From 75e600df28862f17ab13c0c586623c295e3db9f1 Mon Sep 17 00:00:00 2001 From: brendagutman Date: Wed, 27 May 2026 12:21:08 -0500 Subject: [PATCH 01/17] Insert the utils generated pipeline --- dbt_project/dbt_project.yml | 8 + .../inc_chr_18_src_chr_18_phenotype_data.sql | 86 ++++ .../inc_chr_18_src_s3_scrape_cody.sql | 12 + ...c_chr_18_src_ha_delivery_manifest_6735.sql | 19 + .../chr_18/src/_column_descriptions.md | 395 ++++++++++++++++++ .../models/kids_first/chr_18/src/sources.yml | 215 ++++++++++ .../stb/inc_chr_18_stb_accesspolicy.sql | 12 + .../stb/inc_chr_18_stb_activitydefinition.sql | 10 + ..._18_stb_activitydefinition_external_id.sql | 7 + .../chr_18/stb/inc_chr_18_stb_aliquot.sql | 14 + .../inc_chr_18_stb_aliquot_external_id.sql | 7 + .../inc_chr_18_stb_biospecimencollection.sql | 14 + ..._stb_biospecimencollection_external_id.sql | 7 + .../chr_18/stb/inc_chr_18_stb_concept.sql | 7 + .../chr_18/stb/inc_chr_18_stb_dataset.sql | 11 + .../stb/inc_chr_18_stb_dataset_file_id.sql | 7 + .../inc_chr_18_stb_dataset_publication.sql | 7 + .../stb/inc_chr_18_stb_demographics.sql | 14 + ...nc_chr_18_stb_demographics_external_id.sql | 7 + .../stb/inc_chr_18_stb_demographics_race.sql | 7 + .../chr_18/stb/inc_chr_18_stb_doi.sql | 9 + .../stb/inc_chr_18_stb_doi_external_id.sql | 7 + .../chr_18/stb/inc_chr_18_stb_encounter.sql | 11 + .../inc_chr_18_stb_encounter_external_id.sql | 7 + .../inc_chr_18_stb_encounterdefinition.sql | 10 + ...unterdefinition_activity_definition_id.sql | 7 + ...18_stb_encounterdefinition_external_id.sql | 7 + .../chr_18/stb/inc_chr_18_stb_family.sql | 12 + .../stb/inc_chr_18_stb_family_external_id.sql | 7 + .../stb/inc_chr_18_stb_familymember.sql | 11 + ...nc_chr_18_stb_familymember_external_id.sql | 7 + .../stb/inc_chr_18_stb_familyrelationship.sql | 11 + ..._18_stb_familyrelationship_external_id.sql | 7 + .../chr_18/stb/inc_chr_18_stb_file.sql | 17 + .../stb/inc_chr_18_stb_file_external_id.sql | 7 + .../stb/inc_chr_18_stb_file_sample_id.sql | 7 + .../stb/inc_chr_18_stb_file_subject_id.sql | 7 + .../chr_18/stb/inc_chr_18_stb_filehash.sql | 8 + .../stb/inc_chr_18_stb_investigator.sql | 12 + ...nc_chr_18_stb_investigator_external_id.sql | 7 + .../chr_18/stb/inc_chr_18_stb_publication.sql | 10 + ...inc_chr_18_stb_publication_external_id.sql | 7 + .../stb/inc_chr_18_stb_record_external_id.sql | 7 + .../chr_18/stb/inc_chr_18_stb_sample.sql | 14 + .../stb/inc_chr_18_stb_sample_external_id.sql | 7 + .../stb/inc_chr_18_stb_sample_processing.sql | 7 + .../inc_chr_18_stb_sample_storage_method.sql | 7 + .../chr_18/stb/inc_chr_18_stb_study.sql | 16 + ...18_stb_study_clinical_data_source_type.sql | 7 + .../stb/inc_chr_18_stb_study_contact.sql | 7 + .../inc_chr_18_stb_study_data_category.sql | 7 + .../stb/inc_chr_18_stb_study_external_id.sql | 7 + .../inc_chr_18_stb_study_funding_source.sql | 7 + ...8_stb_study_participant_lifespan_stage.sql | 7 + ...hr_18_stb_study_principal_investigator.sql | 7 + .../stb/inc_chr_18_stb_study_program.sql | 7 + .../stb/inc_chr_18_stb_study_publication.sql | 7 + .../inc_chr_18_stb_study_research_domain.sql | 7 + .../stb/inc_chr_18_stb_study_study_design.sql | 7 + .../stb/inc_chr_18_stb_studymetadata.sql | 11 + ...tudymetadata_clinical_data_source_type.sql | 7 + ...chr_18_stb_studymetadata_data_category.sql | 7 + ...c_chr_18_stb_studymetadata_external_id.sql | 7 + ...udymetadata_participant_lifespan_stage.sql | 7 + ...r_18_stb_studymetadata_research_domain.sql | 7 + ..._chr_18_stb_studymetadata_study_design.sql | 7 + .../chr_18/stb/inc_chr_18_stb_subject.sql | 10 + .../inc_chr_18_stb_subject_external_id.sql | 7 + .../stb/inc_chr_18_stb_subjectassertion.sql | 19 + ...nc_chr_18_stb_subjectassertion_concept.sql | 7 + ...hr_18_stb_subjectassertion_external_id.sql | 7 + ..._18_stb_subjectassertion_value_concept.sql | 7 + .../inc_chr_18_stb_virtualbiorepository.sql | 12 + ...hr_18_stb_virtualbiorepository_contact.sql | 7 + ...8_stb_virtualbiorepository_external_id.sql | 7 + .../scripts/run_version_placeholder.sh | 199 +++++++++ 76 files changed, 1531 insertions(+) create mode 100644 dbt_project/models/kids_first/chr_18/src/Clinical_Data/inc_chr_18_src_chr_18_phenotype_data.sql create mode 100644 dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/inc_chr_18_src_s3_scrape_cody.sql create mode 100644 dbt_project/models/kids_first/chr_18/src/Sequencing_Data/inc_chr_18_src_ha_delivery_manifest_6735.sql create mode 100644 dbt_project/models/kids_first/chr_18/src/_column_descriptions.md create mode 100644 dbt_project/models/kids_first/chr_18/src/sources.yml create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_accesspolicy.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_activitydefinition.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_activitydefinition_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_aliquot.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_aliquot_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_biospecimencollection.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_biospecimencollection_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_concept.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset_file_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset_publication.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_race.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_doi.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_doi_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounter.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounter_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition_activity_definition_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_family.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_family_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familymember.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familymember_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familyrelationship.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familyrelationship_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_sample_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_subject_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_filehash.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_investigator.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_investigator_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_publication.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_publication_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_record_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_processing.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_storage_method.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_clinical_data_source_type.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_contact.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_data_category.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_funding_source.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_participant_lifespan_stage.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_principal_investigator.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_program.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_publication.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_research_domain.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_study_design.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_clinical_data_source_type.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_data_category.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_participant_lifespan_stage.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_research_domain.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_study_design.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subject.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subject_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_concept.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_value_concept.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository_contact.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository_external_id.sql create mode 100755 dbt_project/scripts/run_version_placeholder.sh diff --git a/dbt_project/dbt_project.yml b/dbt_project/dbt_project.yml index dd9070b..7ece3e1 100644 --- a/dbt_project/dbt_project.yml +++ b/dbt_project/dbt_project.yml @@ -24,6 +24,11 @@ models: +schema: inc_aadsc_src int: +schema: inc_aadsc_int + chr_18: + src: + +schema: inc_chr_18_src + int: + +schema: inc_chr_18_int kids_first: +tags: [study_stage,kids_first] sd_1nns3k8v: @@ -32,6 +37,9 @@ models: +schema: kf_sd_1nns3k8v_src int: +schema: kf_sd_1nns3k8v_int + chr_18: + +tags: + - chr_18 access: +tags: [access_stage] +schema: access diff --git a/dbt_project/models/kids_first/chr_18/src/Clinical_Data/inc_chr_18_src_chr_18_phenotype_data.sql b/dbt_project/models/kids_first/chr_18/src/Clinical_Data/inc_chr_18_src_chr_18_phenotype_data.sql new file mode 100644 index 0000000..d136438 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/src/Clinical_Data/inc_chr_18_src_chr_18_phenotype_data.sql @@ -0,0 +1,86 @@ +{{ config(materialized='table') }} + + select + ROW_NUMBER() OVER () AS "kf_index", + "Family ID"::text as "family_id", + "Participant ID"::text as "participant_id", + "Family Relationship Target Participant ID"::text as "family_relationship_target_participant_id", + "alliquot_id"::text as "alliquot_id", + "Consent Group"::text as "consent_group", + "Age at Sample"::text as "age_at_sample", + "Sample Composition"::text as "sample_composition", + "Race"::text as "race", + "Sex"::text as "sex", + "Ethnicity"::text as "ethnicity", + "Analyte Type"::text as "analyte_type", + "Age at Phenotype"::text as "age_at_phenotype", + "Affected Status"::text as "affected_status", + "Vital Status"::text as "vital_status", + "chiari 2"::text as "chiari_2", + "pituitary gland abn"::text as "pituitary_gland_abn", + "cleft palate"::text as "cleft_palate", + "hearing loss"::text as "hearing_loss", + "tetralogy of fallot"::text as "tetralogy_of_fallot", + "conductive hearing loss"::text as "conductive_hearing_loss", + "holoprosencephaly"::text as "holoprosencephaly", + "choanal atresia"::text as "choanal_atresia", + "aural atresia"::text as "aural_atresia", + "midface hypoplasia"::text as "midface_hypoplasia", + "dysmyelination"::text as "dysmyelination", + "polymicrogyria"::text as "polymicrogyria", + "cryptorchidism"::text as "cryptorchidism", + "sensorineural hearing loss"::text as "sensorineural_hearing_loss", + "cleft lip"::text as "cleft_lip", + "imperforate anus"::text as "imperforate_anus", + "microcephaly"::text as "microcephaly", + "vertical talus"::text as "vertical_talus", + "hypospadias"::text as "hypospadias", + "rocker bottom foot"::text as "rocker_bottom_foot", + "chiari 1"::text as "chiari_1", + "ptosis"::text as "ptosis", + "strabismus"::text as "strabismus", + "bilateral coxa valga"::text as "bilateral_coxa_valga", + "cardiac_nos"::text as "cardiac_nos", + "corpus callosum abn"::text as "corpus_callosum_abn", + "pulmonary valve stenosis"::text as "pulmonary_valve_stenosis", + "metatarsus varus"::text as "metatarsus_varus", + "decreased white matter volume"::text as "decreased_white_matter_volume", + "macrocephaly"::text as "macrocephaly", + "suprasellar cyst"::text as "suprasellar_cyst", + "hydrocephalus"::text as "hydrocephalus", + "micropenis"::text as "micropenis", + "anal stenosis"::text as "anal_stenosis", + "congenital heart malformation"::text as "congenital_heart_malformation", + "bilateral choanal atresia"::text as "bilateral_choanal_atresia", + "dandy walker malformation"::text as "dandy_walker_malformation", + "dandy walker"::text as "dandy_walker", + "congenital heart defect"::text as "congenital_heart_defect", + "aural stenosis"::text as "aural_stenosis", + "kidney malform"::text as "kidney_malform", + "pituitary fossa enlargement"::text as "pituitary_fossa_enlargement", + "submucous cleft"::text as "submucous_cleft", + "virchow robins spaces"::text as "virchow_robins_spaces", + "retinal coloboma"::text as "retinal_coloboma", + "corneal staphyloma"::text as "corneal_staphyloma", + "club foot"::text as "club_foot", + "macroglossia"::text as "macroglossia", + "dandy walker variant"::text as "dandy_walker_variant", + "coanal atresia"::text as "coanal_atresia", + "occipatal lobe abn"::text as "occipatal_lobe_abn", + "asd"::text as "asd", + "vsd"::text as "vsd", + "pectus excavatum"::text as "pectus_excavatum", + "peripherial pulmonary stenosis"::text as "peripherial_pulmonary_stenosis", + "sagittal stenosis"::text as "sagittal_stenosis", + "hydronephrosis"::text as "hydronephrosis", + "patent ductus arteriosus"::text as "patent_ductus_arteriosus", + "duanes syndrome"::text as "duanes_syndrome", + "laryngomalacia"::text as "laryngomalacia", + "metatarsus adductus"::text as "metatarsus_adductus", + "ptosisbilateral"::text as "ptosisbilateral", + "microphallus"::text as "microphallus", + "sacral agenesis"::text as "sacral_agenesis", + "situs inversus"::text as "situs_inversus", + "Sample Tissue Type"::text as "sample_tissue_type" + from {{ source('chr_18', 'chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/inc_chr_18_src_s3_scrape_cody.sql b/dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/inc_chr_18_src_s3_scrape_cody.sql new file mode 100644 index 0000000..70a74d8 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/inc_chr_18_src_s3_scrape_cody.sql @@ -0,0 +1,12 @@ +{{ config(materialized='table') }} + + select + ROW_NUMBER() OVER () AS "kf_index", + "Size"::integer as "size", + "Key"::text as "key", + "ETag"::text as "etag", + "Bucket"::text as "bucket", + "LastModified"::text as "lastmodified", + "StorageClass"::text as "storageclass" + from {{ source('chr_18', 's3_scrape_cody') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/inc_chr_18_src_ha_delivery_manifest_6735.sql b/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/inc_chr_18_src_ha_delivery_manifest_6735.sql new file mode 100644 index 0000000..1e0c119 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/inc_chr_18_src_ha_delivery_manifest_6735.sql @@ -0,0 +1,19 @@ +{{ config(materialized='table') }} + + select + ROW_NUMBER() OVER () AS "kf_index", + "type"::text as "type", + "sample.sample_id"::text as "sample", + "file_name"::text as "file_name", + "file_type"::text as "file_type", + "file_description"::text as "file_description", + "file_size"::integer as "file_size", + "md5sum"::text as "md5sum", + "library_id"::text as "library_id", + "library_strategy"::text as "library_strategy", + "library_layout"::text as "library_layout", + "library_source"::text as "library_source", + "platform"::text as "platform", + "instrument_model"::text as "instrument_model" + from {{ source('chr_18', 'ha_delivery_manifest_6735') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/src/_column_descriptions.md b/dbt_project/models/kids_first/chr_18/src/_column_descriptions.md new file mode 100644 index 0000000..787b36d --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/src/_column_descriptions.md @@ -0,0 +1,395 @@ +{% docs chr_18_phenotype_data_family_id %} +Family ID +{% enddocs %} + +{% docs chr_18_phenotype_data_participant_id %} +Participant ID +{% enddocs %} + +{% docs chr_18_phenotype_data_family_relationship_target_pa_59d6df7d %} +Family Relationship Target Participant ID +{% enddocs %} + +{% docs chr_18_phenotype_data_alliquot_id %} +alliquot_id +{% enddocs %} + +{% docs chr_18_phenotype_data_consent_group %} +Consent Group +{% enddocs %} + +{% docs chr_18_phenotype_data_age_at_sample %} +Age at Sample +{% enddocs %} + +{% docs chr_18_phenotype_data_sample_composition %} +Sample Composition +{% enddocs %} + +{% docs chr_18_phenotype_data_race %} +Race +{% enddocs %} + +{% docs chr_18_phenotype_data_sex %} +Sex +{% enddocs %} + +{% docs chr_18_phenotype_data_ethnicity %} +Ethnicity +{% enddocs %} + +{% docs chr_18_phenotype_data_analyte_type %} +Analyte Type +{% enddocs %} + +{% docs chr_18_phenotype_data_age_at_phenotype %} +Age at Phenotype +{% enddocs %} + +{% docs chr_18_phenotype_data_affected_status %} +Affected Status +{% enddocs %} + +{% docs chr_18_phenotype_data_vital_status %} +Vital Status +{% enddocs %} + +{% docs chr_18_phenotype_data_chiari_2 %} +chiari 2 +{% enddocs %} + +{% docs chr_18_phenotype_data_pituitary_gland_abn %} +pituitary gland abn +{% enddocs %} + +{% docs chr_18_phenotype_data_cleft_palate %} +cleft palate +{% enddocs %} + +{% docs chr_18_phenotype_data_hearing_loss %} +hearing loss +{% enddocs %} + +{% docs chr_18_phenotype_data_tetralogy_of_fallot %} +tetralogy of fallot +{% enddocs %} + +{% docs chr_18_phenotype_data_conductive_hearing_loss %} +conductive hearing loss +{% enddocs %} + +{% docs chr_18_phenotype_data_holoprosencephaly %} +holoprosencephaly +{% enddocs %} + +{% docs chr_18_phenotype_data_choanal_atresia %} +choanal atresia +{% enddocs %} + +{% docs chr_18_phenotype_data_aural_atresia %} +aural atresia +{% enddocs %} + +{% docs chr_18_phenotype_data_midface_hypoplasia %} +midface hypoplasia +{% enddocs %} + +{% docs chr_18_phenotype_data_dysmyelination %} +dysmyelination +{% enddocs %} + +{% docs chr_18_phenotype_data_polymicrogyria %} +polymicrogyria +{% enddocs %} + +{% docs chr_18_phenotype_data_cryptorchidism %} +cryptorchidism +{% enddocs %} + +{% docs chr_18_phenotype_data_sensorineural_hearing_loss %} +sensorineural hearing loss +{% enddocs %} + +{% docs chr_18_phenotype_data_cleft_lip %} +cleft lip +{% enddocs %} + +{% docs chr_18_phenotype_data_imperforate_anus %} +imperforate anus +{% enddocs %} + +{% docs chr_18_phenotype_data_microcephaly %} +microcephaly +{% enddocs %} + +{% docs chr_18_phenotype_data_vertical_talus %} +vertical talus +{% enddocs %} + +{% docs chr_18_phenotype_data_hypospadias %} +hypospadias +{% enddocs %} + +{% docs chr_18_phenotype_data_rocker_bottom_foot %} +rocker bottom foot +{% enddocs %} + +{% docs chr_18_phenotype_data_chiari_1 %} +chiari 1 +{% enddocs %} + +{% docs chr_18_phenotype_data_ptosis %} +ptosis +{% enddocs %} + +{% docs chr_18_phenotype_data_strabismus %} +strabismus +{% enddocs %} + +{% docs chr_18_phenotype_data_bilateral_coxa_valga %} +bilateral coxa valga +{% enddocs %} + +{% docs chr_18_phenotype_data_cardiac_nos %} +cardiac_nos +{% enddocs %} + +{% docs chr_18_phenotype_data_corpus_callosum_abn %} +corpus callosum abn +{% enddocs %} + +{% docs chr_18_phenotype_data_pulmonary_valve_stenosis %} +pulmonary valve stenosis +{% enddocs %} + +{% docs chr_18_phenotype_data_metatarsus_varus %} +metatarsus varus +{% enddocs %} + +{% docs chr_18_phenotype_data_decreased_white_matter_volume %} +decreased white matter volume +{% enddocs %} + +{% docs chr_18_phenotype_data_macrocephaly %} +macrocephaly +{% enddocs %} + +{% docs chr_18_phenotype_data_suprasellar_cyst %} +suprasellar cyst +{% enddocs %} + +{% docs chr_18_phenotype_data_hydrocephalus %} +hydrocephalus +{% enddocs %} + +{% docs chr_18_phenotype_data_micropenis %} +micropenis +{% enddocs %} + +{% docs chr_18_phenotype_data_anal_stenosis %} +anal stenosis +{% enddocs %} + +{% docs chr_18_phenotype_data_congenital_heart_malformation %} +congenital heart malformation +{% enddocs %} + +{% docs chr_18_phenotype_data_bilateral_choanal_atresia %} +bilateral choanal atresia +{% enddocs %} + +{% docs chr_18_phenotype_data_dandy_walker_malformation %} +dandy walker malformation +{% enddocs %} + +{% docs chr_18_phenotype_data_dandy_walker %} +dandy walker +{% enddocs %} + +{% docs chr_18_phenotype_data_congenital_heart_defect %} +congenital heart defect +{% enddocs %} + +{% docs chr_18_phenotype_data_aural_stenosis %} +aural stenosis +{% enddocs %} + +{% docs chr_18_phenotype_data_kidney_malform %} +kidney malform +{% enddocs %} + +{% docs chr_18_phenotype_data_pituitary_fossa_enlargement %} +pituitary fossa enlargement +{% enddocs %} + +{% docs chr_18_phenotype_data_submucous_cleft %} +submucous cleft +{% enddocs %} + +{% docs chr_18_phenotype_data_virchow_robins_spaces %} +virchow robins spaces +{% enddocs %} + +{% docs chr_18_phenotype_data_retinal_coloboma %} +retinal coloboma +{% enddocs %} + +{% docs chr_18_phenotype_data_corneal_staphyloma %} +corneal staphyloma +{% enddocs %} + +{% docs chr_18_phenotype_data_club_foot %} +club foot +{% enddocs %} + +{% docs chr_18_phenotype_data_macroglossia %} +macroglossia +{% enddocs %} + +{% docs chr_18_phenotype_data_dandy_walker_variant %} +dandy walker variant +{% enddocs %} + +{% docs chr_18_phenotype_data_coanal_atresia %} +coanal atresia +{% enddocs %} + +{% docs chr_18_phenotype_data_occipatal_lobe_abn %} +occipatal lobe abn +{% enddocs %} + +{% docs chr_18_phenotype_data_asd %} +asd +{% enddocs %} + +{% docs chr_18_phenotype_data_vsd %} +vsd +{% enddocs %} + +{% docs chr_18_phenotype_data_pectus_excavatum %} +pectus excavatum +{% enddocs %} + +{% docs chr_18_phenotype_data_peripherial_pulmonary_stenosis %} +peripherial pulmonary stenosis +{% enddocs %} + +{% docs chr_18_phenotype_data_sagittal_stenosis %} +sagittal stenosis +{% enddocs %} + +{% docs chr_18_phenotype_data_hydronephrosis %} +hydronephrosis +{% enddocs %} + +{% docs chr_18_phenotype_data_patent_ductus_arteriosus %} +patent ductus arteriosus +{% enddocs %} + +{% docs chr_18_phenotype_data_duanes_syndrome %} +duanes syndrome +{% enddocs %} + +{% docs chr_18_phenotype_data_laryngomalacia %} +laryngomalacia +{% enddocs %} + +{% docs chr_18_phenotype_data_metatarsus_adductus %} +metatarsus adductus +{% enddocs %} + +{% docs chr_18_phenotype_data_ptosisbilateral %} +ptosisbilateral +{% enddocs %} + +{% docs chr_18_phenotype_data_microphallus %} +microphallus +{% enddocs %} + +{% docs chr_18_phenotype_data_sacral_agenesis %} +sacral agenesis +{% enddocs %} + +{% docs chr_18_phenotype_data_situs_inversus %} +situs inversus +{% enddocs %} + +{% docs chr_18_phenotype_data_sample_tissue_type %} +Sample Tissue Type +{% enddocs %} + +{% docs ha_delivery_manifest_6735_type %} +type +{% enddocs %} + +{% docs ha_delivery_manifest_6735_sample %} +sample.sample_id +{% enddocs %} + +{% docs ha_delivery_manifest_6735_file_name %} +file_name +{% enddocs %} + +{% docs ha_delivery_manifest_6735_file_type %} +file_type +{% enddocs %} + +{% docs ha_delivery_manifest_6735_file_description %} +file_description +{% enddocs %} + +{% docs ha_delivery_manifest_6735_file_size %} +file_size +{% enddocs %} + +{% docs ha_delivery_manifest_6735_md5sum %} +md5sum +{% enddocs %} + +{% docs ha_delivery_manifest_6735_library_id %} +library_id +{% enddocs %} + +{% docs ha_delivery_manifest_6735_library_strategy %} +library_strategy +{% enddocs %} + +{% docs ha_delivery_manifest_6735_library_layout %} +library_layout +{% enddocs %} + +{% docs ha_delivery_manifest_6735_library_source %} +library_source +{% enddocs %} + +{% docs ha_delivery_manifest_6735_platform %} +platform +{% enddocs %} + +{% docs ha_delivery_manifest_6735_instrument_model %} +instrument_model +{% enddocs %} + +{% docs s3_scrape_cody_size %} +Size +{% enddocs %} + +{% docs s3_scrape_cody_key %} +Key +{% enddocs %} + +{% docs s3_scrape_cody_etag %} +ETag +{% enddocs %} + +{% docs s3_scrape_cody_bucket %} +Bucket +{% enddocs %} + +{% docs s3_scrape_cody_lastmodified %} +LastModified +{% enddocs %} + +{% docs s3_scrape_cody_storageclass %} +StorageClass +{% enddocs %} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/src/sources.yml b/dbt_project/models/kids_first/chr_18/src/sources.yml new file mode 100644 index 0000000..d60f199 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/src/sources.yml @@ -0,0 +1,215 @@ +sources: +- name: chr_18 + schema: inc_chr_18_src + tables: + - name: chr_18_phenotype_data + description: Source table for chr_18_phenotype_data. + columns: + - name: Family ID + description: '{{ doc("chr_18_phenotype_data_family_id") }}' + - name: Participant ID + description: '{{ doc("chr_18_phenotype_data_participant_id") }}' + - name: Family Relationship Target Participant ID + description: '{{ doc("chr_18_phenotype_data_family_relationship_target_pa_59d6df7d") + }}' + - name: alliquot_id + description: '{{ doc("chr_18_phenotype_data_alliquot_id") }}' + - name: Consent Group + description: '{{ doc("chr_18_phenotype_data_consent_group") }}' + - name: Age at Sample + description: '{{ doc("chr_18_phenotype_data_age_at_sample") }}' + - name: Sample Composition + description: '{{ doc("chr_18_phenotype_data_sample_composition") }}' + - name: Race + description: '{{ doc("chr_18_phenotype_data_race") }}' + - name: Sex + description: '{{ doc("chr_18_phenotype_data_sex") }}' + - name: Ethnicity + description: '{{ doc("chr_18_phenotype_data_ethnicity") }}' + - name: Analyte Type + description: '{{ doc("chr_18_phenotype_data_analyte_type") }}' + - name: Age at Phenotype + description: '{{ doc("chr_18_phenotype_data_age_at_phenotype") }}' + - name: Affected Status + description: '{{ doc("chr_18_phenotype_data_affected_status") }}' + - name: Vital Status + description: '{{ doc("chr_18_phenotype_data_vital_status") }}' + - name: chiari 2 + description: '{{ doc("chr_18_phenotype_data_chiari_2") }}' + - name: pituitary gland abn + description: '{{ doc("chr_18_phenotype_data_pituitary_gland_abn") }}' + - name: cleft palate + description: '{{ doc("chr_18_phenotype_data_cleft_palate") }}' + - name: hearing loss + description: '{{ doc("chr_18_phenotype_data_hearing_loss") }}' + - name: tetralogy of fallot + description: '{{ doc("chr_18_phenotype_data_tetralogy_of_fallot") }}' + - name: conductive hearing loss + description: '{{ doc("chr_18_phenotype_data_conductive_hearing_loss") }}' + - name: holoprosencephaly + description: '{{ doc("chr_18_phenotype_data_holoprosencephaly") }}' + - name: choanal atresia + description: '{{ doc("chr_18_phenotype_data_choanal_atresia") }}' + - name: aural atresia + description: '{{ doc("chr_18_phenotype_data_aural_atresia") }}' + - name: midface hypoplasia + description: '{{ doc("chr_18_phenotype_data_midface_hypoplasia") }}' + - name: dysmyelination + description: '{{ doc("chr_18_phenotype_data_dysmyelination") }}' + - name: polymicrogyria + description: '{{ doc("chr_18_phenotype_data_polymicrogyria") }}' + - name: cryptorchidism + description: '{{ doc("chr_18_phenotype_data_cryptorchidism") }}' + - name: sensorineural hearing loss + description: '{{ doc("chr_18_phenotype_data_sensorineural_hearing_loss") }}' + - name: cleft lip + description: '{{ doc("chr_18_phenotype_data_cleft_lip") }}' + - name: imperforate anus + description: '{{ doc("chr_18_phenotype_data_imperforate_anus") }}' + - name: microcephaly + description: '{{ doc("chr_18_phenotype_data_microcephaly") }}' + - name: vertical talus + description: '{{ doc("chr_18_phenotype_data_vertical_talus") }}' + - name: hypospadias + description: '{{ doc("chr_18_phenotype_data_hypospadias") }}' + - name: rocker bottom foot + description: '{{ doc("chr_18_phenotype_data_rocker_bottom_foot") }}' + - name: chiari 1 + description: '{{ doc("chr_18_phenotype_data_chiari_1") }}' + - name: ptosis + description: '{{ doc("chr_18_phenotype_data_ptosis") }}' + - name: strabismus + description: '{{ doc("chr_18_phenotype_data_strabismus") }}' + - name: bilateral coxa valga + description: '{{ doc("chr_18_phenotype_data_bilateral_coxa_valga") }}' + - name: cardiac_nos + description: '{{ doc("chr_18_phenotype_data_cardiac_nos") }}' + - name: corpus callosum abn + description: '{{ doc("chr_18_phenotype_data_corpus_callosum_abn") }}' + - name: pulmonary valve stenosis + description: '{{ doc("chr_18_phenotype_data_pulmonary_valve_stenosis") }}' + - name: metatarsus varus + description: '{{ doc("chr_18_phenotype_data_metatarsus_varus") }}' + - name: decreased white matter volume + description: '{{ doc("chr_18_phenotype_data_decreased_white_matter_volume") + }}' + - name: macrocephaly + description: '{{ doc("chr_18_phenotype_data_macrocephaly") }}' + - name: suprasellar cyst + description: '{{ doc("chr_18_phenotype_data_suprasellar_cyst") }}' + - name: hydrocephalus + description: '{{ doc("chr_18_phenotype_data_hydrocephalus") }}' + - name: micropenis + description: '{{ doc("chr_18_phenotype_data_micropenis") }}' + - name: anal stenosis + description: '{{ doc("chr_18_phenotype_data_anal_stenosis") }}' + - name: congenital heart malformation + description: '{{ doc("chr_18_phenotype_data_congenital_heart_malformation") + }}' + - name: bilateral choanal atresia + description: '{{ doc("chr_18_phenotype_data_bilateral_choanal_atresia") }}' + - name: dandy walker malformation + description: '{{ doc("chr_18_phenotype_data_dandy_walker_malformation") }}' + - name: dandy walker + description: '{{ doc("chr_18_phenotype_data_dandy_walker") }}' + - name: congenital heart defect + description: '{{ doc("chr_18_phenotype_data_congenital_heart_defect") }}' + - name: aural stenosis + description: '{{ doc("chr_18_phenotype_data_aural_stenosis") }}' + - name: kidney malform + description: '{{ doc("chr_18_phenotype_data_kidney_malform") }}' + - name: pituitary fossa enlargement + description: '{{ doc("chr_18_phenotype_data_pituitary_fossa_enlargement") }}' + - name: submucous cleft + description: '{{ doc("chr_18_phenotype_data_submucous_cleft") }}' + - name: virchow robins spaces + description: '{{ doc("chr_18_phenotype_data_virchow_robins_spaces") }}' + - name: retinal coloboma + description: '{{ doc("chr_18_phenotype_data_retinal_coloboma") }}' + - name: corneal staphyloma + description: '{{ doc("chr_18_phenotype_data_corneal_staphyloma") }}' + - name: club foot + description: '{{ doc("chr_18_phenotype_data_club_foot") }}' + - name: macroglossia + description: '{{ doc("chr_18_phenotype_data_macroglossia") }}' + - name: dandy walker variant + description: '{{ doc("chr_18_phenotype_data_dandy_walker_variant") }}' + - name: coanal atresia + description: '{{ doc("chr_18_phenotype_data_coanal_atresia") }}' + - name: occipatal lobe abn + description: '{{ doc("chr_18_phenotype_data_occipatal_lobe_abn") }}' + - name: asd + description: '{{ doc("chr_18_phenotype_data_asd") }}' + - name: vsd + description: '{{ doc("chr_18_phenotype_data_vsd") }}' + - name: pectus excavatum + description: '{{ doc("chr_18_phenotype_data_pectus_excavatum") }}' + - name: peripherial pulmonary stenosis + description: '{{ doc("chr_18_phenotype_data_peripherial_pulmonary_stenosis") + }}' + - name: sagittal stenosis + description: '{{ doc("chr_18_phenotype_data_sagittal_stenosis") }}' + - name: hydronephrosis + description: '{{ doc("chr_18_phenotype_data_hydronephrosis") }}' + - name: patent ductus arteriosus + description: '{{ doc("chr_18_phenotype_data_patent_ductus_arteriosus") }}' + - name: duanes syndrome + description: '{{ doc("chr_18_phenotype_data_duanes_syndrome") }}' + - name: laryngomalacia + description: '{{ doc("chr_18_phenotype_data_laryngomalacia") }}' + - name: metatarsus adductus + description: '{{ doc("chr_18_phenotype_data_metatarsus_adductus") }}' + - name: ptosisbilateral + description: '{{ doc("chr_18_phenotype_data_ptosisbilateral") }}' + - name: microphallus + description: '{{ doc("chr_18_phenotype_data_microphallus") }}' + - name: sacral agenesis + description: '{{ doc("chr_18_phenotype_data_sacral_agenesis") }}' + - name: situs inversus + description: '{{ doc("chr_18_phenotype_data_situs_inversus") }}' + - name: Sample Tissue Type + description: '{{ doc("chr_18_phenotype_data_sample_tissue_type") }}' + - name: ha_delivery_manifest_6735 + description: Source table for ha_delivery_manifest_6735. + columns: + - name: type + description: '{{ doc("ha_delivery_manifest_6735_type") }}' + - name: sample.sample_id + description: '{{ doc("ha_delivery_manifest_6735_sample") }}' + - name: file_name + description: '{{ doc("ha_delivery_manifest_6735_file_name") }}' + - name: file_type + description: '{{ doc("ha_delivery_manifest_6735_file_type") }}' + - name: file_description + description: '{{ doc("ha_delivery_manifest_6735_file_description") }}' + - name: file_size + description: '{{ doc("ha_delivery_manifest_6735_file_size") }}' + - name: md5sum + description: '{{ doc("ha_delivery_manifest_6735_md5sum") }}' + - name: library_id + description: '{{ doc("ha_delivery_manifest_6735_library_id") }}' + - name: library_strategy + description: '{{ doc("ha_delivery_manifest_6735_library_strategy") }}' + - name: library_layout + description: '{{ doc("ha_delivery_manifest_6735_library_layout") }}' + - name: library_source + description: '{{ doc("ha_delivery_manifest_6735_library_source") }}' + - name: platform + description: '{{ doc("ha_delivery_manifest_6735_platform") }}' + - name: instrument_model + description: '{{ doc("ha_delivery_manifest_6735_instrument_model") }}' + - name: s3_scrape_cody + description: Source table for s3_scrape_cody. + columns: + - name: Size + description: '{{ doc("s3_scrape_cody_size") }}' + - name: Key + description: '{{ doc("s3_scrape_cody_key") }}' + - name: ETag + description: '{{ doc("s3_scrape_cody_etag") }}' + - name: Bucket + description: '{{ doc("s3_scrape_cody_bucket") }}' + - name: LastModified + description: '{{ doc("s3_scrape_cody_lastmodified") }}' + - name: StorageClass + description: '{{ doc("s3_scrape_cody_storageclass") }}' diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_accesspolicy.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_accesspolicy.sql new file mode 100644 index 0000000..7f9f41d --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_accesspolicy.sql @@ -0,0 +1,12 @@ +{{ config(materialized='table') }} + + select + null::text as "access_policy_id", + null::text as "data_use_accession", + null::text as "data_use_permission", + null::text as "data_use_modifier", + null::text as "disease_limitation", + null::text as "access_description", + null::text as "website" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_activitydefinition.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_activitydefinition.sql new file mode 100644 index 0000000..570da50 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_activitydefinition.sql @@ -0,0 +1,10 @@ +{{ config(materialized='table') }} + + select + null::text as "activity_definition_id", + null::text as "name", + null::text as "description", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_activitydefinition_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_activitydefinition_external_id.sql new file mode 100644 index 0000000..7ecb81a --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_activitydefinition_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "activitydefinition_activity_definition_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_aliquot.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_aliquot.sql new file mode 100644 index 0000000..b2f7bd2 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_aliquot.sql @@ -0,0 +1,14 @@ +{{ config(materialized='table') }} + + select + null::text as "aliquot_id", + null::text as "sample_id", + null::text as "availablity_status", + null::text as "quantity_number", + null::text as "quantity_unit", + null::text as "concentration_number", + null::text as "concentration_unit", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_aliquot_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_aliquot_external_id.sql new file mode 100644 index 0000000..02bf1a0 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_aliquot_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "aliquot_aliquot_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_biospecimencollection.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_biospecimencollection.sql new file mode 100644 index 0000000..eb9b027 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_biospecimencollection.sql @@ -0,0 +1,14 @@ +{{ config(materialized='table') }} + + select + null::text as "biospecimen_collection_id", + null::text as "age_at_collection", + null::text as "method", + null::text as "site", + null::text as "spatial_qualifier", + null::text as "laterality", + null::text as "encounter_id", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_biospecimencollection_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_biospecimencollection_external_id.sql new file mode 100644 index 0000000..11e8404 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_biospecimencollection_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "biospecimencollection_biospecimen_collection_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_concept.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_concept.sql new file mode 100644 index 0000000..4350c7e --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_concept.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "concept_curie", + null::text as "display" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset.sql new file mode 100644 index 0000000..33091c0 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset.sql @@ -0,0 +1,11 @@ +{{ config(materialized='table') }} + + select + null::text as "dataset_id", + null::text as "name", + null::text as "description", + null::text as "do_id", + null::text as "data_collection_start", + null::text as "data_collection_end" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset_file_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset_file_id.sql new file mode 100644 index 0000000..9f8eaa0 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset_file_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "dataset_dataset_id", + null::text as "file_id_file_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset_publication.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset_publication.sql new file mode 100644 index 0000000..41fd529 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset_publication.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "dataset_dataset_id", + null::integer as "publication_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics.sql new file mode 100644 index 0000000..4c0bf43 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics.sql @@ -0,0 +1,14 @@ +{{ config(materialized='table') }} + + select + null::text as "subject_id", + null::text as "sex", + null::text as "ethnicity", + null::text as "down_syndrome_status", + null::integer as "age_at_last_vital_status", + null::text as "vital_status", + null::integer as "age_at_first_engagement", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_external_id.sql new file mode 100644 index 0000000..953521b --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "demographics_subject_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_race.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_race.sql new file mode 100644 index 0000000..1bcfae1 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_race.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "demographics_subject_id", + null::text as "race" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_doi.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_doi.sql new file mode 100644 index 0000000..e330e15 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_doi.sql @@ -0,0 +1,9 @@ +{{ config(materialized='table') }} + + select + null::text as "do_id", + null::text as "bibliographic_reference", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_doi_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_doi_external_id.sql new file mode 100644 index 0000000..6dec0dc --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_doi_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "doi_do_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounter.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounter.sql new file mode 100644 index 0000000..fbb8dc2 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounter.sql @@ -0,0 +1,11 @@ +{{ config(materialized='table') }} + + select + null::text as "encounter_id", + null::text as "subject_id", + null::text as "encounter_definition_id", + null::integer as "age_at_event", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounter_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounter_external_id.sql new file mode 100644 index 0000000..a8f3dc9 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounter_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "encounter_encounter_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition.sql new file mode 100644 index 0000000..492dbe3 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition.sql @@ -0,0 +1,10 @@ +{{ config(materialized='table') }} + + select + null::text as "encounter_definition_id", + null::text as "name", + null::text as "description", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition_activity_definition_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition_activity_definition_id.sql new file mode 100644 index 0000000..a19a472 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition_activity_definition_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "encounterdefinition_encounter_definition_id", + null::text as "activity_definition_id_activity_definition_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition_external_id.sql new file mode 100644 index 0000000..b283c9c --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "encounterdefinition_encounter_definition_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_family.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_family.sql new file mode 100644 index 0000000..affd9d3 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_family.sql @@ -0,0 +1,12 @@ +{{ config(materialized='table') }} + + select + null::text as "family_id", + null::text as "family_type", + null::text as "family_description", + null::text as "consanguinity", + null::text as "family_study_focus", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_family_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_family_external_id.sql new file mode 100644 index 0000000..ed70b01 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_family_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "family_family_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familymember.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familymember.sql new file mode 100644 index 0000000..673f8a2 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familymember.sql @@ -0,0 +1,11 @@ +{{ config(materialized='table') }} + + select + null::integer as "id", + null::text as "family_id", + null::text as "subject_id", + null::text as "family_role", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familymember_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familymember_external_id.sql new file mode 100644 index 0000000..4e41c3e --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familymember_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::integer as "familymember_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familyrelationship.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familyrelationship.sql new file mode 100644 index 0000000..0161392 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familyrelationship.sql @@ -0,0 +1,11 @@ +{{ config(materialized='table') }} + + select + null::text as "family_relationship_id", + null::text as "family_member_id", + null::text as "relationship", + null::text as "subject_id", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familyrelationship_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familyrelationship_external_id.sql new file mode 100644 index 0000000..881cab5 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familyrelationship_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "familyrelationship_family_relationship_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file.sql new file mode 100644 index 0000000..5cba39e --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file.sql @@ -0,0 +1,17 @@ +{{ config(materialized='table') }} + + select + null::text as "file_id", + null::text as "filename", + null::text as "format", + null::text as "data_category", + null::text as "data_type", + null::integer as "size", + null::text as "staging_url", + null::text as "release_url", + null::text as "drs_uri", + null::text as "access_policy_id", + null::text as "study_id", + null::integer as "hash_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_external_id.sql new file mode 100644 index 0000000..cca4563 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "file_file_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_sample_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_sample_id.sql new file mode 100644 index 0000000..c209f6a --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_sample_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "file_file_id", + null::text as "sample_id_sample_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_subject_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_subject_id.sql new file mode 100644 index 0000000..ab988fd --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_subject_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "file_file_id", + null::text as "subject_id_subject_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_filehash.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_filehash.sql new file mode 100644 index 0000000..aea7743 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_filehash.sql @@ -0,0 +1,8 @@ +{{ config(materialized='table') }} + + select + null::integer as "id", + null::text as "hash_type", + null::text as "hash_value" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_investigator.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_investigator.sql new file mode 100644 index 0000000..f37fca3 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_investigator.sql @@ -0,0 +1,12 @@ +{{ config(materialized='table') }} + + select + null::integer as "id", + null::text as "name", + null::text as "institution", + null::text as "investigator_title", + null::text as "email", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_investigator_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_investigator_external_id.sql new file mode 100644 index 0000000..8a6d70f --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_investigator_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::integer as "investigator_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_publication.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_publication.sql new file mode 100644 index 0000000..99f9165 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_publication.sql @@ -0,0 +1,10 @@ +{{ config(materialized='table') }} + + select + null::integer as "id", + null::text as "bibliographic_reference", + null::text as "website", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_publication_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_publication_external_id.sql new file mode 100644 index 0000000..d433a31 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_publication_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::integer as "publication_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_record_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_record_external_id.sql new file mode 100644 index 0000000..2d24622 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_record_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::integer as "record_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample.sql new file mode 100644 index 0000000..539c076 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample.sql @@ -0,0 +1,14 @@ +{{ config(materialized='table') }} + + select + null::text as "sample_id", + null::text as "biospecimen_collection_id", + null::text as "parent_sample_id", + null::text as "sample_type", + null::text as "availablity_status", + null::text as "quantity_number", + null::text as "quantity_unit", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_external_id.sql new file mode 100644 index 0000000..800dae1 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "sample_sample_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_processing.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_processing.sql new file mode 100644 index 0000000..4c4aaf7 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_processing.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "sample_sample_id", + null::text as "processing" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_storage_method.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_storage_method.sql new file mode 100644 index 0000000..96163f6 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_storage_method.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "sample_sample_id", + null::text as "storage_method" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study.sql new file mode 100644 index 0000000..eec3536 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study.sql @@ -0,0 +1,16 @@ +{{ config(materialized='table') }} + + select + null::text as "parent_study", + null::text as "study_title", + null::text as "study_code", + null::text as "study_short_name", + null::text as "study_description", + null::text as "website", + null::text as "acknowledgments", + null::text as "citation_statement", + null::text as "do_id", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_clinical_data_source_type.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_clinical_data_source_type.sql new file mode 100644 index 0000000..8b5f04b --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_clinical_data_source_type.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "study_study_id", + null::text as "clinical_data_source_type" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_contact.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_contact.sql new file mode 100644 index 0000000..51ea7a5 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_contact.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "study_study_id", + null::integer as "contact_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_data_category.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_data_category.sql new file mode 100644 index 0000000..47c5f42 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_data_category.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "study_study_id", + null::text as "data_category" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_external_id.sql new file mode 100644 index 0000000..9431889 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "study_study_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_funding_source.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_funding_source.sql new file mode 100644 index 0000000..fd0f9f5 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_funding_source.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "study_study_id", + null::text as "funding_source" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_participant_lifespan_stage.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_participant_lifespan_stage.sql new file mode 100644 index 0000000..18a0694 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_participant_lifespan_stage.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "study_study_id", + null::text as "participant_lifespan_stage" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_principal_investigator.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_principal_investigator.sql new file mode 100644 index 0000000..323f069 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_principal_investigator.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "study_study_id", + null::integer as "principal_investigator_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_program.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_program.sql new file mode 100644 index 0000000..d2ba0e2 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_program.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "study_study_id", + null::text as "program" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_publication.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_publication.sql new file mode 100644 index 0000000..e543e60 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_publication.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "study_study_id", + null::integer as "publication_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_research_domain.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_research_domain.sql new file mode 100644 index 0000000..38790ef --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_research_domain.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "study_study_id", + null::text as "research_domain" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_study_design.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_study_design.sql new file mode 100644 index 0000000..c6487a4 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_study_design.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "study_study_id", + null::text as "study_design" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata.sql new file mode 100644 index 0000000..3be97a7 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata.sql @@ -0,0 +1,11 @@ +{{ config(materialized='table') }} + + select + null::text as "study_id", + null::text as "selection_criteria", + null::text as "vbr_id", + null::integer as "expected_number_of_participants", + null::integer as "actual_number_of_participants", + null::text as "access_policy_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_clinical_data_source_type.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_clinical_data_source_type.sql new file mode 100644 index 0000000..3147a0a --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_clinical_data_source_type.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "studymetadata_study_id", + null::text as "clinical_data_source_type" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_data_category.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_data_category.sql new file mode 100644 index 0000000..cf9793f --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_data_category.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "studymetadata_study_id", + null::text as "data_category" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_external_id.sql new file mode 100644 index 0000000..d59f31c --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "studymetadata_study_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_participant_lifespan_stage.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_participant_lifespan_stage.sql new file mode 100644 index 0000000..b69a575 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_participant_lifespan_stage.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "studymetadata_study_id", + null::text as "participant_lifespan_stage" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_research_domain.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_research_domain.sql new file mode 100644 index 0000000..9807a99 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_research_domain.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "studymetadata_study_id", + null::text as "research_domain" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_study_design.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_study_design.sql new file mode 100644 index 0000000..e60ea85 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_study_design.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "studymetadata_study_id", + null::text as "study_design" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subject.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subject.sql new file mode 100644 index 0000000..4e05b34 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subject.sql @@ -0,0 +1,10 @@ +{{ config(materialized='table') }} + + select + null::text as "subject_id", + null::text as "subject_type", + null::text as "organism_type", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subject_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subject_external_id.sql new file mode 100644 index 0000000..7dfc140 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subject_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "subject_subject_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion.sql new file mode 100644 index 0000000..e7e3e65 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion.sql @@ -0,0 +1,19 @@ +{{ config(materialized='table') }} + + select + null::text as "assertion_id", + null::text as "subject_id", + null::text as "encounter_id", + null::text as "assertion_provenance", + null::integer as "age_at_assertion", + null::integer as "age_at_event", + null::integer as "age_at_resolution", + null::text as "concept_source", + null::text as "value_number", + null::text as "value_source", + null::text as "value_unit", + null::text as "value_unit_source", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_concept.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_concept.sql new file mode 100644 index 0000000..a24c514 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_concept.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "subjectassertion_assertion_id", + null::text as "concept_concept_curie" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_external_id.sql new file mode 100644 index 0000000..715abdb --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "subjectassertion_assertion_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_value_concept.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_value_concept.sql new file mode 100644 index 0000000..3b170a1 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_value_concept.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "subjectassertion_assertion_id", + null::text as "value_concept_concept_curie" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository.sql new file mode 100644 index 0000000..93927d3 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository.sql @@ -0,0 +1,12 @@ +{{ config(materialized='table') }} + + select + null::text as "vbr_id", + null::text as "name", + null::text as "institution", + null::text as "website", + null::text as "vbr_readme", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository_contact.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository_contact.sql new file mode 100644 index 0000000..25da532 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository_contact.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "virtualbiorepository_vbr_id", + null::integer as "contact_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository_external_id.sql new file mode 100644 index 0000000..3d2a785 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "virtualbiorepository_vbr_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/scripts/run_version_placeholder.sh b/dbt_project/scripts/run_version_placeholder.sh new file mode 100755 index 0000000..e46bff5 --- /dev/null +++ b/dbt_project/scripts/run_version_placeholder.sh @@ -0,0 +1,199 @@ +#!/bin/bash +set -e +dbt clean +dbt deps || { echo "Error: dbt deps failed. Exiting..."; exit 1; } +dbt seed #--full-refresh +# Source tables +dbt run --select inc_chr_18_src_chr_18_phenotype_data +dbt run --select inc_chr_18_src_ha_delivery_manifest_6735 +dbt run --select inc_chr_18_src_s3_scrape_cody +# Stable tables +dbt run --select inc_chr_18_stb_accesspolicy +dbt run --select inc_chr_18_stb_activitydefinition +dbt run --select inc_chr_18_stb_activitydefinition_external_id +dbt run --select inc_chr_18_stb_aliquot +dbt run --select inc_chr_18_stb_aliquot_external_id +dbt run --select inc_chr_18_stb_biospecimencollection +dbt run --select inc_chr_18_stb_biospecimencollection_external_id +dbt run --select inc_chr_18_stb_concept +dbt run --select inc_chr_18_stb_doi +dbt run --select inc_chr_18_stb_doi_external_id +dbt run --select inc_chr_18_stb_dataset +dbt run --select inc_chr_18_stb_dataset_file_id +dbt run --select inc_chr_18_stb_dataset_publication +dbt run --select inc_chr_18_stb_demographics +dbt run --select inc_chr_18_stb_demographics_external_id +dbt run --select inc_chr_18_stb_demographics_race +dbt run --select inc_chr_18_stb_encounter +dbt run --select inc_chr_18_stb_encounterdefinition +dbt run --select inc_chr_18_stb_encounterdefinition_activity_definition_id +dbt run --select inc_chr_18_stb_encounterdefinition_external_id +dbt run --select inc_chr_18_stb_encounter_external_id +dbt run --select inc_chr_18_stb_family +dbt run --select inc_chr_18_stb_familymember +dbt run --select inc_chr_18_stb_familymember_external_id +dbt run --select inc_chr_18_stb_familyrelationship +dbt run --select inc_chr_18_stb_familyrelationship_external_id +dbt run --select inc_chr_18_stb_family_external_id +dbt run --select inc_chr_18_stb_file +dbt run --select inc_chr_18_stb_filehash +dbt run --select inc_chr_18_stb_file_external_id +dbt run --select inc_chr_18_stb_file_sample_id +dbt run --select inc_chr_18_stb_file_subject_id +dbt run --select inc_chr_18_stb_investigator +dbt run --select inc_chr_18_stb_investigator_external_id +dbt run --select inc_chr_18_stb_publication +dbt run --select inc_chr_18_stb_publication_external_id +dbt run --select inc_chr_18_stb_record_external_id +dbt run --select inc_chr_18_stb_sample +dbt run --select inc_chr_18_stb_sample_external_id +dbt run --select inc_chr_18_stb_sample_processing +dbt run --select inc_chr_18_stb_sample_storage_method +dbt run --select inc_chr_18_stb_study +dbt run --select inc_chr_18_stb_studymetadata +dbt run --select inc_chr_18_stb_studymetadata_clinical_data_source_type +dbt run --select inc_chr_18_stb_studymetadata_data_category +dbt run --select inc_chr_18_stb_studymetadata_external_id +dbt run --select inc_chr_18_stb_studymetadata_participant_lifespan_stage +dbt run --select inc_chr_18_stb_studymetadata_research_domain +dbt run --select inc_chr_18_stb_studymetadata_study_design +dbt run --select inc_chr_18_stb_study_clinical_data_source_type +dbt run --select inc_chr_18_stb_study_contact +dbt run --select inc_chr_18_stb_study_data_category +dbt run --select inc_chr_18_stb_study_external_id +dbt run --select inc_chr_18_stb_study_funding_source +dbt run --select inc_chr_18_stb_study_participant_lifespan_stage +dbt run --select inc_chr_18_stb_study_principal_investigator +dbt run --select inc_chr_18_stb_study_program +dbt run --select inc_chr_18_stb_study_publication +dbt run --select inc_chr_18_stb_study_research_domain +dbt run --select inc_chr_18_stb_study_study_design +dbt run --select inc_chr_18_stb_subject +dbt run --select inc_chr_18_stb_subjectassertion +dbt run --select inc_chr_18_stb_subjectassertion_concept +dbt run --select inc_chr_18_stb_subjectassertion_external_id +dbt run --select inc_chr_18_stb_subjectassertion_value_concept +dbt run --select inc_chr_18_stb_subject_external_id +dbt run --select inc_chr_18_stb_virtualbiorepository +dbt run --select inc_chr_18_stb_virtualbiorepository_contact +dbt run --select inc_chr_18_stb_virtualbiorepository_external_id +# Combined tables +dbt run --select combined_accesspolicy +dbt run --select combined_activitydefinition +dbt run --select combined_activitydefinition_external_id +dbt run --select combined_aliquot +dbt run --select combined_aliquot_external_id +dbt run --select combined_biospecimencollection +dbt run --select combined_biospecimencollection_external_id +dbt run --select combined_concept +dbt run --select combined_doi +dbt run --select combined_doi_external_id +dbt run --select combined_dataset +dbt run --select combined_dataset_file_id +dbt run --select combined_dataset_publication +dbt run --select combined_demographics +dbt run --select combined_demographics_external_id +dbt run --select combined_demographics_race +dbt run --select combined_encounter +dbt run --select combined_encounterdefinition +dbt run --select combined_encounterdefinition_activity_definition_id +dbt run --select combined_encounterdefinition_external_id +dbt run --select combined_encounter_external_id +dbt run --select combined_family +dbt run --select combined_familymember +dbt run --select combined_familymember_external_id +dbt run --select combined_familyrelationship +dbt run --select combined_familyrelationship_external_id +dbt run --select combined_family_external_id +dbt run --select combined_file +dbt run --select combined_filehash +dbt run --select combined_file_external_id +dbt run --select combined_file_sample_id +dbt run --select combined_file_subject_id +dbt run --select combined_investigator +dbt run --select combined_investigator_external_id +dbt run --select combined_publication +dbt run --select combined_publication_external_id +dbt run --select combined_record_external_id +dbt run --select combined_sample +dbt run --select combined_sample_external_id +dbt run --select combined_sample_processing +dbt run --select combined_sample_storage_method +dbt run --select combined_study +dbt run --select combined_studymetadata +dbt run --select combined_studymetadata_clinical_data_source_type +dbt run --select combined_studymetadata_data_category +dbt run --select combined_studymetadata_external_id +dbt run --select combined_studymetadata_participant_lifespan_stage +dbt run --select combined_studymetadata_research_domain +dbt run --select combined_studymetadata_study_design +dbt run --select combined_study_clinical_data_source_type +dbt run --select combined_study_contact +dbt run --select combined_study_data_category +dbt run --select combined_study_external_id +dbt run --select combined_study_funding_source +dbt run --select combined_study_participant_lifespan_stage +dbt run --select combined_study_principal_investigator +dbt run --select combined_study_program +dbt run --select combined_study_publication +dbt run --select combined_study_research_domain +dbt run --select combined_study_study_design +dbt run --select combined_subject +dbt run --select combined_subjectassertion +dbt run --select combined_subjectassertion_concept +dbt run --select combined_subjectassertion_external_id +dbt run --select combined_subjectassertion_value_concept +dbt run --select combined_subject_external_id +dbt run --select combined_virtualbiorepository +dbt run --select combined_virtualbiorepository_contact +dbt run --select combined_virtualbiorepository_external_id +# Export tables +dbt run --select fhir_accesspolicy +dbt run --select fhir_accesspolicy_access_policy_code +dbt run --select fhir_ageat +dbt run --select fhir_aliquot +dbt run --select fhir_aliquot_external_id +dbt run --select fhir_associatedparty +dbt run --select fhir_associatedparty_classifier +dbt run --select fhir_associatedparty_period_id +dbt run --select fhir_family +dbt run --select fhir_familyrelationship +dbt run --select fhir_family_external_id +dbt run --select fhir_filelocation +dbt run --select fhir_filemetadata +dbt run --select fhir_filemetadata_samples +dbt run --select fhir_hasexternalid_external_id +dbt run --select fhir_institution +dbt run --select fhir_institution_external_id +dbt run --select fhir_ncpifile +dbt run --select fhir_ncpifile_external_id +dbt run --select fhir_ncpifile_file_location_id +dbt run --select fhir_ncpifile_file_meta_data_id +dbt run --select fhir_participant +dbt run --select fhir_participantassertion +dbt run --select fhir_participant_external_id +dbt run --select fhir_participant_race +dbt run --select fhir_participant_sample_id +dbt run --select fhir_period +dbt run --select fhir_person +dbt run --select fhir_person_participant_id +dbt run --select fhir_practitioner +dbt run --select fhir_practitionerrole +dbt run --select fhir_practitioner_external_id +dbt run --select fhir_relativedatetime +dbt run --select fhir_researchstudy +dbt run --select fhir_researchstudycollection +dbt run --select fhir_researchstudycollection_external_id +dbt run --select fhir_researchstudycollection_label +dbt run --select fhir_researchstudycollection_research_study_collection_member_id +dbt run --select fhir_researchstudy_external_id +dbt run --select fhir_researchstudy_study_acknowledgement +dbt run --select fhir_researchstudy_study_condition +dbt run --select fhir_researchstudy_study_design +dbt run --select fhir_researchstudy_study_focus +dbt run --select fhir_researchstudy_study_personnel +dbt run --select fhir_researchsubject +dbt run --select fhir_sample +dbt run --select fhir_sample_external_id +dbt run --select fhir_sample_processing +dbt run --select fhir_studymembership From 12ba9a00ec27849a2ac1bc9e2c90c724fdee737f Mon Sep 17 00:00:00 2001 From: Amanda Warkow Date: Mon, 22 Jun 2026 09:30:26 -0400 Subject: [PATCH 02/17] =?UTF-8?q?=F0=9F=9A=A7=20WIP?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- ...ql => kf_chr_18_src_chr_18_phenotype_data.sql} | 0 ..._cody.sql => kf_chr_18_src_s3_scrape_cody.sql} | 0 ...> kf_chr_18_src_ha_delivery_manifest_6735.sql} | 0 .../chr_18/stb/inc_chr_18_stb_demographics.sql | 12 ++++++------ .../stb/inc_chr_18_stb_demographics_race.sql | 4 ++-- .../kids_first/chr_18/stb/inc_chr_18_stb_file.sql | 15 ++++++++------- .../chr_18/stb/inc_chr_18_stb_filehash.sql | 6 +++--- .../chr_18/stb/inc_chr_18_stb_sample.sql | 6 +++--- 8 files changed, 22 insertions(+), 21 deletions(-) rename dbt_project/models/kids_first/chr_18/src/Clinical_Data/{inc_chr_18_src_chr_18_phenotype_data.sql => kf_chr_18_src_chr_18_phenotype_data.sql} (100%) rename dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/{inc_chr_18_src_s3_scrape_cody.sql => kf_chr_18_src_s3_scrape_cody.sql} (100%) rename dbt_project/models/kids_first/chr_18/src/Sequencing_Data/{inc_chr_18_src_ha_delivery_manifest_6735.sql => kf_chr_18_src_ha_delivery_manifest_6735.sql} (100%) diff --git a/dbt_project/models/kids_first/chr_18/src/Clinical_Data/inc_chr_18_src_chr_18_phenotype_data.sql b/dbt_project/models/kids_first/chr_18/src/Clinical_Data/kf_chr_18_src_chr_18_phenotype_data.sql similarity index 100% rename from dbt_project/models/kids_first/chr_18/src/Clinical_Data/inc_chr_18_src_chr_18_phenotype_data.sql rename to dbt_project/models/kids_first/chr_18/src/Clinical_Data/kf_chr_18_src_chr_18_phenotype_data.sql diff --git a/dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/inc_chr_18_src_s3_scrape_cody.sql b/dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/kf_chr_18_src_s3_scrape_cody.sql similarity index 100% rename from dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/inc_chr_18_src_s3_scrape_cody.sql rename to dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/kf_chr_18_src_s3_scrape_cody.sql diff --git a/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/inc_chr_18_src_ha_delivery_manifest_6735.sql b/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/kf_chr_18_src_ha_delivery_manifest_6735.sql similarity index 100% rename from dbt_project/models/kids_first/chr_18/src/Sequencing_Data/inc_chr_18_src_ha_delivery_manifest_6735.sql rename to dbt_project/models/kids_first/chr_18/src/Sequencing_Data/kf_chr_18_src_ha_delivery_manifest_6735.sql diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics.sql index 4c0bf43..06cd0c2 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics.sql +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics.sql @@ -2,13 +2,13 @@ select null::text as "subject_id", - null::text as "sex", - null::text as "ethnicity", - null::text as "down_syndrome_status", + sex as "sex", + ethnicity as "ethnicity", + null::text as "down_syndrome_status", -- could map to Not Applicable? null::integer as "age_at_last_vital_status", - null::text as "vital_status", - null::integer as "age_at_first_engagement", + vital_status as "vital_status", + null::integer as "age_at_first_engagement", -- age at phenotype? or sample? null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_race.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_race.sql index 1bcfae1..0e0b421 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_race.sql +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_race.sql @@ -2,6 +2,6 @@ select null::text as "demographics_subject_id", - null::text as "race" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + race as "race" + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file.sql index 5cba39e..f79e037 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file.sql +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file.sql @@ -2,16 +2,17 @@ select null::text as "file_id", - null::text as "filename", + file_name as "filename", null::text as "format", null::text as "data_category", - null::text as "data_type", - null::integer as "size", - null::text as "staging_url", - null::text as "release_url", - null::text as "drs_uri", + file_type as "data_type", + file_size as "size", + -- Need to determine when DRS indexing will happen + -- null::text as "staging_url", + -- null::text as "release_url", + -- null::text as "drs_uri", null::text as "access_policy_id", null::text as "study_id", null::integer as "hash_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_ha_delivery_manifest_6735') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_filehash.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_filehash.sql index aea7743..3e09bd4 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_filehash.sql +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_filehash.sql @@ -2,7 +2,7 @@ select null::integer as "id", - null::text as "hash_type", - null::text as "hash_value" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + 'md5sum' as "hash_type", + md5sum as "hash_value" + from {{ ref('kf_chr_18_src_ha_delivery_manifest_6735') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample.sql index 539c076..1ea159e 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample.sql +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample.sql @@ -1,14 +1,14 @@ {{ config(materialized='table') }} select - null::text as "sample_id", + sample as "sample_id", null::text as "biospecimen_collection_id", null::text as "parent_sample_id", - null::text as "sample_type", + type as "sample_type", null::text as "availablity_status", null::text as "quantity_number", null::text as "quantity_unit", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_ha_delivery_manifest_6735') }} \ No newline at end of file From 014c0b0635704e7eeb66d1678f2b77e8832c8e00 Mon Sep 17 00:00:00 2001 From: Amanda Warkow Date: Mon, 22 Jun 2026 14:14:35 -0400 Subject: [PATCH 03/17] =?UTF-8?q?=E2=99=BB=EF=B8=8F=20reorganizing=20src?= =?UTF-8?q?=20and=20int?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../chr_18/int/kf_chr_18_int_clinical.sql | 118 +++++++++++++ .../chr_18/int/kf_chr_18_int_s3.sql | 12 ++ .../chr_18/int/kf_chr_18_int_sequencing.sql | 19 ++ .../kf_chr_18_src_chr_18_phenotype_data.sql | 162 +++++++++--------- .../kf_chr_18_src_s3_scrape_cody.sql | 14 +- ...f_chr_18_src_ha_delivery_manifest_6735.sql | 28 +-- 6 files changed, 251 insertions(+), 102 deletions(-) create mode 100644 dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_clinical.sql create mode 100644 dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_s3.sql create mode 100644 dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql diff --git a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_clinical.sql b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_clinical.sql new file mode 100644 index 0000000..06a0e9f --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_clinical.sql @@ -0,0 +1,118 @@ +{{ config(materialized='table') }} + +with base_data as ( + select * from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +), +phenotype_list as ( + select phenotype from ( + values + ('chiari_2'), ('pituitary_gland_abn'), ('cleft_palate'), ('hearing_loss'), + ('tetralogy_of_fallot'), ('conductive_hearing_loss'), ('holoprosencephaly'), ('choanal_atresia'), + ('aural_atresia'), ('midface_hypoplasia'), ('dysmyelination'), ('polymicrogyria'), + ('cryptorchidism'), ('sensorineural_hearing_loss'), ('cleft_lip'), ('imperforate_anus'), + ('microcephaly'), ('vertical_talus'), ('hypospadias'), ('rocker_bottom_foot'), + ('chiari_1'), ('ptosis'), ('strabismus'), ('bilateral_coxa_valga'), + ('cardiac_nos'), ('corpus_callosum_abn'), ('pulmonary_valve_stenosis'), ('metatarsus_varus'), + ('decreased_white_matter_volume'), ('macrocephaly'), ('suprasellar_cyst'), ('hydrocephalus'), + ('micropenis'), ('anal_stenosis'), ('congenital_heart_malformation'), ('bilateral_choanal_atresia'), + ('dandy_walker_malformation'), ('dandy_walker'), ('congenital_heart_defect'), ('aural_stenosis'), + ('kidney_malform'), ('pituitary_fossa_enlargement'), ('submucous_cleft'), ('virchow_robins_spaces'), + ('retinal_coloboma'), ('corneal_staphyloma'), ('club_foot'), ('macroglossia'), + ('dandy_walker_variant'), ('coanal_atresia'), ('occipatal_lobe_abn'), ('asd'), + ('vsd'), ('pectus_excavatum'), ('peripherial_pulmonary_stenosis'), ('sagittal_stenosis'), + ('hydronephrosis'), ('patent_ductus_arteriosus'), ('duanes_syndrome'), ('laryngomalacia'), + ('metatarsus_adductus'), ('ptosisbilateral'), ('microphallus'), ('sacral_agenesis'), + ('situs_inversus') + ) as t(phenotype) +), +unpivoted_phenotypes as ( + select + bd.family_id, + bd.participant_id, + bd.family_relationship_target_participant_id, + bd.aliquot_id, + bd.consent_group, + bd.age_at_sample, + bd.sample_composition, + bd.race, + bd.sex, + bd.ethnicity, + bd.analyte_type, + bd.age_at_phenotype, + bd.affected_status, + bd.vital_status, + bd.sample_tissue_type, + pl.phenotype + from base_data bd + cross join phenotype_list pl + where case pl.phenotype + when 'chiari_2' then bd.chiari_2 + when 'pituitary_gland_abn' then bd.pituitary_gland_abn + when 'cleft_palate' then bd.cleft_palate + when 'hearing_loss' then bd.hearing_loss + when 'tetralogy_of_fallot' then bd.tetralogy_of_fallot + when 'conductive_hearing_loss' then bd.conductive_hearing_loss + when 'holoprosencephaly' then bd.holoprosencephaly + when 'choanal_atresia' then bd.choanal_atresia + when 'aural_atresia' then bd.aural_atresia + when 'midface_hypoplasia' then bd.midface_hypoplasia + when 'dysmyelination' then bd.dysmyelination + when 'polymicrogyria' then bd.polymicrogyria + when 'cryptorchidism' then bd.cryptorchidism + when 'sensorineural_hearing_loss' then bd.sensorineural_hearing_loss + when 'cleft_lip' then bd.cleft_lip + when 'imperforate_anus' then bd.imperforate_anus + when 'microcephaly' then bd.microcephaly + when 'vertical_talus' then bd.vertical_talus + when 'hypospadias' then bd.hypospadias + when 'rocker_bottom_foot' then bd.rocker_bottom_foot + when 'chiari_1' then bd.chiari_1 + when 'ptosis' then bd.ptosis + when 'strabismus' then bd.strabismus + when 'bilateral_coxa_valga' then bd.bilateral_coxa_valga + when 'cardiac_nos' then bd.cardiac_nos + when 'corpus_callosum_abn' then bd.corpus_callosum_abn + when 'pulmonary_valve_stenosis' then bd.pulmonary_valve_stenosis + when 'metatarsus_varus' then bd.metatarsus_varus + when 'decreased_white_matter_volume' then bd.decreased_white_matter_volume + when 'macrocephaly' then bd.macrocephaly + when 'suprasellar_cyst' then bd.suprasellar_cyst + when 'hydrocephalus' then bd.hydrocephalus + when 'micropenis' then bd.micropenis + when 'anal_stenosis' then bd.anal_stenosis + when 'congenital_heart_malformation' then bd.congenital_heart_malformation + when 'bilateral_choanal_atresia' then bd.bilateral_choanal_atresia + when 'dandy_walker_malformation' then bd.dandy_walker_malformation + when 'dandy_walker' then bd.dandy_walker + when 'congenital_heart_defect' then bd.congenital_heart_defect + when 'aural_stenosis' then bd.aural_stenosis + when 'kidney_malform' then bd.kidney_malform + when 'pituitary_fossa_enlargement' then bd.pituitary_fossa_enlargement + when 'submucous_cleft' then bd.submucous_cleft + when 'virchow_robins_spaces' then bd.virchow_robins_spaces + when 'retinal_coloboma' then bd.retinal_coloboma + when 'corneal_staphyloma' then bd.corneal_staphyloma + when 'club_foot' then bd.club_foot + when 'macroglossia' then bd.macroglossia + when 'dandy_walker_variant' then bd.dandy_walker_variant + when 'coanal_atresia' then bd.coanal_atresia + when 'occipatal_lobe_abn' then bd.occipatal_lobe_abn + when 'asd' then bd.asd + when 'vsd' then bd.vsd + when 'pectus_excavatum' then bd.pectus_excavatum + when 'peripherial_pulmonary_stenosis' then bd.peripherial_pulmonary_stenosis + when 'sagittal_stenosis' then bd.sagittal_stenosis + when 'hydronephrosis' then bd.hydronephrosis + when 'patent_ductus_arteriosus' then bd.patent_ductus_arteriosus + when 'duanes_syndrome' then bd.duanes_syndrome + when 'laryngomalacia' then bd.laryngomalacia + when 'metatarsus_adductus' then bd.metatarsus_adductus + when 'ptosisbilateral' then bd.ptosisbilateral + when 'microphallus' then bd.microphallus + when 'sacral_agenesis' then bd.sacral_agenesis + when 'situs_inversus' then bd.situs_inversus + end = 'present' +) + +select * from unpivoted_phenotypes + diff --git a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_s3.sql b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_s3.sql new file mode 100644 index 0000000..bedc2f8 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_s3.sql @@ -0,0 +1,12 @@ +{{ config(materialized='table') }} + + select + kf_index, + size, + key, + etag, + bucket, + lastmodified, + storageclass + from {{ ref('kf_chr_18_src_s3_scrape_cody') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql new file mode 100644 index 0000000..7446e88 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql @@ -0,0 +1,19 @@ +{{ config(materialized='table') }} + + select + kf_index, + type, + sample, + file_name, + file_type, + file_description, + file_size, + md5sum, + library_id, + library_strategy, + library_layout, + library_source, + platform, + instrument_model + from {{ source('chr_18', 'ha_delivery_manifest_6735') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/src/Clinical_Data/kf_chr_18_src_chr_18_phenotype_data.sql b/dbt_project/models/kids_first/chr_18/src/Clinical_Data/kf_chr_18_src_chr_18_phenotype_data.sql index d136438..cfb1d99 100644 --- a/dbt_project/models/kids_first/chr_18/src/Clinical_Data/kf_chr_18_src_chr_18_phenotype_data.sql +++ b/dbt_project/models/kids_first/chr_18/src/Clinical_Data/kf_chr_18_src_chr_18_phenotype_data.sql @@ -1,86 +1,86 @@ {{ config(materialized='table') }} select - ROW_NUMBER() OVER () AS "kf_index", - "Family ID"::text as "family_id", - "Participant ID"::text as "participant_id", - "Family Relationship Target Participant ID"::text as "family_relationship_target_participant_id", - "alliquot_id"::text as "alliquot_id", - "Consent Group"::text as "consent_group", - "Age at Sample"::text as "age_at_sample", - "Sample Composition"::text as "sample_composition", - "Race"::text as "race", - "Sex"::text as "sex", - "Ethnicity"::text as "ethnicity", - "Analyte Type"::text as "analyte_type", - "Age at Phenotype"::text as "age_at_phenotype", - "Affected Status"::text as "affected_status", - "Vital Status"::text as "vital_status", - "chiari 2"::text as "chiari_2", - "pituitary gland abn"::text as "pituitary_gland_abn", - "cleft palate"::text as "cleft_palate", - "hearing loss"::text as "hearing_loss", - "tetralogy of fallot"::text as "tetralogy_of_fallot", - "conductive hearing loss"::text as "conductive_hearing_loss", - "holoprosencephaly"::text as "holoprosencephaly", - "choanal atresia"::text as "choanal_atresia", - "aural atresia"::text as "aural_atresia", - "midface hypoplasia"::text as "midface_hypoplasia", - "dysmyelination"::text as "dysmyelination", - "polymicrogyria"::text as "polymicrogyria", - "cryptorchidism"::text as "cryptorchidism", - "sensorineural hearing loss"::text as "sensorineural_hearing_loss", - "cleft lip"::text as "cleft_lip", - "imperforate anus"::text as "imperforate_anus", - "microcephaly"::text as "microcephaly", - "vertical talus"::text as "vertical_talus", - "hypospadias"::text as "hypospadias", - "rocker bottom foot"::text as "rocker_bottom_foot", - "chiari 1"::text as "chiari_1", - "ptosis"::text as "ptosis", - "strabismus"::text as "strabismus", - "bilateral coxa valga"::text as "bilateral_coxa_valga", - "cardiac_nos"::text as "cardiac_nos", - "corpus callosum abn"::text as "corpus_callosum_abn", - "pulmonary valve stenosis"::text as "pulmonary_valve_stenosis", - "metatarsus varus"::text as "metatarsus_varus", - "decreased white matter volume"::text as "decreased_white_matter_volume", - "macrocephaly"::text as "macrocephaly", - "suprasellar cyst"::text as "suprasellar_cyst", - "hydrocephalus"::text as "hydrocephalus", - "micropenis"::text as "micropenis", - "anal stenosis"::text as "anal_stenosis", - "congenital heart malformation"::text as "congenital_heart_malformation", - "bilateral choanal atresia"::text as "bilateral_choanal_atresia", - "dandy walker malformation"::text as "dandy_walker_malformation", - "dandy walker"::text as "dandy_walker", - "congenital heart defect"::text as "congenital_heart_defect", - "aural stenosis"::text as "aural_stenosis", - "kidney malform"::text as "kidney_malform", - "pituitary fossa enlargement"::text as "pituitary_fossa_enlargement", - "submucous cleft"::text as "submucous_cleft", - "virchow robins spaces"::text as "virchow_robins_spaces", - "retinal coloboma"::text as "retinal_coloboma", - "corneal staphyloma"::text as "corneal_staphyloma", - "club foot"::text as "club_foot", - "macroglossia"::text as "macroglossia", - "dandy walker variant"::text as "dandy_walker_variant", - "coanal atresia"::text as "coanal_atresia", - "occipatal lobe abn"::text as "occipatal_lobe_abn", - "asd"::text as "asd", - "vsd"::text as "vsd", - "pectus excavatum"::text as "pectus_excavatum", - "peripherial pulmonary stenosis"::text as "peripherial_pulmonary_stenosis", - "sagittal stenosis"::text as "sagittal_stenosis", - "hydronephrosis"::text as "hydronephrosis", - "patent ductus arteriosus"::text as "patent_ductus_arteriosus", - "duanes syndrome"::text as "duanes_syndrome", - "laryngomalacia"::text as "laryngomalacia", - "metatarsus adductus"::text as "metatarsus_adductus", - "ptosisbilateral"::text as "ptosisbilateral", - "microphallus"::text as "microphallus", - "sacral agenesis"::text as "sacral_agenesis", - "situs inversus"::text as "situs_inversus", - "Sample Tissue Type"::text as "sample_tissue_type" + ROW_NUMBER() OVER () AS kf_index, + "Family ID"::text as family_id, + "Participant ID"::text as participant_id, + "Family Relationship Target Participant ID"::text as family_relationship_target_participant_id, + "alliquot_id"::text as aliquot_id, + "Consent Group"::text as consent_group, + "Age at Sample"::text as age_at_sample, + "Sample Composition"::text as sample_composition, + "Race"::text as race, + "Sex"::text as sex, + "Ethnicity"::text as ethnicity, + "Analyte Type"::text as analyte_type, + "Age at Phenotype"::text as age_at_phenotype, + "Affected Status"::text as affected_status, + "Vital Status"::text as vital_status, + "chiari 2"::text as chiari_2, + "pituitary gland abn"::text as pituitary_gland_abn, + "cleft palate"::text as cleft_palate, + "hearing loss"::text as hearing_loss, + "tetralogy of fallot"::text as tetralogy_of_fallot, + "conductive hearing loss"::text as conductive_hearing_loss, + "holoprosencephaly"::text as holoprosencephaly, + "choanal atresia"::text as choanal_atresia, + "aural atresia"::text as aural_atresia, + "midface hypoplasia"::text as midface_hypoplasia, + "dysmyelination"::text as dysmyelination, + "polymicrogyria"::text as polymicrogyria, + "cryptorchidism"::text as cryptorchidism, + "sensorineural hearing loss"::text as sensorineural_hearing_loss, + "cleft lip"::text as cleft_lip, + "imperforate anus"::text as imperforate_anus, + "microcephaly"::text as microcephaly, + "vertical talus"::text as vertical_talus, + "hypospadias"::text as hypospadias, + "rocker bottom foot"::text as rocker_bottom_foot, + "chiari 1"::text as chiari_1, + "ptosis"::text as ptosis, + "strabismus"::text as strabismus, + "bilateral coxa valga"::text as bilateral_coxa_valga, + "cardiac_nos"::text as cardiac_nos, + "corpus callosum abn"::text as corpus_callosum_abn, + "pulmonary valve stenosis"::text as pulmonary_valve_stenosis, + "metatarsus varus"::text as metatarsus_varus, + "decreased white matter volume"::text as decreased_white_matter_volume, + "macrocephaly"::text as macrocephaly, + "suprasellar cyst"::text as suprasellar_cyst, + "hydrocephalus"::text as hydrocephalus, + "micropenis"::text as micropenis, + "anal stenosis"::text as anal_stenosis, + "congenital heart malformation"::text as congenital_heart_malformation, + "bilateral choanal atresia"::text as bilateral_choanal_atresia, + "dandy walker malformation"::text as dandy_walker_malformation, + "dandy walker"::text as dandy_walker, + "congenital heart defect"::text as congenital_heart_defect, + "aural stenosis"::text as aural_stenosis, + "kidney malform"::text as kidney_malform, + "pituitary fossa enlargement"::text as pituitary_fossa_enlargement, + "submucous cleft"::text as submucous_cleft, + "virchow robins spaces"::text as virchow_robins_spaces, + "retinal coloboma"::text as retinal_coloboma, + "corneal staphyloma"::text as corneal_staphyloma, + "club foot"::text as club_foot, + "macroglossia"::text as macroglossia, + "dandy walker variant"::text as dandy_walker_variant, + "coanal atresia"::text as coanal_atresia, + "occipatal lobe abn"::text as occipatal_lobe_abn, + "asd"::text as asd, + "vsd"::text as vsd, + "pectus excavatum"::text as pectus_excavatum, + "peripherial pulmonary stenosis"::text as peripherial_pulmonary_stenosis, + "sagittal stenosis"::text as sagittal_stenosis, + "hydronephrosis"::text as hydronephrosis, + "patent ductus arteriosus"::text as patent_ductus_arteriosus, + "duanes syndrome"::text as duanes_syndrome, + "laryngomalacia"::text as laryngomalacia, + "metatarsus adductus"::text as metatarsus_adductus, + "ptosisbilateral"::text as ptosisbilateral, + "microphallus"::text as microphallus, + "sacral agenesis"::text as sacral_agenesis, + "situs inversus"::text as situs_inversus, + "Sample Tissue Type"::text as sample_tissue_type from {{ source('chr_18', 'chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/kf_chr_18_src_s3_scrape_cody.sql b/dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/kf_chr_18_src_s3_scrape_cody.sql index 70a74d8..3267410 100644 --- a/dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/kf_chr_18_src_s3_scrape_cody.sql +++ b/dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/kf_chr_18_src_s3_scrape_cody.sql @@ -1,12 +1,12 @@ {{ config(materialized='table') }} select - ROW_NUMBER() OVER () AS "kf_index", - "Size"::integer as "size", - "Key"::text as "key", - "ETag"::text as "etag", - "Bucket"::text as "bucket", - "LastModified"::text as "lastmodified", - "StorageClass"::text as "storageclass" + ROW_NUMBER() OVER () AS kf_index, + "Size"::integer as size, + "Key"::text as key, + "ETag"::text as etag, + "Bucket"::text as bucket, + "LastModified"::text as lastmodified, + "StorageClass"::text as storageclass from {{ source('chr_18', 's3_scrape_cody') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/kf_chr_18_src_ha_delivery_manifest_6735.sql b/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/kf_chr_18_src_ha_delivery_manifest_6735.sql index 1e0c119..6cb41ba 100644 --- a/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/kf_chr_18_src_ha_delivery_manifest_6735.sql +++ b/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/kf_chr_18_src_ha_delivery_manifest_6735.sql @@ -1,19 +1,19 @@ {{ config(materialized='table') }} select - ROW_NUMBER() OVER () AS "kf_index", - "type"::text as "type", - "sample.sample_id"::text as "sample", - "file_name"::text as "file_name", - "file_type"::text as "file_type", - "file_description"::text as "file_description", - "file_size"::integer as "file_size", - "md5sum"::text as "md5sum", - "library_id"::text as "library_id", - "library_strategy"::text as "library_strategy", - "library_layout"::text as "library_layout", - "library_source"::text as "library_source", - "platform"::text as "platform", - "instrument_model"::text as "instrument_model" + ROW_NUMBER() OVER () AS kf_index, + "type"::text as type, + "sample.sample_id"::text as sample, + "file_name"::text as file_name, + "file_type"::text as file_type, + "file_description"::text as file_description, + "file_size"::integer as file_size, + "md5sum"::text as md5sum, + "library_id"::text as library_id, + "library_strategy"::text as library_strategy, + "library_layout"::text as library_layout, + "library_source"::text as library_source, + "platform"::text as platform, + "instrument_model"::text as instrument_model from {{ source('chr_18', 'ha_delivery_manifest_6735') }} \ No newline at end of file From 0ac30b677e08a92745a1b009b5f03eb5b7291d88 Mon Sep 17 00:00:00 2001 From: Amanda Warkow Date: Mon, 22 Jun 2026 14:25:12 -0400 Subject: [PATCH 04/17] =?UTF-8?q?=E2=9C=8F=EF=B8=8F=20rename=20all=20model?= =?UTF-8?q?s=20to=20KF?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- ...18_stb_accesspolicy.sql => kf_chr_18_stb_accesspolicy.sql} | 2 +- ...itydefinition.sql => kf_chr_18_stb_activitydefinition.sql} | 2 +- ...d.sql => kf_chr_18_stb_activitydefinition_external_id.sql} | 2 +- .../{inc_chr_18_stb_aliquot.sql => kf_chr_18_stb_aliquot.sql} | 2 +- ..._external_id.sql => kf_chr_18_stb_aliquot_external_id.sql} | 2 +- ...collection.sql => kf_chr_18_stb_biospecimencollection.sql} | 2 +- ...ql => kf_chr_18_stb_biospecimencollection_external_id.sql} | 2 +- .../{inc_chr_18_stb_concept.sql => kf_chr_18_stb_concept.sql} | 2 +- .../{inc_chr_18_stb_dataset.sql => kf_chr_18_stb_dataset.sql} | 2 +- ..._dataset_file_id.sql => kf_chr_18_stb_dataset_file_id.sql} | 2 +- ..._publication.sql => kf_chr_18_stb_dataset_publication.sql} | 2 +- ...18_stb_demographics.sql => kf_chr_18_stb_demographics.sql} | 0 ...rnal_id.sql => kf_chr_18_stb_demographics_external_id.sql} | 2 +- ...ographics_race.sql => kf_chr_18_stb_demographics_race.sql} | 0 .../stb/{inc_chr_18_stb_doi.sql => kf_chr_18_stb_doi.sql} | 2 +- ..._doi_external_id.sql => kf_chr_18_stb_doi_external_id.sql} | 2 +- ...c_chr_18_stb_encounter.sql => kf_chr_18_stb_encounter.sql} | 2 +- ...xternal_id.sql => kf_chr_18_stb_encounter_external_id.sql} | 2 +- ...erdefinition.sql => kf_chr_18_stb_encounterdefinition.sql} | 2 +- ...chr_18_stb_encounterdefinition_activity_definition_id.sql} | 2 +- ....sql => kf_chr_18_stb_encounterdefinition_external_id.sql} | 2 +- .../{inc_chr_18_stb_family.sql => kf_chr_18_stb_family.sql} | 2 +- ...y_external_id.sql => kf_chr_18_stb_family_external_id.sql} | 2 +- ...18_stb_familymember.sql => kf_chr_18_stb_familymember.sql} | 2 +- ...rnal_id.sql => kf_chr_18_stb_familymember_external_id.sql} | 2 +- ...yrelationship.sql => kf_chr_18_stb_familyrelationship.sql} | 2 +- ...d.sql => kf_chr_18_stb_familyrelationship_external_id.sql} | 2 +- .../stb/{inc_chr_18_stb_file.sql => kf_chr_18_stb_file.sql} | 0 ...ile_external_id.sql => kf_chr_18_stb_file_external_id.sql} | 2 +- ...tb_file_sample_id.sql => kf_chr_18_stb_file_sample_id.sql} | 2 +- ..._file_subject_id.sql => kf_chr_18_stb_file_subject_id.sql} | 2 +- ...inc_chr_18_stb_filehash.sql => kf_chr_18_stb_filehash.sql} | 0 ...18_stb_investigator.sql => kf_chr_18_stb_investigator.sql} | 2 +- ...rnal_id.sql => kf_chr_18_stb_investigator_external_id.sql} | 2 +- ...r_18_stb_publication.sql => kf_chr_18_stb_publication.sql} | 2 +- ...ernal_id.sql => kf_chr_18_stb_publication_external_id.sql} | 2 +- ...d_external_id.sql => kf_chr_18_stb_record_external_id.sql} | 2 +- .../{inc_chr_18_stb_sample.sql => kf_chr_18_stb_sample.sql} | 0 ...e_external_id.sql => kf_chr_18_stb_sample_external_id.sql} | 2 +- ...ple_processing.sql => kf_chr_18_stb_sample_processing.sql} | 2 +- ...age_method.sql => kf_chr_18_stb_sample_storage_method.sql} | 2 +- .../stb/{inc_chr_18_stb_study.sql => kf_chr_18_stb_study.sql} | 2 +- ....sql => kf_chr_18_stb_study_clinical_data_source_type.sql} | 2 +- ..._stb_study_contact.sql => kf_chr_18_stb_study_contact.sql} | 2 +- ...ata_category.sql => kf_chr_18_stb_study_data_category.sql} | 2 +- ...dy_external_id.sql => kf_chr_18_stb_study_external_id.sql} | 2 +- ...ding_source.sql => kf_chr_18_stb_study_funding_source.sql} | 2 +- ...sql => kf_chr_18_stb_study_participant_lifespan_stage.sql} | 2 +- ...tor.sql => kf_chr_18_stb_study_principal_investigator.sql} | 2 +- ..._stb_study_program.sql => kf_chr_18_stb_study_program.sql} | 2 +- ...dy_publication.sql => kf_chr_18_stb_study_publication.sql} | 2 +- ...rch_domain.sql => kf_chr_18_stb_study_research_domain.sql} | 2 +- ..._study_design.sql => kf_chr_18_stb_study_study_design.sql} | 2 +- ..._stb_studymetadata.sql => kf_chr_18_stb_studymetadata.sql} | 2 +- ...kf_chr_18_stb_studymetadata_clinical_data_source_type.sql} | 2 +- ...gory.sql => kf_chr_18_stb_studymetadata_data_category.sql} | 2 +- ...nal_id.sql => kf_chr_18_stb_studymetadata_external_id.sql} | 2 +- ...f_chr_18_stb_studymetadata_participant_lifespan_stage.sql} | 2 +- ...in.sql => kf_chr_18_stb_studymetadata_research_domain.sql} | 2 +- ...esign.sql => kf_chr_18_stb_studymetadata_study_design.sql} | 2 +- .../{inc_chr_18_stb_subject.sql => kf_chr_18_stb_subject.sql} | 2 +- ..._external_id.sql => kf_chr_18_stb_subject_external_id.sql} | 2 +- ...ubjectassertion.sql => kf_chr_18_stb_subjectassertion.sql} | 2 +- ...concept.sql => kf_chr_18_stb_subjectassertion_concept.sql} | 2 +- ..._id.sql => kf_chr_18_stb_subjectassertion_external_id.sql} | 2 +- ...t.sql => kf_chr_18_stb_subjectassertion_value_concept.sql} | 2 +- ...orepository.sql => kf_chr_18_stb_virtualbiorepository.sql} | 2 +- ...act.sql => kf_chr_18_stb_virtualbiorepository_contact.sql} | 2 +- ...sql => kf_chr_18_stb_virtualbiorepository_external_id.sql} | 2 +- dbt_project/package-lock.yml | 4 ++++ 70 files changed, 68 insertions(+), 64 deletions(-) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_accesspolicy.sql => kf_chr_18_stb_accesspolicy.sql} (84%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_activitydefinition.sql => kf_chr_18_stb_activitydefinition.sql} (78%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_activitydefinition_external_id.sql => kf_chr_18_stb_activitydefinition_external_id.sql} (71%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_aliquot.sql => kf_chr_18_stb_aliquot.sql} (86%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_aliquot_external_id.sql => kf_chr_18_stb_aliquot_external_id.sql} (67%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_biospecimencollection.sql => kf_chr_18_stb_biospecimencollection.sql} (86%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_biospecimencollection_external_id.sql => kf_chr_18_stb_biospecimencollection_external_id.sql} (72%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_concept.sql => kf_chr_18_stb_concept.sql} (65%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_dataset.sql => kf_chr_18_stb_dataset.sql} (81%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_dataset_file_id.sql => kf_chr_18_stb_dataset_file_id.sql} (68%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_dataset_publication.sql => kf_chr_18_stb_dataset_publication.sql} (68%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_demographics.sql => kf_chr_18_stb_demographics.sql} (100%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_demographics_external_id.sql => kf_chr_18_stb_demographics_external_id.sql} (68%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_demographics_race.sql => kf_chr_18_stb_demographics_race.sql} (100%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_doi.sql => kf_chr_18_stb_doi.sql} (76%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_doi_external_id.sql => kf_chr_18_stb_doi_external_id.sql} (65%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_encounter.sql => kf_chr_18_stb_encounter.sql} (81%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_encounter_external_id.sql => kf_chr_18_stb_encounter_external_id.sql} (68%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_encounterdefinition.sql => kf_chr_18_stb_encounterdefinition.sql} (79%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_encounterdefinition_activity_definition_id.sql => kf_chr_18_stb_encounterdefinition_activity_definition_id.sql} (75%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_encounterdefinition_external_id.sql => kf_chr_18_stb_encounterdefinition_external_id.sql} (71%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_family.sql => kf_chr_18_stb_family.sql} (83%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_family_external_id.sql => kf_chr_18_stb_family_external_id.sql} (67%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_familymember.sql => kf_chr_18_stb_familymember.sql} (80%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_familymember_external_id.sql => kf_chr_18_stb_familymember_external_id.sql} (67%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_familyrelationship.sql => kf_chr_18_stb_familyrelationship.sql} (81%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_familyrelationship_external_id.sql => kf_chr_18_stb_familyrelationship_external_id.sql} (71%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_file.sql => kf_chr_18_stb_file.sql} (100%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_file_external_id.sql => kf_chr_18_stb_file_external_id.sql} (66%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_file_sample_id.sql => kf_chr_18_stb_file_sample_id.sql} (67%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_file_subject_id.sql => kf_chr_18_stb_file_subject_id.sql} (68%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_filehash.sql => kf_chr_18_stb_filehash.sql} (100%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_investigator.sql => kf_chr_18_stb_investigator.sql} (82%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_investigator_external_id.sql => kf_chr_18_stb_investigator_external_id.sql} (67%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_publication.sql => kf_chr_18_stb_publication.sql} (78%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_publication_external_id.sql => kf_chr_18_stb_publication_external_id.sql} (67%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_record_external_id.sql => kf_chr_18_stb_record_external_id.sql} (66%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_sample.sql => kf_chr_18_stb_sample.sql} (100%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_sample_external_id.sql => kf_chr_18_stb_sample_external_id.sql} (67%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_sample_processing.sql => kf_chr_18_stb_sample_processing.sql} (67%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_sample_storage_method.sql => kf_chr_18_stb_sample_storage_method.sql} (67%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_study.sql => kf_chr_18_stb_study.sql} (87%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_study_clinical_data_source_type.sql => kf_chr_18_stb_study_clinical_data_source_type.sql} (69%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_study_contact.sql => kf_chr_18_stb_study_contact.sql} (67%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_study_data_category.sql => kf_chr_18_stb_study_data_category.sql} (67%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_study_external_id.sql => kf_chr_18_stb_study_external_id.sql} (66%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_study_funding_source.sql => kf_chr_18_stb_study_funding_source.sql} (67%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_study_participant_lifespan_stage.sql => kf_chr_18_stb_study_participant_lifespan_stage.sql} (69%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_study_principal_investigator.sql => kf_chr_18_stb_study_principal_investigator.sql} (69%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_study_program.sql => kf_chr_18_stb_study_program.sql} (66%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_study_publication.sql => kf_chr_18_stb_study_publication.sql} (67%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_study_research_domain.sql => kf_chr_18_stb_study_research_domain.sql} (67%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_study_study_design.sql => kf_chr_18_stb_study_study_design.sql} (67%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_studymetadata.sql => kf_chr_18_stb_studymetadata.sql} (83%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_studymetadata_clinical_data_source_type.sql => kf_chr_18_stb_studymetadata_clinical_data_source_type.sql} (70%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_studymetadata_data_category.sql => kf_chr_18_stb_studymetadata_data_category.sql} (68%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_studymetadata_external_id.sql => kf_chr_18_stb_studymetadata_external_id.sql} (68%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_studymetadata_participant_lifespan_stage.sql => kf_chr_18_stb_studymetadata_participant_lifespan_stage.sql} (70%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_studymetadata_research_domain.sql => kf_chr_18_stb_studymetadata_research_domain.sql} (68%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_studymetadata_study_design.sql => kf_chr_18_stb_studymetadata_study_design.sql} (68%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_subject.sql => kf_chr_18_stb_subject.sql} (78%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_subject_external_id.sql => kf_chr_18_stb_subject_external_id.sql} (67%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_subjectassertion.sql => kf_chr_18_stb_subjectassertion.sql} (90%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_subjectassertion_concept.sql => kf_chr_18_stb_subjectassertion_concept.sql} (70%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_subjectassertion_external_id.sql => kf_chr_18_stb_subjectassertion_external_id.sql} (69%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_subjectassertion_value_concept.sql => kf_chr_18_stb_subjectassertion_value_concept.sql} (71%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_virtualbiorepository.sql => kf_chr_18_stb_virtualbiorepository.sql} (81%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_virtualbiorepository_contact.sql => kf_chr_18_stb_virtualbiorepository_contact.sql} (69%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_virtualbiorepository_external_id.sql => kf_chr_18_stb_virtualbiorepository_external_id.sql} (69%) create mode 100644 dbt_project/package-lock.yml diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_accesspolicy.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_accesspolicy.sql similarity index 84% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_accesspolicy.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_accesspolicy.sql index 7f9f41d..00f3c1b 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_accesspolicy.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_accesspolicy.sql @@ -8,5 +8,5 @@ null::text as "disease_limitation", null::text as "access_description", null::text as "website" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_activitydefinition.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_activitydefinition.sql similarity index 78% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_activitydefinition.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_activitydefinition.sql index 570da50..1cd2bc3 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_activitydefinition.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_activitydefinition.sql @@ -6,5 +6,5 @@ null::text as "description", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_activitydefinition_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_activitydefinition_external_id.sql similarity index 71% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_activitydefinition_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_activitydefinition_external_id.sql index 7ecb81a..0a0bf91 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_activitydefinition_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_activitydefinition_external_id.sql @@ -3,5 +3,5 @@ select null::text as "activitydefinition_activity_definition_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_aliquot.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_aliquot.sql similarity index 86% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_aliquot.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_aliquot.sql index b2f7bd2..d5e2293 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_aliquot.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_aliquot.sql @@ -10,5 +10,5 @@ null::text as "concentration_unit", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_aliquot_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_aliquot_external_id.sql similarity index 67% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_aliquot_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_aliquot_external_id.sql index 02bf1a0..2c49464 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_aliquot_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_aliquot_external_id.sql @@ -3,5 +3,5 @@ select null::text as "aliquot_aliquot_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_biospecimencollection.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_biospecimencollection.sql similarity index 86% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_biospecimencollection.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_biospecimencollection.sql index eb9b027..abbf60c 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_biospecimencollection.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_biospecimencollection.sql @@ -10,5 +10,5 @@ null::text as "encounter_id", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_biospecimencollection_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_biospecimencollection_external_id.sql similarity index 72% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_biospecimencollection_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_biospecimencollection_external_id.sql index 11e8404..11ab9f9 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_biospecimencollection_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_biospecimencollection_external_id.sql @@ -3,5 +3,5 @@ select null::text as "biospecimencollection_biospecimen_collection_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_concept.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_concept.sql similarity index 65% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_concept.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_concept.sql index 4350c7e..436c7e0 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_concept.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_concept.sql @@ -3,5 +3,5 @@ select null::text as "concept_curie", null::text as "display" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_dataset.sql similarity index 81% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_dataset.sql index 33091c0..a1e8495 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_dataset.sql @@ -7,5 +7,5 @@ null::text as "do_id", null::text as "data_collection_start", null::text as "data_collection_end" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset_file_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_dataset_file_id.sql similarity index 68% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset_file_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_dataset_file_id.sql index 9f8eaa0..1ddf2d6 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset_file_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_dataset_file_id.sql @@ -3,5 +3,5 @@ select null::text as "dataset_dataset_id", null::text as "file_id_file_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset_publication.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_dataset_publication.sql similarity index 68% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset_publication.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_dataset_publication.sql index 41fd529..2d08182 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset_publication.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_dataset_publication.sql @@ -3,5 +3,5 @@ select null::text as "dataset_dataset_id", null::integer as "publication_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_demographics.sql similarity index 100% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_demographics.sql diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_demographics_external_id.sql similarity index 68% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_demographics_external_id.sql index 953521b..3b9d002 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_demographics_external_id.sql @@ -3,5 +3,5 @@ select null::text as "demographics_subject_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_race.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_demographics_race.sql similarity index 100% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_race.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_demographics_race.sql diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_doi.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_doi.sql similarity index 76% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_doi.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_doi.sql index e330e15..632d186 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_doi.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_doi.sql @@ -5,5 +5,5 @@ null::text as "bibliographic_reference", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_doi_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_doi_external_id.sql similarity index 65% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_doi_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_doi_external_id.sql index 6dec0dc..4d79e71 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_doi_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_doi_external_id.sql @@ -3,5 +3,5 @@ select null::text as "doi_do_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounter.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounter.sql similarity index 81% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounter.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounter.sql index fbb8dc2..2698417 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounter.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounter.sql @@ -7,5 +7,5 @@ null::integer as "age_at_event", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounter_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounter_external_id.sql similarity index 68% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounter_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounter_external_id.sql index a8f3dc9..a8f68a4 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounter_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounter_external_id.sql @@ -3,5 +3,5 @@ select null::text as "encounter_encounter_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounterdefinition.sql similarity index 79% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounterdefinition.sql index 492dbe3..b82f63a 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounterdefinition.sql @@ -6,5 +6,5 @@ null::text as "description", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition_activity_definition_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounterdefinition_activity_definition_id.sql similarity index 75% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition_activity_definition_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounterdefinition_activity_definition_id.sql index a19a472..d1b003e 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition_activity_definition_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounterdefinition_activity_definition_id.sql @@ -3,5 +3,5 @@ select null::text as "encounterdefinition_encounter_definition_id", null::text as "activity_definition_id_activity_definition_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounterdefinition_external_id.sql similarity index 71% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounterdefinition_external_id.sql index b283c9c..ea0f884 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounterdefinition_external_id.sql @@ -3,5 +3,5 @@ select null::text as "encounterdefinition_encounter_definition_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_family.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_family.sql similarity index 83% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_family.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_family.sql index affd9d3..1497d0c 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_family.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_family.sql @@ -8,5 +8,5 @@ null::text as "family_study_focus", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_family_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_family_external_id.sql similarity index 67% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_family_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_family_external_id.sql index ed70b01..3567c7f 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_family_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_family_external_id.sql @@ -3,5 +3,5 @@ select null::text as "family_family_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familymember.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familymember.sql similarity index 80% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familymember.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familymember.sql index 673f8a2..efbcb26 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familymember.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familymember.sql @@ -7,5 +7,5 @@ null::text as "family_role", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familymember_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familymember_external_id.sql similarity index 67% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familymember_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familymember_external_id.sql index 4e41c3e..a7117d0 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familymember_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familymember_external_id.sql @@ -3,5 +3,5 @@ select null::integer as "familymember_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familyrelationship.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familyrelationship.sql similarity index 81% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familyrelationship.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familyrelationship.sql index 0161392..9e84927 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familyrelationship.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familyrelationship.sql @@ -7,5 +7,5 @@ null::text as "subject_id", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familyrelationship_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familyrelationship_external_id.sql similarity index 71% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familyrelationship_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familyrelationship_external_id.sql index 881cab5..d64ec62 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familyrelationship_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familyrelationship_external_id.sql @@ -3,5 +3,5 @@ select null::text as "familyrelationship_family_relationship_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file.sql similarity index 100% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file.sql diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file_external_id.sql similarity index 66% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file_external_id.sql index cca4563..25567a8 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file_external_id.sql @@ -3,5 +3,5 @@ select null::text as "file_file_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_sample_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file_sample_id.sql similarity index 67% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_sample_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file_sample_id.sql index c209f6a..e6f5a31 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_sample_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file_sample_id.sql @@ -3,5 +3,5 @@ select null::text as "file_file_id", null::text as "sample_id_sample_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_subject_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file_subject_id.sql similarity index 68% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_subject_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file_subject_id.sql index ab988fd..8554e3b 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_subject_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file_subject_id.sql @@ -3,5 +3,5 @@ select null::text as "file_file_id", null::text as "subject_id_subject_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_filehash.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_filehash.sql similarity index 100% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_filehash.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_filehash.sql diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_investigator.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_investigator.sql similarity index 82% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_investigator.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_investigator.sql index f37fca3..f1161de 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_investigator.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_investigator.sql @@ -8,5 +8,5 @@ null::text as "email", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_investigator_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_investigator_external_id.sql similarity index 67% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_investigator_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_investigator_external_id.sql index 8a6d70f..1e6c882 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_investigator_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_investigator_external_id.sql @@ -3,5 +3,5 @@ select null::integer as "investigator_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_publication.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_publication.sql similarity index 78% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_publication.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_publication.sql index 99f9165..758fc43 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_publication.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_publication.sql @@ -6,5 +6,5 @@ null::text as "website", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_publication_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_publication_external_id.sql similarity index 67% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_publication_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_publication_external_id.sql index d433a31..478f978 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_publication_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_publication_external_id.sql @@ -3,5 +3,5 @@ select null::integer as "publication_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_record_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_record_external_id.sql similarity index 66% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_record_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_record_external_id.sql index 2d24622..6873693 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_record_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_record_external_id.sql @@ -3,5 +3,5 @@ select null::integer as "record_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample.sql similarity index 100% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample.sql diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample_external_id.sql similarity index 67% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample_external_id.sql index 800dae1..9f53c14 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample_external_id.sql @@ -3,5 +3,5 @@ select null::text as "sample_sample_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_processing.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample_processing.sql similarity index 67% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_processing.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample_processing.sql index 4c4aaf7..0ca6c7c 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_processing.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample_processing.sql @@ -3,5 +3,5 @@ select null::text as "sample_sample_id", null::text as "processing" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_storage_method.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample_storage_method.sql similarity index 67% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_storage_method.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample_storage_method.sql index 96163f6..09f1a7e 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_storage_method.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample_storage_method.sql @@ -3,5 +3,5 @@ select null::text as "sample_sample_id", null::text as "storage_method" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study.sql similarity index 87% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study.sql index eec3536..b851fe6 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study.sql @@ -12,5 +12,5 @@ null::text as "do_id", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_clinical_data_source_type.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_clinical_data_source_type.sql similarity index 69% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_clinical_data_source_type.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_clinical_data_source_type.sql index 8b5f04b..ad84524 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_clinical_data_source_type.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_clinical_data_source_type.sql @@ -3,5 +3,5 @@ select null::text as "study_study_id", null::text as "clinical_data_source_type" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_contact.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_contact.sql similarity index 67% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_contact.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_contact.sql index 51ea7a5..5f2874e 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_contact.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_contact.sql @@ -3,5 +3,5 @@ select null::text as "study_study_id", null::integer as "contact_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_data_category.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_data_category.sql similarity index 67% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_data_category.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_data_category.sql index 47c5f42..5997d77 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_data_category.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_data_category.sql @@ -3,5 +3,5 @@ select null::text as "study_study_id", null::text as "data_category" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_external_id.sql similarity index 66% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_external_id.sql index 9431889..d7324a2 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_external_id.sql @@ -3,5 +3,5 @@ select null::text as "study_study_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_funding_source.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_funding_source.sql similarity index 67% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_funding_source.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_funding_source.sql index fd0f9f5..d345ec8 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_funding_source.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_funding_source.sql @@ -3,5 +3,5 @@ select null::text as "study_study_id", null::text as "funding_source" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_participant_lifespan_stage.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_participant_lifespan_stage.sql similarity index 69% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_participant_lifespan_stage.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_participant_lifespan_stage.sql index 18a0694..23c43c9 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_participant_lifespan_stage.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_participant_lifespan_stage.sql @@ -3,5 +3,5 @@ select null::text as "study_study_id", null::text as "participant_lifespan_stage" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_principal_investigator.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_principal_investigator.sql similarity index 69% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_principal_investigator.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_principal_investigator.sql index 323f069..dffdf06 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_principal_investigator.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_principal_investigator.sql @@ -3,5 +3,5 @@ select null::text as "study_study_id", null::integer as "principal_investigator_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_program.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_program.sql similarity index 66% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_program.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_program.sql index d2ba0e2..e04a170 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_program.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_program.sql @@ -3,5 +3,5 @@ select null::text as "study_study_id", null::text as "program" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_publication.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_publication.sql similarity index 67% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_publication.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_publication.sql index e543e60..35f2187 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_publication.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_publication.sql @@ -3,5 +3,5 @@ select null::text as "study_study_id", null::integer as "publication_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_research_domain.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_research_domain.sql similarity index 67% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_research_domain.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_research_domain.sql index 38790ef..20ebb9f 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_research_domain.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_research_domain.sql @@ -3,5 +3,5 @@ select null::text as "study_study_id", null::text as "research_domain" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_study_design.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_study_design.sql similarity index 67% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_study_design.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_study_design.sql index c6487a4..2473ea5 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_study_design.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_study_design.sql @@ -3,5 +3,5 @@ select null::text as "study_study_id", null::text as "study_design" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata.sql similarity index 83% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata.sql index 3be97a7..b666f04 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata.sql @@ -7,5 +7,5 @@ null::integer as "expected_number_of_participants", null::integer as "actual_number_of_participants", null::text as "access_policy_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_clinical_data_source_type.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_clinical_data_source_type.sql similarity index 70% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_clinical_data_source_type.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_clinical_data_source_type.sql index 3147a0a..c21df2f 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_clinical_data_source_type.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_clinical_data_source_type.sql @@ -3,5 +3,5 @@ select null::text as "studymetadata_study_id", null::text as "clinical_data_source_type" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_data_category.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_data_category.sql similarity index 68% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_data_category.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_data_category.sql index cf9793f..e956c06 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_data_category.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_data_category.sql @@ -3,5 +3,5 @@ select null::text as "studymetadata_study_id", null::text as "data_category" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_external_id.sql similarity index 68% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_external_id.sql index d59f31c..6f21f7a 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_external_id.sql @@ -3,5 +3,5 @@ select null::text as "studymetadata_study_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_participant_lifespan_stage.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_participant_lifespan_stage.sql similarity index 70% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_participant_lifespan_stage.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_participant_lifespan_stage.sql index b69a575..d351a23 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_participant_lifespan_stage.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_participant_lifespan_stage.sql @@ -3,5 +3,5 @@ select null::text as "studymetadata_study_id", null::text as "participant_lifespan_stage" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_research_domain.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_research_domain.sql similarity index 68% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_research_domain.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_research_domain.sql index 9807a99..cf2c675 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_research_domain.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_research_domain.sql @@ -3,5 +3,5 @@ select null::text as "studymetadata_study_id", null::text as "research_domain" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_study_design.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_study_design.sql similarity index 68% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_study_design.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_study_design.sql index e60ea85..7edc780 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_study_design.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_study_design.sql @@ -3,5 +3,5 @@ select null::text as "studymetadata_study_id", null::text as "study_design" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subject.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subject.sql similarity index 78% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subject.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subject.sql index 4e05b34..0941c6a 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subject.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subject.sql @@ -6,5 +6,5 @@ null::text as "organism_type", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subject_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subject_external_id.sql similarity index 67% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subject_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subject_external_id.sql index 7dfc140..8080cab 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subject_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subject_external_id.sql @@ -3,5 +3,5 @@ select null::text as "subject_subject_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion.sql similarity index 90% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion.sql index e7e3e65..2ae5ad0 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion.sql @@ -15,5 +15,5 @@ null::text as "value_unit_source", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_concept.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion_concept.sql similarity index 70% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_concept.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion_concept.sql index a24c514..9771ae9 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_concept.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion_concept.sql @@ -3,5 +3,5 @@ select null::text as "subjectassertion_assertion_id", null::text as "concept_concept_curie" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion_external_id.sql similarity index 69% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion_external_id.sql index 715abdb..f6af07d 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion_external_id.sql @@ -3,5 +3,5 @@ select null::text as "subjectassertion_assertion_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_value_concept.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion_value_concept.sql similarity index 71% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_value_concept.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion_value_concept.sql index 3b170a1..b6a1e23 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_value_concept.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion_value_concept.sql @@ -3,5 +3,5 @@ select null::text as "subjectassertion_assertion_id", null::text as "value_concept_concept_curie" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_virtualbiorepository.sql similarity index 81% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_virtualbiorepository.sql index 93927d3..dd14313 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_virtualbiorepository.sql @@ -8,5 +8,5 @@ null::text as "vbr_readme", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository_contact.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_virtualbiorepository_contact.sql similarity index 69% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository_contact.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_virtualbiorepository_contact.sql index 25da532..7d01c0e 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository_contact.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_virtualbiorepository_contact.sql @@ -3,5 +3,5 @@ select null::text as "virtualbiorepository_vbr_id", null::integer as "contact_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_virtualbiorepository_external_id.sql similarity index 69% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_virtualbiorepository_external_id.sql index 3d2a785..ccbfcfa 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_virtualbiorepository_external_id.sql @@ -3,5 +3,5 @@ select null::text as "virtualbiorepository_vbr_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/package-lock.yml b/dbt_project/package-lock.yml new file mode 100644 index 0000000..ac29b3f --- /dev/null +++ b/dbt_project/package-lock.yml @@ -0,0 +1,4 @@ +packages: + - package: dbt-labs/dbt_utils + version: 1.3.3 +sha1_hash: 5ffdb7983bbd653b524c5344daf6cb5fd9eaf293 From 37b475c2922abf173596972b248f5ca5695af1df Mon Sep 17 00:00:00 2001 From: Amanda Warkow Date: Thu, 25 Jun 2026 13:07:48 -0400 Subject: [PATCH 05/17] =?UTF-8?q?=E2=99=BB=EF=B8=8F=20separate=20out=20phe?= =?UTF-8?q?notypes?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../chr_18/int/kf_chr_18_int_clinical.sql | 132 +++--------------- .../chr_18/int/kf_chr_18_int_phenotypes.sql | 105 ++++++++++++++ .../chr_18/int/kf_chr_18_int_sequencing.sql | 2 +- .../models/kids_first/chr_18/src/sources.yml | 2 +- .../kf_chr_18_stb_biospecimencollection.sql | 2 +- 5 files changed, 124 insertions(+), 119 deletions(-) create mode 100644 dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_phenotypes.sql diff --git a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_clinical.sql b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_clinical.sql index 06a0e9f..e197697 100644 --- a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_clinical.sql +++ b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_clinical.sql @@ -1,118 +1,18 @@ {{ config(materialized='table') }} - -with base_data as ( - select * from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} -), -phenotype_list as ( - select phenotype from ( - values - ('chiari_2'), ('pituitary_gland_abn'), ('cleft_palate'), ('hearing_loss'), - ('tetralogy_of_fallot'), ('conductive_hearing_loss'), ('holoprosencephaly'), ('choanal_atresia'), - ('aural_atresia'), ('midface_hypoplasia'), ('dysmyelination'), ('polymicrogyria'), - ('cryptorchidism'), ('sensorineural_hearing_loss'), ('cleft_lip'), ('imperforate_anus'), - ('microcephaly'), ('vertical_talus'), ('hypospadias'), ('rocker_bottom_foot'), - ('chiari_1'), ('ptosis'), ('strabismus'), ('bilateral_coxa_valga'), - ('cardiac_nos'), ('corpus_callosum_abn'), ('pulmonary_valve_stenosis'), ('metatarsus_varus'), - ('decreased_white_matter_volume'), ('macrocephaly'), ('suprasellar_cyst'), ('hydrocephalus'), - ('micropenis'), ('anal_stenosis'), ('congenital_heart_malformation'), ('bilateral_choanal_atresia'), - ('dandy_walker_malformation'), ('dandy_walker'), ('congenital_heart_defect'), ('aural_stenosis'), - ('kidney_malform'), ('pituitary_fossa_enlargement'), ('submucous_cleft'), ('virchow_robins_spaces'), - ('retinal_coloboma'), ('corneal_staphyloma'), ('club_foot'), ('macroglossia'), - ('dandy_walker_variant'), ('coanal_atresia'), ('occipatal_lobe_abn'), ('asd'), - ('vsd'), ('pectus_excavatum'), ('peripherial_pulmonary_stenosis'), ('sagittal_stenosis'), - ('hydronephrosis'), ('patent_ductus_arteriosus'), ('duanes_syndrome'), ('laryngomalacia'), - ('metatarsus_adductus'), ('ptosisbilateral'), ('microphallus'), ('sacral_agenesis'), - ('situs_inversus') - ) as t(phenotype) -), -unpivoted_phenotypes as ( select - bd.family_id, - bd.participant_id, - bd.family_relationship_target_participant_id, - bd.aliquot_id, - bd.consent_group, - bd.age_at_sample, - bd.sample_composition, - bd.race, - bd.sex, - bd.ethnicity, - bd.analyte_type, - bd.age_at_phenotype, - bd.affected_status, - bd.vital_status, - bd.sample_tissue_type, - pl.phenotype - from base_data bd - cross join phenotype_list pl - where case pl.phenotype - when 'chiari_2' then bd.chiari_2 - when 'pituitary_gland_abn' then bd.pituitary_gland_abn - when 'cleft_palate' then bd.cleft_palate - when 'hearing_loss' then bd.hearing_loss - when 'tetralogy_of_fallot' then bd.tetralogy_of_fallot - when 'conductive_hearing_loss' then bd.conductive_hearing_loss - when 'holoprosencephaly' then bd.holoprosencephaly - when 'choanal_atresia' then bd.choanal_atresia - when 'aural_atresia' then bd.aural_atresia - when 'midface_hypoplasia' then bd.midface_hypoplasia - when 'dysmyelination' then bd.dysmyelination - when 'polymicrogyria' then bd.polymicrogyria - when 'cryptorchidism' then bd.cryptorchidism - when 'sensorineural_hearing_loss' then bd.sensorineural_hearing_loss - when 'cleft_lip' then bd.cleft_lip - when 'imperforate_anus' then bd.imperforate_anus - when 'microcephaly' then bd.microcephaly - when 'vertical_talus' then bd.vertical_talus - when 'hypospadias' then bd.hypospadias - when 'rocker_bottom_foot' then bd.rocker_bottom_foot - when 'chiari_1' then bd.chiari_1 - when 'ptosis' then bd.ptosis - when 'strabismus' then bd.strabismus - when 'bilateral_coxa_valga' then bd.bilateral_coxa_valga - when 'cardiac_nos' then bd.cardiac_nos - when 'corpus_callosum_abn' then bd.corpus_callosum_abn - when 'pulmonary_valve_stenosis' then bd.pulmonary_valve_stenosis - when 'metatarsus_varus' then bd.metatarsus_varus - when 'decreased_white_matter_volume' then bd.decreased_white_matter_volume - when 'macrocephaly' then bd.macrocephaly - when 'suprasellar_cyst' then bd.suprasellar_cyst - when 'hydrocephalus' then bd.hydrocephalus - when 'micropenis' then bd.micropenis - when 'anal_stenosis' then bd.anal_stenosis - when 'congenital_heart_malformation' then bd.congenital_heart_malformation - when 'bilateral_choanal_atresia' then bd.bilateral_choanal_atresia - when 'dandy_walker_malformation' then bd.dandy_walker_malformation - when 'dandy_walker' then bd.dandy_walker - when 'congenital_heart_defect' then bd.congenital_heart_defect - when 'aural_stenosis' then bd.aural_stenosis - when 'kidney_malform' then bd.kidney_malform - when 'pituitary_fossa_enlargement' then bd.pituitary_fossa_enlargement - when 'submucous_cleft' then bd.submucous_cleft - when 'virchow_robins_spaces' then bd.virchow_robins_spaces - when 'retinal_coloboma' then bd.retinal_coloboma - when 'corneal_staphyloma' then bd.corneal_staphyloma - when 'club_foot' then bd.club_foot - when 'macroglossia' then bd.macroglossia - when 'dandy_walker_variant' then bd.dandy_walker_variant - when 'coanal_atresia' then bd.coanal_atresia - when 'occipatal_lobe_abn' then bd.occipatal_lobe_abn - when 'asd' then bd.asd - when 'vsd' then bd.vsd - when 'pectus_excavatum' then bd.pectus_excavatum - when 'peripherial_pulmonary_stenosis' then bd.peripherial_pulmonary_stenosis - when 'sagittal_stenosis' then bd.sagittal_stenosis - when 'hydronephrosis' then bd.hydronephrosis - when 'patent_ductus_arteriosus' then bd.patent_ductus_arteriosus - when 'duanes_syndrome' then bd.duanes_syndrome - when 'laryngomalacia' then bd.laryngomalacia - when 'metatarsus_adductus' then bd.metatarsus_adductus - when 'ptosisbilateral' then bd.ptosisbilateral - when 'microphallus' then bd.microphallus - when 'sacral_agenesis' then bd.sacral_agenesis - when 'situs_inversus' then bd.situs_inversus - end = 'present' -) - -select * from unpivoted_phenotypes - + family_id, + participant_id, + family_relationship_target_participant_id, + aliquot_id, + consent_group, + age_at_sample, + sample_composition, + race, + sex, + ethnicity, + analyte_type, + age_at_phenotype, + affected_status, + vital_status, + sample_tissue_type, + from ref{{'kf_chr_18_src_chr_18_phenotype_data'}} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_phenotypes.sql b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_phenotypes.sql new file mode 100644 index 0000000..4944cbd --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_phenotypes.sql @@ -0,0 +1,105 @@ +{{ config(materialized='table') }} + +with base_data as ( + select * from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +), +phenotype_list as ( + select phenotype from ( + values + ('chiari_2'), ('pituitary_gland_abn'), ('cleft_palate'), ('hearing_loss'), + ('tetralogy_of_fallot'), ('conductive_hearing_loss'), ('holoprosencephaly'), ('choanal_atresia'), + ('aural_atresia'), ('midface_hypoplasia'), ('dysmyelination'), ('polymicrogyria'), + ('cryptorchidism'), ('sensorineural_hearing_loss'), ('cleft_lip'), ('imperforate_anus'), + ('microcephaly'), ('vertical_talus'), ('hypospadias'), ('rocker_bottom_foot'), + ('chiari_1'), ('ptosis'), ('strabismus'), ('bilateral_coxa_valga'), + ('cardiac_nos'), ('corpus_callosum_abn'), ('pulmonary_valve_stenosis'), ('metatarsus_varus'), + ('decreased_white_matter_volume'), ('macrocephaly'), ('suprasellar_cyst'), ('hydrocephalus'), + ('micropenis'), ('anal_stenosis'), ('congenital_heart_malformation'), ('bilateral_choanal_atresia'), + ('dandy_walker_malformation'), ('dandy_walker'), ('congenital_heart_defect'), ('aural_stenosis'), + ('kidney_malform'), ('pituitary_fossa_enlargement'), ('submucous_cleft'), ('virchow_robins_spaces'), + ('retinal_coloboma'), ('corneal_staphyloma'), ('club_foot'), ('macroglossia'), + ('dandy_walker_variant'), ('coanal_atresia'), ('occipatal_lobe_abn'), ('asd'), + ('vsd'), ('pectus_excavatum'), ('peripherial_pulmonary_stenosis'), ('sagittal_stenosis'), + ('hydronephrosis'), ('patent_ductus_arteriosus'), ('duanes_syndrome'), ('laryngomalacia'), + ('metatarsus_adductus'), ('ptosisbilateral'), ('microphallus'), ('sacral_agenesis'), + ('situs_inversus') + ) as t(phenotype) +), +unpivoted_phenotypes as ( + select + bd.participant_id, + bd.age_at_phenotype, + pl.phenotype + from base_data bd + cross join phenotype_list pl + where case pl.phenotype + when 'chiari_2' then bd.chiari_2 + when 'pituitary_gland_abn' then bd.pituitary_gland_abn + when 'cleft_palate' then bd.cleft_palate + when 'hearing_loss' then bd.hearing_loss + when 'tetralogy_of_fallot' then bd.tetralogy_of_fallot + when 'conductive_hearing_loss' then bd.conductive_hearing_loss + when 'holoprosencephaly' then bd.holoprosencephaly + when 'choanal_atresia' then bd.choanal_atresia + when 'aural_atresia' then bd.aural_atresia + when 'midface_hypoplasia' then bd.midface_hypoplasia + when 'dysmyelination' then bd.dysmyelination + when 'polymicrogyria' then bd.polymicrogyria + when 'cryptorchidism' then bd.cryptorchidism + when 'sensorineural_hearing_loss' then bd.sensorineural_hearing_loss + when 'cleft_lip' then bd.cleft_lip + when 'imperforate_anus' then bd.imperforate_anus + when 'microcephaly' then bd.microcephaly + when 'vertical_talus' then bd.vertical_talus + when 'hypospadias' then bd.hypospadias + when 'rocker_bottom_foot' then bd.rocker_bottom_foot + when 'chiari_1' then bd.chiari_1 + when 'ptosis' then bd.ptosis + when 'strabismus' then bd.strabismus + when 'bilateral_coxa_valga' then bd.bilateral_coxa_valga + when 'cardiac_nos' then bd.cardiac_nos + when 'corpus_callosum_abn' then bd.corpus_callosum_abn + when 'pulmonary_valve_stenosis' then bd.pulmonary_valve_stenosis + when 'metatarsus_varus' then bd.metatarsus_varus + when 'decreased_white_matter_volume' then bd.decreased_white_matter_volume + when 'macrocephaly' then bd.macrocephaly + when 'suprasellar_cyst' then bd.suprasellar_cyst + when 'hydrocephalus' then bd.hydrocephalus + when 'micropenis' then bd.micropenis + when 'anal_stenosis' then bd.anal_stenosis + when 'congenital_heart_malformation' then bd.congenital_heart_malformation + when 'bilateral_choanal_atresia' then bd.bilateral_choanal_atresia + when 'dandy_walker_malformation' then bd.dandy_walker_malformation + when 'dandy_walker' then bd.dandy_walker + when 'congenital_heart_defect' then bd.congenital_heart_defect + when 'aural_stenosis' then bd.aural_stenosis + when 'kidney_malform' then bd.kidney_malform + when 'pituitary_fossa_enlargement' then bd.pituitary_fossa_enlargement + when 'submucous_cleft' then bd.submucous_cleft + when 'virchow_robins_spaces' then bd.virchow_robins_spaces + when 'retinal_coloboma' then bd.retinal_coloboma + when 'corneal_staphyloma' then bd.corneal_staphyloma + when 'club_foot' then bd.club_foot + when 'macroglossia' then bd.macroglossia + when 'dandy_walker_variant' then bd.dandy_walker_variant + when 'coanal_atresia' then bd.coanal_atresia + when 'occipatal_lobe_abn' then bd.occipatal_lobe_abn + when 'asd' then bd.asd + when 'vsd' then bd.vsd + when 'pectus_excavatum' then bd.pectus_excavatum + when 'peripherial_pulmonary_stenosis' then bd.peripherial_pulmonary_stenosis + when 'sagittal_stenosis' then bd.sagittal_stenosis + when 'hydronephrosis' then bd.hydronephrosis + when 'patent_ductus_arteriosus' then bd.patent_ductus_arteriosus + when 'duanes_syndrome' then bd.duanes_syndrome + when 'laryngomalacia' then bd.laryngomalacia + when 'metatarsus_adductus' then bd.metatarsus_adductus + when 'ptosisbilateral' then bd.ptosisbilateral + when 'microphallus' then bd.microphallus + when 'sacral_agenesis' then bd.sacral_agenesis + when 'situs_inversus' then bd.situs_inversus + end = 'present' +) + +select * from unpivoted_phenotypes + diff --git a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql index 7446e88..5b82075 100644 --- a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql +++ b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql @@ -15,5 +15,5 @@ library_source, platform, instrument_model - from {{ source('chr_18', 'ha_delivery_manifest_6735') }} + from {{ ref('kf_chr_18_src_ha_delivery_manifest_6735') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/src/sources.yml b/dbt_project/models/kids_first/chr_18/src/sources.yml index d60f199..4a54e8a 100644 --- a/dbt_project/models/kids_first/chr_18/src/sources.yml +++ b/dbt_project/models/kids_first/chr_18/src/sources.yml @@ -1,6 +1,6 @@ sources: - name: chr_18 - schema: inc_chr_18_src + schema: kf_chr_18_src tables: - name: chr_18_phenotype_data description: Source table for chr_18_phenotype_data. diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_biospecimencollection.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_biospecimencollection.sql index abbf60c..8fcde72 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_biospecimencollection.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_biospecimencollection.sql @@ -2,7 +2,7 @@ select null::text as "biospecimen_collection_id", - null::text as "age_at_collection", + age_at_sample as "age_at_collection", null::text as "method", null::text as "site", null::text as "spatial_qualifier", From 3b6a07c637b064358c7bb5ddc44839b8d36d0187 Mon Sep 17 00:00:00 2001 From: Amanda Warkow Date: Mon, 29 Jun 2026 15:04:55 -0400 Subject: [PATCH 06/17] =?UTF-8?q?=E2=99=BB=EF=B8=8F=20fixing=20seq=20manif?= =?UTF-8?q?est=20source?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- ...f_chr_18_src_ha_delivery_manifest_6735.sql | 19 ------ .../kf_chr_18_src_terra_manifest_v2.sql | 67 +++++++++++++++++++ 2 files changed, 67 insertions(+), 19 deletions(-) delete mode 100644 dbt_project/models/kids_first/chr_18/src/Sequencing_Data/kf_chr_18_src_ha_delivery_manifest_6735.sql create mode 100644 dbt_project/models/kids_first/chr_18/src/Sequencing_Data/kf_chr_18_src_terra_manifest_v2.sql diff --git a/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/kf_chr_18_src_ha_delivery_manifest_6735.sql b/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/kf_chr_18_src_ha_delivery_manifest_6735.sql deleted file mode 100644 index 6cb41ba..0000000 --- a/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/kf_chr_18_src_ha_delivery_manifest_6735.sql +++ /dev/null @@ -1,19 +0,0 @@ -{{ config(materialized='table') }} - - select - ROW_NUMBER() OVER () AS kf_index, - "type"::text as type, - "sample.sample_id"::text as sample, - "file_name"::text as file_name, - "file_type"::text as file_type, - "file_description"::text as file_description, - "file_size"::integer as file_size, - "md5sum"::text as md5sum, - "library_id"::text as library_id, - "library_strategy"::text as library_strategy, - "library_layout"::text as library_layout, - "library_source"::text as library_source, - "platform"::text as platform, - "instrument_model"::text as instrument_model - from {{ source('chr_18', 'ha_delivery_manifest_6735') }} - \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/kf_chr_18_src_terra_manifest_v2.sql b/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/kf_chr_18_src_terra_manifest_v2.sql new file mode 100644 index 0000000..39b5abc --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/kf_chr_18_src_terra_manifest_v2.sql @@ -0,0 +1,67 @@ +{{ config(materialized='table') }} + + select + ROW_NUMBER() OVER () AS kf_index, + "entity:sample_id"::text as sample_id, + "project"::text as project, + "collaborator_sample_id"::text as collaborator_sample_id, + "version"::text as version, + "data_type"::text as data_type, + "pdo"::text as pdo, + "release_date"::date as release_date, + "reference_sequence_name"::text as reference_sequence_name, + "collaborator_participant_id"::text as collaborator_participant_id, + "cram_path"::text as cram_path, + "crai_path"::text as crai_path, + "md5_path"::text as md5_path, + "root_sample_id"::text as root_sample_id, + "mean_coverage"::float as mean_coverage, + "adapter_rate"::float as adapter_rate, + "pf_hq_aligned_q20_bases"::integer as pf_hq_aligned_q20_bases, + "pf_hq_aligned_reads"::integer as pf_hq_aligned_reads, + "pf_mismatch_rate"::float as pf_mismatch_rate, + "pf_noise_reads"::integer as pf_noise_reads, + "pf_reads"::integer as pf_reads, + "pf_reads_aligned"::integer as pf_reads_aligned, + "total_reads"::integer as total_reads, + "mean_read_length"::integer as mean_read_length, + "pf_reads_rate"::integer as pf_reads_rate, + "pf_reads_aligned_rate"::float as pf_reads_aligned_rate, + "pf_aligned_bases"::integer as pf_aligned_bases, + "reads_aligned_in_pairs"::integer as reads_aligned_in_pairs, + "contamination_rate"::integer as contamination_rate, + "genome_territory"::integer as genome_territory, + "exc_baseq_rate"::float as exc_baseq_rate, + "exc_dupe_rate"::float as exc_dupe_rate, + "exc_mapq_rate"::integer as exc_mapq_rate, + "exc_overlap_rate"::float as exc_overlap_rate, + "10x_rate"::float as 10x_rate, + "20x_rate"::float as 20x_rate, + "exc_total_rate"::float as exc_total_rate, + "exc_unpaired_rate"::float as exc_unpaired_rate, + "chimera_rate"::float as chimera_rate, + "het_snp_q"::integer as het_snp_q, + "het_snp_sensitivity"::float as het_snp_sensitivity, + "library-1_estimated_library_size"::integer as library-1_estimated_library_size, + "library-1_mean_insert_size"::float as library-1_mean_insert_size, + "library-1_name"::text as library-1_name, + "library-1_pair_orientation"::text as library-1_pair_orientation, + "library-1_pct_exc_dupe"::integer as library-1_pct_exc_dupe, + "library-1_percent_duplication"::float as library-1_percent_duplication, + "library-1_read_pairs"::integer as library-1_read_pairs, + "mean_insert_size"::float as mean_insert_size, + "median_coverage"::integer as median_coverage, + "median_insert_size"::integer as median_insert_size, + "pf_hq_aligned_bases"::integer as pf_hq_aligned_bases, + "pf_hq_error_rate"::float as pf_hq_error_rate, + "pf_reads_improper_pairs"::integer as pf_reads_improper_pairs, + "read_pair_duplicates"::integer as read_pair_duplicates, + "read_pair_optical_duplicates"::integer as read_pair_optical_duplicates, + "reads_aligned_in_pairs_rate"::float as reads_aligned_in_pairs_rate, + "sample"::text as sample, + "strand_balance"::float as strand_balance, + "width_of_10_percent"::integer as width_of_10_percent, + "width_of_50_percent"::integer as width_of_50_percent, + "width_of_99_percent"::integer as width_of_99_percent +from {{ source('chr_18', 'terra_manifest_v2') }} + \ No newline at end of file From 756383fe5f9882ada8f965922709f4dd0c661f84 Mon Sep 17 00:00:00 2001 From: Amanda Warkow Date: Mon, 29 Jun 2026 15:05:20 -0400 Subject: [PATCH 07/17] =?UTF-8?q?=E2=9C=A8=20int=20model=20for=20terra=20m?= =?UTF-8?q?anifest?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../chr_18/int/kf_chr_18_int_sequencing.sql | 70 ++++++++++++++----- 1 file changed, 53 insertions(+), 17 deletions(-) diff --git a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql index 5b82075..4d731ea 100644 --- a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql +++ b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql @@ -1,19 +1,55 @@ {{ config(materialized='table') }} - select - kf_index, - type, - sample, - file_name, - file_type, - file_description, - file_size, - md5sum, - library_id, - library_strategy, - library_layout, - library_source, - platform, - instrument_model - from {{ ref('kf_chr_18_src_ha_delivery_manifest_6735') }} - \ No newline at end of file + with base as ( + select + sample_id, + collaborator_sample_id, + data_type, + collaborator_participant_id, + root_sample_id, + total_reads, + mean_read_length, + reference_sequence_name + from {{ ref('kf_chr_18_src_terra_manifest_v2') }} + ), + + crams as ( + select + root_sample_id, + cram_path + from {{ ref('kf_chr_18_src_terra_manifest_v2') }} + ), + + crais as ( + select + root_sample_id, + crai_path + from {{ ref('kf_chr_18_src_terra_manifest_v2') }} as crais + ), + + md5s as ( + select + root_sample_id, + md5_path + from {{ ref('kf_chr_18_src_terra_manifest_v2') }} as md5s + ) + + select + base.sample_id, + base.collaborator_sample_id, + base.data_type, + base.collaborator_participant_id, + base.root_sample_id, + base.total_reads, + base.mean_read_length, + base.reference_sequence_name, + crams.cram_path, + crais.crai_path, + md5s.md5_path + from base + left join crams + on base.root_sample_id = crams.root_sample_id + left join crais + on base.root_sample_id = crais.root_sample_id + left join md5s + on base.root_sample_id = md5s.root_sample_id \ No newline at end of file From 09147cd2876a6d6a0081c2751cfedb7e1227d8bf Mon Sep 17 00:00:00 2001 From: Amanda Warkow Date: Tue, 30 Jun 2026 13:49:42 -0400 Subject: [PATCH 08/17] =?UTF-8?q?=F0=9F=93=9D=20fix=20documentation?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../kf_chr_18_src_terra_manifest_v2.sql | 2 +- .../models/kids_first/chr_18/src/sources.yml | 150 ++++++++++++++---- 2 files changed, 123 insertions(+), 29 deletions(-) diff --git a/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/kf_chr_18_src_terra_manifest_v2.sql b/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/kf_chr_18_src_terra_manifest_v2.sql index 39b5abc..fb620e8 100644 --- a/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/kf_chr_18_src_terra_manifest_v2.sql +++ b/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/kf_chr_18_src_terra_manifest_v2.sql @@ -63,5 +63,5 @@ "width_of_10_percent"::integer as width_of_10_percent, "width_of_50_percent"::integer as width_of_50_percent, "width_of_99_percent"::integer as width_of_99_percent -from {{ source('chr_18', 'terra_manifest_v2') }} +from {{ source('chr_18', 'Terra_Manifest_v2') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/src/sources.yml b/dbt_project/models/kids_first/chr_18/src/sources.yml index 4a54e8a..63a7b36 100644 --- a/dbt_project/models/kids_first/chr_18/src/sources.yml +++ b/dbt_project/models/kids_first/chr_18/src/sources.yml @@ -169,35 +169,129 @@ sources: description: '{{ doc("chr_18_phenotype_data_situs_inversus") }}' - name: Sample Tissue Type description: '{{ doc("chr_18_phenotype_data_sample_tissue_type") }}' - - name: ha_delivery_manifest_6735 - description: Source table for ha_delivery_manifest_6735. + - name: terra_manifest_v2 + description: Source table for terra_manifest_v2. columns: - - name: type - description: '{{ doc("ha_delivery_manifest_6735_type") }}' - - name: sample.sample_id - description: '{{ doc("ha_delivery_manifest_6735_sample") }}' - - name: file_name - description: '{{ doc("ha_delivery_manifest_6735_file_name") }}' - - name: file_type - description: '{{ doc("ha_delivery_manifest_6735_file_type") }}' - - name: file_description - description: '{{ doc("ha_delivery_manifest_6735_file_description") }}' - - name: file_size - description: '{{ doc("ha_delivery_manifest_6735_file_size") }}' - - name: md5sum - description: '{{ doc("ha_delivery_manifest_6735_md5sum") }}' - - name: library_id - description: '{{ doc("ha_delivery_manifest_6735_library_id") }}' - - name: library_strategy - description: '{{ doc("ha_delivery_manifest_6735_library_strategy") }}' - - name: library_layout - description: '{{ doc("ha_delivery_manifest_6735_library_layout") }}' - - name: library_source - description: '{{ doc("ha_delivery_manifest_6735_library_source") }}' - - name: platform - description: '{{ doc("ha_delivery_manifest_6735_platform") }}' - - name: instrument_model - description: '{{ doc("ha_delivery_manifest_6735_instrument_model") }}' + - name: entity:sample_id + description: '{{ doc("terra_manifest_v2_entity_sample_id") }}' + - name: project + description: '{{ doc("terra_manifest_v2_project") }}' + - name: collaborator_sample_id + description: '{{ doc("terra_manifest_v2_collaborator_sample_id") }}' + - name: version + description: '{{ doc("terra_manifest_v2_version") }}' + - name: data_type + description: '{{ doc("terra_manifest_v2_data_type") }}' + - name: pdo + description: '{{ doc("terra_manifest_v2_pdo") }}' + - name: release_date + description: '{{ doc("terra_manifest_v2_release_date") }}' + - name: reference_sequence_name + description: '{{ doc("terra_manifest_v2_reference_sequence_name") }}' + - name: collaborator_participant_id + description: '{{ doc("terra_manifest_v2_collaborator_participant_id") }}' + - name: cram_path + description: '{{ doc("terra_manifest_v2_cram_path") }}' + - name: crai_path + description: '{{ doc("terra_manifest_v2_crai_path") }}' + - name: md5_path + description: '{{ doc("terra_manifest_v2_md5_path") }}' + - name: root_sample_id + description: '{{ doc("terra_manifest_v2_root_sample_id") }}' + - name: mean_coverage + description: '{{ doc("terra_manifest_v2_mean_coverage") }}' + - name: adapter_rate + description: '{{ doc("terra_manifest_v2_adapter_rate") }}' + - name: pf_hq_aligned_q20_bases + description: '{{ doc("terra_manifest_v2_pf_hq_aligned_q20_bases") }}' + - name: pf_hq_aligned_reads + description: '{{ doc("terra_manifest_v2_pf_hq_aligned_reads") }}' + - name: pf_mismatch_rate + description: '{{ doc("terra_manifest_v2_pf_mismatch_rate") }}' + - name: pf_noise_reads + description: '{{ doc("terra_manifest_v2_pf_noise_reads") }}' + - name: pf_reads + description: '{{ doc("terra_manifest_v2_pf_reads") }}' + - name: pf_reads_aligned + description: '{{ doc("terra_manifest_v2_pf_reads_aligned") }}' + - name: total_reads + description: '{{ doc("terra_manifest_v2_total_reads") }}' + - name: mean_read_length + description: '{{ doc("terra_manifest_v2_mean_read_length") }}' + - name: pf_reads_rate + description: '{{ doc("terra_manifest_v2_pf_reads_rate") }}' + - name: pf_reads_aligned_rate + description: '{{ doc("terra_manifest_v2_pf_reads_aligned_rate") }}' + - name: pf_aligned_bases + description: '{{ doc("terra_manifest_v2_pf_aligned_bases") }}' + - name: reads_aligned_in_pairs + description: '{{ doc("terra_manifest_v2_reads_aligned_in_pairs") }}' + - name: contamination_rate + description: '{{ doc("terra_manifest_v2_contamination_rate") }}' + - name: genome_territory + description: '{{ doc("terra_manifest_v2_genome_territory") }}' + - name: exc_baseq_rate + description: '{{ doc("terra_manifest_v2_exc_baseq_rate") }}' + - name: exc_dupe_rate + description: '{{ doc("terra_manifest_v2_exc_dupe_rate") }}' + - name: exc_mapq_rate + description: '{{ doc("terra_manifest_v2_exc_mapq_rate") }}' + - name: exc_overlap_rate + description: '{{ doc("terra_manifest_v2_exc_overlap_rate") }}' + - name: 10x_rate + description: '{{ doc("terra_manifest_v2_10x_rate") }}' + - name: 20x_rate + description: '{{ doc("terra_manifest_v2_20x_rate") }}' + - name: exc_total_rate + description: '{{ doc("terra_manifest_v2_exc_total_rate") }}' + - name: exc_unpaired_rate + description: '{{ doc("terra_manifest_v2_exc_unpaired_rate") }}' + - name: chimera_rate + description: '{{ doc("terra_manifest_v2_chimera_rate") }}' + - name: het_snp_q + description: '{{ doc("terra_manifest_v2_het_snp_q") }}' + - name: het_snp_sensitivity + description: '{{ doc("terra_manifest_v2_het_snp_sensitivity") }}' + - name: library-1_estimated_library_size + description: '{{ doc("terra_manifest_v2_library-1_estimated_library_size") }}' + - name: library-1_mean_insert_size + description: '{{ doc("terra_manifest_v2_library-1_mean_insert_size") }}' + - name: library-1_name + description: '{{ doc("terra_manifest_v2_library-1_pair_orientation") }}' + - name: library-1_pct_exc_dupe + description: '{{ doc("terra_manifest_v2_library-1_pct_exc_dupe") }}' + - name: library-1_percent_duplication + description: '{{ doc("terra_manifest_v2_library-1_percent_duplication") }}' + - name: library-1_read_pairs + description: '{{ doc("terra_manifest_v2_library-1_read_pairs") }}' + - name: mean_insert_size + description: '{{ doc("terra_manifest_v2_mean_insert_size") }}' + - name: median_coverage + description: '{{ doc("terra_manifest_v2_median_coverage") }}' + - name: median_insert_size + description: '{{ doc("terra_manifest_v2_median_insert_size") }}' + - name: pf_hq_aligned_bases + description: '{{ doc("terra_manifest_v2_pf_hq_aligned_bases") }}' + - name: pf_hq_error_rate + description: '{{ doc("terra_manifest_v2_pf_hq_error_rate") }}' + - name: pf_reads_improper_pairs + description: '{{ doc("terra_manifest_v2_pf_reads_improper_pairs") }}' + - name: read_pair_duplicates + description: '{{ doc("terra_manifest_v2_read_pair_duplicates") }}' + - name: read_pair_optical_duplicates + description: '{{ doc("terra_manifest_v2_read_pair_optical_duplicates") }}' + - name: reads_aligned_in_pairs_rate + description: '{{ doc("terra_manifest_v2_reads_aligned_in_pairs_rate") }}' + - name: sample + description: '{{ doc("terra_manifest_v2_sample") }}' + - name: strand_balance + description: '{{ doc("terra_manifest_v2_strand_balance") }}' + - name: width_of_10_percent + description: '{{ doc("terra_manifest_v2_width_of_10_percent") }}' + - name: width_of_50_percent + description: '{{ doc("terra_manifest_v2_width_of_50_percent") }}' + - name: width_of_99_percent + description: '{{ doc("terra_manifest_v2_width_of_99_percent") }}' - name: s3_scrape_cody description: Source table for s3_scrape_cody. columns: From 4463f6ade22149e5eb227895a8984a3d1ae37d0b Mon Sep 17 00:00:00 2001 From: Amanda Warkow Date: Tue, 30 Jun 2026 13:50:30 -0400 Subject: [PATCH 09/17] =?UTF-8?q?=E2=9C=A8=20add=20in=20ingest=20transform?= =?UTF-8?q?ations?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../chr_18/int/kf_chr_18_int_s3.sql | 21 ++++++--- .../chr_18/int/kf_chr_18_int_sequencing.sql | 44 ++++++++++++------- 2 files changed, 42 insertions(+), 23 deletions(-) diff --git a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_s3.sql b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_s3.sql index bedc2f8..6fbab6a 100644 --- a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_s3.sql +++ b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_s3.sql @@ -1,12 +1,19 @@ {{ config(materialized='table') }} select - kf_index, - size, - key, - etag, - bucket, - lastmodified, - storageclass + 's3://' + bucket + '/' + key as s3_path, + case + when key.like '%.cram' then 'cram' + when key.like '%.crai' then 'crai' + when key.like '%.md5' then 'md5' + else null + end as file_format, + case + when key.like '%.cram' then 'Aligned Reads' + when key.like '%.crai' then 'Aligned Reads Index' + when key.like '%.md5' then 'Other' + else null + end as data_type, + '{etag' + replace(etag, '"', "") + '}' as hash_dict from {{ ref('kf_chr_18_src_s3_scrape_cody') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql index 4d731ea..a9aef9b 100644 --- a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql +++ b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql @@ -2,11 +2,11 @@ with base as ( select - sample_id, - collaborator_sample_id, - data_type, - collaborator_participant_id, - root_sample_id, + -- sample_id, + -- collaborator_sample_id, + collaborator_participant_id as participant_id, + root_sample_id as sample_id, + data_type as sequencing_strategy, total_reads, mean_read_length, reference_sequence_name @@ -16,40 +16,52 @@ crams as ( select root_sample_id, - cram_path + replace(cram_path, + "gs://fc-2092c58b-ce12-42e7-9a8e-64b78440537a/", + "s3://kf-strides-study-us-east-1-prd-sd-1nns3k8v/source/", + ) as cram_path from {{ ref('kf_chr_18_src_terra_manifest_v2') }} ), crais as ( select root_sample_id, - crai_path + replace(crai_path, + "gs://fc-2092c58b-ce12-42e7-9a8e-64b78440537a/", + "s3://kf-strides-study-us-east-1-prd-sd-1nns3k8v/source/", + ) as crai_path from {{ ref('kf_chr_18_src_terra_manifest_v2') }} as crais ), md5s as ( select root_sample_id, - md5_path + replace(md5_path, + "gs://fc-2092c58b-ce12-42e7-9a8e-64b78440537a/", + "s3://kf-strides-study-us-east-1-prd-sd-1nns3k8v/source/", + ) as md5_path from {{ ref('kf_chr_18_src_terra_manifest_v2') }} as md5s ) select + -- base.sample_id, + -- base.collaborator_sample_id, + base.participant_id, base.sample_id, - base.collaborator_sample_id, - base.data_type, - base.collaborator_participant_id, - base.root_sample_id, + base.sequencing_strategy, base.total_reads, base.mean_read_length, base.reference_sequence_name, crams.cram_path, crais.crai_path, - md5s.md5_path + md5s.md5_path, + 'False' as harmonized, + 'False' as paired_end, + 'Broad Institute' as sequencing_center_name from base left join crams - on base.root_sample_id = crams.root_sample_id + on base.sample_id = crams.root_sample_id left join crais - on base.root_sample_id = crais.root_sample_id + on base.sample_id = crais.root_sample_id left join md5s - on base.root_sample_id = md5s.root_sample_id \ No newline at end of file + on base.sample_id = md5s.root_sample_id \ No newline at end of file From 5894c5673d1f7e5591c3ad1e190fc1367b47db1a Mon Sep 17 00:00:00 2001 From: Amanda Warkow Date: Tue, 30 Jun 2026 14:36:27 -0400 Subject: [PATCH 10/17] =?UTF-8?q?=E2=99=BB=EF=B8=8F=20setup=20stable=20tab?= =?UTF-8?q?les?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../models/kids_first/chr_18/int/kf_chr_18_int_s3.sql | 1 + .../kids_first/chr_18/stb/kf_chr_18_stb_aliquot.sql | 4 ++-- .../kids_first/chr_18/stb/kf_chr_18_stb_demographics.sql | 4 ++-- .../models/kids_first/chr_18/stb/kf_chr_18_stb_file.sql | 8 ++++---- .../kids_first/chr_18/stb/kf_chr_18_stb_filehash.sql | 6 +++--- .../models/kids_first/chr_18/stb/kf_chr_18_stb_sample.sql | 6 +++--- 6 files changed, 15 insertions(+), 14 deletions(-) diff --git a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_s3.sql b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_s3.sql index 6fbab6a..93aef6b 100644 --- a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_s3.sql +++ b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_s3.sql @@ -2,6 +2,7 @@ select 's3://' + bucket + '/' + key as s3_path, + split_part(key, '/', -1) as file_name, case when key.like '%.cram' then 'cram' when key.like '%.crai' then 'crai' diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_aliquot.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_aliquot.sql index d5e2293..d56561f 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_aliquot.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_aliquot.sql @@ -2,7 +2,7 @@ select null::text as "aliquot_id", - null::text as "sample_id", + sample_id as "sample_id", null::text as "availablity_status", null::text as "quantity_number", null::text as "quantity_unit", @@ -10,5 +10,5 @@ null::text as "concentration_unit", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_int_sequencing') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_demographics.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_demographics.sql index 06cd0c2..1437dbe 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_demographics.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_demographics.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} select - null::text as "subject_id", + participant_id as "subject_id", sex as "sex", ethnicity as "ethnicity", null::text as "down_syndrome_status", -- could map to Not Applicable? @@ -10,5 +10,5 @@ null::integer as "age_at_first_engagement", -- age at phenotype? or sample? null::text as "access_policy_id", null::text as "study_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_int_clinical') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file.sql index f79e037..d7ab142 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file.sql @@ -3,10 +3,10 @@ select null::text as "file_id", file_name as "filename", - null::text as "format", + file_format as "format", null::text as "data_category", - file_type as "data_type", - file_size as "size", + data_type as "data_type", + size as "size", -- Need to determine when DRS indexing will happen -- null::text as "staging_url", -- null::text as "release_url", @@ -14,5 +14,5 @@ null::text as "access_policy_id", null::text as "study_id", null::integer as "hash_id" - from {{ ref('kf_chr_18_src_ha_delivery_manifest_6735') }} + from {{ ref('kf_chr_18_int_s3') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_filehash.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_filehash.sql index 3e09bd4..a198eea 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_filehash.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_filehash.sql @@ -2,7 +2,7 @@ select null::integer as "id", - 'md5sum' as "hash_type", - md5sum as "hash_value" - from {{ ref('kf_chr_18_src_ha_delivery_manifest_6735') }} + 'etag' as "hash_type", + etag as "hash_value" + from {{ ref('kf_chr_18_int_s3') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample.sql index 1ea159e..691c86b 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample.sql @@ -1,14 +1,14 @@ {{ config(materialized='table') }} select - sample as "sample_id", + sample_id as "sample_id", null::text as "biospecimen_collection_id", null::text as "parent_sample_id", - type as "sample_type", + sequencing_strategy as "sample_type", null::text as "availablity_status", null::text as "quantity_number", null::text as "quantity_unit", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('kf_chr_18_src_ha_delivery_manifest_6735') }} + from {{ ref('kf_chr_18_int_sequencing') }} \ No newline at end of file From dea998433f28b5350739a8c26b7ce0c623cc703f Mon Sep 17 00:00:00 2001 From: Amanda Warkow Date: Tue, 30 Jun 2026 16:46:25 -0400 Subject: [PATCH 11/17] =?UTF-8?q?=E2=99=BB=EF=B8=8F=20fix=20phenotypes?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../chr_18/int/kf_chr_18_int_phenotypes.sql | 168 ++++++++---------- 1 file changed, 74 insertions(+), 94 deletions(-) diff --git a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_phenotypes.sql b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_phenotypes.sql index 4944cbd..ebb1f76 100644 --- a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_phenotypes.sql +++ b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_phenotypes.sql @@ -3,102 +3,82 @@ with base_data as ( select * from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} ), -phenotype_list as ( - select phenotype from ( - values - ('chiari_2'), ('pituitary_gland_abn'), ('cleft_palate'), ('hearing_loss'), - ('tetralogy_of_fallot'), ('conductive_hearing_loss'), ('holoprosencephaly'), ('choanal_atresia'), - ('aural_atresia'), ('midface_hypoplasia'), ('dysmyelination'), ('polymicrogyria'), - ('cryptorchidism'), ('sensorineural_hearing_loss'), ('cleft_lip'), ('imperforate_anus'), - ('microcephaly'), ('vertical_talus'), ('hypospadias'), ('rocker_bottom_foot'), - ('chiari_1'), ('ptosis'), ('strabismus'), ('bilateral_coxa_valga'), - ('cardiac_nos'), ('corpus_callosum_abn'), ('pulmonary_valve_stenosis'), ('metatarsus_varus'), - ('decreased_white_matter_volume'), ('macrocephaly'), ('suprasellar_cyst'), ('hydrocephalus'), - ('micropenis'), ('anal_stenosis'), ('congenital_heart_malformation'), ('bilateral_choanal_atresia'), - ('dandy_walker_malformation'), ('dandy_walker'), ('congenital_heart_defect'), ('aural_stenosis'), - ('kidney_malform'), ('pituitary_fossa_enlargement'), ('submucous_cleft'), ('virchow_robins_spaces'), - ('retinal_coloboma'), ('corneal_staphyloma'), ('club_foot'), ('macroglossia'), - ('dandy_walker_variant'), ('coanal_atresia'), ('occipatal_lobe_abn'), ('asd'), - ('vsd'), ('pectus_excavatum'), ('peripherial_pulmonary_stenosis'), ('sagittal_stenosis'), - ('hydronephrosis'), ('patent_ductus_arteriosus'), ('duanes_syndrome'), ('laryngomalacia'), - ('metatarsus_adductus'), ('ptosisbilateral'), ('microphallus'), ('sacral_agenesis'), - ('situs_inversus') - ) as t(phenotype) -), unpivoted_phenotypes as ( select - bd.participant_id, - bd.age_at_phenotype, - pl.phenotype - from base_data bd - cross join phenotype_list pl - where case pl.phenotype - when 'chiari_2' then bd.chiari_2 - when 'pituitary_gland_abn' then bd.pituitary_gland_abn - when 'cleft_palate' then bd.cleft_palate - when 'hearing_loss' then bd.hearing_loss - when 'tetralogy_of_fallot' then bd.tetralogy_of_fallot - when 'conductive_hearing_loss' then bd.conductive_hearing_loss - when 'holoprosencephaly' then bd.holoprosencephaly - when 'choanal_atresia' then bd.choanal_atresia - when 'aural_atresia' then bd.aural_atresia - when 'midface_hypoplasia' then bd.midface_hypoplasia - when 'dysmyelination' then bd.dysmyelination - when 'polymicrogyria' then bd.polymicrogyria - when 'cryptorchidism' then bd.cryptorchidism - when 'sensorineural_hearing_loss' then bd.sensorineural_hearing_loss - when 'cleft_lip' then bd.cleft_lip - when 'imperforate_anus' then bd.imperforate_anus - when 'microcephaly' then bd.microcephaly - when 'vertical_talus' then bd.vertical_talus - when 'hypospadias' then bd.hypospadias - when 'rocker_bottom_foot' then bd.rocker_bottom_foot - when 'chiari_1' then bd.chiari_1 - when 'ptosis' then bd.ptosis - when 'strabismus' then bd.strabismus - when 'bilateral_coxa_valga' then bd.bilateral_coxa_valga - when 'cardiac_nos' then bd.cardiac_nos - when 'corpus_callosum_abn' then bd.corpus_callosum_abn - when 'pulmonary_valve_stenosis' then bd.pulmonary_valve_stenosis - when 'metatarsus_varus' then bd.metatarsus_varus - when 'decreased_white_matter_volume' then bd.decreased_white_matter_volume - when 'macrocephaly' then bd.macrocephaly - when 'suprasellar_cyst' then bd.suprasellar_cyst - when 'hydrocephalus' then bd.hydrocephalus - when 'micropenis' then bd.micropenis - when 'anal_stenosis' then bd.anal_stenosis - when 'congenital_heart_malformation' then bd.congenital_heart_malformation - when 'bilateral_choanal_atresia' then bd.bilateral_choanal_atresia - when 'dandy_walker_malformation' then bd.dandy_walker_malformation - when 'dandy_walker' then bd.dandy_walker - when 'congenital_heart_defect' then bd.congenital_heart_defect - when 'aural_stenosis' then bd.aural_stenosis - when 'kidney_malform' then bd.kidney_malform - when 'pituitary_fossa_enlargement' then bd.pituitary_fossa_enlargement - when 'submucous_cleft' then bd.submucous_cleft - when 'virchow_robins_spaces' then bd.virchow_robins_spaces - when 'retinal_coloboma' then bd.retinal_coloboma - when 'corneal_staphyloma' then bd.corneal_staphyloma - when 'club_foot' then bd.club_foot - when 'macroglossia' then bd.macroglossia - when 'dandy_walker_variant' then bd.dandy_walker_variant - when 'coanal_atresia' then bd.coanal_atresia - when 'occipatal_lobe_abn' then bd.occipatal_lobe_abn - when 'asd' then bd.asd - when 'vsd' then bd.vsd - when 'pectus_excavatum' then bd.pectus_excavatum - when 'peripherial_pulmonary_stenosis' then bd.peripherial_pulmonary_stenosis - when 'sagittal_stenosis' then bd.sagittal_stenosis - when 'hydronephrosis' then bd.hydronephrosis - when 'patent_ductus_arteriosus' then bd.patent_ductus_arteriosus - when 'duanes_syndrome' then bd.duanes_syndrome - when 'laryngomalacia' then bd.laryngomalacia - when 'metatarsus_adductus' then bd.metatarsus_adductus - when 'ptosisbilateral' then bd.ptosisbilateral - when 'microphallus' then bd.microphallus - when 'sacral_agenesis' then bd.sacral_agenesis - when 'situs_inversus' then bd.situs_inversus - end = 'present' + participant_id, + age_at_phenotype, + phenotype + from base_data + unpivot ( + value for phenotype in ( + chiari_2, + pituitary_gland_abn, + cleft_palate, + hearing_loss, + tetralogy_of_fallot, + conductive_hearing_loss, + holoprosencephaly, + choanal_atresia, + aural_atresia, + midface_hypoplasia, + dysmyelination, + polymicrogyria, + cryptorchidism, + sensorineural_hearing_loss, + cleft_lip, + imperforate_anus, + microcephaly, + vertical_talus, + hypospadias, + rocker_bottom_foot, + chiari_1, + ptosis, + strabismus, + bilateral_coxa_valga, + cardiac_nos, + corpus_callosum_abn, + pulmonary_valve_stenosis, + metatarsus_varus, + decreased_white_matter_volume, + macrocephaly, + suprasellar_cyst, + hydrocephalus, + micropenis, + anal_stenosis, + congenital_heart_malformation, + bilateral_choanal_atresia, + dandy_walker_malformation, + dandy_walker, + congenital_heart_defect, + aural_stenosis, + kidney_malform, + pituitary_fossa_enlargement, + submucous_cleft, + virchow_robins_spaces, + retinal_coloboma, + corneal_staphyloma, + club_foot, + macroglossia, + dandy_walker_variant, + coanal_atresia, + occipatal_lobe_abn, + asd, + vsd, + pectus_excavatum, + peripherial_pulmonary_stenosis, + sagittal_stenosis, + hydronephrosis, + patent_ductus_arteriosus, + duanes_syndrome, + laryngomalacia, + metatarsus_adductus, + ptosisbilateral, + microphallus, + sacral_agenesis, + situs_inversus + ) + ) + where value = 'present' ) select * from unpivoted_phenotypes From 6e5e509bdb0011aad653e40f25d7b7460ae4ed69 Mon Sep 17 00:00:00 2001 From: Amanda Warkow Date: Tue, 30 Jun 2026 17:00:35 -0400 Subject: [PATCH 12/17] =?UTF-8?q?=E2=9C=8F=EF=B8=8F=20adding=20some=20comm?= =?UTF-8?q?ents?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../kids_first/chr_18/int/kf_chr_18_int_s3.sql | 15 ++++++++------- .../chr_18/int/kf_chr_18_int_sequencing.sql | 3 +++ .../stb/kf_chr_18_stb_familyrelationship.sql | 2 ++ 3 files changed, 13 insertions(+), 7 deletions(-) diff --git a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_s3.sql b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_s3.sql index 93aef6b..b637c65 100644 --- a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_s3.sql +++ b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_s3.sql @@ -4,17 +4,18 @@ 's3://' + bucket + '/' + key as s3_path, split_part(key, '/', -1) as file_name, case - when key.like '%.cram' then 'cram' - when key.like '%.crai' then 'crai' - when key.like '%.md5' then 'md5' + when key like '%.cram' then 'cram' + when key like '%.crai' then 'crai' + when key like '%.md5' then 'md5' else null end as file_format, case - when key.like '%.cram' then 'Aligned Reads' - when key.like '%.crai' then 'Aligned Reads Index' - when key.like '%.md5' then 'Other' + when key like '%.cram' then 'Aligned Reads' + when key like '%.crai' then 'Aligned Reads Index' + when key like '%.md5' then 'Other' else null end as data_type, - '{etag' + replace(etag, '"', "") + '}' as hash_dict + '{etag' + replace(etag, '"', "") + '}' as hash_dict, + 'False' as harmonized, from {{ ref('kf_chr_18_src_s3_scrape_cody') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql index a9aef9b..0dc98cb 100644 --- a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql +++ b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql @@ -2,11 +2,14 @@ with base as ( select + -- commenting these out for now, but linking sample_id differs by study so will be used in some cases -- sample_id, -- collaborator_sample_id, collaborator_participant_id as participant_id, root_sample_id as sample_id, data_type as sequencing_strategy, + + -- these fields are typically included in ingest package but not sure if they will be needed for access model total_reads, mean_read_length, reference_sequence_name diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familyrelationship.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familyrelationship.sql index 9e84927..e7de895 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familyrelationship.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familyrelationship.sql @@ -2,7 +2,9 @@ select null::text as "family_relationship_id", + -- is this participant id? same as subject id? null::text as "family_member_id", + -- this study doesn't have families so should this be null? or mapped to an NA value? null::text as "relationship", null::text as "subject_id", null::text as "access_policy_id", From 33c00bca213bda1f9918f00e21d2eb63b2a0de44 Mon Sep 17 00:00:00 2001 From: Amanda Warkow Date: Wed, 22 Jul 2026 13:36:45 -0400 Subject: [PATCH 13/17] =?UTF-8?q?=F0=9F=93=9D=20fixing=20documentation?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- dbt_project/dbt_project.yml | 6 + .../chr_18/src/_column_descriptions.md | 244 ++++++++++++++++-- 2 files changed, 224 insertions(+), 26 deletions(-) diff --git a/dbt_project/dbt_project.yml b/dbt_project/dbt_project.yml index f5ff314..5a7f849 100644 --- a/dbt_project/dbt_project.yml +++ b/dbt_project/dbt_project.yml @@ -57,6 +57,12 @@ models: chr_18: +tags: - chr_18 + src: + +schema: kf_chr_18_src + int: + +schema: kf_chr_18_int + stb: + +schema: kf_chr_18_stb access: +tags: - access_stage diff --git a/dbt_project/models/kids_first/chr_18/src/_column_descriptions.md b/dbt_project/models/kids_first/chr_18/src/_column_descriptions.md index 787b36d..d7f1f60 100644 --- a/dbt_project/models/kids_first/chr_18/src/_column_descriptions.md +++ b/dbt_project/models/kids_first/chr_18/src/_column_descriptions.md @@ -318,56 +318,248 @@ situs inversus Sample Tissue Type {% enddocs %} -{% docs ha_delivery_manifest_6735_type %} -type +{% docs terra_manifest_v2_sample_id %} +sample_id {% enddocs %} -{% docs ha_delivery_manifest_6735_sample %} -sample.sample_id +{% docs terra_manifest_v2_project %} +project {% enddocs %} -{% docs ha_delivery_manifest_6735_file_name %} -file_name +{% docs terra_manifest_v2_collaborator_sample_id %} +collaborator_sample_id {% enddocs %} -{% docs ha_delivery_manifest_6735_file_type %} -file_type +{% docs terra_manifest_v2_version %} +version {% enddocs %} -{% docs ha_delivery_manifest_6735_file_description %} -file_description +{% docs terra_manifest_v2_data_type %} +data_type {% enddocs %} -{% docs ha_delivery_manifest_6735_file_size %} -file_size +{% docs terra_manifest_v2_pdo %} +pdo {% enddocs %} -{% docs ha_delivery_manifest_6735_md5sum %} -md5sum +{% docs terra_manifest_v2_release_date %} +release_date {% enddocs %} -{% docs ha_delivery_manifest_6735_library_id %} -library_id +{% docs terra_manifest_v2_reference_sequence_name %} +reference_sequence_name {% enddocs %} -{% docs ha_delivery_manifest_6735_library_strategy %} -library_strategy +{% docs terra_manifest_v2_collaborator_participant_id %} +collaborator_participant_id {% enddocs %} -{% docs ha_delivery_manifest_6735_library_layout %} -library_layout +{% docs terra_manifest_v2_cram_path %} +cram_path {% enddocs %} -{% docs ha_delivery_manifest_6735_library_source %} -library_source +{% docs terra_manifest_v2_crai_path %} +crai_path {% enddocs %} -{% docs ha_delivery_manifest_6735_platform %} -platform +{% docs terra_manifest_v2_md5_path %} +md5_path {% enddocs %} -{% docs ha_delivery_manifest_6735_instrument_model %} -instrument_model +{% docs terra_manifest_v2_root_sample_id %} +root_sample_id +{% enddocs %} + +{% docs terra_manifest_v2_mean_coverage %} +mean_coverage +{% enddocs %} + +{% docs terra_manifest_v2_adapter_rate %} +adapter_rate +{% enddocs %} + +{% docs terra_manifest_v2_pf_hq_aligned_q20_bases %} +pf_hq_aligned_q20_bases +{% enddocs %} + +{% docs terra_manifest_v2_pf_hq_aligned_reads %} +pf_hq_aligned_reads +{% enddocs %} + +{% docs terra_manifest_v2_pf_mismatch_rate %} +pf_mismatch_rate +{% enddocs %} + +{% docs terra_manifest_v2_pf_noise_reads %} +pf_noise_reads +{% enddocs %} + +{% docs terra_manifest_v2_pf_reads %} +pf_reads +{% enddocs %} + +{% docs terra_manifest_v2_pf_reads_aligned %} +pf_reads_aligned +{% enddocs %} + +{% docs terra_manifest_v2_total_reads %} +total_reads +{% enddocs %} + +{% docs terra_manifest_v2_mean_read_length %} +mean_read_length +{% enddocs %} + +{% docs terra_manifest_v2_pf_reads_rate %} +pf_reads_rate +{% enddocs %} + +{% docs terra_manifest_v2_pf_reads_aligned_rate %} +pf_reads_aligned_rate +{% enddocs %} + +{% docs terra_manifest_v2_pf_aligned_bases %} +pf_aligned_bases +{% enddocs %} + +{% docs terra_manifest_v2_reads_aligned_in_pairs %} +reads_aligned_in_pairs +{% enddocs %} + +{% docs terra_manifest_v2_contamination_rate %} +contamination_rate +{% enddocs %} + +{% docs terra_manifest_v2_genome_territory %} +genome_territory +{% enddocs %} + +{% docs terra_manifest_v2_exc_baseq_rate %} +exc_baseq_rate +{% enddocs %} + +{% docs terra_manifest_v2_exc_dupe_rate %} +exc_dupe_rate +{% enddocs %} + +{% docs terra_manifest_v2_exc_mapq_rate %} +exc_mapq_rate +{% enddocs %} + +{% docs terra_manifest_v2_exc_overlap_rate %} +exc_overlap_rate +{% enddocs %} + +{% docs terra_manifest_v2_10x_rate %} +10x_rate +{% enddocs %} + +{% docs terra_manifest_v2_20x_rate %} +20x_rate +{% enddocs %} + +{% docs terra_manifest_v2_exc_total_rate %} +exc_total_rate +{% enddocs %} + +{% docs terra_manifest_v2_exc_unpaired_rate %} +exc_unpaired_rate +{% enddocs %} + +{% docs terra_manifest_v2_chimera_rate %} +chimera_rate +{% enddocs %} + +{% docs terra_manifest_v2_het_snp_q %} +het_snp_q +{% enddocs %} + +{% docs terra_manifest_v2_het_snp_sensitivity %} +het_snp_sensitivity +{% enddocs %} + +{% docs terra_manifest_v2_library_1_estimated_library_size %} +library_1_estimated_library_size +{% enddocs %} + +{% docs terra_manifest_v2_library_1_mean_insert_size %} +library_1_mean_insert_size +{% enddocs %} + +{% docs terra_manifest_v2_library_1_name %} +library_1_name +{% enddocs %} + +{% docs terra_manifest_v2_library_1_pair_orientation %} +library_1_pair_orientation +{% enddocs %} + +{% docs terra_manifest_v2_library_1_pct_exc_dupe %} +library_1_pct_exc_dupe +{% enddocs %} + +{% docs terra_manifest_v2_library_1_percent_duplication %} +library_1_percent_duplication +{% enddocs %} + +{% docs terra_manifest_v2_library_1_read_pairs %} +library_1_read_pairs +{% enddocs %} + +{% docs terra_manifest_v2_mean_insert_size %} +mean_insert_size +{% enddocs %} + +{% docs terra_manifest_v2_median_coverage %} +median_coverage +{% enddocs %} + +{% docs terra_manifest_v2_median_insert_size %} +median_insert_size +{% enddocs %} + +{% docs terra_manifest_v2_pf_hq_aligned_bases %} +pf_hq_aligned_bases +{% enddocs %} + +{% docs terra_manifest_v2_pf_hq_error_rate %} +pf_hq_error_rate +{% enddocs %} + +{% docs terra_manifest_v2_pf_reads_improper_pairs %} +pf_reads_improper_pairs +{% enddocs %} + +{% docs terra_manifest_v2_read_pair_duplicates %} +read_pair_duplicates +{% enddocs %} + +{% docs terra_manifest_v2_read_pair_optical_duplicates %} +read_pair_optical_duplicates +{% enddocs %} + +{% docs terra_manifest_v2_reads_aligned_in_pairs_rate %} +reads_aligned_in_pairs_rate +{% enddocs %} + +{% docs terra_manifest_v2_sample %} +sample +{% enddocs %} + +{% docs terra_manifest_v2_strand_balance %} +strand_balance +{% enddocs %} + +{% docs terra_manifest_v2_width_of_10_percent %} +width_of_10_percent +{% enddocs %} + +{% docs terra_manifest_v2_width_of_50_percent %} +width_of_50_percent +{% enddocs %} + +{% docs terra_manifest_v2_width_of_99_percent %} +width_of_99_percent {% enddocs %} {% docs s3_scrape_cody_size %} From 6b4346b19b5dfc91003094e78ff63aeaf5e96d70 Mon Sep 17 00:00:00 2001 From: Amanda Warkow Date: Wed, 22 Jul 2026 13:37:02 -0400 Subject: [PATCH 14/17] =?UTF-8?q?=E2=9C=85=20resolving=20dbt=20run=20error?= =?UTF-8?q?s?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../chr_18/int/kf_chr_18_int_clinical.sql | 4 +-- .../kf_chr_18_src_s3_scrape_cody.sql | 2 +- .../kf_chr_18_src_terra_manifest_v2.sql | 30 +++++++++---------- .../models/kids_first/chr_18/src/sources.yml | 30 ++++++++++--------- 4 files changed, 34 insertions(+), 32 deletions(-) diff --git a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_clinical.sql b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_clinical.sql index e197697..1d5562a 100644 --- a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_clinical.sql +++ b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_clinical.sql @@ -14,5 +14,5 @@ age_at_phenotype, affected_status, vital_status, - sample_tissue_type, - from ref{{'kf_chr_18_src_chr_18_phenotype_data'}} \ No newline at end of file + sample_tissue_type + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/kf_chr_18_src_s3_scrape_cody.sql b/dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/kf_chr_18_src_s3_scrape_cody.sql index 3267410..443154e 100644 --- a/dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/kf_chr_18_src_s3_scrape_cody.sql +++ b/dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/kf_chr_18_src_s3_scrape_cody.sql @@ -2,7 +2,7 @@ select ROW_NUMBER() OVER () AS kf_index, - "Size"::integer as size, + "Size"::bigint as size, "Key"::text as key, "ETag"::text as etag, "Bucket"::text as bucket, diff --git a/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/kf_chr_18_src_terra_manifest_v2.sql b/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/kf_chr_18_src_terra_manifest_v2.sql index fb620e8..30a1595 100644 --- a/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/kf_chr_18_src_terra_manifest_v2.sql +++ b/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/kf_chr_18_src_terra_manifest_v2.sql @@ -17,7 +17,7 @@ "root_sample_id"::text as root_sample_id, "mean_coverage"::float as mean_coverage, "adapter_rate"::float as adapter_rate, - "pf_hq_aligned_q20_bases"::integer as pf_hq_aligned_q20_bases, + "pf_hq_aligned_q20_bases"::float as pf_hq_aligned_q20_bases, "pf_hq_aligned_reads"::integer as pf_hq_aligned_reads, "pf_mismatch_rate"::float as pf_mismatch_rate, "pf_noise_reads"::integer as pf_noise_reads, @@ -27,32 +27,32 @@ "mean_read_length"::integer as mean_read_length, "pf_reads_rate"::integer as pf_reads_rate, "pf_reads_aligned_rate"::float as pf_reads_aligned_rate, - "pf_aligned_bases"::integer as pf_aligned_bases, + "pf_aligned_bases"::float as pf_aligned_bases, "reads_aligned_in_pairs"::integer as reads_aligned_in_pairs, - "contamination_rate"::integer as contamination_rate, - "genome_territory"::integer as genome_territory, + "contamination_rate"::float as contamination_rate, + "genome_territory"::bigint as genome_territory, "exc_baseq_rate"::float as exc_baseq_rate, "exc_dupe_rate"::float as exc_dupe_rate, "exc_mapq_rate"::integer as exc_mapq_rate, "exc_overlap_rate"::float as exc_overlap_rate, - "10x_rate"::float as 10x_rate, - "20x_rate"::float as 20x_rate, + "10x_rate"::float as "10x_rate", + "20x_rate"::float as "20x_rate", "exc_total_rate"::float as exc_total_rate, "exc_unpaired_rate"::float as exc_unpaired_rate, "chimera_rate"::float as chimera_rate, "het_snp_q"::integer as het_snp_q, "het_snp_sensitivity"::float as het_snp_sensitivity, - "library-1_estimated_library_size"::integer as library-1_estimated_library_size, - "library-1_mean_insert_size"::float as library-1_mean_insert_size, - "library-1_name"::text as library-1_name, - "library-1_pair_orientation"::text as library-1_pair_orientation, - "library-1_pct_exc_dupe"::integer as library-1_pct_exc_dupe, - "library-1_percent_duplication"::float as library-1_percent_duplication, - "library-1_read_pairs"::integer as library-1_read_pairs, + "library-1_estimated_library_size"::bigint as library_1_estimated_library_size, + "library-1_mean_insert_size"::float as library_1_mean_insert_size, + "library-1_name"::text as library_1_name, + "library-1_pair_orientation"::text as library_1_pair_orientation, + "library-1_pct_exc_dupe"::integer as library_1_pct_exc_dupe, + "library-1_percent_duplication"::float as library_1_percent_duplication, + "library-1_read_pairs"::integer as library_1_read_pairs, "mean_insert_size"::float as mean_insert_size, "median_coverage"::integer as median_coverage, "median_insert_size"::integer as median_insert_size, - "pf_hq_aligned_bases"::integer as pf_hq_aligned_bases, + "pf_hq_aligned_bases"::float as pf_hq_aligned_bases, "pf_hq_error_rate"::float as pf_hq_error_rate, "pf_reads_improper_pairs"::integer as pf_reads_improper_pairs, "read_pair_duplicates"::integer as read_pair_duplicates, @@ -63,5 +63,5 @@ "width_of_10_percent"::integer as width_of_10_percent, "width_of_50_percent"::integer as width_of_50_percent, "width_of_99_percent"::integer as width_of_99_percent -from {{ source('chr_18', 'Terra_Manifest_v2') }} +from {{ source('chr_18', 'terra_manifest_v2') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/src/sources.yml b/dbt_project/models/kids_first/chr_18/src/sources.yml index 63a7b36..39085f0 100644 --- a/dbt_project/models/kids_first/chr_18/src/sources.yml +++ b/dbt_project/models/kids_first/chr_18/src/sources.yml @@ -172,8 +172,8 @@ sources: - name: terra_manifest_v2 description: Source table for terra_manifest_v2. columns: - - name: entity:sample_id - description: '{{ doc("terra_manifest_v2_entity_sample_id") }}' + - name: sample_id + description: '{{ doc("terra_manifest_v2_sample_id") }}' - name: project description: '{{ doc("terra_manifest_v2_project") }}' - name: collaborator_sample_id @@ -252,18 +252,20 @@ sources: description: '{{ doc("terra_manifest_v2_het_snp_q") }}' - name: het_snp_sensitivity description: '{{ doc("terra_manifest_v2_het_snp_sensitivity") }}' - - name: library-1_estimated_library_size - description: '{{ doc("terra_manifest_v2_library-1_estimated_library_size") }}' - - name: library-1_mean_insert_size - description: '{{ doc("terra_manifest_v2_library-1_mean_insert_size") }}' - - name: library-1_name - description: '{{ doc("terra_manifest_v2_library-1_pair_orientation") }}' - - name: library-1_pct_exc_dupe - description: '{{ doc("terra_manifest_v2_library-1_pct_exc_dupe") }}' - - name: library-1_percent_duplication - description: '{{ doc("terra_manifest_v2_library-1_percent_duplication") }}' - - name: library-1_read_pairs - description: '{{ doc("terra_manifest_v2_library-1_read_pairs") }}' + - name: library_1_estimated_library_size + description: '{{ doc("terra_manifest_v2_library_1_estimated_library_size") }}' + - name: library_1_mean_insert_size + description: '{{ doc("terra_manifest_v2_library_1_mean_insert_size") }}' + - name: library_1_name + description: '{{ doc("terra_manifest_v2_library_1_name") }}' + - name: library_1_pair_orientation + description: '{{ doc("terra_manifest_v2_library_1_pair_orientation") }}' + - name: library_1_pct_exc_dupe + description: '{{ doc("terra_manifest_v2_library_1_pct_exc_dupe") }}' + - name: library_1_percent_duplication + description: '{{ doc("terra_manifest_v2_library_1_percent_duplication") }}' + - name: library_1_read_pairs + description: '{{ doc("terra_manifest_v2_library_1_read_pairs") }}' - name: mean_insert_size description: '{{ doc("terra_manifest_v2_mean_insert_size") }}' - name: median_coverage From 93a6b863e1c12cba01588cce906dfeca13cee67b Mon Sep 17 00:00:00 2001 From: Amanda Warkow Date: Mon, 27 Jul 2026 14:15:38 -0400 Subject: [PATCH 15/17] =?UTF-8?q?=E2=9C=A8=20map=20to=20constants?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../chr_18/int/kf_chr_18_int_clinical.sql | 25 ++++++++++++++----- 1 file changed, 19 insertions(+), 6 deletions(-) diff --git a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_clinical.sql b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_clinical.sql index 1d5562a..f9d5bd3 100644 --- a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_clinical.sql +++ b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_clinical.sql @@ -4,14 +4,27 @@ participant_id, family_relationship_target_participant_id, aliquot_id, - consent_group, + 'GRU' as consent_group, age_at_sample, - sample_composition, - race, - sex, - ethnicity, + case + when sample_composition is 'Blood' then 'Peripheral Whole Blood' + when sample_composition is 'Lymphoblastoid Cells' then 'Lymphoblastoid Cell Lines' + end as sample_composition, + case + when race is 'Native American' then 'American Indian or Alaska Native' + when race is 'Caucasian' then 'White' + else race + end as race, + case + when sex is 'M' then 'Male' + when sex is 'F' then 'Female' + end as sex, + case + when ethnicity is 'Not Hispanic' then 'Not Hispanic or Latino' + when ethnicity is 'Hispanic' then 'Hispanic or Latino' + end as ethnicity, analyte_type, - age_at_phenotype, + -- age_at_phenotype, affected_status, vital_status, sample_tissue_type From b6beeb9c1bd5c4f51d04d8d1caeffc0c9d588a43 Mon Sep 17 00:00:00 2001 From: Amanda Warkow Date: Mon, 27 Jul 2026 16:50:04 -0400 Subject: [PATCH 16/17] =?UTF-8?q?=E2=9C=85=20resolve=20run=20errors?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../chr_18/int/kf_chr_18_int_clinical.sql | 16 ++++++++-------- .../kids_first/chr_18/int/kf_chr_18_int_s3.sql | 6 +++--- .../chr_18/int/kf_chr_18_int_sequencing.sql | 12 ++++++------ 3 files changed, 17 insertions(+), 17 deletions(-) diff --git a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_clinical.sql b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_clinical.sql index f9d5bd3..7364a47 100644 --- a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_clinical.sql +++ b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_clinical.sql @@ -7,21 +7,21 @@ 'GRU' as consent_group, age_at_sample, case - when sample_composition is 'Blood' then 'Peripheral Whole Blood' - when sample_composition is 'Lymphoblastoid Cells' then 'Lymphoblastoid Cell Lines' + when sample_composition = 'Blood' then 'Peripheral Whole Blood' + when sample_composition = 'Lymphoblastoid Cells' then 'Lymphoblastoid Cell Lines' end as sample_composition, case - when race is 'Native American' then 'American Indian or Alaska Native' - when race is 'Caucasian' then 'White' + when race = 'Native American' then 'American Indian or Alaska Native' + when race = 'Caucasian' then 'White' else race end as race, case - when sex is 'M' then 'Male' - when sex is 'F' then 'Female' + when sex = 'M' then 'Male' + when sex = 'F' then 'Female' end as sex, case - when ethnicity is 'Not Hispanic' then 'Not Hispanic or Latino' - when ethnicity is 'Hispanic' then 'Hispanic or Latino' + when ethnicity = 'Not Hispanic' then 'Not Hispanic or Latino' + when ethnicity = 'Hispanic' then 'Hispanic or Latino' end as ethnicity, analyte_type, -- age_at_phenotype, diff --git a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_s3.sql b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_s3.sql index b637c65..43e1c93 100644 --- a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_s3.sql +++ b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_s3.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} select - 's3://' + bucket + '/' + key as s3_path, + concat('s3://', bucket, '/', key) as s3_path, split_part(key, '/', -1) as file_name, case when key like '%.cram' then 'cram' @@ -15,7 +15,7 @@ when key like '%.md5' then 'Other' else null end as data_type, - '{etag' + replace(etag, '"', "") + '}' as hash_dict, - 'False' as harmonized, + concat('{etag', replace(etag, '\"', ''), '}') as hash_dict, + 'False' as harmonized from {{ ref('kf_chr_18_src_s3_scrape_cody') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql index 0dc98cb..6680ee8 100644 --- a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql +++ b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql @@ -20,8 +20,8 @@ select root_sample_id, replace(cram_path, - "gs://fc-2092c58b-ce12-42e7-9a8e-64b78440537a/", - "s3://kf-strides-study-us-east-1-prd-sd-1nns3k8v/source/", + 'gs://fc-2092c58b-ce12-42e7-9a8e-64b78440537a/', + 's3://kf-strides-study-us-east-1-prd-sd-1nns3k8v/source/' ) as cram_path from {{ ref('kf_chr_18_src_terra_manifest_v2') }} ), @@ -30,8 +30,8 @@ select root_sample_id, replace(crai_path, - "gs://fc-2092c58b-ce12-42e7-9a8e-64b78440537a/", - "s3://kf-strides-study-us-east-1-prd-sd-1nns3k8v/source/", + 'gs://fc-2092c58b-ce12-42e7-9a8e-64b78440537a/', + 's3://kf-strides-study-us-east-1-prd-sd-1nns3k8v/source/' ) as crai_path from {{ ref('kf_chr_18_src_terra_manifest_v2') }} as crais ), @@ -40,8 +40,8 @@ select root_sample_id, replace(md5_path, - "gs://fc-2092c58b-ce12-42e7-9a8e-64b78440537a/", - "s3://kf-strides-study-us-east-1-prd-sd-1nns3k8v/source/", + 'gs://fc-2092c58b-ce12-42e7-9a8e-64b78440537a/', + 's3://kf-strides-study-us-east-1-prd-sd-1nns3k8v/source/' ) as md5_path from {{ ref('kf_chr_18_src_terra_manifest_v2') }} as md5s ) From b96edca610d5a312a4c744ceda02fb132fbb5930 Mon Sep 17 00:00:00 2001 From: Amanda Warkow Date: Mon, 27 Jul 2026 17:07:17 -0400 Subject: [PATCH 17/17] =?UTF-8?q?=E2=9C=8F=EF=B8=8F=20sqlfluff=20linting?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../chr_18/int/kf_chr_18_int_clinical.sql | 60 +++---- .../chr_18/int/kf_chr_18_int_s3.sql | 36 ++-- .../chr_18/int/kf_chr_18_int_sequencing.sql | 129 +++++++------- .../kf_chr_18_src_chr_18_phenotype_data.sql | 166 +++++++++--------- .../kf_chr_18_src_s3_scrape_cody.sql | 18 +- .../kf_chr_18_src_terra_manifest_v2.sql | 126 ++++++------- .../chr_18/stb/kf_chr_18_stb_accesspolicy.sql | 18 +- .../stb/kf_chr_18_stb_activitydefinition.sql | 14 +- ..._18_stb_activitydefinition_external_id.sql | 8 +- .../chr_18/stb/kf_chr_18_stb_aliquot.sql | 22 +-- .../stb/kf_chr_18_stb_aliquot_external_id.sql | 8 +- .../kf_chr_18_stb_biospecimencollection.sql | 22 +-- ..._stb_biospecimencollection_external_id.sql | 8 +- .../chr_18/stb/kf_chr_18_stb_concept.sql | 8 +- .../chr_18/stb/kf_chr_18_stb_dataset.sql | 16 +- .../stb/kf_chr_18_stb_dataset_file_id.sql | 8 +- .../stb/kf_chr_18_stb_dataset_publication.sql | 8 +- .../chr_18/stb/kf_chr_18_stb_demographics.sql | 22 +-- ...kf_chr_18_stb_demographics_external_id.sql | 8 +- .../stb/kf_chr_18_stb_demographics_race.sql | 8 +- .../chr_18/stb/kf_chr_18_stb_doi.sql | 12 +- .../stb/kf_chr_18_stb_doi_external_id.sql | 8 +- .../chr_18/stb/kf_chr_18_stb_encounter.sql | 16 +- .../kf_chr_18_stb_encounter_external_id.sql | 8 +- .../stb/kf_chr_18_stb_encounterdefinition.sql | 14 +- ...unterdefinition_activity_definition_id.sql | 8 +- ...18_stb_encounterdefinition_external_id.sql | 8 +- .../chr_18/stb/kf_chr_18_stb_family.sql | 18 +- .../stb/kf_chr_18_stb_family_external_id.sql | 8 +- .../chr_18/stb/kf_chr_18_stb_familymember.sql | 16 +- ...kf_chr_18_stb_familymember_external_id.sql | 8 +- .../stb/kf_chr_18_stb_familyrelationship.sql | 20 +-- ..._18_stb_familyrelationship_external_id.sql | 8 +- .../chr_18/stb/kf_chr_18_stb_file.sql | 30 ++-- .../stb/kf_chr_18_stb_file_external_id.sql | 8 +- .../stb/kf_chr_18_stb_file_sample_id.sql | 8 +- .../stb/kf_chr_18_stb_file_subject_id.sql | 8 +- .../chr_18/stb/kf_chr_18_stb_filehash.sql | 10 +- .../chr_18/stb/kf_chr_18_stb_investigator.sql | 18 +- ...kf_chr_18_stb_investigator_external_id.sql | 8 +- .../chr_18/stb/kf_chr_18_stb_publication.sql | 14 +- .../kf_chr_18_stb_publication_external_id.sql | 8 +- .../stb/kf_chr_18_stb_record_external_id.sql | 8 +- .../chr_18/stb/kf_chr_18_stb_sample.sql | 22 +-- .../stb/kf_chr_18_stb_sample_external_id.sql | 8 +- .../stb/kf_chr_18_stb_sample_processing.sql | 8 +- .../kf_chr_18_stb_sample_storage_method.sql | 8 +- .../chr_18/stb/kf_chr_18_stb_study.sql | 26 +-- ...18_stb_study_clinical_data_source_type.sql | 8 +- .../stb/kf_chr_18_stb_study_contact.sql | 8 +- .../stb/kf_chr_18_stb_study_data_category.sql | 8 +- .../stb/kf_chr_18_stb_study_external_id.sql | 8 +- .../kf_chr_18_stb_study_funding_source.sql | 8 +- ...8_stb_study_participant_lifespan_stage.sql | 8 +- ...hr_18_stb_study_principal_investigator.sql | 8 +- .../stb/kf_chr_18_stb_study_program.sql | 8 +- .../stb/kf_chr_18_stb_study_publication.sql | 8 +- .../kf_chr_18_stb_study_research_domain.sql | 8 +- .../stb/kf_chr_18_stb_study_study_design.sql | 8 +- .../stb/kf_chr_18_stb_studymetadata.sql | 16 +- ...tudymetadata_clinical_data_source_type.sql | 8 +- ...chr_18_stb_studymetadata_data_category.sql | 8 +- ...f_chr_18_stb_studymetadata_external_id.sql | 8 +- ...udymetadata_participant_lifespan_stage.sql | 8 +- ...r_18_stb_studymetadata_research_domain.sql | 8 +- ..._chr_18_stb_studymetadata_study_design.sql | 8 +- .../chr_18/stb/kf_chr_18_stb_subject.sql | 14 +- .../stb/kf_chr_18_stb_subject_external_id.sql | 8 +- .../stb/kf_chr_18_stb_subjectassertion.sql | 32 ++-- ...kf_chr_18_stb_subjectassertion_concept.sql | 8 +- ...hr_18_stb_subjectassertion_external_id.sql | 8 +- ..._18_stb_subjectassertion_value_concept.sql | 8 +- .../kf_chr_18_stb_virtualbiorepository.sql | 18 +- ...hr_18_stb_virtualbiorepository_contact.sql | 8 +- ...8_stb_virtualbiorepository_external_id.sql | 8 +- 75 files changed, 662 insertions(+), 659 deletions(-) diff --git a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_clinical.sql b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_clinical.sql index 7364a47..6f39b4a 100644 --- a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_clinical.sql +++ b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_clinical.sql @@ -1,31 +1,31 @@ {{ config(materialized='table') }} - select - family_id, - participant_id, - family_relationship_target_participant_id, - aliquot_id, - 'GRU' as consent_group, - age_at_sample, - case - when sample_composition = 'Blood' then 'Peripheral Whole Blood' - when sample_composition = 'Lymphoblastoid Cells' then 'Lymphoblastoid Cell Lines' - end as sample_composition, - case - when race = 'Native American' then 'American Indian or Alaska Native' - when race = 'Caucasian' then 'White' - else race - end as race, - case - when sex = 'M' then 'Male' - when sex = 'F' then 'Female' - end as sex, - case - when ethnicity = 'Not Hispanic' then 'Not Hispanic or Latino' - when ethnicity = 'Hispanic' then 'Hispanic or Latino' - end as ethnicity, - analyte_type, - -- age_at_phenotype, - affected_status, - vital_status, - sample_tissue_type - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file +select + family_id, + participant_id, + family_relationship_target_participant_id, + aliquot_id, + 'GRU' as consent_group, + age_at_sample, + case + when sample_composition = 'Blood' then 'Peripheral Whole Blood' + when sample_composition = 'Lymphoblastoid Cells' then 'Lymphoblastoid Cell Lines' + end as sample_composition, + case + when race = 'Native American' then 'American Indian or Alaska Native' + when race = 'Caucasian' then 'White' + else race + end as race, + case + when sex = 'M' then 'Male' + when sex = 'F' then 'Female' + end as sex, + case + when ethnicity = 'Not Hispanic' then 'Not Hispanic or Latino' + when ethnicity = 'Hispanic' then 'Hispanic or Latino' + end as ethnicity, + analyte_type, + -- age_at_phenotype, + affected_status, + vital_status, + sample_tissue_type +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_s3.sql b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_s3.sql index 43e1c93..19ecf2a 100644 --- a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_s3.sql +++ b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_s3.sql @@ -1,21 +1,21 @@ {{ config(materialized='table') }} - select - concat('s3://', bucket, '/', key) as s3_path, - split_part(key, '/', -1) as file_name, - case - when key like '%.cram' then 'cram' - when key like '%.crai' then 'crai' - when key like '%.md5' then 'md5' - else null - end as file_format, - case - when key like '%.cram' then 'Aligned Reads' - when key like '%.crai' then 'Aligned Reads Index' - when key like '%.md5' then 'Other' - else null - end as data_type, - concat('{etag', replace(etag, '\"', ''), '}') as hash_dict, - 'False' as harmonized - from {{ ref('kf_chr_18_src_s3_scrape_cody') }} +select + concat('s3://', bucket, '/', key) as s3_path, + split_part(key, '/', -1) as file_name, + case + when key like '%.cram' then 'cram' + when key like '%.crai' then 'crai' + when key like '%.md5' then 'md5' + else null + end as file_format, + case + when key like '%.cram' then 'Aligned Reads' + when key like '%.crai' then 'Aligned Reads Index' + when key like '%.md5' then 'Other' + else null + end as data_type, + concat('{etag', replace(etag, '\"', ''), '}') as hash_dict, + 'False' as harmonized +from {{ ref('kf_chr_18_src_s3_scrape_cody') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql index 6680ee8..9380ced 100644 --- a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql +++ b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql @@ -1,70 +1,73 @@ {{ config(materialized='table') }} - with base as ( - select - -- commenting these out for now, but linking sample_id differs by study so will be used in some cases - -- sample_id, - -- collaborator_sample_id, - collaborator_participant_id as participant_id, - root_sample_id as sample_id, - data_type as sequencing_strategy, +with base as ( + select + -- commenting these out for now, but linking sample_id differs by study so will be used in some cases + -- sample_id, + -- collaborator_sample_id, + collaborator_participant_id as participant_id, + root_sample_id as sample_id, + data_type as sequencing_strategy, - -- these fields are typically included in ingest package but not sure if they will be needed for access model - total_reads, - mean_read_length, - reference_sequence_name - from {{ ref('kf_chr_18_src_terra_manifest_v2') }} - ), + -- these fields are typically included in ingest package but not sure if they will be needed for access model + total_reads, + mean_read_length, + reference_sequence_name + from {{ ref('kf_chr_18_src_terra_manifest_v2') }} +), - crams as ( - select - root_sample_id, - replace(cram_path, - 'gs://fc-2092c58b-ce12-42e7-9a8e-64b78440537a/', - 's3://kf-strides-study-us-east-1-prd-sd-1nns3k8v/source/' - ) as cram_path - from {{ ref('kf_chr_18_src_terra_manifest_v2') }} - ), +crams as ( + select + root_sample_id, + replace( + cram_path, + 'gs://fc-2092c58b-ce12-42e7-9a8e-64b78440537a/', + 's3://kf-strides-study-us-east-1-prd-sd-1nns3k8v/source/' + ) as cram_path + from {{ ref('kf_chr_18_src_terra_manifest_v2') }} +), - crais as ( - select - root_sample_id, - replace(crai_path, - 'gs://fc-2092c58b-ce12-42e7-9a8e-64b78440537a/', - 's3://kf-strides-study-us-east-1-prd-sd-1nns3k8v/source/' - ) as crai_path - from {{ ref('kf_chr_18_src_terra_manifest_v2') }} as crais - ), +crais as ( + select + root_sample_id, + replace( + crai_path, + 'gs://fc-2092c58b-ce12-42e7-9a8e-64b78440537a/', + 's3://kf-strides-study-us-east-1-prd-sd-1nns3k8v/source/' + ) as crai_path + from {{ ref('kf_chr_18_src_terra_manifest_v2') }} +), - md5s as ( - select - root_sample_id, - replace(md5_path, - 'gs://fc-2092c58b-ce12-42e7-9a8e-64b78440537a/', - 's3://kf-strides-study-us-east-1-prd-sd-1nns3k8v/source/' - ) as md5_path - from {{ ref('kf_chr_18_src_terra_manifest_v2') }} as md5s - ) +md5s as ( + select + root_sample_id, + replace( + md5_path, + 'gs://fc-2092c58b-ce12-42e7-9a8e-64b78440537a/', + 's3://kf-strides-study-us-east-1-prd-sd-1nns3k8v/source/' + ) as md5_path + from {{ ref('kf_chr_18_src_terra_manifest_v2') }} +) - select - -- base.sample_id, - -- base.collaborator_sample_id, - base.participant_id, - base.sample_id, - base.sequencing_strategy, - base.total_reads, - base.mean_read_length, - base.reference_sequence_name, - crams.cram_path, - crais.crai_path, - md5s.md5_path, - 'False' as harmonized, - 'False' as paired_end, - 'Broad Institute' as sequencing_center_name - from base - left join crams - on base.sample_id = crams.root_sample_id - left join crais - on base.sample_id = crais.root_sample_id - left join md5s - on base.sample_id = md5s.root_sample_id \ No newline at end of file +select + -- base.sample_id, + -- base.collaborator_sample_id, + base.participant_id, + base.sample_id, + base.sequencing_strategy, + base.total_reads, + base.mean_read_length, + base.reference_sequence_name, + crams.cram_path, + crais.crai_path, + md5s.md5_path, + 'False' as harmonized, + 'False' as paired_end, + 'Broad Institute' as sequencing_center_name +from base +left join crams + on base.sample_id = crams.root_sample_id +left join crais + on base.sample_id = crais.root_sample_id +left join md5s + on base.sample_id = md5s.root_sample_id \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/src/Clinical_Data/kf_chr_18_src_chr_18_phenotype_data.sql b/dbt_project/models/kids_first/chr_18/src/Clinical_Data/kf_chr_18_src_chr_18_phenotype_data.sql index cfb1d99..9d72108 100644 --- a/dbt_project/models/kids_first/chr_18/src/Clinical_Data/kf_chr_18_src_chr_18_phenotype_data.sql +++ b/dbt_project/models/kids_first/chr_18/src/Clinical_Data/kf_chr_18_src_chr_18_phenotype_data.sql @@ -1,86 +1,86 @@ {{ config(materialized='table') }} - select - ROW_NUMBER() OVER () AS kf_index, - "Family ID"::text as family_id, - "Participant ID"::text as participant_id, - "Family Relationship Target Participant ID"::text as family_relationship_target_participant_id, - "alliquot_id"::text as aliquot_id, - "Consent Group"::text as consent_group, - "Age at Sample"::text as age_at_sample, - "Sample Composition"::text as sample_composition, - "Race"::text as race, - "Sex"::text as sex, - "Ethnicity"::text as ethnicity, - "Analyte Type"::text as analyte_type, - "Age at Phenotype"::text as age_at_phenotype, - "Affected Status"::text as affected_status, - "Vital Status"::text as vital_status, - "chiari 2"::text as chiari_2, - "pituitary gland abn"::text as pituitary_gland_abn, - "cleft palate"::text as cleft_palate, - "hearing loss"::text as hearing_loss, - "tetralogy of fallot"::text as tetralogy_of_fallot, - "conductive hearing loss"::text as conductive_hearing_loss, - "holoprosencephaly"::text as holoprosencephaly, - "choanal atresia"::text as choanal_atresia, - "aural atresia"::text as aural_atresia, - "midface hypoplasia"::text as midface_hypoplasia, - "dysmyelination"::text as dysmyelination, - "polymicrogyria"::text as polymicrogyria, - "cryptorchidism"::text as cryptorchidism, - "sensorineural hearing loss"::text as sensorineural_hearing_loss, - "cleft lip"::text as cleft_lip, - "imperforate anus"::text as imperforate_anus, - "microcephaly"::text as microcephaly, - "vertical talus"::text as vertical_talus, - "hypospadias"::text as hypospadias, - "rocker bottom foot"::text as rocker_bottom_foot, - "chiari 1"::text as chiari_1, - "ptosis"::text as ptosis, - "strabismus"::text as strabismus, - "bilateral coxa valga"::text as bilateral_coxa_valga, - "cardiac_nos"::text as cardiac_nos, - "corpus callosum abn"::text as corpus_callosum_abn, - "pulmonary valve stenosis"::text as pulmonary_valve_stenosis, - "metatarsus varus"::text as metatarsus_varus, - "decreased white matter volume"::text as decreased_white_matter_volume, - "macrocephaly"::text as macrocephaly, - "suprasellar cyst"::text as suprasellar_cyst, - "hydrocephalus"::text as hydrocephalus, - "micropenis"::text as micropenis, - "anal stenosis"::text as anal_stenosis, - "congenital heart malformation"::text as congenital_heart_malformation, - "bilateral choanal atresia"::text as bilateral_choanal_atresia, - "dandy walker malformation"::text as dandy_walker_malformation, - "dandy walker"::text as dandy_walker, - "congenital heart defect"::text as congenital_heart_defect, - "aural stenosis"::text as aural_stenosis, - "kidney malform"::text as kidney_malform, - "pituitary fossa enlargement"::text as pituitary_fossa_enlargement, - "submucous cleft"::text as submucous_cleft, - "virchow robins spaces"::text as virchow_robins_spaces, - "retinal coloboma"::text as retinal_coloboma, - "corneal staphyloma"::text as corneal_staphyloma, - "club foot"::text as club_foot, - "macroglossia"::text as macroglossia, - "dandy walker variant"::text as dandy_walker_variant, - "coanal atresia"::text as coanal_atresia, - "occipatal lobe abn"::text as occipatal_lobe_abn, - "asd"::text as asd, - "vsd"::text as vsd, - "pectus excavatum"::text as pectus_excavatum, - "peripherial pulmonary stenosis"::text as peripherial_pulmonary_stenosis, - "sagittal stenosis"::text as sagittal_stenosis, - "hydronephrosis"::text as hydronephrosis, - "patent ductus arteriosus"::text as patent_ductus_arteriosus, - "duanes syndrome"::text as duanes_syndrome, - "laryngomalacia"::text as laryngomalacia, - "metatarsus adductus"::text as metatarsus_adductus, - "ptosisbilateral"::text as ptosisbilateral, - "microphallus"::text as microphallus, - "sacral agenesis"::text as sacral_agenesis, - "situs inversus"::text as situs_inversus, - "Sample Tissue Type"::text as sample_tissue_type - from {{ source('chr_18', 'chr_18_phenotype_data') }} +select + ROW_NUMBER() over () as kf_index, + "Family ID"::text as family_id, + "Participant ID"::text as participant_id, + "Family Relationship Target Participant ID"::text as family_relationship_target_participant_id, + alliquot_id::text as aliquot_id, + "Consent Group"::text as consent_group, + "Age at Sample"::text as age_at_sample, + "Sample Composition"::text as sample_composition, + "Race"::text as race, + "Sex"::text as sex, + "Ethnicity"::text as ethnicity, + "Analyte Type"::text as analyte_type, + "Age at Phenotype"::text as age_at_phenotype, + "Affected Status"::text as affected_status, + "Vital Status"::text as vital_status, + "chiari 2"::text as chiari_2, + "pituitary gland abn"::text as pituitary_gland_abn, + "cleft palate"::text as cleft_palate, + "hearing loss"::text as hearing_loss, + "tetralogy of fallot"::text as tetralogy_of_fallot, + "conductive hearing loss"::text as conductive_hearing_loss, + holoprosencephaly::text as holoprosencephaly, + "choanal atresia"::text as choanal_atresia, + "aural atresia"::text as aural_atresia, + "midface hypoplasia"::text as midface_hypoplasia, + dysmyelination::text as dysmyelination, + polymicrogyria::text as polymicrogyria, + cryptorchidism::text as cryptorchidism, + "sensorineural hearing loss"::text as sensorineural_hearing_loss, + "cleft lip"::text as cleft_lip, + "imperforate anus"::text as imperforate_anus, + microcephaly::text as microcephaly, + "vertical talus"::text as vertical_talus, + hypospadias::text as hypospadias, + "rocker bottom foot"::text as rocker_bottom_foot, + "chiari 1"::text as chiari_1, + ptosis::text as ptosis, + strabismus::text as strabismus, + "bilateral coxa valga"::text as bilateral_coxa_valga, + cardiac_nos::text as cardiac_nos, + "corpus callosum abn"::text as corpus_callosum_abn, + "pulmonary valve stenosis"::text as pulmonary_valve_stenosis, + "metatarsus varus"::text as metatarsus_varus, + "decreased white matter volume"::text as decreased_white_matter_volume, + macrocephaly::text as macrocephaly, + "suprasellar cyst"::text as suprasellar_cyst, + hydrocephalus::text as hydrocephalus, + micropenis::text as micropenis, + "anal stenosis"::text as anal_stenosis, + "congenital heart malformation"::text as congenital_heart_malformation, + "bilateral choanal atresia"::text as bilateral_choanal_atresia, + "dandy walker malformation"::text as dandy_walker_malformation, + "dandy walker"::text as dandy_walker, + "congenital heart defect"::text as congenital_heart_defect, + "aural stenosis"::text as aural_stenosis, + "kidney malform"::text as kidney_malform, + "pituitary fossa enlargement"::text as pituitary_fossa_enlargement, + "submucous cleft"::text as submucous_cleft, + "virchow robins spaces"::text as virchow_robins_spaces, + "retinal coloboma"::text as retinal_coloboma, + "corneal staphyloma"::text as corneal_staphyloma, + "club foot"::text as club_foot, + macroglossia::text as macroglossia, + "dandy walker variant"::text as dandy_walker_variant, + "coanal atresia"::text as coanal_atresia, + "occipatal lobe abn"::text as occipatal_lobe_abn, + asd::text as asd, + vsd::text as vsd, + "pectus excavatum"::text as pectus_excavatum, + "peripherial pulmonary stenosis"::text as peripherial_pulmonary_stenosis, + "sagittal stenosis"::text as sagittal_stenosis, + hydronephrosis::text as hydronephrosis, + "patent ductus arteriosus"::text as patent_ductus_arteriosus, + "duanes syndrome"::text as duanes_syndrome, + laryngomalacia::text as laryngomalacia, + "metatarsus adductus"::text as metatarsus_adductus, + ptosisbilateral::text as ptosisbilateral, + microphallus::text as microphallus, + "sacral agenesis"::text as sacral_agenesis, + "situs inversus"::text as situs_inversus, + "Sample Tissue Type"::text as sample_tissue_type +from {{ source('chr_18', 'chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/kf_chr_18_src_s3_scrape_cody.sql b/dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/kf_chr_18_src_s3_scrape_cody.sql index 443154e..3644109 100644 --- a/dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/kf_chr_18_src_s3_scrape_cody.sql +++ b/dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/kf_chr_18_src_s3_scrape_cody.sql @@ -1,12 +1,12 @@ {{ config(materialized='table') }} - select - ROW_NUMBER() OVER () AS kf_index, - "Size"::bigint as size, - "Key"::text as key, - "ETag"::text as etag, - "Bucket"::text as bucket, - "LastModified"::text as lastmodified, - "StorageClass"::text as storageclass - from {{ source('chr_18', 's3_scrape_cody') }} +select + ROW_NUMBER() over () as kf_index, + "Size"::bigint as size, + "Key"::text as key, + "ETag"::text as etag, + "Bucket"::text as bucket, + "LastModified"::text as lastmodified, + "StorageClass"::text as storageclass +from {{ source('chr_18', 's3_scrape_cody') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/kf_chr_18_src_terra_manifest_v2.sql b/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/kf_chr_18_src_terra_manifest_v2.sql index 30a1595..5e36e5a 100644 --- a/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/kf_chr_18_src_terra_manifest_v2.sql +++ b/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/kf_chr_18_src_terra_manifest_v2.sql @@ -1,67 +1,67 @@ {{ config(materialized='table') }} - select - ROW_NUMBER() OVER () AS kf_index, - "entity:sample_id"::text as sample_id, - "project"::text as project, - "collaborator_sample_id"::text as collaborator_sample_id, - "version"::text as version, - "data_type"::text as data_type, - "pdo"::text as pdo, - "release_date"::date as release_date, - "reference_sequence_name"::text as reference_sequence_name, - "collaborator_participant_id"::text as collaborator_participant_id, - "cram_path"::text as cram_path, - "crai_path"::text as crai_path, - "md5_path"::text as md5_path, - "root_sample_id"::text as root_sample_id, - "mean_coverage"::float as mean_coverage, - "adapter_rate"::float as adapter_rate, - "pf_hq_aligned_q20_bases"::float as pf_hq_aligned_q20_bases, - "pf_hq_aligned_reads"::integer as pf_hq_aligned_reads, - "pf_mismatch_rate"::float as pf_mismatch_rate, - "pf_noise_reads"::integer as pf_noise_reads, - "pf_reads"::integer as pf_reads, - "pf_reads_aligned"::integer as pf_reads_aligned, - "total_reads"::integer as total_reads, - "mean_read_length"::integer as mean_read_length, - "pf_reads_rate"::integer as pf_reads_rate, - "pf_reads_aligned_rate"::float as pf_reads_aligned_rate, - "pf_aligned_bases"::float as pf_aligned_bases, - "reads_aligned_in_pairs"::integer as reads_aligned_in_pairs, - "contamination_rate"::float as contamination_rate, - "genome_territory"::bigint as genome_territory, - "exc_baseq_rate"::float as exc_baseq_rate, - "exc_dupe_rate"::float as exc_dupe_rate, - "exc_mapq_rate"::integer as exc_mapq_rate, - "exc_overlap_rate"::float as exc_overlap_rate, - "10x_rate"::float as "10x_rate", - "20x_rate"::float as "20x_rate", - "exc_total_rate"::float as exc_total_rate, - "exc_unpaired_rate"::float as exc_unpaired_rate, - "chimera_rate"::float as chimera_rate, - "het_snp_q"::integer as het_snp_q, - "het_snp_sensitivity"::float as het_snp_sensitivity, - "library-1_estimated_library_size"::bigint as library_1_estimated_library_size, - "library-1_mean_insert_size"::float as library_1_mean_insert_size, - "library-1_name"::text as library_1_name, - "library-1_pair_orientation"::text as library_1_pair_orientation, - "library-1_pct_exc_dupe"::integer as library_1_pct_exc_dupe, - "library-1_percent_duplication"::float as library_1_percent_duplication, - "library-1_read_pairs"::integer as library_1_read_pairs, - "mean_insert_size"::float as mean_insert_size, - "median_coverage"::integer as median_coverage, - "median_insert_size"::integer as median_insert_size, - "pf_hq_aligned_bases"::float as pf_hq_aligned_bases, - "pf_hq_error_rate"::float as pf_hq_error_rate, - "pf_reads_improper_pairs"::integer as pf_reads_improper_pairs, - "read_pair_duplicates"::integer as read_pair_duplicates, - "read_pair_optical_duplicates"::integer as read_pair_optical_duplicates, - "reads_aligned_in_pairs_rate"::float as reads_aligned_in_pairs_rate, - "sample"::text as sample, - "strand_balance"::float as strand_balance, - "width_of_10_percent"::integer as width_of_10_percent, - "width_of_50_percent"::integer as width_of_50_percent, - "width_of_99_percent"::integer as width_of_99_percent +select + ROW_NUMBER() over () as kf_index, + "entity:sample_id"::text as sample_id, + project::text as project, + collaborator_sample_id::text as collaborator_sample_id, + version::text as version, + data_type::text as data_type, + pdo::text as pdo, + release_date::date as release_date, + reference_sequence_name::text as reference_sequence_name, + collaborator_participant_id::text as collaborator_participant_id, + cram_path::text as cram_path, + crai_path::text as crai_path, + md5_path::text as md5_path, + root_sample_id::text as root_sample_id, + mean_coverage::float as mean_coverage, + adapter_rate::float as adapter_rate, + pf_hq_aligned_q20_bases::float as pf_hq_aligned_q20_bases, + pf_hq_aligned_reads::integer as pf_hq_aligned_reads, + pf_mismatch_rate::float as pf_mismatch_rate, + pf_noise_reads::integer as pf_noise_reads, + pf_reads::integer as pf_reads, + pf_reads_aligned::integer as pf_reads_aligned, + total_reads::integer as total_reads, + mean_read_length::integer as mean_read_length, + pf_reads_rate::integer as pf_reads_rate, + pf_reads_aligned_rate::float as pf_reads_aligned_rate, + pf_aligned_bases::float as pf_aligned_bases, + reads_aligned_in_pairs::integer as reads_aligned_in_pairs, + contamination_rate::float as contamination_rate, + genome_territory::bigint as genome_territory, + exc_baseq_rate::float as exc_baseq_rate, + exc_dupe_rate::float as exc_dupe_rate, + exc_mapq_rate::integer as exc_mapq_rate, + exc_overlap_rate::float as exc_overlap_rate, + "10x_rate"::float as "10x_rate", + "20x_rate"::float as "20x_rate", + exc_total_rate::float as exc_total_rate, + exc_unpaired_rate::float as exc_unpaired_rate, + chimera_rate::float as chimera_rate, + het_snp_q::integer as het_snp_q, + het_snp_sensitivity::float as het_snp_sensitivity, + "library-1_estimated_library_size"::bigint as library_1_estimated_library_size, + "library-1_mean_insert_size"::float as library_1_mean_insert_size, + "library-1_name"::text as library_1_name, + "library-1_pair_orientation"::text as library_1_pair_orientation, + "library-1_pct_exc_dupe"::integer as library_1_pct_exc_dupe, + "library-1_percent_duplication"::float as library_1_percent_duplication, + "library-1_read_pairs"::integer as library_1_read_pairs, + mean_insert_size::float as mean_insert_size, + median_coverage::integer as median_coverage, + median_insert_size::integer as median_insert_size, + pf_hq_aligned_bases::float as pf_hq_aligned_bases, + pf_hq_error_rate::float as pf_hq_error_rate, + pf_reads_improper_pairs::integer as pf_reads_improper_pairs, + read_pair_duplicates::integer as read_pair_duplicates, + read_pair_optical_duplicates::integer as read_pair_optical_duplicates, + reads_aligned_in_pairs_rate::float as reads_aligned_in_pairs_rate, + sample::text as sample, + strand_balance::float as strand_balance, + width_of_10_percent::integer as width_of_10_percent, + width_of_50_percent::integer as width_of_50_percent, + width_of_99_percent::integer as width_of_99_percent from {{ source('chr_18', 'terra_manifest_v2') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_accesspolicy.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_accesspolicy.sql index 00f3c1b..dabac80 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_accesspolicy.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_accesspolicy.sql @@ -1,12 +1,12 @@ {{ config(materialized='table') }} - select - null::text as "access_policy_id", - null::text as "data_use_accession", - null::text as "data_use_permission", - null::text as "data_use_modifier", - null::text as "disease_limitation", - null::text as "access_description", - null::text as "website" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as access_policy_id, + null::text as data_use_accession, + null::text as data_use_permission, + null::text as data_use_modifier, + null::text as disease_limitation, + null::text as access_description, + null::text as website +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_activitydefinition.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_activitydefinition.sql index 1cd2bc3..6507dc2 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_activitydefinition.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_activitydefinition.sql @@ -1,10 +1,10 @@ {{ config(materialized='table') }} - select - null::text as "activity_definition_id", - null::text as "name", - null::text as "description", - null::text as "access_policy_id", - null::text as "study_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as activity_definition_id, + null::text as name, + null::text as description, + null::text as access_policy_id, + null::text as study_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_activitydefinition_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_activitydefinition_external_id.sql index 0a0bf91..52b10ec 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_activitydefinition_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_activitydefinition_external_id.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "activitydefinition_activity_definition_id", - null::text as "external_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as activitydefinition_activity_definition_id, + null::text as external_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_aliquot.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_aliquot.sql index d56561f..fecd1d6 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_aliquot.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_aliquot.sql @@ -1,14 +1,14 @@ {{ config(materialized='table') }} - select - null::text as "aliquot_id", - sample_id as "sample_id", - null::text as "availablity_status", - null::text as "quantity_number", - null::text as "quantity_unit", - null::text as "concentration_number", - null::text as "concentration_unit", - null::text as "access_policy_id", - null::text as "study_id" - from {{ ref('kf_chr_18_int_sequencing') }} +select + null::text as aliquot_id, + sample_id, + null::text as availablity_status, + null::text as quantity_number, + null::text as quantity_unit, + null::text as concentration_number, + null::text as concentration_unit, + null::text as access_policy_id, + null::text as study_id +from {{ ref('kf_chr_18_int_sequencing') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_aliquot_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_aliquot_external_id.sql index 2c49464..3f9a351 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_aliquot_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_aliquot_external_id.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "aliquot_aliquot_id", - null::text as "external_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as aliquot_aliquot_id, + null::text as external_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_biospecimencollection.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_biospecimencollection.sql index 8fcde72..a9ff943 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_biospecimencollection.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_biospecimencollection.sql @@ -1,14 +1,14 @@ {{ config(materialized='table') }} - select - null::text as "biospecimen_collection_id", - age_at_sample as "age_at_collection", - null::text as "method", - null::text as "site", - null::text as "spatial_qualifier", - null::text as "laterality", - null::text as "encounter_id", - null::text as "access_policy_id", - null::text as "study_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as biospecimen_collection_id, + age_at_sample as age_at_collection, + null::text as method, + null::text as site, + null::text as spatial_qualifier, + null::text as laterality, + null::text as encounter_id, + null::text as access_policy_id, + null::text as study_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_biospecimencollection_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_biospecimencollection_external_id.sql index 11ab9f9..4d55b12 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_biospecimencollection_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_biospecimencollection_external_id.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "biospecimencollection_biospecimen_collection_id", - null::text as "external_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as biospecimencollection_biospecimen_collection_id, + null::text as external_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_concept.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_concept.sql index 436c7e0..9093cf0 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_concept.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_concept.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "concept_curie", - null::text as "display" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as concept_curie, + null::text as display +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_dataset.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_dataset.sql index a1e8495..fc4ccf2 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_dataset.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_dataset.sql @@ -1,11 +1,11 @@ {{ config(materialized='table') }} - select - null::text as "dataset_id", - null::text as "name", - null::text as "description", - null::text as "do_id", - null::text as "data_collection_start", - null::text as "data_collection_end" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as dataset_id, + null::text as name, + null::text as description, + null::text as do_id, + null::text as data_collection_start, + null::text as data_collection_end +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_dataset_file_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_dataset_file_id.sql index 1ddf2d6..d3de502 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_dataset_file_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_dataset_file_id.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "dataset_dataset_id", - null::text as "file_id_file_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as dataset_dataset_id, + null::text as file_id_file_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_dataset_publication.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_dataset_publication.sql index 2d08182..54ba7aa 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_dataset_publication.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_dataset_publication.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "dataset_dataset_id", - null::integer as "publication_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as dataset_dataset_id, + null::integer as publication_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_demographics.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_demographics.sql index 1437dbe..05624f8 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_demographics.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_demographics.sql @@ -1,14 +1,14 @@ {{ config(materialized='table') }} - select - participant_id as "subject_id", - sex as "sex", - ethnicity as "ethnicity", - null::text as "down_syndrome_status", -- could map to Not Applicable? - null::integer as "age_at_last_vital_status", - vital_status as "vital_status", - null::integer as "age_at_first_engagement", -- age at phenotype? or sample? - null::text as "access_policy_id", - null::text as "study_id" - from {{ ref('kf_chr_18_int_clinical') }} +select + participant_id as subject_id, + sex, + ethnicity, + null::text as down_syndrome_status, -- could map to Not Applicable? + null::integer as age_at_last_vital_status, + vital_status, + null::integer as age_at_first_engagement, -- age at phenotype? or sample? + null::text as access_policy_id, + null::text as study_id +from {{ ref('kf_chr_18_int_clinical') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_demographics_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_demographics_external_id.sql index 3b9d002..f62f40e 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_demographics_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_demographics_external_id.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "demographics_subject_id", - null::text as "external_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as demographics_subject_id, + null::text as external_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_demographics_race.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_demographics_race.sql index 0e0b421..d28c482 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_demographics_race.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_demographics_race.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "demographics_subject_id", - race as "race" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as demographics_subject_id, + race +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_doi.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_doi.sql index 632d186..d72114d 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_doi.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_doi.sql @@ -1,9 +1,9 @@ {{ config(materialized='table') }} - select - null::text as "do_id", - null::text as "bibliographic_reference", - null::text as "access_policy_id", - null::text as "study_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as do_id, + null::text as bibliographic_reference, + null::text as access_policy_id, + null::text as study_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_doi_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_doi_external_id.sql index 4d79e71..ead313e 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_doi_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_doi_external_id.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "doi_do_id", - null::text as "external_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as doi_do_id, + null::text as external_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounter.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounter.sql index 2698417..76728f1 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounter.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounter.sql @@ -1,11 +1,11 @@ {{ config(materialized='table') }} - select - null::text as "encounter_id", - null::text as "subject_id", - null::text as "encounter_definition_id", - null::integer as "age_at_event", - null::text as "access_policy_id", - null::text as "study_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as encounter_id, + null::text as subject_id, + null::text as encounter_definition_id, + null::integer as age_at_event, + null::text as access_policy_id, + null::text as study_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounter_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounter_external_id.sql index a8f68a4..fa3cf3a 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounter_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounter_external_id.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "encounter_encounter_id", - null::text as "external_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as encounter_encounter_id, + null::text as external_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounterdefinition.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounterdefinition.sql index b82f63a..de5fa56 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounterdefinition.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounterdefinition.sql @@ -1,10 +1,10 @@ {{ config(materialized='table') }} - select - null::text as "encounter_definition_id", - null::text as "name", - null::text as "description", - null::text as "access_policy_id", - null::text as "study_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as encounter_definition_id, + null::text as name, + null::text as description, + null::text as access_policy_id, + null::text as study_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounterdefinition_activity_definition_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounterdefinition_activity_definition_id.sql index d1b003e..e1c3e98 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounterdefinition_activity_definition_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounterdefinition_activity_definition_id.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "encounterdefinition_encounter_definition_id", - null::text as "activity_definition_id_activity_definition_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as encounterdefinition_encounter_definition_id, + null::text as activity_definition_id_activity_definition_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounterdefinition_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounterdefinition_external_id.sql index ea0f884..fc162aa 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounterdefinition_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounterdefinition_external_id.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "encounterdefinition_encounter_definition_id", - null::text as "external_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as encounterdefinition_encounter_definition_id, + null::text as external_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_family.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_family.sql index 1497d0c..5a75253 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_family.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_family.sql @@ -1,12 +1,12 @@ {{ config(materialized='table') }} - select - null::text as "family_id", - null::text as "family_type", - null::text as "family_description", - null::text as "consanguinity", - null::text as "family_study_focus", - null::text as "access_policy_id", - null::text as "study_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as family_id, + null::text as family_type, + null::text as family_description, + null::text as consanguinity, + null::text as family_study_focus, + null::text as access_policy_id, + null::text as study_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_family_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_family_external_id.sql index 3567c7f..3d01964 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_family_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_family_external_id.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "family_family_id", - null::text as "external_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as family_family_id, + null::text as external_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familymember.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familymember.sql index efbcb26..90c87f6 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familymember.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familymember.sql @@ -1,11 +1,11 @@ {{ config(materialized='table') }} - select - null::integer as "id", - null::text as "family_id", - null::text as "subject_id", - null::text as "family_role", - null::text as "access_policy_id", - null::text as "study_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::integer as id, + null::text as family_id, + null::text as subject_id, + null::text as family_role, + null::text as access_policy_id, + null::text as study_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familymember_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familymember_external_id.sql index a7117d0..8fa0ec3 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familymember_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familymember_external_id.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::integer as "familymember_id", - null::text as "external_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::integer as familymember_id, + null::text as external_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familyrelationship.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familyrelationship.sql index e7de895..5d49b0d 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familyrelationship.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familyrelationship.sql @@ -1,13 +1,13 @@ {{ config(materialized='table') }} - select - null::text as "family_relationship_id", - -- is this participant id? same as subject id? - null::text as "family_member_id", - -- this study doesn't have families so should this be null? or mapped to an NA value? - null::text as "relationship", - null::text as "subject_id", - null::text as "access_policy_id", - null::text as "study_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as family_relationship_id, + -- is this participant id? same as subject id? + null::text as family_member_id, + -- this study doesn't have families so should this be null? or mapped to an NA value? + null::text as relationship, + null::text as subject_id, + null::text as access_policy_id, + null::text as study_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familyrelationship_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familyrelationship_external_id.sql index d64ec62..25b3f68 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familyrelationship_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familyrelationship_external_id.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "familyrelationship_family_relationship_id", - null::text as "external_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as familyrelationship_family_relationship_id, + null::text as external_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file.sql index d7ab142..7f9590c 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file.sql @@ -1,18 +1,18 @@ {{ config(materialized='table') }} - select - null::text as "file_id", - file_name as "filename", - file_format as "format", - null::text as "data_category", - data_type as "data_type", - size as "size", - -- Need to determine when DRS indexing will happen - -- null::text as "staging_url", - -- null::text as "release_url", - -- null::text as "drs_uri", - null::text as "access_policy_id", - null::text as "study_id", - null::integer as "hash_id" - from {{ ref('kf_chr_18_int_s3') }} +select + null::text as file_id, + file_name as filename, + file_format as format, + null::text as data_category, + data_type, + size, + -- Need to determine when DRS indexing will happen + -- null::text as "staging_url", + -- null::text as "release_url", + -- null::text as "drs_uri", + null::text as access_policy_id, + null::text as study_id, + null::integer as hash_id +from {{ ref('kf_chr_18_int_s3') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file_external_id.sql index 25567a8..a2ec374 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file_external_id.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "file_file_id", - null::text as "external_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as file_file_id, + null::text as external_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file_sample_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file_sample_id.sql index e6f5a31..3719d67 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file_sample_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file_sample_id.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "file_file_id", - null::text as "sample_id_sample_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as file_file_id, + null::text as sample_id_sample_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file_subject_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file_subject_id.sql index 8554e3b..ded7be2 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file_subject_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file_subject_id.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "file_file_id", - null::text as "subject_id_subject_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as file_file_id, + null::text as subject_id_subject_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_filehash.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_filehash.sql index a198eea..6d728c9 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_filehash.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_filehash.sql @@ -1,8 +1,8 @@ {{ config(materialized='table') }} - select - null::integer as "id", - 'etag' as "hash_type", - etag as "hash_value" - from {{ ref('kf_chr_18_int_s3') }} +select + null::integer as id, + 'etag' as hash_type, + etag as hash_value +from {{ ref('kf_chr_18_int_s3') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_investigator.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_investigator.sql index f1161de..1b9d840 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_investigator.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_investigator.sql @@ -1,12 +1,12 @@ {{ config(materialized='table') }} - select - null::integer as "id", - null::text as "name", - null::text as "institution", - null::text as "investigator_title", - null::text as "email", - null::text as "access_policy_id", - null::text as "study_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::integer as id, + null::text as name, + null::text as institution, + null::text as investigator_title, + null::text as email, + null::text as access_policy_id, + null::text as study_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_investigator_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_investigator_external_id.sql index 1e6c882..92b599f 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_investigator_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_investigator_external_id.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::integer as "investigator_id", - null::text as "external_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::integer as investigator_id, + null::text as external_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_publication.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_publication.sql index 758fc43..e767929 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_publication.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_publication.sql @@ -1,10 +1,10 @@ {{ config(materialized='table') }} - select - null::integer as "id", - null::text as "bibliographic_reference", - null::text as "website", - null::text as "access_policy_id", - null::text as "study_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::integer as id, + null::text as bibliographic_reference, + null::text as website, + null::text as access_policy_id, + null::text as study_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_publication_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_publication_external_id.sql index 478f978..52f9f8d 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_publication_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_publication_external_id.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::integer as "publication_id", - null::text as "external_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::integer as publication_id, + null::text as external_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_record_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_record_external_id.sql index 6873693..54b92cd 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_record_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_record_external_id.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::integer as "record_id", - null::text as "external_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::integer as record_id, + null::text as external_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample.sql index 691c86b..1d8ef29 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample.sql @@ -1,14 +1,14 @@ {{ config(materialized='table') }} - select - sample_id as "sample_id", - null::text as "biospecimen_collection_id", - null::text as "parent_sample_id", - sequencing_strategy as "sample_type", - null::text as "availablity_status", - null::text as "quantity_number", - null::text as "quantity_unit", - null::text as "access_policy_id", - null::text as "study_id" - from {{ ref('kf_chr_18_int_sequencing') }} +select + sample_id, + null::text as biospecimen_collection_id, + null::text as parent_sample_id, + sequencing_strategy as sample_type, + null::text as availablity_status, + null::text as quantity_number, + null::text as quantity_unit, + null::text as access_policy_id, + null::text as study_id +from {{ ref('kf_chr_18_int_sequencing') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample_external_id.sql index 9f53c14..6cb38db 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample_external_id.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "sample_sample_id", - null::text as "external_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as sample_sample_id, + null::text as external_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample_processing.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample_processing.sql index 0ca6c7c..03f94fb 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample_processing.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample_processing.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "sample_sample_id", - null::text as "processing" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as sample_sample_id, + null::text as processing +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample_storage_method.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample_storage_method.sql index 09f1a7e..2130570 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample_storage_method.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample_storage_method.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "sample_sample_id", - null::text as "storage_method" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as sample_sample_id, + null::text as storage_method +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study.sql index b851fe6..42fa67a 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study.sql @@ -1,16 +1,16 @@ {{ config(materialized='table') }} - select - null::text as "parent_study", - null::text as "study_title", - null::text as "study_code", - null::text as "study_short_name", - null::text as "study_description", - null::text as "website", - null::text as "acknowledgments", - null::text as "citation_statement", - null::text as "do_id", - null::text as "access_policy_id", - null::text as "study_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as parent_study, + null::text as study_title, + null::text as study_code, + null::text as study_short_name, + null::text as study_description, + null::text as website, + null::text as acknowledgments, + null::text as citation_statement, + null::text as do_id, + null::text as access_policy_id, + null::text as study_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_clinical_data_source_type.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_clinical_data_source_type.sql index ad84524..1a407b6 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_clinical_data_source_type.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_clinical_data_source_type.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "study_study_id", - null::text as "clinical_data_source_type" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as study_study_id, + null::text as clinical_data_source_type +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_contact.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_contact.sql index 5f2874e..7a22647 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_contact.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_contact.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "study_study_id", - null::integer as "contact_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as study_study_id, + null::integer as contact_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_data_category.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_data_category.sql index 5997d77..46381ff 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_data_category.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_data_category.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "study_study_id", - null::text as "data_category" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as study_study_id, + null::text as data_category +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_external_id.sql index d7324a2..08afa42 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_external_id.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "study_study_id", - null::text as "external_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as study_study_id, + null::text as external_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_funding_source.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_funding_source.sql index d345ec8..11f7647 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_funding_source.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_funding_source.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "study_study_id", - null::text as "funding_source" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as study_study_id, + null::text as funding_source +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_participant_lifespan_stage.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_participant_lifespan_stage.sql index 23c43c9..802f125 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_participant_lifespan_stage.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_participant_lifespan_stage.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "study_study_id", - null::text as "participant_lifespan_stage" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as study_study_id, + null::text as participant_lifespan_stage +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_principal_investigator.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_principal_investigator.sql index dffdf06..601db2f 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_principal_investigator.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_principal_investigator.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "study_study_id", - null::integer as "principal_investigator_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as study_study_id, + null::integer as principal_investigator_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_program.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_program.sql index e04a170..f0e83c0 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_program.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_program.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "study_study_id", - null::text as "program" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as study_study_id, + null::text as program +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_publication.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_publication.sql index 35f2187..37f71af 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_publication.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_publication.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "study_study_id", - null::integer as "publication_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as study_study_id, + null::integer as publication_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_research_domain.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_research_domain.sql index 20ebb9f..dbb9064 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_research_domain.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_research_domain.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "study_study_id", - null::text as "research_domain" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as study_study_id, + null::text as research_domain +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_study_design.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_study_design.sql index 2473ea5..918c872 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_study_design.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_study_design.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "study_study_id", - null::text as "study_design" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as study_study_id, + null::text as study_design +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata.sql index b666f04..8005372 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata.sql @@ -1,11 +1,11 @@ {{ config(materialized='table') }} - select - null::text as "study_id", - null::text as "selection_criteria", - null::text as "vbr_id", - null::integer as "expected_number_of_participants", - null::integer as "actual_number_of_participants", - null::text as "access_policy_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as study_id, + null::text as selection_criteria, + null::text as vbr_id, + null::integer as expected_number_of_participants, + null::integer as actual_number_of_participants, + null::text as access_policy_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_clinical_data_source_type.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_clinical_data_source_type.sql index c21df2f..8f76350 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_clinical_data_source_type.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_clinical_data_source_type.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "studymetadata_study_id", - null::text as "clinical_data_source_type" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as studymetadata_study_id, + null::text as clinical_data_source_type +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_data_category.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_data_category.sql index e956c06..0e96635 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_data_category.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_data_category.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "studymetadata_study_id", - null::text as "data_category" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as studymetadata_study_id, + null::text as data_category +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_external_id.sql index 6f21f7a..0058736 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_external_id.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "studymetadata_study_id", - null::text as "external_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as studymetadata_study_id, + null::text as external_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_participant_lifespan_stage.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_participant_lifespan_stage.sql index d351a23..502a6bd 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_participant_lifespan_stage.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_participant_lifespan_stage.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "studymetadata_study_id", - null::text as "participant_lifespan_stage" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as studymetadata_study_id, + null::text as participant_lifespan_stage +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_research_domain.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_research_domain.sql index cf2c675..1b4301d 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_research_domain.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_research_domain.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "studymetadata_study_id", - null::text as "research_domain" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as studymetadata_study_id, + null::text as research_domain +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_study_design.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_study_design.sql index 7edc780..6b54487 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_study_design.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_study_design.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "studymetadata_study_id", - null::text as "study_design" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as studymetadata_study_id, + null::text as study_design +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subject.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subject.sql index 0941c6a..60df5cd 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subject.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subject.sql @@ -1,10 +1,10 @@ {{ config(materialized='table') }} - select - null::text as "subject_id", - null::text as "subject_type", - null::text as "organism_type", - null::text as "access_policy_id", - null::text as "study_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as subject_id, + null::text as subject_type, + null::text as organism_type, + null::text as access_policy_id, + null::text as study_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subject_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subject_external_id.sql index 8080cab..73235e8 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subject_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subject_external_id.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "subject_subject_id", - null::text as "external_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as subject_subject_id, + null::text as external_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion.sql index 2ae5ad0..0224cfb 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion.sql @@ -1,19 +1,19 @@ {{ config(materialized='table') }} - select - null::text as "assertion_id", - null::text as "subject_id", - null::text as "encounter_id", - null::text as "assertion_provenance", - null::integer as "age_at_assertion", - null::integer as "age_at_event", - null::integer as "age_at_resolution", - null::text as "concept_source", - null::text as "value_number", - null::text as "value_source", - null::text as "value_unit", - null::text as "value_unit_source", - null::text as "access_policy_id", - null::text as "study_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as assertion_id, + null::text as subject_id, + null::text as encounter_id, + null::text as assertion_provenance, + null::integer as age_at_assertion, + null::integer as age_at_event, + null::integer as age_at_resolution, + null::text as concept_source, + null::text as value_number, + null::text as value_source, + null::text as value_unit, + null::text as value_unit_source, + null::text as access_policy_id, + null::text as study_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion_concept.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion_concept.sql index 9771ae9..6189f35 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion_concept.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion_concept.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "subjectassertion_assertion_id", - null::text as "concept_concept_curie" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as subjectassertion_assertion_id, + null::text as concept_concept_curie +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion_external_id.sql index f6af07d..4b8a8dd 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion_external_id.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "subjectassertion_assertion_id", - null::text as "external_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as subjectassertion_assertion_id, + null::text as external_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion_value_concept.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion_value_concept.sql index b6a1e23..5dfd39a 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion_value_concept.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion_value_concept.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "subjectassertion_assertion_id", - null::text as "value_concept_concept_curie" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as subjectassertion_assertion_id, + null::text as value_concept_concept_curie +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_virtualbiorepository.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_virtualbiorepository.sql index dd14313..e151816 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_virtualbiorepository.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_virtualbiorepository.sql @@ -1,12 +1,12 @@ {{ config(materialized='table') }} - select - null::text as "vbr_id", - null::text as "name", - null::text as "institution", - null::text as "website", - null::text as "vbr_readme", - null::text as "access_policy_id", - null::text as "study_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as vbr_id, + null::text as name, + null::text as institution, + null::text as website, + null::text as vbr_readme, + null::text as access_policy_id, + null::text as study_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_virtualbiorepository_contact.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_virtualbiorepository_contact.sql index 7d01c0e..29321af 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_virtualbiorepository_contact.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_virtualbiorepository_contact.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "virtualbiorepository_vbr_id", - null::integer as "contact_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as virtualbiorepository_vbr_id, + null::integer as contact_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_virtualbiorepository_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_virtualbiorepository_external_id.sql index ccbfcfa..8d007dc 100644 --- a/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_virtualbiorepository_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_virtualbiorepository_external_id.sql @@ -1,7 +1,7 @@ {{ config(materialized='table') }} - select - null::text as "virtualbiorepository_vbr_id", - null::text as "external_id" - from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +select + null::text as virtualbiorepository_vbr_id, + null::text as external_id +from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file