diff --git a/dbt_project/dbt_project.yml b/dbt_project/dbt_project.yml index 40d0eb0..c10a54a 100644 --- a/dbt_project/dbt_project.yml +++ b/dbt_project/dbt_project.yml @@ -45,6 +45,15 @@ models: +schema: kf_sd_1nns3k8v_src int: +schema: kf_sd_1nns3k8v_int + 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/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..6f39b4a --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_clinical.sql @@ -0,0 +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 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..ebb1f76 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_phenotypes.sql @@ -0,0 +1,85 @@ +{{ config(materialized='table') }} + +with base_data as ( + select * from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +), +unpivoted_phenotypes as ( + select + 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 + 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..19ecf2a --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_s3.sql @@ -0,0 +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') }} + \ 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..9380ced --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql @@ -0,0 +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, + + -- 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') }} +), + +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') }} +) + +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 new file mode 100644 index 0000000..9d72108 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/src/Clinical_Data/kf_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 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 new file mode 100644 index 0000000..3644109 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/kf_chr_18_src_s3_scrape_cody.sql @@ -0,0 +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') }} + \ 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..5e36e5a --- /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::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/src/_column_descriptions.md b/dbt_project/models/kids_first/chr_18/src/_column_descriptions.md new file mode 100644 index 0000000..d7f1f60 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/src/_column_descriptions.md @@ -0,0 +1,587 @@ +{% 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 terra_manifest_v2_sample_id %} +sample_id +{% enddocs %} + +{% docs terra_manifest_v2_project %} +project +{% enddocs %} + +{% docs terra_manifest_v2_collaborator_sample_id %} +collaborator_sample_id +{% enddocs %} + +{% docs terra_manifest_v2_version %} +version +{% enddocs %} + +{% docs terra_manifest_v2_data_type %} +data_type +{% enddocs %} + +{% docs terra_manifest_v2_pdo %} +pdo +{% enddocs %} + +{% docs terra_manifest_v2_release_date %} +release_date +{% enddocs %} + +{% docs terra_manifest_v2_reference_sequence_name %} +reference_sequence_name +{% enddocs %} + +{% docs terra_manifest_v2_collaborator_participant_id %} +collaborator_participant_id +{% enddocs %} + +{% docs terra_manifest_v2_cram_path %} +cram_path +{% enddocs %} + +{% docs terra_manifest_v2_crai_path %} +crai_path +{% enddocs %} + +{% docs terra_manifest_v2_md5_path %} +md5_path +{% enddocs %} + +{% 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 %} +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..39085f0 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/src/sources.yml @@ -0,0 +1,311 @@ +sources: +- name: chr_18 + schema: kf_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: terra_manifest_v2 + description: Source table for terra_manifest_v2. + columns: + - name: sample_id + description: '{{ doc("terra_manifest_v2_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_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 + 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: + - 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/kf_chr_18_stb_accesspolicy.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_accesspolicy.sql new file mode 100644 index 0000000..dabac80 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..6507dc2 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..52b10ec --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..fecd1d6 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_aliquot.sql @@ -0,0 +1,14 @@ +{{ config(materialized='table') }} + +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 new file mode 100644 index 0000000..3f9a351 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..a9ff943 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_biospecimencollection.sql @@ -0,0 +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') }} + \ 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 new file mode 100644 index 0000000..4d55b12 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..9093cf0 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_concept.sql @@ -0,0 +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') }} + \ 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 new file mode 100644 index 0000000..fc4ccf2 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..d3de502 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..54ba7aa --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..05624f8 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_demographics.sql @@ -0,0 +1,14 @@ +{{ config(materialized='table') }} + +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 new file mode 100644 index 0000000..f62f40e --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..d28c482 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_demographics_race.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + +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 new file mode 100644 index 0000000..d72114d --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..ead313e --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..76728f1 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..fa3cf3a --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..de5fa56 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..e1c3e98 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..fc162aa --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..5a75253 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..3d01964 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..90c87f6 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..8fa0ec3 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..5d49b0d --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familyrelationship.sql @@ -0,0 +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') }} + \ 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 new file mode 100644 index 0000000..25b3f68 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..7f9590c --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file.sql @@ -0,0 +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, + 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 new file mode 100644 index 0000000..a2ec374 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..3719d67 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..ded7be2 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..6d728c9 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_filehash.sql @@ -0,0 +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') }} + \ 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 new file mode 100644 index 0000000..1b9d840 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..92b599f --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..e767929 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..52f9f8d --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..54b92cd --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..1d8ef29 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample.sql @@ -0,0 +1,14 @@ +{{ config(materialized='table') }} + +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 new file mode 100644 index 0000000..6cb38db --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..03f94fb --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..2130570 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..42fa67a --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..1a407b6 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..7a22647 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..46381ff --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..08afa42 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..11f7647 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..802f125 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..601db2f --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..f0e83c0 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..37f71af --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..dbb9064 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..918c872 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..8005372 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..8f76350 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..0e96635 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..0058736 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..502a6bd --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..1b4301d --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..6b54487 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..60df5cd --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..73235e8 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..0224cfb --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..6189f35 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..4b8a8dd --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..5dfd39a --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..e151816 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..29321af --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 new file mode 100644 index 0000000..8d007dc --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/kf_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('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 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