V2.1

.gitmodules

@@ -1,3 +1,3 @@
 [submodule "metpetdb_api/vendor/djoser"]
 	path = metpetdb_api/vendor/djoser
-	url = https://github.com/IreLynn/djoser.git
+	url = https://github.com/bdrumheller/djoser.git

metpetdb_api/api/bulk_upload/v1/tests.py

@@ -12,10 +12,8 @@
     Subsample
 )
 
-from apps.chemical_analyses.models import(
-    Element,
-    Oxide,
-)
+from apps.chemical_analyses.shared_models import Element, Oxide
+
 
 class BulkUploadTests(APITransactionTestCase):
     """

metpetdb_api/api/bulk_upload/v1/upload_templates.py

@@ -26,6 +26,45 @@
 """
 import copy
 
+# labels are case insensitive!
+sample_label_mappings = {
+    'sample number':'number',
+    'rock type':'rock_type_name',
+    'latitude':'latitude',
+    'longitude':'longitude',
+    'location error':'location_error',
+    'collector':'collector_name',
+    'date of collection':'collection_date',
+    'present sample location':'location_name',
+    'country':'country',
+    # multi-fields 
+    'comment':'description',
+    'reference':'references',
+    'region':'regions',
+    'metamorphic region':'metamorphic_regions',
+    'metamorphic grade':'metamorphic_grades'
+}
+
+chem_analysis_label_mappings = {
+    'sample':'sample',
+    'subsample':'subsample',
+    'mineral':'mineral',
+    'method':'analysis_method',
+    'subsample type':'subsample_type',
+    'reference':'reference',
+    'point':'spot_id',
+    'analytical facility':'where_done',
+    'analysis date':'analysis_date',
+    'analyst':'analyst',
+    'reference x':'reference_x',
+    'reference y':'reference_y',
+    'stage x':'stage_x',
+    'stage y':'stage_y',
+    'total':'total',
+    'comment':'description'
+}
+
+
 class Template:
     def __init__(self, c_types = [], required = [], db_types = [], types = {}): 
         self.complex_types = c_types
@@ -45,12 +84,13 @@ def check_line_len(self):
                 raise Exception("inconsistent line length. Expected {0}, but was {1}".format(len(data[i-1]), len(data[i])))
 
     def check_required(self, row):
-        header = row[0]
+        header = [x for x in row[0]]
+        for i in range(0,len(header)):
+            header[i] = header[i].lower()
         missing ={}
-        for i in range(0, len(header)):
-            if self.is_required(header[i]):
-                if row[1][i] == '':
-                    missing[header[i]] = 'missing'
+        for i in range(0, len(self.required)):
+            if self.required[i] not in header:
+                missing[self.required[i]] = 'missing'
         return missing
 
     def check_type(self, curr_row):
@@ -104,7 +144,7 @@ def parse(self, data):
         for heading in header:
             if self.is_complex(heading): result_template[heading] = []
             else: result_template[heading] = ''
-        result_template['errors'] = '';
+        result_template['errors'] = ''
 
         for i in range(1, len(data)):
             tmp_result = self.TemplateResult(copy.deepcopy(result_template))
@@ -114,17 +154,8 @@ def parse(self, data):
             for j in range(0,len(data[i])):
                 heading = header[j]
 
-                if heading in self.amounts:
-                    name = data[i][j]
-                    amount = self.get_amount(data,i,j)
-                    tmp_result.set_field_complex(heading, {"name": name, "amount": amount})
-                    continue
-
-                if heading == 'mineral' and heading not in self.amounts:
-                    tmp_result.set_field_complex(heading, {"name": data[i][j]})
-                    continue
-
                 field = data[i][j]
+                # print("{}: {}".format(heading,data[i][j]))
                 if self.is_complex(heading):
                     tmp_result.set_field_complex(heading,field)
                 else: tmp_result.set_field_simple(heading, field)
@@ -133,14 +164,14 @@ def parse(self, data):
             result.append(tmp_result.get_rep())
         return result, meta_header
 
-    def is_complex(self, name): return name in self.complex_types
-    def is_required(self, name): return name in self.required
+    def is_complex(self, name): return name.lower() in self.complex_types
+    def is_required(self, name): return name.lower() in self.required
     def is_db_type(self, name): return name in self.db_types
 
 class ChemicalAnalysesTemplate(Template):
     def __init__(self):
-        complex_types = ["comment", "element", "oxide","mineral"]
-        required = ["subsample_id", "spot_id", "mineral", "analysis_method"]
+        complex_types = ["comment","element","oxide"]
+        required = ["sample","subsample","point","mineral","method","subsample type"]
         db_types = ["element", "oxide"]
         types = {"comment": str, "stage_x" : float, "stage_y" : float, "reference_x": float, "reference_y": float}
         Template.__init__(self, complex_types, required, db_types, types)
@@ -168,19 +199,19 @@ def get_meta_header(self,header):
                     meta_header.append((heading, mappings[heading]))
                     added.add(heading)
                 else:
-                    meta_header.append((heading, heading)) 
+                    meta_header.append((heading, heading))
+                    added.add(heading)
         return meta_header
 
 class SampleTemplate(Template):
 
     def __init__(self):
-        complex_types = ["comment", "references", "mineral", "metamorphic_region_id", "metamorphic_grade"]
-        required = ["number", "latitude", "longitude", "rock_type_name"]
+        complex_types = ["comment", "reference", "region", "metamorphic region", "metamorphic grade"]
+        required = ["sample number", "latitude", "longitude", "rock type"]
         types = {"comment": str, "latitude": float, 'longitude': float}
         db_types = ["minerals"]
         #selected_types = {'minerals': ['el1', 'el2', 'el3']}
         Template.__init__(self, complex_types, required, db_types, types)
-        self.amounts.add('mineral')
 
     def check_amounts(self,header):
         pass
@@ -189,18 +220,22 @@ def get_amount(self,data=[],i=0,j=0):
         return 0
 
     def get_meta_header(self,header):
-        mappings = {'mineral' : 'minerals'}
-        added = set()        
+        mappings = {}
+        added = set()
         meta_header = []
         itr = iter(header)
         for heading in itr:
-            if heading == 'latitude':
-                for i in range (0,2): heading = next(itr)
-                meta_header.append((('latitude','longitude'),'location_coords'))
-            elif heading not in added:
-                if heading in mappings.keys():
-                    meta_header.append((heading, mappings[heading]))
+            # if heading.lower() == 'latitude':
+            #     for i in range (0,2): heading = next(itr)
+            #     meta_header.append((('latitude','longitude'),'Location'))
+            if heading not in added:
+                if heading.lower() in mappings.keys():
+                    meta_header.append((heading.lower(),heading))
                     added.add(heading)
                 else:
-                    meta_header.append((heading, heading)) 
+                    meta_header.append((heading, heading))
+                    added.add(heading)
+        # print("\nMETA-HEADER:")
+        # print(meta_header)
+        # print("\n\n")
         return meta_header