insert ages

sedv8808 · sedv8808 · commit 7c19fdd2b6c1 · 2023-10-26T19:13:31.000-07:00
diff --git a/neotomaUploader/__init__.py b/neotomaUploader/__init__.py
@@ -37,4 +37,5 @@
 from .insert_dataset_database import insert_dataset_database
 from .insert_sample import insert_sample
 from .insert_sample_analyst import insert_sample_analyst
-from .insert_data import insert_data
+from .insert_data import insert_data
+from .insert_sample_age import insert_sample_age
diff --git a/neotomaUploader/insertSamples.py b/neotomaUploader/insertSamples.py
diff --git a/neotomaUploader/insert_data.py b/neotomaUploader/insert_data.py
@@ -10,28 +10,24 @@ def insert_data(cur, yml_dict, csv_template, uploader):
     params = ['value']
     inputs = pull_params(params, yml_dict, csv_template, 'ndb.data')
 
-    #print(inputs)
-    #print("uploader sampleid")
-    #print(uploader['samples'])
     data_points = []
     counter = 0
     for i, val_dict in enumerate(inputs):
-        counter +=1
-        print(val_dict)
+        val_dict['value'] = [None if item == 'NA' else item for item in val_dict['value']]
         for j, val in enumerate(val_dict['unitcolumn']):
-            counter +=1
 
             get_varid = """SELECT * FROM ndb.variableunits WHERE variableunits %% %(units)s;"""
             cur.execute(get_varid, {'units': val_dict['unitcolumn'][j]})
             varid = cur.fetchone()[0]
 
-            cur.execute(data_query, {'sampleid': int(4), # int(uploader['sampleid']),
+            cur.execute(data_query, {'sampleid': int(uploader['samples'][counter]),
                                     'variableid': int(varid),
-                                    'value': float(val_dict['value'][i])})
+                                    'value': val_dict['value'][i]})
         
             result = cur.fetchone()[0]
+            counter +=1
             data_points.append(result)
-    print(len(counter))
+    print(counter)
     print(len(uploader['samples']))
 
     return data_points
diff --git a/neotomaUploader/insert_sample_age.py b/neotomaUploader/insert_sample_age.py
@@ -0,0 +1,22 @@
+import logging
+from .pull_params import pull_params
+
+def insert_sample_age(cur, yml_dict, csv_template, uploader):
+    """
+    """
+
+    sample_age_query = """
+                       SELECT ts.insertsampleage(_sampleid := %(sampleid)s, 
+                                                 _chronologyid := %(chronologyid)s, 
+                                                 _age := %(age)s, 
+                                                 _ageyounger := %(ageyounger)s, 
+                                                 _ageolder := %(ageolder)s)
+                       """
+    
+    params = []
+    inputs = pull_params(params, yml_dict, csv_template, 'ndb.ages')
+    
+    print(len(uploader['chronology']))
+    print(len(uploader['samples']))
+
+    return
diff --git a/neotomaUploader/insert_sample_analyst.py b/neotomaUploader/insert_sample_analyst.py
@@ -7,10 +7,28 @@ def insert_sample_analyst(cur, yml_dict, csv_template, uploader):
     
     params = ['contactid']
     inputs = pull_params(params, yml_dict, csv_template, 'ndb.sampleanalysts')
-    
     get_contact = """SELECT * FROM ndb.contacts WHERE contactname %% %(contactname)s;"""
     
-    cur.execute(get_contact, {'contactname': inputs['contactid'][0]})
-    contactid = cur.fetchone()[0]
+    contids = []
+    baseid = 1
+    for i in inputs['contactid']:
+        cur.execute(get_contact, {'contactname': i})
+        contids.append({'contactname': i, 'id': cur.fetchone()[0], 'order': baseid})
+        baseid = baseid + 1
+    
+    result = []
+    counter = 0
+    for i in range(len(uploader['samples'])):
+        for contact in contids:
+            inserter = """
+                        SELECT ts.insertsampleanalyst(_sampleid := %(sampleid)s,
+                                                    _contactid := %(contactid)s,
+                                                    _analystorder := %(analystorder)s)
+                    """
+            cur.execute(inserter, {'sampleid': int(uploader['samples'][counter]), 
+                                'contactid': int(contact['id']),
+                                'analystorder': int(contact['order'])})
+            result.append(cur.fetchone()[0])
+            counter += 1
 
-    return contactid
+    return result
diff --git a/template_upload.py b/template_upload.py
@@ -124,12 +124,12 @@
 
 
 # ts.insertsampleage
-# logfile.append('=== Inserting Sample Analyst ===')
-# uploader['sampleAnalyst'] = nu.insert_sample_analyst(cur, 
-#                                        yml_dict = yml_dict,
-#                                        csv_template = csv_template,
-#                                        uploader = uploader)
-# logfile.append(f"Sample Analyst: {uploader['sampleAnalyst']}")
+logfile.append('=== Inserting Sample Age ===')
+uploader['sampleAge'] = nu.insert_sample_age(cur, 
+                                       yml_dict = yml_dict,
+                                       csv_template = csv_template,
+                                       uploader = uploader)
+logfile.append(f"Sample Age: {uploader['sampleAge']}")
 
 # ts.insertdata
 logfile.append('=== Inserting Data ===')
