feat(#608): add new phenotype guideline

scripts/update.py

@@ -79,14 +79,18 @@ def add_missing_drugs(data, updated_external_data):
             add_log.append(log_item(drug_name))
     return data, add_log
 
+def get_guideline_phenotypes(guidelines):
+    guideline_phenotypes = []
+    for guideline in guidelines:
+        phenotype_key = get_phenotype_key(guideline)
+        if phenotype_key in guideline_phenotypes:
+            raise Exception('Phenotypes should be unique per drug guideline!')
+        guideline_phenotypes.append(phenotype_key)
+    return guideline_phenotypes
+
 def remove_outdated_guidelines(data, drug, guidelines, updated_guidelines):
     remove_log = []
-    updated_guideline_phenotypes = []
-    for updated_guideline in updated_guidelines:
-        phenotype_key = get_phenotype_key(updated_guideline)
-        if phenotype_key in updated_guideline_phenotypes:
-            raise Exception('Phenotypes should be unique per drug guideline!')
-        updated_guideline_phenotypes.append(phenotype_key)
+    updated_guideline_phenotypes = get_guideline_phenotypes(updated_guidelines)
     stale_guidelines = list(filter(
         lambda guideline: get_phenotype_key(guideline) not in \
             updated_guideline_phenotypes,
@@ -115,12 +119,31 @@ def remove_outdated_guidelines(data, drug, guidelines, updated_guidelines):
 def update_guidelines(data, guidelines, updated_guidelines):
     update_log = []
     update_log.append(log_item('TODO: update guidelines', level=1))
-    return guidelines, update_log
+    return update_log
 
-def add_missing_guidelines(data, guidelines, updated_guidelines):
+def add_missing_guidelines(data, drug, guidelines, updated_guidelines):
     add_log = []
-    add_log.append(log_item('TODO: add guidelines', level=1))
-    return guidelines, add_log
+    present_guideline_phenotypes = get_guideline_phenotypes(guidelines)
+    new_guidelines = list(filter(
+        lambda guideline: get_phenotype_key(guideline) not in \
+            present_guideline_phenotypes,
+        updated_guidelines
+    ))
+    new_guideline_ids = list(map(
+        lambda guideline: guideline['_id'],
+        new_guidelines
+    ))
+    if len(new_guidelines) > 0:
+        update_version(data, DRUG_COLLECTION_NAME, drug)
+        drug['guidelines'] += new_guideline_ids
+        data[GUIDELINE_COLLECTION_NAME] += new_guidelines
+        add_log += list(map(
+            lambda guideline: log_item(
+                f'Added guideline for {get_phenotype_key(guideline)}',
+                level=1),
+            new_guidelines
+        ))
+    return add_log
 
 def update_drugs(data, updated_external_data):
     update_log = []
@@ -158,8 +181,8 @@ def update_drugs(data, updated_external_data):
             data, current_drug, current_guidelines, updated_guidelines)
         drug_updates += \
             update_guidelines(data, current_guidelines, updated_guidelines)
-        drug_updates += \
-            add_missing_guidelines(data, current_guidelines, updated_guidelines)
+        drug_updates += add_missing_guidelines(
+            data, current_drug, current_guidelines, updated_guidelines)
 
         if len(drug_updates) != 0:
             update_log.append(drug_log_item)

scripts/update_test.py

@@ -63,6 +63,8 @@ def build_data(drug_guideline_map, rx_norms={}, phenotypes={}):
 ADDED_DRUG = 'drug and guidelines should be added'
 RX_NORM_CHANGED_DRUG = 'drug rxNorm changed'
 GUIDELINE_REMOVED_DRUG = 'drug with guideline for phenotype removed'
+GUIDELINE_ADDED_DRUG = 'drug with guideline for new phenotype'
+ADDED_GUIDELINE_ID = 'new.add-guideline'
 STANDARD_PHENOTYPES = [{
         'CYP2C19': [ 'Poor Metabolizer' ],
         'CYP2D6': [ 'Poor Metabolizer' ]
@@ -82,6 +84,7 @@ def data():
         UNCHANGED_DRUG: ['old.unchanged.1', 'old.unchanged.2'],
         RX_NORM_CHANGED_DRUG: ['old.rx-change.1', 'old.rx-change.2'],
         GUIDELINE_REMOVED_DRUG: ['old.rm-guideline', 'old.keep-guideline'],
+        GUIDELINE_ADDED_DRUG: ['old.present-guideline']
     }
     rx_norms = { RX_NORM_CHANGED_DRUG: 'rx.old' }
     phenotypes = {
@@ -100,6 +103,8 @@ def updated_data():
         ADDED_DRUG: ['new.add-drug.1', 'new.add-drug.2'],
         RX_NORM_CHANGED_DRUG: ['new.rx-change.1', 'new.rx-change.2'],
         GUIDELINE_REMOVED_DRUG: ['new.keep-guideline'],
+        GUIDELINE_ADDED_DRUG: ['new.present-guideline', ADDED_GUIDELINE_ID]
+
     }
     rx_norms = { RX_NORM_CHANGED_DRUG: 'rx.new' }
     phenotypes = {
@@ -150,12 +155,15 @@ def test_update_drugs(data, updated_data):
         copy.deepcopy(expected_data[GUIDELINE_COLLECTION_NAME][7]))
     del expected_data[GUIDELINE_COLLECTION_NAME][7]
 
-    # from pprint import pprint
-    # pprint(data)
-    # pprint(expected_data)
-
-    # New (phenotype) guideline is added to drug and guidelines; drug and
-    # guideline histories added
+    # New (phenotype) guideline is added to drug and guidelines; drug
+    # history added
+    expected_data[DRUG_HISTORY_COLLECTION_NAME].append(
+         copy.deepcopy(expected_data[DRUG_COLLECTION_NAME][4]))
+    expected_data[DRUG_COLLECTION_NAME][4]['guidelines'].append(
+        ADDED_GUIDELINE_ID)
+    expected_data[DRUG_COLLECTION_NAME][4]['_v'] += 1
+    expected_data[GUIDELINE_COLLECTION_NAME].append(
+        copy.deepcopy(updated_data[GUIDELINE_COLLECTION_NAME][8]))
     # TODO
 
     # Guideline lookupkey is updated; guideline history added
@@ -177,6 +185,8 @@ def test_update_drugs(data, updated_data):
         data[DRUG_COLLECTION_NAME][2]['_vDate']
     expected_data[DRUG_COLLECTION_NAME][3]['_vDate'] = \
         data[DRUG_COLLECTION_NAME][3]['_vDate']
+    expected_data[DRUG_COLLECTION_NAME][4]['_vDate'] = \
+        data[DRUG_COLLECTION_NAME][4]['_vDate']
     # import pprint
     # print('Expected:')
     # pprint.pprint(expected_data)