Merge pull request #145 from bcgsc/release-v3.12.3

Release v3.13.0

ipr/annotate.py

@@ -1,6 +1,7 @@
 """
 handles annotating variants with annotation information from graphkb
 """
+
 from requests.exceptions import HTTPError
 
 from graphkb import GraphKBConnection
@@ -55,7 +56,6 @@ def get_ipr_statements_from_variants(
     if not matches:
         return []
     rows = []
-
     statements = get_statements_from_variants(graphkb_conn, matches)
     existing_statements = {s['@rid'] for s in statements}
 
@@ -76,9 +76,8 @@ def get_ipr_statements_from_variants(
     for ipr_row in convert_statements_to_alterations(
         graphkb_conn, inferred_statements, disease_name, convert_to_rid_set(inferred_matches)
     ):
-        new_row = KbMatch({'kbData': {'inferred': True}})
-        new_row.update(ipr_row)
-        rows.append(new_row)
+        ipr_row['kbData']['inferred'] = True
+        rows.append(ipr_row)
 
     return rows
 

ipr/inputs.py

@@ -1,6 +1,7 @@
 """
 Read/Validate the variant input files
 """
+
 import json
 import jsonschema
 import os

ipr/ipr.py

@@ -2,6 +2,7 @@
 Contains functions specific to formatting reports for IPR that are unlikely to be used
 by other reporting systems
 """
+
 from graphkb import GraphKBConnection
 from graphkb import statement as gkb_statement
 from graphkb import vocab as gkb_vocab
@@ -130,6 +131,23 @@ def convert_statements_to_alterations(
     # GERO-318 - add all IPR-A evidence equivalents to the approvedTherapy flag
     approved = set([ev for (ev, ipr) in ev_map.items() if ipr == 'IPR-A'])
 
+    # get the recruitment status for any trial associated with a statement
+    clinical_trials = [
+        s['subject']['@rid'] for s in statements if s['subject']['@class'] == 'ClinicalTrial'
+    ]
+    recruitment_statuses = {}
+    if clinical_trials:
+        clinical_trials = list(set(clinical_trials))
+        for rid in clinical_trials:
+            query_result = graphkb_conn.query(
+                {
+                    'target': {'target': 'ClinicalTrial', 'filters': {'@rid': rid}},
+                    'returnProperties': ['@rid', 'recruitmentStatus'],
+                }
+            )
+            if query_result:
+                recruitment_statuses[rid] = query_result[0]['recruitmentStatus']
+
     for statement in statements:
         variants = [c for c in statement['conditions'] if c['@class'] in VARIANT_CLASSES]
         diseases = [c for c in statement['conditions'] if c['@class'] == 'Disease']
@@ -175,13 +193,20 @@ def convert_statements_to_alterations(
                     'reference': pmid,
                     'relevance': statement['relevance']['displayName'],
                     'kbRelevanceId': statement['relevance']['@rid'],
-                    'externalSource': str(statement['source'].get('displayName', ''))
-                    if statement['source']
-                    else None,
+                    'externalSource': (
+                        str(statement['source'].get('displayName', ''))
+                        if statement['source']
+                        else None
+                    ),
                     'externalStatementId': statement.get('sourceId'),
                     'reviewStatus': statement.get('reviewStatus'),
+                    'kbData': {},
                 }
             )
+            if statement['relevance']['name'] == 'eligibility':
+                row['kbData']['recruitment_status'] = recruitment_statuses.get(
+                    row['kbContextId'], 'not found'
+                )
             rows.append(row)
     return rows
 

ipr/therapeutic_options.py

@@ -1,6 +1,7 @@
 """
 upload variant and report information to IPR
 """
+
 import pandas
 from graphkb import GraphKBConnection
 from typing import Dict, List, Sequence

ipr/types.py

@@ -1,4 +1,4 @@
-from typing import List, Optional, Union
+from typing import List, Optional, Union, Dict
 
 try:
     from typing import TypedDict  # type: ignore
@@ -30,6 +30,7 @@ class KbMatch(TypedDict):
     externalSource: str
     externalStatementId: str
     reviewStatus: str
+    kbData: Optional[Dict]
 
 
 class IprGene(TypedDict):

setup.cfg

@@ -18,7 +18,7 @@ known_standard_library = requests
 
 [metadata]
 name = ipr
-version = 3.12.2
+version = 3.13.0
 author_email = ipr@bcgsc.ca
 author = ipr
 maintainer_email = ipr@bcgsc.ca
@@ -28,7 +28,7 @@ long_description_content_type = text/markdown
 
 [options]
 packages = find:
-python_requires = >=3.6
+python_requires = >=3.7
 dependency_links = []
 include_package_data = True
 install_requires =

tests/test_ipr.py

@@ -179,10 +179,18 @@ def base_graphkb_statement(
                 },
             ],
             "evidence": [],
-            "subject": None,
+            "subject": {
+                "@class": 'dummy_value',
+                "@rid": "101:010",
+                "displayName": 'dummy_display_name',
+            },
             "source": None,
             "sourceId": None,
-            "relevance": {"@rid": relevance_rid, "displayName": "relevance_display_name"},
+            "relevance": {
+                "@rid": relevance_rid,
+                "displayName": "relevance_display_name",
+                "name": "relevance_name",
+            },
             "@rid": "statement_rid",
         }
     )