✨ Add ability to set things to be visible if loaded in dbgap

kf_update_dbgap_consent/app/cli.py

@@ -3,8 +3,8 @@
 from argparse import RawTextHelpFormatter
 from pprint import pprint
 
-from kf_utils.dataservice.patch import send_patches
 from kf_update_dbgap_consent.sample_status import ConsentProcessor
+from kf_utils.dataservice.patch import send_patches
 
 SERVER_DEFAULT = "http://localhost:5000"
 
@@ -46,12 +46,26 @@ def cli():
             " - Defaults to match on `external_sample_id`"
         ),
     )
+    parser.add_argument(
+        "--coerce_visible",
+        action="store_true",
+        default=False,
+        help=(
+            "If a specimen is loaded into dbgap, set the specimen, its "
+            "descendants, the associated participant, and the associated "
+            "participant's non-specimen descendants to visible."
+        ),
+    )
     args = parser.parse_args()
     print(f"Args: {args.__dict__}")
 
     patches, alerts = ConsentProcessor(
         args.server, args.db_url
-    ).get_patches_for_study(args.study, match_aliquot=args.match_aliquot)
+    ).get_patches_for_study(
+        args.study,
+        match_aliquot=args.match_aliquot,
+        coerce_visible=args.coerce_visible,
+    )
 
     all_patches = {}
     for endpoint_patches in patches.values():

kf_update_dbgap_consent/sample_status.py

@@ -60,9 +60,8 @@
 from concurrent.futures import ThreadPoolExecutor, as_completed
 
 from d3b_utils.requests_retry import Session
-
 from kf_utils.dataservice.descendants import find_descendants_by_kfids
-from kf_utils.dataservice.scrape import yield_entities
+from kf_utils.dataservice.scrape import yield_entities, yield_entities_from_kfids
 from kf_utils.dbgap.release import get_latest_sample_status
 
 
@@ -88,7 +87,11 @@ def get_accession(self, study_id):
             )
 
     def get_patches_for_study(
-        self, study_id, dbgap_status="released", match_aliquot=False
+        self,
+        study_id,
+        dbgap_status="released",
+        match_aliquot=False,
+        coerce_visible=False,
     ):
         if match_aliquot:
             match_entity = "external_aliquot_id"
@@ -214,6 +217,56 @@ def entities_dict(endpoint, filt):
                 hidden_specimens[kfid] = bs
 
         """
+        Handle if samples loaded into dbgap should be made visible
+        """
+        if coerce_visible:
+            unhidden_specimens = {}
+            for kfid, bs in storage["biospecimens"].items():
+                sample = dbgap_samples.get(bs[match_entity], {})
+                if sample.get("@dbgap_status") == "Loaded":
+                    # remove the sample from list of hidden specimens if the
+                    # specimen is loaded in dbgap.
+                    hidden_specimens.pop(kfid, None)
+                    unhidden_specimens[kfid] = bs
+            descendants_of_unhidden_specimens = find_descendants_by_kfids(
+                self.db_url or self.api_url,
+                "participants",
+                [bs["participant_id"] for bs in unhidden_specimens.values()],
+                ignore_gfs_with_hidden_external_contribs=True,
+                kfids_only=False,
+            )
+            descendants_of_unhidden_specimens["participants"] = {
+                e["kf_id"]: e
+                for e in yield_entities_from_kfids(
+                    self.api_url,
+                    [
+                        bs["participant_id"]
+                        for bs in unhidden_specimens.values()
+                    ],
+                )
+            }
+            breakpoint()
+            keep_hidden = []
+            for (
+                endpoint,
+                entities,
+            ) in descendants_of_unhidden_specimens.items():
+                for k, e in entities.items():
+                    if endpoint == 'biospecimens'
+                    storage[endpoint][k] = e
+                    patches[endpoint][k]["visible"] = True
+                    if endpoint == "genomic-files":
+                        # remove the genomic file from list of hidden files
+                        hidden_genomic_files.discard(k)
+
+        for k in descendants_of_unhidden_specimens['genomic-files'].keys():
+            if k in [bg['genomic_file_id'] for bg in descendants_of_unhidden_specimens['biospecimen-genomic-files'].values() ]:
+                print(k)
+
+        for bg in descendants_of_unhidden_specimens['biospecimen-genomic-files'].values():
+            if bg['biospecimen_id'] not in unhidden_specimens.keys():
+                print(bg['biospecimen_id'])
+        """
         Rule: If a biospecimen is hidden in the dataservice, its descendants
         should also be hidden.
         """