♻️ Set visibility_reason, visibility_comment for hidden things

kids-first · Jun 23, 2023 · 9c79c2d · 9c79c2d
1 parent e00eecb
commit 9c79c2d
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Showing 3 changed files with 35 additions and 9 deletions.
diff --git a/kf_update_dbgap_consent/sample_status.py b/kf_update_dbgap_consent/sample_status.py
@@ -205,6 +205,8 @@ def entities_dict(endpoint, filt):
                     "consent_type": None,
                     "dbgap_consent_code": None,
                     "visible": False,
+                    "visibility_reason": "Consent Hold",
+                    "visibility_comment": "Sample is not registered in dbGaP",
                 }
                 hidden_specimens[kfid] = bs
 
@@ -225,6 +227,10 @@ def entities_dict(endpoint, filt):
                 for k, e in entities.items():
                     storage[endpoint][k] = e
                     patches[endpoint][k]["visible"] = False
+                    patches[endpoint][k]["visibility_reason"] = "Consent Hold"
+                    patches[endpoint][k][
+                        "visibility_comment"
+                    ] = "Sample is not registered in dbGaP"
                     if endpoint == "genomic-files":
                         hidden_genomic_files.add(k)
 

diff --git a/tests/data/phs999999_patches.json b/tests/data/phs999999_patches.json
@@ -1,20 +1,28 @@
 {
     "biospecimen-diagnoses": {
         "BD_11111111": {
-            "visible": false
+            "visible": false,
+             "visibility_reason": "Consent Hold",
+             "visibility_comment": "Sample is not registered in dbGaP"
         }
     },
     "biospecimen-genomic-files": {
         "BG_00000000": {
-            "visible": false
+            "visible": false,
+             "visibility_reason": "Consent Hold",
+             "visibility_comment": "Sample is not registered in dbGaP"
         },
         "BG_11111111": {
-            "visible": false
+            "visible": false,
+             "visibility_reason": "Consent Hold",
+             "visibility_comment": "Sample is not registered in dbGaP"
         }
     },
     "biospecimens": {
         "BS_11111111": {
-            "visible": false
+            "visible": false,
+             "visibility_reason": "Consent Hold",
+             "visibility_comment": "Sample is not registered in dbGaP"
         },
         "BS_22222222": {
             "consent_type": "LOL",
@@ -28,11 +36,15 @@
     "genomic-files": {
         "GF_00000000": {
             "authz": [],
-            "visible": false
+            "visible": false,
+             "visibility_reason": "Consent Hold",
+             "visibility_comment": "Sample is not registered in dbGaP"
         },
         "GF_11111111": {
             "authz": [],
-            "visible": false
+            "visible": false,
+            "visibility_reason": "Consent Hold",
+            "visibility_comment": "Sample is not registered in dbGaP"
         },
         "GF_22222222": {
             "authz": [
@@ -50,15 +62,21 @@
     },
     "sequencing-experiment-genomic-files": {
         "SG_00000000": {
-            "visible": false
+            "visible": false,
+            "visibility_reason": "Consent Hold",
+            "visibility_comment": "Sample is not registered in dbGaP"
         },
         "SG_11111111": {
-            "visible": false
+            "visible": false,
+            "visibility_reason": "Consent Hold",
+            "visibility_comment": "Sample is not registered in dbGaP"
         }
     },
     "sequencing-experiments": {
         "SE_11111111": {
-            "visible": false
+            "visible": false,
+            "visibility_reason": "Consent Hold",
+            "visibility_comment": "Sample is not registered in dbGaP"
         }
     },
     "studies": {

diff --git a/tests/test_sample_status.py b/tests/test_sample_status.py
@@ -120,6 +120,8 @@ def test_sample_status(requests_mock):
     patches, alerts = ConsentProcessor(host).get_patches_for_study(study_id)
     new_expected_patches["biospecimens"]["BS_44444444"] = {
         "visible": False,
+        "visibility_reason": "Consent Hold",
+        "visibility_comment": "Sample is not registered in dbGaP",
         "consent_type": None,
         "dbgap_consent_code": None,
     }