♻️ DbGaP consent codes are prefixed with /programs

README.md

@@ -29,8 +29,8 @@ The `--match_aliquot` flag will match dbGaP `submitted_sample_id` to `external_a
 ## ACL Definitions
 
 * study_phs: (e.g. "phs001138")
-* consent_acl: f"{study_phs}.c{consent_code}" (consent_code for the specimen) 
-* default_acl: [{consent_acl} from visible biospecimens which contribute to the genomic file]
+* consent_acl: f"/programs/{study_phs}.c{consent_code}" (consent_code for the specimen) 
+* default_acl: set([{consent_acl} from visible biospecimens which contribute to the genomic file])
 * open_acl: ["/open"]
 
 ## ACL Rules
@@ -66,12 +66,12 @@ field set to **False** should get `{open_acl}`.
 * All visible genomic files in the dataservice with their `controlled_access`
 field set to **True** should get the `{default_acl}`.
 
-* The `default_acl` is a list of the `consent_acl` from the visible specimens
-in the study which contribute to the genomic_file.
+* The `default_acl` is the unique set of the `consent_acl` from the visible
+specimens in the study which contribute to the genomic_file.
 
 * The `consent_acl` is composed of the study phs ID and the
-reported sample consent code of the sample. See ACL Definitions for
-details
+reported sample consent code of the sample, prepended with the dbgap
+prefix "/programs" (e.g. "/programs/phs001138.c1")
 
 * All other genomic files in the dataservice should get `{empty_acl}`
 indicating no access.

kf_update_dbgap_consent/sample_status.py

@@ -2,8 +2,8 @@
 ## ACL Definitions
 
 * study_phs: (e.g. "phs001138")
-* consent_acl: f"{study_phs}.c{consent_code}" (consent_code for the specimen)
-* default_acl: [{consent_acl} from visible biospecimens which contribute to the genomic file]
+* consent_acl: f"/programs/{study_phs}.c{consent_code}" (consent_code for the specimen)
+* default_acl: unique([{consent_acl} from visible biospecimens which contribute to the genomic file])
 * open_acl: ["/open"]
 
 ## ACL Rules
@@ -39,15 +39,17 @@
 * All visible genomic files in the dataservice with their `controlled_access`
 field set to **True** should get the `{default_acl}`.
 
-* The `default_acl` is a list of the `consent_acl` from the visible specimens
-in the study which contribute to the genomic_file.
+* The `default_acl` is the unique set of the `consent_acl` from the visible
+specimens in the study which contribute to the genomic_file.
 
 * The `consent_acl` is composed of the study phs ID and the
-reported sample consent code of the sample. See ACL Definitions for
-details
+reported sample consent code of the sample, prepended with the dbgap
+prefix "/programs" (e.g. "/programs/phs001138.c1")
 
-* All hidden genomic files in the dataservice should get `{empty_acl}`
+* All other genomic files in the dataservice should get `{empty_acl}`
 indicating no access.
+
+
 """
 from collections import defaultdict
 from concurrent.futures import ThreadPoolExecutor, as_completed
@@ -266,19 +268,22 @@ def entities_dict(endpoint, filt):
                     their `controlled_access` field set to **True** should get
                     the `{default_acl}`.
 
-                    * The `default_acl` is a list of the `consent_acl`
+                    * The `default_acl` is the unique set of the `consent_acl`
                     from the visible specimens in the study which contribute to
                     the genomic_file.
 
                     * The `consent_acl` is composed of the study phs ID and the
-                    reported consent code of the sample (e.g. phs001138.c1)
+                    reported consent code of the sample, prepended with the
+                    dbgap prefix "/programs" (e.g. "/programs/phs001138.c1")
                     """
                     biospecimen_codes = set(
                         patches["biospecimens"][k].get("dbgap_consent_code")
                         for k in bsids
                     )
                     patches["genomic-files"][gfid].update(
-                        {"authz": sorted(biospecimen_codes)}
+                        {"authz": sorted(
+                            [f"/programs/{code}" for code in biospecimen_codes]
+                        )}
                     )
             # GenomicFile visible = False OR one of contributing Biospecimen
             # visible=False

tests/data/phs999999_patches.json

@@ -36,12 +36,12 @@
         },
         "GF_22222222": {
             "authz": [
-                "phs999999.c1"
+                "/programs/phs999999.c1"
             ]
         },
         "GF_33333333": {
             "authz": [
-                "phs999999.c2"
+                "/programs/phs999999.c2"
             ]
         },
         "GF_44444444": {