more fixes in compliance with updated context

bids-standard · Sep 4, 2023 · 2f9adbc · 2f9adbc
1 parent 5619add
commit 2f9adbc
Show file tree

Hide file tree

Showing 8 changed files with 9 additions and 9 deletions.
diff --git a/bids_prov/afni/afni_parser.py b/bids_prov/afni/afni_parser.py
@@ -220,7 +220,7 @@ def build_records(commands_bloc: list, agent_id: str, verbose: bool = False):
                 activity["Used"].append(existing_input["@id"])
 
         for output_path in outputs:
-            records["prov:Entity"].append(
+            records["Entities"].append(
                 {
                     "@id": f"urn:{get_id()}",
                     "Label": os.path.split(output_path)[1],

diff --git a/bids_prov/fsl/fsl_parser.py b/bids_prov/fsl/fsl_parser.py
@@ -528,7 +528,7 @@ def fsl_to_bids_prov(filename: str, context_url=CONTEXT_URL, output_file=None,
     records = build_records(lines, agent_id)
     graph["Records"].update(records)
 
-    compute_sha_256_entity(graph["Records"]["prov:Entity"])
+    compute_sha_256_entity(graph["Records"]["Entities"])
 
     return writing_jsonld(graph, indent, output_file)
 

diff --git a/bids_prov/spm/spm_parser.py b/bids_prov/spm/spm_parser.py
@@ -227,7 +227,7 @@ def find_output_id_from_closest(closest_activity: dict, records: dict) -> str:
     else:
         output_id = "urn:" + get_id()
     # output_id = next(
-    #     (entity["@id"] for entity in records["prov:Entity"]
+    #     (entity["@id"] for entity in records["Entities"]
     #                   if parts[-1] == entity["Label"] and entity["GeneratedBy"] == closest_activity["@id"]
     #     ), "urn:" + get_id()
     #     ) # find entity id generated by closest activity, if None new get_id
@@ -293,7 +293,7 @@ def get_records(task_groups: dict, agent_id: str, verbose=False) -> dict:
     Returns
     -------
     dict[str, list]
-        records : dict with key "@context", ... "Records":{"prov:Agent": ..."prov:Activity":..."prov:Entity":....}
+        records : dict with key "@context", ... "Records":{"prov:Agent": ..."prov:Activity":..."Entities":....}
 
     """
 

diff --git a/bids_prov/tests/samples_test/batch_example_spm.jsonld b/bids_prov/tests/samples_test/batch_example_spm.jsonld
@@ -270,7 +270,7 @@
         }
       }
     ],
-    "prov:Entity": [
+    "Entities": [
       {
         "@id": "urn:4a800646-417a-4105-bc31-99944567ceb1",
         "Label": "func_sub-01_task-tonecounting_bold.nii.gz",

diff --git a/bids_prov/tests/samples_test/batch_example_spm_ref.jsonld b/bids_prov/tests/samples_test/batch_example_spm_ref.jsonld
@@ -256,7 +256,7 @@
         }
       }
     ],
-    "prov:Entity": [
+    "Entities": [
       {
         "@id": "urn:4a800646-417a-4105-bc31-99944567ceb1",
         "Label": "func_sub-01_task-tonecounting_bold.nii.gz",

diff --git a/bids_prov/tests/samples_test/partial_conjunction.jsonld b/bids_prov/tests/samples_test/partial_conjunction.jsonld
@@ -268,7 +268,7 @@
         }
       }
     ],
-    "prov:Entity": [
+    "Entities": [
       {
         "@id": "urn:4a800646-417a-4105-bc31-99944567ceb1",
         "Label": "func_sub-01_task-tonecounting_bold.nii.gz",

diff --git a/bids_prov/tests/samples_test/partial_conjunction_ref.jsonld b/bids_prov/tests/samples_test/partial_conjunction_ref.jsonld
@@ -254,7 +254,7 @@
         }
       }
     ],
-    "prov:Entity": [
+    "Entities": [
       {
         "@id": "urn:4a800646-417a-4105-bc31-99944567ceb1",
         "Label": "func_sub-01_task-tonecounting_bold.nii.gz",

diff --git a/bids_prov/utils.py b/bids_prov/utils.py
@@ -30,7 +30,7 @@ def get_default_graph(label: str, context_url: str = CONTEXT_URL, soft_ver: str
                        }
                    ],
                    "prov:Activity": [],
-                   "prov:Entity": [],
+                   "Entities": [],
                },
            }, agent_id