Safer URNs for all parsers

bclenet · Oct 3, 2024 · f740415 · f740415
1 parent 5b9d420
commit f740415
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Showing 3 changed files with 24 additions and 9 deletions.
diff --git a/bids_prov/afni/afni_parser.py b/bids_prov/afni/afni_parser.py
@@ -9,7 +9,7 @@
 from bids_prov.fsl.fsl_parser import get_entities
 from bids_prov.utils import (
     get_default_graph, CONTEXT_URL, label_mapping, compute_sha_256_entity,
-    get_activity_urn, get_agent_urn, get_entity_urn,
+    get_activity_urn, get_agent_urn, get_entity_urn, make_alnum, get_uuid,
     writing_jsonld
     )
 
@@ -206,7 +206,11 @@ def build_records(commands_block: list, agent_id: str, verbose: bool = False):
         }
 
         for input_path in inputs:
-            input_id = get_entity_urn(input_path)
+            # Deal with not human readable paths
+            if not make_alnum(input_path):
+                input_id = 'urn:uuid:' + get_uuid()
+            else:
+                input_id = get_entity_urn(input_path)
             existing_input = next(
                 (entity for entity in records["Entities"] if entity["AtLocation"] == input_path), None)
 
@@ -227,9 +231,13 @@ def build_records(commands_block: list, agent_id: str, verbose: bool = False):
         activity["Used"] = sorted(set(activity["Used"]))
 
         for output_path in outputs:
+            if not make_alnum(output_path):
+                output_id = 'urn:uuid:' + get_uuid()
+            else:
+                output_id = get_entity_urn(output_path)
             records["Entities"].append(
                 {
-                    "@id": get_entity_urn(output_path),
+                    "@id": output_id,
                     "Label": os.path.split(output_path)[1],
                     "AtLocation": output_path,
                     "GeneratedBy": activity["@id"],

diff --git a/bids_prov/fsl/fsl_parser.py b/bids_prov/fsl/fsl_parser.py
@@ -10,7 +10,7 @@
 
 from bids_prov.utils import (
     get_default_graph, CONTEXT_URL, label_mapping, compute_sha_256_entity,
-    get_activity_urn, get_agent_urn, get_entity_urn,
+    get_activity_urn, get_agent_urn, get_entity_urn, make_alnum, get_uuid,
     writing_jsonld
     )
 
@@ -502,7 +502,10 @@ def build_records(groups: Mapping[str, List[str]], agent_id: str, verbose: bool
 
             for input_path in inputs:
                 # input_name = input_path.replace("/", "_") # TODO
-                input_id = get_entity_urn(input_path)
+                if not make_alnum(input_path):
+                    input_id = 'urn:uuid:' + get_uuid()
+                else:
+                    input_id = get_entity_urn(input_path)
 
                 existing_input = next(
                     (e for e in records["Entities"] if e["AtLocation"] == input_path), None)
@@ -522,9 +525,14 @@ def build_records(groups: Mapping[str, List[str]], agent_id: str, verbose: bool
 
             for output_path in outputs:
                 # output_name = output_path.replace("/", "_") # TODO
+                if not make_alnum(output_path):
+                    output_id = 'urn:uuid:' + get_uuid()
+                else:
+                    output_id = get_entity_urn(output_path)
+
                 records["Entities"].append(
                     {
-                        "@id": get_entity_urn(output_path),
+                        "@id": output_id,
                         "Label": os.path.split(output_path)[1],
                         "AtLocation": output_path,
                         "GeneratedBy": activity["@id"],

diff --git a/bids_prov/spm/spm_parser.py b/bids_prov/spm/spm_parser.py
@@ -65,12 +65,11 @@ def get_input_entity(right: str) -> List[dict]:
             entity_label_short = "_".join(file_location.split("/")[-2:])  # Sub01_con_0001.nii
             entity = {
                 "@id": get_entity_urn(
-                    "/"+"/".join(file_location.split("/")[1:]),
-                    file_location.split("/")[0]),
+                    "/"+"/".join(file_location.strip("/").split("/")[1:]),
+                    file_location.strip("/").split("/")[0]),
                 "Label": label_mapping(entity_label_short, "spm/spm_activity_labels.json"),
                 "AtLocation": file_location
             }
-
             entities.append(entity)
 
     return entities