New strategies for Id generation

bids_prov/afni/afni_parser.py

@@ -7,8 +7,11 @@
 from itertools import chain
 
 from bids_prov.fsl.fsl_parser import get_entities
-from bids_prov.utils import get_default_graph, CONTEXT_URL, get_id, label_mapping, compute_sha_256_entity, \
+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,
     writing_jsonld
+    )
 
 # regex to catch inputs
 # in `cp /fsl/5.0/doc/fsl.css .files no_ext 5.0` --> only `.files` should match
@@ -117,12 +120,12 @@ def build_records(commands_block: list, agent_id: str, verbose: bool = False):
 
     for (block, cmd) in commands_block:
         cmd_s = re.split(" |=", cmd)
-        a_name = cmd_s[0]
+        activity_name = cmd_s[0]
         cmd_args_remain = cmd_s[1:]
         inputs = []
         outputs = []
         function_in_description_functions = False
-        command_name_end = os.path.split(a_name)[1]
+        command_name_end = os.path.split(activity_name)[1]
 
         for df in description_functions:
             if df["Name"] == command_name_end:
@@ -182,27 +185,28 @@ def build_records(commands_block: list, agent_id: str, verbose: bool = False):
             outputs = list(chain(*(attributes.pop(k)
                                    for k in attributes.keys() & OUTPUT_TAGS)))
             entity_names = [_ for _ in re.findall(
-                INPUT_RE, cmd_without_attributes[len(a_name):])]
+                INPUT_RE, cmd_without_attributes[len(activity_name):])]
 
             if entity_names and entity_names[0] in cmd_without_attributes:
                 outputs.append(entity_names[-1])
                 if len(entity_names) > 1:
                     inputs.append(entity_names[0])
 
         # the file name and possible extension
-        label = f"{os.path.split(a_name)[1]}"
-
+        activity_label = label_mapping(
+            f'{os.path.split(activity_name)[1]}',
+            'afni/afni_labels.json')
         activity = {
-            "@id": f"urn:{get_id()}",
-            "Label": label_mapping(label, "afni/afni_labels.json"),
+            "@id": get_activity_urn(activity_label),
+            "Label": activity_label,
             "AssociatedWith": "urn:" + agent_id,
             "Command": cmd,
             "Parameters": param_dic,
             "Used": list(),
         }
 
         for input_path in inputs:
-            input_id = f"urn:{get_id()}"  # def format_id
+            input_id = get_entity_urn(input_path)
             existing_input = next(
                 (entity for entity in records["Entities"] if entity["AtLocation"] == input_path), None)
 
@@ -225,7 +229,7 @@ def build_records(commands_block: list, agent_id: str, verbose: bool = False):
         for output_path in outputs:
             records["Entities"].append(
                 {
-                    "@id": f"urn:{get_id()}",
+                    "@id": get_entity_urn(output_path),
                     "Label": os.path.split(output_path)[1],
                     "AtLocation": output_path,
                     "GeneratedBy": activity["@id"],
@@ -363,7 +367,7 @@ def fusion_activities(activities, label):
             command += activity["Command"] + "; "
 
         return {
-            "@id": f"urn:{get_id()}",
+            "@id": get_activity_urn(label),
             "Label": label,
             "AssociatedWith": activities[0]["AssociatedWith"],
             "Command": command,

bids_prov/fsl/fsl_parser.py

@@ -8,8 +8,11 @@
 
 from bs4 import BeautifulSoup
 
-from bids_prov.utils import get_default_graph, CONTEXT_URL, get_id, label_mapping, compute_sha_256_entity, \
+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,
     writing_jsonld
+    )
 
 # regex to catch inputs
 # in `cp /fsl/5.0/doc/fsl.css .files no_ext 5.0` --> only `.files` should match
@@ -421,7 +424,7 @@ def build_records(groups: Mapping[str, List[str]], agent_id: str):
             # process to remove + and - in pngappend command
             cmd = cmd.replace(" + ", " ").replace(" - ", " ")
             cmd_s = re.split(" |=", cmd)
-            a_name = cmd_s[0]
+            activity_name = cmd_s[0]
 
             inputs = []
             outputs = []
@@ -430,7 +433,7 @@ def build_records(groups: Mapping[str, List[str]], agent_id: str):
 
             function_in_description_functions = False
 
-            command_name_end = os.path.split(a_name)[1]
+            command_name_end = os.path.split(activity_name)[1]
             for df in description_functions:
                 if df["Name"] == command_name_end:
                     description_of_command = df
@@ -457,9 +460,9 @@ def build_records(groups: Mapping[str, List[str]], agent_id: str):
                 outputs = list(chain(*(attributes.pop(k)
                                for k in attributes.keys() & OUTPUT_TAGS)))
                 entity_names = [_ for _ in re.findall(
-                    INPUT_RE, cmd_without_attributes[len(a_name):])]
+                    INPUT_RE, cmd_without_attributes[len(activity_name):])]
 
-            # # cmd_conf = get_closest_config(a_name)  # with the module boutiques
+            # # cmd_conf = get_closest_config(activity_name)  # with the module boutiques
             # cmd_conf = None  # None because boutiques is not used at this time
             # # if cmd_conf:
             # #     pos_args = filter(lambda e: not e.startswith("-"), cmd_s)  # TODO use "-key value" mappings
@@ -471,12 +474,13 @@ def build_records(groups: Mapping[str, List[str]], agent_id: str):
                     if len(entity_names) > 1:
                         inputs.append(entity_names[0])
 
-            # the file name and possible extension
-            label = f"{os.path.split(a_name)[1]}"
-
-            a = {
-                "@id": f"urn:{get_id()}",
-                "Label": label_mapping(label, "fsl/fsl_labels.json"),
+            # Create activity label & record
+            activity_label = label_mapping(
+                f'{os.path.split(activity_name)[1]}',
+                'fsl/fsl_labels.json')
+            activity = {
+                "@id": get_activity_urn(activity_label),
+                "Label": activity_label,
                 "AssociatedWith": "urn:" + agent_id,
                 "Command": cmd,
                 # "attributes": [
@@ -487,7 +491,7 @@ def build_records(groups: Mapping[str, List[str]], agent_id: str):
 
             for input_path in inputs:
                 # input_name = input_path.replace("/", "_") # TODO
-                input_id = f"urn:{get_id()}"  # def format_id
+                input_id = get_entity_urn(input_path)
 
                 existing_input = next(
                     (entity for entity in records["Entities"] if entity["AtLocation"] == input_path), None)
@@ -509,7 +513,7 @@ def build_records(groups: Mapping[str, List[str]], agent_id: str):
                 # output_name = output_path.replace("/", "_") # TODO
                 records["Entities"].append(
                     {
-                        "@id": f"urn:{get_id()}",
+                        "@id": get_entity_urn(output_path),
                         "Label": os.path.split(output_path)[1],
                         "AtLocation": output_path,
                         "GeneratedBy": a["@id"],

bids_prov/spm/spm_parser.py

@@ -5,8 +5,11 @@
 from typing import List, Dict, Generator
 
 from bids_prov.spm import spm_config as conf
-from bids_prov.utils import get_id, get_default_graph, CONTEXT_URL, label_mapping, compute_sha_256_entity, \
+from bids_prov.utils import (
+    get_uuid, get_default_graph, CONTEXT_URL, label_mapping, compute_sha_256_entity,
+    get_activity_urn, get_agent_urn, get_entity_urn,
     writing_jsonld
+    )
 
 
 def format_activity_name(activity_name: str) -> str:
@@ -61,7 +64,7 @@ def get_input_entity(right: str) -> List[dict]:
             file_location = re.sub(r"\,1", "", file_drop_quotes)  # ds000052/RESULTS/Sub01/con_0001.nii
             entity_label_short = "_".join(file_location.split("/")[-2:])  # Sub01_con_0001.nii
             entity = {
-                "@id": "urn:" + get_id(),
+                "@id": get_entity_urn(file_location),
                 "Label": label_mapping(entity_label_short, "spm/spm_activity_labels.json"),
                 "AtLocation": file_location
             }
@@ -170,7 +173,7 @@ def get_entities_from_ext_config(conf_dic: dict, activity_name: str, activity_id
             # activity_id), None)
             for output in conf_dic[activity]['outputs']:
                 name = conf_dic[activity]['name']
-                entity = {"@id": "urn:" + get_id(),
+                entity = {"@id": get_entity_urn(output),
                           "Label": label_mapping(name, "spm/spm_activity_labels.json"),
                           "Atlocation": output,
                           "GeneratedBy": activity_id,
@@ -217,15 +220,15 @@ def find_output_id_from_closest(closest_activity: dict, records: dict) -> str:
 
     Returns
     -------
-    output_id : entity id, if such one has been  generated by the closest activity, else new id
+    output_id : entity id, if such one has been generated by the closest activity, else new id
     """
     for entity in records["Entities"]:
         if "GeneratedBy" in entity:
             if entity["GeneratedBy"] == closest_activity["@id"]:  # entity["Label"] == parts[-1]
                 output_id = entity["@id"]
                 break
     else:
-        output_id = "urn:" + get_id()
+        output_id = 'urn:uuid:' + get_uuid()
     # output_id = next(
     #     (entity["@id"] for entity in records["Entities"]
     #                   if parts[-1] == entity["Label"] and entity["GeneratedBy"] == closest_activity["@id"]
@@ -309,9 +312,10 @@ def get_records(task_groups: dict, agent_id: str, verbose=False) -> dict:
             command_prefix = command_prefix[:-1]
         command += '\n'.join([command_prefix + c for c in end_line_list])
 
-        activity_id = "urn:" + get_id()
+        activity_label = format_activity_name(common_prefix_act)
+        activity_id = get_activity_urn(activity_label)
         activity = {"@id": activity_id,
-                    "Label": format_activity_name(common_prefix_act),
+                    "Label": activity_label,
                     "Used": list(),
                     "AssociatedWith": "urn:" + agent_id,
                     "Command": command

bids_prov/tests/test_spm_parser.py

@@ -90,11 +90,10 @@ def test_get_input_entity():
     right = "{'ds011/sub-01/func/sub-01_task-tonecounting_bold_trunctest.nii.gz'};"
     # entity label : sub-01_task-tonecounting_bold.nii.gz
     entities = [{
-        "@id": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+        "@id": "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold_trunctest.nii.gz",
         "Label": "func_sub-01_task-tonecounting_bold_trunctest.nii.gz",
         "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold_trunctest.nii.gz"
     }]
-    init_random_state()
     right_entity = get_input_entity(right)[0]
     assert right_entity == entities[0]
 

bids_prov/tests/test_utils.py

@@ -6,25 +6,35 @@
 import hashlib
 
 from bids_prov.utils import (
-    get_id, get_rrid, get_default_graph, CONTEXT_URL, label_mapping, get_sha256
+    get_uuid, get_random_string, get_rrid, make_alnum,
+    get_activity_urn, get_agent_urn, get_entity_urn,
+    get_default_graph, CONTEXT_URL, label_mapping, get_sha256
     )
 from unittest.mock import mock_open, patch
 
-
-def test_get_id():
+def test_get_uuid():
     # Test that the function returns a valid UUID string
-    result = get_id()
+    result = get_uuid()
     assert isinstance(result, str)
     assert isinstance(uuid.UUID(result), uuid.UUID)
 
     # Test that the UUID returned is version 4
     assert uuid.UUID(result).version == 4
 
     # Test that the function returns a different ID each time it's called
-    id1 = get_id()
-    id2 = get_id()
+    id1 = get_uuid()
+    id2 = get_uuid()
     assert id1 != id2
 
+def test_get_random_string():
+    # Test that the function returns a random string
+    result = get_random_string()
+    assert isinstance(result, str)
+    assert len(result) == 8
+    assert result.isalnum()
+    assert len(get_random_string(5)) == 5
+    assert result != get_random_string()
+
 def test_get_rrid():
     # Test that the function returns a RRID string
     result = get_rrid('FSL')
@@ -35,6 +45,32 @@ def test_get_rrid():
     # Test the the function returns None if the software is not referenced
     assert get_rrid('unreferenced_software') is None
 
+def test_make_alnum():
+    # Test that the function that removes all non alphanumeric chars from a string
+    assert make_alnum('¨^$£$êµ*ad45@') == 'ad45'
+    assert make_alnum('\\//:!§.;,?[]()}{}') == '' 
+    assert make_alnum('ezeasdsa45ADA5sdas') == 'ezeasdsa45ADA5sdas'
+
+def test_get_activity_urn():
+    # Test that the function that returns URNs for activities
+    assert 'urn:spm-' in get_activity_urn('SPM')
+    assert len(get_activity_urn('SPM')) == 16
+    assert 'urn:spmv1242-' in get_activity_urn('SPM v. 1242355')
+    assert len(get_activity_urn('SPM v. 1242355')) == 21
+
+def test_get_agent_urn():
+    # Test that the function that returns URNs for agents
+    assert 'urn:bet-' in get_agent_urn('BET')
+    assert len(get_agent_urn('BET')) == 16
+    assert 'urn:movefile-' in get_agent_urn('Move file')
+    assert len(get_agent_urn('SPM v. 1242355')) == 21
+
+def test_get_entity_urn():
+    # Test that the function that returns URNs for entities
+    assert get_entity_urn('') == 'bids::'
+    assert get_entity_urn('sub-001/func/T1.nii') == 'bids::sub-001/func/T1.nii'
+    assert get_entity_urn('T1.nii') == 'bids::T1.nii'
+
 def test_get_default_graph():
     context_url = "http://example.com/context"
     spm_ver = "v1.0"