From 4edd71bca6c6537f1544fa9923dabcf1c418d2af Mon Sep 17 00:00:00 2001 From: cmaumet Date: Mon, 4 Sep 2023 11:33:20 +0200 Subject: [PATCH] more fixes in compliance with updated context --- bids_prov/spm/spm_parser.py | 4 ++-- bids_prov/tests/samples_test/batch_example_spm_ref.jsonld | 2 +- bids_prov/tests/samples_test/partial_conjunction.jsonld | 2 +- bids_prov/tests/samples_test/partial_conjunction_ref.jsonld | 2 +- bids_prov/tests/test_spm_parser.py | 4 ++-- bids_prov/utils.py | 2 +- 6 files changed, 8 insertions(+), 8 deletions(-) diff --git a/bids_prov/spm/spm_parser.py b/bids_prov/spm/spm_parser.py index 6258cf135..d6580f493 100644 --- a/bids_prov/spm/spm_parser.py +++ b/bids_prov/spm/spm_parser.py @@ -166,7 +166,7 @@ def get_entities_from_ext_config(conf_dic: dict, activity_name: str, activity_id for activity in conf_dic.keys(): if activity in activity_name: # {'name': 'segment', 'outputs': ['c1xxx.nii.gz','c2xxx.nii.gz']} - # act_preproc = next((activity for activity in records["prov:Activity"] if activity['@id'] == + # act_preproc = next((activity for activity in records["Activities"] if activity['@id'] == # activity_id), None) for output in conf_dic[activity]['outputs']: name = conf_dic[activity]['name'] @@ -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":..."Entities":....} + records : dict with key "@context", ... "Records":{"prov:Agent": ..."Activities":..."Entities":....} """ diff --git a/bids_prov/tests/samples_test/batch_example_spm_ref.jsonld b/bids_prov/tests/samples_test/batch_example_spm_ref.jsonld index 6129d9a41..dd111bfad 100644 --- a/bids_prov/tests/samples_test/batch_example_spm_ref.jsonld +++ b/bids_prov/tests/samples_test/batch_example_spm_ref.jsonld @@ -12,7 +12,7 @@ "version": "SPM12r7224" } ], - "prov:Activity": [ + "Activities": [ { "@id": "urn:3f372617-f0ba-4f3a-86f0-ce2ea6ec39c1", "Label": "Move file", diff --git a/bids_prov/tests/samples_test/partial_conjunction.jsonld b/bids_prov/tests/samples_test/partial_conjunction.jsonld index ea0058b9b..65c5bb16c 100644 --- a/bids_prov/tests/samples_test/partial_conjunction.jsonld +++ b/bids_prov/tests/samples_test/partial_conjunction.jsonld @@ -12,7 +12,7 @@ "version": "SPM12r7224" } ], - "prov:Activity": [ + "Activities": [ { "@id": "urn:3f372617-f0ba-4f3a-86f0-ce2ea6ec39c1", "Label": "Move file", diff --git a/bids_prov/tests/samples_test/partial_conjunction_ref.jsonld b/bids_prov/tests/samples_test/partial_conjunction_ref.jsonld index 77462f826..376df5ab5 100644 --- a/bids_prov/tests/samples_test/partial_conjunction_ref.jsonld +++ b/bids_prov/tests/samples_test/partial_conjunction_ref.jsonld @@ -12,7 +12,7 @@ "version": "SPM12r7224" } ], - "prov:Activity": [ + "Activities": [ { "@id": "urn:3f372617-f0ba-4f3a-86f0-ce2ea6ec39c1", "Label": "Move file", diff --git a/bids_prov/tests/test_spm_parser.py b/bids_prov/tests/test_spm_parser.py index a98696399..680363a0d 100644 --- a/bids_prov/tests/test_spm_parser.py +++ b/bids_prov/tests/test_spm_parser.py @@ -117,7 +117,7 @@ def test_get_records_copy_attributes(): ] ) recs = get_records(task_groups, str(uuid.uuid4())) - attrs = [activity["parameters"] for activity in recs["prov:Activity"]] + attrs = [activity["parameters"] for activity in recs["Activities"]] assert "action.copyto" in json.dumps(attrs) @@ -126,7 +126,7 @@ def test_get_records_attrs(): ".fwhm = 5;", ] ) recs = get_records(task_groups, "agentUUID") - attrs = [activity["parameters"] for activity in recs["prov:Activity"]] + attrs = [activity["parameters"] for activity in recs["Activities"]] assert "4" in json.dumps(attrs) diff --git a/bids_prov/utils.py b/bids_prov/utils.py index 915d8fa00..b119659c6 100644 --- a/bids_prov/utils.py +++ b/bids_prov/utils.py @@ -29,7 +29,7 @@ def get_default_graph(label: str, context_url: str = CONTEXT_URL, soft_ver: str "version": soft_ver } ], - "prov:Activity": [], + "Activities": [], "Entities": [], }, }, agent_id