From e5f8ca283500592850c16e2f977116574f38c911 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Henrik=20tom=20W=C3=B6rden?= <h.tomwoerden@indiscale.com>
Date: Wed, 19 Mar 2025 15:46:23 +0100
Subject: [PATCH 1/3] FIX: multiple registered identifiables
---
integrationtests/test_bids_folderstructure_cfood.py | 9 ++++-----
src/bids-cfood/cfood.yml | 2 +-
unittests/test_dataset_description.py | 4 ++--
3 files changed, 7 insertions(+), 8 deletions(-)
diff --git a/integrationtests/test_bids_folderstructure_cfood.py b/integrationtests/test_bids_folderstructure_cfood.py
index a43d7f3..210a7e6 100644
--- a/integrationtests/test_bids_folderstructure_cfood.py
+++ b/integrationtests/test_bids_folderstructure_cfood.py
@@ -74,7 +74,7 @@ def test_folders(clear_database, usemodel):
crawler_definition,
converter_registry
)
- crawler.save_debug_data("prov.yml")
+ #crawler.save_debug_data("prov.yml")
files = [fi for fi in records if isinstance(fi, db.File)]
for fi in files:
fi.file = __file__
@@ -84,11 +84,10 @@ def test_folders(clear_database, usemodel):
assert len(datasets) == 1
assert len(subjects) == 5
assert len(sessions) == 10
- ins, ups = crawler.synchronize(commit_changes=False)
+ ins, ups = crawler.synchronize(crawled_data=records, commit_changes=True)
funcs = [el for el in ins + ups if el.parents[0].name == "FunctionalImaging"]
anats = [el for el in ins + ups if el.parents[0].name == "AnatomyImaging"]
assert len(funcs) == 30
assert len(anats) == 10
- for el in funcs:
- assert (len(el.get_property("FunctionalImagingDataFile").value) == 2
- or len(el.get_property("FunctionalImagingDataFile").value) == 3)
+ assert 30 == db.execute_query(
+ "count FunctionalImaging which references FunctionalImagingDataFile")
diff --git a/src/bids-cfood/cfood.yml b/src/bids-cfood/cfood.yml
index 41b210d..cc72a3d 100644
--- a/src/bids-cfood/cfood.yml
+++ b/src/bids-cfood/cfood.yml
@@ -477,7 +477,7 @@ project_level:
parent: "MagnetizationTransferSaturation"
- suffix: T1w
parent: "T1WeightedImage"
- extension: "(nii(\.gz))?"
+ extension: "(nii(\\.gz)?)"
- suffix: T1w
parent: "JSONSidecar"
extension: "json"
diff --git a/unittests/test_dataset_description.py b/unittests/test_dataset_description.py
index d7e26d2..95c6af6 100644
--- a/unittests/test_dataset_description.py
+++ b/unittests/test_dataset_description.py
@@ -63,8 +63,8 @@ def test_dataset():
converter_registry,
restricted_path=["json_only", 'dataset_description.json']
)
- subd = crawler.debug_tree
- subc = crawler.debug_metadata
+ #subd = crawler.debug_tree
+ #subc = crawler.debug_metadata
# print(json.dumps(subc, indent=3))
# print(subd)
# print(subc)
--
GitLab
From 91f386f8cb94e426722c78012d325699975a14ba Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Thu, 20 Mar 2025 13:53:26 +0100
Subject: [PATCH 2/3] DOCS: Update changelog
---
CHANGELOG.md | 2 ++
1 file changed, 2 insertions(+)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index ecc1b5d..6b6c1fd 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -17,6 +17,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Fixed ###
+* Regexp for T1WeightedImage
+
### Security ###
### Documentation ###
--
GitLab
From a4e231c70e68eda5cbb30979ca817ad223b4383f Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Thu, 20 Mar 2025 16:56:08 +0100
Subject: [PATCH 3/3] BUILD: Increase required crawler version
---
CHANGELOG.md | 3 +++
src/bids-cfood/cfood.yml | 2 +-
2 files changed, 4 insertions(+), 1 deletion(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6b6c1fd..0d64d88 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Changed ###
+* Required crawler version was invreased to 0.11.0 to allow for
+ inheritance in identifiables.
+
### Deprecated ###
### Removed ###
diff --git a/src/bids-cfood/cfood.yml b/src/bids-cfood/cfood.yml
index cc72a3d..b2a42e3 100644
--- a/src/bids-cfood/cfood.yml
+++ b/src/bids-cfood/cfood.yml
@@ -1,6 +1,6 @@
---
metadata:
- crawler-version: 0.3.1
+ crawler-version: 0.11.0
macros:
- !defmacro
name: FuncDataFile
--
GitLab