Merge branch 'f-fix-crawler' into 'main'

FIX: multiple registered identifiables

See merge request !3

CHANGELOG.md

@@ -11,12 +11,17 @@ 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 ###
 
 ### Fixed ###
 
+* Regexp for T1WeightedImage
+
 ### Security ###
 
 ### Documentation ###

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")

src/bids-cfood/cfood.yml

 ---
 metadata:
-  crawler-version: 0.3.1
+  crawler-version: 0.11.0
   macros:
   - !defmacro
     name: FuncDataFile
@@ -477,7 +477,7 @@ project_level:
                         parent: "MagnetizationTransferSaturation"
                       - suffix: T1w
                         parent: "T1WeightedImage"
-                        extension: "(nii(\.gz))?"
+                        extension: "(nii(\\.gz)?)"
                       - suffix: T1w
                         parent: "JSONSidecar"
                         extension: "json"

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)