Merge pull request #1110 from nipreps/enh/bids-db-handling

FIX: BIDS database directory handling
nipreps · Apr 4, 2023 · 5bb5947 · 5bb5947
2 parents 21b4aab + d205cdb
commit 5bb5947
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Showing 4 changed files with 21 additions and 8 deletions.
diff --git a/.circleci/circle_T1w.txt b/.circleci/circle_T1w.txt
@@ -1,3 +1,5 @@
+.bids_db
+.bids_db/layout_index.sqlite
 .bidsignore
 dataset_description.json
 group_T1w.html

diff --git a/.circleci/circle_bold.txt b/.circleci/circle_bold.txt
@@ -1,3 +1,5 @@
+.bids_db
+.bids_db/layout_index.sqlite
 .bidsignore
 dataset_description.json
 group_bold.html

diff --git a/mriqc/config.py b/mriqc/config.py
@@ -457,23 +457,31 @@ def init(cls):
                     + r"))"
                 )
 
-            _db_path = cls.bids_database_dir or (
-                cls.work_dir / cls.run_uuid / "bids_db"
-            )
-            _db_path.mkdir(exist_ok=True, parents=True)
-
             # Recommended after PyBIDS 12.1
             _indexer = BIDSLayoutIndexer(
                 validate=False,
                 ignore=ignore_paths,
             )
+
+            # Initialize database in a multiprocessing-safe manner
+            cls.bids_database_dir = cls.output_dir / ".bids_db"
+            if not cls.bids_database_dir.exists():
+                _db_path = cls.output_dir / f".bids_db-{cls.run_uuid}"
+                _db_path.mkdir(exist_ok=True, parents=True)
+
+                BIDSLayout(
+                    str(cls.bids_dir),
+                    database_path=_db_path,
+                    indexer=_indexer,
+                )
+
+                _db_path.replace(cls.bids_database_dir.absolute())
+
             cls._layout = BIDSLayout(
                 str(cls.bids_dir),
-                database_path=_db_path,
-                reset_database=cls.bids_database_dir is None,
+                database_path=cls.bids_database_dir,
                 indexer=_indexer,
             )
-            cls.bids_database_dir = _db_path
 
         cls.layout = cls._layout
 

diff --git a/mriqc/tests/test_config.py b/mriqc/tests/test_config.py
@@ -69,6 +69,7 @@ def test_bids_indexing_manifest(tmp_path, testdata_path, testcase):
 
     reload(config)
 
+    config.execution.output_dir = Path(tmp_path) / "out"
     config.execution.bids_dir = _expand_bids(
         tmp_path,
         testdata_path,