Merge pull request #1095 from bids-standard/fix_recording_regex

Fix recording regex.

Author: rwblair

bids-validator/bids_validator/rules/file_level_rules.json

@@ -74,7 +74,7 @@
   },
 
   "dwi": {
-    "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?dwi[\\/\\\\]\\1(_\\2)?(?:_acq-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_dir-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(_(?:@@@_dwi_type_@@@)\\.(@@@_dwi_ext_@@@)|(?:recording-[a-zA-Z0-9]+)?(?:@@@_cont_ext_@@@))$",
+    "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?dwi[\\/\\\\]\\1(_\\2)?(?:_acq-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_dir-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?((?:_@@@_dwi_type_@@@)\\.(@@@_dwi_ext_@@@)|(?:_recording-[a-zA-Z0-9]+)?(?:@@@_cont_ext_@@@))$",
     "tokens": {
       "@@@_dwi_ext_@@@": ["nii\\.gz", "nii", "json", "bvec", "bval"],
       "@@@_dwi_type_@@@": ["dwi", "sbref"],
@@ -119,7 +119,7 @@
   },
 
   "func": {
-    "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?func[\\/\\\\]\\1(_\\2)?_task-[a-zA-Z0-9]+(?:_acq-[a-zA-Z0-9]+)?(?:_ce-[a-zA-Z0-9]+)?(?:_dir-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_echo-[0-9]+)?((?:@@@_func_ext_@@@)|(?:recording-[a-zA-Z0-9]+)?(?:@@@_cont_ext_@@@))$",
+    "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?func[\\/\\\\]\\1(_\\2)?_task-[a-zA-Z0-9]+(?:_acq-[a-zA-Z0-9]+)?(?:_ce-[a-zA-Z0-9]+)?(?:_dir-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_echo-[0-9]+)?((?:@@@_func_ext_@@@)|(?:_recording-[a-zA-Z0-9]+)?(?:@@@_cont_ext_@@@))$",
     "tokens": {
       "@@@_func_ext_@@@": [
         "_bold\\.nii\\.gz",

bids-validator/bids_validator/rules/top_level_rules.json

@@ -19,16 +19,18 @@
   },
 
   "func_top": {
-    "regexp": "^[\\/\\\\](?:ses-[a-zA-Z0-9]+_)?(?:recording-[a-zA-Z0-9]+_)?task-[a-zA-Z0-9]+(?:_acq-[a-zA-Z0-9]+)?(?:_ce-[a-zA-Z0-9]+)?(?:_dir-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_echo-[0-9]+)?(@@@_func_top_ext_@@@)$",
+    "regexp": "^[\\/\\\\](?:ses-[a-zA-Z0-9]+_)?task-[a-zA-Z0-9]+(?:_acq-[a-zA-Z0-9]+)?(?:_ce-[a-zA-Z0-9]+)?(?:_dir-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_echo-[0-9]+)?((?:@@@_func_top_ext_@@@)|(?:_recording-[a-zA-Z0-9]+)?(?:@@@_cont_ext_@@@))$",
     "tokens": {
       "@@@_func_top_ext_@@@": [
         "_bold\\.json",
         "_sbref\\.json",
         "_events\\.json",
         "_events\\.tsv",
-        "_physio\\.json",
-        "_stim\\.json",
         "_beh\\.json"
+      ],
+      "@@@_cont_ext_@@@": [
+        "_physio\\.json",
+        "_stim\\.json"
       ]
     }
   },
@@ -102,7 +104,7 @@
     "regexp": "^[\\/\\\\](?:acq-[a-zA-Z0-9]+_)?(?:dir-[a-zA-Z0-9]+_)epi\\.json$"
   },
   "other_top_files": {
-    "regexp": "^[\\/\\\\](?:ses-[a-zA-Z0-9]+_)?(?:recording-[a-zA-Z0-9]+_)?(?:task-[a-zA-Z0-9]+_)?(?:acq-[a-zA-Z0-9]+_)?(?:rec-[a-zA-Z0-9]+_)?(?:run-[0-9]+_)?(@@@_other_top_files_ext_@@@)$",
+    "regexp": "^[\\/\\\\](?:ses-[a-zA-Z0-9]+_)?(?:task-[a-zA-Z0-9]+_)?(?:acq-[a-zA-Z0-9]+_)?(?:rec-[a-zA-Z0-9]+_)?(?:run-[0-9]+_)?(?:recording-[a-zA-Z0-9]+_)?(@@@_other_top_files_ext_@@@)$",
     "tokens": {
       "@@@_other_top_files_ext_@@@": ["physio\\.json", "stim\\.json"]
     }

bids-validator/utils/__tests__/type.spec.js

@@ -17,5 +17,24 @@ describe('type.js', () => {
         ),
       ).toBe(true)
     })
+
+    it('does not throw an error for recording entity in physio data at root of the dataset', () => {
+      expect(
+        type.isBIDS(
+          '/task-matchingpennies_recording-eyetracking_physio.json',
+        ),
+      ).toBe(true)
+    })
+
+    const physio_task_modalities = ['eeg', 'ieeg', 'meg', 'func', 'beh']
+    physio_task_modalities.map(mod => {
+      it(`does not throw an error for recording entity in ${mod} physio data`, () => {
+        expect(
+          type.isBIDS(
+            `/sub-05/${mod}/sub-05_task-matchingpennies_recording-eyetracking_physio.tsv.gz`,
+          ),
+        ).toBe(true)
+      })
+    })
   })
 })

package.json

@@ -10,6 +10,7 @@
     "codecov": "./node_modules/.bin/codecov",
     "test": "bids-validator/bin/test-submodule-exists && jest",
     "npmPublish": "cd bids-validator && publish",
+    "lernaPublish": "./node_modules/.bin/lerna publish && ./tools/post_publish.sh",
     "web-dev": "cd bids-validator-web && yarn dev",
     "web-build": "cd bids-validator-web && yarn build",
     "web-export": "yarn web-build && cd bids-validator-web && yarn next export"

tools/post_publish.sh

@@ -0,0 +1,7 @@
+#! /bin/bash
+# Generate a dev version with no tag and push. Meant to be called immediately after publishing new version with tag/npm package.
+set -e
+./node_modules/.bin/lerna version prepatch --preid dev --no-git-tag-version
+git add bids-validator-web/package-lock.json bids-validator-web/package.json bids-validator/package-lock.json bids-validator/package.json lerna.json
+git commit -m "setting dev version"
+git push