escape dots in regexps

bids-standard · Jul 14, 2022 · 24d4351 · 24d4351
1 parent c1a618f
commit 24d4351
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diff --git a/bids-validator/bids_validator/rules/file_level_rules.json b/bids-validator/bids_validator/rules/file_level_rules.json
@@ -467,7 +467,7 @@
  },
 
  "meg": {
- "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?meg[\\/\\\\]\\1(_\\2)?(?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:_split-[0-9]+)?(_digitizer.txt|_meg(@@@_meg_type_@@@[\\/\\\\](.(?!\\.(sqd|con|fif|raw|raw\\.mhd|trg|kdf|chn)$))*|[\\/\\\\](.(?!\\.(sqd|con|fif|raw|raw\\.mhd|trg|kdf|chn)$))*)|(@@@_meg_ext_@@@)|(?:_recording-[a-zA-Z0-9]+)?(?:@@@_cont_ext_@@@))$",
+ "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?meg[\\/\\\\]\\1(_\\2)?(?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:_split-[0-9]+)?(_digitizer\\.txt|_meg(@@@_meg_type_@@@[\\/\\\\](.(?!\\.(sqd|con|fif|raw|raw\\.mhd|trg|kdf|chn)$))*|[\\/\\\\](.(?!\\.(sqd|con|fif|raw|raw\\.mhd|trg|kdf|chn)$))*)|(@@@_meg_ext_@@@)|(?:_recording-[a-zA-Z0-9]+)?(?:@@@_cont_ext_@@@))$",
  "tokens": {
  "@@@_meg_type_@@@": [
  "\\.ds[\\/\\\\].*",
@@ -565,11 +565,11 @@
  "_SPIM"
  ],
  "@@@_microscopy_ext_@@@": [
- ".ome\\.tif",
- ".ome\\.btf",
- ".ome\\.zarr[\\/\\\\].*",
- ".tif",
- ".png"
+ "\\.ome\\.tif",
+ "\\.ome\\.btf",
+ "\\.ome\\.zarr[\\/\\\\].*",
+ "\\.tif",
+ "\\.png"
  ]
  }
  },

diff --git a/bids-validator/bids_validator/rules/session_level_rules.json b/bids-validator/bids_validator/rules/session_level_rules.json
@@ -2,20 +2,20 @@
  "scans": {
  "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?\\1(_\\2)?(@@@_scat_ext_@@@)$",
  "tokens": {
- "@@@_scat_ext_@@@": ["_scans.tsv", "_scans.json"]
+ "@@@_scat_ext_@@@": ["_scans\\.tsv", "_scans\\.json"]
  }
  },
 
  "func_ses": {
  "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?\\1(_\\2)?task-[a-zA-Z0-9]+(?:_acq-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_echo-[0-9]+)?(@@@_func_ses_ext_@@@)$",
  "tokens": {
  "@@@_func_ses_ext_@@@": [
- "_bold.json",
- "_sbref.json",
- "_events.json",
- "_events.tsv",
- "_physio.json",
- "_stim.json"
+ "_bold\\.json",
+ "_sbref\\.json",
+ "_events\\.json",
+ "_events\\.tsv",
+ "_physio\\.json",
+ "_stim\\.json"
  ]
  }
  },
@@ -24,23 +24,23 @@
  "regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)?\\1(_\\2)?(?:_acq-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(@@@_asl_ses_ext_@@@)$",
  "tokens": {
  "@@@_asl_ses_ext_@@@": [
- "_asl.json",
- "_aslcontext.tsv",
- "_m0scan.json",
- "_asllabeling.jpg"
+ "_asl\\.json",
+ "_aslcontext\\.tsv",
+ "_m0scan\\.json",
+ "_asllabeling\\.jpg"
  ]
  }
  },
 
  "pet_ses": {
  "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?\\1(_\\2)?(?:_trc-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_task-[a-zA-Z0-9]+)?(?:_run-[0-9]+_)?(@@@_pet_ses_type_@@@)$",
  "tokens": {
- "@@@_pet_ses_type_@@@": ["_pet.json", "_events.json", "_events.tsv"]
+ "@@@_pet_ses_type_@@@": ["_pet\\.json", "_events\\.json", "_events\\.tsv"]
  }
  },
 
  "anat_ses": {
- "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?\\1(_\\2)?(?:_acq-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_run-[0-9]+_)?(@@@_anat_ses_type_@@@).json$",
+ "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?\\1(_\\2)?(?:_acq-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_run-[0-9]+_)?(@@@_anat_ses_type_@@@)\\.json$",
  "tokens": {
  "@@@_anat_ses_type_@@@": [
  "T1w",
@@ -61,7 +61,7 @@
  },
 
  "dwi_ses": {
- "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?\\1(_\\2)?(?:_acq-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_)?dwi.(?:@@@_dwi_ses_ext_@@@)$",
+ "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?\\1(_\\2)?(?:_acq-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_)?dwi\\.(?:@@@_dwi_ses_ext_@@@)$",
  "tokens": {
  "@@@_dwi_ses_ext_@@@": ["json", "bval", "bvec"]
  }
@@ -71,15 +71,15 @@
  "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?\\1(_\\2)?(?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(@@@_meg_ses_type_@@@)$",
  "tokens": {
  "@@@_meg_ses_type_@@@": [
- "_events.tsv",
- "_channels.tsv",
- "_channels.json",
- "_meg.json",
- "_coordsystem.json",
- "_photo.jpg",
+ "_events\\.tsv",
+ "_channels\\.tsv",
+ "_channels\\.json",
+ "_meg\\.json",
+ "_coordsystem\\.json",
+ "_photo\\.jpg",
  "_photo\\.png",
  "_photo\\.tif",
- "_headshape.pos"
+ "_headshape\\.pos"
  ]
  }
  },
@@ -88,14 +88,14 @@
  "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?\\1(_\\2)?(?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:_space-(@@@_eeg_space_@@@))?(@@@_eeg_ses_type_@@@)$",
  "tokens": {
  "@@@_eeg_ses_type_@@@": [
- "_events.tsv",
- "_channels.tsv",
- "_channels.json",
- "_electrodes.tsv",
- "_electrodes.json",
- "_eeg.json",
- "_coordsystem.json",
- "_photo.jpg",
+ "_events\\.tsv",
+ "_channels\\.tsv",
+ "_channels\\.json",
+ "_electrodes\\.tsv",
+ "_electrodes\\.json",
+ "_eeg\\.json",
+ "_coordsystem\\.json",
+ "_photo\\.jpg",
  "_photo\\.png",
  "_photo\\.tif"
  ],
@@ -153,14 +153,14 @@
  "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?\\1(_\\2)?(?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:_space-(@@@_ieeg_space_@@@))?(@@@_ieeg_ses_type_@@@)$",
  "tokens": {
  "@@@_ieeg_ses_type_@@@": [
- "_events.tsv",
- "_channels.tsv",
- "_channels.json",
- "_electrodes.tsv",
- "_electrodes.json",
- "_ieeg.json",
- "_coordsystem.json",
- "_photo.jpg",
+ "_events\\.tsv",
+ "_channels\\.tsv",
+ "_channels\\.json",
+ "_electrodes\\.tsv",
+ "_electrodes\\.json",
+ "_ieeg\\.json",
+ "_coordsystem\\.json",
+ "_photo\\.jpg",
  "_photo\\.png",
  "_photo\\.tif"
  ],
@@ -226,23 +226,23 @@
  "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?\\1(_\\2)?(?:_sample-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_stain-[a-zA-Z0-9]+)?(?:_run-[0-9]+_)?(?:_chunk-[0-9]+)?(@@@_microscopy_ses_type_@@@)$",
  "tokens": {
  "@@@_microscopy_ses_type_@@@": [
- "_TEM.json",
- "_SEM.json",
- "_uCT.json",
- "_BF.json",
- "_DF.json",
- "_PC.json",
- "_DIC.json",
- "_FLUO.json",
- "_CONF.json",
- "_PLI.json",
- "_CARS.json",
- "_2PE.json",
- "_MPE.json",
- "_SR.json",
- "_NLO.json",
- "_OCT.json",
- "_SPIM.json"
+ "_TEM\\.json",
+ "_SEM\\.json",
+ "_uCT\\.json",
+ "_BF\\.json",
+ "_DF\\.json",
+ "_PC\\.json",
+ "_DIC\\.json",
+ "_FLUO\\.json",
+ "_CONF\\.json",
+ "_PLI\\.json",
+ "_CARS\\.json",
+ "_2PE\\.json",
+ "_MPE\\.json",
+ "_SR\\.json",
+ "_NLO\\.json",
+ "_OCT\\.json",
+ "_SPIM\\.json"
  ]
  }
  }

diff --git a/bids-validator/bids_validator/rules/top_level_rules.json b/bids-validator/bids_validator/rules/top_level_rules.json
@@ -4,23 +4,23 @@
  "tokens": {
  "@@@_root_files_@@@": [
  "README",
- "README.md",
- "README.rst",
- "README.txt",
+ "README\\.md",
+ "README\\.rst",
+ "README\\.txt",
  "CHANGES",
  "LICENSE",
- "dataset_description.json",
- "genetic_info.json",
- "participants.tsv",
- "participants.json",
+ "dataset_description\\.json",
+ "genetic_info\\.json",
+ "participants\\.tsv",
+ "participants\\.json",
  "phasediff.json",
- "phase1.json",
- "phase2.json",
- "fieldmap.json",
- "events.json",
- "scans.json",
- "samples.json",
- "samples.tsv"
+ "phase1\\.json",
+ "phase2\\.json",
+ "fieldmap\\.json",
+ "events\\.json",
+ "scans\\.json",
+ "samples\\.json",
+ "samples\\.tsv"
  ]
  }
  },