Make extensions identifiers contain . to separate extensions where mu…

…ltiple used (bids-standard#1755) * Make extensions identifiers contain . to separate extensions where multiple used * Use underscore since "." is used in path to any object * [DATALAD RUNCMD] sed -i'' -e 's/tsvgz/tsv_gz/g' src/*.md ... === Do not change lines below === { "chain": [], "cmd": "sed -i'' -e 's/tsvgz/tsv_gz/g' src/*.md src/*/*.md", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "." } ^^^ Do not change lines above ^^^ --------- Co-authored-by: Chris Markiewicz <[email protected]>
DimitriPapadopoulos · Apr 19, 2024 · 1afbfe8 · 1afbfe8
1 parent bbe2283
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diff --git a/src/common-principles.md b/src/common-principles.md
@@ -563,7 +563,7 @@ like in the example below.
 ### Compressed tabular files
 
 Large tabular information, such as physiological recordings, MUST be stored with
-[compressed tab-delineated (TSV.GZ) files](glossary.md#tsvgz-extensions) when
+[compressed tab-delineated (TSV.GZ) files](glossary.md#tsv_gz-extensions) when
 so established by the specifications.
 Rules for formatting plain-text tabular files apply to TSVGZ files with three exceptions:
 

diff --git a/src/modality-specific-files/physiological-recordings.md b/src/modality-specific-files/physiological-recordings.md
@@ -2,7 +2,7 @@
 
 Physiological recordings such as cardiac and respiratory signals MAY be
 specified using a [compressed tabular file](../common-principles.md#compressed-tabular-files)
-([TSV.GZ file](../glossary.md#tsvgz-extensions)) and a corresponding
+([TSV.GZ file](../glossary.md#tsv_gz-extensions)) and a corresponding
 JSON file for storing metadata fields (see below).
 
 !!! example "Example datasets"

diff --git a/src/modality-specific-files/task-events.md b/src/modality-specific-files/task-events.md
@@ -325,7 +325,7 @@ in the accompanying JSON sidecar as follows (based on the example of the previou
 Signals related to stimuli (such as parameters of a film or audio stimuli) that are
 evenly recorded at a constant sampling frequency MUST be specified using a
 [compressed tabular file](../common-principles.md#compressed-tabular-files)
-([TSV.GZ file](../glossary.md#tsvgz-extensions)) and a corresponding
+([TSV.GZ file](../glossary.md#tsv_gz-extensions)) and a corresponding
 JSON file for storing metadata fields (see below).
 
 Template:

diff --git a/src/schema/objects/extensions.yaml b/src/schema/objects/extensions.yaml
@@ -184,7 +184,7 @@ nii:
   display_name: NIfTI
   description: |
     A Neuroimaging Informatics Technology Initiative (NIfTI) data file.
-niigz:
+nii_gz:
   value: .nii.gz
   display_name: Compressed NIfTI
   description: |
@@ -274,7 +274,7 @@ tsv:
   display_name: Tab-Delimited
   description: |
     A tab-delimited file.
-tsvgz:
+tsv_gz:
   value: .tsv.gz
   display_name: Compressed Tab-Delimited
   description: |

diff --git a/tools/schemacode/bidsschematools/render/text.py b/tools/schemacode/bidsschematools/render/text.py
@@ -401,8 +401,8 @@ def make_filename_template(
 
             ext_headings = []
             for extension in extensions:
-                # The glossary indexes by the extension identifier (niigz instead of .nii.gz),
-                # but the rules reference the actual suffix string (.nii.gz instead of niigz),
+                # The glossary indexes by the extension identifier (nii_gz instead of .nii.gz),
+                # but the rules reference the actual suffix string (.nii.gz instead of nii_gz),
                 # so we need to look it up.
                 key = ext_key_table.get(extension)
                 if key: