Merge pull request #435 from yarikoptic/deno-validator

Add "master-deno" flavor of validator to use as well

.github/workflows/validate_datasets.yml

@@ -21,7 +21,7 @@ jobs:
       fail-fast: false
       matrix:
         platform: [ubuntu-latest, macos-latest, windows-latest]
-        bids-validator: [master, stable]
+        bids-validator: [master, stable, master-deno]
 
     runs-on: ${{ matrix.platform }}
 
@@ -33,6 +33,7 @@ jobs:
     - uses: actions/checkout@v4
 
     - name: Set up Node.js
+      if: "matrix.bids-validator == 'stable' || matrix.bids-validator == 'master'"
       uses: actions/setup-node@v4
       with:
         node-version: 18
@@ -60,13 +61,32 @@ jobs:
         bash -c "npm install -g bids-validator-*.tgz"
         popd
 
+    - uses: denoland/setup-deno@v1
+      if: "matrix.bids-validator == 'master-deno'"
+      with:
+        deno-version: v1.x
+
+    - name: Install BIDS validator (master deno build)
+      if: "matrix.bids-validator == 'master-deno'"
+      run: |
+        LOCAL_BIN=$HOME/.local/bin
+        VALIDATOR=$LOCAL_BIN/bids-validator
+        mkdir -p $LOCAL_BIN
+        export PATH="$LOCAL_BIN:$PATH"
+        echo PATH="$PATH" >> $GITHUB_ENV
+        echo -e '#!/usr/bin/env'" -S deno run --allow-read --allow-write --allow-env --allow-net --allow-run\nimport 'https://github.com/bids-standard/bids-validator/raw/master/bids-validator/src/bids-validator.ts'" > $VALIDATOR
+        chmod +x $VALIDATOR
+        bids-validator --version
+      shell: bash
+
     - name: Display versions and environment information
       run: |
         echo $TZ
         date
         echo "npm"; npm --version
         echo "node"; node --version
         echo "bids-validator"; bids-validator --version
+      shell: bash
 
     - name: Check that no large files are present
       if: "matrix.bids-validator == 'stable'"
@@ -83,6 +103,12 @@ jobs:
         fi
       shell: bash
 
+    - name: Mark to be skipped some examples for a deno based
+      if: "matrix.bids-validator == 'master-deno'"
+      run: |
+        touch {ds000117,ds000246,ds000247,ds000248,eeg_ds003645s_hed_demo,ieeg_motorMiller2007,ieeg_visual,7t_trt,ds102,fnirs_automaticity,genetics_ukbb,ieeg_epilepsy,ieeg_epilepsyNWB}/.SKIP_VALIDATION
+      shell: bash
+
     - name: Validate all BIDS datasets using bids-validator
       run: |
         cat ./run_tests.sh

run_tests.sh

@@ -1,11 +1,19 @@
 #!/usr/bin/env bash
 
-rc=0;
+failed=
+
+which bids-validator
+if bids-validator --help | grep -q -e '--config'; then
+       VALIDATOR_SUPPORTS_CONFIG=yes
+else
+       VALIDATOR_SUPPORTS_CONFIG=
+fi
+
 for i in $(ls -d */ | grep -v node_modules); do
-    echo "Validating dataset" $i
+    echo -n "Validating dataset $i: "
 
     if [ -f ${i%%/}/.SKIP_VALIDATION ]; then
-        echo "Skipping validation for ${i%%/}"
+        echo "skipping validation"
         continue
     fi
 
@@ -14,18 +22,40 @@ for i in $(ls -d */ | grep -v node_modules); do
     CMD="bids-validator ${i%%/} $VALIDATOR_ARGS"
 
     # Use default configuration unless overridden
-    if [ ! -f ${i%%/}/.bids-validator-config.json ]; then
-        CMD="$CMD -c $PWD/bidsconfig.json"
+    if [ -n "$VALIDATOR_SUPPORTS_CONFIG" ]; then
+        if [ ! -f ${i%%/}/.bids-validator-config.json ]; then
+            CMD="$CMD -c $PWD/bidsconfig.json"
+        fi
+    else
+        # with new one we do not have config so let's get --json and exclude some using jq
+        CMD="$CMD --json"
     fi
 
     # Ignore NIfTI headers except for synthetic dataset
     if [ $i != "synthetic/" ]; then
         CMD="$CMD --ignoreNiftiHeaders"
     else
-        echo "Validating NIfTI headers for dataset" $i
+        echo "validating NIfTI headers. "
     fi
 
-    echo $CMD
-    $CMD || rc=$?
+    echo "Running " $CMD
+
+    if [ -n "$VALIDATOR_SUPPORTS_CONFIG" ]; then
+        $CMD || failed+=" $i"
+    else
+        # exit code is not returned correctly anyways and for the best since we need to ignore
+        # ref: https://github.com/bids-standard/bids-validator/issues/1909
+        # NOTE:  limit to 1 file per error to not flood screen!
+        errors=$($CMD 2>/dev/null \
+          | jq '(.issues | map(select(.severity == "error" and .key != "EMPTY_FILE"))) | map(.files_1 = (.files | if length > 0 then .[0:1] else empty end) | del(.files)) | if length > 0 then . else empty end' \
+        )
+        if [ -n "$errors" ]; then
+            echo -e "$errors" | sed -e 's,^,  ,g'
+            failed+=" $i"
+        fi
+    fi
 done
-exit $rc;
+if [ -n "$failed" ]; then
+    echo "Datasets failed validation: $failed"
+    exit 1
+fi