Support validation using new deno validator while manually skipping E…

…MPTY_FILE errors.

Also adjusted output to make it more concise and easier to identify what errors belong to etc

run_tests.sh

@@ -2,17 +2,18 @@
 
 rc=0;
 
-if bids-validator --version | grep -q 'alpha$'; then
-       VALIDATOR_SUPPORTS_CONFIG=no
-else
+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
 
@@ -21,18 +22,37 @@ for i in $(ls -d */ | grep -v node_modules); do
     CMD="bids-validator ${i%%/} $VALIDATOR_ARGS"
 
     # Use default configuration unless overridden
-    if [ "$VALIDATOR_SUPPORTS_CONFIG" = "yes" ] && [ ! -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
+        $CMD || rc=$?
+    else
+        # rc 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'
+            rc=1
+        fi
+    fi
 done
 exit $rc;