Merge pull request #1420 from bids-standard/enh/blacklist-modality

Update modality blacklist.

Author: rwblair

bids-validator/utils/files/readDir.js

@@ -272,40 +272,41 @@ async function getFilesFromFs(dir, rootPath, ig, options) {
       path.relative(rootPath, fullPath),
     )
     const ignore = ig.ignores(path.relative('/', relativePath))
-    if (!ignore) {
-      const fileObj = {
-        name: file.name,
-        path: fullPath,
-        relativePath,
-      }
-      // Three cases to consider: directories, files, symlinks
-      if (file.isDirectory()) {
-        await recursiveMerge(fullPath)
-      } else if (file.isSymbolicLink()) {
-        // Allow skipping symbolic links which lead to recursion
-        // Disabling this is a big performance advantage on high latency
-        // storage but it's a good default for versatility
-        if (!options.ignoreSymlinks) {
-          try {
-            const targetPath = await fs.promises.realpath(fullPath)
-            const targetStat = await fs.promises.stat(targetPath)
-            // Either add or recurse from the target depending
-            if (targetStat.isDirectory()) {
-              await recursiveMerge(targetPath)
-            } else {
-              filesAccumulator.push(fileObj)
-            }
-          } catch (err) {
-            // Symlink points at an invalid target, skip it
-            return
+    const fileObj = {
+      name: file.name,
+      path: fullPath,
+      relativePath,
+    }
+    if (ignore) {
+      fileObj.ignore = true
+    }
+    // Three cases to consider: directories, files, symlinks
+    if (file.isDirectory()) {
+      await recursiveMerge(fullPath)
+    } else if (file.isSymbolicLink()) {
+      // Allow skipping symbolic links which lead to recursion
+      // Disabling this is a big performance advantage on high latency
+      // storage but it's a good default for versatility
+      if (!options.ignoreSymlinks) {
+        try {
+          const targetPath = await fs.promises.realpath(fullPath)
+          const targetStat = await fs.promises.stat(targetPath)
+          // Either add or recurse from the target depending
+          if (targetStat.isDirectory()) {
+            await recursiveMerge(targetPath)
+          } else {
+            filesAccumulator.push(fileObj)
           }
-        } else {
-          // This branch assumes all symbolic links are not directories
-          filesAccumulator.push(fileObj)
+        } catch (err) {
+          // Symlink points at an invalid target, skip it
+          return
         }
       } else {
+        // This branch assumes all symbolic links are not directories
         filesAccumulator.push(fileObj)
       }
+    } else {
+      filesAccumulator.push(fileObj)
     }
   }
   return filesAccumulator

bids-validator/validators/bids/fullTest.js

@@ -19,6 +19,7 @@ import checkReadme from './checkReadme'
 import validateMisc from '../../utils/files/validateMisc'
 import collectSubjectMetadata from '../../utils/summary/collectSubjectMetadata'
 import collectPetFields from '../../utils/summary/collectPetFields'
+import collectModalities from '../../utils/summary/collectModalities'
 
 /**
  * Full Test
@@ -44,11 +45,13 @@ const fullTest = (fileList, options, annexed, dir, schema, callback) => {
 
   const tsvs = []
 
-  const summary = utils.collectSummary(fileList, self.options, schema)
-
   if (self.options.blacklistModalities) {
+    const relativePaths = Object.keys(fileList).map(
+      file => fileList[file].relativePath,
+    )
+    const preIgnoreModalities = collectModalities(relativePaths)
     self.options.blacklistModalities.map(mod => {
-      if (summary.modalities.includes(mod)) {
+      if (preIgnoreModalities.primary.includes(mod)) {
         self.issues.push(
           new Issue({
             file: mod,
@@ -60,6 +63,8 @@ const fullTest = (fileList, options, annexed, dir, schema, callback) => {
     })
   }
 
+  const summary = utils.collectSummary(fileList, self.options, schema)
+
   // remove size redundancies
   for (const key in fileList) {
     if (fileList.hasOwnProperty(key)) {