Merge pull request #157 from hed-standard/merge-conversion

Rewrite short/long converter
hed-standard · Jul 26, 2024 · 9a4b907 · 9a4b907
2 parents 9c779b7 + 6905aa2
commit 9a4b907
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Showing 37 changed files with 1,309 additions and 1,510 deletions.
diff --git a/bids/tsvParser.js b/bids/tsvParser.js
@@ -20,7 +20,7 @@ export function parseTSV(contents) {
   const rows = stripBOM(normalizeEOL(contents))
     .split('\n')
     .filter(isContentfulRow)
-    .map((str) => str.split('\t'))
+    .map((str) => str.split('\t').map((cell) => cell.trim()))
   const headers = rows.length ? rows[0] : []
 
   headers.forEach((x) => {

diff --git a/bids/types/json.js b/bids/types/json.js
@@ -75,7 +75,7 @@ export class BidsSidecar extends BidsJsonFile {
     const sidecarHedTags = Object.entries(this.jsonData)
       .map(([sidecarKey, sidecarValue]) => {
         if (sidecarValueHasHed(sidecarValue)) {
-          return [sidecarKey, new BidsSidecarKey(sidecarKey, sidecarValue.HED)]
+          return [sidecarKey.trim(), new BidsSidecarKey(sidecarKey.trim(), sidecarValue.HED)]
         } else {
           return null
         }

diff --git a/common/issues/data.js b/common/issues/data.js
@@ -185,10 +185,15 @@ export default {
     level: 'error',
     message: stringTemplate`"${'tag'}" appears as "${'parentTag'}" and cannot be used as an extension. Indices (${0}, ${1}).`,
   },
+  invalidExtension: {
+    hedCode: 'TAG_EXTENSION_INVALID',
+    level: 'error',
+    message: stringTemplate`"${'tag'}" appears as an extension of "${'parentTag'}", which does not allow tag extensions.`,
+  },
   emptyTagFound: {
     hedCode: 'TAG_EMPTY',
     level: 'error',
-    message: stringTemplate`Empty tag cannot be converted.`,
+    message: stringTemplate`Empty tag at index ${'index'} cannot be converted.`,
   },
   duplicateTagsInSchema: {
     hedCode: 'SCHEMA_DUPLICATE_NODE',
@@ -309,4 +314,9 @@ export default {
     level: 'error',
     message: stringTemplate`Unknown HED error "${'internalCode'}" - parameters: "${'parameters'}".`,
   },
+  internalConsistencyError: {
+    hedCode: 'GENERIC_ERROR',
+    level: 'error',
+    message: stringTemplate`Internal consistency error - message: "${'message'}".`,
+  },
 }
diff --git a/common/schema/types.js b/common/schema/types.js
@@ -106,11 +106,6 @@ export class Hed3Schema extends Schema {
    * @type {SchemaEntries}
    */
   entries
-  /**
-   * The mapping between short and long tags.
-   * @type {Mapping}
-   */
-  mapping
   /**
    * The standard HED schema version this schema is linked to.
    * @type {string}
@@ -122,9 +117,8 @@ export class Hed3Schema extends Schema {
    *
    * @param {object} xmlData The schema XML data.
    * @param {SchemaEntries} entries A collection of schema entries.
-   * @param {Mapping} mapping A mapping between short and long tags.
    */
-  constructor(xmlData, entries, mapping) {
+  constructor(xmlData, entries) {
     super(xmlData)
 
     if (!this.library) {
@@ -133,7 +127,6 @@ export class Hed3Schema extends Schema {
       this.withStandard = xmlData.HED?.$?.withStandard
     }
     this.entries = entries
-    this.mapping = mapping
   }
 
   /**
@@ -164,7 +157,7 @@ export class PartneredSchema extends Hed3Schema {
    * @param {Hed3Schema} actualSchema The actual HED 3 schema underlying this partnered schema.
    */
   constructor(actualSchema) {
-    super({}, actualSchema.entries, actualSchema.mapping)
+    super({}, actualSchema.entries)
     this.actualSchema = actualSchema
     this.withStandard = actualSchema.withStandard
     this.library = undefined