dicom-curate 0.7.1 → 0.8.0

package/dist/esm/applyMappingsWorker.js

@@ -25122,6 +25122,9 @@ async function createNestedDirectories(topLevelDirectoryHandle, path) {
   return currentDirectoryHandle;
 }
 
+// src/config/specVersion.ts
+var specVersion = "3.0";
+
 // src/config/dicom/dummyValues.ts
 var dummyValues = {
   AE: "INVALID_AE",
@@ -36337,7 +36340,7 @@ function deidentifyPS315E({
           // We should clean it
           normalName in cleanPolicyMap && // Either cleanDescOpt is off (we handle those separately) or
           // if it's on, it's not one of the exception tags
-          (!cleanDescriptorsOption || !cleanDescriptorsExceptions.includes(normalName)) && // No condition for an exception applies
+          (!cleanDescriptorsOption || cleanDescriptorsExceptions === false || !cleanDescriptorsExceptions.includes(normalName)) && // No condition for an exception applies
           !cleanPolicyMap[normalName].exceptCondition?.(data3) && data3[name] !== ""
         ) {
           const { rule } = cleanPolicyMap[normalName];
@@ -36441,7 +36444,7 @@ function deidentifyPS315E({
           // protocols, though it still could be cleaned as described in Note 2"
           // Note: Removes tags which contain Comment|Desciprion at any location
           // inside the string.
-          cleanDescriptorsOption && normalName.match(/Comment|Description/) && !cleanDescriptorsExceptions.includes(normalName) && data3[name] !== ""
+          cleanDescriptorsOption && normalName.match(/Comment|Description/) && (cleanDescriptorsExceptions === false || !cleanDescriptorsExceptions.includes(normalName)) && data3[name] !== ""
         ) {
           mapResults.mappings[attrPath] = [
             data3[name],
@@ -36537,6 +36540,146 @@ var defaultPs315Options = {
   retainInstitutionIdentityOption: false
 };
 
+// src/defaultSpec.ts
+var defaultSpec = {
+  version: specVersion,
+  hostProps: {},
+  excludedFiletypes: [],
+  dicomPS315EOptions: defaultPs315Options,
+  inputPathPattern: "",
+  modifyDicomHeader: () => ({}),
+  outputFilePathComponents: (parser) => [
+    parser.protectUid(parser.getDicom("SeriesInstanceUID")),
+    parser.getFilePathComp(parser.FILENAME)
+  ],
+  errors: () => []
+};
+
+// src/composeSpecs.ts
+function concatUnique(a, b) {
+  return [.../* @__PURE__ */ new Set([...a, ...b])];
+}
+function mergeRetain(a, b) {
+  if (b === false)
+    return false;
+  if (a === false || a === void 0)
+    return [...b];
+  return concatUnique(a, b);
+}
+function isObj(v) {
+  return !!v && typeof v === "object" && !Array.isArray(v) && !(v instanceof RegExp);
+}
+function mergeHostProps(prev, next) {
+  if (!next)
+    return prev;
+  if (!prev)
+    return next;
+  const res = { ...prev };
+  for (const [k, v] of Object.entries(next)) {
+    const pv = res[k];
+    if (Array.isArray(v)) {
+      res[k] = v;
+    } else if (isObj(v) && isObj(pv)) {
+      res[k] = mergeHostProps(pv, v);
+    } else {
+      res[k] = v;
+    }
+  }
+  return res;
+}
+function mergePs315(chain) {
+  let acc = chain[0];
+  for (let i = 1; i < chain.length; i++) {
+    let cur = chain[i];
+    if (cur === void 0)
+      continue;
+    if (cur === "Off") {
+      acc = "Off";
+      continue;
+    }
+    if (acc === "Off" || acc === void 0) {
+      acc = { ...defaultPs315Options, ...cur };
+      if (Array.isArray(cur.cleanDescriptorsExceptions)) {
+        acc.cleanDescriptorsExceptions = [...cur.cleanDescriptorsExceptions];
+      }
+      const curRetain = cur.retainPatientCharacteristicsOption;
+      if (Array.isArray(curRetain)) {
+        acc.retainPatientCharacteristicsOption = [...curRetain];
+      }
+      continue;
+    }
+    const prevCleanDesc = acc.cleanDescriptorsExceptions ?? [];
+    const prevRetainPatChars = acc.retainPatientCharacteristicsOption;
+    acc = { ...acc, ...cur };
+    if (cur.cleanDescriptorsExceptions !== void 0) {
+      acc.cleanDescriptorsExceptions = mergeRetain(
+        prevCleanDesc,
+        cur.cleanDescriptorsExceptions
+      );
+    }
+    if (cur.retainPatientCharacteristicsOption !== void 0) {
+      acc.retainPatientCharacteristicsOption = mergeRetain(
+        prevRetainPatChars,
+        cur.retainPatientCharacteristicsOption
+      );
+    }
+  }
+  return acc;
+}
+function isTCurationSpec(s) {
+  return typeof s !== "function";
+}
+function composeSpecs(specOrComposedSpec) {
+  const specsIn = Array.isArray(specOrComposedSpec) ? specOrComposedSpec : [specOrComposedSpec];
+  let final = defaultSpec;
+  if (specsIn.length === 0) {
+    throw new Error("composeSpecs requires a non-empty spec array");
+  }
+  const ctx = {};
+  let ps315Chain = [final.dicomPS315EOptions];
+  for (const specIn of specsIn) {
+    let { ctx: c = {}, spec = { version: specVersion } } = isTCurationSpec(
+      specIn
+    ) ? { spec: specIn } : specIn(ctx);
+    Object.assign(ctx, c);
+    if (spec.version !== specVersion) {
+      throw new Error(
+        `All curation specification versions must be '${specVersion}'`
+      );
+    }
+    final.hostProps = mergeHostProps(final.hostProps, spec.hostProps);
+    final.inputPathPattern = spec.inputPathPattern ?? final.inputPathPattern;
+    if (spec.dicomPS315EOptions) {
+      ps315Chain.push(spec.dicomPS315EOptions);
+    }
+    if (spec.excludedFiletypes !== void 0) {
+      const prev = [...final.excludedFiletypes ?? []];
+      const next = spec.excludedFiletypes;
+      final.excludedFiletypes = [...prev, ...next];
+    }
+    if (spec.additionalData !== void 0) {
+      final.additionalData = spec.additionalData;
+    }
+    if (spec.modifyDicomHeader) {
+      const prev = final.modifyDicomHeader;
+      const next = spec.modifyDicomHeader;
+      final.modifyDicomHeader = (p) => ({ ...prev(p), ...next(p) });
+    }
+    if (spec.outputFilePathComponents) {
+      final.outputFilePathComponents = spec.outputFilePathComponents;
+    }
+    if (spec.errors) {
+      const prev = final.errors;
+      const next = spec.errors;
+      final.errors = (p) => {
+        return [...prev(p), ...next(p)];
+      };
+    }
+  }
+  final.dicomPS315EOptions = mergePs315(ps315Chain);
+  return final;
+}
+
 // src/csvMapping.ts
 function getCsvMapping(columnMappings, mapping, mappingKey, value) {
   const rowIdx = columnMappings.rowIndexByFieldValue[mappingKey][value];
@@ -36669,9 +36812,6 @@ function getParser(inputPathPattern, inputFilePath, naturalData, dicomPS315EOpti
   };
 }
 
-// src/config/specVersion.ts
-var specVersion = "3.0";
-
 // src/collectMappings.ts
 var import_lodash2 = __toESM(require_lodash(), 1);
 function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOptions) {
@@ -36690,29 +36830,7 @@ function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOption
     dicomData.dict
   );
   mapResults.sourceInstanceUID = naturalData.SOPInstanceUID;
-  let finalSpec = {
-    dicomPS315EOptions: defaultPs315Options,
-    inputPathPattern: "",
-    modifyDicomHeader: () => ({}),
-    outputFilePathComponents: (parser2) => [
-      parser2.protectUid(parser2.getDicom("SeriesInstanceUID")),
-      parser2.getFilePathComp(parser2.FILENAME)
-    ],
-    errors: () => []
-  };
-  const { modifyDicomHeader, errors, ...restSpec } = mappingOptions.curationSpec();
-  if (restSpec.version !== specVersion) {
-    throw new Error(
-      `Only version ${specVersion} supported in curationSpecification`
-    );
-  }
-  Object.assign(finalSpec, restSpec);
-  if (!mappingOptions.skipModifications) {
-    finalSpec.modifyDicomHeader = modifyDicomHeader;
-  }
-  if (!mappingOptions.skipValidation) {
-    finalSpec.errors = errors;
-  }
+  const finalSpec = composeSpecs(mappingOptions.curationSpec());
   const finalFilePath = finalSpec.dicomPS315EOptions === "Off" ? inputFilePath : inputFilePath.slice(0, inputFilePath.lastIndexOf("/") + 1) + `${String(inputFileIndex + 1).padStart(5, "0")}.dcm`;
   const parser = getParser(
     finalSpec.inputPathPattern,

package/dist/esm/collectMappings.js

@@ -18807,6 +18807,9 @@ ValueRepresentation.setDicomMessageClass(DicomMessage);
 ValueRepresentation.setTagClass(Tag);
 Tag.setDicomMessageClass(DicomMessage);
 
+// src/config/specVersion.ts
+var specVersion = "3.0";
+
 // src/config/dicom/dummyValues.ts
 var dummyValues = {
   AE: "INVALID_AE",
@@ -30008,7 +30011,7 @@ function deidentifyPS315E({
           // We should clean it
           normalName in cleanPolicyMap && // Either cleanDescOpt is off (we handle those separately) or
           // if it's on, it's not one of the exception tags
-          (!cleanDescriptorsOption || !cleanDescriptorsExceptions.includes(normalName)) && // No condition for an exception applies
+          (!cleanDescriptorsOption || cleanDescriptorsExceptions === false || !cleanDescriptorsExceptions.includes(normalName)) && // No condition for an exception applies
           !cleanPolicyMap[normalName].exceptCondition?.(data2) && data2[name] !== ""
         ) {
           const { rule } = cleanPolicyMap[normalName];
@@ -30112,7 +30115,7 @@ function deidentifyPS315E({
           // protocols, though it still could be cleaned as described in Note 2"
           // Note: Removes tags which contain Comment|Desciprion at any location
           // inside the string.
-          cleanDescriptorsOption && normalName.match(/Comment|Description/) && !cleanDescriptorsExceptions.includes(normalName) && data2[name] !== ""
+          cleanDescriptorsOption && normalName.match(/Comment|Description/) && (cleanDescriptorsExceptions === false || !cleanDescriptorsExceptions.includes(normalName)) && data2[name] !== ""
         ) {
           mapResults.mappings[attrPath] = [
             data2[name],
@@ -30208,6 +30211,146 @@ var defaultPs315Options = {
   retainInstitutionIdentityOption: false
 };
 
+// src/defaultSpec.ts
+var defaultSpec = {
+  version: specVersion,
+  hostProps: {},
+  excludedFiletypes: [],
+  dicomPS315EOptions: defaultPs315Options,
+  inputPathPattern: "",
+  modifyDicomHeader: () => ({}),
+  outputFilePathComponents: (parser) => [
+    parser.protectUid(parser.getDicom("SeriesInstanceUID")),
+    parser.getFilePathComp(parser.FILENAME)
+  ],
+  errors: () => []
+};
+
+// src/composeSpecs.ts
+function concatUnique(a, b) {
+  return [.../* @__PURE__ */ new Set([...a, ...b])];
+}
+function mergeRetain(a, b) {
+  if (b === false)
+    return false;
+  if (a === false || a === void 0)
+    return [...b];
+  return concatUnique(a, b);
+}
+function isObj(v) {
+  return !!v && typeof v === "object" && !Array.isArray(v) && !(v instanceof RegExp);
+}
+function mergeHostProps(prev, next) {
+  if (!next)
+    return prev;
+  if (!prev)
+    return next;
+  const res = { ...prev };
+  for (const [k, v] of Object.entries(next)) {
+    const pv = res[k];
+    if (Array.isArray(v)) {
+      res[k] = v;
+    } else if (isObj(v) && isObj(pv)) {
+      res[k] = mergeHostProps(pv, v);
+    } else {
+      res[k] = v;
+    }
+  }
+  return res;
+}
+function mergePs315(chain) {
+  let acc = chain[0];
+  for (let i = 1; i < chain.length; i++) {
+    let cur = chain[i];
+    if (cur === void 0)
+      continue;
+    if (cur === "Off") {
+      acc = "Off";
+      continue;
+    }
+    if (acc === "Off" || acc === void 0) {
+      acc = { ...defaultPs315Options, ...cur };
+      if (Array.isArray(cur.cleanDescriptorsExceptions)) {
+        acc.cleanDescriptorsExceptions = [...cur.cleanDescriptorsExceptions];
+      }
+      const curRetain = cur.retainPatientCharacteristicsOption;
+      if (Array.isArray(curRetain)) {
+        acc.retainPatientCharacteristicsOption = [...curRetain];
+      }
+      continue;
+    }
+    const prevCleanDesc = acc.cleanDescriptorsExceptions ?? [];
+    const prevRetainPatChars = acc.retainPatientCharacteristicsOption;
+    acc = { ...acc, ...cur };
+    if (cur.cleanDescriptorsExceptions !== void 0) {
+      acc.cleanDescriptorsExceptions = mergeRetain(
+        prevCleanDesc,
+        cur.cleanDescriptorsExceptions
+      );
+    }
+    if (cur.retainPatientCharacteristicsOption !== void 0) {
+      acc.retainPatientCharacteristicsOption = mergeRetain(
+        prevRetainPatChars,
+        cur.retainPatientCharacteristicsOption
+      );
+    }
+  }
+  return acc;
+}
+function isTCurationSpec(s) {
+  return typeof s !== "function";
+}
+function composeSpecs(specOrComposedSpec) {
+  const specsIn = Array.isArray(specOrComposedSpec) ? specOrComposedSpec : [specOrComposedSpec];
+  let final = defaultSpec;
+  if (specsIn.length === 0) {
+    throw new Error("composeSpecs requires a non-empty spec array");
+  }
+  const ctx = {};
+  let ps315Chain = [final.dicomPS315EOptions];
+  for (const specIn of specsIn) {
+    let { ctx: c = {}, spec = { version: specVersion } } = isTCurationSpec(
+      specIn
+    ) ? { spec: specIn } : specIn(ctx);
+    Object.assign(ctx, c);
+    if (spec.version !== specVersion) {
+      throw new Error(
+        `All curation specification versions must be '${specVersion}'`
+      );
+    }
+    final.hostProps = mergeHostProps(final.hostProps, spec.hostProps);
+    final.inputPathPattern = spec.inputPathPattern ?? final.inputPathPattern;
+    if (spec.dicomPS315EOptions) {
+      ps315Chain.push(spec.dicomPS315EOptions);
+    }
+    if (spec.excludedFiletypes !== void 0) {
+      const prev = [...final.excludedFiletypes ?? []];
+      const next = spec.excludedFiletypes;
+      final.excludedFiletypes = [...prev, ...next];
+    }
+    if (spec.additionalData !== void 0) {
+      final.additionalData = spec.additionalData;
+    }
+    if (spec.modifyDicomHeader) {
+      const prev = final.modifyDicomHeader;
+      const next = spec.modifyDicomHeader;
+      final.modifyDicomHeader = (p) => ({ ...prev(p), ...next(p) });
+    }
+    if (spec.outputFilePathComponents) {
+      final.outputFilePathComponents = spec.outputFilePathComponents;
+    }
+    if (spec.errors) {
+      const prev = final.errors;
+      const next = spec.errors;
+      final.errors = (p) => {
+        return [...prev(p), ...next(p)];
+      };
+    }
+  }
+  final.dicomPS315EOptions = mergePs315(ps315Chain);
+  return final;
+}
+
 // src/csvMapping.ts
 function getCsvMapping(columnMappings, mapping, mappingKey, value) {
   const rowIdx = columnMappings.rowIndexByFieldValue[mappingKey][value];
@@ -30340,9 +30483,6 @@ function getParser(inputPathPattern, inputFilePath, naturalData, dicomPS315EOpti
   };
 }
 
-// src/config/specVersion.ts
-var specVersion = "3.0";
-
 // src/collectMappings.ts
 var import_lodash2 = __toESM(require_lodash(), 1);
 function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOptions) {
@@ -30361,29 +30501,7 @@ function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOption
     dicomData.dict
   );
   mapResults.sourceInstanceUID = naturalData.SOPInstanceUID;
-  let finalSpec = {
-    dicomPS315EOptions: defaultPs315Options,
-    inputPathPattern: "",
-    modifyDicomHeader: () => ({}),
-    outputFilePathComponents: (parser2) => [
-      parser2.protectUid(parser2.getDicom("SeriesInstanceUID")),
-      parser2.getFilePathComp(parser2.FILENAME)
-    ],
-    errors: () => []
-  };
-  const { modifyDicomHeader, errors, ...restSpec } = mappingOptions.curationSpec();
-  if (restSpec.version !== specVersion) {
-    throw new Error(
-      `Only version ${specVersion} supported in curationSpecification`
-    );
-  }
-  Object.assign(finalSpec, restSpec);
-  if (!mappingOptions.skipModifications) {
-    finalSpec.modifyDicomHeader = modifyDicomHeader;
-  }
-  if (!mappingOptions.skipValidation) {
-    finalSpec.errors = errors;
-  }
+  const finalSpec = composeSpecs(mappingOptions.curationSpec());
   const finalFilePath = finalSpec.dicomPS315EOptions === "Off" ? inputFilePath : inputFilePath.slice(0, inputFilePath.lastIndexOf("/") + 1) + `${String(inputFileIndex + 1).padStart(5, "0")}.dcm`;
   const parser = getParser(
     finalSpec.inputPathPattern,