@radicalimaging/static-wado-creator 1.6.10 → 1.6.11

package/lib/writer/CompleteStudyWriter.js

@@ -1,10 +1,6 @@
-const {
-  JSONReader,
-  JSONWriter,
-  Stats,
-} = require("@radicalimaging/static-wado-util");
-const { Tags } = require("@radicalimaging/static-wado-util");
-const StudyData = require("../operation/StudyData");
+const { JSONReader, JSONWriter, Stats } = require('@radicalimaging/static-wado-util');
+const { Tags } = require('@radicalimaging/static-wado-util');
+const StudyData = require('../operation/StudyData');
 
 /**
  * CompleteStudyWriter takes the deduplicated data values, all loaded into the study parameter,
@@ -12,13 +8,13 @@ const StudyData = require("../operation/StudyData");
  * written out as.
  * The studyData object is then removed, so that a new one can be created if required.
  */
-const CompleteStudyWriter = (options) => {
+const CompleteStudyWriter = options => {
   async function ret() {
     const { studyData } = this;
     if (!studyData) return;
 
     if (!studyData.numberOfInstances) {
-      console.log("studyData.deduplicated is empty");
+      console.log('studyData.deduplicated is empty');
       delete this.studyData;
       return;
     }
@@ -26,28 +22,24 @@ const CompleteStudyWriter = (options) => {
     if (options.isGroup) {
       if (studyData.dirty) {
         await studyData.writeDeduplicatedGroup();
-        console.noQuiet(
-          "Wrote updated deduplicated data for study",
-          studyData.studyInstanceUid,
-        );
+        console.noQuiet('Wrote updated deduplicated data for study', studyData.studyInstanceUid);
       } else {
         console.noQuiet(
-          "Not writing new deduplicated data because it is clean:",
-          studyData.studyInstanceUid,
+          'Not writing new deduplicated data because it is clean:',
+          studyData.studyInstanceUid
         );
         const message = {
-          text: "Metadata clean, not updating",
+          text: 'Metadata clean, not updating',
           status: 0,
           studyInstanceUid: studyData.studyInstanceUid,
         };
-        this.success("metadataClean", message);
+        this.success('metadataClean', message);
       }
       await studyData.deleteInstancesReferenced();
     }
 
     if (!options.isStudyData) {
-      if (options.notifications)
-        this.notificationService.notifyStudy(studyData.studyInstanceUid);
+      if (options.notifications) this.notificationService.notifyStudy(studyData.studyInstanceUid);
       delete this.studyData;
       Stats.StudyStats.summarize();
       return;
@@ -55,47 +47,42 @@ const CompleteStudyWriter = (options) => {
 
     const isDirtyMetadata = await studyData.dirtyMetadata();
     if (!isDirtyMetadata && !options.force) {
-      console.log("Study metadata", studyData.studyInstanceUid, "is clean.");
+      console.log('Study metadata', studyData.studyInstanceUid, 'is clean.');
       delete this.studyData;
       Stats.StudyStats.summarize(
-        `Study metadata ${studyData.studyInstanceUid} has clean metadata, not writing`,
+        `Study metadata ${studyData.studyInstanceUid} has clean metadata, not writing`
       );
       return;
     }
-    console.noQuiet("Writing study metadata", studyData.studyInstanceUid);
+    console.noQuiet('Writing study metadata', studyData.studyInstanceUid);
 
     const studyQuery = await studyData.writeMetadata();
 
-    const allStudies = await JSONReader(
-      options.directoryName,
-      "studies/index.json.gz",
-      [],
-    );
+    const allStudies = await JSONReader(options.directoryName, 'studies/index.json.gz', []);
     const studyUID = Tags.getValue(studyQuery, Tags.StudyInstanceUID);
     if (!studyUID) {
-      console.error("studyQuery=", studyQuery);
-      throw new Error("Study query has null studyUID");
+      console.error('studyQuery=', studyQuery);
+      throw new Error('Study query has null studyUID');
     }
     const studyIndex = allStudies.findIndex(
-      (item) => Tags.getValue(item, Tags.StudyInstanceUID) == studyUID,
+      item => Tags.getValue(item, Tags.StudyInstanceUID) == studyUID
     );
     if (studyIndex == -1) {
       allStudies.push(studyQuery);
     } else {
       allStudies[studyIndex] = studyQuery;
     }
-    await JSONWriter(options.directoryName, "studies", allStudies);
-    if (options.notifications)
-      this.notificationService.notifyStudy(studyData.studyInstanceUid);
+    await JSONWriter(options.directoryName, 'studies', allStudies);
+    if (options.notifications) this.notificationService.notifyStudy(studyData.studyInstanceUid);
     const message = {
-      action: "metadata",
+      action: 'metadata',
       status: 0,
       studyInstanceUid: studyData.studyInstanceUid,
     };
-    this.success("completeStudyWriter", message);
+    this.success('completeStudyWriter', message);
     delete this.studyData;
     Stats.StudyStats.summarize(
-      `Wrote study metadata/query files for ${studyData.studyInstanceUid}`,
+      `Wrote study metadata/query files for ${studyData.studyInstanceUid}`
     );
   }
 
@@ -115,7 +102,7 @@ const CompleteStudyWriter = (options) => {
     }
     callback.setStudyData(new StudyData(id, options));
     if (!options.isSkipStudyScan) {
-      console.verbose("Initiate StudyData");
+      console.verbose('Initiate StudyData');
       await callback.studyData.init(options);
     }
     return callback.studyData;

package/lib/writer/DeduplicateWriter.js

@@ -1,9 +1,9 @@
-const hashFactory = require("node-object-hash");
+const hashFactory = require('node-object-hash');
 
 const hasher = hashFactory.hasher();
-const { JSONWriter } = require("@radicalimaging/static-wado-util");
-const { Tags } = require("@radicalimaging/static-wado-util");
-const TagLists = require("../model/TagLists");
+const { JSONWriter } = require('@radicalimaging/static-wado-util');
+const { Tags } = require('@radicalimaging/static-wado-util');
+const TagLists = require('../model/TagLists');
 
 async function writeDeduplicatedFile(dir, data, hashValueSrc) {
   const hashValue = hashValueSrc || hasher.hash(data);
@@ -19,16 +19,15 @@ const perInstanceWriter = async (id, data) => {
 };
 
 /** Writes out JSON files to the given file name.  Automatically GZips them, and adds the extension */
-const DeduplicateWriter = (options) =>
+const DeduplicateWriter = options =>
   async function DeduplicateWriterInstance(id, data) {
     const studyData = await this.completeStudy.getCurrentStudyData(this, id);
 
     if (options.isDeduplicate) {
-      if (options.verbose)
-        console.log("Writing single instance", id.studyInstanceUid);
+      if (options.verbose) console.log('Writing single instance', id.studyInstanceUid);
       await perInstanceWriter(id, data);
     } else if (options.verbose) {
-      console.log("Not writing single instance deduplicated");
+      console.log('Not writing single instance deduplicated');
     }
     studyData.addDeduplicated(data, id.filename);
   };

package/lib/writer/ExpandUriPath.js

@@ -1,17 +1,15 @@
 const ExpandUriPath = (id, path, options) => {
   const { prependBulkDataUri, expandBulkDataUri, includeSeries } = options;
-  let expandedRelative = "";
+  let expandedRelative = '';
   if (expandBulkDataUri) {
-    let expandedRelativeSeries = "";
+    let expandedRelativeSeries = '';
     if (includeSeries) {
       expandedRelativeSeries = `series/${id.seriesInstanceUid}/`;
     }
     expandedRelative = `studies/${id.studyInstanceUid}/${expandedRelativeSeries}`;
   }
   if (options.verbose)
-    console.log(
-      `Expanded path returned: ${prependBulkDataUri}${expandedRelative}${path}`,
-    );
+    console.log(`Expanded path returned: ${prependBulkDataUri}${expandedRelative}${path}`);
   return `${prependBulkDataUri}${expandedRelative}${path}`;
 };
 

package/lib/writer/HashDataWriter.js

@@ -1,27 +1,27 @@
-const hashFactory = require("node-object-hash");
-const { createHash } = require("crypto");
+const hashFactory = require('node-object-hash');
+const { createHash } = require('crypto');
 
-const path = require("path");
-const { Tags } = require("@radicalimaging/static-wado-util");
-const WriteStream = require("./WriteStream");
-const WriteMultipart = require("./WriteMultipart");
-const ExpandUriPath = require("./ExpandUriPath");
-const { MultipartHeader } = require("./MultipartHeader");
+const path = require('path');
+const { Tags } = require('@radicalimaging/static-wado-util');
+const WriteStream = require('./WriteStream');
+const WriteMultipart = require('./WriteMultipart');
+const ExpandUriPath = require('./ExpandUriPath');
+const { MultipartHeader } = require('./MultipartHeader');
 
 // Extensions for encapsulated content.  Do NOT add any executable content extensions here.
 const extensions = {
-  "application/pdf": ".pdf",
-  "text/json": ".json",
-  "application/xml+cda": ".cda.xml",
+  'application/pdf': '.pdf',
+  'text/json': '.json',
+  'application/xml+cda': '.cda.xml',
 };
 
 const baseHasher = hashFactory.hasher();
 
 const hasher = {
-  hash: (v) => {
+  hash: v => {
     const type = v.constructor?.name;
-    if (type === "Buffer") {
-      return createHash("sha256").update(v).digest("hex");
+    if (type === 'Buffer') {
+      return createHash('sha256').update(v).digest('hex');
     }
     return baseHasher.hash(v);
   },
@@ -29,7 +29,7 @@ const hasher = {
 
 /** Writes out JSON files to the given file name.  Automatically GZips them, and adds the extension */
 const HashDataWriter =
-  (options) =>
+  options =>
   async (id, key, data, additionalOptions = {}) => {
     const isRaw = ArrayBuffer.isView(data);
     const { mimeType } = additionalOptions;
@@ -45,8 +45,8 @@ const HashDataWriter =
     if (isRaw) {
       await WriteMultipart(
         writeStream,
-        [new MultipartHeader("Content-Type", "application/octet-stream")],
-        rawData,
+        [new MultipartHeader('Content-Type', 'application/octet-stream')],
+        rawData
       );
     } else {
       await writeStream.write(rawData);
@@ -61,7 +61,7 @@ const HashDataWriter =
 HashDataWriter.createHashPath = (data, options = {}) => {
   const { mimeType } = options;
   const isRaw = ArrayBuffer.isView(data);
-  const extension = isRaw ? (mimeType && extensions[mimeType]) || "" : ".json";
+  const extension = isRaw ? (mimeType && extensions[mimeType]) || '' : '.json';
   const hashValue = Tags.getValue(data, Tags.DeduppedHash) || hasher.hash(data);
 
   return {

package/lib/writer/ImageFrameWriter.js

@@ -1,10 +1,10 @@
-const uids = require("../model/uids");
-const WriteStream = require("./WriteStream");
-const WriteMultipart = require("./WriteMultipart");
-const ExpandUriPath = require("./ExpandUriPath");
-const { MultipartHeader, MultipartAttribute } = require("./MultipartHeader");
+const uids = require('../model/uids');
+const WriteStream = require('./WriteStream');
+const WriteMultipart = require('./WriteMultipart');
+const ExpandUriPath = require('./ExpandUriPath');
+const { MultipartHeader, MultipartAttribute } = require('./MultipartHeader');
 
-const ImageFrameWriter = (options) => {
+const ImageFrameWriter = options => {
   const { encapsulatedImage, singlePartImage } = options;
   return async (id, index, imageFrame) => {
     const { transferSyntaxUid } = id;
@@ -18,48 +18,35 @@ const ImageFrameWriter = (options) => {
     }
 
     if (encapsulatedImage || !extension) {
-      const writeStream = WriteStream(
-        id.imageFrameRootPath,
-        `${1 + index}.mht`,
-        {
-          gzip: type.gzip,
-          mkdir: true,
-        },
-      );
+      const writeStream = WriteStream(id.imageFrameRootPath, `${1 + index}.mht`, {
+        gzip: type.gzip,
+        mkdir: true,
+      });
       await WriteMultipart(
         writeStream,
         [
-          new MultipartHeader("Content-Type", type.contentType, [
-            new MultipartAttribute("transfer-syntax", transferSyntaxUid),
+          new MultipartHeader('Content-Type', type.contentType, [
+            new MultipartAttribute('transfer-syntax', transferSyntaxUid),
           ]),
         ],
-        content,
+        content
       );
       await writeStream.close();
       console.verbose(
-        "Wrote encapsulated image frame",
+        'Wrote encapsulated image frame',
         id.sopInstanceUid,
         index + 1,
-        type.contentType,
+        type.contentType
       );
     }
     if (extension && singlePartImage) {
-      const writeStreamSingle = WriteStream(
-        id.imageFrameRootPath,
-        `${1 + index}${extension}`,
-        {
-          gzip: type.gzip,
-          mkdir: true,
-        },
-      );
+      const writeStreamSingle = WriteStream(id.imageFrameRootPath, `${1 + index}${extension}`, {
+        gzip: type.gzip,
+        mkdir: true,
+      });
       await writeStreamSingle.write(content);
       await writeStreamSingle.close();
-      console.verbose(
-        "Wrote single part image frame",
-        id.sopInstanceUid,
-        index + 1,
-        extension,
-      );
+      console.verbose('Wrote single part image frame', id.sopInstanceUid, index + 1, extension);
     }
     const includeSeries = true;
     return ExpandUriPath(id, `instances/${id.sopInstanceUid}/frames`, {

package/lib/writer/MultipartHeader.js

@@ -1,4 +1,4 @@
-const MultipartAttribute = require("./MultipartAttribute");
+const MultipartAttribute = require('./MultipartAttribute');
 
 class MultipartHeader {
   constructor(headerName, headerValue, attributes = []) {

package/lib/writer/RawDicomWriter.js

@@ -1,17 +1,16 @@
-const { Tags } = require("@radicalimaging/static-wado-util");
-const WriteStream = require("./WriteStream");
-const WriteMultipart = require("./WriteMultipart");
-const { MultipartHeader } = require("./MultipartHeader");
+const { Tags } = require('@radicalimaging/static-wado-util');
+const WriteStream = require('./WriteStream');
+const WriteMultipart = require('./WriteMultipart');
+const { MultipartHeader } = require('./MultipartHeader');
 
-const modalitiesToRawWrite = ["SEG", "SR"];
-const sopClassesToRawWrite = ["1.2.840.10008.5.1.4.1.1.30"];
+const modalitiesToRawWrite = ['SEG', 'SR'];
+const sopClassesToRawWrite = ['1.2.840.10008.5.1.4.1.1.30'];
 
-const defaultSelector = (instance) => {
+const defaultSelector = instance => {
   const modality = instance.metadata[Tags.Modality]?.Value?.[0];
   const sopClass = instance.metadata[Tags.SOPClassUID]?.Value?.[0];
   return (
-    modalitiesToRawWrite.indexOf(modality) !== -1 ||
-    sopClassesToRawWrite.indexOf(sopClass) !== -1
+    modalitiesToRawWrite.indexOf(modality) !== -1 || sopClassesToRawWrite.indexOf(sopClass) !== -1
   );
 };
 
@@ -26,8 +25,8 @@ const RawDicomWriter =
     if (!selector(instance)) {
       return undefined;
     }
-    const contentType = options.contentType || "application/dicom";
-    const writeStream = WriteStream(id.sopInstanceRootPath, "index.mht", {
+    const contentType = options.contentType || 'application/dicom';
+    const writeStream = WriteStream(id.sopInstanceRootPath, 'index.mht', {
       gzip: options.gzip,
       mkdir: true,
     });
@@ -35,8 +34,8 @@ const RawDicomWriter =
     const buffer = content.slice(0, length);
     await WriteMultipart(
       writeStream,
-      [new MultipartHeader("Content-Type", contentType, [])],
-      buffer,
+      [new MultipartHeader('Content-Type', contentType, [])],
+      buffer
     );
     await writeStream.close();
   };

package/lib/writer/ThumbnailWriter.js

@@ -1,4 +1,4 @@
-const WriteStream = require("./WriteStream");
+const WriteStream = require('./WriteStream');
 
 const ThumbnailWriter = () => async (filePath, fileName, thumbBuffer) => {
   const writeStream = WriteStream(filePath, fileName, {
@@ -7,7 +7,7 @@ const ThumbnailWriter = () => async (filePath, fileName, thumbBuffer) => {
 
   await writeStream.write(thumbBuffer);
 
-  console.verbose("Wrote thumbnail frame", filePath, fileName);
+  console.verbose('Wrote thumbnail frame', filePath, fileName);
   return writeStream.close();
 };
 

package/lib/writer/VideoWriter.js

@@ -1,62 +1,51 @@
 /** Write raw video file */
-const { Tags } = require("@radicalimaging/static-wado-util");
-const WriteStream = require("./WriteStream");
+const { Tags } = require('@radicalimaging/static-wado-util');
+const WriteStream = require('./WriteStream');
 
-const MPEG2 = "mpg";
-const H264 = "mp4";
-const H265 = "h265";
+const MPEG2 = 'mpg';
+const H264 = 'mp4';
+const H265 = 'h265';
 
 const VIDEO_TYPES = {
-  "1.2.840.10008.1.2.4.100": MPEG2,
-  "1.2.840.10008.1.2.4.101": MPEG2,
-  "1.2.840.10008.1.2.4.102": H264,
-  "1.2.840.10008.1.2.4.103": H264,
-  "1.2.840.10008.1.2.4.104": H264,
-  "1.2.840.10008.1.2.4.105": H264,
-  "1.2.840.10008.1.2.4.106": H264,
-  "1.2.840.10008.1.2.4.107": H265,
-  "1.2.840.10008.1.2.4.108": H265,
+  '1.2.840.10008.1.2.4.100': MPEG2,
+  '1.2.840.10008.1.2.4.101': MPEG2,
+  '1.2.840.10008.1.2.4.102': H264,
+  '1.2.840.10008.1.2.4.103': H264,
+  '1.2.840.10008.1.2.4.104': H264,
+  '1.2.840.10008.1.2.4.105': H264,
+  '1.2.840.10008.1.2.4.106': H264,
+  '1.2.840.10008.1.2.4.107': H265,
+  '1.2.840.10008.1.2.4.108': H265,
   // TODO - add the new multi-segment MPEG2 and H264 variants
 };
 
-const isVideo = (value) =>
-  VIDEO_TYPES[
-    value && value.string ? value.string(Tags.RawTransferSyntaxUID) : value
-  ];
+const isVideo = value =>
+  VIDEO_TYPES[value && value.string ? value.string(Tags.RawTransferSyntaxUID) : value];
 
 const VideoWriter = () =>
   async function run(id, dataSet) {
     console.log(`Writing video  ${id.sopInstanceUid}`);
     const extension = VIDEO_TYPES[dataSet.string(Tags.RawTransferSyntaxUID)];
     const filename = `index.${extension}`;
-    const writeStream = WriteStream(
-      `${id.sopInstanceRootPath}/rendered`,
-      filename,
-      {
-        mkdir: true,
-      },
-    );
+    const writeStream = WriteStream(`${id.sopInstanceRootPath}/rendered`, filename, {
+      mkdir: true,
+    });
     let length = 0;
     const { fragments } = dataSet.elements.x7fe00010;
 
     if (!fragments) {
-      console.warn("No video data");
-      return "";
+      console.warn('No video data');
+      return '';
     }
     // The zero position fragment isn't available, even though present in the original data
     for (let i = 0; i < fragments.length; i++) {
       const fragment = fragments[i];
-      const blob = dataSet.byteArray.slice(
-        fragment.position,
-        fragment.position + fragment.length,
-      );
+      const blob = dataSet.byteArray.slice(fragment.position, fragment.position + fragment.length);
       length += blob.length;
       await writeStream.write(blob);
     }
     await writeStream.close();
-    console.log(
-      `Done video ${id.sopInstanceRootPath}\\${filename} of length ${length}`,
-    );
+    console.log(`Done video ${id.sopInstanceRootPath}\\${filename} of length ${length}`);
     return `series/${id.seriesInstanceUid}/instances/${id.sopInstanceUid}/rendered?length=${length}&offset=0&accept=video/mp4`;
   };
 

package/lib/writer/WriteMultipart.js

@@ -1,4 +1,4 @@
-const { v4: uuid } = require("uuid");
+const { v4: uuid } = require('uuid');
 
 const WriteMultipart = async (writeStream, headers, content) => {
   const boundaryId = uuid();
@@ -9,14 +9,12 @@ const WriteMultipart = async (writeStream, headers, content) => {
     if (header.attributes) {
       for (let j = 0; j < header.attributes.length; j++) {
         const attribute = header.attributes[j];
-        await writeStream.write(
-          `;${attribute.attributeName}=${attribute.attributeValue}`,
-        );
+        await writeStream.write(`;${attribute.attributeName}=${attribute.attributeValue}`);
       }
     }
-    await writeStream.write("\r\n");
+    await writeStream.write('\r\n');
   }
-  await writeStream.write("\r\n");
+  await writeStream.write('\r\n');
   await writeStream.write(content);
   await writeStream.write(`\r\n--BOUNDARY_${boundaryId}--`);
 };

package/lib/writer/WriteStream.js

@@ -1,6 +1,6 @@
-const fs = require("fs");
-const zlib = require("zlib");
-const path = require("path");
+const fs = require('fs');
+const zlib = require('zlib');
+const path = require('path');
 
 let writeCount = 0;
 
@@ -10,32 +10,26 @@ let writeCount = 0;
  * requires syncing.
  */
 const WriteStream = (dir, nameSrc, options = {}) => {
-  const isGzip = nameSrc.indexOf(".gz") != -1 || options.gzip;
-  const name =
-    (isGzip && nameSrc.indexOf(".gz") === -1 && `${nameSrc}.gz`) || nameSrc;
-  if (options.mkdir) {
+  const isGzip = nameSrc.indexOf('.gz') != -1 || options.gzip;
+  const name = (isGzip && nameSrc.indexOf('.gz') === -1 && `${nameSrc}.gz`) || nameSrc;
+  if (options.mkdir && !fs.existsSync(dir)) {
     fs.mkdirSync(dir, { recursive: true });
   }
 
-  const tempName = path.join(
-    dir,
-    `tempFile-${Math.round(Math.random() * 1000000000)}`,
-  );
+  const tempName = path.join(dir, `tempFile-${Math.round(Math.random() * 1000000000)}`);
   const finalName = path.join(dir, name);
   writeCount++;
   if (writeCount > 10) {
-    console.log("Write count", tempName, finalName, writeCount);
+    console.log('Write count', tempName, finalName, writeCount);
     if (writeCount > 100) {
-      console.error("Too many open writes", new Error());
-      throw new Error(
-        `Write count too high ${writeCount} destination ${finalName}`,
-      );
+      console.error('Too many open writes', new Error());
+      throw new Error(`Write count too high ${writeCount} destination ${finalName}`);
     }
   }
   const rawStream = fs.createWriteStream(tempName);
-  const closePromise = new Promise((resolve) => {
-    rawStream.on("close", () => {
-      resolve("closed");
+  const closePromise = new Promise(resolve => {
+    rawStream.on('close', () => {
+      resolve('closed');
     });
   });
 
@@ -43,7 +37,7 @@ const WriteStream = (dir, nameSrc, options = {}) => {
   if (isGzip) {
     writeStream = zlib.createGzip();
     writeStream.pipe(rawStream);
-    writeStream.on("close", () => {
+    writeStream.on('close', () => {
       rawStream.close();
     });
   }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@radicalimaging/static-wado-creator",
-  "version": "1.6.10",
+  "version": "1.6.11",
   "description": "Library to convert DICOMP10 to DICOMweb format. Original upstream: https://github.com/chafey/dicomp10-to-dicomweb-js",
   "publishConfig": {
     "access": "public"

package/lib/writer/static-dicomweb.code-workspace

@@ -1,8 +0,0 @@
-{
-	"folders": [
-		{
-			"path": "../../../.."
-		}
-	],
-	"settings": {}
-}