@radicalimaging/static-wado-creator 1.6.10 → 1.6.12

package/lib/mkdicomwebConfig.js

@@ -1,16 +1,16 @@
-const ConfigPoint = require("config-point");
-const { staticWadoConfig } = require("@radicalimaging/static-wado-util");
-const createMain = require("./createMain");
-const createPart10 = require("./createPart10");
-const createThumbnail = require("./createThumbnail");
-const deleteMain = require("./deleteMain");
-const rejectMain = require("./rejectMain");
-const serverMain = require("./serverMain");
-const instanceMain = require("./instanceMain");
-const indexMain = require("./indexMain");
-const groupMain = require("./groupMain");
-const metadataMain = require("./metadataMain");
-const compressionOptionParser = require("./util/compressionOptionParser");
+const ConfigPoint = require('config-point');
+const { staticWadoConfig } = require('@radicalimaging/static-wado-util');
+const createMain = require('./createMain');
+const createPart10 = require('./createPart10');
+const createThumbnail = require('./createThumbnail');
+const deleteMain = require('./deleteMain');
+const rejectMain = require('./rejectMain');
+const serverMain = require('./serverMain');
+const instanceMain = require('./instanceMain');
+const indexMain = require('./indexMain');
+const groupMain = require('./groupMain');
+const metadataMain = require('./metadataMain');
+const compressionOptionParser = require('./util/compressionOptionParser');
 
 /**
  * Defines the basic configuration values for the dicomwebserver component.  See the README for more details.
@@ -24,318 +24,310 @@ const { mkdicomwebConfig } = ConfigPoint.register({
     isGroup: true,
     options: [
       {
-        key: "-c <configFile.json5>",
-        description: "Use an alternate configuration file",
-        defaultValue: "~/static-wado.json5",
+        key: '-c <configFile.json5>',
+        description: 'Use an alternate configuration file',
+        defaultValue: '~/static-wado.json5',
       },
       {
-        key: "--clean",
-        description:
-          "Clean the outputs before generating/starting to write new values.",
+        key: '--clean',
+        description: 'Clean the outputs before generating/starting to write new values.',
         defaultValue: false,
       },
       {
-        key: "-d, --deployments <listvalue...>",
-        description:
-          "List of deployments from configuration to deploy to. Separated by space.",
+        key: '-d, --deployments <listvalue...>',
+        description: 'List of deployments from configuration to deploy to. Separated by space.',
         defaultValue: undefined,
       },
       {
-        key: "--no-notifications",
-        description: "Turns off notifications",
+        key: '--no-notifications',
+        description: 'Turns off notifications',
       },
       {
-        key: "--delete",
-        description: "Delete the imported instances",
+        key: '--delete',
+        description: 'Delete the imported instances',
         defaultValue: false,
       },
       {
-        key: "--lossy",
-        description: "Generate lossy instances instead of lossless",
+        key: '--lossy',
+        description: 'Generate lossy instances instead of lossless',
         defaultValue: false,
       },
       {
-        key: "--alternate <type>",
+        key: '--alternate <type>',
         description:
-          "Generates an alternate representaton of the image generally in the /lossy sub-directory",
-        choices: ["jhc", "jls", "jhcLossless", "jlsLossless"],
+          'Generates an alternate representaton of the image generally in the /lossy sub-directory',
+        choices: ['jhc', 'jls', 'jhcLossless', 'jlsLossless'],
       },
       {
-        key: "--alternate-thumbnail",
-        description: "Generates a thumbnail for the alternate representation",
+        key: '--alternate-thumbnail',
+        description: 'Generates a thumbnail for the alternate representation',
       },
       {
-        key: "--alternate-name <dir>",
-        description: "Uses a given sub directory name",
-        defaultValue: "lossy",
+        key: '--alternate-name <dir>',
+        description: 'Uses a given sub directory name',
+        defaultValue: 'lossy',
       },
       {
-        key: "-v, --verbose",
-        description: "Write verbose output",
+        key: '-v, --verbose',
+        description: 'Write verbose output',
         defaultValue: false,
       },
       {
-        key: "--show-progress",
-        description: "Show progress during DICOM file processing",
+        key: '--show-progress',
+        description: 'Show progress during DICOM file processing',
       },
       {
-        key: "-t, --content-type <type>",
+        key: '-t, --content-type <type>',
         description:
           'Destination type to compress to (choices: "jpeg", "jls", "lei", "jls-lossy", "jhc", "jxl" or DICOM Transfer Syntax UID - default: "jls")',
-        defaultValue: "jls",
+        defaultValue: 'jls',
         customParser: compressionOptionParser,
       },
       {
-        key: "--encapsulated-image",
+        key: '--encapsulated-image',
         description:
-          "Avoid encapsulating the image frame.  Writes with the extension and without multipart",
+          'Avoid encapsulating the image frame.  Writes with the extension and without multipart',
       },
       {
-        key: "-e, --no-encapsulated-image",
+        key: '-e, --no-encapsulated-image',
         description:
-          "Avoid encapsulating the image frame.  Writes with the extension and without multipart",
+          'Avoid encapsulating the image frame.  Writes with the extension and without multipart',
       },
       {
-        key: "--single-part-image",
-        description: "Writes single part image data",
+        key: '--single-part-image',
+        description: 'Writes single part image data',
       },
       {
-        key: "--no-single-part-image",
-        description: "Writes single part image data",
+        key: '--no-single-part-image',
+        description: 'Writes single part image data',
       },
       {
-        key: "-m, --maximum-inline-public-length <value>",
-        description: "Maximum length of public binary data",
+        key: '-m, --maximum-inline-public-length <value>',
+        description: 'Maximum length of public binary data',
         defaultValue: 128 * 1024 + 2,
       },
       {
-        key: "-M, --maximum-inline-private-length <value>",
-        description: "Maximum length of private binary data",
+        key: '-M, --maximum-inline-private-length <value>',
+        description: 'Maximum length of private binary data',
         defaultValue: 64,
       },
       {
-        key: "-r, --recompress <listvalue...>",
-        description: "List of types to recompress separated by space",
-        defaultValue: ["uncompressed", "jp2", "jls", "jll"],
+        key: '-r, --recompress <listvalue...>',
+        description: 'List of types to recompress separated by space',
+        defaultValue: ['uncompressed', 'jp2', 'jls', 'jll'],
         choices: [
-          "uncompressed",
-          "jp2",
-          "jpeg",
-          "jpeglossless",
-          "rle",
-          "jph",
-          "jls",
-          "true",
-          "none",
+          'uncompressed',
+          'jp2',
+          'jpeg',
+          'jpeglossless',
+          'rle',
+          'jph',
+          'jls',
+          'true',
+          'none',
         ],
       },
       {
-        key: "--recompress-color <listvalue...>",
-        description:
-          "List of types to recompress for color images, separated by space",
-        defaultValue: ["uncompressed"],
+        key: '--recompress-color <listvalue...>',
+        description: 'List of types to recompress for color images, separated by space',
+        defaultValue: ['uncompressed'],
         choices: [
-          "uncompressed",
-          "jpeg",
-          "jp2",
-          "jpeglossless",
-          "rle",
-          "jph",
-          "jls",
-          "true",
-          "none",
+          'uncompressed',
+          'jpeg',
+          'jp2',
+          'jpeglossless',
+          'rle',
+          'jph',
+          'jls',
+          'true',
+          'none',
         ],
       },
       {
-        key: "-f, --force",
-        description: "Force the update even if the SOP exists",
+        key: '-f, --force',
+        description: 'Force the update even if the SOP exists',
         defaultValue: false,
       },
       {
-        key: "--delete-input",
-        description: "Deletes successful input files",
+        key: '--delete-input',
+        description: 'Deletes successful input files',
         defaultValue: false,
       },
       {
-        key: "--delete-failed",
-        description: "Deletes unsuccessful input files",
+        key: '--delete-failed',
+        description: 'Deletes unsuccessful input files',
         defaultValue: false,
       },
       {
-        key: "--recompress-thumb <listvalue...>",
-        description: "List of types to recompress thumb separated by space",
-        defaultValue: ["uncompressed", "jp2"],
-        choices: ["uncompressed", "jp2", "jpeglossless", "rle", "none"],
+        key: '--recompress-thumb <listvalue...>',
+        description: 'List of types to recompress thumb separated by space',
+        defaultValue: ['uncompressed', 'jp2'],
+        choices: ['uncompressed', 'jp2', 'jpeglossless', 'rle', 'none'],
       },
       {
-        key: "--no-recompress",
-        description: "Force no recompression",
+        key: '--no-recompress',
+        description: 'Force no recompression',
         defaultValue: false,
       },
       {
-        key: "--no-recompress-thumb",
-        description: "Force no recompression thumbnail",
+        key: '--no-recompress-thumb',
+        description: 'Force no recompression thumbnail',
         defaultValue: false,
       },
       {
-        key: "--no-thumb",
-        description: "Skip generating thumbnails using CS3D internal render",
+        key: '--no-thumb',
+        description: 'Skip generating thumbnails using CS3D internal render',
         defaultValue: true,
       },
       {
-        key: "--dcm2jpg",
-        description: "Use dcm2jpg for thumbnail image generation",
+        key: '--dcm2jpg',
+        description: 'Use dcm2jpg for thumbnail image generation',
         defaultValue: false,
       },
       {
-        key: "--rendered",
-        description: "Use dcm2jpg to generate a rendered PNG image",
+        key: '--rendered',
+        description: 'Use dcm2jpg to generate a rendered PNG image',
         defaultValue: false,
       },
       {
-        key: "-T, --color-content-type <value>",
-        description: "Colour content type",
-        defaultValue: "jpeg",
+        key: '-T, --color-content-type <value>',
+        description: 'Colour content type',
+        defaultValue: 'jpeg',
       },
       {
-        key: "--path-deduplicated <path>",
-        description:
-          "Set the deduplicate data directory path (relative to dir)",
-        defaultValue: "deduplicated",
+        key: '--path-deduplicated <path>',
+        description: 'Set the deduplicate data directory path (relative to dir)',
+        defaultValue: 'deduplicated',
       },
       {
-        key: "--path-instances <path>",
-        description: "Set the instances directory path (relative to dir)",
-        defaultValue: "instances",
+        key: '--path-instances <path>',
+        description: 'Set the instances directory path (relative to dir)',
+        defaultValue: 'instances',
       },
       {
-        key: "--store-multipart-bulk-data",
-        description: "Use multipart encoding for non image frame bulkdata",
+        key: '--store-multipart-bulk-data',
+        description: 'Use multipart encoding for non image frame bulkdata',
         defaultValue: false,
       },
       {
-        key: "--prepend-bulk-data-uri <value>",
+        key: '--prepend-bulk-data-uri <value>',
         description:
-          "Prepend bulkdata uri (ex. to use absolute Uri like http://host:3000/dicomweb)",
-        defaultValue: "",
+          'Prepend bulkdata uri (ex. to use absolute Uri like http://host:3000/dicomweb)',
+        defaultValue: '',
       },
       {
-        key: "--expand-bulk-data-uri",
+        key: '--expand-bulk-data-uri',
         description:
-          "expand bulkdata relative uri to use full relative path (should also be set when using --prepend-bulk-data-uri)",
+          'expand bulkdata relative uri to use full relative path (should also be set when using --prepend-bulk-data-uri)',
         defaultValue: false,
       },
       {
-        key: "--quiet",
-        description: "Run quietly, minimizing extraneous output",
+        key: '--quiet',
+        description: 'Run quietly, minimizing extraneous output',
         defaultValue: false,
       },
       {
-        key: "--multipart",
-        description: "Add a multipart result output",
+        key: '--multipart',
+        description: 'Add a multipart result output',
         defaultValue: false,
       },
       {
-        key: "--no-verify",
-        description: "Verify",
+        key: '--no-verify',
+        description: 'Verify',
         defaultValue: true,
       },
       {
-        key: "-o, --dir <value>",
-        description: "Set output directory",
+        key: '-o, --dir <value>',
+        description: 'Set output directory',
         defaultValue: {
-          configOperation: "reference",
-          source: "staticWadoConfig",
-          reference: "rootDir",
+          configOperation: 'reference',
+          source: 'staticWadoConfig',
+          reference: 'rootDir',
         },
       },
       {
-        key: "--sop-instance-uid <value>",
-        description:
-          "Choose sop instances to run against (only for instance runs)",
+        key: '--sop-instance-uid <value>',
+        description: 'Choose sop instances to run against (only for instance runs)',
       },
       {
-        key: "--series-instance-uid <value>",
-        description:
-          "Choose series instances to run against (only for instance runs)",
+        key: '--series-instance-uid <value>',
+        description: 'Choose series instances to run against (only for instance runs)',
       },
 
       {
-        key: "--hash-study-uid-path",
-        description: "Enable hashing of studyUID folder structure",
+        key: '--hash-study-uid-path',
+        description: 'Enable hashing of studyUID folder structure',
         defaultValue: false,
       },
     ],
     programs: [
       {
-        command: "create",
+        command: 'create',
         isDefault: true,
-        arguments: ["input"],
+        arguments: ['input'],
         main: createMain,
         helpDescription:
-          "Make DICOMweb query and metadata from binary Part 10 DICOM files.  Does a full read\n" +
-          "of deduplicated files each time a study instance UID is found, and only updates\n" +
-          "those studies having at least one ",
+          'Make DICOMweb query and metadata from binary Part 10 DICOM files.  Does a full read\n' +
+          'of deduplicated files each time a study instance UID is found, and only updates\n' +
+          'those studies having at least one ',
       },
       {
-        command: "server",
+        command: 'server',
         main: serverMain,
-        helpDescription:
-          "Run server deploy instances single threaded/separated exec process",
+        helpDescription: 'Run server deploy instances single threaded/separated exec process',
       },
       {
-        command: "part10",
-        arguments: ["studyUID"],
+        command: 'part10',
+        arguments: ['studyUID'],
         main: createPart10,
-        helpDescription: "Store the specified study as part 10 data",
+        helpDescription: 'Store the specified study as part 10 data',
       },
       {
-        command: "index",
+        command: 'index',
         main: indexMain,
-        helpDescription: "Recreate the index for the DICOMweb data.",
+        helpDescription: 'Recreate the index for the DICOMweb data.',
       },
       {
-        command: "thumbnail",
+        command: 'thumbnail',
         main: createThumbnail,
-        helpDescription: "Create a thumbnail for the specified image",
+        helpDescription: 'Create a thumbnail for the specified image',
         options: [
           {
-            key: "--series-thumbnail",
-            description: "Generate a series thumbnail instead of instance",
+            key: '--series-thumbnail',
+            description: 'Generate a series thumbnail instead of instance',
           },
         ],
       },
       {
-        command: "instance",
-        arguments: ["input"],
+        command: 'instance',
+        arguments: ['input'],
         main: instanceMain,
         helpDescription:
           "Make instance level DICOMweb metadata and bulkdata, but don't group or write series metadata",
       },
       {
-        command: "group",
-        arguments: ["input"],
+        command: 'group',
+        arguments: ['input'],
         main: groupMain,
         helpDescription:
-          "Group instance level metadata into deduplicated data.\nDeletes instance level deduplicated information once it is confirmed written.",
+          'Group instance level metadata into deduplicated data.\nDeletes instance level deduplicated information once it is confirmed written.',
       },
       {
-        command: "metadata",
-        arguments: ["input"],
+        command: 'metadata',
+        arguments: ['input'],
         main: metadataMain,
         helpDescription:
-          "Write the metadata object (series and study details) from the grouped deduplicated data.",
+          'Write the metadata object (series and study details) from the grouped deduplicated data.',
       },
       {
-        command: "delete",
+        command: 'delete',
         main: deleteMain,
-        helpDescription:
-          "Delete the given study, series or instance (not yet implemented)",
+        helpDescription: 'Delete the given study, series or instance (not yet implemented)',
       },
       {
-        command: "reject <studyUID...>",
+        command: 'reject <studyUID...>',
         main: rejectMain,
-        helpDescription: "Reject the specified series",
+        helpDescription: 'Reject the specified series',
       },
     ],
   },

package/lib/model/TagLists.js

@@ -1,25 +1,13 @@
-const hashFactory = require("node-object-hash");
-const { Tags } = require("@radicalimaging/static-wado-util");
+const hashFactory = require('node-object-hash');
+const { Tags } = require('@radicalimaging/static-wado-util');
 
 /* eslint "no-param-reassign": "off" */
 
 const hasher = hashFactory.hasher();
 
 const { PatientID, PatientName, IssuerOfPatientID } = Tags;
-const {
-  StudyDescription,
-  AccessionNumber,
-  StudyInstanceUID,
-  StudyDate,
-  StudyTime,
-} = Tags;
-const {
-  SeriesDescription,
-  SeriesNumber,
-  SeriesInstanceUID,
-  SeriesDate,
-  SeriesTime,
-} = Tags;
+const { StudyDescription, AccessionNumber, StudyInstanceUID, StudyDate, StudyTime } = Tags;
+const { SeriesDescription, SeriesNumber, SeriesInstanceUID, SeriesDate, SeriesTime } = Tags;
 
 const { DeduppedHash, DeduppedRef, DeduppedType } = Tags;
 
@@ -153,7 +141,7 @@ const TagSets = {
   extract: (data, type, tagSet, options) => {
     const ret = {};
     const { remove, hashRef } = options || {};
-    tagSet.forEach((tag) => {
+    tagSet.forEach(tag => {
       const value = data[tag];
       if (value) {
         ret[tag] = value;

package/lib/model/uids.js

@@ -1,4 +1,4 @@
-const octetStream = "application/octet-stream";
+const octetStream = 'application/octet-stream';
 const uncompressed = {
   uncompressed: true,
   gzip: true,
@@ -8,41 +8,41 @@ const uncompressed = {
 /**
  * @see {@link https://dicom.nema.org/medical/dicom/current/output/chtml/part18/sect_8.7.3.3.2.html}
  */
-const jpeg = "image/jpeg";
-const jls = "image/jls";
-const jll = "image/jll";
-const jxl = "image/x-jxl";
-const htj2k = "image/jphc";
-const jp2 = "image/jp2";
-const rle = "image/dicom-rle";
+const jpeg = 'image/jpeg';
+const jls = 'image/jls';
+const jll = 'image/jll';
+const jxl = 'image/x-jxl';
+const htj2k = 'image/jphc';
+const jp2 = 'image/jp2';
+const rle = 'image/dicom-rle';
 
 const uids = {
-  "1.2.840.10008.1.2": uncompressed,
-  "1.2.840.10008.1.2.1": uncompressed,
-  "1.2.840.10008.1.2.1.99": uncompressed,
-  "1.2.840.10008.1.2.2": uncompressed,
-  "1.2.840.10008.1.2.4.50": {
+  '1.2.840.10008.1.2': uncompressed,
+  '1.2.840.10008.1.2.1': uncompressed,
+  '1.2.840.10008.1.2.1.99': uncompressed,
+  '1.2.840.10008.1.2.2': uncompressed,
+  '1.2.840.10008.1.2.4.50': {
     contentType: jpeg,
     lossy: true,
-    extension: ".jpeg",
+    extension: '.jpeg',
   },
-  "1.2.840.10008.1.2.4.51": { contentType: jpeg, lossy: true },
-  "1.2.840.10008.1.2.4.57": { contentType: jpeg },
-  "1.2.840.10008.1.2.4.70": { contentType: jll, extension: ".jll" },
-  "1.2.840.10008.1.2.4.140": { contentType: jxl, extension: ".jxl" },
+  '1.2.840.10008.1.2.4.51': { contentType: jpeg, lossy: true },
+  '1.2.840.10008.1.2.4.57': { contentType: jpeg },
+  '1.2.840.10008.1.2.4.70': { contentType: jll, extension: '.jll' },
+  '1.2.840.10008.1.2.4.140': { contentType: jxl, extension: '.jxl' },
   // Lossy, original JPEG reconstruction mode
-  "1.2.840.10008.1.2.4.141": { contentType: jxl, lossy: true },
-  "1.2.840.10008.1.2.4.142": { contentType: jxl, lossy: true },
-  "1.2.840.10008.1.2.4.80": { contentType: jls, extension: ".jls" },
-  "1.2.840.10008.1.2.4.81": { contentType: jls, lossy: true },
-  "1.2.840.10008.1.2.4.90": { contentType: jp2, extension: ".jp2" },
-  "1.2.840.10008.1.2.4.91": { contentType: jp2 },
+  '1.2.840.10008.1.2.4.141': { contentType: jxl, lossy: true },
+  '1.2.840.10008.1.2.4.142': { contentType: jxl, lossy: true },
+  '1.2.840.10008.1.2.4.80': { contentType: jls, extension: '.jls' },
+  '1.2.840.10008.1.2.4.81': { contentType: jls, lossy: true },
+  '1.2.840.10008.1.2.4.90': { contentType: jp2, extension: '.jp2' },
+  '1.2.840.10008.1.2.4.91': { contentType: jp2 },
   // Private/test transfer syntax for HTJ2K
-  "3.2.840.10008.1.2.4.96": { contentType: htj2k },
-  "1.2.840.10008.1.2.4.201": { contentType: htj2k },
-  "1.2.840.10008.1.2.4.202": { contentType: htj2k, extension: ".jhc" },
-  "1.2.840.10008.1.2.4.203": { contentType: htj2k, lossy: true },
-  "1.2.840.10008.1.2.5": { contentType: rle },
+  '3.2.840.10008.1.2.4.96': { contentType: htj2k },
+  '1.2.840.10008.1.2.4.201': { contentType: htj2k },
+  '1.2.840.10008.1.2.4.202': { contentType: htj2k, extension: '.jhc' },
+  '1.2.840.10008.1.2.4.203': { contentType: htj2k, lossy: true },
+  '1.2.840.10008.1.2.5': { contentType: rle },
   default: {},
 };