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feat(WADO) Allow WADO / QIDO requests to originate from client (#222)

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This commit is contained in:
Erik Ziegler 2018-07-17 13:03:36 +02:00 committed by GitHub
parent 92408d4c86
commit ebe0a40f3e
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
43 changed files with 519 additions and 571 deletions
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1
OHIFViewer/.meteor/packages
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@ -39,6 +39,7 @@ ohif:cornerstone-settings
ohif:viewerbase
ohif:study-list
ohif:dicom-services
ohif:dicomweb-client
ohif:hanging-protocols
ohif:metadata

1
OHIFViewer/.meteor/versions
View File

@ -86,6 +86,7 @@ ohif:cornerstone@0.0.1
ohif:cornerstone-settings@0.0.1
ohif:design@0.0.1
ohif:dicom-services@0.0.1
ohif:dicomweb-client@0.0.1
ohif:hanging-protocols@0.0.1
ohif:header@0.0.1
ohif:hotkeys@0.0.1

5
OHIFViewer/client/components/viewer/viewer.js
View File

@ -120,7 +120,7 @@ Template.viewer.onCreated(() => {
const studyMetadata = new OHIF.metadata.StudyMetadata(study, study.studyInstanceUid);
let displaySets = study.displaySets;
if(!study.displaySets) {
if (!study.displaySets) {
displaySets = OHIF.viewerbase.sortingManager.getDisplaySets(studyMetadata);
study.displaySets = displaySets;
}
@ -131,6 +131,9 @@ Template.viewer.onCreated(() => {
OHIF.viewer.Studies.insert(study);
OHIF.viewer.StudyMetadataList.insert(studyMetadata);
OHIF.viewer.data.studyInstanceUids.push(study.studyInstanceUid);
// Updates WADO-RS metaDataManager
OHIF.viewerbase.updateMetaDataManager(study);
});
});

8
OHIFViewer/client/routes.js
View File

@ -3,7 +3,13 @@ import { OHIF } from 'meteor/ohif:core';
Router.configure({
layoutTemplate: 'layout',
loadingTemplate: 'layout'
});
Router.waitOn(function() {
return [
Meteor.subscribe('servers'),
Meteor.subscribe('currentServer')
];
});
Router.onBeforeAction('loading');

14
Packages/ohif-dicom-services/package.js
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@ -1,6 +1,6 @@
Package.describe({
name: 'ohif:dicom-services',
summary: 'DICOM Services: DICOMWeb and DIMSE C-Service functions',
summary: 'DICOM Services: DIMSE C-Service functions',
version: '0.0.1'
});
@ -10,18 +10,6 @@ Package.onUse(function(api) {
api.use('http');
api.use('ecmascript');
// DICOMWeb functions
api.addFiles('server/DICOMWeb/namespace.js', 'server');
api.addFiles('server/DICOMWeb/getJSON.js', 'server');
api.addFiles('server/DICOMWeb/getName.js', 'server');
api.addFiles('server/DICOMWeb/getNumber.js', 'server');
api.addFiles('server/DICOMWeb/getString.js', 'server');
api.addFiles('server/DICOMWeb/getModalities.js', 'server');
api.addFiles('server/DICOMWeb/getAttribute.js', 'server');
api.addFiles('server/DICOMWeb/getBulkData.js', 'server');
api.export('DICOMWeb', 'server');
// DIMSE functions
api.addFiles('server/DIMSE/require.js', 'server');
api.addFiles('server/DIMSE/constants.js', 'server');

230
Packages/ohif-dicom-services/server/DICOMWeb/getBulkData.js
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@ -1,230 +0,0 @@
import { OHIF } from 'meteor/ohif:core';
const ASCII = 'ascii';
const http = Npm.require('http')
const url = Npm.require('url');
function getMultipartContentInfo(headers) {
let dict = null,
multipartRegex = /^\s*multipart\/[^;]+/g,
contentType = headers['content-type'];
if (typeof contentType === 'string' && multipartRegex.test(contentType)) {
let match,
pairRegex = /;\s*([^=]+)=([^;\r\n]+)/g;
pairRegex.lastIndex = multipartRegex.lastIndex;
while ((match = pairRegex.exec(contentType)) !== null) {
let key = match[1], value = match[2];
if (dict === null) {
dict = {};
}
dict[key] = value;
}
}
return dict;
}
function parseContentHeader(data, offset) {
let endOfHeader = data.indexOf('\r\n\r\n', offset, ASCII);
if (endOfHeader < 0 || endOfHeader <= offset || endOfHeader > data.length) {
throw {
name: 'DICOMWebContentParsingError',
message: 'End of content header cannot be determined...'
};
}
let match,
header = {
start: offset,
end: endOfHeader + 4,
fields: {}
},
headerRegex = /([\w\-]+):\s*([^\r\n]+)(?:\r\n)?/g,
headerContentRegex = /\t([^\r\n]+)(?:\r\n)?/g,
headerString = data.toString('ascii', offset, endOfHeader);
while ((match = headerRegex.exec(headerString)) !== null) {
let key = match[1].toLowerCase(), value = match[2];
while (headerString.charAt(headerRegex.lastIndex) === '\t') {
headerContentRegex.lastIndex = headerRegex.lastIndex;
if ((match = headerContentRegex.exec(headerString)) !== null) {
headerRegex.lastIndex = headerContentRegex.lastIndex;
value += ' ' + match[1];
continue;
}
break;
}
header.fields[key] = value;
}
return header;
}
function parseResponse(headers, data) {
let contentInfo = getMultipartContentInfo(headers);
if (!contentInfo || !contentInfo.boundary) {
throw {
name: 'DICOMWebContentParsingError',
message: 'Content boundary not specified...'
};
}
let boundary = contentInfo.boundary,
delimiter = '--' + boundary + '\r\n',
index = data.indexOf(delimiter, 0, ASCII);
if (index < 0) {
throw {
name: 'DICOMWebContentParsingError',
message: 'The specified boundary could not be found...'
};
}
let closingIndex, closingDelimiter = Buffer.from('\r\n--' + boundary + '--', ASCII);
index += delimiter.length;
if (data[index] !== 0x0D || data[index + 1] !== 0x0A) {
// multipart content headers are present, so let's parse them...
let contentHeader = parseContentHeader(data, index);
if (contentHeader && contentHeader.end > index) {
if (contentHeader.fields['content-length'] > 0) {
let endOfData = contentHeader.end + parseInt(contentHeader.fields['content-length'], 10);
if (endOfData === data.indexOf(closingDelimiter, endOfData)) {
// content-length is valid...
return data.slice(contentHeader.end, endOfData);
}
}
index = contentHeader.end;
}
} else {
// no headers, the content comes right after...
index += 2;
}
closingIndex = data.indexOf(closingDelimiter, index);
if (closingIndex < 0 || closingIndex < index) {
throw {
name: 'DICOMWebContentParsingError',
message: 'The end of the content could not be determined...'
};
}
return data.slice(index, closingIndex);
}
function makeRequest(geturl, options, callback) {
const headers = 'multipart/related; type=application/octet-stream';
const parsed = url.parse(geturl);
let requestOpt = {
hostname: parsed.hostname,
headers: {
Accept: headers
},
path: parsed.path,
method: 'GET',
};
let requester;
if (parsed.protocol === 'https:') {
requester = https.request;
const allowUnauthorizedAgent = new https.Agent({ rejectUnauthorized: false });
requestOpt.agent = allowUnauthorizedAgent
} else {
requester = http.request;
}
if (parsed.port) {
requestOpt.port = parsed.port;
}
if (options.auth) {
requestOpt.auth = options.auth;
}
let req = requester(requestOpt, function(resp) {
let data = [];
if (resp.statusCode !== 200) {
callback({
name: 'DICOMWebRequestError',
message: `Unexpected status code for DICOMWeb response (${resp.statusCode})...`
}, null);
}
resp.on('data', function(chunk) {
data.push(chunk);
});
resp.on('error', function (responseError) {
OHIF.log.error('There was an error in the DICOMWeb Server');
OHIF.log.error(responseError.stack);
OHIF.log.trace();
callback(responseError, null);
});
resp.on('end', function() {
try {
callback(null, parseResponse(resp.headers, Buffer.concat(data)));
} catch (error) {
callback(error, null);
}
});
});
req.on('error', function (requestError) {
OHIF.log.error('Couldn\'t connect to DICOMWeb server.');
OHIF.log.error('Make sure you are trying to connect to the right server and that it is up and running.');
OHIF.log.error(requestError.stack);
OHIF.log.trace();
callback(requestError, null);
});
req.end();
}
const makeRequestSync = Meteor.wrapAsync(makeRequest);
// TODO: Unify this stuff with the getJSON code
DICOMWeb.getBulkData = function(geturl, options) {
if (options && options.logRequests) {
OHIF.log.info(geturl);
}
if (options && options.logTiming) {
console.time(geturl);
}
var result = makeRequestSync(geturl, options);
if (options && options.logTiming) {
console.timeEnd(geturl);
}
if (options && options.logResponses) {
OHIF.log.info(result);
}
if (!Buffer.isBuffer(result)) {
throw result;
}
return result;
};

110
Packages/ohif-dicom-services/server/DICOMWeb/getJSON.js
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@ -1,110 +0,0 @@
import { Meteor } from 'meteor/meteor';
import { OHIF } from 'meteor/ohif:core';
const http = Npm.require('http');
const https = Npm.require('https');
const url = Npm.require('url');
function makeRequest(geturl, options, callback) {
const parsed = url.parse(geturl);
const jsonHeaders = ['application/json', 'application/dicom+json'];
let requestOpt = {
hostname: parsed.hostname,
headers: {
Accept: 'application/json'
},
path: parsed.path,
method: 'GET'
};
let requester;
if (parsed.protocol === 'https:') {
requester = https.request;
const allowUnauthorizedAgent = new https.Agent({ rejectUnauthorized: false });
requestOpt.agent = allowUnauthorizedAgent;
} else {
requester = http.request;
}
if (parsed.port) {
requestOpt.port = parsed.port;
}
if (options.auth) {
requestOpt.auth = options.auth;
}
if (options.headers) {
Object.keys(options.headers).forEach(key => {
const value = options.headers[key];
requestOpt.headers[key] = value;
});
}
const req = requester(requestOpt, function(resp) {
// TODO: handle errors with 400+ code
const contentType = (resp.headers['content-type'] || '').split(';')[0];
if (jsonHeaders.indexOf(contentType) === -1) {
const errorMessage = `We only support json but "${contentType}" was sent by the server`;
callback(new Error(errorMessage), null);
return;
}
let output = '';
resp.setEncoding('utf8');
resp.on('data', function(chunk){
output += chunk;
});
resp.on('error', function (responseError) {
OHIF.log.error('There was an error in the DICOMWeb Server')
OHIF.log.error(error.stack);
OHIF.log.trace();
callback(new Meteor.Error('server-internal-error', responseError.message), null);
});
resp.on('end', function(){
callback(null, { data: JSON.parse(output) });
});
});
req.on('error', function (requestError) {
OHIF.log.error('Couldn\'t connect to DICOMWeb server.');
OHIF.log.error('Make sure you are trying to connect to the right server and that it is up and running.');
OHIF.log.error(requestError.stack);
OHIF.log.trace();
callback(new Meteor.Error('server-connection-error', requestError.message), null);
});
req.end();
}
const makeRequestSync = Meteor.wrapAsync(makeRequest);
DICOMWeb.getJSON = function(geturl, options) {
if (options && options.logRequests) {
OHIF.log.info(geturl);
}
if (options && options.logTiming) {
console.time(geturl);
}
const result = makeRequestSync(geturl, options);
if (options && options.logTiming) {
console.timeEnd(geturl);
}
if (options && options.logResponses) {
OHIF.log.info(result);
}
return result;
};

1
Packages/ohif-dicom-services/server/DICOMWeb/namespace.js
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@ -1 +0,0 @@
DICOMWeb = {};

21
Packages/ohif-dicomweb-client/package.js Normal file
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@ -0,0 +1,21 @@
Package.describe({
name: 'ohif:dicomweb-client',
summary: 'DICOM Services: DICOMWeb',
version: '0.0.1'
});
Npm.depends({
'url-parse': '1.4.1',
'isomorphic-fetch': '2.2.1',
});
Package.onUse(function(api) {
api.versionsFrom('1.6');
api.use('ecmascript');
// DICOMWeb functions
api.mainModule('src/index.js');
api.export('DICOMWeb');
});

33
Packages/ohif-dicomweb-client/src/get.js Normal file
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@ -0,0 +1,33 @@
import makeRequest from "./makeRequest";
/**
* Make a request to the URL given a set of options.
* This function will add optional timing, request, and respone logging.
*
* @param {String} url
* @param {Object} options
* @return {Promise<*>}
*/
const get = async function get(url, options) {
if (options.logRequests) {
console.log(url);
}
if (options.logTiming) {
console.time(url);
}
const result = await makeRequest(url, options);
if (options.logTiming) {
console.timeEnd(url);
}
if (options.logResponses) {
console.info(result);
}
return result;
}
export default get;

4
Packages/ohif-dicom-services/server/DICOMWeb/getAttribute.js → Packages/ohif-dicomweb-client/src/getAttribute.js
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@ -5,7 +5,7 @@
* @param [defaultValue] - The value to return if the element is not present
* @returns {*}
*/
DICOMWeb.getAttribute = function(element, defaultValue) {
const getAttribute = function(element, defaultValue) {
if (!element) {
return defaultValue;
}
@ -42,3 +42,5 @@ function convertToInt(input) {
return parseInt(output, 16);
}
export default getAttribute;

133
Packages/ohif-dicomweb-client/src/getBulkData.js Normal file
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@ -0,0 +1,133 @@
import get from './get.js';
const ASCII = 'ascii';
function getMultipartContentInfo(headers) {
const multipartRegex = /^\s*multipart\/[^;]+/g;
const contentType = headers.get('content-type');
let dict = null;
if (typeof contentType === 'string' && multipartRegex.test(contentType)) {
let match;
let pairRegex = /;\s*([^=]+)=([^;\r\n]+)/g;
pairRegex.lastIndex = multipartRegex.lastIndex;
while ((match = pairRegex.exec(contentType)) !== null) {
let key = match[1]
let value = match[2];
if (dict === null) {
dict = {};
}
dict[key] = value;
}
}
return dict;
}
function parseContentHeader(data, offset) {
const endOfHeader = data.indexOf('\r\n\r\n', offset);
if (endOfHeader < 0 || endOfHeader <= offset || endOfHeader > data.length) {
throw new Error('End of content header cannot be determined...');
}
const header = {
start: offset,
end: endOfHeader + 4,
fields: {}
};
const headerRegex = /([\w\-]+):\s*([^\r\n]+)(?:\r\n)?/g;
const headerContentRegex = /\t([^\r\n]+)(?:\r\n)?/g;
const headerString = data.slice(offset, endOfHeader);
let match;
while ((match = headerRegex.exec(headerString)) !== null) {
const key = match[1].toLowerCase(), value = match[2];
while (headerString.charAt(headerRegex.lastIndex) === '\t') {
headerContentRegex.lastIndex = headerRegex.lastIndex;
if ((match = headerContentRegex.exec(headerString)) !== null) {
headerRegex.lastIndex = headerContentRegex.lastIndex;
value += ' ' + match[1];
continue;
}
break;
}
header.fields[key] = value;
}
return header;
}
function toBytes(input) {
const data = [];
for (let i = 0; i < input.length; i++){
data.push(input.charCodeAt(i));
}
return data;
}
function parseResponse(headers, data) {
const contentInfo = getMultipartContentInfo(headers);
if (!contentInfo || !contentInfo.boundary) {
throw new Error('Content boundary not specified...');
}
const boundary = contentInfo.boundary;
const delimiter = '--' + boundary + '\r\n';
let index = data.indexOf(delimiter, 0, ASCII);
if (index < 0) {
throw new Error('DICOMWeb: The specified boundary could not be found...');
}
let closingIndex
let closingDelimiter = '\r\n--' + boundary + '--';
index += delimiter.length;
if (data[index] !== 0x0D || data[index + 1] !== 0x0A) {
// multipart content headers are present, so let's parse them...
let contentHeader = parseContentHeader(data, index);
if (contentHeader && contentHeader.end > index) {
if (contentHeader.fields['content-length'] > 0) {
let endOfData = contentHeader.end + parseInt(contentHeader.fields['content-length'], 10);
if (endOfData === data.indexOf(closingDelimiter, endOfData)) {
// content-length is valid...
return data.slice(contentHeader.end, endOfData);
}
}
index = contentHeader.end;
}
} else {
// no headers, the content comes right after...
index += 2;
}
closingIndex = data.indexOf(closingDelimiter, index);
if (closingIndex < 0 || closingIndex < index) {
throw new Error('DICOMWeb: The end of the content could not be determined...')
}
return toBytes(data.slice(index, closingIndex));
}
const getBulkData = async function(url, options = {}) {
options.headers = options.headers || {};
options.headers.Accept = 'multipart/related; type=application/octet-stream';
const response = await get(url, options);
const data = await response.text();
return parseResponse(response.headers, data);
}
export default getBulkData;

16
Packages/ohif-dicomweb-client/src/getJSON.js Normal file
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@ -0,0 +1,16 @@
import get from './get.js';
import getAttribute from "./getAttribute";
const getJSON = async function (url, options) {
options.headers = options.headers || {};
options.headers.Accept = 'application/json';
return get(url, options).then(response => {
if (!(response instanceof Response)) {
return '';
}
return response.json();
});
};
export default getJSON;

4
Packages/ohif-dicom-services/server/DICOMWeb/getModalities.js → Packages/ohif-dicomweb-client/src/getModalities.js
View File

@ -1,4 +1,4 @@
DICOMWeb.getModalities = function(modality, modalitiesInStudy) {
const getModalities = function(modality, modalitiesInStudy) {
var modalities = {};
if (modality) {
modalities = modality;
@ -19,3 +19,5 @@ DICOMWeb.getModalities = function(modality, modalitiesInStudy) {
}
return modalities;
};
export default getModalities;

2
Packages/ohif-dicom-services/server/DICOMWeb/getName.js → Packages/ohif-dicomweb-client/src/getName.js
View File

@ -5,7 +5,7 @@
* @param [defaultValue] - The default value to return if the element is not found
* @returns {*}
*/
DICOMWeb.getName = function(element, defaultValue) {
export default function getName(element, defaultValue) {
if (!element) {
return defaultValue;
}

2
Packages/ohif-dicom-services/server/DICOMWeb/getNumber.js → Packages/ohif-dicomweb-client/src/getNumber.js
View File

@ -4,7 +4,7 @@
* @param [defaultValue] - The default value to return if the element does not exist
* @returns {*}
*/
DICOMWeb.getNumber = function(element, defaultValue) {
export default function getNumber(element, defaultValue) {
if (!element) {
return defaultValue;
}

2
Packages/ohif-dicom-services/server/DICOMWeb/getString.js → Packages/ohif-dicomweb-client/src/getString.js
View File

@ -5,7 +5,7 @@
* @param [defaultValue] - The value to return if the element is not present
* @returns {*}
*/
DICOMWeb.getString = function(element, defaultValue) {
export default function getString(element, defaultValue) {
if (!element) {
return defaultValue;
}

23
Packages/ohif-dicomweb-client/src/index.js Normal file
View File

@ -0,0 +1,23 @@
import get from './get.js';
import getAttribute from './getAttribute.js';
import getBulkData from './getBulkData.js';
import getJSON from './getJSON.js';
import getModalities from './getModalities.js';
import getName from './getName.js';
import getNumber from './getNumber.js';
import getString from './getString.js';
import makeRequest from './makeRequest.js';
const DICOMWeb = {
get,
getAttribute,
getBulkData,
getJSON,
getModalities,
getName,
getNumber,
getString,
makeRequest
};
export { DICOMWeb };

60
Packages/ohif-dicomweb-client/src/makeRequest.js Normal file
View File

@ -0,0 +1,60 @@
import { Meteor } from "meteor/meteor";
import URL from 'url-parse';
import 'isomorphic-fetch';
async function makeRequest(url, options) {
const parsed = new URL(url);
let requestOpt = {
method: 'GET',
headers: {}
};
// TODO: Clean this up
const accessToken = false //Meteor.user().services.keycloak.accessToken;
if (accessToken) {
requestOpt.headers = {
Authorization: `Bearer ${accessToken}`
};
} else if (requestOpt.auth) {
requestOpt.headers = {
Authorization: requestOpt.auth
};
}
if (options.headers) {
Object.keys(options.headers).forEach(key => {
requestOpt.headers[key] = options.headers[key];
});
}
return new Promise((resolve, reject) => {
// TODO: Kept getting weird build errors from RegExp
const isAbsolute = parsed.href.indexOf('http://') === 0 || parsed.href.indexOf('https://');
let url = parsed.href;
if (isAbsolute === false) {
url = Meteor.absoluteUrl(parsed.href);
}
fetch(url, requestOpt).then((response) => {
if (response.status >= 400) {
reject(new Error(response.status));
}
if (response.status === 204) {
resolve([]);
} else {
// TODO: Handle 204 no content
resolve(response);
}
}, (error) => {
console.error('There was an error in the DICOMWeb Server');
reject(new Error(error));
});
});
}
export default makeRequest;

8
Packages/ohif-servers/both/schema/servers.js
View File

@ -29,6 +29,12 @@ export const DICOMWebRequestOptions = new SimpleSchema({
defaultValue: 'orthanc:orthanc',
optional: true
},
requestFromBrowser: {
type: Boolean,
label: 'Make DICOMWeb requests from the Browser',
defaultValue: false,
optional: true
},
logRequests: {
type: Boolean,
defaultValue: true,
@ -76,7 +82,7 @@ export const DICOMWebServer = new SimpleSchema({
},
qidoSupportsIncludeField: {
type: Boolean,
label: 'QIDO supports including fields',
label: 'QIDO supports "includefield" query key',
defaultValue: false
},
requestOptions: {

11
Packages/ohif-servers/client/components/serverInformation/serverInformationDicomWeb/serverInformationDicomWeb.html
View File

@ -4,11 +4,11 @@
{{>inputText labelClass='form-group' key='wadoUriRoot'}}
</div>
<div class="col-lg-6">
{{>inputText labelClass='form-group' key='wadoRoot'}}
{{>inputSelect labelClass='form-group' key='imageRendering' hideSearch=true
options=(clone placeholder='Select an option')}}
</div>
<div class="col-lg-6">
{{>inputSelect labelClass='form-group' key='imageRendering' hideSearch=true
options=(clone placeholder='Select an option')}}
{{>inputText labelClass='form-group' key='wadoRoot'}}
</div>
<div class="col-lg-6">
{{>inputSelect labelClass='form-group' key='thumbnailRendering' hideSearch=true
@ -30,9 +30,12 @@
</div>
<hr>
<h4>Request options</h4>
{{#group class='row' key='requestOptions'}}
{{#group class='row p-y-1' key='requestOptions'}}
<div class="col-lg-6">
{{>inputText labelClass='form-group' key='auth'}}
<div class="checkbox pull-left">
{{>inputCheckbox key='requestFromBrowser'}}
</div>
</div>
<div class="col-lg-6">
<strong>Logging options</strong>

2
Packages/ohif-studies/imports/both/index.js
View File

@ -0,0 +1,2 @@
import './lib';
import './services';

0
Packages/ohif-studies/imports/server/lib/encodeQueryData.js → Packages/ohif-studies/imports/both/lib/encodeQueryData.js
View File

1
Packages/ohif-studies/imports/server/lib/index.js → Packages/ohif-studies/imports/both/lib/index.js
View File

@ -1 +1,2 @@
import './encodeQueryData.js';
import './parseFloatArray.js';

0
Packages/ohif-studies/imports/server/lib/parseFloatArray.js → Packages/ohif-studies/imports/both/lib/parseFloatArray.js
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6
Packages/ohif-studies/imports/both/services/index.js Normal file
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@ -0,0 +1,6 @@
import './namespace';
// DICOMWeb instance, study, and metadata retrieval
import './qido/instances.js';
import './qido/studies.js';
import './wado/retrieveMetadata.js';

6
Packages/ohif-studies/imports/both/services/namespace.js Normal file
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@ -0,0 +1,6 @@
import { OHIF } from 'meteor/ohif:core';
OHIF.studies.services = {
QIDO: {},
WADO: {}
};

1
Packages/ohif-studies/imports/server/services/qido/instances.js → Packages/ohif-studies/imports/both/services/qido/instances.js
View File

@ -1,4 +1,5 @@
import { OHIF } from 'meteor/ohif:core';
import { DICOMWeb } from 'meteor/ohif:dicomweb-client';
/**
* Creates a QIDO URL given the server settings and a study instance UID

15
Packages/ohif-studies/imports/server/services/qido/studies.js → Packages/ohif-studies/imports/both/services/qido/studies.js
View File

@ -1,4 +1,5 @@
import { OHIF } from 'meteor/ohif:core';
import { DICOMWeb } from 'meteor/ohif:dicomweb-client';
/**
* Creates a QIDO date string for a date range query
@ -99,13 +100,13 @@ function resultDataToStudies(resultData) {
OHIF.studies.services.QIDO.Studies = (server, filter) => {
const url = filterToQIDOURL(server, filter);
try {
const result = DICOMWeb.getJSON(url, server.requestOptions);
return new Promise((resolve, reject) => {
console.warn(DICOMWeb);
return resultDataToStudies(result.data);
} catch (error) {
OHIF.log.trace();
DICOMWeb.getJSON(url, server.requestOptions).then(result => {
const studies = resultDataToStudies(result);
throw error;
}
resolve(studies);
}, reject);
});
};

137
Packages/ohif-studies/imports/server/services/wado/retrieveMetadata.js → Packages/ohif-studies/imports/both/services/wado/retrieveMetadata.js
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@ -1,4 +1,5 @@
import { OHIF } from 'meteor/ohif:core';
import { DICOMWeb } from 'meteor/ohif:dicomweb-client';
import { parseFloatArray } from '../../lib/parseFloatArray';
/**
@ -67,9 +68,8 @@ function buildInstanceWadoUrl(server, studyInstanceUid, seriesInstanceUid, sopIn
params.push('transferSyntax=*');
const paramString = params.join('&');
const uri = encodeURIComponent(paramString);
return `${server.wadoUriRoot}?${uri}`;
return `${server.wadoUriRoot}?${paramString}`;
}
function buildInstanceWadoRsUri(server, studyInstanceUid, seriesInstanceUid, sopInstanceUid) {
@ -106,17 +106,19 @@ function getPaletteColor(server, instance, tag, lutDescriptor) {
const numLutEntries = lutDescriptor[0];
const bits = lutDescriptor[2];
const uri = WADOProxy.convertURL(instance[tag].BulkDataURI, server)
const data = DICOMWeb.getBulkData(uri);
const bulkDataPromise = DICOMWeb.getBulkData(uri);
for (var i = 0; i < numLutEntries; i++) {
if(bits === 16) {
lut[i] = data.readUInt16LE(i*2);
} else {
lut[i] = data.readUInt8(i);
return bulkDataPromise.then(data => {
for (var i = 0; i < numLutEntries; i++) {
if(bits === 16) {
lut[i] = data[i * 65536] + data[i + 1];
} else {
lut[i] = data[i];
}
}
}
return lut;
return lut;
})
}
/**
@ -126,38 +128,33 @@ function getPaletteColor(server, instance, tag, lutDescriptor) {
* @param instance {Object} The retrieved instance metadata;
* @returns {String} The ReferenceSOPInstanceUID
*/
function getPaletteColors(server, instance, lutDescriptor) {
async function getPaletteColors(server, instance, lutDescriptor) {
let entry = null;
let paletteUID = DICOMWeb.getString(instance['00281199']);
let entry = null,
paletteUID = DICOMWeb.getString(instance['00281199']);
if (paletteColorCache.isValidUID(paletteUID)) {
entry = paletteColorCache.get(paletteUID);
} else {
paletteUID = null;
}
if (!entry) {
// no entry on cache... Fetch remote data.
try {
let r, g, b;
r = getPaletteColor(server, instance, '00281201', lutDescriptor);
g = getPaletteColor(server, instance, '00281202', lutDescriptor);;
b = getPaletteColor(server, instance, '00281203', lutDescriptor);;
entry = { red: r, green: g, blue: b };
if (paletteUID !== null) {
// when paletteUID is present, the entry can be cached...
entry.uid = paletteUID;
paletteColorCache.add(entry);
}
} catch (error) {
OHIF.log.error(`(${error.name}) ${error.message}`);
return new Promise((resolve, reject) => {
if (paletteColorCache.isValidUID(paletteUID)) {
entry = paletteColorCache.get(paletteUID);
return resolve(entry);
}
}
return entry;
// no entry in cache... Fetch remote data.
const r = getPaletteColor(server, instance, '00281201', lutDescriptor);
const g = getPaletteColor(server, instance, '00281202', lutDescriptor);;
const b = getPaletteColor(server, instance, '00281203', lutDescriptor);;
const promises = [r, g, b];
Promise.all(promises).then((args) => {
entry = { red: r, green: g, blue: b };
// when paletteUID is present, the entry can be cached...
entry.uid = paletteUID;
paletteColorCache.add(entry);
resolve(entry);
});
});
}
function getFrameIncrementPointer(element) {
@ -204,21 +201,27 @@ function getRadiopharmaceuticalInfo(instance) {
* @param resultData
* @returns {{seriesList: Array, patientName: *, patientId: *, accessionNumber: *, studyDate: *, modalities: *, studyDescription: *, imageCount: *, studyInstanceUid: *}}
*/
function resultDataToStudyMetadata(server, studyInstanceUid, resultData) {
var seriesMap = {};
var seriesList = [];
async function resultDataToStudyMetadata(server, studyInstanceUid, resultData) {
const seriesMap = {};
const seriesList = [];
if (!WADOProxy) {
WADOProxy = {
convertURL: (a => a)
};
}
if (!resultData.length) {
return;
}
var anInstance = resultData[0];
const anInstance = resultData[0];
if (!anInstance) {
return;
}
var studyData = {
seriesList: seriesList,
const studyData = {
seriesList,
patientName: DICOMWeb.getName(anInstance['00100010']),
patientId: DICOMWeb.getString(anInstance['00100020']),
patientAge: DICOMWeb.getNumber(anInstance['00101010']),
@ -233,7 +236,7 @@ function resultDataToStudyMetadata(server, studyInstanceUid, resultData) {
institutionName: DICOMWeb.getString(anInstance['00080080'])
};
resultData.forEach(function(instance) {
await Promise.all(resultData.map(async function(instance) {
var seriesInstanceUid = DICOMWeb.getString(instance['0020000E']);
var series = seriesMap[seriesInstanceUid];
if (!series) {
@ -250,17 +253,16 @@ function resultDataToStudyMetadata(server, studyInstanceUid, resultData) {
seriesList.push(series);
}
var sopInstanceUid = DICOMWeb.getString(instance['00080018']);
const sopInstanceUid = DICOMWeb.getString(instance['00080018']);
const wadouri = buildInstanceWadoUrl(server, studyInstanceUid, seriesInstanceUid, sopInstanceUid);
const baseWadoRsUri = buildInstanceWadoRsUri(server, studyInstanceUid, seriesInstanceUid, sopInstanceUid);
const wadorsuri = buildInstanceFrameWadoRsUri(server, studyInstanceUid, seriesInstanceUid, sopInstanceUid);
var instanceSummary = {
const instanceSummary = {
imageType: DICOMWeb.getString(instance['00080008']),
sopClassUid: DICOMWeb.getString(instance['00080016']),
modality: DICOMWeb.getString(instance['00080060']),
sopInstanceUid: sopInstanceUid,
sopInstanceUid,
instanceNumber: DICOMWeb.getNumber(instance['00200013']),
imagePositionPatient: DICOMWeb.getString(instance['00200032']),
imageOrientationPatient: DICOMWeb.getString(instance['00200037']),
@ -312,12 +314,13 @@ function resultDataToStudyMetadata(server, studyInstanceUid, resultData) {
const redPaletteColorLookupTableDescriptor = parseFloatArray(DICOMWeb.getString(instance['00281101']));
const greenPaletteColorLookupTableDescriptor = parseFloatArray(DICOMWeb.getString(instance['00281102']));
const bluePaletteColorLookupTableDescriptor = parseFloatArray(DICOMWeb.getString(instance['00281103']));
const palettes = getPaletteColors(server, instance, redPaletteColorLookupTableDescriptor);
const palettes = await getPaletteColors(server, instance, redPaletteColorLookupTableDescriptor);
if (palettes) {
if (palettes.uid) {
instanceSummary.paletteColorLookupTableUID = palettes.uid;
}
instanceSummary.redPaletteColorLookupTableData = palettes.red;
instanceSummary.greenPaletteColorLookupTableData = palettes.green;
instanceSummary.bluePaletteColorLookupTableData = palettes.blue;
@ -328,8 +331,7 @@ function resultDataToStudyMetadata(server, studyInstanceUid, resultData) {
}
series.instances.push(instanceSummary);
});
}));
return studyData;
}
@ -338,26 +340,19 @@ function resultDataToStudyMetadata(server, studyInstanceUid, resultData) {
* Retrieved Study MetaData from a DICOM server using a WADO call
* @param server
* @param studyInstanceUid
* @returns {{seriesList: Array, patientName: *, patientId: *, accessionNumber: *, studyDate: *, modalities: *, studyDescription: *, imageCount: *, studyInstanceUid: *}}
* @returns {Promise}
*/
OHIF.studies.services.WADO.RetrieveMetadata = function(server, studyInstanceUid) {
var url = buildUrl(server, studyInstanceUid);
OHIF.studies.services.WADO.RetrieveMetadata = async function(server, studyInstanceUid) {
const url = buildUrl(server, studyInstanceUid);
try {
var result = DICOMWeb.getJSON(url, server.requestOptions);
return new Promise((resolve, reject) => {
DICOMWeb.getJSON(url, server.requestOptions).then(result => {
resultDataToStudyMetadata(server, studyInstanceUid, result).then((study) => {
study.wadoUriRoot = server.wadoUriRoot;
study.studyInstanceUid = studyInstanceUid;
var study = resultDataToStudyMetadata(server, studyInstanceUid, result.data);
if (!study) {
study = {};
}
study.wadoUriRoot = server.wadoUriRoot;
study.studyInstanceUid = studyInstanceUid;
return study;
} catch (error) {
OHIF.log.trace();
throw error;
}
resolve(study);
}, reject);
}, reject);
});
};

33
Packages/ohif-studies/imports/client/lib/loadStudy.js
View File

@ -1,6 +1,7 @@
import { ReactiveDict } from 'meteor/reactive-dict';
import { Tracker } from 'meteor/tracker';
import { OHIF } from 'meteor/ohif:core';
import { Meteor } from "meteor/meteor";
// Create a studies loaded state dictionary to enable reactivity. Values: loading|loaded|failed
OHIF.studies.loadingDict = new ReactiveDict();
@ -24,16 +25,34 @@ OHIF.studies.loadStudy = studyInstanceUid => new Promise((resolve, reject) => {
}
return OHIF.studies.retrieveStudyMetadata(studyInstanceUid).then(study => {
// Add the display sets to the study if not present
if (!study.displaySets) {
const displaySets = OHIF.viewerbase.sortingManager.getDisplaySets(study);
study.displaySets = displaySets;
study.setDisplaySets(displaySets);
study.forEachDisplaySet(displaySet => {
OHIF.viewerbase.stackManager.makeAndAddStack(study, displaySet);
if (window.HipaaLogger && Meteor.user && Meteor.user()) {
window.HipaaLogger.logEvent({
eventType: 'viewed',
userId: Meteor.userId(),
userName: Meteor.user().profile.fullName,
collectionName: 'Study',
recordId: studyInstanceUid,
patientId: study.patientId,
patientName: study.patientName
});
}
// Once the data was retrieved, the series are sorted by series and instance number
OHIF.viewerbase.sortStudy(study);
// Updates WADO-RS metaDataManager
OHIF.viewerbase.updateMetaDataManager(study);
// Transform the study in a StudyMetadata object
const studyMetadata = new OHIF.metadata.StudyMetadata(study);
// Add the display sets to the study
study.displaySets = OHIF.viewerbase.sortingManager.getDisplaySets(studyMetadata);
study.displaySets.forEach(displaySet => {
OHIF.viewerbase.stackManager.makeAndAddStack(study, displaySet);
studyMetadata.addDisplaySet(displaySet);
});
// Double check to make sure this study wasn't already inserted into OHIF.viewer.Studies
// so we don't cause duplicate entry errors
const loaded = OHIF.viewer.Studies.findBy({ studyInstanceUid: study.studyInstanceUid });

102
Packages/ohif-studies/imports/client/lib/retrieveStudyMetadata.js
View File

@ -6,6 +6,18 @@ import 'meteor/ohif:viewerbase';
// promises and prevent unnecessary subsequent calls to the server
const StudyMetaDataPromises = new Map();
/**
* Delete the study promise cached to ensure next retrieve will get it retrieved by server call
*
* @param {String} studyInstanceUid The UID of the Study to be removed from cache
*
*/
OHIF.studies.deleteStudyMetadataPromise = (studyInstanceUid) => {
if (StudyMetaDataPromises.has(studyInstanceUid)) {
StudyMetaDataPromises.delete(studyInstanceUid);
}
};
/**
* Retrieves study metadata using a server call
*
@ -30,70 +42,50 @@ OHIF.studies.retrieveStudyMetadata = (studyInstanceUid, seriesInstanceUids) => {
// Create a promise to handle the data retrieval
const promise = new Promise((resolve, reject) => {
const server = OHIF.servers.getCurrentServer();
// If no study metadata is in the cache variable, we need to retrieve it from
// the server with a call.
Meteor.call('GetStudyMetadata', studyInstanceUid, function(error, study) {
OHIF.log.timeEnd(timingKey);
if (server.type === 'dicomWeb' && server.requestOptions.requestFromBrowser === true) {
OHIF.studies.services.WADO.RetrieveMetadata(server, studyInstanceUid).then(function (data) {
resolve(data)
}, reject);
} else {
Meteor.call('GetStudyMetadata', studyInstanceUid, function (error, study) {
OHIF.log.timeEnd(timingKey);
if (error) {
const errorType = error.error;
let errorMessage = '';
if (error) {
const errorType = error.error;
let errorMessage = '';
if (errorType === 'server-connection-error') {
errorMessage = 'There was an error connecting to the DICOM server, please verify if it is up and running.';
} else if (errorType === 'server-internal-error') {
errorMessage = `There was an internal error with the DICOM server getting metadeta for ${studyInstanceUid}`;
} else {
errorMessage = `For some reason we could not retrieve the study\'s metadata for ${studyInstanceUid}.`;
if (errorType === 'server-connection-error') {
errorMessage = 'There was an error connecting to the DICOM server, please verify if it is up and running.';
} else if (errorType === 'server-internal-error') {
errorMessage = `There was an internal error with the DICOM server getting metadeta for ${studyInstanceUid}`;
} else {
errorMessage = `For some reason we could not retrieve the study\'s metadata for ${studyInstanceUid}.`;
}
OHIF.log.error(errorMessage);
OHIF.log.error(error.stack);
reject(`GetStudyMetadata: ${errorMessage}`);
return;
}
OHIF.log.error(errorMessage);
OHIF.log.error(error.stack);
reject(`GetStudyMetadata: ${errorMessage}`);
return;
}
// Filter series if seriesInstanceUid exists
if (seriesInstanceUids && seriesInstanceUids.length) {
study.seriesList = study.seriesList.filter(series => seriesInstanceUids.indexOf(series.seriesInstanceUid) > -1);
}
// Filter series if seriesInstanceUid exists
if (seriesInstanceUids && seriesInstanceUids.length) {
study.seriesList = study.seriesList.filter(series => seriesInstanceUids.indexOf(series.seriesInstanceUid) > -1);
}
if (!study) {
reject(`GetStudyMetadata: No study data returned from server: ${studyInstanceUid}`);
return;
}
if (!study) {
reject(`GetStudyMetadata: No study data returned from server: ${studyInstanceUid}`);
return;
}
if (window.HipaaLogger && Meteor.user && Meteor.user()) {
window.HipaaLogger.logEvent({
eventType: 'viewed',
userId: Meteor.userId(),
userName: Meteor.user().profile.fullName,
collectionName: 'Study',
recordId: studyInstanceUid,
patientId: study.patientId,
patientName: study.patientName
});
}
// Once the data was retrieved, the series are sorted by series and instance number
OHIF.viewerbase.sortStudy(study);
// Updates WADO-RS metaDataManager
OHIF.viewerbase.updateMetaDataManager(study);
// Transform the study in a StudyMetadata object
const studyMetadata = new OHIF.metadata.StudyMetadata(study);
// Add the display sets to the study
study.displaySets = OHIF.viewerbase.sortingManager.getDisplaySets(studyMetadata);
study.displaySets.forEach(displaySet => {
OHIF.viewerbase.stackManager.makeAndAddStack(study, displaySet);
studyMetadata.addDisplaySet(displaySet);
// Resolve the promise with the final study metadata object
resolve(study);
});
// Resolve the promise with the final study metadata object
resolve(study);
});
}
});
// Store the promise in cache

20
Packages/ohif-studies/imports/client/lib/searchStudies.js
View File

@ -15,13 +15,19 @@ OHIF.studies.searchStudies = filter => {
return studySearchPromises.get(promiseKey);
} else {
const promise = new Promise((resolve, reject) => {
Meteor.call('StudyListSearch', filter, (error, studiesData) => {
if (error) {
reject(error);
} else {
resolve(studiesData);
}
});
const server = OHIF.servers.getCurrentServer();
if (server.type === 'dicomWeb' && server.requestOptions.requestFromBrowser === true) {
OHIF.studies.services.QIDO.Studies(server, filter).then(resolve, reject);
} else {
Meteor.call('StudyListSearch', filter, (error, studiesData) => {
if (error) {
reject(error);
} else {
resolve(studiesData);
}
});
}
});
studySearchPromises.set(promiseKey, promise);
return promise;

1
Packages/ohif-studies/imports/server/index.js
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@ -1,3 +1,2 @@
import './lib';
import './methods';
import './services';

1
Packages/ohif-studies/imports/server/services/dimse/instances.js
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@ -5,6 +5,7 @@ import { OHIF } from 'meteor/ohif:core';
* an array of series that are present in the study
*
* @param resultData
* @param studyInstanceUid
* @returns {Array} Series List
*/
function resultDataToStudyMetadata(resultData, studyInstanceUid) {

2
Packages/ohif-studies/imports/server/services/dimse/retrieveMetadata.js
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@ -1,5 +1,5 @@
import { OHIF } from 'meteor/ohif:core';
import { parseFloatArray } from 'meteor/ohif:studies/imports/server/lib/parseFloatArray';
import { parseFloatArray } from 'meteor/ohif:studies/imports/both/lib/parseFloatArray';
/**
* Returns the value of the element (e.g. '00280009')

5
Packages/ohif-studies/imports/server/services/index.js
View File

@ -1,10 +1,5 @@
import './namespace.js';
// DICOMWeb instance, study, and metadata retrieval
import './qido/instances.js';
import './qido/studies.js';
import './wado/retrieveMetadata.js';
// DIMSE instance, study, and metadata retrieval
import './dimse/instances.js';
import './dimse/studies.js';

7
Packages/ohif-studies/imports/server/services/namespace.js
View File

@ -1,8 +1,3 @@
import { OHIF } from 'meteor/ohif:core';
const Services = {};
Services.QIDO = {};
Services.WADO = {};
Services.DIMSE = {};
OHIF.studies.services = Services;
OHIF.studies.services.DIMSE = {};

3
Packages/ohif-studies/package.js
View File

@ -5,7 +5,7 @@ Package.describe({
});
Package.onUse(function(api) {
api.versionsFrom('1.4');
api.versionsFrom('1.6');
api.use([
'ecmascript',
@ -21,6 +21,7 @@ Package.onUse(function(api) {
'ohif:log',
'ohif:servers',
'ohif:dicom-services',
'ohif:dicomweb-client',
'ohif:viewerbase',
'ohif:wadoproxy'
]);

33
Packages/ohif-study-list/client/components/studylist/studylistResult/studylistResult.js
View File

@ -151,29 +151,12 @@ function search() {
// returned as 'undefined'
const modality = replaceUndefinedColumnValue($('input#modality').val());
Meteor.call('StudyListSearch', filter, (error, studies) => {
OHIF.studies.searchStudies(filter).then((studies) => {
OHIF.log.info('StudyListSearch');
// Hide loading text
Session.set('showLoadingText', false);
if (error) {
Session.set('serverError', true);
const errorType = error.error;
if (errorType === 'server-connection-error') {
OHIF.log.error('There was an error connecting to the DICOM server, please verify if it is up and running.');
} else if (errorType === 'server-internal-error') {
OHIF.log.error('There was an internal error with the DICOM server');
} else {
OHIF.log.error('For some reason we could not list the studies.')
}
OHIF.log.error(error.stack);
return;
}
if (!studies) {
OHIF.log.warn('No studies found');
return;
@ -196,6 +179,20 @@ function search() {
OHIF.studylist.collections.Studies.insert(study);
}
});
}, (error) => {
Session.set('serverError', true);
const errorType = error.error;
if (errorType === 'server-connection-error') {
OHIF.log.error('There was an error connecting to the DICOM server, please verify if it is up and running.');
} else if (errorType === 'server-internal-error') {
OHIF.log.error('There was an internal error with the DICOM server');
} else {
OHIF.log.error('For some reason we could not list the studies.')
}
OHIF.log.error(error.stack);
});
}

2
Packages/ohif-study-list/client/lib/index.js
View File

@ -3,8 +3,6 @@ import './exportStudies.js';
import './getSelectedStudies.js';
import './importStudies.js';
import './queryStudies.js';
import './retrieveStudiesMetadata.js';
import './retrieveStudyMetadata.js';
import './studylist.js';
import './viewSeriesDetails.js';
import './viewStudies.js';

12
Packages/ohif-study-list/client/lib/retrieveStudiesMetadata.js
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@ -1,12 +0,0 @@
import { OHIF } from 'meteor/ohif:core';
const note = 'OHIF.studylist.retrieveStudiesMetadata is deprecated.';
const instructions = 'Please use OHIF.studies.retrieveStudiesMetadata instead.';
/**
* @deprecated Please use OHIF.studies.retrieveStudiesMetadata instead
*/
OHIF.studylist.retrieveStudiesMetadata = function() {
OHIF.log.warn(`${note}\n${instructions}`);
OHIF.studies.retrieveStudiesMetadata.apply(this, arguments);
};

12
Packages/ohif-study-list/client/lib/retrieveStudyMetadata.js
View File

@ -1,12 +0,0 @@
import { OHIF } from 'meteor/ohif:core';
const note = 'OHIF.studylist.retrieveStudyMetadata is deprecated.';
const instructions = 'Please use OHIF.studies.retrieveStudyMetadata instead.';
/**
* @deprecated Please use OHIF.studies.retrieveStudyMetadata instead
*/
OHIF.studylist.retrieveStudyMetadata = function() {
OHIF.log.warn(`${note}\n${instructions}`);
OHIF.studies.retrieveStudyMetadata.apply(this, arguments);
};