grnsight 3.0.0 → 5.1.0

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Files changed (489) hide show
  1. package/.eslintignore +1 -0
  2. package/.travis.yml +1 -1
  3. package/GRNsight - Beta.html +194 -0
  4. package/Gemfile.lock +259 -0
  5. package/README.md +1 -1
  6. package/_gh_pages/about.html +360 -45
  7. package/_gh_pages/assets/css/footer.css +3 -0
  8. package/_gh_pages/assets/css/main.css +28 -14
  9. package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_estimation_output_binary-no-targetless-genes_sif.png +0 -0
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  25. package/{documents/manuscripts/peerj-computerscience-2016/figures/submitted-versions/Figure1_zoom145_900pix-wide.png → _gh_pages/assets/images/demo-3_network-sheet.png} +0 -0
  26. package/{documents/manuscripts/peerj-computerscience-2016/figures/submitted-versions/Figure2_zoom145_900pix-wide.png → _gh_pages/assets/images/demo-4_network-optimized-weights-sheet.png} +0 -0
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  88. package/_gh_pages/documents/manuscripts/peerj-computerscience-2016/revisions/GRNsight_PeerJ-CS_manuscript_2016_text-only_revised-Dondi.docx +0 -0
  89. package/_gh_pages/encryption/server.cert +21 -0
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  109. package/coverage/coverage.json +1 -1
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  145. package/server/app.js +6 -2
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  476. package/test-files/demo-files/21-genes_50-edges_Dahlquist-data_estimation_output.xlsx +0 -0
  477. package/test-files/demo-files/21-genes_50-edges_Dahlquist-data_input.xlsx +0 -0
  478. package/test-files/graph-tests/different-sized-networks/10-genes-max-edges.xlsx +0 -0
  479. package/test-files/graph-tests/different-sized-networks/12-genes-max-edges.xlsx +0 -0
  480. package/test-files/graph-tests/different-sized-networks/35-genes-max-edges.xlsx +0 -0
  481. package/test-files/graph-tests/different-sized-networks/40-genes-0-edges.xlsx +0 -0
  482. package/test-files/graph-tests/different-sized-networks/40-genes-max-edges.xlsx +0 -0
  483. package/test-files/graph-tests/different-sized-networks/42-genes-max-edges.xlsx +0 -0
  484. package/test-files/graph-tests/different-sized-networks/50-genes-max-edges.xlsx +0 -0
  485. package/test-files/graph-tests/different-sized-networks/75-genes-150-edges.xlsx +0 -0
  486. package/web-client/public/js/container.js +0 -121
  487. package/web-client/public/js/node-coloring.js +0 -306
  488. package/web-client/public/js/sliders.js +0 -197
  489. package/web-client/views/upload.jade +0 -458
@@ -0,0 +1,180 @@
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+ import { updateApp } from "./update-app";
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+
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+ import {
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+ DEMO_INFORMATION,
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+ UNWEIGHTED_DEMO_PATH,
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+ WEIGHTED_DEMO_PATH,
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+ SCHADE_INPUT_PATH,
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+ SCHADE_OUTPUT_PATH,
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+ WEIGHTED_DEMO_NAME,
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+ UNWEIGHTED_DEMO_NAME,
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+ SCHADE_INPUT_NAME,
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+ SCHADE_OUTPUT_NAME,
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+ } from "./constants";
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+
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+ const demoFiles = [UNWEIGHTED_DEMO_PATH, WEIGHTED_DEMO_PATH, SCHADE_INPUT_PATH, SCHADE_OUTPUT_PATH];
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+
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+ const submittedFilename = $upload => {
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+ let path = $upload.val();
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+ let fakePathCheck = path.search("\\\\") + 1;
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+
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+ while (fakePathCheck) {
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+ path = path.substring(fakePathCheck);
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+ fakePathCheck = path.search("\\\\") + 1;
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+ }
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+
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+ return path;
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+ };
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+
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+ const createFileForm = $upload => {
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+ const formData = new FormData();
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+ formData.append("file", $upload[0].files[0]);
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+ return formData;
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+ };
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+
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+ const uploadEpilogue = event => {
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+ if (window.ga) {
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+ window.ga("send", "pageview", {
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+ page: "/GRNsight/upload",
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+ sessionControl: "start"
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+ });
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+ }
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+
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+ $("a.upload > input[type=file]").val("");
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+ event.preventDefault();
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+ };
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+ const disableUpload = state => {
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+ $("#upload").attr("disabled", state);
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+ $("#upload-sif").attr("disabled", state);
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+ $("#upload-graphml").attr("disabled", state);
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+ };
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+
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+ const uploadHandler = (uploader) => {
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+ return function (event) { // Must be `function` due to use of `this`.
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+ const $upload = $(this);
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+ const filename = submittedFilename($upload); // TODO: remove before master release (beta@4.0.6)
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+ if ($upload[0].files[0].size < 2000000) {
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+ // disable upload button to prevent multiple uploads
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+ disableUpload(true);
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+ const formData = createFileForm($upload);
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+ uploader(filename, formData);
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+ uploadEpilogue(event);
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+ } else {
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+ let errorString = "The file uploaded is too large. Please try again with a file smaller than 1 MB.";
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+ $("#error").html(errorString);
65
+ $("#errorModal").modal("show");
66
+ }
67
+ };
68
+ };
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+
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+ const workbookErrorDisplayer = xhr => {
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+ // re-enable upload button
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+ disableUpload(false);
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+ // Deleted status, error for argument because it was never used
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+ const err = JSON.parse(xhr.responseText);
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+ let errorString = "Your graph failed to load.<br><br>";
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+
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+ if (!err.errors) { // will be falsy if an error was thrown before the workbook was generated
78
+ errorString += err;
79
+ } else {
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+ errorString = err.errors.reduce(
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+ (currentErrorString, currentError) =>
82
+ `${currentErrorString}${currentError.possibleCause} ${currentError.suggestedFix}<br><br>`,
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+
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+ errorString
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+ );
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+ }
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+
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+ $("#error").html(errorString);
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+ $("#errorModal").modal("show");
90
+ };
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+
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+ let reloader = () => { };
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+
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+ const returnUploadRoute = filename => {
95
+ if (demoFiles.indexOf(filename) !== -1) {
96
+ return filename;
97
+ } else if (filename.includes(".xlsx")) {
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+ return "upload";
99
+ } else if (filename.includes(".sif")) {
100
+ return "upload-sif";
101
+ } else if (filename.includes(".graphml")) {
102
+ return "upload-graphml";
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+ }
104
+ };
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+
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+ export const setupLoadAndImportHandlers = grnState => {
107
+ const loadGrn = (name, formData) => {
108
+ const uploadRoute = returnUploadRoute(name);
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+ const fullUrl = [ $("#service-root").val(), uploadRoute ].join("/");
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+ // The presence of formData is taken to indicate a POST.
111
+ (formData ?
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+ $.ajax({
113
+ url: fullUrl,
114
+ data: formData,
115
+ processData: false,
116
+ contentType: false,
117
+ type: "POST",
118
+ crossDomain: true
119
+ }) :
120
+ $.getJSON(fullUrl)
121
+ ).done((workbook, textStatus, jqXhr) => {
122
+ grnState.name = name || jqXhr.getResponseHeader("X-GRNsight-Filename");
123
+ if (demoFiles.indexOf(name) > -1) {
124
+ switch (name) {
125
+ case WEIGHTED_DEMO_PATH:
126
+ grnState.name = WEIGHTED_DEMO_NAME;
127
+ break;
128
+ case UNWEIGHTED_DEMO_PATH:
129
+ grnState.name = UNWEIGHTED_DEMO_NAME;
130
+ break;
131
+ case SCHADE_INPUT_PATH:
132
+ grnState.name = SCHADE_INPUT_NAME;
133
+ break;
134
+ case SCHADE_OUTPUT_PATH:
135
+ grnState.name = SCHADE_OUTPUT_NAME;
136
+ break;
137
+ }
138
+ }
139
+ grnState.workbook = workbook;
140
+ if (uploadRoute !== "upload") {
141
+ grnState.annotateLinks();
142
+ }
143
+ reloader = () => loadGrn(name, formData);
144
+ // re-enable upload button
145
+ disableUpload(false);
146
+ updateApp(grnState);
147
+ // displayStatistics(workbook);
148
+
149
+ }).error(workbookErrorDisplayer);
150
+ };
151
+ /*
152
+ * Thanks to http://stackoverflow.com/questions/6974684/how-to-send-formdata-objects-with-ajax-requests-in-jquery
153
+ * for helping to resolve this.
154
+ */
155
+
156
+ $("#upload").change(uploadHandler(loadGrn));
157
+
158
+ const loadDemo = url => {
159
+ loadGrn(url);
160
+ reloader = () => loadGrn(url);
161
+
162
+ $("a.upload > input[type=file]").val("");
163
+ };
164
+
165
+ const initializeDemoFile = (demoId, demoPath, demoName) => {
166
+ // Deleted parameter `event`
167
+ $(demoId).on("click", () => loadDemo(demoPath, demoName));
168
+ };
169
+
170
+ DEMO_INFORMATION.forEach(demoInfo => initializeDemoFile.apply(null, demoInfo));
171
+
172
+ $("#reload").click(function () {
173
+ // Deleted `event` parameter but need `function` because of `this`.
174
+ if (!$(this).parent().hasClass("disabled")) {
175
+ if ($.isFunction(reloader)) {
176
+ reloader();
177
+ }
178
+ }
179
+ });
180
+ };