@sjcrh/proteinpaint-client 2.191.3 → 2.191.4

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (888) hide show
  1. package/dist/2dmaf-Z3D2M3FB.js +1373 -0
  2. package/dist/AIProjectAdmin-2OQOQXH4.js +956 -0
  3. package/dist/AppHeader-PXLGVCVS.js +835 -0
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  5. package/dist/CorrelationVolcano-RO6CFLZA.js +619 -0
  6. package/dist/DE-CCA5SBJG.js +95 -0
  7. package/dist/DEinput-MRUQW6X6.js +301 -0
  8. package/dist/DifferentialAnalysis-5YQQLJKR.js +245 -0
  9. package/dist/Disco-4FTOJBLG.js +3237 -0
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  159. package/dist/dnaMethylation-WGJMJL5B.js +38 -0
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  813. /package/dist/{plot.disco-BLNU4I6Q.js.map → plot.disco-OUE4RFHL.js.map} +0 -0
  814. /package/dist/{plot.dzi-FKWY6K5Q.js.map → plot.dzi-T3GPUH36.js.map} +0 -0
  815. /package/dist/{plot.ssgq-3GTTOOMK.js.map → plot.ssgq-WJHGMXW5.js.map} +0 -0
  816. /package/dist/{plot.vaf2cov-UAI64HYN.js.map → plot.vaf2cov-NGD5PCV4.js.map} +0 -0
  817. /package/dist/{plot.wsi-QJ52IJXL.js.map → plot.wsi-2MU5BDG3.js.map} +0 -0
  818. /package/dist/{polar2-6S4IHKK4.js.map → polar2-YCWPBPFU.js.map} +0 -0
  819. /package/dist/{profileForms-WXWHZ56N.js.map → profileForms-OV3I6RK7.js.map} +0 -0
  820. /package/dist/{profilePlot-K7ICCFQ3.js.map → profilePlot-OMVO3K4H.js.map} +0 -0
  821. /package/dist/{proteinView-ALZTEKTC.js.map → proteinView-OAR2RC6U.js.map} +0 -0
  822. /package/dist/{qualitative-QMPO7EY6.js.map → qualitative-MEYBRUC6.js.map} +0 -0
  823. /package/dist/{radar2-LDAFJHSI.js.map → radar2-KREAMGVV.js.map} +0 -0
  824. /package/dist/{radarFacility2-3TX3U243.js.map → radarFacility2-DBPEV7VC.js.map} +0 -0
  825. /package/dist/{regression-DUUCJOFW.js.map → regression-ZPDPLI6G.js.map} +0 -0
  826. /package/dist/{regression.inputs-B6SFFVED.js.map → regression.inputs-QOSBAGL6.js.map} +0 -0
  827. /package/dist/{regression.inputs.term-P5NHX7ME.js.map → regression.inputs.term-HMUMPY7X.js.map} +0 -0
  828. /package/dist/{regression.inputs.values.table-MVPP5VAK.js.map → regression.inputs.values.table-VMCTZHLG.js.map} +0 -0
  829. /package/dist/{regression.integration.spec-T7VH46WO.js.map → regression.integration.spec-RP74JTAA.js.map} +0 -0
  830. /package/dist/{regression.results-QEP4T6JO.js.map → regression.results-5XC6M67C.js.map} +0 -0
  831. /package/dist/{regression.spec-BTBCBKMF.js.map → regression.spec-EZYM24J7.js.map} +0 -0
  832. /package/dist/{report-WYCH4DJX.js.map → report-ZOVQCOGQ.js.map} +0 -0
  833. /package/dist/{sampleScatter.spec-LC6K22FF.js.map → sampleScatter.spec-CD52FEOC.js.map} +0 -0
  834. /package/dist/{sampleView-V3JYDTRA.js.map → sampleView-SVTLSWRG.js.map} +0 -0
  835. /package/dist/{samplelst-JO7UROYA.js.map → samplelst-HXF5POJD.js.map} +0 -0
  836. /package/dist/{samplematrix-6526IJRO.js.map → samplematrix-NYDAH74I.js.map} +0 -0
  837. /package/dist/{sc-EUC7G5OV.js.map → sc-JIDT4W4K.js.map} +0 -0
  838. /package/dist/{scatter-UMK37C4M.js.map → scatter-WNRTPSEE.js.map} +0 -0
  839. /package/dist/{scatter.integration.spec-BTOB6Y4H.js.map → scatter.integration.spec-3EYTPY5B.js.map} +0 -0
  840. /package/dist/{selectGenomeWithTklst-JNEOHP4V.js.map → selectGenomeWithTklst-OSB7B6L3.js.map} +0 -0
  841. /package/dist/{singleCellCellType-ZDMKPQ2Q.js.map → singleCellCellType-3BH7LWQ6.js.map} +0 -0
  842. /package/dist/{singleCellCellType.unit.spec-BKGRNHYP.js.map → singleCellCellType.unit.spec-RU4RJXFF.js.map} +0 -0
  843. /package/dist/{singleCellGeneExpression-J5KFX7TD.js.map → singleCellGeneExpression-3UA4YER7.js.map} +0 -0
  844. /package/dist/{singleCellGeneExpression.unit.spec-6F5YFV7K.js.map → singleCellGeneExpression.unit.spec-4ZTBG37H.js.map} +0 -0
  845. /package/dist/{singleCellPlot-VA6SWR5L.js.map → singleCellPlot-ZUAWK5RE.js.map} +0 -0
  846. /package/dist/{singlecell-A4OHBVJD.js.map → singlecell-BGJZB7MF.js.map} +0 -0
  847. /package/dist/{singlecell-2CWHJR2P.js.map → singlecell-RO3BL5OO.js.map} +0 -0
  848. /package/dist/{snp-PJNNPOSF.js.map → snp-HD7VQKBR.js.map} +0 -0
  849. /package/dist/{snp.unit.spec-JKZCYPNA.js.map → snp.unit.spec-ISXCLMWW.js.map} +0 -0
  850. /package/dist/{snplocus-YY6UIS2R.js.map → snplocus-IL5Z4XWV.js.map} +0 -0
  851. /package/dist/{spliceevent.a53ss.diagram-CEFGK2LA.js.map → spliceevent.a53ss.diagram-LLJSPV7M.js.map} +0 -0
  852. /package/dist/{spliceevent.exonskip.diagram-A24TZTQ7.js.map → spliceevent.exonskip.diagram-LAOIOIST.js.map} +0 -0
  853. /package/dist/{spliceevent.noeventdiagram-USD42ZZB.js.map → spliceevent.noeventdiagram-MVA7Q3HT.js.map} +0 -0
  854. /package/dist/{ssGSEA-A5X56E7U.js.map → ssGSEA-7T6S3DSE.js.map} +0 -0
  855. /package/dist/{ssGSEA.unit.spec-6WMGKWNI.js.map → ssGSEA.unit.spec-XJ3W4NWX.js.map} +0 -0
  856. /package/dist/{summarizeCnvGeneexp-FZJL4Q7O.js.map → summarizeCnvGeneexp-RRP6JUV6.js.map} +0 -0
  857. /package/dist/{summarizeGeneexpSurvival-LRJZBHRW.js.map → summarizeGeneexpSurvival-AFLHDD6Q.js.map} +0 -0
  858. /package/dist/{summarizeMutationCnv-L64CVMHI.js.map → summarizeMutationCnv-NABUYHMX.js.map} +0 -0
  859. /package/dist/{summarizeMutationDiagnosis-S55CKGBO.js.map → summarizeMutationDiagnosis-2LQ7JU3K.js.map} +0 -0
  860. /package/dist/{summarizeMutationSurvival-AM7BZVDP.js.map → summarizeMutationSurvival-3WBT5TXG.js.map} +0 -0
  861. /package/dist/{summary-ANZTET2T.js.map → summary-FRDKOFXW.js.map} +0 -0
  862. /package/dist/{summary.integration.spec-TW3CJTDA.js.map → summary.integration.spec-ZLRIA7G2.js.map} +0 -0
  863. /package/dist/{summaryInput-3JHKZU62.js.map → summaryInput-4JO6MHP4.js.map} +0 -0
  864. /package/dist/{sunburst-ABDTE22P.js.map → sunburst-DRCVSC2X.js.map} +0 -0
  865. /package/dist/{survival-HROP7OR7.js.map → survival-AK75COPY.js.map} +0 -0
  866. /package/dist/{survival-KZDESA36.js.map → survival-IF5NI3A6.js.map} +0 -0
  867. /package/dist/{survival.integration.spec-CMZTALBF.js.map → survival.integration.spec-7IWBTPJG.js.map} +0 -0
  868. /package/dist/{svgraph-TLRXKVWQ.js.map → svgraph-QBDF2SLB.js.map} +0 -0
  869. /package/dist/{svmr-R4QOXWQW.js.map → svmr-O4GJJUT2.js.map} +0 -0
  870. /package/dist/{table-QM3RZQ5R.js.map → table-FQAIXKLE.js.map} +0 -0
  871. /package/dist/{termCollection-WVYJHPIH.js.map → termCollection-GMDDL3L7.js.map} +0 -0
  872. /package/dist/{termCollection-B2A3MSCD.js.map → termCollection-ZO5PZ7E3.js.map} +0 -0
  873. /package/dist/{termCollection.unit.spec-TCPEEZHW.js.map → termCollection.unit.spec-5JBCTXHX.js.map} +0 -0
  874. /package/dist/{tk-DGFFDV7C.js.map → tk-GJX23IV7.js.map} +0 -0
  875. /package/dist/{tp.ui-BEESUHHF.js.map → tp.ui-T7FVMTGQ.js.map} +0 -0
  876. /package/dist/{tvs.dt-UZW3L4MO.js.map → tvs.dt-X7L7NSU6.js.map} +0 -0
  877. /package/dist/{tvs.dtcnv.categorical-OH5NXCDN.js.map → tvs.dtcnv.categorical-73G2V6CH.js.map} +0 -0
  878. /package/dist/{tvs.dtcnv.continuous-VWWTWAX2.js.map → tvs.dtcnv.continuous-DWFJL3X7.js.map} +0 -0
  879. /package/dist/{tvs.dtfusion-YKYYCDJN.js.map → tvs.dtfusion-HQADHCSV.js.map} +0 -0
  880. /package/dist/{tvs.dtsnvindel-Y3WAHLKK.js.map → tvs.dtsnvindel-PY5OBMGW.js.map} +0 -0
  881. /package/dist/{tvs.dtsv-UFLR2XRY.js.map → tvs.dtsv-OTBEEWSW.js.map} +0 -0
  882. /package/dist/{tvs.samplelst-BPWZHD62.js.map → tvs.samplelst-LCXSU5MG.js.map} +0 -0
  883. /package/dist/{tvs.termCollection-JLA3JQFX.js.map → tvs.termCollection-L527XN4X.js.map} +0 -0
  884. /package/dist/{violin-TFNQIETS.js.map → violin-6VKRUQV3.js.map} +0 -0
  885. /package/dist/{violin.integration.spec-XKNZQVN7.js.map → violin.integration.spec-RJATDLQH.js.map} +0 -0
  886. /package/dist/{violin.interactivity-R2EYNWI6.js.map → violin.interactivity-SKF5H7MN.js.map} +0 -0
  887. /package/dist/{violin.renderer-5WA4YLGB.js.map → violin.renderer-GB4TPX3B.js.map} +0 -0
  888. /package/dist/{vocabulary-D2XUEKI6.js.map → vocabulary-D3W44IWE.js.map} +0 -0
@@ -1,956 +0,0 @@
1
- import {
2
- buildAnnotationsCsv
3
- } from "./chunk-XJGPL2JZ.js";
4
- import {
5
- PlotBase,
6
- filterInit,
7
- getNormalRoot,
8
- renderTable,
9
- sayerror
10
- } from "./chunk-APO4BA2P.js";
11
- import "./chunk-HJ6L54YS.js";
12
- import {
13
- require_debounce
14
- } from "./chunk-LSEFWW72.js";
15
- import "./chunk-X3Q6I37T.js";
16
- import "./chunk-HYOEWQ5P.js";
17
- import "./chunk-HBW42TDT.js";
18
- import "./chunk-G6O3URDN.js";
19
- import "./chunk-FN5XPUPH.js";
20
- import "./chunk-IIT367QZ.js";
21
- import "./chunk-RZGEKL77.js";
22
- import "./chunk-XVZ5UJWU.js";
23
- import "./chunk-WS3NUPNV.js";
24
- import {
25
- clearServerDataCache,
26
- dofetch2,
27
- dofetch3
28
- } from "./chunk-6VKTEMFV.js";
29
- import "./chunk-7IYJZZQI.js";
30
- import {
31
- copyMerge,
32
- getCompInit
33
- } from "./chunk-M3J4MINX.js";
34
- import "./chunk-PF4DSFDR.js";
35
- import "./chunk-S4JLRRKK.js";
36
- import "./chunk-TVADJLMF.js";
37
- import {
38
- getColors
39
- } from "./chunk-EBKERML3.js";
40
- import "./chunk-DD4R5P6W.js";
41
- import "./chunk-JNITUVXP.js";
42
- import "./chunk-KSGA62R2.js";
43
- import "./chunk-LOZEKOES.js";
44
- import "./chunk-TOU7EVFQ.js";
45
- import "./chunk-OAWQ6LOO.js";
46
- import "./chunk-TLT4YIG3.js";
47
- import "./chunk-KYBIQBXE.js";
48
- import "./chunk-I6Y4O3RR.js";
49
- import {
50
- rgb
51
- } from "./chunk-OMR2DT66.js";
52
- import "./chunk-DQC5FFGV.js";
53
- import {
54
- __toESM
55
- } from "./chunk-HFNDKYVF.js";
56
-
57
- // plots/aiProjectAdmin/defaults.ts
58
- function getDefaultAIProjectAdminSettings(overrides = {}) {
59
- const defaults = {};
60
- return Object.assign(defaults, overrides);
61
- }
62
-
63
- // plots/aiProjectAdmin/repo/ProjectReposity.ts
64
- var ProjectReposity = class {
65
- async getAuthorization(genome, dslabel, actions) {
66
- const body = {
67
- genome,
68
- dslabel,
69
- for: "auth",
70
- auth: actions
71
- };
72
- try {
73
- const response = await dofetch2("aiProjectAdmin", { body });
74
- return response || {};
75
- } catch (error) {
76
- console.error("Error fetching authorizations:", error);
77
- throw error;
78
- }
79
- }
80
- async getProjects(genome, dslabel) {
81
- const body = {
82
- genome,
83
- dslabel,
84
- for: "list"
85
- };
86
- try {
87
- const response = await dofetch3("aiProjectAdmin", { body });
88
- return response || [];
89
- } catch (error) {
90
- console.error("Error fetching projects:", error);
91
- throw error;
92
- }
93
- }
94
- /** Gets the image paths from db */
95
- async getImagePaths(genome, dslabel, project) {
96
- const body = {
97
- genome,
98
- dslabel,
99
- for: "images",
100
- project
101
- };
102
- try {
103
- return await dofetch3("aiProjectAdmin", { body });
104
- } catch (error) {
105
- console.error("Error fetching images:", error);
106
- throw error;
107
- }
108
- }
109
- async updateProject(_body, method) {
110
- const body = Object.assign({}, _body, { for: "admin" });
111
- try {
112
- if (method == "PUT" || method == "DELETE") {
113
- return await dofetch2("aiProjectAdmin", { method, body }, {});
114
- }
115
- return await dofetch3("aiProjectAdmin", { method, body });
116
- } catch (error) {
117
- console.error("Error fetching projects:", error);
118
- throw error;
119
- }
120
- }
121
- //TODO: Will need a method to call metadata API, then build dictionary
122
- async getTerms(app) {
123
- const root = { id: "__root", name: "root", __tree_isroot: true };
124
- try {
125
- await app.vocabApi.buildAdHocDictionary();
126
- const terms = await app.vocabApi.getTermChildren(root, []);
127
- return terms || [];
128
- } catch (error) {
129
- console.error("Error getting terms:", error);
130
- throw error;
131
- }
132
- }
133
- async getAnnotations(genome, dslabel, projectId) {
134
- try {
135
- const body = {
136
- genome,
137
- dslabel,
138
- projectId,
139
- wsimagesFilenames: ["all"]
140
- };
141
- const response = await dofetch3("aiProjectSelectedWSImages", { body });
142
- const wsimages = response?.wsimages || [];
143
- const annotations = [];
144
- for (const w of wsimages) {
145
- const anns = w.annotations || [];
146
- const filename = w.filename;
147
- if (Array.isArray(anns)) {
148
- for (const a of anns) {
149
- annotations.push(Object.assign({ filename }, a));
150
- }
151
- }
152
- }
153
- return annotations;
154
- } catch (error) {
155
- console.error("Error fetching annotations from server:", error);
156
- throw error;
157
- }
158
- }
159
- };
160
-
161
- // plots/aiProjectAdmin/view/ProjectAdminRender.ts
162
- var import_debounce = __toESM(require_debounce(), 1);
163
- var ProjectAdminRender = class {
164
- constructor(dom, projects, interactions, wsiApp) {
165
- this.dom = dom;
166
- this.projects = projects;
167
- this.interactions = interactions;
168
- this.wsiApp = wsiApp;
169
- }
170
- /** Renders project administration UI, allowing users to
171
- * create new projects or edit existing ones.*/
172
- renderProjectAdmin() {
173
- const projectDiv = this.dom.holder.append("div").attr("id", "sjpp-ai-prjt-admin-projects").attr("class", "sjpp-deletable-ai-prjt-admin-div");
174
- this.interactions.getAuthorization(["addProject"]).then((isAuthorized) => {
175
- console.log(isAuthorized);
176
- if (isAuthorized.addProject) {
177
- this.renderCreateProject(projectDiv);
178
- }
179
- }).catch((e) => {
180
- console.error("Error checking authorization:", e.message || e);
181
- sayerror(this.dom.errorDiv, "Error checking user authorization. Please try again later.");
182
- }).finally(() => {
183
- this.renderProjectSelection(projectDiv);
184
- });
185
- }
186
- /** Users submit a new project name before sample
187
- * filtering UI to finalize project creation.*/
188
- renderCreateProject(projectDiv) {
189
- const newProjectDiv = projectDiv.append("div").attr("class", "sjpp-project-select-new").style("padding", "10px");
190
- const input = newProjectDiv.append("input").attr("id", "sjpp-new-project-name").attr("display", "inline-block").attr("placeholder", "New project name");
191
- const button = newProjectDiv.append("div").text("Create Project").classed("sja_menuoption", true).style("display", "inline-block").property("disabled", true).on("click", async () => {
192
- const projectName = input.property("value");
193
- const prjtNameLen = projectName.trim().length;
194
- const showError = (msg) => {
195
- sayerror(this.dom.errorDiv, msg);
196
- input.property("value", "");
197
- button.property("disabled", true);
198
- setTimeout(() => {
199
- this.dom.errorDiv.selectAll("*").remove();
200
- }, 3e3);
201
- };
202
- if (!(await this.interactions.getAuthorization(["addProject"])).addProject) {
203
- return showError("Only users with admin role can create projects");
204
- }
205
- if (prjtNameLen == 0) {
206
- return showError("Project name cannot be empty");
207
- }
208
- if (prjtNameLen > 50 || prjtNameLen < 3) {
209
- return showError("Project name must be between 3 and 50 characters");
210
- }
211
- const notUnique = this.projects.some((p) => p.name === projectName.trim());
212
- if (notUnique) {
213
- return showError(`Project name '${projectName}' already exists`);
214
- }
215
- if (this.dom.header) this.dom.header.text(`Project: ${projectName}`);
216
- await this.interactions.appDispatchEdit({ project: { name: projectName, type: "new" } });
217
- });
218
- input.on("keydown", () => {
219
- const debouncer = () => {
220
- button.property("disabled", input.property("value").length == 0);
221
- };
222
- (0, import_debounce.debounce)(debouncer, 300)();
223
- });
224
- }
225
- /** Users may select an existing project from a table
226
- * returned for the db to edit or delete, depending
227
- * on user roles.*/
228
- renderProjectSelection(projectDiv) {
229
- if (!this.projects.length) {
230
- projectDiv.append("div").attr("class", "sjpp-project-select-table").style("padding", "10px").append("div").text("No projects found. Please create a new project or request one from your admin.");
231
- return;
232
- }
233
- const tableDiv = projectDiv.append("div").attr("class", "sjpp-project-select-table").style("padding", "10px");
234
- const columns = [{ label: "Project", sortable: true }];
235
- let rows = this.projects.map((p) => [{ value: p.name }]);
236
- const columnButtons = [
237
- {
238
- text: "Edit",
239
- class: "sja_menuoption",
240
- //_ = event, __ = idx
241
- callback: async (_, idx) => {
242
- const project = this.projects[idx];
243
- await this.interactions.appDispatchEdit({ project: { ...project, type: "edit" } });
244
- await this.interactions.launchViewer(this.dom.holder, []);
245
- }
246
- },
247
- {
248
- // Export button - pass only project.id and export will be CSV
249
- text: "Export",
250
- class: "sja_menuoption",
251
- callback: async (_, idx) => {
252
- const project = this.projects[idx];
253
- try {
254
- await this.interactions.exportAnnotations(project.id);
255
- } catch (_2) {
256
- sayerror(this.dom.errorDiv, "Failed to export annotations");
257
- }
258
- }
259
- }
260
- ];
261
- this.interactions.getAuthorization(["deleteProject", "logOut", "required"]).then((isAuthorized) => {
262
- if (isAuthorized.required) {
263
- columns.push({ label: "User", sortable: false });
264
- rows = this.projects.map((p) => [{ value: p.name }, { value: p.current_user ?? "Editable" }]);
265
- }
266
- if (isAuthorized.deleteProject) {
267
- columnButtons.push({
268
- text: "Delete",
269
- class: "sja_menuoption",
270
- callback: async (_, i) => {
271
- const project = this.projects[i];
272
- this.interactions.deleteProject(project).then((success) => {
273
- if (success) {
274
- this.projects.splice(i, 1);
275
- projectDiv.select(".sjpp-project-select-table").remove();
276
- this.renderProjectSelection(projectDiv);
277
- }
278
- });
279
- }
280
- });
281
- }
282
- if (isAuthorized.logOut) {
283
- columnButtons.push({
284
- text: "Force Checkout",
285
- class: "sja_menuoption",
286
- callback: async (_, i) => {
287
- const project = this.projects[i];
288
- await this.interactions.onLogOut(this.interactions.genome, this.interactions.dslabel, project.id);
289
- }
290
- });
291
- }
292
- }).catch((e) => {
293
- console.error("Error checking authorization:", e.message || e);
294
- sayerror(this.dom.errorDiv, "Error checking user authorization. Please try again later.");
295
- }).finally(() => {
296
- renderTable({
297
- div: tableDiv,
298
- rows,
299
- header: {
300
- allowSort: true
301
- },
302
- columns,
303
- singleMode: true,
304
- columnButtons
305
- });
306
- });
307
- }
308
- };
309
-
310
- // plots/aiProjectAdmin/view/LogoutRenderer.ts
311
- var LogoutRenderer = class {
312
- constructor(interactions) {
313
- this.interactions = interactions;
314
- }
315
- render(holder, genome, dslabel, projectId) {
316
- holder.append("div").style("position", "absolute").style("top", "10px").attr("data-testid", "logout-button").style("right", "20px").style("z-index", "1000").append("button").attr("type", "submit").style("font-size", "1.25em").style("padding", "10px 25px").style("border-radius", "20px").style("border", "1px solid black").style("background-color", "white").style("cursor", "pointer").text("Check Out").on("click", async () => {
317
- holder.selectAll("*").remove();
318
- await this.interactions.onLogOut(genome, dslabel, projectId);
319
- });
320
- }
321
- };
322
-
323
- // plots/aiProjectAdmin/interactions/AIProjectAdminInteractions.ts
324
- var AIProjectAdminInteractions = class {
325
- constructor(app, id, prjtRepo) {
326
- this.app = app;
327
- this.id = id;
328
- this.genome = app.vocabApi.vocab.genome;
329
- this.dslabel = app.vocabApi.vocab.dslabel;
330
- this.prjtRepo = prjtRepo;
331
- }
332
- async getAuthorization(actions) {
333
- try {
334
- return await this.prjtRepo.getAuthorization(this.genome, this.dslabel, actions);
335
- } catch (e) {
336
- console.error("Error checking authorization:", e.message || e);
337
- throw e;
338
- }
339
- }
340
- async addProject(opts) {
341
- const config = this.getConfig();
342
- const settings = config.settings || {};
343
- const projectObject = Object.assign({}, settings.project, opts.project);
344
- const body = {
345
- genome: this.genome,
346
- dslabel: this.dslabel,
347
- project: projectObject
348
- };
349
- try {
350
- await this.prjtRepo.updateProject(body, "PUT");
351
- } catch (e) {
352
- console.error("Error adding project:", e.message || e);
353
- throw e;
354
- }
355
- }
356
- async editProject(opts) {
357
- const config = this.getConfig();
358
- const settings = config.settings || {};
359
- const project = Object.assign(
360
- {},
361
- settings.project,
362
- {
363
- type: "edit"
364
- },
365
- opts.project
366
- );
367
- const body = {
368
- genome: this.genome,
369
- dslabel: this.dslabel,
370
- project
371
- };
372
- try {
373
- const res = await this.prjtRepo.updateProject(body, "POST");
374
- if (!project.id) project.id = res.projectId;
375
- } catch (e) {
376
- console.error("Error editing project:", e.message || e);
377
- throw e;
378
- }
379
- await this.appDispatchEdit({ project }, config);
380
- }
381
- async deleteProject(project) {
382
- let success = false;
383
- const body = {
384
- genome: this.genome,
385
- dslabel: this.dslabel,
386
- project: {
387
- name: project.value,
388
- id: project.id
389
- }
390
- };
391
- try {
392
- const response = await this.prjtRepo.updateProject(body, "DELETE");
393
- if (response && response.status === "ok") {
394
- success = true;
395
- }
396
- } catch (e) {
397
- console.error("Error deleting project:", e.message || e);
398
- throw e;
399
- }
400
- return success;
401
- }
402
- async getFilteredImages(filter) {
403
- const config = this.getConfig();
404
- const settings = config.settings || {};
405
- return await this.app.vocabApi.getFilteredAiImages(settings.project, filter);
406
- }
407
- async launchViewer(holder, _images) {
408
- const config = this.getConfig();
409
- const settings = config.settings;
410
- if (!settings.project || !settings.project.id) throw new Error("Project is required to launch viewer");
411
- let images = [];
412
- if (_images && _images.length > 0) {
413
- images = _images;
414
- } else {
415
- const response = await this.prjtRepo.getImagePaths(
416
- this.genome,
417
- this.dslabel,
418
- settings.project
419
- );
420
- if (response.status !== "ok") {
421
- await this.appDispatchEdit({ project: { name: "", type: "logout" } }, config);
422
- sayerror(holder, response.error || "Error fetching images");
423
- return;
424
- }
425
- holder.selectAll(".sjpp-deletable-ai-prjt-admin-div").remove();
426
- images = response.images;
427
- }
428
- const wsiViewer = await import("./plot.wsi-QJ52IJXL.js");
429
- const genome = this.genome;
430
- const dslabel = this.dslabel;
431
- const logoutRenderer = new LogoutRenderer(this);
432
- logoutRenderer.render(holder, genome, dslabel, settings.project.id);
433
- wsiViewer.default(this.dslabel, holder, { name: this.genome }, null, settings.project.id, images, true);
434
- }
435
- async appDispatchEdit(settings, config = {}) {
436
- if (!config?.settings) {
437
- config = this.getConfig();
438
- if (!config) throw new Error(`No plot with id='${this.id}' found.`);
439
- }
440
- const configSettings = config.settings;
441
- const mergedSettings = {
442
- project: { name: "", type: "logout", ...configSettings?.project, ...settings.project }
443
- };
444
- await this.app.dispatch({
445
- type: "plot_edit",
446
- id: this.id,
447
- config: { settings: mergedSettings }
448
- });
449
- }
450
- getConfig() {
451
- return this.app.getState().plots.find((p) => p.id === this.id);
452
- }
453
- async exportAnnotations(projectId) {
454
- const config = this.getConfig();
455
- if (!config || !config.settings) throw new Error(`No plot with id='${this.id}' found.`);
456
- const settings = config.settings || {};
457
- let annotations = [];
458
- try {
459
- annotations = await this.prjtRepo.getAnnotations(this.genome, this.dslabel, projectId);
460
- } catch (e) {
461
- console.error("Error fetching annotations for export:", e?.message || e);
462
- throw e;
463
- }
464
- const mime = "text/csv;charset=utf-8;";
465
- let content;
466
- if (!Array.isArray(annotations) || annotations.length === 0) {
467
- content = "";
468
- } else {
469
- content = buildAnnotationsCsv(annotations);
470
- }
471
- const rawName = settings.project && settings.project.name ? String(settings.project.name) : `project-${projectId}`;
472
- const safeName = rawName.replace(/[^a-z0-9_.-]/gi, "_").slice(0, 200);
473
- const filename = `${safeName}-annotations.csv`;
474
- try {
475
- const blob = new Blob([content], { type: mime });
476
- const url = URL.createObjectURL(blob);
477
- const a = document.createElement("a");
478
- a.href = url;
479
- a.download = filename;
480
- document.body.appendChild(a);
481
- a.click();
482
- a.remove();
483
- setTimeout(() => URL.revokeObjectURL(url), 1e3);
484
- } catch (e) {
485
- console.error("Error creating annotation download:", e?.message || e);
486
- throw e;
487
- }
488
- }
489
- async onLogOut(genome, dslabel, projectId) {
490
- try {
491
- await dofetch3("aiProjectAdmin", {
492
- body: {
493
- genome,
494
- dslabel,
495
- for: "logout",
496
- project: { id: projectId }
497
- }
498
- });
499
- clearServerDataCache();
500
- await this.appDispatchEdit({ project: { name: "", id: projectId, type: "logout" } });
501
- } catch (e) {
502
- console.error("Error logging out: " + (e.message || e));
503
- throw e;
504
- }
505
- }
506
- };
507
-
508
- // plots/aiProjectAdmin/view/ClassesTableRender.ts
509
- var ClassesTableRender = class {
510
- constructor(holder, rows) {
511
- this.dom = {
512
- holder,
513
- tableDiv: holder.append("div"),
514
- btnDiv: holder.append("div")
515
- };
516
- this.columns = [
517
- { label: "" },
518
- // Empty for the delete icon
519
- {
520
- label: "NAME",
521
- editCallback: (rowIdx, cell) => {
522
- const newValue = cell.value.trim();
523
- const foundSameName = this.rows.some((r, i) => newValue === r[1].value.trim() && i !== rowIdx);
524
- if (foundSameName) {
525
- alert(`Class name '${newValue}' already exists`);
526
- cell.value = this.rowsCopy[rowIdx][1].value;
527
- cell.__td.text(this.rowsCopy[rowIdx][1].value);
528
- return;
529
- }
530
- this.rowsCopy = this.rows.map((r) => r.map((c) => ({ ...c })));
531
- }
532
- },
533
- { label: "COLOR" }
534
- ];
535
- const colorScale = getColors(5);
536
- this.rows = rows || this.setDefaultClasses(colorScale);
537
- this.rowsCopy = [];
538
- this.renderTable();
539
- this.renderAddClassBtn(colorScale);
540
- }
541
- renderTable() {
542
- this.dom.tableDiv.select("table").remove();
543
- if (!this.rows || this.rows.length === 0) return;
544
- this.rowsCopy = this.rows.map((r) => r.map((c) => ({ ...c })));
545
- renderTable({
546
- div: this.dom.tableDiv,
547
- columns: this.columns,
548
- rows: this.rows,
549
- striped: false,
550
- showLines: false,
551
- singleMode: false,
552
- resize: true
553
- });
554
- for (const [i, row] of this.rows.entries()) {
555
- const deleteBtn = row[0].__td.select(".sja_menuoption");
556
- deleteBtn.on("click", () => {
557
- this.rows.splice(i, 1);
558
- this.renderTable();
559
- });
560
- }
561
- }
562
- setDefaultClasses(colorScale) {
563
- const rows = [];
564
- for (let i = 0; i < 4; i++) {
565
- this.getNewClass(colorScale, rows);
566
- }
567
- return rows;
568
- }
569
- getNewClass(colorScale, rows) {
570
- const getName = (i2) => `New class ${i2}`;
571
- let i = 1;
572
- let found = true;
573
- while (found) {
574
- const checkName = getName(i);
575
- found = rows.some((r) => r[1].value == checkName);
576
- if (found) i++;
577
- }
578
- rows.push([
579
- { html: `<div class="sja_menuoption">&times;<div>` },
580
- { value: getName(i) },
581
- { color: rgb(colorScale(`${i}`)).formatHex() }
582
- ]);
583
- }
584
- renderAddClassBtn(colorScale) {
585
- this.dom.btnDiv.append("div").text("Add Class").classed("sja_menuoption", true).style("display", "inline-block").style("margin", "10px 0px 0px 0px").on("click", () => {
586
- if (this.rows.length >= 9) {
587
- alert("Maximum number of classes reached.");
588
- return;
589
- }
590
- this.getNewClass(colorScale, this.rows);
591
- this.renderTable();
592
- });
593
- }
594
- };
595
-
596
- // plots/aiProjectAdmin/view/SelectorTableRender.ts
597
- var SelectorTableRender = class {
598
- constructor(holder, interactions, images) {
599
- this.images = { rows: [], cols: [] };
600
- this.selectedRows = /* @__PURE__ */ new Set();
601
- this.sortedIndexMap = [];
602
- this.dom = {
603
- holder,
604
- tableDiv: holder.append("div").attr("class", ".sjpp-deletable-ai-prjt-admin-div").attr("id", "sjpp-selector-table").style("padding", "10px 0"),
605
- btnDiv: holder.append("div").attr("class", ".sjpp-deletable-ai-prjt-admin-div").attr("id", "sjpp-selector-btns")
606
- };
607
- this.images = images;
608
- this.interactions = interactions;
609
- const selectedList = images?.selectedImages;
610
- const normalizeImageName = (s) => String(s ?? "").replace(/\.svs$/i, "").toLowerCase();
611
- const selectedSet = new Set((selectedList || []).map(normalizeImageName));
612
- this.selectedRows = /* @__PURE__ */ new Set();
613
- (this.images?.rows ?? []).forEach((row, i) => {
614
- const candidate = row?.[0]?.value;
615
- const n = normalizeImageName(candidate);
616
- if (selectedSet.has(n)) this.selectedRows.add(i);
617
- });
618
- this.render();
619
- }
620
- render() {
621
- if (this.images === void 0) this.dom.tableDiv.append("div").text("No images found").style("color", "red");
622
- const columns = this.images.cols.map((c) => ({ ...c, sortable: true })) || [];
623
- if (!columns.length) {
624
- this.dom.tableDiv.append("div").text("Missing columns data").style("color", "red");
625
- this.renderApplyBtn(
626
- /*disable=*/
627
- true
628
- );
629
- return;
630
- }
631
- const rows = this.images?.rows ?? [];
632
- const mapped = rows.map((row, origIdx) => ({
633
- row,
634
- origIdx,
635
- selected: this.selectedRows.has(origIdx)
636
- }));
637
- mapped.sort((a, b) => {
638
- const selDiff = Number(b.selected) - Number(a.selected);
639
- return selDiff || a.origIdx - b.origIdx;
640
- });
641
- const rowsSorted = mapped.map((m) => m.row);
642
- this.sortedIndexMap = mapped.map((m) => m.origIdx);
643
- const selectedRowsForRender = mapped.reduce((acc, m, idx) => {
644
- if (m.selected) acc.push(idx);
645
- return acc;
646
- }, []);
647
- renderTable({
648
- div: this.dom.tableDiv,
649
- columns,
650
- rows: rowsSorted,
651
- selectedRows: selectedRowsForRender,
652
- striped: true,
653
- header: { allowSort: true },
654
- noButtonCallback: (sortedIdx, node) => {
655
- const orig = this.sortedIndexMap?.[sortedIdx];
656
- if (orig === void 0) return;
657
- if (node.checked) {
658
- this.selectedRows.add(orig);
659
- } else {
660
- this.selectedRows.delete(orig);
661
- }
662
- }
663
- });
664
- this.renderApplyBtn(
665
- /*disable=*/
666
- false
667
- );
668
- }
669
- renderApplyBtn(disable = false) {
670
- const btn = this.dom.btnDiv.append("div").text("Apply").classed("sja_menuoption", true).style("display", "block").style("width", "fit-content").style("margin-left", "5vw");
671
- if (disable) btn.attr("disabled", true);
672
- btn.on("click", async () => {
673
- if (!this.selectedRows.size) {
674
- alert(`No rows selected. Please select some rows.`);
675
- return;
676
- }
677
- btn.attr("disabled", true);
678
- const images = Array.from(this.selectedRows).map((i) => `${this.images.rows[i][0].value}.svs`);
679
- await this.interactions.editProject({
680
- project: {
681
- images,
682
- type: "edit"
683
- }
684
- });
685
- this.dom.holder.selectAll("*").remove();
686
- await this.interactions.launchViewer(this.dom.holder, images);
687
- });
688
- }
689
- };
690
-
691
- // plots/aiProjectAdmin/view/UsersRender.ts
692
- var UsersRender = class {
693
- constructor(dom, users = []) {
694
- this.dom = dom;
695
- this.users = users.slice();
696
- }
697
- render() {
698
- const container = this.dom.holder.append("div").attr("id", "sjpp-users-render").attr("class", "sjpp-deletable-ai-prjt-admin-div").style("padding", "10px");
699
- const inputRow = container.append("div").attr("class", "sjpp-users-input-row").style("margin-bottom", "10px");
700
- const input = inputRow.append("input").attr("type", "text").attr("placeholder", "user@example.com").attr("id", "sjpp-user-email-input").style("margin-right", "8px").style("width", "300px");
701
- const addBtn = inputRow.append("div").text("Add").classed("sja_menuoption", true).style("display", "inline-block").property("disabled", true).on("click", () => {
702
- const email = input.property("value").trim();
703
- const showError = (msg) => {
704
- sayerror(this.dom.errorDiv, msg);
705
- setTimeout(() => this.dom.errorDiv.selectAll("*").remove(), 3e3);
706
- };
707
- if (email.length === 0) {
708
- return showError("Email cannot be empty");
709
- }
710
- const emailRe = /^[A-Za-z0-9._%+-]+@[A-Za-z0-9.-]+\.[A-Za-z]{2,}$/;
711
- if (!emailRe.test(email)) {
712
- return showError("Invalid email address");
713
- }
714
- if (this.users.includes(email)) {
715
- return showError("Email already added");
716
- }
717
- this.users.push(email);
718
- input.property("value", "");
719
- addBtn.property("disabled", true);
720
- this.renderTableArea(container);
721
- });
722
- input.on("input", () => {
723
- addBtn.property("disabled", input.property("value").trim().length === 0);
724
- });
725
- this.renderTableArea(container);
726
- }
727
- renderTableArea(container) {
728
- container.select(".sjpp-users-table-area").remove();
729
- const tableDiv = container.append("div").attr("class", "sjpp-users-table-area").style("padding", "6px 0");
730
- if (!this.users.length) {
731
- tableDiv.append("div").text("No users added yet.").style("color", "#666");
732
- return;
733
- }
734
- const columns = [{ label: "Email", sortable: true }];
735
- const columnButtons = [
736
- {
737
- text: "\xD7",
738
- class: "sja_menuoption",
739
- callback: (_, idx) => {
740
- this.users.splice(idx, 1);
741
- container.select(".sjpp-users-table-area").remove();
742
- this.renderTableArea(container);
743
- }
744
- }
745
- ];
746
- renderTable({
747
- div: tableDiv,
748
- rows: this.users.map((u) => [{ value: u }]),
749
- columns,
750
- columnButtons,
751
- singleMode: false,
752
- striped: false,
753
- showLines: false,
754
- resize: true
755
- });
756
- tableDiv.selectAll(".sja_menuoption").html("\xD7<div></div>");
757
- }
758
- };
759
-
760
- // plots/aiProjectAdmin/view/CreateProjectRender.ts
761
- var CreateProjectRender = class {
762
- constructor(dom, app, interactions) {
763
- dom.holder.style("padding", "10px 20px").attr("class", "sjpp-deletable-ai-prjt-admin-div");
764
- const filterDiv = dom.holder.append("div").attr("id", "sjpp-ai-prjt-admin-filter-div");
765
- const wrapper = dom.holder.append("div").attr("id", "sjpp-ai-prjt-admin-classes-users-wrapper").style("display", "flex").style("gap", "20px").style("align-items", "flex-start").style("padding", "20px 0px");
766
- const left = wrapper.append("div").attr("id", "sjpp-ai-prjt-admin-classes-table").style("flex", "0 1 auto");
767
- const right = wrapper.append("div").attr("id", "sjpp-ai-prjt-admin-users").style("width", "320px").style("margin-left", "8px");
768
- this.dom = {
769
- holder: dom.holder,
770
- errorDiv: dom.errorDiv,
771
- filterDiv,
772
- classDiv: left,
773
- usersDiv: right
774
- };
775
- this.app = app;
776
- this.interactions = interactions;
777
- this.filter = null;
778
- }
779
- render() {
780
- this.renderFilter();
781
- this.classesTable = new ClassesTableRender(this.dom.classDiv);
782
- this.usersRender = new UsersRender({ holder: this.dom.usersDiv, errorDiv: this.dom.errorDiv }, []);
783
- this.usersRender.render();
784
- this.renderApplyBtn();
785
- }
786
- renderFilter() {
787
- const filter = filterInit({
788
- holder: this.dom.filterDiv,
789
- emptyLabel: "Add filter",
790
- vocabApi: this.app.vocabApi,
791
- termdbConfig: this.app.vocabApi.termdbConfig,
792
- callback: (filter2) => {
793
- this.filter = filter2;
794
- }
795
- });
796
- const state = this.app.getState();
797
- const root = getNormalRoot(state.termfilter.filter);
798
- filter.main(root);
799
- }
800
- renderApplyBtn() {
801
- const btn = this.dom.classDiv.append("div").text("Apply").classed("sja_menuoption", true).style("display", "inline-block").style("margin-left", "200px").on("click", async () => {
802
- btn.attr("disabled", true);
803
- const selections = await this.interactions.getFilteredImages(this.filter);
804
- if (this.filter && selections.status !== "ok" || selections.data?.selectedImages?.length === 0) {
805
- alert("No images match your filter criteria.");
806
- return;
807
- }
808
- if (!this.usersRender || !Array.isArray(this.usersRender.users) || this.usersRender.users.length === 0) {
809
- alert("Please add at least one user.");
810
- btn.attr("disabled", null);
811
- return;
812
- }
813
- await this.interactions.addProject({
814
- project: {
815
- filter: this.filter,
816
- classes: this.classesTable.rows.map((row, i) => {
817
- return { label: row[1].value, color: row[2].color, key_shortcut: `Digit${i + 1}` };
818
- }),
819
- users: this.usersRender?.users || []
820
- }
821
- });
822
- this.dom.holder.selectAll("*").remove();
823
- new SelectorTableRender(this.dom.holder, this.interactions, selections.data);
824
- });
825
- }
826
- /**** Uncomment before production */
827
- // private validateInput() {
828
- // const invalidInfo = {
829
- // entries: [] as { dataType: string; reason: string }[],
830
- // errorMsg: 'Please clear all "Data type: Class" errors before applying changes.'
831
- // }
832
- // //Show user error if no filter is defined.
833
- // if (!this.filter) {
834
- // invalidInfo.entries.push({ dataType: 'Filter', reason: 'No filter defined. Did you mean to add a filter?' })
835
- // }
836
- // //Check if all classes were deleted
837
- // const classes = this.classesTable?.rows.map(row => row[1].value) || []
838
- // if (classes.length === 0) {
839
- // invalidInfo.entries.push({ dataType: 'Class', reason: 'No classes defined. Did you mean to add a class?' })
840
- // }
841
- // //Check to see if any class is still a default class
842
- // const unchangedClasses =
843
- // this.classesTable?.rows
844
- // .filter(row => (row[1]?.value as string)?.startsWith('New class'))
845
- // .map(r => r[1]?.value as string) || []
846
- // for (const c of unchangedClasses) {
847
- // invalidInfo.entries.push({ dataType: 'Class', reason: `${c} is the default class name. Please rename.` })
848
- // }
849
- // return invalidInfo
850
- // }
851
- };
852
-
853
- // plots/aiProjectAdmin/AIProjectAdmin.ts
854
- var AIProjectAdmin = class extends PlotBase {
855
- constructor(opts, api) {
856
- super(opts, api);
857
- this.type = "AIProjectAdmin";
858
- this.opts = opts;
859
- this.dom = {
860
- holder: opts.holder,
861
- errorDiv: opts.holder.append("div").style("margin", "3px").attr("class", "sjpp-ai-prjt-admin-error")
862
- };
863
- if (opts.header) this.dom.header = opts.header;
864
- this.prjtRepo = new ProjectReposity();
865
- }
866
- static {
867
- this.type = "AIProjectAdmin";
868
- }
869
- getState(appState) {
870
- const config = appState.plots.find((p) => p.id === this.id);
871
- if (!config) {
872
- throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
873
- }
874
- return {
875
- config,
876
- vocab: appState.vocab,
877
- filter: appState.termfilter.filter
878
- };
879
- }
880
- async displayProjects(state, interactions) {
881
- try {
882
- this.projects = await this.prjtRepo.getProjects(state.vocab.genome, state.vocab.dslabel);
883
- } catch (e) {
884
- console.error("Error initializing AIProjectAdmin:", e);
885
- throw e;
886
- }
887
- this.prjtAdminUI = new ProjectAdminRender(this.dom, this.projects, interactions, this.app);
888
- this.prjtAdminUI.renderProjectAdmin();
889
- }
890
- async init(appState) {
891
- this.interactions = new AIProjectAdminInteractions(this.app, this.id, this.prjtRepo);
892
- await this.displayProjects(appState, this.interactions);
893
- }
894
- async main() {
895
- const state = structuredClone(this.state);
896
- const config = state.config;
897
- if (config.chartType != this.type) return;
898
- const project = config.settings.project;
899
- if (!project) return;
900
- if (!this.interactions) throw new Error("AIProjectAdminInteractions not initialized");
901
- this.dom.holder.selectAll(".sjpp-deletable-ai-prjt-admin-div").remove();
902
- if (project.type === "new") {
903
- const terms = await this.prjtRepo.getTerms(this.app);
904
- if (!terms || terms.length === 0) {
905
- sayerror(this.dom.errorDiv, "No metadata found.");
906
- return;
907
- }
908
- const createProjectRender = new CreateProjectRender(this.dom, this.app, this.interactions);
909
- createProjectRender.render();
910
- }
911
- if (project.type == "existing") {
912
- if (!project.name) {
913
- sayerror(this.dom.errorDiv, "Project name not provided.");
914
- return;
915
- }
916
- if (!project.id) {
917
- const existingProject = this.projects?.find((p) => p.name === project.name);
918
- if (!existingProject) {
919
- sayerror(this.dom.errorDiv, `Project ${project.name} not found.`);
920
- return;
921
- }
922
- await this.app.save({
923
- type: "plot_edit",
924
- id: this.id,
925
- config: { settings: { project: { id: existingProject.id } } }
926
- });
927
- }
928
- await this.interactions.launchViewer(this.dom.holder, []);
929
- }
930
- if (project.type === "logout") {
931
- await this.displayProjects(state, this.interactions);
932
- }
933
- }
934
- };
935
- var aiProjectAdminInit = getCompInit(AIProjectAdmin);
936
- var componentInit = aiProjectAdminInit;
937
- async function getPlotConfig(opts) {
938
- const config = {
939
- chartType: "AIProjectAdmin",
940
- subfolder: "aiProjectAdmin",
941
- extension: "ts",
942
- hidePlotFilter: true,
943
- //Disable the filter in the sandbox header
944
- settings: getDefaultAIProjectAdminSettings(opts.overrides)
945
- };
946
- if (opts.settings?.project && !opts.settings?.project?.type) {
947
- opts.settings.project.type = "existing";
948
- }
949
- return copyMerge(config, opts);
950
- }
951
- export {
952
- aiProjectAdminInit,
953
- componentInit,
954
- getPlotConfig
955
- };
956
- //# sourceMappingURL=AIProjectAdmin-AYPMZLCD.js.map