@sjcrh/proteinpaint-client 2.190.2 → 2.191.2

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 (932) hide show
  1. package/dist/2dmaf-V4WJ2LEK.js +1373 -0
  2. package/dist/AIProjectAdmin-JMN5O6YU.js +829 -0
  3. package/dist/AppHeader-Y4SEKCEF.js +835 -0
  4. package/dist/BoxPlot-ZXQZGCR3.js +1211 -0
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  6. package/dist/CorrelationVolcano-R5IWD6WA.js +619 -0
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  9. package/dist/DifferentialAnalysis-NLCA766A.js +245 -0
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  15. package/dist/GeneExpInput-CXYRKQU7.js +366 -0
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  179. package/dist/dnaMethylation-72IS3FRI.js +38 -0
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  839. /package/dist/{matrix.layout-FWWM6QQO.js.map → matrix.layout-5DDZWLNX.js.map} +0 -0
  840. /package/dist/{matrix.legend-QT3PMREX.js.map → matrix.legend-RJAFOZHQ.js.map} +0 -0
  841. /package/dist/{matrix.renderers-M6MJO5IU.js.map → matrix.renderers-VFQZG5JP.js.map} +0 -0
  842. /package/dist/{matrix.serieses-NTKMKT22.js.map → matrix.serieses-GJWHSBG4.js.map} +0 -0
  843. /package/dist/{matrix.sort-TTHPJ4XC.js.map → matrix.sort-KIJENIT2.js.map} +0 -0
  844. /package/dist/{matrix.sort.unit.spec-XZI2KPNC.js.map → matrix.sort.unit.spec-ZA5DRNL6.js.map} +0 -0
  845. /package/dist/{matrix.sorterUi-FFLYKBGC.js.map → matrix.sorterUi-3KEDVLGW.js.map} +0 -0
  846. /package/dist/{matrix.sorterUi.unit.spec-6FVHTGSN.js.map → matrix.sorterUi.unit.spec-7TPOJ46U.js.map} +0 -0
  847. /package/dist/{mavb-FZDN27QY.js.map → mavb-73BXZ7MO.js.map} +0 -0
  848. /package/dist/{mds.fimo-SSFKQ3BH.js.map → mds.fimo-L7VVAOXQ.js.map} +0 -0
  849. /package/dist/{mds.samplescatterplot-BMTTX3TB.js.map → mds.samplescatterplot-6P75XEWB.js.map} +0 -0
  850. /package/dist/{mds.survivalplot-PL75RDYI.js.map → mds.survivalplot-GCVE7XGO.js.map} +0 -0
  851. /package/dist/{numericDictTermCluster-NJUXCQYH.js.map → numericDictTermCluster-OMXIURRD.js.map} +0 -0
  852. /package/dist/{oncomatrix-BZDCCEWH.js.map → oncomatrix-BFWV2IC4.js.map} +0 -0
  853. /package/dist/{oncomatrix.spec-5A4A4JLV.js.map → oncomatrix.spec-J6IAY3O6.js.map} +0 -0
  854. /package/dist/{plot.2dvaf-AC7LW56S.js.map → plot.2dvaf-ESJAB2F3.js.map} +0 -0
  855. /package/dist/{plot.app-DOOWDQ3U.js.map → plot.app-T7CQMBRV.js.map} +0 -0
  856. /package/dist/{plot.barplot-RNJWREG5.js.map → plot.barplot-HAWPMPPU.js.map} +0 -0
  857. /package/dist/{plot.boxplot-CRAEUBQF.js.map → plot.boxplot-4QUORFXY.js.map} +0 -0
  858. /package/dist/{plot.brainImaging-ZESEULN6.js.map → plot.brainImaging-HG6I3GJW.js.map} +0 -0
  859. /package/dist/{plot.disco-B4KBP6RK.js.map → plot.disco-LPH7F6YW.js.map} +0 -0
  860. /package/dist/{plot.dzi-2UMRV6IF.js.map → plot.dzi-DYAY4D4E.js.map} +0 -0
  861. /package/dist/{plot.ssgq-FVZ27Z2K.js.map → plot.ssgq-CF5VIGYJ.js.map} +0 -0
  862. /package/dist/{plot.vaf2cov-3OXCIEAX.js.map → plot.vaf2cov-7HZCKNK6.js.map} +0 -0
  863. /package/dist/{plot.wsi-UKTLZSYW.js.map → plot.wsi-MU6AXOWO.js.map} +0 -0
  864. /package/dist/{profileForms-SBNPRIFT.js.map → profileForms-TIT4JUEJ.js.map} +0 -0
  865. /package/dist/{profilePlot-PPI4IDP4.js.map → profilePlot-QFGRAZQA.js.map} +0 -0
  866. /package/dist/{qualitative-4O6KAGEA.js.map → qualitative-YWP4YUPF.js.map} +0 -0
  867. /package/dist/{radar2-ICKCJY4T.js.map → radar2-TKSHL54E.js.map} +0 -0
  868. /package/dist/{radarFacility2-HEBBSM3T.js.map → radarFacility2-FHRFLBLF.js.map} +0 -0
  869. /package/dist/{regression-YFQJE2EP.js.map → regression-5XG5LXP7.js.map} +0 -0
  870. /package/dist/{regression.inputs-A2JVBVZ7.js.map → regression.inputs-QHXK7ZYY.js.map} +0 -0
  871. /package/dist/{regression.inputs.term-CTVNS5MO.js.map → regression.inputs.term-YYO3CR2D.js.map} +0 -0
  872. /package/dist/{regression.inputs.values.table-X7SI6EDO.js.map → regression.inputs.values.table-3I2FCON2.js.map} +0 -0
  873. /package/dist/{regression.integration.spec-NRDEVBWS.js.map → regression.integration.spec-QVDGCKVT.js.map} +0 -0
  874. /package/dist/{regression.results-XVB6CIGW.js.map → regression.results-B7LVT2WG.js.map} +0 -0
  875. /package/dist/{regression.spec-TNB5HBY5.js.map → regression.spec-ISYKKQOM.js.map} +0 -0
  876. /package/dist/{report-5VDIBC2W.js.map → report-TF6Z3Y44.js.map} +0 -0
  877. /package/dist/{sampleScatter.spec-XDW7SCYA.js.map → sampleScatter.spec-2VW55XIZ.js.map} +0 -0
  878. /package/dist/{sampleView-FLUSGZCM.js.map → sampleView-DNNJRAMU.js.map} +0 -0
  879. /package/dist/{samplelst-4WPG5UBN.js.map → samplelst-726II3LN.js.map} +0 -0
  880. /package/dist/{samplematrix-YJGMSXUJ.js.map → samplematrix-TBPW4URH.js.map} +0 -0
  881. /package/dist/{sc-DHU5KSEJ.js.map → sc-GBYH3W4S.js.map} +0 -0
  882. /package/dist/{selectGenomeWithTklst-BVBMVRMQ.js.map → selectGenomeWithTklst-RCAYDV6D.js.map} +0 -0
  883. /package/dist/{singleCellCellType-DADK5UKZ.js.map → singleCellCellType-IQYCKUT6.js.map} +0 -0
  884. /package/dist/{singleCellCellType.unit.spec-X25RMBJ3.js.map → singleCellCellType.unit.spec-ZEWA2IFI.js.map} +0 -0
  885. /package/dist/{singleCellGeneExpression-3UEZWI4E.js.map → singleCellGeneExpression-STLTBXJQ.js.map} +0 -0
  886. /package/dist/{singleCellGeneExpression.unit.spec-5GU3JWE6.js.map → singleCellGeneExpression.unit.spec-W6FPS5ZU.js.map} +0 -0
  887. /package/dist/{singleCellPlot-TFRZG73T.js.map → singleCellPlot-7XH7NIL4.js.map} +0 -0
  888. /package/dist/{singlecell-KR6JYFAY.js.map → singlecell-IDZB2MXW.js.map} +0 -0
  889. /package/dist/{singlecell-HQH6EWJO.js.map → singlecell-JCXR7X5U.js.map} +0 -0
  890. /package/dist/{snp-ACIZ7D5X.js.map → snp-QOKI26PO.js.map} +0 -0
  891. /package/dist/{snp.unit.spec-653HGJBM.js.map → snp.unit.spec-DTPZAALW.js.map} +0 -0
  892. /package/dist/{snplocus-AH6KJCVN.js.map → snplocus-BKUJYANW.js.map} +0 -0
  893. /package/dist/{spliceevent.a53ss.diagram-MKJLJDOG.js.map → spliceevent.a53ss.diagram-4O54ORKZ.js.map} +0 -0
  894. /package/dist/{spliceevent.exonskip.diagram-PSEVCDH4.js.map → spliceevent.exonskip.diagram-KOIOS6IV.js.map} +0 -0
  895. /package/dist/{spliceevent.noeventdiagram-T2LHGFN7.js.map → spliceevent.noeventdiagram-YGUGQMVE.js.map} +0 -0
  896. /package/dist/{ssGSEA-QFMYBITZ.js.map → ssGSEA-UZMBIHVD.js.map} +0 -0
  897. /package/dist/{ssGSEA.unit.spec-SQW7KFWE.js.map → ssGSEA.unit.spec-4YO4E3T7.js.map} +0 -0
  898. /package/dist/{stattable-QDIUQCMG.js.map → stattable-MDABSW3F.js.map} +0 -0
  899. /package/dist/{summarizeCnvGeneexp-EVRTBY3L.js.map → summarizeCnvGeneexp-HV3DHIW4.js.map} +0 -0
  900. /package/dist/{summarizeGeneexpSurvival-O3MGRS6K.js.map → summarizeGeneexpSurvival-VGPRWYQ5.js.map} +0 -0
  901. /package/dist/{summarizeMutationCnv-RZ2DZ2XO.js.map → summarizeMutationCnv-N3JEB4DJ.js.map} +0 -0
  902. /package/dist/{summarizeMutationDiagnosis-V2DISQTC.js.map → summarizeMutationDiagnosis-6U4DBLG5.js.map} +0 -0
  903. /package/dist/{summarizeMutationSurvival-FTTWJBUG.js.map → summarizeMutationSurvival-S7NLAVEI.js.map} +0 -0
  904. /package/dist/{summary-QKBTZINC.js.map → summary-NPR56I4S.js.map} +0 -0
  905. /package/dist/{summary.integration.spec-54HA7BC2.js.map → summary.integration.spec-HWNJWLKT.js.map} +0 -0
  906. /package/dist/{summaryInput-4RLZT6RW.js.map → summaryInput-DO73NGDQ.js.map} +0 -0
  907. /package/dist/{sunburst-SMKD45XD.js.map → sunburst-MMXSGJSL.js.map} +0 -0
  908. /package/dist/{survival-YQNA3WP7.js.map → survival-7AIKFGV5.js.map} +0 -0
  909. /package/dist/{survival-BAW5ME6J.js.map → survival-UK332X6L.js.map} +0 -0
  910. /package/dist/{survival.integration.spec-2AHXNMH2.js.map → survival.integration.spec-YMTEKEGB.js.map} +0 -0
  911. /package/dist/{svgraph-5Z7VAIVR.js.map → svgraph-MLLAYO4A.js.map} +0 -0
  912. /package/dist/{svmr-PHD76RV4.js.map → svmr-PYW4PLT3.js.map} +0 -0
  913. /package/dist/{table-GMRAOIWZ.js.map → table-Y3ED2444.js.map} +0 -0
  914. /package/dist/{termCollection-QLKTRXUR.js.map → termCollection-3XVL75II.js.map} +0 -0
  915. /package/dist/{termCollection-MEBY34TJ.js.map → termCollection-VAB53YGO.js.map} +0 -0
  916. /package/dist/{termCollection.unit.spec-6B53SW2Q.js.map → termCollection.unit.spec-DYPWNVEZ.js.map} +0 -0
  917. /package/dist/{termInfo-2Z4V2QLE.js.map → termInfo-6MJDJSDW.js.map} +0 -0
  918. /package/dist/{tk-X46SEOL7.js.map → tk-GUGJYKJ2.js.map} +0 -0
  919. /package/dist/{tp.ui-XV7CL7CA.js.map → tp.ui-WGETBYJQ.js.map} +0 -0
  920. /package/dist/{tvs.dt-U6SIZTXW.js.map → tvs.dt-JWF4I3KY.js.map} +0 -0
  921. /package/dist/{tvs.dtcnv.categorical-6YGEKMHW.js.map → tvs.dtcnv.categorical-72Y5QMPL.js.map} +0 -0
  922. /package/dist/{tvs.dtcnv.continuous-CQFEENBO.js.map → tvs.dtcnv.continuous-73LHWTU5.js.map} +0 -0
  923. /package/dist/{tvs.dtfusion-NOBT2JPI.js.map → tvs.dtfusion-LP6HUMZU.js.map} +0 -0
  924. /package/dist/{tvs.dtsnvindel-6GTCSVAV.js.map → tvs.dtsnvindel-23N2CFZJ.js.map} +0 -0
  925. /package/dist/{tvs.dtsv-PMI4YVI5.js.map → tvs.dtsv-DILQVKYM.js.map} +0 -0
  926. /package/dist/{tvs.samplelst-HVNYKHXG.js.map → tvs.samplelst-GV4VSCRF.js.map} +0 -0
  927. /package/dist/{tvs.termCollection-EWGTT75Z.js.map → tvs.termCollection-KBDNXK7X.js.map} +0 -0
  928. /package/dist/{violin-MKWRB25Z.js.map → violin-TYUP7FB5.js.map} +0 -0
  929. /package/dist/{violin.integration.spec-CNWJ43SD.js.map → violin.integration.spec-ULRFK2A6.js.map} +0 -0
  930. /package/dist/{violin.interactivity-UXOMTGSD.js.map → violin.interactivity-2QZVQWQJ.js.map} +0 -0
  931. /package/dist/{violin.renderer-67Q6YGYQ.js.map → violin.renderer-HCDSN62Z.js.map} +0 -0
  932. /package/dist/{vocabulary-AKXE7SNU.js.map → vocabulary-I4CMPN2Z.js.map} +0 -0
@@ -0,0 +1,829 @@
1
+ import {
2
+ buildAnnotationsCsv
3
+ } from "./chunk-XJGPL2JZ.js";
4
+ import {
5
+ PlotBase,
6
+ filterInit,
7
+ getNormalRoot,
8
+ renderTable,
9
+ sayerror
10
+ } from "./chunk-L4TUTGTA.js";
11
+ import "./chunk-HJ6L54YS.js";
12
+ import {
13
+ require_debounce
14
+ } from "./chunk-LSEFWW72.js";
15
+ import "./chunk-4FKWINMK.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
+ dofetch2,
26
+ dofetch3
27
+ } from "./chunk-6VKTEMFV.js";
28
+ import "./chunk-7IYJZZQI.js";
29
+ import {
30
+ copyMerge,
31
+ getCompInit
32
+ } from "./chunk-M3J4MINX.js";
33
+ import "./chunk-PF4DSFDR.js";
34
+ import "./chunk-S4JLRRKK.js";
35
+ import "./chunk-TVADJLMF.js";
36
+ import {
37
+ getColors
38
+ } from "./chunk-EBKERML3.js";
39
+ import "./chunk-DD4R5P6W.js";
40
+ import "./chunk-JNITUVXP.js";
41
+ import "./chunk-KSGA62R2.js";
42
+ import "./chunk-LOZEKOES.js";
43
+ import "./chunk-TOU7EVFQ.js";
44
+ import "./chunk-OAWQ6LOO.js";
45
+ import "./chunk-TLT4YIG3.js";
46
+ import "./chunk-KYBIQBXE.js";
47
+ import "./chunk-I6Y4O3RR.js";
48
+ import {
49
+ rgb
50
+ } from "./chunk-OMR2DT66.js";
51
+ import "./chunk-DQC5FFGV.js";
52
+ import {
53
+ __toESM
54
+ } from "./chunk-HFNDKYVF.js";
55
+
56
+ // plots/aiProjectAdmin/defaults.ts
57
+ function getDefaultAIProjectAdminSettings(overrides = {}) {
58
+ const defaults = {};
59
+ return Object.assign(defaults, overrides);
60
+ }
61
+
62
+ // plots/aiProjectAdmin/repo/ProjectReposity.ts
63
+ var ProjectReposity = class {
64
+ async getProjects(genome, dslabel) {
65
+ const body = {
66
+ genome,
67
+ dslabel,
68
+ for: "list"
69
+ };
70
+ try {
71
+ const response = await dofetch3("aiProjectAdmin", { body });
72
+ return response || [];
73
+ } catch (error) {
74
+ console.error("Error fetching projects:", error);
75
+ throw error;
76
+ }
77
+ }
78
+ /** Gets the image paths from db */
79
+ async getImagePaths(genome, dslabel, project) {
80
+ const body = {
81
+ genome,
82
+ dslabel,
83
+ for: "images",
84
+ project
85
+ };
86
+ try {
87
+ return await dofetch3("aiProjectAdmin", { body });
88
+ } catch (error) {
89
+ console.error("Error fetching images:", error);
90
+ throw error;
91
+ }
92
+ }
93
+ async updateProject(_body, method) {
94
+ const body = Object.assign({}, _body, { for: "admin" });
95
+ try {
96
+ if (method == "PUT" || method == "DELETE") {
97
+ return await dofetch2("aiProjectAdmin", { method, body }, {});
98
+ }
99
+ return await dofetch3("aiProjectAdmin", { method, body });
100
+ } catch (error) {
101
+ console.error("Error fetching projects:", error);
102
+ throw error;
103
+ }
104
+ }
105
+ //TODO: Will need a method to call metadata API, then build dictionary
106
+ async getTerms(app) {
107
+ const root = { id: "__root", name: "root", __tree_isroot: true };
108
+ try {
109
+ await app.vocabApi.buildAdHocDictionary();
110
+ const terms = await app.vocabApi.getTermChildren(root, []);
111
+ return terms || [];
112
+ } catch (error) {
113
+ console.error("Error getting terms:", error);
114
+ throw error;
115
+ }
116
+ }
117
+ async getAnnotations(genome, dslabel, projectId) {
118
+ try {
119
+ const body = {
120
+ genome,
121
+ dslabel,
122
+ projectId,
123
+ wsimagesFilenames: ["all"]
124
+ };
125
+ const response = await dofetch3("aiProjectSelectedWSImages", { body });
126
+ const wsimages = response?.wsimages || [];
127
+ const annotations = [];
128
+ for (const w of wsimages) {
129
+ const anns = w.annotations || [];
130
+ const filename = w.filename;
131
+ if (Array.isArray(anns)) {
132
+ for (const a of anns) {
133
+ annotations.push(Object.assign({ filename }, a));
134
+ }
135
+ }
136
+ }
137
+ return annotations;
138
+ } catch (error) {
139
+ console.error("Error fetching annotations from server:", error);
140
+ throw error;
141
+ }
142
+ }
143
+ };
144
+
145
+ // plots/aiProjectAdmin/view/ProjectAdminRender.ts
146
+ var import_debounce = __toESM(require_debounce(), 1);
147
+ var ProjectAdminRender = class {
148
+ constructor(dom, projects, interactions) {
149
+ this.dom = dom;
150
+ this.projects = projects;
151
+ this.interactions = interactions;
152
+ }
153
+ /** Renders project administration UI, allowing users to
154
+ * create new projects or edit existing ones.*/
155
+ renderProjectAdmin() {
156
+ const projectDiv = this.dom.holder.append("div").attr("id", "sjpp-ai-prjt-admin-projects").attr("class", "sjpp-deletable-ai-prjt-admin-div");
157
+ this.renderCreateProject(projectDiv);
158
+ this.renderProjectSelection(projectDiv);
159
+ }
160
+ /** Users submit a new project name before sample
161
+ * filtering UI to finalize project creation.*/
162
+ renderCreateProject(projectDiv) {
163
+ const newProjectDiv = projectDiv.append("div").attr("class", "sjpp-project-select-new").style("padding", "10px");
164
+ const input = newProjectDiv.append("input").attr("id", "sjpp-new-project-name").attr("display", "inline-block").attr("placeholder", "New project name");
165
+ const button = newProjectDiv.append("div").text("Create Project").classed("sja_menuoption", true).style("display", "inline-block").property("disabled", true).on("click", async () => {
166
+ const projectName = input.property("value");
167
+ const prjtNameLen = projectName.trim().length;
168
+ const showError = (msg) => {
169
+ sayerror(this.dom.errorDiv, msg);
170
+ input.property("value", "");
171
+ button.property("disabled", true);
172
+ setTimeout(() => {
173
+ this.dom.errorDiv.selectAll("*").remove();
174
+ }, 3e3);
175
+ };
176
+ if (prjtNameLen == 0) {
177
+ return showError("Project name cannot be empty");
178
+ }
179
+ if (prjtNameLen > 50 || prjtNameLen < 3) {
180
+ return showError("Project name must be between 3 and 50 characters");
181
+ }
182
+ const notUnique = this.projects.some((p) => p.name === projectName.trim());
183
+ if (notUnique) {
184
+ return showError(`Project name '${projectName}' already exists`);
185
+ }
186
+ if (this.dom.header) this.dom.header.text(`Project: ${projectName}`);
187
+ await this.interactions.appDispatchEdit({ settings: { project: { name: projectName, type: "new" } } });
188
+ });
189
+ input.on("keydown", () => {
190
+ const debouncer = () => {
191
+ button.property("disabled", input.property("value").length == 0);
192
+ };
193
+ (0, import_debounce.debounce)(debouncer, 300)();
194
+ });
195
+ }
196
+ /** Users may select an existing project from a table
197
+ * returned for the db to edit or delete, depending
198
+ * on user roles.*/
199
+ renderProjectSelection(projectDiv) {
200
+ if (!this.projects.length) return;
201
+ const tableDiv = projectDiv.append("div").attr("class", "sjpp-project-select-table").style("padding", "10px");
202
+ const columns = [{ label: "Project", sortable: true }];
203
+ const columnButtons = [
204
+ {
205
+ text: "Edit",
206
+ class: "sja_menuoption",
207
+ //_ = event, __ = idx
208
+ callback: async (_, idx) => {
209
+ const project = this.projects[idx];
210
+ await this.interactions.appDispatchEdit({ settings: { project } });
211
+ this.interactions.launchViewer(this.dom.holder, []);
212
+ }
213
+ },
214
+ {
215
+ // Export button - pass only project.id and export will be CSV
216
+ text: "Export",
217
+ class: "sja_menuoption",
218
+ callback: async (_, idx) => {
219
+ const project = this.projects[idx];
220
+ try {
221
+ await this.interactions.exportAnnotations(project.id);
222
+ } catch (_2) {
223
+ sayerror(this.dom.errorDiv, "Failed to export annotations");
224
+ }
225
+ }
226
+ },
227
+ {
228
+ //TODO: Add logic for admins only once user roles are implemented
229
+ //Leave here for development
230
+ text: "Delete",
231
+ class: "sja_menuoption",
232
+ callback: (_, i) => {
233
+ const project = this.projects[i];
234
+ this.interactions.deleteProject(project);
235
+ this.projects.splice(i, 1);
236
+ projectDiv.select(".sjpp-project-select-table").remove();
237
+ this.renderProjectSelection(projectDiv);
238
+ }
239
+ }
240
+ ];
241
+ renderTable({
242
+ div: tableDiv,
243
+ rows: this.projects.map((p) => {
244
+ return [{ value: p.name }];
245
+ }),
246
+ header: {
247
+ allowSort: true
248
+ },
249
+ columns,
250
+ singleMode: true,
251
+ columnButtons
252
+ });
253
+ }
254
+ };
255
+
256
+ // plots/aiProjectAdmin/interactions/AIProjectAdminInteractions.ts
257
+ var AIProjectAdminInteractions = class {
258
+ constructor(app, id, prjtRepo) {
259
+ this.app = app;
260
+ this.id = id;
261
+ this.genome = app.vocabApi.vocab.genome;
262
+ this.dslabel = app.vocabApi.vocab.dslabel;
263
+ this.prjtRepo = prjtRepo;
264
+ }
265
+ async addProject(opts) {
266
+ const config = this.getConfig();
267
+ const projectObject = Object.assign({}, config.settings.project, opts.project);
268
+ const body = {
269
+ genome: this.genome,
270
+ dslabel: this.dslabel,
271
+ project: projectObject
272
+ };
273
+ try {
274
+ await this.prjtRepo.updateProject(body, "PUT");
275
+ } catch (e) {
276
+ console.error("Error adding project:", e.message || e);
277
+ throw e;
278
+ }
279
+ }
280
+ async editProject(opts) {
281
+ const config = this.getConfig();
282
+ const project = Object.assign(
283
+ {},
284
+ config.settings.project,
285
+ {
286
+ type: "edit"
287
+ },
288
+ opts.project
289
+ );
290
+ const body = {
291
+ genome: this.genome,
292
+ dslabel: this.dslabel,
293
+ project
294
+ };
295
+ try {
296
+ const res = await this.prjtRepo.updateProject(body, "POST");
297
+ if (!project.id) project.id = res.projectId;
298
+ } catch (e) {
299
+ console.error("Error editing project:", e.message || e);
300
+ throw e;
301
+ }
302
+ await this.appDispatchEdit({ settings: { project } }, config);
303
+ }
304
+ async deleteProject(project) {
305
+ const body = {
306
+ genome: this.genome,
307
+ dslabel: this.dslabel,
308
+ project: {
309
+ name: project.value,
310
+ id: project.id
311
+ }
312
+ };
313
+ try {
314
+ await this.prjtRepo.updateProject(body, "DELETE");
315
+ } catch (e) {
316
+ console.error("Error deleting project:", e.message || e);
317
+ throw e;
318
+ }
319
+ }
320
+ async getFilteredImages(filter) {
321
+ const config = this.getConfig();
322
+ return await this.app.vocabApi.getFilteredAiImages(config.settings.project, filter);
323
+ }
324
+ async launchViewer(holder, _images) {
325
+ holder.selectAll(".sjpp-deletable-ai-prjt-admin-div").remove();
326
+ const config = this.getConfig();
327
+ let images = [];
328
+ if (_images && _images.length > 0) {
329
+ images = _images;
330
+ } else {
331
+ const response = await this.prjtRepo.getImagePaths(
332
+ this.genome,
333
+ this.dslabel,
334
+ config.settings.project
335
+ );
336
+ images = response.images;
337
+ }
338
+ const wsiViewer = await import("./plot.wsi-MU6AXOWO.js");
339
+ wsiViewer.default(this.dslabel, holder, { name: this.genome }, null, config.settings.project.id, images, true);
340
+ }
341
+ async appDispatchEdit(settings, config = {}) {
342
+ if (!config?.settings) {
343
+ config = this.getConfig();
344
+ if (!config) throw new Error(`No plot with id='${this.id}' found.`);
345
+ }
346
+ await this.app.dispatch({
347
+ type: "plot_edit",
348
+ id: this.id,
349
+ config: Object.assign(settings, config.settings)
350
+ });
351
+ }
352
+ getConfig() {
353
+ return this.app.getState().plots.find((p) => p.id === this.id);
354
+ }
355
+ async exportAnnotations(projectId) {
356
+ const config = this.getConfig();
357
+ if (!config || !config.settings) throw new Error(`No plot with id='${this.id}' found.`);
358
+ let annotations = [];
359
+ try {
360
+ annotations = await this.prjtRepo.getAnnotations(this.genome, this.dslabel, projectId);
361
+ } catch (e) {
362
+ console.error("Error fetching annotations for export:", e?.message || e);
363
+ throw e;
364
+ }
365
+ const mime = "text/csv;charset=utf-8;";
366
+ let content;
367
+ if (!Array.isArray(annotations) || annotations.length === 0) {
368
+ content = "";
369
+ } else {
370
+ content = buildAnnotationsCsv(annotations);
371
+ }
372
+ const rawName = config.settings && config.settings.project && config.settings.project.name ? String(config.settings.project.name) : `project-${projectId}`;
373
+ const safeName = rawName.replace(/[^a-z0-9_.-]/gi, "_").slice(0, 200);
374
+ const filename = `${safeName}-annotations.csv`;
375
+ try {
376
+ const blob = new Blob([content], { type: mime });
377
+ const url = URL.createObjectURL(blob);
378
+ const a = document.createElement("a");
379
+ a.href = url;
380
+ a.download = filename;
381
+ document.body.appendChild(a);
382
+ a.click();
383
+ a.remove();
384
+ setTimeout(() => URL.revokeObjectURL(url), 1e3);
385
+ } catch (e) {
386
+ console.error("Error creating annotation download:", e?.message || e);
387
+ throw e;
388
+ }
389
+ }
390
+ };
391
+
392
+ // plots/aiProjectAdmin/view/ClassesTableRender.ts
393
+ var ClassesTableRender = class {
394
+ constructor(holder, rows) {
395
+ this.dom = {
396
+ holder,
397
+ tableDiv: holder.append("div"),
398
+ btnDiv: holder.append("div")
399
+ };
400
+ this.columns = [
401
+ { label: "" },
402
+ // Empty for the delete icon
403
+ {
404
+ label: "NAME",
405
+ editCallback: (rowIdx, cell) => {
406
+ const newValue = cell.value.trim();
407
+ const foundSameName = this.rows.some((r, i) => newValue === r[1].value.trim() && i !== rowIdx);
408
+ if (foundSameName) {
409
+ alert(`Class name '${newValue}' already exists`);
410
+ cell.value = this.rowsCopy[rowIdx][1].value;
411
+ cell.__td.text(this.rowsCopy[rowIdx][1].value);
412
+ return;
413
+ }
414
+ this.rowsCopy = this.rows.map((r) => r.map((c) => ({ ...c })));
415
+ }
416
+ },
417
+ { label: "COLOR" }
418
+ ];
419
+ const colorScale = getColors(5);
420
+ this.rows = rows || this.setDefaultClasses(colorScale);
421
+ this.rowsCopy = [];
422
+ this.renderTable();
423
+ this.renderAddClassBtn(colorScale);
424
+ }
425
+ renderTable() {
426
+ this.dom.tableDiv.select("table").remove();
427
+ if (!this.rows || this.rows.length === 0) return;
428
+ this.rowsCopy = this.rows.map((r) => r.map((c) => ({ ...c })));
429
+ renderTable({
430
+ div: this.dom.tableDiv,
431
+ columns: this.columns,
432
+ rows: this.rows,
433
+ striped: false,
434
+ showLines: false,
435
+ singleMode: false,
436
+ resize: true
437
+ });
438
+ for (const [i, row] of this.rows.entries()) {
439
+ const deleteBtn = row[0].__td.select(".sja_menuoption");
440
+ deleteBtn.on("click", () => {
441
+ this.rows.splice(i, 1);
442
+ this.renderTable();
443
+ });
444
+ }
445
+ }
446
+ setDefaultClasses(colorScale) {
447
+ const rows = [];
448
+ for (let i = 0; i < 4; i++) {
449
+ this.getNewClass(colorScale, rows);
450
+ }
451
+ return rows;
452
+ }
453
+ getNewClass(colorScale, rows) {
454
+ const getName = (i2) => `New class ${i2}`;
455
+ let i = 1;
456
+ let found = true;
457
+ while (found) {
458
+ const checkName = getName(i);
459
+ found = rows.some((r) => r[1].value == checkName);
460
+ if (found) i++;
461
+ }
462
+ rows.push([
463
+ { html: `<div class="sja_menuoption">&times;<div>` },
464
+ { value: getName(i) },
465
+ { color: rgb(colorScale(`${i}`)).formatHex() }
466
+ ]);
467
+ }
468
+ renderAddClassBtn(colorScale) {
469
+ this.dom.btnDiv.append("div").text("Add Class").classed("sja_menuoption", true).style("display", "inline-block").style("margin", "10px 0px 0px 0px").on("click", () => {
470
+ if (this.rows.length >= 9) {
471
+ alert("Maximum number of classes reached.");
472
+ return;
473
+ }
474
+ this.getNewClass(colorScale, this.rows);
475
+ this.renderTable();
476
+ });
477
+ }
478
+ };
479
+
480
+ // plots/aiProjectAdmin/view/SelectorTableRender.ts
481
+ var SelectorTableRender = class {
482
+ constructor(holder, interactions, images) {
483
+ this.images = { rows: [], cols: [] };
484
+ this.selectedRows = /* @__PURE__ */ new Set();
485
+ this.sortedIndexMap = [];
486
+ this.dom = {
487
+ holder,
488
+ tableDiv: holder.append("div").attr("class", ".sjpp-deletable-ai-prjt-admin-div").attr("id", "sjpp-selector-table").style("padding", "10px 0"),
489
+ btnDiv: holder.append("div").attr("class", ".sjpp-deletable-ai-prjt-admin-div").attr("id", "sjpp-selector-btns")
490
+ };
491
+ this.images = images;
492
+ this.interactions = interactions;
493
+ const selectedList = images?.selectedImages;
494
+ const normalizeImageName = (s) => String(s ?? "").replace(/\.svs$/i, "").toLowerCase();
495
+ const selectedSet = new Set((selectedList || []).map(normalizeImageName));
496
+ this.selectedRows = /* @__PURE__ */ new Set();
497
+ (this.images?.rows ?? []).forEach((row, i) => {
498
+ const candidate = row?.[0]?.value;
499
+ const n = normalizeImageName(candidate);
500
+ if (selectedSet.has(n)) this.selectedRows.add(i);
501
+ });
502
+ this.render();
503
+ }
504
+ render() {
505
+ const columns = this.images.cols.map((c) => ({ ...c, sortable: true })) || [];
506
+ if (!columns.length) {
507
+ this.dom.tableDiv.append("div").text("Missing columns data").style("color", "red");
508
+ this.renderApplyBtn(
509
+ /*disable=*/
510
+ true
511
+ );
512
+ return;
513
+ }
514
+ const rows = this.images?.rows ?? [];
515
+ const mapped = rows.map((row, origIdx) => ({
516
+ row,
517
+ origIdx,
518
+ selected: this.selectedRows.has(origIdx)
519
+ }));
520
+ mapped.sort((a, b) => {
521
+ const selDiff = Number(b.selected) - Number(a.selected);
522
+ return selDiff || a.origIdx - b.origIdx;
523
+ });
524
+ const rowsSorted = mapped.map((m) => m.row);
525
+ this.sortedIndexMap = mapped.map((m) => m.origIdx);
526
+ const selectedRowsForRender = mapped.reduce((acc, m, idx) => {
527
+ if (m.selected) acc.push(idx);
528
+ return acc;
529
+ }, []);
530
+ renderTable({
531
+ div: this.dom.tableDiv,
532
+ columns,
533
+ rows: rowsSorted,
534
+ selectedRows: selectedRowsForRender,
535
+ striped: true,
536
+ header: { allowSort: true },
537
+ noButtonCallback: (sortedIdx, node) => {
538
+ const orig = this.sortedIndexMap?.[sortedIdx];
539
+ if (orig === void 0) return;
540
+ if (node.checked) {
541
+ this.selectedRows.add(orig);
542
+ } else {
543
+ this.selectedRows.delete(orig);
544
+ }
545
+ }
546
+ });
547
+ this.renderApplyBtn(
548
+ /*disable=*/
549
+ false
550
+ );
551
+ }
552
+ renderApplyBtn(disable = false) {
553
+ const btn = this.dom.btnDiv.append("div").text("Apply").classed("sja_menuoption", true).style("display", "block").style("width", "fit-content").style("margin-left", "5vw");
554
+ if (disable) btn.attr("disabled", true);
555
+ btn.on("click", async () => {
556
+ if (!this.selectedRows.size) {
557
+ alert(`No rows selected. Please select some rows.`);
558
+ return;
559
+ }
560
+ btn.attr("disabled", true);
561
+ const images = Array.from(this.selectedRows).map((i) => `${this.images.rows[i][0].value}.svs`);
562
+ await this.interactions.editProject({
563
+ project: {
564
+ images
565
+ }
566
+ });
567
+ this.dom.holder.selectAll("*").remove();
568
+ await this.interactions.launchViewer(this.dom.holder, images);
569
+ });
570
+ }
571
+ };
572
+
573
+ // plots/aiProjectAdmin/view/UsersRender.ts
574
+ var UsersRender = class {
575
+ constructor(dom, users = []) {
576
+ this.dom = dom;
577
+ this.users = users.slice();
578
+ }
579
+ render() {
580
+ if (this.users.length > 0) {
581
+ const container = this.dom.holder.append("div").attr("id", "sjpp-users-render").attr("class", "sjpp-deletable-ai-prjt-admin-div").style("padding", "10px");
582
+ const inputRow = container.append("div").attr("class", "sjpp-users-input-row").style("margin-bottom", "10px");
583
+ 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");
584
+ const addBtn = inputRow.append("div").text("Add").classed("sja_menuoption", true).style("display", "inline-block").property("disabled", true).on("click", () => {
585
+ const email = input.property("value").trim();
586
+ const showError = (msg) => {
587
+ sayerror(this.dom.errorDiv, msg);
588
+ setTimeout(() => this.dom.errorDiv.selectAll("*").remove(), 3e3);
589
+ };
590
+ if (email.length === 0) {
591
+ return showError("Email cannot be empty");
592
+ }
593
+ const emailRe = /^[A-Za-z0-9._%+-]+@[A-Za-z0-9.-]+\.[A-Za-z]{2,}$/;
594
+ if (!emailRe.test(email)) {
595
+ return showError("Invalid email address");
596
+ }
597
+ if (this.users.includes(email)) {
598
+ return showError("Email already added");
599
+ }
600
+ this.users.push(email);
601
+ input.property("value", "");
602
+ addBtn.property("disabled", true);
603
+ this.renderTableArea(container);
604
+ });
605
+ input.on("input", () => {
606
+ addBtn.property("disabled", input.property("value").trim().length === 0);
607
+ });
608
+ this.renderTableArea(container);
609
+ }
610
+ }
611
+ renderTableArea(container) {
612
+ container.select(".sjpp-users-table-area").remove();
613
+ const tableDiv = container.append("div").attr("class", "sjpp-users-table-area").style("padding", "6px 0");
614
+ if (!this.users.length) {
615
+ tableDiv.append("div").text("No users added yet.").style("color", "#666");
616
+ return;
617
+ }
618
+ const columns = [{ label: "Email", sortable: true }];
619
+ const columnButtons = [
620
+ {
621
+ text: "\xD7",
622
+ class: "sja_menuoption",
623
+ callback: (_, idx) => {
624
+ this.users.splice(idx, 1);
625
+ container.select(".sjpp-users-table-area").remove();
626
+ this.renderTableArea(container);
627
+ }
628
+ }
629
+ ];
630
+ renderTable({
631
+ div: tableDiv,
632
+ rows: this.users.map((u) => [{ value: u }]),
633
+ columns,
634
+ columnButtons,
635
+ singleMode: false,
636
+ striped: false,
637
+ showLines: false,
638
+ resize: true
639
+ });
640
+ tableDiv.selectAll(".sja_menuoption").html("\xD7<div></div>");
641
+ }
642
+ };
643
+
644
+ // plots/aiProjectAdmin/view/CreateProjectRender.ts
645
+ var CreateProjectRender = class {
646
+ constructor(dom, app, interactions) {
647
+ dom.holder.style("padding", "10px 20px").attr("class", "sjpp-deletable-ai-prjt-admin-div");
648
+ const filterDiv = dom.holder.append("div").attr("id", "sjpp-ai-prjt-admin-filter-div");
649
+ 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");
650
+ const left = wrapper.append("div").attr("id", "sjpp-ai-prjt-admin-classes-table").style("flex", "0 1 auto");
651
+ const right = wrapper.append("div").attr("id", "sjpp-ai-prjt-admin-users").style("width", "320px").style("margin-left", "8px");
652
+ this.dom = {
653
+ holder: dom.holder,
654
+ errorDiv: dom.errorDiv,
655
+ filterDiv,
656
+ classDiv: left,
657
+ usersDiv: right
658
+ };
659
+ this.app = app;
660
+ this.interactions = interactions;
661
+ this.filter = null;
662
+ }
663
+ render() {
664
+ this.renderFilter();
665
+ this.classesTable = new ClassesTableRender(this.dom.classDiv);
666
+ this.usersRender = new UsersRender({ holder: this.dom.usersDiv, errorDiv: this.dom.errorDiv }, []);
667
+ this.usersRender.render();
668
+ this.renderApplyBtn();
669
+ }
670
+ renderFilter() {
671
+ const filter = filterInit({
672
+ holder: this.dom.filterDiv,
673
+ emptyLabel: "Add filter",
674
+ vocabApi: this.app.vocabApi,
675
+ termdbConfig: this.app.vocabApi.termdbConfig,
676
+ callback: (filter2) => {
677
+ this.filter = filter2;
678
+ }
679
+ });
680
+ const state = this.app.getState();
681
+ const root = getNormalRoot(state.termfilter.filter);
682
+ filter.main(root);
683
+ }
684
+ renderApplyBtn() {
685
+ const btn = this.dom.classDiv.append("div").text("Apply").classed("sja_menuoption", true).style("display", "inline-block").style("margin-left", "200px").on("click", async () => {
686
+ btn.attr("disabled", true);
687
+ const selections = await this.interactions.getFilteredImages(this.filter);
688
+ if (this.filter && selections.status !== "ok" || selections.data?.selectedImages?.length === 0) {
689
+ alert("No images match your filter criteria.");
690
+ return;
691
+ }
692
+ await this.interactions.addProject({
693
+ project: {
694
+ filter: this.filter,
695
+ classes: this.classesTable.rows.map((row, i) => {
696
+ return { label: row[1].value, color: row[2].color, key_shortcut: `Digit${i + 1}` };
697
+ }),
698
+ users: this.usersRender?.users || []
699
+ }
700
+ });
701
+ this.dom.holder.selectAll("*").remove();
702
+ new SelectorTableRender(this.dom.holder, this.interactions, selections.data);
703
+ });
704
+ }
705
+ /**** Uncomment before production */
706
+ // private validateInput() {
707
+ // const invalidInfo = {
708
+ // entries: [] as { dataType: string; reason: string }[],
709
+ // errorMsg: 'Please clear all "Data type: Class" errors before applying changes.'
710
+ // }
711
+ // //Show user error if no filter is defined.
712
+ // if (!this.filter) {
713
+ // invalidInfo.entries.push({ dataType: 'Filter', reason: 'No filter defined. Did you mean to add a filter?' })
714
+ // }
715
+ // //Check if all classes were deleted
716
+ // const classes = this.classesTable?.rows.map(row => row[1].value) || []
717
+ // if (classes.length === 0) {
718
+ // invalidInfo.entries.push({ dataType: 'Class', reason: 'No classes defined. Did you mean to add a class?' })
719
+ // }
720
+ // //Check to see if any class is still a default class
721
+ // const unchangedClasses =
722
+ // this.classesTable?.rows
723
+ // .filter(row => (row[1]?.value as string)?.startsWith('New class'))
724
+ // .map(r => r[1]?.value as string) || []
725
+ // for (const c of unchangedClasses) {
726
+ // invalidInfo.entries.push({ dataType: 'Class', reason: `${c} is the default class name. Please rename.` })
727
+ // }
728
+ // return invalidInfo
729
+ // }
730
+ };
731
+
732
+ // plots/aiProjectAdmin/AIProjectAdmin.ts
733
+ var AIProjectAdmin = class extends PlotBase {
734
+ constructor(opts, api) {
735
+ super(opts, api);
736
+ this.type = "AIProjectAdmin";
737
+ this.opts = opts;
738
+ this.dom = {
739
+ holder: opts.holder,
740
+ errorDiv: opts.holder.append("div").style("margin", "3px").attr("class", "sjpp-ai-prjt-admin-error")
741
+ };
742
+ if (opts.header) this.dom.header = opts.header;
743
+ this.prjtRepo = new ProjectReposity();
744
+ }
745
+ static {
746
+ this.type = "AIProjectAdmin";
747
+ }
748
+ getState(appState) {
749
+ const config = appState.plots.find((p) => p.id === this.id);
750
+ if (!config) {
751
+ throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
752
+ }
753
+ return {
754
+ config,
755
+ vocab: appState.vocab,
756
+ filter: appState.termfilter.filter
757
+ };
758
+ }
759
+ async init(appState) {
760
+ this.interactions = new AIProjectAdminInteractions(this.app, this.id, this.prjtRepo);
761
+ try {
762
+ this.projects = await this.prjtRepo.getProjects(appState.vocab.genome, appState.vocab.dslabel);
763
+ } catch (e) {
764
+ console.error("Error initializing AIProjectAdmin:", e);
765
+ throw e;
766
+ }
767
+ this.prjtAdminUI = new ProjectAdminRender(this.dom, this.projects, this.interactions);
768
+ this.prjtAdminUI.renderProjectAdmin();
769
+ }
770
+ async main() {
771
+ const state = structuredClone(this.state);
772
+ const config = state.config;
773
+ if (config.chartType != this.type) return;
774
+ const project = config.settings.project;
775
+ if (!project) return;
776
+ if (!this.interactions) throw new Error("AIProjectAdminInteractions not initialized");
777
+ this.dom.holder.selectAll(".sjpp-deletable-ai-prjt-admin-div").remove();
778
+ if (project.type === "new") {
779
+ const terms = await this.prjtRepo.getTerms(this.app);
780
+ if (!terms || terms.length === 0) {
781
+ sayerror(this.dom.errorDiv, "No metadata found.");
782
+ return;
783
+ }
784
+ const createProjectRender = new CreateProjectRender(this.dom, this.app, this.interactions);
785
+ createProjectRender.render();
786
+ }
787
+ if (project.type == "existing") {
788
+ if (!project.name) {
789
+ sayerror(this.dom.errorDiv, "Project name not provided.");
790
+ return;
791
+ }
792
+ if (!project.id) {
793
+ const existingProject = this.projects?.find((p) => p.name === project.name);
794
+ if (!existingProject) {
795
+ sayerror(this.dom.errorDiv, `Project ${project.name} not found.`);
796
+ return;
797
+ }
798
+ await this.app.save({
799
+ type: "plot_edit",
800
+ id: this.id,
801
+ config: { settings: { project: { id: existingProject.id } } }
802
+ });
803
+ }
804
+ await this.interactions.launchViewer(this.dom.holder, []);
805
+ }
806
+ }
807
+ };
808
+ var aiProjectAdminInit = getCompInit(AIProjectAdmin);
809
+ var componentInit = aiProjectAdminInit;
810
+ async function getPlotConfig(opts) {
811
+ const config = {
812
+ chartType: "AIProjectAdmin",
813
+ subfolder: "aiProjectAdmin",
814
+ extension: "ts",
815
+ hidePlotFilter: true,
816
+ //Disable the filter in the sandbox header
817
+ settings: getDefaultAIProjectAdminSettings(opts.overrides)
818
+ };
819
+ if (opts.settings?.project && !opts.settings?.project?.type) {
820
+ opts.settings.project.type = "existing";
821
+ }
822
+ return copyMerge(config, opts);
823
+ }
824
+ export {
825
+ aiProjectAdminInit,
826
+ componentInit,
827
+ getPlotConfig
828
+ };
829
+ //# sourceMappingURL=AIProjectAdmin-JMN5O6YU.js.map