@sjcrh/proteinpaint-client 2.191.4 → 2.192.0

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 (957) hide show
  1. package/dist/2dmaf-BNMEUJVM.js +1373 -0
  2. package/dist/AIProjectAdmin-AEXQY5LY.js +958 -0
  3. package/dist/AIProjectAdmin-AEXQY5LY.js.map +7 -0
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  7. package/dist/CorrelationVolcano-V2E566XL.js +619 -0
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  851. /package/dist/{importPlot-YH7ZY6RJ.js.map → importPlot-DQFWY5A7.js.map} +0 -0
  852. /package/dist/{isoformExpression-EV27MKYZ.js.map → isoformExpression-2KANPCBH.js.map} +0 -0
  853. /package/dist/{isoformExpression.unit.spec-7T2GOHH3.js.map → isoformExpression.unit.spec-6FSMHT4K.js.map} +0 -0
  854. /package/dist/{launch.adhoc-NOISOX5E.js.map → launch.adhoc-ZYTIRVIC.js.map} +0 -0
  855. /package/dist/{leftlabel.sample-42AX4KTV.js.map → leftlabel.sample-66U6MHPN.js.map} +0 -0
  856. /package/dist/{legacyDataset-SWJCAWIR.js.map → legacyDataset-TNIIJABK.js.map} +0 -0
  857. /package/dist/{lollipop-LQCQBTSX.js.map → lollipop-PJDUFWEY.js.map} +0 -0
  858. /package/dist/{maf-U237OWZ3.js.map → maf-DLJHCKHJ.js.map} +0 -0
  859. /package/dist/{maftimeline-NLZLMHT2.js.map → maftimeline-NK5QYJMJ.js.map} +0 -0
  860. /package/dist/{matrix-DZJXYRYN.js.map → matrix-7BFYR6QL.js.map} +0 -0
  861. /package/dist/{matrix-Y5345QQG.js.map → matrix-USAB2CHO.js.map} +0 -0
  862. /package/dist/{matrix.cells-PT7S74QP.js.map → matrix.cells-OTAXAJ4N.js.map} +0 -0
  863. /package/dist/{matrix.config-2ORCUWKX.js.map → matrix.config-AL4WSFZ7.js.map} +0 -0
  864. /package/dist/{matrix.data-C6VPQJJ4.js.map → matrix.data-BDHCSN2G.js.map} +0 -0
  865. /package/dist/{matrix.groups-CEOCG2CT.js.map → matrix.groups-MV2D2636.js.map} +0 -0
  866. /package/dist/{matrix.integration.spec-U4B3JB6N.js.map → matrix.integration.spec-DESORC2Y.js.map} +0 -0
  867. /package/dist/{matrix.interactivity-GFLIFIER.js.map → matrix.interactivity-H7EJW3P2.js.map} +0 -0
  868. /package/dist/{matrix.layout-DOVDHTDX.js.map → matrix.layout-7CAS2IBO.js.map} +0 -0
  869. /package/dist/{matrix.legend-JE4ZSLP7.js.map → matrix.legend-JDVG2JDF.js.map} +0 -0
  870. /package/dist/{matrix.renderers-GPUJQ7KF.js.map → matrix.renderers-PDR5FIBC.js.map} +0 -0
  871. /package/dist/{matrix.serieses-REE4DCSR.js.map → matrix.serieses-QVDS5HKK.js.map} +0 -0
  872. /package/dist/{matrix.sort-VD5URUWY.js.map → matrix.sort-HCK4CSTJ.js.map} +0 -0
  873. /package/dist/{matrix.sort.unit.spec-4IOFVHJN.js.map → matrix.sort.unit.spec-2GC4E26N.js.map} +0 -0
  874. /package/dist/{matrix.sorterUi-VQYY6KBK.js.map → matrix.sorterUi-XGBQOPG4.js.map} +0 -0
  875. /package/dist/{matrix.sorterUi.unit.spec-V5O2EJBX.js.map → matrix.sorterUi.unit.spec-BJQKDU2F.js.map} +0 -0
  876. /package/dist/{mavb-SQDA3B2B.js.map → mavb-6E6Z4LPK.js.map} +0 -0
  877. /package/dist/{mds.fimo-ZJSEPLD7.js.map → mds.fimo-5P2TK5U4.js.map} +0 -0
  878. /package/dist/{mds.samplescatterplot-Y5V73GOY.js.map → mds.samplescatterplot-KLKOD4AS.js.map} +0 -0
  879. /package/dist/{mds.survivalplot-CZBRMHYN.js.map → mds.survivalplot-SWQCOFIU.js.map} +0 -0
  880. /package/dist/{numericDictTermCluster-TFXBBUVI.js.map → numericDictTermCluster-WIVO33AV.js.map} +0 -0
  881. /package/dist/{oncomatrix-ZILACPPI.js.map → oncomatrix-SDUUQZCK.js.map} +0 -0
  882. /package/dist/{oncomatrix.spec-RLIVVVD6.js.map → oncomatrix.spec-YGQYIUDT.js.map} +0 -0
  883. /package/dist/{plot.2dvaf-BNRZPIKU.js.map → plot.2dvaf-K53KTP5W.js.map} +0 -0
  884. /package/dist/{plot.app-NRUARQCN.js.map → plot.app-FNJVWLPQ.js.map} +0 -0
  885. /package/dist/{plot.barplot-342AYQC7.js.map → plot.barplot-VTC3N6BR.js.map} +0 -0
  886. /package/dist/{plot.boxplot-OHEJDPTW.js.map → plot.boxplot-RJFGQSLA.js.map} +0 -0
  887. /package/dist/{plot.brainImaging-KV72PAON.js.map → plot.brainImaging-6KVNPPMT.js.map} +0 -0
  888. /package/dist/{plot.disco-OUE4RFHL.js.map → plot.disco-ZFH5RK6B.js.map} +0 -0
  889. /package/dist/{plot.dzi-T3GPUH36.js.map → plot.dzi-IA2SOFUD.js.map} +0 -0
  890. /package/dist/{plot.ssgq-WJHGMXW5.js.map → plot.ssgq-QARGQVKB.js.map} +0 -0
  891. /package/dist/{plot.vaf2cov-NGD5PCV4.js.map → plot.vaf2cov-2JUXYCPG.js.map} +0 -0
  892. /package/dist/{plot.wsi-2MU5BDG3.js.map → plot.wsi-C2DULA7U.js.map} +0 -0
  893. /package/dist/{profilePlot-OMVO3K4H.js.map → profilePlot-SVI3QKMD.js.map} +0 -0
  894. /package/dist/{qualitative-MEYBRUC6.js.map → qualitative-AQFKAZID.js.map} +0 -0
  895. /package/dist/{regression-ZPDPLI6G.js.map → regression-DLPBCDZT.js.map} +0 -0
  896. /package/dist/{regression.inputs-QOSBAGL6.js.map → regression.inputs-42LY4MEZ.js.map} +0 -0
  897. /package/dist/{regression.inputs.term-HMUMPY7X.js.map → regression.inputs.term-TTUFFPG6.js.map} +0 -0
  898. /package/dist/{regression.inputs.values.table-VMCTZHLG.js.map → regression.inputs.values.table-CJAPTSMS.js.map} +0 -0
  899. /package/dist/{regression.integration.spec-RP74JTAA.js.map → regression.integration.spec-UDA26OGS.js.map} +0 -0
  900. /package/dist/{regression.results-5XC6M67C.js.map → regression.results-IA3C7SHR.js.map} +0 -0
  901. /package/dist/{regression.spec-EZYM24J7.js.map → regression.spec-HEXCL3QV.js.map} +0 -0
  902. /package/dist/{report-ZOVQCOGQ.js.map → report-4CFOWNPJ.js.map} +0 -0
  903. /package/dist/{sampleScatter.spec-CD52FEOC.js.map → sampleScatter.spec-N6V4BQ5Q.js.map} +0 -0
  904. /package/dist/{sampleView-SVTLSWRG.js.map → sampleView-CZF7U23I.js.map} +0 -0
  905. /package/dist/{samplelst-HXF5POJD.js.map → samplelst-XUGDS5TU.js.map} +0 -0
  906. /package/dist/{samplematrix-NYDAH74I.js.map → samplematrix-R5PZLZDE.js.map} +0 -0
  907. /package/dist/{sc-JIDT4W4K.js.map → sc-WTZZA5J5.js.map} +0 -0
  908. /package/dist/{selectGenomeWithTklst-OSB7B6L3.js.map → selectGenomeWithTklst-2S2MXVCI.js.map} +0 -0
  909. /package/dist/{singleCellCellType-3BH7LWQ6.js.map → singleCellCellType-LJWFG7MY.js.map} +0 -0
  910. /package/dist/{singleCellCellType.unit.spec-RU4RJXFF.js.map → singleCellCellType.unit.spec-RGN2XVUR.js.map} +0 -0
  911. /package/dist/{singleCellGeneExpression-3UA4YER7.js.map → singleCellGeneExpression-IW2QXTTU.js.map} +0 -0
  912. /package/dist/{singleCellGeneExpression.unit.spec-4ZTBG37H.js.map → singleCellGeneExpression.unit.spec-4PO3Q7TM.js.map} +0 -0
  913. /package/dist/{singleCellPlot-ZUAWK5RE.js.map → singleCellPlot-6EZ6JXCM.js.map} +0 -0
  914. /package/dist/{singlecell-BGJZB7MF.js.map → singlecell-3LFPQ6KO.js.map} +0 -0
  915. /package/dist/{singlecell-RO3BL5OO.js.map → singlecell-NTTAVVMR.js.map} +0 -0
  916. /package/dist/{snp-HD7VQKBR.js.map → snp-XB4IBG4Z.js.map} +0 -0
  917. /package/dist/{snp.unit.spec-ISXCLMWW.js.map → snp.unit.spec-HAJPM53L.js.map} +0 -0
  918. /package/dist/{snplocus-IL5Z4XWV.js.map → snplocus-HE6TITSX.js.map} +0 -0
  919. /package/dist/{spliceevent.a53ss.diagram-LLJSPV7M.js.map → spliceevent.a53ss.diagram-TCZMBMD7.js.map} +0 -0
  920. /package/dist/{spliceevent.exonskip.diagram-LAOIOIST.js.map → spliceevent.exonskip.diagram-VESOF6UC.js.map} +0 -0
  921. /package/dist/{spliceevent.noeventdiagram-MVA7Q3HT.js.map → spliceevent.noeventdiagram-4K7FMO4F.js.map} +0 -0
  922. /package/dist/{ssGSEA-7T6S3DSE.js.map → ssGSEA-2XYMX36P.js.map} +0 -0
  923. /package/dist/{ssGSEA.unit.spec-XJ3W4NWX.js.map → ssGSEA.unit.spec-J36KM2HO.js.map} +0 -0
  924. /package/dist/{summarizeCnvGeneexp-RRP6JUV6.js.map → summarizeCnvGeneexp-LYVDZXXD.js.map} +0 -0
  925. /package/dist/{summarizeGeneexpSurvival-AFLHDD6Q.js.map → summarizeGeneexpSurvival-Y52TGAHF.js.map} +0 -0
  926. /package/dist/{summarizeMutationCnv-NABUYHMX.js.map → summarizeMutationCnv-6EEJT3PV.js.map} +0 -0
  927. /package/dist/{summarizeMutationDiagnosis-2LQ7JU3K.js.map → summarizeMutationDiagnosis-HZKXHOOQ.js.map} +0 -0
  928. /package/dist/{summarizeMutationSurvival-3WBT5TXG.js.map → summarizeMutationSurvival-TU7TQYFQ.js.map} +0 -0
  929. /package/dist/{summary-FRDKOFXW.js.map → summary-4QQZUAMU.js.map} +0 -0
  930. /package/dist/{summary.integration.spec-ZLRIA7G2.js.map → summary.integration.spec-SLIIM4HN.js.map} +0 -0
  931. /package/dist/{summaryInput-4JO6MHP4.js.map → summaryInput-6HROPKCE.js.map} +0 -0
  932. /package/dist/{sunburst-DRCVSC2X.js.map → sunburst-MBJJPERL.js.map} +0 -0
  933. /package/dist/{survival-AK75COPY.js.map → survival-CXLMQSV2.js.map} +0 -0
  934. /package/dist/{survival-IF5NI3A6.js.map → survival-QSL2KDKD.js.map} +0 -0
  935. /package/dist/{survival.integration.spec-7IWBTPJG.js.map → survival.integration.spec-EUAAALVW.js.map} +0 -0
  936. /package/dist/{svgraph-QBDF2SLB.js.map → svgraph-JM5MHQDX.js.map} +0 -0
  937. /package/dist/{svmr-O4GJJUT2.js.map → svmr-MCMST2FL.js.map} +0 -0
  938. /package/dist/{table-FQAIXKLE.js.map → table-MVX3IMAL.js.map} +0 -0
  939. /package/dist/{termCollection-ZO5PZ7E3.js.map → termCollection-FZ2SCVA7.js.map} +0 -0
  940. /package/dist/{termCollection-GMDDL3L7.js.map → termCollection-IGC7REFK.js.map} +0 -0
  941. /package/dist/{termCollection.unit.spec-5JBCTXHX.js.map → termCollection.unit.spec-VY2EZZIP.js.map} +0 -0
  942. /package/dist/{tk-GJX23IV7.js.map → tk-5F3TWZ2G.js.map} +0 -0
  943. /package/dist/{tp.ui-T7FVMTGQ.js.map → tp.ui-IURWTMAS.js.map} +0 -0
  944. /package/dist/{tvs.dt-X7L7NSU6.js.map → tvs.dt-BPZCFPYK.js.map} +0 -0
  945. /package/dist/{tvs.dtcnv.categorical-73G2V6CH.js.map → tvs.dtcnv.categorical-UFS62DTR.js.map} +0 -0
  946. /package/dist/{tvs.dtcnv.continuous-DWFJL3X7.js.map → tvs.dtcnv.continuous-R6YXNNLA.js.map} +0 -0
  947. /package/dist/{tvs.dtfusion-HQADHCSV.js.map → tvs.dtfusion-FGXXS4XX.js.map} +0 -0
  948. /package/dist/{tvs.dtsnvindel-PY5OBMGW.js.map → tvs.dtsnvindel-DR43K7X3.js.map} +0 -0
  949. /package/dist/{tvs.dtsv-OTBEEWSW.js.map → tvs.dtsv-NO34GIOL.js.map} +0 -0
  950. /package/dist/{tvs.numeric-WGDHEBJV.js.map → tvs.numeric-KYAU5OV3.js.map} +0 -0
  951. /package/dist/{tvs.samplelst-LCXSU5MG.js.map → tvs.samplelst-2QP7IV2Y.js.map} +0 -0
  952. /package/dist/{tvs.termCollection-L527XN4X.js.map → tvs.termCollection-UEJDG22G.js.map} +0 -0
  953. /package/dist/{violin-6VKRUQV3.js.map → violin-NBZTGGYF.js.map} +0 -0
  954. /package/dist/{violin.integration.spec-RJATDLQH.js.map → violin.integration.spec-5CLYJSAR.js.map} +0 -0
  955. /package/dist/{violin.interactivity-SKF5H7MN.js.map → violin.interactivity-KXVKTT22.js.map} +0 -0
  956. /package/dist/{violin.renderer-GB4TPX3B.js.map → violin.renderer-37OF6K7Q.js.map} +0 -0
  957. /package/dist/{vocabulary-D3W44IWE.js.map → vocabulary-GR6J3VKW.js.map} +0 -0
@@ -1,193 +0,0 @@
1
- import {
2
- detectGte
3
- } from "./chunk-DJQTUDJM.js";
4
- import {
5
- getRunPp
6
- } from "./chunk-W55XSG6K.js";
7
- import {
8
- require_tape
9
- } from "./chunk-QWOE5YTB.js";
10
- import "./chunk-74ZU4BT6.js";
11
- import "./chunk-IW57W7EQ.js";
12
- import "./chunk-ZTYNN6G5.js";
13
- import "./chunk-DKVUOBIE.js";
14
- import "./chunk-PRZWSBMA.js";
15
- import "./chunk-LTOBEUM2.js";
16
- import "./chunk-MKAF2BHB.js";
17
- import "./chunk-WKNI3HRQ.js";
18
- import "./chunk-VGYTAYFK.js";
19
- import "./chunk-67DBIM6H.js";
20
- import "./chunk-SA7APTJR.js";
21
- import "./chunk-HJ6L54YS.js";
22
- import "./chunk-LSEFWW72.js";
23
- import "./chunk-SKREEF3H.js";
24
- import "./chunk-HYOEWQ5P.js";
25
- import "./chunk-HBW42TDT.js";
26
- import "./chunk-G6O3URDN.js";
27
- import "./chunk-FN5XPUPH.js";
28
- import "./chunk-IIT367QZ.js";
29
- import "./chunk-RZGEKL77.js";
30
- import "./chunk-UI7OCM2A.js";
31
- import "./chunk-YZK37YCC.js";
32
- import "./chunk-7EMWHCVW.js";
33
- import "./chunk-7IYJZZQI.js";
34
- import "./chunk-M3J4MINX.js";
35
- import "./chunk-PF4DSFDR.js";
36
- import "./chunk-QH6W3NVF.js";
37
- import "./chunk-NOEAT6CX.js";
38
- import "./chunk-4UWS5Y3N.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 "./chunk-OMR2DT66.js";
49
- import "./chunk-DQC5FFGV.js";
50
- import {
51
- __toESM
52
- } from "./chunk-HFNDKYVF.js";
53
-
54
- // plots/test/dataDownload.integration.spec.js
55
- var import_tape = __toESM(require_tape(), 1);
56
- var runpp = getRunPp("mass", {
57
- state: {
58
- nav: {
59
- header_mode: "hide_search",
60
- activeTab: 1
61
- },
62
- vocab: {
63
- dslabel: "TermdbTest",
64
- genome: "hg38-test"
65
- }
66
- },
67
- debug: 1
68
- });
69
- (0, import_tape.default)("\n", (test) => {
70
- test.comment("-***- plots/dataDownload -***-");
71
- test.end();
72
- });
73
- (0, import_tape.default)("Data download with no selected terms", (test) => {
74
- test.timeoutAfter(1e3);
75
- runpp({
76
- state: {
77
- plots: [
78
- {
79
- chartType: "dataDownload"
80
- }
81
- ]
82
- },
83
- dataDownload: {
84
- callbacks: {
85
- "postRender.test": runTests
86
- }
87
- }
88
- });
89
- function runTests(dataDownload) {
90
- dataDownload.on("postRender.test", null);
91
- const ddDom = dataDownload.Inner.dom;
92
- test.equal(ddDom.terms.node().querySelectorAll(".term_name_btn").length, 0, `Should render no term pills`);
93
- test.equal(
94
- ddDom.terms.node().querySelectorAll(".sja_filter_tag_btn.add_term_btn").length,
95
- 1,
96
- `Should render 1 'Add variable' button`
97
- );
98
- test.equal(
99
- ddDom.submitNote.node().innerText,
100
- `no sample data`,
101
- `Should render "no sample data" next to Download button`
102
- );
103
- test.ok(ddDom.submitBtn.node().disabled, `Should show Download button as disabled`);
104
- if (test._ok) dataDownload.Inner.app.destroy();
105
- test.end();
106
- }
107
- });
108
- (0, import_tape.default)("Data download with terms selected", (test) => {
109
- test.timeoutAfter(2e3);
110
- const terms = [
111
- { $id: 0, id: "sex" },
112
- { $id: 1, id: "agedx" },
113
- { $id: 2, id: "genetic_race" },
114
- { $id: 3, id: "aaclassic_5" },
115
- { $id: 4, id: "Arrhythmias" }
116
- ];
117
- runpp({
118
- state: {
119
- plots: [
120
- {
121
- chartType: "dataDownload",
122
- terms
123
- }
124
- ]
125
- },
126
- dataDownload: {
127
- callbacks: {
128
- "postRender.test": runTests
129
- }
130
- }
131
- });
132
- async function runTests(dataDownload) {
133
- dataDownload.on("postRender.test", null);
134
- const ddDom = dataDownload.Inner.dom;
135
- await detectGte({
136
- elem: ddDom.terms.node(),
137
- selector: ".term_name_btn",
138
- count: 5
139
- });
140
- test.equal(
141
- ddDom.terms.node().querySelectorAll(".term_name_btn").length,
142
- terms.length,
143
- `Should render ${terms.length} term pills`
144
- );
145
- test.equal(
146
- ddDom.submitNote.node().innerText,
147
- `${dataDownload.Inner.activeSamples.length} samples`,
148
- `Should render "${dataDownload.Inner.activeSamples.length} samples" next to Download button`
149
- );
150
- if (test._ok) dataDownload.Inner.app.destroy();
151
- test.end();
152
- }
153
- });
154
- (0, import_tape.default)("protected dataset", (test) => {
155
- test.timeoutAfter(3e3);
156
- const runpp2 = getRunPp("mass", {
157
- state: {
158
- nav: {
159
- header_mode: "hide_search",
160
- activeTab: 1
161
- },
162
- vocab: {
163
- dslabel: "ProtectedTest",
164
- genome: "hg38-test"
165
- }
166
- },
167
- debug: 1
168
- });
169
- runpp2({
170
- state: {
171
- plots: [
172
- {
173
- chartType: "dataDownload"
174
- }
175
- ]
176
- },
177
- dataDownload: {
178
- callbacks: {
179
- "postRender.test": runTests
180
- }
181
- }
182
- });
183
- async function runTests(dataDownload) {
184
- dataDownload.on("postRender.test", null);
185
- test.true(
186
- dataDownload.Inner.dom.titleDiv.text().includes("Requires sign-in"),
187
- "should not open by default for protected dataset"
188
- );
189
- if (test._ok) dataDownload.Inner.app.destroy();
190
- test.end();
191
- }
192
- });
193
- //# sourceMappingURL=dataDownload.integration.spec-2PKYZ2AY.js.map
@@ -1,433 +0,0 @@
1
- import {
2
- isURL,
3
- makeBtn,
4
- makeFileUpload,
5
- makePrompt,
6
- makeResetBtn,
7
- makeTextAreaInput,
8
- makeTextInput
9
- } from "./chunk-5EBRF6Z7.js";
10
- import {
11
- appInit
12
- } from "./chunk-QNETLNPB.js";
13
- import "./chunk-HKSNADSX.js";
14
- import "./chunk-SKMFMGCD.js";
15
- import "./chunk-BDIKFVWZ.js";
16
- import "./chunk-FFEIP5CT.js";
17
- import "./chunk-DR6H3QAA.js";
18
- import "./chunk-MYF2BWKC.js";
19
- import "./chunk-CXQ6KS3Z.js";
20
- import "./chunk-4KY4XKJV.js";
21
- import "./chunk-OEDZHPBJ.js";
22
- import "./chunk-PCZNTK74.js";
23
- import "./chunk-PRZWSBMA.js";
24
- import {
25
- appear,
26
- sayerror
27
- } from "./chunk-SA7APTJR.js";
28
- import "./chunk-HJ6L54YS.js";
29
- import "./chunk-LSEFWW72.js";
30
- import "./chunk-SKREEF3H.js";
31
- import "./chunk-HYOEWQ5P.js";
32
- import {
33
- Tabs
34
- } from "./chunk-HBW42TDT.js";
35
- import "./chunk-G6O3URDN.js";
36
- import "./chunk-FN5XPUPH.js";
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- import "./chunk-IIT367QZ.js";
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- import "./chunk-RZGEKL77.js";
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- import "./chunk-UI7OCM2A.js";
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- import "./chunk-YZK37YCC.js";
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- import "./chunk-7EMWHCVW.js";
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- import "./chunk-7IYJZZQI.js";
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- import "./chunk-M3J4MINX.js";
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- import "./chunk-PF4DSFDR.js";
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- import "./chunk-QH6W3NVF.js";
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- import "./chunk-NOEAT6CX.js";
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- import "./chunk-4UWS5Y3N.js";
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- import "./chunk-DD4R5P6W.js";
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- import "./chunk-JNITUVXP.js";
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- import "./chunk-KSGA62R2.js";
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- import "./chunk-LOZEKOES.js";
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- import "./chunk-TOU7EVFQ.js";
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- import "./chunk-OAWQ6LOO.js";
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- import "./chunk-TLT4YIG3.js";
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- import "./chunk-KYBIQBXE.js";
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- import "./chunk-I6Y4O3RR.js";
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- import "./chunk-OMR2DT66.js";
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- import "./chunk-DQC5FFGV.js";
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- import "./chunk-HFNDKYVF.js";
60
-
61
- // src/databrowser/dictionary.parse.js
62
- function parseDictionary(input) {
63
- const terms = {};
64
- const lines = input.trim().split(/\r?\n/);
65
- const header = lines[0].split(" ");
66
- const term_idIndex = header.findIndex((l) => l.toLowerCase().includes("term_id"));
67
- const variableIndex = header.findIndex((l) => l.toLowerCase().includes("variable"));
68
- if (term_idIndex != -1) parseDataDictionary(lines, header);
69
- if (variableIndex != -1) parsePhenotree(lines, header);
70
- if (variableIndex == -1 && term_idIndex == -1) {
71
- throw `Unrecognized file format. Please check the header names.`;
72
- }
73
- function parseDataDictionary(lines2, header2) {
74
- const parIdIndex = header2.findIndex((l) => l.toLowerCase().includes("parent_id"));
75
- if (parIdIndex == -1) {
76
- throw `Missing required 'parent_id' header`;
77
- }
78
- const nameIndex = header2.findIndex((l) => l.toLowerCase().includes("name"));
79
- if (nameIndex == -1) {
80
- throw `Missing required 'Name' header`;
81
- }
82
- const typeIndex = header2.findIndex((l) => {
83
- const v = l.trim().toLowerCase();
84
- return v === "type";
85
- });
86
- if (typeIndex == -1) {
87
- throw `Missing required 'Type' header`;
88
- }
89
- const valuesIndex = header2.findIndex((l) => l.toLowerCase().includes("values"));
90
- if (valuesIndex == -1) {
91
- throw `Missing required 'Values' header`;
92
- }
93
- if (parIdIndex == -1 || nameIndex == -1 || typeIndex == -1 || valuesIndex == -1) {
94
- throw `Missing required header(s)`;
95
- }
96
- const parentIds = /* @__PURE__ */ new Set();
97
- for (const [i, line] of lines2.entries()) {
98
- if (i === 0) continue;
99
- const lineNum = i + 1;
100
- try {
101
- const cols = line.split(" ");
102
- for (const [i2, c] of cols.entries()) {
103
- const colNum = i2 + 1;
104
- let foundProblem;
105
- if (i2 == valuesIndex) continue;
106
- if (c == "" || c == "-") {
107
- foundProblem = true;
108
- throw `Blank or '-' entered for line ${lineNum}, column ${colNum}`;
109
- }
110
- if (foundProblem == true) throw `Invalid entry for line ${lineNum}, column ${colNum}`;
111
- }
112
- const termId = cols[term_idIndex];
113
- const type = cols[typeIndex];
114
- terms[termId] = {
115
- id: termId,
116
- name: cols[nameIndex].trim().replace(/"/g, ""),
117
- parent_id: cols[parIdIndex] != "root" ? cols[parIdIndex] : null,
118
- type: cols[typeIndex] != "non graphable" ? cols[typeIndex] : null
119
- };
120
- parentIds.add(terms[termId].parent_id);
121
- if (type == "categorical") {
122
- terms[termId].values = {};
123
- }
124
- const values = cols[valuesIndex].trim().replace(/"/g, "").split(";");
125
- for (const x of values) {
126
- const v = x.trim();
127
- if (v == "") continue;
128
- const segments = v.split("=");
129
- const key = segments.shift();
130
- const label = segments.join("=");
131
- if (!label) throw `Values="${v}" in line ${lineNum} not in a key = value format.`;
132
- if (!terms[termId].values) terms[termId].values = {};
133
- terms[termId].values[key] = { label };
134
- }
135
- const numValues = Object.keys(terms[termId].values).length;
136
- terms[termId].groupsetting = { disabled: numValues < 3 };
137
- validateNumericTermCategories(terms[termId]);
138
- } catch (e) {
139
- throw `Line ${lineNum} error: ${e}`;
140
- }
141
- }
142
- for (const t in terms) terms[t].isleaf = !parentIds.has(terms[t].id);
143
- }
144
- function parsePhenotree(lines2, header2) {
145
- if (variableIndex == -1) {
146
- throw `Missing required 'Variable' header`;
147
- }
148
- const typeIndex = header2.findIndex((l) => {
149
- const v = l.trim().toLowerCase();
150
- return v === "type";
151
- });
152
- if (typeIndex == -1) {
153
- throw `Missing required 'Type' header`;
154
- }
155
- const categoriesIndex = header2.findIndex((l) => l.toLowerCase().includes("categories"));
156
- const levelColIndexes = header2.map((c, i) => c.toLowerCase().includes("level_") ? i : -1).filter((i) => i != -1);
157
- if (!levelColIndexes.length) levelColIndexes.push(variableIndex);
158
- const unitIndex = header2.findIndex((l) => l.toLowerCase().includes("unit"));
159
- const sampleTypeIndex = header2.findIndex((l) => {
160
- const v = l.trim().toLowerCase();
161
- return v === "sample_type";
162
- });
163
- const additionalAttrIndexes = header2.findIndex((l) => l.toLowerCase().includes("additional attributes"));
164
- const termNameToId = {};
165
- const parentTermNames = /* @__PURE__ */ new Set();
166
- const parent2ChildOrder = /* @__PURE__ */ new Map();
167
- parent2ChildOrder.set(null, []);
168
- for (const [i, line] of lines2.entries()) {
169
- if (i === 0) continue;
170
- const lineNum = i + 1;
171
- try {
172
- const cols = line.split(" ");
173
- const levelNames = levelColIndexes.map((i2) => cols[i2].trim().replace(/"/g, "")).filter((c) => c != "-");
174
- if (levelNames.length != new Set(levelNames).size) {
175
- throw `Non-unique levels in line ${lineNum}: ${JSON.stringify(levelNames)}`;
176
- }
177
- for (const [i2, lvlName] of levelNames.entries()) {
178
- if (i2 == 0) {
179
- if (parent2ChildOrder.get(null).indexOf(lvlName) == -1) parent2ChildOrder.get(null).push(lvlName);
180
- }
181
- if (i2 != levelNames.length - 1) {
182
- if (!parent2ChildOrder.has(lvlName)) parent2ChildOrder.set(lvlName, []);
183
- }
184
- for (const n of levelNames) {
185
- if (i2 == levelNames.indexOf(n) - 1) {
186
- if (parent2ChildOrder.get(lvlName).indexOf(n) == -1) parent2ChildOrder.get(lvlName).push(n);
187
- }
188
- }
189
- }
190
- const name = levelNames.pop();
191
- const firstDashIndex = cols.indexOf("-");
192
- if (firstDashIndex != -1 && firstDashIndex < cols.indexOf(name)) {
193
- throw `Blank or '-' value detected between levels in line ${lineNum}`;
194
- }
195
- const term = parseCategories(cols[typeIndex], cols[categoriesIndex], lineNum, name);
196
- const id = cols[variableIndex] || name;
197
- if (id in terms) {
198
- const orig = terms[id];
199
- throw `Error: Multiple config rows for term.id='${id}': lines# ${orig.lineNum} and ${lineNum}`;
200
- }
201
- terms[id] = {
202
- id,
203
- name,
204
- type: term.type,
205
- values: term.values,
206
- groupsetting: term.groupsetting,
207
- // *** temporary attributes to be deleted later ***
208
- ancestry: levelNames.slice(),
209
- // to be deleted later, used to fill in missing terms
210
- parent_name: levelNames.pop() || null,
211
- // will change this later to parent_id
212
- lineNum
213
- // to be deleted later
214
- };
215
- if (cols[unitIndex] != null) terms[id].unit = cols[unitIndex];
216
- if (cols[sampleTypeIndex] != null) terms[id].sample_type = cols[sampleTypeIndex];
217
- if (cols[additionalAttrIndexes]) {
218
- Object.assign(terms[id], JSON.parse(cols[additionalAttrIndexes]));
219
- }
220
- termNameToId[name] = id;
221
- parentTermNames.add(terms[id].parent_name);
222
- } catch (e) {
223
- throw `Line ${lineNum} error: ${e}`;
224
- }
225
- }
226
- trackMissingTerms(termNameToId, terms, parentTermNames, parent2ChildOrder);
227
- for (const id in terms) {
228
- const term = terms[id];
229
- term.child_order = parent2ChildOrder.get(term.parent_name).indexOf(term.name) + 1;
230
- term.isleaf = !parentTermNames.has(term.name);
231
- term.parent_id = termNameToId[term.parent_name] || null;
232
- delete term.parent_name;
233
- delete term.lineNum;
234
- delete term.ancestry;
235
- }
236
- }
237
- return { terms: Object.values(terms) };
238
- }
239
- function parseCategories(type, catJSON, lineNum, varName) {
240
- if (!type) throw `No type provided for variable: ${varName} on line ${lineNum}`;
241
- const term = {
242
- type,
243
- values: catJSON == "" || catJSON == void 0 ? {} : JSON.parse(catJSON)
244
- };
245
- validateNumericTermCategories(term);
246
- if (term.type == "categorical") {
247
- const numValues = Object.keys(term.values).length;
248
- term.groupsetting = { disabled: numValues < 3 };
249
- }
250
- return term;
251
- }
252
- function trackMissingTerms(termNameToId, terms, parentTermNames, parent2ChildOrder) {
253
- for (const id in terms) {
254
- const term = terms[id];
255
- for (const [i, name] of term.ancestry.entries()) {
256
- if (name in termNameToId) {
257
- const id2 = termNameToId[name];
258
- const ancestor = terms[id2];
259
- if (i - 1 < 0 && ancestor.parent_name || ancestor.parent_name != term.ancestry[i - 1]) {
260
- throw `Different parents for term=${name}, '${term.ancestry[i - 1]}' and '${ancestor.parent_name}'`;
261
- }
262
- continue;
263
- }
264
- terms[name] = {
265
- id: name,
266
- name,
267
- isleaf: false,
268
- ancestry: term.ancestry.slice(0, i)
269
- };
270
- terms[name].parent_name = terms[name].ancestry.slice(-1)[0] || null;
271
- termNameToId[name] = name;
272
- parentTermNames.add(name);
273
- }
274
- }
275
- }
276
- function validateNumericTermCategories(term) {
277
- if (term.type != "integer" && term.type != "float") return;
278
- if (!term.values) return;
279
- if (typeof term.values != "object") throw "numeric .values{} is not object";
280
- for (const key in term.values) {
281
- if (key == "") throw "Cannot use empty string as an uncomputable category";
282
- const tmp = Number(key);
283
- if (Number.isNaN(tmp)) {
284
- throw `Uncomputable category of a numeric term is required to be a number (here uses non-numeric value of ${key}).`;
285
- }
286
- term.values[key].uncomputable = true;
287
- }
288
- }
289
-
290
- // src/databrowser/databrowser.ui.js
291
- function init_databrowserUI(holder, debugmode) {
292
- const wrapper = holder.append("div").style("margin", "20px 20px 20px 40px").style(
293
- "font-family",
294
- "'Lucida Sans', 'Lucida Sans Regular', 'Lucida Grande', 'Lucida Sans Unicode', Geneva, Verdana, sans-serif"
295
- ).style("place-items", "center left").style("overflow", "hidden").classed("sjpp-app-ui", true);
296
- const obj = {};
297
- infoSection(wrapper);
298
- makeSectionHeader(wrapper, "Data Dictionary");
299
- const tabs_div = wrapper.append("div").style("margin-left", "2vw");
300
- makeDataDictionaryTabs(tabs_div, obj);
301
- const controlBtns_div = wrapper.append("div").style("display", "flex").style("align-items", "center").style("margin", "40px 0px 40px 130px");
302
- submitButton(controlBtns_div, obj, wrapper, holder);
303
- makeResetBtn(controlBtns_div, obj, ".databrowser_input");
304
- if (debugmode) window.doms = obj;
305
- return obj;
306
- }
307
- function infoSection(div) {
308
- div.append("div").style("margin", "10px").style("opacity", "0.65").html(`
309
- <ul>
310
- <li>
311
- Please see the <a href="https://github.com/stjude/proteinpaint/wiki/Data-Browser" target="_blank">documentation</a> for more information.
312
- </li>
313
- <li>
314
- Download an example data dictionary <a href="https://proteinpaint.stjude.org/ppdemo/databrowser/dictionaryDemoData.tar.gz" target="_self" "download>here</a>.
315
- </li>
316
- </ul>`);
317
- }
318
- function makeSectionHeader(div, text) {
319
- const header = makePrompt(div, text);
320
- header.style("font-size", "1.5em").style("color", "#003366").style("margin", "20px 10px 40px 10px").classed("sjpp-databrowser-section-header", true);
321
- const hr = div.append("hr");
322
- hr.style("color", "ligthgrey").style("margin", "-30px 0px 15px 0px").style("width", "50vw").style("opacity", "0.4");
323
- }
324
- function makeDataDictionaryTabs(tabs_div, obj) {
325
- const tabs = [
326
- {
327
- label: "Select File",
328
- active: true,
329
- width: 95,
330
- callback: async (event, tab) => {
331
- tab.contentHolder.style("border", "none").style("display", "block");
332
- appear(tab.contentHolder);
333
- tab.contentHolder.append("div").html(`<p style="margin-left: 10px; opacity: 0.65;">Select a file from your computer.</p>`);
334
- makeFileUpload2(tab.contentHolder, obj);
335
- delete tab.callback;
336
- }
337
- },
338
- {
339
- label: "Paste Data",
340
- active: false,
341
- width: 95,
342
- callback: async (event, tab) => {
343
- tab.contentHolder.style("border", "none").style("display", "block");
344
- appear(tab.contentHolder);
345
- tab.contentHolder.append("div").html(
346
- `<p style="margin-left: 10px; opacity: 0.65;">Paste data dictionary or phenotree in a tab delimited format.</p>`
347
- );
348
- makeCopyPasteInput(tab.contentHolder, obj);
349
- delete tab.callback;
350
- }
351
- },
352
- {
353
- label: "File Path",
354
- active: false,
355
- width: 95,
356
- callback: async (event, tab) => {
357
- tab.contentHolder.style("border", "none").style("display", "block");
358
- appear(tab.contentHolder);
359
- tab.contentHolder.append("div").html(`<p style="margin-left: 10px; opacity: 0.65;">Provide a URL file path.</p>`);
360
- makePrompt(tab.contentHolder, "URL");
361
- makeTextEntryFilePathInput(tab.contentHolder, obj);
362
- delete tab.callback;
363
- }
364
- }
365
- ];
366
- new Tabs({ holder: tabs_div, tabs }).main();
367
- }
368
- function makeTextEntryFilePathInput(div, obj) {
369
- const filepath_div = div.append("div").style("display", "inline-block");
370
- const filepath = makeTextInput(filepath_div).style("border", "1px solid rgb(138, 177, 212)").classed("databrowser_input", true).on("keyup", async () => {
371
- const data = filepath.property("value").trim();
372
- if (isURL(data)) {
373
- const txt = await fetch(data).then((req) => req.text()).then((txt2) => {
374
- obj.data = parseDictionary(txt2);
375
- });
376
- } else {
377
- }
378
- });
379
- }
380
- function makeFileUpload2(div, obj) {
381
- const upload_div = div.append("div").style("display", "inline-block");
382
- const upload = makeFileUpload(upload_div).classed("databrowser_input", true);
383
- upload.on("change", (event) => {
384
- const file = event.target.files[0];
385
- const reader = new FileReader();
386
- reader.onload = (event2) => {
387
- obj.data = parseDictionary(event2.target.result);
388
- };
389
- reader.readAsText(file, "utf8");
390
- });
391
- }
392
- function makeCopyPasteInput(div, obj) {
393
- const paste_div = div.append("div").style("display", "block");
394
- const paste = makeTextAreaInput({ div: paste_div, rows: 10 }).style("border", "1px solid rgb(138, 177, 212)").style("margin", "0px 0px 0px 20px").classed("databrowser_input", true).on("keyup", async () => {
395
- obj.data = parseDictionary(paste.property("value").trim());
396
- });
397
- }
398
- function submitButton(div, obj, wrapper, holder) {
399
- const submit = makeBtn({
400
- div,
401
- text: "Create Data Browser",
402
- color: "white",
403
- backgroundColor: "#001aff",
404
- border: "2px solid #001aff"
405
- });
406
- const errorMessage_div = div.append("div");
407
- submit.style("margin-right", "10px").style("font-size", "16px").classed("sjpp-ui-submitBtn", true).attr("type", "submit").on("click", () => {
408
- if (!obj.data || obj.data == void 0) {
409
- const sayerrorDiv = errorMessage_div.append("div").style("display", "inline-block").style("max-width", "20vw");
410
- sayerror(sayerrorDiv, "Please provide data");
411
- setTimeout(() => sayerrorDiv.remove(), 3e3);
412
- } else {
413
- wrapper.remove();
414
- appInit({
415
- holder,
416
- state: {
417
- vocab: {
418
- terms: obj.data.terms
419
- },
420
- plots: [
421
- {
422
- chartType: "dictionary"
423
- }
424
- ]
425
- }
426
- });
427
- }
428
- });
429
- }
430
- export {
431
- init_databrowserUI
432
- };
433
- //# sourceMappingURL=databrowser.ui-WGD7D3XV.js.map