@sjcrh/proteinpaint-server 2.84.0 → 2.85.1

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Files changed (48) hide show
  1. package/package.json +4 -5
  2. package/routes/_template_.js +14 -11
  3. package/routes/brainImaging.js +5 -14
  4. package/routes/brainImagingSamples.js +3 -3
  5. package/routes/burden.js +27 -59
  6. package/routes/dataset.js +9 -17
  7. package/routes/dsdata.js +11 -14
  8. package/routes/dzimages.js +11 -16
  9. package/routes/gdc.maf.js +8 -23
  10. package/routes/gdc.mafBuild.js +9 -9
  11. package/routes/gdc.topMutatedGenes.js +7 -7
  12. package/routes/genelookup.js +16 -34
  13. package/routes/genesetEnrichment.js +18 -14
  14. package/routes/genesetOverrepresentation.js +9 -14
  15. package/routes/healthcheck.js +26 -32
  16. package/routes/hicdata.js +7 -28
  17. package/routes/hicgenome.js +6 -27
  18. package/routes/hicstat.js +4 -22
  19. package/routes/isoformlst.js +8 -11
  20. package/routes/ntseq.js +8 -11
  21. package/routes/pdomain.js +8 -11
  22. package/routes/sampledzimages.js +12 -12
  23. package/routes/samplewsimages.js +6 -10
  24. package/routes/snp.js +8 -10
  25. package/routes/termdb.DE.js +8 -10
  26. package/routes/termdb.boxplot.js +8 -9
  27. package/routes/termdb.categories.js +4 -45
  28. package/routes/termdb.cluster.js +9 -9
  29. package/routes/termdb.cohort.summary.js +5 -8
  30. package/routes/termdb.cohorts.js +3 -7
  31. package/routes/{termdb.getdescrstats.js → termdb.descrstats.js} +8 -45
  32. package/routes/termdb.numericcategories.js +51 -0
  33. package/routes/{termdb.getpercentile.js → termdb.percentile.js} +4 -46
  34. package/routes/{termdb.getrootterm.js → termdb.rootterm.js} +4 -24
  35. package/routes/{termdb.getSampleImages.js → termdb.sampleImages.js} +9 -9
  36. package/routes/termdb.singleSampleMutation.js +3 -7
  37. package/routes/termdb.singlecellDEgenes.js +8 -8
  38. package/routes/termdb.singlecellData.js +4 -8
  39. package/routes/termdb.singlecellSamples.js +8 -8
  40. package/routes/{termdb.gettermchildren.js → termdb.termchildren.js} +8 -28
  41. package/routes/termdb.termsbyids.js +9 -16
  42. package/routes/{termdb.getTopTermsByType.js → termdb.topTermsByType.js} +9 -10
  43. package/routes/termdb.topVariablyExpressedGenes.js +8 -8
  44. package/routes/termdb.violin.js +8 -46
  45. package/routes/tileserver.js +5 -10
  46. package/routes/wsimages.js +10 -9
  47. package/src/app.js +1286 -2148
  48. package/routes/termdb.getnumericcategories.js +0 -91
package/routes/termdb.getnumericcategories.js DELETED
@@ -1,91 +0,0 @@
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- import * as termdbsql from "#src/termdb.sql.js";
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- const api = {
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- endpoint: "termdb/numericcategories",
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- methods: {
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- get: {
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- init,
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- request: {
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- typeId: "getnumericcategoriesRequest"
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- },
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- response: {
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- typeId: "getnumericcategoriesResponse"
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- },
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- examples: [
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- {
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- request: {
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- body: {
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- genome: "hg38-test",
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- dslabel: "TermdbTest",
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- embedder: "localhost",
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- tid: "aaclassic_5",
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- filter: {
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- type: "tvslst",
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- in: true,
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- join: "",
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- lst: [
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- {
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- tag: "cohortFilter",
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- type: "tvs",
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- tvs: {
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- term: {
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- name: "Cohort",
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- type: "categorical",
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- values: { ABC: { label: "ABC" }, XYZ: { label: "XYZ" } },
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- id: "subcohort",
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- isleaf: false,
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- groupsetting: { disabled: true }
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- },
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- values: [{ key: "ABC", label: "ABC" }]
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- }
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- }
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- ]
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- }
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- }
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- },
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- response: {
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- header: { status: 200 }
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- }
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- }
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- ]
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- },
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- post: {
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- alternativeFor: "get",
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- init
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- }
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- }
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- };
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- function init({ genomes }) {
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- return async (req, res) => {
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- const q = req.query;
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- try {
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- const g = genomes[req.query.genome];
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- if (!g)
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- throw "invalid genome name";
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- const ds = g.datasets[req.query.dslabel];
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- if (!ds)
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- throw "invalid dataset name";
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- const tdb = ds.cohort.termdb;
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- if (!tdb)
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- throw "invalid termdb object";
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- await trigger_getnumericcategories(q, res, tdb, ds);
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- } catch (e) {
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- res.send({ error: e instanceof Error ? e.message : e });
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- if (e instanceof Error && e.stack)
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- console.log(e);
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- }
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- };
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- }
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- async function trigger_getnumericcategories(q, res, tdb, ds) {
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- if (!q.tid)
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- throw ".tid missing";
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- const arg = {
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- ds,
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- term_id: q.tid,
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- filter: q.filter
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- };
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- const lst = await termdbsql.get_summary_numericcategories(arg);
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- res.send({ lst });
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- }
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- export {
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- api
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- };