@sjcrh/proteinpaint-types 2.152.1-0 → 2.157.0

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Files changed (8) hide show
  1. package/dist/{chunk-EYKGJDKU.js → chunk-4LOGWDCZ.js} +26 -22
  2. package/dist/{chunk-HI2IT25E.js → chunk-WCF7WIJY.js} +73 -38
  3. package/dist/grin2.js +1 -1
  4. package/dist/index.js +2 -2
  5. package/dist/termdb.singlecellDEgenes.js +1 -1
  6. package/package.json +7 -2
  7. package/src/routes/grin2.ts +24 -18
  8. package/src/routes/termdb.singlecellDEgenes.ts +8 -6
package/dist/{chunk-EYKGJDKU.js → chunk-4LOGWDCZ.js} RENAMED
@@ -69,12 +69,12 @@ var validTermdbSingleCellDEgenesResponse = (input) => {
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  const errors = [];
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  const __is = (input2) => {
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  const $io0 = (input3) => "number" === typeof input3.status && "string" === typeof input3.error;
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- const $io1 = (input3) => Array.isArray(input3.genes) && input3.genes.every((elem) => "object" === typeof elem && null !== elem && $io2(elem));
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- const $io2 = (input3) => "string" === typeof input3.name && "number" === typeof input3.p_val_adj && "number" === typeof input3.avg_log2FC;
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+ const $io1 = (input3) => Array.isArray(input3.data) && input3.data.every((elem) => "object" === typeof elem && null !== elem && $io2(elem));
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+ const $io2 = (input3) => "string" === typeof input3.gene_name && "number" === typeof input3.adjusted_p_value && "number" === typeof input3.original_p_value && "number" === typeof input3.fold_change;
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  const $iu0 = (input3) => (() => {
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  if (void 0 !== input3.status)
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  return $io0(input3);
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- if (void 0 !== input3.genes)
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+ if (void 0 !== input3.data)
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  return $io1(input3);
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  return false;
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  })();
@@ -92,40 +92,44 @@ var validTermdbSingleCellDEgenesResponse = (input) => {
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  expected: "string",
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  value: input3.error
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  })].every((flag) => flag);
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- const $vo1 = (input3, _path2, _exceptionable2 = true) => [(Array.isArray(input3.genes) || $report(_exceptionable2, {
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- path: _path2 + ".genes",
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+ const $vo1 = (input3, _path2, _exceptionable2 = true) => [(Array.isArray(input3.data) || $report(_exceptionable2, {
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+ path: _path2 + ".data",
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  expected: "Array<__type>",
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- value: input3.genes
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- })) && input3.genes.map((elem, _index1) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
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- path: _path2 + ".genes[" + _index1 + "]",
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+ value: input3.data
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+ })) && input3.data.map((elem, _index1) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
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+ path: _path2 + ".data[" + _index1 + "]",
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  expected: "__type",
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  value: elem
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- })) && $vo2(elem, _path2 + ".genes[" + _index1 + "]", _exceptionable2) || $report(_exceptionable2, {
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- path: _path2 + ".genes[" + _index1 + "]",
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+ })) && $vo2(elem, _path2 + ".data[" + _index1 + "]", _exceptionable2) || $report(_exceptionable2, {
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+ path: _path2 + ".data[" + _index1 + "]",
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  expected: "__type",
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  value: elem
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  })).every((flag) => flag) || $report(_exceptionable2, {
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- path: _path2 + ".genes",
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+ path: _path2 + ".data",
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  expected: "Array<__type>",
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- value: input3.genes
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+ value: input3.data
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  })].every((flag) => flag);
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- const $vo2 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.name || $report(_exceptionable2, {
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- path: _path2 + ".name",
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+ const $vo2 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.gene_name || $report(_exceptionable2, {
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+ path: _path2 + ".gene_name",
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  expected: "string",
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- value: input3.name
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- }), "number" === typeof input3.p_val_adj || $report(_exceptionable2, {
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- path: _path2 + ".p_val_adj",
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+ value: input3.gene_name
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+ }), "number" === typeof input3.adjusted_p_value || $report(_exceptionable2, {
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+ path: _path2 + ".adjusted_p_value",
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  expected: "number",
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- value: input3.p_val_adj
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- }), "number" === typeof input3.avg_log2FC || $report(_exceptionable2, {
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- path: _path2 + ".avg_log2FC",
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+ value: input3.adjusted_p_value
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+ }), "number" === typeof input3.original_p_value || $report(_exceptionable2, {
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+ path: _path2 + ".original_p_value",
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  expected: "number",
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- value: input3.avg_log2FC
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+ value: input3.original_p_value
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+ }), "number" === typeof input3.fold_change || $report(_exceptionable2, {
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+ path: _path2 + ".fold_change",
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+ expected: "number",
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+ value: input3.fold_change
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  })].every((flag) => flag);
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  const $vu0 = (input3, _path2, _exceptionable2 = true) => (() => {
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  if (void 0 !== input3.status)
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  return $vo0(input3, _path2, _exceptionable2);
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- if (void 0 !== input3.genes)
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+ if (void 0 !== input3.data)
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  return $vo1(input3, _path2, _exceptionable2);
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  return $report(_exceptionable2, {
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  path: _path2,
package/dist/{chunk-HI2IT25E.js → chunk-WCF7WIJY.js} RENAMED
@@ -190,8 +190,8 @@ var validGRIN2Response = (input) => {
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  const __is = (input2) => {
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  const $join = import_typia.createValidate.join;
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  const $io0 = (input3) => ("error" === input3.status || "success" === input3.status) && (void 0 === input3.error || "string" === typeof input3.error) && (void 0 === input3.pngImg || "string" === typeof input3.pngImg) && (void 0 === input3.plotData || "object" === typeof input3.plotData && null !== input3.plotData && $io1(input3.plotData)) && true && (void 0 === input3.topGeneTable || "object" === typeof input3.topGeneTable && null !== input3.topGeneTable && $io5(input3.topGeneTable)) && (void 0 === input3.totalGenes || "number" === typeof input3.totalGenes) && (void 0 === input3.showingTop || "number" === typeof input3.showingTop) && (void 0 === input3.timing || "object" === typeof input3.timing && null !== input3.timing && $io8(input3.timing)) && (void 0 === input3.processingSummary || "object" === typeof input3.processingSummary && null !== input3.processingSummary && false === Array.isArray(input3.processingSummary) && $io9(input3.processingSummary)) && (void 0 === input3.cacheFileName || "string" === typeof input3.cacheFileName);
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- const $io1 = (input3) => Array.isArray(input3.points) && input3.points.every((elem) => "object" === typeof elem && null !== elem && $io2(elem)) && ("object" === typeof input3.chrom_data && null !== input3.chrom_data && false === Array.isArray(input3.chrom_data) && $io3(input3.chrom_data)) && "boolean" === typeof input3.y_axis_scaled && "number" === typeof input3.scale_factor && "number" === typeof input3.total_genome_length && "number" === typeof input3.plot_width && "number" === typeof input3.plot_height && "number" === typeof input3.device_pixel_ratio && "number" === typeof input3.dpi;
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- const $io2 = (input3) => "number" === typeof input3.x && "number" === typeof input3.y && "number" === typeof input3.svg_x && "number" === typeof input3.svg_y && "string" === typeof input3.color && "string" === typeof input3.type && "string" === typeof input3.gene && "string" === typeof input3.chrom && "number" === typeof input3.pos && "number" === typeof input3.q_value;
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+ const $io1 = (input3) => Array.isArray(input3.points) && input3.points.every((elem) => "object" === typeof elem && null !== elem && $io2(elem)) && ("object" === typeof input3.chrom_data && null !== input3.chrom_data && false === Array.isArray(input3.chrom_data) && $io3(input3.chrom_data)) && "number" === typeof input3.total_genome_length;
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+ const $io2 = (input3) => "number" === typeof input3.x && "number" === typeof input3.y && "string" === typeof input3.color && "string" === typeof input3.type && "string" === typeof input3.gene && "string" === typeof input3.chrom && "number" === typeof input3.start && "number" === typeof input3.end && "number" === typeof input3.pos && "number" === typeof input3.nsubj;
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  const $io3 = (input3) => Object.keys(input3).every((key) => {
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  const value = input3[key];
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  if (void 0 === value)
@@ -204,8 +204,17 @@ var validGRIN2Response = (input) => {
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  const $io6 = (input3) => "string" === typeof input3.label && "boolean" === typeof input3.sortable;
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  const $io7 = (input3) => "string" === typeof input3.value || "number" === typeof input3.value;
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  const $io8 = (input3) => "number" === typeof input3.processingTime && "number" === typeof input3.grin2Time && "number" === typeof input3.totalTime;
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- const $io9 = (input3) => (void 0 === input3.totalSamples || "number" === typeof input3.totalSamples) && (void 0 === input3.processedSamples || "number" === typeof input3.processedSamples) && (void 0 === input3.failedSamples || "number" === typeof input3.failedSamples) && (void 0 === input3.failedFiles || Array.isArray(input3.failedFiles) && input3.failedFiles.every((elem) => "object" === typeof elem && null !== elem && $io10(elem))) && (void 0 === input3.totalLesions || "number" === typeof input3.totalLesions) && (void 0 === input3.processedLesions || "number" === typeof input3.processedLesions) && (void 0 === input3.unprocessedSamples || "number" === typeof input3.unprocessedSamples);
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+ const $io9 = (input3) => (void 0 === input3.totalSamples || "number" === typeof input3.totalSamples) && (void 0 === input3.processedSamples || "number" === typeof input3.processedSamples) && (void 0 === input3.failedSamples || "number" === typeof input3.failedSamples) && (void 0 === input3.failedFiles || Array.isArray(input3.failedFiles) && input3.failedFiles.every((elem) => "object" === typeof elem && null !== elem && $io10(elem))) && (void 0 === input3.totalLesions || "number" === typeof input3.totalLesions) && (void 0 === input3.processedLesions || "number" === typeof input3.processedLesions) && (void 0 === input3.unprocessedSamples || "number" === typeof input3.unprocessedSamples) && (void 0 === input3.lesionCounts || "object" === typeof input3.lesionCounts && null !== input3.lesionCounts && false === Array.isArray(input3.lesionCounts) && $io11(input3.lesionCounts));
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  const $io10 = (input3) => "string" === typeof input3.sampleName && "string" === typeof input3.filePath && "string" === typeof input3.error;
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+ const $io11 = (input3) => (void 0 === input3.total || "number" === typeof input3.total) && (void 0 === input3.byType || "object" === typeof input3.byType && null !== input3.byType && false === Array.isArray(input3.byType) && $io12(input3.byType));
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+ const $io12 = (input3) => Object.keys(input3).every((key) => {
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+ const value = input3[key];
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+ if (void 0 === value)
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+ return true;
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+ if (RegExp(/(.*)/).test(key))
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+ return "object" === typeof value && null !== value && ("number" === typeof value.count && "boolean" === typeof value.capped && "number" === typeof value.samples);
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+ return true;
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+ });
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  return "object" === typeof input2 && null !== input2 && $io0(input2);
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  };
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  if (false === __is(input)) {
@@ -293,34 +302,10 @@ var validGRIN2Response = (input) => {
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  path: _path2 + ".chrom_data",
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  expected: "Record<string, __type>",
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  value: input3.chrom_data
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- }), "boolean" === typeof input3.y_axis_scaled || $report(_exceptionable2, {
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- path: _path2 + ".y_axis_scaled",
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- expected: "boolean",
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- value: input3.y_axis_scaled
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- }), "number" === typeof input3.scale_factor || $report(_exceptionable2, {
301
- path: _path2 + ".scale_factor",
302
- expected: "number",
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- value: input3.scale_factor
304
305
  }), "number" === typeof input3.total_genome_length || $report(_exceptionable2, {
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  path: _path2 + ".total_genome_length",
306
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  expected: "number",
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  value: input3.total_genome_length
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- }), "number" === typeof input3.plot_width || $report(_exceptionable2, {
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- path: _path2 + ".plot_width",
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- expected: "number",
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- value: input3.plot_width
312
- }), "number" === typeof input3.plot_height || $report(_exceptionable2, {
313
- path: _path2 + ".plot_height",
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- expected: "number",
315
- value: input3.plot_height
316
- }), "number" === typeof input3.device_pixel_ratio || $report(_exceptionable2, {
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- path: _path2 + ".device_pixel_ratio",
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- expected: "number",
319
- value: input3.device_pixel_ratio
320
- }), "number" === typeof input3.dpi || $report(_exceptionable2, {
321
- path: _path2 + ".dpi",
322
- expected: "number",
323
- value: input3.dpi
324
309
  })].every((flag) => flag);
325
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  const $vo2 = (input3, _path2, _exceptionable2 = true) => ["number" === typeof input3.x || $report(_exceptionable2, {
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  path: _path2 + ".x",
@@ -330,14 +315,6 @@ var validGRIN2Response = (input) => {
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  path: _path2 + ".y",
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  expected: "number",
332
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  value: input3.y
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- }), "number" === typeof input3.svg_x || $report(_exceptionable2, {
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- path: _path2 + ".svg_x",
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- expected: "number",
336
- value: input3.svg_x
337
- }), "number" === typeof input3.svg_y || $report(_exceptionable2, {
338
- path: _path2 + ".svg_y",
339
- expected: "number",
340
- value: input3.svg_y
341
318
  }), "string" === typeof input3.color || $report(_exceptionable2, {
342
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  path: _path2 + ".color",
343
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  expected: "string",
@@ -354,14 +331,22 @@ var validGRIN2Response = (input) => {
354
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  path: _path2 + ".chrom",
355
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  expected: "string",
356
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  value: input3.chrom
334
+ }), "number" === typeof input3.start || $report(_exceptionable2, {
335
+ path: _path2 + ".start",
336
+ expected: "number",
337
+ value: input3.start
338
+ }), "number" === typeof input3.end || $report(_exceptionable2, {
339
+ path: _path2 + ".end",
340
+ expected: "number",
341
+ value: input3.end
357
342
  }), "number" === typeof input3.pos || $report(_exceptionable2, {
358
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  path: _path2 + ".pos",
359
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  expected: "number",
360
345
  value: input3.pos
361
- }), "number" === typeof input3.q_value || $report(_exceptionable2, {
362
- path: _path2 + ".q_value",
346
+ }), "number" === typeof input3.nsubj || $report(_exceptionable2, {
347
+ path: _path2 + ".nsubj",
363
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  expected: "number",
364
- value: input3.q_value
349
+ value: input3.nsubj
365
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  })].every((flag) => flag);
366
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  const $vo3 = (input3, _path2, _exceptionable2 = true) => [false === _exceptionable2 || Object.keys(input3).map((key) => {
367
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  const value = input3[key];
@@ -500,6 +485,14 @@ var validGRIN2Response = (input) => {
500
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  path: _path2 + ".unprocessedSamples",
501
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  expected: "(number | undefined)",
502
487
  value: input3.unprocessedSamples
488
+ }), void 0 === input3.lesionCounts || ("object" === typeof input3.lesionCounts && null !== input3.lesionCounts && false === Array.isArray(input3.lesionCounts) || $report(_exceptionable2, {
489
+ path: _path2 + ".lesionCounts",
490
+ expected: "(__type.o8 | undefined)",
491
+ value: input3.lesionCounts
492
+ })) && $vo11(input3.lesionCounts, _path2 + ".lesionCounts", _exceptionable2) || $report(_exceptionable2, {
493
+ path: _path2 + ".lesionCounts",
494
+ expected: "(__type.o8 | undefined)",
495
+ value: input3.lesionCounts
503
496
  })].every((flag) => flag);
504
497
  const $vo10 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.sampleName || $report(_exceptionable2, {
505
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  path: _path2 + ".sampleName",
@@ -514,6 +507,48 @@ var validGRIN2Response = (input) => {
514
507
  expected: "string",
515
508
  value: input3.error
516
509
  })].every((flag) => flag);
510
+ const $vo11 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.total || "number" === typeof input3.total || $report(_exceptionable2, {
511
+ path: _path2 + ".total",
512
+ expected: "(number | undefined)",
513
+ value: input3.total
514
+ }), void 0 === input3.byType || ("object" === typeof input3.byType && null !== input3.byType && false === Array.isArray(input3.byType) || $report(_exceptionable2, {
515
+ path: _path2 + ".byType",
516
+ expected: "(Record<string, __type>.o1 | undefined)",
517
+ value: input3.byType
518
+ })) && $vo12(input3.byType, _path2 + ".byType", _exceptionable2) || $report(_exceptionable2, {
519
+ path: _path2 + ".byType",
520
+ expected: "(Record<string, __type>.o1 | undefined)",
521
+ value: input3.byType
522
+ })].every((flag) => flag);
523
+ const $vo12 = (input3, _path2, _exceptionable2 = true) => [false === _exceptionable2 || Object.keys(input3).map((key) => {
524
+ const value = input3[key];
525
+ if (void 0 === value)
526
+ return true;
527
+ if (RegExp(/(.*)/).test(key))
528
+ return ("object" === typeof value && null !== value || $report(_exceptionable2, {
529
+ path: _path2 + $join(key),
530
+ expected: "__type.o9",
531
+ value
532
+ })) && $vo13(value, _path2 + $join(key), _exceptionable2) || $report(_exceptionable2, {
533
+ path: _path2 + $join(key),
534
+ expected: "__type.o9",
535
+ value
536
+ });
537
+ return true;
538
+ }).every((flag) => flag)].every((flag) => flag);
539
+ const $vo13 = (input3, _path2, _exceptionable2 = true) => ["number" === typeof input3.count || $report(_exceptionable2, {
540
+ path: _path2 + ".count",
541
+ expected: "number",
542
+ value: input3.count
543
+ }), "boolean" === typeof input3.capped || $report(_exceptionable2, {
544
+ path: _path2 + ".capped",
545
+ expected: "boolean",
546
+ value: input3.capped
547
+ }), "number" === typeof input3.samples || $report(_exceptionable2, {
548
+ path: _path2 + ".samples",
549
+ expected: "number",
550
+ value: input3.samples
551
+ })].every((flag) => flag);
517
552
  return ("object" === typeof input2 && null !== input2 || $report(true, {
518
553
  path: _path + "",
519
554
  expected: "GRIN2Response",
package/dist/grin2.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  GRIN2Payload,
3
3
  validGRIN2Request,
4
4
  validGRIN2Response
5
- } from "./chunk-HI2IT25E.js";
5
+ } from "./chunk-WCF7WIJY.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  GRIN2Payload,
package/dist/index.js CHANGED
@@ -52,7 +52,7 @@ import {
52
52
  termdbSingleCellDEgenesPayload,
53
53
  validTermdbSingleCellDEgenesRequest,
54
54
  validTermdbSingleCellDEgenesResponse
55
- } from "./chunk-EYKGJDKU.js";
55
+ } from "./chunk-4LOGWDCZ.js";
56
56
  import {
57
57
  termdbSingleCellDataPayload,
58
58
  validTermdbSingleCellDataRequest,
@@ -217,7 +217,7 @@ import {
217
217
  GRIN2Payload,
218
218
  validGRIN2Request,
219
219
  validGRIN2Response
220
- } from "./chunk-HI2IT25E.js";
220
+ } from "./chunk-WCF7WIJY.js";
221
221
  import {
222
222
  healthcheckPayload,
223
223
  validHealthCheckRequest,
package/dist/termdb.singlecellDEgenes.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  termdbSingleCellDEgenesPayload,
3
3
  validTermdbSingleCellDEgenesRequest,
4
4
  validTermdbSingleCellDEgenesResponse
5
- } from "./chunk-EYKGJDKU.js";
5
+ } from "./chunk-4LOGWDCZ.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  termdbSingleCellDEgenesPayload,
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@sjcrh/proteinpaint-types",
3
- "version": "2.152.1-0",
3
+ "version": "2.157.0",
4
4
  "type": "module",
5
5
  "description": "Shared type definitions between ProteinPaint server and client code",
6
6
  "main": "src/index.ts",
@@ -36,5 +36,10 @@
36
36
  "files": [
37
37
  "dist/*.js",
38
38
  "src"
39
- ]
39
+ ],
40
+ "repository": {
41
+ "type": "git",
42
+ "url": "https://github.com/stjude/proteinpaint",
43
+ "directory": "server"
44
+ }
40
45
  }
package/src/routes/grin2.ts CHANGED
@@ -82,21 +82,22 @@ export type GRIN2Request = {
82
82
  maxGenesToShow?: number // Default: 500
83
83
  }
84
84
 
85
- /** Simple Interface to store the complex plot data from the python Manhattan plot */
85
+ /** Simple Interface to store the complex plot data from the rust Manhattan plot */
86
86
  interface grin2PlotData {
87
87
  points: Array<{
88
- x: number
89
- y: number
90
- svg_x: number
91
- svg_y: number
92
- color: string
93
- type: string
94
- gene: string
95
- chrom: string
96
- pos: number
97
- q_value: number
88
+ x: number // X-axis position (base pair/genomic position in the pixel space)
89
+ y: number // Y-axis position (-log10(q-value) in the pixel space)
90
+ color: string // Point color (hexadecimal string representing a color for mutation type)
91
+ type: string // Mutation type (e.g., 'mutation', 'loss', 'gain', 'fusion', 'sv')
92
+ gene: string // Gene symbol
93
+ chrom: string // Chromosome in the form of <chrX>
94
+ start: number // Starting position of this chromosome in base pairs/genomic coordinates. Used in hover table
95
+ end: number // Ending position of this chromosome in base pairs/genomic coordinates
96
+ pos: number // Mid-point of this chromosome in base pairs/genomic coordinates
97
+ nsubj: number // Number of subjects with this mutation. Used for hover table subject count
98
98
  }>
99
99
  chrom_data: Record<
100
+ // Data for chromosome labels and positioning on the x-axis
100
101
  string,
101
102
  {
102
103
  start: number
@@ -104,13 +105,7 @@ interface grin2PlotData {
104
105
  center: number
105
106
  }
106
107
  >
107
- y_axis_scaled: boolean
108
- scale_factor: number
109
- total_genome_length: number
110
- plot_width: number
111
- plot_height: number
112
- device_pixel_ratio: number
113
- dpi: number
108
+ total_genome_length: number // Gives us the full length of the genome so we can easily append x buffer space when building d3 x-axis
114
109
  }
115
110
 
116
111
  /**
@@ -166,6 +161,17 @@ export type GRIN2Response = {
166
161
  totalLesions?: number
167
162
  processedLesions?: number
168
163
  unprocessedSamples?: number
164
+ lesionCounts?: {
165
+ total?: number
166
+ byType?: Record<
167
+ string, // Our key is the GRIN2 lesion type
168
+ {
169
+ count: number
170
+ capped: boolean
171
+ samples: number
172
+ }
173
+ >
174
+ }
169
175
  }
170
176
  /** Cache file name for storing GRIN2 results */
171
177
  cacheFileName?: string
package/src/routes/termdb.singlecellDEgenes.ts CHANGED
@@ -18,14 +18,16 @@ export type TermdbSingleCellDEgenesRequest = {
18
18
 
19
19
  export type HasDataResponse = {
20
20
  /** list of significant DE genes for the given category in the sample */
21
- genes: {
21
+ data: {
22
22
  /** gene name */
23
- name: string
23
+ gene_name: string
24
24
  /** adjusted p-value */
25
- p_val_adj: number
26
- /** log foldchange */
27
- avg_log2FC: number
28
- }[]
25
+ adjusted_p_value: number
26
+ /** original p-value */
27
+ original_p_value: number
28
+ /** log2 fold change */
29
+ fold_change: number
30
+ }[] // TODO: May replace with DataEntry from termdb.DE.ts in the future
29
31
  }
30
32
 
31
33
  export type TermdbSingleCellDEgenesResponse = ErrorResponse | HasDataResponse