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feat: allow organisms to have multiple ploidies separately matched with workflows (#334) (#338)
1 parent 8cab2ad commit 7ce865a

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10 files changed

+207
-80
lines changed

10 files changed

+207
-80
lines changed

‎app/apis/catalog/brc-analytics-catalog/common/entities.ts

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -13,7 +13,7 @@ export interface BRCDataCatalogGenome {
1313
length: number;
1414
level: string;
1515
ncbiTaxonomyId: string;
16-
ploidy: ORGANISM_PLOIDY;
16+
ploidy: ORGANISM_PLOIDY[];
1717
scaffoldCount: number | null;
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scaffoldL50: number | null;
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scaffoldN50: number | null;

‎app/components/Entity/components/AnalysisMethodsCatalog/analysisMethodsCatalog.tsx

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@ import { Props } from "./types";
55
import { workflowPloidyMatchesOrganismPloidy } from "../../../../apis/catalog/brc-analytics-catalog/common/utils";
66

77
export const AnalysisMethodsCatalog = ({
8-
assemblyPloidy,
8+
assemblyPloidies,
99
geneModelUrl,
1010
genomeVersionAssemblyId,
1111
}: Props): JSX.Element => {
@@ -14,7 +14,9 @@ export const AnalysisMethodsCatalog = ({
1414
{workflows.map((workflowCategory) => {
1515
const compatibleWorkflows = workflowCategory.workflows.filter(
1616
({ ploidy }) =>
17-
workflowPloidyMatchesOrganismPloidy(ploidy, assemblyPloidy)
17+
assemblyPloidies.some((assemblyPloidy) =>
18+
workflowPloidyMatchesOrganismPloidy(ploidy, assemblyPloidy)
19+
)
1820
);
1921
return (
2022
<AnalysisMethod

‎app/components/Entity/components/AnalysisMethodsCatalog/types.ts

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
import { ORGANISM_PLOIDY } from "../../../../apis/catalog/brc-analytics-catalog/common/schema-entities";
22

33
export interface Props {
4-
assemblyPloidy: ORGANISM_PLOIDY;
4+
assemblyPloidies: ORGANISM_PLOIDY[];
55
geneModelUrl: string | null;
66
genomeVersionAssemblyId: string;
77
}

‎app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -414,7 +414,7 @@ export const buildGenomeAnalysisMethods = (
414414
genome: BRCDataCatalogGenome
415415
): ComponentProps<typeof C.AnalysisMethodsCatalog> => {
416416
return {
417-
assemblyPloidy: genome.ploidy,
417+
assemblyPloidies: genome.ploidy,
418418
geneModelUrl: genome.geneModelUrl,
419419
genomeVersionAssemblyId: genome.accession,
420420
};

‎catalog/output/genomes.json

Lines changed: 75 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -10,7 +10,9 @@
1010
"length": 18891193,
1111
"level": "Chromosome",
1212
"ncbiTaxonomyId": "235443",
13-
"ploidy": "HAPLOID",
13+
"ploidy": [
14+
"HAPLOID"
15+
],
1416
"scaffoldCount": 14,
1517
"scaffoldL50": 6,
1618
"scaffoldN50": 1422463,
@@ -41,7 +43,9 @@
4143
"length": 27583241,
4244
"level": "Scaffold",
4345
"ncbiTaxonomyId": "443226",
44-
"ploidy": "HAPLOID",
46+
"ploidy": [
47+
"HAPLOID"
48+
],
4549
"scaffoldCount": 54,
4650
"scaffoldL50": 8,
4751
"scaffoldN50": 1220107,
@@ -72,7 +76,9 @@
7276
"length": 29040213,
7377
"level": "Chromosome",
7478
"ncbiTaxonomyId": "5855",
75-
"ploidy": "HAPLOID",
79+
"ploidy": [
80+
"HAPLOID"
81+
],
7682
"scaffoldCount": 242,
7783
"scaffoldL50": 6,
7884
"scaffoldN50": 1761288,
@@ -103,7 +109,9 @@
103109
"length": 27007701,
104110
"level": "Chromosome",
105111
"ncbiTaxonomyId": "5855",
106-
"ploidy": "HAPLOID",
112+
"ploidy": [
113+
"HAPLOID"
114+
],
107115
"scaffoldCount": 2747,
108116
"scaffoldL50": 6,
109117
"scaffoldN50": 1678596,
@@ -134,7 +142,9 @@
134142
"length": 26075494,
135143
"level": "Chromosome",
136144
"ncbiTaxonomyId": "185431",
137-
"ploidy": "DIPLOID",
145+
"ploidy": [
146+
"DIPLOID"
147+
],
138148
"scaffoldCount": 12,
139149
"scaffoldL50": 4,
140150
"scaffoldN50": 2481190,
@@ -165,7 +175,9 @@
165175
"length": 29384958,
166176
"level": "Chromosome",
167177
"ncbiTaxonomyId": "330879",
168-
"ploidy": "HAPLOID",
178+
"ploidy": [
179+
"HAPLOID"
180+
],
169181
"scaffoldCount": 8,
170182
"scaffoldL50": 4,
171183
"scaffoldN50": 3948441,
@@ -196,7 +208,9 @@
196208
"length": 32855089,
197209
"level": "Complete Genome",
198210
"ncbiTaxonomyId": "347515",
199-
"ploidy": "DIPLOID",
211+
"ploidy": [
212+
"DIPLOID"
213+
],
200214
"scaffoldCount": 36,
201215
"scaffoldL50": 11,
202216
"scaffoldN50": 1091540,
@@ -227,7 +241,9 @@
227241
"length": 23292622,
228242
"level": "Complete Genome",
229243
"ncbiTaxonomyId": "36329",
230-
"ploidy": "HAPLOID",
244+
"ploidy": [
245+
"HAPLOID"
246+
],
231247
"scaffoldCount": 14,
232248
"scaffoldL50": 5,
233249
"scaffoldN50": 1687656,
@@ -258,7 +274,9 @@
258274
"length": 32068771,
259275
"level": "Chromosome",
260276
"ncbiTaxonomyId": "420245",
261-
"ploidy": "DIPLOID",
277+
"ploidy": [
278+
"DIPLOID"
279+
],
262280
"scaffoldCount": 138,
263281
"scaffoldL50": 11,
264282
"scaffoldN50": 992961,
@@ -289,7 +307,9 @@
289307
"length": 265011681,
290308
"level": "Chromosome",
291309
"ncbiTaxonomyId": "180454",
292-
"ploidy": "DIPLOID",
310+
"ploidy": [
311+
"DIPLOID"
312+
],
293313
"scaffoldCount": 8144,
294314
"scaffoldL50": 9,
295315
"scaffoldN50": 12309988,
@@ -320,7 +340,9 @@
320340
"length": 65633124,
321341
"level": "Chromosome",
322342
"ncbiTaxonomyId": "508771",
323-
"ploidy": "HAPLOID",
343+
"ploidy": [
344+
"HAPLOID"
345+
],
324346
"scaffoldCount": 2276,
325347
"scaffoldL50": 6,
326348
"scaffoldN50": 4973582,
@@ -351,7 +373,9 @@
351373
"length": 19051922,
352374
"level": "Chromosome",
353375
"ncbiTaxonomyId": "214684",
354-
"ploidy": "HAPLOID",
376+
"ploidy": [
377+
"HAPLOID"
378+
],
355379
"scaffoldCount": 14,
356380
"scaffoldL50": 6,
357381
"scaffoldN50": 1438950,
@@ -382,7 +406,9 @@
382406
"length": 28947925,
383407
"level": "Scaffold",
384408
"ncbiTaxonomyId": "246410",
385-
"ploidy": "HAPLOID",
409+
"ploidy": [
410+
"HAPLOID"
411+
],
386412
"scaffoldCount": 6,
387413
"scaffoldL50": 3,
388414
"scaffoldN50": 4323945,
@@ -413,7 +439,9 @@
413439
"length": 14282666,
414440
"level": "Chromosome",
415441
"ncbiTaxonomyId": "237561",
416-
"ploidy": "DIPLOID",
442+
"ploidy": [
443+
"DIPLOID"
444+
],
417445
"scaffoldCount": 8,
418446
"scaffoldL50": 3,
419447
"scaffoldN50": 2231883,
@@ -444,7 +472,9 @@
444472
"length": 4411532,
445473
"level": "Complete Genome",
446474
"ncbiTaxonomyId": "83332",
447-
"ploidy": "HAPLOID",
475+
"ploidy": [
476+
"HAPLOID"
477+
],
448478
"scaffoldCount": 1,
449479
"scaffoldL50": 1,
450480
"scaffoldN50": 4411532,
@@ -475,7 +505,9 @@
475505
"length": 89937456,
476506
"level": "Scaffold",
477507
"ncbiTaxonomyId": "5693",
478-
"ploidy": "DIPLOID",
508+
"ploidy": [
509+
"DIPLOID"
510+
],
479511
"scaffoldCount": 29495,
480512
"scaffoldL50": 212,
481513
"scaffoldN50": 88624,
@@ -506,7 +538,9 @@
506538
"length": 32444968,
507539
"level": "Chromosome",
508540
"ncbiTaxonomyId": "5661",
509-
"ploidy": "DIPLOID",
541+
"ploidy": [
542+
"DIPLOID"
543+
],
510544
"scaffoldCount": 36,
511545
"scaffoldL50": 11,
512546
"scaffoldN50": 1024085,
@@ -537,7 +571,9 @@
537571
"length": 196858,
538572
"level": "Complete Genome",
539573
"ncbiTaxonomyId": "10244",
540-
"ploidy": "HAPLOID",
574+
"ploidy": [
575+
"HAPLOID"
576+
],
541577
"scaffoldCount": 1,
542578
"scaffoldL50": 1,
543579
"scaffoldN50": 196858,
@@ -568,7 +604,9 @@
568604
"length": 29903,
569605
"level": "Complete Genome",
570606
"ncbiTaxonomyId": "2697049",
571-
"ploidy": "HAPLOID",
607+
"ploidy": [
608+
"HAPLOID"
609+
],
572610
"scaffoldCount": 1,
573611
"scaffoldL50": 1,
574612
"scaffoldN50": 29903,
@@ -599,7 +637,9 @@
599637
"length": 573214445,
600638
"level": "Chromosome",
601639
"ncbiTaxonomyId": "7176",
602-
"ploidy": "DIPLOID",
640+
"ploidy": [
641+
"DIPLOID"
642+
],
603643
"scaffoldCount": 56,
604644
"scaffoldL50": 2,
605645
"scaffoldN50": 201550677,
@@ -630,7 +670,9 @@
630670
"length": 566339288,
631671
"level": "Chromosome",
632672
"ncbiTaxonomyId": "42434",
633-
"ploidy": "DIPLOID",
673+
"ploidy": [
674+
"DIPLOID"
675+
],
634676
"scaffoldCount": 289,
635677
"scaffoldL50": 2,
636678
"scaffoldN50": 186194774,
@@ -661,7 +703,9 @@
661703
"length": 28193268,
662704
"level": "Complete Genome",
663705
"ncbiTaxonomyId": "443226",
664-
"ploidy": "HAPLOID",
706+
"ploidy": [
707+
"HAPLOID"
708+
],
665709
"scaffoldCount": 9,
666710
"scaffoldL50": 2,
667711
"scaffoldN50": 8079863,
@@ -692,7 +736,9 @@
692736
"length": 23043114,
693737
"level": "Complete Genome",
694738
"ncbiTaxonomyId": "5861",
695-
"ploidy": "HAPLOID",
739+
"ploidy": [
740+
"HAPLOID"
741+
],
696742
"scaffoldCount": 14,
697743
"scaffoldL50": 5,
698744
"scaffoldN50": 2046250,
@@ -723,7 +769,9 @@
723769
"length": 18338688,
724770
"level": "Chromosome",
725771
"ncbiTaxonomyId": "54757",
726-
"ploidy": "HAPLOID",
772+
"ploidy": [
773+
"HAPLOID"
774+
],
727775
"scaffoldCount": 14,
728776
"scaffoldL50": 5,
729777
"scaffoldN50": 1692345,
@@ -754,7 +802,9 @@
754802
"length": 264451381,
755803
"level": "Chromosome",
756804
"ncbiTaxonomyId": "7165",
757-
"ploidy": "DIPLOID",
805+
"ploidy": [
806+
"DIPLOID"
807+
],
758808
"scaffoldCount": 190,
759809
"scaffoldL50": 2,
760810
"scaffoldN50": 99149756,

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