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Change references to "populations" in API to "ancestry groups" #1457
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5130327
Update schema and API to prefer term "ancestry group" to "population"
phildarnowsky-broad 9b524e4
Clean up CopyNumberVariant associated types
phildarnowsky-broad f218a0e
Change populations to ancestry_groups in CNV page query and associate…
phildarnowsky-broad 540099a
Change populations to ancestry_groups in mitochondrial variant query …
phildarnowsky-broad a42e0e3
Change populations to ancestry_groups in short tandem repat page quer…
phildarnowsky-broad 99641ff
Change populations to ancestry_groups in structural variant page
phildarnowsky-broad 1c390b2
Change populations to ancestry_groups in variant cooccurrence page
phildarnowsky-broad 12869f6
Change populations to ancestry_groups in variant page
phildarnowsky-broad 586e726
Revert frontend references to new ancestry_groups fields
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86 changes: 47 additions & 39 deletions
86
graphql-api/src/graphql/types/copy-number-variant.graphql
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,51 +1,59 @@ | ||
| type CopyNumberVariantAncestryGroup { | ||
| id: String! | ||
| sc: Float! | ||
| sn: Float! | ||
| sf: Float! | ||
| } | ||
|
|
||
| type CopyNumberVariantPopulation { | ||
| id: String! | ||
| sc: Float! | ||
| sn: Float! | ||
| sf: Float! | ||
| id: String! @deprecated(reason: "Use CopyNumberVariantAncestryGroup.id") | ||
| sc: Float! @deprecated(reason: "Use CopyNumberVariantAncestryGroup.sc") | ||
| sn: Float! @deprecated(reason: "Use CopyNumberVariantAncestryGroup.sn") | ||
| sf: Float! @deprecated(reason: "Use CopyNumberVariantAncestryGroup.sf") | ||
| } | ||
|
|
||
| type CopyNumberVariant { | ||
| sc: Float! | ||
| sn: Float! | ||
| sf: Float! | ||
| reference_genome: ReferenceGenomeId! | ||
| chrom: String! | ||
| end: Int! | ||
| filters: [String!] | ||
| length: Int | ||
| pos: Int! | ||
| type: String | ||
| posmin: Int | ||
| posmax: Int | ||
| endmin: Int | ||
| endmax: Int | ||
| variant_id: String! | ||
| sc: Float! | ||
| sn: Float! | ||
| sf: Float! | ||
| reference_genome: ReferenceGenomeId! | ||
| chrom: String! | ||
| end: Int! | ||
| filters: [String!] | ||
| length: Int | ||
| pos: Int! | ||
| type: String | ||
| posmin: Int | ||
| posmax: Int | ||
| endmin: Int | ||
| endmax: Int | ||
| variant_id: String! | ||
| } | ||
|
|
||
| type CopyNumberVariantDetails { | ||
| alts: [String!] | ||
| sc: Float! | ||
| sn: Float! | ||
| sf: Float! | ||
| chrom: String! | ||
| end: Int! | ||
| filters: [String!] | ||
| genes: [String!] | ||
| length: Int | ||
| populations: [CopyNumberVariantPopulation!] | ||
| pos: Int! | ||
| qual: Float | ||
| reference_genome: ReferenceGenomeId! | ||
| type: String | ||
| posmin: Int | ||
| posmax: Int | ||
| endmin: Int | ||
| endmax: Int | ||
| variant_id: String! | ||
| alts: [String!] | ||
| sc: Float! | ||
| sn: Float! | ||
| sf: Float! | ||
| chrom: String! | ||
| end: Int! | ||
| filters: [String!] | ||
| genes: [String!] | ||
| length: Int | ||
| ancestry_groups: [CopyNumberVariantAncestryGroup!] | ||
| populations: [CopyNumberVariantPopulation!] @deprecated(reason: "Use ancestry_groups") | ||
| pos: Int! | ||
| qual: Float | ||
| reference_genome: ReferenceGenomeId! | ||
| type: String | ||
| posmin: Int | ||
| posmax: Int | ||
| endmin: Int | ||
| endmax: Int | ||
| variant_id: String! | ||
| } | ||
|
|
||
| type CNVTrackCallableCoverageBin { | ||
| xpos: Float! | ||
| percent_callable: Float | ||
| } | ||
| } | ||
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15 changes: 13 additions & 2 deletions
15
graphql-api/src/graphql/types/variant-cooccurrence.graphql
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,14 +1,25 @@ | ||
| type VariantCooccurrenceInPopulation { | ||
| type VariantCooccurrenceInAncestryGroup { | ||
| id: String! | ||
| genotype_counts: [Int!]! | ||
| haplotype_counts: [Float!]! | ||
| p_compound_heterozygous: Float | ||
| } | ||
|
|
||
| type VariantCooccurrenceInPopulation { | ||
| id: String! @deprecated(reason: "Use VariantCooccurrenceInAncestryGroup.id") | ||
| genotype_counts: [Int!]! | ||
| @deprecated(reason: "Use VariantCooccurrenceInAncestryGroup.genotype_counts") | ||
| haplotype_counts: [Float!]! | ||
| @deprecated(reason: "Use VariantCooccurrenceInAncestryGroup.haplotype_counts") | ||
| p_compound_heterozygous: Float | ||
| @deprecated(reason: "Use VariantCooccurrenceInAncestryGroup.p_compound_heterozygous") | ||
| } | ||
|
|
||
| type VariantCooccurrence { | ||
| variant_ids: [String!]! | ||
| genotype_counts: [Int!]! | ||
| haplotype_counts: [Float!]! | ||
| p_compound_heterozygous: Float | ||
| populations: [VariantCooccurrenceInPopulation!]! | ||
| ancestry_groups: [VariantCooccurrenceInAncestryGroup!]! | ||
| populations: [VariantCooccurrenceInPopulation!]! @deprecated(reason: "Use ancestry_groups") | ||
| } |
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This field deprecation story is one of the nice things about GraphQL I have to say.