-
Notifications
You must be signed in to change notification settings - Fork 45
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Change references to "populations" in API to "ancestry groups" #1457
Open
phildarnowsky-broad
wants to merge
9
commits into
main
Choose a base branch
from
pop-gag
base: main
Could not load branches
Branch not found: {{ refName }}
Loading
Could not load tags
Nothing to show
Loading
Are you sure you want to change the base?
Some commits from the old base branch may be removed from the timeline,
and old review comments may become outdated.
Open
Changes from all commits
Commits
Show all changes
9 commits
Select commit
Hold shift + click to select a range
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
phildarnowsky-broad File filter
Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
86 changes: 47 additions & 39 deletions
86
graphql-api/src/graphql/types/copy-number-variant.graphql
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 | ||
| } | ||
| } | ||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
15 changes: 13 additions & 2 deletions
15
graphql-api/src/graphql/types/variant-cooccurrence.graphql
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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") | ||
| } |
Oops, something went wrong.
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
This field deprecation story is one of the nice things about GraphQL I have to say.