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Pulling feat/add-links-to-gene-ontology-annotations into develop #197

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Pulling feat/add-links-to-gene-ontology-annotations into develop #197

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2 changes: 1 addition & 1 deletion dist/index.js
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Original file line number Diff line number Diff line change
Expand Up @@ -318,7 +318,7 @@ function useListOrganismsLazyQuery(baseOptions) {
return Apollo.useLazyQuery(exports.ListOrganismsDocument, options);
}
exports.useListOrganismsLazyQuery = useListOrganismsLazyQuery;
exports.GeneDocument = (0, client_1.gql)(templateObject_12 || (templateObject_12 = __makeTemplateObject(["\n query Gene($gene: String!, $limit: Int, $sort_by: String = \"desc\") {\n allStrains(gene: $gene) {\n id\n name\n strains {\n id\n label\n characteristics\n in_stock\n phenotypes {\n phenotype\n publication {\n id\n title\n journal\n pages\n volume\n pub_date\n authors {\n last_name\n rank\n }\n }\n }\n }\n }\n gene(gene: $gene) {\n id\n name\n goas {\n id\n type\n date\n evidence_code\n go_term\n qualifier\n publication\n assigned_by\n with {\n id\n db\n name\n }\n extensions {\n id\n db\n relation\n name\n }\n }\n }\n allPublications(gene: $gene, limit: $limit, sort_by: $sort_by) {\n num_pubs\n publications {\n related_genes {\n id\n name\n }\n id\n doi\n title\n journal\n pub_date\n volume\n pages\n pub_type\n source\n issue\n authors {\n last_name\n rank\n }\n }\n }\n allOrthologs(gene: $gene) {\n id\n name\n orthologs {\n id {\n name\n link\n }\n species\n uniprotkb {\n name\n link\n }\n gene_product\n source\n }\n }\n listGeneProductInfo(gene: $gene) {\n id\n name\n product_info {\n protein_coding_gene {\n name\n link\n }\n protein_length\n protein_molecular_weight\n more_protein_data\n genomic_coords {\n exon\n local_coords\n chrom_coords\n }\n }\n }\n generalInformation(gene: $gene) {\n id\n name\n general_info {\n name_description\n alt_gene_name\n gene_product\n alt_protein_names\n description\n }\n }\n getAssociatedSequnces(gene: $gene) {\n id\n name\n associated_sequences {\n genbank_genomic_fragment {\n name\n link\n }\n genbank_mrna {\n name\n link\n }\n ests {\n name\n link\n }\n more_link\n }\n }\n getLinks(gene: $gene) {\n id\n name\n links {\n expression {\n name\n link\n }\n colleagues {\n name\n link\n }\n ext_resources {\n name\n link\n }\n }\n }\n}\n "], ["\n query Gene($gene: String!, $limit: Int, $sort_by: String = \"desc\") {\n allStrains(gene: $gene) {\n id\n name\n strains {\n id\n label\n characteristics\n in_stock\n phenotypes {\n phenotype\n publication {\n id\n title\n journal\n pages\n volume\n pub_date\n authors {\n last_name\n rank\n }\n }\n }\n }\n }\n gene(gene: $gene) {\n id\n name\n goas {\n id\n type\n date\n evidence_code\n go_term\n qualifier\n publication\n assigned_by\n with {\n id\n db\n name\n }\n extensions {\n id\n db\n relation\n name\n }\n }\n }\n allPublications(gene: $gene, limit: $limit, sort_by: $sort_by) {\n num_pubs\n publications {\n related_genes {\n id\n name\n }\n id\n doi\n title\n journal\n pub_date\n volume\n pages\n pub_type\n source\n issue\n authors {\n last_name\n rank\n }\n }\n }\n allOrthologs(gene: $gene) {\n id\n name\n orthologs {\n id {\n name\n link\n }\n species\n uniprotkb {\n name\n link\n }\n gene_product\n source\n }\n }\n listGeneProductInfo(gene: $gene) {\n id\n name\n product_info {\n protein_coding_gene {\n name\n link\n }\n protein_length\n protein_molecular_weight\n more_protein_data\n genomic_coords {\n exon\n local_coords\n chrom_coords\n }\n }\n }\n generalInformation(gene: $gene) {\n id\n name\n general_info {\n name_description\n alt_gene_name\n gene_product\n alt_protein_names\n description\n }\n }\n getAssociatedSequnces(gene: $gene) {\n id\n name\n associated_sequences {\n genbank_genomic_fragment {\n name\n link\n }\n genbank_mrna {\n name\n link\n }\n ests {\n name\n link\n }\n more_link\n }\n }\n getLinks(gene: $gene) {\n id\n name\n links {\n expression {\n name\n link\n }\n colleagues {\n name\n link\n }\n ext_resources {\n name\n link\n }\n }\n }\n}\n "])));
exports.GeneDocument = (0, client_1.gql)(templateObject_12 || (templateObject_12 = __makeTemplateObject(["\n query Gene($gene: String!, $limit: Int, $sort_by: String = \"desc\") {\n allStrains(gene: $gene) {\n id\n name\n strains {\n id\n label\n characteristics\n in_stock\n phenotypes {\n phenotype\n publication {\n id\n title\n journal\n pages\n volume\n pub_date\n authors {\n last_name\n rank\n }\n }\n }\n }\n }\n gene(gene: $gene) {\n id\n name\n goas {\n id\n type\n date\n evidence_code\n go_term {\n name\n link\n }\n qualifier\n publication\n assigned_by\n with {\n id\n db\n name\n }\n extensions {\n id\n db\n relation\n name\n }\n }\n }\n allPublications(gene: $gene, limit: $limit, sort_by: $sort_by) {\n num_pubs\n publications {\n related_genes {\n id\n name\n }\n id\n doi\n title\n journal\n pub_date\n volume\n pages\n pub_type\n source\n issue\n authors {\n last_name\n rank\n }\n }\n }\n allOrthologs(gene: $gene) {\n id\n name\n orthologs {\n id {\n name\n link\n }\n species\n uniprotkb {\n name\n link\n }\n gene_product\n source\n }\n }\n listGeneProductInfo(gene: $gene) {\n id\n name\n product_info {\n protein_coding_gene {\n name\n link\n }\n protein_length\n protein_molecular_weight\n more_protein_data\n genomic_coords {\n exon\n local_coords\n chrom_coords\n }\n }\n }\n generalInformation(gene: $gene) {\n id\n name\n general_info {\n name_description\n alt_gene_name\n gene_product\n alt_protein_names\n description\n }\n }\n getAssociatedSequnces(gene: $gene) {\n id\n name\n associated_sequences {\n genbank_genomic_fragment {\n name\n link\n }\n genbank_mrna {\n name\n link\n }\n ests {\n name\n link\n }\n more_link\n }\n }\n getLinks(gene: $gene) {\n id\n name\n links {\n expression {\n name\n link\n }\n colleagues {\n name\n link\n }\n ext_resources {\n name\n link\n }\n }\n }\n}\n "], ["\n query Gene($gene: String!, $limit: Int, $sort_by: String = \"desc\") {\n allStrains(gene: $gene) {\n id\n name\n strains {\n id\n label\n characteristics\n in_stock\n phenotypes {\n phenotype\n publication {\n id\n title\n journal\n pages\n volume\n pub_date\n authors {\n last_name\n rank\n }\n }\n }\n }\n }\n gene(gene: $gene) {\n id\n name\n goas {\n id\n type\n date\n evidence_code\n go_term {\n name\n link\n }\n qualifier\n publication\n assigned_by\n with {\n id\n db\n name\n }\n extensions {\n id\n db\n relation\n name\n }\n }\n }\n allPublications(gene: $gene, limit: $limit, sort_by: $sort_by) {\n num_pubs\n publications {\n related_genes {\n id\n name\n }\n id\n doi\n title\n journal\n pub_date\n volume\n pages\n pub_type\n source\n issue\n authors {\n last_name\n rank\n }\n }\n }\n allOrthologs(gene: $gene) {\n id\n name\n orthologs {\n id {\n name\n link\n }\n species\n uniprotkb {\n name\n link\n }\n gene_product\n source\n }\n }\n listGeneProductInfo(gene: $gene) {\n id\n name\n product_info {\n protein_coding_gene {\n name\n link\n }\n protein_length\n protein_molecular_weight\n more_protein_data\n genomic_coords {\n exon\n local_coords\n chrom_coords\n }\n }\n }\n generalInformation(gene: $gene) {\n id\n name\n general_info {\n name_description\n alt_gene_name\n gene_product\n alt_protein_names\n description\n }\n }\n getAssociatedSequnces(gene: $gene) {\n id\n name\n associated_sequences {\n genbank_genomic_fragment {\n name\n link\n }\n genbank_mrna {\n name\n link\n }\n ests {\n name\n link\n }\n more_link\n }\n }\n getLinks(gene: $gene) {\n id\n name\n links {\n expression {\n name\n link\n }\n colleagues {\n name\n link\n }\n ext_resources {\n name\n link\n }\n }\n }\n}\n "])));
/**
* __useGeneQuery__
*
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4 changes: 2 additions & 2 deletions schema.json
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Original file line number Diff line number Diff line change
Expand Up @@ -2145,8 +2145,8 @@
"kind": "NON_NULL",
"name": null,
"ofType": {
"kind": "SCALAR",
"name": "String",
"kind": "OBJECT",
"name": "NameWithLink",
"ofType": null
}
},
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5 changes: 4 additions & 1 deletion src/queries/gene.graphql
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Expand Up @@ -32,7 +32,10 @@ query Gene($gene: String!, $limit: Int, $sort_by: String = "desc") {
type
date
evidence_code
go_term
go_term {
name
link
}
qualifier
publication
assigned_by
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2 changes: 1 addition & 1 deletion src/schema/gene.graphql
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Expand Up @@ -15,7 +15,7 @@ type GOAnnotation {
type: String!
date: String!
evidence_code: String!
go_term: String!
go_term: NameWithLink!
qualifier: String!
publication: String!
with: [With!]
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9 changes: 6 additions & 3 deletions types/index.ts
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Expand Up @@ -215,7 +215,7 @@ export type GoAnnotation = {
date: Scalars['String'];
evidence_code: Scalars['String'];
extensions?: Maybe<Array<Extension>>;
go_term: Scalars['String'];
go_term: NameWithLink;
id: Scalars['String'];
publication: Scalars['String'];
qualifier: Scalars['String'];
Expand Down Expand Up @@ -1046,7 +1046,7 @@ export type GeneQueryVariables = Exact<{
}>;


export type GeneQuery = { __typename?: 'Query', allStrains?: { __typename?: 'Gene', id: string, name: string, strains?: Array<{ __typename?: 'Strain', id: string, label: string, characteristics?: Array<string> | null, in_stock: boolean, phenotypes?: Array<{ __typename?: 'Phenotype', phenotype: string, publication?: { __typename?: 'Publication', id: string, title: string, journal: string, pages?: string | null, volume?: string | null, pub_date?: any | null, authors: Array<{ __typename?: 'Author', last_name: string, rank?: string | null }> } | null }> | null }> | null } | null, gene?: { __typename?: 'Gene', id: string, name: string, goas?: Array<{ __typename?: 'GOAnnotation', id: string, type: string, date: string, evidence_code: string, go_term: string, qualifier: string, publication: string, assigned_by: string, with?: Array<{ __typename?: 'With', id: string, db: string, name: string }> | null, extensions?: Array<{ __typename?: 'Extension', id: string, db: string, relation: string, name: string }> | null }> | null } | null, allPublications: { __typename?: 'NumberOfPublicationsWithGene', num_pubs: number, publications: Array<{ __typename?: 'PublicationWithGene', id: string, doi?: string | null, title: string, journal: string, pub_date?: any | null, volume?: string | null, pages?: string | null, pub_type: string, source: string, issue?: string | null, related_genes: Array<{ __typename?: 'Gene', id: string, name: string }>, authors: Array<{ __typename?: 'Author', last_name: string, rank?: string | null }> }> }, allOrthologs?: { __typename?: 'Gene', id: string, name: string, orthologs?: Array<{ __typename?: 'Orthologs', species: string, gene_product: string, source: Array<string>, id: { __typename?: 'NameWithLink', name: string, link: string }, uniprotkb: { __typename?: 'NameWithLink', name: string, link: string } }> | null } | null, listGeneProductInfo?: { __typename?: 'Gene', id: string, name: string, product_info?: Array<{ __typename?: 'ProductInformation', protein_length: string, protein_molecular_weight: string, more_protein_data: string, protein_coding_gene: { __typename?: 'NameWithLink', name: string, link: string }, genomic_coords: Array<{ __typename?: 'GenomicCoordinates', exon: string, local_coords: string, chrom_coords: string }> }> | null } | null, generalInformation?: { __typename?: 'Gene', id: string, name: string, general_info: { __typename?: 'GeneralInfo', name_description: Array<string>, alt_gene_name?: Array<string> | null, gene_product: string, alt_protein_names?: Array<string> | null, description: string } } | null, getAssociatedSequnces?: { __typename?: 'Gene', id: string, name: string, associated_sequences: { __typename?: 'AssociatedSequences', more_link: string, genbank_genomic_fragment?: { __typename?: 'NameWithLink', name: string, link: string } | null, genbank_mrna?: { __typename?: 'NameWithLink', name: string, link: string } | null, ests: Array<{ __typename?: 'NameWithLink', name: string, link: string }> } } | null, getLinks?: { __typename?: 'Gene', id: string, name: string, links: { __typename?: 'Links', expression: Array<{ __typename?: 'NameWithLink', name: string, link: string }>, colleagues: { __typename?: 'NameWithLink', name: string, link: string }, ext_resources: Array<{ __typename?: 'NameWithLink', name: string, link: string }> } } | null };
export type GeneQuery = { __typename?: 'Query', allStrains?: { __typename?: 'Gene', id: string, name: string, strains?: Array<{ __typename?: 'Strain', id: string, label: string, characteristics?: Array<string> | null, in_stock: boolean, phenotypes?: Array<{ __typename?: 'Phenotype', phenotype: string, publication?: { __typename?: 'Publication', id: string, title: string, journal: string, pages?: string | null, volume?: string | null, pub_date?: any | null, authors: Array<{ __typename?: 'Author', last_name: string, rank?: string | null }> } | null }> | null }> | null } | null, gene?: { __typename?: 'Gene', id: string, name: string, goas?: Array<{ __typename?: 'GOAnnotation', id: string, type: string, date: string, evidence_code: string, qualifier: string, publication: string, assigned_by: string, go_term: { __typename?: 'NameWithLink', name: string, link: string }, with?: Array<{ __typename?: 'With', id: string, db: string, name: string }> | null, extensions?: Array<{ __typename?: 'Extension', id: string, db: string, relation: string, name: string }> | null }> | null } | null, allPublications: { __typename?: 'NumberOfPublicationsWithGene', num_pubs: number, publications: Array<{ __typename?: 'PublicationWithGene', id: string, doi?: string | null, title: string, journal: string, pub_date?: any | null, volume?: string | null, pages?: string | null, pub_type: string, source: string, issue?: string | null, related_genes: Array<{ __typename?: 'Gene', id: string, name: string }>, authors: Array<{ __typename?: 'Author', last_name: string, rank?: string | null }> }> }, allOrthologs?: { __typename?: 'Gene', id: string, name: string, orthologs?: Array<{ __typename?: 'Orthologs', species: string, gene_product: string, source: Array<string>, id: { __typename?: 'NameWithLink', name: string, link: string }, uniprotkb: { __typename?: 'NameWithLink', name: string, link: string } }> | null } | null, listGeneProductInfo?: { __typename?: 'Gene', id: string, name: string, product_info?: Array<{ __typename?: 'ProductInformation', protein_length: string, protein_molecular_weight: string, more_protein_data: string, protein_coding_gene: { __typename?: 'NameWithLink', name: string, link: string }, genomic_coords: Array<{ __typename?: 'GenomicCoordinates', exon: string, local_coords: string, chrom_coords: string }> }> | null } | null, generalInformation?: { __typename?: 'Gene', id: string, name: string, general_info: { __typename?: 'GeneralInfo', name_description: Array<string>, alt_gene_name?: Array<string> | null, gene_product: string, alt_protein_names?: Array<string> | null, description: string } } | null, getAssociatedSequnces?: { __typename?: 'Gene', id: string, name: string, associated_sequences: { __typename?: 'AssociatedSequences', more_link: string, genbank_genomic_fragment?: { __typename?: 'NameWithLink', name: string, link: string } | null, genbank_mrna?: { __typename?: 'NameWithLink', name: string, link: string } | null, ests: Array<{ __typename?: 'NameWithLink', name: string, link: string }> } } | null, getLinks?: { __typename?: 'Gene', id: string, name: string, links: { __typename?: 'Links', expression: Array<{ __typename?: 'NameWithLink', name: string, link: string }>, colleagues: { __typename?: 'NameWithLink', name: string, link: string }, ext_resources: Array<{ __typename?: 'NameWithLink', name: string, link: string }> } } | null };

export type ListRecentGenesQueryVariables = Exact<{
limit?: Scalars['Int'];
Expand Down Expand Up @@ -1656,7 +1656,10 @@ export const GeneDocument = gql`
type
date
evidence_code
go_term
go_term {
name
link
}
qualifier
publication
assigned_by
Expand Down