From 2d0e6451385ce11874d7a21f13e5a5877b75612a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ciar=C3=A1n=20Sch=C3=BCtte?= Date: Tue, 22 Aug 2023 15:47:27 -0400 Subject: [PATCH] Data setup (#74) * Feat/8 Logout (#39) * move global into src, instead of app folder * add some components * configure uikit, emotion and typings * uikit happy * Basic Env Vars * Populating Basic Configs * cleanup * add theme provider * emotion imports * emotion uikit style tpying * First Working Test * Working Redirect w/ URL Join * remove DataCallout uikit re-export wrapper * Basic Reusable Component * Remove .env * Update .gitignore * Remove Duplicate * Stage for UI Kit * Loading Test w/ UI Kit * NavBar Setup * Fix Landing Page * Remove Next logo * Skeleton Cookies * Basic Logout * AuthContext Setup * AuthContext Simplest State * Generic Vars * Major Update w/ Logout + UI Kit * Testing Context + State * Add Copyrights * Update TypeScript, Imports, File Structure * Login Button Component * Use AuthContextValue * Use GoogleLogin * Use URL Join * Local .env updates * Remove Boilerplate * Shuffle Files Around * Refactor w/o Context * Remove Logging * Fix env settings * Add React Query + Mock Login State * Add Copyright * Current Working State * Fix User Badge * Temporary Login Solution * Clean Up State Changes * Remove Redirect * Cleaned Up User Badge * Basic Pathname Solution * Cleaned Up Login Flow * Improved Layout + Header Handling * Remove vscode from gitignore * Fix /public import * Update page names * Refactor Auth / Layout * General Clean Up * Stub Middleware * Tidying * Middleware + Auth Route Setup - Infinite Loop * Current State - Testing * Children prop cleanup * Header UI Updates * Current Working State * Clean Up Use of Stored Token * Remove extra storedToken * First Lint Changes * Hook + Middleware Cleanup * Better fallback, LoggingIn dependency * Move Middleware to Feature Branch * Unnecesary changes * Remove Server side token management * First Setup * Log Out Update * Updated Var name + Conditional * Improve Loading Var Names + Reusable Logout * Use Context logOut * Remove Dummy Logout Button * 1st Header PR Feedback * Remove Unused Imports * Fix Build Issues * ProfileMenu Component * Reusable Login --------- Co-authored-by: Ciaran Schutte Feat/#14 programs list page (#47) * add submission layout * add some components * add All Programs layout * skeleton * cleanup + add linking for programs * remove sidemenu logic for PR * remove program list and search func for PR * fix type error * mmove types around * fix build * clean import --------- Co-authored-by: Ciaran Schutte add All Programs layout skeleton cleanup + add linking for programs remove sidemenu logic for PR remove program list and search func for PR use route groups content additions to sidemenu poor mans sidebar toggle Revert "Merge branch 'develop' into sidemenu-layout-restructure" This reverts commit 640bb4be53ac90eb79b7d9804d885c2e20957dba. clean up add sidemenu toggle fix build lots of styling add page count add table comps, fix font fix percent cell table updates sidemenu styling styling cleanup cleanup * add gql and apollo * add gql codegen * gql data * Update version to 0.5.0 Homepage feedback (#68) * fix footer placement links * fix high res layout not expanding data callout * use chevron icon * Update Footer.tsx --------- Co-authored-by: Ciaran Schutte * add apollo custom auth link remove slice of Programs in comps add sidemenu query * cleanup App * codegen * work manually fix history compared to dev manually fix history compared to dev * move app config provider * update App hooks ref * cleanup data fetching * fix generating types. add checks to satify types * fix build errors * add readme and build step * remove tie in with build from gql compule * remove old file * remove unused types --------- Co-authored-by: Ciaran Schutte --- README.md | 4 + codegen.ts | 41 + package-lock.json | 4976 ++++++++++++++++- package.json | 12 +- src/__generated__/fragment-masking.ts | 71 + src/__generated__/gql.ts | 53 + src/__generated__/graphql.ts | 2516 +++++++++ src/__generated__/index.ts | 2 + .../submission/[shortName]/page.tsx | 4 +- .../submission/components/ProgramMenu.tsx | 29 +- .../components/SideMenu/Content.tsx | 4 +- .../submission/components/SideMenu/Menu.tsx | 4 +- .../submission/components/SideMenu/types.ts | 2 +- .../submission/gql/PROGRAMS_LIST_QUERY.ts | 43 + .../submission/gql/SIDEMENU_PROGRAMS.ts | 30 + src/app/(post-login)/submission/layout.tsx | 4 +- src/app/(post-login)/submission/page.tsx | 14 +- .../(pre-login)/contact/components/form.tsx | 2 +- .../(pre-login)/contact/components/info.tsx | 2 +- src/app/(pre-login)/landing-page/page.tsx | 2 +- src/app/(pre-login)/logging-in/page.tsx | 2 +- src/app/App.tsx | 31 +- src/app/api/config/config.ts | 2 + src/app/components/Footer.tsx | 2 +- src/app/components/Hero.tsx | 2 +- src/app/components/Loader.tsx | 38 + src/app/components/LoginButton.tsx | 2 +- src/app/hooks/ApolloProvider.tsx | 39 + .../AppProvider.tsx} | 3 +- src/app/page.tsx | 2 +- src/global/utils/types.ts | 22 + src/lib/gql.ts | 52 + 32 files changed, 7709 insertions(+), 303 deletions(-) create mode 100644 codegen.ts create mode 100644 src/__generated__/fragment-masking.ts create mode 100644 src/__generated__/gql.ts create mode 100644 src/__generated__/graphql.ts create mode 100644 src/__generated__/index.ts create mode 100644 src/app/(post-login)/submission/gql/PROGRAMS_LIST_QUERY.ts create mode 100644 src/app/(post-login)/submission/gql/SIDEMENU_PROGRAMS.ts create mode 100644 src/app/components/Loader.tsx create mode 100644 src/app/hooks/ApolloProvider.tsx rename src/app/{components/ConfigProvider.tsx => hooks/AppProvider.tsx} (94%) create mode 100644 src/global/utils/types.ts create mode 100644 src/lib/gql.ts diff --git a/README.md b/README.md index dc0d70ea..549b4b91 100644 --- a/README.md +++ b/README.md @@ -35,6 +35,10 @@ docker compose file for local development created an `.env` file based on `.env.schema` in `compose` folder, run `docker-compose up` command +## Apollo GQL Typechecking + +Please recompile Apollo GQL when needed using the `npm run gql-compile` command + ## Learn More To learn more about Next.js, take a look at the following resources: diff --git a/codegen.ts b/codegen.ts new file mode 100644 index 00000000..b54318d6 --- /dev/null +++ b/codegen.ts @@ -0,0 +1,41 @@ +/* + * Copyright (c) 2023 The Ontario Institute for Cancer Research. All rights reserved + * + * This program and the accompanying materials are made available under the terms of + * the GNU Affero General Public License v3.0. You should have received a copy of the + * GNU Affero General Public License along with this program. + * If not, see . + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY + * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT + * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, + * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED + * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; + * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER + * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN + * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +import { CodegenConfig } from '@graphql-codegen/cli'; +import dotenv from 'dotenv'; + +// point to .env.local because .env in nextjs is a default committed file +dotenv.config({ path: '.env.local' }); + +const gqlConfig: CodegenConfig = { + schema: `${process.env.NEXT_PUBLIC_GATEWAY_API_ROOT}/graphql`, + documents: ['src/**/gql/*.ts'], + generates: { + './src/__generated__/': { + preset: 'client', + plugins: [], + presetConfig: { + gqlTagName: 'gql', + }, + }, + }, + ignoreNoDocuments: true, +}; + +export default gqlConfig; diff --git a/package-lock.json b/package-lock.json index c844be42..deb3ba2e 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,17 +1,20 @@ { "name": "rdpc-ui", - "version": "0.5.0", + "version": "0.6.0", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "rdpc-ui", - "version": "0.5.0", + "version": "0.6.0", "dependencies": { + "@apollo/client": "^3.8.1", "@hookform/resolvers": "^3.1.1", "@icgc-argo/ego-token-utils": "^8.2.0", "@icgc-argo/uikit": "^3.0.1", "@types/url-join": "^4.0.1", + "dotenv": "^16.3.1", + "graphql": "^16.8.0", "js-cookie": "^3.0.5", "lodash": "^4.17.21", "next": "^13.4.12", @@ -25,6 +28,9 @@ "zod": "^3.21.4" }, "devDependencies": { + "@graphql-codegen/cli": "^5.0.0", + "@graphql-codegen/client-preset": "^4.1.0", + "@parcel/watcher": "^2.2.0", "@types/js-cookie": "^3.0.3", "@types/lodash": "^4.14.195", "@types/node": "20.2.3", @@ -40,320 +46,2630 @@ 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- "npm": ">= 7" + "node": ">=8" } }, "node_modules/yocto-queue": { @@ -6445,6 +10902,19 @@ "url": "https://github.com/sponsors/sindresorhus" } }, + "node_modules/zen-observable": { + "version": "0.8.15", + "resolved": "https://registry.npmjs.org/zen-observable/-/zen-observable-0.8.15.tgz", + "integrity": "sha512-PQ2PC7R9rslx84ndNBZB/Dkv8V8fZEpk83RLgXtYd0fwUgEjseMn1Dgajh2x6S8QbZAFa9p2qVCEuYZNgve0dQ==" + }, + "node_modules/zen-observable-ts": { + "version": "1.2.5", + "resolved": "https://registry.npmjs.org/zen-observable-ts/-/zen-observable-ts-1.2.5.tgz", + "integrity": "sha512-QZWQekv6iB72Naeake9hS1KxHlotfRpe+WGNbNx5/ta+R3DNjVO2bswf63gXlWDcs+EMd7XY8HfVQyP1X6T4Zg==", + "dependencies": { + "zen-observable": "0.8.15" + } + }, "node_modules/zod": { "version": "3.21.4", "resolved": "https://registry.npmjs.org/zod/-/zod-3.21.4.tgz", diff --git a/package.json b/package.json index f8223e76..4a90deb6 100644 --- a/package.json +++ b/package.json @@ -8,13 +8,18 @@ "start": "next start", "lint": "next lint", "prepare": "husky install", - "test": "echo 'Add tests please :)'" + "test": "echo 'Add tests please :)'", + "gql-compile": "graphql-codegen", + "gql-watch": "graphql-codegen -w" }, "dependencies": { + "@apollo/client": "^3.8.1", "@hookform/resolvers": "^3.1.1", "@icgc-argo/ego-token-utils": "^8.2.0", "@icgc-argo/uikit": "^3.0.1", "@types/url-join": "^4.0.1", + "dotenv": "^16.3.1", + "graphql": "^16.8.0", "js-cookie": "^3.0.5", "lodash": "^4.17.21", "next": "^13.4.12", @@ -32,6 +37,9 @@ "@emotion/styled": "^11.11.0" }, "devDependencies": { + "@graphql-codegen/cli": "^5.0.0", + "@graphql-codegen/client-preset": "^4.1.0", + "@parcel/watcher": "^2.2.0", "@types/js-cookie": "^3.0.3", "@types/lodash": "^4.14.195", "@types/node": "20.2.3", @@ -47,7 +55,7 @@ "lint-staged": "^13.2.2", "prettier": "2.8.8", "prettier-plugin-organize-imports": "^3.2.2", - "typescript": "^5.1.3" + "typescript": "^5.1.6" }, "lint-staged": { "**/*": "prettier --write --ignore-unknown" diff --git a/src/__generated__/fragment-masking.ts b/src/__generated__/fragment-masking.ts new file mode 100644 index 00000000..fc6622f2 --- /dev/null +++ b/src/__generated__/fragment-masking.ts @@ -0,0 +1,71 @@ +import { + DocumentTypeDecoration, + ResultOf, + TypedDocumentNode, +} from '@graphql-typed-document-node/core'; +import { FragmentDefinitionNode } from 'graphql'; +import { Incremental } from './graphql'; + +export type FragmentType> = + TDocumentType extends DocumentTypeDecoration + ? [TType] extends [{ ' $fragmentName'?: infer TKey }] + ? TKey extends string + ? { ' $fragmentRefs'?: { [key in TKey]: TType } } + : never + : never + : never; + +// return non-nullable if `fragmentType` is non-nullable +export function useFragment( + _documentNode: DocumentTypeDecoration, + fragmentType: FragmentType>, +): TType; +// return nullable if `fragmentType` is nullable +export function useFragment( + _documentNode: DocumentTypeDecoration, + fragmentType: FragmentType> | null | undefined, +): TType | null | undefined; +// return array of non-nullable if `fragmentType` is array of non-nullable +export function useFragment( + _documentNode: DocumentTypeDecoration, + fragmentType: ReadonlyArray>>, +): ReadonlyArray; +// return array of nullable if `fragmentType` is array of nullable +export function useFragment( + _documentNode: DocumentTypeDecoration, + fragmentType: ReadonlyArray>> | null | undefined, +): ReadonlyArray | null | undefined; +export function useFragment( + _documentNode: DocumentTypeDecoration, + fragmentType: + | FragmentType> + | ReadonlyArray>> + | null + | undefined, +): TType | ReadonlyArray | null | undefined { + return fragmentType as any; +} + +export function makeFragmentData< + F extends DocumentTypeDecoration, + FT extends ResultOf, +>(data: FT, _fragment: F): FragmentType { + return data as FragmentType; +} +export function isFragmentReady( + queryNode: DocumentTypeDecoration, + fragmentNode: TypedDocumentNode, + data: FragmentType, any>> | null | undefined, +): data is FragmentType { + const deferredFields = ( + queryNode as { __meta__?: { deferredFields: Record } } + ).__meta__?.deferredFields; + + if (!deferredFields) return true; + + const fragDef = fragmentNode.definitions[0] as FragmentDefinitionNode | undefined; + const fragName = fragDef?.name?.value; + + const fields = (fragName && deferredFields[fragName]) || []; + return fields.length > 0 && fields.every((field) => data && field in data); +} diff --git a/src/__generated__/gql.ts b/src/__generated__/gql.ts new file mode 100644 index 00000000..0b2a0fea --- /dev/null +++ b/src/__generated__/gql.ts @@ -0,0 +1,53 @@ +/* eslint-disable */ +import { TypedDocumentNode as DocumentNode } from '@graphql-typed-document-node/core'; +import * as types from './graphql'; + +/** + * Map of all GraphQL operations in the project. + * + * This map has several performance disadvantages: + * 1. It is not tree-shakeable, so it will include all operations in the project. + * 2. It is not minifiable, so the string of a GraphQL query will be multiple times inside the bundle. + * 3. It does not support dead code elimination, so it will add unused operations. + * + * Therefore it is highly recommended to use the babel or swc plugin for production. + */ +const documents = { + '\n\tquery ProgramsList {\n\t\tprograms {\n\t\t\tshortName\n\t\t\tname\n\t\t\tcancerTypes\n\t\t\tcountries\n\t\t\tmembershipType\n\t\t\tgenomicDonors\n\t\t\tsubmittedDonors\n\t\t\tcommitmentDonors\n\t\t\tusers {\n\t\t\t\temail\n\t\t\t\tfirstName\n\t\t\t\tlastName\n\t\t\t\trole\n\t\t\t}\n\t\t}\n\t}\n': + types.ProgramsListDocument, + '\n\tquery SideMenu {\n\t\tprograms {\n\t\t\tshortName\n\t\t}\n\t}\n': types.SideMenuDocument, +}; + +/** + * The gql function is used to parse GraphQL queries into a document that can be used by GraphQL clients. + * + * + * @example + * ```ts + * const query = gql(`query GetUser($id: ID!) { user(id: $id) { name } }`); + * ``` + * + * The query argument is unknown! + * Please regenerate the types. + */ +export function gql(source: string): unknown; + +/** + * The gql function is used to parse GraphQL queries into a document that can be used by GraphQL clients. + */ +export function gql( + source: '\n\tquery ProgramsList {\n\t\tprograms {\n\t\t\tshortName\n\t\t\tname\n\t\t\tcancerTypes\n\t\t\tcountries\n\t\t\tmembershipType\n\t\t\tgenomicDonors\n\t\t\tsubmittedDonors\n\t\t\tcommitmentDonors\n\t\t\tusers {\n\t\t\t\temail\n\t\t\t\tfirstName\n\t\t\t\tlastName\n\t\t\t\trole\n\t\t\t}\n\t\t}\n\t}\n', +): (typeof documents)['\n\tquery ProgramsList {\n\t\tprograms {\n\t\t\tshortName\n\t\t\tname\n\t\t\tcancerTypes\n\t\t\tcountries\n\t\t\tmembershipType\n\t\t\tgenomicDonors\n\t\t\tsubmittedDonors\n\t\t\tcommitmentDonors\n\t\t\tusers {\n\t\t\t\temail\n\t\t\t\tfirstName\n\t\t\t\tlastName\n\t\t\t\trole\n\t\t\t}\n\t\t}\n\t}\n']; +/** + * The gql function is used to parse GraphQL queries into a document that can be used by GraphQL clients. + */ +export function gql( + source: '\n\tquery SideMenu {\n\t\tprograms {\n\t\t\tshortName\n\t\t}\n\t}\n', +): (typeof documents)['\n\tquery SideMenu {\n\t\tprograms {\n\t\t\tshortName\n\t\t}\n\t}\n']; + +export function gql(source: string) { + return (documents as any)[source] ?? {}; +} + +export type DocumentType> = + TDocumentNode extends DocumentNode ? TType : never; diff --git a/src/__generated__/graphql.ts b/src/__generated__/graphql.ts new file mode 100644 index 00000000..5b34a616 --- /dev/null +++ b/src/__generated__/graphql.ts @@ -0,0 +1,2516 @@ +/* eslint-disable */ +import { TypedDocumentNode as DocumentNode } from '@graphql-typed-document-node/core'; +export type Maybe = T | null; +export type InputMaybe = Maybe; +export type Exact = { [K in keyof T]: T[K] }; +export type MakeOptional = Omit & { [SubKey in K]?: Maybe }; +export type MakeMaybe = Omit & { [SubKey in K]: Maybe }; +export type MakeEmpty = { + [_ in K]?: never; +}; +export type Incremental = + | T + | { [P in keyof T]?: P extends ' $fragmentName' | '__typename' ? T[P] : never }; +/** All built-in and custom scalars, mapped to their actual values */ +export type Scalars = { + ID: { input: string; output: string }; + String: { input: string; output: string }; + Boolean: { input: boolean; output: boolean }; + Int: { input: number; output: number }; + Float: { input: number; output: number }; + Date: { input: any; output: any }; + DateTime: { input: any; output: any }; + /** The `JSON` scalar type represents JSON values as specified by [ECMA-404](http://www.ecma-international.org/publications/files/ECMA-ST/ECMA-404.pdf). */ + JSON: { input: any; output: any }; + Upload: { input: any; output: any }; +}; + +export type AccessKey = { + __typename?: 'AccessKey'; + error?: Maybe; + /** Time till expiry in milliseconds */ + exp?: Maybe; + key?: Maybe; +}; + +/** ########## QUERY TYPES ########### */ +export type AggState = { + __typename?: 'AggState'; + active?: Maybe; + field?: Maybe; + show?: Maybe; + /** @deprecated This field is deprecated in favour of client-side deduction of the type using the es mapping and @arranger/mapping-utils/esToAggTypeMap. This computation will already be done with @Arranger/components. Projects created with 0.4.6 will return null for this query */ + type?: Maybe; +}; + +/** ########## INPUT TYPES ########### */ +export type AggStateInput = { + active?: InputMaybe; + field?: InputMaybe; + show?: InputMaybe; +}; + +export type Aggregations = { + __typename?: 'Aggregations'; + bucket_count?: Maybe; + buckets?: Maybe>>; + cardinality?: Maybe; +}; + +export type AggregationsBucketsArgs = { + max?: InputMaybe; +}; + +export type AggregationsCardinalityArgs = { + precision_threshold?: InputMaybe; +}; + +export type AggsState = { + __typename?: 'AggsState'; + state?: Maybe>>; + timestamp?: Maybe; +}; + +/** Date range aggregations for a given donor field. */ +export type AnalysisObject = { + __typename?: 'AnalysisObject'; + buckets?: Maybe>>; + title?: Maybe; +}; + +export type Bucket = { + __typename?: 'Bucket'; + doc_count?: Maybe; + filter_by_term?: Maybe; + key?: Maybe; + key_as_string?: Maybe; + top_hits?: Maybe; +}; + +export type BucketFilter_By_TermArgs = { + filter?: InputMaybe; +}; + +export type BucketTop_HitsArgs = { + _source?: InputMaybe>>; + size?: InputMaybe; +}; + +/** Collated Clinical Data Query Response */ +export type ClinicalData = { + __typename?: 'ClinicalData'; + clinicalEntities: Array>; + clinicalErrors?: Maybe>>; + completionStats?: Maybe>>; + programShortName: Scalars['String']['output']; +}; + +/** Submitted Program Clinical Data arranged by Entity type */ +export type ClinicalDataEntities = { + __typename?: 'ClinicalDataEntities'; + completionStats?: Maybe>>; + entityFields?: Maybe>>; + entityName: Scalars['String']['output']; + records: Array>>>; + totalDocs: Scalars['Int']['output']; +}; + +export type ClinicalEntityError = { + donorId: Scalars['String']['output']; + field: Scalars['String']['output']; + message: Scalars['String']['output']; + row: Scalars['Int']['output']; + type: Scalars['String']['output']; + value: Scalars['String']['output']; +}; + +export type ClinicalErrorInfo = { + __typename?: 'ClinicalErrorInfo'; + message?: Maybe; + value?: Maybe>>; +}; + +/** Specific Error Field + Values */ +export type ClinicalErrorRecord = { + __typename?: 'ClinicalErrorRecord'; + entityName?: Maybe; + errorType?: Maybe; + fieldName?: Maybe; + index?: Maybe; + info?: Maybe; + message?: Maybe; +}; + +/** Data Submission / Schema Errors for a given Donor */ +export type ClinicalErrors = { + __typename?: 'ClinicalErrors'; + donorId?: Maybe; + errors?: Maybe>>; + submitterDonorId?: Maybe; +}; + +/** All schemas below describe clinical errors */ +export type ClinicalFileError = { + __typename?: 'ClinicalFileError'; + code: Scalars['String']['output']; + fileNames: Array>; + message: Scalars['String']['output']; +}; + +/** Query Variables for Pagination & Filtering */ +export type ClinicalInput = { + completionState?: InputMaybe; + donorIds?: InputMaybe>>; + entityTypes?: InputMaybe>>; + page: Scalars['Int']['input']; + pageSize: Scalars['Int']['input']; + sort?: InputMaybe; + submitterDonorIds?: InputMaybe>>; +}; + +/** Generic schema of clinical tsv records */ +export type ClinicalRecord = { + __typename?: 'ClinicalRecord'; + fields: Array; + row: Scalars['Int']['output']; +}; + +export type ClinicalRecordField = { + __typename?: 'ClinicalRecordField'; + name: Scalars['String']['output']; + value?: Maybe; +}; + +/** + * It is possible for there to be no available ClinicalRegistrationData for a program, + * in this case the object will return with id and creator equal to null, and an empty records list. + */ +export type ClinicalRegistrationData = { + __typename?: 'ClinicalRegistrationData'; + alreadyRegistered: ClinicalRegistrationStats; + createdAt?: Maybe; + creator?: Maybe; + errors: Array>; + fileErrors?: Maybe>>; + fileName?: Maybe; + id?: Maybe; + newDonors: ClinicalRegistrationStats; + newSamples: ClinicalRegistrationStats; + newSpecimens: ClinicalRegistrationStats; + programShortName?: Maybe; + records: Array>; +}; + +export type ClinicalRegistrationError = ClinicalEntityError & { + __typename?: 'ClinicalRegistrationError'; + donorId: Scalars['String']['output']; + field: Scalars['String']['output']; + message: Scalars['String']['output']; + row: Scalars['Int']['output']; + sampleId?: Maybe; + specimenId?: Maybe; + type: Scalars['String']['output']; + value: Scalars['String']['output']; +}; + +export type ClinicalRegistrationStatValue = { + __typename?: 'ClinicalRegistrationStatValue'; + name: Scalars['String']['output']; + rows: Array>; +}; + +export type ClinicalRegistrationStats = { + __typename?: 'ClinicalRegistrationStats'; + count: Scalars['Int']['output']; + names: Array>; + rows: Array>; + values: Array>; +}; + +/** Clinical Data DonorId Search Query Response */ +export type ClinicalSearchData = { + __typename?: 'ClinicalSearchData'; + programShortName: Scalars['String']['output']; + searchResults: Array>; + totalResults: Scalars['Int']['output']; +}; + +/** Clinical Data DonorId Search Result Record */ +export type ClinicalSearchResults = { + __typename?: 'ClinicalSearchResults'; + donorId: Scalars['Int']['output']; + submitterDonorId?: Maybe; +}; + +export type ClinicalSubmissionData = { + __typename?: 'ClinicalSubmissionData'; + clinicalEntities: Array>; + fileErrors?: Maybe>>; + id?: Maybe; + programShortName?: Maybe; + state?: Maybe; + updatedAt?: Maybe; + updatedBy?: Maybe; + version?: Maybe; +}; + +export type ClinicalSubmissionDataError = ClinicalEntityError & { + __typename?: 'ClinicalSubmissionDataError'; + donorId: Scalars['String']['output']; + field: Scalars['String']['output']; + message: Scalars['String']['output']; + row: Scalars['Int']['output']; + type: Scalars['String']['output']; + value: Scalars['String']['output']; +}; + +export type ClinicalSubmissionEntity = { + __typename?: 'ClinicalSubmissionEntity'; + batchName?: Maybe; + clinicalType: Scalars['String']['output']; + createdAt?: Maybe; + creator?: Maybe; + dataErrors: Array>; + dataUpdates: Array>; + dataWarnings: Array>; + records: Array>; + schemaErrors: Array>; + stats?: Maybe; +}; + +export type ClinicalSubmissionSchemaError = ClinicalEntityError & { + __typename?: 'ClinicalSubmissionSchemaError'; + clinicalType: Scalars['String']['output']; + donorId: Scalars['String']['output']; + field: Scalars['String']['output']; + message: Scalars['String']['output']; + row: Scalars['Int']['output']; + type: Scalars['String']['output']; + value: Scalars['String']['output']; +}; + +/** Each field is an array of row index referenced in ClinicalSubmissionRecord */ +export type ClinicalSubmissionStats = { + __typename?: 'ClinicalSubmissionStats'; + errorsFound: Array>; + new: Array>; + noUpdate: Array>; + updated: Array>; +}; + +export type ClinicalSubmissionUpdate = { + __typename?: 'ClinicalSubmissionUpdate'; + donorId: Scalars['String']['output']; + field: Scalars['String']['output']; + newValue: Scalars['String']['output']; + oldValue: Scalars['String']['output']; + row: Scalars['Int']['output']; +}; + +export type Column = { + __typename?: 'Column'; + accessor?: Maybe; + canChangeShow?: Maybe; + field?: Maybe; + id?: Maybe; + jsonPath?: Maybe; + query?: Maybe; + show?: Maybe; + sortable?: Maybe; + type?: Maybe; +}; + +/** ########## INPUT TYPES ########### */ +export type ColumnInput = { + accessor?: InputMaybe; + canChangeShow?: InputMaybe; + field?: InputMaybe; + id?: InputMaybe; + jsonPath?: InputMaybe; + query?: InputMaybe; + show?: InputMaybe; + sortable?: InputMaybe; + type?: InputMaybe; +}; + +/** ########## QUERY TYPES ########### */ +export type ColumnSort = { + __typename?: 'ColumnSort'; + desc?: Maybe; + id?: Maybe; +}; + +export type ColumnSortInput = { + desc?: InputMaybe; + id?: InputMaybe; +}; + +export type ColumnState = { + __typename?: 'ColumnState'; + columns?: Maybe>>; + defaultSorted?: Maybe>>; + keyField?: Maybe; + type?: Maybe; +}; + +export type ColumnStateInput = { + columns?: InputMaybe>>; + defaultSorted?: InputMaybe>>; + keyField?: InputMaybe; + type?: InputMaybe; +}; + +export type ColumnsState = { + __typename?: 'ColumnsState'; + state?: Maybe; + timestamp?: Maybe; +}; + +export type ColumnsStates = { + __typename?: 'ColumnsStates'; + index?: Maybe; + states?: Maybe>>; +}; + +/** Display Data For Core Completion Entities */ +export type CompletionEntityData = { + __typename?: 'CompletionEntityData'; + specimens?: Maybe; +}; + +/** Completion Data for a given Donor */ +export type CompletionStats = { + __typename?: 'CompletionStats'; + coreCompletion?: Maybe; + coreCompletionDate?: Maybe; + coreCompletionPercentage?: Maybe; + donorId?: Maybe; + entityData?: Maybe; + overriddenCoreCompletion?: Maybe>>; +}; + +/** Specific Entity Completion Values */ +export type CoreCompletionFields = { + __typename?: 'CoreCompletionFields'; + donor: Scalars['Float']['output']; + followUps: Scalars['Float']['output']; + primaryDiagnosis: Scalars['Float']['output']; + specimens: Scalars['Float']['output']; + treatments: Scalars['Float']['output']; +}; + +export type CoreCompletionStatusCount = { + __typename?: 'CoreCompletionStatusCount'; + completed: Scalars['Int']['output']; + incomplete: Scalars['Int']['output']; + noData: Scalars['Int']['output']; +}; + +export type DataSubmissionStatus = { + __typename?: 'DataSubmissionStatus'; + dataSubmitted: Scalars['Int']['output']; + noDataSubmitted: Scalars['Int']['output']; +}; + +export type DateRangeBucket = { + __typename?: 'DateRangeBucket'; + /** This date is the last day in this date range bucket. */ + date?: Maybe; + /** Number of donors with data published for the relevant analysis, from the beginning of time to this date. */ + donors?: Maybe; +}; + +export enum DonorField { + /** Timestamp of when this donor first had alignment data published */ + AlignmentFirstPublishedDate = 'alignmentFirstPublishedDate', + /** Timestamp of when this donor first had core clinical data completed */ + CoreCompletionDate = 'coreCompletionDate', + /** Timestamp of when this donor first had Mutect2 variant callings data published */ + MutectFirstPublishedDate = 'mutectFirstPublishedDate', + /** Timestamp of when this donor first had Open Access data published */ + OpenAccessFirstPublishedDate = 'openAccessFirstPublishedDate', + /** Timestamp of when this donor first had raw reads data published */ + RawReadsFirstPublishedDate = 'rawReadsFirstPublishedDate', + /** Timestamp of when this donor first had RNA alignment data published */ + RnaAlignmentFirstPublishedDate = 'rnaAlignmentFirstPublishedDate', + /** Timestamp of when this donor first had RNA raw reads data published */ + RnaRawReadsFirstPublishedDate = 'rnaRawReadsFirstPublishedDate', + /** Timestamp of when this donor first had Sanger VC data published */ + SangerVcsFirstPublishedDate = 'sangerVcsFirstPublishedDate', +} + +export enum DonorMolecularDataProcessingStatus { + Complete = 'COMPLETE', + Processing = 'PROCESSING', + Registered = 'REGISTERED', +} + +export enum DonorMolecularDataReleaseStatus { + FullyReleased = 'FULLY_RELEASED', + NoRelease = 'NO_RELEASE', + PartiallyReleased = 'PARTIALLY_RELEASED', +} + +export type DonorSummary = { + __typename?: 'DonorSummary'; + entries?: Maybe>; + stats: ProgramDonorSummaryStats; +}; + +/** Includes status summary of clinical and molecular data processing for the given donor */ +export type DonorSummaryEntry = { + __typename?: 'DonorSummaryEntry'; + /** Number of DNA alignments completed for this donor */ + alignmentsCompleted: Scalars['Int']['output']; + /** Number of DNA alignments that is failing for this donor */ + alignmentsFailed: Scalars['Int']['output']; + /** Number of DNA alignments currently running for this donor */ + alignmentsRunning: Scalars['Int']['output']; + /** Timestamp of when this donor was first registered */ + createdAt: Scalars['DateTime']['output']; + /** Donor id of the donor within the program */ + donorId: Scalars['String']['output']; + /** Unique object ID for this summary object */ + id: Scalars['ID']['output']; + /** Number of matched normal/tumour DNA sample pairs registered for this donor */ + matchedTNPairsDNA: Scalars['Int']['output']; + /** Number of DNA Mutect2 completed for this donor */ + mutectCompleted: Scalars['Int']['output']; + /** Number of DNA Mutect2 that is failed for this donor */ + mutectFailed: Scalars['Int']['output']; + /** Number of DNA Mutect2 currently running for this donor */ + mutectRunning: Scalars['Int']['output']; + /** Number of Open Access completed for this donor */ + openAccessCompleted: Scalars['Int']['output']; + /** Number of DNA Open Access that is failed for this donor */ + openAccessFailed: Scalars['Int']['output']; + /** Number of DNA Open Access currently running for this donor */ + openAccessRunning: Scalars['Int']['output']; + /** Molecular data processing status of this donor */ + processingStatus: DonorMolecularDataProcessingStatus; + /** Short name of the program in which this donor is registered */ + programShortName: Scalars['String']['output']; + /** Number of normal DNA sample analysis that has been published for this donor */ + publishedNormalAnalysis: Scalars['Int']['output']; + /** Number of tumour DNA sample analysis that has been published for this donor */ + publishedTumourAnalysis: Scalars['Int']['output']; + /** Number of normal DNA samples registered for this donor */ + registeredNormalSamples: Scalars['Int']['output']; + /** Number of tumour DNA samples registered for this donor */ + registeredTumourSamples: Scalars['Int']['output']; + /** Release status of the donor's molecular data */ + releaseStatus: DonorMolecularDataReleaseStatus; + /** Number of RNA alignments that are failing for this donor */ + rnaAlignmentFailed: Scalars['Int']['output']; + /** Number of RNA alignments completed for this donor */ + rnaAlignmentsCompleted: Scalars['Int']['output']; + /** Number of RNA alignments currently running for this donor */ + rnaAlignmentsRunning: Scalars['Int']['output']; + /** Number of normal RNA sample analysis that has been published for this donor */ + rnaPublishedNormalAnalysis: Scalars['Int']['output']; + /** Number of tumour RNA sample analysis that has been published for this donor */ + rnaPublishedTumourAnalysis: Scalars['Int']['output']; + /** Number of normal RNA samples registered for this donor */ + rnaRegisteredNormalSamples: Scalars['Int']['output']; + /** Number of tumour RNA samples registered for this donor */ + rnaRegisteredTumourSamples: Scalars['Int']['output']; + /** Number of DNA Sanger VCs completed for this donor */ + sangerVcsCompleted: Scalars['Int']['output']; + /** Number of DNA Sanger VCs that is failing for this donor */ + sangerVcsFailed: Scalars['Int']['output']; + /** Number of DNA Sanger VCs currently running for this donor */ + sangerVcsRunning: Scalars['Int']['output']; + /** Percentage of core clinical data fields that has been submitted for this donor. All core fields are listed at: https://docs.icgc-argo.org/dictionary */ + submittedCoreDataPercent: Scalars['Float']['output']; + /** Percentage of extended clinical data fields that has been submitted for this donor. All extended fields are listed at: https://docs.icgc-argo.org/dictionary */ + submittedExtendedDataPercent: Scalars['Float']['output']; + submitterDonorId: Scalars['String']['output']; + /** Timestamp of the latest update applied to this donor's clinical data */ + updatedAt: Scalars['DateTime']['output']; + /** Whether the donor submitted donor is valid according to the latest data dictionary layed out at: https://docs.icgc-argo.org/dictionary */ + validWithCurrentDictionary: Scalars['Boolean']['output']; +}; + +export type DonorSummaryEntrySort = { + field: ProgramDonorSummaryEntryField; + order?: InputMaybe; +}; + +export enum EsRefresh { + False = 'FALSE', + True = 'TRUE', + WaitFor = 'WAIT_FOR', +} + +export type FileSize = { + __typename?: 'FileSize'; + value?: Maybe; +}; + +export enum InviteStatus { + Accepted = 'ACCEPTED', + Expired = 'EXPIRED', + Pending = 'PENDING', + Revoked = 'REVOKED', +} + +export type InviteUserInput = { + programShortName: Scalars['String']['input']; + userEmail: Scalars['String']['input']; + userFirstName: Scalars['String']['input']; + userLastName: Scalars['String']['input']; + userRole: UserRole; +}; + +export enum JiraTicketCategory { + ApplyingAccess = 'APPLYING_ACCESS', + DataDownload = 'DATA_DOWNLOAD', + DataQuery = 'DATA_QUERY', + DataSubmission = 'DATA_SUBMISSION', + MediaQuery = 'MEDIA_QUERY', + Other = 'OTHER', + PublicationQuery = 'PUBLICATION_QUERY', +} + +export type JoinProgramInput = { + department: Scalars['String']['input']; + institute: Scalars['String']['input']; + invitationId: Scalars['ID']['input']; + piFirstName: Scalars['String']['input']; + piLastName: Scalars['String']['input']; +}; + +export type JoinProgramInvite = { + __typename?: 'JoinProgramInvite'; + acceptedAt?: Maybe; + createdAt: Scalars['DateTime']['output']; + emailSent: Scalars['Boolean']['output']; + expiresAt: Scalars['DateTime']['output']; + id: Scalars['ID']['output']; + program: Program; + status: InviteStatus; + user: ProgramUser; +}; + +export type MatchBoxField = { + __typename?: 'MatchBoxField'; + displayName?: Maybe; + field?: Maybe; + isActive?: Maybe; + keyField?: Maybe; + searchFields?: Maybe>>; +}; + +export type MatchBoxState = { + __typename?: 'MatchBoxState'; + state?: Maybe>>; + timestamp?: Maybe; +}; + +export type MatchBoxStates = { + __typename?: 'MatchBoxStates'; + index?: Maybe; + states?: Maybe>>; +}; + +export enum MembershipType { + Associate = 'ASSOCIATE', + Full = 'FULL', +} + +export enum Missing { + First = 'first', + Last = 'last', +} + +export enum Mode { + Avg = 'avg', + Max = 'max', + Min = 'min', + Sum = 'sum', +} + +export type Mutation = { + __typename?: 'Mutation'; + /** Available for DCC members to approve a clinical submission */ + approveClinicalSubmission: Scalars['Boolean']['output']; + /** Remove the Clinical Registration data currently uploaded and not committed */ + clearClinicalRegistration: Scalars['Boolean']['output']; + /** + * Clear Clinical Submission + * fileType is optional, if it is not provided all fileTypes will be cleared. The values for fileType are the same as the file names from each template (ex. donor, specimen) + */ + clearClinicalSubmission: ClinicalSubmissionData; + /** + * Complete registration of the currently uploaded Clinical Registration data + * On Success, returns a list of the new sample IDs that were committed + */ + commitClinicalRegistration: Array>; + /** + * - If there is update: makes a clinical submission ready for approval by a DCC member, + * returning submission data with updated state + * - If there is NO update: merges clinical data to system, returning an empty submission + */ + commitClinicalSubmission: ClinicalSubmissionData; + createJiraTicketWithReCaptcha: TicketCreationResponse; + /** + * Create new program + * For lists (Cancer Type, Primary Site, Institution, Regions, Countries) the entire new value must be provided, not just values being added. + * Returns Program object details of created program + */ + createProgram?: Maybe; + /** Generate Ego access key */ + generateAccessKey: AccessKey; + /** + * Invite a user to join a program + * Returns the email of the user if the invite is successfully sent + */ + inviteUser?: Maybe; + /** + * Join a program by accepting an invitation + * Returns the user data + */ + joinProgram?: Maybe; + /** + * Remove a user from a program + * Returns message from server + */ + removeUser?: Maybe; + /** Available for DCC members to reopen a clinical submission */ + reopenClinicalSubmission: ClinicalSubmissionData; + saveSet?: Maybe; + /** + * Update Program + * Returns shortName of the program if succesfully updated + */ + updateProgram?: Maybe; + /** + * Update a user's role in a prgoram + * Returns the user data + */ + updateUser?: Maybe; + /** Upload a Registration file */ + uploadClinicalRegistration: ClinicalRegistrationData; + /** Upload Clinical Submission files */ + uploadClinicalSubmissions: ClinicalSubmissionData; + /** Validate the uploaded clinical files */ + validateClinicalSubmissions: ClinicalSubmissionData; +}; + +export type MutationApproveClinicalSubmissionArgs = { + programShortName: Scalars['String']['input']; + version: Scalars['String']['input']; +}; + +export type MutationClearClinicalRegistrationArgs = { + registrationId: Scalars['String']['input']; + shortName: Scalars['String']['input']; +}; + +export type MutationClearClinicalSubmissionArgs = { + fileType?: InputMaybe; + programShortName: Scalars['String']['input']; + version: Scalars['String']['input']; +}; + +export type MutationCommitClinicalRegistrationArgs = { + registrationId: Scalars['String']['input']; + shortName: Scalars['String']['input']; +}; + +export type MutationCommitClinicalSubmissionArgs = { + programShortName: Scalars['String']['input']; + version: Scalars['String']['input']; +}; + +export type MutationCreateJiraTicketWithReCaptchaArgs = { + displayName?: InputMaybe; + emailAddress: Scalars['String']['input']; + messageCategory: JiraTicketCategory; + reCaptchaResponse: Scalars['String']['input']; + requestText: Scalars['String']['input']; +}; + +export type MutationCreateProgramArgs = { + program: ProgramInput; +}; + +export type MutationInviteUserArgs = { + invite: InviteUserInput; +}; + +export type MutationJoinProgramArgs = { + join: JoinProgramInput; +}; + +export type MutationRemoveUserArgs = { + programShortName: Scalars['String']['input']; + userEmail: Scalars['String']['input']; +}; + +export type MutationReopenClinicalSubmissionArgs = { + programShortName: Scalars['String']['input']; + version: Scalars['String']['input']; +}; + +export type MutationSaveSetArgs = { + path: Scalars['String']['input']; + refresh?: InputMaybe; + sort?: InputMaybe>>; + sqon: Scalars['JSON']['input']; + type: ProjectType; + userId?: InputMaybe; +}; + +export type MutationUpdateProgramArgs = { + shortName: Scalars['String']['input']; + updates: UpdateProgramInput; +}; + +export type MutationUpdateUserArgs = { + programShortName: Scalars['String']['input']; + userEmail: Scalars['String']['input']; + userRole: UserRole; +}; + +export type MutationUploadClinicalRegistrationArgs = { + registrationFile: Scalars['Upload']['input']; + shortName: Scalars['String']['input']; +}; + +export type MutationUploadClinicalSubmissionsArgs = { + clinicalFiles?: InputMaybe>; + programShortName: Scalars['String']['input']; +}; + +export type MutationValidateClinicalSubmissionsArgs = { + programShortName: Scalars['String']['input']; + version: Scalars['String']['input']; +}; + +export type Node = { + id: Scalars['ID']['output']; +}; + +export type NumericAggregations = { + __typename?: 'NumericAggregations'; + histogram?: Maybe; + stats?: Maybe; +}; + +export type NumericAggregationsHistogramArgs = { + interval?: InputMaybe; +}; + +export enum Order { + Asc = 'asc', + Desc = 'desc', +} + +export type Profile = { + __typename?: 'Profile'; + apiKey?: Maybe; + isDacoApproved?: Maybe; +}; + +export type Program = { + __typename?: 'Program'; + cancerTypes?: Maybe>>; + commitmentDonors?: Maybe; + countries?: Maybe>>; + description?: Maybe; + genomicDonors?: Maybe; + institutions?: Maybe>>; + membershipType?: Maybe; + name?: Maybe; + primarySites?: Maybe>>; + regions?: Maybe>>; + shortName: Scalars['String']['output']; + submittedDonors?: Maybe; + users?: Maybe>>; + website?: Maybe; +}; + +export enum ProgramDonorSummaryEntryField { + /** + * use this field to filter donor entries by 4 enum values: COMPLETED, IN_PROGRESS, FAILED, NO_DATA. + * COMPLETED = donor has more than 1 completed alignment workflow; + * IN_PROGRESS = donor has more than 1 running alignment workflow; + * FAILED = donor has more than 1 failed alignment workflow; + * NO_DATA = donor has 0 of all the above alignment workflow. + */ + AlignmentStatus = 'alignmentStatus', + AlignmentsCompleted = 'alignmentsCompleted', + AlignmentsFailed = 'alignmentsFailed', + AlignmentsRunning = 'alignmentsRunning', + /** use this field to filter donor entries by partially matching donorId or submitterDonorId, e.g.: "donor", "donor5" */ + CombinedDonorId = 'combinedDonorId', + /** + * use this field to filter donor entries by 3 aggregations of submittedCoreDataPercent, + * 3 enum options to filter by: NO_DATA, COMPLETE, INCOMPLETE. + */ + CoreDataPercentAggregation = 'coreDataPercentAggregation', + CreatedAt = 'createdAt', + /** + * use this field to filter donor entries by 4 enum values: TUMOR_NORMAL_MATCHED_PAIR, TUMOR_NORMAL_NO_MATCHED_PAIR, NO_DATA. + * TUMOR_NORMAL_MATCHED_PAIR = donor has at least 1 tumor/normal matched pair. + * TUMOR_NORMAL_NO_MATCHED_PAIR = donor has at least 1 registered tumour or 1 normal DNA sample, but no matched pairs. + * NO_DATA = donor has not registered any tumour or normal DNA samples. + */ + DnaTnMatchedPair = 'dnaTNMatchedPair', + /** + * use this field to filter donor entries by 3 enum values: TUMOR_AND_NORMAL, TUMOR_OR_NORMAL, NO_DATA. + * TUMOR_AND_NORMAL = donor has at least 1 registered tumour and 1 normal DNA sample. + * TUMOR_OR_NORMAL = donor has at least 1 registered tumour or 1 normal DNA sample, but not both. + * NO_DATA = donor has not registered any tumour or normal DNA samples. + */ + DnaTnRegistered = 'dnaTNRegistered', + DonorId = 'donorId', + MatchedTnPairsDna = 'matchedTNPairsDNA', + MutectCompleted = 'mutectCompleted', + MutectFailed = 'mutectFailed', + MutectRunning = 'mutectRunning', + /** + * use this field to filter donor entries by 4 enum values: COMPLETED, IN_PROGRESS, FAILED, NO_DATA. + * COMPLETED = donor has more than 1 completed Mutect 2 workflow; + * IN_PROGRESS = donor has more than 1 running Mutect 2 workflow; + * FAILED = donor has more than 1 failed Mutect 2 workflow; + * NO_DATA = donor has 0 of all the above Mutect 2 workflow. + */ + MutectStatus = 'mutectStatus', + OpenAccessCompleted = 'openAccessCompleted', + OpenAccessFailed = 'openAccessFailed', + OpenAccessRunning = 'openAccessRunning', + /** + * use this field to filter donor entries by 4 enum values: COMPLETED, IN_PROGRESS, FAILED, NO_DATA. + * COMPLETED = donor has 1 or more completed Open Access workflow; + * IN_PROGRESS = donor has 1 or more running Open Access workflow; + * FAILED = donor has 1 or more failed Open Access workflow; + * NO_DATA = donor has 0 of all the above Open Access workflow. + */ + OpenAccessStatus = 'openAccessStatus', + ProcessingStatus = 'processingStatus', + ProgramShortName = 'programShortName', + PublishedNormalAnalysis = 'publishedNormalAnalysis', + PublishedTumourAnalysis = 'publishedTumourAnalysis', + /** + * use this field to filter donor entries by 2 enum values: VALID, INVALID. + * VALID means the donor has at least 1 submitted tumour/normal sequencing reads. + * INVALID means the donor has not registered any tumour or sequencing reads. + */ + RawReads = 'rawReads', + RegisteredNormalSamples = 'registeredNormalSamples', + /** + * use this field to filter donor entries by 2 enum values: VALID, INVALID. + * VALID means the donor has at least 1 registered tumour/normal sample pair. + * INVALID means the donor has not registered any tumour or normal samples. + */ + RegisteredSamplePairs = 'registeredSamplePairs', + RegisteredTumourSamples = 'registeredTumourSamples', + ReleaseStatus = 'releaseStatus', + RnaAlignmentFailed = 'rnaAlignmentFailed', + /** + * use this field to filter donor entries by 4 enum values: COMPLETED, IN_PROGRESS, FAILED, NO_DATA. + * COMPLETED = donor has more than 1 completed RNA alignment workflow; + * IN_PROGRESS = donor has more than 1 running RNA alignment workflow; + * FAILED = donor has more than 1 failed RNA alignment workflow; + * NO_DATA = donor has 0 of all the above RNA alignment workflow. + */ + RnaAlignmentStatus = 'rnaAlignmentStatus', + RnaAlignmentsCompleted = 'rnaAlignmentsCompleted', + RnaAlignmentsRunning = 'rnaAlignmentsRunning', + RnaPublishedNormalAnalysis = 'rnaPublishedNormalAnalysis', + RnaPublishedTumourAnalysis = 'rnaPublishedTumourAnalysis', + /** + * use this field to filter donor entries by 2 enum values: DATA_SUBMITTED, NO_DATA. + * DATA_SUBMITTED means the donor has at least 1 published tumour or 1 published normal RNA raw reads. + * NO_DATA means the donor has no tumour and normal RNA raw reads. + */ + RnaRawReads = 'rnaRawReads', + RnaRegisteredNormalSamples = 'rnaRegisteredNormalSamples', + /** + * use this field to filter donor entries by 2 enum values: DATA_SUBMITTED, NO_DATA. + * DATA_SUBMITTED means the donor has at least 1 registered tumour or 1 normal RNA sample. + * NO_DATA means the donor has not registered any tumour or normal RNA samples. + */ + RnaRegisteredSample = 'rnaRegisteredSample', + RnaRegisteredTumourSamples = 'rnaRegisteredTumourSamples', + /** + * use this field to filter donor entries by 4 enum values: COMPLETED, IN_PROGRESS, FAILED, NO_DATA. + * COMPLETED = donor has more than 1 completed sanger VC workflow; + * IN_PROGRESS = donor has more than 1 running sanger VC workflow; + * FAILED = donor has more than 1 failed sanger VC workflow; + * NO_DATA = donor has 0 of all the above sanger VC workflow. + */ + SangerVcStatus = 'sangerVCStatus', + SangerVcsCompleted = 'sangerVcsCompleted', + SangerVcsFailed = 'sangerVcsFailed', + SangerVcsRunning = 'sangerVcsRunning', + SubmittedCoreDataPercent = 'submittedCoreDataPercent', + SubmittedExtendedDataPercent = 'submittedExtendedDataPercent', + SubmitterDonorId = 'submitterDonorId', + UpdatedAt = 'updatedAt', + ValidWithCurrentDictionary = 'validWithCurrentDictionary', +} + +export type ProgramDonorSummaryFilter = { + field: ProgramDonorSummaryEntryField; + values: Array; +}; + +/** Contains summary of aggregate clinical and molecular data processing status for the given program */ +export type ProgramDonorSummaryStats = { + __typename?: 'ProgramDonorSummaryStats'; + /** Number of donors that have COMPLETED/IN_PROGRESS/FAILED/NO_DATA as alignment workflow status */ + alignmentStatusCount: WorkflowStatusCount; + /** Total number of genomic files associated with this program */ + allFilesCount: Scalars['Int']['output']; + /** Number of donors whose initiated workflows are all complete */ + completedWorkflowRuns: Scalars['Int']['output']; + /** Number of donors that are clinically completed/incomplete/no core fields */ + coreCompletion: CoreCompletionStatusCount; + /** Number of donors that have tumor & normal matched pairs submitted */ + dnaTNMatchedPairStatus: TumorNormalMatchedPairStatusCount; + /** Number of donors that have tumor and normal data registered */ + dnaTNRegisteredStatus: TumorNormalStatusCount; + /** Number of donors invalidated with current data dictionary version */ + donorsInvalidWithCurrentDictionaryCount: Scalars['Int']['output']; + /** Number of donors whose molecular data is being processed */ + donorsProcessingMolecularDataCount: Scalars['Int']['output']; + /** Number of donors whose files have been released */ + donorsWithReleasedFilesCount: Scalars['Int']['output']; + /** Number of donors with workflow runs that have failed */ + failedWorkflowRuns: Scalars['Int']['output']; + /** Number of files to QC */ + filesToQcCount: Scalars['Int']['output']; + /** Number of donors whose genomic files have been fully released */ + fullyReleasedDonorsCount: Scalars['Int']['output']; + /** Unique ID of this summary object */ + id: Scalars['ID']['output']; + /** Number of donors with workflow runs that are currently running */ + inProgressWorkflowRuns: Scalars['Int']['output']; + /** Date of the most recent update to the donor summary index for this program. Can be null if no documents for this program */ + lastUpdate?: Maybe; + /** Number of donors that have COMPLETED/IN_PROGRESS/FAILED/NO_DATA as mutect2 workflow status */ + mutectStatusCount: WorkflowStatusCount; + /** Number of donors registered to the program who currently has no released genomic file */ + noReleaseDonorsCount: Scalars['Int']['output']; + /** Number of donors that have COMPLETED/IN_PROGRESS/FAILED/NO_DATA as Open Access workflow status */ + openAccessStatusCount: WorkflowStatusCount; + /** Number of donors who only have some genomic files that have been released */ + partiallyReleasedDonorsCount: Scalars['Int']['output']; + /** Percentage of core clinical data fields submitted over total core clinical data fields */ + percentageCoreClinical: Scalars['Float']['output']; + /** Percentage of donors with at least 1 matched tumour/normal DNA raw reads pair */ + percentageTumourAndNormal: Scalars['Float']['output']; + /** Short name of the program which this summary object is associated with */ + programShortName: Scalars['String']['output']; + /** Number of donors that have VALID/INVALID raw reads */ + rawReadsStatus: SamplePairsStatusCount; + /** Total number of donors registered for this program */ + registeredDonorsCount: Scalars['Int']['output']; + /** Number of donors that have COMPLETED/IN_PROGRESS/FAILED/NO_DATA as RNA alignment workflow status */ + rnaAlignmentStatusCount: WorkflowStatusCount; + /** Number of donors that have submitted RNA published raw reads */ + rnaRawReadStatus: DataSubmissionStatus; + /** Number of donors that have submitted RNA samples */ + rnaSampleStatus: DataSubmissionStatus; + /** Number of donors that have VALID/INVALID sample pairs */ + sampleStatus: SamplePairsStatusCount; + /** Number of donors that have COMPLETED/IN_PROGRESS/FAILED/NO_DATA as Sanger VC workflow status */ + sangerStatusCount: WorkflowStatusCount; +}; + +export type ProgramInput = { + admins: Array; + cancerTypes: Array>; + commitmentDonors: Scalars['Int']['input']; + countries: Array; + description?: InputMaybe; + institutions: Array; + membershipType: MembershipType; + name: Scalars['String']['input']; + primarySites: Array>; + regions: Array; + shortName: Scalars['String']['input']; + website: Scalars['String']['input']; +}; + +export type ProgramOptions = { + __typename?: 'ProgramOptions'; + cancerTypes: Array>; + countries: Array>; + institutions: Array>; + primarySites: Array>; + regions: Array>; +}; + +export type ProgramUser = { + __typename?: 'ProgramUser'; + email: Scalars['String']['output']; + firstName: Scalars['String']['output']; + inviteAcceptedAt?: Maybe; + inviteStatus?: Maybe; + isDacoApproved?: Maybe; + lastName: Scalars['String']['output']; + role: UserRole; +}; + +export type ProgramUserInput = { + email: Scalars['String']['input']; + firstName: Scalars['String']['input']; + lastName: Scalars['String']['input']; + role: UserRole; +}; + +export enum ProjectType { + File = 'file', + Sets = 'sets', +} + +export type Query = { + __typename?: 'Query'; + _jiraRootQuery: Scalars['String']['output']; + /** Retrieve all stored Clinical Entity and Donor Completion data for a program */ + clinicalData: ClinicalData; + /** Retrieve all stored Clinical Migration Errors for a program */ + clinicalErrors: Array; + /** Retrieve current stored Clinical Registration data for a program */ + clinicalRegistration: ClinicalRegistrationData; + /** Retrieve DonorIds + Submitter Donor Ids for given Clinical Entity and Program */ + clinicalSearchResults: ClinicalSearchData; + /** Retrieve current stored Clinical Submission Data Dictionary Schema version */ + clinicalSubmissionSchemaVersion: Scalars['String']['output']; + /** Retrieve current Clinical Submission disabled state for both sample_registration and clinical entity files */ + clinicalSubmissionSystemDisabled: Scalars['Boolean']['output']; + /** Retrieve current stored Clinical Submission Types list */ + clinicalSubmissionTypesList?: Maybe>; + /** Retrieve current stored Clinical Submission data for a program */ + clinicalSubmissions: ClinicalSubmissionData; + file?: Maybe; + /** retrieve join program invitation by id */ + joinProgramInvite?: Maybe; + node?: Maybe; + /** retrieve Program data by id */ + program?: Maybe; + /** This query is for finding out how many donors for a given program had data of given types (donorFields) published for the first time before the end of the given date range. The donor count is aggregated into buckets (bucketCount) by date. There must be at least one day per bucket, i.e. the number of days between dateRangeFrom and dateRangeTo must be greater than or equal to bucketCount. */ + programDonorPublishedAnalysisByDateRange: Array>; + /** Paginated list of donor data summary given a program */ + programDonorSummary: DonorSummary; + programOptions: ProgramOptions; + /** retrieve all Programs */ + programs?: Maybe>>; + query?: Maybe; + /** retrive user profile data */ + self?: Maybe; + sets?: Maybe; + systemAlerts?: Maybe>>; + /** retrieve User data by id */ + user?: Maybe; + /** retrieve paginated list of user data */ + users?: Maybe>>; +}; + +export type QueryClinicalDataArgs = { + filters: ClinicalInput; + programShortName: Scalars['String']['input']; +}; + +export type QueryClinicalErrorsArgs = { + donorIds?: InputMaybe>>; + programShortName: Scalars['String']['input']; +}; + +export type QueryClinicalRegistrationArgs = { + shortName: Scalars['String']['input']; +}; + +export type QueryClinicalSearchResultsArgs = { + filters: ClinicalInput; + programShortName: Scalars['String']['input']; +}; + +export type QueryClinicalSubmissionsArgs = { + programShortName: Scalars['String']['input']; +}; + +export type QueryJoinProgramInviteArgs = { + id: Scalars['ID']['input']; +}; + +export type QueryNodeArgs = { + id: Scalars['ID']['input']; +}; + +export type QueryProgramArgs = { + shortName: Scalars['String']['input']; +}; + +export type QueryProgramDonorPublishedAnalysisByDateRangeArgs = { + bucketCount?: InputMaybe; + dateRangeFrom: Scalars['DateTime']['input']; + dateRangeTo: Scalars['DateTime']['input']; + donorFields: Array>; + programShortName: Scalars['String']['input']; +}; + +export type QueryProgramDonorSummaryArgs = { + filters?: InputMaybe>; + first?: InputMaybe; + offset?: InputMaybe; + programShortName: Scalars['String']['input']; + sorts?: InputMaybe>>; +}; + +export type QueryQueryArgs = { + query?: InputMaybe; + types?: InputMaybe>>; +}; + +export type QueryUserArgs = { + id: Scalars['String']['input']; +}; + +export type QueryUsersArgs = { + groups?: InputMaybe>>; + limit?: InputMaybe; + pageNum?: InputMaybe; + query?: InputMaybe; + sort?: InputMaybe; +}; + +export type QueryResults = { + __typename?: 'QueryResults'; + hits?: Maybe>>; + total?: Maybe; +}; + +export type SamplePairsStatusCount = { + __typename?: 'SamplePairsStatusCount'; + invalid: Scalars['Int']['output']; + valid: Scalars['Int']['output']; +}; + +export type Set = { + __typename?: 'Set'; + createdAt?: Maybe; + ids?: Maybe>>; + path?: Maybe; + setId?: Maybe; + size?: Maybe; + sqon?: Maybe; + type?: Maybe; + userId?: Maybe; +}; + +export type Sort = { + field: Scalars['String']['input']; + missing?: InputMaybe; + mode?: InputMaybe; + order?: InputMaybe; +}; + +export enum SortOrder { + Asc = 'asc', + Desc = 'desc', +} + +export type SpecimenCoreCompletion = { + __typename?: 'SpecimenCoreCompletion'; + coreCompletionPercentage: Scalars['Float']['output']; + normalRegistrations: Scalars['Float']['output']; + normalSpecimensPercentage: Scalars['Float']['output']; + normalSubmissions: Scalars['Float']['output']; + tumourRegistrations: Scalars['Float']['output']; + tumourSpecimensPercentage: Scalars['Float']['output']; + tumourSubmissions: Scalars['Float']['output']; +}; + +export type Stats = { + __typename?: 'Stats'; + avg?: Maybe; + count?: Maybe; + max?: Maybe; + min?: Maybe; + sum?: Maybe; +}; + +export enum SubmissionState { + Invalid = 'INVALID', + InvalidByMigration = 'INVALID_BY_MIGRATION', + Open = 'OPEN', + PendingApproval = 'PENDING_APPROVAL', + Valid = 'VALID', +} + +export type SystemAlert = { + __typename?: 'SystemAlert'; + dismissable: Scalars['Boolean']['output']; + id: Scalars['ID']['output']; + level: Scalars['String']['output']; + message?: Maybe; + title: Scalars['String']['output']; +}; + +export type TicketCreationResponse = { + __typename?: 'TicketCreationResponse'; + _links?: Maybe; + issueId?: Maybe; + issueKey?: Maybe; +}; + +export type TicketLink = { + __typename?: 'TicketLink'; + web?: Maybe; +}; + +export type TumorNormalMatchedPairStatusCount = { + __typename?: 'TumorNormalMatchedPairStatusCount'; + noData: Scalars['Int']['output']; + tumorNormalMatchedPair: Scalars['Int']['output']; + tumorNormalMatchedPairMissingRawReads: Scalars['Int']['output']; + tumorNormalNoMatchedPair: Scalars['Int']['output']; +}; + +export type TumorNormalStatusCount = { + __typename?: 'TumorNormalStatusCount'; + noData: Scalars['Int']['output']; + tumorAndNormal: Scalars['Int']['output']; + tumorOrNormal: Scalars['Int']['output']; +}; + +export type UpdateProgramInput = { + cancerTypes?: InputMaybe>>; + commitmentDonors?: InputMaybe; + countries?: InputMaybe>>; + description?: InputMaybe; + institutions?: InputMaybe>>; + membershipType?: InputMaybe; + name?: InputMaybe; + primarySites?: InputMaybe>>; + regions?: InputMaybe>>; + website?: InputMaybe; +}; + +export type User = { + __typename?: 'User'; + applications?: Maybe>>; + /** ISO Formatted DateTime: */ + createdAt?: Maybe; + email: Scalars['String']['output']; + firstName?: Maybe; + groups?: Maybe>>; + id: Scalars['String']['output']; + /** ISO Formatted DateTime: */ + lastLogin?: Maybe; + lastName?: Maybe; + name?: Maybe; + preferredLanguage?: Maybe; + scopes?: Maybe>>; + status?: Maybe; + type?: Maybe; +}; + +export enum UserRole { + Admin = 'ADMIN', + Banned = 'BANNED', + Collaborator = 'COLLABORATOR', + Curator = 'CURATOR', + Submitter = 'SUBMITTER', +} + +export type WorkflowStatusCount = { + __typename?: 'WorkflowStatusCount'; + completed: Scalars['Int']['output']; + failed: Scalars['Int']['output']; + inProgress: Scalars['Int']['output']; + noData: Scalars['Int']['output']; +}; + +export type File = { + __typename?: 'file'; + aggregations?: Maybe; + aggsState?: Maybe; + columnsState?: Maybe; + extended?: Maybe; + hits?: Maybe; + mapping?: Maybe; + matchBoxState?: Maybe; +}; + +export type FileAggregationsArgs = { + aggregations_filter_themselves?: InputMaybe; + filters?: InputMaybe; + include_missing?: InputMaybe; +}; + +export type FileExtendedArgs = { + fields?: InputMaybe>>; +}; + +export type FileHitsArgs = { + after?: InputMaybe; + before?: InputMaybe; + filters?: InputMaybe; + first?: InputMaybe; + last?: InputMaybe; + offset?: InputMaybe; + score?: InputMaybe; + searchAfter?: InputMaybe; + sort?: InputMaybe>>; + trackTotalHits?: InputMaybe; +}; + +export type FileAggregations = { + __typename?: 'fileAggregations'; + analysis__analysis_id?: Maybe; + analysis__analysis_state?: Maybe; + analysis__analysis_type?: Maybe; + analysis__analysis_version?: Maybe; + analysis__experiment__experimental_strategy?: Maybe; + analysis__experiment__platform?: Maybe; + analysis__first_published_at?: Maybe; + analysis__published_at?: Maybe; + analysis__updated_at?: Maybe; + analysis__variant_class?: Maybe; + analysis__workflow__workflow_name?: Maybe; + analysis__workflow__workflow_version?: Maybe; + analysis_tools?: Maybe; + clinical__donor__age_at_menarche?: Maybe; + clinical__donor__bmi?: Maybe; + clinical__donor__cause_of_death?: Maybe; + clinical__donor__donor_id?: Maybe; + clinical__donor__height?: Maybe; + clinical__donor__menopause_status?: Maybe; + clinical__donor__number_of_children?: Maybe; + clinical__donor__number_of_pregnancies?: Maybe; + clinical__donor__primary_site?: Maybe; + clinical__donor__submitter_donor_id?: Maybe; + clinical__donor__survival_time?: Maybe; + clinical__donor__vital_status?: Maybe; + clinical__donor__weight?: Maybe; + clinical__follow_ups__anatomic_site_progression_or_recurrences?: Maybe; + clinical__follow_ups__disease_status_at_followup?: Maybe; + clinical__follow_ups__follow_up_id?: Maybe; + clinical__follow_ups__interval_of_followup?: Maybe; + clinical__follow_ups__is_primary_treatment?: Maybe; + clinical__follow_ups__method_of_progression_status?: Maybe; + clinical__follow_ups__posttherapy_m_category?: Maybe; + clinical__follow_ups__posttherapy_n_category?: Maybe; + clinical__follow_ups__posttherapy_stage_group?: Maybe; + clinical__follow_ups__posttherapy_t_category?: Maybe; + clinical__follow_ups__posttherapy_tumour_staging_system?: Maybe; + clinical__follow_ups__primary_diagnosis_id?: Maybe; + clinical__follow_ups__recurrence_m_category?: Maybe; + clinical__follow_ups__recurrence_n_category?: Maybe; + clinical__follow_ups__recurrence_stage_group?: Maybe; + clinical__follow_ups__recurrence_t_category?: Maybe; + clinical__follow_ups__recurrence_tumour_staging_system?: Maybe; + clinical__follow_ups__relapse_interval?: Maybe; + clinical__follow_ups__relapse_type?: Maybe; + clinical__follow_ups__submitter_follow_up_id?: Maybe; + clinical__follow_ups__submitter_primary_diagnosis_id?: Maybe; + clinical__follow_ups__submitter_treatment_id?: Maybe; + clinical__follow_ups__treatment_id?: Maybe; + clinical__follow_ups__treatment_type?: Maybe; + clinical__follow_ups__weight_at_followup?: Maybe; + clinical__primary_diagnosis__age_at_diagnosis?: Maybe; + clinical__primary_diagnosis__basis_of_diagnosis?: Maybe; + clinical__primary_diagnosis__cancer_type_additional_information?: Maybe; + clinical__primary_diagnosis__cancer_type_code?: Maybe; + clinical__primary_diagnosis__clinical_m_category?: Maybe; + clinical__primary_diagnosis__clinical_n_category?: Maybe; + clinical__primary_diagnosis__clinical_stage_group?: Maybe; + clinical__primary_diagnosis__clinical_t_category?: Maybe; + clinical__primary_diagnosis__clinical_tumour_staging_system?: Maybe; + clinical__primary_diagnosis__number_lymph_nodes_examined?: Maybe; + clinical__primary_diagnosis__number_lymph_nodes_positive?: Maybe; + clinical__primary_diagnosis__performance_status?: Maybe; + clinical__primary_diagnosis__presenting_symptoms?: Maybe; + clinical__primary_diagnosis__primary_diagnosis_id?: Maybe; + clinical__primary_diagnosis__submitter_primary_diagnosis_id?: Maybe; + clinical__specimens__pathological_m_category?: Maybe; + clinical__specimens__pathological_n_category?: Maybe; + clinical__specimens__pathological_stage_group?: Maybe; + clinical__specimens__pathological_t_category?: Maybe; + clinical__specimens__pathological_tumour_staging_system?: Maybe; + clinical__specimens__percent_inflammatory_tissue?: Maybe; + clinical__specimens__percent_necrosis?: Maybe; + clinical__specimens__percent_proliferating_cells?: Maybe; + clinical__specimens__percent_stromal_cells?: Maybe; + clinical__specimens__percent_tumour_cells?: Maybe; + clinical__specimens__primary_diagnosis_id?: Maybe; + clinical__specimens__reference_pathology_confirmed?: Maybe; + clinical__specimens__specimen_acquisition_interval?: Maybe; + clinical__specimens__specimen_anatomic_location?: Maybe; + clinical__specimens__specimen_id?: Maybe; + clinical__specimens__specimen_processing?: Maybe; + clinical__specimens__specimen_storage?: Maybe; + clinical__specimens__submitter_primary_diagnosis_id?: Maybe; + clinical__specimens__submitter_specimen_id?: Maybe; + clinical__specimens__tumour_grade?: Maybe; + clinical__specimens__tumour_grading_system?: Maybe; + clinical__specimens__tumour_histological_type?: Maybe; + clinical__treatments__adverse_events?: Maybe; + clinical__treatments__anatomical_site_irradiated?: Maybe; + clinical__treatments__chemotherapy_dosage_units?: Maybe; + clinical__treatments__clinical_trial_number?: Maybe; + clinical__treatments__clinical_trials_database?: Maybe; + clinical__treatments__cumulative_drug_dosage?: Maybe; + clinical__treatments__days_per_cycle?: Maybe; + clinical__treatments__drug_name?: Maybe; + clinical__treatments__drug_rxnormcui?: Maybe; + clinical__treatments__hemotological_toxicity?: Maybe; + clinical__treatments__hormone_drug_dosage_units?: Maybe; + clinical__treatments__is_primary_treatment?: Maybe; + clinical__treatments__line_of_treatment?: Maybe; + clinical__treatments__number_of_cycles?: Maybe; + clinical__treatments__outcome_of_treatment?: Maybe; + clinical__treatments__primary_diagnosis_id?: Maybe; + clinical__treatments__radiation_therapy_dosage?: Maybe; + clinical__treatments__radiation_therapy_fractions?: Maybe; + clinical__treatments__radiation_therapy_modality?: Maybe; + clinical__treatments__radiation_therapy_type?: Maybe; + clinical__treatments__response_to_treatment?: Maybe; + clinical__treatments__submitter_primary_diagnosis_id?: Maybe; + clinical__treatments__submitter_treatment_id?: Maybe; + clinical__treatments__toxicity_type?: Maybe; + clinical__treatments__treatment_duration?: Maybe; + clinical__treatments__treatment_id?: Maybe; + clinical__treatments__treatment_intent?: Maybe; + clinical__treatments__treatment_setting?: Maybe; + clinical__treatments__treatment_start_interval?: Maybe; + clinical__treatments__treatment_type?: Maybe; + data_category?: Maybe; + data_type?: Maybe; + donors__donor_id?: Maybe; + donors__gender?: Maybe; + donors__specimens__samples__matched_normal_submitter_sample_id?: Maybe; + donors__specimens__samples__sample_id?: Maybe; + donors__specimens__samples__sample_type?: Maybe; + donors__specimens__samples__submitter_sample_id?: Maybe; + donors__specimens__specimen_id?: Maybe; + donors__specimens__specimen_tissue_source?: Maybe; + donors__specimens__specimen_type?: Maybe; + donors__specimens__submitter_specimen_id?: Maybe; + donors__specimens__tumour_normal_designation?: Maybe; + donors__submitter_donor_id?: Maybe; + embargo_stage?: Maybe; + file__index_file__file_type?: Maybe; + file__index_file__md5sum?: Maybe; + file__index_file__name?: Maybe; + file__index_file__object_id?: Maybe; + file__index_file__size?: Maybe; + file__md5sum?: Maybe; + file__name?: Maybe; + file__size?: Maybe; + file_access?: Maybe; + file_autocomplete?: Maybe; + file_id?: Maybe; + file_number?: Maybe; + file_type?: Maybe; + meta__embargo_stage?: Maybe; + meta__release_state?: Maybe; + meta__study_id?: Maybe; + metrics__average_insert_size?: Maybe; + metrics__average_length?: Maybe; + metrics__duplicated_bases?: Maybe; + metrics__error_rate?: Maybe; + metrics__mapped_bases_cigar?: Maybe; + metrics__mapped_reads?: Maybe; + metrics__mismatch_bases?: Maybe; + metrics__paired_reads?: Maybe; + metrics__pairs_on_different_chromosomes?: Maybe; + metrics__properly_paired_reads?: Maybe; + metrics__total_bases?: Maybe; + metrics__total_reads?: Maybe; + object_id?: Maybe; + program_access_date?: Maybe; + release_state?: Maybe; + repositories__code?: Maybe; + repositories__country?: Maybe; + repositories__name?: Maybe; + repositories__organization?: Maybe; + repositories__url?: Maybe; + study_id?: Maybe; +}; + +export type FileAnalysis = { + __typename?: 'fileAnalysis'; + analysis_id?: Maybe; + analysis_state?: Maybe; + analysis_type?: Maybe; + analysis_version?: Maybe; + experiment?: Maybe; + first_published_at?: Maybe; + published_at?: Maybe; + updated_at?: Maybe; + variant_class?: Maybe; + workflow?: Maybe; +}; + +export type FileAnalysisExperiment = { + __typename?: 'fileAnalysisExperiment'; + experimental_strategy?: Maybe; + platform?: Maybe; +}; + +export type FileAnalysisWorkflow = { + __typename?: 'fileAnalysisWorkflow'; + workflow_name?: Maybe; + workflow_version?: Maybe; +}; + +export type FileClinical = { + __typename?: 'fileClinical'; + donor?: Maybe; + follow_ups?: Maybe; + primary_diagnosis?: Maybe; + specimens?: Maybe; + treatments?: Maybe; +}; + +export type FileClinicalDonor = { + __typename?: 'fileClinicalDonor'; + age_at_menarche?: Maybe; + bmi?: Maybe; + cause_of_death?: Maybe; + donor_id?: Maybe; + height?: Maybe; + menopause_status?: Maybe; + number_of_children?: Maybe; + number_of_pregnancies?: Maybe; + primary_site?: Maybe; + submitter_donor_id?: Maybe; + survival_time?: Maybe; + vital_status?: Maybe; + weight?: Maybe; +}; + +export type FileClinicalFollow_Ups = { + __typename?: 'fileClinicalFollow_ups'; + aggregations?: Maybe; + aggsState?: Maybe; + columnsState?: Maybe; + extended?: Maybe; + hits?: Maybe; + mapping?: Maybe; + matchBoxState?: Maybe; +}; + +export type FileClinicalFollow_UpsAggregationsArgs = { + aggregations_filter_themselves?: InputMaybe; + filters?: InputMaybe; + include_missing?: InputMaybe; +}; + +export type FileClinicalFollow_UpsExtendedArgs = { + fields?: InputMaybe>>; +}; + +export type FileClinicalFollow_UpsHitsArgs = { + after?: InputMaybe; + before?: InputMaybe; + filters?: InputMaybe; + first?: InputMaybe; + last?: InputMaybe; + offset?: InputMaybe; + score?: InputMaybe; + searchAfter?: InputMaybe; + sort?: InputMaybe>>; + trackTotalHits?: InputMaybe; +}; + +export type FileClinicalFollow_UpsAggregations = { + __typename?: 'fileClinicalFollow_upsAggregations'; + anatomic_site_progression_or_recurrences?: Maybe; + disease_status_at_followup?: Maybe; + follow_up_id?: Maybe; + interval_of_followup?: Maybe; + is_primary_treatment?: Maybe; + method_of_progression_status?: Maybe; + posttherapy_m_category?: Maybe; + posttherapy_n_category?: Maybe; + posttherapy_stage_group?: Maybe; + posttherapy_t_category?: Maybe; + posttherapy_tumour_staging_system?: Maybe; + primary_diagnosis_id?: Maybe; + recurrence_m_category?: Maybe; + recurrence_n_category?: Maybe; + recurrence_stage_group?: Maybe; + recurrence_t_category?: Maybe; + recurrence_tumour_staging_system?: Maybe; + relapse_interval?: Maybe; + relapse_type?: Maybe; + submitter_follow_up_id?: Maybe; + submitter_primary_diagnosis_id?: Maybe; + submitter_treatment_id?: Maybe; + treatment_id?: Maybe; + treatment_type?: Maybe; + weight_at_followup?: Maybe; +}; + +export type FileClinicalFollow_UpsConnection = { + __typename?: 'fileClinicalFollow_upsConnection'; + edges?: Maybe>>; + total: Scalars['Int']['output']; +}; + +export type FileClinicalFollow_UpsEdge = { + __typename?: 'fileClinicalFollow_upsEdge'; + node?: Maybe; + searchAfter?: Maybe; +}; + +export type FileClinicalFollow_UpsNode = Node & { + __typename?: 'fileClinicalFollow_upsNode'; + anatomic_site_progression_or_recurrences?: Maybe; + disease_status_at_followup?: Maybe; + follow_up_id?: Maybe; + id: Scalars['ID']['output']; + interval_of_followup?: Maybe; + is_primary_treatment?: Maybe; + method_of_progression_status?: Maybe; + posttherapy_m_category?: Maybe; + posttherapy_n_category?: Maybe; + posttherapy_stage_group?: Maybe; + posttherapy_t_category?: Maybe; + posttherapy_tumour_staging_system?: Maybe; + primary_diagnosis_id?: Maybe; + recurrence_m_category?: Maybe; + recurrence_n_category?: Maybe; + recurrence_stage_group?: Maybe; + recurrence_t_category?: Maybe; + recurrence_tumour_staging_system?: Maybe; + relapse_interval?: Maybe; + relapse_type?: Maybe; + score?: Maybe; + submitter_follow_up_id?: Maybe; + submitter_primary_diagnosis_id?: Maybe; + submitter_treatment_id?: Maybe; + treatment_id?: Maybe; + treatment_type?: Maybe; + weight_at_followup?: Maybe; +}; + +export type FileClinicalPrimary_Diagnosis = { + __typename?: 'fileClinicalPrimary_diagnosis'; + aggregations?: Maybe; + aggsState?: Maybe; + columnsState?: Maybe; + extended?: Maybe; + hits?: Maybe; + mapping?: Maybe; + matchBoxState?: Maybe; +}; + +export type FileClinicalPrimary_DiagnosisAggregationsArgs = { + aggregations_filter_themselves?: InputMaybe; + filters?: InputMaybe; + include_missing?: InputMaybe; +}; + +export type FileClinicalPrimary_DiagnosisExtendedArgs = { + fields?: InputMaybe>>; +}; + +export type FileClinicalPrimary_DiagnosisHitsArgs = { + after?: InputMaybe; + before?: InputMaybe; + filters?: InputMaybe; + first?: InputMaybe; + last?: InputMaybe; + offset?: InputMaybe; + score?: InputMaybe; + searchAfter?: InputMaybe; + sort?: InputMaybe>>; + trackTotalHits?: InputMaybe; +}; + +export type FileClinicalPrimary_DiagnosisAggregations = { + __typename?: 'fileClinicalPrimary_diagnosisAggregations'; + age_at_diagnosis?: Maybe; + basis_of_diagnosis?: Maybe; + cancer_type_additional_information?: Maybe; + cancer_type_code?: Maybe; + clinical_m_category?: Maybe; + clinical_n_category?: Maybe; + clinical_stage_group?: Maybe; + clinical_t_category?: Maybe; + clinical_tumour_staging_system?: Maybe; + number_lymph_nodes_examined?: Maybe; + number_lymph_nodes_positive?: Maybe; + performance_status?: Maybe; + presenting_symptoms?: Maybe; + primary_diagnosis_id?: Maybe; + submitter_primary_diagnosis_id?: Maybe; +}; + +export type FileClinicalPrimary_DiagnosisConnection = { + __typename?: 'fileClinicalPrimary_diagnosisConnection'; + edges?: Maybe>>; + total: Scalars['Int']['output']; +}; + +export type FileClinicalPrimary_DiagnosisEdge = { + __typename?: 'fileClinicalPrimary_diagnosisEdge'; + node?: Maybe; + searchAfter?: Maybe; +}; + +export type FileClinicalPrimary_DiagnosisNode = Node & { + __typename?: 'fileClinicalPrimary_diagnosisNode'; + age_at_diagnosis?: Maybe; + basis_of_diagnosis?: Maybe; + cancer_type_additional_information?: Maybe; + cancer_type_code?: Maybe; + clinical_m_category?: Maybe; + clinical_n_category?: Maybe; + clinical_stage_group?: Maybe; + clinical_t_category?: Maybe; + clinical_tumour_staging_system?: Maybe; + id: Scalars['ID']['output']; + number_lymph_nodes_examined?: Maybe; + number_lymph_nodes_positive?: Maybe; + performance_status?: Maybe; + presenting_symptoms?: Maybe; + primary_diagnosis_id?: Maybe; + score?: Maybe; + submitter_primary_diagnosis_id?: Maybe; +}; + +export type FileClinicalSpecimens = { + __typename?: 'fileClinicalSpecimens'; + aggregations?: Maybe; + aggsState?: Maybe; + columnsState?: Maybe; + extended?: Maybe; + hits?: Maybe; + mapping?: Maybe; + matchBoxState?: Maybe; +}; + +export type FileClinicalSpecimensAggregationsArgs = { + aggregations_filter_themselves?: InputMaybe; + filters?: InputMaybe; + include_missing?: InputMaybe; +}; + +export type FileClinicalSpecimensExtendedArgs = { + fields?: InputMaybe>>; +}; + +export type FileClinicalSpecimensHitsArgs = { + after?: InputMaybe; + before?: InputMaybe; + filters?: InputMaybe; + first?: InputMaybe; + last?: InputMaybe; + offset?: InputMaybe; + score?: InputMaybe; + searchAfter?: InputMaybe; + sort?: InputMaybe>>; + trackTotalHits?: InputMaybe; +}; + +export type FileClinicalSpecimensAggregations = { + __typename?: 'fileClinicalSpecimensAggregations'; + pathological_m_category?: Maybe; + pathological_n_category?: Maybe; + pathological_stage_group?: Maybe; + pathological_t_category?: Maybe; + pathological_tumour_staging_system?: Maybe; + percent_inflammatory_tissue?: Maybe; + percent_necrosis?: Maybe; + percent_proliferating_cells?: Maybe; + percent_stromal_cells?: Maybe; + percent_tumour_cells?: Maybe; + primary_diagnosis_id?: Maybe; + reference_pathology_confirmed?: Maybe; + specimen_acquisition_interval?: Maybe; + specimen_anatomic_location?: Maybe; + specimen_id?: Maybe; + specimen_processing?: Maybe; + specimen_storage?: Maybe; + submitter_primary_diagnosis_id?: Maybe; + submitter_specimen_id?: Maybe; + tumour_grade?: Maybe; + tumour_grading_system?: Maybe; + tumour_histological_type?: Maybe; +}; + +export type FileClinicalSpecimensConnection = { + __typename?: 'fileClinicalSpecimensConnection'; + edges?: Maybe>>; + total: Scalars['Int']['output']; +}; + +export type FileClinicalSpecimensEdge = { + __typename?: 'fileClinicalSpecimensEdge'; + node?: Maybe; + searchAfter?: Maybe; +}; + +export type FileClinicalSpecimensNode = Node & { + __typename?: 'fileClinicalSpecimensNode'; + id: Scalars['ID']['output']; + pathological_m_category?: Maybe; + pathological_n_category?: Maybe; + pathological_stage_group?: Maybe; + pathological_t_category?: Maybe; + pathological_tumour_staging_system?: Maybe; + percent_inflammatory_tissue?: Maybe; + percent_necrosis?: Maybe; + percent_proliferating_cells?: Maybe; + percent_stromal_cells?: Maybe; + percent_tumour_cells?: Maybe; + primary_diagnosis_id?: Maybe; + reference_pathology_confirmed?: Maybe; + score?: Maybe; + specimen_acquisition_interval?: Maybe; + specimen_anatomic_location?: Maybe; + specimen_id?: Maybe; + specimen_processing?: Maybe; + specimen_storage?: Maybe; + submitter_primary_diagnosis_id?: Maybe; + submitter_specimen_id?: Maybe; + tumour_grade?: Maybe; + tumour_grading_system?: Maybe; + tumour_histological_type?: Maybe; +}; + +export type FileClinicalTreatments = { + __typename?: 'fileClinicalTreatments'; + aggregations?: Maybe; + aggsState?: Maybe; + columnsState?: Maybe; + extended?: Maybe; + hits?: Maybe; + mapping?: Maybe; + matchBoxState?: Maybe; +}; + +export type FileClinicalTreatmentsAggregationsArgs = { + aggregations_filter_themselves?: InputMaybe; + filters?: InputMaybe; + include_missing?: InputMaybe; +}; + +export type FileClinicalTreatmentsExtendedArgs = { + fields?: InputMaybe>>; +}; + +export type FileClinicalTreatmentsHitsArgs = { + after?: InputMaybe; + before?: InputMaybe; + filters?: InputMaybe; + first?: InputMaybe; + last?: InputMaybe; + offset?: InputMaybe; + score?: InputMaybe; + searchAfter?: InputMaybe; + sort?: InputMaybe>>; + trackTotalHits?: InputMaybe; +}; + +export type FileClinicalTreatmentsAggregations = { + __typename?: 'fileClinicalTreatmentsAggregations'; + adverse_events?: Maybe; + anatomical_site_irradiated?: Maybe; + chemotherapy_dosage_units?: Maybe; + clinical_trial_number?: Maybe; + clinical_trials_database?: Maybe; + cumulative_drug_dosage?: Maybe; + days_per_cycle?: Maybe; + drug_name?: Maybe; + drug_rxnormcui?: Maybe; + hemotological_toxicity?: Maybe; + hormone_drug_dosage_units?: Maybe; + is_primary_treatment?: Maybe; + line_of_treatment?: Maybe; + number_of_cycles?: Maybe; + outcome_of_treatment?: Maybe; + primary_diagnosis_id?: Maybe; + radiation_therapy_dosage?: Maybe; + radiation_therapy_fractions?: Maybe; + radiation_therapy_modality?: Maybe; + radiation_therapy_type?: Maybe; + response_to_treatment?: Maybe; + submitter_primary_diagnosis_id?: Maybe; + submitter_treatment_id?: Maybe; + toxicity_type?: Maybe; + treatment_duration?: Maybe; + treatment_id?: Maybe; + treatment_intent?: Maybe; + treatment_setting?: Maybe; + treatment_start_interval?: Maybe; + treatment_type?: Maybe; +}; + +export type FileClinicalTreatmentsConnection = { + __typename?: 'fileClinicalTreatmentsConnection'; + edges?: Maybe>>; + total: Scalars['Int']['output']; +}; + +export type FileClinicalTreatmentsEdge = { + __typename?: 'fileClinicalTreatmentsEdge'; + node?: Maybe; + searchAfter?: Maybe; +}; + +export type FileClinicalTreatmentsNode = Node & { + __typename?: 'fileClinicalTreatmentsNode'; + adverse_events?: Maybe; + anatomical_site_irradiated?: Maybe; + chemotherapy_dosage_units?: Maybe; + clinical_trial_number?: Maybe; + clinical_trials_database?: Maybe; + cumulative_drug_dosage?: Maybe; + days_per_cycle?: Maybe; + drug_name?: Maybe; + drug_rxnormcui?: Maybe; + hemotological_toxicity?: Maybe; + hormone_drug_dosage_units?: Maybe; + id: Scalars['ID']['output']; + is_primary_treatment?: Maybe; + line_of_treatment?: Maybe; + number_of_cycles?: Maybe; + outcome_of_treatment?: Maybe; + primary_diagnosis_id?: Maybe; + radiation_therapy_dosage?: Maybe; + radiation_therapy_fractions?: Maybe; + radiation_therapy_modality?: Maybe; + radiation_therapy_type?: Maybe; + response_to_treatment?: Maybe; + score?: Maybe; + submitter_primary_diagnosis_id?: Maybe; + submitter_treatment_id?: Maybe; + toxicity_type?: Maybe; + treatment_duration?: Maybe; + treatment_id?: Maybe; + treatment_intent?: Maybe; + treatment_setting?: Maybe; + treatment_start_interval?: Maybe; + treatment_type?: Maybe; +}; + +export type FileConnection = { + __typename?: 'fileConnection'; + edges?: Maybe>>; + total: Scalars['Int']['output']; +}; + +export type FileDonors = { + __typename?: 'fileDonors'; + aggregations?: Maybe; + aggsState?: Maybe; + columnsState?: Maybe; + extended?: Maybe; + hits?: Maybe; + mapping?: Maybe; + matchBoxState?: Maybe; +}; + +export type FileDonorsAggregationsArgs = { + aggregations_filter_themselves?: InputMaybe; + filters?: InputMaybe; + include_missing?: InputMaybe; +}; + +export type FileDonorsExtendedArgs = { + fields?: InputMaybe>>; +}; + +export type FileDonorsHitsArgs = { + after?: InputMaybe; + before?: InputMaybe; + filters?: InputMaybe; + first?: InputMaybe; + last?: InputMaybe; + offset?: InputMaybe; + score?: InputMaybe; + searchAfter?: InputMaybe; + sort?: InputMaybe>>; + trackTotalHits?: InputMaybe; +}; + +export type FileDonorsAggregations = { + __typename?: 'fileDonorsAggregations'; + donor_id?: Maybe; + gender?: Maybe; + specimens__samples__matched_normal_submitter_sample_id?: Maybe; + specimens__samples__sample_id?: Maybe; + specimens__samples__sample_type?: Maybe; + specimens__samples__submitter_sample_id?: Maybe; + specimens__specimen_id?: Maybe; + specimens__specimen_tissue_source?: Maybe; + specimens__specimen_type?: Maybe; + specimens__submitter_specimen_id?: Maybe; + specimens__tumour_normal_designation?: Maybe; + submitter_donor_id?: Maybe; +}; + +export type FileDonorsConnection = { + __typename?: 'fileDonorsConnection'; + edges?: Maybe>>; + total: Scalars['Int']['output']; +}; + +export type FileDonorsEdge = { + __typename?: 'fileDonorsEdge'; + node?: Maybe; + searchAfter?: Maybe; +}; + +export type FileDonorsNode = Node & { + __typename?: 'fileDonorsNode'; + donor_id?: Maybe; + gender?: Maybe; + id: Scalars['ID']['output']; + score?: Maybe; + specimens?: Maybe; + submitter_donor_id?: Maybe; +}; + +export type FileDonorsSpecimens = { + __typename?: 'fileDonorsSpecimens'; + aggregations?: Maybe; + aggsState?: Maybe; + columnsState?: Maybe; + extended?: Maybe; + hits?: Maybe; + mapping?: Maybe; + matchBoxState?: Maybe; +}; + +export type FileDonorsSpecimensAggregationsArgs = { + aggregations_filter_themselves?: InputMaybe; + filters?: InputMaybe; + include_missing?: InputMaybe; +}; + +export type FileDonorsSpecimensExtendedArgs = { + fields?: InputMaybe>>; +}; + +export type FileDonorsSpecimensHitsArgs = { + after?: InputMaybe; + before?: InputMaybe; + filters?: InputMaybe; + first?: InputMaybe; + last?: InputMaybe; + offset?: InputMaybe; + score?: InputMaybe; + searchAfter?: InputMaybe; + sort?: InputMaybe>>; + trackTotalHits?: InputMaybe; +}; + +export type FileDonorsSpecimensAggregations = { + __typename?: 'fileDonorsSpecimensAggregations'; + samples__matched_normal_submitter_sample_id?: Maybe; + samples__sample_id?: Maybe; + samples__sample_type?: Maybe; + samples__submitter_sample_id?: Maybe; + specimen_id?: Maybe; + specimen_tissue_source?: Maybe; + specimen_type?: Maybe; + submitter_specimen_id?: Maybe; + tumour_normal_designation?: Maybe; +}; + +export type FileDonorsSpecimensConnection = { + __typename?: 'fileDonorsSpecimensConnection'; + edges?: Maybe>>; + total: Scalars['Int']['output']; +}; + +export type FileDonorsSpecimensEdge = { + __typename?: 'fileDonorsSpecimensEdge'; + node?: Maybe; + searchAfter?: Maybe; +}; + +export type FileDonorsSpecimensNode = Node & { + __typename?: 'fileDonorsSpecimensNode'; + id: Scalars['ID']['output']; + samples?: Maybe; + score?: Maybe; + specimen_id?: Maybe; + specimen_tissue_source?: Maybe; + specimen_type?: Maybe; + submitter_specimen_id?: Maybe; + tumour_normal_designation?: Maybe; +}; + +export type FileDonorsSpecimensSamples = { + __typename?: 'fileDonorsSpecimensSamples'; + aggregations?: Maybe; + aggsState?: Maybe; + columnsState?: Maybe; + extended?: Maybe; + hits?: Maybe; + mapping?: Maybe; + matchBoxState?: Maybe; +}; + +export type FileDonorsSpecimensSamplesAggregationsArgs = { + aggregations_filter_themselves?: InputMaybe; + filters?: InputMaybe; + include_missing?: InputMaybe; +}; + +export type FileDonorsSpecimensSamplesExtendedArgs = { + fields?: InputMaybe>>; +}; + +export type FileDonorsSpecimensSamplesHitsArgs = { + after?: InputMaybe; + before?: InputMaybe; + filters?: InputMaybe; + first?: InputMaybe; + last?: InputMaybe; + offset?: InputMaybe; + score?: InputMaybe; + searchAfter?: InputMaybe; + sort?: InputMaybe>>; + trackTotalHits?: InputMaybe; +}; + +export type FileDonorsSpecimensSamplesAggregations = { + __typename?: 'fileDonorsSpecimensSamplesAggregations'; + matched_normal_submitter_sample_id?: Maybe; + sample_id?: Maybe; + sample_type?: Maybe; + submitter_sample_id?: Maybe; +}; + +export type FileDonorsSpecimensSamplesConnection = { + __typename?: 'fileDonorsSpecimensSamplesConnection'; + edges?: Maybe>>; + total: Scalars['Int']['output']; +}; + +export type FileDonorsSpecimensSamplesEdge = { + __typename?: 'fileDonorsSpecimensSamplesEdge'; + node?: Maybe; + searchAfter?: Maybe; +}; + +export type FileDonorsSpecimensSamplesNode = Node & { + __typename?: 'fileDonorsSpecimensSamplesNode'; + id: Scalars['ID']['output']; + matched_normal_submitter_sample_id?: Maybe; + sample_id?: Maybe; + sample_type?: Maybe; + score?: Maybe; + submitter_sample_id?: Maybe; +}; + +export type FileEdge = { + __typename?: 'fileEdge'; + node?: Maybe; + searchAfter?: Maybe; +}; + +export type FileFile = { + __typename?: 'fileFile'; + index_file?: Maybe; + md5sum?: Maybe; + name?: Maybe; + size?: Maybe; +}; + +export type FileFileIndex_File = { + __typename?: 'fileFileIndex_file'; + file_type?: Maybe; + md5sum?: Maybe; + name?: Maybe; + object_id?: Maybe; + size?: Maybe; +}; + +export type FileMeta = { + __typename?: 'fileMeta'; + embargo_stage?: Maybe; + release_state?: Maybe; + study_id?: Maybe; +}; + +export type FileMetrics = { + __typename?: 'fileMetrics'; + average_insert_size?: Maybe; + average_length?: Maybe; + duplicated_bases?: Maybe; + error_rate?: Maybe; + mapped_bases_cigar?: Maybe; + mapped_reads?: Maybe; + mismatch_bases?: Maybe; + paired_reads?: Maybe; + pairs_on_different_chromosomes?: Maybe; + properly_paired_reads?: Maybe; + total_bases?: Maybe; + total_reads?: Maybe; +}; + +export type FileNode = Node & { + __typename?: 'fileNode'; + analysis?: Maybe; + analysis_tools?: Maybe>>; + clinical?: Maybe; + data_category?: Maybe; + data_type?: Maybe; + donors?: Maybe; + embargo_stage?: Maybe; + file?: Maybe; + file_access?: Maybe; + file_autocomplete?: Maybe>>; + file_id?: Maybe; + file_number?: Maybe; + file_type?: Maybe; + id: Scalars['ID']['output']; + meta?: Maybe; + metrics?: Maybe; + object_id?: Maybe; + program_access_date?: Maybe; + release_state?: Maybe; + repositories?: Maybe; + score?: Maybe; + study_id?: Maybe; +}; + +export type FileRepositories = { + __typename?: 'fileRepositories'; + aggregations?: Maybe; + aggsState?: Maybe; + columnsState?: Maybe; + extended?: Maybe; + hits?: Maybe; + mapping?: Maybe; + matchBoxState?: Maybe; +}; + +export type FileRepositoriesAggregationsArgs = { + aggregations_filter_themselves?: InputMaybe; + filters?: InputMaybe; + include_missing?: InputMaybe; +}; + +export type FileRepositoriesExtendedArgs = { + fields?: InputMaybe>>; +}; + +export type FileRepositoriesHitsArgs = { + after?: InputMaybe; + before?: InputMaybe; + filters?: InputMaybe; + first?: InputMaybe; + last?: InputMaybe; + offset?: InputMaybe; + score?: InputMaybe; + searchAfter?: InputMaybe; + sort?: InputMaybe>>; + trackTotalHits?: InputMaybe; +}; + +export type FileRepositoriesAggregations = { + __typename?: 'fileRepositoriesAggregations'; + code?: Maybe; + country?: Maybe; + name?: Maybe; + organization?: Maybe; + url?: Maybe; +}; + +export type FileRepositoriesConnection = { + __typename?: 'fileRepositoriesConnection'; + edges?: Maybe>>; + total: Scalars['Int']['output']; +}; + +export type FileRepositoriesEdge = { + __typename?: 'fileRepositoriesEdge'; + node?: Maybe; + searchAfter?: Maybe; +}; + +export type FileRepositoriesNode = Node & { + __typename?: 'fileRepositoriesNode'; + code?: Maybe; + country?: Maybe; + id: Scalars['ID']['output']; + name?: Maybe; + organization?: Maybe; + score?: Maybe; + url?: Maybe; +}; + +export type Sets = { + __typename?: 'sets'; + aggregations?: Maybe; + extended?: Maybe; + hits?: Maybe; + mapping?: Maybe; +}; + +export type SetsAggregationsArgs = { + aggregations_filter_themselves?: InputMaybe; + filters?: InputMaybe; + include_missing?: InputMaybe; +}; + +export type SetsExtendedArgs = { + fields?: InputMaybe>>; +}; + +export type SetsHitsArgs = { + after?: InputMaybe; + before?: InputMaybe; + filters?: InputMaybe; + first?: InputMaybe; + last?: InputMaybe; + offset?: InputMaybe; + score?: InputMaybe; + searchAfter?: InputMaybe; + sort?: InputMaybe>>; + trackTotalHits?: InputMaybe; +}; + +export type SetsAggregations = { + __typename?: 'setsAggregations'; + createdAt?: Maybe; + ids?: Maybe; + path?: Maybe; + setId?: Maybe; + size?: Maybe; + sqon?: Maybe; + type?: Maybe; + userId?: Maybe; +}; + +export type SetsConnection = { + __typename?: 'setsConnection'; + edges?: Maybe>>; + total: Scalars['Int']['output']; +}; + +export type SetsEdge = { + __typename?: 'setsEdge'; + node?: Maybe; + searchAfter?: Maybe; +}; + +export type SetsNode = Node & { + __typename?: 'setsNode'; + createdAt?: Maybe; + id: Scalars['ID']['output']; + ids?: Maybe>>; + path?: Maybe; + score?: Maybe; + setId?: Maybe; + size?: Maybe; + sqon?: Maybe; + type?: Maybe; + userId?: Maybe; +}; + +export type ProgramsListQueryVariables = Exact<{ [key: string]: never }>; + +export type ProgramsListQuery = { + __typename?: 'Query'; + programs?: Array<{ + __typename?: 'Program'; + shortName: string; + name?: string | null; + cancerTypes?: Array | null; + countries?: Array | null; + membershipType?: MembershipType | null; + genomicDonors?: number | null; + submittedDonors?: number | null; + commitmentDonors?: number | null; + users?: Array<{ + __typename?: 'ProgramUser'; + email: string; + firstName: string; + lastName: string; + role: UserRole; + } | null> | null; + } | null> | null; +}; + +export type SideMenuQueryVariables = Exact<{ [key: string]: never }>; + +export type SideMenuQuery = { + __typename?: 'Query'; + programs?: Array<{ __typename?: 'Program'; shortName: string } | null> | null; +}; + +export const ProgramsListDocument = { + kind: 'Document', + definitions: [ + { + kind: 'OperationDefinition', + operation: 'query', + name: { kind: 'Name', value: 'ProgramsList' }, + selectionSet: { + kind: 'SelectionSet', + selections: [ + { + kind: 'Field', + name: { kind: 'Name', value: 'programs' }, + selectionSet: { + kind: 'SelectionSet', + selections: [ + { kind: 'Field', name: { kind: 'Name', value: 'shortName' } }, + { kind: 'Field', name: { kind: 'Name', value: 'name' } }, + { kind: 'Field', name: { kind: 'Name', value: 'cancerTypes' } }, + { kind: 'Field', name: { kind: 'Name', value: 'countries' } }, + { kind: 'Field', name: { kind: 'Name', value: 'membershipType' } }, + { kind: 'Field', name: { kind: 'Name', value: 'genomicDonors' } }, + { kind: 'Field', name: { kind: 'Name', value: 'submittedDonors' } }, + { kind: 'Field', name: { kind: 'Name', value: 'commitmentDonors' } }, + { + kind: 'Field', + name: { kind: 'Name', value: 'users' }, + selectionSet: { + kind: 'SelectionSet', + selections: [ + { kind: 'Field', name: { kind: 'Name', value: 'email' } }, + { kind: 'Field', name: { kind: 'Name', value: 'firstName' } }, + { kind: 'Field', name: { kind: 'Name', value: 'lastName' } }, + { kind: 'Field', name: { kind: 'Name', value: 'role' } }, + ], + }, + }, + ], + }, + }, + ], + }, + }, + ], +} as unknown as DocumentNode; +export const SideMenuDocument = { + kind: 'Document', + definitions: [ + { + kind: 'OperationDefinition', + operation: 'query', + name: { kind: 'Name', value: 'SideMenu' }, + selectionSet: { + kind: 'SelectionSet', + selections: [ + { + kind: 'Field', + name: { kind: 'Name', value: 'programs' }, + selectionSet: { + kind: 'SelectionSet', + selections: [{ kind: 'Field', name: { kind: 'Name', value: 'shortName' } }], + }, + }, + ], + }, + }, + ], +} as unknown as DocumentNode; diff --git a/src/__generated__/index.ts b/src/__generated__/index.ts new file mode 100644 index 00000000..c682b1e2 --- /dev/null +++ b/src/__generated__/index.ts @@ -0,0 +1,2 @@ +export * from './fragment-masking'; +export * from './gql'; diff --git a/src/app/(post-login)/submission/[shortName]/page.tsx b/src/app/(post-login)/submission/[shortName]/page.tsx index 68f2af1b..9b9e79b2 100644 --- a/src/app/(post-login)/submission/[shortName]/page.tsx +++ b/src/app/(post-login)/submission/[shortName]/page.tsx @@ -19,6 +19,6 @@ 'use client'; -export default function Program() { - return
Program
; +export default function Program({ params }: { params: { shortName: string } }) { + return
Program: {params.shortName}
; } diff --git a/src/app/(post-login)/submission/components/ProgramMenu.tsx b/src/app/(post-login)/submission/components/ProgramMenu.tsx index dff4c559..0828552b 100644 --- a/src/app/(post-login)/submission/components/ProgramMenu.tsx +++ b/src/app/(post-login)/submission/components/ProgramMenu.tsx @@ -18,22 +18,23 @@ */ 'use client'; +import Loader from '@/app/components/Loader'; +import { notNull } from '@/global/utils/types'; import { css } from '@/lib/emotion'; +import { useQuery } from '@apollo/client'; import { MenuItem } from '@icgc-argo/uikit'; import Link from 'next/link'; -import { usePathname } from 'next/navigation'; +import { notFound, usePathname } from 'next/navigation'; import { MouseEventHandler, useState } from 'react'; +import SIDEMENU_PROGRAMS from '../gql/SIDEMENU_PROGRAMS'; -export default function ProgramMenu({ - programs, - searchQuery, -}: { - programs: { shortName: string }[]; - searchQuery: string; -}) { - const pathname = usePathname(); +export default function ProgramMenu({ searchQuery }: { searchQuery: string }) { + const { data, loading, error } = useQuery(SIDEMENU_PROGRAMS); const [activeProgramIndex, setActiveProgramIndex] = useState(-1); + const pathname = usePathname(); + + const programs = data?.programs?.filter(notNull) || []; const filteredPrograms = !searchQuery.length ? programs : programs.filter(({ shortName }) => shortName.search(new RegExp(searchQuery, 'i')) > -1); @@ -43,6 +44,8 @@ export default function ProgramMenu({ () => setActiveProgramIndex(index); + if (loading) return ; + if (error) notFound(); return ( <> - {filteredPrograms.map((program, programIndex) => ( + {filteredPrograms.map(({ shortName }, programIndex) => ( - {program.shortName} + {shortName} ))} diff --git a/src/app/(post-login)/submission/components/SideMenu/Content.tsx b/src/app/(post-login)/submission/components/SideMenu/Content.tsx index 3525a078..20ef0ff1 100644 --- a/src/app/(post-login)/submission/components/SideMenu/Content.tsx +++ b/src/app/(post-login)/submission/components/SideMenu/Content.tsx @@ -23,14 +23,14 @@ import { useState } from 'react'; import ProgramMenu from '../ProgramMenu'; import Search from '../Search'; -const SideMenuContent = ({ content }: { content: any[] }) => { +const SideMenuContent = () => { const [programNameSearch, setProgramNameSearch] = useState(''); return ( } content={'My Programs'} selected> - + ); diff --git a/src/app/(post-login)/submission/components/SideMenu/Menu.tsx b/src/app/(post-login)/submission/components/SideMenu/Menu.tsx index f69feb09..9140c0a1 100644 --- a/src/app/(post-login)/submission/components/SideMenu/Menu.tsx +++ b/src/app/(post-login)/submission/components/SideMenu/Menu.tsx @@ -23,7 +23,7 @@ import SideMenuContent from './Content'; import SideMenuToggle, { TOGGLE_HEIGHT_PX } from './Toggle'; import { SideMenuProps } from './types'; -const SideMenu = ({ content, onToggle, isActive }: SideMenuProps) => { +const SideMenu = ({ onToggle, isActive }: SideMenuProps) => { const theme = useTheme(); return ( @@ -43,7 +43,7 @@ const SideMenu = ({ content, onToggle, isActive }: SideMenuProps) => { visibility: ${isActive ? 'visible' : 'hidden'}; `} > - + diff --git a/src/app/(post-login)/submission/components/SideMenu/types.ts b/src/app/(post-login)/submission/components/SideMenu/types.ts index f18bc823..4fcc8497 100644 --- a/src/app/(post-login)/submission/components/SideMenu/types.ts +++ b/src/app/(post-login)/submission/components/SideMenu/types.ts @@ -17,4 +17,4 @@ * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ -export type SideMenuProps = { content: any; onToggle: () => void; isActive: boolean }; +export type SideMenuProps = { onToggle: () => void; isActive: boolean }; diff --git a/src/app/(post-login)/submission/gql/PROGRAMS_LIST_QUERY.ts b/src/app/(post-login)/submission/gql/PROGRAMS_LIST_QUERY.ts new file mode 100644 index 00000000..3782ba98 --- /dev/null +++ b/src/app/(post-login)/submission/gql/PROGRAMS_LIST_QUERY.ts @@ -0,0 +1,43 @@ +/* + * Copyright (c) 2022 The Ontario Institute for Cancer Research. All rights reserved + * + * This program and the accompanying materials are made available under the terms of + * the GNU Affero General Public License v3.0. You should have received a copy of the + * GNU Affero General Public License along with this program. + * If not, see . + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY + * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT + * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, + * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED + * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; + * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER + * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN + * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +import { gql } from '@/__generated__/gql'; + +const PROGRAMS_LIST_QUERY = gql(` + query ProgramsList { + programs { + shortName + name + cancerTypes + countries + membershipType + genomicDonors + submittedDonors + commitmentDonors + users { + email + firstName + lastName + role + } + } + } +`); + +export default PROGRAMS_LIST_QUERY; diff --git a/src/app/(post-login)/submission/gql/SIDEMENU_PROGRAMS.ts b/src/app/(post-login)/submission/gql/SIDEMENU_PROGRAMS.ts new file mode 100644 index 00000000..e75d57a8 --- /dev/null +++ b/src/app/(post-login)/submission/gql/SIDEMENU_PROGRAMS.ts @@ -0,0 +1,30 @@ +/* + * Copyright (c) 2022 The Ontario Institute for Cancer Research. All rights reserved + * + * This program and the accompanying materials are made available under the terms of + * the GNU Affero General Public License v3.0. You should have received a copy of the + * GNU Affero General Public License along with this program. + * If not, see . + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY + * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT + * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, + * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED + * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; + * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER + * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN + * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +import { gql } from '@/__generated__/gql'; + +const SIDEMENU_PROGRAMS = gql(` + query SideMenu { + programs { + shortName + } + } +`); + +export default SIDEMENU_PROGRAMS; diff --git a/src/app/(post-login)/submission/layout.tsx b/src/app/(post-login)/submission/layout.tsx index 549e9734..898c9fa9 100644 --- a/src/app/(post-login)/submission/layout.tsx +++ b/src/app/(post-login)/submission/layout.tsx @@ -20,14 +20,13 @@ import { HEADER_HEIGHT_PX } from '@/app/components/Header'; import { css, useTheme } from '@/lib/emotion'; -import mockData from '@/mockData.json'; import { ReactNode, useState } from 'react'; import SideMenu from './components/SideMenu/Menu'; import TitleBar from './components/TitleBar'; export default function AppLayout({ children }: { children: ReactNode }) { const theme = useTheme(); - const programData = mockData.programs; + const [isSidebarActive, setSidebarActive] = useState(true); return ( @@ -47,7 +46,6 @@ export default function AppLayout({ children }: { children: ReactNode }) { `} > setSidebarActive((active) => !active)} /> diff --git a/src/app/(post-login)/submission/page.tsx b/src/app/(post-login)/submission/page.tsx index 4299a66a..1ffa9056 100644 --- a/src/app/(post-login)/submission/page.tsx +++ b/src/app/(post-login)/submission/page.tsx @@ -19,9 +19,19 @@ 'use client'; -import mockData from '@/mockData.json'; +import Loader from '@/app/components/Loader'; +import { notNull } from '@/global/utils/types'; +import { useQuery } from '@apollo/client'; +import { notFound } from 'next/navigation'; import ProgramList from './components/ProgramList'; +import PROGRAMS_LIST_QUERY from './gql/PROGRAMS_LIST_QUERY'; export default function Submission() { - return ; + const { data, loading, error } = useQuery(PROGRAMS_LIST_QUERY); + + const programs = data?.programs?.filter(notNull) || []; + + if (loading) return ; + if (error) notFound(); + return ; } diff --git a/src/app/(pre-login)/contact/components/form.tsx b/src/app/(pre-login)/contact/components/form.tsx index 667aa67e..df8db483 100644 --- a/src/app/(pre-login)/contact/components/form.tsx +++ b/src/app/(pre-login)/contact/components/form.tsx @@ -17,7 +17,7 @@ * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ -import { useAppConfigContext } from '@/app/components/ConfigProvider'; +import { useAppConfigContext } from '@/app/hooks/AppProvider'; import { zodResolver } from '@hookform/resolvers/zod'; import { Button, diff --git a/src/app/(pre-login)/contact/components/info.tsx b/src/app/(pre-login)/contact/components/info.tsx index b8167b07..f1fdbf9e 100644 --- a/src/app/(pre-login)/contact/components/info.tsx +++ b/src/app/(pre-login)/contact/components/info.tsx @@ -17,7 +17,7 @@ * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ -import { useAppConfigContext } from '@/app/components/ConfigProvider'; +import { useAppConfigContext } from '@/app/hooks/AppProvider'; import { Button, Link, Typography, css, useTheme } from '@icgc-argo/uikit'; import { Col } from 'react-grid-system'; import urljoin from 'url-join'; diff --git a/src/app/(pre-login)/landing-page/page.tsx b/src/app/(pre-login)/landing-page/page.tsx index 561112f3..8283509a 100644 --- a/src/app/(pre-login)/landing-page/page.tsx +++ b/src/app/(pre-login)/landing-page/page.tsx @@ -18,7 +18,7 @@ */ 'use client'; -import { useAppConfigContext } from '@/app/components/ConfigProvider'; +import { useAppConfigContext } from '@/app/hooks/AppProvider'; export default function LandingPage() { const { EGO_CLIENT_ID } = useAppConfigContext(); diff --git a/src/app/(pre-login)/logging-in/page.tsx b/src/app/(pre-login)/logging-in/page.tsx index 51347dea..9f980858 100644 --- a/src/app/(pre-login)/logging-in/page.tsx +++ b/src/app/(pre-login)/logging-in/page.tsx @@ -18,7 +18,7 @@ */ 'use client'; -import { useAppConfigContext } from '@/app/components/ConfigProvider'; +import { useAppConfigContext } from '@/app/hooks/AppProvider'; import { useAuthContext } from '@/global/utils/auth'; import { DnaLoader, css, useTheme } from '@icgc-argo/uikit'; import { useRouter } from 'next/navigation'; diff --git a/src/app/App.tsx b/src/app/App.tsx index 0796ae36..e7c50adb 100644 --- a/src/app/App.tsx +++ b/src/app/App.tsx @@ -19,11 +19,12 @@ // all our context providers won't work server side, beacuse React.Context is client side 'use client'; +import { ApolloProvider } from '@/app/hooks/ApolloProvider'; +import { AppProvider } from '@/app/hooks/AppProvider'; import { AuthProvider } from '@/global/utils/auth'; import { css } from '@/lib/emotion'; import { ReactNode } from 'react'; import { QueryClient, QueryClientProvider } from 'react-query'; -import { AppConfigProvider } from './components/ConfigProvider'; import Footer from './components/Footer'; import Header from './components/Header'; import ThemeProvider from './components/ThemeProvider'; @@ -33,21 +34,23 @@ const queryClient = new QueryClient(); const App = ({ children, config }: { children: ReactNode; config: any }) => ( - + -
-
- {children} -
-
+ +
+
+ {children} +
+
+
-
+
); diff --git a/src/app/api/config/config.ts b/src/app/api/config/config.ts index 7d8c794e..4c131f4d 100644 --- a/src/app/api/config/config.ts +++ b/src/app/api/config/config.ts @@ -32,6 +32,7 @@ export type AppConfig = { ARGO_ROOT: string; EGO_LOGIN_URL: string; DACO_ROOT: string; + GATEWAY_API_ROOT: string; }; /** @@ -73,6 +74,7 @@ export const getAppConfig = (serverEnv: any): AppConfig => { EGO_CLIENT_ID, EGO_LOGIN_URL, DACO_ROOT: serverEnv.DACO_ROOT || process.env.DACO_ROOT || 'https://daco.icgc-argo.org/', + GATEWAY_API_ROOT: serverEnv.GATEWAY_API_ROOT || process.env.NEXT_PUBLIC_GATEWAY_API_ROOT, }; return config; diff --git a/src/app/components/Footer.tsx b/src/app/components/Footer.tsx index 846df0bd..2e415bc0 100644 --- a/src/app/components/Footer.tsx +++ b/src/app/components/Footer.tsx @@ -17,12 +17,12 @@ * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ +import { useAppConfigContext } from '@/app/hooks/AppProvider'; import { css, useTheme } from '@/lib/emotion'; import { Icon, Link } from '@icgc-argo/uikit'; import { Fragment } from 'react'; import { Col, Row } from 'react-grid-system'; import urljoin from 'url-join'; -import { useAppConfigContext } from './ConfigProvider'; const getNavLinks = (docsUrl: string, argoRootUrl: string) => { const privacyUrl = urljoin(argoRootUrl, '/page/2/privacy'); diff --git a/src/app/components/Hero.tsx b/src/app/components/Hero.tsx index 6f692db2..cbe671b8 100644 --- a/src/app/components/Hero.tsx +++ b/src/app/components/Hero.tsx @@ -17,10 +17,10 @@ * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ +import { useAppConfigContext } from '@/app/hooks/AppProvider'; import { BUTTON_SIZES, Button, Icon, Typography, css, useTheme } from '@icgc-argo/uikit'; import Link from 'next/link'; import galaxyImage from '../../../public/assets/galaxy.png'; -import { useAppConfigContext } from './ConfigProvider'; import RegionBanner from './RegionBanner'; const Hero = () => { diff --git a/src/app/components/Loader.tsx b/src/app/components/Loader.tsx new file mode 100644 index 00000000..6058632d --- /dev/null +++ b/src/app/components/Loader.tsx @@ -0,0 +1,38 @@ +/* + * Copyright (c) 2023 The Ontario Institute for Cancer Research. All rights reserved + * + * This program and the accompanying materials are made available under the terms of + * the GNU Affero General Public License v3.0. You should have received a copy of the + * GNU Affero General Public License along with this program. + * If not, see . + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY + * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT + * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, + * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED + * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; + * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER + * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN + * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ +'use client'; + +import { css } from '@/lib/emotion'; +import { DnaLoader } from '@icgc-argo/uikit'; + +const Loader = () => ( +
+ +
+); + +export default Loader; diff --git a/src/app/components/LoginButton.tsx b/src/app/components/LoginButton.tsx index 31c7c9c7..8dcb02d6 100644 --- a/src/app/components/LoginButton.tsx +++ b/src/app/components/LoginButton.tsx @@ -18,9 +18,9 @@ */ 'use client'; +import { useAppConfigContext } from '@/app/hooks/AppProvider'; import { css } from '@/lib/emotion'; import { Button, Icon, useTheme } from '@icgc-argo/uikit'; -import { useAppConfigContext } from './ConfigProvider'; const LoginButton = () => { const { EGO_LOGIN_URL } = useAppConfigContext(); diff --git a/src/app/hooks/ApolloProvider.tsx b/src/app/hooks/ApolloProvider.tsx new file mode 100644 index 00000000..10a0eae8 --- /dev/null +++ b/src/app/hooks/ApolloProvider.tsx @@ -0,0 +1,39 @@ +/* + * Copyright (c) 2023 The Ontario Institute for Cancer Research. All rights reserved + * + * This program and the accompanying materials are made available under the terms of + * the GNU Affero General Public License v3.0. You should have received a copy of the + * GNU Affero General Public License along with this program. + * If not, see . + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY + * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT + * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, + * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED + * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; + * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER + * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN + * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +'use client'; + +import { useAuthContext } from '@/global/utils/auth'; +import { createApolloClient } from '@/lib/gql'; +import { ApolloProvider as DefaultApolloProvider } from '@apollo/client'; +import { ReactNode } from 'react'; +import { useAppConfigContext } from './AppProvider'; + +export const ApolloProvider = ({ children }: { children: ReactNode }) => { + const auth = useAuthContext(); + const { GATEWAY_API_ROOT } = useAppConfigContext(); + const config = { + jwt: auth.egoJwt, + gateway: `${GATEWAY_API_ROOT}/graphql`, + }; + + const apolloClient = createApolloClient(config); + + return {children}; +}; diff --git a/src/app/components/ConfigProvider.tsx b/src/app/hooks/AppProvider.tsx similarity index 94% rename from src/app/components/ConfigProvider.tsx rename to src/app/hooks/AppProvider.tsx index 864a7cb9..fdca77dc 100644 --- a/src/app/components/ConfigProvider.tsx +++ b/src/app/hooks/AppProvider.tsx @@ -34,11 +34,12 @@ const defaultContext = { ARGO_ROOT: '', EGO_LOGIN_URL: '', DACO_ROOT: '', + GATEWAY_API_ROOT: '', }; const AppConfig = createContext(defaultContext); -export const AppConfigProvider = ({ children, config }: { children: ReactNode; config: any }) => { +export const AppProvider = ({ children, config }: { children: ReactNode; config: any }) => { return {children}; }; diff --git a/src/app/page.tsx b/src/app/page.tsx index e602a653..26ad5da4 100644 --- a/src/app/page.tsx +++ b/src/app/page.tsx @@ -18,12 +18,12 @@ */ 'use client'; +import { useAppConfigContext } from '@/app/hooks/AppProvider'; import { css, useTheme } from '@/lib/emotion'; import { DataCallout, Link, Typography, overtureLogo } from '@icgc-argo/uikit'; import Image from 'next/image'; import { ComponentType } from 'react'; import urlJoin from 'url-join'; -import { useAppConfigContext } from './components/ConfigProvider'; import Hero from './components/Hero'; const OvertureBanner: ComponentType = () => { diff --git a/src/global/utils/types.ts b/src/global/utils/types.ts new file mode 100644 index 00000000..635e5ec1 --- /dev/null +++ b/src/global/utils/types.ts @@ -0,0 +1,22 @@ +/* + * Copyright (c) 2023 The Ontario Institute for Cancer Research. All rights reserved + * + * This program and the accompanying materials are made available under the terms of + * the GNU Affero General Public License v3.0. You should have received a copy of the + * GNU Affero General Public License along with this program. + * If not, see . + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY + * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT + * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, + * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED + * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; + * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER + * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN + * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +export function notNull(value: T): value is NonNullable { + return value != null; +} diff --git a/src/lib/gql.ts b/src/lib/gql.ts new file mode 100644 index 00000000..39f2650e --- /dev/null +++ b/src/lib/gql.ts @@ -0,0 +1,52 @@ +/* + * Copyright (c) 2023 The Ontario Institute for Cancer Research. All rights reserved + * + * This program and the accompanying materials are made available under the terms of + * the GNU Affero General Public License v3.0. You should have received a copy of the + * GNU Affero General Public License along with this program. + * If not, see . + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY + * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT + * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, + * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED + * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; + * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER + * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN + * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ +'use client'; + +import { ApolloClient, ApolloLink, InMemoryCache, createHttpLink } from '@apollo/client'; + +export { gql } from '@/__generated__/gql'; + +type Config = { + gateway: string; + jwt: string; +}; +export const createApolloClient = (config: Config) => { + const httpLink = createHttpLink({ + uri: config.gateway, + }); + + const jwt = config.jwt; + + const authLink = new ApolloLink((operation, forward) => { + operation.setContext(({ headers }: { headers: any }) => ({ + headers: { + authorization: `Bearer ${jwt}`, + ...headers, + }, + })); + return forward(operation); + }); + + const additiveLink = ApolloLink.from([authLink, httpLink]); + + return new ApolloClient({ + link: additiveLink, + cache: new InMemoryCache(), + }); +};