From 46212487a4fefd2a289c83414e557a03394b6d88 Mon Sep 17 00:00:00 2001 From: jpfisher72 Date: Tue, 24 Sep 2024 09:34:27 -0400 Subject: [PATCH 1/5] Bump most packages to latest, fix build error --- screen2.0/.yarnrc.yml | 4 + screen2.0/package.json | 52 +- .../app/_biosampleTables/BiosampleTables.tsx | 2 +- screen2.0/yarn.lock | 789 +++++++++--------- 4 files changed, 439 insertions(+), 408 deletions(-) diff --git a/screen2.0/.yarnrc.yml b/screen2.0/.yarnrc.yml index 3186f3f0..e55ce3b3 100644 --- a/screen2.0/.yarnrc.yml +++ b/screen2.0/.yarnrc.yml @@ -1 +1,5 @@ nodeLinker: node-modules + +plugins: + - path: .yarn/plugins/@yarnpkg/plugin-interactive-tools.cjs + spec: "@yarnpkg/plugin-interactive-tools" diff --git a/screen2.0/package.json b/screen2.0/package.json index 50b17de4..e16cf02a 100644 --- a/screen2.0/package.json +++ b/screen2.0/package.json @@ -37,55 +37,55 @@ } }, "dependencies": { - "@apollo/client": "alpha", - "@apollo/experimental-nextjs-app-support": "^0.8.0", - "@emailjs/browser": "^4.3.3", + "@apollo/client": "^3.11.8", + "@apollo/experimental-nextjs-app-support": "^0.11.3", + "@emailjs/browser": "^4.4.1", "@emotion/cache": "^11.13.1", - "@emotion/react": "^11.11.1", - "@emotion/styled": "^11.11.0", + "@emotion/react": "^11.13.3", + "@emotion/styled": "^11.13.0", "@mui/icons-material": "^5.16.7", "@mui/lab": "^5.0.0-alpha.170", "@mui/material": "^5.16.7", "@mui/material-nextjs": "^6.1.0", - "@types/node": "^20.14.6", - "@types/react": "^18.3.3", - "@types/react-dom": "18.2.18", + "@types/node": "^22.6.1", + "@types/react": "^18.3.8", + "@types/react-dom": "18.3.0", "@visx/event": "^3.3.0", "@visx/responsive": "^3.10.2", "@visx/visx": "^3.11.0", - "@weng-lab/psychscreen-ui-components": "^0.9.0", + "@weng-lab/psychscreen-ui-components": "^1.0.4", "@weng-lab/ts-ztable": "^4.0.1", - "autoprefixer": "10.4.17", + "autoprefixer": "10.4.20", "bpnet-ui": "^0.3.8", - "eslint": "8.57.0", - "eslint-config-next": "14.2.5", - "graphql": "^16.8.1", + "eslint": "9.11.1", + "eslint-config-next": "14.2.13", + "graphql": "^16.9.0", "jubilant-carnival": "^0.6.0", - "logots-react": "latest", - "next": "14.2.3", + "logots-react": "^0.2.0", + "next": "14.2.13", "normalize.css": "^8.0.1", "only": "^0.0.2", - "postcss": "8.4.33", + "postcss": "8.4.47", "queryz": "^0.0.3", "react": "18.3.1", - "react-dom": "18.2.0", + "react-dom": "18.3.1", "react-dropzone": "^14.2.3", - "semantic-ui-react": "latest", - "server": "^1.0.38", - "tailwindcss": "3.4.1", - "umap-js": "1.3.3", + "semantic-ui-react": "^2.1.5", + "server": "^1.0.41", + "tailwindcss": "3.4.13", + "umap-js": "1.4.0", "umms-gb": "^3.10.0", - "uuid": "^9.0.0" + "uuid": "^10.0.0" }, "devDependencies": { "@graphql-codegen/cli": "^5.0.2", "@graphql-codegen/client-preset": "^4.3.3", "@graphql-typed-document-node/core": "^3.2.0", "file-loader": "^6.2.0", - "lint-staged": "^15.1.0", - "prettier": "^3.2.5", - "typescript": "5.3.3", - "webpack": "^5.90.1", + "lint-staged": "^15.2.10", + "prettier": "^3.3.3", + "typescript": "5.6.2", + "webpack": "^5.94.0", "webpack-cli": "^5.1.4" }, "prettier": { diff --git a/screen2.0/src/app/_biosampleTables/BiosampleTables.tsx b/screen2.0/src/app/_biosampleTables/BiosampleTables.tsx index ddec5c29..7f4f84d7 100644 --- a/screen2.0/src/app/_biosampleTables/BiosampleTables.tsx +++ b/screen2.0/src/app/_biosampleTables/BiosampleTables.tsx @@ -204,7 +204,7 @@ export const BiosampleTables = ({ if (showRNAseq) cols.push({ header: "RNA-Seq", - value: (row) => +!!row.rnaseq ?? "", + value: (row) => +row.rnaseq, render: (row) => { if (row.rnaseq) { return ( diff --git a/screen2.0/yarn.lock b/screen2.0/yarn.lock index daf994ba..5a5f0e7e 100644 --- a/screen2.0/yarn.lock +++ b/screen2.0/yarn.lock @@ -22,9 +22,21 @@ __metadata: languageName: node linkType: hard -"@apollo/client@alpha": - version: 3.10.0-alpha.1 - resolution: "@apollo/client@npm:3.10.0-alpha.1" +"@apollo/client-react-streaming@npm:0.11.3": + version: 0.11.3 + resolution: "@apollo/client-react-streaming@npm:0.11.3" + dependencies: + ts-invariant: ^0.10.3 + peerDependencies: + "@apollo/client": ^3.10.4 + react: ^18 + checksum: e0fff12744a93d910b8b3600da01b1fb5a23167c13542651043ab038e8e7573d3feec76426b1d8acee3ceba904cfd88bcf6912aee6a17da32ae5d9ce22ae8cae + languageName: node + linkType: hard + +"@apollo/client@npm:^3.11.8": + version: 3.11.8 + resolution: "@apollo/client@npm:3.11.8" dependencies: "@graphql-typed-document-node/core": ^3.1.1 "@wry/caches": ^1.0.0 @@ -34,7 +46,7 @@ __metadata: hoist-non-react-statics: ^3.3.2 optimism: ^0.18.0 prop-types: ^15.7.2 - 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version: 2.2.1 - resolution: "superjson@npm:2.2.1" - dependencies: - copy-anything: ^3.0.2 - checksum: 42f327474a9de80165a70641d66c2afd9ce7f0eb241c32af7e2d5777f893aac6defa6c1584bd35f022658dbdfd2b7bcf0d170acfe62a07e7d1d01238cf5b4a57 - languageName: node - linkType: hard - "supports-color@npm:^5.3.0": version: 5.5.0 resolution: "supports-color@npm:5.5.0" @@ -10936,9 +10970,9 @@ semantic-ui-react@latest: languageName: node linkType: hard -"tailwindcss@npm:3.4.1": - version: 3.4.1 - resolution: "tailwindcss@npm:3.4.1" +"tailwindcss@npm:3.4.13": + version: 3.4.13 + resolution: "tailwindcss@npm:3.4.13" dependencies: "@alloc/quick-lru": ^5.2.0 arg: ^5.0.2 @@ -10948,7 +10982,7 @@ semantic-ui-react@latest: fast-glob: ^3.3.0 glob-parent: ^6.0.2 is-glob: ^4.0.3 - jiti: ^1.19.1 + jiti: ^1.21.0 lilconfig: ^2.1.0 micromatch: ^4.0.5 normalize-path: ^3.0.0 @@ -10965,7 +10999,7 @@ semantic-ui-react@latest: bin: tailwind: lib/cli.js tailwindcss: lib/cli.js - checksum: ef5a587dd32bb4e91e1549ead6162f85f0b78d3e6ffd8b4e8eeb15585b7b886cb3af6ae9df5092ed8ccb7e590608d1b3eec79ca08c862b07cd9ff7e72f73104b + checksum: 0e85717b4276b884c3ba762a72fececcf6c27f54fe4deb660e22b7f278f33e6f806af4e4c4fad27e8de74fa28872cea75fe121b5751ef861cb2cc423a2fc8fc4 languageName: node linkType: hard @@ -11138,7 +11172,7 @@ semantic-ui-react@latest: languageName: node linkType: hard -"ts-api-utils@npm:^1.0.1": +"ts-api-utils@npm:^1.3.0": version: 1.3.0 resolution: "ts-api-utils@npm:1.3.0" peerDependencies: @@ -11223,13 +11257,6 @@ semantic-ui-react@latest: languageName: node linkType: hard -"type-fest@npm:^0.20.2": - version: 0.20.2 - resolution: "type-fest@npm:0.20.2" - checksum: 4fb3272df21ad1c552486f8a2f8e115c09a521ad7a8db3d56d53718d0c907b62c6e9141ba5f584af3f6830d0872c521357e512381f24f7c44acae583ad517d73 - languageName: node - linkType: hard - "type-fest@npm:^0.21.3": version: 0.21.3 resolution: "type-fest@npm:0.21.3" @@ -11299,23 +11326,23 @@ semantic-ui-react@latest: languageName: node linkType: hard -"typescript@npm:5.3.3": - version: 5.3.3 - resolution: "typescript@npm:5.3.3" +"typescript@npm:5.6.2": + version: 5.6.2 + resolution: "typescript@npm:5.6.2" bin: tsc: bin/tsc tsserver: bin/tsserver - checksum: 2007ccb6e51bbbf6fde0a78099efe04dc1c3dfbdff04ca3b6a8bc717991862b39fd6126c0c3ebf2d2d98ac5e960bcaa873826bb2bb241f14277034148f41f6a2 + checksum: 48777e1dabd9044519f56cd012b0296e3b72bafe12b7e8e34222751d45c67e0eba5387ecdaa6c14a53871a29361127798df6dc8d1d35643a0a47cb0b1c65a33a languageName: node linkType: hard -"typescript@patch:typescript@5.3.3#~builtin": - version: 5.3.3 - resolution: "typescript@patch:typescript@npm%3A5.3.3#~builtin::version=5.3.3&hash=85af82" +"typescript@patch:typescript@5.6.2#~builtin": + version: 5.6.2 + resolution: "typescript@patch:typescript@npm%3A5.6.2#~builtin::version=5.6.2&hash=85af82" bin: tsc: bin/tsc tsserver: bin/tsserver - checksum: f61375590b3162599f0f0d5b8737877ac0a7bc52761dbb585d67e7b8753a3a4c42d9a554c4cc929f591ffcf3a2b0602f65ae3ce74714fd5652623a816862b610 + checksum: c084ee1ab865f108c787e6233a5f63c126c482c0c8e87ec998ac5288a2ad54b603e1ea8b8b272355823b833eb31b9fabb99e8c6152283e1cb47e3a76bd6faf6c languageName: node linkType: hard @@ -11346,12 +11373,12 @@ semantic-ui-react@latest: languageName: node linkType: hard -"umap-js@npm:1.3.3": - version: 1.3.3 - resolution: "umap-js@npm:1.3.3" +"umap-js@npm:1.4.0": + version: 1.4.0 + resolution: "umap-js@npm:1.4.0" dependencies: ml-levenberg-marquardt: ^2.0.0 - checksum: 3f5426a19f78b39f291090175e65dad3ce6d59f7622ce32b3b7c2818cf1fc5dcc78935295912fb2f8aa6a85bf48bad55c0615aaa2d80437b1a64f1c6c107fcaa + checksum: c47b96d0aca757813f7710276b4876deac683e37b5ff918509b47d22859554a4237557201c4d6fb5194663c44985ebde7c30d19a22037d9799de00d634c8e714 languageName: node linkType: hard @@ -11582,12 +11609,12 @@ semantic-ui-react@latest: languageName: node linkType: hard -"uuid@npm:^9.0.0": - version: 9.0.1 - resolution: "uuid@npm:9.0.1" +"uuid@npm:^10.0.0": + version: 10.0.0 + resolution: "uuid@npm:10.0.0" bin: uuid: dist/bin/uuid - checksum: 39931f6da74e307f51c0fb463dc2462807531dc80760a9bff1e35af4316131b4fc3203d16da60ae33f07fdca5b56f3f1dd662da0c99fea9aaeab2004780cc5f4 + checksum: 4b81611ade2885d2313ddd8dc865d93d8dccc13ddf901745edca8f86d99bc46d7a330d678e7532e7ebf93ce616679fb19b2e3568873ac0c14c999032acb25869 languageName: node linkType: hard @@ -11726,7 +11753,7 @@ semantic-ui-react@latest: languageName: node linkType: hard -"webpack@npm:^5.90.1": +"webpack@npm:^5.94.0": version: 5.94.0 resolution: "webpack@npm:5.94.0" dependencies: From 479f4fd413540249fcf5e996353db9b35cda78f1 Mon Sep 17 00:00:00 2001 From: jpfisher72 Date: Tue, 24 Sep 2024 12:34:32 -0400 Subject: [PATCH 2/5] Upgrade to MUI v6 --- screen2.0/package.json | 10 +- .../src/app/_mainsearch/ccreautocomplete.tsx | 10 +- .../app/_mainsearch/celltypeautocomplete.tsx | 10 +- .../src/app/_mainsearch/genomicregion.tsx | 20 +- screen2.0/src/app/_mainsearch/queries.ts | 102 +-- .../src/app/_mainsearch/snpautocomplete.tsx | 10 +- screen2.0/src/app/about/page.tsx | 72 ++- .../gene-expression/geneexpressionplot.tsx | 2 +- .../app/applets/gene-expression/queries.ts | 108 ++-- screen2.0/src/app/applets/gwas/page.tsx | 18 +- screen2.0/src/app/applets/gwas/queries.ts | 198 +++--- screen2.0/src/app/downloads/annotations.tsx | 50 +- screen2.0/src/app/downloads/datamatrices.tsx | 48 +- screen2.0/src/app/downloads/downloadrange.tsx | 21 +- screen2.0/src/app/downloads/page.tsx | 20 +- screen2.0/src/app/downloads/queries.ts | 32 +- screen2.0/src/app/page.tsx | 36 +- .../src/app/search/_ccredetails/chromhmm.tsx | 593 +++++++++--------- .../src/app/search/_ccredetails/entexdata.tsx | 287 +++++---- .../search/_ccredetails/functionaldata.tsx | 558 ++++++++-------- .../search/_ccredetails/geneexpression.tsx | 25 +- .../_ccredetails/humanchromhmmtracks.tsx | 292 ++++----- .../_ccredetails/inspecificbiosample.tsx | 133 ++-- .../app/search/_ccredetails/linkedccres.tsx | 17 +- .../app/search/_ccredetails/linkedgenes.tsx | 24 +- .../_ccredetails/nearbygenomicfeatures.tsx | 245 ++++---- .../src/app/search/_ccredetails/rampage.tsx | 304 +++++---- .../search/_ccredetails/tfintersection.tsx | 147 +++-- .../app/search/_gbview/genomebrowserview.tsx | 130 ++-- screen2.0/src/app/search/_gbview/queries.ts | 62 +- .../app/search/_gbview/tfsequencefeatures.tsx | 484 +++++++------- screen2.0/src/app/search/_gbview/types.ts | 40 +- .../_geneAutocomplete/GeneAutocomplete.tsx | 10 +- .../src/app/search/mainresultsfilters.tsx | 96 +-- screen2.0/src/app/search/mainresultstable.tsx | 12 +- screen2.0/src/common/lib/utility.tsx | 10 +- screen2.0/yarn.lock | 235 +++++-- 37 files changed, 2372 insertions(+), 2099 deletions(-) diff --git a/screen2.0/package.json b/screen2.0/package.json index e16cf02a..1203892c 100644 --- a/screen2.0/package.json +++ b/screen2.0/package.json @@ -43,17 +43,17 @@ "@emotion/cache": "^11.13.1", "@emotion/react": "^11.13.3", "@emotion/styled": "^11.13.0", - "@mui/icons-material": "^5.16.7", - "@mui/lab": "^5.0.0-alpha.170", - "@mui/material": "^5.16.7", - "@mui/material-nextjs": "^6.1.0", + "@mui/icons-material": "^6.1.1", + "@mui/lab": "^6.0.0-beta.10", + "@mui/material": "^6.1.1", + "@mui/material-nextjs": "^6.1.1", "@types/node": "^22.6.1", "@types/react": "^18.3.8", "@types/react-dom": "18.3.0", "@visx/event": "^3.3.0", "@visx/responsive": "^3.10.2", "@visx/visx": "^3.11.0", - "@weng-lab/psychscreen-ui-components": "^1.0.4", + "@weng-lab/psychscreen-ui-components": "^2.0.0", "@weng-lab/ts-ztable": "^4.0.1", "autoprefixer": "10.4.20", "bpnet-ui": "^0.3.8", diff --git a/screen2.0/src/app/_mainsearch/ccreautocomplete.tsx b/screen2.0/src/app/_mainsearch/ccreautocomplete.tsx index 42669001..ee5d1011 100644 --- a/screen2.0/src/app/_mainsearch/ccreautocomplete.tsx +++ b/screen2.0/src/app/_mainsearch/ccreautocomplete.tsx @@ -2,7 +2,7 @@ import React, { useState, useCallback } from "react" import Box from "@mui/material/Box" import TextField from "@mui/material/TextField" import Autocomplete from "@mui/material/Autocomplete" -import Grid2 from "@mui/material/Unstable_Grid2/Grid2" +import Grid from "@mui/material/Grid2" import Typography from "@mui/material/Typography" import { debounce } from "@mui/material/utils" import { CCRE_AUTOCOMPLETE_QUERY } from "./queries" @@ -111,8 +111,8 @@ export const CcreAutoComplete: React.FC<{ assembly: string, header?: boolean }> renderOption={(props, option) => { return (
  • - - + + {option} @@ -122,8 +122,8 @@ export const CcreAutoComplete: React.FC<{ assembly: string, header?: boolean }> }-${(ccreAccessions.find((g: { ccreaccession: string }) => g.ccreaccession === option))?.end}`} )} - - + +
    • ) }} diff --git a/screen2.0/src/app/_mainsearch/celltypeautocomplete.tsx b/screen2.0/src/app/_mainsearch/celltypeautocomplete.tsx index 1f4f19e0..8d1f0b99 100644 --- a/screen2.0/src/app/_mainsearch/celltypeautocomplete.tsx +++ b/screen2.0/src/app/_mainsearch/celltypeautocomplete.tsx @@ -2,7 +2,7 @@ import React, { useState, useEffect, SetStateAction, useTransition } from "react import Box from "@mui/material/Box" import TextField from "@mui/material/TextField" import Autocomplete from "@mui/material/Autocomplete" -import Grid2 from "@mui/material/Unstable_Grid2/Grid2" +import Grid from "@mui/material/Grid2" import Typography from "@mui/material/Typography" import { IconButton, Stack } from "@mui/material" import { Search } from "@mui/icons-material" @@ -101,16 +101,16 @@ export const CelltypeAutocomplete: React.FC<{ assembly: string, header?: boolean renderOption={(props, option) => { return (
  • - - + + {option.displayname} {option.ontology} - - + +
    • ) }} diff --git a/screen2.0/src/app/_mainsearch/genomicregion.tsx b/screen2.0/src/app/_mainsearch/genomicregion.tsx index 678a5b81..3afea0e8 100644 --- a/screen2.0/src/app/_mainsearch/genomicregion.tsx +++ b/screen2.0/src/app/_mainsearch/genomicregion.tsx @@ -14,7 +14,7 @@ import { } from "@mui/material" import { useState, SetStateAction, useEffect, useMemo } from "react" import { Search } from "@mui/icons-material" -import Grid2 from "@mui/material/Unstable_Grid2/Grid2" +import Grid from "@mui/material/Grid2" import { parseGenomicRegion } from "./parsegenomicregion" //https://mui.com/material-ui/react-text-field/#integration-with-3rd-party-input-libraries @@ -193,9 +193,9 @@ const GenomicRegion = (props: { assembly: "mm10" | "GRCh38"; header?: boolean }) }, [value, inputType, props.assembly, chromosome, start, end]) return ( - + ( {!props.header && ( - + {/* Input Format */} } label="Individual Inputs" /> - + )} - + {inputType === "Separated" ? ( <> @@ -333,7 +333,7 @@ const GenomicRegion = (props: { assembly: "mm10" | "GRCh38"; header?: boolean }) ) : ( //UCSC Input - + />) )} - - - ) + + ) + ); } export default GenomicRegion diff --git a/screen2.0/src/app/_mainsearch/queries.ts b/screen2.0/src/app/_mainsearch/queries.ts index c5c3cfd3..c5a25199 100644 --- a/screen2.0/src/app/_mainsearch/queries.ts +++ b/screen2.0/src/app/_mainsearch/queries.ts @@ -1,52 +1,52 @@ -import { gql } from "@apollo/client" - -export const CCRE_AUTOCOMPLETE_QUERY = gql` -query cCREQuery($accession_prefix: [String!], $limit: Int, $assembly: String!) { - cCREQuery(accession_prefix: $accession_prefix, assembly: $assembly, limit: $limit) { - accession - coordinates { - start - end - chromosome - } - } -} -` - - -export const GENE_AUTOCOMPLETE_QUERY = ` -query ($assembly: String!, $name_prefix: [String!], $limit: Int, $version: Int) { - gene(assembly: $assembly, name_prefix: $name_prefix, limit: $limit, version: $version) { - name - id - coordinates { - start - chromosome - end - } - } - } - ` - -export const SNP_AUTOCOMPLETE_QUERY = ` -query snpAutocompleteQuery($snpid: String!, $assembly: String!) { - snpAutocompleteQuery(snpid: $snpid, assembly: $assembly) { - id - coordinates { - chromosome - start - end - } - } -} -` - -export const BED_INTERSECT_QUERY = gql` -query bedIntersectCCRE_1 ($user_ccres: [cCRE]!, $assembly: String!, $max_ouput_length: Int) { - intersection ( - userCcres: $user_ccres, - assembly: $assembly, - maxOutputLength: $max_ouput_length - ) -} +import { gql } from "@apollo/client" + +export const CCRE_AUTOCOMPLETE_QUERY = gql` +query cCREQuery($accession_prefix: [String!], $limit: Int, $assembly: String!) { + cCREQuery(accession_prefix: $accession_prefix, assembly: $assembly, limit: $limit) { + accession + coordinates { + start + end + chromosome + } + } +} +` + + +export const GENE_AUTOCOMPLETE_QUERY = ` +query ($assembly: String!, $name_prefix: [String!], $limit: Int, $version: Int) { + gene(assembly: $assembly, name_prefix: $name_prefix, limit: $limit, version: $version) { + name + id + coordinates { + start + chromosome + end + } + } + } + ` + +export const SNP_AUTOCOMPLETE_QUERY = ` +query snpAutocompleteQuery($snpid: String!, $assembly: String!) { + snpAutocompleteQuery(snpid: $snpid, assembly: $assembly) { + id + coordinates { + chromosome + start + end + } + } +} +` + +export const BED_INTERSECT_QUERY = gql` +query bedIntersectCCRE_1 ($user_ccres: [cCRE]!, $assembly: String!, $max_ouput_length: Int) { + intersection ( + userCcres: $user_ccres, + assembly: $assembly, + maxOutputLength: $max_ouput_length + ) +} ` \ No newline at end of file diff --git a/screen2.0/src/app/_mainsearch/snpautocomplete.tsx b/screen2.0/src/app/_mainsearch/snpautocomplete.tsx index 93cc363c..732464e1 100644 --- a/screen2.0/src/app/_mainsearch/snpautocomplete.tsx +++ b/screen2.0/src/app/_mainsearch/snpautocomplete.tsx @@ -6,7 +6,7 @@ import Typography from "@mui/material/Typography" import { debounce } from "@mui/material/utils" import { SNP_AUTOCOMPLETE_QUERY } from "./queries" import Config from "../../config.json" -import Grid2 from "@mui/material/Unstable_Grid2/Grid2" +import Grid from "@mui/material/Grid2" import { IconButton, Stack } from "@mui/material" import { Search } from "@mui/icons-material" @@ -118,8 +118,8 @@ export const SnpAutoComplete: React.FC<{ assembly: string, header?: boolean }> = renderOption={(props, option) => { return (
  • - - + + {option} @@ -128,8 +128,8 @@ export const SnpAutoComplete: React.FC<{ assembly: string, header?: boolean }> = {`${snpids.find((g) => g.id === option)?.chrom}:${snpids.find((g) => g.id === option)?.end}`} )} - - + +
    • ) }} diff --git a/screen2.0/src/app/about/page.tsx b/screen2.0/src/app/about/page.tsx index b3f8453d..cd33affc 100644 --- a/screen2.0/src/app/about/page.tsx +++ b/screen2.0/src/app/about/page.tsx @@ -2,7 +2,7 @@ import React, { useRef, useState } from "react" import emailjs from '@emailjs/browser'; import { Box, Button, Divider, Link, Stack, TextField, Typography } from "@mui/material" -import Grid2 from "@mui/material/Unstable_Grid2/Grid2" +import Grid from "@mui/material/Grid2" import Image from "next/image" import encodeEncyclopedia from "../../../public/assets/about/images/encodeencyclopedia.png" import classifications from "../../../public/assets/about/images/classifications.png" @@ -70,27 +70,35 @@ export default function About() { return ( -
    - + (
    + {/* Header */} - + About SCREEN SCREEN (Search Candidate Regulatory Elements by ENCODE) is a web-based visualization engine designed to allow users to explore and visualize the ENCODE Registry of candidate cis-Regulatory Elements (cCREs) and its connection with other ENCODE Encyclopedia annotations. - + {/* Encode Encyclopedia */} - - + + The ENCODE Encyclopedia The ENCODE Encyclopedia encompasses a comprehensive set of sequence (yellow), element (red), gene (green) and interaction (blue) annotations (Figure 1). These annotations can either derive directly from primary data (primary level) or derive from the integration of multiple data types using innovative computational methods (integrative level). - - + + {"Encode - - + + {/* Reistry of cCREs */} - - + + The Registry of cCREs @@ -151,10 +159,10 @@ export default function About() { Because of the uneven distribution of TF data across biosamples and our desire to reduce false positive annotations, we do not specifically annotate the TF class of elements in individual cell types. We instead provide an aggregate list of these TF cCREs annotated with their supporting TF ChIP-seq peaks. For cell types with TF ChIP-seq data, we annotate CA-TF elements since the accessible chromatin corroborates the TF binding. - - - - + + + + Core Collection @@ -180,13 +188,13 @@ export default function About() { Custom Classification While our classification schemes place each cCRE into specific, individual classes, the signal strengths for all recorded epigenetic features are retained for each cCRE in the Registry and can be used for customized searches by users. For example, users may want promoters that have high DNase, H3K4me3, and H3K27ac to distinguish from poised promoters that often lack H3K27ac signal. Additionally, by default, all chromatin accessibility annotations use DNase signal. If users prefer to use ATAC signal, this can be easily accomplished using the ENCODE API. - - - + + + Integration with other encyclopedia annotations In addition to hosting the Registry of cCREs, SCREEN also hosts other Encyclopedia annotations and displays them in the context of cCREs. Under the cCRE Details page for each cCRE are tabs displaying overlapping Encyclopedia annotations with links to their derived experiments or annotations. Such annotations include TF peaks, histone mark peaks, ChromHMM states, TSS derived from RAMPAGE and long read RNA-seq data, 3D chromatin interactions, and gene expression. - - + + How to Cite the ENCODE Encyclopedia, the Registry of cCREs, and SCREEN The Registry of cCREs and SCREEN
      @@ -200,15 +208,15 @@ export default function About() { The ENCODE Project Consortium, Jill E. Moore, Michael J. Purcaro, Henry E. Pratt, Charles B. Epstein, Noam Shoresh, Jessika Adrian, et al. 2020. “Expanded Encyclopaedias of DNA Elements in the Human and Mouse Genomes.” Nature 583 (7818): 699–710.
    -     -     + + {/* API Documentation */} - + API Documentation - + {/* Contact Us */} - + Contact Us Send us a message and we'll be in touch! As this is a beta site, we would greatly appreciate any feedback you may have. Knowing how our users are using the site and documenting issues they may have are important to make this resource better and easier to use. @@ -284,9 +292,9 @@ export default function About() { {success && Submitted successfully, thank you!} - -     - -
    - ) + + + +
    ) + ); } \ No newline at end of file diff --git a/screen2.0/src/app/applets/gene-expression/geneexpressionplot.tsx b/screen2.0/src/app/applets/gene-expression/geneexpressionplot.tsx index 61470117..c73ea9fb 100644 --- a/screen2.0/src/app/applets/gene-expression/geneexpressionplot.tsx +++ b/screen2.0/src/app/applets/gene-expression/geneexpressionplot.tsx @@ -2,7 +2,7 @@ import React from "react" import { useRouter } from "next/navigation" import { Stack } from "@mui/material" import { Range2D, Point2D, linearTransform2D } from "jubilant-carnival" -import Grid2 from "@mui/material/Unstable_Grid2/Grid2" +import Grid from "@mui/material/Grid2" import { tissueColors } from "../../../common/lib/colors" import { stringToColour } from "../../search/_ccredetails/utils" diff --git a/screen2.0/src/app/applets/gene-expression/queries.ts b/screen2.0/src/app/applets/gene-expression/queries.ts index ded8452a..e3f0f303 100644 --- a/screen2.0/src/app/applets/gene-expression/queries.ts +++ b/screen2.0/src/app/applets/gene-expression/queries.ts @@ -1,55 +1,55 @@ -import { gql } from "@apollo/client" -export const GENE_EXP_QUERY = gql` -query geneexpression($assembly: String!, $accessions: [String], $gene_id: [String]) { - gene_dataset(accession: $accessions) { - biosample - tissue - cell_compartment - biosample_type - assay_term_name - accession - gene_quantification_files(assembly: $assembly) { - accession - biorep - quantifications(gene_id_prefix: $gene_id) { - tpm - file_accession - fpkm - } - } - } -} - ` -export const GENE_QUERY = gql` - query ($assembly: String!, $name: [String!], $limit: Int, $version: Int) { - gene(assembly: $assembly, name: $name, limit: $limit, version: $version) { - name - id - coordinates { - start - chromosome - end - } - } - } ` - -export type GET_ORTHOLOG_VARS = { - name: string[], - assembly: 'grch38' | 'mm10' -} - -export type GET_ORTHOLOG_DATA = { - geneOrthologQuery: { - humanGene: string, - mouseGene: string - }[] -} - -export const GET_ORTHOLOG = gql` - query geneOrthologQuery($name: [String]!, $assembly: String!) { - geneOrthologQuery: geneorthologQuery(name: $name, assembly: $assembly) { - humanGene: external_gene_name - mouseGene: mmusculus_homolog_associated_gene_name - } - } +import { gql } from "@apollo/client" +export const GENE_EXP_QUERY = gql` +query geneexpression($assembly: String!, $accessions: [String], $gene_id: [String]) { + gene_dataset(accession: $accessions) { + biosample + tissue + cell_compartment + biosample_type + assay_term_name + accession + gene_quantification_files(assembly: $assembly) { + accession + biorep + quantifications(gene_id_prefix: $gene_id) { + tpm + file_accession + fpkm + } + } + } +} + ` +export const GENE_QUERY = gql` + query ($assembly: String!, $name: [String!], $limit: Int, $version: Int) { + gene(assembly: $assembly, name: $name, limit: $limit, version: $version) { + name + id + coordinates { + start + chromosome + end + } + } + } ` + +export type GET_ORTHOLOG_VARS = { + name: string[], + assembly: 'grch38' | 'mm10' +} + +export type GET_ORTHOLOG_DATA = { + geneOrthologQuery: { + humanGene: string, + mouseGene: string + }[] +} + +export const GET_ORTHOLOG = gql` + query geneOrthologQuery($name: [String]!, $assembly: String!) { + geneOrthologQuery: geneorthologQuery(name: $name, assembly: $assembly) { + humanGene: external_gene_name + mouseGene: mmusculus_homolog_associated_gene_name + } + } ` \ No newline at end of file diff --git a/screen2.0/src/app/applets/gwas/page.tsx b/screen2.0/src/app/applets/gwas/page.tsx index d2352b94..90368fb4 100644 --- a/screen2.0/src/app/applets/gwas/page.tsx +++ b/screen2.0/src/app/applets/gwas/page.tsx @@ -3,7 +3,7 @@ import { Accordion, AccordionDetails, AccordionSummary, IconButton, Paper, Stack import React, { useState, useMemo } from "react" import { DataTable, DataTableColumn } from "@weng-lab/psychscreen-ui-components" import { CreateLink, createLink, LoadingMessage } from "../../../common/lib/utility" -import Grid from "@mui/material/Unstable_Grid2/Grid2" +import Grid from "@mui/material/Grid2" import { CircularProgress } from "@mui/material" import ExpandMoreIcon from "@mui/icons-material/ExpandMore" import { client } from "../../search/_ccredetails/client" @@ -497,22 +497,28 @@ export default function GWAS() { }, [plotData, study, suggestionsOpen]) return ( -
    + (
    - + {!isLg && } {!isLg && SuggestionsPlot} - + {SuggestionsPlot} -
    - ) +
    ) + ); } diff --git a/screen2.0/src/app/applets/gwas/queries.ts b/screen2.0/src/app/applets/gwas/queries.ts index 554713a9..eed76642 100644 --- a/screen2.0/src/app/applets/gwas/queries.ts +++ b/screen2.0/src/app/applets/gwas/queries.ts @@ -1,100 +1,100 @@ -import { gql } from "../../../graphql/__generated__/gql" - -export const GET_ALL_GWAS_STUDIES = gql(` - query getAllGWASStudies { - getAllGwasStudies { - study - totalldblocks - author - pubmedid - studyname - - } - } -`) - -export const GET_SNPS_FOR_GIVEN_GWASSTUDY= gql(` - query getSNPsforgivengwasStudy($study: [String!]!){ - getSNPsforGWASStudies(study:$study) { - snpid - ldblock - rsquare - chromosome - stop - start - ldblocksnpid - } - }` -) - -export const BED_INTERSECT= gql(` - query bedIntersectCCRE ($inp: [cCRE]!, $assembly: String!) { - intersection ( - userCcres: $inp, - assembly: $assembly - ) - } -`) - -export const CCRE_SEARCH = gql(` - query ccreSearchQuery_2( - $assembly: String! - $celltype: String - $accessions: [String!] - ) { - cCRESCREENSearch( - assembly: $assembly - accessions: $accessions - cellType: $celltype - nearbygeneslimit: 1 - ) { - chrom - start - len - pct - nearestgenes { - gene - distance - } - ctcf_zscore - dnase_zscore - enhancer_zscore - promoter_zscore - atac_zscore - ctspecific { - dnase_zscore - ctcf_zscore - atac_zscore - h3k4me3_zscore - h3k27ac_zscore - } - info { - accession - } - } - } -`) - -export const CT_ENRICHMENT = gql(` - query getGWASCTEnrichmentQuery($study: String!) { - getGWASCtEnrichmentQuery(study: $study) { - celltype - accession - fc - fdr - pvalue - } - } -`) - -export const BIOSAMPLE_DISPLAYNAMES = gql(` - query getDisplayNames($assembly: String!, $samples: [String!]) { - ccREBiosampleQuery(assembly: $assembly, name: $samples) { - biosamples { - name - displayname - ontology - } - } - } +import { gql } from "../../../graphql/__generated__/gql" + +export const GET_ALL_GWAS_STUDIES = gql(` + query getAllGWASStudies { + getAllGwasStudies { + study + totalldblocks + author + pubmedid + studyname + + } + } +`) + +export const GET_SNPS_FOR_GIVEN_GWASSTUDY= gql(` + query getSNPsforgivengwasStudy($study: [String!]!){ + getSNPsforGWASStudies(study:$study) { + snpid + ldblock + rsquare + chromosome + stop + start + ldblocksnpid + } + }` +) + +export const BED_INTERSECT= gql(` + query bedIntersectCCRE ($inp: [cCRE]!, $assembly: String!) { + intersection ( + userCcres: $inp, + assembly: $assembly + ) + } +`) + +export const CCRE_SEARCH = gql(` + query ccreSearchQuery_2( + $assembly: String! + $celltype: String + $accessions: [String!] + ) { + cCRESCREENSearch( + assembly: $assembly + accessions: $accessions + cellType: $celltype + nearbygeneslimit: 1 + ) { + chrom + start + len + pct + nearestgenes { + gene + distance + } + ctcf_zscore + dnase_zscore + enhancer_zscore + promoter_zscore + atac_zscore + ctspecific { + dnase_zscore + ctcf_zscore + atac_zscore + h3k4me3_zscore + h3k27ac_zscore + } + info { + accession + } + } + } +`) + +export const CT_ENRICHMENT = gql(` + query getGWASCTEnrichmentQuery($study: String!) { + getGWASCtEnrichmentQuery(study: $study) { + celltype + accession + fc + fdr + pvalue + } + } +`) + +export const BIOSAMPLE_DISPLAYNAMES = gql(` + query getDisplayNames($assembly: String!, $samples: [String!]) { + ccREBiosampleQuery(assembly: $assembly, name: $samples) { + biosamples { + name + displayname + ontology + } + } + } `) \ No newline at end of file diff --git a/screen2.0/src/app/downloads/annotations.tsx b/screen2.0/src/app/downloads/annotations.tsx index 26e3785d..964109ab 100644 --- a/screen2.0/src/app/downloads/annotations.tsx +++ b/screen2.0/src/app/downloads/annotations.tsx @@ -1,5 +1,5 @@ import { Button, ButtonProps, Paper, Typography, Divider, Stack, Tabs, Tab } from "@mui/material" -import Grid2 from "@mui/material/Unstable_Grid2/Grid2" +import Grid from "@mui/material/Grid2" import React, { useEffect, useState } from "react" import Config from "../../config.json" import DownloadIcon from "@mui/icons-material/Download" @@ -82,14 +82,18 @@ export function Annotations() { } return ( - + ( {species === 0 && ( - - + + @@ -111,19 +115,28 @@ export function Annotations() { - - + + Human cCREs by cell and tissue types - - + + )} {species === 1 && ( - - + + @@ -144,17 +157,22 @@ export function Annotations() { - - + + Mouse cCREs by cell and tissue types - - + + )} - - ) + ) + ); } diff --git a/screen2.0/src/app/downloads/datamatrices.tsx b/screen2.0/src/app/downloads/datamatrices.tsx index 2e20dcda..793468c8 100644 --- a/screen2.0/src/app/downloads/datamatrices.tsx +++ b/screen2.0/src/app/downloads/datamatrices.tsx @@ -19,7 +19,7 @@ import { CircularProgress, } from "@mui/material" import { useQuery } from "@apollo/client" -import Grid2 from "@mui/material/Unstable_Grid2/Grid2" +import Grid from "@mui/material/Grid2" import { ArrowForward, Download, ExpandMore, Visibility } from "@mui/icons-material" import Image from "next/image" import humanTransparentIcon from "../../../public/Transparent_HumanIcon.png" @@ -319,10 +319,10 @@ export function DataMatrices() { ] return ( -
    - - - + (
    + + +
    @@ -334,14 +334,14 @@ export function DataMatrices() {
    {"Human     - - +     + {selectorButton({ assembly: "Human", assay: "DNase" })} {selectorButton({ assembly: "Human", assay: "H3K4me3" })} {selectorButton({ assembly: "Human", assay: "H3K27ac" })} {selectorButton({ assembly: "Human", assay: "CTCF" })} - - + +
    @@ -353,16 +353,16 @@ export function DataMatrices() {
    {"Mouse     - - +     + {selectorButton({ assembly: "Mouse", assay: "DNase" })} {selectorButton({ assembly: "Mouse", assay: "H3K4me3" })} {selectorButton({ assembly: "Mouse", assay: "H3K27ac" })} {selectorButton({ assembly: "Mouse", assay: "CTCF" })} - - - - + +     + + - - + + {tooltip !== -1 && ( //X and Y attributes added due to error. Not sure if setting to zero has unintended consequences - + ( @@ -471,7 +471,7 @@ export function DataMatrices() { {fData[tooltip].experimentAccession} - + ) )} {biosamples.length !== 0 && ( @@ -511,9 +511,9 @@ export function DataMatrices() { } - - - + + +     -
    - ) +
    ) + ); } diff --git a/screen2.0/src/app/downloads/downloadrange.tsx b/screen2.0/src/app/downloads/downloadrange.tsx index 8f05361c..8d3a14b8 100644 --- a/screen2.0/src/app/downloads/downloadrange.tsx +++ b/screen2.0/src/app/downloads/downloadrange.tsx @@ -1,5 +1,5 @@ import { SetStateAction, useState } from "react" -import Grid2 from "@mui/material/Unstable_Grid2/Grid2" +import Grid from "@mui/material/Grid2" import { Box, Button, Checkbox, CircularProgress, CircularProgressProps, FormControl, FormControlLabel, FormLabel, IconButton, Radio, RadioGroup, Stack, TextField, Typography } from "@mui/material" import { downloadBED } from "../search/searchhelpers" import { parseGenomicRegion } from "../_mainsearch/parsegenomicregion" @@ -119,15 +119,15 @@ export const DownloadRange: React.FC = () => { } return ( - - + ( + handleSetSelectedBiosample(selected)} /> - - + + Assembly { indeterminate={ !( //If every value is not true/null - Object.values(selectedConservation).every(x => x || x === null) || - //Or every value is not false/null - Object.values(selectedConservation).every(x => !x || x === null) + (Object.values(selectedConservation).every(x => x || x === null) || //Or every value is not false/null + Object.values(selectedConservation).every(x => !x || x === null)) ) } onChange={(_, checked: boolean) => setSelectedConservation( @@ -335,7 +334,7 @@ export const DownloadRange: React.FC = () => { {bedLoadingPercent !== null && } - - - ) + + ) + ); } \ No newline at end of file diff --git a/screen2.0/src/app/downloads/page.tsx b/screen2.0/src/app/downloads/page.tsx index 98d0ed42..5795b45b 100644 --- a/screen2.0/src/app/downloads/page.tsx +++ b/screen2.0/src/app/downloads/page.tsx @@ -2,7 +2,7 @@ import * as React from "react" import { Tabs, Tab, Box, Container, Divider} from "@mui/material" -import Grid2 from "@mui/material/Unstable_Grid2/Grid2" +import Grid from "@mui/material/Grid2" import { Annotations } from "./annotations" import { DataMatrices } from "./datamatrices" import { useState } from "react" @@ -23,22 +23,22 @@ export default function Downloads() { } return ( - - - + ( + + - - + + {page === 0 && } {page === 1 && } {page === 2 && } - - - - ) + + + ) + ); } diff --git a/screen2.0/src/app/downloads/queries.ts b/screen2.0/src/app/downloads/queries.ts index 55de31d9..34e761ff 100644 --- a/screen2.0/src/app/downloads/queries.ts +++ b/screen2.0/src/app/downloads/queries.ts @@ -1,16 +1,16 @@ -import { gql } from "@apollo/client" -export const UMAP_QUERY = gql` - query q_4($assembly: String!, $assay: [String!], $a: String!) { - ccREBiosampleQuery(assay: $assay, assembly: $assembly) { - biosamples { - name - displayname - ontology - sampleType - lifeStage - umap_coordinates(assay: $a) - experimentAccession(assay: $a) - } - } - } -` +import { gql } from "@apollo/client" +export const UMAP_QUERY = gql` + query q_4($assembly: String!, $assay: [String!], $a: String!) { + ccREBiosampleQuery(assay: $assay, assembly: $assembly) { + biosamples { + name + displayname + ontology + sampleType + lifeStage + umap_coordinates(assay: $a) + experimentAccession(assay: $a) + } + } + } +` diff --git a/screen2.0/src/app/page.tsx b/screen2.0/src/app/page.tsx index cc7a67a2..e2d6b31f 100644 --- a/screen2.0/src/app/page.tsx +++ b/screen2.0/src/app/page.tsx @@ -2,7 +2,7 @@ import { Box, Stack, Typography } from "@mui/material" import { MainSearch } from "./_mainsearch/mainsearch" -import Grid2 from "@mui/material/Unstable_Grid2/Grid2" +import Grid from "@mui/material/Grid2" import homeImage from "../../public/homeImage.png" import Image from "next/image" import humanTransparentIcon from "../../public/Transparent_HumanIcon.png" @@ -11,13 +11,17 @@ import mouseTransparentIcon from "../../public/Transparent_MouseIcon.png" export default function Home() { return ( -
    - - + (
    + + SCREEN Search Candidate cis-Regulatory Elements by ENCODE - - + + What is SCREEN? @@ -31,7 +35,7 @@ export default function Home() { Version 4 Annotations: - + Genome Assembly cCRE Count Cell/Tissue Types Covered @@ -51,12 +55,16 @@ export default function Home() { 926,843 382 - - - + + + {"SCREEN - - -
    - ) + + +
    ) + ); } diff --git a/screen2.0/src/app/search/_ccredetails/chromhmm.tsx b/screen2.0/src/app/search/_ccredetails/chromhmm.tsx index c24c8fd4..44107fc2 100644 --- a/screen2.0/src/app/search/_ccredetails/chromhmm.tsx +++ b/screen2.0/src/app/search/_ccredetails/chromhmm.tsx @@ -1,294 +1,301 @@ -"use client" - -import { BIG_QUERY } from "../_gbview/queries" -import React, { useMemo, useState, useRef, useCallback, useEffect } from "react" -import EGeneTracks from "../_gbview/egenetracks" -import { gql, useQuery } from "@apollo/client" -import { Tab, Tabs, CircularProgress, Box } from "@mui/material" -import CytobandView, { GenomicRange } from "../_gbview/cytobandview" -import { client } from "./client" -import Grid2 from "@mui/material/Unstable_Grid2/Grid2" -import { RulerTrack, GenomeBrowser } from "umms-gb" -import Controls from "../_gbview/controls" -import { HumanChromHmmTracks, stateDetails } from "./humanchromhmmtracks" -import { tissueColors } from "../../../common/lib/colors" -import { BigQueryResponse } from "../_gbview/types" -import { BigBedData } from "bigwig-reader" -import { styled } from '@mui/material/styles'; -import { DataTable } from "@weng-lab/psychscreen-ui-components" -import config from "../../../config.json" -const StyledTab = styled(Tab)(() => ({ - textTransform: "none", - })) - -const GENE_QUERY = gql` - query s_3($chromosome: String, $start: Int, $end: Int, $assembly: String!) { - gene(chromosome: $chromosome, start: $start, end: $end, assembly: $assembly) { - name - strand - transcripts { - name - strand - exons { - coordinates { - chromosome - start - end - } - } - coordinates { - chromosome - start - end - } - } - } - } -` - -export type Transcript = { - id: string - name: string - strand: string - coordinates: GenomicRange -} -export type SNPQueryResponse = { - gene: { - name: string - strand: string - transcripts: Transcript[] - }[] -} -export function expandCoordinates(coordinates, l = 20000) { - return { - chromosome: coordinates.chromosome, - start: coordinates.start - l < 0 ? 0 : coordinates.start - l, - end: coordinates.end + l, - } -} - -export const ChromHMM = (props: { coordinates , assembly, accession }) =>{ - const svgRef = useRef(null) - const expandedCoordinates = useMemo(() => expandCoordinates(props.coordinates), [props.coordinates]) - const [coordinates, setCoordinates] = useState(expandedCoordinates) - - const [page, setPage] = useState(0) - const [chromhmm, seChromHmm] = useState(null) - - - useEffect(() => { - - fetch(config.ChromHMM.HumanChromHMM) - .then((x) => x.text()) - .then((x) => { - const lines = x.split("\n") - let ch = {} - lines.forEach((e) => { - let val = e.split("\t") - if(val[2]) - { - if(ch[val[2]]) - { - let e = ch[val[2]] - e.push([val[0],val[3],`https://downloads.wenglab.org/ChIP_${val[1]}.bigBed`]) - - ch[val[2]] = e - - } else { - ch[val[2]] = [[val[0],val[3],`https://downloads.wenglab.org/ChIP_${val[1]}.bigBed`]] - } - } - - - }) - seChromHmm(ch) - - }) - }, []) - - - const snpResponse = useQuery(GENE_QUERY, { - variables: { ...coordinates, assembly: props.assembly }, - fetchPolicy: "cache-and-network", - nextFetchPolicy: "cache-first", - client, - }) - const groupedTranscripts = useMemo( - () => - snpResponse.data?.gene.map((x) => ({ - ...x, - transcripts: x.transcripts.map((xx) => ({ - ...xx, - color: "#aaaaaa", - })), - })), - [snpResponse,] - ) - const chromhmmtrackswithtissue = useMemo(()=> - chromhmm && Object.keys(chromhmm).map(k=>{ - return chromhmm[k].map(c=>{ - return { tissue:k,url:c[2],biosample: c[1]} - }) - }).flat() - ,[chromhmm]) - - - const { data, loading } = useQuery(BIG_QUERY, { - variables: { bigRequests: chromhmm && Object.keys(chromhmm).map(k=>{ - return chromhmm[k].map(c=>{ - return { chr1: props.coordinates.chromosome!, - start: props.coordinates.start, - end: props.coordinates.end, - preRenderedWidth: 1400, - url: c[2],} - }) - }).flat() }, - skip: !chromhmm, - client, - }) - - const handlePageChange = (_, newValue: number) => { - setPage(newValue) - } - - const chromhmmdata = data && !loading && data.bigRequests.map((b,i)=>{ - let f = b.data[0] as BigBedData - return { - start: f.start, - end: f.end, - name: stateDetails[f.name].description+' ('+ stateDetails[f.name].stateno+')', - chr: f.chr, - color: f.color, - tissue: chromhmmtrackswithtissue[i].tissue, - biosample: chromhmmtrackswithtissue[i].biosample - - } - }) - const onDomainChanged = useCallback( - (d: GenomicRange) => { - const chr = d.chromosome === undefined ? props.coordinates.chromosome : d.chromosome - const start = Math.round(d.start) - const end = Math.round(d.end) - if (end - start > 10) { - setCoordinates({ chromosome: chr, start, end }) - } - }, - [props.coordinates] - ) - const l = useCallback((c) => ((c - coordinates.start) * 1400) / (coordinates.end - coordinates.start), [coordinates]) - - return ( - - - - - - {page==0 && -
    - -
    -
    - -
    -
    -
    - - { Object.keys(stateDetails).map((s, i) => ( - = 9 ? 30 : 0})`} key={s}> - - - {s} - - - ))} - -
    - { - if (Math.ceil(x.end) - Math.floor(x.start) > 10) { - setCoordinates({ - chromosome: coordinates.chromosome, - start: Math.floor(x.start), - end: Math.ceil(x.end), - }) - } - }} - > - - - <> - {props.accession && chromhmm && - - } - - - {chromhmm && Object.keys(chromhmm).map(k=>{ - return( - - ) - })} - -     } - {loading && } - {page==1 && chromhmmdata && - Tissue, - value: (row) => row.tissue, - }, - { - header: "Biosample", - HeaderRender: () => Biosample, - value: (row) => row.biosample, - }, - { - header: "State", - HeaderRender: () => States, - value: (row) => {row.name}, - }, - { - header: "Chromosome", - HeaderRender: () => Chromosome, - value: (row) => row.chr, - }, - { - header: "Start", - HeaderRender: () => Start, - value: (row) => row.start, - }, - { - header: "End", - HeaderRender: () => End, - value: (row) => row.end, - } - ]} - rows={chromhmmdata || []} - sortColumn={0} - sortDescending - itemsPerPage={10} - /> - } -     - - ) +"use client" + +import { BIG_QUERY } from "../_gbview/queries" +import React, { useMemo, useState, useRef, useCallback, useEffect } from "react" +import EGeneTracks from "../_gbview/egenetracks" +import { gql, useQuery } from "@apollo/client" +import { Tab, Tabs, CircularProgress, Box } from "@mui/material" +import CytobandView, { GenomicRange } from "../_gbview/cytobandview" +import { client } from "./client" +import Grid from "@mui/material/Grid2" +import { RulerTrack, GenomeBrowser } from "umms-gb" +import Controls from "../_gbview/controls" +import { HumanChromHmmTracks, stateDetails } from "./humanchromhmmtracks" +import { tissueColors } from "../../../common/lib/colors" +import { BigQueryResponse } from "../_gbview/types" +import { BigBedData } from "bigwig-reader" +import { styled } from '@mui/material/styles'; +import { DataTable } from "@weng-lab/psychscreen-ui-components" +import config from "../../../config.json" +const StyledTab = styled(Tab)(() => ({ + textTransform: "none", + })) + +const GENE_QUERY = gql` + query s_3($chromosome: String, $start: Int, $end: Int, $assembly: String!) { + gene(chromosome: $chromosome, start: $start, end: $end, assembly: $assembly) { + name + strand + transcripts { + name + strand + exons { + coordinates { + chromosome + start + end + } + } + coordinates { + chromosome + start + end + } + } + } + } +` + +export type Transcript = { + id: string + name: string + strand: string + coordinates: GenomicRange +} +export type SNPQueryResponse = { + gene: { + name: string + strand: string + transcripts: Transcript[] + }[] +} +export function expandCoordinates(coordinates, l = 20000) { + return { + chromosome: coordinates.chromosome, + start: coordinates.start - l < 0 ? 0 : coordinates.start - l, + end: coordinates.end + l, + } +} + +export const ChromHMM = (props: { coordinates , assembly, accession }) =>{ + const svgRef = useRef(null) + const expandedCoordinates = useMemo(() => expandCoordinates(props.coordinates), [props.coordinates]) + const [coordinates, setCoordinates] = useState(expandedCoordinates) + + const [page, setPage] = useState(0) + const [chromhmm, seChromHmm] = useState(null) + + + useEffect(() => { + + fetch(config.ChromHMM.HumanChromHMM) + .then((x) => x.text()) + .then((x) => { + const lines = x.split("\n") + let ch = {} + lines.forEach((e) => { + let val = e.split("\t") + if(val[2]) + { + if(ch[val[2]]) + { + let e = ch[val[2]] + e.push([val[0],val[3],`https://downloads.wenglab.org/ChIP_${val[1]}.bigBed`]) + + ch[val[2]] = e + + } else { + ch[val[2]] = [[val[0],val[3],`https://downloads.wenglab.org/ChIP_${val[1]}.bigBed`]] + } + } + + + }) + seChromHmm(ch) + + }) + }, []) + + + const snpResponse = useQuery(GENE_QUERY, { + variables: { ...coordinates, assembly: props.assembly }, + fetchPolicy: "cache-and-network", + nextFetchPolicy: "cache-first", + client, + }) + const groupedTranscripts = useMemo( + () => + snpResponse.data?.gene.map((x) => ({ + ...x, + transcripts: x.transcripts.map((xx) => ({ + ...xx, + color: "#aaaaaa", + })), + })), + [snpResponse,] + ) + const chromhmmtrackswithtissue = useMemo(()=> + chromhmm && Object.keys(chromhmm).map(k=>{ + return chromhmm[k].map(c=>{ + return { tissue:k,url:c[2],biosample: c[1]} + }) + }).flat() + ,[chromhmm]) + + + const { data, loading } = useQuery(BIG_QUERY, { + variables: { bigRequests: chromhmm && Object.keys(chromhmm).map(k=>{ + return chromhmm[k].map(c=>{ + return { chr1: props.coordinates.chromosome!, + start: props.coordinates.start, + end: props.coordinates.end, + preRenderedWidth: 1400, + url: c[2],} + }) + }).flat() }, + skip: !chromhmm, + client, + }) + + const handlePageChange = (_, newValue: number) => { + setPage(newValue) + } + + const chromhmmdata = data && !loading && data.bigRequests.map((b,i)=>{ + let f = b.data[0] as BigBedData + return { + start: f.start, + end: f.end, + name: stateDetails[f.name].description+' ('+ stateDetails[f.name].stateno+')', + chr: f.chr, + color: f.color, + tissue: chromhmmtrackswithtissue[i].tissue, + biosample: chromhmmtrackswithtissue[i].biosample + + } + }) + const onDomainChanged = useCallback( + (d: GenomicRange) => { + const chr = d.chromosome === undefined ? props.coordinates.chromosome : d.chromosome + const start = Math.round(d.start) + const end = Math.round(d.end) + if (end - start > 10) { + setCoordinates({ chromosome: chr, start, end }) + } + }, + [props.coordinates] + ) + const l = useCallback((c) => ((c - coordinates.start) * 1400) / (coordinates.end - coordinates.start), [coordinates]) + + return ( + ( + + + + + {page==0 && +
    + +
    +
    + +
    +
    +
    + + { Object.keys(stateDetails).map((s, i) => ( + = 9 ? 30 : 0})`} key={s}> + + + {s} + + + ))} + +
    + { + if (Math.ceil(x.end) - Math.floor(x.start) > 10) { + setCoordinates({ + chromosome: coordinates.chromosome, + start: Math.floor(x.start), + end: Math.ceil(x.end), + }) + } + }} + > + + + <> + {props.accession && chromhmm && + + } + + + {chromhmm && Object.keys(chromhmm).map(k=>{ + return( + + ) + })} + +     } + {loading && } + {page==1 && chromhmmdata && + Tissue, + value: (row) => row.tissue, + }, + { + header: "Biosample", + HeaderRender: () => Biosample, + value: (row) => row.biosample, + }, + { + header: "State", + HeaderRender: () => States, + value: (row) => {row.name}, + }, + { + header: "Chromosome", + HeaderRender: () => Chromosome, + value: (row) => row.chr, + }, + { + header: "Start", + HeaderRender: () => Start, + value: (row) => row.start, + }, + { + header: "End", + HeaderRender: () => End, + value: (row) => row.end, + } + ]} + rows={chromhmmdata || []} + sortColumn={0} + sortDescending + itemsPerPage={10} + /> + } +     ) + ); } \ No newline at end of file diff --git a/screen2.0/src/app/search/_ccredetails/entexdata.tsx b/screen2.0/src/app/search/_ccredetails/entexdata.tsx index 11bf337d..880f02a2 100644 --- a/screen2.0/src/app/search/_ccredetails/entexdata.tsx +++ b/screen2.0/src/app/search/_ccredetails/entexdata.tsx @@ -1,138 +1,151 @@ -import { gql, useQuery } from "@apollo/client" -import React from "react" -import { DataTable } from "@weng-lab/psychscreen-ui-components" -import Grid2 from "@mui/material/Unstable_Grid2/Grid2" -import { client } from "./client" -import { Typography, CircularProgress } from "@mui/material" -import { createLink } from "../../../common/lib/utility" - -const ENTEx_QUERY = gql` -query ENTEXQuery($accession: String!){ - entexQuery(accession: $accession){ - assay - accession - hap1_count - hap2_count - hap1_allele_ratio - p_betabinom - experiment_accession - tissue - donor - imbalance_significance - } -} -` - -const ENTEx_Active_Annotations_QUERY = gql` -query entexActiveAnnotationsQuery( $coordinates: GenomicRangeInput! ) { - entexActiveAnnotationsQuery(coordinates: $coordinates) { - tissue - assay_score - } - -}` -export const ENTExData = (props: { accession, coordinates }) =>{ - console.log(props.coordinates) - const { data, loading } = useQuery(ENTEx_QUERY, { - variables: { accession: props.accession }, - fetchPolicy: "cache-and-network", - nextFetchPolicy: "cache-first", - client, - }) - - const { data: entexActiveAnno, loading: entexActiveAnnoLoading } = useQuery(ENTEx_Active_Annotations_QUERY, { - variables: { coordinates: props.coordinates }, - fetchPolicy: "cache-and-network", - nextFetchPolicy: "cache-first", - client, - }) - - return( - - {loading && } - {data && !loading && data.entexQuery.length>0 && - - Tissue, - value: (row) => row.tissue.split("_").map(s=>s[0].toUpperCase()+s.slice(1)).join(" "), - }, - { - header: "Assay", - HeaderRender: () => Assay, - value: (row) => row.assay.replaceAll("_"," "), - }, - { - header: "Donor", - HeaderRender: () => Donor, - value: (row) => row.donor, - }, - { - header: "Hap 1 Count", - HeaderRender: () => Hap 1 Count, - value: (row) => row.hap1_count - }, - { - header: "Hap 2 Count", - HeaderRender: () => Hap 2 Count, - value: (row) => row.hap2_count - }, - { - header: "Hap 1 Allele Ratio", - HeaderRender: () => Hap 1 Allele Ratio, - value: (row) => row.hap1_allele_ratio.toFixed(2), - }, - { - header: "Experiment Accession", - HeaderRender: () => Experiment Accession, - value: (row) => createLink("https://www.encodeproject.org/experiments/", row.experiment_accession, row.experiment_accession, true), - }, - { - header: "p beta binom", - HeaderRender: () => p Beta Binom, - value: (row) => row.p_betabinom.toFixed(2), - }, - { - header: "Imbalance Significance", - HeaderRender: () => Imbalance Significance, - value: (row) => row.imbalance_significance, - } - ]} - rows={data.entexQuery || []} - sortColumn={5} - searchable - sortDescending - itemsPerPage={10} - /> - } - { !loading && data && data.entexQuery.length==0 && No data available } - {entexActiveAnno && !entexActiveAnnoLoading && entexActiveAnno.entexActiveAnnotationsQuery.length>0 && - - Tissue, - value: (row) => row.tissue.split("_").map(s=>s[0].toUpperCase()+s.slice(1)).join(" "), - }, - { - header: "Supporting Assays", - HeaderRender: () => Supporting Assays, - value: (row) => row.assay_score.split("|").map(s=>s.split(":")[0]).join(",") - } - ]} - rows={entexActiveAnno.entexActiveAnnotationsQuery || []} - sortColumn={0} - searchable - sortDescending - itemsPerPage={10} - /> - - - } - ) +import { gql, useQuery } from "@apollo/client" +import React from "react" +import { DataTable } from "@weng-lab/psychscreen-ui-components" +import Grid from "@mui/material/Grid2" +import { client } from "./client" +import { Typography, CircularProgress } from "@mui/material" +import { createLink } from "../../../common/lib/utility" + +const ENTEx_QUERY = gql` +query ENTEXQuery($accession: String!){ + entexQuery(accession: $accession){ + assay + accession + hap1_count + hap2_count + hap1_allele_ratio + p_betabinom + experiment_accession + tissue + donor + imbalance_significance + } +} +` + +const ENTEx_Active_Annotations_QUERY = gql` +query entexActiveAnnotationsQuery( $coordinates: GenomicRangeInput! ) { + entexActiveAnnotationsQuery(coordinates: $coordinates) { + tissue + assay_score + } + +}` +export const ENTExData = (props: { accession, coordinates }) =>{ + console.log(props.coordinates) + const { data, loading } = useQuery(ENTEx_QUERY, { + variables: { accession: props.accession }, + fetchPolicy: "cache-and-network", + nextFetchPolicy: "cache-first", + client, + }) + + const { data: entexActiveAnno, loading: entexActiveAnnoLoading } = useQuery(ENTEx_Active_Annotations_QUERY, { + variables: { coordinates: props.coordinates }, + fetchPolicy: "cache-and-network", + nextFetchPolicy: "cache-first", + client, + }) + + return ( + ( + {loading && } + {data && !loading && data.entexQuery.length>0 && + + Tissue, + value: (row) => row.tissue.split("_").map(s=>s[0].toUpperCase()+s.slice(1)).join(" "), + }, + { + header: "Assay", + HeaderRender: () => Assay, + value: (row) => row.assay.replaceAll("_"," "), + }, + { + header: "Donor", + HeaderRender: () => Donor, + value: (row) => row.donor, + }, + { + header: "Hap 1 Count", + HeaderRender: () => Hap 1 Count, + value: (row) => row.hap1_count + }, + { + header: "Hap 2 Count", + HeaderRender: () => Hap 2 Count, + value: (row) => row.hap2_count + }, + { + header: "Hap 1 Allele Ratio", + HeaderRender: () => Hap 1 Allele Ratio, + value: (row) => row.hap1_allele_ratio.toFixed(2), + }, + { + header: "Experiment Accession", + HeaderRender: () => Experiment Accession, + value: (row) => createLink("https://www.encodeproject.org/experiments/", row.experiment_accession, row.experiment_accession, true), + }, + { + header: "p beta binom", + HeaderRender: () => p Beta Binom, + value: (row) => row.p_betabinom.toFixed(2), + }, + { + header: "Imbalance Significance", + HeaderRender: () => Imbalance Significance, + value: (row) => row.imbalance_significance, + } + ]} + rows={data.entexQuery || []} + sortColumn={5} + searchable + sortDescending + itemsPerPage={10} + /> + } + { !loading && data && data.entexQuery.length==0 && No data available } + {entexActiveAnno && !entexActiveAnnoLoading && entexActiveAnno.entexActiveAnnotationsQuery.length>0 && + + Tissue, + value: (row) => row.tissue.split("_").map(s=>s[0].toUpperCase()+s.slice(1)).join(" "), + }, + { + header: "Supporting Assays", + HeaderRender: () => Supporting Assays, + value: (row) => row.assay_score.split("|").map(s=>s.split(":")[0]).join(",") + } + ]} + rows={entexActiveAnno.entexActiveAnnotationsQuery || []} + sortColumn={0} + searchable + sortDescending + itemsPerPage={10} + /> + + + } + ) + ); } \ No newline at end of file diff --git a/screen2.0/src/app/search/_ccredetails/functionaldata.tsx b/screen2.0/src/app/search/_ccredetails/functionaldata.tsx index 448a6e01..9f34e312 100644 --- a/screen2.0/src/app/search/_ccredetails/functionaldata.tsx +++ b/screen2.0/src/app/search/_ccredetails/functionaldata.tsx @@ -1,269 +1,289 @@ -"use client" -import React from "react" -import { client } from "./client" -import { useQuery } from "@apollo/client" -import { FUNCTIONAL_DATA_QUERY, CCRE_RDHS_QUERY, MPRA_FUNCTIONAL_DATA_QUERY, CAPRA_SOLO_FUNCTIONAL_DATA_QUERY, CAPRA_DOUBLE_FUNCTIONAL_DATA_QUERY } from "./queries" -import Grid2 from "@mui/material/Unstable_Grid2/Grid2" -import { DataTable } from "@weng-lab/psychscreen-ui-components" -import { LoadingMessage, ErrorMessage } from "../../../common/lib/utility" -import { Link } from "@mui/material" - -export const FunctionData = ({ coordinates , assembly, accession }) => { - const { loading, error, data } = useQuery(FUNCTIONAL_DATA_QUERY, { - variables: { - assembly: assembly === "GRCh38" ? "grch38" : "mm10", - coordinates, - }, - fetchPolicy: "cache-and-network", - nextFetchPolicy: "cache-first", - client, - }) - - const { loading: mpra_loading, error: mpra_error, data: mpra_data } = useQuery(MPRA_FUNCTIONAL_DATA_QUERY, { - variables: { - coordinates, - }, - skip: assembly === "mm10", - fetchPolicy: "cache-and-network", - nextFetchPolicy: "cache-first", - client, - }) - const { loading: capra_loading, error: capra_error, data: capra_data } = useQuery(CAPRA_SOLO_FUNCTIONAL_DATA_QUERY, { - variables: { - accession: [accession], - }, - skip: assembly === "mm10", - fetchPolicy: "cache-and-network", - nextFetchPolicy: "cache-first", - client, - }) - const { loading: capra_double_loading, error: capra_double_error, data: capra_double_data } = useQuery(CAPRA_DOUBLE_FUNCTIONAL_DATA_QUERY, { - variables: { - accession: [accession], - }, - skip: assembly === "mm10", - fetchPolicy: "cache-and-network", - nextFetchPolicy: "cache-first", - client, - }) - - //CCRE_RDHS_QUERY - const { loading: capra_double_rdhs_loading, error: capra_double_rdhs_error, data: capra_double_rdhs_data } = useQuery(CCRE_RDHS_QUERY, { - variables: { - assembly: "GRCh38", - rDHS: [capra_double_data && capra_double_data.capraFccDoubleQuery.length>0 &&capra_double_data.capraFccDoubleQuery[0].rdhs_p1,capra_double_data && capra_double_data.capraFccDoubleQuery.length>0 && capra_double_data.capraFccDoubleQuery[0].rdhs_p2], - }, - //capra_double_data.capraFccDoubleQuery[0].rdhs_p1,capra_double_data.capraFccDoubleQuery[0].rdhs_p2 - skip: capra_double_data===undefined || !capra_double_data , - fetchPolicy: "cache-and-network", - nextFetchPolicy: "cache-first", - client, - }) - - return loading || mpra_loading || capra_loading || capra_double_loading || capra_double_rdhs_loading? ( - - ) : error ? ( - - ) : ( - - - row.chromosome, - }, - { - header: "Start", - value: (row) => row.start, - }, - { - header: "Stop", - value: (row) => row.stop, - }, - { - header: "Element Id", - value: (row) => row.element_id, - render: (row)=> { - const experiment_id = assembly === "GRCh38" ? row.element_id.split("hs")[1] : row.element_id.split("mm")[1] - const organism_id = assembly === "GRCh38" ? 1: 2 - return ( - - )} - }, - { - header: "Assay Result", - value: (row) => row.assay_result, - }, - { - header: "Tissues [number of embryos positive/number of embryos negative]", - value: (row) => row.tissues, - } - ]} - rows={data.functionalCharacterizationQuery || []} - sortColumn={3} - itemsPerPage={5} - /> - - { mpra_error ? ( - - ) : <> - {assembly!=="mm10" && - row.chromosome, - }, - { - header: "Start", - value: (row) => row.start, - }, - { - header: "Stop", - value: (row) => row.stop, - }, - { - header: "Strand", - value: (row) => row.strand, - }, - { - header: "Log2 FC", - value: (row) => row.log2fc.toFixed(2), - HeaderRender: () => <>Log2(Fold Change) - }, - { - header: "Experiment", - value: (row) => row.experiment, - }, - { - header: "Cell Type", - value: (row) => row.celltype, - }, - { - header: "Assay Type", - value: (row) => row.assay_type, - }, - { - header: "Series", - value: (row) => row.series, - }, - { - header: "Location of element", - value: (row) => row.element_location, - }, - { - header: "Location of barcode", - value: (row) => row.barcode_location, - } - ]} - rows={mpra_data.mpraFccQuery || []} - sortColumn={4} - itemsPerPage={5} - /> - }} - { capra_error ? ( - - ) : <> - {assembly!=="mm10" && - row.experiment, - }, - { - header: "DNA Rep1", - value: (row) => row.dna_rep1, - }, - { - header: "RNA Rep1", - value: (row) => row.rna_rep1, - }, - { - header: "RNA Rep2", - value: (row) => row.rna_rep2, - }, - { - header: "RNA Rep3", - value: (row) => row.rna_rep3, - }, - { - header: "Log2FC", - HeaderRender: () => <>Log2(Fold Change), - value: (row) => row.log2fc.toFixed(2), - }, - { - header: "P", - value: (row) => row.pvalue.toFixed(2), - HeaderRender: () => P - }, - { - header: "FDR", - value: (row) => row.fdr.toFixed(2), - } - ]} - rows={capra_data.capraFccSoloQuery || []} - sortColumn={5} - itemsPerPage={5} - /> - }} - { capra_double_error ? ( - - ) : <> - {assembly!=="mm10" && - row.ccrep1+"-"+row.ccrep2, - }, - { - header: "Experiment", - value: (row) => row.experiment, - }, - { - header: "DNA Rep1", - value: (row) => row.dna_rep1, - }, - { - header: "RNA Rep1", - value: (row) => row.rna_rep1, - }, - { - header: "RNA Rep2", - value: (row) => row.rna_rep2, - }, - { - header: "RNA Rep3", - value: (row) => row.rna_rep3, - }, - { - header: "Log2(Fold Change)", - HeaderRender: () => <>Log2(Fold Change), - value: (row) => row.log2fc.toFixed(2), - }, - { - header: "P", - value: (row) => row.pvalue.toFixed(2), - HeaderRender: () => P, - }, - { - header: "FDR", - value: (row) => row.fdr.toFixed(2), - } - ]} - rows={capra_double_data && - capra_double_data.capraFccDoubleQuery.map(c=>{ return {...c, ccrep1: capra_double_rdhs_data && capra_double_rdhs_data.cCREQuery.length>0 && capra_double_rdhs_data.cCREQuery[0].accession, ccrep2: capra_double_rdhs_data && capra_double_rdhs_data.cCREQuery.length>0 && capra_double_rdhs_data.cCREQuery[1].accession } }) - || []} - sortColumn={6} - itemsPerPage={5} - /> - }} - - ) -} +"use client" +import React from "react" +import { client } from "./client" +import { useQuery } from "@apollo/client" +import { FUNCTIONAL_DATA_QUERY, CCRE_RDHS_QUERY, MPRA_FUNCTIONAL_DATA_QUERY, CAPRA_SOLO_FUNCTIONAL_DATA_QUERY, CAPRA_DOUBLE_FUNCTIONAL_DATA_QUERY } from "./queries" +import Grid from "@mui/material/Grid2" +import { DataTable } from "@weng-lab/psychscreen-ui-components" +import { LoadingMessage, ErrorMessage } from "../../../common/lib/utility" +import { Link } from "@mui/material" + +export const FunctionData = ({ coordinates , assembly, accession }) => { + const { loading, error, data } = useQuery(FUNCTIONAL_DATA_QUERY, { + variables: { + assembly: assembly === "GRCh38" ? "grch38" : "mm10", + coordinates, + }, + fetchPolicy: "cache-and-network", + nextFetchPolicy: "cache-first", + client, + }) + + const { loading: mpra_loading, error: mpra_error, data: mpra_data } = useQuery(MPRA_FUNCTIONAL_DATA_QUERY, { + variables: { + coordinates, + }, + skip: assembly === "mm10", + fetchPolicy: "cache-and-network", + nextFetchPolicy: "cache-first", + client, + }) + const { loading: capra_loading, error: capra_error, data: capra_data } = useQuery(CAPRA_SOLO_FUNCTIONAL_DATA_QUERY, { + variables: { + accession: [accession], + }, + skip: assembly === "mm10", + fetchPolicy: "cache-and-network", + nextFetchPolicy: "cache-first", + client, + }) + const { loading: capra_double_loading, error: capra_double_error, data: capra_double_data } = useQuery(CAPRA_DOUBLE_FUNCTIONAL_DATA_QUERY, { + variables: { + accession: [accession], + }, + skip: assembly === "mm10", + fetchPolicy: "cache-and-network", + nextFetchPolicy: "cache-first", + client, + }) + + //CCRE_RDHS_QUERY + const { loading: capra_double_rdhs_loading, error: capra_double_rdhs_error, data: capra_double_rdhs_data } = useQuery(CCRE_RDHS_QUERY, { + variables: { + assembly: "GRCh38", + rDHS: [capra_double_data && capra_double_data.capraFccDoubleQuery.length>0 &&capra_double_data.capraFccDoubleQuery[0].rdhs_p1,capra_double_data && capra_double_data.capraFccDoubleQuery.length>0 && capra_double_data.capraFccDoubleQuery[0].rdhs_p2], + }, + //capra_double_data.capraFccDoubleQuery[0].rdhs_p1,capra_double_data.capraFccDoubleQuery[0].rdhs_p2 + skip: capra_double_data===undefined || !capra_double_data , + fetchPolicy: "cache-and-network", + nextFetchPolicy: "cache-first", + client, + }) + + return loading || mpra_loading || capra_loading || capra_double_loading || capra_double_rdhs_loading? ( + + ) : error ? ( + + ) : ( + + + row.chromosome, + }, + { + header: "Start", + value: (row) => row.start, + }, + { + header: "Stop", + value: (row) => row.stop, + }, + { + header: "Element Id", + value: (row) => row.element_id, + render: (row)=> { + const experiment_id = assembly === "GRCh38" ? row.element_id.split("hs")[1] : row.element_id.split("mm")[1] + const organism_id = assembly === "GRCh38" ? 1: 2 + return ( + + )} + }, + { + header: "Assay Result", + value: (row) => row.assay_result, + }, + { + header: "Tissues [number of embryos positive/number of embryos negative]", + value: (row) => row.tissues, + } + ]} + rows={data.functionalCharacterizationQuery || []} + sortColumn={3} + itemsPerPage={5} + /> + + { mpra_error ? ( + + ) : <> + {assembly!=="mm10" && + row.chromosome, + }, + { + header: "Start", + value: (row) => row.start, + }, + { + header: "Stop", + value: (row) => row.stop, + }, + { + header: "Strand", + value: (row) => row.strand, + }, + { + header: "Log2 FC", + value: (row) => row.log2fc.toFixed(2), + HeaderRender: () => <>Log2(Fold Change) + }, + { + header: "Experiment", + value: (row) => row.experiment, + }, + { + header: "Cell Type", + value: (row) => row.celltype, + }, + { + header: "Assay Type", + value: (row) => row.assay_type, + }, + { + header: "Series", + value: (row) => row.series, + }, + { + header: "Location of element", + value: (row) => row.element_location, + }, + { + header: "Location of barcode", + value: (row) => row.barcode_location, + } + ]} + rows={mpra_data.mpraFccQuery || []} + sortColumn={4} + itemsPerPage={5} + /> + }} + { capra_error ? ( + + ) : <> + {assembly!=="mm10" && + row.experiment, + }, + { + header: "DNA Rep1", + value: (row) => row.dna_rep1, + }, + { + header: "RNA Rep1", + value: (row) => row.rna_rep1, + }, + { + header: "RNA Rep2", + value: (row) => row.rna_rep2, + }, + { + header: "RNA Rep3", + value: (row) => row.rna_rep3, + }, + { + header: "Log2FC", + HeaderRender: () => <>Log2(Fold Change), + value: (row) => row.log2fc.toFixed(2), + }, + { + header: "P", + value: (row) => row.pvalue.toFixed(2), + HeaderRender: () => P + }, + { + header: "FDR", + value: (row) => row.fdr.toFixed(2), + } + ]} + rows={capra_data.capraFccSoloQuery || []} + sortColumn={5} + itemsPerPage={5} + /> + }} + { capra_double_error ? ( + + ) : <> + {assembly!=="mm10" && + row.ccrep1+"-"+row.ccrep2, + }, + { + header: "Experiment", + value: (row) => row.experiment, + }, + { + header: "DNA Rep1", + value: (row) => row.dna_rep1, + }, + { + header: "RNA Rep1", + value: (row) => row.rna_rep1, + }, + { + header: "RNA Rep2", + value: (row) => row.rna_rep2, + }, + { + header: "RNA Rep3", + value: (row) => row.rna_rep3, + }, + { + header: "Log2(Fold Change)", + HeaderRender: () => <>Log2(Fold Change), + value: (row) => row.log2fc.toFixed(2), + }, + { + header: "P", + value: (row) => row.pvalue.toFixed(2), + HeaderRender: () => P, + }, + { + header: "FDR", + value: (row) => row.fdr.toFixed(2), + } + ]} + rows={capra_double_data && + capra_double_data.capraFccDoubleQuery.map(c=>{ return {...c, ccrep1: capra_double_rdhs_data && capra_double_rdhs_data.cCREQuery.length>0 && capra_double_rdhs_data.cCREQuery[0].accession, ccrep2: capra_double_rdhs_data && capra_double_rdhs_data.cCREQuery.length>0 && capra_double_rdhs_data.cCREQuery[1].accession } }) + || []} + sortColumn={6} + itemsPerPage={5} + /> + }} + + ); +} diff --git a/screen2.0/src/app/search/_ccredetails/geneexpression.tsx b/screen2.0/src/app/search/_ccredetails/geneexpression.tsx index ef56f3a5..30d8563d 100644 --- a/screen2.0/src/app/search/_ccredetails/geneexpression.tsx +++ b/screen2.0/src/app/search/_ccredetails/geneexpression.tsx @@ -4,7 +4,7 @@ import { LoadingMessage } from "../../../common/lib/utility" import { PlotGeneExpression } from "../../applets/gene-expression/geneexpressionplot" import { useQuery } from "@apollo/experimental-nextjs-app-support/ssr" import { Button, Typography, Stack, MenuItem, FormControl, SelectChangeEvent, Checkbox, InputLabel, ListItemText, OutlinedInput, Select, ToggleButton, ToggleButtonGroup, FormLabel, Box } from "@mui/material" -import Grid2 from "@mui/material/Unstable_Grid2/Grid2" +import Grid from "@mui/material/Grid2" import Image from "next/image" import { HUMAN_GENE_EXP, MOUSE_GENE_EXP } from "../../applets/gene-expression/const" import { GENE_EXP_QUERY, GENE_QUERY, GET_ORTHOLOG, GET_ORTHOLOG_DATA, GET_ORTHOLOG_VARS } from "../../applets/gene-expression/queries" @@ -179,7 +179,7 @@ export function GeneExpression(props: { }; return ( - + ( : - + Gene - {props.genes.map((gene) => { - return ( - setCurrentGene(gene.name)}> - {gene.name} - {gene?.linkedBy && Linked By: {gene.linkedBy.join(', ')}} - - ) - })} - - - - Peak - - - - - Sort By - - - - - - - {data_gene?.gene[0] && `Gene ID: ${data_gene.gene[0].id} ${peakDetails ? '(' + peakDetails.locusType + ')' : ''}`} - - - {peak && `${peak}: ${peakDetails?.chrom + ":" + peakDetails?.start.toLocaleString() + "-" + peakDetails?.end.toLocaleString()}`} - - - - {data && data.length == 0 ? (No data available) : - - - + return (loading ? : + + + + TSS Activity Profiles by RAMPAGE + + + + + + + + + + + + + + + Gene + + + + Peak + { + setSort(event.target.value as "byValue" | "byTissueMax" | "byTissue") }} - accession={currentGene} - open={configGBopen} - setOpen={setConfigGBOpen} - /> - - ) + > + Tissue + Tissue Max + Value + + + + + + {data_gene?.gene[0] && `Gene ID: ${data_gene.gene[0].id} ${peakDetails ? '(' + peakDetails.locusType + ')' : ''}`} + + + {peak && `${peak}: ${peakDetails?.chrom + ":" + peakDetails?.start.toLocaleString() + "-" + peakDetails?.end.toLocaleString()}`} + + + + {data && data.length == 0 ? (No data available) : + + + + } + + {/* Configure Trackhub */} + + ); } diff --git a/screen2.0/src/app/search/_ccredetails/tfintersection.tsx b/screen2.0/src/app/search/_ccredetails/tfintersection.tsx index 1747e1f3..3a8db3c6 100644 --- a/screen2.0/src/app/search/_ccredetails/tfintersection.tsx +++ b/screen2.0/src/app/search/_ccredetails/tfintersection.tsx @@ -4,7 +4,7 @@ import { Link } from "@mui/material" import { client } from "./client" import { useQuery } from "@apollo/client" import { TF_INTERSECTION_QUERY, CRE_TF_DCC_QUERY } from "./queries" -import Grid2 from "@mui/material/Unstable_Grid2/Grid2" +import Grid from "@mui/material/Grid2" import { DataTable } from "@weng-lab/psychscreen-ui-components" import { LoadingMessage } from "../../../common/lib/utility" @@ -77,81 +77,92 @@ export const TfIntersection: React.FC<{ assembly: string; coordinates: { chromos } }) - return ( - <> - {loading || !data ? ( - - - - - - ) : ( - <> - - + return (<> + {loading || !data ? ( + + + + + + ) : ( + <> + + + row.name, + render: (row) => ( + + + + ), + }, + { + header: "# of experiments that support TF binding", + value: (row) => row.n, + }, + { + header: "# experiments in total", + value: (row) => row.total, + }, + ]} + tableTitle="TFs that bind this cCRE " + rows={tableData || []} + onRowClick={(row) => { + setFactor(row.name) + setFactorHighlight(row) + }} + sortColumn={1} + itemsPerPage={5} + highlighted={factorHighlight} + /> + + {cre_tf_data && ( + row.name, + header: "cell type", + value: (row) => row.biosample_term_name, + }, + { + header: "experiment/file", + value: (row) => row.expID, render: (row) => ( - - + + ), }, - { - header: "# of experiments that support TF binding", - value: (row) => row.n, - }, - { - header: "# experiments in total", - value: (row) => row.total, - }, ]} - tableTitle="TFs that bind this cCRE " - rows={tableData || []} - onRowClick={(row) => { - setFactor(row.name) - setFactorHighlight(row) - }} - sortColumn={1} + tableTitle={`ChIP-seq ${factor} Experiments`} + rows={cre_tf_data || []} + sortColumn={0} itemsPerPage={5} - highlighted={factorHighlight} /> - - {cre_tf_data && ( - - row.biosample_term_name, - }, - { - header: "experiment/file", - value: (row) => row.expID, - render: (row) => ( - - - - ), - }, - ]} - tableTitle={`ChIP-seq ${factor} Experiments`} - rows={cre_tf_data || []} - sortColumn={0} - itemsPerPage={5} - /> - - )} - - - )} - - ) + + )} + + + )} + ); } diff --git a/screen2.0/src/app/search/_gbview/genomebrowserview.tsx b/screen2.0/src/app/search/_gbview/genomebrowserview.tsx index cf11d158..80eb577e 100644 --- a/screen2.0/src/app/search/_gbview/genomebrowserview.tsx +++ b/screen2.0/src/app/search/_gbview/genomebrowserview.tsx @@ -1,6 +1,6 @@ "use client" import React, { useMemo, useState, useRef, useCallback, useEffect } from "react" -import Grid2 from "@mui/material/Unstable_Grid2/Grid2" +import Grid from "@mui/material/Grid2" import { RulerTrack, GenomeBrowser } from "umms-gb" import Controls from "./controls" import { gql, useQuery } from "@apollo/client" @@ -186,74 +186,76 @@ export const GenomeBrowserView: React.FC = (props) => { } }, [bdata, props.biosample, props.assembly, props.biosampledisplayname]) - return ( - <> - - -
    - -
    -
    - -
    -
    -
    - + + +
    + +
    +
    + +
    +
    +
    + { + if (Math.ceil(x.end) - Math.floor(x.start) > 10) { + setCoordinates({ + chromosome: coordinates.chromosome, + start: Math.floor(x.start), + end: Math.ceil(x.end), + }) + } + }} + > + + + {highlight && ( + + )} + <> + {props.accessions && props.accessions.map((a)=>( + + ))} + + + { - if (Math.ceil(x.end) - Math.floor(x.start) > 10) { - setCoordinates({ - chromosome: coordinates.chromosome, - start: Math.floor(x.start), - end: Math.ceil(x.end), - }) - } + oncCREClicked={(x)=>{ + props.handlecCREClickInTrack && props.handlecCREClickInTrack({ accession: x.name, chromosome: x.coordinates.chromosome,start: x.coordinates.start,end: x.coordinates.end }) }} - > - - - {highlight && ( - - )} - <> - {props.accessions && props.accessions.map((a)=>( - - ))} - - - x && setHighlight(x)} + oncCREMousedOut={() => setHighlight(null)} + /> + {props.biosample && props.assembly != "mm10" && cTracks && ( + { - props.handlecCREClickInTrack && props.handlecCREClickInTrack({ accession: x.name, chromosome: x.coordinates.chromosome,start: x.coordinates.start,end: x.coordinates.end }) - }} + tracks={cTracks} oncCREMousedOver={(x) => x && setHighlight(x)} oncCREMousedOut={() => setHighlight(null)} + oncCREClicked={(x)=>{ + props.handlecCREClickInTrack && props.handlecCREClickInTrack({ accession: x.name, chromosome: x.coordinates.chromosome,start: x.coordinates.start,end: x.coordinates.end }) + }} /> - {props.biosample && props.assembly != "mm10" && cTracks && ( - x && setHighlight(x)} - oncCREMousedOut={() => setHighlight(null)} - oncCREClicked={(x)=>{ - props.handlecCREClickInTrack && props.handlecCREClickInTrack({ accession: x.name, chromosome: x.coordinates.chromosome,start: x.coordinates.start,end: x.coordinates.end }) - }} - /> - )} - -     -     - - ) + )} + + + + ); } diff --git a/screen2.0/src/app/search/_gbview/queries.ts b/screen2.0/src/app/search/_gbview/queries.ts index 7e222b08..7db9fae7 100644 --- a/screen2.0/src/app/search/_gbview/queries.ts +++ b/screen2.0/src/app/search/_gbview/queries.ts @@ -1,31 +1,31 @@ -import { gql } from "@apollo/client" -export const BIG_QUERY = gql` - query BigRequests($bigRequests: [BigRequest!]!) { - bigRequests(requests: $bigRequests) { - data - error { - errortype - message - } - } - } -` - -export const BIOSAMPLE_QUERY = gql` - query q_1($assembly: String!) { - ccREBiosampleQuery(assembly: $assembly) { - biosamples { - name - displayname - dnase: experimentAccession(assay: "DNase") - h3k4me3: experimentAccession(assay: "H3K4me3") - h3k27ac: experimentAccession(assay: "H3K27ac") - ctcf: experimentAccession(assay: "CTCF") - dnase_signal: fileAccession(assay: "DNase") - h3k4me3_signal: fileAccession(assay: "H3K4me3") - h3k27ac_signal: fileAccession(assay: "H3K27ac") - ctcf_signal: fileAccession(assay: "CTCF") - } - } - } -` +import { gql } from "@apollo/client" +export const BIG_QUERY = gql` + query BigRequests($bigRequests: [BigRequest!]!) { + bigRequests(requests: $bigRequests) { + data + error { + errortype + message + } + } + } +` + +export const BIOSAMPLE_QUERY = gql` + query q_1($assembly: String!) { + ccREBiosampleQuery(assembly: $assembly) { + biosamples { + name + displayname + dnase: experimentAccession(assay: "DNase") + h3k4me3: experimentAccession(assay: "H3K4me3") + h3k27ac: experimentAccession(assay: "H3K27ac") + ctcf: experimentAccession(assay: "CTCF") + dnase_signal: fileAccession(assay: "DNase") + h3k4me3_signal: fileAccession(assay: "H3K4me3") + h3k27ac_signal: fileAccession(assay: "H3K27ac") + ctcf_signal: fileAccession(assay: "CTCF") + } + } + } +` diff --git a/screen2.0/src/app/search/_gbview/tfsequencefeatures.tsx b/screen2.0/src/app/search/_gbview/tfsequencefeatures.tsx index f5ad09cc..6c7474d2 100644 --- a/screen2.0/src/app/search/_gbview/tfsequencefeatures.tsx +++ b/screen2.0/src/app/search/_gbview/tfsequencefeatures.tsx @@ -1,241 +1,243 @@ -"use client" -import React, { useMemo, useState, useRef, useCallback, useEffect } from "react" -import Grid2 from "@mui/material/Unstable_Grid2/Grid2" -import { RulerTrack, GenomeBrowser } from "umms-gb" -import Controls from "./controls" -import { gql, useQuery } from "@apollo/client" -import CytobandView, { GenomicRange } from "./cytobandview" -import EGeneTracks from "./egenetracks" -import { client } from "../_ccredetails/client" -import { TfMotifTrack } from "./tfmotiftrack" -import { EmptyTrack, FullBigWig } from "umms-gb" -import { GraphQLImportanceTrack } from "bpnet-ui" -import { BigQueryResponse } from "./types" -import { BIG_QUERY } from "./queries" -import { BigWigData } from "bigwig-reader" -type TfSequenceFeaturesProps = { - coordinates: { - start: number - end: number - chromosome?: string - } - assembly: string -} -const GENE_QUERY = gql` - query s_1($chromosome: String, $start: Int, $end: Int, $assembly: String!, $version: Int) { - gene(chromosome: $chromosome, start: $start, end: $end, assembly: $assembly, version: $version) { - name - strand - transcripts { - name - strand - exons { - coordinates { - chromosome - start - end - } - } - coordinates { - chromosome - start - end - } - } - } - } -` -export type Transcript = { - id: string - name: string - strand: string - coordinates: GenomicRange -} -export type SNPQueryResponse = { - gene: { - name: string - strand: string - transcripts: Transcript[] - }[] -} -export function expandCoordinates(coordinates, l = 0) { - return { - chromosome: coordinates.chromosome, - start: coordinates.start - l < 0 ? 0 : coordinates.start - l, - end: coordinates.end + l, - } -} -const DATA_QUERY = ` -query q($requests: [BigRequest!]!) { - bigRequests(requests: $requests) { - data - } -} -` - -export const TfSequenceFeatures: React.FC = (props) => { - - const [data, setData] = useState([]) - const [loading, setLoading] = useState(true) - const svgRef = useRef(null) - const expandedCoordinates = useMemo(() => expandCoordinates(props.coordinates), [props.coordinates]) - const [coordinates, setCoordinates] = useState(expandedCoordinates) - const [settingsMousedOver, setSettingsMousedOver] = useState(false) - useEffect(() => { - fetch("https://ga.staging.wenglab.org/graphql", { - method: "POST", - headers: { - "Content-Type": "application/json", - Accept: "application/json", - }, - body: JSON.stringify({ - query: DATA_QUERY, - variables: { - requests: [ - { - url: "gs://gcp.wenglab.org/SCREEN/all-sites.sorted.formatted.bigBed", - chr1: coordinates.chromosome, - start: coordinates.start, - chr2: coordinates.chromosome, - end: coordinates.end - }, - ], - }, - }), - }) - .then((x) => x.json()) - .then((x) => { - setData(x.data.bigRequests[0].data.filter((x) => x.name.split("$")[3] === "True")) - setLoading(false) - }) - }, [coordinates]) - const url = props.assembly==="GRCh38" ?"gs://gcp.wenglab.org/241-mammalian-2020v2.bigWig" : "gs://gcp.wenglab.org/mm10.phylop.bigWig" - const { data: sequenceData, loading: sequenceLoading } = useQuery(BIG_QUERY, { - variables: { bigRequests: [{ - url, - chr1: coordinates.chromosome, - start: coordinates.start, - chr2: coordinates.chromosome, - end: coordinates.end - }] }, - client, - }) - //sequenceData?.bigRequests array - const snpResponse = useQuery(GENE_QUERY, { - variables: { ...coordinates, assembly: props.assembly,version: props.assembly.toLowerCase()==="grch38" ? 40: 25 }, - fetchPolicy: "cache-and-network", - nextFetchPolicy: "cache-first", - client, - }) - - const groupedTranscripts = useMemo( - () => - snpResponse.data?.gene.map((x) => ({ - ...x, - transcripts: x.transcripts.map((xx) => ({ - ...xx, - color: "#aaaaaa", - })), - })), - [snpResponse] - ) - const onDomainChanged = useCallback( - (d: GenomicRange) => { - const chr = d.chromosome === undefined ? props.coordinates.chromosome : d.chromosome - const start = Math.round(d.start) - const end = Math.round(d.end) - if (end - start > 10) { - setCoordinates({ chromosome: chr, start, end }) - } - }, - [props.coordinates] - ) - const l = useCallback((c) => ((c - coordinates.start) * 1400) / (coordinates.end - coordinates.start), [coordinates]) - - return ( - <> - - -
    - -
    -
    - -
    -
    -
    - { - if (Math.ceil(x.end) - Math.floor(x.start) > 10) { - setCoordinates({ - chromosome: coordinates.chromosome, - start: Math.floor(x.start), - end: Math.ceil(x.end), - }) - } - }} - > - - <> - {(props.coordinates.start > coordinates.start || props.coordinates.end < coordinates.end ) && - - } - - - {!loading && data && props.assembly!=="mm10" && } - - - {coordinates.end - coordinates.start < 5000 ? : - } - {settingsMousedOver && ( - - )} - - setSettingsMousedOver(true)} - onMouseOut={() => setSettingsMousedOver(false)} - strokeWidth={1} - transform="translate(20,0)" - /> - - Sequence - - - - -     -     - - ) -} +"use client" +import React, { useMemo, useState, useRef, useCallback, useEffect } from "react" +import Grid from "@mui/material/Grid2" +import { RulerTrack, GenomeBrowser } from "umms-gb" +import Controls from "./controls" +import { gql, useQuery } from "@apollo/client" +import CytobandView, { GenomicRange } from "./cytobandview" +import EGeneTracks from "./egenetracks" +import { client } from "../_ccredetails/client" +import { TfMotifTrack } from "./tfmotiftrack" +import { EmptyTrack, FullBigWig } from "umms-gb" +import { GraphQLImportanceTrack } from "bpnet-ui" +import { BigQueryResponse } from "./types" +import { BIG_QUERY } from "./queries" +import { BigWigData } from "bigwig-reader" +type TfSequenceFeaturesProps = { + coordinates: { + start: number + end: number + chromosome?: string + } + assembly: string +} +const GENE_QUERY = gql` + query s_1($chromosome: String, $start: Int, $end: Int, $assembly: String!, $version: Int) { + gene(chromosome: $chromosome, start: $start, end: $end, assembly: $assembly, version: $version) { + name + strand + transcripts { + name + strand + exons { + coordinates { + chromosome + start + end + } + } + coordinates { + chromosome + start + end + } + } + } + } +` +export type Transcript = { + id: string + name: string + strand: string + coordinates: GenomicRange +} +export type SNPQueryResponse = { + gene: { + name: string + strand: string + transcripts: Transcript[] + }[] +} +export function expandCoordinates(coordinates, l = 0) { + return { + chromosome: coordinates.chromosome, + start: coordinates.start - l < 0 ? 0 : coordinates.start - l, + end: coordinates.end + l, + } +} +const DATA_QUERY = ` +query q($requests: [BigRequest!]!) { + bigRequests(requests: $requests) { + data + } +} +` + +export const TfSequenceFeatures: React.FC = (props) => { + + const [data, setData] = useState([]) + const [loading, setLoading] = useState(true) + const svgRef = useRef(null) + const expandedCoordinates = useMemo(() => expandCoordinates(props.coordinates), [props.coordinates]) + const [coordinates, setCoordinates] = useState(expandedCoordinates) + const [settingsMousedOver, setSettingsMousedOver] = useState(false) + useEffect(() => { + fetch("https://ga.staging.wenglab.org/graphql", { + method: "POST", + headers: { + "Content-Type": "application/json", + Accept: "application/json", + }, + body: JSON.stringify({ + query: DATA_QUERY, + variables: { + requests: [ + { + url: "gs://gcp.wenglab.org/SCREEN/all-sites.sorted.formatted.bigBed", + chr1: coordinates.chromosome, + start: coordinates.start, + chr2: coordinates.chromosome, + end: coordinates.end + }, + ], + }, + }), + }) + .then((x) => x.json()) + .then((x) => { + setData(x.data.bigRequests[0].data.filter((x) => x.name.split("$")[3] === "True")) + setLoading(false) + }) + }, [coordinates]) + const url = props.assembly==="GRCh38" ?"gs://gcp.wenglab.org/241-mammalian-2020v2.bigWig" : "gs://gcp.wenglab.org/mm10.phylop.bigWig" + const { data: sequenceData, loading: sequenceLoading } = useQuery(BIG_QUERY, { + variables: { bigRequests: [{ + url, + chr1: coordinates.chromosome, + start: coordinates.start, + chr2: coordinates.chromosome, + end: coordinates.end + }] }, + client, + }) + //sequenceData?.bigRequests array + const snpResponse = useQuery(GENE_QUERY, { + variables: { ...coordinates, assembly: props.assembly,version: props.assembly.toLowerCase()==="grch38" ? 40: 25 }, + fetchPolicy: "cache-and-network", + nextFetchPolicy: "cache-first", + client, + }) + + const groupedTranscripts = useMemo( + () => + snpResponse.data?.gene.map((x) => ({ + ...x, + transcripts: x.transcripts.map((xx) => ({ + ...xx, + color: "#aaaaaa", + })), + })), + [snpResponse] + ) + const onDomainChanged = useCallback( + (d: GenomicRange) => { + const chr = d.chromosome === undefined ? props.coordinates.chromosome : d.chromosome + const start = Math.round(d.start) + const end = Math.round(d.end) + if (end - start > 10) { + setCoordinates({ chromosome: chr, start, end }) + } + }, + [props.coordinates] + ) + const l = useCallback((c) => ((c - coordinates.start) * 1400) / (coordinates.end - coordinates.start), [coordinates]) + + return (<> + + +
    + +
    +
    + +
    +
    +
    + { + if (Math.ceil(x.end) - Math.floor(x.start) > 10) { + setCoordinates({ + chromosome: coordinates.chromosome, + start: Math.floor(x.start), + end: Math.ceil(x.end), + }) + } + }} + > + + <> + {(props.coordinates.start > coordinates.start || props.coordinates.end < coordinates.end ) && + + } + + + {!loading && data && props.assembly!=="mm10" && } + + + {coordinates.end - coordinates.start < 5000 ? : + } + {settingsMousedOver && ( + + )} + + setSettingsMousedOver(true)} + onMouseOut={() => setSettingsMousedOver(false)} + strokeWidth={1} + transform="translate(20,0)" + /> + + Sequence + + + + +     +     + ); +} diff --git a/screen2.0/src/app/search/_gbview/types.ts b/screen2.0/src/app/search/_gbview/types.ts index 983c2e16..3ab9b043 100644 --- a/screen2.0/src/app/search/_gbview/types.ts +++ b/screen2.0/src/app/search/_gbview/types.ts @@ -1,21 +1,21 @@ -import { BigWigData, BigBedData, BigZoomData } from "bigwig-reader" -import { RequestError } from "umms-gb/dist/components/tracks/trackset/types" -import { ValuedPoint } from "umms-gb/dist/utils/types" - - -export type BigResponseData = BigWigData[] | BigBedData[] | BigZoomData[] | ValuedPoint[] - -export type BigResponse = { - data: BigResponseData - error: RequestError -} - -export type BigQueryResponse = { - bigRequests: BigResponse[] -} - -export type GenomicRange = { - chromosome?: string - start: number - end: number +import { BigWigData, BigBedData, BigZoomData } from "bigwig-reader" +import { RequestError } from "umms-gb/dist/components/tracks/trackset/types" +import { ValuedPoint } from "umms-gb/dist/utils/types" + + +export type BigResponseData = BigWigData[] | BigBedData[] | BigZoomData[] | ValuedPoint[] + +export type BigResponse = { + data: BigResponseData + error: RequestError +} + +export type BigQueryResponse = { + bigRequests: BigResponse[] +} + +export type GenomicRange = { + chromosome?: string + start: number + end: number } \ No newline at end of file diff --git a/screen2.0/src/app/search/_geneAutocomplete/GeneAutocomplete.tsx b/screen2.0/src/app/search/_geneAutocomplete/GeneAutocomplete.tsx index a56e1933..411fd879 100644 --- a/screen2.0/src/app/search/_geneAutocomplete/GeneAutocomplete.tsx +++ b/screen2.0/src/app/search/_geneAutocomplete/GeneAutocomplete.tsx @@ -1,6 +1,6 @@ import React, { useState, useEffect, useCallback, useMemo } from "react" import Box from "@mui/material/Box" -import Grid2 from "@mui/material/Unstable_Grid2/Grid2" +import Grid from "@mui/material/Grid2" import Typography from "@mui/material/Typography" import { debounce } from "@mui/material/utils" import { GENE_AUTOCOMPLETE_QUERY } from "../../_mainsearch/queries" @@ -186,16 +186,16 @@ export const GeneAutocomplete = ( } else { return (
  • - - + + {option.name} {descriptions.find((g) => g.name === option.name)?.desc} - - + +
    • ) } diff --git a/screen2.0/src/app/search/mainresultsfilters.tsx b/screen2.0/src/app/search/mainresultsfilters.tsx index 54417aac..440d1248 100644 --- a/screen2.0/src/app/search/mainresultsfilters.tsx +++ b/screen2.0/src/app/search/mainresultsfilters.tsx @@ -27,7 +27,7 @@ import Radio from '@mui/material/Radio'; import RadioGroup from '@mui/material/RadioGroup'; import FormControl from '@mui/material/FormControl'; import ExpandMoreIcon from "@mui/icons-material/ExpandMore" -import Grid2 from "@mui/material/Unstable_Grid2" +import Grid from "@mui/material/Grid2" import { RangeSlider } from "@weng-lab/psychscreen-ui-components" import { FilterCriteria, MainQueryParams, RegistryBiosample } from "./types" import { eQTLsTissues, filtersModified } from "./searchhelpers" @@ -233,8 +233,8 @@ export function MainResultsFilters( const geneInfo = linkedGenesWithNums.find(x => x.geneName === option.name) return (
  • - - + + {loadingLinkedGenes ? @@ -248,8 +248,8 @@ export function MainResultsFilters( {descriptions.find((g) => g.name === option.name)?.desc + ` (Linked: ${geneInfo?.accessions.length ?? 0})`} - - + +
    • ) }, [loadingLinkedGenes, linkedGenesWithNums]) @@ -332,16 +332,16 @@ export function MainResultsFilters( ) => { return (
  • - - + + {option.name} {`${currentGene} linked to ${option.count} in this biosample`} - - + +
    • ) }, []) @@ -385,7 +385,7 @@ export function MainResultsFilters( return ( - + ( {/* cCREs within distance from SNP */} {mainQueryParams.snp.rsID && <> @@ -412,8 +412,8 @@ export function MainResultsFilters( - - + + - - + + @@ -465,8 +465,8 @@ export function MainResultsFilters( {geneTranscripts ? - - + + } label={<>Within distance of TSS of {mainQueryParams.gene.name}} /> - - {mainQueryParams.gene.nearTSS && + + {mainQueryParams.gene.nearTSS && Distance around TSS @@ -499,8 +499,8 @@ export function MainResultsFilters( marks={tssMarks} /> - } - + } + : } @@ -589,8 +589,8 @@ export function MainResultsFilters( - - {(!mainQueryParams.biosample || mainQueryParams.biosample.dnase) && + + {(!mainQueryParams.biosample || mainQueryParams.biosample.dnase) && - } - {(!mainQueryParams.biosample || mainQueryParams.biosample.h3k4me3) && + } + {(!mainQueryParams.biosample || mainQueryParams.biosample.h3k4me3) && - } - {(!mainQueryParams.biosample || mainQueryParams.biosample.h3k27ac) && + } + {(!mainQueryParams.biosample || mainQueryParams.biosample.h3k27ac) && - } - {(!mainQueryParams.biosample || mainQueryParams.biosample.ctcf) && + } + {(!mainQueryParams.biosample || mainQueryParams.biosample.ctcf) && - } - {(!mainQueryParams.biosample || mainQueryParams.biosample.atac) && + } + {(!mainQueryParams.biosample || mainQueryParams.biosample.atac) && - } - + } + {/* Classification */} @@ -722,8 +722,8 @@ export function MainResultsFilters( {/* cCRE Classes */} - - + + - - + + - - + + {/* Conservation */} @@ -817,8 +817,8 @@ export function MainResultsFilters( - - + + - - + + - - + + - - + + } {/* Linked Genes */} @@ -1171,6 +1171,6 @@ export function MainResultsFilters( } } - - ) + ) + ); } diff --git a/screen2.0/src/app/search/mainresultstable.tsx b/screen2.0/src/app/search/mainresultstable.tsx index a8e10c94..b19fd68f 100644 --- a/screen2.0/src/app/search/mainresultstable.tsx +++ b/screen2.0/src/app/search/mainresultstable.tsx @@ -240,7 +240,7 @@ export function MainResultsTable(props: MainResultsTableProps) { return ( //If linked genes data hasn't been fetched, fetch - ) => { event.stopPropagation(); !row.linkedGenes && getLinkedGenes() }} key={row.accession}> + () => { event.stopPropagation(); !row.linkedGenes && getLinkedGenes() }} key={row.accession}> } @@ -312,8 +312,8 @@ export function MainResultsTable(props: MainResultsTableProps) { } - - ) + ) + ); } }) cols.push({ @@ -327,7 +327,7 @@ export function MainResultsTable(props: MainResultsTableProps) { return ( //Box's onClick prevents onRowClick from running when interacting with modal - ) => { event.stopPropagation() }}> + () => { event.stopPropagation() }}> @@ -342,8 +342,8 @@ export function MainResultsTable(props: MainResultsTableProps) { open={open} setOpen={setOpen} /> - - ) + ) + ); } }) props.assembly === "GRCh38" && cols.push({ diff --git a/screen2.0/src/common/lib/utility.tsx b/screen2.0/src/common/lib/utility.tsx index 3fcc3378..6fe9a4b1 100644 --- a/screen2.0/src/common/lib/utility.tsx +++ b/screen2.0/src/common/lib/utility.tsx @@ -1,6 +1,6 @@ import React from "react" import { Link, Alert, AlertTitle, CircularProgress, Typography, TypographyPropsVariantOverrides, Stack, TypographyOwnProps } from "@mui/material" -import Grid2 from "@mui/material/Unstable_Grid2/Grid2" +import Grid from "@mui/material/Grid2" import { Snackbar, Box } from "@mui/material" import { OverridableStringUnion } from '@mui/types'; import { Variant } from "@mui/material/styles/createTypography"; @@ -75,14 +75,14 @@ export const CreateLink: React.FC<{ linkPrefix: string, linkArg?: string, label: */ export function LoadingMessage() { return ( - + Loading... - + ) } @@ -96,7 +96,7 @@ export function ErrorMessage(props: { error: Error }) { // throw error return ( - + - + ) } diff --git a/screen2.0/yarn.lock b/screen2.0/yarn.lock index 5a5f0e7e..002e2f55 100644 --- a/screen2.0/yarn.lock +++ b/screen2.0/yarn.lock @@ -670,7 +670,7 @@ __metadata: languageName: node 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languageName: node linkType: hard +"@mui/private-theming@npm:^6.1.1": + version: 6.1.1 + resolution: "@mui/private-theming@npm:6.1.1" + dependencies: + "@babel/runtime": ^7.25.6 + "@mui/utils": ^6.1.1 + prop-types: ^15.8.1 + peerDependencies: + "@types/react": ^17.0.0 || ^18.0.0 || ^19.0.0 + react: ^17.0.0 || ^18.0.0 || ^19.0.0 + peerDependenciesMeta: + "@types/react": + optional: true + checksum: 20943e600fb8a68b6240cf996d42af9d6fabb0a9be5c728765978fda78bfe6e94d75f4fa16130bdbcad7449cd572d0c4eb480de8749c5e009573e128737d90ea + languageName: node + linkType: hard + "@mui/styled-engine@npm:^5.16.6": version: 5.16.6 resolution: "@mui/styled-engine@npm:5.16.6" @@ -1867,7 +1943,29 @@ __metadata: languageName: node linkType: hard -"@mui/system@npm:^5.16.5, @mui/system@npm:^5.16.7": +"@mui/styled-engine@npm:^6.1.1": + version: 6.1.1 + resolution: "@mui/styled-engine@npm:6.1.1" + dependencies: + "@babel/runtime": ^7.25.6 + "@emotion/cache": ^11.13.1 + "@emotion/sheet": ^1.4.0 + csstype: ^3.1.3 + prop-types: ^15.8.1 + peerDependencies: + "@emotion/react": ^11.4.1 + "@emotion/styled": ^11.3.0 + react: ^17.0.0 || ^18.0.0 || ^19.0.0 + peerDependenciesMeta: + "@emotion/react": + optional: true + "@emotion/styled": + optional: true + checksum: 9ea4396ae71b92eef4db0f9099ec3be757bfa3c09c5cb8573140f473c5b5f9539f1f2f64cf458c0b39a9867096cfea780c07e67fc0b01c7854afb8230c660f0f + languageName: node + linkType: hard + +"@mui/system@npm:^5.16.7": version: 5.16.7 resolution: "@mui/system@npm:5.16.7" dependencies: @@ -1895,6 +1993,34 @@ __metadata: languageName: node linkType: hard +"@mui/system@npm:^6.0.0-dev.240424162023-9968b4889d, @mui/system@npm:^6.1.1": + version: 6.1.1 + resolution: "@mui/system@npm:6.1.1" + dependencies: + "@babel/runtime": ^7.25.6 + "@mui/private-theming": ^6.1.1 + "@mui/styled-engine": ^6.1.1 + "@mui/types": ^7.2.17 + "@mui/utils": ^6.1.1 + clsx: ^2.1.1 + csstype: ^3.1.3 + prop-types: ^15.8.1 + peerDependencies: + "@emotion/react": ^11.5.0 + "@emotion/styled": ^11.3.0 + "@types/react": ^17.0.0 || ^18.0.0 || ^19.0.0 + react: ^17.0.0 || ^18.0.0 || ^19.0.0 + peerDependenciesMeta: + "@emotion/react": + optional: true + "@emotion/styled": + optional: true + "@types/react": + optional: true + checksum: 9d030b9646da961c45411ea4e59113bc41f080ca28a2fd08b8055398a2f5a6fa9a9ba538363384e1db1a7ce0bdadfa290acaf4ac5b4d04aa10bf99b343536276 + languageName: node + linkType: hard + "@mui/types@npm:^7.2.14, @mui/types@npm:^7.2.15": version: 7.2.16 resolution: "@mui/types@npm:7.2.16" @@ -1907,7 +2033,19 @@ __metadata: languageName: node linkType: hard -"@mui/utils@npm:^5.15.14, @mui/utils@npm:^5.16.5, @mui/utils@npm:^5.16.6": +"@mui/types@npm:^7.2.17": + version: 7.2.17 + resolution: "@mui/types@npm:7.2.17" + peerDependencies: + "@types/react": ^17.0.0 || ^18.0.0 || ^19.0.0 + peerDependenciesMeta: + "@types/react": + optional: true + checksum: 21b7f7639f05663f4ba9baa75f8a3f2fbb1e675e0fa4a4ef3b97acdcb81b6290c04b5515d2ae719e8ed2397bbe379f9fb665c74b209a2181fcccd2f83483dd85 + languageName: node + linkType: hard + +"@mui/utils@npm:^5.16.6": version: 5.16.6 resolution: "@mui/utils@npm:5.16.6" dependencies: @@ -1927,6 +2065,26 @@ __metadata: languageName: node linkType: hard +"@mui/utils@npm:^6.0.0-alpha.1, @mui/utils@npm:^6.0.0-alpha.3, @mui/utils@npm:^6.1.1": + version: 6.1.1 + resolution: "@mui/utils@npm:6.1.1" + dependencies: + "@babel/runtime": ^7.25.6 + "@mui/types": ^7.2.17 + "@types/prop-types": ^15.7.12 + clsx: ^2.1.1 + prop-types: ^15.8.1 + react-is: ^18.3.1 + peerDependencies: + "@types/react": ^17.0.0 || ^18.0.0 || ^19.0.0 + react: ^17.0.0 || ^18.0.0 || ^19.0.0 + peerDependenciesMeta: + "@types/react": + optional: true + checksum: 1f8b9d8a71fdabfe7adaf18d2d24b480dce250ad4b9491cc51e1fa503804332fb733c212cfb8601bb4e193f91f635f5b06c378c17c5e91d602033ea319ca3e74 + languageName: node + linkType: hard + "@next/env@npm:14.2.13": version: 14.2.13 resolution: "@next/env@npm:14.2.13" @@ -2409,7 +2567,7 @@ __metadata: languageName: node linkType: hard -"@types/react-transition-group@npm:^4.4.10": +"@types/react-transition-group@npm:^4.4.10, @types/react-transition-group@npm:^4.4.11": version: 4.4.11 resolution: "@types/react-transition-group@npm:4.4.11" dependencies: @@ -3330,9 +3488,9 @@ __metadata: languageName: node linkType: hard -"@weng-lab/psychscreen-ui-components@npm:^1.0.4": - version: 1.0.4 - resolution: "@weng-lab/psychscreen-ui-components@npm:1.0.4" +"@weng-lab/psychscreen-ui-components@npm:^2.0.0": + version: 2.0.0 + resolution: "@weng-lab/psychscreen-ui-components@npm:2.0.0" dependencies: "@visx/tooltip": ^3.3.0 cytoscape: ^3.29.2 @@ -3342,8 +3500,13 @@ __metadata: tippy.js: ^6.3.7 use-react-screenshot: ^4.0.0 peerDependencies: - react: ">=16" - checksum: a96764630b4b13c914699493cad833e1ef13854b93aebc1557d9d7fb78615d5571bcd9a120d75a0ef606ed36dbd245eb1b7badd5b54f972e894419f1406a8be3 + "@emotion/react": ^11.13.3 + "@emotion/styled": ^11.13.0 + "@mui/icons-material": ^6.1.1 + "@mui/material": ^6.1.1 + react: ^18.2.0 + react-dom: ^18.2.0 + checksum: 354a95a94beb1795d30437df2efde9ff88717556c536c660f5d503f29cc5820cca8962cc696d41b581ac4b5550b46a2bd83d0b0c7815997e162990371c94e45b languageName: node linkType: hard @@ -10159,17 +10322,17 @@ __metadata: "@graphql-codegen/cli": ^5.0.2 "@graphql-codegen/client-preset": ^4.3.3 "@graphql-typed-document-node/core": ^3.2.0 - "@mui/icons-material": ^5.16.7 - "@mui/lab": ^5.0.0-alpha.170 - "@mui/material": ^5.16.7 - "@mui/material-nextjs": ^6.1.0 + "@mui/icons-material": ^6.1.1 + "@mui/lab": ^6.0.0-beta.10 + "@mui/material": ^6.1.1 + "@mui/material-nextjs": ^6.1.1 "@types/node": ^22.6.1 "@types/react": ^18.3.8 "@types/react-dom": 18.3.0 "@visx/event": ^3.3.0 "@visx/responsive": ^3.10.2 "@visx/visx": ^3.11.0 - "@weng-lab/psychscreen-ui-components": ^1.0.4 + "@weng-lab/psychscreen-ui-components": ^2.0.0 "@weng-lab/ts-ztable": ^4.0.1 autoprefixer: 10.4.20 bpnet-ui: ^0.3.8 From b66b3f04f3b0e7b21ed4f0ca85cd2e05dc2649e4 Mon Sep 17 00:00:00 2001 From: jpfisher72 Date: Tue, 24 Sep 2024 15:45:40 -0400 Subject: [PATCH 3/5] Cleanup apollo deprecations --- .../src/app/_biosampleTables/BiosampleTables.tsx | 2 +- screen2.0/src/app/search/_ccredetails/ccredetails.tsx | 2 +- .../src/app/search/_ccredetails/geneexpression.tsx | 2 +- .../app/search/_ccredetails/inspecificbiosample.tsx | 2 +- screen2.0/src/app/search/mainresultsfilters.tsx | 3 +-- screen2.0/src/common/lib/apolloprovider.tsx | 11 +++++------ screen2.0/src/common/lib/client.ts | 2 +- 7 files changed, 11 insertions(+), 13 deletions(-) diff --git a/screen2.0/src/app/_biosampleTables/BiosampleTables.tsx b/screen2.0/src/app/_biosampleTables/BiosampleTables.tsx index 7f4f84d7..af637ba0 100644 --- a/screen2.0/src/app/_biosampleTables/BiosampleTables.tsx +++ b/screen2.0/src/app/_biosampleTables/BiosampleTables.tsx @@ -5,7 +5,7 @@ import { CheckboxState, FiltersKey, Props, RegistryBiosample, RegistryBiosampleP import KeyboardArrowRightIcon from "@mui/icons-material/KeyboardArrowRight" import { Check, Close, FilterList } from "@mui/icons-material" import SearchIcon from '@mui/icons-material/Search'; -import { useQuery } from "@apollo/experimental-nextjs-app-support/ssr" +import { useQuery } from "@apollo/client" import { assayHoverInfo, DownloadBiosamplecCREsButton, filterBiosamples } from "./helpers" import { BIOSAMPLE_QUERY, RNA_SEQ_QUERY } from "./queries" diff --git a/screen2.0/src/app/search/_ccredetails/ccredetails.tsx b/screen2.0/src/app/search/_ccredetails/ccredetails.tsx index d96bda9e..8269dd94 100644 --- a/screen2.0/src/app/search/_ccredetails/ccredetails.tsx +++ b/screen2.0/src/app/search/_ccredetails/ccredetails.tsx @@ -14,7 +14,7 @@ import Rampage from "./rampage" import { GeneExpression } from "./geneexpression" import { TfSequenceFeatures } from "../_gbview/tfsequencefeatures" import ConfigureGBTab from "./configuregbtab" -import { useQuery } from "@apollo/experimental-nextjs-app-support/ssr" +import { useQuery } from "@apollo/client" import { NEARBY_AND_LINKED_GENES } from "./queries" import { calcDistToTSS } from "./utils" import { LoadingMessage } from "../../../common/lib/utility" diff --git a/screen2.0/src/app/search/_ccredetails/geneexpression.tsx b/screen2.0/src/app/search/_ccredetails/geneexpression.tsx index 30d8563d..0f7b3148 100644 --- a/screen2.0/src/app/search/_ccredetails/geneexpression.tsx +++ b/screen2.0/src/app/search/_ccredetails/geneexpression.tsx @@ -2,7 +2,7 @@ import React, { useMemo, useState } from "react" import { LoadingMessage } from "../../../common/lib/utility" import { PlotGeneExpression } from "../../applets/gene-expression/geneexpressionplot" -import { useQuery } from "@apollo/experimental-nextjs-app-support/ssr" +import { useQuery } from "@apollo/client" import { Button, Typography, Stack, MenuItem, FormControl, SelectChangeEvent, Checkbox, InputLabel, ListItemText, OutlinedInput, Select, ToggleButton, ToggleButtonGroup, FormLabel, Box } from "@mui/material" import Grid from "@mui/material/Grid2" import Image from "next/image" diff --git a/screen2.0/src/app/search/_ccredetails/inspecificbiosample.tsx b/screen2.0/src/app/search/_ccredetails/inspecificbiosample.tsx index 6d24d03a..7d0f9fa4 100644 --- a/screen2.0/src/app/search/_ccredetails/inspecificbiosample.tsx +++ b/screen2.0/src/app/search/_ccredetails/inspecificbiosample.tsx @@ -1,6 +1,6 @@ "use client" import React from "react" -import { useQuery } from "@apollo/experimental-nextjs-app-support/ssr" +import { useQuery } from "@apollo/client" import { TOP_TISSUES, GET_CCRE_CT_TF } from "./queries" import { DataTable } from "@weng-lab/psychscreen-ui-components" import { z_score, z_score_render, GROUP_COLOR_MAP } from "./utils" diff --git a/screen2.0/src/app/search/mainresultsfilters.tsx b/screen2.0/src/app/search/mainresultsfilters.tsx index 440d1248..c3abd39e 100644 --- a/screen2.0/src/app/search/mainresultsfilters.tsx +++ b/screen2.0/src/app/search/mainresultsfilters.tsx @@ -32,7 +32,7 @@ import { RangeSlider } from "@weng-lab/psychscreen-ui-components" import { FilterCriteria, MainQueryParams, RegistryBiosample } from "./types" import { eQTLsTissues, filtersModified } from "./searchhelpers" import { LazyQueryResultTuple, gql, useLazyQuery } from "@apollo/client" -import { useQuery } from "@apollo/experimental-nextjs-app-support/ssr" +import { useQuery } from "@apollo/client" import { CancelRounded, InfoOutlined } from "@mui/icons-material"; import ClearIcon from '@mui/icons-material/Clear'; import { GeneAutocomplete } from "./_geneAutocomplete/GeneAutocomplete"; @@ -169,7 +169,6 @@ export function MainResultsFilters( skip: !mainQueryParams.gene.name, fetchPolicy: "cache-and-network", nextFetchPolicy: "cache-first" - }) //Recalculate when geneTranscripts available, near diff --git a/screen2.0/src/common/lib/apolloprovider.tsx b/screen2.0/src/common/lib/apolloprovider.tsx index 59109732..3743f47b 100644 --- a/screen2.0/src/common/lib/apolloprovider.tsx +++ b/screen2.0/src/common/lib/apolloprovider.tsx @@ -4,10 +4,10 @@ import React from "react"; import { ApolloLink, HttpLink } from "@apollo/client"; import { ApolloNextAppProvider, - NextSSRInMemoryCache, - NextSSRApolloClient, + InMemoryCache, + ApolloClient, SSRMultipartLink, -} from "@apollo/experimental-nextjs-app-support/ssr"; +} from "@apollo/experimental-nextjs-app-support"; import config from "../../config.json" import { setVerbosity } from "ts-invariant"; @@ -27,9 +27,8 @@ function makeClient() { // const { data } = useSuspenseQuery(MY_QUERY, { context: { fetchOptions: { cache: "force-cache" }}}); }); - return new NextSSRApolloClient({ - // use the `NextSSRInMemoryCache`, not the normal `InMemoryCache` - cache: new NextSSRInMemoryCache(), + return new ApolloClient({ + cache: new InMemoryCache(), link: typeof window === "undefined" ? ApolloLink.from([ diff --git a/screen2.0/src/common/lib/client.ts b/screen2.0/src/common/lib/client.ts index a97aeed7..efaff58c 100644 --- a/screen2.0/src/common/lib/client.ts +++ b/screen2.0/src/common/lib/client.ts @@ -1,5 +1,5 @@ import { ApolloClient, HttpLink, InMemoryCache } from "@apollo/client" -import { registerApolloClient } from "@apollo/experimental-nextjs-app-support/rsc" +import { registerApolloClient } from "@apollo/experimental-nextjs-app-support" import Config from "../../config.json" /** * @returns an ApolloClient instance scoped for the current request From 81b0d6c2a1a7afac8ac48a987d88f1882e34f1a5 Mon Sep 17 00:00:00 2001 From: jpfisher72 Date: Wed, 25 Sep 2024 10:57:19 -0400 Subject: [PATCH 4/5] Cleanup --- .../src/app/applets/gene-expression/geneexpressionplot.tsx | 2 -- screen2.0/src/app/applets/gwas/page.tsx | 4 ++-- screen2.0/src/app/downloads/annotations.tsx | 4 ++-- 3 files changed, 4 insertions(+), 6 deletions(-) diff --git a/screen2.0/src/app/applets/gene-expression/geneexpressionplot.tsx b/screen2.0/src/app/applets/gene-expression/geneexpressionplot.tsx index c73ea9fb..e585e465 100644 --- a/screen2.0/src/app/applets/gene-expression/geneexpressionplot.tsx +++ b/screen2.0/src/app/applets/gene-expression/geneexpressionplot.tsx @@ -2,9 +2,7 @@ import React from "react" import { useRouter } from "next/navigation" import { Stack } from "@mui/material" import { Range2D, Point2D, linearTransform2D } from "jubilant-carnival" -import Grid from "@mui/material/Grid2" import { tissueColors } from "../../../common/lib/colors" -import { stringToColour } from "../../search/_ccredetails/utils" type QuantificationData = { accession: string, diff --git a/screen2.0/src/app/applets/gwas/page.tsx b/screen2.0/src/app/applets/gwas/page.tsx index 90368fb4..77f952e2 100644 --- a/screen2.0/src/app/applets/gwas/page.tsx +++ b/screen2.0/src/app/applets/gwas/page.tsx @@ -497,7 +497,7 @@ export default function GWAS() { }, [plotData, study, suggestionsOpen]) return ( - (
    +
    -
    ) +
    ); } diff --git a/screen2.0/src/app/downloads/annotations.tsx b/screen2.0/src/app/downloads/annotations.tsx index 964109ab..48a48a70 100644 --- a/screen2.0/src/app/downloads/annotations.tsx +++ b/screen2.0/src/app/downloads/annotations.tsx @@ -82,7 +82,7 @@ export function Annotations() { } return ( - ( + @@ -172,7 +172,7 @@ export function Annotations() { )} - ) + ); } From e2ca6cbe59ef62dd7275b9f39910b355eb8dab52 Mon Sep 17 00:00:00 2001 From: jpfisher72 Date: Wed, 25 Sep 2024 12:38:56 -0400 Subject: [PATCH 5/5] More cleanup --- screen2.0/.vscode/settings.json | 4 ---- screen2.0/src/app/_mainsearch/genomicregion.tsx | 4 ++-- screen2.0/src/app/about/page.tsx | 4 ++-- screen2.0/src/app/downloads/datamatrices.tsx | 4 ++-- screen2.0/src/app/downloads/downloadrange.tsx | 4 ++-- screen2.0/src/app/downloads/page.tsx | 6 +++--- screen2.0/src/app/page.tsx | 4 ++-- screen2.0/src/app/search/_ccredetails/chromhmm.tsx | 5 +++-- screen2.0/src/app/search/_ccredetails/entexdata.tsx | 4 ++-- screen2.0/src/app/search/_ccredetails/geneexpression.tsx | 4 ++-- screen2.0/src/app/search/_ccredetails/linkedgenes.tsx | 4 ++-- screen2.0/src/app/search/mainresultsfilters.tsx | 4 ++-- 12 files changed, 24 insertions(+), 27 deletions(-) delete mode 100644 screen2.0/.vscode/settings.json diff --git a/screen2.0/.vscode/settings.json b/screen2.0/.vscode/settings.json deleted file mode 100644 index d0679104..00000000 --- a/screen2.0/.vscode/settings.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "typescript.tsdk": "node_modules/typescript/lib", - "typescript.enablePromptUseWorkspaceTsdk": true -} \ No newline at end of file diff --git a/screen2.0/src/app/_mainsearch/genomicregion.tsx b/screen2.0/src/app/_mainsearch/genomicregion.tsx index 3afea0e8..976253cf 100644 --- a/screen2.0/src/app/_mainsearch/genomicregion.tsx +++ b/screen2.0/src/app/_mainsearch/genomicregion.tsx @@ -193,7 +193,7 @@ const GenomicRegion = (props: { assembly: "mm10" | "GRCh38"; header?: boolean }) }, [value, inputType, props.assembly, chromosome, start, end]) return ( - ( + {!props.header && ( @@ -389,7 +389,7 @@ const GenomicRegion = (props: { assembly: "mm10" | "GRCh38"; header?: boolean }) - ) + ); } diff --git a/screen2.0/src/app/about/page.tsx b/screen2.0/src/app/about/page.tsx index cd33affc..3410b0b8 100644 --- a/screen2.0/src/app/about/page.tsx +++ b/screen2.0/src/app/about/page.tsx @@ -70,7 +70,7 @@ export default function About() { return ( - (
    +
    {/* Header */} @@ -295,6 +295,6 @@ export default function About() { -
    ) +
    ); } \ No newline at end of file diff --git a/screen2.0/src/app/downloads/datamatrices.tsx b/screen2.0/src/app/downloads/datamatrices.tsx index 793468c8..1b4260c3 100644 --- a/screen2.0/src/app/downloads/datamatrices.tsx +++ b/screen2.0/src/app/downloads/datamatrices.tsx @@ -319,7 +319,7 @@ export function DataMatrices() { ] return ( - (
    +
    @@ -526,6 +526,6 @@ export function DataMatrices() { /> -
    ) +
    ); } diff --git a/screen2.0/src/app/downloads/downloadrange.tsx b/screen2.0/src/app/downloads/downloadrange.tsx index 8d3a14b8..7671fb42 100644 --- a/screen2.0/src/app/downloads/downloadrange.tsx +++ b/screen2.0/src/app/downloads/downloadrange.tsx @@ -119,7 +119,7 @@ export const DownloadRange: React.FC = () => { } return ( - ( + { {bedLoadingPercent !== null && } - ) + ); } \ No newline at end of file diff --git a/screen2.0/src/app/downloads/page.tsx b/screen2.0/src/app/downloads/page.tsx index 5795b45b..5ac229da 100644 --- a/screen2.0/src/app/downloads/page.tsx +++ b/screen2.0/src/app/downloads/page.tsx @@ -1,7 +1,7 @@ "use client" import * as React from "react" -import { Tabs, Tab, Box, Container, Divider} from "@mui/material" +import { Tabs, Tab, Container, Divider} from "@mui/material" import Grid from "@mui/material/Grid2" import { Annotations } from "./annotations" import { DataMatrices } from "./datamatrices" @@ -23,7 +23,7 @@ export default function Downloads() { } return ( - ( + @@ -39,6 +39,6 @@ export default function Downloads() { {page === 2 && } - ) + ); } diff --git a/screen2.0/src/app/page.tsx b/screen2.0/src/app/page.tsx index e2d6b31f..7cd68496 100644 --- a/screen2.0/src/app/page.tsx +++ b/screen2.0/src/app/page.tsx @@ -11,7 +11,7 @@ import mouseTransparentIcon from "../../public/Transparent_MouseIcon.png" export default function Home() { return ( - (
    +
    SCREEN @@ -65,6 +65,6 @@ export default function Home() { {"SCREEN -
    ) +
    ); } diff --git a/screen2.0/src/app/search/_ccredetails/chromhmm.tsx b/screen2.0/src/app/search/_ccredetails/chromhmm.tsx index 44107fc2..bcad08fa 100644 --- a/screen2.0/src/app/search/_ccredetails/chromhmm.tsx +++ b/screen2.0/src/app/search/_ccredetails/chromhmm.tsx @@ -17,6 +17,7 @@ import { BigBedData } from "bigwig-reader" import { styled } from '@mui/material/styles'; import { DataTable } from "@weng-lab/psychscreen-ui-components" import config from "../../../config.json" + const StyledTab = styled(Tab)(() => ({ textTransform: "none", })) @@ -178,7 +179,7 @@ export const ChromHMM = (props: { coordinates , assembly, accession }) =>{ const l = useCallback((c) => ((c - coordinates.start) * 1400) / (coordinates.end - coordinates.start), [coordinates]) return ( - ( + @@ -296,6 +297,6 @@ export const ChromHMM = (props: { coordinates , assembly, accession }) =>{ itemsPerPage={10} /> } - ) + ); } \ No newline at end of file diff --git a/screen2.0/src/app/search/_ccredetails/entexdata.tsx b/screen2.0/src/app/search/_ccredetails/entexdata.tsx index 880f02a2..b71ca51d 100644 --- a/screen2.0/src/app/search/_ccredetails/entexdata.tsx +++ b/screen2.0/src/app/search/_ccredetails/entexdata.tsx @@ -48,7 +48,7 @@ export const ENTExData = (props: { accession, coordinates }) =>{ }) return ( - ( + {loading && } {data && !loading && data.entexQuery.length>0 && { } - ) + ); } \ No newline at end of file diff --git a/screen2.0/src/app/search/_ccredetails/geneexpression.tsx b/screen2.0/src/app/search/_ccredetails/geneexpression.tsx index 0f7b3148..b892e22f 100644 --- a/screen2.0/src/app/search/_ccredetails/geneexpression.tsx +++ b/screen2.0/src/app/search/_ccredetails/geneexpression.tsx @@ -179,7 +179,7 @@ export function GeneExpression(props: { }; return ( - ( + - ) + ); } diff --git a/screen2.0/src/app/search/_ccredetails/linkedgenes.tsx b/screen2.0/src/app/search/_ccredetails/linkedgenes.tsx index 73dbf367..e52b200b 100644 --- a/screen2.0/src/app/search/_ccredetails/linkedgenes.tsx +++ b/screen2.0/src/app/search/_ccredetails/linkedgenes.tsx @@ -84,7 +84,7 @@ export const LinkedGenes: React.FC = (props) => { } return ( - ( + {HiCLinked.length > 0 ? = (props) => { } - ) + ); } diff --git a/screen2.0/src/app/search/mainresultsfilters.tsx b/screen2.0/src/app/search/mainresultsfilters.tsx index c3abd39e..9c75f3a2 100644 --- a/screen2.0/src/app/search/mainresultsfilters.tsx +++ b/screen2.0/src/app/search/mainresultsfilters.tsx @@ -384,7 +384,7 @@ export function MainResultsFilters( return ( - ( + {/* cCREs within distance from SNP */} {mainQueryParams.snp.rsID && <> @@ -1170,6 +1170,6 @@ export function MainResultsFilters( } } - ) + ); }