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Release 98 #565

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merged 137 commits into from
Jan 18, 2024
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6fee336
Use the categories of the main domain viewer on the AlphaFold subpage
matthiasblum Nov 22, 2023
a03b907
TS: DropDownButton
gustavo-salazar Nov 24, 2023
bebb846
group download options if job still available in server
gustavo-salazar Nov 28, 2023
5aec18c
group download options if job still available in server
gustavo-salazar Nov 28, 2023
ddc292c
Merge branch 'ipscan-batch-download' of https://github.com/ProteinsWe…
gustavo-salazar Nov 28, 2023
1ce5c81
Merge branch 'dev' into ipscan-batch-download
gustavo-salazar Nov 30, 2023
112fc87
re-sticking the main table header
gustavo-salazar Nov 30, 2023
aadc11e
Increase code reusability
matthiasblum Dec 4, 2023
b49c3cb
Add label for secondary structures
matthiasblum Dec 4, 2023
9e44387
Use categories of the main domain viewer on the Structure subpage
matthiasblum Dec 4, 2023
18e3b6a
Update test and snapshot
matthiasblum Dec 4, 2023
d9851ff
representative domains for ipscan
gustavo-salazar Dec 4, 2023
d8ad094
Merge branch 'dev' into representative-domains-evetywhere
gustavo-salazar Dec 4, 2023
5cfc084
Apply suggestions from code review
gustavo-salazar Dec 4, 2023
d5f6f17
Update src/components/ProteinViewer/Options/index.tsx
gustavo-salazar Dec 4, 2023
d298085
Use the categories of the main domain viewer on the AlphaFold subpage
matthiasblum Nov 22, 2023
e23bd99
Increase code reusability
matthiasblum Dec 4, 2023
40971f6
Add label for secondary structures
matthiasblum Dec 4, 2023
faa61ab
Use categories of the main domain viewer on the Structure subpage
matthiasblum Dec 4, 2023
91ce86e
Update test and snapshot
matthiasblum Dec 4, 2023
5fd3812
Merge remote-tracking branch 'origin/consistent-categories' into cons…
matthiasblum Dec 7, 2023
7436119
Merge pull request #547 from ProteinsWebTeam/ipscan-batch-download
gustavo-salazar Dec 7, 2023
50e9c11
Merge branch 'dev' into representative-domains-evetywhere
gustavo-salazar Dec 7, 2023
f35cf4d
TS: IPScan/Summary/serializers
gustavo-salazar Dec 7, 2023
b5cec3c
removing the genome3d subpage from an entry page
gustavo-salazar Dec 8, 2023
db8c45a
Merge pull request #549 from ProteinsWebTeam/consistent-categories
matthiasblum Dec 11, 2023
f834753
TS: IDA/options + removing idaLabel from redux state
gustavo-salazar Dec 11, 2023
9604cad
TS: ToggleSwitch
gustavo-salazar Dec 11, 2023
936a020
TS: DomainArchitecture/IDAProtVista+TextIDA
gustavo-salazar Dec 11, 2023
f599e82
TS: src/components/Entry/DomainArchitectures
gustavo-salazar Dec 11, 2023
9e8ff99
Update src/utils/removed-pages/index.tsx
gustavo-salazar Dec 12, 2023
e3a3e35
TS: src/components/Entry/DomainArchitectures/IDAResults
gustavo-salazar Dec 12, 2023
fe1e4cf
TS:subPages/DomainArchitecture
gustavo-salazar Dec 12, 2023
1990d24
TS: SimilarProteins
gustavo-salazar Dec 12, 2023
7687c3c
bit of styling
gustavo-salazar Dec 12, 2023
f3d8784
Apply suggestions from code review
gustavo-salazar Dec 14, 2023
b039108
update snapshot
gustavo-salazar Dec 14, 2023
de97769
Merge pull request #550 from ProteinsWebTeam/remove-genome3d-subpage
gustavo-salazar Dec 14, 2023
2a12605
Merge branch 'dev' into IDA-TS-download
gustavo-salazar Dec 14, 2023
c42d16c
remove ProtVistaMatches
gustavo-salazar Dec 14, 2023
e7f1ccf
making the export/web view button more like the others
gustavo-salazar Dec 14, 2023
ab432c9
using floating-ui portal as they reccomend 🙊
gustavo-salazar Dec 14, 2023
c2e4295
Export JSON and TSV in IDA search
gustavo-salazar Dec 14, 2023
dce651a
missing files
gustavo-salazar Dec 14, 2023
4aa6577
Export JSON and TSV in Domain Architectures subpage
gustavo-salazar Dec 14, 2023
4af8228
Merge pull request #551 from ProteinsWebTeam/IDA-TS-download
gustavo-salazar Dec 14, 2023
99d2f5d
removing css row/column from tsx files
gustavo-salazar Dec 15, 2023
1b86623
fix color by domain relationship for ipscan representative domains
gustavo-salazar Dec 15, 2023
a536d2c
naively dealing with the structured description by ignoring the other…
gustavo-salazar Dec 15, 2023
63b62c5
Merge pull request #548 from ProteinsWebTeam/representative-domains-e…
gustavo-salazar Dec 15, 2023
6f6cee8
identifying the type of description: LLM or curated - assumes 1 LLM b…
gustavo-salazar Dec 18, 2023
33e09ab
using the checked flag on LLM descriptions
gustavo-salazar Dec 18, 2023
ee8cf3f
compacting thE TSV DOMAIN STRING
gustavo-salazar Dec 18, 2023
6da3469
description llm & checked per paragraph
gustavo-salazar Dec 21, 2023
dcc6541
installing with npm v6
gustavo-salazar Dec 21, 2023
b468dac
deps bump
gustavo-salazar Dec 22, 2023
60d8bc6
mini depas bump - remove dep @babel/register - update 2024 snapshot
gustavo-salazar Jan 2, 2024
e45d7b2
deps bump
gustavo-salazar Jan 2, 2024
57d919b
lit-labs/react => lit/react
gustavo-salazar Jan 2, 2024
e2f1492
redux dependencies bump
gustavo-salazar Jan 2, 2024
5566396
merge dev conflicts
gustavo-salazar Jan 2, 2024
b13e24c
key in Description
gustavo-salazar Jan 2, 2024
e3166ed
removing create selector when value=>value
gustavo-salazar Jan 2, 2024
509240d
adding 'queued' as an option for the job dispatcher status
gustavo-salazar Jan 2, 2024
ae9a22a
disabling flow for jobs-middleware
gustavo-salazar Jan 2, 2024
cbd37da
Merge branch 'dev' into new-description
gustavo-salazar Jan 3, 2024
b79bbcf
styling the dropdown button
gustavo-salazar Jan 3, 2024
39e39fa
nightingale version: 4.5.0
gustavo-salazar Jan 3, 2024
194d296
simplifying Dynamic tooltip - but still appearing in the top corner
gustavo-salazar Jan 3, 2024
ef0b3cc
TS: IDA domainbutton
gustavo-salazar Jan 3, 2024
9063f33
TS: IdaEntry
gustavo-salazar Jan 3, 2024
26e4198
TS: extracting PanelIDA
gustavo-salazar Jan 3, 2024
71478cf
TS: SearchByIDA
gustavo-salazar Jan 3, 2024
2f4f63d
Apply suggestions from code review
gustavo-salazar Jan 3, 2024
d6c6aa7
snapshot update
gustavo-salazar Jan 3, 2024
ac58f8b
Merge branch 'dev' into IDA-download
gustavo-salazar Jan 4, 2024
9046d71
implementing suggestions from PR
gustavo-salazar Jan 4, 2024
79b5297
description AI badges only visible when there is at least 1 AI paragr…
gustavo-salazar Jan 4, 2024
6bb70d9
updating snapshots
gustavo-salazar Jan 4, 2024
f55f7c9
FIX #517: title in protein viewer for structures
gustavo-salazar Jan 4, 2024
129c816
adding a debounce for the autocomplete in IDA search
gustavo-salazar Jan 4, 2024
42af183
Apply suggestions from code review
gustavo-salazar Jan 5, 2024
b0c4da9
ida search style grab pointer
gustavo-salazar Jan 5, 2024
90c0447
Merge pull request #554 from ProteinsWebTeam/new-description
gustavo-salazar Jan 5, 2024
6810a6f
Merge pull request #557 from ProteinsWebTeam/ts-ida-search
gustavo-salazar Jan 5, 2024
f92494a
merge confilcts
gustavo-salazar Jan 5, 2024
ab700fc
adding a contact-us page
gustavo-salazar Jan 5, 2024
dfe52cb
flow and jest fixes
gustavo-salazar Jan 5, 2024
ea3a9df
Merge pull request #553 from ProteinsWebTeam/IDA-download
gustavo-salazar Jan 5, 2024
86c2b9d
TS: menuConfig
gustavo-salazar Jan 5, 2024
18ab135
flow fix for js importing menuConfig
gustavo-salazar Jan 5, 2024
b4503a8
menuconfig without foundation
gustavo-salazar Jan 5, 2024
3a08d06
TS: src/components/Menu/MenuItem
gustavo-salazar Jan 5, 2024
38de9ed
TS: src/components/Menu/DynamicMenu
gustavo-salazar Jan 5, 2024
75baa7d
TS: src/components/Menu/EBIMenu
gustavo-salazar Jan 5, 2024
53d895a
TS: src/components/Menu/EntitiesMenu
gustavo-salazar Jan 5, 2024
cf8af15
TS: src/components/Menu/InterProMenu
gustavo-salazar Jan 5, 2024
f550b0e
entry.name is an object
matthiasblum Jan 6, 2024
52110a1
removed SingleEntityMenu as it's not in use anymore
gustavo-salazar Jan 8, 2024
f677ce8
TS: Server Status
gustavo-salazar Jan 8, 2024
1ab2727
TS: SideMenu
gustavo-salazar Jan 8, 2024
0e0c7b1
hamburger button toggling the sidemenu
gustavo-salazar Jan 8, 2024
08e446f
fixing hamburger tests
gustavo-salazar Jan 8, 2024
c5b7b62
Merge pull request #559 from ProteinsWebTeam/fix-entryonstructure-popup
gustavo-salazar Jan 8, 2024
a6bb0e3
alignment of actions in table
gustavo-salazar Jan 8, 2024
73132e7
gene in protein list and summary
gustavo-salazar Jan 9, 2024
5ce3604
cleaning up dependencies and now works with npm 10
gustavo-salazar Jan 9, 2024
5de10c0
npm version running on VMs
gustavo-salazar Jan 9, 2024
f7bc73c
downgrading favicons to 7.1.2
gustavo-salazar Jan 9, 2024
0728ddf
remove debug lines from GH workflow
gustavo-salazar Jan 9, 2024
1ecd4a9
removing functional tests - they havent been used in years and were n…
gustavo-salazar Jan 9, 2024
fef172c
removing unused scripts
gustavo-salazar Jan 9, 2024
b2a132c
removing unused custom webpack plugin
gustavo-salazar Jan 9, 2024
23d412d
remove unused index-hydrate
gustavo-salazar Jan 9, 2024
6d78b22
updating GH actions and adding caching to speeding them up
gustavo-salazar Jan 9, 2024
990677b
updating flow-installed
gustavo-salazar Jan 9, 2024
134013d
missing flow typed files
gustavo-salazar Jan 9, 2024
7a4bed4
fixing node & npm version to the ones in the cluster: 19.2.0 & 9.3.1
gustavo-salazar Jan 10, 2024
865fd39
overriding core-js to make sure all dependencies use the latest one
gustavo-salazar Jan 10, 2024
ac0c4c0
sorting the scripts
gustavo-salazar Jan 10, 2024
f75f0ce
deps bump
gustavo-salazar Jan 10, 2024
fa9db34
twitter => X
gustavo-salazar Jan 11, 2024
2d1048f
Apply suggestions from code review
gustavo-salazar Jan 11, 2024
fd49a87
snapshot update
gustavo-salazar Jan 11, 2024
ddd336d
Merge pull request #558 from ProteinsWebTeam/contact-us
gustavo-salazar Jan 12, 2024
3513f78
border and padding only applyes to descriptions with badges
gustavo-salazar Jan 12, 2024
4997f94
styling download alignment button to visual framework
gustavo-salazar Jan 12, 2024
acf81d7
Merge branch 'dev' into ts-menu
gustavo-salazar Jan 12, 2024
be9dcd6
Merge branch 'dev' into displaying-gene
gustavo-salazar Jan 12, 2024
eef569d
protein subpages and similar proteins now include the gene column
gustavo-salazar Jan 12, 2024
4c25eb2
Merge pull request #562 from ProteinsWebTeam/ts-menu
gustavo-salazar Jan 12, 2024
31cd88c
Merge pull request #561 from ProteinsWebTeam/displaying-gene
gustavo-salazar Jan 12, 2024
12b8145
Merge branch 'dev' into npm-update
gustavo-salazar Jan 12, 2024
f5fb4ee
Merge pull request #560 from ProteinsWebTeam/npm-update
gustavo-salazar Jan 12, 2024
46c92b9
Merge branch 'master' into dev
gustavo-salazar Jan 12, 2024
83273ae
fixing css is awesome effect on dropdown
gustavo-salazar Jan 15, 2024
ea281fe
style suggestions in code review
gustavo-salazar Jan 15, 2024
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11 changes: 6 additions & 5 deletions .github/workflows/test-build-report.yml
Original file line number Diff line number Diff line change
Expand Up @@ -6,14 +6,15 @@ jobs:
build:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/setup-node@v3
- uses: actions/checkout@v4
- uses: actions/setup-node@v4
with:
node-version: '18.12.1'
node-version: '19.2.0'
cache: 'npm'
- name: 🔧 - Install
run: |
cp config.yml.example config.yml
npm i -g npm@6.14.9
npm i -g npm@9.3.1
npm ci
- name: 🧪 | 🏗 - Test and Build
run: |
Expand All @@ -24,7 +25,7 @@ jobs:
env:
LHCI_GITHUB_APP_TOKEN: ${{ secrets.LHCI_GITHUB_APP_TOKEN }}
- name: 💾 Archive reports
uses: actions/upload-artifact@v3
uses: actions/upload-artifact@v4
with:
name: reports
path: |
Expand Down
2 changes: 1 addition & 1 deletion .nvmrc
Original file line number Diff line number Diff line change
@@ -1 +1 @@
lts/hydrogen
19.2.0
10 changes: 5 additions & 5 deletions babel.config.js
Original file line number Diff line number Diff line change
Expand Up @@ -17,11 +17,11 @@ module.exports = {
],
'@babel/react',
],
plugins: [
'babel-plugin-dynamic-import-node',
'@babel/plugin-proposal-class-properties',
'@babel/plugin-proposal-optional-chaining',
],
// plugins: [
// 'babel-plugin-dynamic-import-node',
// '@babel/plugin-proposal-class-properties',
// '@babel/plugin-proposal-optional-chaining',
// ],
},
},
};
1 change: 0 additions & 1 deletion config.yml.example
Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,6 @@ pages:
- entry_alignments
- interactions
- pathways
- genome3d
- curation
- subfamilies
protein:
Expand Down
87 changes: 0 additions & 87 deletions flow-typed/npm/@babel/cli_vx.x.x.js

This file was deleted.

11 changes: 2 additions & 9 deletions flow-typed/npm/@babel/core_vx.x.x.js
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
// flow-typed signature: ed1b06309f185cbdc3b282a84fbfdd1a
// flow-typed version: <<STUB>>/@babel/core_v7.20.12/flow_v0.171.0
// flow-typed signature: eca6b73569bb4dfb8c4e455ce20d0fd6
// flow-typed version: <<STUB>>/@babel/core_v7.23.7/flow_v0.171.0

/**
* This is an autogenerated libdef stub for:
Expand Down Expand Up @@ -42,10 +42,6 @@ declare module '@babel/core/lib/config/files/configuration' {
declare module.exports: any;
}

declare module '@babel/core/lib/config/files/import-meta-resolve' {
declare module.exports: any;
}

declare module '@babel/core/lib/config/files/index-browser' {
declare module.exports: any;
}
Expand Down Expand Up @@ -254,9 +250,6 @@ declare module '@babel/core/lib/config/config-descriptors.js' {
declare module '@babel/core/lib/config/files/configuration.js' {
declare module.exports: $Exports<'@babel/core/lib/config/files/configuration'>;
}
declare module '@babel/core/lib/config/files/import-meta-resolve.js' {
declare module.exports: $Exports<'@babel/core/lib/config/files/import-meta-resolve'>;
}
declare module '@babel/core/lib/config/files/index-browser.js' {
declare module.exports: $Exports<'@babel/core/lib/config/files/index-browser'>;
}
Expand Down
4 changes: 2 additions & 2 deletions flow-typed/npm/@babel/eslint-parser_vx.x.x.js
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
// flow-typed signature: f290276e7e3f1665a167045334b7271a
// flow-typed version: <<STUB>>/@babel/eslint-parser_v7.19.1/flow_v0.171.0
// flow-typed signature: 5e6581598f0e1c0e6d84109f69dcb8c2
// flow-typed version: <<STUB>>/@babel/eslint-parser_v7.23.3/flow_v0.171.0

/**
* This is an autogenerated libdef stub for:
Expand Down
35 changes: 0 additions & 35 deletions flow-typed/npm/@babel/plugin-proposal-class-properties_vx.x.x.js

This file was deleted.

35 changes: 0 additions & 35 deletions flow-typed/npm/@babel/plugin-proposal-optional-chaining_vx.x.x.js

This file was deleted.

35 changes: 0 additions & 35 deletions flow-typed/npm/@babel/plugin-syntax-dynamic-import_vx.x.x.js

This file was deleted.

32 changes: 2 additions & 30 deletions flow-typed/npm/@babel/preset-env_vx.x.x.js
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
// flow-typed signature: 4b3831fdae13c2f4225b7b0eb68d9541
// flow-typed version: <<STUB>>/@babel/preset-env_v7.20.2/flow_v0.171.0
// flow-typed signature: 72de2911d54e02689953db69acfa99a2
// flow-typed version: <<STUB>>/@babel/preset-env_v7.23.7/flow_v0.171.0

/**
* This is an autogenerated libdef stub for:
Expand Down Expand Up @@ -78,10 +78,6 @@ declare module '@babel/preset-env/lib/filter-items' {
declare module.exports: any;
}

declare module '@babel/preset-env/lib/get-option-specific-excludes' {
declare module.exports: any;
}

declare module '@babel/preset-env/lib' {
declare module.exports: any;
}
Expand All @@ -102,18 +98,6 @@ declare module '@babel/preset-env/lib/plugins-compat-data' {
declare module.exports: any;
}

declare module '@babel/preset-env/lib/polyfills/babel-polyfill' {
declare module.exports: any;
}

declare module '@babel/preset-env/lib/polyfills/regenerator' {
declare module.exports: any;
}

declare module '@babel/preset-env/lib/polyfills/utils' {
declare module.exports: any;
}

declare module '@babel/preset-env/lib/shipped-proposals' {
declare module.exports: any;
}
Expand Down Expand Up @@ -165,9 +149,6 @@ declare module '@babel/preset-env/lib/debug.js' {
declare module '@babel/preset-env/lib/filter-items.js' {
declare module.exports: $Exports<'@babel/preset-env/lib/filter-items'>;
}
declare module '@babel/preset-env/lib/get-option-specific-excludes.js' {
declare module.exports: $Exports<'@babel/preset-env/lib/get-option-specific-excludes'>;
}
declare module '@babel/preset-env/lib/index' {
declare module.exports: $Exports<'@babel/preset-env/lib'>;
}
Expand All @@ -186,15 +167,6 @@ declare module '@babel/preset-env/lib/options.js' {
declare module '@babel/preset-env/lib/plugins-compat-data.js' {
declare module.exports: $Exports<'@babel/preset-env/lib/plugins-compat-data'>;
}
declare module '@babel/preset-env/lib/polyfills/babel-polyfill.js' {
declare module.exports: $Exports<'@babel/preset-env/lib/polyfills/babel-polyfill'>;
}
declare module '@babel/preset-env/lib/polyfills/regenerator.js' {
declare module.exports: $Exports<'@babel/preset-env/lib/polyfills/regenerator'>;
}
declare module '@babel/preset-env/lib/polyfills/utils.js' {
declare module.exports: $Exports<'@babel/preset-env/lib/polyfills/utils'>;
}
declare module '@babel/preset-env/lib/shipped-proposals.js' {
declare module.exports: $Exports<'@babel/preset-env/lib/shipped-proposals'>;
}
Expand Down
4 changes: 2 additions & 2 deletions flow-typed/npm/@babel/preset-react_vx.x.x.js
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
// flow-typed signature: a2c5556a59f87d25af7a0c40c8c58aee
// flow-typed version: <<STUB>>/@babel/preset-react_v7.18.6/flow_v0.171.0
// flow-typed signature: e919a5bd1e4595885e922b2ac85b9dc6
// flow-typed version: <<STUB>>/@babel/preset-react_v7.23.3/flow_v0.171.0

/**
* This is an autogenerated libdef stub for:
Expand Down
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