GitLab

* Entity viewer design review changes
* Scaleswitcher changed to entityTypeIndicator and move it to global shared component

Also:
- add modal component
- add CloseButton component

- also, disable tabs in gene view for panels that have no content

- Remove message counter from messaging to/from genome browser
- Update useBrowserRouting to avoid reporting location from url back to genome browser
  if it's the same location that genome browser sent to React

The view was always getting set as transcripts as the default value was defined in the wrong place.

The following states are now maintained in entity viewer:
- View
- Expanded transcripts
- Expanded transcript downloads
- Expanded proteins

This commit fixes the issues with restoring the track states in the following scenarios:
- Restoring after browser refresh
- Switching between species
- Switching between apps

Changes that required manual intervention:

- webpack-merge no longer has default export
- replaced apollo-boost and @apollo/react-hooks with apollo-client v.3
- ran npx browserslist@latest --update-db to update caniuse-lite

* add protein sequence download

* fix wrong cds sequence

* fix styling of protein sequend download

* PR suggestions

* fix download wrapper styling

* Export soft-black colour and added to storybook

* fix tabs button alignment

* ENSWBSITES-497: filter and sort component

* PR #303 feedback

* fix classname merging

* PR #303 feedback, renaming component, fix size for smaller screen

* Reduc box sizes so that it align with transcript image below

* Remove entityviewer transcriptfilter as this is not used anywhere

* Improved checkbox and radio styling (same layout for both)

* fix classname issue

* Added checkbox with long labels and in grid layout

* Fix test case failing because of styles empty when no classnames passed as props

* Update the Checkbox component to avoid modifying the scss import

* Update tests

* fullwidth for filterbox is 100% by default
Co-authored-by: Andrey Azov <andrey@ebi.ac.uk>

* Use web thoas endpoint

* Use proper genomeID

* Remove TODO

* Use helper to parse stable_id

* Get objectId

* Change to .build-nginx-wp

* Update Ngnixreview

* Add thoas proxy in dev config

* Remove /thoas from target URL

* Sample date for homo_sapiens_GCA_000001405_14

* Change thoas url
Co-authored-by: Kamal Dodiya <kamal@ebi.ac.uk>

* add uniprot and pdbe ids

* refactor data fetching for protein list item info

* use shared component for displaying external references

* refactor ProteinFeaturesCount

* more PR suggestions

* more PR suggestions

* add collapsed exons image

* fix exon image design issues

* fix wrong reference spliced rna length

* remove introns from image

* redesign changes

* redesign protein domain and collapsed exon images

* fix type issue

* group svg elements properly in exons image

* disable function return type in eslint

* fix protein domain image scale

* draw collapsed exons image using protein info

* add comments to the protein images

* PR suggestions

* rename CollapsedExonsImage to ProteinImage

* fix comments in protein domain image

* Update use outsideclick to support multiple refs

* Fix tests

* Fix more tests

* Update homepage

* Handle removed elements

* Uppercase c

* PR review cleanups

* Simplify loop

* Remove anonymous function

* Fix bugs in useOutsideClick and update the story

* Put back BIG_DESKTOP
Co-authored-by: Andrey Azov <andrey@ebi.ac.uk>

* Fix browser navigation bugs

* Fix tests

* Fix reset issue

* Removed unused props

* Add missing mock function

* Remove unwanted code

* Remove unused css

* Remove if block

* Revert thoas enpoint change

- also, update config of copy-webpack-plugin, which has changed its api in version 6 slightly

Update gitlab-ci to allow deployment of all branches.
(except for special branches whose name begins with the string `nodeploy`)

* add lookup types

* add lookup rest adaptors

* fetch data from lookup for gene

* add protein type and fixture

* add protein list item and refactor EV rest fetching

* fix storybook issues

* fix styling issues

* add coding exon count

* PR suggestions

* PR suggestions

* remove unused protein type

* fix protein domain image story

* add abort controller to cancel api requests on unmount

* add switch to mount current tab content only in gene function

* remove unused class name from protein list item

* change props name from product to protein in ProteinDomainImage

* fix protein domain image not rendering

* PR suggestions and styling fixes

* fix styling issues in protein list item

* add ebi icons package

* add protein features count

* use https for all entity viewer URLs

* PR suggestions

* remove ebi icons package and use static svgs for protein features count

* add licence notice for icons

* name ebi properly

* Fix browser routing - homepage to gb

* Pass genomeId to url for genome browser constructor
Co-authored-by: Andrey Azov <andrey@ebi.ac.uk>

* Add view-in-app component to transcript view accordion on entity viewer

* update test: wrap component inside MemoryRouter to use useParams()

* Headings for new document

* Full draft of ADR

* Move file to correct folder bc Atom is stupid

* Minor updates

* Rewrite to cover more options

* Rewritten to incorporate conclusions from more detailed research

* Datails of chosen software

* Updated after further research

* Clarifications to pricing

* Final draft of ADR

- Add InstantDownloadTranscript to Zmenu
- Add useApiService to fetch data from components

* Gene view tabs availability

* Remove geneId

* Check for protein_Coding transcripts

* Fix overview content and topbar pointer

* Fix JS error and sample data keys

* xref accordion pointer fixes

* Get xrefs from thoas

* Temp genomeId comment

* Better types

* Better namings

* Hide transcript xrefs

* Transcript xref group

Add licence header to all typescript files in the src and stories directories

Add cache with the least-recently-used invalidation strategy