GitLab

* 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

* 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

* use pointer cursor for protein list item to make it look clickable

* add AbortController to sentry ignore errors list

* EV sticky tabs and filter

* Style changes

* Tabs z index

Notable changes:

- typescript got updated to 3.9
- jest got a major update to v.26
- eslint got a major update to v.7

Notice that after updating jest to v.26 test suite is running 25-50% slower.

* ENSWBSITES-543: extending current component to have styled radio buttons

* ENSWBSITES-543: Add radio to storybook

* ENSWBSITES-543: Add radio to storybook and rearrange components alphabetically

* renaming radio to radio group as suggested in PR283 review

* stylesheet not needed anymore

* ENSWBSITES-543: fix data types

* ENSWBSITES-543: git mess when renaming files, now pushing the missing files and removing old files

* ENSWBSITES-543: git mess when renaming files, now pushing the missing files and removing old files

* ENSWBSITES-543: more renaming radio to radioGroup

* fix test error when renaming css classes

* Update tests and class names

* Remove a test
Co-authored-by: Andrey Azov <andrey@ebi.ac.uk>

Also:
- change the black colour across the site, and add soft-black colour
- update the Checkbox component to change cursor appearance to pointer
  when mousing over label, and to catalogue classNames props
  that can be passed to the Checkbox.
- update the Button component so that the active state of the PrimaryButton and
   SecondaryButton have a 1px-wide border (to avoid changes in button size
   when toggling between disabled and enabled states of the button)
- add option to prettier config to remove trailing commas from objects

* Add tests and storybook form

* Match with CDM

* Update storybook directory

* Fix tests

* PR review cleanups

* Add plus one while calculating to exon length

* Fix colours

* Fix tests

* Minor PR review fixes

* Correct scale size

* Remove width +1

* Move +1 inside the scale

* forEach instead of map

* [ENSWEBSITES-491] genome browser link component for entity viewer

* Create ViewInApp shared component and replace all traces of app links created

* Add onClick and remove Link; 

* Add proper tests
Co-authored-by: Andrey Azov <andrey@ebi.ac.uk>

* WIP: add transcript list item info

* add styling and make content dynamic

* use flex instead of grid for list item info

* PR suggestions

* fix import case sensitive warning

* PR suggestions

* fix styling

* add tests

* put transcript list item info inside transcript list item

* add some breathing space for the transcript list items

* Add white stroke for svg rectangles in UnsplicedTranscript in DefaultTranscriptList

* Hide grid bars behind transcript info panel

* Amino acid length is an integer

* PR suggestions

* fix wrong number of coding exons shown

* use formatter to display transcript location str

* use findIndex to get the first and last coding exon indexes

* check if firstcodingexonindex and lastcodingexonindexes exist when calculating amino acid length

* check if first and last coding exon indexes exist when calculating num of coding exons

* remove exon index checks and fix createExons that causes the tests to break
Co-authored-by: Andrey Azov <andrey@ebi.ac.uk>

Co-authored-by: Andrey Azov <andrey@ebi.ac.uk>

* Add sidebar tab content holders

* Add overview tab accordion

* Completed sequence mockup

* Add publications accordion

* Add TARK section

* Add homeologues

* Separate out data

* External references gene

* Completed xrefs UI

* Proper sidebar state

* Add sample data for more species

* Add ExternalLink to Storybook

* Separate out sidebar  entity UI state

* Sidebar acordion states

* Split overview tab file

* Import cleanups

* Update comment

* PR review changes

* Move source to metadata

* Fix typo

* Separate ExternalLink

* Fix tests

* Handle missing data

* Font size changes

* Fix link styles

* Fix tabs overlap

* Revert api uri

Also:
- fix tooltip positioning bug related to window scrolling
- add useRefWithRerender custom hook that makes sure
  that component updates after ref.current has been set
  (useful when rendering of component's children depends on
  existence of refs to other DOM elements).

* sort default transcripts

* PR suggestions

* More PR suggestions