Qa into master 1/12/22 (#371)
Qa into master 1/12/22 (#371)

* undefined formatName bug fix (#317)

* undefined formatName bug fix

* remove unused prop

* restore prop checking: needs clean up in next release

* added Education to tools bar (#318)

* fixed the error message for variant search

* fixed the limit from 200 to 250 (#321)

* fixed the broken links in function summaries (#323)

* minor formatting change

* fixed the broken links in function summaries (#323)

* minor formatting change

* Allele project (#326)

* testing

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* adding allele name to the title

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* adding interaction section to Yeastmine for cellmap paper

* rebased with QA

* get rid of deepscan warning

* adding allele category (#327)

* fixed font issue

* suppressed the ref display associated with the affected gene

* fixing analyze buttons

* markupsafe update

* Allele project (#326)

* testing

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* adding allele name to the title

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* adding interaction section to Yeastmine for cellmap paper

* rebased with QA

* get rid of deepscan warning

* adding allele category (#327)

* fixed font issue

* suppressed the ref display associated with the affected gene

* fixing analyze buttons

* markupsafe update

* fixed font issue in interaction display

* separate interactions into positive & negative in the allele network diagram (#329)

* separate interactions into positive & negative

* separate genetic & physical interaction sections

* moved genetic interaction table above Physical Interactions

* fixed a typo

* adding alliance icons

* adding alliance icon links to LSP (#330)

* order icons by standard 'phylogenetic' order

* fixed 'i' text for allele network diagram and a highlight bug for interaction page (#331)

* minor fix

* fixed i note for network diagram

* fixed the download site url

* fixed download URL

* Fixes to attach allele papers to proper data points (#333)

* fixed to attach the papers with allele name/type/description properly

* fixed to attach the papers with allele name/type/description properly

* fixed to attach the papers with allele name/type/description properly

* adding primary/additional/reviews papers

* adding primary/additional/reviews papers

* adding primary/additional/reviews papers

* fixed to get correct paper count

* adding missed allele name

* testing

* fixed to display multiple affected genes

* fixed display_name to display_text

* rebasing it to master

* changed it back

* adding sgdid to complex page

* adding sgdid to complex page

* fix link for genome-wide analysis papers (#335)

* fixed PTM bug

* fixed default dataset for protein

* fixed to not display Definition for go term if there is no def

* fixed broken seq display

* new code/files for homology tab (#341)

* adding code for homology tab

* adding code for homology tab

* making species names italicized

* fixing yeastmine link

* adding homology tab for narrow window

* making padding smaller for tabs

* redirect the ref index to LSP

* adjust tab padding

* adjust tab padding

* adjust tab padding

* testing

* adding link to fungal homolog gene ID

* expand the 'resistent to chemicals' display

* adding code for complementation data display (#345)

* adding/fixing code for functional complementation data display

* fixing bugs

* fixing bugs

* fixing bugs

* adding Gene column

* adding gene column

* adding gene column

* testing

* testing

* testing

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* updated the dataset update date

* data update date

* fixed go tools to point to https://

* fixing Non-GEO dataset display issue

* fixed the GEO ID link

* fixed to make sure seq type matches blast program

* fixed wiki urls

* fixed YGOB url

* fixed DNA sequence checking part

* rebased

* fixed to work with new/old pip

* fixed to point to BLAST server directly

* 3.8 (#358)

* Dockerize prelim 6082 (#361)

* adding Dockerfile that can run and build frontend

* Dockerfile CMD set to run dev local frontend

* updated readme and Dockerfile

* fixing seq check bug

* fixed  config/deploy.rb

* adding allele section to LSP

* fixed yeastmine link

* Dockerfile update with Vagrant to normalize development environment (#364)

* fixed to group the slim terms

* fixed to display papers for phenotype, htp, disease properly

* change git:// to http:// in deploy script (#367)

* testing

* fixed git:// to http://

* Complex tab pages + complex go annotations + new AlphaFold link etc (#368)

* adding code for complex tab pages

* adding code for complex tab pages

* fixed go annotation download files

* adding AlphaFold link

* adding code for complex tab pages

* fixed to handle ambiguous characters in DNA sequence

* adding AlphaFold link to tools bar for ES search

* fixed a minor complaining

* adding 'i' notes

* fixed to provide a link to yeastmine for paper with tons of go annotations

* fixed to use format_name instead of geo_id

* fixed 'i' notes

* fixed 'i' notes

* adding tabs for cell phone

* adding tabs for allele pages for small screen

* fixed go table display

* fixed the coordinates out of range issue

Co-authored-by: Felix Gondwe <b8e8bd5b2cd8d7797dd22a4a0e272f5730993b61@gmail.com>
Co-authored-by: sweng66 <58f172faaf45db30bd69025d209689a2c5f8681e@stanford.edu>
Co-authored-by: Eric Douglass <7e183368f32859ddecc51441e67bc8229c000ecb@gmail.com>
Co-authored-by: Eric Douglass <7a21dacbcc74ad5312ea7add0fb79a4be0db2736@stanford.edu>
yeastgenome/SGDFrontend,yeastgenome/SGDFrontend,yeastgenome/SGDFrontend,yeastgenome/SGDFrontend