Transition to new BAR API

[alexwaeseperlman]

All the api calls in ePlant 3 are copied from ePlant 2. I am making this issue to track the process of upgrading them.

Here is a list of old api calls we are using:

• Autocomplete for arabidopsis using /eplant/cgi-bin/idautocomplete.cgi
• Gene search for arabidopsis with /eplant/cgi-bin/querygene.cgi
• Gene info view loading for arabidopsis with /webservices/bar_araport/gene_summary_by_locus.php
• Gene info view loading for arabidopsis with /webservices/bar_araport/gene_structure_by_locus.php
• Gene info view loading for arabidopsis with /webservices/bar_araport/get_sequence_by_identifier.php
• Gene info view loading for arabidopsis with /webservices/bar_araport/get_protein_sequence_by_identifier.php

I would like to replace these with calls from the new api, preferably ones that support many species. @asherpasha, if any of these uses are currently supported please let me know.

[asherpasha]

Thanks Alex. I will work on it.

[gabydd]

in the publication viewer we use:

• Publication Data with webservice/bar_araport/publications_by_locus.php
• Gene RIFs Data with webservice/bar_araport/generifs_by_locus.php

[alexwaeseperlman]

I've started working on the eFP views. They need the following:

• An endpoint that serves the svg/xml for requested efp view/species. (e.g. the TissueSpecificShootApicalMeristem svg and TissueSpecificShootApicalMeristem xml)
• An endpoint that can be used to find all of the available plant efp views, and one that can find all of the available tissue/experiment views for a species
• https://bar.utoronto.ca/eplant/cgi-bin/plantefp.cgi doesn't seem to work for every species, it would be great if there was an endpoint that gave this data in one place.

I am only going to implement arabidopsis for now. We should discuss these ideas in todays meeting.

[Yukthiw]

For the Cell EFP:

• https://bar.utoronto.ca/eplant/cgi-bin/groupsuba4.php to get cell efp data for each gene.
• https://bar.utoronto.ca/eplant/data/cell/Arabidopsis_thaliana.svg and https://bar.utoronto.ca/eplant/data/cell/Arabidopsis_thaliana.xml for Cell SVG/XML.

[Yukthiw]

For Gene Expression chart:
https://bar.utoronto.ca/eplant/cgi-bin/get_rank.php