Species Page: Show expression datasets if available for each species.

legumeinfo / legumeinfo.org

general site issues (or a place to log issues if you just want to put them somewhere and triage which repository they properly belong to later)

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Species Page: Show expression datasets if available for each species. #4

Closed sdash-github closed 6 years ago

sdash-github commented 6 years ago

The species page shows most resources available at LIS for each species except expression datasets. We have expr data available for cajca, cicar, phavu, vigun. These items in species page should show the datasets available. Add code to the module to get this info as links?? (To get the link to a gene page for a dataset would be challenging as it needs exemplar)

sdash-github commented 6 years ago

TEMPORARY: SQL to get dataset acc_no starting with genus+spp (available in sp-sheet). Cicer, as always, is the pain-in-the-neck. $ psql -c "SELECT od.accession_no FROM ongenome.dataset AS od WHERE od.genome_id IN (SELECT og.genome_id FROM ongenome.genome AS og WHERE og.organism_id IN (SELECT oo.organism_id from ongenome.organism AS oo WHERE oo.genus='Cicer' AND oo.species='arietinum'))" cicar1 cicar2

If exemplar will be in dataset table; this is possible
Else, use ajax call to query and get links for each dataset. Develop the url in lis_expression with a small function and menu item.

sdash-github commented 6 years ago

Thought most straight forward is to link to the Expression summary page to the specific dataset description.
Added id attrib to'dataset row in /lis_expression/all summary page to be used as named anchor.
Linking to these from species page as: ......./lis_expression/all#phavu1 or #cajca1 or #vigun1, etc (Done in my sandbox)

TO DO: Review; update repo, etc. before closing.

sdash-github commented 6 years ago

Now functional in lis-stage. The following files were modified to accomplish this: lis_expression_all_summary.tpl.php : id attribute added for linking to datasets. lis_species_resources.module : queries ongenome with genus-species to list available datasets with link to expression-summary-page. Done