[InterMine Dev] 'Download' button on bag report

Joe Carlson jwcarlson at lbl.gov
Wed May 27 07:20:25 BST 2015


Hi,

I’m having a little trouble understand how some magic occurs in the enhancement widgets.

On a gene ontology enrichment widget, there are buttons for ‘view’ and ‘download’. The download button results in a tab separated list of GO descriptions, p-values and genes. The GO identifier is not present.

When I trace through what happens when the download button is pressed, I get something of type application/javascript which includes a jQuery function call with a JSON argument:

jQuery18206181168801502899_1432704112334({"extraAttribute":"{\"gene_length\":{\"percentage_gene_length_not_null\":null,\"pathQueryGeneLengthNull\":null,\"gene_length_correction\":false}}","externalLink":"http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=","filterSelectedValue":"biological_process","description":"GO terms enriched for items in this list.","label":"GO Term","filters":"biological_process,cellular_component,molecular_function","type":"Gene","list":"Demo: Poplar list in a pathway","title":"Gene Ontology Enrichment","pathConstraint":"Gene.goAnnotation.ontologyTerm.parents.identifier","notAnalysed":2,"pathQueryForMatches":"{\"model\":{\"name\":\"genomic\"},\"select\":[\"Gene.goAnnotation.ontologyTerm.parents.identifier\",\"Gene.primaryIdentifier\"],\"orderBy\":[{\"Gene.goAnnotation.ontologyTerm.parents.identifier\":\"ASC\"}],\"where\":[{\"path\":\"Gene\",\"op\":\"IN\",\"code\":\"A\",\"value\":\"Demo: Poplar list in a pathway\"}]}","requestedAt":"27 May 2015 06:01:15 GMT","is_logged":false,"current_population":null,"pathQuery":"{\"model\":{\"name\":\"genomic\"},\"select\":[\"Gene.secondaryIdentifier\",\"Gene.symbol\",\"Gene.primaryIdentifier\",\"Gene.organism.name\",\"Gene.goAnnotation.ontologyTerm.identifier\",\"Gene.goAnnotation.ontologyTerm.name\",\"Gene.goAnnotation.ontologyTerm.parents.identifier\",\"Gene.goAnnotation.ontologyTerm.parents.name\"],\"where\":[{\"path\":\"Gene\",\"op\":\"IN\",\"code\":\"A\",\"value\":\"Demo: Poplar list in a pathway\"}]}","filterLabel":"Ontology","results":[
{"identifier":"GO:0009132","p-value":1.2417879361495878E-9,"description":"nucleoside diphosphate metabolic process","matches":4},
….

I’m a little lost at this point in understanding the code. Firebug tells me that the routine jQuery18206181168801502899_1432704112334 is null.

Not knowing anything about the intermine javascript api or bootstrap, I’m sort of lost in trying to see where this function gets defined. is is bootstrap? or intermine.js? Is this described in the section on Cell Formatters? I’m a little lost here.

My goal is to get the GO identifier included in the tsv file you get when you press the Download button. Here is a URL that has some of our enhancement widgets:

http://phytozome.jgi.doe.gov/phytomine/bagDetails.do?scope=all&bagName=Demo%3A+Poplar+list+in+a+pathway 

By the way, I tried the download button on flymine. The button looks ineffective there. firebug tells me there is a javascript error.

Thanks,

Joe





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