Question: Direct Url Links To Img Gene Details Using Gene Locus Tags
1
gravatar for chrismgowen
8.6 years ago by
chrismgowen10
chrismgowen10 wrote:

I am trying to generate reports in Excel that include hyperlinks to the Gene Details provided for my organisms in IMG, but I've so far been unable to find a way to automatically generate the relevant URLs given the gene locus tags.

If you have the object identifiers, it's easy enough to throw that into a URL and get the relevant pages like so:

http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=637798373

but I can't find a comparable keyword for the gene locus, if there even is one. Maybe as an alternative there is a way to link to gene search results using the locus as a search term? As far as I can tell, though, the search terms are not ever passed through the URL:

http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=FindGenes

I'm also open to alternative suggestions. Thanks in advance.

annotation database • 2.1k views
ADD COMMENTlink written 8.6 years ago by chrismgowen10

Have you tried sending a reconstructed POST search as GET request?

ADD REPLYlink written 8.6 years ago by Michael Schubert6.9k

The web developer toolkit plugin for firefox has a handy form tool called "convert POSTs to GETs". of course this cgi might be explicitly looking for POST. It doesn't much care for: http://img.jgi.doe.gov/cgi-bin/w/main.cgi?page=geneSearchForm&searchTerm=Synpcc7942_B2623&searchFilter=locus_tag_list&seqstatus=both&domainfilter=All&displayType=list

This is a valid complaint on your part. Not providing bookmarkable URLs to searches is a big no-no in web application development!

ADD REPLYlink modified 3 months ago by RamRS25k • written 8.6 years ago by Jeremy Leipzig18k
2
gravatar for Michael Schubert
8.6 years ago by
Cambridge, UK
Michael Schubert6.9k wrote:

How you would solve this normally:

  • get all parameters that the form is posting to the cgi script (as Jeremy has done)
  • encode these as a GET request
  • find a GET to POST converter, e.g. on http://get-to-post.nickj.org/
  • bookmark the URL [?]converter>/?[?]your_get_request>

In that case it doesn't work because the POST request also contains some weird cookie data with a total size of 688k(!). Whoever developed the search interface, they either wanted to make it as unusable as possible or didn't know what they were doing.

ADD COMMENTlink modified 4 months ago by RamRS25k • written 8.6 years ago by Michael Schubert6.9k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1732 users visited in the last hour