Direct Url Links To Img Gene Details Using Gene Locus Tags
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12.9 years ago
chrismgowen ▴ 10

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.

database annotation • 3.0k views
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Have you tried sending a reconstructed POST search as GET request?

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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!

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12.9 years ago

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.

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