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PeanutBase / jekyll-peanutbase

A "starter" Jekyll site that uses the jekyll-theme-legumeinfo submodule
Apache License 2.0
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Gene Search Tool and downstream issues encountered #50

Open sdash-github opened 1 year ago

sdash-github commented 1 year ago

I found this while developing a user guide; now work in progress at https://dev.peanutbase.org/userguides/genefamily/geneToFamily.html

Go to gene family starting from a gene

  1. Using Gene Search Tool
    • PeanutBase Home page (use left Tools panel or Tools dropdown in menubar) to [Gene Search Tool](/tools/gene-keyword -search.html){:_blank}.
    • Use the Identifier/Description SEARCH boxex to type your gene name, id, or even partial id. Arahy.H916D0 fails but H916D0 works while in ArachisMine both works. So confusing for user. More confusing because the example shows a Soy pattern that fails, e.g. Glyma.13G357700. We need a Arahy example for PB.
    • If found the Result below will list all the genes and other features that has this id/name.
    • The 'GENE FAMILY ASSIGNMENTS' column will list the link to the Gene Family report page which has a link on the right panel named ,'View on the LIS Funnotate app'. It appears under 'External Links' here while in the alternate ArachisMines search it appears under ‘LIS Linkouts’ which is more appropriate.
    • This links to the Phylogram for the gene family and shows the Taxa composition piechart and the tree diagram below with the searched gene highlighted.
      This link (https://funnotate.legumeinfo.org/?family=legfed_v1_0.L_6RNLR0) is unproductive as it goes to Funnotate but shows perpetual machine loading.
    • (This page is an interface to the ArachisMine from PeanutBase)
adf-ncgr commented 1 year ago

I've created an issue for allowing customization of the examples. I can't reproduce the issue with funnotate not displaying the tree for the linked family. I think we ought to use a gnm2.ann2 gene as the example, and just avoid the mess with "H916D0 vs Arahy.H916D0" which is more of a data issue than anything else. Let me know if there's something else that needs resolving here.

sdash-github commented 1 year ago

This link from the gene family report page is still perpetually loading. It is also labeled under External Links but should be LIS linkout. https://funnotate.legumeinfo.org/?family=legfed_v1_0.L_6RNLR0

Screen Shot 2023-11-24 at 6 29 14 PM
adf-ncgr commented 1 year ago

The URL you provided is still working on my end. Do you see any errors in the browser console?

sdash-github commented 1 year ago

1. Console error: Uncaught SyntaxError: Identifier 'LINKOUTS_BASE_URL' has already been declared (at phylogram.js:1:1) sockjs.min.js:sourcemap:2 WebSocket connection to 'wss://funnotate.legumeinfo.org/__sockjs__/n=HXwiKZfOwB8vargttu/927/spt0mg1d/websocket' failed: n.exports @ sockjs.min.js:sourcemap:2 shiny-server-client.min.js:1 Fri Nov 24 2023 12:22:44 GMT-0600 (Central Standard Time) [INF]: Connection opened. https://funnotate.legumeinfo.org/?family=legfed_v1_0.L_6RNLR0 shiny-server-client.min.js:1 Fri Nov 24 2023 12:22:44 GMT-0600 (Central Standard Time) [DBG]: Open channel 0 funnotate.legumeinfo.org/:1 Uncaught (in promise) Error: A listener indicated an asynchronous response by returning true, but the message channel closed before a response was received

  1. When I opened the URL incognito it worked. So something at my end??
adf-ncgr commented 12 months ago

Yes, I'm not exactly sure how to interpret the error, but I think your browser must have gotten into a problematic state. Maybe try clearing the cache?

svengato commented 12 months ago

This link (https://funnotate.legumeinfo.org/?family=legfed_v1_0.L_6RNLR0) is unproductive as it goes to Funnotate but shows perpetual machine loading.

It works for me too, I get a phylotree in a few seconds.