Details
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Type:
Improvement
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: 10.2.0
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Labels:None
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Story Points:3
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Epic Link:
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Sprint:Summer 4, Summer 5, Summer 6
Description
Situation: The species.txt and synonyms.txt files are used to display human readable species names and genome versions when selecting a genome. They are also used to identify data to the correct genome from UCSC and Galaxy. We are currently storing species.txt and synonyms.txt on our SVN repository and separately within IGB itself. The files are not synced and have diverged significantly.
Task: Synchronize the files between the SVN repository and IGB.
Links:
IGB synonyms.txt file: link
IGB species.txt file: link
SVN repository: link
Species.txt documentation: link
Synonyms.txt documentation: link
Note: There are several entries in the SVN synonyms.txt that are incorrect and will need to be fixed.
Attachments
Issue Links
Activity
Sorry for the delay. The testing-only Quickload is now available at URL http://igbquickload-main.bioviz.org/IGBF-4266/quickload/
cc: Paige Kulzer
We've tested using the test Quickload in IGB 10.1.0 and 10.2.0. All genomes and sequences are loading as expected. Ann Loraine, it should be safe to deploy these changes to the main IGB Quickload for final testing now.
Thank you Paige Kulzer and Nowlan Freese! I am proceeding to deploy the updates to RENCI and UNC Charlotte hosting.
Both quickload main's (primary and mirror) are updated with the new files species.txt and synonyms.txt.
Ready for final testing.
attn: Paige Kulzer and Nowlan Freese
Completed final testing on Mac and found no issues. Closing ticket!
I've combed through both copies of species.txt and synonyms.txt in IGB and the SVN server. They are all identical now. I briefly tested that I didn't mess up any of the genomes during this process by building IGB from my branch and checking that all of the genomes are displaying correctly in the species drop-down menu.
I'm sure there are still some lingering issues, so please carefully review these files and let me know if anything needs to be changed. One thing I would like to point out to the reviewer is line 166 of synonyms.txt - this line seems out of sorts but I'm not sure the best way to fix it.
Branch: https://bitbucket.org/pkulzer-lorainelab/integrated-genome-browser/branch/IGBF-4266