Details
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Type:
Bug
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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: None
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Labels:None
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Story Points:2
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Epic Link:
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Sprint:Fall 3 2022 Sep 26, Fall 4 2022 Oct 10, Fall 5 2022 Oct 24
Description
Situation: Testing on bvctest3.bioviz.org revealed that the Analysis Name and Output file name fields of the Analysis menu are not being autofilled correctly and are appearing blank. The Output file name should be filled with the default value provided by CyVerse (for example: FILE.bw). The Analysis Name I believe we were autofilling with "Analysis Name" though this might have been changed as the current production version of BioViz Connect is behind master.
Task: Provide the appropriate default values for the Analysis Name and Output file name fields.
Note: file extension for "bigwig" format is "bw".
Note: Default file name should resemble the input ".bam" file. For example:
- input file name: "A big old bam filewith stuff in it.sorted.awesome.bam" output file name (filled in by the interface): "A big old bam filewith stuff in it.sorted.awesome.bw"
Attachments
Issue Links
- relates to
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IGBF-3181 Change coverage graph app output to bigwig
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- Closed
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Activity
Trying to find regression:
The issue was not present as of commit 030c3b3 on 2021-09-28 for IGBF-2923 Fix filepath error and add index file to scaled coverage graph
Thinking out loud:
Lots of changes to analyses in commit 08063d6 on 2021-09-22 and we know that commit 030c3b3 the issue with default output was fine as of 2021-09-28 and we know current bioviz connect release does not have commits after 1a2ba49 on 2021-10-12 but there was also a change to analyses on d9ad8c2 on 2021-10-14
Potential change to either rightpanel_tags.py or analysisOperations.js
Every app element in Cyverse has an 'arguments' attribute in its app description and this information is extracted and saved in the 'arguments' table in Bioviz Connect database when SyncAppDatatoBioviz is run. The default value for the output file comes from this table also a unique parameter id.
I am not sure if this is a recent change but for Bioviz Connect apps the arguments attribute is empty but the default value is available in 'defaultValue' attribute. Adding a column in the inputdetails table and changing the UI logic to solves the problem but not sure if this is the best solution.
UPDATE: This is Nowlan: Karthik and I discussed the issue and were able to locate the issue as being refactoring to the sync apps database endpoint (most likely) that requires a change to the database to store the default output information.
Changes have been implemented See commit
Changes to be made in Database before testing:
Open terminal in project virtual environment and type the following commands
- mysql
- USE BioVizCyverse;
- SHOW TABLES;
- SELECT * FROM InputDetails;
[ALTER TABLE InputDetails ADD DefaultValue VARCHAR(5000) AFTER FormType;]
Ready for pull request.
Merged
One change: Need to split off the fileName extension before adding the default filetype extension in analysisOperations.js
Right now a file named test.bam appears as test.bam.bigwig when it should appear as test.bigwig
Changes made. See commit
PR Submitted. https://bitbucket.org/nfreese/bioviz-connect/pull-requests/281/igbf-3186-change-output-filename-format
Merged
[~aloraine] - Could you please rerun the playbooks for bvctest3/7?
Playbooks are run and new code is deployed on bvctest3 and 7.
Output file name looks good.
Note: I am unable to test if an analysis job completes successfully as all jobs on multiple accounts and using multiple owned/not owned apps are all failing immediately. It would appear there is an issue with CyVerse.
Closing ticket.
Note that this bug is a regression. The current production version of Bioviz Connect is behind master and the file name defaults appear correctly. The bvctest3 servers are running the master BioViz Connect and the file name defaults do not appear, so something must have broken in the last year.