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.

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.

PR Submitted. https://bitbucket.org/nfreese/bioviz-connect/pull-requests/278/igbf-3186-fix-analysis-output-filename

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.