Sorry, I was wrong about their not doing anything. I just needed to hover the mouse over them a bit longer. When I did that, a tooltip appeared.

However, most of the tooltips are not very useful. They simply repeat the label, using slightly different wording.

The only tooltip that introduces new information is the tooltip for "Output file name". This tooltip tells the user about where the output file will be saved.

However, there is a problem with putting this information here. The tooltip pertains to the "Output file name" textbox, not the location of the file, which is not something the user can change, so far as I know.

I think this crucial information about where the results files and folders will be saved needs to be added to the interface, not hidden in a tooltip.

Therefore I think we should display this information in another part of the interface. I think it should be added to a new section below the "Run Analysis" button.

Other requests:

• The question mark icons are too close to the preceding letters. Can we add some some whitespace so that the interface looks less crowded?
• Let's also improve the tooltips, making them easier to read and more substantial looking. Can we make them look like the new tooltip for the heading on the "Manage Link" right panel screen?

Dr. [~aloraine], Ill need some help updating the database in the production server for the tooltips (maybe with the Ansible playbook). I need to run the following queries in the inputdetails table:

update inputdetails
set htmldata = replace(htmldata,"title='Output folder saved to current folder if in Home, saved to Analyses folder if data in Shared/Community'",
"title='Output file will be saved in current folder if you are in Home. If you are in Shared or Community, it will be saved in the analyses folder in Home'");

update inputdetails
set htmldata = replace(htmldata,"title='File output to current directory if in Home or Analyses folder if data from Shared or Community'",
"title='Output file will be saved in current folder if you are in Home. If you are in Shared or Community, it will be saved in the analyses folder in Home'");

update inputdetails
set htmldata = replace(htmldata,"title='File is output to current directory if in Home or output to Analyses if file in Community/Shared'",
"title='Output file will be saved in current folder if you are in Home. If you are in Shared or Community, it will be saved in the analyses folder in Home'");

Replying to: Karthik Raveendran
The above queries can be done, but I'm concerned that query success depends on knowing the current value for a row. Instead, it would be better to query based on the App name, or some other value that can function as a primary key.
Can you give me a little more details regarding your strategy for making this solution work on every test server, regardless of the current values in the database?

Merged https://bitbucket.org/nfreese/bioviz-connect/pull-requests/255/igbf-2923-refactor-analyses-ui-and?link_source=email

Submitted PR. Commit

Testing: [~aloraine], it would be great if you could deploy this in the test site. My recommendation is that this commit should be rigorously tested before push to production because the analysis module is quite difficult to test while development as the results of the analysis comes back after a significant delay and this commit has a lot of files with a lot of changes.

Latest main branch from Nowlan Freese repository deployed to bvctest3.bioviz.org.
attn: Karthik Raveendran and Nowlan Freese

Testing:

For the "Make scaled coverage graph", the Input File Index (bai) is no longer being autofilled on bvctest3.

The analysis jobs are failing at "error downloading input_path.list". When I looked at the input param_value the path was listed as "/iplant/home/nowlanf/testFiles/!howLong?//48v37_summits.fasta". Note the double slashes.

Submitted PR for first level review
Commit Includes: File path correction and auto-filling index file

Merged https://bitbucket.org/nfreese/bioviz-connect/pull-requests/256/igbf-2923-fix-filepath-error-and-add-index?link_source=email

Test new functionality using testing host: https://bvctest6.bioviz.org
For background, testers can read latest draft of the bioviz-connect paper: https://www.biorxiv.org/content/10.1101/2020.05.15.098533v4

Analysis jobs are now being completed successfully.
The Input File Index (bai) is now being correctly autofilled.

Problem:
The "Find enriched sequence motifs" analysis is missing the input field for Output Folder Name.

Pushed changes to repo. Commit in branch IGBF-2923

Th conditional statement that handles input fields did not include FolderOutput field which is added in this commit.

Test Protocol:
Search for a .fasta file in Home directory and run Analyse from right-click menu. Click on the "Find enriched sequence motifs" button and check if the Output Folder Name field is present. Try running the analysis and if it appears as 'Submitted' in the Analysis History page

Passes review as per discussion during Oct 19 scrum meeting.

Merged https://bitbucket.org/nfreese/bioviz-connect/pull-requests/261/igbf-2923-fix-folderoutput-input-field-ui?link_source=email

Deployed for testing to https://bvctest6.bioviz.org.

The output folder name field is present, and when the analysis was run the folder was created and named correctly (and the analysis completed correctly).

Closing issue.