Tested using installer for release-10.1.0 as well as main branch installer - the DAS refGene tracks no longer disappear when loading from two different genomes.

Closing ticket.

Both PRs are merged.

notes to: Nowlan Freese and Jaya Sravani Sirigineedi

• Delaying building installers for the main branch because we ought to increment its version code to avoid conflicts with release-10.1.0.
• New release-10.1.0 installers are built and in the Download section of team repository: https://bitbucket.org/lorainelab/integrated-genome-browser/downloads.

Created two PRs one for the release branch and the other for the main, the source branch is based on the release branch. Here are the PRs:
https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1049
https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1050

Tested using Sravani's branch on Mac.

• Able to build branch locally with tests.
• Following the testing instructions above, the DAS refGene tracks no longer disappear when loading from two different genomes.

Ready for pull request to main branch and release-10.1.0

Fixed the test case failure, here is the updated code: https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3936.

I'm seeing a test failure in DASFeatureParserTest.testLinks while building IGB:

DASFeatureParserTest.testLinks -- Time elapsed: 0.053 s <<< FAILURE!
org.opentest4j.AssertionFailedError: expected: <affyU133Plus2> but was: <https://genome.ucsc.edu/cgi-bin/das/hg18affyU133Plus2>

Following the testing instructions above, the DAS refGene tracks no longer disappear when loading from two different genomes.

Fixed the issue by making the type variable unique as it's being used to set the method of a dataset which is important for displaying tracks, that variable has to be unique for each dataset and across genomes too. As this variable was set the same for both the human and mouse genomes, it's loading the human genome dataset in the mouse genome. I have tested the old IGB versions and this issue has been there from the start of DAS, it hasn't been introduced by any UCSC REST changes or any other fixes. Here is the updated code, tested and working as expected: https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3936. Please review and let me know if there are any issues.

Tested all the mentioned tickets in the description and found one issue for DAS provider which is mentioned in this ticket: https://jira.bioviz.org/browse/IGBF-3584. There are two issues mentioned in that ticket and the issue I am seeing for DAS is:

Reproduce the issue:

1. Add UCSC DAS as a custom data provider using this URL (https://genome.ucsc.edu/cgi-bin/das)
2. Select the mouse genome.
3. Select Available Data > UCSC (DAS) > refGene
4. Click Load Data
5. Change to the human genome.
6. Select Available Data > UCSC (DAS) > refGene
7. Click Load Data
8. Go back to the mouse genome
9. The refGene added from UCSC should be missing from the Data Management Table. The data should still be present as a track, but grayed out as if it had not been loaded.