Fixed the Slf4j error and able to see the warning message when linkout URL isn't available. Working on the MissingResourceException issue for the properties file.

Fixed the MissingResourceException issue and the updated code is present at: https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3813. The UCSCRestApiDataProvider class is being initialized from the igb module and the resource stored in the ucsc-rest-service-api module isn't available yet that's the reason for the MissingResourceException error, changed the URL location to igb.properties which is located in the igb module and it's working as expected. Please review and let me know if there are any issues.

Jaya Sravani Sirigineedi - I'm seeing the following error when building the branch with tests. I feel like we ran into a similar issue a little while ago, but I don't remember what the fix was.

Running com.lorainelab.igb.ucsc.rest.api.service.UCSCRestSymloaderTest
10:50:52.565 [main] ERROR org.lorainelab.igb.synonymlookup.services.impl.SynonymLookup - org/apache/commons/csv/CSVFormat
java.lang.NoClassDefFoundError: org/apache/commons/csv/CSVFormat
	at org.lorainelab.igb.synonymlookup.services.impl.SynonymLookup.loadSynonyms(SynonymLookup.java:65)
	at org.lorainelab.igb.synonymlookup.services.impl.ChromosomeSynonymLookupImpl.<init>(ChromosomeSynonymLookupImpl.java:28)
	at com.lorainelab.igb.ucsc.rest.api.service.UCSCRestSymloaderTest.initialise(UCSCRestSymloaderTest.java:68)

Nowlan Freese I understood the root cause of the issue, I changed the location of the URL to igb properties for it to work while initializing, but the test doesn't initialize it from the igb module instead it calls from the ucsc module itself so the igb resource isn't available here. working on fixing the issue.

Changed the location of the URL to igbDefault.prefs file, everything is working as expected and testcases are also working. This location change requires a bit more changes in various places that was the reason I didn't go for this approach in the start but now I see this option only or hardcoding the string directly in code which is not a good coding standard. Here is the updated code: https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3813, I have tested all possible scenarios I can think of that might have an effect because of the changes and there are no issues. Please review and let me know if there are any issues.

Tested Sravani's branch on Mac.
Able to build with tests.
When there is no internet, I can see the error "UCSC Linkout URL isn't responding", but the build still succeeds (correct behavior).
Linkouts work correctly and there are no errors in the logs.

Jaya Sravani Sirigineedi - I'm wondering if the changes required to add the linkouts as a new data provider key may be over engineered? Everything is working correctly, I'm just wondering if we should just hardcode the linkout url and not worry about including it in any kind of prefs file for the time being.

After discussion with Sravani, we have decided to move forward with her implementation for the linkouts as this will make a potential migration of the igbdefaultprefs file easier in the future.

Ready for pull request.

Found this issue while doing the final testing: https://jira.bioviz.org/browse/IGBF-3853. Will raise the pull request after fixing the issue.

As discussed with Nowlan Freese, created a pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1029. The issue mentioned above is part of the Ensembl code which as discussed will not be included in the upcoming release.

PR is merged and new installers are deployed to bioviz.org "early access" section.

Ready for testing.

Testing main branch installer on Mac.

Jaya Sravani Sirigineedi - I noticed that in the Preferences > Data Sources window if I click the "i" icon for UCSC REST I do not see a linkoutUrl variable, but all of the other data sources (IGB Quickload) have a "primarylinkoutUrl". I'm not sure what the primarylinkoutUrl is doing, but it may be confusing that we now have two variables with the phrase linkout in them. Can you investigate the IGB codebase? If you don't think it will be an issue, then I think we can close this ticket.

Note for myself, when testing I saw the below error. This will be handled in IGBF-3853.

16:30:03.111 INFO  o.l.i.u.r.a.s.UCSCRestApiDataProvider - Initializing UCSC Rest Server https://api.genome.ucsc.edu/
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
	at com.google.common.base.Preconditions.checkNotNull(Preconditions.java:903)
	at com.google.common.collect.ImmutableSet.construct(ImmutableSet.java:206)
	at com.google.common.collect.ImmutableSet.copyOf(ImmutableSet.java:243)
	at com.affymetrix.igb.view.load.GeneralLoadUtils.getLoadedSpeciesNames(GeneralLoadUtils.java:197)
	at com.affymetrix.igb.view.load.GeneralLoadUtils.retrieveDataContainer(GeneralLoadUtils.java:172)
	at com.affymetrix.igb.general.DataProviderManager.loadSupportedGenomeVersions(DataProviderManager.java:471)
	at com.affymetrix.igb.general.DataProviderManager.initializeDataProvider(DataProviderManager.java:350)

The primaryLinkoutUrl is present for the Quickload Providers because Quickload implemented a method, getPrimaryLinkoutURl() from the DataProvider interface that is being used to display that as the other providers didn't implement it, that's not shown for them. In the code, they are just returning either mirrorUrl if it is used else the original URL, this may be used to find which URL is being used to retrieve data I guess (is it the original one or the mirrorUrl). Also, I see the URL that is being used for the datasets is named datasetLinkoutUrl and it's not being shown in the info section because it varies for each dataset inside a provider, as the URL that we are storing for the UCSC Rest is just the domain and not complete Url, I think it would be good to rename it to "datasetLinkoutDomainUrl" or something shorter like "datasetDomainUrl" and this won't be shown in the info section for the same reason. Nowlan Freese Please let me know your input on this.

Jaya Sravani Sirigineedi - I think renaming it to "datasetLinkoutDomainUrl" works for me.

Updated the code to rename the variable to "datasetLinkoutDomainUrl" and here is the branch: https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3813 Please review and let me know if there are any issues.

Tested Sravani's branch on Mac.

Linkouts were working correctly, and as far as I could find all of the code was renamed.

Ready for pull request.

Here is the Pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1030

PR is merged and new installers deployed to bioviz.org. Ready for testing.

Tested with main branch installer on Mac.

Link outs to UCSC REST are working, no issues in log.

Closing ticket.