Changes made in IGBF-32 were interfering with bookmarks created from files with spaces being loaded correctly. As the associated changes in the Galaxy codebase associated with IGBF-32 were not pushed, I reverted the changes in the directlyLoadFile and loadUnknownData methods. The loadUnknownData method was also modified to match the loadCyVerseDataMethod (now removed) from IGBF-1632. The loadUnknownData method now does not load a custom genome if a user is already in a genome when opening data that is not associated with a genome.

To test:
To test IGB bookmarks, load the attached files into IGB and create a bookmark. Remove the files from IGB and then double-click on the bookmark to see if it loads correctly.

My IGB branch with changes: https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-2273-SpaceInName

I have tested the issue using the instructions mentioned above.
1) Downloaded the files and the branch installer.
2) Opened those files and created a bookmark.
3) Removed those files and selected a different genome.
4) Double clicked bookmark to check if the custom genome is not being loaded if a user is already in a genome when opening data that is not associated with a genome.
Everything is working fine. Nowlan Freese, please go ahead and submit a PR for the same.

Pull Request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/775/fix-bookmark-issue-when-filename-has/diff

Nowlan Freese - Bookmarks are getting loaded but once I close IGB and try to reload, null pointer exception is thrown.

The issue Noor found is an existing issue with how bookmarks works with custom genomes. What is happening is that when a user loads data without selecting a genome, IGB creates a custom genome. The data is then loaded within this custom genome. When the user creates a bookmark, the version is set as custom genome. When the user closes IGB the custom genome is removed. When the user reopens IGB and tries to load the bookmark, IGB cannot find a genome version of custom genome, and thus generates a null pointer. This behavior has been around for a while. CyVerse and Galaxy use a separate bookmark logic to load custom genomes to avoid this problem. This seems like an edge case as I'm not sure how often users would be creating bookmarks in custom genomes.

Since the other functionality appears to be working, I'm closing this issue.