Some notes that are also mentioned in IGBF-2975:

Sym name is an optional field and may not always be present.
Galaxy and BioViz Connect both use the same method when no genome is set in the bookmark (loadUnknownData).

I made changes to BookmarkUnibrowControlServlet.java in the loadUnknownData method. Previously, the url was being passed as the name of the track instead of the sym name. Now either the sym name or the file name (if no sym name) will be used.

Moving to needs 1st level review.

Commit:https://bitbucket.org/nfreese/nowlanfork-igb/commits/7e845cad7d5750023145d847a155805e733b4798
Downloads: https://bitbucket.org/nfreese/nowlanfork-igb/downloads/

To test:

Download my branch installer for IGBF-2983 and install IGB
In IGB,
Click here to load a bookmark from cyverse that includes the genome version and a sym name. The genome should be automatically selected and the track name and name under available data should be diseaseDa2d.bed.

Remove the file from IGB.

Next, click here to load a bookmark from cyverse that does not include the genome version but does include a sym name. The genome should not change, but the track name and name under available data should be diseaseDa2d.bed. The full URL should not be visible under Available Data.

Before merging this, can we test all the different aspects of how the bookmarks code is used?

Perform functional testing using the below protocols prior to submitting PR:

• https://wiki.transvar.org/display/ITD/Bookmarks (testing protocol)
• https://wiki.transvar.org/display/ITD/Galaxy (testing protocol)

Also, test "View in IGB" functionality of eFP-Seq browser. For information on how to operate the "View in IGB" functionality of eFP-Seq browser, read article available from https://pubmed.ncbi.nlm.nih.gov/31350781.

Test results:

• I followed https://wiki.transvar.org/display/ITD/Bookmarks testing protocol. I am able to perform all the testing steps for bookmarks in IGB.
• For https://wiki.transvar.org/display/ITD/Galaxy testing protocol, the 'View in IGB' link under files in "Open Galaxy files in Integrated Genome Browser" is not working for chrome and Microsoft Edge browser even when IGB was running but It's working with Firefox. I was able to perform rest of the steps. Please check 'screenshot-1' for the error in chrome. ( This issue is unrelated to this ticket, its related to 2987. Dr. Freese is working to fix it.)

Can also test BioViz Connect: https://wiki.transvar.org/display/ITD/BioViz+Connect

Final Test results:

• I am able to perform all the testing steps for bookmarks in IGB.
• For https://wiki.transvar.org/display/ITD/Galaxy testing protocol, the 'View in IGB' link under files in "Open Galaxy files in Integrated Genome Browser" is not working for chrome and Microsoft Edge browser even when IGB was running but It's working with Firefox. I was able to perform rest of the steps. Please check 'screenshot-1' for the error in chrome. ( This issue is unrelated to this ticket, its related to 2987. Dr. Freese is working to fix it.)
• Changes made by Dr. Freese to BookmarkUnibrowControlServlet.java in the loadUnknownData method are working as expected. Now either the sym name or the file name (if no sym name) is getting used.
• Functional testing for https://wiki.transvar.org/display/ITD/BioViz+Connect is also working fine. I am able to perform all the steps.

Pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/890/igbf-2983-sym-name-or-file-name-used-in

Merged and ready for testing using master branch installer(s) from bitbucket repository Downloads folder.

Test results on master branch :

• After clicking the given link the genome got automatically selected and the track name and name under available data was diseaseDa2d.bed. Please see screenshot 2.
• After removing the file and clicking the link again, the genome did not change, but the track name and name under available data was diseaseDa2d.bed. Please see screenshot 3.

A couple of questions with the above comments. Please address:

• Screenshot 2 does not include the title bar. Please always include the title bar as it shows the IGB version and genome. (Genome is also shown in the Current Genome tab)
• The Available Data section is different in the two screenshots. I thought the point of this change was to remove the URL components so that you don't see so many folders, by ensuring that the "sym name" fields is respected regardless of whether a genome version is indicated?
• I was confused as to what "sym name" is being passed in the test bookmarks. Is it the same as the file name?

Here are two new links to try (copy and paste them into web browser). The sym names have been changed so that they are different than the file names.

http://127.0.0.1:7085/IGBControl?
version=A_lyrata_Apr_2011&
cyverse_data=true&
sym_col_0=0x00FF00&
sym_bg_0=0xFF0000&
sym_name_0=exampleSymName1.bed&
query_url=https://data.cyverse.org/dav-anon/iplant/home/kraveend91/diseaseDa2d.bed&
feature_url_0=https://data.cyverse.org/dav-anon/iplant/home/kraveend91/diseaseDa2d.bed&
sym_method_0=https://data.cyverse.org/dav-anon/iplant/home/kraveend91/diseaseDa2d.bed&
loadresidues=false&
server_url=cyverse

http://127.0.0.1:7085/IGBControl?version=?&
cyverse_data=true&
sym_col_0=0x00FF00&
sym_bg_0=0xFF0000&
sym_name_0=exampleSymName2.bed&
query_url=https://data.cyverse.org/dav-anon/iplant/home/kraveend91/diseaseDa2d.bed&
feature_url_0=https://data.cyverse.org/dav-anon/iplant/home/kraveend91/diseaseDa2d.bed&
sym_method_0=https://data.cyverse.org/dav-anon/iplant/home/kraveend91/diseaseDa2d.bed&
loadresidues=false&
server_url=cyverse

Final Test results on the latest master branch.

• After clicking the given link the genome got automatically selected and the track name and name under available data was diseaseDa2d.bed. Please check the sym name in the screenshot 2. The symname is exampleSymName1.bed.
• After removing the file and clicking the link again, the genome did not change, the file name is same which is diseaseDa2d.bed. The symname is exampleSymName2.bed The full URL is not visible in the available data. Please see screenshot 3.

Dr. Freese and I also tested on galaxy and bioviz connect, the results are good.

Closing the ticket.