Issue:- To give a warning message when loading a file without selecting a genome and allow loading of genome sequence data for the FASTA and 2BIT file when file is drag and dropped.

Files changed:-
core/genometry/src/main/resources/genometry.properties
core/genometry/src/main/java/com/affymetrix/genometry/general/DataSet.java
core/igb/src/main/java/com/affymetrix/igb/action/LoadFileAction.java
core/igb/src/main/java/com/affymetrix/igb/view/load/GeneralLoadUtils.java

Testing scenarios:-
1) Drag and drop file in IGB application -
a) If the file is of extension 2bit, bnib, fa, fas, fasta, fna, fsa, mpfa, fa.gz, fas.gz, fasta.gz, fna.gz, fsa.gz or mpfa.gz, it is assumed that the file has
genome sequence data. Once clicked on load sequence button it will load the genome sequence.

b) If the file is of any other extension,
i) If no genome is selected, then once the file is loaded user will get a warning message "A genome sequence has not been selected, some features may be unavailable.". Also on clicking Load Sequence button user will get an error message "A genome sequence has not been selected. Loading sequence data is not possible."

ii) If genome is selected, then no warning message will be displayed and on clicking Load Sequence button, the new file gets loaded on top of the selected genome and there is no error message.

2) Click File -> Open Genome from File... -> select the file from above mentioned extension (as no other file extension will be allowed) --> Click Load Sequence button to load the genome sequence.

Testing results:-
Please check the attached test result for each test scenario.

Code changes:-
https://bitbucket.org/rpatil14/riddhifork-igb/branch/IGBF-1509#diff

1st level review

I'm still getting the "Please Select A Genome" message when I try to load data without first selecting a genome (see attached image).

To reproduce:
Navigate to the IGB start screen.
Select File > Open File...

The behavior should mirror Drag and Drop, where a user can drag and drop a data file (for example .bed) into IGB, and it is loaded as a data track without a selected genome.

This may need to be a separate issue:

I noticed that in the current release (9.0.2), user's cannot load a file through a URL without getting the Please select a Genome warning. However, the user also cannot use a URL to open a genome from a file. Do we not allow a user to use URLs to view custom genomes?

Issue:- Select File by clicking Open File.. option giving error "Please Select A Genome".

Files changed:-
core/igb/src/main/java/com/affymetrix/igb/action/LoadFileAction.java

Testing scenarios:-
1) Navigate to the IGB start screen. Select File > Open File... (It should allow to select the file with/without selecting genome)
2) Click on file open icon from toolbar (It should allow to select the file with/without selecting genome)
3) Select the genome -> Select File -> Open File.. (This is existing behavior which is untouched and working as expected)

Code changes:-
https://bitbucket.org/rpatil14/riddhifork-igb/commits/ee468eef1fc2c90bb32dac4980c2683bdbc6da14

https://bitbucket.org/rpatil14/riddhifork-igb/commits/578bd5f1dac9b23c3665d88ed9a21a23c2cf6cee

1st level review:

Functioning correctly. File > Open File... is now able to open data when no genome is selected.

Issue: I did not see a popup warning when the user loads data (non-sequence file) without first selecting a genome: "A genome sequence has not been selected, some features may be unavailable." I think this is necessary as certain functionality such as showing mismatched bases will not be possible without a genome.

The popup warning when the user loads data (non-sequence file) without first selecting a genome is tied to the popup that informs a user "To display your data, zoom in and click Load Data", in that if the user selects the checkbox "Do not show this message again." the warning "A genome sequence has not been selected, some features may be unavailable." is also skipped. I'm not sure this is the best behavior, as many users opt to ignore the "To display your data" warning, but may want to see the warning about no genome being loaded.

Note: I would like Dr. Loraine to take a look at some of the new functionality. If a sequence file is dragged and dropped with no genome selected, IGB now assumes that the user wanted to load it as the genome. Similarly, if a user selects File > Open File... and selects a sequence file when no genome is selected, IGB assumes the user meant to load it as the genome.

Code changes done :-
https://bitbucket.org/rpatil14/riddhifork-igb/branch/IGBF-1509#diff

Reverted the additional code changes and just fixed the original issue which is open file even when genome is not selected
https://bitbucket.org/rpatil14/riddhifork-igb/commits/ec3a9791a11fa65c0973d0c524178a7189383a5e?at=IGBF-1509

Functional Review - No errors observed.

Pull request submitted:-
https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/667/igbf-1509-open-file-should-work-if-no/diff

Please check comments in modified files for latest commit on this branch. Looks like an unneeded import from experimentation.

Removed unused imports and tested the code locally.

Merged to master.

MacOS successful.

Windows testing successful

Linux testing successful