I have tested it on IGB with the help of the OBR xml file present in the Downloads section of the repo:
https://bitbucket.org/lorainelab/ncbi-primer/src/master/
I can see a new option in the database dropdown for the species mentioned above.
Moving the ticket to done.

Note: Un-assigning from Jay as I don't think he had started working on this yet.

I have checked it and it is working fine. The new database option is now shown for species "danio rerio".
Also, its working for dog and pig's species.
Pooja Nikhare, Please go ahead and submit a PR for the same.

Enabled piplenes. Please check download section. https://bitbucket.org/pnikhare/ncbi-primer-pooja/downloads/

Pooja Nikhare, could you please enable pipelines on you newly forked repo so that I can test it and move it to DONE?

Thank you Prutha Kulkarni to find the issue related to species "danio rerio".

• There was one underscore misplaced. I have edited it.
  For reference dog species name : Canis lupus familiaris, pig species name : Sus scrofa. I was able to view in IGB.
• Modified Reade Me file.
  Please review the changes :
  https://bitbucket.org/pnikhare/ncbi-primer-pooja/branch/IGBF-2287#diff

Pooja Nikhare, I checked it for every genome in the available species and the species in list specified above has the new option in database dropdown which is "Genomes for selected organisms (primary reference assembly only)". Whereas, genomes of other species do not have that option.
Also, I wanted to mention that I could not find dog and pig's genome in IGB though the code has changes related to those genomes. (I checked the code diff for this branch to know the name of the dog & pig species)
I downloaded latest mac installer for mac from IGB repo and still those two species are not visible.

I found one issue in species "danio rerio". The new database input option is not available even though the code is changed to incorporate the option for that species.
Attaching screenshot of IGB for the same.
cc: [~aloraine]

PR is merged and ready for testing.

Please submit PR at your earliest convenience.

Sorry Pooja Nikhare!

Re-opening and moving to previous column for further consideration.

It is not yet merged with the Experimental Apps Repo or new NCBI Primer repo

Moving this forward to completed as no problems have been detected.
cc: Pooja Nikhare and Shamika Gajanan Kulkarni

Pooja Nikhare I have tested the ticket again for "Genomes for selected organisms (primary reference assembly only)" database and it is working fine for that.

To reproduce the result I selected Database "RefSeq representative genomes", species "Ovis arise".
Selected sym and right-click on "Primer blast option". The page to which we are redirected ends up to an error page. Only the "Empty result" is shown in the page after some time.

To verify the behavior, verified with NCBI Site (https://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi)
copied the sequence from IGB console logs, selected Database "RefSeq representative genomes", species "Ovis arise". The same issues occurred, the page ends up to an error page. Only the "Empty result" is shown on the page.

On building the app, the test case related to this database also failed. I think there have been some changes in NCBI Site, with respect to "RefSeq representative genomes" database.
Note: as per this ticket "Genomes for selected organisms (primary reference assembly only) database is not shown on selecting species "Ovis arise". To move forward Commenting out the test case related to "RefSeq representative genomes".

Regarding previous comment from Shamika Gajanan Kulkarni:

I ran a search with Database "RefSeq representative genomes" selected and species "Ovis aries" selected.

Result page contained an error message.

I have reviewed this ticket. It is working as expected for human and mouse, also for A. thaliana where it does not show an option for "Genomes for selected organisms (primary reference assembly only)". However, when I tried for bos taurus, the option appeared as expected, but it did not redirect to the Primer blast site. This maybe due to my laptop and internet issues, I will check and update tomorrow again.

Branch link : https://bitbucket.org/pnikhare/experimental-apps-for-igb/branch/IGBF-2287
steps for testing :

• Install the NCBI Primer app by following the steps given in IGBF-2258.
• Under 'primer options' tab view the database select options.
• Test that database has option "Genomes for selected organisms (primary reference assembly only)" only if following Species are selected :
  apis mellifera
  bos taurus
  danio rerio
  dog
  drosophila melanogaster
  gallus gallus
  human
  mouse
  pan troglodytes
  pig
  rat
• Test "Genomes for selected organisms (primary reference assembly only)" is not visible if any other species apart from the above list is selected
• Zoom in and select syms and right-click and check the appropriate menu item gets populated for the selected database.
• Select one of the species not in the above list and click "Primer blast".
• It will redirect you to the primer blast site.