[IGBF-2287] Update Primer Option Database according to species - JIRA UNCC

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Type: Task
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: None
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2
Epic Link:
Refactor NCBI Primer App
Sprint:
Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun, Summer 2: 22 Jun - 3 Jul, Summer 3: 6 Jul - 17 Jul

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Update Primer Option Database according to species selected.
"Genomes for selected organisms (primary reference assembly only)" works only for few selected organisms.

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15/May/20 6:17 PM

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IGBF-2317 Move NCBI Primer App to its own repository

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IGBF-2258 Make class for default Primer blast options

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Pooja Nikhare (Inactive) added a comment - 18/Mar/20 4:03 PM - edited

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.

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Pooja Nikhare (Inactive) added a comment - 18/Mar/20 4:03 PM - edited 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.

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Prutha Kulkarni (Inactive) added a comment - 15/May/20 7:51 PM

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

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Prutha Kulkarni (Inactive) added a comment - 15/May/20 7:51 PM Pooja Nikhare , could you please enable pipelines on you newly forked repo so that I can test it and move it to DONE?

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Pooja Nikhare (Inactive) added a comment - 15/May/20 7:56 PM

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

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Pooja Nikhare (Inactive) added a comment - 15/May/20 7:56 PM Enabled piplenes. Please check download section. https://bitbucket.org/pnikhare/ncbi-primer-pooja/downloads/

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Prutha Kulkarni (Inactive) added a comment - 15/May/20 8:07 PM - edited

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.

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Prutha Kulkarni (Inactive) added a comment - 15/May/20 8:07 PM - edited 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.

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Ann Loraine added a comment - 20/Jun/20 8:35 PM

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

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Ann Loraine added a comment - 20/Jun/20 8:35 PM Note: Un-assigning from Jay as I don't think he had started working on this yet.

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Prutha Kulkarni (Inactive) added a comment - 14/Jul/20 3:43 PM

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.

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Prutha Kulkarni (Inactive) added a comment - 14/Jul/20 3:43 PM 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.

Update Primer Option Database according to species

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