Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:
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Story Points:2
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Epic Link:
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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
Description
Update Primer Option Database according to species selected.
"Genomes for selected organisms (primary reference assembly only)" works only for few selected organisms.
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link |
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| Sprint | Spring 4 : 2 Mar to 13 Mar [ 89 ] | Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar [ 89, 90 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Sprint | Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar [ 89, 90 ] | Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10 [ 89, 90, 91 ] |
| Rank | Ranked higher |
| Assignee | Pooja Nikhare [ pooja.nikhare ] |
| Story Points | 1 | |
| Labels | Advanced |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
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.
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.
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] | Pooja Nikhare [ pooja.nikhare ] |
| Story Points | 1 | 2 |
| Comment | [ Cannot reproduce above. ] |
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".
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
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.
Moving this forward to completed as no problems have been detected.
cc: Pooja Nikhare and Shamika Gajanan Kulkarni
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
It is not yet merged with the Experimental Apps Repo or new NCBI Primer repo
Sorry Pooja Nikhare!
Re-opening and moving to previous column for further consideration.
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Sprint | Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10 [ 89, 90, 91 ] | 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 [ 89, 90, 91, 92 ] |
| Rank | Ranked higher |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Assignee | Pooja Nikhare [ pooja.nikhare ] | Ann Loraine [ aloraine ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Ann Loraine [ aloraine ] |
PR is merged and ready for testing.
| 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 [ 89, 90, 91, 92 ] | 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 [ 89, 90, 91, 92, 93 ] |
| Rank | Ranked higher |
| 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 [ 89, 90, 91, 92, 93 ] | 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 [ 89, 90, 91, 92, 93, 94 ] |
| Rank | Ranked higher |
| Assignee | Prutha Kulkarni [ prutha ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
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]
| Attachment | Screen Shot 2020-05-15 at 4.23.47 PM.png [ 14731 ] |
| Assignee | Prutha Kulkarni [ prutha ] | Pooja Nikhare [ pooja.nikhare ] |
| Status | Post-merge Testing In Progress [ 10003 ] | To-Do [ 10305 ] |
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
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Pooja Nikhare [ pooja.nikhare ] |
Pooja Nikhare, could you please enable pipelines on you newly forked repo so that I can test it and move it to DONE?
Enabled piplenes. Please check download section. https://bitbucket.org/pnikhare/ncbi-primer-pooja/downloads/
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.
| Assignee | Prutha Kulkarni [ prutha ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Prutha Kulkarni [ prutha ] | Pooja Nikhare [ pooja.nikhare ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Pooja Nikhare [ pooja.nikhare ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| 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 [ 89, 90, 91, 92, 93, 94 ] | 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 [ 89, 90, 91, 92, 93, 94, 95 ] |
| Rank | Ranked higher |
| 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 [ 89, 90, 91, 92, 93, 94, 95 ] | 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 [ 89, 90, 91, 92, 93, 94, 95, 96 ] |
| Rank | Ranked higher |
| Assignee | Nowlan Freese [ nfreese ] |
| Assignee | Nowlan Freese [ nfreese ] |
| 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 [ 89, 90, 91, 92, 93, 94, 95, 96 ] | 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 July [ 89, 90, 91, 92, 93, 94, 95, 96, 97 ] |
| Rank | Ranked higher |
| Assignee | Jay Chamma [ gchamma ] |
| Assignee | Jay Chamma [ gchamma ] |
Note: Un-assigning from Jay as I don't think he had started working on this yet.
| Assignee | Jay Chamma [ gchamma ] |
| Assignee | Jay Chamma [ gchamma ] |
| 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 [ 89, 90, 91, 92, 93, 94, 95, 96, 97 ] | 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: 3 Jul - 14 Jul [ 89, 90, 91, 92, 93, 94, 95, 96, 97, 98 ] |
| Rank | Ranked higher |
| Assignee | Prutha Kulkarni [ prutha ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
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.
| Assignee | Prutha Kulkarni [ prutha ] | Pooja Nikhare [ pooja.nikhare ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
Branch link : https://bitbucket.org/pnikhare/experimental-apps-for-igb/branch/IGBF-2287
steps for testing :
IGBF-2258.apis mellifera
bos taurus
danio rerio
dog
drosophila melanogaster
gallus gallus
human
mouse
pan troglodytes
pig
rat