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:None
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Epic Link:
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Sprint:Fall 5
Description
Steps to reproduce:
- Fork/Clone the repository https://bitbucket.org/lorainelab/ncbi-primer/src/master/.
- Try to run a pipeline for the forked repo master branch or build the cloned repo locally.
- You can see a test case failure
Attachments
Issue Links
- relates to
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- Closed
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Activity
| Assignee | Ann Loraine [ aloraine ] |
| Epic Link | IGBF-1765 [ 17855 ] |
| Sprint | Fall 5 [ 181 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Attachment | Screenshot 2023-11-03 at 9.31.52 AM.png [ 18078 ] |
As discussed, added a random name for the organism to check the failure case. Below is the branch where the changes are present.
https://bitbucket.org/jaya-sravani/ncbi-primer/branch/IGBF-3483
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
| 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 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Nowlan Freese [ nfreese ] |
Testing on Mac
Able to build NCBI Primer app locally using Sravani's IGBF-3483. Code looks good.
Ready for pull request.
| Assignee | Nowlan Freese [ nfreese ] | Jaya Sravani Sirigineedi [ jsirigin ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
Sidenote: It seems odd that we have a hardcoded list of genomes for which the genome_selected_species (Genomes for selected eukaryotic organisms) is available. It looks like NCBI has added many additional genomes, thus it may be difficult for this app to keep up.
Pull request submitted: https://bitbucket.org/lorainelab/ncbi-primer/pull-requests/3
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Assignee | Ann Loraine [ aloraine ] |
The logger code needs to be updated:
logger.info("Test for database : genome_selected_species, Organism : Arabidopsis thaliana ");
because the organism is no longer Arabidopsis thaliana.
| Status | Reviewing Pull Request [ 10303 ] | To-Do [ 10305 ] |
| Assignee | Ann Loraine [ aloraine ] | Jaya Sravani Sirigineedi [ jsirigin ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Made the changes, squashed the commits, and created a new Pull Request. https://bitbucket.org/lorainelab/ncbi-primer/pull-requests/4
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
Merged to master branch. Artifact built successfully. Moving to DONE.
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | 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 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
When I was investigating I found out that the test case which is expecting to give an error when selecting "Arabidopsis thaliana" is written because of this https://jira.bioviz.org/browse/IGBF-2287?focusedCommentId=27078&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-27078 as there is an expectation for this database to work only for few species. But when I debug the test case, I found out that the NCBI primer is giving a response when this organism is selected. [~aloraine] Should it give an error for this particular one? Also, I tried this in the NCBI primer website using the primer blast tool to do the primer calculation through the website and it worked for this organism. Below is the results screenshot.
