Details

    • Type: Task
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Done
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:
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      Description

      Steps to reproduce:

      1. Fork/Clone the repository https://bitbucket.org/lorainelab/ncbi-primer/src/master/.
      2. Try to run a pipeline for the forked repo master branch or build the cloned repo locally.
      3. You can see a test case failure

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            jsirigin Jaya Sravani Sirigineedi added a comment - - edited

            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.

            Show
            jsirigin Jaya Sravani Sirigineedi added a comment - - edited 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.
            Hide
            jsirigin Jaya Sravani Sirigineedi added a comment -

            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

            Show
            jsirigin Jaya Sravani Sirigineedi added a comment - 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
            Hide
            nfreese Nowlan Freese added a comment -

            Testing on Mac
            Able to build NCBI Primer app locally using Sravani's IGBF-3483. Code looks good.

            Ready for pull request.

            Show
            nfreese Nowlan Freese added a comment - Testing on Mac Able to build NCBI Primer app locally using Sravani's IGBF-3483 . Code looks good. Ready for pull request.
            Hide
            nfreese Nowlan Freese added a comment -

            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.

            Show
            nfreese Nowlan Freese added a comment - 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.
            Show
            jsirigin Jaya Sravani Sirigineedi added a comment - Pull request submitted: https://bitbucket.org/lorainelab/ncbi-primer/pull-requests/3
            Hide
            ann.loraine Ann Loraine added a comment -

            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.

            Show
            ann.loraine Ann Loraine added a comment - 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.
            Hide
            jsirigin Jaya Sravani Sirigineedi added a comment -

            Made the changes, squashed the commits, and created a new Pull Request. https://bitbucket.org/lorainelab/ncbi-primer/pull-requests/4

            Show
            jsirigin Jaya Sravani Sirigineedi added a comment - Made the changes, squashed the commits, and created a new Pull Request. https://bitbucket.org/lorainelab/ncbi-primer/pull-requests/4
            Hide
            ann.loraine Ann Loraine added a comment - - edited

            Merged to master branch. Artifact built successfully. Moving to DONE.

            Show
            ann.loraine Ann Loraine added a comment - - edited Merged to master branch. Artifact built successfully. Moving to DONE.

              People

              • Assignee:
                jsirigin Jaya Sravani Sirigineedi
                Reporter:
                jsirigin Jaya Sravani Sirigineedi
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                  Updated:
                  Resolved: