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  1. IGB
  2. IGBF-2805

Describe how to test the feature of adding and using a local quickload on Windows, Mac, Linux to Release Testing.

    Details

    • Type: Task
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Done
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:
      None
    • Story Points:
      1
    • Sprint:
      Winter 6 Mar 8 - Mar 19, Spring 1 2021 Mar 22 - Apr 2, Spring 2 2021 Apr 5 - Apr 16, Spring 3 2021 Apr 19 - Apr 30

      Description

      Please add a step-by-step protocol for testing adding and using a local quickload site on Windows, Mac, and Linux.

      Note that our current testing protocols only cover adding and using a remote quickload site.

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            Hide
            rweidenh Rachel Weidenhammer (Inactive) added a comment - - edited

            When testing IGBF-510 Dr. Freese and I found that my Windows 10 machine was not loading local quickloads normally.
            Today I created new copies of the E. unicornis files tested in IGBF-510,
            expanded the annots.xml file based on the wiki,
            and added a spicies.txt file.

            It was not loading any genomic data in IGB 9.1.6 but was showing data from the contents.txt and genome.txt files.
            Changing the direction of the / characters,
            checking that tabs were used to separate text content,
            moving the files within the local quickload,
            or adding/removing content from the quickload files did not fix the problem.

            I moved the local quickload folder from my two-word user name file path down to the C drive and it began working normally.
            I then moved it up one level to "Program Files", a folder containing a space in the name, and the local quickload stopped working.
            I moved it to another folder with a path not containing any spaces and the local quickload began working again.

            Without spaces anywhere in the file path, local quickloads work on Windows 10.
            Tested on both IGB 9.1.6 and 9.1.8.

            I will now work on creating a wiki page for testing the local quickload function on IGB releases by modifying the instructions from the wiki IGB user's guide.

            Show
            rweidenh Rachel Weidenhammer (Inactive) added a comment - - edited When testing IGBF-510 Dr. Freese and I found that my Windows 10 machine was not loading local quickloads normally. Today I created new copies of the E. unicornis files tested in IGBF-510 , expanded the annots.xml file based on the wiki, and added a spicies.txt file. It was not loading any genomic data in IGB 9.1.6 but was showing data from the contents.txt and genome.txt files. Changing the direction of the / characters, checking that tabs were used to separate text content, moving the files within the local quickload, or adding/removing content from the quickload files did not fix the problem. I moved the local quickload folder from my two-word user name file path down to the C drive and it began working normally. I then moved it up one level to "Program Files", a folder containing a space in the name, and the local quickload stopped working. I moved it to another folder with a path not containing any spaces and the local quickload began working again. Without spaces anywhere in the file path, local quickloads work on Windows 10. Tested on both IGB 9.1.6 and 9.1.8. I will now work on creating a wiki page for testing the local quickload function on IGB releases by modifying the instructions from the wiki IGB user's guide.
            Hide
            rweidenh Rachel Weidenhammer (Inactive) added a comment - - edited

            Document for testing local quickload: https://docs.google.com/document/d/1n2xWo_ZzCvGeVbzFinH7rSu0b33Jf_9A52He8g47Y_k/edit?usp=sharing

            Next I am looking to see where the most appropriate location for this in the IGB Release Documentation Subsystems would be.
            The Data Provider page briefly involves testing remote quickloads. Since it is already a pretty long page I think adding the local quickload testing would make it too long.

            I also wanted to make sure that it was okay to leave out synonyms.txt from the testing.

            We also need to see if these instructions closely relate to those of Quickload Saver that Dr. Freese is working on.

            Show
            rweidenh Rachel Weidenhammer (Inactive) added a comment - - edited Document for testing local quickload: https://docs.google.com/document/d/1n2xWo_ZzCvGeVbzFinH7rSu0b33Jf_9A52He8g47Y_k/edit?usp=sharing Next I am looking to see where the most appropriate location for this in the IGB Release Documentation Subsystems would be. The Data Provider page briefly involves testing remote quickloads. Since it is already a pretty long page I think adding the local quickload testing would make it too long. I also wanted to make sure that it was okay to leave out synonyms.txt from the testing. We also need to see if these instructions closely relate to those of Quickload Saver that Dr. Freese is working on.
            Hide
            rweidenh Rachel Weidenhammer (Inactive) added a comment -

            Draft document is updated and complete: https://docs.google.com/document/d/1n2xWo_ZzCvGeVbzFinH7rSu0b33Jf_9A52He8g47Y_k/edit?usp=sharing

            Please review that the instructions are easy to follow and that we are testing everything we intend to test.

            Show
            rweidenh Rachel Weidenhammer (Inactive) added a comment - Draft document is updated and complete: https://docs.google.com/document/d/1n2xWo_ZzCvGeVbzFinH7rSu0b33Jf_9A52He8g47Y_k/edit?usp=sharing Please review that the instructions are easy to follow and that we are testing everything we intend to test.
            Hide
            nfreese Nowlan Freese added a comment -

            Rachel Weidenhammer - can you attach the quickload files to this jira ticket that will be part of the testing page?

            Show
            nfreese Nowlan Freese added a comment - Rachel Weidenhammer - can you attach the quickload files to this jira ticket that will be part of the testing page?
            Hide
            rweidenh Rachel Weidenhammer (Inactive) added a comment - - edited

            Nowlan Freese,
            The maximum file size on a Jira ticket file upload is 10mb and the 2bit file is almost 28mb compressed.
            So I have uploaded a zip file containing all of the files except for the E_unicornis_Jul_2015.2bit file named "LocalQuickload-Without2bitFile.zip"
            along with the other individual files.

            The entire set of files is available on BioViz Connect here: https://data.cyverse.org/dav-anon/iplant/home/rweidenh/LocalQuickload

            I also have them on google drive here: https://drive.google.com/file/d/1ikK-YenkCiKr3lb8Rq-s3wJDv7E_YNun/view?usp=sharing

            wiki.transvar does accept attachments this large, so it shouldn't be a problem there.

            Show
            rweidenh Rachel Weidenhammer (Inactive) added a comment - - edited Nowlan Freese , The maximum file size on a Jira ticket file upload is 10mb and the 2bit file is almost 28mb compressed. So I have uploaded a zip file containing all of the files except for the E_unicornis_Jul_2015.2bit file named "LocalQuickload-Without2bitFile.zip" along with the other individual files. The entire set of files is available on BioViz Connect here: https://data.cyverse.org/dav-anon/iplant/home/rweidenh/LocalQuickload I also have them on google drive here: https://drive.google.com/file/d/1ikK-YenkCiKr3lb8Rq-s3wJDv7E_YNun/view?usp=sharing wiki.transvar does accept attachments this large, so it shouldn't be a problem there.
            Hide
            nfreese Nowlan Freese added a comment - - edited

            I made a zip folder with two quickloads (quickload.zip). One quickload is for testing absolute paths and the other relative. I would like to use these for the local quickload release documentation.

            Show
            nfreese Nowlan Freese added a comment - - edited I made a zip folder with two quickloads (quickload.zip). One quickload is for testing absolute paths and the other relative. I would like to use these for the local quickload release documentation.
            Hide
            nfreese Nowlan Freese added a comment -

            This issue is blocked until the completion of IGBF-2820

            Show
            nfreese Nowlan Freese added a comment - This issue is blocked until the completion of IGBF-2820
            Hide
            rweidenh Rachel Weidenhammer (Inactive) added a comment -

            Local Quickload (relative path) release testing documentation is complete: https://wiki.transvar.org/display/ITD/Local+Quickload

            Show
            rweidenh Rachel Weidenhammer (Inactive) added a comment - Local Quickload (relative path) release testing documentation is complete: https://wiki.transvar.org/display/ITD/Local+Quickload
            Hide
            nfreese Nowlan Freese added a comment -

            Tested on Mac.

            Closing issue.

            Show
            nfreese Nowlan Freese added a comment - Tested on Mac. Closing issue.

              People

              • Assignee:
                rweidenh Rachel Weidenhammer (Inactive)
                Reporter:
                aloraine Ann Loraine
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                Dates

                • Created:
                  Updated:
                  Resolved: