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  1. IGB
  2. IGBF-2596

Remove repo1 and repo3 from IGB 9.1.8 POM

    Details

    • Type: Task
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Done
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:
    • Story Points:
      0.25
    • Sprint:
      Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5

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          Show
          inaylor Irvin Naylor (Inactive) added a comment - Fork Link: https://bitbucket.org/Inaylor01/integrated-genome-browser/src/IGBF-2596/
          Hide
          ann.loraine Ann Loraine added a comment -

          Quick request for clarification:

          Please confirm:

          • Does it build in bitbucket?
          Show
          ann.loraine Ann Loraine added a comment - Quick request for clarification: Please confirm: Does it build in bitbucket?
          Hide
          inaylor Irvin Naylor (Inactive) added a comment -

          It fails to build, will examine what happened further.

          It says that it cannot find a specific artifact in repo2. Should we remove repo2 along with 1 and 3 as well?

          Show
          inaylor Irvin Naylor (Inactive) added a comment - It fails to build, will examine what happened further. It says that it cannot find a specific artifact in repo2. Should we remove repo2 along with 1 and 3 as well?
          Hide
          ann.loraine Ann Loraine added a comment -

          No, you need to retain repo2.

          Show
          ann.loraine Ann Loraine added a comment - No, you need to retain repo2.
          Hide
          inaylor Irvin Naylor (Inactive) added a comment -

          I've run into an issue. So, building the project with repos 1-3 works perfectly however, if I comment out repo1's reference in the pom.xml file (or comment out repo1 and 3's references), I end up having an issue where the project won't build due to repo2's dependencies not being resolved.

          Just wanted to put that out there but will continue trying to figure out the problem

          Show
          inaylor Irvin Naylor (Inactive) added a comment - I've run into an issue. So, building the project with repos 1-3 works perfectly however, if I comment out repo1's reference in the pom.xml file (or comment out repo1 and 3's references), I end up having an issue where the project won't build due to repo2's dependencies not being resolved. Just wanted to put that out there but will continue trying to figure out the problem
          Hide
          inaylor Irvin Naylor (Inactive) added a comment -

          Curiously, I've found removing just Repo3 from the pom.xml file allows the project to compile without issue but removing both Repo1 and Repo3 causes this error to come up.

          I made sure to run maven on a clean install, and use the -u command to make sure everything was updated and it still wouldn't budge. My thought is that it has something to do with the bioviz repository itself but I am curious to hear what you all think?

          The error screenshot is attached to the issue.

          Show
          inaylor Irvin Naylor (Inactive) added a comment - Curiously, I've found removing just Repo3 from the pom.xml file allows the project to compile without issue but removing both Repo1 and Repo3 causes this error to come up. I made sure to run maven on a clean install, and use the -u command to make sure everything was updated and it still wouldn't budge. My thought is that it has something to do with the bioviz repository itself but I am curious to hear what you all think? The error screenshot is attached to the issue.
          Hide
          inaylor Irvin Naylor (Inactive) added a comment -

          [~aloraine], Me and Chester Dias just met about the maven error I was running into and we both observed how when Repo 1 and 2 are in the pom.xml file, IGB would build properly. According to the error, there was a certain jar file, jlfgr (more details are in the error) that was missing. We found that it was located in repo1 and that's why it wouldn't build unless 1 was there.

          Chester suggested that we could potentially either move the required jars from repo1 to 2, then get rid of repo1 or we could keep the repository references in a separate maven setting.xml file. I currently have my issue branch where Repos 1 and 2 are in the XML file and wasn't sure if I should submit that for review.

          I wanted to get your take about how we should move forward.

          Show
          inaylor Irvin Naylor (Inactive) added a comment - [~aloraine] , Me and Chester Dias just met about the maven error I was running into and we both observed how when Repo 1 and 2 are in the pom.xml file, IGB would build properly. According to the error, there was a certain jar file, jlfgr (more details are in the error) that was missing. We found that it was located in repo1 and that's why it wouldn't build unless 1 was there. Chester suggested that we could potentially either move the required jars from repo1 to 2, then get rid of repo1 or we could keep the repository references in a separate maven setting.xml file. I currently have my issue branch where Repos 1 and 2 are in the XML file and wasn't sure if I should submit that for review. I wanted to get your take about how we should move forward.
          Hide
          cdias1 Chester Dias (Inactive) added a comment -

          [~aloraine] Please let us know if there is any specific reason for having multiple repos? Can we move all the required artifacts into one repo?

          Show
          cdias1 Chester Dias (Inactive) added a comment - [~aloraine] Please let us know if there is any specific reason for having multiple repos? Can we move all the required artifacts into one repo?
          Hide
          ann.loraine Ann Loraine added a comment -

          Yes we can, but it's hard to do because there are a lot of details to consider.

          Show
          ann.loraine Ann Loraine added a comment - Yes we can, but it's hard to do because there are a lot of details to consider.
          Hide
          inaylor Irvin Naylor (Inactive) added a comment - - edited
          Show
          inaylor Irvin Naylor (Inactive) added a comment - - edited Pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/859/igbf-2596-remove-repo1-and-3-from-918 Commit where repo3 is removed, leaving only 1 and 2
          Hide
          ann.loraine Ann Loraine added a comment -

          Request for functional review prior to merging:

          • Please recruit one person on Windows and another person on Mac.

          Test on each platform as follows:

          • Install IGB
          • Review logging messages - look for any "class not found" errors
          • Open Arabidopsis genome and load some data from "Reads" and "Graphs" folders, again observing the console for possible errors
          Show
          ann.loraine Ann Loraine added a comment - Request for functional review prior to merging: Please recruit one person on Windows and another person on Mac. Test on each platform as follows: Install IGB Review logging messages - look for any "class not found" errors Open Arabidopsis genome and load some data from "Reads" and "Graphs" folders, again observing the console for possible errors
          Hide
          ann.loraine Ann Loraine added a comment -

          Logan Weidenhammer] - Could you please test Irvin's branch installer as per the above procedure?

          Show
          ann.loraine Ann Loraine added a comment - Logan Weidenhammer ] - Could you please test Irvin's branch installer as per the above procedure?
          Hide
          rweidenh Logan Weidenhammer (Inactive) added a comment -

          Functional Review on Windows:

          Installed IGB from Irvin's Fork
          Reviewed the Log and did not find any 'class not found' errors.
          Opened Arabidopsis genome
          Loaded data for a read alignment, and a scaled coverage graph
          Reviewed the Log again and did not find a 'class not found' error.

          It looks like we still need a MacOS functional review.

          Show
          rweidenh Logan Weidenhammer (Inactive) added a comment - Functional Review on Windows: Installed IGB from Irvin's Fork Reviewed the Log and did not find any 'class not found' errors. Opened Arabidopsis genome Loaded data for a read alignment, and a scaled coverage graph Reviewed the Log again and did not find a 'class not found' error. It looks like we still need a MacOS functional review.
          Hide
          ann.loraine Ann Loraine added a comment -

          Thanks Logan Weidenhammer!
          Probably a Mac review won't be needed. So would recommend moving ahead with a PR.

          Show
          ann.loraine Ann Loraine added a comment - Thanks Logan Weidenhammer ! Probably a Mac review won't be needed. So would recommend moving ahead with a PR.
          Hide
          ann.loraine Ann Loraine added a comment -

          Change of plan:

          • Do not remove these from the POM at this time.
          • We will need to check that this is feasible after returning DAS1 support.
          • Moving to Done.
          Show
          ann.loraine Ann Loraine added a comment - Change of plan: Do not remove these from the POM at this time. We will need to check that this is feasible after returning DAS1 support. Moving to Done.
          Hide
          ann.loraine Ann Loraine added a comment -

          Note for Irvin Naylor - leaving this assigned to you reflecting the work you have done on it.

          Show
          ann.loraine Ann Loraine added a comment - Note for Irvin Naylor - leaving this assigned to you reflecting the work you have done on it.

            People

            • Assignee:
              inaylor Irvin Naylor (Inactive)
              Reporter:
              ann.loraine Ann Loraine
            • Votes:
              0 Vote for this issue
              Watchers:
              4 Start watching this issue

              Dates

              • Created:
                Updated:
                Resolved: