Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-1419

Add new Nexus repository to top-level POM.xml

        Details

        • Type: Improvement
        • Status: Closed (View Workflow)
        • Priority: Critical
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None
        • Story Points:
          0.25
        • Sprint:
          Fall 2018 Sprint 3, Fall 2018 Sprint 4

          Description

          Edit top-level POM.xml file to include the new Nexus repository for igb releases. This should be a basic repository (for finding .jar artifacts) as well as a plug-in repository. This is for distribution of a Maven plugin that enables App developers to encode a "readme" file in repository.xml's created for their App.

          URL of the nexus site is https://nexus.bioviz.org

          Repositories will have addresses containing this URL but with additional paths.

          You will have to do some digging to find the correct repository URL to use.

          To test:

          • Create a simple maven project and ensure that the artifacts can be retrieved. Ensure that the artifacts are coming from the nexus site and not from a local build process.

            Attachments

              Issue Links

              relates to

              Bug - A problem which impairs or prevents the functions of the product. IGBF-1446 Upgrade Loraine Lab Nexus repository to latest version

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-314 Look into automating the release to nexus of IGB project dependencies (e.g. genoviz). It would be more convenient to not manually manage upload process when making a change to this project. eos.transvar.org/nexus

              • Major - Major loss of function.
              • Closed

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-1213 document and update on-line maven repository

              • Major - Major loss of function.
              • Closed

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-1240 Modify pom.xml to enable upload of IGB artifacts to nexus.bioviz.org

              • Major - Major loss of function.
              • Closed

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-1418 Import htsjdk as OSGi bundle

              • Critical - Crashes, loss of data, severe memory leak.
              • Closed

                Activity

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                ann.loraine Ann Loraine added a comment - - edited

                I'm concerned about the warning message above for the htsjdk artifact.
                We should provide the checksum so that client programs can verify the artifact upon download.
                That's because some clients/IDEs may not trust artifacts that don't have checksums and therefore can't be verified.
                I uploaded this artifact "by hand" using the Nexus3 GUI. I would have expected the checksum files would be generated upon upload.
                I searched for information about this and found this issue from the Nexus vendor:

                Let's do this for the next steps:

                • Add code to our gradle.build script for uploading to our nexus repository. For example for how to do this, see the gradle.build file in our bigwig repository - https://bitbucket.org/lorainelab/bigwig
                • Please add the code to the end of the file; I'm pretty sure it can co-exist with the htsjdk project's current upload code, which hard-codes their repository address. Maybe call our upload function "uploadArtifactsToIgbRepo" (??)
                • You can test the upload process using our Nexus repository's "testuser" user, which has write permission to a test maven repositor - https://nexus.bioviz.org/repository/Test_IGB_Artifact_Deployment/ (Ask Kiran for details, or Dr. Loraine)

                When it's working, I will need to upload it to our maven-releases repository, which is used the IGB project.

                Also, we should upgrade to the newest version of Nexus repository code. Whoever does this will need credentials to access the host. (Ask me.)
                Documentation:
                https://support.sonatype.com/hc/en-us/articles/115000350007?_ga=2.143644791.35725550.1540530730-460053495.1540530730

                Show
                ann.loraine Ann Loraine added a comment - - edited I'm concerned about the warning message above for the htsjdk artifact. We should provide the checksum so that client programs can verify the artifact upon download. That's because some clients/IDEs may not trust artifacts that don't have checksums and therefore can't be verified. I uploaded this artifact "by hand" using the Nexus3 GUI. I would have expected the checksum files would be generated upon upload. I searched for information about this and found this issue from the Nexus vendor: https://issues.sonatype.org/browse/NEXUS-16493 Looks like this is a missing feature in our version of Nexus. We are running Nexus 3.10. Fix appears to have been released with 3.11. Let's do this for the next steps: Add code to our gradle.build script for uploading to our nexus repository. For example for how to do this, see the gradle.build file in our bigwig repository - https://bitbucket.org/lorainelab/bigwig Please add the code to the end of the file; I'm pretty sure it can co-exist with the htsjdk project's current upload code, which hard-codes their repository address. Maybe call our upload function "uploadArtifactsToIgbRepo" (??) You can test the upload process using our Nexus repository's "testuser" user, which has write permission to a test maven repositor - https://nexus.bioviz.org/repository/Test_IGB_Artifact_Deployment/ (Ask Kiran for details, or Dr. Loraine) When it's working, I will need to upload it to our maven-releases repository, which is used the IGB project. Also, we should upgrade to the newest version of Nexus repository code. Whoever does this will need credentials to access the host. (Ask me.) Documentation: https://support.sonatype.com/hc/en-us/articles/115000350007?_ga=2.143644791.35725550.1540530730-460053495.1540530730
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                kkorey Kiran Korey (Inactive) added a comment -

                IGB is able to download the artifacts from the newly added nexus repository,
                Steps followed,
                1. Deleted the HTSJDK and BigWig artifacts from the local repository to trigger the download.
                2. Executed maven clean install
                3. Verified if the artifacts downloaded successfully.
                The below logs also verify the same.

                Downloading from repo1: http://maven.bioviz.org/repo1/htsjdk-igb/htsjdk-igb/2.16.1/htsjdk-igb-2.16.1.jar
                Downloading from repo2: http://maven.bioviz.org/repo2/htsjdk-igb/htsjdk-igb/2.16.1/htsjdk-igb-2.16.1.jar
                Downloading from repo3: http://maven.bioviz.org/repo3/htsjdk-igb/htsjdk-igb/2.16.1/htsjdk-igb-2.16.1.jar
                Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/htsjdk-igb/htsjdk-igb/2.16.1/htsjdk-igb-2.16.1.jar
                [WARNING] Could not validate integrity of download from https://nexus.bioviz.org/repository/maven-releases/htsjdk-igb/htsjdk-igb/2.16.1/htsjdk-igb-2.16.1.jar: Checksum validation failed, no checksums available
                [WARNING] Checksum validation failed, no checksums available from maven-releases for https://nexus.bioviz.org/repository/maven-releases/htsjdk-igb/htsjdk-igb/2.16.1/htsjdk-igb-2.16.1.jar
                Downloaded from maven-releases: https://nexus.bioviz.org/repository/maven-releases/htsjdk-igb/htsjdk-igb/2.16.1/htsjdk-igb-2.16.1.jar (1.6 MB at 352 kB/s)

                Downloading from repo1: http://maven.bioviz.org/repo1/org/broad/igv/bigwig/2.0.0/bigwig-2.0.0.jar
                Downloading from repo2: http://maven.bioviz.org/repo2/org/broad/igv/bigwig/2.0.0/bigwig-2.0.0.jar
                Downloading from repo3: http://maven.bioviz.org/repo3/org/broad/igv/bigwig/2.0.0/bigwig-2.0.0.jar
                Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/broad/igv/bigwig/2.0.0/bigwig-2.0.0.jar
                Downloaded from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/broad/igv/bigwig/2.0.0/bigwig-2.0.0.jar (75 kB at 264 kB/s)

                At this time this issue can be marked Done.
                Please reopen in case of any other issues found.

                Show
                kkorey Kiran Korey (Inactive) added a comment - IGB is able to download the artifacts from the newly added nexus repository, Steps followed, 1. Deleted the HTSJDK and BigWig artifacts from the local repository to trigger the download. 2. Executed maven clean install 3. Verified if the artifacts downloaded successfully. The below logs also verify the same. Downloading from repo1: http://maven.bioviz.org/repo1/htsjdk-igb/htsjdk-igb/2.16.1/htsjdk-igb-2.16.1.jar Downloading from repo2: http://maven.bioviz.org/repo2/htsjdk-igb/htsjdk-igb/2.16.1/htsjdk-igb-2.16.1.jar Downloading from repo3: http://maven.bioviz.org/repo3/htsjdk-igb/htsjdk-igb/2.16.1/htsjdk-igb-2.16.1.jar Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/htsjdk-igb/htsjdk-igb/2.16.1/htsjdk-igb-2.16.1.jar [WARNING] Could not validate integrity of download from https://nexus.bioviz.org/repository/maven-releases/htsjdk-igb/htsjdk-igb/2.16.1/htsjdk-igb-2.16.1.jar: Checksum validation failed, no checksums available [WARNING] Checksum validation failed, no checksums available from maven-releases for https://nexus.bioviz.org/repository/maven-releases/htsjdk-igb/htsjdk-igb/2.16.1/htsjdk-igb-2.16.1.jar Downloaded from maven-releases: https://nexus.bioviz.org/repository/maven-releases/htsjdk-igb/htsjdk-igb/2.16.1/htsjdk-igb-2.16.1.jar (1.6 MB at 352 kB/s) Downloading from repo1: http://maven.bioviz.org/repo1/org/broad/igv/bigwig/2.0.0/bigwig-2.0.0.jar Downloading from repo2: http://maven.bioviz.org/repo2/org/broad/igv/bigwig/2.0.0/bigwig-2.0.0.jar Downloading from repo3: http://maven.bioviz.org/repo3/org/broad/igv/bigwig/2.0.0/bigwig-2.0.0.jar Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/broad/igv/bigwig/2.0.0/bigwig-2.0.0.jar Downloaded from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/broad/igv/bigwig/2.0.0/bigwig-2.0.0.jar (75 kB at 264 kB/s) At this time this issue can be marked Done. Please reopen in case of any other issues found.

                  People

                  • Assignee:
                    kkorey Kiran Korey (Inactive)
                    Reporter:
                    ann.loraine Ann Loraine
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    3 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: