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      Situation: Quickloads that point to files stored in ftp are unable to be loaded in IGB. This feature was last working in version 8.3.4, indicating a change in 8.4.0 broke some of the functionality.

      The issue may be several issues. For example, in FeatureTreeView.java actionPerformed there is a check to see if the data is reachable. In 9.1.6 attempting to load an ftp via quickload causes the isReachable(dataset) to return false. If this is hardcoded to true, then the file will be added to IGB, however, when the data are loaded a bai index file not found error is then thrown.

      Note that loading ftp data directly through IGB works, it is only when the ftp data are attempted to load through the quickload that it fails.

      Task: Implement a fix so that ftp files can be loaded via quickload.

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            nfreese Nowlan Freese added a comment -

            I have attached an example quickload (zip file) for the human genome that includes links to two bam files. The Illumina_2x250 points to an ftp file.

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            nfreese Nowlan Freese added a comment - I have attached an example quickload (zip file) for the human genome that includes links to two bam files. The Illumina_2x250 points to an ftp file.
            Hide
            ssegu Sai Supreeth Segu added a comment - - edited

            Fixed the errors and updated the changes. Please review my changes.
            Link for the branch: https://bitbucket.org/supreeth27/integrated-genome-browser/branch/IGBF-2589#diff

            Show
            ssegu Sai Supreeth Segu added a comment - - edited Fixed the errors and updated the changes. Please review my changes. Link for the branch: https://bitbucket.org/supreeth27/integrated-genome-browser/branch/IGBF-2589#diff
            Hide
            aloraine Ann Loraine added a comment - - edited

            I have a request for clarification:

            It looks like there is some logic intended to handle all the protocols - http, etc.

            FTP was not handled & now it is.

            Should we also address https? I am not seeing where it is handled, but I may be missing it.

            Show
            aloraine Ann Loraine added a comment - - edited I have a request for clarification: It looks like there is some logic intended to handle all the protocols - http, etc. FTP was not handled & now it is. Should we also address https? I am not seeing where it is handled, but I may be missing it.
            Hide
            ssegu Sai Supreeth Segu added a comment -

            Ann Loraine (!file.getName().startsWith("http") handles https as well because https also starts with http. I have already tested https request as well.

            Show
            ssegu Sai Supreeth Segu added a comment - Ann Loraine (!file.getName().startsWith("http") handles https as well because https also starts with http. I have already tested https request as well.
            Hide
            nfreese Nowlan Freese added a comment -

            Tested IGBF-2589 installer on Mac from Supreeth's branch.

            Able to load ftp and http remotely hosted files as specified through the quickload.

            Sai Supreeth Segu please create a pull request.

            Show
            nfreese Nowlan Freese added a comment - Tested IGBF-2589 installer on Mac from Supreeth's branch. Able to load ftp and http remotely hosted files as specified through the quickload. Sai Supreeth Segu please create a pull request.
            Hide
            ssegu Sai Supreeth Segu added a comment -
            Show
            ssegu Sai Supreeth Segu added a comment - Please review my pull request. Link for pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/847/igbf-2589-fixing-ftp-quickload
            Hide
            aloraine Ann Loraine added a comment -

            Merged and master branch installers built.

            Show
            aloraine Ann Loraine added a comment - Merged and master branch installers built.
            Hide
            nfreese Nowlan Freese added a comment -

            Tested master dmg installer on Mac.

            Able to view remote ftp and http data from local quickload.

            Closing issue.

            Show
            nfreese Nowlan Freese added a comment - Tested master dmg installer on Mac. Able to view remote ftp and http data from local quickload. Closing issue.

              People

              • Assignee:
                ssegu Sai Supreeth Segu
                Reporter:
                nfreese Nowlan Freese
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                • Created:
                  Updated:
                  Resolved: