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  1. IGB
  2. IGBF-1425

Investigate & fix error when opening SAM files from Quickload, URL

    Details

    • Story Points:
      1
    • Sprint:
      Fall 2018 Sprint 3, Fall 2018 Sprint 4, Fall 2018 Sprint 5

      Description

      Noticed by Kiran Korey:

      Attempts to open SAM files from Internet fail:

      http://igbquickload.org/smokeTestingQuickload/H_sapiens_Dec_2013/Sam/chr1.p22.3_noHeader.sam
      http://igbquickload.org/smokeTestingQuickload/H_sapiens_Dec_2013/Sam/chr1.p22.3_wHeader.sam

      However, if you download "wHeader" file and try to open it locally, it can be done.

      The "noHeader" file gives an error, however, even if the corresponding human genome is already opened and on display.

        Attachments

          Activity

          Hide
          kkorey Kiran Korey (Inactive) added a comment -

          The following Scenarios needs to be tested for this issue:
          (Scenario --> expected behavior)

          Reachable valid URL --> Sam File should be loaded.

          Reachable valid URL but unauthorized --> Exception in the log saying URL not reachable and HTTP_status code (404)

          Invalid / Unreachable URL --> Exception in the log saying URL not reachable and HTTP_status code ( 401 0r 403)

          Reachable URL but invalid File --> Exception in the log saying invalid file format.

          Show
          kkorey Kiran Korey (Inactive) added a comment - The following Scenarios needs to be tested for this issue: (Scenario --> expected behavior) Reachable valid URL --> Sam File should be loaded. Reachable valid URL but unauthorized --> Exception in the log saying URL not reachable and HTTP_status code (404) Invalid / Unreachable URL --> Exception in the log saying URL not reachable and HTTP_status code ( 401 0r 403) Reachable URL but invalid File --> Exception in the log saying invalid file format.
          Hide
          stiwari8 Srishti Tiwari (Inactive) added a comment -

          For the positive scenario, with a valid reachable URL on the quickload it works. On the console it prints:
          org.lorainelab.igb.bam.SAM initTheSeqs
          SEVERE: Sam file must be sorted by coordinate.

          For a reachable but invalid File, it does not load anything. On the console it prints:
          org.lorainelab.igb.bam.XAM initTheSeqs
          WARNING: Couldn't find sequences in file

          For a reachable valid URL but unauthorized this error message is shown:
          Format not recognized for file: https://drive.google.com/open?id=14KYlPVkMnvUuSnSAwDbwe400hqC3bKFf

          Please have a look.

          Show
          stiwari8 Srishti Tiwari (Inactive) added a comment - For the positive scenario, with a valid reachable URL on the quickload it works. On the console it prints: org.lorainelab.igb.bam.SAM initTheSeqs SEVERE: Sam file must be sorted by coordinate. For a reachable but invalid File, it does not load anything. On the console it prints: org.lorainelab.igb.bam.XAM initTheSeqs WARNING: Couldn't find sequences in file For a reachable valid URL but unauthorized this error message is shown: Format not recognized for file: https://drive.google.com/open?id=14KYlPVkMnvUuSnSAwDbwe400hqC3bKFf Please have a look.
          Hide
          kkorey Kiran Korey (Inactive) added a comment -

          Srishti Tiwari

          I think that is the expected behavior.
          Because when you go to the URL google redirects you to a login page which is an unrecognized format for IGB.

          Show
          kkorey Kiran Korey (Inactive) added a comment - Srishti Tiwari I think that is the expected behavior. Because when you go to the URL google redirects you to a login page which is an unrecognized format for IGB.
          Hide
          stiwari8 Srishti Tiwari (Inactive) added a comment -

          Thank you for confirming this. Marking this as ready for pull request

          Show
          stiwari8 Srishti Tiwari (Inactive) added a comment - Thank you for confirming this. Marking this as ready for pull request
          Hide
          ann.loraine Ann Loraine added a comment -

          Merged to master branch.
          Tagged for release with 9.1.0

          Show
          ann.loraine Ann Loraine added a comment - Merged to master branch. Tagged for release with 9.1.0

            People

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

              Dates

              • Created:
                Updated:
                Resolved: