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  1. IGB
  2. IGBF-2409

Investigate failed tests on windows

    Details

    • Type: Bug
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Done
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:
      None

      Description

      During on-boarding and working on IGBF-1464, both Logan Weidenhammer and Jay Chamma discovered that several tests in the genometry library were running and failing.

      This failure only happens on Windows.

      For this task, investigate the cause of the problem and propose a solution.

      If the solution can be done quickly, go ahead and implement it. Otherwise, make a new ticket to capture all work on the ticket.

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          Activity

          ann.loraine Ann Loraine created issue -
          ann.loraine Ann Loraine made changes -
          Field Original Value New Value
          Epic Link IGBF-1531 [ 17617 ]
          ann.loraine Ann Loraine made changes -
          Rank Ranked higher
          ann.loraine Ann Loraine made changes -
          Assignee Ann Loraine [ aloraine ]
          ann.loraine Ann Loraine made changes -
          Description During on-boarding and working on IGBF-1464, both [~rweidenh] and [~gchamma] discovered that several tests in the genometry library failed to run.

          This failure only happens on Windows.

          For this task, investigate the cause of the problem and propose a solution.

          If the solution can be done quickly, go ahead and implement it. Otherwise, make a new ticket to capture all work on the ticket.
          During on-boarding and working on IGBF-1464, both [~rweidenh] and [~gchamma] discovered that several tests in the genometry library were running and failing.

          This failure only happens on Windows.

          For this task, investigate the cause of the problem and propose a solution.

          If the solution can be done quickly, go ahead and implement it. Otherwise, make a new ticket to capture all work on the ticket.
          chaitanya Chaitanya Kintali (Inactive) made changes -
          Assignee Chaitanya Kintali [ chaitanya ]
          chaitanya Chaitanya Kintali (Inactive) made changes -
          Status To-Do [ 10305 ] In Progress [ 3 ]
          chaitanya Chaitanya Kintali (Inactive) made changes -
          Attachment error - genometry.txt [ 14752 ]
          chaitanya Chaitanya Kintali (Inactive) made changes -
          Comment [ Sample Error log file ]
          Hide
          chaitanya Chaitanya Kintali (Inactive) added a comment -

          [~aloraine]
          It seems that, if IGB is cloned and executed in a folder with space's in its name (ex: C:\sample test) it is causing an issue. Below is the snippet that I found from the error logs.

          Running com.affymetrix.genometry.parsers.BpsParserTest
          Jun 02, 2020 4:41:22 PM com.affymetrix.genometry.parsers.BpsParserTest testConvertToBps
          SEVERE: null
          java.io.FileNotFoundException: C:\test%20sample\core\genometry\target\test-classes\data\psl\test1.psl (The system cannot find the path specified)

          the files are not getting located and finally throwing IO not found an exception. After Cloning the project to a folder name with no spaces, everything worked fine.
          I guess this should be the same behavior with MAC OS as well.

          Show
          chaitanya Chaitanya Kintali (Inactive) added a comment - [~aloraine] It seems that, if IGB is cloned and executed in a folder with space's in its name (ex: C:\sample test) it is causing an issue. Below is the snippet that I found from the error logs. Running com.affymetrix.genometry.parsers.BpsParserTest Jun 02, 2020 4:41:22 PM com.affymetrix.genometry.parsers.BpsParserTest testConvertToBps SEVERE: null java.io.FileNotFoundException: C:\test%20sample\core\genometry\target\test-classes\data\psl\test1.psl (The system cannot find the path specified) the files are not getting located and finally throwing IO not found an exception. After Cloning the project to a folder name with no spaces, everything worked fine. I guess this should be the same behavior with MAC OS as well.
          Hide
          ann.loraine Ann Loraine added a comment -

          So great that you identified the root cause!

          Show
          ann.loraine Ann Loraine added a comment - So great that you identified the root cause!
          Hide
          nfreese Nowlan Freese added a comment -

          Chaitanya Kintali

          Tested on mac in folder with spaces. Throws the same error:

          Jun 02, 2020 8:55:57 PM com.affymetrix.genometry.parsers.BpsParserTest testConvertToBps
          SEVERE: null
          java.io.FileNotFoundException: /Users/lorainelab/Desktop/this%20is%20a%20test/nowlanfork-igb/core/genometry/target/test-classes/data/psl/test1.psl (No such file or directory)

          Show
          nfreese Nowlan Freese added a comment - Chaitanya Kintali Tested on mac in folder with spaces. Throws the same error: Jun 02, 2020 8:55:57 PM com.affymetrix.genometry.parsers.BpsParserTest testConvertToBps SEVERE: null java.io.FileNotFoundException: /Users/lorainelab/Desktop/this%20is%20a%20test/nowlanfork-igb/core/genometry/target/test-classes/data/psl/test1.psl (No such file or directory)
          Hide
          chaitanya Chaitanya Kintali (Inactive) added a comment -

          Recommended Fix:

          Decoding the file path before opening the file can solve this issue.
          for example: String decodedPath = URLDecoder.decode("C:\\test%20sample
          plugins", "UTF-8");

          Moving to Done.

          Show
          chaitanya Chaitanya Kintali (Inactive) added a comment - Recommended Fix: Decoding the file path before opening the file can solve this issue. for example: String decodedPath = URLDecoder.decode("C:\\test%20sample plugins", "UTF-8"); Moving to Done.
          chaitanya Chaitanya Kintali (Inactive) made changes -
          Story Points 0.5 1
          chaitanya Chaitanya Kintali (Inactive) made changes -
          Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
          chaitanya Chaitanya Kintali (Inactive) made changes -
          Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
          chaitanya Chaitanya Kintali (Inactive) made changes -
          Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
          chaitanya Chaitanya Kintali (Inactive) made changes -
          Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
          chaitanya Chaitanya Kintali (Inactive) made changes -
          Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
          chaitanya Chaitanya Kintali (Inactive) made changes -
          Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
          chaitanya Chaitanya Kintali (Inactive) made changes -
          Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
          chaitanya Chaitanya Kintali (Inactive) made changes -
          Resolution Done [ 10000 ]
          Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

            People

            • Assignee:
              chaitanya Chaitanya Kintali (Inactive)
              Reporter:
              ann.loraine Ann Loraine
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              Dates

              • Created:
                Updated:
                Resolved: