Details
-
Type:
Bug
-
Status: Closed (View Workflow)
-
Priority:
Major
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: None
-
Labels:None
-
Story Points:1
-
Epic Link:
-
Sprint:Spring 9 : 25 May to 8 Jun
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.
Attachments
Activity
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)
So great that you identified the root cause!
[~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.
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.