Eroma created AIRAVATA-2674:
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Summary: Re-write file names which has spaces in them
Key: AIRAVATA-2674
URL: https://issues.apache.org/jira/browse/AIRAVATA-2674
Project: Airavata
Issue Type: Bug
Components: Airavata API, PGA PHP Web Gateway
Affects Versions: 0.18
Reporter: Eroma
Fix For: 0.18
Currently airavata could not handle experiment input files with space in the
file name. When an experiment is submitted with a space in the name it fails at
data staging with errors [1] in the log
Users can be educated but this could keep occurring with new users, etc...
File name to rewrite to remove the space or to replace it wth another character.
[1]
org.apache.airavata.gfac.core.GFacException: Error: userFriendly msg :Error
while executing DATA_STAGING task, actual msg :expId:
MACs_in_Metagenomes_27ef130b-9428-4b74-8842-325a36bc544c, processId:
PROCESS_42be4be6-161f-428d-8539-5f375493179a, taskId:
TASK_b8f396cd-0e4e-4564-9101-5bcd4b4ddb6f, type: DATA_STAGING :- DATA_STAGING
failed. Reason: Source or destination uri is not correct source :
file://searchsra.scigap.org:/var/www/portals/gateway-user-data/searching-sra/aalker/DefaultProject/MACs_in_Metagenomes1518210858/SRR_Acc_List
(1).txt, destination :
SCP://g...@js-169-158.jetstream-cloud.org:22/home/gw/airavata-workdirs/PROCESS_42be4be6-161f-428d-8539-5f375493179a/
at
org.apache.airavata.gfac.impl.GFacEngineImpl.checkFailures(GFacEngineImpl.java:628)
at
org.apache.airavata.gfac.impl.GFacEngineImpl.inputDataStaging(GFacEngineImpl.java:609)
at
org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:347)
at
org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(GFacEngineImpl.java:286)
at
org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFacWorker.java:227) at
org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86) at
org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMDC$0(MDCUtil.java:40)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:748)
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