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Posted to issues@airavata.apache.org by "Eroma (JIRA)" <ji...@apache.org> on 2018/02/13 16:03:00 UTC
[jira] [Updated] (AIRAVATA-2674) Re-write file names which has
spaces in them
[ https://issues.apache.org/jira/browse/AIRAVATA-2674?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]
Eroma updated AIRAVATA-2674:
----------------------------
Issue Type: Sub-task (was: Bug)
Parent: AIRAVATA-2675
> 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: Sub-task
> Components: Airavata API, PGA PHP Web Gateway
> Affects Versions: 0.18
> Reporter: Eroma
> Priority: Major
> 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://gw@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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