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    Delete Specimens

    Technical Questions
    #1

    Is there a way to delete specimens that have been put into OpenSpecimen 1.0 in the wrong place? Before, in caTissue, I would dispose a specimen by clicking on event tab on the specimen page, select disposal event and select status as disabled and then submit. It would remove the specimen and open up that location in the storage box. Now it asks for a reason and comments as well as putting in the date and time and it still won’t dispose of the specimen. It gives me the error: form data save failed, at the top of the page.

    #2

    Hi @Amy_Wells,

    You need not go to events to dispose a specimen. Click on dispose button on the specimen page. See below:

    Screen Shot 2015-05-08 at 10.37.53 am.png1270×579 126 KB

    Thanks,
    Poornima

    #3

    Thank you, that’s very helpful to have it on the same page, I only wish it would remove it from the specimen tree so it was no longer seen. Thank you for the quick response and help!

    #4

    Hello,

    I would like to remove test specimens in v1.1. I used the following steps: Select specimen -> Dispose -> “Specimen Updated Successfully”, however the specimen still exists in the database. Is there another workflow to remove specimens and participants from OpenSpecimen?

    Thanks,
    Shannon

    #5

    Here is the server log:

    2015-06-18 16:33:41,407 ERROR [org.apache.catalina.core.ContainerBase.[jboss.web].[localhost].[/openspecimen].[restApi]] (ajp-0.0.0.0-8009-8) Servlet.service() for servlet restApi threw exception
    java.lang.NullPointerException
    at edu.wustl.common.audit.AuditManager.setLoginDetails(AuditManager.java:853)
    at edu.wustl.dao.HibernateDAOImpl.auditLoginEvents(HibernateDAOImpl.java:344)
    at edu.wustl.catissuecore.processor.CatissueLoginProcessor.manageLoginHistory(CatissueLoginProcessor.java:162)
    at edu.wustl.catissuecore.processor.CatissueLoginProcessor.processUserLogin(CatissueLoginProcessor.java:101)
    at krishagni.catissueplus.rest.RestApiAuthFilter.authenticate(RestApiAuthFilter.java:207)
    at krishagni.catissueplus.rest.RestApiAuthFilter.doFilter(RestApiAuthFilter.java:89)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at org.jboss.web.tomcat.filters.ReplyHeaderFilter.doFilter(ReplyHeaderFilter.java:96)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:235)
    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
    at org.jboss.web.tomcat.security.SecurityAssociationValve.invoke(SecurityAssociationValve.java:190)
    at org.jboss.web.tomcat.security.JaccContextValve.invoke(JaccContextValve.java:92)
    at org.jboss.web.tomcat.security.SecurityContextEstablishmentValve.process(SecurityContextEstablishmentValve.java:126)
    at org.jboss.web.tomcat.security.SecurityContextEstablishmentValve.invoke(SecurityContextEstablishmentValve.java:70)
    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
    at org.jboss.web.tomcat.service.jca.CachedConnectionValve.invoke(CachedConnectionValve.java:158)
    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:330)
    at org.apache.coyote.ajp.AjpProcessor.process(AjpProcessor.java:436)
    at org.apache.coyote.ajp.AjpProtocol$AjpConnectionHandler.process(AjpProtocol.java:384)
    at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:447)
    at java.lang.Thread.run(Thread.java:662)

    #6

    @Shannon_Dalton

    When you delete a record from OpenSpecimen, it never gets physically deleted from the database. It is only marked as “disabled”. This is for audit and regulatory purposes.

    If you have to physically delete from database, you will have to write SQL scripts yourself to do it.

    ~Sri

    #7

    We received a request from a user to delete boxes of specimens. I see on the wiki page here that bulk upload can be used to delete data from OpenSpecimen https://openspecimen.atlassian.net/wiki/display/CAT/Bulk+(CSV)+Import. Could you comment on whether the following steps represent the best way to delete boxes of specimens via the UI:

    1. Use the Disposal Event template to delete the specimens of interest
    2. Manually select and delete the boxes of interest, when empty
    #8

    Hi @Matthew_Marcetich,
    Convenient method to delete the specimens through bulk upload would be to-

    1. Use “Specimens” template under Import
    2. In the template mention the Activity status as" Disabled" and Specimen Labels for the specimens you want to delete (rest columns can be left blank).
    3. Upload the template and click on “update” under specimens import option
      Please refer- Update specimens

    Thanks,
    Pooja