DANGERdfEXTRACTDS method

Support Developer support
1

I am trying to create a develop VM, but the script contains:

calltext <- call('DANGERdfEXTRACTDS', dataframeName)

this generates the client side error:

Error: Command 'DANGERdfEXTRACTDS("CM")' failed on 'study1': <no message>

it appears that ‘DANGERdfEXTRACTDS’ method isn’t exported, but I can’t find it. The server side error is:

2019-01-31 04:26:54,346 [R Operations Consumer org.obiba.opal.r.service.OpalRSession$RCommandsConsumer@19dcd514] ERROR org.obiba.opal.r.service.OpalRSession - Error when consuming R command: null org.obiba.opal.datashield.NoSuchDataShieldMethodException: null
    at org.obiba.opal.datashield.DataShieldEnvironment.getMethod(DataShieldEnvironment.java:107) ~[opal-datashield-2.13.1.jar:na]
    at org.obiba.opal.datashield.expr.RScriptGenerator.findMethod(RScriptGenerator.java:98) ~[opal-datashield-2.13.1.jar:na]
    at org.obiba.opal.datashield.expr.RScriptGenerator.visit(RScriptGenerator.java:49) ~[opal-datashield-2.13.1.jar:na]
    at org.obiba.opal.datashield.expr.ASTfuncCall.jjtAccept(ASTfuncCall.java:18) ~[opal-datashield-2.13.1.jar:na]
    at org.obiba.opal.datashield.expr.SimpleNode.childrenAccept(SimpleNode.java:65) ~[opal-datashield-2.13.1.jar:na]
    at org.obiba.opal.datashield.expr.RScriptGenerator.visit(RScriptGenerator.java:88) ~[opal-datashield-2.13.1.jar:na]
    at org.obiba.opal.datashield.expr.ASTroot.jjtAccept(ASTroot.java:18) ~[opal-datashield-2.13.1.jar:na]
    at org.obiba.opal.datashield.expr.RScriptGenerator.toScript(RScriptGenerator.java:28) ~[opal-datashield-2.13.1.jar:na]
    at org.obiba.opal.datashield.AbstractRestrictedRScriptROperation.restricted(AbstractRestrictedRScriptROperation.java:65) ~[opal-datashield-2.13.1.jar:na]
    at org.obiba.opal.datashield.RestrictedRScriptROperation.doWithConnection(RestrictedRScriptROperation.java:33) ~[opal-datashield-2.13.1.jar:na]
    at org.obiba.opal.spi.r.AbstractROperation.doWithConnection(AbstractROperation.java:236) ~[opal-spi-r-2.13.1.jar:na]
    at org.obiba.opal.r.service.OpalRSession.execute(OpalRSession.java:186) ~[opal-r-2.13.1.jar:na]
    at org.obiba.opal.r.service.OpalRSession$RCommandsConsumer.consume(OpalRSession.java:372) [opal-r-2.13.1.jar:na]
    at org.obiba.opal.r.service.OpalRSession$RCommandsConsumer.run(OpalRSession.java:360) [opal-r-2.13.1.jar:na]
    at org.apache.shiro.subject.support.SubjectRunnable.doRun(SubjectRunnable.java:120) [shiro-core-1.3.3-obiba.jar:1.3.3-obiba]
    at org.apache.shiro.subject.support.SubjectRunnable.run(SubjectRunnable.java:108) [shiro-core-1.3.3-obiba.jar:1.3.3-obiba]
    at org.obiba.opal.core.tx.TransactionalThread$1.doInTransactionWithoutResult(TransactionalThread.java:35) [opal-core-2.13.1.jar:na]
    at org.springframework.transaction.support.TransactionCallbackWithoutResult.doInTransaction(TransactionCallbackWithoutResult.java:34) [spring-tx-4.3.19.RELEASE.jar:4.3.19.RELEASE]
    at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:133) [spring-tx-4.3.19.RELEASE.jar:4.3.19.RELEASE]
    at org.obiba.opal.core.tx.TransactionalThread.run(TransactionalThread.java:32) [opal-core-2.13.1.jar:na]
2

All the functions starting with DANGER are @paul.burton 's developer functions. We have not released these onto any repo yet as by their very nature they produce disclosive outputs, but these functions necessary for error checking etc when developing in DataSHIELD. I don’t have a latest version of them all but @demetris.avraam might?

3

Hi, I have checked dsDanger and dsDangerClient but was not able to find any such operation. I will check with Demetris. Thanks, Stuart

4

Yes I don’t think dsDanger and dsDanger client are up to date!