Re: UmlsUserApprover Error [EXTERNAL]
Thanks for the ideas.
There hasn't been any such changes, and network connectivity shouldn't be
an issue. I ran my script earlier, which automatically runs the same
pipeline on several different folders, and only the first run was
successful. The others failed with the same error. My latest attempt is to
remove the .m2 directory and recompile and reinstall, and it is currently
processing the first directory, so I don't know if it will fail on the next
as yet.
My primary interface is over SSH to a remote server, and this is the script:
UmlsLP () { mvn exec:java
-Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline"
-Dexec.args="--input-dir $1/yes/ --output-dir $2/yes/"
-Dctakes.umlsuser= -Dctakes.umlspw= > out.tmp ; mvn exec:java
-Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline"
-Dexec.args="--input-dir $1/no/ --output-dir $2/no/"
-Dctakes.umlsuser= -Dctakes.umlspw= >> out.tmp ; echo Finished
UmlsLP $1 $2 ; cat out.tmp | grep -C 3 "Total time" ;}
Thank you.
*Andrew Phillips*
GitHub: github.com/skeledrew
LinkedIn: www.linkedin.com/in/aphillipstech
On 26 February 2018 at 13:00, Miller, Timothy <
timothy.mil...@childrens.harvard.edu> wrote:
> Is it possible there is some network issue preventing connectivity? New
> institutional firewall maybe?
>
> Otherwise, it looks like somehow your credentials are not getting into
> the right place. Possible a configuration file had them before and it's
> been changed out from under you?
>
> One thing you can try, if you are using an IDE, you can directly put
> your credentials into the VM options for your run configuration with:
> -Dctakes.umlsuser= -Dctakes.umlspw
>
> and see if you still get the issue.
>
> Tim
>
>
> On Sat, 2018-02-24 at 18:42 -0600, Andrew Phillips wrote:
> > Hello,
> >
> > I am getting an error after recompiling a script in my pipeline. My
> > setup
> > was working fine the last time I did a compile several months ago,
> > and I
> > have logged into my UMLS account to ensure it isn't an issue with my
> > credentials, as well as done a complete reinstall from the GitHub
> > repo and
> > checked out the 4.0.0 release. The minor change I made in the script
> > was
> > just uncommenting something that I've used before, so I know there
> > are no
> > errors in it. Any insights as to what the issue may be? I've included
> > the
> > complete output below. Thank you.
> >
> >
> > [INFO] Scanning for projects...
> > [WARNING] The POM for org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 is
> > missing, no dependency information available
> > [WARNING] Failed to retrieve plugin descriptor for
> > org.eclipse.m2e:lifecycle-mapping:1.0.0: Plugin
> > org.eclipse.m2e:lifecycle-mapping:1.0.0 or one of its dependencies
> > could
> > not be resolved: Failure to find
> > org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 in
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__repo.maven.apach
> > e.org_maven2=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU
> > =Heup-IbsIg9Q1TPOylpP9FE4GTK-
> > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=NHws3pftXkncEWsu-
> > Y6fCtMKfY3WWkYQmDYrA4AVcvU=1C-i1p8UnA38es-UT_d0FMIUOx5yrfK0NQh-
> > PSEuxpA= was cached in the local repository,
> > resolution will not be reattempted until the update interval of
> > central has
> > elapsed or updates are forced
> > [INFO]
> > [INFO]
> > ---
> > -
> > [INFO] Building Apache cTAKES Temporal Information Extraction 4.0.1-
> > SNAPSHOT
> > [INFO]
> > ---
> > -
> > [WARNING] The POM for org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 is
> > missing, no dependency information available
> > [WARNING] Failed to retrieve plugin descriptor for
> > org.eclipse.m2e:lifecycle-mapping:1.0.0: Plugin
> > org.eclipse.m2e:lifecycle-mapping:1.0.0 or one of its dependencies
> > could
> > not be resolved: Failure to find
> > org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 in
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__repo.maven.apach
> > e.org_maven2=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU
> > =Heup-IbsIg9Q1TPOylpP9FE4GTK-
> > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=NHws3pftXkncEWsu-
> > Y6fCtMKfY3WWkYQmDYrA4AVcvU=1C-i1p8UnA38es-UT_d0FMIUOx5yrfK0NQh-
> > PSEuxpA= was cached in the local repository,
> > resolution will not be reattempted until the update interval of
> > central has
> > elapsed or updates are forced
> > [INFO]
> > [INFO] >>> exec-maven-plugin:1.2.1:java (default-cli) > validate @
> > ctakes-misc >>>
> > [INFO]
> > [INFO] <<< exec-maven-plugin:1.2.1:java (default-cli) < validate @
> > ctakes-misc <<<
> > [INFO]
> > [INFO]
> > [INFO] --- exec-maven-plugin:1.2.1:java (default-cli) @ ctakes-misc
> > ---
> > log4j: reset attribute= "false".
> > log4j: Threshold ="null".
> > log4j: Retreiving an instance of org.apache.log4j.Logger.
> > log4j: Setting [ProgressAppender] additivity to [false].
> > log4j: Level value for ProgressAppender is
Re: UmlsUserApprover Error [EXTERNAL]
Is it possible there is some network issue preventing connectivity? New
institutional firewall maybe?
Otherwise, it looks like somehow your credentials are not getting into
the right place. Possible a configuration file had them before and it's
been changed out from under you?
One thing you can try, if you are using an IDE, you can directly put
your credentials into the VM options for your run configuration with:
-Dctakes.umlsuser= -Dctakes.umlspw
and see if you still get the issue.
Tim
On Sat, 2018-02-24 at 18:42 -0600, Andrew Phillips wrote:
> Hello,
>
> I am getting an error after recompiling a script in my pipeline. My
> setup
> was working fine the last time I did a compile several months ago,
> and I
> have logged into my UMLS account to ensure it isn't an issue with my
> credentials, as well as done a complete reinstall from the GitHub
> repo and
> checked out the 4.0.0 release. The minor change I made in the script
> was
> just uncommenting something that I've used before, so I know there
> are no
> errors in it. Any insights as to what the issue may be? I've included
> the
> complete output below. Thank you.
>
>
> [INFO] Scanning for projects...
> [WARNING] The POM for org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 is
> missing, no dependency information available
> [WARNING] Failed to retrieve plugin descriptor for
> org.eclipse.m2e:lifecycle-mapping:1.0.0: Plugin
> org.eclipse.m2e:lifecycle-mapping:1.0.0 or one of its dependencies
> could
> not be resolved: Failure to find
> org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 in
> https://urldefense.proofpoint.com/v2/url?u=https-3A__repo.maven.apach
> e.org_maven2=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU
> =Heup-IbsIg9Q1TPOylpP9FE4GTK-
> OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=NHws3pftXkncEWsu-
> Y6fCtMKfY3WWkYQmDYrA4AVcvU=1C-i1p8UnA38es-UT_d0FMIUOx5yrfK0NQh-
> PSEuxpA= was cached in the local repository,
> resolution will not be reattempted until the update interval of
> central has
> elapsed or updates are forced
> [INFO]
> [INFO]
> ---
> -
> [INFO] Building Apache cTAKES Temporal Information Extraction 4.0.1-
> SNAPSHOT
> [INFO]
> ---
> -
> [WARNING] The POM for org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 is
> missing, no dependency information available
> [WARNING] Failed to retrieve plugin descriptor for
> org.eclipse.m2e:lifecycle-mapping:1.0.0: Plugin
> org.eclipse.m2e:lifecycle-mapping:1.0.0 or one of its dependencies
> could
> not be resolved: Failure to find
> org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 in
> https://urldefense.proofpoint.com/v2/url?u=https-3A__repo.maven.apach
> e.org_maven2=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU
> =Heup-IbsIg9Q1TPOylpP9FE4GTK-
> OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=NHws3pftXkncEWsu-
> Y6fCtMKfY3WWkYQmDYrA4AVcvU=1C-i1p8UnA38es-UT_d0FMIUOx5yrfK0NQh-
> PSEuxpA= was cached in the local repository,
> resolution will not be reattempted until the update interval of
> central has
> elapsed or updates are forced
> [INFO]
> [INFO] >>> exec-maven-plugin:1.2.1:java (default-cli) > validate @
> ctakes-misc >>>
> [INFO]
> [INFO] <<< exec-maven-plugin:1.2.1:java (default-cli) < validate @
> ctakes-misc <<<
> [INFO]
> [INFO]
> [INFO] --- exec-maven-plugin:1.2.1:java (default-cli) @ ctakes-misc
> ---
> log4j: reset attribute= "false".
> log4j: Threshold ="null".
> log4j: Retreiving an instance of org.apache.log4j.Logger.
> log4j: Setting [ProgressAppender] additivity to [false].
> log4j: Level value for ProgressAppender is [INFO].
> log4j: ProgressAppender level set to INFO
> log4j: Class name: [org.apache.log4j.ConsoleAppender]
> log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
> log4j: Setting property [conversionPattern] to [%m].
> log4j: Adding appender named [noEolAppender] to category
> [ProgressAppender].
> log4j: Retreiving an instance of org.apache.log4j.Logger.
> log4j: Setting [ProgressDone] additivity to [false].
> log4j: Level value for ProgressDone is [INFO].
> log4j: ProgressDone level set to INFO
> log4j: Class name: [org.apache.log4j.ConsoleAppender]
> log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
> log4j: Setting property [conversionPattern] to [%m%n].
> log4j: Adding appender named [eolAppender] to category
> [ProgressDone].
> log4j: Level value for root is [INFO].
> log4j: root level set to INFO
> log4j: Class name: [org.apache.log4j.ConsoleAppender]
> log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
> log4j: Setting property [conversionPattern] to [%d{dd MMM
> HH:mm:ss}
> %5p %c{1} - %m%n].
> log4j: Adding appender named [consoleAppender] to category [root].
> 24 Feb 2018 18:22:23 INFO LvgAnnotator - URL for lvg.properties
> =/home/aphillips5/ctakes/ctakes-
> misc/target/classes/org/apache/ctakes/lvg/data/config/lvg.properties
> 24 Feb 2018 18:22:23 INFO SentenceDetector - Sentence
