Re: Errors in the tranSMART installation

Keith Nangle

unread,

Nov 17, 2015, 5:18:15 AM11/17/15

to Celia Alvarez Romero, support, transmar...@googlegroups.com

Dear support team, please see the query from Celia below; has she somehow picked up a configuration from the HBase development work ?

------------------------------------------------------------------------

Hello,

What do you think about the error that I showed you? My installation is stoping. I can't deply the web application. I think it doesn't recognise the direction of my database because when PostgreSQL is started it isn´t found and it is replaced for h2 database (h2 isn´t my database).

I hope you can help me.

Thanks you.

Regards,

Celia

From: celiaalva...@hotmail.com
To: keith....@transmartfoundation.org
Subject: RE: Errors in the tranSMART installation
Date: Tue, 10 Nov 2015 14:55:23 +0100

Hello,

I have intended to install both .war files but I obtain the same errors. When PostgreSQL is started it isn´t found and it is replaced for h2 database (h2 isn´t my database). When PostgreSQL is stopped I obtain the previous messages.

catalina.out

org.apache.catalina.core.StandardContext startInternal

GRAVE: One or more listeners failed to start. Full details will be found in the appropriate container log file

org.apache.catalina.util.SessionIdGeneratorBase createSecureRandom

INFORMACIÓN: Creation of SecureRandom instance for session ID generation using [SHA1PRNG] took [19.883] milliseconds.

org.apache.catalina.core.StandardContext startInternal

GRAVE: Falló en arranque del Contexto [/transmart] debido a errores previos

org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc

GRAVE: La aplicación web [/transmart] registró el conductor JDBC [org.postgresql.Driver] pero falló al anular el registro mientras la aplicación web estaba parada. Para prevenir un fallo de memoria, se ha anulado el registro del conductor JDBC por la fuerza.

org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc

GRAVE: La aplicación web [/transmart] registró el conductor JDBC [org.h2.Driver] pero falló al anular el registro mientras la aplicación web estaba parada. Para prevenir un fallo de memoria, se ha anulado el registro del conductor JDBC por la fuerza.

Thanks you,

Celia

On Mon, Nov 16, 2015 at 3:07 PM, Celia Alvarez Romero <celiaalva...@hotmail.com> wrote:

Hello,

What do you think about the error that I showed you? My installation is stoping. I can't deply the web application. I think it doesn't recognise the direction of my database because when PostgreSQL is started it isn´t found and it is replaced for h2 database (h2 isn´t my database).
I hope you can help me.

Thanks you.
Regards,
Celia

From: celiaalva...@hotmail.com
To: keith....@transmartfoundation.org
Subject: RE: Errors in the tranSMART installation
Date: Tue, 10 Nov 2015 14:55:23 +0100

Hello,

I have intended to install both .war files but I obtain the same errors. When PostgreSQL is started it isn´t found and it is replaced for h2 database (h2 isn´t my database). When PostgreSQL is stopped I obtain the previous messages.

catalina.out
org.apache.catalina.core.StandardContext startInternal
GRAVE: One or more listeners failed to start. Full details will be found in the appropriate container log file
org.apache.catalina.util.SessionIdGeneratorBase createSecureRandom
INFORMACIÓN: Creation of SecureRandom instance for session ID generation using [SHA1PRNG] took [19.883] milliseconds.
org.apache.catalina.core.StandardContext startInternal
GRAVE: Falló en arranque del Contexto [/transmart] debido a errores previos
org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
GRAVE: La aplicación web [/transmart] registró el conductor JDBC [org.postgresql.Driver] pero falló al anular el registro mientras la aplicación web estaba parada. Para prevenir un fallo de memoria, se ha anulado el registro del conductor JDBC por la fuerza.
org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
GRAVE: La aplicación web [/transmart] registró el conductor JDBC [org.h2.Driver] pero falló al anular el registro mientras la aplicación web estaba parada. Para prevenir un fallo de memoria, se ha anulado el registro del conductor JDBC por la fuerza.

Thanks you,

Celia

From: celiaalva...@hotmail.com
To: keith....@transmartfoundation.org
Subject: RE: Errors in the tranSMART installation
Date: Mon, 9 Nov 2015 11:37:21 +0100

Hello,
That error is solutioned, I have copied the configuration files in the directory /root/.grails/transmartConfig/
But now I'm obtaining others errors: my database is PosgreSQL, when it is started it isn´t found and it is replaced for h2 database (h2 isn´t my database). When PostgreSQL is stopped I obtain the following messages:

org.postgresql.util.PSQLException: Conexión rechazada. Verifique que el nombre del Host y el puerto sean correctos y que postmaster este aceptando conexiones TCP/IP

catalina.out
org.apache.catalina.core.StandardContext startInternal
GRAVE: One or more listeners failed to start. Full details will be found in the appropriate container log file
org.apache.catalina.util.SessionIdGeneratorBase createSecureRandom
INFORMACIÓN: Creation of SecureRandom instance for session ID generation using [SHA1PRNG] took [19.883] milliseconds.
org.apache.catalina.core.StandardContext startInternal
GRAVE: Falló en arranque del Contexto [/transmart] debido a errores previos
org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
GRAVE: La aplicación web [/transmart] registró el conductor JDBC [org.postgresql.Driver] pero falló al anular el registro mientras la aplicación web estaba parada. Para prevenir un fallo de memoria, se ha anulado el registro del conductor JDBC por la fuerza.
org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
GRAVE: La aplicación web [/transmart] registró el conductor JDBC [org.h2.Driver] pero falló al anular el registro mientras la aplicación web estaba parada. Para prevenir un fallo de memoria, se ha anulado el registro del conductor JDBC por la fuerza.

What could I do?
Thanks you.

Best regards,
Celia

Date: Fri, 6 Nov 2015 22:30:59 +0100
Subject: Re: Errors in the tranSMART installation
From: keith....@transmartfoundation.org
To: celiaalva...@hotmail.com

Dear Celia,

It appears that there is a problem with the Postgres database. If you're not familiar with Postgres I can send you a command to theft whether it's running.

Also could you describe your environment- version of UNIX etc., and the commands you used to pull the code (or just let me know if they were exactly as written on the wiki page).

Best regards,

On Friday, November 6, 2015, Celia Alvarez Romero <celiaalva...@hotmail.com> wrote:

Hello,

I'm Celia Alvarez and I'm installing transmart in my server.
I'm following the installation guide https://wiki.transmartfoundation.org/pages/viewpage.action?pageId=6619205 and I'm in the step 9. I'm deploying tranSMART web application but it doesn't operate.

How could I use the server mode? How could I close all other connections?

I hope you will help me, I want to finish the installation as soon as possible.
Thanks you.

The error is the following:
Catalina.out
feb 11, 2012 3:27:56 PM org.apache.catalina.core.StandardServer await
INFORMACIÓN: Se ha recibido un comando de apagado a través del puerto de apagado. Parando la instancia del Servidor.
feb 11, 2012 3:27:56 PM org.apache.coyote.AbstractProtocol pause
INFORMACIÓN: Pausing ProtocolHandler ["http-apr-8080"]
feb 11, 2012 3:27:56 PM org.apache.coyote.AbstractProtocol pause
INFORMACIÓN: Pausing ProtocolHandler ["http-apr-8081"]
feb 11, 2012 3:27:56 PM org.apache.coyote.AbstractProtocol pause
INFORMACIÓN: Pausing ProtocolHandler ["ajp-apr-8009"]
feb 11, 2012 3:27:56 PM org.apache.catalina.core.StandardService stopInternal
INFORMACIÓN: Parando servicio Catalina
feb 11, 2012 3:27:56 PM org.apache.coyote.AbstractProtocol stop
INFORMACIÓN: Stopping ProtocolHandler ["http-apr-8080"]
feb 11, 2012 3:27:56 PM org.apache.coyote.AbstractProtocol stop
INFORMACIÓN: Stopping ProtocolHandler ["http-apr-8081"]
feb 11, 2012 3:27:57 PM org.apache.coyote.AbstractProtocol stop
INFORMACIÓN: Stopping ProtocolHandler ["ajp-apr-8009"]
feb 11, 2012 3:27:57 PM org.apache.coyote.AbstractProtocol destroy
INFORMACIÓN: Destroying ProtocolHandler ["http-apr-8080"]
feb 11, 2012 3:27:57 PM org.apache.coyote.AbstractProtocol destroy
INFORMACIÓN: Destroying ProtocolHandler ["http-apr-8081"]
feb 11, 2012 3:27:57 PM org.apache.coyote.AbstractProtocol destroy
INFORMACIÓN: Destroying ProtocolHandler ["ajp-apr-8009"]
feb 11, 2012 3:28:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFORMACIÓN: Server version: Apache Tomcat/7.0.64
feb 11, 2012 3:28:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFORMACIÓN: Server built: Aug 19 2015 17:18:06 UTC
feb 11, 2012 3:28:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFORMACIÓN: Server number: 7.0.64.0
feb 11, 2012 3:28:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFORMACIÓN: OS Name: Linux
feb 11, 2012 3:28:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFORMACIÓN: OS Version: 2.6.32-573.7.1.el6.x86_64
feb 11, 2012 3:28:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFORMACIÓN: Architecture: amd64
feb 11, 2012 3:28:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFORMACIÓN: Java Home: /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.91.x86_64/jre
feb 11, 2012 3:28:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFORMACIÓN: JVM Version: 1.7.0_91-mockbuild_2015_10_21_19_56-b00
feb 11, 2012 3:28:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFORMACIÓN: JVM Vendor: Oracle Corporation
feb 11, 2012 3:28:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFORMACIÓN: CATALINA_BASE: /opt/tomcat7/apache-tomcat-7.0.64
feb 11, 2012 3:28:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFORMACIÓN: CATALINA_HOME: /opt/tomcat7/apache-tomcat-7.0.64
feb 11, 2012 3:28:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFORMACIÓN: Command line argument: -Djava.util.logging.config.file=/opt/tomcat7/apache-tomcat-7.0.64/conf/logging.properties
feb 11, 2012 3:28:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFORMACIÓN: Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
feb 11, 2012 3:28:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFORMACIÓN: Command line argument: -Xmx4096M
feb 11, 2012 3:28:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFORMACIÓN: Command line argument: -XX:MaxPermSize=1024M
feb 11, 2012 3:28:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFORMACIÓN: Command line argument: -Djava.endorsed.dirs=/opt/tomcat7/apache-tomcat-7.0.64/endorsed
feb 11, 2012 3:28:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFORMACIÓN: Command line argument: -Dcatalina.base=/opt/tomcat7/apache-tomcat-7.0.64
feb 11, 2012 3:28:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFORMACIÓN: Command line argument: -Dcatalina.home=/opt/tomcat7/apache-tomcat-7.0.64
feb 11, 2012 3:28:02 PM org.apache.catalina.core.AprLifecycleListener lifecycleEvent
INFORMACIÓN: Cargada la biblioteca nativa APR de Apache Tomcat 1.1.33 con la versión APR 1.3.9.
feb 11, 2012 3:28:02 PM org.apache.catalina.core.AprLifecycleListener lifecycleEvent
INFORMACIÓN: Capacidades APR: IPv6 [true], enviar fichero [true], aceptar filtros [false], aleatorio [true].
feb 11, 2012 3:28:02 PM org.apache.catalina.core.AprLifecycleListener initializeSSL
INFORMACIÓN: OpenSSL inicializado correctamente (OpenSSL 1.0.1e 11 Feb 2013)
feb 11, 2012 3:28:02 PM org.apache.coyote.AbstractProtocol init
INFORMACIÓN: Initializing ProtocolHandler ["http-apr-8080"]
feb 11, 2012 3:28:02 PM org.apache.coyote.AbstractProtocol init
INFORMACIÓN: Initializing ProtocolHandler ["http-apr-8081"]
feb 11, 2012 3:28:02 PM org.apache.coyote.AbstractProtocol init
INFORMACIÓN: Initializing ProtocolHandler ["ajp-apr-8009"]
feb 11, 2012 3:28:02 PM org.apache.catalina.startup.Catalina load
INFORMACIÓN: Initialization processed in 618 ms
feb 11, 2012 3:28:02 PM org.apache.catalina.core.StandardService startInternal
INFORMACIÓN: Arrancando servicio Catalina
feb 11, 2012 3:28:02 PM org.apache.catalina.core.StandardEngine startInternal
INFORMACIÓN: Starting Servlet Engine: Apache Tomcat/7.0.64
feb 11, 2012 3:28:02 PM org.apache.catalina.startup.HostConfig deployWAR
INFORMACIÓN: Despliegue del archivo /opt/tomcat7/apache-tomcat-7.0.64/webapps/transmart.war de la aplicación web
feb 11, 2012 3:28:10 PM org.apache.catalina.startup.TaglibUriRule body
INFORMACIÓN: TLD skipped. URI: http://java.sun.com/jsp/jstl/core is already defined
feb 11, 2012 3:28:10 PM org.apache.catalina.startup.TaglibUriRule body
INFORMACIÓN: TLD skipped. URI: http://java.sun.com/jsp/jstl/fmt is already defined
feb 11, 2012 3:28:10 PM org.apache.catalina.startup.TaglibUriRule body
INFORMACIÓN: TLD skipped. URI: http://www.springframework.org/tags is already defined
feb 11, 2012 3:28:10 PM org.apache.catalina.startup.TldConfig execute
INFORMACIÓN: At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
[INFO] Configuration file /root/.grails/transmartConfig/Config.groovy does not exist.
[INFO] Configuration file /root/.grails/transmartConfig/DataSource.groovy does not exist.
[INFO] Configuration file /root/.grails/transmartConfig/Config.groovy does not exist.
[INFO] Configuration file /root/.grails/transmartConfig/DataSource.groovy does not exist.

Configuring Spring Security Core ...
... finished configuring Spring Security Core

2012-02-11 15:28:34,617 [localhost-startStop-1] ERROR pool.ConnectionPool - Unable to create initial connections of pool.
org.h2.jdbc.JdbcSQLException: La base de datos puede que ya esté siendo utilizada: "Locked by another process". Soluciones Posibles: cierre todas las otras conexiones; use el modo server
Database may be already in use: "Locked by another process". Possible solutions: close all other connection(s); use the server mode [90020-176]
at org.h2.message.DbException.getJdbcSQLException(DbException.java:344)
at org.h2.message.DbException.get(DbException.java:178)
at org.h2.message.DbException.get(DbException.java:154)
at org.h2.store.FileLock.getExceptionAlreadyInUse(FileLock.java:462)
at org.h2.store.FileLock.lockFile(FileLock.java:356)
......
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1095)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1930)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
2012-02-11 15:28:37,027 [localhost-startStop-1] ERROR pool.ConnectionPool - Unable to create initial connections of pool.
org.h2.jdbc.JdbcSQLException: La base de datos puede que ya esté siendo utilizada: "Locked by another process". Soluciones Posibles: cierre todas las otras conexiones; use el modo server
Database may be already in use: "Locked by another process". Possible solutions: close all other connection(s); use the server mode [90020-176]
at org.h2.message.DbException.getJdbcSQLException(DbException.java:344)
at org.h2.message.DbException.get(DbException.java:178)
at org.h2.message.DbException.get(DbException.java:154)
at org.h2.store.FileLock.getExceptionAlreadyInUse(FileLock.java:462)
at org.h2.store.FileLock.lockFile(FileLock.java:356)
at org.h2.store.FileLock.lock(FileLock.java:136)
at org.h2.engine.Database.open(Database.java:622)
at org.h2.engine.Database.openDatabase(Database.java:260)
at org.h2.engine.Database.<init>(Database.java:254)
at org.h2.engine.Engine.openSession(Engine.java:57)
.......
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
2012-02-11 15:28:39,134 [localhost-startStop-1] ERROR context.GrailsContextLoader - Error initializing the application: Error creating bean with name 'transactionManagerPostProcessor': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean 'transactionManager_oauth2' while setting constructor argument with key [1]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager_oauth2': Cannot resolve reference to bean 'sessionFactory_oauth2' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory_oauth2': Cannot resolve reference to bean 'hibernateProperties_oauth2' while setting bean property 'hibernateProperties'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'hibernateProperties_oauth2': Cannot resolve reference to bean 'dialectDetector_oauth2' while setting bean property 'properties' with key [hibernate.dialect]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'dialectDetector_oauth2': Invocation of init method failed; nested exception is org.springframework.jdbc.support.MetaDataAccessException: Error while extracting DatabaseMetaData; nested exception is org.h2.jdbc.JdbcSQLException: La base de datos puede que ya esté siendo utilizada: "Locked by another process". Soluciones Posibles: cierre todas las otras conexiones; use el modo server
Database may be already in use: "Locked by another process". Possible solutions: close all other connection(s); use the server mode [90020-176]
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManagerPostProcessor': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean 'transactionManager_oauth2' while setting constructor argument with key [1]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager_oauth2': Cannot resolve reference to bean 'sessionFactory_oauth2' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory_oauth2': Cannot resolve reference to bean 'hibernateProperties_oauth2' while setting bean property 'hibernateProperties'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'hibernateProperties_oauth2': Cannot resolve reference to bean 'dialectDetector_oauth2' while setting bean property 'properties' with key [hibernate.dialect]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'dialectDetector_oauth2': Invocation of init method failed; nested exception is org.springframework.jdbc.support.MetaDataAccessException: Error while extracting DatabaseMetaData; nested exception is org.h2.jdbc.JdbcSQLException: La base de datos puede que ya esté siendo utilizada: "Locked by another process". Soluciones Posibles: cierre todas las otras conexiones; use el modo server
Database may be already in use: "Locked by another process". Possible solutions: close all other connection(s); use the server mode [90020-176]
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean 'transactionManager_oauth2' while setting constructor argument with key [1]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager_oauth2': Cannot resolve reference to bean 'sessionFactory_oauth2' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory_oauth2': Cannot resolve reference to bean 'hibernateProperties_oauth2' while setting bean property 'hibernateProperties'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'hibernateProperties_oauth2': Cannot resolve reference to bean 'dialectDetector_oauth2' while setting bean property 'properties' with key [hibernate.dialect]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'dialectDetector_oauth2': Invocation of init method failed; nested exception is org.springframework.jdbc.support.MetaDataAccessException: Error while extracting DatabaseMetaData; nested exception is org.h2.jdbc.JdbcSQLException: La base de datos puede que ya esté siendo utilizada: "Locked by another process". Soluciones Posibles: cierre todas las otras conexiones; use el modo server
Database may be already in use: "Locked by another process". Possible solutions: close all other connection(s); use the server mode [90020-176]
... 5 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager_oauth2': Cannot resolve reference to bean 'sessionFactory_oauth2' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory_oauth2': Cannot resolve reference to bean 'hibernateProperties_oauth2' while setting bean property 'hibernateProperties'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'hibernateProperties_oauth2': Cannot resolve reference to bean 'dialectDetector_oauth2' while setting bean property 'properties' with key [hibernate.dialect]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'dialectDetector_oauth2': Invocation of init method failed; nested exception is org.springframework.jdbc.support.MetaDataAccessException: Error while extracting DatabaseMetaData; nested exception is org.h2.jdbc.JdbcSQLException: La base de datos puede que ya esté siendo utilizada: "Locked by another process". Soluciones Posibles: cierre todas las otras conexiones; use el modo server
Database may be already in use: "Locked by another process". Possible solutions: close all other connection(s); use the server mode [90020-176]
... 5 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory_oauth2': Cannot resolve reference to bean 'hibernateProperties_oauth2' while setting bean property 'hibernateProperties'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'hibernateProperties_oauth2': Cannot resolve reference to bean 'dialectDetector_oauth2' while setting bean property 'properties' with key [hibernate.dialect]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'dialectDetector_oauth2': Invocation of init method failed; nested exception is org.springframework.jdbc.support.MetaDataAccessException: Error while extracting DatabaseMetaData; nested exception is org.h2.jdbc.JdbcSQLException: La base de datos puede que ya esté siendo utilizada: "Locked by another process". Soluciones Posibles: cierre todas las otras conexiones; use el modo server
.....
feb 11, 2012 3:28:39 PM org.apache.catalina.core.StandardContext startInternal
GRAVE: One or more listeners failed to start. Full details will be found in the appropriate container log file
....
feb 11, 2012 3:29:22 PM org.apache.catalina.core.StandardContext startInternal
GRAVE: Falló en arranque del Contexto [/transmart] debido a errores previos
feb 11, 2012 3:29:22 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
GRAVE: La aplicación web [/transmart] registró el conductor JDBC [org.h2.Driver] pero falló al anular el registro mientras la aplicación web estaba parada. Para prevenir un fallo de memoria, se ha anulado el registro del conductor JDBC por la fuerza.
......

I show you the following files:
TRANSMART CONFIG:
BuildConfig.groovy

/* Clone the pluginsʼ corresponding repository alongside transmartApp and
* uncomment the settings below in order to use those plugins inline. See
* http://grails.org/doc/latest/guide/plugins.html#12.1%20Creating%20and%20Installing%20Plug-ins
* under the heading ‘Specifying Plugin Locations’ for more information. */

//grails.plugin.location.'rdc-rmodules' = '../Rmodules'
//grails.plugin.location.'transmart-core' = '../core-db'
//grails.plugin.location.'dalliance-plugin' = '../dalliance-plugin'
//grails.plugin.location.'transmart-mydas' = '../transmart-mydas'

grails.project.dependency.resolution = {
repositories {
mavenRepo([
name: 'repo.thehyve.nl-public',
url: 'https://repo.thehyve.nl/content/repositories/public/',
])

/* If you set the grails.project.dependency.resolution config property,
* then the tranSMART Foundation repository will not be used (see the
* in-tree BuildConfig.groovy). You can re-add it by uncommenting the
* block below. It will have lower priority than the repositories listed
* in BuildConfig.groovy (which have the highest priority) and the
* repositories that are listed above it in this closure. */
// mavenRepo([
// name: 'repo.transmartfoundation.org-public',
// root: 'https://repo.transmartfoundation.org/content/repositories/public/',
// ])
}

}

// vim: filetype=groovy et ts=4 sts=4 sw=4 tw=80:
Config.groovy
/*
* NOTE
* ----
* This configuration assumes that the development environment will be used with
* run-app and the production environment will be used with the application
* packaged as a WAR and deployed to tomcat. Running grails run-war or otherwise
* running a WAR with the development profile set up or activating the
* production environment when running grails run-app are scenarios that have
* NOT been tested.
*/

// if running as a WAR, we need these
def catalinaBase = System.getProperty('catalina.base') ?: '.'

def explodedWarDir = catalinaBase + '/webapps/transmart'
def solrPort = 8983 //port of appserver where solr runs (under ctx path /solr)
def searchIndex = catalinaBase + '/searchIndex' //create this directory
// for running transmart as WAR, create this directory and then create an alias
def jobsDirectory = "/var/tmp/jobs/"
def oauthEnabled = true
def samlEnabled = false
def gwavaEnabled = false
def transmartURL = "http://10.232.0.114:${System.getProperty('server.port', '8080')}/transmart/"

//Disabling/Enabling UI tabs
ui {
tabs {
//Search was not part of 1.2. It's not working properly. You need to set `show` to `true` to see it on UI
search.show = false
browse.hide = false
//Note: analyze tab is always shown
sampleExplorer.hide = false
geneSignature.hide = false
gwas.hide = false
uploadData.hide = false
}
}

// I001 – Insertion point 'post-WAR-variables'

//transmartURL = 'http://example.com/transmart/'
//oauthEnabled = true
//samlEnabled = false
//gwavaEnabled = false

/* Other things you may want to change:
* – Log4j configuration
* – 'Personalization & login' section
* – Location of Solr instance in 'Faceted Search Configuration'
* – For enabling SAML, editing the corresponding section is mandatory
*/

/* If you want to be able to regenerate this file easily, instead of editing
* the generated file directly, create a Config-extra.groovy file in the root of
* the transmart-data checkout. That file will be appended to this one whenever
* the Config.groovy target is run */

environments { production {
if (transmartURL.startsWith('http://localhost:')) {
println "[WARN] transmartURL not overridden. Some settings (e.g. help page) may be wrong"
}
} }

/* {{{ Log4J Configuration */
log4j = {
environments {
development {
root {
info 'stdout'
}

// for a less verbose startup & shutdown
warn 'org.codehaus.groovy.grails.commons.spring'
warn 'org.codehaus.groovy.grails.orm.hibernate.cfg'
warn 'org.codehaus.groovy.grails.domain.GrailsDomainClassCleaner'

debug 'org.transmartproject'
debug 'com.recomdata'
debug 'grails.app.services.com.recomdata'
debug 'grails.app.services.org.transmartproject'
debug 'grails.app.controllers.com.recomdata'
debug 'grails.app.controllers.org.transmartproject'
debug 'grails.app.domain.com.recomdata'
debug 'grails.app.domain.org.transmartproject'
// debug 'org.springframework.security'
// (very verbose) debug 'org.grails.plugin.resource'
}

production {
def logDirectory = "${catalinaBase}/logs".toString()
appenders {
rollingFile(name: 'transmart',
file: "${logDirectory}/transmart.log",
layout: pattern(conversionPattern: '%d{dd-MM-yyyy HH:mm:ss,SSS} %5p %c{1} - %m%n'),
maxFileSize: '100MB')
}
root {
warn 'transmart'
}
}
}
}
/* }}} */

/* {{{ Faceted Search Configuration */
environments {
development {
com.rwg.solr.scheme = 'http'
com.rwg.solr.host = '127.0.0.1:8983'
com.rwg.solr.path = '/solr/rwg/select/'
}
production {
com.rwg.solr.scheme = 'http'
com.rwg.solr.host = '127.0.0.1:' + solrPort
com.rwg.solr.path = '/solr/rwg/select/'
}
}
/* }}} */

/* {{{ Personalization */
// application logo to be used in the login page
com.recomdata.largeLogo = "transmartlogo.jpg"

// application logo to be used in the search page
com.recomdata.smallLogo="transmartlogosmall.jpg"

// contact email address
com.recomdata.contactUs = "transmar...@googlegroups.com"

// site administrator contact email address
com.recomdata.adminEmail = "transmar...@googlegroups.com"

// application title
com.recomdata.appTitle = "tranSMART v" + org.transmart.originalConfigBinding.appVersion

// Location of the help pages. Should be an absolute URL.
// Currently, these are distribution with transmart,
// so it can also point to that location copy.
com.recomdata.adminHelpURL = "$transmartURL/help/adminHelp/default.htm"

environments { development {
com.recomdata.bugreportURL = 'https://jira.transmartfoundation.org'
} }

// Keys without defaults (see Config-extra.php.sample):
// com.recomdata.projectName
// com.recomdata.providerName
// com.recomdata.providerURL
/* }}} */

/* {{{ Login */
// Session timeout and heartbeat frequency (ping interval)
com.recomdata.sessionTimeout = 300
com.recomdata.heartbeatLaps = 30

environments { development {
com.recomdata.sessionTimeout = Integer.MAX_VALUE / 1000 as int /* ~24 days */
com.recomdata.heartbeatLaps = 900
} }

// Not enabled by default (see Config-extra.php.sample)
//com.recomdata.passwordstrength.pattern
//com.recomdata.passwordstrength.description

// Whether to enable guest auto login.
// If it's enabled no login is required to access tranSMART.
com.recomdata.guestAutoLogin = false
environments { development { com.recomdata.guestAutoLogin = true } }
// Guest account user name - if guestAutoLogin is true, this is the username of
// the account that tranSMART will automatically authenticate users as. This will
// control the level of access anonymous users will have (the access will match
// that of the account specified here).
com.recomdata.guestUserName = 'guest'
/* }}} */

/* {{{ Search tool configuration */

// Lucene index location for documentation search
com.recomdata.searchengine.index = searchIndex

/* }}} */

/* {{{ Sample Explorer configuration */

// This is an object to dictate the names and 'pretty names' of the SOLR fields.
// Optionally you can set the width of each of the columns when rendered.

sampleExplorer {
fieldMapping = [
columns:[
[header:'Sample ID',dataIndex:'id', mainTerm: false, showInGrid: false],
[header:'BioBank', dataIndex:'BioBank', mainTerm: true, showInGrid: true, width:10],
[header:'Source Organism', dataIndex:'Source_Organism', mainTerm: true, showInGrid: true, width:10]
// Continue as you have fields
]
]
resultsGridHeight = 100
resultsGridWidth = 100
idfield = 'id'
}

edu.harvard.transmart.sampleBreakdownMap = [
"id":"Aliquots in Cohort"
]

// Solr configuration for the Sample Explorer
com { recomdata { solr {
maxNewsStories = 10
maxRows = 10000
}}}

/* }}} */

/* {{{ Dataset Explorer configuration */
com { recomdata { datasetExplorer {
// set to 'true' (quotes included) to enable gene pattern integration
genePatternEnabled = 'false'
// The tomcat URL that gene pattern is deployed within -usually it's proxyed through apache
genePatternURL = 'http://23.23.185.167'
// Gene Pattern real URL with port number
genePatternRealURLBehindProxy = 'http://23.23.185.167:8080'
// default Gene pattern user to start up - each tranSMART user will need a separate user account to be created in Gene Pattern
genePatternUser = 'biomart'

// Absolute path to PLINK executables
plinkExcutable = '/usr/local/bin/plink'
} } }
// Metadata view
com.recomdata.view.studyview = 'studydetail'

com.recomdata.plugins.resultSize = 5000
/* }}} */

/* {{{ RModules & Data Export Configuration */
environments {
// This is to target a remove Rserv. Bear in mind the need for shared network storage
RModules.host = "127.0.0.1"
RModules.port = 6311

// This is not used in recent versions; the URL is always /analysisFiles/
RModules.imageURL = "/tempImages/" //must end and start with /

production {
// The working directory for R scripts, where the jobs get created and
// output files get generated
RModules.tempFolderDirectory = jobsDirectory
}
development {
RModules.tempFolderDirectory = "/tmp"

/* we don't need to specify temporaryImageDirectory, because we're not copying */
}

// Used to access R jobs parent directory outside RModules (e.g. data export)
com.recomdata.plugins.tempFolderDirectory = RModules.tempFolderDirectory
}
/* }}} */

/* {{{ GWAS Configuration */

com.recomdata.dataUpload.appTitle="Upload data to tranSMART"
com.recomdata.dataUpload.stageScript="run_analysis_stage"

// Directory path of com.recomdata.dataUpload.stageScript
def gwasEtlDirectory = new File(System.getenv('HOME'), '.grails/transmart-gwasetl')

// Directory to hold GWAS file uploads
def gwasUploadsDirectory = new File(System.getenv('HOME'), '.grails/transmart-datauploads')

// Directory to preload with template files with names <type>-template.txt
def gwasTemplatesDirectory = new File(System.getenv('HOME'), '.grails/transmart-templates')

com.recomdata.dataUpload.templates.dir = gwasTemplatesDirectory.absolutePath
com.recomdata.dataUpload.uploads.dir = gwasUploadsDirectory.absolutePath
com.recomdata.dataUpload.etl.dir = gwasEtlDirectory.absolutePath

[gwasTemplatesDirectory, gwasUploadsDirectory, gwasEtlDirectory].each {
if (!it.exists()) {
it.mkdir()
}
}

/* }}} */
/* {{{ Misc Configuration */

// This can be used to debug JavaScript callbacks in the dataset explorer in
// Chrome. Unfortunately, it also sometimes causes chrome to segfault
com.recomdata.debug.jsCallbacks = 'false'

environments {
production {
com.recomdata.debug.jsCallbacks = 'false'
}
}

grails.resources.adhoc.excludes = [ '/images' + RModules.imageURL + '**' ]

// Adding properties to the Build information panel
buildInfo { properties {
include = [ 'app.grails.version', 'build.groovy' ]
exclude = [ 'env.proc.cores' ]
} }

/* }}} */

/* {{{ Spring Security configuration */

grails { plugin { springsecurity {
// You probably won't want to change these

// customized user GORM class
userLookup.userDomainClassName = 'org.transmart.searchapp.AuthUser'
// customized password field
userLookup.passwordPropertyName = 'passwd'
// customized user /role join GORM class
userLookup.authorityJoinClassName = 'org.transmart.searchapp.AuthUser'
// customized role GORM class
authority.className = 'org.transmart.searchapp.Role'
// request map GORM class name - request map is stored in the db
requestMap.className = 'org.transmart.searchapp.Requestmap'
// requestmap in db
securityConfigType = grails.plugin.springsecurity.SecurityConfigType.Requestmap
// url to redirect after login in
// just_rest branch provides alternative default via org.transmart.defaultLoginRedirect
successHandler.defaultTargetUrl = org.transmart.defaultLoginRedirect ?: '/userLanding'
// logout url
logout.afterLogoutUrl = '/login/forceAuth'

// configurable requestmap functionality in transmart is deprecated
def useRequestMap = false

if (useRequestMap) {
// requestmap in db
securityConfigType = 'Requestmap'
// request map GORM class name - request map is stored in the db
requestMap.className = 'org.transmart.searchapp.Requestmap'
} else {
securityConfigType = 'InterceptUrlMap'
def oauthEndpoints = [
'/oauth/authorize.dispatch': ["isFullyAuthenticated() and (request.getMethod().equals('GET') or request.getMethod().equals('POST'))"],
'/oauth/token.dispatch': ["isFullyAuthenticated() and request.getMethod().equals('POST')"],
]
// This looks dangerous and it possibly is (would need to check), but
// reflects the instructions I got from the developer.
def gwavaMappings = [
'/gwasWeb/**' : ['IS_AUTHENTICATED_ANONYMOUSLY'],
]

interceptUrlMap = [
'/login/**' : ['IS_AUTHENTICATED_ANONYMOUSLY'],
'/css/**' : ['IS_AUTHENTICATED_ANONYMOUSLY'],
'/js/**' : ['IS_AUTHENTICATED_ANONYMOUSLY'],
'/grails-errorhandler' : ['IS_AUTHENTICATED_ANONYMOUSLY'],
'/images/analysisFiles/**' : ['IS_AUTHENTICATED_REMEMBERED'],
'/images/**' : ['IS_AUTHENTICATED_ANONYMOUSLY'],
'/static/**' : ['IS_AUTHENTICATED_ANONYMOUSLY'],
'/search/loadAJAX**' : ['IS_AUTHENTICATED_ANONYMOUSLY'],
'/analysis/getGenePatternFile': ['IS_AUTHENTICATED_ANONYMOUSLY'],
'/analysis/getTestFile' : ['IS_AUTHENTICATED_ANONYMOUSLY'],
'/requestmap/**' : ['ROLE_ADMIN'],
'/role/**' : ['ROLE_ADMIN'],
'/authUser/**' : ['ROLE_ADMIN'],
'/secureObject/**' : ['ROLE_ADMIN'],
'/accessLog/**' : ['ROLE_ADMIN'],
'/authUserSecureAccess/**' : ['ROLE_ADMIN'],
'/secureObjectPath/**' : ['ROLE_ADMIN'],
'/userGroup/**' : ['ROLE_ADMIN'],
'/secureObjectAccess/**' : ['ROLE_ADMIN'],
* : (oauthEnabled ? oauthEndpoints : [:]),
* : (gwavaEnabled ? gwavaMappings : [:]),
'/**' : ['IS_AUTHENTICATED_REMEMBERED'], // must be last
]
rejectIfNoRule = true
}

// Hash algorithm
password.algorithm = 'bcrypt'
// Number of bcrypt rounds
password.bcrypt.logrounds = 14

providerNames = [
'daoAuthenticationProvider',
'anonymousAuthenticationProvider',
'rememberMeAuthenticationProvider',
]

if (oauthEnabled) {
providerNames << 'clientCredentialsAuthenticationProvider'

def securedResourcesFilters = [
'JOINED_FILTERS',
'-securityContextPersistenceFilter',
'-logoutFilter',
'-rememberMeAuthenticationFilter',
'-basicAuthenticationFilter',
'-exceptionTranslationFilter',
].join(',')

filterChain.chainMap = [
'/oauth/token': [
'JOINED_FILTERS',
'-oauth2ProviderFilter',
'-securityContextPersistenceFilter',
'-logoutFilter',
'-rememberMeAuthenticationFilter',
'-exceptionTranslationFilter',
].join(','),
'/studies/**': securedResourcesFilters,
'/observations/**': securedResourcesFilters,
'/patient_sets/**': securedResourcesFilters,
'/oauth/inspectToken': securedResourcesFilters,
'/**': [
'JOINED_FILTERS',
'-statelessSecurityContextPersistenceFilter',
'-oauth2ProviderFilter',
'-clientCredentialsTokenEndpointFilter',
'-basicAuthenticationFilter',
'-oauth2ExceptionTranslationFilter'
].join(','),
]

grails.exceptionresolver.params.exclude = ['password', 'client_secret']

def glowingBearRedirectUris = [
transmartURL - ~/transmart\/$/ + '#/login',
]
if (transmartURL.startsWith('http://localhost:')) {
// for dev, node reverse proxy runs on 8001
glowingBearRedirectUris << 'http://localhost:8001/#/login'
}

oauthProvider {
authorization.requireRegisteredRedirectUri = true
authorization.requireScope = false

clients = [
[
clientId: 'api-client',
clientSecret: 'api-client',
authorities: ['ROLE_CLIENT'],
scopes: ['read', 'write'],
authorizedGrantTypes: ['authorization_code', 'refresh_token'],
redirectUris: [transmartURL + 'oauth/verify']
],

--
Keith Nangle
European Community Fellow
tranSMART Foundation
Cell: +49 151 1563 8609
Skype US: +1 919.647.4741
Skype: klnangle
keith....@transmartfoundation.org

...................................................
Confidentiality Note: This message is intended only for the use of the named recipient(s) and may contain confidential and/or privileged information. If you are not the intended recipient, please contact the sender and delete this message. Any unauthorized use of the information contained in this message is prohibited.

--

Keith Nangle

European Community Fellow

tranSMART Foundation

Cell: +49 151 1563 8609

Skype US: +1 919.647.4741

Skype: klnangle

keith....@transmartfoundation.org

...................................................

Confidentiality Note: This message is intended only for the use of the named recipient(s) and may contain confidential and/or privileged information. If you are not the intended recipient, please contact the sender and delete this message. Any unauthorized use of the information contained in this message is prohibited.

Celia Alvarez

unread,

Nov 18, 2015, 6:00:02 AM11/18/15

to transmart-discuss, celiaalva...@hotmail.com, sup...@transmartfoundation.org

Hello,

I have resolved that problems. I have just deployed tranSMART.

I followed the installation guide https://wiki.transmartfoundation.org/pages/viewpage.action?pageId=6619205

Transmart functions but I haven't uploaded any study (I'm in the step 11).

I try to upload the example study GSE8581 but I obtain the following error:

$ make -C samples/postgres load_clinical_GSE8581

make: *** [datasets] Error 1

Finished fetching datasets

make: se ingresa al directorio `/home/git/transmart-data/samples/postgres'

../common/makefile.inc:42: *** hay varios patrones de objetivos. Alto.

make: se sale del directorio `/home/git/transmart-data/samples/postgres'

If I do: $ sudo make -C samples/postgres load_clinical_GSE8581, I obtain the following:

make: se ingresa al directorio `/home/git/transmart-data/samples/postgres'

Makefile:3: *** You need to set KETTLE_JOBS_PSQL; KETTLE_JOBS has been renamed. Alto.

make: se sale del directorio `/home/git/transmart-data/samples/postgres'

I have defined KETTLE_JOBS_PSQL in vars file.

I don't understand the error, I don't know how I can resolve it for working with tranSMART.

Thanks you very much.

Best regards,

Celia

...

Peter Rice

unread,

Nov 18, 2015, 7:11:59 AM11/18/15

to Celia Alvarez, transmart-discuss, celiaalva...@hotmail.com, sup...@transmartfoundation.org

Hi Celia,

On 18/11/2015 11:00, Celia Alvarez wrote:
> Hello,
> I have resolved that problems. I have just deployed tranSMART.
> I followed the installation guide
> https://wiki.transmartfoundation.org/pages/viewpage.action?pageId=6619205
> Transmart functions but I haven't uploaded any study (I'm in the step 11).
> I try to upload the example study GSE8581 but I obtain the following error:
> |$ make -C samples/postgres load_|clinical_GSE8581

> *make: *** [datasets] Error 1*
> *Finished fetching datasets*
> *make: se ingresa al directorio `/home/git/transmart-data/samples/postgres'*
> *../common/makefile.inc:42: *** hay varios patrones de objetivos. Alto.*
> *make: se sale del directorio `/home/git/transmart-data/samples/postgres'*

I am not familiar with the messages in Spanish, but will try to help...

It appears something is not right in the targets for 'make'

If you have everything configured, when you start to type the make
command line the target should expand when you hit tab, for example
'load_cl' should expand to 'load_clinical_' and then adding 'GSE85'
shoudl expand to 'load_clinical_GSE8581'

If not, then you can update the link to the datasets index:

make update_datasets

this will update the list of available studies in
/home/git/transmart-data/samples/studies/datasets This file is read by
'make' to find the list of load targets.

> If I do: $ sudo |make -C samples/postgres load_|clinical_GSE8581, I
> obtain the following:

> *make: se ingresa al directorio `/home/git/transmart-data/samples/postgres'*
> *Makefile:3: *** You need to set KETTLE_JOBS_PSQL; KETTLE_JOBS has been
> renamed. Alto.*
> *make: se sale del directorio `/home/git/transmart-data/samples/postgres'*
> *
> *

> I have defined KETTLE_JOBS_PSQL in vars file.
> I don't understand the error, I don't know how I can resolve it for
> working with tranSMART.

This one is because sudo starts a new session and has not sourced the
vars file.

regards,

Peter Rice

Celia Alvarez

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Nov 18, 2015, 7:39:36 AM11/18/15

to transmart-discuss, celia....@gmail.com, celiaalva...@hotmail.com, sup...@transmartfoundation.org

Hello,

Thanks for your help.

I have obtain the following error:

make -C samples/studies update_datasets

make[1]: se ingresa al directorio `/home/git/transmart-data/samples/studies'

make[2]: se ingresa al directorio `/home/git/transmart-data/samples/studies'

org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:

General error during conversion: Error grabbing Grapes -- [unresolved dependency: commons-net#commons-net;3.3: not found]

java.lang.RuntimeException: Error grabbing Grapes -- [unresolved dependency: commons-net#commons-net;3.3: not found]

at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)

at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

at java.lang.reflect.Constructor.newInstance(Constructor.java:526)

at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:77)

at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:71)

at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:81)

at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:57)

at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:182)

at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:190)

at groovy.grape.GrapeIvy.getDependencies(GrapeIvy.groovy:420)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.lang.reflect.Method.invoke(Method.java:606)

at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSite.invoke(PogoMetaMethodSite.java:166)

at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:56)

at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:49)

at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:133)

at groovy.grape.GrapeIvy.resolve(GrapeIvy.groovy:565)

at groovy.grape.GrapeIvy$resolve$3.callCurrent(Unknown Source)

at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:49)

at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:133)

at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:153)

at groovy.grape.GrapeIvy.resolve(GrapeIvy.groovy:534)

at groovy.grape.GrapeIvy$resolve$2.callCurrent(Unknown Source)

at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:49)

at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:133)

at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:149)

at groovy.grape.GrapeIvy.grab(GrapeIvy.groovy:251)

at groovy.grape.Grape.grab(Grape.java:163)

at groovy.grape.GrabAnnotationTransformation.visit(GrabAnnotationTransformation.java:360)

at org.codehaus.groovy.transform.ASTTransformationVisitor$3.call(ASTTransformationVisitor.java:319)

at org.codehaus.groovy.control.CompilationUnit.applyToSourceUnits(CompilationUnit.java:923)

at org.codehaus.groovy.control.CompilationUnit.doPhaseOperation(CompilationUnit.java:585)

at org.codehaus.groovy.control.CompilationUnit.processPhaseOperations(CompilationUnit.java:561)

at org.codehaus.groovy.control.CompilationUnit.compile(CompilationUnit.java:538)

at groovy.lang.GroovyClassLoader.doParseClass(GroovyClassLoader.java:286)

at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:259)

at groovy.lang.GroovyShell.parseClass(GroovyShell.java:674)

at groovy.lang.GroovyShell.run(GroovyShell.java:501)

at groovy.lang.GroovyShell.run(GroovyShell.java:491)

at groovy.ui.GroovyMain.processOnce(GroovyMain.java:650)

at groovy.ui.GroovyMain.run(GroovyMain.java:381)

at groovy.ui.GroovyMain.process(GroovyMain.java:367)

at groovy.ui.GroovyMain.processArgs(GroovyMain.java:126)

at groovy.ui.GroovyMain.main(GroovyMain.java:106)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.lang.reflect.Method.invoke(Method.java:606)

at org.codehaus.groovy.tools.GroovyStarter.rootLoader(GroovyStarter.java:106)

at org.codehaus.groovy.tools.GroovyStarter.main(GroovyStarter.java:128)

1 error

make[2]: *** [datasets] Error 1

make[2]: se sale del directorio `/home/git/transmart-data/samples/studies'

make[1]: *** [update_datasets] Error 2

make[1]: se sale del directorio `/home/git/transmart-data/samples/studies'

make: *** [update_datasets] Error 2

Peter Rice

unread,

Nov 18, 2015, 8:14:28 AM11/18/15

to Celia Alvarez, transmart-discuss, celiaalva...@hotmail.com, sup...@transmartfoundation.org

Hi Celia,

On 18/11/2015 12:39, Celia Alvarez wrote:
> Hello,
>
> Thanks for your help.
> I have obtain the following error:
>
> make -C samples/studies update_datasets
> make[1]: se ingresa al directorio `/home/git/transmart-data/samples/studies'
> make[2]: se ingresa al directorio `/home/git/transmart-data/samples/studies'
> org.codehaus.groovy.control.MultipleCompilationErrorsException: startup
> failed:
> General error during conversion: Error grabbing Grapes -- [unresolved
> dependency: commons-net#commons-net;3.3: not found]

What version of groovy are you running? There is a smal groovy script
used to parse the datasets_index file

Try:

groovy --version

and send the result.

regards,

Peter

Celia Alvarez

unread,

Nov 18, 2015, 8:20:42 AM11/18/15

to transmart-discuss, celiaalva...@hotmail.com, sup...@transmartfoundation.org

Hi,

Groovy Version: 2.3.3 JVM: 1.7.0_91 Vendor: Oracle Corporation OS: Linux

Thanks you.

El martes, 17 de noviembre de 2015, 11:18:15 (UTC+1), Keith Nangle escribió:

...

Gustavo Lopes

unread,

Nov 18, 2015, 10:00:24 AM11/18/15

to transmar...@googlegroups.com, celia....@gmail.com, celiaalva...@hotmail.com, sup...@transmartfoundation.org

On 18-11-2015 13:39, Celia Alvarez wrote:
>
> Thanks for your help.
> I have obtain the following error:
>
> make -C samples/studies update_datasets
> make[1]: se ingresa al directorio `/home/git/transmart-data/samples/studies'
> make[2]: se ingresa al directorio `/home/git/transmart-data/samples/studies'
> org.codehaus.groovy.control.MultipleCompilationErrorsException: startup
> failed:
> General error during conversion: Error grabbing Grapes -- [unresolved
> dependency: commons-net#commons-net;3.3: not found]
>
> java.lang.RuntimeException: Error grabbing Grapes -- [unresolved
> dependency: commons-net#commons-net;3.3: not found]
> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native

Maybe you have some firewall in the way and need to configure a proxy.
You can use _JAVA_OPTIONS for this, e.g.w with:

export _JAVA_OPTIONS="-Dhttp.proxyHost=<proxy server address here>
-Dhttp.proxyPort=<proxy port here>"

--
Gustavo Lopes

Celia Alvarez

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Nov 19, 2015, 3:39:41 AM11/19/15

to transmart-discuss, sup...@transmartfoundation.org

Hello,

Thanks you, but I obtain the same message:

$ make -C samples/postgres load_clinical_GSE8581

Fetching datasets...

Picked up _JAVA_OPTIONS

org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:

General error during conversion: Error grabbing Grapes -- [unresolved dependency: commons-net#commons-net;3.3: not found]

java.lang.RuntimeException: Error grabbing Grapes -- [unresolved dependency: commons-net#commons-net;3.3: not found]

make: *** [datasets] Error 1

Finished fetching datasets

make: se ingresa al directorio `/home/git/transmart-data/samples/postgres'

../common/makefile.inc:44: *** hay varios patrones de objetivos. Alto.

make: se sale del directorio `/home/git/transmart-data/samples/postgres'

What could I do?

Regards,

Celia

Celia Alvarez

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Nov 20, 2015, 11:10:38 AM11/20/15

to transmart-discuss

Hello,
My tool correctly functions. I have already uploaded the example study, I had some errors in some dependencies.
Thanks your help.

Regards,
Celia.

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