Hello, The content not allowed in prolog error usually means there is as xml parsing issue with the workflow and that the start of the file has some extraneous characters. I wonder what it means here. Did you get an output from the workflow? The log says it can be found here: Outputs will be saved to the directory: C:\src\_RC3_CL\apache-taverna-commandline-3.1.0-incubating\ taverna-commandline-product\target\apache-taverna- commandline-3.1.0-incubating\Hello_World_output
Cheers, Ian On 7 July 2016 at 19:54, Gale Naylor <[email protected]> wrote: > Update: I ran the example hello world workflow several times without an > issue (other than the "Content is not allowed..." error), but now I am > getting the log4j warnings: > > > C:\src\_RC3_CL\apache-taverna-commandline-3.1.0-incubating\taverna-commandline-product\target\apache-taverna-commandline-3.1.0-incubating>executeworkflow.bat > examples\helloworld.wfbundle > log4j:WARN No appenders could be found for logger > (org.springframework.beans.factory.support.DefaultListableBeanFactory). > log4j:WARN Please initialize the log4j system properly. > log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for > more info. > log4j:WARN No appenders could be found for logger > > (org.springframework.osgi.service.importer.support.OsgiServiceProxyFactoryBean). > log4j:WARN No appenders could be found for logger > > (org.springframework.osgi.extender.internal.dependencies.startup.DependencyServiceManager). > log4j:WARN Please initialize the log4j system properly. > log4j:WARN No appenders could be found for logger > > (org.springframework.osgi.service.importer.support.OsgiServiceCollectionProxyFactoryBean). > log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for > more info. > log4j:WARN Please initialize the log4j system properly. > log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for > more info. > log4j:WARN Please initialize the log4j system properly. > log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for > more info. > Outputs will be saved to the directory: > > C:\src\_RC3_CL\apache-taverna-commandline-3.1.0-incubating\taverna-commandline-product\target\apache-taverna-commandline-3.1.0-incubating\Hello_World_output > ERROR 2016-07-07 11:46:45,132 (org.apache.jena.riot:84) - [line: 1, col: 1 > ] Content is not allowed in prolog. > Workflow completed. > > > > On Thu, Jul 7, 2016 at 11:39 AM Gale Naylor <[email protected]> > wrote: > > > Although the helloworld.wfbundle example gave me an error, it did work. > > For Windows the command is "type Hello_World_output\greeting". I'll > update > > the README. > > > > Gale > > > > On Thu, Jul 7, 2016 at 10:42 AM Gale Naylor <[email protected] > > > > wrote: > > > >> Hello all, > >> > >> I tried running the helloworld.wfbundle example in Windows 10 (Version > >> 10.0.10586) using cmd.exe and got an error: > >> > >> ERROR 2016-07-07 09:27:41,603 (org.apache.jena.riot:84) - [line: 1, col: > >> 1 ] Content is not allowed in prolog. > >> > >> I then tried running the helloanyone.wfbundle example. When I ran it > >> without an input, I got an error that it expected 'Name", but when I > tried > >> entering a name in singe quotes, I still got an error (see below). I > also > >> tried the command with no quotation marks at all (log4j errors) and with > >> double quotation marks (similar/same error as with singe quotes). > >> > >> Is there a step I'm missing? > >> > >> Thanks, > >> Gale > >> > >> > >> HELLOANYONE ERRORS: input = 'Gale' > >> > >> C:\src\_RC3_CL\apache-taverna-commandline-3.1.0-incubating\ > >> taverna-commandline-product\target\apache-taverna- > >> commandline-3.1.0-incubating>executeworkflow.bat > >> examples/helloanyone.wfbundle 'Gale' > >> > >> ERROR 2016-07-07 09:58:28,042 > >> > (org.springframework.osgi.extender.internal.activator.ContextLoaderListener:52) > >> - Application context refresh failed > >> > (OsgiBundleXmlApplicationContext(bundle=org.apache.taverna.commandline.taverna-commandline-common, > >> config=osgibundle:/META-INF/spring/*.xml)) > >> org.springframework.beans.factory.BeanCreationException: Error creating > >> bean with name 'commandLineTool' defined in URL > >> > [bundle://127.0:0/META-INF/spring/taverna-commandline-common-context.xml]: > >> Invocation of init method failed; nested exception is > >> java.lang.reflect.UndeclaredThrowableException > >> at > >> > org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1420) > >> (more error text available) > >> > >> ------------------------------------ > >> > >> HELLOANYONE ERRORS when input does not match expected input > >> > >> ********************************* > >> *** input without single quotes > >> > >> > C:\src\_RC3_CL\apache-taverna-commandline-3.1.0-incubating\taverna-commandline-product\target\apache-taverna-commandline-3.1.0-incubating>executeworkflow.bat > >> examples/helloanyone.wfbundle Gale > >> > >> log4j:WARN No appenders could be found for logger > >> > (org.springframework.osgi.extender.internal.dependencies.startup.DependencyServiceManager). > >> log4j:WARN No appenders could be found for logger > >> > (org.springframework.osgi.service.dependency.internal.DefaultMandatoryDependencyManager). > >> log4j:WARN No appenders could be found for logger > >> > (org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor). > >> log4j:WARN Please initialize the log4j system properly. > >> log4j:WARN No appenders could be found for logger > >> > (org.springframework.osgi.service.importer.support.OsgiServiceProxyFactoryBean). > >> log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig > for > >> more info. > >> log4j:WARN Please initialize the log4j system properly. > >> log4j:WARN Please initialize the log4j system properly. > >> log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig > for > >> more info. > >> log4j:WARN Please initialize the log4j system properly. > >> log4j:WARN See > >> http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info. > >> log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig > for > >> more info. > >> ERROR 2016-07-07 10:01:59,775 > >> > (org.springframework.osgi.extender.internal.activator.ContextLoaderListener:52) > >> - Application context refresh failed > >> > (OsgiBundleXmlApplicationContext(bundle=org.apache.taverna.commandline.taverna-commandline-common, > >> config=osgibundle:/META-INF/spring/*.xml)) > >> org.springframework.beans.factory.BeanCreationException: Error creating > >> bean with name 'commandLineTool' defined in URL > >> > [bundle://127.0:0/META-INF/spring/taverna-commandline-common-context.xml]: > >> Invocation of init method failed; nested exception is > >> java.lang.reflect.UndeclaredThrowableException > >> at > >> > org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1420) > >> > >> ************************************ > >> **** input using double quotes > >> > >> > C:\src\_RC3_CL\apache-taverna-commandline-3.1.0-incubating\taverna-commandline-product\target\apache-taverna-commandline-3.1.0-incubating>executeworkflow.bat > >> examples/helloanyone.wfbundle "Gale" > >> > >> ERROR 2016-07-07 10:15:48,443 > >> > (org.springframework.osgi.extender.internal.activator.ContextLoaderListener:52) > >> - Application context refresh failed > >> > (OsgiBundleXmlApplicationContext(bundle=org.apache.taverna.commandline.taverna-commandline-common, > >> config=osgibundle:/META-INF/spring/*.xml)) > >> org.springframework.beans.factory.BeanCreationException: Error creating > >> bean with name 'commandLineTool' defined in URL > >> > [bundle://127.0:0/META-INF/spring/taverna-commandline-common-context.xml]: > >> Invocation of init method failed; nested exception is > >> java.lang.reflect.UndeclaredThrowableException > >> at > >> > org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1420) > >> > >> > >> ------------------------------------ > >> HELLOANYONE ERRORS: (no input) - included for completeness only > >> > >> > C:\src\_RC3_CL\apache-taverna-commandline-3.1.0-incubating\taverna-commandline-product\target\apache-taverna-commandline-3.1.0-incubating>executeworkflow.bat > >> examples/helloanyone.wfbundle > >> > >> ERROR 2016-07-07 09:57:24,177 > >> (org.apache.taverna.commandline.CommandLineTool:417) - The number of > inputs > >> provided does not match the number of input ports. > >> 1 inputs were expected which are: > >> 'name' > >> 0 inputs were provided > >> org.apache.taverna.commandline.exceptions.InputMismatchException: The > >> number of inputs provided does not match the number of input ports. > >> 1 inputs were expected which are: > >> 'name' > >> 0 inputs were provided > >> at > >> > org.apache.taverna.commandline.data.InputsHandler.checkProvidedInputs(InputsHandler.java:105) > >> at > >> > org.apache.taverna.commandline.CommandLineTool.setupAndExecute(CommandLineTool.java:246) > >> at > >> > org.apache.taverna.commandline.CommandLineTool.run(CommandLineTool.java:109) > >> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > >> at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) > >> at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown > Source) > >> at java.lang.reflect.Method.invoke(Unknown Source) > >> at > >> > org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeCustomInitMethod(AbstractAutowireCapableBeanFactory.java:1544) > >> at > >> > org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1485) > >> at > >> > org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1417) > >> at > >> > org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:519) > >> at > >> > org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456) > >> at > >> > org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:291) > >> at > >> > org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222) > >> at > >> > org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:288) > >> at > >> > org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:190) > >> at > >> > org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:580) > >> at > >> > org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:895) > >> at > >> > org.springframework.osgi.context.support.AbstractDelegatedExecutionApplicationContext.access$1600(AbstractDelegatedExecutionApplicationContext.java:62) > >> at > >> > org.springframework.osgi.context.support.AbstractDelegatedExecutionApplicationContext$4.run(AbstractDelegatedExecutionApplicationContext.java:327) > >> at > >> > org.springframework.osgi.util.internal.PrivilegedUtils.executeWithCustomTCCL(PrivilegedUtils.java:87) > >> at > >> > org.springframework.osgi.context.support.AbstractDelegatedExecutionApplicationContext.completeRefresh(AbstractDelegatedExecutionApplicationContext.java:292) > >> at > >> > org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$CompleteRefreshTask.run(DependencyWaiterApplicationContextExecutor.java:138) > >> at java.lang.Thread.run(Unknown Source) > >> The number of inputs provided does not match the number of input ports. > >> 1 inputs were expected which are: > >> 'name' > >> 0 inputs were provided > >> <end of error output> > >> > >> On Thu, Jul 7, 2016 at 2:01 AM Stian Soiland-Reyes <[email protected]> > >> wrote: > >> > >>> On 7 July 2016 at 09:29, Chamini Prashakthi Jayasinghe > >>> <[email protected]> wrote: > >>> > Can we run taverna command line module in windows 10.if yes please > >>> explain > >>> > >>> Yes, Windows 10 was explicitly tested for the 3.1.0 release. > >>> > >>> If you have downloaded from > >>> https://taverna.incubator.apache.org/download/commandline/ > >>> > >>> Then follow the README from > >>> > >>> > >>> > https://github.com/apache/incubator-taverna-commandline/blob/master/README.md#prerequisites > >>> > >>> > >>> First of all you will need to install JDK 8 for Windows x64 (or for > >>> x86 if you have an older machine): > >>> > >>> > >>> > http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html > >>> > >>> then Apache Maven > >>> > >>> https://maven.apache.org/download.cgi > >>> > >>> > >>> After which you can run > >>> > >>> mvn clean install > >>> > >>> within the unpacked taverna-commandline folder. > >>> > >>> > >>> Note that the README mentions: > >>> > >>> > If you are building on Windows, ensure you unpack this source code to > >>> a folder with a short path name lenght, e.g.C:\src - as Windows has a > >>> limitation on the total path length which might otherwise prevent this > code > >>> from building successfully. > >>> > >>> > >>> After building, see > >>> > >>> > https://github.com/apache/incubator-taverna-commandline/blob/master/README.md#running > >>> > >>> on how to run it. > >>> > >>> > >>> > >>> We would welcome suggestions on how to improve these build > >>> instructions in the README and/or website. :) > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> -- > >>> Stian Soiland-Reyes > >>> Apache Taverna (incubating), Apache Commons > >>> http://orcid.org/0000-0001-9842-9718 > >>> > >> >
