Thanks for checking. I think the "content is not allowed" is coming from Jena when opening or closing the (implicit) workflow bundle when it is reading the manifest 's @context. It should in theory read it from the class path cache instead of the internet, but this being within OSGi the class path might not include the cache file.
Could you try with your network disconnected and see if the warning is the same or if you get a network error? (The helloworld workflow itself does not require internet, so this should in theory work) On 8 Jul 2016 6:11 p.m., "Gale Naylor" <[email protected]> wrote: > Yes, the workflow created the Hello_World_output folder with the greeting > file inside it, which I was then able to write to the console using the > "type" command. So, it looks like it worked, in spite of the error. > > This is the content of the Hello_World.rdf file. (I opened in in Atom.) I'm > not that familiar with XML; does anyone see any extraneous characters?: > > <?xml version="1.0" encoding="UTF-8" standalone="yes"?> > <rdf:RDF xmlns="http://ns.taverna.org.uk/2010/scufl2#"; xmlns:rdf=" > http://www.w3.org/1999/02/22-rdf-syntax-ns#"; xmlns:rdfs=" > http://www.w3.org/2000/01/rdf-schema#"; xmlns:xsi=" > http://www.w3.org/2001/XMLSchema-instance"; xsi:type="WorkflowDocument" > xml:base="Hello_World/" xsi:schemaLocation=" > http://ns.taverna.org.uk/2010/scufl2# > http://ns.taverna.org.uk/2010/scufl2/scufl2.xsd > http://www.w3.org/1999/02/22-rdf-syntax-ns# > http://ns.taverna.org.uk/2010/scufl2/rdf.xsd";> > <Workflow rdf:about=""> > <name>Hello_World</name> > <workflowIdentifier rdf:resource=" > > http://ns.taverna.org.uk/2010/workflow/8781d5f4-d0ba-48a8-a1d1-14281bd8a917/ > "/> > <outputWorkflowPort> > <OutputWorkflowPort rdf:about="out/greeting"> > <name>greeting</name> > </OutputWorkflowPort> > </outputWorkflowPort> > <processor> > <Processor rdf:about="processor/hello/"> > <name>hello</name> > <outputProcessorPort> > <OutputProcessorPort > rdf:about="processor/hello/out/value"> > <name>value</name> > <portDepth rdf:datatype=" > http://www.w3.org/2001/XMLSchema#integer";>0</portDepth> > <granularPortDepth rdf:datatype=" > http://www.w3.org/2001/XMLSchema#integer";>0</granularPortDepth> > </OutputProcessorPort> > </outputProcessorPort> > <iterationStrategyStack> > <IterationStrategyStack > rdf:about="processor/hello/iterationstrategy/"/> > </iterationStrategyStack> > </Processor> > </processor> > <datalink> > <DataLink > rdf:about="datalink?from=processor/hello/out/value&to=out/greeting"> > <receiveFrom rdf:resource="processor/hello/out/value"/> > <sendTo rdf:resource="out/greeting"/> > </DataLink> > </datalink> > </Workflow> > </rdf:RDF> > > > On Fri, Jul 8, 2016 at 8:23 AM Ian Dunlop <[email protected]> wrote: > > > 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 > > > >>> > > > >> > > > > > >
