That seems to be the problem. I disconnected from the network and it ran just fine - no errors.
Can anyone tell me the syntax for running the helloanyone.wfbundle example? Thanks. On Sat, Jul 9, 2016 at 2:02 AM Stian Soiland-Reyes <[email protected]> wrote: > 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 > > > > >>> > > > > >> > > > > > > > > > >
