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 > > >>> > > >> > > >
