Re: newbie question: can't get annotationViewer.sh working...
Hi, There are multiple tools that come with UIMA. It may be there's some confusion about which tool does what. Your first note led me to believe you were running the "UIMA DocumentAnalyzer" tool. That tool is the one which has the OutputDirectory, etc. This note leads me to believe you are running the "UIMA Annotation Viewer". That tool indeed, has the fields you describe in your last note. Its function is to take as input, a directory already populated with xmi files to view. Please try running the "UIMA DocumentAnalyzer" tool, which has the "Output Directory" field, and set that to some writable directory, and see if you get things to run. Then look in that output directory and see if there are .xmi files there. -Marshall On 4/6/2018 3:56 PM, Andrew Logue wrote: > Hi Marshall, > > I tried running the annotationViewer as root and got the same behaviour as I'm > getting as a regular user. > > When I run it I only see the following on screen: > - input and browse button for "Input Directory" > - input and browse button for "TypeSystem or AE Descriptor File" > - a single View button at the bottom. > > It is interesting that I don't see any UI elements for the Output directory as > mentioned. > I had noticed the screen-shot in "tutorials_and_user_guides.html" didn't match > what I see > but thought it was simply a case of the software getting ahead of the > documentation. Now > I'm not so sure. > > After clicking the View button the Analyzed Documents window pops up listing > the xml files > but I cannot locate any *.xmi files nor a directory called "processed". > > Thanks, > Andrew. > > On 2018/04/05 22:47:28, Andrew Logue wrote: > > Hello,> > > > > I'd like to evaluate UIMA for an upcoming project but am having problems > > > trying the examples with annotationViewer.sh.> > > > > It is throwing an error dialog: "java.lang.NumberFormatException: null" > > > when I double click on any of the sample files in the Analyzed> > > Documents window (for example, New_IBM_Fellows.xml).> > > > > I'll paste the partial error message below but is there anywhere else > > > for me to look and try to narrow down the problem on my system?> > > > > I'm using Arch Linux with Sun Java version "1.8.0_162".> > > > > I am able to build from source but am also having the same problem with > > > the binary tarballs. (2.10.2, 2.10.3, and 3.0.0)> > > > > [alogue@freedom bin]$ ./annotationViewer.sh> > > java.lang.NumberFormatException: null> > > at java.lang.Integer.parseInt(Integer.java:542)> > > at java.lang.Integer.parseInt(Integer.java:615)> > > at > > > > org.apache.uima.cas.impl.XmiSerializationSharedData.addOutOfTypeSystemElement(XmiSerializationSharedData.java:202)> > > > at > > > > org.apache.uima.cas.impl.XmiCasDeserializer$XmiCasDeserializerHandler.addToOutOfTypeSystemData(XmiCasDeserializer.java:2015)> > > > at > > > > org.apache.uima.cas.impl.XmiCasDeserializer$XmiCasDeserializerHandler.readFS(XmiCasDeserializer.java:519)> > > > at > > > > org.apache.uima.cas.impl.XmiCasDeserializer$XmiCasDeserializerHandler.startElement(XmiCasDeserializer.java:435)> > > > at > > > > org.apache.uima.util.XmlCasDeserializer$XmlCasDeserializerHandler.startElement(XmlCasDeserializer.java:148)> > > > at > > > > com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(AbstractSAXParser.java:509)> > > > at > > > > com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.scanStartElement(XMLNSDocumentScannerImpl.java:374)> > > > at > > > > com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2784)> > > > at > > > > com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:602)> > > > at > > > > com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:112)> > > > at > > > > com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:505)> > > > at > > > > com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:842)> > > > at > > > > com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:771)> > > > > > > > > Regards,> > > > > Andrew.> > > > > >
Re: newbie question: can't get annotationViewer.sh working...
Hi Marshall, I tried running the annotationViewer as root and got the same behaviour as I'm getting as a regular user. When I run it I only see the following on screen: - input and browse button for "Input Directory" - input and browse button for "TypeSystem or AE Descriptor File" - a single View button at the bottom. It is interesting that I don't see any UI elements for the Output directory as mentioned. I had noticed the screen-shot in "tutorials_and_user_guides.html" didn't match what I see but thought it was simply a case of the software getting ahead of the documentation. Now I'm not so sure. After clicking the View button the Analyzed Documents window pops up listing the xml files but I cannot locate any *.xmi files nor a directory called "processed". Thanks, Andrew. On 2018/04/05 22:47:28, Andrew Logue wrote: > Hello,> > > I'd like to evaluate UIMA for an upcoming project but am having problems > > trying the examples with annotationViewer.sh.> > > It is throwing an error dialog: "java.lang.NumberFormatException: null" > > when I double click on any of the sample files in the Analyzed> > Documents window (for example, New_IBM_Fellows.xml).> > > I'll paste the partial error message below but is there anywhere else > > for me to look and try to narrow down the problem on my system?> > > I'm using Arch Linux with Sun Java version "1.8.0_162".> > > I am able to build from source but am also having the same problem with > > the binary tarballs. (2.10.2, 2.10.3, and 3.0.0)> > > [alogue@freedom bin]$ ./annotationViewer.sh> > java.lang.NumberFormatException: null> > at java.lang.Integer.parseInt(Integer.java:542)> > at java.lang.Integer.parseInt(Integer.java:615)> > at > > org.apache.uima.cas.impl.XmiSerializationSharedData.addOutOfTypeSystemElement(XmiSerializationSharedData.java:202)> > at > > org.apache.uima.cas.impl.XmiCasDeserializer$XmiCasDeserializerHandler.addToOutOfTypeSystemData(XmiCasDeserializer.java:2015)> > at > > org.apache.uima.cas.impl.XmiCasDeserializer$XmiCasDeserializerHandler.readFS(XmiCasDeserializer.java:519)> > at > > org.apache.uima.cas.impl.XmiCasDeserializer$XmiCasDeserializerHandler.startElement(XmiCasDeserializer.java:435)> > at > > org.apache.uima.util.XmlCasDeserializer$XmlCasDeserializerHandler.startElement(XmlCasDeserializer.java:148)> > at > > com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(AbstractSAXParser.java:509)> > at > > com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.scanStartElement(XMLNSDocumentScannerImpl.java:374)> > at > > com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2784)> > at > > com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:602)> > at > > com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:112)> > at > > com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:505)> > at > > com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:842)> > at > > com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:771)> > > > > Regards,> > > Andrew.> > >
Re: newbie question: can't get annotationViewer.sh working...
Hi, sorry you're having troubles. The error message seems to indicate a failure of the viewer to be able to read the results. Here are some things to look at. When you run thd document analyzer, it should put up a "configuration" screen that has a field for an OutputDirectory. Can you check to see that field specifies some directory which is writable by you? After running the document analyzer (which from your note, appears to run OK) instead of trying to view the analysis results, can you instead go to that OutputDirectory, and see what's in it. It should have 8 files of type ".xmi" (not .xml). Open the New_IBM_Fellows.txt.xmi file, for example. It should have a long line, having something like this: http://www.omg.org/XMI"; xmlns:examples="http:///org/apache/uima/examples.ecore"; xmlns:tutorial="http:///org/apache/uima/tutorial.ecore"; xmlns:tcas="http:///uima/tcas.ecore"; xmlns:cas="http:///uima/cas.ecore"; xmlns:tokenizer="http:///org/apache/uima/examples/tokenizer.ecore"; xmi:version="2.0"> etc. Let us know if you can see this data. -Marshall On 4/5/2018 6:47 PM, Andrew Logue wrote: > Hello, > > I'd like to evaluate UIMA for an upcoming project but am having problems > trying the examples with annotationViewer.sh. > > It is throwing an error dialog: "java.lang.NumberFormatException: null" when I > double click on any of the sample files in the Analyzed > Documents window (for example, New_IBM_Fellows.xml). > > I'll paste the partial error message below but is there anywhere else for me > to look and try to narrow down the problem on my system? > > I'm using Arch Linux with Sun Java version "1.8.0_162". > > I am able to build from source but am also having the same problem with the > binary tarballs. (2.10.2, 2.10.3, and 3.0.0) > > [alogue@freedom bin]$ ./annotationViewer.sh > java.lang.NumberFormatException: null > at java.lang.Integer.parseInt(Integer.java:542) > at java.lang.Integer.parseInt(Integer.java:615) > at > org.apache.uima.cas.impl.XmiSerializationSharedData.addOutOfTypeSystemElement(XmiSerializationSharedData.java:202) > at > org.apache.uima.cas.impl.XmiCasDeserializer$XmiCasDeserializerHandler.addToOutOfTypeSystemData(XmiCasDeserializer.java:2015) > at > org.apache.uima.cas.impl.XmiCasDeserializer$XmiCasDeserializerHandler.readFS(XmiCasDeserializer.java:519) > at > org.apache.uima.cas.impl.XmiCasDeserializer$XmiCasDeserializerHandler.startElement(XmiCasDeserializer.java:435) > at > org.apache.uima.util.XmlCasDeserializer$XmlCasDeserializerHandler.startElement(XmlCasDeserializer.java:148) > at > com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(AbstractSAXParser.java:509) > at > com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.scanStartElement(XMLNSDocumentScannerImpl.java:374) > at > com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2784) > at > com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:602) > at > com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:112) > at > com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:505) > at > com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:842) > at > com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:771) > > > Regards, > > Andrew. > >
newbie question: can't get annotationViewer.sh working...
Hello, I'd like to evaluate UIMA for an upcoming project but am having problems trying the examples with annotationViewer.sh. It is throwing an error dialog: "java.lang.NumberFormatException: null" when I double click on any of the sample files in the Analyzed Documents window (for example, New_IBM_Fellows.xml). I'll paste the partial error message below but is there anywhere else for me to look and try to narrow down the problem on my system? I'm using Arch Linux with Sun Java version "1.8.0_162". I am able to build from source but am also having the same problem with the binary tarballs. (2.10.2, 2.10.3, and 3.0.0) [alogue@freedom bin]$ ./annotationViewer.sh java.lang.NumberFormatException: null at java.lang.Integer.parseInt(Integer.java:542) at java.lang.Integer.parseInt(Integer.java:615) at org.apache.uima.cas.impl.XmiSerializationSharedData.addOutOfTypeSystemElement(XmiSerializationSharedData.java:202) at org.apache.uima.cas.impl.XmiCasDeserializer$XmiCasDeserializerHandler.addToOutOfTypeSystemData(XmiCasDeserializer.java:2015) at org.apache.uima.cas.impl.XmiCasDeserializer$XmiCasDeserializerHandler.readFS(XmiCasDeserializer.java:519) at org.apache.uima.cas.impl.XmiCasDeserializer$XmiCasDeserializerHandler.startElement(XmiCasDeserializer.java:435) at org.apache.uima.util.XmlCasDeserializer$XmlCasDeserializerHandler.startElement(XmlCasDeserializer.java:148) at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(AbstractSAXParser.java:509) at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.scanStartElement(XMLNSDocumentScannerImpl.java:374) at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2784) at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:602) at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:112) at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:505) at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:842) at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:771) Regards, Andrew.
