I'm trying to write a Java application that uses the JournalParser to extract authors, citations, etc. from journal articles. The documentation for the GrobidJournalParser gives instructions for the command line app and for TikaServer. I need to point to Grobid running somewhere other than localhost:8080. I have a GrobidExtractor.properties file containing the correct URL on my classpath, but it doesn't seem to get found - I get an error because it's trying to access Grobid on localhost:8080.
WARNING: Interceptor for {http://localhost:8080/processHeaderDocument}WebClient has thrown exception, unwinding now
org.apache.cxf.interceptor.Fault: No message body writer has been found for class org.apache.cxf.jaxrs.ext.multipart.MultipartBody, ContentType: multipart/form-data
at org.apache.cxf.jaxrs.client.WebClient$BodyWriter.doWriteBody(WebClient.java:1220)
Is there some other way to tell Tika or the JournalParser where to find Grobid? The Javadocs were not helpful in this regard.
As explained in the documentation on using GROBID with Tika, if you want to configure Tika to use an alternate GROBID server you do so with a file named org/apache/tika/parser/journal/GrobidExtractor.properties
You have only called yours GrobidExtractor.properties, which is why it isn't being picked up. The full path is required
Assuming you're using Linux, using the Tika app, and with the GROBID properties in the current directory, you'd need to fix it with something like:
mkdir -p org/apache/tika/parser/journal
mv GrobidExtractor.properties org/apache/tika/parser/journal/
java -classpath .:tika-app-1.13.jar org.apache.tika.cli.TikaCLI --metadata journal.pdf
Related
I tried running the example command on Mac from the command line, but it fails to run. I'm wondering what file is not found. My desktop directory does, in fact, exist. Am I missing some configuration or something?
I just downloaded all the dcm4che-5.12.0 code and sample scripts and executed the command from the example when using the --help option.
The example command is what I tried, and is shown in the attached screenshot. I'm not sure what is missing, and it's not exactly clear.
Any guidance will be appreciated, thanks!
According to the documentation, you have to provide a file and not a directory name to the --dicomdir option (with two "-" by the way):
--dicomdir <file> specify path to a DICOMDIR file of
a DICOM File-set into which
received objects are stored and
from which requested objects are
retrieved
Actually, the example from the documentation reads as follows:
Example: dcmqrscp -b DCMQRSCP:11112 --dicomdir /media/cdrom/DICOMDIR
=> Starts server listening on port 11112, accepting association requests
with DCMQRSCP as called AE title.
i am trying run the websphere liberty profile server from the command line. I am following the steps told here : https://developer.ibm.com/wasdev/downloads/liberty-profile-using-non-eclipse-environments/
I have created the server with the name server1.
But when the extraction completes and I try to start the server using the command : server start server1
the server throws an error : CWWKE0054E: Unable to open file C:\wlp\wlp\usr\servers\server1\logs\C:\Users\Furquan\AppData\Local\Temp\\ihp_custom_batches.log.. Now I know this cant be a valid path, but I dont know where and how to change it. Please help !!
This error is related to the LOG_FILE environment variable that you have defined in your environment by some other program. To solve that, you have the following opions:
Remove LOG_FILE env variable, if it is no longer needed by your system
If you cant do that, override it via server.env file, that you can create in the wlp\usr\servers\serverName directory with the following content:
LOG_FILE=console.log
As last resort (this is not recommended, will make your installation NOT SUPPORTED and in certain installations might get overwritten by updates) - modify the server.bat command line script - in the script find the following section:
if not defined LOG_FILE (
set X_LOG_FILE=console.log
) else (
set X_LOG_FILE=!LOG_FILE!
)
And after the line set X_LOG_FILE=!LOG_FILE! just add another line that will override it with the default like this set X_LOG_FILE=console.log
In general, I'd recommend second solution (with the server.env file), as it is the most portable and will work in any environment.
I have the similar problem for IBM Support Assistant V5. After I deleted %LOG_FILE% from Environment Variables, it worked.
I keep having some weird problems. The main one is that I keep getting the following error when trying to add a WSDL to a new project:
Error loading [https://.../token?wsdl]: java.lang.Exception: Failed to load url; https://.../token?wsdl, 0 -
Here's the message recorded in the error.log file:
java.lang.Exception: Failed to load url; https://.../token?wsdl, 0 -
at com.eviware.soapui.impl.wsdl.support.wsdl.UrlWsdlLoader.load(UrlWsdlLoader.java:184)
at com.eviware.soapui.impl.wsdl.support.wsdl.WsdlLoader.loadXmlObject(WsdlLoader.java:121)
at com.eviware.soapui.impl.wsdl.support.xsd.SchemaUtils.getDefinitionParts(SchemaUtils.java:535)
at com.eviware.soapui.impl.wsdl.support.xsd.SchemaUtils.getDefinitionParts(SchemaUtils.java:524)
at com.eviware.soapui.impl.support.definition.support.AbstractDefinitionCache.update(AbstractDefinitionCache.java:97)
at com.eviware.soapui.impl.support.definition.support.AbstractDefinitionContext$Loader.construct(AbstractDefinitionContext.java:226)
at com.eviware.soapui.support.swing.SwingWorkerDelegator.construct(SwingWorkerDelegator.java:46)
at com.eviware.soapui.support.swing.SwingWorker$2.run(SwingWorker.java:149)
at java.lang.Thread.run(Unknown Source)
I verified that the application at that URL is up and running, and I can get to the WSDL from a web browser, but I keep getting this error message no matter what. I am using SoapUI 4.5.0 (32-bit) on a Windows 7 box. I've also tried the 64-bit version with the same results. It happens whether I am on VPN or not.
Do you know why I might be getting this error?
I have had the same problem. I resolved it by disabling the proxy in the SoapUI preferences.
(source : http://www.eviware.com/forum/viewtopic.php?f=13&t=12460)
In my case the server were the service was installed was configured only for TLS. SSL was not allowed. So you have to update SoapUI vmoptions file by adding the server TLS version
-Dsoapui.https.protocols=TLSv1.2
You can find vmoptions file under SoapUI installation folder:
C:\Program Files (x86)\SmartBear\SoapUI-5.0.0\bin\soapUI-5.0.0.vmoptions
I have had similar problems and worked around them by saving the WSDL locally. Don't forget to save any XSD files as well. You may need to edit the WSDL to specify an appropriate location for XSDs.
I got this error when trying to load a WebService implemented in MS Dynamics AX. Because I was connecting via VPN to my network, something went wrong with IPv6 settings. After Googling, I found the solution here: http://support.microsoft.com/kb/929852
In my case the
Error loading [https://.../token?wsdl]: java.lang.Exception: Failed to load url; https://.../token?wsdl, 0
was caused by fake certificate.
If you get the following in browser
"There is a problem with this website’s security certificate."
this is the case.
The resolution was to import a certificate to
C:\Program Files (x86)\SmartBear\SoapUI-5.0.0\jre\lib\security\cacerts
Which is default java used by SOAPUI
This could be a problem with IPV6 address SOAP UI picking. Adding the following JVM option fixed it for me:
-Djava.net.preferIPv4Stack=true
I added it here:
C:\Program Files\SmartBear\soapUI-4.5.2\bin\soapUI-4.5.2.vmoptions
Inside the wsdl file look for the import element, which looks like this :
`<import namespace="nameSpaceValue" location="Users/myname/.../targetxsdName.xsd"/>`
Change the location attribute in the above element to the location of your xsd files stored locally, and it should work.
The following solution helped me:
-Djsse.enableSNIExtension=false
In SoapUI-5.3.0.vmoptions.
This error is due to an erroneous schemaLocation in the WSDL file.
Indicate the correct location (either path on the disk or xsd url) of the xsd file in the wsdl file
exp
<xsd:import namespace="http://xyz:8080/" schemaLocation="http://172.17.16.53:9080/auth/authorizationBS?xsd=1"></xsd:import>
I had this issue when trying to use a SOCKS proxy. It appears that SoapUI does not support SOCKS proxys. I am using the Boomerang Chrome app instead.
I had this error and in my case, the problem was that I was using "localhost" in the URL.
I resolved that changing the localhost word for the respective IP, (Windows + R -> cmd -> ipconfig) then read the IP and write it to the URL replacing the "localhost" word
Close and reopen soapui. Probably is a bug of the application
Update SoapUI version to SoapUI 5.5.0. This error causes when I tried to load wsdl, because of old SoapUI version
If you are running your Web Application with the default port of 8080, please try to change the port to some other value and run your application again and trigger again your SOAPUI request. As you might have history projects in your SOAP UI workspace with port number 8080, might create issues.
My solution was to modify the java.security file:
\SoapUI-5.3.0\jre\lib\security\java.security
Comment code syntax:
#jdk.certpath.disabledAlgorithms=MD2, DSA, RSA keySize < 2048
#jdk.certpath.disabledAlgorithms=MD2, RSA keySize < 1024
For java version above 1.8,
Use below command to setup soapUI jar
java -jar --add-modules java.xml.bind --add-modules java.xml.ws <path for jar file+jar file name.jar>
I get the following error:
org.dbpedia.spotlight.exceptions.ConfigurationException: Cannot find spotter file ../dist/src/deb/control/data/usr/share/dbpedia-spotlight/spotter.dict
at org.dbpedia.spotlight.model.SpotterConfiguration.<init>(SpotterConfiguration.java:54)
at org.dbpedia.spotlight.model.SpotlightConfiguration.<init>(SpotlightConfiguration.java:143)
at org.dbpedia.spotlight.web.rest.Server.main(Server.java:70)
Usage:
java -jar dbpedia-spotlight.jar org.dbpedia.spotlight.web.rest.Server [config file]
or:
mvn scala:run "-DaddArgs=[config file]"
Quick solution:
wget http://spotlight.dbpedia.org/download/release-0.5/dbpedia-spotlight-quickstart.zip
unzip dbpedia-spotlight-quickstart.zip
cd dbpedia-spotlight-quickstart/
./run.sh
Explanation:
DBpedia Spotlight looks for ~3.5M things of ~320 types in text and tries to disambiguate them to their global unique identifiers in DBpedia. Therefore it needs data files to accompany its jar. A minuscule example is distributed along with the source, but for real use cases you may need the larger files. After you've downloaded the files, you need to modify the configuration in server.properties with the correct path to the files. The error message you got tells you that one of the necessary files (spotter.dict) could not be found in the path you indicated in your server.properties.
More information available here:
https://github.com/dbpedia-spotlight/dbpedia-spotlight/wiki/Run-from-a-JAR
Please see the passage "RMI Registry Issue" of this article for the background on Java Update 1.6.0_29 first.
If I understand correctly (I'm german), the update introduces a bug in the rmiregistry which fails to work with the file: pattern in the codebase.
I.E. the following won't work any more with 1.6.0_29:
-Djava.rmi.server.codebase="file:myproject/bin/ ..."
We are currently using the feature of having a codebase with file: syntax. Does anyone know a workaround for making this work?
Note: No, we do not want to start a local webserver or ftp server.
Update:
On Naming.bind this exception is thrown:
java.rmi.ServerException: RemoteException occurred in server thread; nested exception is:
java.rmi.UnmarshalException: error unmarshalling arguments; nested exception is:
java.lang.ClassNotFoundException: access to class loader denied
at sun.rmi.server.UnicastServerRef.oldDispatch(UnicastServerRef.java:400)
at sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:248)
at sun.rmi.transport.Transport$1.run(Transport.java:159)
at java.security.AccessController.doPrivileged(Native Method)
I had the same problem, and can confirm that downgrading JDK to earlier version solves the problem. I know, it's not a solution you're looking for, but at least it makes it to work.
Take running in windows as an example:
Step 1. In C:\Users\Jimmy.java.policy (create it if not exist), append below content:
grant { permission java.security.AllPermission; };
Of course "C:\Users\Jimmy\" is the user home, please change to your home accordingly.
Adding AllPermission is just for quick resolving your issue. you'd better config a more accurate FilePermission here.
Step 2. Start rmiregistry:
C:\JDK\bin>rmiregistry -J-Djava.rmi.server.codebase=file://C:/workspaces/MyLab/target/classes/
(Please note codebase must ended with "/")
Step 3. Run your server and client program.
References:
http://docs.oracle.com/javase/7/docs/technotes/guides/rmi/codebase.html
http://docs.oracle.com/javase/7/docs/technotes/guides/security/spec/security-spec.doc3.html
http://docs.oracle.com/javase/7/docs/technotes/guides/rmi/enhancements-7.html
It looks like there is no workaround because it is a bug, so wait for the fix
See details at
https://bugzilla.redhat.com/show_bug.cgi?id=751203
Code fix
http://icedtea.classpath.org/hg/icedtea6/rev/67df573b0734
If you do not need dynamic code downloading (in which case you can use ftp codebase) the solution is simply to set CLASSPATH environment variable to the path to your jar file:
Windows:
set CLASSPATH="path_to_jarfile"
Linux (batch):
CLASSPATH="path_to_jarfile"
export CLASSPATH
Best place to do it is in some script that invokes the RMI server.
Setting class path in the command line (-cp option) when starting RMI server does not help because it does not affect rmiregistry classpath!
If you start the rmiregistry in the working directory of your project, it works.
So essentially working directory of your project and current directory for rmiregistry should be same.
I recently encountered this issue as well. I can confirm that when using the file: protocol the rmiregistry must either:
be started in the root of the directory containing the shared classes; or
set the classpath to point to the shared classes or shared class jar; or
use a protocol other than file:// (I set up ngnix and served the jar from that).
Maybe not what you want, but you could resolve this with classpath rather than codebase. The client JVM will work fine if you add the required classes to its classpath. If you are using the file: URL scheme, then the classes must already be available on the localhost.
I had the same problem but I couldn't change the JDK version. Turns out you can solve it by running/starting the rmiregistry from the same directory as your code base, which in my case was target/classes. So cd project/target/classes and then run rmiregistry &