I used the example code "Using WebEnv & QueryKey example" from http://www.ncbi.nlm.nih.gov/books/NBK55696/ - the ESearch part seems to work fine, but not EFetch. I added the command "e.printStackTrace()" to get the full error message:
WebEnv: NCID_1_160921978_130.14.18.34_9001_1392822285_1227953195
QueryKey: 1
org.apache.axis2.AxisFault: org.apache.axis2.databinding.ADBException: Unexpected subelement {http://www.ncbi.nlm.nih.gov/soap/eutils/efetch_pubmed}Affiliation
org.apache.axis2.AxisFault: org.apache.axis2.databinding.ADBException: Unexpected subelement {http://www.ncbi.nlm.nih.gov/soap/eutils/efetch_pubmed}Affiliation
at org.apache.axis2.AxisFault.makeFault(AxisFault.java:430)
at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub.fromOM(EFetchPubmedServiceStub.java)
at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub.run_eFetch(EFetchPubmedServiceStub.java:190)
at preparation.Client.main(Client.java:39)
Caused by: java.lang.Exception: org.apache.axis2.databinding.ADBException: Unexpected subelement {http://www.ncbi.nlm.nih.gov/soap/eutils/efetch_pubmed}Affiliation
at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub$AuthorType$Factory.parse(EFetchPubmedServiceStub.java:47561)
at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub$AuthorListType$Factory.parse(EFetchPubmedServiceStub.java:12284)
at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub$ArticleType$Factory.parse(EFetchPubmedServiceStub.java)
at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub$MedlineCitationType$Factory.parse(EFetchPubmedServiceStub.java:27035)
at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub$PubmedArticleType$Factory.parse(EFetchPubmedServiceStub.java:17841)
at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub$PubmedArticleSetChoiceE$Factory.parse(EFetchPubmedServiceStub.java)
at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub$PubmedArticleSet_type0$Factory.parse(EFetchPubmedServiceStub.java:54143)
at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub$EFetchResult$Factory.parse(EFetchPubmedServiceStub.java:48494)
... 3 more
Caused by: org.apache.axis2.databinding.ADBException: Unexpected subelement {http://www.ncbi.nlm.nih.gov/soap/eutils/efetch_pubmed}Affiliation
at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub$AuthorType$Factory.parse(EFetchPubmedServiceStub.java:47555)
... 10 more
I am using Eclipse (Version: 3.7.2) with Ubuntu 12.04 LTS and java-7-openjdk-amd64 as JRE. The NCBI page mentions to use this command before runnning Client.java:
wsdl2java -uri http://eutils.ncbi.nlm.nih.gov/soap/v2.0/efetch_pubmed.wsdl
Instead of that, I simply included the jar files (only binaries) that have been shown as output in console, because this worked fine for all other exapmles on http://www.ncbi.nlm.nih.gov/books/NBK55696/ except the ELink example:
org.apache.axis2.AxisFault: org.apache.axis2.databinding.ADBException: Unexpected subelement {http://www.ncbi.nlm.nih.gov/soap/eutils/elink}error
I will describe which jar files I included in my project.
As the FTP link for downloading eutils_axis2.jar on the above mentioned page did not work, I searched for the current path and added it to my Eclipse project.
Their README says that JDK version 7.0.45 and Axis2 version 1.6.2 should be used and that it was released in December 2013.
I searched for "download wsdl2java.sh" in Google to get the Axis2 version in connection to WSDL and found the package axis2-eclipse-service-plugin-1.6.2.zip . I downloaded the package and added all jar files to my project:
apache-mime4j-core-0.7.2.jar
axiom-api-1.2.13.jar
axiom-impl-1.2.13.jar
axis2-adb-1.6.2.jar
axis2-codegen-1.6.2.jar
axis2-kernel-1.6.2.jar
commons-codec-1.3.jar
commons-fileupload-1.2.jar
commons-httpclient-3.1.jar
geronimo-jta_1.1_spec-1.1.jar
geronimo-ws-metadata_2.0_spec-1.1.2.jar
jaxen-1.1.1.jar
jsr311-api-1.0.jar
neethi-3.0.2.jar
servlet-api-2.3.jar
woden-api-1.0M9.jar
woden-impl-commons-1.0M9.jar
woden-impl-dom-1.0M9.jar
wsdl4j-1.6.2.jar
XmlSchema-1.4.7.jar
Then I searched the packages for the remaining error messages:
axis2-transport-http-1.6.2.jar
axis2-transport-local-1.6.2.jar
commons-logging-1.1.3.jar
geronimo-javamail_1.4_spec-1.7.1.jar
httpcore-4.3.2.jar
I searched for similar cases with Google, but I did not find a solution. How can I fix this message mentioned at the beginning?
The corresponding wsdl file mentioned in the NCBI tutorial is from 2010. Maybe it is outdated, but first, be sure that creating the specified java classes works fine. Do the following steps result in an error?
Download and extract axis2-1.6.2.
Set the environment variables
export AXIS2_HOME=<path/to/axis2-1.6.2>
export JAVA_HOME=<path/to/java-7-openjdk-amd64>
Download the following files
http://eutils.ncbi.nlm.nih.gov/soap/v2.0/efetch_pubmed.xsd
http://eutils.ncbi.nlm.nih.gov/soap/v2.0/efetch_db_pubmed.xsd
http://eutils.ncbi.nlm.nih.gov/soap/v2.0/efetch_pubmed.wsdl
and execute bin/wsdl2java.sh within the axis2-1.6.2 directory using the efetch_pubmed.wsdl file.
sh wsdl2java.sh -uri <path/to/efetch_pubmed.wsdl>
Two java classes should appear in
src/gov/nih/nlm/ncbi/www/soap/eutils
(still in your axis/bin directory). Import and use these files with your Client.java (pointing to the filename in the tutorial).
Works fine for me. Hope that helps.
Related
I have a project in java. Which was currently running in Tomcat-7, JAVA-8 and postgres-9.3. I updated it to openjdk-11 and postgres-13 and tried to deploy it in tomcat9, but it is giving this error.
javax.servlet.ServletException: java.lang.NoSuchMethodError: 'java.lang.Object
org.apache.jasper.runtime.PageContextImpl.proprietaryEvaluate(java.lang.String, java.lan$
at org.apache.jasper.runtime.PageContextImpl.handlePageException(PageContextImpl.java:666)
at org.apache.jsp.layout1_jsp._jspService(Unknown Source)
at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:71)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:733)
I have tried solutions like playing with versions of jar in my WEB-INF/lib folder, but didn't work.
Also tried this and this solutions.
You should clean the $CATALINA_BASE/work directory of your Tomcat installation. You clearly have *.java and *.class files there which were compiled with the Tomcat 7 version of Jasper.
Before deleting the files, stop Tomcat.
This should solve your NoSuchMethodError, but the exception that triggered this message is still in your JSP. As remarked by Scary Wombat, you should consider using only EL expressions and JSTL tags in your JSP pages.
I'm currently wasting my time trying to figure out why WAS won't load my EAR and why said EAR have problem.
Context:
One of my colleague updated a version of a jar and then my m2e seem to have not picked up and was giving thousand of error (was working fine before)
I tried to check if it was Nexus (work fine). My encrypted password in the setting.xml (work fine).
I decided to try maven from the command line, everything worked fine there to.
When I tried again in RAD (IBM eclipse) everything was now ok, no more error.
I then proceeded to put the generated EAR in my websphere server via add and remove project and I get multiple error when I try to start the server with that ear. (see below)
I though that because it was compiled via maven cmd prompt, I might have compiled with the wrong jvm or something so I deleted my maven repo (.m2 in the user) and try to get the jar via m2e in RAD only.
It's worked until I started the server with the new EAR and got the same set of error.
Any idea on what to do to get rid of these error and have a healthy server.
Here some of the error:
[11/10/17 12:08:51:994 EST] 00000075 annotation W
com.ibm.ws.webcontainer.annotation.WASAnnotationHelper collectClasses
SRVE8000W: Skipped class that failed to initialize for annotation
scanning.
java.lang.ClassNotFoundException: org.springframework.web.servlet.tags.form.SelectTag at
java.lang.Class.forNameImpl(Native Method) at
java.lang.Class.forName(Class.java:219) ...
[11/10/17 12:09:00:282 EST] 00000075 wtp W
org.eclipse.jst.j2ee.commonarchivecore.internal.strategy.TempZipFile
clearTempFile Failed to delete temporary file [
C:\IBM\WebSphere\AppServer-x86\profiles\chris_pro\wstemp\appdepl15fa68a2a21\AuthRenfClientWeb-2.0.26.war2406380505527260260.tmp
] [11/10/17 12:09:00:433 EST] 00000075 SinglePathCla E WSVR0120E: An
error occurred processing com.mycom.bla.testalive.TestAliveServlet
java.io.FileNotFoundException:
C:\IBM\WebSphere\AppServer-x86\profiles\chris_pro\wstemp\appdepl15fa68a2a21\Client-1.61.5-SNAPSHOT.jar6655053587500024283.tmp
(The system cannot find the file specified.) ...
SRVE0266E: Error occured while initializing servlets: {0}
javax.servlet.UnavailableException: SRVE0203E: Servlet [SecurityManager]:
com.mycom.bla.pres.request.http.HttpSecurityManagerServlet was found,
but is missing another required class. SRVE0206E: This error typically
implies that the servlet was originally compiled with classes which
cannot be located by the server. SRVE0187E: Check your class path to
ensure that all classes required by the servlet are present.SRVE0210I:
This problem can be debugged by recompiling the servlet using only the
classes in the application's runtime class path SRVE0234I: Application
class
There are steps for building .jar file of SimGrid.
I downloaded archive from here.
Then I made following
cmake -DCMAKE_INSTALL_PREFIX=/home/Documents/simgrid -Denable_maintainer_mode=off -Denable_compile_optimizations=off -Denable_java=on -Denable_model-checking=off
make
make check
100% tests passed, 0 tests failed out of 586
ctest
100% tests passed, 0 tests failed out of 586
make install
There is simgrid.jar in SimGrid-3.13 folder.
But when I write code I can't load classes from this .jar file.
How can I fix it?
UPDATED
If I download ready simgrid.jar from thence, error occurs
Exception in thread "main" java.lang.UnsatisfiedLinkError: /tmp/simgrid-java2166199247712718748/libsimgrid.so: libcgraph.so.6: cannot open shared object file: No such file or directory
Where I have to add libsimgrid-java.so, libsimgrid.so?
UPDATED2
After installing graphviz graphviz-dev. New error occurs
Invalid XML (XML input line 2, state 2): Bad declaration <!DOCTYPE platform SYSTEM "http://simgrid.gforge.inria.fr/simgrid.dtd">.
If your are using a XML v3 file (check the version attribute in <platform>), please update it with tools/simgrid_update_xml.pl
[0.000000] /builds/workspace/SimGrid-Multi/build_mode/Debug/node/simgrid-ubuntu-trusty-64/build/SimGrid-3.13/src/surf/xml/surfxml_sax_cb.cpp:55: [surf_parse/ERROR] Parse error at (null):2: Parse error in /home/ken/IdeaProjects/Sim2Sim/src/main/java/LHCb/platform.xml
[0.000000] /builds/workspace/SimGrid-Multi/build_mode/Debug/node/simgrid-ubuntu-trusty-64/build/SimGrid-3.13/src/surf/xml/surfxml_sax_cb.cpp:57: [xbt/CRITICAL] Exiting now
As for the second update, you should read the error message that you copy-pasted:
If your are using a XML v3 file (check the version attribute in <platform>), please update it with tools/simgrid_update_xml.pl
Can you confirm that:
(1) the version attribute in the <platform> is 3
(2) running the tools/simgrid_update_xml.pl script on the platform fixes the problem?
I just checked the Debian package search page, in the second search box. I looked for /usr/lib/libcgraph.so.6 and it says that this library is in the package libcgraph6. So you have to apt-get install libcgraph6 to get it.
I have been trying to use a home grown test tool and after doing an update to Centos 6.4, I am no longer able to run the tcl based tool. I am getting the following error and I have no internet access on this server. Kindly advise how do I solve this problem?
Thanks
"XpUtils::iload -d /usr/local/testtool/repo/package/linux-glibc2.3-x86_64/lib/tcljava1.4.1 tclblend" failed:
couldn't load file "/usr/local/testtool/repo/package/linux-glibc2.3-x86_64/lib/tcljava1.4.1/libtclblend.so": libjava.so: cannot open shared object file: No such file or directory
while executing
"error "\"XpUtils::iload -d $dir tclblend\" failed:\n $errMsg""
(procedure "loadtclblend" line 168)
invoked from within
"loadtclblend /usr/local/testtool/repo/package/linux-glibc2.3-x86_64/lib/tcljava1.4.1"
("package ifneeded java 1.4.1" script)
invoked from within
"package require java"
("eval" body line 1)
invoked from within
"eval package require $pkg"
("foreach" body line 2)
invoked from within
"foreach pkg $pkgList {
set ::${pkg}Version [eval package require $pkg]
}"
(file "/usr/local/testtool/testtool" line 165)
If you read the error message trace, you'll see that it says that this is all caused by:
libjava.so: cannot open shared object file: No such file or directory
The first steps would then be to ensure that you've got a version of Java actually installed, to check that it includes the file libjava.so, and that the file has been indexed by the system shared library catalog.
It might also be worth checking that all its dependencies are also present and that you've got the architecture for the Tcl library and the Java library matched (e.g., both 32-bit) as those can cause odd failures when they go wrong.
I'm trying to deploy a WAR in GF V3 that has CXF as a dependency and I get the following exception:
[#|2011-02-08T07:34:15.736-0800|WARNING|oracle-glassfish3.0.1|javax.enterprise.system.container.web.com.sun.enterprise.web|_ThreadID=32;_ThreadName=http-thread-pool-8080-(2);|StandardWrapperValve[MyServlet]: PWC1406: Servlet.service() for servlet MyServlet threw exception
com.sun.xml.ws.util.ServiceConfigurationError: com.sun.xml.ws.api.pipe.TransportPipeFactory: Provider com.sun.enterprise.jbi.serviceengine.bridge.transport.JBITransportPipeFactory is specified in bundle://254.0:0/META-INF/services/com.sun.xml.ws.api.pipe.TransportPipeFactory but not found
at com.sun.xml.ws.util.ServiceFinder.fail(ServiceFinder.java:241)
at com.sun.xml.ws.util.ServiceFinder.access$100(ServiceFinder.java:141)
at com.sun.xml.ws.util.ServiceFinder$LazyIterator.next(ServiceFinder.java:376)
at com.sun.xml.ws.api.pipe.TransportTubeFactory.create(TransportTubeFactory.java:129)
at com.sun.xml.ws.transport.DeferredTransportPipe.<init>(DeferredTransportPipe.java:82)
at com.sun.xml.ws.api.pipe.ClientTubeAssemblerContext.createTransportTube(ClientTubeAssemblerContext.java:311)
at com.sun.xml.ws.assembler.jaxws.TransportTubeFactory.createTube(TransportTubeFactory.java:62)
at com.sun.xml.ws.assembler.TubeCreator.createTube(TubeCreator.java:77)
at com.sun.xml.ws.assembler.TubelineAssemblerFactoryImpl$MetroTubelineAssembler.createClient(TubelineAssemblerFactoryImpl.java:121)
at com.sun.xml.ws.client.Stub.createPipeline(Stub.java:224)
at com.sun.xml.ws.client.Stub.<init>(Stub.java:201)
at com.sun.xml.ws.client.Stub.<init>(Stub.java:174)
at com.sun.xml.ws.client.sei.SEIStub.<init>(SEIStub.java:81)
at com.sun.xml.ws.client.WSServiceDelegate.createEndpointIFBaseProxy(WSServiceDelegate.java:602)
at com.sun.xml.ws.client.WSServiceDelegate.getPort(WSServiceDelegate.java:344)
at com.sun.xml.ws.client.WSServiceDelegate.getPort(WSServiceDelegate.java:326)
at com.sun.xml.ws.client.WSServiceDelegate.getPort(WSServiceDelegate.java:308)
at javax.xml.ws.Service.getPort(Service.java:99)
at com.mycompany.myapp.webserviceclient.SomeWebserviceService.getSomeWebservicePort(SomeWebserviceService.java:58)
This sorta indicates to me that there is a bundle in my WAR\lib directory that is causing problems, but when I expand the WAR and do a search on META-INF\services I do not find anything that is close what is outlined in the exception.
I originally had CXF and it's transitive dependencies in the war\lib dir, but I've since removed that and still encounter the same error.
Nothing useful comes up when searching google and I'm at a loss here.
Does anyone know what might be going on here?
EDIT #1
Another symptom of this is that the tester pages for deployed web services will not work properly.
I had a similar problem with my glassfish3.1. Below is a stack trace
Caused by: com.sun.xml.ws.util.ServiceConfigurationError: com.sun.xml.ws.api.pipe.TransportPipeFactory: Provider com.sun.enterprise.jbi.serviceengine.bridge.transport.JBITransportPipeFactory is specified in bundle://96.0:0/META-INF/services/com.sun.xml.ws.api.pipe.TransportPipeFactory but not found
at com.sun.xml.ws.util.ServiceFinder.fail(ServiceFinder.java:245)
at com.sun.xml.ws.util.ServiceFinder.access$100(ServiceFinder.java:145)
at com.sun.xml.ws.util.ServiceFinder$LazyIterator.next(ServiceFinder.java:380)
at com.sun.xml.ws.api.pipe.TransportTubeFactory.create(TransportTubeFactory.java:133)
at com.sun.xml.ws.transport.DeferredTransportPipe.<init>(DeferredTransportPipe.java:86)
at com.sun.xml.ws.api.pipe.ClientTubeAssemblerContext.createTransportTube(ClientTubeAssemblerContext.java:315)
at com.sun.xml.ws.assembler.jaxws.TransportTubeFactory.createTube(TransportTubeFactory.java:67)
at com.sun.xml.ws.assembler.TubeCreator.createTube(TubeCreator.java:84)
at com.sun.xml.ws.assembler.TubelineAssemblerFactoryImpl$MetroTubelineAssembler.createClient(TubelineAssemblerFactoryImpl.java:130)
at com.sun.xml.ws.client.Stub.createPipeline(Stub.java:228)
at com.sun.xml.ws.client.Stub.<init>(Stub.java:205)
at com.sun.xml.ws.client.Stub.<init>(Stub.java:178)
at com.sun.xml.ws.client.sei.SEIStub.<init>(SEIStub.java:85)
at com.sun.xml.ws.client.WSServiceDelegate.createEndpointIFBaseProxy(WSServiceDelegate.java:608)
at com.sun.xml.ws.client.WSServiceDelegate.getPort(WSServiceDelegate.java:348)
at com.sun.xml.ws.client.WSServiceDelegate.getPort(WSServiceDelegate.java:330)
at com.sun.xml.ws.client.WSServiceDelegate.getPort(WSServiceDelegate.java:312)
at javax.xml.ws.Service.getPort(Service.java:134)
at org.glassfish.webservices.monitoring.WebServiceTesterServlet.initializePort(WebServiceTesterServlet.java:563)
at org.glassfish.webservices.monitoring.WebServiceTesterServlet.doGet(WebServiceTesterServlet.java:169)
at org.glassfish.webservices.monitoring.WebServiceTesterServlet.invoke(WebServiceTesterServlet.java:104)
at org.glassfish.webservices.EjbWebServiceServlet.service(EjbWebServiceServlet.java:114)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:848)
at com.sun.grizzly.http.servlet.ServletAdapter$FilterChainImpl.doFilter(ServletAdapter.java:1002)
... 20 more
The problem was traced to the conflicting mappings for "com.sun.xml.ws.api.pipe.TransportPipeFactory" inside two different modules.
prompt> grep -rl com.sun.xml.ws.api.pipe.TransportPipeFactory /usr/local/glassfish-3.1/glassfish/domains/modules*
modules/webservices-osgi.jar
modules/sun-javaee-engine.jar
prompt> grep -rl com.sun.enterprise.jbi.serviceengine.bridge.transport.JBITransportPipeFactory /usr/local/glassfish-3.1/glassfish/domains/modules/*
modules/sun-javaee-engine.jar
Clearly, the required file was sitting in the wrong jar "sun-javaee-engine.jar".
Above, "sun-javaee-engine.jar" is loaded by the "Java EE Service Engine Module". Once I removed the module (using glassfish update tool) everything started working fine.
EDIT #1:
Here is how to remove the module using the update tool on the Unix command line:
sudo ./pkg uninstall sun-javaee-engine