SWORD API: Submitting a dataset with terms when custom dataset terms is disabled results in nondescript command line error and null ptr log error.

[kcondon]

When attempting to create a dataset using the SWORD api with rights/terms defined in the atom file, the command fails with a generic error and with a null ptr server log entry:

<sword:error xmlns="http://www.w3.org/2005/Atom" href="http://purl.org/net/sword/error/ErrorBadRequest" xmlns:sword="http://purl.org/net/sword/terms/">

<title>ERROR</title> 2022-04-05T18:58:03Z

problem calling importXML: javax.ejb.EJBException

Processing failed

[2022-04-05T18:58:03.895+0000] [Payara 5.2021.5] [WARNING] [AS-EJB-00056] [javax.enterprise.ejb.container] [tid: _ThreadID=84 _ThreadName=http-thread-pool::http-listener-1(2)] [timeMillis: 1649185083895] [levelValue: 900] [[
A system exception occurred during an invocation on EJB ImportGenericServiceBean, method: public void edu.harvard.iq.dataverse.api.imports.ImportGenericServiceBean.importXML(java.lang.String,java.lang.String,edu.harvard.iq.dataverse.DatasetVersion)]]

[2022-04-05T18:58:03.895+0000] [Payara 5.2021.5] [WARNING] [] [javax.enterprise.ejb.container] [tid: _ThreadID=84 _ThreadName=http-thread-pool::http-listener-1(2)] [timeMillis: 1649185083895] [levelValue: 900] [[

javax.ejb.EJBException
at com.sun.ejb.containers.EJBContainerTransactionManager.processSystemException(EJBContainerTransactionManager.java:723)
at com.sun.ejb.containers.EJBContainerTransactionManager.completeNewTx(EJBContainerTransactionManager.java:652)
at com.sun.ejb.containers.EJBContainerTransactionManager.postInvokeTx(EJBContainerTransactionManager.java:482)
at com.sun.ejb.containers.BaseContainer.postInvokeTx(BaseContainer.java:4592)
at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2125)
at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2095)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:220)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandlerDelegate.invoke(EJBLocalObjectInvocationHandlerDelegate.java:90)
at com.sun.proxy.$Proxy340.importXML(Unknown Source)
at edu.harvard.iq.dataverse.api.imports.EJB31_Generated__ImportGenericServiceBean__Intf____Bean.importXML(Unknown Source)
at edu.harvard.iq.dataverse.api.datadeposit.CollectionDepositManagerImpl.createNew(CollectionDepositManagerImpl.java:118)
at org.swordapp.server.CollectionAPI.post(CollectionAPI.java:142)
at edu.harvard.iq.dataverse.api.datadeposit.SWORDv2CollectionServlet.doPost(SWORDv2CollectionServlet.java:45)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:665)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:750)
at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1636)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:331)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:211)
at org.glassfish.tyrus.servlet.TyrusServletFilter.doFilter(TyrusServletFilter.java:282)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:253)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:211)
at org.ocpsoft.rewrite.servlet.RewriteFilter.doFilter(RewriteFilter.java:226)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:253)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:211)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:257)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:161)
at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:757)
at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:577)
at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:99)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:158)
at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:371)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:238)
at com.sun.enterprise.v3.services.impl.ContainerMapper$HttpHandlerCallable.call(ContainerMapper.java:520)
at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:217)
at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:182)
at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:156)
at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:218)
at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:95)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:260)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:177)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:109)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:88)
at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:53)
at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:524)
at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:89)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:94)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$100(WorkerThreadIOStrategy.java:33)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:114)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:569)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:549)
at java.base/java.lang.Thread.run(Thread.java:829)
Caused by: java.lang.NullPointerException
at edu.harvard.iq.dataverse.util.json.JsonParser.parseLicense(JsonParser.java:396)
at edu.harvard.iq.dataverse.util.json.JsonParser.parseDatasetVersion(JsonParser.java:348)
at edu.harvard.iq.dataverse.api.imports.ImportGenericServiceBean.importXML(ImportGenericServiceBean.java:106)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.glassfish.ejb.security.application.EJBSecurityManager.runMethod(EJBSecurityManager.java:588)
at org.glassfish.ejb.security.application.EJBSecurityManager.invoke(EJBSecurityManager.java:408)
at com.sun.ejb.containers.BaseContainer.invokeBeanMethod(BaseContainer.java:4826)
at com.sun.ejb.EjbInvocation.invokeBeanMethod(EjbInvocation.java:665)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:834)
at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:615)
at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.doCall(SystemInterceptorProxy.java:163)
at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.aroundInvoke(SystemInterceptorProxy.java:140)
at jdk.internal.reflect.GeneratedMethodAccessor278.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:888)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:833)
at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:615)
at org.jboss.weld.module.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:72)
at org.jboss.weld.module.ejb.SessionBeanInterceptor.aroundInvoke(SessionBeanInterceptor.java:52)
at jdk.internal.reflect.GeneratedMethodAccessor276.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:888)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:833)
at com.sun.ejb.containers.interceptors.InterceptorManager.intercept(InterceptorManager.java:375)
at com.sun.ejb.containers.BaseContainer.__intercept(BaseContainer.java:4798)
at com.sun.ejb.containers.BaseContainer.intercept(BaseContainer.java:4786)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:212)
... 44 more
]]

[pdurbin]

I just wanted to add that to reproduce this on the 8551-sword-license branch (fa9ac6e, PR #8558) you can use the new "testCustomTerms" test in SwordIT to reproduce this if you first disable custom terms like this:

curl -X PUT -d false http://localhost:8080/api/admin/settings/:AllowCustomTermsOfUse

Here's the stacktrace I'm seeing (similar to above):

[2022-04-05T14:56:22.932-0400] [Payara 5.2021.5] [WARNING] [AS-EJB-00056] [javax.enterprise.ejb.container] [tid: _ThreadID=117 _ThreadName=http-thread-pool::http-listener-1(3)] [timeMillis: 1649184982932] [levelValue: 900] [[
A system exception occurred during an invocation on EJB ImportGenericServiceBean, method: public void edu.harvard.iq.dataverse.api.imports.ImportGenericServiceBean.importXML(java.lang.String,java.lang.String,edu.harvard.iq.dataverse.DatasetVersion)]]

[2022-04-05T14:56:22.933-0400] [Payara 5.2021.5] [WARNING] [] [javax.enterprise.ejb.container] [tid: _ThreadID=117 _ThreadName=http-thread-pool::http-listener-1(3)] [timeMillis: 1649184982933] [levelValue: 900] [[

javax.ejb.EJBException
...
at com.sun.proxy.$Proxy421.importXML(Unknown Source)
at edu.harvard.iq.dataverse.api.imports.EJB31_Generated__ImportGenericServiceBean__Intf____Bean.importXML(Unknown Source)
at edu.harvard.iq.dataverse.api.datadeposit.CollectionDepositManagerImpl.createNew(CollectionDepositManagerImpl.java:118)
at org.swordapp.server.CollectionAPI.post(CollectionAPI.java:142)
at edu.harvard.iq.dataverse.api.datadeposit.SWORDv2CollectionServlet.doPost(SWORDv2CollectionServlet.java:45)
...
Caused by: java.lang.NullPointerException
at edu.harvard.iq.dataverse.util.json.JsonParser.parseLicense(JsonParser.java:396)
at edu.harvard.iq.dataverse.util.json.JsonParser.parseDatasetVersion(JsonParser.java:348)
at edu.harvard.iq.dataverse.api.imports.ImportGenericServiceBean.importXML(ImportGenericServiceBean.java:106)

[pdurbin]

at edu.harvard.iq.dataverse.util.json.JsonParser.parseLicense(JsonParser.java:396)

Since what's null is licenseService in the code below...

        if (licenseNameOrUri == null){
            boolean safeDefaultIfKeyNotFound = true;
            if (settingsService.isTrueForKey(SettingsServiceBean.Key.AllowCustomTermsOfUse, safeDefaultIfKeyNotFound)){
                return null;
            } else {
                return licenseService.getDefault();
            }
        }

... something like this might fix it:

$ git diff
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/imports/ImportGenericServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/api/imports/ImportGenericServiceBean.java
index bd7975835e..7b4193cb1c 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/imports/ImportGenericServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/imports/ImportGenericServiceBean.java
@@ -13,6 +13,7 @@ import edu.harvard.iq.dataverse.MetadataBlockServiceBean;
 import edu.harvard.iq.dataverse.api.dto.*;  
 import edu.harvard.iq.dataverse.api.dto.FieldDTO;
 import edu.harvard.iq.dataverse.api.dto.MetadataBlockDTO;
+import edu.harvard.iq.dataverse.license.LicenseServiceBean;
 import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
 import edu.harvard.iq.dataverse.util.StringUtil;
 import edu.harvard.iq.dataverse.util.json.JsonParseException;
@@ -67,6 +68,9 @@ public class ImportGenericServiceBean {
     @EJB
     SettingsServiceBean settingsService;
 
+    @EJB
+    LicenseServiceBean licenseService;
+
     @PersistenceContext(unitName = "VDCNet-ejbPU")
     private EntityManager em;
     
@@ -103,7 +107,7 @@ public class ImportGenericServiceBean {
             logger.fine(json);
             JsonReader jsonReader = Json.createReader(new StringReader(json));
             JsonObject obj = jsonReader.readObject();
-            DatasetVersion dv = new JsonParser(datasetFieldSvc, blockService, settingsService).parseDatasetVersion(obj, datasetVersion);
+            DatasetVersion dv = new JsonParser(datasetFieldSvc, blockService, settingsService, licenseService).parseDatasetVersion(obj, datasetVersion);
         } catch (XMLStreamException ex) {
             //Logger.getLogger("global").log(Level.SEVERE, null, ex);
             throw new EJBException("ERROR occurred while parsing XML fragment  ("+xmlToParse.substring(0, 64)+"...); ", ex);

---

Update: Actually, it might be better to completely remove this constructor without LicenseServiceBean...

public JsonParser(DatasetFieldServiceBean datasetFieldSvc, MetadataBlockServiceBean blockService,
        SettingsServiceBean settingsService {
    this.datasetFieldSvc = datasetFieldSvc;
    this.blockService = blockService;
    this.settingsService = settingsService;
}

... in favor of the one that does have LicenseServiceBean (5 more cases like the change above):

public JsonParser(DatasetFieldServiceBean datasetFieldSvc, MetadataBlockServiceBean blockService, 
        SettingsServiceBean settingsService, LicenseServiceBean licenseService) {
    this.datasetFieldSvc = datasetFieldSvc;
    this.blockService = blockService;
    this.settingsService = settingsService;
    this.licenseService = licenseService;
}

[mreekie]

sprint:

• 5.10.1 testing turned this up.
• It's unclear why this failure occurred.
• we are in this area. we should fix it while we are here.
• Stephen says this may be solved. May work in dev since 5.10.1
• Phil did some investigation. May need to pass in a bean.
  Small