search

bio-ontology-research-group / aberowl-meta

Install script and sub-directories for AberOWL
http://aber-owl.net/
Apache License 2.0
2 stars 1 forks source link

After installing as per Readme (25.11.2015): ArrayIndexOutOfBoundsException #4

Closed Zsar closed 8 years ago

Zsar commented 8 years ago

"Same procedure as last [time], Mrs. Sophie." - Just a different exception.

zsar@IMISE-Aber-OWL-Testrechner:~/aberowl-meta/aberowl-server$ groovy AberOWLServer.groovy
Caught: java.lang.ArrayIndexOutOfBoundsException: 0
java.lang.ArrayIndexOutOfBoundsException: 0
    at AberOWLServer.run(AberOWLServer.groovy:34)
zsar@IMISE-Aber-OWL-Testrechner:~/aberowl-meta/aberowl-server$

May I suggest modifying the readme, so the git command cited under "Installation", first paragraph, points to a revision tagged as stable, for being stable? (Instead of the HEAD revision, which may at any time contain not-actually-executable code for any number of good reasons.)

Furthermore, the error message could use some verbosity. It is not at all visible whether the problem might be a fault in my setup (even though I did again follow the readme to the letter, wherever possible; limitations listed in the linked issue still apply).

... Then again, if 0 is an out-of-bounds array index, I am pretty sure this is a systemic fault, not one in the setup, because clearly the array has a length of zero. (So whatever code computed the desired array length beforehand did not complain about a nonsensical value, when it really should have; if there is no dynamic computation of the array, on the other hand, its definition and use are themselves nonsensical aka should not actually ever happen.)

Incidentally, it is normal to receive Java exceptions using Groovy? I have never used that (latter) language myself, but would have expected at least renaming of the String members if same exceptions are used (for performance? JVM-intrinsic structures?).

... Well, the message does say "caught", not uncaught, so I just attempted to continue as per the readme. It does not get better.

zsar@IMISE-Aber-OWL-Testrechner:~/aberowl-meta/aberowl-web$ bin/www

module.js:340
    throw err;
          ^
Error: Cannot find module 'phantomjs'
    at Function.Module._resolveFilename (module.js:338:15)
    at Function.Module._load (module.js:280:25)
    at Module.require (module.js:364:17)
    at require (module.js:380:17)
    at Object.<anonymous> (/home/zsar/aberowl-meta/aberowl-web/app.js:14:17)
    at Module._compile (module.js:456:26)
    at Object.Module._extensions..js (module.js:474:10)
    at Module.load (module.js:356:32)
    at Function.Module._load (module.js:312:12)
    at Module.require (module.js:364:17)
zsar@IMISE-Aber-OWL-Testrechner:~/aberowl-meta/aberowl-web$ 
zsar@IMISE-Aber-OWL-Testrechner:~/aberowl-meta/aberowl-sync$ groovy RemoteOntologyDiscover.groovy & groovy RemoteOntologyUpdate.groovy 
[1] 2894
org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:
General error during conversion: Error grabbing Grapes -- [unresolved dependency: redis.clients#jedis;2.6.2: not found]

java.lang.RuntimeException: Error grabbing Grapes -- [unresolved dependency: redis.clients#jedis;2.6.2: not found]
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
    at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:77)
    at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:71)
    at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:81)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:54)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:182)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:190)
    at groovy.grape.GrapeIvy.getDependencies(GrapeIvy.groovy:336)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSite.invoke(PogoMetaMethodSite.java:226)
    at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:52)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:46)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:133)
    at groovy.grape.GrapeIvy.resolve(GrapeIvy.groovy:463)
    at groovy.grape.GrapeIvy$resolve$0.callCurrent(Unknown Source)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:46)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:133)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:153)
    at groovy.grape.GrapeIvy.resolve(GrapeIvy.groovy:432)
    at groovy.grape.GrapeIvy$resolve.callCurrent(Unknown Source)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:46)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:133)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:149)
    at groovy.grape.GrapeIvy.grab(GrapeIvy.groovy:248)
    at groovy.grape.Grape.grab(Grape.java:141)
    at groovy.grape.GrabAnnotationTransformation.visit(GrabAnnotationTransformation.java:283)
    at org.codehaus.groovy.transform.ASTTransformationVisitor$3.call(ASTTransformationVisitor.java:302)
    at org.codehaus.groovy.control.CompilationUnit.applyToSourceUnits(CompilationUnit.java:843)
    at org.codehaus.groovy.control.CompilationUnit.doPhaseOperation(CompilationUnit.java:548)
    at org.codehaus.groovy.control.CompilationUnit.processPhaseOperations(CompilationUnit.java:524)
    at org.codehaus.groovy.control.CompilationUnit.compile(CompilationUnit.java:501)
    at groovy.lang.GroovyClassLoader.doParseClass(GroovyClassLoader.java:306)
    at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:283)
    at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:267)
    at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:197)
    at groovy.lang.GroovyShell$2.run(GroovyShell.java:215)
    at groovy.lang.GroovyShell$2.run(GroovyShell.java:213)
    at java.security.AccessController.doPrivileged(Native Method)
    at groovy.lang.GroovyShell.run(GroovyShell.java:213)
    at groovy.lang.GroovyShell.run(GroovyShell.java:159)
    at groovy.ui.GroovyMain.processOnce(GroovyMain.java:550)
    at groovy.ui.GroovyMain.run(GroovyMain.java:337)
    at groovy.ui.GroovyMain.process(GroovyMain.java:323)
    at groovy.ui.GroovyMain.processArgs(GroovyMain.java:120)
    at groovy.ui.GroovyMain.main(GroovyMain.java:100)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at org.codehaus.groovy.tools.GroovyStarter.rootLoader(GroovyStarter.java:108)
    at org.codehaus.groovy.tools.GroovyStarter.main(GroovyStarter.java:130)

1 error

Caught: groovy.lang.MissingMethodException: No signature of method: groovy.json.JsonSlurper.parse() is applicable for argument types: (java.net.URL) values: [http://www.obofoundry.org/registry/ontologies.jsonld]
Possible solutions: parse(java.io.Reader), use([Ljava.lang.Object;), wait(), any(), grep(), wait(long)
groovy.lang.MissingMethodException: No signature of method: groovy.json.JsonSlurper.parse() is applicable for argument types: (java.net.URL) values: [http://www.obofoundry.org/registry/ontologies.jsonld]
Possible solutions: parse(java.io.Reader), use([Ljava.lang.Object;), wait(), any(), grep(), wait(long)
    at RemoteOntologyUpdate.run(RemoteOntologyUpdate.groovy:22)
[1]+  Exit 1                  groovy RemoteOntologyDiscover.groovy
zsar@IMISE-Aber-OWL-Testrechner:~/aberowl-meta/aberowl-sync$
leechuck commented 8 years ago

I can confirm the bug. There are actually two issues:

First, documentation is out of date; AberOWLServer needs to be started with a port number as parameter, e.g., groovy AberOWLServer.groovy 31337 to start on port 31337.

Second, there are now more dependencies for NodeJS; phantomjs needs to be installed using npm install phantomjs in the right directory. @reality could you check the dependencies in the install script?

leechuck commented 8 years ago

@reality The jedis issue seems to be a maven problem; maybe they renamed the maven repo somehow?

leechuck commented 8 years ago

@Zsar Can you confirm that you are using a Groovy version > 2? JsonSlurper.parse(URL) did not exist in 1.8.X and was introduced in 2.X.

Zsar commented 8 years ago

@leechuck : Mayhap it was a mistake going Ubuntu for this. What do you make of this:

zsar@IMISE-Aber-OWL-Testrechner:~$ apt list groovy
Listing... Done
groovy/wily,now 2.0.0~beta2+isreally1.8.6-4ubuntu1 all [installed]
zsar@IMISE-Aber-OWL-Testrechner:~$

"2.0.0 is really 1.8.6"... seriously!? ... Will see to it that I get a proper version - this one is alledgedly groovy is already the newest version. but obviously there exists a version 2.4.5 over there and that is what I will grab.

... And done. Shall I re-run the lines above or wait until further instruction is available regarding phantomjs and jedis?

Zsar commented 8 years ago

... Could you, per chance, tell me a revision where it was still working? So I can continue with my own work?

You do not seem to have any but the master branch and no tagged releases, as far as I can see, so there is no good way to find out myself.

reality commented 8 years ago

The latest master should be working

leechuck commented 8 years ago

Latest master should work. You get ArrayIndexOutOfBounds if you don't start AberOWL with its one required parameter, which is the port number it's supposed to run on. E.g., start it with groovy AberOWLServer 10000 to run on port 10000.

Zsar commented 8 years ago

Mmh. Now works up to this part:

To run the web front-end:
    cd aberowl-web ; bin/www

Same error as before here.

Doing the next step anyway:

To run the sync, follow these commands:
    cd aberowl-sync ; groovy RemoteOntologyDiscover.groovy & groovy RemoteOntologyUpdate.groovy

produces different errors from before (the stack dumps are all identical, as far as I can see; so it's actually just one and the same error triggered each time):

zsar@IMISE-Aber-OWL-Testrechner:~/aberowl-meta$ cd aberowl-sync ; groovy RemoteOntologyDiscover.groovy & groovy RemoteOntologyUpdate.groovy
[1] 2844
getting the list
Processing ICO...
[200] ICO
New version found...
java.io.FileNotFoundException: onts/null (No such file or directory)
    at java.io.FileInputStream.open0(Native Method)
    at java.io.FileInputStream.open(FileInputStream.java:195)
    at java.io.FileInputStream.<init>(FileInputStream.java:138)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
    at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:80)
    at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrapNoCoerce.callConstructor(ConstructorSite.java:105)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:60)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:235)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:247)
    at db.OntologyRecord.addNewSubmission(OntologyRecord.groovy:44)
    at db.OntologyRecord$addNewSubmission.call(Unknown Source)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
    at RemoteOntologyUpdate$_run_closure1$_closure2.doCall(RemoteOntologyUpdate.groovy:52)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
    at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
    at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
    at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1019)
    at groovy.lang.Closure.call(Closure.java:426)
    at groovyx.net.http.HTTPBuilder$1.handleResponse(HTTPBuilder.java:494)
    at org.apache.http.impl.client.AbstractHttpClient.execute(AbstractHttpClient.java:1070)
    at org.apache.http.impl.client.AbstractHttpClient.execute(AbstractHttpClient.java:1044)
    at groovyx.net.http.HTTPBuilder.doRequest(HTTPBuilder.java:506)
    at groovyx.net.http.HTTPBuilder.get(HTTPBuilder.java:276)
    at groovyx.net.http.HTTPBuilder$get$0.call(Unknown Source)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:133)
    at RemoteOntologyUpdate$_run_closure1.doCall(RemoteOntologyUpdate.groovy:39)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
    at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
    at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
    at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1019)
    at groovy.lang.Closure.call(Closure.java:426)
    at groovy.lang.Closure.call(Closure.java:442)
    at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2030)
    at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2015)
    at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2068)
    at org.codehaus.groovy.runtime.dgm$164.invoke(Unknown Source)
    at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274)
    at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
    at RemoteOntologyUpdate.run(RemoteOntologyUpdate.groovy:33)
    at groovy.lang.GroovyShell.runScriptOrMainOrTestOrRunnable(GroovyShell.java:263)
    at groovy.lang.GroovyShell.run(GroovyShell.java:524)
    at groovy.lang.GroovyShell.run(GroovyShell.java:513)
    at groovy.ui.GroovyMain.processOnce(GroovyMain.java:652)
    at groovy.ui.GroovyMain.run(GroovyMain.java:384)
    at groovy.ui.GroovyMain.process(GroovyMain.java:370)
    at groovy.ui.GroovyMain.processArgs(GroovyMain.java:129)
    at groovy.ui.GroovyMain.main(GroovyMain.java:109)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at org.codehaus.groovy.tools.GroovyStarter.rootLoader(GroovyStarter.java:109)
    at org.codehaus.groovy.tools.GroovyStarter.main(GroovyStarter.java:131)
Processing TEO...
[200] TEO
New version found...
java.io.FileNotFoundException: onts/null (No such file or directory)
    at java.io.FileInputStream.open0(Native Method)
    at java.io.FileInputStream.open(FileInputStream.java:195)
    at java.io.FileInputStream.<init>(FileInputStream.java:138)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
    at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:80)
    at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrapNoCoerce.callConstructor(ConstructorSite.java:105)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:247)
    at db.OntologyRecord.addNewSubmission(OntologyRecord.groovy:44)
    at db.OntologyRecord$addNewSubmission.call(Unknown Source)
    at RemoteOntologyUpdate$_run_closure1$_closure2.doCall(RemoteOntologyUpdate.groovy:52)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
    at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
    at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
    at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1019)
    at groovy.lang.Closure.call(Closure.java:426)
    at groovyx.net.http.HTTPBuilder$1.handleResponse(HTTPBuilder.java:494)
    at org.apache.http.impl.client.AbstractHttpClient.execute(AbstractHttpClient.java:1070)
    at org.apache.http.impl.client.AbstractHttpClient.execute(AbstractHttpClient.java:1044)
    at groovyx.net.http.HTTPBuilder.doRequest(HTTPBuilder.java:506)
    at groovyx.net.http.HTTPBuilder.get(HTTPBuilder.java:276)
    at groovyx.net.http.HTTPBuilder$get$0.call(Unknown Source)
    at RemoteOntologyUpdate$_run_closure1.doCall(RemoteOntologyUpdate.groovy:39)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
    at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
    at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
    at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1019)
    at groovy.lang.Closure.call(Closure.java:426)
    at groovy.lang.Closure.call(Closure.java:442)
    at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2030)
    at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2015)
    at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2068)
    at org.codehaus.groovy.runtime.dgm$164.invoke(Unknown Source)
    at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274)
    at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
    at RemoteOntologyUpdate.run(RemoteOntologyUpdate.groovy:33)
    at groovy.lang.GroovyShell.runScriptOrMainOrTestOrRunnable(GroovyShell.java:263)
    at groovy.lang.GroovyShell.run(GroovyShell.java:524)
    at groovy.lang.GroovyShell.run(GroovyShell.java:513)
    at groovy.ui.GroovyMain.processOnce(GroovyMain.java:652)
    at groovy.ui.GroovyMain.run(GroovyMain.java:384)
    at groovy.ui.GroovyMain.process(GroovyMain.java:370)
    at groovy.ui.GroovyMain.processArgs(GroovyMain.java:129)
    at groovy.ui.GroovyMain.main(GroovyMain.java:109)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at org.codehaus.groovy.tools.GroovyStarter.rootLoader(GroovyStarter.java:109)
    at org.codehaus.groovy.tools.GroovyStarter.main(GroovyStarter.java:131)
Processing TMO...
[200] TMO
New version found...
java.io.FileNotFoundException: onts/null (No such file or directory)
    at java.io.FileInputStream.open0(Native Method)
    at java.io.FileInputStream.open(FileInputStream.java:195)
    at java.io.FileInputStream.<init>(FileInputStream.java:138)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
    at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:80)
    at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrapNoCoerce.callConstructor(ConstructorSite.java:105)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:247)
    at db.OntologyRecord.addNewSubmission(OntologyRecord.groovy:44)
    at db.OntologyRecord$addNewSubmission.call(Unknown Source)
    at RemoteOntologyUpdate$_run_closure1$_closure2.doCall(RemoteOntologyUpdate.groovy:52)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
    at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
    at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
    at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1019)
    at groovy.lang.Closure.call(Closure.java:426)
    at groovyx.net.http.HTTPBuilder$1.handleResponse(HTTPBuilder.java:494)
    at org.apache.http.impl.client.AbstractHttpClient.execute(AbstractHttpClient.java:1070)
    at org.apache.http.impl.client.AbstractHttpClient.execute(AbstractHttpClient.java:1044)
    at groovyx.net.http.HTTPBuilder.doRequest(HTTPBuilder.java:506)
    at groovyx.net.http.HTTPBuilder.get(HTTPBuilder.java:276)
    at groovyx.net.http.HTTPBuilder$get$0.call(Unknown Source)
    at RemoteOntologyUpdate$_run_closure1.doCall(RemoteOntologyUpdate.groovy:39)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
    at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
    at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
    at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1019)
    at groovy.lang.Closure.call(Closure.java:426)
    at groovy.lang.Closure.call(Closure.java:442)
    at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2030)
    at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2015)
    at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2068)
    at org.codehaus.groovy.runtime.dgm$164.invoke(Unknown Source)
    at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274)
    at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
    at RemoteOntologyUpdate.run(RemoteOntologyUpdate.groovy:33)
    at groovy.lang.GroovyShell.runScriptOrMainOrTestOrRunnable(GroovyShell.java:263)
    at groovy.lang.GroovyShell.run(GroovyShell.java:524)
    at groovy.lang.GroovyShell.run(GroovyShell.java:513)
    at groovy.ui.GroovyMain.processOnce(GroovyMain.java:652)
    at groovy.ui.GroovyMain.run(GroovyMain.java:384)
    at groovy.ui.GroovyMain.process(GroovyMain.java:370)
    at groovy.ui.GroovyMain.processArgs(GroovyMain.java:129)
    at groovy.ui.GroovyMain.main(GroovyMain.java:109)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at org.codehaus.groovy.tools.GroovyStarter.rootLoader(GroovyStarter.java:109)
    at org.codehaus.groovy.tools.GroovyStarter.main(GroovyStarter.java:131)
Processing OFSMR...
[200] OFSMR
New version found...
java.io.FileNotFoundException: onts/null (No such file or directory)
    at java.io.FileInputStream.open0(Native Method)
    at java.io.FileInputStream.open(FileInputStream.java:195)
    at java.io.FileInputStream.<init>(FileInputStream.java:138)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
    at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:80)
    at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrapNoCoerce.callConstructor(ConstructorSite.java:105)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:247)
    at db.OntologyRecord.addNewSubmission(OntologyRecord.groovy:44)
    at db.OntologyRecord$addNewSubmission.call(Unknown Source)
    at RemoteOntologyUpdate$_run_closure1$_closure2.doCall(RemoteOntologyUpdate.groovy:52)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
    at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
    at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
    at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1019)
    at groovy.lang.Closure.call(Closure.java:426)
    at groovyx.net.http.HTTPBuilder$1.handleResponse(HTTPBuilder.java:494)
    at org.apache.http.impl.client.AbstractHttpClient.execute(AbstractHttpClient.java:1070)
    at org.apache.http.impl.client.AbstractHttpClient.execute(AbstractHttpClient.java:1044)
    at groovyx.net.http.HTTPBuilder.doRequest(HTTPBuilder.java:506)
    at groovyx.net.http.HTTPBuilder.get(HTTPBuilder.java:276)
    at groovyx.net.http.HTTPBuilder$get$0.call(Unknown Source)
    at RemoteOntologyUpdate$_run_closure1.doCall(RemoteOntologyUpdate.groovy:39)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
    at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
    at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
    at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1019)
    at groovy.lang.Closure.call(Closure.java:426)
    at groovy.lang.Closure.call(Closure.java:442)
    at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2030)
    at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2015)
    at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2068)
    at org.codehaus.groovy.runtime.dgm$164.invoke(Unknown Source)
    at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274)
    at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
    at RemoteOntologyUpdate.run(RemoteOntologyUpdate.groovy:33)
    at groovy.lang.GroovyShell.runScriptOrMainOrTestOrRunnable(GroovyShell.java:263)
    at groovy.lang.GroovyShell.run(GroovyShell.java:524)
    at groovy.lang.GroovyShell.run(GroovyShell.java:513)
    at groovy.ui.GroovyMain.processOnce(GroovyMain.java:652)
    at groovy.ui.GroovyMain.run(GroovyMain.java:384)
    at groovy.ui.GroovyMain.process(GroovyMain.java:370)
    at groovy.ui.GroovyMain.processArgs(GroovyMain.java:129)
    at groovy.ui.GroovyMain.main(GroovyMain.java:109)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at org.codehaus.groovy.tools.GroovyStarter.rootLoader(GroovyStarter.java:109)
    at org.codehaus.groovy.tools.GroovyStarter.main(GroovyStarter.java:131)
Processing GEOSPECIES...
[200] GEOSPECIES
New version found...
java.io.FileNotFoundException: onts/null (No such file or directory)
    at java.io.FileInputStream.open0(Native Method)
    at java.io.FileInputStream.open(FileInputStream.java:195)
    at java.io.FileInputStream.<init>(FileInputStream.java:138)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
    at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:80)
    at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrapNoCoerce.callConstructor(ConstructorSite.java:105)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:247)
    at db.OntologyRecord.addNewSubmission(OntologyRecord.groovy:44)
    at db.OntologyRecord$addNewSubmission.call(Unknown Source)
    at RemoteOntologyUpdate$_run_closure1$_closure2.doCall(RemoteOntologyUpdate.groovy:52)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
    at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
    at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
    at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1019)
    at groovy.lang.Closure.call(Closure.java:426)
    at groovyx.net.http.HTTPBuilder$1.handleResponse(HTTPBuilder.java:494)
    at org.apache.http.impl.client.AbstractHttpClient.execute(AbstractHttpClient.java:1070)
    at org.apache.http.impl.client.AbstractHttpClient.execute(AbstractHttpClient.java:1044)
    at groovyx.net.http.HTTPBuilder.doRequest(HTTPBuilder.java:506)
    at groovyx.net.http.HTTPBuilder.get(HTTPBuilder.java:276)
    at groovyx.net.http.HTTPBuilder$get$0.call(Unknown Source)
    at RemoteOntologyUpdate$_run_closure1.doCall(RemoteOntologyUpdate.groovy:39)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
    at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
    at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
    at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1019)
    at groovy.lang.Closure.call(Closure.java:426)
    at groovy.lang.Closure.call(Closure.java:442)
    at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2030)
    at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2015)
    at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2068)
    at org.codehaus.groovy.runtime.dgm$164.invoke(Unknown Source)
    at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274)
    at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
    at RemoteOntologyUpdate.run(RemoteOntologyUpdate.groovy:33)
    at groovy.lang.GroovyShell.runScriptOrMainOrTestOrRunnable(GroovyShell.java:263)
    at groovy.lang.GroovyShell.run(GroovyShell.java:524)
    at groovy.lang.GroovyShell.run(GroovyShell.java:513)
    at groovy.ui.GroovyMain.processOnce(GroovyMain.java:652)
    at groovy.ui.GroovyMain.run(GroovyMain.java:384)
    at groovy.ui.GroovyMain.process(GroovyMain.java:370)
    at groovy.ui.GroovyMain.processArgs(GroovyMain.java:129)
    at groovy.ui.GroovyMain.main(GroovyMain.java:109)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at org.codehaus.groovy.tools.GroovyStarter.rootLoader(GroovyStarter.java:109)
    at org.codehaus.groovy.tools.GroovyStarter.main(GroovyStarter.java:131)
zsar@IMISE-Aber-OWL-Testrechner:~/aberowl-meta/aberowl-sync$ got the list
ICO already exists in AberOWL
GEOSPECIES already exists in AberOWL
TEO already exists in AberOWL
TMO already exists in AberOWL
OFSMR already exists in AberOWL
Creating MOOCCUADO
Caught: java.io.FileNotFoundException: onts/null (No such file or directory)
java.io.FileNotFoundException: onts/null (No such file or directory)
    at db.OntologyRecord.addNewSubmission(OntologyRecord.groovy:44)
    at db.OntologyRecord$addNewSubmission$0.call(Unknown Source)
    at RemoteOntologyDiscover$_run_closure1$_closure2$_closure3.doCall(RemoteOntologyDiscover.groovy:40)
    at groovyx.net.http.HTTPBuilder$1.handleResponse(HTTPBuilder.java:494)
    at org.apache.http.impl.client.AbstractHttpClient.execute(AbstractHttpClient.java:1070)
    at org.apache.http.impl.client.AbstractHttpClient.execute(AbstractHttpClient.java:1044)
    at groovyx.net.http.HTTPBuilder.doRequest(HTTPBuilder.java:506)
    at groovyx.net.http.HTTPBuilder.get(HTTPBuilder.java:276)
    at groovyx.net.http.HTTPBuilder$get.call(Unknown Source)
    at RemoteOntologyDiscover$_run_closure1$_closure2.doCall(RemoteOntologyDiscover.groovy:33)
    at RemoteOntologyDiscover$_run_closure1.doCall(RemoteOntologyDiscover.groovy:22)
    at groovyx.net.http.HTTPBuilder$1.handleResponse(HTTPBuilder.java:494)
    at org.apache.http.impl.client.AbstractHttpClient.execute(AbstractHttpClient.java:1070)
    at org.apache.http.impl.client.AbstractHttpClient.execute(AbstractHttpClient.java:1044)
    at groovyx.net.http.HTTPBuilder.doRequest(HTTPBuilder.java:506)
    at groovyx.net.http.HTTPBuilder.get(HTTPBuilder.java:276)
    at groovyx.net.http.HTTPBuilder$get.call(Unknown Source)
    at RemoteOntologyDiscover.run(RemoteOntologyDiscover.groovy:20)

after which it hangs indefinitely.

Robbie1977 commented 8 years ago

I'm at stuck at roughly the same point.

Got the server running Note: Groovy install details are problematic as the gvm service has been renamed to sdk (http://sdkman.io/install.html) but once installed sdk install groovy works fine.

Got the web service running with the addition of (>):

cd aberowl-web
npm install databank
>npm install phantomjs
>npm install xmldom
cd node_modules/databank/
npm install databank-redis

sync is getting stuck with same multiple errors as Zsar:

java.io.FileNotFoundException: onts/null (No such file or directory)

Are we missing something?

leechuck commented 8 years ago

@reality Could you look into this, please?

reality commented 8 years ago

Hi @Robbie1977 & @Zsar,

It seems there were some problems with the script already assuming there were ontologies present! I have fixed these in the database library, which you can update by doing the following:

cd aberowl-sync ; git submodule update

The discover/update scripts should then work fine.

Another minor issue with the documentation (also fixed now), the command to run the sync should be:

cd aberowl-sync ; groovy RemoteOntologyDiscover.groovy && groovy RemoteOntologyUpdate.groovy

With two ampersands, otherwise the two scripts will run at the same time!

Please let me know if you have any other issues.

Zsar commented 8 years ago

I think this issue can be closed now: I listed all relevant ReadMe changes in my comment to #6.