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Install script and sub-directories for AberOWL

Home Page: http://aber-owl.net/

License: Apache License 2.0

Shell 2.48% Groovy 97.52%

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miguelangelrg

aberowl-meta's Issues

Unable to start bin/www

Whenever I attempt to start bin/www, I'm getting a TypeError after the latest release of aberowl-web.

➜  aberowl-web git:(c1df353) ✗ bin/www 
express-session deprecated undefined resave option; provide resave option app.js:46:9
express-session deprecated undefined saveUninitialized option; provide saveUninitialized option app.js:46:9

TypeError: Cannot set property 'statusCode' of undefined
    at Request._callback (/home/keiron/Documents/Projects/aberowl-meta/aberowl-web/routes/index.js:12:30)
    at self.callback (/home/keiron/Documents/Projects/aberowl-meta/aberowl-web/node_modules/request/request.js:198:22)
    at Request.EventEmitter.emit (events.js:95:17)
    at Request.onRequestError (/home/keiron/Documents/Projects/aberowl-meta/aberowl-web/node_modules/request/request.js:861:8)
    at ClientRequest.EventEmitter.emit (events.js:95:17)
    at Socket.socketErrorListener (http.js:1547:9)
    at Socket.EventEmitter.emit (events.js:95:17)
    at net.js:441:14
    at process._tickCallback (node.js:415:13)

On server start on Ubuntu Server 15.10: MultipleCompilationErrorsException

Starting the server like this (ReadMe line obsolete!):
groovy AberOWLServer.groovy 10000

Error output attached:
log.txt

Network conflict?

There are two network devices on that (virtual) machine:

enp0s3 : DHCP-enabled VirtualBox NAT (internet access)
enp0s8 : static IP VirtualBox host-only network (for browsing the service)
Might it pick the wrong one? Should it then not more informatively complain about lack of internet access?

Note that the previous steps were all successful (in their internet accesses), so this is probably not the case.

Unlisted dependency?

Will try again with Ubuntu Desktop 15.10 and report back whether the issue persists.
(I had previously used Ubuntu Desktop and advanced further than this step.)

Could you add support for zipped OWL file loading

We have large OWL files (>100MB) and are looking at moving to gzip'd versions which is supported by several other ontology tools but you don't appear to currently support it?

A test example would be: https://github.com/VirtualFlyBrain/VFB_owl/raw/master/src/owl/vfb.owl.gz

Confusion in the configuration

Hi guys,

I am a little confused about the configuration of AberOWL. I am running the front-end (aberowl-web) and back-end (aberowl-server) in my own computer (localhost). The problem is that the frontend is not able to communicate with the backend through the API without writing the whole path. For instance, in order to execute the script getStats.groovy is necessary to write: "http:localhost:9222/api/service/getStats.groovy"
Because with the current configuration does not work: "/service/api/service/getStats.groovy"
I think that I made some mistake during the installation of AberOWL because in otherwise I should have to replace "http://localhost:9222" in all javascript files (sparql.js, tree.js, quick search.js,query.js,help, browse.js) and I suppose that this is not the correct solution.

After installing as per Readme (25.11.2015): ArrayIndexOutOfBoundsException

"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.

I am almost sure this has something to do with missing dependencies. But then they would not have been listed (I definitely and triple-checked installed everything the readme told me to)? Should I try to install this "jedis" (there is no such Ubuntu package on the default repository)? Was it a mistake to use Ubuntu, assuming that then the readme could be followed with minimal self-involvement?

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$

On front-end start on Ubuntu Desktop 15.10: Error: Cannot find module 'phantomjs'

Executing bin/www:

zsar@IMISE-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)```

Checking via apt list phantomjs:

Listing... Done
phantomjs/wily,now 1.9.0-1 amd64 [installed]

Probably related to this comment.

After installing as per Readme (20.11.2015): MultipleCompilationErrorsException

On readme entry "Running", first paragraph: groovy AberOWLServer.groovy

org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:
/home/zsar/aberowl-meta/aberowl-server/src/RequestManager.groovy: 281: unable to resolve class AberOWLSyntaxRendererImpl
@ line 281, column 29.
    def manSyntaxRenderer = new AberOWLRendererImpl()
                            ^
1 error

The system is a fresh Ubuntu 15.10 installed from iso and upgraded thereafter.
All installation steps have been done today.

Note that I had to replace the dependency "node" with "nodejs-legacy", as that package does no longer exist. While executing the second installation step "./install", nPM generated warnings regarding the node minor version (is .25, should have been >=.32), but I doubt this is related.

... Any advice? Reproducible? Any hidden dependencies I might have missed?
Can I do anything to further diagnose this fault?

Broken download links

Many on this page: http://aber-owl.net/ontology/go-plus#downloads

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