REST error in UpDownLoading

[Peter Murray-Rust]

I have moved this to DEV. It's a good idea to use DEV if we are hacking and also to choose a different title for different problems

On Tue, Feb 8, 2011 at 12:50 PM, Pablo Echenique <echen...@gmail.com> wrote:

3)

http://quixote.wikispot.org/Tutorials_and_problems#PabloMac

The REST downloading part also fails:

[ERROR] BUILD ERROR

[INFO] ------------------------------------------------------------------------

[INFO] An exception occured while executing the Java class. org.xmlcml.cml.rest.UpDownLoader

[INFO] ------------------------------------------------------------------------

[INFO] Trace

org.apache.maven.lifecycle.LifecycleExecutionException: An exception occured while executing the Java class. org.xmlcml.cml.rest.UpDownLoader

at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoals(DefaultLifecycleExecutor.java:719)

at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeStandaloneGoal(DefaultLifecycleExecutor.java:569)

at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoal(DefaultLifecycleExecutor.java:539)

at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoalAndHandleFailures(DefaultLifecycleExecutor.java:387)

at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeTaskSegments(DefaultLifecycleExecutor.java:348)

at org.apache.maven.lifecycle.DefaultLifecycleExecutor.execute(DefaultLifecycleExecutor.java:180)

at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:328)

at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:138)

at org.apache.maven.cli.MavenCli.main(MavenCli.java:362)

at org.apache.maven.cli.compat.CompatibleMain.main(CompatibleMain.java:60)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

at java.lang.reflect.Method.invoke(Method.java:597)

at org.codehaus.classworlds.Launcher.launchEnhanced(Launcher.java:315)

at org.codehaus.classworlds.Launcher.launch(Launcher.java:255)

at org.codehaus.classworlds.Launcher.mainWithExitCode(Launcher.java:430)

at org.codehaus.classworlds.Launcher.main(Launcher.java:375)

Caused by: org.apache.maven.plugin.MojoExecutionException: An exception occured while executing the Java class. org.xmlcml.cml.rest.UpDownLoader

at org.codehaus.mojo.exec.ExecJavaMojo.execute(ExecJavaMojo.java:346)

at org.apache.maven.plugin.DefaultPluginManager.executeMojo(DefaultPluginManager.java:490)

at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoals(DefaultLifecycleExecutor.java:694)

... 17 more

Caused by: java.lang.ClassNotFoundException: org.xmlcml.cml.rest.UpDownLoader

There may be missing jars.

I think we should concentrate on debugging the compchem first

P.
 

at java.net.URLClassLoader$1.run(URLClassLoader.java:202)

at java.security.AccessController.doPrivileged(Native Method)

at java.net.URLClassLoader.findClass(URLClassLoader.java:190)

at java.lang.ClassLoader.loadClass(ClassLoader.java:307)

at java.lang.ClassLoader.loadClass(ClassLoader.java:248)

at org.codehaus.mojo.exec.ExecJavaMojo$1.run(ExecJavaMojo.java:284)

at java.lang.Thread.run(Thread.java:680)

[INFO] ------------------------------------------------------------------------

[INFO] Total time: 6 seconds

[INFO] Finished at: Tue Feb 08 13:48:16 CET 2011

[INFO] Final Memory: 17M/81M

[INFO] ------------------------------------------------------------------------

On Tue, Feb 8, 2011 at 12:40 PM, Pablo Echenique <echen...@gmail.com> wrote:

2)

http://quixote.wikispot.org/Tutorials_and_problems#PabloMac

The lensfield part.

Everything runs smoothly until

lf gaussianArchive2Cml.lf 

when I get

Lensfield2 (0.1.1)

----------------------------------------

[INFO]  Checking build steps

[INFO]  Resolving build order

[DEBUG]  - files

[DEBUG]  - cml

[INFO]  Resolving dependencies

[DEBUG] Resolving global dependencies

[DEBUG] Resolving dependencies for: cml

[INFO]  Initialising workspace

----------------------------------------

java.lang.ClassNotFoundException: org.xmlcml.cml.converters.compchem.gaussian.GaussianArchive2CMLConverter

at java.net.URLClassLoader$1.run(URLClassLoader.java:202)

at java.security.AccessController.doPrivileged(Native Method)

at java.net.URLClassLoader.findClass(URLClassLoader.java:190)

at java.lang.ClassLoader.loadClass(ClassLoader.java:307)

at java.lang.ClassLoader.loadClass(ClassLoader.java:248)

at org.lensfield.ClassAnalyser.analyseClass(ClassAnalyser.java:44)

at org.lensfield.Lensfield.analyseBuildState(Lensfield.java:312)

at org.lensfield.Lensfield.init(Lensfield.java:87)

at org.lensfield.Lensfield.build(Lensfield.java:123)

at org.lensfield.cli.LensfieldCli.run(LensfieldCli.java:87)

at org.lensfield.cli.LensfieldCli.main(LensfieldCli.java:69)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

at java.lang.reflect.Method.invoke(Method.java:597)

at org.lensfield.launcher.load.Loader.run(Loader.java:65)

at org.lensfield.launcher.load.Loader.main(Loader.java:94)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

at java.lang.reflect.Method.invoke(Method.java:597)

at org.lensfield.launcher.boot.Bootstrap.main(Bootstrap.java:52)

BUILD FAILED

On Tue, Feb 8, 2011 at 12:31 PM, Pablo Echenique <echen...@gmail.com> wrote:

I am rerunning the tutorials we have at the wiki to warm up for the meeting.

I will post here my attempts:

1)

MacOSX 10.6 Snow Leopard.

http://quixote.wikispot.org/Tutorials_and_problems#JUMBO1

Yesterday I could not compile jumbo-converters, now I can,

but,

when I issue

mvn -e exec:java  -Dexec.mainClass=org.xmlcml.cml.converters.compchem.gaussian.ConverterImpl -Dexec.args="-in ./f-15_p-15.gau -out ./f-15_p-15.cml"

I get:

+ Error stacktraces are turned on.

[INFO] Scanning for projects...

[INFO] snapshot wwmm:wwmm-parent:2-SNAPSHOT: checking for updates from com.hp.hpl.jena

[INFO] Searching repository for plugin with prefix: 'exec'.

[INFO] ------------------------------------------------------------------------

[INFO] Building jumbo-converters-gaussian

[INFO]    task-segment: [exec:java]

[INFO] ------------------------------------------------------------------------

[INFO] Preparing exec:java

[INFO] No goals needed for project - skipping

[INFO] snapshot cml:cmlxom:3.0.0-SNAPSHOT: checking for updates from com.hp.hpl.jena

[INFO] snapshot cml:euclid:0.0.1-SNAPSHOT: checking for updates from com.hp.hpl.jena

[INFO] snapshot cml:euclid-testutil:0.0.1-SNAPSHOT: checking for updates from com.hp.hpl.jena

[INFO] snapshot cml:jumbo-converters-core:0.3-SNAPSHOT: checking for updates from com.hp.hpl.jena

[INFO] snapshot cml:jumbo-converters-core:0.3-SNAPSHOT: checking for updates from ucc-repo

[INFO] snapshot cml:jumbo:6.0.0-SNAPSHOT: checking for updates from com.hp.hpl.jena

[INFO] snapshot cml:jumbo-converters-rdf:0.3-SNAPSHOT: checking for updates from com.hp.hpl.jena

[INFO] snapshot cml:jumbo-converters-rdf:0.3-SNAPSHOT: checking for updates from ucc-repo

[INFO] snapshot cml:jumbo-converters-testutils:0.3-SNAPSHOT: checking for updates from com.hp.hpl.jena

[INFO] snapshot cml:jumbo-converters-testutils:0.3-SNAPSHOT: checking for updates from ucc-repo

[INFO] snapshot cml:jumbo-testutil:1.0-SNAPSHOT: checking for updates from com.hp.hpl.jena

[INFO] [exec:java {execution: default-cli}]

Input file: /Volumes/Warehouse/dynamic/Quixote/jumbo-converters/jumbo-converters-compchem/./f-15_p-15.gau

Output file: /Volumes/Warehouse/dynamic/Quixote/jumbo-converters/jumbo-converters-compchem/./f-15_p-15.cml

Input type: gau

Output type: cml

Converter name: org.xmlcml.cml.converters.compchem.gaussian.GaussianArchive2CMLConverter

[INFO] ------------------------------------------------------------------------

[ERROR] BUILD ERROR

[INFO] ------------------------------------------------------------------------

[INFO] An exception occured while executing the Java class. null

org.xmlcml.cml.converters.compchem.gaussian.GaussianArchive2CMLConverter

[INFO] ------------------------------------------------------------------------

[INFO] Trace

org.apache.maven.lifecycle.LifecycleExecutionException: An exception occured while executing the Java class. null

at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoals(DefaultLifecycleExecutor.java:719)

at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeStandaloneGoal(DefaultLifecycleExecutor.java:569)

at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoal(DefaultLifecycleExecutor.java:539)

at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoalAndHandleFailures(DefaultLifecycleExecutor.java:387)

at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeTaskSegments(DefaultLifecycleExecutor.java:348)

at org.apache.maven.lifecycle.DefaultLifecycleExecutor.execute(DefaultLifecycleExecutor.java:180)

at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:328)

at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:138)

at org.apache.maven.cli.MavenCli.main(MavenCli.java:362)

at org.apache.maven.cli.compat.CompatibleMain.main(CompatibleMain.java:60)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

at java.lang.reflect.Method.invoke(Method.java:597)

at org.codehaus.classworlds.Launcher.launchEnhanced(Launcher.java:315)

at org.codehaus.classworlds.Launcher.launch(Launcher.java:255)

at org.codehaus.classworlds.Launcher.mainWithExitCode(Launcher.java:430)

at org.codehaus.classworlds.Launcher.main(Launcher.java:375)

Caused by: org.apache.maven.plugin.MojoExecutionException: An exception occured while executing the Java class. null

at org.codehaus.mojo.exec.ExecJavaMojo.execute(ExecJavaMojo.java:346)

at org.apache.maven.plugin.DefaultPluginManager.executeMojo(DefaultPluginManager.java:490)

at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoals(DefaultLifecycleExecutor.java:694)

... 17 more

Caused by: java.lang.reflect.InvocationTargetException

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

at java.lang.reflect.Method.invoke(Method.java:597)

at org.codehaus.mojo.exec.ExecJavaMojo$1.run(ExecJavaMojo.java:291)

at java.lang.Thread.run(Thread.java:680)

Caused by: java.lang.RuntimeException: Cannot create/run converter

at org.xmlcml.cml.converters.compchem.gaussian.ConverterImpl.process(ConverterImpl.java:108)

at org.xmlcml.cml.converters.compchem.gaussian.ConverterImpl.main(ConverterImpl.java:29)

... 6 more

Caused by: java.lang.ClassNotFoundException: org.xmlcml.cml.converters.compchem.gaussian.GaussianArchive2CMLConverter

at java.net.URLClassLoader$1.run(URLClassLoader.java:202)

at java.security.AccessController.doPrivileged(Native Method)

at java.net.URLClassLoader.findClass(URLClassLoader.java:190)

at java.lang.ClassLoader.loadClass(ClassLoader.java:307)

at java.lang.ClassLoader.loadClass(ClassLoader.java:248)

at java.lang.Class.forName0(Native Method)

at java.lang.Class.forName(Class.java:169)

at org.xmlcml.cml.converters.compchem.gaussian.ConverterImpl.process(ConverterImpl.java:103)

... 7 more

[INFO] ------------------------------------------------------------------------

[INFO] Total time: 5 seconds

[INFO] Finished at: Tue Feb 08 12:24:57 CET 2011

[INFO] Final Memory: 15M/81M

[INFO] ------------------------------------------------------------------------

--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069

[Pablo Echenique]

On Tue, Feb 8, 2011 at 2:01 PM, Peter Murray-Rust <pm...@cam.ac.uk> wrote:

I have moved this to DEV. It's a good idea to use DEV if we are hacking and also to choose a different title for different problems

Totally agree.

I just doubted it because I am not sure if everyone reads DEV.

But they should!

P.

[Peter Murray-Rust]

On Tue, Feb 8, 2011 at 4:28 PM, Pablo Echenique <echen...@gmail.com> wrote:

On Tue, Feb 8, 2011 at 2:01 PM, Peter Murray-Rust <pm...@cam.ac.uk> wrote:

I have moved this to DEV. It's a good idea to use DEV if we are hacking and also to choose a different title for different problems

Totally agree.

I just doubted it because I am not sure if everyone reads DEV.

But they should!

P.

I think all the techies will!

I have opened an issue tracker on bitbucket Jumbo Converters
 

[Pablo Echenique]

On Tue, Feb 8, 2011 at 5:35 PM, Peter Murray-Rust <pm...@cam.ac.uk> wrote:

On Tue, Feb 8, 2011 at 4:28 PM, Pablo Echenique <echen...@gmail.com> wrote:

On Tue, Feb 8, 2011 at 2:01 PM, Peter Murray-Rust <pm...@cam.ac.uk> wrote:

I have moved this to DEV. It's a good idea to use DEV if we are hacking and also to choose a different title for different problems

Totally agree.

I just doubted it because I am not sure if everyone reads DEV.

But they should!

P.

I think all the techies will!

I have opened an issue tracker on bitbucket Jumbo Converters

Yep, I answered, it looks good!

[Pablo Echenique]

I have cloned brand new jumbo-converters and lensfield just in case,

installed them,

and issued, frorm lensfield root,

mvn -e -f ./pom.xml exec:java -Dexec.mainClass=org.xmlcml.cml.rest.UpDownLoader -Dexec.args="-download -url http://neptuno.unizar.es/files/public/datasets/HCO-L-Ala-NH2_g03_BIFIcluster_2007/calcs/homolevel/MP2/6-31G/ -dir /warehouse/dynamic/Quixote/testing"

I still get the error:

+ Error stacktraces are turned on.

[INFO] Scanning for projects...

[INFO] Searching repository for plugin with prefix: 'exec'.

[INFO] ------------------------------------------------------------------------

[INFO] Building Unnamed - wwmm:lensfield-jumbo:jar:0.0.1

[INFO]    task-segment: [exec:java]

[INFO] ------------------------------------------------------------------------

[INFO] Preparing exec:java

[INFO] No goals needed for project - skipping

[INFO] [exec:java {execution: default-cli}]

[INFO] ------------------------------------------------------------------------

[ERROR] BUILD ERROR

[INFO] ------------------------------------------------------------------------

at java.net.URLClassLoader$1.run(URLClassLoader.java:202)

at java.security.AccessController.doPrivileged(Native Method)

at java.net.URLClassLoader.findClass(URLClassLoader.java:190)

at java.lang.ClassLoader.loadClass(ClassLoader.java:307)

at java.lang.ClassLoader.loadClass(ClassLoader.java:248)

at org.codehaus.mojo.exec.ExecJavaMojo$1.run(ExecJavaMojo.java:284)

at java.lang.Thread.run(Thread.java:680)

[INFO] ------------------------------------------------------------------------

[INFO] Total time: 2 seconds

[INFO] Finished at: Tue Feb 08 17:45:13 CET 2011

[INFO] Final Memory: 14M/81M

[INFO] ------------------------------------------------------------------------

[Peter Murray-Rust]

On Tue, Feb 8, 2011 at 4:52 PM, Pablo Echenique <echen...@gmail.com> wrote:

I have cloned brand new jumbo-converters and lensfield just in case,

installed them,

and issued, frorm lensfield root,

mvn -e -f ./pom.xml exec:java -Dexec.mainClass=org.xmlcml.cml.rest.UpDownLoader -Dexec.args="-download -url http://neptuno.unizar.es/files/public/datasets/HCO-L-Ala-NH2_g03_BIFIcluster_2007/calcs/homolevel/MP2/6-31G/ -dir /warehouse/dynamic/Quixote/testing"

Suggest you file this as a bug and I will read it from Bitbucket - stackTraces are easy to read and manage

[Pablo Echenique]

Done:

https://bitbucket.org/wwmm/jumbo-converters/issue/3/rest-error-in-updownloading

[Weerapong Phadungsukanan]

It is probably not a bug. Are you try running org.xmlcml.cml.rest.UpDownLoader from jumbo-converters?

org.xmlcml.cml.rest.UpDownLoader isn't part of jumbo-converters.

I think it's part of lensfield jumbo or something but I cannot find where the repository is.

The current source codes are very scattered on bitbucket. Is it possible to put them under a certain account if it is decided that it will be part of the work? Or have a page on Quixote wikispot for looking up.

Best,

Weerapong

[Pablo Echenique]

On Tue, Feb 8, 2011 at 6:16 PM, Weerapong Phadungsukanan <wp...@cam.ac.uk> wrote:

It is probably not a bug. Are you try running org.xmlcml.cml.rest.UpDownLoader from jumbo-converters?

org.xmlcml.cml.rest.UpDownLoader isn't part of jumbo-converters.

I think it's part of lensfield jumbo or something but I cannot find where the repository is.

I am running it from lensfieldjumbo.

It is part of a tutorial that used to work: http://quixote.wikispot.org/Tutorials_and_problems#PabloMac

 

The current source codes are very scattered on bitbucket. Is it possible to put them under a certain account if it is decided that it will be part of the work? Or have a page on Quixote wikispot for looking up.

That would be great! although I don't know how to do it and I don't know if it fits with the way of working you guys have.

Best,

  Pablo.

[Weerapong Phadungsukanan]

Sorry, I saw you filed an bug under jumbo-converters so I misunderstood.

Have you perfermed "mvn clean install" before executing it?

Weerapong

[Pablo Echenique]

On Tue, Feb 8, 2011 at 6:27 PM, Weerapong Phadungsukanan <wp...@cam.ac.uk> wrote:

Sorry, I saw you filed an bug under jumbo-converters so I misunderstood.

You are right, my fault, I'll delete the unrelated bugs.

 

Have you perfermed "mvn clean install" before executing it?

Yep.

[Weerapong Phadungsukanan]

Make sure you on the lastest version of jumbo lensfield. UpDownLoader doesn't exist until change set 9d59d1db22bd.

I had the same problem because I didn't run on the latest changeset but after I updated it now disappears.

Weerapong

[Pablo Echenique]

I install lensfieldjumbo by

hg clone http://bitbucket.org/petermr/lensfieldjumbo

cd lensfieldjumbo/

unzip lensfield-0.1.1.zip

dos2unix lensfield2-0.1.1/bin/lf

chmod u+x lensfield2-0.1.1/bin/lf

export JAVA_HOME=/usr/lib/jvm/java-6-sun

export PATH=$PATH:$HOME/lensfieldjumbo/lensfield2-0.1.1/bin

lf --update

Is this correct?

P.

[Weerapong Phadungsukanan]

According to your instruction on Quixote wikispot, that should be how it is run. I have tested it on Windows OS, everything works without any problem up to "lf --update"

However, when it comes to actually running the converter over the Gaussian files using "lf gaussianArchive2Cml.lf" over the example data and provided example of gaussianArchive2Cml.lf, it throws me an exception :

java.lang.ClassNotFoundException: org.xmlcml.cml.converters.compchem.gaussian.GaussianArchive2CMLConverter

Due to the upgrading of jumbo-converters to 0.3-SNAPSHOT and refactoring, the class name has been renamed to org.xmlcml.cml.converters.compchem.gaussian.archive.GaussianArchive2CMLConverter.

For a quick fixed and testing, I opened up lensfieldjumbo/examples/gau/gaussianArchive2Cml.lf and change the class name accordingly and rerun it. Now I am hitting a real bug. I originally want to file an issue on bitbucket but I am not sure where the error come from. It seems some required resource must be missing or not being copied over properly during refactoring. The only way to check this is actually running it in debug mode which I do not know how to get started with Lensfield.

Currently, I have a feeling that jumbo, jumbo-converters and lensfield is under going a major changes after the last working demo. If that's true, this problem can be ignored at the moment until the core codes is in place and stable.

Here is the stack trace:

Lensfield2 (0.1.1)
----------------------------------------
[INFO]  Checking build steps
[INFO]  Resolving build order
[DEBUG]  - files
[DEBUG]  - cml
[INFO]  Resolving dependencies
[DEBUG] Resolving global dependencies
[DEBUG] Resolving dependencies for: cml
[INFO]  Initialising workspace

[INFO]  Loading last build log
INFO  org.lensfield.log.BuildStateReader - Reading task: cml / org.xmlcml.cml.converters.compchem.gaussian.archive.GaussianArchive2CMLConverter/convert
[INFO]  Comparing tasks to previous state
[DEBUG] Task files: up-to-date
[DEBUG] Task cml: up-to-date
[INFO]  Starting build log
[INFO]  Processing source: files
[DEBUG] (files) adding a/a.gau
[DEBUG] (files) adding a/a1/C2H5.gau
[DEBUG] (files) adding b/nh2.gau
[INFO]  Processing build step: cml
LOADING CLASS: org.xmlcml.cml.converters.compchem.gaussian.archive.GaussianArchive2CMLConverter
----------
[DEBUG] (cml) reading a/a.gau
----------------------------------------

java.lang.reflect.InvocationTargetException
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:597)

        at org.lensfield.process.ProcessRunner.runArgsTask(ProcessRunner.java:294)
        at org.lensfield.process.ProcessRunner.runProcess(ProcessRunner.java:166)
        at org.lensfield.Lensfield.run(Lensfield.java:655)
        at org.lensfield.Lensfield.runKtoLStep(Lensfield.java:459)
        at org.lensfield.Lensfield.processBuildStep(Lensfield.java:419)
        at org.lensfield.Lensfield.build(Lensfield.java:357)
        at org.lensfield.Lensfield.processBuildSteps(Lensfield.java:712)
        at org.lensfield.Lensfield.build(Lensfield.java:128)

        at org.lensfield.cli.LensfieldCli.run(LensfieldCli.java:87)
        at org.lensfield.cli.LensfieldCli.main(LensfieldCli.java:69)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:597)
        at org.lensfield.launcher.load.Loader.run(Loader.java:65)
        at org.lensfield.launcher.load.Loader.main(Loader.java:94)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:597)
        at org.lensfield.launcher.boot.Bootstrap.main(Bootstrap.java:52)

Caused by: java.lang.RuntimeException: Cannot parse/read/find templateList null
        at org.xmlcml.cml.converters.LegacyProcessor.readTemplates(LegacyProcessor.java:74)
        at org.xmlcml.cml.converters.LegacyProcessor.<init>(LegacyProcessor.java:51)
        at org.xmlcml.cml.converters.compchem.gaussian.archive.GaussianArchiveOrigProcessor.<init>(GaussianArchiveOrigProcessor.java:73)
        at org.xmlcml.cml.converters.compchem.gaussian.archive.GaussianArchive2CMLConverter.convertToXML(GaussianArchive2CMLConverter.java:41)
        at org.xmlcml.cml.converters.AbstractConverter.convert(AbstractConverter.java:377)
        ... 25 more
Caused by: java.lang.NullPointerException
        at org.xmlcml.euclid.Util.getInputStreamFromResource(Util.java:225)
        at org.xmlcml.cml.converters.LegacyProcessor.readTemplates(LegacyProcessor.java:66)
        ... 29 more

BUILD FAILED

Weerapong

[Pablo Echenique]

OK,

the same happens to me.

I also changed the class name in the lf file.

Best,

  Pablo.

[Peter Murray-Rust]

On Wed, Feb 9, 2011 at 6:56 PM, Weerapong Phadungsukanan <wp...@cam.ac.uk> wrote:

According to your instruction on Quixote wikispot, that should be how it is run. I have tested it on Windows OS, everything works without any problem up to "lf --update"

However, when it comes to actually running the converter over the Gaussian files using "lf gaussianArchive2Cml.lf" over the example data and provided example of gaussianArchive2Cml.lf, it throws me an exception :

java.lang.ClassNotFoundException: org.xmlcml.cml.converters.compchem.gaussian.GaussianArchive2CMLConverter

Due to the upgrading of jumbo-converters to 0.3-SNAPSHOT and refactoring, the class name has been renamed to org.xmlcml.cml.converters.compchem.gaussian.archive.GaussianArchive2CMLConverter.

That's correct. Sorry for that - the dependency is not resolved till you come to run Lensfield. We have rationalised the names  (and we soon hope you don't need to know them).

For a quick fixed and testing, I opened up lensfieldjumbo/examples/gau/gaussianArchive2Cml.lf and change the class name accordingly and rerun it. Now I am hitting a real bug. I originally want to file an issue on bitbucket but I am not sure where the error come from. It seems some required resource must be missing or not being copied over properly during refactoring. The only way to check this is actually running it in debug mode which I do not know how to get started with Lensfield.

Currently, I have a feeling that jumbo, jumbo-converters and lensfield is under going a major changes after the last working demo.

Yes