Issues with compiling Snofyre

[Hugo Leroux]

Hi!

After installing and performing an mvn clean install on the project, I
get the following errors at the end of the install for project "srth-
osgi". I'd appreciate it if someone could shed some light on this
error.

Kind regards,
Hugo

----
[ERROR] Failed to execute goal on project distribution: Could not
resolve dependencies for project uk.nhs.cfh.dsp.srth-o
sgi:distribution:jar:1.9-SNAPSHOT: The following artifacts could not
be resolved: uk.nhs.cfh.dsp.snomed:uk.nhs.cfh.dsp.s
nomed.dao:jar:0.8-SNAPSHOT,
uk.nhs.cfh.dsp.snomed:uk.nhs.cfh.dsp.snomed.objectmodel:jar:0.8-
SNAPSHOT, uk.nhs.cfh.dsp.sno
med:uk.nhs.cfh.dsp.snomed.expressiongenerator:jar:0.8-SNAPSHOT,
uk.nhs.cfh.dsp.snomed:uk.nhs.cfh.dsp.snomed.hierarchypro
vider:jar:0.8-SNAPSHOT,
uk.nhs.cfh.dsp.snomed:uk.nhs.cfh.dsp.snomed.normaliser:jar:0.8-
SNAPSHOT, uk.nhs.cfh.dsp.snomed:u
k.nhs.cfh.dsp.snomed.persistence:jar:0.8-SNAPSHOT,
uk.nhs.cfh.dsp.snomed:uk.nhs.cfh.dsp.snomed.mrcm:jar:0.8-SNAPSHOT, uk
.nhs.cfh.dsp.snomed:uk.nhs.cfh.dsp.snomed.expression.model:jar:0.8-
SNAPSHOT, uk.nhs.cfh.dsp.snomed:uk.nhs.cfh.dsp.snomed
.expression.comparator:jar:0.8-SNAPSHOT,
uk.nhs.cfh.dsp.snomed:uk.nhs.cfh.dsp.snomed.converters:jar:0.8-
SNAPSHOT, uk.nhs
.cfh.dsp.yasb:uk.nhs.cfh.dsp.yasb.concept.panel:jar:0.8-SNAPSHOT,
uk.nhs.cfh.dsp.yasb:uk.nhs.cfh.dsp.yasb.searchpanel:ja
r:0.8-SNAPSHOT,
uk.nhs.cfh.dsp.yasb:uk.nhs.cfh.dsp.yasb.concept.hierarchy.panel:jar:
0.8-SNAPSHOT, uk.nhs.cfh.dsp.yasb:uk
.nhs.cfh.dsp.yasb.expression.builder:jar:0.8-SNAPSHOT,
uk.nhs.cfh.dsp.yasb:uk.nhs.cfh.dsp.yasb.expression.renderer:jar:0
.8-SNAPSHOT, uk.nhs.cfh.dsp.yasb:uk.nhs.cfh.dsp.yasb.search:jar:0.8-
SNAPSHOT: Could not find artifact uk.nhs.cfh.dsp.sno
med:uk.nhs.cfh.dsp.snomed.dao:jar:0.8-SNAPSHOT -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with
the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions,
please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
[ERROR]
[ERROR] After correcting the problems, you can resume the build with
the command
[ERROR] mvn <goals> -rf :distribution

[Jay Kola]

Hi Hugo,

Many thanks for reporting this issue. It looks like sometime during
the previous commits, the dependencies in maven regressed to a
snapshot release. I've corrected it now. So hopefully it should
compile properly now. Try to checking out srth-osgi from trunk and
recompile....

Please let me know if this problem persists. I've logged in the issue
tracker at http://code.google.com/p/snofyre/issues/detail?id=42

Cheers,
Jay

> [ERROR] [Help 1]http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolution...

[Hugo Leroux]

Hi Jay,

Many thanks for your prompt reply and your assistance. I've updated
the code from the repository and performed a clean install. The
installl went much further than before and downloaded a significant
number of dependencies. However, it still failed on one dependency,
which you will please find enclosed below. I would greatly appreciate
it if you could have a look at the enclosed log and give me some
insight into it.

By the way, I've downloaded and installed a packaged version of
Snofyre. This is a really neat environment. You guys did a really good
job!

Kind regards,
Hugo

--- Start log

net.sf.launch4j.BuilderException: Application jar doesn't exist.
at net.sf.launch4j.Builder.build(Builder.java:77)
at com.akathist.maven.plugins.launch4j.Launch4jMojo.execute(Launch4jMojo.java:340)
at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:107)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:195)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:148)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:140)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:84)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:59)
at org.apache.maven.lifecycle.internal.LifecycleStarter.singleThreadedBuild(LifecycleStarter.java:183)
at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:161)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:316)
at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:153)
at org.apache.maven.cli.MavenCli.execute(MavenCli.java:451)
at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:188)
at org.apache.maven.cli.MavenCli.main(MavenCli.java:134)
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.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:290)
at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:230)
at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:409)
at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:352)
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] Sappheiros : A query and retrieval framework for SNOMED CT
encoded records - uk.nhs.cfh.dsp.srth-osgi SUCCESS [6
.453s]
[INFO] srth-osgi - plugin configuration .................. SUCCESS [0.328s]
[INFO] srth-osgi - wrapper instructions .................. SUCCESS [0.344s]
[INFO] srth-osgi - bundle instructions ................... SUCCESS [0.313s]
[INFO] Sappheiros Information Model Component ............ SUCCESS [3.500s]
[INFO] Sappheiros Information Model Implementation Bundle SUCCESS [14.188s]
[INFO] Sappheiros Demographics Bundle .................... SUCCESS [6.251s]
[INFO] Sappheiros Query Model ............................ SUCCESS [4.266s]
[INFO] Sappheiros Query Service Bundle ................... SUCCESS [1.828s]
[INFO] srth-osgi - imported bundles ...................... SUCCESS [0.531s]
[INFO] Sappheiros Query Converters ....................... SUCCESS [4.485s]
[INFO] Sappheiros Query Repository ....................... SUCCESS [9.000s]
[INFO] Sappheiros Query CRUD Module ...................... SUCCESS [2.735s]
[INFO] Sappheiros Query Creation Panel ................... SUCCESS [4.047s]
[INFO] Sappheiros Query Renderer View Component .......... SUCCESS [2.125s]
[INFO] Sappheiros Normal Form Expression Repository ...... SUCCESS [8.469s]
[INFO] Sappheiros Query Transform Bundle ................. SUCCESS [2.547s]
[INFO] Sappheiros Query Results View Component ........... SUCCESS [3.000s]
[INFO] Sappheiros Results Explanation View Component ..... SUCCESS [2.453s]
[INFO] Sappherios Data Generator Bundle .................. SUCCESS [12.032s]
[INFO] Simulator ViewComponent ........................... SUCCESS [3.157s]
[INFO] Sappheiros Expression Repository Actions Module ... SUCCESS [2.500s]
[INFO] Query Repository ViewComponent .................... SUCCESS [2.469s]
[INFO] srth-osgi - Distribution .......................... FAILURE [5:17.921s]
[INFO] Snofyre Scripting Bundle -
uk.nhs.cfh.dsp.srth.desktop.modules.scripting SKIPPED
[INFO] uk.nhs.cfh.dsp.srth.desktop.modules.scripting.actions SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 6:57.473s
[INFO] Finished at: Fri Mar 25 10:06:10 EST 2011
[INFO] Final Memory: 25M/63M
[INFO] ------------------------------------------------------------------------

[ERROR] Failed to execute goal

com.akathist.maven.plugins.launch4j:launch4j-maven-plugin:1.3:launch4j
(l4j-snofyre-app)
on project distribution: Failed to build the executable; please verify
your configuration. Application jar doesn't exist
. -> [Help 1]

[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with
the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions,
please read the following articles:
[ERROR] [Help 1]

http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException

[ERROR]
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR] mvn <goals> -rf :distribution

------ end log

[Jay Kola]

Hi Hugo,

Thanks for bringing this up again... You are getting the error because of the  - Distribution module in the srth-osgi project. Some of the hard-coded changes for creating an offline installer are causing the build to fail. I was short of time and didn't get around to cleanly separating the functionality (by creating a fork) and as a consequence the build fails now.

You can resolve this issue by commenting out the distribution module in in the pom.xml file for the srth-osgi project

If you are new to Maven, look for the file pom.xml under srth-osgi folder and in the file comment out the following line

<module>distribution</module> 

After commenting out the above line should look like:

<!-- <module>distribution</module> -->

Hope this little tweak helps you compile the code. I'll try to resolve this issue soonish...by the end of the week.

Cheers,

Jay

[Manisha Rathi]

Hi Jay,

I am also facing the similar issue in building srth-osgi in distribution module.
I took source update from TRUNK.
I don't have experience in using maven but it seems that the mvn build fails to download packages(pom and jars) for the specified repositories e.g., (http://www.9stmaryrd.com/maven).
I checked manually, the repository is not available.

As suggested, I hope the there will be no issues with the code running if If I comment distribution module.

I wanted to use the Snofyre APIs for searching for research purpose. However, I could not locate the developer manual on the site.
Please help in this regard other wise digging in to the code and understanding will take longer and I wanted to do this POC quickly.

[Jay Kola]

Hi,

Snofyre is offered as is and I am unable to support it directly. Please see this post and this post for more information.

As described in the post, you might have some options available, so please provide more details about what you are trying to do with Snofyre.

Regards,

Jay

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[Manisha]

Hi Jay,

Thank you for the reply despite not working on Snofyre currently.
I wanted to use Snofyre query APIs for developing an small POC browser to demonstrate simpler and easier mechanism of using SNOMED CT codes.

- Manisha

[Jay Kola]

Hi Manisha,

There are a few browsers around. If you still want to create your own, then Snofyre is documented well enough to build your own. In fact Snolex, a new online SNOMED CT browser was built using Termlogic, which is Snofyre’s successor.

Unfortunately as a small business startup, I can’t afford to support Snofyre which is almost 5 years old and based on an older release format of SNOMED CT. As I stated in one of my older posts, I am willing to consider offering Termlogic under an open source license if there is sufficient interest and community contribution. Contributions can be either:

• Getting involved in the development
• Sponsoring some of my time for developing a feature
• Or a combination of both or something on those lines.

Otherwise it is available be under a commercial license. 

If you’d like to get in touch about possible contributions, commercial support or opportunities, then please get in touch at in...@noesisinformatica.com

Apologies in advance, if this sounds like a sales pitch, but an open source project like Snofyre without community contributions, license fees or sponsoring clients is just not a viable business model.

Regards,

Jay