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Posted to user@ctakes.apache.org by David Kincaid <ki...@gmail.com> on 2014/11/26 21:31:51 UTC
URI is not hierarchical exception from LvgCmdApiResourceImpl
Does anyone know what is causing this exception:
java.lang.IllegalArgumentException: URI is not hierarchical
at java.io.File.<init>(File.java:418)
at
org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl.load(LvgCmdApiResourceImpl.java:65)
I'm getting that when I try to run the clinical pipeline inside of IntelliJ
using a TestNG unit test. I can run the pipeline from CPE and from a
Clojure REPL no problem, so it must be something in IntelliJ setting
something up wrong.
When I step through a debugger the uri it's trying to use is:
jar:file:/home/davek/.m2/repository/org/apache/ctakes/ctakes-lvg-res/3.2.0/ctakes-lvg-res-3.2.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
which is clearly not a valid file path.
I came across Jira ticket CTAKES-314
<https://issues.apache.org/jira/browse/CTAKES-314> when it's mentioned one
time without any discussion. I haven't found any other references to it yet
though.
Thanks,
Dave
Re: URI is not hierarchical exception from LvgCmdApiResourceImpl
Posted by David Kincaid <ki...@gmail.com>.
Just to close things up I found the problem. I hadn't tagged my resources
directory as containing resources in the IntelliJ project settings. Once I
did that it runs just fine. Thanks for pointing me to it, Kim!
- Dave
On Wed, Nov 26, 2014 at 3:09 PM, David Kincaid <ki...@gmail.com>
wrote:
> Thanks, Kim! That at least gives me somewhere to go. Hopefully it gets
> resolved soon.
>
> - Dave
>
> On Wed, Nov 26, 2014 at 3:06 PM, Kim Ebert <ki...@imatsolutions.com>
> wrote:
>
>> David,
>>
>> See the following ticket.
>>
>> https://issues.apache.org/jira/browse/CTAKES-307
>>
>> Although, looking at the ticket itself seems to indicate that we only
>> fixed the build by extracting the contents of the jar file, and using that
>> in the classpath instead of the jar.
>>
>>
>> [image: IMAT Solutions] <http://imatsolutions.com>
>> Kim Ebert
>> Software Engineer
>> [image: Office:] 801.669.7342
>> kim.ebert@imatsolutions.com <gr...@imatsolutions.com>
>> On 11/26/2014 02:03 PM, Kim Ebert wrote:
>>
>> Hi David,
>>
>> I know that a few people have run into this issue. If it runs
>> successfully in one environment vs the other, you may want to check the
>> ordering of the libraries and resource directory in the classpath.
>>
>> This can be solved by using the resources outside of the jar file. I'm
>> hoping this issue ends up being resolved at some point. I believe Pei Chen
>> has made a few fixes, but I don't think that was in the 3.2.0 release.
>>
>> Thanks,
>>
>> [image: IMAT Solutions] <http://imatsolutions.com>
>> Kim Ebert
>> Software Engineer
>> [image: Office:] 801.669.7342
>> kim.ebert@imatsolutions.com <gr...@imatsolutions.com>
>> On 11/26/2014 01:31 PM, David Kincaid wrote:
>>
>> Does anyone know what is causing this exception:
>>
>> java.lang.IllegalArgumentException: URI is not hierarchical
>> at java.io.File.<init>(File.java:418)
>> at
>> org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl.load(LvgCmdApiResourceImpl.java:65)
>>
>> I'm getting that when I try to run the clinical pipeline inside of
>> IntelliJ using a TestNG unit test. I can run the pipeline from CPE and from
>> a Clojure REPL no problem, so it must be something in IntelliJ setting
>> something up wrong.
>>
>> When I step through a debugger the uri it's trying to use is:
>>
>>
>> jar:file:/home/davek/.m2/repository/org/apache/ctakes/ctakes-lvg-res/3.2.0/ctakes-lvg-res-3.2.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
>>
>> which is clearly not a valid file path.
>>
>> I came across Jira ticket CTAKES-314
>> <https://issues.apache.org/jira/browse/CTAKES-314> when it's mentioned
>> one time without any discussion. I haven't found any other references to it
>> yet though.
>>
>> Thanks,
>>
>> Dave
>>
>>
>>
>>
>
Re: URI is not hierarchical exception from LvgCmdApiResourceImpl
Posted by David Kincaid <ki...@gmail.com>.
Thanks, Kim! That at least gives me somewhere to go. Hopefully it gets
resolved soon.
- Dave
On Wed, Nov 26, 2014 at 3:06 PM, Kim Ebert <ki...@imatsolutions.com>
wrote:
> David,
>
> See the following ticket.
>
> https://issues.apache.org/jira/browse/CTAKES-307
>
> Although, looking at the ticket itself seems to indicate that we only
> fixed the build by extracting the contents of the jar file, and using that
> in the classpath instead of the jar.
>
>
> [image: IMAT Solutions] <http://imatsolutions.com>
> Kim Ebert
> Software Engineer
> [image: Office:] 801.669.7342
> kim.ebert@imatsolutions.com <gr...@imatsolutions.com>
> On 11/26/2014 02:03 PM, Kim Ebert wrote:
>
> Hi David,
>
> I know that a few people have run into this issue. If it runs successfully
> in one environment vs the other, you may want to check the ordering of the
> libraries and resource directory in the classpath.
>
> This can be solved by using the resources outside of the jar file. I'm
> hoping this issue ends up being resolved at some point. I believe Pei Chen
> has made a few fixes, but I don't think that was in the 3.2.0 release.
>
> Thanks,
>
> [image: IMAT Solutions] <http://imatsolutions.com>
> Kim Ebert
> Software Engineer
> [image: Office:] 801.669.7342
> kim.ebert@imatsolutions.com <gr...@imatsolutions.com>
> On 11/26/2014 01:31 PM, David Kincaid wrote:
>
> Does anyone know what is causing this exception:
>
> java.lang.IllegalArgumentException: URI is not hierarchical
> at java.io.File.<init>(File.java:418)
> at
> org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl.load(LvgCmdApiResourceImpl.java:65)
>
> I'm getting that when I try to run the clinical pipeline inside of
> IntelliJ using a TestNG unit test. I can run the pipeline from CPE and from
> a Clojure REPL no problem, so it must be something in IntelliJ setting
> something up wrong.
>
> When I step through a debugger the uri it's trying to use is:
>
>
> jar:file:/home/davek/.m2/repository/org/apache/ctakes/ctakes-lvg-res/3.2.0/ctakes-lvg-res-3.2.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
>
> which is clearly not a valid file path.
>
> I came across Jira ticket CTAKES-314
> <https://issues.apache.org/jira/browse/CTAKES-314> when it's mentioned
> one time without any discussion. I haven't found any other references to it
> yet though.
>
> Thanks,
>
> Dave
>
>
>
>
Re: URI is not hierarchical exception from LvgCmdApiResourceImpl
Posted by Kim Ebert <ki...@imatsolutions.com>.
David,
See the following ticket.
https://issues.apache.org/jira/browse/CTAKES-307
Although, looking at the ticket itself seems to indicate that we only
fixed the build by extracting the contents of the jar file, and using
that in the classpath instead of the jar.
IMAT Solutions <http://imatsolutions.com>
Kim Ebert
Software Engineer
Office: 801.669.7342
kim.ebert@imatsolutions.com <ma...@imatsolutions.com>
On 11/26/2014 02:03 PM, Kim Ebert wrote:
> Hi David,
>
> I know that a few people have run into this issue. If it runs
> successfully in one environment vs the other, you may want to check
> the ordering of the libraries and resource directory in the classpath.
>
> This can be solved by using the resources outside of the jar file. I'm
> hoping this issue ends up being resolved at some point. I believe Pei
> Chen has made a few fixes, but I don't think that was in the 3.2.0
> release.
>
> Thanks,
>
> IMAT Solutions <http://imatsolutions.com>
> Kim Ebert
> Software Engineer
> Office: 801.669.7342
> kim.ebert@imatsolutions.com <ma...@imatsolutions.com>
> On 11/26/2014 01:31 PM, David Kincaid wrote:
>> Does anyone know what is causing this exception:
>>
>> java.lang.IllegalArgumentException: URI is not hierarchical
>> at java.io.File.<init>(File.java:418)
>> at
>> org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl.load(LvgCmdApiResourceImpl.java:65)
>>
>> I'm getting that when I try to run the clinical pipeline inside of
>> IntelliJ using a TestNG unit test. I can run the pipeline from CPE
>> and from a Clojure REPL no problem, so it must be something in
>> IntelliJ setting something up wrong.
>>
>> When I step through a debugger the uri it's trying to use is:
>>
>> jar:file:/home/davek/.m2/repository/org/apache/ctakes/ctakes-lvg-res/3.2.0/ctakes-lvg-res-3.2.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
>>
>> which is clearly not a valid file path.
>>
>> I came across Jira ticket CTAKES-314
>> <https://issues.apache.org/jira/browse/CTAKES-314> when it's
>> mentioned one time without any discussion. I haven't found any other
>> references to it yet though.
>>
>> Thanks,
>>
>> Dave
>
Re: URI is not hierarchical exception from LvgCmdApiResourceImpl
Posted by Kim Ebert <ki...@perfectsearchcorp.com>.
Hi David,
I know that a few people have run into this issue. If it runs
successfully in one environment vs the other, you may want to check the
ordering of the libraries and resource directory in the classpath.
This can be solved by using the resources outside of the jar file. I'm
hoping this issue ends up being resolved at some point. I believe Pei
Chen has made a few fixes, but I don't think that was in the 3.2.0 release.
Thanks,
IMAT Solutions <http://imatsolutions.com>
Kim Ebert
Software Engineer
Office: 801.669.7342
kim.ebert@imatsolutions.com <ma...@imatsolutions.com>
On 11/26/2014 01:31 PM, David Kincaid wrote:
> Does anyone know what is causing this exception:
>
> java.lang.IllegalArgumentException: URI is not hierarchical
> at java.io.File.<init>(File.java:418)
> at
> org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl.load(LvgCmdApiResourceImpl.java:65)
>
> I'm getting that when I try to run the clinical pipeline inside of
> IntelliJ using a TestNG unit test. I can run the pipeline from CPE and
> from a Clojure REPL no problem, so it must be something in IntelliJ
> setting something up wrong.
>
> When I step through a debugger the uri it's trying to use is:
>
> jar:file:/home/davek/.m2/repository/org/apache/ctakes/ctakes-lvg-res/3.2.0/ctakes-lvg-res-3.2.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
>
> which is clearly not a valid file path.
>
> I came across Jira ticket CTAKES-314
> <https://issues.apache.org/jira/browse/CTAKES-314> when it's mentioned
> one time without any discussion. I haven't found any other references
> to it yet though.
>
> Thanks,
>
> Dave