Re: managing ctakes resources on classpath
Hi Pei,
Yes, I was able to get as far as it looks like you did - until I ran into
the same error with ytex:
2014-08-25 22:43:09,596 WARN org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
- sql exception - mrconso probably doesn't exist, check error
However, earlier in the ytex tests, I did get another error:
Running org.apache.ctakes.jdl.data.xml.ValidationTest
org.xml.sax.SAXParseException; schema_reference.4: Failed to read schema
document
'file:/C:/Users/oconnell/workspace/cTakes%20Projects/ctakes/ctakes-ytex/file:/C:/Users/oconnell/workspace/cTakes%2520Projects/ctakes/ctakes-ytex-res/target/ctakes-ytex-res-3.2.1-SNAPSHOT.jar!/org/apache/ctakes/jdl/xdl.xsd',
because 1) could not find the document; 2) the document could not be read;
3) the root element of the document is not xsd:schema.
at
com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:198)
...
Caused by: java.io.FileNotFoundException:
C:\Users\oconnell\workspace\cTakes
Projects\ctakes\ctakes-ytex\file:\C:\Users\oconnell\workspace\cTakes%20Projects\ctakes\ctakes-ytex-res\target\ctakes-ytex-res-3.2.1-SNAPSHOT.jar!\org\apache\ctakes\jdl\xdl.xsd
(The filename, directory name, or volume label syntax is incorrect)
...
Tests run: 3, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.624 sec
FAILURE!
It then goes on to keep running tests, and finds the ytex UMLS/SQL error
above, but at the end of that error dump, it says:
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.539 sec
Results :
Tests in error:
setSchema(org.apache.ctakes.jdl.data.xml.ValidationTest)
Tests run: 36, Failures: 0, Errors: 1, Skipped: 4
Which seems to point towards the earlier test error as being what is
stopping the build. Any thoughts?
Tim
On Mon, Aug 25, 2014 at 8:52 AM, Chen, Pei pei.c...@childrens.harvard.edu
wrote:
Tim/Kim,
After a quick debug, it looks like the DependencyParser Tests looks okay,
however, the test pipeline uses LVG. And during maven 'install', these
files are inside a jar which LVG explicitly needs a File or Directory. I
just committed a step in the pom.xml to unpack the lvg-res. This should be
fine for the junit test; but also keep that in mind when configuring for a
production environment.
If you have a chance, could you try trunk? It should solve the parser
issue (and any other test components that depend on lvg-res), but not sure
about potentially other test errors.
--Pei
-Original Message-
From: Tim O'Connell [mailto:tim.oconn...@gmail.com]
Sent: Monday, August 25, 2014 12:38 AM
To: dev@ctakes.apache.org
Subject: Re: managing ctakes resources on classpath
Thanks Kim Pei. If it helps any, I'm getting the same error in
Eclipse.
I just checked out the code this morning from SVN.
Using -DskipTests=true I was able to get it to build from the command
line.
Tim
On Wed, Aug 20, 2014 at 12:41 PM, Kim Ebert
kim.eb...@perfectsearchcorp.com
wrote:
I've added issue 307.
https://issues.apache.org/jira/browse/CTAKES-307
Kim Ebert
1.801.669.7342
Perfect Search Corp
http://www.perfectsearchcorp.com/
On 08/20/2014 11:52 AM, Chen, Pei wrote:
Thanks Kim- would you mind opening up a Jira to track this?
The cTAKES ClearNLP Dependency Parser and/or Test Cases most likely
need
to be updated to enable resources to be picked up from the jar.
-Original Message-
From: Kim Ebert [mailto:kim.eb...@perfectsearchcorp.com]
Sent: Wednesday, August 20, 2014 1:39 PM
To: dev@ctakes.apache.org
Subject: Re: managing ctakes resources on classpath
I'm just using exactly what came out of SVN, so I haven't modified
the default classpath yet.
Kim Ebert
1.801.669.7342
Perfect Search Corp
http://www.perfectsearchcorp.com/
On 08/20/2014 11:28 AM, Chen, Pei wrote:
Do you happen to have both jars and unpacked in your cp?
Temp workaround: -DskipTests=true?
Sent from my iPhone
On Aug 20, 2014, at 1:25 PM, Kim Ebert
kim.eb...@perfectsearchcorp.com wrote:
I am encountering this same issue when I try to run mvn install
from the command line. Is there a way to get mvn install to work?
---
T E S T S
---
Running
org.apache.ctakes.dependency.parser.ae.util.TestClearNLPAnalysisE
ngin
es
log4j: reset attribute= false.
log4j: Threshold =null.
log4j: Level value for root is [INFO].
log4j: root level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: org.apache.log4j.PatternLayout
log4j: Setting property [conversionPattern] to [%d{dd MMM
HH:mm:ss} %5p %c{1} - %m%n].
log4j: Adding appender named [consoleAppender] to category
[root].
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time
Re: managing ctakes resources on classpath
I'm not too privy to the ytex config details, but yes you're right, it's caused by the xdl.xsd being null. However it looks like it exists in ytex-res.jar but the call being made uses Class.getResource which won't be able to read in from the jar as an InputStream. 1) We can make ytex read in resources directly from jars (as maven central artifacts). We can make AppJdl.class.getResourceAsStream() instead of getResource(). However, are there any other local physical File dependencies? 2) Alternatively, we can add a step to have maven unpack res.jar if required. I think 1 would be nice, but not sure how involved it will be. Caused by: java.io.FileNotFoundException: /Users/pei/workspace/apache-ctakes/trunk/ctakes-ytex/file:/Users/pei/workspace/apache-ctakes/trunk/ctakes-ytex-res/target/ctakes-ytex-res-3.2.1-SNAPSHOT.jar!/org/apache/ctakes/jdl/xdl.xsd (No such file or directory) at java.io.FileInputStream.open(Native Method) at java.io.FileInputStream.lt;initgt;(FileInputStream.java:146) at java.io.FileInputStream.lt;initgt;(FileInputStream.java:101) at sun.net.www.protocol.file.FileURLConnection.connect(FileURLConnection.java:90) Anyhow- https://issues.apache.org/jira/browse/CTAKES-308 opened to track this On Tue, Aug 26, 2014 at 3:01 AM, vijay garla vnga...@gmail.com wrote: Hi The test that is failing has nothing to do with the MRCONSO not found warning. ValidationTest failed because it couldn't find the XSD. The XSD is in the ctakes-ytex-resources, but the corresponding maven artifact is an empty jar. I think it would be best to modify the resource jars to actually contain resources.
RE: managing ctakes resources on classpath
Tim/Kim,
After a quick debug, it looks like the DependencyParser Tests looks okay,
however, the test pipeline uses LVG. And during maven 'install', these files
are inside a jar which LVG explicitly needs a File or Directory. I just
committed a step in the pom.xml to unpack the lvg-res. This should be fine for
the junit test; but also keep that in mind when configuring for a production
environment.
If you have a chance, could you try trunk? It should solve the parser issue
(and any other test components that depend on lvg-res), but not sure about
potentially other test errors.
--Pei
-Original Message-
From: Tim O'Connell [mailto:tim.oconn...@gmail.com]
Sent: Monday, August 25, 2014 12:38 AM
To: dev@ctakes.apache.org
Subject: Re: managing ctakes resources on classpath
Thanks Kim Pei. If it helps any, I'm getting the same error in Eclipse.
I just checked out the code this morning from SVN.
Using -DskipTests=true I was able to get it to build from the command line.
Tim
On Wed, Aug 20, 2014 at 12:41 PM, Kim Ebert
kim.eb...@perfectsearchcorp.com
wrote:
I've added issue 307.
https://issues.apache.org/jira/browse/CTAKES-307
Kim Ebert
1.801.669.7342
Perfect Search Corp
http://www.perfectsearchcorp.com/
On 08/20/2014 11:52 AM, Chen, Pei wrote:
Thanks Kim- would you mind opening up a Jira to track this?
The cTAKES ClearNLP Dependency Parser and/or Test Cases most likely
need
to be updated to enable resources to be picked up from the jar.
-Original Message-
From: Kim Ebert [mailto:kim.eb...@perfectsearchcorp.com]
Sent: Wednesday, August 20, 2014 1:39 PM
To: dev@ctakes.apache.org
Subject: Re: managing ctakes resources on classpath
I'm just using exactly what came out of SVN, so I haven't modified
the default classpath yet.
Kim Ebert
1.801.669.7342
Perfect Search Corp
http://www.perfectsearchcorp.com/
On 08/20/2014 11:28 AM, Chen, Pei wrote:
Do you happen to have both jars and unpacked in your cp?
Temp workaround: -DskipTests=true?
Sent from my iPhone
On Aug 20, 2014, at 1:25 PM, Kim Ebert
kim.eb...@perfectsearchcorp.com wrote:
I am encountering this same issue when I try to run mvn install
from the command line. Is there a way to get mvn install to work?
---
T E S T S
---
Running
org.apache.ctakes.dependency.parser.ae.util.TestClearNLPAnalysisE
ngin
es
log4j: reset attribute= false.
log4j: Threshold =null.
log4j: Level value for root is [INFO].
log4j: root level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: org.apache.log4j.PatternLayout
log4j: Setting property [conversionPattern] to [%d{dd MMM
HH:mm:ss} %5p %c{1} - %m%n].
log4j: Adding appender named [consoleAppender] to category
[root].
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed:
1.397 sec FAILURE!
Results :
Tests in error:
TestClearNLPPipeLine(org.apache.ctakes.dependency.parser.ae.util.Te
stCle
arNLPAnalysisEngines):
URI is not hierarchical
Kim Ebert
1.801.669.7342
Perfect Search Corp
http://www.perfectsearchcorp.com/
On 09/10/2013 07:33 AM, Pei Chen wrote:
Hi Steve,
The URI is not hierarchical is most likely caused by the code
trying to use the resources/models, but they are inside a jar
instead of
unpacked.
-Which version of cTAKES are you using?
-Do you happen to have the resource file name that caused the
above?
--Pei
On Mon, Sep 9, 2013 at 9:48 PM, Steve Hookway
shook...@cra.com wrote:
Hi all,
I'm trying to integrate ctakes into a webapp and am running
into issues getting the resources to load correctly. In a
standalone version of the app, if I add the resources folder to
the buildpath (as described in the install directions)
everything works as expected. However, if I add the folder to
the project classpath instead, I get a URI is not hierarchical
exception from
FileResourceImpl.load:
java.lang.IllegalArgumentException: URI is not hierarchical
at java.io.File.init(File.java:392)
at
org.apache.ctakes.core.resource.FileResourceImpl.load(FileResourceImpl
.ja
va:44)
at
org.apache.uima.resource.impl.ResourceManager_impl.registerResource
(ResourceManager_impl.java:603)
Similarly if I try and run from a webapp - setting up tomcat's
classpath to include the ctakes resource folder, I get the same
URI is not hierarchical error. I found this bug report:
https://issues.apache.org/jira/browse/CTAKES-89 but it
suggests adding the resource folder to my classpath, which
isn't doing the
trick.
If you can steer me in the right direction, I'd really
appreciate
Re: managing ctakes resources on classpath
Thanks Kim Pei. If it helps any, I'm getting the same error in Eclipse.
I just checked out the code this morning from SVN.
Using -DskipTests=true I was able to get it to build from the command line.
Tim
On Wed, Aug 20, 2014 at 12:41 PM, Kim Ebert kim.eb...@perfectsearchcorp.com
wrote:
I've added issue 307.
https://issues.apache.org/jira/browse/CTAKES-307
Kim Ebert
1.801.669.7342
Perfect Search Corp
http://www.perfectsearchcorp.com/
On 08/20/2014 11:52 AM, Chen, Pei wrote:
Thanks Kim- would you mind opening up a Jira to track this?
The cTAKES ClearNLP Dependency Parser and/or Test Cases most likely need
to be updated to enable resources to be picked up from the jar.
-Original Message-
From: Kim Ebert [mailto:kim.eb...@perfectsearchcorp.com]
Sent: Wednesday, August 20, 2014 1:39 PM
To: dev@ctakes.apache.org
Subject: Re: managing ctakes resources on classpath
I'm just using exactly what came out of SVN, so I haven't modified the
default classpath yet.
Kim Ebert
1.801.669.7342
Perfect Search Corp
http://www.perfectsearchcorp.com/
On 08/20/2014 11:28 AM, Chen, Pei wrote:
Do you happen to have both jars and unpacked in your cp?
Temp workaround: -DskipTests=true?
Sent from my iPhone
On Aug 20, 2014, at 1:25 PM, Kim Ebert
kim.eb...@perfectsearchcorp.com wrote:
I am encountering this same issue when I try to run mvn install from
the command line. Is there a way to get mvn install to work?
---
T E S T S
---
Running
org.apache.ctakes.dependency.parser.ae.util.TestClearNLPAnalysisEngin
es
log4j: reset attribute= false.
log4j: Threshold =null.
log4j: Level value for root is [INFO].
log4j: root level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: org.apache.log4j.PatternLayout
log4j: Setting property [conversionPattern] to [%d{dd MMM
HH:mm:ss} %5p %c{1} - %m%n].
log4j: Adding appender named [consoleAppender] to category [root].
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 1.397
sec FAILURE!
Results :
Tests in error:
TestClearNLPPipeLine(org.apache.ctakes.dependency.parser.ae.util.TestCle
arNLPAnalysisEngines):
URI is not hierarchical
Kim Ebert
1.801.669.7342
Perfect Search Corp
http://www.perfectsearchcorp.com/
On 09/10/2013 07:33 AM, Pei Chen wrote:
Hi Steve,
The URI is not hierarchical is most likely caused by the code trying
to use the resources/models, but they are inside a jar instead of
unpacked.
-Which version of cTAKES are you using?
-Do you happen to have the resource file name that caused the above?
--Pei
On Mon, Sep 9, 2013 at 9:48 PM, Steve Hookway
shook...@cra.com wrote:
Hi all,
I'm trying to integrate ctakes into a webapp and am running into
issues getting the resources to load correctly. In a standalone
version of the app, if I add the resources folder to the buildpath
(as described in the install directions) everything works as
expected. However, if I add the folder to the project classpath
instead, I get a URI is not hierarchical exception from
FileResourceImpl.load:
java.lang.IllegalArgumentException: URI is not hierarchical
at java.io.File.init(File.java:392)
at
org.apache.ctakes.core.resource.FileResourceImpl.load(FileResourceImpl.ja
va:44)
at
org.apache.uima.resource.impl.ResourceManager_impl.registerResource
(ResourceManager_impl.java:603)
Similarly if I try and run from a webapp - setting up tomcat's
classpath to include the ctakes resource folder, I get the same URI
is not hierarchical error. I found this bug report:
https://issues.apache.org/jira/browse/CTAKES-89 but it suggests
adding the resource folder to my classpath, which isn't doing the
trick.
If you can steer me in the right direction, I'd really appreciate
it.
Thanks,
Steve
THIS MESSAGE IS INTENDED FOR THE USE OF THE PERSON TO WHOM IT
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ADDRESSED. IT MAY CONTAIN INFORMATION THAT IS PRIVILEGED,
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LAW. If
you are not the intended recipient, your use of this message for any
purpose is strictly prohibited.
If you have received this communication in error, please delete the
message and notify the sender so that we may correct our records.
Re: managing ctakes resources on classpath
I've added issue 307.
https://issues.apache.org/jira/browse/CTAKES-307
Kim Ebert
1.801.669.7342
Perfect Search Corp
http://www.perfectsearchcorp.com/
On 08/20/2014 11:52 AM, Chen, Pei wrote:
Thanks Kim- would you mind opening up a Jira to track this?
The cTAKES ClearNLP Dependency Parser and/or Test Cases most likely need to
be updated to enable resources to be picked up from the jar.
-Original Message-
From: Kim Ebert [mailto:kim.eb...@perfectsearchcorp.com]
Sent: Wednesday, August 20, 2014 1:39 PM
To: dev@ctakes.apache.org
Subject: Re: managing ctakes resources on classpath
I'm just using exactly what came out of SVN, so I haven't modified the
default classpath yet.
Kim Ebert
1.801.669.7342
Perfect Search Corp
http://www.perfectsearchcorp.com/
On 08/20/2014 11:28 AM, Chen, Pei wrote:
Do you happen to have both jars and unpacked in your cp?
Temp workaround: -DskipTests=true?
Sent from my iPhone
On Aug 20, 2014, at 1:25 PM, Kim Ebert
kim.eb...@perfectsearchcorp.com wrote:
I am encountering this same issue when I try to run mvn install from
the command line. Is there a way to get mvn install to work?
---
T E S T S
---
Running
org.apache.ctakes.dependency.parser.ae.util.TestClearNLPAnalysisEngin
es
log4j: reset attribute= false.
log4j: Threshold =null.
log4j: Level value for root is [INFO].
log4j: root level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: org.apache.log4j.PatternLayout
log4j: Setting property [conversionPattern] to [%d{dd MMM
HH:mm:ss} %5p %c{1} - %m%n].
log4j: Adding appender named [consoleAppender] to category [root].
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 1.397
sec FAILURE!
Results :
Tests in error:
TestClearNLPPipeLine(org.apache.ctakes.dependency.parser.ae.util.TestCle
arNLPAnalysisEngines):
URI is not hierarchical
Kim Ebert
1.801.669.7342
Perfect Search Corp
http://www.perfectsearchcorp.com/
On 09/10/2013 07:33 AM, Pei Chen wrote:
Hi Steve,
The URI is not hierarchical is most likely caused by the code trying
to use the resources/models, but they are inside a jar instead of
unpacked.
-Which version of cTAKES are you using?
-Do you happen to have the resource file name that caused the above?
--Pei
On Mon, Sep 9, 2013 at 9:48 PM, Steve Hookway
shook...@cra.com wrote:
Hi all,
I'm trying to integrate ctakes into a webapp and am running into
issues getting the resources to load correctly. In a standalone
version of the app, if I add the resources folder to the buildpath
(as described in the install directions) everything works as
expected. However, if I add the folder to the project classpath
instead, I get a URI is not hierarchical exception from
FileResourceImpl.load:
java.lang.IllegalArgumentException: URI is not hierarchical
at java.io.File.init(File.java:392)
at
org.apache.ctakes.core.resource.FileResourceImpl.load(FileResourceImpl.ja
va:44)
at
org.apache.uima.resource.impl.ResourceManager_impl.registerResource
(ResourceManager_impl.java:603)
Similarly if I try and run from a webapp - setting up tomcat's
classpath to include the ctakes resource folder, I get the same URI
is not hierarchical error. I found this bug report:
https://issues.apache.org/jira/browse/CTAKES-89 but it suggests
adding the resource folder to my classpath, which isn't doing the trick.
If you can steer me in the right direction, I'd really appreciate it.
Thanks,
Steve
THIS MESSAGE IS INTENDED FOR THE USE OF THE PERSON TO WHOM IT
IS
ADDRESSED. IT MAY CONTAIN INFORMATION THAT IS PRIVILEGED,
CONFIDENTIAL AND EXEMPT FROM DISCLOSURE UNDER APPLICABLE
LAW. If
you are not the intended recipient, your use of this message for any
purpose is strictly prohibited.
If you have received this communication in error, please delete the
message and notify the sender so that we may correct our records.
