date:20171114

RE: Lab report [EXTERNAL]

2017-11-14 Thread Abilash.Mathew

Thanks Sean Kean for the help.

Regards,
Abilash Mathew

-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, November 15, 2017 5:40 AM
To: dev@ctakes.apache.org
Subject: RE: Lab report [EXTERNAL]

Hi all,

I checked in Kean's code as LabValueFinder in ctakes-core.  Use is fairly 
straightforward - you can look at the annotator class or the unit test in 
ctakes-regression-test to get a handle on it.

Enjoy,
Sean

-Original Message-
From: Kean Kaufmann [mailto:k...@recordsone.com.INVALID]
Sent: Monday, November 13, 2017 8:12 AM
To: dev@ctakes.apache.org
Subject: Re: Lab report [EXTERNAL]

I wrote a lab annotator that will be checked into the trunk at some point.
Source, unit tests and description attached to this issue:

https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D441=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=vupXKKrBnEXa3M1uhOD2626jlOBVHpUbGwkU1GVWKN4=qrkcg7rc2dbpkMvL3iSKFsQONNpBk1h22lhNWZRBt4Q=

On Mon, Nov 13, 2017 at 6:09 AM,  wrote:

> Hi All,
>
> Can CTAKES process LAB reports and able to extract key findings from
> the report?
>
>
> Thanks,
> Abilash Mathew
>
> This e-mail and any files transmitted with it are for the sole use of
> the intended recipient(s) and may contain confidential and privileged
> information. If you are not the intended recipient(s), please reply to
> the sender and destroy all copies of the original message. Any
> unauthorized review, use, disclosure, dissemination, forwarding,
> printing or copying of this email, and/or any action taken in reliance
> on the contents of this e-mail is strictly prohibited and may be
> unlawful. Where permitted by applicable law, this e-mail and other
> e-mail communications sent to and from Cognizant e-mail addresses may be 
> monitored.
>
This e-mail and any files transmitted with it are for the sole use of the 
intended recipient(s) and may contain confidential and privileged information. 
If you are not the intended recipient(s), please reply to the sender and 
destroy all copies of the original message. Any unauthorized review, use, 
disclosure, dissemination, forwarding, printing or copying of this email, 
and/or any action taken in reliance on the contents of this e-mail is strictly 
prohibited and may be unlawful. Where permitted by applicable law, this e-mail 
and other e-mail communications sent to and from Cognizant e-mail addresses may 
be monitored.

Re: Disable yTEX and Regression tests on Jenkins [EXTERNAL]

2017-11-14 Thread Alexandru Zbarcea

Hi,

It seems that the patch for the org.apache.ctakes.ytex.ConceptDaoTest was
already provided on CTAKES-334.

Applying the fix passes the test.

The only test that needs to be fixed seems to be:
RegressionPipelineTest:testCPE. For this, the fix is to export the UMLS
credentials.

I am currently working on enabling the the test based on the umls
credentials being available and enforcing the execution on a release
profile, which now seems to be disabled:
useReleaseProfile>falsehttps://builds.apache.org/view/C/view/Apache%20cTAKES/job/ctakes-trunk-compiletest/1124/org.apache.ctakes$ctakes-regression-test/testReport/org.apache.ctakes.regression.test/RegressionPipelineTest/testCPE/


On Tue, Nov 14, 2017 at 9:47 AM, Gandhi Rajan Natarajan <
gandhi.natara...@arisglobal.com> wrote:

> Hi Alex,
>
> The error we got in ConceptDaoTest is different from yours. We got the
> following:
>
> testCreateConceptGraph(org.apache.ctakes.ytex.ConceptDaoTest): Unable to
> initialize group definition. Group resource name
> [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key
> [kernelApplicationContext]; nested exception is
> org.springframework.beans.factory.BeanCreationException: Error creating
> bean with name 'kernelApplicationContext' defined in URL
> [file:/D:/Gandhi/ArisG/cTAKES/ctakes_src_new%20-%20Copy/ctak
> es-ytex-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]:
> Instantiation of bean failed; nested exception is
> org.springframework.beans.BeanInstantiationException: Could not
> instantiate bean class [org.springframework.context.s
> upport.ClassPathXmlApplicationContext]: Constructor threw exception;
> nested exception is org.springframework.beans.factory.BeanCreationException:
> Error creating bean with name 'gramMatrixExporter' defined in class path
> resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of
> bean failed; nested exception is org.springframework.beans.FatalBeanException:
> Failed to obtain BeanInfo for class 
> [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl];
> nested exception is java.beans.IntrospectionException: type mismatch
> between read and write methods
>
> Can you do a full build once and try?
>
> Regards,
> Gandhi
>
>
> -Original Message-
> From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
> Sent: Tuesday, November 14, 2017 7:36 PM
> To: dev@ctakes.apache.org
> Subject: RE: Disable yTEX and Regression tests on Jenkins [EXTERNAL]
>
> Hi Alex,
>
> Major kudos for trying to track this down.
>
> I am not sure why you are seeing that particular problem.  Metadata class
> should be auto-generated from the type system, and it does have the
> getPatientIdentifier() method.
> https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-type-sy
> stem/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
>
> Do you think that it is possible that the jcasgen is not being run before
> the test?  I think that it is run for ctakes-util, which is a dependency
> for all modules.
>
> Regardless, I cannot see where getPatientIdentifier() is used in
> ConceptDaoTest.  I can't see where the class Metadata is used in
> ConceptDaoTest.  From a quick code search, Metadata is only used by the
> class SourceMetadataUtil in core.  SourceMetadataUtil is only used by two
> classes, both in core.  I think that the change in test status is actually
> unrelated to the Metadata checkin.  That being said, I don't have any good
> idea about what is causing it.
>
> Thanks,
> Sean
>
> -Original Message-
> From: Alexandru Zbarcea [mailto:zbarce...@gmail.com]
> Sent: Monday, November 13, 2017 6:24 PM
> To: Apache cTAKES Dev
> Subject: RE: Disable yTEX and Regression tests on Jenkins [EXTERNAL]
>
> Hi,
>
> The official Jenkins job (referenced in the pom.xml) is:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__builds.
> apache.org_job_ctakes-2Dtrunk_=DwIBaQ=qS4goWBT7poplM69zy
> _3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpK
> Gd4f7d4gTao=l0_Tnqk6P-iMIhPUpRO8RiW-eImTKvJDGishYy1Jk-o=
> ul6gCHWXUReDCZccgemrhL9EEFs0Id7WilYITMNr5yw=. As one may notice, the
> status is Unstable. I was working on the cTAKES-trunk-Java-1.8 Jenkins job
> [1] to try to fix the issues there. As such the tests failed can be found
> here [2].
>
> So trying to fix one by one, I discovered that for
> ctakes-ytex:ConceptDaoTest.java:testCreateConceptGraph:
>
> There is the construction:
> metadata.getPatientIdentifier()
> (where metadata:org.apache.ctakes.typesystem.type.structured.Metadata).
>
> Researching where this comes (because it seems it is a new issue), I
> realized that is related to:
> ctakes-type-system/target/generated-sources/jcasgen/org/apac
> he/ctakes/typesystem/type/structured/Metadata.java
> :75:  public String getPatientIdentifier() {
>
> more:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
> com_apache_ctakes_commit_bcdc25420eede623a0889b1db26e1307a2b
>

RE: Lab report [EXTERNAL]

2017-11-14 Thread Finan, Sean

Hi all,

I checked in Kean's code as LabValueFinder in ctakes-core.  Use is fairly 
straightforward - you can look at the annotator class or the unit test in 
ctakes-regression-test to get a handle on it.

Enjoy,
Sean

-Original Message-
From: Kean Kaufmann [mailto:k...@recordsone.com.INVALID] 
Sent: Monday, November 13, 2017 8:12 AM
To: dev@ctakes.apache.org
Subject: Re: Lab report [EXTERNAL]

I wrote a lab annotator that will be checked into the trunk at some point.
Source, unit tests and description attached to this issue:

https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D441=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=vupXKKrBnEXa3M1uhOD2626jlOBVHpUbGwkU1GVWKN4=qrkcg7rc2dbpkMvL3iSKFsQONNpBk1h22lhNWZRBt4Q=

On Mon, Nov 13, 2017 at 6:09 AM,  wrote:

> Hi All,
>
> Can CTAKES process LAB reports and able to extract key findings from 
> the report?
>
>
> Thanks,
> Abilash Mathew
>
> This e-mail and any files transmitted with it are for the sole use of 
> the intended recipient(s) and may contain confidential and privileged 
> information. If you are not the intended recipient(s), please reply to 
> the sender and destroy all copies of the original message. Any 
> unauthorized review, use, disclosure, dissemination, forwarding, 
> printing or copying of this email, and/or any action taken in reliance 
> on the contents of this e-mail is strictly prohibited and may be 
> unlawful. Where permitted by applicable law, this e-mail and other 
> e-mail communications sent to and from Cognizant e-mail addresses may be 
> monitored.
>

RE: Disable yTEX and Regression tests on Jenkins [EXTERNAL]

2017-11-14 Thread Gandhi Rajan Natarajan

Hi Alex,

The error we got in ConceptDaoTest is different from yours. We got the 
following:

testCreateConceptGraph(org.apache.ctakes.ytex.ConceptDaoTest): Unable to 
initialize group definition. Group resource name 
[classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key 
[kernelApplicationContext]; nested exception is 
org.springframework.beans.factory.BeanCreationException: Error creating bean 
with name 'kernelApplicationContext' defined in URL 
[file:/D:/Gandhi/ArisG/cTAKES/ctakes_src_new%20-%20Copy/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]:
 Instantiation of bean failed; nested exception is 
org.springframework.beans.BeanInstantiationException: Could not instantiate 
bean class 
[org.springframework.context.support.ClassPathXmlApplicationContext]: 
Constructor threw exception; nested exception is 
org.springframework.beans.factory.BeanCreationException: Error creating bean 
with name 'gramMatrixExporter' defined in class path resource 
[org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; 
nested exception is org.springframework.beans.FatalBeanException: Failed to 
obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; 
nested exception is java.beans.IntrospectionException: type mismatch between 
read and write methods

Can you do a full build once and try?

Regards,
Gandhi


-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Tuesday, November 14, 2017 7:36 PM
To: dev@ctakes.apache.org
Subject: RE: Disable yTEX and Regression tests on Jenkins [EXTERNAL]

Hi Alex,

Major kudos for trying to track this down.

I am not sure why you are seeing that particular problem.  Metadata class 
should be auto-generated from the type system, and it does have the 
getPatientIdentifier() method.
https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml

Do you think that it is possible that the jcasgen is not being run before the 
test?  I think that it is run for ctakes-util, which is a dependency for all 
modules.

Regardless, I cannot see where getPatientIdentifier() is used in 
ConceptDaoTest.  I can't see where the class Metadata is used in 
ConceptDaoTest.  From a quick code search, Metadata is only used by the class 
SourceMetadataUtil in core.  SourceMetadataUtil is only used by two classes, 
both in core.  I think that the change in test status is actually unrelated to 
the Metadata checkin.  That being said, I don't have any good idea about what 
is causing it.

Thanks,
Sean

-Original Message-
From: Alexandru Zbarcea [mailto:zbarce...@gmail.com]
Sent: Monday, November 13, 2017 6:24 PM
To: Apache cTAKES Dev
Subject: RE: Disable yTEX and Regression tests on Jenkins [EXTERNAL]

Hi,

The official Jenkins job (referenced in the pom.xml) is:
https://urldefense.proofpoint.com/v2/url?u=https-3A__builds.apache.org_job_ctakes-2Dtrunk_=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=l0_Tnqk6P-iMIhPUpRO8RiW-eImTKvJDGishYy1Jk-o=ul6gCHWXUReDCZccgemrhL9EEFs0Id7WilYITMNr5yw=.
 As one may notice, the status is Unstable. I was working on the 
cTAKES-trunk-Java-1.8 Jenkins job [1] to try to fix the issues there. As such 
the tests failed can be found here [2].

So trying to fix one by one, I discovered that for
ctakes-ytex:ConceptDaoTest.java:testCreateConceptGraph:

There is the construction:
metadata.getPatientIdentifier()
(where metadata:org.apache.ctakes.typesystem.type.structured.Metadata).

Researching where this comes (because it seems it is a new issue), I realized 
that is related to:
ctakes-type-system/target/generated-sources/jcasgen/org/apache/ctakes/typesystem/type/structured/Metadata.java
:75:  public String getPatientIdentifier() {

more:
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_apache_ctakes_commit_bcdc25420eede623a0889b1db26e1307a2b193bf=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=l0_Tnqk6P-iMIhPUpRO8RiW-eImTKvJDGishYy1Jk-o=c2oayQ5_G3YgHT5iX9AJw9kuhIr94bFRZ7nxj3ebpuw=
(10 Oct 2017)

I thought that it will be a quick fix just replacing:

metadata.getPatientIdentifier()

with

String.format("%d", metadata.getPatientID());


Any feedback?
Alex

[1] -
https://urldefense.proofpoint.com/v2/url?u=https-3A__builds.apache.org_view_C_view_Apache-2520cTAKES_job_cTAKES-2Dtrunk-2DJava-2D1.8_=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=l0_Tnqk6P-iMIhPUpRO8RiW-eImTKvJDGishYy1Jk-o=aRH4KLtGndnC-b7UTdMqjej6vTDKxavocQwUokE6EHw=
[2] -

RE: Disable yTEX and Regression tests on Jenkins [EXTERNAL]

2017-11-14 Thread Finan, Sean

Hi Alex,

Major kudos for trying to track this down.

I am not sure why you are seeing that particular problem.  Metadata class 
should be auto-generated from the type system, and it does have the 
getPatientIdentifier() method.
https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml

Do you think that it is possible that the jcasgen is not being run before the 
test?  I think that it is run for ctakes-util, which is a dependency for all 
modules.

Regardless, I cannot see where getPatientIdentifier() is used in 
ConceptDaoTest.  I can't see where the class Metadata is used in 
ConceptDaoTest.  From a quick code search, Metadata is only used by the class 
SourceMetadataUtil in core.  SourceMetadataUtil is only used by two classes, 
both in core.  I think that the change in test status is actually unrelated to 
the Metadata checkin.  That being said, I don't have any good idea about what 
is causing it.

Thanks,
Sean

-Original Message-
From: Alexandru Zbarcea [mailto:zbarce...@gmail.com] 
Sent: Monday, November 13, 2017 6:24 PM
To: Apache cTAKES Dev
Subject: RE: Disable yTEX and Regression tests on Jenkins [EXTERNAL]

Hi,

The official Jenkins job (referenced in the pom.xml) is:
https://urldefense.proofpoint.com/v2/url?u=https-3A__builds.apache.org_job_ctakes-2Dtrunk_=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=l0_Tnqk6P-iMIhPUpRO8RiW-eImTKvJDGishYy1Jk-o=ul6gCHWXUReDCZccgemrhL9EEFs0Id7WilYITMNr5yw=.
 As one may notice, the status is Unstable. I was working on the 
cTAKES-trunk-Java-1.8 Jenkins job [1] to try to fix the issues there. As such 
the tests failed can be found here [2].

So trying to fix one by one, I discovered that for
ctakes-ytex:ConceptDaoTest.java:testCreateConceptGraph:

There is the construction:
metadata.getPatientIdentifier()
(where metadata:org.apache.ctakes.typesystem.type.structured.Metadata).

Researching where this comes (because it seems it is a new issue), I realized 
that is related to:
ctakes-type-system/target/generated-sources/jcasgen/org/apache/ctakes/typesystem/type/structured/Metadata.java
:75:  public String getPatientIdentifier() {

more:
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_apache_ctakes_commit_bcdc25420eede623a0889b1db26e1307a2b193bf=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=l0_Tnqk6P-iMIhPUpRO8RiW-eImTKvJDGishYy1Jk-o=c2oayQ5_G3YgHT5iX9AJw9kuhIr94bFRZ7nxj3ebpuw=
(10 Oct 2017)

I thought that it will be a quick fix just replacing:

metadata.getPatientIdentifier()

with

String.format("%d", metadata.getPatientID());

Any feedback?
Alex

[1] -
https://urldefense.proofpoint.com/v2/url?u=https-3A__builds.apache.org_view_C_view_Apache-2520cTAKES_job_cTAKES-2Dtrunk-2DJava-2D1.8_=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=l0_Tnqk6P-iMIhPUpRO8RiW-eImTKvJDGishYy1Jk-o=aRH4KLtGndnC-b7UTdMqjej6vTDKxavocQwUokE6EHw=
[2] -
https://urldefense.proofpoint.com/v2/url?u=https-3A__builds.apache.org_view_C_view_Apache-2520cTAKES_job_cTAKES-2Dtrunk-2DJava-2D1.8_25_testReport_=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=l0_Tnqk6P-iMIhPUpRO8RiW-eImTKvJDGishYy1Jk-o=-PwjGWv5MEFT_1Jui9b27fdgkKfFRa29hts-FMalo8I=

On Nov 13, 2017 10:41, "Finan, Sean" 
wrote:

> Thanks Gandhi!
>
> -Original Message-
> From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
> Sent: Monday, November 13, 2017 10:40 AM
> To: dev@ctakes.apache.org
> Subject: RE: Disable yTEX and Regression tests on Jenkins [EXTERNAL]
>
> Hi All,
>
> We had a look at ctakes-Ytex module's failing test cases and looks 
> like it will not have an impact once we upgrade Spring 4x in cTAKES.
>
> We will have a run through at other modules and check the failing test 
> cases if any.
>
> Regards,
> Gandhi
>
>
> -Original Message-
> From: Sandeep Byatha Gururaja rao [mailto:sandeep...@arisglobal.com]
> Sent: Monday, November 13, 2017 6:50 PM
> To: dev@ctakes.apache.org
> Subject: RE: Disable yTEX and Regression tests on Jenkins [EXTERNAL]
>
> Hi Sean,
>
> Myself and Gandhi will work on this and try to fix the issues.
>
> Regards,
> Sandeep
>
> 
>
> Hi Gandhi,
>
> Many thanks for volunteering.  I am slammed with work right now, but 
> if anybody else can also help out ...
>
> Sean
>
> -Original Message-
> From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
> Sent: Thursday, November 09, 2017 12:43 AM
> To: dev@ctakes.apache.org
> Subject: RE: Disable yTEX and Regression tests on Jenkins [EXTERNAL]
>
> Hi Sean,
>
> I can take it up if someone is willing to guide me on this.
>
> Regards,
> Gandhi
>
>
> -Original Message-
> From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
> Sent: Wednesday,

RE: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]

2017-11-14 Thread Finan, Sean

Hi Bhagwat,

To build upon what Tim said, not all of the ctakes modules log in the same 
manor.  Some of the more experimental annotators such as those in the temporal 
module log more 'debug' type events, while some of the standard modules kindly 
log 'progress' events, such as processing "start" and "finish".  In addition, 
the loggers are typically named after the java class, and sometimes the classes 
are oddly named.  Instead of log messages from a "TimeAnnotator" you are seeing 
"BackwardsTimeAnnotator", which is appropriate.

The apache email bounce will get rid of all attachments, so people on the lists 
will not be able to get attachments or embedded images.  This can be 
frustrating, but it does add a bit of security for everybody on the list.  If 
you like you can email me your attachments directly - but piper files are plain 
text that you can just copy and paste into the email.  If you are using test 
data (no phi) then you can send me a zip with the files in your html output 
directory and I will take a look at them.

Also, as Tim noted, capability and behavior of code in trunk are often very 
different from what you get from a release version.  Some things move very 
quickly in ctakes (and some very slowly).  If you are willing to build the code 
then I always recommend using trunk - sometimes because I just plain forget 
what the previous release was doing.

Sean

-Original Message-
From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] 
Sent: Tuesday, November 14, 2017 7:09 AM
To: dev@ctakes.apache.org
Subject: Re: source code of user installation of cTakes. [EXTERNAL] 
[SUSPICIOUS] [SUSPICIOUS]

Hi Bhagwat,

That error comes from the tlink module, but **it should be possible to create 
tlinks even if you are getting it**. In fact, for stupid reasons (i.e. my 
stupidity) you will always see that error when running the tlink annotator. 
However, I do have a fix for the error, that may help the tlink module 
somewhat, checked in to trunk about 2 months ago. If you're working off of 
trunk already, please let me know, because then there is some mistake with my 
fix. If you're working off of a src release and willing to recompile, it should 
be a reasonably small fix:


Replace the existing time annotator model with this one:

https://urldefense.proofpoint.com/v2/url?u=http-3A__svn.apache.org_viewvc_ctakes_trunk_ctakes-2Dtemporal-2Dres_src_main_resources_org_apache_ctakes_temporal_ae_timeannotator_model.jar-3Fview-3Dlog=DwIF-g=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=sKTgd6XX8SzXUjskO039AoLyPc5Bkd30KO2tnioosh0=EPNtkyV_yUzDNfVUlpTVzGIVBkZsqUVt-4tgYL9SM_8=


and then update this java file:

https://urldefense.proofpoint.com/v2/url?u=http-3A__svn.apache.org_viewvc_ctakes_trunk_ctakes-2Dtemporal_src_main_java_org_apache_ctakes_temporal_ae_BackwardsTimeAnnotator.java-3Fview-3Dmarkup=DwIF-g=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=sKTgd6XX8SzXUjskO039AoLyPc5Bkd30KO2tnioosh0=EDaptVRyDuEbjBXQ4F4I4fjxR5qHaPebxKn6smA92fU=


and recompile, and it should remove the error.


Tim



From: Bhagwat Posane 
Sent: Tuesday, November 14, 2017 4:16 AM
To: dev@ctakes.apache.org
Subject: Re: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS]

Hello Sean,

Ok, I understood it now, but in my output, the HTML file doesn't contain 
TimeAnnotator. below is the part of output:

14 Nov 2017 13:03:19  INFO ContextDependentTokenizerAnnotator - process(JCas)
14 Nov 2017 13:03:19  INFO POSTagger - process(JCas)
14 Nov 2017 13:03:19  INFO Chunker -  process(JCas)
14 Nov 2017 13:03:20  INFO ChunkAdjuster -  process(JCas)
14 Nov 2017 13:03:20  INFO ChunkAdjuster -  process(JCas)
14 Nov 2017 13:03:22  INFO BackwardsTimeAnnotator - Starting processing
14 Nov 2017 13:03:22  INFO BackwardsTimeAnnotator - Finished processing
14 Nov 2017 13:03:22  INFO DocTimeRelAnnotator - Starting processing
14 Nov 2017 13:03:22  INFO DocTimeRelAnnotator - Finished processing
14 Nov 2017 13:03:22  INFO EventTimeRelationAnnotator - Starting processing
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
14 Nov 2017 13:03:23  INFO EventTimeRelationAnnotator - Finished processing
14 Nov 2017 13:03:23  INFO HtmlTextWriter - Starting processing
14 Nov 2017 13:03:23  INFO HtmlTextWriter - Finished processing

I doubt, the blue colored output text is the culprit and causing TLINK not 
getting generated. To find the

Re: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS]

2017-11-14 Thread Miller, Timothy

Hi Bhagwat,

That error comes from the tlink module, but **it should be possible to create 
tlinks even if you are getting it**. In fact, for stupid reasons (i.e. my 
stupidity) you will always see that error when running the tlink annotator. 
However, I do have a fix for the error, that may help the tlink module 
somewhat, checked in to trunk about 2 months ago. If you're working off of 
trunk already, please let me know, because then there is some mistake with my 
fix. If you're working off of a src release and willing to recompile, it should 
be a reasonably small fix:


Replace the existing time annotator model with this one:

http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal-res/src/main/resources/org/apache/ctakes/temporal/ae/timeannotator/model.jar?view=log


and then update this java file:

http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotator.java?view=markup


and recompile, and it should remove the error.


Tim



From: Bhagwat Posane 
Sent: Tuesday, November 14, 2017 4:16 AM
To: dev@ctakes.apache.org
Subject: Re: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS]

Hello Sean,

Ok, I understood it now, but in my output, the HTML file doesn't contain 
TimeAnnotator. below is the part of output:

14 Nov 2017 13:03:19  INFO ContextDependentTokenizerAnnotator - process(JCas)
14 Nov 2017 13:03:19  INFO POSTagger - process(JCas)
14 Nov 2017 13:03:19  INFO Chunker -  process(JCas)
14 Nov 2017 13:03:20  INFO ChunkAdjuster -  process(JCas)
14 Nov 2017 13:03:20  INFO ChunkAdjuster -  process(JCas)
14 Nov 2017 13:03:22  INFO BackwardsTimeAnnotator - Starting processing
14 Nov 2017 13:03:22  INFO BackwardsTimeAnnotator - Finished processing
14 Nov 2017 13:03:22  INFO DocTimeRelAnnotator - Starting processing
14 Nov 2017 13:03:22  INFO DocTimeRelAnnotator - Finished processing
14 Nov 2017 13:03:22  INFO EventTimeRelationAnnotator - Starting processing
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
14 Nov 2017 13:03:23  INFO EventTimeRelationAnnotator - Finished processing
14 Nov 2017 13:03:23  INFO HtmlTextWriter - Starting processing
14 Nov 2017 13:03:23  INFO HtmlTextWriter - Finished processing

I doubt, the blue colored output text is the culprit and causing TLINK not 
getting generated. To find the cause, I have checked multiple things with no 
success!
However, event-time-relation is captured in xmi with no problem(P.S. Attached).
For your reference my piper file is also attached.
Could you please have a look at the outputs and guide me to find the root cause 
or please tell me if you are aware of this behavior.

On 13 November 2017 at 18:48, Finan, Sean 
> 
wrote:
Hi Bhagwat,

The image that you’ve attached is not coming through, So I cannot see your html 
file.

You should be able to click on any of the underlined terms in the document.  
When you click on one it will list attributes discovered in the run.  For 
example, clicking on “4:00pm” may display on the right panel “CONTAINS x-ray”.

Sean

From: Bhagwat Posane 
[mailto:bhagwat.pos...@gmail.com]
Sent: Monday, November 13, 2017 3:25 AM
To: dev@ctakes.apache.org
Subject: Re: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS]

Hello Sean,

Thank you for the inputs, I have successfully created HTML output.
My main aim is to understand context out of clinical note and I hope TLINK 
statements may help at some extent.
I am interested TLINK tag output in HTML, Please correct me if my understanding 
is not upto the mark.

But HTML file doesn't contain any TLINK tags,
[Inline images 2]

However I can see some tags(copied below) in xmi file which I suppose useful 
for TLINK tag generation.






I have used TemporalSubPipe.piper file commands to generate the output.

///
// Commands and parameters to create a default temporal processing 
sub-pipeline.  This is not a full pipeline.

// 'Generic' Events.  Use addDescription and let the EventAnnotator set itself 
up with defaults.
addDescription EventAnnotator

// Times.  There aren't default models, so set specifically
add BackwardsTimeAnnotator

Re: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS]

2017-11-14 Thread Bhagwat Posane

Hello Sean,

Ok, I understood it now, but in my output, the HTML file doesn't contain
TimeAnnotator. below is the part of output:

14 Nov 2017 13:03:19  INFO ContextDependentTokenizerAnnotator -
process(JCas)
14 Nov 2017 13:03:19  INFO POSTagger - process(JCas)
14 Nov 2017 13:03:19  INFO Chunker -  process(JCas)
14 Nov 2017 13:03:20  INFO ChunkAdjuster -  process(JCas)
14 Nov 2017 13:03:20  INFO ChunkAdjuster -  process(JCas)
14 Nov 2017 13:03:22  INFO BackwardsTimeAnnotator - Starting processing
14 Nov 2017 13:03:22  INFO BackwardsTimeAnnotator - Finished processing
14 Nov 2017 13:03:22  INFO DocTimeRelAnnotator - Starting processing
14 Nov 2017 13:03:22  INFO DocTimeRelAnnotator - Finished processing
14 Nov 2017 13:03:22  INFO EventTimeRelationAnnotator - Starting processing
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
Null value found in Feature(, )
14 Nov 2017 13:03:23  INFO EventTimeRelationAnnotator - Finished processing
14 Nov 2017 13:03:23  INFO HtmlTextWriter - Starting processing
14 Nov 2017 13:03:23  INFO HtmlTextWriter - Finished processing

I doubt, the blue colored output text is the culprit and causing TLINK not
getting generated. To find the cause, I have checked multiple things with
no success!
However, event-time-relation is captured in xmi with no problem(P.S.
Attached).
For your reference my piper file is also attached.
Could you please have a look at the outputs and guide me to find the root
cause or please tell me if you are aware of this behavior.

On 13 November 2017 at 18:48, Finan, Sean 
wrote:

> Hi Bhagwat,
>
> The image that you’ve attached is not coming through, So I cannot see your
> html file.
>
> You should be able to click on any of the underlined terms in the
> document.  When you click on one it will list attributes discovered in the
> run.  For example, clicking on “4:00pm” may display on the right panel
> “CONTAINS x-ray”.
>
> Sean
>
> From: Bhagwat Posane [mailto:bhagwat.pos...@gmail.com]
> Sent: Monday, November 13, 2017 3:25 AM
> To: dev@ctakes.apache.org
> Subject: Re: source code of user installation of cTakes. [EXTERNAL]
> [SUSPICIOUS]
>
> Hello Sean,
>
> Thank you for the inputs, I have successfully created HTML output.
> My main aim is to understand context out of clinical note and I hope TLINK
> statements may help at some extent.
> I am interested TLINK tag output in HTML, Please correct me if my
> understanding is not upto the mark.
>
> But HTML file doesn't contain any TLINK tags,
> [Inline images 2]
>
> However I can see some tags(copied below) in xmi file which I suppose
> useful for TLINK tag generation.
>
>  role="Arg2"/>
>  discoveryTechnique="0" confidence="0.0" polarity="0" uncertainty="0"
> conditional="false" arg1="8272" arg2="8277"/>
>  discoveryTechnique="0" confidence="0.0" polarity="0" uncertainty="0"
> conditional="false" arg1="8296" arg2="8301"/>
>
>
> I have used TemporalSubPipe.piper file commands to generate the output.
>
> 
> 
> ///
> // Commands and parameters to create a default temporal processing
> sub-pipeline.  This is not a full pipeline.
>
> // 'Generic' Events.  Use addDescription and let the EventAnnotator set
> itself up with defaults.
> addDescription EventAnnotator
>
> // Times.  There aren't default models, so set specifically
> add BackwardsTimeAnnotator classifierJarPath=/org/apache/
> ctakes/temporal/ae/timeannotator/model.jar
>
> // DocTimeRel: the relation bin for Events to the Document Creation Time.
> add DocTimeRelAnnotator classifierJarPath=/org/apache/
> ctakes/temporal/ae/doctimerel/model.jar
>
> // Event - Time binary relations.
> add EventTimeRelationAnnotator classifierJarPath=/org/apache/
> ctakes/temporal/ae/eventtime/model.jar
>
> // Event - Event binary relations.
> add EventEventRelationAnnotator classifierJarPath=/org/apache/
> ctakes/temporal/ae/eventevent/model.jar
>
> // Html output
> set OutputDirectory=D:\Bhagwat\HTMLoutput
> add pretty.html.HtmlTextWriter
>
> //XMI output
> writeXmis D:\Bhagwat\XMI
> 
> 
> ///
>
> Am I missing something?
>
> Could you please guide on this.
>
>
>
> On 10 November 2017 at 18:47, Finan, Sean  edu> wrote:
> Hi Bhagwat,
>
> To get html output, you just need to add the

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Re: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS]

Re: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS]

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