date:20180328

RE: How to change and build project source code?

2018-03-28 Thread Gandhi Rajan Natarajan

Hi Reed,

In this case, I feel 'CTAKES_HOME' environment variable is not required at all. 
Because runPiperCreator.bat considers current directory as 'CTAKES_HOME' if not 
defined.

That's why it worked fine for me when I tried as I don’t have 'CTAKES_HOME' 
environment variable set. I'm not sure whether it should be documented as this 
may not be a common scenario I feel.

Regards,
Gandhi

-Original Message-
From: Reed Villanueva [mailto:villanuevar...@gmail.com]
Sent: Thursday, March 29, 2018 4:17 AM
To: dev@ctakes.apache.org
Subject: Re: How to change and build project source code?

Finally found the problem.

I was initially only using the user binaries, which I installed using the user 
installation guide (https://cwiki.apache.org/conf
luence/display/CTAKES/cTAKES+4.0+User+Install+Guide) (which instructs setting 
the environment variable *CTAKES_HOME=*, maybe you see where this is going).

When later deciding that I wanted to experiment with the dev source code, I 
created a new directory $HOME/projects/ctakes as recommended by the dev install 
guide (https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+
4.0+Developer+Install+Guide) and set and requested environment variables (which 
did not include (in this case re-) setting the CTAKES_HOME env.
variable that was pointing to the user binaries)). After building the project 
and extracting the trunk/ctakes-distribution/target binaries, trying to run the 
binaries in that folder seemed to be using the *exact same**code as the user 
binaries*. The problem was that, looking at the actual code in the extracted 
distribution's bin/runPiperCreator.sh, it could be seen that the java 
class-paths being used were pointing to the resources and jars in CTAKES_HOME, 
which at that point *still referred to the user binaries folder*. Resetting the 
env. variable CTAKES_HOME to point to the location of the extracted dev 
distribution binaries fixed the problem.

*TLDR: extracted binaries from the dev distribution target was still using the 
resources and jars from a previous "user" installation for its
class-paths.*

Perhaps this caveat should be added to the documentation?

On Tue, Mar 27, 2018 at 12:10 PM, Reed Villanueva 
wrote:

> Hi Gandhi,
>
> Apologies for the confusion, I had though that it worked in the way
> you described earlier, but had tried this before and it does not seem
> to have any effect.
> Eg. doing something like:
>
> edit
> trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/MainPane
> l2.java
> to have the snippet
>
> 91 private JComponent createWestPanel() {
>> 92  LOGGER.info( "creating fakeTable placeholder" );
>> 93  LOGGER.info( "creating fakeTable placeholder" );
>> 94  LOGGER.info( "creating fakeTable placeholder" );
>> 95  LOGGER.info( "creating fakeTable placeholder" );
>> 96  LOGGER.info( "creating fakeTable placeholder" );
>> 97  System.out.println( "This is a test" );
>> 98  final JTable fakeTable = new JTable();
>> 99  LOGGER.info( "generating fakeTable header" );
>> 100final JTableHeader fakeHeader = fakeTable.getTableHeader();
>> 101final Component header = fakeHeader.getDefaultRenderer()
>
> 102  
> .getTableCellRendererComponent(
>> fakeTable, "Available Pipe Bits",
>> 103
>>  false, false, -1, -1 );
>
>
> just to add some lines in comparison to the original file (for the
> purpose of seeing change in a later error message, to be shown in a
> bit), then
>
>
>> ➜  trunk $ cd ctakes-gui
>> ➜  ctakes-gui $ mvn clean install
>> 
>> [INFO] --- maven-install-plugin:2.3.1:install (default-install) @
>> ctakes-gui --- [INFO] Installing
>> /home/me/projects/ctakes/trunk/ctakes-gui/target/ctakes-gui-4.0.1-SNA
>> PSHOT.jar to /home/reedv/.m2/repository/org/apache/ctakes/ctakes-gui/
>> 4.0.1-SNAPSHOT/ctakes-gui-4.0.1-SNAPSHOT.jar
>> [INFO] Installing /home/me/projects/ctakes/trunk/ctakes-gui/pom.xml
>> to /home/reedv/.m2/repository/org/apache/ctakes/ctakes-gui/
>> 4.0.1-SNAPSHOT/ctakes-gui-4.0.1-SNAPSHOT.pom
>> [INFO] 
>> 
>> [INFO] BUILD SUCCESS
>> [INFO] 
>> 
>> [INFO] Total time: 5.393 s
>> [INFO] Finished at: 2018-03-27T10:06:57-10:00 [INFO]
>> 
>> 
>>
> 
>
>
>> ➜
>> ctakes-gui
>>
>> $ cd ..
>>
>> ➜
>> trunk
>>
>> $ 
>> cp ctakes-gui/target/ctakes-gui-4.0.1-SNAPSHOT.jar
>> ../apache-ctakes-4.0.1-SNAPSHOT/lib/
>>
>
> (note that the apache-ctakes-4.0.1-SNAPSHOT folder was extracted to
> the same directory level as trunk from trunk/ctakes-distribution/
> target/apache-ctakes-4.0.1-SNAPSHOT-bin.tar.gz from an earlier
> successful build following the dev install guide (skipping the
> tests)), then doing
>
>
>> ➜
>> trunk
>> $ cd

RE: consequences of change to typesystem [EXTERNAL]

2018-03-28 Thread Mullane, Sean *HS

Sean,

Glad I asked. I will try either what you suggested or the similar approach of 
adding some code to handle the bare-annotation-as-feature case similarly to how 
annotations inside FSArrays are handled.

Thanks,
Sean

-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] 
Sent: Wednesday, March 28, 2018 8:40 AM
To: dev@ctakes.apache.org
Subject: Re: consequences of change to typesystem [EXTERNAL]

Hi Sean,

In case nobody else has replied,
Yes, this would definitely break a whole lot of things.  I am not saying that 
it is a bad idea, just that the current BinaryTextRelation interface is used 
as-is in probably a thousand places, and while some refactoring might be 
trivial I wouldn't bet that it all would be as easy as one would like.

I haven't looked at the ytex DBConsumer, but could it possibly be easier to add 
some code there that would check BinaryTextRelations and create a new FSArray 
for each?  Stick those arrays in the cas immediately before and db write() and 
you should be able to do what you want without impacting the rest of ctakes.

Sean

From: Mullane, Sean *HS 
Sent: Tuesday, March 27, 2018 6:05 PM
To: dev@ctakes.apache.org
Subject: consequences of change to typesystem [EXTERNAL]

I am trying out a change to the typesystem (explained below). If it works as I 
hope, I would want to contribute this back to the trunk. Before I invest too 
much time into this, can anyone tell me if this is likely to break things for 
other users? I am thinking of this causing problems reading existing annotated 
corpora, like SHARP.

Problem I'm trying to fix:
The DBConsumer database writer from YTEX seems to ignore 
BinaryTextRelation types (e.g. LocationOfTextRelation, used for the 
bodyLocation feature on annotations like DiseaseDisorderMention). This is 
because they are not added to the default AnnotationIndex index and are not 
contained in FSArrays or FSLists inside other annotation types, like the 
UmlsConcept annotations inside the ontologyConceptArr feature are.

It seems that if I were to change the bodyLocation feature to be a FSArray of 
annotations instead of a bare annotation, the DBConsumer should write it to the 
output table and add an entry in the anno_link table.

Would changing the type of the bodyLocation feature in certain 
IdentifiedAnnotations break things for others?

Thanks,
Sean

Re: How to change and build project source code?

2018-03-28 Thread Reed Villanueva

Finally found the problem.

I was initially only using the user binaries, which I installed using the
user installation guide (https://cwiki.apache.org/conf
luence/display/CTAKES/cTAKES+4.0+User+Install+Guide) (which instructs
setting the environment variable *CTAKES_HOME=*, maybe you see where this is going).

When later deciding that I wanted to experiment with the dev source code, I
created a new directory $HOME/projects/ctakes as recommended by the dev
install guide (https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+
4.0+Developer+Install+Guide) and set and requested environment variables
(which did not include (in this case re-) setting the CTAKES_HOME env.
variable that was pointing to the user binaries)). After building the
project and extracting the trunk/ctakes-distribution/target binaries,
trying to run the binaries in that folder seemed to be using the *exact
same**code as the user binaries*. The problem was that, looking at the
actual code in the extracted distribution's bin/runPiperCreator.sh, it
could be seen that the java class-paths being used were pointing to the
resources and jars in CTAKES_HOME, which at that point *still referred to
the user binaries folder*. Resetting the env. variable CTAKES_HOME to point
to the location of the extracted dev distribution binaries fixed the
problem.

*TLDR: extracted binaries from the dev distribution target was still using
the resources and jars from a previous "user" installation for its
class-paths.*

Perhaps this caveat should be added to the documentation?

On Tue, Mar 27, 2018 at 12:10 PM, Reed Villanueva 
wrote:

> Hi Gandhi,
>
> Apologies for the confusion, I had though that it worked in the way you
> described earlier, but had tried this before and it does not seem to have
> any effect.
> Eg. doing something like:
>
> edit 
> trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/MainPanel2.java
> to have the snippet
>
> 91 private JComponent createWestPanel() {
>> 92  LOGGER.info( "creating fakeTable placeholder" );
>> 93  LOGGER.info( "creating fakeTable placeholder" );
>> 94  LOGGER.info( "creating fakeTable placeholder" );
>> 95  LOGGER.info( "creating fakeTable placeholder" );
>> 96  LOGGER.info( "creating fakeTable placeholder" );
>> 97  System.out.println( "This is a test" );
>> 98  final JTable fakeTable = new JTable();
>> 99  LOGGER.info( "generating fakeTable header" );
>> 100final JTableHeader fakeHeader = fakeTable.getTableHeader();
>> 101final Component header = fakeHeader.getDefaultRenderer()
>
> 102  
> .getTableCellRendererComponent(
>> fakeTable, "Available Pipe Bits",
>> 103
>>  false, false, -1, -1 );
>
>
> just to add some lines in comparison to the original file (for the purpose
> of seeing change in a later error message, to be shown in a bit), then
>
>
>> ➜  trunk $ cd ctakes-gui
>> ➜  ctakes-gui $ mvn clean install
>> 
>> [INFO] --- maven-install-plugin:2.3.1:install (default-install) @
>> ctakes-gui ---
>> [INFO] Installing 
>> /home/me/projects/ctakes/trunk/ctakes-gui/target/ctakes-gui-4.0.1-SNAPSHOT.jar
>> to /home/reedv/.m2/repository/org/apache/ctakes/ctakes-gui/
>> 4.0.1-SNAPSHOT/ctakes-gui-4.0.1-SNAPSHOT.jar
>> [INFO] Installing /home/me/projects/ctakes/trunk/ctakes-gui/pom.xml to
>> /home/reedv/.m2/repository/org/apache/ctakes/ctakes-gui/
>> 4.0.1-SNAPSHOT/ctakes-gui-4.0.1-SNAPSHOT.pom
>> [INFO] 
>> 
>> [INFO] BUILD SUCCESS
>> [INFO] 
>> 
>> [INFO] Total time: 5.393 s
>> [INFO] Finished at: 2018-03-27T10:06:57-10:00
>> [INFO] 
>> 
>>
> 
>
>
>> ➜
>> ctakes-gui
>>
>> $ cd ..
>>
>> ➜
>> trunk
>>
>> $ 
>> cp ctakes-gui/target/ctakes-gui-4.0.1-SNAPSHOT.jar
>> ../apache-ctakes-4.0.1-SNAPSHOT/lib/
>>
>
> (note that the apache-ctakes-4.0.1-SNAPSHOT folder was extracted to the
> same directory level as trunk from trunk/ctakes-distribution/
> target/apache-ctakes-4.0.1-SNAPSHOT-bin.tar.gz from an earlier successful
> build following the dev install guide (skipping the tests)), then doing
>
>
>> ➜
>> trunk
>> $ cd ../apache-ctakes-4.0.1-SNAPSHOT
>>
> 
>> 
>> ➜  apache-ctakes-4.0.1-SNAPSHOT
>>  $
>> ls -lhR lib | grep ctakes-gui
>>  
>>
>
>  -rw-r--r-- 1 reedv reedv 272K  
>> ctakes-gui-4.0.1-SNAPSHOT.jar
>>
>
>  
>
> ➜  apache-ctakes-4.0.1-SNAPSHOT
>>  $
>> ./bin/runPiperCreator.sh
>> 
>> log4j: Setting property [conversionPattern] to [%d{dd MMM  HH:mm:ss}
>> %5p %c{1} - %m%n].
>> log4j: Adding appender named [consoleAppender] to category [root].
>> Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
>> at javax.swing.plaf.synth.SynthTableHeaderUI$HeaderRenderer.
>>

RE: Query on LabValueFinder [EXTERNAL] [SUSPICIOUS]

2018-03-28 Thread Gandhi Rajan Natarajan

Hi Sean,

This is phenomenal commitment.  I appreciate your dedication and passion. You 
are such an inspiration to the open source contributors.

Thanks for taking time out amidst busy schedule and having a look at this. Will 
check this change and keep you posted.

Regards,
Gandhi

-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, March 28, 2018 9:12 PM
To: dev@ctakes.apache.org
Subject: RE: Query on LabValueFinder [EXTERNAL] [SUSPICIOUS]

Guilt is such a powerful motivator ...

The problem is that ctakes traditionally identifies a bunch of those terms as 
Medications, not Labs.  So, I added a parameter named "useDrugs" to the 
LabValueFinder.  If you set that to "true" then the Lab/Medication values come 
through shining.

I also added some (commented out) code to the LabValueFinderTester to use the 
default dictionary instead of the test dictionary.  By default the test 
dictionary is used and all counts match.  If you use the default dictionary you 
can expect the test to fail because it finds 23 labs instead of 24 - but Kean's 
test code kindly prints the labs and values found so you can look at the test 
results.

The code just went into trunk.

Enjoy,
Sean

-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, March 28, 2018 9:03 AM
To: dev@ctakes.apache.org
Subject: Re: Query on LabValueFinder [EXTERNAL] [SUSPICIOUS]

Hi Gandhi,

I know that I just sent an email to the devlist, but that seemed like an item 
that had wide-impact.  Because of some critical work (job that pays the bills) 
I am still "dark" as far as ctakes goes - no free nights and only partial 
weekends.  My apologies.  I know that there are a lot of issues building up, 
and I will try to try to address them asap; I don't know when I'll have the 
time and energy to get back to the devlist.

Feeling a bit guilty,
Sean

From: Gandhi Rajan Natarajan 
Sent: Wednesday, March 28, 2018 8:56 AM
To: dev@ctakes.apache.org
Subject: RE: Query on LabValueFinder [EXTERNAL]

Hi Sean,

Can you throw some light on this?

Regards,

Gandhi

-Original Message-

From: Kean Kaufmann [mailto:k...@recordsone.com]

Sent: Monday, March 19, 2018 8:35 PM

To: dev@ctakes.apache.org

Subject: Re: Query on LabValueFinder

Gandhi, at first blush, I can't replicate your result using the code I 
submitted...

but my code and config differ from trunk, so Sean is probably the best person 
to ask.

I included unit tests with a mini-dictionary for ProcedureMentions, but they 
probably didn't play nicely with the rest of the framework.

Sean, any insight?

On Mon, Mar 19, 2018 at 10:31 AM, Gandhi Rajan Natarajan < 
gandhi.natara...@arisglobal.com> wrote:

> Hi All,

>

> I'm using LabValueFinder annotator in my piper file and when I analyze

> the following text:

>

>

> "HEPATIC FUNCTION PANEL  Result Value Ref Range  Albumin 2.2 (*) 3.7 -

> 5.1 g/dL Total Protein 5.5 (*) 5.8 - 8.0 g/dL Alkaline Phosphatase 844

> (*) 42 -

> 121 IU/L" as mentioned in

> https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D441=DwIGaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=JMvtiTFymmqWfE6zZ1z5oPfqlSFrG0nZKJ0bhEBltrc=2EcJhW06YyWZpdLla-yruHEw4Il9CyHMLBrKoHaDVlc=

>

>

>

> The resulted XML generated using XmiCasSerializer contains only one

> LabMention as mentioned below:

>

>

>  ontologyConceptArr="1089 1109 1079 1099 1069" typeID="0"

> discoveryTechnique="3" confidence="0.0" polarity="0" uncertainty="0"

> conditional="false" generic="false" historyOf="0" labValue="3907" />

>

> 

>

> 

>

>  confidence="0.0" polarity="0" uncertainty="0" conditional="false"

> arg1="3917" arg2="3922" />

>

>  id="0" typeID="0" discoveryTechnique="0" confidence="0.0" polarity="0"

> uncertainty="0" conditional="false" generic="false" historyOf="0" />

>

>

> But as per the comments in the issue, it is supposed to identify 3 lab

> mentions. Any thoughts on this on how to achieve it ?

>

> Regards,

> Gandhi

>

> This email and any files transmitted with it are confidential and

> intended solely for the use of the individual or entity to whom they are 
> addressed.

> If you are not the named addressee you should not disseminate,

> distribute or copy this e-mail. Please notify the sender or system

> manager by email immediately if you have received this e-mail by

> mistake and delete this e-mail from your system. If you are not the

> intended recipient you are notified that disclosing, copying,

> distributing or taking any action in reliance on the contents of this

> information is strictly prohibited and against the law.

>

This email and any files transmitted with it are confidential and intended 
solely for the use of the individual or entity to whom they are addressed. If 
you are not the named

RE: Query on LabValueFinder [EXTERNAL] [SUSPICIOUS]

2018-03-28 Thread Finan, Sean

Guilt is such a powerful motivator ...

The problem is that ctakes traditionally identifies a bunch of those terms as 
Medications, not Labs.  So, I added a parameter named "useDrugs" to the 
LabValueFinder.  If you set that to "true" then the Lab/Medication values come 
through shining.

I also added some (commented out) code to the LabValueFinderTester to use the 
default dictionary instead of the test dictionary.  By default the test 
dictionary is used and all counts match.  If you use the default dictionary you 
can expect the test to fail because it finds 23 labs instead of 24 - but Kean's 
test code kindly prints the labs and values found so you can look at the test 
results.

The code just went into trunk.

Enjoy,
Sean

-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] 
Sent: Wednesday, March 28, 2018 9:03 AM
To: dev@ctakes.apache.org
Subject: Re: Query on LabValueFinder [EXTERNAL] [SUSPICIOUS]

Hi Gandhi,

I know that I just sent an email to the devlist, but that seemed like an item 
that had wide-impact.  Because of some critical work (job that pays the bills) 
I am still "dark" as far as ctakes goes - no free nights and only partial 
weekends.  My apologies.  I know that there are a lot of issues building up, 
and I will try to try to address them asap; I don't know when I'll have the 
time and energy to get back to the devlist.

Feeling a bit guilty,
Sean

From: Gandhi Rajan Natarajan 
Sent: Wednesday, March 28, 2018 8:56 AM
To: dev@ctakes.apache.org
Subject: RE: Query on LabValueFinder [EXTERNAL]

Hi Sean,

Can you throw some light on this?

Regards,

Gandhi

-Original Message-

From: Kean Kaufmann [mailto:k...@recordsone.com]

Sent: Monday, March 19, 2018 8:35 PM

To: dev@ctakes.apache.org

Subject: Re: Query on LabValueFinder

Gandhi, at first blush, I can't replicate your result using the code I 
submitted...

but my code and config differ from trunk, so Sean is probably the best person 
to ask.

I included unit tests with a mini-dictionary for ProcedureMentions, but they 
probably didn't play nicely with the rest of the framework.

Sean, any insight?

On Mon, Mar 19, 2018 at 10:31 AM, Gandhi Rajan Natarajan < 
gandhi.natara...@arisglobal.com> wrote:

> Hi All,

>

> I'm using LabValueFinder annotator in my piper file and when I analyze

> the following text:

>

>

> "HEPATIC FUNCTION PANEL  Result Value Ref Range  Albumin 2.2 (*) 3.7 -

> 5.1 g/dL Total Protein 5.5 (*) 5.8 - 8.0 g/dL Alkaline Phosphatase 844

> (*) 42 -

> 121 IU/L" as mentioned in

> https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D441=DwIGaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=JMvtiTFymmqWfE6zZ1z5oPfqlSFrG0nZKJ0bhEBltrc=2EcJhW06YyWZpdLla-yruHEw4Il9CyHMLBrKoHaDVlc=

>

>

>

> The resulted XML generated using XmiCasSerializer contains only one

> LabMention as mentioned below:

>

>

>  ontologyConceptArr="1089 1109 1079 1099 1069" typeID="0"

> discoveryTechnique="3" confidence="0.0" polarity="0" uncertainty="0"

> conditional="false" generic="false" historyOf="0" labValue="3907" />

>

> 

>

> 

>

>  confidence="0.0" polarity="0" uncertainty="0" conditional="false"

> arg1="3917" arg2="3922" />

>

>  id="0" typeID="0" discoveryTechnique="0" confidence="0.0" polarity="0"

> uncertainty="0" conditional="false" generic="false" historyOf="0" />

>

>

> But as per the comments in the issue, it is supposed to identify 3 lab

> mentions. Any thoughts on this on how to achieve it ?

>

> Regards,

> Gandhi

>

> This email and any files transmitted with it are confidential and

> intended solely for the use of the individual or entity to whom they are 
> addressed.

> If you are not the named addressee you should not disseminate,

> distribute or copy this e-mail. Please notify the sender or system

> manager by email immediately if you have received this e-mail by

> mistake and delete this e-mail from your system. If you are not the

> intended recipient you are notified that disclosing, copying,

> distributing or taking any action in reliance on the contents of this

> information is strictly prohibited and against the law.

>

This email and any files transmitted with it are confidential and intended 
solely for the use of the individual or entity to whom they are addressed. If 
you are not the named addressee you should not disseminate, distribute or copy 
this e-mail. Please notify the sender or system manager by email immediately if 
you have received this e-mail by mistake and delete this e-mail from your 
system. If you are not the intended recipient you are notified that disclosing, 
copying, distributing or taking any action in reliance on the contents of this 
information is strictly prohibited and against the law.

Re: Query on LabValueFinder [EXTERNAL]

2018-03-28 Thread Finan, Sean

Hi Gandhi,

I know that I just sent an email to the devlist, but that seemed like an item 
that had wide-impact.  Because of some critical work (job that pays the bills) 
I am still "dark" as far as ctakes goes - no free nights and only partial 
weekends.  My apologies.  I know that there are a lot of issues building up, 
and I will try to try to address them asap; I don't know when I'll have the 
time and energy to get back to the devlist.

Feeling a bit guilty,
Sean

From: Gandhi Rajan Natarajan 
Sent: Wednesday, March 28, 2018 8:56 AM
To: dev@ctakes.apache.org
Subject: RE: Query on LabValueFinder [EXTERNAL]

Hi Sean,

Can you throw some light on this?

Regards,

Gandhi

-Original Message-

From: Kean Kaufmann [mailto:k...@recordsone.com]

Sent: Monday, March 19, 2018 8:35 PM

To: dev@ctakes.apache.org

Subject: Re: Query on LabValueFinder

Gandhi, at first blush, I can't replicate your result using the code I 
submitted...

but my code and config differ from trunk, so Sean is probably the best person 
to ask.

I included unit tests with a mini-dictionary for ProcedureMentions, but they 
probably didn't play nicely with the rest of the framework.

Sean, any insight?

On Mon, Mar 19, 2018 at 10:31 AM, Gandhi Rajan Natarajan < 
gandhi.natara...@arisglobal.com> wrote:

> Hi All,

>

> I'm using LabValueFinder annotator in my piper file and when I analyze

> the following text:

>

>

> "HEPATIC FUNCTION PANEL  Result Value Ref Range  Albumin 2.2 (*) 3.7 -

> 5.1 g/dL Total Protein 5.5 (*) 5.8 - 8.0 g/dL Alkaline Phosphatase 844

> (*) 42 -

> 121 IU/L" as mentioned in

> https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D441=DwIGaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=JMvtiTFymmqWfE6zZ1z5oPfqlSFrG0nZKJ0bhEBltrc=2EcJhW06YyWZpdLla-yruHEw4Il9CyHMLBrKoHaDVlc=

>

>

>

> The resulted XML generated using XmiCasSerializer contains only one

> LabMention as mentioned below:

>

>

>  ontologyConceptArr="1089 1109 1079 1099 1069" typeID="0"

> discoveryTechnique="3" confidence="0.0" polarity="0" uncertainty="0"

> conditional="false" generic="false" historyOf="0" labValue="3907" />

>

> 

>

> 

>

>  confidence="0.0" polarity="0" uncertainty="0" conditional="false"

> arg1="3917" arg2="3922" />

>

>  id="0" typeID="0" discoveryTechnique="0" confidence="0.0" polarity="0"

> uncertainty="0" conditional="false" generic="false" historyOf="0" />

>

>

> But as per the comments in the issue, it is supposed to identify 3 lab

> mentions. Any thoughts on this on how to achieve it ?

>

> Regards,

> Gandhi

>

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RE: Query on LabValueFinder

2018-03-28 Thread Gandhi Rajan Natarajan

Hi Sean,

Can you throw some light on this?

Regards,
Gandhi


-Original Message-
From: Kean Kaufmann [mailto:k...@recordsone.com]
Sent: Monday, March 19, 2018 8:35 PM
To: dev@ctakes.apache.org
Subject: Re: Query on LabValueFinder

Gandhi, at first blush, I can't replicate your result using the code I 
submitted...
but my code and config differ from trunk, so Sean is probably the best person 
to ask.
I included unit tests with a mini-dictionary for ProcedureMentions, but they 
probably didn't play nicely with the rest of the framework.
Sean, any insight?


On Mon, Mar 19, 2018 at 10:31 AM, Gandhi Rajan Natarajan < 
gandhi.natara...@arisglobal.com> wrote:

> Hi All,
>
> I'm using LabValueFinder annotator in my piper file and when I analyze
> the following text:
>
>
> "HEPATIC FUNCTION PANEL  Result Value Ref Range  Albumin 2.2 (*) 3.7 -
> 5.1 g/dL Total Protein 5.5 (*) 5.8 - 8.0 g/dL Alkaline Phosphatase 844
> (*) 42 -
> 121 IU/L" as mentioned in
> https://issues.apache.org/jira/browse/CTAKES-441
>
>
>
> The resulted XML generated using XmiCasSerializer contains only one
> LabMention as mentioned below:
>
>
>  ontologyConceptArr="1089 1109 1079 1099 1069" typeID="0"
> discoveryTechnique="3" confidence="0.0" polarity="0" uncertainty="0"
> conditional="false" generic="false" historyOf="0" labValue="3907" />
>
> 
>
> 
>
>  confidence="0.0" polarity="0" uncertainty="0" conditional="false"
> arg1="3917" arg2="3922" />
>
>  id="0" typeID="0" discoveryTechnique="0" confidence="0.0" polarity="0"
> uncertainty="0" conditional="false" generic="false" historyOf="0" />
>
>
> But as per the comments in the issue, it is supposed to identify 3 lab
> mentions. Any thoughts on this on how to achieve it ?
>
> Regards,
> Gandhi
>
> This email and any files transmitted with it are confidential and
> intended solely for the use of the individual or entity to whom they are 
> addressed.
> If you are not the named addressee you should not disseminate,
> distribute or copy this e-mail. Please notify the sender or system
> manager by email immediately if you have received this e-mail by
> mistake and delete this e-mail from your system. If you are not the
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> information is strictly prohibited and against the law.
>
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Re: consequences of change to typesystem [EXTERNAL]

2018-03-28 Thread Finan, Sean

Hi Sean,

In case nobody else has replied,
Yes, this would definitely break a whole lot of things.  I am not saying that 
it is a bad idea, just that the current BinaryTextRelation interface is used 
as-is in probably a thousand places, and while some refactoring might be 
trivial I wouldn't bet that it all would be as easy as one would like.

I haven't looked at the ytex DBConsumer, but could it possibly be easier to add 
some code there that would check BinaryTextRelations and create a new FSArray 
for each?  Stick those arrays in the cas immediately before and db write() and 
you should be able to do what you want without impacting the rest of ctakes.

Sean

From: Mullane, Sean *HS 
Sent: Tuesday, March 27, 2018 6:05 PM
To: dev@ctakes.apache.org
Subject: consequences of change to typesystem [EXTERNAL]

I am trying out a change to the typesystem (explained below). If it works as I 
hope, I would want to contribute this back to the trunk. Before I invest too 
much time into this, can anyone tell me if this is likely to break things for 
other users? I am thinking of this causing problems reading existing annotated 
corpora, like SHARP.

Problem I'm trying to fix:
The DBConsumer database writer from YTEX seems to ignore 
BinaryTextRelation types (e.g. LocationOfTextRelation, used for the 
bodyLocation feature on annotations like DiseaseDisorderMention). This is 
because they are not added to the default AnnotationIndex index and are not 
contained in FSArrays or FSLists inside other annotation types, like the 
UmlsConcept annotations inside the ontologyConceptArr feature are.

It seems that if I were to change the bodyLocation feature to be a FSArray of 
annotations instead of a bare annotation, the DBConsumer should write it to the 
output table and add an entry in the anno_link table.

Would changing the type of the bodyLocation feature in certain 
IdentifiedAnnotations break things for others?

Thanks,
Sean

RE: How to change and build project source code?

RE: consequences of change to typesystem [EXTERNAL]

Re: How to change and build project source code?

RE: Query on LabValueFinder [EXTERNAL] [SUSPICIOUS]

RE: Query on LabValueFinder [EXTERNAL] [SUSPICIOUS]

Re: Query on LabValueFinder [EXTERNAL]

RE: Query on LabValueFinder

Re: consequences of change to typesystem [EXTERNAL]

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