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Posted to user@ctakes.apache.org by Abhishek Raj <ab...@iitrpr.ac.in> on 2014/06/11 18:46:47 UTC
Re: [External] Re: Cannot load AggregatePlainTextUmlsProcessor.xml
I think the error is in the ytex.profile file. I am not really sure though.
I am attaching the file. Please let me know if there is anything to be
changed in the file that might fix the issue. Thanks.
On Wed, Jun 11, 2014 at 10:04 PM, Lee, Richard A. [USA] <lee_richard@bah.com
> wrote:
> This is the same error I reported a few weeks ago, but it probably got
> missed because I was also reporting that using the ytex-specific AE failed
> to produce any MedicalAnnotations…
>
>
>
> *From:* Abhishek Raj [mailto:abhishekrm@iitrpr.ac.in]
> *Sent:* Wed, 11 Jun, 2014 12:11
> *To:* user@ctakes.apache.org
> *Subject:* [External] Re: Cannot load AggregatePlainTextUmlsProcessor.xml
>
>
>
> Thanks for the reply. I am using apace-cTakes-3.1.2 and yes, this is using
> YTEX. I followed these
> <https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation> instructions
> for installing ytex and #1 in the installation procedure was " installing ctakes+ytex
> distro 'as usual' " by following these
> <https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1+User+Install+Guide> instructions.
> Not sure what is the reason for the error though. I have UMLS installed in
> my SQL database already.
>
>
>
> On Wed, Jun 11, 2014 at 9:24 PM, Chen, Pei <Pe...@childrens.harvard.edu>
> wrote:
>
> Abhishek,
>
> There is an SQL exception because of the “@db.schema@.” in the sql:
>
> SELECT tui,cui,tok_str FROM @db.schema@.v_snomed_fword_lookup WHERE fword
> = ?
>
>
>
> Which version of cTAKES are you using and also is this using YTEX? As I
> am not sure where the special parameter markers are coming from. Normally,
> it would look something like:
>
>
> http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-dictionary-lookup-res/src/main/resources/org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml
>
>
>
>
>
>
>
>
>
> *From:* Abhishek Raj [mailto:abhishekrm@iitrpr.ac.in]
> *Sent:* Wednesday, June 11, 2014 11:39 AM
> *To:* user@ctakes.apache.org
> *Subject:* Re: Cannot load AggregatePlainTextUmlsProcessor.xml
>
>
>
> Hey! Thanks a lot for the reply. That totally worked. However, I have run
> into another problem now. After loading the
> "AggregatePlainTextUmlsProcessor.xml", when I try to run the it on some
> text sample I get an error saying
>
> org.apache.uima.analysis_engine.AnalysisEngineProcessException . More
> detailed information is in the log file
>
>
> I have attached the log in the attachments. Please do have a look. Any
> help will be appreciated.
>
>
>
> On Wed, Jun 11, 2014 at 7:06 PM, Chen, Pei <Pe...@childrens.harvard.edu>
> wrote:
>
> Abhishek,
>
> Have you tried some of the suggestions from this thread:
>
>
> http://mail-archives.apache.org/mod_mbox/ctakes-dev/201304.mbox/%3CCD84AD35.169BD%25mcoarr%40mitre.org%3E
>
>
>
>
>
> *From:* Abhishek Raj [mailto:abhishekrm@iitrpr.ac.in]
> *Sent:* Wednesday, June 11, 2014 4:17 AM
> *To:* user@ctakes.apache.org
> *Subject:* Cannot load AggregatePlainTextUmlsProcessor.xml
>
>
>
> Hello I installed ctakes following
> https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation and
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1+User+Install+Guide
> . After installation I ran the CVD for annotation purpose. When I try to
> load the AggregatePlainTextUmlsProcessor.xml I get error saying
>
> org.apache.uima.resource.ResourceInitializationException:
>
> Initialization of annotator class
>
> "org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator" failed. (Descriptor: file:/home/gamerboy/apache-ctakes-3.1.2-SNAPSHOT/desc/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml)
>
>
>
> I am behind a proxy network. Not sure this could be the reason though.
>
>
>
>
>
RE: [External] Re: Cannot load AggregatePlainTextUmlsProcessor.xml
Posted by "Lee, Richard A. [USA]" <le...@bah.com>.
Done. It is indeed “the same results” (as when trying to use the old non-ytex AE): the same runtime exception popup. “See the log file”, it says, but as before I’m not seeing anything obvious in ctakes.log (attached).
From: vijay garla [mailto:vngarla@gmail.com]
Sent: Wed, 18 Jun, 2014 10:12
To: user@ctakes.apache.org
Subject: Re: [External] Re: Cannot load AggregatePlainTextUmlsProcessor.xml
The YTEX AggregatePlaintextUMLSProcessor differs from the default AggregatePlaintextUMLSProcessor in the following a ways:
* Use SegmentRegexAnnotator instead of SimpleSegmentAnnotator
* Use SentenceDetectorAnnotator without splitting on newlines
* Added SenseDisambiguatorAnnotator
* Use YTEX DictionaryLookupAnnotatorDB instead of cTAKES DictionaryLookupAnnotatorDB
The YTEX dictionary lookup is different from cTAKES':
* uses the old dictionary lookup
* uses a single dictionary
* uses a single lookup consumer that creates plain-vanilla EntityMention annotations (none of the subtypes)
I think that if you change the YTEX AggregatePlaintextUMLSProcessor to point at the cTAKES dictionary lookup, you will get approximately same annotations (probably more if sentences do not end on newlines, as dictionary lookup is not performed across sentences)
could you try the following please:
In desc\ctakes-ytex-uima\desc\analysis_engine\AggregatePlaintextUMLSProcessor.xml change
<delegateAnalysisEngine key="DictionaryLookupAnnotatorDB">
<import location="./DictionaryLookupAnnotator.xml" />
</delegateAnalysisEngine>
To
<delegateAnalysisEngine key="DictionaryLookupAnnotatorDB">
<import location="../../../ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml"/>
</delegateAnalysisEngine>
And re-run. You should get the same results (keep in mind the newline thing).
On Wed, Jun 18, 2014 at 9:46 AM, Lee, Richard A. [USA] <le...@bah.com>> wrote:
Yes, that exactly the problem I’ve been reporting. I think you’ll see that it you still get the non-Medical annotations, like Date, RomanNumeral, et al, but not DiseaseDisorderMention and the other Medical ones, right?
I’m still hoping someone can assist with this.
From: Abhishek Raj [mailto:abhishekrm@iitrpr.ac.in<ma...@iitrpr.ac.in>]
Sent: Wed, 18 Jun, 2014 04:43
To: user@ctakes.apache.org<ma...@ctakes.apache.org>
Subject: Re: [External] Re: Cannot load AggregatePlainTextUmlsProcessor.xml
Found a fix. Will post it here in case it helps someone. When using ctakes-3.1.2, load the AggregatePlainTextUmlsProcessor.xml from "CTAKES_HOME/desc/ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml" and not from the usual "CTAKES_HOME/desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml" as given here<https://cwiki.apache.org/confluence/display/CTAKES/User%27s+Guide>.
However strangely, "ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml" produced even less annotations than "ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml".
I expected ytex-specific AE to produce better results. But clearly that's not the case.
On Thu, Jun 12, 2014 at 2:51 AM, Abhishek Raj <ab...@iitrpr.ac.in>> wrote:
Hi. Thanks for the reply.
I have a file named LookupDesc_Db.xml which has the line <jdbcImpl tableName="@db.schema@.v_snomed_fword_lookup"/>
instead of LookupDesc_SNOMED.template.xml. Also, my ytex.properties file seems fine. I have attached the file for your reference.
And yes, when running the ant setup by following #7 on this<https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation> link, it sends the output to "setup.out". The build was successful though. I didn't see any errors. I am attaching the file for your reference as well. Please have a look and let me know.
Re: [External] Re: Cannot load AggregatePlainTextUmlsProcessor.xml
Posted by John Green <he...@gmail.com>.
Also, Vijay: What was the thought process behind the lack of subtypes? Was
this more robust? Even with just "plain vanilla" entity mentions as you
say, I find as Mr Lee did that I am only getting a very limited set of
annotations, they seem to be drugs and a few other entities only.
I feel we are all missing something very obvious to inveterate UIMA users
like yourself ...
Thanks as always for your time, I know how limited that can be and how
helping novices can be so frustrating,
Sincerely,
JG
On Wed, Jun 18, 2014 at 10:11 AM, vijay garla <vn...@gmail.com> wrote:
> The YTEX AggregatePlaintextUMLSProcessor differs from the default
> AggregatePlaintextUMLSProcessor in the following a ways:
> * Use SegmentRegexAnnotator instead of SimpleSegmentAnnotator
> * Use SentenceDetectorAnnotator without splitting on newlines
> * Added SenseDisambiguatorAnnotator
> ** Use YTEX DictionaryLookupAnnotatorDB instead of cTAKES
> DictionaryLookupAnnotatorDB*
>
> The YTEX dictionary lookup is different from cTAKES':
> * uses the old dictionary lookup
> * uses a single dictionary
> * uses a single lookup consumer that creates plain-vanilla EntityMention
> annotations (none of the subtypes)
>
> I think that if you change the YTEX AggregatePlaintextUMLSProcessor to
> point at the cTAKES dictionary lookup, you will get approximately same
> annotations (probably more if sentences do not end on newlines, as
> dictionary lookup is not performed across sentences)
>
> could you try the following please:
> In
> desc\ctakes-ytex-uima\desc\analysis_engine\AggregatePlaintextUMLSProcessor.xml
> change
> <delegateAnalysisEngine key="DictionaryLookupAnnotatorDB">
> <import location="./DictionaryLookupAnnotator.xml" />
> </delegateAnalysisEngine>
> To
> <delegateAnalysisEngine key="DictionaryLookupAnnotatorDB">
> <import
> location="../../../ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml"/>
> </delegateAnalysisEngine>
>
> And re-run. You should get the same results (keep in mind the newline
> thing).
>
>
>
>
>
> On Wed, Jun 18, 2014 at 9:46 AM, Lee, Richard A. [USA] <
> lee_richard@bah.com> wrote:
>
>> Yes, that exactly the problem I’ve been reporting. I think you’ll see
>> that it you still get the non-Medical annotations, like Date, RomanNumeral,
>> et al, but not DiseaseDisorderMention and the other Medical ones, right?
>>
>>
>>
>> I’m still hoping someone can assist with this.
>>
>>
>>
>> *From:* Abhishek Raj [mailto:abhishekrm@iitrpr.ac.in]
>> *Sent:* Wed, 18 Jun, 2014 04:43
>> *To:* user@ctakes.apache.org
>> *Subject:* Re: [External] Re: Cannot load
>> AggregatePlainTextUmlsProcessor.xml
>>
>>
>>
>> Found a fix. Will post it here in case it helps someone. When using
>> ctakes-3.1.2, load the AggregatePlainTextUmlsProcessor.xml from "
>> CTAKES_HOME/desc/ytex-uima/desc/analysis_engine/
>> AggregatePlaintextUMLSProcessor.xml" and not from the usual "
>> CTAKES_HOME/desc/ctakes-clinical-pipeline/desc/analysis_engine/
>> AggregatePlaintextUMLSProcessor.xml" as given here
>> <https://cwiki.apache.org/confluence/display/CTAKES/User%27s+Guide>.
>>
>> However strangely, "ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml"
>> produced even less annotations than "
>> ctakes-clinical-pipeline/desc/analysis_engine/
>> AggregatePlaintextUMLSProcessor.xml".
>>
>> I expected ytex-specific AE to produce better results. But clearly that's
>> not the case.
>>
>>
>>
>> On Thu, Jun 12, 2014 at 2:51 AM, Abhishek Raj <ab...@iitrpr.ac.in>
>> wrote:
>>
>> Hi. Thanks for the reply.
>> I have a file named LookupDesc_Db.xml which has the line <jdbcImpl
>> tableName="@db.schema@.v_snomed_fword_lookup"/>
>>
>> instead of LookupDesc_SNOMED.*template*.xml. Also, my ytex.properties
>> file seems fine. I have attached the file for your reference.
>> And yes, when running the ant setup by following #7 on this
>> <https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation> link,
>> it sends the output to "setup.out". The build was successful though. I
>> didn't see any errors. I am attaching the file for your reference as well.
>> Please have a look and let me know.
>>
>>
>>
>
>
Re: [External] Re: Cannot load AggregatePlainTextUmlsProcessor.xml
Posted by John Green <he...@gmail.com>.
Hi Vijay - I tried this again with a fresh install including ant and Im getting the same error. Any hints as to what direction I should turn my investigation? Im a bit at a loss...
Thanks as always for your time,
John
—
Sent from Mailbox for iPhone
On Wed, Jul 16, 2014 at 11:20 AM, vijay garla <vn...@gmail.com> wrote:
> replace db.schema with your database schema name. For sql server, this is
> dbo, for mysql this is the database/schema name, for oracle this is the
> schema name. This should have been done automatically by the ant setup
> script, not sure why it isn't happening in some configs.
> -vj
> On Wed, Jul 16, 2014 at 4:53 PM, John Green <he...@gmail.com>
> wrote:
>> Hi Vijay - I am at the same impasse as Mr Lee and Mr Abhishek, and I didnt
>> come across any other solutions in the archives.
>>
>> Through intuition I figured out what you mention in this post on my own,
>> and tried it. It didnt work. It seems to revolve around this line:
>> Unexpected token: @ in statement [SELECT tui,cui,tok_str FROM @db.schema@.v_snomed_fword_lookup
>> WHERE fword = ?]
>>
>> It seems the query is coming from LookupDesc_SNOMED.xml, but I cant find
>> the @db.schema@... is this a windows/linux issue?
>>
>> Before Vijay spends his precious time on answering this, did anyone else
>> get resolution on this?
>>
>> Best,
>> JG
>>
>>
>> On Wed, Jun 18, 2014 at 10:11 AM, vijay garla <vn...@gmail.com> wrote:
>>
>>> The YTEX AggregatePlaintextUMLSProcessor differs from the default
>>> AggregatePlaintextUMLSProcessor in the following a ways:
>>> * Use SegmentRegexAnnotator instead of SimpleSegmentAnnotator
>>> * Use SentenceDetectorAnnotator without splitting on newlines
>>> * Added SenseDisambiguatorAnnotator
>>> ** Use YTEX DictionaryLookupAnnotatorDB instead of cTAKES
>>> DictionaryLookupAnnotatorDB*
>>>
>>> The YTEX dictionary lookup is different from cTAKES':
>>> * uses the old dictionary lookup
>>> * uses a single dictionary
>>> * uses a single lookup consumer that creates plain-vanilla EntityMention
>>> annotations (none of the subtypes)
>>>
>>> I think that if you change the YTEX AggregatePlaintextUMLSProcessor to
>>> point at the cTAKES dictionary lookup, you will get approximately same
>>> annotations (probably more if sentences do not end on newlines, as
>>> dictionary lookup is not performed across sentences)
>>>
>>> could you try the following please:
>>> In
>>> desc\ctakes-ytex-uima\desc\analysis_engine\AggregatePlaintextUMLSProcessor.xml
>>> change
>>> <delegateAnalysisEngine key="DictionaryLookupAnnotatorDB">
>>> <import location="./DictionaryLookupAnnotator.xml" />
>>> </delegateAnalysisEngine>
>>> To
>>> <delegateAnalysisEngine key="DictionaryLookupAnnotatorDB">
>>> <import
>>> location="../../../ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml"/>
>>> </delegateAnalysisEngine>
>>>
>>> And re-run. You should get the same results (keep in mind the newline
>>> thing).
>>>
>>>
>>>
>>>
>>>
>>> On Wed, Jun 18, 2014 at 9:46 AM, Lee, Richard A. [USA] <
>>> lee_richard@bah.com> wrote:
>>>
>>>> Yes, that exactly the problem I’ve been reporting. I think you’ll see
>>>> that it you still get the non-Medical annotations, like Date, RomanNumeral,
>>>> et al, but not DiseaseDisorderMention and the other Medical ones, right?
>>>>
>>>>
>>>>
>>>> I’m still hoping someone can assist with this.
>>>>
>>>>
>>>>
>>>> *From:* Abhishek Raj [mailto:abhishekrm@iitrpr.ac.in]
>>>> *Sent:* Wed, 18 Jun, 2014 04:43
>>>> *To:* user@ctakes.apache.org
>>>> *Subject:* Re: [External] Re: Cannot load
>>>> AggregatePlainTextUmlsProcessor.xml
>>>>
>>>>
>>>>
>>>> Found a fix. Will post it here in case it helps someone. When using
>>>> ctakes-3.1.2, load the AggregatePlainTextUmlsProcessor.xml from "
>>>> CTAKES_HOME/desc/ytex-uima/desc/analysis_engine/
>>>> AggregatePlaintextUMLSProcessor.xml" and not from the usual "
>>>> CTAKES_HOME/desc/ctakes-clinical-pipeline/desc/analysis_engine/
>>>> AggregatePlaintextUMLSProcessor.xml" as given here
>>>> <https://cwiki.apache.org/confluence/display/CTAKES/User%27s+Guide>.
>>>>
>>>> However strangely, "ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml"
>>>> produced even less annotations than "
>>>> ctakes-clinical-pipeline/desc/analysis_engine/
>>>> AggregatePlaintextUMLSProcessor.xml".
>>>>
>>>> I expected ytex-specific AE to produce better results. But clearly
>>>> that's not the case.
>>>>
>>>>
>>>>
>>>> On Thu, Jun 12, 2014 at 2:51 AM, Abhishek Raj <ab...@iitrpr.ac.in>
>>>> wrote:
>>>>
>>>> Hi. Thanks for the reply.
>>>> I have a file named LookupDesc_Db.xml which has the line <jdbcImpl
>>>> tableName="@db.schema@.v_snomed_fword_lookup"/>
>>>>
>>>> instead of LookupDesc_SNOMED.*template*.xml. Also, my ytex.properties
>>>> file seems fine. I have attached the file for your reference.
>>>> And yes, when running the ant setup by following #7 on this
>>>> <https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation> link,
>>>> it sends the output to "setup.out". The build was successful though. I
>>>> didn't see any errors. I am attaching the file for your reference as well.
>>>> Please have a look and let me know.
>>>>
>>>>
>>>>
>>>
>>>
>>
Re: [External] Re: Cannot load AggregatePlainTextUmlsProcessor.xml
Posted by John Green <he...@gmail.com>.
A manual query such as SELECT * FROM ytex.v_snomed_fword_lookup WHERE
fword="mesna"; works OK btw.
On Wed, Jul 16, 2014 at 11:24 AM, John Green <he...@gmail.com>
wrote:
> So, tableName="@db.schema@.v_snomed_fword_lookup" to
> tableName="ytex.v_snomed_fword_lookup" in LookupDesc_Db.xml?
>
> If so, I tried this and same error, with just the names swapped.
>
> Thanks Vijay,
> JG
>
>
> On Wed, Jul 16, 2014 at 11:20 AM, vijay garla <vn...@gmail.com> wrote:
>
>> replace db.schema with your database schema name. For sql server, this
>> is dbo, for mysql this is the database/schema name, for oracle this is the
>> schema name. This should have been done automatically by the ant setup
>> script, not sure why it isn't happening in some configs.
>>
>> -vj
>>
>>
>> On Wed, Jul 16, 2014 at 4:53 PM, John Green <he...@gmail.com>
>> wrote:
>>
>>> Hi Vijay - I am at the same impasse as Mr Lee and Mr Abhishek, and I
>>> didnt come across any other solutions in the archives.
>>>
>>> Through intuition I figured out what you mention in this post on my own,
>>> and tried it. It didnt work. It seems to revolve around this line:
>>> Unexpected token: @ in statement [SELECT tui,cui,tok_str FROM @db.schema@.v_snomed_fword_lookup
>>> WHERE fword = ?]
>>>
>>> It seems the query is coming from LookupDesc_SNOMED.xml, but I cant find
>>> the @db.schema@... is this a windows/linux issue?
>>>
>>> Before Vijay spends his precious time on answering this, did anyone else
>>> get resolution on this?
>>>
>>> Best,
>>> JG
>>>
>>>
>>> On Wed, Jun 18, 2014 at 10:11 AM, vijay garla <vn...@gmail.com> wrote:
>>>
>>>> The YTEX AggregatePlaintextUMLSProcessor differs from the default
>>>> AggregatePlaintextUMLSProcessor in the following a ways:
>>>> * Use SegmentRegexAnnotator instead of SimpleSegmentAnnotator
>>>> * Use SentenceDetectorAnnotator without splitting on newlines
>>>> * Added SenseDisambiguatorAnnotator
>>>> ** Use YTEX DictionaryLookupAnnotatorDB instead of cTAKES
>>>> DictionaryLookupAnnotatorDB*
>>>>
>>>> The YTEX dictionary lookup is different from cTAKES':
>>>> * uses the old dictionary lookup
>>>> * uses a single dictionary
>>>> * uses a single lookup consumer that creates
>>>> plain-vanilla EntityMention annotations (none of the subtypes)
>>>>
>>>> I think that if you change the YTEX AggregatePlaintextUMLSProcessor to
>>>> point at the cTAKES dictionary lookup, you will get approximately same
>>>> annotations (probably more if sentences do not end on newlines, as
>>>> dictionary lookup is not performed across sentences)
>>>>
>>>> could you try the following please:
>>>> In
>>>> desc\ctakes-ytex-uima\desc\analysis_engine\AggregatePlaintextUMLSProcessor.xml
>>>> change
>>>> <delegateAnalysisEngine key="DictionaryLookupAnnotatorDB">
>>>> <import location="./DictionaryLookupAnnotator.xml" />
>>>> </delegateAnalysisEngine>
>>>> To
>>>> <delegateAnalysisEngine key="DictionaryLookupAnnotatorDB">
>>>> <import
>>>> location="../../../ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml"/>
>>>> </delegateAnalysisEngine>
>>>>
>>>> And re-run. You should get the same results (keep in mind the newline
>>>> thing).
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On Wed, Jun 18, 2014 at 9:46 AM, Lee, Richard A. [USA] <
>>>> lee_richard@bah.com> wrote:
>>>>
>>>>> Yes, that exactly the problem I’ve been reporting. I think you’ll
>>>>> see that it you still get the non-Medical annotations, like Date,
>>>>> RomanNumeral, et al, but not DiseaseDisorderMention and the other Medical
>>>>> ones, right?
>>>>>
>>>>>
>>>>>
>>>>> I’m still hoping someone can assist with this.
>>>>>
>>>>>
>>>>>
>>>>> *From:* Abhishek Raj [mailto:abhishekrm@iitrpr.ac.in]
>>>>> *Sent:* Wed, 18 Jun, 2014 04:43
>>>>> *To:* user@ctakes.apache.org
>>>>> *Subject:* Re: [External] Re: Cannot load
>>>>> AggregatePlainTextUmlsProcessor.xml
>>>>>
>>>>>
>>>>>
>>>>> Found a fix. Will post it here in case it helps someone. When using
>>>>> ctakes-3.1.2, load the AggregatePlainTextUmlsProcessor.xml from "
>>>>> CTAKES_HOME/desc/ytex-uima/desc/analysis_engine/
>>>>> AggregatePlaintextUMLSProcessor.xml" and not from the usual "
>>>>> CTAKES_HOME/desc/ctakes-clinical-pipeline/desc/analysis_engine/
>>>>> AggregatePlaintextUMLSProcessor.xml" as given here
>>>>> <https://cwiki.apache.org/confluence/display/CTAKES/User%27s+Guide>.
>>>>>
>>>>> However strangely, "ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml"
>>>>> produced even less annotations than "
>>>>> ctakes-clinical-pipeline/desc/analysis_engine/
>>>>> AggregatePlaintextUMLSProcessor.xml".
>>>>>
>>>>> I expected ytex-specific AE to produce better results. But clearly
>>>>> that's not the case.
>>>>>
>>>>>
>>>>>
>>>>> On Thu, Jun 12, 2014 at 2:51 AM, Abhishek Raj <ab...@iitrpr.ac.in>
>>>>> wrote:
>>>>>
>>>>> Hi. Thanks for the reply.
>>>>> I have a file named LookupDesc_Db.xml which has the line <jdbcImpl
>>>>> tableName="@db.schema@.v_snomed_fword_lookup"/>
>>>>>
>>>>> instead of LookupDesc_SNOMED.*template*.xml. Also, my ytex.properties
>>>>> file seems fine. I have attached the file for your reference.
>>>>> And yes, when running the ant setup by following #7 on this
>>>>> <https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation> link,
>>>>> it sends the output to "setup.out". The build was successful though. I
>>>>> didn't see any errors. I am attaching the file for your reference as well.
>>>>> Please have a look and let me know.
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>
>
Re: [External] Re: Cannot load AggregatePlainTextUmlsProcessor.xml
Posted by John Green <he...@gmail.com>.
So, tableName="@db.schema@.v_snomed_fword_lookup" to
tableName="ytex.v_snomed_fword_lookup" in LookupDesc_Db.xml?
If so, I tried this and same error, with just the names swapped.
Thanks Vijay,
JG
On Wed, Jul 16, 2014 at 11:20 AM, vijay garla <vn...@gmail.com> wrote:
> replace db.schema with your database schema name. For sql server, this is
> dbo, for mysql this is the database/schema name, for oracle this is the
> schema name. This should have been done automatically by the ant setup
> script, not sure why it isn't happening in some configs.
>
> -vj
>
>
> On Wed, Jul 16, 2014 at 4:53 PM, John Green <he...@gmail.com>
> wrote:
>
>> Hi Vijay - I am at the same impasse as Mr Lee and Mr Abhishek, and I
>> didnt come across any other solutions in the archives.
>>
>> Through intuition I figured out what you mention in this post on my own,
>> and tried it. It didnt work. It seems to revolve around this line:
>> Unexpected token: @ in statement [SELECT tui,cui,tok_str FROM @db.schema@.v_snomed_fword_lookup
>> WHERE fword = ?]
>>
>> It seems the query is coming from LookupDesc_SNOMED.xml, but I cant find
>> the @db.schema@... is this a windows/linux issue?
>>
>> Before Vijay spends his precious time on answering this, did anyone else
>> get resolution on this?
>>
>> Best,
>> JG
>>
>>
>> On Wed, Jun 18, 2014 at 10:11 AM, vijay garla <vn...@gmail.com> wrote:
>>
>>> The YTEX AggregatePlaintextUMLSProcessor differs from the default
>>> AggregatePlaintextUMLSProcessor in the following a ways:
>>> * Use SegmentRegexAnnotator instead of SimpleSegmentAnnotator
>>> * Use SentenceDetectorAnnotator without splitting on newlines
>>> * Added SenseDisambiguatorAnnotator
>>> ** Use YTEX DictionaryLookupAnnotatorDB instead of cTAKES
>>> DictionaryLookupAnnotatorDB*
>>>
>>> The YTEX dictionary lookup is different from cTAKES':
>>> * uses the old dictionary lookup
>>> * uses a single dictionary
>>> * uses a single lookup consumer that creates plain-vanilla EntityMention
>>> annotations (none of the subtypes)
>>>
>>> I think that if you change the YTEX AggregatePlaintextUMLSProcessor to
>>> point at the cTAKES dictionary lookup, you will get approximately same
>>> annotations (probably more if sentences do not end on newlines, as
>>> dictionary lookup is not performed across sentences)
>>>
>>> could you try the following please:
>>> In
>>> desc\ctakes-ytex-uima\desc\analysis_engine\AggregatePlaintextUMLSProcessor.xml
>>> change
>>> <delegateAnalysisEngine key="DictionaryLookupAnnotatorDB">
>>> <import location="./DictionaryLookupAnnotator.xml" />
>>> </delegateAnalysisEngine>
>>> To
>>> <delegateAnalysisEngine key="DictionaryLookupAnnotatorDB">
>>> <import
>>> location="../../../ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml"/>
>>> </delegateAnalysisEngine>
>>>
>>> And re-run. You should get the same results (keep in mind the newline
>>> thing).
>>>
>>>
>>>
>>>
>>>
>>> On Wed, Jun 18, 2014 at 9:46 AM, Lee, Richard A. [USA] <
>>> lee_richard@bah.com> wrote:
>>>
>>>> Yes, that exactly the problem I’ve been reporting. I think you’ll see
>>>> that it you still get the non-Medical annotations, like Date, RomanNumeral,
>>>> et al, but not DiseaseDisorderMention and the other Medical ones, right?
>>>>
>>>>
>>>>
>>>> I’m still hoping someone can assist with this.
>>>>
>>>>
>>>>
>>>> *From:* Abhishek Raj [mailto:abhishekrm@iitrpr.ac.in]
>>>> *Sent:* Wed, 18 Jun, 2014 04:43
>>>> *To:* user@ctakes.apache.org
>>>> *Subject:* Re: [External] Re: Cannot load
>>>> AggregatePlainTextUmlsProcessor.xml
>>>>
>>>>
>>>>
>>>> Found a fix. Will post it here in case it helps someone. When using
>>>> ctakes-3.1.2, load the AggregatePlainTextUmlsProcessor.xml from "
>>>> CTAKES_HOME/desc/ytex-uima/desc/analysis_engine/
>>>> AggregatePlaintextUMLSProcessor.xml" and not from the usual "
>>>> CTAKES_HOME/desc/ctakes-clinical-pipeline/desc/analysis_engine/
>>>> AggregatePlaintextUMLSProcessor.xml" as given here
>>>> <https://cwiki.apache.org/confluence/display/CTAKES/User%27s+Guide>.
>>>>
>>>> However strangely, "ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml"
>>>> produced even less annotations than "
>>>> ctakes-clinical-pipeline/desc/analysis_engine/
>>>> AggregatePlaintextUMLSProcessor.xml".
>>>>
>>>> I expected ytex-specific AE to produce better results. But clearly
>>>> that's not the case.
>>>>
>>>>
>>>>
>>>> On Thu, Jun 12, 2014 at 2:51 AM, Abhishek Raj <ab...@iitrpr.ac.in>
>>>> wrote:
>>>>
>>>> Hi. Thanks for the reply.
>>>> I have a file named LookupDesc_Db.xml which has the line <jdbcImpl
>>>> tableName="@db.schema@.v_snomed_fword_lookup"/>
>>>>
>>>> instead of LookupDesc_SNOMED.*template*.xml. Also, my ytex.properties
>>>> file seems fine. I have attached the file for your reference.
>>>> And yes, when running the ant setup by following #7 on this
>>>> <https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation> link,
>>>> it sends the output to "setup.out". The build was successful though. I
>>>> didn't see any errors. I am attaching the file for your reference as well.
>>>> Please have a look and let me know.
>>>>
>>>>
>>>>
>>>
>>>
>>
>
Re: [External] Re: Cannot load AggregatePlainTextUmlsProcessor.xml
Posted by vijay garla <vn...@gmail.com>.
replace db.schema with your database schema name. For sql server, this is
dbo, for mysql this is the database/schema name, for oracle this is the
schema name. This should have been done automatically by the ant setup
script, not sure why it isn't happening in some configs.
-vj
On Wed, Jul 16, 2014 at 4:53 PM, John Green <he...@gmail.com>
wrote:
> Hi Vijay - I am at the same impasse as Mr Lee and Mr Abhishek, and I didnt
> come across any other solutions in the archives.
>
> Through intuition I figured out what you mention in this post on my own,
> and tried it. It didnt work. It seems to revolve around this line:
> Unexpected token: @ in statement [SELECT tui,cui,tok_str FROM @db.schema@.v_snomed_fword_lookup
> WHERE fword = ?]
>
> It seems the query is coming from LookupDesc_SNOMED.xml, but I cant find
> the @db.schema@... is this a windows/linux issue?
>
> Before Vijay spends his precious time on answering this, did anyone else
> get resolution on this?
>
> Best,
> JG
>
>
> On Wed, Jun 18, 2014 at 10:11 AM, vijay garla <vn...@gmail.com> wrote:
>
>> The YTEX AggregatePlaintextUMLSProcessor differs from the default
>> AggregatePlaintextUMLSProcessor in the following a ways:
>> * Use SegmentRegexAnnotator instead of SimpleSegmentAnnotator
>> * Use SentenceDetectorAnnotator without splitting on newlines
>> * Added SenseDisambiguatorAnnotator
>> ** Use YTEX DictionaryLookupAnnotatorDB instead of cTAKES
>> DictionaryLookupAnnotatorDB*
>>
>> The YTEX dictionary lookup is different from cTAKES':
>> * uses the old dictionary lookup
>> * uses a single dictionary
>> * uses a single lookup consumer that creates plain-vanilla EntityMention
>> annotations (none of the subtypes)
>>
>> I think that if you change the YTEX AggregatePlaintextUMLSProcessor to
>> point at the cTAKES dictionary lookup, you will get approximately same
>> annotations (probably more if sentences do not end on newlines, as
>> dictionary lookup is not performed across sentences)
>>
>> could you try the following please:
>> In
>> desc\ctakes-ytex-uima\desc\analysis_engine\AggregatePlaintextUMLSProcessor.xml
>> change
>> <delegateAnalysisEngine key="DictionaryLookupAnnotatorDB">
>> <import location="./DictionaryLookupAnnotator.xml" />
>> </delegateAnalysisEngine>
>> To
>> <delegateAnalysisEngine key="DictionaryLookupAnnotatorDB">
>> <import
>> location="../../../ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml"/>
>> </delegateAnalysisEngine>
>>
>> And re-run. You should get the same results (keep in mind the newline
>> thing).
>>
>>
>>
>>
>>
>> On Wed, Jun 18, 2014 at 9:46 AM, Lee, Richard A. [USA] <
>> lee_richard@bah.com> wrote:
>>
>>> Yes, that exactly the problem I’ve been reporting. I think you’ll see
>>> that it you still get the non-Medical annotations, like Date, RomanNumeral,
>>> et al, but not DiseaseDisorderMention and the other Medical ones, right?
>>>
>>>
>>>
>>> I’m still hoping someone can assist with this.
>>>
>>>
>>>
>>> *From:* Abhishek Raj [mailto:abhishekrm@iitrpr.ac.in]
>>> *Sent:* Wed, 18 Jun, 2014 04:43
>>> *To:* user@ctakes.apache.org
>>> *Subject:* Re: [External] Re: Cannot load
>>> AggregatePlainTextUmlsProcessor.xml
>>>
>>>
>>>
>>> Found a fix. Will post it here in case it helps someone. When using
>>> ctakes-3.1.2, load the AggregatePlainTextUmlsProcessor.xml from "
>>> CTAKES_HOME/desc/ytex-uima/desc/analysis_engine/
>>> AggregatePlaintextUMLSProcessor.xml" and not from the usual "
>>> CTAKES_HOME/desc/ctakes-clinical-pipeline/desc/analysis_engine/
>>> AggregatePlaintextUMLSProcessor.xml" as given here
>>> <https://cwiki.apache.org/confluence/display/CTAKES/User%27s+Guide>.
>>>
>>> However strangely, "ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml"
>>> produced even less annotations than "
>>> ctakes-clinical-pipeline/desc/analysis_engine/
>>> AggregatePlaintextUMLSProcessor.xml".
>>>
>>> I expected ytex-specific AE to produce better results. But clearly
>>> that's not the case.
>>>
>>>
>>>
>>> On Thu, Jun 12, 2014 at 2:51 AM, Abhishek Raj <ab...@iitrpr.ac.in>
>>> wrote:
>>>
>>> Hi. Thanks for the reply.
>>> I have a file named LookupDesc_Db.xml which has the line <jdbcImpl
>>> tableName="@db.schema@.v_snomed_fword_lookup"/>
>>>
>>> instead of LookupDesc_SNOMED.*template*.xml. Also, my ytex.properties
>>> file seems fine. I have attached the file for your reference.
>>> And yes, when running the ant setup by following #7 on this
>>> <https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation> link,
>>> it sends the output to "setup.out". The build was successful though. I
>>> didn't see any errors. I am attaching the file for your reference as well.
>>> Please have a look and let me know.
>>>
>>>
>>>
>>
>>
>
Re: [External] Re: Cannot load AggregatePlainTextUmlsProcessor.xml
Posted by John Green <he...@gmail.com>.
Hi Vijay - I am at the same impasse as Mr Lee and Mr Abhishek, and I didnt
come across any other solutions in the archives.
Through intuition I figured out what you mention in this post on my own,
and tried it. It didnt work. It seems to revolve around this line:
Unexpected token: @ in statement [SELECT tui,cui,tok_str FROM
@db.schema@.v_snomed_fword_lookup
WHERE fword = ?]
It seems the query is coming from LookupDesc_SNOMED.xml, but I cant find
the @db.schema@... is this a windows/linux issue?
Before Vijay spends his precious time on answering this, did anyone else
get resolution on this?
Best,
JG
On Wed, Jun 18, 2014 at 10:11 AM, vijay garla <vn...@gmail.com> wrote:
> The YTEX AggregatePlaintextUMLSProcessor differs from the default
> AggregatePlaintextUMLSProcessor in the following a ways:
> * Use SegmentRegexAnnotator instead of SimpleSegmentAnnotator
> * Use SentenceDetectorAnnotator without splitting on newlines
> * Added SenseDisambiguatorAnnotator
> ** Use YTEX DictionaryLookupAnnotatorDB instead of cTAKES
> DictionaryLookupAnnotatorDB*
>
> The YTEX dictionary lookup is different from cTAKES':
> * uses the old dictionary lookup
> * uses a single dictionary
> * uses a single lookup consumer that creates plain-vanilla EntityMention
> annotations (none of the subtypes)
>
> I think that if you change the YTEX AggregatePlaintextUMLSProcessor to
> point at the cTAKES dictionary lookup, you will get approximately same
> annotations (probably more if sentences do not end on newlines, as
> dictionary lookup is not performed across sentences)
>
> could you try the following please:
> In
> desc\ctakes-ytex-uima\desc\analysis_engine\AggregatePlaintextUMLSProcessor.xml
> change
> <delegateAnalysisEngine key="DictionaryLookupAnnotatorDB">
> <import location="./DictionaryLookupAnnotator.xml" />
> </delegateAnalysisEngine>
> To
> <delegateAnalysisEngine key="DictionaryLookupAnnotatorDB">
> <import
> location="../../../ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml"/>
> </delegateAnalysisEngine>
>
> And re-run. You should get the same results (keep in mind the newline
> thing).
>
>
>
>
>
> On Wed, Jun 18, 2014 at 9:46 AM, Lee, Richard A. [USA] <
> lee_richard@bah.com> wrote:
>
>> Yes, that exactly the problem I’ve been reporting. I think you’ll see
>> that it you still get the non-Medical annotations, like Date, RomanNumeral,
>> et al, but not DiseaseDisorderMention and the other Medical ones, right?
>>
>>
>>
>> I’m still hoping someone can assist with this.
>>
>>
>>
>> *From:* Abhishek Raj [mailto:abhishekrm@iitrpr.ac.in]
>> *Sent:* Wed, 18 Jun, 2014 04:43
>> *To:* user@ctakes.apache.org
>> *Subject:* Re: [External] Re: Cannot load
>> AggregatePlainTextUmlsProcessor.xml
>>
>>
>>
>> Found a fix. Will post it here in case it helps someone. When using
>> ctakes-3.1.2, load the AggregatePlainTextUmlsProcessor.xml from "
>> CTAKES_HOME/desc/ytex-uima/desc/analysis_engine/
>> AggregatePlaintextUMLSProcessor.xml" and not from the usual "
>> CTAKES_HOME/desc/ctakes-clinical-pipeline/desc/analysis_engine/
>> AggregatePlaintextUMLSProcessor.xml" as given here
>> <https://cwiki.apache.org/confluence/display/CTAKES/User%27s+Guide>.
>>
>> However strangely, "ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml"
>> produced even less annotations than "
>> ctakes-clinical-pipeline/desc/analysis_engine/
>> AggregatePlaintextUMLSProcessor.xml".
>>
>> I expected ytex-specific AE to produce better results. But clearly that's
>> not the case.
>>
>>
>>
>> On Thu, Jun 12, 2014 at 2:51 AM, Abhishek Raj <ab...@iitrpr.ac.in>
>> wrote:
>>
>> Hi. Thanks for the reply.
>> I have a file named LookupDesc_Db.xml which has the line <jdbcImpl
>> tableName="@db.schema@.v_snomed_fword_lookup"/>
>>
>> instead of LookupDesc_SNOMED.*template*.xml. Also, my ytex.properties
>> file seems fine. I have attached the file for your reference.
>> And yes, when running the ant setup by following #7 on this
>> <https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation> link,
>> it sends the output to "setup.out". The build was successful though. I
>> didn't see any errors. I am attaching the file for your reference as well.
>> Please have a look and let me know.
>>
>>
>>
>
>
Re: [External] Re: Cannot load AggregatePlainTextUmlsProcessor.xml
Posted by John Green <he...@gmail.com>.
More info: The issue seems to revolve around how ytex uses
v_snowmed_fword_lookup and how ctakes does... and when you wire the
pipeline together as we've mentioned here, swapping ytex dictionary lookup
for ctakes, this difference is breaking the process.
Still investigating.
On Wed, Jun 18, 2014 at 10:11 AM, vijay garla <vn...@gmail.com> wrote:
> The YTEX AggregatePlaintextUMLSProcessor differs from the default
> AggregatePlaintextUMLSProcessor in the following a ways:
> * Use SegmentRegexAnnotator instead of SimpleSegmentAnnotator
> * Use SentenceDetectorAnnotator without splitting on newlines
> * Added SenseDisambiguatorAnnotator
> ** Use YTEX DictionaryLookupAnnotatorDB instead of cTAKES
> DictionaryLookupAnnotatorDB*
>
> The YTEX dictionary lookup is different from cTAKES':
> * uses the old dictionary lookup
> * uses a single dictionary
> * uses a single lookup consumer that creates plain-vanilla EntityMention
> annotations (none of the subtypes)
>
> I think that if you change the YTEX AggregatePlaintextUMLSProcessor to
> point at the cTAKES dictionary lookup, you will get approximately same
> annotations (probably more if sentences do not end on newlines, as
> dictionary lookup is not performed across sentences)
>
> could you try the following please:
> In
> desc\ctakes-ytex-uima\desc\analysis_engine\AggregatePlaintextUMLSProcessor.xml
> change
> <delegateAnalysisEngine key="DictionaryLookupAnnotatorDB">
> <import location="./DictionaryLookupAnnotator.xml" />
> </delegateAnalysisEngine>
> To
> <delegateAnalysisEngine key="DictionaryLookupAnnotatorDB">
> <import
> location="../../../ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml"/>
> </delegateAnalysisEngine>
>
> And re-run. You should get the same results (keep in mind the newline
> thing).
>
>
>
>
>
> On Wed, Jun 18, 2014 at 9:46 AM, Lee, Richard A. [USA] <
> lee_richard@bah.com> wrote:
>
>> Yes, that exactly the problem I’ve been reporting. I think you’ll see
>> that it you still get the non-Medical annotations, like Date, RomanNumeral,
>> et al, but not DiseaseDisorderMention and the other Medical ones, right?
>>
>>
>>
>> I’m still hoping someone can assist with this.
>>
>>
>>
>> *From:* Abhishek Raj [mailto:abhishekrm@iitrpr.ac.in]
>> *Sent:* Wed, 18 Jun, 2014 04:43
>> *To:* user@ctakes.apache.org
>> *Subject:* Re: [External] Re: Cannot load
>> AggregatePlainTextUmlsProcessor.xml
>>
>>
>>
>> Found a fix. Will post it here in case it helps someone. When using
>> ctakes-3.1.2, load the AggregatePlainTextUmlsProcessor.xml from "
>> CTAKES_HOME/desc/ytex-uima/desc/analysis_engine/
>> AggregatePlaintextUMLSProcessor.xml" and not from the usual "
>> CTAKES_HOME/desc/ctakes-clinical-pipeline/desc/analysis_engine/
>> AggregatePlaintextUMLSProcessor.xml" as given here
>> <https://cwiki.apache.org/confluence/display/CTAKES/User%27s+Guide>.
>>
>> However strangely, "ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml"
>> produced even less annotations than "
>> ctakes-clinical-pipeline/desc/analysis_engine/
>> AggregatePlaintextUMLSProcessor.xml".
>>
>> I expected ytex-specific AE to produce better results. But clearly that's
>> not the case.
>>
>>
>>
>> On Thu, Jun 12, 2014 at 2:51 AM, Abhishek Raj <ab...@iitrpr.ac.in>
>> wrote:
>>
>> Hi. Thanks for the reply.
>> I have a file named LookupDesc_Db.xml which has the line <jdbcImpl
>> tableName="@db.schema@.v_snomed_fword_lookup"/>
>>
>> instead of LookupDesc_SNOMED.*template*.xml. Also, my ytex.properties
>> file seems fine. I have attached the file for your reference.
>> And yes, when running the ant setup by following #7 on this
>> <https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation> link,
>> it sends the output to "setup.out". The build was successful though. I
>> didn't see any errors. I am attaching the file for your reference as well.
>> Please have a look and let me know.
>>
>>
>>
>
>
Re: [External] Re: Cannot load AggregatePlainTextUmlsProcessor.xml
Posted by vijay garla <vn...@gmail.com>.
The YTEX AggregatePlaintextUMLSProcessor differs from the default
AggregatePlaintextUMLSProcessor in the following a ways:
* Use SegmentRegexAnnotator instead of SimpleSegmentAnnotator
* Use SentenceDetectorAnnotator without splitting on newlines
* Added SenseDisambiguatorAnnotator
** Use YTEX DictionaryLookupAnnotatorDB instead of cTAKES
DictionaryLookupAnnotatorDB*
The YTEX dictionary lookup is different from cTAKES':
* uses the old dictionary lookup
* uses a single dictionary
* uses a single lookup consumer that creates plain-vanilla EntityMention
annotations (none of the subtypes)
I think that if you change the YTEX AggregatePlaintextUMLSProcessor to
point at the cTAKES dictionary lookup, you will get approximately same
annotations (probably more if sentences do not end on newlines, as
dictionary lookup is not performed across sentences)
could you try the following please:
In
desc\ctakes-ytex-uima\desc\analysis_engine\AggregatePlaintextUMLSProcessor.xml
change
<delegateAnalysisEngine key="DictionaryLookupAnnotatorDB">
<import location="./DictionaryLookupAnnotator.xml" />
</delegateAnalysisEngine>
To
<delegateAnalysisEngine key="DictionaryLookupAnnotatorDB">
<import
location="../../../ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml"/>
</delegateAnalysisEngine>
And re-run. You should get the same results (keep in mind the newline
thing).
On Wed, Jun 18, 2014 at 9:46 AM, Lee, Richard A. [USA] <le...@bah.com>
wrote:
> Yes, that exactly the problem I’ve been reporting. I think you’ll see
> that it you still get the non-Medical annotations, like Date, RomanNumeral,
> et al, but not DiseaseDisorderMention and the other Medical ones, right?
>
>
>
> I’m still hoping someone can assist with this.
>
>
>
> *From:* Abhishek Raj [mailto:abhishekrm@iitrpr.ac.in]
> *Sent:* Wed, 18 Jun, 2014 04:43
> *To:* user@ctakes.apache.org
> *Subject:* Re: [External] Re: Cannot load
> AggregatePlainTextUmlsProcessor.xml
>
>
>
> Found a fix. Will post it here in case it helps someone. When using
> ctakes-3.1.2, load the AggregatePlainTextUmlsProcessor.xml from "
> CTAKES_HOME/desc/ytex-uima/desc/analysis_engine/
> AggregatePlaintextUMLSProcessor.xml" and not from the usual "
> CTAKES_HOME/desc/ctakes-clinical-pipeline/desc/analysis_engine/
> AggregatePlaintextUMLSProcessor.xml" as given here
> <https://cwiki.apache.org/confluence/display/CTAKES/User%27s+Guide>.
>
> However strangely, "ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml"
> produced even less annotations than "
> ctakes-clinical-pipeline/desc/analysis_engine/
> AggregatePlaintextUMLSProcessor.xml".
>
> I expected ytex-specific AE to produce better results. But clearly that's
> not the case.
>
>
>
> On Thu, Jun 12, 2014 at 2:51 AM, Abhishek Raj <ab...@iitrpr.ac.in>
> wrote:
>
> Hi. Thanks for the reply.
> I have a file named LookupDesc_Db.xml which has the line <jdbcImpl
> tableName="@db.schema@.v_snomed_fword_lookup"/>
>
> instead of LookupDesc_SNOMED.*template*.xml. Also, my ytex.properties
> file seems fine. I have attached the file for your reference.
> And yes, when running the ant setup by following #7 on this
> <https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation> link,
> it sends the output to "setup.out". The build was successful though. I
> didn't see any errors. I am attaching the file for your reference as well.
> Please have a look and let me know.
>
>
>
RE: [External] Re: Cannot load AggregatePlainTextUmlsProcessor.xml
Posted by "Lee, Richard A. [USA]" <le...@bah.com>.
Yes, that exactly the problem I’ve been reporting. I think you’ll see that it you still get the non-Medical annotations, like Date, RomanNumeral, et al, but not DiseaseDisorderMention and the other Medical ones, right?
I’m still hoping someone can assist with this.
From: Abhishek Raj [mailto:abhishekrm@iitrpr.ac.in]
Sent: Wed, 18 Jun, 2014 04:43
To: user@ctakes.apache.org
Subject: Re: [External] Re: Cannot load AggregatePlainTextUmlsProcessor.xml
Found a fix. Will post it here in case it helps someone. When using ctakes-3.1.2, load the AggregatePlainTextUmlsProcessor.xml from "CTAKES_HOME/desc/ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml" and not from the usual "CTAKES_HOME/desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml" as given here<https://cwiki.apache.org/confluence/display/CTAKES/User%27s+Guide>.
However strangely, "ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml" produced even less annotations than "ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml".
I expected ytex-specific AE to produce better results. But clearly that's not the case.
On Thu, Jun 12, 2014 at 2:51 AM, Abhishek Raj <ab...@iitrpr.ac.in>> wrote:
Hi. Thanks for the reply.
I have a file named LookupDesc_Db.xml which has the line <jdbcImpl tableName="@db.schema@.v_snomed_fword_lookup"/>
instead of LookupDesc_SNOMED.template.xml. Also, my ytex.properties file seems fine. I have attached the file for your reference.
And yes, when running the ant setup by following #7 on this<https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation> link, it sends the output to "setup.out". The build was successful though. I didn't see any errors. I am attaching the file for your reference as well. Please have a look and let me know.
Re: [External] Re: Cannot load AggregatePlainTextUmlsProcessor.xml
Posted by Abhishek Raj <ab...@iitrpr.ac.in>.
Found a fix. Will post it here in case it helps someone. When using
ctakes-3.1.2, load the AggregatePlainTextUmlsProcessor.xml from "
CTAKES_HOME/desc/ytex-uima/desc/analysis_engine/
AggregatePlaintextUMLSProcessor.xml" and not from the usual "
CTAKES_HOME/desc/ctakes-clinical-pipeline/desc/analysis_engine/
AggregatePlaintextUMLSProcessor.xml" as given here
<https://cwiki.apache.org/confluence/display/CTAKES/User%27s+Guide>.
However strangely,
"ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml"
produced even less annotations than "
ctakes-clinical-pipeline/desc/analysis_engine/
AggregatePlaintextUMLSProcessor.xml".
I expected ytex-specific AE to produce better results. But clearly that's
not the case.
On Thu, Jun 12, 2014 at 2:51 AM, Abhishek Raj <ab...@iitrpr.ac.in>
wrote:
> Hi. Thanks for the reply.
> I have a file named LookupDesc_Db.xml which has the line <jdbcImpl
> tableName="@db.schema@.v_snomed_fword_lookup"/>
> instead of LookupDesc_SNOMED.*template*.xml. Also, my ytex.properties
> file seems fine. I have attached the file for your reference.
> And yes, when running the ant setup by following #7 on this
> <https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation> link,
> it sends the output to "setup.out". The build was successful though. I
> didn't see any errors. I am attaching the file for your reference as well.
> Please have a look and let me know.
>
Re: [External] Re: Cannot load AggregatePlainTextUmlsProcessor.xml
Posted by Abhishek Raj <ab...@iitrpr.ac.in>.
Hi. Thanks for the reply.
I have a file named LookupDesc_Db.xml which has the line <jdbcImpl
tableName="@db.schema@.v_snomed_fword_lookup"/>
instead of LookupDesc_SNOMED.*template*.xml. Also, my ytex.properties file
seems fine. I have attached the file for your reference.
And yes, when running the ant setup by following #7 on this
<https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation> link,
it sends the output to "setup.out". The build was successful though. I
didn't see any errors. I am attaching the file for your reference as well.
Please have a look and let me know.
Re: [External] Re: Cannot load AggregatePlainTextUmlsProcessor.xml
Posted by vijay garla <vn...@gmail.com>.
CTAKES_HOME\resources\org\apache\ctakes\ytex\dictionary\lookup\LookupDesc_SNOMED.
*template*.xml will have this line:
<jdbcImpl tableName="@db.schema@.v_snomed_fword_lookup"/>
During the setup, ytex looks at the ytex.properties file and substitutes
@db.schema@ with the name of your schema. E.g. if I have this in
ytex.properties:
db.schema=ytex
CTAKES_HOME\resources\org\apache\ctakes\ytex\dictionary\lookup\LookupDesc_SNOMED.xml
will have this line:
<jdbcImpl tableName="ytex.v_snomed_fword_lookup"/>
Either the ytex ant setup failed for some reason (did you send the output
to a file?), or hasn't been run. If it hasn't run, then there might be
other issues.
-vj
On Wed, Jun 11, 2014 at 12:46 PM, Abhishek Raj <ab...@iitrpr.ac.in>
wrote:
> I think the error is in the ytex.profile file. I am not really sure
> though. I am attaching the file. Please let me know if there is anything to
> be changed in the file that might fix the issue. Thanks.
>
>
> On Wed, Jun 11, 2014 at 10:04 PM, Lee, Richard A. [USA] <
> lee_richard@bah.com> wrote:
>
>> This is the same error I reported a few weeks ago, but it probably got
>> missed because I was also reporting that using the ytex-specific AE failed
>> to produce any MedicalAnnotations…
>>
>>
>>
>> *From:* Abhishek Raj [mailto:abhishekrm@iitrpr.ac.in]
>> *Sent:* Wed, 11 Jun, 2014 12:11
>> *To:* user@ctakes.apache.org
>> *Subject:* [External] Re: Cannot load AggregatePlainTextUmlsProcessor.xml
>>
>>
>>
>> Thanks for the reply. I am using apace-cTakes-3.1.2 and yes, this is
>> using YTEX. I followed these
>> <https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation> instructions
>> for installing ytex and #1 in the installation procedure was " installing ctakes+ytex
>> distro 'as usual' " by following these
>> <https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1+User+Install+Guide> instructions.
>> Not sure what is the reason for the error though. I have UMLS installed in
>> my SQL database already.
>>
>>
>>
>> On Wed, Jun 11, 2014 at 9:24 PM, Chen, Pei <
>> Pei.Chen@childrens.harvard.edu> wrote:
>>
>> Abhishek,
>>
>> There is an SQL exception because of the “@db.schema@.” in the sql:
>>
>> SELECT tui,cui,tok_str FROM @db.schema@.v_snomed_fword_lookup WHERE
>> fword = ?
>>
>>
>>
>> Which version of cTAKES are you using and also is this using YTEX? As I
>> am not sure where the special parameter markers are coming from. Normally,
>> it would look something like:
>>
>>
>> http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-dictionary-lookup-res/src/main/resources/org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> *From:* Abhishek Raj [mailto:abhishekrm@iitrpr.ac.in]
>> *Sent:* Wednesday, June 11, 2014 11:39 AM
>> *To:* user@ctakes.apache.org
>> *Subject:* Re: Cannot load AggregatePlainTextUmlsProcessor.xml
>>
>>
>>
>> Hey! Thanks a lot for the reply. That totally worked. However, I have run
>> into another problem now. After loading the
>> "AggregatePlainTextUmlsProcessor.xml", when I try to run the it on some
>> text sample I get an error saying
>>
>> org.apache.uima.analysis_engine.AnalysisEngineProcessException . More
>> detailed information is in the log file
>>
>>
>> I have attached the log in the attachments. Please do have a look. Any
>> help will be appreciated.
>>
>>
>>
>> On Wed, Jun 11, 2014 at 7:06 PM, Chen, Pei <
>> Pei.Chen@childrens.harvard.edu> wrote:
>>
>> Abhishek,
>>
>> Have you tried some of the suggestions from this thread:
>>
>>
>> http://mail-archives.apache.org/mod_mbox/ctakes-dev/201304.mbox/%3CCD84AD35.169BD%25mcoarr%40mitre.org%3E
>>
>>
>>
>>
>>
>> *From:* Abhishek Raj [mailto:abhishekrm@iitrpr.ac.in]
>> *Sent:* Wednesday, June 11, 2014 4:17 AM
>> *To:* user@ctakes.apache.org
>> *Subject:* Cannot load AggregatePlainTextUmlsProcessor.xml
>>
>>
>>
>> Hello I installed ctakes following
>> https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation and
>> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1+User+Install+Guide
>> . After installation I ran the CVD for annotation purpose. When I try to
>> load the AggregatePlainTextUmlsProcessor.xml I get error saying
>>
>> org.apache.uima.resource.ResourceInitializationException:
>>
>> Initialization of annotator class
>>
>> "org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator" failed. (Descriptor: file:/home/gamerboy/apache-ctakes-3.1.2-SNAPSHOT/desc/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml)
>>
>>
>>
>> I am behind a proxy network. Not sure this could be the reason though.
>>
>>
>>
>>
>>
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