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Posted to user@ctakes.apache.org by John Green <he...@gmail.com> on 2014/07/16 16:53:17 UTC
Re: [External] Re: Cannot load AggregatePlainTextUmlsProcessor.xml
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 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.
>>>
>>>
>>>
>>
>>
>