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Posted to dev@ctakes.apache.org by Peter Abramowitsch <pa...@gmail.com> on 2020/07/30 22:48:18 UTC
Problem trying to load a custom dictionary
A couple of questions about installing a custom dictionary in lookup fast.
I hope I'm not too far off the track.
I've used the dictionary creator with a UMLS install to create the
dictionary script, prop file, and xml file in my ctakes resources tree
1. Do I have to manually run this script to execute all its SQL statements
into hsqldb or is this executed by the cTakes program when it encounters
the XML descriptor?
If manual running is needed, are there instructions on how and where to
load the script?
2. The xml file generated by the dictionary creator contains lines with
duplicate names-- see yellow highlight. Is this correct?
<name>my_dict_v1Terms</name>
<property key="jdbcUrl"
value="jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/lookup/fast/
my_dict_v1/my_dict_v1"/>
3. Try as I might I cannot get ctakes to load anything other than
sno_rx. I'm using a piper file with an entry looking like
....
add org.apache.ctakes.dictionary.lookup2.ae.OverlapJCasTermAnnotator
DictionaryDescriptor=org/apache/ctakes/dictionary/lookup/fast/my_dict_v1.xml
....
Not sure if they're looked at any more but I also changed these xml files
under desc as well.
desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsOverlapLookupAnnotator.xml
desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml
But I can't even get it to fail to try to load mine.
my log looks like this
30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator - Exclusion
tagset loaded: CC CD DT EX IN LS MD PDT POS PP PP$ PRP PRP$ RP TO VB VBD
VBG VBN VBP VBZ WDT WP WPS WRB
30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator - Using minimum
term text span: 3
30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator - Using
Dictionary Descriptor: org/apache/ctakes/dictionary/lookup/fast/
sno_rx_16ab.xml
Any suggestions?
Regards, Peter
Re: Problem trying to load a custom dictionary [EXTERNAL] [EXTERNAL]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Cheers!
________________________________________
From: gandhi rajan <ga...@gmail.com>
Sent: Friday, July 31, 2020 10:33 AM
To: dev@ctakes.apache.org
Subject: Re: Problem trying to load a custom dictionary [EXTERNAL] [EXTERNAL]
* External Email - Caution *
Hi Peter,
We can work together on this if you are interested.
On Fri, Jul 31, 2020 at 7:44 PM Peter Abramowitsch <pa...@gmail.com>
wrote:
> I could do it while the experience is fresh, although I only know the happy
> path and not the deeper details in this area of the suite
> If you want me to, let me know how to get editing privileges on the Wiki.
>
> Peter
>
> On Fri, Jul 31, 2020 at 4:28 AM Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
>
> > Obviously Jeff is correct in all of his answers. Thank you Jeff!
> >
> > One comment: DictionaryDescriptor is a deprecated parameter name that is
> > picked up by the piper creator when it inspects the code. However, I am
> > not sure why the deprecated parameter name isn't working ...
> >
> > The wiki needs additional and more thorough information. If anybody can
> > volunteer to work on it I (and future users) would really appreciate it!
> >
> > Thanks,
> > Sean
> >
> >
> > ________________________________________
> > From: Peter Abramowitsch <pa...@gmail.com>
> > Sent: Thursday, July 30, 2020 9:02 PM
> > To: dev@ctakes.apache.org
> > Subject: Re: Problem trying to load a custom dictionary [EXTERNAL]
> >
> > * External Email - Caution *
> >
> >
> > Thanks Jeff
> >
> > That worked!
> >
> > Seems like something that should get fixed in the PiperCreator and in the
> > documentation.
> >
> > With a life of assuming that every mistake is my own error, the last
> thing
> > I would have expected was
> > a generator of incorrect params.
> >
> > Peter
> >
> > On Thu, Jul 30, 2020 at 4:59 PM Jeffrey Miller <je...@gmail.com>
> wrote:
> >
> > > Peter,
> > >
> > > 1) This is loaded by cTAKES, you don't need to manually create the
> > > database.
> > > 2) I can't see the highlights here, but I think that file should be
> okay
> > as
> > > created by the GUI.
> > > 3) I think the parameter name to configure your dictionary location is
> > > LookupXml instead of DictionaryDescriptor
> > >
> > > Jeff
> > >
> > > On Thu, Jul 30, 2020 at 6:49 PM Peter Abramowitsch <
> > > pabramowitsch@gmail.com>
> > > wrote:
> > >
> > > > A couple of questions about installing a custom dictionary in lookup
> > > fast.
> > > > I hope I'm not too far off the track.
> > > >
> > > > I've used the dictionary creator with a UMLS install to create the
> > > > dictionary script, prop file, and xml file in my ctakes resources
> tree
> > > >
> > > > 1. Do I have to manually run this script to execute all its SQL
> > > statements
> > > > into hsqldb or is this executed by the cTakes program when it
> > encounters
> > > > the XML descriptor?
> > > > If manual running is needed, are there instructions on how and where
> to
> > > > load the script?
> > > >
> > > > 2. The xml file generated by the dictionary creator contains lines
> > with
> > > > duplicate names-- see yellow highlight. Is this correct?
> > > > <name>my_dict_v1Terms</name>
> > > > <property key="jdbcUrl"
> > > >
> > >
> >
> value="jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/lookup/fast/
> > > > my_dict_v1/my_dict_v1"/>
> > > >
> > > > 3. Try as I might I cannot get ctakes to load anything other than
> > > > sno_rx. I'm using a piper file with an entry looking like
> > > > ....
> > > > add org.apache.ctakes.dictionary.lookup2.ae
> > > .OverlapJCasTermAnnotator
> > > >
> > > >
> > >
> >
> DictionaryDescriptor=org/apache/ctakes/dictionary/lookup/fast/my_dict_v1.xml
> > > > ....
> > > > Not sure if they're looked at any more but I also changed these xml
> > files
> > > > under desc as well.
> > > >
> > > >
> > > >
> > > >
> > >
> >
> desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsOverlapLookupAnnotator.xml
> > > >
> > > >
> > > >
> > >
> >
> desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml
> > > >
> > > > But I can't even get it to fail to try to load mine.
> > > > my log looks like this
> > > >
> > > > 30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator -
> Exclusion
> > > > tagset loaded: CC CD DT EX IN LS MD PDT POS PP PP$ PRP PRP$ RP TO VB
> > VBD
> > > > VBG VBN VBP VBZ WDT WP WPS WRB
> > > > 30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator - Using
> > > minimum
> > > > term text span: 3
> > > > 30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator - Using
> > > > Dictionary Descriptor: org/apache/ctakes/dictionary/lookup/fast/
> > > > sno_rx_16ab.xml
> > > >
> > > >
> > > > Any suggestions?
> > > >
> > > > Regards, Peter
> > > >
> > >
> >
>
--
Regards,
Gandhi
"The best way to find urself is to lose urself in the service of others !!!"
Re: Problem trying to load a custom dictionary [EXTERNAL] [EXTERNAL]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
To edit the ctakes wiki, you need to obtain a confluence account.
Visit Atlassian.com and navigate until you find something to create a confluence account
or try the direct link
https://id.atlassian.com/login?atlOrigin=eyJpIjoiYTM3ODA4YzFjODJiNGExNzkyZDZjYWZkNDYxNGQ5YzQiLCJwIjoid2FjLWxvZ2luIn0&continue=https%3A%2F%2Fstart.atlassian.com
Once you have an account you might be able to edit ctakes pages.
If you don't see an "edit" option near the central ish - top ish part of a page, send me your user id and I will see if I can give you write permission.
Thanks,
Sean
________________________________________
From: Jeffrey Miller <je...@gmail.com>
Sent: Friday, July 31, 2020 12:44 PM
To: dev@ctakes.apache.org
Subject: Re: Problem trying to load a custom dictionary [EXTERNAL] [EXTERNAL]
* External Email - Caution *
How would I go about getting edit access to the Wiki (is that the preferred
path)?
On Fri, Jul 31, 2020 at 11:08 AM Peter Abramowitsch <pa...@gmail.com>
wrote:
> Thank you Jeff and Gandhi for offers of help. I'm not trying to renege
> on my offer, but as I have only done this once, I'm wondering if your
> combined experience makes it much more appropriate for one of you to do
> this documentation and I do a review rather than the other way round. --
> Especially if Jeff has actually written up the basis for the enhancement.
>
> However I'm willing to give it a shot if neither of you wants to take the
> reins
>
> Peter
>
>
>
> On Fri, Jul 31, 2020 at 7:39 AM Jeffrey Miller <je...@gmail.com> wrote:
>
> > I can help with this as well. I have some documentation that I have
> written
> > for myself that would probably be useful. I've tried to keep a list of
> > useful forum posts that contain information that could probably be more
> > prominently displayed on the wiki.
> >
> > On Fri, Jul 31, 2020 at 10:34 AM gandhi rajan <ga...@gmail.com>
> > wrote:
> >
> > > Hi Peter,
> > >
> > > We can work together on this if you are interested.
> > >
> > > On Fri, Jul 31, 2020 at 7:44 PM Peter Abramowitsch <
> > > pabramowitsch@gmail.com>
> > > wrote:
> > >
> > > > I could do it while the experience is fresh, although I only know the
> > > happy
> > > > path and not the deeper details in this area of the suite
> > > > If you want me to, let me know how to get editing privileges on the
> > Wiki.
> > > >
> > > > Peter
> > > >
> > > > On Fri, Jul 31, 2020 at 4:28 AM Finan, Sean <
> > > > Sean.Finan@childrens.harvard.edu> wrote:
> > > >
> > > > > Obviously Jeff is correct in all of his answers. Thank you Jeff!
> > > > >
> > > > > One comment: DictionaryDescriptor is a deprecated parameter name
> that
> > > is
> > > > > picked up by the piper creator when it inspects the code.
> However, I
> > > am
> > > > > not sure why the deprecated parameter name isn't working ...
> > > > >
> > > > > The wiki needs additional and more thorough information. If
> anybody
> > > can
> > > > > volunteer to work on it I (and future users) would really
> appreciate
> > > it!
> > > > >
> > > > > Thanks,
> > > > > Sean
> > > > >
> > > > >
> > > > > ________________________________________
> > > > > From: Peter Abramowitsch <pa...@gmail.com>
> > > > > Sent: Thursday, July 30, 2020 9:02 PM
> > > > > To: dev@ctakes.apache.org
> > > > > Subject: Re: Problem trying to load a custom dictionary [EXTERNAL]
> > > > >
> > > > > * External Email - Caution *
> > > > >
> > > > >
> > > > > Thanks Jeff
> > > > >
> > > > > That worked!
> > > > >
> > > > > Seems like something that should get fixed in the PiperCreator and
> in
> > > the
> > > > > documentation.
> > > > >
> > > > > With a life of assuming that every mistake is my own error, the
> last
> > > > thing
> > > > > I would have expected was
> > > > > a generator of incorrect params.
> > > > >
> > > > > Peter
> > > > >
> > > > > On Thu, Jul 30, 2020 at 4:59 PM Jeffrey Miller <je...@gmail.com>
> > > > wrote:
> > > > >
> > > > > > Peter,
> > > > > >
> > > > > > 1) This is loaded by cTAKES, you don't need to manually create
> the
> > > > > > database.
> > > > > > 2) I can't see the highlights here, but I think that file should
> be
> > > > okay
> > > > > as
> > > > > > created by the GUI.
> > > > > > 3) I think the parameter name to configure your dictionary
> location
> > > is
> > > > > > LookupXml instead of DictionaryDescriptor
> > > > > >
> > > > > > Jeff
> > > > > >
> > > > > > On Thu, Jul 30, 2020 at 6:49 PM Peter Abramowitsch <
> > > > > > pabramowitsch@gmail.com>
> > > > > > wrote:
> > > > > >
> > > > > > > A couple of questions about installing a custom dictionary in
> > > lookup
> > > > > > fast.
> > > > > > > I hope I'm not too far off the track.
> > > > > > >
> > > > > > > I've used the dictionary creator with a UMLS install to create
> > the
> > > > > > > dictionary script, prop file, and xml file in my ctakes
> resources
> > > > tree
> > > > > > >
> > > > > > > 1. Do I have to manually run this script to execute all its
> SQL
> > > > > > statements
> > > > > > > into hsqldb or is this executed by the cTakes program when it
> > > > > encounters
> > > > > > > the XML descriptor?
> > > > > > > If manual running is needed, are there instructions on how and
> > > where
> > > > to
> > > > > > > load the script?
> > > > > > >
> > > > > > > 2. The xml file generated by the dictionary creator contains
> > lines
> > > > > with
> > > > > > > duplicate names-- see yellow highlight. Is this correct?
> > > > > > > <name>my_dict_v1Terms</name>
> > > > > > > <property key="jdbcUrl"
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> value="jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/lookup/fast/
> > > > > > > my_dict_v1/my_dict_v1"/>
> > > > > > >
> > > > > > > 3. Try as I might I cannot get ctakes to load anything other
> > than
> > > > > > > sno_rx. I'm using a piper file with an entry looking like
> > > > > > > ....
> > > > > > > add org.apache.ctakes.dictionary.lookup2.ae
> > > > > > .OverlapJCasTermAnnotator
> > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> DictionaryDescriptor=org/apache/ctakes/dictionary/lookup/fast/my_dict_v1.xml
> > > > > > > ....
> > > > > > > Not sure if they're looked at any more but I also changed these
> > xml
> > > > > files
> > > > > > > under desc as well.
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsOverlapLookupAnnotator.xml
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml
> > > > > > >
> > > > > > > But I can't even get it to fail to try to load mine.
> > > > > > > my log looks like this
> > > > > > >
> > > > > > > 30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator -
> > > > Exclusion
> > > > > > > tagset loaded: CC CD DT EX IN LS MD PDT POS PP PP$ PRP PRP$ RP
> TO
> > > VB
> > > > > VBD
> > > > > > > VBG VBN VBP VBZ WDT WP WPS WRB
> > > > > > > 30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator -
> > Using
> > > > > > minimum
> > > > > > > term text span: 3
> > > > > > > 30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator -
> > Using
> > > > > > > Dictionary Descriptor:
> org/apache/ctakes/dictionary/lookup/fast/
> > > > > > > sno_rx_16ab.xml
> > > > > > >
> > > > > > >
> > > > > > > Any suggestions?
> > > > > > >
> > > > > > > Regards, Peter
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> > >
> > > --
> > > Regards,
> > > Gandhi
> > >
> > > "The best way to find urself is to lose urself in the service of others
> > > !!!"
> > >
> >
>
Re: Problem trying to load a custom dictionary [EXTERNAL]
Posted by Jeffrey Miller <je...@gmail.com>.
How would I go about getting edit access to the Wiki (is that the preferred
path)?
On Fri, Jul 31, 2020 at 11:08 AM Peter Abramowitsch <pa...@gmail.com>
wrote:
> Thank you Jeff and Gandhi for offers of help. I'm not trying to renege
> on my offer, but as I have only done this once, I'm wondering if your
> combined experience makes it much more appropriate for one of you to do
> this documentation and I do a review rather than the other way round. --
> Especially if Jeff has actually written up the basis for the enhancement.
>
> However I'm willing to give it a shot if neither of you wants to take the
> reins
>
> Peter
>
>
>
> On Fri, Jul 31, 2020 at 7:39 AM Jeffrey Miller <je...@gmail.com> wrote:
>
> > I can help with this as well. I have some documentation that I have
> written
> > for myself that would probably be useful. I've tried to keep a list of
> > useful forum posts that contain information that could probably be more
> > prominently displayed on the wiki.
> >
> > On Fri, Jul 31, 2020 at 10:34 AM gandhi rajan <ga...@gmail.com>
> > wrote:
> >
> > > Hi Peter,
> > >
> > > We can work together on this if you are interested.
> > >
> > > On Fri, Jul 31, 2020 at 7:44 PM Peter Abramowitsch <
> > > pabramowitsch@gmail.com>
> > > wrote:
> > >
> > > > I could do it while the experience is fresh, although I only know the
> > > happy
> > > > path and not the deeper details in this area of the suite
> > > > If you want me to, let me know how to get editing privileges on the
> > Wiki.
> > > >
> > > > Peter
> > > >
> > > > On Fri, Jul 31, 2020 at 4:28 AM Finan, Sean <
> > > > Sean.Finan@childrens.harvard.edu> wrote:
> > > >
> > > > > Obviously Jeff is correct in all of his answers. Thank you Jeff!
> > > > >
> > > > > One comment: DictionaryDescriptor is a deprecated parameter name
> that
> > > is
> > > > > picked up by the piper creator when it inspects the code.
> However, I
> > > am
> > > > > not sure why the deprecated parameter name isn't working ...
> > > > >
> > > > > The wiki needs additional and more thorough information. If
> anybody
> > > can
> > > > > volunteer to work on it I (and future users) would really
> appreciate
> > > it!
> > > > >
> > > > > Thanks,
> > > > > Sean
> > > > >
> > > > >
> > > > > ________________________________________
> > > > > From: Peter Abramowitsch <pa...@gmail.com>
> > > > > Sent: Thursday, July 30, 2020 9:02 PM
> > > > > To: dev@ctakes.apache.org
> > > > > Subject: Re: Problem trying to load a custom dictionary [EXTERNAL]
> > > > >
> > > > > * External Email - Caution *
> > > > >
> > > > >
> > > > > Thanks Jeff
> > > > >
> > > > > That worked!
> > > > >
> > > > > Seems like something that should get fixed in the PiperCreator and
> in
> > > the
> > > > > documentation.
> > > > >
> > > > > With a life of assuming that every mistake is my own error, the
> last
> > > > thing
> > > > > I would have expected was
> > > > > a generator of incorrect params.
> > > > >
> > > > > Peter
> > > > >
> > > > > On Thu, Jul 30, 2020 at 4:59 PM Jeffrey Miller <je...@gmail.com>
> > > > wrote:
> > > > >
> > > > > > Peter,
> > > > > >
> > > > > > 1) This is loaded by cTAKES, you don't need to manually create
> the
> > > > > > database.
> > > > > > 2) I can't see the highlights here, but I think that file should
> be
> > > > okay
> > > > > as
> > > > > > created by the GUI.
> > > > > > 3) I think the parameter name to configure your dictionary
> location
> > > is
> > > > > > LookupXml instead of DictionaryDescriptor
> > > > > >
> > > > > > Jeff
> > > > > >
> > > > > > On Thu, Jul 30, 2020 at 6:49 PM Peter Abramowitsch <
> > > > > > pabramowitsch@gmail.com>
> > > > > > wrote:
> > > > > >
> > > > > > > A couple of questions about installing a custom dictionary in
> > > lookup
> > > > > > fast.
> > > > > > > I hope I'm not too far off the track.
> > > > > > >
> > > > > > > I've used the dictionary creator with a UMLS install to create
> > the
> > > > > > > dictionary script, prop file, and xml file in my ctakes
> resources
> > > > tree
> > > > > > >
> > > > > > > 1. Do I have to manually run this script to execute all its
> SQL
> > > > > > statements
> > > > > > > into hsqldb or is this executed by the cTakes program when it
> > > > > encounters
> > > > > > > the XML descriptor?
> > > > > > > If manual running is needed, are there instructions on how and
> > > where
> > > > to
> > > > > > > load the script?
> > > > > > >
> > > > > > > 2. The xml file generated by the dictionary creator contains
> > lines
> > > > > with
> > > > > > > duplicate names-- see yellow highlight. Is this correct?
> > > > > > > <name>my_dict_v1Terms</name>
> > > > > > > <property key="jdbcUrl"
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> value="jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/lookup/fast/
> > > > > > > my_dict_v1/my_dict_v1"/>
> > > > > > >
> > > > > > > 3. Try as I might I cannot get ctakes to load anything other
> > than
> > > > > > > sno_rx. I'm using a piper file with an entry looking like
> > > > > > > ....
> > > > > > > add org.apache.ctakes.dictionary.lookup2.ae
> > > > > > .OverlapJCasTermAnnotator
> > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> DictionaryDescriptor=org/apache/ctakes/dictionary/lookup/fast/my_dict_v1.xml
> > > > > > > ....
> > > > > > > Not sure if they're looked at any more but I also changed these
> > xml
> > > > > files
> > > > > > > under desc as well.
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsOverlapLookupAnnotator.xml
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml
> > > > > > >
> > > > > > > But I can't even get it to fail to try to load mine.
> > > > > > > my log looks like this
> > > > > > >
> > > > > > > 30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator -
> > > > Exclusion
> > > > > > > tagset loaded: CC CD DT EX IN LS MD PDT POS PP PP$ PRP PRP$ RP
> TO
> > > VB
> > > > > VBD
> > > > > > > VBG VBN VBP VBZ WDT WP WPS WRB
> > > > > > > 30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator -
> > Using
> > > > > > minimum
> > > > > > > term text span: 3
> > > > > > > 30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator -
> > Using
> > > > > > > Dictionary Descriptor:
> org/apache/ctakes/dictionary/lookup/fast/
> > > > > > > sno_rx_16ab.xml
> > > > > > >
> > > > > > >
> > > > > > > Any suggestions?
> > > > > > >
> > > > > > > Regards, Peter
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> > >
> > > --
> > > Regards,
> > > Gandhi
> > >
> > > "The best way to find urself is to lose urself in the service of others
> > > !!!"
> > >
> >
>
Re: Problem trying to load a custom dictionary [EXTERNAL]
Posted by Peter Abramowitsch <pa...@gmail.com>.
Thank you Jeff and Gandhi for offers of help. I'm not trying to renege
on my offer, but as I have only done this once, I'm wondering if your
combined experience makes it much more appropriate for one of you to do
this documentation and I do a review rather than the other way round. --
Especially if Jeff has actually written up the basis for the enhancement.
However I'm willing to give it a shot if neither of you wants to take the
reins
Peter
On Fri, Jul 31, 2020 at 7:39 AM Jeffrey Miller <je...@gmail.com> wrote:
> I can help with this as well. I have some documentation that I have written
> for myself that would probably be useful. I've tried to keep a list of
> useful forum posts that contain information that could probably be more
> prominently displayed on the wiki.
>
> On Fri, Jul 31, 2020 at 10:34 AM gandhi rajan <ga...@gmail.com>
> wrote:
>
> > Hi Peter,
> >
> > We can work together on this if you are interested.
> >
> > On Fri, Jul 31, 2020 at 7:44 PM Peter Abramowitsch <
> > pabramowitsch@gmail.com>
> > wrote:
> >
> > > I could do it while the experience is fresh, although I only know the
> > happy
> > > path and not the deeper details in this area of the suite
> > > If you want me to, let me know how to get editing privileges on the
> Wiki.
> > >
> > > Peter
> > >
> > > On Fri, Jul 31, 2020 at 4:28 AM Finan, Sean <
> > > Sean.Finan@childrens.harvard.edu> wrote:
> > >
> > > > Obviously Jeff is correct in all of his answers. Thank you Jeff!
> > > >
> > > > One comment: DictionaryDescriptor is a deprecated parameter name that
> > is
> > > > picked up by the piper creator when it inspects the code. However, I
> > am
> > > > not sure why the deprecated parameter name isn't working ...
> > > >
> > > > The wiki needs additional and more thorough information. If anybody
> > can
> > > > volunteer to work on it I (and future users) would really appreciate
> > it!
> > > >
> > > > Thanks,
> > > > Sean
> > > >
> > > >
> > > > ________________________________________
> > > > From: Peter Abramowitsch <pa...@gmail.com>
> > > > Sent: Thursday, July 30, 2020 9:02 PM
> > > > To: dev@ctakes.apache.org
> > > > Subject: Re: Problem trying to load a custom dictionary [EXTERNAL]
> > > >
> > > > * External Email - Caution *
> > > >
> > > >
> > > > Thanks Jeff
> > > >
> > > > That worked!
> > > >
> > > > Seems like something that should get fixed in the PiperCreator and in
> > the
> > > > documentation.
> > > >
> > > > With a life of assuming that every mistake is my own error, the last
> > > thing
> > > > I would have expected was
> > > > a generator of incorrect params.
> > > >
> > > > Peter
> > > >
> > > > On Thu, Jul 30, 2020 at 4:59 PM Jeffrey Miller <je...@gmail.com>
> > > wrote:
> > > >
> > > > > Peter,
> > > > >
> > > > > 1) This is loaded by cTAKES, you don't need to manually create the
> > > > > database.
> > > > > 2) I can't see the highlights here, but I think that file should be
> > > okay
> > > > as
> > > > > created by the GUI.
> > > > > 3) I think the parameter name to configure your dictionary location
> > is
> > > > > LookupXml instead of DictionaryDescriptor
> > > > >
> > > > > Jeff
> > > > >
> > > > > On Thu, Jul 30, 2020 at 6:49 PM Peter Abramowitsch <
> > > > > pabramowitsch@gmail.com>
> > > > > wrote:
> > > > >
> > > > > > A couple of questions about installing a custom dictionary in
> > lookup
> > > > > fast.
> > > > > > I hope I'm not too far off the track.
> > > > > >
> > > > > > I've used the dictionary creator with a UMLS install to create
> the
> > > > > > dictionary script, prop file, and xml file in my ctakes resources
> > > tree
> > > > > >
> > > > > > 1. Do I have to manually run this script to execute all its SQL
> > > > > statements
> > > > > > into hsqldb or is this executed by the cTakes program when it
> > > > encounters
> > > > > > the XML descriptor?
> > > > > > If manual running is needed, are there instructions on how and
> > where
> > > to
> > > > > > load the script?
> > > > > >
> > > > > > 2. The xml file generated by the dictionary creator contains
> lines
> > > > with
> > > > > > duplicate names-- see yellow highlight. Is this correct?
> > > > > > <name>my_dict_v1Terms</name>
> > > > > > <property key="jdbcUrl"
> > > > > >
> > > > >
> > > >
> > >
> >
> value="jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/lookup/fast/
> > > > > > my_dict_v1/my_dict_v1"/>
> > > > > >
> > > > > > 3. Try as I might I cannot get ctakes to load anything other
> than
> > > > > > sno_rx. I'm using a piper file with an entry looking like
> > > > > > ....
> > > > > > add org.apache.ctakes.dictionary.lookup2.ae
> > > > > .OverlapJCasTermAnnotator
> > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> DictionaryDescriptor=org/apache/ctakes/dictionary/lookup/fast/my_dict_v1.xml
> > > > > > ....
> > > > > > Not sure if they're looked at any more but I also changed these
> xml
> > > > files
> > > > > > under desc as well.
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsOverlapLookupAnnotator.xml
> > > > > >
> > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml
> > > > > >
> > > > > > But I can't even get it to fail to try to load mine.
> > > > > > my log looks like this
> > > > > >
> > > > > > 30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator -
> > > Exclusion
> > > > > > tagset loaded: CC CD DT EX IN LS MD PDT POS PP PP$ PRP PRP$ RP TO
> > VB
> > > > VBD
> > > > > > VBG VBN VBP VBZ WDT WP WPS WRB
> > > > > > 30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator -
> Using
> > > > > minimum
> > > > > > term text span: 3
> > > > > > 30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator -
> Using
> > > > > > Dictionary Descriptor: org/apache/ctakes/dictionary/lookup/fast/
> > > > > > sno_rx_16ab.xml
> > > > > >
> > > > > >
> > > > > > Any suggestions?
> > > > > >
> > > > > > Regards, Peter
> > > > > >
> > > > >
> > > >
> > >
> >
> >
> > --
> > Regards,
> > Gandhi
> >
> > "The best way to find urself is to lose urself in the service of others
> > !!!"
> >
>
Re: Problem trying to load a custom dictionary [EXTERNAL]
Posted by Jeffrey Miller <je...@gmail.com>.
I can help with this as well. I have some documentation that I have written
for myself that would probably be useful. I've tried to keep a list of
useful forum posts that contain information that could probably be more
prominently displayed on the wiki.
On Fri, Jul 31, 2020 at 10:34 AM gandhi rajan <ga...@gmail.com>
wrote:
> Hi Peter,
>
> We can work together on this if you are interested.
>
> On Fri, Jul 31, 2020 at 7:44 PM Peter Abramowitsch <
> pabramowitsch@gmail.com>
> wrote:
>
> > I could do it while the experience is fresh, although I only know the
> happy
> > path and not the deeper details in this area of the suite
> > If you want me to, let me know how to get editing privileges on the Wiki.
> >
> > Peter
> >
> > On Fri, Jul 31, 2020 at 4:28 AM Finan, Sean <
> > Sean.Finan@childrens.harvard.edu> wrote:
> >
> > > Obviously Jeff is correct in all of his answers. Thank you Jeff!
> > >
> > > One comment: DictionaryDescriptor is a deprecated parameter name that
> is
> > > picked up by the piper creator when it inspects the code. However, I
> am
> > > not sure why the deprecated parameter name isn't working ...
> > >
> > > The wiki needs additional and more thorough information. If anybody
> can
> > > volunteer to work on it I (and future users) would really appreciate
> it!
> > >
> > > Thanks,
> > > Sean
> > >
> > >
> > > ________________________________________
> > > From: Peter Abramowitsch <pa...@gmail.com>
> > > Sent: Thursday, July 30, 2020 9:02 PM
> > > To: dev@ctakes.apache.org
> > > Subject: Re: Problem trying to load a custom dictionary [EXTERNAL]
> > >
> > > * External Email - Caution *
> > >
> > >
> > > Thanks Jeff
> > >
> > > That worked!
> > >
> > > Seems like something that should get fixed in the PiperCreator and in
> the
> > > documentation.
> > >
> > > With a life of assuming that every mistake is my own error, the last
> > thing
> > > I would have expected was
> > > a generator of incorrect params.
> > >
> > > Peter
> > >
> > > On Thu, Jul 30, 2020 at 4:59 PM Jeffrey Miller <je...@gmail.com>
> > wrote:
> > >
> > > > Peter,
> > > >
> > > > 1) This is loaded by cTAKES, you don't need to manually create the
> > > > database.
> > > > 2) I can't see the highlights here, but I think that file should be
> > okay
> > > as
> > > > created by the GUI.
> > > > 3) I think the parameter name to configure your dictionary location
> is
> > > > LookupXml instead of DictionaryDescriptor
> > > >
> > > > Jeff
> > > >
> > > > On Thu, Jul 30, 2020 at 6:49 PM Peter Abramowitsch <
> > > > pabramowitsch@gmail.com>
> > > > wrote:
> > > >
> > > > > A couple of questions about installing a custom dictionary in
> lookup
> > > > fast.
> > > > > I hope I'm not too far off the track.
> > > > >
> > > > > I've used the dictionary creator with a UMLS install to create the
> > > > > dictionary script, prop file, and xml file in my ctakes resources
> > tree
> > > > >
> > > > > 1. Do I have to manually run this script to execute all its SQL
> > > > statements
> > > > > into hsqldb or is this executed by the cTakes program when it
> > > encounters
> > > > > the XML descriptor?
> > > > > If manual running is needed, are there instructions on how and
> where
> > to
> > > > > load the script?
> > > > >
> > > > > 2. The xml file generated by the dictionary creator contains lines
> > > with
> > > > > duplicate names-- see yellow highlight. Is this correct?
> > > > > <name>my_dict_v1Terms</name>
> > > > > <property key="jdbcUrl"
> > > > >
> > > >
> > >
> >
> value="jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/lookup/fast/
> > > > > my_dict_v1/my_dict_v1"/>
> > > > >
> > > > > 3. Try as I might I cannot get ctakes to load anything other than
> > > > > sno_rx. I'm using a piper file with an entry looking like
> > > > > ....
> > > > > add org.apache.ctakes.dictionary.lookup2.ae
> > > > .OverlapJCasTermAnnotator
> > > > >
> > > > >
> > > >
> > >
> >
> DictionaryDescriptor=org/apache/ctakes/dictionary/lookup/fast/my_dict_v1.xml
> > > > > ....
> > > > > Not sure if they're looked at any more but I also changed these xml
> > > files
> > > > > under desc as well.
> > > > >
> > > > >
> > > > >
> > > > >
> > > >
> > >
> >
> desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsOverlapLookupAnnotator.xml
> > > > >
> > > > >
> > > > >
> > > >
> > >
> >
> desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml
> > > > >
> > > > > But I can't even get it to fail to try to load mine.
> > > > > my log looks like this
> > > > >
> > > > > 30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator -
> > Exclusion
> > > > > tagset loaded: CC CD DT EX IN LS MD PDT POS PP PP$ PRP PRP$ RP TO
> VB
> > > VBD
> > > > > VBG VBN VBP VBZ WDT WP WPS WRB
> > > > > 30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator - Using
> > > > minimum
> > > > > term text span: 3
> > > > > 30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator - Using
> > > > > Dictionary Descriptor: org/apache/ctakes/dictionary/lookup/fast/
> > > > > sno_rx_16ab.xml
> > > > >
> > > > >
> > > > > Any suggestions?
> > > > >
> > > > > Regards, Peter
> > > > >
> > > >
> > >
> >
>
>
> --
> Regards,
> Gandhi
>
> "The best way to find urself is to lose urself in the service of others
> !!!"
>
Re: Problem trying to load a custom dictionary [EXTERNAL]
Posted by gandhi rajan <ga...@gmail.com>.
Hi Peter,
We can work together on this if you are interested.
On Fri, Jul 31, 2020 at 7:44 PM Peter Abramowitsch <pa...@gmail.com>
wrote:
> I could do it while the experience is fresh, although I only know the happy
> path and not the deeper details in this area of the suite
> If you want me to, let me know how to get editing privileges on the Wiki.
>
> Peter
>
> On Fri, Jul 31, 2020 at 4:28 AM Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
>
> > Obviously Jeff is correct in all of his answers. Thank you Jeff!
> >
> > One comment: DictionaryDescriptor is a deprecated parameter name that is
> > picked up by the piper creator when it inspects the code. However, I am
> > not sure why the deprecated parameter name isn't working ...
> >
> > The wiki needs additional and more thorough information. If anybody can
> > volunteer to work on it I (and future users) would really appreciate it!
> >
> > Thanks,
> > Sean
> >
> >
> > ________________________________________
> > From: Peter Abramowitsch <pa...@gmail.com>
> > Sent: Thursday, July 30, 2020 9:02 PM
> > To: dev@ctakes.apache.org
> > Subject: Re: Problem trying to load a custom dictionary [EXTERNAL]
> >
> > * External Email - Caution *
> >
> >
> > Thanks Jeff
> >
> > That worked!
> >
> > Seems like something that should get fixed in the PiperCreator and in the
> > documentation.
> >
> > With a life of assuming that every mistake is my own error, the last
> thing
> > I would have expected was
> > a generator of incorrect params.
> >
> > Peter
> >
> > On Thu, Jul 30, 2020 at 4:59 PM Jeffrey Miller <je...@gmail.com>
> wrote:
> >
> > > Peter,
> > >
> > > 1) This is loaded by cTAKES, you don't need to manually create the
> > > database.
> > > 2) I can't see the highlights here, but I think that file should be
> okay
> > as
> > > created by the GUI.
> > > 3) I think the parameter name to configure your dictionary location is
> > > LookupXml instead of DictionaryDescriptor
> > >
> > > Jeff
> > >
> > > On Thu, Jul 30, 2020 at 6:49 PM Peter Abramowitsch <
> > > pabramowitsch@gmail.com>
> > > wrote:
> > >
> > > > A couple of questions about installing a custom dictionary in lookup
> > > fast.
> > > > I hope I'm not too far off the track.
> > > >
> > > > I've used the dictionary creator with a UMLS install to create the
> > > > dictionary script, prop file, and xml file in my ctakes resources
> tree
> > > >
> > > > 1. Do I have to manually run this script to execute all its SQL
> > > statements
> > > > into hsqldb or is this executed by the cTakes program when it
> > encounters
> > > > the XML descriptor?
> > > > If manual running is needed, are there instructions on how and where
> to
> > > > load the script?
> > > >
> > > > 2. The xml file generated by the dictionary creator contains lines
> > with
> > > > duplicate names-- see yellow highlight. Is this correct?
> > > > <name>my_dict_v1Terms</name>
> > > > <property key="jdbcUrl"
> > > >
> > >
> >
> value="jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/lookup/fast/
> > > > my_dict_v1/my_dict_v1"/>
> > > >
> > > > 3. Try as I might I cannot get ctakes to load anything other than
> > > > sno_rx. I'm using a piper file with an entry looking like
> > > > ....
> > > > add org.apache.ctakes.dictionary.lookup2.ae
> > > .OverlapJCasTermAnnotator
> > > >
> > > >
> > >
> >
> DictionaryDescriptor=org/apache/ctakes/dictionary/lookup/fast/my_dict_v1.xml
> > > > ....
> > > > Not sure if they're looked at any more but I also changed these xml
> > files
> > > > under desc as well.
> > > >
> > > >
> > > >
> > > >
> > >
> >
> desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsOverlapLookupAnnotator.xml
> > > >
> > > >
> > > >
> > >
> >
> desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml
> > > >
> > > > But I can't even get it to fail to try to load mine.
> > > > my log looks like this
> > > >
> > > > 30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator -
> Exclusion
> > > > tagset loaded: CC CD DT EX IN LS MD PDT POS PP PP$ PRP PRP$ RP TO VB
> > VBD
> > > > VBG VBN VBP VBZ WDT WP WPS WRB
> > > > 30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator - Using
> > > minimum
> > > > term text span: 3
> > > > 30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator - Using
> > > > Dictionary Descriptor: org/apache/ctakes/dictionary/lookup/fast/
> > > > sno_rx_16ab.xml
> > > >
> > > >
> > > > Any suggestions?
> > > >
> > > > Regards, Peter
> > > >
> > >
> >
>
--
Regards,
Gandhi
"The best way to find urself is to lose urself in the service of others !!!"
Re: Problem trying to load a custom dictionary [EXTERNAL]
Posted by Peter Abramowitsch <pa...@gmail.com>.
I could do it while the experience is fresh, although I only know the happy
path and not the deeper details in this area of the suite
If you want me to, let me know how to get editing privileges on the Wiki.
Peter
On Fri, Jul 31, 2020 at 4:28 AM Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:
> Obviously Jeff is correct in all of his answers. Thank you Jeff!
>
> One comment: DictionaryDescriptor is a deprecated parameter name that is
> picked up by the piper creator when it inspects the code. However, I am
> not sure why the deprecated parameter name isn't working ...
>
> The wiki needs additional and more thorough information. If anybody can
> volunteer to work on it I (and future users) would really appreciate it!
>
> Thanks,
> Sean
>
>
> ________________________________________
> From: Peter Abramowitsch <pa...@gmail.com>
> Sent: Thursday, July 30, 2020 9:02 PM
> To: dev@ctakes.apache.org
> Subject: Re: Problem trying to load a custom dictionary [EXTERNAL]
>
> * External Email - Caution *
>
>
> Thanks Jeff
>
> That worked!
>
> Seems like something that should get fixed in the PiperCreator and in the
> documentation.
>
> With a life of assuming that every mistake is my own error, the last thing
> I would have expected was
> a generator of incorrect params.
>
> Peter
>
> On Thu, Jul 30, 2020 at 4:59 PM Jeffrey Miller <je...@gmail.com> wrote:
>
> > Peter,
> >
> > 1) This is loaded by cTAKES, you don't need to manually create the
> > database.
> > 2) I can't see the highlights here, but I think that file should be okay
> as
> > created by the GUI.
> > 3) I think the parameter name to configure your dictionary location is
> > LookupXml instead of DictionaryDescriptor
> >
> > Jeff
> >
> > On Thu, Jul 30, 2020 at 6:49 PM Peter Abramowitsch <
> > pabramowitsch@gmail.com>
> > wrote:
> >
> > > A couple of questions about installing a custom dictionary in lookup
> > fast.
> > > I hope I'm not too far off the track.
> > >
> > > I've used the dictionary creator with a UMLS install to create the
> > > dictionary script, prop file, and xml file in my ctakes resources tree
> > >
> > > 1. Do I have to manually run this script to execute all its SQL
> > statements
> > > into hsqldb or is this executed by the cTakes program when it
> encounters
> > > the XML descriptor?
> > > If manual running is needed, are there instructions on how and where to
> > > load the script?
> > >
> > > 2. The xml file generated by the dictionary creator contains lines
> with
> > > duplicate names-- see yellow highlight. Is this correct?
> > > <name>my_dict_v1Terms</name>
> > > <property key="jdbcUrl"
> > >
> >
> value="jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/lookup/fast/
> > > my_dict_v1/my_dict_v1"/>
> > >
> > > 3. Try as I might I cannot get ctakes to load anything other than
> > > sno_rx. I'm using a piper file with an entry looking like
> > > ....
> > > add org.apache.ctakes.dictionary.lookup2.ae
> > .OverlapJCasTermAnnotator
> > >
> > >
> >
> DictionaryDescriptor=org/apache/ctakes/dictionary/lookup/fast/my_dict_v1.xml
> > > ....
> > > Not sure if they're looked at any more but I also changed these xml
> files
> > > under desc as well.
> > >
> > >
> > >
> > >
> >
> desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsOverlapLookupAnnotator.xml
> > >
> > >
> > >
> >
> desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml
> > >
> > > But I can't even get it to fail to try to load mine.
> > > my log looks like this
> > >
> > > 30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator - Exclusion
> > > tagset loaded: CC CD DT EX IN LS MD PDT POS PP PP$ PRP PRP$ RP TO VB
> VBD
> > > VBG VBN VBP VBZ WDT WP WPS WRB
> > > 30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator - Using
> > minimum
> > > term text span: 3
> > > 30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator - Using
> > > Dictionary Descriptor: org/apache/ctakes/dictionary/lookup/fast/
> > > sno_rx_16ab.xml
> > >
> > >
> > > Any suggestions?
> > >
> > > Regards, Peter
> > >
> >
>
Re: Problem trying to load a custom dictionary [EXTERNAL]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Obviously Jeff is correct in all of his answers. Thank you Jeff!
One comment: DictionaryDescriptor is a deprecated parameter name that is picked up by the piper creator when it inspects the code. However, I am not sure why the deprecated parameter name isn't working ...
The wiki needs additional and more thorough information. If anybody can volunteer to work on it I (and future users) would really appreciate it!
Thanks,
Sean
________________________________________
From: Peter Abramowitsch <pa...@gmail.com>
Sent: Thursday, July 30, 2020 9:02 PM
To: dev@ctakes.apache.org
Subject: Re: Problem trying to load a custom dictionary [EXTERNAL]
* External Email - Caution *
Thanks Jeff
That worked!
Seems like something that should get fixed in the PiperCreator and in the
documentation.
With a life of assuming that every mistake is my own error, the last thing
I would have expected was
a generator of incorrect params.
Peter
On Thu, Jul 30, 2020 at 4:59 PM Jeffrey Miller <je...@gmail.com> wrote:
> Peter,
>
> 1) This is loaded by cTAKES, you don't need to manually create the
> database.
> 2) I can't see the highlights here, but I think that file should be okay as
> created by the GUI.
> 3) I think the parameter name to configure your dictionary location is
> LookupXml instead of DictionaryDescriptor
>
> Jeff
>
> On Thu, Jul 30, 2020 at 6:49 PM Peter Abramowitsch <
> pabramowitsch@gmail.com>
> wrote:
>
> > A couple of questions about installing a custom dictionary in lookup
> fast.
> > I hope I'm not too far off the track.
> >
> > I've used the dictionary creator with a UMLS install to create the
> > dictionary script, prop file, and xml file in my ctakes resources tree
> >
> > 1. Do I have to manually run this script to execute all its SQL
> statements
> > into hsqldb or is this executed by the cTakes program when it encounters
> > the XML descriptor?
> > If manual running is needed, are there instructions on how and where to
> > load the script?
> >
> > 2. The xml file generated by the dictionary creator contains lines with
> > duplicate names-- see yellow highlight. Is this correct?
> > <name>my_dict_v1Terms</name>
> > <property key="jdbcUrl"
> >
> value="jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/lookup/fast/
> > my_dict_v1/my_dict_v1"/>
> >
> > 3. Try as I might I cannot get ctakes to load anything other than
> > sno_rx. I'm using a piper file with an entry looking like
> > ....
> > add org.apache.ctakes.dictionary.lookup2.ae
> .OverlapJCasTermAnnotator
> >
> >
> DictionaryDescriptor=org/apache/ctakes/dictionary/lookup/fast/my_dict_v1.xml
> > ....
> > Not sure if they're looked at any more but I also changed these xml files
> > under desc as well.
> >
> >
> >
> >
> desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsOverlapLookupAnnotator.xml
> >
> >
> >
> desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml
> >
> > But I can't even get it to fail to try to load mine.
> > my log looks like this
> >
> > 30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator - Exclusion
> > tagset loaded: CC CD DT EX IN LS MD PDT POS PP PP$ PRP PRP$ RP TO VB VBD
> > VBG VBN VBP VBZ WDT WP WPS WRB
> > 30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator - Using
> minimum
> > term text span: 3
> > 30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator - Using
> > Dictionary Descriptor: org/apache/ctakes/dictionary/lookup/fast/
> > sno_rx_16ab.xml
> >
> >
> > Any suggestions?
> >
> > Regards, Peter
> >
>
Re: Problem trying to load a custom dictionary
Posted by Peter Abramowitsch <pa...@gmail.com>.
Thanks Jeff
That worked!
Seems like something that should get fixed in the PiperCreator and in the
documentation.
With a life of assuming that every mistake is my own error, the last thing
I would have expected was
a generator of incorrect params.
Peter
On Thu, Jul 30, 2020 at 4:59 PM Jeffrey Miller <je...@gmail.com> wrote:
> Peter,
>
> 1) This is loaded by cTAKES, you don't need to manually create the
> database.
> 2) I can't see the highlights here, but I think that file should be okay as
> created by the GUI.
> 3) I think the parameter name to configure your dictionary location is
> LookupXml instead of DictionaryDescriptor
>
> Jeff
>
> On Thu, Jul 30, 2020 at 6:49 PM Peter Abramowitsch <
> pabramowitsch@gmail.com>
> wrote:
>
> > A couple of questions about installing a custom dictionary in lookup
> fast.
> > I hope I'm not too far off the track.
> >
> > I've used the dictionary creator with a UMLS install to create the
> > dictionary script, prop file, and xml file in my ctakes resources tree
> >
> > 1. Do I have to manually run this script to execute all its SQL
> statements
> > into hsqldb or is this executed by the cTakes program when it encounters
> > the XML descriptor?
> > If manual running is needed, are there instructions on how and where to
> > load the script?
> >
> > 2. The xml file generated by the dictionary creator contains lines with
> > duplicate names-- see yellow highlight. Is this correct?
> > <name>my_dict_v1Terms</name>
> > <property key="jdbcUrl"
> >
> value="jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/lookup/fast/
> > my_dict_v1/my_dict_v1"/>
> >
> > 3. Try as I might I cannot get ctakes to load anything other than
> > sno_rx. I'm using a piper file with an entry looking like
> > ....
> > add org.apache.ctakes.dictionary.lookup2.ae
> .OverlapJCasTermAnnotator
> >
> >
> DictionaryDescriptor=org/apache/ctakes/dictionary/lookup/fast/my_dict_v1.xml
> > ....
> > Not sure if they're looked at any more but I also changed these xml files
> > under desc as well.
> >
> >
> >
> >
> desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsOverlapLookupAnnotator.xml
> >
> >
> >
> desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml
> >
> > But I can't even get it to fail to try to load mine.
> > my log looks like this
> >
> > 30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator - Exclusion
> > tagset loaded: CC CD DT EX IN LS MD PDT POS PP PP$ PRP PRP$ RP TO VB VBD
> > VBG VBN VBP VBZ WDT WP WPS WRB
> > 30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator - Using
> minimum
> > term text span: 3
> > 30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator - Using
> > Dictionary Descriptor: org/apache/ctakes/dictionary/lookup/fast/
> > sno_rx_16ab.xml
> >
> >
> > Any suggestions?
> >
> > Regards, Peter
> >
>
Re: Problem trying to load a custom dictionary
Posted by Jeffrey Miller <je...@gmail.com>.
Peter,
1) This is loaded by cTAKES, you don't need to manually create the database.
2) I can't see the highlights here, but I think that file should be okay as
created by the GUI.
3) I think the parameter name to configure your dictionary location is
LookupXml instead of DictionaryDescriptor
Jeff
On Thu, Jul 30, 2020 at 6:49 PM Peter Abramowitsch <pa...@gmail.com>
wrote:
> A couple of questions about installing a custom dictionary in lookup fast.
> I hope I'm not too far off the track.
>
> I've used the dictionary creator with a UMLS install to create the
> dictionary script, prop file, and xml file in my ctakes resources tree
>
> 1. Do I have to manually run this script to execute all its SQL statements
> into hsqldb or is this executed by the cTakes program when it encounters
> the XML descriptor?
> If manual running is needed, are there instructions on how and where to
> load the script?
>
> 2. The xml file generated by the dictionary creator contains lines with
> duplicate names-- see yellow highlight. Is this correct?
> <name>my_dict_v1Terms</name>
> <property key="jdbcUrl"
> value="jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/lookup/fast/
> my_dict_v1/my_dict_v1"/>
>
> 3. Try as I might I cannot get ctakes to load anything other than
> sno_rx. I'm using a piper file with an entry looking like
> ....
> add org.apache.ctakes.dictionary.lookup2.ae.OverlapJCasTermAnnotator
>
> DictionaryDescriptor=org/apache/ctakes/dictionary/lookup/fast/my_dict_v1.xml
> ....
> Not sure if they're looked at any more but I also changed these xml files
> under desc as well.
>
>
>
> desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsOverlapLookupAnnotator.xml
>
>
> desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml
>
> But I can't even get it to fail to try to load mine.
> my log looks like this
>
> 30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator - Exclusion
> tagset loaded: CC CD DT EX IN LS MD PDT POS PP PP$ PRP PRP$ RP TO VB VBD
> VBG VBN VBP VBZ WDT WP WPS WRB
> 30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator - Using minimum
> term text span: 3
> 30 Jul 2020 15:43:37 INFO AbstractJCasTermAnnotator - Using
> Dictionary Descriptor: org/apache/ctakes/dictionary/lookup/fast/
> sno_rx_16ab.xml
>
>
> Any suggestions?
>
> Regards, Peter
>