RE: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
Hi Tim,
As you mentioned, the pipeline will be loaded only on the very first request to
the REST service currently. But it can be changed to load the pipelines on
server start too. Every call will not re-load the pipeline. Will incorporate
the change to load the pipelines on server start.
Regards,
Gandhi
-Original Message-
From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu]
Sent: Friday, December 15, 2017 2:28 AM
To: dev@ctakes.apache.org
Subject: Re: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
[SUSPICIOUS] [SUSPICIOUS]
Another thought I just had is that it seems to load the pipeline when the first
call is made -- without knowing the REST APIs that well, is it possible to load
the pipelines when the war is deployed? With some of our larger pipelines the
first call may take quite a while. Would every call re-load the pipeline?
Tim
On Thu, 2017-12-14 at 20:16 +, Finan, Sean wrote:
> Hi Tim,
>
> Many thanks for testing the new rest service! And double that for the
> setup instructions!
>
> >
> > if this whole thing could be wrapped in a docker container that
> > would be really powerful
> - Matthew and I have had a short discussion or two on a docker that he
> is working on. It was working, but performed a lot of the spring
> updates and some workarounds that should no longer be needed. The
> next iteration should be cleaner and simpler. We have also talked
> about making the container more compact. He is busy with real work,
> but I think that this is definitely just over the horizon.
>
> >
> > One other thing I noticed in the code is that in sending back JSON
> > it looks like you're turning the JCas into xml and then parsing it
> > yourself. It should be easier just to access typesystem objects
> > directly. Sean may have some API code laying around to simplify that
> > as well.
> - I am actually looking at the rest/util/XmlParser and had the very
> same thought. It is a great start though, and as far as I know it is
> the first publicly available ctakes json writer. If anybody else out
> there already has or knows of another, please share!
>
>
> Cheers all,
> Sean
>
>
> -Original Message-
> From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu]
> Sent: Thursday, December 14, 2017 2:55 PM
> To: dev@ctakes.apache.org
> Subject: Re: cTAKES as REST service [EXTERNAL] [SUSPICIOUS]
> [SUSPICIOUS] [SUSPICIOUS]
>
> I looked at this today. Looks like a great start!
>
> I was able to get as far as deploying to tomcat, seeing the web form,
> and submitting, but didn't get correct feedback because I don't have a
> mysql dictionary set up, which the default descriptor points at. I
> didn't see any instructions for building that and didn't have time to
> figure that out.
>
> I think I mentioned in a different thread that if this whole thing
> could be wrapped in a docker container that would be really powerful,
> but if not, there are a few things that are obvious to you as
> developers but would make it easier for novices (like me) to deploy.
>
> * download tomcat bin and start with bin/startup.sh (check at
> localhost:8080)
> * run mvn install on my ctakes installation to populate jar files in
> the .m2 directory that were missing
> * run mvn package inside the ctakes-web-rest subdirectory
> * copy the .war file into the webapps directory in my tomcat
> installation.
> * While I couldn't get the dictionary to work pointing to mysql, I
> noticed that the dictionary descriptor file has a hardcoded IP address
> when maybe it should be 127.0.0.1?
>
> One other thing I noticed in the code is that in sending back JSON it
> looks like you're turning the JCas into xml and then parsing it
> yourself. It should be easier just to access typesystem objects
> directly. Sean may have some API code laying around to simplify that
> as well.
>
> To iterate over signs/symptoms, for example, you would do:
>
> for(SignSymptomMention ss : JCasUtil.select(jcas,
> SignSymptomMention.class)){
> int begin = ss.getBegin(); // begin offset
> int end = ss.getEnd(): // end offset ...
> }
>
> Using the typesystem directly may help you to speed up that code or
> make it easier to read. But maybe there is a reason to write it to xml
> that I'm not aware of.
>
> Finally, I see there are two sub-directories with similar names,
> ctakes-rest-service and ctakes-web-rest. If they are duplicates can
> you delete the old one?
>
> I'll keep poking around, but hopefully this is helpful feedback for
> you guys. Thanks again for getting this off the ground!
>
> Tim
>
>
>
>
> On Thu, 2017-12-07 at 14:16 +, Miller, Timothy wrote:
> >
> > I
RE: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
Hi Tim,
The pipelines will soon be preloaded.
Sean
-Original Message-
From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu]
Sent: Thursday, December 14, 2017 3:58 PM
To: dev@ctakes.apache.org
Subject: Re: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
[SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
Another thought I just had is that it seems to load the pipeline when the first
call is made -- without knowing the REST APIs that well, is it possible to load
the pipelines when the war is deployed? With some of our larger pipelines the
first call may take quite a while. Would every call re-load the pipeline?
Tim
On Thu, 2017-12-14 at 20:16 +, Finan, Sean wrote:
> Hi Tim,
>
> Many thanks for testing the new rest service! And double that for the
> setup instructions!
>
> >
> > if this whole thing could be wrapped in a docker container that
> > would be really powerful
> - Matthew and I have had a short discussion or two on a docker that he
> is working on. It was working, but performed a lot of the spring
> updates and some workarounds that should no longer be needed. The
> next iteration should be cleaner and simpler. We have also talked
> about making the container more compact. He is busy with real work,
> but I think that this is definitely just over the horizon.
>
> >
> > One other thing I noticed in the code is that in sending back JSON
> > it looks like you're turning the JCas into xml and then parsing it
> > yourself. It should be easier just to access typesystem objects
> > directly. Sean may have some API code laying around to simplify that
> > as well.
> - I am actually looking at the rest/util/XmlParser and had the very
> same thought. It is a great start though, and as far as I know it is
> the first publicly available ctakes json writer. If anybody else out
> there already has or knows of another, please share!
>
>
> Cheers all,
> Sean
>
>
> -Original Message-
> From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu]
> Sent: Thursday, December 14, 2017 2:55 PM
> To: dev@ctakes.apache.org
> Subject: Re: cTAKES as REST service [EXTERNAL] [SUSPICIOUS]
> [SUSPICIOUS] [SUSPICIOUS]
>
> I looked at this today. Looks like a great start!
>
> I was able to get as far as deploying to tomcat, seeing the web form,
> and submitting, but didn't get correct feedback because I don't have a
> mysql dictionary set up, which the default descriptor points at. I
> didn't see any instructions for building that and didn't have time to
> figure that out.
>
> I think I mentioned in a different thread that if this whole thing
> could be wrapped in a docker container that would be really powerful,
> but if not, there are a few things that are obvious to you as
> developers but would make it easier for novices (like me) to deploy.
>
> * download tomcat bin and start with bin/startup.sh (check at
> localhost:8080)
> * run mvn install on my ctakes installation to populate jar files in
> the .m2 directory that were missing
> * run mvn package inside the ctakes-web-rest subdirectory
> * copy the .war file into the webapps directory in my tomcat
> installation.
> * While I couldn't get the dictionary to work pointing to mysql, I
> noticed that the dictionary descriptor file has a hardcoded IP address
> when maybe it should be 127.0.0.1?
>
> One other thing I noticed in the code is that in sending back JSON it
> looks like you're turning the JCas into xml and then parsing it
> yourself. It should be easier just to access typesystem objects
> directly. Sean may have some API code laying around to simplify that
> as well.
>
> To iterate over signs/symptoms, for example, you would do:
>
> for(SignSymptomMention ss : JCasUtil.select(jcas,
> SignSymptomMention.class)){
> int begin = ss.getBegin(); // begin offset
> int end = ss.getEnd(): // end offset ...
> }
>
> Using the typesystem directly may help you to speed up that code or
> make it easier to read. But maybe there is a reason to write it to xml
> that I'm not aware of.
>
> Finally, I see there are two sub-directories with similar names,
> ctakes-rest-service and ctakes-web-rest. If they are duplicates can
> you delete the old one?
>
> I'll keep poking around, but hopefully this is helpful feedback for
> you guys. Thanks again for getting this off the ground!
>
> Tim
>
>
>
>
> On Thu, 2017-12-07 at 14:16 +, Miller, Timothy wrote:
> >
> > I am really interested in this too, just waiting until I have a few
> > free hours to look around. Don't want you to think it's not of
> > interest.
> >
Re: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
Another thought I just had is that it seems to load the pipeline when
the first call is made -- without knowing the REST APIs that well, is
it possible to load the pipelines when the war is deployed? With some
of our larger pipelines the first call may take quite a while. Would
every call re-load the pipeline?
Tim
On Thu, 2017-12-14 at 20:16 +, Finan, Sean wrote:
> Hi Tim,
>
> Many thanks for testing the new rest service! And double that for
> the setup instructions!
>
> >
> > if this whole thing could be wrapped in a docker container that
> > would be really powerful
> - Matthew and I have had a short discussion or two on a docker that
> he is working on. It was working, but performed a lot of the spring
> updates and some workarounds that should no longer be needed. The
> next iteration should be cleaner and simpler. We have also talked
> about making the container more compact. He is busy with real work,
> but I think that this is definitely just over the horizon.
>
> >
> > One other thing I noticed in the code is that in sending back JSON
> > it looks like you're turning the JCas into xml and then parsing it
> > yourself. It should be easier just to access typesystem objects
> > directly. Sean may have some API code laying around to simplify
> > that as well.
> - I am actually looking at the rest/util/XmlParser and had the very
> same thought. It is a great start though, and as far as I know it is
> the first publicly available ctakes json writer. If anybody else out
> there already has or knows of another, please share!
>
>
> Cheers all,
> Sean
>
>
> -Original Message-
> From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu]
> Sent: Thursday, December 14, 2017 2:55 PM
> To: dev@ctakes.apache.org
> Subject: Re: cTAKES as REST service [EXTERNAL] [SUSPICIOUS]
> [SUSPICIOUS] [SUSPICIOUS]
>
> I looked at this today. Looks like a great start!
>
> I was able to get as far as deploying to tomcat, seeing the web form,
> and submitting, but didn't get correct feedback because I don't have
> a mysql dictionary set up, which the default descriptor points at. I
> didn't see any instructions for building that and didn't have time to
> figure that out.
>
> I think I mentioned in a different thread that if this whole thing
> could be wrapped in a docker container that would be really powerful,
> but if not, there are a few things that are obvious to you as
> developers but would make it easier for novices (like me) to deploy.
>
> * download tomcat bin and start with bin/startup.sh (check at
> localhost:8080)
> * run mvn install on my ctakes installation to populate jar files in
> the .m2 directory that were missing
> * run mvn package inside the ctakes-web-rest subdirectory
> * copy the .war file into the webapps directory in my tomcat
> installation.
> * While I couldn't get the dictionary to work pointing to mysql, I
> noticed that the dictionary descriptor file has a hardcoded IP
> address when maybe it should be 127.0.0.1?
>
> One other thing I noticed in the code is that in sending back JSON it
> looks like you're turning the JCas into xml and then parsing it
> yourself. It should be easier just to access typesystem objects
> directly. Sean may have some API code laying around to simplify that
> as well.
>
> To iterate over signs/symptoms, for example, you would do:
>
> for(SignSymptomMention ss : JCasUtil.select(jcas,
> SignSymptomMention.class)){
> int begin = ss.getBegin(); // begin offset
> int end = ss.getEnd(): // end offset ...
> }
>
> Using the typesystem directly may help you to speed up that code or
> make it easier to read. But maybe there is a reason to write it to
> xml that I'm not aware of.
>
> Finally, I see there are two sub-directories with similar names,
> ctakes-rest-service and ctakes-web-rest. If they are duplicates can
> you delete the old one?
>
> I'll keep poking around, but hopefully this is helpful feedback for
> you guys. Thanks again for getting this off the ground!
>
> Tim
>
>
>
>
> On Thu, 2017-12-07 at 14:16 +, Miller, Timothy wrote:
> >
> > I am really interested in this too, just waiting until I have a
> > few
> > free hours to look around. Don't want you to think it's not of
> > interest.
> > Tim
> >
> >
> > On Tue, 2017-12-05 at 19:18 +, Finan, Sean wrote:
> > >
> > >
> > > Hi all,
> > >
> > > I am trying to clear a backlog at work. I will most likely not
> > > be
> > > able to do anything with ctakes for another week. Hopefully
> > > some
> > > rest e
