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Posted to dev@ctakes.apache.org by Matthew Vita <ma...@gmail.com> on 2018/03/18 22:08:30 UTC
Re: cTAKES Rest Service Development - Dictionary GUI MySQL Progress +
1 Concern [EXTERNAL]
Hi all, I've been quiet around the cTAKES Rest Service because
*all free time has been spent on a OpenEMR release
<https://community.open-emr.org/t/picture-archiving-and-communication-system-pacs/8867/51?u=matthewvita>!
Now that this release is basically out of the door, my free time slots are
opening back up and I'm prioritizing cTAKES Rest Service!*
*Report:*
- I am working on creating a org
.apache.ctakes.gui.dictionary.DictionaryXmlWriter class that is
MySQL-friendly
- Gandhi and Sandeep are working with me on some JSON changes
- Shane and I are working on a refactor of the friendly web ui
Thanks,
Matthew Vita
www.matthewvita.com
On Tue, Jan 2, 2018 at 7:34 AM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:
> 3 cheers Matthew!
>
> -----Original Message-----
> From: John Green [mailto:john.travis.green@gmail.com]
> Sent: Sunday, December 31, 2017 9:12 AM
> To: dev@ctakes.apache.org
> Cc: Sandeep Byatha Gururaja rao; Shane Chesnutt
> Subject: Re: cTAKES Rest Service Development - Dictionary GUI MySQL
> Progress + 1 Concern [EXTERNAL]
>
> Strong work!
>
> --- Sent from VMware Boxer
>
> Just wanted to note that I've made a good bit of progress on the GUI
>
> dictionary piece. I'll post some screenshots when it is further along, but
>
> I am definitely seeing the tables in my MySQL database (tested with CPT and
>
> ICD10).
>
>
>
> I'll aim to setup CouchDB for v2 of the ctakes-rest-service. Next step is
>
> to point cTAKES (within the context of the rest service) at MySQL :).
>
>
>
> Thanks,
>
>
>
> Matthew Vita
>
> www.matthewvita.com
>
>
>
> On Mon, Dec 18, 2017 at 1:27 PM, Finan, Sean <
>
> Sean.Finan@childrens.harvard.edu> wrote:
>
>
>
> > Hi Matthew,
>
> >
>
> > I've heard of CouchDB but know nothing about it. At a glance it looks
>
> > like it is pretty versatile.
>
> >
>
> > Sean
>
> >
>
> > -----Original Message-----
>
> > From: Matthew Vita [mailto:matthewvita48@gmail.com]
>
> > Sent: Monday, December 18, 2017 3:52 PM
>
> > To: dev@ctakes.apache.org
>
> > Cc: Sandeep Byatha Gururaja rao; Shane Chesnutt
>
> > Subject: Re: cTAKES Rest Service Development - Dictionary GUI MySQL
>
> > Progress + 1 Concern [EXTERNAL]
>
> >
>
> > Okay, thanks for that Sean.
>
> >
>
> > I have a CRAZY idea... how about I try it with CouchDB instead? It's a)
> by
>
> > Apache b) can be ran in Docker c) Has a JDBC connector on Github and d)
> Is
>
> > 1 of the 2 databases used in OpenEMR so our cTAKES module users wouldn't
>
> > get too confused.
>
> >
>
> > Again, that last item is nice to have, don't read into it too much :).
>
> >
>
> > Thoughts?
>
> >
>
> > Thanks,
>
> >
>
> > Matthew Vita
>
> > www.matthewvita.com
>
> >
>
> > On Mon, Dec 18, 2017 at 7:23 AM, Finan, Sean <
>
> > Sean.Finan@childrens.harvard.edu> wrote:
>
> >
>
> > > Fantastic!
>
> > >
>
> > > I am glad that you found the issue - that wouldn't have been a
>
> > > straightforward causal to track down.
>
> > >
>
> > > Unfortunately we cannot package and ship any binaries that aren't
>
> > > fully Apache license compliant etc. However, we can do two different
>
> > things:
>
> > > - We can still grab mysql from maven central for developers to use in
>
> > > a developer environment, just like we do with the default umls
>
> > dictionary.
>
> > > - We can provide an easy means for fetching the library
>
> > > post-installation. A Dockerfile for ctakes, a downloader that
>
> > > launches when mysql is selected, or a good old fashioned installation
>
> > script.
>
> > > Luckily the mysql library is easily available and we wouldn't need to
>
> > > put together a runtime package like APR.
>
> > >
>
> > > https://urldefense.proofpoint.com/v2/url?u=https-3A__books.google.com_
>
> > > books-3Fid-3DHTo-5FAmTpQPMC-26pg-3DPA14-26&d=DwIFaQ&c=qS4goWBT7poplM69
>
> > > zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4g
>
> > > Tao&m=n53T6SD3EzUyJps9w7LjgVaYGA5GQjR3h-9GBGppwBc&s=-fxY4QiBU8SayGVEzX
>
> > > 8LVPEPzmgsYP6ANRsuTUkHkrY&e=
>
> > > lpg=PA14&dq=apache+license+mysql&source=bl&ots=uOpifTcI2E&sig=-qlWP2-
>
> > > pXtEkwPM8BsKd73GvX9g&hl=en&sa=X&ved=0ahUKEwjhqrrX55PYAhVm5YMKHTB2A
>
> > > GM4ChDoAQhMMAY#v=onepage&q=apache%20license%20mysql&f=false
>
> > >
>
> > > https://urldefense.proofpoint.com/v2/url?u=https-3A__apr.apache.org_do
>
> > > wnload.cgi&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs
>
> > > 67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=n53T6SD3EzUyJps9w7LjgVaYGA
>
> > > 5GQjR3h-9GBGppwBc&s=Gm3m03xhcJj7rfD05pZkfM9t5l8-aBOOZCwJVf4as5g&e=
>
> > >
>
> > > I think that we could make a class that searches for mysql in the
>
> > > environment if the mysql option is selected. ctakes-gui has a
>
> > dependency
>
> > > that makes this easy. Then a little downloader that throws a driver
>
> > > into the lib/ directory. If needed we could create a factory that
>
> > > returns a wrapper for the required mysql driver classes, and the
>
> > > factory could contain a class loader that guarantees the jar is
>
> > > discovered post-installation. That way a restart of the gui wouldn't
> be
>
> > necessary ...
>
> > > though that may not be a big deal.
>
> > >
>
> > > I am just throwing out some ideas. There is probably a very nice
>
> > > solution that I haven't considered.
>
> > >
>
> > > Sean
>
> > >
>
> > >
>
> > >
>
> > > -----Original Message-----
>
> > > From: Matthew Vita [mailto:matthewvita48@gmail.com]
>
> > > Sent: Monday, December 18, 2017 1:23 AM
>
> > > To: dev@ctakes.apache.org; Sandeep Byatha Gururaja rao; Shane Chesnutt
>
> > > Subject: cTAKES Rest Service Development - Dictionary GUI MySQL
>
> > > Progress +
>
> > > 1 Concern [EXTERNAL]
>
> > >
>
> > > Hi Gandhi, Sean, Tim, Alex, James,
>
> > >
>
> > > Good news, I was able to get MySQL running in the `ctakes-gui` (recall
>
> > > that I am building in a toggle so that folks can create dictionaries
>
> > > using MySQL rather than HSQLDB script files).
>
> > >
>
> > > I found out the source of the issue with bringing in the MySQL
>
> > dependency.
>
> > > This one definitely took me a while and was super subtle! If you visit
>
> > > /ctakes/ctakes-distribution/src/main/assembly/bin.xml,
>
> > > <exclude>mysql:*</exclude>is present because it's a n non-asf
>
> > > compliant dependency used by ytex.
>
> > >
>
> > > Removing the exclude and addingin
>
> > > <include>mysql:mysql-connector-java</include> gets the correct result:
>
> > >
>
> > > /ctakes/ctakes-distribution/target/apache-ctakes-4.0.1-SNAPSHOT/lib
>
> > > matthew
>
> > >
>
> > > % ls -lash | grep mysql
>
> > > 3912 -rw-r--r-- 1 matthew staff 1.9M Dec 14 20:23
>
> > > mysql-connector-java-6.0.6.jar
>
> > >
>
> > > Just for completeness, this is the exact POM entry:
>
> > >
>
> > > <dependency>
>
> > > <groupId>mysql</groupId>
>
> > > <artifactId>mysql-connector-java</artifactId>
>
> > > <version>6.0.6</version>
>
> > > </dependency>
>
> > >
>
> > >
>
> > > Is there anyway we can use MySQL in cTAKES in a way that is compliant
>
> > > with ASF? I wonder if MariaDB or Postgresql would be better because
>
> > > they work with JDBC and are free/open source. Of course, I am biased
>
> > > towards MySQL/MariaDB because the (near) future users of cTAKES Rest
>
> > > Service in the OpenEMR space are going to want MySQL/MariaDB users :).
>
> > > Not a huge deal though.
>
> > >
>
> > > Thanks,
>
> > >
>
> > > Matthew Vita
>
> > > www.matthewvita.com
>
> > >
>
> >
>
>
Re: cTAKES Rest Service Development - Dictionary GUI MySQL Progress +
1 Concern [EXTERNAL]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Ok, thanks!
________________________________________
From: Gandhi Rajan Natarajan <Ga...@arisglobal.com>
Sent: Monday, April 30, 2018 11:53 AM
To: dev@ctakes.apache.org
Subject: RE: cTAKES Rest Service Development - Dictionary GUI MySQL Progress + 1 Concern [EXTERNAL]
HI Sean,
I guess he meant about annotators like Negation annotator, Context annotator etc.. and its short description if I'm right for the write-up.
Regards,
Gandhi
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: Monday, April 30, 2018 8:28 PM
To: dev@ctakes.apache.org; Shane Chesnutt <sh...@gmail.com>; Daniel Ehrlich <Da...@gmail.com>; Erica Rao <oe...@gmail.com>
Subject: Re: cTAKES Rest Service Development - Dictionary GUI MySQL Progress + 1 Concern [EXTERNAL]
Hi Matthew Vita,
Quite excellent!
By
>Also, what would be the best annotators to describe?
Do you mean best pipelines?
Sean
________________________________________
From: Matthew Vita <ma...@gmail.com>
Sent: Sunday, April 29, 2018 11:52 PM
To: dev@ctakes.apache.org; Shane Chesnutt; Daniel Ehrlich; Erica Rao
Subject: Re: cTAKES Rest Service Development - Dictionary GUI MySQL Progress + 1 Concern [EXTERNAL]
Hi Sean, Tim, Alex, James,
I have been working very work on the latest OpenEMR release <https://urldefense.proofpoint.com/v2/url?u=https-3A__news.ycombinator.com_item-3Fid-3D16949974&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=GNOM4G03D19YI2LstCnNlakWTetYMAostEEKkheyKyQ&s=mgOYhS7ByY8mT7B0fmvZI_hJfizUnucV_kZzWyUwyPc&e=> (it is now the open-source EMR golden age!!!) - however, my free time is opening back up a bit!
Gandhi and our humble cTAKES team have made good progress on our first project milestone and wanted to put together a little blog to a) highlight our approach/team b) overview cTAKES and the main annotators c) talk about how the next milestone will integrate it with OpenEMR. This will most likely help with recruiting too!
We started writing it up here (please don't mind the draft state):
https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1SnykahMZft3vkVZmzpYr1NZjdsbW6NCZQn59Jk8xwus_edit-23heading-3Dh.ylkq3w7gocsz&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=GNOM4G03D19YI2LstCnNlakWTetYMAostEEKkheyKyQ&s=jpY51XeM6vbwQgM-0xy-OmWA1qbTx0wDftLEvzt_wB4&e=
Please let Gandhi and myself know your feedback thus far. Also, what would be the best annotators to describe?
Thanks,
Matthew Vita
www.matthewvita.com
On Sun, Mar 18, 2018 at 3:08 PM Matthew Vita <ma...@gmail.com>
wrote:
> Hi all, I've been quiet around the cTAKES Rest Service because
>
> *all free time has been spent on a OpenEMR release
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__community.open-2Demr.org_t_picture-2Darchiving-2Dand-2Dcommunication-2Dsystem-2Dpacs_8867_51-3Fu-3Dmatthewvita&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=GNOM4G03D19YI2LstCnNlakWTetYMAostEEKkheyKyQ&s=8_gH8UQgMpDIXD-4cx3uTqNh4MbOgY6ZYxD0L6gJgPw&e=>!
> Now that this release is basically out of the door, my free time slots
> are opening back up and I'm prioritizing cTAKES Rest Service!*
>
>
> *Report:*
> - I am working on creating a org
> .apache.ctakes.gui.dictionary.DictionaryXmlWriter class that is
> MySQL-friendly
> - Gandhi and Sandeep are working with me on some JSON changes
> - Shane and I are working on a refactor of the friendly web ui
>
> Thanks,
>
> Matthew Vita
> www.matthewvita.com
>
> On Tue, Jan 2, 2018 at 7:34 AM, Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
>
>> 3 cheers Matthew!
>>
>> -----Original Message-----
>> From: John Green [mailto:john.travis.green@gmail.com]
>> Sent: Sunday, December 31, 2017 9:12 AM
>> To: dev@ctakes.apache.org
>> Cc: Sandeep Byatha Gururaja rao; Shane Chesnutt
>> Subject: Re: cTAKES Rest Service Development - Dictionary GUI MySQL
>> Progress + 1 Concern [EXTERNAL]
>>
>> Strong work!
>>
>> --- Sent from VMware Boxer
>>
>> Just wanted to note that I've made a good bit of progress on the GUI
>>
>> dictionary piece. I'll post some screenshots when it is further
>> along, but
>>
>> I am definitely seeing the tables in my MySQL database (tested with
>> CPT and
>>
>> ICD10).
>>
>>
>>
>> I'll aim to setup CouchDB for v2 of the ctakes-rest-service. Next
>> step is
>>
>> to point cTAKES (within the context of the rest service) at MySQL :).
>>
>>
>>
>> Thanks,
>>
>>
>>
>> Matthew Vita
>>
>> www.matthewvita.com
>>
>>
>>
>> On Mon, Dec 18, 2017 at 1:27 PM, Finan, Sean <
>>
>> Sean.Finan@childrens.harvard.edu> wrote:
>>
>>
>>
>> > Hi Matthew,
>>
>> >
>>
>> > I've heard of CouchDB but know nothing about it. At a glance it
>> > looks
>>
>> > like it is pretty versatile.
>>
>> >
>>
>> > Sean
>>
>> >
>>
>> > -----Original Message-----
>>
>> > From: Matthew Vita [mailto:matthewvita48@gmail.com]
>>
>> > Sent: Monday, December 18, 2017 3:52 PM
>>
>> > To: dev@ctakes.apache.org
>>
>> > Cc: Sandeep Byatha Gururaja rao; Shane Chesnutt
>>
>> > Subject: Re: cTAKES Rest Service Development - Dictionary GUI MySQL
>>
>> > Progress + 1 Concern [EXTERNAL]
>>
>> >
>>
>> > Okay, thanks for that Sean.
>>
>> >
>>
>> > I have a CRAZY idea... how about I try it with CouchDB instead?
>> > It's a)
>> by
>>
>> > Apache b) can be ran in Docker c) Has a JDBC connector on Github
>> > and d)
>> Is
>>
>> > 1 of the 2 databases used in OpenEMR so our cTAKES module users
>> > wouldn't
>>
>> > get too confused.
>>
>> >
>>
>> > Again, that last item is nice to have, don't read into it too much :).
>>
>> >
>>
>> > Thoughts?
>>
>> >
>>
>> > Thanks,
>>
>> >
>>
>> > Matthew Vita
>>
>> > www.matthewvita.com
>>
>> >
>>
>> > On Mon, Dec 18, 2017 at 7:23 AM, Finan, Sean <
>>
>> > Sean.Finan@childrens.harvard.edu> wrote:
>>
>> >
>>
>> > > Fantastic!
>>
>> > >
>>
>> > > I am glad that you found the issue - that wouldn't have been a
>>
>> > > straightforward causal to track down.
>>
>> > >
>>
>> > > Unfortunately we cannot package and ship any binaries that aren't
>>
>> > > fully Apache license compliant etc. However, we can do two
>> > > different
>>
>> > things:
>>
>> > > - We can still grab mysql from maven central for developers to
>> > > use in
>>
>> > > a developer environment, just like we do with the default umls
>>
>> > dictionary.
>>
>> > > - We can provide an easy means for fetching the library
>>
>> > > post-installation. A Dockerfile for ctakes, a downloader that
>>
>> > > launches when mysql is selected, or a good old fashioned
>> > > installation
>>
>> > script.
>>
>> > > Luckily the mysql library is easily available and we wouldn't
>> > > need to
>>
>> > > put together a runtime package like APR.
>>
>> > >
>>
>> > >
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__books.google.com
>> _
>>
>> > > books-3Fid-3DHTo-5FAmTpQPMC-26pg-3DPA14-26&d=DwIFaQ&c=qS4goWBT7po
>> > > plM69
>>
>> > > zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4
>> > > f7d4g
>>
>> > > Tao&m=n53T6SD3EzUyJps9w7LjgVaYGA5GQjR3h-9GBGppwBc&s=-fxY4QiBU8Say
>> > > GVEzX
>>
>> > > 8LVPEPzmgsYP6ANRsuTUkHkrY&e=
>>
>> > > lpg=PA14&dq=apache+license+mysql&source=bl&ots=uOpifTcI2E&sig=-ql
>> > > WP2-
>>
>> > > pXtEkwPM8BsKd73GvX9g&hl=en&sa=X&ved=0ahUKEwjhqrrX55PYAhVm5YMKHTB2
>> > > A
>>
>> > > GM4ChDoAQhMMAY#v=onepage&q=apache%20license%20mysql&f=false
>>
>> > >
>>
>> > >
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__apr.apache.org_d
>> o
>>
>> > > wnload.cgi&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU
>> > > &r=fs
>>
>> > > 67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=n53T6SD3EzUyJps9w7Ljg
>> > > VaYGA
>>
>> > > 5GQjR3h-9GBGppwBc&s=Gm3m03xhcJj7rfD05pZkfM9t5l8-aBOOZCwJVf4as5g&e
>> > > =
>>
>> > >
>>
>> > > I think that we could make a class that searches for mysql in the
>>
>> > > environment if the mysql option is selected. ctakes-gui has a
>>
>> > dependency
>>
>> > > that makes this easy. Then a little downloader that throws a
>> > > driver
>>
>> > > into the lib/ directory. If needed we could create a factory
>> > > that
>>
>> > > returns a wrapper for the required mysql driver classes, and the
>>
>> > > factory could contain a class loader that guarantees the jar is
>>
>> > > discovered post-installation. That way a restart of the gui
>> > > wouldn't
>> be
>>
>> > necessary ...
>>
>> > > though that may not be a big deal.
>>
>> > >
>>
>> > > I am just throwing out some ideas. There is probably a very nice
>>
>> > > solution that I haven't considered.
>>
>> > >
>>
>> > > Sean
>>
>> > >
>>
>> > >
>>
>> > >
>>
>> > > -----Original Message-----
>>
>> > > From: Matthew Vita [mailto:matthewvita48@gmail.com]
>>
>> > > Sent: Monday, December 18, 2017 1:23 AM
>>
>> > > To: dev@ctakes.apache.org; Sandeep Byatha Gururaja rao; Shane
>> Chesnutt
>>
>> > > Subject: cTAKES Rest Service Development - Dictionary GUI MySQL
>>
>> > > Progress +
>>
>> > > 1 Concern [EXTERNAL]
>>
>> > >
>>
>> > > Hi Gandhi, Sean, Tim, Alex, James,
>>
>> > >
>>
>> > > Good news, I was able to get MySQL running in the `ctakes-gui`
>> > > (recall
>>
>> > > that I am building in a toggle so that folks can create
>> > > dictionaries
>>
>> > > using MySQL rather than HSQLDB script files).
>>
>> > >
>>
>> > > I found out the source of the issue with bringing in the MySQL
>>
>> > dependency.
>>
>> > > This one definitely took me a while and was super subtle! If you
>> > > visit
>>
>> > > /ctakes/ctakes-distribution/src/main/assembly/bin.xml,
>>
>> > > <exclude>mysql:*</exclude>is present because it's a n non-asf
>>
>> > > compliant dependency used by ytex.
>>
>> > >
>>
>> > > Removing the exclude and addingin
>>
>> > > <include>mysql:mysql-connector-java</include> gets the correct result:
>>
>> > >
>>
>> > > /ctakes/ctakes-distribution/target/apache-ctakes-4.0.1-SNAPSHOT/l
>> > > ib
>>
>> > > matthew
>>
>> > >
>>
>> > > % ls -lash | grep mysql
>>
>> > > 3912 -rw-r--r-- 1 matthew staff 1.9M Dec 14 20:23
>>
>> > > mysql-connector-java-6.0.6.jar
>>
>> > >
>>
>> > > Just for completeness, this is the exact POM entry:
>>
>> > >
>>
>> > > <dependency>
>>
>> > > <groupId>mysql</groupId>
>>
>> > > <artifactId>mysql-connector-java</artifactId>
>>
>> > > <version>6.0.6</version>
>>
>> > > </dependency>
>>
>> > >
>>
>> > >
>>
>> > > Is there anyway we can use MySQL in cTAKES in a way that is
>> > > compliant
>>
>> > > with ASF? I wonder if MariaDB or Postgresql would be better
>> > > because
>>
>> > > they work with JDBC and are free/open source. Of course, I am
>> > > biased
>>
>> > > towards MySQL/MariaDB because the (near) future users of cTAKES
>> > > Rest
>>
>> > > Service in the OpenEMR space are going to want MySQL/MariaDB users :).
>>
>> > > Not a huge deal though.
>>
>> > >
>>
>> > > Thanks,
>>
>> > >
>>
>> > > Matthew Vita
>>
>> > > www.matthewvita.com
>>
>> > >
>>
>> >
>>
>>
>
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RE: cTAKES Rest Service Development - Dictionary GUI MySQL Progress +
1 Concern [EXTERNAL]
Posted by Gandhi Rajan Natarajan <Ga...@arisglobal.com>.
HI Sean,
I guess he meant about annotators like Negation annotator, Context annotator etc.. and its short description if I'm right for the write-up.
Regards,
Gandhi
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: Monday, April 30, 2018 8:28 PM
To: dev@ctakes.apache.org; Shane Chesnutt <sh...@gmail.com>; Daniel Ehrlich <Da...@gmail.com>; Erica Rao <oe...@gmail.com>
Subject: Re: cTAKES Rest Service Development - Dictionary GUI MySQL Progress + 1 Concern [EXTERNAL]
Hi Matthew Vita,
Quite excellent!
By
>Also, what would be the best annotators to describe?
Do you mean best pipelines?
Sean
________________________________________
From: Matthew Vita <ma...@gmail.com>
Sent: Sunday, April 29, 2018 11:52 PM
To: dev@ctakes.apache.org; Shane Chesnutt; Daniel Ehrlich; Erica Rao
Subject: Re: cTAKES Rest Service Development - Dictionary GUI MySQL Progress + 1 Concern [EXTERNAL]
Hi Sean, Tim, Alex, James,
I have been working very work on the latest OpenEMR release <https://urldefense.proofpoint.com/v2/url?u=https-3A__news.ycombinator.com_item-3Fid-3D16949974&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=GNOM4G03D19YI2LstCnNlakWTetYMAostEEKkheyKyQ&s=mgOYhS7ByY8mT7B0fmvZI_hJfizUnucV_kZzWyUwyPc&e=> (it is now the open-source EMR golden age!!!) - however, my free time is opening back up a bit!
Gandhi and our humble cTAKES team have made good progress on our first project milestone and wanted to put together a little blog to a) highlight our approach/team b) overview cTAKES and the main annotators c) talk about how the next milestone will integrate it with OpenEMR. This will most likely help with recruiting too!
We started writing it up here (please don't mind the draft state):
https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1SnykahMZft3vkVZmzpYr1NZjdsbW6NCZQn59Jk8xwus_edit-23heading-3Dh.ylkq3w7gocsz&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=GNOM4G03D19YI2LstCnNlakWTetYMAostEEKkheyKyQ&s=jpY51XeM6vbwQgM-0xy-OmWA1qbTx0wDftLEvzt_wB4&e=
Please let Gandhi and myself know your feedback thus far. Also, what would be the best annotators to describe?
Thanks,
Matthew Vita
www.matthewvita.com
On Sun, Mar 18, 2018 at 3:08 PM Matthew Vita <ma...@gmail.com>
wrote:
> Hi all, I've been quiet around the cTAKES Rest Service because
>
> *all free time has been spent on a OpenEMR release
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__community.open-2Demr.org_t_picture-2Darchiving-2Dand-2Dcommunication-2Dsystem-2Dpacs_8867_51-3Fu-3Dmatthewvita&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=GNOM4G03D19YI2LstCnNlakWTetYMAostEEKkheyKyQ&s=8_gH8UQgMpDIXD-4cx3uTqNh4MbOgY6ZYxD0L6gJgPw&e=>!
> Now that this release is basically out of the door, my free time slots
> are opening back up and I'm prioritizing cTAKES Rest Service!*
>
>
> *Report:*
> - I am working on creating a org
> .apache.ctakes.gui.dictionary.DictionaryXmlWriter class that is
> MySQL-friendly
> - Gandhi and Sandeep are working with me on some JSON changes
> - Shane and I are working on a refactor of the friendly web ui
>
> Thanks,
>
> Matthew Vita
> www.matthewvita.com
>
> On Tue, Jan 2, 2018 at 7:34 AM, Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
>
>> 3 cheers Matthew!
>>
>> -----Original Message-----
>> From: John Green [mailto:john.travis.green@gmail.com]
>> Sent: Sunday, December 31, 2017 9:12 AM
>> To: dev@ctakes.apache.org
>> Cc: Sandeep Byatha Gururaja rao; Shane Chesnutt
>> Subject: Re: cTAKES Rest Service Development - Dictionary GUI MySQL
>> Progress + 1 Concern [EXTERNAL]
>>
>> Strong work!
>>
>> --- Sent from VMware Boxer
>>
>> Just wanted to note that I've made a good bit of progress on the GUI
>>
>> dictionary piece. I'll post some screenshots when it is further
>> along, but
>>
>> I am definitely seeing the tables in my MySQL database (tested with
>> CPT and
>>
>> ICD10).
>>
>>
>>
>> I'll aim to setup CouchDB for v2 of the ctakes-rest-service. Next
>> step is
>>
>> to point cTAKES (within the context of the rest service) at MySQL :).
>>
>>
>>
>> Thanks,
>>
>>
>>
>> Matthew Vita
>>
>> www.matthewvita.com
>>
>>
>>
>> On Mon, Dec 18, 2017 at 1:27 PM, Finan, Sean <
>>
>> Sean.Finan@childrens.harvard.edu> wrote:
>>
>>
>>
>> > Hi Matthew,
>>
>> >
>>
>> > I've heard of CouchDB but know nothing about it. At a glance it
>> > looks
>>
>> > like it is pretty versatile.
>>
>> >
>>
>> > Sean
>>
>> >
>>
>> > -----Original Message-----
>>
>> > From: Matthew Vita [mailto:matthewvita48@gmail.com]
>>
>> > Sent: Monday, December 18, 2017 3:52 PM
>>
>> > To: dev@ctakes.apache.org
>>
>> > Cc: Sandeep Byatha Gururaja rao; Shane Chesnutt
>>
>> > Subject: Re: cTAKES Rest Service Development - Dictionary GUI MySQL
>>
>> > Progress + 1 Concern [EXTERNAL]
>>
>> >
>>
>> > Okay, thanks for that Sean.
>>
>> >
>>
>> > I have a CRAZY idea... how about I try it with CouchDB instead?
>> > It's a)
>> by
>>
>> > Apache b) can be ran in Docker c) Has a JDBC connector on Github
>> > and d)
>> Is
>>
>> > 1 of the 2 databases used in OpenEMR so our cTAKES module users
>> > wouldn't
>>
>> > get too confused.
>>
>> >
>>
>> > Again, that last item is nice to have, don't read into it too much :).
>>
>> >
>>
>> > Thoughts?
>>
>> >
>>
>> > Thanks,
>>
>> >
>>
>> > Matthew Vita
>>
>> > www.matthewvita.com
>>
>> >
>>
>> > On Mon, Dec 18, 2017 at 7:23 AM, Finan, Sean <
>>
>> > Sean.Finan@childrens.harvard.edu> wrote:
>>
>> >
>>
>> > > Fantastic!
>>
>> > >
>>
>> > > I am glad that you found the issue - that wouldn't have been a
>>
>> > > straightforward causal to track down.
>>
>> > >
>>
>> > > Unfortunately we cannot package and ship any binaries that aren't
>>
>> > > fully Apache license compliant etc. However, we can do two
>> > > different
>>
>> > things:
>>
>> > > - We can still grab mysql from maven central for developers to
>> > > use in
>>
>> > > a developer environment, just like we do with the default umls
>>
>> > dictionary.
>>
>> > > - We can provide an easy means for fetching the library
>>
>> > > post-installation. A Dockerfile for ctakes, a downloader that
>>
>> > > launches when mysql is selected, or a good old fashioned
>> > > installation
>>
>> > script.
>>
>> > > Luckily the mysql library is easily available and we wouldn't
>> > > need to
>>
>> > > put together a runtime package like APR.
>>
>> > >
>>
>> > >
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__books.google.com
>> _
>>
>> > > books-3Fid-3DHTo-5FAmTpQPMC-26pg-3DPA14-26&d=DwIFaQ&c=qS4goWBT7po
>> > > plM69
>>
>> > > zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4
>> > > f7d4g
>>
>> > > Tao&m=n53T6SD3EzUyJps9w7LjgVaYGA5GQjR3h-9GBGppwBc&s=-fxY4QiBU8Say
>> > > GVEzX
>>
>> > > 8LVPEPzmgsYP6ANRsuTUkHkrY&e=
>>
>> > > lpg=PA14&dq=apache+license+mysql&source=bl&ots=uOpifTcI2E&sig=-ql
>> > > WP2-
>>
>> > > pXtEkwPM8BsKd73GvX9g&hl=en&sa=X&ved=0ahUKEwjhqrrX55PYAhVm5YMKHTB2
>> > > A
>>
>> > > GM4ChDoAQhMMAY#v=onepage&q=apache%20license%20mysql&f=false
>>
>> > >
>>
>> > >
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__apr.apache.org_d
>> o
>>
>> > > wnload.cgi&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU
>> > > &r=fs
>>
>> > > 67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=n53T6SD3EzUyJps9w7Ljg
>> > > VaYGA
>>
>> > > 5GQjR3h-9GBGppwBc&s=Gm3m03xhcJj7rfD05pZkfM9t5l8-aBOOZCwJVf4as5g&e
>> > > =
>>
>> > >
>>
>> > > I think that we could make a class that searches for mysql in the
>>
>> > > environment if the mysql option is selected. ctakes-gui has a
>>
>> > dependency
>>
>> > > that makes this easy. Then a little downloader that throws a
>> > > driver
>>
>> > > into the lib/ directory. If needed we could create a factory
>> > > that
>>
>> > > returns a wrapper for the required mysql driver classes, and the
>>
>> > > factory could contain a class loader that guarantees the jar is
>>
>> > > discovered post-installation. That way a restart of the gui
>> > > wouldn't
>> be
>>
>> > necessary ...
>>
>> > > though that may not be a big deal.
>>
>> > >
>>
>> > > I am just throwing out some ideas. There is probably a very nice
>>
>> > > solution that I haven't considered.
>>
>> > >
>>
>> > > Sean
>>
>> > >
>>
>> > >
>>
>> > >
>>
>> > > -----Original Message-----
>>
>> > > From: Matthew Vita [mailto:matthewvita48@gmail.com]
>>
>> > > Sent: Monday, December 18, 2017 1:23 AM
>>
>> > > To: dev@ctakes.apache.org; Sandeep Byatha Gururaja rao; Shane
>> Chesnutt
>>
>> > > Subject: cTAKES Rest Service Development - Dictionary GUI MySQL
>>
>> > > Progress +
>>
>> > > 1 Concern [EXTERNAL]
>>
>> > >
>>
>> > > Hi Gandhi, Sean, Tim, Alex, James,
>>
>> > >
>>
>> > > Good news, I was able to get MySQL running in the `ctakes-gui`
>> > > (recall
>>
>> > > that I am building in a toggle so that folks can create
>> > > dictionaries
>>
>> > > using MySQL rather than HSQLDB script files).
>>
>> > >
>>
>> > > I found out the source of the issue with bringing in the MySQL
>>
>> > dependency.
>>
>> > > This one definitely took me a while and was super subtle! If you
>> > > visit
>>
>> > > /ctakes/ctakes-distribution/src/main/assembly/bin.xml,
>>
>> > > <exclude>mysql:*</exclude>is present because it's a n non-asf
>>
>> > > compliant dependency used by ytex.
>>
>> > >
>>
>> > > Removing the exclude and addingin
>>
>> > > <include>mysql:mysql-connector-java</include> gets the correct result:
>>
>> > >
>>
>> > > /ctakes/ctakes-distribution/target/apache-ctakes-4.0.1-SNAPSHOT/l
>> > > ib
>>
>> > > matthew
>>
>> > >
>>
>> > > % ls -lash | grep mysql
>>
>> > > 3912 -rw-r--r-- 1 matthew staff 1.9M Dec 14 20:23
>>
>> > > mysql-connector-java-6.0.6.jar
>>
>> > >
>>
>> > > Just for completeness, this is the exact POM entry:
>>
>> > >
>>
>> > > <dependency>
>>
>> > > <groupId>mysql</groupId>
>>
>> > > <artifactId>mysql-connector-java</artifactId>
>>
>> > > <version>6.0.6</version>
>>
>> > > </dependency>
>>
>> > >
>>
>> > >
>>
>> > > Is there anyway we can use MySQL in cTAKES in a way that is
>> > > compliant
>>
>> > > with ASF? I wonder if MariaDB or Postgresql would be better
>> > > because
>>
>> > > they work with JDBC and are free/open source. Of course, I am
>> > > biased
>>
>> > > towards MySQL/MariaDB because the (near) future users of cTAKES
>> > > Rest
>>
>> > > Service in the OpenEMR space are going to want MySQL/MariaDB users :).
>>
>> > > Not a huge deal though.
>>
>> > >
>>
>> > > Thanks,
>>
>> > >
>>
>> > > Matthew Vita
>>
>> > > www.matthewvita.com
>>
>> > >
>>
>> >
>>
>>
>
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Re: cTAKES Rest Service Development - Dictionary GUI MySQL Progress +
1 Concern [EXTERNAL]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Matthew Vita,
Quite excellent!
By
>Also, what would be the best annotators to describe?
Do you mean best pipelines?
Sean
________________________________________
From: Matthew Vita <ma...@gmail.com>
Sent: Sunday, April 29, 2018 11:52 PM
To: dev@ctakes.apache.org; Shane Chesnutt; Daniel Ehrlich; Erica Rao
Subject: Re: cTAKES Rest Service Development - Dictionary GUI MySQL Progress + 1 Concern [EXTERNAL]
Hi Sean, Tim, Alex, James,
I have been working very work on the latest OpenEMR release
<https://urldefense.proofpoint.com/v2/url?u=https-3A__news.ycombinator.com_item-3Fid-3D16949974&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=GNOM4G03D19YI2LstCnNlakWTetYMAostEEKkheyKyQ&s=mgOYhS7ByY8mT7B0fmvZI_hJfizUnucV_kZzWyUwyPc&e=> (it is now the open-source
EMR golden age!!!) - however, my free time is opening back up a bit!
Gandhi and our humble cTAKES team have made good progress on our first
project milestone and wanted to put together a little blog to a) highlight
our approach/team b) overview cTAKES and the main annotators c) talk about
how the next milestone will integrate it with OpenEMR. This will most
likely help with recruiting too!
We started writing it up here (please don't mind the draft state):
https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1SnykahMZft3vkVZmzpYr1NZjdsbW6NCZQn59Jk8xwus_edit-23heading-3Dh.ylkq3w7gocsz&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=GNOM4G03D19YI2LstCnNlakWTetYMAostEEKkheyKyQ&s=jpY51XeM6vbwQgM-0xy-OmWA1qbTx0wDftLEvzt_wB4&e=
Please let Gandhi and myself know your feedback thus far. Also, what would
be the best annotators to describe?
Thanks,
Matthew Vita
www.matthewvita.com
On Sun, Mar 18, 2018 at 3:08 PM Matthew Vita <ma...@gmail.com>
wrote:
> Hi all, I've been quiet around the cTAKES Rest Service because
>
> *all free time has been spent on a OpenEMR release
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__community.open-2Demr.org_t_picture-2Darchiving-2Dand-2Dcommunication-2Dsystem-2Dpacs_8867_51-3Fu-3Dmatthewvita&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=GNOM4G03D19YI2LstCnNlakWTetYMAostEEKkheyKyQ&s=8_gH8UQgMpDIXD-4cx3uTqNh4MbOgY6ZYxD0L6gJgPw&e=>!
> Now that this release is basically out of the door, my free time slots are
> opening back up and I'm prioritizing cTAKES Rest Service!*
>
>
> *Report:*
> - I am working on creating a org
> .apache.ctakes.gui.dictionary.DictionaryXmlWriter class that is
> MySQL-friendly
> - Gandhi and Sandeep are working with me on some JSON changes
> - Shane and I are working on a refactor of the friendly web ui
>
> Thanks,
>
> Matthew Vita
> www.matthewvita.com
>
> On Tue, Jan 2, 2018 at 7:34 AM, Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
>
>> 3 cheers Matthew!
>>
>> -----Original Message-----
>> From: John Green [mailto:john.travis.green@gmail.com]
>> Sent: Sunday, December 31, 2017 9:12 AM
>> To: dev@ctakes.apache.org
>> Cc: Sandeep Byatha Gururaja rao; Shane Chesnutt
>> Subject: Re: cTAKES Rest Service Development - Dictionary GUI MySQL
>> Progress + 1 Concern [EXTERNAL]
>>
>> Strong work!
>>
>> --- Sent from VMware Boxer
>>
>> Just wanted to note that I've made a good bit of progress on the GUI
>>
>> dictionary piece. I'll post some screenshots when it is further along, but
>>
>> I am definitely seeing the tables in my MySQL database (tested with CPT
>> and
>>
>> ICD10).
>>
>>
>>
>> I'll aim to setup CouchDB for v2 of the ctakes-rest-service. Next step is
>>
>> to point cTAKES (within the context of the rest service) at MySQL :).
>>
>>
>>
>> Thanks,
>>
>>
>>
>> Matthew Vita
>>
>> www.matthewvita.com
>>
>>
>>
>> On Mon, Dec 18, 2017 at 1:27 PM, Finan, Sean <
>>
>> Sean.Finan@childrens.harvard.edu> wrote:
>>
>>
>>
>> > Hi Matthew,
>>
>> >
>>
>> > I've heard of CouchDB but know nothing about it. At a glance it looks
>>
>> > like it is pretty versatile.
>>
>> >
>>
>> > Sean
>>
>> >
>>
>> > -----Original Message-----
>>
>> > From: Matthew Vita [mailto:matthewvita48@gmail.com]
>>
>> > Sent: Monday, December 18, 2017 3:52 PM
>>
>> > To: dev@ctakes.apache.org
>>
>> > Cc: Sandeep Byatha Gururaja rao; Shane Chesnutt
>>
>> > Subject: Re: cTAKES Rest Service Development - Dictionary GUI MySQL
>>
>> > Progress + 1 Concern [EXTERNAL]
>>
>> >
>>
>> > Okay, thanks for that Sean.
>>
>> >
>>
>> > I have a CRAZY idea... how about I try it with CouchDB instead? It's a)
>> by
>>
>> > Apache b) can be ran in Docker c) Has a JDBC connector on Github and d)
>> Is
>>
>> > 1 of the 2 databases used in OpenEMR so our cTAKES module users wouldn't
>>
>> > get too confused.
>>
>> >
>>
>> > Again, that last item is nice to have, don't read into it too much :).
>>
>> >
>>
>> > Thoughts?
>>
>> >
>>
>> > Thanks,
>>
>> >
>>
>> > Matthew Vita
>>
>> > www.matthewvita.com
>>
>> >
>>
>> > On Mon, Dec 18, 2017 at 7:23 AM, Finan, Sean <
>>
>> > Sean.Finan@childrens.harvard.edu> wrote:
>>
>> >
>>
>> > > Fantastic!
>>
>> > >
>>
>> > > I am glad that you found the issue - that wouldn't have been a
>>
>> > > straightforward causal to track down.
>>
>> > >
>>
>> > > Unfortunately we cannot package and ship any binaries that aren't
>>
>> > > fully Apache license compliant etc. However, we can do two different
>>
>> > things:
>>
>> > > - We can still grab mysql from maven central for developers to use in
>>
>> > > a developer environment, just like we do with the default umls
>>
>> > dictionary.
>>
>> > > - We can provide an easy means for fetching the library
>>
>> > > post-installation. A Dockerfile for ctakes, a downloader that
>>
>> > > launches when mysql is selected, or a good old fashioned installation
>>
>> > script.
>>
>> > > Luckily the mysql library is easily available and we wouldn't need to
>>
>> > > put together a runtime package like APR.
>>
>> > >
>>
>> > >
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__books.google.com_
>>
>> > > books-3Fid-3DHTo-5FAmTpQPMC-26pg-3DPA14-26&d=DwIFaQ&c=qS4goWBT7poplM69
>>
>> > > zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4g
>>
>> > > Tao&m=n53T6SD3EzUyJps9w7LjgVaYGA5GQjR3h-9GBGppwBc&s=-fxY4QiBU8SayGVEzX
>>
>> > > 8LVPEPzmgsYP6ANRsuTUkHkrY&e=
>>
>> > > lpg=PA14&dq=apache+license+mysql&source=bl&ots=uOpifTcI2E&sig=-qlWP2-
>>
>> > > pXtEkwPM8BsKd73GvX9g&hl=en&sa=X&ved=0ahUKEwjhqrrX55PYAhVm5YMKHTB2A
>>
>> > > GM4ChDoAQhMMAY#v=onepage&q=apache%20license%20mysql&f=false
>>
>> > >
>>
>> > >
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__apr.apache.org_do
>>
>> > > wnload.cgi&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs
>>
>> > > 67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=n53T6SD3EzUyJps9w7LjgVaYGA
>>
>> > > 5GQjR3h-9GBGppwBc&s=Gm3m03xhcJj7rfD05pZkfM9t5l8-aBOOZCwJVf4as5g&e=
>>
>> > >
>>
>> > > I think that we could make a class that searches for mysql in the
>>
>> > > environment if the mysql option is selected. ctakes-gui has a
>>
>> > dependency
>>
>> > > that makes this easy. Then a little downloader that throws a driver
>>
>> > > into the lib/ directory. If needed we could create a factory that
>>
>> > > returns a wrapper for the required mysql driver classes, and the
>>
>> > > factory could contain a class loader that guarantees the jar is
>>
>> > > discovered post-installation. That way a restart of the gui wouldn't
>> be
>>
>> > necessary ...
>>
>> > > though that may not be a big deal.
>>
>> > >
>>
>> > > I am just throwing out some ideas. There is probably a very nice
>>
>> > > solution that I haven't considered.
>>
>> > >
>>
>> > > Sean
>>
>> > >
>>
>> > >
>>
>> > >
>>
>> > > -----Original Message-----
>>
>> > > From: Matthew Vita [mailto:matthewvita48@gmail.com]
>>
>> > > Sent: Monday, December 18, 2017 1:23 AM
>>
>> > > To: dev@ctakes.apache.org; Sandeep Byatha Gururaja rao; Shane
>> Chesnutt
>>
>> > > Subject: cTAKES Rest Service Development - Dictionary GUI MySQL
>>
>> > > Progress +
>>
>> > > 1 Concern [EXTERNAL]
>>
>> > >
>>
>> > > Hi Gandhi, Sean, Tim, Alex, James,
>>
>> > >
>>
>> > > Good news, I was able to get MySQL running in the `ctakes-gui` (recall
>>
>> > > that I am building in a toggle so that folks can create dictionaries
>>
>> > > using MySQL rather than HSQLDB script files).
>>
>> > >
>>
>> > > I found out the source of the issue with bringing in the MySQL
>>
>> > dependency.
>>
>> > > This one definitely took me a while and was super subtle! If you visit
>>
>> > > /ctakes/ctakes-distribution/src/main/assembly/bin.xml,
>>
>> > > <exclude>mysql:*</exclude>is present because it's a n non-asf
>>
>> > > compliant dependency used by ytex.
>>
>> > >
>>
>> > > Removing the exclude and addingin
>>
>> > > <include>mysql:mysql-connector-java</include> gets the correct result:
>>
>> > >
>>
>> > > /ctakes/ctakes-distribution/target/apache-ctakes-4.0.1-SNAPSHOT/lib
>>
>> > > matthew
>>
>> > >
>>
>> > > % ls -lash | grep mysql
>>
>> > > 3912 -rw-r--r-- 1 matthew staff 1.9M Dec 14 20:23
>>
>> > > mysql-connector-java-6.0.6.jar
>>
>> > >
>>
>> > > Just for completeness, this is the exact POM entry:
>>
>> > >
>>
>> > > <dependency>
>>
>> > > <groupId>mysql</groupId>
>>
>> > > <artifactId>mysql-connector-java</artifactId>
>>
>> > > <version>6.0.6</version>
>>
>> > > </dependency>
>>
>> > >
>>
>> > >
>>
>> > > Is there anyway we can use MySQL in cTAKES in a way that is compliant
>>
>> > > with ASF? I wonder if MariaDB or Postgresql would be better because
>>
>> > > they work with JDBC and are free/open source. Of course, I am biased
>>
>> > > towards MySQL/MariaDB because the (near) future users of cTAKES Rest
>>
>> > > Service in the OpenEMR space are going to want MySQL/MariaDB users :).
>>
>> > > Not a huge deal though.
>>
>> > >
>>
>> > > Thanks,
>>
>> > >
>>
>> > > Matthew Vita
>>
>> > > www.matthewvita.com
>>
>> > >
>>
>> >
>>
>>
>
Re: cTAKES Rest Service Development - Dictionary GUI MySQL Progress +
1 Concern [EXTERNAL]
Posted by Matthew Vita <ma...@gmail.com>.
Hi Sean, Tim, Alex, James,
I have been working very work on the latest OpenEMR release
<https://news.ycombinator.com/item?id=16949974> (it is now the open-source
EMR golden age!!!) - however, my free time is opening back up a bit!
Gandhi and our humble cTAKES team have made good progress on our first
project milestone and wanted to put together a little blog to a) highlight
our approach/team b) overview cTAKES and the main annotators c) talk about
how the next milestone will integrate it with OpenEMR. This will most
likely help with recruiting too!
We started writing it up here (please don't mind the draft state):
https://docs.google.com/document/d/1SnykahMZft3vkVZmzpYr1NZjdsbW6NCZQn59Jk8xwus/edit#heading=h.ylkq3w7gocsz
Please let Gandhi and myself know your feedback thus far. Also, what would
be the best annotators to describe?
Thanks,
Matthew Vita
www.matthewvita.com
On Sun, Mar 18, 2018 at 3:08 PM Matthew Vita <ma...@gmail.com>
wrote:
> Hi all, I've been quiet around the cTAKES Rest Service because
>
> *all free time has been spent on a OpenEMR release
> <https://community.open-emr.org/t/picture-archiving-and-communication-system-pacs/8867/51?u=matthewvita>!
> Now that this release is basically out of the door, my free time slots are
> opening back up and I'm prioritizing cTAKES Rest Service!*
>
>
> *Report:*
> - I am working on creating a org
> .apache.ctakes.gui.dictionary.DictionaryXmlWriter class that is
> MySQL-friendly
> - Gandhi and Sandeep are working with me on some JSON changes
> - Shane and I are working on a refactor of the friendly web ui
>
> Thanks,
>
> Matthew Vita
> www.matthewvita.com
>
> On Tue, Jan 2, 2018 at 7:34 AM, Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
>
>> 3 cheers Matthew!
>>
>> -----Original Message-----
>> From: John Green [mailto:john.travis.green@gmail.com]
>> Sent: Sunday, December 31, 2017 9:12 AM
>> To: dev@ctakes.apache.org
>> Cc: Sandeep Byatha Gururaja rao; Shane Chesnutt
>> Subject: Re: cTAKES Rest Service Development - Dictionary GUI MySQL
>> Progress + 1 Concern [EXTERNAL]
>>
>> Strong work!
>>
>> --- Sent from VMware Boxer
>>
>> Just wanted to note that I've made a good bit of progress on the GUI
>>
>> dictionary piece. I'll post some screenshots when it is further along, but
>>
>> I am definitely seeing the tables in my MySQL database (tested with CPT
>> and
>>
>> ICD10).
>>
>>
>>
>> I'll aim to setup CouchDB for v2 of the ctakes-rest-service. Next step is
>>
>> to point cTAKES (within the context of the rest service) at MySQL :).
>>
>>
>>
>> Thanks,
>>
>>
>>
>> Matthew Vita
>>
>> www.matthewvita.com
>>
>>
>>
>> On Mon, Dec 18, 2017 at 1:27 PM, Finan, Sean <
>>
>> Sean.Finan@childrens.harvard.edu> wrote:
>>
>>
>>
>> > Hi Matthew,
>>
>> >
>>
>> > I've heard of CouchDB but know nothing about it. At a glance it looks
>>
>> > like it is pretty versatile.
>>
>> >
>>
>> > Sean
>>
>> >
>>
>> > -----Original Message-----
>>
>> > From: Matthew Vita [mailto:matthewvita48@gmail.com]
>>
>> > Sent: Monday, December 18, 2017 3:52 PM
>>
>> > To: dev@ctakes.apache.org
>>
>> > Cc: Sandeep Byatha Gururaja rao; Shane Chesnutt
>>
>> > Subject: Re: cTAKES Rest Service Development - Dictionary GUI MySQL
>>
>> > Progress + 1 Concern [EXTERNAL]
>>
>> >
>>
>> > Okay, thanks for that Sean.
>>
>> >
>>
>> > I have a CRAZY idea... how about I try it with CouchDB instead? It's a)
>> by
>>
>> > Apache b) can be ran in Docker c) Has a JDBC connector on Github and d)
>> Is
>>
>> > 1 of the 2 databases used in OpenEMR so our cTAKES module users wouldn't
>>
>> > get too confused.
>>
>> >
>>
>> > Again, that last item is nice to have, don't read into it too much :).
>>
>> >
>>
>> > Thoughts?
>>
>> >
>>
>> > Thanks,
>>
>> >
>>
>> > Matthew Vita
>>
>> > www.matthewvita.com
>>
>> >
>>
>> > On Mon, Dec 18, 2017 at 7:23 AM, Finan, Sean <
>>
>> > Sean.Finan@childrens.harvard.edu> wrote:
>>
>> >
>>
>> > > Fantastic!
>>
>> > >
>>
>> > > I am glad that you found the issue - that wouldn't have been a
>>
>> > > straightforward causal to track down.
>>
>> > >
>>
>> > > Unfortunately we cannot package and ship any binaries that aren't
>>
>> > > fully Apache license compliant etc. However, we can do two different
>>
>> > things:
>>
>> > > - We can still grab mysql from maven central for developers to use in
>>
>> > > a developer environment, just like we do with the default umls
>>
>> > dictionary.
>>
>> > > - We can provide an easy means for fetching the library
>>
>> > > post-installation. A Dockerfile for ctakes, a downloader that
>>
>> > > launches when mysql is selected, or a good old fashioned installation
>>
>> > script.
>>
>> > > Luckily the mysql library is easily available and we wouldn't need to
>>
>> > > put together a runtime package like APR.
>>
>> > >
>>
>> > >
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__books.google.com_
>>
>> > > books-3Fid-3DHTo-5FAmTpQPMC-26pg-3DPA14-26&d=DwIFaQ&c=qS4goWBT7poplM69
>>
>> > > zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4g
>>
>> > > Tao&m=n53T6SD3EzUyJps9w7LjgVaYGA5GQjR3h-9GBGppwBc&s=-fxY4QiBU8SayGVEzX
>>
>> > > 8LVPEPzmgsYP6ANRsuTUkHkrY&e=
>>
>> > > lpg=PA14&dq=apache+license+mysql&source=bl&ots=uOpifTcI2E&sig=-qlWP2-
>>
>> > > pXtEkwPM8BsKd73GvX9g&hl=en&sa=X&ved=0ahUKEwjhqrrX55PYAhVm5YMKHTB2A
>>
>> > > GM4ChDoAQhMMAY#v=onepage&q=apache%20license%20mysql&f=false
>>
>> > >
>>
>> > >
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__apr.apache.org_do
>>
>> > > wnload.cgi&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs
>>
>> > > 67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=n53T6SD3EzUyJps9w7LjgVaYGA
>>
>> > > 5GQjR3h-9GBGppwBc&s=Gm3m03xhcJj7rfD05pZkfM9t5l8-aBOOZCwJVf4as5g&e=
>>
>> > >
>>
>> > > I think that we could make a class that searches for mysql in the
>>
>> > > environment if the mysql option is selected. ctakes-gui has a
>>
>> > dependency
>>
>> > > that makes this easy. Then a little downloader that throws a driver
>>
>> > > into the lib/ directory. If needed we could create a factory that
>>
>> > > returns a wrapper for the required mysql driver classes, and the
>>
>> > > factory could contain a class loader that guarantees the jar is
>>
>> > > discovered post-installation. That way a restart of the gui wouldn't
>> be
>>
>> > necessary ...
>>
>> > > though that may not be a big deal.
>>
>> > >
>>
>> > > I am just throwing out some ideas. There is probably a very nice
>>
>> > > solution that I haven't considered.
>>
>> > >
>>
>> > > Sean
>>
>> > >
>>
>> > >
>>
>> > >
>>
>> > > -----Original Message-----
>>
>> > > From: Matthew Vita [mailto:matthewvita48@gmail.com]
>>
>> > > Sent: Monday, December 18, 2017 1:23 AM
>>
>> > > To: dev@ctakes.apache.org; Sandeep Byatha Gururaja rao; Shane
>> Chesnutt
>>
>> > > Subject: cTAKES Rest Service Development - Dictionary GUI MySQL
>>
>> > > Progress +
>>
>> > > 1 Concern [EXTERNAL]
>>
>> > >
>>
>> > > Hi Gandhi, Sean, Tim, Alex, James,
>>
>> > >
>>
>> > > Good news, I was able to get MySQL running in the `ctakes-gui` (recall
>>
>> > > that I am building in a toggle so that folks can create dictionaries
>>
>> > > using MySQL rather than HSQLDB script files).
>>
>> > >
>>
>> > > I found out the source of the issue with bringing in the MySQL
>>
>> > dependency.
>>
>> > > This one definitely took me a while and was super subtle! If you visit
>>
>> > > /ctakes/ctakes-distribution/src/main/assembly/bin.xml,
>>
>> > > <exclude>mysql:*</exclude>is present because it's a n non-asf
>>
>> > > compliant dependency used by ytex.
>>
>> > >
>>
>> > > Removing the exclude and addingin
>>
>> > > <include>mysql:mysql-connector-java</include> gets the correct result:
>>
>> > >
>>
>> > > /ctakes/ctakes-distribution/target/apache-ctakes-4.0.1-SNAPSHOT/lib
>>
>> > > matthew
>>
>> > >
>>
>> > > % ls -lash | grep mysql
>>
>> > > 3912 -rw-r--r-- 1 matthew staff 1.9M Dec 14 20:23
>>
>> > > mysql-connector-java-6.0.6.jar
>>
>> > >
>>
>> > > Just for completeness, this is the exact POM entry:
>>
>> > >
>>
>> > > <dependency>
>>
>> > > <groupId>mysql</groupId>
>>
>> > > <artifactId>mysql-connector-java</artifactId>
>>
>> > > <version>6.0.6</version>
>>
>> > > </dependency>
>>
>> > >
>>
>> > >
>>
>> > > Is there anyway we can use MySQL in cTAKES in a way that is compliant
>>
>> > > with ASF? I wonder if MariaDB or Postgresql would be better because
>>
>> > > they work with JDBC and are free/open source. Of course, I am biased
>>
>> > > towards MySQL/MariaDB because the (near) future users of cTAKES Rest
>>
>> > > Service in the OpenEMR space are going to want MySQL/MariaDB users :).
>>
>> > > Not a huge deal though.
>>
>> > >
>>
>> > > Thanks,
>>
>> > >
>>
>> > > Matthew Vita
>>
>> > > www.matthewvita.com
>>
>> > >
>>
>> >
>>
>>
>