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://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 <matthewvit...@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.fi...@childrens.harvard.edu> wrote: > >> 3 cheers Matthew! >> >> -Original Message- >> From: John Green [mailto:john.travis.gr...@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.fi...@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:matthewvit...@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.fi...@childrens.harvard.edu> wrote: >> >> > >> >> > > Fantastic! >> >> > > >> >> > > I am glad that you found the issue - that wouldn't have been a >> >> &g
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.fi...@childrens.harvard.edu> wrote: > 3 cheers Matthew! > > -Original Message- > From: John Green [mailto:john.travis.gr...@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.fi...@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:matthewvit...@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.fi...@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=DwIFaQ=qS4goWBT7poplM69 > > > > zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4g > > > > Tao=n53T6SD3EzUyJps9w7LjgVaYGA5GQjR3h-9GBGppwBc=-fxY4QiBU8SayGVEzX > > > > 8LVPEPzmgsYP6ANRsuTUkHkrY= > > > > lpg=PA14=apache+license+mysql=bl=uOpifTcI2E=-qlWP2- > > > > pXtEkwPM8BsKd73GvX9g=en=X=0ahUKEwjhqrrX55PYAhVm5YMKHTB2A > > > > GM4ChDoAQhMMAY#v=onepage=apache%20license%20mysql=false > > > > > > > > https://urldefense.proofpoint.
RE: cTAKES Rest Service Development - Dictionary GUI MySQL Progress + 1 Concern [EXTERNAL]
Great Work Matthew. This will be very handy for cTAKEs MySQL integration. Cheers. Regards, Gandhi -Original Message- From: Matthew Vita [mailto:matthewvit...@gmail.com] Sent: Sunday, December 31, 2017 12:47 PM To: dev@ctakes.apache.org Cc: Sandeep Byatha Gururaja rao <sandeep...@arisglobal.com>; Shane Chesnutt <shanechesn...@gmail.com> Subject: Re: cTAKES Rest Service Development - Dictionary GUI MySQL Progress + 1 Concern [EXTERNAL] 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.fi...@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:matthewvit...@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.fi...@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.co > > m_ > > books-3Fid-3DHTo-5FAmTpQPMC-26pg-3DPA14-26=DwIFaQ=qS4goWBT7poplM > > 69 > > zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d > > 4g > > Tao=n53T6SD3EzUyJps9w7LjgVaYGA5GQjR3h-9GBGppwBc=-fxY4QiBU8SayGVE > > zX > > 8LVPEPzmgsYP6ANRsuTUkHkrY= > > lpg=PA14=apache+license+mysql=bl=uOpifTcI2E=-qlWP2 > > - pXtEkwPM8BsKd73GvX9g=en=X=0ahUKEwjhqrrX55PYAhVm5YMKHTB2A > > GM4ChDoAQhMMAY#v=onepage=apache%20license%20mysql=false > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__apr.apache.org_ > > do > > wnload.cgi=DwIFaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU= > > fs > > 67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=n53T6SD3EzUyJps9w7LjgVaY > > GA > > 5GQjR3h-9GBGppwBc=Gm3m03xhcJj7rfD05pZkfM9t5l8-aBOOZCwJVf4as5g= > > > > 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:matthewvit...@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 Devel
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.fi...@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:matthewvit...@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.fi...@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=DwIFaQ=qS4goWBT7poplM69 > > zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4g > > Tao=n53T6SD3EzUyJps9w7LjgVaYGA5GQjR3h-9GBGppwBc=-fxY4QiBU8SayGVEzX > > 8LVPEPzmgsYP6ANRsuTUkHkrY= > > lpg=PA14=apache+license+mysql=bl=uOpifTcI2E=-qlWP2- > > pXtEkwPM8BsKd73GvX9g=en=X=0ahUKEwjhqrrX55PYAhVm5YMKHTB2A > > GM4ChDoAQhMMAY#v=onepage=apache%20license%20mysql=false > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__apr.apache.org_do > > wnload.cgi=DwIFaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs > > 67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=n53T6SD3EzUyJps9w7LjgVaYGA > > 5GQjR3h-9GBGppwBc=Gm3m03xhcJj7rfD05pZkfM9t5l8-aBOOZCwJVf4as5g= > > > > 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:matthewvit...@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 b
Re: cTAKES Rest Service Development - Dictionary GUI MySQL Progress + 1 Concern [EXTERNAL]
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.fi...@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:matthewvit...@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.fi...@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=DwIFaQ=qS4goWBT7poplM69 > > zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4g > > Tao=n53T6SD3EzUyJps9w7LjgVaYGA5GQjR3h-9GBGppwBc=-fxY4QiBU8SayGVEzX > > 8LVPEPzmgsYP6ANRsuTUkHkrY= > > lpg=PA14=apache+license+mysql=bl=uOpifTcI2E=-qlWP2- > > pXtEkwPM8BsKd73GvX9g=en=X=0ahUKEwjhqrrX55PYAhVm5YMKHTB2A > > GM4ChDoAQhMMAY#v=onepage=apache%20license%20mysql=false > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__apr.apache.org_do > > wnload.cgi=DwIFaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs > > 67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=n53T6SD3EzUyJps9w7LjgVaYGA > > 5GQjR3h-9GBGppwBc=Gm3m03xhcJj7rfD05pZkfM9t5l8-aBOOZCwJVf4as5g= > > > > 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:matthewvit...@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/ctake
RE: cTAKES Rest Service Development - Dictionary GUI MySQL Progress + 1 Concern [EXTERNAL]
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:matthewvit...@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.fi...@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=DwIFaQ=qS4goWBT7poplM69 > zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4g > Tao=n53T6SD3EzUyJps9w7LjgVaYGA5GQjR3h-9GBGppwBc=-fxY4QiBU8SayGVEzX > 8LVPEPzmgsYP6ANRsuTUkHkrY= > lpg=PA14=apache+license+mysql=bl=uOpifTcI2E=-qlWP2- > pXtEkwPM8BsKd73GvX9g=en=X=0ahUKEwjhqrrX55PYAhVm5YMKHTB2A > GM4ChDoAQhMMAY#v=onepage=apache%20license%20mysql=false > > https://urldefense.proofpoint.com/v2/url?u=https-3A__apr.apache.org_do > wnload.cgi=DwIFaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs > 67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=n53T6SD3EzUyJps9w7LjgVaYGA > 5GQjR3h-9GBGppwBc=Gm3m03xhcJj7rfD05pZkfM9t5l8-aBOOZCwJVf4as5g= > > 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:matthewvit...@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, > mysql:*is present because it's a n non-asf > compliant dependency used by ytex. > > Removing the exclude and addingin > mysql:mysql-connector-java 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: > > > mysql > mysql-connector-java > 6.0.6 > > > > 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]
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.fi...@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://books.google.com/books?id=HTo_AmTpQPMC=PA14; > lpg=PA14=apache+license+mysql=bl=uOpifTcI2E=-qlWP2- > pXtEkwPM8BsKd73GvX9g=en=X=0ahUKEwjhqrrX55PYAhVm5YMKHTB2A > GM4ChDoAQhMMAY#v=onepage=apache%20license%20mysql=false > > https://apr.apache.org/download.cgi > > 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:matthewvit...@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, > mysql:*is present because it's a n non-asf compliant > dependency used by ytex. > > Removing the exclude and addingin > mysql:mysql-connector-java 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: > > > mysql > mysql-connector-java > 6.0.6 > > > > 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
Hi Matthew, It's indeed a great news. Glad you cracked it. Cheers. Regards, Gandhi -Original Message- From: Matthew Vita [mailto:matthewvit...@gmail.com] Sent: Monday, December 18, 2017 11:53 AM To: dev@ctakes.apache.org; Sandeep Byatha Gururaja rao <sandeep...@arisglobal.com>; Shane Chesnutt <shanechesn...@gmail.com> Subject: cTAKES Rest Service Development - Dictionary GUI MySQL Progress + 1 Concern 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, mysql:*is present because it's a n non-asf compliant dependency used by ytex. Removing the exclude and addingin mysql:mysql-connector-java 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: mysql mysql-connector-java 6.0.6 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 This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
RE: cTAKES Rest Service Development - Dictionary GUI MySQL Progress + 1 Concern
Hi, Great job Matthew !!! Regards, Sandeep From: Matthew Vita [mailto:matthewvit...@gmail.com] Sent: Monday, December 18, 2017 11:53 AM To: dev@ctakes.apache.org; Sandeep Byatha Gururaja rao; Shane Chesnutt Subject: cTAKES Rest Service Development - Dictionary GUI MySQL Progress + 1 Concern 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, mysql:*is present because it's a n non-asf compliant dependency used by ytex. Removing the exclude and addingin mysql:mysql-connector-java 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: mysql mysql-connector-java 6.0.6 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<http://www.matthewvita.com/> This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
cTAKES Rest Service Development - Dictionary GUI MySQL Progress + 1 Concern
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, mysql:*is present because it's a n non-asf compliant dependency used by ytex. Removing the exclude and addingin mysql:mysql-connector-java 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: mysql mysql-connector-java 6.0.6 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
