Hi Sean, Apropos your last email, I'm never quite sure when/how to let maven access outside repositories. I notice that sometimes it is downloading the very jars I am trying to build., but if I tell it to be local only, then the build will sometimes fail because of other dependencies it needs to update. It's a bit of an octopus. And so, if I were to create a maven submodule with my permissions, how could I be sure not to contaminate the global archive when I sure don't want to..?
Peter On Mon, Mar 1, 2021 at 6:13 PM Finan, Sean <sean.fi...@childrens.harvard.edu> wrote: > Hi Sean (M.), > > I don't know if this helps at all, but I usually keep all custom code in a > separate maven submodule (e.g. ctakes-myproject) and just throw that module > reference into the main ctakes pom. There are a lot of benefits to doing > things this way, including sharing code (vcs or directly), sharing prebuilt > jars, version independency, etc. You might already do this for other > things, in which case this is just a reminder. You can still keep using > the ctakes package system which makes piper specifications easier. > > Sean > > > ________________________________________ > From: Mullane, Sean *HS <sp...@hscmail.mcc.virginia.edu> > Sent: Monday, March 1, 2021 11:19 AM > To: dev@ctakes.apache.org > Subject: RE: 4.0.0.1 patch [EXTERNAL] > > * External Email - Caution * > > > Sean, > > You're right that CuiFilterAnnotator is a custom annotator. It looks like > I will need to merge the auth changes from 4.0.0.1 into our branch and > recompile. > > Thanks, > Sean > > -----Original Message----- > From: Finan, Sean <sean.fi...@childrens.harvard.edu> > Sent: Saturday, February 27, 2021 2:33 PM > To: dev@ctakes.apache.org > Subject: Re: 4.0.0.1 patch [EXTERNAL] > > Hi Sean (Mullane), > > For the original problem: > > No Analysis > > > Component found for org.apache.ctakes.core.ae.CuiFilterAnnotator > > This means that somewhere in your piper file you have an "add" command for > an analysis engine named "CuiFilterAnnotator". > > There is no org.apache.ctakes.core.ae.CuiFilterAnnotator in ctakes 4.0.0 > or trunk: > > https://urldefense.com/v3/__https://svn.apache.org/repos/asf/ctakes/tags/ctakes-4.0.0/ctakes-core/src/main/java/org/apache/ctakes/core/ae/__;!!NZvER7FxgEiBAiR_!9EqSrWbJ5y-PF0tnZc30W49RI0H8lQQb2HgfBO659g3w5yAPh0C-ZyhCeNRsIc7y9t9Q3wkVLpM$ > > https://urldefense.com/v3/__https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/__;!!NZvER7FxgEiBAiR_!9EqSrWbJ5y-PF0tnZc30W49RI0H8lQQb2HgfBO659g3w5yAPh0C-ZyhCeNRsIc7y9t9QkmE1D-E$ > > I also cannot find a class named "CuiFilterAnnotator" in my copy of trunk > in any of the projects - including ytex. > > That leads me to believe that CuiFilterAnnotator is a custom annotator in > your local installation - which I hope that you didn't overwrite with a > copy of 4.0.0.1 > > If you can find the CuiFilterAnnotator file in your previous installation, > just copy it over in a custom jar. After rerunning you may find another > missing class, then another. Such can be the pains of working with custom > alterations. > > Sean > > ________________________________________ > From: Peter Abramowitsch <pabramowit...@gmail.com> > Sent: Friday, February 26, 2021 12:27 PM > To: dev@ctakes.apache.org > Subject: Re: 4.0.0.1 patch [EXTERNAL] > > * External Email - Caution * > > > I don't mean to butt in on another conversation, but for the UMLS > authentication to work in 4.0.0.1, you would need to replace > ctakes-dictionary-lookup-fast jar, the ctakes-dictionary-lookup.jar and for > safety's sake the ctakes-core jar too. > > Peter > > On Fri, Feb 26, 2021 at 6:01 PM Mullane, Sean *HS < > sp...@hscmail.mcc.virginia.edu> wrote: > > > Can you check my understanding of how to apply the patch? I replaced > > the ctakes-core-4.0.0.jar file in ./lib with ctakes-core-4.0.0.1.jar. > > I also replaced the user/pass values in ctakes.profile with the API key > values. > > Are there any steps I missed there? > > > > Sean > > > > -----Original Message----- > > From: Miller, Timothy <timothy.mil...@childrens.harvard.edu> > > Sent: Friday, February 26, 2021 6:41 AM > > To: dev@ctakes.apache.org > > Subject: Re: 4.0.0.1 patch [EXTERNAL] > > > > Hi Sean, > > I can't answer your primary question, but my recollection is that > > 4.0.0.1 was an absolutely minimalist change to just fix the > > authentication, so I don't think ytex would've been touched. > > Tim > > > > > > On Thu, 2021-02-25 at 17:24 +0000, Mullane, Sean *HS wrote: > > > * External Email - Caution * > > > > > > > > > Hello, > > > > > > I am just catching up with the NLM auth changes. I tried replacing > > > the ctakes-core-4.0.0.jar file with ctakes-core-4.0.0.1.jar, and am > > > getting this error: > > > > > > ERROR [PiperFileRunner] MESSAGE LOCALIZATION FAILED: Can't find > > > resource for bundle java.util.PropertyResourceBundle, key No > > > Analysis Component found for > > > org.apache.ctakes.core.ae.CuiFilterAnnotator > > > > > > I saw a message from Tim Miller from December mentioning removing > > > ytex components from ctakes-core. Was this done on the released > > > version of 4.0.0.1? We're using ytex so I wonder if that may be the > > > cause of this error. Or maybe applying the patch isn't as simple as > > > drop-in replacing the jar? (I changed the API key in my config files > > > and that seems to be working as expected). > > > > > > Thanks, > > > Sean > > > > > > > > > >
