I see, thanks. So you're saying that I would do something like: add the option "-LookupXml=$HOME/project/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml" to the VM options in the run configurations for my intellij project? Can this be a comma-seperated list of locations?
On Fri, Apr 6, 2018 at 9:32 AM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Hi Reed, > > Wow, you went through a lot of trouble. There actually is a much simpler > solution. It does need proper documentation as it is only hinted at in [1] > and [2]. You can put a dictionary anywhere you want. Then either in your > piper file (configures pipeline) or the command line, or in the submitter > gui [3], specify the LookupXml file location. That xml file is what > points to the dictionary database and specifies how it should be used. > > The best "how-to" is on the ctakes 4.0 wiki front page, the > "pamphlet/manual" under Documentation. [4] > > Sean > > 1. > https://cwiki.apache.org/confluence/display/CTAKES/Piper+Files > 2. > https://cwiki.apache.org/confluence/display/CTAKES/Dictionary+Creator+GUI > 3. > https://cwiki.apache.org/confluence/display/CTAKES/ > Piper+File+Submitter+GUI > 4. > https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0 > > > > ________________________________________ > From: Reed Villanueva <villanuevar...@gmail.com> > Sent: Friday, April 6, 2018 3:16 PM > To: dev@ctakes.apache.org > Subject: Re: How to add /desc and /resources to intellij IDEA project? > [EXTERNAL] > > > Fixed problem. > > Running similar program in the ctakes source trunk/examples..., > I see that > FileLocator.getResource() method should be using > location=resources/org/apache/ctakes/dictionary/lookup/fast/ > sno_rx_16ab/sno_rx_16ab.script > url=file:/home/ > me > /projects/ctakes/trunk/resources/org/apache/ctakes/ > dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab.script > > Problem appears to be within FileLocator.getSearchPaths() not including the > location that I have the resource > > folder in my project ( > which does not conform to > a certain convention > that the method seems to be expecting > ( > which > was never mentioned in the ctakes documentation > so far as I could find > )). The > relevant > code snippet from the intellij > debugging tool > for the FileLocator.class > when debugging > looks like: > > ------------------------------------------------------------ > ------------------------------- > > private static Collection<String> getFileSearchPaths(String location) { > Collection<String> paths = new ArrayList(); > > // getting current working directory (I assume being registered as > my toplevel intellij project location) > > String dir = System.getProperty("user.dir"); > if (dir != null && !dir.isEmpty()) { > paths.add(dir + "/" + location); > paths.add(dir + "/resources/" + location); > } > > String cTakesHome = System.getenv("CTAKES_HOME"); > if (cTakesHome != null && !cTakesHome.isEmpty()) { > paths.add(cTakesHome + "/" + location); > paths.add(cTakesHome + "/resources/" + location); > } > > if (dir != null && !dir.isEmpty()) { > File ancestor = new File(dir); > > // then starting from the parent folder of the CWD... > > while(ancestor.getParentFile() != null) { > ancestor = ancestor.getParentFile(); > > // ...recursively building back down into each "child" > folder to form a list of possible paths following the conventions > shown here > > paths.add(ancestor + "/" + location); > paths.add(ancestor + "/ctakes/" + location); > paths.add(ancestor + "/resources/" + location); > } > } > > return paths; > } > > ------------------------------------------------------------ > ------------------------------- > > > Examining the "paths" variable before the function returns, I see that it > expects a certain absolute path convention (when the CTAKES_HOME env. > variable is not explicitly set). > > > Solution seemes to be to move the resources/ folder to one of the locations > that the ctakes-core FileLocator.class > is expecting it to be. > My previous project structure looked like: > > $HOME/ > project/ > play-space/ > /resouces ("marked as" resource root in intellij) > /desc (still don't know if I even need this, so please let me > know) > /src > <my java files> > > changing this to > > $HOME/ > project/ > play-space/ > /src > <my java files> > /resouces ("marked as" resource root in intellij) > /desc (still don't know if I even need this, so please let me know) > > seems to have fixed that issue. If there is anything else I should know > related to this issue that is not explicitly documented in the ctakes docs, > please let me know. > > > > > On Wed, Apr 4, 2018 at 1:00 PM, Reed Villanueva <villanuevar...@gmail.com> > wrote: > > > As the title states, I am having trouble understanding where to place the > > /resources (and /desc ?) folders in an intellij IDEA project that is > trying > > to use ctakes (don't work with java often). > > > > *TLDR: In intellij, how do I use the resources/ and des/ folders that > come > > in ctakes binary distributions? What is going on under the surface that > > lets these things be recognized and used (even when outside of > intellij)?* > > > > Currently I have added the jars by copying them to some folder and > > pointing intellij to that folder as a library in the File --> Project > > Structure. The way I am using the resources/ folder right now is by > having > > it in the same folder as a src folder in the intellij project ("marked > as" > > as "source" folder) and using the context menu on this resources/ copy to > > "mark as" a "resource root". > > > > Testing with a simple variation of the HelloWorldAggregatePipeline.java > > that can be found in the ctakes trunk/ctakes-examples/..., the code seems > > to run, but I see errors like: > > > > ** Configuration Error: file:$PROJECT_HOME/project/ > >> out/production/project/org/apache/ctakes/lvg/data/config/lvg.properties > >> (No such file or directory) > >> ** Error: problem of opening/reading config file: 'file:$PROJECT_HOME > >> /project/out/production/project/org/apache/ctakes/lvg/ > data/config/lvg.properties'. > >> Use -x option to specify the config file path. > >> ** Configuration Error: file:$PROJECT_HOME/project/ > >> out/production/project/org/apache/ctakes/lvg/data/config/lvg.properties > >> (No such file or directory) > >> ** Error: problem of opening/reading config file: 'file:$PROJECT_HOME > >> /project/out/production/project/org/apache/ctakes/lvg/ > data/config/lvg.properties'. > >> Use -x option to specify the config file path. > > > > > > even though, checking in that location of the project, properties is > > clearly there and I can open it and see its contents. > > > > This makes me suspect that I have not added them to the project > correctly, > > so what should be done? Thanks for advice. > > >
