Of course! You can submit a jira item regarding the documentation or if you have permissions for the wiki you can create or edit a page yourself.
Sean ________________________________________ From: Reed Villanueva <villanuevar...@gmail.com> Sent: Friday, April 6, 2018 4:20 PM To: dev@ctakes.apache.org Subject: Re: How to add /desc and /resources to intellij IDEA project? [EXTERNAL] Ok, I see, thank you. One final thing, is there some kind of mechanism for myself or others to somehow request to, say, add edits/changes to existing ctakes documentation where someone else reviews and approves it? On Fri, Apr 6, 2018 at 9:52 AM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Hi Reed, > > lookupXml is a parameter that is sent to ctakes, not the vm. But yes, you > can place "--lookupXml <path>" or simply "-l <path>" to the command line if > you are running the default pipeline. > > The lookupXml points to a configuration file that can be anywhere, such as > in your $HOME. However, you will need to edit that configuration file to > make sure that it points to your dictionary. For instance, if you copy the > default sno_rx_16ab.xml from the ctakes resources/ area you should change > the jdbcUrl property to point to your dictionary database. For instance: > > <property key="jdbcUrl" value="jdbc:hsqldb:file: > resources/org/apache/ctakes/dictionary/lookup/fast/ncit_ > plus_16ab/ncit_plus_16ab"/> > > You seem to be pretty savvy, so if you look in the default .xml the change > required should be pretty apparent. Absolute paths are acceptable. > > You can't have more than one .xml file. However, within the xml file you > can specify multiple dictionaries. > > Sean > ________________________________________ > From: Reed Villanueva <villanuevar...@gmail.com> > Sent: Friday, April 6, 2018 3:42 PM > To: dev@ctakes.apache.org > Subject: Re: How to add /desc and /resources to intellij IDEA project? > [EXTERNAL] > > I see, thanks. > So you're saying that I would do something like: add the option > "-LookupXml=$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://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki. > apache.org_confluence_display_CTAKES_Piper-2BFiles&d=DwIFaQ& > c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r= > fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m= > FLRmd8JSLqAXw9SYsRUmX3CPjtNorqZf1HjjYLhacgE&s=MlCXUnzoIy- > QakQAx18Ebp1SCMp26o-7YBvqkDEnufI&e= > > 2. > > https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki. > apache.org_confluence_display_CTAKES_Dictionary-2BCreator- > 2BGUI&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r= > fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m= > FLRmd8JSLqAXw9SYsRUmX3CPjtNorqZf1HjjYLhacgE&s=2oP9-UEq_ > Lhyvq9knIK7RCaPjgG10j_aYFs4HXlIlaQ&e= > > 3. > > https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki. > apache.org_confluence_display_CTAKES_&d=DwIFaQ&c=qS4goWBT7poplM69zy_ > 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m= > FLRmd8JSLqAXw9SYsRUmX3CPjtNorqZf1HjjYLhacgE&s= > MGt75pnvbaQqNsx48w2J8SIWjNjDNtjUGgzA5YkqdIk&e= > > Piper+File+Submitter+GUI > > 4. > > https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki. > apache.org_confluence_display_CTAKES_cTAKES-2B4.0&d=DwIFaQ& > c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r= > fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m= > FLRmd8JSLqAXw9SYsRUmX3CPjtNorqZf1HjjYLhacgE&s= > DcBEnhBIVmzN8ai7tY6bwI1mxt1Unvloz-RdvU_JqWY&e= > > > > > > > > ________________________________________ > > 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. > > > > > >
