I see, I have added a small change proposal to the ctakes JIRA ( https://issues.apache.org/jira/browse/CTAKES-504). Thanks.
On Fri, Apr 6, 2018 at 10:48 AM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > 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=fs67GvlGZstTpyIisCYNYmQCP6r0bc > pKGd4f7d4gTao&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. > > > > > > > > > >
