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.
> >
>
