// Define some global attributes
include::_globattr.adoc[]

[[sec_test_opt_src]]
Test optional components
~~~~~~~~~~~~~~~~~~~~~~~~
This section can be skipped if you have not downloaded any optional components.

Dependency Parser
^^^^^^^^^^^^^^^^^
The dependency parser can be tested in Eclipse:

* Using CVD: Launch ``UIMA_CVD\--dependency parser'', then load
+{inst-root-dir}/dependency parser/desc/analysis_engine/ClearParserPlaintextAggregate.xml+
* Using CPE: Launch ``UIMA_CPE\--dependency parser'', then open the CPE Descriptor
+{inst-root-dir}/dependency parser/desc/collection_processing_engine/ClearParserTestCPE.xml+,
and hit the triangle ``run'' button
* In the clinical documents pipeline: 
** Right-click clinical documents pipeline -> Build Path -> Configure Build Path, 
and add dependency parser to the Projects tab. 
** Open +{inst-root-dir}/clinical documents pipeline/desc/analysis_engine/AggregatePlaintextProcessor.xml+
and +AggregateCdaProcessor.xml+ with the Component Descriptor Editor.
** Under the ``Aggregate'' tab, click ``Add...'' and select
+{inst-root-dir}/dependency parser/desc/analysis_engine/ClearParserAE.xml+
** Re-run the CVD or CPE launch for clinical documents pipeline within Eclipse.

It can also be tested from the command line:

* Using CPE: 
** Change directory to +{inst-root-dir}/dependency parser+ 
** Run +scripts/run_CPE_GUI.sh+.  
This will set up the classpath necessary for the dependency parser,
and launch the same CPE GUI as before.
** Open +{inst-root-dir}/dependency parser/desc/collection_processing_engine/ClearParserTestCPE.xml+,
and hit the triangle ``run'' button
* In the clinical documents pipeline (requires updated source code), viewing with CVD:
** Edit +{inst-root-dir}/clinical documents pipeline/desc/analysis_engine/AggregatePlaintextProcessor.xml+,
deleting the comment marks around all instances of ``ClearParserAE''
** Edit +{inst-root-dir}/build.xml+ to delete comment marks around instances of ``dependency parser''
** While in +{inst-root-dir}+, type +ant testrun+ (assumes a working version of +ant+)

NOTE: For source code, +build.xml+ will not be present; 
copy all files from the +files for pipeline root+ project to +{inst-root-dir}+

Drug NER
^^^^^^^^
The Drug NER project can be tested in Eclipse:

* Process PlainText document:
** Using CVD: Launch ``UIMA_CVD\--Drug NER'', then load
+{inst-root-dir}/Drug NER/desc/analysis_engine/DrugAggregatePlaintextPorcessor.xml+
** Using CPE: Launch ``UIMA_CPE\--Drug NER'', then open the CPE Descriptor
+{inst-root-dir}/Drug NER/desc/collection_processing_engine/DrugNER_PlainText_CPE.xml+,
modify the Input Directory path to point to +{inst-root-dir}/Drug NER/data+, and hit the triangle ``run'' button

* Process CDA document:
** Using CVD: Launch ``UIMA_CVD\--Drug NER'', then load
+{inst-root-dir}/Drug NER/desc/analysis_engine/DrugAggregateCDAPorcessor.xml+
** Using CPE: Launch ``UIMA_CPE\--Drug NER'', then open the CPE Descriptor
+{inst-root-dir}/Drug NER/desc/collection_processing_engine/DrugNER_CPE.xml+,
modify the Input Directory path to point to 
+{inst-root-dir}/clinical documents pipeline/test/data+,
modify the Input Directory path to point to +{inst-root-dir}/clinical documents pipeline/test/data+,
and hit the triangle ``run'' button

//It can also be tested from the command line:
//
//* Using CPE: 
//** Change directory to +{inst-root-dir}/Drug NER+ 
//** Run +scripts/run_CPE_GUI.sh+.  
//This will set up the classpath necessary for the dependency parser,
//and launch the same CPE GUI as before.
//** Open +{inst-root-dir}/Drug NER/desc/collection_processing_engine/DrugNER_CPE.xml+,
//and hit the triangle ``run'' button
//
NOTE: Release {rev-short} does not support Drug NER in +build.xml+;