IntelliJ experience or instructions

[taposh . d . roy]

All -

Did any one use IntelliJ? Are there any instructions using intelliJ?

Regards,

Taposh D. Roy
Health Data Lead
Decision Support Team

Kaiser Permanente
Program Office 
1950 Franklin Street, 17th Floor
Oakland, California 94588
510-987-4121 (Office)
510-206-1633 (cell)



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RE: IntelliJ experience or instructions

[Finan, Sean]

Hi Taposh,

Try the process outlined below.  I have screenshots for each step if you want 
them.  If this works (you are the first tester) then we can put it in the web 
documentation.

Sean

Fresh checkout from SVN
===
1. Start IntelliJ IDEa.
2. In the "Quick Start" menu, select "Check out from Version Control" (VCS 
icon).  
This will display a drop-down box.
3. In the drop-down box, select "Subversion".  
This will open a "Checkout from Subversion" dialog.

4. In the "Checkout from Subversion" dialog, click the "+" button in the top 
left to add a new Repository.  
This will open a "New Repository Location" dialog.
5. In the "New Repository Location" dialog, enter the svn checkout location of 
cTakes.
6. Click "Ok".  
This will inspect the repository.
7. Click the "Expand" triangle.  
This should display the directory listing of trunk.
8. Click "Checkout".  
This will open a "Destination Directory" dialog.

9. Enter a local directory in which to keep trunk (your sandbox).
10. Click "Ok".  This will open a "Checkout Options" dialog.  
The default options ("Head", etc.) are fine for most users.
11. Click "Ok".  
This will open a "Working Copy Format" dialog.
12. Select a (version) format and click "Ok".  I use version 1.8, but any 
should be fine.  
This will start the actual checkout and display a progress dialog.  The 
checkout may take a little while.

13. After the checkout has completed, you a new dialog will ask you if you'd 
like to open the project.  Click "No".


Import Project from Maven
=
A local repository is needed.  If you do not yet have one, follow any 
instructions on this wiki for checking out cTakes.
1. Start IntelliJ IDEa.
2. In the "Quick Start" menu, select "Import Project".
This will open a "Select File or Directory to Import" dialog.
3. Browse to your local cTakes repository root directory and select the pom.xml 
file.
4. Click "Ok".
This will open an "Import Project from Maven" dialog.
5. Make sure the "Search for projects recursively" box is selected, just in 
case any cTakes modules are not in the pom.
6. Make sure that "Create IntelliJ IDEa modules for aggregator projects" is not 
selected.
If you plan to add new module, 'disable' a present cTakes module or make other 
changes to the main pom.xml, check the "Import Maven projects automatically" 
box.
See also: http://www.jetbrains.com/idea/webhelp/maven-importing.html
7. Make sure that "Create module rgoups for multi-module Maven projects" is not 
selected.
8. Make sure that "Keep source and test folders on reimport is selected.
9. Make sure that "Exclude build directory (%PROJECT_ROOT%/target)" is selected.
10. Make sure that "Use Maven output directories" is selected.
11. Make sure that the "Generated sources folders" option "Detect 
automatically" is selected.
12. For the "Phase to be used for folders update" the default option 
"process-resources" should be fine.
13. For the "Automatically download" options, you may select what you like, but 
be wary that if broken code has been checked in you may need to revert manually.
14. The default "Dependency types" are fine.
15. Click "Environment settings...".
This will open a dialog that can be used to set options about the Maven 
environment.
16. The default maven environment settings should be fine.  If $M2_HOME is not 
set in your environment you may select a "Maven home directory", but it is 
better to set $M2_HOME in your environment.
17. Click "Next".
This will inspect the cTakes Maven settings and search for profiles.  It should 
display a dialog with the possible cTakes profiles.
If you plan to run the UIMA CVD or CPE then select the appropriate profile.  
Neither is necessary
18. Click "Next".
This will open an "Import" dialog with the current version of cTakes displayed.
19. Click "Next".
This will open a dialog allowing you to select a Java SDK version.
20. Click the "+" button in the top left.
This will display a drop-down box with options for an SDK.
21. Select "JDK".
This will open a dialog to select a Java JDK directory.
22. Navigate to a directory with a JDK and click "Ok".  
This will display a listing of the file paths associated with the selected JDK.
23. Click "Next".

24. Click "Ok/Next???"  Didn't see dialog.
The project will load.  This may take a while.
25. Important: If you are asked about adding and .iml files to svn, click "No". 
 

26. You should now see the full cTakes project structure in IntelliJ.


Compile with Maven
===
1. Open the "Maven Projects" Tool Window using the button on the left side of 
the window.  
If you do not see it, Use the main Menu > View > Tool Windows > Maven Projects.
If you would like to permanently add the button to the UI, use Menu > View > 
Tool Buttons.
See also: http://www.jetbrains.com/idea/webhelp/maven-projects-tool-window.html
2. Select the "Expand" triangle next to "Apache cTAKES" and then its child node 
"Lifecycle".
This will display standard maven goals.

BagOfCuisGenerator.java, same idea for getConceptText()

[Maite Meseure Hugues]

Hi everyone,

I am currently working on BagOfCuisGenerator, and I would like to add the
concept text to the output.
I 've seen some discussions about getting the original text and UMLS
preferred text in addition to the cui. Can someone give me pointers to do
that?
Thanks in advance for your time.

Maite

-- 
--
 Maïté Meseure Hugues

RE: BagOfCuisGenerator.java, same idea for getConceptText()

[Finan, Sean]

Try something like the following for output:

   private int extractFeatures( final IdentifiedAnnotation annotation )  {
  // Extract the IdentifiedAnnotation itself
  final Collection umlsInfos = getUmlsInfos( annotation, 
_printSnomed );
  if ( umlsInfos  == null ) {
 return 0;
  }
  final int begin = annotation.getBegin();
  final int end = annotation.getEnd();
  final String annotationText = annotation.getCoveredText();
  final int polarity = annotation.getPolarity();
  int count = 0;
  for ( String umlsInfo : umlsInfos ) {
 saveAnnotation( annotationText, umlsInfo, polarity, begin, end );
 count++;
  }
  return count;
   }

   static private Collection getUmlsInfos( final IdentifiedAnnotation 
identifiedAnnotation ) {
  final FSArray fsArray = identifiedAnnotation.getOntologyConceptArr();
  if ( fsArray == null ) {
 return Collections.emptySet();
  }
  final FeatureStructure[] featureStructures = fsArray.toArray();
  final Set umlsInfos = new HashSet( 
featureStructures.length );
  for ( FeatureStructure featureStructure : featureStructures ) {
 final OntologyConcept ontologyConcept = (OntologyConcept) 
featureStructure;
 String info = null;
 if ( ontologyConcept instanceof UmlsConcept ) {
final UmlsConcept umlsConcept = (UmlsConcept) ontologyConcept;
info = umlsConcept.getCui();
final String tui = umlsConcept.getTui();
if ( tui != null && !tui.isEmpty() ) {
   info += "_" + tui;
}
final String preferredText = umlsConcept.getPreferredText();
if ( preferredText != null && !preferredText.isEmpty() ) {
   info += " = \"" + preferredText + "\"";
}
umlsInfos.add( info );
 }
  }
  return umlsInfos;
   }

   public void saveAnnotation( final String spannedText, final String umlsInfo, 
final int polarity,
   final int begin, final int end  )  {
  final String text = begin + "," + end + " " + (polarity < 0 ? "-" : " ") 
+ umlsInfo + " " + spannedText;
  if ( _writer == null ) {
 System.out.println( text );
 return;
  }
  try {
 _writer.write( text );
 _writer.newLine();
  } catch ( IOException ioE ) {
 logger.error( ioE.getMessage() );
  }
   }
-Original Message-
From: Maite Meseure Hugues [mailto:meseure.ma...@gmail.com] 
Sent: Thursday, February 12, 2015 2:46 PM
To: dev@ctakes.apache.org
Subject: BagOfCuisGenerator.java, same idea for getConceptText()

Hi everyone,

I am currently working on BagOfCuisGenerator, and I would like to add the 
concept text to the output.
I 've seen some discussions about getting the original text and UMLS preferred 
text in addition to the cui. Can someone give me pointers to do that?
Thanks in advance for your time.

Maite

--
--
 Maïté Meseure Hugues

RE: BagOfCuisGenerator.java, same idea for getConceptText()

[Finan, Sean]

Oh yeah - use the -fast dictionary to get preferred text.  The fastest way to 
get cuis only is with CuisOnlyPlaintextUMLSProcessor.  If you want polarity 
make sure you uncomment the section with PolarityCleartkAnalysisEngine.

Sean

-Original Message-
From: Maite Meseure Hugues [mailto:meseure.ma...@gmail.com] 
Sent: Thursday, February 12, 2015 2:46 PM
To: dev@ctakes.apache.org
Subject: BagOfCuisGenerator.java, same idea for getConceptText()

Hi everyone,

I am currently working on BagOfCuisGenerator, and I would like to add the 
concept text to the output.
I 've seen some discussions about getting the original text and UMLS preferred 
text in addition to the cui. Can someone give me pointers to do that?
Thanks in advance for your time.

Maite

--
--
 Maïté Meseure Hugues