You are viewing a plain text version of this content. The canonical link for it is here.
Posted to commits@ctakes.apache.org by ja...@apache.org on 2013/07/08 11:21:39 UTC
svn commit: r1500619 -
/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/AssertionConst.java
Author: james-masanz
Date: Mon Jul 8 09:21:39 2013
New Revision: 1500619
URL: http://svn.apache.org/r1500619
Log:
add additional constants for newly checked in classes. also, add a BASE_DIRECTORY constant, so different users just have 1 constant to set
Modified:
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/AssertionConst.java
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/AssertionConst.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/AssertionConst.java?rev=1500619&r1=1500618&r2=1500619&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/AssertionConst.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/AssertionConst.java Mon Jul 8 09:21:39 2013
@@ -3,21 +3,31 @@ package org.apache.ctakes.assertion.util
import java.util.ArrayList;
import java.util.HashMap;
+import javax.swing.JFrame;
+import javax.swing.JOptionPane;
+
public class AssertionConst {
/*** CHANGE THESE ***/
// Locally-stored data models
+ public static final String BASE_DIRECTORY = "/Users/m081914/"; //"/usr/data/work/data/assertion/"; // "/usr/data";
+ static {
+ if (!BASE_DIRECTORY.endsWith("/") && !BASE_DIRECTORY.endsWith("\\")) {
+ throw new RuntimeException("BASE_DIRECTORY should end with a slash");
+ }
+ }
+
// expects subdirectories: "Mayo/UMLS_CEM/*batch*/Knowtator*" "Seattle Group Health/UMLS_CEM/*batch*/Knowtator*"
- public static final String SHARP_SEED_CORPUS = "/Users/m081914/work/data/sharp/Seed Corpus/";
+ public static final String SHARP_SEED_CORPUS = BASE_DIRECTORY + "work/data/sharp/Seed Corpus/";
// expects subdirectories: ast, txt
- public static final String I2B2_2010_CORPUS = "/Users/m081914/work/data/i2b2Challenge2010/Data/i2b2Challenge2010AllTrain/";
+ public static final String I2B2_2010_CORPUS = BASE_DIRECTORY + "work/data/i2b2Challenge2010/Data/i2b2Challenge2010AllTrain/";
// expects subdirectories: ast, txt
- public static final String I2B2_2010_TEST_CORPUS = "/Users/m081914/work/data/i2b2Challenge2010/Data/Test/reports/";
+ public static final String I2B2_2010_TEST_CORPUS = BASE_DIRECTORY + "work/data/i2b2Challenge2010/Data/Test/reports/";
// raw and processed text, expects subdirectories for different sources, then subsubdirectories for train/test/dev
- public static final String DATA_DIR = "/Users/m081914/work/data/assertion/";
+ public static final String DATA_DIR = BASE_DIRECTORY + "work/data/assertion/";
// specify the model to write (train/crossvalidate) or read (test/crossvalidate).
// please rename for different configurations of training data
@@ -31,14 +41,25 @@ public class AssertionConst {
// Specify training directories for each attribute in a (semi)colon-separated list, e.g., "sharp_data/dev:sharp_data/train"
public static HashMap<String,String> trainingDirectories = new HashMap<String,String>();
static {
- trainingDirectories.put("polarity",DATA_DIR+"fromtim_sharp_data/train");
+ trainingDirectories.put("polarity", DATA_DIR + "fromtim_sharp_data/train");
// trainingDirectories.put("polarity","sharp_data/train");
// trainingDirectories.put("polarity","i2b2_data/train");
- trainingDirectories.put("conditional",DATA_DIR+"fromtim_sharp_data/train");
- trainingDirectories.put("uncertainty",DATA_DIR+"fromtim_sharp_data/train");
- trainingDirectories.put("subject",DATA_DIR+"fromtim_sharp_data/train");
- trainingDirectories.put("generic",DATA_DIR+"fromtim_sharp_data/train");
- trainingDirectories.put("historyOf",DATA_DIR+"fromtim_sharp_data/train");
+ trainingDirectories.put("conditional", DATA_DIR + "fromtim_sharp_data/train");
+ trainingDirectories.put("uncertainty", DATA_DIR + "fromtim_sharp_data/train");
+ trainingDirectories.put("subject", DATA_DIR + "fromtim_sharp_data/train");
+ trainingDirectories.put("generic", DATA_DIR + "fromtim_sharp_data/train");
+ trainingDirectories.put("historyOf", DATA_DIR + "fromtim_sharp_data/train");
+ }
+
+ public static HashMap<String,String> testDirectories = new HashMap<String,String>();
+ static {
+ testDirectories.put("polarity", DATA_DIR + "fromtim_sharp_data/test");
+// testDirectories.put("polarity","i2b2_data/test");
+ testDirectories.put("conditional", DATA_DIR + "fromtim_sharp_data/test");
+ testDirectories.put("uncertainty", DATA_DIR + "fromtim_sharp_data/test");
+ testDirectories.put("subject", DATA_DIR + "fromtim_sharp_data/test");
+ testDirectories.put("generic", DATA_DIR + "fromtim_sharp_data/test");
+ testDirectories.put("historyOf", DATA_DIR + "fromtim_sharp_data/test");
}
// If you don't want to train/cross-validate everything, comment these out
@@ -53,29 +74,48 @@ public class AssertionConst {
}
- /*** DON'T CHANGE THESE ***/
+ /*** DON'T CHANGE THESE ***/ /* TODO - please comment why these should not be changed */
// Specify input and output data locations for preprocessing. Results will be used for model training
public static HashMap<String,String> preprocessRootDirectory = new HashMap<String,String>();
static {
- preprocessRootDirectory.put(SHARP_SEED_CORPUS+"Mayo/UMLS_CEM", DATA_DIR+"sharp_data/train");
- preprocessRootDirectory.put(SHARP_SEED_CORPUS+"Seattle Group Health/UMLS_CEM", DATA_DIR+"sharp_data/train");
- preprocessRootDirectory.put(I2B2_2010_CORPUS, DATA_DIR+"i2b2_data/train");
- preprocessRootDirectory.put(I2B2_2010_TEST_CORPUS, DATA_DIR+"i2b2_data/test");
+ preprocessRootDirectory.put(SHARP_SEED_CORPUS+"Mayo/UMLS_CEM", DATA_DIR + "sharp_data/train");
+ preprocessRootDirectory.put(SHARP_SEED_CORPUS+"Seattle Group Health/UMLS_CEM", DATA_DIR + "sharp_data/train");
+ preprocessRootDirectory.put(I2B2_2010_CORPUS, DATA_DIR + "i2b2_data/train");
+ preprocessRootDirectory.put(I2B2_2010_TEST_CORPUS, DATA_DIR + "i2b2_data/test");
+
+ // If one of the preprocessRootDirectory entries above is commented out, warn user with a popup
+ if (preprocessRootDirectory.keySet().size()<4) {
+ JFrame frame = new JFrame("DialogDemo");
+ frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+
+ //Create and set up the content pane.
+ JOptionPane.showMessageDialog(frame, "Commented out one or more data dir(s) for now.. add back before using for real.");
+ frame.dispose();
+ //frame.setContentPane(newContentPane);
+
+ //Display the window.
+ //frame.pack();
+ //frame.setVisible(true);
+ }
}
+
// Specify input and output data locations for preprocessing. Results will be used for model test
public static HashMap<String,String> preprocessForTest = new HashMap<String,String>();
static {
- preprocessForTest.put(SHARP_SEED_CORPUS+"/Mayo/UMLS_CEM", DATA_DIR+"sharp_data/test");
- preprocessForTest.put(SHARP_SEED_CORPUS+"/Seattle Group Health/UMLS_CEM", DATA_DIR+"sharp_data/test");
+ preprocessForTest.put(SHARP_SEED_CORPUS+"/Mayo/UMLS_CEM", DATA_DIR + "sharp_data/test");
+ preprocessForTest.put(SHARP_SEED_CORPUS+"/Seattle Group Health/UMLS_CEM", DATA_DIR + "sharp_data/test");
}
// Specify input and output data locations for preprocessing. Results will be used for model dev
public static HashMap<String,String> preprocessForDev = new HashMap<String,String>();
static {
- preprocessForDev.put(SHARP_SEED_CORPUS+"/Mayo/UMLS_CEM", DATA_DIR+"sharp_data/dev");
- preprocessForDev.put(SHARP_SEED_CORPUS+"/Seattle Group Health/UMLS_CEM", DATA_DIR+"sharp_data/dev");
+ preprocessForDev.put(SHARP_SEED_CORPUS+"/Mayo/UMLS_CEM", DATA_DIR + "sharp_data/dev");
+ preprocessForDev.put(SHARP_SEED_CORPUS+"/Seattle Group Health/UMLS_CEM", DATA_DIR + "sharp_data/dev");
}
+ public static String evalOutputDir = "sharp_data/output";
+
+ public static String instanceGatheringOutputDir = "sharp_data/output_instancegathering";
}