Section |
---|
Column |
---|
| Panel |
---|
title | Contents of this Page |
---|
| |
|
Column |
---|
Include Page |
---|
| CTAKES:Menu cTAKES 3.0 to IncludeCTAKES: |
---|
| Menu cTAKES 3.0 to Include |
---|
|
|
|
...
Eclipse step by step install instructions
Preparing Java
...
...
Preparing Eclipse
If you are going to use Eclipse for development then follow these instructions.
Step | Example |
---|
1. Download and install Eclipse 4.2+.
(optional) It is recommended that you start a new workspace to keep your cTAKES projects separate from other work. | No example |
2. Subversion Eclipse plug-in (based on Subversive site). We will use the one called "Subversive - SVN Team Provider"
Help -> Install New Software... Select the current Eclipse release (in the case of Eclipse 4 it is Juno) for the "Work with" field:
Code Block |
---|
| Juno - http://download.eclipse.org/releases/juno |
Expand the Collaboration category. Select "Subversive SVN Team Provider". Click Next. Click Next. Agree to the license agreement. Click Finish. Restart Eclipse. |
|
3. Subversion team provider connectors 1.7+.
After restarting Eclipse a dialog will ask you to install an SVN Kit for the Team Provider. Select SVN Kit 1.7 or greater. Click Finish. Click Next. Click Next. Agree to the license agreement. Click Finish. Accept the security warning (if one appears). Restart Eclipse. |
|
4. Maven is already part of Eclipse, but more integration to Maven commands is needed.
Help -> Install New Software... Select the current Eclipse release (in the case of Eclipse 4 it is Juno) for the "Work with" field:
Code Block |
---|
| Juno - http://download.eclipse.org/releases/juno |
Expand the Collaboration category. Select "m2e - Maven Integration for Eclipse". Click Next. Click Finish. Restart Eclipse. |
|
5. Maven SCM connector.
File -> Import ... -> Maven -> Check out Maven Projects from SCM. Click Next. Click the "m2e Marketplace" link. You are now in the m2e Marketplace not the Eclipse Marketplace. Scroll to and select m2e-subversive. Click Finish. Leave the defaults to install the "Maven SCM Handler for Subversive" and click Next. Click Next. Accept the license agreement. Click Finish. Accept the security warning (if one appears). Restart Eclipse. |
|
Compile a release in Eclipse
Step | Example |
---|
1. Import the cTAKES projects using Maven.
File -> Import ... -> Maven -> Check out Maven Projects from SCM. Click Next. |
|
Info |
---|
The following location is the main trunk of cTAKES. See how cTAKES treats the trunk, branches, and tags in the developer FAQs. |
2. For SCM URL use "svn" in the drop-down and this in the text field Code Block |
---|
| https://svn.apache.org/repos/asf/ctakes/trunk |
Click Finish. Eclipse will download and build all of the cTAKES sub-projects including running jcasgen as needed. Info |
---|
Due to the way Maven and Eclipse work together you will see two copies of the sub-projects in Eclipse. If you look into your workspace directories there is only one set of underlying files. |
|
|
3. Download cTAKES 3.0 Dictionaries and models. Info |
---|
Due to licensing considerations and easy of installability, one download from an external location was established with all the resources you will need. Licensing for these resources is found within the download. |
Info |
---|
Download time will be commensurate with 1GB of data. |
Windows: Go to cTAKES resources and download the ZIP file with a matching version from the ctakesresources project. Unzip the files into a temporary location such as C:\temp.
Linux: Obtain the URL of the version matching ZIP file from cTAKES resources, get the file, and unzip to a temporary location.
| Windows:
Linux: Code Block |
---|
| cd /tmp
wget http://sourceforge.net/projects/ctakesresources/files/ctakes-resources-3.0.1.zip
sudo unzip ctakes-resources-3.0.1.zip |
|
4. Copy (or move) the resources to cTAKES_HOME. With Eclipse, cTAKES_HOME will be your workspace location followed by the project name "ctakes". Copy the contents of the temporary resources directory (and all sub-directories) to <cTAKES_HOME>/ctakes-dictionary-lookup/resources. Info |
---|
There may be conflicts while taking this action. Overwrite the cTAKES_HOME files with those in the resources download. |
| Windows: Code Block |
---|
| xcopy /s C:\temp\ctakes-resources-3.0.1\resources C:\Users\<userID>\workspace\ctakes\ctakes-dictionary-lookup\resources |
Linux: Code Block |
---|
| cp -R /tmp/resources/* <LINUX_ECLIPSE_WORKSPACE_HOME>/ctakes/ctakes-dictionary-lookup/resources |
|
5. Refresh Eclipse.
You must refresh your Eclipse projects to make sure that Eclipse knows about the new directories and data. | No example |
6. Add ctakes-dictionary-lookup/resources as a folder to the classpath. You will need to repeat this step for EACH project that needs access to those resources (nearly all of them do except for ctakes-relation-extractor). For example:
Open the properties on the top-level project ctakes-clinical-pipeline. For Eclipse, do not select the one under the ctakes project but the sibling to that at the highest level. Select Java Build Path -> Libraries tab -> Add Class Folder ... button. Select the resources directory under the ctakes-dictionary-lookup. Click OK on all dialogs until you are out of the sequence.
|
|
7. UMLS user ID and password. Usually the dictionaries are required to process data. If you plan to utilize the UMLS dictionaries you must pass your UMLS user ID and password to the pipeline. There are several ways to do this - select one. Environment variable - Set or export environment variable
No Format |
---|
ctakes.umlsuser=<username>, ctakes.umlspw=<password>
|
Add the system properties to the Java arguments for a run configuration (shown in the next cell). Navigate to ctakes-clinical-pipeline -> resources -> launch > UIMA_<CVD | CPE>GUI--clinical_documents pipeline.launch. Right-click on the launch file and select Run-As -> Run Configurations... In the Arguments tab enter these parameters in the VM. Click Apply.
No Format |
---|
-Dctakes.umlsuser=<username> -Dctakes.umlspw=<password>
|
- Change the UMLSUser and UMLSPW <nameValuePair> strings in these descriptor files with your UMLS username and password.
|
|
...
Step | Example |
---|
1. Launching the UIMA CAS Visual Debugger (CVD) or the Collection Processing Engine (CPE) from Eclipse can now be accomplished in the ctakes-clinical-pipeline project. Navigate to:
Code Block |
---|
| <cTAKES_HOME>
\ctakes-clinical-pipeline
\resources
\launch
\UIMA_<CVD | CPE>GUI--clinical_documents pipeline.launch |
where you must select between CVD and CPE in the command. Right-click on the launch file and select Run-As -> UIMA_<CVD | CPE>GUI-clinical_documents. Info |
---|
Note: Don't forget to set the location of the resources and your UMLS user ID and password if you have not done so for a particular project or run configuration. |
|
|
2. (Optional) Process data.
Now that you can launch the tools, the User Guide has steps to walk you through processing test data if you want to go there. Note |
---|
The User Guide describes files in the form that they came in the binary distributions. That form does not match the form when you checkout the code as we have done here.
For developers there is only one directory named "desc" in a path. When you use the User Guide you must ignore the first "desc" shown in a path. |
| No example |
...
Step | Example |
---|
1. Find UIMA Eclipse plug-ins.
Help> Install New Software...> Add... button Set a repository name and this site location Code Block |
---|
| http://www.apache.org/dist/uima/eclipse-update-site
|
Click OK.
|
|
2. Install UIMA Eclipse plug-ins.
Select the UIMA Eclipse tooling and runtime support. Click Next. Leave the defaults and click Next. Accept the license agreement. Click Finish. Restart Eclipse. |
|
3. (optional) Verify the installation of the UIMA Plug-ins. Go to Help -> About Eclipse -> Installation Details -> Plug-ins. You will see a dialog such as that i the next cell with plug-in names starting with "UIMA Eclipse:". |
|
Command line minimal install instructions
...
Command line step by step install instructions
Preparing Java
...
...
Preparing command line tools
Step | Example |
---|
1. Install an SVN client. Info |
---|
Run this command to check the setup. svn --version |
Windows: We used a binary package of Apache Subversion from SlikSVN. Apache has a larger list here. Download and run the MSI file. Click Next. Accept the license agreement. Click Next. Click Next. Select Typical. Select Install. Wait Click Finish. Exit and restart any command prompts that were open.
Linux:
Code Block |
---|
| sudo apt-get install subversion |
| Windows:
Linux:
Code Block |
---|
| The following extra packages will be installed:
libapr1 libaprutil1 libneon27-gnutls libsvn1
Suggested packages:
subversion-tools db4.8-util
The following NEW packages will be installed:
libapr1 libaprutil1 libneon27-gnutls libsvn1 subversion
...
Processing triggers for python-central ...
Processing triggers for man-db ...
Setting up libapr1 (1.4.2-7ubuntu2) ...
Setting up libaprutil1 (1.3.9+dfsg-5ubuntu3) ...
Setting up libneon27-gnutls (0.29.5-3) ...
Setting up libsvn1 (1.6.12dfsg-4ubuntu2) ...
Setting up subversion (1.6.12dfsg-4ubuntu2) ... |
|
2. Install a Maven 3.0+ client.
Windows: We downloaded Apache Maven file apache-maven- 3.0.4 -bin.zip. Install instructions are on the same page. from http://archive.apache.org/dist/maven/binaries/ Unzip the file to the root drive. C:\apache-maven-3.0.4 will be your MAVEN_HOME.
Linux: We downloaded Apache Maven file apache-maven- 3.0.4 -bin.tar.gz. Install instructions are on the same page. from http://archive.apache.org/dist/maven/binaries/ Unzip the file to /usr/local/apache-maven-3.0.4 which will be your MAVEN_HOME.
Code Block |
---|
| cd /tmp
wget http://archive.apache.mirrors.pair.com/maven/maven-3/3.0.4org/dist/maven/binaries/apache-maven-3.0.4-bin.tar.gz
tar -xvf apache-maven-3.0.4-bin.tar.gz -C /usr/local |
| Windows:
Linux:
|
3. Set the Maven environment variable values - M2_HOME=<MAVEN_HOME> M2=<MAVEN_HOME>/bin PATH=<existing Path>;<MAVEN_HOME> where MAVEN_HOME is the path you unzipped to. Info |
---|
Run this command to check the setup. mvn --version |
Windows: Right-click on Computer > Properties > Advanced System Settings > Advanced tab > Environment Variables button > New button for User variables. Once the values are entered click OK until you are out of the dialog series.
Linux:
Code Block |
---|
| export M2_HOME=/usr/local/apache-maven-3.0.4
export M2=$M2_HOME/bin
export PATH=$PATH:$M2 |
Note |
---|
It is left to the user to make environment variables permanent in their development environment. |
| Windows:
Linux:
Code Block |
---|
| tbleeker@system:~$ export
...
declare -x M2="/usr/local/apache-maven-3.0.4/bin"
declare -x M2_HOME="/usr/local/apache-maven-3.0.4"
declare -x PATH="/usr/lib/jvm/java-6-sun/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/apache-maven-3.0.4/bin" |
|
...
Step | Example |
---|
1. Checkout the cTAKES project. Info |
---|
The following location is the main trunk of cTAKES. See how cTAKES treats the trunk, branches, and tags in the developer FAQs. |
Windows/Linux:
Code Block |
---|
| cd /
svn co https://svn.apache.org/repos/asf/ctakes/trunk cTAKES-3.0 |
The parameter on the end will be created as a new directory in your current location. Note |
---|
For Linux, make sure that you have write access to the directory that you are in. |
We will refer to the directory you specify at the end of the checkout command as <cTAKES_HOME>. | Windows: Code Block |
---|
| C:\>cd /
C:\>svn co https://svn.apache.org/repos/asf/ctakes/trunk cTAKES-3.0
...
A ctakes-3.0\ctakes-type-system\pom.xml
A ctakes-3.0\ctakes-type-system\.settings
A ctakes-3.0\ctakes-type-system\.settings\org.eclipse.jdt.core.prefs
A ctakes-3.0\ctakes-type-system\.settings\org.eclipse.core.resources.prefs
A ctakes-3.0\ctakes-type-system\desc
A ctakes-3.0\DISCLAIMER
Checked out revision 1433729.
C:\>cd cTAKES-3.0
C:\cTAKES-3.0> |
Linux: Code Block |
---|
| tbleeker@system:~$ cd /
tbleeker@system:/$ svn co https://svn.apache.org/repos/asf/ctakes/trunk cTAKES-3.0
...
A ctakes-3.0/ctakes-type-system/pom.xml
A ctakes-3.0/ctakes-type-system/.settings
A ctakes-3.0/ctakes-type-system/.settings/org.eclipse.jdt.core.prefs
A ctakes-3.0/ctakes-type-system/.settings/org.eclipse.core.resources.prefs
A ctakes-3.0/ctakes-type-system/desc
A ctakes-3.0/DISCLAIMER
Checked out revision 1434842.
tbleeker@system:/$ cd cTAKES-3.0/
tbleeker@system:/cTAKES-3.0$ |
|
2. Download cTAKES 3.0 Dictionaries and models. Info |
---|
Due to licensing considerations and easy of installability, one download from an external location was established with all the resources you will need. Licensing for these resources is found within the download. |
Info |
---|
Download time will be commensurate with 1GB of data. |
Windows: Go to cTAKES resources and download the ZIP file with a matching version from the ctakesresources project. Unzip the files into a temporary location such as C:\temp.
Linux: Obtain the URL of the version matching ZIP file from cTAKES resources, get the file, and unzip to a temporary location.
| Windows:
Linux: Code Block |
---|
| cd /tmp
wget http://sourceforge.net/projects/ctakesresources/files/ctakes-resources-3.0.1.zip
sudo unzip ctakes-resources-3.0.1.zip |
|
3. Copy (or move) the resources to cTAKES_HOME. Copy the contents of the temporary resources directory (and all sub-directories) to <cTAKES_HOME>/ctakes-dictionary-lookup/resources. Info |
---|
There may be conflicts while taking this action. Overwrite the cTAKES_HOME files with those in the resources download. |
| Windows: Code Block |
---|
| xcopy /s C:\temp\ctakes-resources-3.0.1\resources C:\cTAKES-3.0\ctakes-dictionary-lookup\resources |
Linux: Code Block |
---|
| sudo cp -R /tmp/resources/* /cTAKES-3.0/ctakes-dictionary-lookup/resources |
|
4. Compile the complete set.
Make sure you are in the proper directory.
Windows/Linux: Code Block |
---|
| cd cTAKES-3.0
mvn clean compile |
Note |
---|
For Linux, make sure you are using the user that has access to the files in your cTAKES directory. |
Info |
---|
Instead of "compile" you can use the maven target called "package" to compile and build all the cTAKES deliverables. Package is convenient in situations like running cTAKES outside of maven with custom processes/scripts because it will bundle up all of the 3rd party and transient dependencies.
|
| Windows/Linux: Code Block |
---|
| ...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] Apache cTAKES ..................................... SUCCESS [59.140s]
[INFO] Apache cTAKES common type system .................. SUCCESS [41.856s]
[INFO] Apache cTAKES utils ............................... SUCCESS [6.255s]
[INFO] Apache cTAKES core ................................ SUCCESS [17.940s]
[INFO] Apache cTAKES part-of-speech tagger ............... SUCCESS [5.148s]
[INFO] Apache cTAKES chunker ............................. SUCCESS [3.027s]
[INFO] Apache cTAKES document preprocessor ............... SUCCESS [4.118s]
[INFO] Apache cTAKES dictionary lookup ................... SUCCESS [1:14.740s]
[INFO] Apache cTAKES context dependent tokenizer ......... SUCCESS [5.975s]
[INFO] Apache cTAKES LVG lexical tools ................... SUCCESS [7.831s]
[INFO] Apache cTAKES named entity contexts ............... SUCCESS [4.743s]
[INFO] Apache cTAKES Constituency Parser ................. SUCCESS [9.516s]
[INFO] Apache cTAKES Dependency Parser ................... SUCCESS [32.386s]
[INFO] Apache cTAKES Assertion's zoner ................... SUCCESS [2.152s]
[INFO] Apache cTAKES Assertion ........................... SUCCESS [12.200s]
[INFO] Apache cTAKES ctakes-clinical-pipeline ............ SUCCESS [4.446s]
[INFO] Apache cTAKES Relation Extractor .................. SUCCESS [13.634s]
[INFO] Apache cTAKES CoReference Resolver ................ SUCCESS [8.923s]
[INFO] Apache cTAKES Drug NER ............................ SUCCESS [6.958s]
[INFO] Apache cTAKES Side Effects ........................ SUCCESS [7.566s]
[INFO] Apache cTAKES Smoking Status ...................... SUCCESS [8.377s]
[INFO] Apache cTAKES Pad Term Spotter .................... SUCCESS [9.048s]
[INFO] Apache cTAKES Temporal Information Extraction ..... SUCCESS [33.993s]
[INFO] Apache cTAKES Distribution ........................ SUCCESS [17:59.809s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 24:22.120s
[INFO] Finished at: Wed Jan 16 17:44:35 CST 2013
[INFO] Final Memory: 41M/181M
[INFO] ------------------------------------------------------------------------
... |
|
5. Add the resources as a folder to the classpath. Make sure the current path or dot (.) is in your CLASSPATH environment variable accessible to the process maven is running in. | No example |
6. UMLS user ID and password. Usually the dictionaries are required to process data. If you plan to utilize the UMLS dictionaries you must pass your UMLS user ID and password to the pipeline. There are several ways to do this - select one. - Environment variable - Set or export environment variables.
Refer to the Eclipse documentation above for more information. Add the system properties to the Java arguments for the maven environment. Add these parameters to the MAVEN_OPTS environment variable in the next section as you run the commands to process documents. No Format |
---|
-Dctakes.umlsuser=<username> -Dctakes.umlspw=<password>
|
Make the ID and password specific to you. - Change the UMLSUser and UMLSPW <nameValuePair> strings in these descriptor files with your UMLS username and password.
Refer to the Eclipse documentation above for more information.
| No example |
...
Step | Example |
---|
1. Launching the UIMA CAS Visual Debugger (CVD) or the Collection Processing Engine (CPE) can now be accomplished in the ctakes-clinical-pipeline project:
Windows: Code Block |
---|
| cd \cTAKES-3.0
set MAVEN_OPTS=-Xmx2g -Xms1g
mvn -Prun<CVD|CPE> compile |
Linux: Code Block |
---|
| cd /cTAKES-3.0
export MAVEN_OPTS="-Xmx2g -Xms1g"
mvn -Prun<CVD|CPE> compile |
where you must select between CVD and CPE in the command. |
|
2. (Optional) Process data.
Now that you can launch the tools, the User Guide has steps to walk you through processing test data if you want to go there. Note |
---|
The User Guide describes files in the form that they came in the binary distributions. That form does not match the form when you checkout the code as we have done here.
For developers there is only one directory named "desc" in a path. When you use the User Guide you must ignore the first "desc" shown in a path. |
| No example |
Next Steps
The cTAKES 3.0 Component Use Guide will help you to understand, in great detail, each of the cTAKES components that have been installed. In some cases you can learn how to improve the components.
Also, before you go on to process text in production you will need to consider dictionaries and models. cTAKES does not distribute from Apache a complete dictionary capable of annotating production data. The models provided have been trained on data that may not match your data well enough to be effective. In most cases, you will need to modify the dictionaries and train models on your own data to be effective.