Document Contents
- Items required to install the MMTx program
- Guide to the installation process
- Installing Tools to Support Data File Builder on Solaris
- Loading of optional data models after install
- Running MMTx
Items required to install and run the MMTx program and the associated programs:
- Compliance with the
MMTx Terms and Conditions
- We are currently supporting the following Operating Systems:
- Solaris
- Windows NT/2000
- Linux
- Mac OS/X
- Sun's Version of Java ®
1.4.2 or higher.
NOTE: We have confirmed this release builds
and runs with Java 1.4.2.
Please Note: The GNU version of Java does not work with MMTx.
- Ant (Only required if you plan to compile MMTx source code)
1.6 or better
- ~400mb of disk space for the programs and data files.
- ~3gb of disk space for database space to load data.
- Use of the Data File Builder module to
construct a custom target thesaurus for the Solaris platform requires
the installation of additional GNU utilities. For details, please see
Installing Tools to Support
Data File Builder section of the
Installation
instructions. The additional utilities are distributed in the
Windows® platform version and already
included in most other versions of Unix.
The Data File Builder workspace will require disk space about five times the size of your knowledge sources or at least 8.6GB.
- Copyright issues --
Please Note: Users are responsible for compliance with the UMLS copyright restrictions.
To use this application, you must have signed the UMLS agreement. The UMLS agreement requires those who use the UMLS to file a brief report once a year to summarize their use of the UMLS. It also requires the acknowledgment that the UMLS contains copyrighted material and that those copyright restrictions be respected. The UMLS agreement requires users to agree to obtain agreements for EACH copyrighted source prior to it's use within a commercial or production application.[Use of all the sources is permitted if the application is for research only.]
If you are installing this on a Windows® based machine, open a DOS command window to perform the installation. There is no InstallShield® installation process for this application. Note that on Windows®, shell environment variables have the form %VariableName%, rather than $VariableName as would be seen on in a Unix or bash shell. Installation differences due to platform will be noted below.
To Install MMTx V2.4.C do the following:
On Windows
- Make a top level directory to store the MMTx program. This will become your $MMTX_PATH area.
- Go to the Download page from the MMTx homepage.
- Download the latest version of MMTx and any of the optional data models into the directory created in #1.
- Change directory to the directory created in #1: cd $MMTX_PATH
- Extract the jar files using winzip, pkzip, or zip! There is a
bug in the java jar program that removes file permissions leaving
the embedded cygwin executables un-runable.:
- Run winzip, pkzip, or zip on the mmtx_V2.4.C_base.jar
- Run winzip, pkzip, or zip on the mmtx_V2.4.C_2006_common_data.jar
- Run winzip, pkzip, or zip on the mmtx_V2.4.C_2006_strict_data.jar
NOTE: You don't need to unjar the optional data model files if you downloaded them - they will be processed via the install program.
- This will create the nls/mmtx directory under your $MMTX_PATH directory and fill it with all of the program files needed to run the MMTx program. Now, change to the mmtx directory: cd nls/mmtx
- Run the install script: .\bin\install.bat from the DOS command window. Clicking on the script name from the explorer window will not work.
- If you have successfully installed the programs and data, you no longer need the optional data files that you might have downloaded. The *.jar files located in the $MMTX_PATH directory are no longer needed. If you are concerned about disk space, these files may now be deleted.
On Unix/Solaris/Linux
- Make a top level directory to store the MMTx program. This will become your $MMTX_PATH area.
- Go to the Download page from the MMTx homepage.
- Download the latest version of MMTx and any of the optional data models into the directory created in #1.
- Change directory to the directory created in #1: cd $MMTX_PATH
- Extract the jar files:
- Run the java jar program on the mmtx_V2.4.C_base.jar file: java sun.tools.jar.Main xf mmtx_V2.4.C_base.jar
- Run the java jar program on the mmtx_V2.4.C_2006_common_data.jar file: java sun.tools.jar.Main xf mmtx_V2.4.C_2006_common_data.jar
- Run the java jar program on the mmtx_V2.4.C_2006_strict_data.jar file: java sun.tools.jar.Main xf mmtx_V2.4.C_2006_strict_data.jar
NOTE: You don't need to unjar the optional data model files if you downloaded them - they will be processed via the install program.
- This will create the nls/mmtx directory under your $MMTX_PATH directory and fill it with all of the program files needed to run the MMTx program. Now, change to the mmtx directory: cd nls/mmtx
- Run the install script: sh ./bin/install.sh
- If you have successfully installed the programs and data, you no longer need the optional data files that you might have downloaded. The *.jar files located in the $MMTX_PATH directory are no longer needed. If you are concerned about disk space, these files may now be deleted.
A Detail for Windows users only
- Go to Sunfreeware.com (www.sunfreeware.com).
- Select your processor and Solaris OS version from the list at the top of the right frame.
- Select textutils-2.0 from the list of packages.
- Pick the full package, not the source code. Download to a temporary location on your system.
- Repeat for the other packages:
- sed-3.02
- grep-2.5
- pkgadd -d textutils-2.0-sol8-sparc-local
- pkgadd -d sed-3.02-sol8-sparc-local
- pkgadd -d grep-2.5-sol8-sparc-local
- setenv PATH /usr/local/bin:$PATH
- Change directory to the
"nls/mmtx"directory under the directory you created in Step #1 of the installation process: cd $MMTX_PATH/nls/mmtx, or under Windows: cd $MMTX_PATH\nls\mmtx. - Go to the Download page from the MMTx homepage.
- Download the optional data models you wish to have loaded into the
current directory.
NOTE: For each year you will need the YYYY_common.zip file along with any of the three models for that year (e.g., YYYY_relaxed_model.zip). You DO NOT need to download the YYYY_common.zip file IF you have already installed one of the three models previously (e.g., during the install process). - Once all of the optional models you wanted loaded have finished downloading, run unzip on each of the optional data model file such as the
2004_relaxed_model.zip or 2004_relaxed_model.zip file:
> unzip xvf 2004_relaxed_model.zip
or
> java sun.tools.jar.Main xvf 2004_relaxed_model.zip
or
> winzip 2004_relaxed_model.zip
- This will add the data model and indexes into the nls/mmtx/data directory under your $MMTX_PATH directory.
- Once done, the mmtx program can now use each optional data model
by adding one or more parameters to the mmtx command line options.
- --KSYear=2004
- --moderate_model or -B
- --relaxed_model or -C
The Datafile Builder (DFBuilder) uses CYGWIN Unix tools, when running in Windows. This install includes CYGWIN tools for Windows, and asks to add an entry in the Windows Registry to point to the version of the CYGWIN tools included here.
If you already have the CYGWIN tools loaded on your machine, answering yes to this question will point the tools to use the version that comes with MMTx.
WARNING: Answering yest to this question will change a variable in the Registry. Be sure you do not have installed software that will be affected by this change. If you are using any unix untilities like sed or grep, then you may have cygwin tools installed. If you have these tools already installed do not run this script. In particular, this script sets the HKEY_CURRENT_USER\Software\Cygnus Solutions\Cygwin\mounts v2\
If you already have GNU tools from Cygnus Solutions or other vendors, we can not assure that the Data File Builder scripts will run or create exactly the same output produced by a standard installation. If you get errors while running the scripts due to missing tools (Command not found.) then you may need to download additional CYGWIN packages. The tools distributed with the Data File Builder in mmtx/cygwin are the following packages:
In order to assure that the results are consistent, we ask that you
run the Data File Builder in an environment with the GNU
utilities. The scripts of the Data File Builder module use grep, cut,
join, sort, etc. These utilities vary slightly in behavior and options
from those found in /bin for Solaris.
The necessary utilities may be downloaded freely and are installed
using the Solaris package manager. Knowledge of the use of pkgadd and
root privileges are required to install them but you don't need a C
compiler.
If the GNU utilities are already available on your system you may skip
to the Configuring the Shell Environment section below.
Installing Tools to Support Data File Builder on the Solaris Platform:
Use if the Data File Builder module to construct a
custom target thesaurus for the Solaris platform requires an installation
of GNU utilities. If you do not wish to generate a custom thesaurus
and are using one of the provided data models
(see the next section for more), you do not need need to do this installation. If you are
going to use the Data File Builder, but are not installing on a
Solaris platform, you will not need to do this installation.
Downloading Software:
See Sunfreeware.com's Downloading/Installation page for more details.
Installing GNU Packages:
Use the tools or commands you are familar with or ask your system
administrator to install the packages you downloaded. If you have root
privileges then following sample commands may be sufficient. From the
directory into which you downloaded the packages, enter:
The tool may ask about conflicts or reuse of files. If the questions
only concern directories such as /usr/local/bin, then it is probably
OK to go ahead.
Configuring the Shell Environment:
The GNU utilities were installed above in /usr/local/bin. Before you
run BuildDataFiles, you need to run the following command or otheriwse
see to it that a 'which grep' returns "/usr/local/bin/grep" and not
"/bin/grep" or some other location.
See the Data File Builder Documentation
for complete instructions on running BuildDataFiles.
Loading of optional data models after install:
This section describes the steps necessary to install optional data models
that were either not included in the original installation process or,
missing due to errors occurring in the initial installation.
