DFB and Source Code Readme for the Solaris Platform:

Preliminaries:

This document is a reference on installing tools to support Data File Builder or Source Code compilation on the Solaris Platform.

This document is relevant only if

1. You do not want to use one of the data models provided with MetaMap, but want instead to build a custom Metathesaurus, and
2. You plan to build your custom Metathesaurus on Solaris.

The Data File Builder module, which constructs a custom Metathesaurus, requires certain GNU utilities, which are included in Linux distributions, but not with Solaris. If you plan to use the Data File Builder on Solaris, you need to download and install the GNU utilities.

It is *essential* that the GNU utilities be available, because the Data File Builder scripts use the GNU versions of programs such as grep, cut, join, sort, etc., and will not work properly if the Solaris versions of these programs in /bin are used instead.

The necessary GNU utilities may be freely downloaded and can be installed using the Solaris package manager. Knowledge of pkgadd and root privileges are required to install the GNU utilities; no C compiler is required, however.

If the GNU utilities are already available on your system, you may skip to the Configuring the Shell Environment: section below.

Downloading Software:

Software necessary for the use of Data FIle Builder

GNU coreutils

The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system.

GNU sed

This is a stream editor. A stream editor is used to perform basic text transformations on an input stream (a file or input from a pipeline). The data file builder scripts are written to use GNU sed rather than the original BSD/UNIX sed.

GNu grep

Used to print lines matching a pattern from a pipe or a file. The data file builder scripts are written to use GNU grep rather than the original BSD/UNIX grep.

1. Go to Sunfreeware.com (http://www.sunfreeware.com).
2. Select your processor and Solaris OS version from the list at the top of the right frame.
3. Select coreutils-8.5 from the list of packages.
4. Pick the full package, not the source code. Download to a temporary location on your system.
5. Repeat for the other packages:
• sed
• grep

See Sunfreeware.com's Downloading/Installation page (http://www.sunfreeware.com/) for more details.

The source code to these utilities are available at http://www.gnu.org/software/.

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:

• pkgadd -d textutils-package_version-solaris_version-sparc-local
• pkgadd -d sed-package_version-solaris_version-sparc-local
• pkgadd -d grep-package_version-solaris_version-sparc-local

The tool may ask about conflicts or reuse of files. Be careful about overwriting any existing versions of these tools, e.g., in /usr/local/bin.

Configuring the Shell Environment:

The GNU utilities were installed above in /usr/local/bin. Before running BuildDataFiles, ensure that the programs grep, sed, sort, cut, join, etc. are run from /usr/local/bin and not /bin, /usr/bin, or another directory. The simplest way to do this is to run the following command (using csh or tcsh):

$ set path = ( /usr/local/bin $path )

or using sh or bash:

$ PATH=/usr/local/bin:$PATH
$ export PATH

The appropriate command should be added to your .cshrc or .bashrc file.

See the Data File Builder Documentation (http://lhncbc.nlm.nih.gov/ii/tools/MetaMap/Docs/datafilebuilder.pdf) for complete instructions on running BuildDataFiles.

Installing LVG on Solaris

If you are using something other than Linux or Windows there are special instructions for installing LVG:

Download the "Lite" version of Lvg for the year you wish to use (the example uses LVG 2010.) (see Lexical Tools Download Page: http://lexsrv3.nlm.nih.gov/LexSysGroup/Projects/lvg/current/web/release/index.html)

extract it using tar and then for each of the files in the lvg2010lite/bin directory replace:

JAVA=/export/home/lu/Development/LVG/lvg2010/bin/jre1.6.0_14/bin/java

with:

JAVA=java  (or JAVA=<jdk or jre directory path>/bin/java)

and:

LVG_DIR=/export/home/lu/Development/LVG/lvg2010

with:

LVG_DIR={where lvg is extracted}/lvg2010lite

Also modify the CLASSPATH variable: include both ${LVG_DIR} and lvg2011dist.jar.

Make sure all of the files in lvg2010lite/bin are executable:

chmod +x lvg2010lite/bin/*

Also modify the configuration file (${LVG_DIR}/data/config/lvg.properties.

More detailed instructions on how to install Lvg manually are available at the Lexical Systems WebSite. See details at URL:

http://lexsrv3.nlm.nih.gov/LexSysGroup/Projects/lvg/current/docs/userDoc/install/installManual.html

This document was generated using AFT v5.098