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Code Block
Copyright: (c) 2004-2006 Mayo Foundation for Medical Education and Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the triple-shield Mayo logo are trademarks and service marks of MFMER. Except as contained in the copyright notice above, the trade names, trademarks, service marks, or product names of the copyright holder shall not be used in advertising, promotion or otherwise in connection with this Software without prior written authorization of the copyright holder. Licensed under the Eclipse Public License, Version 1.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.eclipse.org/legal/epl-v10.html Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

Code Block

Copyright: (c) 2004-2006 Mayo Foundation for Medical Education and
Research (MFMER).  All rights reserved.  MAYO, MAYO CLINIC, and the
triple-shield Mayo logo are trademarks and service marks of MFMER.
 
Except as contained in the copyright notice above, the trade names,
trademarks, service marks, or product names of the copyright holder shall
not be used in advertising, promotion or otherwise in connection with
this Software without prior written authorization of the copyright holder.
Licensed under the Eclipse Public License, Version 1.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
 
              http://www.eclipse.org/legal/epl-v10.html
 
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

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Type	Contact
Training contact	VKC VocabKC@mayo.edu
Developer	Division of Biomedical Informatics Mayo Clinic 200 1st ST SW Rochester, MN 55905 informatics@mayo.edu

Facilities Pertinent to Software Teams

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Directory

Description of Content

admin

Installed by default. This directory provides a centralized point for command line scripts that can be executed to perform administrative functions such as the loading, activation/deactivation, and removal of vocabulary resources.

Info

title	Note

Programmers may be interested in the code used to execute these functions. In that light, it is perhaps noteworthy to mention that this directory does not contain any source or binary code, only the scripts used to launch the admin functions.

Object code used to carry out these functions is included directly in the LexBIG runtime components. Source code is included in the /source directory in the lbAdmin-src.jar (described below).

doc

Optionally installed. This directory provides documentation related to LexBIG services, configuration, and execution. This guide is distributed in the /doc top-level directory.

/doc/javadoc

Of special interest to programmers. This directory provides the generated javadoc for model classes and public interfaces available to LexBIG programmers. Also included with each object representation is a UML-based model diagram that shows the object, its attributes and operations, and immediately linked objects. The diagrams work to provide clickable navigation through the javadoc materials.

/examples

Optionally installed. This directory provides a small number of example programs.
Refer to the README.txt file in this directory for instructions used to configure and run the example programs. The examples are intended to provide a limited interactive demonstration of LexBIG capabilities. Source and object code for the example programs is provided under the /examples/org subdirectory. Source materials are also centrally archived under the /source directory in the file lbExamples-src.jar.

/examples
/resources

Contains sample vocabulary content for reference by the example programs; use the /examples/LoadSampleData command-line script to load.

/gui

Optionally installed. This folder contains programs and supporting files to launch the LexBIG Graphical User Interface (GUI). The GUI provides convenient centralized access to administrative functions as well as support to test and exercise most of the LexBIG API. The GUI is launched using a platform-specific script file in the /gui directory. The name of the platform (e.g. Windows, OSX, etc) is included in the file name. Program source and related materials are centrally archived under the /source directory in the file lbGUI-src.jar.

/logs

Default location for log files, which can be modified by the LOG_FILE_LOCATION entry in the config.props file (see next section).

/resources

Installed by default. This directory contains resources referenced and written directly by the LexBIG runtime. It should, in general, be considered off-limits to modify or remove the content of this directory without specific guidance and reason to do so. Files typically stored to this location include the vocabulary registry (tracking certain metadata for installed content) and indexes used to facilitate query over the installed content. One file of particular interest in this directory is the /resources/config/config.props file. This file controls access to the database repository and other settings used to tune the LexBIG runtime behavior. Contents of this file should be set according to instructions provided by the LexBIG Administrator's Guide.

/runtime

Installed by default. This directory contains a Java archive (.jar) file containing the combined object code of the LexBIG runtime, LexBIG administrative interfaces, and any additional code they are dependent on. All required code for execution of LexBIG administrative and runtime services is installed to this directory.

Info

title	Note

Java programmers writing to the LexBIG runtime interfaces should always include the following files in their java classpath (listed in order of inclusion):

/runtime/lbPatch.jar - In the course of the product lifecycle, it is possible that smaller fixes will be introduced as a patch to the initially distributed runtime. Including this file in the classpath ensures automatic accessibility to the calling program without requiring adjustment. All patches are cumulative (there is at most one patch file introduced per release; all patch-level fixes are cumulative).
/runtime/lbRuntime.jar - This is the standard runtime file, including all LexBIG and dependency code required for program execution except for SQL drivers (see next).

/runtime
/sqldrivers

The JDBC drivers used to connect to database repositories are not included in the lbRuntime.jar. Instead, the runtime scans this directory for the drivers to include. This can be overridden by path settings in the config.props file.

Info

title	Note

While the LexBIG software package ships with JDBC drivers to certain open source databases such as mySQL and PostgreSQL, this folder provides a mechanism to introduce updated drivers or to add drivers for additional supported database systems. For example, the Oracle database is supported by the runtime environment. However, the drivers are not redistributed with the LexBIG software. To run against Oracle, an administrator would add a jar with the appropriate JDBC driver to this directory and then reference it in the config.props settings.

/runtime-components

Optionally installed. Due to license considerations for additional materials (as described by the license.pdf and license.txt files in the install directory), the cumulative runtime provided in the lbRuntime.jar is not redistributable. This directory contains a finer grain breakdown of object code into logical components and 3rd party inclusions. All components are redistributable under their own license agreements, which are provided along with each archive. The top-level of the /runtime-components directory contains all code produced for the LexBIG project in a single lexbig.jar file.

Info

title	Note

These files are included as an alternative to the lbRuntime.jar for code execution and redistribution. There is no need to include any of these files in the Java classpath if you are already including the lbPatch.jar and lbRuntime.jar described above.

/runtime-components/extlib

This subdirectory includes all 3rd party code redistributed with the LexBIG runtime, along with respective license agreements.

/source

Archive source directories and files described in further detail in the next table below.

/test

Optionally installed. This directory provides an automated test bucket that can be used by System Administrators to verify node installation. Note that the /runtime/config/config.props file must still be configured for database access prior to invoking the test bucket. Testcases are launched via the TestRunner command-line script. Several reporting options are provided and are further described in the LexBIG Administrator's Guide.

Info

title	Note

Programmers may be interested in referencing the source code for the test programs. These are provided in the /source directory (described in the next table).

/uninstaller

Contains an executable jar that can be invoked by an administrator to uninstall files originally introduced by the LexBIG installation.

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Component	Description
changeType	Atomic modification actions. Currently populated from a combination of Concordia, SNOMED-CT list and NCI's action list.
NCIChangeEvent	A change event as documented in ftp://ftp1.nci.nih.gov/pub/cacore/EVS/ReadMe_history.txt ^{Image Removed} . Note that date and time of the change event is recorded in the containing version. All change events for the same/date and time a recorded in the same version.

Component

Description

changeType

Atomic modification actions. Currently populated from a combination of Concordia, SNOMED-CT list and NCI's action list.

NCIChangeEvent

A change event as documented in ftp://ftp1.nci.nih.gov/pub/cacore/EVS/ReadMe_history.txt

^{Image Removed}

. Note that date and time of the change event is recorded in the containing version. All change events for the same/date and time a recorded in the same version.

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Code Block
Linux_64-lbGUI.sh Linux-lbGUI.sh OSX-lbGUI.command Windows-lbGUI.bat

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This appendix includes lists and hypertext links, where appropriate, to technical manuals, articles, scientific publications and online resources related to the LexBIG project.

Appendix B Included Materials

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`lexbig`	This archive includes the LexBIG runtime code, excluding all dependencies.
`lbGUI`	The LexBIG graphical user interface runtime code, excluding all dependencies.
`activation`	Provided by Sun's reference implementation of the JavaBeans Activation Framework (JAF) standard extension. Used for e-mail notification when runtime errors occur.
`caGrid`	Grid infrastructure to support the caBIG® community. Contains tools for creating and deploying caBIG®-compliant grid services.
`commons-cli`	Provides a simple API for working with command line arguments, options, option groups, mandatory options and so forth.
`commons-codec`	Provides implementations of common encoders and decoders such as Base64, Hex, Phonetic and URLs.
`commons-collections`	Provides a suite of classes that extend or augment the Java Collections Framework.
`commons-lang`	Provides a very common set of utility classes that provide extra functionality for classes in the `java.lang` package.
`commons-logging`	Provides a bridge between different logging libraries.
`commons-pool`	Provides a generic object pooling interface, a toolkit for creating modular object pools and several general purpose pool implementations.
`gnu-regexp`	Provides a Java language implementation of standard NFA regular expression features.
`hsqldb`	SQL relational database engine written in Java.
`icu4j`	International components for Unicode processing.
`jakarta-regexp`	Java package for processing regular expressions.
`jcalendar`	Java date chooser bean for graphically picking a date.
`jdom`	Java-based solution for accessing, manipulating, and outputting XML data from Java code.
`jena`	Java framework for building Semantic Web applications.
`junit`	Java regression test framework.
`log4j`	Runtime logging services.
`lucene-core`	Text search engine library written in Java. Provides support for regular expression-based queries. Provides stemming support for indexed concepts.
`mail`	Provided by the Sun JavaMail API. Used for e-mail notification when runtime errors occur.
`mm.mysql (drivers, 2.0.6)`	JDBC drivers for MySQL database.
`org.eclipse.*`	Used internally by LexBIG load and export extensions to access and manipulate Eclipse Modeling Framework (EMF) model representations.
`postgresql (drivers)`	JDBC drivers for PostgreSQL database.
`prefuse`	Used for graph representations in the LexBIG GUI.
`swt` `(swt.jar)`	Provides the underlying widget toolkit used by the LexBIG GUI.
`xerces`	XML parsing services.

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Appendix B Included Materials