Merge branch 'release-staging/1.6.0' into release

Author: benknoll-umn

.gitignore

@@ -9,3 +9,4 @@ target/
 *.orig
 ./distribution/src/main/resources/logs/biomedicus.log
 distribution/src/main/resources/logs/biomedicus.log
+~$*

Pipeline.pptx

@@ -10,198 +10,18 @@ This is a collaborative project that aims to serve biomedical and clinical resea
 with different texts.
 
 
-Install Guide
+Wiki
 ========================================================================================================================
 
-Along with the source code, we also release distribution of all the files required to immediately start running. You can
-download this file and appropriate model files at [http://athena.ahc.umn.edu/biomedicus-downloads/](http://athena.ahc.umn.edu/biomedicus-downloads/).
+[Our wiki on GitHub](https://github.com/nlpie/biomedicus/wiki) contains information about installation, configuration,
+use, and development of BioMedICUS.
 
-Prerequisites
-------------------------------------------------------------------------------------------------------------------------
-
-The following 3rd-party tools need to be installed to download, compile and run BioMedICUS:
-
- 1.  Java SE Development Kit 8: [download](http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html)
-
- 2.  Git: [download](http://git-scm.com) \(optional, only required for checking out the project source code\)
-
- 3.  Maven: [download](http://maven.apache.org) \(optional, only required for building the project from source\)
-
-Environment Variables
-------------------------------------------------------------------------------------------------------------------------
-
-The following environment variables need to be set:
-
- 1. JAVA_HOME: 
-
-    *   On OS X, after installing Java SE Development Kit, you can find the path to the installation by typing this
-    command:
-
-        /usr/libexec/java_home
-
-    *   Open the .bash_profile file in your favorite text editor and add the following statement:
-
-        export JAVA_HOME="path-to-java-home-from-previous-step"
-
-    *   Save the .bash_profile, close it and then run the following:
-
-        source .bash_profile
-
-    *   Try 'echo $JAVA_HOME' to make sure the environment is pointing to the right Java version (currently 1.8.0)
- 
-
-Getting BioMedICUS
-------------------------------------------------------------------------------------------------------------------------
-
-If you wish to compile BioMedICUS from source, instead of using the prepackaged version above, the following 
-instructions are provided.
-
-At a command prompt, change directories to where you want to install BioMedICUS, and then enter:
-
-    git clone https://github.com/nlpie/biomedicus.git
-
-Notes: 
-
-*    FYI: This clone command will create a subdirectory called 'biomedicus' in the current working directory and create
-     a git repository under that subdirectory.
-
-
-Downloading Large Model Files
-------------------------------------------------------------------------------------------------------------------------
-
-After having checked out biomedicus from git using the steps above, you will need to download the models file for the
-version of biomedicus you are running. You can download the data zip at
-[http://athena.ahc.umn.edu/biomedicus-downloads/](http://athena.ahc.umn.edu/biomedicus-downloads/).
-There are two options, the first is an open data set which is freely licensed UMLS data, the second zip is a umls data
-set which uses SNOMED data and requires you to log in to a NIH UTS account to verify your UMLS Metathesaurus License.
-After extracting, set the BIOMEDICUS_JAVA_OPTS java parameter biomedicus.paths.data to the location of the
-extracted data. If you are using a release version of BioMedICUS, you may instead set the paths.data configuration
-property in config/biomedicusConfiguration.yml to the location of the BioMedICUS data.
-
-    export BIOMEDICUS_JAVA_OPTS=-Dbiomedicus.paths.data=[location of data]
-
-
-Building BioMedICUS
-------------------------------------------------------------------------------------------------------------------------
-
-After cloning completes, run the following to build BioMedICUS
-
-    cd biomedicus
-    mvn clean install
-
-
-Running BioMedICUS
-------------------------------------------------------------------------------------------------------------------------
-
-Then maven install phase will create a "release" folder in the root directory of BioMedICUS. This root directory
-contains all resources necessary to run biomedicus.
-
-*   config: configuration files such as .properties
-
-*   **desc: UIMA descriptor files**
-
-    -   ae - location for pipelines/aggregates of multiple annotators
-    -   ae/annotator - standard location for annotators
-    -   ae/writer - location for writers to output analyzed documents in a specific format
-    -   ae/util - utility analysis engines
-    -   cr - location for Collection Readers, to read in documents
-    -   tools - descriptors for analysis engines in the tools module.
-    
-*   lib: Compiled and packaged modules of biomedicus and third-party libraries necessary to run biomedicus
-
-*   bin: scripts for running biomedicus tools or uima tools with the correct classpath for biomedicus
-    
-    -   AV.sh run the UIMA Annotation Viewer.
-        [UIMA help](https://uima.apache.org/d/uimaj-2.6.0/tools.html#ugr.tools.annotation_viewer)
-    -   CPM.sh run the UIMA Collection Processing Engine Configurator.
-        [UIMA help](https://uima.apache.org/d/uimaj-2.6.0/tools.html#ugr.tools.cpe)
-    -   CVD.sh run the UIMA CAS Visual Debugger.
-        [UIMA help](https://uima.apache.org/d/uimaj-2.6.0/tools.html#ugr.tools.cvd)
-    -   runClass.sh run any executable java class within the biomedicus classpath
-    -   runCPE.sh run a cpe desciptor directly without opening the visual interface
-
-After successful installation is completed, the simplest way to start is to use the default annotation pipeline with a
-UIMA provided graphical user interface - Collection Processing Manager (CPM). The simplest format for the input files is
-plain text; however, our system also currently has collection readers defined for certain XML formats as well as text
-stored in a database. Here, we will show how to run BioMedICUS on a collection of plain text files. To run the pipeline,
-first, you will need to create a local directory containing only the files to be processed
-(e.g., ./examples/plaintext/input) and move the files to be processed into the newly created directory. We would also
-recommend creating an output directory in a nearby location that will contain the output of the pipeline
-(e.g., ./examples/plaintext/output).
-
-Next, navigate to the "bin" directory under the BioMedICUS installation directory:
-
-    cd ./release/bin
-
-Next, run the CPM.sh shell script:
-
-    ./CPM.sh
-
-If you have a cpe descriptor file already created, you can load the CPM descriptor by browsing to the "File" menu in the
-CPM and selecting "Open CPE Descriptor." From there a file dialog will popup and you can browse to your CPE Descriptor
-file.
-
-You can also run a CPE directly without launching the UI by using the runCPE.sh script:
-
-    ./runCPE.sh /path/to/CpeDescriptor.xml
-
-To make it easier to start for users new to BioMedICUS and UIMA, we have included an "examples/plaintext" folder with
-the BioMedICUS distribution. This folder contains an "input" and "output" subfolders. The ./examples/plaintext/input
-folder has a few plain ASCII text files. The ./examples/plaintext/ folder also contains a predefined
-PlainTextCPM_Example.launch descriptor file that can be used to start the CPM or be loaded after the CPM has been
-started. This launch configuration has relative paths defined - relative to the current working directory from which
-CPM.sh is started. So, the best way to use it is to first switch to the "scripts" directory. Try the following:
-
-    cd ./release/scripts
-    ./CPM.sh
-
-Follow the instructions for opening a CPE Descriptor and select
-${BIOMEDICUS_HOME}/release/examples/plaintext/PlainTextCPM_Example.xml
-
-After the process completes, you can view the results with the Annotation Viewer (AV.sh) like this:
-
-    ./AV.sh 
-
-When AV starts, you can point it to the output directory ../examples/plaintext/output. You will also need to point AV to
-the type system that was used by the BioMedICUS pipeline, the type system is outputted to the same directory as the XMI
-files.
-
-
-
-IntelliJ IDEA Setup (Recommended)
-------------------------------------------------------------------------------------------------------------------------
-
-IntelliJ is Java IDE with a Community Edition licensed under the Apache 2.0 license developed by JetBrains S.R.O. You
-can find it [here](https://www.jetbrains.com/idea/)
-
-1. Select Import Project
-2. Browse to the folder that you cloned the biomedicus code into
-3. Select 'Import from external model' and 'Maven'
-
-
-Eclipse Setup
-------------------------------------------------------------------------------------------------------------------------
-
-Prerequisites: Install m2e. [link](http://eclipse.org/m2e/). Recent versions of Eclipse have maven included.
-
-1.  Open eclipse with a workspace folder that is not the BioMedICUS root directory.
-2.  Right click in the package explorer and select 'Import'
-3.  Expand the 'Maven' folder and select 'Existing Maven Projects'
-4.  Select the root directory of the BioMedICUS project using the 'Browse' button
-5.  Confirm that 'pom.xml' and a list of modules appear in the 'Projects' pane
-6.  Select 'Finish'
-7.  Under the 'Biomedicus' project in the 'developer' folder there are .launch files for the Annotation Viewer and the
-    Collection Processing Engine Configurator, they should be automatically included in the Run and Debug favorites.
-            
-
-Changing settings
-------------------------------------------------------------------------------------------------------------------------
-
-UIMA defines an annotator's settings in an XML descriptor file. These files are located in the
-release/desc folder. To change the behavior of any of the annotators,
-the available settings can be changed in the files within that folder.
+Contact and Support
+========================================================================================================================
 
-The config/biomedicus.properties contains some system-wide per-launch constants such as the location of data models.
+BioMedICUS has a [Google Group](https://groups.google.com/a/umn.edu/forum/#!forum/biomedicus) for contacting developers 
+with questions, suggestions or feedback. Also, bug reports and feature suggestions can be submitted to the Issues tab on 
+GitHub.
 
 About Us
 ========================================================================================================================
@@ -215,11 +35,6 @@ with assistance from the
 Other Resources
 ========================================================================================================================
 
-### BioMedICUS
-
- *   [Demo](http://athena.ahc.umn.edu/biomedicus/)
- *   [Source Code](https://github.org/nlpie/biomedicus)
-
 ### NLP-TAB
 
  *   [Demo](http://athena.ahc.umn.edu/nlptab)

README.md

@@ -19,27 +19,57 @@
     <parent>
         <artifactId>biomedicus</artifactId>
         <groupId>edu.umn.biomedicus</groupId>
-        <version>1.5.0</version>
+        <version>1.6.0</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 
     <artifactId>biomedicus-core</artifactId>
 
+    <properties>
+        <jackson.version>2.8.3</jackson.version>
+    </properties>
+
     <dependencies>
         <dependency>
             <groupId>com.google.inject</groupId>
             <artifactId>guice</artifactId>
-            <version>4.0</version>
+            <version>4.1.0</version>
         </dependency>
         <dependency>
             <groupId>com.google.inject.extensions</groupId>
             <artifactId>guice-multibindings</artifactId>
-            <version>4.0</version>
+            <version>4.1.0</version>
         </dependency>
         <dependency>
             <groupId>org.yaml</groupId>
             <artifactId>snakeyaml</artifactId>
-            <version>1.15</version>
+            <version>1.17</version>
+        </dependency>
+        <dependency>
+            <groupId>org.mapdb</groupId>
+            <artifactId>mapdb</artifactId>
+            <version>3.0.4</version>
+        </dependency>
+        <dependency>
+            <groupId>args4j</groupId>
+            <artifactId>args4j</artifactId>
+            <version>2.33</version>
+        </dependency>
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-databind</artifactId>
+            <version>${jackson.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.immutables</groupId>
+            <artifactId>value</artifactId>
+            <version>2.4.4</version>
+            <scope>provided</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.opennlp</groupId>
+            <artifactId>opennlp-tools</artifactId>
+            <version>1.7.2</version>
         </dependency>
     </dependencies>