Merge pull request #164 from JULIELab/v2.6

V2.6

.github/maven-settings.xml

@@ -0,0 +1,24 @@
+<?xml version="1.0" ?>
+<settings>
+    <profiles>
+        <profile>
+            <id>sonatype-snapshots</id>
+            <repositories>
+                <repository>
+                    <id>sonatype-nexus-snapshots</id>
+                    <name>Sonatype Nexus Snapshots</name>
+                    <url>https://oss.sonatype.org/content/repositories/snapshots</url>
+                    <releases>
+                        <enabled>false</enabled>
+                    </releases>
+                    <snapshots>
+                        <enabled>true</enabled>
+                    </snapshots>
+                </repository>
+            </repositories>
+        </profile>
+    </profiles>
+    <activeProfiles>
+        <activeProfile>sonatype-snapshots</activeProfile>
+    </activeProfiles>
+</settings>

.github/workflows/maven.yml

@@ -0,0 +1,33 @@
+# This workflow will build a Java project with Maven
+# For more information see: https://help.github.com/actions/language-and-framework-guides/building-and-testing-java-with-maven
+
+name: Java CI with Maven
+
+on:
+  push:
+    branches: [ master, v2.6 ]
+  pull_request:
+    branches: [ master, v2.6 ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Set up Python 3.7
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.7
+      - name: Install python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flair==0.11.3
+      - uses: actions/checkout@v2
+      - name: Set up JDK 11
+        uses: actions/setup-java@v2
+        with:
+          java-version: '11'
+          distribution: 'adopt'
+      - name: Build with Maven
+        run: mvn -B package --file pom.xml --settings .github/maven-settings.xml

.gitignore

@@ -11,3 +11,4 @@ target
 **/*.iml
 /julie-xml-tools.jar
 
+/jcore-pmc-db-reader/src/test/resources/hiddenConfig

.travis.yml

@@ -6,8 +6,8 @@ addons:
     sources:
       - deadsnakes
     packages:
-      - python3.6
-      - python3.6-dev
+      - python3.7
+      - python3.7-dev
 
 env:
   global:
@@ -19,7 +19,7 @@ env:
   - # GPG_KEY_NAME
   - secure: 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
   - # GPG_PASSPHRASE
-  - PYTHON=/usr/bin/python3.6
+  - PYTHON=/usr/bin/python3.7
 
 before_install:
   - |
@@ -31,11 +31,11 @@ before_install:
     if ! find "$HOME/pip-cache" -mindepth 1 -print -quit 2>/dev/null | grep -q .; then
       $PYTHON -m pip download --destination-directory="$HOME/pip-cache" flair
     fi
-    sudo -H $PYTHON -m pip install --find-links="$HOME/pip-cache" flair==0.4.5
+    sudo -H $PYTHON -m pip install --find-links="$HOME/pip-cache" flair==0.6.1 torch==1.7.1
   - #./travis-deployment/install-flair-nightly.sh
   - export BOTO_CONFIG=/dev/null
 install: mvn install -DskipTests=true -Dmaven.javadoc.skip=true -B -V
-script: mvn -T 1C test -B
+script: mvn -T 2C test -B
 
 cache:
   directories:
@@ -51,4 +51,4 @@ deploy:
   skip_cleanup: true
   on:
     all_branches: true
-    condition: $TRAVIS_BRANCH =~ ^v2.5|master$
+    condition: $TRAVIS_BRANCH =~ ^v2.6|master$

LICENSE

@@ -0,0 +1,25 @@
+BSD 2-Clause License
+
+Copyright (c) 2022, JULIE Lab
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -12,24 +12,29 @@ In order to automate the builds of complex NLP pipelines and properly represent
 A description for each individual component can be found in their respective `README.md`.
 
 ### Requirements & Dependencies
-In order to use our components you need at least [JDK 11](https://www.oracle.com/technetwork/java/javase/downloads/jdk11-downloads-5066655.html) (Java SE Development Kit 11), [UIMA 2.10](https://uima.apache.org/index.html) & [Maven 3](https://maven.apache.org/). We develop with the [Eclipse IDE for Java Developers](http://www.eclipse.org/downloads/) and [IntelliJ IDEA](https://www.jetbrains.com/idea/) Java IDEs. If course you're free to try it with different versions or tools than those mentioned, but we can't make promises for a flawless functioning of our components in these cases.
+In order to use our components you need at least [JDK 11](https://www.oracle.com/technetwork/java/javase/downloads/jdk11-downloads-5066655.html) (Java SE Development Kit 11), [UIMA 2.x](https://uima.apache.org/index.html) & [Maven 3](https://maven.apache.org/). We develop with the [Eclipse IDE for Java Developers](http://www.eclipse.org/downloads/) and [IntelliJ IDEA](https://www.jetbrains.com/idea/) Java IDEs. If course you're free to try it with different versions or tools than those mentioned, but we can't make promises for a flawless functioning of our components in these cases.
 
 ### UIMA's Collection Processing Engine (CPE)
-UIMA features a relatively easy way to combine UIMA components together in order to analyze a collection of artifacts. If you're not firm or willing to deal with Java Code, the usage of a CPE might be the right choice.
+UIMA offers a relatively easy way to combine UIMA components together in order to analyze a collection of artifacts. If you're not firm or willing to deal with Java Code, the usage of a CPE might be the right choice.
 For more detailed information see [UIMA's CPE Documentation](https://uima.apache.org/downloads/releaseDocs/2.1.0-incubating/docs/html/tutorials_and_users_guides/tutorials_and_users_guides.html#ugr.tug.cpe).
 
-We're also working on a simple [Python script](https://github.com/JULIELab/jcore-misc/tree/master/jcore-cpe-builder) that builds rudimentary and preconfigured CPEs of your choice. It's working but still work in progress so please bear with us and post issues.
+A newer alternative is [UIMA AS](https://uima.apache.org/doc-uimaas-what.html). It is today's officially recommended way to use and scale UIMA pipelines. Our existing CPE infrastructure serves us well, however, so we mostly stick to those for the time being.
+
+### JCoRe UIMA Pipeline Builder
+
+Most CPE configurations consisting of JCoRe components can be easily built using the [JCoRe UIMA Pipeline Builder](https://github.com/JULIELab/jcore-pipeline-modules).
+This is a Java program that offers a simple command line interface for the creation of CPEs. There is also support for UIMA AS.
 
 ### Maven Artifacts
 If not stated otherwise, all the components found in this project are at least in their latest release version also available as Maven artifacts:
 ```
 <dependency>
     <groupId>de.julielab</groupId>
-    <artifactId>#COMPONENT-NAME</artifactId>
+    <artifactId>COMPONENT-NAME</artifactId>
     <version>${jcore-version}</version>
 </dependency>
 ```
-Where `#COMPONENT-NAME` is exactly the same as the name on GitHub.
+Where `COMPONENT-NAME` is exactly the same as the name on GitHub.
 For instance, to get the Acronym Resolver, include this in your Maven dependencies:
 ```
 <dependency>

jcore-ace-reader/component.meta

@@ -14,7 +14,7 @@
     "maven-artifact": {
         "artifactId": "jcore-ace-reader",
         "groupId": "de.julielab",
-        "version": "2.5.1-SNAPSHOT"
+        "version": "2.6.0"
     },
     "name": "JCoRe ACE Reader"
 }

jcore-ace-reader/pom.xml

@@ -13,7 +13,7 @@
     <parent>
         <groupId>de.julielab</groupId>
         <artifactId>jcore-base</artifactId>
-        <version>2.5.1-SNAPSHOT</version>
+        <version>2.6.0</version>
     </parent>
 
     <dependencies>
@@ -32,8 +32,8 @@
             <version>${jcore-types-version}</version>
         </dependency>
         <dependency>
-            <groupId>junit</groupId>
-            <artifactId>junit</artifactId>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter-engine</artifactId>
         </dependency>
         <dependency>
             <groupId>de.julielab</groupId>

jcore-ace-reader/src/main/resources/de/julielab/jcore/reader/ace/desc/jcore-ace-reader.xml

@@ -5,7 +5,7 @@
     <processingResourceMetaData>
         <name>AceReader</name>
         <description>Descriptor automatically generated by uimaFIT</description>
-        <version>2.5.1-SNAPSHOT</version>
+        <version>2.6.0</version>
         <vendor>JULIE Lab Jena, Germany</vendor>
         <configurationParameters>
             <configurationParameter>