initial release

README.md

@@ -1,2 +1,93 @@
-# semantic-assistants-2.0
-SA2.0 - An upgraded version of the Semantic Assistants Framework
+# Semantic Assistants 2.0 - spring boot application
+
+This spring boot application uses several NLP services for Named Entity Recognition tasks with two micro services.
+
+The first micro service provides three GATE pipelines:
+
+* [GATE ANNIE](https://github.com/GateNLP)
+* [BiodivTagger](https://github.com/fusion-jena/BiodivTagger)
+* [OrganismTagger](https://www.semanticsoftware.info/organism-tagger)
+
+As a second microservice, a Python based application offers access to language models:
+
+* Huggingface Bert-base-NER (ToDo: Link oder citation!!!) extracting people, locations and organizations
+* [SciSpacy with the BioNLP model](https://github.com/allenai/scispacy) recognizing for instance cancer, cells and anatomical structures. 
+
+## Prerequisites
+
+### JDK 11
+Install Adopt Open JDK 11 (https://adoptopenjdk.net/)
+
+### Maven
+Install Maven from [Maven](https://maven.apache.org/install.html "Download Maven")
+
+### Python
+
+Python version 3.9
+
+### GATE pipelines
+
+TODO: please download the BiodivTagger and OrganismTagger
+
+
+## Installation and running
+
+run below commands in order:
+
+
+```cd SA2.0/nlp```
+
+```mvn spring-boot:run```
+
+## Get started
+It takes a little time until the application starts.
+
+This project contains a Swagger API platform.
+
+http://localhost:8080/swagger-ui.html#/
+
+## Settings
+
+go to the:
+
+src/main/resources/application.properties
+
+set the Annie, BioTagger and OrganismTagger location on your system
+
+# PythonAPI
+
+For using the Huggingface service, you need to run this app.
+
+## Prerequisites
+
+### Anaconda
+
+Install Anaconda from [Anaconda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html "Download Python")
+
+
+## Installation and running
+
+run blow commands in order:
+
+```cd SA2.0/pythonAPI```
+
+```python -m venv myenv```
+
+```.\myenv\Scripts\activate```
+
+Linux: ```./myenv/bin/activate```
+
+```pip install -r requirements.txt```
+
+```python main.py```
+
+## Semantic Assistants
+
+Further information on the first version of the Semantic Assistants framwork can be obtained from the website of the Semantic Software Lab: https://www.semanticsoftware.info/semantic-assistants-architecture
+
+## Changelog
+
+03.12.2022 initial release 0.1
+
+## License
+Semantic Assistants 2.0 is distributed under the terms of the GNU LGPL v3.0. (https://www.gnu.org/licenses/lgpl-3.0.en.html) 

nlp/.mvn/wrapper/MavenWrapperDownloader.java

@@ -0,0 +1,117 @@
+/*
+ * Copyright 2007-present the original author or authors.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * 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.
+ */
+import java.net.*;
+import java.io.*;
+import java.nio.channels.*;
+import java.util.Properties;
+
+public class MavenWrapperDownloader {
+
+    private static final String WRAPPER_VERSION = "0.5.6";
+    /**
+     * Default URL to download the maven-wrapper.jar from, if no 'downloadUrl' is provided.
+     */
+    private static final String DEFAULT_DOWNLOAD_URL = "https://repo.maven.apache.org/maven2/io/takari/maven-wrapper/"
+        + WRAPPER_VERSION + "/maven-wrapper-" + WRAPPER_VERSION + ".jar";
+
+    /**
+     * Path to the maven-wrapper.properties file, which might contain a downloadUrl property to
+     * use instead of the default one.
+     */
+    private static final String MAVEN_WRAPPER_PROPERTIES_PATH =
+            ".mvn/wrapper/maven-wrapper.properties";
+
+    /**
+     * Path where the maven-wrapper.jar will be saved to.
+     */
+    private static final String MAVEN_WRAPPER_JAR_PATH =
+            ".mvn/wrapper/maven-wrapper.jar";
+
+    /**
+     * Name of the property which should be used to override the default download url for the wrapper.
+     */
+    private static final String PROPERTY_NAME_WRAPPER_URL = "wrapperUrl";
+
+    public static void main(String args[]) {
+        System.out.println("- Downloader started");
+        File baseDirectory = new File(args[0]);
+        System.out.println("- Using base directory: " + baseDirectory.getAbsolutePath());
+
+        // If the maven-wrapper.properties exists, read it and check if it contains a custom
+        // wrapperUrl parameter.
+        File mavenWrapperPropertyFile = new File(baseDirectory, MAVEN_WRAPPER_PROPERTIES_PATH);
+        String url = DEFAULT_DOWNLOAD_URL;
+        if(mavenWrapperPropertyFile.exists()) {
+            FileInputStream mavenWrapperPropertyFileInputStream = null;
+            try {
+                mavenWrapperPropertyFileInputStream = new FileInputStream(mavenWrapperPropertyFile);
+                Properties mavenWrapperProperties = new Properties();
+                mavenWrapperProperties.load(mavenWrapperPropertyFileInputStream);
+                url = mavenWrapperProperties.getProperty(PROPERTY_NAME_WRAPPER_URL, url);
+            } catch (IOException e) {
+                System.out.println("- ERROR loading '" + MAVEN_WRAPPER_PROPERTIES_PATH + "'");
+            } finally {
+                try {
+                    if(mavenWrapperPropertyFileInputStream != null) {
+                        mavenWrapperPropertyFileInputStream.close();
+                    }
+                } catch (IOException e) {
+                    // Ignore ...
+                }
+            }
+        }
+        System.out.println("- Downloading from: " + url);
+
+        File outputFile = new File(baseDirectory.getAbsolutePath(), MAVEN_WRAPPER_JAR_PATH);
+        if(!outputFile.getParentFile().exists()) {
+            if(!outputFile.getParentFile().mkdirs()) {
+                System.out.println(
+                        "- ERROR creating output directory '" + outputFile.getParentFile().getAbsolutePath() + "'");
+            }
+        }
+        System.out.println("- Downloading to: " + outputFile.getAbsolutePath());
+        try {
+            downloadFileFromURL(url, outputFile);
+            System.out.println("Done");
+            System.exit(0);
+        } catch (Throwable e) {
+            System.out.println("- Error downloading");
+            e.printStackTrace();
+            System.exit(1);
+        }
+    }
+
+    private static void downloadFileFromURL(String urlString, File destination) throws Exception {
+        if (System.getenv("MVNW_USERNAME") != null && System.getenv("MVNW_PASSWORD") != null) {
+            String username = System.getenv("MVNW_USERNAME");
+            char[] password = System.getenv("MVNW_PASSWORD").toCharArray();
+            Authenticator.setDefault(new Authenticator() {
+                @Override
+                protected PasswordAuthentication getPasswordAuthentication() {
+                    return new PasswordAuthentication(username, password);
+                }
+            });
+        }
+        URL website = new URL(urlString);
+        ReadableByteChannel rbc;
+        rbc = Channels.newChannel(website.openStream());
+        FileOutputStream fos = new FileOutputStream(destination);
+        fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);
+        fos.close();
+        rbc.close();
+    }
+
+}

nlp/.mvn/wrapper/maven-wrapper.properties

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+distributionUrl=https://repo.maven.apache.org/maven2/org/apache/maven/apache-maven/3.8.2/apache-maven-3.8.2-bin.zip
+wrapperUrl=https://repo.maven.apache.org/maven2/io/takari/maven-wrapper/0.5.6/maven-wrapper-0.5.6.jar