Beacon v2 abstract endpoints

elixir-europe · Oct 17, 2023 · a63b2e1 · a63b2e1
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diff --git a/README.md b/README.md
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+These are Java Beans classes for the Beacon API v2.0.0 specification JSON schema.
+
+Compiling:
+```shell
+>git https://github.com/elixir-europe/java-beacon-v2.api.git
+>cd java-beacon-v2-api
+>mvn install
+```
+Maven will build three libraries:
+1. beacon-framework/target/beacon-framework-2.x.x.jar
+these are java model classes for Beacon v2 framwork
+2. beacon-data-model/target/beacon-data-model-2.x.x.jar
+these are the java interfaces for Beacon v2 models
+3. beacon-model/target/beacon-model-2.x.x.jar
+these are the java interfaces for Beacon v2 endpoints
+
+Most probably, you wont be needed to manually compile this project, but rather include the libararies in your own project  
+
+To include Beacon beans in a maven project (pom.xml):
+
+```xml
+<dependencies>
+    <dependency>
+        <groupId>es.bsc.inb.ga4gh</groupId>
+        <artifactId>beacon-model</artifactId>
+        <version>2.x.x</version>
+    </dependency>
+</dependencies>
+
+<repositories>
+    <repository>
+        <id>gitlab-bsc-maven</id>
+        <url>https://inb.bsc.es/maven</url>
+    </repository>
+</repositories>
+```
diff --git a/beacon-model/LICENSE b/beacon-model/LICENSE
diff --git a/beacon-model/pom.xml b/beacon-model/pom.xml
@@ -0,0 +1,105 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+  Copyright (C) 2023 Spanish National Bioinformatics Institute (INB) and
+  Barcelona Supercomputing Center
+
+  Modifications to the initial code base are copyright of their respective
+  authors, or their employers as appropriate.
+ 
+  This library is free software; you can redistribute it and/or
+  modify it under the terms of the GNU Lesser General Public
+  License as published by the Free Software Foundation; either
+  version 2.1 of the License, or (at your option) any later version.
+
+  This library is distributed in the hope that it will be useful,
+  but WITHOUT ANY WARRANTY; without even the implied warranty of
+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+  Lesser General Public License for more details.
+
+  You should have received a copy of the GNU Lesser General Public
+  License along with this library; if not, write to the Free Software
+  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+  MA 02110-1301  USA
+-->
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+
+    <parent>
+        <groupId>es.bsc.inb.ga4gh</groupId>
+        <artifactId>beacon-v2-api</artifactId>
+        <version>2.0.4</version>
+    </parent>
+
+    <artifactId>beacon-model</artifactId>
+    <packaging>jar</packaging>
+
+    <description>
+        Beacon Java Data Model version 2.0.0
+    </description>
+
+    <organization>
+        <name>Barcelona Supercomputing Center</name>
+        <url>https://www.bsc.es/</url>
+    </organization>
+
+    <licenses>
+      <license>
+        <name>LGPL-2.1-or-later</name>
+        <url>https://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt</url>
+        <distribution>repo</distribution>
+      </license>
+    </licenses>
+
+    <developers>
+        <developer>
+          <id>redmitry</id>
+          <name>Dmitry Repchevsky</name>
+          <email>[email protected]</email>
+        </developer>
+    </developers>
+
+    <properties>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+        <maven.compiler.source>17</maven.compiler.source>
+        <maven.compiler.target>17</maven.compiler.target>
+
+        <jakarta.ws.rs-api.version>3.1.0</jakarta.ws.rs-api.version>
+    </properties>
+
+    <dependencies>
+
+        <dependency>        
+            <groupId>es.bsc.inb.ga4gh</groupId>
+            <artifactId>beacon-framework</artifactId>
+            <version>2.0.4</version>
+        </dependency>
+
+        <dependency>        
+            <groupId>es.bsc.inb.ga4gh</groupId>
+            <artifactId>beacon-data-model</artifactId>
+            <version>2.0.4</version>
+        </dependency>
+
+        <dependency>
+            <groupId>jakarta.ws.rs</groupId>
+            <artifactId>jakarta.ws.rs-api</artifactId>
+            <version>${jakarta.ws.rs-api.version}</version>
+            <scope>provided</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>jakarta.json</groupId>
+            <artifactId>jakarta.json-api</artifactId>
+            <version>${jakarta.json.version}</version>
+            <scope>provided</scope>
+        </dependency>
+        <dependency>
+            <groupId>jakarta.json.bind</groupId>
+            <artifactId>jakarta.json.bind-api</artifactId>
+            <version>${jakarta.json.bind.version}</version>
+            <scope>provided</scope>
+        </dependency>
+
+    </dependencies>
+
+</project>
diff --git a/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/AnalysesInterface.java b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/AnalysesInterface.java
@@ -0,0 +1,120 @@
+/**
+ * *****************************************************************************
+ * Copyright (C) 2023 ELIXIR ES, Spanish National Bioinformatics Institute (INB)
+ * and Barcelona Supercomputing Center (BSC)
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ * 
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301  USA
+ * *****************************************************************************
+ */
+
+package es.bsc.inb.ga4gh.beacon.framework;
+
+import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconQueryFilter;
+import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconRequestBody;
+import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconFilteringTermsResponse;
+import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconResultsetsResponse;
+import java.util.List;
+
+/**
+ * GA4GH Beacon API Specification - Analysis endpoints
+ * 
+ * @author Dmitry Repchevsky
+ */
+
+public interface AnalysesInterface {
+
+    /**
+     * Get a list of bioinformatics analyses.
+     * 
+     * @param requested_schema
+     * @param skip
+     * @param limit
+     * @param include_responses
+     * @param filters
+     * 
+     * @return 
+     */
+    BeaconResultsetsResponse getAnalyses(
+            String requested_schema, Integer skip, Integer limit, 
+            String include_responses, List<BeaconQueryFilter> filters);
+
+    /**
+     * Get a list of bioinformatics analyses.
+     * 
+     * @param request
+     * @return 
+     */
+    BeaconResultsetsResponse postAnalyses(BeaconRequestBody request);
+
+    /**
+     * Get details about one bioinformatics analysis, identified by its (unique) 'id'
+     * 
+     * @param id
+     * @return 
+     */
+    BeaconResultsetsResponse getOneAnalysis(String id);
+
+    /**
+     * Get details about one bioinformatics analysis, identified by its (unique) 'id'
+     * 
+     * @param id
+     * @param request
+     * @return 
+     */
+    BeaconResultsetsResponse postOneAnalysisRequest(String id, BeaconRequestBody request);
+
+    /**
+     * Get the list of variants instances for one bioinformatics analysis, identified by its (unique) 'id'
+     * 
+     * @param id
+     * @param requested_schema
+     * @param skip
+     * @param limit
+     * @return 
+     */
+    BeaconResultsetsResponse getOneAnalysisGenomicVariants(
+            String id, String requested_schema, Integer skip, Integer limit);
+
+    /**
+     * Get the list of variants instances for one bioinformatics analysis, identified by its (unique) 'id'
+     * 
+     * @param id
+     * @param request
+     * @return 
+     */
+    BeaconResultsetsResponse postOneAnalysisGenomicVariantsRequest(String id, BeaconRequestBody request);
+
+    /**
+     * Get the list of filtering terms that could be used with analyses.
+     * 
+     * @param skip
+     * @param limit
+     * @return 
+     */
+    BeaconFilteringTermsResponse getAnalysesFilteringTerms(Integer skip, Integer limit);
+
+    /**
+     * Get the list of filtering terms that could be used with analyses.
+     * 
+     * @param request
+     * @return 
+     */
+    BeaconFilteringTermsResponse postAnalysesFilteringTermsRequest(BeaconRequestBody request);
+
+}