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beacon-data-model/pom.xml

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+<?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-data-model</artifactId>
+    <packaging>jar</packaging>
+
+    <description>
+        Beacon Java Data Model version 2.0.1
+    </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>
+    </properties>
+
+    <dependencies>
+        <dependency>
+            <groupId>es.bsc.inb.ga4gh</groupId>
+            <artifactId>vrs-model</artifactId>
+            <version>1.2.1</version>
+        </dependency>
+
+        <dependency>
+            <groupId>jakarta.json</groupId>
+            <artifactId>jakarta.json-api</artifactId>
+            <version>${jakarta.json.version}</version>
+            <scope>provided</scope>
+        </dependency>
+    </dependencies>
+
+</project>

beacon-data-model/src/main/java/es/bsc/inb/ga4gh/beacon/model/v200/analysis/Analysis.java

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+/**
+ * *****************************************************************************
+ * Copyright (C) 2022 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.model.v200.analysis;
+
+import jakarta.json.JsonObject;
+import java.io.Serializable;
+import java.time.LocalDate;
+
+/**
+ * @author Dmitry Repchevsky
+ */
+
+public interface Analysis extends Serializable {
+
+    String getId();
+    void setId(String id);
+
+    String getRunId();
+    void setRunId(String runId);
+
+    String getBiosampleId();
+    void setBiosampleId(String biosampleId);
+
+    String getIndividualId();
+    void setIndividualId(String individualId);
+
+    LocalDate getAnalysisDate();
+    void setAnalysisDate(LocalDate analysisDate);
+
+    String getPipelineName();
+    void setPipelineName(String pipelineName);
+
+    String getPipelineRef();
+    void setPipelineRef(String pipelineRef);
+
+    String getAligner();
+    void setAligner(String aligner);
+
+    String getVariantCaller();
+    void setVariantCaller(String variantCaller);
+
+    JsonObject getInfo();
+    void setInfo(JsonObject info);
+
+}

beacon-data-model/src/main/java/es/bsc/inb/ga4gh/beacon/model/v200/biosample/Biosample.java

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+/**
+ * *****************************************************************************
+ * Copyright (C) 2022 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.model.v200.biosample;
+
+import es.bsc.inb.ga4gh.beacon.model.v200.common.PhenotypicFeature;
+import es.bsc.inb.ga4gh.beacon.model.v200.common.OntologyTerm;
+import jakarta.json.JsonObject;
+import java.io.Serializable;
+import java.time.LocalDate;
+import java.util.List;
+
+/**
+ * @author Dmitry Repchevsky
+ * 
+ * @param <K> OntologyTerm implementation class
+ * @param <L> Procedure implementation class
+ * @param <M> PhenotypicFeature implementation class
+ * @param <N> Measurement implementation class
+ */
+
+public interface Biosample<K extends OntologyTerm, L extends Procedure,
+        M extends PhenotypicFeature, N extends Measurement> extends Serializable {
+
+    /**
+     * Get biosample identifier (external accession or internal ID).
+     * 
+     * @return biosample identifier
+     */    
+    String getId();
+    void setId(String id);
+
+    /**
+     * Get the individual of the biosample.
+     * 
+     * @return individual id
+     */    
+    String getIndividualId();
+    void setIndividualId(String individualId);
+
+    /**
+     * Get relevant info about the biosample that does not fit into any 
+     * other field in the schema.
+     * 
+     * @return 
+     */    
+    String getNotes();
+    void setNotes(String notes);
+
+    /**
+     * Ontology value from Experimental Factor Ontology (EFO) Material 
+     * Sample ontology (OBI:0000747).Classification of the sample in abnormal 
+     * sample (EFO:0009655) or reference sample (EFO:0009654).
+     * 
+     * @return 
+     */    
+    K getBiosampleStatus();
+    void setBiosampleStatus(K biosampleStatus);
+
+    /**
+     * Get the date of biosample collection in the ISO8601 date format.
+     * 
+     * @return 
+     */    
+    LocalDate getCollectionDate();
+    void getCollectionDate(LocalDate collectionDate);
+
+    /**
+     * Get the individual's age at the time of sample collection 
+     * in the ISO8601 duration format `P[n]Y[n]M[n]DT[n]H[n]M[n]S`.
+     * 
+     * @return 
+     */    
+    String getCollectionMoment();
+    void setCollectionMoment(String collectionMoment);
+
+    /**
+     * Category of sample origin.Value from Ontology for Biomedical Investigations (OBI)
+     * material entity (BFO:0000040) ontology, e.g. 'specimen from organism' 
+     * (OBI:0001479),'xenograft' (OBI:0100058), 'cell culture' (OBI:0001876).
+     * 
+     * @return 
+     */
+    K getSampleOriginType();
+    void setSampleOriginType(K sampleOriginType);
+
+    K getSampleOriginDetail();
+    void setSampleOriginDetail(K sampleOriginDetail);
+
+    L getObtentionProcedure();
+    void setObtentionProcedure(L obtentionProcedure);
+
+    K getTumorProgression();
+    void setTumorProgression(K tumorProgression);
+
+    K getTumorGrade();
+    void setTumorGrade(K tumorGrade);
+
+    K getPathologicalStage();
+    void setPathologicalStage(K pathologicalStage);
+
+    K getPathologicalTnmFinding();
+    void setPathologicalTnmFinding(K pathologicalTnmFinding);
+
+    K getHistologicalDiagnosis();
+    void setHistologicalDiagnosis(K histologicalDiagnosis);
+
+    K getDiagnosticMarkers();
+    void setDiagnosticMarkers(K diagnosticMarkers);
+
+    List<M> getPhenotypicFeatures();
+    void setPhenotypicFeatures(List<M> phenotypicFeatures);
+
+    List<N> getMeasurements();
+    void setMeasurements(List<N> measurements);
+
+    K getSampleProcessing();
+    void setSampleProcessing(K sampleProcessing);
+
+    K getSampleStorage();
+    void setSampleStorage(K sampleStorage);
+
+    JsonObject getInfo();
+    void setInfo(JsonObject info);
+}

beacon-data-model/src/main/java/es/bsc/inb/ga4gh/beacon/model/v200/biosample/ComplexValue.java

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+/**
+ * *****************************************************************************
+ * Copyright (C) 2022 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.model.v200.biosample;
+
+import java.util.List;
+
+/**
+ * @author Dmitry Repchevsky
+ * 
+ * @param <K> TypedQuantity implementation class
+ */
+
+public interface ComplexValue<K extends TypedQuantity> extends MeasurementValue {
+
+    List<K> getTypedQuantities();
+    void setTypedQuantities(List<K> typedQuantities);
+}

beacon-data-model/src/main/java/es/bsc/inb/ga4gh/beacon/model/v200/biosample/Evidence.java

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+/**
+ * *****************************************************************************
+ * Copyright (C) 2022 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.model.v200.biosample;
+
+import es.bsc.inb.ga4gh.beacon.model.v200.common.OntologyTerm;
+import java.io.Serializable;
+
+/**
+ * @author Dmitry Repchevsky
+ * 
+ * @param <K> OntologyTerm implementation class
+ * @param <L> ExternalReference implementation class
+ */
+
+public interface Evidence<K extends OntologyTerm, L extends ExternalReference>
+        extends Serializable {
+
+    K getEvidenceCode();
+    void setEvidenceCode(K evidenceCode);
+
+    L getReference();
+    void setReference(L reference);
+}