Added array

src/main/java/uk/ac/ebi/ega/accession/array/model/Array.java

@@ -0,0 +1,26 @@
+/*
+ *
+ * Copyright 2018 EMBL - European Bioinformatics Institute
+ *
+ * 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
+ *
+ *      http://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.
+ *
+ */
+package uk.ac.ebi.ega.accession.array.model;
+
+public interface Array {
+
+    String getSubmissionAccount();
+
+    String getAlias();
+
+}

src/main/java/uk/ac/ebi/ega/accession/array/persistence/ArrayEntity.java

@@ -0,0 +1,64 @@
+/*
+ *
+ * Copyright 2018 EMBL - European Bioinformatics Institute
+ *
+ * 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
+ *
+ *      http://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.
+ *
+ */
+package uk.ac.ebi.ega.accession.array.persistence;
+
+import uk.ac.ebi.ampt2d.commons.accession.core.models.AccessionWrapper;
+import uk.ac.ebi.ampt2d.commons.accession.persistence.jpa.entities.AccessionedEntity;
+import uk.ac.ebi.ega.accession.array.model.Array;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+
+@Entity
+public class ArrayEntity extends AccessionedEntity<Array, Long> implements Array {
+
+    @Column(nullable = false)
+    private String submissionAccount;
+
+    @Column(nullable = false)
+    private String alias;
+
+    ArrayEntity() {
+        super(null, null, -1);
+    }
+
+    public ArrayEntity(Array array, Long accession, String hashedMessage, int version) {
+        super(hashedMessage, accession, version);
+        this.submissionAccount = array.getSubmissionAccount();
+        this.alias = array.getAlias();
+    }
+
+    public ArrayEntity(AccessionWrapper<Array, String, Long> wrapper) {
+        this(wrapper.getData(), wrapper.getAccession(), wrapper.getHash(), wrapper.getVersion());
+    }
+
+    @Override
+    public Array getModel() {
+        return this;
+    }
+
+    @Override
+    public String getSubmissionAccount() {
+        return submissionAccount;
+    }
+
+    @Override
+    public String getAlias() {
+        return alias;
+    }
+}

src/main/java/uk/ac/ebi/ega/accession/array/persistence/ArrayEntityRepository.java

@@ -0,0 +1,26 @@
+/*
+ *
+ * Copyright 2018 EMBL - European Bioinformatics Institute
+ *
+ * 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
+ *
+ *      http://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.
+ *
+ */
+package uk.ac.ebi.ega.accession.array.persistence;
+
+import org.springframework.stereotype.Repository;
+import uk.ac.ebi.ampt2d.commons.accession.persistence.repositories.IAccessionedObjectRepository;
+
+@Repository
+public interface ArrayEntityRepository extends IAccessionedObjectRepository<ArrayEntity, Long> {
+
+}

src/main/java/uk/ac/ebi/ega/accession/array/persistence/ArrayEntityRepositoryImpl.java

@@ -0,0 +1,30 @@
+/*
+ *
+ * Copyright 2018 EMBL - European Bioinformatics Institute
+ *
+ * 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
+ *
+ *      http://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.
+ *
+ */
+package uk.ac.ebi.ega.accession.array.persistence;
+
+import org.springframework.transaction.PlatformTransactionManager;
+import uk.ac.ebi.ampt2d.commons.accession.persistence.jpa.repositories.BasicJpaAccessionedObjectCustomRepositoryImpl;
+
+import javax.persistence.EntityManager;
+
+public class ArrayEntityRepositoryImpl extends BasicJpaAccessionedObjectCustomRepositoryImpl<Long, ArrayEntity> {
+
+    public ArrayEntityRepositoryImpl(PlatformTransactionManager platformTransactionManager, EntityManager entityManager) {
+        super(ArrayEntity.class, platformTransactionManager, entityManager);
+    }
+}

src/main/java/uk/ac/ebi/ega/accession/array/persistence/HistoricArrayEntity.java

@@ -0,0 +1,59 @@
+/*
+ *
+ * Copyright 2018 EMBL - European Bioinformatics Institute
+ *
+ * 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
+ *
+ *      http://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.
+ *
+ */
+package uk.ac.ebi.ega.accession.array.persistence;
+
+import uk.ac.ebi.ampt2d.commons.accession.persistence.jpa.entities.InactiveAccessionEntity;
+import uk.ac.ebi.ega.accession.array.model.Array;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+
+@Entity
+public class HistoricArrayEntity extends InactiveAccessionEntity<Array, Long> implements Array {
+
+    @Column(nullable = false)
+    private String submissionAccount;
+
+    @Column(nullable = false)
+    private String alias;
+
+    HistoricArrayEntity() {
+        super();
+    }
+
+    public HistoricArrayEntity(ArrayEntity entity) {
+        super(entity);
+        this.submissionAccount = entity.getSubmissionAccount();
+        this.alias = entity.getAlias();
+    }
+
+    @Override
+    public Array getModel() {
+        return this;
+    }
+
+    @Override
+    public String getSubmissionAccount() {
+        return submissionAccount;
+    }
+
+    @Override
+    public String getAlias() {
+        return alias;
+    }
+}

src/main/java/uk/ac/ebi/ega/accession/array/persistence/HistoricArrayRepository.java

@@ -0,0 +1,26 @@
+/*
+ *
+ * Copyright 2018 EMBL - European Bioinformatics Institute
+ *
+ * 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
+ *
+ *      http://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.
+ *
+ */
+package uk.ac.ebi.ega.accession.array.persistence;
+
+import org.springframework.stereotype.Repository;
+import uk.ac.ebi.ampt2d.commons.accession.persistence.jpa.repositories.InactiveAccessionRepository;
+
+@Repository
+public interface HistoricArrayRepository extends InactiveAccessionRepository<HistoricArrayEntity> {
+
+}

src/main/java/uk/ac/ebi/ega/accession/array/persistence/HistoricLogArrayEntity.java

@@ -0,0 +1,26 @@
+/*
+ *
+ * Copyright 2018 EMBL - European Bioinformatics Institute
+ *
+ * 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
+ *
+ *      http://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.
+ *
+ */
+package uk.ac.ebi.ega.accession.array.persistence;
+
+import uk.ac.ebi.ampt2d.commons.accession.persistence.jpa.entities.OperationEntity;
+
+import javax.persistence.Entity;
+
+@Entity
+public class HistoricLogArrayEntity extends OperationEntity<Long> {
+}

src/main/java/uk/ac/ebi/ega/accession/array/persistence/HistoricLogArrayRepository.java

@@ -0,0 +1,26 @@
+/*
+ *
+ * Copyright 2018 EMBL - European Bioinformatics Institute
+ *
+ * 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
+ *
+ *      http://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.
+ *
+ */
+package uk.ac.ebi.ega.accession.array.persistence;
+
+import org.springframework.stereotype.Repository;
+import uk.ac.ebi.ampt2d.commons.accession.persistence.repositories.IHistoryRepository;
+
+@Repository
+public interface HistoricLogArrayRepository extends IHistoryRepository<Long, HistoricLogArrayEntity, Long> {
+
+}

src/main/java/uk/ac/ebi/ega/accession/array/rest/ArrayDTO.java

@@ -0,0 +1,51 @@
+/*
+ *
+ * Copyright 2018 EMBL - European Bioinformatics Institute
+ *
+ * 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
+ *
+ *      http://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.
+ *
+ */
+package uk.ac.ebi.ega.accession.array.rest;
+
+import uk.ac.ebi.ega.accession.array.model.Array;
+
+import javax.persistence.Column;
+
+public class ArrayDTO implements Array {
+
+    @Column(nullable = false)
+    private String submissionAccount;
+
+    @Column(nullable = false)
+    private String alias;
+
+    public ArrayDTO(Array array) {
+        this(array.getSubmissionAccount(), array.getAlias());
+    }
+
+    public ArrayDTO(String submissionAccount, String alias) {
+        this.submissionAccount = submissionAccount;
+        this.alias = alias;
+    }
+
+    @Override
+    public String getSubmissionAccount() {
+        return submissionAccount;
+    }
+
+    @Override
+    public String getAlias() {
+        return alias;
+    }
+
+}

src/main/java/uk/ac/ebi/ega/accession/array/rest/ArrayRestController.java

@@ -0,0 +1,34 @@
+/*
+ *
+ * Copyright 2018 EMBL - European Bioinformatics Institute
+ *
+ * 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
+ *
+ *      http://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.
+ *
+ */
+package uk.ac.ebi.ega.accession.array.rest;
+
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RestController;
+import uk.ac.ebi.ampt2d.commons.accession.core.AccessioningService;
+import uk.ac.ebi.ampt2d.commons.accession.rest.controllers.BasicRestController;
+import uk.ac.ebi.ega.accession.array.model.Array;
+
+@RestController
+@RequestMapping(value = "/v1/array")
+public class ArrayRestController extends BasicRestController<ArrayDTO, Array, String, String> {
+
+    public ArrayRestController(AccessioningService<Array, String, String> arrayAccessionService) {
+        super(arrayAccessionService, ArrayDTO::new);
+    }
+
+}