Added dataset

src/main/java/uk/ac/ebi/ega/accession/configuration/DatasetServiceConfiguration.java

@@ -0,0 +1,113 @@
+/*
+ *
+ * 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.configuration;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.autoconfigure.domain.EntityScan;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
+import uk.ac.ebi.ampt2d.commons.accession.core.AccessioningService;
+import uk.ac.ebi.ampt2d.commons.accession.core.BasicAccessioningService;
+import uk.ac.ebi.ampt2d.commons.accession.core.DatabaseService;
+import uk.ac.ebi.ampt2d.commons.accession.core.DecoratedAccessioningService;
+import uk.ac.ebi.ampt2d.commons.accession.generators.monotonic.MonotonicAccessionGenerator;
+import uk.ac.ebi.ampt2d.commons.accession.generators.monotonic.MonotonicRange;
+import uk.ac.ebi.ampt2d.commons.accession.hashing.SHA1HashingFunction;
+import uk.ac.ebi.ampt2d.commons.accession.persistence.jpa.monotonic.service.ContiguousIdBlockService;
+import uk.ac.ebi.ampt2d.commons.accession.persistence.jpa.monotonic.service.MonotonicDatabaseService;
+import uk.ac.ebi.ampt2d.commons.accession.persistence.jpa.service.BasicJpaInactiveAccessionService;
+import uk.ac.ebi.ampt2d.commons.accession.persistence.services.BasicSpringDataRepositoryDatabaseService;
+import uk.ac.ebi.ampt2d.commons.accession.persistence.services.InactiveAccessionService;
+import uk.ac.ebi.ega.accession.dataset.model.Dataset;
+import uk.ac.ebi.ega.accession.dataset.persistence.HistoricLogDatasetEntity;
+import uk.ac.ebi.ega.accession.dataset.persistence.HistoricLogDatasetRepository;
+import uk.ac.ebi.ega.accession.dataset.persistence.HistoricDatasetEntity;
+import uk.ac.ebi.ega.accession.dataset.persistence.HistoricDatasetRepository;
+import uk.ac.ebi.ega.accession.dataset.persistence.DatasetEntity;
+import uk.ac.ebi.ega.accession.dataset.persistence.DatasetEntityRepository;
+
+import java.util.Collection;
+
+@Configuration
+@EntityScan({"uk.ac.ebi.ega.accession.dataset.persistence"})
+@EnableJpaRepositories(basePackages = {"uk.ac.ebi.ega.accession.dataset.persistence"})
+public class DatasetServiceConfiguration {
+
+    private final String PAD_FORMAT = "%011d";
+
+    private final String PREFIX = "EGAD";
+
+    private final String CATEGORY_ID = "dataset";
+
+    @Autowired
+    private ContiguousIdBlockService blockService;
+
+    @Autowired
+    private DatasetEntityRepository repository;
+
+    @Autowired
+    private HistoricDatasetRepository historicRepository;
+
+    @Autowired
+    private HistoricLogDatasetRepository historicLogRepository;
+
+    @Bean
+    public AccessioningService<Dataset, String, String> prefixDatasetAccessionService() {
+        return DecoratedAccessioningService.buildPrefixPaddedLongAccessionService(datasetAccessionService(), PREFIX,
+                PAD_FORMAT, Long::parseLong);
+    }
+
+    @Bean
+    public AccessioningService<Dataset, String, Long> datasetAccessionService() {
+        return new BasicAccessioningService<>(
+                new MonotonicAccessionGenerator<>(CATEGORY_ID, "ega-accession-01", blockService,
+                        monotonicDatabaseService()),
+                datasetAccessioningDatabaseService(),
+                dataset -> dataset.getSubmissionAccount() + "_" + dataset.getAlias(),
+                new SHA1HashingFunction());
+    }
+
+    public MonotonicDatabaseService monotonicDatabaseService() {
+        return new MonotonicDatabaseService() {
+            @Override
+            public long[] getAccessionsInRanges(Collection<MonotonicRange> collection) {
+                //Not implemented yet
+                return new long[0];
+            }
+        };
+    }
+
+    @Bean
+    public DatabaseService<Dataset, String, Long> datasetAccessioningDatabaseService() {
+        return new BasicSpringDataRepositoryDatabaseService<>(repository,
+                DatasetEntity::new,
+                historicDatasetAccessionService());
+    }
+
+    @Bean
+    public InactiveAccessionService<Dataset, Long, DatasetEntity> historicDatasetAccessionService() {
+        return new BasicJpaInactiveAccessionService<>(
+                historicLogRepository,
+                HistoricDatasetEntity::new,
+                historicRepository,
+                HistoricLogDatasetEntity::new);
+    }
+
+}

src/main/java/uk/ac/ebi/ega/accession/dataset/model/Dataset.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.dataset.model;
+
+public interface Dataset {
+
+    String getSubmissionAccount();
+
+    String getAlias();
+
+}

src/main/java/uk/ac/ebi/ega/accession/dataset/persistence/DatasetEntity.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.dataset.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.dataset.model.Dataset;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+
+@Entity
+public class DatasetEntity extends AccessionedEntity<Dataset, Long> implements Dataset {
+
+    @Column(nullable = false)
+    private String submissionAccount;
+
+    @Column(nullable = false)
+    private String alias;
+
+    DatasetEntity() {
+        super(null, null, -1);
+    }
+
+    public DatasetEntity(Dataset dataset, Long accession, String hashedMessage, int version) {
+        super(hashedMessage, accession, version);
+        this.submissionAccount = dataset.getSubmissionAccount();
+        this.alias = dataset.getAlias();
+    }
+
+    public DatasetEntity(AccessionWrapper<Dataset, String, Long> wrapper) {
+        this(wrapper.getData(), wrapper.getAccession(), wrapper.getHash(), wrapper.getVersion());
+    }
+
+    @Override
+    public Dataset getModel() {
+        return this;
+    }
+
+    @Override
+    public String getSubmissionAccount() {
+        return submissionAccount;
+    }
+
+    @Override
+    public String getAlias() {
+        return alias;
+    }
+}

src/main/java/uk/ac/ebi/ega/accession/dataset/persistence/DatasetEntityRepository.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.dataset.persistence;
+
+import org.springframework.stereotype.Repository;
+import uk.ac.ebi.ampt2d.commons.accession.persistence.repositories.IAccessionedObjectRepository;
+
+@Repository
+public interface DatasetEntityRepository extends IAccessionedObjectRepository<DatasetEntity, Long> {
+
+}

src/main/java/uk/ac/ebi/ega/accession/dataset/persistence/DatasetEntityRepositoryImpl.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.dataset.persistence;
+
+import org.springframework.transaction.PlatformTransactionManager;
+import uk.ac.ebi.ampt2d.commons.accession.persistence.jpa.repositories.BasicJpaAccessionedObjectCustomRepositoryImpl;
+
+import javax.persistence.EntityManager;
+
+public class DatasetEntityRepositoryImpl extends BasicJpaAccessionedObjectCustomRepositoryImpl<Long, DatasetEntity> {
+
+    public DatasetEntityRepositoryImpl(PlatformTransactionManager platformTransactionManager, EntityManager entityManager) {
+        super(DatasetEntity.class, platformTransactionManager, entityManager);
+    }
+}

src/main/java/uk/ac/ebi/ega/accession/dataset/persistence/HistoricDatasetEntity.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.dataset.persistence;
+
+import uk.ac.ebi.ampt2d.commons.accession.persistence.jpa.entities.InactiveAccessionEntity;
+import uk.ac.ebi.ega.accession.dataset.model.Dataset;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+
+@Entity
+public class HistoricDatasetEntity extends InactiveAccessionEntity<Dataset, Long> implements Dataset {
+
+    @Column(nullable = false)
+    private String submissionAccount;
+
+    @Column(nullable = false)
+    private String alias;
+
+    HistoricDatasetEntity() {
+        super();
+    }
+
+    public HistoricDatasetEntity(DatasetEntity entity) {
+        super(entity);
+        this.submissionAccount = entity.getSubmissionAccount();
+        this.alias = entity.getAlias();
+    }
+
+    @Override
+    public Dataset getModel() {
+        return this;
+    }
+
+    @Override
+    public String getSubmissionAccount() {
+        return submissionAccount;
+    }
+
+    @Override
+    public String getAlias() {
+        return alias;
+    }
+}

src/main/java/uk/ac/ebi/ega/accession/dataset/persistence/HistoricDatasetRepository.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.dataset.persistence;
+
+import org.springframework.stereotype.Repository;
+import uk.ac.ebi.ampt2d.commons.accession.persistence.jpa.repositories.InactiveAccessionRepository;
+
+@Repository
+public interface HistoricDatasetRepository extends InactiveAccessionRepository<HistoricDatasetEntity> {
+
+}

src/main/java/uk/ac/ebi/ega/accession/dataset/persistence/HistoricLogDatasetEntity.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.dataset.persistence;
+
+import uk.ac.ebi.ampt2d.commons.accession.persistence.jpa.entities.OperationEntity;
+
+import javax.persistence.Entity;
+
+@Entity
+public class HistoricLogDatasetEntity extends OperationEntity<Long> {
+}