Merge branch '327-subsets-model' into 'master'

Resolve "Subsets model"

Closes #327

See merge request genesys-pgr/genesys-server!224

pom.xml

@@ -856,7 +856,7 @@
 			<plugin>
 				<groupId>org.liquibase</groupId>
 				<artifactId>liquibase-maven-plugin</artifactId>
-				<version>${liquibase.version}</version>
+				<version>${liquibase.version}.2</version>
 				<configuration>
 					<propertyFile>src/main/resources/liquibase.properties</propertyFile>
 					<verbose>true</verbose>

src/main/java/org/genesys/catalog/model/dataset/Dataset.java

@@ -29,6 +29,7 @@ import org.genesys.catalog.model.traits.Descriptor;
 import org.genesys.catalog.service.PublishValidationInterface;
 import org.genesys.filerepository.model.RepositoryFile;
 import org.genesys2.server.model.PublishState;
+import org.genesys2.server.model.impl.Crop;
 import org.genesys2.util.MCPDUtil;
 import org.springframework.data.elasticsearch.annotations.Document;
 import org.springframework.data.elasticsearch.annotations.Field;
@@ -132,7 +133,7 @@ public class Dataset extends UuidModel implements Publishable, SelfCleaning, Pub
 	@CollectionTable(name = "dataset_crops", joinColumns = @JoinColumn(name = "datasetId"),
 			// index
 			indexes = { @Index(columnList = "datasetId, crop") })
-	@Column(name = "crop", nullable = false, length = 20)
+	@Column(name = "crop", nullable = false, length = Crop.CROP_SHORTNAME_LENGTH)
 	@JsonView({ JsonViews.Minimal.class })
 	private Set<String> crops;
 

src/main/java/org/genesys/catalog/model/traits/Descriptor.java

@@ -24,6 +24,7 @@ import org.genesys.catalog.model.dataset.Dataset;
 import org.genesys.catalog.model.vocab.ControlledVocabulary;
 import org.genesys.catalog.model.vocab.VocabularyTerm;
 import org.genesys2.server.model.PublishState;
+import org.genesys2.server.model.impl.Crop;
 import org.springframework.dao.DataIntegrityViolationException;
 import org.springframework.data.elasticsearch.annotations.Document;
 import org.springframework.data.elasticsearch.annotations.Field;
@@ -200,7 +201,7 @@ public class Descriptor extends UuidModel implements SelfCleaning, Publishable,
 	private List<Dataset> datasets;
 
 	/** The crop. */
-	@Column(name = "crop", length = 100, nullable = true)
+	@Column(name = "crop", length = Crop.CROP_SHORTNAME_LENGTH, nullable = true)
 	private String crop;
 
 	/** Descriptor classification. */

src/main/java/org/genesys/catalog/model/traits/DescriptorList.java

@@ -27,6 +27,7 @@ import org.genesys.blocks.model.UuidModel;
 import org.genesys.blocks.security.model.AclAwareModel;
 import org.genesys.catalog.model.Partner;
 import org.genesys2.server.model.PublishState;
+import org.genesys2.server.model.impl.Crop;
 import org.springframework.data.elasticsearch.annotations.Document;
 import org.springframework.data.elasticsearch.annotations.Field;
 import org.springframework.data.elasticsearch.annotations.FieldType;
@@ -108,7 +109,7 @@ public class DescriptorList extends UuidModel implements Publishable, SelfCleani
 	private String publisher;
 
 	/** The crop. */
-	@Column(name = "crop", length = 100, nullable = true)
+	@Column(name = "crop", length = Crop.CROP_SHORTNAME_LENGTH, nullable = true)
 	private String crop;
 
 	/** Extra information associated with the descriptor list */

src/main/java/org/genesys2/server/model/impl/Crop.java

@@ -61,11 +61,13 @@ public class Crop extends GlobalVersionedAuditedModel implements AclAwareModel {
 
     public static final Logger LOG = LoggerFactory.getLogger(Crop.class);
 
+	public static final int CROP_SHORTNAME_LENGTH = 50;
+
 
 	/**
 	 * Crop short name used as short name in URLs
 	 */
-	@Column(nullable = false, length = 50, unique = true)
+	@Column(nullable = false, length = CROP_SHORTNAME_LENGTH, unique = true)
 	private String shortName;
 
 	@Column(name = "otherName", nullable = false, unique = true, length = 255)

src/main/java/org/genesys2/server/model/impl/Subset.java

@@ -17,23 +17,40 @@
 package org.genesys2.server.model.impl;
 
 import java.util.List;
-
-import javax.persistence.*;
+import java.util.Set;
+
+import javax.persistence.CascadeType;
+import javax.persistence.CollectionTable;
+import javax.persistence.Column;
+import javax.persistence.ElementCollection;
+import javax.persistence.Entity;
+import javax.persistence.EnumType;
+import javax.persistence.Enumerated;
+import javax.persistence.FetchType;
+import javax.persistence.Index;
+import javax.persistence.JoinColumn;
+import javax.persistence.JoinTable;
+import javax.persistence.Lob;
+import javax.persistence.ManyToMany;
+import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
+import javax.persistence.PrePersist;
+import javax.persistence.PreUpdate;
+import javax.persistence.Table;
 
 import org.genesys.blocks.model.JsonViews;
 import org.genesys.blocks.model.SelfCleaning;
 import org.genesys.blocks.model.UuidModel;
 import org.genesys.blocks.security.model.AclAwareModel;
-import org.genesys.catalog.annotations.PublishValidation;
 import org.genesys2.server.model.PublishState;
 import org.genesys2.server.model.genesys.AccessionId;
+import org.genesys2.util.MCPDUtil;
 import org.hibernate.annotations.Type;
+import org.springframework.data.elasticsearch.annotations.Field;
+import org.springframework.data.elasticsearch.annotations.FieldType;
 
 import com.fasterxml.jackson.annotation.JsonIdentityReference;
-import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonView;
-import org.springframework.data.elasticsearch.annotations.Field;
-import org.springframework.data.elasticsearch.annotations.FieldType;
 
 // TODO: Auto-generated Javadoc
 /**
@@ -99,6 +116,22 @@ public class Subset extends UuidModel implements AclAwareModel, SelfCleaning {
 	private List<SubsetCreator> creators;
 
 
+	/** The crops. */
+	@ElementCollection(fetch = FetchType.EAGER)
+	@CollectionTable(name = "subset_crops", joinColumns = @JoinColumn(name = "subsetId"),
+			indexes = { @Index(columnList = "subsetId, crop") })
+	@Column(name = "crop", nullable = false, length = Crop.CROP_SHORTNAME_LENGTH)
+	@JsonView({ JsonViews.Minimal.class })
+	private Set<String> crops;
+
+	/** The date when subset was authored. */
+	@Column(length = 8)
+	private String date;
+
+	/** The source. */
+	@Column(length = 200)
+	private String source;
+
 	/**
 	 * Generate UUID if missing.
 	 */
@@ -114,6 +147,9 @@ public class Subset extends UuidModel implements AclAwareModel, SelfCleaning {
 		}
 	}
 	
+	/* (non-Javadoc)
+	 * @see org.genesys.blocks.security.model.AclAwareModel#aclParentObject()
+	 */
 	@Override
 	public AclAwareModel aclParentObject() {
 		return institute;
@@ -300,7 +336,7 @@ public class Subset extends UuidModel implements AclAwareModel, SelfCleaning {
 	}
 
 	/**
-	 * Gets subset creators
+	 * Gets subset creators.
 	 *
 	 * @return subset creators
 	 */
@@ -309,11 +345,67 @@ public class Subset extends UuidModel implements AclAwareModel, SelfCleaning {
 	}
 
 	/**
-	 * Sets subset creators
+	 * Sets subset creators.
 	 *
 	 * @param creators new creators
 	 */
 	public void setCreators(List<SubsetCreator> creators) {
 		this.creators = creators;
 	}
+
+	/**
+	 * Gets the crops.
+	 *
+	 * @return the crops
+	 */
+	public Set<String> getCrops() {
+		return crops;
+	}
+
+	/**
+	 * Sets the crops.
+	 *
+	 * @param crops the new crops
+	 */
+	public void setCrops(Set<String> crops) {
+		this.crops = crops;
+	}
+
+	/**
+	 * Gets the date when subset was authored
+	 *
+	 * @return the date
+	 */
+	public String getDate() {
+		return date;
+	}
+
+	/**
+	 * Sets the date when subset was authored
+	 *
+	 * @param date the new date
+	 */
+	public void setDate(String date) {
+		if (MCPDUtil.isMcpdDate(date)) {
+			this.date = date;
+		}
+	}
+
+	/**
+	 * Gets the source.
+	 *
+	 * @return the source
+	 */
+	public String getSource() {
+		return source;
+	}
+
+	/**
+	 * Sets the source.
+	 *
+	 * @param source the new source
+	 */
+	public void setSource(String source) {
+		this.source = source;
+	}
 }

src/main/java/org/genesys2/server/service/filter/SubsetFilter.java

@@ -56,6 +56,8 @@ public class SubsetFilter extends UuidModelFilter<SubsetFilter, Subset> {
     /** The publish state. */
     public Set<PublishState> state;
 
+    public Set<String> crop;
+
     /**
      * Builds the query.
      *
@@ -86,6 +88,9 @@ public class SubsetFilter extends UuidModelFilter<SubsetFilter, Subset> {
         if (state != null && !state.isEmpty()) {
             and.and(subset.state.in(state));
         }
+        if (crop != null && !crop.isEmpty()) {
+            and.and(subset.crops.any().in(crop));
+        }
         return and;
     }
 }

src/main/java/org/genesys2/server/service/impl/SubsetServiceImpl.java

@@ -93,9 +93,7 @@ public class SubsetServiceImpl implements SubsetService {
 	@Override
 	public Page<Subset> list(final SubsetFilter filter, final Pageable page) {
 		final BooleanBuilder published = new BooleanBuilder();
-		if (!securityUtils.hasRole(UserRole.ADMINISTRATOR)) {
-			published.and(QSubset.subset.state.eq(PublishState.PUBLISHED));
-		}
+		published.and(QSubset.subset.state.eq(PublishState.PUBLISHED));
 		published.and(filter.buildQuery());
 		return subsetRepository.findAll(published, page);
 	}
@@ -167,6 +165,16 @@ public class SubsetServiceImpl implements SubsetService {
 		target.setDateCreated(source.getDateCreated());
 		target.setRights(source.getRights());
 		target.setUuid(source.getUuid());
+		target.setDate(source.getDate());
+		target.setSource(source.getSource());
+
+		if (source.getCrops() != null) {
+			if (target.getCrops() == null) {
+				target.setCrops(new HashSet<>());
+			}
+			target.getCrops().clear();
+			target.getCrops().addAll(source.getCrops());
+		}
 	}
 
 	/**
@@ -180,6 +188,8 @@ public class SubsetServiceImpl implements SubsetService {
 			throw new NotFoundElement("No such subset");
 
 		subset.getInstitute().getId();
+		if (subset.getCrops() != null)
+		    subset.getCrops().size();
 		if (subset.getAccessionIds() != null)
 			subset.getAccessionIds().size();
 		if (subset.getCreators() != null)

src/main/resources/liquibase/liquibase-changeLog.yml

@@ -3875,3 +3875,63 @@ databaseChangeLog:
         onUpdate: NO ACTION
         referencedColumnNames: id
         referencedTableName: subset
+
+- changeSet:
+    id:              1536945927974-1
+    author:          mobreza (generated)
+    comment:         Fix crop shortName (code) to 50
+    changes:
+    - modifyDataType:
+        columnName:  crop
+        newDataType: varchar(50)
+        tableName:   dataset_crops
+    - modifyDataType:
+        columnName:  crop
+        newDataType: varchar(50)
+        tableName:   descriptor
+    - modifyDataType:
+        columnName:  crop
+        newDataType: varchar(50)
+        tableName:   descriptorlist
+
+- changeSet:
+    id:                        1536945927974-4
+    author:                    vpavlov
+    comment:                   Add crops to Subset
+    changes:
+    - addColumn:
+        columns:
+        - column:
+            name:              date
+            type:              VARCHAR(8)
+        tableName:             subset
+    - addColumn:
+        columns:
+        - column:
+            name:              source
+            type:              VARCHAR(200)
+        tableName:             subset
+    - createTable:
+        columns:
+        - column:
+            constraints:
+              primaryKey:      true
+            name:              subsetId
+            type:              BIGINT
+        - column:
+            constraints:
+              primaryKey:      true
+            name:              crop
+            type:              VARCHAR(50)
+        tableName:             subset_crops
+    - addForeignKeyConstraint:
+        baseColumnNames:       subsetId
+        baseTableName:         subset_crops
+        constraintName:        FK_hny3je51ro3jv72dubq9lt4o2
+        deferrable:            false
+        initiallyDeferred:     false
+        onDelete:              NO ACTION
+        onUpdate:              NO ACTION
+        referencedColumnNames: id
+        referencedTableName:   subset
+        validate:              true