Merge Catalog continued

- Updated JPA table and column names
- Annotated Catalog services with "catalog*" name
- Vocabulary source beans with name "*VocabularySource"
- Registered keys missing in application.properties

src/main/java/org/genesys/catalog/model/Partner.java

@@ -38,8 +38,8 @@ import java.util.Set;
  * @author Matija Obreza
  */
 @Entity
-@Cacheable
 @Table(name = "partner")
+@Cacheable
 @JsonIdentityInfo(generator = ObjectIdGenerators.PropertyGenerator.class, property = "uuid")
 @Document(indexName = "catalog")
 public class Partner extends UuidModel implements SelfCleaning, AclAwareModel {
@@ -74,17 +74,17 @@ public class Partner extends UuidModel implements SelfCleaning, AclAwareModel {
 
 	/// partner-associated web links
 	@ElementCollection
-	@CollectionTable(name = "partnerUrl", joinColumns = @JoinColumn(name = "partnerId"))
+	@CollectionTable(name = "partner_url", joinColumns = @JoinColumn(name = "partnerId"))
 	private Set<URL> urls;
 
 	/// FAO WIEWS codes associated with this partner
 	@ElementCollection
-	@CollectionTable(name = "partnerWiews", joinColumns = @JoinColumn(name = "partnerId"))
+	@CollectionTable(name = "partner_wiews", joinColumns = @JoinColumn(name = "partnerId"))
 	@Column(name = "wiews")
 	private Set<String> wiewsCodes;
 
 	@ElementCollection
-	@CollectionTable(name = "PartnerCountry", joinColumns = @JoinColumn(name = "partnerId"), uniqueConstraints = { @UniqueConstraint(columnNames = { "partnerId", "code" }) })
+	@CollectionTable(name = "partner_country", joinColumns = @JoinColumn(name = "partnerId"), uniqueConstraints = { @UniqueConstraint(columnNames = { "partnerId", "code" }) })
 	@Column(name = "code", length = 3, nullable = false)
 	private Set<String> countryCodes;
 

src/main/java/org/genesys/catalog/model/ShortFilter.java

@@ -26,8 +26,12 @@ import java.util.Objects;
  * @author Maxym Borodenko
  */
 @Entity
+@Table(name = "short_filter"
+// TODO Manually create an index on json field! (length limited)
+// , indexes = { @Index(name="UK_1my8xep8hi5fv42o3ivu0t41o", columnList =
+// "json") }
+)
 @Cacheable
-@Table(indexes = { @Index(name="UK_1my8xep8hi5fv42o3ivu0t41o", columnList = "json") })
 public class ShortFilter implements Serializable, EntityId {
 
 	/** The Constant serialVersionUID. */
@@ -52,12 +56,13 @@ public class ShortFilter implements Serializable, EntityId {
 	/**
 	 * Default constructor.
 	 */
-	public ShortFilter() {}
+	public ShortFilter() {
+	}
 
 	/**
 	 * Instantiates a new ShortFilter.
 	 *
-	 * @param code the short  name
+	 * @param code the short name
 	 * @param json the json filters
 	 */
 	public ShortFilter(final String code, final String json) {
@@ -108,11 +113,12 @@ public class ShortFilter implements Serializable, EntityId {
 
 	@Override
 	public boolean equals(final Object o) {
-		if (this == o) return true;
-		if (!(o instanceof ShortFilter)) return false;
+		if (this == o)
+			return true;
+		if (!(o instanceof ShortFilter))
+			return false;
 		final ShortFilter that = (ShortFilter) o;
-		return Objects.equals(id, that.id) && Objects.equals(code, that.code)
-				&& Objects.equals(json, that.json);
+		return Objects.equals(id, that.id) && Objects.equals(code, that.code) && Objects.equals(json, that.json);
 	}
 
 	@Override

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

@@ -45,6 +45,7 @@ import java.util.Set;
  * @author Maxim Borodenko
  */
 @Entity
+@Table(name="dataset")
 @Cacheable
 @Audited
 @Document(indexName = "catalog")
@@ -69,7 +70,7 @@ public class Dataset extends UuidModel implements Publishable, SelfCleaning, Pub
 
 	/** The accession identifiers. */
 	@ElementCollection(fetch = FetchType.LAZY)
-	@CollectionTable(name = "datasetAccessions", joinColumns = @JoinColumn(name = "datasetId"),
+	@CollectionTable(name = "dataset_accessions", joinColumns = @JoinColumn(name = "datasetId"),
 			// index
 			indexes = { @Index(columnList = "datasetId, instCode, acceNumb"), @Index(columnList = "datasetId, genus") })
 	@Field(type=FieldType.Object)
@@ -78,7 +79,7 @@ public class Dataset extends UuidModel implements Publishable, SelfCleaning, Pub
 
 	/** The descriptors. */
 	@ManyToMany(fetch = FetchType.LAZY, cascade = {})
-	@JoinTable(name = "datasetDescriptor", joinColumns = @JoinColumn(name = "datasetId", referencedColumnName = "id"), inverseJoinColumns = @JoinColumn(name = "descriptorId", referencedColumnName = "id"))
+	@JoinTable(name = "dataset_descriptor", joinColumns = @JoinColumn(name = "datasetId", referencedColumnName = "id"), inverseJoinColumns = @JoinColumn(name = "descriptorId", referencedColumnName = "id"))
 	@OrderColumn(name = "position")
 	@JsonView({ JsonViews.Public.class })
 	private List<Descriptor> descriptors;
@@ -86,7 +87,7 @@ public class Dataset extends UuidModel implements Publishable, SelfCleaning, Pub
 	/** The repository files. */
 	@PublishValidation
 	@OneToMany(fetch = FetchType.LAZY, cascade = {})
-	@JoinTable(name = "datasetRepositoryfile", joinColumns = @JoinColumn(name = "datasetId", referencedColumnName = "id"), inverseJoinColumns = @JoinColumn(name = "repositoryfileId", referencedColumnName = "id"))
+	@JoinTable(name = "dataset_repositoryfile", joinColumns = @JoinColumn(name = "datasetId", referencedColumnName = "id"), inverseJoinColumns = @JoinColumn(name = "repositoryfileId", referencedColumnName = "id"))
 	@OrderColumn(name = "position")
 	@Field(type=FieldType.Object)
 	@JsonView({ JsonViews.Public.class })
@@ -118,7 +119,7 @@ public class Dataset extends UuidModel implements Publishable, SelfCleaning, Pub
 
 	/** The crops. */
 	@ElementCollection(fetch = FetchType.EAGER)
-	@CollectionTable(name = "datasetCrops", joinColumns = @JoinColumn(name = "datasetId"),
+	@CollectionTable(name = "dataset_crops", joinColumns = @JoinColumn(name = "datasetId"),
 			// index
 			indexes = { @Index(columnList = "datasetId, crop") })
 	@Column(name = "crop", nullable = false, length = 20)

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

@@ -29,6 +29,7 @@ import java.util.Map;
  * @author Andrey Lugovskoy.
  */
 @Entity
+@Table(name="dataset_creator")
 public class DatasetCreator extends UuidModel implements PublishValidationInterface {
 
 	/**

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

@@ -29,6 +29,7 @@ import java.util.Map;
  * @author Andrey Lugovskoy.
  */
 @Entity
+@Table(name="dataset_location")
 public class DatasetLocation extends UuidModel implements PublishValidationInterface {
 
 	/**

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

@@ -22,6 +22,8 @@ import javax.persistence.Entity;
 import javax.persistence.FetchType;
 import javax.persistence.OneToMany;
 import javax.persistence.OneToOne;
+import javax.persistence.Table;
+
 import java.util.List;
 
 /**
@@ -31,6 +33,7 @@ import java.util.List;
  *
  */
 @Entity
+@Table(name="dataset_version")
 public class DatasetVersions extends UuidModel {
 
 	/** The Constant serialVersionUID. */

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

@@ -135,8 +135,13 @@ public class Descriptor extends UuidModel implements SelfCleaning, Publishable,
 	/** Allow only integers, no decimal numbers. */
 	private Boolean integerOnly;
 
-	/** Data constraints, min and max allowed numeric values. */
-	private Double minValue, maxValue;
+	/** Data constraints: minimum allowed numeric values. */
+	@Column(name = "min_value")
+	private Double minValue;
+
+	/** Data constraints: maximum allowed numeric values. */
+	@Column(name = "max_value")
+	private Double maxValue;
 
 	/** The uom. */
 	@Column(name = "uom", length = 20)
@@ -164,7 +169,7 @@ public class Descriptor extends UuidModel implements SelfCleaning, Publishable,
 	 * Vocabulary terms specific to this descriptor (99% of the cases).
 	 */
 	@OneToMany(fetch = FetchType.LAZY, cascade = { CascadeType.MERGE, CascadeType.PERSIST, CascadeType.REFRESH }, orphanRemoval = true)
-	@JoinTable(name = "DescriptorTerm", joinColumns = @JoinColumn(name = "descriptorId"),
+	@JoinTable(name = "descriptor_term", joinColumns = @JoinColumn(name = "descriptorId"),
 			// other side
 			inverseJoinColumns = @JoinColumn(name = "termId", unique = true),
 			// unique constraints

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

@@ -40,6 +40,7 @@ import java.util.Map;
  * @author Andrey Lugovskoy
  */
 @Entity
+@Table(name="descriptorlist")
 @Audited
 @Cacheable
 @JsonIdentityInfo(generator = ObjectIdGenerators.PropertyGenerator.class, property = "uuid")
@@ -87,7 +88,7 @@ public class DescriptorList extends UuidModel implements Publishable, SelfCleani
 
 	/** The descriptors. */
 	@ManyToMany(cascade = { CascadeType.REFRESH }, fetch = FetchType.LAZY)
-	@JoinTable(name = "descriptorListDescriptor", joinColumns = @JoinColumn(name = "descriptorListId", referencedColumnName = "id"), inverseJoinColumns = @JoinColumn(name = "descriptorId", referencedColumnName = "id"))
+	@JoinTable(name = "descriptorlist_descriptor", joinColumns = @JoinColumn(name = "descriptorListId", referencedColumnName = "id"), inverseJoinColumns = @JoinColumn(name = "descriptorId", referencedColumnName = "id"))
 	@OrderColumn(name = "position")
 	@JsonView({ JsonViews.Public.class })
 	@JsonIgnoreProperties(value = { "descriptorLists", "datasets", "owner", "vocabulary", "terms" })
@@ -111,7 +112,7 @@ public class DescriptorList extends UuidModel implements Publishable, SelfCleani
 	/** Extra information associated with the descriptor list */
 	@JsonView({ JsonViews.Update.class, JsonViews.Public.class })
 	@ElementCollection(fetch = FetchType.EAGER)
-	@JoinTable(name = "DescriptorListExtra", joinColumns = { @JoinColumn(name = "descriptorListId") })
+	@JoinTable(name = "descriptorlist_extra", joinColumns = { @JoinColumn(name = "descriptorListId") })
 	@MapKeyColumn(name = "extra", length = 25)
 	@MapKeyEnumerated(EnumType.STRING)
 	@Column(name = "v")

src/main/java/org/genesys/catalog/model/vocab/ControlledVocabulary.java

@@ -40,6 +40,7 @@ import java.util.List;
  * @author Matija Obreza
  */
 @Entity
+@Table(name = "vocabulary")
 @JsonIdentityInfo(generator = ObjectIdGenerators.PropertyGenerator.class, property = "uuid")
 @Document(indexName = "catalog")
 public class ControlledVocabulary extends UuidModel implements Publishable, SelfCleaning, AclAwareModel {
@@ -82,7 +83,7 @@ public class ControlledVocabulary extends UuidModel implements Publishable, Self
 
 	/** The terms. */
 	@OneToMany(fetch = FetchType.LAZY, cascade = { CascadeType.MERGE, CascadeType.PERSIST, CascadeType.REFRESH }, orphanRemoval = true)
-	@JoinTable(name = "ControlledVocabularyTerm", joinColumns = @JoinColumn(name = "vocabularyId"),
+	@JoinTable(name = "vocabulary_term", joinColumns = @JoinColumn(name = "vocabularyId"),
 			// other side
 			inverseJoinColumns = @JoinColumn(name = "termId", unique = true),
 			// unique constraints

src/main/java/org/genesys/catalog/model/vocab/VocabularyTerm.java

@@ -43,7 +43,7 @@ import java.text.MessageFormat;
  * @author Matija Obreza
  */
 @Entity
-@Table(name = "Term")
+@Table(name = "term")
 @Document(indexName = "catalog")
 public class VocabularyTerm extends BasicModel implements SelfCleaning {
 
@@ -64,7 +64,7 @@ public class VocabularyTerm extends BasicModel implements SelfCleaning {
 	 * Link back to Descriptor
 	 */
 	@ManyToOne(fetch = FetchType.LAZY, cascade = { CascadeType.REFRESH })
-	@JoinTable(name = "DescriptorTerm", joinColumns = @JoinColumn(name = "termId"),
+	@JoinTable(name = "descriptor_term", joinColumns = @JoinColumn(name = "termId"),
 			// other side
 			inverseJoinColumns = @JoinColumn(name = "descriptorId"))
 	@JsonView({ JsonViews.Indexed.class, JsonViews.Minimal.class })
@@ -77,7 +77,7 @@ public class VocabularyTerm extends BasicModel implements SelfCleaning {
 	 * Link back to Descriptor
 	 */
 	@ManyToOne(fetch = FetchType.LAZY, cascade = { CascadeType.REFRESH })
-	@JoinTable(name = "ControlledVocabularyTerm", joinColumns = @JoinColumn(name = "termId"),
+	@JoinTable(name = "vocabulary_term", joinColumns = @JoinColumn(name = "termId"),
 			// other side
 			inverseJoinColumns = @JoinColumn(name = "vocabularyId"))
 	@JsonView({ JsonViews.Indexed.class, JsonViews.Minimal.class })

src/main/java/org/genesys/catalog/server/controller/api/v0/DatasetController.java

@@ -43,7 +43,7 @@ import java.util.stream.Collectors;
  * @author Andrey Lugovskoy
  * @author Matija Obreza
  */
-@RestController
+@RestController("catalogDatasetController")
 @RequestMapping(DatasetController.API_BASE)
 @PreAuthorize("isAuthenticated()")
 public class DatasetController {

src/main/java/org/genesys/catalog/server/controller/api/v0/DescriptorController.java

@@ -39,7 +39,7 @@ import java.util.UUID;
  *
  * @author Maxym Borodenko
  */
-@RestController
+@RestController("catalogDescriptorController")
 @RequestMapping(DescriptorController.API_BASE)
 @PreAuthorize("isAuthenticated()")
 public class DescriptorController {

src/main/java/org/genesys/catalog/server/controller/api/v0/MetadataController.java → src/main/java/org/genesys/catalog/server/controller/api/v0/FileMetadataController.java

@@ -15,28 +15,23 @@
  */
 package org.genesys.catalog.server.controller.api.v0;
 
-import com.fasterxml.jackson.databind.node.ObjectNode;
-import org.apache.commons.io.FileUtils;
-import org.genesys.catalog.service.MetadataService;
+import org.genesys.catalog.service.FileMetadataService;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.security.access.prepost.PreAuthorize;
-import org.springframework.web.bind.annotation.*;
-import org.springframework.web.multipart.MultipartFile;
-
-import java.io.File;
-import java.io.IOException;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RestController;
 
 /**
- * The Class MetadataController.
+ * The Class FileMetadataController.
  *
  * @author Maxym Borodenko
  */
 @RestController
-@RequestMapping(MetadataController.API_BASE)
+@RequestMapping(FileMetadataController.API_BASE)
 @PreAuthorize("isAuthenticated()")
-public class MetadataController {
+public class FileMetadataController {
 
 	/**
 	 * The Constant API_BASE.
@@ -46,13 +41,13 @@ public class MetadataController {
 	/**
 	 * The Constant LOG.
 	 */
-	private static final Logger LOG = LoggerFactory.getLogger(MetadataController.class);
+	private static final Logger LOG = LoggerFactory.getLogger(FileMetadataController.class);
 
 	private static final String APPLICATION_OXML_SHEET = "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet";
 	private static final String APPLICATION_MS_EXCEL = "application/vnd.ms-excel";
 
 	@Autowired
-	private MetadataService metadataService;
+	private FileMetadataService fileMetadataService;
 
 	/**
 	 * Metadata.
@@ -87,7 +82,7 @@ public class MetadataController {
 //		final File tempFile = File.createTempFile("metadata", ".xlsx");
 //		try {
 //			FileUtils.copyInputStreamToFile(file.getInputStream(), tempFile);
-//			return metadataService.getExcelMetadata(tempFile);
+//			return fileMetadataService.getExcelMetadata(tempFile);
 //		} finally {
 //			FileUtils.deleteQuietly(tempFile);
 //		}

src/main/java/org/genesys/catalog/service/MetadataService.java → src/main/java/org/genesys/catalog/service/FileMetadataService.java

@@ -21,11 +21,11 @@ import java.io.File;
 import java.io.IOException;
 
 /**
- * The Class MetadataService.
+ * The Class FileMetadataService.
  *
  * @author Maxym Borodenko
  */
-public interface MetadataService {
+public interface FileMetadataService {
 
     /**
      * generate JSON with Excel metadata.

src/main/java/org/genesys/catalog/service/impl/DatasetServiceImpl.java

@@ -65,7 +65,7 @@ import com.querydsl.core.BooleanBuilder;
 /**
  * The Class DatasetServiceImpl.
  */
-@Service
+@Service("catalogDatasetService")
 @Transactional(readOnly = true)
 public class DatasetServiceImpl implements DatasetService {
 

src/main/java/org/genesys/catalog/service/impl/DescriptorServiceImpl.java

@@ -56,11 +56,10 @@ import org.springframework.transaction.annotation.Transactional;
 
 import com.querydsl.core.BooleanBuilder;
 
-
 /**
  * The Class DescriptorServiceImpl.
  */
-@Service
+@Service("catalogDescriptorService")
 @Transactional(readOnly = true)
 public class DescriptorServiceImpl implements DescriptorService {
 

src/main/java/org/genesys/catalog/service/impl/MetadataServiceImpl.java → src/main/java/org/genesys/catalog/service/impl/FileMetadataServiceImpl.java

@@ -22,7 +22,7 @@ import java.util.Iterator;
 import java.util.List;
 
 import org.apache.poi.ss.usermodel.Cell;
-import org.genesys.catalog.service.MetadataService;
+import org.genesys.catalog.service.FileMetadataService;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.stereotype.Service;
@@ -31,17 +31,17 @@ import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.node.ObjectNode;
 
 /**
- * The Class MetadataServiceImpl.
+ * The Class FileMetadataServiceImpl.
  *
  * @author Maxym Borodenko
  */
 @Service
-public class MetadataServiceImpl implements MetadataService {
+public class FileMetadataServiceImpl implements FileMetadataService {
 
 	/**
 	 * The Constant LOG.
 	 */
-	private static final Logger LOG = LoggerFactory.getLogger(MetadataServiceImpl.class);
+	private static final Logger LOG = LoggerFactory.getLogger(FileMetadataServiceImpl.class);
 
 	/**
 	 * The Constant ROWS_TO_READ.

src/main/java/org/genesys/catalog/service/worker/DavrosCountrySource.java

@@ -40,7 +40,7 @@ import java.util.stream.Collectors;
  * @author Matija Obreza
  * @author Maxym Borodenko
  */
-@Component
+@Component("davrosVocabularySource")
 public class DavrosCountrySource {
 	public static final String DAVROS_ISO3166_URL = "http://www.davros.org/misc/iso3166.txt";
 

src/main/java/org/genesys/catalog/service/worker/GeonamesISOLanguageSource.java

@@ -38,7 +38,7 @@ import java.util.stream.Collectors;
  *
  * @author Maxym Borodenko
  */
-@Component
+@Component("genonamesVocabularySource")
 public class GeonamesISOLanguageSource {
 	public static final String GEONAMES_ISO639_URL = "http://download.geonames.org/export/dump/iso-languagecodes.txt";
 

src/main/java/org/genesys/catalog/service/worker/WiewsVocabularySource.java

@@ -40,7 +40,7 @@ import java.util.zip.ZipInputStream;
  *
  * @author Maxym Borodenko
  */
-@Component
+@Component("wiewsVocabularySource")
 public class WiewsVocabularySource {
 	public static final String WIEWS_EXPORT_URL = "http://www.fao.org/wiews-archive/export_c.zip";
 	public static final String[] WIEWS_EXPORT_C_HEADERS = { "INSTCODE", "ACRONYM", "ECPACRONYM", "FULL_NAME", "TYPE", "GENEBANK_LONG_TERM_COLLECTIONS", "BOTANICAL_GARDEN",

src/main/java/org/genesys2/server/servlet/controller/admin/RepositoryController.java

@@ -51,7 +51,7 @@ import org.springframework.web.servlet.HandlerMapping;
 import org.springframework.web.servlet.mvc.support.RedirectAttributes;
 import org.springframework.web.util.UriUtils;
 
-@Controller
+@Controller("adminRepositoryController")
 @RequestMapping(RepositoryController.CONTROLLER_PATH)
 @PreAuthorize("hasRole('ADMINISTRATOR')")
 public class RepositoryController extends BaseController {

src/main/java/org/genesys2/spring/config/DatabaseConfig.java

@@ -45,7 +45,7 @@ import liquibase.integration.spring.SpringLiquibase;
 
 @EnableJpaRepositories(basePackages = { "org.genesys.blocks.persistence", "org.genesys.blocks.security.persistence", "org.genesys.blocks.oauth.persistence",
 		"org.genesys.blocks.auditlog.persistence", "org.genesys2.server.persistence.domain", "org.genesys2.server.persistence.acl",
-		"org.genesys.filerepository.persistence" }, entityManagerFactoryRef = "entityManagerFactory", transactionManagerRef = "transactionManager", repositoryImplementationPostfix = "CustomImpl")
+		"org.genesys.filerepository.persistence", "org.genesys.catalog.persistence" }, entityManagerFactoryRef = "entityManagerFactory", transactionManagerRef = "transactionManager", repositoryImplementationPostfix = "CustomImpl")
 @EnableJpaAuditing(auditorAwareRef = "auditorAware")
 @EnableTransactionManagement
 @Configuration

src/main/resources/application.properties

@@ -182,6 +182,7 @@ transifex.content.template=<html xmlns="http://www.w3.org/1999/xhtml">\
 
 # File repository
 file.repository.dir=${data.dir}/repository
+file.repository.datasets.folder=/datasets
 
 # File repository S3 parameter values
 s3.accessKey=
@@ -202,3 +203,9 @@ itpgrfa.glis.basepath=https://glistest.planttreaty.org
 itpgrfa.glis.username=
 itpgrfa.glis.password=
 itpgrfa.glis.ratelimit=20
+
+
+# Catalogy thingies
+partner.primary.uuid=39d3022b-dfca-45d8-98f1-3eeaa6c3e605
+default.jwt.signingKey=genesys-signing-key-changeme
+