Added csv loader, removed types from biologicalEntities and Studies, …

…removed URI as it is represented through the mongo _id, modified collections

.gitignore

@@ -7,6 +7,8 @@ etc
 .idea
 # Maven
 **/target/**
+#Application properties
+*.properties
 
 # Mac specific files
 .DS_Store

pom.xml

@@ -49,6 +49,7 @@
 	<modules>
 		<module>zooma-api</module>
 		<module>zooma-mongo</module>
+		<module>zooma-csv-loader</module>
 	</modules>
 
 

zooma-api/src/main/java/uk/ac/ebi/spot/datasource/AnnotationFactory.java

@@ -48,11 +48,9 @@ public interface AnnotationFactory {
      * @param studyAccession   the accession of the study.  Unique across this datasource
      * @param studyURI         the URI of the study that will be created, if present
      * @param studyID          the ID of the study in the datasource.  If present, will be used to generate the URI
-     * @param studyType        the URI that specifies the type of Study e.g. an experiment or pubmed article
      * @param bioentityName    the name of the bioentity.  Should be unique per study in the datasource
      * @param bioentityURI     the URI of the bioentity that will be created, if present
      * @param bioentityID      the ID of the bioentity in the datasource.  If present, will be used to generate the URI
-     * @param bioentityTypeURI the URI of the bioentity type in the datasource.
      * @param propertyType     the property type
      * @param propertyValue    the property value
      * @param propertyURI      the URI of the property that will be created, if present
@@ -67,12 +65,9 @@ Annotation createAnnotation(URI annotationURI,
                                 String studyAccession,
                                 URI studyURI,
                                 String studyID,
-                                URI studyType,
                                 String bioentityName,
                                 URI bioentityURI,
                                 String bioentityID,
-                                String bioentityTypeName,
-                                URI bioentityTypeURI,
                                 String propertyType,
                                 String propertyValue,
                                 URI propertyURI,

zooma-api/src/main/java/uk/ac/ebi/spot/datasource/AnnotationLoadingSession.java

@@ -18,57 +18,46 @@
 public interface AnnotationLoadingSession {
     String getDatasourceName();
 
-    Study getOrCreateStudy(String studyAccession, Collection<URI> studyTypes);
+    Study getOrCreateStudy(String studyAccession);
 
-    Study getOrCreateStudy(String studyAccession, String studyID, Collection<URI> studyTypes);
+    Study getOrCreateStudy(String studyAccession, String studyID);
+
+    Study getOrCreateStudy(String studyAccession, URI studyURI);
 
-    Study getOrCreateStudy(String studyAccession, URI studyURI, Collection<URI> studyTypes);
 
     /**
      * A method to create a biological entity object based on the bioentity name, types and set of studies
      *
      * @param bioentityName       A name to identity the biological entity
-     * @param bioentityTypesNames An optional collection of names to represent the type of biological entity
-     * @param bioentityTypesURIs  An optional collection of URIs to represent the type of biological entity
      * @param studies             A collection of studies linked to the biological entity
      * @return BiologicalEntity
      */
     BiologicalEntity getOrCreateBiologicalEntity(String bioentityName,
-                                                 Collection<String> bioentityTypesNames,
-                                                 Collection<URI> bioentityTypesURIs,
-                                                 Study... studies);
+                                                 Collection<Study> studies);
 
     /**
      * A method to create a biological entity object based on the bioentity name, types and set of studies
      *
      * @param bioentityName       A name to identity the biological entity
      * @param bioentityID         An id that can be used to form the URI of the biological entity
-     * @param bioentityTypesNames An optional collection of names to represent the type of biological entity
-     * @param bioentityTypesURIs  An optional collection of URIs to represent the type of biological entity
      * @param studies             A collection of studies linked to the biological entity
      * @return BiologicalEntity
      */
     BiologicalEntity getOrCreateBiologicalEntity(String bioentityName,
                                                  String bioentityID,
-                                                 Collection<String> bioentityTypesNames,
-                                                 Collection<URI> bioentityTypesURIs,
-                                                 Study... studies);
+                                                 Collection<Study> studies);
 
     /**
      * A method to create a biological entity object based on the bioentity name, types and set of studies
      *
      * @param bioentityName       A name to identity the biological entity
      * @param bioentityURI        A URI that will be used to identify the biological entity
-     * @param bioentityTypesNames An optional collection of names to represent the type of biological entity
-     * @param bioentityTypesURIs  An optional collection of URIs to represent the type of biological entity
      * @param studies             A collection of studies linked to the biological entity
      * @return BiologicalEntity
      */
     BiologicalEntity getOrCreateBiologicalEntity(String bioentityName,
                                                  URI bioentityURI,
-                                                 Collection<String> bioentityTypesNames,
-                                                 Collection<URI> bioentityTypesURIs,
-                                                 Study... studies);
+                                                 Collection<Study> studies);
 
     Property getOrCreateProperty(String propertyType, String propertyValue);
 

zooma-api/src/main/java/uk/ac/ebi/spot/datasource/ZoomaDAO.java

@@ -17,7 +17,7 @@
  * @author Tony Burdett
  * @date 30/03/12
  */
-public interface ZoomaDAO<I extends Identifiable> {
+public interface ZoomaDAO<I> {
     /**
      * Retrieves a name that represents the datasource that this DAO retrieves data from.  Although this is not treated
      * as a unique key, it is best to take care to ensure that implementations define a reasonably unique name so as to

zooma-api/src/main/java/uk/ac/ebi/spot/model/Annotation.java

@@ -14,7 +14,7 @@
  * @author Tony Burdett
  * @date 08/03/12
  */
-public interface Annotation extends Identifiable {
+public interface Annotation {
     /**
      * Returns a collection of biological entities to which this annotation applies
      *

zooma-api/src/main/java/uk/ac/ebi/spot/model/AnnotationSource.java

@@ -11,7 +11,7 @@
  * @author Tony Burdett
  * @date 04/10/13
  */
-public interface AnnotationSource extends Identifiable {
+public interface AnnotationSource {
     /**
      * Returns the type of this annotation source
      *

zooma-api/src/main/java/uk/ac/ebi/spot/model/AnnotationTarget.java

@@ -10,7 +10,7 @@
  * @author Simon Jupp
  * @date 07/10/2013 Functional Genomics Group EMBL-EBI
  */
-public interface AnnotationTarget extends Identifiable {
+public interface AnnotationTarget {
     /**
      * Returns the type that was assigned to this annotation target entity
      *

zooma-api/src/main/java/uk/ac/ebi/spot/model/BiologicalEntity.java

@@ -9,7 +9,7 @@
  * @author Tony Burdett
  * @date 13/03/12
  */
-public interface BiologicalEntity extends AnnotationTarget {
+public interface BiologicalEntity {
     /**
      * Returns the name that was assigned to this biological entity to identify it within the context of the study in
      * which it was described.

zooma-api/src/main/java/uk/ac/ebi/spot/model/Property.java

@@ -18,7 +18,7 @@
  * @author Tony Burdett
  * @date 08/03/12
  */
-public interface Property extends Identifiable, Comparable<Property> {
+public interface Property extends Comparable<Property> {
     /**
      * Returns the property value for this property.
      *

zooma-api/src/main/java/uk/ac/ebi/spot/model/Study.java

@@ -11,7 +11,7 @@
  * @author Tony Burdett
  * @date 13/03/12
  */
-public interface Study extends TargetSource {
+public interface Study {
     /**
      * An accession attributed to this study, usually unique within the context of the datasource it was derived from.
      * This accession may not be globally unique (for instance, in the case of studies present in several datasources

zooma-api/src/main/java/uk/ac/ebi/spot/service/StatusService.java

@@ -2,7 +2,7 @@
 
 
 /**
- * A ZOOMA service that indicates the status of backend services.  This is used to indicate whether ZOOMA is ready to
+ * A ZOOMA service that indicates the status of backend service.  This is used to indicate whether ZOOMA is ready to
  * serve requests, or force a reinitialization of backend infrastructure to ZOOMA.
  * <p/>
  * Any service implementations that require initialization, startup or indexing should implement this service to only

zooma-api/src/main/java/uk/ac/ebi/spot/service/StudySearchService.java

@@ -6,7 +6,6 @@
 
 import java.net.URI;
 import java.util.Collection;
-import java.util.Map;
 
 /**
  * A ZOOMA service that allows searching over the set of {@link Study}s known to ZOOMA.  The search facililty on this

zooma-api/src/main/java/uk/ac/ebi/spot/util/SearchStringProcessor.java

@@ -6,7 +6,7 @@
  * Encapsulates rules that allow ZOOMA search strings to be processed. How this processing is performed is up to
  * individual implementations.
  * <p/>
- * Some of the ZOOMA search services declare methods that take property value search strings and use the supplied search
+ * Some of the ZOOMA search service declare methods that take property value search strings and use the supplied search
  * string to query for matching annotations.  This class will return processed versions of the search string, allowing,
  * for example, partial matches to be evaluated
  *

zooma-api/src/main/java/uk/ac/ebi/spot/util/ZoomaUtils.java

@@ -67,8 +67,9 @@ public static String generateHashEncodedID(MessageDigest messageDigest, boolean
             idContent.append(s);
         }
         try {
+            String s = idContent.toString();
             // encode the content using the supplied message digest
-            byte[] digest = messageDigest.digest(idContent.toString().getBytes("UTF-8"));
+            byte[] digest = messageDigest.digest(s.getBytes("UTF-8"));
 
             // now translate the resulting byte array to hex
             String idKey = getHexRepresentation(digest);