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[Obo-svn-commit] SF.net SVN: obo:[3216] OBD-WS/trunk
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From: <ba...@us...> - 2010-03-29 15:41:14
|
Revision: 3216
http://obo.svn.sourceforge.net/obo/?rev=3216&view=rev
Author: balhoff
Date: 2010-03-29 15:41:06 +0000 (Mon, 29 Mar 2010)
Log Message:
-----------
Migrated project to Restlet 2.0. Refactored various resources to reduce duplicated code.
Modified Paths:
--------------
OBD-WS/trunk/.classpath
OBD-WS/trunk/WebContent/WEB-INF/lib/org.json.jar
OBD-WS/trunk/WebContent/WEB-INF/lib/org.restlet.jar
OBD-WS/trunk/WebContent/WEB-INF/web.xml
OBD-WS/trunk/src/org/obd/ws/application/OBDApplication.java
OBD-WS/trunk/src/org/obd/ws/resources/AbstractOBDResource.java
OBD-WS/trunk/src/org/obd/ws/resources/AnnotationResource.java
OBD-WS/trunk/src/org/obd/ws/resources/AutoCompleteResource.java
OBD-WS/trunk/src/org/obd/ws/resources/HomologyResource.java
OBD-WS/trunk/src/org/obd/ws/resources/KbRefreshTimestampResource.java
OBD-WS/trunk/src/org/obd/ws/resources/PhenotypeDetailsResource.java
OBD-WS/trunk/src/org/obd/ws/resources/PhenotypeSummaryResource.java
OBD-WS/trunk/src/org/obd/ws/resources/SquarifiedTaxonMapResource.java
OBD-WS/trunk/src/org/obd/ws/resources/TermResource.java
OBD-WS/trunk/src/org/obd/ws/statistics/reports/resources/AbstractStatisticalReportGenerator.java
OBD-WS/trunk/src/org/obd/ws/statistics/reports/resources/DataConsistencyReportGeneratorForQuestion13.java
OBD-WS/trunk/src/org/obd/ws/statistics/reports/resources/DataConsistencyReportGeneratorForQuestion21A.java
OBD-WS/trunk/src/org/obd/ws/statistics/reports/resources/DataConsistencyReportGeneratorForQuestion21B.java
OBD-WS/trunk/src/org/obd/ws/statistics/reports/resources/DataConsistencyReportGeneratorForQuestion9.java
OBD-WS/trunk/src/org/obd/ws/statistics/resources/AbstractStatisticsGenerator.java
OBD-WS/trunk/src/org/obd/ws/statistics/resources/CharactersAndGenesByAttribute.java
OBD-WS/trunk/src/org/obd/ws/statistics/resources/CharactersAndGenesBySystem.java
OBD-WS/trunk/src/org/obd/ws/statistics/resources/CharactersAndGenesBySystemAndClade.java
OBD-WS/trunk/src/org/obd/ws/statistics/resources/CharactersDatasetsAndTaxaByClade.java
OBD-WS/trunk/src/org/obd/ws/statistics/resources/PhenotypeAnnotationCounts.java
OBD-WS/trunk/test/org/obd/ws/resources/OBDResourceTest.java
Removed Paths:
-------------
OBD-WS/trunk/WebContent/WEB-INF/lib/com.noelios.restlet.ext.servlet_2.5.jar
OBD-WS/trunk/WebContent/WEB-INF/lib/com.noelios.restlet.jar
OBD-WS/trunk/WebContent/WEB-INF/lib/org.restlet.ext.json_2.0.jar
Modified: OBD-WS/trunk/.classpath
===================================================================
--- OBD-WS/trunk/.classpath 2010-03-25 17:20:59 UTC (rev 3215)
+++ OBD-WS/trunk/.classpath 2010-03-29 15:41:06 UTC (rev 3216)
@@ -4,8 +4,19 @@
<classpathentry kind="src" path="test"/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
<classpathentry kind="con" path="org.eclipse.jst.server.core.container/org.eclipse.jst.server.tomcat.runtimeTarget/Apache Tomcat v5.5"/>
- <classpathentry kind="con" path="org.eclipse.jst.j2ee.internal.web.container"/>
<classpathentry kind="con" path="org.eclipse.jst.j2ee.internal.module.container"/>
<classpathentry kind="lib" path="lib/junit-4.5.jar"/>
+ <classpathentry kind="lib" path="WebContent/WEB-INF/lib/bbop.jar"/>
+ <classpathentry kind="lib" path="WebContent/WEB-INF/lib/log4j-1.2.13.jar"/>
+ <classpathentry kind="lib" path="WebContent/WEB-INF/lib/obdapi.jar"/>
+ <classpathentry kind="lib" path="WebContent/WEB-INF/lib/obo-vocab.jar"/>
+ <classpathentry kind="lib" path="WebContent/WEB-INF/lib/obo.jar"/>
+ <classpathentry kind="lib" path="WebContent/WEB-INF/lib/postgresql-8.2-506.jdbc3.jar"/>
+ <classpathentry kind="lib" path="WebContent/WEB-INF/lib/javax.servlet.jar"/>
+ <classpathentry kind="lib" path="WebContent/WEB-INF/lib/org.json.jar"/>
+ <classpathentry kind="lib" path="WebContent/WEB-INF/lib/org.osgi.core.jar"/>
+ <classpathentry kind="lib" path="WebContent/WEB-INF/lib/org.restlet.ext.json.jar"/>
+ <classpathentry kind="lib" path="WebContent/WEB-INF/lib/org.restlet.ext.servlet.jar"/>
+ <classpathentry kind="lib" path="WebContent/WEB-INF/lib/org.restlet.jar"/>
<classpathentry kind="output" path="build/classes"/>
</classpath>
Deleted: OBD-WS/trunk/WebContent/WEB-INF/lib/com.noelios.restlet.ext.servlet_2.5.jar
===================================================================
(Binary files differ)
Deleted: OBD-WS/trunk/WebContent/WEB-INF/lib/com.noelios.restlet.jar
===================================================================
(Binary files differ)
Modified: OBD-WS/trunk/WebContent/WEB-INF/lib/org.json.jar
===================================================================
(Binary files differ)
Deleted: OBD-WS/trunk/WebContent/WEB-INF/lib/org.restlet.ext.json_2.0.jar
===================================================================
(Binary files differ)
Modified: OBD-WS/trunk/WebContent/WEB-INF/lib/org.restlet.jar
===================================================================
(Binary files differ)
Modified: OBD-WS/trunk/WebContent/WEB-INF/web.xml
===================================================================
--- OBD-WS/trunk/WebContent/WEB-INF/web.xml 2010-03-25 17:20:59 UTC (rev 3215)
+++ OBD-WS/trunk/WebContent/WEB-INF/web.xml 2010-03-29 15:41:06 UTC (rev 3216)
@@ -10,7 +10,7 @@
<!-- Restlet adapter -->
<servlet>
<servlet-name>ServerServlet</servlet-name>
- <servlet-class>com.noelios.restlet.ext.servlet.ServerServlet</servlet-class>
+ <servlet-class>org.restlet.ext.servlet.ServerServlet</servlet-class>
</servlet>
<servlet-mapping>
Modified: OBD-WS/trunk/src/org/obd/ws/application/OBDApplication.java
===================================================================
--- OBD-WS/trunk/src/org/obd/ws/application/OBDApplication.java 2010-03-25 17:20:59 UTC (rev 3215)
+++ OBD-WS/trunk/src/org/obd/ws/application/OBDApplication.java 2010-03-29 15:41:06 UTC (rev 3216)
@@ -19,98 +19,90 @@
import org.obd.ws.util.Queries;
import org.obd.ws.util.TTOTaxonomy;
import org.restlet.Application;
-import org.restlet.Context;
import org.restlet.Restlet;
-import org.restlet.Router;
+import org.restlet.routing.Router;
+import org.restlet.routing.Template;
public class OBDApplication extends Application {
- private Queries queries;
- private OBDSQLShard obdsql;
- /* Database connection parameters */
- private String selectedDatabaseName,dbHost,uid,pwd;
-
- /** A structure which maps ontology prefixes to their
- * default namespaces */
- private Map<String, Set<String>> prefixToDefaultNamespacesMap;
- /** A structure to map default namespaces of ontologies to their
- * node ids in the database */
- private Map<String, String> defaultNamespaceToNodeIdMap;
+ private Queries queries;
+ private OBDSQLShard obdsql;
+ /* Database connection parameters */
+ private String selectedDatabaseName,dbHost,uid,pwd;
- /** GETTER for the map from default namespaces of ontologies
- * to their node ids in the database */
- public Map<String, String> getDefaultNamespaceToNodeIdMap() {
- return defaultNamespaceToNodeIdMap;
- }
- /** GETTER for the map from ontology prefixes to default namespaces
- */
- public Map<String, Set<String>> getPrefixToDefaultNamespacesMap() {
- return prefixToDefaultNamespacesMap;
- }
+ /** A structure which maps ontology prefixes to their
+ * default namespaces */
+ private Map<String, Set<String>> prefixToDefaultNamespacesMap;
+ /** A structure to map default namespaces of ontologies to their
+ * node ids in the database */
+ private Map<String, String> defaultNamespaceToNodeIdMap;
- /* Some static Strings */
- public static final String PREFIX_TO_NS_FILE =
- "PrefixToDefaultNamespaceOfOntology.properties";
- public static final String PREFIX_TO_DEFAULT_NAMESPACE_MAP_STRING =
- "prefixToDefaultNamespacesMap";
- public static final String DEFAULT_NAMESPACE_TO_SOURCE_ID_MAP_STRING =
- "defaultNamespacesToSourceIdMap";
- public static final String TTO_TAXONOMY_STRING = "ttoTaxonomy";
- public static final String QUERIES_STRING = "queries";
- public static final String SHARD_STRING = "shard";
- public static final String SELECTED_DATABASE_NAME_STRING = "selectedDatabaseName";
- public static final String DB_HOST_NAME_STRING = "dbHost";
- public static final String UID_STRING = "uid";
- public static final String PWD_STRING = "pwd";
-
- /**
- * Constructor extends the default superclass constructor
- * @param context
- */
- public OBDApplication(Context context){
- super(context);
+ /** GETTER for the map from default namespaces of ontologies
+ * to their node ids in the database */
+ public Map<String, String> getDefaultNamespaceToNodeIdMap() {
+ return defaultNamespaceToNodeIdMap;
}
+ /** GETTER for the map from ontology prefixes to default namespaces
+ */
+ public Map<String, Set<String>> getPrefixToDefaultNamespacesMap() {
+ return prefixToDefaultNamespacesMap;
+ }
- /**
- * Selects the Shard pointing to the most recently updated database to be used by the
- * data services
- * Then this method sets a number of context level parameters
- * @throws SQLException
- * @throws ClassNotFoundException
- * @throws IOException
- * @throws ParseException
- * @throws PhenoscapeDbConnectionException
- * @throws DataAdapterException
- */
+ /* Some static Strings */
+ public static final String PREFIX_TO_NS_FILE =
+ "PrefixToDefaultNamespaceOfOntology.properties";
+ public static final String PREFIX_TO_DEFAULT_NAMESPACE_MAP_STRING =
+ "prefixToDefaultNamespacesMap";
+ public static final String DEFAULT_NAMESPACE_TO_SOURCE_ID_MAP_STRING =
+ "defaultNamespacesToSourceIdMap";
+ public static final String TTO_TAXONOMY_STRING = "ttoTaxonomy";
+ public static final String QUERIES_STRING = "queries";
+ public static final String SHARD_STRING = "shard";
+ public static final String SELECTED_DATABASE_NAME_STRING = "selectedDatabaseName";
+ public static final String DB_HOST_NAME_STRING = "dbHost";
+ public static final String UID_STRING = "uid";
+ public static final String PWD_STRING = "pwd";
+
+ /**
+ * Selects the Shard pointing to the most recently updated database to be used by the
+ * data services
+ * Then this method sets a number of context level parameters
+ * @throws SQLException
+ * @throws ClassNotFoundException
+ * @throws IOException
+ * @throws ParseException
+ * @throws PhenoscapeDbConnectionException
+ * @throws DataAdapterException
+ */
private void connect() throws SQLException, ClassNotFoundException, IOException, ParseException,
- PhenoscapeDbConnectionException, DataAdapterException{
-
- DatabaseToggler dbToggler = new DatabaseToggler();
- this.prefixToDefaultNamespacesMap = new HashMap<String, Set<String>>();
- this.defaultNamespaceToNodeIdMap = new HashMap<String, String>();
-
- obdsql = dbToggler.chooseDatabase();
+ PhenoscapeDbConnectionException, DataAdapterException{
+
+ DatabaseToggler dbToggler = new DatabaseToggler();
+ this.prefixToDefaultNamespacesMap = new HashMap<String, Set<String>>();
+ this.defaultNamespaceToNodeIdMap = new HashMap<String, String>();
+
+ obdsql = dbToggler.chooseDatabase();
selectedDatabaseName = dbToggler.getSelectedDatabaseName();
dbHost = dbToggler.getDbHost();
uid = dbToggler.getUid();
pwd = dbToggler.getPwd();
-
+
if(obdsql != null && selectedDatabaseName != null && dbHost != null && uid != null && pwd != null){
- this.getContext().getAttributes().put(SHARD_STRING, obdsql);
- this.getContext().getAttributes().put(SELECTED_DATABASE_NAME_STRING, selectedDatabaseName);
- this.getContext().getAttributes().put(DB_HOST_NAME_STRING, dbHost);
- this.getContext().getAttributes().put(UID_STRING, uid);
- this.getContext().getAttributes().put(PWD_STRING, pwd);
- queries = new Queries(obdsql);
- this.getContext().getAttributes().put(QUERIES_STRING, queries);
- this.constructPrefixToDefaultNamespacesMap();
- this.constructDefaultNamespaceToNodeIdMap();
- this.getContext().getAttributes().put(PREFIX_TO_DEFAULT_NAMESPACE_MAP_STRING, this.prefixToDefaultNamespacesMap);
- this.getContext().getAttributes().put(DEFAULT_NAMESPACE_TO_SOURCE_ID_MAP_STRING, this.defaultNamespaceToNodeIdMap);
+ this.getContext().getAttributes().put(SHARD_STRING, obdsql);
+ this.getContext().getAttributes().put(SELECTED_DATABASE_NAME_STRING, selectedDatabaseName);
+ this.getContext().getAttributes().put(DB_HOST_NAME_STRING, dbHost);
+ this.getContext().getAttributes().put(UID_STRING, uid);
+ this.getContext().getAttributes().put(PWD_STRING, pwd);
+ queries = new Queries(obdsql);
+ this.getContext().getAttributes().put(QUERIES_STRING, queries);
+ this.constructPrefixToDefaultNamespacesMap();
+ this.constructDefaultNamespaceToNodeIdMap();
+ this.getContext().getAttributes().put(PREFIX_TO_DEFAULT_NAMESPACE_MAP_STRING, this.prefixToDefaultNamespacesMap);
+ this.getContext().getAttributes().put(DEFAULT_NAMESPACE_TO_SOURCE_ID_MAP_STRING, this.defaultNamespaceToNodeIdMap);
}else
- throw new PhenoscapeDbConnectionException("Failed to obtain a connection to the database. " +
- "This is because neither database is ready to be queried. ");
-
+ throw new PhenoscapeDbConnectionException("Failed to obtain a connection to the database. " +
+ "This is because neither database is ready to be queried. ");
+
TTOTaxonomy ttoTaxonomy = new TTOTaxonomy();
this.getContext().getAttributes().put(TTO_TAXONOMY_STRING, ttoTaxonomy);
}
@@ -119,9 +111,10 @@
* The router method.
* It holds mappings from URL patterns to the appropriate REST service to be invoked
*/
- public Restlet createRoot() {
+ @Override
+ public Restlet createInboundRoot() {
try {
- connect();
+ connect();
} catch (SQLException e) {
log().fatal("Error connecting to SQL shard", e);
} catch (ClassNotFoundException e) {
@@ -129,13 +122,13 @@
} catch (IOException e) {
log().fatal("Error reading connection properties file", e);
} catch (ParseException e) {
- log().fatal("Error parsing the date", e);
+ log().fatal("Error parsing the date", e);
} catch (PhenoscapeDbConnectionException e) {
- log().fatal("Error with the database connection", e);
+ log().fatal("Error with the database connection", e);
} catch (DataAdapterException e) {
- log().fatal("Error reading in the OBO files", e);
- }
-
+ log().fatal("Error reading in the OBO files", e);
+ }
+
final Router router = new Router(this.getContext());
// URL mappings
router.attach("/phenotypes", org.obd.ws.resources.PhenotypeDetailsResource.class);
@@ -144,81 +137,81 @@
router.attach("/term/search", org.obd.ws.resources.AutoCompleteResource.class);
router.attach("/term/{termID}", org.obd.ws.resources.TermResource.class);
router.attach("/term/{termID}/homology", org.obd.ws.resources.HomologyResource.class);
- router.attach("/timestamp", org.obd.ws.resources.KbRefreshTimestampResource.class);
+ router.attach("/timestamp", org.obd.ws.resources.KbRefreshTimestampResource.class).setMatchingMode(Template.MODE_STARTS_WITH);
router.attach("/taxon/{taxonID}/treemap/",org.obd.ws.resources.SquarifiedTaxonMapResource.class);
/* These resources generate data consistency reports*/
router.attach("/statistics/consistencyreports/relationalqualitieswithoutrelatedentities",
- org.obd.ws.statistics.reports.resources.DataConsistencyReportGeneratorForQuestion21A.class);
+ org.obd.ws.statistics.reports.resources.DataConsistencyReportGeneratorForQuestion21A.class);
router.attach("/statistics/consistencyreports/nonrelationalqualitieswithrelatedentities",
- org.obd.ws.statistics.reports.resources.DataConsistencyReportGeneratorForQuestion21B.class);
+ org.obd.ws.statistics.reports.resources.DataConsistencyReportGeneratorForQuestion21B.class);
router.attach("/statistics/consistencyreports/characterswithonlyoneannotatedstate",
- org.obd.ws.statistics.reports.resources.DataConsistencyReportGeneratorForQuestion9.class);
+ org.obd.ws.statistics.reports.resources.DataConsistencyReportGeneratorForQuestion9.class);
router.attach("/statistics/consistencyreports/characterswithonlyoneoftwopossibleannotations",
- org.obd.ws.statistics.reports.resources.DataConsistencyReportGeneratorForQuestion13.class);
+ org.obd.ws.statistics.reports.resources.DataConsistencyReportGeneratorForQuestion13.class);
/* These resources generate summary statistics of the data */
router.attach("/statistics/phenotypeannotationcount",
- org.obd.ws.statistics.resources.PhenotypeAnnotationCounts.class);
+ org.obd.ws.statistics.resources.PhenotypeAnnotationCounts.class);
router.attach("/statistics/countsofgenesandcharactersbyattribute",
- org.obd.ws.statistics.resources.CharactersAndGenesByAttribute.class);
+ org.obd.ws.statistics.resources.CharactersAndGenesByAttribute.class);
router.attach("/statistics/countsofgenesandcharactersbysystem",
- org.obd.ws.statistics.resources.CharactersAndGenesBySystem.class);
+ org.obd.ws.statistics.resources.CharactersAndGenesBySystem.class);
router.attach("/statistics/countsofgenesandcharactersbysystemandclade",
- org.obd.ws.statistics.resources.CharactersAndGenesBySystemAndClade.class);
+ org.obd.ws.statistics.resources.CharactersAndGenesBySystemAndClade.class);
router.attach("/statistics/countsofcharactersdatasetsandtaxabyclade",
- org.obd.ws.statistics.resources.CharactersDatasetsAndTaxaByClade.class);
+ org.obd.ws.statistics.resources.CharactersDatasetsAndTaxaByClade.class);
return router;
}
-
+
private Logger log() {
return Logger.getLogger(this.getClass());
}
/**
- * PURPOSE This method reads in the list of default namespaces from a file and
- * adds the corresponding node ids to a map
- * @throws IOException
- * @throws SQLException
- */
- private void constructDefaultNamespaceToNodeIdMap() throws SQLException{
- String sourceNodeQuery = queries.getQueryForNodeIdsForOntologies();
- String nodeId, uid;
- Connection conn = obdsql.getConnection();
- java.sql.Statement stmt = conn.createStatement();
- ResultSet rs = stmt.executeQuery(sourceNodeQuery);
- while(rs.next()){
- nodeId = rs.getString(1);
- uid = rs.getString(2);
- if(uid.length() > 0){
- this.defaultNamespaceToNodeIdMap.put(uid, nodeId);
- }
- }
- }
-
- /**
- * PURPOSE This method constructs a mapping
- * from every prefix used in the autocompletion
- * service to the set of default namespaces of the
- * ontologies the prefix comes from\n
- * PROCEDURE This method reads the allowed
- * prefix to namespace mappings from a static text
- * file. This is converted into a map
- * @throws IOException
- */
- private void constructPrefixToDefaultNamespacesMap()
- throws IOException{
- InputStream inStream =
- this.getClass().getResourceAsStream(PREFIX_TO_NS_FILE);
- Properties props = new Properties();
- props.load(inStream);
- Set<String> namespaceSet;
- for(Object key : props.keySet()){
- String prefix = key.toString();
- String commaDelimitedNamespaces = props.get(key).toString();
- namespaceSet = new HashSet<String>();
- for(String namespace : commaDelimitedNamespaces.split(",")){
- namespaceSet.add(namespace);
- }
- prefixToDefaultNamespacesMap.put(prefix, namespaceSet);
- }
- }
+ * PURPOSE This method reads in the list of default namespaces from a file and
+ * adds the corresponding node ids to a map
+ * @throws IOException
+ * @throws SQLException
+ */
+ private void constructDefaultNamespaceToNodeIdMap() throws SQLException{
+ String sourceNodeQuery = queries.getQueryForNodeIdsForOntologies();
+ String nodeId, uid;
+ Connection conn = obdsql.getConnection();
+ java.sql.Statement stmt = conn.createStatement();
+ ResultSet rs = stmt.executeQuery(sourceNodeQuery);
+ while(rs.next()){
+ nodeId = rs.getString(1);
+ uid = rs.getString(2);
+ if(uid.length() > 0){
+ this.defaultNamespaceToNodeIdMap.put(uid, nodeId);
+ }
+ }
+ }
+
+ /**
+ * PURPOSE This method constructs a mapping
+ * from every prefix used in the autocompletion
+ * service to the set of default namespaces of the
+ * ontologies the prefix comes from\n
+ * PROCEDURE This method reads the allowed
+ * prefix to namespace mappings from a static text
+ * file. This is converted into a map
+ * @throws IOException
+ */
+ private void constructPrefixToDefaultNamespacesMap()
+ throws IOException{
+ InputStream inStream =
+ this.getClass().getResourceAsStream(PREFIX_TO_NS_FILE);
+ Properties props = new Properties();
+ props.load(inStream);
+ Set<String> namespaceSet;
+ for(Object key : props.keySet()){
+ String prefix = key.toString();
+ String commaDelimitedNamespaces = props.get(key).toString();
+ namespaceSet = new HashSet<String>();
+ for(String namespace : commaDelimitedNamespaces.split(",")){
+ namespaceSet.add(namespace);
+ }
+ prefixToDefaultNamespacesMap.put(prefix, namespaceSet);
+ }
+ }
}
Modified: OBD-WS/trunk/src/org/obd/ws/resources/AbstractOBDResource.java
===================================================================
--- OBD-WS/trunk/src/org/obd/ws/resources/AbstractOBDResource.java 2010-03-25 17:20:59 UTC (rev 3215)
+++ OBD-WS/trunk/src/org/obd/ws/resources/AbstractOBDResource.java 2010-03-29 15:41:06 UTC (rev 3216)
@@ -5,25 +5,28 @@
import org.apache.log4j.Logger;
import org.obd.query.impl.OBDSQLShard;
import org.obd.ws.application.OBDApplication;
-import org.restlet.Context;
-import org.restlet.data.Request;
-import org.restlet.data.Response;
-import org.restlet.resource.Resource;
+import org.restlet.resource.ResourceException;
+import org.restlet.resource.ServerResource;
-public abstract class AbstractOBDResource extends Resource {
+public abstract class AbstractOBDResource extends ServerResource {
private static final String DRIVER_NAME = "jdbc:postgresql://";
- protected OBDSQLShard shard;
+ private OBDSQLShard shard;
- public AbstractOBDResource(Context context, Request request, Response response) {
- super(context, request, response);
+ /* (non-Javadoc)
+ * @see org.restlet.resource.UniformResource#doInit()
+ * If a subclass overrides this method, it should call super's before its own implementation.
+ */
+ @Override
+ protected void doInit() throws ResourceException {
+ super.doInit();
try {
this.shard = new OBDSQLShard();
} catch (SQLException e) {
log().fatal("Failed to create shard", e);
} catch (ClassNotFoundException e) {
log().fatal("Failed to create shard", e);
- }
+ }
}
protected OBDSQLShard getShard() {
Modified: OBD-WS/trunk/src/org/obd/ws/resources/AnnotationResource.java
===================================================================
--- OBD-WS/trunk/src/org/obd/ws/resources/AnnotationResource.java 2010-03-25 17:20:59 UTC (rev 3215)
+++ OBD-WS/trunk/src/org/obd/ws/resources/AnnotationResource.java 2010-03-29 15:41:06 UTC (rev 3216)
@@ -4,27 +4,21 @@
import java.util.ArrayList;
import java.util.List;
-import org.apache.log4j.Logger;
import org.json.JSONException;
import org.json.JSONObject;
-import org.obd.query.impl.OBDSQLShard;
import org.obd.ws.application.OBDApplication;
import org.obd.ws.util.Queries;
import org.obd.ws.util.TTOTaxonomy;
import org.obd.ws.util.dto.AnnotationDTO;
import org.obd.ws.util.dto.NodeDTO;
import org.phenoscape.obd.OBDQuery;
-import org.restlet.Context;
-import org.restlet.data.MediaType;
import org.restlet.data.Reference;
-import org.restlet.data.Request;
-import org.restlet.data.Response;
import org.restlet.data.Status;
import org.restlet.ext.json.JsonRepresentation;
-import org.restlet.resource.Representation;
-import org.restlet.resource.Resource;
+import org.restlet.representation.Representation;
+import org.restlet.representation.Variant;
+import org.restlet.resource.Get;
import org.restlet.resource.ResourceException;
-import org.restlet.resource.Variant;
/**
* The purpose of this resource is to invoke a query
@@ -35,37 +29,23 @@
* endpoint
*/
-public class AnnotationResource extends Resource {
+public class AnnotationResource extends AbstractOBDResource {
- private final String driverName = "jdbc:postgresql://";
-
- private JSONObject jObjs;
-
- private OBDSQLShard obdsqlShard;
- private final String annotationId;
-
+ private JSONObject jObjs;
+
+ private String annotationId;
+
private OBDQuery obdq;
private Queries queries;
-
+
private TTOTaxonomy ttoTaxonomy;
-
- /**
- * Constructor extends the default constructor
- * Initializes the Shard, Queries, OBDQuery and the JSON Object which
- * will be returned
- * @param context
- * @param request
- * @param response
- * @throws ClassNotFoundException
- * @throws SQLException
- */
- public AnnotationResource(Context context, Request request, Response response) throws SQLException, ClassNotFoundException {
- super(context, request, response);
- this.obdsqlShard = new OBDSQLShard();
+
+ @Override
+ protected void doInit() throws ResourceException {
+ super.doInit();
this.queries = (Queries)this.getContext().getAttributes().get(OBDApplication.QUERIES_STRING);
this.ttoTaxonomy = (TTOTaxonomy)this.getContext().getAttributes().get(OBDApplication.TTO_TAXONOMY_STRING);
- this.annotationId = Reference.decode((String)(request.getAttributes().get("annotation_id")));
- this.getVariants().add(new Variant(MediaType.APPLICATION_JSON));
+ this.annotationId = Reference.decode(this.getRequestAttributes().get("annotation_id").toString());
this.jObjs = new JSONObject();
}
@@ -75,60 +55,34 @@
* packaged into a JSON Object using the {@link #assembleJSONObjectFromAnnotations(List)}
* method
*/
- public Representation represent(Variant variant) throws ResourceException {
-
- List<List<String[]>> annots;
-
- try{
- connectShardToDatabase();
- obdq = new OBDQuery(obdsqlShard, queries);
- annots = getMetadata(annotationId);
- assembleJSONObjectFromAnnotations(annots);
- }catch(SQLException sqle){
- getResponse().setStatus(Status.SERVER_ERROR_INTERNAL,
- "[SQL EXCEPTION] Something broke server side. Consult server logs");
- return null;
- } catch (ClassNotFoundException e) {
- getResponse().setStatus(Status.SERVER_ERROR_INTERNAL,
- "[CLASS NOT FOUND EXCEPTION] Something broke server side. Consult server logs");
- return null;
- } catch(JSONException jsone){
- getResponse().setStatus(Status.CLIENT_ERROR_UNPROCESSABLE_ENTITY,
- "[JSON EXCEPTION] JSON object error.");
- log().error(jsone);
+ @Get("json")
+ public Representation getJSONRepresentation() throws ResourceException {
+ List<List<String[]>> annots;
+ try{
+ connectShardToDatabase();
+ obdq = new OBDQuery(this.getShard(), queries);
+ annots = getMetadata(annotationId);
+ assembleJSONObjectFromAnnotations(annots);
+ }catch(SQLException sqle){
+ getResponse().setStatus(Status.SERVER_ERROR_INTERNAL,
+ "[SQL EXCEPTION] Something broke server side. Consult server logs");
return null;
- } finally{
- disconnectShardFromDatabase();
- }
- return new JsonRepresentation(this.jObjs);
+ } catch (ClassNotFoundException e) {
+ getResponse().setStatus(Status.SERVER_ERROR_INTERNAL,
+ "[CLASS NOT FOUND EXCEPTION] Something broke server side. Consult server logs");
+ return null;
+ } catch(JSONException jsone){
+ getResponse().setStatus(Status.CLIENT_ERROR_UNPROCESSABLE_ENTITY,
+ "[JSON EXCEPTION] JSON object error.");
+ log().error(jsone);
+ return null;
+ } finally{
+ disconnectShardFromDatabase();
+ }
+ return new JsonRepresentation(this.jObjs);
}
-
+
/**
- * This method reads in db connection parameters from app context before connecting
- * the Shard to the database
- * @throws SQLException
- * @throws ClassNotFoundException
- */
- private void connectShardToDatabase() throws SQLException, ClassNotFoundException{
- String dbName = (String)this.getContext().getAttributes().get(OBDApplication.SELECTED_DATABASE_NAME_STRING);
- String dbHost = (String)this.getContext().getAttributes().get(OBDApplication.DB_HOST_NAME_STRING);
- String uid = (String)this.getContext().getAttributes().get(OBDApplication.UID_STRING);
- String pwd = (String)this.getContext().getAttributes().get(OBDApplication.PWD_STRING);
-
- String dbConnString = driverName + dbHost + "/" + dbName;
- long connStartTime = System.currentTimeMillis();
- obdsqlShard.connect(dbConnString, uid, pwd);
- long connEndTime = System.currentTimeMillis();
- log().trace("It took " + (connEndTime - connStartTime) + " msecs to connect");
- }
-
- private void disconnectShardFromDatabase(){
- if(obdsqlShard != null)
- obdsqlShard.disconnect();
- obdsqlShard = null;
- }
-
- /**
* PURPOSE This method invokes the metadata query from
* the Queries object and loads it for execution by invoking
* the {@link OBDQuery#executeFreeTextQueryAndAssembleResults(Integer)} method.
@@ -142,54 +96,54 @@
* @throws SQLException
*/
private List<List<String[]>> getMetadata(String annotId) throws SQLException{
-
- List<List<String[]>> results = new ArrayList<List<String[]>>();
- List<String[]> annots;
-
- String taxonId, taxon, entityId, entity, qualityId, quality,
- publication, curators, charText, charComments, stateText, stateComments,
- charNumber;
-
- String[] annotIds = annotId.split(",");
-
- try{
- for(String id : annotIds){
- for(AnnotationDTO node : obdq.executeFreeTextQueryAndAssembleResults(Integer.parseInt(id))){
- taxonId = node.getTaxonId();
- taxon = node.getTaxon();
- entityId = node.getEntityId();
- entity = node.getEntity();
- qualityId = node.getQualityId();
- quality = node.getQuality();
-
- publication = node.getPublication();
- curators = node.getCurators();
- charText = node.getCharText();
- charComments = node.getCharComments();
- stateText = node.getStateText();
- stateComments = node.getStateComments();
- charNumber = node.getCharNumber();
- annots = new ArrayList<String[]>();
- annots.add(new String[]{taxonId, taxon});
- annots.add(new String[]{entityId, entity});
- annots.add(new String[]{qualityId, quality});
- annots.add(new String[]{publication});
- annots.add(new String[]{curators});
- annots.add(new String[]{charText, charComments, charNumber});
- annots.add(new String[]{stateText, stateComments});
-
- results.add(annots);
- }
- }
- }
- catch (SQLException sqle){
- sqle.printStackTrace();
- log().error(sqle);
- throw sqle;
- }
- return results;
+
+ List<List<String[]>> results = new ArrayList<List<String[]>>();
+ List<String[]> annots;
+
+ String taxonId, taxon, entityId, entity, qualityId, quality,
+ publication, curators, charText, charComments, stateText, stateComments,
+ charNumber;
+
+ String[] annotIds = annotId.split(",");
+
+ try{
+ for(String id : annotIds){
+ for(AnnotationDTO node : obdq.executeFreeTextQueryAndAssembleResults(Integer.parseInt(id))){
+ taxonId = node.getTaxonId();
+ taxon = node.getTaxon();
+ entityId = node.getEntityId();
+ entity = node.getEntity();
+ qualityId = node.getQualityId();
+ quality = node.getQuality();
+
+ publication = node.getPublication();
+ curators = node.getCurators();
+ charText = node.getCharText();
+ charComments = node.getCharComments();
+ stateText = node.getStateText();
+ stateComments = node.getStateComments();
+ charNumber = node.getCharNumber();
+ annots = new ArrayList<String[]>();
+ annots.add(new String[]{taxonId, taxon});
+ annots.add(new String[]{entityId, entity});
+ annots.add(new String[]{qualityId, quality});
+ annots.add(new String[]{publication});
+ annots.add(new String[]{curators});
+ annots.add(new String[]{charText, charComments, charNumber});
+ annots.add(new String[]{stateText, stateComments});
+
+ results.add(annots);
+ }
+ }
+ }
+ catch (SQLException sqle){
+ sqle.printStackTrace();
+ log().error(sqle);
+ throw sqle;
+ }
+ return results;
}
-
+
/**
* This method takes in a data structure of the annotations
* obtained from the {@link #getMetadata(String)} method and
@@ -198,66 +152,60 @@
* @throws JSONException
*/
private void assembleJSONObjectFromAnnotations(List<List<String[]>> annots) throws JSONException{
- List<JSONObject> sourceObjs = new ArrayList<JSONObject>();
- JSONObject phenotypeObj, sourceObj;
- JSONObject entityObj, taxonObj, qualityObj, rankObj;
-
- if(annots != null && annots.size() > 0){
- phenotypeObj = new JSONObject();
- for(List<String[]> annot : annots){
- entityObj = new JSONObject();
- taxonObj = new JSONObject();
- qualityObj = new JSONObject();
-
- sourceObj = new JSONObject();
-
- taxonObj.put("id", annot.get(0)[0]);
- taxonObj.put("name", annot.get(0)[1]);
-
- if(annot.get(0)[0].startsWith("TTO")){
- NodeDTO taxonDTO = new NodeDTO(annot.get(0)[0]);
- taxonDTO.setName(annot.get(0)[1]);
- rankObj = new JSONObject();
- NodeDTO rankDTO = ttoTaxonomy.getTaxonToRankMap().get(taxonDTO);
- if(rankDTO != null){
- rankObj.put("id", rankDTO.getId());
- rankObj.put("name", rankDTO.getName());
- }
- else{
- rankObj.put("id", "");
- rankObj.put("name", "");
- }
- taxonObj.put("rank", rankObj);
- }
-
- entityObj.put("id", annot.get(1)[0]);
- entityObj.put("name", annot.get(1)[1]);
- qualityObj.put("id", annot.get(2)[0]);
- qualityObj.put("name", annot.get(2)[1]);
-
- phenotypeObj.put("subject", taxonObj);
- phenotypeObj.put("entity", entityObj);
- phenotypeObj.put("quality", qualityObj);
-
- sourceObj.put("publication", annot.get(3)[0]);
- sourceObj.put("curated_by", annot.get(4)[0]);
- sourceObj.put("character_text", annot.get(5)[0]);
- sourceObj.put("character_comment", annot.get(5)[1]);
- sourceObj.put("character_number", annot.get(5)[2]);
- sourceObj.put("state_text", annot.get(6)[0]);
- sourceObj.put("state_comment", annot.get(6)[1]);
-
- sourceObjs.add(sourceObj);
- }
- jObjs.put("phenotype", phenotypeObj);
- jObjs.put("sources", sourceObjs);
- }
+ List<JSONObject> sourceObjs = new ArrayList<JSONObject>();
+ JSONObject phenotypeObj, sourceObj;
+ JSONObject entityObj, taxonObj, qualityObj, rankObj;
+
+ if(annots != null && annots.size() > 0){
+ phenotypeObj = new JSONObject();
+ for(List<String[]> annot : annots){
+ entityObj = new JSONObject();
+ taxonObj = new JSONObject();
+ qualityObj = new JSONObject();
+
+ sourceObj = new JSONObject();
+
+ taxonObj.put("id", annot.get(0)[0]);
+ taxonObj.put("name", annot.get(0)[1]);
+
+ if(annot.get(0)[0].startsWith("TTO")){
+ NodeDTO taxonDTO = new NodeDTO(annot.get(0)[0]);
+ taxonDTO.setName(annot.get(0)[1]);
+ rankObj = new JSONObject();
+ NodeDTO rankDTO = ttoTaxonomy.getTaxonToRankMap().get(taxonDTO);
+ if(rankDTO != null){
+ rankObj.put("id", rankDTO.getId());
+ rankObj.put("name", rankDTO.getName());
+ }
+ else{
+ rankObj.put("id", "");
+ rankObj.put("name", "");
+ }
+ taxonObj.put("rank", rankObj);
+ }
+
+ entityObj.put("id", annot.get(1)[0]);
+ entityObj.put("name", annot.get(1)[1]);
+ qualityObj.put("id", annot.get(2)[0]);
+ qualityObj.put("name", annot.get(2)[1]);
+
+ phenotypeObj.put("subject", taxonObj);
+ phenotypeObj.put("entity", entityObj);
+ phenotypeObj.put("quality", qualityObj);
+
+ sourceObj.put("publication", annot.get(3)[0]);
+ sourceObj.put("curated_by", annot.get(4)[0]);
+ sourceObj.put("character_text", annot.get(5)[0]);
+ sourceObj.put("character_comment", annot.get(5)[1]);
+ sourceObj.put("character_number", annot.get(5)[2]);
+ sourceObj.put("state_text", annot.get(6)[0]);
+ sourceObj.put("state_comment", annot.get(6)[1]);
+
+ sourceObjs.add(sourceObj);
+ }
+ jObjs.put("phenotype", phenotypeObj);
+ jObjs.put("sources", sourceObjs);
+ }
}
-
- /**
- * This method returns a logger (log4j)
- */
- private Logger log() {
- return Logger.getLogger(this.getClass());
- }
+
}
Modified: OBD-WS/trunk/src/org/obd/ws/resources/AutoCompleteResource.java
===================================================================
--- OBD-WS/trunk/src/org/obd/ws/resources/AutoCompleteResource.java 2010-03-25 17:20:59 UTC (rev 3215)
+++ OBD-WS/trunk/src/org/obd/ws/resources/AutoCompleteResource.java 2010-03-29 15:41:06 UTC (rev 3216)
@@ -11,339 +11,289 @@
import java.util.Map;
import java.util.Set;
-import org.apache.log4j.Logger;
import org.json.JSONException;
import org.json.JSONObject;
-import org.obd.query.impl.OBDSQLShard;
import org.obd.ws.application.OBDApplication;
import org.obd.ws.util.Queries;
import org.phenoscape.obd.OBDQuery;
-import org.restlet.Context;
-import org.restlet.data.MediaType;
import org.restlet.data.Reference;
-import org.restlet.data.Request;
-import org.restlet.data.Response;
import org.restlet.data.Status;
import org.restlet.ext.json.JsonRepresentation;
-import org.restlet.resource.Representation;
-import org.restlet.resource.Resource;
+import org.restlet.representation.Representation;
+import org.restlet.resource.Get;
import org.restlet.resource.ResourceException;
-import org.restlet.resource.Variant;
-public class AutoCompleteResource extends Resource {
+public class AutoCompleteResource extends AbstractOBDResource {
- private final String driverName = "jdbc:postgresql://";
-
- private String searchTerm;
- private String synonymOption;
- private String definitionOption;
- /** The list of ontologies whose terms are to be searched */
- private String ontologyOption;
-
- private JSONObject jObjs;
- private OBDSQLShard obdsqlShard;
- private Logger log;
- private Queries queries;
- /** The map from default namespaces of the ontologies to their corr. node ids in the database */
- private Map<String, String> nsToSourceIdMap;
- /** The map from prefixes of the terms to the default namespaces of the ontologies they come from */
- private Map<String, Set<String>> prefixToNSMap;
-
+ private String searchTerm;
+ private String synonymOption;
+ private String definitionOption;
+ /** The list of ontologies whose terms are to be searched */
+ private String ontologyOption;
- /** A parameter to limit the number of matches */
- private Integer limitOfMatches = null;
-
- /** A structure to keep track of the search options input
- * from the form such as ontologyList, synonyms, definitions
- * etc.
- */
- private Map<String, String> searchOptions;
-
- private static final String ID_STRING = "id";
- private static final String NAME_STRING = "name";
- private static final String SYNONYM_STRING = "synonym";
- private static final String DEF_STRING = "definition";
- private static final String MATCH_TYPE_STRING = "match_type";
- private static final String MATCH_TEXT_STRING = "match_text";
- private static final String MATCHES_STRING = "matches";
-
- private static final String ONTOLOGY_OPTION_STRING = "ontologyOption";
- private static final String SYNONYM_OPTION_STRING = "synonymOption";
- private static final String DEFINITION_OPTION_STRING = "definitionOption";
-
- private static final String INPUT_TEXT_STRING = "text";
- private static final String INPUT_SYN_STRING = "syn";
- private static final String INPUT_DEF_STRING = "def";
- private static final String INPUT_ONTOLOGY_STRING = "ontology";
- private static final String INPUT_LIMIT_STRING = "limit";
-
- /**
- * This comparator is used to order collections of JSON objects.
- * The property values for the {@literal #MATCH_TEXT_STRING} is used
- * to compare the JSON objects
- */
- private static final Comparator<JSONObject> MATCHES_COMPARATOR = new Comparator<JSONObject>() {
- public int compare(JSONObject o1, JSONObject o2) {
- try {
- return ((String)o1.get(MATCH_TEXT_STRING)).compareToIgnoreCase((String)o2.get(MATCH_TEXT_STRING));
- } catch (JSONException e) {
- return 0;
- }
- }
- };
-
- /**
- * PURPOSE This construnctor instantiates all the instance variables and also
- * reads in the form parameters. It also does a little work towards setting up the final query
- * to be executed\n
- * @param context - the application context
- * @param request - the Rest request
- * @param response - the Rest response
- * @throws SQLException
- * @throws ClassNotFoundException
- */
- public AutoCompleteResource(Context context, Request request, Response response) throws SQLException, ClassNotFoundException {
- super(context, request, response);
- this.obdsqlShard = new OBDSQLShard();
- this.queries = (Queries)this.getContext().getAttributes().get(OBDApplication.QUERIES_STRING);
- this.prefixToNSMap =
- (Map<String, Set<String>>)this.getContext().getAttributes().get(OBDApplication.PREFIX_TO_DEFAULT_NAMESPACE_MAP_STRING);
- this.nsToSourceIdMap =
- (Map<String, String>)this.getContext().getAttributes().get(OBDApplication.DEFAULT_NAMESPACE_TO_SOURCE_ID_MAP_STRING);
- this.log = Logger.getLogger(this.getClass());
- this.searchOptions = new HashMap<String, String>();
-
- this.getVariants().add(new Variant(MediaType.APPLICATION_JSON));
-
- this.searchTerm = Reference.decode((String) request.getResourceRef().getQueryAsForm().getFirstValue(INPUT_TEXT_STRING));
+ private JSONObject jObjs;
+ private Queries queries;
+ /** The map from default namespaces of the ontologies to their corr. node ids in the database */
+ private Map<String, String> nsToSourceIdMap;
+ /** The map from prefixes of the terms to the default namespaces of the ontologies they come from */
+ private Map<String, Set<String>> prefixToNSMap;
+
+
+ /** A parameter to limit the number of matches */
+ private Integer limitOfMatches = null;
+
+ /** A structure to keep track of the search options input
+ * from the form such as ontologyList, synonyms, definitions
+ * etc.
+ */
+ private Map<String, String> searchOptions;
+
+ private static final String ID_STRING = "id";
+ private static final String NAME_STRING = "name";
+ private static final String SYNONYM_STRING = "synonym";
+ private static final String DEF_STRING = "definition";
+ private static final String MATCH_TYPE_STRING = "match_type";
+ private static final String MATCH_TEXT_STRING = "match_text";
+ private static final String MATCHES_STRING = "matches";
+
+ private static final String ONTOLOGY_OPTION_STRING = "ontologyOption";
+ private static final String SYNONYM_OPTION_STRING = "synonymOption";
+ private static final String DEFINITION_OPTION_STRING = "definitionOption";
+
+ private static final String INPUT_TEXT_STRING = "text";
+ private static final String INPUT_SYN_STRING = "syn";
+ private static final String INPUT_DEF_STRING = "def";
+ private static final String INPUT_ONTOLOGY_STRING = "ontology";
+ private static final String INPUT_LIMIT_STRING = "limit";
+
+ /**
+ * This comparator is used to order collections of JSON objects.
+ * The property values for the {@literal #MATCH_TEXT_STRING} is used
+ * to compare the JSON objects
+ */
+ private static final Comparator<JSONObject> MATCHES_COMPARATOR = new Comparator<JSONObject>() {
+ public int compare(JSONObject o1, JSONObject o2) {
+ try {
+ return ((String)o1.get(MATCH_TEXT_STRING)).compareToIgnoreCase((String)o2.get(MATCH_TEXT_STRING));
+ } catch (JSONException e) {
+ return 0;
+ }
+ }
+ };
+
+ @SuppressWarnings("unchecked")
+ @Override
+ protected void doInit() throws ResourceException {
+ super.doInit();
+ this.queries = (Queries)this.getContext().getAttributes().get(OBDApplication.QUERIES_STRING);
+ this.prefixToNSMap = (Map<String, Set<String>>)this.getContext().getAttributes().get(OBDApplication.PREFIX_TO_DEFAULT_NAMESPACE_MAP_STRING);
+ this.nsToSourceIdMap = (Map<String, String>)this.getContext().getAttributes().get(OBDApplication.DEFAULT_NAMESPACE_TO_SOURCE_ID_MAP_STRING);
+ this.searchOptions = new HashMap<String, String>();
+
+ this.searchTerm = Reference.decode((String) this.getQuery().getFirstValue(INPUT_TEXT_STRING));
searchTerm = searchTerm.trim().toLowerCase();
- if(request.getResourceRef().getQueryAsForm().getFirstValue(INPUT_SYN_STRING) != null)
- synonymOption = Reference.decode((String) request.getResourceRef().getQueryAsForm().getFirstValue(INPUT_SYN_STRING));
- if(request.getResourceRef().getQueryAsForm().getFirstValue(INPUT_DEF_STRING ) != null)
- definitionOption = Reference.decode((String) request.getResourceRef().getQueryAsForm().getFirstValue(INPUT_DEF_STRING ));
- if(request.getResourceRef().getQueryAsForm().getFirstValue(INPUT_ONTOLOGY_STRING) != null)
- ontologyOption = Reference.decode((String) request.getResourceRef().getQueryAsForm().getFirstValue(INPUT_ONTOLOGY_STRING));
-
- final String limitParameter = request.getResourceRef().getQueryAsForm().getFirstValue(INPUT_LIMIT_STRING);
- if (limitParameter != null)
- this.limitOfMatches = Integer.parseInt(limitParameter);
- if(!inputFormParametersAreValid()){
- throw new IllegalArgumentException("Invalid form parameters");
- }
- searchOptions.put(SYNONYM_OPTION_STRING, synonymOption);
- searchOptions.put(DEFINITION_OPTION_STRING, definitionOption);
- searchOptions.put(ONTOLOGY_OPTION_STRING, ontologyOption);
- }
-
- /**
- * A method to check if input parameters from the form are valid
- * @return a boolean to indicate if the input form parameters are valid
- */
- private boolean inputFormParametersAreValid(){
- if(searchTerm == null){
- getResponse().setStatus(
- Status.CLIENT_ERROR_BAD_REQUEST,
- "ERROR: Please specify a string to search for");
- return false;
- }
- if (limitOfMatches != null) {
- try {
- if (this.limitOfMatches < 1) {
- this.limitOfMatches = null;
- }
- } catch (NumberFormatException e) {
- log.error("The value for the limit parameter was not a valid integer", e);
- this.limitOfMatches = null;
- return false;
- }
- }
- return true;
- }
+ if(this.getQuery().getFirstValue(INPUT_SYN_STRING) != null)
+ synonymOption = Reference.decode((String) this.getQuery().getFirstValue(INPUT_SYN_STRING));
+ if(this.getQuery().getFirstValue(INPUT_DEF_STRING ) != null)
+ definitionOption = Reference.decode((String) this.getQuery().getFirstValue(INPUT_DEF_STRING ));
+ if(this.getQuery().getFirstValue(INPUT_ONTOLOGY_STRING) != null)
+ ontologyOption = Reference.decode((String) this.getQuery().getFirstValue(INPUT_ONTOLOGY_STRING));
+ final String limitParameter = this.getQuery().getFirstValue(INPUT_LIMIT_STRING);
+ if (limitParameter != null)
+ this.limitOfMatches = Integer.parseInt(limitParameter);
+ if(!inputFormParametersAreValid()){
+ throw new IllegalArgumentException("Invalid form parameters");
+ }
+ searchOptions.put(SYNONYM_OPTION_STRING, synonymOption);
+ searchOptions.put(DEFINITION_OPTION_STRING, definitionOption);
+ searchOptions.put(ONTOLOGY_OPTION_STRING, ontologyOption);
+ }
+
+
+
/**
+ * A method to check if input parameters from the form are valid
+ * @return a boolean to indicate if the input form parameters are valid
+ */
+ private boolean inputFormParametersAreValid(){
+ if(searchTerm == null){
+ getResponse().setStatus(
+ Status.CLIENT_ERROR_BAD_REQUEST,
+ "ERROR: Please specify a string to search for");
+ return false;
+ }
+ if (limitOfMatches != null) {
+ try {
+ if (this.limitOfMatches < 1) {
+ this.limitOfMatches = null;
+ }
+ } catch (NumberFormatException e) {
+ log().error("The value for the limit parameter was not a valid integer", e);
+ this.limitOfMatches = null;
+ return false;
+ }
+ }
+ return true;
+ }
+
+ /**
* This method is responsible for creating the representation of the JSON Object
* from the query results which will be forwarded to the invoking client
*/
- @Override
- public Representation represent(Variant variant)
- throws ResourceException {
+ @Get("json")
+ public Representation getJSONRepresentation() throws ResourceException {
- Representation rep = null;
- try {
- connectShardToDatabase();
- this.jObjs = getTextMatches();
- } catch (JSONException e) {
- getResponse().setStatus(Status.SERVER_ERROR_INTERNAL,
- "[JSON EXCEPTION] Something broke on the JSON Object side. Consult server logs");
- log.error(e);
+ Representation rep = null;
+ try {
+ connectShardToDatabase();
+ this.jObjs = getTextMatches();
+ } catch (JSONException e) {
+ getResponse().setStatus(Status.SERVER_ERROR_INTERNAL,
+ "[JSON EXCEPTION] Something broke on the JSON Object side. Consult server logs");
+ log().error(e);
return null;
- } catch (SQLException e) {
- getResponse().setStatus(Status.SERVER_ERROR_INTERNAL,
- "[SQL EXCEPTION] Something broke on the SQL query. Consult server logs");
- log.error(e);
+ } catch (SQLException e) {
+ getResponse().setStatus(Status.SERVER_ERROR_INTERNAL,
+ "[SQL EXCEPTION] Something broke on the SQL query. Consult server logs");
+ log().error(e);
return null;
- } catch (ClassNotFoundException e) {
- getResponse().setStatus(Status.SERVER_ERROR_INTERNAL,
- "[CLASS NOT FOUND EXCEPTION] Something broke on the SQL query. Consult server logs");
- log.error(e);
- return null;
- } finally{
- disconnectShardFromDatabase();
- }
- rep = new JsonRepresentation(this.jObjs);
- return rep;
- }
+ } catch (ClassNotFoundException e) {
+ getResponse().setStatus(Status.SERVER_ERROR_INTERNAL,
+ "[CLASS NOT FOUND EXCEPTION] Something broke on the SQL query. Consult server logs");
+ log().error(e);
+ return null;
+ } finally{
+ disconnectShardFromDatabase();
+ }
+ rep = new JsonRepresentation(this.jObjs);
+ return rep;
+ }
/**
- * This method reads in db connection parameters from app context and connects the Shard to the
- * database
+ * This method arranges the user defined options and invokes the
+ * {@link OBDQuery#getAutocompletionsForSearchTerm(String, Map)} method to find
+ * label (default), synonym and definition (optional) matches for the search string.
+ * @return JSON object to be sent to the UI
+ * @throws IOException
* @throws SQLException
* @throws ClassNotFoundException
+ * @throws JSONException
*/
- private void connectShardToDatabase() throws SQLException, ClassNotFoundException{
- String dbName = (String)this.getContext().getAttributes().get(OBDApplication.SELECTED_DATABASE_NAME_STRING);
- String dbHost = (String)this.getContext().getAttributes().get(OBDApplication.DB_HOST_NAME_STRING);
- String uid = (String)this.getContext().getAttributes().get(OBDApplication.UID_STRING);
- String pwd = (String)this.getContext().getAttributes().get(OBDApplication.PWD_STRING);
-
- String dbConnString = driverName + dbHost + "/" + dbName;
- long connStartTime = System.currentTimeMillis();
- obdsqlShard.connect(dbConnString, uid, pwd);
- long connEndTime = System.currentTimeMillis();
- log.trace("It took " + (connEndTime - connStartTime) + " msecs to connect");
+ private JSONObject getTextMatches() throws JSONException, SQLException {
+
+ JSONObject jObj = new JSONObject();
+ OBDQuery obdq = new OBDQuery(this.getShard(), this.queries, this.nsToSourceIdMap, this.prefixToNSMap);
+ //For search terms shorter than 3, only "begins with" searches are done
+ String term = searchTerm.length() > 3 ? "%" + searchTerm + "%" : searchTerm + "%";
+ Map<String, List<List<String>>> results =
+ obdq.getAutocompletionsForSearchTerm(term, searchOptions);
+
+ List<List<String>> labelMatches =
+ results.get(OBDQuery.AutoCompletionMatchTypes.LABEL_MATCH.name());
+ List<List<String>> synonymMatches =
+ results.get(OBDQuery.AutoCompletionMatchTypes.SYNONYM_MATCH.name());
+ List<List<String>> definitionMatches =
+ results.get(OBDQuery.AutoCompletionMatchTypes.DEFINITION_MATCH.name());
+
+ Set<JSONObject> matches = new HashSet<JSONObject>();
+ int i = 0, j = 0, k = 0;
+ if(labelMatches.size() > 0){
+ for(List<String> label : labelMatches){
+ JSONObject nameMatch = new JSONObject();
+ nameMatch.put(ID_STRING, label.get(0));
+ nameMatch.put(NAME_STRING, label.get(1));
+ nameMatch.put(MATCH_TYPE_STRING, NAME_STRING);
+ nameMatch.put(MATCH_TEXT_STRING, label.get(1));
+ matches.add(nameMatch);
+ log().debug( ++i + ". Name matches for search term: " + searchTerm + "\tID: " + label.get(0) + "\tLABEL: " + label.get(1));
+ }
+ }
+ if(synonymMatches != null && synonymMatches.size() > 0){
+ for(List<String> synonym : synonymMatches){
+ JSONObject synonymMatch = new JSONObject();
+ synonymMatch.put(ID_STRING, synonym.get(0));
+ synonymMatch.put(NAME_STRING, synonym.get(1));
+ synonymMatch.put(MATCH_TYPE_STRING, SYNONYM_STRING);
+ synonymMatch.put(MATCH_TEXT_STRING, synonym.get(2));
+ matches.add(synonymMatch);
+ log().debug(++j + ". Synonym matches for search term: " + searchTerm + "\tID: " + synonym.get(0) + "\tLABEL: " +
+ synonym.get(1) + "\tSYNONYM: " + synonym.get(2));
+ }
+ }
+ if(definitionMatches != null && definitionMatches.size() > 0){
+ for(List<String> definition : definitionMatches){
+ JSONObject definitionMatch = new JSONObject();
+ definitionMatch.put(ID_STRING, definition.get(0));
+ definitionMatch.put(NAME_STRING, definition.get(1));
+ definitionMatch.put(MATCH_TYPE_STRING, DEF_STRING);
+ definitionMatch.put(MATCH_TEXT_STRING, definition.get(3));
+ matches.add(definitionMatch);
+ log().debug(++k + ". Definition matches for search term: " + searchTerm + "\tID: " + definition.get(0) + "\tLABEL: " +
+ definition.get(1) + "\tDefinition: " + definition.get(3));
+ }
+ }
+ jObj.put("search_term", searchTerm);
+ try{
+ List<JSONObject> sortedMatches = sortJsonObjects(matches, searchTerm);
+ jObj.put(MATCHES_STRING, sortedMatches);
+ }
+ catch(JSONException e){
+ log().error("JSON Exception: " + e.getMessage());
+ jObj.put(MATCHES_STRING, matches);
+ /* FIXME why are we swallowing this exception? */
+ }
+ return jObj;
}
-
- private void disconnectShardFromDatabase(){
- if(obdsqlShard != null)
- obdsqlShard.disconnect();
- obdsqlShard = null;
- }
-
- /**
- * This method arranges the user defined options and invokes the
- * {@link OBDQuery#getAutocompletionsForSearchTerm(String, Map)} method to find
- * label (default), synonym and definition (optional) matches for the search string.
- * @return JSON object to be sent to the UI
- * @throws IOException
- * @throws SQLException
- * @throws ClassNotFoundException
- * @throws JSONException
- */
- private JSONObject getTextMatches()
- throws JSONException, SQLException {
- JSONObject jObj = new JSONObject();
- OBDQuery obdq = new OBDQuery(obdsqlShard, this.queries, this.nsToSourceIdMap, this.prefixToNSMap);
- //For search terms shorter than 3, only "begins with" searches are done
- String term = searchTerm.length() > 3 ? "%" + searchTerm + "%" : searchTerm + "%";
- Map<String, List<List<String>>> results =
- obdq.getAutocompletionsForSearchTerm(term, searchOptions);
-
- List<List<String>> labelMatches =
- results.get(OBDQuery.AutoCompletionMatchTypes.LABEL_MATCH.name());
- List<List<String>> synonymMatches =
- results.get(OBDQuery.AutoCompletionMatchTypes.SYNONYM_MATCH.name());
- List<List<String>> definitionMatches =
- results.get(OBDQuery.AutoCompletionMatchTypes.DEFINITION_MATCH.name());
-
- Set<JSONObject> matches = new HashSet<JSONObject>();
- int i = 0, j = 0, k = 0;
- if(labelMatches.size() > 0){
- for(List<String> label : labelMatches){
- JSONObject nameMatch = new JSONObject();
- nameMatch.put(ID_STRING, label.get(0));
- nameMatch.put(NAME_STRING, label.get(1));
- nameMatch.put(MATCH_TYPE_STRING, NAME_STRING);
- nameMatch.put(MATCH_TEXT_STRING, label.get(1));
- matches.add(nameMatch);
- log.debug( ++i + ". Name matches for search term: " + searchTerm + "\tID: " + label.get(0) + "\tLABEL: " + label.ge...
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