[MOBY-guts] biomoby commit
Eddie Kawas
kawas at pub.open-bio.org
Tue Mar 14 16:23:06 UTC 2006
kawas
Tue Mar 14 11:23:06 EST 2006
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/definitions/types
In directory pub.open-bio.org:/tmp/cvs-serv25768/org/biomoby/registry/definitions/types
Modified Files:
JServicesSqlImpl.java JNamespacesSqlImpl.java
Log Message:
new method to retrieve full service type information, like lsid, contact_email, authority, etc for use (in the RDF) by registry clients
moby-live/Java/src/main/org/biomoby/registry/definitions/types JServicesSqlImpl.java,1.1,1.2 JNamespacesSqlImpl.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/definitions/types/JServicesSqlImpl.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/definitions/types/JServicesSqlImpl.java 2005/08/29 20:19:20 1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/definitions/types/JServicesSqlImpl.java 2006/03/14 16:23:06 1.2
@@ -16,115 +16,175 @@
import org.biomoby.shared.MobyException;
/**
- * @author Eddie Kawas
- * mySQL implementation of JServicesI
- * <p>email me at edward.kawas at gmail.com
+ * @author Eddie Kawas mySQL implementation of JServicesI
+ * <p>
+ * email me at edward.kawas at gmail.com
*/
-public final class JServicesSqlImpl implements JServiceI{
- private static final String sql = "SELECT ot1.service_type, rt.relationship_type, ot2.service_type, ot1.description "
- + "FROM service as ot1, service_term2term as rt, service as ot2 "
- + "WHERE ot1.service_id = rt.service1_id and ot2.service_id = rt.service2_id order by ot1.service_type";
-
- private Connection connection = null;
-
- private final String newline = System.getProperty("line.separator");
-
- /**
- *
- * @throws MobyException if database driver cannot be found or there is an database access error.
- */
- public JServicesSqlImpl() throws MobyException {
- try {
- // Load the JDBC driver
- String driverName = "com.mysql.jdbc.Driver";
- Class.forName(driverName);
- // get certain properties from mobycentral.config
- Map map = MobyCentralConfig.getMobyService();
- // Create a connection to the database
- String serverName = map.get("url") + ":" + map.get("port");//localhost:3306"; //TODO - make this a property
- String mydatabase = (String) map.get("dbname");//"mobyobject";
- String url = "jdbc:mysql://" + serverName + "/" + mydatabase;
- String username = (String) map.get("username");//"moby_external";
- String password = (String) map.get("password");//"";
-
- /* String serverName = "mobycentral.icapture.ubc.ca:3306";
- String mydatabase = "mobyservice";
- String url = "jdbc:mysql://" + serverName + "/" + mydatabase;
- String username = "moby_external";
- String password = "";*/
- this.connection = DriverManager.getConnection(url, username,
- password);
- } catch (ClassNotFoundException e) {
- throw new MobyException(
- "Could not find database driver. Please ensure that you have the right libraries present");
- } catch (SQLException e) {
- e.printStackTrace();
- throw new MobyException("Database access error.");
- }
- }
-
- /* (non-Javadoc)
- * @see org.biomoby.registry.definitions.types.JServiceI#getServices()
- */
- public final String getServices() {
- StringBuffer sb = new StringBuffer();
- /*ensure connection is not null*/
- if (connection == null)
- return "";
-
- ResultSet rs = null;
- try {
- Statement stmt = connection.createStatement();
- rs = stmt.executeQuery(sql);
- } catch (SQLException ex) {
- // TODO - throw exception - Error in sql
- return ex.getMessage();
- }
- try {
- while (rs.next()) {
- // Get the data from the row using the column index
- sb.append(rs.getString(1) + "\t" + rs.getString(2) + "\t"
- + rs.getString(3) + "\t" + rs.getString(4) + newline);
- }
- } catch (SQLException e) {
- // TODO - throw exception - Database access error
- return e.getMessage();
- }
- return sb.toString();
- }
-
- /* (non-Javadoc)
- * @see org.biomoby.registry.definitions.types.JServiceI#getServicesAsArray()
- */
- public String[][] getServicesAsArray() {
- ArrayList sb = new ArrayList();
- /*ensure connection is not null*/
- if (connection == null)
- return null;
-
- ResultSet rs = null;
- try {
- Statement stmt = connection.createStatement();
- rs = stmt.executeQuery(sql);
- } catch (SQLException ex) {
- // TODO - throw exception - Error in sql
- return null;
- }
- try {
- while (rs.next()) {
- // Get the data from the row using the column index
- sb.add(new String[] {rs.getString(1) , rs.getString(2), rs.getString(3), rs.getString(4)});
- }
- } catch (SQLException e) {
- // TODO - throw exception - Database access error
- return null;
- }
- String[][] array = new String[sb.size()][];
- sb.toArray( array );
- return array;
- }
-
- public static void main(String[] args) throws MobyException {
- System.out.println(new JServicesSqlImpl().getServicesAsArray());
- }
+public final class JServicesSqlImpl implements JServiceI {
+ private static final String sql = "SELECT ot1.service_type, rt.relationship_type, ot2.service_type, ot1.description "
+ + "FROM service as ot1, service_term2term as rt, service as ot2 "
+ + "WHERE ot1.service_id = rt.service1_id and ot2.service_id = rt.service2_id order by ot1.service_type";
+
+ private static final String sql_all = "SELECT ot1.service_type, rt.relationship_type, ot2.service_type, ot1.description, ot1.service_lsid, ot1.authority, ot1.contact_email "
+ + "FROM service as ot1, service_term2term as rt, service as ot2 "
+ + "WHERE ot1.service_id = rt.service1_id and ot2.service_id = rt.service2_id order by ot1.service_type";
+
+ private Connection connection = null;
+
+ private final String newline = System.getProperty("line.separator");
+
+ /**
+ *
+ * @throws MobyException
+ * if database driver cannot be found or there is an database
+ * access error.
+ */
+ public JServicesSqlImpl() throws MobyException {
+ try {
+ // Load the JDBC driver
+ String driverName = "com.mysql.jdbc.Driver";
+ Class.forName(driverName);
+ // get certain properties from mobycentral.config
+ Map map = MobyCentralConfig.getMobyService();
+ // Create a connection to the database
+ String serverName = map.get("url") + ":" + map.get("port");// localhost:3306";
+ // //TODO
+ // -
+ // make
+ // this
+ // a
+ // property
+ String mydatabase = (String) map.get("dbname");// "mobyobject";
+ String url = "jdbc:mysql://" + serverName + "/" + mydatabase;
+ String username = (String) map.get("username");// "moby_external";
+ String password = (String) map.get("password");// "";
+
+ /*
+ * String serverName = "mobycentral.icapture.ubc.ca:3306"; String
+ * mydatabase = "mobyservice"; String url = "jdbc:mysql://" +
+ * serverName + "/" + mydatabase; String username = "moby_external";
+ * String password = "";
+ */
+ this.connection = DriverManager.getConnection(url, username, password);
+ } catch (ClassNotFoundException e) {
+ throw new MobyException(
+ "Could not find database driver. Please ensure that you have the right libraries present");
+ } catch (SQLException e) {
+ e.printStackTrace();
+ throw new MobyException("Database access error.");
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.biomoby.registry.definitions.types.JServiceI#getServices()
+ */
+ public final String getServices() {
+ StringBuffer sb = new StringBuffer();
+ /* ensure connection is not null */
+ if (connection == null)
+ return "";
+
+ ResultSet rs = null;
+ try {
+ Statement stmt = connection.createStatement();
+ rs = stmt.executeQuery(sql);
+ } catch (SQLException ex) {
+ // TODO - throw exception - Error in sql
+ return ex.getMessage();
+ }
+ try {
+ while (rs.next()) {
+ // Get the data from the row using the column index
+ sb.append(rs.getString(1) + "\t" + rs.getString(2) + "\t" + rs.getString(3) + "\t"
+ + rs.getString(4) + newline);
+ }
+ } catch (SQLException e) {
+ // TODO - throw exception - Database access error
+ return e.getMessage();
+ }
+ return sb.toString();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.biomoby.registry.definitions.types.JServiceI#getServicesAsArray()
+ */
+ public String[][] getServicesAsArray() {
+ ArrayList sb = new ArrayList();
+ /* ensure connection is not null */
+ if (connection == null)
+ return null;
+
+ ResultSet rs = null;
+ try {
+ Statement stmt = connection.createStatement();
+ rs = stmt.executeQuery(sql);
+ } catch (SQLException ex) {
+ // TODO - throw exception - Error in sql
+ return null;
+ }
+ try {
+ while (rs.next()) {
+ // Get the data from the row using the column index
+ sb.add(new String[] { rs.getString(1), rs.getString(2), rs.getString(3),
+ rs.getString(4) });
+ }
+ } catch (SQLException e) {
+ // TODO - throw exception - Database access error
+ return null;
+ }
+ String[][] array = new String[sb.size()][];
+ sb.toArray(array);
+ return array;
+ }
+
+ /**
+ * Get all the data in the db regrading service types.
+ * @return an array of String[] objects. The String[] consists of
+ * {service_type, relationship_type, to_service_type, description, service_lsid, authority,
+ * contact_email}. <em>Note that relationship_type is the relationship that service_type has
+ * with to_service_type.</em>
+ */
+ public String[][] getFullServicesAsArray() {
+ ArrayList sb = new ArrayList();
+ /* ensure connection is not null */
+ if (connection == null)
+ return null;
+
+ ResultSet rs = null;
+ try {
+ Statement stmt = connection.createStatement();
+ rs = stmt.executeQuery(sql_all);
+ } catch (SQLException ex) {
+ // TODO - throw exception - Error in sql
+ return null;
+ }
+ try {
+ while (rs.next()) {
+ // Get the data from the row using the column index
+ sb.add(new String[] { rs.getString(1), rs.getString(2), rs.getString(3),
+ rs.getString(4), rs.getString(5), rs.getString(6), rs.getString(7) });
+ }
+ } catch (SQLException e) {
+ // TODO - throw exception - Database access error
+ return null;
+ }
+ String[][] array = new String[sb.size()][];
+ sb.toArray(array);
+ return array;
+ }
+
+ public static void main(String[] args) throws MobyException {
+ String[][] services = new JServicesSqlImpl().getFullServicesAsArray();
+ for (int i = 0; i < services.length; i++) {
+ String[] service = services[i];
+ for (int j = 0; j < service.length; j++) {
+ System.out.print(service[j] + " ");
+ }
+ System.out.println();
+ }
+ }
}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/definitions/types/JNamespacesSqlImpl.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/definitions/types/JNamespacesSqlImpl.java 2006/03/14 16:11:43 1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/definitions/types/JNamespacesSqlImpl.java 2006/03/14 16:23:06 1.3
@@ -16,149 +16,165 @@
import org.biomoby.shared.MobyException;
/**
- * @author Eddie Kawas
- * mySQL implementation of JNamespaceI.
- * <p>email me at edward.kawas at gmail.com
+ * @author Eddie Kawas mySQL implementation of JNamespaceI.
+ * <p>
+ * email me at edward.kawas at gmail.com
*/
-public final class JNamespacesSqlImpl implements JNamespaceI{
- private static final String sql = "SELECT namespace_type, description FROM namespace ORDER BY namespace_type asc";
-
- private static final String sql_all = "SELECT namespace_type, description, namespace_lsid, authority, contact_email FROM namespace ORDER BY namespace_type asc";
-
- private final String newline = System.getProperty("line.separator");
-
- private Connection connection = null;
-
- /**
- *
- * @throws MobyException if database driver cannot be found or there is an database access error.
- */
- public JNamespacesSqlImpl() throws MobyException {
- try {
- // Load the JDBC driver
- String driverName = "com.mysql.jdbc.Driver";
- Class.forName(driverName);
- // get certain properties from mobycentral.config
- Map map = MobyCentralConfig.getMobyNamespace();
- // Create a connection to the database
- String serverName = map.get("url") + ":" + map.get("port");//localhost:3306"; //TODO - make this a property
- String mydatabase = (String) map.get("dbname");//"mobyobject";
- String url = "jdbc:mysql://" + serverName + "/" + mydatabase;
- String username = (String) map.get("username");//"moby_external";
- String password = (String) map.get("password");//"";
-
- /* String serverName = "mobycentral.icapture.ubc.ca:3306";
- String mydatabase = "mobynamespace";
- String url = "jdbc:mysql://" + serverName + "/" + mydatabase;
- String username = "moby_external";
- String password = "";*/
- this.connection = DriverManager.getConnection(url, username,
- password);
- } catch (ClassNotFoundException e) {
- throw new MobyException(
- "Could not find database driver. Please ensure that you have the right libraries present");
- } catch (SQLException e) {
- e.printStackTrace();
- throw new MobyException("Database access error.");
- }
- }
-
- /* (non-Javadoc)
- * @see org.biomoby.registry.definitions.types.JNamespaceI#getNamespaces()
- */
- public final String getNamespaces() {
- /*ensure that the connection isnt null*/
- if (connection == null)
- return "";
-
- StringBuffer sb = new StringBuffer();
- ResultSet rs = null;
- try {
- Statement stmt = connection.createStatement();
- rs = stmt.executeQuery(sql);
- } catch (SQLException ex) {
- // TODO - throw exception - Error in sql
- return ex.getMessage();
- }
- try {
- while (rs.next()) {
- // Get the data from the row using the column index
- sb.append(rs.getString(1) + "\t" + rs.getString(2) + newline);
- }
- } catch (SQLException e) {
- // TODO - throw exception - Database access error
- return e.getMessage();
- }
- return sb.toString();
- }
-
- /* (non-Javadoc)
- * @see org.biomoby.registry.definitions.types.JNamespaceI#getNamespacesAsArray()
- */
- public String[][] getNamespacesAsArray() {
- /*ensure that the connection isnt null*/
- if (connection == null)
- return null;
-
- ArrayList sb = new ArrayList();
- ResultSet rs = null;
- try {
- Statement stmt = connection.createStatement();
- rs = stmt.executeQuery(sql);
- } catch (SQLException ex) {
- return null;
- }
- try {
- while (rs.next()) {
- // Get the data from the row using the column index
- sb.add(new String[]{ rs.getString(1), rs.getString(2)});
- }
- } catch (SQLException e) {
- return null;
- }
- String[][] array = new String[sb.size()][];
- sb.toArray(array);
- return array;
- }
-
- /**
- * Get all the data in the db regrading namespaces.
- * @return
- */
- public String[][] getFullNamespacesAsArray() {
- /*ensure that the connection isnt null*/
- if (connection == null)
- return null;
-
- ArrayList sb = new ArrayList();
- ResultSet rs = null;
- try {
- Statement stmt = connection.createStatement();
- rs = stmt.executeQuery(sql_all);
- } catch (SQLException ex) {
- return null;
- }
- try {
- while (rs.next()) {
- // Get the data from the row using the column index
- sb.add(new String[]{ rs.getString(1), rs.getString(2), rs.getString(3), rs.getString(4), rs.getString(5)});
- }
- } catch (SQLException e) {
- return null;
- }
- String[][] array = new String[sb.size()][];
- sb.toArray(array);
- return array;
- }
-
- public static void main(String[] args) throws MobyException {
- String[][] namespaces =new JNamespacesSqlImpl().getFullNamespacesAsArray();
- for (int i = 0; i < namespaces.length; i++) {
- String[] namespace = namespaces[i];
- for (int j = 0; j < namespace.length; j++) {
- System.out.print(namespace[j] + " ");
+public final class JNamespacesSqlImpl implements JNamespaceI {
+ private static final String sql = "SELECT namespace_type, description FROM namespace ORDER BY namespace_type asc";
+
+ private static final String sql_all = "SELECT namespace_type, description, namespace_lsid, authority, contact_email FROM namespace ORDER BY namespace_type asc";
+
+ private final String newline = System.getProperty("line.separator");
+
+ private Connection connection = null;
+
+ /**
+ *
+ * @throws MobyException
+ * if database driver cannot be found or there is an database
+ * access error.
+ */
+ public JNamespacesSqlImpl() throws MobyException {
+ try {
+ // Load the JDBC driver
+ String driverName = "com.mysql.jdbc.Driver";
+ Class.forName(driverName);
+ // get certain properties from mobycentral.config
+ Map map = MobyCentralConfig.getMobyNamespace();
+ // Create a connection to the database
+ String serverName = map.get("url") + ":" + map.get("port");// localhost:3306";
+ // //TODO
+ // -
+ // make
+ // this
+ // a
+ // property
+ String mydatabase = (String) map.get("dbname");// "mobyobject";
+ String url = "jdbc:mysql://" + serverName + "/" + mydatabase;
+ String username = (String) map.get("username");// "moby_external";
+ String password = (String) map.get("password");// "";
+
+ /*
+ * String serverName = "mobycentral.icapture.ubc.ca:3306"; String
+ * mydatabase = "mobynamespace"; String url = "jdbc:mysql://" +
+ * serverName + "/" + mydatabase; String username = "moby_external";
+ * String password = "";
+ */
+ this.connection = DriverManager.getConnection(url, username, password);
+ } catch (ClassNotFoundException e) {
+ throw new MobyException(
+ "Could not find database driver. Please ensure that you have the right libraries present");
+ } catch (SQLException e) {
+ e.printStackTrace();
+ throw new MobyException("Database access error.");
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.biomoby.registry.definitions.types.JNamespaceI#getNamespaces()
+ */
+ public final String getNamespaces() {
+ /* ensure that the connection isnt null */
+ if (connection == null)
+ return "";
+
+ StringBuffer sb = new StringBuffer();
+ ResultSet rs = null;
+ try {
+ Statement stmt = connection.createStatement();
+ rs = stmt.executeQuery(sql);
+ } catch (SQLException ex) {
+ // TODO - throw exception - Error in sql
+ return ex.getMessage();
+ }
+ try {
+ while (rs.next()) {
+ // Get the data from the row using the column index
+ sb.append(rs.getString(1) + "\t" + rs.getString(2) + newline);
+ }
+ } catch (SQLException e) {
+ // TODO - throw exception - Database access error
+ return e.getMessage();
+ }
+ return sb.toString();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.biomoby.registry.definitions.types.JNamespaceI#getNamespacesAsArray()
+ */
+ public String[][] getNamespacesAsArray() {
+ /* ensure that the connection isnt null */
+ if (connection == null)
+ return null;
+
+ ArrayList sb = new ArrayList();
+ ResultSet rs = null;
+ try {
+ Statement stmt = connection.createStatement();
+ rs = stmt.executeQuery(sql);
+ } catch (SQLException ex) {
+ return null;
+ }
+ try {
+ while (rs.next()) {
+ // Get the data from the row using the column index
+ sb.add(new String[] { rs.getString(1), rs.getString(2) });
+ }
+ } catch (SQLException e) {
+ return null;
+ }
+ String[][] array = new String[sb.size()][];
+ sb.toArray(array);
+ return array;
+ }
+
+ /**
+ * Get all the data in the db regrading namespaces.
+ *
+ * @return an array of String[] objects. The String[] consists of
+ * {namespace_type, description, namespace_lsid, authority,
+ * contact_email}.
+ */
+ public String[][] getFullNamespacesAsArray() {
+ /* ensure that the connection isnt null */
+ if (connection == null)
+ return null;
+
+ ArrayList sb = new ArrayList();
+ ResultSet rs = null;
+ try {
+ Statement stmt = connection.createStatement();
+ rs = stmt.executeQuery(sql_all);
+ } catch (SQLException ex) {
+ return null;
+ }
+ try {
+ while (rs.next()) {
+ // Get the data from the row using the column index
+ sb.add(new String[] { rs.getString(1), rs.getString(2), rs.getString(3),
+ rs.getString(4), rs.getString(5) });
+ }
+ } catch (SQLException e) {
+ return null;
+ }
+ String[][] array = new String[sb.size()][];
+ sb.toArray(array);
+ return array;
+ }
+
+ public static void main(String[] args) throws MobyException {
+ String[][] namespaces = new JNamespacesSqlImpl().getFullNamespacesAsArray();
+ for (int i = 0; i < namespaces.length; i++) {
+ String[] namespace = namespaces[i];
+ for (int j = 0; j < namespace.length; j++) {
+ System.out.print(namespace[j] + " ");
}
- System.out.println();
- }
- }
+ System.out.println();
+ }
+ }
}
More information about the MOBY-guts
mailing list