[MOBY-guts] biomoby commit
Eddie Kawas
kawas at pub.open-bio.org
Wed Mar 15 16:22:38 UTC 2006
kawas
Wed Mar 15 11:22:37 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-serv32102/org/biomoby/registry/definitions/types
Modified Files:
JServicesSqlImpl.java JObjectsSqlImpl.java
JNamespacesSqlImpl.java
Log Message:
updated RDF generators and clients so that LSIDs with versioining information is used. This is only preliminary. More updates to come
moby-live/Java/src/main/org/biomoby/registry/definitions/types JServicesSqlImpl.java,1.2,1.3 JObjectsSqlImpl.java,1.1,1.2 JNamespacesSqlImpl.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/definitions/types/JServicesSqlImpl.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/JServicesSqlImpl.java 2006/03/14 16:23:06 1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/definitions/types/JServicesSqlImpl.java 2006/03/15 16:22:37 1.3
@@ -25,7 +25,7 @@
+ "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 "
+ 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, ot2.service_lsid "
+ "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";
@@ -48,12 +48,12 @@
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
+ // //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";
@@ -143,9 +143,11 @@
/**
* 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
+ * {service_type, relationship_type, to_service_type, description,
+ * service_lsid, authority, contact_email, to_service_type_lsid}.
+ * <em>Note that relationship_type is the relationship that service_type has
* with to_service_type.</em>
*/
public String[][] getFullServicesAsArray() {
@@ -166,7 +168,7 @@
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) });
+ rs.getString(4), rs.getString(5), rs.getString(6), rs.getString(7), rs.getString(8) });
}
} catch (SQLException e) {
// TODO - throw exception - Database access error
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/definitions/types/JObjectsSqlImpl.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/JObjectsSqlImpl.java 2005/08/29 20:19:20 1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/definitions/types/JObjectsSqlImpl.java 2006/03/15 16:22:37 1.2
@@ -21,179 +21,221 @@
* email me at edward.kawas at gmail.com
*/
public final class JObjectsSqlImpl implements JObjectsI {
- private static final String sql = "SELECT ot1.object_type, rt.relationship_type, ot2.object_type, rt.object2_articlename, ot1.description "
- + "FROM object as ot1, object_term2term as rt, object as ot2 "
- + "WHERE ot1.object_id = rt.object1_id and ot2.object_id = rt.object2_id "
- + "ORDER BY ot1.object_type";
-
- 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 JObjectsSqlImpl() 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.getMobyObject();
- // 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 = "mobyobject"; 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: " + e.getSQLState());
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.biomoby.registry.definitions.types.JObjectsI#getObjects()
- */
- public final String getObjects() {
- 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)
- + ((rs.getString(4) == null || rs.getString(4).equals(
- "")) ? "\t" : "(" + rs.getString(4) + ")\t")
- + rs.getString(5) + newline);
- }
- } catch (SQLException e) {
- // TODO - throw exception - Database access error
- return e.getMessage();
- }
- return sb.toString();
- }
-
- /**
- *
- * @param name
- * the name of the object to get information on
- * @return a tab delimited string containing object, object relationship,
- * object type that this relationship is with, the articlename (if
- * it exists), and description
- */
- public final String getObject(String name) {
- String _SQL = "SELECT ot1.object_type, rt.relationship_type, ot2.object_type, rt.object2_articlename, ot1.description "
- + "FROM object as ot1, object_term2term as rt, object as ot2 "
- + "WHERE ot1.object_id = rt.object1_id and ot2.object_id = rt.object2_id and ot1.object_type = '"
- + name + "' " + "ORDER BY ot1.object_type";
- 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)
- + ((rs.getString(4) == null || rs.getString(4).equals(
- "")) ? "\t" : "(" + rs.getString(4) + ")\t")
- + rs.getString(5) + newline);
- }
- } catch (SQLException e) {
- // TODO - throw exception - Database access error
- return e.getMessage();
- }
- return sb.toString();
- }
-
- public static void main(String[] args) throws MobyException {
- System.out.println(new JObjectsSqlImpl().getObjectsAsArray());
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.biomoby.registry.definitions.types.JObjectsI#getObjectsAsArray()
- */
- public String[][] getObjectsAsArray() {
- 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) {
- 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) == null ||
- rs.getString(4).equals("")) ?
- "" : "(" + rs.getString(4) + ")"),
- rs.getString(5) });
- }
- } catch (SQLException e) {
- return null;
- }
- String[][] array = new String[sb.size()][];
- sb.toArray(array);
- return array;
- }
+ private static final String sql = "SELECT ot1.object_type, rt.relationship_type, ot2.object_type, rt.object2_articlename, ot1.description "
+ + "FROM object as ot1, object_term2term as rt, object as ot2 "
+ + "WHERE ot1.object_id = rt.object1_id and ot2.object_id = rt.object2_id "
+ + "ORDER BY ot1.object_type";
+
+ private static final String sql_all = "SELECT ot1.object_type, rt.relationship_type, ot2.object_type, rt.object2_articlename, ot1.description,"
+ + " ot1.object_lsid, ot1.authority, ot1.contact_email, ot2.object_lsid "
+ + "FROM object as ot1, object_term2term as rt, object as ot2 "
+ + "WHERE ot1.object_id = rt.object1_id and ot2.object_id = rt.object2_id "
+ + "ORDER BY ot1.object_type";
+
+ 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 JObjectsSqlImpl() 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.getMobyObject();
+ // 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 = "mobyobject"; 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: " + e.getSQLState());
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.biomoby.registry.definitions.types.JObjectsI#getObjects()
+ */
+ public final String getObjects() {
+ 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)
+ + ((rs.getString(4) == null || rs.getString(4).equals("")) ? "\t" : "("
+ + rs.getString(4) + ")\t") + rs.getString(5) + newline);
+ }
+ } catch (SQLException e) {
+ // TODO - throw exception - Database access error
+ return e.getMessage();
+ }
+ return sb.toString();
+ }
+
+ /**
+ *
+ * @param name
+ * the name of the object to get information on
+ * @return a tab delimited string containing object, object relationship,
+ * object type that this relationship is with, the articlename (if
+ * it exists), and description
+ */
+ public final String getObject(String name) {
+ String _SQL = "SELECT ot1.object_type, rt.relationship_type, ot2.object_type, rt.object2_articlename, ot1.description "
+ + "FROM object as ot1, object_term2term as rt, object as ot2 "
+ + "WHERE ot1.object_id = rt.object1_id and ot2.object_id = rt.object2_id and ot1.object_type = '"
+ + name + "' " + "ORDER BY ot1.object_type";
+ 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)
+ + ((rs.getString(4) == null || rs.getString(4).equals("")) ? "\t" : "("
+ + rs.getString(4) + ")\t") + rs.getString(5) + newline);
+ }
+ } catch (SQLException e) {
+ // TODO - throw exception - Database access error
+ return e.getMessage();
+ }
+ return sb.toString();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.biomoby.registry.definitions.types.JObjectsI#getObjectsAsArray()
+ */
+ public String[][] getObjectsAsArray() {
+ 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) {
+ 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) == null || rs.getString(4).equals("")) ? "" : "("
+ + rs.getString(4) + ")"), rs.getString(5) });
+ }
+ } catch (SQLException e) {
+ return null;
+ }
+ String[][] array = new String[sb.size()][];
+ sb.toArray(array);
+ return array;
+ }
+
+ /**
+ *
+ * @return
+ */
+ public String[][] getFullObjectsAsArray() {
+ 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) {
+ 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) == null || rs.getString(4).equals("")) ? "" : "("
+ + rs.getString(4) + ")"), rs.getString(5), rs.getString(6),
+ rs.getString(7), rs.getString(8), rs.getString(9) });
+ }
+ } 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[][] datatypes = new JObjectsSqlImpl().getFullObjectsAsArray();
+ for (int i = 0; i < datatypes.length; i++) {
+ String[] datatype = datatypes[i];
+ for (int j = 0; j < datatype.length; j++) {
+ System.out.print(datatype[j] + " ");
+ }
+ System.out.println();
+ }
+ }
}
\ No newline at end of file
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/definitions/types/JNamespacesSqlImpl.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/definitions/types/JNamespacesSqlImpl.java 2006/03/14 16:23:06 1.3
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/definitions/types/JNamespacesSqlImpl.java 2006/03/15 16:22:37 1.4
@@ -43,24 +43,12 @@
// 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 serverName = map.get("url") + ":" + map.get("port");
+ String mydatabase = (String) map.get("dbname");
String url = "jdbc:mysql://" + serverName + "/" + mydatabase;
- String username = (String) map.get("username");// "moby_external";
- String password = (String) map.get("password");// "";
+ String username = (String) map.get("username");
+ 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(
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