POST: All of the relationships, inheritance and containment, are removed.
POST: - * @return + * @return Registration */ public Registration getRegistration() { return registration; =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/MobyUtilities.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/client/ui/graphical/applets/objectCreationTool/MobyUtilities.java 2005/04/07 16:42:26 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/MobyUtilities.java 2005/06/02 15:48:01 1.2 @@ -16,7 +16,7 @@ /** * Utilities that are useful for retrieving information about certain objects, parsing objects, etc. * @author Eddie Kawas - * @Jun 10, 2004 + * Jun 10, 2004 * */ public class MobyUtilities { @@ -27,7 +27,7 @@ * => The first item in the list is a string representation of the parent* => The second item is a linked list of all the 'HAS' container relationships
* => The third item is a linked list of all the 'HASA' container relationships - * @param name, the name of the object to query for. + * @param name - the name of the object to query for. * @return returns a linked list {String, LinkedList, LinkedList} of relationships */ public static LinkedList GetRelations(String name) throws IOException { @@ -119,7 +119,6 @@ * PRE: ll is a valid linkedlist, panelDetails is a valid MobyUserPanel.
* POST: All the relations of child are outputted to the MobyUserPanel panelDetails. * @param ll - a linked list created via GetRelations() - * @param panelDetails - the MobyUserPanel to output the relationships * @param child - the object that GetRelations() was called with. */ public static String WriteToPanel(LinkedList ll, String child) { =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/Registration.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/client/ui/graphical/applets/objectCreationTool/Registration.java 2005/04/20 21:42:10 1.2 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/Registration.java 2005/06/02 15:48:01 1.3 @@ -12,7 +12,7 @@ /** * @author Eddie Kawas - * @Jun 21, 2004 + * Jun 21, 2004 * */ public class Registration extends MobyDataType{ =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/Pair.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/client/ui/graphical/applets/objectCreationTool/Pair.java 2005/04/07 16:42:26 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/Pair.java 2005/06/02 15:48:01 1.2 @@ -5,7 +5,7 @@ * This class contains the methods required to encapsulate
the container relationships * 'HAS' and 'HASA' from the BioMoby Object Ontology. * @author Eddie Kawas - * @May 31, 2004 + * May 31, 2004 * */ public class Pair { @@ -28,7 +28,6 @@ /** * PRE: None.
* POST: The article name is retrieved. - * @param - none. * @return the contained objects name */ public String getArticlename() { @@ -38,7 +37,6 @@ /** * PRE: None.
* POST: The attribute is retrieved - * @param - none. * @return the contained objects attribute */ public String getAttribute() { @@ -48,7 +46,6 @@ /** * PRE: none.
* POST: a String representation of a Pair is returned. - * @param - none. * @return returns the string representation of a pair. */ public String toString() { =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/MobyPlainText.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/client/ui/graphical/applets/objectCreationTool/MobyPlainText.java 2005/04/07 16:42:26 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/MobyPlainText.java 2005/06/02 15:48:01 1.2 @@ -10,7 +10,7 @@ * This class is used to maintain and then output a plain * text representation of an object. * @author Eddie Kawas - * @Jun 12, 2004 + * Jun 12, 2004 * */ public class MobyPlainText { @@ -145,7 +145,6 @@ * * PRE: None.
* POST: All of the relationships, inheritance and containment, are removed. - * @return nothing. */ public void clear() { renameRoot("MyObject"); From kawas at pub.open-bio.org Thu Jun 2 11:48:28 2005 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Thu Jun 2 11:27:41 2005 Subject: [MOBY-guts] biomoby commit Message-ID: <200506021548.j52FmSBZ015655@pub.open-bio.org> kawas Thu Jun 2 11:48:28 EDT 2005 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool In directory pub.open-bio.org:/tmp/cvs-serv15594/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool Modified Files: ServiceFocusListener.java MobyCollection.java InputOutputActionListener.java MobyUtilities.java HelpActionListener.java ServiceCreationTool.java ButtonBeautifier.java NamespaceTree.java ServiceTypeTree.java Pair.java Log Message: Fixed the javadoc comments in order to get rid of warnings. moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool ServiceFocusListener.java,1.1,1.2 MobyCollection.java,1.1,1.2 InputOutputActionListener.java,1.1,1.2 MobyUtilities.java,1.1,1.2 HelpActionListener.java,1.1,1.2 ServiceCreationTool.java,1.2,1.3 ButtonBeautifier.java,1.2,1.3 NamespaceTree.java,1.1,1.2 ServiceTypeTree.java,1.1,1.2 Pair.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/ServiceFocusListener.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/client/ui/graphical/applets/serviceInstanceCreationTool/ServiceFocusListener.java 2005/04/07 16:42:27 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/ServiceFocusListener.java 2005/06/02 15:48:28 1.2 @@ -11,7 +11,7 @@ /** * * @author Edward Kawas - * @date July 7, 2004 + * date July 7, 2004 * This class implements the FocusListener for the Service Creation Tool. *
For questions, comments, or bugs *
email me at edward.kawas@gmail.com =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/MobyCollection.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/client/ui/graphical/applets/serviceInstanceCreationTool/MobyCollection.java 2005/04/07 16:42:27 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/MobyCollection.java 2005/06/02 15:48:28 1.2 @@ -11,7 +11,7 @@ /** * * @author Edward Kawas - * @date July 19, 2004 + * date July 19, 2004 * This class represents a collection, either input or output, for the Moby Services. *
For questions, comments, or bugs *
email me at edward.kawas@gmail.com =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/InputOutputActionListener.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/client/ui/graphical/applets/serviceInstanceCreationTool/InputOutputActionListener.java 2005/04/07 16:42:27 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/InputOutputActionListener.java 2005/06/02 15:48:28 1.2 @@ -12,7 +12,7 @@ /** * * @author Edward Kawas
- * @date July 16, 2004
+ * date July 16, 2004
* This class implements the ActionListener interface. *
For questions, comments, or bugs *
email me at edward.kawas@gmail.com =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/MobyUtilities.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/client/ui/graphical/applets/serviceInstanceCreationTool/MobyUtilities.java 2005/04/07 16:42:27 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/MobyUtilities.java 2005/06/02 15:48:28 1.2 @@ -9,7 +9,7 @@ /** * Utilities that are useful for retrieving information about certain objects, parsing objects, etc. * @author Eddie Kawas - * @Jun 10, 2004 + * Jun 10, 2004 *
For questions, comments, or bugs *
email me at edward.kawas@gmail.com */ @@ -74,7 +74,6 @@ * PRE: ll is a valid linkedlist, panelDetails is a valid MobyUserPanel.
* POST: All the relations of child are outputted to the MobyUserPanel panelDetails. * @param ll - a linked list created via GetRelations() - * @param panelDetails - the MobyUserPanel to output the relationships * @param child - the object that GetRelations() was called with. */ public static String WriteToPanel(LinkedList ll, String child) { =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/HelpActionListener.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/client/ui/graphical/applets/serviceInstanceCreationTool/HelpActionListener.java 2005/04/07 16:42:27 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/HelpActionListener.java 2005/06/02 15:48:28 1.2 @@ -12,7 +12,7 @@ /** * @author Edward Kawas - * @date Sep 1, 2004 + * Sep 1, 2004 *
This class implements the ActionListener interface. *
The sole purpose of this class is to provide messages to *
the user regarding the form inputs for a service instance. =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/ServiceCreationTool.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/client/ui/graphical/applets/serviceInstanceCreationTool/ServiceCreationTool.java 2005/04/07 21:01:13 1.2 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/ServiceCreationTool.java 2005/06/02 15:48:28 1.3 @@ -22,7 +22,7 @@ /** * * @author Edward Kawas - * @date Jul 7, 2004 + * date Jul 7, 2004 * This class is the main class for the service instance creation tool. *
For questions, comments, or bugs *
email me at edward.kawas@gmail.com @@ -215,7 +215,7 @@ } /** - * @param i, the radio button id. + * @param i - the radio button id. * -1 => no button is selected. * 1 => Primary button is selected. * 2 => Secondary button is selected. @@ -227,7 +227,7 @@ /** * * @return an int reprepresenting the radio button that is selected. - * @see setRadioButtonID(int i) + * @see #setRadioButtonID(int i) */ public int getRadioButtonID() { return radioButtonID; =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/ButtonBeautifier.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/client/ui/graphical/applets/serviceInstanceCreationTool/ButtonBeautifier.java 2005/04/20 21:42:10 1.2 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/ButtonBeautifier.java 2005/06/02 15:48:28 1.3 @@ -16,7 +16,7 @@ /** * @author Eddie Kawas - * @Jun 30, 2004 + * Jun 30, 2004 *
* This class enhances the esthetic look of buttons. *
@@ -206,7 +206,7 @@ * POST: The powered by moby services image is returned in a label. *
* - * @param cls - + * @param c - * the class where program execution began. */ public static JLabel getMobyImage(Class c) { =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/NamespaceTree.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/client/ui/graphical/applets/serviceInstanceCreationTool/NamespaceTree.java 2005/04/07 16:42:27 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/NamespaceTree.java 2005/06/02 15:48:28 1.2 @@ -25,9 +25,9 @@ /** * This class encapsulates everything that is needed to create the tree
* representation of all the Services contained in the BioMoby Service Ontology. - * @see http://biomoby.org + * @link http://biomoby.org * @author Eddie Kawas - * @May 31, 2004 + * May 31, 2004 *
For questions, comments, or bugs *
email me at edward.kawas@gmail.com */ @@ -50,7 +50,8 @@ * POST: A moby tree is constructed with the root node labeled as 'Namespace'
* and the material for the tree taken from the RDF located at * @link http://biomoby.org/RESOURCES/MOBY-S/Namespace - * @param canEdit, if true, then the nodes are editable, else they are not. + * @param canEdit - if true, then the nodes are editable, else they are not. + * @param rdf - rdf for namespaces. */ public NamespaceTree(boolean canEdit, String rdf) { @@ -92,7 +93,6 @@ /** * PRE: None.
* POST: The MobyTree Namespace contains an empty tree with a single node labeled 'Namespace' - * @return - none. * */ public void clear() { @@ -103,7 +103,6 @@ /** * PRE: A node other then the root node is selected.
* POST: if a node has been selected, then it is removed, otherwise nothing happens. - * @return - none. */ public void removeCurrentNode() { TreePath currentSelection = tree.getSelectionPath(); @@ -124,7 +123,7 @@ * PRE: None.
* POST: Child will be added to the tree at the root node or if a node is selected,
* then the node will be added as a child of the selected node. - * @param child, the object to insert into the tree. + * @param child - the object to insert into the tree. * @return returns the newly inserted node. */ public DefaultMutableTreeNode addObject(Object child) { @@ -216,7 +215,6 @@ * PRE: None.
* POST: The tree will be refreshed to show all changes and user renamed. * @param name the name for the root node in the tree. - * @return - none. */ public void refreshTree(String name) { if (!name.equals("")) @@ -268,8 +266,6 @@ * * PRE: None.
* POST: The tree representation of the RDF taken from MobyCentral is created. - * @param none. - * @return nothing. * */ public void makeObjectTree() { =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/ServiceTypeTree.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/client/ui/graphical/applets/serviceInstanceCreationTool/ServiceTypeTree.java 2005/04/07 16:42:27 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/ServiceTypeTree.java 2005/06/02 15:48:28 1.2 @@ -25,9 +25,9 @@ /** * This class encapsulates everything that is needed to create the tree
* representation of all the Services contained in the BioMoby Service Ontology. - * @see http://biomoby.org + * @link http://biomoby.org * @author Eddie Kawas - * @May 31, 2004 + * May 31, 2004 *
For questions, comments, or bugs *
email me at edward.kawas@gmail.com * @@ -51,8 +51,8 @@ * POST: A moby tree is constructed with the root node labeled as 'Service'
* and the material for the tree taken from the RDF located at * @link http://biomoby.org/RESOURCES/MOBY-S/Service - * @param canEdit, if true, then the nodes are editable, else they are not. - * @param rdf, the location of the RDF for the service type tree. + * @param canEdit - if true, then the nodes are editable, else they are not. + * @param rdf - the location of the RDF for the service type tree. */ public ServiceTypeTree(boolean canEdit, String rdf) { @@ -96,7 +96,6 @@ /** * PRE: None.
* POST: The MobyTree object contains an empty tree with a single node labeled 'Object' - * @return - none. * */ public void clear() { @@ -107,7 +106,6 @@ /** * PRE: A node other then the root node is selected.
* POST: if a node has been selected, then it is removed, otherwise nothing happens. - * @return - none. */ public void removeCurrentNode() { TreePath currentSelection = tree.getSelectionPath(); @@ -128,7 +126,7 @@ * PRE: None.
* POST: Child will be added to the tree at the root node or if a node is selected,
* then the node will be added as a child of the selected node. - * @param child, the object to insert into the tree. + * @param child - the object to insert into the tree. * @return returns the newly inserted node. */ public DefaultMutableTreeNode addObject(Object child) { @@ -220,7 +218,6 @@ * PRE: None.
* POST: The tree will be refreshed to show all changes and user renamed. * @param name the name for the root node in the tree. - * @return - none. */ public void refreshTree(String name) { if (!name.equals("")) @@ -272,8 +269,6 @@ * * PRE: None.
* POST: The tree representation of the RDF taken from MobyCentral is created. - * @param none. - * @return nothing. * */ public void makeObjectTree() { =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/Pair.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/client/ui/graphical/applets/serviceInstanceCreationTool/Pair.java 2005/04/07 16:42:27 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/Pair.java 2005/06/02 15:48:28 1.2 @@ -5,7 +5,7 @@ * This class contains the methods required to encapsulate
the container relationships * 'HAS' and 'HASA' from the BioMoby Object Ontology. * @author Eddie Kawas - * @May 31, 2004 + * May 31, 2004 *
For questions, comments, or bugs *
email me at edward.kawas@gmail.com */ @@ -30,7 +30,6 @@ /** * PRE: None.
* POST: The article name is retrieved. - * @param - none. * @return the contained objects name */ public String getArticlename() { @@ -40,7 +39,6 @@ /** * PRE: None.
* POST: The attribute is retrieved - * @param - none. * @return the contained objects attribute */ public String getAttribute() { @@ -50,7 +48,6 @@ /** * PRE: none.
* POST: a String representation of a Pair is returned. - * @param - none. * @return returns the string representation of a pair. */ public String toString() { From kawas at pub.open-bio.org Thu Jun 2 11:48:54 2005 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Thu Jun 2 11:27:42 2005 Subject: [MOBY-guts] biomoby commit Message-ID: <200506021548.j52Fms7Z015697@pub.open-bio.org> kawas Thu Jun 2 11:48:54 EDT 2005 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/shared In directory pub.open-bio.org:/tmp/cvs-serv15668/org/biomoby/client/ui/graphical/applets/shared Modified Files: Household.java MobyTree.java Log Message: Fixed the javadoc comments in order to get rid of warnings. moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/shared Household.java,1.1,1.2 MobyTree.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/shared/Household.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/client/ui/graphical/applets/shared/Household.java 2005/04/07 16:42:27 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/shared/Household.java 2005/06/02 15:48:54 1.2 @@ -9,7 +9,7 @@ * @author Eddie Kawas *
For questions, comments, or bugs *
email me at edward.kawas@gmail.com - * @Jun 4, 2004 + * Jun 4, 2004 * */ =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/shared/MobyTree.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/client/ui/graphical/applets/shared/MobyTree.java 2005/04/07 16:42:27 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/shared/MobyTree.java 2005/06/02 15:48:54 1.2 @@ -23,11 +23,11 @@ /** * This class encapsulates everything that is needed to create the tree
* representation of all the objects contained in the BioMoby Object Ontology. - * @see http://biomoby.org + * @link http://biomoby.org * @author Eddie Kawas *
For questions, comments, or bugs *
email me at edward.kawas@gmail.com - * @May 31, 2004 + * May 31, 2004 * */ public class MobyTree extends JPanel { @@ -47,11 +47,12 @@ String name = ""; private static final boolean DEBUG = false; /** - * PRE: None
- * POST: A moby tree is constructed with the root node labeled as 'Object'
- * and the material for the tree taken from the RDF located at - * @link http://biomoby.org/RESOURCES/MOBY-S/Objects - * @param canEdit, if true, then the nodes are editable, else they are not. + * A moby tree is constructed with the root node labeled as 'name'
+ * and the material for the tree taken from the RDF located at + * the url rdf. + * @param canEdit - if true then nodes in tree can be edited, otherwise they cannot. + * @param rdf - the url of the RDF describing Moby Objects, Services, Service Types, and Namespaces + * @param name - the name of the root node in the tree. */ public MobyTree(boolean canEdit, String rdf, String name) { @@ -94,7 +95,6 @@ /** * PRE: None.
* POST: The MobyTree object contains an empty tree with a single node labeled 'Object' - * @return - none. * */ public void clear() { @@ -105,7 +105,6 @@ /** * PRE: A node other then the root node is selected.
* POST: if a node has been selected, then it is removed, otherwise nothing happens. - * @return - none. */ public void removeCurrentNode() { TreePath currentSelection = tree.getSelectionPath(); @@ -126,7 +125,7 @@ * PRE: None.
* POST: Child will be added to the tree at the root node or if a node is selected,
* then the node will be added as a child of the selected node. - * @param child, the object to insert into the tree. + * @param child - the object to insert into the tree. * @return returns the newly inserted node. */ public DefaultMutableTreeNode addObject(Object child) { @@ -218,7 +217,6 @@ * PRE: None.
* POST: The tree will be refreshed to show all changes and user renamed. * @param name the name for the root node in the tree. - * @return - none. */ public void refreshTree(String name) { if (!name.equals("")) @@ -270,8 +268,7 @@ * * PRE: None.
* POST: The tree representation of the RDF taken from MobyCentral is created. - * @param none. - * @return nothing. + * @param name - name of the object to create tree for. * */ public void makeObjectTree(String name) { From kawas at pub.open-bio.org Thu Jun 2 11:49:28 2005 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Thu Jun 2 11:27:43 2005 Subject: [MOBY-guts] biomoby commit Message-ID: <200506021549.j52FnSfC015751@pub.open-bio.org> kawas Thu Jun 2 11:49:28 EDT 2005 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util In directory pub.open-bio.org:/tmp/cvs-serv15726/org/biomoby/client/ui/graphical/applets/util Modified Files: TreeLoaderThread.java Log Message: Fixed the javadoc comments in order to get rid of warnings. moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util TreeLoaderThread.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util/TreeLoaderThread.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/client/ui/graphical/applets/util/TreeLoaderThread.java 2005/04/07 20:21:18 1.2 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util/TreeLoaderThread.java 2005/06/02 15:49:28 1.3 @@ -5,7 +5,7 @@ * @author Sun Micro Systems *
This class was created to provide an abstract class that you subclass to *
perform GUI-related work in a dedicated thread. - * @see http://java.sun.com/docs/books/tutorial/uiswing/misc/threads.html + * @link http://java.sun.com/docs/books/tutorial/uiswing/misc/threads.html *
For questions, comments, or bugs *
email me at edward.kawas@gmail.com
*/
From kawas at pub.open-bio.org Thu Jun 2 11:50:26 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Thu Jun 2 11:27:44 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200506021550.j52FoQFg015804@pub.open-bio.org>
kawas
Thu Jun 2 11:50:26 EDT 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier
In directory pub.open-bio.org:/tmp/cvs-serv15779/org/biomoby/registry/rdfagent/verifier
Modified Files:
DataMngr.java
Log Message:
Fixed the javadoc comments in order to get rid of warnings.
moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier DataMngr.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier/DataMngr.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier/DataMngr.java 2005/04/16 14:32:12 1.4
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier/DataMngr.java 2005/06/02 15:50:26 1.5
@@ -160,16 +160,15 @@
/** This method use for the update service_instance table, simple_input/output table,
* collection_input/output table, secondary_input table in accordance with data
* from RDF file.
- * @param Hashtable servSign - set of the serviceSignature data (name - value, an example: servicename - GoTerm);
+ * @param servSign - set of the serviceSignature data (name - value, an example: servicename - GoTerm);
* Hashtable of hashtables represented by a pair:
* a name of the input = hashtable for this output
* example:{siminp1={object_type_uri=urn:lsid:biomoby.org:objectclass:Object, namespace_type_uris=urn:lsid:biomoby.org:namespacetype:taxon}}
- * @param Hashtable of hashtables represented by a pair:
+ * @param servInp - Hashtable of hashtables represented by a pair:
* a name of the output = hashtable for this output
* @param servname - the name of service
* @param authURI - the authority URI
* @param signURL - URL of resource
- * @return .
*/
public static void processService( Hashtable servSign, Hashtable servInp, Hashtable servOut, String servname,String authURI,String signURL){
@@ -582,7 +581,7 @@
/** delete the service instance by service name and signature URL
* @param servName the name of service which we want delete.
- * @param rdfURL the authority URI for service which we want delete.
+ * @param signURL the authority URI for service which we want delete.
*
*/
@@ -667,7 +666,7 @@
/** add the record about new service instance in the service_instance table of mobycentral database
* @param servName - the name of service instance the record was added for.
* @param cat - the category of service instance.
- * @param servTypeUri - the service type URI of service instance.
+ * @param servTypeURI - the service type URI of service instance.
* @param authId - the authority Id of service instance.
* @param url - the URL of service instance.
* @param email - the contact e-Mail of service instance.
@@ -778,7 +777,6 @@
* @param objTypeUri the object type URI of the simple input.
* @param nsTypeUris the string with set of the nameSpaces for this simple input.
* @param colInpId the collection input Id if this simple input belongs to a collection, and blank otherwise.
- * @return ret=1 if the record has added, and ret=-1 otherwise
*/
public static void insIntoSimpleInput(Integer servInstId,String articleName,String objTypeUri,String nsTypeUris,Integer colInpId){
@@ -876,7 +874,6 @@
* @param max the maximum value of the secondary input
* @param min the minimum value of the secondary input
* * @param enum the enumeration value for the secondary input
- * @return ret=1 if the record has added, and ret=-1 otherwise
*/
public static void insIntoSecondary(int servInstId,String article_name,String def,String dataType,BigDecimal max,BigDecimal min,String enumeration){
@@ -921,9 +918,8 @@
* @param dataType the type of data of the secondary input.
* @param max the maximum value of the secondary input
* @param min the minimum value of the secondary input
- * @param enum the enumeration value for the secondary input
+ * @param enumeration the enumeration value for the secondary input
* @param minSecNum minimum free number for secondary_input_id
- * @return ret=1 if the record has added, and ret=-1 otherwise
*/
public static void updateSec(int servInstId,String article_name,String def,String dataType,BigDecimal max,BigDecimal min,String enumeration, int minSecNum){
@@ -968,7 +964,6 @@
* @param objTypeUri the object type URI of the simple output.
* @param nsTypeUris the string with set of the nameSpaces for this simple output.
* @param colOutId the collection input Id if this simple output belongs to a collection, and blank otherwise.
- * @return ret=1 if the record has added, and ret=-1 otherwise
*/
public static void insIntoSimpleOutput(Integer servInstId,String articleName,String objTypeUri,String nsTypeUris,Integer colOutId){
@@ -1186,7 +1181,7 @@
}
/** get the secondary input data by the secondary input Id
- * @param secInpId - the secondary input Id
+ * @param servInstId - the secondary input Id
* @return carrier class Secondary
*/
@@ -1247,7 +1242,6 @@
/** get the simple/collection output data by the service instance Id
* and build xml representation
* @param servInstId - the service instance Id
- * @
*/
public static void getSimpleCollectOutput(int servInstId){
@@ -1300,7 +1294,6 @@
/** get the simple/collection input data by the service instance Id
* and build xml representation
* @param servInstId - the service instance Id
- * @
*/
public static void getSimpleCollectInput(int servInstId){
@@ -1516,7 +1509,7 @@
/** get the service instance Id for the given service name and signatureURL
* @param servName - the name of service instance .
- * @param signatureURL - URL of resource for the service instance.
+ * @param signURL - URL of resource for the service instance.
* @return Intrger service instance Id if was found in the database, zero otherwise
*/
@@ -1646,7 +1639,6 @@
/** delete a record from simple table by a service instance Id and collection_input_id
* (the metod is working for simple_input/output, collection input/output tables)
* @param servInstId - the service instance Id.
- * @return Intrger ret=1 if the record was deleted, ret=-1 otherwise.
*/
public static void delCollectionMember(String inout, int servInstId){
@@ -1707,7 +1699,8 @@
}
/** delete a record from service_instance table by a servicename and authority Id
- * @param servInstId - the service instance Id.
+ * @param servName - the service instance name.
+ * @param authId - the id of the authority
* @return Intrger ret=1 if the record was deleted, ret=-1 otherwise.
*/
@@ -1920,7 +1913,7 @@
/** get the service authority Id from service_instance table by the servicename and signatureURL
- * @param servName - the name of service
+ * @param serviceName - the name of service
* @param signURL - the signatureURL for the given service
* @return int authority Id if was found, zero otherwise.
*/
@@ -2100,10 +2093,13 @@
}
- /** get the contact e-Mail from service_instance table by the servicename
- * @param signURL - the URL of a resource
- * @return String contact e-Mail if was found, empty string otherwise.
- */
+ /**
+ *
+ * gets the min number of records with service instance id = 0
+ * @param table
+ * @param key_field
+ * @return the number of records
+ */
public static int getMinFreeNumber(String table, String key_field){
From kawas at pub.open-bio.org Thu Jun 2 11:52:19 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Thu Jun 2 11:28:35 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200506021552.j52FqJhN015901@pub.open-bio.org>
kawas
Thu Jun 2 11:52:19 EDT 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/mobyxml/w3c/dom3
In directory pub.open-bio.org:/tmp/cvs-serv15877/org/biomoby/shared/mobyxml/w3c/dom3
Modified Files:
Tag: java_1_5_compat
MobyObjectClassImpl.java MobyObjectClassNSImpl.java
MobyObjectClass.java
Log Message:
Fixed the javadoc comments in order to get rid of warnings and fixed some parsing logic.
moby-live/Java/src/main/org/biomoby/shared/mobyxml/w3c/dom3 MobyObjectClassImpl.java,1.1,1.1.2.1 MobyObjectClassNSImpl.java,1.1,1.1.2.1 MobyObjectClass.java,1.1,1.1.2.1
rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/mobyxml/w3c/dom3/RCS/MobyObjectClassImpl.java,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/mobyxml/w3c/dom3/RCS/MobyObjectClassNSImpl.java,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/mobyxml/w3c/dom3/RCS/MobyObjectClass.java,v: No such file or directory
From dwang at pub.open-bio.org Wed Jun 1 21:33:24 2005
From: dwang at pub.open-bio.org (Dennis Wang)
Date: Thu Jun 2 13:21:58 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200506020133.j521XOhH012494@pub.open-bio.org>
dwang
Wed Jun 1 21:33:24 EDT 2005
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby
In directory pub.open-bio.org:/tmp/cvs-serv12468/Perl/MOBY/Adaptor/moby
Modified Files:
Tag: moby-DennisVersion
queryapi.pm
Log Message:
test
moby-live/Perl/MOBY/Adaptor/moby queryapi.pm,1.2,1.2.2.1
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi.pm,v
retrieving revision 1.2
retrieving revision 1.2.2.1
diff -u -r1.2 -r1.2.2.1
--- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi.pm 2004/07/09 00:21:53 1.2
+++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi.pm 2005/06/02 01:33:23 1.2.2.1
@@ -3,6 +3,7 @@
use Carp;
use vars qw($AUTOLOAD);
+# Modified by Dennis
{
#Encapsulated class data
From yanwong at pub.open-bio.org Thu Jun 9 04:19:46 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Thu Jun 9 03:55:55 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200506090819.j598Jkw3026903@pub.open-bio.org>
yanwong
Thu Jun 9 04:19:46 EDT 2005
Update of /home/repository/moby/moby-live/Python
In directory pub.open-bio.org:/tmp/cvs-serv26869
Modified Files:
PKG-INFO changelog setup.py
Log Message:
Version 0.9p2:
Changed the namespace URI from http://biomoby.org/moby to http://biomoby.org/moby-s
Corrected: Unicode strings can now be unmarshalled
Corrected: the prefix of this object was Object instead of moby
moby-live/Python PKG-INFO,1.6,1.7 changelog,1.8,1.9 setup.py,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Python/PKG-INFO,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Python/PKG-INFO 2005/02/18 15:58:21 1.6
+++ /home/repository/moby/moby-live/Python/PKG-INFO 2005/06/09 08:19:46 1.7
@@ -1,6 +1,6 @@
Metadata-Version: 1.0
Name: bioMoby
-Version: 0.9
+Version: 0.9p2
Summary: Python interface for bioMoby
Home-page: http://bioserv.rpbs.jussieu.fr
Author: Yan Wong
===================================================================
RCS file: /home/repository/moby/moby-live/Python/changelog,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Python/changelog 2005/04/22 10:13:48 1.8
+++ /home/repository/moby/moby-live/Python/changelog 2005/06/09 08:19:46 1.9
@@ -69,5 +69,5 @@
0.9: PIB implemented as a set of string in the __PIB__ field
0.9p1: added a SQL invocator and SQL dispatcher in order to help the building of DB webservices.
-
+0.9p2: changed the deserialization code for TCBioMoby and MobyObject. Added a new constant MOBYNAMESPACEURI
===================================================================
RCS file: /home/repository/moby/moby-live/Python/setup.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/setup.py 2005/01/27 08:44:04 1.5
+++ /home/repository/moby/moby-live/Python/setup.py 2005/06/09 08:19:46 1.6
@@ -3,7 +3,7 @@
from distutils.core import setup
setup(name="bioMoby",
- version=0.8,
+ version="0.9p2",
description="An implementation of bioMoby in Python",
author="Yan Wong",
author_email="yanwong@ebgm.jussieu.fr",
From yanwong at pub.open-bio.org Thu Jun 9 04:19:47 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Thu Jun 9 03:56:20 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200506090819.j598JlTR026965@pub.open-bio.org>
yanwong
Thu Jun 9 04:19:46 EDT 2005
Update of /home/repository/moby/moby-live/Python/bioMoby/webservice
In directory pub.open-bio.org:/tmp/cvs-serv26869/bioMoby/webservice
Modified Files:
TCBioMoby.py
Log Message:
Version 0.9p2:
Changed the namespace URI from http://biomoby.org/moby to http://biomoby.org/moby-s
Corrected: Unicode strings can now be unmarshalled
Corrected: the prefix of this object was Object instead of moby
moby-live/Python/bioMoby/webservice TCBioMoby.py,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/webservice/TCBioMoby.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/webservice/TCBioMoby.py 2005/02/01 08:52:17 1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/webservice/TCBioMoby.py 2005/06/09 08:19:46 1.4
@@ -9,6 +9,7 @@
Date: 12/06/2004
01/17/2005: solve the problem with GBrowse :) return a raw string instead of the text embbeded in a Body tag.
+ 06/08/2005: Return a string containing the MobyContent instead of the Python object
"""
from ZSI import _copyright, _children, \
@@ -23,12 +24,7 @@
def parse(self, elt, ps):
#self.checkname(elt, ps)
if _children(elt):
- from bioMoby import MobyContent
- mc=MobyContent()
-
- mc.fromMoby(elt.firstChild.nodeValue)
-
- return mc
+ return elt.firstChild.nodeValue
class body(TypeCode):
From yanwong at pub.open-bio.org Thu Jun 9 04:27:47 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Thu Jun 9 04:16:57 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200506090827.j598RlHS027027@pub.open-bio.org>
yanwong
Thu Jun 9 04:27:47 EDT 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv27001/bioMoby
Modified Files:
mobyService.py
Log Message:
moby-live/Python/bioMoby mobyService.py,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyService.py,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Python/bioMoby/mobyService.py 2005/06/09 08:19:46 1.6
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyService.py 2005/06/09 08:27:47 1.7
@@ -455,7 +455,7 @@
def join(self):
"""Same as Thread.join
"""
-self._execThread.join()
+ self._execThread.join()
From yanwong at pub.open-bio.org Thu Jun 9 04:39:26 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Thu Jun 9 04:17:15 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200506090839.j598dQDp027169@pub.open-bio.org>
yanwong
Thu Jun 9 04:39:26 EDT 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv27146
Removed Files:
mobyService.py
Log Message:
moby-live/Python/bioMoby mobyService.py,1.7,NONE
rcsdiff: /home/repository/moby/moby-live/Python/bioMoby/RCS/mobyService.py,v: No such file or directory
From yanwong at pub.open-bio.org Thu Jun 9 04:40:13 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Thu Jun 9 04:17:24 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200506090840.j598eDh1027223@pub.open-bio.org>
yanwong
Thu Jun 9 04:40:13 EDT 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv27197
Added Files:
mobyService.py
Log Message:
corrected a mistakenly placed \t
moby-live/Python/bioMoby mobyService.py,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyService.py,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
From kawas at pub.open-bio.org Thu Jun 9 13:36:00 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Thu Jun 9 13:13:17 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200506091736.j59Ha0PF029340@pub.open-bio.org>
kawas
Thu Jun 9 13:35:59 EDT 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder
In directory pub.open-bio.org:/tmp/cvs-serv29315/org/biomoby/client/rdf/builder
Modified Files:
ServiceInstanceRDF.java
Log Message:
Modified how the lsid domain is retrieved. Eddie
moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder/ServiceInstanceRDF.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/client/rdf/builder/ServiceInstanceRDF.java 2005/05/31 18:11:07 1.3
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder/ServiceInstanceRDF.java 2005/06/09 17:35:59 1.4
@@ -296,7 +296,7 @@
.getURL()));
subject.addProperty(DC.identifier, model
.createTypedLiteral("urn:lsid:"
- + properties.getProperty("domain")
+ + properties.getProperty("lsid_domain")
+ ":serviceinstance:" + services[i].getAuthority()
+ "," + services[i].getName()));
subject.addProperty(Predicates.performs_task, model
From kawas at pub.open-bio.org Thu Jun 9 13:39:00 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Thu Jun 9 13:14:35 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200506091739.j59Hd0vw029457@pub.open-bio.org>
kawas
Thu Jun 9 13:39:00 EDT 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources
In directory pub.open-bio.org:/tmp/cvs-serv29432/org/biomoby/client/ui/graphical/servlet/jresources
Modified Files:
RESOURCE.java
Log Message:
Modified how the lsid domain is retrieved. Eddie
moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources RESOURCE.java,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources/RESOURCE.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources/RESOURCE.java 2005/05/31 18:09:24 1.5
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources/RESOURCE.java 2005/06/09 17:39:00 1.6
@@ -366,7 +366,7 @@
.getURL()));
subject.addProperty(DC.identifier, model
.createTypedLiteral("urn:lsid:"
- + properties.getProperty("domain")
+ + properties.getProperty("lsid_domain")
+ ":serviceinstance:" + services[i].getAuthority()
+ "," + services[i].getName()));
subject.addProperty(Predicates.performs_task, model
From yanwong at pub.open-bio.org Fri Jun 10 03:47:15 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Fri Jun 10 03:22:59 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200506100747.j5A7lFCx000503@pub.open-bio.org>
yanwong
Fri Jun 10 03:47:15 EDT 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv477
Modified Files:
mobyMarshal.py
Log Message:
A generated object can now have a field content
moby-live/Python/bioMoby mobyMarshal.py,1.9,1.10
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyMarshal.py,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Python/bioMoby/mobyMarshal.py 2005/06/09 08:19:46 1.9
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyMarshal.py 2005/06/10 07:47:15 1.10
@@ -3,7 +3,7 @@
""" Creation date 19th of May 2004
- Latest modification date: 9th of June 2005
+ Latest modification date: 10th of June 2005
Author: Wong Yan
Topic: Marshalling moby Objects
@@ -15,6 +15,7 @@
06/09/2005: Change the doc.getElementsByTagNameNS("http://biomoby.org/moby",'mobyContent') to
doc.getElementsByTagNameNS(doc.firstChild.namespaceURI,'mobyContent') Parsing is now
independant from the namespace.
+ 06/10/2005: A generated object can now have a field content!
"""
from xml.dom.minidom import parseString
@@ -336,7 +337,7 @@
content.append(str(elem.nodeValue))
if content:
- anObject.content(r"".join(content))
+ anObject.content=r"".join(content)
return anObject
From senger at pub.open-bio.org Fri Jun 10 09:48:10 2005
From: senger at pub.open-bio.org (Martin Senger)
Date: Fri Jun 10 09:23:39 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200506101348.j5ADmAcA003762@pub.open-bio.org>
senger
Fri Jun 10 09:48:10 EDT 2005
Update of /home/repository/moby/jars-archive
In directory pub.open-bio.org:/tmp/cvs-serv3744
Log Message:
Module for third-party libraries created
Status:
Vendor Tag: jars-archive
Release Tags: v1
N jars-archive/README
N jars-archive/current/.keep-me
No conflicts created by this import
jars-archive - Imported sources
rcsdiff: /home/repository/moby/jars-archive/RCS/-,v: No such file or directory
rcsdiff: /home/repository/moby/jars-archive/RCS/Imported,v: No such file or directory
rcsdiff: /home/repository/moby/jars-archive/RCS/sources,v: No such file or directory
From senger at pub.open-bio.org Fri Jun 10 09:53:03 2005
From: senger at pub.open-bio.org (Martin Senger)
Date: Fri Jun 10 09:28:21 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200506101353.j5ADr3Jf003851@pub.open-bio.org>
senger
Fri Jun 10 09:53:03 EDT 2005
Update of /home/repository/moby/jars-archive
In directory pub.open-bio.org:/tmp/cvs-serv3832
Modified Files:
README
Log Message:
jars-archive README,1.1.1.1,1.2
===================================================================
RCS file: /home/repository/moby/jars-archive/README,v
retrieving revision 1.1.1.1
retrieving revision 1.2
diff -u -r1.1.1.1 -r1.2
--- /home/repository/moby/jars-archive/README 2005/06/10 13:48:10 1.1.1.1
+++ /home/repository/moby/jars-archive/README 2005/06/10 13:53:03 1.2
@@ -3,7 +3,7 @@
This module serves just one purpose: to store commonly (or less
commonly) used third-party Java libraries (jar files) in order to
-share them by several other CVS modules withouyt the need to include
+share them by several other CVS modules without the need to include
them separately in all those CVS modules.
I guess that the purpose is similar to the CVS-native notion of the
@@ -16,6 +16,12 @@
first time it builds everything. An example can be found in the
moby-live module (subdirectory Java).
+It started as a BioMoby initiative so it is located as a module within
+the 'moby' CVS repository. But it can used by others, as well - one
+does not use it as a CVS module, but like a normal HTTP resource. Only
+when you want to add a new library, or to udate an existing one, you
+need to check-out it as usual.
+
Directory structure
-------------------
@@ -37,5 +43,5 @@
----------------------------------------------------------------------
Started by: Martin Senger (martin.senger@gmail.com), June 2005
-$Id
+$Id$
----------------------------------------------------------------------
From senger at pub.open-bio.org Fri Jun 10 09:55:36 2005
From: senger at pub.open-bio.org (Martin Senger)
Date: Fri Jun 10 09:30:54 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200506101355.j5ADtais003920@pub.open-bio.org>
senger
Fri Jun 10 09:55:36 EDT 2005
Update of /home/repository/moby/jars-archive/current
In directory pub.open-bio.org:/tmp/cvs-serv3904/current
Added Files:
activation.jar adenine.jar alltools.jar axis-ant.jar axis.jar
commons-discovery.jar commons-logging.jar concurrent.jar
icu4j.jar jakarta-oro-2.0.5.jar jaxen-core.jar jaxen-jdom.jar
jaxrpc.jar jdom.jar jena.jar junit.jar log4j-1.2.4.jar
lsid-client-1.1.2.jar lsid-server-1.1.2.jar mail.jar
mysql-connector-java-3.1.7-bin.jar rdf-api-2001-01-19.jar
saaj.jar saxpath.jar servlet.jar taverna.jar wsdl4j.jar
xalan.jar xercesImpl.jar xercesSamples.jar xml-apis.jar
xmlParserAPIs.jar
Removed Files:
.keep-me
Log Message:
jars-archive/current activation.jar,NONE,1.1 adenine.jar,NONE,1.1 alltools.jar,NONE,1.1 axis-ant.jar,NONE,1.1 axis.jar,NONE,1.1 commons-discovery.jar,NONE,1.1 commons-logging.jar,NONE,1.1 concurrent.jar,NONE,1.1 icu4j.jar,NONE,1.1 jakarta-oro-2.0.5.jar,NONE,1.1 jaxen-core.jar,NONE,1.1 jaxen-jdom.jar,NONE,1.1 jaxrpc.jar,NONE,1.1 jdom.jar,NONE,1.1 jena.jar,NONE,1.1 junit.jar,NONE,1.1 log4j-1.2.4.jar,NONE,1.1 lsid-client-1.1.2.jar,NONE,1.1 lsid-server-1.1.2.jar,NONE,1.1 mail.jar,NONE,1.1 mysql-connector-java-3.1.7-bin.jar,NONE,1.1 rdf-api-2001-01-19.jar,NONE,1.1 saaj.jar,NONE,1.1 saxpath.jar,NONE,1.1 servlet.jar,NONE,1.1 taverna.jar,NONE,1.1 wsdl4j.jar,NONE,1.1 xalan.jar,NONE,1.1 xercesImpl.jar,NONE,1.1 xercesSamples.jar,NONE,1.1 xml-apis.jar,NONE,1.1 xmlParserAPIs.jar,NONE,1.1 .keep-me,1.1.1.1,NONE
rcsdiff: /home/repository/moby/jars-archive/current/RCS/.keep-me,v: No such file or directory
From senger at pub.open-bio.org Fri Jun 10 10:07:45 2005
From: senger at pub.open-bio.org (Martin Senger)
Date: Fri Jun 10 09:43:01 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200506101407.j5AE7jJY004023@pub.open-bio.org>
senger
Fri Jun 10 10:07:45 EDT 2005
Update of /home/repository/moby/jars-archive
In directory pub.open-bio.org:/tmp/cvs-serv4004
Modified Files:
README
Log Message:
jars-archive README,1.2,1.3
===================================================================
RCS file: /home/repository/moby/jars-archive/README,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/jars-archive/README 2005/06/10 13:53:03 1.2
+++ /home/repository/moby/jars-archive/README 2005/06/10 14:07:45 1.3
@@ -19,7 +19,7 @@
It started as a BioMoby initiative so it is located as a module within
the 'moby' CVS repository. But it can used by others, as well - one
does not use it as a CVS module, but like a normal HTTP resource. Only
-when you want to add a new library, or to udate an existing one, you
+when you want to add a new library, or to update an existing one, you
need to check-out it as usual.
From kawas at pub.open-bio.org Mon Jun 13 14:14:36 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Mon Jun 13 13:49:40 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200506131814.j5DIEabl026259@pub.open-bio.org>
kawas
Mon Jun 13 14:14:35 EDT 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier
In directory pub.open-bio.org:/tmp/cvs-serv26234/org/biomoby/registry/rdfagent/verifier
Modified Files:
Communicator.java
Log Message:
Fixed a bug that crashed the agent when an RDF document retrieved from an author contained invalid xml. Eddie
moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier Communicator.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier/Communicator.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier/Communicator.java 2005/04/16 14:32:12 1.4
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier/Communicator.java 2005/06/13 18:14:35 1.5
@@ -1,4 +1,3 @@
-
package org.biomoby.registry.rdfagent.verifier;
import java.io.BufferedReader;
@@ -25,223 +24,260 @@
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.RDFException;
+import com.hp.hpl.jena.shared.JenaException;
+
/**
* @author Nina Opushneva
- *
- * The Communicator class allows a Java application to communicate with
- * servers of service providers by HTTP protocol, and with SMTP server by message
+ *
+ * The Communicator class allows a Java application to communicate with servers
+ * of service providers by HTTP protocol, and with SMTP server by message
*/
public class Communicator {
-/** get RDF model of service by signatureURL
- * (make HTTP connect to server, open a file,read a file into a streem, build the model)
- * @param signURL - the URL of resource (signatureURL)
- * @param servNames - set of service names located at this signatureURL
- * @return Model the RDF model of services located at this signatureURL
- */
-
- public static Model getServiceRDF(String servNames,String signURL){
-
- Model model = ModelFactory.createDefaultModel();
- String mes1 = "";
- try {
- URL u = new URL(signURL);
-
- HttpURLConnection huc = (HttpURLConnection) u.openConnection();
- huc.connect();
-
- int code = huc.getResponseCode();
- Log.info("GET <"+signURL+" > - HTTP CODE: "+ code);
- Report.doWrite("");
- Report.doWrite("GET SIGNATURE_URL <"+signURL+" > - HTTP CODE: "+ code);
- Report.add("GET SIGNATURE_URL <"+signURL+" > - HTTP CODE: "+ code);
-
- if (code == 200 || code == 202 ) {
-
- try{
- model.read(huc.getInputStream(),"");
- }catch(RDFException e){
- Log.severe("Failed : "+e);
- Report.add("Error 1: "+e);
-// e.getMessage();
- }catch(IOException e){
- Log.severe("Failed : "+e);
- Report.add("Error 3: "+e);
-// e.getMessage();
- }
-
- }
- else {
- if (code == 400){
- Log.warning("The request had bad syntax or was inherently impossible to be satisfied.");
- Report.add("The request had bad syntax or was inherently impossible to be satisfied.");
- }
- else if (code == 401){
- Log.warning("The parameter to this message gives a specification of authorization schemes which are acceptable.");
- Report.add("The parameter to this message gives a specification of authorization schemes which are acceptable.");
- }
- else if (code == 402){
- Report.add("The parameter to this message gives a specification of charging schemes acceptable.");
- }
- else if (code == 403){
- Report.add("The request is for something forbidden. Authorization will not help.");
- mes1 = "The request is for something forbidden.";
- }
- else if (code == 404){
- Report.doWrite("The server has not found anything matching the URI given");
- Report.add("The server has not found anything matching the URI given");
- mes1 = "The RDF file was not found on the server";
+ /**
+ * get RDF model of service by signatureURL (make HTTP connect to server,
+ * open a file,read a file into a streem, build the model)
+ *
+ * @param signURL -
+ * the URL of resource (signatureURL)
+ * @param servNames -
+ * set of service names located at this signatureURL
+ * @return Model the RDF model of services located at this signatureURL
+ */
+
+ public static Model getServiceRDF(String servNames, String signURL) {
+
+ Model model = ModelFactory.createDefaultModel();
+ String mes1 = "";
+ try {
+ URL u = new URL(signURL);
+
+ HttpURLConnection huc = (HttpURLConnection) u.openConnection();
+ huc.connect();
+
+ int code = huc.getResponseCode();
+ Log.info("GET <" + signURL + " > - HTTP CODE: " + code);
+ Report.doWrite("");
+ Report.doWrite("GET SIGNATURE_URL <" + signURL
+ + " > - HTTP CODE: " + code);
+ Report.add("GET SIGNATURE_URL <" + signURL + " > - HTTP CODE: "
+ + code);
+ if (code == 200 || code == 202) {
+
+ try {
+ model.read(huc.getInputStream(), "");
+ } catch (RDFException e) {
+ Log.severe("Failed : " + e);
+ Report.add("Error 1: " + e);
+
+
+ // e.getMessage();
+ } catch (JenaException e) {
+ //reset code to
+ code = 417;
}
- else if (code == 500){
+ //http://www.w3.org/RDF/Validator/RDF/Validator/ARPServlet?URI=
+ }
+
+ //////////////////////////
+ // no else if here purposely, because i reset the code if an
+ // exception is thrown due to invalid rdfs being returned.
+ //////////////////////////
+ if (code != 200 && code != 202)
+ if (code == 400) {
+ Log
+ .warning("The request had bad syntax or was inherently impossible to be satisfied.");
+ Report
+ .add("The request had bad syntax or was inherently impossible to be satisfied.");
+ } else if (code == 401) {
+ Log
+ .warning("The parameter to this message gives a specification of authorization schemes which are acceptable.");
+ Report
+ .add("The parameter to this message gives a specification of authorization schemes which are acceptable.");
+ } else if (code == 402) {
+ Report
+ .add("The parameter to this message gives a specification of charging schemes acceptable.");
+ } else if (code == 403) {
+ Report
+ .add("The request is for something forbidden. Authorization will not help.");
+ mes1 = "The request is for something forbidden.";
+ } else if (code == 404) {
+ Report
+ .doWrite("The server has not found anything matching the URI given");
+ Report
+ .add("The server has not found anything matching the URI given");
+ mes1 = "The RDF file was not found on the server";
+ } else if (code == 417) {
+ Report.add(" RDF Parsing error. Possible reason being that multiple
-
+
Semantic MOBY Developer Tools
-
-
Convert a graph to a different format
-
-
-
- List all statements in the S-MOBY metadata
- repository
-
-
-
- Validate an OWL Graph using Jena
-
-
-
- Validate that a graph is MOBY canonical form
-
-