[MOBY-guts] biomoby commit
senger@ebi.ac.uk
senger at pub.open-bio.org
Mon Oct 18 14:35:07 UTC 2004
senger
Mon Oct 18 10:35:06 EDT 2004
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory pub.open-bio.org:/tmp/cvs-serv2405/src/main/org/biomoby/shared
Modified Files:
Central.java MobyData.java MobyDataType.java
MobyPrimaryDataSimple.java MobyRelationship.java
MobyService.java MobyServiceType.java
Added Files:
CentralAll.java
Log Message:
searching data paths and more, see docs/ChangeLog
moby-live/Java/src/main/org/biomoby/shared CentralAll.java,NONE,1.1 Central.java,1.7,1.8 MobyData.java,1.1,1.2 MobyDataType.java,1.4,1.5 MobyPrimaryDataSimple.java,1.2,1.3 MobyRelationship.java,1.2,1.3 MobyService.java,1.3,1.4 MobyServiceType.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java 2004/09/24 19:52:56 1.7
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java 2004/10/18 14:35:06 1.8
@@ -12,21 +12,19 @@
import java.net.*;
/**
- * An interface to the Moby Registry.
- *<p>
- * The Moby Registry service (or Moby Central service) is used to do
- * various transactions, including registering new Data and Service
- * types, querying for these types, registering new Services, or
- * querying for available services given certain input/output or
- * service type constraints.
- *<P>
+ * An interface to the Moby Registry. <p>
+ *
+ * The Moby Registry (or Moby Central) is used to do various
+ * transactions, including registering new Data and Service types,
+ * querying for these types, registering new Services, or querying for
+ * available services given certain input/output or service type
+ * constraints. <P>
*
* The main purpose of this interface is to express the Moby Registry
* functionality in Java language, and to hide complexity of the
* parameters required by the Moby Registry. The Moby Registry gets
* most parameters as small XML documents while this interface defines
- * the same parameters as various Java method signatures.
- *<p>
+ * the same parameters as various Java method signatures. <p>
*
* For details describing and explaining the methods see the original documentation at
* <a href="http://biomoby.org/" target="_top">
@@ -35,7 +33,11 @@
*
* <H5>Last changes (in backwards order)</H5>
* <UL>
- * <LI> New methods retrieving various types of relationships has been added:
+ * <li> New methods retrieving location of a Moby registry have been added:
+ * {@link #getRegistryEndpoint},
+ * {@link #getRegistryNamespace},
+ * <li> Added new constants defining relationship types as integers.
+ * <LI> New methods retrieving various types of relationships have been added:
* {@link #getDataTypeRelationships},
* {@link #getServiceTypeRelationships}
* <LI> Added constants defining recognizable relationship types
@@ -375,12 +377,17 @@
*************************************************************************/
boolean getCacheMode();
+ /**************************************************************************
+ * Return an endpoint (a stringified URL) representing a Moby
+ * registry that an instance of this implementation is connected
+ * to.
+ *************************************************************************/
+ String getRegistryEndpoint();
- // Work in progress:
-// http://biomoby.org/RESOURCES/MOBY-S/Objects
-// http://biomoby.org/RESOURCES/MOBY-S/Services
-// http://biomoby.org/RESOURCES/MOBY-S/Namespaces
-// http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances
-// http://biomoby.org/RESOURCES/MOBY-S/FULL
+ /**************************************************************************
+ * Return a namespace (a URI) used by a Moby registry that an
+ * instance of this implementation is connected to.
+ *************************************************************************/
+ String getRegistryNamespace();
}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyData.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/shared/MobyData.java 2003/09/24 14:33:37 1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyData.java 2004/10/18 14:35:06 1.2
@@ -28,16 +28,26 @@
protected String id = null;
/**************************************************************************
- * Default constructor. Other characteristics are empty - which is usually
+ * Default constructor.
+ *************************************************************************/
+ public MobyData() {
+ this ("_dummy_");
+ }
+
+ /**************************************************************************
+ * Normal constructor. Other characteristics are empty - which is usually
* wrong - therefore use 'set' method to fill them.
*************************************************************************/
public MobyData (String name) {
- this.name = name;
+ setName (name);
}
public String getName() {
return name;
}
+ public void setName (String value) {
+ name = value;
+ }
public String getId() {
return id;
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.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/shared/MobyDataType.java 2004/09/23 10:20:29 1.4
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java 2004/10/18 14:35:06 1.5
@@ -35,7 +35,14 @@
protected String id = null;
/**************************************************************************
- * Default constructor. Other characteristics are empty - which is
+ * Default constructor.
+ *************************************************************************/
+ public MobyDataType() {
+ this ("_dummy_");
+ }
+
+ /**************************************************************************
+ * Normal constructor. Other characteristics are empty - which is
* usually wrong - you should use 'set' methods to fill them
* before using this instance. <p>
*
@@ -45,13 +52,17 @@
* (e.g. urn:lsid:biomoby.org:objectclass:Object).
*************************************************************************/
public MobyDataType (String name) {
- this.name = name;
+ setName (name);
}
public String getName() {
return name;
}
+ public void setName (String value) {
+ name = value;
+ }
+
/**
* Return an ID that is given to this data type during its
* registration. The ID seems to be used only for de-registration
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrimaryDataSimple.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/shared/MobyPrimaryDataSimple.java 2004/09/22 21:11:17 1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrimaryDataSimple.java 2004/10/18 14:35:06 1.3
@@ -27,7 +27,14 @@
protected MobyDataType dataType;
/**************************************************************************
- * Default constructor. Other characteristics are empty - which is usually
+ * Default constructor.
+ *************************************************************************/
+ public MobyPrimaryDataSimple() {
+ super();
+ }
+
+ /**************************************************************************
+ * Normal constructor. Other characteristics are empty - which is usually
* wrong - therefore use 'set' method to fill them.
*************************************************************************/
public MobyPrimaryDataSimple (String name) {
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyRelationship.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/shared/MobyRelationship.java 2004/09/23 10:20:29 1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyRelationship.java 2004/10/18 14:35:06 1.3
@@ -25,7 +25,14 @@
protected int relationshipType = Central.iHASA;
/**************************************************************************
- * Default (and only) constructor. <p>
+ * Default constructor. <p>
+ *************************************************************************/
+ public MobyRelationship() {
+ this ("_dummy_", "Object", Central.iISA);
+ }
+
+ /**************************************************************************
+ * Normal constructor. <p>
*
* @param name is a name how this relationship is known (an
* "article name" in the BioMoby speak), e.g. 'length'. Because of
@@ -52,6 +59,9 @@
public String getName() {
return name;
}
+ public void setName (String value) {
+ name = value;
+ }
/**
* Return a name of a data type that is linked by this
@@ -60,6 +70,9 @@
public String getDataTypeName() {
return dataTypeName;
}
+ public void setDataTypeName (String value) {
+ dataTypeName = value;
+ }
/**
* Return type of this relationship. It is either {@link Central#iHASA HASA} or
@@ -68,6 +81,9 @@
public int getRelationshipType() {
return relationshipType;
}
+ public void setRelationshipType (int value) {
+ relationshipType = value;
+ }
/**
* A static method converting a relationship type to its string
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.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/shared/MobyService.java 2004/09/22 21:11:17 1.3
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java 2004/10/18 14:35:06 1.4
@@ -42,17 +42,31 @@
protected Vector primaryOutputs = new Vector();
/**************************************************************************
- * Default constructor. Other characteristics are empty - which is
+ * Default constructor.
+ *************************************************************************/
+ public MobyService() {
+ this ("_dummy_");
+ }
+
+ /**************************************************************************
+ * Normal constructor. Other characteristics are empty - which is
* usually wrong - therefore use 'set' methods to fill them before
* using this instance.
*************************************************************************/
public MobyService (String name) {
- this.name = name;
+ setName (name);
+ }
+
+ public String getUniqueName() {
+ return name + "/" + authority;
}
public String getName() {
return name;
}
+ public void setName (String value) {
+ name = value;
+ }
/**
* Return an ID that is given to this service instance during its
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyServiceType.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/shared/MobyServiceType.java 2003/09/24 14:33:37 1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyServiceType.java 2004/10/18 14:35:06 1.2
@@ -29,16 +29,26 @@
protected String id = null;
/**************************************************************************
- * Default constructor. Other characteristics are empty - which is usually
+ * Default constructor.
+ *************************************************************************/
+ public MobyServiceType() {
+ this ("_dummy_");
+ }
+
+ /**************************************************************************
+ * Normal constructor. Other characteristics are empty - which is usually
* wrong - therefore use 'set' method to fill them.
*************************************************************************/
public MobyServiceType (String name) {
- this.name = name;
+ setName (name);
}
public String getName() {
return name;
}
+ public void setName (String value) {
+ name = value;
+ }
public String getId() {
return id;
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