[MOBY-guts] biomoby commit
Martin Senger
senger at pub.open-bio.org
Thu Sep 22 16:07:09 UTC 2005
senger
Thu Sep 22 12:07:09 EDT 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory pub.open-bio.org:/tmp/cvs-serv17235/src/main/org/biomoby/shared
Modified Files:
CentralDigest.java MobyDataType.java MobyNamespace.java
MobyPrimaryDataSet.java MobyPrimaryDataSimple.java
MobySecondaryData.java MobyService.java
Log Message:
moby-live/Java/src/main/org/biomoby/shared CentralDigest.java,1.1,1.2 MobyDataType.java,1.7,1.8 MobyNamespace.java,1.1,1.2 MobyPrimaryDataSet.java,1.2,1.3 MobyPrimaryDataSimple.java,1.4,1.5 MobySecondaryData.java,1.3,1.4 MobyService.java,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/CentralDigest.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/CentralDigest.java 2004/10/18 14:49:30 1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/CentralDigest.java 2005/09/22 16:07:09 1.2
@@ -1,14 +1,16 @@
// CentralDigest.java
//
-// senger at ebi.ac.uk
-// September 2004
+// Created: September 2004
+//
+// This file is a component of the BioMoby project.
+// Copyright Martin Senger (martin.senger at gmail.com).
//
package org.biomoby.shared;
/**
- * An interface to the cumulated (digested) contents of the Moby Registry.
- *<p>
+ * An interface to the cumulated (digested) contents of the Moby
+ * Registry. <p>
*
* The main purpose of this interface is for those clients that are
* accessing the whole, or a substantial part of, Moby registry. The
@@ -16,7 +18,7 @@
* registry API that allow to get more information in one go - saving
* significantly network and time. <p>
*
- * @author <A HREF="mailto:senger at ebi.ac.uk">Martin Senger</A>
+ * @author <A HREF="mailto:martin.senger at gmail.com">Martin Senger</A>
* @version $Id$
*/
@@ -44,6 +46,17 @@
throws MobyException;
/*************************************************************************
+ * Get definition of all known namespaces. It differs from the
+ * {@link Central#getNamespaces} because it returns an array of
+ * full definitions of namespaces, and not just their names and
+ * descriptions. <p>
+ *
+ * @throws MobyException if communication with the Moby Registry fails
+ *************************************************************************/
+ MobyNamespace[] getFullNamespaces()
+ throws MobyException;
+
+ /*************************************************************************
* Get definition of all registered service instances. It is a
* cumulation of many individual calls to {@link
* Central#findService(MobyService) findService by name} for all
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.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/MobyDataType.java 2005/08/26 06:27:04 1.7
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java 2005/09/22 16:07:09 1.8
@@ -7,6 +7,7 @@
package org.biomoby.shared;
+import org.tulsoft.shared.UUtils;
/**
@@ -246,20 +247,27 @@
public String toString() {
StringBuffer buf = new StringBuffer();
buf.append ("Name: " + name + "\n");
- buf.append ("Auth: " + authority + "\n");
- buf.append ("Desc: " + description + "\n");
- buf.append ("Contact: " + emailContact + "\n");
+ if (UUtils.notEmpty (authority)) buf.append ("Auth: " + authority + "\n");
+ if (UUtils.notEmpty (description)) buf.append ("Desc: " + description + "\n");
+ if (UUtils.notEmpty (emailContact)) buf.append ("Contact: " + emailContact + "\n");
if (id != null) buf.append ("ID: " + id + "\n");
- buf.append ("Parents:\n");
- for (int i = 0 ; i < parentNames.length; i++) {
- buf.append (Utils.format (null, 1));
- buf.append (parentNames [i]);
+ if (parentNames.length > 0) {
+ buf.append ("Parents: ");
+ for (int i = 0 ; i < parentNames.length; i++) {
+ if (i > 0) buf.append (", ");
+ buf.append (parentNames [i]);
+ }
buf.append ("\n");
}
- buf.append ("Children (only those registered here):\n");
- for (int i = 0 ; i < children.length; i++) {
- buf.append (Utils.format (null, 1));
- buf.append (children[i].toString());
+ int chLen = children.length;
+ if (chLen > 0) {
+ buf.append ("Children (only those registered here): ");
+ if (chLen > 1)
+ buf.append ("\n");
+ for (int i = 0 ; i < chLen; i++) {
+ if (i > 0) buf.append ("\n\t");
+ buf.append (children[i].toString());
+ }
buf.append ("\n");
}
return new String (buf);
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyNamespace.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/MobyNamespace.java 2003/09/24 14:33:37 1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyNamespace.java 2005/09/22 16:07:09 1.2
@@ -6,6 +6,7 @@
//
package org.biomoby.shared;
+import org.tulsoft.shared.UUtils;
/**
* A container representing a namespace used in the Moby registry.
@@ -69,10 +70,12 @@
public String toString() {
StringBuffer buf = new StringBuffer();
- buf.append ("Name: " + name + "\n");
- buf.append ("Auth: " + authority + "\n");
- buf.append ("Desc: " + description + "\n");
- buf.append ("ID: " + id + "\n");
+ buf.append ("Name: " + name);
+ if (UUtils.notEmpty (authority))
+ buf.append (", Auth: " + authority);
+ if (id != null) buf.append (", ID: " + id);
+ if (UUtils.notEmpty (description))
+ buf.append ("\n\t" + description);
return new String (buf);
}
public String format (int indent) {
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrimaryDataSet.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/MobyPrimaryDataSet.java 2005/04/07 16:37:02 1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrimaryDataSet.java 2005/09/22 16:07:09 1.3
@@ -6,6 +6,8 @@
package org.biomoby.shared;
+import org.tulsoft.shared.UUtils;
+
import java.util.Enumeration;
import java.util.Vector;
@@ -106,8 +108,9 @@
public String toString() {
StringBuffer buf = new StringBuffer();
- buf.append ("Name: " + name + "\n");
- buf.append ("ID: " + id + "\n");
+ if (UUtils.notEmpty (name))
+ buf.append ("Name: " + name + "\n");
+ if (id != null) buf.append ("ID: " + id + "\n");
buf.append ("Elements in collection:\n");
for (Enumeration en = elements.elements(); en.hasMoreElements(); ) {
buf.append (((MobyPrimaryDataSimple)en.nextElement()).format (1));
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrimaryDataSimple.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/MobyPrimaryDataSimple.java 2005/04/07 16:37:02 1.4
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrimaryDataSimple.java 2005/09/22 16:07:09 1.5
@@ -6,6 +6,8 @@
package org.biomoby.shared;
+import org.tulsoft.shared.UUtils;
+
import java.util.Enumeration;
import java.util.Vector;
@@ -130,15 +132,18 @@
public String toString() {
StringBuffer buf = new StringBuffer();
- buf.append ("Name: " + name + "\n");
+ if (UUtils.notEmpty (name))
+ buf.append ("Name: " + name + "\n");
if (id != null) buf.append ("ID: " + id + "\n");
if (dataType != null)
buf.append ("Data Type:\n" + dataType.format (1));
- buf.append ("Namespaces:\n");
- for (Enumeration en = namespaces.elements(); en.hasMoreElements(); ) {
- buf.append (((MobyNamespace)en.nextElement()).format (1));
+ if (namespaces.size() > 0) {
+ buf.append ("Namespaces:\n");
+ for (Enumeration en = namespaces.elements(); en.hasMoreElements(); ) {
+ buf.append (((MobyNamespace)en.nextElement()).format (1));
+ buf.append ("\n");
+ }
}
- buf.append ("\n");
return new String (buf);
}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobySecondaryData.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/MobySecondaryData.java 2005/04/19 17:58:49 1.3
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobySecondaryData.java 2005/09/22 16:07:09 1.4
@@ -6,6 +6,8 @@
package org.biomoby.shared;
+import org.tulsoft.shared.UUtils;
+
import java.util.Enumeration;
import java.util.Vector;
@@ -178,19 +180,23 @@
public String toString() {
StringBuffer buf = new StringBuffer();
- buf.append ("Name: " + name + "\n");
- buf.append ("ID: " + id + "\n");
+ if (UUtils.notEmpty (name))
+ buf.append ("Name: " + name + "\n");
+ if (id != null) buf.append ("ID: " + id + "\n");
buf.append ("Data Type: " + dataType + "\n");
- buf.append ("Default: " + defaultValue + "\n");
+ if (UUtils.notEmpty (defaultValue))
+ buf.append ("Default: " + defaultValue + "\n");
if (minimumValue != Integer.MIN_VALUE)
buf.append ("Min: " + minimumValue + "\n");
if (maximumValue != Integer.MAX_VALUE)
buf.append ("Max: " + maximumValue + "\n");
- buf.append ("Allowed values: ");
- for (Enumeration en = allowedValues.elements(); en.hasMoreElements(); ) {
- buf.append (en.nextElement() + " ");
+ if (allowedValues.size() > 0) {
+ buf.append ("Allowed values: ");
+ for (Enumeration en = allowedValues.elements(); en.hasMoreElements(); ) {
+ buf.append (en.nextElement() + " ");
+ }
+ buf.append ("\n");
}
- buf.append ("\n");
return new String (buf);
}
}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java 2005/08/26 06:27:04 1.6
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java 2005/09/22 16:07:09 1.7
@@ -7,6 +7,8 @@
package org.biomoby.shared;
+import org.tulsoft.shared.UUtils;
+
import java.util.Enumeration;
import java.util.Vector;
@@ -70,6 +72,15 @@
setName (name);
}
+ /**************************************************************************
+ * Even more normal constructor - because a service is fully
+ * qualified only by its name <b>and</b> its authority. <p>
+ *************************************************************************/
+ public MobyService (String name, String authority) {
+ setName (name);
+ setAuthority (authority);
+ }
+
public String getUniqueName() {
return name + "/" + authority;
}
@@ -302,24 +313,25 @@
buf.append ("Desc: " + description + "\n");
buf.append ("URL: " + url + "\n");
buf.append ("Contact: " + emailContact + "\n");
- buf.append ("Signature URL: " + signatureURL + "\n");
- buf.append ("Path to RDF: " + pathToRDF + "\n");
+ if (UUtils.notEmpty (signatureURL))
+ buf.append ("Signature URL: " + signatureURL + "\n");
+ if (UUtils.notEmpty (pathToRDF))
+ buf.append ("Path to RDF: " + pathToRDF + "\n");
if (id != null) buf.append ("ID: " + id + "\n");
- buf.append ("\nPrimary inputs:\n");
+ buf.append ("Primary inputs:\n");
for (Enumeration en = primaryInputs.elements(); en.hasMoreElements(); )
buf.append (((MobyData)en.nextElement()).format (1));
- buf.append ("\n");
- buf.append ("\nSecondary inputs:\n");
- for (Enumeration en = secondaryInputs.elements(); en.hasMoreElements(); )
- buf.append (en.nextElement().toString());
- buf.append ("\n");
+ if (secondaryInputs.size() > 0) {
+ buf.append ("Secondary inputs:\n");
+ for (Enumeration en = secondaryInputs.elements(); en.hasMoreElements(); )
+ buf.append (((MobyData)en.nextElement()).format (1));
+ }
- buf.append ("\nOutputs:\n");
+ buf.append ("Outputs:\n");
for (Enumeration en = primaryOutputs.elements(); en.hasMoreElements(); )
- buf.append (en.nextElement().toString());
- buf.append ("\n");
+ buf.append (((MobyData)en.nextElement()).format (1));
return new String (buf);
}
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