[MOBY-guts] biomoby commit
Eddie Kawas
kawas at pub.open-bio.org
Thu Apr 7 16:37:02 UTC 2005
kawas
Thu Apr 7 12:37:02 EDT 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory pub.open-bio.org:/tmp/cvs-serv1723/org/biomoby/client
Modified Files:
CentralImpl.java Graphviz.java MobyRequest.java FileCache.java
CentralDigestImpl.java ServicesEdge.java SimpleCache.java
DataTypeConnector.java RDF.java GraphsServlet.java
FilterServices.java ServletFileCache.java DataServiceEdge.java
Taverna.java CentralDigestCachedImpl.java
ServiceConnections.java SimpleFileCache.java
Log Message:
Okay, i am trying again ...
-----------------------
Adding the packages and files:
org.biomoby.client.rdf.*
org.biomoby.client.ui.*
org.biomoby.shared.mobyxml.*
org.biomoby.registry.properties.*
org.biomoby.registry.definitions.*
as well as some empty packages:
org.biomoby.client.exceptions
I have also removed various import statements in source files that were not needed.
Eddie
moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.19,1.20 Graphviz.java,1.5,1.6 MobyRequest.java,1.7,1.8 FileCache.java,1.4,1.5 CentralDigestImpl.java,1.1,1.2 ServicesEdge.java,1.4,1.5 SimpleCache.java,1.2,1.3 DataTypeConnector.java,1.1,1.2 RDF.java,1.1,1.2 GraphsServlet.java,1.7,1.8 FilterServices.java,1.4,1.5 ServletFileCache.java,1.3,1.4 DataServiceEdge.java,1.1,1.2 Taverna.java,1.1,1.2 CentralDigestCachedImpl.java,1.2,1.3 ServiceConnections.java,1.3,1.4 SimpleFileCache.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v
retrieving revision 1.19
retrieving revision 1.20
diff -u -r1.19 -r1.20
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2004/12/05 22:28:02 1.19
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2005/04/07 16:37:02 1.20
@@ -7,17 +7,41 @@
package org.biomoby.client;
-import org.biomoby.shared.*;
-
-import org.apache.axis.client.*;
-import org.apache.axis.*;
-import javax.xml.namespace.QName;
-
-import org.w3c.dom.*;
-
-import java.util.*;
-import java.io.*;
-import java.net.*;
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.PrintStream;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.Map;
+import java.util.Properties;
+import java.util.Vector;
+
+import org.apache.axis.AxisFault;
+import org.apache.axis.client.Call;
+import org.apache.axis.client.Service;
+import org.biomoby.shared.Central;
+import org.biomoby.shared.MobyData;
+import org.biomoby.shared.MobyDataType;
+import org.biomoby.shared.MobyException;
+import org.biomoby.shared.MobyNamespace;
+import org.biomoby.shared.MobyPrimaryDataSet;
+import org.biomoby.shared.MobyPrimaryDataSimple;
+import org.biomoby.shared.MobyRelationship;
+import org.biomoby.shared.MobySecondaryData;
+import org.biomoby.shared.MobyService;
+import org.biomoby.shared.MobyServiceType;
+import org.biomoby.shared.NoSuccessException;
+import org.biomoby.shared.PendingCurationException;
+import org.biomoby.shared.Utils;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
/**
* A default implementation of the
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/Graphviz.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/Graphviz.java 2004/10/18 14:35:06 1.5
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/Graphviz.java 2005/04/07 16:37:02 1.6
@@ -6,14 +6,12 @@
package org.biomoby.client;
-import java.util.Enumeration;
-import java.util.Hashtable;
import java.util.HashSet;
import java.util.Properties;
-import org.biomoby.shared.MobyService;
import org.biomoby.shared.MobyDataType;
import org.biomoby.shared.MobyRelationship;
+import org.biomoby.shared.MobyService;
import org.biomoby.shared.MobyServiceType;
import org.biomoby.shared.Utils;
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.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/client/MobyRequest.java 2005/02/15 17:47:39 1.7
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java 2005/04/07 16:37:02 1.8
@@ -1,38 +1,43 @@
package org.biomoby.client;
// Defines Web service input, output, access
-import org.biomoby.shared.*;
-
-// Transport
-import org.apache.axis.message.SOAPBody;
-import org.apache.axis.client.Call;
-import javax.xml.rpc.encoding.XMLType;
-import javax.xml.rpc.ParameterMode;
-import javax.xml.rpc.Service;
+import java.io.PrintStream;
+import java.io.StringBufferInputStream;
+import java.util.Hashtable;
+import java.util.Vector;
-// JAXP Parsing
-import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.namespace.QName;
import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.rpc.Service;
import javax.xml.transform.TransformerException;
-import javax.xml.namespace.QName;
-import org.w3c.dom.*;
-
-// Utilities
-import java.util.Hashtable;
-import java.util.Vector;
-import java.io.ByteArrayInputStream;
-import org.apache.xpath.XPath; // compiled xpath statement
-import org.apache.xpath.XPathContext; //runtime environment in which XPath is executed
-import org.apache.xpath.objects.XObject;
+import org.apache.axis.client.Call;
+import org.apache.axis.message.MessageElement;
import org.apache.xml.utils.PrefixResolver;
import org.apache.xml.utils.PrefixResolverDefault;
+import org.apache.xpath.XPath;
+import org.apache.xpath.XPathContext;
import org.apache.xpath.objects.XNodeSet;
+import org.apache.xpath.objects.XObject;
+import org.biomoby.shared.Central;
+import org.biomoby.shared.MobyData;
+import org.biomoby.shared.MobyDataInstance;
+import org.biomoby.shared.MobyDataSecondaryInstance;
+import org.biomoby.shared.MobyDataSetInstance;
+import org.biomoby.shared.MobyDataSimpleInstance;
+import org.biomoby.shared.MobyException;
+import org.biomoby.shared.MobyPrefixResolver;
+import org.biomoby.shared.MobyService;
+import org.biomoby.shared.NoSuccessException;
+import org.biomoby.shared.SOAPException;
+import org.w3c.dom.CDATASection;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
-import org.apache.axis.message.MessageElement;
-import java.io.PrintStream;
-import java.io.StringBufferInputStream;
+import org.w3c.dom.Text;
/**
* This class handles the WSDL transaction to request a response
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/FileCache.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/client/FileCache.java 2004/10/18 14:35:06 1.4
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/FileCache.java 2005/04/07 16:37:02 1.5
@@ -9,8 +9,14 @@
// TBD: this may go later to the general tools
package org.biomoby.client;
-import java.util.*;
-import java.io.*;
+import java.io.BufferedOutputStream;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.Properties;
/**
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestImpl.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/CentralDigestImpl.java 2004/10/18 14:35:06 1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestImpl.java 2005/04/07 16:37:02 1.2
@@ -6,11 +6,17 @@
package org.biomoby.client;
-import org.biomoby.shared.*;
-import embl.ebi.utils.*;
+import java.util.Iterator;
+import java.util.Map;
+import java.util.Vector;
+
+import org.biomoby.shared.CentralDigest;
+import org.biomoby.shared.MobyDataType;
+import org.biomoby.shared.MobyException;
+import org.biomoby.shared.MobyService;
+import org.biomoby.shared.MobyServiceType;
-import java.util.*;
-import java.io.*;
+import embl.ebi.utils.DGUtils;
// import java.net.*;
/**
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ServicesEdge.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/client/ServicesEdge.java 2005/03/03 23:18:35 1.4
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ServicesEdge.java 2005/04/07 16:37:02 1.5
@@ -6,11 +6,7 @@
package org.biomoby.client;
-import org.biomoby.shared.*;
-
-import java.net.*;
-import java.util.*;
-import java.io.*;
+import org.biomoby.shared.MobyService;
/**
* An instance of this class is a container for a pair of Moby service
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/SimpleCache.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/SimpleCache.java 2004/10/18 14:35:06 1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/SimpleCache.java 2005/04/07 16:37:02 1.3
@@ -9,8 +9,8 @@
// TBD: this may go later to the general tools
package org.biomoby.client;
-import java.util.*;
-import java.io.*;
+import java.io.IOException;
+import java.util.Properties;
/**
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/DataTypeConnector.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/DataTypeConnector.java 2004/10/18 14:35:06 1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/DataTypeConnector.java 2005/04/07 16:37:02 1.2
@@ -6,7 +6,8 @@
package org.biomoby.client;
-import org.biomoby.shared.*;
+import org.biomoby.shared.MobyDataType;
+import org.biomoby.shared.Utils;
/**
* A simple container for a connection between two data types. <p>
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/RDF.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/RDF.java 2003/11/08 00:27:24 1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/RDF.java 2005/04/07 16:37:02 1.2
@@ -6,12 +6,16 @@
package org.biomoby.client;
-import org.biomoby.shared.*;
-import edu.mit.lcs.haystack.rdf.*;
+import java.util.Properties;
-import java.net.*;
-import java.util.*;
-import java.io.*;
+import org.biomoby.shared.MobyService;
+
+import edu.mit.lcs.haystack.rdf.Literal;
+import edu.mit.lcs.haystack.rdf.LocalRDFContainer;
+import edu.mit.lcs.haystack.rdf.RDFException;
+import edu.mit.lcs.haystack.rdf.Resource;
+import edu.mit.lcs.haystack.rdf.Statement;
+import edu.mit.lcs.haystack.rdf.Utilities;
/**
* A utility class that understands how to create
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/GraphsServlet.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/client/GraphsServlet.java 2004/10/18 14:35:06 1.7
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/GraphsServlet.java 2005/04/07 16:37:02 1.8
@@ -8,16 +8,45 @@
package org.biomoby.client;
-import org.biomoby.shared.*;
-
-import embl.ebi.tools.*;
-import embl.ebi.utils.*;
-import embl.ebi.servlets.*;
-
-import javax.servlet.*;
-import javax.servlet.http.*;
-import java.util.*;
-import java.io.*;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.PrintWriter;
+import java.util.Arrays;
+import java.util.Date;
+import java.util.Enumeration;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.Map;
+import java.util.Properties;
+import java.util.Vector;
+
+import javax.servlet.ServletContext;
+import javax.servlet.ServletException;
+import javax.servlet.http.HttpServlet;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+import org.biomoby.shared.CentralAll;
+import org.biomoby.shared.MobyDataType;
+import org.biomoby.shared.MobyException;
+import org.biomoby.shared.MobyNamespace;
+import org.biomoby.shared.MobyPrimaryDataSimple;
+import org.biomoby.shared.MobyService;
+import org.biomoby.shared.MobyServiceType;
+import org.biomoby.shared.Utils;
+
+import embl.ebi.servlets.Html;
+import embl.ebi.servlets.HtmlConstants;
+import embl.ebi.tools.CatchOutputDefaultImpl;
+import embl.ebi.tools.Executor;
+import embl.ebi.tools.Printf;
+import embl.ebi.tools.Sorter;
+import embl.ebi.utils.GException;
+import embl.ebi.utils.StringUtils;
+import embl.ebi.utils.UUtils;
/**
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/FilterServices.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/client/FilterServices.java 2004/11/12 23:07:08 1.4
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/FilterServices.java 2005/04/07 16:37:02 1.5
@@ -6,8 +6,13 @@
package org.biomoby.client;
-import org.biomoby.shared.*;
-import java.util.*;
+import java.util.Enumeration;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.Vector;
+
+import org.biomoby.shared.MobyService;
/**
* This class allows to filter a set of services using some criteria.
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ServletFileCache.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/ServletFileCache.java 2004/10/18 14:35:06 1.3
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ServletFileCache.java 2005/04/07 16:37:02 1.4
@@ -9,9 +9,7 @@
// TBD: this may go later to the general tools
package org.biomoby.client;
-import javax.servlet.*;
-import java.util.*;
-import java.io.*;
+import javax.servlet.ServletContext;
/**
* A simple cache implementation meant to be used in a servlet
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/DataServiceEdge.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/DataServiceEdge.java 2004/10/18 14:35:06 1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/DataServiceEdge.java 2005/04/07 16:37:02 1.2
@@ -6,11 +6,9 @@
package org.biomoby.client;
-import org.biomoby.shared.*;
-
-import java.net.*;
-import java.util.*;
-import java.io.*;
+import org.biomoby.shared.MobyDataType;
+import org.biomoby.shared.MobyService;
+import org.biomoby.shared.Utils;
/**
* An instance of this class is a container for a pair of a data type
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/Taverna.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/Taverna.java 2004/10/18 14:35:06 1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/Taverna.java 2005/04/07 16:37:02 1.2
@@ -6,13 +6,21 @@
package org.biomoby.client;
-import org.biomoby.shared.*;
-import org.embl.ebi.escience.scufl.*;
-import org.embl.ebi.escience.scufl.view.*;
-import org.embl.ebi.escience.scuflworkers.biomoby.*;
-import org.embl.ebi.escience.scuflworkers.java.*;
-import org.embl.ebi.escience.scuflworkers.stringconstant.*;
-import java.util.*;
+import java.util.Hashtable;
+import java.util.Properties;
+
+import org.biomoby.shared.MobyException;
+import org.biomoby.shared.MobyService;
+import org.biomoby.shared.Utils;
+import org.embl.ebi.escience.scufl.DataConstraint;
+import org.embl.ebi.escience.scufl.InputPort;
+import org.embl.ebi.escience.scufl.OutputPort;
+import org.embl.ebi.escience.scufl.Processor;
+import org.embl.ebi.escience.scufl.ScuflModel;
+import org.embl.ebi.escience.scufl.view.XScuflView;
+import org.embl.ebi.escience.scuflworkers.biomoby.BiomobyProcessor;
+import org.embl.ebi.escience.scuflworkers.java.LocalServiceProcessor;
+import org.embl.ebi.escience.scuflworkers.stringconstant.StringConstantProcessor;
/**
* A utility class that understands how to create workflow definitions
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.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/CentralDigestCachedImpl.java 2004/11/14 16:12:50 1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2005/04/07 16:37:02 1.3
@@ -6,11 +6,22 @@
package org.biomoby.client;
-import org.biomoby.shared.*;
-import embl.ebi.utils.*;
-
-import java.util.*;
-import java.io.*;
+import java.io.BufferedOutputStream;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.Iterator;
+import java.util.Map;
+import java.util.Vector;
+
+import org.biomoby.shared.CentralAll;
+import org.biomoby.shared.MobyDataType;
+import org.biomoby.shared.MobyException;
+import org.biomoby.shared.MobyService;
+import org.biomoby.shared.NoSuccessException;
/**
* An implementation of {@link org.biomoby.shared.CentralAll},
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ServiceConnections.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/ServiceConnections.java 2004/10/18 14:35:06 1.3
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ServiceConnections.java 2005/04/07 16:37:02 1.4
@@ -6,8 +6,16 @@
package org.biomoby.client;
-import org.biomoby.shared.*;
-import java.util.*;
+import java.util.Hashtable;
+import java.util.Vector;
+
+import org.biomoby.shared.MobyData;
+import org.biomoby.shared.MobyDataType;
+import org.biomoby.shared.MobyNamespace;
+import org.biomoby.shared.MobyPrimaryDataSet;
+import org.biomoby.shared.MobyPrimaryDataSimple;
+import org.biomoby.shared.MobyService;
+import org.biomoby.shared.Utils;
/**
* This class contains knowledge (an algorithm) how individual Moby
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/SimpleFileCache.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/SimpleFileCache.java 2004/10/18 14:35:06 1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/SimpleFileCache.java 2005/04/07 16:37:02 1.2
@@ -7,8 +7,7 @@
// TBD: this may go later to the general tools
package org.biomoby.client;
-import java.util.*;
-import java.io.*;
+import java.io.IOException;
/**
More information about the MOBY-guts
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