Third-party Libraries Guidelines

Martin Senger · Comming soon..

.jar
xmls/libraries.xml
jar
remote.dir
xmls/libraries
jar
jars-archive
+export CVS_RSH=ssh
+cvs -d :ext:your-user-name@pub.open-bio.org:/home/repository/moby co -P jars-archive
+
remote.dir
moby-live/Java
moby-live/Java
            
+import org.biomoby.client.*;
+import org.biomoby.shared.*;
+import org.biomoby.shared.data.*;
+
+public class HelloMOBY {
+    public static void main(String[] args) throws Exception{
+
+        Central worker = new CentralImpl();
+        MobyService templateService = new MobyService("MOBYSHoundGetGenBankff");
+        MobyService[] validServices = worker.findService(templateService);
+
+	MobyRequest mr = new MobyRequest(worker);
+	mr.setService(validServices[0]);
+	mr.setInput(new MobyDataObject("NCBI_gi", "111076"));
+	System.out.println(mr.invokeService().toString());
+    }
+}
+	  
+String aaSequence = "MPGGFILAIDEGTTSARAIIYNQDLEVLGIGQYDFPQHYPSPGYVEHNPDEIWNAQMLAI";
+MobyDataComposite aaSequenceObject = new MobyDataComposite("AminoAcidSequence");
+aaSequence.put("SequenceString", new MobyDataString(aaSequence));
+aaSequence.put("Length", new MobyDataInt(aaSequence.length()));
+
+MobyContentInstance queries = new MobyContentInstance();
+data.put(new MobyDataObject("gi", "100089"));
+data.put(new MobyDataObject("gi", "324442"));
+MobyDataUtils.toXMLDocument(System.out, queries);
+
+MobyContentInstance queries = MobyDataUtils.fromXMLDocument(System.in);
+System.out.println("The document contained " + ((queries.size() == 1) ? "1 query" : (query.size() + " queries")));
+
.jar
xmls/libraries.xml
jar
remote.dir
xmls/libraries
jar
jars-archive
+export CVS_RSH=ssh
+cvs -d :ext:your-user-name at pub.open-bio.org:/home/repository/moby co -P jars-archive
+
remote.dir
moby-live/Java
moby-live/Java
            
+import org.biomoby.client.*;
+import org.biomoby.shared.*;
+import org.biomoby.shared.data.*;
+
+public class HelloMOBY {
+    public static void main(String[] args) throws Exception{
+
+        Central worker = new CentralImpl();
+        MobyService templateService = new MobyService("MOBYSHoundGetGenBankff");
+        MobyService[] validServices = worker.findService(templateService);
+
+	MobyRequest mr = new MobyRequest(worker);
+	mr.setService(validServices[0]);
+	mr.setInput(new MobyDataObject("NCBI_gi", "111076"));
+	System.out.println(mr.invokeService().toString());
+    }
+}
+	  
+String aaSequence = "MPGGFILAIDEGTTSARAIIYNQDLEVLGIGQYDFPQHYPSPGYVEHNPDEIWNAQMLAI";
+MobyDataComposite aaSequenceObject = new MobyDataComposite("AminoAcidSequence");
+aaSequence.put("SequenceString", new MobyDataString(aaSequence));
+aaSequence.put("Length", new MobyDataInt(aaSequence.length()));
+
+MobyContentInstance queries = new MobyContentInstance();
+data.put(new MobyDataObject("gi", "100089"));
+data.put(new MobyDataObject("gi", "324442"));
+MobyDataUtils.toXMLDocument(System.out, queries);
+
+MobyContentInstance queries = MobyDataUtils.fromXMLDocument(System.in);
+System.out.println("The document contained " + ((queries.size() == 1) ? "1 query" : (query.size() + " queries")));
+
.jar
xmls/libraries.xml
jar
remote.dir
xmls/libraries
jar
jars-archive
+export CVS_RSH=ssh
+cvs -d :ext:your-user-name at pub.open-bio.org:/home/repository/moby co -P jars-archive
+
remote.dir
moby-live/Java
moby-live/Java
            
+import org.biomoby.client.*;
+import org.biomoby.shared.*;
+import org.biomoby.shared.data.*;
+
+public class HelloMOBY {
+    public static void main(String[] args) throws Exception{
+
+        Central worker = new CentralImpl();
+        MobyService templateService = new MobyService("MOBYSHoundGetGenBankff");
+        MobyService[] validServices = worker.findService(templateService);
+
+	MobyRequest mr = new MobyRequest(worker);
+	mr.setService(validServices[0]);
+	mr.setInput(new MobyDataObject("NCBI_gi", "111076"));
+	System.out.println(mr.invokeService().toString());
+    }
+}
+	  
+String aaSequence = "MPGGFILAIDEGTTSARAIIYNQDLEVLGIGQYDFPQHYPSPGYVEHNPDEIWNAQMLAI";
+MobyDataComposite aaSequenceObject = new MobyDataComposite("AminoAcidSequence");
+aaSequence.put("SequenceString", new MobyDataString(aaSequence));
+aaSequence.put("Length", new MobyDataInt(aaSequence.length()));
+
+MobyContentInstance queries = new MobyContentInstance();
+data.put(new MobyDataObject("gi", "100089"));
+data.put(new MobyDataObject("gi", "324442"));
+MobyDataUtils.toXMLDocument(System.out, queries);
+
+MobyContentInstance queries = MobyDataUtils.fromXMLDocument(System.in);
+System.out.println("The document contained " + ((queries.size() == 1) ? "1 query" : (query.size() + " queries")));
+

MOBY Specification	jMOBY class in `org.biomoby.shared.data`	underlying Java implementation	Can be instantiated using any one of
Object	`MobyDataObject`	implements `Comparable`	"namespace", "id" MOBYDataObject (cloning)
String	`MobyDataString`	`java.lang.StringBuffer`	java.lang.CharSequence (i.e. CharBuffer, String, StringBuffer, StringBuilder)
Integer	`MobyDataInt`	`java.math.BigInteger`	int java.lang.Number (i.e. Byte, Double, Float, Integer, Long, Short, BigInteger, BigDecimal) Strings like "2005"
Float	`MobyDataFloat`	`java.math.BigDecimal`	double java.lang.Number Strings like "2.0-e4" or "0.0002"
DateTime	`MobyDataDateTime`	`java.util.GregorianCalendar`	java.util.GregorianCalendar Strings like "2005-07-21" (a W3C profile version of an ISO 8601 date-time string)

MOBY Specification	jMOBY class in `org.biomoby.shared.data`	underlying Java implementation	Can be instantiated using any one of
Object	`MobyDataObject`	implements `Comparable`	"namespace", "id" MOBYDataObject (cloning)
String	`MobyDataString`	`java.lang.StringBuffer`	java.lang.CharSequence (i.e. CharBuffer, String, StringBuffer, StringBuilder)
Integer	`MobyDataInt`	`java.math.BigInteger`	int java.lang.Number (i.e. Byte, Double, Float, Integer, Long, Short, BigInteger, BigDecimal) Strings like "2005"
Float	`MobyDataFloat`	`java.math.BigDecimal`	double java.lang.Number Strings like "2.0-e4" or "0.0002"
DateTime	`MobyDataDateTime`	`java.util.GregorianCalendar`	java.util.GregorianCalendar Strings like "2005-07-21" (a W3C profile version of an ISO 8601 date-time string)

MOBY Specification	jMOBY class in `org.biomoby.shared.data`	underlying Java implementation	Can be instantiated using any one of
Object	`MobyDataObject`	implements `Comparable`	"namespace", "id" MOBYDataObject (cloning)
String	`MobyDataString`	`java.lang.StringBuffer`	java.lang.CharSequence (i.e. CharBuffer, String, StringBuffer, StringBuilder)
Integer	`MobyDataInt`	`java.math.BigInteger`	int java.lang.Number (i.e. Byte, Double, Float, Integer, Long, Short, BigInteger, BigDecimal) Strings like "2005"
Float	`MobyDataFloat`	`java.math.BigDecimal`	double java.lang.Number Strings like "2.0-e4" or "0.0002"
DateTime	`MobyDataDateTime`	`java.util.GregorianCalendar`	java.util.GregorianCalendar Strings like "2005-07-21" (a W3C profile version of an ISO 8601 date-time string)

Last changes (in backwards order)

Third-party Libraries Guidelines

Using jMoby from CVS

Unable to update your information

Make sure that you specify a valid signature url! This field looks like the following: http://myAuthority.domain/path/to/rdf/for/service. Also make sure that you have specified the right case-sensitive service name, if applicable.

Simple Client

jMOBY Client/Server Quickstart

Motivation

Syntax Notes

Sections

Basic Anatomy of the Java API

Hello World (or its bioinformatics equivalent)

Creating jMOBY Data

Creating a database identifier object

Creating a "primitive" data object

Creating composite objects

Manipulating jMOBY data

Dissecting queries and responses

Changing data objects

Creating MOBY XML (responses and queries)

Create a blank MOBY XML response

Create a MOBY XML response or query with a single data object

Create a MOBY XML response or query envelope with multiple invocations

Parsing MOBY XML

Last changes (in backwards order)

Third-party Libraries Guidelines

Using jMoby from CVS

Unable to update your information

Make sure that you specify a valid signature url! This field looks like the following: http://myAuthority.domain/path/to/rdf/for/service. Also make sure that you have specified the right case-sensitive service name, if applicable.

Simple Client

jMOBY Client/Server Quickstart

Motivation

Syntax Notes

Sections

Basic Anatomy of the Java API

Hello World (or its bioinformatics equivalent)

Creating jMOBY Data

Creating a database identifier object

Creating a "primitive" data object

Creating composite objects

Manipulating jMOBY data

Dissecting queries and responses

Changing data objects

Creating MOBY XML (responses and queries)

Create a blank MOBY XML response

Create a MOBY XML response or query with a single data object

Create a MOBY XML response or query envelope with multiple invocations

Parsing MOBY XML

Last changes (in backwards order)

Third-party Libraries Guidelines

Using jMoby from CVS

Unable to update your information

Make sure that you specify a valid signature url! This field looks like the following: http://myAuthority.domain/path/to/rdf/for/service. Also make sure that you have specified the right case-sensitive service name, if applicable.

Simple Client

jMOBY Client/Server Quickstart

Motivation

Syntax Notes

Sections

Basic Anatomy of the Java API

Hello World (or its bioinformatics equivalent)

Creating jMOBY Data

Creating a database identifier object

Creating a "primitive" data object

Creating composite objects

Manipulating jMOBY data

Dissecting queries and responses

Changing data objects

Creating MOBY XML (responses and queries)

Create a blank MOBY XML response

Create a MOBY XML response or query with a single data object

Create a MOBY XML response or query envelope with multiple invocations

Parsing MOBY XML