JAXB implementation of query

README.md

-Common API for the AKTIN data warehouse
\ No newline at end of file
+Common API for the AKTIN data warehouse
+---------------------------------------
+
+Generate XSD files:
+```
+"$JAVA_HOME"/bin/schemagen -d target -cp target/classes org.aktin.exchange.Query
+```
+
+Query exchange
+--------------
+```
+<request>
+	<id>unique request id</id>
+	<date-reference>2016-04-11</date-reference>
+	<published>
+	<query>
+		<id>unique query id</id>
+		<description>
+		
+		</description>
+		<principal>
+			<name></name>
+			<organisation></organisation>
+			<location></location>
+			<email></email>
+			<phone></phone>
+			<url></url>
+		</principal>
+
+		<schedule type="single|repeating|benchmark">
+			<duration>-P1Y</duration>
+			<interval>P1Y</interval>
+		</schedule>
+
+		<concepts>
+			<concept id="CEDIS30:XXX" type="raw"/>
+			<concept id="XXX1" type="aggregate">
+				<count group-by="fact.value">
+			</concept>
+			<concept id="XXX1" type="aggregate">
+				<!-- by arrival time -->
+				<count group-by="substr(8,10,fact.start)">
+				<max/>
+				<min/>
+			</concept>
+		</concepts>
+		<definition xsi:type="sql">
+			
+		</definition>
+	</query>
+	<signature from="broker" algorithm="SHA256withRSA">...</signature>
+	<signature from="me" algorithm="SHA256withRSA">...</signature>
+	<broker>
+		<last-modified>max timestamp der nachfolgenden</last-modified>
+		<!-- timestamp the query was published by the broker -->
+		<published>2015-12-01T18:30:14</published>
+		<!-- later, the query can be either canceled or closed -->
+		<closed>2015-12-02T18:30:00</closed>
+		<canceled>2015-12-02T18:30:14</canceled>
+	</broker>
+</query>
+
+	<request-status ref="123">
+		<last-modified>max timestampt der nachfolgenden</last-modified>
+		<received>XXXtimestamp</received>
+		<confirmation method="single|double|automatic">xxx</confirmation>
+		<!-- confirmation or rejection -->
+		<rejected></rejected>
+		<comment></comment>
+		<last-execution>
+			<completed>XXXtimestamp</completed>
+			<failed></failed>
+			
+		</last-execution>
+		<last-contact>
+		<result-submitted>XXX timestamp</result-submitted>
+	</request-status>
+
+
+<query-result id-ref="">
+</query-result>
+```

TODO.txt

+Error in maven schemagen:
+
+Post error in maven schemagen:
+
+Should not convert spaces to %20:
+
+schemagen -encoding UTF-8 -d D:\Users\marap1\Projects\2014-09 AKTIN\repo-v2\aktin\dwh-api\target\schemagen-work\compile_scope -classpath /D:/Users/marap1/Projects/2014-09%20AKTIN/repo-v2/aktin/dwh-api/src/main/java/ -episode D:\Users\marap1\Projects\2014-09 AKTIN\repo-v2\aktin\dwh-api\target\generated-resources\schemagen\META-INF\sun-jaxb.episode src\main\java\org\aktin\exchange\AbstractConcept.java src\main\java\org\aktin\exchange\Principal.java src\main\java\org\aktin\exchange\Query.java src\main\java\org\aktin\exchange\RawConcept.java src\main\java\org\aktin\exchange\XMLConstants.java src\main\java\org\aktin\exchange\package-info.java
+
+
+
+https://github.com/mojohaus/jaxb2-maven-plugin/issues/
+

pom.xml

@@ -12,16 +12,37 @@
 		<version>0.1-SNAPSHOT</version>
 	</parent>
 	<build>
-		<!--
 		<resources>
 			<resource>
 				<directory>src/main/resources</directory>
 			</resource>
+			<resource>
+				<directory>target/generated-resources</directory>
+			</resource>
 		</resources>
-		-->
 		<plugins>
+			<plugin>
+				<groupId>org.codehaus.mojo</groupId>
+				<artifactId>jaxb2-maven-plugin</artifactId>
+				<version>2.2</version>
+				<executions>
+					<execution>
+						<id>schemagen</id>
+						<goals>
+							<goal>schemagen</goal>
+						</goals>
+					</execution>
+				</executions>
+				<configuration>
+					<locale>en</locale>
+					<sources>
+						<source>src/main/java/org/aktin/exchange</source>
+					</sources>
+				</configuration>
+			</plugin>
 		</plugins>
-	</build>
+		
+	</build> 
 	<dependencies>
 		<!-- unit tests -->
 		<dependency>

src/main/java/org/aktin/exchange/AbstractConcept.java

+package org.aktin.exchange;
+
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlSeeAlso;
+
+@XmlSeeAlso({RawConcept.class})
+public abstract class AbstractConcept {
+
+	/**
+	 * Unique identifier of the concept.
+	 */
+	@XmlAttribute
+	public String id;
+}

src/main/java/org/aktin/exchange/Principal.java

+package org.aktin.exchange;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlElement;
+
+/**
+ * Principal of a query.
+ * @author R.W.Majeed
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+public class Principal {
+
+	/**
+	 * Principal's full name
+	 */
+	@XmlElement(required=true)
+	public String name;
+	/**
+	 * Principal's organisation
+	 */
+	@XmlElement(required=true)
+	public String organisation;
+	@XmlElement(required=true)
+	public String email;
+	@XmlElement(required=true)
+	public String phone;
+	/**
+	 * Postal address
+	 */
+	public String address;
+	/**
+	 * Web page URL
+	 */
+	public String url;
+}

src/main/java/org/aktin/exchange/Query.java

+package org.aktin.exchange;
+
+import java.util.List;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlElementWrapper;
+import javax.xml.bind.annotation.XmlRootElement;
+
+/**
+ * Query which can be executed in an i2b2
+ * data warehouse by the AKTIN remote query 
+ * plugin.
+ * 
+ * @author R.W.Majeed
+ *
+ */
+@XmlRootElement
+@XmlAccessorType(XmlAccessType.NONE)
+public class Query {
+
+	/**
+	 * Unique identifier for this query. This identifier
+	 * will not change, even if a query scheduled for repeated
+	 * executions.
+	 */
+	@XmlElement(required=true)
+	public String id;
+	
+	/**
+	 * Human readable description of the query.
+	 */
+	@XmlElement(required=true)
+	public String description;
+	
+	/**
+	 * Contact for inquiries and further
+	 * information about the query and research
+	 * project.
+	 */
+	@XmlElement(required=true)
+	public Principal principal;
+
+	/**
+	 * Execution schedule for the query. For now,
+	 * only {@link SingleExecution} and {@link RepeatedExecution} 
+	 * are supported.
+	 */
+	@XmlElement(required=true)
+	public QuerySchedule schedule;
+	
+	@XmlElementWrapper(name="concepts",required=true)
+	@XmlElement(name="concept",required=true)
+	public List<AbstractConcept> concepts;
+}

src/main/java/org/aktin/exchange/QueryRequest.java

+package org.aktin.exchange;
+
+import java.time.Instant;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlRootElement;
+
+@XmlRootElement
+@XmlAccessorType(XmlAccessType.FIELD)
+public class QueryRequest {
+
+	/**
+	 * Unique id for the query request.
+	 * This id will always be unique and different
+	 * for multiple (e.g. recurring) requests for 
+	 * the same query.
+	 * The id is given by the broker.
+	 */
+	@XmlElement(required=true)
+	String id;
+	
+	/**
+	 * Date reference for recurring queries. A recurring
+	 * query may be requested once per month. The reference
+	 * date will then be used to determine the time frame
+	 * for the query. In other words, the reference date is used
+	 * to fill a placeholder in the recurring query. 
+	 */
+	@XmlElement(required=false)
+	Instant referenceDate;
+	
+	/**
+	 * Time stamp when the request was published at the query broker.
+	 */
+	Instant published;
+	/**
+	 * Due date until which the query results have to be submitted.
+	 */
+	Instant deadline;
+	/**
+	 * Date when the request was closed by the query broker. While
+	 * this date is unset/null, results can be sumitted at any time.
+	 */
+	Instant closed;
+	/**
+	 * Date when the request was canceled. This indicates abnormal
+	 * or unsuccessful termination of the request.
+	 * A request can not be closed and canceled at the same time.
+	 */
+	Instant canceled;
+	
+	/**
+	 * Query to execute
+	 */
+	@XmlElement(required=true)
+	Query query;
+	
+	@XmlElement(name="signature", required=false)
+	Signature[] signatures;
+}

src/main/java/org/aktin/exchange/QuerySchedule.java

+package org.aktin.exchange;
+
+import java.time.Period;
+
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlSeeAlso;
+
+/**
+ * Abstract query schedule
+ * @author R.W.Majeed
+ *
+ */
+@XmlSeeAlso({SingleExecution.class, RepeatedExecution.class})
+public abstract class QuerySchedule {
+
+	/**
+	 * Duration for the query. The duration is relative
+	 * to the {@link #reference} timestamp and might also be negative.
+	 */
+	@XmlElement(required=true)
+	public Period duration;
+
+}

src/main/java/org/aktin/exchange/RawConcept.java

+package org.aktin.exchange;
+
+import javax.xml.bind.annotation.XmlType;
+
+@XmlType(name="raw")
+public class RawConcept extends AbstractConcept{
+	
+}

src/main/java/org/aktin/exchange/RepeatedExecution.java

+package org.aktin.exchange;
+
+import java.time.Duration;
+
+/**
+ * Repeated execution schedule for a query.
+ * 
+ * The repeated execution does not contain a reference timestamp. Instead, the reference
+ * timestamp is provided by the query request from the broker.
+ * 
+ * @author R.W.Majeed
+ *
+ */
+public class RepeatedExecution extends QuerySchedule{
+
+	/**
+	 * Estimated repeating interval. Only positive periods allowed.
+	 * This property will not cause any execution on the data warehouse side.
+	 * It is solely for information purposes.
+	 */
+	public Duration repeats;
+}

src/main/java/org/aktin/exchange/Signature.java

+package org.aktin.exchange;
+
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlValue;
+
+/**
+ * Signature during query exchange
+ * 
+ * @author R.W.Majeed
+ *
+ */
+public class Signature {
+
+	/** Signature author */
+	@XmlAttribute
+	String from;
+	
+	/** Signature algorithm */
+	@XmlAttribute
+	String algorithm;
+	
+	@XmlValue
+	byte[] value;
+	
+	// TODO add code to verify content
+}

src/main/java/org/aktin/exchange/SingleExecution.java

+package org.aktin.exchange;
+
+import java.time.Instant;
+
+import javax.xml.bind.annotation.XmlElement;
+
+/**
+ * Single execution schedule for a query.
+ * 
+ * A reference time stamp is provided.
+ * 
+ * @author R.W.Majeed
+ *
+ */
+public class SingleExecution extends QuerySchedule{
+	/**
+	 * Reference time stamp for queries. If 
+	 */
+	@XmlElement(required=false)
+	public Instant reference;
+	
+	
+}

src/main/java/org/aktin/exchange/XMLConstants.java

+package org.aktin.exchange;
+
+import javax.xml.bind.annotation.XmlTransient;
+
+@XmlTransient
+public class XMLConstants {
+
+	public static final String XML_NAMESPACE="http://aktin.org/ns/exchange";
+}

src/main/java/org/aktin/exchange/package-info.java

+/**
+ * Interfaces for the AKTIN data exchange.
+ * Requests for query executions, query definitions,
+ * query responses.
+ * 
+ * @author R.W.Majeed
+ *
+ */
+@XmlSchema(namespace=XMLConstants.XML_NAMESPACE,
+elementFormDefault=XmlNsForm.QUALIFIED,
+	xmlns = {
+			
+		@XmlNs(prefix = "xsi", namespaceURI = javax.xml.XMLConstants.W3C_XML_SCHEMA_INSTANCE_NS_URI) 
+		//"http://www.w3.org/2001/XMLSchema-instance"
+	}
+)
+@javax.xml.bind.annotation.adapters.XmlJavaTypeAdapters({
+	@javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter(type=java.time.Duration.class,value=org.aktin.xml.DurationAdapter.class),
+	@javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter(type=java.time.Period.class,value=org.aktin.xml.PeriodAdapter.class),
+	@javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter(type=java.time.Instant.class,value=org.aktin.xml.InstantAdapter.class)
+})
+
+package org.aktin.exchange;
+import javax.xml.bind.annotation.*;
\ No newline at end of file

src/main/java/org/aktin/xml/DurationAdapter.java

+package org.aktin.xml;
+
+import java.time.Duration;
+
+import javax.xml.bind.annotation.adapters.XmlAdapter;
+
+/**
+ * JAXB adapter for processing java.time.Duration.
+ * This can be removed later on when native support is added to the JAXB implementation
+ *
+ */
+public class DurationAdapter extends XmlAdapter<String, Duration>{
+
+	@Override
+	public String marshal(Duration v) throws Exception {
+		if( v == null )return null;
+		else return v.toString();
+	}
+
+	@Override
+	public Duration unmarshal(String v) throws Exception {
+		if( v == null )return null;
+		else return Duration.parse(v);
+	}
+	
+}
\ No newline at end of file

src/main/java/org/aktin/xml/InstantAdapter.java

+package org.aktin.xml;
+
+import java.time.Instant;
+
+import javax.xml.bind.annotation.adapters.XmlAdapter;
+
+/**
+ * JAXB adapter for processing java.time.Instant.
+ * This can be removed later on when native support is added to the JAXB implementation
+ *
+ */
+public class InstantAdapter extends XmlAdapter<String, Instant>{
+
+	@Override
+	public Instant unmarshal(String v) throws Exception {
+		if( v == null )return null;
+		else return Instant.parse(v);
+	}
+
+	@Override
+	public String marshal(Instant v) throws Exception {
+		if( v == null )return null;
+		else return v.toString();
+	}
+	
+}
\ No newline at end of file

src/main/java/org/aktin/xml/PeriodAdapter.java

+package org.aktin.xml;
+
+import java.time.Period;
+
+import javax.xml.bind.annotation.adapters.XmlAdapter;
+
+/**
+ * JAXB adapter for processing java.time.Duration.
+ * This can be removed later on when native support is added to the JAXB implementation
+ *
+ */
+public class PeriodAdapter extends XmlAdapter<String, Period>{
+
+	@Override
+	public String marshal(Period v) throws Exception {
+		if( v == null )return null;
+		else return v.toString();
+	}
+
+	@Override
+	public Period unmarshal(String v) throws Exception {
+		if( v == null )return null;
+		else return Period.parse(v);
+	}
+	
+}
\ No newline at end of file