Import module for any table based format

histream-import/.gitignore

+.settings/
+.classpath
+.project
+target/

histream-import/pom.xml

+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<name>HIStream : Import</name>
+
+	<groupId>de.sekmi.histream</groupId>
+	<artifactId>histream-import</artifactId>
+	<version>0.2-alpha</version>
+
+	<parent>
+		<groupId>de.sekmi.histream</groupId>
+		<artifactId>histream</artifactId>
+		<version>0.2-alpha</version>
+	</parent>
+  
+	<build>
+		<plugins>
+		</plugins>
+	</build>
+	<dependencies>
+		<dependency>
+			<groupId>de.sekmi.histream</groupId>
+			<artifactId>histream-core</artifactId>
+			<version>0.2-alpha</version>
+		</dependency>
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+		</dependency>
+	</dependencies>
+</project>
\ No newline at end of file

histream-import/src/main/java/de/sekmi/histream/etl/ETLObservationSupplier.java

+package de.sekmi.histream.etl;
+
+import de.sekmi.histream.Observation;
+import de.sekmi.histream.ObservationSupplier;
+
+public class ETLObservationSupplier implements ObservationSupplier{
+
+	@Override
+	public Observation get() {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	@Override
+	public void close() throws Exception {
+		// TODO Auto-generated method stub
+		
+	}
+
+	@Override
+	public String getMeta(String arg0) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+}

histream-import/src/main/java/de/sekmi/histream/etl/config/Column.java

+package de.sekmi.histream.etl.config;
+
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlValue;
+
+public class Column {
+	private Column(){
+	}
+	public Column(String name){
+		this();
+		this.name = name;
+	}
+	@XmlAttribute
+	String na;
+	
+	@XmlAttribute(name="constant-value")
+	String constantValue;
+	
+	@XmlValue
+	String name;
+}

histream-import/src/main/java/de/sekmi/histream/etl/config/Concept.java

+package de.sekmi.histream.etl.config;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
+
+/**
+ * Concept from a wide table
+ * @author Raphael
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+public class Concept{
+	@XmlAttribute(required=true)
+	String id;
+	// TODO: value should contain also type (string,decimal,integer,...)
+	Column value;
+	Column unit;
+	@XmlElement(required=true)
+	Column start;
+	Column end;
+	@XmlElement(name="modifier")
+	Modifier[] modifiers;
+	// ...
+	
+	@XmlAccessorType(XmlAccessType.FIELD)
+	public static class Modifier{
+		@XmlAttribute(required=true)
+		String id;
+		// TODO: value with type
+		Column value;
+		Column unit;
+		
+		private Modifier(){
+		}
+		public Modifier(String id){
+			this();
+			this.id = id;
+		}
+	}
+	
+	private Concept(){
+	}
+	
+	public Concept(String id, String startColumn){
+		this();
+		this.id = id;
+		this.start = new Column(startColumn);
+	}
+	
+}
\ No newline at end of file

histream-import/src/main/java/de/sekmi/histream/etl/config/DataSource.java

+package de.sekmi.histream.etl.config;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlElementWrapper;
+
+@XmlAccessorType(XmlAccessType.FIELD)
+public class DataSource {
+	@XmlElement
+	Meta meta;
+	
+	@XmlElementWrapper(name="transformation")
+	@XmlElement(name="xml-source")
+	XmlSource[] xmlSources;
+
+	@XmlElement(name="patient-table",required=true)
+	PatientTable patientTable;
+	
+	@XmlElement(name="visit-table")
+	VisitTable visitTable;
+	
+	@XmlElement(name="wide-table")
+	WideTable[] wideTables;
+	
+	
+	
+}

histream-import/src/main/java/de/sekmi/histream/etl/config/DataTableIdat.java

+package de.sekmi.histream.etl.config;
+
+import javax.xml.bind.annotation.XmlElement;
+
+public class DataTableIdat extends IdatColumns {
+	@XmlElement(name="visit-id")
+	Column visitId;
+}

histream-import/src/main/java/de/sekmi/histream/etl/config/FileSource.java

+package de.sekmi.histream.etl.config;
+
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.stream.Stream;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlElement;
+
+@XmlAccessorType(XmlAccessType.FIELD)
+public class FileSource extends TableSource{
+	@XmlElement
+	URL url;
+	
+	@XmlElement
+	String type;
+	
+	private FileSource(){
+	}
+	public FileSource(String url, String type) throws MalformedURLException{
+		this();
+		this.url = new URL(url);
+		this.type = type;
+	}
+	@Override
+	public String[] getHeaders() {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	@Override
+	public Stream<String[]> rows() {
+		return null;
+	}
+
+}

histream-import/src/main/java/de/sekmi/histream/etl/config/IdatColumns.java

+package de.sekmi.histream.etl.config;
+
+import javax.xml.bind.annotation.XmlElement;
+
+public class IdatColumns {
+	@XmlElement(name="patient-id")
+	Column patientId;
+}

histream-import/src/main/java/de/sekmi/histream/etl/config/Meta.java

+package de.sekmi.histream.etl.config;
+
+import javax.xml.bind.annotation.XmlElement;
+
+public class Meta {
+	@XmlElement(name="source-id")
+	String sourceId;
+
+	@XmlElement(name="etl-strategy")
+	String etlStrategy;
+}

histream-import/src/main/java/de/sekmi/histream/etl/config/PatientTable.java

+package de.sekmi.histream.etl.config;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlElementWrapper;
+
+/**
+ * Patient table. Contains patient id and other identifying information.
+ * Can also contain medical data
+ * @author marap1
+ *
+ */
+public class PatientTable extends Table implements WideInterface{
+	@XmlElement
+	IDAT idat;
+	
+	@XmlElementWrapper(name="mdat")
+	@XmlElement(name="concept")
+	Concept[] concepts;
+
+	@XmlAccessorType(XmlAccessType.FIELD)
+	public static class IDAT extends IdatColumns{
+		Column firstname;
+		Column lastname;
+		Column birthdate;
+		Column deathdate;
+		Column gender;
+		Column[] ignore;
+	}
+
+}

histream-import/src/main/java/de/sekmi/histream/etl/config/SQLSource.java

+package de.sekmi.histream.etl.config;
+
+import java.util.stream.Stream;
+
+import javax.xml.bind.annotation.XmlElement;
+
+public class SQLSource extends TableSource {
+	@XmlElement
+	String jdbcDriver;
+	@XmlElement
+	String connectString;
+	@XmlElement
+	String sql;
+	
+	private SQLSource() {
+	}
+	public SQLSource(String driver, String connectString){
+		this();
+		this.jdbcDriver = driver;
+		this.connectString = connectString;
+	}
+	
+	@Override
+	public String[] getHeaders() {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	@Override
+	public Stream<String[]> rows() {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+}

histream-import/src/main/java/de/sekmi/histream/etl/config/Table.java

+package de.sekmi.histream.etl.config;
+
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlTransient;
+
+@XmlTransient
+public class Table {
+
+	@XmlElement(required=true)
+	TableSource source;
+}

histream-import/src/main/java/de/sekmi/histream/etl/config/TableSource.java

+package de.sekmi.histream.etl.config;
+
+import java.util.stream.Stream;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlSeeAlso;
+import javax.xml.bind.annotation.XmlTransient;
+
+@XmlTransient
+@XmlAccessorType(XmlAccessType.NONE)
+
+@XmlSeeAlso({FileSource.class, SQLSource.class})
+public abstract class TableSource{
+	public abstract String[] getHeaders();
+	public abstract Stream<String[]> rows();
+}
\ No newline at end of file

histream-import/src/main/java/de/sekmi/histream/etl/config/VisitTable.java

+package de.sekmi.histream.etl.config;
+
+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.XmlType;
+
+public class VisitTable extends Table implements WideInterface{
+	@XmlElement
+	IDAT idat;
+	
+	@XmlElementWrapper(name="mdat")
+	@XmlElement(name="concept")
+	Concept[] concepts;
+	
+	@XmlType(name="patient-idat")
+	@XmlAccessorType(XmlAccessType.FIELD)
+	public static class IDAT extends IdatColumns{
+		@XmlElement(name="visit-id")
+		Column visitId;
+		Column start;
+		Column end;
+		// TODO inpatient/outpatient state
+		Column[] ignore;
+	}
+}

histream-import/src/main/java/de/sekmi/histream/etl/config/WideInterface.java

+package de.sekmi.histream.etl.config;
+
+
+public interface WideInterface {
+}

histream-import/src/main/java/de/sekmi/histream/etl/config/WideTable.java

+package de.sekmi.histream.etl.config;
+
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlElementWrapper;
+
+public class WideTable extends Table {
+
+	@XmlElement
+	DataTableIdat idat;
+	
+	@XmlElementWrapper(name="mdat")
+	@XmlElement(name="concept")
+	Concept[] concepts;
+}

histream-import/src/main/java/de/sekmi/histream/etl/config/XmlSource.java

+package de.sekmi.histream.etl.config;
+
+import java.net.MalformedURLException;
+import java.net.URL;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
+
+@XmlAccessorType(XmlAccessType.FIELD)
+public class XmlSource {
+
+	@XmlAttribute
+	URL url;
+	@XmlElement
+	Transform[] transform;
+	
+	public static class Transform{
+		@XmlAttribute
+		URL with;
+		@XmlAttribute
+		String to; // TODO use Path internally
+		
+		public Transform(){
+		}
+		public Transform(String with, String to) throws MalformedURLException{
+			this.with = new URL(with);
+			this.to = to;
+		}
+	}
+}

histream-import/src/main/java/de/sekmi/histream/etl/config/package-info.java

+/**
+ * 
+ */
+/**
+ * @author marap1
+ *
+ */
+package de.sekmi.histream.etl.config;
\ No newline at end of file

histream-import/src/main/java/de/sekmi/histream/etl/package-info.java

+/**
+ * 
+ */
+/**
+ * @author marap1
+ *
+ */
+package de.sekmi.histream.etl;
\ No newline at end of file