retrieve slightly different list of patients (based on the reports), …

…instead of the Doe family
Data2Semantics · Oct 31, 2012 · 7400e68 · 7400e68
1 parent 5531939
commit 7400e68
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Showing 7 changed files with 101 additions and 56 deletions.
diff --git a/pom.xml b/pom.xml
@@ -183,6 +183,25 @@
 										<ignore></ignore>
 									</action>
 								</pluginExecution>
+								<pluginExecution>
+									<pluginExecutionFilter>
+										<groupId>
+											org.apache.maven.plugins
+										</groupId>
+										<artifactId>
+											maven-war-plugin
+										</artifactId>
+										<versionRange>
+											[2.1.1,)
+										</versionRange>
+										<goals>
+											<goal>exploded</goal>
+										</goals>
+									</pluginExecutionFilter>
+									<action>
+										<ignore></ignore>
+									</action>
+								</pluginExecution>
 							</pluginExecutions>
 						</lifecycleMappingMetadata>
 					</configuration>

diff --git a/src/main/java/com/data2semantics/hubble/client/helpers/Helper.java b/src/main/java/com/data2semantics/hubble/client/helpers/Helper.java
@@ -31,6 +31,8 @@ public static ArrayList<String> getSparqlPrefixes(String prefixTypes) {
 			namespaceList.add("PREFIX ns1: <http://purl.org/cpr/0.75#>");
 			namespaceList.add("PREFIX : <http://aers.data2semantics.org/vocab/>");
 			namespaceList.add("PREFIX patient: <http://www.data2semantics.org/ontology/patient/>");
+			namespaceList.add("PREFIX aers: <http://aers.data2semantics.org/>");
+			namespaceList.add("PREFIX aersv: <http://aers.data2semantics.org/vocab/>");
 		} else if (prefixTypes.equals("annotations")) {
 			namespaceList.add("PREFIX ao: <http://purl.org/ao/core#>");
 			namespaceList.add("PREFIX aot: <http://purl.org/ao/types#>");
@@ -50,7 +52,6 @@ public static ArrayList<String> getSparqlPrefixes(String prefixTypes) {
 			namespaceList.add("PREFIX cnt: <http://www.w3.org/2011/content#>"); 
 			namespaceList.add("PREFIX dc: <http://purl.org/dc/elements/1.1/>"); 
 			namespaceList.add("PREFIX dcterms: <http://purl.org/dc/terms/>"); 
-			namespaceList.add("PREFIX aers: <http://aers.data2semantics.org/>");
 			namespaceList.add("PREFIX swanrel: <http://purl.org/swan/2.0/discourse-relationships/>");		
 			namespaceList.add("PREFIX d2sa: <http://aers.data2semantics.org/vocab/annotation/>");
 		}

diff --git a/src/main/java/com/data2semantics/hubble/client/view/patientinfo/PatientDetails.java b/src/main/java/com/data2semantics/hubble/client/view/patientinfo/PatientDetails.java
@@ -16,7 +16,6 @@
 import com.data2semantics.hubble.shared.models.Indication;
 import com.data2semantics.hubble.shared.models.Measurement;
 import com.data2semantics.hubble.shared.models.Patient;
-import com.data2semantics.hubble.shared.models.Treatment;
 import com.google.gwt.user.client.Window;
 import com.google.gwt.user.client.rpc.AsyncCallback;
 import com.smartgwt.client.types.Alignment;
@@ -220,13 +219,23 @@ public String hoverHTML(Object value, ListGridRecord record, int rowNum, int col
 	private void drawInfoIntoTable(Patient patientInfo) {
 		rows = new ArrayList<PatientInfoRecord>();
 		rows.add(new PatientInfoRecord("Patient ID", patientInfo.getPatientID()));
-		rows.add(new PatientInfoRecord("Comment", patientInfo.getComment()));
-		rows.add(new PatientInfoRecord("Age", Integer.toString(patientInfo.getAge())));
+		String comment = patientInfo.getComment();
+		if (comment != null) {
+			rows.add(new PatientInfoRecord("Comment", patientInfo.getComment()));
+		}
+		int age = patientInfo.getAge();
+		if (age != 0) {
+			rows.add(new PatientInfoRecord("Age", Integer.toString(patientInfo.getAge())));
+		}
+		String weight = patientInfo.getWeight();
+		if (weight != null) {
+			rows.add(new PatientInfoRecord("Weight", weight));
+		}
 		drawIndications(patientInfo);
-		drawPreviousIndications(patientInfo);
+		//drawPreviousIndications(patientInfo);
 		drawDrugs(patientInfo);
 		drawMeasurements(patientInfo);
-		drawRecentTreatments(patientInfo);
+		//drawRecentTreatments(patientInfo);
 
 		PatientInfoRecord[] rowsArray = new PatientInfoRecord[rows.size()];
 		rows.toArray(rowsArray);
@@ -242,14 +251,14 @@ private void drawIndications(Patient patientInfo) {
 			rows.add(row);
 		}
 	}
-	private void drawPreviousIndications(Patient patientInfo) {
-		for (Map.Entry<String, Indication> entry : patientInfo.getPreviousIndications().entrySet()) {
-			final Indication indication = entry.getValue();
-			PatientInfoRecord row = new PatientInfoRecord(RowHeaders.PREV_INDICATION, indication.getLabel(), indication.getDefinition());
-			row.setUri(entry.getKey());
-			rows.add(row);
-		}
-	}
+//	private void drawPreviousIndications(Patient patientInfo) {
+//		for (Map.Entry<String, Indication> entry : patientInfo.getPreviousIndications().entrySet()) {
+//			final Indication indication = entry.getValue();
+//			PatientInfoRecord row = new PatientInfoRecord(RowHeaders.PREV_INDICATION, indication.getLabel(), indication.getDefinition());
+//			row.setUri(entry.getKey());
+//			rows.add(row);
+//		}
+//	}
 	private void drawMeasurements(Patient patientInfo) {
 		for (Map.Entry<String, Measurement> entry : patientInfo.getMeasurements().entrySet()) {
 			final Measurement measurement = entry.getValue();
@@ -261,14 +270,14 @@ private void drawMeasurements(Patient patientInfo) {
 		}
 
 	}
-	private void drawRecentTreatments(Patient patientInfo) {
-		for (Map.Entry<String, Treatment> entry : patientInfo.getRecentTreatments().entrySet()) {
-			final Treatment treatment = entry.getValue();
-			PatientInfoRecord row = new PatientInfoRecord(RowHeaders.TREATMENT, treatment.getLabel());
-			row.setUri(entry.getKey());
-			rows.add(row);
-		}
-	}
+//	private void drawRecentTreatments(Patient patientInfo) {
+//		for (Map.Entry<String, Treatment> entry : patientInfo.getRecentTreatments().entrySet()) {
+//			final Treatment treatment = entry.getValue();
+//			PatientInfoRecord row = new PatientInfoRecord(RowHeaders.TREATMENT, treatment.getLabel());
+//			row.setUri(entry.getKey());
+//			rows.add(row);
+//		}
+//	}
 
 	private void drawDrugs(Patient patientInfo) {
 		for (Map.Entry<String, Drug> entry : patientInfo.getDrugs().entrySet()) {

diff --git a/src/main/java/com/data2semantics/hubble/client/view/patientlisting/PatientListing.java b/src/main/java/com/data2semantics/hubble/client/view/patientlisting/PatientListing.java
@@ -25,6 +25,7 @@ public PatientListing(final View view) {
 		setSelectionType(SelectionStyle.SINGLE);
 		ListGridField nameField = new ListGridField("patientId", "Patient");
 		setFields(nameField);
+
 		setLeaveScrollbarGap(false);
 		addSelectionChangedHandler(new SelectionChangedHandler() {
 			public void onSelectionChanged(SelectionEvent event) {

diff --git a/src/main/java/com/data2semantics/hubble/server/RdfNodeHelper.java b/src/main/java/com/data2semantics/hubble/server/RdfNodeHelper.java
@@ -16,6 +16,13 @@ public static int getInt(RDFNode node) {
 		return node.asLiteral().getInt();
 	}
 
+	public static double getDouble(RDFNode node) {
+		return node.asLiteral().getDouble();
+	}
+
+//	public static BigDecimal getBigDecimal(RDFNode node) {
+//		return node.asLiteral().getString();
+//	}
 	public static String getString(QuerySolution solution, String variable) {
 		return getString(solution.get(variable));
 	}

diff --git a/src/main/java/com/data2semantics/hubble/server/loaders/PatientLoader.java b/src/main/java/com/data2semantics/hubble/server/loaders/PatientLoader.java
@@ -94,7 +94,7 @@ private void parseValue(String varName, QuerySolution solution) {
 			 * These are values (not uri's). Set them in the patient object
 			 */
 			if (varName.equals("age")) {
-				patientObject.setAge(RdfNodeHelper.getInt(rdfNode));
+				patientObject.setAge(RdfNodeHelper.getDurationYears(rdfNode));
 			} else if (varName.equals("comment")) {
 				patientObject.setComment(RdfNodeHelper.getString(rdfNode));
 			} else if (varName.equals("status")) {
@@ -126,6 +126,8 @@ private void parseValue(String varName, QuerySolution solution) {
 				String drugbankID = sameAs.substring(Drug.DRUGBANK_PREFIX.length());
 				String imageLocation = Drug.IMGLOCATION_PREFIX + drugbankID + Drug.IMGLOCATION_POSTFIX;
 				patientObject.getDrug(uri).setImgLocation(imageLocation);
+			} else if (varName.equals("weight")) {
+				patientObject.setWeight(RdfNodeHelper.getString(rdfNode));
 			}
 		} catch (NullPointerException e) {
 			System.out.println("Nullpointer exception for var " + varName + " and rdfNode " + solution.get(varName).toString());
@@ -136,47 +138,46 @@ private void parseValue(String varName, QuerySolution solution) {
 
 	private ResultSet queryPatientData() throws IllegalArgumentException, SparqlException {
 		String queryString = Helper.getSparqlPrefixesAsString("aers") + "\n" +
+			"PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>\n" + 
 			"SELECT DISTINCT " +
 				"?age \n" +
-				"?comment \n" +
-				"?status \n" +
-				"?measurement \n" +
+//				"?comment \n" +
+//				"?status \n" +
+//				"?measurement \n" +
 				"?indication \n" +
 				"?indication_label \n" +
-				"?recentTreatment \n" +
-				"?recentTreatment_label \n" +
-				"?previousIndication \n" +
+//				"?recentTreatment \n" +
+//				"?recentTreatment_label \n" +
+//				"?previousIndication \n" +
 				"?drug \n" +
 				"?drug_label \n" +
 				"?drug_sameAs \n" +
+				"?weight\n" +
 			"{\n" + 
-				"?patient rdf:type patient:Patient.\n" + 
-				"?patient rdfs:label '" + patientId + "'@en.\n" + 
-				"?patient patient:hasAge ?age.\n" + 
-				"?patient rdfs:comment ?comment.\n" + 
-				"OPTIONAL{?patient patient:usesMedication ?drug.\n" +
-					"?drug rdfs:label ?drug_label;\n" +
-						"skos:exactMatch ?drug_sameAs.\n" +
-					"?drug_sameAs <http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/primaryAccessionNo> ?pan .\n" +
-//					"FILTER regex(str(?drug_sameAs), \"^http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugs/DB\", \"i\")\n" + 
-				"}.\n" + 
-				"OPTIONAL{?patient patient:hasStatus ?status}.\n" + 
-				"OPTIONAL{?patient patient:hasMeasurement ?measurement}.\n" + 
-				"OPTIONAL{\n" +
-					"?patient patient:hasDiagnosis ?indication.\n" +
-					"OPTIONAL{\n" + 
-						"?indication rdfs:label ?indication_label.\n" +
-					"}\n" +
-				"}.\n" + 
-
-				//Workaround to get 'hadRecentTreatment' from our own 4store. This SHOULD BE in the lld rdf, but isnt :(
-				"OPTIONAL{\n" +
-					"?patient patient:hadRecentTreatment ?recentTreatment.\n" +
-					"?recentTreatment rdfs:label ?recentTreatment_label.\n" +
-				"}.\n" + 
-				"OPTIONAL{?patient patient:hadPreviousIndication ?previousIndication}.\n" + 
-			"}\n" + 
+				"?patient rdf:type patient:Patient;\n" + 
+				"	rdfs:label '" + patientId + "'^^xsd:string;\n" + 
+				" 	patient:hasDiagnosis ?indication.\n" +
+				"OPTIONAL {\n" +
+				"	?patient aersv:age ?age.\n" +
+				"}\n" + 
+				"  OPTIONAL {\n" +
+				"		?patient aersv:weight ?weight\n" + 
+				"}\n" + 
+				"  OPTIONAL {\n" + 
+				"    ?indication rdfs:label ?indication_label\n" + 
+				"  }\n" + 
+				"  OPTIONAL {\n" + 
+				"     ?patient patient:usesMedication ?medication.\n" + 
+				"     ?medication aersv:drug ?drug.\n" + 
+				"     ?drug rdfs:label ?drug_label;\n" + 
+				"    		skos:exactMatch ?drug_sameAs.\n" + 
+				"    ?drug_sameAs <http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/primaryAccessionNo> ?pan.\n" + 
+				"    FILTER regex(str(?drug_sameAs), \"^http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugs/DB\", \"i\")\n" + 
+				"  }\n" + 
+				"  \n" + 
+				"} " + 
 			"";
+		System.out.println(queryString);
 		return Endpoint.query(Endpoint.ECULTURE2, queryString);
 	}
 

diff --git a/src/main/java/com/data2semantics/hubble/shared/models/Patient.java b/src/main/java/com/data2semantics/hubble/shared/models/Patient.java
@@ -8,9 +8,10 @@ public class Patient implements Serializable {
 	private static final long serialVersionUID = 1L;
 
 	private String patientID;
-	private int age;
+	private int age = 0;
 	private String comment;
 	private String status;
+	private String weight;
 
 	/**
 	 * For these hashmaps, use URI as key
@@ -142,5 +143,11 @@ public Drug getDrug(String uri) {
 		}
 		return drug;
 	}
+	public String getWeight() {
+		return weight;
+	}
+	public void setWeight(String weight) {
+		this.weight = weight;
+	}
 
 }