fix broken javadoc and add missing license header

IPK-BIT · Mar 24, 2020 · 60f686a · 60f686a
1 parent 2097676
commit 60f686a
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Showing 2 changed files with 76 additions and 57 deletions.
diff --git a/src/main/java/de/ipk_gatersleben/bit/bi/isa4j/components/Process.java b/src/main/java/de/ipk_gatersleben/bit/bi/isa4j/components/Process.java
@@ -20,33 +20,35 @@
 import de.ipk_gatersleben.bit.bi.isa4j.exceptions.RedundantItemException;
 
 public class Process extends StudyOrAssayTableObject implements Commentable {
-	
+
 	private CommentCollection comments = new CommentCollection();
-	
+
 	private LocalDate date;
-	
+
 	private LocalDateTime dateTime;
-	
+
 	private StudyOrAssayTableObject input;
-	
+
 	private List<ParameterValue> parameterValues = new ArrayList<ParameterValue>();
-	
+
 	private Protocol protocol;
-	
+
 	public Process(Protocol protocol) {
 		this.setProtocol(protocol);
 	}
-	
+
 	public void addParameterValue(ParameterValue parameterValue) {
-		if(this.parameterValues.stream().map(ParameterValue::getCategory).anyMatch(parameterValue.getCategory()::equals))
-			throw new RedundantItemException("Multiple ParameterValues for Parameter: " + parameterValue.getCategory().getName());
+		if (this.parameterValues.stream().map(ParameterValue::getCategory)
+				.anyMatch(parameterValue.getCategory()::equals))
+			throw new RedundantItemException(
+					"Multiple ParameterValues for Parameter: " + parameterValue.getCategory().getName());
 		this.parameterValues.add(parameterValue);
 	}
-	
+
 	public CommentCollection comments() {
 		return this.comments;
 	}
-	
+
 	/**
 	 * @return the date
 	 */
@@ -60,40 +62,43 @@ public LocalDate getDate() {
 	public LocalDateTime getDateTime() {
 		return dateTime;
 	}
-	
+
 	Map<String, String[]> getFields() {
 		HashMap<String, String[]> fields = new HashMap<String, String[]>();
-
-		fields.put(StudyAssayAttribute.PROTOCOL.toString(), new String[]{this.protocol.getName()});
-		fields.putAll(this.getFieldsForValues(StudyAssayAttribute.PARAMETER_VALUE, this.parameterValues, pv -> pv.getCategory().getName().getTerm()));
-		if(this.dateTime != null)
-			fields.put(StudyAssayAttribute.PROTOCOL_DATE.toString(), new String[]{this.dateTime.toString()});
-		else if(this.date != null)
-			fields.put(StudyAssayAttribute.PROTOCOL_DATE.toString(), new String[]{this.date.toString()});
+
+		fields.put(StudyAssayAttribute.PROTOCOL.toString(), new String[] { this.protocol.getName() });
+		fields.putAll(this.getFieldsForValues(StudyAssayAttribute.PARAMETER_VALUE, this.parameterValues,
+				pv -> pv.getCategory().getName().getTerm()));
+		if (this.dateTime != null)
+			fields.put(StudyAssayAttribute.PROTOCOL_DATE.toString(), new String[] { this.dateTime.toString() });
+		else if (this.date != null)
+			fields.put(StudyAssayAttribute.PROTOCOL_DATE.toString(), new String[] { this.date.toString() });
 		fields.putAll(this.getFieldsForComments(this.comments));
 
 		return fields;
 	}
 
 	LinkedHashMap<String, String[]> getHeaders() {
 		LinkedHashMap<String, String[]> headers = new LinkedHashMap<String, String[]>();
-
-		headers.put(StudyAssayAttribute.PROTOCOL.toString(), new String[]{StudyAssayAttribute.PROTOCOL.toString()});
-		headers.putAll(this.getHeadersForValues(StudyAssayAttribute.PARAMETER_VALUE, this.parameterValues, pv -> pv.getCategory().getName().getTerm()));
-		if(this.dateTime != null || this.date != null)
-			headers.put(StudyAssayAttribute.PROTOCOL_DATE.toString(), new String[]{StudyAssayAttribute.PROTOCOL_DATE.toString()});
+
+		headers.put(StudyAssayAttribute.PROTOCOL.toString(), new String[] { StudyAssayAttribute.PROTOCOL.toString() });
+		headers.putAll(this.getHeadersForValues(StudyAssayAttribute.PARAMETER_VALUE, this.parameterValues,
+				pv -> pv.getCategory().getName().getTerm()));
+		if (this.dateTime != null || this.date != null)
+			headers.put(StudyAssayAttribute.PROTOCOL_DATE.toString(),
+					new String[] { StudyAssayAttribute.PROTOCOL_DATE.toString() });
 		headers.putAll(this.getHeadersForComments(this.comments));
-		
+
 		return headers;
 	}
 
 	public StudyOrAssayTableObject getInput() {
-    	return this.input;
-    }
+		return this.input;
+	}
 
 	public StudyOrAssayTableObject getOutput() {
-    	return this.getNextStudyOrAssayTableObject();
-    }
+		return this.getNextStudyOrAssayTableObject();
+	}
 
 	/**
 	 * @return the factorValues
@@ -110,60 +115,67 @@ public Protocol getProtocol() {
 	}
 
 	/**
-	 * Sets a Date for this Process (without time of day). Overwrites any Date or DateTime set before.
+	 * Sets a Date for this Process (without time of day). Overwrites any Date or
+	 * DateTime set before.
+	 * 
 	 * @param date the date to set
 	 */
 	public void setDate(LocalDate date) {
 		this.date = date;
 		this.dateTime = null;
 	}
-    
+
 	/**
 	 * Sets a DateTime for this Process. Overwrites any Date or DateTime set before.
+	 * 
 	 * @param dateTime the dateTime to set
 	 */
 	public void setDateTime(LocalDateTime dateTime) {
 		this.dateTime = dateTime;
 		this.date = null;
 	}
-
+
+	/**
+	 * Declares the input to this Process. This information is used to link
+	 * different entities together in the output Study and Assay Files through
+	 * Processes, e.g. Source-&gt;Process-&gt;Sample.
+	 * 
+	 * @param input to set
+	 */
+	public void setInput(StudyOrAssayTableObject input) {
+		// Remove myself from previously defined input
+		if (this.input != null)
+			this.input.setNextStudyOrAssayTableObject(null);
+		input.setNextStudyOrAssayTableObject(this);
+		this.input = input;
+	}
+
 	/**
-	 * Declares the input to this Process. This information is used to link different entities
-	 * together in the output Study and Assay Files through Processes, e.g. Source->Process->Sample.
-	 * @param input
+	 * Declares the output of this Process. This information is used to link
+	 * different entities together in the output Study and Assay Files through
+	 * Processes, e.g. Source-&gt;Process-&gt;Sample.
+	 * 
+	 * @param output to set
 	 */
-    public void setInput(StudyOrAssayTableObject input) {
-    	// Remove myself from previously defined input
-    	if(this.input != null)
-    		this.input.setNextStudyOrAssayTableObject(null);
-    	input.setNextStudyOrAssayTableObject(this);
-    	this.input = input;
-    }
-
-    /**
-     * Declares the output of this Process. This information is used to link different entities
-	 * together in the output Study and Assay Files through Processes, e.g. Source->Process->Sample.
-     * @param output
-     */
-    public void setOutput(StudyOrAssayTableObject output) {
-    	this.setNextStudyOrAssayTableObject(output);
-    }
-
-    /**
+	public void setOutput(StudyOrAssayTableObject output) {
+		this.setNextStudyOrAssayTableObject(output);
+	}
+
+	/**
 	 * @param parameterValues the factorValues to set
 	 */
 	public void setParameterValues(List<ParameterValue> parameterValues) {
 		parameterValues.stream().forEach(Objects::requireNonNull);
 		this.parameterValues = parameterValues;
 	}
-    
-    /**
+
+	/**
 	 * @param protocol the protocol to set
 	 */
 	public void setProtocol(Protocol protocol) {
 		this.protocol = Objects.requireNonNull(protocol, "Protocol cannot be null");
 	}
-	
+
 	@Override
 	public String toString() {
 		return "<Process> '" + this.protocol.getName() + "' on input " + this.input.toString();

diff --git a/src/test/java/isa4J/SimpleWorkingExample.java b/src/test/java/isa4J/SimpleWorkingExample.java
@@ -1,3 +1,10 @@
+/**
+ * Copyright (c) 2020 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.
+ * All rights reserved. This program and the accompanying materials are made available under the terms of the GNU GPLv3 license (https://www.gnu.org/licenses/gpl-3.0.en.html)
+ *
+ * Contributors:
+ *      Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
+ */
 package isa4J;
 
 import java.io.IOException;