Fix boxplot whiskers bug; Include outliers on chart

mpi2 · Mar 10, 2020 · c5ee8ab · c5ee8ab
1 parent 4fcbb0a
commit c5ee8ab
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Showing 10 changed files with 270 additions and 133 deletions.
diff --git a/data-model-solr/src/main/java/org/mousephenotype/cda/solr/service/ImpressService.java b/data-model-solr/src/main/java/org/mousephenotype/cda/solr/service/ImpressService.java
@@ -251,12 +251,39 @@ public ImpressBaseDTO getPipeline(String pipelineStableId)
 		SolrDocument doc = pipelineCore.query(query).getResults().get(0);
 
 		return new ImpressBaseDTO((Long)doc.getFirstValue(ImpressDTO.PIPELINE_ID),
-				Long.getLong(doc.getFirstValue(ImpressDTO.PIPELINE_STABLE_KEY).toString()),
+				(Long) doc.getFirstValue(ImpressDTO.PIPELINE_STABLE_KEY),
 				doc.getFirstValue(ImpressDTO.PIPELINE_STABLE_ID).toString(),
 				doc.getFirstValue(ImpressDTO.PIPELINE_NAME).toString());
 
 	}
 
+	public ProcedureDTO getProcedureByStableId(String pipelineStableId, String procedureStableId) {
+
+		ProcedureDTO procedure = new ProcedureDTO();
+		try {
+			SolrQuery query = new SolrQuery()
+					.setQuery(ImpressDTO.PROCEDURE_STABLE_ID + ":" + procedureStableId + " AND " + ImpressDTO.PIPELINE_STABLE_ID +":"+pipelineStableId)
+					.setFields(ImpressDTO.PROCEDURE_ID,
+							ImpressDTO.PROCEDURE_NAME,
+							ImpressDTO.PROCEDURE_STABLE_ID,
+							ImpressDTO.PROCEDURE_STABLE_KEY);
+
+			QueryResponse response = pipelineCore.query(query);
+
+			ImpressDTO imd = response.getBeans(ImpressDTO.class).get(0);
+
+			procedure.setStableId(imd.getProcedureStableId().toString());
+			procedure.setName(imd.getProcedureName().toString());
+			procedure.setStableKey(imd.getProcedureStableKey());
+			return procedure;
+
+		} catch (SolrServerException | IOException | IndexOutOfBoundsException e) {
+			e.printStackTrace();
+		}
+
+		return null;
+	}
+
 
 	public ProcedureDTO getProcedureByStableId(String procedureStableId) {
 
@@ -417,10 +444,16 @@ public Long getPipelineStableKey(String pipelineStableId) {
 		return null;
 	}
 
+	public String getProcedureUrlByStableKeyAndPipelineStableKey(Long procedureStableKey, Long pipelineStableKey) {
 
+		return String.format("%s/impress/ProcedureInfo?action=list&procID=%s&pipeID=%s",
+				cmsBaseUrl,
+				procedureStableKey,
+				pipelineStableKey);
+	}
 	public String getProcedureUrlByKey(String procedureStableKey) {
 
-		return cmsBaseUrl + "/impress/protocol/" + procedureStableKey;
+		return cmsBaseUrl + "/impress/ProcedureInfo?action=list&procID=" + procedureStableKey;
 	}
 
 
@@ -449,12 +482,8 @@ public String getAnchorForProcedure(String procedureName, String procedureStable
 	}
 
 
-	public String getPipelineUrlByStableId(String stableId){
-		Long pipelineKey = getPipelineStableKey(stableId);
-		if (pipelineKey != null ){
-			return cmsBaseUrl + "/impress/procedures/" + pipelineKey;
-		}
-		else return "#";
+	public String getPipelineUrlByStableKey(Long stableKey){
+		return cmsBaseUrl + "/impress/PipelineInfo?id=" + stableKey;
 	}
 
 
@@ -539,20 +568,71 @@ public ImpressDTO getParameterByStableIdSpecifyFields(String stableId, List<Stri
 
 
 	/**
-	 * @author tudose
+	 * @since 2015/08/20
+	 * @param parameterStableId stable ID of the parameter in question
+	 */
+	public ParameterDTO getParameterByPipelineProcedureParameterStableKey(Long pipelineStableKey, Long procedureStableKey, String parameterStableId)
+			throws SolrServerException, IOException  {
+
+		ParameterDTO param = new ParameterDTO();
+		SolrQuery query = new SolrQuery()
+				.setQuery(String.format("%s:%s AND %s:%S AND %s:%s",
+						ImpressDTO.PIPELINE_STABLE_KEY, pipelineStableKey,
+						ImpressDTO.PROCEDURE_STABLE_KEY, procedureStableKey,
+						ImpressDTO.PARAMETER_STABLE_ID, parameterStableId))
+				.setFields(ImpressDTO.PARAMETER_NAME,
+						ImpressDTO.PARAMETER_ID,
+						ImpressDTO.PARAMETER_STABLE_KEY,
+						ImpressDTO.PARAMETER_STABLE_ID,
+						ImpressDTO.OBSERVATION_TYPE,
+						ImpressDTO.CATEGORIES,
+						ImpressDTO.UNITX,
+						ImpressDTO.UNITY,
+						ImpressDTO.PROCEDURE_NAME)
+				.setRows(1);
+		QueryResponse response = pipelineCore.query(query);
+
+		List<ImpressDTO> dtoList = response.getBeans(ImpressDTO.class);
+		if ((dtoList == null) || (dtoList.isEmpty())) {
+			return null;
+		}
+
+		ImpressDTO dto = response.getBeans(ImpressDTO.class).get(0);
+		param.setId(dto.getParameterId());
+		param.setStableId(dto.getParameterStableId());
+		param.setStableKey(dto.getParameterStableKey());
+		param.setUnitX(dto.getUnitX());
+		param.setUnitY(dto.getUnitY());
+		param.setName(dto.getParameterName());
+		param.setObservationType(ObservationType.valueOf(dto.getObservationType()));
+		param.setCategories(dto.getCategories());
+		List<String> procedures = new ArrayList<String>();
+		procedures.add(dto.getProcedureName());
+		param.setProcedureNames(procedures);
+
+		return param;
+	}
+
+
+	/**
 	 * @since 2015/08/20
 	 * @param stableId
-	 * @return
-	 * @throws SolrServerException, IOException
 	 */
 	public ParameterDTO getParameterByStableId(String stableId)
 	throws SolrServerException, IOException  {
 
 		ParameterDTO param = new ParameterDTO();
 		SolrQuery query = new SolrQuery()
 				.setQuery(ImpressDTO.PARAMETER_STABLE_ID + ":" + stableId )
-				.setFields(ImpressDTO.PARAMETER_NAME, ImpressDTO.PARAMETER_ID, ImpressDTO.PARAMETER_STABLE_KEY, ImpressDTO.PARAMETER_STABLE_ID, ImpressDTO.OBSERVATION_TYPE, ImpressDTO.CATEGORIES,
-						ImpressDTO.UNITX, ImpressDTO.UNITY, ImpressDTO.PROCEDURE_NAME )
+				.setFields(ImpressDTO.PARAMETER_NAME,
+						ImpressDTO.PARAMETER_ID,
+						ImpressDTO.PARAMETER_STABLE_KEY,
+						ImpressDTO.PARAMETER_STABLE_ID,
+						ImpressDTO.OBSERVATION_TYPE,
+						ImpressDTO.CATEGORIES,
+						ImpressDTO.UNITX,
+						ImpressDTO.UNITY,
+						ImpressDTO.PROCEDURE_NAME)
 				.setRows(1);
 		QueryResponse response = pipelineCore.query(query);
 
@@ -642,6 +722,6 @@ public static String getParameterUrl(Long parameterStableKey){
 
 	public String getParameterUrlByProcedureAndParameterKey(Long procedureKey,Long parameterKey) {
 
-		return cmsBaseUrl + "/impress/parameterontologies/"+parameterKey + "/"+procedureKey;
+		return cmsBaseUrl + "/impress/OntologyInfo?action=list&procID="+procedureKey+"#"+parameterKey;
 	}
 }
diff --git a/data-model-solr/src/main/java/org/mousephenotype/cda/solr/service/dto/ImpressBaseDTO.java b/data-model-solr/src/main/java/org/mousephenotype/cda/solr/service/dto/ImpressBaseDTO.java
@@ -105,13 +105,7 @@ public String toString() {
 	 */
 	public static Comparator<ImpressBaseDTO> getComparatorByName()
 	{   
-		Comparator<ImpressBaseDTO> comp = new Comparator<ImpressBaseDTO>(){
-	    @Override
-	    public int compare(ImpressBaseDTO a, ImpressBaseDTO b)
-	    {
-	        return a.getName().compareTo(b.getName());
-	    }        
-		};
+		Comparator<ImpressBaseDTO> comp = Comparator.comparing(ImpressBaseDTO::getName);
 		return comp;
 	}  
 
@@ -121,13 +115,7 @@ public int compare(ImpressBaseDTO a, ImpressBaseDTO b)
 	 * @return Sort by stable id.
 	 */
 	public static Comparator<ImpressBaseDTO> getComparatorByStableId()	{   
-		Comparator<ImpressBaseDTO> comp = new Comparator<ImpressBaseDTO>(){
-	    @Override
-	    public int compare(ImpressBaseDTO a, ImpressBaseDTO b)
-	    {
-	        return a.getStableId().compareTo(b.getStableId());
-	    }        
-		};
+		Comparator<ImpressBaseDTO> comp = Comparator.comparing(ImpressBaseDTO::getStableId);
 		return comp;
 	}  
 

diff --git a/data-model/src/main/java/org/mousephenotype/cda/web/ChartType.java b/data-model/src/main/java/org/mousephenotype/cda/web/ChartType.java
@@ -24,7 +24,8 @@ public enum ChartType {
   , CATEGORICAL_STACKED_COLUMN
   , TIME_SERIES_LINE
   , PIE
-  , TIME_SERIES_LINE_BODYWEIGHT;
+  , TIME_SERIES_LINE_BODYWEIGHT
+  , TEXT;
 
     public String getName() {
         return this.toString();

diff --git a/web/src/main/java/uk/ac/ebi/phenotype/chart/ChartsSeriesElement.java b/web/src/main/java/uk/ac/ebi/phenotype/chart/ChartsSeriesElement.java
@@ -38,84 +38,108 @@
 //]
 public class ChartsSeriesElement {
 
-	List<Float>originalData=new ArrayList<>();//to hold original data before being processsed to chart objects
+	private String name;
+	private String colorString;
+	private String chartTypeString;
+	private JSONArray boxPlotArray;
+	private JSONArray boxPlotOutliersArray;
+	private SexType sexType;
+	private ZygosityType zygosityType;
+
+	//to hold original data before being processsed to chart objects
+	List<Float> originalData = new ArrayList<>();
+
+	// to record the column of this data if say for boxplots we need this to determine how many other [] arrays to add before us
+	int column;
+
 	public List<Float> getOriginalData() {
 		return originalData;
 	}
+
 	public void setOriginalData(List<Float> originalData) {
 		this.originalData = originalData;
 	}
-	@Override
-	public String toString() {
-		return "ChartsSeriesElement [originalData=" + originalData
-				+ ", column=" + column + ", sexType=" + sexType
-				+ ", controlOrZygosity=" + zygosityType + ", name=" + name
-				+ ", colorString=" + colorString + ", chartTypeString="
-				+ chartTypeString + ", dataArray=" + boxPlotArray + "]\n";
+
+	public JSONArray getBoxPlotOutliersArray() {
+		return boxPlotOutliersArray;
+	}
+
+	public void setBoxPlotOutliersArray(JSONArray boxPlotOutliersArray) {
+		this.boxPlotOutliersArray = boxPlotOutliersArray;
 	}
-	int column;//to record the column of this data if say for boxplots we need this to determine how many other [] arrays to add before us
-	SexType sexType;
-	ZygosityType zygosityType;
 
-	/**
-	 * if zygosity type is null then it must be wildtype
-	 * @return
-	 */
 	public ZygosityType getZygosityType() {
 		return zygosityType;
 	}
+
 	public void setZygosityType(ZygosityType zygosityType) {
 		this.zygosityType = zygosityType;
 	}
 
 	String getControlOrZygosityString() {
-		if(zygosityType==null) {
+		if (zygosityType == null) {
 			return "WT";
-		}else {
+		} else {
 			return zygosityType.getShortName();
 		}
 
 	}
+
 	public int getColumn() {
 		return column;
 	}
+
 	public void setColumn(int column) {
 		this.column = column;
 	}
 
 	public SexType getSexType() {
 		return sexType;
 	}
+
 	public void setSexType(SexType sexType) {
 		this.sexType = sexType;
 	}
+
 	public String getName() {
 		return name;
 	}
+
 	public void setName(String name) {
 		this.name = name;
 	}
+
 	public String getColorString() {
 		return colorString;
 	}
+
 	public void setColorString(String colorString) {
 		this.colorString = colorString;
 	}
+
 	public String getChartTypeString() {
 		return chartTypeString;
 	}
+
 	public void setChartTypeString(String chartTypeString) {
 		this.chartTypeString = chartTypeString;
 	}
+
 	public JSONArray getBoxPlotArray() {
 		return boxPlotArray;
 	}
+
 	public void setBoxPlotArray(JSONArray dataArray) {
 		this.boxPlotArray = dataArray;
 	}
-	String name;
-	String colorString;
-	String chartTypeString;
-	JSONArray boxPlotArray;
+
+	@Override
+	public String toString() {
+		return "ChartsSeriesElement [originalData=" + originalData
+				+ ", column=" + column + ", sexType=" + sexType
+				+ ", controlOrZygosity=" + zygosityType + ", name=" + name
+				+ ", colorString=" + colorString + ", chartTypeString="
+				+ chartTypeString + ", dataArray=" + boxPlotArray + "]\n";
+	}
 
 }
diff --git a/web/src/main/java/uk/ac/ebi/phenotype/chart/GraphUtils.java b/web/src/main/java/uk/ac/ebi/phenotype/chart/GraphUtils.java
@@ -15,7 +15,6 @@
  *******************************************************************************/
 package uk.ac.ebi.phenotype.chart;
 
-import org.apache.commons.lang3.StringUtils;
 import org.apache.solr.client.solrj.SolrServerException;
 import org.mousephenotype.cda.enumerations.ObservationType;
 import org.mousephenotype.cda.solr.service.ExperimentService;
@@ -241,6 +240,9 @@ public static ChartType getDefaultChartType(ParameterDTO parameter) {
                 case time_series:
                     return ChartType.TIME_SERIES_LINE;
 
+                case text:
+                    return ChartType.TEXT;
+
             }
         }
         return null;

diff --git a/web/src/main/java/uk/ac/ebi/phenotype/chart/ScatterChartAndTableProvider.java b/web/src/main/java/uk/ac/ebi/phenotype/chart/ScatterChartAndTableProvider.java
@@ -54,6 +54,12 @@ public String createScatter(ExperimentDTO experiment, Float min, Float max, Stri
 		}else if(parameter.getUnitX()!=null && !parameter.getUnitX().equals("")){
 			yTitle=parameter.getUnitX();
 		}
+
+		String yAxisLabel = parameter.getName() + " (" + yTitle + ")";
+		if (yTitle.trim().isEmpty()) {
+			yAxisLabel = parameter.getName();
+		}
+
 		String chartString="	$(function () { "
 			+ "  chart71maleWTSI = new Highcharts.Chart({ "
 			+ "     chart: {"
@@ -63,7 +69,7 @@ public String createScatter(ExperimentDTO experiment, Float min, Float max, Stri
 			+ "         zoomType: 'xy'"
 
 			+ "     },"
-			+ "   title: {  text: 'Scatterplot of the data' },"
+			+ "   title: {  useHTML:true, text: 'Scatterplot of the data <a href=\"/help/quick-guide-to-the-website/chart-page/\" target=\"_blank\"><i class=\"fa fa-question-circle\" style=\"color: #ce6211;\"></i></a>' },"
 			+ "     xAxis: {"
 			+ "       type: 'datetime',"
 			+ "       labels: { "
@@ -82,7 +88,7 @@ public String createScatter(ExperimentDTO experiment, Float min, Float max, Stri
 			+ (max != null ? "       max: " + max + ", " : "")
 			+ (min != null ? "       min: " + min + ", " : "")
 			+ "       title: { "
-			+ "         text: '" + yTitle + "' "
+			+ "         text: '" + yAxisLabel + "' "
 			+ "       } "
 			+ "     }, "
 			+ "     credits: { "
@@ -115,7 +121,7 @@ public String createScatter(ExperimentDTO experiment, Float min, Float max, Stri
 			+ "      }, "
 			+ "     series: " +
 			series.toString()
-			+ "    }); console.log('HERE');"
+			+ "    });"
 			+ "	}); ";
 
 		return chartString;