Bugfix berlin v4

CHANGELOG.md

@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
 ## [7.4.1 - 2021-10-18]
 ### Fixed
 - Quality Report for large amount of data
+- QB-Generator: Cache number of patients per mdrid (and per mdr id and value)
 
 ## [7.4.0 - 2021-09-13]
 ### Added

src/main/java/de/samply/share/client/model/EnumConfiguration.java

@@ -78,6 +78,7 @@ public enum EnumConfiguration {
   QUALITY_REPORT_SHOW_STATISTICS_SHEET,
   QUALITY_REPORT_WORKBOOK_WINDOW,
   QUALITY_REPORT_MAX_NUMBER_OF_ROWS_PER_SHEET,
+  QUALITY_REPORT_COLUMNS_TO_BE_FILTERED,
   MONITORING_REPORT_COUNT_TOTAL,
   MONITORING_REPORT_COUNT_DKTKFLAG,
   MONITORING_REPORT_COUNT_REFERENCEQUERY,

src/main/java/de/samply/share/client/quality/report/file/excel/row/factory/ExcelRowFactoryImpl.java

@@ -1,9 +1,13 @@
 package de.samply.share.client.quality.report.file.excel.row.factory;
 
+import de.samply.share.client.model.EnumConfiguration;
 import de.samply.share.client.quality.report.file.excel.cell.element.ExcelCellElement;
 import de.samply.share.client.quality.report.file.excel.cell.element.StringExcelCellElement;
 import de.samply.share.client.quality.report.file.excel.row.context.ExcelRowContext;
 import de.samply.share.client.quality.report.file.excel.row.elements.ExcelRowElements;
+import de.samply.share.client.quality.report.properties.PropertyUtils;
+import java.util.HashSet;
+import java.util.Set;
 import org.apache.poi.ss.SpreadsheetVersion;
 import org.apache.poi.ss.usermodel.CellStyle;
 import org.apache.poi.ss.usermodel.Font;
@@ -16,7 +20,29 @@
 public class ExcelRowFactoryImpl implements ExcelRowFactory {
 
   private final StringExcelCellElement emptyElement = new StringExcelCellElement("");
+  //TO DELETE:
+  private Set<Integer> toBeFiltered = getColumnsToBeFiltered();
+  // new HashSet<>(
+  //Arrays.asList(new Integer[]{0, 3, 4, 7, 9, 10}));
+  //Arrays.asList(new Integer[]{0, 3, 4, 5, 6, 7, 8, 9, 10}));
 
+  private Set<Integer> getColumnsToBeFiltered() {
+
+    Set<Integer> columnstoBeFilteredI = new HashSet<>();
+
+    String[] columnsToBeFilteredS = PropertyUtils.getListOfProperties(
+        EnumConfiguration.QUALITY_REPORT_COLUMNS_TO_BE_FILTERED);
+
+    for (String columnToBeFilteredS : columnsToBeFilteredS) {
+      Integer columnToBeFilteredI = new Integer(columnToBeFilteredS);
+      if (columnToBeFilteredI != null) {
+        columnstoBeFilteredI.add(columnToBeFilteredI);
+      }
+    }
+
+    return columnstoBeFilteredI;
+
+  }
 
   @Override
   public SXSSFSheet addRowTitles(SXSSFSheet sheet, ExcelRowContext excelRowContext)
@@ -72,20 +98,22 @@ public SXSSFSheet addRow(SXSSFSheet sheet, ExcelRowElements excelRowElements)
 
     SXSSFRow row = sheet.createRow(rowNum);
 
-    addElementsToRow(row, excelRowElements);
+    boolean isToBeFiltered = sheet.getSheetName().equals("all elements");
+    addElementsToRow(row, excelRowElements, isToBeFiltered);
 
     return sheet;
   }
 
-  private SXSSFRow addElementsToRow(SXSSFRow row, ExcelRowElements elements) {
+  private SXSSFRow addElementsToRow(SXSSFRow row, ExcelRowElements elements,
+      boolean isToBeFiltered) {
 
     for (int i = 0;
         i < elements.getMaxNumberOfElements() && i < SpreadsheetVersion.EXCEL2007.getMaxColumns();
         i++) {
 
       ExcelCellElement element = elements.getElement(i);
 
-      if (element != null) {
+      if ((element != null) && (!isToBeFiltered || !toBeFiltered.contains(i))) {
         element.addAsCell(row);
       } else {
         emptyElement.addAsCell(row);

src/main/java/de/samply/share/client/quality/report/file/excel/sheet/ExplanatoryExcelSheetFactory.java

@@ -17,6 +17,7 @@ public class ExplanatoryExcelSheetFactory implements ExcelSheetFactory {
 
 
   protected static final Logger logger = LogManager.getLogger(ExplanatoryExcelSheetFactory.class);
+  private Integer workbookWindow;
   //private ExplanatoryExcelFileDownloader explanatoryExcelFileDownloader =
   // new ExplanatoryExcelFileDownloader();
 
@@ -74,7 +75,8 @@ private SXSSFWorkbook readWorkbook(File explanatoryExcelFile) throws ExcelSheetF
 
       logger.info("reading explanatory excel file");
       XSSFWorkbook workbook = new XSSFWorkbook(fileInputStream);
-      return new SXSSFWorkbook(workbook);
+      return (workbookWindow != null) ? new SXSSFWorkbook(workbook, workbookWindow)
+          : new SXSSFWorkbook(workbook);
 
     } catch (IOException e) {
       throw new ExcelSheetFactoryException(e);
@@ -84,7 +86,7 @@ private SXSSFWorkbook readWorkbook(File explanatoryExcelFile) throws ExcelSheetF
 
   @Override
   public void setMaxNumberOfRowsPerSheet(int maxNumberOfRowsPerSheet) {
-    // This method does not make sense here.
+    workbookWindow = maxNumberOfRowsPerSheet;
   }
 
 

src/main/java/de/samply/share/client/quality/report/file/excel/workbook/ExcelWorkbookFactoryImpl002.java

@@ -86,7 +86,7 @@ public SXSSFWorkbook createWorkbook(QualityResults qualityResults)
     if (isSheetSelectedToBeWritten(EnumConfiguration.QUALITY_REPORT_SHOW_INFO_SHEET)) {
       logger.info("Adding explanatory sheet to Excel quality report file");
       if (explanatoryExcelSheetFactory != null) {
-        SXSSFWorkbook workbook2 = addExplanatorySheet(workbook);
+        SXSSFWorkbook workbook2 = addExplanatorySheet(workbook, workbookWindow);
         if (workbook2 != null) {
           workbook = workbook2;
         }
@@ -220,10 +220,11 @@ private ExcelRowContext createExcelRowContext(QualityResults qualityResults,
         .createExcelRowContext(qualityResults, asmQualityResults, qualityResultsStatistics);
   }
 
-  private SXSSFWorkbook addExplanatorySheet(SXSSFWorkbook workbook)
+  private SXSSFWorkbook addExplanatorySheet(SXSSFWorkbook workbook, int workbookWindow)
       throws ExcelWorkbookFactoryException {
 
     try {
+      explanatoryExcelSheetFactory.setMaxNumberOfRowsPerSheet(workbookWindow);
       return explanatoryExcelSheetFactory.addSheet(workbook, null, null);
     } catch (ExcelSheetFactoryException e) {
       throw new ExcelWorkbookFactoryException(e);

src/main/java/de/samply/share/client/quality/report/results/QualityResult.java

@@ -6,15 +6,26 @@
 public class QualityResult {
 
 
-  private int numberOfPatients = 0;
+  private Integer numberOfPatients = null;
   private boolean isValid = false;
   private final Set<String> patientLocalIds = new HashSet<>();
   private final Set<String> patientDktkIds = new HashSet<>();
 
 
+  /**
+   * Get number of patients.
+   *
+   * @return number of patients.
+   *
+   */
   public int getNumberOfPatients() {
-    return (numberOfPatients > 0) ? numberOfPatients
-        : Math.max(patientLocalIds.size(), patientDktkIds.size());
+
+    if (numberOfPatients == null) {
+      numberOfPatients = Math.max(patientLocalIds.size(), patientDktkIds.size());
+    }
+
+    return numberOfPatients;
+
   }
 
   public void setNumberOfPatients(int numberOfPatients) {
@@ -52,6 +63,7 @@ public void addPatientLocalIds(Set<String> patientLocalIds) {
 
     if (patientLocalIds != null && patientLocalIds.size() > 0) {
       this.patientLocalIds.addAll(patientLocalIds);
+      this.numberOfPatients = null;
     }
 
   }
@@ -65,6 +77,7 @@ public void addPatientDktkId(String patientDktkId) {
 
     if (patientDktkId != null) {
       patientDktkIds.add(patientDktkId);
+      this.numberOfPatients = null;
     }
 
   }

src/main/java/de/samply/share/client/quality/report/results/statistics/QualityResultsStatisticsImpl.java

@@ -4,7 +4,9 @@
 import de.samply.share.client.quality.report.results.QualityResult;
 import de.samply.share.client.quality.report.results.QualityResults;
 import de.samply.share.common.utils.MdrIdDatatype;
+import java.util.HashMap;
 import java.util.HashSet;
+import java.util.Map;
 import java.util.Set;
 
 public class QualityResultsStatisticsImpl implements QualityResultsStatistics,
@@ -17,6 +19,8 @@ public class QualityResultsStatisticsImpl implements QualityResultsStatistics,
   private final OrConditionsEvaluator orConditionsEvaluator = new OrConditionsEvaluator();
 
   private Integer totalNumberOfPatients;
+  private Map<MdrIdDatatype, Integer> mdrIdNumberOfPatients = new HashMap<>();
+  private MdrIdValueNumberOfPatients mdrIdValueNumberOfPatients = new MdrIdValueNumberOfPatients();
 
 
   public QualityResultsStatisticsImpl(QualityResults qualityResults,
@@ -30,6 +34,37 @@ private double getPercentage(int part, int total) {
     return (total > 0) ? 100.0d * ((double) part) / ((double) total) : 0;
   }
 
+  private class MdrIdValueNumberOfPatients {
+
+    private Map<String, Integer> mdrIdValueNumberOfPatients = new HashMap<>();
+
+    public void addMdrIdValueNumberOfPatients(MdrIdDatatype mdrId, String value,
+        Integer numberOfPatients) {
+      String id = convertToId(mdrId, value);
+      mdrIdValueNumberOfPatients.put(id, numberOfPatients);
+    }
+
+    public Integer getNumberOfPatients(MdrIdDatatype mdrId, String value) {
+
+      Integer numberOfPatients = null;
+
+      if (mdrId != null && value != null) {
+        String id = convertToId(mdrId, value);
+        if (id != null) {
+          numberOfPatients = mdrIdValueNumberOfPatients.get(id);
+        }
+      }
+
+      return numberOfPatients;
+
+    }
+
+    private String convertToId(MdrIdDatatype mdrId, String value) {
+      return mdrId.getMajor() + '-' + value;
+    }
+
+  }
+
   @Override
   public double getPercentageOfPatientsWithValueOutOfPatientsWithMdrId(MdrIdDatatype mdrId,
       String value) {
@@ -53,8 +88,16 @@ public double getPercentageOfPatientsWithValueOutOfTotalPatients(MdrIdDatatype m
 
   private int getPatientsWithValue(MdrIdDatatype mdrID, String value) {
 
-    QualityResult result = qualityResults.getResult(mdrID, value);
-    return (result == null) ? 0 : result.getNumberOfPatients();
+    Integer numberOfPatients = mdrIdValueNumberOfPatients.getNumberOfPatients(mdrID, value);
+    if (numberOfPatients == null) {
+
+      QualityResult result = qualityResults.getResult(mdrID, value);
+      numberOfPatients = (result == null) ? 0 : result.getNumberOfPatients();
+      mdrIdValueNumberOfPatients.addMdrIdValueNumberOfPatients(mdrID, value, numberOfPatients);
+
+    }
+
+    return numberOfPatients;
 
   }
 
@@ -82,7 +125,13 @@ private int countPatients(MdrIdDatatype mdrId, QualityResultPatientIdsGetter pro
 
   private int getPatientsWithMdrId(MdrIdDatatype mdrId) {
 
-    return countPatients(mdrId, qualityResult -> qualityResult.getPatientLocalIds());
+    Integer numberOfPatients = mdrIdNumberOfPatients.get(mdrId);
+    if (numberOfPatients == null) {
+      numberOfPatients = countPatients(mdrId, qualityResult -> qualityResult.getPatientLocalIds());
+      mdrIdNumberOfPatients.put(mdrId, numberOfPatients);
+    }
+
+    return numberOfPatients;
 
   }