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oicr-gsi · Apr 1, 2024 · 4b0fe6e · 4b0fe6e
2 parents d9ecc00 + 8a58e76
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diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -1,3 +1,6 @@
 Jira ticket or GitHub issue:
 
 - [ ] Includes a change file
+- [ ] Updated tests (or n/a)
+- [ ] Updated documentation (or n/a)
+- [ ] Discussed with CGI (or n/a; see release procedure on wiki for applicability)
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,26 @@ This file is updated automatically as described in [Unreleased Changes](changes/
 
 ---------------------------------------------------------------------------------------------------
 
+## [1.29.0] - 2024-03-28
+
+### Added
+
+* Format option for case downloads, allowing CSV and TSV formats in addition to Excel
+* Full-Depth Summary Download from the Cases table
+* DARE Input Sheet Download from the Cases table
+
+### Changed
+
+* Button text in first "Case QC" dialog from "Submit" to "Next" to clarify that there will be another step
+
+
+## [1.28.1] - 2024-03-25
+
+### Fixed
+
+* Error when attempting to record sign offs
+
+
 ## [1.28.0] - 2024-03-14
 
 ### Added

diff --git a/pom.xml b/pom.xml
@@ -12,7 +12,7 @@
   </parent>
   <groupId>ca.on.oicr.gsi</groupId>
   <artifactId>dimsum</artifactId>
-  <version>1.28.1-SNAPSHOT</version>
+  <version>1.29.1-SNAPSHOT</version>
   <name>Dimsum</name>
   <description>QC Tracking Dashboard</description>
   <properties>

diff --git a/src/main/java/ca/on/oicr/gsi/dimsum/controller/rest/DownloadRestController.java b/src/main/java/ca/on/oicr/gsi/dimsum/controller/rest/DownloadRestController.java
@@ -1,16 +1,13 @@
 package ca.on.oicr.gsi.dimsum.controller.rest;
 
-import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.time.ZonedDateTime;
 import java.time.format.DateTimeFormatter;
 import java.util.Map;
 import javax.servlet.http.HttpServletResponse;
-import org.apache.poi.xssf.usermodel.XSSFWorkbook;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.HttpEntity;
 import org.springframework.http.HttpHeaders;
-import org.springframework.http.MediaType;
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.PostMapping;
 import org.springframework.web.bind.annotation.RequestBody;
@@ -19,7 +16,9 @@
 import ca.on.oicr.gsi.dimsum.controller.BadRequestException;
 import ca.on.oicr.gsi.dimsum.service.CaseService;
 import ca.on.oicr.gsi.dimsum.util.reporting.Report;
-import ca.on.oicr.gsi.dimsum.util.reporting.reports.CaseReport;
+import ca.on.oicr.gsi.dimsum.util.reporting.ReportFormat;
+import ca.on.oicr.gsi.dimsum.util.reporting.reports.DareInputSheet;
+import ca.on.oicr.gsi.dimsum.util.reporting.reports.FullDepthSummary;
 import ca.on.oicr.gsi.dimsum.util.reporting.reports.TglTrackingReport;
 
 @RestController
@@ -34,36 +33,31 @@ public HttpEntity<byte[]> generateReport(@PathVariable String reportName,
       @RequestBody Map<String, String> parameters, HttpServletResponse response)
       throws IOException {
 
+    ReportFormat format = Report.getFormat(parameters);
     Report report = getReport(reportName);
-    XSSFWorkbook workbook = report.writeExcelFile(caseService, parameters);
+    byte[] bytes = report.writeFile(caseService, parameters);
 
     HttpHeaders headers = new HttpHeaders();
-    headers.setContentType(new MediaType("application", "vnd.ms-excel"));
+    headers.setContentType(format.getMediaType());
     response.setHeader("Content-Disposition",
         "attachment; filename="
-            + String.format("%s-%s.xlsx", reportName, DateTimeFormatter.ISO_LOCAL_DATE.format(
-                ZonedDateTime.now())));
+            + String.format("%s-%s.%s", reportName, DateTimeFormatter.ISO_LOCAL_DATE.format(
+                ZonedDateTime.now()), format.getExtension()));
 
-    byte[] bytes = getReportBytes(workbook);
     return new HttpEntity<byte[]>(bytes, headers);
   }
 
   private static Report getReport(String reportName) {
     switch (reportName) {
       case "tgl-tracking-sheet":
         return TglTrackingReport.INSTANCE;
-      case "case-report":
-        return CaseReport.INSTANCE;
+      case "full-depth-summary":
+        return FullDepthSummary.INSTANCE;
+      case "dare-input-sheet":
+        return DareInputSheet.INSTANCE;
       default:
         throw new BadRequestException("Invalid report name");
     }
   }
 
-  private static byte[] getReportBytes(XSSFWorkbook workbook) throws IOException {
-    try (ByteArrayOutputStream output = new ByteArrayOutputStream()) {
-      workbook.write(output);
-      return output.toByteArray();
-    }
-  }
-
 }
diff --git a/src/main/java/ca/on/oicr/gsi/dimsum/service/CaseService.java b/src/main/java/ca/on/oicr/gsi/dimsum/service/CaseService.java
@@ -10,6 +10,7 @@
 import java.util.Collections;
 import java.util.Comparator;
 import java.util.HashMap;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -728,11 +729,13 @@ private void refreshCacheUpdatedCases() {
 
   private void removeExpiredCachedSignoffs() {
     ZonedDateTime cutoff = caseData.getTimestamp().minus(CACHE_OVERLAP_MINUTES, ChronoUnit.MINUTES);
-    for (String caseId : cachedSignoffsByCaseId.keySet()) {
+    Iterator<String> iterator = cachedSignoffsByCaseId.keySet().iterator();
+    while (iterator.hasNext()) {
+      String caseId = iterator.next();
       List<NabuSavedSignoff> signoffs = cachedSignoffsByCaseId.get(caseId);
       signoffs.removeIf(signoff -> signoff.getCreated().isBefore(cutoff));
       if (signoffs.isEmpty()) {
-        cachedSignoffsByCaseId.remove(caseId);
+        iterator.remove();
       }
     }
   }

diff --git a/src/main/java/ca/on/oicr/gsi/dimsum/util/reporting/Column.java b/src/main/java/ca/on/oicr/gsi/dimsum/util/reporting/Column.java
@@ -15,6 +15,19 @@ public void writeExcelCell(Cell cell, T object) {
         cell.setCellValue(value);
       }
 
+      @Override
+      public String getDelimitedColumnString(String delimiter, T object) {
+        String value = getter.apply(object);
+        if (value == null || value.isBlank()) {
+          return "";
+        }
+        // Quote string with double quotes if necessary; escape double quotes with double quotes
+        if (value.contains(delimiter) || value.contains("\"") || value.contains("'")) {
+          return "\"" + value.replace("\"", "\"\"") + "\"";
+        }
+        return value;
+      }
+
     };
   }
 
@@ -29,6 +42,12 @@ public void writeExcelCell(Cell cell, T object) {
         }
       }
 
+      @Override
+      public String getDelimitedColumnString(String delimiter, T object) {
+        BigDecimal value = getter.apply(object);
+        return value.toPlainString();
+      }
+
     };
   }
 
@@ -57,4 +76,6 @@ public String getTitle() {
 
   public abstract void writeExcelCell(Cell cell, T object);
 
+  public abstract String getDelimitedColumnString(String delimiter, T object);
+
 }
diff --git a/src/main/java/ca/on/oicr/gsi/dimsum/util/reporting/Report.java b/src/main/java/ca/on/oicr/gsi/dimsum/util/reporting/Report.java
@@ -1,14 +1,21 @@
 package ca.on.oicr.gsi.dimsum.util.reporting;
 
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
 import java.util.Map;
+import java.util.Objects;
 import org.apache.poi.xssf.usermodel.XSSFWorkbook;
+import ca.on.oicr.gsi.dimsum.controller.BadRequestException;
 import ca.on.oicr.gsi.dimsum.service.CaseService;
 
 public abstract class Report {
 
+  private static final String PARAM_FORMAT = "format";
+  private static final String PARAM_HEADINGS = "includeHeadings";
+
   private final String title;
   private final List<ReportSection<?>> sections;
 
@@ -21,12 +28,58 @@ public String getTitle() {
     return title;
   }
 
-  public XSSFWorkbook writeExcelFile(CaseService caseService, Map<String, String> parameters) {
+  public static ReportFormat getFormat(Map<String, String> parameters) {
+    String format = parameters.get(PARAM_FORMAT);
+    if (format == null) {
+      return ReportFormat.EXCEL;
+    }
+    switch (format) {
+      case "excel":
+        return ReportFormat.EXCEL;
+      case "csv":
+        return ReportFormat.CSV;
+      case "tsv":
+        return ReportFormat.TSV;
+      default:
+        throw new BadRequestException("Invalid report format: " + format);
+    }
+  }
+
+  public byte[] writeFile(CaseService caseService, Map<String, String> parameters)
+      throws IOException {
+    ReportFormat format = getFormat(parameters);
+
+    switch (format) {
+      case EXCEL:
+        return writeExcelFile(caseService, parameters);
+      case CSV:
+        return writeDelimitedFile(caseService, ",", parameters);
+      case TSV:
+        return writeDelimitedFile(caseService, "\t", parameters);
+      default:
+        throw new BadRequestException("Invalid download format: " + format);
+    }
+  }
+
+  private byte[] writeExcelFile(CaseService caseService, Map<String, String> parameters)
+      throws IOException {
     XSSFWorkbook workbook = new XSSFWorkbook();
     for (ReportSection<?> section : sections) {
       section.createExcelSheet(workbook, caseService, parameters);
     }
-    return workbook;
+    try (ByteArrayOutputStream output = new ByteArrayOutputStream()) {
+      workbook.write(output);
+      return output.toByteArray();
+    }
+  }
+
+  private byte[] writeDelimitedFile(CaseService caseService, String delimiter,
+      Map<String, String> parameters) {
+    StringBuilder sb = new StringBuilder();
+    boolean includeHeadings = Objects.equals("true", parameters.get(PARAM_HEADINGS));
+    // This does not support multiple sections
+    sections.get(0).createDelimitedText(sb, caseService, delimiter, includeHeadings, parameters);
+    return sb.toString().getBytes();
   }
 
 }
diff --git a/src/main/java/ca/on/oicr/gsi/dimsum/util/reporting/ReportFormat.java b/src/main/java/ca/on/oicr/gsi/dimsum/util/reporting/ReportFormat.java
@@ -0,0 +1,27 @@
+package ca.on.oicr.gsi.dimsum.util.reporting;
+
+import org.springframework.http.MediaType;
+
+public enum ReportFormat {
+  // @formatter:off
+  EXCEL(new MediaType("application", "vnd.ms-excel"), "xlsx"),
+  CSV(new MediaType("text", "csv"), "csv"),
+  TSV(new MediaType("text", "tab-separated-values"), "tsv");
+  // @formatter:on
+
+  private final MediaType mediaType;
+  private final String extension;
+
+  private ReportFormat(MediaType mediaType, String extension) {
+    this.mediaType = mediaType;
+    this.extension = extension;
+  }
+
+  public MediaType getMediaType() {
+    return mediaType;
+  }
+
+  public String getExtension() {
+    return extension;
+  }
+}
diff --git a/src/main/java/ca/on/oicr/gsi/dimsum/util/reporting/ReportSection.java b/src/main/java/ca/on/oicr/gsi/dimsum/util/reporting/ReportSection.java
@@ -10,6 +10,7 @@
 import org.apache.poi.ss.usermodel.Row;
 import org.apache.poi.xssf.usermodel.XSSFSheet;
 import org.apache.poi.xssf.usermodel.XSSFWorkbook;
+import ca.on.oicr.gsi.dimsum.controller.BadRequestException;
 import ca.on.oicr.gsi.dimsum.service.CaseService;
 
 public abstract class ReportSection<T> {
@@ -41,6 +42,29 @@ public void writeExcelSheet(XSSFSheet worksheet, List<T> objects) {
       }
     }
 
+    @Override
+    public void writeDelimitedText(StringBuilder sb, List<T> objects, String delimiter,
+        boolean includeHeaders) {
+      List<Column<T>> columns = getColumns();
+      if (includeHeaders) {
+        for (int i = 0; i < columns.size(); i++) {
+          if (i > 0) {
+            sb.append(delimiter);
+          }
+          sb.append(columns.get(i).getTitle());
+        }
+      }
+      for (T object : objects) {
+        for (int i = 0; i < columns.size(); i++) {
+          if (i > 0) {
+            sb.append(delimiter);
+          }
+          sb.append(columns.get(i).getDelimitedColumnString(delimiter, object));
+        }
+        sb.append("\r\n");
+      }
+    }
+
   }
 
   private final String title;
@@ -68,6 +92,15 @@ public void createExcelSheet(XSSFWorkbook workbook, CaseService caseService,
 
   protected abstract void writeExcelSheet(XSSFSheet worksheet, List<T> objects);
 
+  public void createDelimitedText(StringBuilder sb, CaseService caseService,
+      String delimiter, boolean includeHeadings, Map<String, String> parameters) {
+    List<T> objects = getData(caseService, parameters);
+    writeDelimitedText(sb, objects, delimiter, includeHeadings);
+  }
+
+  protected abstract void writeDelimitedText(StringBuilder sb, List<T> objects, String delimiter,
+      boolean includeHeaders);
+
   /**
    * Fetches data from the CaseService based on parameters provided
    * 

diff --git a/src/main/java/ca/on/oicr/gsi/dimsum/util/reporting/reports/DareInputSheet.java b/src/main/java/ca/on/oicr/gsi/dimsum/util/reporting/reports/DareInputSheet.java
@@ -0,0 +1,40 @@
+package ca.on.oicr.gsi.dimsum.util.reporting.reports;
+
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import ca.on.oicr.gsi.dimsum.controller.BadRequestException;
+import ca.on.oicr.gsi.dimsum.service.CaseService;
+import ca.on.oicr.gsi.dimsum.util.reporting.Column;
+import ca.on.oicr.gsi.dimsum.util.reporting.Report;
+import ca.on.oicr.gsi.dimsum.util.reporting.ReportSection;
+import ca.on.oicr.gsi.dimsum.util.reporting.ReportSection.TableReportSection;
+import ca.on.oicr.gsi.dimsum.util.reporting.reports.shared.CaseSampleRowData;
+
+public class DareInputSheet extends Report {
+
+  private static final ReportSection<CaseSampleRowData> mainSection =
+      new TableReportSection<CaseSampleRowData>("Full-Depth Sequencing", Arrays.asList(
+          Column.forString("Library", x -> x.getSample().getName()),
+          Column.forString("Run", x -> x.getSample().getRun().getName()))) {
+
+        @Override
+        public List<CaseSampleRowData> getData(CaseService caseService,
+            Map<String, String> parameters) {
+          Set<String> caseIds = getParameterStringSet(parameters, "caseIds");
+          if (caseIds == null) {
+            throw new BadRequestException("caseIds parameter missing");
+          }
+          return CaseSampleRowData.listByCaseIds(caseService, caseIds);
+        }
+
+      };
+
+  public static final DareInputSheet INSTANCE = new DareInputSheet();
+
+  private DareInputSheet() {
+    super("Dare Input Sheet", mainSection);
+  }
+
+}