x1520 support downloading a file of data about imaging qc op

src/main/java/uk/ac/sanger/sccp/stan/ImageDataFileController.java

@@ -0,0 +1,41 @@
+package uk.ac.sanger.sccp.stan;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Controller;
+import org.springframework.web.bind.annotation.*;
+import uk.ac.sanger.sccp.stan.model.Operation;
+import uk.ac.sanger.sccp.stan.repo.OperationRepo;
+import uk.ac.sanger.sccp.stan.service.imagedatafile.ImageDataFileService;
+import uk.ac.sanger.sccp.utils.tsv.TsvFile;
+
+import javax.persistence.EntityNotFoundException;
+
+/**
+ * Controller for delivering image data files (excel).
+ * @author dr6
+ */
+@Controller
+public class ImageDataFileController {
+    public static final String IMAGING_QC_OP_NAME = "Imaging QC";
+
+    private final OperationRepo opRepo;
+    private final ImageDataFileService imageDataFileService;
+
+    @Autowired
+    public ImageDataFileController(OperationRepo opRepo, ImageDataFileService imageDataFileService) {
+        this.opRepo = opRepo;
+        this.imageDataFileService = imageDataFileService;
+    }
+
+    @RequestMapping(value="/imageqc", method=RequestMethod.GET,
+                    produces="application/vnd.openxmlformats-officedocument.spreadsheetml.sheet")
+    @ResponseBody
+    public TsvFile<?> getImageDataFile(@RequestParam(name="id") Integer id) {
+        Operation op = opRepo.findById(id).orElseThrow(() -> new EntityNotFoundException("No operation found with id " + id+"."));
+        if (!op.getOperationType().getName().equalsIgnoreCase(IMAGING_QC_OP_NAME)) {
+            throw new IllegalArgumentException("Operation " + id + " is not an imaging QC operation");
+        }
+        return imageDataFileService.generateFile(op);
+        // TsvFileConverter will convert the data to an excel file
+    }
+}

src/main/java/uk/ac/sanger/sccp/stan/repo/WorkRepo.java

@@ -13,8 +13,7 @@
 
 import static java.util.stream.Collectors.toMap;
 import static java.util.stream.Collectors.toSet;
-import static uk.ac.sanger.sccp.utils.BasicUtils.inMap;
-import static uk.ac.sanger.sccp.utils.BasicUtils.stream;
+import static uk.ac.sanger.sccp.utils.BasicUtils.*;
 
 public interface WorkRepo extends CrudRepository<Work, Integer> {
     Optional<Work> findByWorkNumber(String workNumber);
@@ -83,6 +82,15 @@ default Map<Integer, Set<String>> findWorkNumbersForOpIds(Collection<Integer> op
         return opWork;
     }
 
+    @Query(value = "select work_id from work_op where operation_id=?1", nativeQuery = true)
+    List<Integer> findWorkIdsForOperationId(Integer opId);
+
+    /** Gets list of works linked to the given operation id. */
+    default List<Work> findWorksForOperationId(Integer opId) {
+        List<Integer> workIds = findWorkIdsForOperationId(opId);
+        return (workIds.isEmpty() ? List.of() : asList(findAllById(workIds)));
+    }
+
     @Query(value="select release_id as releaseId, work_number as workNumber from work_release join work on (work_id=work.id) where release_id IN (?1)", nativeQuery=true)
     List<Object[]> _releaseIdWorkNumbersForReleaseIds(Collection<Integer> releaseIds);
 

src/main/java/uk/ac/sanger/sccp/stan/service/imagedatafile/ImageDataColumn.java

@@ -0,0 +1,30 @@
+package uk.ac.sanger.sccp.stan.service.imagedatafile;
+
+import uk.ac.sanger.sccp.utils.tsv.TsvColumn;
+
+import java.util.function.Function;
+
+/** Columns in the image data file */
+public enum ImageDataColumn implements TsvColumn<ImageDataRow> {
+    location(null),
+    filename(ImageDataRow::getBarcode),
+    omero_name(ImageDataRow::getExternalName),
+    omero_group(ImageDataRow::getOmeroProject),
+    omero_project(ImageDataRow::getWorkNumber),
+    omero_dataset(ImageDataRow::getExternalName),
+    omero_username(ImageDataRow::getUserName),
+    tags(null),
+    comments(ImageDataRow::getComments),
+    ;
+
+    private final Function<ImageDataRow, String> dataGetter;
+
+    ImageDataColumn(Function<ImageDataRow, String> dataGetter) {
+        this.dataGetter = dataGetter;
+    }
+
+    @Override
+    public String get(ImageDataRow entry) {
+        return (dataGetter==null ? null : dataGetter.apply(entry));
+    }
+}

src/main/java/uk/ac/sanger/sccp/stan/service/imagedatafile/ImageDataFileService.java

@@ -0,0 +1,14 @@
+package uk.ac.sanger.sccp.stan.service.imagedatafile;
+
+import uk.ac.sanger.sccp.stan.model.Operation;
+import uk.ac.sanger.sccp.utils.tsv.TsvFile;
+
+/** Service for generating file data for image qc ops */
+public interface ImageDataFileService {
+    /**
+     * Generate file data containing the image data for the given operation.
+     * @param op the operation
+     * @return the file data
+     */
+    TsvFile<?> generateFile(Operation op);
+}

src/main/java/uk/ac/sanger/sccp/stan/service/imagedatafile/ImageDataFileServiceImp.java

@@ -0,0 +1,119 @@
+package uk.ac.sanger.sccp.stan.service.imagedatafile;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+import uk.ac.sanger.sccp.stan.model.*;
+import uk.ac.sanger.sccp.stan.repo.*;
+import uk.ac.sanger.sccp.utils.tsv.TsvColumn;
+import uk.ac.sanger.sccp.utils.tsv.TsvFile;
+
+import java.util.*;
+
+import static java.util.stream.Collectors.joining;
+import static java.util.stream.Collectors.toSet;
+import static uk.ac.sanger.sccp.utils.BasicUtils.*;
+
+/**
+ * @author dr6
+ */
+@Service
+public class ImageDataFileServiceImp implements ImageDataFileService {
+    private final WorkRepo workRepo;
+    private final OperationCommentRepo opComRepo;
+    private final LabwareRepo lwRepo;
+
+    @Autowired
+    public ImageDataFileServiceImp(WorkRepo workRepo, OperationCommentRepo opComRepo, LabwareRepo lwRepo) {
+        this.workRepo = workRepo;
+        this.opComRepo = opComRepo;
+        this.lwRepo = lwRepo;
+    }
+
+    @Override
+    public TsvFile<?> generateFile(Operation op) {
+        String filename = getFilename(op);
+        List<? extends TsvColumn<ImageDataRow>> columns = getColumns();
+        List<ImageDataRow> rows = getRows(op);
+        return new TsvFile<>(filename, rows, columns);
+    }
+
+    /** Filename for the given operation */
+    public String getFilename(Operation op) {
+        return "imaging-qc-" + op.getId() + ".xlsx";
+    }
+
+    /** The columns in the file */
+    public List<ImageDataColumn> getColumns() {
+        return Arrays.asList(ImageDataColumn.values());
+    }
+
+    /** Gets the comments for the operation, mapped from slot/sample id */
+    public Map<Integer, List<Comment>> compileCommentMap(Integer opId) {
+        List<OperationComment> opcoms = opComRepo.findAllByOperationIdIn(List.of(opId));
+        if (opcoms.isEmpty()) {
+            return Map.of();
+        }
+        Map<Integer, List<Comment>> map = new HashMap<>();
+        for (OperationComment opCom : opcoms) {
+            map.computeIfAbsent(opCom.getSampleId(), k -> new ArrayList<>())
+                    .add(opCom.getComment());
+        }
+        map.replaceAll((k, v) -> v.stream().sorted(Comparator.comparingInt(Comment::getId)).distinct().toList());
+        return map;
+    }
+
+    /** Gets the labware for the operation, mapped from their ids */
+    public Map<Integer, Labware> compileLabwareMap(Operation op) {
+        Set<Integer> labwareIds = op.getActions().stream()
+                .map(ac -> ac.getDestination().getLabwareId())
+                .collect(toSet());
+        return lwRepo.findAllByIdIn(labwareIds).stream()
+                .collect(inMap(Labware::getId));
+    }
+
+    /** Gets the rows for the operation */
+    public List<ImageDataRow> getRows(Operation op) {
+        List<Work> works = workRepo.findWorksForOperationId(op.getId());
+        String workNumber = works.stream().map(Work::getWorkNumber).collect(joining(", "));
+        String omeroProject = works.stream()
+                .map(Work::getOmeroProject)
+                .filter(Objects::nonNull)
+                .distinct()
+                .map(OmeroProject::getName)
+                .collect(joining(", "));
+        Map<Integer, List<Comment>> sampleComments = compileCommentMap(op.getId());
+        Map<Integer, Labware> lwMap = compileLabwareMap(op);
+        return compileRows(op, omeroProject, workNumber, op.getUser().getUsername(), lwMap, sampleComments);
+    }
+
+    /** Puts together rows given various data. One row per sample */
+    public List<ImageDataRow> compileRows(Operation op, String omeroProject, String workNumber, String user,
+                                          Map<Integer, Labware> lwMap, Map<Integer, List<Comment>> sampleComments) {
+        return op.getActions().stream()
+                .filter(distinctBySerial(ac -> ac.getSample().getId()))
+                .map(ac -> makeRow(ac, omeroProject, workNumber, user, lwMap, sampleComments))
+                .distinct()
+                .toList();
+    }
+
+    /** Converts an action to a row */
+    public ImageDataRow makeRow(Action ac, String omeroProject, String workNumber, String user,
+                                Map<Integer, Labware> lwMap, Map<Integer, List<Comment>> slotSampleComments) {
+        Slot slot = ac.getDestination();
+        Sample sample = ac.getSample();
+        Labware lw = lwMap.get(slot.getLabwareId());
+        List<Comment> comments = slotSampleComments.get(sample.getId());
+        String commentString;
+        if (nullOrEmpty(comments)) {
+            commentString = null;
+        } else {
+            commentString = comments.stream()
+                    .map(Comment::getText)
+                    .map(s -> s.endsWith(".") ? s : (s + "."))
+                    .collect(joining(" "));
+        }
+        return new ImageDataRow(lw.getBarcode(), sample.getTissue().getExternalName(), omeroProject, workNumber, user,
+                commentString);
+    }
+
+}

src/main/java/uk/ac/sanger/sccp/stan/service/imagedatafile/ImageDataRow.java

@@ -0,0 +1,105 @@
+package uk.ac.sanger.sccp.stan.service.imagedatafile;
+
+import java.util.Objects;
+
+import static uk.ac.sanger.sccp.utils.BasicUtils.describe;
+
+/**
+ * @author dr6
+ */
+public class ImageDataRow {
+    private String barcode;
+    private String externalName;
+    private String omeroProject;
+    private String workNumber;
+    private String userName;
+    private String comments;
+
+    public ImageDataRow(String barcode, String externalName, String omeroProject, String workNumber, String userName,
+                        String comments) {
+        this.barcode = barcode;
+        this.externalName = externalName;
+        this.omeroProject = omeroProject;
+        this.workNumber = workNumber;
+        this.userName = userName;
+        this.comments = comments;
+    }
+
+    public String getBarcode() {
+        return this.barcode;
+    }
+
+    public void setBarcode(String barcode) {
+        this.barcode = barcode;
+    }
+
+    public String getExternalName() {
+        return this.externalName;
+    }
+
+    public void setExternalName(String externalName) {
+        this.externalName = externalName;
+    }
+
+    public String getOmeroProject() {
+        return this.omeroProject;
+    }
+
+    public void setOmeroProject(String omeroProject) {
+        this.omeroProject = omeroProject;
+    }
+
+    public String getWorkNumber() {
+        return this.workNumber;
+    }
+
+    public void setWorkNumber(String workNumber) {
+        this.workNumber = workNumber;
+    }
+
+    public String getUserName() {
+        return this.userName;
+    }
+
+    public void setUserName(String userName) {
+        this.userName = userName;
+    }
+
+    public String getComments() {
+        return this.comments;
+    }
+
+    public void setComments(String comments) {
+        this.comments = comments;
+    }
+
+    @Override
+    public boolean equals(Object o) {
+        if (o == null || getClass() != o.getClass()) return false;
+        ImageDataRow that = (ImageDataRow) o;
+        return (Objects.equals(this.barcode, that.barcode)
+                && Objects.equals(this.externalName, that.externalName)
+                && Objects.equals(this.omeroProject, that.omeroProject)
+                && Objects.equals(this.workNumber, that.workNumber)
+                && Objects.equals(this.userName, that.userName)
+                && Objects.equals(this.comments, that.comments));
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(barcode, externalName, omeroProject, workNumber, userName, comments);
+    }
+
+    @Override
+    public String toString() {
+        return describe(this)
+                .add("barcode", barcode)
+                .add("externalName", externalName)
+                .add("omeroProject", omeroProject)
+                .add("workNumber", workNumber)
+                .add("userName", userName)
+                .add("comments", comments)
+                .reprStringValues()
+                .toString();
+    }
+}

src/main/java/uk/ac/sanger/sccp/utils/tsv/TsvData.java

@@ -4,6 +4,8 @@
 
 /**
  * The data required for a tsv file
+ * @param <C> the type of the columns
+ * @param <E> the type of the data
  * @author dr6
  */
 public interface TsvData<C, E> {