Allow aliquot receipt (GLT-1055)

core/src/main/java/uk/ac/bbsrc/tgac/miso/core/data/impl/DetailedSampleBuilder.java

@@ -1,9 +1,11 @@
 package uk.ac.bbsrc.tgac.miso.core.data.impl;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collection;
 import java.util.Date;
 import java.util.HashSet;
+import java.util.List;
 import java.util.Set;
 import java.util.TreeSet;
 
@@ -43,12 +45,15 @@
 import uk.ac.bbsrc.tgac.miso.core.exception.ReportingException;
 import uk.ac.bbsrc.tgac.miso.core.security.SecurableByProfile;
 
-public class DetailedSampleBuilder implements DetailedSample, SampleAliquot, SampleStock, SampleTissue, SampleTissueProcessing,
-    SampleCVSlide, SampleLCMTube, Identity {
+public class DetailedSampleBuilder
+    implements DetailedSample, SampleAliquot, SampleStock, SampleTissue, SampleTissueProcessing, SampleCVSlide, SampleLCMTube, Identity {
 
   @SuppressWarnings("unused")
   private static final long serialVersionUID = 1L;
 
+  private static final List<String> CATEGORY_ORDER = Arrays.asList(Identity.CATEGORY_NAME, SampleTissue.CATEGORY_NAME,
+      SampleStock.CATEGORY_NAME, SampleAliquot.CATEGORY_NAME);
+
   // Sample attributes
   private long sampleId = AbstractSample.UNSAVED_ID;
   private Project project;
@@ -109,6 +114,7 @@ public class DetailedSampleBuilder implements DetailedSample, SampleAliquot, Sam
   private SamplePurpose samplePurpose;
 
   // SampleStock attributes
+  private SampleClass stockClass;
   private StrStatus strStatus = StrStatus.NOT_SUBMITTED;
   private Double concentration;
   private Boolean dnaseTreated;
@@ -156,7 +162,7 @@ public void setProject(Project project) {
   public void addQc(SampleQC sampleQc) throws MalformedSampleQcException {
     this.sampleQCs.add(sampleQc);
     try {
-    sampleQc.setSample(this);
+      sampleQc.setSample(this);
     } catch (MalformedSampleException e) {
       // This is never actually thrown
       throw new RuntimeException(e);
@@ -629,6 +635,14 @@ public void setTissueMaterial(TissueMaterial tissueMaterial) {
     this.tissueMaterial = tissueMaterial;
   }
 
+  public SampleClass getStockClass() {
+    return stockClass;
+  }
+
+  public void setStockClass(SampleClass stockClass) {
+    this.stockClass = stockClass;
+  }
+
   @Override
   public StrStatus getStrStatus() {
     return strStatus;
@@ -853,10 +867,7 @@ public DetailedSample build() {
     DetailedSample sample = null;
     switch (sampleClass.getSampleCategory()) {
     case Identity.CATEGORY_NAME:
-      Identity identity = new IdentityImpl();
-      identity.setInternalName(internalName);
-      identity.setExternalName(externalName);
-      identity.setDonorSex(donorSex);
+      Identity identity = buildIdentity();
       sample = identity;
       break;
     case SampleTissue.CATEGORY_NAME:
@@ -879,11 +890,7 @@ public DetailedSample build() {
       }
       break;
     case SampleStock.CATEGORY_NAME:
-      SampleStock stock = new SampleStockImpl();
-      stock.setStrStatus(strStatus);
-      stock.setConcentration(concentration);
-      stock.setDNAseTreated(dnaseTreated);
-      stock.setQCs(sampleQCs);
+      SampleStock stock = buildStock();
       sample = stock;
       break;
     case SampleAliquot.CATEGORY_NAME:
@@ -897,23 +904,28 @@ public DetailedSample build() {
 
     if (parent != null) {
       sample.setParent(parent);
-    } else if (!Identity.CATEGORY_NAME.equals(sampleClass.getSampleCategory())) {
-      Identity identity = new IdentityImpl();
-      if (externalName == null) {
-        throw new NullPointerException("Missing externalName");
+    } else {
+      DetailedSample parent = null;
+      int categoryIndex = CATEGORY_ORDER.indexOf(sampleClass.getSampleCategory());
+      if (categoryIndex < 0) {
+        throw new IllegalArgumentException("Sample has no parent and cannot infer order from sample category.");
       }
-      identity.setExternalName(externalName);
-      identity.setInternalName(internalName);
-      identity.setDonorSex(donorSex);
-      if (SampleTissue.CATEGORY_NAME.equals(sampleClass.getSampleCategory())) {
-        sample.setParent(identity);
-      } else {
-        if (tissueClass == null) throw new NullPointerException("Missing tissue class");
+      if (categoryIndex > 0 && externalName != null) {
+        parent = buildIdentity();
+      }
+      if (categoryIndex > 1 && tissueClass != null) {
         SampleTissue tissue = buildTissue();
+        tissue.setParent(parent);
         tissue.setSampleClass(tissueClass);
-        tissue.setParent(identity);
-        sample.setParent(tissue);
+        parent = tissue;
+      }
+      if (categoryIndex > 2 && stockClass != null) {
+        SampleStock stock = buildStock();
+        stock.setParent(parent);
+        stock.setSampleClass(stockClass);
+        parent = stock;
       }
+      sample.setParent(parent);
     }
 
     sample.setId(sampleId);
@@ -953,6 +965,26 @@ public DetailedSample build() {
     return sample;
   }
 
+  private Identity buildIdentity() {
+    if (externalName == null) {
+      throw new NullPointerException("Missing externalName");
+    }
+    Identity identity = new IdentityImpl();
+    identity.setInternalName(internalName);
+    identity.setExternalName(externalName);
+    identity.setDonorSex(donorSex);
+    return identity;
+  }
+
+  private SampleStock buildStock() {
+    SampleStock stock = new SampleStockImpl();
+    stock.setStrStatus(strStatus);
+    stock.setConcentration(concentration);
+    stock.setDNAseTreated(dnaseTreated);
+    stock.setQCs(sampleQCs);
+    return stock;
+  }
+
   private SampleTissue buildTissue() {
     SampleTissue tissue = new SampleTissueImpl();
     tissue.setTimesReceived(timesReceived);

core/src/main/java/uk/ac/bbsrc/tgac/miso/core/util/LimsUtils.java

@@ -890,4 +890,13 @@ public static boolean isAliquotSample(Sample sample) {
     return sample instanceof SampleAliquot;
   }
 
+  public static boolean hasStockParent(Long id, Iterable<SampleValidRelationship> relationships) throws IOException {
+    for (SampleValidRelationship relationship : relationships) {
+      if (!relationship.getArchived() && relationship.getChild().getId() == id
+          && relationship.getParent().getSampleCategory().equals(SampleStock.CATEGORY_NAME)) {
+        return true;
+      }
+    }
+    return false;
+  }
 }

miso-dto/src/main/java/uk/ac/bbsrc/tgac/miso/dto/DetailedSampleDto.java

@@ -11,7 +11,7 @@ public class DetailedSampleDto extends SampleDto {
   private Long parentId;
   private String parentUrl;
   private String parentAlias;
-  private Long parentSampleClassId;
+  private Long parentTissueSampleClassId;
   private Long sampleClassId;
   private String sampleClassUrl;
   private Long detailedQcStatusId;
@@ -50,12 +50,12 @@ public void setParentAlias(String parentAlias) {
     this.parentAlias = parentAlias;
   }
 
-  public Long getParentSampleClassId() {
-    return parentSampleClassId;
+  public Long getParentTissueSampleClassId() {
+    return parentTissueSampleClassId;
   }
 
-  public void setParentSampleClassId(Long parentSampleClassId) {
-    this.parentSampleClassId = parentSampleClassId;
+  public void setParentTissueSampleClassId(Long parentSampleClassId) {
+    this.parentTissueSampleClassId = parentSampleClassId;
   }
 
   public Long getDetailedQcStatusId() {

miso-dto/src/main/java/uk/ac/bbsrc/tgac/miso/dto/Dtos.java

@@ -1,13 +1,6 @@
 package uk.ac.bbsrc.tgac.miso.dto;
 
-import static uk.ac.bbsrc.tgac.miso.core.util.LimsUtils.getDateAsString;
-import static uk.ac.bbsrc.tgac.miso.core.util.LimsUtils.isAliquotSample;
-import static uk.ac.bbsrc.tgac.miso.core.util.LimsUtils.isDetailedSample;
-import static uk.ac.bbsrc.tgac.miso.core.util.LimsUtils.isIdentitySample;
-import static uk.ac.bbsrc.tgac.miso.core.util.LimsUtils.isStockSample;
-import static uk.ac.bbsrc.tgac.miso.core.util.LimsUtils.isStringEmptyOrNull;
-import static uk.ac.bbsrc.tgac.miso.core.util.LimsUtils.isTissueProcessingSample;
-import static uk.ac.bbsrc.tgac.miso.core.util.LimsUtils.isTissueSample;
+import static uk.ac.bbsrc.tgac.miso.core.util.LimsUtils.*;
 
 import java.text.DateFormat;
 import java.text.ParseException;
@@ -276,7 +269,7 @@ private static DetailedSampleDto asDetailedSampleDto(DetailedSample from) {
     if (from.getParent() != null) {
       dto.setParentId(from.getParent().getId());
       dto.setParentAlias(from.getParent().getAlias());
-      dto.setParentSampleClassId(from.getParent().getSampleClass().getId());
+      dto.setParentTissueSampleClassId(from.getParent().getSampleClass().getId());
     }
     if (from.getGroupId() != null) {
       dto.setGroupId(from.getGroupId());
@@ -348,14 +341,13 @@ private static DetailedSample toDetailedSample(DetailedSampleDto from) {
   }
 
   /**
-   * Extracts parent details from the DTO, according to three possible cases:
+   * Extracts parent details from the DTO, according to these possible cases:
    * 
    * <ol>
    * <li>parent ID is provided. This implies that the parent exists, so no other parent information will be required</li>
-   * <li>identity information and parentSampleClassId are provided. This implies that a tissue parent should be created, and that the
-   * identity may or may not yet exist</li>
-   * <li>identity information is provided, but no parentSampleClassId. This implies that the direct parent of this sample will be an
-   * identity, which may or may not yet exist</li>
+   * <li>identity information and parentTissueSampleClassId are provided. This implies that a tissue parent should be created, and that the
+   * identity may or may not yet exist. If the sampleClassId is an aliquot, a stockClassId must be provided.</li>
+   * <li>identity information is provided, but no parentTissueSampleClassId. You must be creating a tissue in this case.</li>
    * </ol>
    * 
    * @param childDto
@@ -365,21 +357,29 @@ private static DetailedSample toDetailedSample(DetailedSampleDto from) {
   private static DetailedSample getParent(DetailedSampleDto childDto) {
     DetailedSample parent = null;
     if (childDto.getParentId() != null) {
-      // Case 1
       parent = new DetailedSampleImpl();
       parent.setId(childDto.getParentId());
-    } else if (childDto instanceof SampleIdentityDto && childDto.getClass() != SampleIdentityDto.class) {
-      // Case 2 or 3 require Identity details
-      Identity identity = toIdentitySample((SampleIdentityDto) childDto);
-      if (childDto instanceof SampleTissueDto && childDto.getParentSampleClassId() != null) {
-        // Case 2
-        parent = toTissueSample((SampleTissueDto) childDto);
-        parent.setSampleClass(new SampleClassImpl());
-        parent.getSampleClass().setId(childDto.getParentSampleClassId());
-        parent.setParent(identity);
-      } else {
-        // Case 3
-        parent = identity;
+    } else {
+      if (childDto instanceof SampleIdentityDto && childDto.getClass() != SampleIdentityDto.class) {
+        parent = toIdentitySample((SampleIdentityDto) childDto);
+      }
+
+      if (childDto instanceof SampleTissueDto && childDto.getClass() != SampleTissueDto.class) {
+        if (childDto.getParentTissueSampleClassId() == null) {
+          throw new IllegalArgumentException("No tissue class specified.");
+        }
+        DetailedSample tissue = toTissueSample((SampleTissueDto) childDto);
+        tissue.setSampleClass(new SampleClassImpl());
+        tissue.getSampleClass().setId(childDto.getParentTissueSampleClassId());
+        tissue.setParent(parent);
+        parent = tissue;
+      }
+      if (childDto instanceof SampleStockDto && childDto.getClass() != SampleStockDto.class) {
+        DetailedSample stock = toStockSample((SampleStockDto) childDto);
+        stock.setSampleClass(new SampleClassImpl());
+        stock.getSampleClass().setId(((SampleAliquotDto) childDto).getStockClassId());
+        stock.setParent(parent);
+        parent = stock;
       }
     }
     return parent;
@@ -1157,7 +1157,7 @@ public static PoolDto asDto(Pool<? extends Poolable<?, ?>> from) {
     if (from.getLastModified() != null) {
       dto.setLastModified(getDateAsString(from.getLastModified()));
     }
-    Set<DilutionDto> pooledElements = new HashSet<DilutionDto>();
+    Set<DilutionDto> pooledElements = new HashSet<>();
     for (Dilution ld : from.getDilutions()) {
       if (ld != null) {
         pooledElements.add(asDto(ld));

miso-dto/src/main/java/uk/ac/bbsrc/tgac/miso/dto/SampleAliquotDto.java

@@ -2,12 +2,15 @@
 
 import java.net.URI;
 
+import org.codehaus.jackson.annotate.JsonIgnore;
 import org.springframework.web.util.UriComponentsBuilder;
 
 public class SampleAliquotDto extends SampleStockDto {
 
   private Long samplePurposeId;
   private String samplePurposeUrl;
+  @JsonIgnore
+  private Long stockClassId;
 
   public Long getSamplePurposeId() {
     return samplePurposeId;
@@ -25,6 +28,14 @@ public void setSamplePurposeUrl(String samplePurposeUrl) {
     this.samplePurposeUrl = samplePurposeUrl;
   }
 
+  public Long getStockClassId() {
+    return stockClassId;
+  }
+
+  public void setStockClassId(Long stockClassId) {
+    this.stockClassId = stockClassId;
+  }
+
   @Override
   public void writeUrls(URI baseUri) {
     super.writeUrls(baseUri);

miso-dto/src/main/java/uk/ac/bbsrc/tgac/miso/dto/SampleClassDto.java

@@ -17,6 +17,7 @@ public class SampleClassDto {
   private String updatedByUrl;
   private String lastUpdated;
   private Boolean dnaseTreatable;
+  private boolean canCreateNew;
 
   public Long getId() {
     return id;
@@ -114,11 +115,18 @@ public void setDNAseTreatable(Boolean dnaseTreatable) {
     this.dnaseTreatable = dnaseTreatable;
   }
 
+  public boolean getCanCreateNew() {
+    return canCreateNew;
+  }
+
+  public void setCanCreateNew(boolean canCreateNew) {
+    this.canCreateNew = canCreateNew;
+  }
+
   @Override
   public String toString() {
     return "SampleClassDto [id=" + id + ", url=" + url + ", alias=" + alias + ", sampleCategory=" + sampleCategory + ", suffix=" + suffix
         + ", createdById=" + createdById + ", createdByUrl=" + createdByUrl + ", creationDate=" + creationDate + ", updatedById="
         + updatedById + ", updatedByUrl=" + updatedByUrl + ", lastUpdated=" + lastUpdated + ", dnaseTreatable=" + dnaseTreatable + "]";
   }
-
 }