Merge pull request #57 from DiamondLightSource/I15_1-563

I'm merging now as I don't expect anyone else to chip in at this point. We'll see if it does the job, and if not we'll just have to make another version.

pom.xml

@@ -11,7 +11,7 @@
     <organization>
         <name>Diamond Light Source</name>
     </organization>
-    <version>2.1.1</version>
+    <version>2.3.0</version>
 
     <packaging>bundle</packaging>
 
@@ -147,4 +147,3 @@
     </dependencies>
 
 </project>
-

src/main/java/uk/ac/diamond/ispyb/api/IspybXpdfApi.java

@@ -22,10 +22,12 @@
 public interface IspybXpdfApi extends Closeable {
     List<Sample> retrieveSamplesAssignedForProposal(String proposalCode, Long proposalNumber);
     List<SampleGroup> retrieveSampleGroupsForSample(Long sampleId);
-    List<SampleGroup> retrieveSamplesForSampleGroup(Long sampleGroupId);
+    List<Sample> retrieveSamplesForSampleGroup(Long sampleGroupId);
     List<Component> retrieveComponentsForSampleType(Long sampleTypeId);
     List<DataCollectionPlan> retrieveDataCollectionPlansForSample(Long sampleId);
     Optional<DataCollectionPlanInfo> retrieveDataCollectionPlanInfoForSample(Long sampleId);
     List<ComponentLattice> retrieveComponentLatticesForComponent(Long componentId);
     Optional<ContainerInfo> retrieveContainerInfoForId(Long containerId) throws SQLException;
+    Optional<SampleType> retrieveSampleTypeForSample(Long sampleId) throws SQLException;
+    List<PDB> retrievePDBsForComponent(Long componentId) throws SQLException;
 }

src/main/java/uk/ac/diamond/ispyb/api/PDB.java

@@ -0,0 +1,70 @@
+/*-
+ *******************************************************************************
+ * Copyright (c) 2011, 2018 Diamond Light Source Ltd.
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors:
+ *    See git history
+ *******************************************************************************/
+package uk.ac.diamond.ispyb.api;
+
+import org.apache.commons.lang3.builder.EqualsBuilder;
+import org.apache.commons.lang3.builder.HashCodeBuilder;
+import org.apache.commons.lang3.builder.ReflectionToStringBuilder;
+
+public class PDB {
+    private Long pdbId;
+    private String name;
+    private String contents;
+    private String code;
+
+    public Long getPdbId() {
+        return pdbId;
+    }
+
+    public void setPdbId(Long pdbId) {
+        this.pdbId = pdbId;
+    }
+
+    public String getName() {
+        return name;
+    }
+
+    public void setName(String name) {
+        this.name = name;
+    }
+
+    public String getContents() {
+        return contents;
+    }
+
+    public void setContents(String contents) {
+        this.contents = contents;
+    }
+
+    public String getCode() {
+        return code;
+    }
+
+    public void setCode(String code) {
+        this.code = code;
+    }
+
+    @Override
+    public String toString() {
+        return ReflectionToStringBuilder.toString(this);
+    }
+
+    @Override
+    public int hashCode() {
+        return HashCodeBuilder.reflectionHashCode(this);
+    }
+
+    @Override
+    public boolean equals(Object that) {
+        return EqualsBuilder.reflectionEquals(this, that);
+    };
+}

src/main/java/uk/ac/diamond/ispyb/api/Sample.java

@@ -31,7 +31,8 @@ public class Sample {
     private String sampleTypeName;
     private String sampleTypeComments;
     private String sampleTypeSpaceGroup;
-
+    private Long orderInGroup;
+    private String typeInGroup;
 
     public Long getSampleId() {
         return sampleId;
@@ -153,6 +154,22 @@ public void setSampleTypeSpaceGroup(String sampleTypeSpaceGroup) {
         this.sampleTypeSpaceGroup = sampleTypeSpaceGroup;
     }
 
+    public Long getOrderInGroup() {
+        return orderInGroup;
+    }
+
+    public void setOrderInGroup(Long orderInGroup) {
+        this.orderInGroup = orderInGroup;
+    }
+
+    public String getTypeInGroup() {
+        return typeInGroup;
+    }
+
+    public void setTypeInGroup(String typeInGroup) {
+        this.typeInGroup = typeInGroup;
+    }
+
     @Override
     public String toString() {
         return ReflectionToStringBuilder.toString(this);

src/main/java/uk/ac/diamond/ispyb/api/SampleType.java

@@ -0,0 +1,70 @@
+/*-
+ *******************************************************************************
+ * Copyright (c) 2011, 2018 Diamond Light Source Ltd.
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors:
+ *    See git history
+ *******************************************************************************/
+package uk.ac.diamond.ispyb.api;
+
+import org.apache.commons.lang3.builder.EqualsBuilder;
+import org.apache.commons.lang3.builder.HashCodeBuilder;
+import org.apache.commons.lang3.builder.ReflectionToStringBuilder;
+
+public class SampleType {
+    private Long sampleTypeId;
+    private Long componentId;
+    private String name;
+    private String comments;
+
+    public Long getSampleTypeId() {
+        return sampleTypeId;
+    }
+
+    public void setSampleTypeId(Long sampleTypeId) {
+        this.sampleTypeId = sampleTypeId;
+    }
+
+    public Long getComponentId() {
+        return componentId;
+    }
+
+    public void setComponentId(Long componentId) {
+        this.componentId = componentId;
+    }
+
+    public String getName() {
+        return name;
+    }
+
+    public void setName(String name) {
+        this.name = name;
+    }
+
+    public String getComments() {
+        return comments;
+    }
+
+    public void setComments(String comments) {
+        this.comments = comments;
+    }
+
+    @Override
+    public String toString() {
+        return ReflectionToStringBuilder.toString(this);
+    }
+
+    @Override
+    public int hashCode() {
+        return HashCodeBuilder.reflectionHashCode(this);
+    }
+
+    @Override
+    public boolean equals(Object that) {
+        return EqualsBuilder.reflectionEquals(this, that);
+    };
+}

src/main/java/uk/ac/diamond/ispyb/dao/IspybXpdfDAO.java

@@ -41,10 +41,10 @@ public List<SampleGroup> retrieveSampleGroupsForSample(Long sampleId){
         return templateWrapper.callIspybForListBeans("retrieve_sample_groups_for_sample", SampleGroup.class, map);
     }
 
-    public List<SampleGroup> retrieveSamplesForSampleGroup(Long sampleGroupId){
+    public List<Sample> retrieveSamplesForSampleGroup(Long sampleGroupId){
         Map<String, Object> map = new HashMap<>();
         map.put("sampleGroupId", sampleGroupId);
-        return templateWrapper.callIspybForListBeans("retrieve_samples_for_sample_group", SampleGroup.class, map);
+        return templateWrapper.callIspybForListBeans("retrieve_samples_for_sample_group", Sample.class, map);
     }
 
     public List<Component> retrieveComponentsForSampleType(Long sampleTypeId){
@@ -83,6 +83,20 @@ public Optional<ContainerInfo> retrieveContainerInfoForId(Long containerId) thro
   		return templateWrapper.callIspybForBean("retrieve_container_info_for_id", ContainerInfo.class, map);
   	}
 
+    @Override
+  	public Optional<SampleType> retrieveSampleTypeForSample(Long sampleId) throws SQLException {
+      Map<String, Object> map = new HashMap<>();
+      map.put("sampleId", sampleId);
+  		return templateWrapper.callIspybForBean("retrieve_sample_type_for_sample", SampleType.class, map);
+  	}
+
+    @Override
+  	public List<PDB> retrievePDBsForComponent(Long componentId) throws SQLException {
+      Map<String, Object> map = new HashMap<>();
+      map.put("componentId", componentId);
+      return templateWrapper.callIspybForListBeans("retrieve_pdbs_for_component", PDB.class, map);
+  	}
+
     @Override
     public void close() throws IOException {
         try {

src/test/java/uk/ac/diamond/ispyb/test/XpdfIntegrationTest.java

@@ -27,6 +27,9 @@
 import java.util.List;
 import java.util.ArrayList;
 
+import java.nio.file.Files;
+import java.nio.file.Paths;
+
 import uk.ac.diamond.ispyb.api.*;
 import uk.ac.diamond.ispyb.dao.IspybXpdfDaoFactory;
 
@@ -84,23 +87,43 @@ public void testRetrieveSampleGroupsForSample()throws SQLException, IOException,
 	}
 
 	@Test
-	public void testRetrieveSamplesForSampleGroups()throws SQLException, IOException, InterruptedException {
-		List<SampleGroup> groups = helper.execute(api -> api.retrieveSamplesForSampleGroup(5L));
-		List<SampleGroup> sampleGroups = new ArrayList<SampleGroup>();
-
-		SampleGroup sampleGroup1 = new SampleGroup();
-		sampleGroup1.setSampleId(398824L);
-		sampleGroup1.setOrder(1L);
-		sampleGroup1.setType(SampleGroupType.BACKGROUND.name());
-		sampleGroups.add(sampleGroup1);
-
-		SampleGroup sampleGroup2 = new SampleGroup();
-		sampleGroup2.setSampleId(398827L);
-		sampleGroup2.setOrder(2L);
-		sampleGroup2.setType(SampleGroupType.SAMPLE.name());
-		sampleGroups.add(sampleGroup2);
-
-		assertThat(groups , is(equalTo(sampleGroups)));
+	public void testRetrieveSamplesForSampleGroup()throws SQLException, IOException, InterruptedException {
+		List<Sample> samples = helper.execute(api -> api.retrieveSamplesForSampleGroup(5L));
+		List<Sample> expected = new ArrayList<Sample>();
+
+		Sample sample1 = new Sample();
+		sample1.setSampleId(398824L);
+		sample1.setContainerId(34883L);
+		sample1.setSampleTypeId(333308L);
+		sample1.setSampleName("XPDF-1");
+		sample1.setSampleCode("XPDF-0001");
+		sample1.setSampleComments("Test sample for XPDF");
+
+		sample1.setSampleTypeName("SampleType01");
+		sample1.setSampleTypeComments("sample type comments ...");
+		sample1.setSampleTypeSpaceGroup("P12121");
+
+		sample1.setTypeInGroup("background");
+		sample1.setOrderInGroup(1L);
+		expected.add(sample1);
+
+		Sample sample2 = new Sample();
+		sample2.setSampleId(398827L);
+		sample2.setContainerId(34883L);
+		sample2.setSampleTypeId(333308L);
+		sample2.setSampleName("XPDF-2");
+		sample2.setSampleCode("XPDF-0002");
+		sample2.setSampleComments("Test sample for XPDF");
+
+		sample2.setSampleTypeName("SampleType01");
+		sample2.setSampleTypeComments("sample type comments ...");
+		sample2.setSampleTypeSpaceGroup("P12121");
+
+		sample2.setTypeInGroup("sample");
+		sample2.setOrderInGroup(2L);
+		expected.add(sample2);
+
+		assertThat(samples , is(equalTo(expected)));
 	}
 
 	@Test
@@ -114,6 +137,32 @@ public void testRetrieveComponentsForSampleType()throws SQLException, IOExceptio
 		assertThat(components, is(equalTo(Arrays.asList(component))));
 	}
 
+	@Test
+	public void testRetrieveSampleTypeForSample() throws SQLException, IOException, InterruptedException {
+		Optional<SampleType> sampleType = helper.execute(api -> api.retrieveSampleTypeForSample(398827L));
+
+		SampleType expected = new SampleType();
+		expected.setSampleTypeId(333308L);
+		expected.setComponentId(123497L);
+		expected.setName("SampleType01");
+		expected.setComments("sample type comments ...");
+
+		assertThat(sampleType.get(), is(equalTo(expected)));
+	}
+
+	@Test
+	public void testRetrievePDBsForComponent()throws SQLException, IOException, InterruptedException {
+		List<PDB> pdbs = helper.execute(api -> api.retrievePDBsForComponent(123497L));
+
+		PDB pdb = new PDB();
+		pdb.setPdbId(6L);
+		pdb.setName("ceo2");
+		pdb.setContents(new String(Files.readAllBytes(Paths.get(System.getProperty("user.dir").toString(), "src", "test", "resources", "ceo2.cif"))));
+
+		assertThat(pdbs, is(equalTo(Arrays.asList(pdb))));
+	}
+
+
 	@Test
 	public void testRetrieveDataCollectionPlansForSample()throws SQLException, IOException, InterruptedException {
 		List<DataCollectionPlan> components = helper.execute(api -> api.retrieveDataCollectionPlansForSample(398824L));