From f209db54e72f7996e8ac7bd51788ab30c5d5da28 Mon Sep 17 00:00:00 2001
From: David Hoksza <david.hoksza@uni.lu>
Date: Thu, 20 Jul 2017 17:54:02 +0200
Subject: [PATCH] Model extended to include pdb annotation (species class
extended and added 1:N to uniprot and 1:N to structure). ORM mapping. Unit
tests working. Tested on web server with SNCA.
---
.../services/annotators/PdbAnnotator.java | 97 +++--
.../annotators/PdbBestMappingEntry.java | 25 +-
.../services/annotators/PdbAnnotatorTest.java | 29 +-
.../mapviewer/model/map/species/Species.java | 27 ++
.../model/map/species/field/Structure.java | 344 ++++++++++++++++++
.../map/species/field/UniprotRecord.java | 181 +++++++++
.../map/species/field/AllFieldTests.java | 2 +
.../map/species/field/StructureTest.java | 68 ++++
.../map/species/field/UniprotRecordTest.java | 61 ++++
...ix_db_20171307.sql => fix_db_20170713.sql} | 2 +-
persist/src/db/11.0.1/fix_db_20170720.sql | 62 ++++
.../resources/applicationContext-persist.xml | 2 +
12 files changed, 852 insertions(+), 48 deletions(-)
create mode 100644 model/src/main/java/lcsb/mapviewer/model/map/species/field/Structure.java
create mode 100644 model/src/main/java/lcsb/mapviewer/model/map/species/field/UniprotRecord.java
create mode 100644 model/src/test/java/lcsb/mapviewer/model/map/species/field/StructureTest.java
create mode 100644 model/src/test/java/lcsb/mapviewer/model/map/species/field/UniprotRecordTest.java
rename persist/src/db/11.0.1/{fix_db_20171307.sql => fix_db_20170713.sql} (99%)
create mode 100644 persist/src/db/11.0.1/fix_db_20170720.sql
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java
index 3995f04896..fc3b02a9bf 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java
@@ -24,7 +24,10 @@ import lcsb.mapviewer.model.map.MiriamType;
//import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.modelutils.map.ElementUtils;
+import lcsb.mapviewer.model.map.species.field.Structure;
+import lcsb.mapviewer.model.map.species.field.UniprotRecord;
import com.google.gson.Gson;
import com.google.gson.reflect.TypeToken;
@@ -82,10 +85,10 @@ public class PdbAnnotator extends ElementAnnotator implements IExternalService {
this.setCache(null);
try {
- Collection<MiriamData> pdbMiriamData = uniProtToPdb(new MiriamData(MiriamType.UNIPROT, "P29373"));
+ Collection<Structure> structures = uniProtToPdb(new MiriamData(MiriamType.UNIPROT, "P29373"));
- if (pdbMiriamData.size() > 0){
- if (pdbMiriamData.iterator().next().getResource() != null) { //TODO - is this id?
+ if (structures.size() > 0){
+ if (structures.iterator().next().getPdbId() != null) { //TODO - is this id?
status.setStatus(ExternalServiceStatusType.OK);
} else {
status.setStatus(ExternalServiceStatusType.CHANGED);
@@ -102,48 +105,72 @@ public class PdbAnnotator extends ElementAnnotator implements IExternalService {
return status;
}
- public MiriamData getUnitProt(BioEntity bioEntity) {
+ public Set<MiriamData> getUnitProts(BioEntity bioEntity) {
+ HashSet<MiriamData> mds = new HashSet<MiriamData>();
for (MiriamData md : bioEntity.getMiriamData()) {
if (md.getDataType().equals(MiriamType.UNIPROT)) {
- return md;
+ mds.add(md);
}
}
- return null;
+ return mds.size() > 0 ? mds : null;
}
@Override
public void annotateElement(BioEntity bioEntity) throws AnnotatorException {
if (isAnnotatable(bioEntity)) {
- MiriamData md = getUnitProt(bioEntity);
- if (md == null) {
+ Set<MiriamData> mds = getUnitProts(bioEntity);
+ if (mds == null) {
uniprotAnnotator.annotateElement(bioEntity);
- md = getUnitProt(bioEntity);
+ mds = getUnitProts(bioEntity);
}
/*If no UniProt ID was found, try to search HGNC which then searches UNIPROT
* based on the gene name.
*/
- if (md == null) {
+ if (mds == null) {
hgncAnnotator.annotateElement(bioEntity);
- md = getUnitProt(bioEntity);
+ mds = getUnitProts(bioEntity);
}
- if (md == null) {
+ if (mds == null) {
return;
}
- try {
- Set<MiriamData> annotations = (Set<MiriamData>)uniProtToPdb(md);
- if (annotations.size() == 0) {
- logger.warn(elementUtils.getElementTag(bioEntity) + " No PDB mapping for UniProt ID: " + md.getResource());
- } else {
- bioEntity.addMiriamData(annotations);
- }
- } catch (WrongResponseCodeIOException exception) {
- logger.warn("Response error when trying to find PDB mapping for UniProt ID: " + md.getResource());
- } catch (IOException exception) {
- throw new AnnotatorException(exception);
+ for (MiriamData md : mds) {
+ try {
+ Set<Structure> structures = (Set<Structure>)uniProtToPdb(md);
+ if (structures.size() == 0) {
+ logger.warn(elementUtils.getElementTag(bioEntity) + " No PDB mapping for UniProt ID: " + md.getResource());
+ } else {
+ //add the annotations to the set of annotation irrespective on
+ //which uniprot record the structures belong to (since annotations do
+ //not include concept of hierarchy or complex data types)
+ Set<MiriamData> annotations = new HashSet<MiriamData>();
+ for (Structure s : structures) {
+ annotations.add(new MiriamData(MiriamType.PDB, s.getPdbId()));
+ }
+ bioEntity.addMiriamData(annotations);
+
+ //insert the full information directly into species, .i.e.
+ //create new uniprot record which includes the mapped structures
+ //and add it to the species (bioentity)
+ UniprotRecord ur = new UniprotRecord();
+ ur.setUniprotId(md.getResource());
+ ur.setSpecies((Species)bioEntity);
+ for (Structure s : structures) {
+ s.setUniprot(ur);
+ }
+ ur.setStructures(structures);
+ ((Species)bioEntity).getUniprots().add(ur);
+ }
+ } catch (WrongResponseCodeIOException exception) {
+ logger.warn("Response error when trying to find PDB mapping for UniProt ID: " + md.getResource());
+ } catch (IOException exception) {
+ throw new AnnotatorException(exception);
+ }
+
}
+
}
}
@@ -166,8 +193,8 @@ public class PdbAnnotator extends ElementAnnotator implements IExternalService {
* JSON file with the UniProt to PDB mapping
* @return set of PDB identifiers found on the webpage
*/
- private Collection<MiriamData> processMappingData(String pageContentJson) {
- Collection<MiriamData> result = new HashSet<MiriamData>();
+ private Collection<Structure> processMappingData(String pageContentJson) {
+ Collection<Structure> result = new HashSet<Structure>();
Gson g = new Gson();
java.lang.reflect.Type t = new TypeToken<Map<String, List<PdbBestMappingEntry>>>(){}.getType();
Map<String, List<PdbBestMappingEntry>> m = g.fromJson(pageContentJson, t);
@@ -175,7 +202,8 @@ public class PdbAnnotator extends ElementAnnotator implements IExternalService {
for (String key : m.keySet()){
for(PdbBestMappingEntry e : m.get(key)) {
if (e != null){
- result.add(new MiriamData(MiriamType.PDB, e.pdb_id));
+ result.add(e.convertToStructure());
+ //result.add(new MiriamData(MiriamType.PDB, e.pdb_id));
}
}
}
@@ -231,7 +259,7 @@ public class PdbAnnotator extends ElementAnnotator implements IExternalService {
* @return JSON String with mapping.
* thrown when there is a problem with accessing external database
*/
- public Collection<MiriamData> uniProtToPdb(MiriamData uniprot) throws IOException /*throws UniprotSearchException*/ {
+ public Collection<Structure> uniProtToPdb(MiriamData uniprot) throws IOException {
if (uniprot == null) {
return null;
}
@@ -241,18 +269,9 @@ public class PdbAnnotator extends ElementAnnotator implements IExternalService {
}
String accessUrl = getPdbMappingUrl(uniprot.getResource());
-// try {
- String json = getWebPageContent(accessUrl);
- if (!isJson(json)) {
- return null;
- } else {
- return processMappingData(json);
- }
-
-// } catch (IOException e) {
-// throw new UniprotSearchException("Problem with accessing mapping data: ", e); //TODO
-// }
-
+ String json = getWebPageContent(accessUrl);
+
+ return isJson(json) ? processMappingData(json) : null;
}
@Override
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbBestMappingEntry.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbBestMappingEntry.java
index 00f63e8ddd..c3cf1c9b2c 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbBestMappingEntry.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbBestMappingEntry.java
@@ -1,21 +1,40 @@
package lcsb.mapviewer.annotation.services.annotators;
+import lcsb.mapviewer.model.map.species.field.Structure;
+
/**
* Structure of the PDB entries returned by the PDBe REST API "Best Structures"
*
* @author David Hoksza
*
*/
-public class PdbBestMappingEntry {
- public String end;
+public class PdbBestMappingEntry {
public String chain_id;
public String experimental_method;
public String pdb_id;
public int start;
+ public int end;
public int unp_end;
public double coverage;
public int unp_start;
public double resolution;
public int tax_id;
-
+
+ public Structure convertToStructure() {
+
+ Structure s = new Structure();
+
+ s.setPdbId(this.pdb_id);
+ s.setChainId(this.chain_id);
+ s.setCoverage(this.coverage);
+ s.setResolution(this.resolution);
+ s.setStructStart(this.start);
+ s.setStructEnd(this.end);
+ s.setUnpStart(this.unp_start);
+ s.setUnpEnd(this.unp_end);
+ s.setExperimentalMethod(this.experimental_method);
+ s.setTaxId(this.tax_id);
+
+ return s;
+ }
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotatorTest.java
index c417885b45..a5af588359 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotatorTest.java
@@ -1,10 +1,13 @@
package lcsb.mapviewer.annotation.services.annotators;
import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import static org.mockito.Matchers.anyString;
import static org.mockito.Mockito.when;
+import java.util.Set;
+
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
@@ -18,6 +21,8 @@ import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.Structure;
+import lcsb.mapviewer.model.map.species.field.UniprotRecord;
public class PdbAnnotatorTest extends AnnotationTestFunctions {
@@ -38,8 +43,9 @@ public class PdbAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testAnnotate1() throws Exception {
try {
+ String uniprotId = "P29373";
Species protein = new GenericProtein("id");
- protein.setName("P29373");
+ protein.setName(uniprotId);
/* One needs to have the UniProt ID first.
* This tests simulates situation when the Uniprot annotator
* is called first.
@@ -60,7 +66,20 @@ public class PdbAnnotatorTest extends AnnotationTestFunctions {
}
}
assertTrue("No PDB annotation extracted from pdb annotator", pdb);
-
+
+ Set<UniprotRecord> urs = protein.getUniprots();
+ assertTrue(urs.size() > 0);
+ UniprotRecord ur = null;
+ for (UniprotRecord ur1 : urs) {
+ if (ur1.getUniprotId() == uniprotId) {
+ ur = ur1;
+ }
+ }
+ assertNotNull(ur);
+ Set<Structure> ss = ur.getStructures();
+ assertNotNull(ss);
+ assertTrue(ss.size() > 0);
+ assertTrue(ss.iterator().next().getUniprot() == ur);
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -197,7 +216,7 @@ public class PdbAnnotatorTest extends AnnotationTestFunctions {
WebPageDownloader downloader = pdbAnnotator.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("");
pdbAnnotator.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.DOWN, pdbAnnotator.getServiceStatus().getStatus());
} catch (Exception e) {
@@ -213,7 +232,7 @@ public class PdbAnnotatorTest extends AnnotationTestFunctions {
WebPageDownloader downloader = pdbAnnotator.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("{\"P29373\": [{\"xxx\": 140}]}");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("{\"P29373\": [{\"xxx\": 140}]}");
pdbAnnotator.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.CHANGED, pdbAnnotator.getServiceStatus().getStatus());
} catch (Exception e) {
@@ -234,7 +253,7 @@ public class PdbAnnotatorTest extends AnnotationTestFunctions {
int cntAnnotations1 = protein.getMiriamData().size();
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("\"P29373\": [{\"xxx\": 140}]}");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("\"P29373\": [{\"xxx\": 140}]}");
pdbAnnotator.setWebPageDownloader(mockDownloader);
pdbAnnotator.annotateElement(protein);
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java
index 62875191ca..a873e01f7d 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java
@@ -18,6 +18,7 @@ import org.hibernate.annotations.CascadeType;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
+import lcsb.mapviewer.model.map.species.field.UniprotRecord;
/**
* Structure used for representing information about single element.
@@ -121,6 +122,13 @@ public abstract class Species extends Element {
* Is species hypothetical.
*/
private Boolean hypothetical = null;
+
+ /**
+ * List of uniprot records which are associated with this species.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(fetch = FetchType.EAGER, mappedBy = "species", orphanRemoval = true)
+ private Set<UniprotRecord> uniprots = new HashSet<>();
/**
* Constructor that set element identifier.
@@ -168,6 +176,8 @@ public abstract class Species extends Element {
homodimer = original.getHomodimer();
positionToCompartment = original.getPositionToCompartment();
hypothetical = original.getHypothetical();
+
+ uniprots = original.getUniprots();
// don't copy reaction nodes
}
@@ -404,6 +414,23 @@ public abstract class Species extends Element {
return hypothetical;
}
+ /**
+ * @param uniprots
+ * set of uniprot records for this species
+ * @see #uniprots
+ */
+ public void setUniprots(Set<UniprotRecord> uniprots) {
+ this.uniprots = uniprots;
+ }
+
+ /**
+ * @return the uniprot
+ * @see #uniprots
+ */
+ public Set<UniprotRecord> getUniprots() {
+ return uniprots;
+ }
+
/**
* @param hypothetical
* the hypothetical to set
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/Structure.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/Structure.java
new file mode 100644
index 0000000000..5dbe0b9053
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/Structure.java
@@ -0,0 +1,344 @@
+package lcsb.mapviewer.model.map.species.field;
+
+import java.io.Serializable;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * This class stores structure information as obtained from the SIFTS API
+ * (https://www.ebi.ac.uk/pdbe/api/doc/sifts.html best_structures), which provides
+ * the following fields
+ * pdb_id: the PDB ID which maps to the UniProt ID
+ * chain_id: the specific chain of the PDB which maps to the UniProt ID
+ * coverage: the percent coverage of the entire UniProt sequence
+ * resolution: the resolution of the structure
+ * start: the structure residue number which maps to the start of the mapped sequence
+ * end: the structure residue number which maps to the end of the mapped sequence
+ * unp_start: the sequence residue number which maps to the structure start
+ * unp_end: the sequence residue number which maps to the structure end
+ * experimental_method: type of experiment used to determine structure
+ * tax_id: taxonomic ID of the protein's original organism
+ *
+ * @author David Hoksza
+ *
+ */
+@Entity
+@Table(name = "structure_table")
+//@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
+public class Structure implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+
+ /**
+ * Unique identifier in the database.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "iddb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * Uniprot record to which this structure belongs to.
+ */
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = "uniprot_id", nullable = false)
+ private UniprotRecord uniprot;
+
+ /**
+ * the PDB ID which maps to the UniProt ID
+ */
+ @Column(name = "pdb_id")
+ private String pdbId = null;
+
+ /**
+ * the specific chain of the PDB which maps to the UniProt ID
+ */
+ @Column(name = "chain_id")
+ private String chainId = null;
+
+ /**
+ * the percent coverage of the entire UniProt sequence
+ */
+ @Column(name = "coverage")
+ private Double coverage = null;
+
+ /**
+ * the resolution of the structure
+ */
+ @Column(name = "resolution")
+ private Double resolution = null;
+
+ /**
+ * the structure residue number which maps to the start of the mapped sequence
+ */
+ @Column(name = "struct_start")
+ private Integer structStart = null;
+
+ /**
+ * the structure residue number which maps to the end of the mapped sequence
+ */
+ @Column(name = "struct_end")
+ private Integer structEnd = null;
+
+ /**
+ * the sequence residue number which maps to the structure start
+ */
+ @Column(name = "unp_start")
+ private Integer unpStart = null;
+
+ /**
+ * the sequence residue number which maps to the structure end
+ */
+ @Column(name = "unp_end")
+ private Integer unpEnd = null;
+
+ /**
+ * type of experiment used to determine structure
+ */
+ @Column(name = "experimental_method")
+ private String experimentalMethod = null;
+
+ /**
+ * taxonomic ID of the protein's original organism
+ */
+ @Column(name = "tax_id")
+ private Integer taxId = null;
+
+ /**
+ * Default constructor.
+ */
+ public Structure() {
+ }
+
+ /**
+ * Constructor that initialize object with the data taken from the parameter.
+ *
+ * @param s
+ * original object from which data is taken
+ */
+ public Structure(Structure s) {
+ this.id = s.id;
+ this.uniprot = s.uniprot;
+ this.pdbId = s.pdbId;
+ this.chainId = s.chainId;
+ this.coverage = s.coverage;
+ this.resolution = s.resolution;
+ this.structStart = s.structStart;
+ this.structEnd = s.structEnd;
+ this.unpStart = s.unpStart;
+ this.unpEnd = s.unpEnd;
+ this.experimentalMethod = s.experimentalMethod;
+ this.taxId = s.taxId;
+ }
+
+ /**
+ * Creates copy of the object.
+ *
+ * @return copy of the object.
+ */
+ public Structure copy() {
+ if (this.getClass() == Structure.class) {
+ return new Structure(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ /**
+ * @return the idModificationResidue
+ * @see #id
+ */
+ public int getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ /**
+ * @return the uniprot
+ */
+ public UniprotRecord getUniprot() {
+ return uniprot;
+ }
+
+ /**
+ * @param uniprot the uniprot to set
+ */
+ public void setUniprot(UniprotRecord uniprot) {
+ this.uniprot = uniprot;
+ }
+
+ /**
+ * @return the pdbId
+ */
+ public String getPdbId() {
+ return pdbId;
+ }
+
+ /**
+ * @param pdbId the pdbId to set
+ */
+ public void setPdbId(String pdbId) {
+ this.pdbId = pdbId;
+ }
+
+ /**
+ * @return the chainId
+ */
+ public String getChainId() {
+ return chainId;
+ }
+
+ /**
+ * @param chainId the chainId to set
+ */
+ public void setChainId(String chainId) {
+ this.chainId = chainId;
+ }
+
+ /**
+ * @return the coverage
+ */
+ public Double getCoverage() {
+ return coverage;
+ }
+
+ /**
+ * @param coverage the coverage to set
+ */
+ public void setCoverage(Double coverage) {
+ this.coverage = coverage;
+ }
+
+ /**
+ * @return the resolution
+ */
+ public Double getResolution() {
+ return resolution;
+ }
+
+ /**
+ * @param resolution the resolution to set
+ */
+ public void setResolution(Double resolution) {
+ this.resolution = resolution;
+ }
+
+ /**
+ * @return the structStart
+ */
+ public Integer getStructStart() {
+ return structStart;
+ }
+
+ /**
+ * @param structStart the structStart to set
+ */
+ public void setStructStart(Integer structStart) {
+ this.structStart = structStart;
+ }
+
+ /**
+ * @return the structEnd
+ */
+ public Integer getStructEnd() {
+ return structEnd;
+ }
+
+ /**
+ * @param structEnd the structEnd to set
+ */
+ public void setStructEnd(Integer structEnd) {
+ this.structEnd = structEnd;
+ }
+
+ /**
+ * @return the unpStart
+ */
+ public Integer getUnpStart() {
+ return unpStart;
+ }
+
+ /**
+ * @param unpStart the unpStart to set
+ */
+ public void setUnpStart(Integer unpStart) {
+ this.unpStart = unpStart;
+ }
+
+ /**
+ * @return the unpEnd
+ */
+ public Integer getUnpEnd() {
+ return unpEnd;
+ }
+
+ /**
+ * @param unpEnd the unpEnd to set
+ */
+ public void setUnpEnd(Integer unpEnd) {
+ this.unpEnd = unpEnd;
+ }
+
+ /**
+ * @return the experimentalMethod
+ */
+ public String getExperimentalMethod() {
+ return experimentalMethod;
+ }
+
+ /**
+ * @param experimentalMethod the experimentalMethod to set
+ */
+ public void setExperimentalMethod(String experimentalMethod) {
+ this.experimentalMethod = experimentalMethod;
+ }
+
+ /**
+ * @return the taxId
+ */
+ public Integer getTaxId() {
+ return taxId;
+ }
+
+ /**
+ * @param taxId the taxId to set
+ */
+ public void setTaxId(Integer taxId) {
+ this.taxId = taxId;
+ }
+
+ /* (non-Javadoc)
+ * @see java.lang.Object#toString()
+ */
+ @Override
+ public String toString() {
+ return "Structure [pdbId=" + pdbId + ", chainId=" + chainId + ", coverage=" + coverage + ", resolution="
+ + resolution + ", structStart=" + structStart + ", structEnd=" + structEnd + ", unpStart=" + unpStart
+ + ", unpEnd=" + unpEnd + ", experimentalMethod=" + experimentalMethod + ", taxId=" + taxId + "]";
+ }
+
+
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/UniprotRecord.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/UniprotRecord.java
new file mode 100644
index 0000000000..92346cb4f2
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/UniprotRecord.java
@@ -0,0 +1,181 @@
+package lcsb.mapviewer.model.map.species.field;
+
+import java.io.Serializable;
+import java.util.HashSet;
+import java.util.Set;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
+import javax.persistence.Table;
+
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * This class stores basically only uniprot Id which is used as mapping between
+ * species and uniprot record.
+ *
+ * @author David Hoksza
+ *
+ */
+
+@Entity
+@Table(name = "uniprot_table")
+//@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
+public class UniprotRecord implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+
+ /**
+ * Unique identifier in the database.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "iddb", unique = true, nullable = false)
+ private int id;
+
+
+ /**
+ * ID of the uniprot record
+ */
+ @Column(name = "uniprot_id", nullable = false)
+ private String uniprotId = "";
+
+ /**
+ * Species to which this uniprot record belongs to.
+ */
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = "element_id", nullable = false)
+ private Species species;
+
+ /**
+ * List of uniprot records which are associated with this species.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(fetch = FetchType.EAGER, mappedBy = "uniprot", orphanRemoval = true)
+ private Set<Structure> structures = new HashSet<>();
+
+ /**
+ * Default constructor.
+ */
+ public UniprotRecord() {
+ }
+
+ /**
+ * Constructor that initialize object with the data taken from the parameter.
+ *
+ * @param ur
+ * original object from which data is taken
+ */
+ public UniprotRecord(UniprotRecord ur) {
+ this.id = ur.id;
+ this.uniprotId = ur.uniprotId;
+ this.species = ur.species;
+ }
+
+ /**
+ * Creates copy of the object.
+ *
+ * @return copy of the object.
+ */
+ public UniprotRecord copy() {
+ if (this.getClass() == UniprotRecord.class) {
+ return new UniprotRecord(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+
+
+ /* (non-Javadoc)
+ * @see java.lang.Object#toString()
+ */
+ @Override
+ public String toString() {
+ return "UniprotRecord [id=" + id + ", uniprotId=" + uniprotId + ", species=" + species + ", structures="
+ + structures + "]";
+ }
+
+ /**
+ * @return the idModificationResidue
+ * @see #id
+ */
+ public int getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ /**
+ * @return the uniprot id
+ * @see #uniprotId
+ */
+ public String getUniprotId() {
+ return uniprotId;
+ }
+
+ /**
+ * @param uniprot id
+ * the id to set
+ * @see #idModificationResidue
+ */
+ public void setUniprotId(String uniprotId) {
+ this.uniprotId = uniprotId;
+ }
+
+ /**
+ * @param species
+ * species to which this uniprot record belongs
+ * @see #species
+ */
+ public void setSpecies(Species species) {
+ this.species = species;
+ }
+
+ /**
+ * @return the species
+ * @see #species
+ */
+ public Species getSpecies() {
+ return species;
+ }
+
+ /**
+ * @param structures
+ * set of structures mapped to this uniprot record
+ * @see #structures
+ */
+ public void setStructures(Set<Structure> structures) {
+ this.structures = structures;
+ }
+
+ /**
+ * @return the structures
+ * @see #structures
+ */
+ public Set<Structure> getStructures() {
+ return structures;
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/field/AllFieldTests.java b/model/src/test/java/lcsb/mapviewer/model/map/species/field/AllFieldTests.java
index 3cc809ba3b..512ff1dab9 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/field/AllFieldTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/field/AllFieldTests.java
@@ -11,6 +11,8 @@ import org.junit.runners.Suite.SuiteClasses;
ModificationResidueTest.class, //
PositionToCompartmentTest.class, //
RnaRegionTest.class,//
+ StructureTest.class,//
+ UniprotRecordTest.class,//
})
public class AllFieldTests {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/field/StructureTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/field/StructureTest.java
new file mode 100644
index 0000000000..ddcce64170
--- /dev/null
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/field/StructureTest.java
@@ -0,0 +1,68 @@
+package lcsb.mapviewer.model.map.species.field;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import java.util.HashSet;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class StructureTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetters() {
+ Structure s = new Structure();
+ UniprotRecord ur = new UniprotRecord();
+ ur.setId(100);
+ ur.setUniprotId("P29373");
+
+ int id = 101;
+ s.setUniprot(ur);
+ s.setId(id);
+
+ ur.setStructures(new HashSet<Structure>() {private static final long serialVersionUID = 1L; {add(s);} });
+
+ assertEquals(ur, s.getUniprot());
+ assertEquals(id, s.getId());
+ assertEquals(s, ur.getStructures().iterator().next());
+ }
+
+ @Test
+ public void testCopy() {
+ Structure s = new Structure().copy();
+ assertNotNull(s);
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ Structure s = Mockito.spy(Structure.class);
+ try {
+ s.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/field/UniprotRecordTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/field/UniprotRecordTest.java
new file mode 100644
index 0000000000..38460ffb23
--- /dev/null
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/field/UniprotRecordTest.java
@@ -0,0 +1,61 @@
+package lcsb.mapviewer.model.map.species.field;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class UniprotRecordTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetters() {
+ UniprotRecord ur = new UniprotRecord();
+ Species species = new GenericProtein("id");
+ int id = 94;
+
+ ur.setSpecies(species);
+ ur.setId(id);
+
+ assertEquals(species, ur.getSpecies());
+ assertEquals(id, ur.getId());
+ }
+
+ @Test
+ public void testCopy() {
+ UniprotRecord ur = new UniprotRecord().copy();
+ assertNotNull(ur);
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ UniprotRecord ur = Mockito.spy(UniprotRecord.class);
+ try {
+ ur.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+
+ }
+ }
+
+}
diff --git a/persist/src/db/11.0.1/fix_db_20171307.sql b/persist/src/db/11.0.1/fix_db_20170713.sql
similarity index 99%
rename from persist/src/db/11.0.1/fix_db_20171307.sql
rename to persist/src/db/11.0.1/fix_db_20170713.sql
index 94523a2c4d..c0f3e49c8e 100644
--- a/persist/src/db/11.0.1/fix_db_20171307.sql
+++ b/persist/src/db/11.0.1/fix_db_20170713.sql
@@ -1,2 +1,2 @@
-DELETE FROM cache_type WHERE classname = 'lcsb.mapviewer.annotation.services.annotators.PdbAnnotator'
+DELETE FROM cache_type WHERE classname = 'lcsb.mapviewer.annotation.services.annotators.PdbAnnotator'
INSERT INTO cache_type(validity, classname) VALUES (365, 'lcsb.mapviewer.annotation.services.annotators.PdbAnnotator')
\ No newline at end of file
diff --git a/persist/src/db/11.0.1/fix_db_20170720.sql b/persist/src/db/11.0.1/fix_db_20170720.sql
new file mode 100644
index 0000000000..71cf63626c
--- /dev/null
+++ b/persist/src/db/11.0.1/fix_db_20170720.sql
@@ -0,0 +1,62 @@
+CREATE SEQUENCE uniprot_table_iddb_seq
+ INCREMENT 1
+ MINVALUE 1
+ MAXVALUE 9223372036854775807
+ START 1
+ CACHE 1;
+
+-- 1:N mapping between element and its uniprot mappings, each of which is then used to map (PDB) structures to it
+CREATE TABLE uniprot_table
+(
+ iddb integer NOT NULL DEFAULT nextval('uniprot_table_iddb_seq'::regclass),
+ element_id integer NOT NULL,
+ uniprot_id character varying(255) NOT NULL,
+ CONSTRAINT uniprot_pkey PRIMARY KEY (iddb),
+ CONSTRAINT uniprot_element_fk FOREIGN KEY (element_id)
+ REFERENCES public.element_table (iddb) MATCH SIMPLE
+ ON UPDATE CASCADE ON DELETE CASCADE
+);
+
+
+CREATE SEQUENCE structure_table_iddb_seq
+ INCREMENT 1
+ MINVALUE 1
+ MAXVALUE 9223372036854775807
+ START 1
+ CACHE 1;
+
+/*
+based on https://www.ebi.ac.uk/pdbe/api/doc/sifts.html best_structures API
+
+ pdb_id: the PDB ID which maps to the UniProt ID
+ chain_id: the specific chain of the PDB which maps to the UniProt ID
+ coverage: the percent coverage of the entire UniProt sequence
+ resolution: the resolution of the structure
+ start: the structure residue number which maps to the start of the mapped sequence
+ end: the structure residue number which maps to the end of the mapped sequence
+ unp_start: the sequence residue number which maps to the structure start
+ unp_end: the sequence residue number which maps to the structure end
+ experimental_method: type of experiment used to determine structure
+ tax_id: taxonomic ID of the protein's original organism
+*/
+CREATE TABLE structure_table
+(
+ iddb integer NOT NULL DEFAULT nextval('structure_table_iddb_seq'::regclass),
+ uniprot_id integer NOT NULL,
+ pdb_id character varying(255) NOT NULL, --should be character(4), but to be on the safe side...
+ chain_id character varying(1)NOT NULL,
+ struct_start integer,
+ struct_end integer,
+ unp_start integer,
+ unp_end integer,
+ experimental_method character varying(255),
+ coverage double precision,
+ resolution double precision,
+ tax_id integer,
+ CONSTRAINT structure_pkey PRIMARY KEY (iddb),
+ CONSTRAINT structure_uniprot_fk FOREIGN KEY (uniprot_id)
+ REFERENCES public.uniprot_table (iddb) MATCH SIMPLE
+ ON UPDATE CASCADE ON DELETE CASCADE
+);
+
+
diff --git a/persist/src/main/resources/applicationContext-persist.xml b/persist/src/main/resources/applicationContext-persist.xml
index 896e204ca1..896a8cafaf 100644
--- a/persist/src/main/resources/applicationContext-persist.xml
+++ b/persist/src/main/resources/applicationContext-persist.xml
@@ -185,6 +185,8 @@
<value>lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion</value>
<value>lcsb.mapviewer.model.map.species.field.ModificationResidue</value>
<value>lcsb.mapviewer.model.map.species.field.RnaRegion</value>
+ <value>lcsb.mapviewer.model.map.species.field.UniprotRecord</value>
+ <value>lcsb.mapviewer.model.map.species.field.Structure</value>
<value>lcsb.mapviewer.model.map.layout.graphics.Layer</value>
<value>lcsb.mapviewer.model.map.layout.graphics.LayerText</value>
--
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