diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
index fb21e1e31b1a74f5dfe67cd9121e222938112d03..b82f08768c430eb57a03f6a152bc2e8c9fa391bc 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
@@ -23,6 +23,7 @@ import lcsb.mapviewer.annotation.services.annotators.EnsemblAnnotator;
import lcsb.mapviewer.annotation.services.annotators.EntrezAnnotator;
import lcsb.mapviewer.annotation.services.annotators.GoAnnotator;
import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
+import lcsb.mapviewer.annotation.services.annotators.PdbAnnotator;
import lcsb.mapviewer.annotation.services.annotators.ReconAnnotator;
import lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator;
import lcsb.mapviewer.common.IProgressUpdater;
@@ -85,6 +86,12 @@ public class ModelAnnotator {
*/
@Autowired
private UniprotAnnotator uniprotAnnotator;
+
+ /**
+ * PDB annotator.
+ */
+ @Autowired
+ private PdbAnnotator pdbAnnotator;
/**
* Recon annotator.
@@ -142,6 +149,7 @@ public class ModelAnnotator {
addAnnotator(uniprotAnnotator);
addAnnotator(goAnnotator);
addAnnotator(hgncAnnotator);
+ addAnnotator(pdbAnnotator);
addAnnotator(reconAnnotator);
addAnnotator(entrezAnnotator);
addAnnotator(ensemblAnnotator);
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
index dde647a3bf294e8e2aaeeb1e3744ae451ee458c8..7c28ab4f17f65dc43031067f609509afd2d17ed2 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
@@ -40,7 +40,7 @@ public abstract class ElementAnnotator extends CachableInterface {
private final List<Class<? extends BioEntity>> validClasses = new ArrayList<>();
/**
- * Should be this annotator used as a default annotatior.
+ * Should be this annotator used as a default annotator.
*/
private boolean isDefault = false;
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
new file mode 100644
index 0000000000000000000000000000000000000000..4c2d0110f86ab6b7db470889fc34cba371caff6c
--- /dev/null
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java
@@ -0,0 +1,260 @@
+package lcsb.mapviewer.annotation.services.annotators;
+
+import java.io.IOException;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.Set;
+import java.util.Map;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.WebPageDownloader;
+import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
+import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
+import lcsb.mapviewer.annotation.services.IExternalService;
+import lcsb.mapviewer.annotation.services.WrongResponseCodeIOException;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+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.modelutils.map.ElementUtils;
+
+import com.google.gson.Gson;
+import com.google.gson.reflect.TypeToken;
+
+/**
+ * This is a class that implements a backend to the EBI's PDB SIFTS REST API mapping.
+ *
+ * @author David Hoksza
+ *
+ */
+/**
+ * @author hellb
+ *
+ */
+public class PdbAnnotator extends ElementAnnotator implements IExternalService {
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(PdbAnnotator.class);
+
+ /**
+ * Class used for some simple operations on {@link BioEntity} elements.
+ */
+ private ElementUtils elementUtils = new ElementUtils();
+
+ /**
+ * Service used for annotation of proteins using {@link MiriamType#UNIPROT
+ * uniprot}.
+ */
+ @Autowired
+ private UniprotAnnotator uniprotAnnotator;
+
+
+ /**
+ * Default constructor.
+ */
+ public PdbAnnotator() {
+ super(PdbAnnotator.class, new Class[] { Protein.class, Rna.class }, false);
+ }
+
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
+
+ GeneralCacheInterface cacheCopy = getCache();
+ this.setCache(null);
+
+ try {
+ Collection<MiriamData> pdbMiriamData = uniProtToPdb(new MiriamData(MiriamType.UNIPROT, "P29373"));
+
+ if (pdbMiriamData.size() > 0){
+ if (pdbMiriamData.iterator().next().getResource() != null) { //TODO - is this id?
+ status.setStatus(ExternalServiceStatusType.OK);
+ } else {
+ status.setStatus(ExternalServiceStatusType.CHANGED);
+ }
+ }
+ else {
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ }
+ } catch (Exception e) {
+ logger.error(status.getName() + " is down", e);
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ }
+ this.setCache(cacheCopy);
+ return status;
+ }
+
+ public MiriamData getUnitProt(BioEntity bioEntity) {
+ for (MiriamData md : bioEntity.getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.UNIPROT)) {
+ return md;
+ }
+ }
+ return null;
+ }
+
+ @Override
+ public void annotateElement(BioEntity bioEntity) throws AnnotatorException {
+ if (isAnnotatable(bioEntity)) {
+ MiriamData md = getUnitProt(bioEntity);
+ if (md == null) {
+ uniprotAnnotator.annotateElement(bioEntity);
+ md = getUnitProt(bioEntity);
+ }
+
+ if (md == 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);
+ }
+ }
+ }
+
+ /**
+ * Returns url to JSON with best mapping PDB entries given the UniProt entry.
+ *
+ * @param uniprotId
+ * uniprot identifier
+ * @return url with best mapping PDB entries to the UniProt entry
+ */
+ private String getPdbMappingUrl(String uniprotId) {
+ return "https://www.ebi.ac.uk/pdbe/api/mappings/best_structures/" + uniprotId;
+ }
+
+ /**
+ * Parse UniProt-to-PDB mapping JSON file.
+ * {@link MiriamType#PDB} and returns them.
+ *
+ * @param pageContentJson
+ * 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>();
+ 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);
+ if (m != null){
+ for (String key : m.keySet()){
+ for(PdbBestMappingEntry e : m.get(key)) {
+ result.add(new MiriamData(MiriamType.PDB, e.pdb_id));
+ }
+ }
+ }
+
+ return result;
+ }
+
+ @Override
+ public Object refreshCacheQuery(Object query) throws SourceNotAvailable {
+ String name;
+ String result = null;
+ if (query instanceof String) {
+ name = (String) query;
+ if (name.startsWith("http")) {
+ try {
+ result = getWebPageContent(name);
+ } catch (IOException e) {
+ throw new SourceNotAvailable(e);
+ }
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with query: " + query);
+ }
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
+ }
+ return result;
+ }
+
+
+ /**
+ * Tests if given input string is a valid JSON document.
+ *
+ * @param json
+ * Input document as a string.
+ * @return True or false dependent on whether the input string is a valid JSON document
+ */
+ public static boolean isJson(String json) {
+ Gson gson = new Gson();
+ try {
+ gson.fromJson(json, Object.class);
+ return true;
+ } catch (com.google.gson.JsonSyntaxException ex) {
+ return false;
+ }
+ }
+
+ /**
+ * Transform UniProt identifier into PDB IDs.
+ *
+ * @param uniprot
+ * {@link MiriamData} with UniProt identifier
+ * @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*/ {
+ if (uniprot == null) {
+ return null;
+ }
+
+ if (!MiriamType.UNIPROT.equals(uniprot.getDataType())) {
+ throw new InvalidArgumentException(MiriamType.UNIPROT + " expected.");
+ }
+
+ 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
+// }
+
+ }
+
+ @Override
+ public String getCommonName() {
+ return MiriamType.PDB.getCommonName();
+ }
+
+ @Override
+ public String getUrl() {
+ return MiriamType.PDB.getDbHomepage();
+ }
+
+ @Override
+ protected WebPageDownloader getWebPageDownloader() {
+ return super.getWebPageDownloader();
+ }
+
+ @Override
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ super.setWebPageDownloader(webPageDownloader);
+ }
+
+}
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
new file mode 100644
index 0000000000000000000000000000000000000000..00f63e8ddd84ed391415351cf9cbd8126ee9b691
--- /dev/null
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbBestMappingEntry.java
@@ -0,0 +1,21 @@
+package lcsb.mapviewer.annotation.services.annotators;
+
+/**
+ * Structure of the PDB entries returned by the PDBe REST API "Best Structures"
+ *
+ * @author David Hoksza
+ *
+ */
+public class PdbBestMappingEntry {
+ public String end;
+ public String chain_id;
+ public String experimental_method;
+ public String pdb_id;
+ public int start;
+ public int unp_end;
+ public double coverage;
+ public int unp_start;
+ public double resolution;
+ public int tax_id;
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AllAnnotatorTests.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AllAnnotatorTests.java
index 71dae4246b80c0f32a5ea1543bb31b73120d149d..218bd397eec6b1d0c43b14046b61f4db209aa6ed 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AllAnnotatorTests.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AllAnnotatorTests.java
@@ -13,6 +13,7 @@ import org.junit.runners.Suite.SuiteClasses;
EntrezAnnotatorTest.class, //
GoAnnotatorTest.class, //
HgncAnnotatorTest.class, //
+ PdbAnnotatorTest.class, //
ReconAnnotatorTest.class, //
UniprotAnnotatorTest.class, //
})
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
new file mode 100644
index 0000000000000000000000000000000000000000..f50382c6fb8e2512988e7bc90dbe1a3b964efece
--- /dev/null
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotatorTest.java
@@ -0,0 +1,194 @@
+package lcsb.mapviewer.annotation.services.annotators;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import static org.mockito.Matchers.anyString;
+import static org.mockito.Mockito.when;
+
+import java.io.IOException;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.AnnotationTestFunctions;
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.GeneralCacheWithExclusion;
+import lcsb.mapviewer.annotation.cache.WebPageDownloader;
+import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+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;
+
+public class PdbAnnotatorTest extends AnnotationTestFunctions {
+
+ @Autowired
+ PdbAnnotator pdbAnnotator;
+
+ @Autowired
+ UniprotAnnotator uniprotAnnotator;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testAnnotate1() throws Exception {
+ try {
+ Species protein = new GenericProtein("id");
+ protein.setName("P29373");
+ //First, annotate protein by UniProt which is the used in the PDB annotator
+ uniprotAnnotator.annotateElement(protein);
+ int cntAnnotations1 = protein.getMiriamData().size();
+ pdbAnnotator.annotateElement(protein);
+ int cntAnnotations2 = protein.getMiriamData().size();
+
+ assertTrue(cntAnnotations2 > cntAnnotations1);
+
+ boolean pdb = false;
+
+ for (MiriamData md : protein.getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.PDB)) {
+ pdb = true;
+ break;
+ }
+ }
+ assertTrue("No PDB annotation extracted from pdb annotator", pdb);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotateNotUniprotAnnodated() throws Exception {
+ try {
+ Species protein = new GenericProtein("id");
+ protein.setName("P29373");
+ pdbAnnotator.annotateElement(protein);
+
+ assertTrue("UniProt annotation in PDB annotator failed", protein.getMiriamData().size() > 0);
+
+ boolean pdb = false;
+
+ for (MiriamData md : protein.getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.PDB)) {
+ pdb = true;
+ break;
+ }
+ }
+ assertTrue("No PDB annotation extracted from PDB annotator", pdb);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotateInvalidUniprot() throws Exception {
+ try {
+ Species protein = new GenericProtein("id");
+ protein.setName("bla");
+ pdbAnnotator.annotateElement(protein);
+
+ assertEquals(0, protein.getMiriamData().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotateValidUniprotInexistingPdb() throws Exception {
+ try {
+ Species protein = new GenericProtein("id");
+ protein.setName("Q88VP8");
+ pdbAnnotator.annotateElement(protein);
+
+ boolean pdb = false;
+ for (MiriamData md : protein.getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.PDB)) {
+ pdb = true;
+ break;
+ }
+ }
+ assertTrue("PDB mapping found for structure for which no should be available", !pdb);
+ assertEquals(1, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSimulateDownStatus() throws Exception {
+ WebPageDownloader downloader = pdbAnnotator.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString())).thenReturn("");
+ pdbAnnotator.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.DOWN, pdbAnnotator.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ pdbAnnotator.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testSimulateChangedStatus() throws Exception {
+ WebPageDownloader downloader = pdbAnnotator.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString())).thenReturn("{\"P29373\": [{\"xxx\": 140}]}");
+ pdbAnnotator.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.CHANGED, pdbAnnotator.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ pdbAnnotator.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testSimulateInvalidJson() throws Exception {
+ WebPageDownloader downloader = pdbAnnotator.getWebPageDownloader();
+ try {
+ Species protein = new GenericProtein("id");
+ protein.setName("Q88VP8");
+ uniprotAnnotator.annotateElement(protein);
+ int cntAnnotations1 = protein.getMiriamData().size();
+
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString())).thenReturn("\"P29373\": [{\"xxx\": 140}]}");
+ pdbAnnotator.setWebPageDownloader(mockDownloader);
+
+ pdbAnnotator.annotateElement(protein);
+ int cntAnnotations2 = protein.getMiriamData().size();
+ assertTrue(cntAnnotations1 == cntAnnotations2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ pdbAnnotator.setWebPageDownloader(downloader);
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
index cd8b930f1703058b08f2138e4688354fc45bfa4a..31fa7c1338738febf5798debcde11f33fafa604a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
@@ -265,6 +265,14 @@ public enum MiriamType {
"http://www.pantherdb.org/", //
new String[] { "urn:miriam:panther.family", "urn:miriam:panther" }, //
new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000060"), //
+
+ /**
+ * PDB: http://www.pdbe.org/.
+ */
+ PDB("Protein Data Bank", //
+ "http://www.pdbe.org/", //
+ "urn:miriam:pdb", //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000020"),
/**
* Protein Family Database: http://pfam.xfam.org/.
diff --git a/persist/src/db/11.0.1/fix_db_20171307.sql b/persist/src/db/11.0.1/fix_db_20171307.sql
new file mode 100644
index 0000000000000000000000000000000000000000..94523a2c4d08e87d3b5af2767a02ebd675043bea
--- /dev/null
+++ b/persist/src/db/11.0.1/fix_db_20171307.sql
@@ -0,0 +1,2 @@
+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