diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java
index 7cae5de69da970c92262fe42c47ea5c0be0d4203..45c6daa1ebe3375bfb63983866742ab91bd960b3 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java
@@ -3,6 +3,7 @@ package lcsb.mapviewer.annotation.services;
import java.io.IOException;
import java.net.URLEncoder;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
@@ -111,11 +112,6 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
@Autowired
private HgncAnnotator hgncAnnotator;
- /**
- * Object used to access information about organism taxonomy.
- */
- @Autowired
- private TaxonomyBackend taxonomyBackend;
/**
* Default constructor.
@@ -180,7 +176,7 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
if (node.getNodeType() == Node.ELEMENT_NODE) {
if (node.getNodeName().equalsIgnoreCase("organism")) {
// node with information abou organism
- target.setOrganism(taxonomyBackend.getByName(node.getTextContent()));
+ target.setOrganism(getTaxonomyBackend().getByName(node.getTextContent()));
} else if (node.getNodeName().equalsIgnoreCase("pref_name")) {
// node with information about name
target.setName(node.getTextContent());
@@ -541,9 +537,9 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
}
@Override
- public List<Drug> getDrugListByTarget(MiriamData target) throws DrugSearchException {
- List<Drug> result = new ArrayList<Drug>();
- List<MiriamData> uniprotData = new ArrayList<MiriamData>();
+ public List<Drug> getDrugListByTarget(MiriamData target, Collection<MiriamData> organisms) throws DrugSearchException {
+ List<Drug> result = new ArrayList<>();
+ List<MiriamData> uniprotData = new ArrayList<>();
if (MiriamType.HGNC_SYMBOL.equals(target.getDataType())) {
try {
uniprotData = hgncAnnotator.hgncToUniprot(target);
@@ -561,7 +557,10 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
logger.warn("Too many uniprot ids. Only first will be taken");
}
try {
- String page = getWebPageContent(URL_TARGET_FROM_UNIPROT + uniprotData.get(0).getResource());
+ String url = URL_TARGET_FROM_UNIPROT + uniprotData.get(0).getResource();
+ logger.debug(url);
+
+ String page = getWebPageContent(url);
Set<String> drugNames = new HashSet<>();
Document document = getXmlDocumentFromString(page);
@@ -573,14 +572,17 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
Node node = nodeList.item(i);
if (node.getNodeType() == Node.ELEMENT_NODE) {
if (node.getNodeName().equalsIgnoreCase("target")) {
- Node chemblTargetIdNode = getNode("target_chembl_id", node);
- MiriamData targetMiriam = new MiriamData(MiriamType.CHEMBL_TARGET, chemblTargetIdNode.getTextContent());
- List<Drug> drugs = getDrugsByChemblTarget(targetMiriam);
- for (Drug drug : drugs) {
- // don't add duplicates
- if (!drugNames.contains(drug.getName())) {
- drugNames.add(drug.getName());
- result.add(drug);
+ String organismName = getNode("organism", node).getTextContent();
+ if (organismMatch(organismName, organisms)) {
+ Node chemblTargetIdNode = getNode("target_chembl_id", node);
+ MiriamData targetMiriam = new MiriamData(MiriamType.CHEMBL_TARGET, chemblTargetIdNode.getTextContent());
+ List<Drug> drugs = getDrugsByChemblTarget(targetMiriam);
+ for (Drug drug : drugs) {
+ // don't add duplicates
+ if (!drugNames.contains(drug.getName())) {
+ drugNames.add(drug.getName());
+ result.add(drug);
+ }
}
}
}
@@ -597,6 +599,7 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
}
+
/**
* Returns list of drugs found by target identified in the paramter.
*
@@ -664,23 +667,6 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
super.setWebPageDownloader(webPageDownloader);
}
- /**
- * @return the taxonomyBackend
- * @see #taxonomyBackend
- */
- protected TaxonomyBackend getTaxonomyBackend() {
- return taxonomyBackend;
- }
-
- /**
- * @param taxonomyBackend
- * the taxonomyBackend to set
- * @see #taxonomyBackend
- */
- protected void setTaxonomyBackend(TaxonomyBackend taxonomyBackend) {
- this.taxonomyBackend = taxonomyBackend;
- }
-
/**
* @return the hgncAnnotator
* @see #hgncAnnotator
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugAnnotation.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugAnnotation.java
index 64d4f11adc23464be114a36f4f4eb37902a1f814..9873ea124319c2cad0f9750e5f85e9d56af1a1ba 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugAnnotation.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugAnnotation.java
@@ -6,6 +6,9 @@ import java.util.HashSet;
import java.util.List;
import java.util.Set;
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+
import lcsb.mapviewer.annotation.cache.CachableInterface;
import lcsb.mapviewer.annotation.cache.XmlSerializer;
import lcsb.mapviewer.annotation.data.Drug;
@@ -20,11 +23,22 @@ import lcsb.mapviewer.model.map.MiriamData;
*/
public abstract class DrugAnnotation extends CachableInterface {
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(DrugAnnotation.class);
+
/**
* Object that allows to serialize {@link Drug} elements into xml string and
* deserialize xml into {@link Drug} objects.
*/
- private XmlSerializer<Drug> drugSerializer;
+ private XmlSerializer<Drug> drugSerializer;
+
+ /**
+ * Object used to access information about organism taxonomy.
+ */
+ @Autowired
+ private TaxonomyBackend taxonomyBackend;
/**
* Default constructor. Initializes structures used for transforming
@@ -59,7 +73,11 @@ public abstract class DrugAnnotation extends CachableInterface {
* thrown when there are problems with finding drug
*/
- public abstract List<Drug> getDrugListByTarget(MiriamData target) throws DrugSearchException;
+ public abstract List<Drug> getDrugListByTarget(MiriamData target, Collection<MiriamData> organisms) throws DrugSearchException;
+
+ public List<Drug> getDrugListByTarget(MiriamData target) throws DrugSearchException {
+ return getDrugListByTarget(target, new ArrayList<>());
+ }
/**
* Returns list of drugs that target at least one protein from the parameter
@@ -71,7 +89,7 @@ public abstract class DrugAnnotation extends CachableInterface {
* @throws DrugSearchException
* thrown when there are problems with connection to drug database
*/
- public List<Drug> getDrugListByTargets(Collection<MiriamData> targets) throws DrugSearchException {
+ public List<Drug> getDrugListByTargets(Collection<MiriamData> targets, Collection<MiriamData> organisms) throws DrugSearchException {
List<Drug> result = new ArrayList<Drug>();
Set<String> set = new HashSet<String>();
Set<MiriamData> searchedResult = new HashSet<MiriamData>();
@@ -80,7 +98,7 @@ public abstract class DrugAnnotation extends CachableInterface {
continue;
}
searchedResult.add(md);
- List<Drug> drugs = getDrugListByTarget(md);
+ List<Drug> drugs = getDrugListByTarget(md, organisms);
for (Drug drug : drugs) {
if (!set.contains(drug.getSources().get(0).getResource())) {
result.add(drug);
@@ -93,6 +111,10 @@ public abstract class DrugAnnotation extends CachableInterface {
return result;
}
+ public List<Drug> getDrugListByTargets(Collection<MiriamData> targets) throws DrugSearchException {
+ return getDrugListByTargets(targets, new ArrayList<>());
+ }
+
/**
* @return the drugSerializer
* @see #drugSerializer
@@ -110,4 +132,34 @@ public abstract class DrugAnnotation extends CachableInterface {
this.drugSerializer = drugSerializer;
}
+ protected boolean organismMatch(String organismName, Collection<MiriamData> organisms) {
+ if (organismName == null || organismName.isEmpty() || organisms.size() == 0) {
+ return true;
+ }
+ try {
+ MiriamData organism = taxonomyBackend.getByName(organismName);
+ return organisms.contains(organism);
+ } catch (TaxonomySearchException e) {
+ logger.error("Problem with taxonomy search for: " + organismName, e);
+ return true;
+ }
+ }
+
+ /**
+ * @return the taxonomyBackend
+ * @see #taxonomyBackend
+ */
+ public TaxonomyBackend getTaxonomyBackend() {
+ return taxonomyBackend;
+ }
+
+ /**
+ * @param taxonomyBackend
+ * the taxonomyBackend to set
+ * @see #taxonomyBackend
+ */
+ public void setTaxonomyBackend(TaxonomyBackend taxonomyBackend) {
+ this.taxonomyBackend = taxonomyBackend;
+ }
+
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java
index cb9b4ac8032611e54f010bf40c662521b5f111be..cd79dcf68058ca4ec56b689e18b19b21938f9d7f 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java
@@ -3,6 +3,7 @@ package lcsb.mapviewer.annotation.services;
import java.io.IOException;
import java.net.URLEncoder;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
@@ -107,12 +108,6 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
*/
private Pattern targetPattern = Pattern.compile("(?<=\"/biodb/bio_entities/)([\\s\\S]*?)(?=\")");
- /**
- * Object used to access information about organism taxonomy.
- */
- @Autowired
- private TaxonomyBackend taxonomyBackend;
-
/**
* Default constructor.
*/
@@ -354,7 +349,7 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
i = page.indexOf("Organism</dt><dd>", i);
i = i + "Organism</dt><dd>".length();
j = page.indexOf("</dd>", i);
- target.setOrganism(taxonomyBackend.getByName(page.substring(i, j)));
+ target.setOrganism(getTaxonomyBackend().getByName(page.substring(i, j)));
// Getting References
i = page.indexOf("<strong>References</strong>", i);
@@ -554,8 +549,8 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
}
@Override
- public List<Drug> getDrugListByTarget(MiriamData target) throws DrugSearchException {
- List<Drug> result = new ArrayList<Drug>();
+ public List<Drug> getDrugListByTarget(MiriamData target, Collection<MiriamData> organisms) throws DrugSearchException {
+ List<Drug> result = new ArrayList<>();
if (target == null) {
return result;
}
@@ -571,12 +566,12 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
throw new DrugSearchException("Cannot access drug database", e);
}
- Set<String> drugNames = new HashSet<String>();
+ Set<String> drugNames = new HashSet<>();
Matcher matcher = targetPattern.matcher(page);
while (matcher.find()) {
String drugbankTargetId = matcher.group(0);
- drugNames.addAll(getDrugNamesForTarget(new MiriamData(MiriamType.DRUGBANK_TARGET_V4, drugbankTargetId), target));
+ drugNames.addAll(getDrugNamesForTarget(new MiriamData(MiriamType.DRUGBANK_TARGET_V4, drugbankTargetId), target, organisms));
}
for (String string : drugNames) {
Drug drug = findDrug(string);
@@ -605,27 +600,28 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
* thrown when there are problems with connection to DrugBank
* database
*/
- private Set<String> getDrugNamesForTarget(MiriamData drugbankTarget, MiriamData hgncTarget) throws DrugSearchException {
+ private Set<String> getDrugNamesForTarget(MiriamData drugbankTarget, MiriamData hgncTarget, Collection<MiriamData> organisms) throws DrugSearchException {
if (!MiriamType.DRUGBANK_TARGET_V4.equals(drugbankTarget.getDataType())) {
throw new InvalidArgumentException("drugbankTarget must be of type: " + MiriamType.DRUGBANK_TARGET_V4);
}
try {
- Set<String> drugNames = new HashSet<String>();
+ Set<String> drugNames = new HashSet<>();
+ String url = URL_TARGET_DETAIL + drugbankTarget.getResource();
- String page = getWebPageContent(URL_TARGET_DETAIL + drugbankTarget.getResource());
+ String page = getWebPageContent(url);
- int id = page.indexOf("<th>DrugBank ID</th>");
- if (id < 0) {
+ int idPosition = page.indexOf("<th>DrugBank ID</th>");
+ if (idPosition < 0) {
throw new DrugSearchException("Problematic web page for target: " + drugbankTarget + "(" + hgncTarget + ")");
}
- int i = page.indexOf("/polypeptides/");
+ int protienLinkPosition = page.indexOf("/polypeptides/");
// sometimes there might not be an element
- if (i >= 0) {
- i = i + "/polypeptides/".length(); // 20;
- int j = page.indexOf('"', i);
- String uniprotId = page.substring(i, j);
+ if (protienLinkPosition >= 0) {
+ protienLinkPosition = protienLinkPosition + "/polypeptides/".length(); // 20;
+ int j = page.indexOf('"', protienLinkPosition);
+ String uniprotId = page.substring(protienLinkPosition, j);
MiriamData uniprotMiriam = new MiriamData(MiriamType.UNIPROT, uniprotId);
MiriamData hgncMiriam = uniprotAnnotator.uniProtToHgnc(uniprotMiriam);
if (hgncMiriam == null || !hgncMiriam.equals(hgncTarget)) {
@@ -638,7 +634,18 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
return drugNames;
}
- Matcher matcher = drugNamePattern.matcher(page.substring(id));
+ int organismPosition = page.indexOf("Organism<");
+ if (organismPosition >= 0) {
+ int organismStart = page.indexOf("<td>", organismPosition) + "<td>".length();
+ int organismEnd = page.indexOf("<", organismStart + 1);
+ String organismName = page.substring(organismStart, organismEnd);
+ if (!organismMatch(organismName, organisms)) {
+ logger.debug("Organism doesn't match. Found" + organismName + ". Expected: " + organisms);
+ return drugNames;
+ }
+ }
+
+ Matcher matcher = drugNamePattern.matcher(page.substring(idPosition));
while (matcher.find()) {
drugNames.add(matcher.group(1));
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java
index ea227a5b9e0f9bebade68b6979535e7c13dcf655..8a2ccae9ca521c17970dc194fe339b1ff1308628 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java
@@ -694,6 +694,34 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
}
+ @Test
+ public void testFindDrugByHgncTargetAndFilteredOutByOrganism() throws Exception {
+ try {
+ List<MiriamData> organisms = new ArrayList<>();
+ organisms.add(new MiriamData(MiriamType.TAXONOMY, "-1"));
+ List<Drug> drugs = chemblParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "GRIN3B"), organisms);
+ assertNotNull(drugs);
+ assertEquals("No drugs for this organisms should be found", 0, drugs.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindDrugByHgncTargetAndFilteredByOrganism() throws Exception {
+ try {
+ List<MiriamData> organisms = new ArrayList<>();
+ organisms.add(TaxonomyBackend.HUMAN_TAXONOMY);
+ List<Drug> drugs = chemblParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "GRIN3B"), organisms);
+ assertNotNull(drugs);
+ assertTrue(drugs.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void testFindDrugsByRepeatingHgncTargets() throws Exception {
try {
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugAnnotationTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugAnnotationTest.java
index d80c1c51c617a8802e68cd0eb1cb8b27f6925997..45ca75b80eaba935ebe495c9ddcd5ba7bb905e94 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugAnnotationTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugAnnotationTest.java
@@ -2,6 +2,7 @@ package lcsb.mapviewer.annotation.services;
import static org.junit.Assert.assertEquals;
+import java.util.Collection;
import java.util.List;
import org.apache.log4j.Logger;
@@ -47,7 +48,7 @@ public class DrugAnnotationTest extends AnnotationTestFunctions {
}
@Override
- public List<Drug> getDrugListByTarget(MiriamData target) {
+ public List<Drug> getDrugListByTarget(MiriamData target, Collection<MiriamData> organisms) {
// TODO Auto-generated method stub
return null;
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java
index 11a288170b287626cb2314ea41bdc538f5fd21a2..5b0dafb3ff8daaca8c4d615f9a1ee79d6e25bf8d 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java
@@ -302,6 +302,34 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
}
}
+ @Test
+ public void testFindDrugByHgncTargetAndFilteredOutByOrganism() throws Exception {
+ try {
+ List<MiriamData> organisms = new ArrayList<>();
+ organisms.add(new MiriamData(MiriamType.TAXONOMY, "-1"));
+ List<Drug> drugs = drugBankHTMLParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "NFKB2"), organisms);
+ assertNotNull(drugs);
+ assertEquals("No drugs for this organisms should be found", 0, drugs.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindDrugByHgncTargetAndFilteredByOrganism() throws Exception {
+ try {
+ List<MiriamData> organisms = new ArrayList<>();
+ organisms.add(TaxonomyBackend.HUMAN_TAXONOMY);
+ List<Drug> drugs = drugBankHTMLParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "NFKB2"), organisms);
+ assertNotNull(drugs);
+ assertTrue(drugs.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void testFindDrugByInvalidTarget() throws Exception {
try {
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
index 85fed9a13c9f0af2de55ba2d27fbf0b93bcbbff6..b566144f91d2f600e98b483ae143341ffb7c644f 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
@@ -46,9 +46,6 @@ public class DrugRestImpl extends BaseRestImpl {
@Autowired
private IUserService userService;
- @Autowired
- private ElementMatcher elementMatcher;
-
public List<Map<String, Object>> getDrugsByQuery(String token, String projectId, String columns, String query) throws SecurityException, QueryException {
AuthenticationToken authenticationToken = userService.getToken(token);
Model model = modelService.getLastModelByProjectId(projectId, authenticationToken);
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java b/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java
index e1bb55227d5eb21f88d83557c69df96d62a2e9e7..584dfa0811af34460401f681e91418800cd9bf05 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java
@@ -282,14 +282,14 @@ public class DrugService implements IDrugService {
}
}
try {
- List<Drug> drugs = drugBankParser.getDrugListByTargets(targetsMiriam);
+ List<Drug> drugs = drugBankParser.getDrugListByTargets(targetsMiriam, searchCriteria.getOrganisms());
drugList.addAll(drugs);
} catch (DrugSearchException e) {
logger.error("Problem with accessing drugBank parser", e);
}
try {
- List<Drug> drugs = chEMBLParser.getDrugListByTargets(targetsMiriam);
+ List<Drug> drugs = chEMBLParser.getDrugListByTargets(targetsMiriam, searchCriteria.getOrganisms());
drugList.addAll(drugs);
} catch (DrugSearchException e) {
logger.error("Problem with accessing chembl parser", e);
@@ -386,9 +386,10 @@ public class DrugService implements IDrugService {
}
}
double counter = 0.0;
+ List<MiriamData> organisms = new ArrayList<>();
for (MiriamData md : targetMiriams) {
try {
- List<Drug> chemicalList = drugBankParser.getDrugListByTarget(md);
+ List<Drug> chemicalList = drugBankParser.getDrugListByTarget(md, organisms);
for (Drug chemical : chemicalList) {
cacheMiriamData(chemical);
}
@@ -396,7 +397,7 @@ public class DrugService implements IDrugService {
logger.error("Problem with accessing info about drugbank for target: " + md, e);
}
try {
- List<Drug> chemicalList = chEMBLParser.getDrugListByTarget(md);
+ List<Drug> chemicalList = chEMBLParser.getDrugListByTarget(md, organisms);
for (Drug chemical : chemicalList) {
cacheMiriamData(chemical);
}