From b77c155bc78c53771616b0cf48375c7d88675038 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 4 Aug 2017 13:59:18 +0200
Subject: [PATCH] drugbank results are manually limited by the name match
searched name must match at least on of:
* drug name
* brand name
* synonym
---
.../services/DrugbankHTMLParser.java | 34 +++++++++++++++++++
.../services/DrugbankHTMLParserTest.java | 33 ++++++++++--------
2 files changed, 52 insertions(+), 15 deletions(-)
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 be48b0c568..69a0265fcf 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.annotation.services;
import java.io.IOException;
+import java.io.UnsupportedEncodingException;
import java.net.URLEncoder;
import java.util.ArrayList;
import java.util.Collection;
@@ -447,6 +448,10 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
result.setBloodBrainBarrier(getBloodBrainBarrier(page));
result.setApproved(getApproved(page));
+
+ if (!nameMatch(result, name)) {
+ result = null;
+ }
}
} catch (IOException e) {
throw new DrugSearchException(e);
@@ -454,6 +459,35 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
return result;
}
+ /**
+ * Check if drug data mateches with the search name.
+ *
+ * @param drug
+ * drug to be checked
+ * @param name
+ * name of the drug that we were looking for
+ * @return true if if drug data matches with the search name
+ */
+ private boolean nameMatch(Drug drug, String name) {
+ Set<String> foundNames = new HashSet<>();
+ foundNames.add(drug.getName());
+ foundNames.addAll(drug.getSynonyms());
+ foundNames.addAll(drug.getBrandNames());
+ String lowerCaseName;
+ try {
+ lowerCaseName = java.net.URLDecoder.decode(name, "UTF-8").toLowerCase().replaceAll("[^A-Za-z0-9]", "");
+ } catch (UnsupportedEncodingException e) {
+ lowerCaseName = name.toLowerCase().replaceAll("[^A-Za-z0-9]", "");
+ }
+ for (String string : foundNames) {
+ String query = string.toLowerCase().replaceAll("[^A-Za-z0-9]", "");
+ if (query.contains(lowerCaseName)) {
+ return true;
+ }
+ }
+ return false;
+ }
+
/**
* Finds blood brain barrier info about drug in the webpage content.
*
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 d1c78db1f9..7f77e45006 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java
@@ -197,18 +197,6 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
}
}
- // at some point this search threw exception
- @Test
- public void testFindDrugKainicAcid() throws Exception {
- try {
- Drug test = drugBankHTMLParser.findDrug("kainic acid");
- assertNotNull(test);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
@Test
public void testFindDrugAmantadineWithBrandNames() throws Exception {
try {
@@ -305,7 +293,7 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
@Test
public void testFindAluminiumByName() throws Exception {
try {
- Drug drug = drugBankHTMLParser.findDrug("Aluminium");
+ Drug drug = drugBankHTMLParser.findDrug("Aluminium");
assertTrue(drug.getName().equalsIgnoreCase("Aluminium"));
} catch (Exception e) {
@@ -314,6 +302,21 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
}
}
+ @Test
+ public void testFindBIIB054ByName() throws Exception {
+ try {
+ Drug drug = drugBankHTMLParser.findDrug("BIIB054");
+ if (drug != null) {
+ // check if are not pointint to BIIB021
+ assertFalse(drug.getSources().get(0).getResource().equalsIgnoreCase("DB12359"));
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void testFindDrugByHgncTargetAndFilteredOutByOrganism() throws Exception {
try {
@@ -483,7 +486,7 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
assertEquals("Ibuprofen", test.getName());
assertEquals("DB01050", test.getSources().get(0).getResource());
assertNotNull(test.getDescription());
- assertEquals(8, test.getTargets().size());
+ assertTrue(test.getTargets().size()>=8);
} catch (Exception e) {
e.printStackTrace();
@@ -731,5 +734,5 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
assertEquals(2, target.getReferences().size());
assertEquals("Galactoside O-acetyltransferase", target.getName());
}
-
+
}
--
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