From 3eccf8c431d1f705bd441186ac331ad87ea69d11 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 10 Sep 2018 11:42:16 +0200
Subject: [PATCH] small refactor - methods extracted for better unit testing
---
.../services/DrugbankHTMLParser.java | 74 ++++++++++++-------
.../services/DrugbankHTMLParserTest.java | 44 ++++++++---
2 files changed, 84 insertions(+), 34 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 1e8e8af9ed..89338e9847 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java
@@ -642,15 +642,7 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
if (drug == null) {
logger.warn("Cannot find drug that should be there: " + string);
} else {
- boolean targets = false;
- for (Target target : drug.getTargets()) {
- for (MiriamData gene : target.getGenes()) {
- if (gene.equals(targetMiriamData)) {
- targets = true;
- }
- }
- }
- if (targets) {
+ if (isDrugContainTarget(targetMiriamData, drug)) {
result.add(drug);
} else {
logger.debug("Skipping drug that doesn't target required target. Drug name: " + drug.getName()
@@ -665,6 +657,18 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
}
}
+ boolean isDrugContainTarget(MiriamData targetMiriamData, Drug drug) {
+ boolean targets = false;
+ for (Target target : drug.getTargets()) {
+ for (MiriamData gene : target.getGenes()) {
+ if (gene.equals(targetMiriamData)) {
+ targets = true;
+ }
+ }
+ }
+ return targets;
+ }
+
/**
* Returns list of drugs that target element (target) identified be drugbank
* identifier.
@@ -698,25 +702,13 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
throw new DrugSearchException("Problematic web page for target: " + drugbankTarget + "(" + hgncTarget + ")");
}
- int protienLinkPosition = page.indexOf("/polypeptides/");
- // sometimes there might not be an element
- 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.setAnnotator(null);
- if (hgncMiriam == null || !hgncMiriam.equals(hgncTarget)) {
- logger.debug("Invalid target found. Expected " + hgncTarget + ", but found: " + hgncMiriam + " ("
- + uniprotMiriam + ")");
- return drugNames;
- }
-
- } else {
+ if (!isValidTargetPage(page)) {
logger.warn("Invalid target found. No protein data available.");
return drugNames;
}
+ if (!targetPageMatchTarget(page, hgncTarget)) {
+ return drugNames;
+ }
int organismPosition = page.indexOf("Organism</dt><dd class=\"col-md-10 col-sm-8\">");
if (organismPosition >= 0) {
@@ -743,6 +735,38 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
}
}
+ /**
+ * Checks if the content of the page matches our expectations about target.
+ * Sometimes when we search for targets drugbank returns something similar to
+ * the target and we need to filter it out (here is an example for TF targets:
+ * https://www.drugbank.ca/unearth/q?utf8=%E2%9C%93&searcher=targets&query=TF)
+ *
+ * @param page - target webpage content
+ * @param hgncTarget - HGNC identifier that should match the target
+ * @return
+ * @throws UniprotSearchException - when there is problem with translating HGNC<->uniprot
+ */
+ boolean targetPageMatchTarget(String page, MiriamData hgncTarget) throws UniprotSearchException {
+ int protienLinkPosition = page.indexOf("/polypeptides/");
+ 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.setAnnotator(null);
+ if (hgncMiriam == null || !hgncMiriam.equals(hgncTarget)) {
+ logger.debug(
+ "Invalid target found. Expected " + hgncTarget + ", but found: " + hgncMiriam + " (" + uniprotMiriam + ")");
+ return false;
+ }
+ return true;
+ }
+
+ private boolean isValidTargetPage(String page) {
+ return page.indexOf("/polypeptides/") >= 0;
+ }
+
/**
* @return the uniprotAnnotator
* @see #uniprotAnnotator
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 56d4ff56be..62801c46e8 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java
@@ -96,9 +96,9 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
public void testFindAfegostat() throws Exception {
try {
// finding synonym
- Drug rapamycinDrug = drugBankHTMLParser.findDrug("Afegostat");
- assertNotNull(rapamycinDrug);
- assertFalse(rapamycinDrug.getApproved());
+ Drug afegostatDrug = drugBankHTMLParser.findDrug("Afegostat");
+ assertNotNull(afegostatDrug);
+ assertFalse(afegostatDrug.getApproved());
} catch (Exception e) {
e.printStackTrace();
@@ -269,13 +269,39 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
}
@Test
- public void testFindDrugByTFTarget() throws Exception {
+ public void testTargetPageMatchTargetForTFProtein() throws Exception {
try {
- List<Drug> drugs = drugBankHTMLParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "TF"));
- assertNotNull(drugs);
- for (Drug drug : drugs) {
- assertFalse(drug.getName().equalsIgnoreCase("Iron saccharate"));
- }
+ MiriamData tfMiriam = new MiriamData(MiriamType.HGNC_SYMBOL, "TF");
+ String content = drugBankHTMLParser.getWebPageDownloader().getFromNetwork("https://www.drugbank.ca/biodb/bio_entities/BE0000510");
+ assertTrue(drugBankHTMLParser.targetPageMatchTarget(content, tfMiriam));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTargetPageMatchTargetForNotMatchingTFProtein() throws Exception {
+ try {
+ MiriamData tfMiriam = new MiriamData(MiriamType.HGNC_SYMBOL, "TF");
+ String content = drugBankHTMLParser.getWebPageDownloader().getFromNetwork("https://www.drugbank.ca/biodb/bio_entities/BE0002803");
+ assertFalse(drugBankHTMLParser.targetPageMatchTarget(content, tfMiriam));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testIsDrugContainTarget() throws Exception {
+ try {
+ Drug afegostat = drugBankHTMLParser.findDrug("Urokinase");
+ MiriamData plgMiriam = new MiriamData(MiriamType.HGNC_SYMBOL, "PLG");
+ MiriamData tfMiriam = new MiriamData(MiriamType.HGNC_SYMBOL, "TF");
+ assertTrue(drugBankHTMLParser.isDrugContainTarget(plgMiriam, afegostat));
+ assertFalse(drugBankHTMLParser.isDrugContainTarget(tfMiriam, afegostat));
} catch (Exception e) {
e.printStackTrace();
--
GitLab