Adding new tests for the configurations and for testing the publicati…

…on searcher.
ISA-tools · Jul 14, 2011 · 9ab6cb6 · 9ab6cb6
1 parent 2ac539f
commit 9ab6cb6
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Showing 5 changed files with 162 additions and 47 deletions.
diff --git a/run_tests.sh b/run_tests.sh
@@ -0,0 +1,32 @@
+#!/bin/sh
+
+rm -rf Configurations
+
+echo "Retreiving configuration from GitHub repo"
+mkdir Configurations
+cd Configurations
+wget https://github.com/downloads/ISA-tools/Configuration-Files/isaconfig-default_v2011-02-18.zip --no-check-certificate
+wget https://github.com/downloads/ISA-tools/Configuration-Files/isaconfig-default_v2011-02-18-MIMARKS-soil_v2011-02-18.zip --no-check-certificate
+wget https://github.com/downloads/ISA-tools/Configuration-Files/isaconfig-default_v2011-02-18-MIMARKS-water_v2011-02-18.zip --no-check-certificate
+wget https://github.com/downloads/ISA-tools/Configuration-Files/isaconfig-MISFISHIE-rodent-january-2011.zip --no-check-certificate
+
+echo "Unzipping files"
+
+unzip isaconfig-default_v2011-02-18.zip
+unzip isaconfig-default_v2011-02-18-MIMARKS-soil_v2011-02-18.zip
+unzip isaconfig-default_v2011-02-18-MIMARKS-water_v2011-02-18.zip
+unzip isaconfig-MISFISHIE-rodent-january-2011.zip
+
+echo "Cleaning up directory"
+rm -rf __*
+rm *.zip
+
+cd ../
+
+echo "Running tests"
+
+# now run tests
+mvn $MVNOPTS clean test
+
+echo "Testing completed successfully!"
+
diff --git a/...acreator/ontologymanager/bioportal/xmlresulthandlers/BioPortalAnnotatorResultHandler.java b/...acreator/ontologymanager/bioportal/xmlresulthandlers/BioPortalAnnotatorResultHandler.java
@@ -13,14 +13,6 @@
 import java.util.Map;
 import java.util.Set;
 
-/**
- * Created by the ISA team
- *
- * @author Eamonn Maguire (eamonnmag@gmail.com)
- *         <p/>
- *         Date: 26/01/2011
- *         Time: 18:39
- */
 public class BioPortalAnnotatorResultHandler {
 
     public SuccessDocument getDocument(String fileLocation) {
@@ -58,8 +50,6 @@ public Map<String, Map<String, AnnotatorResult>> getSearchResults(String fileLoc
 
                     if (annotatorResult != null) {
 
-                        System.out.println("Original test to annotate: " + originalTextToAnnotate);
-
                         String originalTerm = originalTextToAnnotate.substring(annotatorResult.getStartIndex() - 1, annotatorResult.getEndIndex());
 
                         if (originalTerms.contains(originalTerm)) {

diff --git a/src/main/java/org/isatools/isacreator/publicationlocator/CiteExploreClient.java b/src/main/java/org/isatools/isacreator/publicationlocator/CiteExploreClient.java
@@ -44,10 +44,9 @@ The ISA Team and the ISA software suite have been funded by the EU Carcinogenomi
 import org.isatools.isacreator.model.StudyPublication;
 import uk.ac.ebi.cdb.client.*;
 
+import javax.print.attribute.ResolutionSyntax;
 import javax.xml.ws.WebServiceRef;
-import java.util.HashMap;
+import java.util.*;
-import java.util.List;
-import java.util.Map;
 
 
 public class CiteExploreClient {
@@ -74,55 +73,58 @@ private String formDOIQueryString(String doi) {
     public Map<String, Publication> getPublication(SearchOption searchOption, String query, DataEntryForm parent) throws NoPublicationFoundException {
         Map<String, Publication> publications = new HashMap<String, Publication>();
         try {
-            WSCitationImpl port = service.getWSCitationImplPort();
 
-            String fullQueryString = searchOption == SearchOption.DOI ? formDOIQueryString(query) : formPubMedQueryString(query);
+            List<ResultBean> resultBeanCollection = searchForPublication(searchOption, query);
 
-            ResultListBean resultListBean = port.searchCitations(fullQueryString, "all", 0, "");
+            for (ResultBean resultBean : resultBeanCollection) {
+                uk.ac.ebi.cdb.client.Citation citation = resultBean.getCitation();
 
-            if (resultListBean.getHitCount() > 0) {
-                List<ResultBean> resultBeanCollection = resultListBean.getResultBeanCollection();
 
-                for (ResultBean resultBean : resultBeanCollection) {
+                String authorList = "";
-                    uk.ac.ebi.cdb.client.Citation citation = resultBean.getCitation();
+                for (Author author : citation.getAuthorCollection()) {
-
+                    authorList += author.getLastName() + " " + author.getInitials() + ",";
-
+                }
-                    String authorList = "";
+                if (authorList.length() > 1) {
-                    for (Author author : citation.getAuthorCollection()) {
+                    authorList = authorList.substring(0, authorList.length() - 1);
-                        authorList += author.getLastName() + " " + author.getInitials() + ",";
+                }
-                    }
-                    if (authorList.length() > 1) {
-                        authorList = authorList.substring(0, authorList.length() - 1);
-                    }
-
-                    String doi = "";
-                    for (FullTextURL ftURL : citation.getUrlCollection()) {
-                        if (ftURL.getUrl().contains("doi")) {
-                            doi = ftURL.getUrl();
-                            break;
-                        }
-                    }
 
-                    Publication pub;
+                String doi = "";
-                    if (parent instanceof StudyDataEntry) {
+                for (FullTextURL ftURL : citation.getUrlCollection()) {
-                        pub = new StudyPublication(citation.getExternalId(), doi, authorList, citation.getTitle().replaceAll("\\[|\\]", ""), "Published");
+                    if (ftURL.getUrl().contains("doi")) {
-                    } else {
+                        doi = ftURL.getUrl();
-                        pub = new InvestigationPublication(citation.getExternalId(), doi, authorList, citation.getTitle().replaceAll("\\[|\\]", ""), "Published");
+                        break;
                     }
-                    pub.setAbstractText(citation.getAbstractText());
+                }
-                    publications.put(citation.getExternalId(), pub);
 
+                Publication pub;
+                if (parent instanceof StudyDataEntry) {
+                    pub = new StudyPublication(citation.getExternalId(), doi, authorList, citation.getTitle().replaceAll("\\[|\\]", ""), "Published");
+                } else {
+                    pub = new InvestigationPublication(citation.getExternalId(), doi, authorList, citation.getTitle().replaceAll("\\[|\\]", ""), "Published");
                 }
-            } else {
+                pub.setAbstractText(citation.getAbstractText());
-                throw new NoPublicationFoundException(searchOption, query);
+                publications.put(citation.getExternalId(), pub);
             }
-
         } catch (QueryException_Exception qex) {
             System.out.printf("Caught QueryException_Exception: %s\n", qex.getFaultInfo().getMessage());
         }
 
         return publications;
     }
 
+    public List<ResultBean> searchForPublication(SearchOption searchOption, String query) throws QueryException_Exception, NoPublicationFoundException {
+        WSCitationImpl port = service.getWSCitationImplPort();
+
+        String fullQueryString = searchOption == SearchOption.DOI ? formDOIQueryString(query) : formPubMedQueryString(query);
+
+        ResultListBean resultListBean = port.searchCitations(fullQueryString, "all", 0, "");
+
+        if (resultListBean.getHitCount() > 0) {
+            return resultListBean.getResultBeanCollection();
+        } else {
+            throw new NoPublicationFoundException(searchOption, query);
+        }
+    }
+
 
 }
diff --git a/src/test/java/org/isatools/isacreator/configuration/io/ConfigurationLoadTest.java b/src/test/java/org/isatools/isacreator/configuration/io/ConfigurationLoadTest.java
@@ -0,0 +1,38 @@
+package org.isatools.isacreator.configuration.io;
+
+import org.junit.Test;
+
+import java.io.File;
+
+import static org.junit.Assert.assertTrue;
+
+public class ConfigurationLoadTest {
+
+    @Test
+    public void configurationTestLoad() {
+        System.out.println("_____TESTING configurationTestLoad()");
+
+        File configurationDirectory = new File("Configurations");
+        if(configurationDirectory.exists() && configurationDirectory.isDirectory()) {
+
+            File[] configurationFiles = configurationDirectory.listFiles();
+
+            for(File file : configurationFiles) {
+
+                if(!file.isHidden() && !file.getName().startsWith(".")) {
+
+                    ConfigXMLParser parser = new ConfigXMLParser(ConfigurationLoadingSource.ISACREATOR, file.getAbsolutePath());
+
+                    System.out.println("___loading configuration " + file.getName().toLowerCase());
+
+                    parser.loadConfiguration();
+
+                    assertTrue("Oh, the configuration size is 0!", parser.getTables().size() > 0);
+
+                    System.out.println("Configuration " + file.getName().toLowerCase() +  " loaded successfully");
+                }
+            }
+        }
+    }
+
+}
diff --git a/src/test/java/org/isatools/isacreator/publicationlocator/CiteXploreTest.java b/src/test/java/org/isatools/isacreator/publicationlocator/CiteXploreTest.java
@@ -0,0 +1,53 @@
+package org.isatools.isacreator.publicationlocator;
+
+import org.junit.Test;
+import uk.ac.ebi.cdb.client.Citation;
+import uk.ac.ebi.cdb.client.QueryException_Exception;
+import uk.ac.ebi.cdb.client.ResultBean;
+
+import java.util.Collection;
+import java.util.List;
+
+/**
+ * Created by the ISA team
+ *
+ * @author Eamonn Maguire (eamonnmag@gmail.com)
+ *         <p/>
+ *         Date: 14/07/2011
+ *         Time: 13:45
+ */
+public class CiteXploreTest {
+
+    @Test
+    public void testCiteXplorePubMed() {
+        runTest(SearchOption.PUBMED, "19815759");
+    }
+
+    @Test
+    public void testCiteXploreDOI() {
+        runTest(SearchOption.DOI, "10.1093/bioinformatics/btq415");
+    }
+
+    private void runTest(SearchOption searchOption, String query) {
+        CiteExploreClient publicationSearcher = new CiteExploreClient();
+
+        try {
+            List<ResultBean> result = publicationSearcher.searchForPublication(searchOption, query);
+            printResultBeans(result);
+        } catch (QueryException_Exception qex) {
+            System.out.printf("Caught QueryException_Exception: %s\n", qex.getFaultInfo().getMessage());
+        } catch (NoPublicationFoundException e) {
+            System.out.println("No publication found");
+        }
+    }
+
+    private void printResultBeans(Collection<ResultBean> resultBeans) {
+        for(ResultBean resultBean : resultBeans) {
+            Citation citation = resultBean.getCitation();
+
+            System.out.println("citation.getTitle() = " + citation.getTitle());
+            System.out.println("citation.getAbstractText() = " + citation.getAbstractText());
+            System.out.println("citation.getAffiliation() = " + citation.getAffiliation());
+        }
+    }
+}