Merge pull request #124 from HHS/develop

Bump version to 1.0.7
HHS · Feb 27, 2019 · c06c290 · c06c290
2 parents 26be3a7 + da322f9
commit c06c290
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Showing 12 changed files with 166 additions and 1,547 deletions.
diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
     <groupId>gov.nih.nlm.lode</groupId>
     <artifactId>meshrdf</artifactId>
     <packaging>pom</packaging>
-    <version>1.0.6</version>
+    <version>1.0.7</version>
     <name>NLM MeSH RDF parent project</name>
     <scm>
         <url>https://github.com/HHS/meshrdf</url>

diff --git a/webui/pom.xml b/webui/pom.xml
@@ -12,7 +12,7 @@
     <parent>
         <groupId>gov.nih.nlm.lode</groupId>
         <artifactId>meshrdf</artifactId>
-        <version>1.0.6</version>
+        <version>1.0.7</version>
     </parent>
 
     <properties>
@@ -50,10 +50,22 @@
                 <artifactId>maven-war-plugin</artifactId>
                 <version>3.2.0</version>
                 <configuration>
+                    <webResources>
+                        <resource>
+                            <directory>src/main/webapp</directory>
+                        </resource>
+                        <resource>
+                            <directory>../meta</directory>
+                            <includes>
+                                <include>*.ttl</include>
+                                <include>*.owl</include>
+                            </includes>
+                        </resource>
+                    </webResources>
                     <overlays>
                         <overlay>
                             <groupId>ebi-lode</groupId>
-                            <artifactId>web-ui</artifactId>
+                            <artifactId>web-ui</artifactId>                        
                             <excludes>
                                 <exclude>index.html</exclude>
                                 <exclude>query.html</exclude>

diff --git a/webui/src/main/resources/lode.properties b/webui/src/main/resources/lode.properties
@@ -43,7 +43,7 @@ lode.explorer.max.objects=50
 # Specifies if the query engine should use any inference when answering queries. This should be 
 # false when querying over http and is only relevant when using the virtuoso JDBC configuration 
 # at the moment
-lode.explorer.useInference=true
+lode.explorer.useInference=false
 
 # Specify the baseURI to be used when the API uri is relative
 lode.explorer.service.baseuri=http://id.nlm.nih.gov/mesh/

diff --git a/webui/src/main/webapp/WEB-INF/urlrewrite.xml b/webui/src/main/webapp/WEB-INF/urlrewrite.xml
@@ -126,6 +126,12 @@
       <to type="redirect">vocabulary.owl</to>
   </rule>
 
+  <rule>
+      <name>void-to-ttl-file</name>
+      <from casesensitive="true">^/void(#.*)?$</from>
+      <to type="redirect">void.ttl</to>
+  </rule>
+
 <!--
     <rule>
       <name>commented-1</name>

diff --git a/webui/src/main/webapp/scripts/lode.js b/webui/src/main/webapp/scripts/lode.js
@@ -1000,7 +1000,6 @@ function createTableHeader (names) {
     return htmlString;
 }
 
-
 function renderResourceTypes(element) {
     var identifier = getIdentifier(document.location.href);
 
@@ -1070,6 +1069,7 @@ function renderResourceTypes(element) {
     }
 }
 
+
 function renderAllResourceTypes(element, exclude) {
     var match = document.location.href.match(/\?(.*)/);
     var queryString = match ? match[1] : '';

diff --git a/webui/src/main/webapp/vocabulary.owl b/webui/src/main/webapp/vocabulary.owl
diff --git a/webui/src/main/webapp/vocabulary.ttl b/webui/src/main/webapp/vocabulary.ttl
diff --git a/webui/src/main/webapp/void.ttl b/webui/src/main/webapp/void.ttl
diff --git a/webui/src/test/java/gov/nih/nlm/lode/tests/BasicsTest.java b/webui/src/test/java/gov/nih/nlm/lode/tests/BasicsTest.java
@@ -1,14 +1,9 @@
 package gov.nih.nlm.lode.tests;
 
-import java.util.List;
-import java.util.ArrayList;
 import org.openqa.selenium.WebElement;
 import org.openqa.selenium.By;
 import org.testng.annotations.Test;
 
-import static org.testng.Assert.*;
-import static org.hamcrest.CoreMatchers.*;
-import static org.hamcrest.MatcherAssert.assertThat;
 
 @Test(groups = "basics")
 public class BasicsTest extends LodeBaseTest {
@@ -35,17 +30,7 @@ public void testQueryPage() {
 
   @Test
   public void testExplorerPage() {
-    openExplorerPage(false);
-    titleShouldBe("MeSH RDF Explorer");
-    elementShouldContain(By.cssSelector(".meshrdf-heading > h1"), "Medical Subject Headings");
-    WebElement navi = navigationShouldBeValid();
-    shouldBeValidLinks(navi.findElements(By.tagName("a")));
-    noPageErrors();
-  }
-
-  @Test
-  public void testExplorerYearPage() {
-    openExplorerPage(true);
+    openExplorerPage();
     titleShouldBe("MeSH RDF Explorer");
     elementShouldContain(By.cssSelector(".meshrdf-heading > h1"), "Medical Subject Headings");
     WebElement navi = navigationShouldBeValid();
@@ -61,6 +46,14 @@ public void testVocabularyTurtle() {
     vocablink.shouldBeValid();
   }
 
+  @Test
+  public void testVoidTurtle() {
+      LinkChecker vocablink = new LinkChecker();
+      vocablink.add(getLodeBaseUrl()+"/void.ttl");
+      vocablink.shouldMatchContentType("^text/turtle");
+      vocablink.shouldBeValid();
+  }
+
   @Test
   public void testVocabularyOwl() {
     LinkChecker vocablink = new LinkChecker();
@@ -73,9 +66,16 @@ public void testVocabularyOwl() {
   public void testVocabularyRedirect() {
     LinkChecker vocablink = new LinkChecker();
     vocablink.add(getLodeBaseUrl()+"/vocab#CheckTag");
-    // NOTE: link points to production, always, so don't check Content-Type
-    //   vocablink.shouldMatchContentType("^text/turtle");
+    vocablink.shouldMatchContentType("^application/rdf\\+xml");
     vocablink.shouldBeValid();
   }
 
+  @Test
+  public void testVoidRedirect() {
+    LinkChecker voidlink = new LinkChecker();
+    voidlink.add(getLodeBaseUrl()+"/void#MeSHRDF");
+    voidlink.add(getLodeBaseUrl()+"/void");
+    voidlink.shouldMatchContentType("^text/turtle");
+    voidlink.shouldBeValid();
+  }
 }
diff --git a/webui/src/test/java/gov/nih/nlm/lode/tests/ExplorerTest.java b/webui/src/test/java/gov/nih/nlm/lode/tests/ExplorerTest.java
@@ -0,0 +1,82 @@
+package gov.nih.nlm.lode.tests;
+
+import org.openqa.selenium.WebElement;
+import org.openqa.selenium.By;
+import org.testng.annotations.Test;
+
+public class ExplorerTest extends LodeBaseTest {
+
+    @Test
+    public void testTopicalDescriptor() {
+        openExplorerPage("D000420");
+        shouldBeExplorerPage();
+        shouldBeAbout("Albuterol");
+        shouldBeResourceType("MeSH TopicalDescriptor");
+
+        /* First test - test navigation */
+        WebElement navi = navigationShouldBeValid();
+        shouldBeValidLinks(navi.findElements(By.tagName("a")));
+        noPageErrors();
+    }
+
+    @Test
+    public void testExplorerYearPage() {
+        openExplorerPage(true);
+        shouldBeExplorerPage();
+        shouldBeAbout("Ofloxacin");
+        shouldBeResourceType("MeSH TopicalDescriptor");
+
+        /* Test again as this is a URI with a deeper URI */
+        WebElement navi = navigationShouldBeValid();
+        shouldBeValidLinks(navi.findElements(By.tagName("a")));
+        noPageErrors();
+    }
+
+    @Test
+    public void testPublicationType() {
+        openExplorerPage("D000077825");
+        shouldBeExplorerPage();
+        shouldBeAbout("Dictionary, Pharmaceutic");
+        shouldBeResourceType("MeSH PublicationType");
+    }
+
+    @Test
+    public void testGeographicalDescriptor() {
+        openExplorerPage("D008922");
+        shouldBeExplorerPage();
+        shouldBeAbout("Mississippi");
+        shouldBeResourceType("MeSH GeographicalDescriptor");
+    }
+
+    @Test
+    public void testCheckTag() {
+        openExplorerPage("D005260");
+        shouldBeExplorerPage();
+        shouldBeAbout("Female");
+        shouldBeResourceType("MeSH CheckTag");
+    }
+
+    @Test
+    public void testSCRChemical() {
+        openExplorerPage("C000621506");
+        shouldBeExplorerPage();
+        shouldBeAbout("CXXC5 protein, zebrafish");
+        shouldBeResourceType("MeSH SCR Chemical");
+    }
+
+    @Test
+    public void testSCRDisease() {
+        openExplorerPage("C000598941");
+        shouldBeExplorerPage();
+        shouldBeAbout("Keratoactinomycosis");
+        shouldBeResourceType("MeSH SCR Disease");
+    }
+
+    @Test
+    public void testSCROrganism() {
+        openExplorerPage("C000623735");
+        shouldBeExplorerPage();
+        shouldBeAbout("Rhinovirus B");
+        shouldBeResourceType("MeSH SCR Organism");
+    }
+}
diff --git a/webui/src/test/java/gov/nih/nlm/lode/tests/LinkChecker.java b/webui/src/test/java/gov/nih/nlm/lode/tests/LinkChecker.java
@@ -20,16 +20,11 @@
 import org.apache.http.Header;
 import org.apache.http.HttpRequest;
 import org.apache.http.HttpResponse;
-import org.apache.http.StatusLine;
 import org.apache.http.message.BasicHeader;
 
-import org.apache.commons.lang3.tuple.Pair;
-
 import org.testng.Reporter;
-
 import static org.testng.Assert.*;
-import static org.hamcrest.CoreMatchers.*;
-import static org.hamcrest.MatcherAssert.assertThat;
+
 
 public class LinkChecker {
 
@@ -134,6 +129,7 @@ public void addRequestHeader(String name, String value) {
 
     public void addRequestHeader(final Header header) {
         addRequestCallback(new LinkChecker.RequestCallback() {
+            @Override
             public void withRequest(HttpRequest request) {
                 request.setHeader(header);
             }
@@ -148,6 +144,7 @@ public void shouldMatchResponseHeader(final String name, final String valueExpr)
         try {
             final Pattern pattern = Pattern.compile(valueExpr);
             addResponseCallback(new LinkChecker.ResponseCallback() {
+                @Override
                 public void withResponse(HttpResponse response) {
                     Header header = response.getFirstHeader(name);
                     assertNotNull(header);
@@ -201,9 +198,9 @@ public void shouldBeValid() {
         URI lastbadlink = null;
         RequestConfig.Builder config = RequestConfig.custom();
         if (connectTimeout != null)
-            config.setConnectTimeout((int)connectTimeout * 1000);
+            config.setConnectTimeout(connectTimeout * 1000);
         if (socketTimeout != null)
-            config.setSocketTimeout((int)socketTimeout * 1000);
+            config.setSocketTimeout(socketTimeout * 1000);
         HttpClientBuilder builder = HttpClients.custom();
         builder.setDefaultRequestConfig(config.build());
         if (!followRedirects)

diff --git a/webui/src/test/java/gov/nih/nlm/lode/tests/LodeBaseTest.java b/webui/src/test/java/gov/nih/nlm/lode/tests/LodeBaseTest.java
@@ -97,6 +97,25 @@ public void shouldBeValidLinks(List<WebElement> links) {
     linkcheck.shouldBeValid();
   }
 
+  public void shouldBeExplorerPage() {
+      titleShouldBe("MeSH RDF Explorer");
+      elementShouldContain(By.cssSelector(".meshrdf-heading > h1"), "Medical Subject Headings");
+  }
+
+  public void shouldBeResourceType(String expectedTypeLabel) {
+      WebElement typeElement = findElement(By.cssSelector("#lodestar-contents_lode_explore_resourceType a.graph-link"));
+      assertThat(typeElement, not(nullValue()));
+      String actualTypeLabel = typeElement.getText().trim();
+      assertThat(actualTypeLabel, equalTo(expectedTypeLabel));
+  }
+
+  public void shouldBeAbout(String expectedAboutLabel) {
+      WebElement aboutElement = findElement(By.cssSelector("#lodestar-contents_lode_explore_resourceTopObject a.graph-link"));
+      assertThat(aboutElement, not(nullValue()));
+      String actualAboutLabel = aboutElement.getText().trim();
+      assertThat(actualAboutLabel, equalTo(expectedAboutLabel));
+  }
+
   public void openHomePage() {
     driver.get(getLodeBaseUrl());
   }
@@ -105,10 +124,25 @@ public void openQueryPage() {
     driver.get(getLodeBaseUrl() + "/query");
   }
 
-  public void openExplorerPage(Boolean useprefix) {
-    String prefix = (useprefix ? YEAR_PREFIX : "");
-    String uri = getLodeBaseUrl() + prefix + OFLAXIN_RELURI;
-    driver.get(uri);
+  public void openExplorerPage(String relativeUri, boolean usePrefix) {
+      if (relativeUri == null || relativeUri.length() == 0) {
+          relativeUri = OFLAXIN_RELURI;
+      }
+      if (relativeUri.charAt(0) != '/') {
+          relativeUri = '/'+relativeUri;
+      }
+      String prefix = (usePrefix ? YEAR_PREFIX : "");
+      String uri = getLodeBaseUrl() + prefix + relativeUri;
+      driver.get(uri);
+  }
+  public void openExplorerPage(String relativeUri) {
+      openExplorerPage(relativeUri, false);
+  }
+  public void openExplorerPage(Boolean usePrefix) {
+      openExplorerPage(null, usePrefix);
+  }
+  public void openExplorerPage() {
+      openExplorerPage(null, false);
   }
 
   public void noPageErrors() {