new implementation of miriam connector (using identifiers.org API)

annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnector.java

 package lcsb.mapviewer.annotation.services;
 
 import java.io.IOException;
+import java.util.Map;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
@@ -9,13 +10,14 @@ import org.springframework.stereotype.Service;
 import org.w3c.dom.Document;
 import org.w3c.dom.Node;
 
+import com.google.gson.Gson;
+
 import lcsb.mapviewer.annotation.cache.CachableInterface;
 import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
 import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
 import lcsb.mapviewer.annotation.cache.WebPageDownloader;
 import lcsb.mapviewer.common.XmlParser;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.MiriamRelationType;
 import lcsb.mapviewer.model.map.MiriamType;
@@ -35,11 +37,6 @@ public final class MiriamConnector extends CachableInterface implements IExterna
    */
   static final String LINK_DB_PREFIX = "Link: ";
 
-  /**
-   * String used to distinguish cached data for checking if uri is valid.
-   */
-  protected static final String VALID_URI_PREFIX = "Validity: ";
-
   /**
    * String describing invalid miriam entries that will be put into db (instead of
    * null).
@@ -79,23 +76,43 @@ public final class MiriamConnector extends CachableInterface implements IExterna
       }
       return result;
     }
-    String uri = miriamData.getDataType().getUris().get(0) + ":" + miriamData.getResource();
-    throw new NotImplementedException();
-//    String[] urls = getLink().getLocations(uri);
-//    if (urls == null) {
-//      result = null;
-//    } else if (urls.length > 0) {
-//      result = urls[0];
-//    }
-//    if (result != null) {
-//      setCacheValue(query, result);
-//      return result;
-//    } else {
-//      logger.warn("Cannot find url for miriam: " + miriamData);
-//      // if url cannot be found then mark miriam data as invalid for one day
-//      setCacheValue(query, INVALID_LINK, 1);
-//      return null;
-//    }
+    String id;
+    if (miriamData.getDataType().getNamespace().isEmpty()) {
+      id = miriamData.getResource();
+    } else {
+      id = miriamData.getDataType().getNamespace() + ":" + miriamData.getResource();
+    }
+
+    query = "https://identifiers.org/rest/identifiers/validate/" + id;
+    String page;
+    try {
+      page = getWebPageContent(query);
+      Gson gson = new Gson();
+      Map<?, ?> map = gson.fromJson(page, Map.class);
+      return (String) map.get("url");
+
+    } catch (Exception e) {
+      throw new AnnotationException("Problem with accessing identifiers.org", e);
+    }
+    // Document document = XmlParser.getXmlDocumentFromString(page);
+    // Node uri = XmlParser.getNode("uri", document.getChildNodes());
+    // return XmlParser.getNodeValue(uri);
+
+    // String[] urls = getLink().getLocations(uri);
+    // if (urls == null) {
+    // result = null;
+    // } else if (urls.length > 0) {
+    // result = urls[0];
+    // }
+    // if (result != null) {
+    // setCacheValue(query, result);
+    // return result;
+    // } else {
+    // logger.warn("Cannot find url for miriam: " + miriamData);
+    // // if url cannot be found then mark miriam data as invalid for one day
+    // setCacheValue(query, INVALID_LINK, 1);
+    // return null;
+    // }
   }
 
   @Override
@@ -151,9 +168,6 @@ public final class MiriamConnector extends CachableInterface implements IExterna
         MiriamType dataType = MiriamType.getTypeByUri(rows[0]);
         String resource = rows[1];
         result = getUrlString(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, dataType, resource));
-      } else if (name.startsWith(VALID_URI_PREFIX)) {
-        String tmp = name.substring(VALID_URI_PREFIX.length());
-        result = "" + isValid(tmp);
       } else if (name.startsWith("http")) {
         try {
           result = getWebPageContent(name);
@@ -171,23 +185,18 @@ public final class MiriamConnector extends CachableInterface implements IExterna
   }
 
   /**
-   * Checks if uri (like the one defined in {@link MiriamType#getUris()}) is valid.
+   * Checks if {@link MiriamType} is valid.
    * 
-   * @param uri
-   *          uri to check
-   * @return <code>true</code> if uri in parameter is valid, <code>false</code>
+   * @param type
+   *          type to be checked
+   * @return <code>true</code> if {@link MiriamType} is valid, <code>false</code>
    *         otherwise
    */
-  public boolean isValid(String uri) {
-    throw new NotImplementedException();
-//    boolean result = false;
-//    String name = getLink().getName(uri);
-//    if (name == null) {
-//      result = false;
-//    } else {
-//      result = !name.isEmpty();
-//    }
-//    return result;
+  public boolean isValidMiriamType(MiriamType type) {
+    if (type.getNamespace() == null || type.getExampleIdentifier() == null) {
+      return false;
+    }
+    return getUrlString(new MiriamData(type, type.getExampleIdentifier())) != null;
   }
 
   /**

annotation/src/test/java/lcsb/mapviewer/annotation/services/MiriamConnectorTest.java

@@ -136,8 +136,7 @@ public class MiriamConnectorTest extends AnnotationTestFunctions {
     try {
       for (MiriamType mt : MiriamType.values()) {
         if (!MiriamType.UNKNOWN.equals(mt)) {
-          String uri = mt.getUris().get(0);
-          assertTrue("Invalid URI (" + uri + ") for MiriamType: " + mt, miriamConnector.isValid(mt.getUris().get(0)));
+          assertTrue("Invalid MiriamType (" + mt + ") for MiriamType: " + mt, miriamConnector.isValidMiriamType(mt));
         }
       }
 
@@ -147,18 +146,6 @@ public class MiriamConnectorTest extends AnnotationTestFunctions {
     }
   }
 
-  @Test
-  public void testRefresh() throws Exception {
-    String query = MiriamConnector.VALID_URI_PREFIX + MiriamType.HGNC.getUris().get(0);
-    try {
-      String res = miriamConnector.refreshCacheQuery(query);
-      assertNotNull(res);
-    } catch (Exception e) {
-      e.printStackTrace();
-      throw e;
-    }
-  }
-
   @Test
   public void testRefresh2() throws Exception {
     MiriamData md = TaxonomyBackend.HUMAN_TAXONOMY;
@@ -306,10 +293,10 @@ public class MiriamConnectorTest extends AnnotationTestFunctions {
   }
 
   @Test
-  public void testCheckValidyOfEmptyUri() throws Exception {
+  public void testCheckValidyOfUnknownMiriamType() throws Exception {
     try {
       // user connector without cache
-      boolean value = new MiriamConnector().isValid("");
+      boolean value = miriamConnector.isValidMiriamType(MiriamType.UNKNOWN);
       assertFalse(value);
     } catch (Exception e) {
       e.printStackTrace();

persist/src/main/resources/db/migration/14.0.0~alpha.0/V14.0.0.20190514__old_miriam_queries.sql

+delete from cache_query_table where query like 'Validity:%';
\ No newline at end of file