old unused code removed

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.http.HttpStatus;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.hibernate.AnnotationException;
 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.model.map.MiriamData;
 import lcsb.mapviewer.model.map.MiriamRelationType;
@@ -31,18 +27,6 @@ import lcsb.mapviewer.model.map.MiriamType;
  */
 @Service
 public final class MiriamConnector extends CachableInterface implements IExternalService {
-
-  /**
-   * String used to distinguish cached data for links.
-   */
-  static final String LINK_DB_PREFIX = "Link: ";
-
-  /**
-   * String describing invalid miriam entries that will be put into db (instead of
-   * null).
-   */
-  private static final String INVALID_LINK = "INVALID";
-
   /**
    * Default class logger.
    */
@@ -68,14 +52,6 @@ public final class MiriamConnector extends CachableInterface implements IExterna
     } else if (miriamData.getDataType().getUris().size() == 0) {
       throw new InvalidArgumentException("Url for " + miriamData.getDataType() + " cannot be retreived.");
     }
-    String query = LINK_DB_PREFIX + miriamData.getDataType().getUris().get(0) + "\n" + miriamData.getResource();
-    String result = getCacheValue(query);
-    if (result != null) {
-      if (INVALID_LINK.equals(result)) {
-        return null;
-      }
-      return result;
-    }
     String id;
     if (miriamData.getDataType().getNamespace().isEmpty()) {
       id = miriamData.getResource();
@@ -83,14 +59,18 @@ public final class MiriamConnector extends CachableInterface implements IExterna
       id = miriamData.getDataType().getNamespace() + ":" + miriamData.getResource();
     }
 
-    query = "https://identifiers.org/rest/identifiers/validate/" + id;
-    String page;
+    String query = "https://identifiers.org/rest/identifiers/validate/" + id;
     try {
-      page = getWebPageContent(query);
+      String page = getWebPageContent(query);
       Gson gson = new Gson();
       Map<?, ?> map = gson.fromJson(page, Map.class);
       return (String) map.get("url");
-
+    } catch (WrongResponseCodeIOException e) {
+      if (HttpStatus.SC_NOT_FOUND == e.getResponseCode()) {
+        return null;
+      } else {
+        throw new AnnotationException("Problem with accessing identifiers.org", e);
+      }
     } catch (Exception e) {
       throw new AnnotationException("Problem with accessing identifiers.org", e);
     }
@@ -135,36 +115,6 @@ public final class MiriamConnector extends CachableInterface implements IExterna
     }
   }
 
-  @Override
-  public String refreshCacheQuery(Object query) throws SourceNotAvailable {
-    String result = null;
-    if (query instanceof String) {
-      String name = (String) query;
-      if (name.startsWith(LINK_DB_PREFIX)) {
-        String tmp = name.substring(LINK_DB_PREFIX.length());
-        String[] rows = tmp.split("\n");
-        if (rows.length != 2) {
-          throw new InvalidArgumentException("Miriam link query is invalid: " + query);
-        }
-        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("http")) {
-        try {
-          result = getWebPageContent(name);
-        } catch (IOException e) {
-          throw new SourceNotAvailable(e);
-        }
-      } else {
-        throw new InvalidArgumentException("Don't know what to do with string \"" + query + "\"");
-      }
-    } else {
-      throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
-    }
-
-    return result;
-  }
-
   /**
    * Checks if {@link MiriamType} is valid.
    * 

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

@@ -14,7 +14,6 @@ import java.io.IOException;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
-import org.hibernate.AnnotationException;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
@@ -146,30 +145,6 @@ public class MiriamConnectorTest extends AnnotationTestFunctions {
     }
   }
 
-  @Test
-  public void testRefresh2() throws Exception {
-    MiriamData md = TaxonomyBackend.HUMAN_TAXONOMY;
-    String query = MiriamConnector.LINK_DB_PREFIX + md.getDataType().getUris().get(0) + "\n" + md.getResource();
-    try {
-      String res = miriamConnector.refreshCacheQuery(query);
-      assertNotNull(res);
-    } catch (Exception e) {
-      e.printStackTrace();
-      throw e;
-    }
-  }
-
-  @Test
-  public void testRefresh3() throws Exception {
-    try {
-      String res = miriamConnector.refreshCacheQuery("https://www.google.pl/");
-      assertNotNull(res);
-    } catch (Exception e) {
-      e.printStackTrace();
-      throw e;
-    }
-  }
-
   @Test
   public void testGetUrlForDoi() throws Exception {
     try {
@@ -241,19 +216,6 @@ public class MiriamConnectorTest extends AnnotationTestFunctions {
     }
   }
 
-  @Test
-  public void testRefreshInvalidCacheQuery3() throws Exception {
-    try {
-      miriamConnector.refreshCacheQuery(MiriamConnector.LINK_DB_PREFIX);
-      fail("Exception expected");
-    } catch (InvalidArgumentException e) {
-      assertTrue(e.getMessage().contains("Miriam link query is invalid"));
-    } catch (Exception e) {
-      e.printStackTrace();
-      throw e;
-    }
-  }
-
   @Test
   public void testCheckValidyOfUnknownMiriamType() throws Exception {
     try {

persist/src/main/resources/db/migration/14.0.0~alpha.0/V14.0.0.20190515__old_miriam_queries.sql

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