SSDM-689 : Add Javascript facade method for API extension for BLAST searchs

SVN: 32156

datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v2/sequencedatabases/EchoDatabase.java

+/*
+ * Copyright 2014 ETH Zuerich, SIS
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.dss.generic.server.api.v2.sequencedatabases;
+
+import java.io.File;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SequenceSearchResult;
+
+/**
+ * A test database that returns a search result that was stored in the parameters map under a key equal to the searched sequence snippet.
+ * 
+ * @author pkupczyk
+ */
+public class EchoDatabase extends AbstractSequenceDatabase
+{
+    public EchoDatabase(Properties properties, File storeRoot)
+    {
+        super(properties, storeRoot);
+    }
+
+    @Override
+    public boolean isAvailable()
+    {
+        return true;
+    }
+
+    @Override
+    public List<SequenceSearchResult> search(String sequenceSnippet, Map<String, String> optionalParametersOrNull)
+    {
+        String resultStr = optionalParametersOrNull.get(sequenceSnippet);
+        if (resultStr != null)
+        {
+            try
+            {
+                ObjectMapper mapper = new ObjectMapper();
+                SequenceSearchResult result = mapper.readValue(resultStr, SequenceSearchResult.class);
+                return Collections.singletonList(result);
+            } catch (Exception e)
+            {
+                throw CheckedExceptionTunnel.wrapIfNecessary(e);
+            }
+        } else
+        {
+            return Collections.emptyList();
+        }
+    }
+}

js-test/build.gradle

@@ -56,7 +56,7 @@ test {
     useTestNG()
     options.suites('source/java/tests.xml')    
 
-    jvmArgs '-Xmx2048m', '-XX:MaxPermSize=256m', '-Duser.timezone=Europe/Zurich'
+    jvmArgs '-Xmx2048m', '-XX:MaxPermSize=256m', '-Duser.timezone=Europe/Zurich', '-Xdebug', '-Xrunjdwp:transport=dt_socket,address=20010,server=y,suspend=n'
     
     testLogging.showStandardStreams = true
     ignoreFailures = true

js-test/servers/common/core-plugins/tests/1/dss/miscellaneous/echo-db/plugin.properties

+sequence-databases = echo-database
+echo-database.label = Echo database
+echo-database.class = ch.systemsx.cisd.openbis.dss.generic.server.api.v2.sequencedatabases.EchoDatabase

js-test/source/java/ch/systemsx/cisd/openbis/jstest/suite/common/JsTestCommonSelenium.java

@@ -97,7 +97,7 @@ public class JsTestCommonSelenium extends SeleniumTest
         runTests("runOpenbisScreeningJsTests", new OpenbisScreeningJsWebappLocation());
     }
 
-    private void runTests(String method, Location<OpenbisJsCommonWebapp> location)
+    protected void runTests(String method, Location<OpenbisJsCommonWebapp> location)
     {
         try
         {

js-test/source/java/ch/systemsx/cisd/openbis/jstest/suite/dev/JsTestDevSelenium.java

+/*
+ * Copyright 2012 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.jstest.suite.dev;
+
+import ch.systemsx.cisd.openbis.jstest.page.OpenbisJsCommonWebapp;
+import ch.systemsx.cisd.openbis.jstest.suite.common.JsTestCommonSelenium;
+import ch.systemsx.cisd.openbis.uitest.layout.Location;
+
+/**
+ * @author pkupczyk
+ */
+public class JsTestDevSelenium extends JsTestCommonSelenium
+{
+    @Override
+    protected void runTests(String method, Location<OpenbisJsCommonWebapp> location)
+    {
+        try
+        {
+            Thread.sleep(1000 * 60 * 60 * 24);
+        } catch (Exception e)
+        {
+            new RuntimeException(e);
+        }
+    }
+
+}

js-test/source/java/tests-dev.xml

+<suite name="All" verbose="2" >
+  <test name="Main" annotations="JDK">
+    <classes>
+       <class name="ch.systemsx.cisd.openbis.jstest.suite.dev.JsTestDevSelenium" />
+    </classes>  
+  </test>
+</suite>

openbis/source/java/ch/systemsx/cisd/openbis/public/resources/js/openbis.js

@@ -860,6 +860,21 @@ openbis.prototype.searchForDataSetsOnBehalfOfUser = function(searchCriteria, use
 	});
 }
 
+/**
+ * @see IGeneralInformationService.searchForDataSetsWithSequences(String, String, String, Map<String, String>)
+ * @method
+ */
+openbis.prototype.searchForDataSetsWithSequences = function(preferredSequenceDatabaseOrNull, sequenceSnippet, optionalParametersOrNull, action) {
+	this._internal.ajaxRequest({
+		url: this._internal.generalInfoServiceUrl,
+		data: { "method" : "searchForDataSetsWithSequences",
+				"params" : [ this.getSession(),
+							 preferredSequenceDatabaseOrNull,
+							 sequenceSnippet, optionalParametersOrNull ] },
+		success: action
+	});
+}
+
 /**
  * @see IGeneralInformationService.filterDataSetsVisibleToUser(String, List<DataSet>, String)
  * @method