LMS-2392 Refactored and added data set search.

SVN: 22198

eu_basynthec/source/java/eu/basynthec/cisd/client/examples/BaSynthecClient.java

@@ -16,6 +16,8 @@
 
 package eu.basynthec.cisd.client.examples;
 
+import java.util.Arrays;
+import java.util.List;
 import java.util.Properties;
 
 import org.apache.commons.lang.time.DateUtils;
@@ -122,9 +124,18 @@ public class BaSynthecClient extends AbstractBaSynthecClient
      */
     public void run()
     {
-        logInfo("Listing experiments...");
+        List<String> projectIdentifiers = Arrays.asList("/PRIVATE/TEST");
+        logInfo("Listing experiments in projects " + projectIdentifiers + "...");
         ExperimentLister experimentLister = new ExperimentLister(openBis);
-        experimentLister.run();
+        experimentLister.run(projectIdentifiers);
+
+        println("\n");
+
+        List<String> strainNames = Arrays.asList("MGP100");
+        logInfo("Listing data sets containing data for strains " + strainNames + "...");
+        DataSetSearch dataSetSearch = new DataSetSearch(openBis);
+        dataSetSearch.run(strainNames);
+
     }
 
     private void logout()

eu_basynthec/source/java/eu/basynthec/cisd/client/examples/DataSetSearch.java

+/*
+ * Copyright 2011 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 eu.basynthec.cisd.client.examples;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet;
+import ch.systemsx.cisd.openbis.dss.client.api.v1.IOpenbisServiceFacade;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.SearchOperator;
+
+/**
+ * A class that, given a live connection to openBIS, searches for data sets where one of the
+ * specified strains appear, downloads the data set and prints information about the data set and
+ * experiment.
+ * 
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class DataSetSearch extends AbstractBaSynthecClient
+{
+    private static final String STRAIN_NAMES_PROPERTY = "STRAIN_NAMES";
+
+    private static final String STRAINS_HEADER = "Strains";
+
+    private static final String REGISTERED_BY_HEADER = "Contact Person";
+
+    private static final String DATA_SET_HEADER = "Data Set";
+
+    /**
+     * An enum for keeping track of the metadata fields we are interested in, in the order we want
+     * to display them.
+     * 
+     * @author Chandrasekhar Ramakrishnan
+     */
+    private enum MetadataField
+    {
+        EXPERIMENT_DATE("Date"), DESCRIPTION("Description"), MEDIUM("Medium"), TEMPERATURE(
+                "Temperature"), MISC_GROWTH_CONDITIONS("Growth Conditions");
+
+        MetadataField(String headerText)
+        {
+            this.headerText = headerText;
+        }
+
+        private final String headerText;
+    }
+
+    // State we compute as part of the operation of this class
+
+    // The data sets we are interested in
+    private List<DataSet> matchingDataSets;
+
+    // The experiments that contain the data sets we are interested in
+    private List<Experiment> experiments;
+
+    // A mapping from experiments to data sets
+    private HashMap<String, ArrayList<DataSet>> experimentDataSets;
+
+    /**
+     * The public constructor
+     * 
+     * @param facade The facade for interacting with openBIS.
+     */
+    public DataSetSearch(IOpenbisServiceFacade facade)
+    {
+        super(facade);
+    }
+
+    /**
+     * Using the connection to openBIS, get search for data sets that contain data on the specified
+     * strains. Download the data set and print information about the data set and its experiment.<br>
+     * <ul>
+     * <li>Experiment Date</li>
+     * <li>Description</li>
+     * <li>Medium</li>
+     * <li>Temperature</li>
+     * <li>Growth Conditions</li>
+     * <li>Data Set Strains</li>
+     * <li>Data Set Path</li>
+     * </ul>
+     */
+    public void run(List<String> strainNames)
+    {
+        printHeader();
+        retrieveInformationFromOpenBis(strainNames);
+
+        for (Experiment experiment : experiments)
+        {
+            printExperiment(experiment);
+        }
+    }
+
+    /**
+     * Connect to openBis to get the information we need.
+     */
+    private void retrieveInformationFromOpenBis(List<String> strainNames)
+    {
+        // Find all data sets that match the strain names
+        matchingDataSets = retrieveDataSetsReferencingStrains(strainNames);
+
+        // Get the experiments for the specified data sets
+        List<String> experimentIdentifiers = new ArrayList<String>();
+        for (DataSet dataSet : matchingDataSets)
+        {
+            experimentIdentifiers.add(dataSet.getExperimentIdentifier());
+        }
+        experiments = openBis.getExperiments(experimentIdentifiers);
+
+        // Create a map from experiment to data set
+        experimentDataSets = new HashMap<String, ArrayList<DataSet>>();
+        for (DataSet dataSet : matchingDataSets)
+        {
+            ArrayList<DataSet> dataSetsForExperiment =
+                    experimentDataSets.get(dataSet.getExperimentIdentifier());
+            if (null == dataSetsForExperiment)
+            {
+                dataSetsForExperiment = new ArrayList<DataSet>();
+                experimentDataSets.put(dataSet.getExperimentIdentifier(), dataSetsForExperiment);
+            }
+            dataSetsForExperiment.add(dataSet);
+        }
+    }
+
+    /**
+     * Find data sets that contain data for the specified strains.
+     */
+    private List<DataSet> retrieveDataSetsReferencingStrains(List<String> strainNames)
+    {
+        // Construct a search criteria that matches any of the strains specified.
+        SearchCriteria searchCriteria = new SearchCriteria();
+        searchCriteria.setOperator(SearchOperator.MATCH_ANY_CLAUSES);
+        for (String strainName : strainNames)
+        {
+            searchCriteria.addMatchClause(MatchClause.createPropertyMatch(STRAIN_NAMES_PROPERTY,
+                    strainName));
+        }
+        println("Searching for data sets that match the following criteria: ");
+        println(searchCriteria.toString());
+        return openBis.searchForDataSets(searchCriteria);
+    }
+
+    private void printHeader()
+    {
+        StringBuffer sb = new StringBuffer();
+        sb.append("Experiment");
+        for (MetadataField field : MetadataField.values())
+        {
+            sb.append("\t");
+            sb.append(field.headerText);
+        }
+        sb.append("\t");
+        sb.append(REGISTERED_BY_HEADER);
+        sb.append("\t");
+        sb.append(DATA_SET_HEADER);
+        sb.append("\t");
+        sb.append(STRAINS_HEADER);
+        println(sb.toString());
+    }
+
+    private void printEmptyExperimentInformationOn(StringBuffer sb)
+    {
+        // Experiment Identifier
+        sb.append("\t");
+        for (@SuppressWarnings("unused")
+        MetadataField field : MetadataField.values())
+        {
+            sb.append("\t");
+        }
+        // REGISTERED_BY_HEADER
+        sb.append("\t");
+
+        // We have now tabbed to allign with the data set information
+    }
+
+    private void printExperiment(Experiment experiment)
+    {
+        StringBuffer sb = new StringBuffer();
+        sb.append(experiment.getIdentifier());
+        printExperimentPropertiesOn(experiment.getProperties(), sb);
+        printRegisteredByOn(experiment.getRegistrationDetails(), sb);
+        printDataSetsOn(experiment, sb);
+        println(sb.toString());
+    }
+
+    private void printExperimentPropertiesOn(Map<String, String> properties, StringBuffer sb)
+    {
+        for (MetadataField field : MetadataField.values())
+        {
+            sb.append("\t");
+            String value = properties.get(field.toString());
+            if (null != value)
+            {
+                sb.append(value);
+            }
+        }
+    }
+
+    /**
+     * Get the strains for the experiment and print them to the string buffer.
+     */
+    private void printDataSetsOn(Experiment experiment, StringBuffer sb)
+    {
+        sb.append("\t");
+
+        // dataSets cannot be null, because we only have experiments that have data sets here
+        ArrayList<DataSet> dataSets = experimentDataSets.get(experiment.getIdentifier());
+
+        boolean isFirstLine = true;
+        for (DataSet dataSet : dataSets)
+        {
+            String dataSetCode = dataSet.getCode();
+            String strainNames = dataSet.getProperties().get(STRAIN_NAMES_PROPERTY);
+            if (false == isFirstLine)
+            {
+                sb.append("\n");
+                printEmptyExperimentInformationOn(sb);
+            }
+            sb.append(dataSetCode);
+            sb.append("\t");
+            sb.append(strainNames);
+        }
+    }
+
+    private void printRegisteredByOn(EntityRegistrationDetails registrationDetails, StringBuffer sb)
+    {
+        sb.append("\t");
+        sb.append(registrationDetails.getUserEmail());
+    }
+}

eu_basynthec/source/java/eu/basynthec/cisd/client/examples/ExperimentLister.java

@@ -17,13 +17,13 @@
 package eu.basynthec.cisd.client.examples;
 
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
 import ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet;
 import ch.systemsx.cisd.openbis.dss.client.api.v1.IOpenbisServiceFacade;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails;
 import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
 
 /**
@@ -37,6 +37,8 @@ public class ExperimentLister extends AbstractBaSynthecClient
 
     private static final String STRAINS_HEADER = "Strains";
 
+    private static final String REGISTERED_BY_HEADER = "Contact Person";
+
     /**
      * An enum for keeping track of the metadata fields we are interested in, in the order we want
      * to display them.
@@ -75,8 +77,8 @@ public class ExperimentLister extends AbstractBaSynthecClient
     }
 
     /**
-     * Using the connection to openBIS, get all experiments in the project <i>/PRIVATE/TEST</i> and
-     * print the following information about the experiment:<br>
+     * Using the connection to openBIS, get all experiments in the specified projects and print the
+     * following information about the experiment:<br>
      * <ul>
      * <li>Experiment Date</li>
      * <li>Description</li>
@@ -85,11 +87,13 @@ public class ExperimentLister extends AbstractBaSynthecClient
      * <li>Growth Conditions</li>
      * <li>Strains</li>
      * </ul>
+     * 
+     * @param projectIdentifiers The projects in which the experiments we are interested in are
+     *            housed.
      */
-    public void run()
+    public void run(List<String> projectIdentifiers)
     {
         printHeader();
-        List<String> projectIdentifiers = Arrays.asList("/PRIVATE/TEST");
         retrieveInformationFromOpenBis(projectIdentifiers);
 
         for (Experiment experiment : experiments)
@@ -113,7 +117,6 @@ public class ExperimentLister extends AbstractBaSynthecClient
             experimentIdentifiers.add(experiment.getIdentifier());
         }
 
-        experimentIdentifiers = Arrays.asList("/PRIVATE/TEST/TEST");
         List<DataSet> dataSets = openBis.listDataSetsForExperiments(experimentIdentifiers);
 
         experimentDataSets = new HashMap<String, ArrayList<DataSet>>();
@@ -141,6 +144,8 @@ public class ExperimentLister extends AbstractBaSynthecClient
         }
         sb.append("\t");
         sb.append(STRAINS_HEADER);
+        sb.append("\t");
+        sb.append(REGISTERED_BY_HEADER);
         println(sb.toString());
     }
 
@@ -150,6 +155,7 @@ public class ExperimentLister extends AbstractBaSynthecClient
         sb.append(experiment.getIdentifier());
         printExperimentPropertiesOn(experiment.getProperties(), sb);
         printExperimentStrainsOn(experiment, sb);
+        printRegisteredByOn(experiment.getRegistrationDetails(), sb);
         println(sb.toString());
     }
 
@@ -203,4 +209,10 @@ public class ExperimentLister extends AbstractBaSynthecClient
             sb.append(strains.get(i));
         }
     }
+
+    private void printRegisteredByOn(EntityRegistrationDetails registrationDetails, StringBuffer sb)
+    {
+        sb.append("\t");
+        sb.append(registrationDetails.getUserEmail());
+    }
 }