From 04c723458028a6ddfddf927ecd613abff83e2ca9 Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Tue, 19 Jul 2011 09:38:00 +0000
Subject: [PATCH] LMS-2392 Refactored and added data set search.
SVN: 22198
---
.../cisd/client/examples/BaSynthecClient.java | 15 +-
.../cisd/client/examples/DataSetSearch.java | 249 ++++++++++++++++++
.../client/examples/ExperimentLister.java | 24 +-
3 files changed, 280 insertions(+), 8 deletions(-)
create mode 100644 eu_basynthec/source/java/eu/basynthec/cisd/client/examples/DataSetSearch.java
diff --git a/eu_basynthec/source/java/eu/basynthec/cisd/client/examples/BaSynthecClient.java b/eu_basynthec/source/java/eu/basynthec/cisd/client/examples/BaSynthecClient.java
index 6ffaee9b05b..f77ff86557d 100644
--- a/eu_basynthec/source/java/eu/basynthec/cisd/client/examples/BaSynthecClient.java
+++ b/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()
diff --git a/eu_basynthec/source/java/eu/basynthec/cisd/client/examples/DataSetSearch.java b/eu_basynthec/source/java/eu/basynthec/cisd/client/examples/DataSetSearch.java
new file mode 100644
index 00000000000..7e896a29dde
--- /dev/null
+++ b/eu_basynthec/source/java/eu/basynthec/cisd/client/examples/DataSetSearch.java
@@ -0,0 +1,249 @@
+/*
+ * 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());
+ }
+}
diff --git a/eu_basynthec/source/java/eu/basynthec/cisd/client/examples/ExperimentLister.java b/eu_basynthec/source/java/eu/basynthec/cisd/client/examples/ExperimentLister.java
index 7652e191e8b..421ab0f9367 100644
--- a/eu_basynthec/source/java/eu/basynthec/cisd/client/examples/ExperimentLister.java
+++ b/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());
+ }
}
--
GitLab