From af1bcb1c89ff2c93a28fb41c6ac9366cfec313a6 Mon Sep 17 00:00:00 2001
From: buczekp <buczekp>
Date: Fri, 24 Jun 2011 15:11:50 +0000
Subject: [PATCH] [LMS-2301] sketch of the framework
SVN: 21843
---
.../jython/JythonBasedPluginUtils.java | 133 ++++++++++++++++++
.../jython/JythonBasedProcessingPlugin.java | 88 ++++++++++++
.../jython/JythonBasedReportingPlugin.java | 86 +++++++++++
.../server/plugins/jython/api/IDataSet.java | 68 +++++++++
4 files changed, 375 insertions(+)
create mode 100644 datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedPluginUtils.java
create mode 100644 datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedProcessingPlugin.java
create mode 100644 datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedReportingPlugin.java
create mode 100644 datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/api/IDataSet.java
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedPluginUtils.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedPluginUtils.java
new file mode 100644
index 00000000000..8388fdc91d0
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedPluginUtils.java
@@ -0,0 +1,133 @@
+/*
+ * Copyright 2009 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.dss.generic.server.plugins.jython;
+
+import ch.systemsx.cisd.common.io.IHierarchicalContent;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.api.IDataSet;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
+
+/**
+ * Utility methods for reporting and processing plugins delegating the work to a Jython script.
+ *
+ * @author Piotr Buczek
+ */
+public class JythonBasedPluginUtils
+{
+ /**
+ * @return an instance of {@link IDataSet} based on given {@link DatasetDescription} and
+ * {@link IHierarchicalContent}
+ */
+ static IDataSet createDataSet(final DatasetDescription description,
+ final IHierarchicalContent content)
+ {
+ return new IDataSet()
+ {
+ public IHierarchicalContent getContent()
+ {
+ return content;
+ }
+
+ // delegator to description
+
+ public int getSpeedHint()
+ {
+ return description.getSpeedHint();
+ }
+
+ public String getSpaceCode()
+ {
+ return description.getSpaceCode();
+ }
+
+ public String getSampleTypeCode()
+ {
+ return description.getSampleTypeCode();
+ }
+
+ public String getSampleIdentifier()
+ {
+ return description.getSampleIdentifier();
+ }
+
+ public String getSampleCode()
+ {
+ return description.getSampleCode();
+ }
+
+ public String getProjectCode()
+ {
+ return description.getProjectCode();
+ }
+
+ public String getMainDataSetPattern()
+ {
+ return description.getMainDataSetPattern();
+ }
+
+ public String getMainDataSetPath()
+ {
+ return description.getMainDataSetPath();
+ }
+
+ public String getInstanceCode()
+ {
+ return description.getInstanceCode();
+ }
+
+ public String getExperimentTypeCode()
+ {
+ return description.getExperimentTypeCode();
+ }
+
+ public String getExperimentIdentifier()
+ {
+ return description.getExperimentIdentifier();
+ }
+
+ public String getExperimentCode()
+ {
+ return description.getExperimentCode();
+ }
+
+ public String getDatasetTypeCode()
+ {
+ return description.getDatasetTypeCode();
+ }
+
+ public String getDatabaseInstanceCode()
+ {
+ return description.getDatabaseInstanceCode();
+ }
+
+ public Long getDataSetSize()
+ {
+ return description.getDataSetSize();
+ }
+
+ public String getDataSetLocation()
+ {
+ return description.getDataSetLocation();
+ }
+
+ public String getDataSetCode()
+ {
+ return description.getDataSetCode();
+ }
+
+ };
+ }
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedProcessingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedProcessingPlugin.java
new file mode 100644
index 00000000000..030cc54c81b
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedProcessingPlugin.java
@@ -0,0 +1,88 @@
+/*
+ * Copyright 2009 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.dss.generic.server.plugins.jython;
+
+import java.io.File;
+import java.util.List;
+import java.util.Properties;
+
+import org.apache.log4j.Logger;
+
+import ch.systemsx.cisd.common.exceptions.Status;
+import ch.systemsx.cisd.common.io.IHierarchicalContent;
+import ch.systemsx.cisd.common.logging.LogCategory;
+import ch.systemsx.cisd.common.logging.LogFactory;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.api.IDataSet;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IProcessingPluginTask;
+import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IHierarchicalContentProvider;
+import ch.systemsx.cisd.openbis.dss.generic.shared.ProcessingStatus;
+import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
+
+/**
+ * Processing plugin which delegates the processing to a Jython script.
+ *
+ * @author Piotr Buczek
+ */
+public class JythonBasedProcessingPlugin implements IProcessingPluginTask
+{
+ private static final long serialVersionUID = 1L;
+
+ private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
+ JythonBasedProcessingPlugin.class);
+
+ public JythonBasedProcessingPlugin(Properties properties, File storeRoot)
+ {
+ }
+
+ public ProcessingStatus process(List<DatasetDescription> datasets,
+ DataSetProcessingContext context)
+ {
+ operationLog.info("Processing of the following datasets has been requested: " + datasets);
+ final IHierarchicalContentProvider contentProvider =
+ ServiceProvider.getHierarchicalContentProvider();
+
+ ProcessingStatus result = new ProcessingStatus();
+
+ for (DatasetDescription dataset : datasets)
+ {
+ String dataSetCode = dataset.getDataSetCode();
+ IHierarchicalContent content = null;
+ try
+ {
+ content = contentProvider.asContent(dataSetCode);
+ IDataSet iDataSet = JythonBasedPluginUtils.createDataSet(dataset, content);
+ result.addDatasetStatus(dataSetCode, delegateProcessing(iDataSet));
+ } finally
+ {
+ if (content != null)
+ {
+ content.close();
+ }
+ }
+ }
+ operationLog.info("Processing done.");
+ return null;
+ }
+
+ private Status delegateProcessing(IDataSet iDataSet)
+ {
+ return Status.OK; // TODO
+ }
+
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedReportingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedReportingPlugin.java
new file mode 100644
index 00000000000..ae364e1d1b1
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedReportingPlugin.java
@@ -0,0 +1,86 @@
+/*
+ * Copyright 2009 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.dss.generic.server.plugins.jython;
+
+import java.io.File;
+import java.util.List;
+import java.util.Properties;
+
+import ch.systemsx.cisd.common.io.IHierarchicalContent;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.api.IDataSet;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractTableModelReportingPlugin;
+import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IHierarchicalContentProvider;
+import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
+import ch.systemsx.cisd.openbis.generic.shared.util.SimpleTableModelBuilder;
+
+/**
+ * Reporting plugin which delegates the creation of report to a Jython script.
+ *
+ * @author Piotr Buczek
+ */
+public class JythonBasedReportingPlugin extends AbstractTableModelReportingPlugin
+{
+ private static final long serialVersionUID = 1L;
+
+ public JythonBasedReportingPlugin(Properties properties, File storeRoot)
+ {
+ super(properties, storeRoot);
+ }
+
+ public TableModel createReport(List<DatasetDescription> datasets,
+ DataSetProcessingContext context)
+ {
+ operationLog.info("Reporting for the following datasets has been requested: " + datasets);
+ IHierarchicalContentProvider contentProvider =
+ ServiceProvider.getHierarchicalContentProvider();
+ SimpleTableModelBuilder builder = new SimpleTableModelBuilder();
+
+ for (DatasetDescription dataset : datasets)
+ {
+ describe(builder, dataset, contentProvider);
+ }
+ return builder.getTableModel();
+ }
+
+ private void describe(SimpleTableModelBuilder builder, DatasetDescription dataset,
+ IHierarchicalContentProvider contentProvider)
+ {
+ String dataSetCode = dataset.getDataSetCode();
+ IHierarchicalContent content = null;
+ try
+ {
+ content = contentProvider.asContent(dataSetCode);
+ IDataSet iDataSet = JythonBasedPluginUtils.createDataSet(dataset, content);
+ delegateDescribe(builder, iDataSet);
+ } finally
+ {
+ if (content != null)
+ {
+ content.close();
+ }
+ }
+ }
+
+ private void delegateDescribe(SimpleTableModelBuilder builder, IDataSet iDataSet)
+ {
+ // TODO Auto-generated method stub
+ }
+
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/api/IDataSet.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/api/IDataSet.java
new file mode 100644
index 00000000000..5b778f574bf
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/api/IDataSet.java
@@ -0,0 +1,68 @@
+/*
+ * 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 ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.api;
+
+import ch.systemsx.cisd.common.io.IHierarchicalContent;
+
+/**
+ * @author Piotr Buczek
+ */
+public interface IDataSet
+{
+ // TODO move IHierarchicalContent to an API package
+ IHierarchicalContent getContent();
+
+ // DatasetDescription
+
+ String getDataSetCode();
+
+ String getDatasetTypeCode();
+
+ Long getDataSetSize();
+
+ String getDataSetLocation();
+
+ String getInstanceCode();
+
+ int getSpeedHint();
+
+ String getMainDataSetPattern();
+
+ String getMainDataSetPath();
+
+ String getSpaceCode();
+
+ String getProjectCode();
+
+ String getDatabaseInstanceCode();
+
+ String getExperimentCode();
+
+ String getExperimentIdentifier();
+
+ String getExperimentTypeCode();
+
+ /**
+ * NOTE: below methods may return null
+ */
+
+ String getSampleCode();
+
+ String getSampleIdentifier();
+
+ String getSampleTypeCode();
+}
--
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