Metacat

package edu.ucsb.nceas.metacat.annotation;

import java.io.InputStream;

import java.sql.PreparedStatement;

import java.sql.SQLException;

import java.util.ArrayList;

import java.util.List;

import java.util.Vector;

import org.apache.log4j.Logger;

import org.apache.wicket.protocol.http.mock.MockHttpServletRequest;

import org.dataone.service.types.v1.Identifier;

import org.dataone.service.types.v1.Session;

import org.dataone.service.types.v1.Subject;

import org.ecoinformatics.datamanager.parser.Attribute;

import org.ecoinformatics.datamanager.parser.DataPackage;

import org.ecoinformatics.datamanager.parser.Entity;

import org.ecoinformatics.datamanager.parser.generic.DataPackageParserInterface;

import org.ecoinformatics.datamanager.parser.generic.Eml200DataPackageParser;

import edu.ucsb.nceas.metacat.DBUtil;

import edu.ucsb.nceas.metacat.DocumentImpl;

import edu.ucsb.nceas.metacat.IdentifierManager;

import edu.ucsb.nceas.metacat.McdbDocNotFoundException;

import edu.ucsb.nceas.metacat.database.DBConnection;

import edu.ucsb.nceas.metacat.database.DBConnectionPool;

import edu.ucsb.nceas.metacat.dataone.MNodeService;

import edu.ucsb.nceas.metacat.properties.PropertyService;

import edu.ucsb.nceas.metacat.util.DocumentUtil;

import edu.ucsb.nceas.utilities.SortedProperties;

public class DatapackageSummarizer {

	private static Logger logMetacat = Logger.getLogger(DatapackageSummarizer.class);

	public void summarize(List<Identifier> identifiers) throws SQLException {

		DBConnection dbconn = null;

		try {

			dbconn = DBConnectionPool.getDBConnection("DatapackageSummarizer.summarize");

			PreparedStatement dropStatement = dbconn.prepareStatement("DROP TABLE IF EXISTS entity_summary");

			dropStatement.execute();

			PreparedStatement createStatement = dbconn.prepareStatement(

					"CREATE TABLE entity_summary (" +

					"guid text, " +

					"title text, " +

					"entity text," +

					"attributeName text," +

					"attributeLabel text," +

					"attributeDefinition text," +

					"attributeType text," +

					"attributeScale text," +

					"attributeUnitType text," +

					"attributeUnit text," +

					"attributeDomain text" +

					")");

			createStatement.execute();

			PreparedStatement insertStatement = dbconn.prepareStatement(

					"INSERT INTO entity_summary " +

					"VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)");

			for (Identifier pid: identifiers) {

				logMetacat.debug("Parsing pid: " + pid.getValue());

				try {

					// for using the MN API as the MN itself

					MockHttpServletRequest request = new MockHttpServletRequest(null, null, null);

					Session session = new Session();

			        Subject subject = MNodeService.getInstance(request).getCapabilities().getSubject(0);

			        session.setSubject(subject);

					InputStream emlStream = MNodeService.getInstance(request).get(session, pid);

					// parse the metadata

					DataPackageParserInterface parser = new Eml200DataPackageParser();

					parser.parse(emlStream);

					DataPackage dataPackage = parser.getDataPackage();

					String title = dataPackage.getTitle();

					logMetacat.debug("Title: " + title);

					Entity[] entities = dataPackage.getEntityList();

					if (entities != null) {

						for (Entity entity: entities) {

							String entityName = entity.getName();

							logMetacat.debug("Entity name: " + entityName);

							Attribute[] attributes = entity.getAttributeList().getAttributes();

							for (Attribute attribute: attributes) {

								String attributeName = attribute.getName();

								String attributeLabel = attribute.getLabel();

								String attributeDefinition = attribute.getDefinition();

								String attributeType = attribute.getAttributeType();

								String attributeScale = attribute.getMeasurementScale();

								String attributeUnitType = attribute.getUnitType();

								String attributeUnit = attribute.getUnit();

								String attributeDomain = attribute.getDomain().getClass().getSimpleName();

								logMetacat.debug("Attribute name: " + attributeName);

								logMetacat.debug("Attribute label: " + attributeLabel);

								logMetacat.debug("Attribute definition: " + attributeDefinition);

								logMetacat.debug("Attribute type: " + attributeType);

								logMetacat.debug("Attribute scale: " + attributeScale);

								logMetacat.debug("Attribute unit type: " + attributeUnitType);

								logMetacat.debug("Attribute unit: " + attributeUnit);

								logMetacat.debug("Attribute domain: " + attributeDomain);

								// set the values for this attribute

								insertStatement.setString(1, pid.getValue());

								insertStatement.setString(2, title);

								insertStatement.setString(3, entityName);

								insertStatement.setString(4, attributeName);

								insertStatement.setString(5, attributeLabel);

								insertStatement.setString(6, attributeDefinition);

								insertStatement.setString(7, attributeType);

								insertStatement.setString(8, attributeScale);

								insertStatement.setString(9, attributeUnitType);

								insertStatement.setString(10, attributeUnit);

								insertStatement.setString(11, attributeDomain);

								insertStatement.execute();

							}		

						}

					}

				} catch (Exception e) {

					logMetacat.warn("error parsing metadata for: " + pid.getValue(), e);

				}

			}

		} catch (SQLException sqle) {

			// just throw it

			throw sqle;

		} finally {

			if (dbconn != null) {

				DBConnectionPool.returnDBConnection(dbconn, 0);

				dbconn.close();

			}

		}

	}

	public static void main(String[] args) throws Exception {

		// set up the properties based on the test/deployed configuration of the workspace

		SortedProperties testProperties = new SortedProperties("test/test.properties");

		testProperties.load();

		String metacatContextDir = testProperties.getProperty("metacat.contextDir");

		PropertyService.getInstance(metacatContextDir + "/WEB-INF");

		// summarize the packages

		DatapackageSummarizer ds = new DatapackageSummarizer();

		List<Identifier> identifiers = new ArrayList<Identifier>();

		Vector<String> idList = DBUtil.getAllDocidsByType(DocumentImpl.EML2_0_0NAMESPACE, false, 1);

		Vector<String> idList1 = DBUtil.getAllDocidsByType(DocumentImpl.EML2_0_1NAMESPACE, false, 1);

		Vector<String> idList2 = DBUtil.getAllDocidsByType(DocumentImpl.EML2_1_0NAMESPACE, false, 1);

		Vector<String> idList3 = DBUtil.getAllDocidsByType(DocumentImpl.EML2_1_1NAMESPACE, false, 1);

		idList.addAll(idList1);

		idList.addAll(idList2);

		idList.addAll(idList3);

		for (String localId : idList) {

			try {

				String guid = IdentifierManager.getInstance().getGUID(

						DocumentUtil.getDocIdFromAccessionNumber(localId), 

						DocumentUtil.getRevisionFromAccessionNumber(localId));

				Identifier pid = new Identifier();

				pid.setValue(guid);

				identifiers.add(pid);

			} catch (McdbDocNotFoundException nfe) {

				// just skip it

				continue;

			}

		}

		ds.summarize(identifiers);

		System.exit(0);

	}

}