Author: [log in to unmask]
Date: Tue Sep 1 19:04:51 2015
New Revision: 3487
Log:
Rework extraction of EVIO metadata so it is included with the event processing via EvioLoop.
Added:
java/trunk/crawler/src/main/java/org/hps/crawler/EvioDatacatUtilities.java
java/trunk/record-util/src/main/java/org/hps/record/evio/EvioFileMetadata.java
- copied, changed from r3467, java/trunk/record-util/src/main/java/org/hps/record/evio/EvioFileMetaData.java
java/trunk/record-util/src/main/java/org/hps/record/evio/EvioFileMetadataAdapter.java
java/trunk/record-util/src/main/java/org/hps/record/evio/EvioFileMetadataProcessor.java
Removed:
java/trunk/record-util/src/main/java/org/hps/record/evio/EvioFileMetaData.java
Modified:
java/trunk/crawler/src/main/java/org/hps/crawler/Crawler.java
java/trunk/crawler/src/main/java/org/hps/crawler/CrawlerConfig.java
java/trunk/crawler/src/main/java/org/hps/crawler/RunProcessor.java
Modified: java/trunk/crawler/src/main/java/org/hps/crawler/Crawler.java
=============================================================================
--- java/trunk/crawler/src/main/java/org/hps/crawler/Crawler.java (original)
+++ java/trunk/crawler/src/main/java/org/hps/crawler/Crawler.java Tue Sep 1 19:04:51 2015
@@ -7,10 +7,10 @@
import java.nio.file.attribute.BasicFileAttributes;
import java.sql.Connection;
import java.sql.SQLException;
-import java.util.ArrayList;
import java.util.Date;
import java.util.EnumSet;
import java.util.HashSet;
+import java.util.List;
import java.util.Set;
import java.util.logging.Level;
import java.util.logging.Logger;
@@ -21,8 +21,10 @@
import org.apache.commons.cli.ParseException;
import org.apache.commons.cli.PosixParser;
import org.hps.conditions.database.ConnectionParameters;
+import org.hps.record.evio.EvioFileMetadata;
import org.hps.run.database.RunDatabaseDaoFactory;
import org.hps.run.database.RunSummary;
+import org.hps.run.database.RunSummaryDao;
import org.hps.run.database.RunSummaryImpl;
import org.lcsim.util.log.DefaultLogFormatter;
import org.lcsim.util.log.LogUtil;
@@ -55,18 +57,19 @@
*/
static {
OPTIONS.addOption("b", "min-date", true, "min date for a file (example \"2015-03-26 11:28:59\")");
- OPTIONS.addOption("C", "cache", false, "automatically cache files from MSS to cache disk (JLAB only)");
+ OPTIONS.addOption("c", "datacat", true, "update the data catalog using the specified folder (off by default)");
+ OPTIONS.addOption("C", "cache", false, "cache files from MSS (JLAB only and not for batch farm use!)");
OPTIONS.addOption("p", "connection-properties", true, "database connection properties file (required)");
OPTIONS.addOption("d", "directory", true, "root directory to start crawling (default is current dir)");
OPTIONS.addOption("E", "evio-processor", true, "class name of an EvioEventProcessor to execute");
OPTIONS.addOption("h", "help", false, "print help and exit (overrides all other arguments)");
OPTIONS.addOption("i", "insert", false, "insert information into the run database (not done by default)");
OPTIONS.addOption("L", "log-level", true, "set the log level (INFO, FINE, etc.)");
- OPTIONS.addOption("r", "run", true, "add a run number to accept (when used others will be excluded)");
+ OPTIONS.addOption("r", "run", true, "add a run number to accept (others will be excluded)");
OPTIONS.addOption("t", "timestamp-file", true, "existing or new timestamp file name");
- OPTIONS.addOption("w", "max-cache-wait", true, "total time to allow for file caching (seconds)");
+ OPTIONS.addOption("w", "max-cache-wait", true, "time per run allowed for file caching in seconds");
OPTIONS.addOption("u", "update", false, "allow replacement of existing data in the run db (off by default)");
- OPTIONS.addOption("x", "max-depth", true, "max depth to crawl in the directory tree");
+ OPTIONS.addOption("x", "max-depth", true, "max depth to crawl");
}
/**
@@ -88,26 +91,21 @@
* @param runs the run log containing the list of run summaries
* @throws Exception if there is an error processing one of the runs
*/
- static void processRuns(final JCacheManager cacheManager, final RunSummaryMap runs, final boolean useFileCache)
- throws Exception {
-
- // Process all of the runs that were found.
- for (final RunSummary runSummary : runs.getRunSummaries()) {
-
- // Clear the cache manager.
- if (useFileCache) {
- LOGGER.info("clearing file cache");
- cacheManager.clear();
- }
-
- // Create a processor to process all the EVIO events in the run.
- LOGGER.info("creating run processor for " + runSummary.getRun());
- final RunProcessor runProcessor = new RunProcessor(cacheManager, (RunSummaryImpl) runSummary, useFileCache);
-
- // Process all of the files from the run.
- LOGGER.info("processing run " + runSummary.getRun());
- runProcessor.processRun();
- }
+ static RunProcessor processRun(final RunSummary runSummary) throws Exception {
+
+ LOGGER.info("processing run" + runSummary.getRun());
+
+ // Create a processor to process all the EVIO events in the run.
+ LOGGER.info("creating run processor for " + runSummary.getRun());
+ final RunProcessor runProcessor = new RunProcessor((RunSummaryImpl) runSummary);
+
+ // Process all of the files from the run.
+ LOGGER.info("processing run " + runSummary.getRun());
+ runProcessor.processRun();
+
+ LOGGER.getHandlers()[0].flush();
+
+ return runProcessor;
}
/**
@@ -124,6 +122,35 @@
* The options parser.
*/
private final PosixParser parser = new PosixParser();
+
+ /**
+ * Cache all files and wait for the operation to complete.
+ * <p>
+ * Potentially, this operation can take a very long time. This can be managed using the
+ * {@link JCacheManager#setWaitTime(long)} method to set a timeout.
+ */
+ private void cacheFiles(final RunSummary runSummary) {
+ if (this.config.useFileCache()) {
+
+ LOGGER.info("caching files for run " + runSummary.getRun());
+
+ // Cache all the files and wait for the operation to complete.
+ this.cacheManager.cache(runSummary.getEvioFiles());
+ final boolean cached = this.cacheManager.waitForCache();
+
+ // If the files weren't cached then die.
+ if (!cached) {
+ throw new RuntimeException("The cache process did not complete in time.");
+ }
+
+ LOGGER.info("done caching files from run " + runSummary.getRun());
+
+ } else {
+ LOGGER.info("file caching disabled");
+ }
+
+ LOGGER.getHandlers()[0].flush();
+ }
/**
* Parse command line options and create a new {@link Crawler} object from the configuration.
@@ -263,6 +290,7 @@
final String[] classNames = cl.getOptionValues("E");
for (final String className : classNames) {
try {
+ LOGGER.config("adding extra EVIO processor " + className);
config.addProcessor(className);
} catch (final Exception e) {
throw new RuntimeException(e);
@@ -277,6 +305,18 @@
throw new IllegalArgumentException("invalid -x argument for maxDepth: " + maxDepth);
}
config.setMaxDepth(maxDepth);
+ LOGGER.config("set max depth to " + maxDepth);
+ }
+
+ // Update data catalog.
+ if (cl.hasOption("c")) {
+ final String datacatFolder = cl.getOptionValue("c");
+ if (datacatFolder == null) {
+ throw new IllegalArgumentException("missing -c argument with data catalog folder");
+ }
+ LOGGER.config("using data catalog folder " + datacatFolder);
+ config.setDatacatFolder(datacatFolder);
+ config.setUpdateDatacat(true);
}
} catch (final ParseException e) {
@@ -310,37 +350,59 @@
*/
public void run() throws Exception {
- LOGGER.info("running Crawler job");
+ LOGGER.info("starting Crawler job");
// Create the file visitor for crawling the root directory with the given date filter.
- LOGGER.info("creating file visitor");
- LOGGER.getHandlers()[0].flush();
final EvioFileVisitor visitor = new EvioFileVisitor(config.timestamp());
// Walk the file tree using the visitor.
- LOGGER.info("walking the dir tree");
- LOGGER.getHandlers()[0].flush();
this.walk(visitor);
// Get the list of run data created by the visitor.
- final RunSummaryMap runs = visitor.getRunMap();
-
- // Process all the files, performing caching from the MSS if necessary.
- LOGGER.info("processing all runs");
- processRuns(this.cacheManager, runs, config.useFileCache());
- LOGGER.getHandlers()[0].flush();
-
- // Execute the run database update.
- LOGGER.info("updating run database");
- this.updateRunDatabase(runs);
- LOGGER.getHandlers()[0].flush();
+ final RunSummaryMap runMap = visitor.getRunMap();
+
+ // Process all runs that were found.
+ for (RunSummary runSummary : runMap.getRunSummaries()) {
+
+ if (runSummary == null) {
+ throw new IllegalArgumentException("The run summary is null for some weird reason.");
+ }
+
+ LOGGER.info("starting full processing of run " + runSummary.getRun());
+
+ // Cache files from MSS.
+ this.cacheFiles(runSummary);
+
+ // Process the run's files.
+ RunProcessor runProcessor = processRun(runSummary);
+
+ // Execute the run database update.
+ this.updateRunDatabase(runSummary);
+
+ // Update the data catalog.
+ this.updateDatacat(runProcessor.getEvioFileMetaData());
+
+ LOGGER.info("completed full processing of run " + runSummary);
+ }
// Update the timestamp output file.
- LOGGER.info("updating the timestamp");
this.updateTimestamp();
- LOGGER.getHandlers()[0].flush();
LOGGER.info("Crawler job is done!");
+ }
+
+ /**
+ * Update the data catalog.
+ *
+ * @param runMap the map of run information including the EVIO file list
+ */
+ private void updateDatacat(List<EvioFileMetadata> metadataList) {
+ if (this.config.updateDatacat()) {
+ EvioDatacatUtilities.addEvioFiles(metadataList, config.datacatFolder());
+ LOGGER.info("done updating data catalog");
+ } else {
+ LOGGER.info("updating data catalog is disabled");
+ }
}
/**
@@ -349,20 +411,33 @@
* @param runs the list of runs to update
* @throws SQLException if there is a database query error
*/
- private void updateRunDatabase(final RunSummaryMap runs) throws SQLException {
+ private void updateRunDatabase(final RunSummary runSummary) throws SQLException {
// Insert the run information into the database.
if (config.updateRunDatabase()) {
- LOGGER.info("updating run database is enabled");
+ LOGGER.info("updating run database for run " + runSummary.getRun());
// Open a DB connection.
final Connection connection = config.connectionParameters().createConnection();
+ // Create factory for interfacing to run database.
final RunDatabaseDaoFactory dbFactory = new RunDatabaseDaoFactory(connection);
- // Insert all run summaries into the database.
- dbFactory.createRunSummaryDao().insertFullRunSummaries(new ArrayList<RunSummary>(runs.getRunSummaries()),
- config.allowUpdates());
+ // Create object for updating run info in the database.
+ final RunSummaryDao runSummaryDao = dbFactory.createRunSummaryDao();
+
+ // Delete existing run summary if necessary.
+ if (runSummaryDao.runSummaryExists(runSummary.getRun())) {
+ if (this.config.allowUpdates()) {
+ LOGGER.info("deleting existing information for run " + runSummary.getRun());
+ runSummaryDao.deleteFullRunSummary(runSummary);
+ } else {
+ throw new RuntimeException("Run " + runSummary.getRun() + " exists in database and deletion is not enabled.");
+ }
+ }
+
+ // Insert run summary into database.
+ runSummaryDao.insertFullRunSummary(runSummary);
// Close the DB connection.
connection.close();
@@ -370,28 +445,32 @@
LOGGER.info("done updating run database");
} else {
- LOGGER.info("updating run database is not enabled");
- }
+ LOGGER.info("updating run database is disabled");
+ }
+
+ LOGGER.getHandlers()[0].flush();
}
/**
* Update the timestamp file's modification date to the time when this job ended.
* <p>
- * This can be then be used in subsequent crawl jobs to filter out files that have already been seen.
+ * This can be then be used in subsequent crawl jobs to filter out files that have already been processed.
*/
private void updateTimestamp() {
- // Update the timestamp file which can be used to tell which files have been processed by their creation date.
if (config.timestampFile() == null) {
+
+ LOGGER.info("creating default timestamp file");
+
config.setTimestampFile(new File("timestamp"));
try {
config.timestampFile().createNewFile();
} catch (final IOException e) {
throw new RuntimeException(e);
}
- LOGGER.config("created new timestamp file: " + config.timestampFile().getPath());
}
config.timestampFile().setLastModified(System.currentTimeMillis());
- LOGGER.config("set modified on timestamp file: " + new Date(config.timestampFile().lastModified()));
+ LOGGER.info("touching timestamp file " + config.timestampFile().getPath());
+ LOGGER.info("set modified on timestamp file: " + new Date(config.timestampFile().lastModified()));
}
/**
Modified: java/trunk/crawler/src/main/java/org/hps/crawler/CrawlerConfig.java
=============================================================================
--- java/trunk/crawler/src/main/java/org/hps/crawler/CrawlerConfig.java (original)
+++ java/trunk/crawler/src/main/java/org/hps/crawler/CrawlerConfig.java Tue Sep 1 19:04:51 2015
@@ -43,6 +43,13 @@
private ConnectionParameters connectionParameters;
/**
+ * The name of the folder in the data catalog for inserting data (under "/HPS" root folder).
+ * <p>
+ * Default provided for Eng Run 2015 data.
+ */
+ private String datacatFolder = null;
+
+ /**
* The maximum depth to crawl.
*/
private Integer maxDepth = Integer.MAX_VALUE;
@@ -71,6 +78,11 @@
* A file to use for getting the timestamp date.
*/
private File timestampFile = null;
+
+ /**
+ * <code>true</code> if the data catalog should be updated (off by default).
+ */
+ private boolean updateDatacat = false;
/**
* <code>true</code> if the run database should be updated from results of the job.
@@ -141,6 +153,15 @@
}
/**
+ * Get the data catalog folder.
+ *
+ * @return the data catalog folder
+ */
+ String datacatFolder() {
+ return this.datacatFolder;
+ }
+
+ /**
* Get the max depth in the directory tree to crawl.
*
* @return the max depth
@@ -212,6 +233,16 @@
}
/**
+ * Set the data catalog folder.
+ *
+ * @param datacatFolder the data catalog folder
+ */
+ CrawlerConfig setDatacatFolder(final String datacatFolder) {
+ this.datacatFolder = datacatFolder;
+ return this;
+ }
+
+ /**
* Set the max depth.
*
* @param maxDepth the max depth
@@ -284,6 +315,16 @@
}
/**
+ * Set to <code>true</code> to update data catalog.
+ *
+ * @param updateDatacat <code>true</code> to update data catalog
+ */
+ CrawlerConfig setUpdateDatacat(final boolean updateDatacat) {
+ this.updateDatacat = updateDatacat;
+ return this;
+ }
+
+ /**
* Set whether the run database should be updated in the job.
* <p>
* This will not allow replacement of existing run log records. The {@link #allowUpdates()} flag must be on for this
@@ -344,6 +385,15 @@
}
/**
+ * Get whether data catalog should be updated or not.
+ *
+ * @return <code>true</code> if data catalog should be update
+ */
+ boolean updateDatacat() {
+ return this.updateDatacat;
+ }
+
+ /**
* Return <code>true</code> if the run database should be updated.
*
* @return <code>true</code> if the run database should be updated
Added: java/trunk/crawler/src/main/java/org/hps/crawler/EvioDatacatUtilities.java
=============================================================================
--- java/trunk/crawler/src/main/java/org/hps/crawler/EvioDatacatUtilities.java (added)
+++ java/trunk/crawler/src/main/java/org/hps/crawler/EvioDatacatUtilities.java Tue Sep 1 19:04:51 2015
@@ -0,0 +1,100 @@
+package org.hps.crawler;
+
+import java.io.File;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+import org.hps.datacat.client.DatacatClient;
+import org.hps.datacat.client.DatacatClientFactory;
+import org.hps.datacat.client.DatasetDataType;
+import org.hps.datacat.client.DatasetFileFormat;
+import org.hps.datacat.client.DatasetSite;
+import org.hps.record.evio.EvioFileMetadata;
+import org.lcsim.util.log.DefaultLogFormatter;
+import org.lcsim.util.log.LogUtil;
+
+/**
+ * Utility for inserting EVIO files into the SRS data catalog.
+ *
+ * @author Jeremy McCormick, SLAC
+ */
+final class EvioDatacatUtilities {
+
+ /**
+ * Setup logger.
+ */
+ private static final Logger LOGGER = LogUtil.create(EvioDatacatUtilities.class, new DefaultLogFormatter(), Level.FINE);
+
+ /**
+ * Add an EVIO to the data catalog.
+ *
+ * @param client the data catalog client
+ * @param folder the folder name e.g. "data/raw"
+ * @param evioFile the evio file to add to the data catalog
+ * @param evioMetadata the EVIO file's meta data
+ * @return the HTTP response code
+ */
+ static int addEvioFile(final DatacatClient client, final String folder, final EvioFileMetadata evioMetadata) {
+
+ // Create metadata map for adding dataset.
+ final Map<String, Object> metadataMap = createMetadataMap(evioMetadata);
+
+ // Get the EVIO file.
+ File evioFile = evioMetadata.getEvioFile();
+
+ // Add the dataset to the data catalog using the REST API.
+ final int response = client.addDataset(folder, DatasetDataType.RAW, evioFile.getPath(), DatasetSite.SLAC,
+ DatasetFileFormat.EVIO, evioFile.getName(), metadataMap);
+
+ return response;
+ }
+
+ /**
+ * Add a list of EVIO files to the data catalog.
+ *
+ * @param evioFiles the list of EVIO files
+ * @param folder the folder in the data catalog
+ */
+ static void addEvioFiles(List<EvioFileMetadata> metadataList, final String folder) {
+ LOGGER.info("adding " + metadataList.size() + " EVIO files to data catalog in folder " + folder);
+ final DatacatClientFactory datacatFactory = new DatacatClientFactory();
+ final DatacatClient datacatClient = datacatFactory.createClient();
+ for (EvioFileMetadata metadata : metadataList) {
+ LOGGER.info("adding " + metadata.getEvioFile().getPath() + " to data catalog");
+ EvioDatacatUtilities.addEvioFile(datacatClient, folder, metadata);
+ }
+ }
+
+ /**
+ * Create a map of metadata keys and values suitable for making a new dataset.
+ *
+ * @param evioMetadata the EVIO metadata object
+ * @return the metadata map
+ */
+ static Map<String, Object> createMetadataMap(EvioFileMetadata evioMetadata) {
+ final Map<String, Object> metadataMap = new HashMap<String, Object>();
+ metadataMap.put("runMin", evioMetadata.getRun());
+ metadataMap.put("runMax", evioMetadata.getRun());
+ metadataMap.put("eventCount", evioMetadata.getEventCount());
+ metadataMap.put("size", evioMetadata.getByteCount());
+ metadataMap.put("fileNumber", evioMetadata.getSequence());
+ metadataMap.put("badEventCount", evioMetadata.getBadEventCount());
+ metadataMap.put("endTimestamp", evioMetadata.getEndDate().getTime());
+ metadataMap.put("startTimestamp", evioMetadata.getStartDate().getTime());
+ metadataMap.put("startEvent", evioMetadata.getStartEvent());
+ metadataMap.put("endEvent", evioMetadata.getEndEvent());
+ metadataMap.put("hasEnd", evioMetadata.hasEnd() ? 1 : 0);
+ metadataMap.put("hasPrestart", evioMetadata.hasPrestart() ? 1 : 0);
+ return metadataMap;
+ }
+
+ /**
+ * Class constructor which is private.
+ */
+ private EvioDatacatUtilities() {
+ throw new RuntimeException("Do not instantiate this class.");
+ }
+}
Modified: java/trunk/crawler/src/main/java/org/hps/crawler/RunProcessor.java
=============================================================================
--- java/trunk/crawler/src/main/java/org/hps/crawler/RunProcessor.java (original)
+++ java/trunk/crawler/src/main/java/org/hps/crawler/RunProcessor.java Tue Sep 1 19:04:51 2015
@@ -1,13 +1,13 @@
package org.hps.crawler;
-import java.io.File;
import java.util.Collections;
+import java.util.List;
import java.util.logging.Level;
import java.util.logging.Logger;
import org.hps.record.epics.EpicsRunProcessor;
-import org.hps.record.evio.EvioFileMetaData;
-import org.hps.record.evio.EvioFileMetaDataReader;
+import org.hps.record.evio.EvioFileMetadata;
+import org.hps.record.evio.EvioFileMetadataAdapter;
import org.hps.record.evio.EvioFileSequenceComparator;
import org.hps.record.evio.EvioFileSource;
import org.hps.record.evio.EvioLoop;
@@ -37,11 +37,6 @@
private static final Logger LOGGER = LogUtil.create(RunProcessor.class, new DefaultLogFormatter(), Level.FINE);
/**
- * The cache manager.
- */
- private final JCacheManager cacheManager;
-
- /**
* Processor for extracting EPICS information.
*/
private final EpicsRunProcessor epicsProcessor;
@@ -70,11 +65,11 @@
* Processor for extracting TI time offset.
*/
private final TiTimeOffsetEvioProcessor triggerTimeProcessor;
-
- /**
- * Set to <code>true</code> to use file caching.
- */
- private final boolean useFileCache;
+
+ /**
+ * Record loop adapter for getting file metadata.
+ */
+ private final EvioFileMetadataAdapter metadataAdapter = new EvioFileMetadataAdapter();
/**
* Create a run processor.
@@ -82,13 +77,9 @@
* @param runSummary the run summary object for the run
* @return the run processor
*/
- RunProcessor(final JCacheManager cacheManager, final RunSummaryImpl runSummary, final boolean useFileCache) {
+ RunProcessor(final RunSummaryImpl runSummary) {
this.runSummary = runSummary;
- this.cacheManager = cacheManager;
-
- // Set whether file caching from MSS is enabled.
- this.useFileCache = useFileCache;
// Sort the list of EVIO files.
Collections.sort(runSummary.getEvioFiles(), new EvioFileSequenceComparator());
@@ -109,63 +100,46 @@
// Add processor for extracting TI time offset.
triggerTimeProcessor = new TiTimeOffsetEvioProcessor();
evioLoop.addEvioEventProcessor(triggerTimeProcessor);
- }
-
- /**
- * Cache all files and wait for the operation to complete.
- * <p>
- * Potentially, this operation can take a very long time. This can be managed using the
- * {@link JCacheManager#setWaitTime(long)} method to set a timeout.
- */
- private void cacheFiles() {
-
- LOGGER.info("caching files from run " + this.runSummary.getRun());
-
- // Cache all the files and wait for the operation to complete.
- this.cacheManager.cache(this.runSummary.getEvioFiles());
- final boolean cached = this.cacheManager.waitForCache();
-
- // If the files weren't cached then die.
- if (!cached) {
- throw new RuntimeException("The cache process did not complete in time.");
- }
-
- LOGGER.info("done caching files from run " + this.runSummary.getRun());
+
+ // Add file metadata processor.
+ evioLoop.addRecordListener(metadataAdapter);
+ evioLoop.addLoopListener(metadataAdapter);
}
/**
* Extract meta data from first file in run.
*/
- private void processFirstFile() {
- final File firstEvioFile = runSummary.getEvioFiles().get(0);
- LOGGER.info("getting meta data for " + firstEvioFile.getPath());
- final EvioFileMetaDataReader metaDataReader = new EvioFileMetaDataReader();
- final EvioFileMetaData metaData = metaDataReader.getMetaData(firstEvioFile);
- LOGGER.info(metaData.toString());
- if (metaData.getStartDate() == null) {
- throw new IllegalStateException("The start date is not set in the EVIO file meta data from "
- + firstEvioFile.getPath());
- }
- LOGGER.info("setting unix start time to " + metaData.getStartDate().getTime() + " from meta data");
- runSummary.setStartDate(metaData.getStartDate());
+ private void processFirstFile() {
+ final EvioFileMetadata metadata = metadataAdapter.getEvioFileMetadata().get(0);
+ if (metadata == null) {
+ throw new IllegalStateException("No meta data exists for first file.");
+ }
+ LOGGER.info("first file metadata: " + metadata.toString());
+ if (metadata.getStartDate() == null) {
+ throw new IllegalStateException("The start date is not set in the metadata.");
+ }
+ LOGGER.info("setting unix start time to " + metadata.getStartDate().getTime() + " from meta data");
+ runSummary.setStartDate(metadata.getStartDate());
}
/**
* Extract meta data from last file in run.
*/
private void processLastFile() {
- final File lastEvioFile = runSummary.getEvioFiles().get(runSummary.getEvioFiles().size() - 1);
- LOGGER.info("getting meta data for " + lastEvioFile.getPath());
- final EvioFileMetaDataReader metaDataReader = new EvioFileMetaDataReader();
- final EvioFileMetaData metaData = metaDataReader.getMetaData(lastEvioFile);
- LOGGER.info(metaData.toString());
- if (metaData.getEndDate() == null) {
- throw new IllegalStateException("The end date is not set in the EVIO file meta data from "
- + lastEvioFile.getPath());
- }
- LOGGER.info("setting unix end time to " + metaData.getEndDate().getTime() + " from meta data");
- runSummary.setEndDate(metaData.getEndDate());
- runSummary.setEndOkay(metaData.hasEnd());
+ LOGGER.info("looking for " + runSummary.getEvioFiles().get(runSummary.getEvioFiles().size() - 1).getPath() + " metadata");
+ LOGGER.getHandlers()[0].flush();
+ final EvioFileMetadata metadata = this.metadataAdapter.getEvioFileMetadata().get(this.metadataAdapter.getEvioFileMetadata().size() - 1);
+ if (metadata == null) {
+ throw new IllegalStateException("Failed to find metadata for last file.");
+ }
+ LOGGER.info("last file metadata: " + metadata.toString());
+ if (metadata.getEndDate() == null) {
+ throw new IllegalStateException("The end date is not set in the metadata.");
+ }
+ LOGGER.info("setting unix end time to " + metadata.getEndDate().getTime() + " from meta data");
+ runSummary.setEndDate(metadata.getEndDate());
+ LOGGER.info("setting has END to " + metadata.hasEnd());
+ runSummary.setEndOkay(metadata.hasEnd());
}
/**
@@ -181,21 +155,18 @@
LOGGER.info("processing " + this.runSummary.getEvioFiles().size() + " files from run "
+ this.runSummary.getRun());
- // Cache files from MSS if this is enabled.
- if (this.useFileCache) {
- LOGGER.info("caching files from MSS");
- this.cacheFiles();
- }
-
// Run processors over all files.
LOGGER.info("looping over all events");
evioLoop.loop(-1);
-
- // Get run start date.
+
+ LOGGER.info("got " + metadataAdapter.getEvioFileMetadata().size() + " metadata objects from loop");
+ LOGGER.getHandlers()[0].flush();
+
+ // Set start date from first file.
LOGGER.info("processing first file");
this.processFirstFile();
- // Get run end date.
+ // Set end date from last file.
LOGGER.info("processing last file");
this.processLastFile();
@@ -203,7 +174,7 @@
LOGGER.info("updating run summary");
this.updateRunSummary();
- LOGGER.info("done processing run " + this.runSummary.getRun());
+ LOGGER.info("run processor done with run " + this.runSummary.getRun());
}
/**
@@ -211,8 +182,8 @@
*/
private void updateRunSummary() {
+ // Set total number of events from the event loop.
LOGGER.info("setting total events " + evioLoop.getTotalCountableConsumed());
- // Set total number of events from the event loop.
runSummary.setTotalEvents((int) evioLoop.getTotalCountableConsumed());
// Add scaler data from the scalers EVIO processor.
@@ -231,5 +202,14 @@
runSummary.setTriggerConfigInt(triggerConfig);
LOGGER.getHandlers()[0].flush();
+ }
+
+ /**
+ * Get list of metadata created by processing the files.
+ *
+ * @return the list of metadata
+ */
+ List<EvioFileMetadata> getEvioFileMetaData() {
+ return this.metadataAdapter.getEvioFileMetadata();
}
}
Copied: java/trunk/record-util/src/main/java/org/hps/record/evio/EvioFileMetadata.java (from r3467, java/trunk/record-util/src/main/java/org/hps/record/evio/EvioFileMetaData.java)
=============================================================================
--- java/trunk/record-util/src/main/java/org/hps/record/evio/EvioFileMetaData.java (original)
+++ java/trunk/record-util/src/main/java/org/hps/record/evio/EvioFileMetadata.java Tue Sep 1 19:04:51 2015
@@ -2,15 +2,13 @@
import java.io.File;
import java.util.Date;
-import java.util.HashMap;
-import java.util.Map;
/**
* Meta data that can be extracted from EVIO files.
*
* @author Jeremy McCormick, SLAC
*/
-public final class EvioFileMetaData {
+public final class EvioFileMetadata {
/**
* The number of bad events in the file that are unreadable.
@@ -77,15 +75,17 @@
*
* @param evioFile the EVIO file to which the meta data applies
*/
- public EvioFileMetaData(final File evioFile) {
+ public EvioFileMetadata(final File evioFile) {
if (evioFile == null) {
throw new IllegalArgumentException("The EVIO file argument is null.");
}
if (!evioFile.exists()) {
- throw new IllegalArgumentException("The file " + evioFile.getPath()
- + " does not exist or it is inaccessible.");
+ throw new IllegalArgumentException("The file " + evioFile.getPath() + " does not exist.");
}
this.evioFile = evioFile;
+
+ // Set sequence number.
+ setSequence(EvioFileUtilities.getSequenceFromName(this.evioFile));
}
/**
@@ -314,28 +314,4 @@
+ this.hasEnd + ", run: " + this.run + ", fileNumber: " + sequence + ", startEvent: "
+ this.startEvent + ", endEvent: " + endEvent + " }";
}
-
- /**
- * Convert data to a map with names and values (int, float or string).
- *
- * @return the metadata converted to a map
- */
- public Map<String, Object> toMap() {
- Map<String, Object> metadataMap = new HashMap<String, Object>();
- metadataMap.put("badEventCount", badEventCount);
- metadataMap.put("size", byteCount);
- metadataMap.put("endDate", endDate.getTime());
- metadataMap.put("endEvent", endEvent);
- metadataMap.put("endDate", endDate.getTime());
- metadataMap.put("endEvent", endEvent);
- metadataMap.put("eventCount", eventCount);
- metadataMap.put("evioFile", evioFile.getPath());
- metadataMap.put("hasEnd", hasEnd ? 1 : 0);
- metadataMap.put("hasPrestart", hasPrestart ? 1 : 0);
- metadataMap.put("run", run);
- metadataMap.put("fileNumber", sequence);
- metadataMap.put("startDate", startDate.getTime());
- metadataMap.put("startEvent", startEvent);
- return metadataMap;
- }
}
Added: java/trunk/record-util/src/main/java/org/hps/record/evio/EvioFileMetadataAdapter.java
=============================================================================
--- java/trunk/record-util/src/main/java/org/hps/record/evio/EvioFileMetadataAdapter.java (added)
+++ java/trunk/record-util/src/main/java/org/hps/record/evio/EvioFileMetadataAdapter.java Tue Sep 1 19:04:51 2015
@@ -0,0 +1,104 @@
+package org.hps.record.evio;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+import org.freehep.record.loop.AbstractLoopListener;
+import org.freehep.record.loop.LoopEvent;
+import org.freehep.record.loop.LoopListener;
+import org.freehep.record.loop.RecordEvent;
+import org.freehep.record.loop.RecordListener;
+import org.jlab.coda.jevio.EvioEvent;
+import org.lcsim.util.log.DefaultLogFormatter;
+import org.lcsim.util.log.LogUtil;
+
+/**
+ * Loop adapter for creating a list of metadata from processed EVIO files.
+ *
+ * @author Jeremy McCormick, SLAC
+ */
+public class EvioFileMetadataAdapter extends AbstractLoopListener implements RecordListener, LoopListener {
+
+ /**
+ * Setup logging.
+ */
+ private static Logger LOGGER = LogUtil.create(EvioFileMetadataProcessor.class, new DefaultLogFormatter(), Level.ALL);
+
+ /**
+ * The EVIO file currently being processed.
+ */
+ File currentEvioFile = null;
+
+ /**
+ * The list of metadata created by the job.
+ */
+ List<EvioFileMetadata> metadataList = new ArrayList<EvioFileMetadata>();
+
+ /**
+ * The processor that creates the metadata for each file.
+ */
+ EvioFileMetadataProcessor metadataProcessor = null;
+
+ /**
+ * Perform single record processing of EVIO events.
+ *
+ * @param recordEvent the record event with the EVIO event
+ */
+ @Override
+ public void recordSupplied(RecordEvent recordEvent) {
+ EvioEvent evioEvent = (EvioEvent) recordEvent.getRecord();
+ if (evioEvent == null) {
+ throw new RuntimeException("Record has wrong type.");
+ }
+ EvioFileSource evioSource = (EvioFileSource) recordEvent.getSource().getRecordSource();
+ if (evioSource == null) {
+ throw new RuntimeException("Wrong record source type.");
+ }
+
+ // First time setup.
+ if (currentEvioFile == null) {
+ currentEvioFile = evioSource.getCurrentFile();
+ LOGGER.info("got first file " + currentEvioFile.getPath());
+ metadataProcessor = new EvioFileMetadataProcessor(currentEvioFile);
+ }
+
+ // Start of new file.
+ if (evioSource.getCurrentFile() != currentEvioFile) {
+ LOGGER.info("putting metadata for " + currentEvioFile.getPath() + " into output");
+ EvioFileMetadata metadata = this.metadataProcessor.createEvioFileMetadata();
+ metadataList.add(metadata);
+
+ LOGGER.info("starting metadata for new file " + evioSource.getCurrentFile().getPath());
+ currentEvioFile = evioSource.getCurrentFile();
+ metadataProcessor = new EvioFileMetadataProcessor(currentEvioFile);
+ }
+
+ // Process an EVIO event.
+ metadataProcessor.process(evioEvent);
+ }
+
+ /**
+ * End of job hook.
+ *
+ * @param event the loop event (contents ignored)
+ */
+ public void finish(final LoopEvent event) {
+ LOGGER.info("finish");
+ metadataList.add(metadataProcessor.createEvioFileMetadata());
+ LOGGER.info("created " + metadataList.size() + " metadata objects in job");
+ LOGGER.getHandlers()[0].flush();
+ }
+
+ /**
+ * Get the list of metadata generated by the job.
+ *
+ * @return the list of metadata generated by the job
+ */
+ public List<EvioFileMetadata> getEvioFileMetadata() {
+ return this.metadataList;
+ }
+
+}
Added: java/trunk/record-util/src/main/java/org/hps/record/evio/EvioFileMetadataProcessor.java
=============================================================================
--- java/trunk/record-util/src/main/java/org/hps/record/evio/EvioFileMetadataProcessor.java (added)
+++ java/trunk/record-util/src/main/java/org/hps/record/evio/EvioFileMetadataProcessor.java Tue Sep 1 19:04:51 2015
@@ -0,0 +1,113 @@
+package org.hps.record.evio;
+
+import java.io.File;
+import java.util.Date;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+import org.jlab.coda.jevio.EvioEvent;
+import org.lcsim.util.log.DefaultLogFormatter;
+import org.lcsim.util.log.LogUtil;
+
+
+public class EvioFileMetadataProcessor extends EvioEventProcessor {
+
+ private static Logger LOGGER = LogUtil.create(EvioFileMetadataProcessor.class, new DefaultLogFormatter(), Level.ALL);
+
+ private File evioFile = null;
+ private Date startDate = null;
+ private Date endDate = null;
+ private int badEventCount = 0;
+ private int eventCount = 0;
+ private int byteCount = 0;
+ private boolean hasPrestart = false;
+ private boolean hasEnd = false;
+ private int[] eventIdData = null;
+ private Integer run = null;
+ private Integer endEvent = null;
+ private Integer startEvent = null;
+ private Long lastTimestamp = null;
+
+ EvioFileMetadataProcessor(File evioFile) {
+ this.evioFile = evioFile;
+ }
+
+ public void process(EvioEvent evioEvent) {
+ byteCount += evioEvent.getTotalBytes();
+ if (EventTagConstant.PRESTART.equals(evioEvent)) {
+ LOGGER.info("found PRESTART");
+ hasPrestart = true;
+ final int[] controlEventData = EvioEventUtilities.getControlEventData(evioEvent);
+ final long timestamp = controlEventData[0] * 1000L;
+ startDate = new Date(timestamp);
+ LOGGER.info("set start date to " + startDate + " from PRESTART");
+ if (run == null) {
+ run = controlEventData[1];
+ LOGGER.info("set run to " + run);
+ }
+ } else if (EventTagConstant.END.equals(evioEvent)) {
+ LOGGER.info("found END event");
+ hasEnd = true;
+ final int[] controlEventData = EvioEventUtilities.getControlEventData(evioEvent);
+ final long timestamp = controlEventData[0] * 1000L;
+ endDate = new Date(timestamp);
+ LOGGER.info("set end date to " + endDate);
+ if (run == null) {
+ run = controlEventData[1];
+ LOGGER.info("set run to " + run);
+ }
+ } else if (EvioEventUtilities.isPhysicsEvent(evioEvent)) {
+ final int[] headBankData = EvioEventUtilities.getHeadBankData(evioEvent);
+ if (startDate == null) {
+ if (headBankData[3] != 0) {
+ startDate = new Date(headBankData[3] * 1000L);
+ LOGGER.info("set start date to " + startDate + " from physics event");
+ }
+ }
+ if (run == null) {
+ run = headBankData[1];
+ LOGGER.info("set run to " + run + " from physics event");
+ }
+ eventIdData = EvioEventUtilities.getEventIdData(evioEvent);
+ if (startEvent == null) {
+ startEvent = eventIdData[0];
+ LOGGER.info("set start event " + startEvent);
+ }
+ if (headBankData[3] != 0) {
+ lastTimestamp = headBankData[3] * 1000L;
+ }
+ ++eventCount;
+ }
+ }
+
+ EvioFileMetadata createEvioFileMetadata() {
+
+ EvioFileMetadata metadata = new EvioFileMetadata(evioFile);
+
+ // Set end date from last valid timestamp.
+ if (endDate == null) {
+ endDate = new Date(lastTimestamp);
+ LOGGER.info("set end date to " + endDate + " from last timestamp " + lastTimestamp);
+ }
+
+ // Set end event number.
+ if (eventIdData != null) {
+ endEvent = eventIdData[0];
+ LOGGER.info("set end event " + endEvent);
+ }
+
+ // Set values on the metadata object.
+ metadata.setStartDate(startDate);
+ metadata.setEndDate(endDate);
+ metadata.setBadEventCount(badEventCount);
+ metadata.setByteCount(byteCount);
+ metadata.setEventCount(eventCount);
+ metadata.setHasPrestart(hasPrestart);
+ metadata.setHasEnd(hasEnd);
+ metadata.setRun(run);
+ metadata.setEndEvent(endEvent);
+ metadata.setStartEvent(startEvent);
+
+ return metadata;
+ }
+}
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