1371

Committed 28 Jun 2024 05:54AM UTC coverage: 25.453% (-0.05%) from 25.503%

Build # 1371

Build Type

push

jenkins

Committed by

web-flow

Commit Message

Closes #2474: Store the entity id in saml session once user logs in with the identity provider (#2486)

Run Details

49 of 54 new or added lines in 4 files covered. (90.74%)

860 existing lines in 14 files now uncovered.

17805 of 69953 relevant lines covered (25.45%)

0.25 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

0.47

/dataverse-webapp/src/main/java/edu/harvard/iq/dataverse/timer/DataverseTimerServiceBean.java

package edu.harvard.iq.dataverse.timer;

import com.google.api.client.util.Preconditions;
import edu.harvard.iq.dataverse.DatasetDao;
import edu.harvard.iq.dataverse.featured.FeaturedDataverseServiceBean;
import edu.harvard.iq.dataverse.authorization.AuthenticationServiceBean;
import edu.harvard.iq.dataverse.datafile.FileIntegrityChecker;
import edu.harvard.iq.dataverse.datafile.pojo.FilesIntegrityReport;
import edu.harvard.iq.dataverse.dataset.DatasetCitationsCountUpdater;
import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
import edu.harvard.iq.dataverse.harvest.client.HarvestTimerInfo;
import edu.harvard.iq.dataverse.harvest.client.HarvesterServiceBean;
import edu.harvard.iq.dataverse.harvest.client.HarvestingClientDao;
import edu.harvard.iq.dataverse.harvest.server.OAISetServiceBean;
import edu.harvard.iq.dataverse.persistence.dataset.Dataset;
import edu.harvard.iq.dataverse.persistence.harvest.HarvestingClient;
import edu.harvard.iq.dataverse.persistence.user.AuthenticatedUser;
import edu.harvard.iq.dataverse.search.index.IndexServiceBean;
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
import edu.harvard.iq.dataverse.settings.SettingsServiceBean.Key;
import edu.harvard.iq.dataverse.util.SystemConfig;
import org.apache.commons.lang3.StringUtils;

import javax.annotation.PostConstruct;
import javax.annotation.Resource;
import javax.ejb.DependsOn;
import javax.ejb.EJB;
import javax.ejb.ScheduleExpression;
import javax.ejb.Singleton;
import javax.ejb.Startup;
import javax.ejb.Timeout;
import javax.ejb.Timer;
import javax.ejb.TimerConfig;
import javax.ejb.TransactionAttribute;
import javax.ejb.TransactionAttributeType;
import javax.inject.Inject;
import javax.servlet.http.HttpServletRequest;
import java.io.IOException;
import java.io.Serializable;
import java.net.InetAddress;
import java.net.UnknownHostException;
import java.util.Calendar;
import java.util.Date;
import java.util.Iterator;
import java.util.List;
import java.util.logging.Level;
import java.util.logging.Logger;


/**
 * This is a largely intact DVN3 implementation.
 * original
 *
 * @author roberttreacy
 * ported by
 * @author Leonid Andreev
 */
@Singleton
@Startup
@DependsOn("StartupFlywayMigrator")
public class DataverseTimerServiceBean implements Serializable {
    private static final Logger logger = Logger.getLogger(DataverseTimerServiceBean.class.getCanonicalName());

    @Resource
    javax.ejb.TimerService timerService;

    @EJB
    HarvesterServiceBean harvesterService;
    @EJB
    HarvestingClientDao harvestingClientService;
    @EJB
    AuthenticationServiceBean authSvc;
    @EJB
    OAISetServiceBean oaiSetService;
    @EJB
    SystemConfig systemConfig;
    @Inject
    SettingsServiceBean settingsService;
    @EJB
    FileIntegrityChecker fileIntegrityChecker;
    @Inject
    DatasetCitationsCountUpdater datasetCitationsCountUpdater;
    @Inject
    FeaturedDataverseServiceBean featuredDataverseServiceBean;

    @Inject
    DatasetDao datasetDao;
    
    @Inject
    IndexServiceBean indexServiceBean;

    @PostConstruct
    public void init() {
        logger.info("PostConstruct timer check.");

        if (systemConfig.isReadonlyMode()) {
            logger.info("Timers not allowed in readonly mode");
            return;
        }

        if (systemConfig.isTimerServer()) {
            logger.info("I am the dedicated timer server. Initializing mother timer.");

            removeAllTimers();
            // create mother timer:
            createMotherTimer();
            // And the export timer (there is only one)
            createExportTimer();

            createIntegrityCheckTimer();
            createCitationCountUpdateTimer();
            createFeaturedDataversesSortingUpdateTimer();
            
            createReindexAfterEmbargoTimer();

        } else {
            logger.info("Skipping timer server init (I am not the dedicated timer server)");
        }
    }

    private void createReindexAfterEmbargoTimer() {
        String cronExpression = settingsService.getValueForKey(Key.ReindexAfterEmbargoTimerExpression);

        if (StringUtils.isNotBlank(cronExpression)) {
            ScheduleExpression expression = cronToScheduleExpression(cronExpression);

            TimerConfig timerConfig = new TimerConfig();
            timerConfig.setPersistent(false);
            timerConfig.setInfo(new AfterEmbargoReindexTimerInfo());
            Timer timer = timerService.createCalendarTimer(expression, timerConfig);
            logger.info("ReindexAfterEmbargoTimerExpression: timer created, initial expiration: " + timer.getNextTimeout());
        } else {
            logger.info("ReindexAfterEmbargoTimerExpression is empty. Skipping creation of timer.");
        }
    }

    public void createTimer(Date initialExpiration, long intervalDuration, Serializable info) {
        try {
            logger.log(Level.INFO, "Creating timer on " + InetAddress.getLocalHost().getCanonicalHostName());
        } catch (UnknownHostException ex) {
            Logger.getLogger(DataverseTimerServiceBean.class.getName()).log(Level.SEVERE, null, ex);
        }
        timerService.createIntervalTimer(initialExpiration, intervalDuration, new TimerConfig(info, false));
    }

    /**
     * This method is called whenever an EJB Timer goes off.
     * Check to see if this is a Harvest Timer, and if it is
     * Run the harvest for the given (scheduled) dataverse
     *
     * @param timer
     */
    @Timeout
    @TransactionAttribute(TransactionAttributeType.NOT_SUPPORTED)
    public void handleTimeout(Timer timer) {
        // We have to put all the code in a try/catch block because
        // if an exception is thrown from this method, Glassfish will automatically
        // call the method a second time. (The minimum number of re-tries for a Timer method is 1)
        if (systemConfig.isReadonlyMode()) {
            Logger.getLogger(DataverseTimerServiceBean.class.getName()).log(Level.WARNING, null, "handleTimeout() was called in readonly mode - skipping timeout handling");
            return;
        }

        if (!systemConfig.isTimerServer()) {
            //logger.info("I am not the timer server! - bailing out of handleTimeout()");
            Logger.getLogger(DataverseTimerServiceBean.class.getName()).log(Level.WARNING, null, "I am not the timer server! - but handleTimeout() got called. Please investigate!");
        }

        try {
            logger.log(Level.INFO, "Handling timeout on " + InetAddress.getLocalHost().getCanonicalHostName());
        } catch (UnknownHostException ex) {
            Logger.getLogger(DataverseTimerServiceBean.class.getName()).log(Level.SEVERE, null, ex);
        }

        if (timer.getInfo() instanceof MotherTimerInfo) {
            logger.info("Behold! I am the Master Timer, king of all timers! I'm here to create all the lesser timers!");
            removeHarvestTimers();
            for (HarvestingClient client : harvestingClientService.getAllHarvestingClients()) {
                createHarvestTimer(client);
            }
        } else if (timer.getInfo() instanceof HarvestTimerInfo) {
            HarvestTimerInfo info = (HarvestTimerInfo) timer.getInfo();
            try {

                logger.log(Level.INFO, "running a harvesting client: id=" + info.getHarvestingClientId());
                // Timer batch jobs are run by the main Admin user.
                // TODO: revisit how we retrieve the superuser here.
                // Should it be configurable somewhere, which superuser
                // runs these jobs? Should there be a central mechanism for obtaining
                // the "major", builtin superuser for this Dataverse instance?
                // -- L.A. 4.5, Aug. 2016
                AuthenticatedUser adminUser = authSvc.getAdminUser(); // getAuthenticatedUser("admin");
                if (adminUser == null) {
                    logger.info("Scheduled harvest: failed to locate the admin user! Exiting.");
                    throw new IOException("Scheduled harvest: failed to locate the admin user");
                }
                logger.info("found admin user " + adminUser.getName());
                DataverseRequest dataverseRequest = new DataverseRequest(adminUser, (HttpServletRequest) null);
                harvesterService.doHarvest(dataverseRequest, info.getHarvestingClientId());

            } catch (Throwable e) {
                // Harvester Service should be handling any error notifications,
                // if/when things go wrong.
                // (TODO: -- verify this logic; harvesterService may still be able
                // to throw an IOException, if it could not run the harvest at all,
                // or could not for whatever reason modify the database record...
                // in this case we should, probably, log the error and try to send
                // a mail notification. -- L.A. 4.4)
                //dataverseService.setHarvestResult(info.getHarvestingDataverseId(), harvesterService.HARVEST_RESULT_FAILED);
                //mailService.sendHarvestErrorNotification(dataverseService.find().getSystemEmail(), dataverseService.find().getName());
                logException(e, logger);
            }
        } else if (timer.getInfo() instanceof ExportTimerInfo) {
            try {
                ExportTimerInfo info = (ExportTimerInfo) timer.getInfo();
                logger.info("Timer Service: Running a scheduled export job.");

                // and update all oai sets:
                oaiSetService.exportAllSets();
            } catch (Throwable e) {
                logException(e, logger);
            }
        } else if (timer.getInfo() instanceof FilesIntegrityCheckTimerInfo) {
            FilesIntegrityReport report = fileIntegrityChecker.checkFilesIntegrity();

            logger.info(report.getSummaryInfo());
        } else if (timer.getInfo() instanceof CitationCountUpdateTimerInfo) {
            datasetCitationsCountUpdater.updateCitationCount();
        } else if (timer.getInfo() instanceof AfterEmbargoReindexTimerInfo) {
            reindexAfterEmbargo();
        } else if (timer.getInfo() instanceof FeaturedDataversesSortingUpdateTimerInfo) {
            featuredDataverseServiceBean.refreshFeaturedDataversesAutomaticSorting();
        }

    }

    private void reindexAfterEmbargo() {
        List<Dataset> datasetsAfterEmbargo = datasetDao.findNotIndexedAfterEmbargo();
        for (Dataset dataset:datasetsAfterEmbargo) {
            indexServiceBean.indexDataset(dataset, true);
        }
    }

    public void removeAllTimers() {
        logger.info("Removing ALL existing timers.");

        int i = 0;

        for (Iterator it = timerService.getTimers().iterator(); it.hasNext(); ) {

            Timer timer = (Timer) it.next();

            logger.info("Removing timer " + i + ";");
            timer.cancel();

            i++;
        }
        logger.info("Done!");
    }

    public void removeHarvestTimers() {
        // Remove all the harvest timers, if exist:
        //
        // (the logging messages below are set to level INFO; it's ok,
        // since this code is only called on startup of the application,
        // and it may be useful to know what existing timers were encountered).

        logger.log(Level.INFO, "Removing existing harvest timers..");

        int i = 1;
        for (Iterator it = timerService.getTimers().iterator(); it.hasNext(); ) {

            Timer timer = (Timer) it.next();
            logger.log(Level.INFO, "HarvesterService: checking timer " + i);

            if (timer.getInfo() instanceof HarvestTimerInfo) {
                logger.log(Level.INFO, "HarvesterService: timer " + i + " is a harvesting one; removing.");
                timer.cancel();
            }

            i++;
        }
    }

    public void createMotherTimer() {
        MotherTimerInfo info = new MotherTimerInfo();
        Calendar initExpiration = Calendar.getInstance();
        long intervalDuration = 60 * 60 * 1000; // every hour
        initExpiration.set(Calendar.MINUTE, 50);
        initExpiration.set(Calendar.SECOND, 0);

        Date initExpirationDate = initExpiration.getTime();
        Date currTime = new Date();
        if (initExpirationDate.before(currTime)) {
            initExpirationDate.setTime(initExpiration.getTimeInMillis() + intervalDuration);
        }

        logger.info("Setting the \"Mother Timer\", initial expiration: " + initExpirationDate);
        createTimer(initExpirationDate, intervalDuration, info);
    }

    public void createHarvestTimer(HarvestingClient harvestingClient) {

        if (harvestingClient.isScheduled()) {
            long intervalDuration = 0;
            Calendar initExpiration = Calendar.getInstance();
            initExpiration.set(Calendar.MINUTE, 0);
            initExpiration.set(Calendar.SECOND, 0);
            if (harvestingClient.getSchedulePeriod().equals(HarvestingClient.SCHEDULE_PERIOD_DAILY)) {
                intervalDuration = 1000 * 60 * 60 * 24;
                initExpiration.set(Calendar.HOUR_OF_DAY, harvestingClient.getScheduleHourOfDay());

            } else if (harvestingClient.getSchedulePeriod().equals(HarvestingClient.SCHEDULE_PERIOD_WEEKLY)) {
                intervalDuration = 1000 * 60 * 60 * 24 * 7;
                initExpiration.set(Calendar.HOUR_OF_DAY, harvestingClient.getScheduleHourOfDay());
                initExpiration.set(Calendar.DAY_OF_WEEK, harvestingClient.getScheduleDayOfWeek() + 1); //(saved as zero-based array but Calendar is one-based.)

            } else {
                logger.log(Level.WARNING, "Could not set timer for harvesting client id=" + harvestingClient.getId() + ", unknown schedule period: " + harvestingClient.getSchedulePeriod());
                return;
            }
            Date initExpirationDate = initExpiration.getTime();
            Date currTime = new Date();
            if (initExpirationDate.before(currTime)) {
                initExpirationDate.setTime(initExpiration.getTimeInMillis() + intervalDuration);
            }
            logger.log(Level.INFO, "Setting timer for harvesting client " + harvestingClient.getName() + ", initial expiration: " + initExpirationDate);
            createTimer(initExpirationDate, intervalDuration, new HarvestTimerInfo(harvestingClient.getId()));
        }
    }

    public void removeHarvestTimer(HarvestingClient harvestingClient) {
        // Clear dataverse timer, if one exists
        try {
            logger.log(Level.INFO, "Removing harvest timer on " + InetAddress.getLocalHost().getCanonicalHostName());
        } catch (UnknownHostException ex) {
            Logger.getLogger(DataverseTimerServiceBean.class.getName()).log(Level.SEVERE, null, ex);
        }
        for (Iterator it = timerService.getTimers().iterator(); it.hasNext(); ) {
            Timer timer = (Timer) it.next();
            if (timer.getInfo() instanceof HarvestTimerInfo) {
                HarvestTimerInfo info = (HarvestTimerInfo) timer.getInfo();
                if (info.getHarvestingClientId().equals(harvestingClient.getId())) {
                    timer.cancel();
                }
            }
        }
    }

    public void createExportTimer() {
        ExportTimerInfo info = new ExportTimerInfo();
        Calendar initExpiration = Calendar.getInstance();
        long intervalDuration = 24 * 60 * 60 * 1000; // every day
        initExpiration.set(Calendar.MINUTE, 0);
        initExpiration.set(Calendar.SECOND, 0);
        initExpiration.set(Calendar.HOUR_OF_DAY, 2); // 2AM, fixed.


        Date initExpirationDate = initExpiration.getTime();
        Date currTime = new Date();
        if (initExpirationDate.before(currTime)) {
            initExpirationDate.setTime(initExpiration.getTimeInMillis() + intervalDuration);
        }

        logger.info("Setting the Export Timer, initial expiration: " + initExpirationDate);
        createTimer(initExpirationDate, intervalDuration, info);
    }

    public void createIntegrityCheckTimer() {
        String cronExpression = settingsService.getValueForKey(Key.FilesIntegrityCheckTimerExpression);

        if (StringUtils.isNotBlank(cronExpression)) {
            ScheduleExpression expression = cronToScheduleExpression(cronExpression);

            TimerConfig timerConfig = new TimerConfig();
            timerConfig.setInfo(new FilesIntegrityCheckTimerInfo());
            timerConfig.setPersistent(false);
            timerService.createCalendarTimer(expression, timerConfig);
        }
    }

    public void createCitationCountUpdateTimer() {
        String cronExpression = settingsService.getValueForKey(Key.CitationCountUpdateTimerExpression);

        if (StringUtils.isNotBlank(cronExpression)) {
            ScheduleExpression expression = cronToScheduleExpression(cronExpression);

            TimerConfig timerConfig = new TimerConfig();
            timerConfig.setPersistent(false);
            timerConfig.setInfo(new CitationCountUpdateTimerInfo());
            Timer timer = timerService.createCalendarTimer(expression, timerConfig);
            logger.info("CitationCountUpdateTimerExpression: timer created, initial expiration: " + timer.getNextTimeout());
        } else {
            logger.info("CitationCountUpdateTimerExpression is empty. Skipping creation of timer.");
        }

    }

    public void createFeaturedDataversesSortingUpdateTimer() {
        String cronExpression = settingsService.getValueForKey(Key.FeaturedDataversesSortingUpdateTimerExpression);

        if (StringUtils.isNotBlank(cronExpression)) {
            ScheduleExpression expression = cronToScheduleExpression(cronExpression);

            TimerConfig timerConfig = new TimerConfig();
            timerConfig.setPersistent(false);
            timerConfig.setInfo(new FeaturedDataversesSortingUpdateTimerInfo());
            Timer timer = timerService.createCalendarTimer(expression, timerConfig);
            logger.info("FeaturedDataversesSortingUpdateTimerExpression: timer created, initial expiration: " + timer.getNextTimeout());
        } else {
            logger.info("FeaturedDataversesSortingUpdateTimerExpression is empty. Skipping creation of timer.");
        }

    }

    /* Utility methods: */
    private ScheduleExpression cronToScheduleExpression(String cronExpression) {
        final String[] parts = cronExpression.split(" ");
        Preconditions.checkArgument(parts.length == 5, "Invalid cron expression {} Expression should have 5 parts", cronExpression);

        return new ScheduleExpression()
            .minute(parts[0])
            .hour(parts[1])
            .dayOfMonth(parts[2])
            .month(parts[3])
            .dayOfWeek(parts[4]);
    }

    private void logException(Throwable e, Logger logger) {

        boolean cause = false;
        String fullMessage = "";
        do {
            String message = e.getClass().getName() + " " + e.getMessage();
            if (cause) {
                message = "\nCaused By Exception.................... " + e.getClass().getName() + " " + e.getMessage();
            }
            StackTraceElement[] ste = e.getStackTrace();
            message += "\nStackTrace: \n";
            for (int m = 0; m < ste.length; m++) {
                message += ste[m].toString() + "\n";
            }
            fullMessage += message;
            cause = true;
        } while ((e = e.getCause()) != null);
        logger.severe(fullMessage);
    }

}

1	package edu.harvard.iq.dataverse.timer;
2
3	import com.google.api.client.util.Preconditions;
4	import edu.harvard.iq.dataverse.DatasetDao;
5	import edu.harvard.iq.dataverse.featured.FeaturedDataverseServiceBean;
6	import edu.harvard.iq.dataverse.authorization.AuthenticationServiceBean;
7	import edu.harvard.iq.dataverse.datafile.FileIntegrityChecker;
8	import edu.harvard.iq.dataverse.datafile.pojo.FilesIntegrityReport;
9	import edu.harvard.iq.dataverse.dataset.DatasetCitationsCountUpdater;
10	import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
11	import edu.harvard.iq.dataverse.harvest.client.HarvestTimerInfo;
12	import edu.harvard.iq.dataverse.harvest.client.HarvesterServiceBean;
13	import edu.harvard.iq.dataverse.harvest.client.HarvestingClientDao;
14	import edu.harvard.iq.dataverse.harvest.server.OAISetServiceBean;
15	import edu.harvard.iq.dataverse.persistence.dataset.Dataset;
16	import edu.harvard.iq.dataverse.persistence.harvest.HarvestingClient;
17	import edu.harvard.iq.dataverse.persistence.user.AuthenticatedUser;
18	import edu.harvard.iq.dataverse.search.index.IndexServiceBean;
19	import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
20	import edu.harvard.iq.dataverse.settings.SettingsServiceBean.Key;
21	import edu.harvard.iq.dataverse.util.SystemConfig;
22	import org.apache.commons.lang3.StringUtils;
23
24	import javax.annotation.PostConstruct;
25	import javax.annotation.Resource;
26	import javax.ejb.DependsOn;
27	import javax.ejb.EJB;
28	import javax.ejb.ScheduleExpression;
29	import javax.ejb.Singleton;
30	import javax.ejb.Startup;
31	import javax.ejb.Timeout;
32	import javax.ejb.Timer;
33	import javax.ejb.TimerConfig;
34	import javax.ejb.TransactionAttribute;
35	import javax.ejb.TransactionAttributeType;
36	import javax.inject.Inject;
37	import javax.servlet.http.HttpServletRequest;
38	import java.io.IOException;
39	import java.io.Serializable;
40	import java.net.InetAddress;
41	import java.net.UnknownHostException;
42	import java.util.Calendar;
43	import java.util.Date;
44	import java.util.Iterator;
45	import java.util.List;
46	import java.util.logging.Level;
47	import java.util.logging.Logger;
48
49
50	/**
51	* This is a largely intact DVN3 implementation.
52	* original
53	*
54	* @author roberttreacy
55	* ported by
56	* @author Leonid Andreev
57	*/
58	@Singleton
59	@Startup
60	@DependsOn("StartupFlywayMigrator")
UNCOV 61	public class DataverseTimerServiceBean implements Serializable {	×
62	private static final Logger logger = Logger.getLogger(DataverseTimerServiceBean.class.getCanonicalName());	1✔
63
64	@Resource
65	javax.ejb.TimerService timerService;
66
67	@EJB
68	HarvesterServiceBean harvesterService;
69	@EJB
70	HarvestingClientDao harvestingClientService;
71	@EJB
72	AuthenticationServiceBean authSvc;
73	@EJB
74	OAISetServiceBean oaiSetService;
75	@EJB
76	SystemConfig systemConfig;
77	@Inject
78	SettingsServiceBean settingsService;
79	@EJB
80	FileIntegrityChecker fileIntegrityChecker;
81	@Inject
82	DatasetCitationsCountUpdater datasetCitationsCountUpdater;
83	@Inject
84	FeaturedDataverseServiceBean featuredDataverseServiceBean;
85
86	@Inject
87	DatasetDao datasetDao;
88
89	@Inject
90	IndexServiceBean indexServiceBean;
91
92	@PostConstruct
93	public void init() {
94	logger.info("PostConstruct timer check.");	×
95
UNCOV 96	if (systemConfig.isReadonlyMode()) {	×
UNCOV 97	logger.info("Timers not allowed in readonly mode");	×
98	return;	×
99	}
100
101	if (systemConfig.isTimerServer()) {	×
UNCOV 102	logger.info("I am the dedicated timer server. Initializing mother timer.");	×
103
UNCOV 104	removeAllTimers();	×
105	// create mother timer:
UNCOV 106	createMotherTimer();	×
107	// And the export timer (there is only one)
108	createExportTimer();	×
109
110	createIntegrityCheckTimer();	×
UNCOV 111	createCitationCountUpdateTimer();	×
UNCOV 112	createFeaturedDataversesSortingUpdateTimer();	×
113
UNCOV 114	createReindexAfterEmbargoTimer();	×
115
116	} else {
UNCOV 117	logger.info("Skipping timer server init (I am not the dedicated timer server)");	×
118	}
UNCOV 119	}	×
120
121	private void createReindexAfterEmbargoTimer() {
UNCOV 122	String cronExpression = settingsService.getValueForKey(Key.ReindexAfterEmbargoTimerExpression);	×
123
124	if (StringUtils.isNotBlank(cronExpression)) {	×
125	ScheduleExpression expression = cronToScheduleExpression(cronExpression);	×
126
127	TimerConfig timerConfig = new TimerConfig();	×
128	timerConfig.setPersistent(false);	×
129	timerConfig.setInfo(new AfterEmbargoReindexTimerInfo());	×
UNCOV 130	Timer timer = timerService.createCalendarTimer(expression, timerConfig);	×
131	logger.info("ReindexAfterEmbargoTimerExpression: timer created, initial expiration: " + timer.getNextTimeout());	×
UNCOV 132	} else {	×
UNCOV 133	logger.info("ReindexAfterEmbargoTimerExpression is empty. Skipping creation of timer.");	×
134	}
135	}	×
136
137	public void createTimer(Date initialExpiration, long intervalDuration, Serializable info) {
138	try {
139	logger.log(Level.INFO, "Creating timer on " + InetAddress.getLocalHost().getCanonicalHostName());	×
140	} catch (UnknownHostException ex) {	×
UNCOV 141	Logger.getLogger(DataverseTimerServiceBean.class.getName()).log(Level.SEVERE, null, ex);	×
UNCOV 142	}	×
UNCOV 143	timerService.createIntervalTimer(initialExpiration, intervalDuration, new TimerConfig(info, false));	×
UNCOV 144	}	×
145
146	/**
147	* This method is called whenever an EJB Timer goes off.
148	* Check to see if this is a Harvest Timer, and if it is
149	* Run the harvest for the given (scheduled) dataverse
150	*
151	* @param timer
152	*/
153	@Timeout
154	@TransactionAttribute(TransactionAttributeType.NOT_SUPPORTED)
155	public void handleTimeout(Timer timer) {
156	// We have to put all the code in a try/catch block because
157	// if an exception is thrown from this method, Glassfish will automatically
158	// call the method a second time. (The minimum number of re-tries for a Timer method is 1)
UNCOV 159	if (systemConfig.isReadonlyMode()) {	×
160	Logger.getLogger(DataverseTimerServiceBean.class.getName()).log(Level.WARNING, null, "handleTimeout() was called in readonly mode - skipping timeout handling");	×
UNCOV 161	return;	×
162	}
163
UNCOV 164	if (!systemConfig.isTimerServer()) {	×
165	//logger.info("I am not the timer server! - bailing out of handleTimeout()");
166	Logger.getLogger(DataverseTimerServiceBean.class.getName()).log(Level.WARNING, null, "I am not the timer server! - but handleTimeout() got called. Please investigate!");	×
167	}
168
169	try {
UNCOV 170	logger.log(Level.INFO, "Handling timeout on " + InetAddress.getLocalHost().getCanonicalHostName());	×
171	} catch (UnknownHostException ex) {	×
172	Logger.getLogger(DataverseTimerServiceBean.class.getName()).log(Level.SEVERE, null, ex);	×
173	}	×
174
175	if (timer.getInfo() instanceof MotherTimerInfo) {	×
176	logger.info("Behold! I am the Master Timer, king of all timers! I'm here to create all the lesser timers!");	×
177	removeHarvestTimers();	×
178	for (HarvestingClient client : harvestingClientService.getAllHarvestingClients()) {	×
UNCOV 179	createHarvestTimer(client);	×
UNCOV 180	}	×
181	} else if (timer.getInfo() instanceof HarvestTimerInfo) {	×
UNCOV 182	HarvestTimerInfo info = (HarvestTimerInfo) timer.getInfo();	×
183	try {
184
UNCOV 185	logger.log(Level.INFO, "running a harvesting client: id=" + info.getHarvestingClientId());	×
186	// Timer batch jobs are run by the main Admin user.
187	// TODO: revisit how we retrieve the superuser here.
188	// Should it be configurable somewhere, which superuser
189	// runs these jobs? Should there be a central mechanism for obtaining
190	// the "major", builtin superuser for this Dataverse instance?
191	// -- L.A. 4.5, Aug. 2016
UNCOV 192	AuthenticatedUser adminUser = authSvc.getAdminUser(); // getAuthenticatedUser("admin");	×
193	if (adminUser == null) {	×
194	logger.info("Scheduled harvest: failed to locate the admin user! Exiting.");	×
195	throw new IOException("Scheduled harvest: failed to locate the admin user");	×
196	}
197	logger.info("found admin user " + adminUser.getName());	×
UNCOV 198	DataverseRequest dataverseRequest = new DataverseRequest(adminUser, (HttpServletRequest) null);	×
UNCOV 199	harvesterService.doHarvest(dataverseRequest, info.getHarvestingClientId());	×
200
UNCOV 201	} catch (Throwable e) {	×
202	// Harvester Service should be handling any error notifications,
203	// if/when things go wrong.
204	// (TODO: -- verify this logic; harvesterService may still be able
205	// to throw an IOException, if it could not run the harvest at all,
206	// or could not for whatever reason modify the database record...
207	// in this case we should, probably, log the error and try to send
208	// a mail notification. -- L.A. 4.4)
209	//dataverseService.setHarvestResult(info.getHarvestingDataverseId(), harvesterService.HARVEST_RESULT_FAILED);
210	//mailService.sendHarvestErrorNotification(dataverseService.find().getSystemEmail(), dataverseService.find().getName());
211	logException(e, logger);	×
212	}	×
UNCOV 213	} else if (timer.getInfo() instanceof ExportTimerInfo) {	×
214	try {
215	ExportTimerInfo info = (ExportTimerInfo) timer.getInfo();	×
216	logger.info("Timer Service: Running a scheduled export job.");	×
217
218	// and update all oai sets:
219	oaiSetService.exportAllSets();	×
220	} catch (Throwable e) {	×
UNCOV 221	logException(e, logger);	×
222	}	×
223	} else if (timer.getInfo() instanceof FilesIntegrityCheckTimerInfo) {	×
224	FilesIntegrityReport report = fileIntegrityChecker.checkFilesIntegrity();	×
225
226	logger.info(report.getSummaryInfo());	×
UNCOV 227	} else if (timer.getInfo() instanceof CitationCountUpdateTimerInfo) {	×
UNCOV 228	datasetCitationsCountUpdater.updateCitationCount();	×
229	} else if (timer.getInfo() instanceof AfterEmbargoReindexTimerInfo) {	×
UNCOV 230	reindexAfterEmbargo();	×
UNCOV 231	} else if (timer.getInfo() instanceof FeaturedDataversesSortingUpdateTimerInfo) {	×
232	featuredDataverseServiceBean.refreshFeaturedDataversesAutomaticSorting();	×
233	}
234
235	}	×
236
237	private void reindexAfterEmbargo() {
UNCOV 238	List<Dataset> datasetsAfterEmbargo = datasetDao.findNotIndexedAfterEmbargo();	×
239	for (Dataset dataset:datasetsAfterEmbargo) {	×
UNCOV 240	indexServiceBean.indexDataset(dataset, true);	×
241	}	×
UNCOV 242	}	×
243
244	public void removeAllTimers() {
245	logger.info("Removing ALL existing timers.");	×
246
247	int i = 0;	×
248
UNCOV 249	for (Iterator it = timerService.getTimers().iterator(); it.hasNext(); ) {	×
250
251	Timer timer = (Timer) it.next();	×
252
253	logger.info("Removing timer " + i + ";");	×
UNCOV 254	timer.cancel();	×
255
UNCOV 256	i++;	×
UNCOV 257	}	×
UNCOV 258	logger.info("Done!");	×
UNCOV 259	}	×
260
261	public void removeHarvestTimers() {
262	// Remove all the harvest timers, if exist:
263	//
264	// (the logging messages below are set to level INFO; it's ok,
265	// since this code is only called on startup of the application,
266	// and it may be useful to know what existing timers were encountered).
267
268	logger.log(Level.INFO, "Removing existing harvest timers..");	×
269
270	int i = 1;	×
271	for (Iterator it = timerService.getTimers().iterator(); it.hasNext(); ) {	×
272
UNCOV 273	Timer timer = (Timer) it.next();	×
UNCOV 274	logger.log(Level.INFO, "HarvesterService: checking timer " + i);	×
275
276	if (timer.getInfo() instanceof HarvestTimerInfo) {	×
277	logger.log(Level.INFO, "HarvesterService: timer " + i + " is a harvesting one; removing.");	×
UNCOV 278	timer.cancel();	×
279	}
280
281	i++;	×
282	}	×
283	}	×
284
285	public void createMotherTimer() {
286	MotherTimerInfo info = new MotherTimerInfo();	×
287	Calendar initExpiration = Calendar.getInstance();	×
288	long intervalDuration = 60 * 60 * 1000; // every hour	×
289	initExpiration.set(Calendar.MINUTE, 50);	×
UNCOV 290	initExpiration.set(Calendar.SECOND, 0);	×
291
292	Date initExpirationDate = initExpiration.getTime();	×
293	Date currTime = new Date();	×
294	if (initExpirationDate.before(currTime)) {	×
UNCOV 295	initExpirationDate.setTime(initExpiration.getTimeInMillis() + intervalDuration);	×
296	}
297
298	logger.info("Setting the \"Mother Timer\", initial expiration: " + initExpirationDate);	×
299	createTimer(initExpirationDate, intervalDuration, info);	×
300	}	×
301
302	public void createHarvestTimer(HarvestingClient harvestingClient) {
303
304	if (harvestingClient.isScheduled()) {	×
305	long intervalDuration = 0;	×
UNCOV 306	Calendar initExpiration = Calendar.getInstance();	×
307	initExpiration.set(Calendar.MINUTE, 0);	×
308	initExpiration.set(Calendar.SECOND, 0);	×
309	if (harvestingClient.getSchedulePeriod().equals(HarvestingClient.SCHEDULE_PERIOD_DAILY)) {	×
310	intervalDuration = 1000 * 60 * 60 * 24;	×
UNCOV 311	initExpiration.set(Calendar.HOUR_OF_DAY, harvestingClient.getScheduleHourOfDay());	×
312
313	} else if (harvestingClient.getSchedulePeriod().equals(HarvestingClient.SCHEDULE_PERIOD_WEEKLY)) {	×
314	intervalDuration = 1000 * 60 * 60 * 24 * 7;	×
UNCOV 315	initExpiration.set(Calendar.HOUR_OF_DAY, harvestingClient.getScheduleHourOfDay());	×
316	initExpiration.set(Calendar.DAY_OF_WEEK, harvestingClient.getScheduleDayOfWeek() + 1); //(saved as zero-based array but Calendar is one-based.)	×
317
318	} else {
319	logger.log(Level.WARNING, "Could not set timer for harvesting client id=" + harvestingClient.getId() + ", unknown schedule period: " + harvestingClient.getSchedulePeriod());	×
UNCOV 320	return;	×
321	}
322	Date initExpirationDate = initExpiration.getTime();	×
UNCOV 323	Date currTime = new Date();	×
324	if (initExpirationDate.before(currTime)) {	×
UNCOV 325	initExpirationDate.setTime(initExpiration.getTimeInMillis() + intervalDuration);	×
326	}
UNCOV 327	logger.log(Level.INFO, "Setting timer for harvesting client " + harvestingClient.getName() + ", initial expiration: " + initExpirationDate);	×
UNCOV 328	createTimer(initExpirationDate, intervalDuration, new HarvestTimerInfo(harvestingClient.getId()));	×
329	}
330	}	×
331
332	public void removeHarvestTimer(HarvestingClient harvestingClient) {
333	// Clear dataverse timer, if one exists
334	try {
335	logger.log(Level.INFO, "Removing harvest timer on " + InetAddress.getLocalHost().getCanonicalHostName());	×
336	} catch (UnknownHostException ex) {	×
337	Logger.getLogger(DataverseTimerServiceBean.class.getName()).log(Level.SEVERE, null, ex);	×
338	}	×
UNCOV 339	for (Iterator it = timerService.getTimers().iterator(); it.hasNext(); ) {	×
UNCOV 340	Timer timer = (Timer) it.next();	×
341	if (timer.getInfo() instanceof HarvestTimerInfo) {	×
342	HarvestTimerInfo info = (HarvestTimerInfo) timer.getInfo();	×
UNCOV 343	if (info.getHarvestingClientId().equals(harvestingClient.getId())) {	×
UNCOV 344	timer.cancel();	×
345	}
346	}
347	}	×
348	}	×
349
350	public void createExportTimer() {
UNCOV 351	ExportTimerInfo info = new ExportTimerInfo();	×
UNCOV 352	Calendar initExpiration = Calendar.getInstance();	×
353	long intervalDuration = 24 * 60 * 60 * 1000; // every day	×
354	initExpiration.set(Calendar.MINUTE, 0);	×
355	initExpiration.set(Calendar.SECOND, 0);	×
356	initExpiration.set(Calendar.HOUR_OF_DAY, 2); // 2AM, fixed.	×
357
358
359	Date initExpirationDate = initExpiration.getTime();	×
360	Date currTime = new Date();	×
361	if (initExpirationDate.before(currTime)) {	×
UNCOV 362	initExpirationDate.setTime(initExpiration.getTimeInMillis() + intervalDuration);	×
363	}
364
UNCOV 365	logger.info("Setting the Export Timer, initial expiration: " + initExpirationDate);	×
366	createTimer(initExpirationDate, intervalDuration, info);	×
367	}	×
368
369	public void createIntegrityCheckTimer() {
370	String cronExpression = settingsService.getValueForKey(Key.FilesIntegrityCheckTimerExpression);	×
371
372	if (StringUtils.isNotBlank(cronExpression)) {	×
UNCOV 373	ScheduleExpression expression = cronToScheduleExpression(cronExpression);	×
374
UNCOV 375	TimerConfig timerConfig = new TimerConfig();	×
UNCOV 376	timerConfig.setInfo(new FilesIntegrityCheckTimerInfo());	×
377	timerConfig.setPersistent(false);	×
UNCOV 378	timerService.createCalendarTimer(expression, timerConfig);	×
379	}
380	}	×
381
382	public void createCitationCountUpdateTimer() {
383	String cronExpression = settingsService.getValueForKey(Key.CitationCountUpdateTimerExpression);	×
384
385	if (StringUtils.isNotBlank(cronExpression)) {	×
386	ScheduleExpression expression = cronToScheduleExpression(cronExpression);	×
387
388	TimerConfig timerConfig = new TimerConfig();	×
UNCOV 389	timerConfig.setPersistent(false);	×
UNCOV 390	timerConfig.setInfo(new CitationCountUpdateTimerInfo());	×
391	Timer timer = timerService.createCalendarTimer(expression, timerConfig);	×
UNCOV 392	logger.info("CitationCountUpdateTimerExpression: timer created, initial expiration: " + timer.getNextTimeout());	×
UNCOV 393	} else {	×
UNCOV 394	logger.info("CitationCountUpdateTimerExpression is empty. Skipping creation of timer.");	×
395	}
396
UNCOV 397	}	×
398
399	public void createFeaturedDataversesSortingUpdateTimer() {
400	String cronExpression = settingsService.getValueForKey(Key.FeaturedDataversesSortingUpdateTimerExpression);	×
401
402	if (StringUtils.isNotBlank(cronExpression)) {	×
403	ScheduleExpression expression = cronToScheduleExpression(cronExpression);	×
404
UNCOV 405	TimerConfig timerConfig = new TimerConfig();	×
UNCOV 406	timerConfig.setPersistent(false);	×
UNCOV 407	timerConfig.setInfo(new FeaturedDataversesSortingUpdateTimerInfo());	×
408	Timer timer = timerService.createCalendarTimer(expression, timerConfig);	×
409	logger.info("FeaturedDataversesSortingUpdateTimerExpression: timer created, initial expiration: " + timer.getNextTimeout());	×
UNCOV 410	} else {	×
411	logger.info("FeaturedDataversesSortingUpdateTimerExpression is empty. Skipping creation of timer.");	×
412	}
413
UNCOV 414	}	×
415
416	/* Utility methods: */
417	private ScheduleExpression cronToScheduleExpression(String cronExpression) {
418	final String[] parts = cronExpression.split(" ");	×
UNCOV 419	Preconditions.checkArgument(parts.length == 5, "Invalid cron expression {} Expression should have 5 parts", cronExpression);	×
420
421	return new ScheduleExpression()	×
422	.minute(parts[0])	×
423	.hour(parts[1])	×
424	.dayOfMonth(parts[2])	×
UNCOV 425	.month(parts[3])	×
UNCOV 426	.dayOfWeek(parts[4]);	×
427	}
428
429	private void logException(Throwable e, Logger logger) {
430
UNCOV 431	boolean cause = false;	×
UNCOV 432	String fullMessage = "";	×
433	do {
UNCOV 434	String message = e.getClass().getName() + " " + e.getMessage();	×
UNCOV 435	if (cause) {	×
UNCOV 436	message = "\nCaused By Exception.................... " + e.getClass().getName() + " " + e.getMessage();	×
437	}
UNCOV 438	StackTraceElement[] ste = e.getStackTrace();	×
UNCOV 439	message += "\nStackTrace: \n";	×
UNCOV 440	for (int m = 0; m < ste.length; m++) {	×
UNCOV 441	message += ste[m].toString() + "\n";	×
442	}
UNCOV 443	fullMessage += message;	×
UNCOV 444	cause = true;	×
UNCOV 445	} while ((e = e.getCause()) != null);	×
UNCOV 446	logger.severe(fullMessage);	×
UNCOV 447	}	×
448
449	}

CeON / dataverse / 1371

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous