Java tutorial
/* * $Id$ * * Copyright 2010 University of Dundee. All rights reserved. * Use is subject to license terms supplied in LICENSE.txt */ package ome.services; import java.awt.Dimension; import java.io.IOException; import java.sql.Timestamp; import java.util.ArrayList; import java.util.Collections; import java.util.HashMap; import java.util.HashSet; import java.util.List; import java.util.Map; import java.util.Set; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.perf4j.StopWatch; import org.perf4j.commonslog.CommonsLogStopWatch; import ome.api.IPixels; import ome.api.IQuery; import ome.api.IRenderingSettings; import ome.api.IUpdate; import ome.conditions.ApiUsageException; import ome.conditions.InternalException; import ome.conditions.ResourceError; import ome.conditions.ValidationException; import ome.io.nio.ThumbnailService; import ome.model.IObject; import ome.model.core.Image; import ome.model.core.Pixels; import ome.model.display.RenderingDef; import ome.model.display.Thumbnail; import ome.model.internal.Details; import ome.model.internal.Permissions; import ome.model.meta.Session; import ome.parameters.Parameters; import ome.security.SecuritySystem; import ome.system.EventContext; /** * */ public class ThumbnailCtx { /** Logger for this class. */ private static final Log log = LogFactory.getLog(ThumbnailCtx.class); /** Default thumbnail MIME type. */ public static final String DEFAULT_MIME_TYPE = "image/jpeg"; /** OMERO query service. */ private IQuery queryService; /** OMERO update service. */ private IUpdate updateService; /** OMERO pixels service. */ private IPixels pixelsService; /** ROMIO thumbnail service. */ private ThumbnailService thumbnailService; /** OMERO rendering settings service. */ private IRenderingSettings settingsService; /** OMERO security system for this session. */ private SecuritySystem securitySystem; /** User ID to use in queries. */ private long userId; /** Pixels ID vs. Pixels object map. */ private Map<Long, Pixels> pixelsIdPixelsMap = new HashMap<Long, Pixels>(); /** * Pixels ID vs. owner ID map. We don't access these RenderingDef object * properties directly due to load/unload issues with Hibernate * (ObjectUnloadedExceptions) when multiple objects were created with or * updated by the same event. */ private Map<Long, Long> pixelsIdOwnerIdMap = new HashMap<Long, Long>(); /** Pixels ID vs. RenderingDef object map. */ private Map<Long, RenderingDef> pixelsIdSettingsMap = new HashMap<Long, RenderingDef>(); /** Pixels ID vs. Thumbnail object map. */ private Map<Long, Thumbnail> pixelsIdMetadataMap = new HashMap<Long, Thumbnail>(); /** * Pixels ID vs. RenderingDef object last modified time map. We don't access * these RenderingDef object properties directly due to load/unload issues * with Hibernate (ObjectUnloadedExceptions) when multiple objects were * created with or updated by the same event. */ private Map<Long, Timestamp> pixelsIdSettingsLastModifiedTimeMap = new HashMap<Long, Timestamp>(); /** * Pixels ID vs. Thumbnail object last modified time map. We don't access * these Thumbnail object properties directly due to load/unload issues * with Hibernate (ObjectUnloadedExceptions) when multiple objects were * created with or updated by the same event. */ private Map<Long, Timestamp> pixelsIdMetadataLastModifiedTimeMap = new HashMap<Long, Timestamp>(); /** * Pixels ID vs. RenderingDef object owner. We don't access these * RenderingDef object properties directly due to load/unload issues * with Hibernate (ObjectUnloadedExceptions) when multiple objects were * created with or updated by the same event. */ private Map<Long, Long> pixelsIdSettingsOwnerIdMap = new HashMap<Long, Long>(); /** * Default constructor. * @param queryService OMERO query service to use. * @param updateService OMERO update service to use. * @param pixelsService OMERO pixels service to use. * @param settingsService OMERO rendering settings service to use. * @param thumbnailService OMERO thumbnail service to use. * @param securitySystem OMERO security system for this session. * @param userId Current user ID. */ public ThumbnailCtx(IQuery queryService, IUpdate updateService, IPixels pixelsService, IRenderingSettings settingsService, ThumbnailService thumbnailService, SecuritySystem securitySystem, long userId) { this.queryService = queryService; this.updateService = updateService; this.pixelsService = pixelsService; this.settingsService = settingsService; this.thumbnailService = thumbnailService; this.securitySystem = securitySystem; this.userId = userId; } /** * Retrieves the current user ID to use for queries. * @return See above. */ public long getUserId() { return userId; } /** * Sets the user ID to use for queries. * @param userId The user ID to use for queries. */ public void setUserId(long userId) { this.userId = userId; } /** * Bulk loads a set of rendering settings for a group of pixels sets and * prepares our internal data structures. * @param pixelsIds Set of Pixels IDs to prepare rendering settings for. */ public void loadAndPrepareRenderingSettings(Set<Long> pixelsIds) { loadAndPrepareRenderingSettings(Pixels.class, pixelsIds); } /** * Bulk loads a set of rendering settings for a group of pixels sets and * prepares our internal data structures. * @param ids Set of IDs to prepare rendering settings for. * @param klass Either <code>Image</code> or <code>Pixels</code> qualifying * the type that <code>ids</code> are identifiers for. */ private void loadAndPrepareRenderingSettings(Class<? extends IObject> klass, Set<Long> ids) { // Sanity check our ID set if (ids == null || ids.size() == 0) { log.warn("Preparation of null or zero length ID set requested."); return; } // First we need to load our rendering settings either by Image ID or // by Pixels ID. List<RenderingDef> settingsList = null; Set<Long> pixelsIds = null; if (klass.equals(Pixels.class)) { // Populate our hash maps asking for our settings by Pixels ID settingsList = bulkLoadRenderingSettingsByPixelsId(ids); pixelsIds = ids; } else if (klass.equals((Image.class))) { // Populate our hash maps asking for our settings by Image ID settingsList = bulkLoadRenderingSettingsByImageId(ids); pixelsIds = new HashSet<Long>(); for (RenderingDef def : settingsList) { pixelsIds.add(def.getPixels().getId()); } } else { throw new ApiUsageException("Unexpected preparation source type: " + klass.getName()); } // Now prepare the loaded rendering settings for (RenderingDef settings : settingsList) { prepareRenderingSettings(settings, settings.getPixels()); } // Locate the Pixels sets we have no settings for this user for. Set<Long> pixelsIdsWithoutSettings = getPixelsIdsWithoutSettings(pixelsIds); // For dimension pooling and checks of graph criticality to work // correctly for the purpose of thumbnail metadata creation we now need // to load the Pixels sets that had no rendering settings. loadMissingPixels(pixelsIdsWithoutSettings); // Now check to see if we're in a state where missing settings requires // us to use the owner's settings (we're "graph critical") and load // them if possible. if (pixelsIdsWithoutSettings.size() > 0 && isExtendedGraphCritical(pixelsIdsWithoutSettings)) { settingsList = bulkLoadOwnerRenderingSettings(pixelsIdsWithoutSettings); for (RenderingDef settings : settingsList) { prepareRenderingSettings(settings, settings.getPixels()); } pixelsIdsWithoutSettings = getPixelsIdsWithoutSettings(pixelsIds); } } /** * Loads and prepares a rendering settings for a Pixels ID and RenderingDef * ID. * @param pixelsId Pixels ID to load. * @param settingsId RenderingDef ID to load an prepare settings for. */ public void loadAndPrepareRenderingSettings(long pixelsId, long settingsId) { Pixels pixels = pixelsService.retrievePixDescription(pixelsId); RenderingDef settings = pixelsService.loadRndSettings(settingsId); if (settings == null) { throw new ValidationException("No rendering definition exists with ID = " + settingsId); } if (!settingsService.sanityCheckPixels(pixels, settings.getPixels())) { throw new ValidationException("The rendering definition " + settingsId + " is incompatible with pixels set " + pixels.getId()); } prepareRenderingSettings(settings, pixels); } /** * Bulk loads and prepares metadata for a group of pixels sets. Calling * this method guarantees that metadata are available, creating them if * they are not. * @param pixelsIds Pixels IDs to prepare metadata for. * @param longestSide The longest side of the thumbnails requested. */ public void loadAndPrepareMetadata(Set<Long> pixelsIds, int longestSide) { // Now we're going to attempt to efficiently retrieve the thumbnail // metadata based on our dimension pools above. To save significant // time later we're also going to pre-create thumbnail metadata where // it is missing. Map<Dimension, Set<Long>> dimensionPools = createDimensionPools(longestSide); loadMetadataByDimensionPool(dimensionPools); createMissingThumbnailMetadata(dimensionPools); } /** * Bulk loads and prepares metadata for a group of pixels sets. Calling * this method guarantees that metadata are available, creating them if * they are not. * @param pixelsIds Pixels IDs to prepare metadata for. * @param dimensions X-Y dimensions of the thumbnails requested. */ public void loadAndPrepareMetadata(Set<Long> pixelsIds, Dimension dimensions) { // Now we're going to attempt to efficiently retrieve the thumbnail // metadata based on our dimension pools above. To save significant // time later we're also going to pre-create thumbnail metadata where // it is missing. Map<Dimension, Set<Long>> dimensionPools = new HashMap<Dimension, Set<Long>>(); dimensionPools.put(dimensions, pixelsIds); loadMetadataByDimensionPool(dimensionPools); createMissingThumbnailMetadata(dimensionPools); } /** * Retrieves all thumbnail metadata available in the database for a given * Pixels ID. * @param pixelsId Pixels ID to retrieve thumbnail metadata for. * @return See above. */ public List<Thumbnail> loadAllMetadata(long pixelsId) { Parameters params = new Parameters(); params.addId(pixelsId); params.addLong("o_id", userId); StopWatch s1 = new CommonsLogStopWatch("omero.loadAllMetadata"); List<Thumbnail> toReturn = queryService.findAllByQuery( "select t from Thumbnail as t " + "join t.pixels " + "join fetch t.details.updateEvent " + "where t.details.owner.id = :o_id " + "and t.pixels.id = :id", params); s1.stop(); return toReturn; } /** * Resets a given set of Pixels rendering settings to the default * effectively creating any which do not exist. * @param pixelsIds Pixels IDs */ public void createAndPrepareMissingRenderingSettings(Set<Long> pixelsIds) { // Now check to see if we're in a state where missing rendering // settings and our state requires us to not save. if (isExtendedGraphCritical(pixelsIds)) { // TODO: Could possibly "su" to the user and create a thumbnail return; } StopWatch s1 = new CommonsLogStopWatch("omero.createAndPrepareMissingRenderingSettings"); Set<Long> pixelsIdsWithoutSettings = getPixelsIdsWithoutSettings(pixelsIds); int count = pixelsIdsWithoutSettings.size(); if (count > 0) { log.info(count + " pixels without settings"); Set<Long> imageIds = settingsService.resetDefaultsInSet(Pixels.class, pixelsIdsWithoutSettings); if (count != imageIds.size()) { log.warn(String.format( "Return value ID count %d does not match pixels " + "without settings count %d", imageIds.size(), count)); } loadAndPrepareRenderingSettings(Image.class, imageIds); } s1.stop(); } /** * Whether or not settings are available for a given Pixels ID. * @param pixelsId Pixels ID to check for availability. * @return <code>true</code> if settings are available and * <code>false</code> otherwise. */ public boolean hasSettings(long pixelsId) { return pixelsIdSettingsMap.containsKey(pixelsId); } /** * Whether or not thumbnail metadata is available for a given Pixels ID. * @param pixelsId Pixels ID to check for availability. * @return <code>true</code> if metadata is available and * <code>false</code> otherwise. */ public boolean hasMetadata(long pixelsId) { return pixelsIdMetadataMap.containsKey(pixelsId); } /** * Retrieves the Pixels object for a given Pixels ID. * @param pixelsId Pixels ID to retrieve the Pixels object for. * @return See above. */ public Pixels getPixels(long pixelsId) { Pixels pixels = pixelsIdPixelsMap.get(pixelsId); if (pixels == null) { throw new ResourceError(String.format( "Error retrieving Pixels id:%d. Pixels set does not " + "exist or the user id:%d has insufficient permissions " + "to retrieve it.", pixelsId, userId)); } return pixelsIdPixelsMap.get(pixelsId); } /** * Retrieves the RenderingDef object for a given Pixels ID. * @param pixelsId Pixels ID to retrieve the RenderingDef object for. * @return See above. */ public RenderingDef getSettings(long pixelsId) { return pixelsIdSettingsMap.get(pixelsId); } /** * Retrieves the Thumbnail object for a given Pixels ID. * @param pixelsId Pixels ID to retrieve the Thumbnail object for. * @return See above. */ public Thumbnail getMetadata(long pixelsId) { Thumbnail thumbnail = pixelsIdMetadataMap.get(pixelsId); if (thumbnail == null && securitySystem.isGraphCritical()) { Pixels pixels = pixelsIdPixelsMap.get(pixelsId); long ownerId = pixels.getDetails().getOwner().getId(); throw new ResourceError(String.format( "The user id:%s may not be the owner id:%d. The owner " + "has not viewed the Pixels set id:%d and thumbnail " + "metadata is missing.", userId, ownerId, pixelsId)); } else if (thumbnail == null) { throw new InternalException( "Fatal error retrieving thumbnail metadata for Pixels " + "set id:" + pixelsId); } return thumbnail; } /** * Whether or not the thumbnail metadata for a given Pixels ID is dirty * (the RenderingDef has been updated since the Thumbnail was). * @param pixelsId Pixels ID to check for dirty metadata. * @return <code>true</code> if the metadata is dirty <code>false</code> * otherwise. */ public boolean dirtyMetadata(long pixelsId) { Timestamp metadataLastUpdated = pixelsIdMetadataLastModifiedTimeMap.get(pixelsId); Timestamp settingsLastUpdated = pixelsIdSettingsLastModifiedTimeMap.get(pixelsId); if (log.isDebugEnabled()) { log.debug("Thumb time: " + metadataLastUpdated); log.debug("Settings time: " + settingsLastUpdated); } return settingsLastUpdated.after(metadataLastUpdated); } /** * Checks to see if a thumbnail is in the on disk cache or not. * * @param pixelsId The Pixels set the thumbnail is for. * @return Whether or not the thumbnail is in the on disk cache. */ public boolean isThumbnailCached(long pixelsId) { Thumbnail metadata = pixelsIdMetadataMap.get(pixelsId); try { boolean dirtyMetadata = dirtyMetadata(pixelsId); boolean thumbnailExists = thumbnailService.getThumbnailExists(metadata); boolean isExtendedGraphCritical = isExtendedGraphCritical(Collections.singleton(pixelsId)); Long metadataOwnerId = metadata.getDetails().getOwner().getId(); Long sessionUserId = getCurrentUserId(); boolean isMyMetadata = sessionUserId.equals(metadataOwnerId); if (!dirtyMetadata) { if (thumbnailExists) { return true; } else if (!thumbnailExists && isExtendedGraphCritical) { throw new ResourceError(String.format("Error retrieving Pixels id:%d. Thumbnail " + "metadata exists but a thumbnail is not " + "available in the cache. User id:%d has " + "insufficient permissions to create it.", pixelsId, userId)); } } else if (thumbnailExists && !isMyMetadata) { log.warn(String.format( "Thumbnail metadata is dirty for Pixels Id:%d and " + "the metadata is owned User id:%d which is not us " + "User id:%d. Ignoring this and returning the cached " + "thumbnail.", pixelsId, metadataOwnerId, sessionUserId)); return true; } else if (thumbnailExists && isExtendedGraphCritical) { log.warn(String.format("Thumbnail metadata is dirty for Pixels Id:%d and " + "graph is critical for User id:%d. Ignoring this " + "and returning the cached thumbnail.", pixelsId, userId)); return true; } } catch (IOException e) { String s = "Could not check if thumbnail is cached: "; log.error(s, e); throw new ResourceError(s + e.getMessage()); } return false; } /** * Calculates the ratio of the two sides of a Pixel set and returns the * X and Y widths based on the longest side maintaining aspect ratio. * * @param pixels The Pixels set to calculate against. * @param longestSide The size of the longest side of the thumbnail * requested. * @return The calculated width (X) and height (Y). */ public Dimension calculateXYWidths(Pixels pixels, int longestSide) { int sizeX = pixels.getSizeX(); int sizeY = pixels.getSizeY(); if (sizeX > sizeY) { float ratio = (float) longestSide / sizeX; return new Dimension(longestSide, (int) (sizeY * ratio)); } float ratio = (float) longestSide / sizeY; return new Dimension((int) (sizeX * ratio), longestSide); } /** * Returns the Id of the currently logged in user. * Returns owner of the share while in share * @return See above. */ private Long getCurrentUserId() { EventContext ec = securitySystem.getEventContext(); Long shareId = ec.getCurrentShareId(); if (shareId != null) { Session s = queryService.get(Session.class, shareId); return s.getOwner().getId(); } return ec.getCurrentUserId(); } /** * Whether or not we're extended graph critical for a given set of * dimension pools. We're extended graph critical if: * <ul> * <li> * <code>isGraphGritical() == true</code> and the Pixels set does not * belong to us. * </li> * <li> * <code>isGraphCritical() == false</code>, the Pixels set does not * belong to us and the group is READ-ONLY. * </li> * </ul> * @param dimensionPools Dimension pools to check if we're graph critical * for. * @return <code>true</code> if we're graph critical, and * <code>false</code> otherwise. * @see #isExtendedGraphCritical(Set) */ private boolean isExtendedGraphCritical(Map<Dimension, Set<Long>> dimensionPools) { for (Set<Long> pool : dimensionPools.values()) { if (isExtendedGraphCritical(pool)) { return true; } } return false; } /** * Whether or not we're extended graph critical for a given set of * dimension pools. We're extended graph critical if: * <ul> * <li> * <code>isGraphGritical() == true</code> and the Pixels set does not * belong to us. * </li> * <li> * <code>isGraphCritical() == false</code>, the Pixels set does not * belong to us and the group is READ-ONLY. * </li> * </ul> * @param pixelsIds Set of Pixels to check if we're graph critical for. * @return <code>true</code> if we're graph critical, and * <code>false</code> otherwise. */ public boolean isExtendedGraphCritical(Set<Long> pixelsIds) { EventContext ec = securitySystem.getEventContext(); Permissions currentGroupPermissions = ec.getCurrentGroupPermissions(); Permissions readOnly = Permissions.parseString("rwr---"); if (ec.getCurrentShareId() != null) { return true; } if (securitySystem.isGraphCritical() || currentGroupPermissions.identical(readOnly)) { for (Long pixelsId : pixelsIds) { // Check if the Pixels ID vs. Owner ID map is missing, which // signifies that we were completely unable to load any of the // Pixels sets identified in pixelsIds. if (pixelsIdOwnerIdMap == null) { throw new ResourceError(String.format("Error retrieving Pixels id:%d. Pixels set does " + "not exist or the user id:%d has insufficient " + "permissions to retrieve it.", pixelsId, userId)); } Long pixelsOwner = pixelsIdOwnerIdMap.get(pixelsId); // Check if the Owner ID is missing from the map, which as // above signifies that we unable to load this particular // Pixels set as identified by Pixels ID. This will be a hard // failure due to the crazy state that this potentially // suggests. if (pixelsOwner == null) { throw new ResourceError(String.format("Error retrieving Pixels id:%d. Pixels set does " + "not exist or the user id:%d has insufficient " + "permissions to retrieve it.", pixelsId, userId)); } if (pixelsOwner != userId) { return true; } } } return false; } /** * Creates X-Y dimension pools based on a requested longest side. * @param longestSide Requested longest side of the thumbnail. * @return Map of X-Y dimension vs. Pixels ID (a set of dimension pools). */ private Map<Dimension, Set<Long>> createDimensionPools(int longestSide) { Map<Dimension, Set<Long>> dimensionPools = new HashMap<Dimension, Set<Long>>(); for (Pixels pixels : pixelsIdPixelsMap.values()) { // Calculate the XY widths we would use for a thumbnail of Pixels Dimension dimensions = calculateXYWidths(pixels, longestSide); addToDimensionPool(dimensionPools, pixels, dimensions); } return dimensionPools; } /** * Adds the Id of a particular set of Pixels to the correct dimension pool * based on the requested longest side. * * @param pools Map of the current dimension pools. * @param pixels Pixels set to add to the correct dimension pool. * @param dimensions Dimensions pool to add to. */ private void addToDimensionPool(Map<Dimension, Set<Long>> pools, Pixels pixels, Dimension dimensions) { // Insert the Pixels set into the dimension pool Set<Long> pool = pools.get(dimensions); if (pool == null) { pool = new HashSet<Long>(); } pool.add(pixels.getId()); pools.put(dimensions, pool); } /** * Examines the currently prepared data structures for Pixels IDs without * settings. * @param pixelsIds Pixels IDs to check. * @return Set of Pixels IDs which do not have settings prepared. */ private Set<Long> getPixelsIdsWithoutSettings(Set<Long> pixelsIds) { Set<Long> pixelsIdsWithoutSettings = new HashSet<Long>(); for (Long pixelsId : pixelsIds) { if (!hasSettings(pixelsId)) { pixelsIdsWithoutSettings.add(pixelsId); } } return pixelsIdsWithoutSettings; } /** * Examines the currently prepared data structures for Pixels IDs without * thumbnail metadata. * @param pixelsIds Pixels IDs to check. * @return Set of Pixels IDs which do not have thumbnail metadata prepared. */ private Set<Long> getPixelsIdsWithoutMetadata(Set<Long> pixelsIds) { Set<Long> pixelsIdsWithoutMetadata = new HashSet<Long>(); for (Long pixelsId : pixelsIds) { if (!hasMetadata(pixelsId)) { pixelsIdsWithoutMetadata.add(pixelsId); } } return pixelsIdsWithoutMetadata; } /** * Bulk loads a set of rendering sets for a group of pixels sets. * @param pixelsIds the Pixels sets to retrieve thumbnails for. * @return Loaded rendering settings for <code>pixelsIds</code>. */ private List<RenderingDef> bulkLoadRenderingSettingsByPixelsId(Set<Long> pixelsIds) { StopWatch s1 = new CommonsLogStopWatch("omero.bulkLoadRenderingSettings"); List<RenderingDef> toReturn = queryService.findAllByQuery( "select r from RenderingDef as r " + "join fetch r.pixels as p " + "join fetch r.details.updateEvent " + "join p.details.updateEvent " + "where r.details.owner.id = :id and r.pixels.id in (:ids)", new Parameters().addId(userId).addIds(pixelsIds)); s1.stop(); return toReturn; } /** * Bulk loads a set of rendering sets for a group of Images. * @param imageIds the Images retrieve thumbnails for. * @return Loaded rendering settings for <code>imageIds</code>. */ private List<RenderingDef> bulkLoadRenderingSettingsByImageId(Set<Long> imageIds) { StopWatch s1 = new CommonsLogStopWatch("omero.bulkLoadRenderingSettings"); List<RenderingDef> toReturn = queryService.findAllByQuery( "select r from RenderingDef as r " + "join fetch r.pixels as p " + "join fetch r.details.updateEvent " + "join fetch p.details.updateEvent " + "where r.details.owner.id = :id " + "and r.pixels.image.id in (:ids)", new Parameters().addId(userId).addIds(imageIds)); s1.stop(); return toReturn; } /** * Bulk loads a set of rendering sets for a group of pixels sets. * @param pixelsIds the Pixels sets to retrieve thumbnails for. * @return Loaded rendering settings for <code>pixelsIds</code>. */ private List<RenderingDef> bulkLoadOwnerRenderingSettings(Set<Long> pixelsIds) { StopWatch s1 = new CommonsLogStopWatch("omero.bulkLoadOwnerRenderingSettings"); List<RenderingDef> toReturn = queryService.findAllByQuery( "select r from RenderingDef as r " + "join fetch r.pixels as p " + "join fetch r.details.updateEvent " + "join fetch p.details.updateEvent " + "where r.details.owner.id = p.details.owner.id " + "and r.pixels.id in (:ids)", new Parameters().addIds(pixelsIds)); s1.stop(); return toReturn; } /** * Bulk loads thumbnail metadata. * @param dimensions X-Y dimensions to bulk load metdata for. * @param pixelsIds Pixels IDs to bulk load metadata for. * @return List of thumbnail objects with <code>thumbnail.pixels</code> and * <code>thumbnail.details.updateEvent</code> loaded. */ private List<Thumbnail> bulkLoadMetadata(Dimension dimensions, Set<Long> pixelsIds) { Parameters params = new Parameters(); params.addInteger("x", (int) dimensions.getWidth()); params.addInteger("y", (int) dimensions.getHeight()); params.addLong("o_id", userId); params.addIds(pixelsIds); StopWatch s1 = new CommonsLogStopWatch("omero.bulkLoadMetadata"); List<Thumbnail> toReturn = queryService.findAllByQuery("select t from Thumbnail as t " + "join t.pixels " + "join fetch t.details.updateEvent " + "where t.sizeX = :x and t.sizeY = :y " + "and t.details.owner.id = :o_id " + "and t.pixels.id in (:ids)", params); s1.stop(); return toReturn; } /** * Bulk loads thumbnail metadata that is owned by the owner of the Pixels * set.. * @param dimensions X-Y dimensions to bulk load metadata for. * @param pixelsIds Pixels IDs to bulk load metadata for. * @return List of thumbnail objects with <code>thumbnail.pixels</code> and * <code>thumbnail.details.updateEvent</code> loaded. */ private List<Thumbnail> bulkLoadOwnerMetadata(Dimension dimensions, Set<Long> pixelsIds) { Parameters params = new Parameters(); params.addInteger("x", (int) dimensions.getWidth()); params.addInteger("y", (int) dimensions.getHeight()); params.addIds(pixelsIds); StopWatch s1 = new CommonsLogStopWatch("omero.bulkLoadOwnerMetadata"); List<Thumbnail> toReturn = queryService .findAllByQuery( "select t from Thumbnail as t " + "join t.pixels as p " + "join fetch t.details.updateEvent " + "where t.sizeX = :x and t.sizeY = :y " + "and t.details.owner.id = p.details.owner.id " + "and t.pixels.id in (:ids)", params); s1.stop(); return toReturn; } /** * Attempts to efficiently retrieve the thumbnail metadata based on a set * of dimension pools. At worst, the result of maintaining the aspect ratio * (calculating the new XY widths) is that we have to retrieve each * thumbnail object separately. * @param dimensionPools Dimension pools to query based upon. * @param metadataMap Dictionary of Pixels ID vs. thumbnail metadata. Will * be updated by this method. * @param metadataTimeMap Dictionary of Pixels ID vs. thumbnail metadata * last modification time. Will be updated by this method. */ private void loadMetadataByDimensionPool(Map<Dimension, Set<Long>> dimensionPools) { StopWatch s1 = new CommonsLogStopWatch("omero.loadMetadataByDimensionPool"); for (Dimension dimensions : dimensionPools.keySet()) { Set<Long> pool = dimensionPools.get(dimensions); // First populate our hash maps asking for our metadata. List<Thumbnail> thumbnailList = bulkLoadMetadata(dimensions, pool); for (Thumbnail metadata : thumbnailList) { prepareMetadata(metadata, metadata.getPixels().getId()); } // Now check to see if we're in a state where missing metadata // requires us to use the owner's metadata (we're "graph critical") // and load them if possible. Set<Long> pixelsIdsWithoutMetadata = getPixelsIdsWithoutMetadata(pool); if (pixelsIdsWithoutMetadata.size() > 0 && isExtendedGraphCritical(pixelsIdsWithoutMetadata)) { thumbnailList = bulkLoadOwnerMetadata(dimensions, pixelsIdsWithoutMetadata); for (Thumbnail metadata : thumbnailList) { prepareMetadata(metadata, metadata.getPixels().getId()); } } } s1.stop(); } /** * Loads and prepares missing Pixels sets. * @param pixelsIds Pixels IDs to load missing Pixels objects for. */ private void loadMissingPixels(Set<Long> pixelsIds) { if (pixelsIds.size() > 0) { Parameters parameters = new Parameters(); parameters.addIds(pixelsIds); if (log.isDebugEnabled()) { log.debug("Loading " + pixelsIds.size() + " missing Pixels."); } StopWatch s1 = new CommonsLogStopWatch("omero.loadMissingPixels"); List<Pixels> pixelsWithoutSettings = queryService .findAllByQuery("select p from Pixels as p where id in (:ids)", parameters); s1.stop(); for (Pixels pixels : pixelsWithoutSettings) { Long pixelsId = pixels.getId(); pixelsIdPixelsMap.put(pixelsId, pixels); pixelsIdOwnerIdMap.put(pixelsId, pixels.getDetails().getOwner().getId()); } } } /** * Prepares a set of rendering settings, extracting relevant metadata and * preparing the internal maps. * @param settings RenderingDef object to prepare. * @param pixels Pixels object to prepare. */ private void prepareRenderingSettings(RenderingDef settings, Pixels pixels) { Long pixelsId = pixels.getId(); pixelsIdPixelsMap.put(pixelsId, pixels); pixelsIdOwnerIdMap.put(pixelsId, pixels.getDetails().getOwner().getId()); Details details = settings.getDetails(); Timestamp timestemp = details.getUpdateEvent().getTime(); pixelsIdSettingsMap.put(pixelsId, settings); pixelsIdSettingsLastModifiedTimeMap.put(pixelsId, timestemp); pixelsIdSettingsOwnerIdMap.put(pixelsId, details.getOwner().getId()); } /** * Prepares thumbnail metadata extracting relevant metadata and prepares * the internal maps. * @param metadata Thumbnail object to prepare. * @param pixelsId Pixels ID to prepare. */ private void prepareMetadata(Thumbnail metadata, long pixelsId) { Timestamp t = metadata.getDetails().getUpdateEvent().getTime(); pixelsIdMetadataMap.put(pixelsId, metadata); pixelsIdMetadataLastModifiedTimeMap.put(pixelsId, t); } /** * Creates missing thumbnail metadata for a set of Pixels IDs that have * been prepared. * @param dimensionPools Dimension pools to retrieve pre-calculated, * requested dimensions from. */ private void createMissingThumbnailMetadata(Map<Dimension, Set<Long>> dimensionPools) { // Now check to see if we're in a state where missing metadata // and our state requires us to not save. if (isExtendedGraphCritical(dimensionPools)) { // TODO: Could possibly "su" to the user and create a thumbnail return; } StopWatch s1 = new CommonsLogStopWatch("omero.createMissingThumbnailMetadata"); List<Thumbnail> toSave = new ArrayList<Thumbnail>(); Map<Dimension, Set<Long>> temporaryDimensionPools = new HashMap<Dimension, Set<Long>>(); Set<Long> pixelsIdsWithoutMetadata = getPixelsIdsWithoutMetadata(pixelsIdPixelsMap.keySet()); for (Long pixelsId : pixelsIdsWithoutMetadata) { Pixels pixels = pixelsIdPixelsMap.get(pixelsId); for (Dimension dimension : dimensionPools.keySet()) { Set<Long> pool = dimensionPools.get(dimension); if (pool.contains(pixelsId)) { toSave.add(createThumbnailMetadata(pixels, dimension)); addToDimensionPool(temporaryDimensionPools, pixels, dimension); break; } } } log.info("New thumbnail object set size: " + toSave.size()); log.info("Dimension pool size: " + temporaryDimensionPools.size()); if (toSave.size() > 0) { updateService.saveAndReturnIds(toSave.toArray(new Thumbnail[toSave.size()])); loadMetadataByDimensionPool(temporaryDimensionPools); } s1.stop(); } /** * Creates metadata for a thumbnail of a given set of pixels set and X-Y * dimensions. * * @param pixels The Pixels set to create thumbnail metadata for. * @param dimensions The dimensions of the thumbnail. * * @return the thumbnail metadata as created. * @see getThumbnailMetadata() */ public Thumbnail createThumbnailMetadata(Pixels pixels, Dimension dimensions) { // Unload the pixels object to avoid transactional headaches Pixels unloadedPixels = new Pixels(pixels.getId(), false); Thumbnail thumb = new Thumbnail(); thumb.setPixels(unloadedPixels); thumb.setMimeType(DEFAULT_MIME_TYPE); thumb.setSizeX((int) dimensions.getWidth()); thumb.setSizeY((int) dimensions.getHeight()); return thumb; } }