Source code for girder_large_image

#  Copyright Kitware Inc.
#  Licensed under the Apache License, Version 2.0 ( the "License" );
#  you may not use this file except in compliance with the License.
#  You may obtain a copy of the License at
#  Unless required by applicable law or agreed to in writing, software
#  distributed under the License is distributed on an "AS IS" BASIS,
#  See the License for the specific language governing permissions and
#  limitations under the License.

import datetime
import json
import re
import threading
import warnings
from importlib.metadata import PackageNotFoundError
from importlib.metadata import version as _importlib_version

import yaml
from girder_jobs.constants import JobStatus
from girder_jobs.models.job import Job

import girder
import large_image
from girder import events, logger
from girder.api import filter_logging
from girder.constants import AccessType, SortDir
from girder.exceptions import RestException, ValidationException
from girder.models.file import File
from girder.models.folder import Folder
from import Group
from girder.models.item import Item
from girder.models.notification import Notification
from girder.models.setting import Setting
from girder.models.upload import Upload
from girder.plugin import GirderPlugin, getPlugin
from girder.settings import SettingDefault
from girder.utility import config, search, setting_utilities
from girder.utility.model_importer import ModelImporter

from . import constants, girder_tilesource
from .girder_tilesource import getGirderTileSource  # noqa
from .loadmodelcache import invalidateLoadModelCache
from .models.image_item import ImageItem
from .rest import addSystemEndpoints
from .rest.item_meta import InternalMetadataItemResource
from .rest.large_image_resource import LargeImageResource
from .rest.tiles import TilesItemResource

    __version__ = _importlib_version(__name__)
except PackageNotFoundError:
    # package is not installed

mimetypes = None
_configWriteLock = threading.RLock()

# Girder 3 is pinned to use pymongo < 4; its warnings aren't relevant until
# that changes.
warnings.filterwarnings('ignore', category=UserWarning, module='pymongo')

def _postUpload(event):
    Called when a file is uploaded. We check the parent item to see if it is
    expecting a large image upload, and if so we register this file as the
    result image.
    fileObj =['file']
    # There may not be an itemId (on thumbnails, for instance)
    if not fileObj.get('itemId'):

    item = Item().load(fileObj['itemId'], force=True, exc=True)

    if item.get('largeImage', {}).get('expected') and (
            fileObj['name'].endswith('.tiff') or
            fileObj.get('mimeType') == 'image/tiff'):
        if fileObj.get('mimeType') != 'image/tiff':
            fileObj['mimeType'] = 'image/tiff'
        del item['largeImage']['expected']
        item['largeImage']['fileId'] = fileObj['_id']
        item['largeImage']['sourceName'] = 'tiff'
        if fileObj['name'].endswith('.geo.tiff'):
            item['largeImage']['sourceName'] = 'gdal'
        # If the job looks finished, update it once more to force notifications
        if 'jobId' in item['largeImage'] and item['largeImage'].get('notify'):
            job = Job().load(item['largeImage']['jobId'], force=True)
            if job and job['status'] == JobStatus.SUCCESS:

def _updateJob(event):
    Called when a job is saved, updated, or removed.  If this is a large image
    job and it is ended, clean up after it.
    job =['job'] if == 'jobs.job.update.after' else
    meta = job.get('meta', {})
    if (meta.get('creator') != 'large_image' or not meta.get('itemId') or
            meta.get('task') != 'createImageItem'):
    status = job['status']
    if == 'model.job.remove' and status not in (
            JobStatus.ERROR, JobStatus.CANCELED, JobStatus.SUCCESS):
        status = JobStatus.CANCELED
    if status not in (JobStatus.ERROR, JobStatus.CANCELED, JobStatus.SUCCESS):
    item = Item().load(meta['itemId'], force=True)
    if not item or 'largeImage' not in item:
    if item.get('largeImage', {}).get('expected'):
        # We can get a SUCCESS message before we get the upload message, so
        # don't clear the expected status on success.
        if status != JobStatus.SUCCESS:
            del item['largeImage']['expected']
    notify = item.get('largeImage', {}).get('notify')
    msg = None
    if notify:
        del item['largeImage']['notify']
        if status == JobStatus.SUCCESS:
            msg = 'Large image created'
        elif status == JobStatus.CANCELED:
            msg = 'Large image creation canceled'
        else:  # ERROR
            msg = 'FAILED: Large image creation failed'
        msg += ' for item %s' % item['name']
    if (status in (JobStatus.ERROR, JobStatus.CANCELED) and
            'largeImage' in item):
        del item['largeImage']
    if msg and != 'model.job.remove':
        Job().updateJob(job, progressMessage=msg)
    if notify:
                'job_id': job['_id'],
                'item_id': item['_id'],
                'success': status == JobStatus.SUCCESS,
                'status': status,
            user={'_id': job.get('userId')},
            expires=( +

[docs] def checkForLargeImageFiles(event): file ='Handling file %s (%s)', file['_id'], file['name']) possible = False mimeType = file.get('mimeType') if mimeType in girder_tilesource.KnownMimeTypes: possible = True exts = [ext.split()[0] for ext in file.get('exts') if ext] if set(exts[-2:]).intersection(girder_tilesource.KnownExtensions): possible = True if not file.get('itemId'): return autoset = Setting().get(constants.PluginSettings.LARGE_IMAGE_AUTO_SET) if not autoset or (not possible and autoset != 'all'): return item = Item().load(file['itemId'], force=True, exc=False) if not item or item.get('largeImage'): return try: ImageItem().createImageItem(item, file, createJob=False) except Exception: # We couldn't automatically set this as a large image 'Saved file %s cannot be automatically used as a largeImage' % str(file['_id']))
[docs] def removeThumbnails(event): ImageItem().removeThumbnailFiles(
[docs] def prepareCopyItem(event): """ When copying an item, adjust the largeImage fileId reference so it can be matched to the to-be-copied file. """ srcItem, newItem = if 'largeImage' in newItem: li = newItem['largeImage'] for pos, file in enumerate(Item().childFiles(item=srcItem)): for key in ('fileId', 'originalId'): if li.get(key) == file['_id']: li['_index_' + key] = pos Item().save(newItem, triggerEvents=False)
[docs] def handleCopyItem(event): """ When copying an item, finish adjusting the largeImage fileId reference to the copied file. """ newItem = if 'largeImage' in newItem: li = newItem['largeImage'] files = list(Item().childFiles(item=newItem)) for key in ('fileId', 'originalId'): pos = li.pop('_index_' + key, None) if pos is not None and 0 <= pos < len(files): li[key] = files[pos]['_id'] Item().save(newItem, triggerEvents=False)
[docs] def handleRemoveFile(event): """ When a file is removed, check if it is a largeImage fileId. If so, delete the largeImage record. """ fileObj = if fileObj.get('itemId'): item = Item().load(fileObj['itemId'], force=True, exc=False) if item and 'largeImage' in item and item['largeImage'].get('fileId') == fileObj['_id']: ImageItem().delete(item, [fileObj['_id']])
[docs] def handleFileSave(event): """ When a file is first saved, mark its mime type based on its extension if we would otherwise just mark it as generic application/octet-stream. """ fileObj = if fileObj.get('mimeType', None) in {None, ''} or ( '_id' not in fileObj and fileObj.get('mimeType', None) in {'application/octet-stream'}): global mimetypes if not mimetypes: import mimetypes if not mimetypes.inited: mimetypes.init() # Augment the standard mimetypes with some additional values for mimeType, ext, std in [ ('text/yaml', '.yaml', True), ('text/yaml', '.yml', True), ('application/vnd.geo+json', '.geojson', True), ]: if ext not in mimetypes.types_map: mimetypes.add_type(mimeType, ext, std) alt = mimetypes.guess_type(fileObj.get('name', ''))[0] if alt is not None: fileObj['mimeType'] = alt
[docs] def handleSettingSave(event): """ When certain settings are changed, clear the caches. """ if'key') == constants.PluginSettings.LARGE_IMAGE_ICC_CORRECTION: if['value'] == Setting().get( constants.PluginSettings.LARGE_IMAGE_ICC_CORRECTION): return import gc from import setResponseHeader large_image.config.setConfig('icc_correction',['value']) large_image.cache_util.cachesClear() gc.collect() try: # ask the browser to clear the cache; it probably won't be honored setResponseHeader('Clear-Site-Data', '"cache"') except Exception: pass
[docs] def metadataSearchHandler( # noqa query, types, user=None, level=None, limit=0, offset=0, models=None, searchModels=None, metakey='meta'): """ Provide a substring search on metadata. """ models = models or {'item', 'folder'} if any(typ not in models for typ in types): raise RestException('The metadata search is only able to search in %r.' % models) if not isinstance(query, str): msg = 'The search query must be a string.' raise RestException(msg) # If we have the beginning of the field specifier, don't do a search if re.match(r'^(k|ke|key|key:)$', query.strip()): return {k: [] for k in types} phrases = re.findall(r'"[^"]*"|\'[^\']*\'|\S+', query) fields = {phrase.split('key:', 1)[1] for phrase in phrases if phrase.startswith('key:') and len(phrase.split('key:', 1)[1])} phrases = [phrase for phrase in phrases if not phrase.startswith('key:') or not len(phrase.split('key:', 1)[1])] if not len(fields): pipeline = [ {'$project': {'arrayofkeyvalue': {'$objectToArray': '$$ROOT.%s' % metakey}}}, {'$unwind': '$arrayofkeyvalue'}, {'$group': {'_id': None, 'allkeys': {'$addToSet': '$arrayofkeyvalue.k'}}}, ] for model in (searchModels or types): modelInst = ModelImporter.model(*model if isinstance(model, tuple) else [model]) result = list(modelInst.collection.aggregate(pipeline, allowDiskUse=True)) if len(result): fields.update(list(result)[0]['allkeys']) if not len(fields): return {k: [] for k in types} logger.debug('Will search the following fields: %r', fields) usedPhrases = set() filter = [] for phrase in phrases: if phrase[0] == phrase[-1] and phrase[0] in '"\'': phrase = phrase[1:-1] if not len(phrase) or phrase in usedPhrases: continue usedPhrases.add(phrase) try: numval = float(phrase) delta = abs(float(re.sub(r'[1-9]', '1', re.sub( r'\d(?=.*[1-9](0*\.|)0*$)', '0', str(numval))))) except Exception: numval = None phrase = re.escape(phrase) clause = [] for field in fields: key = '%s.%s' % (metakey, field) clause.append({key: {'$regex': phrase, '$options': 'i'}}) if numval is not None: clause.append({key: {'$eq': numval}}) if numval > 0 and delta: clause.append({key: {'$gte': numval, '$lt': numval + delta}}) elif numval < 0 and delta: clause.append({key: {'$lte': numval, '$gt': numval + delta}}) if len(clause) > 1: filter.append({'$or': clause}) else: filter.append(clause[0]) if not len(filter): return [] filter = {'$and': filter} if len(filter) > 1 else filter[0] result = {} logger.debug('Metadata search uses filter: %r' % filter) for model in searchModels or types: modelInst = ModelImporter.model(*model if isinstance(model, tuple) else [model]) if searchModels is None: result[model] = [ modelInst.filter(doc, user) for doc in modelInst.filterResultsByPermission( modelInst.find(filter), user, level, limit, offset)] else: resultModelInst = ModelImporter.model(searchModels[model]['model']) result[searchModels[model]['model']] = [] foundIds = set() for doc in modelInst.filterResultsByPermission(modelInst.find(filter), user, level): id = doc[searchModels[model]['reference']] if id in foundIds: continue foundIds.add(id) entry = resultModelInst.load(id=id, user=user, level=level, exc=False) if entry is not None and offset: offset -= 1 continue elif entry is not None: result[searchModels[model]['model']].append(resultModelInst.filter(entry, user)) if limit and len(result[searchModels[model]['model']]) == limit: break return result
def _mergeDictionaries(a, b): """ Merge two dictionaries recursively. If the second dictionary (or any sub-dictionary) has a special key, value of '__all__': True, the updated dictionary only contains values from the second dictionary and excludes the __all__ key. :param a: the first dictionary. Modified. :param b: the second dictionary that gets added to the first. :returns: the modified first dictionary. """ if b.get('__all__') is True: a.clear() for key in b: if isinstance(a.get(key), dict) and isinstance(b[key], dict): _mergeDictionaries(a[key], b[key]) elif key != '__all__' or b[key] is not True: a[key] = b[key] return a
[docs] def adjustConfigForUser(config, user): """ Given the current user, adjust the config so that only relevant and combined values are used. If the root of the config dictionary contains "access": {"user": <dict>, "admin": <dict>}, the base values are updated based on the user's access level. If the root of the config contains "group": {<group-name>: <dict>, ...}, the base values are updated for every group the user is a part of. The order of update is groups in C-sort alphabetical order followed by access/user and then access/admin as they apply. :param config: a config dictionary. """ if not isinstance(config, dict): return config if isinstance(config.get('groups'), dict): groups = config.pop('groups') if user: for group in Group().find( {'_id': {'$in': user['groups']}}, sort=[('name', SortDir.ASCENDING)]): if isinstance(groups.get(group['name']), dict): config = _mergeDictionaries(config, groups[group['name']]) if isinstance(config.get('access'), dict): accessList = config.pop('access') if user and isinstance(accessList.get('user'), dict): config = _mergeDictionaries(config, accessList['user']) if user and user.get('admin') and isinstance(accessList.get('admin'), dict): config = _mergeDictionaries(config, accessList['admin']) return config
[docs] def yamlConfigFile(folder, name, user): """ Get a resolved named config file based on a folder and user. :param folder: a Girder folder model. :param name: the name of the config file. :param user: the user that the response if adjusted for. :returns: either None if no config file, or a yaml record. """ addConfig = None last = False while folder: item = Item().findOne({'folderId': folder['_id'], 'name': name}) if item: for file in Item().childFiles(item): if file['size'] > 10 * 1024 ** 2:'Not loading %s -- too large' % file['name']) continue with File().open(file) as fptr: config = yaml.safe_load(fptr) if isinstance(config, list) and len(config) == 1: config = config[0] # combine and adjust config values based on current user if isinstance(config, dict) and 'access' in config or 'group' in config: config = adjustConfigForUser(config, user) if addConfig and isinstance(config, dict): config = _mergeDictionaries(config, addConfig) if not isinstance(config, dict) or config.get('__inherit__') is not True: return config config.pop('__inherit__') addConfig = config if last: break if folder['parentCollection'] != 'folder': if folder['name'] != '.config': folder = Folder().findOne({ 'parentId': folder['parentId'], 'parentCollection': folder['parentCollection'], 'name': '.config'}) else: last = 'setting' if not folder or last == 'setting': folderId = Setting().get(constants.PluginSettings.LARGE_IMAGE_CONFIG_FOLDER) if not folderId: break folder = Folder().load(folderId, force=True) last = True else: folder = Folder().load(folder['parentId'], user=user, level=AccessType.READ) return addConfig
[docs] def yamlConfigFileWrite(folder, name, user, yaml_config): """ If the user has appropriate permissions, create or modify an item in the specified folder with the specified name, storing the config value as a file. :param folder: a Girder folder model. :param name: the name of the config file. :param user: the user that the response if adjusted for. :param yaml_config: a yaml config string. """ # Check that we have valid yaml yaml.safe_load(yaml_config) item = Item().createItem(name, user, folder, reuseExisting=True) existingFiles = list(Item().childFiles(item)) if (len(existingFiles) == 1 and existingFiles[0]['mimeType'] == 'text/yaml' and existingFiles[0]['name'] == name): upload = Upload().createUploadToFile( existingFiles[0], user, size=len(yaml_config)) else: upload = Upload().createUpload( user, name, 'item', item, size=len(yaml_config), mimeType='text/yaml', save=True) newfile = Upload().handleChunk(upload, yaml_config) with _configWriteLock: for entry in list(Item().childFiles(item)): if entry['_id'] != newfile['_id'] and len(Item().childFiles(item)) > 1: File().remove(entry)
# Validators
[docs] @setting_utilities.validator({ constants.PluginSettings.LARGE_IMAGE_SHOW_THUMBNAILS, constants.PluginSettings.LARGE_IMAGE_SHOW_VIEWER, constants.PluginSettings.LARGE_IMAGE_NOTIFICATION_STREAM_FALLBACK, }) def validateBoolean(doc): val = doc['value'] if str(val).lower() not in ('false', 'true', ''): raise ValidationException('%s must be a boolean.' % doc['key'], 'value') doc['value'] = (str(val).lower() != 'false')
[docs] @setting_utilities.validator({ constants.PluginSettings.LARGE_IMAGE_ICC_CORRECTION, }) def validateBooleanOrICCIntent(doc): import PIL.ImageCms val = doc['value'] if ((hasattr(PIL.ImageCms, 'Intent') and hasattr(PIL.ImageCms.Intent, str(val).upper())) or hasattr(PIL.ImageCms, 'INTENT_' + str(val).upper())): doc['value'] = str(val).upper() else: if str(val).lower() not in ('false', 'true', ''): raise ValidationException( '%s must be a boolean or a named intent.' % doc['key'], 'value') doc['value'] = (str(val).lower() != 'false')
[docs] @setting_utilities.validator({ constants.PluginSettings.LARGE_IMAGE_AUTO_SET, }) def validateBooleanOrAll(doc): val = doc['value'] if str(val).lower() not in ('false', 'true', 'all', ''): raise ValidationException('%s must be a boolean or "all".' % doc['key'], 'value') doc['value'] = val if val in {'all'} else (str(val).lower() != 'false')
[docs] @setting_utilities.validator({ constants.PluginSettings.LARGE_IMAGE_SHOW_EXTRA_PUBLIC, constants.PluginSettings.LARGE_IMAGE_SHOW_EXTRA, constants.PluginSettings.LARGE_IMAGE_SHOW_EXTRA_ADMIN, constants.PluginSettings.LARGE_IMAGE_SHOW_ITEM_EXTRA_PUBLIC, constants.PluginSettings.LARGE_IMAGE_SHOW_ITEM_EXTRA, constants.PluginSettings.LARGE_IMAGE_SHOW_ITEM_EXTRA_ADMIN, }) def validateDictOrJSON(doc): val = doc['value'] try: if isinstance(val, dict): doc['value'] = json.dumps(val) elif val is None or val.strip() == '': doc['value'] = '' else: parsed = json.loads(val) if not isinstance(parsed, dict): raise ValidationException('%s must be a JSON object.' % doc['key'], 'value') doc['value'] = val.strip() except (ValueError, AttributeError): raise ValidationException('%s must be a JSON object.' % doc['key'], 'value')
[docs] @setting_utilities.validator({ constants.PluginSettings.LARGE_IMAGE_MAX_THUMBNAIL_FILES, constants.PluginSettings.LARGE_IMAGE_MAX_SMALL_IMAGE_SIZE, }) def validateNonnegativeInteger(doc): val = doc['value'] try: val = int(val) if val < 0: raise ValueError except ValueError: raise ValidationException('%s must be a non-negative integer.' % ( doc['key'], ), 'value') doc['value'] = val
[docs] @setting_utilities.validator({ constants.PluginSettings.LARGE_IMAGE_DEFAULT_VIEWER, }) def validateDefaultViewer(doc): doc['value'] = str(doc['value']).strip()
[docs] @setting_utilities.validator(constants.PluginSettings.LARGE_IMAGE_CONFIG_FOLDER) def validateFolder(doc): if not doc.get('value', None): doc['value'] = None else: Folder().load(doc['value'], force=True, exc=True)
# Defaults # Defaults that have fixed values can just be added to the system defaults # dictionary. SettingDefault.defaults.update({ constants.PluginSettings.LARGE_IMAGE_SHOW_THUMBNAILS: True, constants.PluginSettings.LARGE_IMAGE_SHOW_VIEWER: True, constants.PluginSettings.LARGE_IMAGE_AUTO_SET: True, constants.PluginSettings.LARGE_IMAGE_MAX_THUMBNAIL_FILES: 10, constants.PluginSettings.LARGE_IMAGE_MAX_SMALL_IMAGE_SIZE: 4096, constants.PluginSettings.LARGE_IMAGE_NOTIFICATION_STREAM_FALLBACK: True, constants.PluginSettings.LARGE_IMAGE_ICC_CORRECTION: True, })
[docs] def unbindGirderEventsByHandlerName(handlerName): for eventName in events._mapping: events.unbind(eventName, handlerName)
[docs] class LargeImagePlugin(GirderPlugin): DISPLAY_NAME = 'Large Image' CLIENT_SOURCE_PATH = 'web_client'
[docs] def load(self, info): try: getPlugin('worker').load(info) except Exception: logger.debug('worker plugin is unavailable') unbindGirderEventsByHandlerName('large_image') ModelImporter.registerModel('image_item', ImageItem, 'large_image') large_image.config.setConfig('logger', girder.logger) large_image.config.setConfig('logprint', girder.logprint) # Load girder's large_image config curConfig = config.getConfig().get('large_image') for key, value in (curConfig or {}).items(): large_image.config.setConfig(key, value) large_image.config.setConfig('icc_correction', Setting().get( constants.PluginSettings.LARGE_IMAGE_ICC_CORRECTION)) addSystemEndpoints(info['apiRoot']) girder_tilesource.loadGirderTileSources() TilesItemResource(info['apiRoot']) InternalMetadataItemResource(info['apiRoot']) info['apiRoot'].large_image = LargeImageResource() Item().exposeFields(level=AccessType.READ, fields='largeImage') events.bind('data.process', 'large_image', _postUpload) events.bind('jobs.job.update.after', 'large_image', _updateJob) events.bind('', 'large_image', _updateJob) events.bind('model.job.remove', 'large_image', _updateJob) events.bind('', 'large_image', invalidateLoadModelCache) events.bind('', 'large_image', invalidateLoadModelCache) events.bind('', 'large_image', invalidateLoadModelCache) events.bind('', 'large_image', invalidateLoadModelCache) events.bind('model.item.remove', 'large_image', invalidateLoadModelCache) events.bind('model.item.copy.prepare', 'large_image', prepareCopyItem) events.bind('model.item.copy.after', 'large_image', handleCopyItem) events.bind('', 'large_image', invalidateLoadModelCache) events.bind('', 'large_image', checkForLargeImageFiles) filter_logging.addLoggingFilter( r'Handling file ([0-9a-f]{24}) \(', frequency=1000, duration=10) events.bind('model.item.remove', 'large_image.removeThumbnails', removeThumbnails) events.bind('server_fuse.unmount', 'large_image', large_image.cache_util.cachesClear) events.bind('model.file.remove', 'large_image', handleRemoveFile) events.bind('', 'large_image', handleFileSave) events.bind('', 'large_image', handleSettingSave) search._allowedSearchMode.pop('li_metadata', None) search.addSearchMode('li_metadata', metadataSearchHandler)