def getByHash(self, algo, hash):
self._validateAlgo(algo)
model = FileModel()
user = self.getCurrentUser()
cursor = model.find({algo: hash})
return [file for file in cursor if model.hasAccess(file, user, AccessType.READ)]
def _checkUploadSize(self, upload):
"""
Check if an upload will fit within a quota restriction.
:param upload: an upload document.
:returns: None if the upload is allowed, otherwise a dictionary of
information about the quota restriction.
"""
origSize = 0
if 'fileId' in upload:
file = File().load(id=upload['fileId'], force=True)
origSize = int(file.get('size', 0))
model, resource = self._getBaseResource('file', file)
else:
model, resource = self._getBaseResource(upload['parentType'], upload['parentId'])
if resource is None:
return None
fileSizeQuota = self._getFileSizeQuota(model, resource)
if not fileSizeQuota:
return None
newSize = resource['size'] + upload['size'] - origSize
# always allow replacement with a smaller object
if newSize <= fileSizeQuota or upload['size'] < origSize:
return None
left = fileSizeQuota - resource['size']
if left < 0:
left = 0
return {'fileSizeQuota': fileSizeQuota,
'sizeNeeded': upload['size'] - origSize,
'quotaLeft': left,
'quotaUsed': resource['size']}
def _computeHash(file, progress=noProgress):
"""
Computes all supported checksums on a given file. Downloads the
file data and stream-computes all required hashes on it, saving
the results in the file document.
In the case of assetstore impls that already compute the sha512,
and when sha512 is the only supported algorithm, we will not download
the file to the server.
"""
toCompute = SUPPORTED_ALGORITHMS - set(file)
toCompute = {alg: getattr(hashlib, alg)() for alg in toCompute}
if not toCompute:
return
fileModel = FileModel()
with fileModel.open(file) as fh:
while True:
chunk = fh.read(_CHUNK_LEN)
if not chunk:
break
for digest in six.viewvalues(toCompute):
digest.update(chunk)
progress.update(increment=len(chunk))
digests = {alg: digest.hexdigest() for alg, digest in six.viewitems(toCompute)}
fileModel.update({'_id': file['_id']}, update={
'$set': digests
}, multi=False)
return digests
def _getFirstFileByHash(self, algo, hash, user=None):
"""
Return the first file that the user has access to given its hash and its
associated hashsum algorithm name.
:param algo: Algorithm the given hash is encoded with.
:param hash: Hash of the file to find.
:param user: User to test access against.
Default (none) is the current user.
:return: A file document.
"""
self._validateAlgo(algo)
query = {algo: hash}
fileModel = FileModel()
cursor = fileModel.find(query)
if not user:
user = self.getCurrentUser()
for file in cursor:
if fileModel.hasAccess(file, user, AccessType.READ):
return file
return None
def testFilePath(self):
"""
Test that all files report a FUSE path, and that this results in the
same file as the non-fuse path.
"""
from girder.plugins import fuse as girder_fuse
files = list(File().find())
for file in files:
adapter = File().getAssetstoreAdapter(file)
filesystempath = adapter.fullPath(file)
filepath = girder_fuse.getFilePath(file)
fusepath = girder_fuse.getFuseFilePath(file)
self.assertTrue(os.path.exists(filesystempath))
self.assertTrue(os.path.exists(filepath))
self.assertTrue(os.path.exists(fusepath))
self.assertEqual(filesystempath, filepath)
self.assertNotEqual(filesystempath, fusepath)
self.assertEqual(fusepath[:len(self.mainMountPath)], self.mainMountPath)
with open(filepath) as file1:
with open(fusepath) as file2:
self.assertEqual(file1.read(), file2.read())
subpath = fusepath[len(self.mainMountPath):].lstrip('/')
if self.knownPaths.get(subpath):
with open(fusepath) as file1:
self.assertEqual(file1.read().strip(), self.knownPaths[subpath])
def adjustDBUri(cls, uri, *args, **kwargs):
"""
Adjust a uri to match the form sqlite requires. This can convert a
Girder resource path to an aprpopriate physical file reference.
:param uri: the uri to adjust.
:returns: the adjusted uri
"""
uri = super(SqliteSAConnector, cls).adjustDBUri(uri, *args, **kwargs)
if '://' in uri:
uri = uri.split('://', 1)[0] + ':////' + uri.split('://', 1)[1].lstrip('/')
uri = super(SqliteSAConnector, cls).adjustDBUri(uri, *args, **kwargs)
# If we have a Girder resource path, convert it. If this looks like a
# file but doesn't exist, check if it is a resource path. If this is
# not a resoruce path to a file that we can read directly, treat this
# the same as a missing file.
if (':///' in uri and not os.path.exists(uri.split(':///', 1)[1])):
resourcepath = path_util.lookUpPath(
uri.split(':///', 1)[1], test=True, filter=False, force=True)
if resourcepath and resourcepath['model'] == 'file':
file = resourcepath['document']
adapter = File().getAssetstoreAdapter(file)
if hasattr(adapter, 'fullPath'):
filepath = adapter.fullPath(file)
if os.path.exists(filepath):
uri = uri.split(':///', 1)[0] + ':///' + filepath
log.debug('Using Girder file for SQLite database')
return uri
def removeThumbnails(event):
"""
When a resource containing thumbnails is about to be deleted, we delete
all of the thumbnails that are attached to it.
"""
thumbs = event.info.get('_thumbnails', ())
fileModel = File()
for fileId in thumbs:
file = fileModel.load(fileId, force=True)
if file:
fileModel.remove(file)
def girderInputSpec(resource, resourceType='file', name=None, token=None,
dataType='string', dataFormat='text', fetchParent=False):
"""
Downstream plugins that are building Girder worker jobs that use Girder IO
should use this to generate the input specs more easily.
:param resource: The resource document to be downloaded at runtime.
:type resource: dict
:param resourceType: The resource type to download for the input. Should
be "folder", "item", or "file".
:type resourceType: str
:param name: The name of the resource to download. If not passed, uses
the "name" field of the resource document.
:type name: str or None
:param token: The Girder token document or raw token string to use to
authenticate when downloading. Pass `None` for anonymous downloads.
:type token: dict, str, or None
:param dataType: The worker `type` field.
:type dataType: str
:param dataFormat: The worker `format` field.
:type dataFormat: str
:param fetchParent: Whether to fetch the whole parent resource of the
specified resource as a side effect.
:type fetchParent: bool
"""
if isinstance(token, dict):
token = token['_id']
result = {
'mode': 'girder',
'api_url': getWorkerApiUrl(),
'token': token,
'id': str(resource['_id']),
'name': name or resource['name'],
'resource_type': resourceType,
'type': dataType,
'format': dataFormat,
'fetch_parent': fetchParent
}
if resourceType == 'file' and not fetchParent and Setting().get(PluginSettings.DIRECT_PATH):
# If we are adding a file and it exists on the local filesystem include
# that location. This can permit the user of the specification to
# access the file directly instead of downloading the file.
adapter = File().getAssetstoreAdapter(resource)
if callable(getattr(adapter, 'fullPath', None)):
result['direct_path'] = adapter.fullPath(resource)
return result
def testAssetstoreOpen(self):
for userAssetstore in (False, True):
townItem, townFile, assetstore1 = self._createTownItem(userAssetstore=userAssetstore)
adapter = File().getAssetstoreAdapter(townFile)
handle = adapter.open(townFile)
data = handle.read(200)
self.assertEqual(data[:2], b'{"')
data += handle.read(200)
self.assertNotEqual(data[:200], data[200:])
handle.seek(100)
data100 = handle.read(200)
self.assertEqual(data100, data[100:300])
handle.seek(-100, os.SEEK_END)
dataend = handle.read(200)
self.assertEqual(len(dataend), 100)
self.assertNotEqual(dataend, data[:100])
def __init__(self):
super(HdfsAssetstoreResource, self).__init__()
self.resourceName = 'hdfs_assetstore'
self.route('PUT', (':id', 'import'), self.importData)
self.folderModel = Folder() # Save to avoid many lookups
self.itemModel = Item()
self.fileModel = File()
def findInvalidFiles(self, progress=progress.noProgress, filters=None,
checkSize=True, **kwargs):
"""
Goes through every file in this assetstore and finds those whose
underlying data is missing or invalid. This is a generator function --
for each invalid file found, a dictionary is yielded to the caller that
contains the file, its absolute path on disk, and a reason for invalid,
e.g. "missing" or "size".
:param progress: Pass a progress context to record progress.
:type progress: :py:class:`girder.utility.progress.ProgressContext`
:param filters: Additional query dictionary to restrict the search for
files. There is no need to set the ``assetstoreId`` in the filters,
since that is done automatically.
:type filters: dict or None
:param checkSize: Whether to make sure the size of the underlying
data matches the size of the file.
:type checkSize: bool
"""
filters = filters or {}
q = dict({
'assetstoreId': self.assetstore['_id']
}, **filters)
cursor = File().find(q)
progress.update(total=cursor.count(), current=0)
for file in cursor:
progress.update(increment=1, message=file['name'])
path = self.fullPath(file)
if not os.path.isfile(path):
yield {
'reason': 'missing',
'file': file,
'path': path
}
elif checkSize and os.path.getsize(path) != file['size']:
yield {
'reason': 'size',
'file': file,
'path': path
}
def __init__(self, file):
"""
Create a file-like object representing a file blob stored in Girder.
:param file: The file object being opened.
:type file: dict
"""
super(_FileHandle, self).__init__()
self.file = file
self._handle = File().open(file)
def __init__(self):
super().__init__()
self.resourceName = 'label'
self.coll_m = Collection()
self.file_m = File()
self.folder_m = Folder()
self.item_m = Item()
self.upload_m = Upload()
self.asset_m = Assetstore()
self.setupRoutes()
def deleteFile(self, file):
"""
We want to queue up files to be deleted asynchronously since it requires
an external HTTP request per file in order to delete them, and we don't
want to wait on that.
Files that were imported as pre-existing data will not actually be
deleted from S3, only their references in Girder will be deleted.
"""
if file['size'] > 0 and 'relpath' in file:
q = {
'relpath': file['relpath'],
'assetstoreId': self.assetstore['_id']
}
matching = File().find(q, limit=2, fields=[])
if matching.count(True) == 1:
events.daemon.trigger(info={
'client': self.client,
'bucket': self.assetstore['bucket'],
'key': file['s3Key']
}, callback=_deleteFileImpl)
class _FileHandle(paramiko.SFTPHandle):
def __init__(self, file):
"""
Create a file-like object representing a file blob stored in Girder.
:param file: The file object being opened.
:type file: dict
"""
super(_FileHandle, self).__init__()
self.file = file
self._handle = File().open(file)
def read(self, offset, length):
if length > MAX_BUF_LEN:
raise IOError(
'Requested chunk length (%d) is larger than the maximum allowed.' % length)
if offset != self._handle.tell() and offset < self.file['size']:
self._handle.seek(offset)
return self._handle.read(length)
def stat(self):
return _stat(self.file, 'file')
def close(self):
self._handle.close()
return paramiko.SFTP_OK
def deleteFile(self, file):
"""
Delete all of the chunks in the collection that correspond to the
given file.
"""
q = {
'chunkUuid': file['chunkUuid'],
'assetstoreId': self.assetstore['_id']
}
matching = File().find(q, limit=2, projection=[])
if matching.count(True) == 1:
# If we can't reach the database, we return anyway. A system check
# will be necessary to remove the abandoned file. Since we already
# can handle that case, tell Mongo to use a 0 write concern -- we
# don't need to know that the chunks have been deleted, and this
# can be faster.
try:
self.chunkColl.with_options(
write_concern=pymongo.WriteConcern(w=0)).delete_many(
{'uuid': file['chunkUuid']})
except pymongo.errors.AutoReconnect:
pass
def deleteFile(self, file):
"""
Deletes the file from disk if it is the only File in this assetstore
with the given sha512. Imported files are not actually deleted.
"""
from girder.models.file import File
if file.get('imported') or 'path' not in file:
return
q = {
'sha512': file['sha512'],
'assetstoreId': self.assetstore['_id']
}
path = os.path.join(self.assetstore['root'], file['path'])
if os.path.isfile(path):
with filelock.FileLock(path + '.deleteLock'):
matching = File().find(q, limit=2, fields=[])
matchingUpload = Upload().findOne(q)
if matching.count(True) == 1 and matchingUpload is None:
try:
os.unlink(path)
except Exception:
logger.exception('Failed to delete file %s' % path)
def __init__(self):
super(File, self).__init__()
self._model = FileModel()
self.resourceName = 'file'
self.route('DELETE', (':id',), self.deleteFile)
self.route('DELETE', ('upload', ':id'), self.cancelUpload)
self.route('GET', ('offset',), self.requestOffset)
self.route('GET', (':id',), self.getFile)
self.route('GET', (':id', 'download'), self.download)
self.route('GET', (':id', 'download', ':name'), self.downloadWithName)
self.route('POST', (), self.initUpload)
self.route('POST', ('chunk',), self.readChunk)
self.route('POST', ('completion',), self.finalizeUpload)
self.route('POST', (':id', 'copy'), self.copy)
self.route('PUT', (':id',), self.updateFile)
self.route('PUT', (':id', 'contents'), self.updateFileContents)
self.route('PUT', (':id', 'move'), self.moveFileToAssetstore)
def testFilesystemAssetstoreFindInvalidFiles(self):
# Create several files in the assetstore, some of which point to real
# files on disk and some that don't
folder = next(Folder().childFolders(
parent=self.admin, parentType='user', force=True, limit=1))
item = Item().createItem('test', self.admin, folder)
path = os.path.join(
ROOT_DIR, 'tests', 'cases', 'py_client', 'testdata', 'hello.txt')
real = File().createFile(
name='hello.txt', creator=self.admin, item=item,
assetstore=self.assetstore, size=os.path.getsize(path))
real['imported'] = True
real['path'] = path
File().save(real)
fake = File().createFile(
name='fake', creator=self.admin, item=item, size=1, assetstore=self.assetstore)
fake['path'] = 'nonexistent/path/to/file'
fake['sha512'] = '...'
fake = File().save(fake)
fakeImport = File().createFile(
name='fakeImport', creator=self.admin, item=item, size=1, assetstore=self.assetstore)
fakeImport['imported'] = True
fakeImport['path'] = '/nonexistent/path/to/file'
fakeImport = File().save(fakeImport)
adapter = assetstore_utilities.getAssetstoreAdapter(self.assetstore)
self.assertTrue(inspect.isgeneratorfunction(adapter.findInvalidFiles))
with ProgressContext(True, user=self.admin, title='test') as p:
invalidFiles = list(adapter.findInvalidFiles(progress=p, filters={
'imported': True
}))
self.assertEqual(len(invalidFiles), 1)
self.assertEqual(invalidFiles[0]['reason'], 'missing')
self.assertEqual(invalidFiles[0]['file']['_id'], fakeImport['_id'])
self.assertEqual(p.progress['data']['current'], 2)
self.assertEqual(p.progress['data']['total'], 2)
invalidFiles = list(adapter.findInvalidFiles(progress=p))
self.assertEqual(len(invalidFiles), 2)
for invalidFile in invalidFiles:
self.assertEqual(invalidFile['reason'], 'missing')
self.assertIn(invalidFile['file']['_id'], (fakeImport['_id'], fake['_id']))
self.assertEqual(p.progress['data']['current'], 3)
self.assertEqual(p.progress['data']['total'], 3)
def _testEmptyUpload(self, name):
"""
Uploads an empty file to the server.
"""
resp = self.request(
path='/file', method='POST', user=self.user, params={
'parentType': 'folder',
'parentId': self.privateFolder['_id'],
'name': name,
'size': 0
})
self.assertStatusOk(resp)
file = resp.json
self.assertHasKeys(file, ['itemId'])
self.assertEqual(file['size'], 0)
self.assertEqual(file['name'], name)
self.assertEqual(file['assetstoreId'], str(self.assetstore['_id']))
return File().load(file['_id'], force=True)
def _countCachedImages(self, spec, associatedImages=False):
if spec is not None:
try:
spec = json.loads(spec)
if not isinstance(spec, list):
raise ValueError()
except ValueError:
raise RestException('The spec parameter must be a JSON list.')
spec = [json.dumps(entry, sort_keys=True, separators=(',', ':'))
for entry in spec]
else:
spec = [None]
count = 0
for entry in spec:
query = {'isLargeImageThumbnail': True, 'attachedToType': 'item'}
if entry is not None:
query['thumbnailKey'] = entry
elif associatedImages:
query['thumbnailKey'] = {'$regex': '"imageKey":'}
count += File().find(query).count()
return count
def ingestDataset(self, params):
params = self._decodeParams(params)
self.requireParams(['zipFileId', 'name', 'owner'], params)
user = self.getCurrentUser()
User().requireCreateDataset(user)
zipFileId = params.get('zipFileId')
if not zipFileId:
raise ValidationException('No file was uploaded.', 'zipFileId')
zipFile = File().load(zipFileId, user=user, level=AccessType.WRITE, exc=False)
if not zipFile:
raise ValidationException('Invalid upload file ID.', 'zipFileId')
if not self._checkFileFormat(zipFile, ZIP_FORMATS):
raise ValidationException('File must be in .zip format.', 'zipFileId')
name = params['name'].strip()
owner = params['owner'].strip()
if not owner:
raise ValidationException('Owner must be specified.', 'owner')
description = params.get('description', '').strip()
# Enforce valid licensing metadata only at API level
licenseValue = params.get('license', '').strip()
if licenseValue not in {'CC-0', 'CC-BY', 'CC-BY-NC'}:
raise ValidationException('Unknown license type.', 'license')
signature = params.get('signature', '').strip()
if not signature:
raise ValidationException('Signature must be specified.', 'signature')
anonymous = self.boolParam('anonymous', params, False)
attribution = params.get('attribution', '').strip()
if not anonymous and not attribution:
raise ValidationException(
'Attribution must be specified when not contributing anonymously.', 'attribution')
# TODO: make this return only the dataset fields
return Dataset().ingestDataset(
zipFile=zipFile, user=user, name=name, owner=owner,
description=description, license=licenseValue, signature=signature,
anonymous=anonymous, attribution=attribution, sendMail=True)
def _uploadFile(self, path, name=None, private=False):
"""
Upload the specified path to the admin user's public or private folder
and return the resulting item.
:param path: path to upload.
:param name: optional name for the file.
:param private: True to upload to the private folder, False for public.
'user' for the user's private folder.
:returns: file: the created file.
"""
if not name:
name = os.path.basename(path)
with open(path, 'rb') as file:
data = file.read()
if private == 'user':
folderId = self.userPrivateFolder['_id']
elif private:
folderId = self.privateFolder['_id']
else:
folderId = self.publicFolder['_id']
resp = self.request(
path='/file', method='POST', user=self.admin, params={
'parentType': 'folder',
'parentId': folderId,
'name': name,
'size': len(data)
})
self.assertStatusOk(resp)
uploadId = resp.json['_id']
fields = [('offset', 0), ('uploadId', uploadId)]
files = [('chunk', name, data)]
resp = self.multipartRequest(
path='/file/chunk', fields=fields, files=files, user=self.admin)
self.assertStatusOk(resp)
self.assertIn('itemId', resp.json)
file = File().load(resp.json['_id'], user=self.admin, exc=True)
item = Item().load(file['itemId'], user=self.admin, exc=True)
return file, item
def downloadArchiveFile(self, file, path, offset, endByte, contentDisposition,
extraParameters):
"""
Requires read permission on the folder that contains the file's item.
"""
with ArchiveFileHandle(File(), file, path) as fileobj:
info = fileobj.info()
rangeHeader = cherrypy.lib.httputil.get_ranges(
cherrypy.request.headers.get('Range'), info['size'])
# The HTTP Range header takes precedence over query params
if rangeHeader and len(rangeHeader):
# Currently we only support a single range.
offset, endByte = rangeHeader[0]
if offset:
fileobj.seek(offset)
else:
offset = 0
if endByte is None or endByte > info['size']:
endByte = info['size']
setResponseHeader('Accept-Ranges', 'bytes')
setResponseHeader('Content-Type', 'application/octet-stream')
setContentDisposition(os.path.basename(path), contentDisposition
or 'attachment')
setResponseHeader('Content-Length', max(endByte - offset, 0))
if (offset or endByte < file['size']) and file['size']:
setResponseHeader(
'Content-Range',
'bytes %d-%d/%d' % (offset, endByte - 1, file['size']))
def downloadGenerator():
pos = offset
while pos < endByte:
data = fileobj.read(min(65536, endByte - pos))
yield data
pos += len(data)
if pos >= endByte:
break
return downloadGenerator
def createTiles(self, item, params):
largeImageFileId = params.get('fileId')
if largeImageFileId is None:
files = list(Item().childFiles(item=item, limit=2))
if len(files) == 1:
largeImageFileId = str(files[0]['_id'])
if not largeImageFileId:
raise RestException('Missing "fileId" parameter.')
largeImageFile = File().load(largeImageFileId, force=True, exc=True)
user = self.getCurrentUser()
token = self.getCurrentToken()
try:
return self.imageItemModel.createImageItem(item,
largeImageFile,
user,
token,
notify=self.boolParam(
'notify',
params,
default=True))
except TileGeneralException as e:
raise RestException(e.args[0])
def find_file(p_folder, name, user, assetstore, create=False):
"""
Find file by name. If not found create the file.
:param p_folder: parent folder
:param name: name of the file
:param user: user trying to access this file
:param assetstore: assetstore where this file exists
:param create: boolean, whether or not to create the file if not found
:return: file doc or None
"""
item = list(Item().find({'folderId': p_folder['_id'], 'name': name}).limit(1))
if not item:
# check if you are allowed to create, else return nothing
if create:
file = create_new_file(p_folder, name, user, assetstore)
else:
return None
else:
item = item[0]
file = list(File().find({'itemId': item['_id']}).limit(1))[0]
return file
def create_new_file(p_folder, name, user, assetstore):
"""
create a new file
:param p_folder: parent folder
:param name: name of the file you want to create
:param user: user trying to create this file
:param assetstore: assetstore where this file is going to be created
:return: file doc
"""
item = Item().createItem(name,
creator=user,
folder=p_folder,
description='label file',
reuseExisting=False)
file = File().createFile(size=0,
item=item,
name=name,
creator=user,
assetstore=assetstore,
mimeType="application/json")
return file
def handler(path, girder_item, girder_file):
if ".obj" not in girder_file['name'] and \
".OBJ" not in girder_file['name']:
raise CannotHandleError(girder_file['name'] + ' is not an OBJ file')
try:
jsonItem = Item().findOne({
'name':
girder_file['name'].replace("obj", "json"),
'folderId':
girder_item['folderId']
})
jsonFile = [i for i in Item().childFiles(jsonItem, limit=1)][0]
jsonContent = json.loads(''.join(
list(File().download(jsonFile, headers=False)())))
projectionParams = jsonContent['scenes'][0]['coordinate_system'][
'parameters']
ellps = projectionParams[0].upper()
m = re.compile('(utm) zone ([0-9]+)N',
re.IGNORECASE).match(projectionParams[1])
proj = m.group(1).lower()
zone = m.group(2)
sourceSrs = Proj(proj=proj, zone=zone, ellps=ellps).srs
offset = [
projectionParams[2], projectionParams[3], projectionParams[4]
]
bounds = getOBJBounds(path, offset)
geoJsonBounds = from_bounds_to_geojson(bounds, sourceSrs)
geometa = {
'crs': sourceSrs,
'nativeBounds': bounds,
'bounds': geoJsonBounds,
'type_': 'vector',
'driver': 'OBJ'
}
schema = OBJSchema()
return schema.load(geometa)
except Exception:
raise CannotHandleError('Failed to add geometa to OBJ file' +
girder_file['name'])
def _file_to_cjson(self, file, file_format):
readers = {
'cjson': oc.CjsonReader
}
if file_format not in readers:
raise Exception('Unknown file format %s' % file_format)
reader = readers[file_format]
with File().open(file) as f:
calc_data = f.read().decode()
# SpooledTemporaryFile doesn't implement next(),
# workaround in case any reader needs it
tempfile.SpooledTemporaryFile.__next__ = lambda self: self.__iter__().__next__()
with tempfile.SpooledTemporaryFile(mode='w+', max_size=10*1024*1024) as tf:
tf.write(calc_data)
tf.seek(0)
cjson = reader(tf).read()
return cjson
def testFilePathNoLocalPath(self):
"""
Test that if an assetstore adapter doesn't respond to getLocalFilePath,
we always get the fuse path.
"""
from girder.plugins import fuse as girder_fuse
from girder.utility.filesystem_assetstore_adapter import FilesystemAssetstoreAdapter
def getLocalFilePath(self, file):
return super(FilesystemAssetstoreAdapter,
self).getLocalFilePath(file)
file = File().findOne()
origGetLocalFilePath = FilesystemAssetstoreAdapter.getLocalFilePath
FilesystemAssetstoreAdapter.getLocalFilePath = getLocalFilePath
filepath = girder_fuse.getFilePath(file)
fusepath = girder_fuse.getFuseFilePath(file)
FilesystemAssetstoreAdapter.getLocalFilePath = origGetLocalFilePath
self.assertTrue(os.path.exists(filepath))
self.assertTrue(os.path.exists(fusepath))
self.assertEqual(filepath, fusepath)
def testUserImportedFolders(self):
user = User().findOne({'login': '******'})
self.assertDictContains(
{
'firstName': 'User',
'lastName': 'Two',
'admin': False
}, user, 'defaultFolders user')
folder = Folder().findOne({'parentId': user['_id']})
self.assertDictContains({'name': 'folder'}, folder, 'imported folder')
item = Item().findOne({'folderId': folder['_id']})
self.assertDictContains({'name': 'file.txt'}, item, 'imported item')
file = File().findOne({'itemId': item['_id']})
self.assertDictContains(
{
'name': 'file.txt',
'mimeType': 'text/plain',
'size': 5
}, file, 'imported file')
def _getLargeImagePath(self):
# If self.mayHaveAdjacentFiles is True, we try to use the girder
# mount where companion files appear next to each other.
try:
largeImageFileId = self.item['largeImage']['fileId']
if not hasattr(self, 'mayHaveAdjacentFiles'):
# The item has adjacent files if there are any files that
# are not the large image file or an original file it
# was derived from. This is always the case if there are 3
# or more files.
fileIds = [
str(file['_id'])
for file in Item().childFiles(self.item, limit=3)
]
knownIds = [str(largeImageFileId)]
if 'originalId' in self.item['largeImage']:
knownIds.append(str(self.item['largeImage']['originalId']))
self.mayHaveAdjacentFiles = (len(fileIds) >= 3
or fileIds[0] not in knownIds
or fileIds[-1] not in knownIds)
largeImageFile = File().load(largeImageFileId, force=True)
if (any(ext in KnownExtensionsWithAdjacentFiles
for ext in largeImageFile['exts'])
or largeImageFile.get('mimeType')
in KnownMimeTypesWithAdjacentFiles):
self.mayHaveAdjacentFiles = True
largeImagePath = None
if self.mayHaveAdjacentFiles and hasattr(File(),
'getGirderMountFilePath'):
try:
largeImagePath = File().getGirderMountFilePath(
largeImageFile)
except FilePathException:
pass
if not largeImagePath:
try:
largeImagePath = File().getLocalFilePath(largeImageFile)
except AttributeError as e:
raise TileSourceException(
'No local file path for this file: %s' % e.args[0])
return largeImagePath
except (TileSourceAssetstoreException, FilePathException):
raise
except (KeyError, ValidationException, TileSourceException) as e:
raise TileSourceException('No large image file in this item: %s' %
e.args[0])
def test_direct_docker_run(mocker, server, adminToken, file):
from girder.models.file import File
docker_run_mock = mocker.patch(
'slicer_cli_web.girder_worker_plugin.direct_docker_run._docker_run')
docker_run_mock.return_value = []
gc_mock = MockedGirderClient()
path = File().getLocalFilePath(file)
run(image='test', container_args=[DirectGirderFileIdToVolume(
file['_id'], filename=basename(path), direct_file_path=None, gc=gc_mock)])
docker_run_mock.assert_called_once()
kwargs = docker_run_mock.call_args[1]
# image
assert kwargs['image'] == 'test'
# container args
assert len(kwargs['container_args']) == 1
assert kwargs['container_args'][0].endswith(basename(path))
# volumes
assert len(kwargs['volumes']) == 1
target_path = '%s/%s' % (TEMP_VOLUME_DIRECT_MOUNT_PREFIX, basename(path))
docker_run_mock.reset_mock()
run(image='test', container_args=[DirectGirderFileIdToVolume(
file['_id'], direct_file_path=path, gc=gc_mock)])
docker_run_mock.assert_called_once()
kwargs = docker_run_mock.call_args[1]
# image
assert kwargs['image'] == 'test'
# container args
assert kwargs['container_args'] == [target_path]
# volumes
assert len(kwargs['volumes']) == 2
def boundaryThumbnail(self, segmentation, image=None, width=256):
if not image:
image = Image().load(segmentation['imageId'], force=True, exc=True)
# An alternative approach to the below method is to use OpenCV to create a morphological
# gradient image of the mask (using a square or cross structuring element, a circle is
# slower), which produces a mask of the outline. However, while this part is quite fast,
# using NumPy to set the pixels of the rendered image is not quite as fast as Pillow's line
# drawing and encoding the image as JPEG is also faster with Pillow than NumPy.
mask = self.maskData(segmentation)
if mask is None:
return None
contour = OpenCVSegmentationHelper.maskToContour(
mask, paddedInput=False)
originalFilePath = File().getLocalFilePath(Image().originalFile(image))
with PIL_Image.open(originalFilePath) as pilImageData:
pilDraw = PIL_ImageDraw.Draw(pilImageData)
pilDraw.line(
list(map(tuple, contour)),
fill=(0, 255, 0), # TODO: make color an option
width=int(pilImageData.size[0] / 300.0)
)
# Saving using native PIL is much faster than converting to a NumPy array to save with
# ScikitSegmentationHelper
if width is not None:
height = width * pilImageData.size[1] // pilImageData.size[0]
pilImageData = pilImageData.resize(
size=(width, height),
# A PIL_Image.LANCZOS downsampling filter takes ~350ms to resize a 7k image to
# 700, whereas default downsampling filter (nearest neighbor) is <1ms with
# minimal noticeable difference in quality.
)
imageStream = io.BytesIO()
pilImageData.save(imageStream, format='jpeg')
return imageStream
def make_girder_file():
files = []
def _make_girder_file(assetstore, user, name, contents=b''):
folder = Folder().find({
'parentId': user['_id'],
'name': 'Public'
})[0]
file = Upload().uploadFromFile(
six.BytesIO(contents), size=len(contents), name=name,
parentType='folder', parent=folder,
user=user, assetstore=assetstore)
if not contents:
file = Upload().finalizeUpload(file, assetstore)
files.append(file)
return file
yield _make_girder_file
for file in files:
File().remove(file)
def testAdmin(self):
admin = User().findOne({'login': '******'})
self.assertDictContains(
{
'firstName': 'First',
'lastName': 'Last',
'email': '*****@*****.**',
'admin': True
}, admin, 'Admin user')
folder = Folder().findOne({'parentId': admin['_id']})
self.assertDictContains({'name': 'folder'}, folder, 'imported folder')
item = Item().findOne({'folderId': folder['_id']})
self.assertDictContains({'name': 'file.txt'}, item, 'imported item')
file = File().findOne({'itemId': item['_id']})
self.assertDictContains(
{
'name': 'file.txt',
'mimeType': 'text/plain',
'size': 5
}, file, 'imported file')
def createTiles(self, item, params):
if 'concurrent' in params:
params['_concurrency'] = params.pop('concurrent')
largeImageFileId = params.get('fileId')
if largeImageFileId is None:
files = list(Item().childFiles(item=item, limit=2))
if len(files) == 1:
largeImageFileId = str(files[0]['_id'])
if not largeImageFileId:
raise RestException('Missing "fileId" parameter.')
largeImageFile = File().load(largeImageFileId, force=True, exc=True)
user = self.getCurrentUser()
token = self.getCurrentToken()
notify = self.boolParam('notify', params, default=True)
params.pop('notify', None)
try:
return self.imageItemModel.createImageItem(
item, largeImageFile, user, token,
createJob='always' if self.boolParam('force', params, default=False) else True,
notify=notify,
**params)
except TileGeneralException as e:
raise RestException(e.args[0])
def addZipBatch(self, dataset, params):
params = self._decodeParams(params)
self.requireParams(['zipFileId', 'signature'], params)
user = self.getCurrentUser()
User().requireCreateDataset(user)
zipFileId = params['zipFileId']
if not zipFileId:
raise ValidationException('No file was uploaded.', 'zipFileId')
zipFile = File().load(zipFileId, user=user, level=AccessType.WRITE, exc=False)
if not zipFile:
raise ValidationException('Invalid upload file ID.', 'zipFileId')
if not self._checkFileFormat(zipFile, ZIP_FORMATS):
raise ValidationException('File must be in .zip format.', 'zipFileId')
signature = params['signature'].strip()
if not signature:
raise ValidationException('Signature must be specified.', 'owner')
# TODO: make this return something
Dataset().addZipBatch(
dataset=dataset, zipFile=zipFile, signature=signature, user=user, sendMail=True)
def mask(self, segmentation, params):
contentDisp = params.get('contentDisposition', None)
if contentDisp is not None and contentDisp not in {
'inline', 'attachment'
}:
raise ValidationException(
'Unallowed contentDisposition type "%s".' % contentDisp,
'contentDisposition')
# TODO: convert this to make Segmentation use an AccessControlMixin
Image().load(segmentation['imageId'],
level=AccessType.READ,
user=self.getCurrentUser(),
exc=True)
maskFile = Segmentation().maskFile(segmentation)
if maskFile is None:
raise RestException(
'This segmentation is failed, and thus has no mask.', code=410)
return File().download(maskFile,
headers=True,
contentDisposition=contentDisp)
def _handleUpload(event):
upload, file = event.info['upload'], event.info['file']
try:
reference = json.loads(upload.get('reference'))
except (TypeError, ValueError):
return
if isinstance(reference, dict) and 'interactive_thumbnail' in reference:
item = Item().load(file['itemId'], force=True, exc=True)
file['interactive_thumbnails_uid'] = file['name']
file['attachedToId'] = item['_id']
file['attachedToType'] = 'item'
file['itemId'] = None
File().save(file)
if not item.get('hasInteractiveThumbnail'):
Item().update({'_id': item['_id']},
{'$set': {
'hasInteractiveThumbnail': True
}},
multi=False)
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 = event.info['file']
# There may not be an itemId (on thumbnails, for instance)
if not fileObj.get('itemId'):
return
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'
File().save(fileObj)
del item['largeImage']['expected']
item['largeImage']['fileId'] = fileObj['_id']
item['largeImage']['sourceName'] = 'tiff'
Item().save(item)
def attachThumbnail(file, thumbnail, attachToType, attachToId, width, height):
"""
Add the required information to the thumbnail file and the resource it
is being attached to, and save the documents.
:param file: The file from which the thumbnail was derived.
:type file: dict
:param thumbnail: The newly generated thumbnail file document.
:type thumbnail: dict
:param attachToType: The type to which the thumbnail is being attached.
:type attachToType: str
:param attachToId: The ID of the document to attach the thumbnail to.
:type attachToId: str or ObjectId
:param width: Thumbnail width.
:type width: int
:param height: Thumbnail height.
:type height: int
:returns: The updated thumbnail file document.
"""
parentModel = ModelImporter.model(attachToType)
parent = parentModel.load(attachToId, force=True)
parent['_thumbnails'] = parent.get('_thumbnails', [])
parent['_thumbnails'].append(thumbnail['_id'])
parentModel.save(parent)
thumbnail['attachedToType'] = attachToType
thumbnail['attachedToId'] = parent['_id']
thumbnail['isThumbnail'] = True
thumbnail['derivedFrom'] = {
'type': 'file',
'id': file['_id'],
'process': 'thumbnail',
'width': width,
'height': height
}
return File().save(thumbnail)
def create_calc(self, params):
body = getBodyJson()
if 'cjson' not in body and ('fileId' not in body or 'format' not in body):
raise RestException('Either cjson or fileId is required.')
user = getCurrentUser()
cjson = body.get('cjson')
props = body.get('properties', {})
molecule_id = body.get('moleculeId', None)
public = body.get('public', False)
notebooks = body.get('notebooks', [])
image = body.get('image')
input_parameters = body.get('input', {}).get('parameters')
file_id = None
file_format = body.get('format', 'cjson')
if 'fileId' in body:
file = File().load(body['fileId'], user=getCurrentUser())
file_id = file['_id']
cjson = self._file_to_cjson(file, file_format)
if molecule_id is None:
mol = create_molecule(json.dumps(cjson), 'cjson', user, public)
molecule_id = mol['_id']
calc = CalculationModel().create_cjson(user, cjson, props, molecule_id,
image=image,
input_parameters=input_parameters,
file_id=file_id,
notebooks=notebooks, public=public)
cherrypy.response.status = 201
cherrypy.response.headers['Location'] \
= '/calculations/%s' % (str(calc['_id']))
return CalculationModel().filter(calc, user)
def testImportToItemAndFile(self):
from girder.plugins.database_assetstore.base import DB_ASSETSTORE_ID
userstore = Assetstore().load(DB_ASSETSTORE_ID)
resp = self.request(path='/assetstore', method='POST', user=self.admin,
params=self.dbParams)
self.assertStatusOk(resp)
assetstore1 = resp.json
for store in (assetstore1, userstore):
adapter = assetstore_utilities.getAssetstoreAdapter(store)
adapter.importData(self.item1, 'item', {
'tables': ['towns'],
'uri': self.dbParams['dburi'],
}, progress.noProgress, self.admin)
self.assertEqual(Item().childFiles(item=self.item1).count(), 1)
file = Item().childFiles(item=self.item1)[0]
adapter.importData(file, 'file', {
'tables': ['towns'],
'limit': 5,
'uri': self.dbParams['dburi'],
}, progress.noProgress, self.admin)
self.assertEqual(Item().childFiles(item=self.item1).count(), 1)
for file in Item().childFiles(item=self.item1):
File().remove(file)
def setUp(self):
import datetime
from girder.api import rest
from girder.plugins import worker
from girder.plugins.worker import utils as worker_utils
from girder.models.file import File
from girder.models.folder import Folder
from girder.models.item import Item
from girder.models.user import User
base.TestCase.setUp(self)
self.admin = User().createUser('admin', 'passwd', 'admin', 'admin', '*****@*****.**')
self.folder = Folder().createFolder(self.admin, 'folder', parentType='user')
self.item = Item().createItem('item', self.admin, self.folder)
self.file = File().createFile(self.admin, self.item, 'file', 7, self.assetstore)
# Mock several functions so we can fake creating jobs
def getCurrentToken():
return {
'_id': str(self.admin['_id']),
'expires': datetime.datetime.utcnow() + datetime.timedelta(hours=1)
}
def getWorkerApiUrl():
return '/api/v1'
self._origRestGetCurrentToken = rest.getCurrentToken
self._origRestGetApiUrl = rest.getApiUrl
self._origWorkerGetWorkerApiUrl = worker.getWorkerApiUrl
rest.getCurrentToken = getCurrentToken
rest.getApiUrl = lambda x: '/api/v1'
rest.setCurrentUser(self.admin)
worker.getWorkerApiUrl = worker_utils.getWorkerApiUrl = getWorkerApiUrl
def update(self, projection, projection_updates, user=None, public=None ):
query = {
'_id': projection['_id']
}
projection_updates = self.validate(projection_updates)
updates = {}
mutable_props = ['voltage', 'convergenceSemiAngle', 'probeSize',
'detectorInnerAngle', 'detectorOuterAngle',
'depthOfFocus', 'pixelSize', 'tiltRange',
'electronDose', 'nProjections']
for prop in projection_updates:
if prop in mutable_props:
updates.setdefault('$set', {})[prop] = projection_updates[prop]
if 'emdFileId' in projection_updates:
updates.setdefault('$set', {})['emdFileId'] = ObjectId(projection_updates['emdFileId'])
if public is not None:
updates.setdefault('$set', {})['public'] = public
if updates:
file_id = projection['emdFileId']
super(Projection, self).update(query, update=updates, multi=False)
if 'emdFileId' in projection_updates and \
projection_updates['emdFileId'] != file_id:
f = File().load(file_id, force=True)
if f is not None:
item = Item().load(f['itemId'], force=True)
Item().remove(item)
return self.load(projection['_id'], user=user, level=AccessType.READ)
return projection
def validate(self, doc):
try:
assert set(six.viewkeys(doc)) >= {
'imageId', 'creatorId', 'created', 'maskId', 'reviews', 'meta'}
assert set(six.viewkeys(doc)) <= {
'_id', 'imageId', 'creatorId', 'created', 'maskId', 'reviews',
'meta'}
assert isinstance(doc['imageId'], ObjectId)
assert Image().find({'_id': doc['imageId']}).count()
assert isinstance(doc['creatorId'], ObjectId)
assert User().find({'_id': doc['creatorId']}).count()
assert isinstance(doc['created'], datetime.datetime)
if doc['maskId']:
assert isinstance(doc['maskId'], ObjectId)
assert File().find({'_id': doc['maskId']}).count()
assert isinstance(doc['reviews'], list)
for review in doc['reviews']:
assert set(six.viewkeys(review)) == {
'userId', 'skill', 'time', 'approved'}
assert isinstance(review['userId'], ObjectId)
assert User().find({'_id': review['userId']}).count()
assert review['skill'] in {self.Skill.NOVICE, self.Skill.EXPERT}
assert isinstance(review['time'], datetime.datetime)
assert isinstance(review['approved'], bool)
assert isinstance(doc['meta'], dict)
except (AssertionError, KeyError):
# TODO: message
raise ValidationException('')
return doc
def testDownloadLogging(server, admin, fsAssetstore, freshLog):
folder = Folder().find({'parentId': admin['_id'], 'name': 'Public'})[0]
file = Upload().uploadFromFile(io.BytesIO(b'hello'),
size=5,
name='test',
parentType='folder',
parent=folder,
user=admin,
assetstore=fsAssetstore)
Record().collection.remove({}) # Clear existing records
File().download(file, headers=False, offset=2, endByte=4)
records = Record().find()
assert records.count() == 1
record = records[0]
assert record['ip'] == '127.0.0.1'
assert record['type'] == 'file.download'
assert record['details']['fileId'] == file['_id']
assert record['details']['startByte'] == 2
assert record['details']['endByte'] == 4
assert isinstance(record['when'], datetime.datetime)
class File(Resource):
"""
API Endpoint for files. Includes utilities for uploading and downloading
them.
"""
def __init__(self):
super(File, self).__init__()
self._model = FileModel()
self.resourceName = 'file'
self.route('DELETE', (':id',), self.deleteFile)
self.route('DELETE', ('upload', ':id'), self.cancelUpload)
self.route('GET', ('offset',), self.requestOffset)
self.route('GET', (':id',), self.getFile)
self.route('GET', (':id', 'download'), self.download)
self.route('GET', (':id', 'download', ':name'), self.downloadWithName)
self.route('POST', (), self.initUpload)
self.route('POST', ('chunk',), self.readChunk)
self.route('POST', ('completion',), self.finalizeUpload)
self.route('POST', (':id', 'copy'), self.copy)
self.route('PUT', (':id',), self.updateFile)
self.route('PUT', (':id', 'contents'), self.updateFileContents)
self.route('PUT', (':id', 'move'), self.moveFileToAssetstore)
@access.public(scope=TokenScope.DATA_READ)
@filtermodel(model=FileModel)
@autoDescribeRoute(
Description('Get a file\'s information.')
.modelParam('id', model=FileModel, level=AccessType.READ)
.errorResponse()
.errorResponse('Read access was denied on the file.', 403)
)
def getFile(self, file):
return file
@access.user(scope=TokenScope.DATA_WRITE)
@autoDescribeRoute(
Description('Start a new upload or create an empty or link file.')
.notes('Use POST /file/chunk to send the contents of the file. '
'The data for the first chunk of the file can be included with '
'this query by sending it as the body of the request using an '
'appropriate content-type and with the other parameters as '
'part of the query string. If the entire file is uploaded via '
'this call, the resulting file is returned.')
.responseClass('Upload')
.param('parentType', 'Type being uploaded into.', enum=['folder', 'item'])
.param('parentId', 'The ID of the parent.')
.param('name', 'Name of the file being created.')
.param('size', 'Size in bytes of the file.', dataType='integer', required=False)
.param('mimeType', 'The MIME type of the file.', required=False)
.param('linkUrl', 'If this is a link file, pass its URL instead '
'of size and mimeType using this parameter.', required=False)
.param('reference', 'If included, this information is passed to the '
'data.process event when the upload is complete.',
required=False)
.param('assetstoreId', 'Direct the upload to a specific assetstore (admin-only).',
required=False)
.errorResponse()
.errorResponse('Write access was denied on the parent folder.', 403)
.errorResponse('Failed to create upload.', 500)
)
def initUpload(self, parentType, parentId, name, size, mimeType, linkUrl, reference,
assetstoreId):
"""
Before any bytes of the actual file are sent, a request should be made
to initialize the upload. This creates the temporary record of the
forthcoming upload that will be passed in chunks to the readChunk
method. If you pass a "linkUrl" parameter, it will make a link file
in the designated parent.
"""
user = self.getCurrentUser()
parent = self.model(parentType).load(
id=parentId, user=user, level=AccessType.WRITE, exc=True)
if linkUrl is not None:
return self._model.filter(
self._model.createLinkFile(
url=linkUrl, parent=parent, name=name, parentType=parentType, creator=user,
size=size, mimeType=mimeType), user)
else:
self.requireParams({'size': size})
assetstore = None
if assetstoreId:
self.requireAdmin(
user, message='You must be an admin to select a destination assetstore.')
assetstore = Assetstore().load(assetstoreId)
chunk = None
if size > 0 and cherrypy.request.headers.get('Content-Length'):
ct = cherrypy.request.body.content_type.value
if (ct not in cherrypy.request.body.processors and
ct.split('/', 1)[0] not in cherrypy.request.body.processors):
chunk = RequestBodyStream(cherrypy.request.body)
if chunk is not None and chunk.getSize() <= 0:
chunk = None
try:
# TODO: This can be made more efficient by adding
# save=chunk is None
# to the createUpload call parameters. However, since this is
# a breaking change, that should be deferred until a major
# version upgrade.
upload = Upload().createUpload(
user=user, name=name, parentType=parentType, parent=parent, size=size,
mimeType=mimeType, reference=reference, assetstore=assetstore)
except OSError as exc:
if exc.errno == errno.EACCES:
raise GirderException(
'Failed to create upload.', 'girder.api.v1.file.create-upload-failed')
raise
if upload['size'] > 0:
if chunk:
return Upload().handleChunk(upload, chunk, filter=True, user=user)
return upload
else:
return self._model.filter(Upload().finalizeUpload(upload), user)
@access.user(scope=TokenScope.DATA_WRITE)
@autoDescribeRoute(
Description('Finalize an upload explicitly if necessary.')
.notes('This is only required in certain non-standard upload '
'behaviors. Clients should know which behavior models require '
'the finalize step to be called in their behavior handlers.')
.modelParam('uploadId', paramType='formData', model=Upload)
.errorResponse(('ID was invalid.',
'The upload does not require finalization.',
'Not enough bytes have been uploaded.'))
.errorResponse('You are not the user who initiated the upload.', 403)
)
def finalizeUpload(self, upload):
user = self.getCurrentUser()
if upload['userId'] != user['_id']:
raise AccessException('You did not initiate this upload.')
# If we don't have as much data as we were told would be uploaded and
# the upload hasn't specified it has an alternate behavior, refuse to
# complete the upload.
if upload['received'] != upload['size'] and 'behavior' not in upload:
raise RestException(
'Server has only received %s bytes, but the file should be %s bytes.' %
(upload['received'], upload['size']))
file = Upload().finalizeUpload(upload)
extraKeys = file.get('additionalFinalizeKeys', ())
return self._model.filter(file, user, additionalKeys=extraKeys)
@access.user(scope=TokenScope.DATA_WRITE)
@autoDescribeRoute(
Description('Request required offset before resuming an upload.')
.modelParam('uploadId', paramType='formData', model=Upload)
.errorResponse("The ID was invalid, or the offset did not match the server's record.")
)
def requestOffset(self, upload):
"""
This should be called when resuming an interrupted upload. It will
report the offset into the upload that should be used to resume.
:param uploadId: The _id of the temp upload record being resumed.
:returns: The offset in bytes that the client should use.
"""
offset = Upload().requestOffset(upload)
if isinstance(offset, six.integer_types):
upload['received'] = offset
Upload().save(upload)
return {'offset': offset}
else:
return offset
@access.user(scope=TokenScope.DATA_WRITE)
@autoDescribeRoute(
Description('Upload a chunk of a file.')
.notes('The data for the chunk should be sent as the body of the '
'request using an appropriate content-type and with the other '
'parameters as part of the query string. Alternately, the '
'data can be sent as a file in the "chunk" field in multipart '
'form data. Multipart uploads are much less efficient and '
'their use is deprecated.')
.modelParam('uploadId', paramType='formData', model=Upload)
.param('offset', 'Offset of the chunk in the file.', dataType='integer',
paramType='formData')
.errorResponse(('ID was invalid.',
'Received too many bytes.',
'Chunk is smaller than the minimum size.'))
.errorResponse('You are not the user who initiated the upload.', 403)
.errorResponse('Failed to store upload.', 500)
)
def readChunk(self, upload, offset, params):
"""
After the temporary upload record has been created (see initUpload),
the bytes themselves should be passed up in ordered chunks. The user
must remain logged in when passing each chunk, to authenticate that
the writer of the chunk is the same as the person who initiated the
upload. The passed offset is a verification mechanism for ensuring the
server and client agree on the number of bytes sent/received.
This method accepts both the legacy multipart content encoding, as
well as passing offset and uploadId as query parameters and passing
the chunk as the body, which is the recommended method.
.. deprecated :: 2.2.0
"""
if 'chunk' in params:
chunk = params['chunk']
if isinstance(chunk, cherrypy._cpreqbody.Part):
# Seek is the only obvious way to get the length of the part
chunk.file.seek(0, os.SEEK_END)
size = chunk.file.tell()
chunk.file.seek(0, os.SEEK_SET)
chunk = RequestBodyStream(chunk.file, size=size)
else:
chunk = RequestBodyStream(cherrypy.request.body)
user = self.getCurrentUser()
if upload['userId'] != user['_id']:
raise AccessException('You did not initiate this upload.')
if upload['received'] != offset:
raise RestException(
'Server has received %s bytes, but client sent offset %s.' % (
upload['received'], offset))
try:
return Upload().handleChunk(upload, chunk, filter=True, user=user)
except IOError as exc:
if exc.errno == errno.EACCES:
raise Exception('Failed to store upload.')
raise
@access.cookie
@access.public(scope=TokenScope.DATA_READ)
@autoDescribeRoute(
Description('Download a file.')
.notes('This endpoint also accepts the HTTP "Range" header for partial '
'file downloads.')
.modelParam('id', model=FileModel, level=AccessType.READ)
.param('offset', 'Start downloading at this offset in bytes within '
'the file.', dataType='integer', required=False, default=0)
.param('endByte', 'If you only wish to download part of the file, '
'pass this as the index of the last byte to download. Unlike '
'the HTTP Range header, the endByte parameter is non-inclusive, '
'so you should set it to the index of the byte one past the '
'final byte you wish to receive.', dataType='integer',
required=False)
.param('contentDisposition', 'Specify the Content-Disposition response '
'header disposition-type value.', required=False,
enum=['inline', 'attachment'], default='attachment')
.param('extraParameters', 'Arbitrary data to send along with the download request.',
required=False)
.errorResponse('ID was invalid.')
.errorResponse('Read access was denied on the parent folder.', 403)
)
def download(self, file, offset, endByte, contentDisposition, extraParameters):
"""
Defers to the underlying assetstore adapter to stream a file out.
Requires read permission on the folder that contains the file's item.
"""
rangeHeader = cherrypy.lib.httputil.get_ranges(
cherrypy.request.headers.get('Range'), file.get('size', 0))
# The HTTP Range header takes precedence over query params
if rangeHeader and len(rangeHeader):
# Currently we only support a single range.
offset, endByte = rangeHeader[0]
return self._model.download(
file, offset, endByte=endByte, contentDisposition=contentDisposition,
extraParameters=extraParameters)
@access.cookie
@access.public(scope=TokenScope.DATA_READ)
@describeRoute(
Description('Download a file.')
.param('id', 'The ID of the file.', paramType='path')
.param('name', 'The name of the file. This is ignored.',
paramType='path')
.param('offset', 'Start downloading at this offset in bytes within '
'the file.', dataType='integer', required=False)
.notes('The name parameter doesn\'t alter the download. Some '
'download clients save files based on the last part of a path, '
'and specifying the name satisfies those clients.')
.errorResponse('ID was invalid.')
.errorResponse('Read access was denied on the parent folder.', 403)
)
def downloadWithName(self, id, name, params):
return self.download(id=id, params=params)
@access.user(scope=TokenScope.DATA_WRITE)
@autoDescribeRoute(
Description('Delete a file by ID.')
.modelParam('id', model=FileModel, level=AccessType.WRITE)
.errorResponse('ID was invalid.')
.errorResponse('Write access was denied on the parent folder.', 403)
)
def deleteFile(self, file):
self._model.remove(file)
@access.user(scope=TokenScope.DATA_WRITE)
@autoDescribeRoute(
Description('Cancel a partially completed upload.')
.modelParam('id', model=Upload)
.errorResponse('ID was invalid.')
.errorResponse('You lack permission to cancel this upload.', 403)
)
def cancelUpload(self, upload):
user = self.getCurrentUser()
if upload['userId'] != user['_id'] and not user['admin']:
raise AccessException('You did not initiate this upload.')
Upload().cancelUpload(upload)
return {'message': 'Upload canceled.'}
@access.user(scope=TokenScope.DATA_WRITE)
@filtermodel(model=FileModel)
@autoDescribeRoute(
Description('Change file metadata such as name or MIME type.')
.modelParam('id', model=FileModel, level=AccessType.WRITE)
.param('name', 'The name to set on the file.', required=False, strip=True)
.param('mimeType', 'The MIME type of the file.', required=False, strip=True)
.errorResponse('ID was invalid.')
.errorResponse('Write access was denied on the parent folder.', 403)
)
def updateFile(self, file, name, mimeType):
if name is not None:
file['name'] = name
if mimeType is not None:
file['mimeType'] = mimeType
return self._model.updateFile(file)
@access.user(scope=TokenScope.DATA_WRITE)
@autoDescribeRoute(
Description('Change the contents of an existing file.')
.modelParam('id', model=FileModel, level=AccessType.WRITE)
.param('size', 'Size in bytes of the new file.', dataType='integer')
.param('reference', 'If included, this information is passed to the '
'data.process event when the upload is complete.', required=False)
.param('assetstoreId', 'Direct the upload to a specific assetstore (admin-only).',
required=False)
.notes('After calling this, send the chunks just like you would with a '
'normal file upload.')
)
def updateFileContents(self, file, size, reference, assetstoreId):
user = self.getCurrentUser()
assetstore = None
if assetstoreId:
self.requireAdmin(
user, message='You must be an admin to select a destination assetstore.')
assetstore = Assetstore().load(assetstoreId)
# Create a new upload record into the existing file
upload = Upload().createUploadToFile(
file=file, user=user, size=size, reference=reference, assetstore=assetstore)
if upload['size'] > 0:
return upload
else:
return self._model.filter(Upload().finalizeUpload(upload), user)
@access.admin(scope=TokenScope.DATA_WRITE)
@filtermodel(model=FileModel)
@autoDescribeRoute(
Description('Move a file to a different assetstore.')
.modelParam('id', model=FileModel, level=AccessType.WRITE)
.modelParam('assetstoreId', 'The destination assetstore.', paramType='formData',
model=Assetstore)
.param('progress', 'Controls whether progress notifications will be sent.',
dataType='boolean', default=False, required=False)
)
def moveFileToAssetstore(self, file, assetstore, progress):
user = self.getCurrentUser()
title = 'Moving file "%s" to assetstore "%s"' % (file['name'], assetstore['name'])
with ProgressContext(progress, user=user, title=title, total=file['size']) as ctx:
return Upload().moveFileToAssetstore(
file=file, user=user, assetstore=assetstore, progress=ctx)
@access.user(scope=TokenScope.DATA_WRITE)
@filtermodel(model=FileModel)
@autoDescribeRoute(
Description('Copy a file.')
.modelParam('id', model=FileModel, level=AccessType.READ)
.modelParam('itemId', description='The ID of the item to copy the file to.',
level=AccessType.WRITE, paramType='formData', model=Item)
)
def copy(self, file, item):
return self._model.copyFile(file, self.getCurrentUser(), item=item)
def importData(self, parent, parentType, params, progress, user, **kwargs):
"""
Import a list of tables, each to a file within a distinct item. Each
table specification in the list is an object which must have a 'table'
key. It may optionally have other connection information such as
'database' and 'schema'. If there is a 'name' key, the name is used
for the item and file. If there is a 'database' key, a subfolder is
created within the specified parent with that name. If a user or
collection is specified for the top level and no database key is
specified, the default database name (from the assetstore) is used.
If the specific item and file already exists and is from the same
assetstore, it is updated. If the specific item already exists and is
not from the same assetstore (or not marked that it was imported), an
error is given.
:param parent: The parent object to import into. Must be a folder,
user, collection, item, or file.
:param parentType: The model type of the parent object.
:param params: Additional parameters required for the import process:
tables: a list of tables to add. If there is already an item with
an exact table name, it is updated.
sort: default sort parameter. Used in plain downloads.
fields: default fields parameter. Used in plain downloads.
filters: default filters parameter. Used in plain downloads.
group: default group parameter. Used in plain downloads.
format: default format parameter. Used in plain downloads.
replace: if False, don't replace an existing file/item with the
name, but always create new entries. A parentType of file
will always replace the existing data of a file
:type params: dict
:param progress: Object on which to record progress if possible.
:type progress: :py:class:`girder.utility.progress.ProgressContext`
:param user: The Girder user performing the import.
:type user: dict or None
:return: a list of objects, each of which has an item and file entry
with the items and files that were imported.
"""
uri = (self.assetstore['database'].get('uri')
if self.assetstore['database'].get('uri') else params['uri'])
defaultDatabase = dbs.databaseFromUri(uri)
response = []
createdFolder = createdItem = createdFile = False
for table in params['tables']:
if isinstance(table, six.string_types):
dbinfo = {'table': table}
else:
dbinfo = table.copy()
if not self.assetstore['database'].get('uri'):
dbinfo['uri'] = uri
name = dbinfo.pop('name', dbinfo['table'])
progress.update(message='Importing %s' % name)
# Find or create a folder if needed
if 'database' not in dbinfo and parentType == 'folder':
folder = parent
elif parentType not in ('file', 'item'):
folderName = dbinfo.get('database', defaultDatabase)
folder = Folder().findOne({
'parentId': parent['_id'],
'name': folderName,
'parentCollection': parentType
})
if folder is None:
folder = Folder().createFolder(
parent, folderName, parentType=parentType,
creator=user)
createdFolder = True
if parentType == 'file':
# for files, we'll create a provisional file below, then
# delete the original assetstore entry and modify the
# existing file entry with the updated values before saving.
item = Item().load(parent['itemId'], force=True)
elif parentType == 'item':
item = parent
else:
# Create an item if needed
item = Item().findOne({
'folderId': folder['_id'],
'name': name
})
if item is None or params.get('replace') is False:
item = Item().createItem(
name=name, creator=user, folder=folder)
createdItem = True
# Create a file if needed
file = File().findOne({
'name': name,
'itemId': item['_id']
})
if file is None or params.get('replace') is False or parentType == 'file':
file = File().createFile(
creator=user, item=item, name=name, size=0,
assetstore=self.assetstore,
mimeType=dbFormatList.get(preferredFormat(params.get(
'format'))),
saveFile=False)
createdFile = True
if file.get(DB_INFO_KEY) and not file[DB_INFO_KEY].get('imported'):
raise GirderException(
'A file for table %s is present but cannot be updated '
'because it wasn\'t imported.' % name)
try:
file = self._importDataFile(file, parent, parentType, dbinfo, params)
except GirderException as exc:
self._importDataCleanup(
file if createdFile else None,
item if createdItem else None,
folder if createdFolder else None)
raise exc
response.append({'item': item, 'file': file})
return response
def testAssetstoreDownload(self):
from girder.plugins.database_assetstore import assetstore
from girder.plugins.database_assetstore import query
for userAssetstore in (False, True):
townItem, townFile, assetstore1 = self._createTownItem({
'format': 'list',
'fields': 'town,pop2010',
'limit': '10'
}, userAssetstore)
resp = self.request(path='/item/%s/download' % str(townItem['_id']))
self.assertStatusOk(resp)
data = resp.json
self.assertEqual(data['datacount'], 10)
self.assertEqual(data['fields'], ['town', 'pop2010'])
# Test extraParameters for format
params = {
'extraParameters': urllib.parse.urlencode({
'format': 'csv',
'limit': 5
}),
'contentDisposition': 'inline'
}
resp = self.request(
path='/item/%s/download' % str(townItem['_id']), params=params,
isJson=False)
self.assertStatusOk(resp)
data = self.getBody(resp)
self.assertEqual(len(data.split('\r\n')), 7)
self.assertEqual(data.split('\r\n', 1)[0], 'town,pop2010')
# Test range requests
resp = self.request(
path='/item/%s/download' % str(townItem['_id']), params=params,
isJson=False, additionalHeaders=[('Range', 'bytes=10-19')])
self.assertStatus(resp, 206)
self.assertEqual(self.getBody(resp), data[10:20])
resp = self.request(
path='/item/%s/download' % str(townItem['_id']), params=params,
isJson=False, additionalHeaders=[('Range', 'bytes=50-')])
self.assertStatus(resp, 206)
self.assertEqual(self.getBody(resp), data[50:])
resp = self.request(
path='/item/%s/download' % str(townItem['_id']), params=params,
isJson=False, additionalHeaders=[('Range', 'bytes=5000-')])
self.assertStatus(resp, 206)
self.assertEqual(self.getBody(resp), '')
# Test more complex extraParameters
extra = {
'format': 'list',
'fields': json.dumps(['town', 'pop2000', 'pop2010']),
'sort': json.dumps([['pop2000', -1]]),
'filters': json.dumps([{
'field': 'pop2000', 'operator': '<', 'value': 100000}]),
'limit': 5
}
params = {'extraParameters': urllib.parse.urlencode(extra)}
resp = self.request(
path='/item/%s/download' % str(townItem['_id']), params=params)
self.assertStatusOk(resp)
data = resp.json
self.assertEqual(data['datacount'], 5)
self.assertEqual(data['fields'], ['town', 'pop2000', 'pop2010'])
self.assertLess(int(data['data'][0][1]), 100000)
self.assertLess(int(data['data'][1][1]), int(data['data'][0][1]))
# Test with JSON extraParameters
params = {'extraParameters': json.dumps(extra)}
resp = self.request(
path='/item/%s/download' % str(townItem['_id']), params=params)
self.assertStatusOk(resp)
data = resp.json
self.assertEqual(data['datacount'], 5)
self.assertEqual(data['fields'], ['town', 'pop2000', 'pop2010'])
self.assertLess(int(data['data'][0][1]), 100000)
self.assertLess(int(data['data'][1][1]), int(data['data'][0][1]))
# Test a direct call
townFile = list(Item().childFiles(item=townItem))[0]
adapter = File().getAssetstoreAdapter(townFile)
params = {
'format': 'list',
'fields': ['town', 'pop2000', 'pop2010'],
'sort': [['pop2000', -1]],
'filters': [{
'field': 'pop2000', 'operator': '<', 'value': 100000}],
'limit': 5
}
func = adapter.downloadFile(townFile, headers=False,
extraParameters=params)
data = b''.join([part for part in func()])
data = json.loads(data.decode('utf8'))
self.assertEqual(data['datacount'], 5)
self.assertEqual(data['fields'], ['town', 'pop2000', 'pop2010'])
self.assertLess(int(data['data'][0][1]), 100000)
self.assertLess(int(data['data'][1][1]), int(data['data'][0][1]))
# Test a direct query with group
params = {
'format': 'rawlist',
'sort': [
[{'func': 'count', 'param': {'field': 'town'}}, -1],
[{'func': 'max', 'param': {'field': 'town'}}, 1]
],
'fields': [
{'func': 'max', 'param': {'field': 'town'}},
'pop2010',
{'func': 'count', 'param': {'field': 'town'}}
],
'group': 'pop2010,popch80_90',
'limit': 5,
}
data = query.queryDatabase(
townFile['_id'], assetstore.getDbInfoForFile(townFile), params)
data = list(data[0]())
self.assertEqual(len(data), 5)
self.assertEqual(data[0][0], 'ABINGTON')
self.assertEqual(data[4][0], 'AGAWAM')
# Test with bad extraParameters
with six.assertRaisesRegex(self, Exception,
'JSON-encoded dictionary, or a url'):
adapter.downloadFile(townFile, headers=False, extraParameters=6)
# Test with 0 and none limits
params = {
'format': 'list',
'fields': 'town,pop2000',
'sort': 'pop2000',
'filters': json.dumps([{
'field': 'pop2000', 'operator': '>', 'value': 25000}]),
}
params['limit'] = 0
func = adapter.downloadFile(
townFile, headers=False, extraParameters=params)
jsondata = b''.join([part for part in func()])
data = json.loads(jsondata.decode('utf8'))
self.assertEqual(data['datacount'], 0)
self.assertEqual(data['fields'], ['town', 'pop2000'])
# It shouldn't matter if we ask for this via json, query, or object
func = adapter.downloadFile(
townFile, headers=False,
extraParameters=urllib.parse.urlencode(params))
self.assertEqual(b''.join([part for part in func()]), jsondata)
func = adapter.downloadFile(
townFile, headers=False, extraParameters=json.dumps(params))
self.assertEqual(b''.join([part for part in func()]), jsondata)
params['limit'] = 'none'
func = adapter.downloadFile(
townFile, headers=False, extraParameters=params)
jsondata = b''.join([part for part in func()])
data = json.loads(jsondata.decode('utf8'))
self.assertEqual(data['datacount'], 71)
self.assertEqual(data['fields'], ['town', 'pop2000'])
# It shouldn't matter if we ask for this via json, query, or object
func = adapter.downloadFile(
townFile, headers=False,
extraParameters=urllib.parse.urlencode(params))
self.assertEqual(b''.join([part for part in func()]), jsondata)
func = adapter.downloadFile(
townFile, headers=False, extraParameters=json.dumps(params))
self.assertEqual(b''.join([part for part in func()]), jsondata)
# None can also be used as unlimited
params['limit'] = None
func = adapter.downloadFile(
townFile, headers=False, extraParameters=params)
self.assertEqual(b''.join([part for part in func()]), jsondata)
func = adapter.downloadFile(
townFile, headers=False,
extraParameters=urllib.parse.urlencode(params))
self.assertEqual(b''.join([part for part in func()]), jsondata)
func = adapter.downloadFile(
townFile, headers=False, extraParameters=json.dumps(params))
self.assertEqual(b''.join([part for part in func()]), jsondata)
# filters can also be an object or tuple
params['filters'] = json.loads(params['filters'])
func = adapter.downloadFile(
townFile, headers=False, extraParameters=params)
self.assertEqual(b''.join([part for part in func()]), jsondata)
params['filters'] = tuple(params['filters'])
func = adapter.downloadFile(
townFile, headers=False, extraParameters=params)
self.assertEqual(b''.join([part for part in func()]), jsondata)
# Test with group
params['sort'] = [
[{'func': 'count', 'param': {'field': 'town'}}, -1],
[{'func': 'max', 'param': {'field': 'town'}}, 1]]
params['fields'] = [
{'func': 'max', 'param': {'field': 'town'}},
'pop2010',
{'func': 'count', 'param': {'field': 'town'}}]
params['group'] = 'pop2010'
params['limit'] = 5
del params['filters']
func = adapter.downloadFile(
townFile, headers=False, extraParameters=params)
jsondata = b''.join([part for part in func()])
data = json.loads(jsondata.decode('utf8'))
self.assertEqual(data['datacount'], 5)
self.assertEqual(data['data'][0][0], 'DEDHAM')
self.assertEqual(data['data'][0][2], 2)
self.assertEqual(data['data'][4][0], 'ACTON')
self.assertEqual(data['data'][4][2], 1)
class LabelResource(Resource):
def __init__(self):
super().__init__()
self.resourceName = 'label'
self.coll_m = Collection()
self.file_m = File()
self.folder_m = Folder()
self.item_m = Item()
self.upload_m = Upload()
self.asset_m = Assetstore()
self.setupRoutes()
def setupRoutes(self):
self.route('GET', (), handler=self.getLabelList)
self.route('GET', (':label_id',), self.getLabel)
self.route('GET', ('meta',), self.getLabelMeta)
self.route('GET', ('create',), self.createLabelFile)
self.route('GET', ('by_name',), self.getLabelByName)
self.route('POST', (), self.postLabel)
def createNewFile(self, folder, file_name):
item = self.item_m.createItem(file_name,
creator=self.getCurrentUser(),
folder=folder,
description='label file',
reuseExisting=False)
file = self.file_m.createFile(size=0,
item=item,
name=file_name,
creator=self.getCurrentUser(),
assetstore=self.asset_m.getCurrent(),
mimeType="application/json")
return file
def copy(self, srcFile, destFile):
upload = self.upload_m.createUploadToFile(destFile, self.getCurrentUser(), srcFile['size'])
self.upload_m.handleChunk(upload=upload,
chunk=RequestBodyStream(self.file_m.open(srcFile), size=destFile['size']),
user=self.getCurrentUser())
return upload
@access.public
@autoDescribeRoute(
Description('Get label list'))
@rest.rawResponse
def getLabelList(self):
printOk('getLabelsList() was called!')
try:
collection = list(self.coll_m.list(user=self.getCurrentUser(), offset=0, limit=1))[0]
files = self.coll_m.fileList(collection, user=self.getCurrentUser(), data=False,
includeMetadata=True, mimeFilter=['application/json'])
files = list(files)
cherrypy.response.headers["Content-Type"] = "application/json"
return dumps(files)
except:
printFail(traceback.print_exc)
@staticmethod
def getOwnerId(folder):
aclList = Folder().getFullAccessList(folder)
for acl in aclList['users']:
if acl['level'] == AccessType.ADMIN:
return str(acl['id'])
return None
def getConfigFolder(self, label_folder_id):
label_folder = Folder().load(label_folder_id,
user=self.getCurrentUser(),
level=AccessType.READ)
ownerId = self.getOwnerId(label_folder)
config_folder = self.folder_m.load(label_folder['meta'][ownerId], level=AccessType.READ,
user=self.getCurrentUser())
return config_folder
def findConfig(self, folder_id):
folder = self.getConfigFolder(folder_id)
printOk2("Config folder {}".format(folder))
files = self.folder_m.fileList(folder, self.getCurrentUser(), data=False)
for file_path, file in files:
printOk(file)
if file['name'] == "config.json":
return file
def __findFile(self, folder, file_name):
item = list(self.item_m.find({'folderId': folder['_id'], 'name': file_name}).limit(1))
if not item:
return None
item = item[0]
file = list(self.file_m.find({'itemId': item['_id']}).limit(1))
if not file:
return None
return file[0]
@access.public
@autoDescribeRoute(
Description('Create a new label file if it doesnt exist')
.param('file_name', 'label file name').param('folder_id', 'the parent folder id'))
@rest.rawResponse
def createLabelFile(self, file_name, folder_id):
try:
folder = self.folder_m.load(folder_id, user=self.getCurrentUser(), level=AccessType.WRITE)
file = self.__findFile(folder, file_name)
if not file:
file = self.createNewFile(folder, file_name)
config_file = self.findConfig(folder_id)
if not config_file:
printFail("No config file found")
return errorMessage("No config file found")
else:
res = self.copy(config_file, file)
return dumps({
"label_id": res['fileId']
})
return dumps({
"label_id": file['_id']
})
except:
printFail(traceback.print_exc)
cherrypy.response.status = 500
@access.public
@autoDescribeRoute(
Description('Get labels by file_name')
.param('file_name', 'label file name').param('folder_id', 'the parent folder id'))
@rest.rawResponse
def getLabelByName(self, file_name, folder_id):
try:
folder = self.folder_m.load(folder_id, user=self.getCurrentUser(), level=AccessType.READ)
file = self.__findFile(folder, file_name)
cherrypy.response.headers["Content-Type"] = "application/json"
if file:
return self.file_m.download(file)
else:
return dumps({})
except:
printFail(traceback.print_exc)
cherrypy.response.status = 500
@access.public
@autoDescribeRoute(
Description('Get label by id')
.param('label_id', 'label file id'))
@rest.rawResponse
def getLabel(self, label_id):
try:
file = self.file_m.load(label_id, level=AccessType.READ, user=self.getCurrentUser())
printOk2(file)
cherrypy.response.headers["Content-Type"] = "application/json"
return self.file_m.download(file)
except:
# Unknown slug
printFail(traceback.print_exc)
cherrypy.response.status = 404
@access.public
@autoDescribeRoute(
Description('Get label by id')
.param('label_id', 'label file id'))
def getLabelMeta(self, label_id):
try:
file = self.file_m.load(label_id, level=AccessType.READ, user=self.getCurrentUser())
cherrypy.response.headers["Content-Type"] = "application/json"
return dumps(file)
except:
# Unknown slug
printFail(traceback.print_exc)
cherrypy.response.status = 404
@access.public
@autoDescribeRoute(
Description('Post label by id')
.param('label_id', 'label file id'))
@rest.rawResponse
def postLabel(self, label_id, params):
try:
file = self.file_m.load(label_id, level=AccessType.WRITE, user=self.getCurrentUser())
cherrypy.response.headers["Content-Type"] = "application/json"
params['labels'] = json.loads(params['labels'])
data = json.dumps(params, indent=2, sort_keys=True)
upload = writeData(self.getCurrentUser(), file, data)
printOk2(file)
printOk(upload)
return dumps(upload)
except:
# Unknown slug
printFail(traceback.print_exc)
cherrypy.response.status = 404
@access.public
@autoDescribeRoute(
Description('Post label by id')
.param('label_id', 'label file id'))
@rest.rawResponse
def strokeToOutline(self, strokes):
pass
def createThumbnail(width, height, crop, fileId, attachToType, attachToId):
"""
Creates the thumbnail. Validation and access control must be done prior
to the invocation of this method.
"""
fileModel = File()
file = fileModel.load(fileId, force=True)
streamFn = functools.partial(fileModel.download, file, headers=False)
event = events.trigger('thumbnails.create', info={
'file': file,
'width': width,
'height': height,
'crop': crop,
'attachToType': attachToType,
'attachToId': attachToId,
'streamFn': streamFn
})
if len(event.responses):
resp = event.responses[-1]
newFile = resp['file']
if event.defaultPrevented:
if resp.get('attach', True):
newFile = attachThumbnail(file, newFile, attachToType, attachToId, width, height)
return newFile
else:
file = newFile
streamFn = functools.partial(
fileModel.download, file, headers=False)
if 'assetstoreId' not in file:
# TODO we could thumbnail link files if we really wanted.
raise Exception('File %s has no assetstore.' % fileId)
stream = streamFn()
data = b''.join(stream())
image = _getImage(file['mimeType'], file['exts'], data)
if not width:
width = int(height * image.size[0] / image.size[1])
elif not height:
height = int(width * image.size[1] / image.size[0])
elif crop:
x1 = y1 = 0
x2, y2 = image.size
wr = float(image.size[0]) / width
hr = float(image.size[1]) / height
if hr > wr:
y1 = int(y2 / 2 - height * wr / 2)
y2 = int(y2 / 2 + height * wr / 2)
else:
x1 = int(x2 / 2 - width * hr / 2)
x2 = int(x2 / 2 + width * hr / 2)
image = image.crop((x1, y1, x2, y2))
image.thumbnail((width, height), Image.ANTIALIAS)
out = six.BytesIO()
image.convert('RGB').save(out, 'JPEG', quality=85)
size = out.tell()
out.seek(0)
thumbnail = Upload().uploadFromFile(
out, size=size, name='_thumb.jpg', parentType=attachToType,
parent={'_id': ObjectId(attachToId)}, user=None, mimeType='image/jpeg',
attachParent=True)
return attachThumbnail(file, thumbnail, attachToType, attachToId, width, height)
class HdfsAssetstoreResource(Resource):
def __init__(self):
super(HdfsAssetstoreResource, self).__init__()
self.resourceName = 'hdfs_assetstore'
self.route('PUT', (':id', 'import'), self.importData)
self.folderModel = Folder() # Save to avoid many lookups
self.itemModel = Item()
self.fileModel = File()
def _importFile(self, parent, name, user, assetstore, node):
item = self.itemModel.findOne({
'folderId': parent['_id'],
'name': name
})
if item is None:
item = self.itemModel.createItem(
name=name, creator=user, folder=parent)
file = self.fileModel.findOne({
'name': name,
'itemId': item['_id']
})
if file is None:
file = self.fileModel.createFile(
creator=user, item=item, name=name, size=node['length'],
assetstore=assetstore, mimeType=None, saveFile=False)
file['hdfs'] = {
'imported': True,
'path': node['path']
}
self.fileModel.save(file)
def _importData(self, parentType, parent, assetstore, client, path, ctx,
user):
for node in client.ls([path]):
ctx.update(message='Importing ' + node['path'])
name = posixpath.basename(node['path'])
if node['file_type'] == 'd':
folder = self.folderModel.findOne({
'parentId': parent['_id'],
'name': name,
'parentCollection': parentType
})
if folder is None:
folder = self.folderModel.createFolder(
parent, name, parentType=parentType, creator=user)
self._importData('folder', folder, assetstore, client,
node['path'], ctx, user)
elif node['file_type'] == 'f' and parentType == 'folder':
self._importFile(parent, name, user, assetstore, node)
@access.admin
@loadmodel(model='assetstore')
@describeRoute(
Description('Import a data hierarchy from an HDFS instance.')
.notes('Only site administrators may use this endpoint.')
.param('id', 'The ID of the assetstore representing the HDFS instance.',
paramType='path')
.param('parentId', 'The ID of the parent object in the Girder data '
'hierarchy under which to import the files.')
.param('parentType', 'The type of the parent object to import into.',
enum=('folder', 'user', 'collection'), required=False)
.param('path', 'Root of the directory structure (relative to the root '
'of the HDFS) to import.')
.param('progress', 'Whether to record progress on this operation ('
'default=False)', required=False, dataType='boolean')
.errorResponse()
.errorResponse('You are not an administrator.', 403)
)
def importData(self, assetstore, params):
self.requireParams(('parentId', 'path'), params)
user = self.getCurrentUser()
parentType = params.get('parentType', 'folder')
if parentType not in ('user', 'collection', 'folder'):
raise RestException('Invalid parentType.')
parent = self.model(parentType).load(params['parentId'], force=True, exc=True)
progress = self.boolParam('progress', params, default=False)
client = HdfsClient(
host=assetstore['hdfs']['host'], port=assetstore['hdfs']['port'], use_trash=False)
path = params['path']
with ProgressContext(progress, user=user, title='Importing data from HDFS') as ctx:
try:
self._importData(parentType, parent, assetstore, client, path, ctx, user)
except FileNotFoundException:
raise RestException('File not found: %s.' % path)
