def testFilePath(self):
"""
Test that all files report a FUSE path, and that this results in the
same file as the non-fuse path.
"""
files = list(File().find())
for file in files:
adapter = File().getAssetstoreAdapter(file)
filesystempath = adapter.fullPath(file)
filepath = File().getLocalFilePath(file)
fusepath = File().getGirderMountFilePath(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.mountPath)], self.mountPath)
with open(filepath) as file1:
with open(fusepath) as file2:
self.assertEqual(file1.read(), file2.read())
subpath = fusepath[len(self.mountPath):].lstrip('/')
if self.knownPaths.get(subpath):
with open(fusepath) as file1:
self.assertEqual(file1.read().strip(),
self.knownPaths[subpath])
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 getFilePath(file):
"""
Given a file resource, return a path on the local file system. For
assetstores that have a fullPath method, this returns the results of that
call. Otherwise, it returns a path on the main mounted FUSE.
:param file: file resource document.
:returns: a path on the local file system.
"""
adapter = File().getAssetstoreAdapter(file)
if callable(getattr(adapter, 'fullPath', None)):
return adapter.fullPath(file)
return server_fuse.getServerFusePath(MAIN_FUSE_KEY, 'file', 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
