def get_uploaded_datasets(self,
trans,
context,
override_name=None,
override_info=None):
def get_data_file_filename(data_file,
override_name=None,
override_info=None,
purge=True):
dataset_name = override_name
def get_file_name(file_name):
file_name = file_name.split('\\')[-1]
file_name = file_name.split('/')[-1]
return file_name
try:
# Use the existing file
if not dataset_name and 'filename' in data_file:
dataset_name = get_file_name(data_file['filename'])
return Bunch(type='file',
path=data_file['local_filename'],
name=dataset_name,
purge_source=purge)
except Exception:
# The uploaded file should've been persisted by the upload tool action
return Bunch(type=None, path=None, name=None)
def get_url_paste_urls_or_filename(group_incoming,
override_name=None,
override_info=None):
url_paste_file = group_incoming.get('url_paste', None)
if url_paste_file is not None:
url_paste = open(url_paste_file).read()
def start_of_url(content):
start_of_url_paste = content.lstrip()[0:10].lower()
looks_like_url = False
for url_prefix in URI_PREFIXES:
if start_of_url_paste.startswith(url_prefix):
looks_like_url = True
break
return looks_like_url
if start_of_url(url_paste):
url_paste = url_paste.replace('\r', '').split('\n')
for line in url_paste:
line = line.strip()
if line:
if not start_of_url(line):
continue # non-url line, ignore
if "file://" in line:
if not trans.user_is_admin:
raise AdminRequiredException()
elif not trans.app.config.allow_path_paste:
raise ConfigDoesNotAllowException()
upload_path = line[len("file://"):]
dataset_name = os.path.basename(upload_path)
else:
dataset_name = line
if override_name:
dataset_name = override_name
yield Bunch(type='url',
path=line,
name=dataset_name)
else:
dataset_name = 'Pasted Entry' # we need to differentiate between various url pastes here
if override_name:
dataset_name = override_name
yield Bunch(type='file',
path=url_paste_file,
name=dataset_name)
def get_one_filename(context):
data_file = context['file_data']
url_paste = context['url_paste']
ftp_files = context['ftp_files']
name = context.get('NAME', None)
info = context.get('INFO', None)
uuid = context.get('uuid', None) or None # Turn '' to None
file_type = context.get('file_type', None)
dbkey = self.get_dbkey(context)
warnings = []
to_posix_lines = False
if context.get('to_posix_lines',
None) not in ["None", None, False]:
to_posix_lines = True
auto_decompress = False
if context.get('auto_decompress',
None) not in ["None", None, False]:
auto_decompress = True
space_to_tab = False
if context.get('space_to_tab', None) not in ["None", None, False]:
space_to_tab = True
file_bunch = get_data_file_filename(data_file,
override_name=name,
override_info=info)
if file_bunch.path:
if url_paste is not None and url_paste.strip():
warnings.append(
"All file contents specified in the paste box were ignored."
)
if ftp_files:
warnings.append(
"All FTP uploaded file selections were ignored.")
elif url_paste is not None and url_paste.strip(
): # we need to use url_paste
for file_bunch in get_url_paste_urls_or_filename(
context, override_name=name, override_info=info):
if file_bunch.path:
break
if file_bunch.path and ftp_files is not None:
warnings.append(
"All FTP uploaded file selections were ignored.")
elif ftp_files is not None and trans.user is not None: # look for files uploaded via FTP
user_ftp_dir = trans.user_ftp_dir
assert not os.path.islink(
user_ftp_dir
), "User FTP directory cannot be a symbolic link"
for dirpath, _dirnames, filenames in os.walk(user_ftp_dir):
for filename in filenames:
for ftp_filename in ftp_files:
if ftp_filename == filename:
path = relpath(os.path.join(dirpath, filename),
user_ftp_dir)
if not os.path.islink(
os.path.join(dirpath, filename)):
ftp_data_file = {
'local_filename':
os.path.abspath(
os.path.join(user_ftp_dir, path)),
'filename':
os.path.basename(path)
}
purge = getattr(trans.app.config,
'ftp_upload_purge', True)
file_bunch = get_data_file_filename(
ftp_data_file,
override_name=name,
override_info=info,
purge=purge,
)
if file_bunch.path:
break
if file_bunch.path:
break
if file_bunch.path:
break
file_bunch.to_posix_lines = to_posix_lines
file_bunch.auto_decompress = auto_decompress
file_bunch.space_to_tab = space_to_tab
file_bunch.uuid = uuid
if file_type is not None:
file_bunch.file_type = file_type
if dbkey is not None:
file_bunch.dbkey = dbkey
return file_bunch, warnings
def get_filenames(context):
rval = []
data_file = context['file_data']
ftp_files = context['ftp_files']
uuid = context.get('uuid', None) or None # Turn '' to None
name = context.get('NAME', None)
info = context.get('INFO', None)
file_type = context.get('file_type', None)
dbkey = self.get_dbkey(context)
to_posix_lines = False
if context.get('to_posix_lines',
None) not in ["None", None, False]:
to_posix_lines = True
auto_decompress = False
if context.get('auto_decompress',
None) not in ["None", None, False]:
auto_decompress = True
space_to_tab = False
if context.get('space_to_tab', None) not in ["None", None, False]:
space_to_tab = True
file_bunch = get_data_file_filename(data_file,
override_name=name,
override_info=info)
file_bunch.uuid = uuid
if file_bunch.path:
file_bunch.to_posix_lines = to_posix_lines
file_bunch.auto_decompress = auto_decompress
file_bunch.space_to_tab = space_to_tab
if file_type is not None:
file_bunch.file_type = file_type
if dbkey is not None:
file_bunch.dbkey = dbkey
rval.append(file_bunch)
for file_bunch in get_url_paste_urls_or_filename(
context, override_name=name, override_info=info):
if file_bunch.path:
file_bunch.uuid = uuid
file_bunch.to_posix_lines = to_posix_lines
file_bunch.auto_decompress = auto_decompress
file_bunch.space_to_tab = space_to_tab
if file_type is not None:
file_bunch.file_type = file_type
if dbkey is not None:
file_bunch.dbkey = dbkey
rval.append(file_bunch)
# look for files uploaded via FTP
valid_files = []
if ftp_files is not None:
# Normalize input paths to ensure utf-8 encoding is normal form c.
# This allows for comparison when the filesystem uses a different encoding than the browser.
ftp_files = [
unicodedata.normalize('NFC', f) for f in ftp_files
if isinstance(f, str)
]
if trans.user is None:
log.warning(
'Anonymous user passed values in ftp_files: %s' %
ftp_files)
ftp_files = []
# TODO: warning to the user (could happen if session has become invalid)
else:
user_ftp_dir = trans.user_ftp_dir
assert not os.path.islink(
user_ftp_dir
), "User FTP directory cannot be a symbolic link"
for dirpath, _dirnames, filenames in os.walk(user_ftp_dir):
for filename in filenames:
path = relpath(os.path.join(dirpath, filename),
user_ftp_dir)
if not os.path.islink(
os.path.join(dirpath, filename)):
# Normalize filesystem paths
if isinstance(path, str):
valid_files.append(
unicodedata.normalize('NFC', path))
else:
valid_files.append(path)
else:
ftp_files = []
for ftp_file in ftp_files:
if ftp_file not in valid_files:
log.warning(
'User passed an invalid file path in ftp_files: %s' %
ftp_file)
continue
# TODO: warning to the user (could happen if file is already imported)
ftp_data_file = {
'local_filename':
os.path.abspath(os.path.join(user_ftp_dir, ftp_file)),
'filename':
os.path.basename(ftp_file)
}
purge = getattr(trans.app.config, 'ftp_upload_purge', True)
file_bunch = get_data_file_filename(ftp_data_file,
override_name=name,
override_info=info,
purge=purge)
if file_bunch.path:
file_bunch.to_posix_lines = to_posix_lines
file_bunch.auto_decompress = auto_decompress
file_bunch.space_to_tab = space_to_tab
if file_type is not None:
file_bunch.file_type = file_type
if dbkey is not None:
file_bunch.dbkey = dbkey
rval.append(file_bunch)
return rval
file_type = self.get_file_type(context)
file_count = self.get_file_count(trans, context)
d_type = self.get_datatype(trans, context)
dbkey = self.get_dbkey(context)
tag_using_filenames = context.get('tag_using_filenames', False)
tags = context.get('tags', False)
force_composite = asbool(context.get('force_composite', 'False'))
writable_files = d_type.writable_files
writable_files_offset = 0
groups_incoming = [None for _ in range(file_count)]
for group_incoming in context.get(self.name, []):
i = int(group_incoming['__index__'])
groups_incoming[i] = group_incoming
if d_type.composite_type is not None or force_composite:
# handle uploading of composite datatypes
# Only one Dataset can be created
dataset = Bunch()
dataset.type = 'composite'
dataset.file_type = file_type
dataset.dbkey = dbkey
dataset.datatype = d_type
dataset.warnings = []
dataset.metadata = {}
dataset.composite_files = {}
dataset.uuid = None
dataset.tag_using_filenames = None
dataset.tags = None
# load metadata
files_metadata = context.get(self.metadata_ref, {})
metadata_name_substition_default_dict = {
composite_file.substitute_name_with_metadata:
d_type.metadata_spec[
composite_file.substitute_name_with_metadata].default
for composite_file in d_type.composite_files.values()
if composite_file.substitute_name_with_metadata
}
for meta_name, meta_spec in d_type.metadata_spec.items():
if meta_spec.set_in_upload:
if meta_name in files_metadata:
meta_value = files_metadata[meta_name]
if meta_name in metadata_name_substition_default_dict:
meta_value = sanitize_for_filename(
meta_value,
default=metadata_name_substition_default_dict[
meta_name])
dataset.metadata[meta_name] = meta_value
dataset.name = self.get_composite_dataset_name(context)
if dataset.datatype.composite_type == 'auto_primary_file':
# replace sniff here with just creating an empty file
temp_name = sniff.stream_to_file(
io.StringIO(d_type.generate_primary_file(dataset)),
prefix='upload_auto_primary_file')
dataset.primary_file = temp_name
dataset.to_posix_lines = True
dataset.auto_decompress = True
dataset.space_to_tab = False
else:
file_bunch, warnings = get_one_filename(groups_incoming[0])
writable_files_offset = 1
dataset.primary_file = file_bunch.path
dataset.to_posix_lines = file_bunch.to_posix_lines
dataset.auto_decompress = file_bunch.auto_decompress
dataset.space_to_tab = file_bunch.space_to_tab
if file_bunch.file_type:
dataset.file_type = file_type
if file_bunch.dbkey:
dataset.dbkey = dbkey
dataset.warnings.extend(warnings)
if dataset.primary_file is None: # remove this before finish, this should create an empty dataset
raise Exception(
'No primary dataset file was available for composite upload'
)
if not force_composite:
keys = [value.name for value in writable_files.values()]
else:
keys = [str(index) for index in range(file_count)]
for i, group_incoming in enumerate(
groups_incoming[writable_files_offset:]):
key = keys[i + writable_files_offset]
if not force_composite and group_incoming is None and not writable_files[
list(writable_files.keys())[keys.index(key)]].optional:
dataset.warnings.append(
"A required composite file (%s) was not specified." %
(key))
dataset.composite_files[key] = None
else:
file_bunch, warnings = get_one_filename(group_incoming)
dataset.warnings.extend(warnings)
if file_bunch.path:
if force_composite:
key = group_incoming.get("NAME") or i
dataset.composite_files[key] = file_bunch.__dict__
elif not force_composite:
dataset.composite_files[key] = None
if not writable_files[list(writable_files.keys())[
keys.index(key)]].optional:
dataset.warnings.append(
"A required composite file (%s) was not specified."
% (key))
return [dataset]
else:
rval = []
for i, file_contexts in enumerate(context[self.name]):
datasets = get_filenames(file_contexts)
for dataset in datasets:
override_file_type = self.get_file_type(
context[self.name][i], parent_context=context)
d_type = self.get_datatype(trans,
context[self.name][i],
parent_context=context)
dataset.file_type = override_file_type
dataset.datatype = d_type
dataset.ext = self.get_datatype_ext(trans,
context[self.name][i],
parent_context=context)
dataset.dbkey = self.get_dbkey(context[self.name][i],
parent_context=context)
dataset.tag_using_filenames = tag_using_filenames
dataset.tags = tags
rval.append(dataset)
return rval
def get_uploaded_datasets(self, trans, context, override_name=None, override_info=None):
def get_data_file_filename(data_file, override_name=None, override_info=None, purge=True):
dataset_name = override_name
def get_file_name(file_name):
file_name = file_name.split('\\')[-1]
file_name = file_name.split('/')[-1]
return file_name
try:
# Use the existing file
if not dataset_name and 'filename' in data_file:
dataset_name = get_file_name(data_file['filename'])
return Bunch(type='file', path=data_file['local_filename'], name=dataset_name, purge_source=purge)
except:
# The uploaded file should've been persisted by the upload tool action
return Bunch(type=None, path=None, name=None)
def get_url_paste_urls_or_filename(group_incoming, override_name=None, override_info=None):
url_paste_file = group_incoming.get('url_paste', None)
if url_paste_file is not None:
url_paste = open(url_paste_file, 'r').read(1024)
def start_of_url(content):
start_of_url_paste = content.lstrip()[0:8].lower()
looks_like_url = False
for url_prefix in ["http://", "https://", "ftp://", "file://"]:
if start_of_url_paste.startswith(url_prefix):
looks_like_url = True
break
return looks_like_url
if start_of_url(url_paste):
url_paste = url_paste.replace('\r', '').split('\n')
for line in url_paste:
line = line.strip()
if line:
if not start_of_url(line):
continue # non-url line, ignore
if "file://" in line:
if not trans.user_is_admin():
raise AdminRequiredException()
elif not trans.app.config.allow_path_paste:
raise ConfigDoesNotAllowException()
upload_path = line[len("file://"):]
dataset_name = os.path.basename(upload_path)
else:
dataset_name = line
if override_name:
dataset_name = override_name
yield Bunch(type='url', path=line, name=dataset_name)
else:
dataset_name = 'Pasted Entry' # we need to differentiate between various url pastes here
if override_name:
dataset_name = override_name
yield Bunch(type='file', path=url_paste_file, name=dataset_name)
def get_one_filename(context):
data_file = context['file_data']
url_paste = context['url_paste']
ftp_files = context['ftp_files']
name = context.get('NAME', None)
info = context.get('INFO', None)
uuid = context.get('uuid', None) or None # Turn '' to None
warnings = []
to_posix_lines = False
if context.get('to_posix_lines', None) not in ["None", None, False]:
to_posix_lines = True
auto_decompress = False
if context.get('auto_decompress', None) not in ["None", None, False]:
auto_decompress = True
space_to_tab = False
if context.get('space_to_tab', None) not in ["None", None, False]:
space_to_tab = True
file_bunch = get_data_file_filename(data_file, override_name=name, override_info=info)
if file_bunch.path:
if url_paste is not None and url_paste.strip():
warnings.append("All file contents specified in the paste box were ignored.")
if ftp_files:
warnings.append("All FTP uploaded file selections were ignored.")
elif url_paste is not None and url_paste.strip(): # we need to use url_paste
for file_bunch in get_url_paste_urls_or_filename(context, override_name=name, override_info=info):
if file_bunch.path:
break
if file_bunch.path and ftp_files is not None:
warnings.append("All FTP uploaded file selections were ignored.")
elif ftp_files is not None and trans.user is not None: # look for files uploaded via FTP
user_ftp_dir = trans.user_ftp_dir
assert not os.path.islink(user_ftp_dir), "User FTP directory cannot be a symbolic link"
for (dirpath, dirnames, filenames) in os.walk(user_ftp_dir):
for filename in filenames:
for ftp_filename in ftp_files:
if ftp_filename == filename:
path = relpath(os.path.join(dirpath, filename), user_ftp_dir)
if not os.path.islink(os.path.join(dirpath, filename)):
ftp_data_file = {'local_filename' : os.path.abspath(os.path.join(user_ftp_dir, path)),
'filename' : os.path.basename(path)}
purge = getattr(trans.app.config, 'ftp_upload_purge', True)
file_bunch = get_data_file_filename(
ftp_data_file,
override_name=name,
override_info=info,
purge=purge,
)
if file_bunch.path:
break
if file_bunch.path:
break
if file_bunch.path:
break
file_bunch.to_posix_lines = to_posix_lines
file_bunch.auto_decompress = auto_decompress
file_bunch.space_to_tab = space_to_tab
file_bunch.uuid = uuid
return file_bunch, warnings
def get_filenames(context):
rval = []
data_file = context['file_data']
ftp_files = context['ftp_files']
uuid = context.get('uuid', None) or None # Turn '' to None
name = context.get('NAME', None)
info = context.get('INFO', None)
to_posix_lines = False
if context.get('to_posix_lines', None) not in ["None", None, False]:
to_posix_lines = True
auto_decompress = False
if context.get('auto_decompress', None) not in ["None", None, False]:
auto_decompress = True
space_to_tab = False
if context.get('space_to_tab', None) not in ["None", None, False]:
space_to_tab = True
file_bunch = get_data_file_filename(data_file, override_name=name, override_info=info)
file_bunch.uuid = uuid
if file_bunch.path:
file_bunch.to_posix_lines = to_posix_lines
file_bunch.auto_decompress = auto_decompress
file_bunch.space_to_tab = space_to_tab
rval.append(file_bunch)
for file_bunch in get_url_paste_urls_or_filename(context, override_name=name, override_info=info):
if file_bunch.path:
file_bunch.uuid = uuid
file_bunch.to_posix_lines = to_posix_lines
file_bunch.auto_decompress = auto_decompress
file_bunch.space_to_tab = space_to_tab
rval.append(file_bunch)
# look for files uploaded via FTP
valid_files = []
if ftp_files is not None:
# Normalize input paths to ensure utf-8 encoding is normal form c.
# This allows for comparison when the filesystem uses a different encoding than the browser.
ftp_files = [unicodedata.normalize('NFC', f) for f in ftp_files if isinstance(f, text_type)]
if trans.user is None:
log.warning('Anonymous user passed values in ftp_files: %s' % ftp_files)
ftp_files = []
# TODO: warning to the user (could happen if session has become invalid)
else:
user_ftp_dir = trans.user_ftp_dir
assert not os.path.islink(user_ftp_dir), "User FTP directory cannot be a symbolic link"
for (dirpath, dirnames, filenames) in os.walk(user_ftp_dir):
for filename in filenames:
path = relpath(os.path.join(dirpath, filename), user_ftp_dir)
if not os.path.islink(os.path.join(dirpath, filename)):
# Normalize filesystem paths
if isinstance(path, text_type):
valid_files.append(unicodedata.normalize('NFC', path))
else:
valid_files.append(path)
else:
ftp_files = []
for ftp_file in ftp_files:
if ftp_file not in valid_files:
log.warning('User passed an invalid file path in ftp_files: %s' % ftp_file)
continue
# TODO: warning to the user (could happen if file is already imported)
ftp_data_file = {'local_filename' : os.path.abspath(os.path.join(user_ftp_dir, ftp_file)),
'filename' : os.path.basename(ftp_file)}
purge = getattr(trans.app.config, 'ftp_upload_purge', True)
file_bunch = get_data_file_filename(ftp_data_file, override_name=name, override_info=info, purge=purge)
if file_bunch.path:
file_bunch.to_posix_lines = to_posix_lines
file_bunch.auto_decompress = auto_decompress
file_bunch.space_to_tab = space_to_tab
rval.append(file_bunch)
return rval
file_type = self.get_file_type(context)
d_type = self.get_datatype(trans, context)
dbkey = context.get('dbkey', None)
tag_using_filenames = context.get('tag_using_filenames', False)
writable_files = d_type.writable_files
writable_files_offset = 0
groups_incoming = [None for _ in writable_files]
for group_incoming in context.get(self.name, []):
i = int(group_incoming['__index__'])
groups_incoming[i] = group_incoming
if d_type.composite_type is not None:
# handle uploading of composite datatypes
# Only one Dataset can be created
dataset = Bunch()
dataset.type = 'composite'
dataset.file_type = file_type
dataset.dbkey = dbkey
dataset.datatype = d_type
dataset.warnings = []
dataset.metadata = {}
dataset.composite_files = {}
dataset.uuid = None
dataset.tag_using_filenames = None
# load metadata
files_metadata = context.get(self.metadata_ref, {})
metadata_name_substition_default_dict = dict((composite_file.substitute_name_with_metadata, d_type.metadata_spec[composite_file.substitute_name_with_metadata].default) for composite_file in d_type.composite_files.values() if composite_file.substitute_name_with_metadata)
for meta_name, meta_spec in d_type.metadata_spec.items():
if meta_spec.set_in_upload:
if meta_name in files_metadata:
meta_value = files_metadata[meta_name]
if meta_name in metadata_name_substition_default_dict:
meta_value = sanitize_for_filename(meta_value, default=metadata_name_substition_default_dict[meta_name])
dataset.metadata[meta_name] = meta_value
dataset.precreated_name = dataset.name = self.get_composite_dataset_name(context)
if dataset.datatype.composite_type == 'auto_primary_file':
# replace sniff here with just creating an empty file
temp_name, is_multi_byte = sniff.stream_to_file(StringIO(d_type.generate_primary_file(dataset)), prefix='upload_auto_primary_file')
dataset.primary_file = temp_name
dataset.to_posix_lines = True
dataset.auto_decompress = True
dataset.space_to_tab = False
else:
file_bunch, warnings = get_one_filename(groups_incoming[0])
writable_files_offset = 1
dataset.primary_file = file_bunch.path
dataset.to_posix_lines = file_bunch.to_posix_lines
dataset.auto_decompress = file_bunch.auto_decompress
dataset.space_to_tab = file_bunch.space_to_tab
dataset.warnings.extend(warnings)
if dataset.primary_file is None: # remove this before finish, this should create an empty dataset
raise Exception('No primary dataset file was available for composite upload')
keys = [value.name for value in writable_files.values()]
for i, group_incoming in enumerate(groups_incoming[writable_files_offset :]):
key = keys[i + writable_files_offset]
if group_incoming is None and not writable_files[list(writable_files.keys())[keys.index(key)]].optional:
dataset.warnings.append("A required composite file (%s) was not specified." % (key))
dataset.composite_files[key] = None
else:
file_bunch, warnings = get_one_filename(group_incoming)
dataset.warnings.extend(warnings)
if file_bunch.path:
dataset.composite_files[key] = file_bunch.__dict__
else:
dataset.composite_files[key] = None
if not writable_files[list(writable_files.keys())[keys.index(key)]].optional:
dataset.warnings.append("A required composite file (%s) was not specified." % (key))
return [dataset]
else:
datasets = get_filenames(context[self.name][0])
rval = []
for dataset in datasets:
dataset.file_type = file_type
dataset.datatype = d_type
dataset.ext = self.get_datatype_ext(trans, context)
dataset.dbkey = dbkey
dataset.tag_using_filenames = tag_using_filenames
rval.append(dataset)
return rval
