def prepare_argument_path(self, argument_noun, raw_arguments, draft_folder,
default_path):
data_type = get_data_type(argument_noun)
# If client sent direct content (x_table_csv), save it
for file_format in data_type.formats:
raw_argument_name = '%s_%s' % (argument_noun, file_format)
if raw_argument_name not in raw_arguments:
continue
source_text = raw_arguments[raw_argument_name]
target_name = '%s.%s' % (argument_noun, file_format)
return copy_text(join(draft_folder, target_name), source_text)
# Raise KeyError if client did not specify noun (x_table)
v = raw_arguments[argument_noun]
# If client sent multipart content, save it
if hasattr(v, 'file'):
target_name = argument_noun + get_file_extension(v.filename)
return copy_file(join(draft_folder, target_name), v.file)
# If client sent empty content, use default
if v == '':
if not default_path:
raise KeyError
target_name = argument_noun + get_file_extension(default_path)
return link_path(join(draft_folder, target_name), default_path)
# If client sent a relative path (x_table=11/x/y.csv), find it
if '/' in v:
source_path = self.get_file_path(*parse_result_relative_path(v))
target_name = argument_noun + get_file_extension(source_path)
return link_path(join(draft_folder, target_name), source_path)
# If client sent an upload id (x_table=x), find it
upload = get_upload(self, upload_id=v)
source_path = realpath(join(upload.folder, data_type.get_file_name()))
target_name = argument_noun + get_file_extension(source_path)
target_path = move_path(join(draft_folder, target_name), source_path)
remove_safely(upload.folder)
return target_path
def prepare_argument_path(
self, argument_noun, raw_arguments, draft_folder, default_path):
data_type = get_data_type(argument_noun)
# If client sent direct content (x_table_csv), save it
for file_format in data_type.formats:
raw_argument_name = '%s_%s' % (argument_noun, file_format)
if raw_argument_name not in raw_arguments:
continue
source_text = raw_arguments[raw_argument_name]
target_name = '%s.%s' % (argument_noun, file_format)
return copy_text(join(draft_folder, target_name), source_text)
# Raise KeyError if client did not specify noun (x_table)
v = raw_arguments[argument_noun]
# If client sent multipart content, save it
if hasattr(v, 'file'):
target_name = argument_noun + get_file_extension(v.filename)
return copy_file(join(draft_folder, target_name), v.file)
# If client sent empty content, use default
if v == '':
if not default_path:
raise KeyError
target_name = argument_noun + get_file_extension(default_path)
return link_path(join(draft_folder, target_name), default_path)
# If client sent a relative path (x_table=11/x/y.csv), find it
if '/' in v:
source_path = self.get_file_path(*parse_result_relative_path(v))
target_name = argument_noun + get_file_extension(source_path)
return link_path(join(draft_folder, target_name), source_path)
# If client sent an upload id (x_table=x), find it
upload = get_upload(self, upload_id=v)
source_path = join(upload.folder, data_type.get_file_name())
target_name = argument_noun + get_file_extension(source_path)
target_path = move_path(join(draft_folder, target_name), source_path)
remove_safely(upload.folder)
return target_path
def save(Class, path, table):
if path.endswith(".csv"):
table.to_csv(path, encoding="utf-8", index=False)
elif path.endswith(".msg"):
table.to_msgpack(path, compress="blosc")
elif path.endswith(".json"):
table.to_json(path)
elif path.endswith(".xls") or path.endswith(".xlsx"):
table.to_excel(path)
else:
raise DataTypeError("file format not supported (%s)" % get_file_extension(path))
def save(Class, data_folder, owner_id, id_length, source_name, source_x):
source_extension = get_file_extension(source_name)
source_file = prepare_file(source_x)
instance = Class.spawn(data_folder, id_length, owner_id)
instance.name = source_name
instance.path = join(instance.folder, 'raw' + source_extension)
# Save name
open(join(instance.folder, 'name.txt'), 'wt').write(source_name)
# Save path
temporary_path = join(instance.folder, 'temporary.bin')
with open(temporary_path, 'wb') as temporary_file:
copyfileobj(source_file, temporary_file)
rename(temporary_path, instance.path)
return instance
def load(Class, path):
if not exists(path):
raise IOError
if path.endswith(".csv"):
try:
table = pandas.read_csv(path, encoding="utf-8", skipinitialspace=True)
except UnicodeDecodeError:
encoding = _get_encoding(open(path).read())
table = pandas.read_csv(path, encoding=encoding, skipinitialspace=True)
elif path.endswith(".msg"):
table = pandas.read_msgpack(path)
elif path.endswith(".json"):
table = pandas.read_json(path, orient="split")
elif path.endswith(".xls") or path.endswith(".xlsx"):
table = pandas.read_excel(path)
else:
raise DataTypeError("file format not supported (%s)" % get_file_extension(path))
return table
def prepare_script_folder(target_folder, notebook, notebook_name):
tool_arguments = load_tool_arguments(notebook)
# Prepare paths
for k, v in tool_arguments.items():
if not k.endswith('_path'):
continue
path = make_unique_path(target_folder, get_file_extension(v))
shutil.copy(v, path)
tool_arguments[k] = basename(path)
# Prepare command-line script
script_lines = []
script_lines.append('from sys import argv')
for i, arg in zip(range(1, len(tool_arguments) + 1), tool_arguments):
if arg.endswith('_integer'):
script_lines.append('%s = int(argv[%s])' % (arg, i))
else:
script_lines.append('%s = argv[%s]' % (arg, i))
#script_lines.append('%s = argv[1:]' % ', '.join(tool_arguments))
notebook.cells[0]['source'] = '\n'.join(script_lines)
script_content, script_info = nbconvert.export_script(notebook)
script_name = 'run' + script_info['output_extension']
if script_name.endswith('.py'):
command_name = 'python'
else:
raise CrossComputeError
# Save script
script_path = join(target_folder, script_name)
codecs.open(script_path, 'w', encoding='utf-8').write(script_content)
# Save configuration
configuration_path = join(target_folder, 'cc.ini')
configuration_lines = []
configuration_lines.append('[crosscompute %s]' % notebook_name)
configuration_lines.append(
'command_template = %s %s %s' %
(command_name, script_name, ' '.join('{%s}' % x
for x in tool_arguments).strip()))
for k, v in tool_arguments.items():
if k in RESERVED_ARGUMENT_NAMES:
continue
configuration_lines.append('%s = %s' % (k, v))
codecs.open(configuration_path, 'w',
encoding='utf-8').write('\n'.join(configuration_lines).strip())
return target_folder
def prepare_script_folder(target_folder, notebook, notebook_name):
tool_arguments = load_tool_arguments(notebook)
# Prepare paths
for k, v in tool_arguments.items():
if not k.endswith("_path"):
continue
path = make_unique_path(target_folder, get_file_extension(v))
shutil.copy(v, path)
tool_arguments[k] = basename(path)
# Prepare command-line script
script_lines = []
script_lines.append("from sys import argv")
script_lines.append("%s = argv[1:]" % ", ".join(tool_arguments))
notebook.cells[0]["source"] = "\n".join(script_lines)
script_content, script_info = nbconvert.export_script(notebook)
script_name = "run" + script_info["output_extension"]
if script_name.endswith(".py"):
command_name = "python"
else:
raise CrossComputeError
# Save script
script_path = join(target_folder, script_name)
codecs.open(script_path, "w", encoding="utf-8").write(script_content)
# Save configuration
configuration_path = join(target_folder, "cc.ini")
configuration_lines = []
configuration_lines.append("[crosscompute %s]" % notebook_name)
configuration_lines.append(
"command_template = %s %s %s"
% (command_name, script_name, " ".join("{%s}" % x for x in tool_arguments).strip())
)
for k, v in tool_arguments.items():
if k in RESERVED_ARGUMENT_NAMES:
continue
configuration_lines.append("%s = %s" % (k, v))
codecs.open(configuration_path, "w", encoding="utf-8").write("\n".join(configuration_lines).strip())
return target_folder
def test_get_file_extension():
assert get_file_extension('file.txt.zip') == '.txt.zip'
def test_get_file_extension():
assert get_file_extension('file.txt.zip') == '.txt.zip'
