def load():
try:
if context().get_storage_file().exists():
with context().get_storage_file().open('rb') as f:
_store.update(pickle.load(f))
else:
_persist()
except (pickle.PickleError, IOError) as e:
raise McmdError("Unable to read storage from file: {}".format(
e.message))
def _install(default_config):
mcmd.io.io.info("Looks like this is your first time running {}!\n "
"Let's take a moment to set things up. It's OK to leave some fields empty, you can always change "
"them later.".format(highlight("Molgenis Commander")))
mcmd.io.io.newline()
for configurer in property_configurers().values():
configurer(default_config)
config.set_config(default_config, context().get_properties_file())
mcmd.io.io.newline()
mcmd.io.io.info(
'The configuration file has been created at {}'.format(highlight(str(context().get_properties_file()))))
def _upgrade(default_config, user_config):
mcmd.io.io.info("Some properties haven't been configured yet. Let's take a moment to fix that.")
mcmd.io.io.newline()
for prop, configurer in property_configurers().items():
if prop not in user_config:
configurer(default_config)
config.set_config(default_config, context().get_properties_file())
mcmd.io.io.newline()
mcmd.io.io.info(
'The configuration file has been updated successfully ({})'.format(
highlight(str(context().get_properties_file()))))
exit(0)
def set_(args):
"""
set sets the specified row of the specified table (or setting of specified settings table) to the specified value
:param args: command line arguments containing: the settings type, the setting to set, and the value to set it to,
if not a setting also the --for (which row to alter)
if --from-path or --from-resource is passed the value is assumed to be a file containing the value data to be set
:return: None
"""
value = args.value
value_desc = highlight(value)
if args.from_path:
path = Path(args.value)
value = files.read_file(path)
value_desc = 'contents of {}'.format(highlight(args.value))
elif args.from_resource:
path = files.select_file_from_folders(context().get_resource_folders(),
args.value)
value = files.read_file(path)
value_desc = 'contents of {}'.format(highlight(args.value))
if args.for_:
entity = args.type
row = args.for_
io.start('Updating {} of {} for id {} to {}'.format(
highlight(args.attribute), highlight(args.type),
highlight(args.for_), value_desc))
else:
entity = _get_settings_entity(args.type)
io.start('Updating {} of {} settings to {}'.format(
highlight(args.attribute), highlight(args.type), value_desc))
row = _get_first_row_id(entity)
url = api.rest1('{}/{}/{}'.format(entity, row, args.attribute))
put(url, json.dumps(value))
def _remove_script(script_name):
path = context().get_scripts_folder().joinpath(script_name)
_check_script_exists(path)
try:
io.start('Removing script %s' % highlight(script_name))
path.unlink()
except OSError as e:
raise McmdError('Error removing script: %s' % str(e))
def _get_script(args):
if args.from_path:
script = Path(args.script)
else:
script = context().get_scripts_folder().joinpath(args.script)
if not script.exists():
raise McmdError("The script {} doesn't exist".format(script))
return script
def _read_script(script_name):
path = context().get_scripts_folder().joinpath(script_name)
_check_script_exists(path)
try:
with path.open() as f:
for line in f.readlines():
log.info(line.strip())
except OSError as e:
raise McmdError('Error reading script: %s' % str(e))
def load_config():
yaml = YAML()
default_config = _try_load_yaml(yaml, _DEFAULT_PROPERTIES)
if _is_install_required():
_install(default_config)
user_config = _try_load_yaml(yaml, context().get_properties_file())
if _is_upgrade_required(user_config):
_upgrade(default_config, user_config)
# merge the configs so that new properties and list items are added
_merge(default_config, user_config)
# pass result to the config module and save to disk
config.set_config(default_config, context().get_properties_file())
def write(arg_string, success):
try:
history = open(str(context().get_history_file()), 'a')
indicator = _INDICATOR_SUCCESS
if not success:
indicator = _INDICATOR_FAILURE
history.write('%s %s\n' % (indicator, arg_string))
except OSError as e:
raise McmdError("Error writing to history: %s" % str(e))
def _input_script_name():
file_name = ''
while not file_name:
name = mcmd.io.ask.input_('Supply the name of the script:')
if context().get_scripts_folder().joinpath(name).exists():
overwrite = confirm('%s already exists. Overwrite?' % name)
if overwrite:
file_name = name
else:
file_name = name
return file_name
def load_config():
yaml = YAML()
default_config = _try_load_yaml(yaml, _DEFAULT_PROPERTIES)
if _is_install_required():
if os.getenv('MCMD_INSTALL_NON_INTERACTIVE', 'False').lower() == 'true':
_install_non_interactive(default_config)
else:
_install(default_config)
exit(0)
user_config = _try_load_yaml(yaml, context().get_properties_file())
if _is_upgrade_required(user_config):
_upgrade(default_config, user_config)
# merge the configs so that new properties and list items are added
_merge(default_config, user_config)
# pass result to the config module and save to disk
config.set_config(default_config, context().get_properties_file())
def read(num_lines, include_fails):
lines = deque()
if not context().get_history_file().is_file():
return lines
try:
with open(str(context().get_history_file()), 'r') as history:
for line in history:
line = line.rstrip('\n')
if line.startswith(_INDICATOR_FAILURE):
if include_fails:
lines.append((False, line[2:]))
else:
lines.append((True, line[2:]))
if len(lines) > num_lines:
lines.popleft()
except OSError as e:
raise McmdError("Error reading from history: %s" % str(e))
return lines
def _create_script(args):
lines = history.read(args.number, args.show_fails)
if len(lines) == 0:
log.info('History is empty.')
return
options = [line[1] for line in lines]
commands = mcmd.io.ask.checkbox('Pick the lines that will form the script:', options)
file_name = _input_script_name()
try:
with open(str(context().get_scripts_folder().joinpath(file_name)), 'w') as script_file:
for cmd in commands:
script_file.write(cmd + '\n')
except OSError as e:
raise McmdError("Error writing to script: %s" % str(e))
def _download_attachment(attachment, issue_num):
issue_folder = context().get_issues_folder().joinpath(issue_num)
issue_folder.mkdir(parents=True, exist_ok=True)
file_path = issue_folder.joinpath(attachment.name)
if file_path.exists():
overwrite = mcmd.io.ask.confirm(
'File %s already exists. Re-download?' % file_path.name)
if not overwrite:
return file_path
io.start('Downloading %s from GitHub issue %s' %
(highlight(attachment.name), highlight('#' + issue_num)))
try:
r = requests.get(attachment.url)
r.raise_for_status()
with file_path.open('wb') as f:
f.write(r.content)
except (OSError, requests.RequestException, requests.HTTPError) as e:
raise McmdError('Error downloading GitHub attachment: %s' % str(e))
io.succeed()
return file_path
def _list_scripts():
for path in context().get_scripts_folder().iterdir():
if not path.name.startswith('.'):
log.info(path.name)
def clear():
try:
open(str(context().get_history_file()), 'w').close()
except OSError as e:
raise McmdError("Error clearing history: %s" % str(e))
def _is_install_required():
return not context().get_properties_file().exists() or context().get_properties_file().stat().st_size == 0
def _persist():
try:
with context().get_storage_file().open('wb') as f:
pickle.dump(_store, f)
except (pickle.PickleError, IOError) as e:
raise McmdError("Unable to save storage to file: {}".format(e.message))
def _get_path_from_quick_folders(file_name):
file_name = os_path.splitext(file_name)[0]
file_map = scan_folders_for_files(context().get_resource_folders())
path = select_path(file_map, file_name)
return str(path)
def _import_from_quick_folders(args):
file_name = os_path.splitext(args.resource)[0]
path = files.select_file_from_folders(folders=context().get_git_folders() +
context().get_dataset_folders(),
file_name=file_name)
_do_import(path, args.to_package, args.entity_type_id, args.import_action)
def _get_path_from_quick_folders(file_name):
file_name = os_path.splitext(file_name)[0]
path = file_utils.select_file_from_folders(
context().get_resource_folders(), file_name)
return str(path)
def _install_non_interactive(default_config):
config.set_config(default_config, context().get_properties_file())
config.set_non_interactive(True)
mcmd.io.io.info(
'The configuration file has been created at {}'.format(highlight(str(context().get_properties_file()))))
def _import_from_quick_folders(args):
file_name = os_path.splitext(args.resource)[0]
file_map = scan_folders_for_files(context().get_git_folders() +
context().get_dataset_folders())
path = select_path(file_map, file_name)
_do_import(path, args.to_package, args.entity_type_id)
