def test_capsys_err(capsys):
try:
fatal('goodbye world')
except SystemExit:
pass
cap = capsys.readouterr()
assert 'goodbye world' in cap.err
def main():
with Inform(notify_if_no_tty=True, version=version) as inform:
try:
# assure config and log directories exist
to_path(CONFIG_DIR).mkdir(parents=True, exist_ok=True)
to_path(DATA_DIR).mkdir(parents=True, exist_ok=True)
inform.set_logfile(to_path(DATA_DIR, LOG_FILE))
# read command line
cmdline = docopt(synopsis, options_first=True, version=version)
command = cmdline["<command>"]
args = cmdline["<args>"]
if cmdline["--quiet"]:
inform.quiet = True
# find and run command
settings = Settings(cmdline)
cmd, cmd_name = Command.find(command)
cmd.execute(cmd_name, args, settings, cmdline)
except KeyboardInterrupt:
display("Terminated by user.")
except Error as e:
e.terminate()
except OSError as e:
fatal(os_error(e))
done()
def initialize(cls, gpg_path=None, gpg_home=None, armor=None):
cls.gpg_path = to_path(
gpg_path if gpg_path else get_setting('gpg_executable'))
override_setting('gpg_executable', cls.gpg_path)
cls.gpg_home = to_path(
gpg_home if gpg_home else get_setting('gpg_home'))
override_setting('gpg_home', cls.gpg_home)
armor = armor if armor is not None else get_setting('gpg_armor')
if armor not in ARMOR_CHOICES:
warn("'%s' is not valid, choose from %s." %
(armor, conjoin(ARMOR_CHOICES)),
culprit=setting_path('gpg_armor'))
armor = 'extension'
cls.armor = armor
override_setting('gpg_armor', armor)
gpg_args = {}
if cls.gpg_path:
gpg_args.update({'gpgbinary': str(cls.gpg_path)})
if cls.gpg_home:
gpg_args.update({'gnupghome': str(cls.gpg_home)})
try:
cls.gpg = gnupg.GPG(**gpg_args)
except ValueError as e:
fatal(e)
def main():
try:
# read config file
read_config()
# read command line
cmdline = docopt(
__doc__.format(commands=Command.summarize()),
version='avendesora {} ({})'.format(__version__, __released__),
options_first=True,
)
# start logging
logfile = BufferedFile(get_setting('log_file'), True)
Inform(logfile=logfile,
hanging_indent=False,
stream_policy='header',
notify_if_no_tty=True)
shlib.set_prefs(use_inform=True, log_cmd=True)
# run the requested command
Command.execute(cmdline['<command>'], cmdline['<args>'])
done()
except KeyboardInterrupt:
output('\nTerminated by user.')
terminate()
except (PasswordError, Error) as e:
e.terminate()
except OSError as e:
fatal(os_error(e))
done()
def main():
with Inform() as inform:
# read command line
cmdline = docopt(
__doc__.format(commands=Command.summarize()),
options_first=True
)
config = cmdline['--config']
command = cmdline['<command>']
args = cmdline['<args>']
options = cull([
'verbose' if cmdline['--verbose'] else '',
'narrate' if cmdline['--narrate'] else '',
'trial-run' if cmdline['--trial-run'] else '',
])
if cmdline['--narrate']:
inform.narrate = True
try:
cmd, name = Command.find(command)
with Settings(config, cmd.REQUIRES_EXCLUSIVITY) as settings:
cmd.execute(name, args, settings, options)
except KeyboardInterrupt:
display('Terminated by user.')
except Error as err:
err.terminate()
except OSError as err:
fatal(os_error(err))
terminate()
def main():
with Inform(error_status=2, flush=True, version=version) as inform:
# read command line
cmdline = docopt(expanded_synopsis, options_first=True, version=version)
config = cmdline["--config"]
command = cmdline["<command>"]
args = cmdline["<args>"]
if cmdline["--mute"]:
inform.mute = True
if cmdline["--quiet"]:
inform.quiet = True
emborg_opts = cull(
[
"verbose" if cmdline["--verbose"] else "",
"narrate" if cmdline["--narrate"] else "",
"dry-run" if cmdline["--dry-run"] else "",
"no-log" if cmdline["--no-log"] else "",
]
)
if cmdline["--narrate"]:
inform.narrate = True
try:
# find the command
cmd, cmd_name = Command.find(command)
# execute the command initialization
exit_status = cmd.execute_early(cmd_name, args, None, emborg_opts)
if exit_status is not None:
terminate(exit_status)
worst_exit_status = 0
try:
while True:
with Settings(config, cmd, emborg_opts) as settings:
try:
exit_status = cmd.execute(
cmd_name, args, settings, emborg_opts
)
except Error as e:
settings.fail(e, cmd=' '.join(sys.argv))
e.terminate()
if exit_status and exit_status > worst_exit_status:
worst_exit_status = exit_status
except NoMoreConfigs:
pass
# execute the command termination
exit_status = cmd.execute_late(cmd_name, args, None, emborg_opts)
if exit_status and exit_status > worst_exit_status:
worst_exit_status = exit_status
except KeyboardInterrupt:
display("Terminated by user.")
except Error as e:
e.terminate()
except OSError as e:
fatal(os_error(e))
terminate(worst_exit_status)
def main():
with Inform(error_status=2, flush=True, version=version) as inform:
# read command line
cmdline = docopt(expanded_synopsis, options_first=True, version=version)
config = cmdline['--config']
command = cmdline['<command>']
args = cmdline['<args>']
if cmdline['--mute']:
inform.mute = True
if cmdline['--quiet']:
inform.quiet = True
options = cull([
'verbose' if cmdline['--verbose'] else '',
'narrate' if cmdline['--narrate'] else '',
'trial-run' if cmdline['--trial-run'] else '',
'no-log' if cmdline['--no-log'] else '',
])
if cmdline['--narrate']:
inform.narrate = True
try:
# find the command
cmd, cmd_name = Command.find(command)
# execute the command initialization
exit_status = cmd.execute_early(cmd_name, args, None, options)
if exit_status is not None:
terminate(exit_status)
worst_exit_status = 0
try:
while True:
with Settings(config, cmd, options) as settings:
try:
exit_status = cmd.execute(cmd_name, args, settings, options)
except Error as e:
settings.fail(e)
e.terminate()
if exit_status and exit_status > worst_exit_status:
worst_exit_status = exit_status
except NoMoreConfigs:
pass
# execute the command termination
exit_status = cmd.execute_late(cmd_name, args, None, options)
if exit_status and exit_status > worst_exit_status:
worst_exit_status = exit_status
except KeyboardInterrupt:
display('Terminated by user.')
except Error as e:
e.terminate()
except OSError as e:
fatal(os_error(e))
terminate(worst_exit_status)
def update_params(self, **params):
prev_params = self.metadata['parameters']
curr_params = params
if prev_params and prev_params != curr_params:
error(f"{self.repr} parameters differ from those used previously!")
for key in params:
prev = prev_params.get(key, '')
curr = curr_params.get(key, '')
if prev != curr:
codicil(f" {key!r} was {prev!r}, now {curr!r}")
fatal("Use the -f flag to overwrite. Aborting.")
self.metadata['parameters'] = curr_params
def get_psf_filename(psf_file):
if not psf_file:
try:
with open(saved_psf_file_filename) as f:
psf_file = f.read().strip()
display('Using PSF file:', psf_file)
except OSError:
fatal('missing PSF file name.')
try:
with open(saved_psf_file_filename, 'w') as f:
f.write(psf_file)
except OSError as e:
warn(os_error(e))
return psf_file
def main():
"""
Construct, encrypt, and publish backup keys.
As the primary entry point for the end user, this function is also
responsible for integrating information from command-line arguments,
configuration files, and `setuptools` plugins.
"""
set_shlib_prefs(use_inform=True, log_cmd=True)
args = docopt.docopt(__doc__)
if args['--verbose']:
set_output_prefs(verbose=True, narrate=True)
elif args['--quiet']:
set_output_prefs(quiet=True)
try:
config_path, config = load_config()
try:
if args['plugins']:
list_plugins(config)
sys.exit()
# Get the passcode before building the archive, so if something
# goes wrong with the passcode, we don't need to worry about
# cleaning up the unencrypted archive.
passcode = query_passcode(config)
batch = args['--yes'] or args['--quiet']
archive = build_archive(config, not batch)
encrypt_archive(config, archive, passcode)
publish_archive(config, archive)
except ConfigError as e:
e.reraise(culprit=config_path)
finally:
if 'archive' in locals():
delete_archive(config, archive)
except KeyboardInterrupt:
print()
except Error as e:
if args['--verbose']: raise
else: e.report()
except OSError as e:
fatal(os_error(e))
terminate()
def generate(self):
comment(' creating key')
keyname = self.keyname
data = self.data
servers = self.data.get('servers', [])
opts = data['keygen-options']
account_name = data['abraxas-account']
if account_name:
pw.get_account(account_name)
passcode = pw.generate_password()
description = fmt("{keyname} (created {date})")
else:
passcode = ''
self.warning = 'This key is not protected with a passcode!'
description = fmt("{keyname} (created {date} -- no passcode!)")
# warn user if they have a key with no passcode and no restrictions
for server in servers:
server_data = servers[server]
restrictions = server_data.get('restrictions')
if not restrictions:
warn(
'unprotected key being sent to', server,
'without restrictions.'
)
args = ['-C', description, '-f', keyname] + opts.split()
try:
comment(' running:', 'ssh-keygen', *args)
keygen = pexpect.spawn('ssh-keygen', args, timeout=None)
keygen.expect('Enter passphrase.*: ')
keygen.sendline(passcode)
keygen.expect('Enter same passphrase again: ')
keygen.sendline(passcode)
keygen.expect(pexpect.EOF)
keygen.close()
except pexpect.ExceptionPexpect as err:
fatal(err)
# remove group/other permissions from keyfiles
to_path(keyname).chmod(0o600)
to_path(keyname + '.pub').chmod(0o600)
def main():
import docopt
args = docopt.docopt(__doc__)
# Create the workspace directory:
work = SharedWorkspace(args['<workspace>'])
if args['--force']:
work.rmdir()
if work.exists():
error(f"Workspace '{args['<workspace>']}' already exists.")
fatal("Use the -f flag to overwrite. Aborting.")
work.mkdir()
# Fill in the workspace:
copyfile(args['<fasta>'], work.target_fasta)
copyfile(args['<pdb>'], work.get_target_pdb(args['<pdb>']))
work.loophash_db.symlink_to(
os.path.relpath(
Path(args['<loophash_db>']).resolve(),
work.root,
),
target_is_directory=True,
)
work.params['target'] = {
'pdb_chain': args['<pdb_chain>'],
}
work.params['user'] = {
'email': args['--user-email'],
}
work.write_params()
display("Workspace successfully initialized.")
def find_matching_command(given_cmd, known_cmds):
matching_cmds = find_matching_commands(given_cmd, known_cmds)
pseudo_cmd = shlex.join([Path(sys.argv[0]).name] + sys.argv[1:])
if len(matching_cmds) == 0:
guessed_cmd = did_you_mean(given_cmd, known_cmds)
fatal(f"""\
Unknown command '{given_cmd}'. Did you mean:
$ {pseudo_cmd.replace(given_cmd, guessed_cmd)}
""")
elif len(matching_cmds) > 1:
err = f"Command '{given_cmd}' is ambiguous. Did you mean:\n\n"
for cmd, main in matching_cmds:
err += f" $ {pseudo_cmd.replace(given_cmd, cmd)}\n"
err += '\n'
fatal(err)
else:
return matching_cmds[0]
def main():
# read config file
read_config()
# read command line
cmdline = docopt(
__doc__.format(commands=Command.summarize()),
options_first=True
)
# start logging
logfile = BufferedFile(get_setting('log_file'), True)
with Inform(logfile=logfile, hanging_indent=False):
try:
Command.execute(cmdline['<command>'], cmdline['<args>'])
except KeyboardInterrupt:
output('Terminated by user.')
except Error as err:
err.terminate()
except OSError as err:
fatal(os_error(err))
terminate()
def main():
with Inform(error_status=2, flush=True, version=version) as inform:
# read command line
cmdline = docopt(expanded_synopsis, options_first=True, version=version)
config = cmdline['--config']
command = cmdline['<command>']
args = cmdline['<args>']
if cmdline['--mute']:
inform.mute = True
options = cull([
'verbose' if cmdline['--verbose'] else '',
'narrate' if cmdline['--narrate'] else '',
'trial-run' if cmdline['--trial-run'] else '',
'no-log' if cmdline['--no-log'] else '',
])
if cmdline['--narrate']:
inform.narrate = True
try:
cmd, cmd_name = Command.find(command)
with Settings(config, cmd.REQUIRES_EXCLUSIVITY, options) as settings:
try:
exit_status = cmd.execute(cmd_name, args, settings, options)
except Error as e:
settings.fail(e)
e.terminate(True)
except KeyboardInterrupt:
display('Terminated by user.')
exit_status = 0
except Error as e:
e.terminate()
except OSError as e:
fatal(os_error(e))
terminate(exit_status)
def main(self):
appcli.load(self)
io = ProtocolIO.from_stdin()
if io.errors:
fatal("protocol has errors, not adding footnote.")
if not io.protocol:
fatal("no protocol specified.")
p = io.protocol
footnote = self.text if self.wrap else pre(self.text)
pattern = re.compile(self.where or '(?=[.:])')
try:
p.insert_footnotes(footnote, pattern=pattern)
except ValueError:
fatal(f"pattern {pattern!r} not found in protocol.")
p.merge_footnotes()
io.to_stdout(self.force_text)
def protocol_from_stdin():
io = ProtocolIO.from_stdin()
if io.errors:
fatal("protocol has errors, not stashing.")
return io.protocol
def main():
import docopt
args = docopt.docopt(__doc__)
plots = []
for path in args['<dels_workspace>']:
work_dels = DeletionsWorkspace.from_path(path)
msa = load_weighted_msa(work_dels.msa)
dels = pd.read_hdf(work_dels.deletions_hdf5)
plot = Plot()
plot.y = count_deletions(msa, dels)
plot.x = np.arange(len(plot.y))
plot.label = f'{work_dels.relpath} (N={len(dels)})'
plot.seq = msa.ref_ungapped
plots.append(plot)
if args['--align']:
if len(plots) != 2:
fatal("Must specify 2 worksapces to use the --align option.")
# I decided to use BLOSUM62 because the two sequences in this case may
# not be particularly similar. I used the corresponding gap penalties
# from BLAST 2.2.27, which I found in the reference below:
#
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3848038/
alignments = align.globalds(
plots[0].seq,
plots[1].seq,
blosum62,
-11,
-1,
)
aligned_seq1, aligned_seq2, score, start, end = alignments[0]
aligned_x1 = []
aligned_x2 = []
for i, (aa1, aa2) in enumerate(zip(aligned_seq1, aligned_seq2)):
if aa1 not in '-':
aligned_x1.append(i)
if aa2 not in '-':
aligned_x2.append(i)
plots[0].x = np.array(aligned_x1)
plots[1].x = np.array(aligned_x2)
percent_id = sum(x[0] == x[1] and '-' not in x
for x in zip(aligned_seq1, aligned_seq2))
percent_id /= max(len(p.seq) for p in plots)
print(f"Scaffolds aligned with {100*percent_id:.2f}% identity.")
if os.fork():
sys.exit()
for p in plots:
plt.plot(p.x, p.y, label=p.label)
plt.xlabel("aligned residue index" if args['--align'] else "residue index")
plt.ylabel("relative deletions" if args['--normalize'] else "deletions")
plt.xlim((0, max(p.x[-1] for x in plots)))
plt.legend(loc='best')
plt.show()
def format_text(self, *args, **kwargs):
fatal(
f"failed to unpickle stashed protocol:\n{self.err.__class__.__name__}: {self.err}"
)
def main():
try:
# Read command line {{{1
cmdline = docopt(__doc__)
keys = cmdline["--keys"].split(",") if cmdline["--keys"] else []
update = cmdline["--update"].split(",") if cmdline["--update"] else []
skip = cmdline["--skip"].split(",") if cmdline["--skip"] else []
Inform(
narrate=cmdline["--narrate"] or cmdline["--verbose"],
verbose=cmdline["--verbose"],
logfile=".sshdeploy.log",
prog_name=False,
flush=True,
version=__version__,
)
if keys and not cmdline["--trial-run"]:
fatal(
"Using the --keys option results in incomplete authorized_keys files.",
"It may only be used for testing purposes.",
"As such, --trial-run must also be specified when using --keys.",
sep="\n",
)
# Generated detailed help {{{1
if cmdline["manual"]:
from pkg_resources import resource_string
try:
Run(cmd=["less"], modes="soeW0", stdin=resource_string("src", "manual.rst").decode("utf8"))
except OSError as err:
error(os_error(err))
terminate()
# Read config file {{{1
try:
config_file = cmdline.get("--config-file")
config_file = config_file if config_file else "sshdeploy.conf"
contents = to_path(config_file).read_text()
except OSError as err:
fatal(os_error(err))
code = compile(contents, config_file, "exec")
config = {}
try:
exec(code, config)
except Exception as err:
fatal(err)
# Move into keydir {{{1
keydir = cmdline["--keydir"]
keydir = to_path(keydir if keydir else "keys-" + date)
if cmdline["generate"]:
comment("creating key directory:", keydir)
rm(keydir)
mkdir(keydir)
cd(keydir)
elif cmdline["distribute"]:
cd(keydir)
# determine default values for key options
defaults = {}
for name, default in [
("keygen-options", DefaultKeygenOpts),
("abraxas-account", DefaultAbraxasAccount),
("remote-include-filename", DefaultRemoteIncludeFilename),
]:
defaults[name] = config.get(name, default)
# Generate keys {{{1
if cmdline["generate"]:
for keyname in sorted(config["keys"].keys()):
data = config["keys"][keyname]
if keys and keyname not in keys:
# user did not request this key
continue
# get default values for missing key options
for option in defaults:
data[option] = data.get(option, defaults[option])
# generate the key
key = Key(keyname, data, update, skip, cmdline["--trial-run"])
key.generate()
# Publish keys {{{1
elif cmdline["distribute"]:
for keyname in sorted(config["keys"].keys()):
data = config["keys"][keyname]
if keys and keyname not in keys:
continue # user did not request this key
# get default values for missing key options
for option in defaults:
data[option] = data.get(option, defaults[option])
# publish the key pair to clients
key = Key(keyname, data, update, skip, cmdline["--trial-run"])
key.publish_private_key()
key.gather_public_keys()
# publish authorized_keys files to servers {{{1
if cmdline["distribute"]:
for each in sorted(AuthKeys.known):
authkey = AuthKeys.known[each]
authkey.publish()
authkey.verify()
# Process hosts {{{1
elif cmdline["test"] or cmdline["clean"] or cmdline["hosts"]:
hosts = set()
for keyname, data in config["keys"].items():
if keys and keyname not in keys:
continue # user did not request this key
# add servers to list of hosts
for server, options in data["servers"].items():
if update and server not in update or server in skip:
continue
if "bypass" not in options:
hosts.add(server)
# add clients to list of hosts
for client in data["clients"].keys():
if update and client not in update or client in skip:
continue
hosts.add(client)
# process the hosts
if cmdline["test"]:
# test host
for host in sorted(hosts):
test_access(host)
elif cmdline["clean"]:
# clean host
for host in sorted(hosts):
clean(host)
else:
# list hosts
for host in sorted(hosts):
display(host)
except OSError as err:
error(os_error(err))
except KeyboardInterrupt:
display("Killed by user")
done()
def show_list_dialog(options):
msg = 'selection dialog not available, you must install python3-gobject.'
notify(msg)
fatal(msg)
if path.is_symlink():
notes = f" (symlink to {path.resolve().name})"
doc += f" {path.name}{notes}\n"
return doc.strip()
if __name__ == '__main__':
template_docs = document_templates()
args = docopt.docopt(__doc__.format(indent(template_docs, 8*' ')))
case = name_test_dir(args['<family>'], args['--num'])
template = TEMPLATE_DIR / args['<template>']
if not template.is_dir():
fatal("template not found", culprit=template.name)
shutil.copytree(template, case, symlinks=True)
print(case)
if args['--readme']:
readme = case / 'README'
readme.touch()
editor = args['--editor'] or os.environ.get('EDITOR', 'vim')
editor_args = [
str(p)
for p in sorted(
case.iterdir(),
key=lambda p: FILE_ORDER.get(p.name, len(FILE_ORDER)),
)
import nestedtext as nt
from voluptuous import Schema, Coerce, Invalid
from inform import fatal, full_stop
from pprint import pprint
schema = Schema({
'debug': Coerce(bool),
'secret_key': str,
'allowed_hosts': [str],
'database': {
'engine': str,
'host': str,
'port': Coerce(int),
'user': str,
},
'webmaster_email': str,
})
try:
keymap = {}
raw = nt.load('deploy.nt', keymap=keymap)
config = schema(raw)
except nt.NestedTextError as e:
e.terminate()
except Invalid as e:
kind = 'key' if 'key' in e.msg else 'value'
loc = keymap[tuple(e.path)]
fatal(full_stop(e.msg), culprit=e.path, codicil=loc.as_line(kind))
pprint(config)
def run_script(self, account, script):
def run_xdotool(args):
try:
#[get_setting('xdotool_executable'), 'getactivewindow'] +
Run(get_setting('xdotool_executable').split() + args, 'soeW')
except OSError as err:
fatal(os_error(err))
def autotype(text):
# Split the text into individual key strokes and convert the special
# characters to their xkeysym names
keysyms = []
for char in text:
if char in string.ascii_letters + string.digits:
keysym = char
else:
keysym = KEYSYMS.get(char)
if not keysym:
error('cannot map to keysym, unknown', culprit=char)
else:
keysyms.append(keysym)
run_xdotool('key --clearmodifiers'.split() + keysyms)
# Create the default script if a script was not given
if script is True:
# this bit of trickery gets the name of the default field
name, key = account.split_name(None)
name = account.combine_name(name, key)
script = "{%s}{return}" % name
# Run the script
regex = re.compile(r'({\w+})')
out = []
scrubbed = []
sleep(INITIAL_AUTOTYPE_DELAY)
for term in regex.split(script):
if term and term[0] == '{' and term[-1] == '}':
# we have found a command
cmd = term[1:-1].lower()
if cmd == 'tab':
out.append('\t')
scrubbed.append('\t')
elif cmd == 'return':
out.append('\n')
scrubbed.append('\n')
elif cmd.startswith('sleep '):
cmd = cmd.split()
try:
assert cmd[0] == 'sleep'
assert len(cmd) == 2
if out:
autotype(''.join(out))
out = []
sleep(float(cmd[1]))
scrubbed.append('<sleep %s>' % cmd[1])
except (AssertionError, TypeError):
raise
fatal('syntax error in keyboard script.', culprit=term)
else:
name, key = account.split_name(cmd)
try:
value = dedent(str(account.get_field(name, key))).strip()
out.append(value)
if account.is_secret(name, key):
scrubbed.append('<%s>' % cmd)
else:
scrubbed.append('%s' % value)
except Error as err:
err.terminate()
else:
out.append(term)
log('Autotyping "%s".' % ''.join(scrubbed).replace('\t', '→').replace('\n', '↲'))
autotype(''.join(out))
def run_xdotool(args):
try:
#[get_setting('xdotool_executable'), 'getactivewindow'] +
Run(get_setting('xdotool_executable').split() + args, 'soeW')
except OSError as err:
fatal(os_error(err))
def template_stock_nM(self, x):
if x is not None:
return x
fatal("Must specify a template stock concentration")
def show_error_dialog(message):
msg = 'error dialog not available, you must install python3-gobject.'
notify(msg)
fatal(msg)
path = Path(args['<table>'])
keys = args['--key']
loaders = {
'.xlsx': lambda p: pd.read_excel(p, header=None, dtype=str),
'.csv': lambda p: pd.read_csv(p, header=None, dtype=str),
'.tsv': lambda p: pd.read_csv(p, sep='\t', header=None, dtype=str),
}
try:
df = loaders[path.suffix](path)
except KeyError:
err = f"""\
Unsupported file extension: *{path.suffix}
Expected one of the following: *.xlsx *.csv *.tsv"""
fatal(err, culprit=path)
except FileNotFoundError:
fatal("no such file", culprit=path)
# Add colons to the condition names:
df[0] = df[0].map(lambda x: x.rstrip(':') + ':')
# Replace hyphens with true minus-signs:
for c in df.columns[1:]:
df[c] = df[c].str.replace(r'^-$', '−')
rows = df.values.tolist()
align = ['<'] + (len(df.columns) - 1) * ['^']
br = '\n'
p = Protocol()
def main(self):
appcli.load(self)
# Defer importing `sqlalchemy`.
from . import model
with model.open_db() as db:
if self.ls:
model.list_protocols(
db,
categories=self.categories,
dependencies=self.dependencies,
include_dependents=self.show_dependents,
include_complete=self.show_all,
)
elif self.edit:
model.edit_protocol(
db, self.id,
protocol=protocol_from_stdin(),
message=self.message,
categories=self.categories,
dependencies=self.dependencies,
explicit=self.explicit,
)
elif self.peek:
model.peek_protocol(
db, self.id,
quiet=self.quiet,
force_text=self.force_text,
)
elif self.pop:
model.pop_protocol(
db, self.id,
quiet=self.quiet,
force_text=self.force_text,
)
elif self.drop:
model.drop_protocols(db, self.ids)
elif self.restore:
model.restore_protocols(db, self.ids)
elif self.clear:
model.clear_protocols(db)
elif self.reset:
model.reset_protocols(db)
else:
protocol = protocol_from_stdin()
if not protocol:
if self.add: fatal("no protocol specified.")
model.list_protocols(
db,
categories=self.categories,
dependencies=self.dependencies,
include_dependents=self.show_dependents,
include_complete=self.show_all,
)
else:
model.add_protocol(
db, protocol,
message=self.message,
categories=self.categories,
dependencies=self.dependencies,
)