def __init__(self, *args, **kwargs):
import re
import sys
unicodes = ["\u2018", "\u2019", "\u201C", "\u201D", "\u2014", "\u2013"]
category_regex = re.compile(r'--m-(\S+)-category')
invalid_chars = []
categories = []
for command in sys.argv:
if any(x in command for x in unicodes):
invalid_chars.append(command)
match = category_regex.fullmatch(command)
if match is not None:
param_name, = match.groups()
# Maps old-style option name to new name.
categories.append((command, '--m-%s-column' % param_name))
if invalid_chars or categories:
if invalid_chars:
msg = ("Error: Detected invalid character in: %s\nVerify the "
"correct quotes or dashes (ASCII) are being used." %
', '.join(invalid_chars))
click.echo(CONFIG.cfg_style('error', msg), err=True)
if categories:
old_to_new_names = '\n'.join('Instead of %s, trying using %s' %
(old, new)
for old, new in categories)
msg = ("Error: The following options no longer exist because "
"metadata *categories* are now called metadata "
"*columns* in QIIME 2.\n\n%s" % old_to_new_names)
click.echo(CONFIG.cfg_style('error', msg), err=True)
sys.exit(-1)
super().__init__(*args, **kwargs)
# Plugin state for current deployment that will be loaded from cache.
# Used to construct the dynamic CLI.
self._plugins = None
def extract(input_path, output_path):
import zipfile
import qiime2.sdk
from q2cli.core.config import CONFIG
try:
extracted_dir = qiime2.sdk.Result.extract(input_path, output_path)
except (zipfile.BadZipFile, ValueError):
raise click.BadParameter(
'%s is not a valid QIIME 2 Result. Only QIIME 2 Artifacts and '
'Visualizations can be extracted.' % input_path)
else:
success = 'Extracted %s to directory %s' % (input_path, extracted_dir)
click.echo(CONFIG.cfg_style('success', success))
def export_data(input_path, output_path, output_format):
import qiime2.util
import qiime2.sdk
import distutils
from q2cli.core.config import CONFIG
result = qiime2.sdk.Result.load(input_path)
if output_format is None:
if isinstance(result, qiime2.sdk.Artifact):
output_format = result.format.__name__
else:
output_format = 'Visualization'
result.export_data(output_path)
else:
if isinstance(result, qiime2.sdk.Visualization):
error = '--output-format cannot be used with visualizations'
click.echo(CONFIG.cfg_style('error', error), err=True)
click.get_current_context().exit(1)
else:
source = result.view(qiime2.sdk.parse_format(output_format))
if os.path.isfile(str(source)):
if os.path.isfile(output_path):
os.remove(output_path)
elif os.path.dirname(output_path) == '':
# This allows the user to pass a filename as a path if they
# want their output in the current working directory
output_path = os.path.join('.', output_path)
if os.path.dirname(output_path) != '':
# create directory (recursively) if it doesn't exist yet
os.makedirs(os.path.dirname(output_path), exist_ok=True)
qiime2.util.duplicate(str(source), output_path)
else:
distutils.dir_util.copy_tree(str(source), output_path)
output_type = 'file' if os.path.isfile(output_path) else 'directory'
success = 'Exported %s as %s to %s %s' % (input_path, output_format,
output_type, output_path)
click.echo(CONFIG.cfg_style('success', success))
def _color_important(self, tokens, ctx):
import re
from q2cli.core.config import CONFIG
for t in tokens:
if '_' in t:
names = self.get_option_names(ctx)
if re.sub(r'[^\w]', '', t) in names:
m = re.search(r'(\w+)', t)
word = t[m.start():m.end()]
word = CONFIG.cfg_style('emphasis', word.replace('_', '-'))
token = t[:m.start()] + word + t[m.end():]
yield token
continue
yield t
def assert_result_data(input_path, zip_data_path, expression):
import re
import q2cli.util
import qiime2.sdk
from q2cli.core.config import CONFIG
q2cli.util.get_plugin_manager()
try:
result = qiime2.sdk.Result.load(input_path)
except Exception as e:
header = 'There was a problem loading %s as a QIIME 2 result:' % \
input_path
q2cli.util.exit_with_error(e, header=header)
try:
hits = sorted(result._archiver.data_dir.glob(zip_data_path))
if len(hits) != 1:
data_dir = result._archiver.data_dir
all_fps = sorted(data_dir.glob('**/*'))
all_fps = [x.relative_to(data_dir).name for x in all_fps]
raise ValueError('Value provided for zip_data_path (%s) did not '
'produce exactly one match.\nMatches: %s\n'
'Paths observed: %s' %
(zip_data_path, hits, all_fps))
except Exception as e:
header = 'There was a problem locating the zip_data_path (%s)' % \
zip_data_path
q2cli.util.exit_with_error(e, header=header)
try:
target = hits[0].read_text()
match = re.search(expression, target, flags=re.MULTILINE)
if match is None:
raise AssertionError('Expression %r not found in %s.' %
(expression, hits[0]))
except Exception as e:
header = 'There was a problem finding the expression.'
q2cli.util.exit_with_error(e, header=header)
msg = '"%s" was found in %s' % (str(expression), str(zip_data_path))
click.echo(CONFIG.cfg_style('success', msg))
def get_command(self, ctx, name):
try:
action = self._action_lookup[name]
except KeyError:
from q2cli.util import get_close_matches
possibilities = get_close_matches(name, self._action_lookup)
if len(possibilities) == 1:
hint = ' Did you mean %r?' % possibilities[0]
elif possibilities:
hint = ' (Possible commands: %s)' % ', '.join(possibilities)
else:
hint = ''
click.echo(CONFIG.cfg_style(
'error', "Error: QIIME 2 plugin %r has no "
"action %r." % (self._plugin['name'], name) + hint),
err=True)
ctx.exit(2) # Match exit code of `return None`
return ActionCommand(name, self._plugin, action)
def callback(ctx, param, value):
if not value or ctx.resilient_parsing:
return
records = get_citation_records()
if records:
import io
import qiime2.sdk
citations = qiime2.sdk.Citations([('key%d' % i, r)
for i, r in enumerate(records)])
with io.StringIO() as fh:
fh.write('% use `qiime tools citations` on a QIIME 2 result'
' for complete list\n\n')
citations.save(fh)
click.echo(fh.getvalue(), nl=False)
ctx.exit()
else:
click.echo(CONFIG.cfg_style('problem', 'No citations found.'),
err=True)
ctx.exit(1)
def import_data(type, input_path, output_path, input_format):
import qiime2.sdk
import qiime2.plugin
from q2cli.core.config import CONFIG
try:
artifact = qiime2.sdk.Artifact.import_data(type, input_path,
view_type=input_format)
except qiime2.plugin.ValidationError as e:
header = 'There was a problem importing %s:' % input_path
q2cli.util.exit_with_error(e, header=header, traceback=None)
except Exception as e:
header = 'An unexpected error has occurred:'
q2cli.util.exit_with_error(e, header=header)
artifact.save(output_path)
if input_format is None:
input_format = artifact.format.__name__
success = 'Imported %s as %s to %s' % (input_path,
input_format,
output_path)
click.echo(CONFIG.cfg_style('success', success))
def citations(path):
import qiime2.sdk
import io
from q2cli.core.config import CONFIG
ctx = click.get_current_context()
try:
result = qiime2.sdk.Result.load(path)
except Exception as e:
header = 'There was a problem loading %s as a QIIME 2 result:' % path
q2cli.util.exit_with_error(e, header=header)
if result.citations:
with io.StringIO() as fh:
result.citations.save(fh)
click.echo(fh.getvalue(), nl=False)
ctx.exit(0)
else:
click.echo(CONFIG.cfg_style('problem', 'No citations found.'),
err=True)
ctx.exit(1)
def __init__(self, name, plugin, action):
import q2cli.util
import q2cli.click.type
self.plugin = plugin
self.action = action
self._inputs, self._params, self._outputs = \
self._build_generated_options()
self._misc = [
click.Option(['--output-dir'],
type=q2cli.click.type.OutDirType(),
help='Output unspecified results to a directory'),
click.Option(['--verbose / --quiet'],
default=None,
required=False,
help='Display verbose output to stdout and/or stderr '
'during execution of this action. Or silence '
'output if execution is successful (silence is '
'golden).'),
q2cli.util.example_data_option(self._get_plugin,
self.action['id']),
q2cli.util.citations_option(self._get_citation_records)
]
options = [*self._inputs, *self._params, *self._outputs, *self._misc]
help_ = [action['description']]
if self.action['deprecated']:
help_.append(
CONFIG.cfg_style(
'warning',
'WARNING:\n\nThis command is deprecated and will '
'be removed in a future version of this plugin.'))
super().__init__(name,
params=options,
callback=self,
short_help=action['name'],
help='\n\n'.join(help_))
def validate(path, level):
import qiime2.sdk
from q2cli.core.config import CONFIG
try:
result = qiime2.sdk.Result.load(path)
except Exception as e:
header = 'There was a problem loading %s as a QIIME 2 Result:' % path
q2cli.util.exit_with_error(e, header=header)
try:
result.validate(level)
except qiime2.plugin.ValidationError as e:
header = 'Result %s does not appear to be valid at level=%s:' % (
path, level)
q2cli.util.exit_with_error(e, header=header, traceback=None)
except Exception as e:
header = ('An unexpected error has occurred while attempting to '
'validate result %s:' % path)
q2cli.util.exit_with_error(e, header=header)
else:
click.echo(CONFIG.cfg_style('success', f'Result {path} appears to be '
f'valid at level={level}.'))
def get_command(self, ctx, name):
if name in self._builtin_commands:
return self._builtin_commands[name]
try:
plugin = self._plugin_lookup[name]
except KeyError:
from q2cli.util import get_close_matches
possibilities = get_close_matches(name, self._plugin_lookup)
if len(possibilities) == 1:
hint = ' Did you mean %r?' % possibilities[0]
elif possibilities:
hint = ' (Possible commands: %s)' % ', '.join(possibilities)
else:
hint = ''
click.echo(CONFIG.cfg_style(
'error', "Error: QIIME 2 has no "
"plugin/command named %r." % name + hint),
err=True)
ctx.exit(2) # Match exit code of `return None`
return PluginCommand(plugin, name)
def assert_result_type(input_path, qiime_type):
import q2cli.util
import qiime2.sdk
from q2cli.core.config import CONFIG
q2cli.util.get_plugin_manager()
try:
result = qiime2.sdk.Result.load(input_path)
except Exception as e:
header = 'There was a problem loading %s as a QIIME 2 Result:' % \
input_path
q2cli.util.exit_with_error(e, header=header)
if str(result.type) != qiime_type:
try:
msg = 'Expected %s, observed %s' % (qiime_type, result.type)
raise AssertionError(msg)
except Exception as e:
header = 'There was a problem asserting the type:'
q2cli.util.exit_with_error(e, header=header)
else:
msg = 'The input file (%s) type and the expected type (%s)' \
' match' % (input_path, qiime_type)
click.echo(CONFIG.cfg_style('success', msg))
def view(visualization_path, index_extension):
# Guard headless envs from having to import anything large
import sys
from q2cli.core.config import CONFIG
if not os.getenv("DISPLAY") and sys.platform != "darwin":
raise click.UsageError(
'Visualization viewing is currently not supported in headless '
'environments. You can view Visualizations (and Artifacts) at '
'https://view.qiime2.org, or move the Visualization to an '
'environment with a display and view it with `qiime tools view`.')
import zipfile
import qiime2.sdk
if index_extension.startswith('.'):
index_extension = index_extension[1:]
try:
visualization = qiime2.sdk.Visualization.load(visualization_path)
# TODO: currently a KeyError is raised if a zipped file that is not a
# QIIME 2 result is passed. This should be handled better by the framework.
except (zipfile.BadZipFile, KeyError, TypeError):
raise click.BadParameter(
'%s is not a QIIME 2 Visualization. Only QIIME 2 Visualizations '
'can be viewed.' % visualization_path)
index_paths = visualization.get_index_paths(relative=False)
if index_extension not in index_paths:
raise click.BadParameter(
'No index %s file is present in the archive. Available index '
'extensions are: %s' %
(index_extension, ', '.join(index_paths.keys())))
else:
index_path = index_paths[index_extension]
launch_status = click.launch(index_path)
if launch_status != 0:
click.echo(CONFIG.cfg_style(
'error', 'Viewing visualization '
'failed while attempting to open '
f'{index_path}'),
err=True)
else:
while True:
click.echo(
"Press the 'q' key, Control-C, or Control-D to quit. This "
"view may no longer be accessible or work correctly after "
"quitting.",
nl=False)
# There is currently a bug in click.getchar where translation
# of Control-C and Control-D into KeyboardInterrupt and
# EOFError (respectively) does not work on Python 3. The code
# here should continue to work as expected when the bug is
# fixed in Click.
#
# https://github.com/pallets/click/issues/583
try:
char = click.getchar()
click.echo()
if char in {'q', '\x03', '\x04'}:
break
except (KeyboardInterrupt, EOFError):
break
def write_option(self, ctx, formatter, opt, record, border, COL_SPACING=2):
import itertools
from q2cli.core.config import CONFIG
full_width = formatter.width - formatter.current_indent
indent_text = ' ' * formatter.current_indent
opt_text, help_text = record
opt_text_secondary = None
if type(opt_text) is tuple:
opt_text, opt_text_secondary = opt_text
help_text, requirements = self._clean_help(help_text)
type_placement = None
type_repr = None
type_indent = 2 * indent_text
if hasattr(opt.type, 'get_type_repr'):
type_repr = opt.type.get_type_repr(opt)
if type_repr is not None:
if len(type_repr) <= border - len(type_indent):
type_placement = 'under'
else:
type_placement = 'beside'
if len(opt_text) > border:
lines = simple_wrap(opt_text, full_width)
else:
lines = [opt_text.split(' ')]
if opt_text_secondary is not None:
lines.append(opt_text_secondary.split(' '))
to_write = []
for tokens in lines:
dangling_edge = formatter.current_indent
styled = []
for token in tokens:
dangling_edge += len(token) + 1
if token.startswith('--'):
token = CONFIG.cfg_style('option',
token,
required=opt.required)
styled.append(token)
line = indent_text + ' '.join(styled)
to_write.append(line)
formatter.write('\n'.join(to_write))
dangling_edge -= 1
if type_placement == 'beside':
lines = simple_wrap(type_repr,
formatter.width - len(type_indent),
start_col=dangling_edge - 1)
to_write = []
first_iter = True
for tokens in lines:
line = ' '.join(tokens)
if first_iter:
dangling_edge += 1 + len(line)
line = " " + CONFIG.cfg_style('type', line)
first_iter = False
else:
dangling_edge = len(type_indent) + len(line)
line = type_indent + CONFIG.cfg_style('type', line)
to_write.append(line)
formatter.write('\n'.join(to_write))
if dangling_edge + 1 > border + COL_SPACING:
formatter.write('\n')
left_col = []
else:
padding = ' ' * (border + COL_SPACING - dangling_edge)
formatter.write(padding)
dangling_edge += len(padding)
left_col = [''] # jagged start
if type_placement == 'under':
padding = ' ' * (border + COL_SPACING - len(type_repr) -
len(type_indent))
line = ''.join(
[type_indent,
CONFIG.cfg_style('type', type_repr), padding])
left_col.append(line)
if hasattr(opt, 'meta_help') and opt.meta_help is not None:
meta_help = simple_wrap(opt.meta_help,
border - len(type_indent) - 1)
for idx, line in enumerate([' '.join(t) for t in meta_help]):
if idx == 0:
line = type_indent + '(' + line
else:
line = type_indent + ' ' + line
if idx == len(meta_help) - 1:
line += ')'
line += ' ' * (border - len(line) + COL_SPACING)
left_col.append(line)
right_col = simple_wrap(help_text,
formatter.width - border - COL_SPACING)
right_col = [
' '.join(self._color_important(tokens, ctx))
for tokens in right_col
]
to_write = []
for left, right in itertools.zip_longest(left_col,
right_col,
fillvalue=' ' *
(border + COL_SPACING)):
to_write.append(left)
if right.strip():
to_write[-1] += right
formatter.write('\n'.join(to_write))
if requirements is None:
formatter.write('\n')
else:
if to_write:
if len(to_write) > 1 or ((not left_col) or left_col[0] != ''):
dangling_edge = 0
dangling_edge += click.formatting.term_len(to_write[-1])
else:
pass # dangling_edge is still correct
if dangling_edge + 1 + len(requirements) > formatter.width:
formatter.write('\n')
pad = formatter.width - len(requirements)
else:
pad = formatter.width - len(requirements) - dangling_edge
formatter.write((' ' * pad) +
CONFIG.cfg_style('default_arg', requirements) +
'\n')
def format_usage(self, ctx, formatter):
from q2cli.core.config import CONFIG
"""Writes the usage line into the formatter."""
pieces = self.collect_usage_pieces(ctx)
formatter.write_usage(CONFIG.cfg_style('command', ctx.command_path),
' '.join(pieces))
def __call__(self, **kwargs):
"""Called when user hits return, **kwargs are Dict[click_names, Obj]"""
import os
import qiime2.util
output_dir = kwargs.pop('output_dir')
verbose = kwargs.pop('verbose')
if verbose is None:
verbose = False
quiet = False
elif verbose:
quiet = False
else:
quiet = True
arguments = {}
init_outputs = {}
for key, value in kwargs.items():
prefix, *parts = key.split('_')
key = '_'.join(parts)
if prefix == 'o':
if value is None:
value = os.path.join(output_dir, key)
init_outputs[key] = value
elif prefix == 'm':
arguments[key[:-len('_file')]] = value
else:
arguments[key] = value
outputs = self._order_outputs(init_outputs)
action = self._get_action()
# `qiime2.util.redirected_stdio` defaults to stdout/stderr when
# supplied `None`.
log = None
if not verbose:
import tempfile
log = tempfile.NamedTemporaryFile(prefix='qiime2-q2cli-err-',
suffix='.log',
delete=False,
mode='w')
if action.deprecated:
# We don't need to worry about redirecting this, since it should a)
# always be shown to the user and b) the framework-originated
# FutureWarning will wind up in the log file in quiet mode.
msg = ('Plugin warning from %s:\n\n%s is deprecated and '
'will be removed in a future version of this plugin.' %
(q2cli.util.to_cli_name(self.plugin['name']), self.name))
click.echo(CONFIG.cfg_style('warning', msg))
cleanup_logfile = False
try:
with qiime2.util.redirected_stdio(stdout=log, stderr=log):
results = action(**arguments)
except Exception as e:
header = ('Plugin error from %s:' %
q2cli.util.to_cli_name(self.plugin['name']))
if verbose:
# log is not a file
log = 'stderr'
q2cli.util.exit_with_error(e, header=header, traceback=log)
else:
cleanup_logfile = True
finally:
# OS X will reap temporary files that haven't been touched in
# 36 hours, double check that the log is still on the filesystem
# before trying to delete. Otherwise this will fail and the
# output won't be written.
if log and cleanup_logfile and os.path.exists(log.name):
log.close()
os.remove(log.name)
if output_dir is not None:
os.makedirs(output_dir)
for result, output in zip(results, outputs):
path = result.save(output)
if not quiet:
click.echo(
CONFIG.cfg_style('success',
'Saved %s to: %s' % (result.type, path)))
