New upstream version 2019.7.0 (7b94726b) · Commits · Debian Med / q2cli

q2cli/_version.py

+3 −3

Original line number	Diff line number	Diff line
		@@ -23,9 +23,9 @@ def get_keywords():
		# setup.py/versioneer.py will grep for the variable names, so they must
		# each be defined on a line of their own. _version.py will just call
		# get_keywords().
		git_refnames = " (tag: 2019.4.0)"
		git_full = "dc80fad32777035091692ce1083088380a6ac509"
		git_date = "2019-05-03 04:14:45 +0000"
		git_refnames = " (tag: 2019.7.0)"
		git_full = "06b978c96c8efce8be0c8213e744cb4b389f2bc6"
		git_date = "2019-07-30 18:15:53 +0000"
		keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
		return keywords

q2cli/builtin/dev.py

+110 −0

Original line number	Diff line number	Diff line
		@@ -7,6 +7,7 @@
		# ----------------------------------------------------------------------------

		import click

		from q2cli.click.command import ToolCommand, ToolGroupCommand


		@@ -29,3 +30,112 @@ def dev():
		def refresh_cache():
		import q2cli.core.cache
		q2cli.core.cache.CACHE.refresh()


		import_theme_help = \
		("Allows for customization of q2cli's command line styling based on an "
		"imported .theme (INI formatted) file. If you are unfamiliar with .ini "
		"formatted files look here https://en.wikipedia.org/wiki/INI_file."
		"\n"
		"\n"
		"The .theme file allows you to customize text on the basis of what that "
		"text represents with the following supported text types: command, "
		"option, type, default_arg, required, emphasis, problem, warning, error, "
		"and success. These will be your headers in the '[]' brackets. "
		"\n"
		"\n"
		"`command` refers to the name of the command you issued. `option` refers "
		"to the arguments you give to the command when running it. `type` refers "
		"to the QIIME 2 semantic typing of these arguments (where applicable). "
		"`default_arg` refers to the label next to the argument indicating its "
		"default value (where applicable), and if it is required (where "
		"applicable). `required` refers to any arguments that must be passed to "
		"the command for it to work and gives them special formatting on top of "
		"your normal `option` formatting. `emphasis` refers to any emphasized "
		"pieces of text within help text. `problem` refers to the text informing "
		"you there were issues with the command. `warning` refers to the text "
		"for non-fatal issues while `error` refers to the text for fatal issues."
		"`success` refers to text indicating a process completed as expected."
		"\n"
		"\n"
		"Depending on what your terminal supports, some or all of the following "
		"pieces of the text's formatting may be customized: bold, dim (if true "
		"the text's brightness is reduced), underline, blink, reverse (if true "
		"foreground and background colors are reversed), and finally fg "
		"(foreground color) and bg (background color). The first five may each "
		"be either true or false, while the colors may be set to any of the "
		"following: black, red, green, yellow, blue, magenta, cyan, white, "
		"bright_black, bright_red, bright_green, bright_yellow, bright_blue, "
		"bright_magenta, bright_cyan, or bright_white.")


		@dev.command(name='import-theme',
		short_help='Install new command line theme.',
		help=import_theme_help,
		cls=ToolCommand)
		@click.option('--theme', required=True,
		type=click.Path(exists=True, file_okay=True,
		dir_okay=False, readable=True),
		help='Path to file containing new theme info')
		def import_theme(theme):
		import os
		import shutil
		from configparser import Error

		import q2cli.util
		from q2cli.core.config import CONFIG

		try:
		CONFIG.parse_file(theme)
		except Error as e:
		# If they tried to change [error] in a valid manner before we hit our
		# parsing error, we don't want to use their imported error settings
		CONFIG.styles = CONFIG.get_default_styles()
		header = 'Something went wrong while parsing your theme: '
		q2cli.util.exit_with_error(e, header=header, traceback=None)
		shutil.copy(theme, os.path.join(q2cli.util.get_app_dir(),
		'cli-colors.theme'))


		@dev.command(name='export-default-theme',
		short_help='Export the default settings.',
		help='Create a .theme (INI formatted) file from the default '
		'settings at the specified filepath.',
		cls=ToolCommand)
		@click.option('--output-path', required=True,
		type=click.Path(exists=False, file_okay=True,
		dir_okay=False, readable=True),
		help='Path to output the config to')
		def export_default_theme(output_path):
		import configparser
		from q2cli.core.config import CONFIG

		parser = configparser.ConfigParser()
		parser.read_dict(CONFIG.get_default_styles())
		with open(output_path, 'w') as fh:
		parser.write(fh)


		def abort_if_false(ctx, param, value):
		if not value:
		ctx.abort()


		@dev.command(name='reset-theme',
		short_help='Reset command line theme to default.',
		help="Reset command line theme to default. Requres the '--yes' "
		"parameter to be passed asserting you do want to reset.",
		cls=ToolCommand)
		@click.option('--yes', is_flag=True, callback=abort_if_false,
		expose_value=False,
		prompt='Are you sure you want to reset your theme?')
		def reset_theme():
		import os
		import q2cli.util

		path = os.path.join(q2cli.util.get_app_dir(), 'cli-colors.theme')
		if os.path.exists(path):
		os.unlink(path)
		click.echo('Theme reset.')
		else:
		click.echo('Theme was already default.')

q2cli/builtin/tools.py

+26 −17

Original line number	Diff line number	Diff line
		@@ -46,6 +46,7 @@ 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):
		@@ -56,7 +57,7 @@ def export_data(input_path, output_path, output_format):
		else:
		if isinstance(result, qiime2.sdk.Visualization):
		error = '--output-format cannot be used with visualizations'
		click.secho(error, fg='red', bold=True, err=True)
		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))
		@@ -73,7 +74,7 @@ def export_data(input_path, output_path, output_format):
		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.secho(success, fg='green')
		click.echo(CONFIG.cfg_style('success', success))


		def show_importable_types(ctx, param, value):
		@@ -147,6 +148,7 @@ def show_importable_formats(ctx, param, value):
		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)
		@@ -163,7 +165,7 @@ def import_data(type, input_path, output_path, input_format):
		success = 'Imported %s as %s to %s' % (input_path,
		input_format,
		output_path)
		click.secho(success, fg='green')
		click.echo(CONFIG.cfg_style('success', success))


		@tools.command(short_help='Take a peek at a QIIME 2 Artifact or '
		@@ -176,16 +178,17 @@ def import_data(type, input_path, output_path, input_format):
		metavar=_COMBO_METAVAR)
		def peek(path):
		import qiime2.sdk
		from q2cli.core.config import CONFIG

		metadata = qiime2.sdk.Result.peek(path)

		click.secho("UUID: ", fg="green", nl=False)
		click.secho(metadata.uuid)
		click.secho("Type: ", fg="green", nl=False)
		click.secho(metadata.type)
		click.echo(CONFIG.cfg_style('type', "UUID")+": ", nl=False)
		click.echo(metadata.uuid)
		click.echo(CONFIG.cfg_style('type', "Type")+": ", nl=False)
		click.echo(metadata.type)
		if metadata.format is not None:
		click.secho("Data format: ", fg="green", nl=False)
		click.secho(metadata.format)
		click.echo(CONFIG.cfg_style('type', "Data format")+": ", nl=False)
		click.echo(metadata.format)


		@tools.command('inspect-metadata',
		@@ -274,7 +277,7 @@ def _load_metadata(path):
		@tools.command(short_help='View a QIIME 2 Visualization.',
		help="Displays a QIIME 2 Visualization until the command "
		"exits. To open a QIIME 2 Visualization so it can be "
		"used after the command exits, use 'qiime extract'.",
		"used after the command exits, use 'qiime tools extract'.",
		cls=ToolCommand)
		@click.argument('visualization-path', metavar='VISUALIZATION',
		type=click.Path(exists=True, file_okay=True, dir_okay=False,
		@@ -285,6 +288,7 @@ def _load_metadata(path):
		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 '
		@@ -310,15 +314,16 @@ def view(visualization_path, index_extension):

		if index_extension not in index_paths:
		raise click.BadParameter(
		'No index %s file with is present in the archive. Available index '
		'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('Viewing visualization failed while attempting to '
		'open %s' % index_path, err=True)
		click.echo(CONFIG.cfg_style('error', 'Viewing visualization '
		'failed while attempting to open '
		f'{index_path}'), err=True)
		else:
		while True:
		click.echo(
		@@ -362,6 +367,7 @@ def view(visualization_path, index_extension):
		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)
		@@ -371,7 +377,7 @@ def extract(input_path, output_path):
		'Visualizations can be extracted.' % input_path)
		else:
		success = 'Extracted %s to directory %s' % (input_path, extracted_dir)
		click.secho(success, fg='green')
		click.echo(CONFIG.cfg_style('success', success))


		@tools.command(short_help='Validate data in a QIIME 2 Artifact.',
		@@ -393,6 +399,7 @@ def extract(input_path, output_path):
		default='max', show_default=True)
		def validate(path, level):
		import qiime2.sdk
		from q2cli.core.config import CONFIG

		try:
		result = qiime2.sdk.Result.load(path)
		@@ -411,8 +418,8 @@ def validate(path, level):
		'validate result %s:' % path)
		q2cli.util.exit_with_error(e, header=header)
		else:
		click.secho('Result %s appears to be valid at level=%s.'
		% (path, level), fg="green")
		click.echo(CONFIG.cfg_style('success', f'Result {path} appears to be '
		f'valid at level={level}.'))


		@tools.command(short_help='Print citations for a QIIME 2 result.',
		@@ -425,6 +432,7 @@ def validate(path, level):
		def citations(path):
		import qiime2.sdk
		import io
		from q2cli.core.config import CONFIG
		ctx = click.get_current_context()

		try:
		@@ -439,5 +447,6 @@ def citations(path):
		click.echo(fh.getvalue(), nl=False)
		ctx.exit(0)
		else:
		click.secho('No citations found.', fg='yellow', err=True)
		click.echo(CONFIG.cfg_style('problem', 'No citations found.'),
		err=True)
		ctx.exit(1)

q2cli/click/command.py

+20 −30

Original line number	Diff line number	Diff line
		@@ -38,6 +38,7 @@ class BaseCommandMixin:
		# c6042bf2607c5be22b1efef2e42a94ffd281434c/click/core.py#L934 >
		# Copyright (c) 2014 by the Pallets team.
		def parse_args(self, ctx, args):
		from q2cli.core.config import CONFIG
		if isinstance(self, click.MultiCommand):
		return super().parse_args(ctx, args)

		@@ -71,14 +72,15 @@ class BaseCommandMixin:
		problems = 'There were some problems with the command:'
		else:
		problems = 'There was a problem with the command:'
		click.secho(problems.center(78, ' '), fg='yellow', err=True)
		click.echo(CONFIG.cfg_style('problem',
		problems.center(78, ' ')), err=True)
		for idx, e in enumerate(errors, 1):
		msg = click.formatting.wrap_text(
		e.format_message(),
		initial_indent=' (%d/%d%s) ' % (idx, len(errors),
		'?' if skip_rest else ''),
		subsequent_indent=' ')
		click.secho(msg, err=True, fg='red', bold=True)
		click.secho(CONFIG.cfg_style('error', msg), err=True)
		ctx.exit(1)

		ctx.args = args
		@@ -113,12 +115,14 @@ class BaseCommandMixin:
		# /c6042bf2607c5be22b1efef2e42a94ffd281434c/click/core.py#L830 >
		# Copyright (c) 2014 by the Pallets team.
		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(_style_command(ctx.command_path),
		formatter.write_usage(CONFIG.cfg_style('command', ctx.command_path),
		' '.join(pieces))

		def format_options(self, ctx, formatter, COL_MAX=23, COL_MIN=10):
		from q2cli.core.config import CONFIG
		# write options
		opt_groups = {}
		records = []
		@@ -167,7 +171,7 @@ class BaseCommandMixin:
		rows = []
		for subcommand, cmd in commands:
		help = cmd.get_short_help_str(limit)
		rows.append((_style_command(subcommand), help))
		rows.append((CONFIG.cfg_style('command', subcommand), help))

		if rows:
		with formatter.section(click.style('Commands', bold=True)):
		@@ -175,6 +179,7 @@ class BaseCommandMixin:

		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
		@@ -208,7 +213,8 @@ class BaseCommandMixin:
		for token in tokens:
		dangling_edge += len(token) + 1
		if token.startswith('--'):
		token = _style_option(token, required=opt.required)
		token = CONFIG.cfg_style('option', token,
		required=opt.required)
		styled.append(token)
		line = indent_text + ' '.join(styled)
		to_write.append(line)
		@@ -224,11 +230,11 @@ class BaseCommandMixin:
		line = ' '.join(tokens)
		if first_iter:
		dangling_edge += 1 + len(line)
		line = " " + _style_type(line)
		line = " " + CONFIG.cfg_style('type', line)
		first_iter = False
		else:
		dangling_edge = len(type_indent) + len(line)
		line = type_indent + _style_type(line)
		line = type_indent + CONFIG.cfg_style('type', line)
		to_write.append(line)
		formatter.write('\n'.join(to_write))

		@@ -244,7 +250,8 @@ class BaseCommandMixin:
		if type_placement == 'under':
		padding = ' ' * (border + COL_SPACING
		- len(type_repr) - len(type_indent))
		line = ''.join([type_indent, _style_type(type_repr), padding])
		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:
		@@ -290,10 +297,13 @@ class BaseCommandMixin:
		else:
		pad = formatter.width - len(requirements) - dangling_edge

		formatter.write((' ' * pad) + _style_reqs(requirements) + '\n')
		formatter.write(
		(' ' * pad) + CONFIG.cfg_style(
		'default_arg', requirements) + '\n')

		def _color_important(self, tokens, ctx):
		import re
		from q2cli.core.config import CONFIG

		for t in tokens:
		if '_' in t:
		@@ -301,7 +311,7 @@ class BaseCommandMixin:
		if re.sub(r'[^\w]', '', t) in names:
		m = re.search(r'(\w+)', t)
		word = t[m.start():m.end()]
		word = _style_emphasis(word.replace('_', '-'))
		word = CONFIG.cfg_style('emphasis', word.replace('_', '-'))
		token = t[:m.start()] + word + t[m.end():]
		yield token
		continue
		@@ -353,23 +363,3 @@ def simple_wrap(text, target, start_col=0):
		current_width += 1 + token_len

		return result


		def _style_option(text, required=False):
		return click.style(text, fg='blue', underline=required)


		def _style_type(text):
		return click.style(text, fg='green')


		def _style_reqs(text):
		return click.style(text, fg='magenta')


		def _style_command(text):
		return _style_option(text)


		def _style_emphasis(text):
		return click.style(text, underline=True)

q2cli/click/type.py

+27 −4

Original line number	Diff line number	Diff line
		@@ -46,6 +46,10 @@ class OutDirType(click.Path):
		return value


		class ControlFlowException(Exception):
		pass


		class QIIME2Type(click.ParamType):
		def __init__(self, type_ast, type_repr, is_output=False):
		self.type_repr = type_repr
		@@ -94,14 +98,33 @@ class QIIME2Type(click.ParamType):

		def _convert_input(self, value, param, ctx):
		import os
		import tempfile
		import qiime2.sdk
		import qiime2.sdk.util

		try:
		try:
		result = qiime2.sdk.Result.load(value)
		except OSError as e:
		if e.errno == 28:
		temp = tempfile.tempdir
		self.fail(f'There was not enough space left on {temp!r} '
		f'to extract the artifact {value!r}. '
		'(Try setting $TMPDIR to a directory with '
		'more space, or increasing the size of '
		f'{temp!r})', param, ctx)
		else:
		raise ControlFlowException
		except ValueError as e:
		if 'does not exist' in str(e):
		self.fail(f'{value!r} is not a valid filepath', param, ctx)
		else:
		raise ControlFlowException
		except Exception:
		self.fail('%r is not a QIIME 2 Artifact (.qza)' % value,
		param, ctx)
		raise ControlFlowException
		except ControlFlowException:
		self.fail('%r is not a QIIME 2 Artifact (.qza)' % value, param,
		ctx)

		if isinstance(result, qiime2.sdk.Visualization):
		maybe = value[:-1] + 'a'