def select(self):
"""Toggles selection of the current label."""
LOGGER.debug('Select command triggered.')
# get current label
label, cur_y = self.get_current_label()
# toggle selection
if label not in self.selection:
LOGGER.info("Adding '%s' to the selection.", label)
self.selection.add(label)
# Note, that we use an additional two spaces to attempt to uniquely identify the label
# in the list mode. Otherwise it might be possible that the same text (as used for the
# label) can occur elsewhere in the buffer.
# We do not need this outside of the list view because then the line indexed by `cur_y`
# will surely only include the one label which we actually want to operate on.
offset = ' ' if self.list_mode == -1 else ''
self.buffer.replace(
cur_y, label + offset,
CONFIG.get_ansi_color('selection') + label + '\x1b[0m' +
offset)
else:
LOGGER.info("Removing '%s' from the selection.", label)
self.selection.remove(label)
self.buffer.replace(
cur_y,
CONFIG.get_ansi_color('selection') + label + '\x1b[0m', label)
# update buffer view
self.buffer.view(self.viewport,
self.visible,
self.width - 1,
ansi_map=self.ANSI_MAP)
def test_add_overwrite_label():
"""Test add command while specifying a label manually.
Regression test against #4.
"""
# use temporary config
tmp_config = "[DATABASE]\nfile=/tmp/cobib_test_database.yaml\n"
with open('/tmp/cobib_test_config.ini', 'w') as file:
file.write(tmp_config)
CONFIG.set_config(Path('/tmp/cobib_test_config.ini'))
# ensure database file exists and is empty
open('/tmp/cobib_test_database.yaml', 'w').close()
# freshly read in database to overwrite anything that was read in during setup()
read_database(fresh=True)
# add some data
commands.AddCommand().execute(['-b', './test/example_literature.bib'])
# add potentially duplicate entry
commands.AddCommand().execute([
'-b', './test/example_duplicate_entry.bib', '--label',
'duplicate_resolver'
])
# compare with reference file
with open('./test/example_literature.yaml', 'r') as expected:
true_lines = expected.readlines()
with open('./test/example_duplicate_entry.yaml', 'r') as extra:
true_lines += extra.readlines()
with open('/tmp/cobib_test_database.yaml', 'r') as file:
for line, truth in zip_longest(file, true_lines):
assert line == truth
# clean up file system
os.remove('/tmp/cobib_test_database.yaml')
os.remove('/tmp/cobib_test_config.ini')
def test_tui_quit_prompt(setting, keys):
"""Test the prompt_before_quit setting of the TUI."""
# ensure configuration is empty
CONFIG.config = {}
root = os.path.abspath(os.path.dirname(__file__))
CONFIG.set_config(Path(root + '/../cobib/docs/debug.ini'))
# set prompt_before_quit setting
CONFIG.config['TUI']['prompt_before_quit'] = setting
read_database()
test_tui(None, keys, assert_quit, {'prompt': setting})
def test_tui_scrolling(keys, assertion, assertion_kwargs):
"""Test TUI scrolling behavior."""
# ensure configuration is empty
CONFIG.config = {}
root = os.path.abspath(os.path.dirname(__file__))
CONFIG.set_config(Path(root + '/../cobib/docs/debug.ini'))
# overwrite database file
CONFIG.config['DATABASE']['file'] = './test/scrolling_database.yaml'
read_database()
test_tui(None, keys, assertion, assertion_kwargs)
def setup():
"""Setup."""
# ensure configuration is empty
CONFIG.config = {}
root = os.path.abspath(os.path.dirname(__file__))
CONFIG.set_config(Path(root + '/../cobib/docs/debug.ini'))
# NOTE: normally you would never trigger an Add command before reading the database but in this
# controlled testing scenario we can be certain that this is fine
AddCommand().execute(['-b', './test/dummy_scrolling_entry.bib'])
read_database()
yield setup
DeleteCommand().execute(['dummy_entry_for_scroll_testing'])
def test_set_config(setup):
"""Test config setting.
Args:
setup: runs pytest fixture.
"""
# from setup
assert CONFIG.config['DATABASE'][
'file'] == './test/example_literature.yaml'
# change back to default
CONFIG.set_config()
assert CONFIG.config['DATABASE']['file'] == \
os.path.expanduser('~/.local/share/cobib/literature.yaml')
def test_tui_open_menu():
"""Test the open prompt menu for multiple associated files."""
# ensure configuration is empty
CONFIG.config = {}
root = os.path.abspath(os.path.dirname(__file__))
CONFIG.set_config(Path(root + '/../cobib/docs/debug.ini'))
# NOTE: normally you would never trigger an Add command before reading the database but in this
# controlled testing scenario we can be certain that this is fine
AddCommand().execute(['-b', './test/dummy_multi_file_entry.bib'])
read_database()
try:
test_tui(None, 'o', assert_open, {})
finally:
DeleteCommand().execute(['dummy_multi_file_entry'])
def test_tui_config_color():
"""Test TUI color configuration."""
# ensure configuration is empty
CONFIG.config = {}
root = os.path.abspath(os.path.dirname(__file__))
CONFIG.set_config(Path(root + '/../cobib/docs/debug.ini'))
# overwrite color configuration
CONFIG.config['COLORS']['top_statusbar_bg'] = 'red'
CONFIG.config['COLORS']['top_statusbar_fg'] = 'blue'
CONFIG.config['COLORS']['bottom_statusbar_bg'] = 'green'
CONFIG.config['COLORS']['bottom_statusbar_fg'] = 'magenta'
CONFIG.config['COLORS']['cursor_line_bg'] = 'white'
CONFIG.config['COLORS']['cursor_line_fg'] = 'black'
read_database()
test_tui(None, '', assert_config_color, {'colors': CONFIG.config['COLORS']})
def list_tags(args=None):
"""List all tags.
Args:
args (dict, optional): dictionary of keyword arguments.
Returns:
A list of all available tags in the database.
"""
if not args:
args = {}
CONFIG.set_config(args.get('config', None))
read_database()
tags = list(CONFIG.config['BIB_DATA'].keys())
return tags
def tui(tui):
"""See base class."""
LOGGER.debug('Show command triggered from TUI.')
# get current label
label, cur_y = tui.get_current_label()
# populate buffer with entry data
LOGGER.debug('Clearing current buffer contents.')
tui.buffer.clear()
ShowCommand().execute([label], out=tui.buffer)
tui.buffer.split()
if label in tui.selection:
LOGGER.debug('Current entry is selected. Applying highlighting.')
tui.buffer.replace(0, label, CONFIG.get_ansi_color('selection') + label + '\x1b[0m')
LOGGER.debug('Populating buffer with ShowCommand result.')
tui.buffer.view(tui.viewport, tui.visible, tui.width-1, ansi_map=tui.ANSI_MAP)
# reset current cursor position
tui.top_line = 0
tui.current_line = 0
# update top statusbar
tui.topstatus = "CoBib v{} - {}".format(__version__, label)
tui.statusbar(tui.topbar, tui.topstatus)
# enter show menu
tui.list_mode = cur_y
tui.inactive_commands = ['Add', 'Filter', 'Search', 'Show', 'Sort']
def test_tui_config_keys(command, key):
"""Test TUI key binding configuration."""
# ensure configuration is empty
CONFIG.config = {}
root = os.path.abspath(os.path.dirname(__file__))
CONFIG.set_config(Path(root + '/../cobib/docs/debug.ini'))
# overwrite key binding configuration
CONFIG.config['KEY_BINDINGS'][command] = key
# NOTE: normally you would never trigger an Add command before reading the database but in this
# controlled testing scenario we can be certain that this is fine
AddCommand().execute(['-b', './test/dummy_scrolling_entry.bib'])
read_database()
try:
test_tui(None, key, assert_show, {})
finally:
DeleteCommand().execute(['dummy_entry_for_scroll_testing'])
def test_init():
"""Test init command."""
# use temporary config
tmp_config = "[DATABASE]\nfile=/tmp/cobib_test_database.yaml\n"
with open('/tmp/cobib_test_config.ini', 'w') as file:
file.write(tmp_config)
CONFIG.set_config(Path('/tmp/cobib_test_config.ini'))
# store current time
now = float(datetime.now().timestamp())
commands.InitCommand().execute({})
# check creation time of temporary database file
ctime = os.stat('/tmp/cobib_test_database.yaml').st_ctime
# assert these times are close
assert ctime - now < 0.1 or now - ctime < 0.1
# clean up file system
os.remove('/tmp/cobib_test_database.yaml')
os.remove('/tmp/cobib_test_config.ini')
def test_init_force():
"""Test init can be forced when database file exists."""
# use temporary config
tmp_config = "[DATABASE]\nfile=/tmp/cobib_test_database.yaml\n"
with open('/tmp/cobib_test_config.ini', 'w') as file:
file.write(tmp_config)
CONFIG.set_config(Path('/tmp/cobib_test_config.ini'))
# fill database file
with open('/tmp/cobib_test_database.yaml', 'w') as file:
file.write('test')
# try running init
commands.InitCommand().execute(['-f'])
# check init was forced and database file was overwritten
assert os.stat('/tmp/cobib_test_database.yaml').st_size == 0
# clean up file system
os.remove('/tmp/cobib_test_database.yaml')
os.remove('/tmp/cobib_test_config.ini')
def list_filters(args=None):
"""List all filters.
Args:
args (dict, optional): dictionary of keyword arguments.
Returns:
A list of all field names available for filtering.
"""
if not args:
args = {}
CONFIG.set_config(args.get('config', None))
read_database()
filters = set()
for entry in CONFIG.config['BIB_DATA'].values():
filters.update(entry.data.keys())
return filters
def test_init_safe():
"""Test init aborts when database file exists."""
# use temporary config
tmp_config = "[DATABASE]\nfile=/tmp/cobib_test_database.yaml\n"
with open('/tmp/cobib_test_config.ini', 'w') as file:
file.write(tmp_config)
CONFIG.set_config(Path('/tmp/cobib_test_config.ini'))
# fill database file
with open('/tmp/cobib_test_database.yaml', 'w') as file:
file.write('test')
# try running init
commands.InitCommand().execute({})
# check init aborted and database file still contains 'test'
with open('/tmp/cobib_test_database.yaml', 'r') as file:
assert file.read() == 'test'
# clean up file system
os.remove('/tmp/cobib_test_database.yaml')
os.remove('/tmp/cobib_test_config.ini')
def test_add():
"""Test add command."""
# use temporary config
tmp_config = "[DATABASE]\nfile=/tmp/cobib_test_database.yaml\n"
with open('/tmp/cobib_test_config.ini', 'w') as file:
file.write(tmp_config)
CONFIG.set_config(Path('/tmp/cobib_test_config.ini'))
# ensure database file exists and is empty
open('/tmp/cobib_test_database.yaml', 'w').close()
# freshly read in database to overwrite anything that was read in during setup()
read_database(fresh=True)
# add some data
commands.AddCommand().execute(['-b', './test/example_literature.bib'])
# compare with reference file
with open('/tmp/cobib_test_database.yaml', 'r') as file:
with open('./test/example_literature.yaml', 'r') as expected:
for line, truth in zip_longest(file, expected):
assert line == truth
# clean up file system
os.remove('/tmp/cobib_test_database.yaml')
os.remove('/tmp/cobib_test_config.ini')
def test_delete(labels):
"""Test delete command."""
# use temporary config
tmp_config = "[DATABASE]\nfile=/tmp/cobib_test_database.yaml\n"
with open('/tmp/cobib_test_config.ini', 'w') as file:
file.write(tmp_config)
CONFIG.set_config(Path('/tmp/cobib_test_config.ini'))
# copy example database to configured location
copyfile(Path('./test/example_literature.yaml'),
Path('/tmp/cobib_test_database.yaml'))
# delete some data
# NOTE: for testing simplicity we delete the last entry
commands.DeleteCommand().execute(labels)
with open('/tmp/cobib_test_database.yaml', 'r') as file:
with open('./test/example_literature.yaml', 'r') as expected:
# NOTE: do NOT use zip_longest to omit last entry (thus, we deleted the last one)
for line, truth in zip(file, expected):
assert line == truth
with pytest.raises(StopIteration):
file.__next__()
# clean up file system
os.remove('/tmp/cobib_test_database.yaml')
os.remove('/tmp/cobib_test_config.ini')
def tui(tui):
"""See base class."""
LOGGER.debug('Search command triggered from TUI.')
tui.buffer.clear()
# handle input via prompt
command, results = tui.execute_command('search', out=tui.buffer)
if tui.buffer.lines and results is not None:
hits, labels = results
tui.list_mode, _ = tui.viewport.getyx()
tui.buffer.split()
LOGGER.debug('Applying selection highlighting in search results.')
for label in labels:
if label not in tui.selection:
continue
# we match the label including its 'search_label' highlight to ensure that we really
# only match this specific occurrence of whatever the label may be
tui.buffer.replace(range(tui.buffer.height),
CONFIG.get_ansi_color('search_label') + label + '\x1b[0m',
CONFIG.get_ansi_color('search_label') +
CONFIG.get_ansi_color('selection') + label + '\x1b[0m\x1b[0m')
LOGGER.debug('Populating viewport with search results.')
tui.buffer.view(tui.viewport, tui.visible, tui.width-1, ansi_map=tui.ANSI_MAP)
# reset current cursor position
LOGGER.debug('Resetting cursor position to top.')
tui.top_line = 0
tui.current_line = 0
# update top statusbar
tui.topstatus = "CoBib v{} - {} hit{}".format(__version__, hits,
"s" if hits > 1 else "")
tui.statusbar(tui.topbar, tui.topstatus)
tui.inactive_commands = ['Add', 'Filter', 'Sort']
elif command[1:]:
msg = f"No search hits for '{shlex.join(command[1:])}'!"
LOGGER.info(msg)
tui.prompt_print(msg)
tui.update_list()
def colors():
"""Initialize the color pairs for the curses TUI."""
# Start colors in curses
curses.start_color()
# parse user color configuration
color_cfg = CONFIG.config['COLORS']
colors = {col: {} for col in TUI.COLOR_NAMES}
for attr, col in color_cfg.items():
if attr in TUI.COLOR_VALUES.keys():
if not curses.can_change_color():
# cannot change curses default colors
LOGGER.warning(
'Curses cannot change the default colors. Skipping color setup.'
)
continue
# update curses-internal color with HEX-color
rgb_color = tuple(
int(col.strip('#')[i:i + 2], 16) for i in (0, 2, 4))
# curses colors range from 0 to 1000
curses_color = tuple(col * 1000 // 255 for col in rgb_color)
curses.init_color(TUI.COLOR_VALUES[attr], *curses_color)
else:
if attr[:-3] not in TUI.COLOR_NAMES:
LOGGER.warning(
'Detected unknown TUI color name specification: %s',
attr[:-3])
continue
colors[attr[:-3]][attr[-2:]] = col
# initialize color pairs for TUI elements
for idx, attr in enumerate(TUI.COLOR_NAMES):
foreground = colors[attr].get('fg', 'white')
background = colors[attr].get('bg', 'black')
LOGGER.debug('Initiliazing color pair %d for %s', idx + 1, attr)
curses.init_pair(idx + 1, TUI.COLOR_VALUES[foreground],
TUI.COLOR_VALUES[background])
LOGGER.debug('Adding ANSI color code for %s', attr)
TUI.ANSI_MAP[CONFIG.get_ansi_color(
attr)] = TUI.COLOR_NAMES.index(attr) + 1
def update_list(self):
"""Updates the default list view."""
LOGGER.debug('Re-populating the viewport with the list command.')
self.buffer.clear()
labels = commands.ListCommand().execute(self.list_args,
out=self.buffer)
labels = labels or [] # convert to empty list if labels is None
# populate buffer with the list
if self.list_mode >= 0:
self.current_line = self.list_mode
self.list_mode = -1
# reset viewport
self.top_line = 0
self.left_edge = 0
self.inactive_commands = []
# highlight current selection
for label in self.selection:
# Note: the two spaces are explained in the `select()` method.
# Also: this step may become a performance bottleneck because we replace inside the
# whole buffer for each selected label!
self.buffer.replace(
range(self.buffer.height), label + ' ',
CONFIG.get_ansi_color('selection') + label + '\x1b[0m ')
# display buffer in viewport
self.buffer.view(self.viewport,
self.visible,
self.width - 1,
ansi_map=self.ANSI_MAP)
# update top statusbar
self.topstatus = "CoBib v{} - {} Entries".format(
__version__, len(labels))
self.statusbar(self.topbar, self.topstatus)
# if cursor position is out-of-view (due to e.g. top-line reset in Show command), reset the
# top-line such that the current line becomes visible again
if self.current_line > self.top_line + self.visible:
self.top_line = min(self.current_line,
self.buffer.height - self.visible)
def execute(self, args, out=sys.stdout):
"""Search database.
Searches the database recursively (i.e. including any associated files) using `grep` for a
query string.
Args: See base class.
"""
LOGGER.debug('Starting Search command.')
parser = ArgumentParser(prog="search", description="Search subcommand parser.")
parser.add_argument("query", type=str, help="text to search for")
parser.add_argument("-c", "--context", type=int, default=1,
help="number of context lines to provide for each match")
parser.add_argument("-i", "--ignore-case", action="store_true",
help="ignore case for searching")
parser.add_argument('list_arg', nargs='*',
help="Any arguments for the List subcommand." +
"\nUse this to add filters to specify a subset of searched entries." +
"\nYou can add a '--' before the List arguments to ensure separation." +
"\nSee also `list --help` for more information on the List arguments.")
if not args:
parser.print_usage(sys.stderr)
sys.exit(1)
try:
largs = parser.parse_intermixed_args(args)
except argparse.ArgumentError as exc:
print("{}: {}".format(exc.argument_name, exc.message), file=sys.stderr)
return None
labels = ListCommand().execute(largs.list_arg, out=open(os.devnull, 'w'))
LOGGER.debug('Available entries to search: %s', labels)
ignore_case = CONFIG.config['DATABASE'].getboolean('search_ignore_case', False) or \
largs.ignore_case
re_flags = re.IGNORECASE if ignore_case else 0
LOGGER.debug('The search will be performed case %ssensitive', 'in' if ignore_case else '')
hits = 0
output = []
for label in labels.copy():
entry = CONFIG.config['BIB_DATA'][label]
matches = entry.search(largs.query, largs.context, ignore_case)
if not matches:
labels.remove(label)
continue
hits += len(matches)
LOGGER.debug('Entry "%s" includes %d hits.', label, hits)
title = f"{label} - {len(matches)} match" + ("es" if len(matches) > 1 else "")
title = title.replace(label, CONFIG.get_ansi_color('search_label') + label + '\x1b[0m')
output.append(title)
for idx, match in enumerate(matches):
for line in match:
line = re.sub(rf'({largs.query})',
CONFIG.get_ansi_color('search_query') + r'\1' + '\x1b[0m',
line, flags=re_flags)
output.append(f"[{idx+1}]\t".expandtabs(8) + line)
print('\n'.join(output), file=out)
return (hits, labels)
def main():
"""Main executable.
CoBib's main function used to parse optional keyword arguments and subcommands.
"""
if len(sys.argv) > 1 and any([a[0] == '_' for a in sys.argv]):
# zsh helper function called
zsh_main()
sys.exit()
# initialize logging
log_to_stream()
subcommands = [cmd.split(':')[0] for cmd in zsh_helper.list_commands()]
parser = argparse.ArgumentParser(prog='CoBib',
description="""
Cobib input arguments.
If no arguments are given, the TUI will start as a default.
""")
parser.add_argument("--version",
action="version",
version="%(prog)s v{}".format(__version__))
parser.add_argument('--verbose', '-v', action='count', default=0)
parser.add_argument("-l",
"--logfile",
type=argparse.FileType('w'),
help="Alternative log file")
parser.add_argument("-c",
"--config",
type=argparse.FileType('r'),
help="Alternative config file")
parser.add_argument('command',
help="subcommand to be called",
choices=subcommands,
nargs='?')
parser.add_argument('args', nargs=argparse.REMAINDER)
args = parser.parse_args()
if args.logfile:
LOGGER.info('Switching to FileHandler logger in %s', args.logfile.name)
log_to_file('DEBUG' if args.verbose > 1 else 'INFO',
logfile=args.logfile.name)
# set logging verbosity level
if args.verbose == 1:
logging.getLogger().setLevel(logging.INFO)
LOGGER.info('Logging level set to INFO.')
elif args.verbose > 1:
logging.getLogger().setLevel(logging.DEBUG)
LOGGER.info('Logging level set to DEBUG.')
CONFIG.set_config(args.config)
try:
CONFIG.validate()
except RuntimeError as exc:
LOGGER.error(exc)
sys.exit(1)
if args.command == 'init':
# the database file may not exist yet, thus we ensure to execute the command before trying
# to read the database file
subcmd = getattr(commands, 'InitCommand')()
subcmd.execute(args.args)
return
read_database()
if not args.command:
if args.logfile is None:
LOGGER.info('Switching to FileHandler logger in %s',
'/tmp/cobib.log')
log_to_file('DEBUG' if args.verbose > 1 else 'INFO')
else:
LOGGER.info(
'Already logging to %s. NOT switching to "/tmp/cobib.log"',
args.logfile)
tui()
else:
subcmd = getattr(commands, args.command.title() + 'Command')()
subcmd.execute(args.args)
def test_valid_tui_colors(setup, color):
"""Test curses color specification validation."""
with pytest.raises(RuntimeError) as exc_info:
CONFIG.config.get('COLORS', {})[color] = 'test'
CONFIG.validate()
assert str(exc_info.value) == 'Unknown color specification: test'
def test_database_section(setup, section, field):
"""Test raised RuntimeError for missing config fields."""
with pytest.raises(RuntimeError) as exc_info:
del CONFIG.config.get(section, {})[field]
CONFIG.validate()
assert f'{section}/{field}' in str(exc_info.value)
def test_missing_section(setup, section):
"""Test raised RuntimeError for missing configuration section."""
with pytest.raises(RuntimeError) as exc_info:
del CONFIG.config[section]
CONFIG.validate()
assert section in str(exc_info.value)
def test_base_config(setup):
"""Test the initial configuration passes all validation checks."""
CONFIG.validate()
def setup():
"""Setup."""
# ensure configuration is empty
CONFIG.config = {}
root = os.path.abspath(os.path.dirname(__file__))
CONFIG.set_config(Path(root + '/../cobib/docs/debug.ini'))
def setup():
"""Setup."""
root = os.path.abspath(os.path.dirname(__file__))
CONFIG.set_config(Path(root + '/../cobib/docs/debug.ini'))
read_database()