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ajslater/picopt | picopt/walk.py | _is_skippable | def _is_skippable(filename_full):
"""Handle things that are not optimizable files."""
# File types
if not Settings.follow_symlinks and os.path.islink(filename_full):
return True
if os.path.basename(filename_full) == timestamp.RECORD_FILENAME:
return True
if not os.path.exists(filena... | python | def _is_skippable(filename_full):
"""Handle things that are not optimizable files."""
# File types
if not Settings.follow_symlinks and os.path.islink(filename_full):
return True
if os.path.basename(filename_full) == timestamp.RECORD_FILENAME:
return True
if not os.path.exists(filena... | [
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ajslater/picopt | picopt/walk.py | walk_file | def walk_file(filename, walk_after, recurse=None, archive_mtime=None):
"""Optimize an individual file."""
filename = os.path.normpath(filename)
result_set = set()
if _is_skippable(filename):
return result_set
walk_after = timestamp.get_walk_after(filename, walk_after)
# File is a dir... | python | def walk_file(filename, walk_after, recurse=None, archive_mtime=None):
"""Optimize an individual file."""
filename = os.path.normpath(filename)
result_set = set()
if _is_skippable(filename):
return result_set
walk_after = timestamp.get_walk_after(filename, walk_after)
# File is a dir... | [
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ajslater/picopt | picopt/walk.py | walk_dir | def walk_dir(dir_path, walk_after, recurse=None, archive_mtime=None):
"""Recursively optimize a directory."""
if recurse is None:
recurse = Settings.recurse
result_set = set()
if not recurse:
return result_set
for root, _, filenames in os.walk(dir_path):
for filename in fil... | python | def walk_dir(dir_path, walk_after, recurse=None, archive_mtime=None):
"""Recursively optimize a directory."""
if recurse is None:
recurse = Settings.recurse
result_set = set()
if not recurse:
return result_set
for root, _, filenames in os.walk(dir_path):
for filename in fil... | [
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ajslater/picopt | picopt/walk.py | _walk_all_files | def _walk_all_files():
"""
Optimize the files from the arugments list in two batches.
One for absolute paths which are probably outside the current
working directory tree and one for relative files.
"""
# Init records
record_dirs = set()
result_set = set()
for filename in Settings.... | python | def _walk_all_files():
"""
Optimize the files from the arugments list in two batches.
One for absolute paths which are probably outside the current
working directory tree and one for relative files.
"""
# Init records
record_dirs = set()
result_set = set()
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ajslater/picopt | picopt/walk.py | run | def run():
"""Use preconfigured settings to optimize files."""
# Setup Multiprocessing
# manager = multiprocessing.Manager()
Settings.pool = multiprocessing.Pool(Settings.jobs)
# Optimize Files
record_dirs, bytes_in, bytes_out, nag_about_gifs, errors = \
_walk_all_files()
# Shut do... | python | def run():
"""Use preconfigured settings to optimize files."""
# Setup Multiprocessing
# manager = multiprocessing.Manager()
Settings.pool = multiprocessing.Pool(Settings.jobs)
# Optimize Files
record_dirs, bytes_in, bytes_out, nag_about_gifs, errors = \
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ajslater/picopt | picopt/files.py | replace_ext | def replace_ext(filename, new_ext):
"""Replace the file extention."""
filename_base = os.path.splitext(filename)[0]
new_filename = '{}.{}'.format(filename_base, new_ext)
return new_filename | python | def replace_ext(filename, new_ext):
"""Replace the file extention."""
filename_base = os.path.splitext(filename)[0]
new_filename = '{}.{}'.format(filename_base, new_ext)
return new_filename | [
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ajslater/picopt | picopt/files.py | _cleanup_after_optimize_aux | def _cleanup_after_optimize_aux(filename, new_filename, old_format,
new_format):
"""
Replace old file with better one or discard new wasteful file.
"""
bytes_in = 0
bytes_out = 0
final_filename = filename
try:
bytes_in = os.stat(filename).st_size
... | python | def _cleanup_after_optimize_aux(filename, new_filename, old_format,
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"""
Replace old file with better one or discard new wasteful file.
"""
bytes_in = 0
bytes_out = 0
final_filename = filename
try:
bytes_in = os.stat(filename).st_size
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ajslater/picopt | picopt/files.py | cleanup_after_optimize | def cleanup_after_optimize(filename, new_filename, old_format, new_format):
"""
Replace old file with better one or discard new wasteful file.
And report results using the stats module.
"""
final_filename, bytes_in, bytes_out = _cleanup_after_optimize_aux(
filename, new_filename, old_format... | python | def cleanup_after_optimize(filename, new_filename, old_format, new_format):
"""
Replace old file with better one or discard new wasteful file.
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final_filename, bytes_in, bytes_out = _cleanup_after_optimize_aux(
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ajslater/picopt | setup.py | parse_reqs | def parse_reqs(filename):
"""Parse setup requirements from a requirements.txt file."""
install_reqs = parse_requirements(filename, session=False)
return [str(ir.req) for ir in install_reqs] | python | def parse_reqs(filename):
"""Parse setup requirements from a requirements.txt file."""
install_reqs = parse_requirements(filename, session=False)
return [str(ir.req) for ir in install_reqs] | [
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ajslater/picopt | setup.py | get_req_list | def get_req_list():
"""Get the requirements by weather we're building develop or not."""
req_list = parse_reqs(REQUIREMENTS['prod'])
if len(sys.argv) > 2 and sys.argv[2] == ('develop'):
req_list += parse_reqs(REQUIREMENTS['dev'])
return req_list | python | def get_req_list():
"""Get the requirements by weather we're building develop or not."""
req_list = parse_reqs(REQUIREMENTS['prod'])
if len(sys.argv) > 2 and sys.argv[2] == ('develop'):
req_list += parse_reqs(REQUIREMENTS['dev'])
return req_list | [
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ajslater/picopt | picopt/formats/comic.py | get_comic_format | def get_comic_format(filename):
"""Return the comic format if it is a comic archive."""
image_format = None
filename_ext = os.path.splitext(filename)[-1].lower()
if filename_ext in _COMIC_EXTS:
if zipfile.is_zipfile(filename):
image_format = _CBZ_FORMAT
elif rarfile.is_rarfil... | python | def get_comic_format(filename):
"""Return the comic format if it is a comic archive."""
image_format = None
filename_ext = os.path.splitext(filename)[-1].lower()
if filename_ext in _COMIC_EXTS:
if zipfile.is_zipfile(filename):
image_format = _CBZ_FORMAT
elif rarfile.is_rarfil... | [
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ajslater/picopt | picopt/formats/comic.py | _get_archive_tmp_dir | def _get_archive_tmp_dir(filename):
"""Get the name of the working dir to use for this filename."""
head, tail = os.path.split(filename)
return os.path.join(head, _ARCHIVE_TMP_DIR_TEMPLATE.format(tail)) | python | def _get_archive_tmp_dir(filename):
"""Get the name of the working dir to use for this filename."""
head, tail = os.path.split(filename)
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ajslater/picopt | picopt/formats/comic.py | comic_archive_uncompress | def comic_archive_uncompress(filename, image_format):
"""
Uncompress comic archives.
Return the name of the working directory we uncompressed into.
"""
if not Settings.comics:
report = ['Skipping archive file: {}'.format(filename)]
return None, ReportStats(filename, report=report)
... | python | def comic_archive_uncompress(filename, image_format):
"""
Uncompress comic archives.
Return the name of the working directory we uncompressed into.
"""
if not Settings.comics:
report = ['Skipping archive file: {}'.format(filename)]
return None, ReportStats(filename, report=report)
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ajslater/picopt | picopt/formats/comic.py | _comic_archive_write_zipfile | def _comic_archive_write_zipfile(new_filename, tmp_dir):
"""Zip up the files in the tempdir into the new filename."""
if Settings.verbose:
print('Rezipping archive', end='')
with zipfile.ZipFile(new_filename, 'w',
compression=zipfile.ZIP_DEFLATED) as new_zf:
root_len... | python | def _comic_archive_write_zipfile(new_filename, tmp_dir):
"""Zip up the files in the tempdir into the new filename."""
if Settings.verbose:
print('Rezipping archive', end='')
with zipfile.ZipFile(new_filename, 'w',
compression=zipfile.ZIP_DEFLATED) as new_zf:
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ajslater/picopt | picopt/formats/comic.py | comic_archive_compress | def comic_archive_compress(args):
"""
Called back by every optimization inside a comic archive.
When they're all done it creates the new archive and cleans up.
"""
try:
filename, old_format, settings, nag_about_gifs = args
Settings.update(settings)
tmp_dir = _get_archive_tmp... | python | def comic_archive_compress(args):
"""
Called back by every optimization inside a comic archive.
When they're all done it creates the new archive and cleans up.
"""
try:
filename, old_format, settings, nag_about_gifs = args
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ajslater/picopt | picopt/formats/jpeg.py | mozjpeg | def mozjpeg(ext_args):
"""Create argument list for mozjpeg."""
args = copy.copy(_MOZJPEG_ARGS)
if Settings.destroy_metadata:
args += ["-copy", "none"]
else:
args += ["-copy", "all"]
args += ['-outfile']
args += [ext_args.new_filename, ext_args.old_filename]
extern.run_ext(arg... | python | def mozjpeg(ext_args):
"""Create argument list for mozjpeg."""
args = copy.copy(_MOZJPEG_ARGS)
if Settings.destroy_metadata:
args += ["-copy", "none"]
else:
args += ["-copy", "all"]
args += ['-outfile']
args += [ext_args.new_filename, ext_args.old_filename]
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ajslater/picopt | picopt/formats/jpeg.py | jpegtran | def jpegtran(ext_args):
"""Create argument list for jpegtran."""
args = copy.copy(_JPEGTRAN_ARGS)
if Settings.destroy_metadata:
args += ["-copy", "none"]
else:
args += ["-copy", "all"]
if Settings.jpegtran_prog:
args += ["-progressive"]
args += ['-outfile']
args += [e... | python | def jpegtran(ext_args):
"""Create argument list for jpegtran."""
args = copy.copy(_JPEGTRAN_ARGS)
if Settings.destroy_metadata:
args += ["-copy", "none"]
else:
args += ["-copy", "all"]
if Settings.jpegtran_prog:
args += ["-progressive"]
args += ['-outfile']
args += [e... | [
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ajslater/picopt | picopt/formats/jpeg.py | jpegrescan | def jpegrescan(ext_args):
"""Run the EXTERNAL program jpegrescan."""
args = copy.copy(_JPEGRESCAN_ARGS)
if Settings.jpegrescan_multithread:
args += ['-t']
if Settings.destroy_metadata:
args += ['-s']
args += [ext_args.old_filename, ext_args.new_filename]
extern.run_ext(args)
... | python | def jpegrescan(ext_args):
"""Run the EXTERNAL program jpegrescan."""
args = copy.copy(_JPEGRESCAN_ARGS)
if Settings.jpegrescan_multithread:
args += ['-t']
if Settings.destroy_metadata:
args += ['-s']
args += [ext_args.old_filename, ext_args.new_filename]
extern.run_ext(args)
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ajslater/picopt | picopt/cli.py | get_arguments | def get_arguments(args):
"""Parse the command line."""
usage = "%(prog)s [arguments] [image files]"
programs_str = ', '.join([prog.__name__ for prog in PROGRAMS])
description = "Uses "+programs_str+" if they are on the path."
parser = argparse.ArgumentParser(usage=usage, description=description)
... | python | def get_arguments(args):
"""Parse the command line."""
usage = "%(prog)s [arguments] [image files]"
programs_str = ', '.join([prog.__name__ for prog in PROGRAMS])
description = "Uses "+programs_str+" if they are on the path."
parser = argparse.ArgumentParser(usage=usage, description=description)
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ajslater/picopt | picopt/cli.py | process_arguments | def process_arguments(arguments):
"""Recompute special cases for input arguments."""
Settings.update(arguments)
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Settings.paths = set(arguments.paths)
if arguments.formats == DEFAULT_FORMATS:
Settings.forma... | python | def process_arguments(arguments):
"""Recompute special cases for input arguments."""
Settings.update(arguments)
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Settings.paths = set(arguments.paths)
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ajslater/picopt | picopt/cli.py | run | def run(args):
"""Process command line arguments and walk inputs."""
raw_arguments = get_arguments(args[1:])
process_arguments(raw_arguments)
walk.run()
return True | python | def run(args):
"""Process command line arguments and walk inputs."""
raw_arguments = get_arguments(args[1:])
process_arguments(raw_arguments)
walk.run()
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ajslater/picopt | picopt/extern.py | does_external_program_run | def does_external_program_run(prog, verbose):
"""Test to see if the external programs can be run."""
try:
with open('/dev/null') as null:
subprocess.call([prog, '-h'], stdout=null, stderr=null)
result = True
except OSError:
if verbose > 1:
print("couldn't run ... | python | def does_external_program_run(prog, verbose):
"""Test to see if the external programs can be run."""
try:
with open('/dev/null') as null:
subprocess.call([prog, '-h'], stdout=null, stderr=null)
result = True
except OSError:
if verbose > 1:
print("couldn't run ... | [
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ajslater/picopt | picopt/extern.py | run_ext | def run_ext(args):
"""Run EXTERNAL program."""
try:
subprocess.check_call(args)
except subprocess.CalledProcessError as exc:
print(exc)
print(exc.cmd)
print(exc.returncode)
print(exc.output)
raise | python | def run_ext(args):
"""Run EXTERNAL program."""
try:
subprocess.check_call(args)
except subprocess.CalledProcessError as exc:
print(exc)
print(exc.cmd)
print(exc.returncode)
print(exc.output)
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ajslater/picopt | picopt/stats.py | _humanize_bytes | def _humanize_bytes(num_bytes, precision=1):
"""
Return a humanized string representation of a number of num_bytes.
from:
http://code.activestate.com/recipes/
577081-humanized-representation-of-a-number-of-num_bytes/
Assumes `from __future__ import division`.
>>> humanize_bytes(1)
... | python | def _humanize_bytes(num_bytes, precision=1):
"""
Return a humanized string representation of a number of num_bytes.
from:
http://code.activestate.com/recipes/
577081-humanized-representation-of-a-number-of-num_bytes/
Assumes `from __future__ import division`.
>>> humanize_bytes(1)
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'1.0 kB'
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ajslater/picopt | picopt/stats.py | new_percent_saved | def new_percent_saved(report_stats):
"""Spit out how much space the optimization saved."""
size_in = report_stats.bytes_in
if size_in > 0:
size_out = report_stats.bytes_out
ratio = size_out / size_in
kb_saved = _humanize_bytes(size_in - size_out)
else:
ratio = 0
k... | python | def new_percent_saved(report_stats):
"""Spit out how much space the optimization saved."""
size_in = report_stats.bytes_in
if size_in > 0:
size_out = report_stats.bytes_out
ratio = size_out / size_in
kb_saved = _humanize_bytes(size_in - size_out)
else:
ratio = 0
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ajslater/picopt | picopt/stats.py | truncate_cwd | def truncate_cwd(full_filename):
"""Remove the cwd from the full filename."""
if full_filename.startswith(os.getcwd()):
truncated_filename = full_filename.split(os.getcwd(), 1)[1]
truncated_filename = truncated_filename.split(os.sep, 1)[1]
else:
truncated_filename = full_filename
... | python | def truncate_cwd(full_filename):
"""Remove the cwd from the full filename."""
if full_filename.startswith(os.getcwd()):
truncated_filename = full_filename.split(os.getcwd(), 1)[1]
truncated_filename = truncated_filename.split(os.sep, 1)[1]
else:
truncated_filename = full_filename
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ajslater/picopt | picopt/stats.py | report_saved | def report_saved(report_stats):
"""Record the percent saved & print it."""
if Settings.verbose:
report = ''
truncated_filename = truncate_cwd(report_stats.final_filename)
report += '{}: '.format(truncated_filename)
total = new_percent_saved(report_stats)
if total:
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"""Record the percent saved & print it."""
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report = ''
truncated_filename = truncate_cwd(report_stats.final_filename)
report += '{}: '.format(truncated_filename)
total = new_percent_saved(report_stats)
if total:
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ajslater/picopt | picopt/stats.py | report_totals | def report_totals(bytes_in, bytes_out, nag_about_gifs, errors):
"""Report the total number and percent of bytes saved."""
if bytes_in:
bytes_saved = bytes_in - bytes_out
percent_bytes_saved = bytes_saved / bytes_in * 100
msg = ''
if Settings.test:
if percent_bytes_sav... | python | def report_totals(bytes_in, bytes_out, nag_about_gifs, errors):
"""Report the total number and percent of bytes saved."""
if bytes_in:
bytes_saved = bytes_in - bytes_out
percent_bytes_saved = bytes_saved / bytes_in * 100
msg = ''
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ajslater/picopt | picopt/stats.py | skip | def skip(type_name, filename):
"""Provide reporting statistics for a skipped file."""
report = ['Skipping {} file: {}'.format(type_name, filename)]
report_stats = ReportStats(filename, report=report)
return report_stats | python | def skip(type_name, filename):
"""Provide reporting statistics for a skipped file."""
report = ['Skipping {} file: {}'.format(type_name, filename)]
report_stats = ReportStats(filename, report=report)
return report_stats | [
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ajslater/picopt | picopt/formats/gif.py | gifsicle | def gifsicle(ext_args):
"""Run the EXTERNAL program gifsicle."""
args = _GIFSICLE_ARGS + [ext_args.new_filename]
extern.run_ext(args)
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"""Run the EXTERNAL program gifsicle."""
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extern.run_ext(args)
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ajslater/picopt | picopt/optimize.py | _optimize_image_external | def _optimize_image_external(filename, func, image_format, new_ext):
"""Optimize the file with the external function."""
new_filename = filename + TMP_SUFFIX + new_ext
new_filename = os.path.normpath(new_filename)
shutil.copy2(filename, new_filename)
ext_args = ExtArgs(filename, new_filename)
n... | python | def _optimize_image_external(filename, func, image_format, new_ext):
"""Optimize the file with the external function."""
new_filename = filename + TMP_SUFFIX + new_ext
new_filename = os.path.normpath(new_filename)
shutil.copy2(filename, new_filename)
ext_args = ExtArgs(filename, new_filename)
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ajslater/picopt | picopt/optimize.py | _optimize_with_progs | def _optimize_with_progs(format_module, filename, image_format):
"""
Use the correct optimizing functions in sequence.
And report back statistics.
"""
filesize_in = os.stat(filename).st_size
report_stats = None
for func in format_module.PROGRAMS:
if not getattr(Settings, func.__nam... | python | def _optimize_with_progs(format_module, filename, image_format):
"""
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filesize_in = os.stat(filename).st_size
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ajslater/picopt | picopt/optimize.py | _get_format_module | def _get_format_module(image_format):
"""Get the format module to use for optimizing the image."""
format_module = None
nag_about_gifs = False
if detect_format.is_format_selected(image_format,
Settings.to_png_formats,
png.P... | python | def _get_format_module(image_format):
"""Get the format module to use for optimizing the image."""
format_module = None
nag_about_gifs = False
if detect_format.is_format_selected(image_format,
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ajslater/picopt | picopt/optimize.py | optimize_image | def optimize_image(arg):
"""Optimize a given image from a filename."""
try:
filename, image_format, settings = arg
Settings.update(settings)
format_module, nag_about_gifs = _get_format_module(image_format)
if format_module is None:
if Settings.verbose > 1:
... | python | def optimize_image(arg):
"""Optimize a given image from a filename."""
try:
filename, image_format, settings = arg
Settings.update(settings)
format_module, nag_about_gifs = _get_format_module(image_format)
if format_module is None:
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ajslater/picopt | picopt/detect_format.py | _is_program_selected | def _is_program_selected(progs):
"""Determine if the program is enabled in the settings."""
mode = False
for prog in progs:
if getattr(Settings, prog.__name__):
mode = True
break
return mode | python | def _is_program_selected(progs):
"""Determine if the program is enabled in the settings."""
mode = False
for prog in progs:
if getattr(Settings, prog.__name__):
mode = True
break
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ajslater/picopt | picopt/detect_format.py | is_format_selected | def is_format_selected(image_format, formats, progs):
"""Determine if the image format is selected by command line arguments."""
intersection = formats & Settings.formats
mode = _is_program_selected(progs)
result = (image_format in intersection) and mode
return result | python | def is_format_selected(image_format, formats, progs):
"""Determine if the image format is selected by command line arguments."""
intersection = formats & Settings.formats
mode = _is_program_selected(progs)
result = (image_format in intersection) and mode
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ajslater/picopt | picopt/detect_format.py | _is_image_sequenced | def _is_image_sequenced(image):
"""Determine if the image is a sequenced image."""
try:
image.seek(1)
image.seek(0)
result = True
except EOFError:
result = False
return result | python | def _is_image_sequenced(image):
"""Determine if the image is a sequenced image."""
try:
image.seek(1)
image.seek(0)
result = True
except EOFError:
result = False
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ajslater/picopt | picopt/detect_format.py | get_image_format | def get_image_format(filename):
"""Get the image format."""
image = None
bad_image = 1
image_format = NONE_FORMAT
sequenced = False
try:
bad_image = Image.open(filename).verify()
image = Image.open(filename)
image_format = image.format
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"""Get the image format."""
image = None
bad_image = 1
image_format = NONE_FORMAT
sequenced = False
try:
bad_image = Image.open(filename).verify()
image = Image.open(filename)
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ajslater/picopt | picopt/detect_format.py | detect_file | def detect_file(filename):
"""Decide what to do with the file."""
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if image_format in Settings.formats:
return image_format
if image_format in (NONE_FORMAT, ERROR_FORMAT):
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return image_format
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ajslater/picopt | picopt/settings.py | Settings.update | def update(cls, settings):
"""Update settings with a dict."""
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"""Update settings with a dict."""
for key, val in settings.__dict__.items():
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ajslater/picopt | picopt/settings.py | Settings._set_program_defaults | def _set_program_defaults(cls, programs):
"""Run the external program tester on the required binaries."""
for program in programs:
val = getattr(cls, program.__name__) \
and extern.does_external_program_run(program.__name__,
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"""Run the external program tester on the required binaries."""
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ajslater/picopt | picopt/settings.py | Settings.config_program_reqs | def config_program_reqs(cls, programs):
"""Run the program tester and determine if we can do anything."""
cls._set_program_defaults(programs)
do_png = cls.optipng or cls.pngout or cls.advpng
do_jpeg = cls.mozjpeg or cls.jpegrescan or cls.jpegtran
do_comics = cls.comics
... | python | def config_program_reqs(cls, programs):
"""Run the program tester and determine if we can do anything."""
cls._set_program_defaults(programs)
do_png = cls.optipng or cls.pngout or cls.advpng
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ajslater/picopt | picopt/formats/png.py | optipng | def optipng(ext_args):
"""Run the external program optipng on the file."""
args = _OPTIPNG_ARGS + [ext_args.new_filename]
extern.run_ext(args)
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"""Run the external program optipng on the file."""
args = _OPTIPNG_ARGS + [ext_args.new_filename]
extern.run_ext(args)
return _PNG_FORMAT | [
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ajslater/picopt | picopt/formats/png.py | advpng | def advpng(ext_args):
"""Run the external program advpng on the file."""
args = _ADVPNG_ARGS + [ext_args.new_filename]
extern.run_ext(args)
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"""Run the external program advpng on the file."""
args = _ADVPNG_ARGS + [ext_args.new_filename]
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ajslater/picopt | picopt/formats/png.py | pngout | def pngout(ext_args):
"""Run the external program pngout on the file."""
args = _PNGOUT_ARGS + [ext_args.old_filename, ext_args.new_filename]
extern.run_ext(args)
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"""Run the external program pngout on the file."""
args = _PNGOUT_ARGS + [ext_args.old_filename, ext_args.new_filename]
extern.run_ext(args)
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datacamp/protowhat | protowhat/sct_syntax.py | F._from_func | def _from_func(cls, f, *args, _attr_scts=None, **kwargs):
"""Creates a function chain starting with the specified SCT (f), and its arguments."""
func_chain = cls(attr_scts=_attr_scts)
func_chain._stack.append([f, args, kwargs])
return func_chain | python | def _from_func(cls, f, *args, _attr_scts=None, **kwargs):
"""Creates a function chain starting with the specified SCT (f), and its arguments."""
func_chain = cls(attr_scts=_attr_scts)
func_chain._stack.append([f, args, kwargs])
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AtteqCom/zsl | src/zsl/resource/guard.py | _nested_transactional | def _nested_transactional(fn):
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# type: (Callable) -> Callable
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datacamp/protowhat | protowhat/checks/check_files.py | check_file | def check_file(
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parse=True,
use_fs=True,
use_solution=False,
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state,
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is_dir_msg="Want to check a file named `{}`, but found a directory.",
parse=True,
use_fs=True,
use_solution=False,
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datacamp/protowhat | protowhat/checks/check_files.py | has_dir | def has_dir(state, fname, incorrect_msg="Did you create a directory named `{}`?"):
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if not Path(fname).is_dir():
state.report(Feedback(incorrect_msg.format(fname)))
return state | python | def has_dir(state, fname, incorrect_msg="Did you create a directory named `{}`?"):
"""Test whether a directory exists."""
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state.report(Feedback(incorrect_msg.format(fname)))
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AtteqCom/zsl | src/zsl/interface/task.py | exec_task | def exec_task(task_path, data):
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:type task_path: str|Callable
:param data: task's data
:type data: Any
:return:
"""
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elif not isinstance(data, (str, bytes)):
data = {'d... | python | def exec_task(task_path, data):
"""Execute task.
:param task_path: task path
:type task_path: str|Callable
:param data: task's data
:type data: Any
:return:
"""
if not data:
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datacamp/protowhat | protowhat/utils_ast.py | dump | def dump(node, config):
"""
Convert a node tree to a simple nested dict
All steps in this conversion are configurable using DumpConfig
dump dictionary node: {"type": str, "data": dict}
"""
if config.is_node(node):
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for name in config.fields_iter(node):
... | python | def dump(node, config):
"""
Convert a node tree to a simple nested dict
All steps in this conversion are configurable using DumpConfig
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AtteqCom/zsl | src/zsl/db/helpers/pagination.py | Pagination.apply_pagination | def apply_pagination(self, q):
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:param q: Query to be paged.
:return: Paged query.
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# type: (Query)->Query
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:return: Paged query.
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AtteqCom/zsl | src/zsl/db/helpers/pagination.py | Pagination.paginate | def paginate(self, q):
"""
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:param q: Query to be paged.
:return: Paged query.
"""
self.record_count = q.count()
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briney/abutils | abutils/utils/cluster.py | cluster | def cluster(seqs, threshold=0.975, out_file=None, temp_dir=None, make_db=True,
quiet=False, threads=0, return_just_seq_ids=False, max_memory=800, debug=False):
'''
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briney/abutils | abutils/utils/cluster.py | cdhit | def cdhit(seqs, out_file=None, temp_dir=None, threshold=0.975, make_db=True, quiet=False, threads=0, max_memory=800, retries=5, debug=False):
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briney/abutils | abutils/utils/cluster.py | parse_clusters | def parse_clusters(out_file, clust_file, seq_db=None, db_path=None, seq_dict=None, return_just_seq_ids=False):
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Parses CD-HIT output.
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AtteqCom/zsl | src/zsl/task/task_decorator.py | log_output | def log_output(f):
"""
Logs the output value.
"""
@wraps(f)
def wrapper_fn(*args, **kwargs):
res = f(*args, **kwargs)
logging.debug("Logging result %s.", res)
return res
return wrapper_fn | python | def log_output(f):
"""
Logs the output value.
"""
@wraps(f)
def wrapper_fn(*args, **kwargs):
res = f(*args, **kwargs)
logging.debug("Logging result %s.", res)
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AtteqCom/zsl | src/zsl/task/task_decorator.py | save_to_file | def save_to_file(destination_filename, append=False):
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Save the output value to file.
"""
def decorator_fn(f):
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def wrapper_fn(*args, **kwargs):
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AtteqCom/zsl | src/zsl/task/task_decorator.py | json_input | def json_input(f):
"""
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"""
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def json_input_decorator(*args, **kwargs):
# If the data is already transformed, we do not transform it any
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"""
Expects task input data in json format and parse this data.
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@wraps(f)
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AtteqCom/zsl | src/zsl/task/task_decorator.py | json_output | def json_output(f):
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AtteqCom/zsl | src/zsl/task/task_decorator.py | jsonp_wrap | def jsonp_wrap(callback_key='callback'):
"""
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"""
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AtteqCom/zsl | src/zsl/task/task_decorator.py | jsend_output | def jsend_output(fail_exception_classes=None):
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@param fail_exception_classes: exceptions which will produce 'fail' response
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"""
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"""
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AtteqCom/zsl | src/zsl/task/task_decorator.py | web_error_and_result | def web_error_and_result(f):
"""
Same as error_and_result decorator, except:
If no exception was raised during task execution, ONLY IN CASE OF WEB
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"""
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def web_error_and_result_decorator(*args, **kwargs):
... | python | def web_error_and_result(f):
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AtteqCom/zsl | src/zsl/task/task_decorator.py | required_data | def required_data(*data):
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"""
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def required_data_decorator(*args, **kwargs):
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AtteqCom/zsl | src/zsl/task/task_decorator.py | append_get_parameters | def append_get_parameters(accept_only_web=True):
# type: (bool) -> Callable
"""
Task decorator which appends the GET data to the task data.
:param accept_only_web: Parameter which limits using this task only
with web requests.
"""
def wrapper(f):
@wraps(f)
... | python | def append_get_parameters(accept_only_web=True):
# type: (bool) -> Callable
"""
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AtteqCom/zsl | src/zsl/task/task_decorator.py | web_task | def web_task(f):
"""
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"""
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AtteqCom/zsl | src/zsl/task/task_decorator.py | secured_task | def secured_task(f):
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def secured_task_decorator(*args, **kwargs):
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"""
Secured task decorator.
"""
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AtteqCom/zsl | src/zsl/task/task_decorator.py | xml_output | def xml_output(f):
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AtteqCom/zsl | src/zsl/task/task_decorator.py | file_upload | def file_upload(f):
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Return list of `werkzeug.datastructures.FileStorage` objects - files to be
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"""
@wraps(f)
def file_upload_decorator(*args, **kwargs):
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Return list of `werkzeug.datastructures.FileStorage` objects - files to be
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AtteqCom/zsl | src/zsl/task/task_decorator.py | forbid_web_access | def forbid_web_access(f):
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Forbids running task using http request.
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"""
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def wrapper_fn(*args, **kwargs):
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Forbids running task using http request.
:param f: Callable
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def wrapper_fn(*args, **kwargs):
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AtteqCom/zsl | src/zsl/resource/resource_helper.py | filter_from_url_arg | def filter_from_url_arg(model_cls, query, arg, query_operator=and_,
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"""
Parse filter URL argument ``arg`` and apply to ``query``
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AtteqCom/zsl | src/zsl/resource/resource_helper.py | model_tree | def model_tree(name, model_cls, visited=None):
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:param name: name of the model
:type name: str
:param model_cls: model class
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AtteqCom/zsl | src/zsl/resource/resource_helper.py | flat_model | def flat_model(tree):
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names = []
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for col in columns:
if isinstance(col, dict):
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AtteqCom/zsl | src/zsl/interface/task_queue.py | execute_job | def execute_job(job, app=Injected, task_router=Injected):
# type: (Job, Zsl, TaskRouter) -> dict
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:param job: job to execute
:type job: Job
:param app: service application instance, injected
:type app: ServiceApplication
:param task_router: task router instance, injected
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AtteqCom/zsl | src/zsl/interface/task_queue.py | TaskQueueWorker.handle_exception | def handle_exception(self, e, task_path):
# type: (Exception, str) -> dict
"""Handle exception raised during task execution.
:param e: exception
:type e: Exception
:param task_path: task path
:type task_path: str
:return: exception as task result
:rtype: ... | python | def handle_exception(self, e, task_path):
# type: (Exception, str) -> dict
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AtteqCom/zsl | src/zsl/interface/task_queue.py | TaskQueueWorker.execute_job | def execute_job(self, job):
# type: (Job) -> dict
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:param job: job
:type job: Job
:return: task result
:rtype: dict
"""
try:
return execute_job(job)
except KillWorkerException:
self._... | python | def execute_job(self, job):
# type: (Job) -> dict
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datacamp/protowhat | protowhat/utils.py | legacy_signature | def legacy_signature(**kwargs_mapping):
"""
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@legacy_signature(old_arg1='arg1', old_arg2='arg2')
def func(arg1, arg2=1):
return arg1 + arg2
func(old_arg1=1) == 2
f... | python | def legacy_signature(**kwargs_mapping):
"""
This decorator makes it possible to call a function using old argument names
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@legacy_signature(old_arg1='arg1', old_arg2='arg2')
def func(arg1, arg2=1):
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AtteqCom/zsl | src/zsl/application/initializers/service_initializer.py | ServiceInitializer._bind_service | def _bind_service(package_name, cls_name, binder=Injected):
"""Bind service to application injector.
:param package_name: service package
:type package_name: str
:param cls_name: service class
:type cls_name: str
:param binder: current application binder, injected
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AtteqCom/zsl | src/zsl/application/initializers/service_initializer.py | ServiceInitializer.initialize | def initialize(config):
"""Initialize method.
:param config: current application config, injected
:type config: Config
"""
service_injection_config = config.get('SERVICE_INJECTION', ())
if not isinstance(service_injection_config, (tuple, list)):
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AtteqCom/zsl | src/zsl/utils/background_task.py | background_task_method | def background_task_method(task):
"""Decorate an object method as a background task (called with help of
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You have to create a task which will handle the gearman call. The
method arguments will be encoded as JSON.
:param task: name of the task
:type task: str
:return: decorated fu... | python | def background_task_method(task):
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AtteqCom/zsl | src/zsl/resource/json_server_resource.py | _get_link_pages | def _get_link_pages(page, per_page, count, page_url):
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:param page: current page
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AtteqCom/zsl | src/zsl/resource/json_server_resource.py | JsonServerResource.to_filter | def to_filter(self, query, arg):
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return filter_from_url_arg(self.model_cls, query, arg, query_operator=or_) | python | def to_filter(self, query, arg):
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AtteqCom/zsl | src/zsl/resource/json_server_resource.py | JsonServerResource.create | def create(self, *args, **kwargs):
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resource = super(JsonServerResource, self).create(*args, **kwargs)
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status=get_http_status_code_value(http.client.CREATED),
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AtteqCom/zsl | src/zsl/resource/json_server_resource.py | JsonServerResource._create_filter_by | def _create_filter_by(self):
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filter_by = []
for name, values in request.args.copy().lists(): # copy.lists works in py2 and py3
if name not in _SKIPPED_ARGUMENTS:
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AtteqCom/zsl | src/zsl/resource/json_server_resource.py | JsonServerResource._create_related | def _create_related(args):
# type: (Dict) -> None
"""Create related field from `_embed` arguments."""
if '_embed' in request.args:
embeds = request.args.getlist('_embed')
args['related'] = ','.join(embeds)
del args['_embed'] | python | def _create_related(args):
# type: (Dict) -> None
"""Create related field from `_embed` arguments."""
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embeds = request.args.getlist('_embed')
args['related'] = ','.join(embeds)
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AtteqCom/zsl | src/zsl/resource/json_server_resource.py | JsonServerResource._create_fulltext_query | def _create_fulltext_query(self):
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filter_by = []
if 'q' in request.args:
columns = flat_model(model_tree(self.__class__.__name__, self.model_cls))
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"""Support the json-server fulltext search with a broad LIKE filter."""
filter_by = []
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columns = flat_model(model_tree(self.__class__.__name__, self.model_cls))
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AtteqCom/zsl | src/zsl/resource/json_server_resource.py | JsonServerResource._transform_list_args | def _transform_list_args(self, args):
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AtteqCom/zsl | src/zsl/resource/json_server_resource.py | JsonServerResource.read | def read(self, params, args, data):
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result_count = None
result_links = None
if params is None:
params = []
if args:
args = args.copy()
else:
args = {}
ctx = sel... | python | def read(self, params, args, data):
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AtteqCom/zsl | src/zsl/resource/json_server_resource.py | JsonServerResource.update | def update(self, *args, **kwargs):
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AtteqCom/zsl | src/zsl/resource/json_server_resource.py | JsonServerResource.delete | def delete(self, params, args, data):
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deleted = self._delete_one(row_id, ctx)
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return ... | python | def delete(self, params, args, data):
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ctx = self._create_context(params, args, data)
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AtteqCom/zsl | src/zsl/utils/task_helper.py | run_task | def run_task(task_cls, task_data):
"""Instantiate and run the perform method od given task data.
:param task_cls: task class
:param task_data: task data
:type task_data: TaskData
:return: task's result
"""
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task_callable = get_callable(task)
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:param task_cls: task class
:param task_data: task data
:type task_data: TaskData
:return: task's result
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AtteqCom/zsl | src/zsl/utils/task_helper.py | run_task_json | def run_task_json(task_cls, task_data):
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:param task_cls: task class
:param task_data: task data
:type task_data: TaskData
:return: task's result
"""
# TODO what does set_skipping_json do?
task = instantiate(task_cls)
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briney/abutils | abutils/plots/summary.py | _aggregate | def _aggregate(data, norm=True, sort_by='value', keys=None):
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Counts the number of occurances of each item in 'data'.
Inputs
data: a list of values.
norm: normalize the resulting counts (as percent)
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data: a list of values.
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AtteqCom/zsl | src/zsl/utils/deploy/apiari_doc_generator.py | generate_apiary_doc | def generate_apiary_doc(task_router):
"""Generate apiary documentation.
Create a Apiary generator and add application packages to it.
:param task_router: task router, injected
:type task_router: TaskRouter
:return: apiary generator
:rtype: ApiaryDoc
"""
generator = ApiaryDoc()
for... | python | def generate_apiary_doc(task_router):
"""Generate apiary documentation.
Create a Apiary generator and add application packages to it.
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briney/abutils | abutils/utils/log.py | setup_logging | def setup_logging(logfile, print_log_location=True, debug=False):
'''
Set up logging using the built-in ``logging`` package.
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``logging.INFO`` level are printed to screen as well as written
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Arguments:
logf... | python | def setup_logging(logfile, print_log_location=True, debug=False):
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] | train | https://github.com/briney/abutils/blob/944755fc7d28bfc7d4f1ffad94ca0bf9d74ec54b/abutils/utils/log.py#L34-L70 |
briney/abutils | abutils/utils/log.py | get_logger | def get_logger(name=None):
'''
Get a logging handle.
As with ``setup_logging``, a stream handler is added to the
log handle.
Arguments:
name (str): Name of the log handle. Default is ``None``.
'''
logger = logging.getLogger(name)
if len(logger.handlers) == 0:
logger = ... | python | def get_logger(name=None):
'''
Get a logging handle.
As with ``setup_logging``, a stream handler is added to the
log handle.
Arguments:
name (str): Name of the log handle. Default is ``None``.
'''
logger = logging.getLogger(name)
if len(logger.handlers) == 0:
logger = ... | [
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AtteqCom/zsl | src/zsl/utils/injection_helper.py | inject | def inject(**bindings):
"""
Decorator for injecting parameters for ASL objects.
"""
def outer_wrapper(f):
def function_wrapper(ff):
for key, value in viewitems(bindings):
bindings[key] = BindingKey(value)
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def _inject(*arg... | python | def inject(**bindings):
"""
Decorator for injecting parameters for ASL objects.
"""
def outer_wrapper(f):
def function_wrapper(ff):
for key, value in viewitems(bindings):
bindings[key] = BindingKey(value)
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briney/abutils | abutils/utils/phylogeny.py | phylogeny | def phylogeny(sequences=None, project_dir=None, name=None, aln_file=None, tree_file=None,
seq_field=None, name_field=None, aa=False, species='human', unrooted=False, ladderize=True,
root=None, root_name=None, show_root_name=False, color_dict=None, color_function=None,
order_dict=None, order_func... | python | def phylogeny(sequences=None, project_dir=None, name=None, aln_file=None, tree_file=None,
seq_field=None, name_field=None, aa=False, species='human', unrooted=False, ladderize=True,
root=None, root_name=None, show_root_name=False, color_dict=None, color_function=None,
order_dict=None, order_func... | [
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Args:
sequences (list(Sequence)): A list of ``Sequence`` objects from which a phylogeny
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briney/abutils | abutils/utils/phylogeny.py | igphyml | def igphyml(input_file=None, tree_file=None, root=None, verbose=False):
'''
Computes a phylogenetic tree using IgPhyML.
.. note::
IgPhyML must be installed. It can be downloaded from https://github.com/kbhoehn/IgPhyML.
Args:
input_file (str): Path to a Phylip-formatted multip... | python | def igphyml(input_file=None, tree_file=None, root=None, verbose=False):
'''
Computes a phylogenetic tree using IgPhyML.
.. note::
IgPhyML must be installed. It can be downloaded from https://github.com/kbhoehn/IgPhyML.
Args:
input_file (str): Path to a Phylip-formatted multip... | [
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.. note::
IgPhyML must be installed. It can be downloaded from https://github.com/kbhoehn/IgPhyML.
Args:
input_file (str): Path to a Phylip-formatted multiple sequence alignment. Required.
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