How to use make_excluded method in Behave

Best Python code snippet using behave

invoke_cleanup.py

Source:invoke_cleanup.py

...83                print("FAILURE in CLEANUP TASK: %s (GRACEFULLY-IGNORED)" % cleanup_task)84                failure_count += 185    if failure_count:86        print("CLEANUP TASKS: %d failure(s) occured" % failure_count)87def make_excluded(excluded, config_dir=None, workdir=None):88    workdir = workdir or Path.getcwd()89    config_dir = config_dir or workdir90    workdir = Path(workdir)91    config_dir = Path(config_dir)92    excluded2 = []93    for p in excluded:94        assert p, "REQUIRE: non-empty"95        p = Path(p)96        if p.isabs():97            excluded2.append(p.normpath())98        else:99            # -- RELATIVE PATH:100            # Described relative to config_dir.101            # Recompute it relative to current workdir.102            p = Path(config_dir)/p103            p = workdir.relpathto(p)104            excluded2.append(p.normpath())105            excluded2.append(p.abspath())106    return set(excluded2)107def is_directory_excluded(directory, excluded):108    directory = Path(directory).normpath()109    directory2 = directory.abspath()110    if (directory in excluded) or (directory2 in excluded):111        return True112    # -- OTHERWISE:113    return False114def cleanup_dirs(patterns, workdir=".", excluded=None,115                 dry_run=False, verbose=False, show_skipped=False):116    """Remove directories (and their contents) recursively.117    Skips removal if directories does not exist.118    :param patterns:    Directory name patterns, like "**/tmp*" (as list).119    :param workdir:     Current work directory (default=".")120    :param dry_run:     Dry-run mode indicator (as bool).121    """122    excluded = excluded or []123    excluded = set([Path(p) for p in excluded])124    show_skipped = show_skipped or verbose125    current_dir = Path(workdir)126    python_basedir = Path(Path(sys.executable).dirname()).joinpath("..").abspath()127    warn2_counter = 0128    for dir_pattern in patterns:129        for directory in path_glob(dir_pattern, current_dir):130            if is_directory_excluded(directory, excluded):131                print("SKIP-DIR: %s (excluded)" % directory)132                continue133            directory2 = directory.abspath()134            if sys.executable.startswith(directory2):135                # -- PROTECT VIRTUAL ENVIRONMENT (currently in use):136                # pylint: disable=line-too-long137                print("SKIP-SUICIDE: '%s' contains current python executable" % directory)138                continue139            elif directory2.startswith(python_basedir):140                # -- PROTECT VIRTUAL ENVIRONMENT (currently in use):141                # HINT: Limit noise in DIAGNOSTIC OUTPUT to X messages.142                if warn2_counter <= 4:  # noqa143                    print("SKIP-SUICIDE: '%s'" % directory)144                warn2_counter += 1145                continue146            if not directory.isdir():147                if show_skipped:148                    print("RMTREE: %s (SKIPPED: Not a directory)" % directory)149                continue150            if dry_run:151                print("RMTREE: %s (dry-run)" % directory)152            else:153                try:154                    # -- MAYBE: directory.rmtree(ignore_errors=True)155                    print("RMTREE: %s" % directory)156                    directory.rmtree_p()157                except OSError as e:158                    print("RMTREE-FAILED: %s (for: %s)" % (e, directory))159def cleanup_files(patterns, workdir=".", dry_run=False, verbose=False, show_skipped=False):160    """Remove files or files selected by file patterns.161    Skips removal if file does not exist.162    :param patterns:    File patterns, like "**/*.pyc" (as list).163    :param workdir:     Current work directory (default=".")164    :param dry_run:     Dry-run mode indicator (as bool).165    """166    show_skipped = show_skipped or verbose167    current_dir = Path(workdir)168    python_basedir = Path(Path(sys.executable).dirname()).joinpath("..").abspath()169    error_message = None170    error_count = 0171    for file_pattern in patterns:172        for file_ in path_glob(file_pattern, current_dir):173            if file_.abspath().startswith(python_basedir):174                # -- PROTECT VIRTUAL ENVIRONMENT (currently in use):175                continue176            if not file_.isfile():177                if show_skipped:178                    print("REMOVE: %s (SKIPPED: Not a file)" % file_)179                continue180            if dry_run:181                print("REMOVE: %s (dry-run)" % file_)182            else:183                print("REMOVE: %s" % file_)184                try:185                    file_.remove_p()186                except os.error as e:187                    message = "%s: %s" % (e.__class__.__name__, e)188                    print(message + " basedir: "+ python_basedir)189                    error_count += 1190                    if not error_message:191                        error_message = message192    if False and error_message: # noqa193        class CleanupError(RuntimeError):194            pass195        raise CleanupError(error_message)196def path_glob(pattern, current_dir=None):197    """Use pathlib for ant-like patterns, like: "**/*.py"198    :param pattern:      File/directory pattern to use (as string).199    :param current_dir:  Current working directory (as Path, pathlib.Path, str)200    :return Resolved Path (as path.Path).201    """202    if not current_dir: # noqa203        current_dir = pathlib.Path.cwd()204    elif not isinstance(current_dir, pathlib.Path):205        # -- CASE: string, path.Path (string-like)206        current_dir = pathlib.Path(str(current_dir))207    pattern_path = Path(pattern)208    if pattern_path.isabs():209        # -- SPECIAL CASE: Path.glob() only supports relative-path(s) / pattern(s).210        if pattern_path.isdir():211            yield pattern_path212        return213    # -- HINT: OSError is no longer raised in pathlib2 or python35.pathlib214    # try:215    for p in current_dir.glob(pattern):216        yield Path(str(p))217    # except OSError as e:218    #     # -- CORNER-CASE 1: x.glob(pattern) may fail with:219    #     # OSError: [Errno 13] Permission denied: <filename>220    #     # HINT: Directory lacks excutable permissions for traversal.221    #     # -- CORNER-CASE 2: symlinked endless loop222    #     # OSError: [Errno 62] Too many levels of symbolic links: <filename>223    #     print("{0}: {1}".format(e.__class__.__name__, e))224# -----------------------------------------------------------------------------225# GENERIC CLEANUP TASKS:226# -----------------------------------------------------------------------------227@task(help={228    "workdir": "Directory to clean(up) (default: $CWD).",229    "verbose": "Enable verbose mode (default: OFF).",230})231def clean(ctx, workdir=".", verbose=False):232    """Cleanup temporary dirs/files to regain a clean state."""233    dry_run = ctx.config.run.dry234    config_dir = getattr(ctx.config, "config_dir", workdir)235    directories = list(ctx.config.cleanup.directories or [])236    directories.extend(ctx.config.cleanup.extra_directories or [])237    files = list(ctx.config.cleanup.files or [])238    files.extend(ctx.config.cleanup.extra_files or [])239    excluded_directories = list(ctx.config.cleanup.excluded_directories or [])240    excluded_directories = make_excluded(excluded_directories,241                                         config_dir=config_dir, workdir=".")242    # -- PERFORM CLEANUP:243    execute_cleanup_tasks(ctx, cleanup_tasks)244    cleanup_dirs(directories, workdir=workdir, excluded=excluded_directories,245                 dry_run=dry_run, verbose=verbose)246    cleanup_files(files, workdir=workdir, dry_run=dry_run, verbose=verbose)247    # -- CONFIGURABLE EXTENSION-POINT:248    # use_cleanup_python = ctx.config.cleanup.use_cleanup_python or False249    # if use_cleanup_python:250    #     clean_python(ctx)251@task(name="all", aliases=("distclean",),252      help={253        "workdir": "Directory to clean(up) (default: $CWD).",254        "verbose": "Enable verbose mode (default: OFF).",255})256def clean_all(ctx, workdir=".", verbose=False):257    """Clean up everything, even the precious stuff.258    NOTE: clean task is executed last.259    """260    dry_run = ctx.config.run.dry261    config_dir = getattr(ctx.config, "config_dir", workdir)262    directories = list(ctx.config.cleanup_all.directories or [])263    directories.extend(ctx.config.cleanup_all.extra_directories or [])264    files = list(ctx.config.cleanup_all.files or [])265    files.extend(ctx.config.cleanup_all.extra_files or [])266    excluded_directories = list(ctx.config.cleanup_all.excluded_directories or [])267    excluded_directories.extend(ctx.config.cleanup.excluded_directories or [])268    excluded_directories = make_excluded(excluded_directories,269                                         config_dir=config_dir, workdir=".")270    # -- PERFORM CLEANUP:271    # HINT: Remove now directories, files first before cleanup-tasks.272    cleanup_dirs(directories, workdir=workdir, excluded=excluded_directories,273                 dry_run=dry_run, verbose=verbose)274    cleanup_files(files, workdir=workdir, dry_run=dry_run, verbose=verbose)275    execute_cleanup_tasks(ctx, cleanup_all_tasks)276    clean(ctx, workdir=workdir, verbose=verbose)277    # -- CONFIGURABLE EXTENSION-POINT:278    # use_cleanup_python1 = ctx.config.cleanup.use_cleanup_python or False279    # use_cleanup_python2 = ctx.config.cleanup_all.use_cleanup_python or False280    # if use_cleanup_python2 and not use_cleanup_python1:281    #     clean_python(ctx)282@task(aliases=["python"])...

base.py

Source:base.py

...272    def __exit__(self, exc_type, exc_val, exc_tb):273        self.close()274DEFAULT_EXCLUDES = fnmatch.translate(".*")275DEFAULT_EXCLUDES_RE = re.compile(DEFAULT_EXCLUDES).match276def make_excluded(excludes=None):277    if excludes is None:278        return DEFAULT_EXCLUDES_RE279    patterns = [DEFAULT_EXCLUDES]280    patterns.extend(fnmatch.translated(x) for x in excludes)281    return re.compile("|".join(patterns)).match282def generate_paths(roots, excludes=None):283    """284    Walk set of paths in local filesystem, and for each file and directory generate a tuple of285    (is directory, absolute path, path relative root used to get to that file)286    """287    excluded = make_excluded(excludes)288    for root in roots:289        base = os.path.basename(root)290        if not excluded(base):291            is_dir = os.path.isdir(root)292            yield is_dir, root, base293            if is_dir:294                prefix_len = len(os.path.dirname(root))295                for dirpath, dirnames, filenames in os.walk(root, topdown=True, followlinks=True):296                    relpath = dirpath[prefix_len:].strip('/')297                    for is_dir, names in ((False, filenames), (True, dirnames)):298                        for name in names:299                            if not excluded(name):300                                yield is_dir, os.path.join(dirpath, name), "%s/%s" % (relpath, name)301def filter_none_values(dict):...

choose_samples.py

Source:choose_samples.py

1#!/usr/bin/env python2from __future__ import (print_function)3import argparse4from operator import itemgetter5import os.path6import subprocess7import sys8import yaml9parser = argparse.ArgumentParser(description="Choose samples for bin reassembly")10parser.add_argument("-r", "--reads", type=str, help="Directory with reads")11parser.add_argument("-o", "--output", type=str, help="Output path")12parser.add_argument("prof", type=str, help="File with bin profiles")13parser.add_argument("-f", "--filtered", type=str, help="File with filtered bins")14parser.add_argument("--min-sample", type=float, default=4, help="Minimal coverage in a single sample to be used")15parser.add_argument("--min-total", type=float, default=1, help="Minimal total coverage of the bin to be reassembled")16args = parser.parse_args()17BINS = set()18if args.filtered:19    with open(args.filtered) as input:20        for line in input:21            bin = line.split()[0]22            BINS.add(bin)23prof_dict = dict()24make_excluded = True25excluded_dir = os.path.join(args.output, "excluded")26input = open(args.prof)27for line in input:28    exclude = False29    samples = []30    params = line.split()31    bin = params[0]32    profile = list(map(float, params[1:]))33    print("Profile of", bin, ":", profile)34    if BINS and bin not in BINS:35        print(bin, "was excluded from the reassembly")36        exclude = True37    total = 038    #Current strategy: choose all samples larger than soft threshold.39    #If there's not enough, use the lower hard threshold.40    #Sort samples by their abundancies41    weighted_profile = list((i, ab)42        for i, ab in enumerate(profile, start=1) if ab >= args.min_sample)43    weighted_profile.sort(key=itemgetter(1), reverse=True)44    for i, cov in weighted_profile:45        if not os.path.exists(os.path.join(args.reads, bin, "sample{}_1.fastq.gz".format(i))):46            print("WARNING: sample", i, "does not contain reads for", bin)47            continue48        total += cov49        samples.append(i)50    print("Chosen samples are", samples, "with total mean abundance", total)51    prof_dict[bin] = total52    if total < args.min_total:53        print(bin, "is too scarce; excluding from the reassembly")54        exclude = True55    config_dir = args.output56    if exclude:57        if make_excluded and not os.path.isdir(excluded_dir):58            os.mkdir(excluded_dir)59        make_excluded = False60        config_dir = excluded_dir61    config_path = os.path.join(config_dir, bin + ".info")62    print("Dumping config into", config_path)63    with open(config_path, "w") as out:64        print("total", sum(profile), file=out)65        for i, ab in enumerate(profile, start=1):66            line = "sample" + str(i)67            if i in samples:68                line = "+" + line...

complete_lp.py

Source:complete_lp.py

...22            else:23                fout.write('presc: ' + var + ' = 0\n')24        25    fout.write('binary\n' + ' '.join(vars))26def make_excluded(db):27    c = db.cursor()28    c.execute("""29select id from casteller where nickname in ('AE', 'Aina', 'Alaitz', 'Aleix', 'Alvarito', 'Berta', 'Eva', 'Joana', 'Joanet', 'Laia O', 'Lali', 'Marco', 'Martina', 'Montxi', 'Oriolet', 'Rafols', 'Rai', 'Santako', 'Stefano');30""")31    ans = []32    for row in c.fetchall():33        ans.append(int(row[0]))34    return ans35def make_segons(db):36    c = db.cursor()37    c.execute("""38select id from casteller where nickname in ('Abdul', 'Arnau', 'Quim');39""")40    ans = []41    for row in c.fetchall():42        ans.append(int(row[0]))43    print ans44    return ans45def complete_lp():46    db = get_db()47    excluded = make_excluded(db)48    prescribed = dict([(2, 79), (14, 80), (72, 81)]) # Abdul, Arnau, Quim as segons49    print prescribed50    print excluded 51    [castell_id_name, colla_id_name] = ['cvg.3de9f', 'cvg']52    complete_lp_impl(prescribed, excluded, castell_id_name, colla_id_name)53if __name__=="__main__":...

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