comparison data_manager/fetch_mothur_reference_data.py @ 3:9d09724f2bf1 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"

2:0e532fc0a0a6

    NB the directory pointed to by 'extra_files_path'
    doesn't exist initially, it is the job of the script
    to create it if necessary.

    """
    params = json.loads(open(jsonfile).read())
    return (params['param_dict'],
            params['output_data'][0]['extra_files_path'])


# Utility functions for creating data table dictionaries

# Example usage:
# >>> d = create_data_tables_dict()
# >>> add_data_table(d,'my_data')
# >>> add_data_table_entry(dict(dbkey='hg19',value='human'))
# >>> add_data_table_entry(dict(dbkey='mm9',value='mouse'))
# >>> print str(json.dumps(d))
def create_data_tables_dict():
    """Return a dictionary for storing data table information

    Returns a dictionary that can be used with 'add_data_table'
    and 'add_data_table_entry' to store information about a

    if not target:
        target = os.path.basename(url)
    if wd:
        target = os.path.join(wd, target)
    print("Saving to %s" % target)
    open(target, 'wb').write(urllib2.urlopen(url).read())
    return target


def unpack_zip_archive(filen, wd=None):
    """Extract files from a ZIP archive

    """
    if not zipfile.is_zipfile(filen):
        print("%s: not ZIP formatted file")
        return [filen]
    file_list = []
    z = zipfile.ZipFile(filen)
    for name in z.namelist():
        if reduce(lambda x, y: x or name.startswith(y), IGNORE_PATHS, False):
            print("Ignoring %s" % name)
            continue
        if wd:
            target = os.path.join(wd, name)
        else:
            target = name
        if name.endswith('/'):
            # Make directory
            print("Creating dir %s" % target)
            try:
                os.makedirs(target)
            except OSError:
                pass
        else:
            # Extract file
            print("Extracting %s" % name)
            try:
                os.makedirs(os.path.dirname(target))
            except OSError:
                pass
            open(target, 'wb').write(z.read(name))
            file_list.append(target)
    print("Removing %s" % filen)
    os.remove(filen)
    return file_list

    """
    file_list = []
    if not tarfile.is_tarfile(filen):
        print("%s: not TAR file")
        return [filen]
    t = tarfile.open(filen)
    for name in t.getnames():
        # Check for unwanted files
        if reduce(lambda x, y: x or name.startswith(y), IGNORE_PATHS, False):
            print("Ignoring %s" % name)
            continue
        # Extract file
        print("Extracting %s" % name)
        t.extract(name, wd)
        if wd:
            target = os.path.join(wd, name)
        else:
            target = name
        file_list.append(target)
    print("Removing %s" % filen)
    os.remove(filen)
    return file_list

        # that might have been inserted by Galaxy)
        paths = options.paths.replace('__cn__', '\n').replace('__cr__', '\r').split()
        import_from_server(data_tables, target_dir, paths, description, link_to_data=options.link_to_data)
    # Write output JSON
    print("Outputting JSON")
    print(json.dumps(data_tables))
    open(jsonfile, 'w').write(json.dumps(data_tables, sort_keys=True))
    print("Done.")

3:9d09724f2bf1

    NB the directory pointed to by 'extra_files_path'
    doesn't exist initially, it is the job of the script
    to create it if necessary.

    """
    with open(jsonfile) as fh:
        params = json.load(fh)
    return (params['param_dict'],
            params['output_data'][0]['extra_files_path'])


# Utility functions for creating data table dictionaries

# Example usage:
# >>> d = create_data_tables_dict()
# >>> add_data_table(d,'my_data')
# >>> add_data_table_entry(dict(dbkey='hg19',value='human'))
# >>> add_data_table_entry(dict(dbkey='mm9',value='mouse'))
# >>> print(json.dumps(d))
def create_data_tables_dict():
    """Return a dictionary for storing data table information

    Returns a dictionary that can be used with 'add_data_table'
    and 'add_data_table_entry' to store information about a

    if not target:
        target = os.path.basename(url)
    if wd:
        target = os.path.join(wd, target)
    print("Saving to %s" % target)
    with open(target, 'wb') as fh:
        fh.write(urllib2.urlopen(url).read())
    return target


def unpack_zip_archive(filen, wd=None):
    """Extract files from a ZIP archive

    """
    if not zipfile.is_zipfile(filen):
        print("%s: not ZIP formatted file")
        return [filen]
    file_list = []
    with zipfile.ZipFile(filen) as z:
        for name in z.namelist():
            if reduce(lambda x, y: x or name.startswith(y), IGNORE_PATHS, False):
                print("Ignoring %s" % name)
                continue
            if wd:
                target = os.path.join(wd, name)
            else:
                target = name
            if name.endswith('/'):
                # Make directory
                print("Creating dir %s" % target)
                try:
                    os.makedirs(target)
                except OSError:
                    pass
            else:
                # Extract file
                print("Extracting %s" % name)
                try:
                    os.makedirs(os.path.dirname(target))
                except OSError:
                    pass
                with open(target, 'wb') as fh:
                    fh.write(z.read(name))
                file_list.append(target)
    print("Removing %s" % filen)
    os.remove(filen)
    return file_list

    """
    file_list = []
    if not tarfile.is_tarfile(filen):
        print("%s: not TAR file")
        return [filen]
    with tarfile.open(filen) as t:
        for name in t.getnames():
            # Check for unwanted files
            if reduce(lambda x, y: x or name.startswith(y), IGNORE_PATHS, False):
                print("Ignoring %s" % name)
                continue
            # Extract file
            print("Extracting %s" % name)
            t.extract(name, wd)
            if wd:
                target = os.path.join(wd, name)
            else:
                target = name
            file_list.append(target)
    print("Removing %s" % filen)
    os.remove(filen)
    return file_list

        # that might have been inserted by Galaxy)
        paths = options.paths.replace('__cn__', '\n').replace('__cr__', '\r').split()
        import_from_server(data_tables, target_dir, paths, description, link_to_data=options.link_to_data)
    # Write output JSON
    print("Outputting JSON")
    with open(jsonfile, 'w') as fh:
        json.dump(data_tables, fh, sort_keys=True)
    print("Done.")