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How to use parse_pict_output method in avocado

Best Python code snippet using avocado_python

varianter_pict.py

Source:varianter_pict.py

...92        pass93def run_pict(binary, parameter_file, order):94    cmd = f"{binary} {parameter_file} /o:{order}"95    return process.run(cmd, shell=True).stdout_text96def parse_pict_output(output):97    variants = []98    lines = output.splitlines()99    header = lines[0]100    headers = header.split("\t")101    for line in lines[1:]:102        variants.append(dict(zip(headers, line.split("\t"))))103    return (headers, variants)104class VarianterPict(Varianter):105    """106    Processes the pict file into variants107    """108    name = "pict"109    description = "PICT based Varianter"110    def initialize(self, config):111        self.variants = None  # pylint: disable=W0201112        error = False113        subcommand = config.get("subcommand", "run")114        namespace = f"{subcommand}.pict_parameter_file"115        pict_parameter_file = config.get(namespace)116        if pict_parameter_file is None:117            return118        else:119            pict_parameter_file = os.path.expanduser(pict_parameter_file)120            if not os.access(pict_parameter_file, os.R_OK):121                LOG_UI.error(122                    "pict parameter file '%s' could not be found or " "is not readable",123                    pict_parameter_file,124                )125                error = True126        pict_binary = config.get(f"{subcommand}.pict_binary")127        if pict_binary is None:128            LOG_UI.error(129                "pict binary could not be found in $PATH. Please set "130                "its location with --pict-binary or put it in your "131                "$PATH"132            )133            error = True134        else:135            pict_binary = os.path.expanduser(pict_binary)136            if not os.access(pict_binary, os.R_OK | os.X_OK):137                LOG_UI.error(138                    "pict binary '%s' can not be executed, please check "139                    "the option given with --pict-binary and/or the file "140                    "permissions",141                    pict_binary,142                )143                error = True144        if error:145            if subcommand == "run":146                sys.exit(exit_codes.AVOCADO_JOB_FAIL)147            else:148                sys.exit(exit_codes.AVOCADO_FAIL)149        path_namespace = f"{subcommand}.pict_parameter_path"150        self.parameter_path = config.get(path_namespace)  # pylint: disable=W0201151        order_namespace = f"{subcommand}.pict_combinations_order"152        output = run_pict(pict_binary, pict_parameter_file, config.get(order_namespace))153        self.headers, self.variants = parse_pict_output(output)  # pylint: disable=W0201154    def __iter__(self):155        if self.variants is None:156            return157        variant_ids = []158        for variant in self.variants:159            base_id = "-".join([variant.get(key) for key in self.headers])160            variant_ids.append(161                base_id + "-" + hashlib.sha1(base_id.encode()).hexdigest()[:4]162            )163        for vid, variant in zip(variant_ids, self.variants):164            variant_tree_nodes = []165            for key, val in variant.items():166                variant_tree_nodes.append(TreeNode(key, {key: val}))167            yield {...

__init__.py

Source:__init__.py

...60        pass61def run_pict(binary, parameter_file, order):62    cmd = "%s %s /o:%s" % (binary, parameter_file, order)63    return process.system_output(cmd, shell=True)64def parse_pict_output(output):65    variants = []66    lines = output.splitlines()67    header = lines[0]68    headers = header.split('\t')69    for line in lines[1:]:70        variants.append(dict(zip(headers, line.split('\t'))))71    return (headers, variants)72class VarianterPict(Varianter):73    """74    Processes the pict file into variants75    """76    name = 'pict'77    description = "PICT based Varianter"78    def initialize(self, args):79        self.variants = None80        error = False81        pict_parameter_file = getattr(args, "pict_parameter_file", None)82        if pict_parameter_file is None:83            return84        else:85            pict_parameter_file = os.path.expanduser(pict_parameter_file)86            if not os.access(pict_parameter_file, os.R_OK):87                LOG_UI.error("pict parameter file '%s' could not be found or "88                             "is not readable", pict_parameter_file)89                error = True90        pict_binary = getattr(args, "pict_binary", None)91        if pict_binary is None:92            LOG_UI.error("pict binary could not be found in $PATH. Please set "93                         "its location with --pict-binary or put it in your "94                         "$PATH")95            error = True96        else:97            pict_binary = os.path.expanduser(pict_binary)98            if not os.access(pict_binary, os.R_OK | os.X_OK):99                LOG_UI.error("pict binary '%s' can not be executed, please check "100                             "the option given with --pict-binary and/or the file "101                             "permissions", pict_binary)102                error = True103        if error:104            if args.subcommand == 'run':105                sys.exit(exit_codes.AVOCADO_JOB_FAIL)106            else:107                sys.exit(exit_codes.AVOCADO_FAIL)108        self.parameter_path = getattr(args, "pict_parameter_path")109        output = run_pict(pict_binary,110                          pict_parameter_file,111                          getattr(args, "pict_order_of_combinations"))112        self.headers, self.variants = parse_pict_output(output)113    def __iter__(self):114        if self.variants is None:115            return116        variant_ids = []117        for variant in self.variants:118            base_id = "-".join([variant.get(key) for key in self.headers])119            variant_ids.append(base_id + '-' +120                               hashlib.sha1(base_id).hexdigest()[:4])121        for vid, variant in itertools.izip(variant_ids, self.variants):122            variant_tree_nodes = []123            for key, val in variant.items():124                variant_tree_nodes.append(TreeNode(key, {key: val}))125            yield {"variant_id": vid,126                   "variant": variant_tree_nodes,...

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