Python get_file_timestampの例

コード例 #1

ファイル: __init__.py プロジェクト: kevyin/bcbio-nextgen

def _add_meta(xs, sample):
    out = []
    for x in xs:
        x["mtime"] = shared.get_file_timestamp(x["path"])
        x["sample"] = sample["name"][-1]
        out.append(x)
    return out

コード例 #2

ファイル: __init__.py プロジェクト: ohofmann/bcbio-nextgen

def _add_meta(xs, sample=None, config=None):
    """Add top level information about the sample or flowcell to output.

    Sorts outputs into sample names (sample input) and project (config input).
    """
    out = []
    for x in xs:
        if not isinstance(x["path"], basestring) or not os.path.exists(
                x["path"]):
            raise ValueError("Unexpected path for upload: %s" % x)
        x["mtime"] = shared.get_file_timestamp(x["path"])
        if sample:
            sample_name = dd.get_sample_name(sample)
            if "sample" not in x:
                x["sample"] = sample_name
            elif x["sample"] != sample_name:
                x["run"] = sample_name
        if config:
            if "fc_name" in config and "fc_date" in config:
                x["run"] = "%s_%s" % (config["fc_date"], config["fc_name"])
            else:
                x["run"] = "project_%s" % datetime.datetime.now().strftime(
                    "%Y-%m-%d")
        out.append(x)
    return out

コード例 #3

ファイル: __init__.py プロジェクト: janusz005/bcbio-nextgen

def _add_meta(xs, sample=None, config=None):
    out = []
    for x in xs:
        x["mtime"] = shared.get_file_timestamp(x["path"])
        if sample:
            x["sample"] = sample["name"][-1]
        if config:
            x["run"] = "%s_%s" % (config["fc_date"], config["fc_name"])
        out.append(x)
    return out

コード例 #4

ファイル: __init__.py プロジェクト: alneberg/bcbio-nextgen

def _add_meta(xs, sample=None, config=None):
    out = []
    for x in xs:
        x["mtime"] = shared.get_file_timestamp(x["path"])
        if sample:
            x["sample"] = sample["name"][-1]
        if config:
            x["run"] = "%s_%s" % (config["fc_date"], config["fc_name"])
        out.append(x)
    return out

コード例 #5

ファイル: __init__.py プロジェクト: abushoy/bcbio-nextgen

def _add_meta(xs, sample=None, config=None):
    out = []
    for x in xs:
        x["mtime"] = shared.get_file_timestamp(x["path"])
        if sample:
            x["sample"] = sample["name"][-1]
        if config:
            if "fc_name" in config and "fc_date" in config:
                x["run"] = "%s_%s" % (config["fc_date"], config["fc_name"])
            else:
                x["run"] = "project_%s" % datetime.datetime.now().strftime("%Y-%m-%d")
        out.append(x)
    return out

コード例 #6

ファイル: __init__.py プロジェクト: senthil10/bcbio-nextgen

def _add_meta(xs, sample=None, config=None):
    out = []
    for x in xs:
        x["mtime"] = shared.get_file_timestamp(x["path"])
        if sample:
            x["sample"] = sample["name"][-1]
        if config:
            if "fc_name" in config and "fc_date" in config:
                x["run"] = "%s_%s" % (config["fc_date"], config["fc_name"])
            else:
                x["run"] = "project_%s" % datetime.datetime.now().strftime("%Y-%m-%d")
        out.append(x)
    return out

コード例 #7

ファイル: __init__.py プロジェクト: tiehan/bcbio-nextgen

def _add_meta(xs, sample=None, config=None):
    out = []
    for x in xs:
        if not isinstance(x["path"], basestring) or not os.path.exists(x["path"]):
            raise ValueError("Unexpected path for upload: %s" % x)
        x["mtime"] = shared.get_file_timestamp(x["path"])
        if sample and "sample" not in x:
            x["sample"] = dd.get_sample_name(sample)
        if config:
            if "fc_name" in config and "fc_date" in config:
                x["run"] = "%s_%s" % (config["fc_date"], config["fc_name"])
            else:
                x["run"] = "project_%s" % datetime.datetime.now().strftime("%Y-%m-%d")
        out.append(x)
    return out

コード例 #8

ファイル: __init__.py プロジェクト: tanglingfung/bcbio-nextgen

def _add_meta(xs, sample=None, config=None):
    out = []
    for x in xs:
        x["mtime"] = shared.get_file_timestamp(x["path"])
        if sample and "sample" not in x:
            if isinstance(sample["name"], (tuple, list)):
                name = sample["name"][-1]
            else:
                name = "%s-%s" % (sample["name"], run_info.clean_name(sample["description"]))
            x["sample"] = name
        if config:
            if "fc_name" in config and "fc_date" in config:
                x["run"] = "%s_%s" % (config["fc_date"], config["fc_name"])
            else:
                x["run"] = "project_%s" % datetime.datetime.now().strftime("%Y-%m-%d")
        out.append(x)
    return out

コード例 #9

def _add_meta(xs, sample=None, config=None):
    out = []
    for x in xs:
        x["mtime"] = shared.get_file_timestamp(x["path"])
        if sample and "sample" not in x:
            if isinstance(sample["name"], (tuple, list)):
                name = sample["name"][-1]
            else:
                name = "%s-%s" % (sample["name"], run_info.clean_name(sample["description"]))
            x["sample"] = name
        if config:
            if "fc_name" in config and "fc_date" in config:
                x["run"] = "%s_%s" % (config["fc_date"], config["fc_name"])
            else:
                x["run"] = "project_%s" % datetime.datetime.now().strftime("%Y-%m-%d")
        out.append(x)
    return out

コード例 #10

ファイル: __init__.py プロジェクト: chapmanb/bcbio-nextgen

def _add_meta(xs, sample=None, config=None):
    """Add top level information about the sample or flowcell to output.

    Sorts outputs into sample names (sample input) and project (config input).
    """
    out = []
    for x in xs:
        if not isinstance(x["path"], six.string_types) or not os.path.exists(x["path"]):
            raise ValueError("Unexpected path for upload: %s" % x)
        x["mtime"] = shared.get_file_timestamp(x["path"])
        if sample:
            sample_name = dd.get_sample_name(sample)
            if "sample" not in x:
                x["sample"] = sample_name
            elif x["sample"] != sample_name:
                x["run"] = sample_name
        if config:
            fc_name = config.get("fc_name") or "project"
            fc_date = config.get("fc_date") or datetime.datetime.now().strftime("%Y-%m-%d")
            x["run"] = "%s_%s" % (fc_date, fc_name)
        out.append(x)
    return out