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
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
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
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
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
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
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
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
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
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