def _read_input_csv(in_file):
"""Parse useful details from SampleSheet CSV file.
"""
# Sanitize raw file before opening with csv reader
#_sanitize(in_file)
try:
with open(in_file, "rU") as in_handle:
dialect = csv.excel
reader = csv.DictReader(in_handle, dialect=dialect)
for line in reader:
if line: # skip empty lines
# convert '__' to '.'
for key, val in line.items():
if val is not None and type(val) is str:
line[key] = val.replace('__', '.')
yield line['FCID'], line['Lane'], line['SampleID'], \
line['SampleRef'], line['Index'], line['Description'], \
line.get('Recipe', None), line.get('Operator', None), \
line.get('SampleProject', line['Description'])
except ValueError:
log.warning("Corrupt samplesheet %s, please fix it" % in_file)
pass
def _read_input_csv(in_file):
"""Parse useful details from SampleSheet CSV file.
"""
# Sanitize raw file before opening with csv reader
# _sanitize(in_file)
try:
with open(in_file, "rU") as in_handle:
dialect = csv.excel
reader = csv.DictReader(in_handle, dialect=dialect)
for line in reader:
if line: # skip empty lines
# convert '__' to '.'
for key, val in line.items():
if val is not None and type(val) is str:
line[key] = val.replace("__", ".")
yield line["FCID"], line["Lane"], line["SampleID"], line["SampleRef"], line["Index"], line[
"Description"
], line.get("Recipe", None), line.get("Operator", None), line.get(
"SampleProject", line["Description"]
)
except ValueError:
log.warning("Corrupt samplesheet %s, please fix it" % in_file)
pass
def __init__(self, project_name, config):
"""Initialize the object"""
col_mapping = self.column_mapping()
name_column = col_mapping["project_name"]
columns = []
attributes = []
for attr, col in col_mapping.items():
columns.append(col)
attributes.append(attr)
setattr(self, attr, None)
# Get the credentials
encoded_credentials = bcbio.google.get_credentials(config)
assert encoded_credentials is not None, \
"The Google Docs credentials could not be found."
# Get the name of the spreadsheet where uppnex ids can be found
gdocs_config = config.get("gdocs_upload", {})
ssheet_title = gdocs_config.get("projects_spreadsheet", None)
wsheet_title = gdocs_config.get("projects_worksheet", None)
assert ssheet_title is not None and wsheet_title is not None, \
"The names of the projects spreadsheet and worksheet on Google \
Docs could not be found."
# Connect to the spread- and worksheet
client = bcbio.google.spreadsheet.get_client(encoded_credentials)
ssheet = bcbio.google.spreadsheet.get_spreadsheet(client, ssheet_title)
assert ssheet is not None, \
"Could not fetch %s from Google Docs." % ssheet_title
# We allow multiple, comma-separated worksheets to be searched
for wtitle in wsheet_title.split(','):
wsheet = bcbio.google.spreadsheet.get_worksheet(client, ssheet, wtitle.strip())
if not wsheet:
logger2.warning("Could not locate %s in %s." % (wsheet_title, ssheet_title))
continue
# Get the rows for the project
rows = bcbio.google.spreadsheet.get_rows_columns_with_constraint( \
client, ssheet, wsheet, columns, {name_column: project_name})
if len(rows) == 0:
continue
# Will only use the first result found to set each attribute
for i, val in enumerate(rows[0]):
setattr(self, attributes[i], val)
# We have found the project data so stop iterating
break
def _log_messages(self, log_handler, subject="Test email"):
try:
with log_handler.applicationbound():
with logbook.Processor(lambda record: record.extra.__setitem__('run', subject)):
logger2.debug("DEBUG record test generated @ %s" % time.strftime("%x - %X"))
logger2.info("INFO record test generated @ %s" % time.strftime("%x - %X"))
logger2.notice("NOTICE record test generated @ %s" % time.strftime("%x - %X"))
logger2.warning("WARNING record test generated @ %s" % time.strftime("%x - %X"))
logger2.error("ERROR record test generated @ %s" % time.strftime("%x - %X"))
logger2.critical("CRITICAL record test generated @ %s" % time.strftime("%x - %X"))
except Exception as e:
return e
return None
def _log_messages(self, log_handler, subject="Test email"):
try:
with log_handler.applicationbound():
with logbook.Processor(lambda record: record.extra.__setitem__(
'run', subject)):
logger2.debug("DEBUG record test generated @ %s" %
time.strftime("%x - %X"))
logger2.info("INFO record test generated @ %s" %
time.strftime("%x - %X"))
logger2.notice("NOTICE record test generated @ %s" %
time.strftime("%x - %X"))
logger2.warning("WARNING record test generated @ %s" %
time.strftime("%x - %X"))
logger2.error("ERROR record test generated @ %s" %
time.strftime("%x - %X"))
logger2.critical("CRITICAL record test generated @ %s" %
time.strftime("%x - %X"))
except Exception as e:
return e
return None