def normalize_timedelta(timedelta):
"""
Given a string like "1w" or "5d", convert it to an integer in seconds.
Integers without a suffix are interpreted as seconds.
Note: not related to the datetime timedelta class.
"""
try:
return int(timedelta)
except ValueError as e:
suffix_multipliers = {'s': 1, 'm': 60, 'h': 60*60, 'd': 60*60*24, 'w': 60*60*24*7,
'M': 60*60*24*30, 'y': 60*60*24*365}
re_match = re.match('([0-9]+)([\s]*)([a-zA-Z]*)', timedelta)
if re_match is None:
msg = 'Could not parse time delta {0}'.format(timedelta)
raise dxpy.AppInternalError(msg)
t, space, suffix = re_match.groups()
if suffix in suffix_multipliers:
normalized_time = int(t) * suffix_multipliers[suffix]
elif suffix not in suffix_multipliers and len(suffix) > 1 and suffix[0] in suffix_multipliers:
old_suffix = suffix
suffix = suffix[0]
print('Not familiar with suffix {0}. Assuming you meant {1}.'.format(old_suffix, suffix), file=sys.stderr)
normalized_time = int(t) * suffix_multipliers[suffix]
else:
msg = 'Valid suffixes for time duration are {0}.'.format(str(suffix_multipliers.keys()))
raise dxpy.AppInternalError(msg)
return normalized_time
def normalize_timedelta(timedelta):
"""
Given a string like "1w" or "5d", convert it to an integer in seconds.
Integers without a suffix are interpreted as seconds. It is assumed this
function is run inside a dnanexus job.
Note: not related to the datetime timedelta class.
Args:
timedelta (int or str): An integer in seconds or a string of the form "1w" or "5d"
Returns:
normalized_time (int): An integer in seconds
Raises:
dxpy.AppInternalError if suffixes are not known. Known suffixes are
defined in the dictionary suffix_multipliers.
Examples:
>>> normalize_timedelta(500)
500
>>> normalize_timedelta('5w')
3024000
>>> normalize_timedelta('1d')
86400
>>> normalize_timedelta('1h')
3600
"""
try:
return int(timedelta)
except ValueError as e:
suffix_multipliers = {'s': 1, 'm': 60, 'h': 60*60, 'd': 60*60*24,
'w': 60*60*24*7,
'M': 60*60*24*30, 'y': 60*60*24*365}
re_match = re.match('([0-9]+)([\s]*)([a-zA-Z]*)', timedelta)
if re_match is None:
msg = 'Could not parse time delta {0}'.format(timedelta)
raise dxpy.AppInternalError(msg)
t, _, suffix = re_match.groups()
if suffix in suffix_multipliers:
normalized_time = int(t) * suffix_multipliers[suffix]
elif suffix not in suffix_multipliers and len(suffix) > 1 and suffix[0] in suffix_multipliers:
old_suffix = suffix
suffix = suffix[0]
print('Not familiar with suffix {0}. Assuming you meant {1}.'.format(old_suffix, suffix), file=sys.stderr)
normalized_time = int(t) * suffix_multipliers[suffix]
else:
msg = 'Valid suffixes for time duration are {0}.'.format(str(suffix_multipliers.keys()))
raise dxpy.AppInternalError(msg)
return normalized_time
def DownloadFilesFromArray(input_ids):
print "\nDownloading {n} files".format(n=len(input_ids))
if len(input_ids) < 1:
raise dxpy.AppInternalError("No files were given as input")
filenames = []
start_time = time.time()
for id in input_ids:
fn = dxpy.describe(id)["name"]
filenames.append(fn)
dxpy.download_dxfile(dxid=id, filename=fn)
print "Downloaded {files} in {min} minutes".format(
files=sorted(filenames), min=float((time.time() - start_time) / 60))
return sorted(filenames)
def normalize_timedelta(timedelta):
"""
Given a string like "1w" or "5d", convert it to an integer in seconds.
Integers without a suffix are interpreted as seconds.
Note: not related to the datetime timedelta class.
"""
try:
return int(timedelta)
except ValueError as e:
t, suffix = timedelta[:-1], timedelta[-1:]
suffix_multipliers = {'s': 1, 'm': 60, 'h': 60*60, 'd': 60*60*24, 'w': 60*60*24*7,
'M': 60*60*24*30, 'y': 60*60*24*365}
if suffix not in suffix_multipliers:
msg = 'Valid suffixes for time duration are shdwMy'
raise dxpy.AppInternalError(msg)
return int(t) * suffix_multipliers[suffix]
def locate_or_create_dx_drive():
# findDrives is an API method that has not been explicitly added to dxpy yet, so call the API method explicitly.
drives = dxpy.DXHTTPRequest('/system/findDrives', {'name': DX_DRIVE_NAME}, always_retry=True)['results']
if len(drives) == 1:
return drives[0]
elif len(drives) == 0:
# if no drive exists, create it
access_key, secret_access_key = _get_aws_key()
print('Creating drive with name: {0}'.format(DX_DRIVE_NAME))
# create drive using API call
new_drive_def = {'name': DX_DRIVE_NAME,
'cloud': 'aws',
'credentials': {'accessKeyId': access_key,
'secretAccessKey': secret_access_key}}
drive_id = dxpy.DXHTTPRequest('/drive/new', new_drive_def)
print('Created drive with id: {0}'.format(DX_DRIVE_NAME))
return drive_id
elif len(drives) > 1:
msg = 'More than one drives found with name "{0}"'.format(DX_DRIVE_NAME)
raise dxpy.AppInternalError(msg)
def _get_species_name():
project_desc = dxpy.describe(dxpy.PROJECT_CONTEXT_ID, input_params={'properties': True})
if 'species_name' in project_desc['properties']:
return project_desc['properties']['species_name']
else:
raise dxpy.AppInternalError('No species name was provided as input or as a property of this project.')