def main():
context = get_context()
try:
m = context['message_dict']['text']
reducer = context['message_dict']['reducer']
print("Got JSON.")
except Exception:
print("Didnt get JSON, using raw message.")
reducer = None
m = context.raw_message
wordcount = {}
for word in m.split():
w = word.lower()
if w in wordcount:
wordcount[w] += 1
else:
wordcount[w] = 1
print("Final word count:")
for k, v in wordcount.items():
print("{}: {}".format(k, v))
if reducer:
print("Sending message to reducer {}".format(reducer))
ag = get_client()
ag.actors.sendMessage(actorId=reducer,
body={'message': {
'count': wordcount
}})
def main():
print("executing")
context = get_context()
path = context['message_dict'].get('path', '/data/samples')
system_id = context['message_dict'].get('system_id',
'reactors.storage.sample')
ag = get_client()
try:
fs = ag.files.list(systemId=system_id, filePath=path)
except Exception as e:
try:
print("files error; content: {}".format(e.response.content))
except Exception as e2:
print("files original: {}; 2nd: {}".format(e, e2))
try:
p = ag.profiles.get()
except Exception as e:
try:
print("profiles error; content: {}".format(e.response.content))
except Exception as e2:
print("profiles original: {}; 2nd: {}".format(e, e2))
try:
a = ag.apps.list()
except Exception as e:
try:
print("apps error; content: {}".format(e.response.content))
except Exception as e2:
print("apps original: {}; 2nd: {}".format(e, e2))
try:
print(len(fs))
print(p)
print(a)
except Exception as e:
print("failure: {}".format(e))
def main():
context = get_context()
print("Contents of context:")
for k, v in context.items():
print("key: {}. value: {}".format(k, v))
print("Contents of env: {}".format(os.environ))
# check identity:
print("*** Posix Identity Information ***")
try:
print("Posix username: {}".format(getpass.getuser()))
except Exception as e:
# it is possible to get an exception trying to look up the username because the uid may not
# exist there. Swallow it and keep going.
print("Got an exception trying to look up the username: {}".format(e))
print("Posix uid: {}".format(os.getuid()))
print("Posix gid: {}".format(os.getgid()))
# instantiate the agavepy client:
try:
ag = get_client()
except Exception as e:
print("Got exception {} trying to get client.".format(e))
sys.exit()
try:
prof = ag.profiles.get()
print("This actor was executed by the user with profile: {}".format(
prof))
except Exception as e:
print(
"Got an exception trying to get the profile. Exception: {}".format(
e))
def main():
context = get_context()
path = context['message_dict'].get('path', '/data/samples')
system_id = context['message_dict'].get('system_id',
'reactors.storage.sample')
ag = get_client()
fs = ag.files.list(systemId=system_id, filePath=path)
print("Files: {}".format(fs))
def get_apy_client(context):
"""Instantiate the agavepy client:
"""
try:
ag = get_client()
except Exception as e:
print("Got exception {} trying to get client.".format(e))
sys.exit()
return ag
def main():
context = get_context()
ag = get_client()
try:
job = ag.jobs.submit(body=context['message_dict'])
print("jobs {} submitted successfully.".format(job))
except Exception as e:
print("Exception submitting job: {}".format(e))
def main():
ag = get_client()
context = get_context()
m = context.message_dict
file_m = m.get('file')
if not file_m:
print "Not a file event."
sys.exit()
status = file_m['status']
path = file_m['path']
system_id = file_m['systemId']
native_format = file_m['nativeFormat']
print "Status: {} path:{} system_id:{} format:{} ".format(
status, path, system_id, native_format)
try:
rsp = ag.files.list(systemId=system_id, filePath=path)
except Exception as e:
print "Got an exception trying to list files: {}".format(e)
print "URL on the request: {}".format(e.request.url)
print "Request headers: {}".format(e.request.headers)
print "Request body: {}".format(e.request.body)
print "Agave files response: {}".format(rsp)
if status == 'STAGING_COMPLETED' or status == 'TRANSFORMING_COMPLETED':
if native_format == 'dir':
# new project directory, let's add our project skeleton
ag.files.manage(systemId=system_id,
filePath=path,
body={
'action': 'mkdir',
'path': 'data'
})
ag.files.manage(systemId=system_id,
filePath=path,
body={
'action': 'mkdir',
'path': 'analysis'
})
ag.files.manage(systemId=system_id,
filePath=path,
body={
'action': 'mkdir',
'path': 'logs'
})
else:
print "Skipping since native_format was {}, not 'dir'".format(
native_format)
else:
print "Skipping since status was {}".format(status)
def get_client_with_mock_support():
"""
Return the Abaco actor's API client if
running as a function. Try to return
user's local Agave client for debug
and test purposes.
"""
_client = None
if os.environ.get('_abaco_access_token') is None:
from agavepy.agave import Agave
try:
_client = Agave.restore()
except TypeError:
_client = None
else:
_client = get_client()
return _client
def load_client(permissive=False):
"""Gets the current Tapis API client
Returns the Abaco actor's client if running deployed. Attempts to
bootstrap a client from supplied credentials if running in local or
debug mode.
"""
# Resolution order (agavepy.actors#getclient)
#
# 1. Abaco context variables
# 2. Values from TAPIS_BASE_URL + TAPIS_TOKEN
# 3. Cache from ~/.agave/current
try:
return get_client()
except Exception:
if permissive is True:
return None
else:
raise
def get_client_with_mock_support():
'''
Get the current Actor API client
Returns the Abaco actor's client if running deployed. Attempts to
bootstrap a client from supplied credentials if running in local or
debug mode.
'''
_client = None
if os.environ.get('_abaco_access_token') is None:
from agavepy.agave import Agave
try:
_client = Agave.restore()
except TypeError:
_client = None
else:
_client = get_client()
return _client
def main():
ag = get_client()
context = get_context()
m = context.message_dict
print "new_project actor running for message: {}".format(m)
file_m = m.get('file')
if not file_m:
print "Not a file event."
sys.exit()
status = file_m.get('status')
if status == 'STAGING_COMPLETED':
native_format = file_m['nativeFormat']
if native_format == 'raw':
path = file_m['path']
system_id = file_m['systemId']
process_image(ag, path, system_id)
else:
print "Skipping since native_format was {}, not 'raw'".format(
native_format)
else:
print "Skipping since status was {}".format(status)
def get_client_with_mock_support():
'''
Get the current Actor API client
Returns the Abaco actor's client if running deployed. Attempts to
bootstrap a client from supplied credentials if running in local or
debug mode.
'''
client = None
if '_abaco_access_token' not in os.environ:
try:
client = Agave.restore()
except TypeError as err:
raise AgaveError('Unable to restore Agave client: {}'.format(err))
else:
try:
client = get_client()
except Exception as err:
raise AgaveError('Unable to get Agave client from context: {}'.format(err))
return client
def get_vars(agave_context):
'''Returns container, system, and outdir variables'''
# check if passed as JSON
if type(context.message_dict) is dict:
c, s, o = get_vars_json(agave_context)
else:
c, s, o = get_vars_env(agave_context)
return (c, s, o)
if __name__ == '__main__':
# get context and client
context = get_context()
ag = get_client()
# container, agave system, and path to outdir
container, system, outdir = get_vars(context)
# execute d2s with bash
d2s_cmd = 'bash /docker2singularity.sh {}'.format(container)
process = Popen(d2s_cmd.split()).wait()
assert int(
process) == 0, 'd2s command finished with non-zero status: {}'.format(
str(process))
# find image file produced
files = ' '.join(listdir('/output'))
regex = container.replace('/', '_').replace(
':', '_') + '-[0-9]{4}-[0-9]{2}-[0-9]{2}-\w{12}\.img'
