class Client:
def __init__(self, url, user, token):
self.url = utils.verify_url(url)
self.user = user
self.token = token
self.headers = {'Authorization': '{}'.format(self.token),
'Content-type': 'application/json',
'Accept': 'text/plain'}
self.shock = None
def init_shock(self):
if self.shock is None:
shockres = self.req_get('{}/shock'.format(self.url))
self.shockurl = utils.verify_url(json.loads(shockres)['shockurl'])
self.shock = Shock(self.shockurl, self.user, self.token)
def upload_data_shock(self, filename, curl=False):
self.init_shock()
res = self.shock.upload_reads(filename, curl=curl)
shock_info = {'filename': os.path.basename(filename),
'filesize': os.path.getsize(filename),
'shock_url': self.shockurl,
'shock_id': res['data']['id'],
'upload_time': str(datetime.datetime.utcnow())}
return res, shock_info
def upload_data_file_info(self, filename, curl=False):
""" Returns FileInfo Object """
self.init_shock()
res = self.shock.upload_reads(filename, curl=curl)
return asmtypes.FileInfo(filename, shock_url=self.shockurl, shock_id=res['data']['id'],
create_time=str(datetime.datetime.utcnow()))
def submit_job(self, data):
url = '{}/user/{}/job/new'.format(self.url, self.user)
return self.req_post(url, data=data)
def submit_data(self, data):
url = '{}/user/{}/data/new'.format(self.url, self.user)
return self.req_post(url, data=data)
def get_job_status(self, stat_n, job_id=None, detail=False):
if job_id:
url = '{}/user/{}/job/{}/status'.format(self.url, self.user, job_id)
else:
if detail:
url = '{}/user/{}/job/status?records={}&detail=True'.format(
self.url, self.user, stat_n)
else:
url = '{}/user/{}/job/status?records={}'.format(
self.url, self.user, stat_n)
return self.req_get(url)
def get_data_list(self):
url = '{}/user/{}/data'.format(self.url, self.user)
li = json.loads(self.req_get(url))
li.sort(key=lambda e: e["data_id"])
return li
def get_data_list_table(self, stat_n=10):
li = self.get_data_list()
li = li[-stat_n:]
rows = []
for data in li:
data_id = data.get("data_id", "")
message = data.get("message")
if 'kbase_assembly_input' in data:
message = data['kbase_assembly_input'].get(
'dataset_description')
data_rows = assembly_data_to_rows(data)
data_rows = [ [''] * 2 + r for r in data_rows]
rows += [[data_id, message] + [''] * 2]
rows += data_rows
pt = PrettyTable(["Data ID", "Description", "Type", "Files"]);
for r in rows: pt.add_row(r)
return pt.get_string()
def get_data_json(self, data_id):
url = '{}/user/{}/data/{}'.format(self.url, self.user, data_id)
return self.req_get(url)
def is_job_valid(self, job_id):
stat = self.get_job_status(1, job_id)
return False if stat.startswith("Could not get job status") else True
def is_job_done(self, job_id):
stat = self.get_job_status(1, job_id)
match = re.search('(complete|fail|terminated)', stat, re.IGNORECASE)
return True if match else False
def validate_job(self, job_id):
if not self.is_job_valid(job_id):
sys.exit("Invalid job ID: {}".format(job_id))
return
def wait_for_job(self, job_id):
self.validate_job(job_id)
while not self.is_job_done(job_id):
time.sleep(5)
return self.get_job_status(1, job_id)
def check_job(self, job_id):
if not self.is_job_done(job_id):
sys.stderr.write("Job in progress. Use -w to wait for the job.\n")
sys.exit()
def get_job_report(self, job_id):
"""Get the stats section of job report"""
url = '{}/user/{}/job/{}/report'.format(self.url, self.user, job_id)
return self.req_get(url)
def get_job_log(self, job_id):
"""Get the log section of job report"""
url = '{}/user/{}/job/{}/log'.format(self.url, self.user, job_id)
return self.req_get(url)
def get_job_report_full(self, job_id, stdout=False, outdir=None):
url = '{}/user/{}/job/{}/report_handle'.format(self.url, self.user, job_id)
handle = json.loads(self.req_get(url))
self.download_shock_handle(handle, stdout=stdout, outdir=outdir)
def get_assemblies(self, job_id, asm=None, stdout=False, outdir=None):
""" Assembly ID cases: None => all, 'auto' => best, numerical/string => label"""
if not asm: asm = ''
url = '{}/user/{}/job/{}/assemblies/{}'.format(self.url, self.user, job_id, asm)
handles = json.loads(self.req_get(url))
if asm and not handles:
# result-not-found exception handled by router
raise Error('Invalid assembly ID: ' + asm)
for h in handles:
self.download_shock_handle(h, stdout, outdir, prefix=job_id+'_')
return
def get_job_analysis_tarball(self, job_id, outdir=None, remove=True):
"""Download and extract quast tarball"""
url = '{}/user/{}/job/{}/analysis'.format(self.url, self.user, job_id)
handle = json.loads(self.req_get(url))
filename = self.download_shock_handle(handle, outdir=outdir)
dirname = filename.split('/')[-1].split('.')[0]
destpath = os.path.join(outdir, dirname) if outdir else dirname
tar = tarfile.open(filename)
tar.extractall(path=destpath)
tar.close()
sys.stderr.write("HTML extracted: {}/report.html\n".format(destpath))
if remove: os.remove(filename)
return '{}/report.html\n'.format(destpath)
def get_job_data(self, job_id, outdir=None):
self.get_assemblies(job_id, outdir=outdir)
self.get_job_report_full(job_id, outdir=outdir)
self.get_job_analysis_tarball(job_id, outdir=outdir)
def get_available_modules(self):
url = '{}/module/all/avail/'.format(self.url)
return self.req_get(url)
def get_available_recipes(self):
url = '{}/recipe/all/avail/'.format(self.url)
return self.req_get(url)
def kill_jobs(self, job_id=None):
if job_id:
url = '{}/user/{}/job/{}/kill'.format(self.url, self.user, job_id)
else:
url = '{}/user/{}/job/all/kill'.format(self.url, self.user)
return self.req_get(url)
def get_config(self):
return self.req_get('{}/admin/system/config'.format(self.url))
def req(self, url, req_type='get', data=None, ret=None):
"""Authenticated request. Parses CherryPy message and raises HTTPError"""
# print "req_{}: {}".format(req_type, url)
try:
if req_type == 'get':
r = requests.get(url, headers=self.headers)
elif req_type == 'post':
r = requests.post(url, data=data, headers=self.headers)
except requests.exceptions.ConnectionError as e:
raise ConnectionError(e)
if r.status_code != requests.codes.ok:
cherry = re.compile("^HTTPError: \(\d+, '(.*?)'", re.MULTILINE)
match = cherry.search(r.content)
msg = match.group(1) if match else r.reason
raise HTTPError("{} (HTTP status code {})".format(msg, r.status_code))
return {'text': r.text, 'json': r.json}.get(ret, r.content)
def req_get(self, url, ret=None):
return self.req(url, req_type='get', ret=ret)
def req_post(self, url, data=None, ret=None):
return self.req(url, req_type='post', data=data, ret=ret)
@contextlib.contextmanager
def smart_open(self, filename=None):
if filename and filename != '-':
fh = open(filename, 'w')
else:
fh = sys.stdout
try:
yield fh
finally:
if fh is not sys.stdout:
fh.close()
def download_shock_handle(self, handle, stdout=False, outdir=None, prefix=''):
shock_url = handle.get('shock_url') or handle.get('url')
shock_id = handle.get('shock_id') or handle.get('id')
if not shock_url or not shock_id:
raise Error("Invalid shock handle: {}".format(handle))
url = "{}/node/{}?download".format(shock_url, shock_id)
if stdout:
filename = None
else:
outdir = utils.verify_dir(outdir) if outdir else None
filename = handle.get('filename') or handle.get('local_file') or shock_id
filename = prefix + filename.split('/')[-1]
filename = os.path.join(outdir, filename) if outdir else filename
headers = {'Authorization': 'OAuth {}'.format(self.token)}
r = requests.get(url, stream=True, headers=headers)
with self.smart_open(filename) as f:
for chunk in r.iter_content(chunk_size=1024):
if chunk: # filter out keep-alive new chunks
f.write(chunk)
f.flush()
if filename:
if not os.path.exists(filename):
raise Error('Data exists but file not properly saved')
else:
sys.stderr.write("File downloaded: {}\n".format(filename))
return filename
class Client:
def __init__(self, url, user, token):
self.url = utils.verify_url(url)
self.user = user
self.token = token
self.headers = {'Authorization': '{}'.format(self.token),
'Content-type': 'application/json',
'Accept': 'text/plain'}
self.shock = None
def init_shock(self):
if self.shock is None:
shockres = self.req_get('{}/shock'.format(self.url))
self.shockurl = utils.verify_url(json.loads(shockres)['shockurl'])
self.shock = Shock(self.shockurl, self.user, self.token)
def upload_data_shock(self, filename, curl=False):
self.init_shock()
res = self.shock.upload_reads(filename, curl=curl)
shock_info = {'filename': os.path.basename(filename),
'filesize': os.path.getsize(filename),
'shock_url': self.shockurl,
'shock_id': res['data']['id'],
'upload_time': str(datetime.datetime.utcnow())}
return res, shock_info
def upload_data_file_info(self, filename, curl=False):
""" Returns FileInfo Object """
self.init_shock()
res = self.shock.upload_reads(filename, curl=curl)
return asmtypes.FileInfo(filename, shock_url=self.shockurl, shock_id=res['data']['id'],
create_time=str(datetime.datetime.utcnow()))
def submit_job(self, data):
url = '{}/user/{}/job/new'.format(self.url, self.user)
return self.req_post(url, data=data)
def submit_data(self, data):
url = '{}/user/{}/data/new'.format(self.url, self.user)
return self.req_post(url, data=data)
def get_job_status(self, stat_n, job_id=None, detail=False):
if job_id:
url = '{}/user/{}/job/{}/status'.format(self.url, self.user, job_id)
else:
if detail:
url = '{}/user/{}/job/status?records={}&detail=True'.format(
self.url, self.user, stat_n)
else:
url = '{}/user/{}/job/status?records={}'.format(
self.url, self.user, stat_n)
return self.req_get(url)
def get_data_list(self):
url = '{}/user/{}/data'.format(self.url, self.user)
li = json.loads(self.req_get(url))
li.sort(key=lambda e: e["data_id"])
return li
def get_data_list_table(self, stat_n=10):
li = self.get_data_list()
li = li[-stat_n:]
rows = []
for data in li:
data_id = data.get("data_id", "")
message = data.get("message")
if 'kbase_assembly_input' in data:
message = data['kbase_assembly_input'].get(
'dataset_description')
data_rows = assembly_data_to_rows(data)
data_rows = [ [''] * 2 + r for r in data_rows]
rows += [[data_id, message] + [''] * 2]
rows += data_rows
pt = PrettyTable(["Data ID", "Description", "Type", "Files"]);
for r in rows: pt.add_row(r)
return pt.get_string()
def get_data_json(self, data_id):
url = '{}/user/{}/data/{}'.format(self.url, self.user, data_id)
return self.req_get(url)
def is_job_valid(self, job_id):
stat = self.get_job_status(1, job_id)
return False if stat.startswith("Could not get job status") else True
def is_job_done(self, job_id):
stat = self.get_job_status(1, job_id)
match = re.search('(complete|fail|terminated)', stat, re.IGNORECASE)
return True if match else False
def validate_job(self, job_id):
if not self.is_job_valid(job_id):
sys.exit("Invalid job ID: {}".format(job_id))
return
def wait_for_job(self, job_id, interval=30):
self.validate_job(job_id)
try:
interval = int(interval)
except ValueError:
interval = 30
if interval < 2:
interval = 2
while not self.is_job_done(job_id):
time.sleep(interval)
return self.get_job_status(1, job_id)
def check_job(self, job_id):
if not self.is_job_done(job_id):
sys.stderr.write("Job in progress. Use -w to wait for the job.\n")
sys.exit()
def get_job_report(self, job_id):
"""Get the stats section of job report"""
url = '{}/user/{}/job/{}/report'.format(self.url, self.user, job_id)
return self.req_get(url)
def get_job_log(self, job_id):
"""Get the log section of job report"""
url = '{}/user/{}/job/{}/log'.format(self.url, self.user, job_id)
return self.req_get(url)
def get_job_report_full(self, job_id, stdout=False, outdir=None):
url = '{}/user/{}/job/{}/report_handle'.format(self.url, self.user, job_id)
handle = json.loads(self.req_get(url))
self.download_shock_handle(handle, stdout=stdout, outdir=outdir)
def get_assemblies(self, job_id, asm=None, stdout=False, outdir=None):
""" Assembly ID cases: None => all, 'auto' => best, numerical/string => label"""
if not asm: asm = ''
url = '{}/user/{}/job/{}/assemblies/{}'.format(self.url, self.user, job_id, asm)
handles = json.loads(self.req_get(url))
if asm and not handles:
# result-not-found exception handled by router
raise Error('Invalid assembly ID: ' + asm)
for h in handles:
self.download_shock_handle(h, stdout, outdir, prefix=job_id+'_')
return
def get_job_analysis_tarball(self, job_id, outdir=None, remove=True):
"""Download and extract quast tarball"""
url = '{}/user/{}/job/{}/analysis'.format(self.url, self.user, job_id)
handle = json.loads(self.req_get(url))
filename = self.download_shock_handle(handle, outdir=outdir)
dirname = filename.split('/')[-1].split('.')[0]
destpath = os.path.join(outdir, dirname) if outdir else dirname
tar = tarfile.open(filename)
tar.extractall(path=destpath)
tar.close()
sys.stderr.write("HTML extracted: {}/report.html\n".format(destpath))
if remove: os.remove(filename)
return '{}/report.html\n'.format(destpath)
def get_job_data(self, job_id, outdir=None):
self.get_assemblies(job_id, outdir=outdir)
self.get_job_report_full(job_id, outdir=outdir)
self.get_job_analysis_tarball(job_id, outdir=outdir)
def get_available_modules(self):
url = '{}/module/all/avail/'.format(self.url)
return self.req_get(url)
def get_available_recipes(self):
url = '{}/recipe/all/avail/'.format(self.url)
return self.req_get(url)
def kill_jobs(self, job_id=None):
if job_id:
url = '{}/user/{}/job/{}/kill'.format(self.url, self.user, job_id)
else:
url = '{}/user/{}/job/all/kill'.format(self.url, self.user)
return self.req_get(url)
def get_config(self):
return self.req_get('{}/admin/system/config'.format(self.url))
def req(self, url, req_type='get', data=None, ret=None):
"""Authenticated request. Parses CherryPy message and raises HTTPError"""
try:
if req_type == 'get':
r = requests.get(url, headers=self.headers)
elif req_type == 'post':
r = requests.post(url, data=data, headers=self.headers)
except requests.exceptions.ConnectionError as e:
raise ConnectionError(e)
if r.status_code != requests.codes.ok:
cherry = re.compile("^HTTPError: \(\d+, '(.*?)'", re.MULTILINE)
match = cherry.search(r.content)
msg = match.group(1) if match else r.reason
raise HTTPError("{} (HTTP status code {})".format(msg, r.status_code))
return {'text': r.text, 'json': r.json}.get(ret, r.content)
def req_get(self, url, ret=None):
return self.req(url, req_type='get', ret=ret)
def req_post(self, url, data=None, ret=None):
return self.req(url, req_type='post', data=data, ret=ret)
@contextlib.contextmanager
def smart_open(self, filename=None):
if filename and filename != '-':
fh = open(filename, 'w')
else:
fh = sys.stdout
try:
yield fh
finally:
if fh is not sys.stdout:
fh.close()
def download_shock_handle(self, handle, stdout=False, outdir=None, prefix=''):
shock_url = handle.get('shock_url') or handle.get('url')
shock_id = handle.get('shock_id') or handle.get('id')
if not shock_url or not shock_id:
raise Error("Invalid shock handle: {}".format(handle))
url = "{}/node/{}?download".format(shock_url, shock_id)
if stdout:
filename = None
else:
outdir = utils.verify_dir(outdir) if outdir else None
filename = handle.get('filename') or handle.get('local_file') or shock_id
filename = prefix + filename.split('/')[-1]
filename = os.path.join(outdir, filename) if outdir else filename
headers = {'Authorization': 'OAuth {}'.format(self.token)}
r = requests.get(url, stream=True, headers=headers)
with self.smart_open(filename) as f:
for chunk in r.iter_content(chunk_size=1024):
if chunk: # filter out keep-alive new chunks
f.write(chunk)
f.flush()
if filename:
if not os.path.exists(filename):
raise Error('Data exists but file not properly saved')
else:
sys.stderr.write("File downloaded: {}\n".format(filename))
return filename
class Client:
def __init__(self, url, user, token):
self.port = 8000 ## change
if url.find(':') == -1: # Port not included
self.url = url + ':{}'.format(self.port)
else:
self.url = url
self.user = user
self.token = token
self.headers = {'Authorization': '{}'.format(self.token),
'Content-type': 'application/json',
'Accept': 'text/plain'}
shockres = requests.get('http://{}/shock'.format(self.url), headers=self.headers).text
self.shockurl = 'http://{}/'.format(json.loads(shockres)['shockurl'])
self.shock = Shock(self.shockurl, self.user, self.token)
def get_job_data(self, job_id=None, outdir=None):
if not job_id:
raise NotImplementedError('Job id required')
# Get node id
res = requests.get('http://{}/user/{}/job/{}/shock_node'.format(
self.url, self.user, job_id), headers=self.headers)
# Download files
try:
nodes_map = json.loads(res.text)
for node_id in nodes_map.values():
self.shock.download_file(node_id, outdir=outdir)
except:
print traceback.format_tb(sys.exc_info()[2])
print sys.exc_info()
raise Exception("Error retrieving results")
return
def get_assemblies(self, job_id=None, asm_id=None, stdout=False, outdir=None):
if not job_id:
raise NotImplementedError('Job id required')
# Get node id
res = requests.get('http://{}/user/{}/job/{}/assembly'.format(
self.url, self.user, job_id), headers=self.headers)
# Download files
try:
nodes_map = json.loads(res.text)
if stdout: # Get first one and print
asm_file = self.shock.download_file(nodes_map.values()[0], outdir=outdir)
with open(asm_file) as f:
for line in f:
print line
elif asm_id:
ordered = collections.OrderedDict(sorted(nodes_map.items()))
id = ordered.values()[int(asm_id)-1]
self.shock.download_file(id , outdir=outdir)
else:
for node_id in nodes_map.values():
self.shock.download_file(node_id, outdir=outdir)
except:
print traceback.format_tb(sys.exc_info()[2])
print sys.exc_info()
raise Exception("Error retrieving results")
return
def upload_data_shock(self, filename, curl=False):
res = self.shock.upload_reads(filename, curl=curl)
shock_info = {'filename': os.path.basename(filename),
'filesize': os.path.getsize(filename),
'shock_url': self.shockurl,
'shock_id': res['data']['id'],
'upload_time': str(datetime.datetime.utcnow())}
return res, shock_info
def upload_data_file_info(self, filename, curl=False):
""" Returns FileInfo Object """
res = self.shock.upload_reads(filename, curl=curl)
return FileInfo(self.shockurl, res['data']['id'], os.path.getsize(filename),
os.path.basename(filename), str(datetime.datetime.utcnow()))
def submit_job(self, data):
url = 'http://{}/user/{}/job/new'.format(self.url, self.user)
r = requests.post(url, data=data, headers=self.headers)
return r.content
def submit_data(self, data):
url = 'http://{}/user/{}/data/new'.format(self.url, self.user)
r = requests.post(url, data=data, headers=self.headers)
return r.content
def get_job_status(self, stat_n, job_id=None):
if job_id:
url = 'http://{}/user/{}/job/{}/status'.format(self.url, self.user, job_id)
else:
url = 'http://{}/user/{}/job/status?records={}'.format(
self.url, self.user, stat_n)
r = requests.get(url, headers=self.headers)
return r.content
def get_available_modules(self):
url = 'http://{}/module/all/avail/'.format(self.url, self.user)
r = requests.get(url, headers=self.headers)
return r.content
def kill_jobs(self, job_id=None):
if job_id:
url = 'http://{}/user/{}/job/{}/kill'.format(self.url, self.user, job_id)
else:
url = 'http://{}/user/{}/job/all/kill'.format(
self.url, self.user)
r = requests.get(url, headers=self.headers)
return r.content
def get_config(self):
return requests.get('http://{}/admin/system/config'.format(self.url)).content
class Client:
def __init__(self, url, user, token):
self.port = 8000 ## change
if url.find(':') == -1: # Port not included
self.url = url + ':{}'.format(self.port)
else:
self.url = url
self.user = user
self.token = token
self.headers = {
'Authorization': '{}'.format(self.token),
'Content-type': 'application/json',
'Accept': 'text/plain'
}
shockres = requests.get('http://{}/shock'.format(self.url),
headers=self.headers).text
self.shockurl = 'http://{}/'.format(json.loads(shockres)['shockurl'])
self.shock = Shock(self.shockurl, self.user, self.token)
def get_job_data(self, job_id=None, outdir=None):
if not job_id:
raise NotImplementedError('Job id required')
# Get node id
res = requests.get('http://{}/user/{}/job/{}/shock_node'.format(
self.url, self.user, job_id),
headers=self.headers)
# Download files
try:
nodes_map = json.loads(res.text)
for node_id in nodes_map.values():
self.shock.download_file(node_id, outdir=outdir)
except:
print traceback.format_tb(sys.exc_info()[2])
print sys.exc_info()
raise Exception("Error retrieving results")
return
def get_assemblies(self,
job_id=None,
asm_id=None,
stdout=False,
outdir=None):
if not job_id:
raise NotImplementedError('Job id required')
# Get node id
res = requests.get('http://{}/user/{}/job/{}/assembly'.format(
self.url, self.user, job_id),
headers=self.headers)
# Download files
try:
nodes_map = json.loads(res.text)
if stdout: # Get first one and print
asm_file = self.shock.download_file(nodes_map.values()[0],
outdir=outdir)
with open(asm_file) as f:
for line in f:
print line
elif asm_id:
ordered = collections.OrderedDict(sorted(nodes_map.items()))
id = ordered.values()[int(asm_id) - 1]
self.shock.download_file(id, outdir=outdir)
else:
for node_id in nodes_map.values():
self.shock.download_file(node_id, outdir=outdir)
except:
print traceback.format_tb(sys.exc_info()[2])
print sys.exc_info()
raise Exception("Error retrieving results")
return
def upload_data_shock(self, filename, curl=False):
res = self.shock.upload_reads(filename, curl=curl)
shock_info = {
'filename': os.path.basename(filename),
'filesize': os.path.getsize(filename),
'shock_url': self.shockurl,
'shock_id': res['data']['id'],
'upload_time': str(datetime.datetime.utcnow())
}
return res, shock_info
def upload_data_file_info(self, filename, curl=False):
""" Returns FileInfo Object """
res = self.shock.upload_reads(filename, curl=curl)
return FileInfo(self.shockurl, res['data']['id'],
os.path.getsize(filename), os.path.basename(filename),
str(datetime.datetime.utcnow()))
def submit_job(self, data):
url = 'http://{}/user/{}/job/new'.format(self.url, self.user)
r = requests.post(url, data=data, headers=self.headers)
return r.content
def submit_data(self, data):
url = 'http://{}/user/{}/data/new'.format(self.url, self.user)
r = requests.post(url, data=data, headers=self.headers)
return r.content
def get_job_status(self, stat_n, job_id=None):
if job_id:
url = 'http://{}/user/{}/job/{}/status'.format(
self.url, self.user, job_id)
else:
url = 'http://{}/user/{}/job/status?records={}'.format(
self.url, self.user, stat_n)
r = requests.get(url, headers=self.headers)
return r.content
def get_available_modules(self):
url = 'http://{}/module/all/avail/'.format(self.url, self.user)
r = requests.get(url, headers=self.headers)
return r.content
def kill_jobs(self, job_id=None):
if job_id:
url = 'http://{}/user/{}/job/{}/kill'.format(
self.url, self.user, job_id)
else:
url = 'http://{}/user/{}/job/all/kill'.format(self.url, self.user)
r = requests.get(url, headers=self.headers)
return r.content
def get_config(self):
return requests.get('http://{}/admin/system/config'.format(
self.url)).content
class Client:
def __init__(self, url, user, token):
self.port = 8000 ## change
if url.find(':') == -1: # Port not included
self.url = url + ':{}'.format(self.port)
else:
self.url = url
self.user = user
self.token = token
self.headers = {'Authorization': '{}'.format(self.token),
'Content-type': 'application/json',
'Accept': 'text/plain'}
shockres = requests.get('http://{}/shock'.format(self.url), headers=self.headers).text
self.shockurl = 'http://{}/'.format(json.loads(shockres)['shockurl'])
self.shock = Shock(self.shockurl, self.user, self.token)
def get_job_data(self, job_id=None, outdir=None):
if not job_id:
raise NotImplementedError('Job id required')
# Get node id
res = requests.get('http://{}/user/{}/job/{}/shock_node'.format(
self.url, self.user, job_id), headers=self.headers)
if res.status_code == 403:
raise ValueError('Invalid Job Id')
# Download files
try:
nodes_map = json.loads(res.text)
for node_id in nodes_map.values():
self.shock.download_file(node_id, outdir=outdir)
except Exception as e:
print e
raise Exception("Error retrieving results")
return
def get_assemblies(self, job_id=None, asm_id=None, stdout=False, outdir=None):
if not job_id:
raise NotImplementedError('Job id required')
# Get node id
res = requests.get('http://{}/user/{}/job/{}/assembly'.format(
self.url, self.user, job_id), headers=self.headers)
# Download files
try:
nodes_map = json.loads(res.text)
if stdout: # Get first one and print
asm_file = self.shock.download_file(nodes_map.values()[0], outdir=outdir)
with open(asm_file) as f:
for line in f:
print line
elif asm_id:
ordered = collections.OrderedDict(sorted(nodes_map.items()))
id = ordered.values()[int(asm_id)-1]
self.shock.download_file(id , outdir=outdir)
else:
for node_id in nodes_map.values():
self.shock.download_file(node_id, outdir=outdir)
except:
print traceback.format_tb(sys.exc_info()[2])
print sys.exc_info()
raise Exception("Error retrieving results")
return
def upload_data_shock(self, filename, curl=False):
res = self.shock.upload_reads(filename, curl=curl)
shock_info = {'filename': os.path.basename(filename),
'filesize': os.path.getsize(filename),
'shock_url': self.shockurl,
'shock_id': res['data']['id'],
'upload_time': str(datetime.datetime.utcnow())}
return res, shock_info
def upload_data_file_info(self, filename, curl=False):
""" Returns FileInfo Object """
res = self.shock.upload_reads(filename, curl=curl)
return asmtypes.FileInfo(filename, shock_url=self.shockurl, shock_id=res['data']['id'],
create_time=str(datetime.datetime.utcnow()))
# return FileInfo(self.shockurl, res['data']['id'], os.path.getsize(filename),
# os.path.basename(filename), str(datetime.datetime.utcnow()))
def submit_job(self, data):
url = 'http://{}/user/{}/job/new'.format(self.url, self.user)
r = requests.post(url, data=data, headers=self.headers)
return r.content
def submit_data(self, data):
url = 'http://{}/user/{}/data/new'.format(self.url, self.user)
r = requests.post(url, data=data, headers=self.headers)
return r.content
def get_job_status(self, stat_n, job_id=None):
if job_id:
url = 'http://{}/user/{}/job/{}/status'.format(self.url, self.user, job_id)
else:
url = 'http://{}/user/{}/job/status?records={}'.format(
self.url, self.user, stat_n)
r = requests.get(url, headers=self.headers)
return r.content
def get_data_list(self):
url = 'http://{}/user/{}/data'.format(self.url, self.user)
r = requests.get(url, headers=self.headers)
li = json.loads(r.content)
li.sort(key=lambda e: e["data_id"])
return li
def get_data_list_table(self, stat_n=10):
li = self.get_data_list()
li = li[-stat_n:]
rows = []
for data in li:
data_id = data.get("data_id", "")
message = data.get("message", "")
data_rows = assembly_data_to_rows(data)
data_rows = [ [''] * 2 + r for r in data_rows]
rows += [[data_id, message] + [''] * 2]
rows += data_rows
pt = PrettyTable(["Data ID", "Description", "Type", "Files"]);
for r in rows: pt.add_row(r)
return pt.get_string()
def get_data_json(self, data_id):
url = 'http://{}/user/{}/data/{}'.format(self.url, self.user, data_id)
r = requests.get(url, headers=self.headers)
return r.content
def is_job_valid(self, job_id):
stat = self.get_job_status(1, job_id)
return False if stat.startswith("Could not") else True
def validate_job(self, job_id):
if not self.is_job_valid(job_id):
sys.stderr.write("Invalid job ID: {}\n".format(job_id))
sys.exit()
return
def wait_for_job(self, job_id):
self.validate_job(job_id)
stat = self.get_job_status(1, job_id)
while not re.search('(complete|fail)', stat, re.IGNORECASE):
time.sleep(5)
stat = self.get_job_status(1, job_id)
return stat
def get_job_report(self, job_id, log=False):
url = 'http://{}/user/{}/job/{}/report'.format(self.url, self.user, job_id)
r = requests.get(url, headers=self.headers)
if not r.content:
sys.stderr.write("Job in progress. Use -w to wait for the job.\n")
sys.exit()
try:
info = json.loads(r.content)[0]['file_infos'][0]
url = '{}/node/{}?download'.format(info['shock_url'], info['shock_id'])
report = shock_get(url).content
if not log:
lines = str.splitlines(report, 1)
report = ''.join(lines[0:20])
except Exception as e:
print e
raise Exception("Error retrieving job report")
return report
def get_available_modules(self):
url = 'http://{}/module/all/avail/'.format(self.url, self.user)
r = requests.get(url, headers=self.headers)
return r.content
def kill_jobs(self, job_id=None):
if job_id:
url = 'http://{}/user/{}/job/{}/kill'.format(self.url, self.user, job_id)
else:
url = 'http://{}/user/{}/job/all/kill'.format(
self.url, self.user)
r = requests.get(url, headers=self.headers)
return r.content
def get_config(self):
return requests.get('http://{}/admin/system/config'.format(self.url)).content
