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tgbugs/pyontutils | pyontutils/sheets.py | Sheet.fetch | def fetch(self, fetch_notes=None):
""" update remote values (called automatically at __init__) """
if fetch_notes is None:
fetch_notes = self.fetch_notes
values, notes_index = get_sheet_values(self.name, self.sheet_name,
spreadsheet_serv... | python | def fetch(self, fetch_notes=None):
""" update remote values (called automatically at __init__) """
if fetch_notes is None:
fetch_notes = self.fetch_notes
values, notes_index = get_sheet_values(self.name, self.sheet_name,
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tgbugs/pyontutils | neurondm/neurondm/build.py | add_types | def add_types(graph, phenotypes): # TODO missing expression phenotypes! also basket type somehow :(
""" Add disjoint union classes so that it is possible to see the invariants
associated with individual phenotypes """
collect = defaultdict(set)
def recurse(id_, start, level=0):
#print(leve... | python | def add_types(graph, phenotypes): # TODO missing expression phenotypes! also basket type somehow :(
""" Add disjoint union classes so that it is possible to see the invariants
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collect = defaultdict(set)
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tgbugs/pyontutils | neurondm/neurondm/build.py | _rest_make_phenotypes | def _rest_make_phenotypes():
#phenotype sources
neuroner = Path(devconfig.git_local_base,
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#phenotype sources
neuroner = Path(devconfig.git_local_base,
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tgbugs/pyontutils | pyontutils/config.py | DevConfig.config | def config(self):
""" Allows changing the config on the fly """
# TODO more efficient to read once and put watch on the file
config = {}
if self.config_file.exists():
with open(self.config_file.as_posix(), 'rt') as f: # 3.5/pypy3 can't open Path directly
conf... | python | def config(self):
""" Allows changing the config on the fly """
# TODO more efficient to read once and put watch on the file
config = {}
if self.config_file.exists():
with open(self.config_file.as_posix(), 'rt') as f: # 3.5/pypy3 can't open Path directly
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SUSE-Enceladus/ipa | ipa/ipa_gce.py | GCECloud._get_service_account_info | def _get_service_account_info(self):
"""Retrieve json dict from service account file."""
with open(self.service_account_file, 'r') as f:
info = json.load(f)
self.service_account_email = info.get('client_email')
if not self.service_account_email:
raise GCECloudExc... | python | def _get_service_account_info(self):
"""Retrieve json dict from service account file."""
with open(self.service_account_file, 'r') as f:
info = json.load(f)
self.service_account_email = info.get('client_email')
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SUSE-Enceladus/ipa | ipa/ipa_gce.py | GCECloud._get_driver | def _get_driver(self):
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ComputeEngine = get_driver(Provider.GCE)
return ComputeEngine(
self.service_account_email,
self.service_account_file,
project=self.service_account_project
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"""Get authenticated GCE driver."""
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SUSE-Enceladus/ipa | ipa/ipa_gce.py | GCECloud._get_instance | def _get_instance(self):
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SUSE-Enceladus/ipa | ipa/ipa_gce.py | GCECloud._get_ssh_public_key | def _get_ssh_public_key(self):
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key = ipa_utils.generate_public_ssh_key(self.ssh_private_key_file)
return '{user}:{key} {user}'.format(
user=self.ssh_user,
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key = ipa_utils.generate_public_ssh_key(self.ssh_private_key_file)
return '{user}:{key} {user}'.format(
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SUSE-Enceladus/ipa | ipa/ipa_gce.py | GCECloud._launch_instance | def _launch_instance(self):
"""Launch an instance of the given image."""
metadata = {'key': 'ssh-keys', 'value': self.ssh_public_key}
self.running_instance_id = ipa_utils.generate_instance_name(
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self.logger.debug('ID of instance: %s' % self.running_in... | python | def _launch_instance(self):
"""Launch an instance of the given image."""
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SUSE-Enceladus/ipa | ipa/ipa_gce.py | GCECloud._validate_region | def _validate_region(self):
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SUSE-Enceladus/ipa | ipa/ipa_gce.py | GCECloud._set_instance_ip | def _set_instance_ip(self):
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SUSE-Enceladus/ipa | ipa/ipa_gce.py | GCECloud._start_instance | def _start_instance(self):
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tgbugs/pyontutils | ilxutils/ilxutils/interlex_ingestion.py | InterLexIngestion.grab_rdflib_graph_version | def grab_rdflib_graph_version(g: Graph) -> str:
''' Crap-shot for ontology iri if its properly in the header and correctly formated '''
version = g.subject_objects( predicate = URIRef( OWL.versionIRI ) )
version = [o for s, o in version]
if len(version) != 1:
print('versionin... | python | def grab_rdflib_graph_version(g: Graph) -> str:
''' Crap-shot for ontology iri if its properly in the header and correctly formated '''
version = g.subject_objects( predicate = URIRef( OWL.versionIRI ) )
version = [o for s, o in version]
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tgbugs/pyontutils | ilxutils/ilxutils/interlex_ingestion.py | InterLexIngestion.fix_ilx | def fix_ilx(self, ilx_id: str) -> str:
''' Database only excepts lower case and underscore version of ID '''
ilx_id = ilx_id.replace('http://uri.interlex.org/base/', '')
if ilx_id[:4] not in ['TMP:', 'tmp_', 'ILX:', 'ilx_']:
raise ValueError(
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''' Database only excepts lower case and underscore version of ID '''
ilx_id = ilx_id.replace('http://uri.interlex.org/base/', '')
if ilx_id[:4] not in ['TMP:', 'tmp_', 'ILX:', 'ilx_']:
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tgbugs/pyontutils | ilxutils/ilxutils/interlex_ingestion.py | InterLexIngestion.pull_int_tail | def pull_int_tail(self, string: str) -> str:
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int_tail = ''
for element in string[::-1]:
try:
int(element)
int_tail = element + int_tail
except:
pass
... | python | def pull_int_tail(self, string: str) -> str:
''' Useful for IDs that have giberish in the front of the real ID '''
int_tail = ''
for element in string[::-1]:
try:
int(element)
int_tail = element + int_tail
except:
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tgbugs/pyontutils | ilxutils/ilxutils/interlex_ingestion.py | InterLexIngestion.extract_fragment | def extract_fragment(self, iri: str) -> str:
''' Pulls only for code/ID from the iri
I only add the str() conversion for the iri because rdflib objects need to be converted.
'''
fragment = str(iri).rsplit('/')[-1].split(':', 1)[-1].split('#', 1)[-1].split('_', 1)[-1]
return frag... | python | def extract_fragment(self, iri: str) -> str:
''' Pulls only for code/ID from the iri
I only add the str() conversion for the iri because rdflib objects need to be converted.
'''
fragment = str(iri).rsplit('/')[-1].split(':', 1)[-1].split('#', 1)[-1].split('_', 1)[-1]
return frag... | [
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tgbugs/pyontutils | ilxutils/ilxutils/interlex_ingestion.py | InterLexIngestion.curie_search | def curie_search(self, curie:str) -> dict:
''' Returns the row in InterLex associated with the curie
Note:
Pressumed to not have duplicate curies in InterLex
Args:
curie: The "prefix:fragment_id" of the existing_id pertaining to the ontology
Returns:
... | python | def curie_search(self, curie:str) -> dict:
''' Returns the row in InterLex associated with the curie
Note:
Pressumed to not have duplicate curies in InterLex
Args:
curie: The "prefix:fragment_id" of the existing_id pertaining to the ontology
Returns:
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tgbugs/pyontutils | ilxutils/ilxutils/interlex_ingestion.py | InterLexIngestion.fragment_search | def fragment_search(self, fragement:str) -> List[dict]:
''' Returns the rows in InterLex associated with the fragment
Note:
Pressumed to have duplicate fragements in InterLex
Args:
fragment: The fragment_id of the curie pertaining to the ontology
Returns:
... | python | def fragment_search(self, fragement:str) -> List[dict]:
''' Returns the rows in InterLex associated with the fragment
Note:
Pressumed to have duplicate fragements in InterLex
Args:
fragment: The fragment_id of the curie pertaining to the ontology
Returns:
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tgbugs/pyontutils | ilxutils/ilxutils/interlex_ingestion.py | InterLexIngestion.label_search | def label_search(self, label:str) -> List[dict]:
''' Returns the rows in InterLex associated with that label
Note:
Pressumed to have duplicated labels in InterLex
Args:
label: label of the entity you want to find
Returns:
None or List[dict]
''... | python | def label_search(self, label:str) -> List[dict]:
''' Returns the rows in InterLex associated with that label
Note:
Pressumed to have duplicated labels in InterLex
Args:
label: label of the entity you want to find
Returns:
None or List[dict]
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tgbugs/pyontutils | ilxutils/ilxutils/interlex_ingestion.py | InterLexIngestion.readyup_entity | def readyup_entity(
self,
label: str,
type: str,
uid: Union[int, str] = None,
comment: str = None,
definition: str = None,
superclass: str = None,
synonyms: list = None,
existing_ids: List[dict] = None, ) -> dict:
''' Setups the entity to b... | python | def readyup_entity(
self,
label: str,
type: str,
uid: Union[int, str] = None,
comment: str = None,
definition: str = None,
superclass: str = None,
synonyms: list = None,
existing_ids: List[dict] = None, ) -> dict:
''' Setups the entity to b... | [
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Args:
label: name of entity
type: entities type
Can be any of the following: term, cde, fde, pde, annotation, relationship
uid: usually fine and auto completes to api user ID, but if you provide one with a
... | [
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tgbugs/pyontutils | ilxutils/ilxutils/interlex_ingestion.py | InterLexIngestion.__exhaustive_diff | def __exhaustive_diff(self, check_list:List[dict]) -> List[List[dict]]:
''' Helper for exhaustive checks to see if there any matches at all besides the anchor
OUTPUT:
[
{
'external_ontology_row' : {},
'interlex_row' ... | python | def __exhaustive_diff(self, check_list:List[dict]) -> List[List[dict]]:
''' Helper for exhaustive checks to see if there any matches at all besides the anchor
OUTPUT:
[
{
'external_ontology_row' : {},
'interlex_row' ... | [
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... | [
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tgbugs/pyontutils | ilxutils/ilxutils/interlex_ingestion.py | InterLexIngestion.exhaustive_label_check | def exhaustive_label_check( self,
ontology:pd.DataFrame,
label_predicate='rdfs:label',
diff:bool=True, ) -> Tuple[list]:
''' All entities with conflicting labels gets a full diff
Args:
on... | python | def exhaustive_label_check( self,
ontology:pd.DataFrame,
label_predicate='rdfs:label',
diff:bool=True, ) -> Tuple[list]:
''' All entities with conflicting labels gets a full diff
Args:
on... | [
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tgbugs/pyontutils | ilxutils/ilxutils/interlex_ingestion.py | InterLexIngestion.exhaustive_iri_check | def exhaustive_iri_check( self,
ontology:pd.DataFrame,
iri_predicate:str,
diff:bool=True, ) -> Tuple[list]:
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Args:
o... | python | def exhaustive_iri_check( self,
ontology:pd.DataFrame,
iri_predicate:str,
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Args:
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tgbugs/pyontutils | ilxutils/ilxutils/interlex_ingestion.py | InterLexIngestion.exhaustive_curie_check | def exhaustive_curie_check( self,
ontology:pd.DataFrame,
curie_predicate:str,
curie_prefix:str,
diff:bool=True, ) -> Tuple[list]:
''' All entities with conflicting curies gets a full d... | python | def exhaustive_curie_check( self,
ontology:pd.DataFrame,
curie_predicate:str,
curie_prefix:str,
diff:bool=True, ) -> Tuple[list]:
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tgbugs/pyontutils | ilxutils/ilxutils/interlex_ingestion.py | InterLexIngestion.exhaustive_fragment_check | def exhaustive_fragment_check( self,
ontology:pd.DataFrame,
iri_curie_fragment_predicate:str = 'iri',
cross_reference_iris:bool = False,
cross_reference_fragments:bool = False,
... | python | def exhaustive_fragment_check( self,
ontology:pd.DataFrame,
iri_curie_fragment_predicate:str = 'iri',
cross_reference_iris:bool = False,
cross_reference_fragments:bool = False,
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tgbugs/pyontutils | ilxutils/ilxutils/interlex_ingestion.py | InterLexIngestion.exhaustive_ontology_ilx_diff_row_only | def exhaustive_ontology_ilx_diff_row_only( self, ontology_row: dict ) -> dict:
''' WARNING RUNTIME IS AWEFUL '''
results = []
header = ['Index'] + list(self.existing_ids.columns)
for row in self.existing_ids.itertuples():
row = {header[i]:val for i, val in enumerate(row)}
... | python | def exhaustive_ontology_ilx_diff_row_only( self, ontology_row: dict ) -> dict:
''' WARNING RUNTIME IS AWEFUL '''
results = []
header = ['Index'] + list(self.existing_ids.columns)
for row in self.existing_ids.itertuples():
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tgbugs/pyontutils | ilxutils/ilxutils/interlex_ingestion.py | InterLexIngestion.combo_exhaustive_label_definition_check | def combo_exhaustive_label_definition_check( self,
ontology: pd.DataFrame,
label_predicate:str,
definition_predicates:str,
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ontology: pd.DataFrame,
label_predicate:str,
definition_predicates:str,
d... | [
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SUSE-Enceladus/ipa | ipa/ipa_utils.py | clear_cache | def clear_cache(ip=None):
"""Clear the client cache or remove key matching the given ip."""
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with ignored(Exception):
client = CLIENT_CACHE[ip]
del CLIENT_CACHE[ip]
client.close()
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with ignored(Ex... | python | def clear_cache(ip=None):
"""Clear the client cache or remove key matching the given ip."""
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del CLIENT_CACHE[ip]
client.close()
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ssh_private_key_file,
ssh_user,
port,
attempts=5,
timeout=None):
"""
Establish ssh connection and return paramiko client.
Raises:... | python | def establish_ssh_connection(ip,
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SUSE-Enceladus/ipa | ipa/ipa_utils.py | execute_ssh_command | def execute_ssh_command(client, cmd):
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Execute given command using paramiko.
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String output of cmd execution.
Raises:
IpaSSHException: If stderr returns a non-empty string.
"""
try:
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err = stderr.read()
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"""
Execute given command using paramiko.
Returns:
String output of cmd execution.
Raises:
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"""
try:
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SUSE-Enceladus/ipa | ipa/ipa_utils.py | extract_archive | def extract_archive(client, archive_path, extract_path=None):
"""
Extract the archive in current path using the provided client.
If extract_path is provided extract the archive there.
"""
command = 'tar -xf {path}'.format(path=archive_path)
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"""
Extract the archive in current path using the provided client.
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"""
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SUSE-Enceladus/ipa | ipa/ipa_utils.py | generate_public_ssh_key | def generate_public_ssh_key(ssh_private_key_file):
"""Generate SSH public key from private key file."""
try:
with open(ssh_private_key_file, "rb") as key_file:
key = key_file.read()
except FileNotFoundError:
raise IpaUtilsException(
'SSH private key file: %s cannot be... | python | def generate_public_ssh_key(ssh_private_key_file):
"""Generate SSH public key from private key file."""
try:
with open(ssh_private_key_file, "rb") as key_file:
key = key_file.read()
except FileNotFoundError:
raise IpaUtilsException(
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SUSE-Enceladus/ipa | ipa/ipa_utils.py | get_config_values | def get_config_values(config_path, section, default='default'):
"""
Parse ini config file and return a dict of values.
The provided section overrides any values in default section.
"""
values = {}
if not os.path.isfile(config_path):
raise IpaUtilsException(
'Config file not... | python | def get_config_values(config_path, section, default='default'):
"""
Parse ini config file and return a dict of values.
The provided section overrides any values in default section.
"""
values = {}
if not os.path.isfile(config_path):
raise IpaUtilsException(
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SUSE-Enceladus/ipa | ipa/ipa_utils.py | get_ssh_client | def get_ssh_client(ip,
ssh_private_key_file,
ssh_user='root',
port=22,
timeout=600,
wait_period=10):
"""Attempt to establish and test ssh connection."""
if ip in CLIENT_CACHE:
return CLIENT_CACHE[ip]
star... | python | def get_ssh_client(ip,
ssh_private_key_file,
ssh_user='root',
port=22,
timeout=600,
wait_period=10):
"""Attempt to establish and test ssh connection."""
if ip in CLIENT_CACHE:
return CLIENT_CACHE[ip]
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SUSE-Enceladus/ipa | ipa/ipa_utils.py | get_yaml_config | def get_yaml_config(config_path):
"""
Load yaml config file and return dictionary.
Todo:
* This will need refactoring similar to the test search.
"""
config_path = os.path.expanduser(config_path)
if not os.path.isfile(config_path):
raise IpaUtilsException(
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"""
Load yaml config file and return dictionary.
Todo:
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config_path = os.path.expanduser(config_path)
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SUSE-Enceladus/ipa | ipa/ipa_utils.py | parse_sync_points | def parse_sync_points(names, tests):
"""
Slice list of test names on sync points.
If test is test file find full path to file.
Returns:
A list of test file sets and sync point strings.
Examples:
['test_hard_reboot']
[set('test1', 'test2')]
[set('test1', 'test2'), 't... | python | def parse_sync_points(names, tests):
"""
Slice list of test names on sync points.
If test is test file find full path to file.
Returns:
A list of test file sets and sync point strings.
Examples:
['test_hard_reboot']
[set('test1', 'test2')]
[set('test1', 'test2'), 't... | [
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SUSE-Enceladus/ipa | ipa/ipa_utils.py | put_file | def put_file(client, source_file, destination_file):
"""
Copy file to instance using Paramiko client connection.
"""
try:
sftp_client = client.open_sftp()
sftp_client.put(source_file, destination_file)
except Exception as error:
raise IpaUtilsException(
'Error cop... | python | def put_file(client, source_file, destination_file):
"""
Copy file to instance using Paramiko client connection.
"""
try:
sftp_client = client.open_sftp()
sftp_client.put(source_file, destination_file)
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SUSE-Enceladus/ipa | ipa/ipa_utils.py | redirect_output | def redirect_output(fileobj):
"""Redirect standard out to file."""
old = sys.stdout
sys.stdout = fileobj
try:
yield fileobj
finally:
sys.stdout = old | python | def redirect_output(fileobj):
"""Redirect standard out to file."""
old = sys.stdout
sys.stdout = fileobj
try:
yield fileobj
finally:
sys.stdout = old | [
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SUSE-Enceladus/ipa | ipa/ipa_utils.py | ssh_config | def ssh_config(ssh_user, ssh_private_key_file):
"""Create temporary ssh config file."""
try:
ssh_file = NamedTemporaryFile(delete=False, mode='w+')
ssh_file.write('Host *\n')
ssh_file.write(' IdentityFile %s\n' % ssh_private_key_file)
ssh_file.write(' User %s' % ssh_user)
... | python | def ssh_config(ssh_user, ssh_private_key_file):
"""Create temporary ssh config file."""
try:
ssh_file = NamedTemporaryFile(delete=False, mode='w+')
ssh_file.write('Host *\n')
ssh_file.write(' IdentityFile %s\n' % ssh_private_key_file)
ssh_file.write(' User %s' % ssh_user)
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SUSE-Enceladus/ipa | ipa/ipa_utils.py | update_history_log | def update_history_log(history_log,
clear=False,
description=None,
test_log=None):
"""
Update the history log file with item.
If clear flag is provided the log file is deleted.
"""
if not test_log and not clear:
raise IpaUt... | python | def update_history_log(history_log,
clear=False,
description=None,
test_log=None):
"""
Update the history log file with item.
If clear flag is provided the log file is deleted.
"""
if not test_log and not clear:
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shanbay/peeweext | peeweext/validation.py | RegexValidator.validate | def validate(self, value):
"""Validate string by regex
:param value: str
:return:
"""
if not self._compiled_regex.match(value):
raise ValidationError(
'value {:s} not match r"{:s}"'.format(value, self._regex)) | python | def validate(self, value):
"""Validate string by regex
:param value: str
:return:
"""
if not self._compiled_regex.match(value):
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tgbugs/pyontutils | ilxutils/ontoutils/create_strict_records_from_ontology.py | Ontology2DataFrame.ontology2df | def ontology2df(self):
'''Updates self.g or self.path bc you could only choose 1'''
if isinstance(self.path, str) or isinstance(self.path, p):
self.path = str(self.path)
filetype = p(self.path).suffix
if filetype == '.json':
self.g = None
... | python | def ontology2df(self):
'''Updates self.g or self.path bc you could only choose 1'''
if isinstance(self.path, str) or isinstance(self.path, p):
self.path = str(self.path)
filetype = p(self.path).suffix
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self.g = None
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tgbugs/pyontutils | ilxutils/ontoutils/create_strict_records_from_ontology.py | CommonPredMap.create_pred2common | def create_pred2common(self):
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and their respected suffixes to decrease sensitivity.
'''
self.pred2common = {}
for common_name, ext_preds in self.common2preds.items():
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self.pred2common = {}
for common_name, ext_preds in self.common2preds.items():
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tgbugs/pyontutils | ilxutils/ontoutils/create_strict_records_from_ontology.py | CommonPredMap.clean_pred | def clean_pred(self, pred, ignore_warning=False):
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'''
original_pred = pred
pred = pred.lower().strip()
if 'http' in pred:
pred = pred.split('/')[-1]
elif ':' in pred:
if p... | python | def clean_pred(self, pred, ignore_warning=False):
''' Takes the predicate and returns the suffix, lower case, stripped version
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tgbugs/pyontutils | ilxutils/ontoutils/create_strict_records_from_ontology.py | CommonPredMap.get_common_pred | def get_common_pred(self, pred):
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OUTPUT:
Common relationship or None
'''
pred = self.clean_pred(pred)
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pred = self.clean_pred(pred)
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SUSE-Enceladus/ipa | ipa/ipa_azure.py | AzureCloud._create_network_interface | def _create_network_interface(
self, ip_config_name, nic_name, public_ip, region,
resource_group_name, subnet, accelerated_networking=False
):
"""
Create a network interface in the resource group.
Attach NIC to the subnet and public IP provided.
"""
nic_confi... | python | def _create_network_interface(
self, ip_config_name, nic_name, public_ip, region,
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):
"""
Create a network interface in the resource group.
Attach NIC to the subnet and public IP provided.
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SUSE-Enceladus/ipa | ipa/ipa_azure.py | AzureCloud._create_public_ip | def _create_public_ip(self, public_ip_name, resource_group_name, region):
"""
Create dynamic public IP address in the resource group.
"""
public_ip_config = {
'location': region,
'public_ip_allocation_method': 'Dynamic'
}
try:
public_i... | python | def _create_public_ip(self, public_ip_name, resource_group_name, region):
"""
Create dynamic public IP address in the resource group.
"""
public_ip_config = {
'location': region,
'public_ip_allocation_method': 'Dynamic'
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SUSE-Enceladus/ipa | ipa/ipa_azure.py | AzureCloud._create_resource_group | def _create_resource_group(self, region, resource_group_name):
"""
Create resource group if it does not exist.
"""
resource_group_config = {'location': region}
try:
self.resource.resource_groups.create_or_update(
resource_group_name, resource_group_co... | python | def _create_resource_group(self, region, resource_group_name):
"""
Create resource group if it does not exist.
"""
resource_group_config = {'location': region}
try:
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SUSE-Enceladus/ipa | ipa/ipa_azure.py | AzureCloud._create_storage_profile | def _create_storage_profile(self):
"""
Create the storage profile for the instance.
Image reference can be a custom image name or a published urn.
"""
if self.image_publisher:
storage_profile = {
'image_reference': {
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"""
Create the storage profile for the instance.
Image reference can be a custom image name or a published urn.
"""
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SUSE-Enceladus/ipa | ipa/ipa_azure.py | AzureCloud._create_subnet | def _create_subnet(self, resource_group_name, subnet_id, vnet_name):
"""
Create a subnet in the provided vnet and resource group.
"""
subnet_config = {'address_prefix': '10.0.0.0/29'}
try:
subnet_setup = self.network.subnets.create_or_update(
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"""
Create a subnet in the provided vnet and resource group.
"""
subnet_config = {'address_prefix': '10.0.0.0/29'}
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"""
Create a vnet in the given resource group with default address space.
"""
vnet_config = {
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... | python | def _create_virtual_network(self, region, resource_group_name, vnet_name):
"""
Create a vnet in the given resource group with default address space.
"""
vnet_config = {
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SUSE-Enceladus/ipa | ipa/ipa_azure.py | AzureCloud._create_vm | def _create_vm(self, vm_config):
"""
Attempt to create or update VM instance based on vm_parameters config.
"""
try:
vm_setup = self.compute.virtual_machines.create_or_update(
self.running_instance_id, self.running_instance_id,
vm_config
... | python | def _create_vm(self, vm_config):
"""
Attempt to create or update VM instance based on vm_parameters config.
"""
try:
vm_setup = self.compute.virtual_machines.create_or_update(
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SUSE-Enceladus/ipa | ipa/ipa_azure.py | AzureCloud._create_vm_config | def _create_vm_config(self, interface):
"""
Create the VM config dictionary.
Requires an existing network interface object.
"""
# Split image ID into it's components.
self._process_image_id()
hardware_profile = {
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"""
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SUSE-Enceladus/ipa | ipa/ipa_azure.py | AzureCloud._get_instance | def _get_instance(self):
"""
Return the instance matching the running_instance_id.
"""
try:
instance = self.compute.virtual_machines.get(
self.running_instance_id, self.running_instance_id,
expand='instanceView'
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"""
Return the instance matching the running_instance_id.
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SUSE-Enceladus/ipa | ipa/ipa_azure.py | AzureCloud._get_instance_state | def _get_instance_state(self):
"""
Retrieve state of instance.
"""
instance = self._get_instance()
statuses = instance.instance_view.statuses
for status in statuses:
if status.code.startswith('PowerState'):
return status.display_status | python | def _get_instance_state(self):
"""
Retrieve state of instance.
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instance = self._get_instance()
statuses = instance.instance_view.statuses
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SUSE-Enceladus/ipa | ipa/ipa_azure.py | AzureCloud._get_management_client | def _get_management_client(self, client_class):
"""
Return instance of resource management client.
"""
try:
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client_class, auth_path=self.service_account_file
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Return instance of resource management client.
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SUSE-Enceladus/ipa | ipa/ipa_azure.py | AzureCloud._launch_instance | def _launch_instance(self):
"""
Create new test instance in a resource group with the same name.
"""
self.running_instance_id = ipa_utils.generate_instance_name(
'azure-ipa-test'
)
self.logger.debug('ID of instance: %s' % self.running_instance_id)
self... | python | def _launch_instance(self):
"""
Create new test instance in a resource group with the same name.
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self.running_instance_id = ipa_utils.generate_instance_name(
'azure-ipa-test'
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SUSE-Enceladus/ipa | ipa/ipa_azure.py | AzureCloud._process_image_id | def _process_image_id(self):
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Split image id into component values.
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Publisher:Offer:Sku:Version
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If image_id is not a valid format.
"""
try:
image_info = self.image_id.strip().split(... | python | def _process_image_id(self):
"""
Split image id into component values.
Example: SUSE:SLES:12-SP3:2018.01.04
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SUSE-Enceladus/ipa | ipa/ipa_azure.py | AzureCloud._set_default_resource_names | def _set_default_resource_names(self):
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self.running_instance_id, '-ip-config'
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self.nic_name = ''.join([self.running_instance_id, '-nic'])
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"""
Generate names for resources based on the running_instance_id.
"""
self.ip_config_name = ''.join([
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SUSE-Enceladus/ipa | ipa/ipa_azure.py | AzureCloud._set_image_id | def _set_image_id(self):
"""
If an existing instance is used get image id from deployment.
"""
instance = self._get_instance()
image_info = instance.storage_profile.image_reference
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"""
If an existing instance is used get image id from deployment.
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SUSE-Enceladus/ipa | ipa/ipa_azure.py | AzureCloud._set_instance_ip | def _set_instance_ip(self):
"""
Get the IP address based on instance ID.
If public IP address not found attempt to get private IP.
"""
try:
ip_address = self.network.public_ip_addresses.get(
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).... | python | def _set_instance_ip(self):
"""
Get the IP address based on instance ID.
If public IP address not found attempt to get private IP.
"""
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ip_address = self.network.public_ip_addresses.get(
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SUSE-Enceladus/ipa | ipa/ipa_azure.py | AzureCloud._start_instance | def _start_instance(self):
"""
Start the instance.
"""
try:
vm_start = self.compute.virtual_machines.start(
self.running_instance_id, self.running_instance_id
)
except Exception as error:
raise AzureCloudException(
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"""
Start the instance.
"""
try:
vm_start = self.compute.virtual_machines.start(
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except Exception as error:
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SUSE-Enceladus/ipa | ipa/ipa_azure.py | AzureCloud._stop_instance | def _stop_instance(self):
"""
Stop the instance.
"""
try:
vm_stop = self.compute.virtual_machines.power_off(
self.running_instance_id, self.running_instance_id
)
except Exception as error:
raise AzureCloudException(
... | python | def _stop_instance(self):
"""
Stop the instance.
"""
try:
vm_stop = self.compute.virtual_machines.power_off(
self.running_instance_id, self.running_instance_id
)
except Exception as error:
raise AzureCloudException(
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SUSE-Enceladus/ipa | ipa/ipa_azure.py | AzureCloud._terminate_instance | def _terminate_instance(self):
"""
Terminate the resource group and instance.
"""
try:
self.resource.resource_groups.delete(self.running_instance_id)
except Exception as error:
raise AzureCloudException(
'Unable to terminate resource group:... | python | def _terminate_instance(self):
"""
Terminate the resource group and instance.
"""
try:
self.resource.resource_groups.delete(self.running_instance_id)
except Exception as error:
raise AzureCloudException(
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SUSE-Enceladus/ipa | ipa/scripts/cli.py | main | def main(context, no_color):
"""
Ipa provides a Python API and command line utility for testing images.
It can be used to test images in the Public Cloud (AWS, Azure, GCE, etc.).
"""
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context.obj['no_color'] = no_color | python | def main(context, no_color):
"""
Ipa provides a Python API and command line utility for testing images.
It can be used to test images in the Public Cloud (AWS, Azure, GCE, etc.).
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"""Process provided history log and results files."""
if context.obj is None:
context.obj = {}
context.obj['history_log'] = history_log
if context.invoked_subcommand is None:
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"""Process provided history log and results files."""
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Archive the history log and all results/log files.
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Archive the history log and all results/log files.
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SUSE-Enceladus/ipa | ipa/scripts/cli.py | delete | def delete(context, item):
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Delete the specified history item from the history log.
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history = lines.pop(len(lines) - it... | python | def delete(context, item):
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Delete the specified history item from the history log.
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Print test results info from provided results json file.
If no results file is supplied echo results from most recent
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If verbose option selected, echo all test cases.
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SUSE-Enceladus/ipa | ipa/ipa_cloud.py | IpaCloud._get_ssh_client | def _get_ssh_client(self):
"""Return a new or existing SSH client for given ip."""
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self.ssh_private_key_file,
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SUSE-Enceladus/ipa | ipa/ipa_cloud.py | IpaCloud._log_info | def _log_info(self):
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'distro': self.distro_name,
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'timestamp': self.time_st... | python | def _log_info(self):
"""Output test run information to top of log file."""
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SUSE-Enceladus/ipa | ipa/ipa_cloud.py | IpaCloud._write_to_log | def _write_to_log(self, output):
"""Write the output string to the log file."""
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log_file.write(output)
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"""Write the output string to the log file."""
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SUSE-Enceladus/ipa | ipa/ipa_cloud.py | IpaCloud._merge_results | def _merge_results(self, results):
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SUSE-Enceladus/ipa | ipa/ipa_cloud.py | IpaCloud._set_distro | def _set_distro(self):
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self.distro = SLES()
elif self.distro_name == 'opensuse_leap':
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raise IpaCloudException(
... | python | def _set_distro(self):
"""Determine distro for image and create instance of class."""
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SUSE-Enceladus/ipa | ipa/ipa_cloud.py | IpaCloud._set_results_dir | def _set_results_dir(self):
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self.results_dir,
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self.image_id,
self.running_instance_id
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... | python | def _set_results_dir(self):
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SUSE-Enceladus/ipa | ipa/ipa_cloud.py | IpaCloud._collect_vm_info | def _collect_vm_info(self):
"""
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self.logger.info('Collecting basic info about VM')
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out = self.distro.get_vm_info(client)
self._write_to_log(out) | python | def _collect_vm_info(self):
"""
Gather basic info about VM
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SUSE-Enceladus/ipa | ipa/ipa_cloud.py | IpaCloud._update_history | def _update_history(self):
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SUSE-Enceladus/ipa | ipa/ipa_cloud.py | IpaCloud._wait_on_instance | def _wait_on_instance(self, state, timeout=600, wait_period=10):
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start = time.time()
end = start + timeout
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SUSE-Enceladus/ipa | ipa/ipa_cloud.py | IpaCloud.execute_ssh_command | def execute_ssh_command(self, client, command):
"""Execute the provided command and log output."""
try:
out = ipa_utils.execute_ssh_command(client, command)
except Exception as error:
raise IpaCloudException(
'Command: "{0}", failed execution: {1}.'.format... | python | def execute_ssh_command(self, client, command):
"""Execute the provided command and log output."""
try:
out = ipa_utils.execute_ssh_command(client, command)
except Exception as error:
raise IpaCloudException(
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SUSE-Enceladus/ipa | ipa/ipa_cloud.py | IpaCloud.extract_archive | def extract_archive(self, client, archive_path, extract_path=None):
"""Extract the archive files using the client in the current path."""
try:
out = ipa_utils.extract_archive(client, archive_path, extract_path)
except Exception as error:
raise IpaCloudException(
... | python | def extract_archive(self, client, archive_path, extract_path=None):
"""Extract the archive files using the client in the current path."""
try:
out = ipa_utils.extract_archive(client, archive_path, extract_path)
except Exception as error:
raise IpaCloudException(
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SUSE-Enceladus/ipa | ipa/ipa_cloud.py | IpaCloud.hard_reboot_instance | def hard_reboot_instance(self):
"""Stop then start the instance."""
self._stop_instance()
self._start_instance()
self._set_instance_ip()
self.logger.debug('IP of instance: %s' % self.instance_ip)
ipa_utils.clear_cache() | python | def hard_reboot_instance(self):
"""Stop then start the instance."""
self._stop_instance()
self._start_instance()
self._set_instance_ip()
self.logger.debug('IP of instance: %s' % self.instance_ip)
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SUSE-Enceladus/ipa | ipa/ipa_cloud.py | IpaCloud.install_package | def install_package(self, client, package):
"""
Install package using distro specific install method.
"""
try:
out = self.distro.install_package(client, package)
except Exception as error:
raise IpaCloudException(
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"""
Install package using distro specific install method.
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SUSE-Enceladus/ipa | ipa/ipa_cloud.py | IpaCloud.process_injection_file | def process_injection_file(self, client):
"""
Load yaml file and process injection configuration.
There are 5 injection options:
:inject_packages: an rpm path or list of rpm paths which will be
copied and installed on the test instance.
:inject_archive... | python | def process_injection_file(self, client):
"""
Load yaml file and process injection configuration.
There are 5 injection options:
:inject_packages: an rpm path or list of rpm paths which will be
copied and installed on the test instance.
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SUSE-Enceladus/ipa | ipa/ipa_cloud.py | IpaCloud.put_file | def put_file(self, client, source_file):
"""
Put file on instance in default SSH directory.
"""
try:
file_name = os.path.basename(source_file)
ipa_utils.put_file(client, source_file, file_name)
except Exception as error:
raise IpaCloudException... | python | def put_file(self, client, source_file):
"""
Put file on instance in default SSH directory.
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try:
file_name = os.path.basename(source_file)
ipa_utils.put_file(client, source_file, file_name)
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tgbugs/pyontutils | neurondm/neurondm/models/allen_cell_types.py | AllenCellTypes.build_transgenic_lines | def build_transgenic_lines(self):
"""
init class | "transgenic_line_source_name":"stock_number" a Class
add superClass | rdfs:subClassOf ilxtr:transgenicLine
add *order* | ilxtr:useObjectProperty ilxtr:<order>
add name | rdfs:label "name"
add def |... | python | def build_transgenic_lines(self):
"""
init class | "transgenic_line_source_name":"stock_number" a Class
add superClass | rdfs:subClassOf ilxtr:transgenicLine
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tgbugs/pyontutils | nifstd/nifstd_tools/ilx_utils.py | decodeIlxResp | def decodeIlxResp(resp):
""" We need this until we can get json back directly and this is SUPER nasty"""
lines = [_ for _ in resp.text.split('\n') if _] # strip empties
if 'successfull' in lines[0]:
return [(_.split('"')[1],
ilxIdFix(_.split(': ')[-1]))
for _ in li... | python | def decodeIlxResp(resp):
""" We need this until we can get json back directly and this is SUPER nasty"""
lines = [_ for _ in resp.text.split('\n') if _] # strip empties
if 'successfull' in lines[0]:
return [(_.split('"')[1],
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tgbugs/pyontutils | nifstd/nifstd_tools/ilx_utils.py | getSubOrder | def getSubOrder(existing):
""" Alpha sort by the full chain of parents. """
alpha = list(zip(*sorted(((k, v['rec']['label']) for k, v in existing.items()), key=lambda a: a[1])))[0]
depths = {}
def getDepth(id_):
if id_ in depths:
return depths[id_]
else:
if id_ in... | python | def getSubOrder(existing):
""" Alpha sort by the full chain of parents. """
alpha = list(zip(*sorted(((k, v['rec']['label']) for k, v in existing.items()), key=lambda a: a[1])))[0]
depths = {}
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tgbugs/pyontutils | nifstd/nifstd_tools/parcellation/berman.py | clean | def clean(string):
''' Begining of the string can sometimes have odd noise '''
# manual fixes in the source
# 24/1.png
# 9/1.png
# 3/1.png
#if ')' in string: # fix in the source data
#string = string.split(')')[0] + ')' # remove trailing garbage
return (string
.replace(... | python | def clean(string):
''' Begining of the string can sometimes have odd noise '''
# manual fixes in the source
# 24/1.png
# 9/1.png
# 3/1.png
#if ')' in string: # fix in the source data
#string = string.split(')')[0] + ')' # remove trailing garbage
return (string
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tgbugs/pyontutils | nifstd/nifstd_tools/parcellation/berman.py | BermanSrc.loadData | def loadData(cls):
""" Sigh, this was indeed a poorly conceived approach
since it hard blocks when the files are not in the source
so you can't easily bootstrap from another source and the
cognitive overhead is way, way too high :/
Adding dry_run/bootstrap to __new__ sort of he... | python | def loadData(cls):
""" Sigh, this was indeed a poorly conceived approach
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tgbugs/pyontutils | nifstd/nifstd_tools/hbp_cells.py | ilx_conv | def ilx_conv(graph, prefix, ilx_start):
""" convert a set of temporary identifiers to ilx and modify the graph in place """
to_sub = set()
for subject in graph.subjects(rdflib.RDF.type, rdflib.OWL.Class):
if PREFIXES[prefix] in subject:
to_sub.add(subject)
ilx_base = 'ilx_{:0>7}'
... | python | def ilx_conv(graph, prefix, ilx_start):
""" convert a set of temporary identifiers to ilx and modify the graph in place """
to_sub = set()
for subject in graph.subjects(rdflib.RDF.type, rdflib.OWL.Class):
if PREFIXES[prefix] in subject:
to_sub.add(subject)
ilx_base = 'ilx_{:0>7}'
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tgbugs/pyontutils | pyontutils/necromancy.py | alreadyHasEntry | def alreadyHasEntry(oldClassString, og):
""" Return true if there is already an owl:Class with the old id"""
namespace = oldClassString.split(':')[0]
if namespace == 'http':
target = rdflib.URIRef(oldClassString)
print('OLD CLASS ID IS A URL', oldClassString)
else:
try:
... | python | def alreadyHasEntry(oldClassString, og):
""" Return true if there is already an owl:Class with the old id"""
namespace = oldClassString.split(':')[0]
if namespace == 'http':
target = rdflib.URIRef(oldClassString)
print('OLD CLASS ID IS A URL', oldClassString)
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tgbugs/pyontutils | neurondm/neurondm/lang.py | config | def config(remote_base= 'https://raw.githubusercontent.com/SciCrunch/NIF-Ontology/',
local_base= None, # devconfig.ontology_local_repo by default
branch= devconfig.neurons_branch,
core_graph_paths= ['ttl/phenotype-core.ttl',
'ttl/ph... | python | def config(remote_base= 'https://raw.githubusercontent.com/SciCrunch/NIF-Ontology/',
local_base= None, # devconfig.ontology_local_repo by default
branch= devconfig.neurons_branch,
core_graph_paths= ['ttl/phenotype-core.ttl',
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tgbugs/pyontutils | pyontutils/ontutils.py | add_version_iri | def add_version_iri(graph, epoch):
""" Also remove the previous versionIRI if there was one."""
for ont in graph.subjects(rdf.type, owl.Ontology):
for versionIRI in graph.objects(ont, owl.versionIRI):
graph.remove((ont, owl.versionIRI, versionIRI))
t = ont, owl.versionIRI, make_versi... | python | def add_version_iri(graph, epoch):
""" Also remove the previous versionIRI if there was one."""
for ont in graph.subjects(rdf.type, owl.Ontology):
for versionIRI in graph.objects(ont, owl.versionIRI):
graph.remove((ont, owl.versionIRI, versionIRI))
t = ont, owl.versionIRI, make_versi... | [
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] | train | https://github.com/tgbugs/pyontutils/blob/3d913db29c177db39151592909a4f56170ef8b35/pyontutils/ontutils.py#L323-L329 |
Sheeprider/BitBucket-api | bitbucket/bitbucket.py | Bitbucket.auth | def auth(self):
""" Return credentials for current Bitbucket user. """
if self.oauth:
return self.oauth
return (self.username, self.password) | python | def auth(self):
""" Return credentials for current Bitbucket user. """
if self.oauth:
return self.oauth
return (self.username, self.password) | [
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Sheeprider/BitBucket-api | bitbucket/bitbucket.py | Bitbucket.authorize | def authorize(self, consumer_key, consumer_secret, callback_url=None,
access_token=None, access_token_secret=None):
"""
Call this with your consumer key, secret and callback URL, to
generate a token for verification.
"""
self.consumer_key = consumer_key
... | python | def authorize(self, consumer_key, consumer_secret, callback_url=None,
access_token=None, access_token_secret=None):
"""
Call this with your consumer key, secret and callback URL, to
generate a token for verification.
"""
self.consumer_key = consumer_key
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Sheeprider/BitBucket-api | bitbucket/bitbucket.py | Bitbucket.verify | def verify(self, verifier, consumer_key=None, consumer_secret=None,
access_token=None, access_token_secret=None):
"""
After converting the token into verifier, call this to finalize the
authorization.
"""
# Stored values can be supplied to verify
self.consu... | python | def verify(self, verifier, consumer_key=None, consumer_secret=None,
access_token=None, access_token_secret=None):
"""
After converting the token into verifier, call this to finalize the
authorization.
"""
# Stored values can be supplied to verify
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