sentence1 stringlengths 52 3.87M | sentence2 stringlengths 1 47.2k | label stringclasses 1
value |
|---|---|---|
def remove_triple(
self,
subj: URIRef,
pred: URIRef,
obj: Union[URIRef, Literal]
) -> None:
""" Removes triple from rdflib Graph
You must input the triple in its URIRef or Literal form for each node exactly the way it
was inputed or it wil... | Removes triple from rdflib Graph
You must input the triple in its URIRef or Literal form for each node exactly the way it
was inputed or it will not delete the triple.
Args:
subj: Entity subject to be removed it its the only node with this subject; else this is
just... | entailment |
def print_graph(self, format: str = 'turtle') -> str:
""" prints serialized formated rdflib Graph """
print(self.g.serialize(format=format).decode('utf-8')) | prints serialized formated rdflib Graph | entailment |
def identifierSearches(self,
ids=None,
LIMIT=25,
_print=True,
crawl=False):
"""parameters( data = "list of term_ids" )"""
url_base = self.base_url + '/api/1/term/view/{id}' + '?key=' + self.api_ke... | parameters( data = "list of term_ids" ) | entailment |
def ilxSearches(self,
ilx_ids=None,
LIMIT=25,
_print=True,
crawl=False):
"""parameters( data = "list of ilx_ids" )"""
url_base = self.base_url + "/api/1/ilx/search/identifier/{identifier}?key={APIKEY}"
urls = [url_ba... | parameters( data = "list of ilx_ids" ) | entailment |
def updateTerms(self, data:list, LIMIT:int=20, _print:bool=True, crawl:bool=False,) -> list:
""" Updates existing entities
Args:
data:
needs:
id <str>
ilx_id <str>
options:
... | Updates existing entities
Args:
data:
needs:
id <str>
ilx_id <str>
options:
definition <str> #bug with qutations
superclasses ... | entailment |
def addTerms(self, data, LIMIT=25, _print=True, crawl=False):
"""
need:
label <str>
type term, cde, anntation, or relationship <str>
options:
definition <str> #bug with qutations
sup... | need:
label <str>
type term, cde, anntation, or relationship <str>
options:
definition <str> #bug with qutations
superclasses [{'id':<int>}]
synonyms [{'literal':<str>}]
... | entailment |
def getAnnotations_via_tid(self,
tids,
LIMIT=25,
_print=True,
crawl=False):
"""
tids = list of term ids that possess the annoations
"""
url_base = self.base_url + \... | tids = list of term ids that possess the annoations | entailment |
def getAnnotations_via_id(self,
annotation_ids,
LIMIT=25,
_print=True,
crawl=False):
"""tids = list of strings or ints that are the ids of the annotations themselves"""
url_base = self... | tids = list of strings or ints that are the ids of the annotations themselves | entailment |
def updateAnnotations(self,
data,
LIMIT=25,
_print=True,
crawl=False,):
"""data = [{'id', 'tid', 'annotation_tid', 'value', 'comment', 'upvote', 'downvote',
'curator_status', 'withdrawn', 'term_versio... | data = [{'id', 'tid', 'annotation_tid', 'value', 'comment', 'upvote', 'downvote',
'curator_status', 'withdrawn', 'term_version', 'annotation_term_version', 'orig_uid',
'orig_time'}] | entailment |
def deleteAnnotations(self,
annotation_ids,
LIMIT=25,
_print=True,
crawl=False,):
"""data = list of ids"""
url_base = self.base_url + \
'/api/1/term/edit-annotation/{annotation_id}' # id ... | data = list of ids | entailment |
def addRelationships(
self,
data: list,
LIMIT: int = 20,
_print: bool = True,
crawl: bool = False,
) -> list:
"""
data = [{
"term1_id", "term2_id", "relationship_tid",
"term1_version", "term2_version",
"relationship_term... | data = [{
"term1_id", "term2_id", "relationship_tid",
"term1_version", "term2_version",
"relationship_term_version",}] | entailment |
def deprecate_entity(
self,
ilx_id: str,
note = None,
) -> None:
""" Tagged term in interlex to warn this term is no longer used
There isn't an proper way to delete a term and so we have to mark it so I can
extrapolate that in mysql/ttl loads.
Args:
... | Tagged term in interlex to warn this term is no longer used
There isn't an proper way to delete a term and so we have to mark it so I can
extrapolate that in mysql/ttl loads.
Args:
term_id: id of the term of which to be deprecated
term_version: version of the term of wh... | entailment |
def force_add_term(self, entity: dict):
""" Need to add an entity that already has a label existing in InterLex?
Well this is the function for you!
entity:
need:
label <str>
type term, cde, pde, fde, an... | Need to add an entity that already has a label existing in InterLex?
Well this is the function for you!
entity:
need:
label <str>
type term, cde, pde, fde, anntation, or relationship <str>
optio... | entailment |
def create_df_file_with_query(self, query, output):
""" Dumps in df in chunks to avoid crashes.
"""
chunk_size = 100000
offset = 0
data = defaultdict(lambda : defaultdict(list))
with open(output, 'wb') as outfile:
query = query.replace(';', '')
qu... | Dumps in df in chunks to avoid crashes. | entailment |
def diff(s1, s2):
''' --word-diff=porcelain clone'''
delta = difflib.Differ().compare(s1.split(), s2.split())
difflist = []
fullline = ''
for line in delta:
if line[0] == '?':
continue
elif line[0] == ' ':
fullline += line.strip() + ' '
else:
... | --word-diff=porcelain clone | entailment |
def diffcolor(s1, s2):
''' --word-diff=color clone '''
string = ''
for line in diff(s1, s2):
if line[0] == '-':
string += ' ' + TermColors.red(line[2:])
elif line[0] == '+':
string += ' ' + TermColors.green(line[2:])
else:
string += ' ' + line
... | --word-diff=color clone | entailment |
def create_html(s1, s2, output='test.html'):
''' creates basic html based on the diff of 2 strings '''
html = difflib.HtmlDiff().make_file(s1.split(), s2.split())
with open(output, 'w') as f:
f.write(html) | creates basic html based on the diff of 2 strings | entailment |
def traverse_data(obj, key_target):
''' will traverse nested list and dicts until key_target equals the current dict key '''
if isinstance(obj, str) and '.json' in str(obj):
obj = json.load(open(obj, 'r'))
if isinstance(obj, list):
queue = obj.copy()
elif isinstance(obj, dict):
q... | will traverse nested list and dicts until key_target equals the current dict key | entailment |
def json_diff(json1, json2, key_target, get_just_diff=True, porcelain=False):
''' creates a (keyname + diff) key within the json of the same layer which key_target resides.
Ex: json1={'definition':'data of key_target'}, json2={'definition':'data of key_target'}
key_target = 'definition'
Usage:
... | creates a (keyname + diff) key within the json of the same layer which key_target resides.
Ex: json1={'definition':'data of key_target'}, json2={'definition':'data of key_target'}
key_target = 'definition'
Usage:
json_diff (
json_data1, json_data1 can be both [{..}] ... | entailment |
def memoryCheck(vms_max_kb):
""" Lookup vms_max using getCurrentVMSKb """
safety_factor = 1.2
vms_max = vms_max_kb
vms_gigs = vms_max / 1024 ** 2
buffer = safety_factor * vms_max
buffer_gigs = buffer / 1024 ** 2
vm = psutil.virtual_memory()
free_gigs = vm.available / 1024 ** 2
if vm.... | Lookup vms_max using getCurrentVMSKb | entailment |
def _sequence_query(self):
"""
query all sequence rows
"""
klass = self.__class__
query = klass.select().where(klass.sequence.is_null(False))
seq_scope_field_names =\
(self.__seq_scope_field_name__ or '').split(',')
for name in seq_scope_field_names:
... | query all sequence rows | entailment |
def update_sheet_values(spreadsheet_name, sheet_name, values, spreadsheet_service=None):
SPREADSHEET_ID = devconfig.secrets(spreadsheet_name)
if spreadsheet_service is None:
service = get_oauth_service(readonly=False)
ss = service.spreadsheets()
else:
ss = spreadsheet_service
"""... | requests = [
{'updateCells': {
'start': {'sheetId': TODO,
'rowIndex': 0,
'columnIndex': 0}
'rows': {'values'}
}
}]
response = ss.batchUpdate(
spreadsheetId=SPREADSHEET_ID, range=sheet_name,
body=body).execute... | entailment |
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... | update remote values (called automatically at __init__) | entailment |
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... | Add disjoint union classes so that it is possible to see the invariants
associated with individual phenotypes | entailment |
def _rest_make_phenotypes():
#phenotype sources
neuroner = Path(devconfig.git_local_base,
'neuroNER/resources/bluima/neuroner/hbp_morphology_ontology.obo').as_posix()
neuroner1 = Path(devconfig.git_local_base,
'neuroNER/resources/bluima/neuroner/hbp_electrophysiology_ontolog... | print stuff
print('matches')
pprint(exact)
pprint(similar)
#print('EXACT', exact)
print()
for k, v in s2.items():
print(k)
for k, v2 in sorted(v.items()):
print(' ', k, ':', v2)
# | entailment |
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... | Allows changing the config on the fly | entailment |
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... | Retrieve json dict from service account file. | entailment |
def _get_driver(self):
"""Get authenticated GCE driver."""
ComputeEngine = get_driver(Provider.GCE)
return ComputeEngine(
self.service_account_email,
self.service_account_file,
project=self.service_account_project
) | Get authenticated GCE driver. | entailment |
def _get_instance(self):
"""Retrieve instance matching instance_id."""
try:
instance = self.compute_driver.ex_get_node(
self.running_instance_id,
zone=self.region
)
except ResourceNotFoundError as e:
raise GCECloudException(
... | Retrieve instance matching instance_id. | entailment |
def _get_ssh_public_key(self):
"""Generate SSH public key from private key."""
key = ipa_utils.generate_public_ssh_key(self.ssh_private_key_file)
return '{user}:{key} {user}'.format(
user=self.ssh_user,
key=key.decode()
) | Generate SSH public key from private key. | entailment |
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(
'gce-ipa-test'
)
self.logger.debug('ID of instance: %s' % self.running_in... | Launch an instance of the given image. | entailment |
def _validate_region(self):
"""Validate region was passed in and is a valid GCE zone."""
if not self.region:
raise GCECloudException(
'Zone is required for GCE cloud framework: '
'Example: us-west1-a'
)
try:
zone = self.compute... | Validate region was passed in and is a valid GCE zone. | entailment |
def _set_instance_ip(self):
"""Retrieve and set the instance ip address."""
instance = self._get_instance()
if instance.public_ips:
self.instance_ip = instance.public_ips[0]
elif instance.private_ips:
self.instance_ip = instance.private_ips[0]
else:
... | Retrieve and set the instance ip address. | entailment |
def _start_instance(self):
"""Start the instance."""
instance = self._get_instance()
self.compute_driver.ex_start_node(instance)
self.compute_driver.wait_until_running(
[instance],
timeout=self.timeout
) | Start the instance. | entailment |
def _stop_instance(self):
"""Stop the instance."""
instance = self._get_instance()
self.compute_driver.ex_stop_node(instance)
self._wait_on_instance('stopped', timeout=self.timeout) | Stop the instance. | entailment |
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... | Crap-shot for ontology iri if its properly in the header and correctly formated | entailment |
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(
'Need to provide ilx ID w... | Database only excepts lower case and underscore version of ID | entailment |
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:
pass
... | Useful for IDs that have giberish in the front of the real ID | entailment |
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... | Pulls only for code/ID from the iri
I only add the str() conversion for the iri because rdflib objects need to be converted. | entailment |
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:
... | 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:
None or dict | entailment |
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:
... | 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:
None or List[dict] | entailment |
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]
''... | 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] | entailment |
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... | Setups the entity to be InterLex ready
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
... | entailment |
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' ... | Helper for exhaustive checks to see if there any matches at all besides the anchor
OUTPUT:
[
{
'external_ontology_row' : {},
'interlex_row' : {},
'same': {},
},
... | entailment |
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... | All entities with conflicting labels gets a full diff
Args:
ontology: pandas DataFrame created from an ontology where the colnames are predicates
and if classes exist it is also thrown into a the colnames.
label_predicate: usually in qname form and is the... | entailment |
def exhaustive_iri_check( self,
ontology:pd.DataFrame,
iri_predicate:str,
diff:bool=True, ) -> Tuple[list]:
''' All entities with conflicting iris gets a full diff to see if they belong
Args:
o... | All entities with conflicting iris gets a full diff to see if they belong
Args:
ontology: pandas DataFrame created from an ontology where the colnames are predicates
and if classes exist it is also thrown into a the colnames.
iri_predicate: usually in qna... | entailment |
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... | All entities with conflicting curies gets a full diff to see if they belong
Args:
ontology: pandas DataFrame created from an ontology where the colnames are predicates
and if classes exist it is also thrown into a the colnames.
curie_predicate: usually in... | entailment |
def exhaustive_fragment_check( self,
ontology:pd.DataFrame,
iri_curie_fragment_predicate:str = 'iri',
cross_reference_iris:bool = False,
cross_reference_fragments:bool = False,
... | All entities with conflicting fragments gets a full diff to see if they belong
Args:
ontology: pandas DataFrame created from an ontology where the colnames are predicates
and if classes exist it is also thrown into a the colnames.
iri_curie_fragment_predi... | entailment |
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)}
... | WARNING RUNTIME IS AWEFUL | entailment |
def combo_exhaustive_label_definition_check( self,
ontology: pd.DataFrame,
label_predicate:str,
definition_predicates:str,
d... | Combo of label & definition exhaustive check out of convenience
Args:
ontology: pandas DataFrame created from an ontology where the colnames are predicates
and if classes exist it is also thrown into a the colnames.
label_predicate: usually in qname form ... | entailment |
def clear_cache(ip=None):
"""Clear the client cache or remove key matching the given ip."""
if ip:
with ignored(Exception):
client = CLIENT_CACHE[ip]
del CLIENT_CACHE[ip]
client.close()
else:
for client in CLIENT_CACHE.values():
with ignored(Ex... | Clear the client cache or remove key matching the given ip. | entailment |
def establish_ssh_connection(ip,
ssh_private_key_file,
ssh_user,
port,
attempts=5,
timeout=None):
"""
Establish ssh connection and return paramiko client.
Raises:... | Establish ssh connection and return paramiko client.
Raises:
IpaSSHException: If connection cannot be established
in given number of attempts. | entailment |
def execute_ssh_command(client, cmd):
"""
Execute given command using paramiko.
Returns:
String output of cmd execution.
Raises:
IpaSSHException: If stderr returns a non-empty string.
"""
try:
stdin, stdout, stderr = client.exec_command(cmd)
err = stderr.read()
... | Execute given command using paramiko.
Returns:
String output of cmd execution.
Raises:
IpaSSHException: If stderr returns a non-empty string. | entailment |
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)
if extract_path:
command += ' -C {extract_pat... | Extract the archive in current path using the provided client.
If extract_path is provided extract the archive there. | entailment |
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... | Generate SSH public key from private key file. | entailment |
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... | Parse ini config file and return a dict of values.
The provided section overrides any values in default section. | entailment |
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... | Attempt to establish and test ssh connection. | entailment |
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(
'Config fi... | Load yaml config file and return dictionary.
Todo:
* This will need refactoring similar to the test search. | entailment |
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... | 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'), 'test_soft_reboot']
[set('test1', 'test2'),... | entailment |
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... | Copy file to instance using Paramiko client connection. | entailment |
def redirect_output(fileobj):
"""Redirect standard out to file."""
old = sys.stdout
sys.stdout = fileobj
try:
yield fileobj
finally:
sys.stdout = old | Redirect standard out to file. | entailment |
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)
... | Create temporary ssh config file. | entailment |
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... | Update the history log file with item.
If clear flag is provided the log file is deleted. | entailment |
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)) | Validate string by regex
:param value: str
:return: | entailment |
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
... | Updates self.g or self.path bc you could only choose 1 | entailment |
def create_pred2common(self):
''' Takes list linked to common name and maps common name to accepted predicate
and their respected suffixes to decrease sensitivity.
'''
self.pred2common = {}
for common_name, ext_preds in self.common2preds.items():
for pred in ext_p... | Takes list linked to common name and maps common name to accepted predicate
and their respected suffixes to decrease sensitivity. | entailment |
def clean_pred(self, pred, ignore_warning=False):
''' Takes the predicate and returns the suffix, lower case, stripped version
'''
original_pred = pred
pred = pred.lower().strip()
if 'http' in pred:
pred = pred.split('/')[-1]
elif ':' in pred:
if p... | Takes the predicate and returns the suffix, lower case, stripped version | entailment |
def get_common_pred(self, pred):
''' Gets version of predicate and sees if we have a translation to a common relation.
INPUT:
pred = predicate from the triple
OUTPUT:
Common relationship or None
'''
pred = self.clean_pred(pred)
comm... | Gets version of predicate and sees if we have a translation to a common relation.
INPUT:
pred = predicate from the triple
OUTPUT:
Common relationship or None | entailment |
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... | Create a network interface in the resource group.
Attach NIC to the subnet and public IP provided. | entailment |
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... | Create dynamic public IP address in the resource group. | entailment |
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... | Create resource group if it does not exist. | entailment |
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': {
'publisher': s... | Create the storage profile for the instance.
Image reference can be a custom image name or a published urn. | entailment |
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(
resource... | Create a subnet in the provided vnet and resource group. | entailment |
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 = {
'location': region,
'address_space': {
'address_prefixes': ['10.0.0.0/27']
... | Create a vnet in the given resource group with default address space. | entailment |
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
... | Attempt to create or update VM instance based on vm_parameters config. | entailment |
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 = {
'vm_size': self.instance_type or AZUR... | Create the VM config dictionary.
Requires an existing network interface object. | entailment |
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'
)
except Exc... | Return the instance matching the running_instance_id. | entailment |
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 | Retrieve state of instance. | entailment |
def _get_management_client(self, client_class):
"""
Return instance of resource management client.
"""
try:
client = get_client_from_auth_file(
client_class, auth_path=self.service_account_file
)
except ValueError as error:
rais... | Return instance of resource management client. | entailment |
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... | Create new test instance in a resource group with the same name. | entailment |
def _process_image_id(self):
"""
Split image id into component values.
Example: SUSE:SLES:12-SP3:2018.01.04
Publisher:Offer:Sku:Version
Raises:
If image_id is not a valid format.
"""
try:
image_info = self.image_id.strip().split(... | Split image id into component values.
Example: SUSE:SLES:12-SP3:2018.01.04
Publisher:Offer:Sku:Version
Raises:
If image_id is not a valid format. | entailment |
def _set_default_resource_names(self):
"""
Generate names for resources based on the running_instance_id.
"""
self.ip_config_name = ''.join([
self.running_instance_id, '-ip-config'
])
self.nic_name = ''.join([self.running_instance_id, '-nic'])
self.pub... | Generate names for resources based on the running_instance_id. | entailment |
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
if image_info.publisher:
self.image_id = ':'.join([
image_info... | If an existing instance is used get image id from deployment. | entailment |
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(
self.running_instance_id, self.public_ip_name
).... | Get the IP address based on instance ID.
If public IP address not found attempt to get private IP. | entailment |
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(
... | Start the instance. | entailment |
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(
... | Stop the instance. | entailment |
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:... | Terminate the resource group and instance. | entailment |
def preferred_change(data):
''' Determines preferred existing id based on curie prefix in the ranking list '''
ranking = [
'CHEBI',
'NCBITaxon',
'COGPO',
'CAO',
'DICOM',
'UBERON',
'NLX',
'NLXANAT',
'NLXCELL',
'NLXFUNC',
'NLX... | Determines preferred existing id based on curie prefix in the ranking list | entailment |
def merge(new, old):
''' synonyms and existing_ids are part of an object bug that can create duplicates if in the same batch '''
for k, vals in new.items():
if k == 'synonyms':
new_synonyms = vals
if old['synonyms']:
old_literals = [syn['literal'].lower().strip(... | synonyms and existing_ids are part of an object bug that can create duplicates if in the same batch | entailment |
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.).
"""
if context.obj is None:
context.obj = {}
context.obj['no_color'] = 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.). | entailment |
def results(context, history_log):
"""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:
context.invoke(show, item=1) | Process provided history log and results files. | entailment |
def archive(context, clear_log, items, path, name):
"""
Archive the history log and all results/log files.
After archive is created optionally clear the history log.
"""
history_log = context.obj['history_log']
no_color = context.obj['no_color']
with open(history_log, 'r') as f:
# ... | Archive the history log and all results/log files.
After archive is created optionally clear the history log. | entailment |
def delete(context, item):
"""
Delete the specified history item from the history log.
"""
history_log = context.obj['history_log']
no_color = context.obj['no_color']
try:
with open(history_log, 'r+') as f:
lines = f.readlines()
history = lines.pop(len(lines) - it... | Delete the specified history item from the history log. | entailment |
def show(context,
log,
results_file,
verbose,
item):
"""
Print test results info from provided results json file.
If no results file is supplied echo results from most recent
test in history if it exists.
If verbose option selected, echo all test cases.
If ... | Print test results info from provided results json file.
If no results file is supplied echo results from most recent
test in history if it exists.
If verbose option selected, echo all test cases.
If log option selected echo test log. | entailment |
def _get_ssh_client(self):
"""Return a new or existing SSH client for given ip."""
return ipa_utils.get_ssh_client(
self.instance_ip,
self.ssh_private_key_file,
self.ssh_user,
timeout=self.timeout
) | Return a new or existing SSH client for given ip. | entailment |
def _log_info(self):
"""Output test run information to top of log file."""
if self.cloud == 'ssh':
self.results['info'] = {
'platform': self.cloud,
'distro': self.distro_name,
'image': self.instance_ip,
'timestamp': self.time_st... | Output test run information to top of log file. | entailment |
def _write_to_log(self, output):
"""Write the output string to the log file."""
with open(self.log_file, 'a') as log_file:
log_file.write('\n')
log_file.write(output)
log_file.write('\n') | Write the output string to the log file. | entailment |
def _merge_results(self, results):
"""Combine results of test run with exisiting dict."""
self.results['tests'] += results['tests']
for key, value in results['summary'].items():
self.results['summary'][key] += value | Combine results of test run with exisiting dict. | entailment |
def _save_results(self):
"""Save results dictionary to json file."""
with open(self.results_file, 'w') as results_file:
json.dump(self.results, results_file) | Save results dictionary to json file. | entailment |
def _set_distro(self):
"""Determine distro for image and create instance of class."""
if self.distro_name == 'sles':
self.distro = SLES()
elif self.distro_name == 'opensuse_leap':
self.distro = openSUSE_Leap()
else:
raise IpaCloudException(
... | Determine distro for image and create instance of class. | entailment |
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