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ghukill/pyfc4 | pyfc4/models.py | Repository.start_txn | def start_txn(self, txn_name=None):
'''
Request new transaction from repository, init new Transaction,
store in self.txns
Args:
txn_name (str): human name for transaction
Return:
(Transaction): returns intance of newly created transaction
'''
# if no name provided, create one
if not txn_name:
txn_name = uuid.uuid4().hex
# request new transaction
txn_response = self.api.http_request('POST','%s/fcr:tx' % self.root, data=None, headers=None)
# if 201, transaction was created
if txn_response.status_code == 201:
txn_uri = txn_response.headers['Location']
logger.debug("spawning transaction: %s" % txn_uri)
# init new Transaction, and pass Expires header
txn = Transaction(
self, # pass the repository
txn_name,
txn_uri,
expires = txn_response.headers['Expires'])
# append to self
self.txns[txn_name] = txn
# return
return txn | python | def start_txn(self, txn_name=None):
'''
Request new transaction from repository, init new Transaction,
store in self.txns
Args:
txn_name (str): human name for transaction
Return:
(Transaction): returns intance of newly created transaction
'''
# if no name provided, create one
if not txn_name:
txn_name = uuid.uuid4().hex
# request new transaction
txn_response = self.api.http_request('POST','%s/fcr:tx' % self.root, data=None, headers=None)
# if 201, transaction was created
if txn_response.status_code == 201:
txn_uri = txn_response.headers['Location']
logger.debug("spawning transaction: %s" % txn_uri)
# init new Transaction, and pass Expires header
txn = Transaction(
self, # pass the repository
txn_name,
txn_uri,
expires = txn_response.headers['Expires'])
# append to self
self.txns[txn_name] = txn
# return
return txn | [
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store in self.txns
Args:
txn_name (str): human name for transaction
Return:
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L229-L266 | train |
ghukill/pyfc4 | pyfc4/models.py | Repository.get_txn | def get_txn(self, txn_name, txn_uri):
'''
Retrieves known transaction and adds to self.txns.
TODO:
Perhaps this should send a keep-alive request as well? Obviously still needed, and would reset timer.
Args:
txn_prefix (str, rdflib.term.URIRef): uri of the transaction. e.g. http://localhost:8080/rest/txn:123456789
txn_name (str): local, human name for transaction
Return:
(Transaction) local instance of transactions from self.txns[txn_uri]
'''
# parse uri
txn_uri = self.parse_uri(txn_uri)
# request new transaction
txn_response = self.api.http_request('GET',txn_uri, data=None, headers=None)
# if 200, transaction exists
if txn_response.status_code == 200:
logger.debug("transactoin found: %s" % txn_uri)
# init new Transaction, and pass Expires header
txn = Transaction(
self, # pass the repository
txn_name,
txn_uri,
expires = None)
# append to self
self.txns[txn_name] = txn
# return
return txn
# if 404, transaction does not exist
elif txn_response.status_code in [404, 410]:
logger.debug("transaction does not exist: %s" % txn_uri)
return False
else:
raise Exception('HTTP %s, could not retrieve transaction' % txn_response.status_code) | python | def get_txn(self, txn_name, txn_uri):
'''
Retrieves known transaction and adds to self.txns.
TODO:
Perhaps this should send a keep-alive request as well? Obviously still needed, and would reset timer.
Args:
txn_prefix (str, rdflib.term.URIRef): uri of the transaction. e.g. http://localhost:8080/rest/txn:123456789
txn_name (str): local, human name for transaction
Return:
(Transaction) local instance of transactions from self.txns[txn_uri]
'''
# parse uri
txn_uri = self.parse_uri(txn_uri)
# request new transaction
txn_response = self.api.http_request('GET',txn_uri, data=None, headers=None)
# if 200, transaction exists
if txn_response.status_code == 200:
logger.debug("transactoin found: %s" % txn_uri)
# init new Transaction, and pass Expires header
txn = Transaction(
self, # pass the repository
txn_name,
txn_uri,
expires = None)
# append to self
self.txns[txn_name] = txn
# return
return txn
# if 404, transaction does not exist
elif txn_response.status_code in [404, 410]:
logger.debug("transaction does not exist: %s" % txn_uri)
return False
else:
raise Exception('HTTP %s, could not retrieve transaction' % txn_response.status_code) | [
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TODO:
Perhaps this should send a keep-alive request as well? Obviously still needed, and would reset timer.
Args:
txn_prefix (str, rdflib.term.URIRef): uri of the transaction. e.g. http://localhost:8080/rest/txn:123456789
txn_name (str): local, human name for transaction
Return:
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L269-L314 | train |
ghukill/pyfc4 | pyfc4/models.py | Transaction.keep_alive | def keep_alive(self):
'''
Keep current transaction alive, updates self.expires
Args:
None
Return:
None: sets new self.expires
'''
# keep transaction alive
txn_response = self.api.http_request('POST','%sfcr:tx' % self.root, data=None, headers=None)
# if 204, transaction kept alive
if txn_response.status_code == 204:
logger.debug("continuing transaction: %s" % self.root)
# update status and timer
self.active = True
self.expires = txn_response.headers['Expires']
return True
# if 410, transaction does not exist
elif txn_response.status_code == 410:
logger.debug("transaction does not exist: %s" % self.root)
self.active = False
return False
else:
raise Exception('HTTP %s, could not continue transaction' % txn_response.status_code) | python | def keep_alive(self):
'''
Keep current transaction alive, updates self.expires
Args:
None
Return:
None: sets new self.expires
'''
# keep transaction alive
txn_response = self.api.http_request('POST','%sfcr:tx' % self.root, data=None, headers=None)
# if 204, transaction kept alive
if txn_response.status_code == 204:
logger.debug("continuing transaction: %s" % self.root)
# update status and timer
self.active = True
self.expires = txn_response.headers['Expires']
return True
# if 410, transaction does not exist
elif txn_response.status_code == 410:
logger.debug("transaction does not exist: %s" % self.root)
self.active = False
return False
else:
raise Exception('HTTP %s, could not continue transaction' % txn_response.status_code) | [
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L357-L387 | train |
ghukill/pyfc4 | pyfc4/models.py | Transaction._close | def _close(self, close_type):
'''
Ends transaction by committing, or rolling back, all changes during transaction.
Args:
close_type (str): expects "commit" or "rollback"
Return:
(bool)
'''
# commit transaction
txn_response = self.api.http_request('POST','%sfcr:tx/fcr:%s' % (self.root, close_type), data=None, headers=None)
# if 204, transaction was closed
if txn_response.status_code == 204:
logger.debug("%s for transaction: %s, successful" % (close_type, self.root))
# update self.active
self.active = False
# return
return True
# if 410 or 404, transaction does not exist
elif txn_response.status_code in [404, 410]:
logger.debug("transaction does not exist: %s" % self.root)
# update self.active
self.active = False
return False
else:
raise Exception('HTTP %s, could not commit transaction' % txn_response.status_code) | python | def _close(self, close_type):
'''
Ends transaction by committing, or rolling back, all changes during transaction.
Args:
close_type (str): expects "commit" or "rollback"
Return:
(bool)
'''
# commit transaction
txn_response = self.api.http_request('POST','%sfcr:tx/fcr:%s' % (self.root, close_type), data=None, headers=None)
# if 204, transaction was closed
if txn_response.status_code == 204:
logger.debug("%s for transaction: %s, successful" % (close_type, self.root))
# update self.active
self.active = False
# return
return True
# if 410 or 404, transaction does not exist
elif txn_response.status_code in [404, 410]:
logger.debug("transaction does not exist: %s" % self.root)
# update self.active
self.active = False
return False
else:
raise Exception('HTTP %s, could not commit transaction' % txn_response.status_code) | [
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L390-L421 | train |
ghukill/pyfc4 | pyfc4/models.py | API.http_request | def http_request(self,
verb,
uri,
data=None,
headers=None,
files=None,
response_format=None,
is_rdf = True,
stream = False
):
'''
Primary route for all HTTP requests to repository. Ability to set most parameters for requests library,
with some additional convenience parameters as well.
Args:
verb (str): HTTP verb to use for request, e.g. PUT, POST, GET, HEAD, PATCH, etc.
uri (rdflib.term.URIRef,str): input URI
data (str,file): payload of data to send for request, may be overridden in preperation of request
headers (dict): optional dictionary of headers passed directly to requests.request
files (dict): optional dictionary of files passed directly to requests.request
response_format (str): desired response format for resource's payload, e.g. 'application/rdf+xml', 'text/turtle', etc.
is_rdf (bool): if True, set Accept header based on combination of response_format and headers
stream (bool): passed directly to requests.request for stream parameter
Returns:
requests.models.Response
'''
# set content negotiated response format for RDFSources
if is_rdf:
'''
Acceptable content negotiated response formats include:
application/ld+json (discouraged, if not prohibited, as it drops prefixes used in repository)
application/n-triples
application/rdf+xml
text/n3 (or text/rdf+n3)
text/plain
text/turtle (or application/x-turtle)
'''
# set for GET requests only
if verb == 'GET':
# if no response_format has been requested to this point, use repository instance default
if not response_format:
response_format = self.repo.default_serialization
# if headers present, append
if headers and 'Accept' not in headers.keys():
headers['Accept'] = response_format
# if headers are blank, init dictionary
else:
headers = {'Accept':response_format}
# prepare uri for HTTP request
if type(uri) == rdflib.term.URIRef:
uri = uri.toPython()
logger.debug("%s request for %s, format %s, headers %s" %
(verb, uri, response_format, headers))
# manually prepare request
session = requests.Session()
request = requests.Request(verb, uri, auth=(self.repo.username, self.repo.password), data=data, headers=headers, files=files)
prepped_request = session.prepare_request(request)
response = session.send(prepped_request,
stream=stream,
)
return response | python | def http_request(self,
verb,
uri,
data=None,
headers=None,
files=None,
response_format=None,
is_rdf = True,
stream = False
):
'''
Primary route for all HTTP requests to repository. Ability to set most parameters for requests library,
with some additional convenience parameters as well.
Args:
verb (str): HTTP verb to use for request, e.g. PUT, POST, GET, HEAD, PATCH, etc.
uri (rdflib.term.URIRef,str): input URI
data (str,file): payload of data to send for request, may be overridden in preperation of request
headers (dict): optional dictionary of headers passed directly to requests.request
files (dict): optional dictionary of files passed directly to requests.request
response_format (str): desired response format for resource's payload, e.g. 'application/rdf+xml', 'text/turtle', etc.
is_rdf (bool): if True, set Accept header based on combination of response_format and headers
stream (bool): passed directly to requests.request for stream parameter
Returns:
requests.models.Response
'''
# set content negotiated response format for RDFSources
if is_rdf:
'''
Acceptable content negotiated response formats include:
application/ld+json (discouraged, if not prohibited, as it drops prefixes used in repository)
application/n-triples
application/rdf+xml
text/n3 (or text/rdf+n3)
text/plain
text/turtle (or application/x-turtle)
'''
# set for GET requests only
if verb == 'GET':
# if no response_format has been requested to this point, use repository instance default
if not response_format:
response_format = self.repo.default_serialization
# if headers present, append
if headers and 'Accept' not in headers.keys():
headers['Accept'] = response_format
# if headers are blank, init dictionary
else:
headers = {'Accept':response_format}
# prepare uri for HTTP request
if type(uri) == rdflib.term.URIRef:
uri = uri.toPython()
logger.debug("%s request for %s, format %s, headers %s" %
(verb, uri, response_format, headers))
# manually prepare request
session = requests.Session()
request = requests.Request(verb, uri, auth=(self.repo.username, self.repo.password), data=data, headers=headers, files=files)
prepped_request = session.prepare_request(request)
response = session.send(prepped_request,
stream=stream,
)
return response | [
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verb (str): HTTP verb to use for request, e.g. PUT, POST, GET, HEAD, PATCH, etc.
uri (rdflib.term.URIRef,str): input URI
data (str,file): payload of data to send for request, may be overridden in preperation of request
headers (dict): optional dictionary of headers passed directly to requests.request
files (dict): optional dictionary of files passed directly to requests.request
response_format (str): desired response format for resource's payload, e.g. 'application/rdf+xml', 'text/turtle', etc.
is_rdf (bool): if True, set Accept header based on combination of response_format and headers
stream (bool): passed directly to requests.request for stream parameter
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requests.models.Response | [
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L471-L537 | train |
ghukill/pyfc4 | pyfc4/models.py | API.parse_rdf_payload | def parse_rdf_payload(self, data, headers):
'''
small function to parse RDF payloads from various repository endpoints
Args:
data (response.data): data from requests response
headers (response.headers): headers from requests response
Returns:
(rdflib.Graph): parsed graph
'''
# handle edge case for content-types not recognized by rdflib parser
if headers['Content-Type'].startswith('text/plain'):
logger.debug('text/plain Content-Type detected, using application/n-triples for parser')
parse_format = 'application/n-triples'
else:
parse_format = headers['Content-Type']
# clean parse format for rdf parser (see: https://www.w3.org/2008/01/rdf-media-types)
if ';charset' in parse_format:
parse_format = parse_format.split(';')[0]
# parse graph
graph = rdflib.Graph().parse(
data=data.decode('utf-8'),
format=parse_format)
# return graph
return graph | python | def parse_rdf_payload(self, data, headers):
'''
small function to parse RDF payloads from various repository endpoints
Args:
data (response.data): data from requests response
headers (response.headers): headers from requests response
Returns:
(rdflib.Graph): parsed graph
'''
# handle edge case for content-types not recognized by rdflib parser
if headers['Content-Type'].startswith('text/plain'):
logger.debug('text/plain Content-Type detected, using application/n-triples for parser')
parse_format = 'application/n-triples'
else:
parse_format = headers['Content-Type']
# clean parse format for rdf parser (see: https://www.w3.org/2008/01/rdf-media-types)
if ';charset' in parse_format:
parse_format = parse_format.split(';')[0]
# parse graph
graph = rdflib.Graph().parse(
data=data.decode('utf-8'),
format=parse_format)
# return graph
return graph | [
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headers (response.headers): headers from requests response
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L585-L615 | train |
ghukill/pyfc4 | pyfc4/models.py | SparqlUpdate._derive_namespaces | def _derive_namespaces(self):
'''
Small method to loop through three graphs in self.diffs, identify unique namespace URIs.
Then, loop through provided dictionary of prefixes and pin one to another.
Args:
None: uses self.prefixes and self.diffs
Returns:
None: sets self.update_namespaces and self.update_prefixes
'''
# iterate through graphs and get unique namespace uris
for graph in [self.diffs.overlap, self.diffs.removed, self.diffs.added]:
for s,p,o in graph:
try:
ns_prefix, ns_uri, predicate = graph.compute_qname(p) # predicates
self.update_namespaces.add(ns_uri)
except:
logger.debug('could not parse Object URI: %s' % ns_uri)
try:
ns_prefix, ns_uri, predicate = graph.compute_qname(o) # objects
self.update_namespaces.add(ns_uri)
except:
logger.debug('could not parse Object URI: %s' % ns_uri)
logger.debug(self.update_namespaces)
# build unique prefixes dictionary
# NOTE: can improve by using self.rdf.uris (reverse lookup of self.rdf.prefixes)
for ns_uri in self.update_namespaces:
for k in self.prefixes.__dict__:
if str(ns_uri) == str(self.prefixes.__dict__[k]):
logger.debug('adding prefix %s for uri %s to unique_prefixes' % (k,str(ns_uri)))
self.update_prefixes[k] = self.prefixes.__dict__[k] | python | def _derive_namespaces(self):
'''
Small method to loop through three graphs in self.diffs, identify unique namespace URIs.
Then, loop through provided dictionary of prefixes and pin one to another.
Args:
None: uses self.prefixes and self.diffs
Returns:
None: sets self.update_namespaces and self.update_prefixes
'''
# iterate through graphs and get unique namespace uris
for graph in [self.diffs.overlap, self.diffs.removed, self.diffs.added]:
for s,p,o in graph:
try:
ns_prefix, ns_uri, predicate = graph.compute_qname(p) # predicates
self.update_namespaces.add(ns_uri)
except:
logger.debug('could not parse Object URI: %s' % ns_uri)
try:
ns_prefix, ns_uri, predicate = graph.compute_qname(o) # objects
self.update_namespaces.add(ns_uri)
except:
logger.debug('could not parse Object URI: %s' % ns_uri)
logger.debug(self.update_namespaces)
# build unique prefixes dictionary
# NOTE: can improve by using self.rdf.uris (reverse lookup of self.rdf.prefixes)
for ns_uri in self.update_namespaces:
for k in self.prefixes.__dict__:
if str(ns_uri) == str(self.prefixes.__dict__[k]):
logger.debug('adding prefix %s for uri %s to unique_prefixes' % (k,str(ns_uri)))
self.update_prefixes[k] = self.prefixes.__dict__[k] | [
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L641-L675 | train |
ghukill/pyfc4 | pyfc4/models.py | Resource.check_exists | def check_exists(self):
'''
Check if resource exists, update self.exists, returns
Returns:
None: sets self.exists
'''
response = self.repo.api.http_request('HEAD', self.uri)
self.status_code = response.status_code
# resource exists
if self.status_code == 200:
self.exists = True
# resource no longer here
elif self.status_code == 410:
self.exists = False
# resource not found
elif self.status_code == 404:
self.exists = False
return self.exists | python | def check_exists(self):
'''
Check if resource exists, update self.exists, returns
Returns:
None: sets self.exists
'''
response = self.repo.api.http_request('HEAD', self.uri)
self.status_code = response.status_code
# resource exists
if self.status_code == 200:
self.exists = True
# resource no longer here
elif self.status_code == 410:
self.exists = False
# resource not found
elif self.status_code == 404:
self.exists = False
return self.exists | [
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L801-L821 | train |
ghukill/pyfc4 | pyfc4/models.py | Resource.create | def create(self, specify_uri=False, ignore_tombstone=False, serialization_format=None, stream=False, auto_refresh=None):
'''
Primary method to create resources.
Args:
specify_uri (bool): If True, uses PUT verb and sets the URI during creation. If False, uses POST and gets repository minted URI
ignore_tombstone (bool): If True, will attempt creation, if tombstone exists (409), will delete tombstone and retry
serialization_format(str): Content-Type header / mimetype that will be used to serialize self.rdf.graph, and set headers for PUT/POST requests
auto_refresh (bool): If True, refreshes resource after update. If left None, defaults to repo.default_auto_refresh
'''
# if resource claims existence, raise exception
if self.exists:
raise Exception('resource exists attribute True, aborting')
# else, continue
else:
# determine verb based on specify_uri parameter
if specify_uri:
verb = 'PUT'
else:
verb = 'POST'
logger.debug('creating resource %s with verb %s' % (self.uri, verb))
# check if NonRDFSource, or extension thereof
#if so, run self.binary._prep_binary()
if issubclass(type(self),NonRDFSource):
self.binary._prep_binary()
data = self.binary.data
# otherwise, prep for RDF
else:
# determine serialization
if not serialization_format:
serialization_format = self.repo.default_serialization
data = self.rdf.graph.serialize(format=serialization_format)
logger.debug('Serialized graph used for resource creation:')
logger.debug(data.decode('utf-8'))
self.headers['Content-Type'] = serialization_format
# fire creation request
response = self.repo.api.http_request(verb, self.uri, data=data, headers=self.headers, stream=stream)
return self._handle_create(response, ignore_tombstone, auto_refresh) | python | def create(self, specify_uri=False, ignore_tombstone=False, serialization_format=None, stream=False, auto_refresh=None):
'''
Primary method to create resources.
Args:
specify_uri (bool): If True, uses PUT verb and sets the URI during creation. If False, uses POST and gets repository minted URI
ignore_tombstone (bool): If True, will attempt creation, if tombstone exists (409), will delete tombstone and retry
serialization_format(str): Content-Type header / mimetype that will be used to serialize self.rdf.graph, and set headers for PUT/POST requests
auto_refresh (bool): If True, refreshes resource after update. If left None, defaults to repo.default_auto_refresh
'''
# if resource claims existence, raise exception
if self.exists:
raise Exception('resource exists attribute True, aborting')
# else, continue
else:
# determine verb based on specify_uri parameter
if specify_uri:
verb = 'PUT'
else:
verb = 'POST'
logger.debug('creating resource %s with verb %s' % (self.uri, verb))
# check if NonRDFSource, or extension thereof
#if so, run self.binary._prep_binary()
if issubclass(type(self),NonRDFSource):
self.binary._prep_binary()
data = self.binary.data
# otherwise, prep for RDF
else:
# determine serialization
if not serialization_format:
serialization_format = self.repo.default_serialization
data = self.rdf.graph.serialize(format=serialization_format)
logger.debug('Serialized graph used for resource creation:')
logger.debug(data.decode('utf-8'))
self.headers['Content-Type'] = serialization_format
# fire creation request
response = self.repo.api.http_request(verb, self.uri, data=data, headers=self.headers, stream=stream)
return self._handle_create(response, ignore_tombstone, auto_refresh) | [
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serialization_format(str): Content-Type header / mimetype that will be used to serialize self.rdf.graph, and set headers for PUT/POST requests
auto_refresh (bool): If True, refreshes resource after update. If left None, defaults to repo.default_auto_refresh | [
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L824-L869 | train |
ghukill/pyfc4 | pyfc4/models.py | Resource.options | def options(self):
'''
Small method to return headers of an OPTIONS request to self.uri
Args:
None
Return:
(dict) response headers from OPTIONS request
'''
# http request
response = self.repo.api.http_request('OPTIONS', self.uri)
return response.headers | python | def options(self):
'''
Small method to return headers of an OPTIONS request to self.uri
Args:
None
Return:
(dict) response headers from OPTIONS request
'''
# http request
response = self.repo.api.http_request('OPTIONS', self.uri)
return response.headers | [
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Return:
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L928-L942 | train |
ghukill/pyfc4 | pyfc4/models.py | Resource.copy | def copy(self, destination):
'''
Method to copy resource to another location
Args:
destination (rdflib.term.URIRef, str): URI location to move resource
Returns:
(Resource) new, moved instance of resource
'''
# set move headers
destination_uri = self.repo.parse_uri(destination)
# http request
response = self.repo.api.http_request('COPY', self.uri, data=None, headers={'Destination':destination_uri.toPython()})
# handle response
if response.status_code == 201:
return destination_uri
else:
raise Exception('HTTP %s, could not move resource %s to %s' % (response.status_code, self.uri, destination_uri)) | python | def copy(self, destination):
'''
Method to copy resource to another location
Args:
destination (rdflib.term.URIRef, str): URI location to move resource
Returns:
(Resource) new, moved instance of resource
'''
# set move headers
destination_uri = self.repo.parse_uri(destination)
# http request
response = self.repo.api.http_request('COPY', self.uri, data=None, headers={'Destination':destination_uri.toPython()})
# handle response
if response.status_code == 201:
return destination_uri
else:
raise Exception('HTTP %s, could not move resource %s to %s' % (response.status_code, self.uri, destination_uri)) | [
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L986-L1008 | train |
ghukill/pyfc4 | pyfc4/models.py | Resource.delete | def delete(self, remove_tombstone=True):
'''
Method to delete resources.
Args:
remove_tombstone (bool): If True, will remove tombstone at uri/fcr:tombstone when removing resource.
Returns:
(bool)
'''
response = self.repo.api.http_request('DELETE', self.uri)
# update exists
if response.status_code == 204:
# removal successful, updating self
self._empty_resource_attributes()
if remove_tombstone:
self.repo.api.http_request('DELETE', '%s/fcr:tombstone' % self.uri)
return True | python | def delete(self, remove_tombstone=True):
'''
Method to delete resources.
Args:
remove_tombstone (bool): If True, will remove tombstone at uri/fcr:tombstone when removing resource.
Returns:
(bool)
'''
response = self.repo.api.http_request('DELETE', self.uri)
# update exists
if response.status_code == 204:
# removal successful, updating self
self._empty_resource_attributes()
if remove_tombstone:
self.repo.api.http_request('DELETE', '%s/fcr:tombstone' % self.uri)
return True | [
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L1011-L1033 | train |
ghukill/pyfc4 | pyfc4/models.py | Resource.refresh | def refresh(self, refresh_binary=True):
'''
Performs GET request and refreshes RDF information for resource.
Args:
None
Returns:
None
'''
updated_self = self.repo.get_resource(self.uri)
# if resource type of updated_self != self, raise exception
if not isinstance(self, type(updated_self)):
raise Exception('Instantiated %s, but repository reports this resource is %s' % (type(updated_self), type(self)) )
if updated_self:
# update attributes
self.status_code = updated_self.status_code
self.rdf.data = updated_self.rdf.data
self.headers = updated_self.headers
self.exists = updated_self.exists
# update graph if RDFSource
if type(self) != NonRDFSource:
self._parse_graph()
# empty versions
self.versions = SimpleNamespace()
# if NonRDF, set binary attributes
if type(updated_self) == NonRDFSource and refresh_binary:
self.binary.refresh(updated_self)
# fire resource._post_create hook if exists
if hasattr(self,'_post_refresh'):
self._post_refresh()
# cleanup
del(updated_self)
else:
logger.debug('resource %s not found, dumping values')
self._empty_resource_attributes() | python | def refresh(self, refresh_binary=True):
'''
Performs GET request and refreshes RDF information for resource.
Args:
None
Returns:
None
'''
updated_self = self.repo.get_resource(self.uri)
# if resource type of updated_self != self, raise exception
if not isinstance(self, type(updated_self)):
raise Exception('Instantiated %s, but repository reports this resource is %s' % (type(updated_self), type(self)) )
if updated_self:
# update attributes
self.status_code = updated_self.status_code
self.rdf.data = updated_self.rdf.data
self.headers = updated_self.headers
self.exists = updated_self.exists
# update graph if RDFSource
if type(self) != NonRDFSource:
self._parse_graph()
# empty versions
self.versions = SimpleNamespace()
# if NonRDF, set binary attributes
if type(updated_self) == NonRDFSource and refresh_binary:
self.binary.refresh(updated_self)
# fire resource._post_create hook if exists
if hasattr(self,'_post_refresh'):
self._post_refresh()
# cleanup
del(updated_self)
else:
logger.debug('resource %s not found, dumping values')
self._empty_resource_attributes() | [
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L1036-L1082 | train |
ghukill/pyfc4 | pyfc4/models.py | Resource._build_rdf | def _build_rdf(self, data=None):
'''
Parse incoming rdf as self.rdf.orig_graph, create copy at self.rdf.graph
Args:
data (): payload from GET request, expected RDF content in various serialization formats
Returns:
None
'''
# recreate rdf data
self.rdf = SimpleNamespace()
self.rdf.data = data
self.rdf.prefixes = SimpleNamespace()
self.rdf.uris = SimpleNamespace()
# populate prefixes
for prefix,uri in self.repo.context.items():
setattr(self.rdf.prefixes, prefix, rdflib.Namespace(uri))
# graph
self._parse_graph() | python | def _build_rdf(self, data=None):
'''
Parse incoming rdf as self.rdf.orig_graph, create copy at self.rdf.graph
Args:
data (): payload from GET request, expected RDF content in various serialization formats
Returns:
None
'''
# recreate rdf data
self.rdf = SimpleNamespace()
self.rdf.data = data
self.rdf.prefixes = SimpleNamespace()
self.rdf.uris = SimpleNamespace()
# populate prefixes
for prefix,uri in self.repo.context.items():
setattr(self.rdf.prefixes, prefix, rdflib.Namespace(uri))
# graph
self._parse_graph() | [
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L1085-L1106 | train |
ghukill/pyfc4 | pyfc4/models.py | Resource._parse_graph | def _parse_graph(self):
'''
use Content-Type from headers to determine parsing method
Args:
None
Return:
None: sets self.rdf by parsing data from GET request, or setting blank graph of resource does not yet exist
'''
# if resource exists, parse self.rdf.data
if self.exists:
self.rdf.graph = self.repo.api.parse_rdf_payload(self.rdf.data, self.headers)
# else, create empty graph
else:
self.rdf.graph = rdflib.Graph()
# bind any additional namespaces from repo instance, but do not override
self.rdf.namespace_manager = rdflib.namespace.NamespaceManager(self.rdf.graph)
for ns_prefix, ns_uri in self.rdf.prefixes.__dict__.items():
self.rdf.namespace_manager.bind(ns_prefix, ns_uri, override=False)
# conversely, add namespaces from parsed graph to self.rdf.prefixes
for ns_prefix, ns_uri in self.rdf.graph.namespaces():
setattr(self.rdf.prefixes, ns_prefix, rdflib.Namespace(ns_uri))
setattr(self.rdf.uris, rdflib.Namespace(ns_uri), ns_prefix)
# pin old graph to resource, create copy graph for modifications
self.rdf._orig_graph = copy.deepcopy(self.rdf.graph)
# parse triples for object-like access
self.parse_object_like_triples() | python | def _parse_graph(self):
'''
use Content-Type from headers to determine parsing method
Args:
None
Return:
None: sets self.rdf by parsing data from GET request, or setting blank graph of resource does not yet exist
'''
# if resource exists, parse self.rdf.data
if self.exists:
self.rdf.graph = self.repo.api.parse_rdf_payload(self.rdf.data, self.headers)
# else, create empty graph
else:
self.rdf.graph = rdflib.Graph()
# bind any additional namespaces from repo instance, but do not override
self.rdf.namespace_manager = rdflib.namespace.NamespaceManager(self.rdf.graph)
for ns_prefix, ns_uri in self.rdf.prefixes.__dict__.items():
self.rdf.namespace_manager.bind(ns_prefix, ns_uri, override=False)
# conversely, add namespaces from parsed graph to self.rdf.prefixes
for ns_prefix, ns_uri in self.rdf.graph.namespaces():
setattr(self.rdf.prefixes, ns_prefix, rdflib.Namespace(ns_uri))
setattr(self.rdf.uris, rdflib.Namespace(ns_uri), ns_prefix)
# pin old graph to resource, create copy graph for modifications
self.rdf._orig_graph = copy.deepcopy(self.rdf.graph)
# parse triples for object-like access
self.parse_object_like_triples() | [
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L1109-L1143 | train |
ghukill/pyfc4 | pyfc4/models.py | Resource.parse_object_like_triples | def parse_object_like_triples(self):
'''
method to parse triples from self.rdf.graph for object-like
access
Args:
None
Returns:
None: sets self.rdf.triples
'''
# parse triples as object-like attributes in self.rdf.triples
self.rdf.triples = SimpleNamespace() # prepare triples
for s,p,o in self.rdf.graph:
# get ns info
ns_prefix, ns_uri, predicate = self.rdf.graph.compute_qname(p)
# if prefix as list not yet added, add
if not hasattr(self.rdf.triples, ns_prefix):
setattr(self.rdf.triples, ns_prefix, SimpleNamespace())
# same for predicate
if not hasattr(getattr(self.rdf.triples, ns_prefix), predicate):
setattr(getattr(self.rdf.triples, ns_prefix), predicate, [])
# append object for this prefix
getattr(getattr(self.rdf.triples, ns_prefix), predicate).append(o) | python | def parse_object_like_triples(self):
'''
method to parse triples from self.rdf.graph for object-like
access
Args:
None
Returns:
None: sets self.rdf.triples
'''
# parse triples as object-like attributes in self.rdf.triples
self.rdf.triples = SimpleNamespace() # prepare triples
for s,p,o in self.rdf.graph:
# get ns info
ns_prefix, ns_uri, predicate = self.rdf.graph.compute_qname(p)
# if prefix as list not yet added, add
if not hasattr(self.rdf.triples, ns_prefix):
setattr(self.rdf.triples, ns_prefix, SimpleNamespace())
# same for predicate
if not hasattr(getattr(self.rdf.triples, ns_prefix), predicate):
setattr(getattr(self.rdf.triples, ns_prefix), predicate, [])
# append object for this prefix
getattr(getattr(self.rdf.triples, ns_prefix), predicate).append(o) | [
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L1146-L1175 | train |
ghukill/pyfc4 | pyfc4/models.py | Resource._empty_resource_attributes | def _empty_resource_attributes(self):
'''
small method to empty values if resource is removed or absent
Args:
None
Return:
None: empties selected resource attributes
'''
self.status_code = 404
self.headers = {}
self.exists = False
# build RDF
self.rdf = self._build_rdf()
# if NonRDF, empty binary data
if type(self) == NonRDFSource:
self.binary.empty() | python | def _empty_resource_attributes(self):
'''
small method to empty values if resource is removed or absent
Args:
None
Return:
None: empties selected resource attributes
'''
self.status_code = 404
self.headers = {}
self.exists = False
# build RDF
self.rdf = self._build_rdf()
# if NonRDF, empty binary data
if type(self) == NonRDFSource:
self.binary.empty() | [
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Args:
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Return:
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L1233-L1254 | train |
ghukill/pyfc4 | pyfc4/models.py | Resource.add_triple | def add_triple(self, p, o, auto_refresh=True):
'''
add triple by providing p,o, assumes s = subject
Args:
p (rdflib.term.URIRef): predicate
o (): object
auto_refresh (bool): whether or not to update object-like self.rdf.triples
Returns:
None: adds triple to self.rdf.graph
'''
self.rdf.graph.add((self.uri, p, self._handle_object(o)))
# determine if triples refreshed
self._handle_triple_refresh(auto_refresh) | python | def add_triple(self, p, o, auto_refresh=True):
'''
add triple by providing p,o, assumes s = subject
Args:
p (rdflib.term.URIRef): predicate
o (): object
auto_refresh (bool): whether or not to update object-like self.rdf.triples
Returns:
None: adds triple to self.rdf.graph
'''
self.rdf.graph.add((self.uri, p, self._handle_object(o)))
# determine if triples refreshed
self._handle_triple_refresh(auto_refresh) | [
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L1290-L1307 | train |
ghukill/pyfc4 | pyfc4/models.py | Resource.set_triple | def set_triple(self, p, o, auto_refresh=True):
'''
Assuming the predicate or object matches a single triple, sets the other for that triple.
Args:
p (rdflib.term.URIRef): predicate
o (): object
auto_refresh (bool): whether or not to update object-like self.rdf.triples
Returns:
None: modifies pre-existing triple in self.rdf.graph
'''
self.rdf.graph.set((self.uri, p, self._handle_object(o)))
# determine if triples refreshed
self._handle_triple_refresh(auto_refresh) | python | def set_triple(self, p, o, auto_refresh=True):
'''
Assuming the predicate or object matches a single triple, sets the other for that triple.
Args:
p (rdflib.term.URIRef): predicate
o (): object
auto_refresh (bool): whether or not to update object-like self.rdf.triples
Returns:
None: modifies pre-existing triple in self.rdf.graph
'''
self.rdf.graph.set((self.uri, p, self._handle_object(o)))
# determine if triples refreshed
self._handle_triple_refresh(auto_refresh) | [
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L1310-L1327 | train |
ghukill/pyfc4 | pyfc4/models.py | Resource.remove_triple | def remove_triple(self, p, o, auto_refresh=True):
'''
remove triple by supplying p,o
Args:
p (rdflib.term.URIRef): predicate
o (): object
auto_refresh (bool): whether or not to update object-like self.rdf.triples
Returns:
None: removes triple from self.rdf.graph
'''
self.rdf.graph.remove((self.uri, p, self._handle_object(o)))
# determine if triples refreshed
self._handle_triple_refresh(auto_refresh) | python | def remove_triple(self, p, o, auto_refresh=True):
'''
remove triple by supplying p,o
Args:
p (rdflib.term.URIRef): predicate
o (): object
auto_refresh (bool): whether or not to update object-like self.rdf.triples
Returns:
None: removes triple from self.rdf.graph
'''
self.rdf.graph.remove((self.uri, p, self._handle_object(o)))
# determine if triples refreshed
self._handle_triple_refresh(auto_refresh) | [
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L1330-L1347 | train |
ghukill/pyfc4 | pyfc4/models.py | Resource._handle_triple_refresh | def _handle_triple_refresh(self, auto_refresh):
'''
method to refresh self.rdf.triples if auto_refresh or defaults set to True
'''
# if auto_refresh set, and True, refresh
if auto_refresh:
self.parse_object_like_triples()
# else, if auto_refresh is not set (None), check repository instance default
elif auto_refresh == None:
if self.repo.default_auto_refresh:
self.parse_object_like_triples() | python | def _handle_triple_refresh(self, auto_refresh):
'''
method to refresh self.rdf.triples if auto_refresh or defaults set to True
'''
# if auto_refresh set, and True, refresh
if auto_refresh:
self.parse_object_like_triples()
# else, if auto_refresh is not set (None), check repository instance default
elif auto_refresh == None:
if self.repo.default_auto_refresh:
self.parse_object_like_triples() | [
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L1350-L1363 | train |
ghukill/pyfc4 | pyfc4/models.py | Resource.update | def update(self, sparql_query_only=False, auto_refresh=None, update_binary=True):
'''
Method to update resources in repository. Firing this method computes the difference in the local modified graph and the original one,
creates an instance of SparqlUpdate and builds a sparql query that represents these differences, and sends this as a PATCH request.
Note: send PATCH request, regardless of RDF or NonRDF, to [uri]/fcr:metadata
If the resource is NonRDF (Binary), this also method also updates the binary data.
Args:
sparql_query_only (bool): If True, returns only the sparql query string and does not perform any actual updates
auto_refresh (bool): If True, refreshes resource after update. If left None, defaults to repo.default_auto_refresh
update_binary (bool): If True, and resource is NonRDF, updates binary data as well
Returns:
(bool)
'''
# run diff on graphs, send as PATCH request
self._diff_graph()
sq = SparqlUpdate(self.rdf.prefixes, self.rdf.diffs)
if sparql_query_only:
return sq.build_query()
response = self.repo.api.http_request(
'PATCH',
'%s/fcr:metadata' % self.uri, # send RDF updates to URI/fcr:metadata
data=sq.build_query(),
headers={'Content-Type':'application/sparql-update'})
# if RDF update not 204, raise Exception
if response.status_code != 204:
logger.debug(response.content)
raise Exception('HTTP %s, expecting 204' % response.status_code)
# if NonRDFSource, and self.binary.data is not a Response object, update binary as well
if type(self) == NonRDFSource and update_binary and type(self.binary.data) != requests.models.Response:
self.binary._prep_binary()
binary_data = self.binary.data
binary_response = self.repo.api.http_request(
'PUT',
self.uri,
data=binary_data,
headers={'Content-Type':self.binary.mimetype})
# if not refreshing RDF, still update binary here
if not auto_refresh and not self.repo.default_auto_refresh:
logger.debug("not refreshing resource RDF, but updated binary, so must refresh binary data")
updated_self = self.repo.get_resource(self.uri)
self.binary.refresh(updated_self)
# fire optional post-update hook
if hasattr(self,'_post_update'):
self._post_update()
# determine refreshing
'''
If not updating binary, pass that bool to refresh as refresh_binary flag to avoid touching binary data
'''
if auto_refresh:
self.refresh(refresh_binary=update_binary)
elif auto_refresh == None:
if self.repo.default_auto_refresh:
self.refresh(refresh_binary=update_binary)
return True | python | def update(self, sparql_query_only=False, auto_refresh=None, update_binary=True):
'''
Method to update resources in repository. Firing this method computes the difference in the local modified graph and the original one,
creates an instance of SparqlUpdate and builds a sparql query that represents these differences, and sends this as a PATCH request.
Note: send PATCH request, regardless of RDF or NonRDF, to [uri]/fcr:metadata
If the resource is NonRDF (Binary), this also method also updates the binary data.
Args:
sparql_query_only (bool): If True, returns only the sparql query string and does not perform any actual updates
auto_refresh (bool): If True, refreshes resource after update. If left None, defaults to repo.default_auto_refresh
update_binary (bool): If True, and resource is NonRDF, updates binary data as well
Returns:
(bool)
'''
# run diff on graphs, send as PATCH request
self._diff_graph()
sq = SparqlUpdate(self.rdf.prefixes, self.rdf.diffs)
if sparql_query_only:
return sq.build_query()
response = self.repo.api.http_request(
'PATCH',
'%s/fcr:metadata' % self.uri, # send RDF updates to URI/fcr:metadata
data=sq.build_query(),
headers={'Content-Type':'application/sparql-update'})
# if RDF update not 204, raise Exception
if response.status_code != 204:
logger.debug(response.content)
raise Exception('HTTP %s, expecting 204' % response.status_code)
# if NonRDFSource, and self.binary.data is not a Response object, update binary as well
if type(self) == NonRDFSource and update_binary and type(self.binary.data) != requests.models.Response:
self.binary._prep_binary()
binary_data = self.binary.data
binary_response = self.repo.api.http_request(
'PUT',
self.uri,
data=binary_data,
headers={'Content-Type':self.binary.mimetype})
# if not refreshing RDF, still update binary here
if not auto_refresh and not self.repo.default_auto_refresh:
logger.debug("not refreshing resource RDF, but updated binary, so must refresh binary data")
updated_self = self.repo.get_resource(self.uri)
self.binary.refresh(updated_self)
# fire optional post-update hook
if hasattr(self,'_post_update'):
self._post_update()
# determine refreshing
'''
If not updating binary, pass that bool to refresh as refresh_binary flag to avoid touching binary data
'''
if auto_refresh:
self.refresh(refresh_binary=update_binary)
elif auto_refresh == None:
if self.repo.default_auto_refresh:
self.refresh(refresh_binary=update_binary)
return True | [
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Note: send PATCH request, regardless of RDF or NonRDF, to [uri]/fcr:metadata
If the resource is NonRDF (Binary), this also method also updates the binary data.
Args:
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auto_refresh (bool): If True, refreshes resource after update. If left None, defaults to repo.default_auto_refresh
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L1366-L1430 | train |
ghukill/pyfc4 | pyfc4/models.py | Resource.children | def children(self, as_resources=False):
'''
method to return hierarchical children of this resource
Args:
as_resources (bool): if True, opens each as appropriate resource type instead of return URI only
Returns:
(list): list of resources
'''
children = [o for s,p,o in self.rdf.graph.triples((None, self.rdf.prefixes.ldp.contains, None))]
# if as_resources, issue GET requests for children and return
if as_resources:
logger.debug('retrieving children as resources')
children = [ self.repo.get_resource(child) for child in children ]
return children | python | def children(self, as_resources=False):
'''
method to return hierarchical children of this resource
Args:
as_resources (bool): if True, opens each as appropriate resource type instead of return URI only
Returns:
(list): list of resources
'''
children = [o for s,p,o in self.rdf.graph.triples((None, self.rdf.prefixes.ldp.contains, None))]
# if as_resources, issue GET requests for children and return
if as_resources:
logger.debug('retrieving children as resources')
children = [ self.repo.get_resource(child) for child in children ]
return children | [
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Args:
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Returns:
(list): list of resources | [
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L1433-L1452 | train |
ghukill/pyfc4 | pyfc4/models.py | Resource.parents | def parents(self, as_resources=False):
'''
method to return hierarchical parents of this resource
Args:
as_resources (bool): if True, opens each as appropriate resource type instead of return URI only
Returns:
(list): list of resources
'''
parents = [o for s,p,o in self.rdf.graph.triples((None, self.rdf.prefixes.fedora.hasParent, None))]
# if as_resources, issue GET requests for children and return
if as_resources:
logger.debug('retrieving parent as resource')
parents = [ self.repo.get_resource(parent) for parent in parents ]
return parents | python | def parents(self, as_resources=False):
'''
method to return hierarchical parents of this resource
Args:
as_resources (bool): if True, opens each as appropriate resource type instead of return URI only
Returns:
(list): list of resources
'''
parents = [o for s,p,o in self.rdf.graph.triples((None, self.rdf.prefixes.fedora.hasParent, None))]
# if as_resources, issue GET requests for children and return
if as_resources:
logger.debug('retrieving parent as resource')
parents = [ self.repo.get_resource(parent) for parent in parents ]
return parents | [
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as_resources (bool): if True, opens each as appropriate resource type instead of return URI only
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L1455-L1474 | train |
ghukill/pyfc4 | pyfc4/models.py | Resource.siblings | def siblings(self, as_resources=False):
'''
method to return hierarchical siblings of this resource.
Args:
as_resources (bool): if True, opens each as appropriate resource type instead of return URI only
Returns:
(list): list of resources
'''
siblings = set()
# loop through parents and get children
for parent in self.parents(as_resources=True):
for sibling in parent.children(as_resources=as_resources):
siblings.add(sibling)
# remove self
if as_resources:
siblings.remove(self)
if not as_resources:
siblings.remove(self.uri)
return list(siblings) | python | def siblings(self, as_resources=False):
'''
method to return hierarchical siblings of this resource.
Args:
as_resources (bool): if True, opens each as appropriate resource type instead of return URI only
Returns:
(list): list of resources
'''
siblings = set()
# loop through parents and get children
for parent in self.parents(as_resources=True):
for sibling in parent.children(as_resources=as_resources):
siblings.add(sibling)
# remove self
if as_resources:
siblings.remove(self)
if not as_resources:
siblings.remove(self.uri)
return list(siblings) | [
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as_resources (bool): if True, opens each as appropriate resource type instead of return URI only
Returns:
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L1477-L1502 | train |
ghukill/pyfc4 | pyfc4/models.py | Resource.create_version | def create_version(self, version_label):
'''
method to create a new version of the resource as it currently stands
- Note: this will create a version based on the current live instance of the resource,
not the local version, which might require self.update() to update.
Args:
version_label (str): label to be used for version
Returns:
(ResourceVersion): instance of ResourceVersion, also appended to self.versions
'''
# create version
version_response = self.repo.api.http_request('POST', '%s/fcr:versions' % self.uri, data=None, headers={'Slug':version_label})
# if 201, assume success
if version_response.status_code == 201:
logger.debug('version created: %s' % version_response.headers['Location'])
# affix version
self._affix_version(version_response.headers['Location'], version_label) | python | def create_version(self, version_label):
'''
method to create a new version of the resource as it currently stands
- Note: this will create a version based on the current live instance of the resource,
not the local version, which might require self.update() to update.
Args:
version_label (str): label to be used for version
Returns:
(ResourceVersion): instance of ResourceVersion, also appended to self.versions
'''
# create version
version_response = self.repo.api.http_request('POST', '%s/fcr:versions' % self.uri, data=None, headers={'Slug':version_label})
# if 201, assume success
if version_response.status_code == 201:
logger.debug('version created: %s' % version_response.headers['Location'])
# affix version
self._affix_version(version_response.headers['Location'], version_label) | [
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- Note: this will create a version based on the current live instance of the resource,
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Args:
version_label (str): label to be used for version
Returns:
(ResourceVersion): instance of ResourceVersion, also appended to self.versions | [
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L1517-L1540 | train |
ghukill/pyfc4 | pyfc4/models.py | Resource.get_versions | def get_versions(self):
'''
retrieves all versions of an object, and stores them at self.versions
Args:
None
Returns:
None: appends instances
'''
# get all versions
versions_response = self.repo.api.http_request('GET', '%s/fcr:versions' % self.uri)
# parse response
versions_graph = self.repo.api.parse_rdf_payload(versions_response.content, versions_response.headers)
# loop through fedora.hasVersion
for version_uri in versions_graph.objects(self.uri, self.rdf.prefixes.fedora.hasVersion):
# get label
version_label = versions_graph.value(version_uri, self.rdf.prefixes.fedora.hasVersionLabel, None).toPython()
# affix version
self._affix_version(version_uri, version_label) | python | def get_versions(self):
'''
retrieves all versions of an object, and stores them at self.versions
Args:
None
Returns:
None: appends instances
'''
# get all versions
versions_response = self.repo.api.http_request('GET', '%s/fcr:versions' % self.uri)
# parse response
versions_graph = self.repo.api.parse_rdf_payload(versions_response.content, versions_response.headers)
# loop through fedora.hasVersion
for version_uri in versions_graph.objects(self.uri, self.rdf.prefixes.fedora.hasVersion):
# get label
version_label = versions_graph.value(version_uri, self.rdf.prefixes.fedora.hasVersionLabel, None).toPython()
# affix version
self._affix_version(version_uri, version_label) | [
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L1543-L1568 | train |
ghukill/pyfc4 | pyfc4/models.py | Resource.dump | def dump(self,format='ttl'):
'''
Convenience method to return RDF data for resource,
optionally selecting serialization format.
Inspired by .dump from Samvera.
Args:
format (str): expecting serialization formats accepted by rdflib.serialization(format=)
'''
return self.rdf.graph.serialize(format=format).decode('utf-8') | python | def dump(self,format='ttl'):
'''
Convenience method to return RDF data for resource,
optionally selecting serialization format.
Inspired by .dump from Samvera.
Args:
format (str): expecting serialization formats accepted by rdflib.serialization(format=)
'''
return self.rdf.graph.serialize(format=format).decode('utf-8') | [
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L1571-L1582 | train |
ghukill/pyfc4 | pyfc4/models.py | ResourceVersion.revert_to | def revert_to(self):
'''
method to revert resource to this version by issuing PATCH
Args:
None
Returns:
None: sends PATCH request, and refreshes parent resource
'''
# send patch
response = self.resource.repo.api.http_request('PATCH', self.uri)
# if response 204
if response.status_code == 204:
logger.debug('reverting to previous version of resource, %s' % self.uri)
# refresh current resource handle
self._current_resource.refresh()
else:
raise Exception('HTTP %s, could not revert to resource version, %s' % (response.status_code, self.uri)) | python | def revert_to(self):
'''
method to revert resource to this version by issuing PATCH
Args:
None
Returns:
None: sends PATCH request, and refreshes parent resource
'''
# send patch
response = self.resource.repo.api.http_request('PATCH', self.uri)
# if response 204
if response.status_code == 204:
logger.debug('reverting to previous version of resource, %s' % self.uri)
# refresh current resource handle
self._current_resource.refresh()
else:
raise Exception('HTTP %s, could not revert to resource version, %s' % (response.status_code, self.uri)) | [
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L1609-L1632 | train |
ghukill/pyfc4 | pyfc4/models.py | ResourceVersion.delete | def delete(self):
'''
method to remove version from resource's history
'''
# send patch
response = self.resource.repo.api.http_request('DELETE', self.uri)
# if response 204
if response.status_code == 204:
logger.debug('deleting previous version of resource, %s' % self.uri)
# remove from resource versions
delattr(self._current_resource.versions, self.label)
# if 400, likely most recent version and cannot remove
elif response.status_code == 400:
raise Exception('HTTP 400, likely most recent resource version which cannot be removed')
else:
raise Exception('HTTP %s, could not delete resource version: %s' % (response.status_code, self.uri)) | python | def delete(self):
'''
method to remove version from resource's history
'''
# send patch
response = self.resource.repo.api.http_request('DELETE', self.uri)
# if response 204
if response.status_code == 204:
logger.debug('deleting previous version of resource, %s' % self.uri)
# remove from resource versions
delattr(self._current_resource.versions, self.label)
# if 400, likely most recent version and cannot remove
elif response.status_code == 400:
raise Exception('HTTP 400, likely most recent resource version which cannot be removed')
else:
raise Exception('HTTP %s, could not delete resource version: %s' % (response.status_code, self.uri)) | [
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L1635-L1656 | train |
ghukill/pyfc4 | pyfc4/models.py | BinaryData.empty | def empty(self):
'''
Method to empty attributes, particularly for use when
object is deleted but remains as variable
'''
self.resource = None
self.delivery = None
self.data = None
self.stream = False
self.mimetype = None
self.location = None | python | def empty(self):
'''
Method to empty attributes, particularly for use when
object is deleted but remains as variable
'''
self.resource = None
self.delivery = None
self.data = None
self.stream = False
self.mimetype = None
self.location = None | [
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L1686-L1698 | train |
ghukill/pyfc4 | pyfc4/models.py | BinaryData.refresh | def refresh(self, updated_self):
'''
method to refresh binary attributes and data
Args:
updated_self (Resource): resource this binary data attaches to
Returns:
None: updates attributes
'''
logger.debug('refreshing binary attributes')
self.mimetype = updated_self.binary.mimetype
self.data = updated_self.binary.data | python | def refresh(self, updated_self):
'''
method to refresh binary attributes and data
Args:
updated_self (Resource): resource this binary data attaches to
Returns:
None: updates attributes
'''
logger.debug('refreshing binary attributes')
self.mimetype = updated_self.binary.mimetype
self.data = updated_self.binary.data | [
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L1701-L1715 | train |
ghukill/pyfc4 | pyfc4/models.py | BinaryData.parse_binary | def parse_binary(self):
'''
when retrieving a NonRDF resource, parse binary data and make available
via generators
'''
# derive mimetype
self.mimetype = self.resource.rdf.graph.value(
self.resource.uri,
self.resource.rdf.prefixes.ebucore.hasMimeType).toPython()
# get binary content as stremable response
self.data = self.resource.repo.api.http_request(
'GET',
self.resource.uri,
data=None,
headers={'Content-Type':self.resource.mimetype},
is_rdf=False,
stream=True) | python | def parse_binary(self):
'''
when retrieving a NonRDF resource, parse binary data and make available
via generators
'''
# derive mimetype
self.mimetype = self.resource.rdf.graph.value(
self.resource.uri,
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# get binary content as stremable response
self.data = self.resource.repo.api.http_request(
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data=None,
headers={'Content-Type':self.resource.mimetype},
is_rdf=False,
stream=True) | [
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| when retrieving a NonRDF resource, parse binary data and make available
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L1718-L1737 | train |
ghukill/pyfc4 | pyfc4/models.py | BinaryData._prep_binary_content | def _prep_binary_content(self):
'''
Sets delivery method of either payload or header
Favors Content-Location header if set
Args:
None
Returns:
None: sets attributes in self.binary and headers
'''
# nothing present
if not self.data and not self.location and 'Content-Location' not in self.resource.headers.keys():
raise Exception('creating/updating NonRDFSource requires content from self.binary.data, self.binary.location, or the Content-Location header')
elif 'Content-Location' in self.resource.headers.keys():
logger.debug('Content-Location header found, using')
self.delivery = 'header'
# if Content-Location is not set, look for self.data_location then self.data
elif 'Content-Location' not in self.resource.headers.keys():
# data_location set, trumps Content self.data
if self.location:
# set appropriate header
self.resource.headers['Content-Location'] = self.location
self.delivery = 'header'
# data attribute is plain text, binary, or file-like object
elif self.data:
# if file-like object, set flag for api.http_request
if isinstance(self.data, io.BufferedIOBase):
logger.debug('detected file-like object')
self.delivery = 'payload'
# else, just bytes
else:
logger.debug('detected bytes')
self.delivery = 'payload' | python | def _prep_binary_content(self):
'''
Sets delivery method of either payload or header
Favors Content-Location header if set
Args:
None
Returns:
None: sets attributes in self.binary and headers
'''
# nothing present
if not self.data and not self.location and 'Content-Location' not in self.resource.headers.keys():
raise Exception('creating/updating NonRDFSource requires content from self.binary.data, self.binary.location, or the Content-Location header')
elif 'Content-Location' in self.resource.headers.keys():
logger.debug('Content-Location header found, using')
self.delivery = 'header'
# if Content-Location is not set, look for self.data_location then self.data
elif 'Content-Location' not in self.resource.headers.keys():
# data_location set, trumps Content self.data
if self.location:
# set appropriate header
self.resource.headers['Content-Location'] = self.location
self.delivery = 'header'
# data attribute is plain text, binary, or file-like object
elif self.data:
# if file-like object, set flag for api.http_request
if isinstance(self.data, io.BufferedIOBase):
logger.debug('detected file-like object')
self.delivery = 'payload'
# else, just bytes
else:
logger.debug('detected bytes')
self.delivery = 'payload' | [
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L1785-L1826 | train |
ghukill/pyfc4 | pyfc4/models.py | NonRDFSource.fixity | def fixity(self, response_format=None):
'''
Issues fixity check, return parsed graph
Args:
None
Returns:
(dict): ('verdict':(bool): verdict of fixity check, 'premis_graph':(rdflib.Graph): parsed PREMIS graph from check)
'''
# if no response_format, use default
if not response_format:
response_format = self.repo.default_serialization
# issue GET request for fixity check
response = self.repo.api.http_request('GET', '%s/fcr:fixity' % self.uri)
# parse
fixity_graph = self.repo.api.parse_rdf_payload(response.content, response.headers)
# determine verdict
for outcome in fixity_graph.objects(None, self.rdf.prefixes.premis.hasEventOutcome):
if outcome.toPython() == 'SUCCESS':
verdict = True
else:
verdict = False
return {
'verdict':verdict,
'premis_graph':fixity_graph
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'''
Issues fixity check, return parsed graph
Args:
None
Returns:
(dict): ('verdict':(bool): verdict of fixity check, 'premis_graph':(rdflib.Graph): parsed PREMIS graph from check)
'''
# if no response_format, use default
if not response_format:
response_format = self.repo.default_serialization
# issue GET request for fixity check
response = self.repo.api.http_request('GET', '%s/fcr:fixity' % self.uri)
# parse
fixity_graph = self.repo.api.parse_rdf_payload(response.content, response.headers)
# determine verdict
for outcome in fixity_graph.objects(None, self.rdf.prefixes.premis.hasEventOutcome):
if outcome.toPython() == 'SUCCESS':
verdict = True
else:
verdict = False
return {
'verdict':verdict,
'premis_graph':fixity_graph
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| 59011df592f08978c4a901a908862d112a5dcf02 | https://github.com/ghukill/pyfc4/blob/59011df592f08978c4a901a908862d112a5dcf02/pyfc4/models.py#L1896-L1928 | train |
sleibman/python-conduit | conduit/core.py | Channel.get_value | def get_value(self, consumer=None):
"""
If consumer is specified, the channel will record that consumer as having consumed the value.
"""
if consumer:
self.consumers[consumer] = True
return self.value | python | def get_value(self, consumer=None):
"""
If consumer is specified, the channel will record that consumer as having consumed the value.
"""
if consumer:
self.consumers[consumer] = True
return self.value | [
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| f6002d45c4f25e4418591a72fdac9ac6fb422d80 | https://github.com/sleibman/python-conduit/blob/f6002d45c4f25e4418591a72fdac9ac6fb422d80/conduit/core.py#L105-L111 | train |
sleibman/python-conduit | conduit/core.py | DataBlock.set_input_data | def set_input_data(self, key, value):
"""
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"""
if not key in self.input_channels.keys():
self.set_input_channel(key, Channel())
self.input_channels[key].set_value(Data(self.time, value)) | python | def set_input_data(self, key, value):
"""
set_input_data will automatically create an input channel if necessary.
Automatic channel creation is intended for the case where users are trying to set initial values on a block
whose input channels aren't subscribed to anything in the graph.
"""
if not key in self.input_channels.keys():
self.set_input_channel(key, Channel())
self.input_channels[key].set_value(Data(self.time, value)) | [
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| f6002d45c4f25e4418591a72fdac9ac6fb422d80 | https://github.com/sleibman/python-conduit/blob/f6002d45c4f25e4418591a72fdac9ac6fb422d80/conduit/core.py#L276-L284 | train |
sleibman/python-conduit | conduit/core.py | DataBlock.get_output_channel | def get_output_channel(self, output_channel_name):
"""
get_output_channel will create a new channel object if necessary.
"""
if not output_channel_name in self.output_channels.keys():
self.output_channels[output_channel_name] = Channel()
self.output_channels[output_channel_name].add_producer(self)
return self.output_channels[output_channel_name] | python | def get_output_channel(self, output_channel_name):
"""
get_output_channel will create a new channel object if necessary.
"""
if not output_channel_name in self.output_channels.keys():
self.output_channels[output_channel_name] = Channel()
self.output_channels[output_channel_name].add_producer(self)
return self.output_channels[output_channel_name] | [
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| f6002d45c4f25e4418591a72fdac9ac6fb422d80 | https://github.com/sleibman/python-conduit/blob/f6002d45c4f25e4418591a72fdac9ac6fb422d80/conduit/core.py#L336-L343 | train |
adamhadani/python-yelp | yelp/api.py | ReviewSearchApi.by_bounding_box | def by_bounding_box(self, tl_lat, tl_long, br_lat, br_long, term=None, num_biz_requested=None, category=None):
"""
Perform a Yelp Review Search based on a map bounding box.
Args:
tl_lat - bounding box top left latitude
tl_long - bounding box top left longitude
br_lat - bounding box bottom right latitude
br_long - bounding box bottom right longitude
term - Search term to filter by (Optional)
num_biz_requested - Maximum number of matching results to return (Optional)
category - '+'-seperated list of categories to filter by. See
http://www.yelp.com/developers/documentation/category_list
for list of valid categories. (Optional)
"""
header, content = self._http_request(
self.BASE_URL,
tl_lat = tl_lat,
tl_long = tl_long,
br_lat = br_lat,
br_long = br_long,
term = term,
category = category,
num_biz_requested = num_biz_requested
)
return json.loads(content) | python | def by_bounding_box(self, tl_lat, tl_long, br_lat, br_long, term=None, num_biz_requested=None, category=None):
"""
Perform a Yelp Review Search based on a map bounding box.
Args:
tl_lat - bounding box top left latitude
tl_long - bounding box top left longitude
br_lat - bounding box bottom right latitude
br_long - bounding box bottom right longitude
term - Search term to filter by (Optional)
num_biz_requested - Maximum number of matching results to return (Optional)
category - '+'-seperated list of categories to filter by. See
http://www.yelp.com/developers/documentation/category_list
for list of valid categories. (Optional)
"""
header, content = self._http_request(
self.BASE_URL,
tl_lat = tl_lat,
tl_long = tl_long,
br_lat = br_lat,
br_long = br_long,
term = term,
category = category,
num_biz_requested = num_biz_requested
)
return json.loads(content) | [
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| 7694ccb7274cc3c5783250ed0c3396cda2fcfa1a | https://github.com/adamhadani/python-yelp/blob/7694ccb7274cc3c5783250ed0c3396cda2fcfa1a/yelp/api.py#L104-L131 | train |
adamhadani/python-yelp | yelp/api.py | ReviewSearchApi.by_geopoint | def by_geopoint(self, lat, long, radius, term=None, num_biz_requested=None, category=None):
"""
Perform a Yelp Review Search based on a geopoint and radius tuple.
Args:
lat - geopoint latitude
long - geopoint longitude
radius - search radius (in miles)
term - Search term to filter by (Optional)
num_biz_requested - Maximum number of matching results to return (Optional)
category - '+'-seperated list of categories to filter by. See
http://www.yelp.com/developers/documentation/category_list
for list of valid categories. (Optional)
"""
header, content = self._http_request(
self.BASE_URL,
lat = lat,
long = long,
radius = radius,
term = None,
num_biz_requested = None
)
return json.loads(content) | python | def by_geopoint(self, lat, long, radius, term=None, num_biz_requested=None, category=None):
"""
Perform a Yelp Review Search based on a geopoint and radius tuple.
Args:
lat - geopoint latitude
long - geopoint longitude
radius - search radius (in miles)
term - Search term to filter by (Optional)
num_biz_requested - Maximum number of matching results to return (Optional)
category - '+'-seperated list of categories to filter by. See
http://www.yelp.com/developers/documentation/category_list
for list of valid categories. (Optional)
"""
header, content = self._http_request(
self.BASE_URL,
lat = lat,
long = long,
radius = radius,
term = None,
num_biz_requested = None
)
return json.loads(content) | [
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| 7694ccb7274cc3c5783250ed0c3396cda2fcfa1a | https://github.com/adamhadani/python-yelp/blob/7694ccb7274cc3c5783250ed0c3396cda2fcfa1a/yelp/api.py#L134-L158 | train |
adamhadani/python-yelp | yelp/api.py | ReviewSearchApi.by_location | def by_location(self, location, cc=None, radius=None, term=None, num_biz_requested=None, category=None):
"""
Perform a Yelp Review Search based on a location specifier.
Args:
location - textual location specifier of form: "address, neighborhood, city, state or zip, optional country"
cc - ISO 3166-1 alpha-2 country code. (Optional)
radius - search radius (in miles) (Optional)
term - Search term to filter by (Optional)
num_biz_requested - Maximum number of matching results to return (Optional)
category - '+'-seperated list of categories to filter by. See
http://www.yelp.com/developers/documentation/category_list
for list of valid categories. (Optional)
"""
header, content = self._http_request(
self.BASE_URL,
location = location,
cc = cc,
radius = radius,
term = term,
num_biz_requested = num_biz_requested
)
return json.loads(content) | python | def by_location(self, location, cc=None, radius=None, term=None, num_biz_requested=None, category=None):
"""
Perform a Yelp Review Search based on a location specifier.
Args:
location - textual location specifier of form: "address, neighborhood, city, state or zip, optional country"
cc - ISO 3166-1 alpha-2 country code. (Optional)
radius - search radius (in miles) (Optional)
term - Search term to filter by (Optional)
num_biz_requested - Maximum number of matching results to return (Optional)
category - '+'-seperated list of categories to filter by. See
http://www.yelp.com/developers/documentation/category_list
for list of valid categories. (Optional)
"""
header, content = self._http_request(
self.BASE_URL,
location = location,
cc = cc,
radius = radius,
term = term,
num_biz_requested = num_biz_requested
)
return json.loads(content) | [
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radius - search radius (in miles) (Optional)
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| 7694ccb7274cc3c5783250ed0c3396cda2fcfa1a | https://github.com/adamhadani/python-yelp/blob/7694ccb7274cc3c5783250ed0c3396cda2fcfa1a/yelp/api.py#L161-L184 | train |
adamhadani/python-yelp | yelp/api.py | PhoneApi.by_phone | def by_phone(self, phone, cc=None):
"""
Perform a Yelp Phone API Search based on phone number given.
Args:
phone - Phone number to search by
cc - ISO 3166-1 alpha-2 country code. (Optional)
"""
header, content = self._http_request(self.BASE_URL, phone=phone, cc=cc)
return json.loads(content) | python | def by_phone(self, phone, cc=None):
"""
Perform a Yelp Phone API Search based on phone number given.
Args:
phone - Phone number to search by
cc - ISO 3166-1 alpha-2 country code. (Optional)
"""
header, content = self._http_request(self.BASE_URL, phone=phone, cc=cc)
return json.loads(content) | [
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| 7694ccb7274cc3c5783250ed0c3396cda2fcfa1a | https://github.com/adamhadani/python-yelp/blob/7694ccb7274cc3c5783250ed0c3396cda2fcfa1a/yelp/api.py#L203-L214 | train |
adamhadani/python-yelp | yelp/api.py | NeighborhoodApi.by_geopoint | def by_geopoint(self, lat, long):
"""
Perform a Yelp Neighborhood API Search based on a geopoint.
Args:
lat - geopoint latitude
long - geopoint longitude
"""
header, content = self._http_request(self.BASE_URL, lat=lat, long=long)
return json.loads(content) | python | def by_geopoint(self, lat, long):
"""
Perform a Yelp Neighborhood API Search based on a geopoint.
Args:
lat - geopoint latitude
long - geopoint longitude
"""
header, content = self._http_request(self.BASE_URL, lat=lat, long=long)
return json.loads(content) | [
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| 7694ccb7274cc3c5783250ed0c3396cda2fcfa1a | https://github.com/adamhadani/python-yelp/blob/7694ccb7274cc3c5783250ed0c3396cda2fcfa1a/yelp/api.py#L233-L243 | train |
adamhadani/python-yelp | yelp/api.py | NeighborhoodApi.by_location | def by_location(self, location, cc=None):
"""
Perform a Yelp Neighborhood API Search based on a location specifier.
Args:
location - textual location specifier of form: "address, city, state or zip, optional country"
cc - ISO 3166-1 alpha-2 country code. (Optional)
"""
header, content = self._http_request(self.BASE_URL, location=location, cc=cc)
return json.loads(content) | python | def by_location(self, location, cc=None):
"""
Perform a Yelp Neighborhood API Search based on a location specifier.
Args:
location - textual location specifier of form: "address, city, state or zip, optional country"
cc - ISO 3166-1 alpha-2 country code. (Optional)
"""
header, content = self._http_request(self.BASE_URL, location=location, cc=cc)
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| 7694ccb7274cc3c5783250ed0c3396cda2fcfa1a | https://github.com/adamhadani/python-yelp/blob/7694ccb7274cc3c5783250ed0c3396cda2fcfa1a/yelp/api.py#L246-L256 | train |
eventifyio/eventify | eventify/drivers/zeromq.py | Service.check_transport_host | def check_transport_host(self):
"""
Check if zeromq socket is available
on transport host
"""
sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
result = sock.connect_ex(('events-server', 8080))
if result == 0:
logging.info('port 8080 on zmq is open!')
return True
return False | python | def check_transport_host(self):
"""
Check if zeromq socket is available
on transport host
"""
sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
result = sock.connect_ex(('events-server', 8080))
if result == 0:
logging.info('port 8080 on zmq is open!')
return True
return False | [
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255BITS/hyperchamber | hyperchamber/io/__init__.py | sample | def sample(config, samples):
"""Upload a series of samples. Each sample has keys 'image' and 'label'.
Images are ignored if the rate limit is hit."""
url = get_api_path('sample.json')
multiple_files = []
images = [s['image'] for s in samples]
labels = [s['label'] for s in samples]
for image in images:
multiple_files.append(('images', (image, open(image, 'rb'), 'image/png')))
headers=get_headers(no_content_type=True)
headers["config"]= json.dumps(config, cls=HCEncoder)
headers["labels"]= json.dumps(labels)
print("With headers", headers)
try:
r = requests.post(url, files=multiple_files, headers=headers, timeout=30)
return r.text
except requests.exceptions.RequestException:
e = sys.exc_info()[0]
print("Error while calling hyperchamber - ", e)
return None | python | def sample(config, samples):
"""Upload a series of samples. Each sample has keys 'image' and 'label'.
Images are ignored if the rate limit is hit."""
url = get_api_path('sample.json')
multiple_files = []
images = [s['image'] for s in samples]
labels = [s['label'] for s in samples]
for image in images:
multiple_files.append(('images', (image, open(image, 'rb'), 'image/png')))
headers=get_headers(no_content_type=True)
headers["config"]= json.dumps(config, cls=HCEncoder)
headers["labels"]= json.dumps(labels)
print("With headers", headers)
try:
r = requests.post(url, files=multiple_files, headers=headers, timeout=30)
return r.text
except requests.exceptions.RequestException:
e = sys.exc_info()[0]
print("Error while calling hyperchamber - ", e)
return None | [
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| 4d5774bde9ea6ce1113f77a069ffc605148482b8 | https://github.com/255BITS/hyperchamber/blob/4d5774bde9ea6ce1113f77a069ffc605148482b8/hyperchamber/io/__init__.py#L43-L63 | train |
255BITS/hyperchamber | hyperchamber/io/__init__.py | measure | def measure(config, result, max_retries=10):
"""Records results on hyperchamber.io. Used when you are done testing a config."""
url = get_api_path('measurement.json')
data = {'config': config, 'result': result}
retries = 0
while(retries < max_retries):
try:
r = requests.post(url, data=json.dumps(data, cls=HCEncoder), headers=get_headers(), timeout=30)
return r.text
except requests.exceptions.RequestException:
e = sys.exc_info()[0]
print("Error while calling hyperchamber - retrying ", e)
retries += 1 | python | def measure(config, result, max_retries=10):
"""Records results on hyperchamber.io. Used when you are done testing a config."""
url = get_api_path('measurement.json')
data = {'config': config, 'result': result}
retries = 0
while(retries < max_retries):
try:
r = requests.post(url, data=json.dumps(data, cls=HCEncoder), headers=get_headers(), timeout=30)
return r.text
except requests.exceptions.RequestException:
e = sys.exc_info()[0]
print("Error while calling hyperchamber - retrying ", e)
retries += 1 | [
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| 4d5774bde9ea6ce1113f77a069ffc605148482b8 | https://github.com/255BITS/hyperchamber/blob/4d5774bde9ea6ce1113f77a069ffc605148482b8/hyperchamber/io/__init__.py#L65-L77 | train |
stephenmcd/gunicorn-console | gunicorn_console.py | move_selection | def move_selection(reverse=False):
"""
Goes through the list of gunicorns, setting the selected as the one after
the currently selected.
"""
global selected_pid
if selected_pid not in gunicorns:
selected_pid = None
found = False
pids = sorted(gunicorns.keys(), reverse=reverse)
# Iterate items twice to enable wrapping.
for pid in pids + pids:
if selected_pid is None or found:
selected_pid = pid
return
found = pid == selected_pid | python | def move_selection(reverse=False):
"""
Goes through the list of gunicorns, setting the selected as the one after
the currently selected.
"""
global selected_pid
if selected_pid not in gunicorns:
selected_pid = None
found = False
pids = sorted(gunicorns.keys(), reverse=reverse)
# Iterate items twice to enable wrapping.
for pid in pids + pids:
if selected_pid is None or found:
selected_pid = pid
return
found = pid == selected_pid | [
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| f5c9b9a69ea1f2ca00aac3565cb99491684d868a | https://github.com/stephenmcd/gunicorn-console/blob/f5c9b9a69ea1f2ca00aac3565cb99491684d868a/gunicorn_console.py#L87-L102 | train |
stephenmcd/gunicorn-console | gunicorn_console.py | update_gunicorns | def update_gunicorns():
"""
Updates the dict of gunicorn processes. Run the ps command and parse its
output for processes named after gunicorn, building up a dict of gunicorn
processes. When new gunicorns are discovered, run the netstat command to
determine the ports they're serving on.
"""
global tick
tick += 1
if (tick * screen_delay) % ps_delay != 0:
return
tick = 0
for pid in gunicorns:
gunicorns[pid].update({"workers": 0, "mem": 0})
ps = Popen(PS_ARGS, stdout=PIPE).communicate()[0].split("\n")
headings = ps.pop(0).split()
name_col = headings.index(cmd_heading)
num_cols = len(headings) - 1
for row in ps:
cols = row.split(None, num_cols)
if cols and "gunicorn: " in cols[name_col]:
if "gunicorn: worker" in cols[name_col]:
is_worker = True
else:
is_worker = False
if is_worker:
pid = cols[headings.index("PPID")]
else:
pid = cols[headings.index("PID")]
if pid not in gunicorns:
gunicorns[pid] = {"workers": 0, "mem": 0, "port": None, "name":
cols[name_col].strip().split("[",1)[1].split("]",1)[:-1]}
gunicorns[pid]["mem"] += int(cols[headings.index("RSS")])
if is_worker:
gunicorns[pid]["workers"] += 1
# Remove gunicorns that were not found in the process list.
for pid in gunicorns.keys()[:]:
if gunicorns[pid]["workers"] == 0:
del gunicorns[pid]
# Determine ports if any are missing.
if not [g for g in gunicorns.values() if g["port"] is None]:
return
for (pid, port) in ports_for_pids(gunicorns.keys()):
if pid in gunicorns:
gunicorns[pid]["port"] = port | python | def update_gunicorns():
"""
Updates the dict of gunicorn processes. Run the ps command and parse its
output for processes named after gunicorn, building up a dict of gunicorn
processes. When new gunicorns are discovered, run the netstat command to
determine the ports they're serving on.
"""
global tick
tick += 1
if (tick * screen_delay) % ps_delay != 0:
return
tick = 0
for pid in gunicorns:
gunicorns[pid].update({"workers": 0, "mem": 0})
ps = Popen(PS_ARGS, stdout=PIPE).communicate()[0].split("\n")
headings = ps.pop(0).split()
name_col = headings.index(cmd_heading)
num_cols = len(headings) - 1
for row in ps:
cols = row.split(None, num_cols)
if cols and "gunicorn: " in cols[name_col]:
if "gunicorn: worker" in cols[name_col]:
is_worker = True
else:
is_worker = False
if is_worker:
pid = cols[headings.index("PPID")]
else:
pid = cols[headings.index("PID")]
if pid not in gunicorns:
gunicorns[pid] = {"workers": 0, "mem": 0, "port": None, "name":
cols[name_col].strip().split("[",1)[1].split("]",1)[:-1]}
gunicorns[pid]["mem"] += int(cols[headings.index("RSS")])
if is_worker:
gunicorns[pid]["workers"] += 1
# Remove gunicorns that were not found in the process list.
for pid in gunicorns.keys()[:]:
if gunicorns[pid]["workers"] == 0:
del gunicorns[pid]
# Determine ports if any are missing.
if not [g for g in gunicorns.values() if g["port"] is None]:
return
for (pid, port) in ports_for_pids(gunicorns.keys()):
if pid in gunicorns:
gunicorns[pid]["port"] = port | [
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| f5c9b9a69ea1f2ca00aac3565cb99491684d868a | https://github.com/stephenmcd/gunicorn-console/blob/f5c9b9a69ea1f2ca00aac3565cb99491684d868a/gunicorn_console.py#L105-L150 | train |
stephenmcd/gunicorn-console | gunicorn_console.py | handle_keypress | def handle_keypress(screen):
"""
Check for a key being pressed and handle it if applicable.
"""
global selected_pid
try:
key = screen.getkey().upper()
except:
return
if key in ("KEY_DOWN", "J"):
move_selection()
elif key in ("KEY_UP", "K"):
move_selection(reverse=True)
elif key in ("A", "+"):
send_signal("TTIN")
if selected_pid in gunicorns:
gunicorns[selected_pid]["workers"] = 0
elif key in ("W", "-"):
if selected_pid in gunicorns:
if gunicorns[selected_pid]["workers"] != 1:
send_signal("TTOU")
gunicorns[selected_pid]["workers"] = 0
elif key in ("R",):
if selected_pid in gunicorns:
send_signal("HUP")
del gunicorns[selected_pid]
selected_pid = None
elif key in ("T",):
for pid in gunicorns.copy().iterkeys():
selected_pid = pid
send_signal("HUP")
del gunicorns[selected_pid]
selected_pid = None
elif key in ("M", "-"):
if selected_pid in gunicorns:
send_signal("QUIT")
del gunicorns[selected_pid]
selected_pid = None
elif key in ("Q",):
raise KeyboardInterrupt | python | def handle_keypress(screen):
"""
Check for a key being pressed and handle it if applicable.
"""
global selected_pid
try:
key = screen.getkey().upper()
except:
return
if key in ("KEY_DOWN", "J"):
move_selection()
elif key in ("KEY_UP", "K"):
move_selection(reverse=True)
elif key in ("A", "+"):
send_signal("TTIN")
if selected_pid in gunicorns:
gunicorns[selected_pid]["workers"] = 0
elif key in ("W", "-"):
if selected_pid in gunicorns:
if gunicorns[selected_pid]["workers"] != 1:
send_signal("TTOU")
gunicorns[selected_pid]["workers"] = 0
elif key in ("R",):
if selected_pid in gunicorns:
send_signal("HUP")
del gunicorns[selected_pid]
selected_pid = None
elif key in ("T",):
for pid in gunicorns.copy().iterkeys():
selected_pid = pid
send_signal("HUP")
del gunicorns[selected_pid]
selected_pid = None
elif key in ("M", "-"):
if selected_pid in gunicorns:
send_signal("QUIT")
del gunicorns[selected_pid]
selected_pid = None
elif key in ("Q",):
raise KeyboardInterrupt | [
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| f5c9b9a69ea1f2ca00aac3565cb99491684d868a | https://github.com/stephenmcd/gunicorn-console/blob/f5c9b9a69ea1f2ca00aac3565cb99491684d868a/gunicorn_console.py#L153-L192 | train |
stephenmcd/gunicorn-console | gunicorn_console.py | format_row | def format_row(pid="", port="", name="", mem="", workers="", prefix_char=" "):
"""
Applies consistant padding to each of the columns in a row and serves as
the source of the overall screen width.
"""
row = "%s%-5s %-6s %-25s %8s %7s " \
% (prefix_char, pid, port, name, mem, workers)
global screen_width
if screen_width is None:
screen_width = len(row)
return row | python | def format_row(pid="", port="", name="", mem="", workers="", prefix_char=" "):
"""
Applies consistant padding to each of the columns in a row and serves as
the source of the overall screen width.
"""
row = "%s%-5s %-6s %-25s %8s %7s " \
% (prefix_char, pid, port, name, mem, workers)
global screen_width
if screen_width is None:
screen_width = len(row)
return row | [
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| f5c9b9a69ea1f2ca00aac3565cb99491684d868a | https://github.com/stephenmcd/gunicorn-console/blob/f5c9b9a69ea1f2ca00aac3565cb99491684d868a/gunicorn_console.py#L195-L206 | train |
stephenmcd/gunicorn-console | gunicorn_console.py | display_output | def display_output(screen):
"""
Display the menu list of gunicorns.
"""
format_row() # Sets up the screen width.
screen_height = len(gunicorns) + len(instructions.split("\n")) + 9
if not gunicorns:
screen_height += 2 # A couple of blank lines are added when empty.
screen.erase()
win = curses.newwin(screen_height, screen_width + 6, 1, 3)
win.bkgd(" ", curses.color_pair(1))
win.border()
x = 3
blank_line = y = count(2).next
win.addstr(y(), x, title.center(screen_width), curses.A_NORMAL)
blank_line()
win.addstr(y(), x, format_row(" PID", "PORT", "NAME", "MEM (MB)", "WORKERS"),
curses.A_STANDOUT)
if not gunicorns:
blank_line()
win.addstr(y(), x, no_gunicorns.center(screen_width),
curses.A_NORMAL)
blank_line()
else:
win.hline(y(), x, curses.ACS_HLINE, screen_width)
for (i, pid) in enumerate(sorted(gunicorns.keys())):
port = gunicorns[pid]["port"]
name = gunicorns[pid]["name"]
mem = "%#.3f" % (gunicorns[pid]["mem"] / 1000.)
workers = gunicorns[pid]["workers"]
# When a signal is sent to update the number of workers, the number
# of workers is set to zero as a marker to signify an update has
# occurred. We then piggyback this variable and use it as a counter
# to animate the display until the gunicorn is next updated.
if workers < 1:
gunicorns[pid]["workers"] -= 1
chars = "|/-\\"
workers *= -1
if workers == len(chars):
gunicorns[pid]["workers"] = workers = 0
workers = chars[workers]
if pid == selected_pid:
attr = curses.A_STANDOUT
prefix_char = '> '
else:
attr = curses.A_NORMAL
prefix_char = ' '
win.addstr(y(), x, format_row(pid, port, name, mem, workers,
prefix_char), attr)
win.hline(y(), x, curses.ACS_HLINE, screen_width)
blank_line()
for line in instructions.split("\n"):
win.addstr(y(), x, line.center(screen_width), curses.A_NORMAL)
win.refresh() | python | def display_output(screen):
"""
Display the menu list of gunicorns.
"""
format_row() # Sets up the screen width.
screen_height = len(gunicorns) + len(instructions.split("\n")) + 9
if not gunicorns:
screen_height += 2 # A couple of blank lines are added when empty.
screen.erase()
win = curses.newwin(screen_height, screen_width + 6, 1, 3)
win.bkgd(" ", curses.color_pair(1))
win.border()
x = 3
blank_line = y = count(2).next
win.addstr(y(), x, title.center(screen_width), curses.A_NORMAL)
blank_line()
win.addstr(y(), x, format_row(" PID", "PORT", "NAME", "MEM (MB)", "WORKERS"),
curses.A_STANDOUT)
if not gunicorns:
blank_line()
win.addstr(y(), x, no_gunicorns.center(screen_width),
curses.A_NORMAL)
blank_line()
else:
win.hline(y(), x, curses.ACS_HLINE, screen_width)
for (i, pid) in enumerate(sorted(gunicorns.keys())):
port = gunicorns[pid]["port"]
name = gunicorns[pid]["name"]
mem = "%#.3f" % (gunicorns[pid]["mem"] / 1000.)
workers = gunicorns[pid]["workers"]
# When a signal is sent to update the number of workers, the number
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# to animate the display until the gunicorn is next updated.
if workers < 1:
gunicorns[pid]["workers"] -= 1
chars = "|/-\\"
workers *= -1
if workers == len(chars):
gunicorns[pid]["workers"] = workers = 0
workers = chars[workers]
if pid == selected_pid:
attr = curses.A_STANDOUT
prefix_char = '> '
else:
attr = curses.A_NORMAL
prefix_char = ' '
win.addstr(y(), x, format_row(pid, port, name, mem, workers,
prefix_char), attr)
win.hline(y(), x, curses.ACS_HLINE, screen_width)
blank_line()
for line in instructions.split("\n"):
win.addstr(y(), x, line.center(screen_width), curses.A_NORMAL)
win.refresh() | [
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| f5c9b9a69ea1f2ca00aac3565cb99491684d868a | https://github.com/stephenmcd/gunicorn-console/blob/f5c9b9a69ea1f2ca00aac3565cb99491684d868a/gunicorn_console.py#L209-L262 | train |
stephenmcd/gunicorn-console | gunicorn_console.py | main | def main():
"""
Main entry point for gunicorn_console.
"""
# Set up curses.
stdscr = curses.initscr()
curses.start_color()
curses.init_pair(1, foreground_colour, background_colour)
curses.noecho()
stdscr.keypad(True)
stdscr.nodelay(True)
try:
curses.curs_set(False)
except:
pass
try:
# Run main event loop until quit.
while True:
try:
update_gunicorns()
handle_keypress(stdscr)
display_output(stdscr)
curses.napms(int(screen_delay * 1000))
except KeyboardInterrupt:
break
finally:
# Tear down curses.
curses.nocbreak()
stdscr.keypad(False)
curses.echo()
curses.endwin() | python | def main():
"""
Main entry point for gunicorn_console.
"""
# Set up curses.
stdscr = curses.initscr()
curses.start_color()
curses.init_pair(1, foreground_colour, background_colour)
curses.noecho()
stdscr.keypad(True)
stdscr.nodelay(True)
try:
curses.curs_set(False)
except:
pass
try:
# Run main event loop until quit.
while True:
try:
update_gunicorns()
handle_keypress(stdscr)
display_output(stdscr)
curses.napms(int(screen_delay * 1000))
except KeyboardInterrupt:
break
finally:
# Tear down curses.
curses.nocbreak()
stdscr.keypad(False)
curses.echo()
curses.endwin() | [
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| f5c9b9a69ea1f2ca00aac3565cb99491684d868a | https://github.com/stephenmcd/gunicorn-console/blob/f5c9b9a69ea1f2ca00aac3565cb99491684d868a/gunicorn_console.py#L265-L295 | train |
pgxcentre/geneparse | geneparse/extract/extractor.py | _get_variant_silent | def _get_variant_silent(parser, variant):
"""Gets a variant from the parser while disabling logging."""
prev_log = config.LOG_NOT_FOUND
config.LOG_NOT_FOUND = False
results = parser.get_variant_genotypes(variant)
config.LOG_NOT_FOUND = prev_log
return results | python | def _get_variant_silent(parser, variant):
"""Gets a variant from the parser while disabling logging."""
prev_log = config.LOG_NOT_FOUND
config.LOG_NOT_FOUND = False
results = parser.get_variant_genotypes(variant)
config.LOG_NOT_FOUND = prev_log
return results | [
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| f698f9708af4c7962d384a70a5a14006b1cb7108 | https://github.com/pgxcentre/geneparse/blob/f698f9708af4c7962d384a70a5a14006b1cb7108/geneparse/extract/extractor.py#L93-L99 | train |
KnightConan/sspdatatables | src/sspdatatables/utils/enum.py | ExtendedEnumMeta._attrs_ | def _attrs_(mcs, cls, attr_name: str) -> Tuple[Any, ...]:
"""
Returns a tuple containing just the value of the given attr_name of all
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:return: tuple of different types
"""
return tuple(map(lambda x: getattr(x, attr_name), list(cls))) | python | def _attrs_(mcs, cls, attr_name: str) -> Tuple[Any, ...]:
"""
Returns a tuple containing just the value of the given attr_name of all
the elements from the cls.
:return: tuple of different types
"""
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| 1179a11358734e5e472e5eee703e8d34fa49e9bf | https://github.com/KnightConan/sspdatatables/blob/1179a11358734e5e472e5eee703e8d34fa49e9bf/src/sspdatatables/utils/enum.py#L55-L62 | train |
KnightConan/sspdatatables | src/sspdatatables/utils/enum.py | ExtendedEnumMeta._from_attr_ | def _from_attr_(mcs, cls, attr_name: str, attr_value: Any) -> TypeVar:
"""
Returns the enumeration item regarding to the attribute name and value,
or None if not found for the given cls
:param attr_name: str: attribute's name
:param attr_value: different values: key to search for
:return: Enumeration Item
"""
return next(iter(filter(lambda x: getattr(x, attr_name) == attr_value,
list(cls))), None) | python | def _from_attr_(mcs, cls, attr_name: str, attr_value: Any) -> TypeVar:
"""
Returns the enumeration item regarding to the attribute name and value,
or None if not found for the given cls
:param attr_name: str: attribute's name
:param attr_value: different values: key to search for
:return: Enumeration Item
"""
return next(iter(filter(lambda x: getattr(x, attr_name) == attr_value,
list(cls))), None) | [
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| 1179a11358734e5e472e5eee703e8d34fa49e9bf | https://github.com/KnightConan/sspdatatables/blob/1179a11358734e5e472e5eee703e8d34fa49e9bf/src/sspdatatables/utils/enum.py#L65-L75 | train |
KnightConan/sspdatatables | src/sspdatatables/utils/enum.py | ExtendedEnum.describe | def describe(cls) -> None:
"""
Prints in the console a table showing all the attributes for all the
definitions inside the class
:return: None
"""
max_lengths = []
for attr_name in cls.attr_names():
attr_func = "%ss" % attr_name
attr_list = list(map(str, getattr(cls, attr_func)())) + [attr_name]
max_lengths.append(max(list(map(len, attr_list))))
row_format = "{:>%d} | {:>%d} | {:>%d}" % tuple(max_lengths)
headers = [attr_name.capitalize() for attr_name in cls.attr_names()]
header_line = row_format.format(*headers)
output = "Class: %s\n" % cls.__name__
output += header_line + "\n"
output += "-"*(len(header_line)) + "\n"
for item in cls:
format_list = [str(getattr(item, attr_name))
for attr_name in cls.attr_names()]
output += row_format.format(*format_list) + "\n"
print(output) | python | def describe(cls) -> None:
"""
Prints in the console a table showing all the attributes for all the
definitions inside the class
:return: None
"""
max_lengths = []
for attr_name in cls.attr_names():
attr_func = "%ss" % attr_name
attr_list = list(map(str, getattr(cls, attr_func)())) + [attr_name]
max_lengths.append(max(list(map(len, attr_list))))
row_format = "{:>%d} | {:>%d} | {:>%d}" % tuple(max_lengths)
headers = [attr_name.capitalize() for attr_name in cls.attr_names()]
header_line = row_format.format(*headers)
output = "Class: %s\n" % cls.__name__
output += header_line + "\n"
output += "-"*(len(header_line)) + "\n"
for item in cls:
format_list = [str(getattr(item, attr_name))
for attr_name in cls.attr_names()]
output += row_format.format(*format_list) + "\n"
print(output) | [
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| 1179a11358734e5e472e5eee703e8d34fa49e9bf | https://github.com/KnightConan/sspdatatables/blob/1179a11358734e5e472e5eee703e8d34fa49e9bf/src/sspdatatables/utils/enum.py#L135-L157 | train |
geophysics-ubonn/crtomo_tools | src/td_plot.py | read_iter | def read_iter(use_fpi):
'''Return the path to the final .mag file either for the complex or the fpi
inversion.
'''
filename_rhosuffix = 'exe/inv.lastmod_rho'
filename = 'exe/inv.lastmod'
# filename HAS to exist. Otherwise the inversion was not finished
if(not os.path.isfile(filename)):
print('Inversion was not finished! No last iteration found.')
if(use_fpi is True):
if(os.path.isfile(filename_rhosuffix)):
filename = filename_rhosuffix
linestring = open(filename, 'r').readline().strip()
linestring = linestring.replace('\n', '')
linestring = linestring.replace('../', '')
return linestring | python | def read_iter(use_fpi):
'''Return the path to the final .mag file either for the complex or the fpi
inversion.
'''
filename_rhosuffix = 'exe/inv.lastmod_rho'
filename = 'exe/inv.lastmod'
# filename HAS to exist. Otherwise the inversion was not finished
if(not os.path.isfile(filename)):
print('Inversion was not finished! No last iteration found.')
if(use_fpi is True):
if(os.path.isfile(filename_rhosuffix)):
filename = filename_rhosuffix
linestring = open(filename, 'r').readline().strip()
linestring = linestring.replace('\n', '')
linestring = linestring.replace('../', '')
return linestring | [
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| 27c3e21a557f8df1c12455b96c4c2e00e08a5b4a | https://github.com/geophysics-ubonn/crtomo_tools/blob/27c3e21a557f8df1c12455b96c4c2e00e08a5b4a/src/td_plot.py#L228-L245 | train |
geophysics-ubonn/crtomo_tools | src/td_plot.py | list_datafiles | def list_datafiles():
'''Get the type of the tomodir and the highest iteration to list all files,
which will be plotted.
'''
is_cplx, is_fpi = td_type()
# get the highest iteration
it_rho = read_iter(is_fpi)
it_phase = read_iter(False)
# list the files
files = ['inv/coverage.mag']
dtype = ['cov']
files.append(it_rho)
dtype.append('mag')
if is_cplx:
files.append(it_rho.replace('mag', 'pha'))
dtype.append('pha')
if is_fpi:
files.append(it_phase.replace('mag', 'pha'))
dtype.append('pha_fpi')
return files, dtype | python | def list_datafiles():
'''Get the type of the tomodir and the highest iteration to list all files,
which will be plotted.
'''
is_cplx, is_fpi = td_type()
# get the highest iteration
it_rho = read_iter(is_fpi)
it_phase = read_iter(False)
# list the files
files = ['inv/coverage.mag']
dtype = ['cov']
files.append(it_rho)
dtype.append('mag')
if is_cplx:
files.append(it_rho.replace('mag', 'pha'))
dtype.append('pha')
if is_fpi:
files.append(it_phase.replace('mag', 'pha'))
dtype.append('pha_fpi')
return files, dtype | [
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| 27c3e21a557f8df1c12455b96c4c2e00e08a5b4a | https://github.com/geophysics-ubonn/crtomo_tools/blob/27c3e21a557f8df1c12455b96c4c2e00e08a5b4a/src/td_plot.py#L265-L285 | train |
geophysics-ubonn/crtomo_tools | src/td_plot.py | read_datafiles | def read_datafiles(files, dtype, column):
'''Load the datafiles and return cov, mag, phase and fpi phase values.
'''
pha = []
pha_fpi = []
for filename, filetype in zip(files, dtype):
if filetype == 'cov':
cov = load_cov(filename)
elif filetype == 'mag':
mag = load_rho(filename, column)
elif filetype == 'pha':
pha = load_rho(filename, 2)
elif filetype == 'pha_fpi':
pha_fpi = load_rho(filename, 2)
return cov, mag, pha, pha_fpi | python | def read_datafiles(files, dtype, column):
'''Load the datafiles and return cov, mag, phase and fpi phase values.
'''
pha = []
pha_fpi = []
for filename, filetype in zip(files, dtype):
if filetype == 'cov':
cov = load_cov(filename)
elif filetype == 'mag':
mag = load_rho(filename, column)
elif filetype == 'pha':
pha = load_rho(filename, 2)
elif filetype == 'pha_fpi':
pha_fpi = load_rho(filename, 2)
return cov, mag, pha, pha_fpi | [
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| 27c3e21a557f8df1c12455b96c4c2e00e08a5b4a | https://github.com/geophysics-ubonn/crtomo_tools/blob/27c3e21a557f8df1c12455b96c4c2e00e08a5b4a/src/td_plot.py#L288-L303 | train |
geophysics-ubonn/crtomo_tools | src/td_plot.py | load_cov | def load_cov(name):
'''Load a datafile with coverage file structure.
'''
content = np.genfromtxt(name, skip_header=1, skip_footer=1, usecols=([2]))
return content | python | def load_cov(name):
'''Load a datafile with coverage file structure.
'''
content = np.genfromtxt(name, skip_header=1, skip_footer=1, usecols=([2]))
return content | [
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| 27c3e21a557f8df1c12455b96c4c2e00e08a5b4a | https://github.com/geophysics-ubonn/crtomo_tools/blob/27c3e21a557f8df1c12455b96c4c2e00e08a5b4a/src/td_plot.py#L306-L311 | train |
geophysics-ubonn/crtomo_tools | src/td_plot.py | load_rho | def load_rho(name, column):
'''Load a datafile with rho structure like mag and phase
'''
try:
content = np.loadtxt(name, skiprows=1, usecols=([column]))
except:
raise ValueError('Given column to open does not exist.')
return content | python | def load_rho(name, column):
'''Load a datafile with rho structure like mag and phase
'''
try:
content = np.loadtxt(name, skiprows=1, usecols=([column]))
except:
raise ValueError('Given column to open does not exist.')
return content | [
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| 27c3e21a557f8df1c12455b96c4c2e00e08a5b4a | https://github.com/geophysics-ubonn/crtomo_tools/blob/27c3e21a557f8df1c12455b96c4c2e00e08a5b4a/src/td_plot.py#L314-L322 | train |
geophysics-ubonn/crtomo_tools | src/td_plot.py | calc_complex | def calc_complex(mag, pha):
''' Calculate real and imaginary part of the complex conductivity from
magnitude and phase in log10.
'''
complx = [10 ** m * math.e ** (1j * p / 1e3) for m, p in zip(mag, pha)]
real = [math.log10((1 / c).real) for c in complx]
imag = []
for c in complx:
if ((1 / c).imag) == 0:
imag.append(math.nan)
else:
i = math.log10(abs((1 / c).imag))
imag.append(i)
return real, imag | python | def calc_complex(mag, pha):
''' Calculate real and imaginary part of the complex conductivity from
magnitude and phase in log10.
'''
complx = [10 ** m * math.e ** (1j * p / 1e3) for m, p in zip(mag, pha)]
real = [math.log10((1 / c).real) for c in complx]
imag = []
for c in complx:
if ((1 / c).imag) == 0:
imag.append(math.nan)
else:
i = math.log10(abs((1 / c).imag))
imag.append(i)
return real, imag | [
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| 27c3e21a557f8df1c12455b96c4c2e00e08a5b4a | https://github.com/geophysics-ubonn/crtomo_tools/blob/27c3e21a557f8df1c12455b96c4c2e00e08a5b4a/src/td_plot.py#L325-L338 | train |
geophysics-ubonn/crtomo_tools | src/td_plot.py | plot_ratio | def plot_ratio(cid, ax, plotman, title, alpha, vmin, vmax,
xmin, xmax, zmin, zmax, xunit, cbtiks, elecs):
'''Plot ratio of two conductivity directions.
'''
# handle options
cblabel = 'anisotropy ratio'
zlabel = 'z [' + xunit + ']'
xlabel = 'x [' + xunit + ']'
# cm = 'brg'
cm = 'RdYlGn'
xmin, xmax, zmin, zmax, vmin, vmax = check_minmax(
plotman,
cid,
xmin, xmax,
zmin, zmax,
vmin, vmax,
)
# plot
fig, ax, cnorm, cmap, cb, scalarMap = plotman.plot_elements_to_ax(
cid=cid,
ax=ax,
xmin=xmin,
xmax=xmax,
zmin=zmin,
zmax=zmax,
cblabel=cblabel,
cbnrticks=cbtiks,
title=title,
zlabel=zlabel,
xlabel=xlabel,
plot_colorbar=True,
cmap_name=cm,
no_elecs=elecs,
cbmin=vmin,
cbmax=vmax,
)
return fig, ax, cnorm, cmap, cb | python | def plot_ratio(cid, ax, plotman, title, alpha, vmin, vmax,
xmin, xmax, zmin, zmax, xunit, cbtiks, elecs):
'''Plot ratio of two conductivity directions.
'''
# handle options
cblabel = 'anisotropy ratio'
zlabel = 'z [' + xunit + ']'
xlabel = 'x [' + xunit + ']'
# cm = 'brg'
cm = 'RdYlGn'
xmin, xmax, zmin, zmax, vmin, vmax = check_minmax(
plotman,
cid,
xmin, xmax,
zmin, zmax,
vmin, vmax,
)
# plot
fig, ax, cnorm, cmap, cb, scalarMap = plotman.plot_elements_to_ax(
cid=cid,
ax=ax,
xmin=xmin,
xmax=xmax,
zmin=zmin,
zmax=zmax,
cblabel=cblabel,
cbnrticks=cbtiks,
title=title,
zlabel=zlabel,
xlabel=xlabel,
plot_colorbar=True,
cmap_name=cm,
no_elecs=elecs,
cbmin=vmin,
cbmax=vmax,
)
return fig, ax, cnorm, cmap, cb | [
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| 27c3e21a557f8df1c12455b96c4c2e00e08a5b4a | https://github.com/geophysics-ubonn/crtomo_tools/blob/27c3e21a557f8df1c12455b96c4c2e00e08a5b4a/src/td_plot.py#L534-L570 | train |
geophysics-ubonn/crtomo_tools | src/td_plot.py | check_minmax | def check_minmax(plotman, cid, xmin, xmax, zmin, zmax, vmin, vmax):
'''Get min and max values for axes and colorbar if not given
'''
if xmin is None:
xmin = plotman.grid.grid['x'].min()
if xmax is None:
xmax = plotman.grid.grid['x'].max()
if zmin is None:
zmin = plotman.grid.grid['z'].min()
if zmax is None:
zmax = plotman.grid.grid['z'].max()
if isinstance(cid, int):
subdata = plotman.parman.parsets[cid]
else:
subdata = cid
if vmin is None:
vmin = subdata.min()
if vmax is None:
vmax = subdata.max()
return xmin, xmax, zmin, zmax, vmin, vmax | python | def check_minmax(plotman, cid, xmin, xmax, zmin, zmax, vmin, vmax):
'''Get min and max values for axes and colorbar if not given
'''
if xmin is None:
xmin = plotman.grid.grid['x'].min()
if xmax is None:
xmax = plotman.grid.grid['x'].max()
if zmin is None:
zmin = plotman.grid.grid['z'].min()
if zmax is None:
zmax = plotman.grid.grid['z'].max()
if isinstance(cid, int):
subdata = plotman.parman.parsets[cid]
else:
subdata = cid
if vmin is None:
vmin = subdata.min()
if vmax is None:
vmax = subdata.max()
return xmin, xmax, zmin, zmax, vmin, vmax | [
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| 27c3e21a557f8df1c12455b96c4c2e00e08a5b4a | https://github.com/geophysics-ubonn/crtomo_tools/blob/27c3e21a557f8df1c12455b96c4c2e00e08a5b4a/src/td_plot.py#L587-L607 | train |
unt-libraries/pyuntl | pyuntl/highwire_structure.py | citation_director | def citation_director(**kwargs):
"""Direct the citation elements based on their qualifier."""
qualifier = kwargs.get('qualifier', '')
content = kwargs.get('content', '')
if qualifier == 'publicationTitle':
return CitationJournalTitle(content=content)
elif qualifier == 'volume':
return CitationVolume(content=content)
elif qualifier == 'issue':
return CitationIssue(content=content)
elif qualifier == 'pageStart':
return CitationFirstpage(content=content)
elif qualifier == 'pageEnd':
return CitationLastpage(content=content)
else:
return None | python | def citation_director(**kwargs):
"""Direct the citation elements based on their qualifier."""
qualifier = kwargs.get('qualifier', '')
content = kwargs.get('content', '')
if qualifier == 'publicationTitle':
return CitationJournalTitle(content=content)
elif qualifier == 'volume':
return CitationVolume(content=content)
elif qualifier == 'issue':
return CitationIssue(content=content)
elif qualifier == 'pageStart':
return CitationFirstpage(content=content)
elif qualifier == 'pageEnd':
return CitationLastpage(content=content)
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| f92413302897dab948aac18ee9e482ace0187bd4 | https://github.com/unt-libraries/pyuntl/blob/f92413302897dab948aac18ee9e482ace0187bd4/pyuntl/highwire_structure.py#L237-L252 | train |
unt-libraries/pyuntl | pyuntl/highwire_structure.py | identifier_director | def identifier_director(**kwargs):
"""Direct the identifier elements based on their qualifier."""
qualifier = kwargs.get('qualifier', '')
content = kwargs.get('content', '')
if qualifier == 'ISBN':
return CitationISBN(content=content)
elif qualifier == 'ISSN':
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elif qualifier == 'DOI':
return CitationDOI(content=content)
elif qualifier == 'REP-NO':
return CitationTechnicalReportNumber(content=content)
else:
return None | python | def identifier_director(**kwargs):
"""Direct the identifier elements based on their qualifier."""
qualifier = kwargs.get('qualifier', '')
content = kwargs.get('content', '')
if qualifier == 'ISBN':
return CitationISBN(content=content)
elif qualifier == 'ISSN':
return CitationISSN(content=content)
elif qualifier == 'DOI':
return CitationDOI(content=content)
elif qualifier == 'REP-NO':
return CitationTechnicalReportNumber(content=content)
else:
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| f92413302897dab948aac18ee9e482ace0187bd4 | https://github.com/unt-libraries/pyuntl/blob/f92413302897dab948aac18ee9e482ace0187bd4/pyuntl/highwire_structure.py#L255-L268 | train |
unt-libraries/pyuntl | pyuntl/highwire_structure.py | CitationAuthor.get_author | def get_author(self, **kwargs):
"""Determine the authors from the creator field."""
qualifier = kwargs.get('qualifier', '')
children = kwargs.get('children', [])
creator_type_per = False
author_name = None
# Find the creator type in children.
for child in children:
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# Get the author name.
elif child.tag == 'name':
author_name = child.content
if qualifier == 'aut' and creator_type_per and author_name:
return author_name
return None | python | def get_author(self, **kwargs):
"""Determine the authors from the creator field."""
qualifier = kwargs.get('qualifier', '')
children = kwargs.get('children', [])
creator_type_per = False
author_name = None
# Find the creator type in children.
for child in children:
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| f92413302897dab948aac18ee9e482ace0187bd4 | https://github.com/unt-libraries/pyuntl/blob/f92413302897dab948aac18ee9e482ace0187bd4/pyuntl/highwire_structure.py#L52-L68 | train |
unt-libraries/pyuntl | pyuntl/highwire_structure.py | CitationPublisher.get_publisher_name | def get_publisher_name(self, **kwargs):
"""Get the publisher name."""
children = kwargs.get('children', [])
# Find the creator type in children.
for child in children:
if child.tag == 'name':
return child.content
return None | python | def get_publisher_name(self, **kwargs):
"""Get the publisher name."""
children = kwargs.get('children', [])
# Find the creator type in children.
for child in children:
if child.tag == 'name':
return child.content
return None | [
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| f92413302897dab948aac18ee9e482ace0187bd4 | https://github.com/unt-libraries/pyuntl/blob/f92413302897dab948aac18ee9e482ace0187bd4/pyuntl/highwire_structure.py#L77-L84 | train |
unt-libraries/pyuntl | pyuntl/highwire_structure.py | CitationPublicationDate.get_publication_date | def get_publication_date(self, **kwargs):
"""Determine the creation date for the publication date."""
date_string = kwargs.get('content', '')
date_match = CREATION_DATE_REGEX.match(date_string)
month_match = CREATION_MONTH_REGEX.match(date_string)
year_match = CREATION_YEAR_REGEX.match(date_string)
# Check if a date match exists.
if date_match:
(year, month, day) = date_match.groups('')
# Create the date.
try:
creation_date = datetime.date(int(year), int(month), int(day))
except ValueError:
return None
else:
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format_date_string(creation_date.month),
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creation_date.year,
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elif month_match:
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# Create the date.
try:
creation_date = datetime.date(int(year), int(month), 1)
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format_date_string(creation_date.month),
creation_date.year,
)
elif year_match:
year = year_match.groups('')[0]
return year
else:
return None | python | def get_publication_date(self, **kwargs):
"""Determine the creation date for the publication date."""
date_string = kwargs.get('content', '')
date_match = CREATION_DATE_REGEX.match(date_string)
month_match = CREATION_MONTH_REGEX.match(date_string)
year_match = CREATION_YEAR_REGEX.match(date_string)
# Check if a date match exists.
if date_match:
(year, month, day) = date_match.groups('')
# Create the date.
try:
creation_date = datetime.date(int(year), int(month), int(day))
except ValueError:
return None
else:
return '%s/%s/%s' % (
format_date_string(creation_date.month),
format_date_string(creation_date.day),
creation_date.year,
)
elif month_match:
(year, month) = month_match.groups('')
# Create the date.
try:
creation_date = datetime.date(int(year), int(month), 1)
except ValueError:
return None
else:
return '%s/%s' % (
format_date_string(creation_date.month),
creation_date.year,
)
elif year_match:
year = year_match.groups('')[0]
return year
else:
return None | [
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| f92413302897dab948aac18ee9e482ace0187bd4 | https://github.com/unt-libraries/pyuntl/blob/f92413302897dab948aac18ee9e482ace0187bd4/pyuntl/highwire_structure.py#L93-L129 | train |
unt-libraries/pyuntl | pyuntl/highwire_structure.py | CitationOnlineDate.get_online_date | def get_online_date(self, **kwargs):
"""Get the online date from the meta creation date."""
qualifier = kwargs.get('qualifier', '')
content = kwargs.get('content', '')
# Handle meta-creation-date element.
if qualifier == 'metadataCreationDate':
date_match = META_CREATION_DATE_REGEX.match(content)
(year, month, day) = date_match.groups('')
# Create the date.
creation_date = datetime.date(int(year), int(month), int(day))
return '%s/%s/%s' % (
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format_date_string(creation_date.day),
creation_date.year,
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return None | python | def get_online_date(self, **kwargs):
"""Get the online date from the meta creation date."""
qualifier = kwargs.get('qualifier', '')
content = kwargs.get('content', '')
# Handle meta-creation-date element.
if qualifier == 'metadataCreationDate':
date_match = META_CREATION_DATE_REGEX.match(content)
(year, month, day) = date_match.groups('')
# Create the date.
creation_date = datetime.date(int(year), int(month), int(day))
return '%s/%s/%s' % (
format_date_string(creation_date.month),
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unt-libraries/pyuntl | pyuntl/highwire_structure.py | CitationDissertationInstitution.get_institution | def get_institution(self, **kwargs):
"""Get the dissertation institution."""
qualifier = kwargs.get('qualifier', '')
content = kwargs.get('content', '')
if qualifier == 'grantor':
return content
return None | python | def get_institution(self, **kwargs):
"""Get the dissertation institution."""
qualifier = kwargs.get('qualifier', '')
content = kwargs.get('content', '')
if qualifier == 'grantor':
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rhayes777/PyAutoFit | autofit/aggregator.py | PhaseOutput.model_results | def model_results(self) -> str:
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Reads the model.results file
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rhayes777/PyAutoFit | autofit/aggregator.py | PhaseOutput.header | def header(self) -> str:
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A header created by joining the pipeline, phase and data names
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rhayes777/PyAutoFit | autofit/aggregator.py | PhaseOutput.optimizer | def optimizer(self) -> non_linear.NonLinearOptimizer:
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The optimizer object that was used in this phase
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rhayes777/PyAutoFit | autofit/aggregator.py | Aggregator.phases_with | def phases_with(self, **kwargs) -> [PhaseOutput]:
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Parameters
----------
kwargs
Filters, e.g. pipeline=pipeline1
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Parameters
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rhayes777/PyAutoFit | autofit/aggregator.py | Aggregator.optimizers_with | def optimizers_with(self, **kwargs) -> [non_linear.NonLinearOptimizer]:
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kwargs
Filters, e.g. pipeline=pipeline1
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kwargs
Filters, e.g. pipeline=pipeline1
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A list of optimizers, one for each phase in the directory that matches the filters.
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rhayes777/PyAutoFit | autofit/aggregator.py | Aggregator.model_results | def model_results(self, **kwargs) -> str:
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Collates model results from all phases in the directory or some subset if filters are applied.
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kwargs
Filters, e.g. pipeline=pipeline1
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Collates model results from all phases in the directory or some subset if filters are applied.
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kwargs
Filters, e.g. pipeline=pipeline1
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| a9e6144abb08edfc6a6906c4030d7119bf8d3e14 | https://github.com/rhayes777/PyAutoFit/blob/a9e6144abb08edfc6a6906c4030d7119bf8d3e14/autofit/aggregator.py#L123-L138 | train |
peterbe/gg | gg/builtins/branches/gg_branches.py | branches | def branches(config, searchstring=""):
"""List all branches. And if exactly 1 found, offer to check it out."""
repo = config.repo
branches_ = list(find(repo, searchstring))
if branches_:
merged = get_merged_branches(repo)
info_out("Found existing branches...")
print_list(branches_, merged)
if len(branches_) == 1 and searchstring:
# If the found branch is the current one, error
active_branch = repo.active_branch
if active_branch == branches_[0]:
error_out("You're already on '{}'".format(branches_[0].name))
branch_name = branches_[0].name
if len(branch_name) > 50:
branch_name = branch_name[:47] + "…"
check_it_out = (
input("Check out '{}'? [Y/n] ".format(branch_name)).lower().strip()
!= "n"
)
if check_it_out:
branches_[0].checkout()
elif searchstring:
error_out("Found no branches matching '{}'.".format(searchstring))
else:
error_out("Found no branches.") | python | def branches(config, searchstring=""):
"""List all branches. And if exactly 1 found, offer to check it out."""
repo = config.repo
branches_ = list(find(repo, searchstring))
if branches_:
merged = get_merged_branches(repo)
info_out("Found existing branches...")
print_list(branches_, merged)
if len(branches_) == 1 and searchstring:
# If the found branch is the current one, error
active_branch = repo.active_branch
if active_branch == branches_[0]:
error_out("You're already on '{}'".format(branches_[0].name))
branch_name = branches_[0].name
if len(branch_name) > 50:
branch_name = branch_name[:47] + "…"
check_it_out = (
input("Check out '{}'? [Y/n] ".format(branch_name)).lower().strip()
!= "n"
)
if check_it_out:
branches_[0].checkout()
elif searchstring:
error_out("Found no branches matching '{}'.".format(searchstring))
else:
error_out("Found no branches.") | [
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| 2aace5bdb4a9b1cb65bea717784edf54c63b7bad | https://github.com/peterbe/gg/blob/2aace5bdb4a9b1cb65bea717784edf54c63b7bad/gg/builtins/branches/gg_branches.py#L13-L39 | train |
Riminder/python-riminder-api | riminder/base64Wrapper.py | decodebytes | def decodebytes(input):
"""Decode base64 string to byte array."""
py_version = sys.version_info[0]
if py_version >= 3:
return _decodebytes_py3(input)
return _decodebytes_py2(input) | python | def decodebytes(input):
"""Decode base64 string to byte array."""
py_version = sys.version_info[0]
if py_version >= 3:
return _decodebytes_py3(input)
return _decodebytes_py2(input) | [
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| 01279f0ece08cf3d1dd45f76de6d9edf7fafec90 | https://github.com/Riminder/python-riminder-api/blob/01279f0ece08cf3d1dd45f76de6d9edf7fafec90/riminder/base64Wrapper.py#L14-L19 | train |
gofed/gofedlib | gofedlib/snapshot/capturer.py | ProjectCapturer.capture | def capture(self, commit = ""):
"""Capture the current state of a project based on its provider
Commit is relevant only for upstream providers.
If empty, the latest commit from provider repository is taken.
It is ignored for distribution providers.
:param provider: project provider, e.g. upstream repository, distribution builder
:type provider: json/dict
:param commit: project's original commit
:type commit: string
"""
self._validateProvider(self._provider)
# get client for repository
# TODO(jchaloup): read config file to switch between local and remove clients
# TODO(jchaloup): remote client can cover gofed infratructure or any remove source for repository info
client = RepositoryClientBuilder().buildWithRemoteClient(self._provider)
if self._provider["provider"] == "github":
self._signature = ProjectGithubRepositoryCapturer(self._provider, client).capture(commit).signature()
elif self._provider["provider"] == "bitbucket":
self._signature = ProjectBitbucketRepositoryCapturer(self._provider, client).capture(commit).signature()
else:
raise KeyError("Provider '%s' not recognized" % self._provider["provider"])
return self | python | def capture(self, commit = ""):
"""Capture the current state of a project based on its provider
Commit is relevant only for upstream providers.
If empty, the latest commit from provider repository is taken.
It is ignored for distribution providers.
:param provider: project provider, e.g. upstream repository, distribution builder
:type provider: json/dict
:param commit: project's original commit
:type commit: string
"""
self._validateProvider(self._provider)
# get client for repository
# TODO(jchaloup): read config file to switch between local and remove clients
# TODO(jchaloup): remote client can cover gofed infratructure or any remove source for repository info
client = RepositoryClientBuilder().buildWithRemoteClient(self._provider)
if self._provider["provider"] == "github":
self._signature = ProjectGithubRepositoryCapturer(self._provider, client).capture(commit).signature()
elif self._provider["provider"] == "bitbucket":
self._signature = ProjectBitbucketRepositoryCapturer(self._provider, client).capture(commit).signature()
else:
raise KeyError("Provider '%s' not recognized" % self._provider["provider"])
return self | [
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| 0674c248fe3d8706f98f912996b65af469f96b10 | https://github.com/gofed/gofedlib/blob/0674c248fe3d8706f98f912996b65af469f96b10/gofedlib/snapshot/capturer.py#L25-L51 | train |
pgxcentre/geneparse | geneparse/logging.py | found_duplicates | def found_duplicates(counts):
"""Log that duplicates were found.
:param counts: A list of duplicate marker names along with their number
of occurences.
:type counts: list
"""
_logger.warning("Duplicated markers found")
for marker, count in counts:
_logger.warning(" - {}: {:,d} times".format(marker, count))
_logger.warning("Appending ':dupX' to the duplicated markers according "
"to their location in the file.") | python | def found_duplicates(counts):
"""Log that duplicates were found.
:param counts: A list of duplicate marker names along with their number
of occurences.
:type counts: list
"""
_logger.warning("Duplicated markers found")
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_logger.warning(" - {}: {:,d} times".format(marker, count))
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| f698f9708af4c7962d384a70a5a14006b1cb7108 | https://github.com/pgxcentre/geneparse/blob/f698f9708af4c7962d384a70a5a14006b1cb7108/geneparse/logging.py#L45-L57 | train |
lalinsky/mbdata | mbdata/utils/__init__.py | patch_model_schemas | def patch_model_schemas(mapping):
"""Update mbdata.models to use different schema names
The function accepts a dictionary with schema name mapping
and updates the schema for all MusicBrainz tables.
If you want to use the default schema:
>>> patch_model_schemas(NO_SCHEMAS)
If you have just one 'musicbrainz' schema:
>>> patch_model_schemas(SINGLE_MUSICBRAINZ_SCHEMA)
"""
from mbdata.models import Base
for table in Base.metadata.sorted_tables:
if table.schema is None:
continue
table.schema = mapping.get(table.schema, table.schema) | python | def patch_model_schemas(mapping):
"""Update mbdata.models to use different schema names
The function accepts a dictionary with schema name mapping
and updates the schema for all MusicBrainz tables.
If you want to use the default schema:
>>> patch_model_schemas(NO_SCHEMAS)
If you have just one 'musicbrainz' schema:
>>> patch_model_schemas(SINGLE_MUSICBRAINZ_SCHEMA)
"""
from mbdata.models import Base
for table in Base.metadata.sorted_tables:
if table.schema is None:
continue
table.schema = mapping.get(table.schema, table.schema) | [
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Nic30/hwtGraph | hwtGraph/elk/fromHwt/statementRenderer.py | detectRamPorts | def detectRamPorts(stm: IfContainer, current_en: RtlSignalBase):
"""
Detect RAM ports in If statement
:param stm: statement to detect the ram ports in
:param current_en: curent en/clk signal
"""
if stm.ifFalse or stm.elIfs:
return
for _stm in stm.ifTrue:
if isinstance(_stm, IfContainer):
yield from detectRamPorts(_stm, _stm.cond & current_en)
elif isinstance(_stm, Assignment):
if isinstance(_stm.dst._dtype, HArray):
assert len(_stm.indexes) == 1, "one address per RAM port"
w_addr = _stm.indexes[0]
mem = _stm.dst
yield (RAM_WRITE, mem, w_addr, current_en, _stm.src)
elif _stm.src.hidden and len(_stm.src.drivers) == 1:
op = _stm.src.drivers[0]
mem = op.operands[0]
if isinstance(mem._dtype, HArray) and op.operator == AllOps.INDEX:
r_addr = op.operands[1]
if _stm.indexes:
raise NotImplementedError()
yield (RAM_READ, mem, r_addr, current_en, _stm.dst) | python | def detectRamPorts(stm: IfContainer, current_en: RtlSignalBase):
"""
Detect RAM ports in If statement
:param stm: statement to detect the ram ports in
:param current_en: curent en/clk signal
"""
if stm.ifFalse or stm.elIfs:
return
for _stm in stm.ifTrue:
if isinstance(_stm, IfContainer):
yield from detectRamPorts(_stm, _stm.cond & current_en)
elif isinstance(_stm, Assignment):
if isinstance(_stm.dst._dtype, HArray):
assert len(_stm.indexes) == 1, "one address per RAM port"
w_addr = _stm.indexes[0]
mem = _stm.dst
yield (RAM_WRITE, mem, w_addr, current_en, _stm.src)
elif _stm.src.hidden and len(_stm.src.drivers) == 1:
op = _stm.src.drivers[0]
mem = op.operands[0]
if isinstance(mem._dtype, HArray) and op.operator == AllOps.INDEX:
r_addr = op.operands[1]
if _stm.indexes:
raise NotImplementedError()
yield (RAM_READ, mem, r_addr, current_en, _stm.dst) | [
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| 6b7d4fdd759f263a0fdd2736f02f123e44e4354f | https://github.com/Nic30/hwtGraph/blob/6b7d4fdd759f263a0fdd2736f02f123e44e4354f/hwtGraph/elk/fromHwt/statementRenderer.py#L42-L67 | train |
Nic30/hwtGraph | hwtGraph/elk/fromHwt/statementRenderer.py | StatementRenderer.addInputPort | def addInputPort(self, node, name,
i: Union[Value, RtlSignalBase],
side=PortSide.WEST):
"""
Add and connect input port on subnode
:param node: node where to add input port
:param name: name of newly added port
:param i: input value
:param side: side where input port should be added
"""
root = self.node
port = node.addPort(name, PortType.INPUT, side)
netCtxs = self.netCtxs
if isinstance(i, LPort):
root.addEdge(i, port)
elif isConst(i):
i = i.staticEval()
c, wasThereBefore = self.netCtxs.getDefault(i)
if not wasThereBefore:
v = ValueAsLNode(root, i).east[0]
c.addDriver(v)
c.addEndpoint(port)
elif i.hidden:
# later connect driver of this signal to output port
ctx, wasThereBefore = netCtxs.getDefault(i)
if not wasThereBefore:
self.lazyLoadNet(i)
ctx.addEndpoint(port)
else:
portCtx = self.portCtx
rootCtx, _ = self.rootNetCtxs.getDefault(i)
if self.isVirtual:
# later connect signal in root to input port or input port of
# wrap node
rootCtx.addEndpoint(port)
else:
# spot input port on this wrap node if required
isNewlySpotted = (i, PortType.INPUT) not in portCtx.data
src = portCtx.register(i, PortType.INPUT)
# connect input port on wrap node with specified output port
ctx, _ = netCtxs.getDefault(i)
ctx.addDriver(src)
ctx.addEndpoint(port)
if isNewlySpotted:
# get input port from parent view
_port = portCtx.getOutside(i, PortType.INPUT)
rootCtx.addEndpoint(_port) | python | def addInputPort(self, node, name,
i: Union[Value, RtlSignalBase],
side=PortSide.WEST):
"""
Add and connect input port on subnode
:param node: node where to add input port
:param name: name of newly added port
:param i: input value
:param side: side where input port should be added
"""
root = self.node
port = node.addPort(name, PortType.INPUT, side)
netCtxs = self.netCtxs
if isinstance(i, LPort):
root.addEdge(i, port)
elif isConst(i):
i = i.staticEval()
c, wasThereBefore = self.netCtxs.getDefault(i)
if not wasThereBefore:
v = ValueAsLNode(root, i).east[0]
c.addDriver(v)
c.addEndpoint(port)
elif i.hidden:
# later connect driver of this signal to output port
ctx, wasThereBefore = netCtxs.getDefault(i)
if not wasThereBefore:
self.lazyLoadNet(i)
ctx.addEndpoint(port)
else:
portCtx = self.portCtx
rootCtx, _ = self.rootNetCtxs.getDefault(i)
if self.isVirtual:
# later connect signal in root to input port or input port of
# wrap node
rootCtx.addEndpoint(port)
else:
# spot input port on this wrap node if required
isNewlySpotted = (i, PortType.INPUT) not in portCtx.data
src = portCtx.register(i, PortType.INPUT)
# connect input port on wrap node with specified output port
ctx, _ = netCtxs.getDefault(i)
ctx.addDriver(src)
ctx.addEndpoint(port)
if isNewlySpotted:
# get input port from parent view
_port = portCtx.getOutside(i, PortType.INPUT)
rootCtx.addEndpoint(_port) | [
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:param side: side where input port should be added | [
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| 6b7d4fdd759f263a0fdd2736f02f123e44e4354f | https://github.com/Nic30/hwtGraph/blob/6b7d4fdd759f263a0fdd2736f02f123e44e4354f/hwtGraph/elk/fromHwt/statementRenderer.py#L99-L149 | train |
Nic30/hwtGraph | hwtGraph/elk/fromHwt/statementRenderer.py | StatementRenderer.addOutputPort | def addOutputPort(self, node: LNode, name: str,
out: Optional[Union[RtlSignalBase, LPort]],
side=PortSide.EAST):
"""
Add and connect output port on subnode
"""
oPort = node.addPort(name, PortType.OUTPUT, side)
if out is not None:
if isinstance(out, LPort):
self.node.addEdge(oPort, out)
elif out.hidden:
raise ValueError("Hidden signals should not be connected to outside", name)
elif self.isVirtual:
# This node is inlined inside of parent.
# Mark that this output of subnode should be connected
# to output of parent node.
ctx, _ = self.netCtxs.getDefault(out)
ctx.addDriver(oPort)
else:
# connect my signal to my output port
_out = self.portCtx.getInside(out, PortType.OUTPUT)
self.node.addEdge(oPort, _out, originObj=out)
# mark connection of output port to parent net
ooPort = self.portCtx.getOutside(out, PortType.OUTPUT)
ctx, _ = self.rootNetCtxs.getDefault(out)
ctx.addDriver(ooPort)
return oPort | python | def addOutputPort(self, node: LNode, name: str,
out: Optional[Union[RtlSignalBase, LPort]],
side=PortSide.EAST):
"""
Add and connect output port on subnode
"""
oPort = node.addPort(name, PortType.OUTPUT, side)
if out is not None:
if isinstance(out, LPort):
self.node.addEdge(oPort, out)
elif out.hidden:
raise ValueError("Hidden signals should not be connected to outside", name)
elif self.isVirtual:
# This node is inlined inside of parent.
# Mark that this output of subnode should be connected
# to output of parent node.
ctx, _ = self.netCtxs.getDefault(out)
ctx.addDriver(oPort)
else:
# connect my signal to my output port
_out = self.portCtx.getInside(out, PortType.OUTPUT)
self.node.addEdge(oPort, _out, originObj=out)
# mark connection of output port to parent net
ooPort = self.portCtx.getOutside(out, PortType.OUTPUT)
ctx, _ = self.rootNetCtxs.getDefault(out)
ctx.addDriver(ooPort)
return oPort | [
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| 6b7d4fdd759f263a0fdd2736f02f123e44e4354f | https://github.com/Nic30/hwtGraph/blob/6b7d4fdd759f263a0fdd2736f02f123e44e4354f/hwtGraph/elk/fromHwt/statementRenderer.py#L151-L178 | train |
Nic30/hwtGraph | hwtGraph/elk/fromHwt/statementRenderer.py | StatementRenderer.renderContent | def renderContent(self):
"""
Walk from outputs to inputs
for each public signal register port of wrap node if required
lazy load all operator and statement nodes for signals
"""
stm = self.stm
portCtx = self.portCtx
# for each inputs and outputs render expression trees
# walk statements and render muxs and memories
for o in stm._outputs:
if not self.isVirtual:
portCtx.register(o, PortType.OUTPUT)
canHaveRamPorts = isinstance(stm, IfContainer) and arr_any(
chain(stm._inputs, stm._outputs),
lambda s: isinstance(s._dtype, HArray))
# render RAM ports
consumedOutputs = set()
if canHaveRamPorts:
for pType, memSig, addrSig, enSig, io in detectRamPorts(stm, stm.cond):
if pType == RAM_READ:
self.createRamReadNode(memSig, enSig, addrSig,
io, True)
consumedOutputs.add(io)
elif pType == RAM_WRITE:
self.createRamWriteNode(memSig, enSig, addrSig,
io, True)
consumedOutputs.add(memSig)
else:
raise TypeError()
for o in stm._outputs:
if o not in consumedOutputs:
self.renderForSignal(stm, o, True)
if not self.isVirtual:
self.netCtxs.applyConnections(self.node) | python | def renderContent(self):
"""
Walk from outputs to inputs
for each public signal register port of wrap node if required
lazy load all operator and statement nodes for signals
"""
stm = self.stm
portCtx = self.portCtx
# for each inputs and outputs render expression trees
# walk statements and render muxs and memories
for o in stm._outputs:
if not self.isVirtual:
portCtx.register(o, PortType.OUTPUT)
canHaveRamPorts = isinstance(stm, IfContainer) and arr_any(
chain(stm._inputs, stm._outputs),
lambda s: isinstance(s._dtype, HArray))
# render RAM ports
consumedOutputs = set()
if canHaveRamPorts:
for pType, memSig, addrSig, enSig, io in detectRamPorts(stm, stm.cond):
if pType == RAM_READ:
self.createRamReadNode(memSig, enSig, addrSig,
io, True)
consumedOutputs.add(io)
elif pType == RAM_WRITE:
self.createRamWriteNode(memSig, enSig, addrSig,
io, True)
consumedOutputs.add(memSig)
else:
raise TypeError()
for o in stm._outputs:
if o not in consumedOutputs:
self.renderForSignal(stm, o, True)
if not self.isVirtual:
self.netCtxs.applyConnections(self.node) | [
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| 6b7d4fdd759f263a0fdd2736f02f123e44e4354f | https://github.com/Nic30/hwtGraph/blob/6b7d4fdd759f263a0fdd2736f02f123e44e4354f/hwtGraph/elk/fromHwt/statementRenderer.py#L385-L425 | train |
gofed/gofedlib | gofedlib/distribution/packagenamegenerator.py | PackageNameGenerator.generate | def generate(self, project):
"""
Package name construction is based on provider, not on prefix.
Prefix does not have to equal provider_prefix.
"""
for assignment in self.s2n_mapping:
if assignment["ipprefix"] == project:
self._name = assignment["package"]
return self
#
# github.com -> github
# code.google.com/p/ -> googlecode
# golang.org/x/ -> golangorg
# gopkg.in/check.v1 -> gopkg-check
# camlistore.org
#
name = project
if name.startswith("github.com"):
name = re.sub(r"^github\.com", "github", name)
if name.startswith("gopkg.in"):
name = re.sub(r"gopkg\.in", "gopkg", name)
# any version marks?
name = re.sub(r"\.v\d", "", name)
name = re.sub(r"/v\d/", "/", name)
if name.startswith("code.google.com/p"):
name = re.sub(r"^code\.google\.com/p", "googlecode", name)
if name.startswith("golang.org/x"):
name = re.sub(r"^golang\.org/x", "golangorg", name)
if name.startswith("google.golang.org"):
name = re.sub(r"^google\.golang\.org", "googlegolangorg", name)
if name.startswith("bitbucket.org"):
name = re.sub(r"^bitbucket\.org", "bitbucket", name)
if name.startswith("k8s.io"):
name = re.sub(r"^k8s\.io", "k8s", name)
if name.endswith(".org"):
name = re.sub(r"\.org$", "", name)
name = name.replace("/", "-")
self._name = "golang-%s" % name
return self | python | def generate(self, project):
"""
Package name construction is based on provider, not on prefix.
Prefix does not have to equal provider_prefix.
"""
for assignment in self.s2n_mapping:
if assignment["ipprefix"] == project:
self._name = assignment["package"]
return self
#
# github.com -> github
# code.google.com/p/ -> googlecode
# golang.org/x/ -> golangorg
# gopkg.in/check.v1 -> gopkg-check
# camlistore.org
#
name = project
if name.startswith("github.com"):
name = re.sub(r"^github\.com", "github", name)
if name.startswith("gopkg.in"):
name = re.sub(r"gopkg\.in", "gopkg", name)
# any version marks?
name = re.sub(r"\.v\d", "", name)
name = re.sub(r"/v\d/", "/", name)
if name.startswith("code.google.com/p"):
name = re.sub(r"^code\.google\.com/p", "googlecode", name)
if name.startswith("golang.org/x"):
name = re.sub(r"^golang\.org/x", "golangorg", name)
if name.startswith("google.golang.org"):
name = re.sub(r"^google\.golang\.org", "googlegolangorg", name)
if name.startswith("bitbucket.org"):
name = re.sub(r"^bitbucket\.org", "bitbucket", name)
if name.startswith("k8s.io"):
name = re.sub(r"^k8s\.io", "k8s", name)
if name.endswith(".org"):
name = re.sub(r"\.org$", "", name)
name = name.replace("/", "-")
self._name = "golang-%s" % name
return self | [
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| 0674c248fe3d8706f98f912996b65af469f96b10 | https://github.com/gofed/gofedlib/blob/0674c248fe3d8706f98f912996b65af469f96b10/gofedlib/distribution/packagenamegenerator.py#L9-L59 | train |
NikolayDachev/jadm | lib/paramiko-1.14.1/paramiko/hostkeys.py | HostKeys.hash_host | def hash_host(hostname, salt=None):
"""
Return a "hashed" form of the hostname, as used by OpenSSH when storing
hashed hostnames in the known_hosts file.
:param str hostname: the hostname to hash
:param str salt: optional salt to use when hashing (must be 20 bytes long)
:return: the hashed hostname as a `str`
"""
if salt is None:
salt = os.urandom(sha1().digest_size)
else:
if salt.startswith('|1|'):
salt = salt.split('|')[2]
salt = decodebytes(b(salt))
assert len(salt) == sha1().digest_size
hmac = HMAC(salt, b(hostname), sha1).digest()
hostkey = '|1|%s|%s' % (u(encodebytes(salt)), u(encodebytes(hmac)))
return hostkey.replace('\n', '') | python | def hash_host(hostname, salt=None):
"""
Return a "hashed" form of the hostname, as used by OpenSSH when storing
hashed hostnames in the known_hosts file.
:param str hostname: the hostname to hash
:param str salt: optional salt to use when hashing (must be 20 bytes long)
:return: the hashed hostname as a `str`
"""
if salt is None:
salt = os.urandom(sha1().digest_size)
else:
if salt.startswith('|1|'):
salt = salt.split('|')[2]
salt = decodebytes(b(salt))
assert len(salt) == sha1().digest_size
hmac = HMAC(salt, b(hostname), sha1).digest()
hostkey = '|1|%s|%s' % (u(encodebytes(salt)), u(encodebytes(hmac)))
return hostkey.replace('\n', '') | [
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| 12bb550445edfcd87506f7cba7a6a35d413c5511 | https://github.com/NikolayDachev/jadm/blob/12bb550445edfcd87506f7cba7a6a35d413c5511/lib/paramiko-1.14.1/paramiko/hostkeys.py#L258-L276 | train |
geophysics-ubonn/crtomo_tools | lib/crtomo/grid.py | crt_grid._read_elem_nodes | def _read_elem_nodes(self, fid):
""" Read the nodes from an opened elem.dat file. Correct for CutMcK
transformations.
We store three typed of nodes in the dict 'nodes':
* "raw" : as read from the elem.dat file
* "presort" : pre-sorted so we can directly read node numbers from
a elec.dat file and use them as indices.
* "sorted" : completely sorted as in the original grid (before any
CutMcK)
For completeness, we also store the following keys:
* "cutmck_index" : Array containing the indices in "presort" to
obtain the "sorted" values:
nodes['sorted'] = nodes['presort'] [nodes['cutmck_index'], :]
* "rev_cutmck_index" : argsort(cutmck_index)
"""
nodes = {}
# # prepare nodes
# nodes_sorted = np.zeros((number_of_nodes, 3), dtype=float)
# nodes = np.zeros((number_of_nodes, 3), dtype=float)
# read in nodes
nodes_raw = np.empty((self.header['nr_nodes'], 3), dtype=float)
for nr in range(0, self.header['nr_nodes']):
node_line = fid.readline().lstrip()
nodes_raw[nr, :] = np.fromstring(
node_line, dtype=float, sep=' ')
# round node coordinates to 5th decimal point. Sometimes this is
# important when we deal with mal-formatted node data
nodes_raw[:, 1:3] = np.round(nodes_raw[:, 1:3], 5)
# check for CutMcK
# The check is based on the first node, but if one node was renumbered,
# so were all the others.
if(nodes_raw[:, 0] != list(range(1, nodes_raw.shape[0]))):
self.header['cutmck'] = True
print(
'This grid was sorted using CutMcK. The nodes were resorted!')
else:
self.header['cutmck'] = False
# Rearrange nodes when CutMcK was used.
if(self.header['cutmck']):
nodes_cutmck = np.empty_like(nodes_raw)
nodes_cutmck_index = np.zeros(nodes_raw.shape[0], dtype=int)
for node in range(0, self.header['nr_nodes']):
new_index = np.where(nodes_raw[:, 0].astype(int) == (node + 1))
nodes_cutmck[new_index[0], 1:3] = nodes_raw[node, 1:3]
nodes_cutmck[new_index[0], 0] = new_index[0]
nodes_cutmck_index[node] = new_index[0]
# sort them
nodes_sorted = nodes_cutmck[nodes_cutmck_index, :]
nodes['presort'] = nodes_cutmck
nodes['cutmck_index'] = nodes_cutmck_index
nodes['rev_cutmck_index'] = np.argsort(nodes_cutmck_index)
else:
nodes_sorted = nodes_raw
nodes['presort'] = nodes_raw
# prepare node dict
nodes['raw'] = nodes_raw
nodes['sorted'] = nodes_sorted
self.nodes = nodes
self.nr_of_nodes = nodes['raw'].shape[0] | python | def _read_elem_nodes(self, fid):
""" Read the nodes from an opened elem.dat file. Correct for CutMcK
transformations.
We store three typed of nodes in the dict 'nodes':
* "raw" : as read from the elem.dat file
* "presort" : pre-sorted so we can directly read node numbers from
a elec.dat file and use them as indices.
* "sorted" : completely sorted as in the original grid (before any
CutMcK)
For completeness, we also store the following keys:
* "cutmck_index" : Array containing the indices in "presort" to
obtain the "sorted" values:
nodes['sorted'] = nodes['presort'] [nodes['cutmck_index'], :]
* "rev_cutmck_index" : argsort(cutmck_index)
"""
nodes = {}
# # prepare nodes
# nodes_sorted = np.zeros((number_of_nodes, 3), dtype=float)
# nodes = np.zeros((number_of_nodes, 3), dtype=float)
# read in nodes
nodes_raw = np.empty((self.header['nr_nodes'], 3), dtype=float)
for nr in range(0, self.header['nr_nodes']):
node_line = fid.readline().lstrip()
nodes_raw[nr, :] = np.fromstring(
node_line, dtype=float, sep=' ')
# round node coordinates to 5th decimal point. Sometimes this is
# important when we deal with mal-formatted node data
nodes_raw[:, 1:3] = np.round(nodes_raw[:, 1:3], 5)
# check for CutMcK
# The check is based on the first node, but if one node was renumbered,
# so were all the others.
if(nodes_raw[:, 0] != list(range(1, nodes_raw.shape[0]))):
self.header['cutmck'] = True
print(
'This grid was sorted using CutMcK. The nodes were resorted!')
else:
self.header['cutmck'] = False
# Rearrange nodes when CutMcK was used.
if(self.header['cutmck']):
nodes_cutmck = np.empty_like(nodes_raw)
nodes_cutmck_index = np.zeros(nodes_raw.shape[0], dtype=int)
for node in range(0, self.header['nr_nodes']):
new_index = np.where(nodes_raw[:, 0].astype(int) == (node + 1))
nodes_cutmck[new_index[0], 1:3] = nodes_raw[node, 1:3]
nodes_cutmck[new_index[0], 0] = new_index[0]
nodes_cutmck_index[node] = new_index[0]
# sort them
nodes_sorted = nodes_cutmck[nodes_cutmck_index, :]
nodes['presort'] = nodes_cutmck
nodes['cutmck_index'] = nodes_cutmck_index
nodes['rev_cutmck_index'] = np.argsort(nodes_cutmck_index)
else:
nodes_sorted = nodes_raw
nodes['presort'] = nodes_raw
# prepare node dict
nodes['raw'] = nodes_raw
nodes['sorted'] = nodes_sorted
self.nodes = nodes
self.nr_of_nodes = nodes['raw'].shape[0] | [
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| 27c3e21a557f8df1c12455b96c4c2e00e08a5b4a | https://github.com/geophysics-ubonn/crtomo_tools/blob/27c3e21a557f8df1c12455b96c4c2e00e08a5b4a/lib/crtomo/grid.py#L160-L229 | train |
geophysics-ubonn/crtomo_tools | lib/crtomo/grid.py | crt_grid.calculate_dimensions | def calculate_dimensions(self):
"""For a regular grid, calculate the element and node dimensions
"""
x_coordinates = np.sort(self.grid['x'][:, 0]) # first x node
self.nr_nodes_z = np.where(x_coordinates == x_coordinates[0])[0].size
self.nr_elements_x = self.elements.shape[0] / (self.nr_nodes_z - 1)
self.nr_nodes_x = self.nr_elements_x + 1
self.nr_elements_z = self.nr_nodes_z - 1 | python | def calculate_dimensions(self):
"""For a regular grid, calculate the element and node dimensions
"""
x_coordinates = np.sort(self.grid['x'][:, 0]) # first x node
self.nr_nodes_z = np.where(x_coordinates == x_coordinates[0])[0].size
self.nr_elements_x = self.elements.shape[0] / (self.nr_nodes_z - 1)
self.nr_nodes_x = self.nr_elements_x + 1
self.nr_elements_z = self.nr_nodes_z - 1 | [
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| 27c3e21a557f8df1c12455b96c4c2e00e08a5b4a | https://github.com/geophysics-ubonn/crtomo_tools/blob/27c3e21a557f8df1c12455b96c4c2e00e08a5b4a/lib/crtomo/grid.py#L306-L313 | train |
geophysics-ubonn/crtomo_tools | lib/crtomo/grid.py | crt_grid._read_elem_neighbors | def _read_elem_neighbors(self, fid):
"""Read the boundary-element-neighbors from the end of the file
"""
# get number of boundary elements
# types 11 and 12 are boundary elements
sizes = sum([len(self.element_data[key]) for key in (11, 12) if
self.element_data.get(key, None) is not None])
self.neighbors = []
try:
for i in range(0, sizes):
self.neighbors.append(int(fid.readline().strip()))
except Exception as e:
raise Exception('Not enough neighbors in file') | python | def _read_elem_neighbors(self, fid):
"""Read the boundary-element-neighbors from the end of the file
"""
# get number of boundary elements
# types 11 and 12 are boundary elements
sizes = sum([len(self.element_data[key]) for key in (11, 12) if
self.element_data.get(key, None) is not None])
self.neighbors = []
try:
for i in range(0, sizes):
self.neighbors.append(int(fid.readline().strip()))
except Exception as e:
raise Exception('Not enough neighbors in file') | [
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| 27c3e21a557f8df1c12455b96c4c2e00e08a5b4a | https://github.com/geophysics-ubonn/crtomo_tools/blob/27c3e21a557f8df1c12455b96c4c2e00e08a5b4a/lib/crtomo/grid.py#L330-L343 | train |
geophysics-ubonn/crtomo_tools | lib/crtomo/grid.py | crt_grid.load_grid | def load_grid(self, elem_file, elec_file):
"""Load elem.dat and elec.dat
"""
self.load_elem_file(elem_file)
self.load_elec_file(elec_file) | python | def load_grid(self, elem_file, elec_file):
"""Load elem.dat and elec.dat
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self.load_elem_file(elem_file)
self.load_elec_file(elec_file) | [
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| 27c3e21a557f8df1c12455b96c4c2e00e08a5b4a | https://github.com/geophysics-ubonn/crtomo_tools/blob/27c3e21a557f8df1c12455b96c4c2e00e08a5b4a/lib/crtomo/grid.py#L411-L415 | train |
geophysics-ubonn/crtomo_tools | lib/crtomo/grid.py | crt_grid.get_element_centroids | def get_element_centroids(self):
"""return the central points of all elements
Returns
-------
Nx2 array
x/z coordinates for all (N) elements
"""
centroids = np.vstack((
np.mean(self.grid['x'], axis=1), np.mean(self.grid['z'], axis=1)
)).T
return centroids | python | def get_element_centroids(self):
"""return the central points of all elements
Returns
-------
Nx2 array
x/z coordinates for all (N) elements
"""
centroids = np.vstack((
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x/z coordinates for all (N) elements | [
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| 27c3e21a557f8df1c12455b96c4c2e00e08a5b4a | https://github.com/geophysics-ubonn/crtomo_tools/blob/27c3e21a557f8df1c12455b96c4c2e00e08a5b4a/lib/crtomo/grid.py#L494-L506 | train |
geophysics-ubonn/crtomo_tools | lib/crtomo/grid.py | crt_grid.get_internal_angles | def get_internal_angles(self):
"""Compute all internal angles of the grid
Returns
-------
numpy.ndarray
NxK array with N the number of elements, and K the number of nodes,
filled with the internal angles in degrees
"""
angles = []
for elx, elz in zip(self.grid['x'], self.grid['z']):
el_angles = []
xy = np.vstack((elx, elz))
for i in range(0, elx.size):
i1 = (i - 1) % elx.size
i2 = (i + 1) % elx.size
a = (xy[:, i] - xy[:, i1])
b = (xy[:, i2] - xy[:, i])
# note that nodes are ordered counter-clockwise!
angle = np.pi - np.arctan2(
a[0] * b[1] - a[1] * b[0],
a[0] * b[0] + a[1] * b[1]
)
el_angles.append(angle * 180 / np.pi)
angles.append(el_angles)
return np.array(angles) | python | def get_internal_angles(self):
"""Compute all internal angles of the grid
Returns
-------
numpy.ndarray
NxK array with N the number of elements, and K the number of nodes,
filled with the internal angles in degrees
"""
angles = []
for elx, elz in zip(self.grid['x'], self.grid['z']):
el_angles = []
xy = np.vstack((elx, elz))
for i in range(0, elx.size):
i1 = (i - 1) % elx.size
i2 = (i + 1) % elx.size
a = (xy[:, i] - xy[:, i1])
b = (xy[:, i2] - xy[:, i])
# note that nodes are ordered counter-clockwise!
angle = np.pi - np.arctan2(
a[0] * b[1] - a[1] * b[0],
a[0] * b[0] + a[1] * b[1]
)
el_angles.append(angle * 180 / np.pi)
angles.append(el_angles)
return np.array(angles) | [
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| 27c3e21a557f8df1c12455b96c4c2e00e08a5b4a | https://github.com/geophysics-ubonn/crtomo_tools/blob/27c3e21a557f8df1c12455b96c4c2e00e08a5b4a/lib/crtomo/grid.py#L519-L547 | train |
geophysics-ubonn/crtomo_tools | lib/crtomo/grid.py | crt_grid.Wm | def Wm(self):
"""Return the smoothing regularization matrix Wm of the grid
"""
centroids = self.get_element_centroids()
Wm = scipy.sparse.csr_matrix(
(self.nr_of_elements, self.nr_of_elements))
# Wm = np.zeros((self.nr_of_elements, self.nr_of_elements))
for i, nb in enumerate(self.element_neighbors):
for j, edges in zip(nb, self.element_neighbors_edges[i]):
# side length
edge_coords = self.nodes['presort'][edges][:, 1:]
edge_length = np.linalg.norm(
edge_coords[1, :] - edge_coords[0, :]
)
distance = np.linalg.norm(centroids[i] - centroids[j])
# main diagonal
Wm[i, i] += edge_length / distance
# side diagonals
Wm[i, j] -= edge_length / distance
return Wm | python | def Wm(self):
"""Return the smoothing regularization matrix Wm of the grid
"""
centroids = self.get_element_centroids()
Wm = scipy.sparse.csr_matrix(
(self.nr_of_elements, self.nr_of_elements))
# Wm = np.zeros((self.nr_of_elements, self.nr_of_elements))
for i, nb in enumerate(self.element_neighbors):
for j, edges in zip(nb, self.element_neighbors_edges[i]):
# side length
edge_coords = self.nodes['presort'][edges][:, 1:]
edge_length = np.linalg.norm(
edge_coords[1, :] - edge_coords[0, :]
)
distance = np.linalg.norm(centroids[i] - centroids[j])
# main diagonal
Wm[i, i] += edge_length / distance
# side diagonals
Wm[i, j] -= edge_length / distance
return Wm | [
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| 27c3e21a557f8df1c12455b96c4c2e00e08a5b4a | https://github.com/geophysics-ubonn/crtomo_tools/blob/27c3e21a557f8df1c12455b96c4c2e00e08a5b4a/lib/crtomo/grid.py#L672-L694 | train |
geophysics-ubonn/crtomo_tools | lib/crtomo/tdManager.py | tdMan.create_tomodir | def create_tomodir(self, directory):
"""Create a tomodir subdirectory structure in the given directory
"""
pwd = os.getcwd()
if not os.path.isdir(directory):
os.makedirs(directory)
os.chdir(directory)
directories = (
'config',
'exe',
'grid',
'mod',
'mod/pot',
'mod/sens',
'rho',
)
for directory in directories:
if not os.path.isdir(directory):
os.makedirs(directory)
os.chdir(pwd) | python | def create_tomodir(self, directory):
"""Create a tomodir subdirectory structure in the given directory
"""
pwd = os.getcwd()
if not os.path.isdir(directory):
os.makedirs(directory)
os.chdir(directory)
directories = (
'config',
'exe',
'grid',
'mod',
'mod/pot',
'mod/sens',
'rho',
)
for directory in directories:
if not os.path.isdir(directory):
os.makedirs(directory)
os.chdir(pwd) | [
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| 27c3e21a557f8df1c12455b96c4c2e00e08a5b4a | https://github.com/geophysics-ubonn/crtomo_tools/blob/27c3e21a557f8df1c12455b96c4c2e00e08a5b4a/lib/crtomo/tdManager.py#L260-L281 | train |
geophysics-ubonn/crtomo_tools | lib/crtomo/tdManager.py | tdMan.load_rho_file | def load_rho_file(self, filename):
"""Load a forward model from a rho.dat file
Parameters
----------
filename: string
filename to rho.dat file
Returns
-------
pid_mag: int
parameter id for the magnitude model
pid_pha: int
parameter id for the phase model
"""
pids = self.parman.load_from_rho_file(filename)
self.register_magnitude_model(pids[0])
self.register_phase_model(pids[1])
return pids | python | def load_rho_file(self, filename):
"""Load a forward model from a rho.dat file
Parameters
----------
filename: string
filename to rho.dat file
Returns
-------
pid_mag: int
parameter id for the magnitude model
pid_pha: int
parameter id for the phase model
"""
pids = self.parman.load_from_rho_file(filename)
self.register_magnitude_model(pids[0])
self.register_phase_model(pids[1])
return pids | [
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Returns
-------
pid_mag: int
parameter id for the magnitude model
pid_pha: int
parameter id for the phase model | [
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| 27c3e21a557f8df1c12455b96c4c2e00e08a5b4a | https://github.com/geophysics-ubonn/crtomo_tools/blob/27c3e21a557f8df1c12455b96c4c2e00e08a5b4a/lib/crtomo/tdManager.py#L295-L314 | train |
geophysics-ubonn/crtomo_tools | lib/crtomo/tdManager.py | tdMan.save_to_tomodir | def save_to_tomodir(self, directory):
"""Save the tomodir instance to a directory structure.
Note
----
Test cases:
* modeling only
* inversion only
* modeling and inversion
"""
self.create_tomodir(directory)
self.grid.save_elem_file(
directory + os.sep + 'grid/elem.dat'
)
self.grid.save_elec_file(
directory + os.sep + 'grid/elec.dat'
)
# modeling
if self.configs.configs is not None:
self.configs.write_crmod_config(
directory + os.sep + 'config/config.dat'
)
if self.assignments['forward_model'] is not None:
self.parman.save_to_rho_file(
directory + os.sep + 'rho/rho.dat',
self.assignments['forward_model'][0],
self.assignments['forward_model'][1],
)
self.crmod_cfg.write_to_file(
directory + os.sep + 'exe/crmod.cfg'
)
if self.assignments['measurements'] is not None:
self.configs.write_crmod_volt(
directory + os.sep + 'mod/volt.dat',
self.assignments['measurements']
)
if self.assignments['sensitivities'] is not None:
self._save_sensitivities(
directory + os.sep + 'mod/sens',
)
if self.assignments['potentials'] is not None:
self._save_potentials(
directory + os.sep + 'mod/pot',
)
# inversion
self.crtomo_cfg.write_to_file(
directory + os.sep + 'exe/crtomo.cfg'
)
if self.noise_model is not None:
self.noise_model.write_crt_noisemod(
directory + os.sep + 'exe/crt.noisemod'
)
if not os.path.isdir(directory + os.sep + 'inv'):
os.makedirs(directory + os.sep + 'inv') | python | def save_to_tomodir(self, directory):
"""Save the tomodir instance to a directory structure.
Note
----
Test cases:
* modeling only
* inversion only
* modeling and inversion
"""
self.create_tomodir(directory)
self.grid.save_elem_file(
directory + os.sep + 'grid/elem.dat'
)
self.grid.save_elec_file(
directory + os.sep + 'grid/elec.dat'
)
# modeling
if self.configs.configs is not None:
self.configs.write_crmod_config(
directory + os.sep + 'config/config.dat'
)
if self.assignments['forward_model'] is not None:
self.parman.save_to_rho_file(
directory + os.sep + 'rho/rho.dat',
self.assignments['forward_model'][0],
self.assignments['forward_model'][1],
)
self.crmod_cfg.write_to_file(
directory + os.sep + 'exe/crmod.cfg'
)
if self.assignments['measurements'] is not None:
self.configs.write_crmod_volt(
directory + os.sep + 'mod/volt.dat',
self.assignments['measurements']
)
if self.assignments['sensitivities'] is not None:
self._save_sensitivities(
directory + os.sep + 'mod/sens',
)
if self.assignments['potentials'] is not None:
self._save_potentials(
directory + os.sep + 'mod/pot',
)
# inversion
self.crtomo_cfg.write_to_file(
directory + os.sep + 'exe/crtomo.cfg'
)
if self.noise_model is not None:
self.noise_model.write_crt_noisemod(
directory + os.sep + 'exe/crt.noisemod'
)
if not os.path.isdir(directory + os.sep + 'inv'):
os.makedirs(directory + os.sep + 'inv') | [
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* inversion only
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| 27c3e21a557f8df1c12455b96c4c2e00e08a5b4a | https://github.com/geophysics-ubonn/crtomo_tools/blob/27c3e21a557f8df1c12455b96c4c2e00e08a5b4a/lib/crtomo/tdManager.py#L316-L383 | train |
geophysics-ubonn/crtomo_tools | lib/crtomo/tdManager.py | tdMan._save_sensitivities | def _save_sensitivities(self, directory):
"""save sensitivities to a directory
"""
print('saving sensitivities')
digits = int(np.ceil(np.log10(self.configs.configs.shape[0])))
for i in range(0, self.configs.configs.shape[0]):
sens_data, meta_data = self.get_sensitivity(i)
filename_raw = 'sens{0:0' + '{0}'.format(digits) + '}.dat'
filename = directory + os.sep + filename_raw.format(i + 1)
grid_xz = self.grid.get_element_centroids()
all_data = np.vstack((
grid_xz[:, 0],
grid_xz[:, 0],
sens_data[0],
sens_data[1],
)).T
with open(filename, 'wb') as fid:
fid.write(bytes(
'{0} {1}\n'.format(meta_data[0], meta_data[1]),
'utf-8'
))
np.savetxt(fid, all_data) | python | def _save_sensitivities(self, directory):
"""save sensitivities to a directory
"""
print('saving sensitivities')
digits = int(np.ceil(np.log10(self.configs.configs.shape[0])))
for i in range(0, self.configs.configs.shape[0]):
sens_data, meta_data = self.get_sensitivity(i)
filename_raw = 'sens{0:0' + '{0}'.format(digits) + '}.dat'
filename = directory + os.sep + filename_raw.format(i + 1)
grid_xz = self.grid.get_element_centroids()
all_data = np.vstack((
grid_xz[:, 0],
grid_xz[:, 0],
sens_data[0],
sens_data[1],
)).T
with open(filename, 'wb') as fid:
fid.write(bytes(
'{0} {1}\n'.format(meta_data[0], meta_data[1]),
'utf-8'
))
np.savetxt(fid, all_data) | [
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| 27c3e21a557f8df1c12455b96c4c2e00e08a5b4a | https://github.com/geophysics-ubonn/crtomo_tools/blob/27c3e21a557f8df1c12455b96c4c2e00e08a5b4a/lib/crtomo/tdManager.py#L385-L407 | train |
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