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phac-nml/sistr_cmd | sistr/src/cgmlst/extras/centroid_cgmlst_alleles.py | seq_int_arr | def seq_int_arr(seqs):
"""Convert list of ACGT strings to matix of 1-4 ints
Args:
seqs (list of str): nucleotide sequences with only 'ACGT' characters
Returns:
numpy.array of int: matrix of integers from 1 to 4 inclusive representing A, C, G, and T
str: nucleotide sequence string
... | python | def seq_int_arr(seqs):
"""Convert list of ACGT strings to matix of 1-4 ints
Args:
seqs (list of str): nucleotide sequences with only 'ACGT' characters
Returns:
numpy.array of int: matrix of integers from 1 to 4 inclusive representing A, C, G, and T
str: nucleotide sequence string
... | [
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phac-nml/sistr_cmd | sistr/src/cgmlst/extras/centroid_cgmlst_alleles.py | group_alleles_by_start_end_Xbp | def group_alleles_by_start_end_Xbp(arr, bp=28):
"""Group alleles by matching ends
Args:
arr (numpy.array): 2D int matrix of alleles
bp (int): length of ends to group by
Returns:
dict of lists: key of start + end strings to list of indices of alleles with matching ends
"""
s... | python | def group_alleles_by_start_end_Xbp(arr, bp=28):
"""Group alleles by matching ends
Args:
arr (numpy.array): 2D int matrix of alleles
bp (int): length of ends to group by
Returns:
dict of lists: key of start + end strings to list of indices of alleles with matching ends
"""
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phac-nml/sistr_cmd | sistr/src/cgmlst/extras/centroid_cgmlst_alleles.py | allele_clusters | def allele_clusters(dists, t=0.025):
"""Flat clusters from distance matrix
Args:
dists (numpy.array): pdist distance matrix
t (float): fcluster (tree cutting) distance threshold
Returns:
dict of lists: cluster number to list of indices of distances in cluster
"""
clusters =... | python | def allele_clusters(dists, t=0.025):
"""Flat clusters from distance matrix
Args:
dists (numpy.array): pdist distance matrix
t (float): fcluster (tree cutting) distance threshold
Returns:
dict of lists: cluster number to list of indices of distances in cluster
"""
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phac-nml/sistr_cmd | sistr/src/cgmlst/extras/centroid_cgmlst_alleles.py | min_row_dist_sum_idx | def min_row_dist_sum_idx(dists):
"""Find the index of the row with the minimum row distance sum
This should return the index of the row index with the least distance overall
to all other rows.
Args:
dists (np.array): must be square distance matrix
Returns:
int: index of row wit... | python | def min_row_dist_sum_idx(dists):
"""Find the index of the row with the minimum row distance sum
This should return the index of the row index with the least distance overall
to all other rows.
Args:
dists (np.array): must be square distance matrix
Returns:
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phac-nml/sistr_cmd | sistr/src/cgmlst/extras/centroid_cgmlst_alleles.py | find_centroid_alleles | def find_centroid_alleles(alleles, bp=28, t=0.025):
"""Reduce list of alleles to set of centroid alleles based on size grouping, ends matching and hierarchical clustering
Workflow for finding centroid alleles:
- grouping by size (e.g. 100bp, 101bp, 103bp, etc)
- then grouped by `bp` nucleotides at end... | python | def find_centroid_alleles(alleles, bp=28, t=0.025):
"""Reduce list of alleles to set of centroid alleles based on size grouping, ends matching and hierarchical clustering
Workflow for finding centroid alleles:
- grouping by size (e.g. 100bp, 101bp, 103bp, etc)
- then grouped by `bp` nucleotides at end... | [
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phac-nml/sistr_cmd | sistr/src/mash.py | mash_dist_trusted | def mash_dist_trusted(fasta_path):
"""
Compute Mash distances of sketch file of genome fasta to RefSeq sketch DB.
Args:
mash_bin (str): Mash binary path
Returns:
(str): Mash STDOUT string
"""
args = [MASH_BIN,
'dist',
MASH_SKETCH_FILE,
fasta_... | python | def mash_dist_trusted(fasta_path):
"""
Compute Mash distances of sketch file of genome fasta to RefSeq sketch DB.
Args:
mash_bin (str): Mash binary path
Returns:
(str): Mash STDOUT string
"""
args = [MASH_BIN,
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phac-nml/sistr_cmd | sistr/src/cgmlst/extras/hclust_cutree.py | nr_profiles | def nr_profiles(arr, genomes):
"""
Get a condensed cgMLST pairwise distance matrix for specified Genomes_
where condensed means redundant cgMLST profiles are only represented once in the distance matrix.
Args:
user_name (list): List of Genome_ names to retrieve condensed distance matrix for
... | python | def nr_profiles(arr, genomes):
"""
Get a condensed cgMLST pairwise distance matrix for specified Genomes_
where condensed means redundant cgMLST profiles are only represented once in the distance matrix.
Args:
user_name (list): List of Genome_ names to retrieve condensed distance matrix for
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phac-nml/sistr_cmd | sistr/src/serovar_prediction/__init__.py | overall_serovar_call | def overall_serovar_call(serovar_prediction, antigen_predictor):
"""
Predict serovar from cgMLST cluster membership analysis and antigen BLAST results.
SerovarPrediction object is assigned H1, H2 and Serogroup from the antigen BLAST results.
Antigen BLAST results will predict a particular serovar or lis... | python | def overall_serovar_call(serovar_prediction, antigen_predictor):
"""
Predict serovar from cgMLST cluster membership analysis and antigen BLAST results.
SerovarPrediction object is assigned H1, H2 and Serogroup from the antigen BLAST results.
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phac-nml/sistr_cmd | sistr/src/cgmlst/__init__.py | process_cgmlst_results | def process_cgmlst_results(df):
"""Append informative fields to cgMLST330 BLAST results DataFrame
The `qseqid` column must contain cgMLST330 query IDs with `{marker name}|{allele number}` format.
The `qseqid` parsed allele numbers and marker names are appended as new fields.
`is_perfect` column contai... | python | def process_cgmlst_results(df):
"""Append informative fields to cgMLST330 BLAST results DataFrame
The `qseqid` column must contain cgMLST330 query IDs with `{marker name}|{allele number}` format.
The `qseqid` parsed allele numbers and marker names are appended as new fields.
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phac-nml/sistr_cmd | sistr/src/cgmlst/__init__.py | alleles_to_retrieve | def alleles_to_retrieve(df):
"""Alleles to retrieve from genome fasta
Get a dict of the genome fasta contig title to a list of blastn results of the allele sequences that must be
retrieved from the genome contig.
Args:
df (pandas.DataFrame): blastn results dataframe
Returns:
{str:... | python | def alleles_to_retrieve(df):
"""Alleles to retrieve from genome fasta
Get a dict of the genome fasta contig title to a list of blastn results of the allele sequences that must be
retrieved from the genome contig.
Args:
df (pandas.DataFrame): blastn results dataframe
Returns:
{str:... | [
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phac-nml/sistr_cmd | sistr/src/cgmlst/__init__.py | matches_to_marker_results | def matches_to_marker_results(df):
"""Perfect BLAST matches to marker results dict
Parse perfect BLAST matches to marker results dict.
Args:
df (pandas.DataFrame): DataFrame of perfect BLAST matches
Returns:
dict: cgMLST330 marker names to matching allele numbers
"""
assert i... | python | def matches_to_marker_results(df):
"""Perfect BLAST matches to marker results dict
Parse perfect BLAST matches to marker results dict.
Args:
df (pandas.DataFrame): DataFrame of perfect BLAST matches
Returns:
dict: cgMLST330 marker names to matching allele numbers
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phac-nml/sistr_cmd | sistr/src/cgmlst/__init__.py | cgmlst_subspecies_call | def cgmlst_subspecies_call(df_relatives):
"""Call Salmonella subspecies based on cgMLST results
This method attempts to find the majority subspecies type within curated
public genomes above a cgMLST allelic profile distance threshold.
Note:
``CGMLST_SUBSPECIATION_DISTANCE_THRESHOLD`` is the cg... | python | def cgmlst_subspecies_call(df_relatives):
"""Call Salmonella subspecies based on cgMLST results
This method attempts to find the majority subspecies type within curated
public genomes above a cgMLST allelic profile distance threshold.
Note:
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phac-nml/sistr_cmd | sistr/sistr_cmd.py | genome_name_from_fasta_path | def genome_name_from_fasta_path(fasta_path):
"""Extract genome name from fasta filename
Get the filename without directory and remove the file extension.
Example:
With fasta file path ``/path/to/genome_1.fasta``::
fasta_path = '/path/to/genome_1.fasta'
genome_name = genome... | python | def genome_name_from_fasta_path(fasta_path):
"""Extract genome name from fasta filename
Get the filename without directory and remove the file extension.
Example:
With fasta file path ``/path/to/genome_1.fasta``::
fasta_path = '/path/to/genome_1.fasta'
genome_name = genome... | [
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phac-nml/sistr_cmd | sistr/misc/add_ref_genomes.py | sketch_fasta | def sketch_fasta(fasta_path, outdir):
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fasta_path (str): input fasta file path. Genome name in fasta filename
outdir (str): output directory path to write Mash sketch file to
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str: output Mash sketch file path
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outdir (str): output directory path to write Mash sketch file to
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mbr/simplekv | simplekv/__init__.py | KeyValueStore.get_file | def get_file(self, key, file):
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mbr/simplekv | simplekv/__init__.py | KeyValueStore.put_file | def put_file(self, key, file):
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mbr/simplekv | simplekv/__init__.py | CopyMixin.copy | def copy(self, source, dest):
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:param dest: The destination for the copy
:returns: The destination key
:raises: exceptions.ValueError: If the source or target key are not valid
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napalm-automation/napalm-eos | napalm_eos/eos.py | EOSDriver.compare_config | def compare_config(self):
"""Implementation of NAPALM method compare_config."""
if self.config_session is None:
return ''
else:
commands = ['show session-config named %s diffs' % self.config_session]
result = self.device.run_commands(commands, encoding='text')... | python | def compare_config(self):
"""Implementation of NAPALM method compare_config."""
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napalm-automation/napalm-eos | napalm_eos/eos.py | EOSDriver.discard_config | def discard_config(self):
"""Implementation of NAPALM method discard_config."""
if self.config_session is not None:
commands = []
commands.append('configure session {}'.format(self.config_session))
commands.append('abort')
self.device.run_commands(commands... | python | def discard_config(self):
"""Implementation of NAPALM method discard_config."""
if self.config_session is not None:
commands = []
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napalm-automation/napalm-eos | napalm_eos/eos.py | EOSDriver.rollback | def rollback(self):
"""Implementation of NAPALM method rollback."""
commands = []
commands.append('configure replace flash:rollback-0')
commands.append('write memory')
self.device.run_commands(commands) | python | def rollback(self):
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commands = []
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napalm-automation/napalm-eos | napalm_eos/eos.py | EOSDriver.get_facts | def get_facts(self):
"""Implementation of NAPALM method get_facts."""
commands = []
commands.append('show version')
commands.append('show hostname')
commands.append('show interfaces')
result = self.device.run_commands(commands)
version = result[0]
hostna... | python | def get_facts(self):
"""Implementation of NAPALM method get_facts."""
commands = []
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napalm-automation/napalm-eos | napalm_eos/eos.py | EOSDriver.get_config | def get_config(self, retrieve="all"):
"""get_config implementation for EOS."""
get_startup = retrieve == "all" or retrieve == "startup"
get_running = retrieve == "all" or retrieve == "running"
get_candidate = (retrieve == "all" or retrieve == "candidate") and self.config_session
... | python | def get_config(self, retrieve="all"):
"""get_config implementation for EOS."""
get_startup = retrieve == "all" or retrieve == "startup"
get_running = retrieve == "all" or retrieve == "running"
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mbr/simplekv | simplekv/net/botostore.py | map_boto_exceptions | def map_boto_exceptions(key=None, exc_pass=()):
"""Map boto-specific exceptions to the simplekv-API."""
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try:
yield
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if e.code == 'NoSuchKey':
raise Key... | python | def map_boto_exceptions(key=None, exc_pass=()):
"""Map boto-specific exceptions to the simplekv-API."""
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mbr/simplekv | simplekv/net/azurestore.py | _file_md5 | def _file_md5(file_):
"""
Compute the md5 digest of a file in base64 encoding.
"""
md5 = hashlib.md5()
chunk_size = 128 * md5.block_size
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byte_digest = md5.digest()
return base64.b64encode(... | python | def _file_md5(file_):
"""
Compute the md5 digest of a file in base64 encoding.
"""
md5 = hashlib.md5()
chunk_size = 128 * md5.block_size
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mbr/simplekv | simplekv/net/azurestore.py | _byte_buffer_md5 | def _byte_buffer_md5(buffer_):
"""
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byte_digest = md5.digest()
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"""
Computes the md5 digest of a byte buffer in base64 encoding.
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mbr/simplekv | simplekv/net/azurestore.py | map_azure_exceptions | def map_azure_exceptions(key=None, exc_pass=()):
"""Map Azure-specific exceptions to the simplekv-API."""
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AzureException
try:
yield
except AzureMissingResourceHttpError as ex:
if ex.__class__.__name__ not in... | python | def map_azure_exceptions(key=None, exc_pass=()):
"""Map Azure-specific exceptions to the simplekv-API."""
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mbr/simplekv | simplekv/net/azurestore.py | IOInterface.read | def read(self, size=-1):
"""Returns 'size' amount of bytes or less if there is no more data.
If no size is given all data is returned. size can be >= 0."""
if self.closed:
raise ValueError("I/O operation on closed file")
with map_azure_exceptions(key=self.key):
if... | python | def read(self, size=-1):
"""Returns 'size' amount of bytes or less if there is no more data.
If no size is given all data is returned. size can be >= 0."""
if self.closed:
raise ValueError("I/O operation on closed file")
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mbr/simplekv | simplekv/net/azurestore.py | IOInterface.seek | def seek(self, offset, whence=0):
"""Move to a new offset either relative or absolute. whence=0 is
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Any relative or absolute seek operation which would result in a
negative position is undefined and that case can be ignored... | python | def seek(self, offset, whence=0):
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mbr/simplekv | simplekv/git.py | _on_tree | def _on_tree(repo, tree, components, obj):
"""Mounts an object on a tree, using the given path components.
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:param components: A list of strings of subpaths (i.e. ['foo', 'bar'] is
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:param obj: Object to mount. If None... | python | def _on_tree(repo, tree, components, obj):
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SUSE-Enceladus/ipa | ipa/ipa_ec2.py | EC2Cloud._connect | def _connect(self):
"""Connect to ec2 resource."""
resource = None
try:
resource = boto3.resource(
'ec2',
aws_access_key_id=self.access_key_id,
aws_secret_access_key=self.secret_access_key,
region_name=self.region
... | python | def _connect(self):
"""Connect to ec2 resource."""
resource = None
try:
resource = boto3.resource(
'ec2',
aws_access_key_id=self.access_key_id,
aws_secret_access_key=self.secret_access_key,
region_name=self.region
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SUSE-Enceladus/ipa | ipa/ipa_ec2.py | EC2Cloud._get_user_data | def _get_user_data(self):
"""
Return formatted bash script string.
The public ssh key is added by cloud init to the instance based on
the ssh user and private key file.
"""
key = ipa_utils.generate_public_ssh_key(
self.ssh_private_key_file
).decode()
... | python | def _get_user_data(self):
"""
Return formatted bash script string.
The public ssh key is added by cloud init to the instance based on
the ssh user and private key file.
"""
key = ipa_utils.generate_public_ssh_key(
self.ssh_private_key_file
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SUSE-Enceladus/ipa | ipa/ipa_ec2.py | EC2Cloud._set_instance_ip | def _set_instance_ip(self):
"""
Retrieve instance ip and cache it.
Current preference is for public ipv4, ipv6 and private.
"""
instance = self._get_instance()
# ipv6
try:
ipv6 = instance.network_interfaces[0].ipv6_addresses[0]
except (IndexE... | python | def _set_instance_ip(self):
"""
Retrieve instance ip and cache it.
Current preference is for public ipv4, ipv6 and private.
"""
instance = self._get_instance()
# ipv6
try:
ipv6 = instance.network_interfaces[0].ipv6_addresses[0]
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tgbugs/pyontutils | pyontutils/process_fixed.py | _process_worker | def _process_worker(call_queue, result_queue):
""" This worker is wrapped to block KeyboardInterrupt """
signal.signal(signal.SIGINT, signal.SIG_IGN) #block ctrl-c
return _process_worker_base(call_queue, result_queue) | python | def _process_worker(call_queue, result_queue):
""" This worker is wrapped to block KeyboardInterrupt """
signal.signal(signal.SIGINT, signal.SIG_IGN) #block ctrl-c
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SUSE-Enceladus/ipa | ipa/ipa_distro.py | Distro._set_init_system | def _set_init_system(self, client):
"""Determine the init system of distribution."""
if not self.init_system:
try:
out = ipa_utils.execute_ssh_command(
client,
'ps -p 1 -o comm='
)
except Exception as e:
... | python | def _set_init_system(self, client):
"""Determine the init system of distribution."""
if not self.init_system:
try:
out = ipa_utils.execute_ssh_command(
client,
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except Exception as e:
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SUSE-Enceladus/ipa | ipa/ipa_distro.py | Distro.get_vm_info | def get_vm_info(self, client):
"""Return vm info."""
out = ''
self._set_init_system(client)
if self.init_system == 'systemd':
try:
out += 'systemd-analyze:\n\n'
out += ipa_utils.execute_ssh_command(
client,
... | python | def get_vm_info(self, client):
"""Return vm info."""
out = ''
self._set_init_system(client)
if self.init_system == 'systemd':
try:
out += 'systemd-analyze:\n\n'
out += ipa_utils.execute_ssh_command(
client,
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SUSE-Enceladus/ipa | ipa/ipa_distro.py | Distro.install_package | def install_package(self, client, package):
"""Install package on instance."""
install_cmd = "{sudo} '{install} {package}'".format(
sudo=self.get_sudo_exec_wrapper(),
install=self.get_install_cmd(),
package=package
)
try:
out = ipa_utils.e... | python | def install_package(self, client, package):
"""Install package on instance."""
install_cmd = "{sudo} '{install} {package}'".format(
sudo=self.get_sudo_exec_wrapper(),
install=self.get_install_cmd(),
package=package
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try:
out = ipa_utils.e... | [
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SUSE-Enceladus/ipa | ipa/ipa_distro.py | Distro.reboot | def reboot(self, client):
"""Execute reboot command on instance."""
self._set_init_system(client)
reboot_cmd = "{sudo} '{stop_ssh};{reboot}'".format(
sudo=self.get_sudo_exec_wrapper(),
stop_ssh=self.get_stop_ssh_service_cmd(),
reboot=self.get_reboot_cmd()
... | python | def reboot(self, client):
"""Execute reboot command on instance."""
self._set_init_system(client)
reboot_cmd = "{sudo} '{stop_ssh};{reboot}'".format(
sudo=self.get_sudo_exec_wrapper(),
stop_ssh=self.get_stop_ssh_service_cmd(),
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SUSE-Enceladus/ipa | ipa/ipa_distro.py | Distro.update | def update(self, client):
"""Execute update command on instance."""
update_cmd = "{sudo} '{refresh};{update}'".format(
sudo=self.get_sudo_exec_wrapper(),
refresh=self.get_refresh_repo_cmd(),
update=self.get_update_cmd()
)
out = ''
try:
... | python | def update(self, client):
"""Execute update command on instance."""
update_cmd = "{sudo} '{refresh};{update}'".format(
sudo=self.get_sudo_exec_wrapper(),
refresh=self.get_refresh_repo_cmd(),
update=self.get_update_cmd()
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out = ''
try:
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tgbugs/pyontutils | pyontutils/scigraph_client.py | Graph.ordered | def ordered(start, edges, predicate=None, inverse=False):
""" Depth first edges from a SciGraph response. """
s, o = 'sub', 'obj'
if inverse:
s, o = o, s
for edge in edges:
if predicate is not None and edge['pred'] != predicate:
print('scoop!')
... | python | def ordered(start, edges, predicate=None, inverse=False):
""" Depth first edges from a SciGraph response. """
s, o = 'sub', 'obj'
if inverse:
s, o = o, s
for edge in edges:
if predicate is not None and edge['pred'] != predicate:
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tgbugs/pyontutils | pyontutils/hierarchies.py | tcsort | def tcsort(item): # FIXME SUCH WOW SO INEFFICIENT O_O
""" get len of transitive closure assume type items is tree... """
return len(item[1]) + sum(tcsort(kv) for kv in item[1].items()) | python | def tcsort(item): # FIXME SUCH WOW SO INEFFICIENT O_O
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tgbugs/pyontutils | pyontutils/hierarchies.py | get_node | def get_node(start, tree, pnames):
""" for each parent find a single branch to root """
def get_first_branch(node):
if node not in pnames: # one way to hit a root
return []
if pnames[node]: # mmmm names
fp = pnames[node][0]
if cycle_check(node, fp, pnames):
... | python | def get_node(start, tree, pnames):
""" for each parent find a single branch to root """
def get_first_branch(node):
if node not in pnames: # one way to hit a root
return []
if pnames[node]: # mmmm names
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tgbugs/pyontutils | pyontutils/hierarchies.py | dematerialize | def dematerialize(parent_name, parent_node): # FIXME we need to demat more than just leaves!
#FIXME still an issue: Fornix, Striatum, Diagonal Band
""" Remove nodes higher in the tree that occur further down the
SAME branch. If they occur down OTHER branchs leave them alone.
NOTE: modifies in ... | python | def dematerialize(parent_name, parent_node): # FIXME we need to demat more than just leaves!
#FIXME still an issue: Fornix, Striatum, Diagonal Band
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tgbugs/pyontutils | ilxutils/ilxutils/interlex_sql.py | IlxSql.get_terms | def get_terms(self):
''' GROUP BY is a shortcut to only getting the first in every list of group '''
if not self.terms.empty:
return self.terms
if self.from_backup:
self.terms = open_pickle(TERMS_BACKUP_PATH)
return self.terms
engine = create_engine(se... | python | def get_terms(self):
''' GROUP BY is a shortcut to only getting the first in every list of group '''
if not self.terms.empty:
return self.terms
if self.from_backup:
self.terms = open_pickle(TERMS_BACKUP_PATH)
return self.terms
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tgbugs/pyontutils | ilxutils/ilxutils/simple_scicrunch_client.py | superclasses_bug_fix | def superclasses_bug_fix(data):
''' PHP returns "id" in superclass but only accepts superclass_tid '''
for i, value in enumerate(data['superclasses']):
data['superclasses'][i]['superclass_tid'] = data['superclasses'][i].pop('id')
return data | python | def superclasses_bug_fix(data):
''' PHP returns "id" in superclass but only accepts superclass_tid '''
for i, value in enumerate(data['superclasses']):
data['superclasses'][i]['superclass_tid'] = data['superclasses'][i].pop('id')
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tgbugs/pyontutils | ilxutils/ilxutils/simple_scicrunch_client.py | Client.log_info | def log_info(self, data):
''' Logs successful responses '''
info = 'label={label}, id={id}, ilx={ilx}, superclass_tid={super_id}'
info_filled = info.format(label = data['label'],
id = data['id'],
ilx = data['ilx'],... | python | def log_info(self, data):
''' Logs successful responses '''
info = 'label={label}, id={id}, ilx={ilx}, superclass_tid={super_id}'
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tgbugs/pyontutils | ilxutils/ilxutils/simple_scicrunch_client.py | Client.process_request | def process_request(self, req):
''' Checks to see if data returned from database is useable '''
# Check status code of request
req.raise_for_status() # if codes not in 200s; error raise
# Proper status code, but check if server returned a warning
try:
output = req.jso... | python | def process_request(self, req):
''' Checks to see if data returned from database is useable '''
# Check status code of request
req.raise_for_status() # if codes not in 200s; error raise
# Proper status code, but check if server returned a warning
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tgbugs/pyontutils | ilxutils/ilxutils/simple_scicrunch_client.py | Client.is_equal | def is_equal(self, string1, string2):
''' Simple string comparator '''
return string1.lower().strip() == string2.lower().strip() | python | def is_equal(self, string1, string2):
''' Simple string comparator '''
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tgbugs/pyontutils | ilxutils/ilxutils/simple_scicrunch_client.py | Client.are_ilx | def are_ilx(self, ilx_ids):
''' Checks list of objects to see if they are usable ILX IDs '''
total_data = []
for ilx_id in ilx_ids:
ilx_id = ilx_id.replace('http', '').replace('.', '').replace('/', '')
data, success = self.get_data_from_ilx(ilx_id)
if success:... | python | def are_ilx(self, ilx_ids):
''' Checks list of objects to see if they are usable ILX IDs '''
total_data = []
for ilx_id in ilx_ids:
ilx_id = ilx_id.replace('http', '').replace('.', '').replace('/', '')
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tgbugs/pyontutils | ilxutils/ilxutils/simple_scicrunch_client.py | Client.add_triple | def add_triple(self, subj, pred, obj):
''' Adds an entity property to an existing entity '''
subj_data, pred_data, obj_data = self.are_ilx([subj, pred, obj])
# RELATIONSHIP PROPERTY
if subj_data.get('id') and pred_data.get('id') and obj_data.get('id'):
if pred_data['type'] !=... | python | def add_triple(self, subj, pred, obj):
''' Adds an entity property to an existing entity '''
subj_data, pred_data, obj_data = self.are_ilx([subj, pred, obj])
# RELATIONSHIP PROPERTY
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tgbugs/pyontutils | ilxutils/ilxutils/simple_scicrunch_client.py | Client.add_relationship | def add_relationship(self, term1, relationship, term2):
''' Creates a relationship between 3 entities in database '''
url = self.base_path + 'term/add-relationship'
data = {'term1_id': term1['id'],
'relationship_tid': relationship['id'],
'term2_id': term2['id'],
... | python | def add_relationship(self, term1, relationship, term2):
''' Creates a relationship between 3 entities in database '''
url = self.base_path + 'term/add-relationship'
data = {'term1_id': term1['id'],
'relationship_tid': relationship['id'],
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tgbugs/pyontutils | ilxutils/ilxutils/simple_scicrunch_client.py | Client.add_annotation | def add_annotation(self, entity, annotation, value):
''' Adds an annotation proprty to existing entity '''
url = self.base_path + 'term/add-annotation'
data = {'tid': entity['id'],
'annotation_tid': annotation['id'],
'value': value,
'term_version':... | python | def add_annotation(self, entity, annotation, value):
''' Adds an annotation proprty to existing entity '''
url = self.base_path + 'term/add-annotation'
data = {'tid': entity['id'],
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tgbugs/pyontutils | ilxutils/ilxutils/simple_scicrunch_client.py | Client.custom_update | def custom_update(self, data, pred, obj):
''' Updates existing entity proprty based on the predicate input '''
if isinstance(data[pred], str): # for all simple properties of str value
data[pred] = str(obj)
else: # synonyms, superclasses, and existing_ids have special requirements
... | python | def custom_update(self, data, pred, obj):
''' Updates existing entity proprty based on the predicate input '''
if isinstance(data[pred], str): # for all simple properties of str value
data[pred] = str(obj)
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tgbugs/pyontutils | ttlser/ttlser/serializers.py | CustomTurtleSerializer.sortProperties | def sortProperties(self, properties): # modified to sort objects using their global rank
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Sort the lists of values. Return a sorted list of properties."""
# Sort object lists
for prop, objects in properties.items():
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Sort the lists of values. Return a sorted list of properties."""
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tgbugs/pyontutils | ttlser/ttlser/serializers.py | CustomTurtleSerializer._buildPredicateHash | def _buildPredicateHash(self, subject): # XXX unmodified
"""
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subject
"""
properties = {}
for s, p, o in self.store.triples((subject, None, None)):
oList = properties.get(p, [])
oList... | python | def _buildPredicateHash(self, subject): # XXX unmodified
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Build a hash key by predicate to a list of objects for the given
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tgbugs/pyontutils | ttlser/ttlser/serializers.py | CustomTurtleSerializer.isValidList | def isValidList(self, l): # modified to flatten lists specified using [ a rdf:List; ] syntax
"""
Checks if l is a valid RDF list, i.e. no nodes have other properties.
"""
try:
if self.store.value(l, RDF.first) is None:
return False
except:
... | python | def isValidList(self, l): # modified to flatten lists specified using [ a rdf:List; ] syntax
"""
Checks if l is a valid RDF list, i.e. no nodes have other properties.
"""
try:
if self.store.value(l, RDF.first) is None:
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tgbugs/pyontutils | ttlser/ttlser/serializers.py | CustomTurtleSerializer._write | def _write(self, value):
""" rename to write and import inspect to debut the callstack """
if ' ' in value:
s = inspect.stack()
fn = s[1].function
super().write('%%DEBUG {} %%'.format(fn))
super().write(value) | python | def _write(self, value):
""" rename to write and import inspect to debut the callstack """
if ' ' in value:
s = inspect.stack()
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super().write('%%DEBUG {} %%'.format(fn))
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tgbugs/pyontutils | ttlser/ttlser/serializers.py | HtmlTurtleSerializer.serialize | def serialize(self, *args, **kwargs):
""" Modified to allow additional labels to be passed in. """
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# populate labels from outside the local graph
self._labels.update(kwargs['labels'])
super(HtmlTurtleSerializer, self).serialize(*args, **kwargs) | python | def serialize(self, *args, **kwargs):
""" Modified to allow additional labels to be passed in. """
if 'labels' in kwargs:
# populate labels from outside the local graph
self._labels.update(kwargs['labels'])
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tgbugs/pyontutils | neurondm/neurondm/core.py | addLNT | def addLNT(LocalName, phenoId, predicate, g=None): # XXX deprecated
""" Add a local name for a phenotype from a pair of identifiers """
if g is None:
s = inspect.stack(0) # horribly inefficient
checkCalledInside('LocalNameManager', s)
g = s[1][0].f_locals # get globals of calling scop... | python | def addLNT(LocalName, phenoId, predicate, g=None): # XXX deprecated
""" Add a local name for a phenotype from a pair of identifiers """
if g is None:
s = inspect.stack(0) # horribly inefficient
checkCalledInside('LocalNameManager', s)
g = s[1][0].f_locals # get globals of calling scop... | [
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tgbugs/pyontutils | neurondm/neurondm/core.py | Config.load_existing | def load_existing(self):
""" advanced usage allows loading multiple sets of neurons and using a config
object to keep track of the different graphs """
from pyontutils.closed_namespaces import rdfs
# bag existing
try:
next(iter(self.neurons()))
raise ... | python | def load_existing(self):
""" advanced usage allows loading multiple sets of neurons and using a config
object to keep track of the different graphs """
from pyontutils.closed_namespaces import rdfs
# bag existing
try:
next(iter(self.neurons()))
raise ... | [
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tgbugs/pyontutils | neurondm/neurondm/core.py | graphBase.label_maker | def label_maker(self):
""" needed to defer loading of local conventions to avoid circular dependency issue """
if (not hasattr(graphBase, '_label_maker') or
graphBase._label_maker.local_conventions != graphBase.local_conventions):
graphBase._label_maker = LabelMaker(graphBase.loc... | python | def label_maker(self):
""" needed to defer loading of local conventions to avoid circular dependency issue """
if (not hasattr(graphBase, '_label_maker') or
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tgbugs/pyontutils | neurondm/neurondm/core.py | Neuron._graphify | def _graphify(self, *args, graph=None): # defined
""" Lift phenotypeEdges to Restrictions """
if graph is None:
graph = self.out_graph
################## LABELS ARE DEFINED HERE ##################
gl = self.genLabel
ll = self.localLabel
ol = self.origLabel
... | python | def _graphify(self, *args, graph=None): # defined
""" Lift phenotypeEdges to Restrictions """
if graph is None:
graph = self.out_graph
################## LABELS ARE DEFINED HERE ##################
gl = self.genLabel
ll = self.localLabel
ol = self.origLabel
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tgbugs/pyontutils | pyontutils/core.py | qname | def qname(uri, warning=False):
""" compute qname from defaults """
if warning:
print(tc.red('WARNING:'), tc.yellow(f'qname({uri}) is deprecated! please use OntId({uri}).curie'))
return __helper_graph.qname(uri) | python | def qname(uri, warning=False):
""" compute qname from defaults """
if warning:
print(tc.red('WARNING:'), tc.yellow(f'qname({uri}) is deprecated! please use OntId({uri}).curie'))
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tgbugs/pyontutils | pyontutils/core.py | cull_prefixes | def cull_prefixes(graph, prefixes={k:v for k, v in uPREFIXES.items() if k != 'NIFTTL'},
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""" Remove unused curie prefixes and normalize to a standard set. """
prefs = ['']
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""" Remove unused curie prefixes and normalize to a standard set. """
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tgbugs/pyontutils | pyontutils/core.py | displayTriples | def displayTriples(triples, qname=qname):
""" triples can also be an rdflib Graph instance """
[print(*(e[:5]
if isinstance(e, rdflib.BNode) else
qname(e)
for e in t), '.')
for t in sorted(triples)] | python | def displayTriples(triples, qname=qname):
""" triples can also be an rdflib Graph instance """
[print(*(e[:5]
if isinstance(e, rdflib.BNode) else
qname(e)
for e in t), '.')
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tgbugs/pyontutils | pyontutils/core.py | makeGraph.write | def write(self, cull=False):
""" Serialize self.g and write to self.filename, set cull to true to remove unwanted prefixes """
if cull:
cull_prefixes(self).write()
else:
ser = self.g.serialize(format='nifttl')
with open(self.filename, 'wb') as f:
... | python | def write(self, cull=False):
""" Serialize self.g and write to self.filename, set cull to true to remove unwanted prefixes """
if cull:
cull_prefixes(self).write()
else:
ser = self.g.serialize(format='nifttl')
with open(self.filename, 'wb') as f:
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tgbugs/pyontutils | pyontutils/core.py | makeGraph.add_hierarchy | def add_hierarchy(self, parent, edge, child): # XXX DEPRECATED
""" Helper function to simplify the addition of part_of style
objectProperties to graphs. FIXME make a method of makeGraph?
"""
if type(parent) != rdflib.URIRef:
parent = self.check_thing(parent)
if ... | python | def add_hierarchy(self, parent, edge, child): # XXX DEPRECATED
""" Helper function to simplify the addition of part_of style
objectProperties to graphs. FIXME make a method of makeGraph?
"""
if type(parent) != rdflib.URIRef:
parent = self.check_thing(parent)
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tgbugs/pyontutils | pyontutils/core.py | makeGraph.add_restriction | def add_restriction(self, subject, predicate, object_):
""" Lift normal triples into restrictions using someValuesFrom. """
if type(object_) != rdflib.URIRef:
object_ = self.check_thing(object_)
if type(predicate) != rdflib.URIRef:
predicate = self.check_thing(predicate)... | python | def add_restriction(self, subject, predicate, object_):
""" Lift normal triples into restrictions using someValuesFrom. """
if type(object_) != rdflib.URIRef:
object_ = self.check_thing(object_)
if type(predicate) != rdflib.URIRef:
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tgbugs/pyontutils | pyontutils/core.py | makeGraph.qname | def qname(self, uri, generate=False):
""" Given a uri return the qname if it exists, otherwise return the uri. """
try:
prefix, namespace, name = self.g.namespace_manager.compute_qname(uri, generate=generate)
qname = ':'.join((prefix, name))
return qname
excep... | python | def qname(self, uri, generate=False):
""" Given a uri return the qname if it exists, otherwise return the uri. """
try:
prefix, namespace, name = self.g.namespace_manager.compute_qname(uri, generate=generate)
qname = ':'.join((prefix, name))
return qname
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SUSE-Enceladus/ipa | ipa/scripts/cli_utils.py | archive_history_item | def archive_history_item(item, destination, no_color):
"""
Archive the log and results file for the given history item.
Copy the files and update the results file in destination directory.
"""
log_src, description = split_history_item(item.strip())
# Get relative path for log:
# {provider}... | python | def archive_history_item(item, destination, no_color):
"""
Archive the log and results file for the given history item.
Copy the files and update the results file in destination directory.
"""
log_src, description = split_history_item(item.strip())
# Get relative path for log:
# {provider}... | [
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SUSE-Enceladus/ipa | ipa/scripts/cli_utils.py | echo_verbose_results | def echo_verbose_results(data, no_color):
"""Print list of tests and result of each test."""
click.echo()
click.echo(
'\n'.join(
'{}: {}'.format(key, val) for key, val in data['info'].items()
)
)
click.echo()
for test in data['tests']:
if test['outcome'] == 'p... | python | def echo_verbose_results(data, no_color):
"""Print list of tests and result of each test."""
click.echo()
click.echo(
'\n'.join(
'{}: {}'.format(key, val) for key, val in data['info'].items()
)
)
click.echo()
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SUSE-Enceladus/ipa | ipa/scripts/cli_utils.py | get_log_file_from_item | def get_log_file_from_item(history):
"""
Return the log file based on provided history item.
Description is optional.
"""
try:
log_file, description = shlex.split(history)
except ValueError:
log_file = history.strip()
return log_file | python | def get_log_file_from_item(history):
"""
Return the log file based on provided history item.
Description is optional.
"""
try:
log_file, description = shlex.split(history)
except ValueError:
log_file = history.strip()
return log_file | [
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SUSE-Enceladus/ipa | ipa/scripts/cli_utils.py | results_history | def results_history(history_log, no_color):
"""Display a list of ipa test results history."""
try:
with open(history_log, 'r') as f:
lines = f.readlines()
except Exception as error:
echo_style(
'Unable to process results history log: %s' % error,
no_color,... | python | def results_history(history_log, no_color):
"""Display a list of ipa test results history."""
try:
with open(history_log, 'r') as f:
lines = f.readlines()
except Exception as error:
echo_style(
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SUSE-Enceladus/ipa | ipa/scripts/cli_utils.py | split_history_item | def split_history_item(history):
"""
Return the log file and optional description for item.
"""
try:
log_file, description = shlex.split(history)
except ValueError:
log_file = history.strip()
description = None
return log_file, description | python | def split_history_item(history):
"""
Return the log file and optional description for item.
"""
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log_file = history.strip()
description = None
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tgbugs/pyontutils | pyontutils/utils.py | get_working_dir | def get_working_dir(script__file__):
""" hardcoded sets the 'equivalent' working directory if not in git """
start = Path(script__file__).resolve()
_root = Path(start.root)
working_dir = start
while not list(working_dir.glob('.git')):
if working_dir == _root:
return
work... | python | def get_working_dir(script__file__):
""" hardcoded sets the 'equivalent' working directory if not in git """
start = Path(script__file__).resolve()
_root = Path(start.root)
working_dir = start
while not list(working_dir.glob('.git')):
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tgbugs/pyontutils | pyontutils/utils.py | sysidpath | def sysidpath(ignore_options=False):
""" get a unique identifier for the machine running this function """
# in the event we have to make our own
# this should not be passed in a as a parameter
# since we need these definitions to be more or less static
failover = Path('/tmp/machine-id')
if not... | python | def sysidpath(ignore_options=False):
""" get a unique identifier for the machine running this function """
# in the event we have to make our own
# this should not be passed in a as a parameter
# since we need these definitions to be more or less static
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tgbugs/pyontutils | pyontutils/scigraph_codegen.py | State.gencode | def gencode(self):
""" Run this to generate the code """
ledict = requests.get(self.api_url).json()
ledict = self.dotopdict(ledict)
out = self.dodict(ledict)
self._code = out | python | def gencode(self):
""" Run this to generate the code """
ledict = requests.get(self.api_url).json()
ledict = self.dotopdict(ledict)
out = self.dodict(ledict)
self._code = out | [
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tgbugs/pyontutils | pyontutils/scigraph_codegen.py | State2.dotopdict | def dotopdict(self, dict_):
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mlookup = {'get':'GET', 'post':'POST'}
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method_dict['nickname'] = ... | python | def dotopdict(self, dict_):
""" Rewrite the 2.0 json to match what we feed the code for 1.2 """
mlookup = {'get':'GET', 'post':'POST'}
def rearrange(path, method_dict, method):
oid = method_dict['operationId']
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tgbugs/pyontutils | pyontutils/obo_io.py | OboFile.write | def write(self, filename, type_='obo'): #FIXME this is bugged
""" Write file, will not overwrite files with the same name
outputs to obo by default but can also output to ttl if
passed type_='ttl' when called.
"""
if os.path.exists(filename):
name, ext = file... | python | def write(self, filename, type_='obo'): #FIXME this is bugged
""" Write file, will not overwrite files with the same name
outputs to obo by default but can also output to ttl if
passed type_='ttl' when called.
"""
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tgbugs/pyontutils | librdflib/librdflib/__init__.py | main | def main():
from IPython import embed
""" Python 3.6.6
ibttl 2.605194091796875
ttl 3.8316309452056885
diff lt - ttl -1.2264368534088135
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diff lr - rl -26.983628273010254
simple time 17.405116319656372
"""
""" Python 3.5.3 ... | python | def main():
from IPython import embed
""" Python 3.6.6
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ttl 3.8316309452056885
diff lt - ttl -1.2264368534088135
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"""
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tgbugs/pyontutils | pyontutils/combinators.py | make_predicate_object_combinator | def make_predicate_object_combinator(function, p, o):
""" Combinator to hold predicate object pairs until a subject is supplied and then
call a function that accepts a subject, predicate, and object.
Create a combinator to defer production of a triple until the missing pieces are supplied.
... | python | def make_predicate_object_combinator(function, p, o):
""" Combinator to hold predicate object pairs until a subject is supplied and then
call a function that accepts a subject, predicate, and object.
Create a combinator to defer production of a triple until the missing pieces are supplied.
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tgbugs/pyontutils | pyontutils/combinators.py | EquivalentClass.serialize | def serialize(self, subject, *objects_or_combinators):
""" object_combinators may also be URIRefs or Literals """
ec_s = rdflib.BNode()
if self.operator is not None:
if subject is not None:
yield subject, self.predicate, ec_s
yield from oc(ec_s)
... | python | def serialize(self, subject, *objects_or_combinators):
""" object_combinators may also be URIRefs or Literals """
ec_s = rdflib.BNode()
if self.operator is not None:
if subject is not None:
yield subject, self.predicate, ec_s
yield from oc(ec_s)
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shanbay/peeweext | peeweext/model.py | Model.update_with | def update_with(self, **query):
"""
secure update, mass assignment protected
"""
for k, v in self._filter_attrs(query).items():
setattr(self, k, v)
return self.save() | python | def update_with(self, **query):
"""
secure update, mass assignment protected
"""
for k, v in self._filter_attrs(query).items():
setattr(self, k, v)
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shanbay/peeweext | peeweext/model.py | Model._validate | def _validate(self):
"""Validate model data and save errors
"""
errors = {}
for name, validator in self._validators.items():
value = getattr(self, name)
try:
validator(self, value)
except ValidationError as e:
errors[n... | python | def _validate(self):
"""Validate model data and save errors
"""
errors = {}
for name, validator in self._validators.items():
value = getattr(self, name)
try:
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tgbugs/pyontutils | ilxutils/ilxutils/nltklib.py | penn_to_wn | def penn_to_wn(tag):
""" Convert between a Penn Treebank tag to a simplified Wordnet tag """
if tag.startswith('N'):
return 'n'
if tag.startswith('V'):
return 'v'
if tag.startswith('J'):
return 'a'
if tag.startswith('R'):
return 'r'
return None | python | def penn_to_wn(tag):
""" Convert between a Penn Treebank tag to a simplified Wordnet tag """
if tag.startswith('N'):
return 'n'
if tag.startswith('V'):
return 'v'
if tag.startswith('J'):
return 'a'
if tag.startswith('R'):
return 'r'
return None | [
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tgbugs/pyontutils | ilxutils/ilxutils/nltklib.py | sentence_similarity | def sentence_similarity(sentence1, sentence2):
""" compute the sentence similarity using Wordnet """
# Tokenize and tag
sentence1 = pos_tag(word_tokenize(sentence1))
sentence2 = pos_tag(word_tokenize(sentence2))
# Get the synsets for the tagged words
synsets1 = [tagged_to_synset(*tagged_word) f... | python | def sentence_similarity(sentence1, sentence2):
""" compute the sentence similarity using Wordnet """
# Tokenize and tag
sentence1 = pos_tag(word_tokenize(sentence1))
sentence2 = pos_tag(word_tokenize(sentence2))
# Get the synsets for the tagged words
synsets1 = [tagged_to_synset(*tagged_word) f... | [
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tgbugs/pyontutils | ilxutils/ilxutils/ontopandas.py | command_line | def command_line():
''' If you want to use the command line '''
from docopt import docopt
doc = docopt( __doc__, version=VERSION )
args = pd.Series({k.replace('--', ''): v for k, v in doc.items()})
if args.all:
graph = Graph2Pandas(args.file, _type='all')
elif args.type:
graph = ... | python | def command_line():
''' If you want to use the command line '''
from docopt import docopt
doc = docopt( __doc__, version=VERSION )
args = pd.Series({k.replace('--', ''): v for k, v in doc.items()})
if args.all:
graph = Graph2Pandas(args.file, _type='all')
elif args.type:
graph = ... | [
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tgbugs/pyontutils | ilxutils/ilxutils/ontopandas.py | OntoPandas.save | def save(self, foldername: str, path_to_folder: str=None) -> None:
''' Saves entities into multiple files within the same folder because of pickle-recursive
errors that would happen if squeezed into one '''
self.create_pickle((self.g.namespaces, ))
self.df.to_pickle(output) | python | def save(self, foldername: str, path_to_folder: str=None) -> None:
''' Saves entities into multiple files within the same folder because of pickle-recursive
errors that would happen if squeezed into one '''
self.create_pickle((self.g.namespaces, ))
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] | 3d913db29c177db39151592909a4f56170ef8b35 | https://github.com/tgbugs/pyontutils/blob/3d913db29c177db39151592909a4f56170ef8b35/ilxutils/ilxutils/ontopandas.py#L54-L58 | train |
tgbugs/pyontutils | ilxutils/ilxutils/ontopandas.py | OntoPandas.qname | def qname(self, uri: str) -> str:
''' Returns qname of uri in rdflib graph while also saving it '''
try:
prefix, namespace, name = self.g.compute_qname(uri)
qname = prefix + ':' + name
return qname
except:
try:
print('prefix:', pref... | python | def qname(self, uri: str) -> str:
''' Returns qname of uri in rdflib graph while also saving it '''
try:
prefix, namespace, name = self.g.compute_qname(uri)
qname = prefix + ':' + name
return qname
except:
try:
print('prefix:', pref... | [
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tgbugs/pyontutils | ilxutils/ilxutils/ontopandas.py | OntoPandas.get_sparql_dataframe | def get_sparql_dataframe( self ):
''' Iterates through the sparql table and condenses it into a Pandas DataFrame '''
self.result = self.g.query(self.query)
cols = set() # set(['qname'])
indx = set()
data = {}
curr_subj = None # place marker for first subj to be processed
... | python | def get_sparql_dataframe( self ):
''' Iterates through the sparql table and condenses it into a Pandas DataFrame '''
self.result = self.g.query(self.query)
cols = set() # set(['qname'])
indx = set()
data = {}
curr_subj = None # place marker for first subj to be processed
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tgbugs/pyontutils | ilxutils/ilxutils/ontopandas.py | OntoPandas.df | def df(self, qname_predicates:bool=False, keep_variable_type:bool=True) -> pd.DataFrame:
''' Multi funcitonal DataFrame with settings '''
local_df = self.df.copy()
if qname_predicates:
for col in self.columns:
local_df.rename({col: self.g.qname(col)})
if not k... | python | def df(self, qname_predicates:bool=False, keep_variable_type:bool=True) -> pd.DataFrame:
''' Multi funcitonal DataFrame with settings '''
local_df = self.df.copy()
if qname_predicates:
for col in self.columns:
local_df.rename({col: self.g.qname(col)})
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tgbugs/pyontutils | ilxutils/ilxutils/simple_rdflib.py | SimpleGraph.qname | def qname(self, iri: str) -> str:
""" Get qualified name of uri in rdflib graph while also saving it
Args: iri: The iri that you want to replace the uri with a known prefix with
Returns: qualified name of the iri to be used as the new predicate
"""
prefix, namespace, name = sel... | python | def qname(self, iri: str) -> str:
""" Get qualified name of uri in rdflib graph while also saving it
Args: iri: The iri that you want to replace the uri with a known prefix with
Returns: qualified name of the iri to be used as the new predicate
"""
prefix, namespace, name = sel... | [
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tgbugs/pyontutils | ilxutils/ilxutils/simple_rdflib.py | SimpleGraph.find_prefix | def find_prefix(self, iri: Union[URIRef, Literal, str]) -> Union[None, str]:
""" Finds if uri is in common_namespaces
Auto adds prefix if incoming iri has a uri in common_namespaces. If its not in the local
library, then it will just be spit out as the iri and not saved/condensed into qualified... | python | def find_prefix(self, iri: Union[URIRef, Literal, str]) -> Union[None, str]:
""" Finds if uri is in common_namespaces
Auto adds prefix if incoming iri has a uri in common_namespaces. If its not in the local
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tgbugs/pyontutils | ilxutils/ilxutils/simple_rdflib.py | SimpleGraph.add_annotation | def add_annotation(
self,
subj: URIRef,
pred: URIRef,
obj: Union[Literal, URIRef],
a_p: URIRef ,
a_o: Union[Literal, URIRef],
) -> BNode:
""" Adds annotation to rdflib graph.
The annotation axiom will filled in if this is a... | python | def add_annotation(
self,
subj: URIRef,
pred: URIRef,
obj: Union[Literal, URIRef],
a_p: URIRef ,
a_o: Union[Literal, URIRef],
) -> BNode:
""" Adds annotation to rdflib graph.
The annotation axiom will filled in if this is a... | [
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tgbugs/pyontutils | ilxutils/ilxutils/simple_rdflib.py | SimpleGraph.add_triple | def add_triple(
self,
subj: Union[URIRef, str],
pred: Union[URIRef, str],
obj: Union[URIRef, Literal, str]
) -> None:
""" Adds triple to rdflib Graph
Triple can be of any subject, predicate, and object of the entity without a need for order.
... | python | def add_triple(
self,
subj: Union[URIRef, str],
pred: Union[URIRef, str],
obj: Union[URIRef, Literal, str]
) -> None:
""" Adds triple to rdflib Graph
Triple can be of any subject, predicate, and object of the entity without a need for order.
... | [
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Args:
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pred: Entity predicate
obj: Entity object
Example:
In [1]: add_triple(
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] | 3d913db29c177db39151592909a4f56170ef8b35 | https://github.com/tgbugs/pyontutils/blob/3d913db29c177db39151592909a4f56170ef8b35/ilxutils/ilxutils/simple_rdflib.py#L165-L191 | train |
tgbugs/pyontutils | ilxutils/ilxutils/simple_rdflib.py | SimpleGraph.process_prefix | def process_prefix(self, prefix: str) -> Union[Namespace, None]:
""" Add namespace to graph if it has a local match
This allows qnames to be used without adding their respected namespaces if they are in
the common_namespaces local dict. This is is to save a butt-ton of time trying to see what
... | python | def process_prefix(self, prefix: str) -> Union[Namespace, None]:
""" Add namespace to graph if it has a local match
This allows qnames to be used without adding their respected namespaces if they are in
the common_namespaces local dict. This is is to save a butt-ton of time trying to see what
... | [
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tgbugs/pyontutils | ilxutils/ilxutils/simple_rdflib.py | SimpleGraph.process_subj_or_pred | def process_subj_or_pred(self, component: Union[URIRef, str]) -> URIRef:
""" Adds viable uri from iri or expands viable qname to iri to be triple ready
Need to have a viable qualified name (qname) in order to use a qname. You can make it
viable by either add the namespace beforehand with add_na... | python | def process_subj_or_pred(self, component: Union[URIRef, str]) -> URIRef:
""" Adds viable uri from iri or expands viable qname to iri to be triple ready
Need to have a viable qualified name (qname) in order to use a qname. You can make it
viable by either add the namespace beforehand with add_na... | [
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tgbugs/pyontutils | ilxutils/ilxutils/simple_rdflib.py | SimpleGraph.process_obj | def process_obj(self, obj: Union[URIRef, Literal, str]) -> Union[URIRef, Literal]:
""" Gives component the proper node type
Args:
obj: Entity object to be converted to its appropriate node type
Returns:
URIRef or Literal type of the object provided.
Raises:
... | python | def process_obj(self, obj: Union[URIRef, Literal, str]) -> Union[URIRef, Literal]:
""" Gives component the proper node type
Args:
obj: Entity object to be converted to its appropriate node type
Returns:
URIRef or Literal type of the object provided.
Raises:
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tgbugs/pyontutils | ilxutils/ilxutils/simple_rdflib.py | SimpleGraph.remove_triple | def remove_triple(
self,
subj: URIRef,
pred: URIRef,
obj: Union[URIRef, Literal]
) -> None:
""" Removes triple from rdflib Graph
You must input the triple in its URIRef or Literal form for each node exactly the way it
was inputed or it wil... | python | def remove_triple(
self,
subj: URIRef,
pred: URIRef,
obj: Union[URIRef, Literal]
) -> None:
""" Removes triple from rdflib Graph
You must input the triple in its URIRef or Literal form for each node exactly the way it
was inputed or it wil... | [
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Args:
subj: Entity subject to be removed it its the only node with this subject; else this is
just... | [
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