repository_name stringlengths 5 67 | func_path_in_repository stringlengths 4 234 | func_name stringlengths 0 314 | whole_func_string stringlengths 52 3.87M | language stringclasses 6
values | func_code_string stringlengths 52 3.87M | func_documentation_string stringlengths 1 47.2k | func_code_url stringlengths 85 339 |
|---|---|---|---|---|---|---|---|
sorgerlab/indra | indra/tools/reading/submit_reading_pipeline.py | submit_reading | def submit_reading(basename, pmid_list_filename, readers, start_ix=None,
end_ix=None, pmids_per_job=3000, num_tries=2,
force_read=False, force_fulltext=False, project_name=None):
"""Submit an old-style pmid-centered no-database s3 only reading job.
This function is provide... | python | def submit_reading(basename, pmid_list_filename, readers, start_ix=None,
end_ix=None, pmids_per_job=3000, num_tries=2,
force_read=False, force_fulltext=False, project_name=None):
"""Submit an old-style pmid-centered no-database s3 only reading job.
This function is provide... | Submit an old-style pmid-centered no-database s3 only reading job.
This function is provided for the sake of backward compatibility. It is
preferred that you use the object-oriented PmidSubmitter and the
submit_reading job going forward. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/tools/reading/submit_reading_pipeline.py#L555-L568 |
sorgerlab/indra | indra/tools/reading/submit_reading_pipeline.py | submit_combine | def submit_combine(basename, readers, job_ids=None, project_name=None):
"""Submit a batch job to combine the outputs of a reading job.
This function is provided for backwards compatibility. You should use the
PmidSubmitter and submit_combine methods.
"""
sub = PmidSubmitter(basename, readers, proje... | python | def submit_combine(basename, readers, job_ids=None, project_name=None):
"""Submit a batch job to combine the outputs of a reading job.
This function is provided for backwards compatibility. You should use the
PmidSubmitter and submit_combine methods.
"""
sub = PmidSubmitter(basename, readers, proje... | Submit a batch job to combine the outputs of a reading job.
This function is provided for backwards compatibility. You should use the
PmidSubmitter and submit_combine methods. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/tools/reading/submit_reading_pipeline.py#L571-L580 |
sorgerlab/indra | indra/tools/reading/submit_reading_pipeline.py | create_read_parser | def create_read_parser():
import argparse
parent_read_parser = argparse.ArgumentParser(add_help=False)
parent_read_parser.add_argument(
'input_file',
help=('Path to file containing input ids of content to read. For the '
'no-db options, this is simply a file with each line bein... | python | def create_read_parser():
import argparse
parent_read_parser = argparse.ArgumentParser(add_help=False)
parent_read_parser.add_argument(
'input_file',
help=('Path to file containing input ids of content to read. For the '
'no-db options, this is simply a file with each line bein... | Not currently supported.
parent_read_parser.add_argument(
'--num_tries',
default=2,
type=int,
help='Maximum number of times to try running job.'
) | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/tools/reading/submit_reading_pipeline.py#L606-L650 |
sorgerlab/indra | indra/tools/reading/submit_reading_pipeline.py | Submitter.submit_reading | def submit_reading(self, input_fname, start_ix, end_ix, ids_per_job,
num_tries=1, stagger=0):
"""Submit a batch of reading jobs
Parameters
----------
input_fname : str
The name of the file containing the ids to be read.
start_ix : int
... | python | def submit_reading(self, input_fname, start_ix, end_ix, ids_per_job,
num_tries=1, stagger=0):
"""Submit a batch of reading jobs
Parameters
----------
input_fname : str
The name of the file containing the ids to be read.
start_ix : int
... | Submit a batch of reading jobs
Parameters
----------
input_fname : str
The name of the file containing the ids to be read.
start_ix : int
The line index of the first item in the list to read.
end_ix : int
The line index of the last item in the... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/tools/reading/submit_reading_pipeline.py#L397-L466 |
sorgerlab/indra | indra/tools/reading/submit_reading_pipeline.py | Submitter.watch_and_wait | def watch_and_wait(self, poll_interval=10, idle_log_timeout=None,
kill_on_timeout=False, stash_log_method=None,
tag_instances=False, **kwargs):
"""This provides shortcut access to the wait_for_complete_function."""
return wait_for_complete(self._job_queue, j... | python | def watch_and_wait(self, poll_interval=10, idle_log_timeout=None,
kill_on_timeout=False, stash_log_method=None,
tag_instances=False, **kwargs):
"""This provides shortcut access to the wait_for_complete_function."""
return wait_for_complete(self._job_queue, j... | This provides shortcut access to the wait_for_complete_function. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/tools/reading/submit_reading_pipeline.py#L468-L478 |
sorgerlab/indra | indra/tools/reading/submit_reading_pipeline.py | Submitter.run | def run(self, input_fname, ids_per_job, stagger=0, **wait_params):
"""Run this submission all the way.
This method will run both `submit_reading` and `watch_and_wait`,
blocking on the latter.
"""
submit_thread = Thread(target=self.submit_reading,
a... | python | def run(self, input_fname, ids_per_job, stagger=0, **wait_params):
"""Run this submission all the way.
This method will run both `submit_reading` and `watch_and_wait`,
blocking on the latter.
"""
submit_thread = Thread(target=self.submit_reading,
a... | Run this submission all the way.
This method will run both `submit_reading` and `watch_and_wait`,
blocking on the latter. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/tools/reading/submit_reading_pipeline.py#L480-L496 |
sorgerlab/indra | indra/tools/reading/submit_reading_pipeline.py | PmidSubmitter.set_options | def set_options(self, force_read=False, force_fulltext=False):
"""Set the options for this run."""
self.options['force_read'] = force_read
self.options['force_fulltext'] = force_fulltext
return | python | def set_options(self, force_read=False, force_fulltext=False):
"""Set the options for this run."""
self.options['force_read'] = force_read
self.options['force_fulltext'] = force_fulltext
return | Set the options for this run. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/tools/reading/submit_reading_pipeline.py#L517-L521 |
sorgerlab/indra | indra/databases/chebi_client.py | get_chebi_name_from_id | def get_chebi_name_from_id(chebi_id, offline=False):
"""Return a ChEBI name corresponding to the given ChEBI ID.
Parameters
----------
chebi_id : str
The ChEBI ID whose name is to be returned.
offline : Optional[bool]
Choose whether to allow an online lookup if the local lookup fail... | python | def get_chebi_name_from_id(chebi_id, offline=False):
"""Return a ChEBI name corresponding to the given ChEBI ID.
Parameters
----------
chebi_id : str
The ChEBI ID whose name is to be returned.
offline : Optional[bool]
Choose whether to allow an online lookup if the local lookup fail... | Return a ChEBI name corresponding to the given ChEBI ID.
Parameters
----------
chebi_id : str
The ChEBI ID whose name is to be returned.
offline : Optional[bool]
Choose whether to allow an online lookup if the local lookup fails. If
True, the online lookup is not attempted. Defa... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/databases/chebi_client.py#L86-L106 |
sorgerlab/indra | indra/databases/chebi_client.py | get_chebi_name_from_id_web | def get_chebi_name_from_id_web(chebi_id):
"""Return a ChEBI mame corresponding to a given ChEBI ID using a REST API.
Parameters
----------
chebi_id : str
The ChEBI ID whose name is to be returned.
Returns
-------
chebi_name : str
The name corresponding to the given ChEBI ID... | python | def get_chebi_name_from_id_web(chebi_id):
"""Return a ChEBI mame corresponding to a given ChEBI ID using a REST API.
Parameters
----------
chebi_id : str
The ChEBI ID whose name is to be returned.
Returns
-------
chebi_name : str
The name corresponding to the given ChEBI ID... | Return a ChEBI mame corresponding to a given ChEBI ID using a REST API.
Parameters
----------
chebi_id : str
The ChEBI ID whose name is to be returned.
Returns
-------
chebi_name : str
The name corresponding to the given ChEBI ID. If the lookup
fails, None is returned. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/databases/chebi_client.py#L179-L214 |
sorgerlab/indra | indra/tools/executable_subnetwork.py | get_subnetwork | def get_subnetwork(statements, nodes, relevance_network=None,
relevance_node_lim=10):
"""Return a PySB model based on a subset of given INDRA Statements.
Statements are first filtered for nodes in the given list and other nodes
are optionally added based on relevance in a given network. ... | python | def get_subnetwork(statements, nodes, relevance_network=None,
relevance_node_lim=10):
"""Return a PySB model based on a subset of given INDRA Statements.
Statements are first filtered for nodes in the given list and other nodes
are optionally added based on relevance in a given network. ... | Return a PySB model based on a subset of given INDRA Statements.
Statements are first filtered for nodes in the given list and other nodes
are optionally added based on relevance in a given network. The filtered
statements are then assembled into an executable model using INDRA's
PySB Assembler.
P... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/tools/executable_subnetwork.py#L7-L45 |
sorgerlab/indra | indra/tools/executable_subnetwork.py | _filter_statements | def _filter_statements(statements, agents):
"""Return INDRA Statements which have Agents in the given list.
Only statements are returned in which all appearing Agents as in the
agents list.
Parameters
----------
statements : list[indra.statements.Statement]
A list of INDRA Statements t... | python | def _filter_statements(statements, agents):
"""Return INDRA Statements which have Agents in the given list.
Only statements are returned in which all appearing Agents as in the
agents list.
Parameters
----------
statements : list[indra.statements.Statement]
A list of INDRA Statements t... | Return INDRA Statements which have Agents in the given list.
Only statements are returned in which all appearing Agents as in the
agents list.
Parameters
----------
statements : list[indra.statements.Statement]
A list of INDRA Statements to filter.
agents : list[str]
A list of ... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/tools/executable_subnetwork.py#L47-L70 |
sorgerlab/indra | indra/tools/executable_subnetwork.py | _find_relevant_nodes | def _find_relevant_nodes(query_nodes, relevance_network, relevance_node_lim):
"""Return a list of nodes that are relevant for the query.
Parameters
----------
query_nodes : list[str]
A list of node names to query for.
relevance_network : str
The UUID of the NDEx network to query rel... | python | def _find_relevant_nodes(query_nodes, relevance_network, relevance_node_lim):
"""Return a list of nodes that are relevant for the query.
Parameters
----------
query_nodes : list[str]
A list of node names to query for.
relevance_network : str
The UUID of the NDEx network to query rel... | Return a list of nodes that are relevant for the query.
Parameters
----------
query_nodes : list[str]
A list of node names to query for.
relevance_network : str
The UUID of the NDEx network to query relevance in.
relevance_node_lim : int
The number of top relevant nodes to r... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/tools/executable_subnetwork.py#L72-L92 |
sorgerlab/indra | indra/sources/hume/api.py | process_jsonld_file | def process_jsonld_file(fname):
"""Process a JSON-LD file in the new format to extract Statements.
Parameters
----------
fname : str
The path to the JSON-LD file to be processed.
Returns
-------
indra.sources.hume.HumeProcessor
A HumeProcessor instance, which contains a lis... | python | def process_jsonld_file(fname):
"""Process a JSON-LD file in the new format to extract Statements.
Parameters
----------
fname : str
The path to the JSON-LD file to be processed.
Returns
-------
indra.sources.hume.HumeProcessor
A HumeProcessor instance, which contains a lis... | Process a JSON-LD file in the new format to extract Statements.
Parameters
----------
fname : str
The path to the JSON-LD file to be processed.
Returns
-------
indra.sources.hume.HumeProcessor
A HumeProcessor instance, which contains a list of INDRA Statements
as its st... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/hume/api.py#L10-L26 |
sorgerlab/indra | indra/util/aws.py | kill_all | def kill_all(job_queue, reason='None given', states=None):
"""Terminates/cancels all RUNNING, RUNNABLE, and STARTING jobs."""
if states is None:
states = ['STARTING', 'RUNNABLE', 'RUNNING']
batch = boto3.client('batch')
runnable = batch.list_jobs(jobQueue=job_queue, jobStatus='RUNNABLE')
job... | python | def kill_all(job_queue, reason='None given', states=None):
"""Terminates/cancels all RUNNING, RUNNABLE, and STARTING jobs."""
if states is None:
states = ['STARTING', 'RUNNABLE', 'RUNNING']
batch = boto3.client('batch')
runnable = batch.list_jobs(jobQueue=job_queue, jobStatus='RUNNABLE')
job... | Terminates/cancels all RUNNING, RUNNABLE, and STARTING jobs. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/util/aws.py#L11-L33 |
sorgerlab/indra | indra/util/aws.py | tag_instance | def tag_instance(instance_id, **tags):
"""Tag a single ec2 instance."""
logger.debug("Got request to add tags %s to instance %s."
% (str(tags), instance_id))
ec2 = boto3.resource('ec2')
instance = ec2.Instance(instance_id)
# Remove None's from `tags`
filtered_tags = {k: v for k... | python | def tag_instance(instance_id, **tags):
"""Tag a single ec2 instance."""
logger.debug("Got request to add tags %s to instance %s."
% (str(tags), instance_id))
ec2 = boto3.resource('ec2')
instance = ec2.Instance(instance_id)
# Remove None's from `tags`
filtered_tags = {k: v for k... | Tag a single ec2 instance. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/util/aws.py#L36-L62 |
sorgerlab/indra | indra/util/aws.py | tag_myself | def tag_myself(project='cwc', **other_tags):
"""Function run when indra is used in an EC2 instance to apply tags."""
base_url = "http://169.254.169.254"
try:
resp = requests.get(base_url + "/latest/meta-data/instance-id")
except requests.exceptions.ConnectionError:
logger.warning("Could ... | python | def tag_myself(project='cwc', **other_tags):
"""Function run when indra is used in an EC2 instance to apply tags."""
base_url = "http://169.254.169.254"
try:
resp = requests.get(base_url + "/latest/meta-data/instance-id")
except requests.exceptions.ConnectionError:
logger.warning("Could ... | Function run when indra is used in an EC2 instance to apply tags. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/util/aws.py#L65-L76 |
sorgerlab/indra | indra/util/aws.py | get_batch_command | def get_batch_command(command_list, project=None, purpose=None):
"""Get the command appropriate for running something on batch."""
command_str = ' '.join(command_list)
ret = ['python', '-m', 'indra.util.aws', 'run_in_batch', command_str]
if not project and has_config('DEFAULT_AWS_PROJECT'):
proj... | python | def get_batch_command(command_list, project=None, purpose=None):
"""Get the command appropriate for running something on batch."""
command_str = ' '.join(command_list)
ret = ['python', '-m', 'indra.util.aws', 'run_in_batch', command_str]
if not project and has_config('DEFAULT_AWS_PROJECT'):
proj... | Get the command appropriate for running something on batch. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/util/aws.py#L79-L89 |
sorgerlab/indra | indra/util/aws.py | get_jobs | def get_jobs(job_queue='run_reach_queue', job_status='RUNNING'):
"""Returns a list of dicts with jobName and jobId for each job with the
given status."""
batch = boto3.client('batch')
jobs = batch.list_jobs(jobQueue=job_queue, jobStatus=job_status)
return jobs.get('jobSummaryList') | python | def get_jobs(job_queue='run_reach_queue', job_status='RUNNING'):
"""Returns a list of dicts with jobName and jobId for each job with the
given status."""
batch = boto3.client('batch')
jobs = batch.list_jobs(jobQueue=job_queue, jobStatus=job_status)
return jobs.get('jobSummaryList') | Returns a list of dicts with jobName and jobId for each job with the
given status. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/util/aws.py#L101-L106 |
sorgerlab/indra | indra/util/aws.py | get_job_log | def get_job_log(job_info, log_group_name='/aws/batch/job',
write_file=True, verbose=False):
"""Gets the Cloudwatch log associated with the given job.
Parameters
----------
job_info : dict
dict containing entries for 'jobName' and 'jobId', e.g., as returned
by get_jobs()
... | python | def get_job_log(job_info, log_group_name='/aws/batch/job',
write_file=True, verbose=False):
"""Gets the Cloudwatch log associated with the given job.
Parameters
----------
job_info : dict
dict containing entries for 'jobName' and 'jobId', e.g., as returned
by get_jobs()
... | Gets the Cloudwatch log associated with the given job.
Parameters
----------
job_info : dict
dict containing entries for 'jobName' and 'jobId', e.g., as returned
by get_jobs()
log_group_name : string
Name of the log group; defaults to '/aws/batch/job'
write_file : boolean
... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/util/aws.py#L109-L153 |
sorgerlab/indra | indra/util/aws.py | get_log_by_name | def get_log_by_name(log_group_name, log_stream_name, out_file=None,
verbose=True):
"""Download a log given the log's group and stream name.
Parameters
----------
log_group_name : str
The name of the log group, e.g. /aws/batch/job.
log_stream_name : str
The name ... | python | def get_log_by_name(log_group_name, log_stream_name, out_file=None,
verbose=True):
"""Download a log given the log's group and stream name.
Parameters
----------
log_group_name : str
The name of the log group, e.g. /aws/batch/job.
log_stream_name : str
The name ... | Download a log given the log's group and stream name.
Parameters
----------
log_group_name : str
The name of the log group, e.g. /aws/batch/job.
log_stream_name : str
The name of the log stream, e.g. run_reach_jobdef/default/<UUID>
Returns
-------
lines : list[str]
... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/util/aws.py#L156-L196 |
sorgerlab/indra | indra/util/aws.py | dump_logs | def dump_logs(job_queue='run_reach_queue', job_status='RUNNING'):
"""Write logs for all jobs with given the status to files."""
jobs = get_jobs(job_queue, job_status)
for job in jobs:
get_job_log(job, write_file=True) | python | def dump_logs(job_queue='run_reach_queue', job_status='RUNNING'):
"""Write logs for all jobs with given the status to files."""
jobs = get_jobs(job_queue, job_status)
for job in jobs:
get_job_log(job, write_file=True) | Write logs for all jobs with given the status to files. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/util/aws.py#L199-L203 |
sorgerlab/indra | indra/util/aws.py | get_s3_file_tree | def get_s3_file_tree(s3, bucket, prefix):
"""Overcome s3 response limit and return NestedDict tree of paths.
The NestedDict object also allows the user to search by the ends of a path.
The tree mimics a file directory structure, with the leave nodes being the
full unbroken key. For example, 'path/to/f... | python | def get_s3_file_tree(s3, bucket, prefix):
"""Overcome s3 response limit and return NestedDict tree of paths.
The NestedDict object also allows the user to search by the ends of a path.
The tree mimics a file directory structure, with the leave nodes being the
full unbroken key. For example, 'path/to/f... | Overcome s3 response limit and return NestedDict tree of paths.
The NestedDict object also allows the user to search by the ends of a path.
The tree mimics a file directory structure, with the leave nodes being the
full unbroken key. For example, 'path/to/file.txt' would be retrieved by
ret['path... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/util/aws.py#L206-L248 |
sorgerlab/indra | indra/assemblers/sif/assembler.py | SifAssembler.make_model | def make_model(self, use_name_as_key=False, include_mods=False,
include_complexes=False):
"""Assemble the graph from the assembler's list of INDRA Statements.
Parameters
----------
use_name_as_key : boolean
If True, uses the name of the agent as the key to... | python | def make_model(self, use_name_as_key=False, include_mods=False,
include_complexes=False):
"""Assemble the graph from the assembler's list of INDRA Statements.
Parameters
----------
use_name_as_key : boolean
If True, uses the name of the agent as the key to... | Assemble the graph from the assembler's list of INDRA Statements.
Parameters
----------
use_name_as_key : boolean
If True, uses the name of the agent as the key to the nodes in
the network. If False (default) uses the matches_key() of the
agent.
inclu... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/sif/assembler.py#L38-L81 |
sorgerlab/indra | indra/assemblers/sif/assembler.py | SifAssembler.print_model | def print_model(self, include_unsigned_edges=False):
"""Return a SIF string of the assembled model.
Parameters
----------
include_unsigned_edges : bool
If True, includes edges with an unknown activating/inactivating
relationship (e.g., most PTMs). Default is Fals... | python | def print_model(self, include_unsigned_edges=False):
"""Return a SIF string of the assembled model.
Parameters
----------
include_unsigned_edges : bool
If True, includes edges with an unknown activating/inactivating
relationship (e.g., most PTMs). Default is Fals... | Return a SIF string of the assembled model.
Parameters
----------
include_unsigned_edges : bool
If True, includes edges with an unknown activating/inactivating
relationship (e.g., most PTMs). Default is False. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/sif/assembler.py#L98-L122 |
sorgerlab/indra | indra/assemblers/sif/assembler.py | SifAssembler.save_model | def save_model(self, fname, include_unsigned_edges=False):
"""Save the assembled model's SIF string into a file.
Parameters
----------
fname : str
The name of the file to save the SIF into.
include_unsigned_edges : bool
If True, includes edges with an unk... | python | def save_model(self, fname, include_unsigned_edges=False):
"""Save the assembled model's SIF string into a file.
Parameters
----------
fname : str
The name of the file to save the SIF into.
include_unsigned_edges : bool
If True, includes edges with an unk... | Save the assembled model's SIF string into a file.
Parameters
----------
fname : str
The name of the file to save the SIF into.
include_unsigned_edges : bool
If True, includes edges with an unknown activating/inactivating
relationship (e.g., most PTMs... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/sif/assembler.py#L124-L137 |
sorgerlab/indra | indra/assemblers/sif/assembler.py | SifAssembler.print_loopy | def print_loopy(self, as_url=True):
"""Return
Parameters
----------
out_file : Optional[str]
A file name in which the Loopy network is saved.
Returns
-------
full_str : str
The string representing the Loopy network.
"""
i... | python | def print_loopy(self, as_url=True):
"""Return
Parameters
----------
out_file : Optional[str]
A file name in which the Loopy network is saved.
Returns
-------
full_str : str
The string representing the Loopy network.
"""
i... | Return
Parameters
----------
out_file : Optional[str]
A file name in which the Loopy network is saved.
Returns
-------
full_str : str
The string representing the Loopy network. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/sif/assembler.py#L139-L181 |
sorgerlab/indra | indra/assemblers/sif/assembler.py | SifAssembler.print_boolean_net | def print_boolean_net(self, out_file=None):
"""Return a Boolean network from the assembled graph.
See https://github.com/ialbert/booleannet for details about
the format used to encode the Boolean rules.
Parameters
----------
out_file : Optional[str]
A file n... | python | def print_boolean_net(self, out_file=None):
"""Return a Boolean network from the assembled graph.
See https://github.com/ialbert/booleannet for details about
the format used to encode the Boolean rules.
Parameters
----------
out_file : Optional[str]
A file n... | Return a Boolean network from the assembled graph.
See https://github.com/ialbert/booleannet for details about
the format used to encode the Boolean rules.
Parameters
----------
out_file : Optional[str]
A file name in which the Boolean network is saved.
Ret... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/sif/assembler.py#L183-L242 |
sorgerlab/indra | indra/literature/elsevier_client.py | _ensure_api_keys | def _ensure_api_keys(task_desc, failure_ret=None):
"""Wrap Elsevier methods which directly use the API keys.
Ensure that the keys are retrieved from the environment or config file when
first called, and store global scope. Subsequently use globally stashed
results and check for required ids.
"""
... | python | def _ensure_api_keys(task_desc, failure_ret=None):
"""Wrap Elsevier methods which directly use the API keys.
Ensure that the keys are retrieved from the environment or config file when
first called, and store global scope. Subsequently use globally stashed
results and check for required ids.
"""
... | Wrap Elsevier methods which directly use the API keys.
Ensure that the keys are retrieved from the environment or config file when
first called, and store global scope. Subsequently use globally stashed
results and check for required ids. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/literature/elsevier_client.py#L51-L85 |
sorgerlab/indra | indra/literature/elsevier_client.py | check_entitlement | def check_entitlement(doi):
"""Check whether IP and credentials enable access to content for a doi.
This function uses the entitlement endpoint of the Elsevier API to check
whether an article is available to a given institution. Note that this
feature of the API is itself not available for all institut... | python | def check_entitlement(doi):
"""Check whether IP and credentials enable access to content for a doi.
This function uses the entitlement endpoint of the Elsevier API to check
whether an article is available to a given institution. Note that this
feature of the API is itself not available for all institut... | Check whether IP and credentials enable access to content for a doi.
This function uses the entitlement endpoint of the Elsevier API to check
whether an article is available to a given institution. Note that this
feature of the API is itself not available for all institution keys. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/literature/elsevier_client.py#L89-L106 |
sorgerlab/indra | indra/literature/elsevier_client.py | download_article | def download_article(id_val, id_type='doi', on_retry=False):
"""Low level function to get an XML article for a particular id.
Parameters
----------
id_val : str
The value of the id.
id_type : str
The type of id, such as pmid (a.k.a. pubmed_id), doi, or eid.
on_retry : bool
... | python | def download_article(id_val, id_type='doi', on_retry=False):
"""Low level function to get an XML article for a particular id.
Parameters
----------
id_val : str
The value of the id.
id_type : str
The type of id, such as pmid (a.k.a. pubmed_id), doi, or eid.
on_retry : bool
... | Low level function to get an XML article for a particular id.
Parameters
----------
id_val : str
The value of the id.
id_type : str
The type of id, such as pmid (a.k.a. pubmed_id), doi, or eid.
on_retry : bool
This function has a recursive retry feature, and this is the only... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/literature/elsevier_client.py#L110-L158 |
sorgerlab/indra | indra/literature/elsevier_client.py | download_article_from_ids | def download_article_from_ids(**id_dict):
"""Download an article in XML format from Elsevier matching the set of ids.
Parameters
----------
<id_type> : str
You can enter any combination of eid, doi, pmid, and/or pii. Ids will be
checked in that order, until either content has been found... | python | def download_article_from_ids(**id_dict):
"""Download an article in XML format from Elsevier matching the set of ids.
Parameters
----------
<id_type> : str
You can enter any combination of eid, doi, pmid, and/or pii. Ids will be
checked in that order, until either content has been found... | Download an article in XML format from Elsevier matching the set of ids.
Parameters
----------
<id_type> : str
You can enter any combination of eid, doi, pmid, and/or pii. Ids will be
checked in that order, until either content has been found or all ids
have been checked.
Retur... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/literature/elsevier_client.py#L161-L192 |
sorgerlab/indra | indra/literature/elsevier_client.py | get_abstract | def get_abstract(doi):
"""Get the abstract text of an article from Elsevier given a doi."""
xml_string = download_article(doi)
if xml_string is None:
return None
assert isinstance(xml_string, str)
xml_tree = ET.XML(xml_string.encode('utf-8'), parser=UTB())
if xml_tree is None:
re... | python | def get_abstract(doi):
"""Get the abstract text of an article from Elsevier given a doi."""
xml_string = download_article(doi)
if xml_string is None:
return None
assert isinstance(xml_string, str)
xml_tree = ET.XML(xml_string.encode('utf-8'), parser=UTB())
if xml_tree is None:
re... | Get the abstract text of an article from Elsevier given a doi. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/literature/elsevier_client.py#L195-L207 |
sorgerlab/indra | indra/literature/elsevier_client.py | get_article | def get_article(doi, output_format='txt'):
"""Get the full body of an article from Elsevier.
Parameters
----------
doi : str
The doi for the desired article.
output_format : 'txt' or 'xml'
The desired format for the output. Selecting 'txt' (default) strips all
xml tags and j... | python | def get_article(doi, output_format='txt'):
"""Get the full body of an article from Elsevier.
Parameters
----------
doi : str
The doi for the desired article.
output_format : 'txt' or 'xml'
The desired format for the output. Selecting 'txt' (default) strips all
xml tags and j... | Get the full body of an article from Elsevier.
Parameters
----------
doi : str
The doi for the desired article.
output_format : 'txt' or 'xml'
The desired format for the output. Selecting 'txt' (default) strips all
xml tags and joins the pieces of text in the main text, while 'x... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/literature/elsevier_client.py#L210-L233 |
sorgerlab/indra | indra/literature/elsevier_client.py | extract_paragraphs | def extract_paragraphs(xml_string):
"""Get paragraphs from the body of the given Elsevier xml."""
assert isinstance(xml_string, str)
xml_tree = ET.XML(xml_string.encode('utf-8'), parser=UTB())
full_text = xml_tree.find('article:originalText', elsevier_ns)
if full_text is None:
logger.info('C... | python | def extract_paragraphs(xml_string):
"""Get paragraphs from the body of the given Elsevier xml."""
assert isinstance(xml_string, str)
xml_tree = ET.XML(xml_string.encode('utf-8'), parser=UTB())
full_text = xml_tree.find('article:originalText', elsevier_ns)
if full_text is None:
logger.info('C... | Get paragraphs from the body of the given Elsevier xml. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/literature/elsevier_client.py#L245-L259 |
sorgerlab/indra | indra/literature/elsevier_client.py | get_dois | def get_dois(query_str, count=100):
"""Search ScienceDirect through the API for articles.
See http://api.elsevier.com/content/search/fields/scidir for constructing a
query string to pass here. Example: 'abstract(BRAF) AND all("colorectal
cancer")'
"""
url = '%s/%s' % (elsevier_search_url, quer... | python | def get_dois(query_str, count=100):
"""Search ScienceDirect through the API for articles.
See http://api.elsevier.com/content/search/fields/scidir for constructing a
query string to pass here. Example: 'abstract(BRAF) AND all("colorectal
cancer")'
"""
url = '%s/%s' % (elsevier_search_url, quer... | Search ScienceDirect through the API for articles.
See http://api.elsevier.com/content/search/fields/scidir for constructing a
query string to pass here. Example: 'abstract(BRAF) AND all("colorectal
cancer")' | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/literature/elsevier_client.py#L264-L283 |
sorgerlab/indra | indra/literature/elsevier_client.py | get_piis | def get_piis(query_str):
"""Search ScienceDirect through the API for articles and return PIIs.
Note that ScienceDirect has a limitation in which a maximum of 6,000
PIIs can be retrieved for a given search and therefore this call is
internally broken up into multiple queries by a range of years and the
... | python | def get_piis(query_str):
"""Search ScienceDirect through the API for articles and return PIIs.
Note that ScienceDirect has a limitation in which a maximum of 6,000
PIIs can be retrieved for a given search and therefore this call is
internally broken up into multiple queries by a range of years and the
... | Search ScienceDirect through the API for articles and return PIIs.
Note that ScienceDirect has a limitation in which a maximum of 6,000
PIIs can be retrieved for a given search and therefore this call is
internally broken up into multiple queries by a range of years and the
results are combined.
P... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/literature/elsevier_client.py#L286-L306 |
sorgerlab/indra | indra/literature/elsevier_client.py | get_piis_for_date | def get_piis_for_date(query_str, date):
"""Search ScienceDirect with a query string constrained to a given year.
Parameters
----------
query_str : str
The query string to search with
date : str
The year to constrain the search to
Returns
-------
piis : list[str]
... | python | def get_piis_for_date(query_str, date):
"""Search ScienceDirect with a query string constrained to a given year.
Parameters
----------
query_str : str
The query string to search with
date : str
The year to constrain the search to
Returns
-------
piis : list[str]
... | Search ScienceDirect with a query string constrained to a given year.
Parameters
----------
query_str : str
The query string to search with
date : str
The year to constrain the search to
Returns
-------
piis : list[str]
The list of PIIs identifying the papers return... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/literature/elsevier_client.py#L311-L358 |
sorgerlab/indra | indra/literature/elsevier_client.py | download_from_search | def download_from_search(query_str, folder, do_extract_text=True,
max_results=None):
"""Save raw text files based on a search for papers on ScienceDirect.
This performs a search to get PIIs, downloads the XML corresponding to
the PII, extracts the raw text and then saves the text i... | python | def download_from_search(query_str, folder, do_extract_text=True,
max_results=None):
"""Save raw text files based on a search for papers on ScienceDirect.
This performs a search to get PIIs, downloads the XML corresponding to
the PII, extracts the raw text and then saves the text i... | Save raw text files based on a search for papers on ScienceDirect.
This performs a search to get PIIs, downloads the XML corresponding to
the PII, extracts the raw text and then saves the text into a file
in the designated folder.
Parameters
----------
query_str : str
The query string ... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/literature/elsevier_client.py#L361-L400 |
sorgerlab/indra | indra/sources/cwms/rdf_processor.py | CWMSRDFProcessor.extract_statement_from_query_result | def extract_statement_from_query_result(self, res):
"""Adds a statement based on one element of a rdflib SPARQL query.
Parameters
----------
res: rdflib.query.ResultRow
Element of rdflib SPARQL query result
"""
agent_start, agent_end, affected_start, affected... | python | def extract_statement_from_query_result(self, res):
"""Adds a statement based on one element of a rdflib SPARQL query.
Parameters
----------
res: rdflib.query.ResultRow
Element of rdflib SPARQL query result
"""
agent_start, agent_end, affected_start, affected... | Adds a statement based on one element of a rdflib SPARQL query.
Parameters
----------
res: rdflib.query.ResultRow
Element of rdflib SPARQL query result | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/cwms/rdf_processor.py#L45-L77 |
sorgerlab/indra | indra/sources/cwms/rdf_processor.py | CWMSRDFProcessor.extract_statements | def extract_statements(self):
"""Extracts INDRA statements from the RDF graph via SPARQL queries.
"""
# Look for events that have an AGENT and an AFFECTED, and get the
# start and ending text indices for each.
query = prefixes + """
SELECT
?agent_start
... | python | def extract_statements(self):
"""Extracts INDRA statements from the RDF graph via SPARQL queries.
"""
# Look for events that have an AGENT and an AFFECTED, and get the
# start and ending text indices for each.
query = prefixes + """
SELECT
?agent_start
... | Extracts INDRA statements from the RDF graph via SPARQL queries. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/cwms/rdf_processor.py#L79-L111 |
sorgerlab/indra | indra/sources/signor/processor.py | SignorProcessor._recursively_lookup_complex | def _recursively_lookup_complex(self, complex_id):
"""Looks up the constitutents of a complex. If any constituent is
itself a complex, recursively expands until all constituents are
not complexes."""
assert complex_id in self.complex_map
expanded_agent_strings = []
expan... | python | def _recursively_lookup_complex(self, complex_id):
"""Looks up the constitutents of a complex. If any constituent is
itself a complex, recursively expands until all constituents are
not complexes."""
assert complex_id in self.complex_map
expanded_agent_strings = []
expan... | Looks up the constitutents of a complex. If any constituent is
itself a complex, recursively expands until all constituents are
not complexes. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/signor/processor.py#L223-L244 |
sorgerlab/indra | indra/sources/signor/processor.py | SignorProcessor._get_complex_agents | def _get_complex_agents(self, complex_id):
"""Returns a list of agents corresponding to each of the constituents
in a SIGNOR complex."""
agents = []
components = self._recursively_lookup_complex(complex_id)
for c in components:
db_refs = {}
name = uniprot... | python | def _get_complex_agents(self, complex_id):
"""Returns a list of agents corresponding to each of the constituents
in a SIGNOR complex."""
agents = []
components = self._recursively_lookup_complex(complex_id)
for c in components:
db_refs = {}
name = uniprot... | Returns a list of agents corresponding to each of the constituents
in a SIGNOR complex. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/signor/processor.py#L246-L280 |
sorgerlab/indra | indra/statements/io.py | stmts_from_json | def stmts_from_json(json_in, on_missing_support='handle'):
"""Get a list of Statements from Statement jsons.
In the case of pre-assembled Statements which have `supports` and
`supported_by` lists, the uuids will be replaced with references to
Statement objects from the json, where possible. The method ... | python | def stmts_from_json(json_in, on_missing_support='handle'):
"""Get a list of Statements from Statement jsons.
In the case of pre-assembled Statements which have `supports` and
`supported_by` lists, the uuids will be replaced with references to
Statement objects from the json, where possible. The method ... | Get a list of Statements from Statement jsons.
In the case of pre-assembled Statements which have `supports` and
`supported_by` lists, the uuids will be replaced with references to
Statement objects from the json, where possible. The method of handling
missing support is controled by the `on_missing_su... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/statements/io.py#L16-L64 |
sorgerlab/indra | indra/statements/io.py | stmts_to_json_file | def stmts_to_json_file(stmts, fname):
"""Serialize a list of INDRA Statements into a JSON file.
Parameters
----------
stmts : list[indra.statement.Statements]
The list of INDRA Statements to serialize into the JSON file.
fname : str
Path to the JSON file to serialize Statements into... | python | def stmts_to_json_file(stmts, fname):
"""Serialize a list of INDRA Statements into a JSON file.
Parameters
----------
stmts : list[indra.statement.Statements]
The list of INDRA Statements to serialize into the JSON file.
fname : str
Path to the JSON file to serialize Statements into... | Serialize a list of INDRA Statements into a JSON file.
Parameters
----------
stmts : list[indra.statement.Statements]
The list of INDRA Statements to serialize into the JSON file.
fname : str
Path to the JSON file to serialize Statements into. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/statements/io.py#L84-L95 |
sorgerlab/indra | indra/statements/io.py | stmts_to_json | def stmts_to_json(stmts_in, use_sbo=False):
"""Return the JSON-serialized form of one or more INDRA Statements.
Parameters
----------
stmts_in : Statement or list[Statement]
A Statement or list of Statement objects to serialize into JSON.
use_sbo : Optional[bool]
If True, SBO annota... | python | def stmts_to_json(stmts_in, use_sbo=False):
"""Return the JSON-serialized form of one or more INDRA Statements.
Parameters
----------
stmts_in : Statement or list[Statement]
A Statement or list of Statement objects to serialize into JSON.
use_sbo : Optional[bool]
If True, SBO annota... | Return the JSON-serialized form of one or more INDRA Statements.
Parameters
----------
stmts_in : Statement or list[Statement]
A Statement or list of Statement objects to serialize into JSON.
use_sbo : Optional[bool]
If True, SBO annotations are added to each applicable element of the
... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/statements/io.py#L98-L119 |
sorgerlab/indra | indra/statements/io.py | _promote_support | def _promote_support(sup_list, uuid_dict, on_missing='handle'):
"""Promote the list of support-related uuids to Statements, if possible."""
valid_handling_choices = ['handle', 'error', 'ignore']
if on_missing not in valid_handling_choices:
raise InputError('Invalid option for `on_missing_support`: \... | python | def _promote_support(sup_list, uuid_dict, on_missing='handle'):
"""Promote the list of support-related uuids to Statements, if possible."""
valid_handling_choices = ['handle', 'error', 'ignore']
if on_missing not in valid_handling_choices:
raise InputError('Invalid option for `on_missing_support`: \... | Promote the list of support-related uuids to Statements, if possible. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/statements/io.py#L122-L139 |
sorgerlab/indra | indra/statements/io.py | draw_stmt_graph | def draw_stmt_graph(stmts):
"""Render the attributes of a list of Statements as directed graphs.
The layout works well for a single Statement or a few Statements at a time.
This function displays the plot of the graph using plt.show().
Parameters
----------
stmts : list[indra.statements.Statem... | python | def draw_stmt_graph(stmts):
"""Render the attributes of a list of Statements as directed graphs.
The layout works well for a single Statement or a few Statements at a time.
This function displays the plot of the graph using plt.show().
Parameters
----------
stmts : list[indra.statements.Statem... | Render the attributes of a list of Statements as directed graphs.
The layout works well for a single Statement or a few Statements at a time.
This function displays the plot of the graph using plt.show().
Parameters
----------
stmts : list[indra.statements.Statement]
A list of one or more ... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/statements/io.py#L142-L201 |
sorgerlab/indra | indra/sources/sparser/processor.py | _fix_json_agents | def _fix_json_agents(ag_obj):
"""Fix the json representation of an agent."""
if isinstance(ag_obj, str):
logger.info("Fixing string agent: %s." % ag_obj)
ret = {'name': ag_obj, 'db_refs': {'TEXT': ag_obj}}
elif isinstance(ag_obj, list):
# Recursive for complexes and similar.
... | python | def _fix_json_agents(ag_obj):
"""Fix the json representation of an agent."""
if isinstance(ag_obj, str):
logger.info("Fixing string agent: %s." % ag_obj)
ret = {'name': ag_obj, 'db_refs': {'TEXT': ag_obj}}
elif isinstance(ag_obj, list):
# Recursive for complexes and similar.
... | Fix the json representation of an agent. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/sparser/processor.py#L23-L37 |
sorgerlab/indra | indra/sources/sparser/processor.py | SparserJSONProcessor.set_statements_pmid | def set_statements_pmid(self, pmid):
"""Set the evidence PMID of Statements that have been extracted.
Parameters
----------
pmid : str or None
The PMID to be used in the Evidence objects of the Statements
that were extracted by the processor.
"""
... | python | def set_statements_pmid(self, pmid):
"""Set the evidence PMID of Statements that have been extracted.
Parameters
----------
pmid : str or None
The PMID to be used in the Evidence objects of the Statements
that were extracted by the processor.
"""
... | Set the evidence PMID of Statements that have been extracted.
Parameters
----------
pmid : str or None
The PMID to be used in the Evidence objects of the Statements
that were extracted by the processor. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/sparser/processor.py#L155-L172 |
sorgerlab/indra | indra/sources/trips/analyze_ekbs.py | get_args | def get_args(node):
"""Return the arguments of a node in the event graph."""
arg_roles = {}
args = node.findall('arg') + \
[node.find('arg1'), node.find('arg2'), node.find('arg3')]
for arg in args:
if arg is not None:
id = arg.attrib.get('id')
if id is not None:
... | python | def get_args(node):
"""Return the arguments of a node in the event graph."""
arg_roles = {}
args = node.findall('arg') + \
[node.find('arg1'), node.find('arg2'), node.find('arg3')]
for arg in args:
if arg is not None:
id = arg.attrib.get('id')
if id is not None:
... | Return the arguments of a node in the event graph. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/trips/analyze_ekbs.py#L20-L47 |
sorgerlab/indra | indra/sources/trips/analyze_ekbs.py | type_match | def type_match(a, b):
"""Return True of the types of a and b are compatible, False otherwise."""
# If the types are the same, return True
if a['type'] == b['type']:
return True
# Otherwise, look at some special cases
eq_groups = [
{'ONT::GENE-PROTEIN', 'ONT::GENE', 'ONT::PROTEIN'},
... | python | def type_match(a, b):
"""Return True of the types of a and b are compatible, False otherwise."""
# If the types are the same, return True
if a['type'] == b['type']:
return True
# Otherwise, look at some special cases
eq_groups = [
{'ONT::GENE-PROTEIN', 'ONT::GENE', 'ONT::PROTEIN'},
... | Return True of the types of a and b are compatible, False otherwise. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/trips/analyze_ekbs.py#L58-L71 |
sorgerlab/indra | indra/sources/trips/analyze_ekbs.py | add_graph | def add_graph(patterns, G):
"""Add a graph to a set of unique patterns."""
if not patterns:
patterns.append([G])
return
for i, graphs in enumerate(patterns):
if networkx.is_isomorphic(graphs[0], G, node_match=type_match,
edge_match=type_match):
... | python | def add_graph(patterns, G):
"""Add a graph to a set of unique patterns."""
if not patterns:
patterns.append([G])
return
for i, graphs in enumerate(patterns):
if networkx.is_isomorphic(graphs[0], G, node_match=type_match,
edge_match=type_match):
... | Add a graph to a set of unique patterns. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/trips/analyze_ekbs.py#L74-L84 |
sorgerlab/indra | indra/sources/trips/analyze_ekbs.py | draw | def draw(graph, fname):
"""Draw a graph and save it into a file"""
ag = networkx.nx_agraph.to_agraph(graph)
ag.draw(fname, prog='dot') | python | def draw(graph, fname):
"""Draw a graph and save it into a file"""
ag = networkx.nx_agraph.to_agraph(graph)
ag.draw(fname, prog='dot') | Draw a graph and save it into a file | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/trips/analyze_ekbs.py#L87-L90 |
sorgerlab/indra | indra/sources/trips/analyze_ekbs.py | build_patterns | def build_patterns(fnames):
"""Return a list of CC/EVENT graph patterns from a list of EKB files"""
patterns = []
for fn in fnames:
et = ET.parse(fn)
res = et.findall('CC') + et.findall('EVENT')
for event in res:
G = networkx.DiGraph()
build_event_graph(G, et,... | python | def build_patterns(fnames):
"""Return a list of CC/EVENT graph patterns from a list of EKB files"""
patterns = []
for fn in fnames:
et = ET.parse(fn)
res = et.findall('CC') + et.findall('EVENT')
for event in res:
G = networkx.DiGraph()
build_event_graph(G, et,... | Return a list of CC/EVENT graph patterns from a list of EKB files | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/trips/analyze_ekbs.py#L93-L104 |
sorgerlab/indra | indra/sources/trips/analyze_ekbs.py | build_event_graph | def build_event_graph(graph, tree, node):
"""Return a DiGraph of a specific event structure, built recursively"""
# If we have already added this node then let's return
if node_key(node) in graph:
return
type = get_type(node)
text = get_text(node)
label = '%s (%s)' % (type, text)
gra... | python | def build_event_graph(graph, tree, node):
"""Return a DiGraph of a specific event structure, built recursively"""
# If we have already added this node then let's return
if node_key(node) in graph:
return
type = get_type(node)
text = get_text(node)
label = '%s (%s)' % (type, text)
gra... | Return a DiGraph of a specific event structure, built recursively | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/trips/analyze_ekbs.py#L107-L123 |
sorgerlab/indra | indra/sources/trips/analyze_ekbs.py | get_extracted_events | def get_extracted_events(fnames):
"""Get a full list of all extracted event IDs from a list of EKB files"""
event_list = []
for fn in fnames:
tp = trips.process_xml_file(fn)
ed = tp.extracted_events
for k, v in ed.items():
event_list += v
return event_list | python | def get_extracted_events(fnames):
"""Get a full list of all extracted event IDs from a list of EKB files"""
event_list = []
for fn in fnames:
tp = trips.process_xml_file(fn)
ed = tp.extracted_events
for k, v in ed.items():
event_list += v
return event_list | Get a full list of all extracted event IDs from a list of EKB files | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/trips/analyze_ekbs.py#L126-L134 |
sorgerlab/indra | indra/sources/trips/analyze_ekbs.py | check_event_coverage | def check_event_coverage(patterns, event_list):
"""Calculate the ratio of patterns that were extracted."""
proportions = []
for pattern_list in patterns:
proportion = 0
for pattern in pattern_list:
for node in pattern.nodes():
if node in event_list:
... | python | def check_event_coverage(patterns, event_list):
"""Calculate the ratio of patterns that were extracted."""
proportions = []
for pattern_list in patterns:
proportion = 0
for pattern in pattern_list:
for node in pattern.nodes():
if node in event_list:
... | Calculate the ratio of patterns that were extracted. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/trips/analyze_ekbs.py#L137-L148 |
sorgerlab/indra | indra/preassembler/ontology_mapper.py | _load_wm_map | def _load_wm_map(exclude_auto=None):
"""Load an ontology map for world models.
exclude_auto : None or list[tuple]
A list of ontology mappings for which automated mappings should be
excluded, e.g. [(HUME, UN)] would result in not using mappings
from HUME to UN.
"""
exclude_auto =... | python | def _load_wm_map(exclude_auto=None):
"""Load an ontology map for world models.
exclude_auto : None or list[tuple]
A list of ontology mappings for which automated mappings should be
excluded, e.g. [(HUME, UN)] would result in not using mappings
from HUME to UN.
"""
exclude_auto =... | Load an ontology map for world models.
exclude_auto : None or list[tuple]
A list of ontology mappings for which automated mappings should be
excluded, e.g. [(HUME, UN)] would result in not using mappings
from HUME to UN. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/preassembler/ontology_mapper.py#L102-L215 |
sorgerlab/indra | indra/preassembler/ontology_mapper.py | OntologyMapper.map_statements | def map_statements(self):
"""Run the ontology mapping on the statements."""
for stmt in self.statements:
for agent in stmt.agent_list():
if agent is None:
continue
all_mappings = []
for db_name, db_id in agent.db_refs.items(... | python | def map_statements(self):
"""Run the ontology mapping on the statements."""
for stmt in self.statements:
for agent in stmt.agent_list():
if agent is None:
continue
all_mappings = []
for db_name, db_id in agent.db_refs.items(... | Run the ontology mapping on the statements. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/preassembler/ontology_mapper.py#L45-L74 |
sorgerlab/indra | indra/preassembler/grounding_mapper.py | load_grounding_map | def load_grounding_map(grounding_map_path, ignore_path=None,
lineterminator='\r\n'):
"""Return a grounding map dictionary loaded from a csv file.
In the file pointed to by grounding_map_path, the number of name_space ID
pairs can vary per row and commas are
used to pad out entrie... | python | def load_grounding_map(grounding_map_path, ignore_path=None,
lineterminator='\r\n'):
"""Return a grounding map dictionary loaded from a csv file.
In the file pointed to by grounding_map_path, the number of name_space ID
pairs can vary per row and commas are
used to pad out entrie... | Return a grounding map dictionary loaded from a csv file.
In the file pointed to by grounding_map_path, the number of name_space ID
pairs can vary per row and commas are
used to pad out entries containing fewer than the maximum amount of
name spaces appearing in the file. Lines should be terminated wit... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/preassembler/grounding_mapper.py#L360-L421 |
sorgerlab/indra | indra/preassembler/grounding_mapper.py | all_agents | def all_agents(stmts):
"""Return a list of all of the agents from a list of statements.
Only agents that are not None and have a TEXT entry are returned.
Parameters
----------
stmts : list of :py:class:`indra.statements.Statement`
Returns
-------
agents : list of :py:class:`indra.stat... | python | def all_agents(stmts):
"""Return a list of all of the agents from a list of statements.
Only agents that are not None and have a TEXT entry are returned.
Parameters
----------
stmts : list of :py:class:`indra.statements.Statement`
Returns
-------
agents : list of :py:class:`indra.stat... | Return a list of all of the agents from a list of statements.
Only agents that are not None and have a TEXT entry are returned.
Parameters
----------
stmts : list of :py:class:`indra.statements.Statement`
Returns
-------
agents : list of :py:class:`indra.statements.Agent`
List of ... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/preassembler/grounding_mapper.py#L426-L447 |
sorgerlab/indra | indra/preassembler/grounding_mapper.py | get_sentences_for_agent | def get_sentences_for_agent(text, stmts, max_sentences=None):
"""Returns evidence sentences with a given agent text from a list of statements
Parameters
----------
text : str
An agent text
stmts : list of :py:class:`indra.statements.Statement`
INDRA Statements to search in for evid... | python | def get_sentences_for_agent(text, stmts, max_sentences=None):
"""Returns evidence sentences with a given agent text from a list of statements
Parameters
----------
text : str
An agent text
stmts : list of :py:class:`indra.statements.Statement`
INDRA Statements to search in for evid... | Returns evidence sentences with a given agent text from a list of statements
Parameters
----------
text : str
An agent text
stmts : list of :py:class:`indra.statements.Statement`
INDRA Statements to search in for evidence statements.
max_sentences : Optional[int/None]
Cap ... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/preassembler/grounding_mapper.py#L467-L496 |
sorgerlab/indra | indra/preassembler/grounding_mapper.py | agent_texts_with_grounding | def agent_texts_with_grounding(stmts):
"""Return agent text groundings in a list of statements with their counts
Parameters
----------
stmts: list of :py:class:`indra.statements.Statement`
Returns
-------
list of tuple
List of tuples of the form
(text: str, ((name_space: st... | python | def agent_texts_with_grounding(stmts):
"""Return agent text groundings in a list of statements with their counts
Parameters
----------
stmts: list of :py:class:`indra.statements.Statement`
Returns
-------
list of tuple
List of tuples of the form
(text: str, ((name_space: st... | Return agent text groundings in a list of statements with their counts
Parameters
----------
stmts: list of :py:class:`indra.statements.Statement`
Returns
-------
list of tuple
List of tuples of the form
(text: str, ((name_space: str, ID: str, count: int)...),
total_cou... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/preassembler/grounding_mapper.py#L499-L559 |
sorgerlab/indra | indra/preassembler/grounding_mapper.py | ungrounded_texts | def ungrounded_texts(stmts):
"""Return a list of all ungrounded entities ordered by number of mentions
Parameters
----------
stmts : list of :py:class:`indra.statements.Statement`
Returns
-------
ungroundc : list of tuple
list of tuples of the form (text: str, count: int) sorted in ... | python | def ungrounded_texts(stmts):
"""Return a list of all ungrounded entities ordered by number of mentions
Parameters
----------
stmts : list of :py:class:`indra.statements.Statement`
Returns
-------
ungroundc : list of tuple
list of tuples of the form (text: str, count: int) sorted in ... | Return a list of all ungrounded entities ordered by number of mentions
Parameters
----------
stmts : list of :py:class:`indra.statements.Statement`
Returns
-------
ungroundc : list of tuple
list of tuples of the form (text: str, count: int) sorted in descending
order by count. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/preassembler/grounding_mapper.py#L563-L583 |
sorgerlab/indra | indra/preassembler/grounding_mapper.py | get_agents_with_name | def get_agents_with_name(name, stmts):
"""Return all agents within a list of statements with a particular name."""
return [ag for stmt in stmts for ag in stmt.agent_list()
if ag is not None and ag.name == name] | python | def get_agents_with_name(name, stmts):
"""Return all agents within a list of statements with a particular name."""
return [ag for stmt in stmts for ag in stmt.agent_list()
if ag is not None and ag.name == name] | Return all agents within a list of statements with a particular name. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/preassembler/grounding_mapper.py#L586-L589 |
sorgerlab/indra | indra/preassembler/grounding_mapper.py | save_base_map | def save_base_map(filename, grouped_by_text):
"""Dump a list of agents along with groundings and counts into a csv file
Parameters
----------
filename : str
Filepath for output file
grouped_by_text : list of tuple
List of tuples of the form output by agent_texts_with_grounding
"... | python | def save_base_map(filename, grouped_by_text):
"""Dump a list of agents along with groundings and counts into a csv file
Parameters
----------
filename : str
Filepath for output file
grouped_by_text : list of tuple
List of tuples of the form output by agent_texts_with_grounding
"... | Dump a list of agents along with groundings and counts into a csv file
Parameters
----------
filename : str
Filepath for output file
grouped_by_text : list of tuple
List of tuples of the form output by agent_texts_with_grounding | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/preassembler/grounding_mapper.py#L592-L614 |
sorgerlab/indra | indra/preassembler/grounding_mapper.py | protein_map_from_twg | def protein_map_from_twg(twg):
"""Build map of entity texts to validate protein grounding.
Looks at the grounding of the entity texts extracted from the statements
and finds proteins where there is grounding to a human protein that maps to
an HGNC name that is an exact match to the entity text. Return... | python | def protein_map_from_twg(twg):
"""Build map of entity texts to validate protein grounding.
Looks at the grounding of the entity texts extracted from the statements
and finds proteins where there is grounding to a human protein that maps to
an HGNC name that is an exact match to the entity text. Return... | Build map of entity texts to validate protein grounding.
Looks at the grounding of the entity texts extracted from the statements
and finds proteins where there is grounding to a human protein that maps to
an HGNC name that is an exact match to the entity text. Returns a dict that
can be used to updat... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/preassembler/grounding_mapper.py#L617-L671 |
sorgerlab/indra | indra/preassembler/grounding_mapper.py | save_sentences | def save_sentences(twg, stmts, filename, agent_limit=300):
"""Write evidence sentences for stmts with ungrounded agents to csv file.
Parameters
----------
twg: list of tuple
list of tuples of ungrounded agent_texts with counts of the
number of times they are mentioned in the list of sta... | python | def save_sentences(twg, stmts, filename, agent_limit=300):
"""Write evidence sentences for stmts with ungrounded agents to csv file.
Parameters
----------
twg: list of tuple
list of tuples of ungrounded agent_texts with counts of the
number of times they are mentioned in the list of sta... | Write evidence sentences for stmts with ungrounded agents to csv file.
Parameters
----------
twg: list of tuple
list of tuples of ungrounded agent_texts with counts of the
number of times they are mentioned in the list of statements.
Should be sorted in descending order by the count... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/preassembler/grounding_mapper.py#L674-L707 |
sorgerlab/indra | indra/preassembler/grounding_mapper.py | _get_text_for_grounding | def _get_text_for_grounding(stmt, agent_text):
"""Get text context for Deft disambiguation
If the INDRA database is available, attempts to get the fulltext from
which the statement was extracted. If the fulltext is not available, the
abstract is returned. If the indra database is not available, uses th... | python | def _get_text_for_grounding(stmt, agent_text):
"""Get text context for Deft disambiguation
If the INDRA database is available, attempts to get the fulltext from
which the statement was extracted. If the fulltext is not available, the
abstract is returned. If the indra database is not available, uses th... | Get text context for Deft disambiguation
If the INDRA database is available, attempts to get the fulltext from
which the statement was extracted. If the fulltext is not available, the
abstract is returned. If the indra database is not available, uses the
pubmed client to get the abstract. If no abstrac... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/preassembler/grounding_mapper.py#L743-L798 |
sorgerlab/indra | indra/preassembler/grounding_mapper.py | GroundingMapper.update_agent_db_refs | def update_agent_db_refs(self, agent, agent_text, do_rename=True):
"""Update db_refs of agent using the grounding map
If the grounding map is missing one of the HGNC symbol or Uniprot ID,
attempts to reconstruct one from the other.
Parameters
----------
agent : :py:clas... | python | def update_agent_db_refs(self, agent, agent_text, do_rename=True):
"""Update db_refs of agent using the grounding map
If the grounding map is missing one of the HGNC symbol or Uniprot ID,
attempts to reconstruct one from the other.
Parameters
----------
agent : :py:clas... | Update db_refs of agent using the grounding map
If the grounding map is missing one of the HGNC symbol or Uniprot ID,
attempts to reconstruct one from the other.
Parameters
----------
agent : :py:class:`indra.statements.Agent`
The agent whose db_refs will be updated... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/preassembler/grounding_mapper.py#L51-L83 |
sorgerlab/indra | indra/preassembler/grounding_mapper.py | GroundingMapper.map_agents_for_stmt | def map_agents_for_stmt(self, stmt, do_rename=True):
"""Return a new Statement whose agents have been grounding mapped.
Parameters
----------
stmt : :py:class:`indra.statements.Statement`
The Statement whose agents need mapping.
do_rename: Optional[bool]
... | python | def map_agents_for_stmt(self, stmt, do_rename=True):
"""Return a new Statement whose agents have been grounding mapped.
Parameters
----------
stmt : :py:class:`indra.statements.Statement`
The Statement whose agents need mapping.
do_rename: Optional[bool]
... | Return a new Statement whose agents have been grounding mapped.
Parameters
----------
stmt : :py:class:`indra.statements.Statement`
The Statement whose agents need mapping.
do_rename: Optional[bool]
If True, the Agent name is updated based on the mapped grounding... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/preassembler/grounding_mapper.py#L150-L217 |
sorgerlab/indra | indra/preassembler/grounding_mapper.py | GroundingMapper.map_agent | def map_agent(self, agent, do_rename):
"""Return the given Agent with its grounding mapped.
This function grounds a single agent. It returns the new Agent object
(which might be a different object if we load a new agent state
from json) or the same object otherwise.
Parameters
... | python | def map_agent(self, agent, do_rename):
"""Return the given Agent with its grounding mapped.
This function grounds a single agent. It returns the new Agent object
(which might be a different object if we load a new agent state
from json) or the same object otherwise.
Parameters
... | Return the given Agent with its grounding mapped.
This function grounds a single agent. It returns the new Agent object
(which might be a different object if we load a new agent state
from json) or the same object otherwise.
Parameters
----------
agent : :py:class:`indr... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/preassembler/grounding_mapper.py#L219-L268 |
sorgerlab/indra | indra/preassembler/grounding_mapper.py | GroundingMapper.map_agents | def map_agents(self, stmts, do_rename=True):
"""Return a new list of statements whose agents have been mapped
Parameters
----------
stmts : list of :py:class:`indra.statements.Statement`
The statements whose agents need mapping
do_rename: Optional[bool]
I... | python | def map_agents(self, stmts, do_rename=True):
"""Return a new list of statements whose agents have been mapped
Parameters
----------
stmts : list of :py:class:`indra.statements.Statement`
The statements whose agents need mapping
do_rename: Optional[bool]
I... | Return a new list of statements whose agents have been mapped
Parameters
----------
stmts : list of :py:class:`indra.statements.Statement`
The statements whose agents need mapping
do_rename: Optional[bool]
If True, the Agent name is updated based on the mapped gr... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/preassembler/grounding_mapper.py#L270-L301 |
sorgerlab/indra | indra/preassembler/grounding_mapper.py | GroundingMapper.rename_agents | def rename_agents(self, stmts):
"""Return a list of mapped statements with updated agent names.
Creates a new list of statements without modifying the original list.
The agents in a statement should be renamed if the grounding map has
updated their db_refs. If an agent contains a FamPl... | python | def rename_agents(self, stmts):
"""Return a list of mapped statements with updated agent names.
Creates a new list of statements without modifying the original list.
The agents in a statement should be renamed if the grounding map has
updated their db_refs. If an agent contains a FamPl... | Return a list of mapped statements with updated agent names.
Creates a new list of statements without modifying the original list.
The agents in a statement should be renamed if the grounding map has
updated their db_refs. If an agent contains a FamPlex grounding, the
FamPlex ID is use... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/preassembler/grounding_mapper.py#L303-L355 |
sorgerlab/indra | indra/sources/hprd/processor.py | HprdProcessor.get_complexes | def get_complexes(self, cplx_df):
"""Generate Complex Statements from the HPRD protein complexes data.
Parameters
----------
cplx_df : pandas.DataFrame
DataFrame loaded from the PROTEIN_COMPLEXES.txt file.
"""
# Group the agents for the complex
logg... | python | def get_complexes(self, cplx_df):
"""Generate Complex Statements from the HPRD protein complexes data.
Parameters
----------
cplx_df : pandas.DataFrame
DataFrame loaded from the PROTEIN_COMPLEXES.txt file.
"""
# Group the agents for the complex
logg... | Generate Complex Statements from the HPRD protein complexes data.
Parameters
----------
cplx_df : pandas.DataFrame
DataFrame loaded from the PROTEIN_COMPLEXES.txt file. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/hprd/processor.py#L151-L176 |
sorgerlab/indra | indra/sources/hprd/processor.py | HprdProcessor.get_ptms | def get_ptms(self, ptm_df):
"""Generate Modification statements from the HPRD PTM data.
Parameters
----------
ptm_df : pandas.DataFrame
DataFrame loaded from the POST_TRANSLATIONAL_MODIFICATIONS.txt file.
"""
logger.info('Processing PTMs...')
# Iterat... | python | def get_ptms(self, ptm_df):
"""Generate Modification statements from the HPRD PTM data.
Parameters
----------
ptm_df : pandas.DataFrame
DataFrame loaded from the POST_TRANSLATIONAL_MODIFICATIONS.txt file.
"""
logger.info('Processing PTMs...')
# Iterat... | Generate Modification statements from the HPRD PTM data.
Parameters
----------
ptm_df : pandas.DataFrame
DataFrame loaded from the POST_TRANSLATIONAL_MODIFICATIONS.txt file. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/hprd/processor.py#L178-L220 |
sorgerlab/indra | indra/sources/hprd/processor.py | HprdProcessor.get_ppis | def get_ppis(self, ppi_df):
"""Generate Complex Statements from the HPRD PPI data.
Parameters
----------
ppi_df : pandas.DataFrame
DataFrame loaded from the BINARY_PROTEIN_PROTEIN_INTERACTIONS.txt
file.
"""
logger.info('Processing PPIs...')
... | python | def get_ppis(self, ppi_df):
"""Generate Complex Statements from the HPRD PPI data.
Parameters
----------
ppi_df : pandas.DataFrame
DataFrame loaded from the BINARY_PROTEIN_PROTEIN_INTERACTIONS.txt
file.
"""
logger.info('Processing PPIs...')
... | Generate Complex Statements from the HPRD PPI data.
Parameters
----------
ppi_df : pandas.DataFrame
DataFrame loaded from the BINARY_PROTEIN_PROTEIN_INTERACTIONS.txt
file. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/hprd/processor.py#L222-L243 |
sorgerlab/indra | indra/sources/isi/processor.py | _build_verb_statement_mapping | def _build_verb_statement_mapping():
"""Build the mapping between ISI verb strings and INDRA statement classes.
Looks up the INDRA statement class name, if any, in a resource file,
and resolves this class name to a class.
Returns
-------
verb_to_statement_type : dict
Dictionary mapping... | python | def _build_verb_statement_mapping():
"""Build the mapping between ISI verb strings and INDRA statement classes.
Looks up the INDRA statement class name, if any, in a resource file,
and resolves this class name to a class.
Returns
-------
verb_to_statement_type : dict
Dictionary mapping... | Build the mapping between ISI verb strings and INDRA statement classes.
Looks up the INDRA statement class name, if any, in a resource file,
and resolves this class name to a class.
Returns
-------
verb_to_statement_type : dict
Dictionary mapping verb name to an INDRA statment class | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/isi/processor.py#L167-L198 |
sorgerlab/indra | indra/sources/isi/processor.py | IsiProcessor.get_statements | def get_statements(self):
"""Process reader output to produce INDRA Statements."""
for k, v in self.reader_output.items():
for interaction in v['interactions']:
self._process_interaction(k, interaction, v['text'], self.pmid,
self.extr... | python | def get_statements(self):
"""Process reader output to produce INDRA Statements."""
for k, v in self.reader_output.items():
for interaction in v['interactions']:
self._process_interaction(k, interaction, v['text'], self.pmid,
self.extr... | Process reader output to produce INDRA Statements. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/isi/processor.py#L38-L43 |
sorgerlab/indra | indra/sources/isi/processor.py | IsiProcessor._process_interaction | def _process_interaction(self, source_id, interaction, text, pmid,
extra_annotations):
"""Process an interaction JSON tuple from the ISI output, and adds up
to one statement to the list of extracted statements.
Parameters
----------
source_id : str
... | python | def _process_interaction(self, source_id, interaction, text, pmid,
extra_annotations):
"""Process an interaction JSON tuple from the ISI output, and adds up
to one statement to the list of extracted statements.
Parameters
----------
source_id : str
... | Process an interaction JSON tuple from the ISI output, and adds up
to one statement to the list of extracted statements.
Parameters
----------
source_id : str
the JSON key corresponding to the sentence in the ISI output
interaction: the JSON list with subject/ver... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/isi/processor.py#L59-L146 |
sorgerlab/indra | indra/sources/geneways/actionmention_parser.py | GenewaysActionMention.make_annotation | def make_annotation(self):
"""Returns a dictionary with all properties of the action mention."""
annotation = dict()
# Put all properties of the action object into the annotation
for item in dir(self):
if len(item) > 0 and item[0] != '_' and \
not inspect... | python | def make_annotation(self):
"""Returns a dictionary with all properties of the action mention."""
annotation = dict()
# Put all properties of the action object into the annotation
for item in dir(self):
if len(item) > 0 and item[0] != '_' and \
not inspect... | Returns a dictionary with all properties of the action mention. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/geneways/actionmention_parser.py#L31-L41 |
sorgerlab/indra | indra/sources/biopax/processor.py | _match_to_array | def _match_to_array(m):
""" Returns an array consisting of the elements obtained from a pattern
search cast into their appropriate classes. """
return [_cast_biopax_element(m.get(i)) for i in range(m.varSize())] | python | def _match_to_array(m):
""" Returns an array consisting of the elements obtained from a pattern
search cast into their appropriate classes. """
return [_cast_biopax_element(m.get(i)) for i in range(m.varSize())] | Returns an array consisting of the elements obtained from a pattern
search cast into their appropriate classes. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/biopax/processor.py#L1374-L1377 |
sorgerlab/indra | indra/sources/biopax/processor.py | _is_complex | def _is_complex(pe):
"""Return True if the physical entity is a complex"""
val = isinstance(pe, _bp('Complex')) or \
isinstance(pe, _bpimpl('Complex'))
return val | python | def _is_complex(pe):
"""Return True if the physical entity is a complex"""
val = isinstance(pe, _bp('Complex')) or \
isinstance(pe, _bpimpl('Complex'))
return val | Return True if the physical entity is a complex | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/biopax/processor.py#L1379-L1383 |
sorgerlab/indra | indra/sources/biopax/processor.py | _is_protein | def _is_protein(pe):
"""Return True if the element is a protein"""
val = isinstance(pe, _bp('Protein')) or \
isinstance(pe, _bpimpl('Protein')) or \
isinstance(pe, _bp('ProteinReference')) or \
isinstance(pe, _bpimpl('ProteinReference'))
return val | python | def _is_protein(pe):
"""Return True if the element is a protein"""
val = isinstance(pe, _bp('Protein')) or \
isinstance(pe, _bpimpl('Protein')) or \
isinstance(pe, _bp('ProteinReference')) or \
isinstance(pe, _bpimpl('ProteinReference'))
return val | Return True if the element is a protein | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/biopax/processor.py#L1385-L1391 |
sorgerlab/indra | indra/sources/biopax/processor.py | _is_rna | def _is_rna(pe):
"""Return True if the element is an RNA"""
val = isinstance(pe, _bp('Rna')) or isinstance(pe, _bpimpl('Rna'))
return val | python | def _is_rna(pe):
"""Return True if the element is an RNA"""
val = isinstance(pe, _bp('Rna')) or isinstance(pe, _bpimpl('Rna'))
return val | Return True if the element is an RNA | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/biopax/processor.py#L1393-L1396 |
sorgerlab/indra | indra/sources/biopax/processor.py | _is_small_molecule | def _is_small_molecule(pe):
"""Return True if the element is a small molecule"""
val = isinstance(pe, _bp('SmallMolecule')) or \
isinstance(pe, _bpimpl('SmallMolecule')) or \
isinstance(pe, _bp('SmallMoleculeReference')) or \
isinstance(pe, _bpimpl('SmallMoleculeReference'))
... | python | def _is_small_molecule(pe):
"""Return True if the element is a small molecule"""
val = isinstance(pe, _bp('SmallMolecule')) or \
isinstance(pe, _bpimpl('SmallMolecule')) or \
isinstance(pe, _bp('SmallMoleculeReference')) or \
isinstance(pe, _bpimpl('SmallMoleculeReference'))
... | Return True if the element is a small molecule | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/biopax/processor.py#L1398-L1404 |
sorgerlab/indra | indra/sources/biopax/processor.py | _is_physical_entity | def _is_physical_entity(pe):
"""Return True if the element is a physical entity"""
val = isinstance(pe, _bp('PhysicalEntity')) or \
isinstance(pe, _bpimpl('PhysicalEntity'))
return val | python | def _is_physical_entity(pe):
"""Return True if the element is a physical entity"""
val = isinstance(pe, _bp('PhysicalEntity')) or \
isinstance(pe, _bpimpl('PhysicalEntity'))
return val | Return True if the element is a physical entity | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/biopax/processor.py#L1406-L1410 |
sorgerlab/indra | indra/sources/biopax/processor.py | _is_modification_or_activity | def _is_modification_or_activity(feature):
"""Return True if the feature is a modification"""
if not (isinstance(feature, _bp('ModificationFeature')) or \
isinstance(feature, _bpimpl('ModificationFeature'))):
return None
mf_type = feature.getModificationType()
if mf_type is None:
... | python | def _is_modification_or_activity(feature):
"""Return True if the feature is a modification"""
if not (isinstance(feature, _bp('ModificationFeature')) or \
isinstance(feature, _bpimpl('ModificationFeature'))):
return None
mf_type = feature.getModificationType()
if mf_type is None:
... | Return True if the feature is a modification | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/biopax/processor.py#L1418-L1432 |
sorgerlab/indra | indra/sources/biopax/processor.py | _is_reference | def _is_reference(bpe):
"""Return True if the element is an entity reference."""
if isinstance(bpe, _bp('ProteinReference')) or \
isinstance(bpe, _bpimpl('ProteinReference')) or \
isinstance(bpe, _bp('SmallMoleculeReference')) or \
isinstance(bpe, _bpimpl('SmallMoleculeReference')) or \
... | python | def _is_reference(bpe):
"""Return True if the element is an entity reference."""
if isinstance(bpe, _bp('ProteinReference')) or \
isinstance(bpe, _bpimpl('ProteinReference')) or \
isinstance(bpe, _bp('SmallMoleculeReference')) or \
isinstance(bpe, _bpimpl('SmallMoleculeReference')) or \
... | Return True if the element is an entity reference. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/biopax/processor.py#L1434-L1446 |
sorgerlab/indra | indra/sources/biopax/processor.py | _is_entity | def _is_entity(bpe):
"""Return True if the element is a physical entity."""
if isinstance(bpe, _bp('Protein')) or \
isinstance(bpe, _bpimpl('Protein')) or \
isinstance(bpe, _bp('SmallMolecule')) or \
isinstance(bpe, _bpimpl('SmallMolecule')) or \
isinstance(bpe, _bp('Complex')) o... | python | def _is_entity(bpe):
"""Return True if the element is a physical entity."""
if isinstance(bpe, _bp('Protein')) or \
isinstance(bpe, _bpimpl('Protein')) or \
isinstance(bpe, _bp('SmallMolecule')) or \
isinstance(bpe, _bpimpl('SmallMolecule')) or \
isinstance(bpe, _bp('Complex')) o... | Return True if the element is a physical entity. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/biopax/processor.py#L1448-L1466 |
sorgerlab/indra | indra/sources/biopax/processor.py | _is_catalysis | def _is_catalysis(bpe):
"""Return True if the element is Catalysis."""
if isinstance(bpe, _bp('Catalysis')) or \
isinstance(bpe, _bpimpl('Catalysis')):
return True
else:
return False | python | def _is_catalysis(bpe):
"""Return True if the element is Catalysis."""
if isinstance(bpe, _bp('Catalysis')) or \
isinstance(bpe, _bpimpl('Catalysis')):
return True
else:
return False | Return True if the element is Catalysis. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/biopax/processor.py#L1468-L1474 |
sorgerlab/indra | indra/sources/biopax/processor.py | BiopaxProcessor.print_statements | def print_statements(self):
"""Print all INDRA Statements collected by the processors."""
for i, stmt in enumerate(self.statements):
print("%s: %s" % (i, stmt)) | python | def print_statements(self):
"""Print all INDRA Statements collected by the processors."""
for i, stmt in enumerate(self.statements):
print("%s: %s" % (i, stmt)) | Print all INDRA Statements collected by the processors. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/biopax/processor.py#L53-L56 |
sorgerlab/indra | indra/sources/biopax/processor.py | BiopaxProcessor.save_model | def save_model(self, file_name=None):
"""Save the BioPAX model object in an OWL file.
Parameters
----------
file_name : Optional[str]
The name of the OWL file to save the model in.
"""
if file_name is None:
logger.error('Missing file name')
... | python | def save_model(self, file_name=None):
"""Save the BioPAX model object in an OWL file.
Parameters
----------
file_name : Optional[str]
The name of the OWL file to save the model in.
"""
if file_name is None:
logger.error('Missing file name')
... | Save the BioPAX model object in an OWL file.
Parameters
----------
file_name : Optional[str]
The name of the OWL file to save the model in. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/biopax/processor.py#L58-L69 |
sorgerlab/indra | indra/sources/biopax/processor.py | BiopaxProcessor.eliminate_exact_duplicates | def eliminate_exact_duplicates(self):
"""Eliminate Statements that were extracted multiple times.
Due to the way the patterns are implemented, they can sometimes yield
the same Statement information multiple times, in which case,
we end up with redundant Statements that aren't from inde... | python | def eliminate_exact_duplicates(self):
"""Eliminate Statements that were extracted multiple times.
Due to the way the patterns are implemented, they can sometimes yield
the same Statement information multiple times, in which case,
we end up with redundant Statements that aren't from inde... | Eliminate Statements that were extracted multiple times.
Due to the way the patterns are implemented, they can sometimes yield
the same Statement information multiple times, in which case,
we end up with redundant Statements that aren't from independent
underlying entries. To avoid this... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/biopax/processor.py#L71-L83 |
sorgerlab/indra | indra/sources/biopax/processor.py | BiopaxProcessor.get_complexes | def get_complexes(self):
"""Extract INDRA Complex Statements from the BioPAX model.
This method searches for org.biopax.paxtools.model.level3.Complex
objects which represent molecular complexes. It doesn't reuse
BioPAX Pattern's org.biopax.paxtools.pattern.PatternBox.inComplexWith
... | python | def get_complexes(self):
"""Extract INDRA Complex Statements from the BioPAX model.
This method searches for org.biopax.paxtools.model.level3.Complex
objects which represent molecular complexes. It doesn't reuse
BioPAX Pattern's org.biopax.paxtools.pattern.PatternBox.inComplexWith
... | Extract INDRA Complex Statements from the BioPAX model.
This method searches for org.biopax.paxtools.model.level3.Complex
objects which represent molecular complexes. It doesn't reuse
BioPAX Pattern's org.biopax.paxtools.pattern.PatternBox.inComplexWith
query since that retrieves pairs ... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/biopax/processor.py#L86-L109 |
sorgerlab/indra | indra/sources/biopax/processor.py | BiopaxProcessor.get_modifications | def get_modifications(self):
"""Extract INDRA Modification Statements from the BioPAX model.
To extract Modifications, this method reuses the structure of
BioPAX Pattern's
org.biopax.paxtools.pattern.PatternBox.constrolsStateChange pattern
with additional constraints to specify ... | python | def get_modifications(self):
"""Extract INDRA Modification Statements from the BioPAX model.
To extract Modifications, this method reuses the structure of
BioPAX Pattern's
org.biopax.paxtools.pattern.PatternBox.constrolsStateChange pattern
with additional constraints to specify ... | Extract INDRA Modification Statements from the BioPAX model.
To extract Modifications, this method reuses the structure of
BioPAX Pattern's
org.biopax.paxtools.pattern.PatternBox.constrolsStateChange pattern
with additional constraints to specify the type of state change
occurri... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/biopax/processor.py#L111-L126 |
sorgerlab/indra | indra/sources/biopax/processor.py | BiopaxProcessor.get_activity_modification | def get_activity_modification(self):
"""Extract INDRA ActiveForm statements from the BioPAX model.
This method extracts ActiveForm Statements that are due to
protein modifications. This method reuses the structure of
BioPAX Pattern's
org.biopax.paxtools.pattern.PatternBox.constr... | python | def get_activity_modification(self):
"""Extract INDRA ActiveForm statements from the BioPAX model.
This method extracts ActiveForm Statements that are due to
protein modifications. This method reuses the structure of
BioPAX Pattern's
org.biopax.paxtools.pattern.PatternBox.constr... | Extract INDRA ActiveForm statements from the BioPAX model.
This method extracts ActiveForm Statements that are due to
protein modifications. This method reuses the structure of
BioPAX Pattern's
org.biopax.paxtools.pattern.PatternBox.constrolsStateChange pattern
with additional c... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/biopax/processor.py#L128-L185 |
sorgerlab/indra | indra/sources/biopax/processor.py | BiopaxProcessor.get_regulate_activities | def get_regulate_activities(self):
"""Get Activation/Inhibition INDRA Statements from the BioPAX model.
This method extracts Activation/Inhibition Statements and reuses the
structure of BioPAX Pattern's
org.biopax.paxtools.pattern.PatternBox.constrolsStateChange pattern
with add... | python | def get_regulate_activities(self):
"""Get Activation/Inhibition INDRA Statements from the BioPAX model.
This method extracts Activation/Inhibition Statements and reuses the
structure of BioPAX Pattern's
org.biopax.paxtools.pattern.PatternBox.constrolsStateChange pattern
with add... | Get Activation/Inhibition INDRA Statements from the BioPAX model.
This method extracts Activation/Inhibition Statements and reuses the
structure of BioPAX Pattern's
org.biopax.paxtools.pattern.PatternBox.constrolsStateChange pattern
with additional constraints to specify the gain or los... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/biopax/processor.py#L187-L259 |
sorgerlab/indra | indra/sources/biopax/processor.py | BiopaxProcessor.get_regulate_amounts | def get_regulate_amounts(self):
"""Extract INDRA RegulateAmount Statements from the BioPAX model.
This method extracts IncreaseAmount/DecreaseAmount Statements from
the BioPAX model. It fully reuses BioPAX Pattern's
org.biopax.paxtools.pattern.PatternBox.controlsExpressionWithTemplateRe... | python | def get_regulate_amounts(self):
"""Extract INDRA RegulateAmount Statements from the BioPAX model.
This method extracts IncreaseAmount/DecreaseAmount Statements from
the BioPAX model. It fully reuses BioPAX Pattern's
org.biopax.paxtools.pattern.PatternBox.controlsExpressionWithTemplateRe... | Extract INDRA RegulateAmount Statements from the BioPAX model.
This method extracts IncreaseAmount/DecreaseAmount Statements from
the BioPAX model. It fully reuses BioPAX Pattern's
org.biopax.paxtools.pattern.PatternBox.controlsExpressionWithTemplateReac
pattern to find TemplateReaction... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/biopax/processor.py#L261-L342 |
sorgerlab/indra | indra/sources/biopax/processor.py | BiopaxProcessor.get_conversions | def get_conversions(self):
"""Extract Conversion INDRA Statements from the BioPAX model.
This method uses a custom BioPAX Pattern
(one that is not implemented PatternBox) to query for
BiochemicalReactions whose left and right hand sides are collections
of SmallMolecules. This pa... | python | def get_conversions(self):
"""Extract Conversion INDRA Statements from the BioPAX model.
This method uses a custom BioPAX Pattern
(one that is not implemented PatternBox) to query for
BiochemicalReactions whose left and right hand sides are collections
of SmallMolecules. This pa... | Extract Conversion INDRA Statements from the BioPAX model.
This method uses a custom BioPAX Pattern
(one that is not implemented PatternBox) to query for
BiochemicalReactions whose left and right hand sides are collections
of SmallMolecules. This pattern thereby extracts metabolic
... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/biopax/processor.py#L344-L433 |
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