Source code for allensdk.api.queries.glif_api

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import simplejson as json
import logging
from ...deprecated import deprecated
from .rma_template import RmaTemplate


[docs]class GlifApi(RmaTemplate): _log = logging.getLogger('allensdk.api.queries.glif_api') NWB_FILE_TYPE = None rma_templates = \ {"glif_queries": [ {'name': 'neuronal_model_templates', 'description': 'see name', 'model': 'NeuronalModelTemplate', 'num_rows': 'all', 'count': False, }, {'name': 'neuronal_models', 'description': 'see name', 'model': 'Specimen', 'include': 'neuronal_models(well_known_files,neuronal_model_template,neuronal_model_runs(well_known_files))', 'criteria':'[id$in{{ ephys_experiment_ids }}]', 'num_rows': 'all', 'criteria_params':['ephys_experiment_ids'], 'count': False, }, {'name': 'neuron_config', 'description': 'see name', 'model': 'NeuronalModel', 'include': 'well_known_files(well_known_file_type)', 'criteria':'[id$in{{ neuronal_model_ids }}]', 'num_rows': 'all', 'criteria_params':['neuronal_model_ids'], 'count': False, } ] } def __init__(self, base_uri=None): super(GlifApi, self).__init__(base_uri, query_manifest=GlifApi.rma_templates)
[docs] def get_neuronal_model_templates(self): return self.template_query('glif_queries', 'neuronal_model_templates')
[docs] def get_neuronal_models(self, ephys_experiment_ids=None): return self.template_query('glif_queries', 'neuronal_models', ephys_experiment_ids=ephys_experiment_ids)
[docs] def get_neuronal_models_by_id(self, neuronal_model_ids=None): return self.template_query('glif_queries', 'neuron_config', neuronal_model_ids=neuronal_model_ids)
[docs] def get_neuron_configs(self, neuronal_model_ids=None): data = self.template_query('glif_queries', 'neuron_config', neuronal_model_ids=neuronal_model_ids) return_dict = {} for curr_config in data: # print curr_config neuron_config_url = curr_config['well_known_files'][0]['download_link'] return_dict[curr_config['id']] = self.retrieve_parsed_json_over_http(self.api_url + neuron_config_url) return return_dict
@deprecated()
[docs] def list_neuronal_models(self): ''' DEPRECATED Query the API for a list of all GLIF neuronal models. Returns ------- list Meta data for all GLIF neuronal models. ''' include = "specimen(ephys_result[failed$eqfalse]),neuronal_model_template[name$il'*LIF*']" return self.model_query('NeuronalModel', include=include, num_rows='all')
@deprecated()
[docs] def get_neuronal_model(self, neuronal_model_id): '''DEPRECATED Query the current RMA endpoint with a neuronal_model id to get the corresponding well known files and meta data. Returns ------- dict A dictionary containing ''' include = ('neuronal_model_template(well_known_files(well_known_file_type)),' + 'specimen(ephys_sweeps,ephys_result(well_known_files(well_known_file_type))),' + 'well_known_files(well_known_file_type)') criteria = "[id$eq%d]" % neuronal_model_id self.neuronal_model = self.model_query('NeuronalModel', criteria=criteria, include=include, num_rows='all')[0] self.ephys_sweeps = None self.neuron_config_url = None self.stimulus_url = None # sweeps come from the specimen try: specimen = self.neuronal_model['specimen'] self.ephys_sweeps = specimen['ephys_sweeps'] except Exception as e: logging.info(e.args) self.ephys_sweeps = None if self.ephys_sweeps is None: logging.warning( "Could not find ephys_sweeps for this model (%d)" % self.neuronal_model['id']) # neuron config file comes from the neuronal model's well known files try: for wkf in self.neuronal_model['well_known_files']: if wkf['path'].endswith('neuron_config.json'): self.neuron_config_url = wkf['download_link'] break except Exception as e: self.neuron_config_url = None if self.neuron_config_url is None: logging.warning( "Could not find neuron config well_known_file for this model (%d)" % self.neuronal_model['id']) # NWB file comes from the ephys_result's well known files try: ephys_result = specimen['ephys_result'] for wkf in ephys_result['well_known_files']: if wkf['well_known_file_type']['name'] == 'NWBDownload': self.stimulus_url = wkf['download_link'] break except Exception as e: self.stimulus_url = None if self.stimulus_url is None: logging.warning( "Could not find stimulus well_known_file for this model (%d)" % self.neuronal_model['id']) self.metadata = { 'neuron_config_url': self.neuron_config_url, 'stimulus_url': self.stimulus_url, 'ephys_sweeps': self.ephys_sweeps, 'neuronal_model': self.neuronal_model } return self.metadata
@deprecated()
[docs] def get_ephys_sweeps(self): ''' DEPRECATED Retrieve ephys sweep information out of downloaded metadata for a neuronal model Returns ------- list A list of sweeps metadata dictionaries ''' return self.ephys_sweeps
@deprecated()
[docs] def get_neuron_config(self, output_file_name=None): ''' DEPRECATED Retrieve a model configuration file from the API, optionally save it to disk, and return the contents of that file as a dictionary. Parameters ---------- output_file_name: string File name to store the neuron configuration (optional). ''' if self.neuron_config_url is None: raise Exception("URL for neuron config file is empty.") logging.info(self.api_url + self.neuron_config_url) neuron_config = self.retrieve_parsed_json_over_http( self.api_url + self.neuron_config_url) if output_file_name: with open(output_file_name, 'wb') as f: f.write(json.dumps(neuron_config, indent=2)) return neuron_config
@deprecated()
[docs] def cache_stimulus_file(self, output_file_name): ''' DEPRECATED Download the NWB file for the current neuronal model and save it to a file. Parameters ---------- output_file_name: string File name to store the NWB file. ''' if self.stimulus_url is None: raise Exception("URL for stimulus file is empty.") self.retrieve_file_over_http( self.api_url + self.metadata['stimulus_url'], output_file_name)