Source code for indra.sources.eidos.cli

"""
This is a Python based command line interface to Eidos
to complement the Python-Java bridge based interface.
EIDOSPATH (in the INDRA config.ini or as an environmental variable)
needs to be pointing to a fat JAR of the Eidos system.
"""
import os
import glob
import logging
import subprocess
from indra import get_config
from .api import process_json_file


eip = get_config('EIDOSPATH')
eidos_package = 'org.clulab.wm.eidos'
logger = logging.getLogger(__name__)


[docs]def run_eidos(endpoint, *args): """Run a given enpoint of Eidos through the command line. Parameters ---------- endpoint : str The class within the Eidos package to run, for instance 'apps.ExtractFromDirectory' will run 'org.clulab.wm.eidos.apps.ExtractFromDirectory' *args Any further arguments to be passed as inputs to the class being run. """ # Make the full path to the class that should be used call_class = '%s.%s' % (eidos_package, endpoint) # Assemble the command line command and append optonal args cmd = ['java', '-Xmx12G', '-cp', eip, call_class] + list(args) logger.info('Running Eidos with command "%s"' % (' '.join(cmd))) subprocess.call(cmd)
[docs]def extract_from_directory(path_in, path_out): """Run Eidos on a set of text files in a folder. The output is produced in the specified output folder but the output files aren't processed by this function. Parameters ---------- path_in : str Path to an input folder with some text files path_out : str Path to an output folder in which Eidos places the output JSON-LD files """ path_in = os.path.realpath(os.path.expanduser(path_in)) path_out = os.path.realpath(os.path.expanduser(path_out)) logger.info('Running Eidos on input folder %s' % path_in) run_eidos('apps.ExtractFromDirectory', path_in, path_out)
[docs]def extract_and_process(path_in, path_out): """Run Eidos on a set of text files and process output with INDRA. The output is produced in the specified output folder but the output files aren't processed by this function. Parameters ---------- path_in : str Path to an input folder with some text files path_out : str Path to an output folder in which Eidos places the output JSON-LD files Returns ------- stmts : list[indra.statements.Statements] A list of INDRA Statements """ path_in = os.path.realpath(os.path.expanduser(path_in)) path_out = os.path.realpath(os.path.expanduser(path_out)) extract_from_directory(path_in, path_out) jsons = glob.glob(os.path.join(path_out, '*.jsonld')) logger.info('Found %d JSON-LD files to process in %s' % (len(jsons), path_out)) stmts = [] for json in jsons: ep = process_json_file(json) if ep: stmts += ep.statements return stmts