#!/usr/bin/env python
"""
Search queries
Type:
biogorl-search -h
For instructions
Examples:
biogolr-search.py -vv -f relation -P subject_category object_category
biogolr-search.py -vv -f relation -P subject_taxon object_category
biogolr-search.py -vv -f relation -P subject_taxon is_defined_by
"""
import argparse
from ontobio.golr.golr_associations import search_query_as_matrix
import networkx as nx
from networkx.algorithms.dag import ancestors, descendants
from networkx.drawing.nx_pydot import write_dot
from prefixcommons.curie_util import expand_uri
from ontobio.slimmer import get_minimal_subgraph
import yaml
import json
import logging
import plotly.plotly as py
import plotly.graph_objs as go
def main():
"""
Wrapper for OGR
"""
parser = argparse.ArgumentParser(
description='Command line interface to python-ontobio.golr library'
"""
Provides command line interface onto the ontobio.golr python library, a high level
abstraction layer over Monarch and GO solr indices.
""",
formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument('-o', '--outfile', type=str, required=False,
help='Path to output file')
parser.add_argument('-f', '--facet', type=str, required=True,
help='Facet field to query')
parser.add_argument('-q', '--fq', type=json.loads, default={}, required=False,
help='Facet query (solr fq) - should be json')
parser.add_argument('-Q', '--qargs', type=json.loads, default={}, required=False,
help='Query to be passed directly to python golr_associations query')
parser.add_argument('-P', '--search', nargs='*', type=str, required=False,
help='Search fields. E.f subject_category object_category, relation')
parser.add_argument('-u', '--url', type=str, required=False,
help='Solr URL. E.g. http://localhost:8983/solr/golr')
parser.add_argument('-v', '--verbosity', default=0, action='count',
help='Increase output verbosity')
args = parser.parse_args()
if args.verbosity >= 2:
logging.basicConfig(level=logging.DEBUG)
elif args.verbosity == 1:
logging.basicConfig(level=logging.INFO)
else:
logging.basicConfig(level=logging.WARNING)
logging.info("Welcome!")
r = search_query_as_matrix(facet=args.facet,
fq=args.fq,
facet_search_fields=args.search,
url=args.url,
**args.qargs)
print(str(r))
trace = go.Heatmap(z=r['z'],
x=r['xaxis'],
y=r['yaxis'])
data=[trace]
py.plot(data, filename='search-heatmap')
if __name__ == "__main__":
main()
