Delete ipro.py after doubling file by renaming it to interpro.py

dbxref/retrieve/ipro.py

-#!/usr/bin/env python3
-
-import dbxref.resolver
-import requests
-import logging
-import json
-import argparse
-
-logger = logging.getLogger(__name__)
-
-def main():
-    """main()method for script usage"""
-    # AVAILABLE for implementation:
-    # 'go_terms', 'member_databases', 'integrated', 'entry_annotations', ''
-    #
-    # USED:
-    # basics: 'accession', 'type', 'description', 'counters', 'entry_id', 'source_database', 'name'
-    # hierarchy
-    # wikipedia
-    # literature
-    # cross_references
-    # overlaps_with
-
-    parser = argparse.ArgumentParser(description="Retrieve InterPro documents and convert them into json")
-    parser.add_argument("--basics", "-b", action="store_true", help="Include basic information such as accession, "
-                                                                    "type, name, description, counters, entry_id and "
-                                                                    "source_database")
-    parser.add_argument("--hierarchy", "-hi", action="store_true", help="")
-    parser.add_argument("--wikipedia", "-w", action="store_true", help="")
-    parser.add_argument("--literature", "-l", action="store_true", help="")
-    parser.add_argument("--cross_references", "-cr", action="store_true", help="")
-    parser.add_argument("--overlaps", "-o", action="store_true", help="")
-    parser.add_argument("dbxrefs", nargs=argparse.REMAINDER)
-    args = parser.parse_args()
-
-    # if nothing specified, output all available information for the entry
-    if None not in (args.basics, args.hierarchy, args.wikipedia, args.literature, args.cross_references, args.overlaps):
-        args.basics = True
-        args.hierarchy = True
-        args.wikipedia = True
-        args.literature = True
-        args.cross_references = True
-        args.overlaps = True
-
-    dbxrefs = dbxref.resolver.convert_to_dbxrefs(args.dbxrefs)
-
-    documents = retrieve(dbxrefs, basics=args.basics, hierarchy=args.hierarchy, wikipedia=args.wikipedia,
-                         literature=args.literature, cross_references=args.cross_references, overlaps=args.overlaps)
-    print(json.dumps(documents, sort_keys=True, indent=4))
-
-
-def retrieve(dbxrefs, basics, hierarchy, wikipedia, literature, cross_references, overlaps):
-    """Retrieve json document from InterPro REST api, filter information by selected Options and parse into new json"""
-    resolved = dbxref.resolver.resolve(dbxrefs, check_existence=False)
-    documents = []
-    for entry in resolved:
-        # Construct URL for retrieve
-        json_url = entry['locations']['json'][0]
-        logger.debug('URL: %s', json_url)
-        r = requests.get(json_url)
-        logger.debug('Content: %s', r.text)
-        ipro = json.loads(r.text)
-
-        # Parse retrieved json file by selected Options
-        output = {}
-        if basics:
-            try:
-                output.update(accession=ipro["metadata"]["accession"], entry_type=ipro["metadata"]["type"],
-                              description=ipro["metadata"]["description"], counters=ipro["metadata"]["counters"],
-                              entry_id=ipro["metadata"]["entry_id"], name=ipro["metadata"]["name"],
-                              source_database=ipro["metadata"]["source_database"])
-            except KeyError:
-                print("One or more basic information were not available for the given entry. Please check your output.")
-        if hierarchy:
-            try:
-                output.update(hierarchy=ipro["metadata"]["hierarchy"])
-            except KeyError:
-                print("Hierarchy information was not available for the given entry.")
-        if wikipedia:
-            try:
-                output.update(wikipedia=ipro["metadata"]["wikipedia"])
-            except KeyError:
-                print("Wikipedia articel were not available for the given entry.")
-        if literature:
-            try:
-                output.update(literature=ipro["metadata"]["literature"])
-            except KeyError:
-                print("Literature was not available for the given entry.")
-        if cross_references:
-            try:
-                output.update(cross_references=ipro["metadata"]["cross_references"])
-            except KeyError:
-                print("Cross_references were not available for the given entry.")
-        if overlaps:
-            try:
-                output.update(overlaps=ipro["metadata"]["overlaps_with"])
-            except KeyError:
-                print("Overlap information was not available for the given entry.")
-        documents.append(output)
-    return documents
-
-
-if __name__ == "__main__":
-    main()