whynot-list.py

#!/usr/bin/python3

import os,sys,re

import update_settings as settings
from storage import storage
storage.uri = settings.MONGODB_URI
storage.db_name = settings.MONGODB_DB_NAME
storage.connect()

from utils import (get_obsolete_entries, get_present_entries, get_valid_entries, get_entries_with_comment,
                   get_missing_entries, get_annotated_entries, get_unannotated_entries, get_entries_with_pdbid)

# This is simply a commandline tool for quick listing of the database contents.

usage='Usage: %s [DB] [present|missing|valid|obsolete|annotated|unannotated|comment:*|pdbid:????]'%sys.argv[0]
if len(sys.argv) < 2:
    print(usage)
    sys.exit(0)

dbname=sys.argv[1]

if len(sys.argv) == 3:
    category=sys.argv[2]

    entries=[]
    if category.lower()=='present':
        entries=get_present_entries(dbname)
    elif category.lower()=='missing':
        entries=get_missing_entries(dbname)
    elif category.lower()=='valid':
        entries=get_valid_entries(dbname)
    elif category.lower()=='obsolete':
        entries=get_obsolete_entries(dbname)
    elif category.lower()=='annotated':
        entries=get_annotated_entries(dbname)
    elif category.lower()=='unannotated':
        entries=get_unannotated_entries(dbname)
    elif category.lower().startswith('comment:'):
        entries=get_entries_with_comment(dbname,category[8:].strip())
    elif category.lower().startswith('pdbid:'):
        print(get_entries_with_pdbid(dbname,category[6:].strip()))
    else:
        print(usage)
        sys.exit(0)

    for entry in entries:
        print(entry['pdbid'])

else:
    print('valid', len(get_valid_entries(dbname)))
    print('obsolete', len(get_obsolete_entries(dbname)))
    print('present', len(get_present_entries(dbname)))
    print('annotated', len(get_annotated_entries(dbname)))
    print('unannotated', len(get_unannotated_entries(dbname)))
    print('missing', len(get_missing_entries(dbname)))