shell.py

#!/usr/bin/env python

import os
os.environ['DJANGO_SETTINGS_MODULE'] = 'settings'
import django
django.setup()

import pymongo
from xbrowse.reference import Reference
from xbrowse.annotation import VariantAnnotator
from xbrowse.coverage import CoverageDatastore
from xbrowse.datastore import MongoDatastore
import reference_settings
import annotator_settings
from seqr.models import Project as SeqrProject, Family as SeqrFamily, Individual as SeqrIndividual, Sample as SeqrSample, \
    VariantTagType as SeqrVariantTagType, VariantTag as SeqrVariantTag, VariantNote as SeqrVariantNote, \
    SavedVariant as SeqrSavedVariant, \
    LocusList as SeqrLocusList, LocusListGene as SeqrLocusListGene, LocusListInterval as SeqrLocusListInterval
from django.contrib.auth.models import User
from xbrowse_server.base.models import UserProfile
from xbrowse_server.base.models import Project as BaseProject, Family as BaseFamily, Individual as BaseIndividual, \
    VariantTag as BaseVariantTag, ProjectTag as BaseProjectTag, VCFFile
from xbrowse_server.gene_lists.models import GeneList

annotator = datastore = None
try:
    reference_db = pymongo.MongoClient('xbrowse_reference')
    reference = Reference(reference_settings) 

    annotator_db = pymongo.MongoClient('xbrowse_annotator')
    annotator = VariantAnnotator(annotator_settings, reference)
    annotator._ensure_indices()

    datastore_db = pymongo.MongoClient('xbrowse_datastore')
    datastore = MongoDatastore(datastore_db, annotator)
except Exception as e:
    print("Error while connecting to mongo: " + str(e))

user_ns = {
    'annotator': annotator, 
    'datastore': datastore,
    'BaseProject': BaseProject,
    'BaseFamily': BaseFamily,
    'BaseIndividual': BaseIndividual,
    'ProjectTag': BaseProjectTag,
    'VariantTag': BaseVariantTag,

    'SeqrProject': SeqrProject,
    'Project': SeqrProject,

    'SeqrFamily': SeqrFamily,
    'Family': SeqrFamily,

    'SeqrIndividual': SeqrIndividual,
    'Individual': SeqrIndividual,

    'SeqrLocusList': SeqrLocusList,
    'LocusList': SeqrLocusList,

    'SeqrLocusListGene': SeqrLocusListGene,
    'LocusListGene': SeqrLocusListGene,

    'SeqrLocusListInterval': SeqrLocusListInterval,
    'LocusListInterval': SeqrLocusListInterval,

    'SeqrSample': SeqrSample,
    'Sample': SeqrSample,

    'SeqrSavedVariant': SeqrSavedVariant,
    'SavedVariant': SeqrSavedVariant,

    'SeqrVariantTagType': SeqrVariantTagType,
    'VariantTagType': SeqrVariantTagType,

    'SeqrVariantTag': SeqrVariantTag,
    'VariantTag': SeqrVariantTag,

    'SeqrVariantNote': SeqrVariantNote,
    'VariantNote': SeqrVariantNote,


    'User': User,
    'BaseUser': User,
    'UserProfile': UserProfile,
    'GeneList': GeneList,
    'VCFFile': VCFFile,
}

import IPython
IPython.embed(user_ns=user_ns)