from __future__ import print_function from __future__ import unicode_literals import re import time import pstats import argparse import cProfile import guppy import glue import ga4gh.schemas.protocol as protocol glue.ga4ghImportGlue() import ga4gh.server.backend as backend # noqa import ga4gh.server.datarepo as datarepo # noqa class HeapProfilerBackend(backend.Backend): def __init__(self, registryDb): repo = datarepo.SqlDataRepository(registryDb) repo.open(datarepo.MODE_READ) super(HeapProfilerBackend, self).__init__(repo) self.profiler = guppy.hpy() def startProfile(self): self.profiler.setrelheap() def endProfile(self):
import argparse import os import shutil import json import pysam import generate_gff3_db import tempfile import zipfile import glob import file_downloader import ga4gh.common.utils as utils import glue glue.ga4ghImportGlue() # We need to turn off QA because of the import glue import ga4gh.server # NOQA import ga4gh.server.datarepo as datarepo # NOQA import ga4gh.server.datamodel.references as references # NOQA import ga4gh.server.datamodel.datasets as datasets # NOQA import ga4gh.server.datamodel.variants as variants # NOQA import ga4gh.server.datamodel.reads as reads # NOQA import ga4gh.server.datamodel.ontologies as ontologies # NOQA import ga4gh.server.datamodel.sequence_annotations as sequence_annotations # NOQA import ga4gh.server.datamodel.bio_metadata as biodata # NOQA import ga4gh.server.datamodel.genotype_phenotype_featureset as g2p_featureset # NOQA import ga4gh.server.datamodel.genotype_phenotype as g2p_associationset # NOQA import ga4gh.server.datamodel.rna_quantification as rna_quantification # NOQA import ga4gh.server.repo.rnaseq2ga as rnaseq2ga # NOQA