database and arranges them for use in the analysis code. A data folder (mouse_struc_data_dir or human_struc_data_dir) should appear within this directory. Note that that cleaned up versions of these directories are provided in this repository and are available in the root directory.''' import os import sys relative_path=os.path.dirname(os.getcwd()) from allensdk.api.queries.glif_api import GlifApi from allensdk.core.cell_types_cache import CellTypesCache ctc = CellTypesCache(manifest_file=os.path.join(relative_path,'cell_types_manifest.json')) import pandas as pd from shutil import copyfile import numpy as np from allensdk.config import enable_console_log enable_console_log() #--------------------------------------------------------------------------- #----------------------SPECIFY SPECIES-------------------------------------- #--------------------------------------------------------------------------- species="mouse" #species="human" #--------------------------------------------------------------------------- #--------------------------------------------------------------------------- #--------------------------------------------------------------------------- model_template_ids=[395310469, 395310479, 395310475, 471355161, 395310498] #model template ids associated with data in database model_names=['GLIF1', 'GLIF2', 'GLIF3', 'GLIF4', 'GLIF5'] def get_files_from_LIMS_public(output_path, glif_sp_ids=None, type='mouse'): '''This will grab cre positive data config files from LIMS and sort them and put them in
def console_log(): enable_console_log()
def test_list_cells_unmocked(cell_types_api): from allensdk.config import enable_console_log enable_console_log() # this test will always require the latest warehouse cells = cell_types_api.list_cells()