def constuct_req_file(args): ''' read the input requirements from user and create a new txt file in the data_env that includes the requirements given by the user. if a value wasn't provided by the user, use the defaults''' print("Summarising the structural requirements...") req_dict = {} ## 1. Load default params: with open(os.path.join(args.sling_dir,"default.txt")) as f: ## get all the values from the req file for line in f: key, val = line.strip().split() if key != "order": val = int(val) req_dict[key] = val orders = ["upstream", "downstream", "either", "both"] args_dict = vars(args) for key in req_dict: if args_dict[key] is not None: if key == "order": args_dict[key] = args_dict[key].lower() req_dict[key] = args_dict[key] utils.check_reqs(req_dict) with open(os.path.join(args.sling_dir, args.name + ".txt"), "w") as out: for key in req_dict: out.write(key + "\t" + str(req_dict[key]) + "\n") return
def get_requirements(args, data_env): # path to the requirement document of each built in DB reqs = utils.databases if args["hmm_db"] in reqs: # built in collections req_file = os.path.join(data_env, args["hmm_db"] + ".txt") else: # not a built in collection, take the default values req_file = os.path.join(data_env, "default.txt") with open(req_file) as f: # get all the values from the req file for line in f: key, val = line.strip().split() if key != "order": val = int(val) if args[key] is None: # otherwise, keep what the user gave args[key] = val utils.check_reqs(args) return
#!/usr/bin/env python from utils import check_reqs check_reqs() """ Converts an image stack to an MRC file. Runs either as a command line program or as an importable function. """ def stack2mrc(stack, mrc, imfilter = lambda im: im): """ Converts an image stack to an MRC file. Returns the new MRC file object. Arguments: stack -- the images to read, an iterable of file names mrc -- the MRC filename to save to Optional Arguments: imfilter -- a function/callable that takes and returns an image """ from mrc import MRC from images import imread stack = iter(stack) try: img = imfilter(imread(stack.next())) except StopIteration: raise ValueError("Must provide at least one image") mrc = MRC(mrc, nx=img.shape[1], ny=img.shape[0], dtype=img.dtype) mrc.append(img) mrc.append_all(imfilter(imread(img)) for img in stack) # will skip the first one mrc.write_header() return mrc
manager.types[person].override_property('occupant_age', MockFn(PERSON.get_age)) manager.types[person].override_property('occupant_gender', MockFn(PERSON.get_sex)) manager.types[person].override_property('occupant_name', MockFn(PERSON.get_name)) for _ in range(SEED_ENTITIES): manager.register(person) for mocker in manager.types.values(): if mocker.killed: manager.kill() return break manager.kill() if __name__ == '__main__': check_reqs(reqs=['KERNEL_URL', 'KERNEL_USER', 'KERNEL_PASSWORD']) NAMES = file_to_json(f'{RESOURCES_DIR}/sample-names.json') POP_CENTERS = file_to_json(f'{RESOURCES_DIR}/sample-locations.json') args = sys.argv seed = 1000 try: if len(args) > 1 and isinstance(int(args[1]), int): seed = int(args[1]) except ValueError: pass main(seed_size=seed)
#!/usr/bin/env python from utils import check_reqs check_reqs() """ Converts an image file to a new format. """ def help_msg(err=0, msg=None): from os.path import basename from sys import stderr, argv, exit from textwrap import fill, TextWrapper from utils import get_terminal_width import imfilter_util w = max(get_terminal_width(), 20) tw = TextWrapper(width=w, subsequent_indent=' ' * 18) if msg != None: print >> stderr, fill(msg, w) print "Usage:" print tw.fill(" %s [args] input.xxx output.xxx" % basename(argv[0])) print "" print "Supports numerous file formats based on extension. The extension should be accurate to the filetype otherwise it may not work." print "" print "Optional arguments:" print tw.fill(" -h --help Display this help") for l in imfilter_util.usage: print tw.fill(l) if len(l) > 20 and l[0] == ' ' else l exit(err) if __name__ == "__main__":
schema_decorators = schema_decorator(project_id, schema_ids) LOGGER.debug(schema_decorators) ps_ids = {ps.name: ps.id for ps in schema_decorators.values()} ms = mappingset(project_id) sub_id = mapping(project_id, ms.id, ps_ids) LOGGER.debug(sub_id) if __name__ == '__main__': check_reqs(reqs=[ 'KERNEL_URL', 'KERNEL_USER', 'KERNEL_PASSWORD', 'PROJECT_NAME', 'MAPPING_NAME', ]) try: client = Client(KERNEL_URL, KERNEL_USER, KERNEL_PASSWORD, log_level=CLIENT_LOGLEVEL, realm=REALM, keycloak_url=KEYCLOAK_URL) except Exception as err: LOGGER.error(f'Kernel is not ready. Please check ' f'''it's status or wait a moment and try again : {err}''') sys.exit(1)