diff --git a/gga_load_data.py b/gga_load_data.py index 6bffec7f457ac2f2f84dd179489d0c3b7ebf5552..9d2277017b38b2ab97253892967248945a584cd5 100755 --- a/gga_load_data.py +++ b/gga_load_data.py @@ -11,6 +11,7 @@ import json import yaml from bioblend import galaxy +from bioblend.galaxy.objects import GalaxyInstance import utilities import speciesData @@ -100,7 +101,7 @@ class LoadData(speciesData.SpeciesData): return histories - def setup_library(self, instance): + def setup_library(self, instance, data_dir_root='./src_data'): """ Create a "Project Data" library in galaxy, mirroring the "src_data" folder of the current organism directory tree @@ -110,10 +111,16 @@ class LoadData(speciesData.SpeciesData): self.goto_species_dir() + gio = GalaxyInstance(url=self.instance_url, + email=self.config["galaxy_default_admin_email"], + password=self.config["galaxy_default_admin_password"] + ) + + logging.info("Looking for project data in %s" % data_dir_root) folders = dict() post_renaming = {} - for root, dirs, files in os.walk("./src_data", followlinks=True): + for root, dirs, files in os.walk(data_dir_root, followlinks=True): file_list = [os.path.join(root, filename) for filename in files] folders[root] = file_list @@ -132,7 +139,7 @@ class LoadData(speciesData.SpeciesData): for fname, files in folders.items(): if fname and files: - folder_name = fname[len("./src_data") + 1:] + folder_name = fname[len(data_dir_root) + 1:] logging.info("Creating folder: %s" % folder_name) folder = self.create_deep_folder(prj_lib, folder_name)