def main(json_json_files_to_process,
runtime_json,
collection_name_override=None):
with open(runtime_json, "r") as fj:
runtime_config = json.load(fj)
mongo_db_config = runtime_config["mongo_db_config"]
connection_string = mongo_db_config["connection_string"]
database_name = mongo_db_config["database_name"]
if collection_name_override is None:
collection_name = mongo_db_config["collection_name"]
else:
collection_name = collection_name_override
refresh_collection = mongo_db_config["refresh_collection"]
print("Connecting to MongoDB '%s'" % connection_string)
client = pymongo.MongoClient(connection_string)
database = client[database_name]
collection = database[collection_name]
if refresh_collection:
collection.delete_many({})
initial_collection_count = collection.count()
with open(json_json_files_to_process, "r") as fj:
json_files_to_to_process = json.load(fj)
j = 0
for json_file_dict in json_files_to_to_process:
json_file_name = json_file_dict["data_json_file"]
print("Loading '%s'" % json_file_name)
data_dict = data_dict_load(json_file_name)
i = 0
for datum_key in data_dict:
collection.insert(
data_dict[datum_key], check_keys=False
) # Have to makes sure keys do not have a "." or "$" in it
if i > 0 and i % 500 == 0:
print("Inserted '%s' documents" % i)
i += 1
j += i
print("Inserted '%s' total documents" % j)
print("Added %s items in collection '%s' housed in database '%s'" %
(collection.count() - initial_collection_count, collection_name,
database_name))
def main(json_json_files_to_process, runtime_json, collection_name_override=None):
with open(runtime_json, "r") as fj:
runtime_config = json.load(fj)
mongo_db_config = runtime_config["mongo_db_config"]
connection_string = mongo_db_config["connection_string"]
database_name = mongo_db_config["database_name"]
if collection_name_override is None:
collection_name = mongo_db_config["collection_name"]
else:
collection_name = collection_name_override
refresh_collection = mongo_db_config["refresh_collection"]
print("Connecting to MongoDB '%s'" % connection_string)
client = pymongo.MongoClient(connection_string)
database = client[database_name]
collection = database[collection_name]
if refresh_collection:
collection.delete_many({})
initial_collection_count = collection.count()
with open(json_json_files_to_process, "r") as fj:
json_files_to_to_process = json.load(fj)
j = 0
for json_file_dict in json_files_to_to_process:
json_file_name = json_file_dict["data_json_file"]
print("Loading '%s'" % json_file_name)
data_dict = data_dict_load(json_file_name)
i = 0
for datum_key in data_dict:
collection.insert(data_dict[datum_key], check_keys=False) # Have to makes sure keys do not have a "." or "$" in it
if i > 0 and i % 500 == 0:
print("Inserted '%s' documents" % i)
i += 1
j += i
print("Inserted '%s' total documents" % j)
print("Added %s items in collection '%s' housed in database '%s'" % (collection.count() - initial_collection_count, collection_name, database_name))
def main(hdf5_base_name, batch_json_file_name, data_template_json, refresh_template=True, output_directory=None):
"""Convert a JSON file to a HDF5 matrix format using a template"""
with open(batch_json_file_name) as fj: # Load names of files to process
batch_list_dict = json.load(fj)
data_json_files = [x["data_json_file"] for x in batch_list_dict]
sort_order_dict = {}
batch_ids = []
for list_dict in batch_list_dict:
batch_id = list_dict["batch_id"]
batch_ids += [batch_id]
if "sort_order_file_name" in list_dict:
sort_order_file_name = list_dict["sort_order_file_name"]
sort_order_dict[batch_id] = sort_order_file_name
if output_directory is None:
output_directory = os.path.abspath(os.path.split(data_json_files[0])[0])
generated_data_templates_names = []
ks = 0
for data_json_file in data_json_files: # For each subset generate a template
batch_number = batch_ids[ks]
data_dict = data_dict_load(data_json_file)
with open(data_template_json, "r") as f:
data_template_dict = json.load(f)
data_template_dict = expand_template_dict(data_dict, data_template_dict)
data_translate_dict = build_translation_dict(data_dict, data_template_dict)
data_translate_dict = add_offsets_to_translation_dict(data_translate_dict)
data_translate_dict_json_name = os.path.join(output_directory, hdf5_base_name + "_" + str(batch_number) + "_data_template.json")
generated_data_templates_names += [data_translate_dict_json_name]
print("Generated: '%s'" % data_translate_dict_json_name)
with open(data_translate_dict_json_name, "w") as fjw:
try:
json.dump(data_translate_dict, fjw, indent=4, separators=(", ", ": "), sort_keys=True)
except:
json.dump(data_translate_dict, fjw)
ks += 1
master_data_translate_dict = []
for data_template_name in generated_data_templates_names: # Combine templates into a single master template
print("Merging '%s' to master data template" % data_template_name)
with open(data_template_name) as fj:
data_translate_dict = json.load(fj)
master_data_translate_dict = merge_data_translate_dicts(master_data_translate_dict, data_translate_dict)
master_data_translate_dict_name = os.path.join(output_directory, hdf5_base_name + "_master_data_template.json")
with open(master_data_translate_dict_name, "w") as fjw:
try:
json.dump(master_data_translate_dict, fjw, indent=4, separators=(", ", ": "), sort_keys=True)
except TypeError:
json.dump(master_data_translate_dict, fjw)
generated_hdf5_file_names = []
ks = 0
total_number_of_rows = 0
for data_json_file in data_json_files: # Export each subset into a HDF5 matrix
batch_number = batch_ids[ks]
data_dict = data_dict_load(data_json_file)
total_number_of_rows += len(data_dict)
hdf5_file_name = os.path.join(output_directory, hdf5_base_name + "_" + str(batch_number) + ".hdf5")
generated_hdf5_file_names += [hdf5_file_name]
f5p = h5py.File(hdf5_file_name, "w")
if batch_number in sort_order_dict:
sort_order_json_name = sort_order_dict[batch_number]
with open(sort_order_json_name, "r") as fj:
sort_order_list = json.load(fj)
else:
sort_order_list = None
build_hdf5_matrix(f5p, data_dict, master_data_translate_dict, sort_order_list)
ks += 1
print("Exported %s rows across %s files" % (total_number_of_rows, len(data_json_files)))
all_hdf5_file_name = os.path.join(output_directory, hdf5_base_name + "_combined.hdf5")
combined_hdf5 = h5py.File(all_hdf5_file_name, "w")
combine_exported_hdf5_files_into_single_file(combined_hdf5, generated_hdf5_file_names, total_number_of_rows)
def main(hdf5_base_name,
batch_json_file_name,
data_template_json,
refresh_template=True,
output_directory=None):
"""Convert a JSON file to a HDF5 matrix format using a template"""
with open(batch_json_file_name) as fj: # Load names of files to process
batch_list_dict = json.load(fj)
data_json_files = [x["data_json_file"] for x in batch_list_dict]
sort_order_dict = {}
batch_ids = []
for list_dict in batch_list_dict:
batch_id = list_dict["batch_id"]
batch_ids += [batch_id]
if "sort_order_file_name" in list_dict:
sort_order_file_name = list_dict["sort_order_file_name"]
sort_order_dict[batch_id] = sort_order_file_name
if output_directory is None:
output_directory = os.path.abspath(
os.path.split(data_json_files[0])[0])
generated_data_templates_names = []
ks = 0
for data_json_file in data_json_files: # For each subset generate a template
batch_number = batch_ids[ks]
data_dict = data_dict_load(data_json_file)
with open(data_template_json, "r") as f:
data_template_dict = json.load(f)
data_template_dict = expand_template_dict(data_dict,
data_template_dict)
data_translate_dict = build_translation_dict(data_dict,
data_template_dict)
data_translate_dict = add_offsets_to_translation_dict(
data_translate_dict)
data_translate_dict_json_name = os.path.join(
output_directory,
hdf5_base_name + "_" + str(batch_number) + "_data_template.json")
generated_data_templates_names += [data_translate_dict_json_name]
print("Generated: '%s'" % data_translate_dict_json_name)
with open(data_translate_dict_json_name, "w") as fjw:
try:
json.dump(data_translate_dict,
fjw,
indent=4,
separators=(", ", ": "),
sort_keys=True)
except:
json.dump(data_translate_dict, fjw)
ks += 1
master_data_translate_dict = []
for data_template_name in generated_data_templates_names: # Combine templates into a single master template
print("Merging '%s' to master data template" % data_template_name)
with open(data_template_name) as fj:
data_translate_dict = json.load(fj)
master_data_translate_dict = merge_data_translate_dicts(
master_data_translate_dict, data_translate_dict)
master_data_translate_dict_name = os.path.join(
output_directory, hdf5_base_name + "_master_data_template.json")
with open(master_data_translate_dict_name, "w") as fjw:
try:
json.dump(master_data_translate_dict,
fjw,
indent=4,
separators=(", ", ": "),
sort_keys=True)
except TypeError:
json.dump(master_data_translate_dict, fjw)
generated_hdf5_file_names = []
ks = 0
total_number_of_rows = 0
for data_json_file in data_json_files: # Export each subset into a HDF5 matrix
batch_number = batch_ids[ks]
data_dict = data_dict_load(data_json_file)
total_number_of_rows += len(data_dict)
hdf5_file_name = os.path.join(
output_directory,
hdf5_base_name + "_" + str(batch_number) + ".hdf5")
generated_hdf5_file_names += [hdf5_file_name]
f5p = h5py.File(hdf5_file_name, "w")
if batch_number in sort_order_dict:
sort_order_json_name = sort_order_dict[batch_number]
with open(sort_order_json_name, "r") as fj:
sort_order_list = json.load(fj)
else:
sort_order_list = None
build_hdf5_matrix(f5p, data_dict, master_data_translate_dict,
sort_order_list)
ks += 1
print("Exported %s rows across %s files" %
(total_number_of_rows, len(data_json_files)))
all_hdf5_file_name = os.path.join(output_directory,
hdf5_base_name + "_combined.hdf5")
combined_hdf5 = h5py.File(all_hdf5_file_name, "w")
combine_exported_hdf5_files_into_single_file(combined_hdf5,
generated_hdf5_file_names,
total_number_of_rows)