diff options
| -rw-r--r-- | scripts/sampledata.py | 55 |
1 files changed, 36 insertions, 19 deletions
diff --git a/scripts/sampledata.py b/scripts/sampledata.py index 8b060e82..3c6ad808 100644 --- a/scripts/sampledata.py +++ b/scripts/sampledata.py @@ -6,6 +6,7 @@ import sys from flask import g from wqflask import app +from wqflask.api.gen_menu import gen_dropdown_json from wqflask.show_trait import show_trait from wqflask.database import database_connection from wqflask.search_results import SearchResultPage @@ -62,25 +63,41 @@ def fetch_all_traits(species, group, type_, dataset): }).trait_list: yield result.get('name') or result.get('display_name') + +def main(): + # Dump all sampledata into a given directory + with database_connection() as conn: + for species, group in gen_dropdown_json(conn).get("datasets").items(): + for group_name, type_ in group.items(): + for dataset_type, datasets in type_.items(): + for dataset in datasets: + dataset_name = dataset[1] + if not os.path.isdir( + BASE_DIR:=os.path.join( + sys.argv[1], + dataset_name) + ): + os.makedirs(BASE_DIR) + print("\n\n======================================\n\n") + print(f"Dumping {dataset_name} into {sys.argv[1]}:\n\n") + for trait in fetch_all_traits( + species=species, + group=group_name, + type_=dataset_type, + dataset=dataset_name + ): + # Dump all sample data into a given directory: + print(f"\033[FDumping: {dataset_name}/{trait}") + with open( + os.path.join(BASE_DIR, f"{trait}.json"), "w" + ) as f: + json.dump( + dump_sample_data(dataset_name, trait), f + ) + print(f"\033[FDONE DUMPING: {BASE_DIR} !!") + -if __name__ == "__main__": - DATASET_NAME = "BXDPublish" - if not os.path.isdir( - BASE_DIR:=os.path.join(sys.argv[1],DATASET_NAME) - ): - os.makedirs(BASE_DIR) - print("\n\n======================================\n\n") - print(f"Dumping Sampledata into {sys.argv[1]}:\n\n") - for trait in fetch_all_traits( - species="mouse", - group="BXD", - type_="Phenotypes", - dataset="BXDPublish", - ): - # Dump all sample data into a given directory: - print(f"\033[FDumping: {DATASET_NAME}/{trait}") - with open(os.path.join(BASE_DIR, f"{trait}.json"), "w") as f: - json.dump(dump_sample_data(DATASET_NAME, trait), f) - print("DONE DUMPING!") +if __name__ == "__main__": + main() |