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authorMunyoki Kilyungi2023-01-17 11:51:24 +0300
committerBonfaceKilz2023-01-20 15:02:46 +0300
commit6357001a7a413595b7fdcd5959fbb63a2d074f3f (patch)
tree81bac4b03cd63dcea506776c7eef5f5abcb492fb /scripts
parent5cc778e3db7035b49a8c5f37b98dcd3a07fafa26 (diff)
downloadgenenetwork2-6357001a7a413595b7fdcd5959fbb63a2d074f3f.tar.gz
Dump all sample data into a given directory
* scripts/sampledata.py: Import gen_dropdown_json. (main): Dump all the sample data from all the datasets into a given directory.
Diffstat (limited to 'scripts')
-rw-r--r--scripts/sampledata.py55
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()