diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/correlation/correlation_gn3_api.py | 6 | ||||
| -rw-r--r-- | wqflask/wqflask/correlation/rust_correlation.py | 19 | ||||
| -rw-r--r-- | wqflask/wqflask/partial_correlations_views.py | 6 |
3 files changed, 20 insertions, 11 deletions
diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py index 1af54867..b09f3ae2 100644 --- a/wqflask/wqflask/correlation/correlation_gn3_api.py +++ b/wqflask/wqflask/correlation/correlation_gn3_api.py @@ -3,6 +3,8 @@ import json import time from functools import wraps +from flask import current_app + from wqflask.correlation import correlation_functions from wqflask.correlation.pre_computes import fetch_precompute_results from wqflask.correlation.pre_computes import cache_compute_results @@ -11,7 +13,7 @@ from base import data_set from base.trait import create_trait from base.trait import retrieve_sample_data -from gn3.db_utils import database_connector +from gn3.db_utils import database_connection from gn3.commands import run_sample_corr_cmd from gn3.computations.correlations import map_shared_keys_to_values from gn3.computations.correlations import compute_all_lit_correlation @@ -146,7 +148,7 @@ def lit_for_trait_list(corr_results, this_dataset, this_trait): geneid_dict = {trait_name: geneid for (trait_name, geneid) in geneid_dict.items() if trait_lists.get(trait_name)} - with database_connector() as conn: + with database_connection(current_app.config["SQL_URI"]) as conn: correlation_results = compute_all_lit_correlation( conn=conn, trait_lists=list(geneid_dict.items()), species=species, gene_id=this_trait_geneid) diff --git a/wqflask/wqflask/correlation/rust_correlation.py b/wqflask/wqflask/correlation/rust_correlation.py index 188278d8..cfec1ae3 100644 --- a/wqflask/wqflask/correlation/rust_correlation.py +++ b/wqflask/wqflask/correlation/rust_correlation.py @@ -1,6 +1,9 @@ """module contains integration code for rust-gn3""" import json from functools import reduce + +from flask import current_app + from utility.db_tools import mescape from utility.db_tools import create_in_clause from wqflask.correlation.correlation_functions\ @@ -15,7 +18,7 @@ from gn3.computations.correlations import compute_all_lit_correlation from gn3.computations.rust_correlation import run_correlation from gn3.computations.rust_correlation import get_sample_corr_data from gn3.computations.rust_correlation import parse_tissue_corr_data -from gn3.db_utils import database_connector +from gn3.db_utils import database_connection from wqflask.correlation.exceptions import WrongCorrelationType @@ -26,7 +29,7 @@ def query_probes_metadata(dataset, trait_list): if not bool(trait_list) or dataset.type!="ProbeSet": return [] - with database_connector() as conn: + with database_connection(current_app.config["SQL_URI"]) as conn: with conn.cursor() as cursor: query = """ @@ -96,7 +99,7 @@ def chunk_dataset(dataset, steps, name): ProbeSetXRef.ProbeSetId = ProbeSet.Id """.format(name) - with database_connector() as conn: + with database_connection(current_app.config["SQL_URI"]) as conn: with conn.cursor() as curr: curr.execute(query) traits_name_dict = dict(curr.fetchall()) @@ -120,7 +123,7 @@ def compute_top_n_sample(start_vars, dataset, trait_list): sample_data=json.loads(samples_vals), dataset_samples=dataset.group.all_samples_ordered()) - with database_connector() as conn: + with database_connection(current_app.config["SQL_URI"]) as conn: with conn.cursor() as curr: curr.execute( """ @@ -138,7 +141,7 @@ def compute_top_n_sample(start_vars, dataset, trait_list): if len(trait_list) == 0: return {} - with database_connector() as conn: + with database_connection(current_app.config["SQL_URI"]) as conn: with conn.cursor() as curr: # fetching strain data in bulk query = ( @@ -174,7 +177,7 @@ def compute_top_n_lit(corr_results, target_dataset, this_trait) -> dict: geneid_dict = {trait_name: geneid for (trait_name, geneid) in geneid_dict.items() if corr_results.get(trait_name)} - with database_connector() as conn: + with database_connection(current_app.config["SQL_URI"]) as conn: return reduce( lambda acc, corr: {**acc, **corr}, compute_all_lit_correlation( @@ -249,7 +252,7 @@ def __compute_sample_corr__( if target_dataset.type == "ProbeSet" and start_vars.get("use_cache") == "true": - with database_connector() as conn: + with database_connection(current_app.config["SQL_URI"]) as conn: file_path = fetch_text_file(target_dataset.name, conn) if file_path: (sample_vals, target_data) = read_text_file( @@ -336,7 +339,7 @@ def __compute_lit_corr__( (this_trait_geneid, geneid_dict, species) = do_lit_correlation( this_trait, target_dataset) - with database_connector() as conn: + with database_connection(current_app.config["SQL_URI"]) as conn: return reduce( lambda acc, lit: {**acc, **lit}, compute_all_lit_correlation( diff --git a/wqflask/wqflask/partial_correlations_views.py b/wqflask/wqflask/partial_correlations_views.py index b3ebc4c5..a11d902c 100644 --- a/wqflask/wqflask/partial_correlations_views.py +++ b/wqflask/wqflask/partial_correlations_views.py @@ -348,7 +348,7 @@ def process_pcorrs_command_output(result): @app.route("/partial_correlations/<command_id>", methods=["GET"]) def poll_partial_correlation_results(command_id): response = requests.get( - url=urljoin(GN_SERVER_URL, "async_commands/state/{command_id}")) + url=urljoin(GN_SERVER_URL, f"async_commands/state/{command_id}")) if response.status_code == 200: data = response.json() @@ -366,3 +366,7 @@ def poll_partial_correlation_results(command_id): return render_template( "partial_correlations/pcorrs_poll_results.html", command_id = command_id) + return render_error( + "We messed up, and the computation failed due to a system " + "error.", + command_id) |