fix exceeded number of requests to CLUE

clreda · Oct 28, 2024 · 356a685 · 356a685
1 parent e057bb5
commit 356a685
Show file tree

Hide file tree

Showing 2 changed files with 6 additions and 4 deletions.
diff --git a/src/NORDic/NORDic_NI/functions.py b/src/NORDic/NORDic_NI/functions.py
@@ -85,7 +85,7 @@ def network_identification(file_folder, taxon_id, path_to_genes=None, disgenet_a
 
     return solution
 
-def solution_generation(file_folder, taxon_id, path_to_genes=None, disgenet_args=None, network_fname=None, string_args=None, experiments_fname=None, lincs_args=None, edge_args=None, sig_args=None, bonesis_args=None, weights=None, seed=0, njobs=1, force_experiments=True, accept_nonRNA=False,preserve_network_sign=True):
+def solution_generation(file_folder, taxon_id, path_to_genes=None, disgenet_args=None, network_fname=None, string_args=None, experiments_fname=None, lincs_args=None, edge_args=None, sig_args=None, bonesis_args=None, weights=None, seed=0, njobs=1, force_experiments=True, accept_nonRNA=False,preserve_network_sign=True, pause_time=0.3):
     '''
     Generates or retrieves the optimal network model
 
@@ -123,6 +123,8 @@ def solution_generation(file_folder, taxon_id, path_to_genes=None, disgenet_args
         [default=True] : if set to True, returns an error if no experimental profile associated with the genes is found
     accept_nonRNA : Python bool
         [default=False] : if set to False, ignores gene names which cannot be converted to EntrezIDs or which are not present in LINCS L1000
+    pause_time : Python float
+    	[default=0.3] : pause between requests to the CLUE.io API
 
     Returns
     ----------
@@ -292,7 +294,7 @@ def solution_generation(file_folder, taxon_id, path_to_genes=None, disgenet_args
         symbols_fname=file_folder+"SYMBOLS.csv"
         if (not os.path.exists(symbols_fname)):
             user_key = get_user_key(lincs_args["credentials"])
-            pert_df = convert_EntrezGene_LINCSL1000(file_folder, list(probes["Gene ID"]), user_key)
+            pert_df = convert_EntrezGene_LINCSL1000(file_folder, list(probes["Gene ID"]), user_key, pause_time=pause_time)
             pert_df.to_csv(symbols_fname)
         pert_df = pd.read_csv(symbols_fname, index_col=0)
 

diff --git a/src/NORDic/UTILS/utils_data.py b/src/NORDic/UTILS/utils_data.py
@@ -137,7 +137,7 @@ def convert_genes_EntrezGene(gene_list, taxon_id, app_name, chunksize=100, missi
         print("%d probes (successful %d, unsuccessful %d)" % (len(probes), len(probes.loc[probes["Gene ID"]!='-']), len(probes.loc[probes["Gene ID"]=="-"])))
     return probes
 
-def convert_EntrezGene_LINCSL1000(file_folder, EntrezGenes, user_key, quiet=False):
+def convert_EntrezGene_LINCSL1000(file_folder, EntrezGenes, user_key, pause_time=3.7, quiet=False):
     '''
     Converts EntrezIDs to Gene Symbols present in LINCS L1000
 
@@ -180,7 +180,7 @@ def convert_EntrezGene_LINCSL1000(file_folder, EntrezGenes, user_key, quiet=Fals
         for entrezid in all_entrezid:
             params = {"where":{"entrez_id": str(entrezid)},"fields":["gene_symbol"]}
             request_url = build_url(endpoint, method, params, user_key=user_key)
-            data = post_request(request_url, quiet=True, pause_time=0.3)
+            data = post_request(request_url, quiet=True, pause_time=pause_time)
             if (len(data)==0):
                 continue
             else: