remove debugging print statements

geneontology · Feb 13, 2024 · a16d119 · a16d119
1 parent a6a3843
commit a16d119
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Showing 2 changed files with 6 additions and 8 deletions.
diff --git a/src/gopreprocess/goa_annotation_creation_controller.py b/src/gopreprocess/goa_annotation_creation_controller.py
@@ -41,9 +41,9 @@ def generate_annotation(
         # PR:Q9DAQ4-1 = UniProtKB:Q9DAQ4-1
         if isoform:
             pr_id = protein_xrefs[str(annotation.subject.id)]
-            print("pr_id", pr_id)
-            print("parent_xrefs", parent_xrefs[pr_id])
-            print("annotation.subject.id", annotation.subject.id)
+            # print("pr_id", pr_id)
+            # print("parent_xrefs", parent_xrefs[pr_id])
+            # print("annotation.subject.id", annotation.subject.id)
             # PR:Q9DAQ4-1 = MGI:MGI:1918911
             mgi_id = parent_xrefs[pr_id]
             new_gene = Curie(namespace=mgi_id.split(":")[0], identity=mgi_id.replace("MGI:MGI:", "MGI:"))

diff --git a/src/utils/download.py b/src/utils/download.py
@@ -33,7 +33,7 @@ def download_files(source_taxon: str, target_taxon: str) -> tuple[Path, Path, Pa
     return ortho_path, source_gaf_path, target_gpi_path
 
 
-def download_with_retry(target_directory_name, config_key, gunzip=True, retries=3, timeout=60):
+def download_with_retry(target_directory_name, config_key, gunzip=True, retries=3):
     attempt = 0
     while attempt < retries:
         try:
@@ -57,13 +57,11 @@ def download_file(target_directory_name: str, config_key: str, gunzip=False) ->
     if gunzip:
         file_path = pystow.ensure_gunzip(target_directory_name,
                                          url=get_url(config_key),
-                                         force=True,
-                                         download_kwargs={"timeout": 60})
+                                         force=True)
     else:
         file_path = pystow.ensure(target_directory_name,
                                   url=get_url(config_key),
-                                  force=True,
-                                  download_kwargs={"timeout": 60})
+                                  force=True)
     return file_path