Making a small change so I can test this on AWS:

Author: jjacobson95

build/build_all.py

@@ -40,7 +40,7 @@ def main():
     parser.add_argument('--figshare', action='store_true', help="Upload all local data to Figshare. FIGSHARE_TOKEN must be set in local environment.")
     parser.add_argument('--all',dest='all',default=False,action='store_true', help="Run all data build commands. This includes docker, samples, omics, drugs, exp arguments. This does not run the validate or figshare commands")
     parser.add_argument('--high_mem',dest='high_mem',default=False,action='store_true',help = "If you have 32 or more CPUs, this option is recommended. It will run many code portions in parallel. If you don't have enough memory, this will cause a run failure.")
-    parser.add_argument('--dataset',dest='datasets',default='broad_sanger,hcmi,beataml,cptac,mpnst,mpnstpdx,pancpdo',help='Datasets to process. Defaults to all available.')
+    parser.add_argument('--dataset',dest='datasets',default='broad_sanger,hcmi,beataml,cptac,mpnst,mpnstpdx,pancpdo,bladderpdo',help='Datasets to process. Defaults to all available.')
     parser.add_argument('--version', type=str, required=False, help='Version number for the Figshare upload title (e.g., "0.1.29"). This is required for Figshare upload. This must be a higher version than previously published versions.')
     parser.add_argument('--github-username', type=str, required=False, help='GitHub username for the repository.')
     parser.add_argument('--github-email', type=str, required=False, help='GitHub email for the repository.')
@@ -121,6 +121,7 @@ def process_docker(datasets):
             'mpnst': ['mpnst'],
             'mpnstpdx': ['mpnstpdx'],
             'pancpdo': ['pancpdo'],
+            'bladderpdo': ['bladderpdo'],
             'cptac': ['cptac'],
             'genes': ['genes'],
             'upload': ['upload']
@@ -328,7 +329,7 @@ def get_latest_commit_hash(owner, repo, branch='main'):
     # Error handling for required tokens
     if args.figshare and not figshare_token:
         raise ValueError("FIGSHARE_TOKEN environment variable is not set.")
-    if ('beataml' in args.datasets or 'mpnst' in args.datasets) and not synapse_auth_token:
+    if any(dataset in args.datasets for dataset in ['beataml', 'mpnst', 'bladderpdo', 'pancpdo']) and not synapse_auth_token:
         if args.docker or args.samples or args.omics or args.drugs or args.exp or args.all: # Token only required if building data, not upload or validate.
             raise ValueError("SYNAPSE_AUTH_TOKEN is required for accessing MPNST and beatAML datasets.")
 
@@ -407,7 +408,7 @@ def get_latest_commit_hash(owner, repo, branch='main'):
     # if args.figshare or args.validate:
         # FigShare File Prefixes:
 
-        prefixes = ['beataml', 'hcmi', 'cptac', 'mpnst', 'genes', 'drugs']
+        prefixes = ['beataml', 'hcmi', 'cptac', 'mpnst', 'mpnstpdx', 'pancpdo', 'bladderpdo', 'genes', 'drugs']
         broad_sanger_datasets = ["ccle","ctrpv2","fimm","gdscv1","gdscv2","gcsi","prism","nci60"]
         if "broad_sanger" in datasets:
             prefixes.extend(broad_sanger_datasets)