Add Synapse upload command with RecordSet routing

.env.example

@@ -0,0 +1,11 @@
+# Synapse credentials
+# Copy this file to .env and fill in your values.
+# Then load before running htan:
+#   source .env
+# Or for a single command:
+#   SYNAPSE_AUTH_TOKEN=your_token htan upload synapse file ...
+#
+# Get your token at: https://www.synapse.org/#!Profile:v/settings (Access Tokens tab)
+# IMPORTANT: Never commit .env to git. It is already in .gitignore.
+
+SYNAPSE_AUTH_TOKEN=your_personal_access_token_here

.gitignore

@@ -19,6 +19,11 @@ htmlcov/
 # OS
 .DS_Store
 
+# Credentials — never commit
+.env
+.env.*
+!.env.example
+
 # Local Claude Code config
 .claude/settings.local.json
 

src/htan/cli.py

@@ -36,10 +36,14 @@ def main():
     if command == "init":
         from htan.init import cli_main
         cli_main(rest)
+    elif command == "etl":
+        _dispatch_etl(rest)
     elif command == "query":
         _dispatch_query(rest)
     elif command == "download":
         _dispatch_download(rest)
+    elif command == "upload":
+        _dispatch_upload(rest)
     elif command == "pubs":
         from htan.pubs import cli_main
         cli_main(rest)
@@ -57,6 +61,22 @@ def main():
         sys.exit(1)
 
 
+def _dispatch_etl(args):
+    if not args:
+        print("Usage: htan etl {omop} ...", file=sys.stderr)
+        sys.exit(1)
+
+    subcommand = args[0]
+    rest = args[1:]
+
+    if subcommand == "omop":
+        from htan.etl.omop import cli_main
+        cli_main(rest)
+    else:
+        print(f"Unknown etl subcommand: {subcommand}. Use 'omop'.", file=sys.stderr)
+        sys.exit(1)
+
+
 def _dispatch_query(args):
     if not args:
         print("Usage: htan query {portal,bq} ...", file=sys.stderr)
@@ -95,6 +115,22 @@ def _dispatch_download(args):
         sys.exit(1)
 
 
+def _dispatch_upload(args):
+    if not args:
+        print("Usage: htan upload {synapse} ...", file=sys.stderr)
+        sys.exit(1)
+
+    backend = args[0]
+    rest = args[1:]
+
+    if backend == "synapse":
+        from htan.upload.synapse import cli_main
+        cli_main(rest)
+    else:
+        print(f"Unknown upload backend: {backend}. Use 'synapse'.", file=sys.stderr)
+        sys.exit(1)
+
+
 def _dispatch_config(args):
     import json
     from htan.config import check_setup
@@ -123,9 +159,11 @@ def _print_usage():
 
 Commands:
   init                Interactive setup wizard (configure credentials)
+  etl omop ...        ETL lung cancer data to OMOP CDM in DuckDB
   query portal ...    Query HTAN portal ClickHouse database
   query bq ...        Query HTAN metadata in ISB-CGC BigQuery
   download synapse .. Download open-access files from Synapse
+  upload synapse ...  Upload files to Synapse (single, bulk, with annotations)
   download gen3 ...   Download controlled-access files from Gen3/CRDC
   pubs ...            Search HTAN publications on PubMed
   model ...           Query HTAN data model (components, attributes, valid values)

src/htan/upload/__init__.py

@@ -0,0 +1 @@
+"""Upload HTAN data files to Synapse."""