scientiflow-cli 0.4.5__py3-none-any.whl → 0.4.6__py3-none-any.whl

scientiflow_cli/pipeline/decode_and_execute.py

@@ -1,7 +1,7 @@
 import subprocess
 import tempfile
 import os
-import re
+import re, shlex
 import multiprocessing
 import threading
 from concurrent.futures import ProcessPoolExecutor, as_completed
@@ -114,9 +114,23 @@ class PipelineExecutor:
             print(f"[ERROR] Failed to update terminal output: {e}")
 
     def replace_variables(self, command: str) -> str:
-        """Replace placeholders like ${VAR} with environment values."""
-        return re.sub(r'\$\{(\w+)\}', lambda m: self.environment_variables.get(m.group(1), m.group(0)), command)
-
+        #     """Replace placeholders like ${VAR} with environment values."""
+        #     print(self.environment_variables)
+        #     return re.sub(r'\$\{(\w+)\}', lambda m: self.environment_variables.get(m.group(1), m.group(0)), command)
+        """Replace placeholders like ${VAR} with environment values.
+        - If value is a list: safely join into space-separated arguments (quoted).
+        - Otherwise: use the old behavior (direct substitution).
+        """
+        def replacer(match):
+            key = match.group(1)
+            value = self.environment_variables.get(key, match.group(0))
+            # ✅ Special handling for lists
+            if isinstance(value, list):
+                return " ".join(shlex.quote(str(v)) for v in value)
+            # ✅ Default: keep original behavior for strings, numbers, None
+            return self.environment_variables.get(key, match.group(0))
+        return re.sub(r'\$\{(\w+)\}', replacer, command)
+        
     def execute_command(self, command: str):
         """Run the command in the terminal, display output in real-time, and log the captured output."""
         import sys

{scientiflow_cli-0.4.5.dist-info → scientiflow_cli-0.4.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scientiflow-cli
-Version: 0.4.5
+Version: 0.4.6
 Summary: CLI tool for scientiflow. This application runs on the client side, decodes pipelines, and executes them in the configured order!
 License: Proprietary
 Author: ScientiFlow

{scientiflow_cli-0.4.5.dist-info → scientiflow_cli-0.4.6.dist-info}/RECORD

@@ -8,7 +8,7 @@ scientiflow_cli/config.py,sha256=MlNscMiu7G9VsZxqQFYVuU6_HKhGC7Y9pU0yRZPN9Ms,337
 scientiflow_cli/main.py,sha256=PbZRL4GatzXVK95GGPWJnpBCKPqyn1dVmiwNHDyjXkU,6584
 scientiflow_cli/pipeline/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 scientiflow_cli/pipeline/container_manager.py,sha256=KAnE5AvsSg4cewLc_v4gWCqhKGoc7ycHOtl_HYxUK7E,8444
-scientiflow_cli/pipeline/decode_and_execute.py,sha256=wZ3CWTq57gYYxNkfpk1YsLnEWNAuSl1idiCQ2EspvfE,17461
+scientiflow_cli/pipeline/decode_and_execute.py,sha256=UhmIQrFxhJvtwqcbFIeg1wiDt2DAhVowASKiYSl5mDk,18257
 scientiflow_cli/pipeline/get_jobs.py,sha256=69jOIVwXd8j2lAYy28r2QcsjFT4yRpXNOqsfopiZhFs,1498
 scientiflow_cli/services/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 scientiflow_cli/services/auth_service.py,sha256=lknARfVTjRCH-4yWVPKiS330NIVHxFw3HlQdN2Lw3Og,3343
@@ -23,8 +23,8 @@ scientiflow_cli/utils/file_manager.py,sha256=J6FBaZ0xz6OH4vcArOGj5KqKSZ2AD78HNei
 scientiflow_cli/utils/logger.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 scientiflow_cli/utils/mock.py,sha256=UZ9cN2Qx3EAXcxnLQY5z4DQWy4jflnWFnfNTsuvnFH8,11237
 scientiflow_cli/utils/singularity.py,sha256=jy8ep7Xa1Eg4fptNjyXLPuVN2KA8l4dFil-w-KaVNkw,4956
-scientiflow_cli-0.4.5.dist-info/LICENSE.md,sha256=nb6GGGYuS_KXe33mSNwcEW-QzvwM475NQ4cNE7KBb34,425
-scientiflow_cli-0.4.5.dist-info/METADATA,sha256=vw30zHjWRRk_PTEOs3d2xPnI53eTBTLNoc9iroeWz2o,2491
-scientiflow_cli-0.4.5.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-scientiflow_cli-0.4.5.dist-info/entry_points.txt,sha256=0lq2mjcG5hGfODrQodeMSAy9RfE2EX1MZSHRpfSncxc,61
-scientiflow_cli-0.4.5.dist-info/RECORD,,
+scientiflow_cli-0.4.6.dist-info/LICENSE.md,sha256=nb6GGGYuS_KXe33mSNwcEW-QzvwM475NQ4cNE7KBb34,425
+scientiflow_cli-0.4.6.dist-info/METADATA,sha256=rf9_MkUiB5am5x6W4laHvD_yVH_1uBO1k1dhxFBg6fk,2491
+scientiflow_cli-0.4.6.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+scientiflow_cli-0.4.6.dist-info/entry_points.txt,sha256=0lq2mjcG5hGfODrQodeMSAy9RfE2EX1MZSHRpfSncxc,61
+scientiflow_cli-0.4.6.dist-info/RECORD,,