scientiflow-cli 0.4.12__py3-none-any.whl → 0.4.15__py3-none-any.whl

scientiflow_cli/pipeline/decode_and_execute.py

@@ -12,85 +12,6 @@ from scientiflow_cli.services.rich_printer import RichPrinter
 
 printer = RichPrinter()
 
-# Global background job tracker
-class GlobalBackgroundJobTracker:
-    _instance = None
-    _lock = threading.Lock()
-    
-    def __new__(cls):
-        if cls._instance is None:
-            with cls._lock:
-                if cls._instance is None:
-                    cls._instance = super().__new__(cls)
-                    cls._instance._initialize()
-        return cls._instance
-    
-    def _initialize(self):
-        self.background_executors = []
-        self.background_jobs_count = 0
-        self.background_jobs_completed = 0
-        self.background_jobs_lock = threading.Lock()
-    
-    def register_background_job(self, executor, futures, node_label, log_file_path):
-        """Register a background job for global tracking."""
-        with self.background_jobs_lock:
-            self.background_jobs_count += 1
-            self.background_executors.append(executor)
-        
-        # Start monitoring in a separate thread
-        monitor_thread = threading.Thread(
-            target=self._monitor_job,
-            args=(futures, node_label, executor, log_file_path),
-            daemon=True
-        )
-        monitor_thread.start()
-    
-    def _monitor_job(self, futures, node_label, executor, log_file_path):
-        """Monitor background job completion."""
-        all_successful = True
-        for future in as_completed(futures):
-            success = future.result()
-            if not success:
-                all_successful = False
-        
-        if not all_successful:
-            with open(log_file_path, 'a') as f:
-                f.write(f"[ERROR] Background job {node_label} failed\n")
-            printer.print_message(f"[BACKGROUND JOB] {node_label} Failed - some commands in background job failed", style="bold red")
-        else:
-            printer.print_message(f"[BACKGROUND JOB] {node_label} Execution completed in the background", style="bold green")
-        
-        # Clean up executor
-        executor.shutdown(wait=False)
-        with self.background_jobs_lock:
-            if executor in self.background_executors:
-                self.background_executors.remove(executor)
-            self.background_jobs_completed += 1
-    
-    def wait_for_all_jobs(self):
-        """Wait for all background jobs to complete."""
-        import time
-        if self.background_jobs_count > 0:
-            printer.print_message(f"[INFO] Waiting for {self.background_jobs_count} background job(s) to complete...", style="bold yellow")
-            
-            while True:
-                with self.background_jobs_lock:
-                    if self.background_jobs_completed >= self.background_jobs_count:
-                        break
-                time.sleep(0.5)  # Check every 500ms
-            
-            printer.print_message("[INFO] All background jobs completed.", style="bold green")
-    
-    def reset(self):
-        """Reset the tracker for a new execution cycle."""
-        with self.background_jobs_lock:
-            self.background_executors = []
-            self.background_jobs_count = 0
-            self.background_jobs_completed = 0
-
-# Global tracker instance
-global_bg_tracker = GlobalBackgroundJobTracker()
-
 def execute_background_command_standalone(command: str, log_file_path: str):
     """Execute a command in background without real-time output display - standalone function for multiprocessing."""
     try:
@@ -130,6 +51,10 @@ class PipelineExecutor:
         self.current_node = None
         self.job_status = job_status
         self.current_node_from_config = current_node_from_config
+        self.background_executors = []  # Keep track of background executors
+        self.background_jobs_count = 0  # Track number of active background jobs
+        self.background_jobs_completed = 0  # Track completed background jobs
+        self.background_jobs_lock = threading.Lock()  # Thread-safe counter updates
         
         # For resuming: flag to track if we've reached the resume point
         self.resume_mode = (job_status == "running" and current_node_from_config is not None)
@@ -240,7 +165,47 @@ class PipelineExecutor:
             self.update_terminal_output()
             raise SystemExit("[ERROR] Pipeline execution terminated due to an unexpected error.")
 
+    def monitor_background_job(self, futures, node_label, executor):
+        """Monitor background job completion in a separate thread."""
+        def monitor():
+            all_successful = True
+            for future in as_completed(futures):
+                success = future.result()
+                if not success:
+                    all_successful = False
+            
+            if not all_successful:
+                self.log_output(f"[ERROR] Background job {node_label} failed")
+                printer.print_message(f"[BACKGROUND JOB] {node_label} Failed - some commands in background job failed", style="bold red")
+            else:
+                printer.print_message(f"[BACKGROUND JOB] {node_label} Execution completed in the background", style="bold green")
+            
+            # Clean up executor
+            executor.shutdown(wait=False)
+            if executor in self.background_executors:
+                self.background_executors.remove(executor)
+            
+            # Update background job completion count
+            with self.background_jobs_lock:
+                self.background_jobs_completed += 1
+        
+        # Start monitoring thread
+        monitor_thread = threading.Thread(target=monitor, daemon=True)
+        monitor_thread.start()
 
+    def wait_for_background_jobs(self):
+        """Wait for all background jobs to complete."""
+        import time
+        if self.background_jobs_count > 0:
+            printer.print_message(f"[INFO] Waiting for {self.background_jobs_count} background job(s) to complete...", style="bold yellow")
+            
+            while True:
+                with self.background_jobs_lock:
+                    if self.background_jobs_completed >= self.background_jobs_count:
+                        break
+                time.sleep(0.5)  # Check every 500ms
+            
+            printer.print_message("[INFO] All background jobs completed.", style="bold green")
 
     def dfs(self, node: str):
         """Perform Depth-First Search (DFS) for executing pipeline nodes."""
@@ -319,14 +284,19 @@ class PipelineExecutor:
                 
                 # Execute commands in background using ProcessPoolExecutor (non-blocking)
                 if command_list:
+                    # Increment background jobs counter
+                    with self.background_jobs_lock:
+                        self.background_jobs_count += 1
+                    
                     executor = ProcessPoolExecutor(max_workers=numberOfThreads)
+                    self.background_executors.append(executor)  # Keep reference to prevent garbage collection
                     futures = []
                     for cmd in command_list:
                         future = executor.submit(execute_background_command_standalone, cmd, self.log_file_path)
                         futures.append(future)
                     
-                    # Register with global tracker (non-blocking)
-                    global_bg_tracker.register_background_job(executor, futures, node_label, self.log_file_path)
+                    # Start monitoring in a separate thread (non-blocking)
+                    self.monitor_background_job(futures, node_label, executor)
                     
                     # Don't wait for completion, immediately continue to next node
                 else:
@@ -374,9 +344,9 @@ class PipelineExecutor:
         if starting_node:
             self.dfs(starting_node)
 
-        # Don't wait for background jobs here - let them continue across multiple jobs
-        # Background jobs will be waited for at the end of all job executions
-        
+        # Wait for all background jobs to complete before marking pipeline as completed
+        self.wait_for_background_jobs()
+
         update_job_status(self.project_job_id, "completed")
         update_stopped_at_node(self.project_id, self.project_job_id, self.current_node)
 

scientiflow_cli/services/executor.py

@@ -1,7 +1,7 @@
 from concurrent.futures import ThreadPoolExecutor
 import asyncio
 from scientiflow_cli.pipeline.get_jobs import get_jobs
-from scientiflow_cli.pipeline.decode_and_execute import decode_and_execute_pipeline, global_bg_tracker
+from scientiflow_cli.pipeline.decode_and_execute import decode_and_execute_pipeline
 from scientiflow_cli.pipeline.container_manager import get_job_containers
 from scientiflow_cli.utils.file_manager import create_job_dirs, get_job_files
 from scientiflow_cli.services.rich_printer import RichPrinter
@@ -37,6 +37,7 @@ def execute_jobs(job_ids: list[int] = None, parallel: bool = False, is_cloud: bo
             if matching_jobs:
                 if is_cloud:
                     for job in matching_jobs:
+                        job['project_title'] = str(job['project']['id']) + '_' + job['project']['project_title']
                         if 'server' not in job or job['server'] is None:
                             job['server'] = {'base_directory':None}
                         job['server']['base_directory'] = get_base_directory()
@@ -116,9 +117,6 @@ async def execute_async(jobs: list[dict]) -> None:
 
     await asyncio.gather(*running_jobs)  # Wait for all jobs to complete
     printer.print_success("[ASYNC COMPLETE] All jobs finished!")
-    
-    # Wait for all background jobs from all executed jobs to complete
-    global_bg_tracker.wait_for_all_jobs()
 
 
 def execute_single_job(job: dict, is_cloud: bool = False) -> None:
@@ -158,7 +156,7 @@ def execute_single_job(job: dict, is_cloud: bool = False) -> None:
         if job_status != "running":
             if job["new_job"] == 1:
                 # Initialize folders for the project / project_job 
-                create_job_dirs(job, is_cloud)
+                create_job_dirs(job)
 
             # Fetch the files and folder from the backend
             get_job_files(job)

scientiflow_cli/services/request_handler.py

@@ -21,6 +21,7 @@ def make_auth_request(endpoint, method, data=None, params=None, error_message=No
         return handle_response(response, error_message)
 
     except requests.RequestException as e:
+        print(e)
         return "Request failed"
 
 
@@ -32,10 +33,12 @@ def make_no_auth_request(endpoint, method, data=None, error_message=None):
             response = requests.get(base_url + endpoint)
         elif method == 'POST':
             response = requests.post(base_url + endpoint, json=data)
+            print(response)
         else:
             raise ValueError("Unsupported HTTP method")
 
         return handle_response(response, error_message)
 
     except requests.RequestException as e:
+        print(e)
         return "Request failed"

scientiflow_cli/utils/file_manager.py

@@ -37,12 +37,9 @@ def get_job_files(job: dict) -> None:
 
     printer.print_success(f"[+] Files extracted to {str(project_dir_name).strip()}")
         
-def create_job_dirs(job: dict, is_cloud: bool = False) -> None:
+def create_job_dirs(job: dict) -> None:
     base_dir = Path(job['server']['base_directory'])
-    if is_cloud:
-        project_dir = base_dir / (str(job['project']['id'])+"_"+job['project']['project_title'])
-    else:
-        project_dir = base_dir / job['project']['project_title']       
+    project_dir = base_dir / job['project']['project_title']       
     job_dir = project_dir / job['project_job']['job_directory']
     job_dir.mkdir(parents=True, exist_ok=True)
 

{scientiflow_cli-0.4.12.dist-info → scientiflow_cli-0.4.15.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scientiflow-cli
-Version: 0.4.12
+Version: 0.4.15
 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-0.4.12.dist-info → scientiflow_cli-0.4.15.dist-info}/RECORD

@@ -7,25 +7,25 @@ scientiflow_cli/cli/logout.py,sha256=EzpFPA1ENoXqLvduo6rxaVF09GqgO5GCRvnGMDr5BEw
 scientiflow_cli/main.py,sha256=AliEFU3bebJV2tbvxQYbiMY1bqVGqq3-a6dzkVUXong,6982
 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=M_0RPiJhenPc9HShGIB7CLzb-Jc0MPsHClGhNQYh-Xk,18926
+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
 scientiflow_cli/services/base_directory.py,sha256=2dUvGYk4enLe3Cagcs_bfv2kNuHg1ws-dtMDEW_tccI,2726
-scientiflow_cli/services/executor.py,sha256=TC3-0-rOOzTKQGlV0Dbi__6iqIlp8RZFJuPlwHrfcss,11846
+scientiflow_cli/services/executor.py,sha256=1TAST7zokikecTJZ5Pdd9hrlNncAzcuDeJnlGJhGGk0,11813
 scientiflow_cli/services/modes.py,sha256=-Bk1CJO0vgc8v_rXktfKAyHSF6cr5bGbufSGa_DtvY4,1241
-scientiflow_cli/services/request_handler.py,sha256=CjJqEjXt8AOzyZq6UwUBzRBhahqWHj1_OKUyPG3PpFs,1335
+scientiflow_cli/services/request_handler.py,sha256=5Y1B84kpHP-EDAI9d6fjaPtQE1-dMKCtoCaqvixifSU,1397
 scientiflow_cli/services/rich_printer.py,sha256=5ORAaZOa_84m6vP-novpPOI70UPxt0pEvmRq9999Ifg,2129
 scientiflow_cli/services/status_updater.py,sha256=VjC2V6lWzjwBN7ZhCQzW_h_sMG25Poeh35MNTeVdt5E,2910
 scientiflow_cli/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 scientiflow_cli/utils/config.py,sha256=iq9aEVwlJA-KLPWX6Vtx6SaEgH3UAuKjNIODw2mGYxY,256
 scientiflow_cli/utils/encryption.py,sha256=iQ-b40i75JvoB1cGANDqzZXLztD54toO_6loX1m5W9Q,1107
-scientiflow_cli/utils/file_manager.py,sha256=OjIXM_VV8t4ctLQDFo7g2sYf9ewPb2n5pe07J7OcvrY,2075
+scientiflow_cli/utils/file_manager.py,sha256=KLdJlIzFng_BfKHHZzQNp35hXsFMWfgy4OUqodadzss,1923
 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-0.4.12.dist-info/LICENSE.md,sha256=nb6GGGYuS_KXe33mSNwcEW-QzvwM475NQ4cNE7KBb34,425
-scientiflow_cli-0.4.12.dist-info/METADATA,sha256=6MtglJyLBVH4phBij1cJgUF2c7AqPkD_jnK-96pFjnc,2492
-scientiflow_cli-0.4.12.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-scientiflow_cli-0.4.12.dist-info/entry_points.txt,sha256=0lq2mjcG5hGfODrQodeMSAy9RfE2EX1MZSHRpfSncxc,61
-scientiflow_cli-0.4.12.dist-info/RECORD,,
+scientiflow_cli-0.4.15.dist-info/LICENSE.md,sha256=nb6GGGYuS_KXe33mSNwcEW-QzvwM475NQ4cNE7KBb34,425
+scientiflow_cli-0.4.15.dist-info/METADATA,sha256=LBG22lfG_UFtnbrC64_MXN8FK86HgPpPehq4hMFmrbM,2492
+scientiflow_cli-0.4.15.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+scientiflow_cli-0.4.15.dist-info/entry_points.txt,sha256=0lq2mjcG5hGfODrQodeMSAy9RfE2EX1MZSHRpfSncxc,61
+scientiflow_cli-0.4.15.dist-info/RECORD,,