refine: oton endpoint

src/server/operandi_server/routers/workflow.py

@@ -17,7 +17,6 @@
 from operandi_utils.database import (
     db_create_workflow, db_create_workflow_job, db_get_hpc_slurm_job, db_get_workflow, db_update_workspace,
     db_increase_processing_stats_with_handling)
-from operandi_utils.oton import OTONConverter
 from operandi_utils.rabbitmq import (
     get_connection_publisher, RABBITMQ_QUEUE_JOB_STATUSES, RABBITMQ_QUEUE_HARVESTER, RABBITMQ_QUEUE_USERS)
 from operandi_server.constants import (
@@ -30,7 +29,8 @@
     convert_oton_with_handling,
     get_db_workflow_job_with_handling,
     get_db_workflow_with_handling,
-    nf_script_uses_mets_server_with_handling
+    nf_script_uses_mets_server_with_handling,
+    validate_oton_with_handling
 )
 from .workspace_utils import check_if_file_group_exists_with_handling, get_db_workspace_with_handling
 from .user import RouterUser
@@ -51,7 +51,7 @@ def __init__(self):
         self.router = APIRouter(tags=[ServerApiTag.WORKFLOW])
         self.router.add_api_route(
             path=f"/workflow", endpoint=self.list_workflows, methods=["GET"], status_code=status.HTTP_200_OK,
-            summary="Get a list of existing nextflow workflows.",
+            summary="Get a list of existing nextflow from operandi_utils.oton import OTONConverter, OCRDValidatorworkflows.",
             response_model=List[WorkflowRsrc], response_model_exclude_unset=True, response_model_exclude_none=True
         )
         self.router.add_api_route(
@@ -108,13 +108,12 @@ def __init__(self):
         # Added by Faizan
         self.router.add_api_route(
             path="/convert_workflow",
-            endpoint=self.convert_txt_to_nextflow,
-            methods=["POST"],
-            status_code=status.HTTP_201_CREATED,
+            endpoint=self.convert_txt_to_nextflow, methods=["POST"], status_code=status.HTTP_201_CREATED,
             summary="""
             Upload a text file containing a workflow in ocrd process format and
             convert it to a Nextflow script in the desired format (local/docker)
-            """
+            """,
+            response_model=None, response_model_exclude_unset=False, response_model_exclude_none=False
         )
 
     def __del__(self):
@@ -448,12 +447,6 @@ async def convert_txt_to_nextflow(
         # Authenticate the user
         await self.user_authenticator.user_login(auth)
 
-        environments = ["local", "docker", "apptainer"]
-        if environment not in environments:
-            message = f"Unknown environment value: {environment}. Must be one of: {environments}"
-            self.logger.error(message)
-            raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=message)
-
         oton_id, oton_dir = create_resource_dir(SERVER_OTON_CONVERSIONS, resource_id=None)
         ocrd_process_txt = join(oton_dir, f"ocrd_process_input.txt")
         nf_script_dest = join(oton_dir, f"nextflow_output.nf")
@@ -465,19 +458,6 @@ async def convert_txt_to_nextflow(
             self.logger.error(f"{message}, error: {error}")
             raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=message)
 
-        # Use the Converter's convert_OtoN function instead of directly calling OCRDValidator
-        converter = OTONConverter()
-        try:
-            # Call the conversion function (this will also perform validation inside)
-            if environment == "local":
-                converter.convert_oton_env_local(str(ocrd_process_txt), str(nf_script_dest))
-            elif environment == "docker":
-                converter.convert_oton_env_docker(str(ocrd_process_txt), str(nf_script_dest))
-            elif environment == "apptainer":
-                converter.convert_oton_env_apptainer(str(ocrd_process_txt), str(nf_script_dest))
-        except ValueError as e:
-            raise HTTPException(status_code=400, detail=str(e))
-
-        # Return the generated Nextflow (.nf) file as a response
-
+        await validate_oton_with_handling(self.logger, ocrd_process_txt)
+        await convert_oton_with_handling(self.logger, environment, ocrd_process_txt, nf_script_dest)
         return FileResponse(nf_script_dest, filename=f'{oton_id}.nf')

src/server/operandi_server/routers/workflow_utils.py

@@ -3,6 +3,7 @@
 
 from operandi_utils.database import db_get_workflow, db_get_workflow_job
 from operandi_utils.database.models import DBWorkflow, DBWorkflowJob
+from operandi_utils.oton import OTONConverter, OCRDValidator
 
 
 async def get_db_workflow_with_handling(
@@ -56,5 +57,31 @@ async def nf_script_uses_mets_server_with_handling(
         raise HTTPException(status_code=status.HTTP_422_UNPROCESSABLE_ENTITY, detail=message)
 
 
-async def convert_oton_with_handling():
-    pass
+async def validate_oton_with_handling(logger, ocrd_process_txt_path: str):
+    try:
+        # Separate validation for refined error logging
+        validator = OCRDValidator()
+        validator.validate(input_file=ocrd_process_txt_path)
+    except ValueError as error:
+        message = "Failed to validate the ocrd process workflow txt file"
+        logger.error(f"{message}, error: {error}")
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=message)
+
+async def convert_oton_with_handling(logger, environment: str, ocrd_process_txt_path: str, nf_script_dest_path: str):
+    environments = ["local", "docker", "apptainer"]
+    if environment not in environments:
+        message = f"Unknown environment value: {environment}. Must be one of: {environments}"
+        logger.error(message)
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=message)
+    try:
+        converter = OTONConverter()
+        if environment == "local":
+            converter.convert_oton_env_local(str(ocrd_process_txt_path), str(nf_script_dest_path))
+        elif environment == "docker":
+            converter.convert_oton_env_docker(str(ocrd_process_txt_path), str(nf_script_dest_path))
+        elif environment == "apptainer":
+            converter.convert_oton_env_apptainer(str(ocrd_process_txt_path), str(nf_script_dest_path))
+    except ValueError as error:
+        message = "Failed to convert ocrd process workflow to nextflow workflow"
+        logger.error(f"{message}, error: {error}")
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=message)

src/server/operandi_server/server.py

@@ -10,7 +10,8 @@
 from operandi_utils.database import db_initiate_database
 from operandi_utils import safe_init_logging
 
-from operandi_server.constants import SERVER_WORKFLOW_JOBS_ROUTER, SERVER_WORKFLOWS_ROUTER, SERVER_WORKSPACES_ROUTER
+from operandi_server.constants import (
+    SERVER_OTON_CONVERSIONS, SERVER_WORKFLOW_JOBS_ROUTER, SERVER_WORKFLOWS_ROUTER, SERVER_WORKSPACES_ROUTER)
 from operandi_server.files_manager import create_resource_base_dir
 from operandi_server.routers import RouterAdminPanel, RouterDiscovery, RouterUser, RouterWorkflow, RouterWorkspace
 from operandi_server.routers.user_utils import create_user_if_not_available
@@ -81,6 +82,7 @@ async def startup_event(self):
         # Reconfigure all loggers to the same format
         reconfigure_all_loggers(log_level=LOG_LEVEL_SERVER, log_file_path=log_file_path)
 
+        create_resource_base_dir(SERVER_OTON_CONVERSIONS)
         create_resource_base_dir(SERVER_WORKFLOW_JOBS_ROUTER)
         create_resource_base_dir(SERVER_WORKFLOWS_ROUTER)
         create_resource_base_dir(SERVER_WORKSPACES_ROUTER)

src/utils/operandi_utils/oton/ocrd_validator.py

@@ -64,7 +64,7 @@ def validate_processor_params(
         report = ParameterValidator(processor_args.ocrd_tool_json).validate(processor_args.parameters)
         if not report.is_valid:
             self.logger.error(report.errors)
-            raise Exception(report.errors)
+            raise ValueError(report.errors)
 
         # Remove the overwritten defaults to keep the produced NF executable file less populated
         # Note: The defaults, still get overwritten in run-time

src/utils/operandi_utils/oton/oton_converter.py

@@ -7,7 +7,6 @@ def __init__(self):
         self.ocrd_validator = OCRDValidator()
 
     def __convert_oton(self, input_path: str, output_path: str, environment: str):
-        self.ocrd_validator.validate(input_path)
         list_processor_call_arguments = self.ocrd_validator.validate(input_path)
         nf_file_executable = NextflowFileExecutable()
         if environment == "local":

tests/tests_server/test_endpoint_workflow.py

@@ -167,7 +167,7 @@ def test_convert_txt_to_nextflow_validator_failure(operandi, auth):
 
     response = operandi.post(url="/convert_workflow", files=files, auth=auth, params=params)
     assert_response_status_code(response.status_code, expected_floor=4)
-    assert "Invalid first line. Expected: 'ocrd process', got: 'Invalid ocrd process text" in response.json()["detail"]
+    assert "Failed to validate the ocrd process workflow txt file" in response.json()["detail"]
 
 
 # Added by Faizan

tests/tests_utils/test_2_oton/test_2_validator_2_validate_processor_params.py

@@ -46,16 +46,16 @@ def test_falseness_basic(ocrd_parser, ocrd_validator):
 def test_falseness_with_params_separated(ocrd_parser, ocrd_validator):
     call_args: ProcessorCallArguments = ocrd_parser.parse_arguments(
         "cis-ocropy-binarize -I OCR-D-IMG -O OCR-D-BIN -P dpi 177.0 -P non-existing-param 0.42")
-    with raises(Exception):
+    with raises(ValueError):
         ocrd_validator.validate_processor_params(processor_args=call_args, overwrite_with_defaults=False)
-    with raises(Exception):
+    with raises(ValueError):
         ocrd_validator.validate_processor_params(processor_args=call_args, overwrite_with_defaults=True)
 
 
 def test_falseness_with_params_clustered(ocrd_parser, ocrd_validator):
     call_args: ProcessorCallArguments = ocrd_parser.parse_arguments(
         """cis-ocropy-binarize -I OCR-D-IMG -O OCR-D-BIN -p '{"dpi": 177.0, "non-existing-param": 0.42}'""")
-    with raises(Exception):
+    with raises(ValueError):
         ocrd_validator.validate_processor_params(processor_args=call_args, overwrite_with_defaults=False)
-    with raises(Exception):
+    with raises(ValueError):
         ocrd_validator.validate_processor_params(processor_args=call_args, overwrite_with_defaults=True)