WIP - its just caos right now.

crc/api/spec_file.py

@@ -1,4 +1,4 @@
-from crc import session, WorkflowSpecService
+from crc import session
 from crc.api.common import ApiError
 from crc.models.file import FileSchema, FileType
 from crc.services.spec_file_service import SpecFileService
@@ -8,12 +8,15 @@ from flask import send_file
 import io
 import connexion
 
+from crc.services.workflow_spec_service import WorkflowSpecService
+
+workflow_spec_service = WorkflowSpecService()
 
 def get_files(spec_id, include_libraries=False):
     if spec_id is None:
         raise ApiError(code='missing_spec_id',
                        message='Please specify the workflow_spec_id.')
-    workflow_spec = WorkflowSpecService.get_spec(spec_id)
+    workflow_spec = workflow_spec_service.get_spec(spec_id)
     if workflow_spec is None:
         raise ApiError(code='unknown_spec',
                        message=f'Unknown Spec: {spec_id}')
@@ -23,7 +26,7 @@ def get_files(spec_id, include_libraries=False):
 
 
 def get_file(spec_id, file_name):
-    workflow_spec = WorkflowSpecService.get_spec(spec_id)
+    workflow_spec = workflow_spec_service.get_spec(spec_id)
     files = SpecFileService.get_files(workflow_spec, file_name)
     if len(files) == 0:
         raise ApiError(code='unknown file',
@@ -33,7 +36,7 @@ def get_file(spec_id, file_name):
 
 
 def add_file(spec_id):
-    workflow_spec = WorkflowSpecService.get_spec(spec_id)
+    workflow_spec = workflow_spec_service.get_spec(spec_id)
     file = connexion.request.files['file']
     file = SpecFileService.add_file(workflow_spec, file.filename, file.stream.read())
     if not workflow_spec.primary_process_name and file.type == FileType.bpmn:
@@ -42,7 +45,7 @@ def add_file(spec_id):
 
 
 def update(spec_id, file_name, is_primary):
-    workflow_spec = WorkflowSpecService.get_spec(spec_id)
+    workflow_spec = workflow_spec_service.get_spec(spec_id)
     files = SpecFileService.get_files(workflow_spec, file_name)
     if len(files) < 1:
         raise ApiError(code='unknown file',
@@ -55,7 +58,7 @@ def update(spec_id, file_name, is_primary):
 
 
 def update_data(spec_id, file_name):
-    workflow_spec_model = WorkflowSpecService.get_spec(spec_id)
+    workflow_spec_model = workflow_spec_service.get_spec(spec_id)
     if workflow_spec_model is None:
         raise ApiError(code='missing_spec',
                        message=f'The workflow spec for id {spec_id} does not exist.')
@@ -65,7 +68,7 @@ def update_data(spec_id, file_name):
 
 
 def get_data(spec_id, file_name):
-    workflow_spec = WorkflowSpecService.get_spec(spec_id)
+    workflow_spec = workflow_spec_service.get_spec(spec_id)
     file_data = SpecFileService.get_data(workflow_spec, file_name)
     if file_data is not None:
         file_info = SpecFileService.get_files(workflow_spec, file_name)[0]
@@ -82,5 +85,5 @@ def get_data(spec_id, file_name):
 
 
 def delete(spec_id, file_name):
-    workflow_spec = WorkflowSpecService.get_spec(spec_id)
+    workflow_spec = workflow_spec_service.get_spec(spec_id)
     SpecFileService.delete_file(workflow_spec, file_name)

crc/api/workflow.py

@@ -2,7 +2,7 @@ import uuid
 
 from flask import g
 
-from crc import session, WorkflowSpecService
+from crc import session
 from crc.api.common import ApiError, ApiErrorSchema
 from crc.models.api_models import WorkflowApiSchema
 from crc.models.study import StudyModel, WorkflowMetadata, StudyStatus
@@ -18,20 +18,22 @@ from crc.services.task_logging_service import TaskLoggingService
 from crc.services.user_service import UserService
 from crc.services.workflow_processor import WorkflowProcessor
 from crc.services.workflow_service import WorkflowService
+from crc.services.workflow_spec_service import WorkflowSpecService
 
+workflow_spec_service = WorkflowSpecService()
 
 def all_specifications(libraries=False,standalone=False):
     if libraries and standalone:
         raise ApiError('inconceivable!', 'You should specify libraries or standalone, but not both')
 
     if libraries:
-        return WorkflowSpecService.get_libraries()
+        return workflow_spec_service.get_libraries()
 
     if standalone:
-        return WorkflowSpecService.get_standalones()
+        return workflow_spec_service.get_standalones()
 
     # return standard workflows (not library, not standalone)
-    categories = WorkflowSpecService.get_categories()
+    categories = workflow_spec_service.get_categories()
     workflows = []
     for cat in categories:
         workflows.extend(cat.workflows)
@@ -47,14 +49,14 @@ def add_workflow_specification(body):
     if body['library'] is True or body['standalone'] is True:
         body['category_id'] = None
 
-    new_spec = WorkflowSpecService.add_spec(body)
+    new_spec = workflow_spec_service.add_spec(body)
     return new_spec
 
 
 def get_workflow_specification(spec_id):
     if spec_id is None:
         raise ApiError('unknown_spec', 'Please provide a valid Workflow Specification ID.')
-    spec = WorkflowSpecService.get_spec(spec_id)
+    spec = workflow_spec_service.get_spec(spec_id)
 
     if spec is None:
         raise ApiError('unknown_spec', 'The Workflow Specification "' + spec_id + '" is not recognized.')
@@ -67,8 +69,8 @@ def validate_spec_and_library(spec_id,library_id):
     if library_id is None:
         raise ApiError('unknown_spec', 'Please provide a valid Library Specification ID.')
 
-    spec = WorkflowSpecService.get_spec(spec_id)
+    spec = workflow_spec_service.get_spec(spec_id)
-    library = WorkflowSpecService.get_library(library_id);
+    library = workflow_spec_service.get_library(library_id);
     if spec is None:
         raise ApiError('unknown_spec', 'The Workflow Specification "' + spec_id + '" is not recognized.')
     if library is None:
@@ -79,27 +81,27 @@ def validate_spec_and_library(spec_id,library_id):
 
 def add_workflow_spec_library(spec_id, library_id):
     validate_spec_and_library(spec_id, library_id)
-    libraries: WorkflowSpecService.get_libraries()
+    libraries: workflow_spec_service.get_libraries()
     libraryids = [x.library_spec_id for x in libraries]
     if library_id in libraryids:
         raise ApiError('unknown_spec', 'The Library Specification "' + library_id + '" is already attached.')
 
-    spec = WorkflowSpecService.get_spec(spec_id)
+    spec = workflow_spec_service.get_spec(spec_id)
-    library = WorkflowSpecService.get_spec(library_id)
+    library = workflow_spec_service.get_spec(library_id)
     spec.libraries.push(library)
-    WorkflowSpecService.update_spec(spec_id)
+    workflow_spec_service.update_spec(spec_id)
     return spec
 
 
 def drop_workflow_spec_library(spec_id, library_id):
     validate_spec_and_library(spec_id, library_id)
-    spec = WorkflowSpecService.get_spec(spec_id)
+    spec = workflow_spec_service.get_spec(spec_id)
 
     # heres a piece of code that certainly wont work
-    library = WorkflowSpecService.get_spec(library_id)
+    library = workflow_spec_service.get_spec(library_id)
     if library in spec.libraries:
         spec.libraries.pop(library)
-    WorkflowSpecService.update_spec(spec_id)
+    workflow_spec_service.update_spec(spec_id)
     return spec
 
 
@@ -118,7 +120,7 @@ def validate_workflow_specification(spec_id, study_id=None, test_until=None):
 def update_workflow_specification(spec_id, body):
     if spec_id is None:
         raise ApiError('unknown_spec', 'Please provide a valid Workflow Spec ID.')
-    spec = WorkflowSpecService.get_spec(spec_id)
+    spec = workflow_spec_service.get_spec(spec_id)
 
     if spec is None:
         raise ApiError('unknown_study', 'The spec "' + spec_id + '" is not recognized.')
@@ -131,7 +133,7 @@ def update_workflow_specification(spec_id, body):
     if body['library'] is True or body['standalone'] is True:
         body['category_id'] = None
 
-    spec = WorkflowSpecService.update_spec(spec_id, body)
+    spec = workflow_spec_service.update_spec(spec_id, body)
     return spec
 
 
@@ -139,7 +141,7 @@ def delete_workflow_specification(spec_id):
     if spec_id is None:
         raise ApiError('unknown_spec', 'Please provide a valid Workflow Specification ID.')
 
-    spec = WorkflowSpecService.get_spec(spec_id)
+    spec = workflow_spec_service.get_spec(spec_id)
 
     if spec is None:
         raise ApiError('unknown_spec', 'The Workflow Specification "' + spec_id + '" is not recognized.')
@@ -155,7 +157,7 @@ def delete_workflow_specification(spec_id):
     WorkflowService.delete_workflow_spec_task_events(spec_id)
 
     # .delete() doesn't work when we need a cascade. Must grab the record, and explicitly delete
-    WorkflowSpecService.delete_spec(spec_id)
+    workflow_spec_service.delete_spec(spec_id)
 
     # Reorder the remaining specs
     WorkflowService.cleanup_workflow_spec_display_order(spec.category_id)
@@ -165,9 +167,9 @@ def reorder_workflow_specification(spec_id, direction):
     if direction not in ('up', 'down'):
         raise ApiError(code='bad_direction',
                        message='The direction must be `up` or `down`.')
-    spec = WorkflowSpecService.get_spec(spec_id)
+    spec = workflow_spec_service.get_spec(spec_id)
     if spec:
-        ordered_specs = WorkflowSpecService.reorder_spec(spec, direction)
+        ordered_specs = workflow_spec_service.reorder_spec(spec, direction)
     else:
         raise ApiError(code='bad_spec_id',
                        message=f'The spec_id {spec_id} did not return a specification. Please check that it is valid.')
@@ -322,22 +324,22 @@ def __update_task(processor, task, data, user):
 
 
 def list_workflow_spec_categories():
-    return WorkflowSpecService.get_workflow_categories()
+    return workflow_spec_service.get_workflow_categories()
 
 
 def get_workflow_spec_category(cat_id):
-    return WorkflowSpecService.get_workflow_category(cat_id)
+    return workflow_spec_service.get_workflow_category(cat_id)
 
 
 def add_workflow_spec_category(body):
-    return WorkflowSpecService.add_category(body)
+    return workflow_spec_service.add_category(body)
 
 
 def update_workflow_spec_category(cat_id, body):
     if cat_id is None:
         raise ApiError('unknown_category', 'Please provide a valid Workflow Spec Category ID.')
 
-    category = WorkflowSpecService.update_category(cat_id, body)
+    category = workflow_spec_service.update_category(cat_id, body)
 
     if category is None:
         raise ApiError('unknown_category', 'The category "' + cat_id + '" is not recognized.')
@@ -358,9 +360,9 @@ def reorder_workflow_spec_category(cat_id, direction):
         raise ApiError(code='bad_direction',
                        message='The direction must be `up` or `down`.')
     WorkflowService.cleanup_workflow_spec_category_display_order()
-    category = WorkflowSpecService.get_category(cat_id)
+    category = workflow_spec_service.get_category(cat_id)
     if category:
-        ordered_categories = WorkflowSpecService.reorder_workflow_spec_category(category, direction)
+        ordered_categories = workflow_spec_service.reorder_workflow_spec_category(category, direction)
         return ordered_categories
     else:
         raise ApiError(code='bad_category_id',

crc/services/workflow_spec_service.py

@@ -29,7 +29,6 @@ class WorkflowSpecService(FileSystemService):
         self.master_spec = None
         self.libraries = {}
         self.standalone = {}
-        self.scan_file_system()
 
     def add_spec(self, spec: WorkflowSpecInfo):
         self.update_spec(spec)

tests/base_test.py

@@ -12,7 +12,7 @@ import datetime
 import shutil
 from flask import g
 
-from crc import app, db, session, WorkflowSpecService
+from crc import app, db, session
 from crc.models.api_models import WorkflowApiSchema, MultiInstanceType
 from crc.models.file import FileModel, CONTENT_TYPES
 from crc.models.task_event import TaskEventModel
@@ -26,7 +26,7 @@ from crc.services.user_service import UserService
 from crc.services.workflow_service import WorkflowService
 from crc.services.document_service import DocumentService
 from example_data import ExampleDataLoader
-from crc.services.user_file_service import UserFileService
+from crc.services.workflow_spec_service import WorkflowSpecService
 
 # UNCOMMENT THIS FOR DEBUGGING SQL ALCHEMY QUERIES
 import logging

tests/workflow/cr_connect.log

@@ -1,3 +1,5 @@
 2022-01-26 15:05:47,955 - connexion.apis.abstract - ERROR - Failed to add operation for GET /v1.0/workflow_sync/pullall
 2022-01-26 15:06:36,303 - connexion.apis.abstract - ERROR - Failed to add operation for GET /v1.0/workflow_sync/pullall
 2022-01-26 15:08:01,978 - connexion.apis.abstract - ERROR - Failed to add operation for GET /v1.0/file/{md5_hash}/hash_data
+2022-02-07 12:46:21,875 - connexion.apis.abstract - ERROR - Failed to add operation for GET /v1.0/ldap
+2022-02-07 12:49:13,793 - connexion.apis.abstract - ERROR - Failed to add operation for GET /v1.0/ldap

tests/workflow/test_workflow_spec_service.py

@@ -7,13 +7,15 @@ from tests.base_test import BaseTest
 from crc.models.workflow import WorkflowSpecInfo, WorkflowSpecCategory
 from crc.services.file_system_service import FileSystemService
 from crc.services.spec_file_service import SpecFileService
-from crc import db, app, workflow_spec_service
+from crc.services.workflow_spec_service import WorkflowSpecService
+from crc import db, app
 
 
 class TestWorkflowSync(BaseTest):
 
     spec_path = FileSystemService.root_path()
     import_spec_path = os.path.join(app.root_path, '..', 'tests', 'data', 'IMPORT_TEST')
+    service = WorkflowSpecService()
 
     def copy_files_to_file_system(self):
         """Some tests rely on a well populated file system """
@@ -34,24 +36,24 @@ class TestWorkflowSync(BaseTest):
         self.load_test_spec('email', category_id=c1.id, library=True)
 
     def test_from_file_system_blank_slate(self):
-        self.assertEquals(0, len(workflow_spec_service.get_categories()))
+        self.assertEquals(0, len(self.service.get_categories()))
-        self.assertEquals(0, len(workflow_spec_service.get_specs()))
+        self.assertEquals(0, len(self.service.get_specs()))
         self.copy_files_to_file_system()
-        workflow_spec_service.scan_file_system()
+        self.service.scan_file_system()
-        self.assertEquals(2, len(workflow_spec_service.get_categories()))
+        self.assertEquals(2, len(self.service.get_categories()))
-        self.assertEquals(5, len(workflow_spec_service.get_specs()))
+        self.assertEquals(5, len(self.service.get_specs()))
-        self.assertEquals(1, len(workflow_spec_service.get_category('Category Number One').workflows))
+        self.assertEquals(1, len(self.service.get_category('Category Number One').workflows))
-        self.assertEquals(2, len(workflow_spec_service.get_category('Category Number Two').workflows))
+        self.assertEquals(2, len(self.service.get_category('Category Number Two').workflows))
-        self.assertIsNotNone(workflow_spec_service.master_spec)
+        self.assertIsNotNone(self.service.master_spec)
-        self.assertEquals(1, len(workflow_spec_service.get_libraries()))
+        self.assertEquals(1, len(self.service.get_libraries()))
-        self.assertEquals(1, len(workflow_spec_service.master_spec.libraries))
+        self.assertEquals(1, len(self.service.master_spec.libraries))
 
     def test_delete_category_and_workflows(self):
         self.copy_files_to_file_system()
         cat_path = SpecFileService().category_path('Category Number One')
         shutil.rmtree(cat_path) # Remove the path, as if from a git pull and the path was removed.
-        self.assertEquals(3, len(workflow_spec_service.get_categories()))
+        self.assertEquals(3, len(self.service.get_categories()))
-        self.assertEquals(4, len(workflow_spec_service.get_specs()))
+        self.assertEquals(4, len(self.service.get_specs()))