sartography/cr-connect-workflow
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Merge branch 'feature/spec_files_wthout_db' of github.com:sartography/cr-connect-workflow into feature/spec_files_wthout_db

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This commit is contained in:
Dan 2022-02-07 14:58:42 -05:00
commit 1d7ecad51f
2 changed files with 28 additions and 32 deletions
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57
crc/api/workflow.py
View File

@ -9,7 +9,6 @@ from crc.models.study import StudyModel, WorkflowMetadata, StudyStatus
from crc.models.task_event import TaskEventModel, TaskEvent, TaskEventSchema from crc.models.task_event import TaskEventModel, TaskEvent, TaskEventSchema
from crc.models.task_log import TaskLogModelSchema, TaskLogQuery, TaskLogQuerySchema from crc.models.task_log import TaskLogModelSchema, TaskLogQuery, TaskLogQuerySchema
from crc.models.workflow import WorkflowModel from crc.models.workflow import WorkflowModel
from crc.services import workflow_spec_service
from crc.services.error_service import ValidationErrorService from crc.services.error_service import ValidationErrorService
from crc.services.lookup_service import LookupService from crc.services.lookup_service import LookupService
from crc.services.spec_file_service import SpecFileService from crc.services.spec_file_service import SpecFileService
@ -20,20 +19,20 @@ from crc.services.workflow_processor import WorkflowProcessor
from crc.services.workflow_service import WorkflowService from crc.services.workflow_service import WorkflowService
from crc.services.workflow_spec_service import WorkflowSpecService from crc.services.workflow_spec_service import WorkflowSpecService
workflow_spec_service = WorkflowSpecService() spec_service = WorkflowSpecService()
def all_specifications(libraries=False,standalone=False): def all_specifications(libraries=False,standalone=False):
if libraries and standalone: if libraries and standalone:
raise ApiError('inconceivable!', 'You should specify libraries or standalone, but not both') raise ApiError('inconceivable!', 'You should specify libraries or standalone, but not both')
if libraries: if libraries:
return workflow_spec_service.get_libraries() return spec_service.get_libraries()
if standalone: if standalone:
return workflow_spec_service.get_standalones() return spec_service.get_standalones()
# return standard workflows (not library, not standalone) # return standard workflows (not library, not standalone)
categories = workflow_spec_service.get_categories() categories = spec_service.get_categories()
workflows = [] workflows = []
for cat in categories: for cat in categories:
workflows.extend(cat.workflows) workflows.extend(cat.workflows)
@ -49,14 +48,14 @@ def add_workflow_specification(body):
if body['library'] is True or body['standalone'] is True: if body['library'] is True or body['standalone'] is True:
body['category_id'] = None body['category_id'] = None
new_spec = workflow_spec_service.add_spec(body) new_spec = spec_service.add_spec(body)
return new_spec return new_spec
def get_workflow_specification(spec_id): def get_workflow_specification(spec_id):
if spec_id is None: if spec_id is None:
raise ApiError('unknown_spec', 'Please provide a valid Workflow Specification ID.') raise ApiError('unknown_spec', 'Please provide a valid Workflow Specification ID.')
spec = workflow_spec_service.get_spec(spec_id) spec = spec_service.get_spec(spec_id)
if spec is None: if spec is None:
raise ApiError('unknown_spec', 'The Workflow Specification "' + spec_id + '" is not recognized.') raise ApiError('unknown_spec', 'The Workflow Specification "' + spec_id + '" is not recognized.')
@ -69,8 +68,8 @@ def validate_spec_and_library(spec_id,library_id):
if library_id is None: if library_id is None:
raise ApiError('unknown_spec', 'Please provide a valid Library Specification ID.') raise ApiError('unknown_spec', 'Please provide a valid Library Specification ID.')
spec = workflow_spec_service.get_spec(spec_id) spec = spec_service.get_spec(spec_id)
library = workflow_spec_service.get_library(library_id); library = spec_service.get_library(library_id);
if spec is None: if spec is None:
raise ApiError('unknown_spec', 'The Workflow Specification "' + spec_id + '" is not recognized.') raise ApiError('unknown_spec', 'The Workflow Specification "' + spec_id + '" is not recognized.')
if library is None: if library is None:
@ -81,27 +80,27 @@ def validate_spec_and_library(spec_id,library_id):
def add_workflow_spec_library(spec_id, library_id): def add_workflow_spec_library(spec_id, library_id):
validate_spec_and_library(spec_id, library_id) validate_spec_and_library(spec_id, library_id)
libraries: workflow_spec_service.get_libraries() libraries: spec_service.get_libraries()
libraryids = [x.library_spec_id for x in libraries] libraryids = [x.library_spec_id for x in libraries]
if library_id in libraryids: if library_id in libraryids:
raise ApiError('unknown_spec', 'The Library Specification "' + library_id + '" is already attached.') raise ApiError('unknown_spec', 'The Library Specification "' + library_id + '" is already attached.')
spec = workflow_spec_service.get_spec(spec_id) spec = spec_service.get_spec(spec_id)
library = workflow_spec_service.get_spec(library_id) library = spec_service.get_spec(library_id)
spec.libraries.push(library) spec.libraries.push(library)
workflow_spec_service.update_spec(spec_id) spec_service.update_spec(spec_id)
return spec return spec
def drop_workflow_spec_library(spec_id, library_id): def drop_workflow_spec_library(spec_id, library_id):
validate_spec_and_library(spec_id, library_id) validate_spec_and_library(spec_id, library_id)
spec = workflow_spec_service.get_spec(spec_id) spec = spec_service.get_spec(spec_id)
# heres a piece of code that certainly wont work # heres a piece of code that certainly wont work
library = workflow_spec_service.get_spec(library_id) library = spec_service.get_spec(library_id)
if library in spec.libraries: if library in spec.libraries:
spec.libraries.pop(library) spec.libraries.pop(library)
workflow_spec_service.update_spec(spec_id) spec_service.update_spec(spec_id)
return spec return spec
@ -120,7 +119,7 @@ def validate_workflow_specification(spec_id, study_id=None, test_until=None):
def update_workflow_specification(spec_id, body): def update_workflow_specification(spec_id, body):
if spec_id is None: if spec_id is None:
raise ApiError('unknown_spec', 'Please provide a valid Workflow Spec ID.') raise ApiError('unknown_spec', 'Please provide a valid Workflow Spec ID.')
spec = workflow_spec_service.get_spec(spec_id) spec = spec_service.get_spec(spec_id)
if spec is None: if spec is None:
raise ApiError('unknown_study', 'The spec "' + spec_id + '" is not recognized.') raise ApiError('unknown_study', 'The spec "' + spec_id + '" is not recognized.')
@ -133,7 +132,7 @@ def update_workflow_specification(spec_id, body):
if body['library'] is True or body['standalone'] is True: if body['library'] is True or body['standalone'] is True:
body['category_id'] = None body['category_id'] = None
spec = workflow_spec_service.update_spec(spec_id, body) spec = spec_service.update_spec(spec_id, body)
return spec return spec
@ -141,7 +140,7 @@ def delete_workflow_specification(spec_id):
if spec_id is None: if spec_id is None:
raise ApiError('unknown_spec', 'Please provide a valid Workflow Specification ID.') raise ApiError('unknown_spec', 'Please provide a valid Workflow Specification ID.')
spec = workflow_spec_service.get_spec(spec_id) spec = spec_service.get_spec(spec_id)
if spec is None: if spec is None:
raise ApiError('unknown_spec', 'The Workflow Specification "' + spec_id + '" is not recognized.') raise ApiError('unknown_spec', 'The Workflow Specification "' + spec_id + '" is not recognized.')
@ -157,7 +156,7 @@ def delete_workflow_specification(spec_id):
WorkflowService.delete_workflow_spec_task_events(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 # .delete() doesn't work when we need a cascade. Must grab the record, and explicitly delete
workflow_spec_service.delete_spec(spec_id) spec_service.delete_spec(spec_id)
# Reorder the remaining specs # Reorder the remaining specs
WorkflowService.cleanup_workflow_spec_display_order(spec.category_id) WorkflowService.cleanup_workflow_spec_display_order(spec.category_id)
@ -167,9 +166,9 @@ def reorder_workflow_specification(spec_id, direction):
if direction not in ('up', 'down'): if direction not in ('up', 'down'):
raise ApiError(code='bad_direction', raise ApiError(code='bad_direction',
message='The direction must be `up` or `down`.') message='The direction must be `up` or `down`.')
spec = workflow_spec_service.get_spec(spec_id) spec = spec_service.get_spec(spec_id)
if spec: if spec:
ordered_specs = workflow_spec_service.reorder_spec(spec, direction) ordered_specs = spec_service.reorder_spec(spec, direction)
else: else:
raise ApiError(code='bad_spec_id', raise ApiError(code='bad_spec_id',
message=f'The spec_id {spec_id} did not return a specification. Please check that it is valid.') message=f'The spec_id {spec_id} did not return a specification. Please check that it is valid.')
@ -323,22 +322,22 @@ def __update_task(processor, task, data, user):
def list_workflow_spec_categories(): def list_workflow_spec_categories():
return workflow_spec_service.get_workflow_categories() return spec_service.get_categories()
def get_workflow_spec_category(cat_id): def get_workflow_spec_category(cat_id):
return workflow_spec_service.get_workflow_category(cat_id) return spec_service.get_category(cat_id)
def add_workflow_spec_category(body): def add_workflow_spec_category(body):
return workflow_spec_service.add_category(body) return spec_service.add_category(body)
def update_workflow_spec_category(cat_id, body): def update_workflow_spec_category(cat_id, body):
if cat_id is None: if cat_id is None:
raise ApiError('unknown_category', 'Please provide a valid Workflow Spec Category ID.') raise ApiError('unknown_category', 'Please provide a valid Workflow Spec Category ID.')
category = workflow_spec_service.update_category(cat_id, body) category = spec_service.update_category(cat_id, body)
if category is None: if category is None:
raise ApiError('unknown_category', 'The category "' + cat_id + '" is not recognized.') raise ApiError('unknown_category', 'The category "' + cat_id + '" is not recognized.')
@ -351,7 +350,7 @@ def update_workflow_spec_category(cat_id, body):
def delete_workflow_spec_category(cat_id): def delete_workflow_spec_category(cat_id):
workflow_spec_service.delete_category(cat_id) spec_service.delete_category(cat_id)
def reorder_workflow_spec_category(cat_id, direction): def reorder_workflow_spec_category(cat_id, direction):
@ -359,9 +358,9 @@ def reorder_workflow_spec_category(cat_id, direction):
raise ApiError(code='bad_direction', raise ApiError(code='bad_direction',
message='The direction must be `up` or `down`.') message='The direction must be `up` or `down`.')
WorkflowService.cleanup_workflow_spec_category_display_order() WorkflowService.cleanup_workflow_spec_category_display_order()
category = workflow_spec_service.get_category(cat_id) category = spec_service.get_category(cat_id)
if category: if category:
ordered_categories = workflow_spec_service.reorder_workflow_spec_category(category, direction) ordered_categories = spec_service.reorder_workflow_spec_category(category, direction)
return ordered_categories return ordered_categories
else: else:
raise ApiError(code='bad_category_id', raise ApiError(code='bad_category_id',

3
crc/services/workflow_spec_service.py
View File

@ -78,9 +78,6 @@ class WorkflowSpecService(FileSystemService):
spec_list.sort(key=lambda w: w.display_order) spec_list.sort(key=lambda w: w.display_order)
return spec_list return spec_list
def get_standalones(self) -> List[WorkflowSpecInfo]:
pass
def get_categories(self) -> List[WorkflowSpecCategory]: def get_categories(self) -> List[WorkflowSpecCategory]:
"""Returns the categories as a list in display order""" """Returns the categories as a list in display order"""
cat_list = list(self.categories.values()) cat_list = list(self.categories.values())