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https://github.com/sartography/cr-connect-workflow.git
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8c88de35cd
In get_validate_common, we first look in validate_data_store, then in the real data_store. This allows us the flexibility to use temp values for current workflow or real values set by previous workflows. Also, lots of cleanup: - we didn't use the dictionary returned by the set_data_common method, so removed it and only return the value we set. - this allowed us to delete the `overwritten` method and some other code. - renamed some variables to better represent what we are doing
105 lines
5.2 KiB
Python
105 lines
5.2 KiB
Python
from crc import session
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from crc.api.common import ApiError
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from crc.models.data_store import DataStoreModel
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from crc.models.workflow import WorkflowModel
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from flask import g
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class DataStoreBase(object):
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def set_validate_common(self, task_id, study_id, workflow_id, script_name, user_id, file_id, *args):
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self.check_args_2(args, script_name)
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if script_name == 'study_data_set':
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record = {'task_id': task_id, 'study_id': study_id, 'workflow_id': workflow_id, args[0]: args[1]}
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elif script_name == 'file_data_set':
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record = {'task_id': task_id, 'study_id': study_id, 'workflow_id': workflow_id, 'file_id': file_id, args[0]: args[1]}
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elif script_name == 'user_data_set':
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record = {'task_id': task_id, 'study_id': study_id, 'workflow_id': workflow_id, 'user_id': user_id, args[0]: args[1]}
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g.validation_data_store.append(record)
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return record
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def get_validate_common(self, script_name, study_id=None, user_id=None, file_id=None, *args):
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# This method uses a temporary validation_data_store that is only available for the current validation request.
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# This allows us to set data_store values during validation that don't affect the real data_store.
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# For data_store `gets`, we first look in the temporary validation_data_store.
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# If we don't find an entry in validation_data_store, we look in the real data_store.
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if script_name == 'study_data_get':
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# If it's in the validation data store, return it
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for record in g.validation_data_store:
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if 'study_id' in record and record['study_id'] == study_id and args[0] in record:
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return record[args[0]]
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# If not in validation_data_store, look for in the actual data_store
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return self.get_data_common(study_id, user_id, 'study_data_get', file_id, *args)
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elif script_name == 'file_data_get':
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for record in g.validation_data_store:
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if 'file_id' in record and record['file_id'] == file_id and args[0] in record:
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return record[args[0]]
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return self.get_data_common(study_id, user_id, 'file_data_get', file_id, *args)
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elif script_name == 'user_data_get':
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for record in g.validation_data_store:
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if 'user_id' in record and record['user_id'] == user_id and args[0] in record:
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return record[args[0]]
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return self.get_data_common(study_id, user_id, 'user_data_get', file_id, *args)
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@staticmethod
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def check_args(args, maxlen=1, script_name='study_data_get'):
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if len(args) < 1 or len(args) > maxlen:
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raise ApiError(code="missing_argument",
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message=f"The {script_name} script takes either one or two arguments, "
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f"starting with the key and an optional default")
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@staticmethod
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def check_args_2(args, script_name='study_data_set'):
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if len(args) != 2:
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raise ApiError(code="missing_argument",
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message=f"The {script_name} script takes two arguments, key and value, in that order.")
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def set_data_common(self,
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task_spec,
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study_id,
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user_id,
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workflow_id,
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workflow_spec_id,
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script_name,
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file_id,
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*args,
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**kwargs):
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self.check_args_2(args, script_name=script_name)
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if workflow_spec_id is None and workflow_id is not None:
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workflow = session.query(WorkflowModel).filter(WorkflowModel.id == workflow_id).first()
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workflow_spec_id = workflow.workflow_spec_id
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dsm = DataStoreModel(key=args[0],
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value=args[1],
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study_id=study_id,
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task_spec=task_spec,
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user_id=user_id, # Make this available to any User
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file_id=file_id,
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workflow_id=workflow_id,
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spec_id=workflow_spec_id)
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session.add(dsm)
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session.commit()
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return dsm.value
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def get_data_common(self, study_id, user_id, script_name, file_id=None, *args):
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self.check_args(args, 2, script_name)
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record = session.query(DataStoreModel).filter_by(study_id=study_id,
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user_id=user_id,
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file_id=file_id,
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key=args[0]).first()
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if record:
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return record.value
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else:
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# This is a possible default value passed in from the data_store get methods
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if len(args) == 2:
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return args[1]
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@staticmethod
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def get_multi_common(study_id, user_id, file_id=None):
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results = session.query(DataStoreModel).filter_by(study_id=study_id,
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user_id=user_id,
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file_id=file_id)
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return results
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