Add file_data_get and file_data_set functions that can be accessed in a bpmn script function
Fixes #299
This commit is contained in:
Kelly McDonald
parent
277beb345f
commit
d3d7eeb309
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@ -7,30 +7,30 @@ from crc.models.data_store import DataStoreModel, DataStoreSchema
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from crc.scripts.data_store_base import DataStoreBase
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def study_data_set(study_id, key, value):
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"""Set a study data value in the data_store, mimic the script endpoint"""
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if study_id is None:
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raise ApiError('unknown_study', 'Please provide a valid Study ID.')
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if key is None:
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raise ApiError('invalid_key', 'Please provide a valid key')
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dsb = DataStoreBase()
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retval = dsb.set_data_common('api', study_id, None, None, None, 'api_study_data_set', key, value)
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json_value = json.dumps(retval, ensure_ascii=False, indent=2)
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return json_value
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# def study_data_set(study_id, key, value):
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# """Set a study data value in the data_store, mimic the script endpoint"""
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# if study_id is None:
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# raise ApiError('unknown_study', 'Please provide a valid Study ID.')
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#
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# if key is None:
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# raise ApiError('invalid_key', 'Please provide a valid key')
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# dsb = DataStoreBase()
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# retval = dsb.set_data_common('api', study_id, None, None, None, 'api_study_data_set', key, value)
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# json_value = json.dumps(retval, ensure_ascii=False, indent=2)
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# return json_value
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def study_data_get(study_id, key, default=None):
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"""Get a study data value in the data_store, mimic the script endpoint"""
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if study_id is None:
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raise ApiError('unknown_study', 'Please provide a valid Study ID.')
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if key is None:
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raise ApiError('invalid_key', 'Please provide a valid key')
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dsb = DataStoreBase()
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retval = dsb.get_data_common(study_id, None, 'api_study_data_get', key, default)
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# json_value = json.dumps(retval, ensure_ascii=False, indent=2) # just return raw text
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return retval
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# def study_data_get(study_id, key, default=None):
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# """Get a study data value in the data_store, mimic the script endpoint"""
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# if study_id is None:
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# raise ApiError('unknown_study', 'Please provide a valid Study ID.')
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#
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# if key is None:
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# raise ApiError('invalid_key', 'Please provide a valid key')
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# dsb = DataStoreBase()
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# retval = dsb.get_data_common(study_id, None, 'api_study_data_get', key, default)
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# # json_value = json.dumps(retval, ensure_ascii=False, indent=2) # just return raw text
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# return retval
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def study_multi_get(study_id):
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@ -44,56 +44,56 @@ def study_multi_get(study_id):
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return results
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def study_data_del(study_id, key):
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"""Delete a study data value in the data store"""
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if study_id is None:
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raise ApiError('unknown_study', 'Please provide a valid Study ID.')
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if key is None:
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raise ApiError('invalid_key', 'Please provide a valid key')
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dsb = DataStoreBase()
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dsb.del_data_common(study_id, None, 'api_study_data_get', key)
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json_value = json.dumps('deleted', ensure_ascii=False, indent=2)
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return json_value
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# def study_data_del(study_id, key):
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# """Delete a study data value in the data store"""
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# if study_id is None:
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# raise ApiError('unknown_study', 'Please provide a valid Study ID.')
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#
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# if key is None:
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# raise ApiError('invalid_key', 'Please provide a valid key')
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# dsb = DataStoreBase()
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# dsb.del_data_common(study_id, None, 'api_study_data_get', key)
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# json_value = json.dumps('deleted', ensure_ascii=False, indent=2)
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# return json_value
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def user_data_set(user_id, key, value):
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"""Set a user data value in the data_store, mimic the script endpoint"""
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if user_id is None:
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raise ApiError('unknown_study', 'Please provide a valid UserID.')
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if key is None:
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raise ApiError('invalid_key', 'Please provide a valid key')
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dsb = DataStoreBase()
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retval = dsb.set_data_common('api',
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None,
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user_id,
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None,
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None,
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'api_user_data_set',
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key, value)
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json_value = json.dumps(retval, ensure_ascii=False, indent=2)
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return json_value
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# def user_data_set(user_id, key, value):
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# """Set a user data value in the data_store, mimic the script endpoint"""
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# if user_id is None:
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# raise ApiError('unknown_study', 'Please provide a valid UserID.')
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#
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# if key is None:
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# raise ApiError('invalid_key', 'Please provide a valid key')
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# dsb = DataStoreBase()
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#
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# retval = dsb.set_data_common('api',
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# None,
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# user_id,
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# None,
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# None,
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# 'api_user_data_set',
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# key, value)
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#
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# json_value = json.dumps(retval, ensure_ascii=False, indent=2)
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# return json_value
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def user_data_get(user_id, key, default=None):
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"""Get a user data value from the data_store, mimic the script endpoint"""
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if user_id is None:
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raise ApiError('unknown_study', 'Please provide a valid UserID.')
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if key is None:
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raise ApiError('invalid_key', 'Please provide a valid key')
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dsb = DataStoreBase()
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retval = dsb.get_data_common(None,
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user_id,
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'api_user_data_get',
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key, default)
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# json_value = json.dumps(retval, ensure_ascii=False, indent=2) # just return raw text
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return retval
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# def user_data_get(user_id, key, default=None):
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# """Get a user data value from the data_store, mimic the script endpoint"""
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# if user_id is None:
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# raise ApiError('unknown_study', 'Please provide a valid UserID.')
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#
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# if key is None:
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# raise ApiError('invalid_key', 'Please provide a valid key')
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# dsb = DataStoreBase()
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# retval = dsb.get_data_common(None,
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# user_id,
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# 'api_user_data_get',
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# key, default)
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#
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# # json_value = json.dumps(retval, ensure_ascii=False, indent=2) # just return raw text
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# return retval
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#
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def user_multi_get(user_id):
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"""Get all data values in the data_store for a userid"""
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@ -130,7 +130,7 @@ def update_datastore(id, body):
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item = session.query(DataStoreModel).filter_by(id=id).first()
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if item is None:
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raise ApiError('unknown_item', 'The item "' + id + '" is not recognized.')
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print(body)
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#print(body)
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# I'm not sure if there is a generic way to use the
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# schema to both parse the body and update the SQLAlchemy record
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for key in body:
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@ -155,12 +155,16 @@ def add_datastore(body):
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if 'value' not in body:
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raise ApiError('no_value', 'You need to specify a value to add a datastore item')
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if (not 'user_id' in body) and (not 'study_id' in body):
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raise ApiError('conflicting_values', 'A datastore item should have either a study_id or a user_id')
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if ('user_id' not in body) and ('study_id' not in body) and ('file_id' not in body):
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raise ApiError('conflicting_values', 'A datastore item should have either a study_id, user_id or file_id ')
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if 'user_id' in body and 'study_id' in body:
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raise ApiError('conflicting_values', 'A datastore item should have either a study_id or a user_id, '
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'but not both')
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present = 0
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for field in ['user_id','study_id','file_id']:
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if field in body:
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present = present+1
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if present > 1:
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raise ApiError('conflicting_values', 'A datastore item should have one of a study_id, user_id or a file_id '
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'but not more than one of these')
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item = DataStoreModel(key=body['key'], value=body['value'])
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# I'm not sure if there is a generic way to use the
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@ -20,10 +20,11 @@ class DataStoreBase(object):
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overwritten = True
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return overwritten
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def set_validate_common(self, study_id, workflow_id, user_id, script_name, *args):
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def set_validate_common(self, study_id, workflow_id, user_id, script_name, file_id, *args):
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self.check_args_2(args, script_name)
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workflow = session.query(WorkflowModel).filter(WorkflowModel.id == workflow_id).first()
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self.get_prev_value(study_id=study_id, user_id=user_id, key=args[0])
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self.get_prev_value(study_id=study_id, user_id=user_id, file_id=file_id, key=args[0])
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def check_args(self, args, maxlen=1, script_name='study_data_get'):
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if len(args) < 1 or len(args) > maxlen:
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@ -0,0 +1,34 @@
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from flask import g
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from crc.api.common import ApiError
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from crc.scripts.data_store_base import DataStoreBase
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from crc.scripts.script import Script
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class FileDataGet(Script, DataStoreBase):
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def get_description(self):
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return """Gets user data from the data store - takes only two keyword arguments arguments: 'file_id' and 'key' """
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def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
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self.do_task(task, study_id, workflow_id, *args, **kwargs)
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def validate_kw_args(self,**kwargs):
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if kwargs.get('key',None) is None:
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raise ApiError(code="missing_argument",
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message=f"The 'file_data_get' script requires a keyword argument of 'key'")
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if kwargs.get('file_id',None) is None:
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raise ApiError(code="missing_argument",
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message=f"The 'file_data_get' script requires a keyword argument of 'file_id'")
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return True
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def do_task(self, task, study_id, workflow_id, *args, **kwargs):
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if self.validate_kw_args(**kwargs):
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myargs = [kwargs['key']]
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return self.get_data_common(None,
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None,
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'file_data_get',
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kwargs['file_id'],
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*myargs)
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@ -0,0 +1,44 @@
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from flask import g
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from crc.api.common import ApiError
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from crc.scripts.data_store_base import DataStoreBase
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from crc.scripts.script import Script
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class FileDataSet(Script, DataStoreBase):
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def get_description(self):
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return """Sets data the data store - takes three keyword arguments arguments: 'file_id' and 'key' and 'value'"""
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def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
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self.do_task(task, study_id, workflow_id, *args, **kwargs)
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def validate_kw_args(self,**kwargs):
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if kwargs.get('key',None) is None:
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raise ApiError(code="missing_argument",
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message=f"The 'file_data_get' script requires a keyword argument of 'key'")
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if kwargs.get('file_id',None) is None:
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raise ApiError(code="missing_argument",
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message=f"The 'file_data_get' script requires a keyword argument of 'file_id'")
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if kwargs.get('value',None) is None:
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raise ApiError(code="missing_argument",
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message=f"The 'file_data_get' script requires a keyword argument of 'value'")
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return True
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def do_task(self, task, study_id, workflow_id, *args, **kwargs):
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if self.validate_kw_args(**kwargs):
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myargs = [kwargs['key'],kwargs['value']]
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fileid = kwargs['file_id']
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del(kwargs['file_id'])
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return self.set_data_common(task.id,
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None,
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None,
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workflow_id,
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None,
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'file_data_set',
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fileid,
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*myargs,
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**kwargs)
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@ -11,6 +11,7 @@ class StudyDataSet(Script,DataStoreBase):
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workflow_id,
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None,
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'study_data_set',
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None,
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*args)
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def do_task(self, task, study_id, workflow_id, *args, **kwargs):
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@ -20,6 +21,7 @@ class StudyDataSet(Script,DataStoreBase):
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workflow_id,
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None,
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'study_data_set',
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None,
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*args,
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**kwargs)
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@ -15,6 +15,7 @@ class UserDataSet(Script,DataStoreBase):
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workflow_id,
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g.user.uid,
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'user_data_set',
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None,
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*args)
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def do_task(self, task, study_id, workflow_id, *args, **kwargs):
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@ -24,6 +25,7 @@ class UserDataSet(Script,DataStoreBase):
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workflow_id,
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None,
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'user_data_set',
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None,
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*args,
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**kwargs)
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@ -0,0 +1,70 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_1j7idla" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.0">
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<bpmn:process id="Process_18biih5" isExecutable="true">
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<bpmn:startEvent id="StartEvent_1">
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<bpmn:outgoing>SequenceFlow_1pnq3kg</bpmn:outgoing>
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</bpmn:startEvent>
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<bpmn:sequenceFlow id="SequenceFlow_1pnq3kg" sourceRef="StartEvent_1" targetRef="Task_Has_Bananas" />
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<bpmn:scriptTask id="Task_Has_Bananas" name="get Documents">
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<bpmn:incoming>SequenceFlow_1pnq3kg</bpmn:incoming>
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<bpmn:outgoing>Flow_1xqewuk</bpmn:outgoing>
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<bpmn:script>documents = study_info('documents')</bpmn:script>
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</bpmn:scriptTask>
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<bpmn:sequenceFlow id="Flow_1xqewuk" sourceRef="Task_Has_Bananas" targetRef="Activity_0yikdu7" />
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<bpmn:scriptTask id="Activity_0yikdu7" name="save arbitrary value">
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<bpmn:incoming>Flow_1xqewuk</bpmn:incoming>
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<bpmn:outgoing>Flow_0z7kamo</bpmn:outgoing>
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<bpmn:script>filelist = list(documents.keys())
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fileid = documents['UVACompl_PRCAppr'].files[0]['file_id']
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file_data_set(file_id=fileid,key='test',value='me')</bpmn:script>
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</bpmn:scriptTask>
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<bpmn:endEvent id="Event_1pdyoyv">
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<bpmn:incoming>Flow_15mmymi</bpmn:incoming>
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</bpmn:endEvent>
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<bpmn:sequenceFlow id="Flow_0z7kamo" sourceRef="Activity_0yikdu7" targetRef="Activity_19x6e2e" />
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<bpmn:sequenceFlow id="Flow_15mmymi" sourceRef="Activity_19x6e2e" targetRef="Event_1pdyoyv" />
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<bpmn:scriptTask id="Activity_19x6e2e" name="get output">
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<bpmn:incoming>Flow_0z7kamo</bpmn:incoming>
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<bpmn:outgoing>Flow_15mmymi</bpmn:outgoing>
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<bpmn:script>output=file_data_get(file_id=fileid,key='test')
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</bpmn:script>
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</bpmn:scriptTask>
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</bpmn:process>
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<bpmndi:BPMNDiagram id="BPMNDiagram_1">
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<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_18biih5">
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<bpmndi:BPMNEdge id="SequenceFlow_1pnq3kg_di" bpmnElement="SequenceFlow_1pnq3kg">
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<di:waypoint x="215" y="117" />
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<di:waypoint x="270" y="117" />
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</bpmndi:BPMNEdge>
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<bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
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<dc:Bounds x="179" y="99" width="36" height="36" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="Activity_01ekdl8_di" bpmnElement="Task_Has_Bananas">
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<dc:Bounds x="270" y="77" width="100" height="80" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNEdge id="Flow_1xqewuk_di" bpmnElement="Flow_1xqewuk">
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<di:waypoint x="370" y="117" />
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<di:waypoint x="430" y="117" />
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</bpmndi:BPMNEdge>
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<bpmndi:BPMNShape id="Activity_0g5namy_di" bpmnElement="Activity_0yikdu7">
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<dc:Bounds x="430" y="77" width="100" height="80" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="Event_1pdyoyv_di" bpmnElement="Event_1pdyoyv">
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<dc:Bounds x="782" y="99" width="36" height="36" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNEdge id="Flow_0z7kamo_di" bpmnElement="Flow_0z7kamo">
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<di:waypoint x="530" y="117" />
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<di:waypoint x="590" y="117" />
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</bpmndi:BPMNEdge>
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<bpmndi:BPMNEdge id="Flow_15mmymi_di" bpmnElement="Flow_15mmymi">
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<di:waypoint x="690" y="117" />
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<di:waypoint x="782" y="117" />
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</bpmndi:BPMNEdge>
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<bpmndi:BPMNShape id="Activity_0ma7ela_di" bpmnElement="Activity_19x6e2e">
|
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<dc:Bounds x="590" y="77" width="100" height="80" />
|
||||
</bpmndi:BPMNShape>
|
||||
</bpmndi:BPMNPlane>
|
||||
</bpmndi:BPMNDiagram>
|
||||
</bpmn:definitions>
|
||||
|
|
@ -0,0 +1,31 @@
|
|||
import json
|
||||
|
||||
from crc.services.file_service import FileService
|
||||
from crc.services.workflow_processor import WorkflowProcessor
|
||||
from tests.base_test import BaseTest
|
||||
from crc.models.workflow import WorkflowStatus
|
||||
from crc import db
|
||||
from crc.api.common import ApiError
|
||||
from crc.models.task_event import TaskEventModel, TaskEventSchema
|
||||
from crc.services.workflow_service import WorkflowService
|
||||
|
||||
|
||||
class TestFileDatastore(BaseTest):
|
||||
|
||||
|
||||
def test_file_datastore_workflow(self):
|
||||
self.load_example_data()
|
||||
self.create_reference_document()
|
||||
# we need to create a file with an IRB code
|
||||
# for this study
|
||||
workflow = self.create_workflow('file_data_store')
|
||||
irb_code = "UVACompl_PRCAppr" # The first file referenced in pb required docs.
|
||||
FileService.add_workflow_file(workflow_id=workflow.id,
|
||||
name="anything.png", content_type="text",
|
||||
binary_data=b'1234', irb_doc_code=irb_code)
|
||||
|
||||
processor = WorkflowProcessor(workflow)
|
||||
processor.do_engine_steps()
|
||||
task_data = processor.bpmn_workflow.last_task.data
|
||||
self.assertEqual(task_data['output'],'me')
|
||||
|
||||
Loading…
Reference in New Issue