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cr-connect-workflow
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Assure that all script tasks place data in a dictionary that is named exactly the same as the class - which is also the same as the Script tag.

This commit is contained in:
Dan Funk 2020-04-07 14:09:21 -04:00
parent c6b6ee5d70
commit 697127660f
11 changed files with 22 additions and 19 deletions
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10
crc/scripts/documents.py
View File

@ -19,7 +19,7 @@ is also provided.
This place a dictionary of values in the current task, where the key is the code in the lookup table.
For example:
``` "documents" :
``` "Documents" :
{
"UVACompliance_PRCApproval": {
"name": "Cancer Center's PRC Approval Form",
@ -28,8 +28,8 @@ For example:
"category3": "",
"Who Uploads?": "CRC",
"required": True,
"requirement_id": 6
"upload_count": 0
"Id": 6
"count": 0
},
24: { ...
}
@ -38,13 +38,13 @@ For example:
def do_task_validate_only(self, task, study_id, *args, **kwargs):
"""For validation only, pretend no results come back from pb"""
pb_docs = []
task.data["required_docs"] = self.get_documents(study_id, pb_docs)
self.add_data_to_task(task, self.get_documents(study_id, pb_docs))
def do_task(self, task, study_id, *args, **kwargs):
"""Takes data from the protocol builder, and merges it with data from the IRB Pro Categories
spreadsheet to return pertinent details about the required documents."""
pb_docs = self.pb.get_required_docs(study_id, as_objects=True)
task.data["documents"] = self.get_documents(study_id, pb_docs)
self.add_data_to_task(task, self.get_documents(study_id, pb_docs))
def get_documents(self, study_id, pb_docs):
"""Takes data from the protocol builder, and merges it with data from the IRB Pro Categories spreadsheet to return

3
crc/scripts/fact_service.py
View File

@ -40,6 +40,7 @@ class FactService(Script):
else:
details = "unknown fact type."
task.data['details'] = details
self.add_data_to_task(task, details)
print(details)
return details

2
crc/scripts/script.py
View File

@ -53,6 +53,8 @@ class Script:
return all_subclasses
def add_data_to_task(self, task, data):
task.data[self.__class__.__name__] = data
class ScriptValidationError:

6
crc/scripts/study_info.py
View File

@ -45,15 +45,15 @@ class StudyInfo(Script):
{}
}
}
task.data["study"] = data["study"]
self.add_data_to_task(task=task, data=data["study"])
def do_task(self, task, study_id, *args, **kwargs):
self.check_args(args)
cmd = args[0]
study_info = {}
if "study" in task.data:
study_info = task.data["study"]
if self.__class__.__name__ in task.data:
study_info = task.data[self.__class__.__name__]
if cmd == 'info':
study = session.query(StudyModel).filter_by(id=study_id).first()

4
crc/static/bpmn/top_level_workflow/data_security_plan.dmn
View File

@ -5,9 +5,9 @@
<biodi:bounds x="190" y="80" width="180" height="80" />
</extensionElements>
<decisionTable id="DecisionTable_1mjqwlv">
<input id="InputClause_18pwfqu" label="Required Doc Keys">
<input id="InputClause_18pwfqu" label="Data Plan Required in PB?">
<inputExpression id="LiteralExpression_1y84stb" typeRef="boolean" expressionLanguage="feel">
<text>documents['UVACompl_PRCAppr']['required']</text>
<text>Documents['Study_DataSecurityPlan']['required']</text>
</inputExpression>
</input>
<output id="OutputClause_05y0j7c" label="data_security_plan" name="data_security_plan" typeRef="string" />

2
crc/static/bpmn/top_level_workflow/enter_core_info.dmn
View File

@ -7,7 +7,7 @@
<decisionTable id="decisionTable_1">
<input id="InputClause_1ki80j6" label="required doc ids">
<inputExpression id="LiteralExpression_10mfcy7" typeRef="boolean" expressionLanguage="Python">
<text>documents['UVACompl_PRCAppr']['required']</text>
<text>Documents['UVACompl_PRCAppr']['required']</text>
</inputExpression>
</input>
<output id="output_1" label="enter_core_info" name="enter_core_info" typeRef="string" />

4
crc/static/bpmn/top_level_workflow/sponsor_funding_source.dmn
View File

@ -5,9 +5,9 @@
<biodi:bounds x="190" y="70" width="180" height="80" />
</extensionElements>
<decisionTable id="DecisionTable_00zdxg0">
<input id="InputClause_02n3ccs" label="CoCApplication Required?">
<input id="InputClause_02n3ccs" label="Sponsor Document Required in PB?">
<inputExpression id="LiteralExpression_1ju4o1o" typeRef="boolean" expressionLanguage="feel">
<text>documents['AD_LabManual']['required']</text>
<text>Documents['AD_LabManual']['required']</text>
</inputExpression>
</input>
<output id="OutputClause_1ybi1ud" label="sponsor_funding_source" name="eat_my_shorts" typeRef="string" />

2
tests/data/top_level_workflow/data_security_plan.dmn
View File

@ -7,7 +7,7 @@
<decisionTable id="DecisionTable_1mjqwlv">
<input id="InputClause_18pwfqu" label="Data Plan Required in PB?">
<inputExpression id="LiteralExpression_1y84stb" typeRef="boolean" expressionLanguage="feel">
<text>documents['Study_DataSecurityPlan']['required']</text>
<text>Documents['Study_DataSecurityPlan']['required']</text>
</inputExpression>
</input>
<output id="OutputClause_05y0j7c" label="data_security_plan" name="data_security_plan" typeRef="string" />

2
tests/data/top_level_workflow/enter_core_info.dmn
View File

@ -7,7 +7,7 @@
<decisionTable id="decisionTable_1">
<input id="InputClause_1ki80j6" label="required doc ids">
<inputExpression id="LiteralExpression_10mfcy7" typeRef="boolean" expressionLanguage="Python">
<text>documents['UVACompl_PRCAppr']['required']</text>
<text>Documents['UVACompl_PRCAppr']['required']</text>
</inputExpression>
</input>
<output id="output_1" label="enter_core_info" name="enter_core_info" typeRef="string" />

2
tests/data/top_level_workflow/sponsor_funding_source.dmn
View File

@ -7,7 +7,7 @@
<decisionTable id="DecisionTable_00zdxg0">
<input id="InputClause_02n3ccs" label="Sponsor Document Required in PB?">
<inputExpression id="LiteralExpression_1ju4o1o" typeRef="boolean" expressionLanguage="feel">
<text>documents['AD_LabManual']['required']</text>
<text>Documents['AD_LabManual']['required']</text>
</inputExpression>
</input>
<output id="OutputClause_1ybi1ud" label="sponsor_funding_source" name="eat_my_shorts" typeRef="string" />

4
tests/test_workflow_processor.py
View File

@ -48,7 +48,7 @@ class TestWorkflowProcessor(BaseTest):
self.assertEqual(WorkflowStatus.complete, processor.get_status())
data = processor.get_data()
self.assertIsNotNone(data)
self.assertIn("details", data)
self.assertIn("FactService", data)
def test_workflow_with_dmn(self):
self.load_example_data()
@ -152,7 +152,7 @@ class TestWorkflowProcessor(BaseTest):
self.assertEqual(WorkflowStatus.complete, processor.get_status())
task = processor.next_task()
self.assertIsNotNone(task)
self.assertIn("details", task.data)
self.assertIn("FactService", task.data)
self.assertIsInstance(task.task_spec, EndEvent)
def test_workflow_validation_error_is_properly_raised(self):