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cr-connect-workflow/crc/scripts/study_info.py

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Adding a new reference file that provides greater details about the investigators related to a study. Improving the study_info script documentation to provide detailed examples of values returned based on arguments. Making the tests a little more targetted and less subject to breaking through better mocks. Allow all tests to pass even when ther protocol builder mock isn't running locally. Removing the duplication of reference files in tests and static, as this seems silly to me at the moment.
2020-05-07 17:57:24 +00:00
import json
Connect LDAP Requests to the StudyInfo service so we get back additional details.
2020-04-20 20:02:13 +00:00
Adding a new reference file that provides greater details about the investigators related to a study. Improving the study_info script documentation to provide detailed examples of values returned based on arguments. Making the tests a little more targetted and less subject to breaking through better mocks. Allow all tests to pass even when ther protocol builder mock isn't running locally. Removing the duplication of reference files in tests and static, as this seems silly to me at the moment.
2020-05-07 17:57:24 +00:00
from crc import session
Standardizing the script tasks that can be executed on the server, adding tons of error messages for when things go wrong. All scripts must exist in side of the crc/scripts directory. Adding a new script that script tasks can use to add in data about the study. Moving all the test workflow specifications out of the main load. fixing a pile of tests so they can find workflow specs that are now moved into the test directory.
2020-03-03 18:50:22 +00:00
from crc.api.common import ApiError
Makes Sonar happy.
2020-08-04 20:42:35 +00:00
from crc.models.protocol_builder import ProtocolBuilderInvestigatorType
Created a "StudyService" and moved all complex logic around study manipulation out of the study api, and this service, as things were getting complicated. The Workflow Processor no longer creates the WorkflowModel, the study object handles that, and only passes the model into the workflow processor when it is ready to start the workflow. Created a Study object (seperate from the StudyModel) that can cronstructed on request, and contains a different data structure than we store in the DB. This allows us to return underlying Categories and Workflows in a clean way. Added a new status to workflows called "not_started", meaning we have not yet instantiated a processor or created a BPMN, they have no version yet and no stored data, just the possiblity of being started. The Top Level Workflow or "Master" workflow is now a part of the sample data, and loaded at all times. Removed the ability to "add a workflow to a study" and "remove a workflow from a study", a study contains all possible workflows by definition. Example data no longer creates users or studies, it just creates the specs.
2020-03-30 12:00:16 +00:00
from crc.models.study import StudyModel, StudySchema
Adds documents_status StudyInfo script. Adds Documents & Approvals workflow spec.
2020-04-23 23:25:01 +00:00
from crc.models.workflow import WorkflowStatus
Adding a new reference file that provides greater details about the investigators related to a study. Improving the study_info script documentation to provide detailed examples of values returned based on arguments. Making the tests a little more targetted and less subject to breaking through better mocks. Allow all tests to pass even when ther protocol builder mock isn't running locally. Removing the duplication of reference files in tests and static, as this seems silly to me at the moment.
2020-05-07 17:57:24 +00:00
from crc.scripts.script import Script
missed a file in the last commit.
2020-05-11 21:42:24 +00:00
from crc.services.file_service import FileService
Standardizing the script tasks that can be executed on the server, adding tons of error messages for when things go wrong. All scripts must exist in side of the crc/scripts directory. Adding a new script that script tasks can use to add in data about the study. Moving all the test workflow specifications out of the main load. fixing a pile of tests so they can find workflow specs that are now moved into the test directory.
2020-03-03 18:50:22 +00:00
from crc.services.protocol_builder import ProtocolBuilderService
Adds approvals to study service
2020-04-23 18:40:05 +00:00
from crc.services.study_service import StudyService
Test of adding in the ability of augmenting the workflow to include internal scripts like StudyInfo This is the first waypoint on a larger effort to make all of the 'special scripts' that currently require a shebang to be just another python function.
2020-07-24 16:08:46 +00:00
from box import Box
Standardizing the script tasks that can be executed on the server, adding tons of error messages for when things go wrong. All scripts must exist in side of the crc/scripts directory. Adding a new script that script tasks can use to add in data about the study. Moving all the test workflow specifications out of the main load. fixing a pile of tests so they can find workflow specs that are now moved into the test directory.
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class StudyInfo(Script):
Adding a new reference file that provides greater details about the investigators related to a study. Improving the study_info script documentation to provide detailed examples of values returned based on arguments. Making the tests a little more targetted and less subject to breaking through better mocks. Allow all tests to pass even when ther protocol builder mock isn't running locally. Removing the duplication of reference files in tests and static, as this seems silly to me at the moment.
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"""Please see the detailed description that is provided below. """
Connect LDAP Requests to the StudyInfo service so we get back additional details.
2020-04-20 20:02:13 +00:00
Standardizing the script tasks that can be executed on the server, adding tons of error messages for when things go wrong. All scripts must exist in side of the crc/scripts directory. Adding a new script that script tasks can use to add in data about the study. Moving all the test workflow specifications out of the main load. fixing a pile of tests so they can find workflow specs that are now moved into the test directory.
2020-03-03 18:50:22 +00:00
pb = ProtocolBuilderService()
Add 'sponsors' to study_info call
2020-11-04 19:34:10 +00:00
type_options = ['info', 'investigators', 'roles', 'details', 'approvals', 'documents', 'protocol','sponsors']
Standardizing the script tasks that can be executed on the server, adding tons of error messages for when things go wrong. All scripts must exist in side of the crc/scripts directory. Adding a new script that script tasks can use to add in data about the study. Moving all the test workflow specifications out of the main load. fixing a pile of tests so they can find workflow specs that are now moved into the test directory.
2020-03-03 18:50:22 +00:00
Adding a new reference file that provides greater details about the investigators related to a study. Improving the study_info script documentation to provide detailed examples of values returned based on arguments. Making the tests a little more targetted and less subject to breaking through better mocks. Allow all tests to pass even when ther protocol builder mock isn't running locally. Removing the duplication of reference files in tests and static, as this seems silly to me at the moment.
2020-05-07 17:57:24 +00:00
# This is used for test/workflow validation, as well as documentation.
example_data = {
"StudyInfo": {
"info": {
"id": 12,
"title": "test",
"primary_investigator_id": 21,
"user_uid": "dif84",
"sponsor": "sponsor",
"ind_number": "1234",
"inactive": False
},
Change the study_sponsors script so that we can actually call it : var = study_info('sponsors') to keep it more in line with other scripts that we have
2020-11-05 15:31:47 +00:00
"sponsors": [
{
"COMMONRULEAGENCY": None,
"SPONSOR_ID": 2453,
"SP_NAME": "Abbott Ltd",
"SP_TYPE": "Private",
"SP_TYPE_GROUP_NAME": None,
"SS_STUDY": 2
},
{
"COMMONRULEAGENCY": None,
"SPONSOR_ID": 2387,
"SP_NAME": "Abbott-Price",
"SP_TYPE": "Incoming Sub Award",
"SP_TYPE_GROUP_NAME": "Government",
"SS_STUDY": 2
},
{
"COMMONRULEAGENCY": None,
"SPONSOR_ID": 1996,
"SP_NAME": "Abernathy-Heidenreich",
"SP_TYPE": "Foundation/Not for Profit",
"SP_TYPE_GROUP_NAME": "Other External Funding",
"SS_STUDY": 2
}
],
Adding a new reference file that provides greater details about the investigators related to a study. Improving the study_info script documentation to provide detailed examples of values returned based on arguments. Making the tests a little more targetted and less subject to breaking through better mocks. Allow all tests to pass even when ther protocol builder mock isn't running locally. Removing the duplication of reference files in tests and static, as this seems silly to me at the moment.
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"investigators": {
'PI': {
Makes Sonar happy.
2020-08-04 20:42:35 +00:00
'label': ProtocolBuilderInvestigatorType.PI.value,
Adding a new reference file that provides greater details about the investigators related to a study. Improving the study_info script documentation to provide detailed examples of values returned based on arguments. Making the tests a little more targetted and less subject to breaking through better mocks. Allow all tests to pass even when ther protocol builder mock isn't running locally. Removing the duplication of reference files in tests and static, as this seems silly to me at the moment.
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'display': 'Always',
'unique': 'Yes',
'user_id': 'dhf8r',
'display_name': 'Dan Funk',
'given_name': 'Dan',
'email': 'dhf8r@virginia.edu',
'telephone_number': '+1 (434) 924-1723',
'title': "E42:He's a hoopy frood",
'department': 'E0:EN-Eng Study of Parallel Universes',
'affiliation': 'faculty',
'sponsor_type': 'Staff'},
'SC_I': {
'label': 'Study Coordinator I',
'display': 'Always',
'unique': 'Yes',
'user_id': None},
'DC': {
'label': 'Department Contact',
'display': 'Optional',
'unique': 'Yes',
'user_id': 'asd3v',
'error': 'Unable to locate a user with id asd3v in LDAP'}
},
"documents": {
'AD_CoCApp': {'category1': 'Ancillary Document', 'category2': 'CoC Application', 'category3': '',
'Who Uploads?': 'CRC', 'id': '12',
'description': 'Certificate of Confidentiality Application', 'required': False,
'study_id': 1, 'code': 'AD_CoCApp', 'display_name': 'Ancillary Document / CoC Application',
'count': 0, 'files': []},
'UVACompl_PRCAppr': {'category1': 'UVA Compliance', 'category2': 'PRC Approval', 'category3': '',
'Who Uploads?': 'CRC', 'id': '6', 'description': "Cancer Center's PRC Approval Form",
'required': True, 'study_id': 1, 'code': 'UVACompl_PRCAppr',
'display_name': 'UVA Compliance / PRC Approval', 'count': 1, 'files': [
{'file_id': 10,
'task_id': 'fakingthisout',
'workflow_id': 2,
'workflow_spec_id': 'docx'}],
'status': 'complete'}
},
"details":
{},
"approvals": {
"study_id": 12,
"workflow_id": 321,
"display_name": "IRB API Details",
"name": "irb_api_details",
"status": WorkflowStatus.not_started.value,
"workflow_spec_id": "irb_api_details",
},
'protocol': {
id: 0,
}
}
}
def example_to_string(self, key):
return json.dumps(self.example_data['StudyInfo'][key], indent=2, separators=(',', ': '))
Standardizing the script tasks that can be executed on the server, adding tons of error messages for when things go wrong. All scripts must exist in side of the crc/scripts directory. Adding a new script that script tasks can use to add in data about the study. Moving all the test workflow specifications out of the main load. fixing a pile of tests so they can find workflow specs that are now moved into the test directory.
2020-03-03 18:50:22 +00:00
def get_description(self):
Adding a new reference file that provides greater details about the investigators related to a study. Improving the study_info script documentation to provide detailed examples of values returned based on arguments. Making the tests a little more targetted and less subject to breaking through better mocks. Allow all tests to pass even when ther protocol builder mock isn't running locally. Removing the duplication of reference files in tests and static, as this seems silly to me at the moment.
2020-05-07 17:57:24 +00:00
return """
StudyInfo [TYPE], where TYPE is one of 'info', 'investigators', 'details', 'approvals',
'documents' or 'protocol'.
Adds details about the current study to the Task Data. The type of information required should be
provided as an argument. The following arguments are available:
### Info ###
Returns the basic information such as the id and title
```
{info_example}
```
### Investigators ###
Returns detailed information about related personnel.
The order returned is guaranteed to match the order provided in the investigators.xslx reference file.
* Modifying the StudyInfo script to return both "investigators" and "roles", the investigators argument will return only the current active investigators according to the protocol builder. The "roles" argument returns all possible roles - it is what "investigators" use to be. * The Task.title returned to the front end will now attempt to process the "display_name" property for dot-notation syntax, making it possible to use this for multi-instance tasks, but will work in all cases where we want he title to change based on values in the data model. * Fixing a bug the test_study_api where it wasn't updated when we made recent changes to the different states of a study. *
2020-07-06 16:09:21 +00:00
Detailed information is added in from LDAP about each personnel based on their user_id.
Adding a new reference file that provides greater details about the investigators related to a study. Improving the study_info script documentation to provide detailed examples of values returned based on arguments. Making the tests a little more targetted and less subject to breaking through better mocks. Allow all tests to pass even when ther protocol builder mock isn't running locally. Removing the duplication of reference files in tests and static, as this seems silly to me at the moment.
2020-05-07 17:57:24 +00:00
```
{investigators_example}
```
* Modifying the StudyInfo script to return both "investigators" and "roles", the investigators argument will return only the current active investigators according to the protocol builder. The "roles" argument returns all possible roles - it is what "investigators" use to be. * The Task.title returned to the front end will now attempt to process the "display_name" property for dot-notation syntax, making it possible to use this for multi-instance tasks, but will work in all cases where we want he title to change based on values in the data model. * Fixing a bug the test_study_api where it wasn't updated when we made recent changes to the different states of a study. *
2020-07-06 16:09:21 +00:00
### Investigator Roles ###
Returns a list of all investigator roles, populating any roles with additional information available from
the Protocol Builder and LDAP. Its basically just like Investigators, but it includes all the roles, rather
that just those that were set in Protocol Builder.
```
{investigators_example}
```
Adding a new reference file that provides greater details about the investigators related to a study. Improving the study_info script documentation to provide detailed examples of values returned based on arguments. Making the tests a little more targetted and less subject to breaking through better mocks. Allow all tests to pass even when ther protocol builder mock isn't running locally. Removing the duplication of reference files in tests and static, as this seems silly to me at the moment.
2020-05-07 17:57:24 +00:00
### Details ###
Returns detailed information about variable keys read in from the Protocol Builder.
### Approvals ###
Returns data about the status of approvals related to a study.
```
{approvals_example}
```
### Documents ###
Returns a list of all documents that might be related to a study, reading all columns from the irb_documents.xsl
file. Including information about any files that were uploaded or generated that relate to a given document.
Please note this is just a few examples, ALL known document types are returned in an actual call.
```
{documents_example}
```
### Protocol ###
Returns information specific to the protocol.
""".format(info_example=self.example_to_string("info"),
investigators_example=self.example_to_string("investigators"),
approvals_example=self.example_to_string("approvals"),
documents_example=self.example_to_string("documents"),
)
Standardizing the script tasks that can be executed on the server, adding tons of error messages for when things go wrong. All scripts must exist in side of the crc/scripts directory. Adding a new script that script tasks can use to add in data about the study. Moving all the test workflow specifications out of the main load. fixing a pile of tests so they can find workflow specs that are now moved into the test directory.
2020-03-03 18:50:22 +00:00
As we now have an approval_service.py, I moved all the business logic into this service and out of the request_approval.py script. And moved all tests for these features into a test file for the service. Will make it easier to cross reference what is happening, as everything all happens in one file. As many of the scripts need to know the workflow, and it's down in a weird parameter, moved this so it is passed in each time.
2020-05-24 20:13:15 +00:00
def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
Vastly more informative ApiError model that provides details on the underlying task where the error occured. Added a validate_workflow_specification endpoint that allows you to check if the workflow will execute from beginning to end using random data. Minor fixes to existing bpmns to allow them to pass. All scripts must include a "do_task_validate_only" that restricts external calls and database modifications, but performs as much logic as possible.
2020-03-27 12:29:31 +00:00
"""For validation only, pretend no results come back from pb"""
All tests are passing - may need to refactor a bit, / remove comments
2020-07-28 15:02:49 +00:00
self.check_args(args,2)
Refactor the document details scripts. Now there is one script, it returns data in a consistent format, and has all the details required. The script is located in StudyInfo, with the argument documents. Make note that it returns a dictionary of ALL the documents, with a field to mark which ones are required according to the protocol builder. Others may become required if a workflow determines such, in which case the workflow will enforce this, and the document will have a count > 0, and additional details in a list of files within the document. I modified the XLS file to use lower case variable names, because it disturbed me, and we have to reference them frequently. Removed devious "as_object" variable on get_required_docs, so it behaves like the other methods all the time, and returns a dictionary. All the core business logic for finding the documents list now resides in the StudyService. Because this changes the endpoint for all existing document details, I've modified all the test and static bpmn files to use the new format. Shorting up the SponsorsList.xls file makes for slightly faster tests. seems senseless to load 5000 everytime we reset the data. Tried to test all of this carefully in the test_study_details_documents.py test.
2020-04-29 19:08:11 +00:00
# Assure the reference file exists (a bit hacky, but we want to raise this error early, and cleanly.)
missed a file in the last commit.
2020-05-11 21:42:24 +00:00
FileService.get_reference_file_data(FileService.DOCUMENT_LIST)
FileService.get_reference_file_data(FileService.INVESTIGATOR_LIST)
All tests are passing - may need to refactor a bit, / remove comments
2020-07-28 15:02:49 +00:00
data = Box({
Renamed the required_docs script to just "documents", and it returns all documented in the irb_documents look up table indexed on the "Code" - so details become available in the task data like "documents.IRB_INFOSEC_DOC.required". Updated the irb_documents with shorter code names, thanks to Alex. Re-worked the DMN models so they can properly read from this new datastructure.
2020-04-06 20:56:00 +00:00
"study":{
"info": {
"id": 12,
"title": "test",
"primary_investigator_id":21,
"user_uid": "dif84",
"sponsor": "sponsor",
"ind_number": "1234",
"inactive": False
},
Change the study_sponsors script so that we can actually call it : var = study_info('sponsors') to keep it more in line with other scripts that we have
2020-11-05 15:31:47 +00:00
"sponsors": [
{
"COMMONRULEAGENCY": None,
"SPONSOR_ID": 2453,
"SP_NAME": "Abbott Ltd",
"SP_TYPE": "Private",
"SP_TYPE_GROUP_NAME": None,
"SS_STUDY": 2
},
{
"COMMONRULEAGENCY": None,
"SPONSOR_ID": 2387,
"SP_NAME": "Abbott-Price",
"SP_TYPE": "Incoming Sub Award",
"SP_TYPE_GROUP_NAME": "Government",
"SS_STUDY": 2
},
{
"COMMONRULEAGENCY": None,
"SPONSOR_ID": 1996,
"SP_NAME": "Abernathy-Heidenreich",
"SP_TYPE": "Foundation/Not for Profit",
"SP_TYPE_GROUP_NAME": "Other External Funding",
"SS_STUDY": 2
}
],
Fleshes out fake PB response, so workflows that pull from PB actually trigger validation errors
2020-08-04 19:50:29 +00:00
"investigators": {
"PI": {
Makes Sonar happy.
2020-08-04 20:42:35 +00:00
"label": ProtocolBuilderInvestigatorType.PI.value,
Fleshes out fake PB response, so workflows that pull from PB actually trigger validation errors
2020-08-04 19:50:29 +00:00
"display": "Always",
"unique": "Yes",
"user_id": "dhf8r",
"title": "",
"display_name": "Daniel Harold Funk",
"sponsor_type": "Contractor",
"telephone_number": "0000000000",
"department": "",
"email_address": "dhf8r@virginia.edu",
"given_name": "Daniel",
"uid": "dhf8r",
"affiliation": "",
"date_cached": "2020-08-04T19:32:08.006128+00:00"
Renamed the required_docs script to just "documents", and it returns all documented in the irb_documents look up table indexed on the "Code" - so details become available in the task data like "documents.IRB_INFOSEC_DOC.required". Updated the irb_documents with shorter code names, thanks to Alex. Re-worked the DMN models so they can properly read from this new datastructure.
2020-04-06 20:56:00 +00:00
},
Fleshes out fake PB response, so workflows that pull from PB actually trigger validation errors
2020-08-04 19:50:29 +00:00
"SC_I": {
Makes Sonar happy.
2020-08-04 20:42:35 +00:00
"label": ProtocolBuilderInvestigatorType.SC_I.value,
Fleshes out fake PB response, so workflows that pull from PB actually trigger validation errors
2020-08-04 19:50:29 +00:00
"display": "Always",
"unique": "Yes",
"user_id": "ajl2j",
"title": "",
"display_name": "Aaron Louie",
"sponsor_type": "Contractor",
"telephone_number": "0000000000",
"department": "",
"email_address": "ajl2j@virginia.edu",
"given_name": "Aaron",
"uid": "ajl2j",
"affiliation": "sponsored",
"date_cached": "2020-08-04T19:32:10.699666+00:00"
},
"SC_II": {
Makes Sonar happy.
2020-08-04 20:42:35 +00:00
"label": ProtocolBuilderInvestigatorType.SC_II.value,
Fleshes out fake PB response, so workflows that pull from PB actually trigger validation errors
2020-08-04 19:50:29 +00:00
"display": "Optional",
"unique": "Yes",
"user_id": "cah3us",
"title": "",
"display_name": "Alex Herron",
"sponsor_type": "Contractor",
"telephone_number": "0000000000",
"department": "",
"email_address": "cah3us@virginia.edu",
"given_name": "Alex",
"uid": "cah3us",
"affiliation": "sponsored",
"date_cached": "2020-08-04T19:32:10.075852+00:00"
1. Updating Personnel BPMN diagram to debug some issues. 2. Disabling the token timeout for now, to see if this corrects the issues Alex is having with lost work. 3. Raising more thoughtful error messages for unknown lookup options. 4. Providing better validation of default values and injecting the correct value for defaults related to enum lists of all types. 5. Bumping Spiffworkflow library which contains some better error messages and checks.
2020-09-01 19:58:50 +00:00
},
Fleshes out fake PB response, so workflows that pull from PB actually trigger validation errors
2020-08-04 19:50:29 +00:00
},
"pi": {
"PI": {
Makes Sonar happy.
2020-08-04 20:42:35 +00:00
"label": ProtocolBuilderInvestigatorType.PI.value,
Fleshes out fake PB response, so workflows that pull from PB actually trigger validation errors
2020-08-04 19:50:29 +00:00
"display": "Always",
"unique": "Yes",
"user_id": "dhf8r",
"title": "",
"display_name": "Daniel Harold Funk",
"sponsor_type": "Contractor",
"telephone_number": "0000000000",
"department": "",
"email_address": "dhf8r@virginia.edu",
"given_name": "Daniel",
"uid": "dhf8r",
"affiliation": "",
"date_cached": "2020-08-04T19:32:08.006128+00:00"
}
},
* Modifying the StudyInfo script to return both "investigators" and "roles", the investigators argument will return only the current active investigators according to the protocol builder. The "roles" argument returns all possible roles - it is what "investigators" use to be. * The Task.title returned to the front end will now attempt to process the "display_name" property for dot-notation syntax, making it possible to use this for multi-instance tasks, but will work in all cases where we want he title to change based on values in the data model. * Fixing a bug the test_study_api where it wasn't updated when we made recent changes to the different states of a study. *
2020-07-06 16:09:21 +00:00
"roles":
{
"INVESTIGATORTYPE": "PI",
Makes Sonar happy.
2020-08-04 20:42:35 +00:00
"INVESTIGATORTYPEFULL": ProtocolBuilderInvestigatorType.PI.value,
* Modifying the StudyInfo script to return both "investigators" and "roles", the investigators argument will return only the current active investigators according to the protocol builder. The "roles" argument returns all possible roles - it is what "investigators" use to be. * The Task.title returned to the front end will now attempt to process the "display_name" property for dot-notation syntax, making it possible to use this for multi-instance tasks, but will work in all cases where we want he title to change based on values in the data model. * Fixing a bug the test_study_api where it wasn't updated when we made recent changes to the different states of a study. *
2020-07-06 16:09:21 +00:00
"NETBADGEID": "dhf8r"
},
Renamed the required_docs script to just "documents", and it returns all documented in the irb_documents look up table indexed on the "Code" - so details become available in the task data like "documents.IRB_INFOSEC_DOC.required". Updated the irb_documents with shorter code names, thanks to Alex. Re-worked the DMN models so they can properly read from this new datastructure.
2020-04-06 20:56:00 +00:00
"details":
Updated to use the latest script engine / evaluation engine that creates a single location where all values used in BPMN/DMN are processed. Right now this is a python based interpreter, but we will eventually base this on FEEL expressions. The validation process needs to take the api model into account so we catch errors with bad file names.
2020-05-11 21:04:05 +00:00
{
adding additional data to the study details returned during validation/shield testing.
2020-08-12 21:04:59 +00:00
"DSMB": None,
"DSMB_FREQUENCY": None,
"GCRC_NUMBER": None,
"IBC_NUMBER": None,
"IDE": None,
"IND_1": 1234,
"IND_2": None,
"IND_3": None,
"IRBREVIEWERADMIN": None,
"IS_ADULT_PARTICIPANT": None,
"IS_APPROVED_DEVICE": None,
"IS_AUX": None,
"IS_BIOMEDICAL": None,
"IS_CANCER_PATIENT": None,
"IS_CENTRAL_REG_DB": None,
"IS_CHART_REVIEW": None,
"IS_COMMITTEE_CONFLICT": None,
"IS_CONSENT_WAIVER": None,
"IS_DB": None,
"IS_ELDERLY_POP": None,
"IS_ENGAGED_RESEARCH": None,
"IS_FETUS_POP": None,
"IS_FINANCIAL_CONFLICT": None,
"IS_FOR_CANCER_CENTER": None,
"IS_FUNDING_SOURCE": None,
"IS_GCRC": None,
"IS_GENE_TRANSFER": None,
"IS_GRANT": None,
"IS_HGT": None,
"IS_IBC": None,
"IS_IDE": None,
"IS_IND": None,
"IS_MENTAL_IMPAIRMENT_POP": None,
"IS_MINOR": None,
"IS_MINOR_PARTICIPANT": None,
"IS_MULTI_SITE": None,
"IS_NOT_CONSENT_WAIVER": None,
"IS_NOT_PRC_WAIVER": None,
"IS_OTHER_VULNERABLE_POP": None,
"IS_OUTSIDE_CONTRACT": None,
"IS_PI_INITIATED": None,
"IS_PI_SCHOOL": None,
"IS_PRC": None,
"IS_PRC_DSMP": None,
"IS_PREGNANT_POP": None,
"IS_PRISONERS_POP": None,
"IS_QUALITATIVE": None,
"IS_RADIATION": None,
"IS_REVIEW_BY_CENTRAL_IRB": None,
"IS_SPONSOR": None,
"IS_SPONSOR_MONITORING": None,
"IS_SURROGATE_CONSENT": None,
"IS_TISSUE_BANKING": None,
"IS_UVA_DB": None,
"IS_UVA_IDE": None,
"IS_UVA_IND": None,
"IS_UVA_LOCATION": None,
"IS_UVA_PI_MULTI": None,
"MULTI_SITE_LOCATIONS": None,
"NON_UVA_LOCATION": None,
"OTHER_VULNERABLE_DESC": None,
"PRC_NUMBER": None,
"SPONSORS_PROTOCOL_REVISION_DATE": None,
"UPLOAD_COMPLETE": None
Updated to use the latest script engine / evaluation engine that creates a single location where all values used in BPMN/DMN are processed. Right now this is a python based interpreter, but we will eventually base this on FEEL expressions. The validation process needs to take the api model into account so we catch errors with bad file names.
2020-05-11 21:04:05 +00:00
},
Adds documents_status StudyInfo script. Adds Documents & Approvals workflow spec.
2020-04-23 23:25:01 +00:00
"approvals": {
Adds more useful metadata to approvals and documents status scripts. Fleshes out and pretties up Documents & Approvals screen
2020-04-24 03:32:20 +00:00
"study_id": 12,
"workflow_id": 321,
Adds documents_status StudyInfo script. Adds Documents & Approvals workflow spec.
2020-04-23 23:25:01 +00:00
"display_name": "IRB API Details",
"name": "irb_api_details",
"status": WorkflowStatus.not_started.value,
"workflow_spec_id": "irb_api_details",
},
Adds protocol script to study service
2020-04-29 14:21:24 +00:00
'protocol': {
Fixing a stupid mistake where I used an unquoted value in the mock data for validation, which created a dict that could not be serilized.
2020-07-16 17:28:00 +00:00
'id': 0,
Adds protocol script to study service
2020-04-29 14:21:24 +00:00
}
Renamed the required_docs script to just "documents", and it returns all documented in the irb_documents look up table indexed on the "Code" - so details become available in the task data like "documents.IRB_INFOSEC_DOC.required". Updated the irb_documents with shorter code names, thanks to Alex. Re-worked the DMN models so they can properly read from this new datastructure.
2020-04-06 20:56:00 +00:00
}
All tests are passing - may need to refactor a bit, / remove comments
2020-07-28 15:02:49 +00:00
})
if args[0]=='documents':
return StudyService().get_documents_status(study_id)
return data['study'][args[0]]
Change exception name
2020-07-27 16:18:28 +00:00
#self.add_data_to_task(task=task, data=data["study"])
#self.add_data_to_task(task, {"documents": StudyService().get_documents_status(study_id)})
Vastly more informative ApiError model that provides details on the underlying task where the error occured. Added a validate_workflow_specification endpoint that allows you to check if the workflow will execute from beginning to end using random data. Minor fixes to existing bpmns to allow them to pass. All scripts must include a "do_task_validate_only" that restricts external calls and database modifications, but performs as much logic as possible.
2020-03-27 12:29:31 +00:00
Replace all legacy style calls with new calls. Still having issues where we try to eval an empty definition, not quite sure why there is a difference from what we had before. I may need to revert some of it and determine what is going on.
2020-07-24 18:33:24 +00:00
def do_task(self, task, study_id, workflow_id, *args, **kwargs):
Test of adding in the ability of augmenting the workflow to include internal scripts like StudyInfo This is the first waypoint on a larger effort to make all of the 'special scripts' that currently require a shebang to be just another python function.
2020-07-24 16:08:46 +00:00
self.check_args(args,2)
prefix = None
if len(args) > 1:
prefix = args[1]
cmd = args[0]
All tests are passing - may need to refactor a bit, / remove comments
2020-07-28 15:02:49 +00:00
# study_info = {}
# if self.__class__.__name__ in task.data:
# study_info = task.data[self.__class__.__name__]
Test of adding in the ability of augmenting the workflow to include internal scripts like StudyInfo This is the first waypoint on a larger effort to make all of the 'special scripts' that currently require a shebang to be just another python function.
2020-07-24 16:08:46 +00:00
retval = None
if cmd == 'info':
study = session.query(StudyModel).filter_by(id=study_id).first()
schema = StudySchema()
retval = schema.dump(study)
if cmd == 'investigators':
retval = StudyService().get_investigators(study_id)
if cmd == 'roles':
retval = StudyService().get_investigators(study_id, all=True)
if cmd == 'details':
retval = self.pb.get_study_details(study_id)
Add 'sponsors' to study_info call
2020-11-04 19:34:10 +00:00
if cmd == 'sponsors':
retval = self.pb.get_sponsors(study_id)
Test of adding in the ability of augmenting the workflow to include internal scripts like StudyInfo This is the first waypoint on a larger effort to make all of the 'special scripts' that currently require a shebang to be just another python function.
2020-07-24 16:08:46 +00:00
if cmd == 'approvals':
retval = StudyService().get_approvals(study_id)
if cmd == 'documents':
retval = StudyService().get_documents_status(study_id)
if cmd == 'protocol':
retval = StudyService().get_protocol(study_id)
StudyInfo sometimes returns arrays of items, each item in the array should be coverted to a Box dictionary if possible.
2020-12-30 19:51:51 +00:00
if isinstance(retval, list):
retval = [Box(item) for item in retval]
Test of adding in the ability of augmenting the workflow to include internal scripts like StudyInfo This is the first waypoint on a larger effort to make all of the 'special scripts' that currently require a shebang to be just another python function.
2020-07-24 16:08:46 +00:00
if isinstance(retval,dict) and prefix is not None:
return Box({x:retval[x] for x in retval.keys() if x[:len(prefix)] == prefix})
StudyInfo sometimes returns arrays of items, each item in the array should be coverted to a Box dictionary if possible.
2020-12-30 19:51:51 +00:00
elif isinstance(retval,dict) :
Test of adding in the ability of augmenting the workflow to include internal scripts like StudyInfo This is the first waypoint on a larger effort to make all of the 'special scripts' that currently require a shebang to be just another python function.
2020-07-24 16:08:46 +00:00
return Box(retval)
else:
return retval
Adds documents_status StudyInfo script. Adds Documents & Approvals workflow spec.
2020-04-23 23:25:01 +00:00
Vastly more informative ApiError model that provides details on the underlying task where the error occured. Added a validate_workflow_specification endpoint that allows you to check if the workflow will execute from beginning to end using random data. Minor fixes to existing bpmns to allow them to pass. All scripts must include a "do_task_validate_only" that restricts external calls and database modifications, but performs as much logic as possible.
2020-03-27 12:29:31 +00:00
Test of adding in the ability of augmenting the workflow to include internal scripts like StudyInfo This is the first waypoint on a larger effort to make all of the 'special scripts' that currently require a shebang to be just another python function.
2020-07-24 16:08:46 +00:00
def check_args(self, args, maxlen=1):
if len(args) < 1 or len(args) > maxlen or (args[0] not in StudyInfo.type_options):
Vastly more informative ApiError model that provides details on the underlying task where the error occured. Added a validate_workflow_specification endpoint that allows you to check if the workflow will execute from beginning to end using random data. Minor fixes to existing bpmns to allow them to pass. All scripts must include a "do_task_validate_only" that restricts external calls and database modifications, but performs as much logic as possible.
2020-03-27 12:29:31 +00:00
raise ApiError(code="missing_argument",
message="The StudyInfo script requires a single argument which must be "
"one of %s" % ",".join(StudyInfo.type_options))
Updating libraries, modifying study_info script to save data in a consistent way, waiting on more fixes in spiffworkflow before continuing.
2020-04-13 20:23:31 +00:00