428 lines
17 KiB
Python
428 lines
17 KiB
Python
import json
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from crc import session
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from crc.api.common import ApiError
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from crc.models.protocol_builder import ProtocolBuilderInvestigatorType
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from crc.models.study import StudyModel, StudySchema
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from crc.models.workflow import WorkflowStatus
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from crc.scripts.script import Script
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from crc.services.file_service import FileService
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from crc.services.protocol_builder import ProtocolBuilderService
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from crc.services.study_service import StudyService
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from box import Box
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class StudyInfo(Script):
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"""Please see the detailed description that is provided below. """
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pb = ProtocolBuilderService()
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type_options = ['info', 'investigators', 'roles', 'details', 'approvals', 'documents', 'protocol','sponsors']
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# This is used for test/workflow validation, as well as documentation.
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example_data = {
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"StudyInfo": {
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"info": {
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"id": 12,
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"title": "test",
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"primary_investigator_id": 21,
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"user_uid": "dif84",
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"sponsor": "sponsor",
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"ind_number": "1234",
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"inactive": False
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},
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"sponsors": [
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{
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"COMMONRULEAGENCY": None,
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"SPONSOR_ID": 2453,
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"SP_NAME": "Abbott Ltd",
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"SP_TYPE": "Private",
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"SP_TYPE_GROUP_NAME": None,
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"SS_STUDY": 2
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},
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{
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"COMMONRULEAGENCY": None,
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"SPONSOR_ID": 2387,
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"SP_NAME": "Abbott-Price",
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"SP_TYPE": "Incoming Sub Award",
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"SP_TYPE_GROUP_NAME": "Government",
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"SS_STUDY": 2
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},
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{
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"COMMONRULEAGENCY": None,
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"SPONSOR_ID": 1996,
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"SP_NAME": "Abernathy-Heidenreich",
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"SP_TYPE": "Foundation/Not for Profit",
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"SP_TYPE_GROUP_NAME": "Other External Funding",
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"SS_STUDY": 2
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}
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],
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"investigators": {
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'PI': {
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'label': ProtocolBuilderInvestigatorType.PI.value,
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'display': 'Always',
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'unique': 'Yes',
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'user_id': 'dhf8r',
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'display_name': 'Dan Funk',
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'given_name': 'Dan',
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'email': 'dhf8r@virginia.edu',
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'telephone_number': '+1 (434) 924-1723',
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'title': "E42:He's a hoopy frood",
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'department': 'E0:EN-Eng Study of Parallel Universes',
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'affiliation': 'faculty',
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'sponsor_type': 'Staff'},
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'SC_I': {
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'label': 'Study Coordinator I',
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'display': 'Always',
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'unique': 'Yes',
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'user_id': None},
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'DC': {
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'label': 'Department Contact',
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'display': 'Optional',
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'unique': 'Yes',
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'user_id': 'asd3v',
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'error': 'Unable to locate a user with id asd3v in LDAP'}
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},
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"documents": {
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'AD_CoCApp': {'category1': 'Ancillary Document', 'category2': 'CoC Application', 'category3': '',
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'Who Uploads?': 'CRC', 'id': '12',
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'description': 'Certificate of Confidentiality Application', 'required': False,
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'study_id': 1, 'code': 'AD_CoCApp', 'display_name': 'Ancillary Document / CoC Application',
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'count': 0, 'files': []},
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'UVACompl_PRCAppr': {'category1': 'UVA Compliance', 'category2': 'PRC Approval', 'category3': '',
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'Who Uploads?': 'CRC', 'id': '6', 'description': "Cancer Center's PRC Approval Form",
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'required': True, 'study_id': 1, 'code': 'UVACompl_PRCAppr',
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'display_name': 'UVA Compliance / PRC Approval', 'count': 1, 'files': [
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{'file_id': 10,
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'task_id': 'fakingthisout',
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'workflow_id': 2,
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'workflow_spec_id': 'docx'}],
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'status': 'complete'}
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},
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"details":
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{},
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"approvals": {
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"study_id": 12,
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"workflow_id": 321,
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"display_name": "IRB API Details",
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"name": "irb_api_details",
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"status": WorkflowStatus.not_started.value,
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"workflow_spec_id": "irb_api_details",
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},
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'protocol': {
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id: 0,
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}
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}
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}
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def example_to_string(self, key):
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return json.dumps(self.example_data['StudyInfo'][key], indent=2, separators=(',', ': '))
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def get_description(self):
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return """
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StudyInfo [TYPE], where TYPE is one of 'info', 'investigators', 'details', 'approvals',
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'documents' or 'protocol'.
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Adds details about the current study to the Task Data. The type of information required should be
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provided as an argument. The following arguments are available:
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### Info ###
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Returns the basic information such as the id and title
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```
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{info_example}
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```
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### Investigators ###
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Returns detailed information about related personnel.
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The order returned is guaranteed to match the order provided in the investigators.xslx reference file.
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Detailed information is added in from LDAP about each personnel based on their user_id.
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```
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{investigators_example}
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```
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### Investigator Roles ###
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Returns a list of all investigator roles, populating any roles with additional information available from
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the Protocol Builder and LDAP. Its basically just like Investigators, but it includes all the roles, rather
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that just those that were set in Protocol Builder.
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```
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{investigators_example}
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```
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### Details ###
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Returns detailed information about variable keys read in from the Protocol Builder.
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### Approvals ###
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Returns data about the status of approvals related to a study.
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```
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{approvals_example}
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```
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### Documents ###
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Returns a list of all documents that might be related to a study, reading all columns from the irb_documents.xsl
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file. Including information about any files that were uploaded or generated that relate to a given document.
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Please note this is just a few examples, ALL known document types are returned in an actual call.
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```
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{documents_example}
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```
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### Protocol ###
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Returns information specific to the protocol.
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""".format(info_example=self.example_to_string("info"),
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investigators_example=self.example_to_string("investigators"),
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approvals_example=self.example_to_string("approvals"),
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documents_example=self.example_to_string("documents"),
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)
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def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
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"""For validation only, pretend no results come back from pb"""
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self.check_args(args,2)
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# Assure the reference file exists (a bit hacky, but we want to raise this error early, and cleanly.)
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FileService.get_reference_file_data(FileService.DOCUMENT_LIST)
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FileService.get_reference_file_data(FileService.INVESTIGATOR_LIST)
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data = Box({
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"study":{
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"info": {
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"id": 12,
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"title": "test",
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"primary_investigator_id":21,
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"user_uid": "dif84",
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"sponsor": "sponsor",
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"ind_number": "1234",
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"inactive": False
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},
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"sponsors": [
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{
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"COMMONRULEAGENCY": None,
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"SPONSOR_ID": 2453,
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"SP_NAME": "Abbott Ltd",
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"SP_TYPE": "Private",
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"SP_TYPE_GROUP_NAME": None,
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"SS_STUDY": 2
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},
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{
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"COMMONRULEAGENCY": None,
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"SPONSOR_ID": 2387,
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"SP_NAME": "Abbott-Price",
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"SP_TYPE": "Incoming Sub Award",
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"SP_TYPE_GROUP_NAME": "Government",
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"SS_STUDY": 2
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},
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{
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"COMMONRULEAGENCY": None,
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"SPONSOR_ID": 1996,
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"SP_NAME": "Abernathy-Heidenreich",
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"SP_TYPE": "Foundation/Not for Profit",
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"SP_TYPE_GROUP_NAME": "Other External Funding",
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"SS_STUDY": 2
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}
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],
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"investigators": {
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"PI": {
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"label": ProtocolBuilderInvestigatorType.PI.value,
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"display": "Always",
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"unique": "Yes",
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"user_id": "dhf8r",
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"title": "",
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"display_name": "Daniel Harold Funk",
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"sponsor_type": "Contractor",
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"telephone_number": "0000000000",
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"department": "",
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"email_address": "dhf8r@virginia.edu",
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"given_name": "Daniel",
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"uid": "dhf8r",
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"affiliation": "",
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"date_cached": "2020-08-04T19:32:08.006128+00:00"
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},
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"SC_I": {
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"label": ProtocolBuilderInvestigatorType.SC_I.value,
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"display": "Always",
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"unique": "Yes",
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"user_id": "ajl2j",
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"title": "",
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"display_name": "Aaron Louie",
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"sponsor_type": "Contractor",
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"telephone_number": "0000000000",
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"department": "",
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"email_address": "ajl2j@virginia.edu",
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"given_name": "Aaron",
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"uid": "ajl2j",
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"affiliation": "sponsored",
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"date_cached": "2020-08-04T19:32:10.699666+00:00"
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},
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"SC_II": {
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"label": ProtocolBuilderInvestigatorType.SC_II.value,
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"display": "Optional",
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"unique": "Yes",
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"user_id": "cah3us",
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"title": "",
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"display_name": "Alex Herron",
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"sponsor_type": "Contractor",
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"telephone_number": "0000000000",
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"department": "",
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"email_address": "cah3us@virginia.edu",
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"given_name": "Alex",
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"uid": "cah3us",
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"affiliation": "sponsored",
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"date_cached": "2020-08-04T19:32:10.075852+00:00"
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},
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},
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"pi": {
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"PI": {
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"label": ProtocolBuilderInvestigatorType.PI.value,
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"display": "Always",
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"unique": "Yes",
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"user_id": "dhf8r",
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"title": "",
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"display_name": "Daniel Harold Funk",
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"sponsor_type": "Contractor",
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"telephone_number": "0000000000",
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"department": "",
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"email_address": "dhf8r@virginia.edu",
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"given_name": "Daniel",
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"uid": "dhf8r",
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"affiliation": "",
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"date_cached": "2020-08-04T19:32:08.006128+00:00"
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}
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},
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"roles":
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{
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"INVESTIGATORTYPE": "PI",
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"INVESTIGATORTYPEFULL": ProtocolBuilderInvestigatorType.PI.value,
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"NETBADGEID": "dhf8r"
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},
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"details":
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{
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"DSMB": None,
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"DSMB_FREQUENCY": None,
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"GCRC_NUMBER": None,
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"IBC_NUMBER": None,
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"IDE": None,
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"IND_1": 1234,
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"IND_2": None,
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"IND_3": None,
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"IRBREVIEWERADMIN": None,
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"IS_ADULT_PARTICIPANT": None,
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"IS_APPROVED_DEVICE": None,
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"IS_AUX": None,
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"IS_BIOMEDICAL": None,
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"IS_CANCER_PATIENT": None,
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"IS_CENTRAL_REG_DB": None,
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"IS_CHART_REVIEW": None,
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"IS_COMMITTEE_CONFLICT": None,
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"IS_CONSENT_WAIVER": None,
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"IS_DB": None,
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"IS_ELDERLY_POP": None,
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"IS_ENGAGED_RESEARCH": None,
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"IS_FETUS_POP": None,
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"IS_FINANCIAL_CONFLICT": None,
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"IS_FOR_CANCER_CENTER": None,
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"IS_FUNDING_SOURCE": None,
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"IS_GCRC": None,
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"IS_GENE_TRANSFER": None,
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"IS_GRANT": None,
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"IS_HGT": None,
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"IS_IBC": None,
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"IS_IDE": None,
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"IS_IND": 1,
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"IS_MENTAL_IMPAIRMENT_POP": None,
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"IS_MINOR": None,
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"IS_MINOR_PARTICIPANT": None,
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"IS_MULTI_SITE": None,
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"IS_NOT_CONSENT_WAIVER": None,
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"IS_NOT_PRC_WAIVER": None,
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"IS_OTHER_VULNERABLE_POP": None,
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"IS_OUTSIDE_CONTRACT": None,
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"IS_PI_INITIATED": None,
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"IS_PI_SCHOOL": None,
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"IS_PRC": None,
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"IS_PRC_DSMP": None,
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"IS_PREGNANT_POP": None,
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"IS_PRISONERS_POP": None,
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"IS_QUALITATIVE": None,
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"IS_RADIATION": None,
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"IS_REVIEW_BY_CENTRAL_IRB": None,
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"IS_SPONSOR": None,
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"IS_SPONSOR_MONITORING": None,
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"IS_SURROGATE_CONSENT": None,
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"IS_TISSUE_BANKING": None,
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"IS_UVA_DB": None,
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"IS_UVA_IDE": None,
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"IS_UVA_IND": None,
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"IS_UVA_LOCATION": None,
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"IS_UVA_PI_MULTI": None,
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"MULTI_SITE_LOCATIONS": None,
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"NON_UVA_LOCATION": None,
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"OTHER_VULNERABLE_DESC": None,
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"PRC_NUMBER": None,
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"SPONSORS_PROTOCOL_REVISION_DATE": None,
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"UPLOAD_COMPLETE": None
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},
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"approvals": {
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"study_id": 12,
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"workflow_id": 321,
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"display_name": "IRB API Details",
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"name": "irb_api_details",
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"status": WorkflowStatus.not_started.value,
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"workflow_spec_id": "irb_api_details",
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},
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'protocol': {
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'id': 0,
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}
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}
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})
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if args[0]=='documents':
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return StudyService().get_documents_status(study_id)
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return data['study'][args[0]]
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#self.add_data_to_task(task=task, data=data["study"])
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#self.add_data_to_task(task, {"documents": StudyService().get_documents_status(study_id)})
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def do_task(self, task, study_id, workflow_id, *args, **kwargs):
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self.check_args(args,2)
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prefix = None
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if len(args) > 1:
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prefix = args[1]
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cmd = args[0]
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# study_info = {}
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# if self.__class__.__name__ in task.data:
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# study_info = task.data[self.__class__.__name__]
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retval = None
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if cmd == 'info':
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study = session.query(StudyModel).filter_by(id=study_id).first()
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schema = StudySchema()
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retval = schema.dump(study)
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if cmd == 'investigators':
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retval = StudyService().get_investigators(study_id)
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if cmd == 'roles':
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retval = StudyService().get_investigators(study_id, all=True)
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if cmd == 'details':
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retval = self.pb.get_study_details(study_id)
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if cmd == 'sponsors':
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retval = self.pb.get_sponsors(study_id)
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if cmd == 'approvals':
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retval = StudyService().get_approvals(study_id)
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if cmd == 'documents':
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retval = StudyService().get_documents_status(study_id)
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if cmd == 'protocol':
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retval = StudyService().get_protocol(study_id)
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if isinstance(retval, list):
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retval = [Box(item) for item in retval]
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if isinstance(retval,dict) and prefix is not None:
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return Box({x:retval[x] for x in retval.keys() if x[:len(prefix)] == prefix})
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elif isinstance(retval,dict) :
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return Box(retval)
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else:
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return retval
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def check_args(self, args, maxlen=1):
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if len(args) < 1 or len(args) > maxlen or (args[0] not in StudyInfo.type_options):
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raise ApiError(code="missing_argument",
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message="The StudyInfo script requires a single argument which must be "
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"one of %s" % ",".join(StudyInfo.type_options))
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