Merge remote-tracking branch 'origin/dev' into token_reset_message

This commit is contained in:
mike cullerton 2020-11-16 14:48:04 -05:00
commit 781f62df64
11 changed files with 428 additions and 397 deletions

664
Pipfile.lock generated
View File

@ -25,10 +25,11 @@
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"sha256:ed53209b5f0f383acb49a927179fa51a6e2259878e164273ebc6815f3a752465",
"sha256:f605f348f4e6a2ba00acb3399c71d213b92f27f2383fc4abebf7a37368c12142",
"sha256:fcdb3755a7c355bc29df1b5e6fb8226d5c8b90551d202d69d0076a8a5649d68b"
],
"version": "==1.3.19"
"version": "==1.3.20"
},
"swagger-ui-bundle": {
"hashes": [
@ -849,10 +892,10 @@
},
"urllib3": {
"hashes": [
"sha256:91056c15fa70756691db97756772bb1eb9678fa585d9184f24534b100dc60f4a",
"sha256:e7983572181f5e1522d9c98453462384ee92a0be7fac5f1413a1e35c56cc0461"
"sha256:8d7eaa5a82a1cac232164990f04874c594c9453ec55eef02eab885aa02fc17a2",
"sha256:f5321fbe4bf3fefa0efd0bfe7fb14e90909eb62a48ccda331726b4319897dd5e"
],
"version": "==1.25.10"
"version": "==1.25.11"
},
"waitress": {
"hashes": [
@ -907,74 +950,67 @@
},
"xlsxwriter": {
"hashes": [
"sha256:830cad0a88f0f95e5a8945ee082182aa68ab89e7d9725d0c32c196207634244b",
"sha256:88ab71d464e8f6c3923335cc92d6035260aa9e7c8b27fcbb3a5bc07e2c671d22"
"sha256:9b1ade2d1ba5d9b40a6d1de1d55ded4394ab8002718092ae80a08532c2add2e6",
"sha256:b807c2d3e379bf6a925f472955beef3e07495c1bac708640696876e68675b49b"
],
"index": "pypi",
"version": "==1.3.3"
"version": "==1.3.7"
}
},
"develop": {
"attrs": {
"hashes": [
"sha256:0ef97238856430dcf9228e07f316aefc17e8939fc8507e18c6501b761ef1a42a",
"sha256:2867b7b9f8326499ab5b0e2d12801fa5c98842d2cbd22b35112ae04bf85b4dff"
"sha256:31b2eced602aa8423c2aea9c76a724617ed67cf9513173fd3a4f03e3a929c7e6",
"sha256:832aa3cde19744e49938b91fea06d69ecb9e649c93ba974535d08ad92164f700"
],
"version": "==20.1.0"
"version": "==20.3.0"
},
"coverage": {
"hashes": [
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"sha256:78e93cc3571fd928a39c0b26767c986188a4118edc67bc0695bc7a284da22e82",
"sha256:7f43286f13d91a34fadf61ae252a51a130223c52bfefb50310d5b2deb062cf0f",
"sha256:86e9f8cd4b0cdd57b4ae71a9c186717daa4c5a99f3238a8723f416256e0b064d",
"sha256:8f264ba2701b8c9f815b272ad568d555ef98dfe1576802ab3149c3629a9f2221",
"sha256:9342dd70a1e151684727c9c91ea003b2fb33523bf19385d4554f7897ca0141d4",
"sha256:9361de40701666b034c59ad9e317bae95c973b9ff92513dd0eced11c6adf2e21",
"sha256:9669179786254a2e7e57f0ecf224e978471491d660aaca833f845b72a2df3709",
"sha256:aac1ba0a253e17889550ddb1b60a2063f7474155465577caa2a3b131224cfd54",
"sha256:aef72eae10b5e3116bac6957de1df4d75909fc76d1499a53fb6387434b6bcd8d",
"sha256:bd3166bb3b111e76a4f8e2980fa1addf2920a4ca9b2b8ca36a3bc3dedc618270",
"sha256:c1b78fb9700fc961f53386ad2fd86d87091e06ede5d118b8a50dea285a071c24",
"sha256:c3888a051226e676e383de03bf49eb633cd39fc829516e5334e69b8d81aae751",
"sha256:c5f17ad25d2c1286436761b462e22b5020d83316f8e8fcb5deb2b3151f8f1d3a",
"sha256:c851b35fc078389bc16b915a0a7c1d5923e12e2c5aeec58c52f4aa8085ac8237",
"sha256:cb7df71de0af56000115eafd000b867d1261f786b5eebd88a0ca6360cccfaca7",
"sha256:cedb2f9e1f990918ea061f28a0f0077a07702e3819602d3507e2ff98c8d20636",
"sha256:e8caf961e1b1a945db76f1b5fa9c91498d15f545ac0ababbe575cfab185d3bd8"
],
"index": "pypi",
"version": "==5.2.1"
"version": "==5.3"
},
"iniconfig": {
"hashes": [
"sha256:80cf40c597eb564e86346103f609d74efce0f6b4d4f30ec8ce9e2c26411ba437",
"sha256:e5f92f89355a67de0595932a6c6c02ab4afddc6fcdc0bfc5becd0d60884d3f69"
"sha256:011e24c64b7f47f6ebd835bb12a743f2fbe9a26d4cecaa7f53bc4f35ee9da8b3",
"sha256:bc3af051d7d14b2ee5ef9969666def0cd1a000e121eaea580d4a313df4b37f32"
],
"version": "==1.0.1"
},
"more-itertools": {
"hashes": [
"sha256:6f83822ae94818eae2612063a5101a7311e68ae8002005b5e05f03fd74a86a20",
"sha256:9b30f12df9393f0d28af9210ff8efe48d10c94f73e5daf886f10c4b0b0b4f03c"
],
"version": "==8.5.0"
"version": "==1.1.1"
},
"packaging": {
"hashes": [
@ -985,11 +1021,11 @@
},
"pbr": {
"hashes": [
"sha256:07f558fece33b05caf857474a366dfcc00562bca13dd8b47b2b3e22d9f9bf55c",
"sha256:579170e23f8e0c2f24b0de612f71f648eccb79fb1322c814ae6b3c07b5ba23e8"
"sha256:5fad80b613c402d5b7df7bd84812548b2a61e9977387a80a5fc5c396492b13c9",
"sha256:b236cde0ac9a6aedd5e3c34517b423cd4fd97ef723849da6b0d2231142d89c00"
],
"index": "pypi",
"version": "==5.4.5"
"version": "==5.5.1"
},
"pluggy": {
"hashes": [
@ -1014,11 +1050,11 @@
},
"pytest": {
"hashes": [
"sha256:85228d75db9f45e06e57ef9bf4429267f81ac7c0d742cc9ed63d09886a9fe6f4",
"sha256:8b6007800c53fdacd5a5c192203f4e531eb2a1540ad9c752e052ec0f7143dbad"
"sha256:4288fed0d9153d9646bfcdf0c0428197dba1ecb27a33bb6e031d002fa88653fe",
"sha256:c0a7e94a8cdbc5422a51ccdad8e6f1024795939cc89159a0ae7f0b316ad3823e"
],
"index": "pypi",
"version": "==6.0.1"
"version": "==6.1.2"
},
"six": {
"hashes": [
@ -1029,10 +1065,10 @@
},
"toml": {
"hashes": [
"sha256:926b612be1e5ce0634a2ca03470f95169cf16f939018233a670519cb4ac58b0f",
"sha256:bda89d5935c2eac546d648028b9901107a595863cb36bae0c73ac804a9b4ce88"
"sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b",
"sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f"
],
"version": "==0.10.1"
"version": "==0.10.2"
}
}
}

View File

@ -42,7 +42,7 @@ PB_USER_STUDIES_URL = environ.get('PB_USER_STUDIES_URL', default=PB_BASE_URL + "
PB_INVESTIGATORS_URL = environ.get('PB_INVESTIGATORS_URL', default=PB_BASE_URL + "investigators?studyid=%i")
PB_REQUIRED_DOCS_URL = environ.get('PB_REQUIRED_DOCS_URL', default=PB_BASE_URL + "required_docs?studyid=%i")
PB_STUDY_DETAILS_URL = environ.get('PB_STUDY_DETAILS_URL', default=PB_BASE_URL + "study?studyid=%i")
PB_SPONSORS_URL = environ.get('PB_SPONSORS_URL', default=PB_BASE_URL + "sponsors?studyid=%i")
LDAP_URL = environ.get('LDAP_URL', default="ldap.virginia.edu").strip('/') # No trailing slash or http://
LDAP_TIMEOUT_SEC = int(environ.get('LDAP_TIMEOUT_SEC', default=1))

View File

@ -15,7 +15,7 @@ class StudyInfo(Script):
"""Please see the detailed description that is provided below. """
pb = ProtocolBuilderService()
type_options = ['info', 'investigators', 'roles', 'details', 'approvals', 'documents', 'protocol']
type_options = ['info', 'investigators', 'roles', 'details', 'approvals', 'documents', 'protocol','sponsors']
# This is used for test/workflow validation, as well as documentation.
example_data = {
@ -29,6 +29,33 @@ class StudyInfo(Script):
"ind_number": "1234",
"inactive": False
},
"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
}
],
"investigators": {
'PI': {
'label': ProtocolBuilderInvestigatorType.PI.value,
@ -165,6 +192,33 @@ Returns information specific to the protocol.
"ind_number": "1234",
"inactive": False
},
"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
}
],
"investigators": {
"PI": {
"label": ProtocolBuilderInvestigatorType.PI.value,
@ -345,6 +399,8 @@ Returns information specific to the protocol.
retval = StudyService().get_investigators(study_id, all=True)
if cmd == 'details':
retval = self.pb.get_study_details(study_id)
if cmd == 'sponsors':
retval = self.pb.get_sponsors(study_id)
if cmd == 'approvals':
retval = StudyService().get_approvals(study_id)
if cmd == 'documents':

View File

@ -1,70 +0,0 @@
import json
from crc.api.common import ApiError
from crc.scripts.script import Script
from crc.services.protocol_builder import ProtocolBuilderService
class StudySponsors(Script):
"""Please see the detailed description that is provided below. """
pb = ProtocolBuilderService()
# This is used for test/workflow validation, as well as documentation.
example_data = [
{
"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
}
]
def example_to_string(self, key):
return json.dumps(self.example_data['StudyInfo'][key], indent=2, separators=(',', ': '))
def get_description(self):
return ""
# return """
# Returns a list of sponsors related to a study in the following format:
# {{example}}
#z """.format(example=json.dumps(self.example_data, index=2, separators=(',', ': ')))
def check_args(self, args):
if len(args) > 0:
raise ApiError(code="invalid_argument",
message="The Sponsor script does not take any arguments. "
"It returns the list of sponsors for the current study only. ")
def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
"""For validation only, pretend no results come back from pb"""
self.check_args(args)
return self.example_data
def do_task(self, task, study_id, workflow_id, *args, **kwargs):
self.check_args(args)
retval = ProtocolBuilderService.get_sponsors(study_id)
# Check on returning box, as in return Box(retval) - may not work with list.
return retval

View File

@ -227,7 +227,7 @@ class FileService(object):
def get_spec_data_files(workflow_spec_id, workflow_id=None, name=None):
"""Returns all the FileDataModels related to a workflow specification.
If a workflow is specified, returns the version of the spec relatted
to that workflow, otherwise, returns the lastes files."""
to that workflow, otherwise, returns the lastest files."""
if workflow_id:
query = session.query(FileDataModel) \
.join(WorkflowSpecDependencyFile) \

View File

@ -13,7 +13,7 @@ class ProtocolBuilderService(object):
INVESTIGATOR_URL = app.config['PB_INVESTIGATORS_URL']
REQUIRED_DOCS_URL = app.config['PB_REQUIRED_DOCS_URL']
STUDY_DETAILS_URL = app.config['PB_STUDY_DETAILS_URL']
SPONSORS_URL = app.config['PB_STUDY_DETAILS_URL']
SPONSORS_URL = app.config['PB_SPONSORS_URL']
@staticmethod
def is_enabled():

View File

@ -134,17 +134,19 @@ class WorkflowProcessor(object):
which should work in casees where a soft reset fails.
If neither flag is set, it will use the same version of the specification that was used to originally
create the workflow model. """
self.workflow_model = workflow_model
if soft_reset or len(workflow_model.dependencies) == 0: # Depenencies of 0 means the workflow was never started.
self.spec_data_files = FileService.get_spec_data_files(
workflow_spec_id=workflow_model.workflow_spec_id)
spec = self.get_spec(self.spec_data_files, workflow_model.workflow_spec_id)
else:
self.spec_data_files = FileService.get_spec_data_files(
workflow_spec_id=workflow_model.workflow_spec_id,
workflow_id=workflow_model.id)
spec = None
spec = self.get_spec(self.spec_data_files, workflow_model.workflow_spec_id)
self.workflow_spec_id = workflow_model.workflow_spec_id
try:
self.bpmn_workflow = self.__get_bpmn_workflow(workflow_model, spec, validate_only)
@ -159,7 +161,8 @@ class WorkflowProcessor(object):
# database model to which it is associated, and scripts running within the model
# can then load data as needed.
self.bpmn_workflow.data[WorkflowProcessor.WORKFLOW_ID_KEY] = workflow_model.id
workflow_model.bpmn_workflow_json = WorkflowProcessor._serializer.serialize_workflow(self.bpmn_workflow)
workflow_model.bpmn_workflow_json = WorkflowProcessor._serializer.serialize_workflow(
self.bpmn_workflow,include_spec=True)
self.save()
except MissingSpecError as ke:
@ -184,7 +187,8 @@ class WorkflowProcessor(object):
def __get_bpmn_workflow(self, workflow_model: WorkflowModel, spec: WorkflowSpec, validate_only=False):
if workflow_model.bpmn_workflow_json:
bpmn_workflow = self._serializer.deserialize_workflow(workflow_model.bpmn_workflow_json, workflow_spec=spec)
bpmn_workflow = self._serializer.deserialize_workflow(workflow_model.bpmn_workflow_json,
workflow_spec=spec)
else:
bpmn_workflow = BpmnWorkflow(spec, script_engine=self._script_engine)
bpmn_workflow.data[WorkflowProcessor.STUDY_ID_KEY] = workflow_model.study_id
@ -349,7 +353,7 @@ class WorkflowProcessor(object):
raise ApiError.from_task("task_error", str(we), we.task)
def serialize(self):
return self._serializer.serialize_workflow(self.bpmn_workflow)
return self._serializer.serialize_workflow(self.bpmn_workflow,include_spec=True)
def next_user_tasks(self):
return self.bpmn_workflow.get_ready_user_tasks()

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@ -141,7 +141,7 @@ class WorkflowService(object):
continue
# If there is a default value, set it.
if field.has_property('default_value') and field.default_value:
if hasattr(field,'default_value') and field.default_value:
form_data[field.id] = WorkflowService.get_default_value(field, task)
# If we are only populating required fields, and this isn't required. stop here.

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@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<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:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_0kmksnn" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.3">
<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:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_0kmksnn" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.0">
<bpmn:process id="Process_0exnnpv" isExecutable="true">
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>SequenceFlow_1nfe5m9</bpmn:outgoing>
@ -8,7 +8,8 @@
<bpmn:scriptTask id="Task_Script_Load_Study_Sponsors" name="Load Study Sponsors">
<bpmn:incoming>SequenceFlow_1nfe5m9</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_1bqiin0</bpmn:outgoing>
<bpmn:script>sponsors = study_sponsors()</bpmn:script>
<bpmn:script>sponsors = study_info('sponsors')
</bpmn:script>
</bpmn:scriptTask>
<bpmn:sequenceFlow id="SequenceFlow_1bqiin0" sourceRef="Task_Script_Load_Study_Sponsors" targetRef="EndEvent_171dj09" />
<bpmn:endEvent id="EndEvent_171dj09">

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@ -4,7 +4,6 @@ from tests.base_test import BaseTest
from crc import session, app
from crc.models.study import StudyModel
from crc.scripts.study_sponsors import StudySponsors
from crc.services.study_service import StudyService
from crc.services.workflow_processor import WorkflowProcessor
from crc.services.workflow_service import WorkflowService
@ -13,7 +12,12 @@ class TestSudySponsorsScript(BaseTest):
test_uid = "dhf8r"
test_study_id = 1
def test_study_sponsors_script_validation(self):
self.load_example_data() # study_info script complains if irb_documents.xls is not loaded
# during the validate phase I'm going to assume that we will never
# have a case where irb_documents.xls is not loaded ??
self.load_test_spec("study_sponsors")
WorkflowService.test_spec("study_sponsors") # This would raise errors if it didn't validate

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@ -188,7 +188,7 @@ class TestWorkflowProcessorMultiInstance(BaseTest):
task = next_user_tasks[1]
api_task = WorkflowService.spiff_task_to_api_task(task)
self.assertEqual("MultiInstanceTask", task.get_name())
self.assertEqual("MultiInstanceTask_0", task.get_name())
task.update_data({"investigator":{"email":"asdf32@virginia.edu"}})
processor.complete_task(task)
processor.do_engine_steps()