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cr-connect-workflow
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Loads of bug fixes. 

Modifed the request_approval to take a list of arguments, which works better for us... today.
UpdateStudy correctly handles validation.
WorkflowService correctly populates random values from lookup tables.
And several fixes down in Spiffworkflow, including a big bug where only the last item in a decision table made it through.
This commit is contained in:
Dan Funk 2020-05-26 20:06:50 -04:00
parent e9645fa3fd
commit ccbf374b40
5 changed files with 70 additions and 37 deletions
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14
Pipfile.lock generated
View File

@ -296,10 +296,10 @@
},
"flask-sqlalchemy": {
"hashes": [
"sha256:0078d8663330dc05a74bc72b3b6ddc441b9a744e2f56fe60af1a5bfc81334327",
"sha256:6974785d913666587949f7c2946f7001e4fa2cb2d19f4e69ead02e4b8f50b33d"
"sha256:0b656fbf87c5f24109d859bafa791d29751fabbda2302b606881ae5485b557a5",
"sha256:fcfe6df52cd2ed8a63008ca36b86a51fa7a4b70cef1c39e5625f722fca32308e"
],
"version": "==2.4.1"
"version": "==2.4.3"
},
"future": {
"hashes": [
@ -727,11 +727,11 @@
},
"sphinx": {
"hashes": [
"sha256:62edfd92d955b868d6c124c0942eba966d54b5f3dcb4ded39e65f74abac3f572",
"sha256:f5505d74cf9592f3b997380f9bdb2d2d0320ed74dd69691e3ee0644b956b8d83"
"sha256:779a519adbd3a70fc7c468af08c5e74829868b0a5b34587b33340e010291856c",
"sha256:ea64df287958ee5aac46be7ac2b7277305b0381d213728c3a49d8bb9b8415807"
],
"index": "pypi",
"version": "==3.0.3"
"version": "==3.0.4"
},
"sphinxcontrib-applehelp": {
"hashes": [
@ -778,7 +778,7 @@
"spiffworkflow": {
"editable": true,
"git": "https://github.com/sartography/SpiffWorkflow.git",
"ref": "cb098ee6d55b85bf7795997f4ad5f78c27d15381"
"ref": "c8d87826d496af825a184bdc3f0a751e603cfe44"
},
"sqlalchemy": {
"hashes": [

21
crc/scripts/request_approval.py
View File

@ -10,11 +10,11 @@ class RequestApproval(Script):
def get_description(self):
return """
Creates an approval request on this workflow, by the given approver_uid(s),"
Takes one argument, which should point to data located in current task.
Takes multiple arguments, which should point to data located in current task
or be quoted strings.
Example:
RequestApproval required_approvals.uids
RequestApproval approver1 "dhf8r"
"""
def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
@ -29,15 +29,16 @@ RequestApproval required_approvals.uids
ApprovalService.add_approval(study_id, workflow_id, id)
def get_uids(self, task, args):
if len(args) != 1:
if len(args) < 1:
raise ApiError(code="missing_argument",
message="The RequestApproval script requires 1 argument. The "
message="The RequestApproval script requires at least one argument. The "
"the name of the variable in the task data that contains user"
"ids to process.")
uids = task.workflow.script_engine.evaluate_expression(task, args[0])
if not isinstance(uids, str) and not isinstance(uids, list):
"id to process. Multiple arguments are accepted.")
uids = []
for arg in args:
id = task.workflow.script_engine.evaluate_expression(task, arg)
uids.append(id)
if not isinstance(id, str):
raise ApiError(code="invalid_argument",
message="The RequestApproval script requires 1 argument. The "
"the name of the variable in the task data that contains user"

13
crc/scripts/update_study.py
View File

@ -6,6 +6,12 @@ from crc.models.study import StudyModel
from crc.scripts.script import Script
class mock_study:
def __init__(self):
self.title = ""
self.principle_investigator_id = ""
class UpdateStudy(Script):
argument_error_message = "You must supply at least one argument to the " \
@ -21,11 +27,15 @@ Example:
UpdateStudy title:PIComputingID.label pi:PIComputingID.value
"""
def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
self.do_task(task, study_id, workflow_id, *args, **kwargs)
study = mock_study
self.__update_study(task, study, *args)
def do_task(self, task, study_id, workflow_id, *args, **kwargs):
study = db.session.query(StudyModel).filter(StudyModel.id == study_id).first()
self.__update_study(task, study, *args)
db.session.add(study)
def __update_study(self, task, study, *args):
if len(args) < 1:
raise ApiError.from_task("missing_argument", self.argument_error_message,
task=task)
@ -46,4 +56,3 @@ UpdateStudy title:PIComputingID.label pi:PIComputingID.value
else:
raise ApiError.from_task("invalid_argument", self.argument_error_message,
task=task)
db.session.add(study)

39
crc/services/workflow_service.py
View File

@ -61,7 +61,6 @@ class WorkflowService(object):
raise ApiError.from_task_spec("workflow_execution_exception", str(we),
we.sender)
@staticmethod
def populate_form_with_random_data(task, task_api):
"""populates a task with random data - useful for testing a spec."""
@ -72,22 +71,42 @@ class WorkflowService(object):
for field in task_api.form.fields:
if field.type == "enum":
if len(field.options) > 0:
form_data[field.id] = random.choice(field.options)
random_choice = random.choice(field.options)
if isinstance(random_choice, dict):
form_data[field.id] = random.choice(field.options)['id']
else:
# fixme: why it is sometimes an EnumFormFieldOption, and other times not?
form_data[field.id] = random_choice.id ## Assume it is an EnumFormFieldOption
else:
raise ApiError.from_task("invalid_enum", "You specified an enumeration field (%s),"
" with no options" % field.id,
task)
if field.type == "autocomplete":
elif field.type == "autocomplete":
lookup_model = LookupService.get_lookup_table(task, field)
if not lookup_model:
raise ApiError.from_task("invalid_autocomplete", "The settings for this auto complete field "
"(%s) are incorrect: " % field.id)
data = db.session.query(LookupDataModel).filter(LookupDataModel.lookup_file_model == lookup_model).limit(10).all()
if field.has_property(Task.PROP_LDAP_LOOKUP):
form_data[field.id] = {
"label": "dhf8r",
"value": "Dan Funk",
"data": {
"uid": "dhf8r",
"display_name": "Dan Funk",
"given_name": "Dan",
"email_address": "dhf8r@virginia.edu",
"department": "Depertment of Psychocosmographictology",
"affiliation": "Rousabout",
"sponsor_type": "Staff"
}
}
elif lookup_model:
data = db.session.query(LookupDataModel).filter(
LookupDataModel.lookup_file_model == lookup_model).limit(10).all()
options = []
for d in data:
options.append({"id": d.value, "name": d.label})
form_data[field.id] = random.choice(options)
else:
raise ApiError.from_task("invalid_autocomplete", "The settings for this auto complete field "
"are incorrect: %s " % field.id, task)
elif field.type == "long":
form_data[field.id] = random.randint(1, 1000)
elif field.type == 'boolean':
@ -102,6 +121,10 @@ class WorkflowService(object):
task.data = {}
task.data.update(form_data)
def __get_options(self):
pass
@staticmethod
def _random_string(string_length=10):
"""Generate a random string of fixed length """

10
tests/test_request_approval_script.py
View File

@ -16,10 +16,10 @@ class TestRequestApprovalScript(BaseTest):
workflow = self.create_workflow('empty_workflow')
processor = WorkflowProcessor(workflow)
task = processor.next_task()
task.data = {"study": {"approvals": ['dhf8r', 'lb3dp']}}
task.data = {"study": {"approval1": "dhf8r", 'approval2':'lb3dp'}}
script = RequestApproval()
script.do_task(task, workflow.study_id, workflow.id, "study.approvals")
script.do_task(task, workflow.study_id, workflow.id, "study.approval1", "study.approval2")
self.assertEquals(2, db.session.query(ApprovalModel).count())
def test_do_task_with_incorrect_argument(self):
@ -29,7 +29,7 @@ class TestRequestApprovalScript(BaseTest):
workflow = self.create_workflow('empty_workflow')
processor = WorkflowProcessor(workflow)
task = processor.next_task()
task.data = {"approvals": {'dhf8r':"invalid", 'lb3dp':"invalid"}}
task.data = {"approvals": {'dhf8r':["invalid"], 'lb3dp':"invalid"}}
script = RequestApproval()
with self.assertRaises(ApiError):
script.do_task(task, workflow.study_id, workflow.id, "approvals")
@ -40,9 +40,9 @@ class TestRequestApprovalScript(BaseTest):
workflow = self.create_workflow('empty_workflow')
processor = WorkflowProcessor(workflow)
task = processor.next_task()
task.data = {"approvals": ['dhf8r', 'lb3dp']}
task.data = {"study": {"approval1": "dhf8r", 'approval2':'lb3dp'}}
script = RequestApproval()
script.do_task_validate_only(task, workflow.study_id, workflow.id, "approvals")
script.do_task_validate_only(task, workflow.study_id, workflow.id, "study.approval1")
self.assertEquals(0, db.session.query(ApprovalModel).count())