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cr-connect-workflow
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Adds enrollment_date to study model

This commit is contained in:
Aaron Louie 2020-07-22 09:35:08 -04:00 committed by Carlos Lopez
parent 6379b26a71
commit 4adb6a1b44
4 changed files with 122 additions and 18 deletions
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7
crc/models/study.py
View File

@ -25,6 +25,7 @@ class StudyModel(db.Model):
investigator_uids = db.Column(db.ARRAY(db.String), nullable=True)
requirements = db.Column(db.ARRAY(db.Integer), nullable=True)
on_hold = db.Column(db.Boolean, default=False)
enrollment_date = db.Column(db.DateTime(timezone=True), nullable=True)
def update_from_protocol_builder(self, pbs: ProtocolBuilderStudy):
self.hsr_number = pbs.HSRNUMBER
@ -108,7 +109,7 @@ class Study(object):
id=None,
protocol_builder_status=None,
sponsor="", hsr_number="", ind_number="", categories=[],
files=[], approvals=[], **argsv):
files=[], approvals=[], enrollment_date=None, **argsv):
self.id = id
self.user_uid = user_uid
self.title = title
@ -122,6 +123,7 @@ class Study(object):
self.approvals = approvals
self.warnings = []
self.files = files
self.enrollment_date = enrollment_date
@classmethod
def from_model(cls, study_model: StudyModel):
@ -154,11 +156,12 @@ class StudySchema(ma.Schema):
ind_number = fields.String(allow_none=True)
files = fields.List(fields.Nested(FileSchema), dump_only=True)
approvals = fields.List(fields.Nested('ApprovalSchema'), dump_only=True)
enrollment_date = fields.Date(allow_none=True)
class Meta:
model = Study
additional = ["id", "title", "last_updated", "primary_investigator_id", "user_uid",
"sponsor", "ind_number", "approvals", "files"]
"sponsor", "ind_number", "approvals", "files", "enrollment_date"]
unknown = INCLUDE
@marshmallow.post_load

5
crc/services/workflow_service.py
View File

@ -154,10 +154,9 @@ class WorkflowService(object):
if len(field.options) > 0:
random_choice = random.choice(field.options)
if isinstance(random_choice, dict):
choice = random.choice(field.options)
return {
'value': choice['id'],
'label': choice['name']
'value': random_choice['id'],
'label': random_choice['name']
}
else:
# fixme: why it is sometimes an EnumFormFieldOption, and other times not?

100
crc/static/bpmn/notifications/notifications.bpmn
View File

@ -1,42 +1,116 @@
<?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:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_300b2c3" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.0.0-dev">
<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:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" id="Definitions_300b2c3" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="4.0.0">
<bpmn:collaboration id="Collaboration_163c7c8">
<bpmn:participant id="Participant_1mnua71" name="team" processRef="Process_cd666f3" />
</bpmn:collaboration>
<bpmn:process id="Process_cd666f3" isExecutable="true">
<bpmn:laneSet id="LaneSet_0ucxzw3">
<bpmn:lane id="Lane_16ml9fk">
<bpmn:flowNodeRef>StartEvent_1</bpmn:flowNodeRef>
<bpmn:flowNodeRef>Activity_1qpy9ra</bpmn:flowNodeRef>
<bpmn:flowNodeRef>Event_1m9fnmv</bpmn:flowNodeRef>
</bpmn:lane>
<bpmn:lane id="Lane_1jw70kl" name="supervisor">
<bpmn:flowNodeRef>Gateway_0ved0t9</bpmn:flowNodeRef>
<bpmn:flowNodeRef>Activity_107ojvq</bpmn:flowNodeRef>
</bpmn:lane>
</bpmn:laneSet>
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>Flow_0q51aiq</bpmn:outgoing>
</bpmn:startEvent>
<bpmn:sequenceFlow id="Flow_0q51aiq" sourceRef="StartEvent_1" targetRef="Activity_1qpy9ra" />
<bpmn:userTask id="Activity_1qpy9ra" name="Placeholder" camunda:formKey="Formkey_placeholder">
<bpmn:userTask id="Activity_1qpy9ra" name="Assign Approver" camunda:formKey="form_assign_approver">
<bpmn:extensionElements>
<camunda:formData>
<camunda:formField id="FormField_2t2220o" label="Will this be updated later" type="boolean" />
<camunda:formField id="supervisor" label="Approver UID" type="string" defaultValue="dhf8r" />
</camunda:formData>
</bpmn:extensionElements>
<bpmn:incoming>Flow_0q51aiq</bpmn:incoming>
<bpmn:outgoing>Flow_0ai4j1x</bpmn:outgoing>
<bpmn:incoming>Flow_11tnx3n</bpmn:incoming>
<bpmn:outgoing>Flow_0d2snmk</bpmn:outgoing>
</bpmn:userTask>
<bpmn:sequenceFlow id="Flow_0q51aiq" sourceRef="StartEvent_1" targetRef="Activity_1qpy9ra" />
<bpmn:sequenceFlow id="Flow_0d2snmk" sourceRef="Activity_1qpy9ra" targetRef="Activity_107ojvq" />
<bpmn:exclusiveGateway id="Gateway_0ved0t9" name="Approved?">
<bpmn:incoming>Flow_0apr3nj</bpmn:incoming>
<bpmn:outgoing>Flow_0mhtlkt</bpmn:outgoing>
<bpmn:outgoing>Flow_11tnx3n</bpmn:outgoing>
</bpmn:exclusiveGateway>
<bpmn:sequenceFlow id="Flow_0apr3nj" sourceRef="Activity_107ojvq" targetRef="Gateway_0ved0t9" />
<bpmn:sequenceFlow id="Flow_0mhtlkt" name="Yes" sourceRef="Gateway_0ved0t9" targetRef="Event_1m9fnmv">
<bpmn:conditionExpression xsi:type="bpmn:tFormalExpression">is_study_approved == True</bpmn:conditionExpression>
</bpmn:sequenceFlow>
<bpmn:endEvent id="Event_1m9fnmv">
<bpmn:incoming>Flow_0ai4j1x</bpmn:incoming>
<bpmn:incoming>Flow_0mhtlkt</bpmn:incoming>
</bpmn:endEvent>
<bpmn:sequenceFlow id="Flow_0ai4j1x" sourceRef="Activity_1qpy9ra" targetRef="Event_1m9fnmv" />
<bpmn:sequenceFlow id="Flow_11tnx3n" name="No" sourceRef="Gateway_0ved0t9" targetRef="Activity_1qpy9ra">
<bpmn:conditionExpression xsi:type="bpmn:tFormalExpression">is_study_approved == False</bpmn:conditionExpression>
</bpmn:sequenceFlow>
<bpmn:userTask id="Activity_107ojvq" name="Approve Study" camunda:formKey="form_approve_study">
<bpmn:extensionElements>
<camunda:formData>
<camunda:formField id="is_study_approved" label="Approve this study?" type="boolean" />
</camunda:formData>
</bpmn:extensionElements>
<bpmn:incoming>Flow_0d2snmk</bpmn:incoming>
<bpmn:outgoing>Flow_0apr3nj</bpmn:outgoing>
</bpmn:userTask>
</bpmn:process>
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_cd666f3">
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Collaboration_163c7c8">
<bpmndi:BPMNShape id="Participant_1mnua71_di" bpmnElement="Participant_1mnua71" isHorizontal="true">
<dc:Bounds x="129" y="117" width="600" height="250" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Lane_1jw70kl_di" bpmnElement="Lane_1jw70kl" isHorizontal="true">
<dc:Bounds x="159" y="242" width="570" height="125" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Lane_16ml9fk_di" bpmnElement="Lane_16ml9fk" isHorizontal="true">
<dc:Bounds x="159" y="117" width="570" height="125" />
</bpmndi:BPMNShape>
<bpmndi:BPMNEdge id="Flow_11tnx3n_di" bpmnElement="Flow_11tnx3n">
<di:waypoint x="460" y="275" />
<di:waypoint x="460" y="177" />
<di:waypoint x="370" y="177" />
<bpmndi:BPMNLabel>
<dc:Bounds x="468" y="223" width="15" height="14" />
</bpmndi:BPMNLabel>
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_0mhtlkt_di" bpmnElement="Flow_0mhtlkt">
<di:waypoint x="485" y="300" />
<di:waypoint x="660" y="300" />
<di:waypoint x="660" y="195" />
<bpmndi:BPMNLabel>
<dc:Bounds x="563" y="282" width="19" height="14" />
</bpmndi:BPMNLabel>
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_0apr3nj_di" bpmnElement="Flow_0apr3nj">
<di:waypoint x="370" y="300" />
<di:waypoint x="435" y="300" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_0d2snmk_di" bpmnElement="Flow_0d2snmk">
<di:waypoint x="320" y="217" />
<di:waypoint x="320" y="260" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_0q51aiq_di" bpmnElement="Flow_0q51aiq">
<di:waypoint x="215" y="177" />
<di:waypoint x="270" y="177" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_0ai4j1x_di" bpmnElement="Flow_0ai4j1x">
<di:waypoint x="370" y="177" />
<di:waypoint x="432" y="177" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
<dc:Bounds x="179" y="159" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_14cpuv6_di" bpmnElement="Activity_1qpy9ra">
<dc:Bounds x="270" y="137" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Gateway_0ved0t9_di" bpmnElement="Gateway_0ved0t9" isMarkerVisible="true">
<dc:Bounds x="435" y="275" width="50" height="50" />
<bpmndi:BPMNLabel>
<dc:Bounds x="435" y="332" width="54" height="14" />
</bpmndi:BPMNLabel>
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Event_1m9fnmv_di" bpmnElement="Event_1m9fnmv">
<dc:Bounds x="432" y="159" width="36" height="36" />
<dc:Bounds x="642" y="159" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_1ps6jft_di" bpmnElement="Activity_107ojvq">
<dc:Bounds x="270" y="260" width="100" height="80" />
</bpmndi:BPMNShape>
</bpmndi:BPMNPlane>
</bpmndi:BPMNDiagram>

28
migrations/versions/c4ddb69e7ef4_.py Normal file
View File

@ -0,0 +1,28 @@
"""empty message
Revision ID: c4ddb69e7ef4
Revises: ffef4661a37d
Create Date: 2020-07-22 09:04:09.769239
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = 'c4ddb69e7ef4'
down_revision = 'ffef4661a37d'
branch_labels = None
depends_on = None
def upgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.add_column('study', sa.Column('enrollment_date', sa.DateTime(timezone=True), nullable=True))
# ### end Alembic commands ###
def downgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.drop_column('study', 'enrollment_date')
# ### end Alembic commands ###