Merge branch 'dev' into 201-changes-to-in-progress
This commit is contained in:
Dan Funk
GitHub
commit
349c3d657a
20
README.md
20
README.md
|
|
@ -141,6 +141,26 @@ additional edits required.)
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## Documentation
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Additional Documentation is available on [ReadTheDocs](https://cr-connect-workflow.readthedocs.io/en/latest/#)
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## Manual Synch
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You can move all the BPMN diagrams from one system to another (upgrading and replacing as needed) This is how
|
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we will transfer files from staging to production.
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Eventually we will connect this into the front end code for the BPMN Editor, but for now, you can do so by:
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1. Run flask clear-db to clear out your local database if desried (this isn't reuired, but will give you a clean slate
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to get an exact replica of production/testing whatever)
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2. Log into the Swagger UI for the system you want to move all files to (this could be a local development machine)
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3. Set the API Token under authentication. This token must match what is on the testing server. This might
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match what is in the default config, at least, that will work for staging.
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4. Run the workflow_synch/pullall in swagger, using the url for the site you want to pull from:
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something like "https://testing.crconnect.uvadcos.io/api"
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5. Be patient. It may take a minute or more to pull everything down.
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### Additional Reading
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1. [BPMN](https://www.process.st/bpmn-tutorial/) Is the tool we are using to create diagrams
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|
|
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150
crc/api.yml
150
crc/api.yml
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@ -357,30 +357,6 @@ paths:
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application/json:
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schema:
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$ref: "#/components/schemas/Study"
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/study/{study_id}/approvals:
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parameters:
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- name: study_id
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in: path
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required: true
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description: The id of the study for which workflows should be returned.
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schema:
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type: integer
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format: int32
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get:
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operationId: crc.api.approval.get_approvals_for_study
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summary: Returns approvals for a single study
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tags:
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- Studies
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- Approvals
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responses:
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'200':
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description: An array of approvals
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content:
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application/json:
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schema:
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type: array
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items:
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$ref: "#/components/schemas/Approval"
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/workflow-specification:
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get:
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operationId: crc.api.workflow.all_specifications
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@ -1135,132 +1111,6 @@ paths:
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text/plain:
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schema:
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type: string
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/approval-counts:
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parameters:
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- name: as_user
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in: query
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required: false
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description: If provided, returns the approval counts for that user.
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schema:
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type: string
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get:
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operationId: crc.api.approval.get_approval_counts
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summary: Provides counts for approvals by status for the given user, or all users if no user is provided
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tags:
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- Approvals
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responses:
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'200':
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description: An dictionary of Approval Statuses and the counts for each
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content:
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application/json:
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schema:
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type: array
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items:
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$ref: "#/components/schemas/ApprovalCounts"
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/all_approvals:
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parameters:
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- name: status
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in: query
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required: false
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description: If set to true, returns all the approvals with any status. Defaults to false, leaving out canceled approvals.
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schema:
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type: boolean
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get:
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operationId: crc.api.approval.get_all_approvals
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summary: Provides a list of all workflows approvals
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tags:
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- Approvals
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responses:
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'200':
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description: An array of approvals
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content:
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application/json:
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schema:
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type: array
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items:
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$ref: "#/components/schemas/Approval"
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/approval:
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parameters:
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- name: status
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in: query
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required: false
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description: If provided, returns just approvals for the given status.
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schema:
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type: string
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- name: as_user
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in: query
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required: false
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description: If provided, returns the approval results as they would appear for that user.
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schema:
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type: string
|
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get:
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operationId: crc.api.approval.get_approvals
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summary: Provides a list of workflows approvals
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tags:
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- Approvals
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responses:
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'200':
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description: An array of approvals
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content:
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application/json:
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schema:
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type: array
|
||||
items:
|
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$ref: "#/components/schemas/Approval"
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/approval/{approval_id}:
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parameters:
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- name: approval_id
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in: path
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required: true
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description: The id of the approval in question.
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schema:
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type: integer
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format: int32
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put:
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operationId: crc.api.approval.update_approval
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summary: Updates an approval with the given parameters
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tags:
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- Approvals
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requestBody:
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content:
|
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application/json:
|
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schema:
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$ref: '#/components/schemas/Approval'
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responses:
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'200':
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description: Study updated successfully.
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content:
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application/json:
|
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schema:
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$ref: "#/components/schemas/Approval"
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/approval/csv:
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get:
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operationId: crc.api.approval.get_csv
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summary: Provides a list of all users for all approved studies
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tags:
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- Approvals
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responses:
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'200':
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||||
description: An array of approvals
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content:
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application/json:
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schema:
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type: object
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/health_attesting:
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get:
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operationId: crc.api.approval.get_health_attesting_csv
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summary: Returns a CSV file with health attesting records
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tags:
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- Approvals
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responses:
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'200':
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description: A CSV file
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content:
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||||
application/json:
|
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schema:
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type: array
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items:
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$ref: "#/components/schemas/Approval"
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/datastore:
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post:
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operationId: crc.api.data_store.add_datastore
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|
|
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@ -12,7 +12,6 @@ from jinja2 import Markup
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from crc import db, app
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from crc.api.user import verify_token, verify_token_admin
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from crc.models.approval import ApprovalModel
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from crc.models.file import FileModel, FileDataModel
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from crc.models.task_event import TaskEventModel
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from crc.models.study import StudyModel
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@ -83,7 +82,6 @@ class TaskEventView(AdminModelView):
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admin = Admin(app)
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admin.add_view(StudyView(StudyModel, db.session))
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admin.add_view(ApprovalView(ApprovalModel, db.session))
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admin.add_view(UserView(UserModel, db.session))
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admin.add_view(WorkflowView(WorkflowModel, db.session))
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admin.add_view(FileView(FileModel, db.session))
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|
|
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@ -1,137 +0,0 @@
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|||
import csv
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import io
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import json
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import pickle
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||||
from base64 import b64decode
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||||
from datetime import datetime
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||||
|
||||
from flask import g, make_response
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from crc import db, session
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from crc.api.common import ApiError
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from crc.models.approval import Approval, ApprovalModel, ApprovalSchema, ApprovalStatus
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from crc.models.workflow import WorkflowModel
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from crc.services.approval_service import ApprovalService
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from crc.services.ldap_service import LdapService
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|
||||
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# Returns counts of approvals in each status group assigned to the given user.
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# The goal is to return results as quickly as possible.
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def get_approval_counts(as_user=None):
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uid = as_user or g.user.uid
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db_user_approvals = db.session.query(ApprovalModel)\
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.filter_by(approver_uid=uid)\
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||||
.filter(ApprovalModel.status != ApprovalStatus.CANCELED.name)\
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.all()
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|
||||
study_ids = [a.study_id for a in db_user_approvals]
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||||
|
||||
db_other_approvals = db.session.query(ApprovalModel)\
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.filter(ApprovalModel.study_id.in_(study_ids))\
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.filter(ApprovalModel.approver_uid != uid)\
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.filter(ApprovalModel.status != ApprovalStatus.CANCELED.name)\
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.all()
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# Make a dict of the other approvals where the key is the study id and the value is the approval
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# TODO: This won't work if there are more than 2 approvals with the same study_id
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other_approvals = {}
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for approval in db_other_approvals:
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other_approvals[approval.study_id] = approval
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||||
|
||||
counts = {}
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||||
for name, value in ApprovalStatus.__members__.items():
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||||
counts[name] = 0
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||||
|
||||
for approval in db_user_approvals:
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# Check if another approval has the same study id
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||||
if approval.study_id in other_approvals:
|
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other_approval = other_approvals[approval.study_id]
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||||
# Other approval takes precedence over this one
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||||
if other_approval.id < approval.id:
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if other_approval.status == ApprovalStatus.PENDING.name:
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counts[ApprovalStatus.AWAITING.name] += 1
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elif other_approval.status == ApprovalStatus.DECLINED.name:
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counts[ApprovalStatus.DECLINED.name] += 1
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elif other_approval.status == ApprovalStatus.CANCELED.name:
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counts[ApprovalStatus.CANCELED.name] += 1
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||||
elif other_approval.status == ApprovalStatus.APPROVED.name:
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||||
counts[approval.status] += 1
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||||
else:
|
||||
counts[approval.status] += 1
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||||
else:
|
||||
counts[approval.status] += 1
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||||
|
||||
return counts
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||||
|
||||
|
||||
def get_all_approvals(status=None):
|
||||
approvals = ApprovalService.get_all_approvals(include_cancelled=status is True)
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||||
results = ApprovalSchema(many=True).dump(approvals)
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return results
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||||
|
||||
|
||||
def get_approvals(status=None, as_user=None):
|
||||
#status = ApprovalStatus.PENDING.value
|
||||
user = g.user.uid
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||||
if as_user:
|
||||
user = as_user
|
||||
approvals = ApprovalService.get_approvals_per_user(user, status,
|
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include_cancelled=False)
|
||||
results = ApprovalSchema(many=True).dump(approvals)
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return results
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||||
|
||||
|
||||
def get_approvals_for_study(study_id=None):
|
||||
db_approvals = ApprovalService.get_approvals_for_study(study_id)
|
||||
approvals = [Approval.from_model(approval_model) for approval_model in db_approvals]
|
||||
results = ApprovalSchema(many=True).dump(approvals)
|
||||
return results
|
||||
|
||||
|
||||
def get_health_attesting_csv():
|
||||
records = ApprovalService.get_health_attesting_records()
|
||||
si = io.StringIO()
|
||||
cw = csv.writer(si)
|
||||
cw.writerows(records)
|
||||
output = make_response(si.getvalue())
|
||||
output.headers["Content-Disposition"] = "attachment; filename=health_attesting.csv"
|
||||
output.headers["Content-type"] = "text/csv"
|
||||
return output
|
||||
|
||||
|
||||
# ----- Begin descent into madness ---- #
|
||||
def get_csv():
|
||||
"""A damn lie, it's a json file. A huge bit of a one-off for RRT, but 3 weeks of midnight work can convince a
|
||||
man to do just about anything"""
|
||||
content = ApprovalService.get_not_really_csv_content()
|
||||
|
||||
return content
|
||||
|
||||
# ----- come back to the world of the living ---- #
|
||||
|
||||
|
||||
def update_approval(approval_id, body):
|
||||
if approval_id is None:
|
||||
raise ApiError('unknown_approval', 'Please provide a valid Approval ID.')
|
||||
|
||||
approval_model = session.query(ApprovalModel).get(approval_id)
|
||||
if approval_model is None:
|
||||
raise ApiError('unknown_approval', 'The approval "' + str(approval_id) + '" is not recognized.')
|
||||
|
||||
if approval_model.approver_uid != g.user.uid:
|
||||
raise ApiError("not_your_approval", "You may not modify this approval. It belongs to another user.")
|
||||
|
||||
approval_model.status = body['status']
|
||||
approval_model.message = body['message']
|
||||
approval_model.date_approved = datetime.now()
|
||||
session.add(approval_model)
|
||||
session.commit()
|
||||
|
||||
# Called only to send emails
|
||||
approver = body['approver']['uid']
|
||||
ApprovalService.update_approval(approval_id, approver)
|
||||
|
||||
result = ApprovalSchema().dump(approval_model)
|
||||
return result
|
||||
|
|
@ -1,118 +0,0 @@
|
|||
import enum
|
||||
|
||||
import marshmallow
|
||||
from marshmallow import INCLUDE, fields
|
||||
from sqlalchemy import func
|
||||
|
||||
from crc import db, ma, app
|
||||
from crc.api.common import ApiError
|
||||
from crc.models.file import FileDataModel
|
||||
from crc.models.ldap import LdapSchema
|
||||
from crc.models.study import StudyModel
|
||||
from crc.models.workflow import WorkflowModel
|
||||
from crc.services.file_service import FileService
|
||||
from crc.services.ldap_service import LdapService
|
||||
|
||||
|
||||
class ApprovalStatus(enum.Enum):
|
||||
PENDING = "PENDING" # no one has done jack.
|
||||
APPROVED = "APPROVED" # approved by the reviewer
|
||||
DECLINED = "DECLINED" # rejected by the reviewer
|
||||
CANCELED = "CANCELED" # The document was replaced with a new version and this review is no longer needed.
|
||||
|
||||
# Used for overall status only, never set on a task.
|
||||
AWAITING = "AWAITING" # awaiting another approval
|
||||
|
||||
|
||||
class ApprovalFile(db.Model):
|
||||
file_data_id = db.Column(db.Integer, db.ForeignKey(FileDataModel.id), primary_key=True)
|
||||
approval_id = db.Column(db.Integer, db.ForeignKey("approval.id"), primary_key=True)
|
||||
|
||||
approval = db.relationship("ApprovalModel")
|
||||
file_data = db.relationship(FileDataModel)
|
||||
|
||||
|
||||
class ApprovalModel(db.Model):
|
||||
__tablename__ = 'approval'
|
||||
id = db.Column(db.Integer, primary_key=True)
|
||||
study_id = db.Column(db.Integer, db.ForeignKey(StudyModel.id), nullable=False)
|
||||
study = db.relationship(StudyModel)
|
||||
workflow_id = db.Column(db.Integer, db.ForeignKey(WorkflowModel.id), nullable=False)
|
||||
workflow = db.relationship(WorkflowModel)
|
||||
approver_uid = db.Column(db.String) # Not linked to user model, as they may not have logged in yet.
|
||||
status = db.Column(db.String)
|
||||
message = db.Column(db.String, default='')
|
||||
date_created = db.Column(db.DateTime(timezone=True), default=func.now())
|
||||
date_approved = db.Column(db.DateTime(timezone=True), default=None)
|
||||
version = db.Column(db.Integer) # Incremented integer, so 1,2,3 as requests are made.
|
||||
approval_files = db.relationship(ApprovalFile, back_populates="approval",
|
||||
cascade="all, delete, delete-orphan",
|
||||
order_by=ApprovalFile.file_data_id)
|
||||
|
||||
|
||||
class Approval(object):
|
||||
|
||||
def __init__(self, **kwargs):
|
||||
self.__dict__.update(kwargs)
|
||||
|
||||
@classmethod
|
||||
def from_model(cls, model: ApprovalModel):
|
||||
args = dict((k, v) for k, v in model.__dict__.items() if not k.startswith('_'))
|
||||
instance = cls(**args)
|
||||
instance.related_approvals = []
|
||||
instance.title = model.study.title if model.study else ''
|
||||
|
||||
try:
|
||||
instance.approver = LdapService.user_info(model.approver_uid)
|
||||
instance.primary_investigator = LdapService.user_info(model.study.primary_investigator_id)
|
||||
except ApiError as ae:
|
||||
app.logger.error(f'Ldap lookup failed for approval record {model.id}', exc_info=True)
|
||||
|
||||
doc_dictionary = FileService.get_doc_dictionary()
|
||||
instance.associated_files = []
|
||||
for approval_file in model.approval_files:
|
||||
try:
|
||||
# fixme: This is slow because we are doing a ton of queries to find the irb code.
|
||||
extra_info = doc_dictionary[approval_file.file_data.file_model.irb_doc_code]
|
||||
except:
|
||||
extra_info = None
|
||||
associated_file = {}
|
||||
associated_file['id'] = approval_file.file_data.file_model.id
|
||||
if extra_info:
|
||||
associated_file['name'] = '_'.join((extra_info['category1'],
|
||||
approval_file.file_data.file_model.name))
|
||||
associated_file['description'] = extra_info['description']
|
||||
else:
|
||||
associated_file['name'] = approval_file.file_data.file_model.name
|
||||
associated_file['description'] = 'No description available'
|
||||
associated_file['name'] = '(' + model.study.primary_investigator_id + ')' + associated_file['name']
|
||||
associated_file['content_type'] = approval_file.file_data.file_model.content_type
|
||||
instance.associated_files.append(associated_file)
|
||||
|
||||
return instance
|
||||
|
||||
def update_model(self, approval_model: ApprovalModel):
|
||||
approval_model.status = self.status
|
||||
approval_model.message = self.message
|
||||
|
||||
|
||||
class ApprovalSchema(ma.Schema):
|
||||
|
||||
approver = fields.Nested(LdapSchema, dump_only=True)
|
||||
primary_investigator = fields.Nested(LdapSchema, dump_only=True)
|
||||
related_approvals = fields.List(fields.Nested('ApprovalSchema', allow_none=True, dump_only=True))
|
||||
|
||||
class Meta:
|
||||
model = Approval
|
||||
fields = ["id", "study_id", "workflow_id", "version", "title",
|
||||
"status", "message", "approver", "primary_investigator",
|
||||
"associated_files", "date_created", "date_approved",
|
||||
"related_approvals"]
|
||||
unknown = INCLUDE
|
||||
|
||||
@marshmallow.post_load
|
||||
def make_approval(self, data, **kwargs):
|
||||
"""Loads the basic approval data for updates to the database"""
|
||||
return Approval(**data)
|
||||
|
||||
|
||||
|
|
@ -230,14 +230,13 @@ class StudySchema(ma.Schema):
|
|||
sponsor = fields.String(allow_none=True)
|
||||
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)
|
||||
events_history = fields.List(fields.Nested('StudyEventSchema'), dump_only=True)
|
||||
|
||||
class Meta:
|
||||
model = Study
|
||||
additional = ["id", "title", "last_updated", "primary_investigator_id", "user_uid",
|
||||
"sponsor", "ind_number", "approvals", "files", "enrollment_date",
|
||||
"sponsor", "ind_number", "files", "enrollment_date",
|
||||
"create_user_display", "last_activity_date","last_activity_user",
|
||||
"events_history"]
|
||||
unknown = INCLUDE
|
||||
|
|
|
|||
|
|
@ -1,51 +0,0 @@
|
|||
from crc.api.common import ApiError
|
||||
from crc.scripts.script import Script
|
||||
from crc.services.approval_service import ApprovalService
|
||||
|
||||
|
||||
class RequestApproval(Script):
|
||||
"""This still needs to be fully wired up as a Script task callable from the workflow
|
||||
But the basic logic is here just to get the tests passing and logic sound. """
|
||||
|
||||
def get_description(self):
|
||||
return """
|
||||
Creates an approval request on this workflow, by the given approver_uid(s),"
|
||||
Takes multiple arguments, which should point to data located in current task
|
||||
or be quoted strings. The order is important. Approvals will be processed
|
||||
in this order.
|
||||
|
||||
Example:
|
||||
RequestApproval approver1 "dhf8r"
|
||||
"""
|
||||
|
||||
def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
|
||||
self.get_uids(task, args)
|
||||
|
||||
def do_task(self, task, study_id, workflow_id, *args, **kwargs):
|
||||
uids = self.get_uids(task, args)
|
||||
if isinstance(uids, str):
|
||||
ApprovalService.add_approval(study_id, workflow_id, args)
|
||||
elif isinstance(uids, list):
|
||||
for id in uids:
|
||||
if id: ## Assure it's not empty or null
|
||||
ApprovalService.add_approval(study_id, workflow_id, id)
|
||||
|
||||
def get_uids(self, task, args):
|
||||
if len(args) < 1:
|
||||
raise ApiError(code="missing_argument",
|
||||
message="The RequestApproval script requires at least one argument. The "
|
||||
"the name of the variable in the task data that contains user"
|
||||
"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"
|
||||
"ids to process. This must point to an array or a string, but "
|
||||
"it currently points to a %s " % uids.__class__.__name__)
|
||||
|
||||
return uids
|
||||
|
||||
|
|
@ -1,385 +0,0 @@
|
|||
import json
|
||||
import pickle
|
||||
import sys
|
||||
from base64 import b64decode
|
||||
from datetime import datetime, timedelta
|
||||
|
||||
from sqlalchemy import desc, func
|
||||
|
||||
from crc import app, db, session
|
||||
from crc.api.common import ApiError
|
||||
|
||||
from crc.models.approval import ApprovalModel, ApprovalStatus, ApprovalFile, Approval
|
||||
from crc.models.study import StudyModel
|
||||
from crc.models.workflow import WorkflowModel
|
||||
from crc.services.file_service import FileService
|
||||
from crc.services.ldap_service import LdapService
|
||||
from crc.services.mails import (
|
||||
send_ramp_up_submission_email,
|
||||
send_ramp_up_approval_request_email,
|
||||
send_ramp_up_approval_request_first_review_email,
|
||||
send_ramp_up_approved_email,
|
||||
send_ramp_up_denied_email,
|
||||
send_ramp_up_denied_email_to_approver
|
||||
)
|
||||
|
||||
class ApprovalService(object):
|
||||
"""Provides common tools for working with an Approval"""
|
||||
|
||||
@staticmethod
|
||||
def __one_approval_from_study(study, approver_uid = None, status=None,
|
||||
include_cancelled=True):
|
||||
"""Returns one approval, with all additional approvals as 'related_approvals',
|
||||
the main approval can be pinned to an approver with an optional argument.
|
||||
Will return null if no approvals exist on the study."""
|
||||
main_approval = None
|
||||
related_approvals = []
|
||||
query = db.session.query(ApprovalModel).filter(ApprovalModel.study_id == study.id)
|
||||
if not include_cancelled:
|
||||
query=query.filter(ApprovalModel.status != ApprovalStatus.CANCELED.value)
|
||||
approvals = query.all() # All non-cancelled approvals.
|
||||
|
||||
for approval_model in approvals:
|
||||
if approval_model.approver_uid == approver_uid:
|
||||
main_approval = approval_model
|
||||
else:
|
||||
related_approvals.append(approval_model)
|
||||
|
||||
# IF WE ARE JUST RETURNING ALL OF THE APPROVALS PER STUDY
|
||||
if not main_approval and len(related_approvals) > 0:
|
||||
main_approval = related_approvals[0]
|
||||
related_approvals = related_approvals[1:]
|
||||
|
||||
if main_approval is not None: # May be null if the study has no approvals.
|
||||
final_status = ApprovalService.__calculate_overall_approval_status(main_approval, related_approvals)
|
||||
if status and final_status != status: return # Now that we are certain of the status, filter on it.
|
||||
|
||||
main_approval = Approval.from_model(main_approval)
|
||||
main_approval.status = final_status
|
||||
for ra in related_approvals:
|
||||
main_approval.related_approvals.append(Approval.from_model(ra))
|
||||
|
||||
return main_approval
|
||||
|
||||
@staticmethod
|
||||
def __calculate_overall_approval_status(approval, related):
|
||||
# In the case of pending approvals, check to see if there is a related approval
|
||||
# that proceeds this approval - and if it is declined, or still pending, then change
|
||||
# the state of the approval to be Declined, or Waiting respectively.
|
||||
if approval.status == ApprovalStatus.PENDING.value:
|
||||
for ra in related:
|
||||
if ra.id < approval.id:
|
||||
if ra.status == ApprovalStatus.DECLINED.value or ra.status == ApprovalStatus.CANCELED.value:
|
||||
return ra.status # If any prior approval id declined or cancelled so is this approval.
|
||||
elif ra.status == ApprovalStatus.PENDING.value:
|
||||
return ApprovalStatus.AWAITING.value # if any prior approval is pending, then this is waiting.
|
||||
return approval.status
|
||||
else:
|
||||
return approval.status
|
||||
|
||||
@staticmethod
|
||||
def get_approvals_per_user(approver_uid, status=None, include_cancelled=False):
|
||||
"""Returns a list of approval objects (not db models) for the given
|
||||
approver. """
|
||||
studies = db.session.query(StudyModel).join(ApprovalModel).\
|
||||
filter(ApprovalModel.approver_uid == approver_uid).all()
|
||||
approvals = []
|
||||
for study in studies:
|
||||
approval = ApprovalService.__one_approval_from_study(study, approver_uid,
|
||||
status, include_cancelled)
|
||||
if approval:
|
||||
approvals.append(approval)
|
||||
return approvals
|
||||
|
||||
@staticmethod
|
||||
def get_all_approvals(include_cancelled=True):
|
||||
"""Returns a list of all approval objects (not db models), one record
|
||||
per study, with any associated approvals grouped under the first approval."""
|
||||
studies = db.session.query(StudyModel).all()
|
||||
approvals = []
|
||||
for study in studies:
|
||||
approval = ApprovalService.__one_approval_from_study(study, include_cancelled=include_cancelled)
|
||||
if approval:
|
||||
approvals.append(approval)
|
||||
return approvals
|
||||
|
||||
@staticmethod
|
||||
def get_approvals_for_study(study_id, include_cancelled=True):
|
||||
"""Returns an array of Approval objects for the study, it does not
|
||||
compute the related approvals."""
|
||||
query = session.query(ApprovalModel).filter_by(study_id=study_id)
|
||||
if not include_cancelled:
|
||||
query = query.filter(ApprovalModel.status != ApprovalStatus.CANCELED.value)
|
||||
db_approvals = query.all()
|
||||
return [Approval.from_model(approval_model) for approval_model in db_approvals]
|
||||
|
||||
@staticmethod
|
||||
def get_approval_details(approval):
|
||||
"""Returns a list of packed approval details, obtained from
|
||||
the task data sent during the workflow """
|
||||
def extract_value(task, key):
|
||||
if key in task['data']:
|
||||
return pickle.loads(b64decode(task['data'][key]['__bytes__']))
|
||||
else:
|
||||
return ""
|
||||
|
||||
def find_task(uuid, task):
|
||||
if task['id']['__uuid__'] == uuid:
|
||||
return task
|
||||
for child in task['children']:
|
||||
task = find_task(uuid, child)
|
||||
if task:
|
||||
return task
|
||||
|
||||
if approval.status != ApprovalStatus.APPROVED.value:
|
||||
return {}
|
||||
for related_approval in approval.related_approvals:
|
||||
if related_approval.status != ApprovalStatus.APPROVED.value:
|
||||
continue
|
||||
workflow = db.session.query(WorkflowModel).filter(WorkflowModel.id == approval.workflow_id).first()
|
||||
data = json.loads(workflow.bpmn_workflow_json)
|
||||
last_task = find_task(data['last_task']['__uuid__'], data['task_tree'])
|
||||
personnel = extract_value(last_task, 'personnel')
|
||||
training_val = extract_value(last_task, 'RequiredTraining')
|
||||
pi_supervisor = extract_value(last_task, 'PISupervisor')['value']
|
||||
review_complete = 'AllRequiredTraining' in training_val
|
||||
pi_uid = workflow.study.primary_investigator_id
|
||||
pi_details = LdapService.user_info(pi_uid)
|
||||
details = {
|
||||
'Supervisor': pi_supervisor,
|
||||
'PI_Details': pi_details,
|
||||
'Review': review_complete
|
||||
}
|
||||
details['person_details'] = []
|
||||
details['person_details'].append(pi_details)
|
||||
for person in personnel:
|
||||
uid = person['PersonnelComputingID']['value']
|
||||
details['person_details'].append(LdapService.user_info(uid))
|
||||
|
||||
return details
|
||||
|
||||
@staticmethod
|
||||
def get_health_attesting_records():
|
||||
"""Return a list with prepared information related to all approvals """
|
||||
|
||||
approvals = ApprovalService.get_all_approvals(include_cancelled=False)
|
||||
|
||||
health_attesting_rows = [
|
||||
['university_computing_id',
|
||||
'last_name',
|
||||
'first_name',
|
||||
'department',
|
||||
'job_title',
|
||||
'supervisor_university_computing_id']
|
||||
]
|
||||
|
||||
for approval in approvals:
|
||||
try:
|
||||
details = ApprovalService.get_approval_details(approval)
|
||||
if not details:
|
||||
continue
|
||||
|
||||
for person in details['person_details']:
|
||||
first_name = person.given_name
|
||||
last_name = person.display_name.replace(first_name, '').strip()
|
||||
record = [
|
||||
person.uid,
|
||||
last_name,
|
||||
first_name,
|
||||
'',
|
||||
'Academic Researcher',
|
||||
details['Supervisor'] if person.uid == details['person_details'][0].uid else 'askresearch'
|
||||
]
|
||||
|
||||
if record not in health_attesting_rows:
|
||||
health_attesting_rows.append(record)
|
||||
|
||||
except Exception as e:
|
||||
app.logger.error(f'Error pulling data for workflow {approval.workflow_id}', exc_info=True)
|
||||
|
||||
return health_attesting_rows
|
||||
|
||||
@staticmethod
|
||||
def get_not_really_csv_content():
|
||||
approvals = ApprovalService.get_all_approvals(include_cancelled=False)
|
||||
output = []
|
||||
errors = []
|
||||
for approval in approvals:
|
||||
try:
|
||||
details = ApprovalService.get_approval_details(approval)
|
||||
|
||||
for person in details['person_details']:
|
||||
record = {
|
||||
"study_id": approval.study_id,
|
||||
"pi_uid": details['PI_Details'].uid,
|
||||
"pi": details['PI_Details'].display_name,
|
||||
"name": person.display_name,
|
||||
"uid": person.uid,
|
||||
"email": person.email_address,
|
||||
"supervisor": details['Supervisor'] if person.uid == details['person_details'][0].uid else "",
|
||||
"review_complete": details['Review'],
|
||||
}
|
||||
|
||||
output.append(record)
|
||||
|
||||
except Exception as e:
|
||||
errors.append(
|
||||
f'Error pulling data for workflow #{approval.workflow_id} '
|
||||
f'(Approval status: {approval.status} - '
|
||||
f'More details in Sentry): {str(e)}'
|
||||
)
|
||||
# Detailed information sent to Sentry
|
||||
app.logger.error(f'Error pulling data for workflow {approval.workflow_id}', exc_info=True)
|
||||
return {"results": output, "errors": errors }
|
||||
|
||||
@staticmethod
|
||||
def update_approval(approval_id, approver_uid):
|
||||
"""Update a specific approval
|
||||
NOTE: Actual update happens in the API layer, this
|
||||
funtion is currently in charge of only sending
|
||||
corresponding emails
|
||||
"""
|
||||
db_approval = session.query(ApprovalModel).get(approval_id)
|
||||
status = db_approval.status
|
||||
if db_approval:
|
||||
if status == ApprovalStatus.APPROVED.value:
|
||||
# second_approval = ApprovalModel().query.filter_by(
|
||||
# study_id=db_approval.study_id, workflow_id=db_approval.workflow_id,
|
||||
# status=ApprovalStatus.PENDING.value, version=db_approval.version).first()
|
||||
# if second_approval:
|
||||
# send rrp approval request for second approver
|
||||
ldap_service = LdapService()
|
||||
pi_user_info = ldap_service.user_info(db_approval.study.primary_investigator_id)
|
||||
approver_info = ldap_service.user_info(approver_uid)
|
||||
# send rrp submission
|
||||
mail_result = send_ramp_up_approved_email(
|
||||
'askresearch@virginia.edu',
|
||||
[pi_user_info.email_address],
|
||||
f'{approver_info.display_name} - ({approver_info.uid})'
|
||||
)
|
||||
if mail_result:
|
||||
app.logger.error(mail_result, exc_info=True)
|
||||
elif status == ApprovalStatus.DECLINED.value:
|
||||
ldap_service = LdapService()
|
||||
pi_user_info = ldap_service.user_info(db_approval.study.primary_investigator_id)
|
||||
approver_info = ldap_service.user_info(approver_uid)
|
||||
# send rrp submission
|
||||
mail_result = send_ramp_up_denied_email(
|
||||
'askresearch@virginia.edu',
|
||||
[pi_user_info.email_address],
|
||||
f'{approver_info.display_name} - ({approver_info.uid})'
|
||||
)
|
||||
if mail_result:
|
||||
app.logger.error(mail_result, exc_info=True)
|
||||
first_approval = ApprovalModel().query.filter_by(
|
||||
study_id=db_approval.study_id, workflow_id=db_approval.workflow_id,
|
||||
status=ApprovalStatus.APPROVED.value, version=db_approval.version).first()
|
||||
if first_approval:
|
||||
# Second approver denies
|
||||
first_approver_info = ldap_service.user_info(first_approval.approver_uid)
|
||||
approver_email = [first_approver_info.email_address] if first_approver_info.email_address else app.config['FALLBACK_EMAILS']
|
||||
# send rrp denied by second approver email to first approver
|
||||
mail_result = send_ramp_up_denied_email_to_approver(
|
||||
'askresearch@virginia.edu',
|
||||
approver_email,
|
||||
f'{pi_user_info.display_name} - ({pi_user_info.uid})',
|
||||
f'{approver_info.display_name} - ({approver_info.uid})'
|
||||
)
|
||||
if mail_result:
|
||||
app.logger.error(mail_result, exc_info=True)
|
||||
|
||||
return db_approval
|
||||
|
||||
@staticmethod
|
||||
def add_approval(study_id, workflow_id, approver_uid):
|
||||
"""we might have multiple approvals for a workflow, so I would expect this
|
||||
method to get called multiple times for the same workflow. This will
|
||||
only add a new approval if no approval already exists for the approver_uid,
|
||||
unless the workflow has changed, at which point, it will CANCEL any
|
||||
pending approvals and create a new approval for the latest version
|
||||
of the workflow."""
|
||||
|
||||
# Find any existing approvals for this workflow.
|
||||
latest_approval_requests = db.session.query(ApprovalModel). \
|
||||
filter(ApprovalModel.workflow_id == workflow_id). \
|
||||
order_by(desc(ApprovalModel.version))
|
||||
|
||||
latest_approver_request = latest_approval_requests.filter(ApprovalModel.approver_uid == approver_uid).first()
|
||||
|
||||
# Construct as hash of the latest files to see if things have changed since
|
||||
# the last approval.
|
||||
workflow = db.session.query(WorkflowModel).filter(WorkflowModel.id == workflow_id).first()
|
||||
workflow_data_files = FileService.get_workflow_data_files(workflow_id)
|
||||
current_data_file_ids = list(data_file.id for data_file in workflow_data_files)
|
||||
|
||||
if len(current_data_file_ids) == 0:
|
||||
raise ApiError("invalid_workflow_approval", "You can't create an approval for a workflow that has"
|
||||
"no files to approve in it.")
|
||||
|
||||
# If an existing approval request exists and no changes were made, do nothing.
|
||||
# If there is an existing approval request for a previous version of the workflow
|
||||
# then add a new request, and cancel any waiting/pending requests.
|
||||
if latest_approver_request:
|
||||
request_file_ids = list(file.file_data_id for file in latest_approver_request.approval_files)
|
||||
current_data_file_ids.sort()
|
||||
request_file_ids.sort()
|
||||
other_approver = latest_approval_requests.filter(ApprovalModel.approver_uid != approver_uid).first()
|
||||
if current_data_file_ids == request_file_ids:
|
||||
return # This approval already exists or we're updating other approver.
|
||||
else:
|
||||
for approval_request in latest_approval_requests:
|
||||
if (approval_request.version == latest_approver_request.version and
|
||||
approval_request.status != ApprovalStatus.CANCELED.value):
|
||||
approval_request.status = ApprovalStatus.CANCELED.value
|
||||
db.session.add(approval_request)
|
||||
version = latest_approver_request.version + 1
|
||||
else:
|
||||
version = 1
|
||||
|
||||
model = ApprovalModel(study_id=study_id, workflow_id=workflow_id,
|
||||
approver_uid=approver_uid, status=ApprovalStatus.PENDING.value,
|
||||
message="", date_created=datetime.now(),
|
||||
version=version)
|
||||
approval_files = ApprovalService._create_approval_files(workflow_data_files, model)
|
||||
|
||||
# Check approvals count
|
||||
approvals_count = ApprovalModel().query.filter_by(study_id=study_id, workflow_id=workflow_id,
|
||||
version=version).count()
|
||||
|
||||
db.session.add(model)
|
||||
db.session.add_all(approval_files)
|
||||
db.session.commit()
|
||||
|
||||
# Send first email
|
||||
if approvals_count == 0:
|
||||
ldap_service = LdapService()
|
||||
pi_user_info = ldap_service.user_info(model.study.primary_investigator_id)
|
||||
approver_info = ldap_service.user_info(approver_uid)
|
||||
# send rrp submission
|
||||
mail_result = send_ramp_up_submission_email(
|
||||
'askresearch@virginia.edu',
|
||||
[pi_user_info.email_address],
|
||||
f'{approver_info.display_name} - ({approver_info.uid})'
|
||||
)
|
||||
if mail_result:
|
||||
app.logger.error(mail_result, exc_info=True)
|
||||
# send rrp approval request for first approver
|
||||
# enhance the second part in case it bombs
|
||||
approver_email = [approver_info.email_address] if approver_info.email_address else app.config['FALLBACK_EMAILS']
|
||||
mail_result = send_ramp_up_approval_request_first_review_email(
|
||||
'askresearch@virginia.edu',
|
||||
approver_email,
|
||||
f'{pi_user_info.display_name} - ({pi_user_info.uid})'
|
||||
)
|
||||
if mail_result:
|
||||
app.logger.error(mail_result, exc_info=True)
|
||||
|
||||
@staticmethod
|
||||
def _create_approval_files(workflow_data_files, approval):
|
||||
"""Currently based exclusively on the status of files associated with a workflow."""
|
||||
file_approval_models = []
|
||||
for file_data in workflow_data_files:
|
||||
file_approval_models.append(ApprovalFile(file_data_id=file_data.id,
|
||||
approval=approval))
|
||||
return file_approval_models
|
||||
|
||||
|
|
@ -9,7 +9,6 @@ from ldap3.core.exceptions import LDAPSocketOpenError
|
|||
|
||||
from crc import db, session, app
|
||||
from crc.api.common import ApiError
|
||||
from crc.models.approval import ApprovalFile, ApprovalModel
|
||||
from crc.models.file import FileDataModel, FileModel, FileModelSchema, File, LookupFileModel, LookupDataModel
|
||||
from crc.models.ldap import LdapSchema
|
||||
from crc.models.protocol_builder import ProtocolBuilderStudy, ProtocolBuilderStatus
|
||||
|
|
@ -18,7 +17,6 @@ from crc.models.study import StudyModel, Study, StudyStatus, Category, WorkflowM
|
|||
from crc.models.task_event import TaskEventModel, TaskEvent
|
||||
from crc.models.workflow import WorkflowSpecCategoryModel, WorkflowModel, WorkflowSpecModel, WorkflowState, \
|
||||
WorkflowStatus, WorkflowSpecDependencyFile
|
||||
from crc.services.approval_service import ApprovalService
|
||||
from crc.services.file_service import FileService
|
||||
from crc.services.ldap_service import LdapService
|
||||
from crc.services.protocol_builder import ProtocolBuilderService
|
||||
|
|
@ -69,7 +67,6 @@ class StudyService(object):
|
|||
study.last_activity_date = last_event.date
|
||||
study.categories = StudyService.get_categories()
|
||||
workflow_metas = StudyService.__get_workflow_metas(study_id)
|
||||
study.approvals = ApprovalService.get_approvals_for_study(study.id)
|
||||
files = FileService.get_files_for_study(study.id)
|
||||
files = (File.from_models(model, FileService.get_file_data(model.id),
|
||||
FileService.get_doc_dictionary()) for model in files)
|
||||
|
|
@ -108,10 +105,6 @@ class StudyService(object):
|
|||
session.query(WorkflowSpecDependencyFile).filter_by(workflow_id=workflow_id).delete(synchronize_session='fetch')
|
||||
session.query(FileModel).filter_by(workflow_id=workflow_id).update({'archived': True, 'workflow_id': None})
|
||||
|
||||
# Todo: Remove approvals completely.
|
||||
session.query(ApprovalFile).filter(ApprovalModel.workflow_id == workflow_id).delete(synchronize_session='fetch')
|
||||
session.query(ApprovalModel).filter_by(workflow_id=workflow.id).delete()
|
||||
|
||||
session.delete(workflow)
|
||||
session.commit()
|
||||
|
||||
|
|
@ -125,32 +118,6 @@ class StudyService(object):
|
|||
categories.append(Category(cat_model))
|
||||
return categories
|
||||
|
||||
@staticmethod
|
||||
def get_approvals(study_id):
|
||||
"""Returns a list of non-hidden approval workflows."""
|
||||
study = StudyService.get_study(study_id)
|
||||
cat = next(c for c in study.categories if c.name == 'approvals')
|
||||
|
||||
approvals = []
|
||||
for wf in cat.workflows:
|
||||
if wf.state is WorkflowState.hidden:
|
||||
continue
|
||||
|
||||
workflow = db.session.query(WorkflowModel).filter_by(id=wf.id).first()
|
||||
approvals.append({
|
||||
'study_id': study_id,
|
||||
'workflow_id': wf.id,
|
||||
'display_name': wf.display_name,
|
||||
'display_order': wf.display_order or 0,
|
||||
'name': wf.name,
|
||||
'state': wf.state.value,
|
||||
'status': wf.status.value,
|
||||
'workflow_spec_id': workflow.workflow_spec_id,
|
||||
})
|
||||
|
||||
approvals.sort(key=lambda k: k['display_order'])
|
||||
return approvals
|
||||
|
||||
@staticmethod
|
||||
def get_documents_status(study_id):
|
||||
"""Returns a list of documents related to the study, and any file information
|
||||
|
|
|
|||
|
|
@ -158,7 +158,9 @@ class WorkflowService(object):
|
|||
if field.has_property(Task.FIELD_PROP_HIDE_EXPRESSION) and field.has_validation(Task.FIELD_CONSTRAINT_REQUIRED):
|
||||
if not field.has_property(Task.FIELD_PROP_VALUE_EXPRESSION) or not (hasattr(field, 'default_value')):
|
||||
raise ApiError(code='hidden and required field missing default',
|
||||
message='Fields that are required but can be hidden must have either a default value or a value_expression')
|
||||
message='Fields that are required but can be hidden must have either a default value or a value_expression',
|
||||
task_id='task.id',
|
||||
task_name=task.get_name())
|
||||
|
||||
# If the field is hidden and not required, it should not produce a value.
|
||||
if field.has_property(Task.FIELD_PROP_HIDE_EXPRESSION) and not field.has_validation(Task.FIELD_CONSTRAINT_REQUIRED):
|
||||
|
|
@ -212,7 +214,7 @@ class WorkflowService(object):
|
|||
if not id[0].isalpha():
|
||||
return False
|
||||
for char in id[1:len(id)]:
|
||||
if char.isalnum() or char == '_':
|
||||
if char.isalnum() or char == '_' or char == '.':
|
||||
pass
|
||||
else:
|
||||
return False
|
||||
|
|
|
|||
|
|
@ -0,0 +1,48 @@
|
|||
"""empty message
|
||||
|
||||
Revision ID: ff29528a9909
|
||||
Revises: c6261ac7a7bc
|
||||
Create Date: 2021-02-16 09:00:38.674050
|
||||
|
||||
"""
|
||||
from alembic import op
|
||||
import sqlalchemy as sa
|
||||
from sqlalchemy.dialects import postgresql
|
||||
|
||||
# revision identifiers, used by Alembic.
|
||||
revision = 'ff29528a9909'
|
||||
down_revision = 'c6261ac7a7bc'
|
||||
branch_labels = None
|
||||
depends_on = None
|
||||
|
||||
|
||||
def upgrade():
|
||||
# ### commands auto generated by Alembic - please adjust! ###
|
||||
op.drop_table('approval_file')
|
||||
op.drop_table('approval')
|
||||
# ### end Alembic commands ###
|
||||
|
||||
|
||||
def downgrade():
|
||||
# ### commands auto generated by Alembic - please adjust! ###
|
||||
op.create_table('approval_file',
|
||||
sa.Column('approval_id', sa.INTEGER(), autoincrement=False, nullable=False),
|
||||
sa.Column('file_data_id', sa.INTEGER(), autoincrement=False, nullable=False),
|
||||
sa.ForeignKeyConstraint(['approval_id'], ['approval.id'], name='approval_file_approval_id_fkey'),
|
||||
sa.ForeignKeyConstraint(['file_data_id'], ['file_data.id'], name='approval_file_file_data_id_fkey')
|
||||
)
|
||||
op.create_table('approval',
|
||||
sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False),
|
||||
sa.Column('study_id', sa.INTEGER(), autoincrement=False, nullable=False),
|
||||
sa.Column('workflow_id', sa.INTEGER(), autoincrement=False, nullable=False),
|
||||
sa.Column('approver_uid', sa.VARCHAR(), autoincrement=False, nullable=True),
|
||||
sa.Column('status', sa.VARCHAR(), autoincrement=False, nullable=True),
|
||||
sa.Column('message', sa.VARCHAR(), autoincrement=False, nullable=True),
|
||||
sa.Column('date_created', postgresql.TIMESTAMP(timezone=True), autoincrement=False, nullable=True),
|
||||
sa.Column('version', sa.INTEGER(), autoincrement=False, nullable=True),
|
||||
sa.Column('date_approved', postgresql.TIMESTAMP(timezone=True), autoincrement=False, nullable=True),
|
||||
sa.ForeignKeyConstraint(['study_id'], ['study.id'], name='approval_study_id_fkey'),
|
||||
sa.ForeignKeyConstraint(['workflow_id'], ['workflow.id'], name='approval_workflow_id_fkey'),
|
||||
sa.PrimaryKeyConstraint('id', name='approval_pkey')
|
||||
)
|
||||
# ### end Alembic commands ###
|
||||
|
|
@ -1,239 +0,0 @@
|
|||
import json
|
||||
import random
|
||||
import string
|
||||
|
||||
from flask import g
|
||||
|
||||
from tests.base_test import BaseTest
|
||||
from crc import session, db
|
||||
from crc.models.approval import ApprovalModel, ApprovalStatus
|
||||
from crc.models.study import StudyModel
|
||||
from crc.models.workflow import WorkflowModel
|
||||
|
||||
|
||||
class TestApprovals(BaseTest):
|
||||
def setUp(self):
|
||||
"""Initial setup shared by all TestApprovals tests"""
|
||||
self.load_example_data()
|
||||
|
||||
# Add a study with 2 approvers
|
||||
study_workflow_approvals_1 = self._create_study_workflow_approvals(
|
||||
user_uid="dhf8r", title="first study", primary_investigator_id="lb3dp",
|
||||
approver_uids=["lb3dp", "dhf8r"], statuses=[ApprovalStatus.PENDING.value, ApprovalStatus.PENDING.value]
|
||||
)
|
||||
self.study = study_workflow_approvals_1['study']
|
||||
self.workflow = study_workflow_approvals_1['workflow']
|
||||
self.approval = study_workflow_approvals_1['approvals'][0]
|
||||
self.approval_2 = study_workflow_approvals_1['approvals'][1]
|
||||
|
||||
# Add a study with 1 approver
|
||||
study_workflow_approvals_2 = self._create_study_workflow_approvals(
|
||||
user_uid="dhf8r", title="second study", primary_investigator_id="dhf8r",
|
||||
approver_uids=["lb3dp"], statuses=[ApprovalStatus.PENDING.value]
|
||||
)
|
||||
self.unrelated_study = study_workflow_approvals_2['study']
|
||||
self.unrelated_workflow = study_workflow_approvals_2['workflow']
|
||||
self.approval_3 = study_workflow_approvals_2['approvals'][0]
|
||||
|
||||
def test_list_approvals_per_approver(self):
|
||||
"""Only approvals associated with approver should be returned"""
|
||||
approver_uid = self.approval_2.approver_uid
|
||||
rv = self.app.get(f'/v1.0/approval', headers=self.logged_in_headers())
|
||||
self.assert_success(rv)
|
||||
|
||||
response = json.loads(rv.get_data(as_text=True))
|
||||
|
||||
# Stored approvals are 3
|
||||
approvals_count = ApprovalModel.query.count()
|
||||
self.assertEqual(approvals_count, 3)
|
||||
|
||||
# but Dan's approvals should be only 1
|
||||
self.assertEqual(len(response), 1)
|
||||
|
||||
# Confirm approver UID matches returned payload
|
||||
approval = response[0]
|
||||
self.assertEqual(approval['approver']['uid'], approver_uid)
|
||||
|
||||
def test_list_approvals_as_user(self):
|
||||
"""All approvals as different user"""
|
||||
rv = self.app.get('/v1.0/approval?as_user=lb3dp', headers=self.logged_in_headers())
|
||||
self.assert_success(rv)
|
||||
|
||||
response = json.loads(rv.get_data(as_text=True))
|
||||
|
||||
# Returned approvals should match what's in the db for user ld3dp, we should get one
|
||||
# approval back per study (2 studies), and that approval should have one related approval.
|
||||
response_count = len(response)
|
||||
self.assertEqual(2, response_count)
|
||||
|
||||
rv = self.app.get('/v1.0/approval', headers=self.logged_in_headers())
|
||||
self.assert_success(rv)
|
||||
response = json.loads(rv.get_data(as_text=True))
|
||||
response_count = len(response)
|
||||
self.assertEqual(1, response_count)
|
||||
self.assertEqual(1, len(response[0]['related_approvals'])) # this approval has a related approval.
|
||||
|
||||
def test_update_approval_fails_if_not_the_approver(self):
|
||||
approval = session.query(ApprovalModel).filter_by(approver_uid='lb3dp').first()
|
||||
data = {'id': approval.id,
|
||||
"approver_uid": "dhf8r",
|
||||
'message': "Approved. I like the cut of your jib.",
|
||||
'status': ApprovalStatus.APPROVED.value}
|
||||
|
||||
self.assertEqual(approval.status, ApprovalStatus.PENDING.value)
|
||||
|
||||
rv = self.app.put(f'/v1.0/approval/{approval.id}',
|
||||
content_type="application/json",
|
||||
headers=self.logged_in_headers(), # As dhf8r
|
||||
data=json.dumps(data))
|
||||
self.assert_failure(rv)
|
||||
|
||||
def test_accept_approval(self):
|
||||
approval = session.query(ApprovalModel).filter_by(approver_uid='dhf8r').first()
|
||||
data = {'id': approval.id,
|
||||
"approver": {"uid": "dhf8r"},
|
||||
'message': "Approved. I like the cut of your jib.",
|
||||
'status': ApprovalStatus.APPROVED.value}
|
||||
|
||||
self.assertEqual(approval.status, ApprovalStatus.PENDING.value)
|
||||
|
||||
rv = self.app.put(f'/v1.0/approval/{approval.id}',
|
||||
content_type="application/json",
|
||||
headers=self.logged_in_headers(), # As dhf8r
|
||||
data=json.dumps(data))
|
||||
self.assert_success(rv)
|
||||
|
||||
session.refresh(approval)
|
||||
|
||||
# Updated record should now have the data sent to the endpoint
|
||||
self.assertEqual(approval.message, data['message'])
|
||||
self.assertEqual(approval.status, ApprovalStatus.APPROVED.value)
|
||||
|
||||
def test_decline_approval(self):
|
||||
approval = session.query(ApprovalModel).filter_by(approver_uid='dhf8r').first()
|
||||
data = {'id': approval.id,
|
||||
"approver": {"uid": "dhf8r"},
|
||||
'message': "Approved. I find the cut of your jib lacking.",
|
||||
'status': ApprovalStatus.DECLINED.value}
|
||||
|
||||
self.assertEqual(approval.status, ApprovalStatus.PENDING.value)
|
||||
|
||||
rv = self.app.put(f'/v1.0/approval/{approval.id}',
|
||||
content_type="application/json",
|
||||
headers=self.logged_in_headers(), # As dhf8r
|
||||
data=json.dumps(data))
|
||||
self.assert_success(rv)
|
||||
|
||||
session.refresh(approval)
|
||||
|
||||
# Updated record should now have the data sent to the endpoint
|
||||
self.assertEqual(approval.message, data['message'])
|
||||
self.assertEqual(approval.status, ApprovalStatus.DECLINED.value)
|
||||
|
||||
def test_csv_export(self):
|
||||
self.load_test_spec('two_forms')
|
||||
self._add_lots_of_random_approvals(n=50, workflow_spec_name='two_forms')
|
||||
|
||||
# Get all workflows
|
||||
workflows = db.session.query(WorkflowModel).filter_by(workflow_spec_id='two_forms').all()
|
||||
|
||||
# For each workflow, complete all tasks
|
||||
for workflow in workflows:
|
||||
workflow_api = self.get_workflow_api(workflow, user_uid=workflow.study.user_uid)
|
||||
self.assertEqual('two_forms', workflow_api.workflow_spec_id)
|
||||
|
||||
# Log current user out.
|
||||
g.user = None
|
||||
self.assertIsNone(g.user)
|
||||
|
||||
# Complete the form for Step one and post it.
|
||||
self.complete_form(workflow, workflow_api.next_task, {"color": "blue"}, error_code=None, user_uid=workflow.study.user_uid)
|
||||
|
||||
# Get the next Task
|
||||
workflow_api = self.get_workflow_api(workflow, user_uid=workflow.study.user_uid)
|
||||
self.assertEqual("StepTwo", workflow_api.next_task.name)
|
||||
|
||||
# Get all user Tasks and check that the data have been saved
|
||||
task = workflow_api.next_task
|
||||
self.assertIsNotNone(task.data)
|
||||
for val in task.data.values():
|
||||
self.assertIsNotNone(val)
|
||||
|
||||
rv = self.app.get(f'/v1.0/approval/csv', headers=self.logged_in_headers())
|
||||
self.assert_success(rv)
|
||||
|
||||
def test_all_approvals(self):
|
||||
self._add_lots_of_random_approvals()
|
||||
|
||||
not_canceled = session.query(ApprovalModel).filter(ApprovalModel.status != 'CANCELED').all()
|
||||
not_canceled_study_ids = []
|
||||
for a in not_canceled:
|
||||
if a.study_id not in not_canceled_study_ids:
|
||||
not_canceled_study_ids.append(a.study_id)
|
||||
|
||||
rv_all = self.app.get(f'/v1.0/all_approvals?status=false', headers=self.logged_in_headers())
|
||||
self.assert_success(rv_all)
|
||||
all_data = json.loads(rv_all.get_data(as_text=True))
|
||||
self.assertEqual(len(all_data), len(not_canceled_study_ids), 'Should return all non-canceled approvals, grouped by study')
|
||||
|
||||
all_approvals = session.query(ApprovalModel).all()
|
||||
all_approvals_study_ids = []
|
||||
for a in all_approvals:
|
||||
if a.study_id not in all_approvals_study_ids:
|
||||
all_approvals_study_ids.append(a.study_id)
|
||||
|
||||
rv_all = self.app.get(f'/v1.0/all_approvals?status=true', headers=self.logged_in_headers())
|
||||
self.assert_success(rv_all)
|
||||
all_data = json.loads(rv_all.get_data(as_text=True))
|
||||
self.assertEqual(len(all_data), len(all_approvals_study_ids), 'Should return all approvals, grouped by study')
|
||||
|
||||
def test_approvals_counts(self):
|
||||
statuses = [name for name, value in ApprovalStatus.__members__.items()]
|
||||
self._add_lots_of_random_approvals()
|
||||
|
||||
# Get the counts
|
||||
rv_counts = self.app.get(f'/v1.0/approval-counts', headers=self.logged_in_headers())
|
||||
self.assert_success(rv_counts)
|
||||
counts = json.loads(rv_counts.get_data(as_text=True))
|
||||
|
||||
# Get the actual approvals
|
||||
rv_approvals = self.app.get(f'/v1.0/approval', headers=self.logged_in_headers())
|
||||
self.assert_success(rv_approvals)
|
||||
approvals = json.loads(rv_approvals.get_data(as_text=True))
|
||||
|
||||
# Tally up the number of approvals in each status category
|
||||
manual_counts = {}
|
||||
for status in statuses:
|
||||
manual_counts[status] = 0
|
||||
|
||||
for approval in approvals:
|
||||
manual_counts[approval['status']] += 1
|
||||
|
||||
# Numbers in each category should match
|
||||
for status in statuses:
|
||||
self.assertEqual(counts[status], manual_counts[status], 'Approval counts for status %s should match' % status)
|
||||
|
||||
# Total number of approvals should match
|
||||
total_counts = sum(counts[status] for status in statuses)
|
||||
self.assertEqual(total_counts, len(approvals), 'Total approval counts for user should match number of approvals for user')
|
||||
|
||||
def _add_lots_of_random_approvals(self, n=100, workflow_spec_name="random_fact"):
|
||||
num_studies_before = db.session.query(StudyModel).count()
|
||||
statuses = [name for name, value in ApprovalStatus.__members__.items()]
|
||||
|
||||
# Add a whole bunch of approvals with random statuses
|
||||
for i in range(n):
|
||||
approver_uids = random.choices(["lb3dp", "dhf8r"])
|
||||
self._create_study_workflow_approvals(
|
||||
user_uid=random.choice(["lb3dp", "dhf8r"]),
|
||||
title="".join(random.choices(string.ascii_lowercase, k=64)),
|
||||
primary_investigator_id=random.choice(["lb3dp", "dhf8r"]),
|
||||
approver_uids=approver_uids,
|
||||
statuses=random.choices(statuses, k=len(approver_uids)),
|
||||
workflow_spec_name=workflow_spec_name
|
||||
)
|
||||
|
||||
session.flush()
|
||||
num_studies_after = db.session.query(StudyModel).count()
|
||||
self.assertEqual(num_studies_after, num_studies_before + n)
|
||||
|
||||
|
|
@ -1,125 +0,0 @@
|
|||
from tests.base_test import BaseTest
|
||||
from crc import db
|
||||
from crc.models.approval import ApprovalModel
|
||||
from crc.services.approval_service import ApprovalService, ApprovalStatus
|
||||
from crc.services.file_service import FileService
|
||||
from crc.services.workflow_processor import WorkflowProcessor
|
||||
|
||||
|
||||
class TestApprovalsService(BaseTest):
|
||||
|
||||
def test_create_approval_record(self):
|
||||
self.create_reference_document()
|
||||
workflow = self.create_workflow("empty_workflow")
|
||||
FileService.add_workflow_file(workflow_id=workflow.id,
|
||||
name="anything.png", content_type="text",
|
||||
binary_data=b'5678', irb_doc_code="UVACompl_PRCAppr" )
|
||||
|
||||
|
||||
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
|
||||
self.assertEqual(1, db.session.query(ApprovalModel).count())
|
||||
model = db.session.query(ApprovalModel).first()
|
||||
self.assertEqual(workflow.study_id, model.study_id)
|
||||
self.assertEqual(workflow.id, model.workflow_id)
|
||||
self.assertEqual("dhf8r", model.approver_uid)
|
||||
self.assertEqual(1, model.version)
|
||||
|
||||
def test_new_requests_dont_add_if_approval_exists_for_current_workflow(self):
|
||||
self.create_reference_document()
|
||||
workflow = self.create_workflow("empty_workflow")
|
||||
FileService.add_workflow_file(workflow_id=workflow.id,
|
||||
name="anything.png", content_type="text",
|
||||
binary_data=b'5678', irb_doc_code="UVACompl_PRCAppr" )
|
||||
|
||||
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
|
||||
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
|
||||
self.assertEqual(1, db.session.query(ApprovalModel).count())
|
||||
model = db.session.query(ApprovalModel).first()
|
||||
self.assertEqual(1, model.version)
|
||||
|
||||
def test_new_approval_requests_after_file_modification_create_new_requests(self):
|
||||
self.load_example_data()
|
||||
self.create_reference_document()
|
||||
workflow = self.create_workflow('empty_workflow')
|
||||
FileService.add_workflow_file(workflow_id=workflow.id,
|
||||
name="anything.png", content_type="text",
|
||||
binary_data=b'5678', irb_doc_code="AD_CoCAppr")
|
||||
|
||||
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
|
||||
|
||||
FileService.add_workflow_file(workflow_id=workflow.id,
|
||||
name="anything.png", content_type="text",
|
||||
binary_data=b'5678', irb_doc_code="UVACompl_PRCAppr")
|
||||
|
||||
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
|
||||
self.assertEqual(2, db.session.query(ApprovalModel).count())
|
||||
models = db.session.query(ApprovalModel).order_by(ApprovalModel.version).all()
|
||||
self.assertEqual(1, models[0].version)
|
||||
self.assertEqual(2, models[1].version)
|
||||
|
||||
def test_get_health_attesting_records(self):
|
||||
self.load_example_data()
|
||||
self.create_reference_document()
|
||||
workflow = self.create_workflow('empty_workflow')
|
||||
FileService.add_workflow_file(workflow_id=workflow.id,
|
||||
name="anything.png", content_type="text",
|
||||
binary_data=b'5678', irb_doc_code="AD_CoCAppr")
|
||||
|
||||
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
|
||||
records = ApprovalService.get_health_attesting_records()
|
||||
|
||||
self.assertEqual(len(records), 1)
|
||||
|
||||
def test_get_not_really_csv_content(self):
|
||||
self.load_example_data()
|
||||
self.create_reference_document()
|
||||
workflow = self.create_workflow('empty_workflow')
|
||||
FileService.add_workflow_file(workflow_id=workflow.id,
|
||||
name="anything.png", content_type="text",
|
||||
binary_data=b'5678', irb_doc_code="AD_CoCAppr")
|
||||
|
||||
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
|
||||
records = ApprovalService.get_not_really_csv_content()
|
||||
|
||||
self.assertEqual(len(records), 2)
|
||||
|
||||
def test_new_approval_cancels_all_previous_approvals(self):
|
||||
self.create_reference_document()
|
||||
workflow = self.create_workflow("empty_workflow")
|
||||
FileService.add_workflow_file(workflow_id=workflow.id,
|
||||
name="anything.png", content_type="text",
|
||||
binary_data=b'5678', irb_doc_code="UVACompl_PRCAppr" )
|
||||
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
|
||||
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="lb3dp")
|
||||
|
||||
current_count = ApprovalModel.query.count()
|
||||
self.assertTrue(current_count, 2)
|
||||
|
||||
FileService.add_workflow_file(workflow_id=workflow.id,
|
||||
name="borderline.png", content_type="text",
|
||||
binary_data=b'906090', irb_doc_code="AD_CoCAppr" )
|
||||
|
||||
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
|
||||
|
||||
current_count = ApprovalModel.query.count()
|
||||
canceled_count = ApprovalModel.query.filter(ApprovalModel.status == ApprovalStatus.CANCELED.value)
|
||||
self.assertTrue(current_count, 2)
|
||||
self.assertTrue(current_count, 3)
|
||||
|
||||
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="lb3dp")
|
||||
|
||||
current_count = ApprovalModel.query.count()
|
||||
self.assertTrue(current_count, 4)
|
||||
|
||||
def test_new_approval_sends_proper_emails(self):
|
||||
self.assertEqual(1, 1)
|
||||
|
||||
def test_new_approval_failed_ldap_lookup(self):
|
||||
# failed lookup should send email to sartographysupport@googlegroups.com + Cheryl
|
||||
self.assertEqual(1, 1)
|
||||
|
||||
def test_approve_approval_sends_proper_emails(self):
|
||||
self.assertEqual(1, 1)
|
||||
|
||||
def test_deny_approval_sends_proper_emails(self):
|
||||
self.assertEqual(1, 1)
|
||||
|
|
@ -1,68 +0,0 @@
|
|||
from tests.base_test import BaseTest
|
||||
|
||||
from crc.services.file_service import FileService
|
||||
from crc.scripts.request_approval import RequestApproval
|
||||
from crc.services.workflow_processor import WorkflowProcessor
|
||||
from crc.api.common import ApiError
|
||||
|
||||
from crc import db
|
||||
from crc.models.approval import ApprovalModel
|
||||
|
||||
|
||||
class TestRequestApprovalScript(BaseTest):
|
||||
|
||||
def test_do_task(self):
|
||||
self.load_example_data()
|
||||
self.create_reference_document()
|
||||
workflow = self.create_workflow('empty_workflow')
|
||||
processor = WorkflowProcessor(workflow)
|
||||
task = processor.next_task()
|
||||
task.data = {"study": {"approval1": "dhf8r", 'approval2':'lb3dp'}}
|
||||
FileService.add_workflow_file(workflow_id=workflow.id,
|
||||
irb_doc_code="UVACompl_PRCAppr",
|
||||
name="anything.png", content_type="text",
|
||||
binary_data=b'1234')
|
||||
script = RequestApproval()
|
||||
script.do_task(task, workflow.study_id, workflow.id, "study.approval1", "study.approval2")
|
||||
self.assertEqual(2, db.session.query(ApprovalModel).count())
|
||||
|
||||
def test_do_task_with_blank_second_approver(self):
|
||||
self.load_example_data()
|
||||
self.create_reference_document()
|
||||
workflow = self.create_workflow('empty_workflow')
|
||||
processor = WorkflowProcessor(workflow)
|
||||
task = processor.next_task()
|
||||
task.data = {"study": {"approval1": "dhf8r", 'approval2':''}}
|
||||
FileService.add_workflow_file(workflow_id=workflow.id,
|
||||
irb_doc_code="UVACompl_PRCAppr",
|
||||
name="anything.png", content_type="text",
|
||||
binary_data=b'1234')
|
||||
script = RequestApproval()
|
||||
script.do_task(task, workflow.study_id, workflow.id, "study.approval1", "study.approval2")
|
||||
self.assertEqual(1, db.session.query(ApprovalModel).count())
|
||||
|
||||
|
||||
def test_do_task_with_incorrect_argument(self):
|
||||
"""This script should raise an error if it can't figure out the approvers."""
|
||||
self.load_example_data()
|
||||
self.create_reference_document()
|
||||
workflow = self.create_workflow('empty_workflow')
|
||||
processor = WorkflowProcessor(workflow)
|
||||
task = processor.next_task()
|
||||
task.data = {"approvals": {'dhf8r':["invalid"], 'lb3dp':"invalid"}}
|
||||
script = RequestApproval()
|
||||
with self.assertRaises(ApiError):
|
||||
script.do_task(task, workflow.study_id, workflow.id, "approvals")
|
||||
|
||||
def test_do_task_validate_only(self):
|
||||
self.load_example_data()
|
||||
self.create_reference_document()
|
||||
workflow = self.create_workflow('empty_workflow')
|
||||
processor = WorkflowProcessor(workflow)
|
||||
task = processor.next_task()
|
||||
task.data = {"study": {"approval1": "dhf8r", 'approval2':'lb3dp'}}
|
||||
|
||||
script = RequestApproval()
|
||||
script.do_task_validate_only(task, workflow.study_id, workflow.id, "study.approval1")
|
||||
self.assertEqual(0, db.session.query(ApprovalModel).count())
|
||||
|
||||
|
|
@ -13,7 +13,6 @@ from sqlalchemy import Sequence
|
|||
|
||||
from crc import app, db, session
|
||||
from crc.models.api_models import WorkflowApiSchema, MultiInstanceType
|
||||
from crc.models.approval import ApprovalModel, ApprovalStatus
|
||||
from crc.models.file import FileModel, FileDataModel, CONTENT_TYPES
|
||||
from crc.models.task_event import TaskEventModel
|
||||
from crc.models.study import StudyModel, StudyStatus
|
||||
|
|
|
|||
|
|
@ -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:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_06dpn07" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="4.2.0">
|
||||
<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_06dpn07" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.5.0">
|
||||
<bpmn:process id="Process_1iqn8uk" isExecutable="true">
|
||||
<bpmn:startEvent id="StartEvent_1">
|
||||
<bpmn:outgoing>Flow_0dbfi6t</bpmn:outgoing>
|
||||
|
|
@ -8,16 +8,16 @@
|
|||
<bpmn:manualTask id="Activity_09rr8u7" name="Hello">
|
||||
<bpmn:documentation><H1>Hello</H1></bpmn:documentation>
|
||||
<bpmn:incoming>Flow_0dbfi6t</bpmn:incoming>
|
||||
<bpmn:outgoing>Flow_02rje6r</bpmn:outgoing>
|
||||
<bpmn:outgoing>SequenceFlow_0o1egpu</bpmn:outgoing>
|
||||
</bpmn:manualTask>
|
||||
<bpmn:sequenceFlow id="Flow_02rje6r" sourceRef="Activity_09rr8u7" targetRef="Activity_GetName" />
|
||||
<bpmn:userTask id="Activity_GetName" name="Get Name" camunda:formKey="GetName">
|
||||
<bpmn:extensionElements>
|
||||
<camunda:formData>
|
||||
<camunda:formField id="name" label="Name" type="string" defaultValue="World" />
|
||||
<camunda:formField id="me.name" label="Enter" type="string" />
|
||||
</camunda:formData>
|
||||
</bpmn:extensionElements>
|
||||
<bpmn:incoming>Flow_02rje6r</bpmn:incoming>
|
||||
<bpmn:incoming>SequenceFlow_1hytves</bpmn:incoming>
|
||||
<bpmn:outgoing>Flow_1iphrck</bpmn:outgoing>
|
||||
</bpmn:userTask>
|
||||
<bpmn:sequenceFlow id="Flow_1iphrck" sourceRef="Activity_GetName" targetRef="Activity_GetTitle" />
|
||||
|
|
@ -40,47 +40,61 @@
|
|||
<bpmn:incoming>Flow_0hbiuz4</bpmn:incoming>
|
||||
</bpmn:endEvent>
|
||||
<bpmn:sequenceFlow id="Flow_0hbiuz4" sourceRef="Activity_SayHello" targetRef="Event_13veu8t" />
|
||||
<bpmn:sequenceFlow id="SequenceFlow_0o1egpu" sourceRef="Activity_09rr8u7" targetRef="Task_SeedData" />
|
||||
<bpmn:scriptTask id="Task_SeedData" name="Seed Data">
|
||||
<bpmn:incoming>SequenceFlow_0o1egpu</bpmn:incoming>
|
||||
<bpmn:outgoing>SequenceFlow_1hytves</bpmn:outgoing>
|
||||
<bpmn:script>me = {'name': 'my_name'}</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
<bpmn:sequenceFlow id="SequenceFlow_1hytves" sourceRef="Task_SeedData" targetRef="Activity_GetName" />
|
||||
</bpmn:process>
|
||||
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
|
||||
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_1iqn8uk">
|
||||
<bpmndi:BPMNEdge id="Flow_0dbfi6t_di" bpmnElement="Flow_0dbfi6t">
|
||||
<di:waypoint x="215" y="117" />
|
||||
<di:waypoint x="270" y="117" />
|
||||
</bpmndi:BPMNEdge>
|
||||
<bpmndi:BPMNEdge id="Flow_02rje6r_di" bpmnElement="Flow_02rje6r">
|
||||
<di:waypoint x="370" y="117" />
|
||||
<di:waypoint x="430" y="117" />
|
||||
<di:waypoint x="195" y="117" />
|
||||
<di:waypoint x="250" y="117" />
|
||||
</bpmndi:BPMNEdge>
|
||||
<bpmndi:BPMNEdge id="Flow_1iphrck_di" bpmnElement="Flow_1iphrck">
|
||||
<di:waypoint x="530" y="117" />
|
||||
<di:waypoint x="590" y="117" />
|
||||
<di:waypoint x="660" y="117" />
|
||||
<di:waypoint x="720" y="117" />
|
||||
</bpmndi:BPMNEdge>
|
||||
<bpmndi:BPMNEdge id="Flow_0cxh51h_di" bpmnElement="Flow_0cxh51h">
|
||||
<di:waypoint x="690" y="117" />
|
||||
<di:waypoint x="750" y="117" />
|
||||
<di:waypoint x="820" y="117" />
|
||||
<di:waypoint x="880" y="117" />
|
||||
</bpmndi:BPMNEdge>
|
||||
<bpmndi:BPMNEdge id="Flow_0hbiuz4_di" bpmnElement="Flow_0hbiuz4">
|
||||
<di:waypoint x="850" y="117" />
|
||||
<di:waypoint x="912" y="117" />
|
||||
<di:waypoint x="980" y="117" />
|
||||
<di:waypoint x="1042" y="117" />
|
||||
</bpmndi:BPMNEdge>
|
||||
<bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
|
||||
<dc:Bounds x="179" y="99" width="36" height="36" />
|
||||
<dc:Bounds x="159" y="99" width="36" height="36" />
|
||||
</bpmndi:BPMNShape>
|
||||
<bpmndi:BPMNShape id="Activity_132twgr_di" bpmnElement="Activity_09rr8u7">
|
||||
<dc:Bounds x="270" y="77" width="100" height="80" />
|
||||
<dc:Bounds x="250" y="77" width="100" height="80" />
|
||||
</bpmndi:BPMNShape>
|
||||
<bpmndi:BPMNShape id="Activity_0it9qzi_di" bpmnElement="Activity_GetName">
|
||||
<dc:Bounds x="430" y="77" width="100" height="80" />
|
||||
<dc:Bounds x="560" y="77" width="100" height="80" />
|
||||
</bpmndi:BPMNShape>
|
||||
<bpmndi:BPMNShape id="Activity_19s9l3h_di" bpmnElement="Activity_GetTitle">
|
||||
<dc:Bounds x="590" y="77" width="100" height="80" />
|
||||
<dc:Bounds x="720" y="77" width="100" height="80" />
|
||||
</bpmndi:BPMNShape>
|
||||
<bpmndi:BPMNShape id="Activity_05qpklh_di" bpmnElement="Activity_SayHello">
|
||||
<dc:Bounds x="750" y="77" width="100" height="80" />
|
||||
<dc:Bounds x="880" y="77" width="100" height="80" />
|
||||
</bpmndi:BPMNShape>
|
||||
<bpmndi:BPMNShape id="Event_13veu8t_di" bpmnElement="Event_13veu8t">
|
||||
<dc:Bounds x="912" y="99" width="36" height="36" />
|
||||
<dc:Bounds x="1042" y="99" width="36" height="36" />
|
||||
</bpmndi:BPMNShape>
|
||||
<bpmndi:BPMNEdge id="SequenceFlow_0o1egpu_di" bpmnElement="SequenceFlow_0o1egpu">
|
||||
<di:waypoint x="350" y="117" />
|
||||
<di:waypoint x="410" y="117" />
|
||||
</bpmndi:BPMNEdge>
|
||||
<bpmndi:BPMNShape id="ScriptTask_09ok9u2_di" bpmnElement="Task_SeedData">
|
||||
<dc:Bounds x="410" y="77" width="100" height="80" />
|
||||
</bpmndi:BPMNShape>
|
||||
<bpmndi:BPMNEdge id="SequenceFlow_1hytves_di" bpmnElement="SequenceFlow_1hytves">
|
||||
<di:waypoint x="510" y="117" />
|
||||
<di:waypoint x="560" y="117" />
|
||||
</bpmndi:BPMNEdge>
|
||||
</bpmndi:BPMNPlane>
|
||||
</bpmndi:BPMNDiagram>
|
||||
</bpmn:definitions>
|
||||
|
|
|
|||
|
|
@ -1,7 +1,6 @@
|
|||
from tests.base_test import BaseTest
|
||||
|
||||
from crc import session
|
||||
from crc.models.approval import ApprovalModel, ApprovalStatus
|
||||
from crc.models.email import EmailModel
|
||||
from crc.services.email_service import EmailService
|
||||
|
||||
|
|
|
|||
|
|
@ -9,8 +9,6 @@ from crc.models.workflow import WorkflowSpecModel
|
|||
from crc.services.file_service import FileService
|
||||
from crc.services.workflow_processor import WorkflowProcessor
|
||||
from example_data import ExampleDataLoader
|
||||
from crc.services.approval_service import ApprovalService
|
||||
from crc.models.approval import ApprovalModel, ApprovalStatus
|
||||
|
||||
|
||||
class TestFilesApi(BaseTest):
|
||||
|
|
@ -251,39 +249,6 @@ class TestFilesApi(BaseTest):
|
|||
rv = self.app.get('/v1.0/file/%i' % file_id, headers=self.logged_in_headers())
|
||||
self.assertEqual(404, rv.status_code)
|
||||
|
||||
def test_delete_file_after_approval(self):
|
||||
self.create_reference_document()
|
||||
workflow = self.create_workflow("empty_workflow")
|
||||
FileService.add_workflow_file(workflow_id=workflow.id,
|
||||
name="anything.png", content_type="text",
|
||||
binary_data=b'5678', irb_doc_code="UVACompl_PRCAppr")
|
||||
FileService.add_workflow_file(workflow_id=workflow.id,
|
||||
name="anotother_anything.png", content_type="text",
|
||||
binary_data=b'1234', irb_doc_code="Study_App_Doc")
|
||||
|
||||
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
|
||||
|
||||
file = session.query(FileModel).\
|
||||
filter(FileModel.workflow_id == workflow.id).\
|
||||
filter(FileModel.name == "anything.png").first()
|
||||
self.assertFalse(file.archived)
|
||||
rv = self.app.get('/v1.0/file/%i' % file.id, headers=self.logged_in_headers())
|
||||
self.assert_success(rv)
|
||||
|
||||
rv = self.app.delete('/v1.0/file/%i' % file.id, headers=self.logged_in_headers())
|
||||
self.assert_success(rv)
|
||||
|
||||
session.refresh(file)
|
||||
self.assertTrue(file.archived)
|
||||
|
||||
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
|
||||
|
||||
approvals = session.query(ApprovalModel)\
|
||||
.filter(ApprovalModel.status == ApprovalStatus.PENDING.value)\
|
||||
.filter(ApprovalModel.study_id == workflow.study_id).all()
|
||||
|
||||
self.assertEqual(1, len(approvals))
|
||||
self.assertEqual(1, len(approvals[0].approval_files))
|
||||
|
||||
|
||||
def test_change_primary_bpmn(self):
|
||||
|
|
|
|||
|
|
@ -9,14 +9,13 @@ from unittest.mock import patch
|
|||
from crc import session, app
|
||||
from crc.models.protocol_builder import ProtocolBuilderStatus, \
|
||||
ProtocolBuilderStudySchema
|
||||
from crc.models.approval import ApprovalStatus
|
||||
from crc.models.file import FileModel
|
||||
from crc.models.task_event import TaskEventModel
|
||||
from crc.models.study import StudyEvent, StudyModel, StudySchema, StudyStatus, StudyEventType
|
||||
from crc.models.workflow import WorkflowSpecModel, WorkflowModel
|
||||
from crc.services.file_service import FileService
|
||||
from crc.services.workflow_processor import WorkflowProcessor
|
||||
from crc.services.workflow_service import WorkflowService
|
||||
|
||||
|
||||
|
||||
class TestStudyApi(BaseTest):
|
||||
|
|
@ -100,22 +99,6 @@ class TestStudyApi(BaseTest):
|
|||
|
||||
# TODO: WRITE A TEST FOR STUDY FILES
|
||||
|
||||
def test_get_study_has_details_about_approvals(self):
|
||||
self.load_example_data()
|
||||
full_study = self._create_study_workflow_approvals(
|
||||
user_uid="dhf8r", title="first study", primary_investigator_id="lb3dp",
|
||||
approver_uids=["lb3dp", "dhf8r"], statuses=[ApprovalStatus.PENDING.value, ApprovalStatus.PENDING.value]
|
||||
)
|
||||
|
||||
api_response = self.app.get('/v1.0/study/%i' % full_study['study'].id,
|
||||
headers=self.logged_in_headers(), content_type="application/json")
|
||||
self.assert_success(api_response)
|
||||
study = StudySchema().loads(api_response.get_data(as_text=True))
|
||||
|
||||
self.assertEqual(len(study.approvals), 2)
|
||||
|
||||
for approval in study.approvals:
|
||||
self.assertEqual(full_study['study'].title, approval['title'])
|
||||
|
||||
def test_add_study(self):
|
||||
self.load_example_data()
|
||||
|
|
|
|||
|
|
@ -100,9 +100,6 @@ class TestStudyService(BaseTest):
|
|||
self.assertEqual(1, workflow.completed_tasks)
|
||||
|
||||
# Get approvals
|
||||
approvals = StudyService.get_approvals(studies[0].id)
|
||||
self.assertGreater(len(approvals), 0)
|
||||
self.assertIsNotNone(approvals[0]['display_order'])
|
||||
|
||||
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_required_docs') # mock_docs
|
||||
def test_get_required_docs(self, mock_docs):
|
||||
|
|
|
|||
|
|
@ -12,3 +12,14 @@ class TestFormFieldName(BaseTest):
|
|||
self.assertEqual(json_data[0]['message'],
|
||||
'When populating all fields ... Invalid Field name: "user-title". A field ID must begin '
|
||||
'with a letter, and can only contain letters, numbers, and "_"')
|
||||
|
||||
def test_form_field_name_with_period(self):
|
||||
workflow = self.create_workflow('workflow_form_field_name')
|
||||
|
||||
workflow_api = self.get_workflow_api(workflow)
|
||||
first_task = workflow_api.next_task
|
||||
self.complete_form(workflow_api, first_task, {})
|
||||
|
||||
workflow_api = self.get_workflow_api(workflow)
|
||||
second_task = workflow_api.next_task
|
||||
self.assertEqual('me.name', second_task.form['fields'][1]['id'])
|
||||
|
|
|
|||
|
|
@ -12,6 +12,8 @@ class TestWorkflowHiddenRequiredField(BaseTest):
|
|||
|
||||
json_data = json.loads(rv.get_data(as_text=True))
|
||||
self.assertEqual(json_data[0]['code'], 'hidden and required field missing default')
|
||||
self.assertIn('task_id', json_data[0])
|
||||
self.assertIn('task_name', json_data[0])
|
||||
|
||||
def test_default_used(self):
|
||||
# If a field is hidden and required, make sure we use the default value
|
||||
|
|
|
|||
Loading…
Reference in New Issue