Adds study inactive flag. Sets study to inactive if not found in Protocol Builder.

This commit is contained in:
Aaron Louie 2020-02-27 11:17:58 -05:00
parent f3068e68db
commit 0cc59d0974
5 changed files with 43 additions and 8 deletions

View File

@ -1,18 +1,16 @@
from typing import List
from dateutil.parser import parse
from connexion import NoContent
from flask import g
from crc import session, auth
from crc.api.common import ApiError, ApiErrorSchema
from crc.api.workflow import __get_workflow_api_model
from crc.models.protocol_builder import ProtocolBuilderStatus, ProtocolBuilderStudy
from crc.models.study import StudyModelSchema, StudyModel
from models.protocol_builder import ProtocolBuilderStatus, ProtocolBuilderStudy
from crc.models.workflow import WorkflowModel, WorkflowApiSchema, WorkflowSpecModel
from crc.services import protocol_builder
from crc.services.workflow_processor import WorkflowProcessor
from services.protocol_builder import ProtocolBuilderService
from crc.services.protocol_builder import ProtocolBuilderService
@auth.login_required
@ -77,10 +75,13 @@ def update_from_protocol_builder():
db_studies = session.query(StudyModel).filter_by(user_uid=user.uid).all()
db_study_ids = list(map(lambda s: s.id, db_studies))
pb_study_ids = list(map(lambda s: s.id, pb_studies))
# Add studies from Protocol Builder that aren't in the database yet
for pb_study in pb_studies:
if pb_study['HSRNUMBER'] not in db_study_ids:
status = ProtocolBuilderStatus.complete._value_ if pb_study['Q_COMPLETE'] else ProtocolBuilderStatus.in_process._value_
status = ProtocolBuilderStatus.complete._value_ if pb_study[
'Q_COMPLETE'] else ProtocolBuilderStatus.in_process._value_
add_study({
'id': pb_study['HSRNUMBER'],
'title': pb_study['TITLE'],
@ -89,6 +90,11 @@ def update_from_protocol_builder():
'last_updated': pb_study['DATE_MODIFIED']
})
# Mark studies as inactive that are no longer in Protocol Builder
for study_id in db_study_ids:
if study_id not in pb_study_ids:
update_study(study_id=study_id, body={'inactive': True})
def post_update_study_from_protocol_builder(study_id):
"""Update a single study based on data received from

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@ -3,7 +3,7 @@ from marshmallow_sqlalchemy import ModelSchema
from sqlalchemy import func
from crc import db
from models.protocol_builder import ProtocolBuilderStatus
from crc.models.protocol_builder import ProtocolBuilderStatus
class StudyModel(db.Model):
@ -17,6 +17,7 @@ class StudyModel(db.Model):
ind_number = db.Column(db.String)
user_uid = db.Column(db.String, db.ForeignKey('user.uid'), nullable=True)
investigator_uids = db.Column(db.ARRAY(db.String))
inactive = db.Column(db.Boolean, default=False)
class StudyModelSchema(ModelSchema):

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@ -4,7 +4,7 @@ from typing import List, Optional
import requests
from crc import app
from models.protocol_builder import ProtocolBuilderStudy, ProtocolBuilderStudySchema, ProtocolBuilderInvestigator, \
from crc.models.protocol_builder import ProtocolBuilderStudy, ProtocolBuilderStudySchema, ProtocolBuilderInvestigator, \
ProtocolBuilderRequiredDocument, ProtocolBuilderStudyDetails, ProtocolBuilderInvestigatorSchema, \
ProtocolBuilderRequiredDocumentSchema, ProtocolBuilderStudyDetailsSchema

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@ -0,0 +1,28 @@
"""empty message
Revision ID: 2c88e49d0ffc
Revises: 726d09a4fa0c
Create Date: 2020-02-27 11:17:01.768161
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '2c88e49d0ffc'
down_revision = '726d09a4fa0c'
branch_labels = None
depends_on = None
def upgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.add_column('study', sa.Column('inactive', sa.Boolean(), nullable=True))
# ### end Alembic commands ###
def downgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.drop_column('study', 'inactive')
# ### end Alembic commands ###

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@ -3,7 +3,7 @@ from datetime import datetime, timezone
from crc import session
from crc.models.study import StudyModel, StudyModelSchema
from models.protocol_builder import ProtocolBuilderStatus
from crc.models.protocol_builder import ProtocolBuilderStatus
from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel, WorkflowStatus, \
WorkflowApiSchema
from tests.base_test import BaseTest