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cr-connect-workflow
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Merge pull request #32 from sartography/feature/new_study_states 

Updated the study status to use a different enumeration.  Migration c…
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Dan Funk 2020-04-21 17:21:10 -04:00 committed by GitHub
parent b10f72c085 fd0adb1d43
commit 79d9a66ce3
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10 changed files with 91 additions and 40 deletions
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2
crc/api.yml
View File

@ -828,7 +828,7 @@ components:
example: dhf8r
protocol_builder_status:
type: string
enum: [DRAFT, IN_PROCESS, IN_REVIEW, REVIEW_COMPLETE, INACTIVE]
enum: [INCOMPLETE, ACTIVE, HOLD, OPEN, ABANDONED]
example: done
sponsor:
type: string

2
crc/api/study.py
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@ -82,7 +82,7 @@ def post_update_study_from_protocol_builder(study_id):
db_study.update_from_protocol_builder(pb_study)
else:
db_study.inactive = True
db_study.protocol_builder_status = ProtocolBuilderStatus.INACTIVE
db_study.protocol_builder_status = ProtocolBuilderStatus.ABANDONED
return NoContent, 304

22
crc/models/protocol_builder.py
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@ -18,11 +18,23 @@ class ProtocolBuilderInvestigatorType(enum.Enum):
class ProtocolBuilderStatus(enum.Enum):
DRAFT = 'draft', # !Q_COMPLETE
IN_PROCESS = 'in_process', # Q_COMPLETE && !UPLOAD_COMPLETE && !HSRNUMBER
IN_REVIEW = 'in_review', # Q_COMPLETE && (!UPLOAD_COMPLETE || !HSRNUMBER)
REVIEW_COMPLETE = 'review_complete', # Q_COMPLETE && UPLOAD_COMPLETE && HSRNUMBER
INACTIVE = 'inactive', # Not found in PB
# • Active: found in PB and no HSR number and not hold
# • Hold: store boolean value in CR Connect (add to Study Model)
# • Open To Enrollment: has start date and HSR number?
# • Abandoned: deleted in PB
INCOMPLETE = 'incomplete' # Found in PB but not ready to start (not q_complete)
ACTIVE = 'active', # found in PB, marked as "q_complete" and no HSR number and not hold
HOLD = 'hold', # CR Connect side, if the Study ias marked as "hold".
OPEN = 'open', # Open To Enrollment: has start date and HSR number?
ABANDONED = 'Abandoned' # Not found in PB
#DRAFT = 'draft', # !Q_COMPLETE
#IN_PROCESS = 'in_process', # Q_COMPLETE && !UPLOAD_COMPLETE && !HSRNUMBER
#IN_REVIEW = 'in_review', # Q_COMPLETE && (!UPLOAD_COMPLETE || !HSRNUMBER)
#REVIEW_COMPLETE = 'review_complete', # Q_COMPLETE && UPLOAD_COMPLETE && HSRNUMBER
#INACTIVE = 'inactive', # Not found in PB
class ProtocolBuilderStudy(object):

23
crc/models/study.py
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@ -22,24 +22,22 @@ class StudyModel(db.Model):
ind_number = db.Column(db.String, nullable=True)
user_uid = db.Column(db.String, db.ForeignKey('user.uid'), nullable=False)
investigator_uids = db.Column(db.ARRAY(db.String), nullable=True)
inactive = db.Column(db.Boolean, default=False)
requirements = db.Column(db.ARRAY(db.Integer), nullable=True)
on_hold = db.Column(db.Boolean, default=False)
def update_from_protocol_builder(self, pbs: ProtocolBuilderStudy):
self.hsr_number = pbs.HSRNUMBER
self.title = pbs.TITLE
self.user_uid = pbs.NETBADGEID
self.last_updated = pbs.DATE_MODIFIED
self.protocol_builder_status = ProtocolBuilderStatus.DRAFT
self.inactive = False
if pbs.HSRNUMBER: # And Up load complete?
self.protocol_builder_status = ProtocolBuilderStatus.REVIEW_COMPLETE
elif pbs.Q_COMPLETE:
self.protocol_builder_status = ProtocolBuilderStatus.IN_PROCESS
self.protocol_builder_status = ProtocolBuilderStatus.INCOMPLETE
if pbs.Q_COMPLETE:
self.protocol_builder_status = ProtocolBuilderStatus.ACTIVE
if pbs.HSRNUMBER:
self.protocol_builder_status = ProtocolBuilderStatus.OPEN
if self.on_hold:
self.protocol_builder_status = ProtocolBuilderStatus.HOLD
class WorkflowMetadata(object):
@ -106,7 +104,7 @@ class Study(object):
def __init__(self, id, title, last_updated, primary_investigator_id, user_uid,
protocol_builder_status=None,
sponsor="", hsr_number="", ind_number="", inactive=False, categories=[], **argsv):
sponsor="", hsr_number="", ind_number="", categories=[], **argsv):
self.id = id
self.user_uid = user_uid
self.title = title
@ -116,7 +114,6 @@ class Study(object):
self.sponsor = sponsor
self.hsr_number = hsr_number
self.ind_number = ind_number
self.inactive = inactive
self.categories = categories
self.warnings = []
@ -149,7 +146,7 @@ class StudySchema(ma.Schema):
class Meta:
model = Study
additional = ["id", "title", "last_updated", "primary_investigator_id", "user_uid",
"sponsor", "ind_number", "inactive"]
"sponsor", "ind_number"]
unknown = INCLUDE
@marshmallow.post_load

3
crc/services/study_service.py
View File

@ -88,8 +88,7 @@ class StudyService(object):
for study in db_studies:
pb_study = next((pbs for pbs in pb_studies if pbs.STUDYID == study.id), None)
if not pb_study:
study.inactive = True
study.protocol_builder_status = ProtocolBuilderStatus.INACTIVE
study.protocol_builder_status = ProtocolBuilderStatus.ABANDONED
db.session.commit()

38
migrations/versions/0f38d7a36f21_.py Normal file
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@ -0,0 +1,38 @@
"""empty message
Revision ID: 0f38d7a36f21
Revises: 476f8a4933ba
Create Date: 2020-04-21 15:42:46.430272
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '0f38d7a36f21'
down_revision = '476f8a4933ba'
branch_labels = None
depends_on = None
def upgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.add_column('study', sa.Column('on_hold', sa.Boolean(), nullable=True))
op.drop_column('study', 'inactive')
# ### end Alembic commands ###
op.execute('ALTER TYPE protocolbuilderstatus RENAME TO pbs_old;')
op.execute("CREATE TYPE protocolbuilderstatus AS ENUM('INCOMPLETE', 'ACTIVE', 'HOLD', 'OPEN', 'ABANDONED')")
op.execute("ALTER TABLE study ALTER COLUMN protocol_builder_status TYPE protocolbuilderstatus USING protocol_builder_status::text::protocolbuilderstatus;")
op.execute('DROP TYPE pbs_old;')
def downgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.add_column('study', sa.Column('inactive', sa.BOOLEAN(), autoincrement=False, nullable=True))
op.drop_column('study', 'on_hold')
# ### end Alembic commands ###
op.execute('ALTER TYPE protocolbuilderstatus RENAME TO pbs_old;')
op.execute("CREATE TYPE protocolbuilderstatus AS ENUM('DRAFT', 'IN_PROCESS', 'IN_REVIEW', 'REVIEW_COMPLETE', 'INACTIVE')")
op.execute("ALTER TABLE study ALTER COLUMN protocol_builder_status TYPE protocolbuilderstatus USING protocol_builder_status::text::protocolbuilderstatus;")
op.execute('DROP TYPE pbs_old;')

4
tests/base_test.py
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@ -53,7 +53,7 @@ class BaseTest(unittest.TestCase):
'id':0,
'title':'The impact of fried pickles on beer consumption in bipedal software developers.',
'last_updated':datetime.datetime.now(),
'protocol_builder_status':ProtocolBuilderStatus.IN_PROCESS,
'protocol_builder_status':ProtocolBuilderStatus.ACTIVE,
'primary_investigator_id':'dhf8r',
'sponsor':'Sartography Pharmaceuticals',
'ind_number':'1234',
@ -63,7 +63,7 @@ class BaseTest(unittest.TestCase):
'id':1,
'title':'Requirement of hippocampal neurogenesis for the behavioral effects of soft pretzels',
'last_updated':datetime.datetime.now(),
'protocol_builder_status':ProtocolBuilderStatus.IN_PROCESS,
'protocol_builder_status':ProtocolBuilderStatus.ACTIVE,
'primary_investigator_id':'dhf8r',
'sponsor':'Makerspace & Co.',
'ind_number':'5678',

6
tests/data/pb_responses/user_studies.json
View File

@ -9,7 +9,7 @@
},
{
"DATE_MODIFIED": "2020-02-19T14:24:55.101695",
"HSRNUMBER": "56753",
"HSRNUMBER": "",
"NETBADGEID": "dhf8r",
"Q_COMPLETE": true,
"STUDYID": 65432,
@ -17,9 +17,9 @@
},
{
"DATE_MODIFIED": "2020-02-19T14:24:55.101695",
"HSRNUMBER": "45678",
"HSRNUMBER": "",
"NETBADGEID": "dhf8r",
"Q_COMPLETE": true,
"Q_COMPLETE": false,
"STUDYID": 1,
"TITLE": "Efficacy of xenomorph bio-augmented circuits on dexterity of cybernetic prostheses"
}

29
tests/test_study_api.py
View File

@ -21,7 +21,7 @@ class TestStudyApi(BaseTest):
"title": "Phase III Trial of Genuine People Personalities (GPP) Autonomous Intelligent Emotional Agents "
"for Interstellar Spacecraft",
"last_updated": datetime.now(tz=timezone.utc),
"protocol_builder_status": ProtocolBuilderStatus.IN_PROCESS,
"protocol_builder_status": ProtocolBuilderStatus.ACTIVE,
"primary_investigator_id": "tricia.marie.mcmillan@heartofgold.edu",
"sponsor": "Sirius Cybernetics Corporation",
"ind_number": "567890",
@ -104,7 +104,7 @@ class TestStudyApi(BaseTest):
self.load_example_data()
study: StudyModel = session.query(StudyModel).first()
study.title = "Pilot Study of Fjord Placement for Single Fraction Outcomes to Cortisol Susceptibility"
study.protocol_builder_status = ProtocolBuilderStatus.REVIEW_COMPLETE
study.protocol_builder_status = ProtocolBuilderStatus.ACTIVE
rv = self.app.put('/v1.0/study/%i' % study.id,
content_type="application/json",
headers=self.logged_in_headers(),
@ -142,26 +142,31 @@ class TestStudyApi(BaseTest):
self.assert_success(api_response)
json_data = json.loads(api_response.get_data(as_text=True))
num_inactive = 0
num_incomplete = 0
num_abandoned = 0
num_active = 0
num_open = 0
for study in json_data:
if study['inactive']:
num_inactive += 1
else:
if study['protocol_builder_status'] == 'INCOMPLETE': # One study in user_studies.json is not q_complete
num_incomplete += 1
if study['protocol_builder_status'] == 'ABANDONED': # One study does not exist in user_studies.json
num_abandoned += 1
if study['protocol_builder_status'] == 'ACTIVE': # One study is marked complete without HSR Number
num_active += 1
if study['protocol_builder_status'] == 'OPEN': # One study is marked complete and has an HSR Number
num_open += 1
db_studies_after = session.query(StudyModel).all()
num_db_studies_after = len(db_studies_after)
self.assertGreater(num_db_studies_after, num_db_studies_before)
self.assertGreater(num_inactive, 0)
self.assertGreater(num_active, 0)
self.assertEquals(num_abandoned, 1)
self.assertEquals(num_open, 1)
self.assertEquals(num_active, 1)
self.assertEquals(num_incomplete, 1)
self.assertEqual(len(json_data), num_db_studies_after)
self.assertEqual(num_active + num_inactive, num_db_studies_after)
self.assertEqual(num_open + num_active + num_incomplete + num_abandoned, num_db_studies_after)
# Assure that the existing study is properly updated.
test_study = session.query(StudyModel).filter_by(id=54321).first()
self.assertFalse(test_study.inactive)
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_required_docs') # mock_docs
def test_get_single_study(self, mock_docs):

2
tests/test_study_service.py
View File

@ -29,7 +29,7 @@ class TestStudyService(BaseTest):
user = UserModel(uid="dhf8r", email_address="whatever@stuff.com", display_name="Stayathome Smellalots")
db.session.add(user)
db.session.commit()
study = StudyModel(title="My title", protocol_builder_status=ProtocolBuilderStatus.IN_PROCESS, user_uid=user.uid)
study = StudyModel(title="My title", protocol_builder_status=ProtocolBuilderStatus.ACTIVE, user_uid=user.uid)
cat = WorkflowSpecCategoryModel(name="cat", display_name="cat", display_order=0)
db.session.add_all([study, cat])
db.session.commit()