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Merge pull request #357 from sartography/426-remove-hsr-number 

remove hsr number #426
This commit is contained in:
Dan Funk 2021-08-17 09:58:56 -04:00 committed by GitHub
parent 0a2597ae36 fcebc6ac2b
commit c831ee7e4a
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GPG Key ID: 4AEE18F83AFDEB23
7 changed files with 61 additions and 34 deletions
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4
crc/api.yml
View File

@ -1627,10 +1627,6 @@ components:
type: string
x-nullable: true
example: "27b-6-42"
hsr_number:
type: string
x-nullable: true
example: "27b-6-1212"
StudyAssociate:
properties:
uid:

19
crc/models/protocol_builder.py
View File

@ -19,32 +19,31 @@ class ProtocolBuilderInvestigatorType(enum.Enum):
# Deprecated: Marked for removal
class ProtocolBuilderStatus(enum.Enum):
# • Active: found in PB and no HSR number and not hold
# • Active: found in PB and not hold
# • Hold: store boolean value in CR Connect (add to Study Model)
# • Open To Enrollment: has start date and HSR number?
# • Open To Enrollment: has start date?
# • 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
active = 'active' # found in PB, marked as "q_complete" 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?
open = 'open' # Open To Enrollment: has start date?
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
#IN_PROCESS = 'in_process', # Q_COMPLETE && !UPLOAD_COMPLETE
#IN_REVIEW = 'in_review', # Q_COMPLETE && (!UPLOAD_COMPLETE)
#REVIEW_COMPLETE = 'review_complete', # Q_COMPLETE && UPLOAD_COMPLETE
#INACTIVE = 'inactive', # Not found in PB
class ProtocolBuilderStudy(object):
def __init__(
self, STUDYID: int, HSRNUMBER: str, TITLE: str, NETBADGEID: str,
self, STUDYID: int, TITLE: str, NETBADGEID: str,
DATE_MODIFIED: str
):
self.STUDYID = STUDYID
self.HSRNUMBER = HSRNUMBER
self.TITLE = TITLE
self.NETBADGEID = NETBADGEID
self.DATE_MODIFIED = DATE_MODIFIED
@ -54,7 +53,7 @@ class ProtocolBuilderStudySchema(ma.Schema):
class Meta:
model = ProtocolBuilderStudy
unknown = INCLUDE
fields = ["STUDYID", "HSRNUMBER", "TITLE", "NETBADGEID",
fields = ["STUDYID", "TITLE", "NETBADGEID",
"DATE_MODIFIED"]
@post_load

8
crc/models/study.py
View File

@ -27,7 +27,6 @@ class StudyStatus(enum.Enum):
class IrbStatus(enum.Enum):
incomplete_in_protocol_builder = 'incomplete in protocol builder'
completed_in_protocol_builder = 'completed in protocol builder'
hsr_assigned = 'hsr number assigned'
class StudyEventType(enum.Enum):
@ -46,7 +45,6 @@ class StudyModel(db.Model):
irb_status = db.Column(db.Enum(IrbStatus))
primary_investigator_id = db.Column(db.String, nullable=True)
sponsor = db.Column(db.String, nullable=True)
hsr_number = db.Column(db.String, nullable=True)
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)
@ -57,7 +55,6 @@ class StudyModel(db.Model):
events_history = db.relationship("StudyEvent", cascade="all, delete, delete-orphan")
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
@ -172,7 +169,7 @@ class Study(object):
def __init__(self, title, short_title, last_updated, primary_investigator_id, user_uid,
id=None, status=None, irb_status=None, comment="",
sponsor="", hsr_number="", ind_number="", categories=[],
sponsor="", ind_number="", categories=[],
files=[], approvals=[], enrollment_date=None, events_history=[],
last_activity_user="",last_activity_date =None,create_user_display="", **argsv):
self.id = id
@ -188,7 +185,6 @@ class Study(object):
self.comment = comment
self.primary_investigator_id = primary_investigator_id
self.sponsor = sponsor
self.hsr_number = hsr_number
self.ind_number = ind_number
self.categories = categories
self.approvals = approvals
@ -220,7 +216,6 @@ class StudyForUpdateSchema(ma.Schema):
id = fields.Integer(required=False, allow_none=True)
status = EnumField(StudyStatus, by_value=True)
hsr_number = fields.String(allow_none=True)
sponsor = fields.String(allow_none=True)
ind_number = fields.String(allow_none=True)
enrollment_date = fields.DateTime(allow_none=True)
@ -252,7 +247,6 @@ class StudySchema(ma.Schema):
warnings = fields.List(fields.Nested(ApiErrorSchema), dump_only=True)
protocol_builder_status = EnumField(StudyStatus, by_value=True)
status = EnumField(StudyStatus, by_value=True)
hsr_number = fields.String(allow_none=True)
short_title = fields.String(allow_none=True)
sponsor = fields.String(allow_none=True)
ind_number = fields.String(allow_none=True)

5
crc/services/study_service.py
View File

@ -398,11 +398,6 @@ class StudyService(object):
session.add(db_study)
db_studies.append(db_study)
if pb_study.HSRNUMBER:
db_study.irb_status = IrbStatus.hsr_assigned
if db_study.status != StudyStatus.open_for_enrollment:
new_status = StudyStatus.open_for_enrollment
db_study.update_from_protocol_builder(pb_study)
StudyService._add_all_workflow_specs_to_study(db_study)

40
migrations/versions/3d9ae7cfc231_.py Normal file
View File

@ -0,0 +1,40 @@
"""Remove HSR Number
Revision ID: 3d9ae7cfc231
Revises: 2a6f7ea00e5f
Create Date: 2021-08-16 11:28:40.027495
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '3d9ae7cfc231'
down_revision = '2a6f7ea00e5f'
branch_labels = None
depends_on = None
def upgrade():
# Remove `hsr_assigned` values from Study table
op.execute("UPDATE study SET irb_status = 'incomplete_in_protocol_builder' where irb_status = 'hsr_assigned'")
# Remove `hsr_assigned` from IRB Status Enum
op.execute("ALTER TYPE irbstatus RENAME TO irbstatus_old")
op.execute("CREATE TYPE irbstatus AS ENUM('incomplete_in_protocol_builder', 'completed_in_protocol_builder')")
op.execute("ALTER TABLE study ALTER COLUMN irb_status TYPE irbstatus USING irb_status::text::irbstatus")
op.execute("DROP TYPE irbstatus_old")
# Remove hsr_number column from Study table
op.drop_column('study', 'hsr_number')
def downgrade():
op.execute("ALTER TYPE irbstatus RENAME TO irbstatus_old")
op.execute("CREATE TYPE irbstatus AS ENUM('incomplete_in_protocol_builder', 'completed_in_protocol_builder', 'hsr_assigned')")
op.execute("ALTER TABLE study ALTER COLUMN irb_status TYPE irbstatus USING irb_status::text::irbstatus")
op.execute("DROP TYPE irbstatus_old")
op.add_column('study', sa.Column('hsr_number', sa.String(), nullable=True))

3
tests/data/pb_responses/user_studies.json
View File

@ -1,21 +1,18 @@
[
{
"DATE_MODIFIED": "2020-02-19T14:26:49.127756",
"HSRNUMBER": "12345",
"NETBADGEID": "dhf8r",
"STUDYID": 54321,
"TITLE": "Another study about the effect of a naked mannequin on software productivity"
},
{
"DATE_MODIFIED": "2020-02-19T14:24:55.101695",
"HSRNUMBER": "",
"NETBADGEID": "dhf8r",
"STUDYID": 65432,
"TITLE": "Peanut butter consumption among quiet dogs"
},
{
"DATE_MODIFIED": "2020-02-19T14:24:55.101695",
"HSRNUMBER": "",
"NETBADGEID": "dhf8r",
"STUDYID": 1,
"TITLE": "Efficacy of xenomorph bio-augmented circuits on dexterity of cybernetic prostheses"

16
tests/study/test_study_api.py
View File

@ -190,17 +190,20 @@ class TestStudyApi(BaseTest):
num_abandoned += 1
if study['status'] == 'in_progress': # One study is marked complete without HSR Number
num_in_progress += 1
if study['status'] == 'open_for_enrollment': # One study is marked complete and has an HSR Number
if study['status'] == 'open_for_enrollment': # Currently, we don't automatically set studies to open for enrollment
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.assertEqual(num_abandoned, 1)
self.assertEqual(num_open, 1)
self.assertEqual(num_open, 0) # Currently, we don't automatically set studies to open for enrollment
self.assertEqual(num_in_progress, 2)
self.assertEqual(len(json_data), num_db_studies_after)
self.assertEqual(num_open + num_in_progress + num_abandoned, num_db_studies_after)
# The sum below is off, since we don't automatically set studies to Open for Enrollment
# Leaving the test here because we will need it again
# when we implement a new way to set Open for Enrollment
# self.assertEqual(num_open + num_in_progress + num_abandoned, num_db_studies_after)
# Automatic events check
in_progress_events = session.query(StudyEvent).filter_by(status=StudyStatus.in_progress)
@ -209,8 +212,11 @@ class TestStudyApi(BaseTest):
abandoned_events = session.query(StudyEvent).filter_by(status=StudyStatus.abandoned)
self.assertEqual(abandoned_events.count(), 1) # 1 study has been abandoned
open_for_enrollment_events = session.query(StudyEvent).filter_by(status=StudyStatus.open_for_enrollment)
self.assertEqual(open_for_enrollment_events.count(), 1) # 1 study was moved to open for enrollment
# We don't currently set any studies to Open for Enrollment automatically
# Leaving the test here because we will need it again
# when we implement a new way to set Open for Enrollment
# open_for_enrollment_events = session.query(StudyEvent).filter_by(status=StudyStatus.open_for_enrollment)
# self.assertEqual(open_for_enrollment_events.count(), 1) # 1 study was moved to open for enrollment
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_investigators') # mock_studies
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_required_docs') # mock_docs