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protocol-builder-mock
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Ticket 275 - adding new API endpoint for IRB Study Info 

models.py
 - Added new IRBInfo model
 - Added relationship to Study table

forms.py
 - Added form to edit the data
 - Added column in Study table for link to edit new info

__init__.py
 - Added route for new form page
 - Added method to update the db
This commit is contained in:
mike cullerton 2021-04-08 17:35:24 -04:00
parent 2c780c9028
commit 40f45202df
4 changed files with 119 additions and 4 deletions
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37
migrations/versions/277f05065db0_.py Normal file
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@ -0,0 +1,37 @@
"""empty message
Revision ID: 277f05065db0
Revises: 119c1269ee7c
Create Date: 2021-04-07 16:14:01.470659
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '277f05065db0'
down_revision = '119c1269ee7c'
branch_labels = None
depends_on = None
def upgrade():
op.create_table('irb_info',
sa.Column('SS_STUDY_ID', sa.Integer(), nullable=False),
sa.Column('UVA_STUDY_TRACKING', sa.String(), nullable=False, default=''),
sa.Column('DATE_MODIFIED', sa.DateTime(timezone=True), nullable=True),
sa.Column('IRB_ADMINISTRATIVE_REVIEWER', sa.String(), nullable=False, default=''),
sa.Column('AGENDA_DATE', sa.DateTime(timezone=True), nullable=True),
sa.Column('IRB_REVIEW_TYPE', sa.String(), nullable=False, default=''),
sa.Column('IRBEVENT', sa.String(), nullable=False, default=''),
sa.Column('IRB_STATUS', sa.String(), nullable=False, default=''),
sa.Column('RB_OF_RECORD', sa.String(), nullable=False, default=''),
sa.Column('UVA_IRB_HSR_IS_IRB_OF_RECORD_FOR_ALL_SITES', sa.Integer(), nullable=True),
sa.Column('STUDYIRBREVIEWERADMIN', sa.String(), nullable=False, default=''),
sa.ForeignKeyConstraint(['SS_STUDY_ID'], ['study.STUDYID'],),
sa.PrimaryKeyConstraint('SS_STUDY_ID'))
def downgrade():
op.drop_table('irb_info')

49
pb/__init__.py
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@ -160,9 +160,11 @@ def site_map():
# **************************
# WEB FORMS
# **************************
from pb.forms import StudyForm, StudyTable, InvestigatorForm, StudyDetailsForm, ConfirmDeleteForm, StudySponsorForm
from pb.forms import StudyForm, StudyTable, InvestigatorForm, StudyDetailsForm, ConfirmDeleteForm, StudySponsorForm, \
IRBInfoForm
from pb.models import Study, RequiredDocument, Investigator, StudySchema, RequiredDocumentSchema, InvestigatorSchema, \
StudyDetails, StudyDetailsSchema, StudySponsor, Sponsor, SponsorSchema, StudySponsorSchema, IRBStatus, IRBStatusSchema
StudyDetails, StudyDetailsSchema, StudySponsor, Sponsor, SponsorSchema, StudySponsorSchema, IRBStatus, \
IRBStatusSchema, IRBInfo, IRBInfoSchema
from pb.ldap.ldap_service import LdapService
@ -245,6 +247,29 @@ def edit_study(study_id):
)
@app.route('/irb_info/<study_id>', methods=['GET', 'POST'])
def edit_irb_info(study_id):
irb_info = db.session.query(IRBInfo).filter(IRBInfo.SS_STUDY_ID == study_id).first()
form = IRBInfoForm(request.form, obj=irb_info)
action = BASE_HREF + "/irb_info/" + study_id
title = "Edit IRB Info #" + study_id
# if request.method == 'GET':
# form.SS_STUDY_ID.data = study_id
if request.method == 'POST':
if form.validate():
_update_irb_info(study_id, irb_info, form)
flash('IRB Info updated successfully!', 'success')
return redirect_home()
return render_template(
'form.html',
form=form,
action=action,
title=title,
description_map={},
base_href=BASE_HREF
)
@app.route('/investigator/<study_id>', methods=['GET', 'POST'])
def new_investigator(study_id):
form = InvestigatorForm(request.form)
@ -473,6 +498,26 @@ def _update_study(study, form):
db.session.commit()
def _update_irb_info(study_id, irb_info, form):
if irb_info is None:
irb_info = IRBInfo(SS_STUDY_ID=study_id)
irb_info.UVA_STUDY_TRACKING = form.UVA_STUDY_TRACKING.data
irb_info.DATE_MODIFIED = form.DATE_MODIFIED.data
irb_info.IRB_ADMINISTRATIVE_REVIEWER = form.IRB_ADMINISTRATIVE_REVIEWER.data
irb_info.AGENDA_DATE = form.AGENDA_DATE.data
irb_info.IRB_REVIEW_TYPE = form.IRB_REVIEW_TYPE.data
irb_info.IRBEVENT = form.IRBEVENT.data
irb_info.IRB_STATUS = form.IRB_STATUS.data
irb_info.RB_OF_RECORD = form.RB_OF_RECORD.data
irb_info.UVA_IRB_HSR_IS_IRB_OF_RECORD_FOR_ALL_SITES = form.UVA_IRB_HSR_IS_IRB_OF_RECORD_FOR_ALL_SITES.data
irb_info.STUDYIRBREVIEWERADMIN = form.STUDYIRBREVIEWERADMIN.data
db.session.add(irb_info)
db.session.commit()
print('_update_irb_info')
def _allowed_file(filename):
allowed_extensions = ['csv', 'xls', 'xlsx']
return '.' in filename and \

15
pb/forms.py
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@ -1,9 +1,9 @@
from flask_table import Table, Col, LinkCol, BoolCol, DatetimeCol, NestedTableCol
from flask_wtf import FlaskForm
from wtforms import SelectMultipleField, StringField, BooleanField, SelectField, validators, HiddenField
from wtforms import SelectMultipleField, StringField, BooleanField, SelectField, validators, HiddenField, DateField, IntegerField
from wtforms_alchemy import ModelForm
from pb.models import RequiredDocument, Investigator, StudyDetails, IRBStatus
from pb.models import RequiredDocument, Investigator, StudyDetails, IRBStatus, IRBInfo
class StudyForm(FlaskForm):
@ -18,6 +18,12 @@ class StudyForm(FlaskForm):
choices=[((q.STATUS, q.DETAIL), q.DETAIL) for q in IRBStatus.all()])
class IRBInfoForm(ModelForm, FlaskForm):
class Meta:
model = IRBInfo
hidden = 'SS_STUDY_ID'
class InvestigatorForm(FlaskForm):
NETBADGEID = StringField('UVA Id')
INVESTIGATORTYPE = SelectField("InvestigatorType", choices=[(i.INVESTIGATORTYPE, i.INVESTIGATORTYPEFULL) for i in Investigator.all_types()])
@ -115,6 +121,11 @@ class StudyTable(Table):
anchor_attrs={'class': 'btn btn-icon btn-accent', 'title': 'Edit Sponsor(s)'},
th_html_attrs={'class': 'mat-icon text-center', 'title': 'Edit Sponsor(s)'}
)
irb_info = LinkCol(
'irb_info', 'edit_irb_info', url_kwargs=dict(study_id='STUDYID'),
anchor_attrs={'class': 'btn btn-icon btn-accent', 'title': 'Edit Info'},
th_html_attrs={'class': 'mat-icon text-center', 'title': 'Edit Info'}
)
STUDYID = Col('Study Id')
TITLE = Col('Title')
NETBADGEID = Col('User')

22
pb/models.py
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@ -69,6 +69,7 @@ class Study(db.Model):
NETBADGEID = db.Column(db.String(), nullable=False)
DATE_MODIFIED = db.Column(db.DateTime(timezone=True), default=func.now())
Q_COMPLETE = db.relationship("IRBStatus", backref="study", lazy='dynamic')
irb_info = db.relationship("IRBInfo", backref="study", lazy='dynamic')
requirements = db.relationship("RequiredDocument", backref="study", lazy='dynamic')
investigators = db.relationship("Investigator", backref="study", lazy='dynamic')
study_details = db.relationship("StudyDetails", uselist=False, backref="study")
@ -82,6 +83,27 @@ class StudySchema(ma.Schema):
"DATE_MODIFIED")
class IRBInfo(db.Model):
SS_STUDY_ID = db.Column(db.Integer, db.ForeignKey('study.STUDYID'), primary_key=True)
UVA_STUDY_TRACKING = db.Column(db.String(), nullable=False, default='')
DATE_MODIFIED = db.Column(db.Date, nullable=True)
IRB_ADMINISTRATIVE_REVIEWER = db.Column(db.String(), nullable=False, default='')
AGENDA_DATE = db.Column(db.Date, nullable=True)
IRB_REVIEW_TYPE = db.Column(db.String(), nullable=False, default='')
IRBEVENT = db.Column(db.String(), nullable=False, default='')
IRB_STATUS = db.Column(db.String(), nullable=False, default='')
RB_OF_RECORD = db.Column(db.String(), nullable=False, default='')
UVA_IRB_HSR_IS_IRB_OF_RECORD_FOR_ALL_SITES = db.Column(db.Integer(), nullable=True)
STUDYIRBREVIEWERADMIN = db.Column(db.String(), nullable=False, default='')
class IRBInfoSchema(ma.Schema):
class Meta:
# Fields to expose
fields = ("UVA_STUDY_TRACKING", "DATE_MODIFIED", "IRB_ADMINISTRATIVE_REVIEWER",
"AGENDA_DATE", "IRB_REVIEW_TYPE", "IRBEVENT", "IRB_STATUS", "RB_OF_RECORD",
"UVA_IRB_HSR_IS_IRB_OF_RECORD_FOR_ALL_SITES", "STUDYIRBREVIEWERADMIN")
class Investigator(db.Model):
id = db.Column(db.Integer, primary_key=True)
STUDYID = db.Column(db.Integer, db.ForeignKey('study.STUDYID'))