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

migrations/versions/277f05065db0_.py

@@ -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')

pb/__init__.py

@@ -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 \

pb/forms.py

@@ -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')

pb/models.py

@@ -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'))