Merge pull request #49 from sartography/irb-api-endpoints-273

Irb api endpoints #273

migrations/versions/119c1269ee7c_.py

@@ -0,0 +1,33 @@
+"""empty message
+
+Revision ID: 119c1269ee7c
+Revises: 93a1e2ce38dc
+Create Date: 2021-03-31 12:30:19.645458
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '119c1269ee7c'
+down_revision = '93a1e2ce38dc'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    op.drop_column('study', 'Q_COMPLETE')
+    op.create_table('irb_status',
+    sa.Column('STUDYID', sa.Integer(), nullable=False),
+    sa.Column('STATUS', sa.String(), nullable=False, default=''),
+    sa.Column('DETAIL', sa.String(), nullable=False, default=''),
+    sa.ForeignKeyConstraint(['STUDYID'], ['study.STUDYID'],),
+    sa.PrimaryKeyConstraint('STUDYID')
+    )
+
+
+
+def downgrade():
+    op.drop_table('irb_status')
+    op.add_column('study', sa.Column('Q_COMPLETE', sa.Boolean(), nullable=True))

pb/__init__.py

@@ -41,6 +41,11 @@ def sponsors(studyid):
     return StudySponsorSchema(many=True).dump(sponsors)
 
 
+def check_study(studyid):
+    irb_status = db.session.query(IRBStatus).filter(IRBStatus.STUDYID == studyid).first()
+    return IRBStatusSchema().dump(irb_status)
+
+
 def get_form(id, requirement_code):
     return
 
@@ -157,7 +162,7 @@ def site_map():
 # **************************
 from pb.forms import StudyForm, StudyTable, InvestigatorForm, StudyDetailsForm, ConfirmDeleteForm, StudySponsorForm
 from pb.models import Study, RequiredDocument, Investigator, StudySchema, RequiredDocumentSchema, InvestigatorSchema, \
-    StudyDetails, StudyDetailsSchema, StudySponsor, Sponsor, SponsorSchema, StudySponsorSchema
+    StudyDetails, StudyDetailsSchema, StudySponsor, Sponsor, SponsorSchema, StudySponsorSchema, IRBStatus, IRBStatusSchema
 from pb.ldap.ldap_service import LdapService
 
 
@@ -201,6 +206,8 @@ def new_study():
         flash('Study created successfully!', 'success')
         return redirect_home()
 
+    # set default first time
+    form.Q_COMPLETE.data = "('No Error', 'Passed validation.')"
     return render_template(
         'form.html',
         form=form,
@@ -220,8 +227,10 @@ def edit_study(study_id):
         title = "Edit Study #" + study_id
         if study.requirements:
             form.requirements.data = list(map(lambda r: r.AUXDOCID, list(study.requirements)))
-        if study.Q_COMPLETE:
-            form.Q_COMPLETE.checked = True
+        if study.Q_COMPLETE and study.Q_COMPLETE.first():
+            form.Q_COMPLETE.data = "('" + study.Q_COMPLETE.first().STATUS + "', '" + study.Q_COMPLETE.first().DETAIL + "')"
+        else:
+            form.Q_COMPLETE.data = "('No Error', 'Passed validation.')"
     if request.method == 'POST':
         _update_study(study, form)
         flash('Study updated successfully!', 'success')
@@ -441,7 +450,6 @@ def _update_study(study, form):
     study.TITLE = form.TITLE.data
     study.NETBADGEID = form.NETBADGEID.data
     study.DATE_MODIFIED = datetime.datetime.now()
-    study.Q_COMPLETE = form.Q_COMPLETE.data
     study.HSRNUMBER = form.HSRNUMBER.data
 
     for r in form.requirements:
@@ -449,6 +457,18 @@ def _update_study(study, form):
             requirement = RequiredDocument(AUXDOCID=r.data, AUXDOC=r.label.text, study=study)
             db.session.add(requirement)
 
+    q_data = eval(form.Q_COMPLETE.data)
+    if q_data:
+        q_data_status = q_data[0]
+        q_data_detail = q_data[1]
+        q_status = db.session.query(IRBStatus).filter(IRBStatus.STUDYID == study.STUDYID).first()
+        if q_status:
+            q_status.STATUS = q_data_status
+            q_status.DETAIL = q_data_detail
+        else:
+            q_status = IRBStatus(STATUS=q_data_status, DETAIL=q_data_detail, STUDYID=study.STUDYID)
+        db.session.add(q_status)
+
     db.session.add(study)
     db.session.commit()
 

pb/api.yml

@@ -133,6 +133,27 @@ paths:
             application/json:
               schema:
                 $ref: "#/components/schemas/StudyDetail"
+  /check_study/{studyid}:
+    parameters:
+      - name: studyid
+        in: path
+        required: true
+        description: The id of the study.
+        schema:
+          type: integer
+          format: int32
+    get:
+      tags:
+      - CR-Connect
+      operationId: pb.check_study
+      summary: IRB Status about a particular study.
+      responses:
+        200:
+          description: Details about the protocol
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/IRBStatus"
 components:
   schemas:
     Study:
@@ -156,11 +177,6 @@ components:
           format: string
           example: jfg6n
           description: The UVA Id of of the principle investigator for the study.
-        Q_COMPLETE:
-          type: number
-          enum: [0,1]
-          example: 0
-          description: If 1, then this study is complete in the Protocol Builder, and is ready for processing by CR Connect.
         DATE_MODIFIED:
           type: string
           format: date_time
@@ -233,6 +249,21 @@ components:
           type: string
           example: Principal Investigator
           description: A human readable descriptive string of the INVESTIGATORTYPE.
+    IRBStatus:
+      type: object
+      properties:
+        STUDYID:
+          type: number
+          example: 12345
+          description: The study id from the Protocol Builder
+        STATUS:
+          type: string
+          example: No Error
+          description: The study status
+        DETAIL:
+          type: string
+          example: Passed Validation
+          description: Detail about the study status
     StudyDetail:
       type: object
       properties:

pb/forms.py

@@ -3,7 +3,7 @@ from flask_wtf import FlaskForm
 from wtforms import SelectMultipleField, StringField, BooleanField, SelectField, validators, HiddenField
 from wtforms_alchemy import ModelForm
 
-from pb.models import RequiredDocument, Investigator, StudyDetails
+from pb.models import RequiredDocument, Investigator, StudyDetails, IRBStatus
 
 
 class StudyForm(FlaskForm):
@@ -14,8 +14,8 @@ class StudyForm(FlaskForm):
                                        render_kw={'class': 'multi'},
                                        choices=[(rd.AUXDOCID, rd.AUXDOC) for rd in RequiredDocument.all()])
     HSRNUMBER = StringField('HSR Number')
-    Q_COMPLETE = BooleanField('Complete in Protocol Builder?', default='checked',
-                              false_values=(False, 'false', 0, '0'))
+    Q_COMPLETE = SelectField("IRBStatus",
+                             choices=[((q.STATUS, q.DETAIL), q.DETAIL) for q in IRBStatus.all()])
 
 
 class InvestigatorForm(FlaskForm):

pb/models.py

@@ -67,8 +67,8 @@ class Study(db.Model):
     HSRNUMBER = db.Column(db.String())
     TITLE = db.Column(db.Text(), nullable=False)
     NETBADGEID = db.Column(db.String(), nullable=False)
-    Q_COMPLETE = db.Column(db.Boolean, nullable=True)
     DATE_MODIFIED = db.Column(db.DateTime(timezone=True), default=func.now())
+    Q_COMPLETE = db.relationship("IRBStatus", 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")
@@ -79,7 +79,7 @@ class StudySchema(ma.Schema):
     class Meta:
         # Fields to expose
         fields = ("STUDYID", "HSRNUMBER", "TITLE", "NETBADGEID",
-                  "Q_COMPLETE", "DATE_MODIFIED")
+                  "DATE_MODIFIED")
 
 
 class Investigator(db.Model):
@@ -163,6 +163,24 @@ class RequiredDocumentSchema(ma.Schema):
         fields = ("AUXDOCID", "AUXDOC")
 
 
+class IRBStatus(db.Model):
+    STUDYID = db.Column(db.Integer, db.ForeignKey('study.STUDYID'), primary_key=True)
+    STATUS = db.Column(db.String(), nullable=False, default="")
+    DETAIL = db.Column(db.String(), nullable=False, default="")
+
+    @staticmethod
+    def all():
+        status = [IRBStatus(STATUS="Error", DETAIL="Study ID does not exist."),
+                  IRBStatus(STATUS="Error", DETAIL="General study errors. UVA Study Tracking Number is missing or not formatted correctly."),
+                  IRBStatus(STATUS="No Error", DETAIL="Passed validation.")]
+        return status
+
+
+class IRBStatusSchema(ma.Schema):
+    class Meta:
+        fields = ("STATUS", "DETAIL")
+
+
 class StudyDetails(db.Model):
     STUDYID = db.Column(db.Integer, db.ForeignKey('study.STUDYID'), primary_key=True)
     IS_IND = db.Column(db.Integer, nullable=True)

tests/test_sanity.py

@@ -57,6 +57,8 @@ class Sanity_Check_Test(unittest.TestCase):
         for r in form.requirements:
             form.data['requirements'].append(r.data)
 
+        form.Q_COMPLETE.data = "('No Error', 'Passed validation.')"
+
         r = self.app.post('/new_study', data=form.data, follow_redirects=False)
         assert r.status_code == 302
         added_study = Study.query.filter(Study.TITLE == study_title).first()
@@ -79,6 +81,7 @@ class Sanity_Check_Test(unittest.TestCase):
 
         for r in form_2.requirements:
             form_2.data['requirements'].append(r.data)
+        form_2.Q_COMPLETE.data = "('No Error', 'Passed validation.')"
 
         r_2 = self.app.post('/study/%i' % added_study.STUDYID, data=form_2.data, follow_redirects=False)
         assert r_2.status_code == 302