Merge branch 'rrt/staging' into rrt/production

config/default.py

@@ -44,5 +44,11 @@ PB_STUDY_DETAILS_URL = environ.get('PB_STUDY_DETAILS_URL', default=PB_BASE_URL +
 LDAP_URL = environ.get('LDAP_URL', default="ldap.virginia.edu").strip('/')  # No trailing slash or http://
 LDAP_TIMEOUT_SEC = int(environ.get('LDAP_TIMEOUT_SEC', default=1))
 
-# Fallback emails
+# Email configuration
 FALLBACK_EMAILS = ['askresearch@virginia.edu', 'sartographysupport@googlegroups.com']
+MAIL_SERVER = environ.get('MAIL_SERVER', default='smtp.mailtrap.io')
+MAIL_PORT = environ.get('MAIL_PORT', default=2525)
+MAIL_USE_SSL = environ.get('MAIL_USE_SSL', default=False)
+MAIL_USE_TLS = environ.get('MAIL_USE_TLS', default=True)
+MAIL_USERNAME = environ.get('MAIL_USERNAME', default='5f012d0108d374')
+MAIL_PASSWORD = environ.get('MAIL_PASSWORD', default='08442c04e98d50')

crc/__init__.py

@@ -54,12 +54,6 @@ if app.config['ENABLE_SENTRY']:
 template_dir = os.getcwd() + '/crc/static/templates/mails'
 env = Environment(loader=FileSystemLoader(template_dir))
 # Mail settings
-app.config['MAIL_SERVER']='smtp.mailtrap.io'
-app.config['MAIL_PORT'] = 2525
-app.config['MAIL_USERNAME'] = '5f012d0108d374'
-app.config['MAIL_PASSWORD'] = '08442c04e98d50'
-app.config['MAIL_USE_TLS'] = True
-app.config['MAIL_USE_SSL'] = False
 mail = Mail(app)
 
 print('=== USING THESE CONFIG SETTINGS: ===')

crc/api.yml

@@ -806,12 +806,34 @@ paths:
                 type: array
                 items:
                   $ref: "#/components/schemas/Script"
+  /approval-counts:
+    parameters:
+      - name: as_user
+        in: query
+        required: false
+        description: If provided, returns the approval counts for that user.
+        schema:
+          type: string
+    get:
+      operationId: crc.api.approval.get_approval_counts
+      summary: Provides counts for approvals by status for the given user, or all users if no user is provided
+      tags:
+      - Approvals
+      responses:
+        '200':
+          description: An dictionary of Approval Statuses and the counts for each
+          content:
+            application/json:
+              schema:
+                type: array
+                items:
+                  $ref: "#/components/schemas/ApprovalCounts"
   /approval:
     parameters:
       - name: status
         in: query
         required: false
-        description: If set to true, returns all the approvals with any status.
+        description: If provided, returns just approvals for the given status.
         schema:
           type: string
       - name: as_user
@@ -1286,4 +1308,26 @@ components:
           type: number
           format: integer
           example: 5
+    ApprovalCounts:
+      properties:
+        PENDING:
+          type: number
+          format: integer
+          example: 5
+        APPROVED:
+          type: number
+          format: integer
+          example: 5
+        DECLINED:
+          type: number
+          format: integer
+          example: 5
+        CANCELED:
+          type: number
+          format: integer
+          example: 5
+        AWAITING:
+          type: number
+          format: integer
+          example: 5
 

crc/api/approval.py

@@ -13,6 +13,56 @@ from crc.services.approval_service import ApprovalService
 from crc.services.ldap_service import LdapService
 
 
+# Returns counts of approvals in each status group assigned to the given user.
+# The goal is to return results as quickly as possible.
+def get_approval_counts(as_user=None):
+    uid = as_user or g.user.uid
+
+    db_user_approvals = db.session.query(ApprovalModel)\
+        .filter_by(approver_uid=uid)\
+        .filter(ApprovalModel.status != ApprovalStatus.CANCELED.name)\
+        .all()
+
+    study_ids = [a.study_id for a in db_user_approvals]
+    print('study_ids', study_ids)
+
+    db_other_approvals = db.session.query(ApprovalModel)\
+        .filter(ApprovalModel.study_id.in_(study_ids))\
+        .filter(ApprovalModel.approver_uid != uid)\
+        .filter(ApprovalModel.status != ApprovalStatus.CANCELED.name)\
+        .all()
+
+    # Make a dict of the other approvals where the key is the study id and the value is the approval
+    # TODO: This won't work if there are more than 2 approvals with the same study_id
+    other_approvals = {}
+    for approval in db_other_approvals:
+        other_approvals[approval.study_id] = approval
+
+    counts = {}
+    for status in ApprovalStatus:
+        counts[status.name] = 0
+
+    for approval in db_user_approvals:
+        # Check if another approval has the same study id
+        if approval.study_id in other_approvals:
+            other_approval = other_approvals[approval.study_id]
+
+            # Other approval takes precedence over this one
+            if other_approval.id < approval.id:
+                if other_approval.status == ApprovalStatus.PENDING.name:
+                    counts[ApprovalStatus.AWAITING.name] += 1
+                elif other_approval.status == ApprovalStatus.DECLINED.name:
+                    counts[ApprovalStatus.DECLINED.name] += 1
+                elif other_approval.status == ApprovalStatus.CANCELED.name:
+                    counts[ApprovalStatus.CANCELED.name] += 1
+                elif other_approval.status == ApprovalStatus.APPROVED.name:
+                    counts[approval.status] += 1
+        else:
+            counts[approval.status] += 1
+
+    return counts
+
+
 def get_approvals(status=None, as_user=None):
     #status = ApprovalStatus.PENDING.value
     user = g.user.uid
@@ -31,7 +81,7 @@ def get_approvals_for_study(study_id=None):
     return results
 
 
-# ----- Being decent into madness ---- #
+# ----- Begin descent into madness ---- #
 def get_csv():
     """A damn lie, it's a json file. A huge bit of a one-off for RRT, but 3 weeks of midnight work can convince a
     man to do just about anything"""
@@ -81,12 +131,14 @@ def get_csv():
             errors.append("Error pulling data for workflow #%i: %s" % (approval.workflow_id, str(e)))
     return {"results": output, "errors": errors }
 
+
 def extract_value(task, key):
     if key in task['data']:
         return pickle.loads(b64decode(task['data'][key]['__bytes__']))
     else:
         return ""
 
+
 def find_task(uuid, task):
     if task['id']['__uuid__'] == uuid:
         return task
@@ -96,6 +148,7 @@ def find_task(uuid, task):
             return task
 # ----- come back to the world of the living ---- #
 
+
 def update_approval(approval_id, body):
     if approval_id is None:
         raise ApiError('unknown_approval', 'Please provide a valid Approval ID.')
@@ -113,5 +166,9 @@ def update_approval(approval_id, body):
     session.add(approval_model)
     session.commit()
 
+    # Called only to send emails
+    approver = body['approver']['uid']
+    ApprovalService.update_approval(approval_id, approver)
+
     result = ApprovalSchema().dump(approval_model)
     return result

crc/services/approval_service.py

@@ -111,13 +111,14 @@ class ApprovalService(object):
 
 
     @staticmethod
-    def update_approval(approval_id, approver_uid, status):
+    def update_approval(approval_id, approver_uid):
         """Update a specific approval"""
         db_approval = session.query(ApprovalModel).get(approval_id)
+        status = db_approval.status
         if db_approval:
-            db_approval.status = status
+            # db_approval.status = status
-            session.add(db_approval)
+            # session.add(db_approval)
-            session.commit()
+            # session.commit()
             if status == ApprovalStatus.APPROVED.value:
                 # second_approval = ApprovalModel().query.filter_by(
                 #     study_id=db_approval.study_id, workflow_id=db_approval.workflow_id,
@@ -125,7 +126,7 @@ class ApprovalService(object):
                 # if second_approval:
                     # send rrp approval request for second approver
                 ldap_service = LdapService()
-                pi_user_info = ldap_service.user_info(model.study.primary_investigator_id)
+                pi_user_info = ldap_service.user_info(db_approval.study.primary_investigator_id)
                 approver_info = ldap_service.user_info(approver_uid)
                 # send rrp submission
                 send_ramp_up_approved_email(
@@ -135,7 +136,7 @@ class ApprovalService(object):
                 )
             elif status == ApprovalStatus.DECLINED.value:
                 ldap_service = LdapService()
-                pi_user_info = ldap_service.user_info(model.study.primary_investigator_id)
+                pi_user_info = ldap_service.user_info(db_approval.study.primary_investigator_id)
                 approver_info = ldap_service.user_info(approver_uid)
                 # send rrp submission
                 send_ramp_up_denied_email(

crc/services/mails.py

@@ -11,7 +11,6 @@ def send_ramp_up_submission_email(sender, recipients, approver_1, approver_2=Non
         msg = Message('Research Ramp-up Plan Submitted',
               sender=sender,
               recipients=recipients)
-
         from crc import env, mail
         template = env.get_template('ramp_up_submission.txt')
         template_vars = {'approver_1': approver_1, 'approver_2': approver_2}
@@ -28,7 +27,6 @@ def send_ramp_up_approval_request_email(sender, recipients, primary_investigator
         msg = Message('Research Ramp-up Plan Approval Request',
               sender=sender,
               recipients=recipients)
-
         from crc import env, mail
         template = env.get_template('ramp_up_approval_request.txt')
         template_vars = {'primary_investigator': primary_investigator}
@@ -45,7 +43,6 @@ def send_ramp_up_approval_request_first_review_email(sender, recipients, primary
         msg = Message('Research Ramp-up Plan Approval Request',
               sender=sender,
               recipients=recipients)
-
         from crc import env, mail
         template = env.get_template('ramp_up_approval_request_first_review.txt')
         template_vars = {'primary_investigator': primary_investigator}

crc/static/templates/mails/ramp_up_denied.html

@@ -1 +1 @@
-<p>Your Research Ramp-up Plan has been denied by {{ approver_1 }}.  Please return to the Research Ramp-up Plan application and review the comments from {{ approver_1 }} on the home page.  Next, open the application and locate the first step where changes are needed.  Continue to complete additional steps saving your work along the way. Review your revised Research Ramp-up Plan and res-submit for approval.</p>
+<p>Your Research Ramp-up Plan has been denied by {{ approver }}.  Please return to the Research Ramp-up Plan application and review the comments from {{ approver }} on the home page.  Next, open the application and locate the first step where changes are needed.  Continue to complete additional steps saving your work along the way. Review your revised Research Ramp-up Plan and res-submit for approval.</p>

tests/test_approvals_api.py

@@ -105,7 +105,7 @@ class TestApprovals(BaseTest):
     def test_accept_approval(self):
         approval = session.query(ApprovalModel).filter_by(approver_uid='dhf8r').first()
         data = {'id': approval.id,
-                "approver_uid": "dhf8r",
+                "approver": {"uid": "dhf8r"},
                 'message': "Approved.  I like the cut of your jib.",
                 'status': ApprovalStatus.APPROVED.value}
 
@@ -126,7 +126,7 @@ class TestApprovals(BaseTest):
     def test_decline_approval(self):
         approval = session.query(ApprovalModel).filter_by(approver_uid='dhf8r').first()
         data = {'id': approval.id,
-                "approver_uid": "dhf8r",
+                "approver": {"uid": "dhf8r"},
                 'message': "Approved.  I find the cut of your jib lacking.",
                 'status': ApprovalStatus.DECLINED.value}