submissions

docker-compose.yml

@@ -41,10 +41,10 @@ services:
     dockerfile: services/server/dockerfiles/Dockerfile
   restart: always
   volumes:
+   - ./utils/dev.py:/flaski/flaski/apps/external.py # this needs to be the first volume as otherwise it will be overwritten by `- ./:/flaski`
    - data:/flaski_data/users
    - ./:/flaski
    - ~/flaski_private:/flaski_private:ro
-   - ./utils/dev.py:/flaski/flaski/apps/external.py
   environment:
    - LOGS=/var/log/flaski/
    - SECRET_KEY=${SECRET_KEY}

flaski/apps/main/submissions.py

@@ -1,9 +1,63 @@
-def check_rnaseq(df):
-  status=True
-  msg=None
+import pandas as pd
+import io
+from werkzeug.utils import secure_filename
+import re
+
+
+def check_rnaseq(EXC):
+  if "samples" not in EXC.sheet_names:
+    status=False
+    msg="Could not find sample information - 'samples' sheet - in the submission file."
+    return status, msg
+  metadata=EXC.parse("RNAseq")
+  email=metadata[  metadata["Field"] == "email"][ "Value" ].values[0]
+  email=str(email).rstrip().lstrip()
+  email=email.split(",")
+  email=[ re.search("([^@|\s]+@[^@]+\.[^@|\s]+)",e,re.I) for e in email ]
+  email=[ e.group(1) for e in email if e ]
+  if not email :
+    status=False
+    msg="Contact email is not a valid email. Please provide a valid email in the 'email' field of your submission file."
+    return status, msg
+  nas=metadata[metadata["Value"].isna()]["Field"].tolist()
+  if nas:
+    status=False
+    msg="The following fields require a valid value: {fields} ".format(fields=", ".join(nas) )
+    return status, msg
+
+  status="RNAseq"
+  msg="Submission successuful. Please check for email confirmation."
   return status, msg
 
-def submission_check(df, submission_type="RNAseq"):
-  if submission_type=="RNAseq":
-    status, msg=check_rnaseq(df)
+def submission_check(inputfile):
+  valid_submissions=["RNAseq"]
+
+  filename = secure_filename(inputfile.filename)
+  fileread = inputfile.read()
+  filestream=io.BytesIO(fileread)
+  extension=filename.rsplit('.', 1)[1].lower()
+  if extension != "xlsx":
+    status=False
+    msg="Wrong file extension detected."
+    return status, msg
+
+  EXC=pd.ExcelFile(filestream)
+  sheets=EXC.sheet_names
+  submission_type=[ s for s in sheets if s in valid_submissions ]
+  if len(submission_type) > 1 :
+    status=False
+    msg="More than one submission type detected."
+    return status, msg
+
+  elif len(submission_type) == 0 :
+    status=False
+    msg="This submission file did not contain a valid submission sheet. Make sure you do not change the sheet names when editing the submission file."
+    return status, msg
+
+  if submission_type[0]=="RNAseq":
+    status, msg=check_rnaseq(EXC)
+  else:
+    status=False
+    msg="Submission failed."
+
   return status, msg

flaski/apps/routes/submissions.py

@@ -1,4 +1,5 @@
 from flask import render_template, Flask, Response, request, url_for, redirect, session, send_file, flash, jsonify
+from flask import Markup
 from flaski import app
 from werkzeug.utils import secure_filename
 from flask_session import Session
@@ -7,9 +8,9 @@
 from datetime import datetime
 from flaski import db
 from werkzeug.urls import url_parse
-from flaski.apps.main.submission import submission_check #, submission_defaults
+from flaski.apps.main.submissions import submission_check #, submission_defaults
 from flaski.models import User, UserLogging
-from flaski.email import send_exception_email
+from flaski.email import send_exception_email, send_submission_email
 from flaski.routines import session_to_file, check_session_app, handle_exception, read_request, read_tables, allowed_file, read_argument_file, read_session_file
 
 
@@ -45,6 +46,7 @@ def submissions():
     reset_info=check_session_app(session,"submissions",apps)
     if reset_info:
         flash(reset_info,'error')
+
         # INITIATE SESSION
         session["filename"]="Select file.."
 
@@ -72,25 +74,27 @@ def submissions():
             #     flash(msg,"info")
 
             # if not request.files["inputsessionfile"] and not request.files["inputargumentsfile"] :
-            plot_arguments=read_request(request)
+            # plot_arguments=read_request(request)
 
             inputfile = request.files["inputfile"]
             if inputfile:
                 filename = secure_filename(inputfile.filename)
-                if allowed_file(inputfile.filename):
-                    df=read_tables(inputfile)
+                if not allowed_file(inputfile.filename):
+                    msg="This file is not allowed."
+                    flash(msg,"error")
+                    return render_template('/apps/submissions.html', apps=apps)
 
             # CALL FIGURE FUNCTION
-            status, msg=submission_check(df)
+            status, msg=submission_check(inputfile)
             if not status:
                 flash(msg,"error")
                 return render_template('/apps/submissions.html', apps=apps) #, **plot_arguments)
 
             if status:
                 flash(msg)
+                send_submission_email(user=current_user, submission_type=status, submission_file=inputfile)
                 return render_template('/apps/submissions.html', apps=apps) #, **plot_arguments)
 
-
             # return render_template('/apps/submissions.html', apps=apps, **plot_arguments)
 
         except Exception as e:
@@ -99,5 +103,6 @@ def submissions():
             return render_template('/apps/submissions.html', apps=apps) #, **plot_arguments)
 
     else:
-
+        initial_message=Markup('For submitting samples please follow the instructions in  <a href="https://github.com/mpg-age-bioinformatics/submissions/blob/main/README.md#submissions" class="alert-link">here</a>.')
+        flash(initial_message)
         return render_template('apps/submissions.html',  apps=apps) #, **session["plot_arguments"])

flaski/email.py

@@ -3,15 +3,23 @@
 from flaski import app
 from flask_mail import Message
 from flaski import mail
+from werkzeug.utils import secure_filename
+
 
 def send_async_email(app, msg):
     with app.app_context():
         mail.send(msg)
 
-def send_email(subject, sender, recipients, text_body, html_body, reply_to):
+def send_email(subject, sender, recipients, text_body, html_body, reply_to, attatchment=None):
     msg = Message(subject, sender=sender, recipients=recipients, reply_to = reply_to)
     msg.body = text_body
     msg.html = html_body
+    if attatchment:
+        msg.attach(
+            secure_filename(attatchment.filename),
+            'application/octect-stream',
+            attatchment.read())
+
     Thread(target=send_async_email, args=(app, msg)).start()
 
 def send_password_reset_email(user):
@@ -80,3 +88,15 @@ def send_help_email(user,eapp,emsg,etime,session_file):
                 html_body=render_template('email/app_help.html',
                                             user=user, eapp=eapp, emsg=emsg_html, etime=etime, session_file=session_file),\
                 reply_to=user.email )                                   
+
+def send_submission_email(user,submission_type,submission_file):
+    with app.app_context():
+        send_email('[Flaski][Automation][{submission_type}] Files have been submited for analysis.'.format(submission_type=submission_type),
+                sender=app.config['MAIL_USERNAME'],
+                recipients=[user.email,"[email protected]"],
+                text_body=render_template('email/submissions.txt',
+                                            user=user, submission_type=submission_type),
+                html_body=render_template('email/submissions.html',
+                                            user=user, submission_type=submission_type),\
+                reply_to='[email protected]',\
+                attatchment=submission_file   )

flaski/templates/apps/submissions.html

@@ -3,7 +3,7 @@
 {% block app_title %}
 
 <div class="d-none d-sm-inline-block form-inline mr-auto ml-md-3 my-2 my-md-0 mw-100">
-    <h1 class="h3 mb-0 text-gray-800">DAVID</h1>
+    <h1 class="h3 mb-0 text-gray-800">Submissions</h1>
 </div>
 
 {% endblock %}
@@ -36,7 +36,7 @@ <h1 class="h3 mb-0 text-gray-800">DAVID</h1>
 
     <div id="" style="overflow-y:auto;height:calc(100vh - 80px);">
 
-        <form action="{{ url_for('david') }}" method="post" enctype="multipart/form-data">
+        <form action="{{ url_for('submissions') }}" method="post" enctype="multipart/form-data">
 
             <!-- -------------------- INPUT FILE SELECTION ---------------------- -->
             <!-- Heading -->

flaski/templates/email/submissions.html

@@ -0,0 +1,6 @@
+<p>Files have been submitted by {{ user.firstname }} for {{ submission_type }} analysis.</p>
+<p>Submission form attached.</p>
+
+<br>
+<p>Cheers!</p>
+<p>Flaski</p>

flaski/templates/email/submissions.txt

@@ -0,0 +1,7 @@
+Files have been submitted by {{ user.firstname }} for {{ submission_type }} analysis.
+
+Submission form attached.
+
+Cheers!
+
+Flaski