Merge branch 'master' into feature-scheduler

.travis.yml

@@ -21,7 +21,6 @@ install:
 env:
   global:
     - TESTING=true
-    - PB_ENABLED=false
     - SQLALCHEMY_DATABASE_URI="postgresql://postgres:@localhost:5432/communicator_test"
 
 script:

Dockerfile

@@ -1,23 +1,20 @@
 FROM python:3.8-slim
 
-WORKDIR /app
+RUN apt-get update -q \
-COPY Pipfile Pipfile.lock /app/
+ && apt-get install -y -q \
-
+     gcc \
-RUN set -xe \
+     libssl-dev \
-  pip install pipenv \
+     curl \
-  && apt-get update -q \
+     postgresql-client \
-  && apt-get install -y -q \
+     gunicorn3
-        gcc python3-dev libssl-dev \
+RUN useradd _gunicorn --no-create-home --user-group
-        curl postgresql-client git-core \
-        gunicorn3 postgresql-client
-
-RUN set -xe \
-  pipenv install --dev \
-  && apt-get remove -y gcc python3-dev libssl-dev \
-  && apt-get autoremove -y \
-  && apt-get clean -y \
-  && rm -rf /var/lib/apt/lists/* \
-  && useradd _gunicorn --no-create-home --user-group
 
 COPY . /app/
 WORKDIR /app
+
+RUN chmod +x "/app/docker_run.sh" \
+  && pip install pipenv \
+  && pipenv install --dev --deploy --system --ignore-pipfile
+
+ENTRYPOINT ["/app/docker_run.sh"]
+

Pipfile

@@ -21,18 +21,24 @@ flask-mail = "*"
 flask-marshmallow = "*"
 flask-migrate = "*"
 flask-restful = "*"
+flask-wtf = "*"
+flask-table = "*"
 marshmallow = "*"
 marshmallow-enum = "*"
 marshmallow-sqlalchemy = "*"
 sentry-sdk = {extras = ["flask"],version = "==0.14.4"}
 swagger-ui-bundle = "*"
-spiffworkflow = {git = "https://github.com/sartography/SpiffWorkflow.git",ref = "master"}
 webtest = "*"
 python-box = "*"
 psycopg2-binary = "*"
 google-cloud-firestore = "*"
 globus-sdk = "*"
 apscheduler = "*"
+gunicorn = "*"
+twilio = "*"
+flask-paginate = "*"
+flask-assets = "*"
+pyscss = "*"
 
 [requires]
 python_version = "3.8"

Pipfile.lock

@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "11bbdfff553eecca38caef64677e8e9fb43705ea35b83f220c663cb8396d1cd6"
+            "sha256": "490cbcef70664a97232f019f8c20c17cea8035fac4904aa2e997c2f288832b87"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -55,6 +55,13 @@
             "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
             "version": "==20.2.0"
         },
+        "babel": {
+            "hashes": [
+                "sha256:1aac2ae2d0d8ea368fa90906567f5c08463d98ade155c0c4bfedd6a0f7160e38",
+                "sha256:d670ea0b10f8b723672d3a6abeb87b565b244da220d76b4dba1b66269ec152d4"
+            ],
+            "version": "==2.8.0"
+        },
         "bcrypt": {
             "hashes": [
                 "sha256:5b93c1726e50a93a033c36e5ca7fdcd29a5c7395af50a6892f5d9e7c6cfbfb29",
@@ -236,30 +243,30 @@
         },
         "cryptography": {
             "hashes": [
-                "sha256:10c9775a3f31610cf6b694d1fe598f2183441de81cedcf1814451ae53d71b13a",
+                "sha256:21b47c59fcb1c36f1113f3709d37935368e34815ea1d7073862e92f810dc7499",
-                "sha256:180c9f855a8ea280e72a5d61cf05681b230c2dce804c48e9b2983f491ecc44ed",
+                "sha256:451cdf60be4dafb6a3b78802006a020e6cd709c22d240f94f7a0696240a17154",
-                "sha256:247df238bc05c7d2e934a761243bfdc67db03f339948b1e2e80c75d41fc7cc36",
+                "sha256:4549b137d8cbe3c2eadfa56c0c858b78acbeff956bd461e40000b2164d9167c6",
-                "sha256:26409a473cc6278e4c90f782cd5968ebad04d3911ed1c402fc86908c17633e08",
+                "sha256:48ee615a779ffa749d7d50c291761dc921d93d7cf203dca2db663b4f193f0e49",
-                "sha256:2a27615c965173c4c88f2961cf18115c08fedfb8bdc121347f26e8458dc6d237",
+                "sha256:559d622aef2a2dff98a892eef321433ba5bc55b2485220a8ca289c1ecc2bd54f",
-                "sha256:2e26223ac636ca216e855748e7d435a1bf846809ed12ed898179587d0cf74618",
+                "sha256:5d52c72449bb02dd45a773a203196e6d4fae34e158769c896012401f33064396",
-                "sha256:321761d55fb7cb256b771ee4ed78e69486a7336be9143b90c52be59d7657f50f",
+                "sha256:65beb15e7f9c16e15934569d29fb4def74ea1469d8781f6b3507ab896d6d8719",
-                "sha256:4005b38cd86fc51c955db40b0f0e52ff65340874495af72efabb1bb8ca881695",
+                "sha256:680da076cad81cdf5ffcac50c477b6790be81768d30f9da9e01960c4b18a66db",
-                "sha256:4b9e96543d0784acebb70991ebc2dbd99aa287f6217546bb993df22dd361d41c",
+                "sha256:762bc5a0df03c51ee3f09c621e1cee64e3a079a2b5020de82f1613873d79ee70",
-                "sha256:548b0818e88792318dc137d8b1ec82a0ab0af96c7f0603a00bb94f896fbf5e10",
+                "sha256:89aceb31cd5f9fc2449fe8cf3810797ca52b65f1489002d58fe190bfb265c536",
-                "sha256:725875681afe50b41aee7fdd629cedbc4720bab350142b12c55c0a4d17c7416c",
+                "sha256:983c0c3de4cb9fcba68fd3f45ed846eb86a2a8b8d8bc5bb18364c4d00b3c61fe",
-                "sha256:7a63e97355f3cd77c94bd98c59cb85fe0efd76ea7ef904c9b0316b5bbfde6ed1",
+                "sha256:99d4984aabd4c7182050bca76176ce2dbc9fa9748afe583a7865c12954d714ba",
-                "sha256:94191501e4b4009642be21dde2a78bd3c2701a81ee57d3d3d02f1d99f8b64a9e",
+                "sha256:9d9fc6a16357965d282dd4ab6531013935425d0dc4950df2e0cf2a1b1ac1017d",
-                "sha256:969ae512a250f869c1738ca63be843488ff5cc031987d302c1f59c7dbe1b225f",
+                "sha256:a7597ffc67987b37b12e09c029bd1dc43965f75d328076ae85721b84046e9ca7",
-                "sha256:9f734423eb9c2ea85000aa2476e0d7a58e021bc34f0a373ac52a5454cd52f791",
+                "sha256:ab010e461bb6b444eaf7f8c813bb716be2d78ab786103f9608ffd37a4bd7d490",
-                "sha256:b45ab1c6ece7c471f01c56f5d19818ca797c34541f0b2351635a5c9fe09ac2e0",
+                "sha256:b12e715c10a13ca1bd27fbceed9adc8c5ff640f8e1f7ea76416352de703523c8",
-                "sha256:cc6096c86ec0de26e2263c228fb25ee01c3ff1346d3cfc219d67d49f303585af",
+                "sha256:b2bded09c578d19e08bd2c5bb8fed7f103e089752c9cf7ca7ca7de522326e921",
-                "sha256:dc3f437ca6353979aace181f1b790f0fc79e446235b14306241633ab7d61b8f8",
+                "sha256:b372026ebf32fe2523159f27d9f0e9f485092e43b00a5adacf732192a70ba118",
-                "sha256:e7563eb7bc5c7e75a213281715155248cceba88b11cb4b22957ad45b85903761",
+                "sha256:cb179acdd4ae1e4a5a160d80b87841b3d0e0be84af46c7bb2cd7ece57a39c4ba",
-                "sha256:e7dad66a9e5684a40f270bd4aee1906878193ae50a4831922e454a2a457f1716",
+                "sha256:e97a3b627e3cb63c415a16245d6cef2139cca18bb1183d1b9375a1c14e83f3b3",
-                "sha256:eb80a288e3cfc08f679f95da72d2ef90cb74f6d8a8ba69d2f215c5e110b2ca32",
+                "sha256:f0e099fc4cc697450c3dd4031791559692dd941a95254cb9aeded66a7aa8b9bc",
-                "sha256:fa7fbcc40e2210aca26c7ac8a39467eae444d90a2c346cbcffd9133a166bcc67"
+                "sha256:f99317a0fa2e49917689b8cf977510addcfaaab769b3f899b9c481bbd76730c2"
             ],
-            "version": "==3.1"
+            "version": "==3.1.1"
         },
         "docxtpl": {
             "hashes": [
@@ -284,6 +291,21 @@
             "index": "pypi",
             "version": "==1.5.6"
         },
+        "flask-assets": {
+            "hashes": [
+                "sha256:1dfdea35e40744d46aada72831f7613d67bf38e8b20ccaaa9e91fdc37aa3b8c2",
+                "sha256:2845bd3b479be9db8556801e7ebc2746ce2d9edb4e7b64a1c786ecbfc1e5867b"
+            ],
+            "index": "pypi",
+            "version": "==2.0"
+        },
+        "flask-babel": {
+            "hashes": [
+                "sha256:e6820a052a8d344e178cdd36dd4bb8aea09b4bda3d5f9fa9f008df2c7f2f5468",
+                "sha256:f9faf45cdb2e1a32ea2ec14403587d4295108f35017a7821a2b1acb8cfd9257d"
+            ],
+            "version": "==2.0.0"
+        },
         "flask-bcrypt": {
             "hashes": [
                 "sha256:d71c8585b2ee1c62024392ebdbc447438564e2c8c02b4e57b56a4cafd8d13c5f"
@@ -322,6 +344,13 @@
             "index": "pypi",
             "version": "==2.5.3"
         },
+        "flask-paginate": {
+            "hashes": [
+                "sha256:4d5c746e4f7b639a9bb72fac0c2452d58e5297b88d6ecda3340153a59453d581"
+            ],
+            "index": "pypi",
+            "version": "==0.7.0"
+        },
         "flask-restful": {
             "hashes": [
                 "sha256:5ea9a5991abf2cb69b4aac19793faac6c032300505b325687d7c305ffaa76915",
@@ -344,6 +373,20 @@
             ],
             "markers": "python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'",
             "version": "==0.18.2"
+        "flask-table": {
+            "hashes": [
+                "sha256:320e5756cd7252e902e03b6cd1087f2c7ebc31364341b482f41f30074d10a770"
+            ],
+            "index": "pypi",
+            "version": "==0.5.0"
+        },
+        "flask-wtf": {
+            "hashes": [
+                "sha256:57b3faf6fe5d6168bda0c36b0df1d05770f8e205e18332d0376ddb954d17aef2",
+                "sha256:d417e3a0008b5ba583da1763e4db0f55a1269d9dd91dcc3eb3c026d3c5dbd720"
+            ],
+            "index": "pypi",
+            "version": "==0.14.3"
         },
         "globus-sdk": {
             "hashes": [
@@ -440,6 +483,14 @@
             ],
             "version": "==1.32.0"
         },
+        "gunicorn": {
+            "hashes": [
+                "sha256:1904bb2b8a43658807108d59c3f3d56c2b6121a701161de0ddf9ad140073c626",
+                "sha256:cd4a810dd51bf497552cf3f863b575dabd73d6ad6a91075b65936b151cbf4f9c"
+            ],
+            "index": "pypi",
+            "version": "==20.0.4"
+        },
         "idna": {
             "hashes": [
                 "sha256:b307872f855b18632ce0c21c5e45be78c0ea7ae4c15c828c20788b26921eb3f6",
@@ -448,6 +499,14 @@
             "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
             "version": "==2.10"
         },
+        "importlib-metadata": {
+            "hashes": [
+                "sha256:77a540690e24b0305878c37ffd421785a6f7e53c8b5720d211b211de8d0e95da",
+                "sha256:cefa1a2f919b866c5beb7c9f7b0ebb4061f30a8a9bf16d609b000e2dfaceb9c3"
+            ],
+            "markers": "python_version < '3.8'",
+            "version": "==2.0.0"
+        },
         "inflection": {
             "hashes": [
                 "sha256:1a29730d366e996aaacffb2f1f1cb9593dc38e2ddd30c91250c6dde09ea9b417",
@@ -725,6 +784,13 @@
             "markers": "python_version >= '3.5'",
             "version": "==0.17.3"
         },
+        "pyscss": {
+            "hashes": [
+                "sha256:f1df571569021a23941a538eb154405dde80bed35dc1ea7c5f3e18e0144746bf"
+            ],
+            "index": "pypi",
+            "version": "==1.3.7"
+        },
         "python-box": {
             "hashes": [
                 "sha256:b7a6f3edd2f71e2475d93163b6465f637a2714b155acafef17408b06e55282b3",
@@ -829,10 +895,6 @@
             "markers": "python_version >= '3.5'",
             "version": "==2.0.1"
         },
-        "spiffworkflow": {
-            "git": "https://github.com/sartography/SpiffWorkflow.git",
-            "ref": "cfd1b994ac3bcc7f1d6459b00ab7455b76b942bc"
-        },
         "sqlalchemy": {
             "hashes": [
                 "sha256:072766c3bd09294d716b2d114d46ffc5ccf8ea0b714a4e1c48253014b771c6bb",
@@ -885,6 +947,12 @@
                 "sha256:e2cb6c6b5b604af38597403e9852872d7f534962ae2954c7f35efcb1ccacf4a4"
             ],
             "version": "==2.1"
+        "twilio": {
+            "hashes": [
+                "sha256:df1cf8f7e62fbe4d412e66204ee7f948cd31ff18173ff4690475834174eedaf0"
+            ],
+            "index": "pypi",
+            "version": "==6.45.3"
         },
         "urllib3": {
             "hashes": [
@@ -910,6 +978,13 @@
             "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
             "version": "==1.4.4"
         },
+        "webassets": {
+            "hashes": [
+                "sha256:167132337677c8cedc9705090f6d48da3fb262c8e0b2773b29f3352f050181cd",
+                "sha256:a31a55147752ba1b3dc07dee0ad8c8efff274464e08bbdb88c1fd59ffd552724"
+            ],
+            "version": "==2.0"
+        },
         "webob": {
             "hashes": [
                 "sha256:a3c89a8e9ba0aeb17382836cdb73c516d0ecf6630ec40ec28288f3ed459ce87b",
@@ -940,6 +1015,13 @@
                 "sha256:81195de0ac94fbc8368abbaf9197b88c4f3ffd6c2719b5bf5fc9da744f3d829c"
             ],
             "version": "==2.3.3"
+        },
+        "zipp": {
+            "hashes": [
+                "sha256:43f4fa8d8bb313e65d8323a3952ef8756bf40f9a5c3ea7334be23ee4ec8278b6",
+                "sha256:b52f22895f4cfce194bc8172f3819ee8de7540aa6d873535a8668b730b8b411f"
+            ],
+            "version": "==3.2.0"
         }
     },
     "develop": {
@@ -991,6 +1073,14 @@
             "index": "pypi",
             "version": "==5.3"
         },
+        "importlib-metadata": {
+            "hashes": [
+                "sha256:77a540690e24b0305878c37ffd421785a6f7e53c8b5720d211b211de8d0e95da",
+                "sha256:cefa1a2f919b866c5beb7c9f7b0ebb4061f30a8a9bf16d609b000e2dfaceb9c3"
+            ],
+            "markers": "python_version < '3.8'",
+            "version": "==2.0.0"
+        },
         "iniconfig": {
             "hashes": [
                 "sha256:80cf40c597eb564e86346103f609d74efce0f6b4d4f30ec8ce9e2c26411ba437",
@@ -1068,6 +1158,13 @@
                 "sha256:bda89d5935c2eac546d648028b9901107a595863cb36bae0c73ac804a9b4ce88"
             ],
             "version": "==0.10.1"
+        },
+        "zipp": {
+            "hashes": [
+                "sha256:43f4fa8d8bb313e65d8323a3952ef8756bf40f9a5c3ea7334be23ee4ec8278b6",
+                "sha256:b52f22895f4cfce194bc8172f3819ee8de7540aa6d873535a8668b730b8b411f"
+            ],
+            "version": "==3.2.0"
         }
     }
 }

communicator/__init__.py

@@ -3,13 +3,16 @@ import os
 
 import connexion
 import sentry_sdk
+from flask import render_template, request, redirect, url_for
+from flask_assets import Environment
 from flask_cors import CORS
 from flask_mail import Mail
 from flask_marshmallow import Marshmallow
 from flask_migrate import Migrate
+from flask_paginate import Pagination, get_page_parameter
 from flask_sqlalchemy import SQLAlchemy
 from sentry_sdk.integrations.flask import FlaskIntegration
-
+from webassets import Bundle
 
 logging.basicConfig(level=logging.INFO)
 
@@ -34,8 +37,31 @@ db = SQLAlchemy(app)
 migrate = Migrate(app, db)
 ma = Marshmallow(app)
 
+# Asset management
+url_map = app.url_map
+try:
+    for rule in url_map.iter_rules('static'):
+        url_map._rules.remove(rule)
+except ValueError:
+    # no static view was created yet
+    pass
+app.add_url_rule(
+    app.static_url_path + '/<path:filename>',
+    endpoint='static', view_func=app.send_static_file)
+assets = Environment(app)
+assets.init_app(app)
+assets.url = app.static_url_path
+scss = Bundle(
+    'scss/app.scss',
+    filters='pyscss',
+    output='app.css'
+)
+assets.register('app_scss', scss)
+
 from communicator import models
 from communicator import api
+from communicator import forms
+
 connexion_app.add_api('api.yml', base_path='/v1.0')
 
 # Convert list of allowed origins to list of regexes
@@ -50,6 +76,88 @@ if app.config['SENTRY_ENVIRONMENT']:
         integrations=[FlaskIntegration()]
     )
 
+### HTML Pages
+BASE_HREF = app.config['APPLICATION_ROOT'].strip('/')
+
+
+@app.route('/', methods=['GET'])
+def index():
+    from communicator.models import Sample
+    from communicator.tables import SampleTable
+    # display results
+    page = request.args.get(get_page_parameter(), type=int, default=1)
+    samples = db.session.query(Sample).order_by(Sample.date.desc())
+    pagination = Pagination(page=page, total=samples.count(), search=False, record_name='samples')
+
+    table = SampleTable(samples.paginate(page,10,error_out=False).items)
+    return render_template(
+        'index.html',
+        table=table,
+        pagination=pagination,
+        base_href=BASE_HREF
+    )
+
+@app.route('/invitation', methods=['GET', 'POST'])
+def send_invitation():
+    from communicator.models.invitation import Invitation
+    from communicator.tables import InvitationTable
+
+    form = forms.InvitationForm(request.form)
+    action = BASE_HREF + "/invitation"
+    title = "Send invitation to students"
+    if request.method == 'POST' and form.validate():
+        from communicator.services.notification_service import NotificationService
+        with NotificationService(app) as ns:
+            ns.send_invitations(form.date.data, form.location.data, form.emails.data)
+            return redirect(url_for('send_invitation'))
+    # display results
+    page = request.args.get(get_page_parameter(), type=int, default=1)
+    invites = db.session.query(Invitation).order_by(Invitation.date_sent.desc())
+    pagination = Pagination(page=page, total=invites.count(), search=False, record_name='samples')
+
+    table = InvitationTable(invites.paginate(page,10,error_out=False).items)
+
+    return render_template(
+        'form.html',
+        form=form,
+        table=table,
+        pagination=pagination,
+        action=action,
+        title=title,
+        description_map={},
+        base_href=BASE_HREF
+    )
+
+@app.route('/imported_files', methods=['GET'])
+def list_imported_files_from_ivy():
+    from communicator.models.ivy_file import IvyFile
+    from communicator.tables import IvyFileTable
+
+    # display results
+    page = request.args.get(get_page_parameter(), type=int, default=1)
+    files = db.session.query(IvyFile).order_by(IvyFile.date_added.desc())
+    pagination = Pagination(page=page, total=files.count(), search=False, record_name='samples')
+
+    table = IvyFileTable(files.paginate(page, 10, error_out=False).items)
+    return render_template(
+        'imported_files.html',
+        table=table,
+        pagination=pagination,
+        base_href=BASE_HREF
+    )
+
+@app.route('/sso')
+def sso():
+    response = ""
+    response += "<h1>Headers</h1>"
+    response += "<ul>"
+    for k, v in request.headers:
+        response += "<li><b>%s</b> %s</li>\n" % (k, v)
+    response += "<h1>Environment</h1>"
+    for k, v in request.environ:
+        response += "<li><b>%s</b> %s</li>\n" % (k, v)
+    return response
+
 # Access tokens
 @app.cli.command()
 def globus_token():
@@ -57,18 +165,21 @@ def globus_token():
     ivy_service = IvyService()
     ivy_service.get_access_token()
 
+
 @app.cli.command()
 def list_files():
     from communicator.services.ivy_service import IvyService
     ivy_service = IvyService()
     ivy_service.list_files()
 
+
 @app.cli.command()
 def transfer():
     from communicator.services.ivy_service import IvyService
     ivy_service = IvyService()
     ivy_service.request_transfer()
 
+
 @app.cli.command()
 def delete():
     from communicator.services.ivy_service import IvyService

communicator/api.yml

@@ -6,8 +6,6 @@ info:
     name: MIT
 servers:
   - url: http://localhost:5000/v1.0
-security:
-  - jwt: ['secret']
 paths:
   /status:
     get:
@@ -45,10 +43,52 @@ paths:
             text/plain:
               schema:
                 type: string
-
+  /sample:
+    post:
+      operationId: communicator.api.admin.add_sample
+      summary: Creates a new sample
+      tags:
+        - Samples
+      requestBody:
+        content:
+          application/json:
+            schema:
+              $ref: '#/components/schemas/Sample'
+      responses:
+        '200':
+          description: Sample created successfully
+          content:
+            application/json:
+              schema:
+                type: array
+                items:
+                  $ref: "#/components/schemas/Sample"
+    delete:
+      operationId: communicator.api.admin.clear_samples
+      summary: Removes the given samples completely.
+      tags:
+        - Studies
+      responses:
+        '204':
+          description: All Samples removed.
 components:
   schemas:
     Status:
       properties:
         status:
-          type: string
+          type: string
+    Sample:
+      properties:
+        barcode:
+          type: string
+          example: "000000111-202009091449-4321"
+        student_id:
+          type: string
+          example: "000000111"
+        date:
+          type: string
+          format: date_time
+          example: "2019-12-25T09:12:33.001Z"
+        location:
+          type: string
+          example: "0001"

communicator/api/admin.py

@@ -12,16 +12,25 @@ from communicator.services.sample_service import SampleService
 def status():
     return {"status":"good"}
 
+def add_sample(body):
+    sample = Sample(barcode=body['barcode'],
+                    student_id=body['student_id'],
+                    date=body['date'],
+                    location=body['location'])
+    db.session.add(sample)
+    db.session.commit()
+
+def clear_samples():
+    db.session.query(Sample).delete()
+    db.session.commit()
 
 def update_data():
-    """Updates the database based on local files placed by IVY and recoreds
+    """Updates the database based on local files placed by IVY.  No longer attempts
-    read in from the firecloud database."""
+    to pull files from the Firebase service."""
-    fb_service = FirebaseService()
     ivy_service = IvyService()
-
+    samples = ivy_service.load_directory()
-    samples = fb_service.get_samples()
-    samples.extend(ivy_service.load_directory())
     SampleService().add_or_update_records(samples)
+    db.session.commit()
 
 
 def notify_by_email():

communicator/forms.py

@@ -0,0 +1,20 @@
+import re
+
+from flask_table import Table, Col, LinkCol, BoolCol, DatetimeCol, NestedTableCol
+from flask_wtf import FlaskForm
+from wtforms import SelectMultipleField, StringField, BooleanField, SelectField, validators, HiddenField, TextAreaField, \
+    ValidationError
+from wtforms.widgets import TextArea
+
+
+class InvitationForm(FlaskForm):
+    location = StringField('Location (ex. Newcomb Hall, South Meeting Room)', [validators.DataRequired()])
+    date = StringField('Date (ex. Monday, September 23 from 10:00 am-5:00 pm ', [validators.DataRequired()])
+    emails = TextAreaField('Emails (newline delimited)', render_kw={'rows': 10, 'cols': 50})
+
+    def validate_emails(form, field):
+        all_emails = field.data.splitlines()
+        EMAIL_REGEX = re.compile('^[a-z0-9]+[._a-z0-9]+[@]\w+[.]\w{2,3}$')
+        for email in all_emails:
+            if not re.search(EMAIL_REGEX, email):
+                raise ValidationError(f'Invalid email \'{email}\', Emails must each be on a seperate line.')

communicator/models/invitation.py

@@ -0,0 +1,11 @@
+from sqlalchemy import func
+
+from communicator import db
+
+
+class Invitation(db.Model):
+    id = db.Column(db.Integer, primary_key=True)
+    date_sent = db.Column(db.DateTime(timezone=True), default=func.now())
+    location = db.Column(db.String)
+    date = db.Column(db.String)
+    total_recipients = db.Column(db.Integer)

communicator/models/ivy_file.py

@@ -0,0 +1,9 @@
+from sqlalchemy import func
+
+from communicator import db
+
+
+class IvyFile(db.Model):
+    file_name = db.Column(db.String, primary_key=True)
+    date_added = db.Column(db.DateTime(timezone=True), default=func.now())
+    sample_count = db.Column(db.Integer)

communicator/services/firebase_service.py

@@ -1,7 +1,5 @@
 import json
-import os
 
-from google.auth.credentials import Credentials
 from google.cloud import firestore
 from google.oauth2 import service_account
 
@@ -18,7 +16,6 @@ class FirebaseService(object):
         self.db = firestore.Client(project="uva-covid19-testing-kiosk",
                                    credentials= credentials)
 
-
     def get_samples(self):
         # Then query for documents
         fb_samples = self.db.collection(u'samples')

communicator/services/ivy_service.py

@@ -1,10 +1,12 @@
 import csv
+from datetime import datetime
 
 import globus_sdk
 from dateutil import parser
 
-from communicator import app
+from communicator import app, db
 from communicator.errors import CommError
+from communicator.models.ivy_file import IvyFile
 from communicator.models.sample import Sample
 from os import listdir
 from os.path import isfile, join
@@ -22,16 +24,20 @@ class IvyService(object):
         self.GLOBUS_IVY_ENDPOINT = app.config['GLOBUS_IVY_ENDPOINT']
         self.GLOBUS_DTN_ENDPOINT = app.config['GLOBUS_DTN_ENDPOINT']
 
-        print("Client ID:" + self.GLOBUS_CLIENT_ID)
-
-        self.client = globus_sdk.NativeAppAuthClient(self.GLOBUS_CLIENT_ID)
-        self.client.oauth2_start_flow(refresh_tokens=True)
 
     def load_directory(self):
         onlyfiles = [f for f in listdir(self.path) if isfile(join(self.path, f))]
         samples = []
-        for file in onlyfiles:
+        for file_name in onlyfiles:
-            samples.extend(IvyService.samples_from_ivy_file(join(self.path, file)))
+            samples = IvyService.samples_from_ivy_file(join(self.path, file_name))
+            ivy_file = db.session.query(IvyFile).filter(IvyFile.file_name == file_name).first()
+            if not ivy_file:
+                ivy_file = IvyFile(file_name=file_name, sample_count=len(samples))
+            else:
+                ivy_file.date_added = datetime.now()
+                ivy_file.sample_count = len(samples)
+            db.session.add(ivy_file)
+            db.session.commit()
         return samples
 
     @staticmethod
@@ -102,6 +108,9 @@ class IvyService(object):
 
 
     def get_transfer_client(self):
+        self.client = globus_sdk.NativeAppAuthClient(self.GLOBUS_CLIENT_ID)
+        self.client.oauth2_start_flow(refresh_tokens=True)
+
         authorizer = globus_sdk.RefreshTokenAuthorizer(
             self.GLOBUS_TRANSFER_RT, self.client, access_token=self.GLOBUS_TRANSFER_AT, expires_at=self.EXPIRES_AT)
         tc = globus_sdk.TransferClient(authorizer=authorizer)

communicator/services/notification_service.py

@@ -3,24 +3,105 @@ import uuid
 from email.header import Header
 from email.mime.multipart import MIMEMultipart
 from email.mime.text import MIMEText
+import re
 
 from flask import render_template
-from flask_mail import Message
+from twilio.rest import Client
 
-from communicator import db, mail, app
+from communicator import app, db
-from communicator.errors import ApiError, CommError
+from communicator.errors import CommError
+from communicator.models.invitation import Invitation
 
 TEST_MESSAGES = []
 
+
 class NotificationService(object):
-    """Provides common tools for working with an Email"""
+    """Provides common tools for working with email and text messages, please use this
+    using the "with" syntax, to assure connections are properly closed.
+    ex:
+
+    with NotificationService() as notifier:
+        notifier.send_result_email(sample)
+        notifier.send_result_text(sample)
+
+    """
 
     def __init__(self, app):
         self.app = app
         self.sender = app.config['MAIL_SENDER']
+        self.BASE_HREF = app.config['APPLICATION_ROOT'].strip('/')
+
+    def __enter__(self):
+        if 'TESTING' in self.app.config and self.app.config['TESTING']:
+            return self
+        self.email_server = self._get_email_server()
+        self.twilio_client = self._get_twilio_client()
+        return self
+
+    def __exit__(self, exc_type, exc_value, traceback):
+        if 'TESTING' in self.app.config and self.app.config['TESTING']:
+            return
+        self.email_server.close()
+        # No way to close the twilio client that I can see.
+
+    def get_link(self, sample):
+        return f"https://besafe.virginia.edu/result-demo?code={sample.result_code}"
+
+    def send_result_sms(self, sample):
+        link = self.get_link(sample)
+        message = self.twilio_client.messages.create(
+            to=sample.phone,
+            from_=self.app.config['TWILIO_NUMBER'],
+            body=f"You have an important notification from UVA Be Safe, please visit: {link}")
+        print(message.sid)
+
+    def send_result_email(self, sample):
+        link = self.get_link(sample)
+        subject = "UVA: BE SAFE Notification"
+        tracking_code = self._tracking_code()
+        text_body = render_template("result_email.txt",
+                                    link=link,
+                                    base_url = self.BASE_HREF,
+                                    sample=sample,
+                                    tracking_code=tracking_code)
+
+        html_body = render_template("result_email.html",
+                                    link=link,
+                                    base_url = self.BASE_HREF,
+                                    sample=sample,
+                                    tracking_code=tracking_code)
+
+        self._send_email(subject, recipients=[sample.email], text_body=text_body, html_body=html_body)
+
+        return tracking_code
+
+    def send_invitations(self, date, location, email_string):
+        emails = email_string.splitlines()
+        subject = "UVA: BE SAFE - Appointment"
+        tracking_code = self._tracking_code()
+        text_body = render_template("invitation_email.txt",
+                                    date=date,
+                                    location=location,
+                                    base_url = self.BASE_HREF,
+                                    tracking_code=tracking_code)
+
+        html_body = render_template("invitation_email.html",
+                                    date=date,
+                                    location=location,
+                                    base_url = self.BASE_HREF,
+                                    tracking_code=tracking_code)
+
+        self._send_email(subject, recipients=[self.sender], bcc=emails, text_body=text_body, html_body=html_body)
+
+        invitation_log = Invitation(location=location, date=date, total_recipients=len(emails))
+        db.session.add(invitation_log)
+        db.session.commit()
+
+    def _tracking_code(self):
+        return str(uuid.uuid4())[:16]
+
+    def _get_email_server(self):
 
-    def email_server(self):
-        print("Server:" + self.app.config['MAIL_SERVER'])
         server = smtplib.SMTP(host=self.app.config['MAIL_SERVER'],
                               port=self.app.config['MAIL_PORT'],
                               timeout=self.app.config['MAIL_TIMEOUT'])
@@ -32,30 +113,11 @@ class NotificationService(object):
                          self.app.config['MAIL_PASSWORD'])
         return server
 
-    def tracking_code(self):
+    def _get_twilio_client(self):
-        return str(uuid.uuid4())[:16]
+        return Client(self.app.config['TWILIO_SID'],
+                      self.app.config['TWILIO_TOKEN'])
 
-    def send_result_email(self, sample):
+    def _send_email(self, subject, recipients, text_body, html_body, bcc=[], sender=None, ical=None):
-        subject = "UVA: BE SAFE Notification"
-        link = f"https://besafe.virginia.edu/result-demo?code={sample.result_code}"
-        tracking_code = self.tracking_code()
-        text_body = render_template("result_email.txt",
-                                    link=link,
-                                    sample=sample,
-                                    tracking_code=tracking_code)
-
-        html_body = render_template("result_email.html",
-                                    link=link,
-                                    sample=sample,
-                                    tracking_code=tracking_code)
-
-        self.send_email(subject, recipients=[sample.email], text_body=text_body, html_body=html_body)
-
-        return tracking_code
-
-
-
-    def send_email(self, subject, recipients, text_body, html_body, sender=None, ical=None):
         msgRoot = MIMEMultipart('related')
         msgRoot.set_charset('utf8')
 
@@ -78,9 +140,9 @@ class NotificationService(object):
 
         # Leaving this on here, just in case we need it later.
         if ical:
-            ical_atch = MIMEText(ical.decode("utf-8"),'calendar')
+            ical_atch = MIMEText(ical.decode("utf-8"), 'calendar')
-            ical_atch.add_header('Filename','event.ics')
+            ical_atch.add_header('Filename', 'event.ics')
-            ical_atch.add_header('Content-Disposition','attachment; filename=event.ics')
+            ical_atch.add_header('Content-Disposition', 'attachment; filename=event.ics')
             msgRoot.attach(ical_atch)
 
         if 'TESTING' in self.app.config and self.app.config['TESTING']:
@@ -88,12 +150,11 @@ class NotificationService(object):
             TEST_MESSAGES.append(msgRoot)
             return
 
+        all_recipients = recipients + bcc
+
         try:
-            server = self.email_server()
+            self.email_server.sendmail(sender, all_recipients, msgRoot.as_bytes())
-            server.sendmail(sender, recipients, msgRoot.as_bytes())
-            server.quit()
         except Exception as e:
             app.logger.error('An exception happened in EmailService', exc_info=True)
             app.logger.error(str(e))
             raise CommError(5000, f"failed to send email to {', '.join(recipients)}", e)
-

communicator/static/app.css

@@ -0,0 +1,201 @@
+.mat-icon {
+  font-family: 'Material Icons', sans-serif;
+  font-size: 24px; }
+
+  .text-center {
+    text-align: center; }
+
+    html, body {
+      padding: 1em;
+      margin: 0;
+      font-family: Arial, sans-serif;
+      font-size: 16px; }
+
+      table {
+        border: 1px solid #cacaca;
+        background-color: white;
+        width: 100%;
+        text-align: left;
+        border-collapse: collapse; }
+        table th, table td {
+          padding: 0.5em; }
+          table td, table.blueTable th {
+            border: 1px solid #cacaca; }
+            table tbody td {
+              font-size: 14px; }
+              table tr:nth-child(even) {
+                background: #ededed; }
+                table thead {
+                  background-color: #495e9d; }
+                  table thead th {
+                    font-size: 16px;
+                    font-weight: bold;
+                    color: white;
+                    border-left: 1px solid #cacaca; }
+        table thead th:first-child {
+          border-left: none; }
+          table tfoot {
+            font-size: 16px;
+            font-weight: bold;
+            color: white;
+            background-color: #cacaca; }
+            table tfoot td {
+              font-size: 16px; }
+              table tfoot .links {
+                text-align: right; }
+                table tfoot .links a {
+                  display: inline-block;
+                  background: #495e9d;
+                  color: white;
+                  padding: 2px 8px;
+                  border-radius: 5px; }
+
+.btn {
+  font-size: 16px;
+  padding: 0.5em 1em;
+  border-radius: 5px;
+  text-decoration: none;
+  color: white;
+  white-space: nowrap;
+  border: none; }
+  .btn:hover {
+    text-decoration: none; }
+    .btn.btn-icon {
+      font-family: 'Material Icons', sans-serif;
+      font-size: 24px;
+      border: none; }
+      .btn.btn-icon.btn-default {
+        color: #4e4e4e;
+        background-color: transparent;
+        border: none; }
+        .btn.btn-icon.btn-default:hover {
+          color: #373737;
+          background-color: transparent; }
+      .btn.btn-icon.btn-primary {
+        color: #232D4B;
+        background-color: transparent; }
+        .btn.btn-icon.btn-primary:hover {
+          color: #191f34;
+          background-color: transparent; }
+      .btn.btn-icon.btn-accent {
+        color: #E57200;
+        background-color: transparent; }
+        .btn.btn-icon.btn-accent:hover {
+          color: #a05000;
+          background-color: transparent; }
+      .btn.btn-icon.btn-warn {
+        color: #DF1E43;
+        background-color: transparent; }
+        .btn.btn-icon.btn-warn:hover {
+          color: #9c152f;
+          background-color: transparent; }
+  .btn.btn-default {
+    color: #373737;
+    background-color: white;
+    border: 1px solid #cacaca; }
+    .btn.btn-default:hover {
+      background-color: #ededed; }
+  .btn.btn-primary {
+    background-color: #232D4B; }
+    .btn.btn-primary:hover {
+      background-color: #191f34; }
+  .btn.btn-warn {
+    background-color: #DF1E43; }
+    .btn.btn-warn:hover {
+      background-color: #9c152f; }
+  .btn.btn-accent {
+    background-color: #E57200; }
+    .btn.btn-accent:hover {
+      background-color: #a05000; }
+
+select.multi {
+  height: 600px; }
+
+  .form-field {
+    display: flex;
+    max-width: 100vw;
+    margin-bottom: 40px;
+    padding: 2em; }
+    .form-field.hidden {
+      display: none; }
+      .form-field:nth-child(even) {
+        background-color: #ededed; }
+        .form-field .form-field-label, .form-field .form-field-help,
+        .form-field .form-field-input {
+          width: 30%;
+          text-align: left;
+          margin-right: 24px; }
+          .form-field .form-field-label {
+            font-weight: bold;
+            text-align: right; }
+            .form-field .form-field-input input {
+              width: 100%;
+              text-align: left; }
+              .form-field .form-field-input input[type=checkbox] {
+                width: 24px; }
+    .form-field .form-field-help {
+      font-style: italic; }
+      .form-field .form-field-error {
+        color: #DF1E43; }
+
+.alert {
+  padding: 20px;
+  background-color: #4e4e4e;
+  color: white;
+  margin-bottom: 15px;
+  opacity: 1;
+  border-radius: 5px;
+  transform: scale3d(1, 1, 1);
+  transition: all 0.5s ease-in-out; }
+  .alert.warn {
+    background-color: #DF1E43; }
+    .alert.success {
+      background-color: #64B343; }
+      .alert.info {
+        background-color: #cacaca;
+        color: black; }
+        .alert .btn-close {
+          margin-left: 15px;
+          color: white;
+          font-weight: bold;
+          float: right;
+          font-size: 22px;
+          line-height: 20px;
+          cursor: pointer;
+          transition: 0.3s; }
+          .alert .btn-close:hover {
+            color: black; }
+  .alert.fade-out {
+    opacity: 0; }
+    .alert.shrink {
+      transform: scale3d(0, 0, 0);
+      padding: 0;
+      margin: 0; }
+
+.highlight {
+  font-weight: bolder;
+  font-style: italic; }
+
+  .pagination-page-info {
+    padding: 0.6em;
+    padding-left: 0;
+    width: 40em;
+    margin: 0.5em;
+    margin-left: 0;
+    font-size: 12px; }
+
+    .pagination-page-info b {
+      color: black;
+      background: #6aa6ed;
+      padding-left: 2px;
+      padding: 0.1em 0.25em;
+      font-size: 150%; }
+
+      .pagination ul li {
+        display: inline-block;
+        width: 30px;
+        height: 20px;
+        border: 1px solid black;
+        text-align: center; }
+        .pagination ul li.active {
+          background-color: #ededed; }

communicator/static/scss/app.scss

@@ -0,0 +1,334 @@
+// COLOR PALETTE
+
+// gray
+$color-gray: #4e4e4e;
+$color-gray-light-2: scale-color($color-gray, $lightness: +90%);
+$color-gray-light-1: scale-color($color-gray, $lightness: +70%);
+$color-gray-light: $color-gray-light-1;
+$color-gray-dark: scale-color($color-gray, $lightness: -30%);
+
+// primary (UVA "Jefferson Blue")
+$color-primary: #232D4B;
+$color-primary-light: scale-color($color-primary, $lightness: +30%);
+$color-primary-dark: scale-color($color-primary, $lightness: -30%);
+
+// accent (UVA "Rotunda Orange")
+$color-accent: #E57200;
+$color-accent-light: scale-color($color-accent, $lightness: +30%);
+$color-accent-dark: scale-color($color-accent, $lightness: -30%);
+
+// warn (UVA "Emergency Red")
+$color-warn: #DF1E43;
+$color-warn-light: scale-color($color-warn, $lightness: +30%);
+$color-warn-dark: scale-color($color-warn, $lightness: -30%);
+
+// success (Green)
+$color-success: #64B343;
+$color-success-light: scale-color($color-success, $lightness: +30%);
+$color-success-dark: scale-color($color-success, $lightness: -30%);
+
+$font-size-default: 16px;
+$font-size-lg: 24px;
+$font-size-md: 16px;
+$font-size-sm: 14px;
+
+@mixin mat-icon {
+  font-family: 'Material Icons', sans-serif;
+  font-size: $font-size-lg;
+}
+
+.mat-icon {
+  @include mat-icon;
+}
+
+.text-center {
+  text-align: center;
+}
+
+html, body {
+  padding: 1em;
+  margin: 0;
+  font-family: Arial, sans-serif;
+  font-size: $font-size-default;
+}
+
+table {
+  border: 1px solid $color-gray-light;
+  background-color: white;
+  width: 100%;
+  text-align: left;
+  border-collapse: collapse;
+
+  th, td {
+    padding: 0.5em;
+  }
+
+  td, &.blueTable th {
+    border: 1px solid $color-gray-light;
+  }
+
+  tbody td {
+    font-size: $font-size-sm;
+  }
+
+  tr:nth-child(even) {
+    background: $color-gray-light-2;
+  }
+
+  thead {
+    background-color: $color-primary-light;
+
+    th {
+      font-size: $font-size-default;
+      font-weight: bold;
+      color: white;
+      border-left: 1px solid $color-gray-light;
+    }
+  }
+
+  thead th:first-child {
+    border-left: none;
+  }
+
+  tfoot {
+    font-size: $font-size-default;
+    font-weight: bold;
+    color: white;
+    background-color: $color-gray-light;
+
+    td {
+      font-size: $font-size-default;
+    }
+
+    .links {
+      text-align: right;
+
+      a {
+        display: inline-block;
+        background: $color-primary-light;
+        color: white;
+        padding: 2px 8px;
+        border-radius: 5px;
+      }
+    }
+  }
+}
+
+.btn {
+  font-size: $font-size-default;
+  padding: 0.5em 1em;
+  border-radius: 5px;
+  text-decoration: none;
+  color: white;
+  white-space: nowrap;
+  border: none;
+
+  &:hover {
+    text-decoration: none;
+  }
+
+  &.btn-icon {
+    @include mat-icon;
+    border: none;
+
+    &.btn-default {
+      color: $color-gray;
+      background-color: transparent;
+      border: none;
+
+      &:hover {
+        color: $color-gray-dark;
+        background-color: transparent;
+      }
+    }
+
+    &.btn-primary {
+      color: $color-primary;
+      background-color: transparent;
+
+      &:hover {
+        color: $color-primary-dark;
+        background-color: transparent;
+      }
+    }
+
+    &.btn-accent {
+      color: $color-accent;
+      background-color: transparent;
+
+      &:hover {
+        color: $color-accent-dark;
+        background-color: transparent;
+      }
+    }
+
+    &.btn-warn {
+      color: $color-warn;
+      background-color: transparent;
+
+      &:hover {
+        color: $color-warn-dark;
+        background-color: transparent;
+      }
+    }
+  }
+
+  &.btn-default {
+    color: $color-gray-dark;
+    background-color: white;
+    border: 1px solid $color-gray-light;
+
+    &:hover {
+      background-color: $color-gray-light-2;
+    }
+  }
+
+  &.btn-primary {
+    background-color: $color-primary;
+
+    &:hover {
+      background-color: $color-primary-dark;
+    }
+  }
+
+  &.btn-warn {
+    background-color: $color-warn;
+
+    &:hover {
+      background-color: $color-warn-dark;
+    }
+  }
+
+  &.btn-accent {
+    background-color: $color-accent;
+
+    &:hover {
+      background-color: $color-accent-dark;
+    }
+  }
+}
+
+select.multi {
+  height: 600px;
+}
+
+.form-field {
+  display: flex;
+  max-width: 100vw;
+  margin-bottom: 40px;
+  padding: 2em;
+
+  &.hidden {
+    display: none;
+  }
+
+  &:nth-child(even) {
+    background-color: $color-gray-light-2;
+  }
+
+  .form-field-label,
+  .form-field-help,
+  .form-field-input {
+    width: 30%;
+    text-align: left;
+    margin-right: 24px;
+  }
+
+  .form-field-label {
+    font-weight: bold;
+    text-align: right;
+  }
+
+  .form-field-input input {
+    width: 100%;
+    text-align: left;
+
+    &[type=checkbox] {
+      width: 24px;
+    }
+  }
+
+  .form-field-help {
+    font-style: italic;
+  }
+
+  .form-field-error {
+    color: $color-warn;
+  }
+}
+
+.alert {
+  padding: 20px;
+  background-color: $color-gray;
+  color: white;
+  margin-bottom: 15px;
+  opacity: 1;
+  border-radius: 5px;
+  transform: scale3d(1, 1, 1);
+  transition: all 0.5s ease-in-out;
+
+  &.warn { background-color: $color-warn; }
+  &.success { background-color: $color-success; }
+  &.info { background-color: $color-gray-light; color: black; }
+
+  .btn-close {
+    margin-left: 15px;
+    color: white;
+    font-weight: bold;
+    float: right;
+    font-size: 22px;
+    line-height: 20px;
+    cursor: pointer;
+    transition: 0.3s;
+
+    &:hover {
+      color: black;
+    }
+  }
+
+  &.fade-out {
+    opacity: 0;
+  }
+
+  &.shrink {
+    transform: scale3d(0, 0, 0);
+    padding: 0;
+    margin: 0;
+  }
+}
+
+.highlight {
+  font-weight: bolder;
+  font-style: italic;
+}
+
+.pagination-page-info {
+    padding: .6em;
+    padding-left: 0;
+    width: 40em;
+    margin: .5em;
+    margin-left: 0;
+    font-size: 12px;
+}
+.pagination-page-info b {
+    color: black;
+    background: #6aa6ed;
+    padding-left: 2px;
+    padding: .1em .25em;
+    font-size: 150%;
+}
+
+.pagination {
+  ul {
+    li {
+      display: inline-block;
+      width: 30px;
+      height: 20px;
+      border: 1px solid black;
+      text-align: center;
+    }
+    li.active {
+      background-color: $color-gray-light-2;
+    }
+  }
+}

communicator/tables.py

@@ -0,0 +1,29 @@
+from flask_table import Table, Col, DatetimeCol, BoolCol
+
+
+class SampleTable(Table):
+    def sort_url(self, col_id, reverse=False):
+        pass
+    barcode = Col('Barcode')
+    student_id = Col('Student Id')
+    date = DatetimeCol('Date', "medium")
+    location = Col('Location')
+    email_notified = BoolCol('Emailed?')
+    text_notified = BoolCol('Texted?')
+
+
+class IvyFileTable(Table):
+    def sort_url(self, col_id, reverse=False):
+        pass
+    file_name = Col('File Name')
+    date_added = DatetimeCol('Date', "medium")
+    sample_count = Col('Total Records')
+
+
+class InvitationTable(Table):
+    def sort_url(self, col_id, reverse=False):
+        pass
+    date_sent = DatetimeCol('Date Sent', "medium")
+    location = Col('Location')
+    date = Col('Date')
+    total_recipients = Col('# Recipients')

communicator/templates/base_email.html

@@ -103,7 +103,7 @@
                   <table border="0" cellpadding="0" cellspacing="0" style="border-collapse: separate; mso-table-lspace: 0pt; mso-table-rspace: 0pt; width: 100%;">
                     <tr>
                       <td style="font-family: sans-serif; font-size: 14px; vertical-align: top; background-color:#232d4b; padding: 12px">
-                    <img src="https://besafe.virginia.edu/themes/custom/de_theme/logo.svg">
+                        <img src="{{base_url + '/images/uva_logo.png'}}" alt="University of Virginia"/>
                       </td>
                     </tr>
 
@@ -132,7 +132,7 @@
                 </tr>
                 <tr>
                   <td class="content-block powered-by" style="font-family: sans-serif; vertical-align: top; padding-bottom: 10px; padding-top: 10px; font-size: 12px; color: #999999; text-align: center;">
-                    Powered by <a href=" {{ site_url }}" style="color: #999999; font-size: 12px; text-align: center; text-decoration: none;">BE SAFE</a>.
+                    Powered by <div style="color: #999999; font-size: 12px; text-align: center; text-decoration: none;">BE SAFE</div>.
                   </td>
                 </tr>
               </table>

communicator/templates/form.html

@@ -0,0 +1,52 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <title>Be SAFE Notification System</title>
+    <base href="/">
+    <link href="https://fonts.googleapis.com/icon?family=Material+Icons" rel="stylesheet">
+    <link rel="stylesheet" href="https://use.typekit.net/kwp6dli.css">
+    <link rel="shortcut icon" href="{{ base_href + url_for('static', filename='favicon.ico') }}">
+    {% assets 'app_scss' %}
+        <link href="{{ base_href + ASSET_URL }}" rel="stylesheet" type="text/css">
+    {% endassets %}
+    <link rel="shortcut icon" href="{{ base_href + url_for('static', filename='favicon.ico') }}">
+</head>
+    <style type="text/css">
+        input {
+            width: 500px;
+            margin-bottom: 20px;
+        }
+    </style>
+<body>
+<a href="{{base_href}}"><< Home</a>
+
+<h3>Previous Entries</h3>
+{{ pagination.info }}
+{{ pagination.links }}
+{{ table }}
+{{ pagination.links }}
+
+<h2>{{ title }}</h2>
+<p>{{ details|safe }}</p>
+<form action="{{ action }}" method="post">
+
+    {{ form.csrf_token() }}
+
+    {% for field in form if field.name != "csrf_token" %}
+        <div class="form-field {{ field.widget.input_type }}">
+            <div class="form-field-label">{{ field.label() }}:</div>
+            <div class="form-field-input">{{ field }}</div>
+            <div class="form-field-help">{{ description_map[field.name] }}</div>
+            {% for error in field.errors %}
+                <div class="form-field-error">{{ error }}</div>
+            {% endfor %}
+        </div>
+    {% endfor %}
+    <button class="btn btn-primary" type="submit">Submit</button>
+    <a href="{{ url_for('index') }}" class="btn btn-default">Cancel</a>
+</form>
+
+
+</body>
+</html>

communicator/templates/imported_files.html

@@ -0,0 +1,25 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <title>UVA Be Safe Communicator</title>
+    <base href="/">
+    <link href="https://fonts.googleapis.com/icon?family=Material+Icons" rel="stylesheet">
+    <link rel="stylesheet" href="https://use.typekit.net/kwp6dli.css">
+    <link rel="shortcut icon" href="{{ base_href + url_for('static', filename='favicon.ico') }}">
+    {% assets 'app_scss' %}
+        <link href="{{ base_href + ASSET_URL }}" rel="stylesheet" type="text/css">
+    {% endassets %}
+    <link rel="shortcut icon" href="{{ base_href + url_for('static', filename='favicon.ico') }}">
+</head>
+<body>
+<a href="{{base_href}}"><< Home</a>
+
+<h2>UVA Be Safe Communicator</h2>
+
+<h3>The following files were imported from IVY</h3>
+{{ pagination.info }}
+{{ pagination.links }}
+{{ table }}
+{{ pagination.links }}
+</body>
+</html>

communicator/templates/index.html

@@ -0,0 +1,24 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <title>UVA Be Safe Communicator</title>
+    <base href="/">
+    <link href="https://fonts.googleapis.com/icon?family=Material+Icons" rel="stylesheet">
+    <link rel="stylesheet" href="https://use.typekit.net/kwp6dli.css">
+    <link rel="shortcut icon" href="{{ base_href + url_for('static', filename='favicon.ico') }}">
+    {% assets 'app_scss' %}
+        <link href="{{ base_href + ASSET_URL }}" rel="stylesheet" type="text/css">
+    {% endassets %}
+    <link rel="shortcut icon" href="{{ base_href + url_for('static', filename='favicon.ico') }}">
+</head>
+<body>
+<h2>UVA Be Safe Communicator</h2>
+<a href="{{base_href + '/invitation'}}">Send Invitations</a> | <a href="{{base_href + '/imported_files'}}">View imported files</a>
+
+<h3>Records to be processed</h3>
+{{ pagination.info }}
+{{ pagination.links }}
+{{ table }}
+{{ pagination.links }}
+</body>
+</html>

communicator/templates/invitation_email.html

@@ -0,0 +1,39 @@
+{% extends "base_email.html" %}
+{% block content %}
+    <p style="font-family: sans-serif; font-size: 24px; font-weight: bold; margin: 0; Margin-bottom: 15px;">
+        This is your invitation from the University of Virginia Be SAFE System.
+    </p>
+
+    <p style="font-family: sans-serif; font-size: 14px; font-weight: normal; margin: 0; Margin-bottom: 15px;">
+        To help keep our classes in-person, and to help keep our community safe, we are launching Be SAFE*
+        (Screening Asymptomatic Finding Effort). Be SAFE is a quick and easy coronavirus screening
+        program that will rely on saliva samples to detect the virus, with the goal of identifying silent
+        carriers before they have the opportunity to transmit the coronavirus. The saliva screenings are
+        mandatory and free of charge. The screenings will be done at multiple locations around Grounds and
+        only take about 2-3 minutes. The ultimate goal is to test all asymptomatic students who are coming
+        on Grounds periodically throughout the semester and to get them results within hours (rather than days).
+    </p>
+    <p style="font-family: sans-serif; font-size: 14px; font-weight: normal; margin: 0; Margin-bottom: 15px;">
+        Your next screening test is scheduled at:
+    </p>
+    <p style="font-family: sans-serif; font-size: 24px; font-weight: bold; margin: 0; Margin-bottom: 15px;">
+        {{location}}
+    </p>
+    <p style="font-family: sans-serif; font-size: 24px; font-weight: bold; margin: 0; Margin-bottom: 15px;">
+        {{date}}
+    </p>
+
+    <p style="font-family: sans-serif; font-size: 24px; font-weight: bold; margin: 0; Margin-bottom: 15px;">
+        You will need to bring your student ID card with you.
+    </p>
+
+    <p style="font-family: sans-serif; font-size: 14px; font-weight: normal; margin: 0; Margin-bottom: 15px;">
+        For more information please visit https://besafe.virginia.edu/
+    </p>
+    <p style="font-family: sans-serif; font-size: 14px; font-weight: normal; margin: 0; Margin-bottom: 15px;">
+        Questions? Email us at asksafe@virginia.edu
+    </p>
+
+
+
+{% endblock %}

communicator/templates/invitation_email.txt

@@ -0,0 +1,22 @@
+This is your invitation from the University of Virginia Be SAFE System.
+-----------------------------------------------------------------------
+
+To help keep our classes in-person, and to help keep our community safe, we are launching Be SAFE*
+(Screening Asymptomatic Finding Effort). Be SAFE is a quick and easy coronavirus screening
+program that will rely on saliva samples to detect the virus, with the goal of identifying silent
+carriers before they have the opportunity to transmit the coronavirus. The saliva screenings are
+mandatory and free of charge. The screenings will be done at multiple locations around Grounds and
+only take about 2-3 minutes. The ultimate goal is to test all asymptomatic students who are coming
+on Grounds periodically throughout the semester and to get them results within hours (rather than days).
+
+==========================================
+Your next screening test is scheduled at:
+{{location}}
+{{date}}
+==========================================
+
+You will need to bring your student ID card with you.
+
+For more information please visit https://besafe.virginia.edu/
+Questions? Email us at asksafe@virginia.edu
+

config/default.py

@@ -39,17 +39,18 @@ GITHUB_REPO = environ.get('GITHUB_REPO', None)
 TARGET_BRANCH = environ.get('TARGET_BRANCH', None)
 
 # Email configuration
-MAIL_DEBUG = environ.get('MAIL_DEBUG', default=True)
+MAIL_DEBUG = environ.get('MAIL_DEBUG', default="false") == "true"
 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_SSL = environ.get('MAIL_USE_SSL', default="false") == "true"
-MAIL_USE_TLS = environ.get('MAIL_USE_TLS', default=False)
+MAIL_USE_TLS = environ.get('MAIL_USE_TLS', default="false") == "true"
-MAIL_USERNAME = environ.get('MAIL_USERNAME', default='xxx')
+MAIL_USERNAME = environ.get('MAIL_USERNAME', default='')
-MAIL_PASSWORD = environ.get('MAIL_PASSWORD', default='yyy')
+MAIL_PASSWORD = environ.get('MAIL_PASSWORD', default='')
 MAIL_SENDER = 'askresearch@virginia.edu'
+MAIL_TIMEOUT = 10
 
 # Ivy Directory
-IVY_IMPORT_DIR = os.path.join(basedir, '..', 'example_ivy_data')
+IVY_IMPORT_DIR = environ.get('IVY_IMPORT_DIR', default='')
 
 # Globus endpoint connections
 GLOBUS_CLIENT_ID = environ.get('GLOBUS_CLIENT_ID')
@@ -57,3 +58,12 @@ GLOBUS_TRANSFER_RT = environ.get('GLOBUS_TRANSFER_RT')
 GLOBUS_TRANSFER_AT = environ.get('GLOBUS_TRANSFER_AT')
 GLOBUS_IVY_ENDPOINT = environ.get('GLOBUS_IVY_ENDPOINT')
 GLOBUS_DTN_ENDPOINT = environ.get('GLOBUS_DTN_ENDPOINT')
+
+# Twilio SMS Messages
+TWILIO_SID = environ.get('TWILIO_SID')
+TWILIO_TOKEN = environ.get('TWILIO_TOKEN')
+TWILIO_NUMBER =  environ.get('TWILIO_NUMBER')
+
+# Firestore configuration
+FIRESTORE_JSON = environ.get('FIRESTORE_JSON')
+

deploy.sh

@@ -19,15 +19,8 @@ function branch_to_tag () {
   if [ "$1" == "master" ]; then echo "latest"; else echo "$1" ; fi
 }
 
-function branch_to_deploy_group() {
-  echo "covid";
-  # if [[ $1 =~ ^(rrt\/.*)$ ]]; then echo "rrt"; else echo "crconnect" ; fi
-}
-
 DOCKER_TAG=$(branch_to_tag "$TRAVIS_BRANCH")
 
-DEPLOY_GROUP=$(branch_to_deploy_group "$TRAVIS_BRANCH")
-
 echo "DOCKER_REPO = $DOCKER_REPO"
 echo "DOCKER_TAG = $DOCKER_TAG"
 

docker_run.sh

@@ -19,6 +19,12 @@ if [ "$RESET_DB" = "true" ]; then
 fi
 
 # THIS MUST BE THE LAST COMMAND!
+if [ -z "$PORT0" ]
+then
+  echo "$PORT0 is not set, setting to 5000"
+  PORT0=5000
+fi
+
 if [ "$APPLICATION_ROOT" = "/" ]; then
   pipenv run gunicorn --bind 0.0.0.0:$PORT0 wsgi:app
 else

migrations/versions/3525dcf128cb_.py

@@ -0,0 +1,35 @@
+"""empty message
+
+Revision ID: 3525dcf128cb
+Revises: 39a845579587
+Create Date: 2020-09-23 16:23:09.383030
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '3525dcf128cb'
+down_revision = '39a845579587'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table('invitation',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('date_sent', sa.DateTime(timezone=True), nullable=True),
+    sa.Column('location', sa.String(), nullable=True),
+    sa.Column('date', sa.String(), nullable=True),
+    sa.Column('total_recipients', sa.Integer(), nullable=True),
+    sa.PrimaryKeyConstraint('id')
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_table('invitation')
+    # ### end Alembic commands ###

migrations/versions/39a845579587_.py

@@ -0,0 +1,28 @@
+"""empty message
+
+Revision ID: 39a845579587
+Revises: fa4b41e0bfe6
+Create Date: 2020-09-23 15:50:44.987745
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '39a845579587'
+down_revision = 'fa4b41e0bfe6'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column('ivy_file', sa.Column('sample_count', sa.Integer(), nullable=True))
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_column('ivy_file', 'sample_count')
+    # ### end Alembic commands ###

migrations/versions/fa4b41e0bfe6_.py

@@ -0,0 +1,32 @@
+"""empty message
+
+Revision ID: fa4b41e0bfe6
+Revises: d904b7b3c1c0
+Create Date: 2020-09-23 14:05:50.766928
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = 'fa4b41e0bfe6'
+down_revision = 'd904b7b3c1c0'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table('ivy_file',
+    sa.Column('file_name', sa.String(), nullable=False),
+    sa.Column('date_added', sa.DateTime(timezone=True), nullable=True),
+    sa.PrimaryKeyConstraint('file_name')
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_table('ivy_file')
+    # ### end Alembic commands ###

tests/data/import_directory/file1.csv

@@ -0,0 +1,2 @@
+Student ID|Student Cellphone|Student Email|Test Date Time|Test Kiosk Loc|Test Result Code
+987654321|555/555-5555|rkc7h@virginia.edu|202009030809|4321|8726520277

tests/data/import_directory/file2.csv

@@ -0,0 +1,3 @@
+Student ID|Student Cellphone|Student Email|Test Date Time|Test Kiosk Loc|Test Result Code
+987655321|555/555-5558|testnegetive@virginia.edu|202009070719|4321|1142270225
+

tests/data/import_directory/file3.csv

@@ -0,0 +1,3 @@
+Student ID|Student Cellphone|Student Email|Test Date Time|Test Kiosk Loc|Test Result Code
+000000222|555/555-5556|testpositive@virginia.edu|202009091449|4321|8269722523
+000000333|555/555-5558|testnegetive@virginia.edu|202009091449|4321|1142270225

tests/data/import_directory/file4.csv

@@ -0,0 +1,4 @@
+Student ID|Student Cellphone|Student Email|Test Date Time|Test Kiosk Loc|Test Result Code
+987654321|555/555-5555|rkc7h@virginia.edu|202009030809|4321|8726520277
+987654322|555/555-5556|testpositive@virginia.edu|202009060919|4321|8269722523
+

tests/services/test_ivy_service.py

@@ -1,9 +1,11 @@
+from tests.base_test import BaseTest
 import os
 import unittest
 import globus_sdk
-from tests.base_test import BaseTest
 
-from communicator import app
+from communicator.models.ivy_file import IvyFile
+
+from communicator import app, db
 
 from communicator.errors import CommError
 from communicator.services.ivy_service import IvyService
@@ -22,5 +24,11 @@ class IvyServiceTest(BaseTest):
             ivy_incorrect_file = os.path.join(app.root_path, '..', 'tests', 'data', 'incorrect.csv')
             IvyService.samples_from_ivy_file(ivy_incorrect_file)
 
+    def test_load_directory(self):
+        self.assertEquals(0, db.session.query(IvyFile).count())
+        app.config['IVY_IMPORT_DIR'] = os.path.join(app.root_path, '..', 'tests', 'data', 'import_directory')
+        records = IvyService().load_directory()
+        files = db.session.query(IvyFile).all()
+        self.assertEquals(4, len(files))
 
 

tests/services/test_notification_service.py

@@ -10,8 +10,9 @@ class TestNotificationService(BaseTest):
 
     def test_send_notification(self):
         message_count = len(TEST_MESSAGES)
-        notifier = NotificationService(app)
         sample = Sample(email="dan@stauntonmakerspace.com", result_code="1234")
-        notifier.send_result_email(sample)
+        with NotificationService(app) as notifier:
+            notifier.send_result_email(sample)
         self.assertEqual(len(TEST_MESSAGES), message_count + 1)
-        self.assertEqual("UVA: BE SAFE Notification", self.decode(TEST_MESSAGES[-1]['subject']))
+        self.assertEqual("UVA: BE SAFE Notification", self.decode(TEST_MESSAGES[-1]['subject']))
+

tests/services/test_sample_endpoints.py

@@ -0,0 +1,27 @@
+from tests.base_test import BaseTest
+
+import json
+from communicator.models import Sample
+from communicator import db
+
+
+class TestSampleEndpoint(BaseTest):
+
+    def test_create_sample(self):
+
+        sample_json = {"barcode": "000000111-202009091449-4321",
+                "location": "4321",
+                "date": "2020-09-09T14:49:00+0000",
+                "student_id": "000000111"}
+
+        # Test add sample
+        samples = db.session.query(Sample).all()
+        self.assertEquals(0, len(samples))
+
+        rv = self.app.post('/v1.0/sample',
+                           content_type="application/json",
+                           data=json.dumps(sample_json))
+
+        samples = db.session.query(Sample).all()
+        self.assertEquals(1, len(samples))
+