Reorganizes files for consistency between repos. Completely refactors…

… Dockerfile to install from wheel.

.gitignore

@@ -2,4 +2,4 @@
 __pycache__/
 app.db
 static/.webassets-cache*
-static/*.css
+pb/static/*.css

Dockerfile

@@ -1,30 +1,48 @@
-FROM python:3.7
-
-ENV PATH=/root/.local/bin:/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/local/sbin
-
-# install node and yarn
-RUN apt-get update
-RUN apt-get -y install postgresql-client libpcre3 libpcre3-dev
-
-# config project dir
-RUN mkdir /protocol-builder-mock
-WORKDIR /protocol-builder-mock
-
-# install python requirements
-RUN pip install pipenv
-ADD Pipfile /protocol-builder-mock/
-ADD Pipfile.lock /protocol-builder-mock/
-RUN pipenv install --dev
-
-# include rejoiner code (gets overriden by local changes)
-COPY . /protocol-builder-mock/
-
-ENV FLASK_APP=/protocol-builder-mock/app.py
-
-# run webserver by default
-CMD ["pipenv", "run", "python", "/protocol-builder-mock/run.py"]
-
-# expose ports
-EXPOSE 5001
-
-
+#
+# https://medium.com/@greut/building-a-python-package-a-docker-image-using-pipenv-233d8793b6cc
+# https://github.com/greut/pipenv-to-wheel
+#
+FROM kennethreitz/pipenv as pipenv
+
+ADD . /app
+WORKDIR /app
+
+RUN pipenv install --dev \
+ && pipenv lock -r > requirements.txt \
+ && pipenv run python setup.py bdist_wheel
+
+# ----------------------------------------------------------------------------
+FROM ubuntu:bionic
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+COPY --from=pipenv /app/dist/*.whl .
+
+RUN set -xe \
+ && apt-get update -q \
+ && apt-get install -y -q \
+        python3-minimal \
+        python3-wheel \
+        python3-pip \
+        gunicorn3 \
+        postgresql-client \
+ && python3 -m pip install *.whl \
+ && apt-get remove -y python3-pip python3-wheel \
+ && apt-get autoremove -y \
+ && apt-get clean -y \
+ && rm -f *.whl \
+ && rm -rf /root/.cache \
+ && rm -rf /var/lib/apt/lists/* \
+ && mkdir -p /app \
+ && useradd _gunicorn --no-create-home --user-group
+
+USER _gunicorn
+
+COPY ./static /app/static
+COPY ./docker_run.sh /app/
+COPY ./wait-for-it.sh /app/
+WORKDIR /app
+
+CMD ["gunicorn3", \
+     "--bind", "0.0.0.0:8000", \
+     "pb:app"]

Pipfile

@@ -4,6 +4,7 @@ url = "https://pypi.org/simple"
 verify_ssl = true
 
 [dev-packages]
+pbr = "*"
 
 [packages]
 flask = "*"

app.py → pb/__init__.py

@@ -11,7 +11,6 @@
 from flask_marshmallow import Marshmallow
 from flask_migrate import Migrate
 from sqlalchemy import func
-
 from wtforms.ext.appengine.db import model_form
 
 PROTOCOLS = {}
@@ -40,8 +39,7 @@ def get_study_details(studyid):
 def get_form(id, requirement_code):
     return
 
-
-conn = connexion.App('Protocol Builder', specification_dir='./')
+conn = connexion.App('Protocol Builder', specification_dir='pb')
 
 app = conn.app
 
@@ -66,7 +64,7 @@ def get_form(id, requirement_code):
 
 # Loads all the descriptions from the API so we can display them in the editor.
 description_map = {}
-with open(r'api.yml') as file:
+with open(r'pb/api.yml') as file:
     api_config = yaml.load(file, Loader=yaml.FullLoader)
     study_detail_properties = api_config['components']['schemas']['StudyDetail']['properties']
     for schema in api_config['components']['schemas']:
@@ -98,8 +96,8 @@ def site_map():
 # **************************
 # WEB FORMS
 # **************************
-from forms import StudyForm, StudyTable, InvestigatorForm, StudyDetailsForm
-from models import Study, RequiredDocument, Investigator, StudySchema, RequiredDocumentSchema, InvestigatorSchema, \
+from pb.forms import StudyForm, StudyTable, InvestigatorForm, StudyDetailsForm
+from pb.models import Study, RequiredDocument, Investigator, StudySchema, RequiredDocumentSchema, InvestigatorSchema, \
     StudyDetails, StudyDetailsSchema
 
 

api.yml → pb/api.yml

@@ -20,7 +20,7 @@ paths:
       tags:
       - CR-Connect
       summary: A list of all studies related to a given UVA ID
-      operationId: app.get_user_studies
+      operationId: pb.get_user_studies
       description: "By passing in a valid UVA Id (ex: dhf8r) it will return a list of all studies that exist for that user in Protocol Builder"
       parameters:
       - in: query
@@ -49,7 +49,7 @@ paths:
       tags:
         - CR-Connect
       summary: Required documents
-      operationId: app.required_docs
+      operationId: pb.required_docs
       description: A list of all documents Protocol Builder considers required, given input from the PI
       parameters:
       - in: query
@@ -72,7 +72,7 @@ paths:
       tags:
         - CR-Connect
       summary: Personnel associated with this study.
-      operationId: app.investigators
+      operationId: pb.investigators
       description: A list of everyone that is associated with the study, including the PI, Study Coordinator, etc... This is currently returned on the "study" endpoint with other information.
       parameters:
       - in: query
@@ -101,7 +101,7 @@ paths:
     get:
       tags:
       - CR-Connect
-      operationId: app.get_study_details
+      operationId: pb.get_study_details
       summary: Details about a specific protocol.
       responses:
         200:

forms.py → pb/forms.py

@@ -1,12 +1,9 @@
-import sys
-
-from flask_table import Table, Col, DateCol, LinkCol, BoolCol, DatetimeCol, NestedTableCol
+from flask_table import Table, Col, LinkCol, BoolCol, DatetimeCol, NestedTableCol
 from flask_wtf import FlaskForm
-from wtforms import SelectMultipleField, SubmitField, StringField, IntegerField, BooleanField, DateField, widgets, \
-    SelectField, validators, HiddenField
+from wtforms import SelectMultipleField, StringField, BooleanField, SelectField, validators, HiddenField
 from wtforms_alchemy import ModelForm
 
-from models import RequiredDocument, Investigator, StudyDetails
+from pb.models import RequiredDocument, Investigator, StudyDetails
 
 
 class StudyForm(FlaskForm):

models.py → pb/models.py

@@ -1,5 +1,5 @@
 from sqlalchemy import func
-from app import db, ma
+from pb import db, ma
 
 
 class Study(db.Model):

run.py

@@ -1,4 +1,4 @@
-from app import app
+from pb import app
 if __name__ == "__main__":
     flask_port = app.config['FLASK_PORT']
     app.run(host='0.0.0.0', port=flask_port)

setup.cfg

@@ -0,0 +1,5 @@
+[metadata]
+name = pb
+
+[files]
+packages = pb

setup.py

@@ -0,0 +1,3 @@
+from setuptools import setup
+
+setup(setup_requires=["pbr"], pbr=True)

static/app.css

@@ -0,0 +1,133 @@
+.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;
+    width: 100%;
+    margin-bottom: 40px;
+    padding: 2em; }
+    .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: 40px; }
+        .form-field .form-field-label {
+          font-weight: bold; }
+          .form-field .form-field-input input {
+            width: 100%; }
+            .form-field .form-field-help {
+              font-style: italic; }
+              .form-field .form-field-error {
+                color: #DF1E43; }

test_sanity.py → tests/test_sanity.py

@@ -3,9 +3,9 @@
 os.environ["TESTING"] = "true"
 
 import unittest
-from app import app, db
-from forms import StudyForm
-from models import Study, RequiredDocument
+from pb import app, db
+from pb.forms import StudyForm
+from pb.models import Study, RequiredDocument
 
 
 class Sanity_Check_Test(unittest.TestCase):