sartography
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protocol-builder-mock
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Fixes all the paths and routing errors

This commit is contained in:
Aaron Louie 2020-05-24 23:05:57 -04:00
parent d54160600e
commit 07d0c43e8e
12 changed files with 121 additions and 175 deletions
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2
.gitignore vendored
View File

@ -1,5 +1,7 @@
.idea
__pycache__/
app.db
pb/static/.webassets-cache*
pb/static/*.css
static/.webassets-cache*
static/*.css

4
Dockerfile
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@ -23,8 +23,8 @@ WORKDIR /app
ENV FLASK_APP=/app/pb/__init__.py
# Don't run gunicorn until the DC/OS container actually starts.
# Otherwise, environment variables will not be availabele.
# Otherwise, environment variables will not be available.
#CMD ["pipenv", "run", "gunicorn", \
# "--bind", "0.0.0.0:8000", \
# "-e", "SCRIPT_NAME=/api", \
# "crc:app"]
# "wsgi:app"]

1
Pipfile
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@ -23,6 +23,7 @@ wtforms-alchemy = "*"
psycopg2-binary = "*"
pyscss = "*"
gunicorn = "*"
werkzeug = "*"
[requires]
python_version = "3.7"

3
Pipfile.lock generated
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@ -1,7 +1,7 @@
{
"_meta": {
"hash": {
"sha256": "22303ab4362e0b95f21f7c949b2d43a4ec58b42add20699c159d2a7cc3eaf0be"
"sha256": "42147b649c5838de2eba97ebf9360b65d4bdbb8b3ae94ba23c813660a9490ed3"
},
"pipfile-spec": 6,
"requires": {
@ -518,6 +518,7 @@
"sha256:2de2a5db0baeae7b2d2664949077c2ac63fbd16d98da0ff71837f7d1dea3fd43",
"sha256:6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c"
],
"index": "pypi",
"version": "==1.0.1"
},
"wtforms": {

2
docker_run.sh
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@ -18,4 +18,4 @@ if [ "$RESET_DB" = "true" ]; then
pipenv run flask load-example-data
fi
pipenv run gunicorn -e SCRIPT_NAME="$APPLICATION_ROOT" --bind 0.0.0.0:$PORT0 run:app
pipenv run gunicorn -e SCRIPT_NAME="$APPLICATION_ROOT" --bind 0.0.0.0:$PORT0 wsgi:app

119
pb/__init__.py
View File

@ -39,8 +39,7 @@ def get_study_details(studyid):
def get_form(id, requirement_code):
return
conn = connexion.App('Protocol Builder', specification_dir='pb')
conn = connexion.FlaskApp('Protocol Builder', specification_dir='pb')
app = conn.app
app.config.from_object('config.default')
@ -53,13 +52,43 @@ else:
app.config.root_path = app.instance_path
app.config.from_pyfile('config.py', silent=True)
conn.add_api('api.yml', base_path='/pb')
conn.add_api('api.yml', base_path='/v2.0')
db = SQLAlchemy(app)
migrate = Migrate(app, db)
ma = Marshmallow(app)
# Set the path of the static directory
APP_ROOT = os.path.dirname(os.path.abspath(__file__))
APP_STATIC = os.path.join(APP_ROOT, 'static')
BASE_HREF = app.config['APPLICATION_ROOT'].strip('/')
app.static_folder = APP_STATIC
app.static_url_path = app.config['APPLICATION_ROOT'] + 'static'
print('app.static_folder', app.static_folder)
print('app.static_url_path', app.static_url_path)
# remove old static map
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
# register new; the same view function is used
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')
scss = Bundle(
'scss/app.scss',
filters='pyscss',
output='app.css'
)
assets.register('app_scss', scss)
# Loads all the descriptions from the API so we can display them in the editor.
@ -88,7 +117,7 @@ def site_map():
# Filter out rules we can't navigate to in a browser
# and rules that require parameters
if "GET" in rule.methods and has_no_empty_params(rule):
url = url_for(rule.endpoint, **(rule.defaults or {}))
url = app.confg['APPLICATION_ROOT'].strip('/') + url_for(rule.endpoint, **(rule.defaults or {}))
links.append((url, rule.endpoint))
return json.dumps({"links": links})
@ -106,25 +135,33 @@ def index():
# display results
studies = db.session.query(Study).order_by(Study.DATE_MODIFIED.desc()).all()
table = StudyTable(studies)
return render_template('index.html', table=table, APPLICATION_ROOT=app.config['APPLICATION_ROOT'])
return render_template(
'index.html',
table=table,
base_href=BASE_HREF
)
@app.route('/new_study', methods=['GET', 'POST'])
def new_study():
form = StudyForm(request.form)
action = "/new_study"
action = BASE_HREF + "/new_study"
title = "New Study"
if request.method == 'POST':
study = Study()
study.study_details = StudyDetails()
_update_study(study, form)
flash('Study created successfully!')
return redirect('/')
return redirect_home()
return render_template('form.html', form=form,
action=action,
title=title,
description_map=description_map)
return render_template(
'form.html',
form=form,
action=action,
title=title,
description_map=description_map,
base_href=BASE_HREF
)
@app.route('/study/<study_id>', methods=['GET', 'POST'])
@ -132,7 +169,7 @@ def edit_study(study_id):
study = db.session.query(Study).filter(Study.STUDYID == study_id).first()
form = StudyForm(request.form, obj=study)
if request.method == 'GET':
action = "/study/" + study_id
action = BASE_HREF + "/study/" + study_id
title = "Edit Study #" + study_id
if study.requirements:
form.requirements.data = list(map(lambda r: r.AUXDOCID, list(study.requirements)))
@ -141,17 +178,21 @@ def edit_study(study_id):
if request.method == 'POST':
_update_study(study, form)
flash('Study updated successfully!')
return redirect('/')
return render_template('form.html', form=form,
action=action,
title=title,
description_map={})
return redirect_home()
return render_template(
'form.html',
form=form,
action=action,
title=title,
description_map={},
base_href=BASE_HREF
)
@app.route('/investigator/<study_id>', methods=['GET', 'POST'])
def new_investigator(study_id):
form = InvestigatorForm(request.form)
action = "/investigator/" + study_id
action = BASE_HREF + "/investigator/" + study_id
title = "Add Investigator to Study " + study_id
if request.method == 'POST':
investigator = Investigator(STUDYID=study_id)
@ -160,19 +201,23 @@ def new_investigator(study_id):
db.session.add(investigator)
db.session.commit()
flash('Investigator created successfully!')
return redirect('/')
return redirect_home()
return render_template('form.html', form=form,
action=action,
title=title,
description_map={})
return render_template(
'form.html',
form=form,
action=action,
title=title,
description_map={},
base_href=BASE_HREF
)
@app.route('/del_investigator/<inv_id>', methods=['GET'])
def del_investigator(inv_id):
db.session.query(Investigator).filter(Investigator.id == inv_id).delete()
db.session.commit()
return redirect('/')
return redirect_home()
@app.route('/del_study/<study_id>', methods=['GET'])
@ -182,7 +227,7 @@ def del_study(study_id):
db.session.query(StudyDetails).filter(StudyDetails.STUDYID == study_id).delete()
db.session.query(Study).filter(Study.STUDYID == study_id).delete()
db.session.commit()
return redirect('/')
return redirect_home()
def _update_study(study, form):
@ -217,7 +262,7 @@ def study_details(study_id):
study_details = StudyDetails(STUDYID=study_id)
form = StudyDetailsForm(request.form, obj=study_details)
if request.method == 'GET':
action = "/study_details/" + study_id
action = BASE_HREF + "/study_details/" + study_id
title = "Edit Study Details for Study #" + study_id
details = "Numeric fields can be 1 for true, 0 or false, or Null if not applicable."
if request.method == 'POST':
@ -225,12 +270,20 @@ def study_details(study_id):
db.session.add(study_details)
db.session.commit()
flash('Study updated successfully!')
return redirect('/')
return render_template('form.html', form=form,
action=action,
title=title,
details=details,
description_map=description_map)
return redirect_home()
return render_template(
'form.html',
form=form,
action=action,
title=title,
details=details,
description_map=description_map,
base_href=BASE_HREF
)
def redirect_home():
return redirect('/' + BASE_HREF)
if __name__ == '__main__':

0
static/favicon.ico → pb/static/favicon.ico
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Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 15 KiB

After

Width:  |  Height:  |  Size: 15 KiB

0
static/scss/app.scss → pb/static/scss/app.scss
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133
static/app.css
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@ -1,133 +0,0 @@
.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; }

6
templates/form.html
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@ -3,11 +3,13 @@
<head>
<meta charset="UTF-8">
<title>Protocol Builder Mock Configuration</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">
{% assets 'app_scss' %}
<link href="{{ ASSET_URL }}" rel="stylesheet" type="text/css">
<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>{{ title }}</h2>
@ -27,7 +29,7 @@
</div>
{% endfor %}
<button class="btn btn-primary" type="submit">Submit</button>
<a href="/" class="btn btn-default">Cancel</a>
<a href="{{ base_href + "/" }}" class="btn btn-default">Cancel</a>
</form>
</body>

6
templates/index.html
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@ -2,13 +2,13 @@
<html lang="en">
<head>
<title>Protocol Builder Mock</title>
<base href="{{ APPLICATION_ROOT }}">
<base href="/">
<link href="https://fonts.googleapis.com/icon?family=Material+Icons" rel="stylesheet">
<link rel="stylesheet" href="https://use.typekit.net/kwp6dli.css">
{% assets 'app_scss' %}
<link href="{{ ASSET_URL }}" rel="stylesheet" type="text/css">
<link href="{{ base_href + ASSET_URL }}" rel="stylesheet" type="text/css">
{% endassets %}
<link rel="shortcut icon" href="{{ url_for('static', filename='favicon.ico') }}">
<link rel="shortcut icon" href="{{ base_href + url_for('static', filename='favicon.ico') }}">
</head>
<body>
<h2>Protocol Builder Mock</h2>

20
wsgi.py Normal file
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@ -0,0 +1,20 @@
from werkzeug.exceptions import NotFound
from werkzeug.middleware.dispatcher import DispatcherMiddleware
from werkzeug.middleware.proxy_fix import ProxyFix
from pb import app
if __name__ == "__main__":
def no_app(environ, start_response):
return NotFound()(environ, start_response)
# Remove trailing slash, but add leading slash
base_url = '/' + app.config['APPLICATION_ROOT'].strip('/')
app.wsgi_app = DispatcherMiddleware(no_app, {app.config['APPLICATION_ROOT']: app.wsgi_app})
app.wsgi_app = ProxyFix(app.wsgi_app)
flask_port = app.config['FLASK_PORT']
app.run(host='0.0.0.0', port=flask_port)