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fix Deep Sequencing Request PDF generator
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@anatskiy
anatskiy committed Jan 30, 2017
1 parent a691d08 commit 38439c0
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99 changes: 99 additions & 0 deletions request/templates/deepseq_request_pdf.html
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Original file line number Diff line number Diff line change
@@ -0,0 +1,99 @@
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<title>Deep Sequencing Request</title>
<style type="text/css">
body {
font-family: Helvetica, Arial, sans-serif;
font-size: 3.5em;
}

h2 {
text-align: center;
margin-bottom: 2em;
}

h3 {
text-align: center;
margin-bottom: 1.5em;
}

hr {
margin: 1.5em 0;
}

.info p {
margin: 0.5em 0;
}

.info p.description {
line-height: 1.5;
}

.libraries {
font-size: 0.9em;
width: 100%;
}

.libraries tr th {
text-align: left;
}

.signature {
font-size: 0.8em;
text-align: center;
margin-top: 5em;
float: right;
width: 50%;
}
</style>
</head>
<body>
<h2>Deep Sequencing Request</h2>

<div class="info">
<p><strong>Request name:</strong> {{ request_name }}</p>
<p><strong>Date:</strong> {{ date }}</p>
<p><strong>User:</strong> {{ user }}</p>
<p><strong>Phone:</strong> {{ phone }}</p>
<p><strong>Email:</strong> {{ email }}</p>
<p><strong>Organization:</strong> {{ organization }}</p>
<p><strong>Cost unit(s):</strong> {{ cost_unit }}</p>
<p class="description"><strong>Description:</strong> {{ description }}</p>
</div>

<hr />

<h3>List of libraries/samples to be submitted for sequencing</h3>
<table class="libraries">
<tr>
<th style="width:10%">#</th>
<th style="width:50%">Name</th>
<th style="width:20%">Type</th>
<th style="width:20%">Barcode</th>
</tr>
{% for record in records %}
<tr>
<td>{{ forloop.counter }}</td>
<td>{{ record.name }}</td>
<td>{{ record.type }}</td>
<td>{{ record.barcode }}</td>
</tr>
{% endfor %}
</table>

<hr />

<table class="signature">
<tr>
<td style="width:50%">____________________</td>
<td style="width:50%">____________________</td>
</tr>
<tr>
<td>(Date, Signature)</td>
<td>(Principal Investigator)</td>
</tr>
</table>
</body>
</html>
208 changes: 34 additions & 174 deletions request/views.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,16 +3,15 @@
from django.contrib.auth import get_user_model
from django.views.decorators.csrf import csrf_exempt
from django.contrib.auth.decorators import login_required
from django.template.loader import render_to_string
from .models import Request
from .forms import RequestForm

import json
from datetime import datetime
import logging

from reportlab.pdfgen import canvas
from reportlab.lib.units import inch
from reportlab.rl_config import defaultPageSize
import pdfkit

User = get_user_model()
logger = logging.getLogger('db')
Expand Down Expand Up @@ -153,164 +152,16 @@ def delete_request(request):
return JsonResponse({'success': not error, 'error': error})


# Helper functions

def draw_page_header(p, font, font_size):
""" """
page_width = defaultPageSize[0]
page_height = defaultPageSize[1]
title = 'Deep Sequencing Request'
p.setFont(font, font_size)
p.drawCentredString(page_width / 2.0, page_height - 75, title)


def draw_string(p, x, _x, y, font, font_bold, font_size, label, string):
""" """
p.setFont(font_bold, font_size)
p.drawString(x, y, label)
p.setFont(font, font_size)
p.drawString(_x, y, string)


def draw_table_row(p, x, y, string):
""" """
_x, _y = x, y
_y -= 30
p.drawString(_x, _y, string[0])
_x += 25
p.drawString(_x, _y, string[1])
_x += 300
p.drawString(_x, _y, string[2])
_x += 70
p.drawString(_x, _y, string[3])


@csrf_exempt
@login_required
def generate_deep_sequencing_request(request):
""" """
request_id = request.GET.get('request_id')
response = HttpResponse(content_type='application/pdf')
""" Generate Deep Sequencing Request form in PDF. """
request_id = request.POST.get('request_id', '')

try:
req = Request.objects.get(id=request_id)
user = User.objects.get(id=req.researcher_id)
cost_unit = sorted([u.name for u in user.cost_unit.all()])
filename = req.name + '_Deep_Sequencing_Request.pdf'
response['Content-Disposition'] = 'inline; filename="%s"' % filename

p = canvas.Canvas(response)
FONT_BOLD = 'Helvetica-Bold'
FONT = 'Helvetica'
HEADER_FONT_SIZE = 14
DEFAULT_FONT_SIZE = 12
SMALL_FONT_SIZE = 10
LINE_SPACING = 20

x = inch
y = 10 * inch + 25

# Strings
request_name = req.name
description = req.description
submitted_libraries_samples = 'List of samples/libraries to be ' + \
'submitted for sequencing:'
page_1 = 'Page 1 of 2'
page_2 = 'Page 2 of 2'

# Page 1
_x = x + 150
_y = y - 10
draw_page_header(p, FONT_BOLD, HEADER_FONT_SIZE)

draw_string(
p, x, _x, _y, FONT, FONT_BOLD, DEFAULT_FONT_SIZE,
'Request Name:', request_name,
)
_y -= LINE_SPACING

draw_string(
p, x, _x, _y, FONT, FONT_BOLD, DEFAULT_FONT_SIZE,
'Date:', datetime.now().strftime('%d.%m.%Y'),
)
_y -= LINE_SPACING

draw_string(
p, x, _x, _y, FONT, FONT_BOLD, DEFAULT_FONT_SIZE,
'Request Number:', '',
)
_y -= LINE_SPACING

draw_string(
p, x, _x, _y, FONT, FONT_BOLD, DEFAULT_FONT_SIZE,
'Provider:', '',
)
_y -= LINE_SPACING * 1.5

draw_string(
p, x, _x, _y, FONT, FONT_BOLD, DEFAULT_FONT_SIZE,
'User:', user.name,
)
_y -= LINE_SPACING

draw_string(
p, x, _x, _y, FONT, FONT_BOLD, DEFAULT_FONT_SIZE,
'Phone:', user.phone,
)
_y -= LINE_SPACING

draw_string(
p, x, _x, _y, FONT, FONT_BOLD, DEFAULT_FONT_SIZE,
'Email:', user.email
)
_y -= LINE_SPACING

draw_string(
p, x, _x, _y, FONT, FONT_BOLD, DEFAULT_FONT_SIZE,
'Organization:', user.organization.name,
)
_y -= LINE_SPACING

draw_string(
p, x, _x, _y, FONT, FONT_BOLD, DEFAULT_FONT_SIZE,
'Principal Investigator:',
user.pi.name if user.pi is not None else '',
)
_y -= LINE_SPACING

draw_string(
p, x, _x, _y, FONT, FONT_BOLD, DEFAULT_FONT_SIZE,
'Cost Unit(s):',
', '.join(cost_unit) if any(cost_unit) else '',
)
_y -= LINE_SPACING * 1.5

draw_string(
p, x, _x, _y, FONT, FONT_BOLD, DEFAULT_FONT_SIZE,
'Description:', description,
)
_y -= LINE_SPACING

# Signature
signature_y = 1.5 * inch
p.setFont(FONT, SMALL_FONT_SIZE - 1)
p.line(x, signature_y + 10, x + 125, signature_y + 10)
p.drawString(x + 30, signature_y, '(Date, Signature)')
p.line(x + 150, signature_y + 10, x + 300, signature_y + 10)
p.drawString(x + 180, signature_y, '(Principal Investigator)')

p.setFont(FONT, SMALL_FONT_SIZE)
p.drawString(x * 6.5, inch, page_1) # Page counter
p.showPage()

# Page 2
_y = y - 10
draw_page_header(p, FONT_BOLD, HEADER_FONT_SIZE)
p.setFont(FONT_BOLD, DEFAULT_FONT_SIZE)
p.drawString(x, _y, submitted_libraries_samples)
p.setFont(FONT_BOLD, SMALL_FONT_SIZE)
draw_table_row(p, x, y - 10, ('#', 'Name', 'Type', 'Barcode'))
p.setFont(FONT, SMALL_FONT_SIZE)
req = Request.objects.get(pk=request_id)
user = User.objects.get(id=req.user.id)
cost_unit = ','.join(sorted([u.name for u in user.cost_unit.all()]))

libraries = [
{
Expand All @@ -320,6 +171,7 @@ def generate_deep_sequencing_request(request):
}
for library in req.libraries.all()
]

samples = [
{
'name': sample.name,
Expand All @@ -328,24 +180,32 @@ def generate_deep_sequencing_request(request):
}
for sample in req.samples.all()
]
data = sorted(libraries + samples, key=lambda x: x['barcode'])

# Only ~55 records fit into the page
for i, record in enumerate(data):
draw_table_row(
p,
x,
y - (15 + (i + 1) * 10),
(str(i + 1), record['name'], record['type'], record['barcode']),
)

p.drawString(x * 6.5, inch, page_2) # Page counter
p.showPage()
p.save()

except:
# TODO@me: Error handling
pass

records = sorted(libraries + samples, key=lambda x: x['barcode'])

html = render_to_string('deepseq_request_pdf.html', {
'request_name': req.name,
'date': datetime.now().strftime('%d.%m.%Y'),
'user': user.name,
'phone': user.phone if user.phone else '',
'email': user.email,
'organization': user.organization.name if user.organization else '',
'cost_unit': cost_unit,
'description': req.description,
'records': records,
})

pdf = pdfkit.from_string(html, False, options=settings.PDF_OPTIONS)

# Generate response
filename = req.name + '_Deep_Sequencing_Request.pdf'
response = HttpResponse(pdf, content_type='application/pdf')
response['Content-Disposition'] = 'attachment; filename="%s"' % filename

except (Request.DoesNotExist, ValueError) as e:
error = str(e)
logger.exception(e)
response = JsonResponse({'success': False, 'error': error})

return response

Expand Down
8 changes: 4 additions & 4 deletions static/main-hub/app/view/startpage/RequestWindowController.js
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Original file line number Diff line number Diff line change
Expand Up @@ -73,10 +73,10 @@ Ext.define('MainHub.view.startpage.RequestWindowController', {

showContextMenu: function(grid, record, item, index, e) {
var me = this;

e.stopEvent();
Ext.create('Ext.menu.Menu', {
items: [
{
items: [{
text: 'Edit',
iconCls: 'x-fa fa-pencil',
handler: function() {
Expand Down Expand Up @@ -156,8 +156,8 @@ Ext.define('MainHub.view.startpage.RequestWindowController', {
},

generatePDF: function(btn) {
var wnd = btn.up('request_wnd'),
url = 'request/generate_pdf/';
var wnd = btn.up('window'),
url = 'request/generate_deep_sequencing_request/';

Ext.getCmp('generatePDFForm').submit({
target: '_blank',
Expand Down
15 changes: 15 additions & 0 deletions wui/settings.py
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Original file line number Diff line number Diff line change
Expand Up @@ -220,6 +220,21 @@
}


# pdfkit
PDF_OPTIONS = {
'encoding': 'UTF-8',
'quiet': '',

# 'header-center': 'Deep Sequencing Request',
# 'header-font-name': 'Helvetica',
# 'header-font-size': 12,
# 'header-spacing': 20,

'footer-center': 'Page [page] of [topage]',
'footer-font-size': 8,
}


# Honor the 'X-Forwarded-Proto' header for request.is_secure()
# SECURE_PROXY_SSL_HEADER = ('HTTP_X_FORWARDED_PROTO', 'https')

Expand Down

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