def generate_eva_report():
geometry_options = {
"head": "40pt",
"margin": "0.5in",
"bottom": "0.6in",
"includeheadfoot": True
}
doc = Document(geometry_options=geometry_options)
reportStyle = PageStyle("reportStyle")
with reportStyle.create(Head("R")) as left_header:
with left_header.create(
MiniPage(width=NoEscape(r"0.49\textwidth"), pos='c',
align='l')) as title_wrapper:
title_wrapper.append(LargeText(bold("RiMEA-Projekt")))
title_wrapper.append(LineBreak())
title_wrapper.append(MediumText(bold("Anlyse")))
doc.preamble.append(reportStyle)
doc.change_document_style("reportStyle")
with doc.create(LongTabu("X[c] X[c]", row_height=1.5)) as report_table:
report_table.add_row(["Test", "evacuation time(s)"], mapper=bold)
report_table.add_hline()
for i in range(1, 4):
report_table.add_row(i, get_evac_time(i)[0])
doc.append(NewPage())
doc.generate_pdf("RiMEA-Projekt-Evacution-Analyse", clean_tex=False)
def test_document():
geometry_options = {
"includeheadfoot": True,
"headheight": "12pt",
"headsep": "10pt",
"landscape": True
}
doc = Document(default_filepath='default_filepath',
documentclass='article',
fontenc='T1',
inputenc='utf8',
lmodern=True,
data=None,
page_numbers=True,
indent=False,
document_options=["a4paper", "12pt"],
geometry_options=geometry_options)
repr(doc)
doc.append('Some text.')
doc.change_page_style(style="empty")
doc.change_document_style(style="plain")
doc.add_color(name="lightgray", model="gray", description="0.6")
doc.add_color(name="abitless", model="gray", description="0.8")
doc.set_variable(name="myVar", value="1234")
doc.set_variable(name="myVar", value="1234")
doc.change_length(parameter=r"\headheight", value="0.5in")
doc.generate_tex(filepath='')
doc.generate_pdf(filepath='', clean=True)
def generate_pdf(stroka):
pdf_path = get_dir('odli_pdf') + '\\' +stroka.Surname +' '+ stroka.Firstname +' '+ stroka.Patronymic
logo_image = r'miaclogo.png'
pdf = Document(pdf_path)
pdf.packages.add(Package('babel',options='russian'))
pdf.packages.add(Package('pdfx', options= NoEscape('a-1b') ))
pdf.packages.add(Package('inputenc',options='utf8'))
pdf.packages.add(Package('fontenc',options='T2A'))
pdf.packages.add(Package('geometry',options='a5paper'))
first_page = PageStyle("firstpage")
with first_page.create(Head("L")) as header_left:
with header_left.create(MiniPage(width=NoEscape(r"0.49\textwidth"),pos='l')) as logo_wrapper:
logo_wrapper.append(StandAloneGraphic(image_options="width=120px",filename=logo_image))
with header_left.create(MiniPage(width=NoEscape(r"0.49\textwidth"),pos='c')) as logo_wrapper:
logo_wrapper.append(NoEscape("Сгенерированно в СПб ГБУЗ МИАЦ"))
logo_wrapper.append(NewLine())
logo_wrapper.append(NoEscape("В основе данные, предоставленные лабораториями"))
pdf.preamble.append(first_page)
pdf.change_document_style("firstpage")
pdf.add_color(name="lightgray", model="gray", description="0.80")
pdf.append(HorizontalSpace(size="500px"))
with pdf.create(Section(NoEscape("Исследование на COVID-19"),numbering=False)):
pdf.append(NoEscape("Наименование лаборатории: " + stroka.Name_Lab ))
pdf.append(NewLine())
pdf.append(NoEscape("Дата исследования: " + stroka.Date_Test))
pdf.append(NewLine())
pdf.append(NoEscape("Ответственный за исследование: "))
pdf.append(NewLine())
pdf.append(NoEscape(stroka.lab_familia +' '+ stroka.lab_name +' '+ stroka.lab_secondname))
with pdf.create(Section(NoEscape("Пациент: ") ,numbering=False)):
pdf.append(LargeText(NoEscape(stroka.Surname +' '+ stroka.Firstname +' '+ stroka.Patronymic)))
pdf.append(NewLine())
pdf.append(NewLine())
pdf.append(NoEscape("Дата рождения: " + stroka.Birthday))
pdf.append(NewLine())
pdf.append(NoEscape("Паспорт: " + stroka.Passport))
pdf.append(NewLine())
pdf.append(NoEscape("СНИЛС: " + stroka.Snils))
pdf.append(NewLine())
pdf.append(NoEscape("ОМС: " + stroka.Policy_OMS))
pdf.append(NewLine())
pdf.append(NoEscape("Контактный номер: " + stroka.Phone))
pdf.append(NewLine())
with pdf.create(Section(NoEscape("Результат: "),numbering=False)):
pdf.append(NoEscape("Качественное обнаружение короновируса SARS 2 в различных образцах: "))
pdf.append(NewLine())
pdf.append(NewLine())
if stroka.Result_Test == 'ND':
pdf.append(TextColor('green',LargeText(NoEscape('Не обнаружено'))))
if stroka.Result_Test == 'DET':
pdf.append(TextColor('red',LargeText(NoEscape('Обнаружено'))))
pdf.generate_pdf(clean_tex=True,compiler='pdflatex')
with open(pdf_path+'.pdf', "rb") as pdf_file:
encoded_pdf = base64.b64encode(pdf_file.read()).decode()
return encoded_pdf
def create_document(self):
geometry = {
"head": "40pt",
"margin": "1in",
"bottom": "1in",
}
doc = Document(geometry_options=geometry)
page = PageStyle("pagestyle")
with page.create(Head("L")) as header_left:
with header_left.create(
MiniPage(width=NoEscape(r"0.5\textwidth"),
pos="c")) as logo_wrapper:
logo_file = os.path.join(get_current_directory(),
"assets/" + LOGO).replace("\\", "/")
logo_wrapper.append(
StandAloneGraphic(image_options="width=120px",
filename=logo_file))
with page.create(Head("R")) as right_header:
with right_header.create(
MiniPage(width=NoEscape(r"0.5\textwidth"),
pos="c",
align="r")) as title_wrapper:
title_wrapper.append(LargeText(bold("Vindskjerming")))
doc.preamble.append(page)
doc.change_document_style("pagestyle")
return doc
class PdfFront(AbstractFront):
FILE_EXTENSION = 'pdf'
PAGE_GEOMETRY = {
'margin': '2.0cm'
}
PACKAGES = ['amsfonts']
def __init__(self):
self._doc = Document(
geometry_options=PdfFront.PAGE_GEOMETRY,
page_numbers=False
)
for package in PdfFront.PACKAGES:
self._doc.preamble.append(Command('usepackage', arguments=package))
def _create_header(self, info):
style_name = NoEscape('header{}'.format(info['run']))
header = PageStyle(style_name)
with header.create(Head('L')):
header.append(info['name'])
header.append(LineBreak())
header.append('Date: {}'.format(self._date()))
with header.create(Head('R')):
header.append('Seed: {}'.format(info['seed']))
header.append(LineBreak())
header.append('Run: {}'.format(info['run']))
self._doc.preamble.append(header)
self._doc.change_document_style(style_name)
def _write_questions(self, info):
self._doc.append(NoEscape(r'\flushleft'))
i = 1
for question, answers, options in info['questions']:
self._doc.append('{}. {}'.format(i, question))
self._doc.append(LineBreak())
for image in options['images']:
with self._doc.create(Figure(position='h!')) as fig:
fig.add_image(image['src'], width='{}px'.format(image.get('width', 100)))
if image.get('description'):
fig.add_caption(image.get('description'))
i += 1
if len(answers) == 0:
for _ in range(options['hints'].get('max_lines', 1)):
self._doc.append(NewLine())
else:
l = options['hints'].get('max_cols', 1)
table_data = [answers[j:j+l] for j in range(0, len(answers), l)]
with self._doc.create(Tabular('l'*l)) as table:
for row in table_data:
table.add_row(row, mapper = lambda x: NoEscape(r'$\Box~~$') + x, strict=False)
self._doc.append(LineBreak())
def _save(self, info):
self._doc.generate_pdf(self._filename(info))
def _add_page_separator(self):
self._doc.append(NoEscape(r'\clearpage'))
def make_doc(self, foirequest):
doc = Document(
lmodern=True,
geometry_options={
"a4paper": True,
"margin": "1in",
},
)
# Change font
doc.packages.append(Package('fontspec,xunicode,array'))
doc.packages.append(Package('sectsty'))
doc.preamble.append(NoEscape("\\usepackage{helvet}"))
doc.preamble.append(
NoEscape("\\sectionfont{\\fontsize{12}{15}\\selectfont}"))
# Adjust description list
doc.packages.append(Package('enumitem'))
doc.preamble.append(
NoEscape(
"\\setlist[description]{labelindent=0cm,style=multiline,leftmargin=1.5cm}"
))
# Hyphenation
doc.append(NoEscape("\\lefthyphenmin=5"))
doc.append(NoEscape("\\sloppy"))
# doc.preamble.append(Command('title', foirequest.title))
# doc.preamble.append(Command('author', foirequest.get_absolute_domain_short_url()))
# doc.preamble.append(Command('date', NoEscape('\\today')))
# doc.append(NoEscape('\\maketitle'))
# Set up header and footer
header = PageStyle("header")
with header.create(Foot("L")):
header.append(italic(settings.SITE_NAME))
with header.create(Head("C")):
header.append(foirequest.title)
with header.create(Foot("R")):
header.append(
str(
_('Request #{request_no}').format(
request_no=foirequest.pk)))
with header.create(Foot("C")):
header.append(
italic(NoEscape(r'Seite \thepage\ von \pageref{LastPage}')))
doc.preamble.append(header)
doc.change_document_style("header")
for i, message in enumerate(foirequest.messages):
last = i == len(foirequest.messages) - 1
add_message_to_doc(doc, message)
if not last:
doc.append(NewPage())
return doc
def make_doc(file,
title,
author,
geometry_options={"margin": "1.15cm"},
options=""):
""" Create and return a formatted Pylatex Document with my data
Parameters
----------
file = Path() (from pathlib) to ifentify the tex and pdf output files
Returns
----------
The document class
"""
# geometry_options = {"tmargin": "1.5cm", "lmargin": "2.5cm"},
doc = Document(default_filepath=file.as_posix(),
documentclass='article',
document_options=['12pt', 'titlepage'] + options,
fontenc="T1",
inputenc=ENCODING,
font_size="normalsize",
lmodern=True,
page_numbers=False,
indent=False,
geometry_options=geometry_options)
doc.change_document_style("empty")
date = str(datetime.datetime.date(datetime.datetime.now()))
comment(doc.preamble, "Automatically generated by make on " + date)
doc.preamble.append(Command("usepackage", "graphicx"))
doc.preamble.append(Command("usepackage", "enumitem"))
doc.preamble.append(Command("usepackage", "url"))
doc.preamble.append(NoEscape("\\setcounter{secnumdepth}{0}"))
doc.preamble.append(Command("usepackage", "titlesec"))
doc.preamble.append(NoEscape("\\titlespacing\\section{0pt}{12pt}{12pt}"))
doc.preamble.append(
NoEscape("\\titlespacing\\subsection{0pt}{12pt}{12pt}"))
doc.preamble.append(Command("title", title.title()))
doc.preamble.append(Command("author", author.title()))
doc.preamble.append(Command("date", NoEscape(r'\today')))
doc.append(NoEscape(r'\maketitle'))
return doc
def generate_style(schema: PLDSchema, locale: LocaleDictionary,
document: Document) -> Document:
document.preamble.append(
UnsafeCommand("newcommand",
Command("rowWidth"),
extra_arguments=NoEscape("\\linewidth-(\\tabcolsep*2)")))
document.preamble.append(
Command('renewcommand',
NoEscape('\\familydefault'),
extra_arguments=NoEscape('\\sfdefault')))
document.preamble.append(
Command("graphicspath", NoEscape("{assets/}{../assets/}")))
header = PageStyle("header")
with header.create(Head("L")) as left_header:
left_header: Head
left_header.create(
StandAloneGraphic("primary_logo.pdf", NoEscape("width=30pt")))
with header.create(Head("R")) as right_header:
right_header: Head
right_header.append(LargeText(locale.project_log_document))
with header.create(Foot("R")) as right_footer:
right_footer: Foot
right_footer.append(
NoEscape(
f"{locale.page} \\thepage\\ {locale.of} \\pageref{{LastPage}}")
)
with header.create(Foot("L")) as left_footer:
left_footer: Foot
left_footer.append(
StandAloneGraphic("secondary_logo.pdf", NoEscape("width=100pt")))
document.preamble.append(
Command(
"title",
NoEscape(
StandAloneGraphic("primary_logo.pdf", NoEscape(
"width=100pt")).dumps() + "~\\\\[1cm]\n" +
locale.project_log_document)))
now = datetime.date.today()
document.preamble.append(
Command("date", f"{now.day}/{now.month}/{now.year}"))
document.preamble.append(
Command("author", NoEscape("\\and ".join(schema.authors))))
document.preamble.append(header)
document.change_document_style("header")
return document
def compile_document_week(no):
"produce a pdf of the weeks workout"
# input accessory lifts for main lifts
bench = [('Decline DB Press (4 x 12)'), ('Face pull (4 x 12)'),
('Low/High flyes ss/w press (4 x 12)'), ('Press ups (4 x Max)')]
# squat = [('Leg press (4 x 15)'), ('Leg extension (4 x 12)'),
# ('Leg curl (4 x 12)'), ('Roll out (4 x Max)')]
squat = [('Smith Front/Back (4 x 12)'), ('Calf Raises (4 x 12)'),
('Walking Lunges (4 x 12)'), ('Roll out (4 x Max)')]
dead = [('Pendlay Row (4 x 8-12)'), ('Hip thrust (4 x 8-12)'),
('Pull up (4 x Max)'), ('Leg raise (4 x 8-12)')]
press = [('Landmine press (4 x 8-12)'), ('Lateral/Rear raises (4 x 8-12)'),
('DB Curls (4 x 8-12)'), ('Roll outs (4 x Max)')]
acc = [bench, squat, press, dead]
# input main lifts and one rep maxes
# last updated 21/03/2017
main_lifts = [('Bench', 90), ('Squat', 128), ('Military Press', 63),
('Deadlift', 143)]
date = t.strftime("%d/%m/%Y")
doc = Document()
doc.packages.append(Package('geometry', options=['margin=2cm']))
doc.packages.append(Package('times'))
doc.packages.append(Package('float'))
doc.packages.append(Package('graphicx'))
header = generate_header()
doc.preamble.append(header)
doc.change_document_style("header")
# Add title
doc.append(LineBreak())
doc.append(LargeText(bold("8/6/3 Workout Routine")))
doc.append(LineBreak())
doc.append(MediumText(bold("As of: " + date)))
doc.append(LineBreak())
# Add workout for a week
gen_week(doc, main_lifts, no, acc)
date_1 = t.strftime("%Y%m%d")
directory = "/home/thomas/Documents/workout_print/workouts"
filename = (directory + "/workout_routine_week_" + str(no) + "_" + date_1)
doc.generate_pdf(filename, clean_tex=True)
def generate_labels():
geometry_options = {"margin": "0.5in"}
doc = Document(geometry_options=geometry_options)
doc.change_document_style("empty")
for i in range(10):
with doc.create(MiniPage(width=r"0.5\textwidth")):
doc.append("Vladimir Gorovikov")
doc.append("\n")
doc.append("Company Name")
doc.append("\n")
doc.append("Somewhere, City")
doc.append("\n")
doc.append("Country")
if (i % 2) == 1:
doc.append(VerticalSpace("20pt"))
doc.append(LineBreak())
doc.generate_pdf("minipage", clean_tex=False)
def generate_header():
geometry_options = {"margin": "0.7in"}
doc = Document(geometry_options=geometry_options)
# Add document header
header = PageStyle("header")
# Create left header
with header.create(Head("L")):
header.append("__")
header.append(LineBreak())
header.append("_")
# Create center header
with header.create(Head("C")):
header.append("____")
# Create right header
with header.create(Head("R")):
header.append(simple_page_number())
# Create left footer
with header.create(Foot("L")):
header.append("Left Footer")
# Create center footer
with header.create(Foot("C")):
header.append("Center Footer")
# Create right footer
with header.create(Foot("R")):
header.append("Right Footer")
doc.preamble.append(header)
doc.change_document_style("header")
# Add Heading
with doc.create(MiniPage(align='l')):
doc.append(LargeText(bold("INVESTMENT PROPERTY - BUY & HOLD")))
doc.append(LineBreak())
doc.append(MediumText(bold(" ")))
doc.generate_pdf("header", clean_tex=False)
return print('nice')
def wrap_table_in_latex_document(table: str,
landscape: bool = False,
margin: float = 1.5) -> str:
"""
Wraps a table inside a proper latex document.
Uses ``\\longtable`` instead of ``\\tabular`` to fit data on multiple pages.
Args:
table: table string to wrap the document around
landscape: whether to layout the table in landscape mode
margin: margin around the table in cm
Returns:
the resulting latex document as a string
"""
doc = Document(documentclass="scrbook",
document_options="paper=a4",
geometry_options={
"margin": f"{margin}cm",
"landscape": "true" if landscape else "false"
})
# set monospace font
monospace_comm = UnsafeCommand('renewcommand',
r'\familydefault',
extra_arguments=r'\ttdefault')
doc.preamble.append(monospace_comm)
doc.packages.append(Package('longtable'))
doc.packages.append(Package('booktabs'))
doc.change_document_style("empty")
# embed latex table inside document
doc.append(NoEscape(table))
return tp.cast(str, doc.dumps())
def generate_header():
geometry_options = {"margin": "0.7in"}
doc = Document(geometry_options=geometry_options)
# Add document header
header = PageStyle("header")
# Create left header
with header.create(Head("L")):
header.append("Page date: ")
header.append(LineBreak())
header.append("R3")
# Create center header
with header.create(Head("C")):
header.append("Company")
# Create right header
with header.create(Head("R")):
header.append(simple_page_number())
# Create left footer
with header.create(Foot("L")):
header.append("Left Footer")
# Create center footer
with header.create(Foot("C")):
header.append("Center Footer")
# Create right footer
with header.create(Foot("R")):
header.append("Right Footer")
doc.preamble.append(header)
doc.change_document_style("header")
# Add Heading
with doc.create(MiniPage(align='c')):
doc.append(LargeText(bold("Title")))
doc.append(LineBreak())
doc.append(MediumText(bold("As at:")))
doc.generate_pdf("header", clean_tex=False)
def generate_unique():
geometry_options = {
"head": "40pt",
"margin": "0.5in",
"bottom": "0.6in",
"includeheadfoot": True
}
doc = Document(geometry_options=geometry_options,
document_options="a4paper")
# Generating first page style
first_page = PageStyle("firstpage")
# Header image
with first_page.create(Head("L")) as header_left:
with header_left.create(
MiniPage(width=NoEscape(r"0.49\textwidth"),
pos='c')) as logo_wrapper:
logo_file = os.path.join(os.path.dirname(__file__), logo_name)
logo_wrapper.append(
StandAloneGraphic(image_options="width=50px",
filename=logo_file))
# Add document title
with first_page.create(Head("R")) as right_header:
with right_header.create(
MiniPage(width=NoEscape(r"0.49\textwidth"), pos='c',
align='r')) as title_wrapper:
title_wrapper.append(LargeText(bold("Sjain ventures ltd")))
title_wrapper.append(LineBreak())
title_wrapper.append(MediumText(bold("C-246, Vallabhnagar")))
title_wrapper.append(LineBreak())
# title_wrapper.append(TextColor("gray", MediumText(bold("Raipur, CG"))))
title_wrapper.append(MediumText(bold("Raipur, CG")))
# Add footer
# with first_page.create(Foot("C")) as footer:
# message = "Important message please read"
# with footer.create(Tabularx(
# "X X X X",
# width_argument=NoEscape(r"\textwidth"))) as footer_table:
# footer_table.add_row(
# [MultiColumn(4, align='l', data=TextColor("blue", message))])
# footer_table.add_hline(color="blue")
# footer_table.add_empty_row()
# branch_address = MiniPage(
# width=NoEscape(r"0.25\textwidth"),
# pos='t')
# branch_address.append("960 - 22nd street east")
# branch_address.append("\n")
# branch_address.append("Saskatoon, SK")
# document_details = MiniPage(width=NoEscape(r"0.25\textwidth"),
# pos='t', align='r')
# document_details.append("1000")
# document_details.append(LineBreak())
# document_details.append(simple_page_number())
# footer_table.add_row([branch_address, branch_address,
# branch_address, document_details])
# Newly added
with first_page.create(Foot("L")) as right_footer:
with right_footer.create(
MiniPage(width=NoEscape(r"0.49\textwidth"), pos='l',
align='l')) as contact_wrapper:
contact_wrapper.append(MediumText(bold("Alok Kumar Sharma")))
contact_wrapper.append(LineBreak())
contact_wrapper.append(MediumText("*****@*****.**"))
contact_wrapper.append(LineBreak())
contact_wrapper.append(MediumText("+91 7877681234"))
doc.preamble.append(first_page)
# End first page style
# Add customer information
with doc.create(Tabu("X[r]")) as first_page_table:
# customer = MiniPage(width=NoEscape(r"0.9\textwidth"), pos='h')
# customer.append("Verna Volcano")
# customer.append("\n")
# customer.append("For some Person")
# customer.append("\n")
# customer.append("Address1")
# customer.append("\n")
# customer.append("Address2")
# customer.append("\n")
# customer.append("Address3")
# Add branch information
branch = MiniPage(width=NoEscape(r"0.49\textwidth"),
pos='t!',
align='r')
branch.append("http://sjainventures.com")
branch.append(LineBreak())
branch.append("*****@*****.**")
# branch.append(LineBreak())
# branch.append("+91 7877681234")
first_page_table.add_row([branch]) # [customer, branch]
first_page_table.add_empty_row()
doc.change_document_style("firstpage")
doc.add_color(name="lightgray", model="gray", description="0.80")
# Add statement table
# with doc.create(LongTabu("X[l] X[2l] X[r] X[r] X[r]",
# row_height=1.5)) as data_table:
# data_table.add_row(["date",
# "description",
# "debits($)",
# "credits($)",
# "balance($)"],
# mapper=bold,
# color="lightgray")
# data_table.add_empty_row()
# data_table.add_hline()
# row = ["2016-JUN-01", "Test", "$100", "$1000", "-$900"]
# for i in range(25):
# if (i % 2) == 0:
# data_table.add_row(row, color="lightgray")
# else:
# data_table.add_row(row)
with doc.create(Paragraph("Dear Rishikesh,")) as para1:
para1.append(lorem_ipsum.LOREM_IPSUM_TEXT2)
# doc.append(NewPage())
# Add cheque images
# with doc.create(LongTabu("X[c] X[c]")) as cheque_table:
# cheque_file = os.path.join(os.path.dirname(__file__),
# 'facebook_logo.png')
# cheque = StandAloneGraphic(cheque_file, image_options="width=200px")
# for i in range(0, 20):
# cheque_table.add_row([cheque, cheque])
doc.generate_pdf("complex_report", clean_tex=False)
def get_document(document_title='Report',
author='Entail AS',
fig_ext=u'.pdf',
header_logofilename='entail.pdf',
logo_image_option_header="width=250px",
workflow_ID=0):
global _fig_ext
_fig_ext = fig_ext
geometry_options = {
"head": "70pt",
"margin": "1.5cm",
"bottom": "1.5cm",
"includeheadfoot": True
}
document_options = ['a4paper']
doc = Document(geometry_options=geometry_options,
document_options=document_options)
# packages
doc.packages.append(Package('booktabs'))
doc.packages.append(Package('chngcntr'))
doc.packages.append(Package('longtable'))
doc.packages.append(Package('titlepic'))
doc.packages.append(Package('float'))
# page style
first_page = PageStyle("firstpage")
# Header image
with first_page.create(Head("L")) as header_left:
with header_left.create(
MiniPage(width=NoEscape(r"0.25\textwidth"),
pos='c')) as logo_wrapper:
logo_file = os.path.join(
os.path.dirname(os.path.abspath(__file__)),
header_logofilename).replace('\\', '/')
logo_wrapper.append(
StandAloneGraphic(image_options="width=80px",
filename=logo_file))
# Add document title
with first_page.create(Head("R")) as right_header:
with right_header.create(
MiniPage(width=NoEscape(r"0.75\textwidth"), pos='c',
align='r')) as title_wrapper:
title_wrapper.append(LargeText(bold(document_title)))
title_wrapper.append(LineBreak())
title_wrapper.append(MediumText(bold(NoEscape(r'\today'))))
# Add footer
with first_page.create(Foot("C")) as center_footer:
center_footer.append(simple_page_number())
with first_page.create(Foot("R")) as right_footer:
with right_footer.create(
MiniPage(width=NoEscape(r"0.15\textwidth"),
pos='r')) as logo_wrapper:
logo_file = os.path.join(
os.path.dirname(os.path.abspath(__file__)),
'tailor.png').replace('\\', '/')
logo_wrapper.append(
StandAloneGraphic(image_options="width=50px",
filename=logo_file))
doc.preamble.append(first_page)
doc.change_document_style("firstpage")
doc.preamble.append(Command('title', document_title))
logo_file = os.path.join(os.path.dirname(os.path.abspath(__file__)),
header_logofilename).replace('\\', '/')
doc.preamble.append(
Command(
'titlepic',
StandAloneGraphic(image_options=logo_image_option_header,
filename=logo_file)))
# doc.preamble.append(Command('author', author))
doc.preamble.append(Command('date', NoEscape(r'\today')))
doc.preamble.append(
Command(
'hypersetup',
arguments=
'colorlinks, citecolor=black, filecolor=black, linkcolor=black, urlcolor=black',
packages=[Package('hyperref')]))
doc.preamble.append(NoEscape(r'\counterwithin{figure}{section}'))
doc.append(NoEscape(r'\maketitle'))
# Add disclaimer
doc.append(NewPage())
doc.append(NoEscape(r'\textbf{Disclaimer}'))
doc.append(NoEscape(r'\newline'))
doc.append(NoEscape(r'\vspace{0.2in}'))
temptext = f'This is in automatically generated report. '
if workflow_ID == 0:
temptext += f'The report was generated '
else:
temptext += f'The results are extracted from Workflow ID {workflow_ID} '
temptext += f'on the {datetime.datetime.now().strftime("%m/%d/%Y at %H:%M:%S")}. '
temptext += f'Errors may occur and it is the user’s responsibility to interpret the reported data '
temptext += f'with sound engineering judgement.'
doc.append(temptext)
doc.append(NewPage())
doc.append(Command('tableofcontents'))
doc.append(NewPage())
return doc
def save_latex(self,
uiObj,
Design_Check,
reportsummary,
filename,
rel_path,
Disp_2d_image,
Disp_3d_image,
module=''):
companyname = str(reportsummary["ProfileSummary"]['CompanyName'])
companylogo = str(reportsummary["ProfileSummary"]['CompanyLogo'])
groupteamname = str(reportsummary["ProfileSummary"]['Group/TeamName'])
designer = str(reportsummary["ProfileSummary"]['Designer'])
projecttitle = str(reportsummary['ProjectTitle'])
subtitle = str(reportsummary['Subtitle'])
jobnumber = str(reportsummary['JobNumber'])
client = str(reportsummary['Client'])
does_design_exist = reportsummary['does_design_exist']
osdagheader = '/ResourceFiles/images/Osdag_header_report.png'
# Add document header
geometry_options = {
"top": "5cm",
"hmargin": "2cm",
"headheight": "100pt",
"footskip": "100pt",
"bottom": "5cm"
}
doc = Document(geometry_options=geometry_options, indent=False)
doc.packages.append(Package('amsmath'))
doc.packages.append(Package('graphicx'))
doc.packages.append(Package('needspace'))
doc.append(pyl.Command('fontsize', arguments=[8, 12]))
doc.append(pyl.Command('selectfont'))
doc.add_color('OsdagGreen', 'RGB', '153,169,36')
doc.add_color('PassColor', 'RGB', '153,169,36')
doc.add_color('Red', 'RGB', '255,0,0')
doc.add_color('Green', 'RGB', '0,200,0')
doc.add_color('FailColor', 'HTML', '933A16')
header = PageStyle("header")
# Create center header
with header.create(Head("C")):
with header.create(Tabularx('|l|p{4cm}|l|X|')) as table:
table.add_hline()
# MultiColumn(4)
table.add_row((
MultiColumn(
2,
align='|c|',
data=('' if companylogo is '' else StandAloneGraphic(
image_options="height=0.95cm",
filename=companylogo))),
MultiColumn(2,
align='|c|',
data=[
'Created with',
StandAloneGraphic(
image_options="width=4.0cm,height=1cm",
filename=rel_path + osdagheader)
]),
))
table.add_hline()
table.add_row(('Company Name', companyname, 'Project Title',
projecttitle),
color='OsdagGreen')
table.add_hline()
table.add_row(
('Group/Team Name', groupteamname, 'Subtitle', subtitle),
color='OsdagGreen')
table.add_hline()
table.add_row(('Designer', designer, 'Job Number', jobnumber),
color='OsdagGreen')
table.add_hline()
table.add_row(
('Date', time.strftime("%d /%m /%Y"), 'Client', client),
color='OsdagGreen')
table.add_hline()
# Create right footer
with header.create(Foot("R")):
header.append(NoEscape(r'Page \thepage'))
#
# doc.preamble.append(header)
# doc.change_document_style("header")
# Add Heading
# with doc.create(MiniPage(align='c')):
doc.preamble.append(header)
doc.change_document_style("header")
with doc.create(Section('Input Parameters')):
with doc.create(
LongTable('|p{5cm}|p{2.5cm}|p{1.5cm}|p{3cm}|p{3.5cm}|',
row_height=1.2)) as table:
table.add_hline()
for i in uiObj:
# row_cells = ('9', MultiColumn(3, align='|c|', data='Multicolumn not on left'))
if i == "Selected Section Details" or i == KEY_DISP_ANGLE_LIST or i == KEY_DISP_TOPANGLE_LIST or i == KEY_DISP_CLEAT_ANGLE_LIST:
# if type(uiObj[i]) == list:
continue
if type(uiObj[i]) == dict:
table.add_hline()
sectiondetails = uiObj[i]
image_name = sectiondetails[KEY_DISP_SEC_PROFILE]
Img_path = '/ResourceFiles/images/' + image_name + '.png'
if (len(sectiondetails)) % 2 == 0:
# merge_rows = int(round_up(len(sectiondetails),2)/2 + 2)
merge_rows = int((len(sectiondetails) / 2)) + 2
else:
merge_rows = round_up((len(sectiondetails) / 2), 2)
if (len(sectiondetails)) % 2 == 0:
sectiondetails[''] = ''
a = list(sectiondetails.keys())
# index=0
for x in range(1, (merge_rows + 1)):
# table.add_row("Col.Det.",i,columndetails[i])
if x == 1:
table.add_row((
MultiRow(
merge_rows,
data=StandAloneGraphic(
image_options=
"width=5cm,height=5cm",
filename=rel_path + Img_path)),
MultiColumn(2, align='|c|', data=a[x]),
MultiColumn(2,
align='|c|',
data=sectiondetails[a[x]]),
))
elif x <= 4:
table.add_row((
'',
MultiColumn(2,
align='|c|',
data=NoEscape(a[x])),
MultiColumn(2,
align='|c|',
data=NoEscape(
sectiondetails[a[x]])),
))
else:
table.add_row((
'',
NoEscape(a[x]),
sectiondetails[a[x]],
NoEscape(a[merge_rows + x - 4]),
sectiondetails[a[merge_rows + x - 4]],
))
table.add_hline(2, 5)
elif uiObj[i] == "TITLE":
table.add_hline()
table.add_row((MultiColumn(
5,
align='|c|',
data=bold(i),
), ))
table.add_hline()
elif i == 'Section Size*':
table.add_hline()
table.add_row((
MultiColumn(
3,
align='|c|',
data=i,
),
MultiColumn(2,
align='|c|',
data="Ref List of Input Section"),
))
table.add_hline()
elif len(str(uiObj[i])) > 55 and type(
uiObj[i]) != pyl.math.Math:
str_len = len(str(uiObj[i]))
loop_len = round_up((str_len / 55), 1, 1)
for j in range(1, loop_len + 1):
b = 55 * j + 1
if j == 1:
table.add_row((
MultiColumn(3,
align='|c|',
data=MultiRow(loop_len,
data=i)),
MultiColumn(2,
align='|c|',
data=uiObj[i][0:b]),
))
else:
table.add_row((
MultiColumn(3,
align='|c|',
data=MultiRow(loop_len,
data="")),
MultiColumn(2,
align='|c|',
data=uiObj[i][b - 55:b]),
))
table.add_hline()
else:
table.add_hline()
table.add_row((
MultiColumn(3, align='|c|', data=NoEscape(i)),
MultiColumn(2, align='|c|', data=uiObj[i]),
))
table.add_hline()
for i in uiObj:
if i == 'Section Size*' or i == KEY_DISP_ANGLE_LIST or i == KEY_DISP_TOPANGLE_LIST or i == KEY_DISP_CLEAT_ANGLE_LIST:
with doc.create(Subsection("List of Input Section")):
# with doc.create(LongTable('|p{8cm}|p{8cm}|', row_height=1.2)) as table:
with doc.create(Tabularx('|p{4cm}|X|',
row_height=1.2)) as table:
table.add_hline()
table.add_row((
MultiColumn(
1,
align='|c|',
data=i,
),
MultiColumn(1,
align='|X|',
data=uiObj[i].strip("[]")),
))
# str_len = len(uiObj[i])
# loop_len = round_up((str_len/100),1,1)
# table.add_hline()
# for j in range(1,loop_len+1):
# b= 100*j+1
# if j ==1:
# table.add_row((MultiColumn(1, align='|c|', data=i, ),
# MultiColumn(1, align='|X|', data=uiObj[i][0:b]),))
# else:
# table.add_row((MultiColumn(1, align='|c|', data=" ", ),
# MultiColumn(1, align='|X|', data=uiObj[i][b-100:b]),))
table.add_hline()
doc.append(
pyl.Command('Needspace', arguments=NoEscape(r'10\baselineskip')))
doc.append(NewPage())
count = 0
with doc.create(Section('Design Checks')):
with doc.create(
Tabularx(
r'|>{\centering}p{12.5cm}|>{\centering\arraybackslash}X|',
row_height=1.2)) as table:
table.add_hline()
# Fail = TextColor("FailColor", bold("Fail"))
# Pass = TextColor("PassColor", bold("Pass"))
if does_design_exist != True:
table.add_row(bold('Design Status'),
color_cell("Red", bold("Fail")))
else:
table.add_row(bold('Design Status'),
color_cell("OsdagGreen", bold("Pass")))
table.add_hline()
for check in Design_Check:
if check[0] == 'SubSection':
if count >= 1:
# doc.append(NewPage())
doc.append(
pyl.Command(
'Needspace',
arguments=NoEscape(r'10\baselineskip')))
with doc.create(Subsection(check[1])):
#########################
# if uiObj== "WELDImage":
# table.add_hline()
# table.add_row((MultiColumn(5, align='|c|', data=bold(i), ),))
# table.add_hline()
# else:
#########################
with doc.create(LongTable(check[2], row_height=1.2)
) as table: # todo anjali remove
table.add_hline()
table.add_row(
('Check', 'Required', 'Provided', 'Remarks'),
color='OsdagGreen')
table.add_hline()
table.end_table_header()
table.add_hline()
count = count + 1
elif check[0] == "Selected":
if count >= 1:
# doc.append(NewPage())
doc.append(
pyl.Command(
'Needspace',
arguments=NoEscape(r'10\baselineskip')))
with doc.create(Subsection(check[1])):
with doc.create(LongTable(check[2],
row_height=1.2)) as table:
table.add_hline()
for i in uiObj:
# row_cells = ('9', MultiColumn(3, align='|c|', data='Multicolumn not on left'))
print(i)
if type(
uiObj[i]
) == dict and i == 'Selected Section Details':
table.add_hline()
sectiondetails = uiObj[i]
image_name = sectiondetails[
KEY_DISP_SEC_PROFILE]
Img_path = '/ResourceFiles/images/' + image_name + '.png'
if (len(sectiondetails)) % 2 == 0:
# merge_rows = int(round_up(len(sectiondetails),2)/2 + 2)
merge_rows = int(
round_up((len(sectiondetails) /
2), 1, 0) + 2)
else:
merge_rows = int(
round_up((len(sectiondetails) /
2), 1, 0) + 1)
print('Hi',
len(sectiondetails) / 2,
round_up(len(sectiondetails), 2) / 2,
merge_rows)
if (len(sectiondetails)) % 2 == 0:
sectiondetails[''] = ''
a = list(sectiondetails.keys())
# index=0
for x in range(1, (merge_rows + 1)):
# table.add_row("Col.Det.",i,columndetails[i])
if x == 1:
table.add_row((
MultiRow(
merge_rows,
data=StandAloneGraphic(
image_options=
"width=5cm,height=5cm",
filename=rel_path +
Img_path)),
MultiColumn(2,
align='|c|',
data=NoEscape(
a[x])),
MultiColumn(
2,
align='|c|',
data=NoEscape(
sectiondetails[a[x]])),
))
elif x <= 4:
table.add_row((
'',
MultiColumn(2,
align='|c|',
data=NoEscape(
a[x])),
MultiColumn(
2,
align='|c|',
data=sectiondetails[a[x]]),
))
else:
table.add_row((
'',
NoEscape(a[x]),
sectiondetails[a[x]],
NoEscape(a[merge_rows + x -
4]),
sectiondetails[a[merge_rows +
x - 4]],
))
table.add_hline(2, 5)
table.add_hline()
count = count + 1
else:
if check[3] == 'Fail':
table.add_row((NoEscape(check[0])), check[1], check[2],
TextColor("Red", bold(check[3])))
else:
table.add_row((NoEscape(check[0])), check[1], check[2],
TextColor("OsdagGreen", bold(check[3])))
table.add_hline()
# 2D images
if len(Disp_2d_image) != 0:
if module == KEY_DISP_BCENDPLATE or module == KEY_DISP_BB_EP_SPLICE:
if does_design_exist and sys.platform != 'darwin':
doc.append(NewPage())
weld_details = rel_path + Disp_2d_image[0]
detailing_details = rel_path + Disp_2d_image[1]
stiffener_details = rel_path + Disp_2d_image[2]
with doc.create(Section('2D Drawings (Typical)')):
with doc.create(Figure()) as image:
image.add_image(weld_details,
width=NoEscape(r'0.7\textwidth'),
placement=NoEscape(r'\centering'))
image.add_caption(
'Typical Weld Details -- Beam to End Plate Connection'
)
# doc.append(NewPage())
with doc.create(Figure()) as image_2:
image_2.add_image(
detailing_details,
width=NoEscape(r'0.7\textwidth'),
placement=NoEscape(r'\centering'))
image_2.add_caption('Typical Detailing')
# doc.append(NewPage())
with doc.create(Figure()) as image_3:
image_3.add_image(
stiffener_details,
width=NoEscape(r'0.9\textwidth'),
placement=NoEscape(r'\centering'))
image_3.add_caption('Typical Stiffener Details')
# doc.append(NewPage())
elif module == KEY_DISP_BASE_PLATE:
if does_design_exist and sys.platform != 'darwin':
doc.append(NewPage())
bp_sketch = rel_path + Disp_2d_image[0]
bp_detailing = rel_path + Disp_2d_image[1]
bp_weld = rel_path + Disp_2d_image[2]
bp_anchor = rel_path + Disp_2d_image[3]
bp_key = rel_path + Disp_2d_image[4]
with doc.create(Section('2D Drawings (Typical)')):
with doc.create(Figure()) as image_1:
image_1.add_image(
bp_sketch,
width=NoEscape(r'1.0\textwidth'),
placement=NoEscape(r'\centering'))
image_1.add_caption('Typical Base Plate Details')
# doc.append(NewPage())
with doc.create(Figure()) as image_2:
image_2.add_image(
bp_detailing,
width=NoEscape(r'1.0\textwidth'),
placement=NoEscape(r'\centering'))
image_2.add_caption('Typical Base Plate Detailing')
# doc.append(NewPage())
with doc.create(Figure()) as image_3:
image_3.add_image(
bp_weld,
width=NoEscape(r'1.0\textwidth'),
placement=NoEscape(r'\centering'))
image_3.add_caption('Typical Weld Details')
# doc.append(NewPage())
with doc.create(Figure()) as image_4:
image_4.add_image(
bp_anchor,
width=NoEscape(r'0.5\textwidth'),
placement=NoEscape(r'\centering'))
image_4.add_caption('Typical Anchor Bolt Details')
# doc.append(NewPage())
if len(Disp_2d_image[-1]) > 0:
with doc.create(Figure()) as image_5:
image_5.add_image(
bp_key,
width=NoEscape(r'0.9\textwidth'),
placement=NoEscape(r'\centering'))
image_5.add_caption(
'Typical Shear Key Details')
# doc.append(NewPage())
if does_design_exist and sys.platform != 'darwin':
doc.append(NewPage())
Disp_top_image = "/ResourceFiles/images/top.png"
Disp_side_image = "/ResourceFiles/images/side.png"
Disp_front_image = "/ResourceFiles/images/front.png"
view_3dimg_path = rel_path + Disp_3d_image
view_topimg_path = rel_path + Disp_top_image
view_sideimg_path = rel_path + Disp_side_image
view_frontimg_path = rel_path + Disp_front_image
with doc.create(Section('3D Views')):
with doc.create(
Tabularx(
r'|>{\centering}X|>{\centering\arraybackslash}X|',
row_height=1.2)) as table:
view_3dimg_path = rel_path + Disp_3d_image
view_topimg_path = rel_path + Disp_top_image
view_sideimg_path = rel_path + Disp_side_image
view_frontimg_path = rel_path + Disp_front_image
table.add_hline()
table.add_row([
StandAloneGraphic(image_options="height=4cm",
filename=view_3dimg_path),
StandAloneGraphic(image_options="height=4cm",
filename=view_topimg_path)
])
table.add_row('(a) 3D View', '(b) Top View')
table.add_hline()
table.add_row([
StandAloneGraphic(image_options="height=4cm",
filename=view_sideimg_path),
StandAloneGraphic(image_options="height=4cm",
filename=view_frontimg_path)
])
table.add_row('(c) Side View', '(d) Front View')
table.add_hline()
# with doc.create(Figure(position='h!')) as view_3D:
# view_3dimg_path = rel_path + Disp_3d_image
# # view_3D.add_image(filename=view_3dimg_path, width=NoEscape(r'\linewidth'))
#
# view_3D.add_image(filename=view_3dimg_path,width=NoEscape(r'\linewidth,height=6.5cm'))
#
# view_3D.add_caption('3D View')
with doc.create(Section('Design Log')):
doc.append(
pyl.Command('Needspace',
arguments=NoEscape(r'10\baselineskip')))
logger_msgs = reportsummary['logger_messages'].split('\n')
for msg in logger_msgs:
if ('WARNING' in msg):
colour = 'blue'
elif ('INFO' in msg):
colour = 'OsdagGreen'
elif ('ERROR' in msg):
colour = 'red'
else:
continue
doc.append(TextColor(colour, '\n' + msg))
try:
doc.generate_pdf(filename, compiler='pdflatex', clean_tex=False)
except:
pass
def generar(self, Carrera, Asignatura, Curso, listaPreguntas, aleatorio):
today = str(self.__fecha)
geometry_options = {
"head": "48pt",
"margin": "0.5in",
"bottom": "0.6in",
"includeheadfoot": True
}
doc = Document(geometry_options=geometry_options)
header = PageStyle("header") # DEFINIMOS LA VARIABLE CON ESTILO
#image_filename = os.path.join(os.path.dirname("__file__"), '../static/zigmap.png') # IMAGEN UNAB
#data_folder = os.path.join("../", "static/zigmap.png")
#file_to_open = os.path.join(data_folder, "zigmap.png")
#image_filename = data_folder
image_filename = "zigmap.png"
# Generating first page style
first_page = PageStyle("firstpage")
# Header image
with first_page.create(Head("L")) as header_left:
with header_left.create(
SubFigure(
position='L',
width=NoEscape(r'0.10\linewidth'))) as logo_wrapper:
print("IMAGEN")
#logo_wrapper.add_image('zigmap.png', width=NoEscape(r'\linewidth'))
# Add document title
with first_page.create(Head("C")) as center_header:
with center_header.create(
MiniPage(width=NoEscape(r"0.49\textwidth"),
pos='c',
align='c')) as title_wrapper:
title_wrapper.append(LargeText(bold(self.__nombre)))
# Add document title
with first_page.create(Head("R")) as right_header:
with right_header.create(
MiniPage(width=NoEscape(r"0.49\textwidth"),
pos='c',
align='r')) as title_wrapper:
#title_wrapper.append(LargeText(bold("Solemne II")))
#title_wrapper.append(LineBreak())
title_wrapper.append(MediumText(bold(
Asignatura.get_nombreA())))
# Add footer
with first_page.create(Foot("C")) as footer:
message = "Programación II"
with footer.create(
Tabularx("X X X X", width_argument=NoEscape(
r"\textwidth"))) as footer_table:
footer_table.add_row([
MultiColumn(4, align='l', data=TextColor("black", message))
])
footer_table.add_hline(color="black")
footer_table.add_empty_row()
branch_address = MiniPage(width=NoEscape(r"0.45\textwidth"),
pos='t',
align='l')
branch_address.append(
MediumText("Facultad de " + Carrera.get_facultad()))
branch_address.append("\n")
branch_address.append("")
branch_address2 = MiniPage(width=NoEscape(r"0.10\textwidth"),
pos='t')
branch_address2.append("")
branch_address2.append("\n")
branch_address2.append("")
document_details = MiniPage(width=NoEscape(r"0.25\textwidth"),
pos='t',
align='r')
document_details.append(self.__fecha)
document_details.append(LineBreak())
document_details.append("") # simple_page_number()
footer_table.add_row([
branch_address, branch_address2, branch_address2,
document_details
])
doc.preamble.append(first_page)
# End first page style
############################################
####################################################
# Add customer information
with doc.create(Tabu("X[l] X[r]")) as first_page_table:
customer = MiniPage(width=NoEscape(r"0.55\textwidth"), pos='h')
customer.append("Nombre: ___________________________________")
customer.append("\n")
customer.append(" Rut: _______________")
customer.append("\n")
customer.append("Nota: ______________")
customer.append("\n")
customer.append("\n")
# Add branch information
branch = MiniPage(width=NoEscape(r"0.35\textwidth"),
pos='t!',
align='r')
if self.__unidad == "unidad1":
branch.append(bold("Unidad: 1"))
elif self.__unidad == "unidad2":
branch.append(bold("Unidad: 2"))
else:
branch.append(bold("Unidades: 1 & 2"))
branch.append(LineBreak())
branch.append(bold("Curso: "))
branch.append(bold(Curso.get_cod()))
branch.append(LineBreak())
branch.append(bold("Ponderación: "))
branch.append(bold(self.__ponderacion + "%"))
branch.append(LineBreak())
first_page_table.add_row([customer, branch])
doc.append(LargeText(bold("Indicaciones:")))
# INDICACIONES
with doc.create(Itemize()) as itemize:
doc.append(LineBreak())
itemize.add_item(
" Lea atentamente los enunciados de cada pregunta antes de contestar."
)
itemize.add_item(
" Conteste su evaluación en silencio, está prohibido conversar o gesticulizar en la sala durante la prueba."
)
itemize.add_item(
" Dispone de 90 minutos para realizar esta evaluación.")
itemize.add_item(
" Marque la alternativa con lapiz pasta, no se aceptan marcadas con lapiz grafito."
)
itemize.add_item(
" Utilice solamente sus materiales, está prohibido solicitar materiales a sus compañeros."
)
# you can append to existing items
itemize.append(Command("ldots"))
doc.change_document_style("firstpage")
doc.add_color(name="lightgray", model="gray", description="0.80")
customer.append(LineBreak())
now = str(datetime.today())
for p in listaPreguntas:
with doc.create(Section('Pregunta - ' + p.get_tipo())):
doc.append(p.get_contenido())
doc.append(NewPage())
nombreFile = str(
self.__nombre) + " - " + self.get_fecha() + " - " + str(aleatorio)
print(
"--------------------------ANTES DE DIR------------------------------"
)
try:
# GENERANDO PDF
doc.generate_pdf(filepath="tests/" + nombreFile,
clean_tex=True,
clean=True)
#doc.generate_pdf(dirName + "/" + nombreFile, clean_tex=False)
except FileNotFoundError as e:
doc.generate_pdf(filepath="../tests/" + nombreFile,
clean_tex=True,
clean=True)
class RelatorioCliente:
def __init__(self, nomeArquivo, usuario, db=None):
self.nomeArquivo = nomeArquivo
self.usuarioModel = UsuarioModel().fromList(usuario)
self.geometry = {
'head': '40pt',
'margin': '1.5cm',
'tmargin': '1cm',
'includeheadfoot': True
}
self.documento = Document(f'{self.nomeArquivo}',
geometry_options=self.geometry,
page_numbers=False)
self.firstPage = None
self.daoClientes = DaoCliente(db=db)
# Estatísticas
self.totalClientes = 0
self.clientesAtivos = 0
self.clientesInativos = 0
self.mediaClientesAtivos = 0
self.clientesList = None
self.carregarClientes()
self.contaTotalClientes()
def constroiCabecalho(self):
self.firstPage = PageStyle('firstpage')
with self.firstPage.create(Head("L")) as header_left:
with header_left.create(
MiniPage(width=NoEscape(r"0.3\textwidth"),
pos='l')) as logo_wrapper:
with logo_wrapper.create(
Tabularx('X X',
width_argument=NoEscape(
r"0.5\textwidth"))) as logo:
logo.add_row([MultiColumn(2, align='c')])
logo_file = os.path.join(os.getcwd(), 'Telas', 'Imagens',
'nautilusDash.png')
imagem = StandAloneGraphic(image_options="width=36px",
filename=logo_file)
textLogo = MiniPage(width=NoEscape(r"0.6\textwidth"),
content_pos='t',
align='l')
textLogo.append(LargeText(bold('Nautilus')))
textLogo.append(LineBreak())
textLogo.append('Navegue sem medo')
textLogo.append(LineBreak())
textLogo.append('\n')
logo.add_row([imagem, textLogo])
with self.firstPage.create(Head("C")) as headerCenter:
with headerCenter.create(
MiniPage(width=NoEscape(r"0.4\textwidth"),
pos='c')) as centro:
centro.append(LargeText(bold('Relatório geral de clientes')))
# Add document title
with self.firstPage.create(Head("R")) as right_header:
with right_header.create(
MiniPage(width=NoEscape(r"0.3\textwidth"),
pos='R',
align='r')) as title_wrapper:
title_wrapper.append(
LargeText(bold(self.usuarioModel.nomeEmpresa)))
title_wrapper.append(LineBreak())
title_wrapper.append(
MediumText(mascaraMeses(data=datetime.date.today())))
def constroiCorpo(self):
with self.documento.create(Tabu("X[l] X[r]")) as first_page_table:
customer = MiniPage(width=NoEscape(r"0.49\textwidth"), pos='h')
customer.append(bold("Nome fantasia: "))
customer.append(self.usuarioModel.nomeFantasia)
customer.append("\n")
customer.append(bold("CNPJ: "))
customer.append(mascaraCNPJ(self.usuarioModel.cnpj))
customer.append("\n")
customer.append(bold("Endereço: "))
if self.usuarioModel.endereco == 'None':
customer.append('---')
else:
customer.append(self.usuarioModel.endereco)
# Add branch information
branch = MiniPage(width=NoEscape(r"0.49\textwidth"),
pos='t!',
align='r')
branch.append(f"Total de clientes: {self.totalClientes}")
branch.append(LineBreak())
branch.append(f"Total de clientes Ativos: {self.clientesAtivos}")
branch.append(LineBreak())
branch.append(
f"Média de clientes ativos: {round((self.clientesAtivos / self.totalClientes)*100)} % "
)
branch.append(LineBreak())
first_page_table.add_row([customer, branch])
first_page_table.add_empty_row()
self.documento.change_document_style("firstpage")
with self.documento.create(
LongTabu("X[1.5l] X[2l] X[r] X[r] X[r]",
row_height=1.5)) as data_table:
data_table.add_row([
"Última atualização", "Nome do cliente", "Turma", "credits($)",
"balance($)"
],
mapper=bold,
color="lightgray")
data_table.add_empty_row()
data_table.add_hline()
for i, cliente in enumerate(self.clientesList):
clienteRow = list()
clienteRow.append(mascaraMeses(cliente[13]))
clienteRow.append(cliente[1] + ' ' + cliente[2])
clienteRow.append('Teste 1')
clienteRow.append('Teste 2')
clienteRow.append('Teste 3')
if (i % 2) == 0:
data_table.add_row(clienteRow, color="lightgray")
else:
data_table.add_row(clienteRow)
def exportaRelatorio(self, tipo='pdf'):
# Desenvolvimento
fileName = QFileDialog.getSaveFileName(
directory=str(Path.home()),
options=QFileDialog.DontUseNativeDialog,
filter="Adobe Pdf (*.pdf);;Excel (*.xlsx)")
# Produção
# fileName = QFileDialog.getSaveFileName(directory=str(Path.home()), filter="Adobe Pdf (*.pdf);;Excel (*.xlsx)")
print(f'\033[33m{fileName}')
if fileName[0] != '':
if '*.pdf' in fileName[1]:
self.constroiCabecalho()
self.constroiCorpo()
self.documento.preamble.append(self.firstPage)
self.documento.generate_pdf(fileName[0], clean_tex=False)
else:
self.exportaExcel(fileName[0])
def contaTotalClientes(self):
self.totalClientes = self.daoClientes.contaTotal()
self.clientesAtivos = self.daoClientes.contaTotal(
where='WHERE ativo = TRUE')
self.clientesInativos = self.totalClientes - self.clientesAtivos
def carregarClientes(self):
self.clientesList = self.daoClientes.findAll(all=True)
def exportaExcel(self, path):
colunas = [
'Inscrição', 'Nome', 'Sobrenome', 'Telefone', 'E-mail', 'CPF',
'Endereço', 'Complemento', 'CEP', 'Bairro', 'Meio de Pagamento',
'Usuário ativo', 'Data do Cadastro', 'Última atualização'
]
dataFrameClientes = pd.DataFrame(self.clientesList, columns=colunas)
excelWriter = pd.ExcelWriter(f'{path}.xlsx', endine='openpyxl')
dataFrameClientes.to_excel(excel_writer=excelWriter, index=False)
excelWriter.save()
class PimaReport:
def __init__(self, analysis):
self.analysis = analysis
self.report = analysis.report
self.doc = None
def start_doc(self):
geometry_options = {"margin": "0.75in"}
self.doc = Document(geometry_options=geometry_options)
self.doc.preamble.append(Command('usepackage{float}'))
def add_header(self):
header_text = 'Analysis of ' + self.report['name']
header = PageStyle('header')
with header.create(Head('L')):
header.append(header_text)
header.append(LineBreak())
with header.create(Foot('R')):
header.append(simple_page_number())
self.doc.preamble.append(header)
self.doc.change_document_style('header')
def add_summary(self):
with self.doc.create(
Section(self.analysis.summary_title, numbering=False)):
with self.doc.create(Subsection('Run information',
numbering=False)):
with self.doc.create(Tabular('lp{6cm}lp{20cm}',
width=2)) as table:
table.add_row(('Date', self.analysis.start_time))
if self.analysis.ont_fast5:
table.add_row(('ONT FAST5', self.analysis.ont_fast5))
if self.analysis.ont_raw_fastq:
table.add_row(
('ONT FASTQ', self.analysis.ont_raw_fastq))
if self.analysis.illumina_fastq:
table.add_row(
('Illumina FASTQ',
', '.join(self.analysis.illumina_fastq)))
if self.analysis.genome_fasta:
table.add_row(('Assembly', self.analysis.genome_fasta))
if self.analysis.reference_fasta:
table.add_row(
('Reference', self.analysis.reference_fasta))
self.doc.append(VerticalSpace("10pt"))
if not (self.analysis.ont_n50 is None):
with self.doc.create(
Subsection('ONT library statistics', numbering=False)):
with self.doc.create(Tabular('ll', width=2)) as table:
table.add_row(
('ONT N50', '{:,}'.format(self.analysis.ont_n50)))
table.add_row(
('ONT reads',
'{:,}'.format(self.analysis.ont_read_count)))
table.add_row(('ONT bases',
'{:s}'.format(self.analysis.ont_bases)))
self.doc.append(VerticalSpace("10pt"))
if not (self.analysis.illumina_length_mean is None):
with self.doc.create(
Subsection('Illumina library statistics',
numbering=False)):
with self.doc.create(Tabular('ll', width=2)) as table:
table.add_row(('Illumina mean length', '{:.1f}'.format(
self.analysis.illumina_length_mean)))
table.add_row(
('Illumina reads',
'{:,}'.format(self.analysis.illumina_read_count)))
table.add_row(
('Illumina bases',
'{:s}'.format(self.analysis.illumina_bases)))
self.doc.append(VerticalSpace("10pt"))
if not (self.analysis.genome is None):
with self.doc.create(
Subsection('Assembly statistics', numbering=False)):
with self.doc.create(Tabular('ll', width=2)) as table:
table.add_row(('Contigs', len(self.analysis.genome)))
genome_size = 0
for i in self.analysis.genome:
genome_size += len(i.seq)
genome_size = si_format(genome_size, precision=1)
table.add_row(('Assembly size', genome_size))
self.doc.append(VerticalSpace("10pt"))
if len(self.report[self.analysis.assembly_title]) > 0:
if len(self.report[self.analysis.assembly_title][
self.analysis.assembly_notes_title]) > 0:
with self.doc.create(
Subsection(self.analysis.assembly_notes_title,
numbering=False)):
left = FlushLeft()
for note in self.report[self.analysis.assembly_title][
self.analysis.assembly_notes_title]:
left.append(note)
left.append(LineBreak())
self.doc.append(left)
self.doc.append(VerticalSpace("10pt"))
if not (self.analysis.contig_info is None):
for method in ['ONT', 'Illumina']:
if not method in self.analysis.contig_info.index:
continue
with self.doc.create(
Subsection('Assembly coverage by ' + method,
numbering=False)):
table_format = 'l' * self.analysis.contig_info[
method].shape[1]
self.doc.append('')
with self.doc.create(Tabular(table_format)) as table:
table.add_row(
('Contig', 'Length (bp)', 'Coverage (X)'))
table.add_hline()
formatted = self.analysis.contig_info[method].copy(
)
formatted.iloc[:, 1] = formatted.iloc[:, 1].apply(
lambda x: '{:,}'.format(x))
for i in range(self.analysis.contig_info[method].
shape[0]):
table.add_row(
formatted.iloc[i, :].values.tolist())
self.doc.append(LineBreak())
self.doc.append(VerticalSpace("10pt"))
def add_alignment(self):
if len(self.report[self.analysis.alignment_title][
self.analysis.contig_alignment_title]) > 0:
alignments = self.report[self.analysis.alignment_title][
self.analysis.contig_alignment_title]
else:
return
self.doc.append(NewPage())
with self.doc.create(
Section(self.analysis.alignment_title, numbering=False)):
with self.doc.create(
Subsection(self.analysis.snp_indel_title,
numbering=False)):
with self.doc.create(Tabular('ll', width=2)) as table:
table.add_row(
('SNPs',
'{:,}'.format(self.analysis.quast_mismatches)))
table.add_row(('Small indels',
'{:,}'.format(self.analysis.quast_indels)))
self.doc.append(LineBreak())
if len(self.report[self.analysis.alignment_title][
self.analysis.alignment_notes_title]) > 0:
with self.doc.create(
Subsection(self.analysis.alignment_notes_title,
numbering=False)):
left = FlushLeft()
for note in self.report[self.analysis.alignment_title][
self.analysis.alignment_notes_title]:
left.append(note)
left.append(LineBreak())
self.doc.append(left)
for contig in alignments.index.tolist():
contig_title = 'Alignment to ' + contig
self.doc.append(
Command('graphicspath{{../circos/' + contig + '/}}'))
image_png = os.path.basename(alignments[contig])
with self.doc.create(Subsection(contig_title,
numbering=False)):
with self.doc.create(Figure(position='H')) as figure:
figure.add_image(image_png, width='5in')
def add_features(self):
if len(self.report[self.analysis.feature_title]) == 0:
return
self.doc.append(NewPage())
with self.doc.create(
Section(self.analysis.feature_title, numbering=False)):
for feature_name in self.report[
self.analysis.feature_title].index.tolist():
features = self.report[
self.analysis.feature_title][feature_name].copy()
if features.shape[0] == 0:
continue
features.iloc[:, 1] = features.iloc[:, 1].apply(
lambda x: '{:,}'.format(x))
features.iloc[:, 2] = features.iloc[:, 2].apply(
lambda x: '{:,}'.format(x))
table_format = 'l' * (features.shape[1] - 1)
with self.doc.create(Subsection(feature_name,
numbering=False)):
if (features.shape[0] == 0):
self.doc.append('None')
continue
for contig in pandas.unique(features.iloc[:, 0]):
self.doc.append(contig)
contig_features = features.loc[(
features.iloc[:, 0] == contig), :]
with self.doc.create(Tabular(table_format)) as table:
table.add_row(('Start', 'Stop', 'Feature',
'Identity (%)', 'Strand'))
table.add_hline()
for i in range(contig_features.shape[0]):
feature = contig_features.iloc[i, :].copy(
deep=True)
feature[4] = '{:.3f}'.format(feature[4])
table.add_row(feature[1:].values.tolist())
self.doc.append(LineBreak())
self.doc.append(VerticalSpace("10pt"))
def add_feature_plots(self):
if len(self.report[self.analysis.feature_plot_title]) == 0:
return
self.doc.append(NewPage())
self.doc.append(Command('graphicspath{{../drawing/}}'))
with self.doc.create(Section('Feature plots', numbering=False)):
self.doc.append('Only contigs with features are shown')
for contig in self.report[
self.analysis.feature_plot_title].index.tolist():
image_png = os.path.basename(
self.report[self.analysis.feature_plot_title][contig])
with self.doc.create(Figure(position='h!')) as figure:
figure.add_image(image_png, width='7in')
def add_mutations(self):
# Make sure we looked for mutations
if len(self.report[self.analysis.mutation_title]) == 0:
return
mutations = self.report[self.analysis.mutation_title]
self.doc.append(NewPage())
table_format = 'l' * 4
with self.doc.create(
Section(self.analysis.mutation_title, numbering=False)):
for region_name in mutations.index.tolist():
region_mutations = mutations[region_name].copy()
with self.doc.create(Subsection(region_name, numbering=False)):
if (region_mutations.shape[0] == 0):
self.doc.append('None')
continue
region_mutations.iloc[:,
1] = region_mutations.iloc[:, 1].apply(
lambda x: '{:,}'.format(x))
with self.doc.create(Tabular(table_format)) as table:
table.add_row(('Reference contig', 'Position',
'Reference', 'Alternate'))
table.add_hline()
for i in range(region_mutations.shape[0]):
table.add_row(region_mutations.iloc[
i, [0, 1, 3, 4]].values.tolist())
def add_amr_matrix(self):
# Make sure that we have an AMR matrix to plot
amr_matrix = self.report[self.analysis.amr_matrix_title]
if len(amr_matrix) == 0:
return
if amr_matrix is None:
return
self.doc.append(NewPage())
with self.doc.create(
Section(self.analysis.amr_matrix_title, numbering=False)):
self.doc.append(
'AMR genes and mutations with their corresponding drugs.')
self.doc.append(Command('graphicspath{{../}}'))
with self.doc.create(Figure(position='h!')) as figure:
figure.add_image(amr_matrix['png'], width='7in')
def add_large_indels(self):
# Make sure we looked for mutations
if len(self.report[self.analysis.large_indel_title]) == 0:
return
large_indels = self.report[self.analysis.large_indel_title]
if large_indels is None:
return
self.doc.append(NewPage())
with self.doc.create(
Section(self.analysis.large_indel_title, numbering=False)):
for genome in ['Reference insertions', 'Query insertions']:
genome_indels = large_indels[genome].copy()
with self.doc.create(Subsection(genome, numbering=False)):
if (genome_indels.shape[0] == 0):
self.doc.append('None')
continue
genome_indels.iloc[:, 1] = genome_indels.iloc[:, 1].apply(
lambda x: '{:,}'.format(x))
genome_indels.iloc[:, 2] = genome_indels.iloc[:, 2].apply(
lambda x: '{:,}'.format(x))
genome_indels.iloc[:, 3] = genome_indels.iloc[:, 3].apply(
lambda x: '{:,}'.format(x))
table_format = 'l' * genome_indels.shape[1]
with self.doc.create(Tabular(table_format)) as table:
table.add_row(
('Reference contig', 'Start', 'Stop', 'Size (bp)'))
table.add_hline()
for i in range(genome_indels.shape[0]):
table.add_row(
genome_indels.iloc[i, :].values.tolist())
def add_plasmids(self):
if len(self.report[self.analysis.plasmid_title]) == 0:
return
# Make sure we looked for mutations
plasmids = self.report[self.analysis.plasmid_title].copy()
if plasmids is None:
return
self.doc.append(NewPage())
with self.doc.create(
Section(self.analysis.plasmid_title, numbering=False)):
if (plasmids.shape[0] == 0):
self.doc.append('None')
return
plasmids.iloc[:, 3] = plasmids.iloc[:, 3].apply(
lambda x: '{:,}'.format(x))
plasmids.iloc[:, 4] = plasmids.iloc[:, 4].apply(
lambda x: '{:,}'.format(x))
plasmids.iloc[:, 5] = plasmids.iloc[:, 5].apply(
lambda x: '{:,}'.format(x))
table_format = 'p{0.15\linewidth}p{0.3\linewidth}p{0.1\linewidth}p{0.08\linewidth}p{0.08\linewidth}p{0.08\linewidth}'
with self.doc.create(Tabular(table_format)) as table:
table.add_row(('Genome contig', 'Plasmid hit', 'Plasmid acc.',
'Contig size', 'Aliged', 'Plasmid size'))
table.add_hline()
for i in range(plasmids.shape[0]):
table.add_row(plasmids.iloc[i, 0:6].values.tolist())
def add_methods(self):
self.doc.append(NewPage())
methods = self.report[self.analysis.methods_title]
with self.doc.create(
Section(self.analysis.methods_title, numbering=False)):
for methods_section in methods.index.tolist():
if len(methods[methods_section]) == 0:
continue
with self.doc.create(
Subsection(methods_section, numbering=False)):
self.doc.append(' '.join(methods[methods_section]))
def make_tex(self):
self.doc.generate_tex(self.analysis.report_prefix)
def make_report(self):
self.start_doc()
self.add_header()
self.add_summary()
self.add_alignment()
self.add_features()
self.add_feature_plots()
self.add_mutations()
self.add_large_indels()
self.add_plasmids()
self.add_amr_matrix()
#self.add_snps()
self.add_methods()
self.make_tex()
def save_latex(self, reportsummary, filename, rel_path, Disp_3d_image):
companyname = str(reportsummary["ProfileSummary"]['CompanyName'])
companylogo = str(reportsummary["ProfileSummary"]['CompanyLogo'])
groupteamname = str(reportsummary["ProfileSummary"]['Group/TeamName'])
designer = str(reportsummary["ProfileSummary"]['Designer'])
projecttitle = str(reportsummary['ProjectTitle'])
subtitle = str(reportsummary['Subtitle'])
jobnumber = str(reportsummary['JobNumber'])
client = str(reportsummary['Client'])
header = PageStyle("header")
# Create center header
with header.create(Head("C")):
with header.create(Tabularx('|l|p{6cm}|l|X|')) as table:
table.add_hline()
# MultiColumn(4)
table.add_row(('Company Name', companyname, 'Project Title',
projecttitle),
color='OsdagGreen')
table.add_hline()
table.add_row(
('Group/Team Name', groupteamname, 'Subtitle', subtitle),
color='OsdagGreen')
table.add_hline()
table.add_row(('Designer', designer, 'Job Number', jobnumber),
color='OsdagGreen')
table.add_hline()
table.add_row(
('Date', time.strftime("%d /%m /%Y"), 'Client', client),
color='OsdagGreen')
table.add_hline()
# Create right footer
with header.create(Foot("R")):
header.append(NoEscape(r'Page \thepage'))
geometry_options = {
"top": "1.2in",
"bottom": "1in",
"left": "0.6in",
"right": "0.6in",
"headsep": "0.8in"
}
doc = Document(geometry_options=geometry_options, indent=False)
doc.packages.append(Package('amsmath'))
doc.packages.append(Package('graphicx'))
doc.packages.append(Package('needspace'))
doc.add_color('OsdagGreen', 'HTML', 'D5DF93')
doc.preamble.append(header)
doc.change_document_style("header")
with doc.create(Section('Design Conclusion')):
with doc.create(Tabularx('|X|X|', row_height=1.2)) as table:
table.add_hline()
table.add_row(('Section Designation', 'Remarks'),
color='OsdagGreen')
table.add_hline()
table.add_row(
(reportsummary['Define Section']['Section Designation'],
'Pass'))
table.add_hline()
with doc.create(Section('Section Details')):
with doc.create(Tabularx('|X|X|', row_height=1.2)) as table:
table.add_hline()
table.add_row(
(bold('Section Type'),
reportsummary['Define Section']['Section Type']))
table.add_hline()
table.add_row(
(bold('Section Template'),
reportsummary['Define Section']['Section Template']))
table.add_hline()
with doc.create(Section('Section Parameters')):
with doc.create(Tabularx('|X|X|', row_height=1.2)) as table:
for parameter in reportsummary['Define Section'][
'Section Parameters']:
para = reportsummary['Define Section'][
'Section Parameters'][parameter]
table.add_hline()
table.add_row((bold(para[0]), para[1]))
table.add_hline()
labels = [
'Area, a(cm²)',
'Moment of Inertia',
'I_zz(cm4)',
'I_yy(cm4)',
'Radius of Gyration',
'r_zz(cm)',
'r_yy(cm)',
'Centriod',
'c_z(cm)',
'c_y(cm)',
'Plastic Section modulus',
'Z_pz(cm³)',
'Z_py(cm³)',
'Elastic Section modulus',
'Z_zz(cm³)',
'Z_yy(cm³)',
]
values = list(reportsummary['Section Properties'].values())
Properties = [
(labels[0], values[0]),
(labels[1], ""),
(labels[2], values[1]),
(labels[3], values[2]),
(labels[4], ""),
(labels[5], values[3]),
(labels[6], values[4]),
(labels[7], ""),
(labels[8], values[5]),
(labels[9], values[6]),
(labels[10], ""),
(labels[11], values[7]),
(labels[12], values[8]),
(labels[13], ""),
(labels[14], values[9]),
(labels[15], values[10]),
]
with doc.create(Section('Section Properties')):
with doc.create(Tabularx('|X|X|', row_height=1.2)) as table:
for ppty in Properties:
table.add_hline()
table.add_row((bold(ppty[0]), ppty[1]))
table.add_hline()
doc.append(NewPage())
if (not 'TRAVIS' in os.environ):
with doc.create(Section('3D View')):
with doc.create(Figure(position='h!')) as view_3D:
view_3dimg_path = rel_path + Disp_3d_image
# view_3D.add_image(filename=view_3dimg_path, width=NoEscape(r'\linewidth'))
view_3D.add_image(filename=view_3dimg_path)
view_3D.add_caption('3D View')
try:
doc.generate_pdf(filename, compiler='pdflatex', clean_tex=False)
except:
pass
def generate_unique(cpm):
geometry_options = {
"head": "60pt",
"margin": "0.5in",
"bottom": "0.6in",
"includeheadfoot": True
}
doc = Document(geometry_options=geometry_options)
first_page = PageStyle("firstpage")
with first_page.create(Head("L")) as header_left:
with header_left.create(
MiniPage(width=NoEscape(r"0.49\textwidth"), pos='c',
align='L')) as logo_wrapper:
logo_file = os.path.join(current_app.root_path,
"static/logo/sf.png")
logo_wrapper.append(
StandAloneGraphic(image_options="width=120px",
filename=logo_file))
with first_page.create(Head("R")) as header_right:
with header_right.create(
MiniPage(width=NoEscape(r'0.49\textwidth'), pos='c',
align='r')) as wrapper_right:
wrapper_right.append(LargeText(bold('SOCIALFISH')))
wrapper_right.append(LineBreak())
wrapper_right.append(MediumText(bold('UNDEADSEC')))
wrapper_right.append(LineBreak())
wrapper_right.append(NoEscape(r'\today'))
with first_page.create(Head('C')) as header_center:
header_center.append('CAPTURE REPORT')
with first_page.create(Foot("C")) as footer:
message = "Important message please read"
doc.preamble.append(first_page)
with doc.create(Tabu("X[l] X[r]")) as first_page_table:
customer = MiniPage(width=NoEscape(r"0.49\textwidth"), pos='h')
branch = MiniPage(width=NoEscape(r"0.49\textwidth"),
pos='t!',
align='r')
first_page_table.add_row([customer, branch])
first_page_table.add_empty_row()
doc.change_document_style("firstpage")
doc.add_color(name="lightgray", model="gray", description="0.80")
with doc.create(LongTabu("X[15l]", row_height=1.8)) as data_table:
data_table.add_row(["Organization\nCapture IP\nBrowser\nLog\n"],
mapper=bold,
color="lightgray")
data_table.add_empty_row()
data_table.add_hline()
result_query, result_count = generate_report(cpm)
x = 0
for i in range(result_count):
url = result_query[1 + x].split('//')[1]
ip = result_query[7 + x]
log_dict = literal_eval(result_query[2 + x])
if 'skstamp' in log_dict.keys():
rm_trash = log_dict.pop('skstamp')
elif 'utf8' in log_dict.keys():
rm_trash = log_dict.pop('utf8')
browser = result_query[4 + x] + ' v' + result_query[5 + x]
x = 8 * (i + 1)
row_tex = [
url + '\n' + ip + '\n' + browser + '\n' + str(log_dict) + '\n'
]
if (i % 2) == 0:
data_table.add_row(row_tex, color="lightgray")
else:
data_table.add_row(row_tex)
doc.append(NewPage())
pdf_name = 'Report{}'.format(strftime('-%y%m'))
doc.generate_pdf(pdf_name, clean_tex=False)
open_new(os.getcwd() + '/' + pdf_name + '.pdf')
class TestCreator:
def __init__(self, questions):
self.all_qs = questions.all_questions
self.headers = questions.headings
self.folder = questions.folder
self.filename, self.extension = os.path.splitext(
os.path.basename(questions.wordfile))
self.doc = None
self.convert()
def generate_header(self,
output="Exam",
instructor="Vaccaro",
section="English",
test_name="Final Exam",
version=1):
header = PageStyle("header")
with header.create(Head("C")):
header.append(instructor)
header.append(LineBreak())
with header.create(Head("L")):
header.append(section)
header.append(LineBreak())
header.append(test_name +
str(version) if output != 'key' else test_name)
with header.create(Head("R")):
if (output == "exam"):
header.append("Student: _____________")
elif (output == "answers"):
header.append("Answers v" + str(version))
else:
header.append("Key")
with header.create(Foot("R")):
header.append(simple_page_number())
return header
def mcExamOptions(self,
output='concept',
versions=4,
version=1,
randomq='true',
randoma='true'):
#output=concept, exam, key, answers, analysis
options = 'output=' + output + ', '
options += 'numberofversions=' + str(versions) + ', '
options += 'version=' + str(version) + ', '
options += 'seed=' + str(7) + ', '
options += 'randomizequestions=' + randomq + ', '
options += 'randomizeanswers=' + randoma + ', '
options += 'writeRfile=' + 'false'
return options
def keep_qandas_together(self):
# Code to keep the questions and answers on the same page
# Returns an Arguments type
linewidthCmd = Command(command='linewidth')
labelWidthCmd = Command(command='labelwidth')
beginMiniPgCmd = Command(
command='begin',
arguments='minipage',
options='t',
extra_arguments=NoEscape(linewidthCmd.dumps() + '-' +
labelWidthCmd.dumps()))
endMiniPgCmd = Command(command='end', arguments='minipage')
parCmd = Command(command='par')
arg2 = NoEscape(beginMiniPgCmd.dumps())
arg3 = NoEscape(endMiniPgCmd.dumps() + parCmd.dumps())
return Arguments('setmcquestion', arg2, arg3)
def addAnswerList(self, question):
self.doc.append(Command('begin', arguments='mcanswerslist'))
if question.alloftheabove and question.noneoftheabove:
self.doc.append(NoEscape("[permutenone]"))
elif question.alloftheabove or question.noneoftheabove:
self.doc.append(NoEscape("[fixlast]"))
for index in range(0, len(question.choices)):
if str(index + 1) == question.answer:
opt = 'correct'
else:
opt = ''
self.doc.append(Command('answer', options=opt))
self.strip_tags(question.choices[index])
self.doc.append(Command('end', 'mcanswerslist'))
def addQuestion(self, question):
if question.instructions != None:
self.doc.append(Command('begin', 'mcquestioninstruction'))
self.doc.append(question.instructions)
self.doc.append(Command('end', 'mcquestioninstruction'))
self.doc.append(Command('question'))
self.strip_tags(question.question)
self.addAnswerList(question)
def add_allQs(self):
for quest in self.all_qs:
self.addQuestion(quest)
def strip_tags(self, string):
while '\\' in string:
# Find slash, grab the text before the slash (left), find the other locations
# that are key - the braces - and grab the key and the emphaszied text, then
# send the rest of the rest of the string back through the while loop in case
# there are other tags that need to be stripped
# TODO: what happens if text is both italicized and underlined?
slashLocation = string.find('\\')
left = string[:slashLocation]
textStart = string.find('{')
tag = string[slashLocation + 1:textStart]
tagEnd = string.find('}')
emphasizedText = string[textStart + 1:tagEnd]
# if '\\' in emphasizedText:
# so ... with a double tag ... you have to
# update where the tagEnd is, put the left stuff in the document
# put the first tag in and the first part of the emphasized text in
# then the strip the tags from the new emphasized text
# and what do you do with the right side ... hmmmm
# self.strip_tags(emphasizedText)
# Append the text as appropriate
self.doc.append(left)
if tag == 'underline':
self.doc.append(Command('underline', emphasizedText))
elif tag == 'textit':
self.doc.append(italic(emphasizedText))
elif tag == 'textbf':
self.doc.append(bold(emphasizedText))
else:
self.doc.append(emphasizedText)
if string[tagEnd + 1:tagEnd + 2] == ' ': # Force a space
self.doc.append(bold(' '))
string = string[
tagEnd +
1:] # remove what was added to the doc already from the string
# After the while loop is done, if there is any string left, append it (it is not emphasized)
self.doc.append(string)
def add_instructions(self, instructions):
# Leaving this in its own method in case we want to add different formatting for the instructions
self.strip_tags(instructions)
def add_mcexam_package(self,
output='exam',
version=1,
versions=4,
randomq='true',
randoma='true'):
return Package(
'mcexam',
self.mcExamOptions(
output=output, #concept, exam, key, answers, analysis
versions=versions,
version=version,
randomq=randomq,
randoma=randoma))
def add_packages(self,
output,
version,
versions=4,
randomq='true',
randoma='true'):
# self.doc.packages.append(Package('mcexam', self.mcExamOptions('concept', 4, 1, 'true', 'true')))
self.doc.packages.append(
self.add_mcexam_package(output, version, versions, randomq,
randoma))
self.doc.packages.append(Package('calc'))
self.doc.packages.append(Package('geometry', options='margin=0.75in'))
def convert(self, versions=4, randomq='true', randoma='true'):
#create_qs()
newfolder = self.folder + '/' + self.filename
if not os.path.exists(newfolder):
os.mkdir(newfolder)
output = 'exam' # output needs to run through a list to get all versions
for output in {'exam', 'answers', 'key'}:
for version in range(1, versions + 1):
if output == 'key' and version > 1: # Only create 1 key document with all versions
break
self.doc = Document(document_options="letter")
self.add_packages(output, version, versions, randomq, randoma)
self.doc.preamble.append(
Command(command='renewenvironment',
arguments=self.keep_qandas_together()))
self.doc.preamble.append(
self.generate_header(output, Teacher.NAME,
self.headers.section,
self.headers.test_name, version))
self.doc.change_document_style("header")
self.add_instructions(self.headers.instructions)
self.doc.append(Command('begin', 'mcquestions'))
self.add_allQs()
self.doc.append(Command('end', 'mcquestions'))
# self.doc.generate_pdf('basic_maketitle2', clean_tex=False, compiler='pdflatex')
if (output == 'key'):
newfilename = newfolder + '/' + self.filename + '_' + output
else:
newfilename = newfolder + '/' + self.filename + '_' + output + '_v' + str(
version)
self.doc.generate_pdf(newfilename,
clean_tex=False,
compiler='pdflatex')
print("." + " " + newfilename)
class PimaReport:
def __init__(self, analysis):
self.analysis = analysis
self.doc = None
self.summary_title = 'Summary'
self.basecalling_title = 'Basecalling'
self.assembly_notes_title = 'Assembly notes'
self.alignment_title = 'Comparison with reference'
self.alignment_notes_title = 'Alignment notes'
self.contig_alignment_title = 'Alignment vs. reference contigs'
self.large_indel_title = 'Large insertions & deletions'
self.snp_indel_title = 'SNPs and small indels'
self.feature_title = 'Features found in the assembly'
self.feature_plot_title = 'Feature annotation plots'
self.mutation_title = 'Mutations found in the sample'
self.amr_matrix_title = 'AMR matrix'
self.methods = pd.Series(dtype='float64')
self.methods_title = 'Methods'
self.basecalling_methods_title = 'Basecalling'
self.contamination_methods_title = 'Contamination check'
self.methods[self.contamination_methods_title] = pd.Series(
dtype='float64')
self.assembly_methods_title = 'Assembly'
self.methods[self.assembly_methods_title] = pd.Series(dtype='float64')
self.reference_methods_title = 'Reference comparison'
self.methods[self.reference_methods_title] = pd.Series(dtype='float64')
self.mutation_methods_title = 'Mutation screening'
self.methods[self.mutation_methods_title] = pd.Series(dtype='float64')
self.feature_methods_title = 'Feature annotation'
self.methods[self.feature_methods_title] = pd.Series(dtype='float64')
self.plasmid_methods_title = 'Plasmid annotation'
self.methods[self.plasmid_methods_title] = pd.Series(dtype='float64')
def start_doc(self):
geometry_options = {"margin": "0.75in"}
self.doc = Document(geometry_options=geometry_options)
self.doc.preamble.append(Command('usepackage{float}'))
def add_header(self):
header_text = 'Analysis of ' + self.analysis.analysis_name
header = PageStyle('header')
with header.create(Head('L')):
header.append(header_text)
header.append(LineBreak())
with header.create(Foot('R')):
header.append(simple_page_number())
self.doc.preamble.append(header)
self.doc.change_document_style('header')
def add_summary(self):
with self.doc.create(Section(self.summary_title, numbering=False)):
with self.doc.create(Subsection('CDC Advisory',
numbering=False)) as subsection:
self.doc.append(cdc_advisory)
self.add_run_information()
self.add_ont_library_information()
methods = []
if self.analysis.did_guppy_ont_fast5:
methods += [
'ONT reads were basecalled using guppy (v ' +
self.analysis.versions['guppy'] + ').'
]
if self.analysis.did_qcat_ont_fastq:
methods += [
'ONT reads were demultiplexed and trimmed using qcat (v ' +
self.analysis.versions['qcat'] + ').'
]
self.methods[self.basecalling_methods_title] = pd.Series(methods)
self.add_illumina_library_information()
self.add_assembly_information()
self.add_contig_info()
self.add_assembly_notes()
if self.analysis.did_flye_ont_fastq:
method = 'ONT reads were assembled using Flye (v ' + self.analysis.versions[
'flye'] + ').'
self.methods[self.assembly_methods_title] = self.methods[
self.assembly_methods_title].append(pd.Series(method))
if self.analysis.did_medaka_ont_assembly:
method = 'The genome assembly was polished using ONT reads and Medaka (v ' +\
self.analysis.versions['medaka'] + ').'
self.methods[self.assembly_methods_title] = self.methods[
self.assembly_methods_title].append(pd.Series(method))
def add_run_information(self):
with self.doc.create(Subsection('Run information', numbering=False)):
with self.doc.create(
Tabular('p{0.15\linewidth}p{0.65\linewidth}',
width=2)) as table:
table.add_row(('Date', self.analysis.start_time))
if self.analysis.ont_fast5:
table.add_row(('ONT FAST5', self.analysis.ont_fast5))
if self.analysis.ont_raw_fastq:
table.add_row(('ONT FASTQ', self.analysis.ont_raw_fastq))
if self.analysis.illumina_fastq:
table.add_row(('Illumina FASTQ',
', '.join(self.analysis.illumina_fastq)))
if self.analysis.genome_fasta:
table.add_row(('Assembly', self.analysis.genome_fasta))
if self.analysis.reference_fasta:
table.add_row(('Reference', self.analysis.reference_fasta))
self.doc.append(VerticalSpace("10pt"))
def add_ont_library_information(self):
if self.analysis.ont_n50 is None:
return
with self.doc.create(
Subsection('ONT library statistics', numbering=False)):
with self.doc.create(Tabular('ll', width=2)) as table:
table.add_row(
('ONT N50', '{:,}'.format(self.analysis.ont_n50)))
table.add_row(
('ONT reads', '{:,}'.format(self.analysis.ont_read_count)))
table.add_row(
('ONT bases', '{:s}'.format(self.analysis.ont_bases)))
self.doc.append(VerticalSpace("10pt"))
def add_illumina_library_information(self):
if self.analysis.illumina_length_mean is None:
return
with self.doc.create(
Subsection('Illumina library statistics', numbering=False)):
with self.doc.create(Tabular('ll', width=2)) as table:
table.add_row(
('Illumina mean length',
'{:.1f}'.format(self.analysis.illumina_length_mean)))
table.add_row(
('Illumina reads',
'{:,}'.format(self.analysis.illumina_read_count)))
table.add_row(('Illumina bases',
'{:s}'.format(self.analysis.illumina_bases)))
self.doc.append(VerticalSpace("10pt"))
def add_assembly_information(self):
if self.analysis.genome is None:
return
with self.doc.create(Subsection('Assembly statistics',
numbering=False)):
with self.doc.create(Tabular('ll', width=2)) as table:
table.add_row(('Contigs', len(self.analysis.genome)))
genome_size = 0
for i in self.analysis.genome:
genome_size += len(i.seq)
genome_size = si_format(genome_size, precision=1)
table.add_row(('Assembly size', genome_size))
self.doc.append(VerticalSpace("10pt"))
def add_contig_info(self):
if self.analysis.contig_info is None:
return
for method in ['ONT', 'Illumina']:
if not method in self.analysis.contig_info.index:
continue
with self.doc.create(
Subsection('Assembly coverage by ' + method,
numbering=False)):
table_format = 'l' * self.analysis.contig_info[method].shape[1]
self.doc.append('')
with self.doc.create(Tabular(table_format)) as table:
table.add_row(('Contig', 'Length (bp)', 'Coverage (X)'))
table.add_hline()
formatted = self.analysis.contig_info[method].copy()
formatted.iloc[:, 1] = formatted.iloc[:, 1].apply(
lambda x: '{:,}'.format(x))
for i in range(self.analysis.contig_info[method].shape[0]):
table.add_row(formatted.iloc[i, :].values.tolist())
self.doc.append(LineBreak())
self.doc.append(VerticalSpace("10pt"))
def add_assembly_notes(self):
if len(self.analysis.assembly_notes) == 0:
return
with self.doc.create(
Subsection(self.assembly_notes_title, numbering=False)):
left = FlushLeft()
for _, note in self.analysis.assembly_notes.iteritems():
left.append(note)
left.append(LineBreak())
self.doc.append(left)
self.doc.append(VerticalSpace("10pt"))
def add_contamination(self):
if len(self.analysis.kraken_fracs) == 0:
return
self.doc.append(NewPage())
with self.doc.create(Section('Contamination check', numbering=False)):
for read_type, kraken_fracs in self.analysis.kraken_fracs.iteritems(
):
left = FlushLeft()
left.append(read_type + ' classifications')
left.append(VerticalSpace('5pt'))
self.doc.append(left)
with self.doc.create(
Tabular(''.join(['l'] * kraken_fracs.shape[1]),
width=kraken_fracs.shape[1])) as table:
table.add_row(
('Percent of reads', 'Reads', 'Level', 'Label'))
table.add_hline()
for index, row in kraken_fracs.iterrows():
table.add_row(row.tolist())
self.doc.append(LineBreak())
self.doc.append(VerticalSpace('5pt'))
if not self.contamination_methods_title in self.methods:
self.methods[self.contamination_methods_title] = ''
method = 'Kraken2 (' + self.analysis.versions[
'kraken2'] + ') was used to assign the raw reads into taxa.'
self.methods[self.contamination_methods_title] = self.methods[
self.contamination_methods_title].append(pd.Series(method))
def add_alignment(self):
if len(self.analysis.contig_alignment) > 0:
alignments = self.analysis.contig_alignment
else:
return
self.doc.append(NewPage())
with self.doc.create(Section(self.alignment_title, numbering=False)):
with self.doc.create(
Subsection(self.snp_indel_title, numbering=False)):
with self.doc.create(Tabular('ll', width=2)) as table:
table.add_row(
('SNPs',
'{:,}'.format(self.analysis.quast_mismatches)))
table.add_row(('Small indels',
'{:,}'.format(self.analysis.quast_indels)))
self.doc.append(LineBreak())
if len(self.analysis.alignment_notes) > 0:
with self.doc.create(
Subsection(self.alignment_notes_title,
numbering=False)):
left = FlushLeft()
for note in self.analysis.alignment_notes:
left.append(note)
left.append(LineBreak())
self.doc.append(left)
for contig in alignments.index.tolist():
contig_title = 'Alignment to ' + contig
self.doc.append(
Command('graphicspath{{../circos/' + contig + '/}}'))
image_png = os.path.basename(alignments[contig])
with self.doc.create(Subsection(contig_title,
numbering=False)):
with self.doc.create(Figure(position='H')) as figure:
figure.add_image(image_png, width='5in')
method = 'The genome assembly was aligned against the reference sequencing using dnadiff (v ' \
+ self.analysis.versions['dnadiff'] + ').'
self.methods[self.reference_methods_title] = self.methods[
self.reference_methods_title].append(pd.Series(method))
def add_features(self):
if len(self.analysis.feature_hits) == 0:
return
self.doc.append(NewPage())
with self.doc.create(Section(self.feature_title, numbering=False)):
for feature_name in self.analysis.feature_hits.index.tolist():
features = self.analysis.feature_hits[feature_name].copy()
if features.shape[0] == 0:
continue
features.iloc[:, 1] = features.iloc[:, 1].apply(
lambda x: '{:,}'.format(x))
features.iloc[:, 2] = features.iloc[:, 2].apply(
lambda x: '{:,}'.format(x))
table_format = 'l' * (features.shape[1] - 1)
with self.doc.create(Subsection(feature_name,
numbering=False)):
if (features.shape[0] == 0):
self.doc.append('None')
continue
for contig in pd.unique(features.iloc[:, 0]):
self.doc.append(contig)
contig_features = features.loc[(
features.iloc[:, 0] == contig), :]
with self.doc.create(Tabular(table_format)) as table:
table.add_row(('Start', 'Stop', 'Feature',
'Identity (%)', 'Strand'))
table.add_hline()
for i in range(contig_features.shape[0]):
feature = contig_features.iloc[i, :].copy(
deep=True)
feature[4] = '{:.3f}'.format(feature[4])
table.add_row(feature[1:].values.tolist())
self.doc.append(LineBreak())
self.doc.append(VerticalSpace("10pt"))
method = 'The genome assembly was queried for features using blastn (v ' + self.analysis.versions['blastn'] + '). ' + \
'Feature hits were clustered using bedtools (v ' + self.analysis.versions['bedtools'] + ') ' + \
'and the highest scoring hit for each cluster was reported.'
self.methods[self.feature_methods_title] = self.methods[
self.feature_methods_title].append(pd.Series(method))
def add_feature_plots(self):
if len(self.analysis.feature_plots) == 0:
return
self.doc.append(NewPage())
self.doc.append(Command('graphicspath{{../drawing/}}'))
with self.doc.create(Section('Feature plots', numbering=False)):
self.doc.append('Only contigs with features are shown')
for contig in self.analysis.feature_plots.index.tolist():
image_png = os.path.basename(
self.analysis.feature_plots[contig])
with self.doc.create(Figure(position='h!')) as figure:
figure.add_image(image_png, width='7in')
def add_mutations(self):
# Make sure we looked for mutations
if not getattr(self.analysis, 'did_call_amr_mutations', False):
return
mutations = self.analysis.amr_mutations
self.doc.append(NewPage())
table_format = 'p{0.1\linewidth}p{0.1\linewidth}p{0.12\linewidth}p{0.12\linewidth}p{0.12\linewidth}p{0.34\linewidth}'
with self.doc.create(Section(self.mutation_title, numbering=False)):
for region_name in mutations.index.tolist():
region_mutations = mutations[region_name].copy()
with self.doc.create(Subsection(region_name, numbering=False)):
if (region_mutations.shape[0] == 0):
self.doc.append('None')
continue
region_mutations.iloc[:,
1] = region_mutations.iloc[:, 1].apply(
lambda x: '{:,}'.format(x))
with self.doc.create(Tabular(table_format)) as table:
table.add_row(
('Reference contig', 'Position', 'Reference',
'Alternate', 'Drug', 'Note'))
table.add_hline()
for i in range(region_mutations.shape[0]):
table.add_row(region_mutations.iloc[
i, [0, 1, 3, 4, 5, 6]].values.tolist())
method = self.analysis.mutations_read_type + ' reads were mapped to the reference sequence using minimap2 (v '\
+ self.analysis.versions['minimap2'] + ').'
self.methods[self.mutation_methods_title] = self.methods[
self.mutation_methods_title].append(pd.Series(method))
method = ' '.join([
'Mutations were identified using'
'samtools mpileup (v', self.analysis.versions['samtools'], ')',
'and varscan (v', self.analysis.versions['varscan'], ').'
])
self.methods[self.mutation_methods_title] = self.methods[
self.mutation_methods_title].append(pd.Series(method))
def add_amr_matrix(self):
# Make sure that we have an AMR matrix to plot
if not getattr(self.analysis, 'did_draw_amr_matrix', False):
return
amr_matrix_png = self.analysis.amr_matrix_png
self.doc.append(NewPage())
with self.doc.create(Section(self.amr_matrix_title, numbering=False)):
self.doc.append(
'AMR genes and mutations with their corresponding drugs.')
self.doc.append(Command('graphicspath{{../}}'))
with self.doc.create(Figure(position='h!')) as figure:
figure.add_image(amr_matrix_png, width='7in')
def add_large_indels(self):
# Make sure we looked for mutations
if len(self.analysis.large_indels) == 0:
return
large_indels = self.analysis.large_indels
self.doc.append(NewPage())
with self.doc.create(Section(self.large_indel_title, numbering=False)):
for genome in ['Reference insertions', 'Query insertions']:
genome_indels = large_indels[genome].copy()
with self.doc.create(Subsection(genome, numbering=False)):
if (genome_indels.shape[0] == 0):
self.doc.append('None')
continue
genome_indels.iloc[:, 1] = genome_indels.iloc[:, 1].apply(
lambda x: '{:,}'.format(x))
genome_indels.iloc[:, 2] = genome_indels.iloc[:, 2].apply(
lambda x: '{:,}'.format(x))
genome_indels.iloc[:, 3] = genome_indels.iloc[:, 3].apply(
lambda x: '{:,}'.format(x))
table_format = 'l' * genome_indels.shape[1]
with self.doc.create(Tabular(table_format)) as table:
table.add_row(
('Reference contig', 'Start', 'Stop', 'Size (bp)'))
table.add_hline()
for i in range(genome_indels.shape[0]):
table.add_row(
genome_indels.iloc[i, :].values.tolist())
method = 'Large insertions or deletions were found as the complement of aligned ' + \
'regions using bedtools (v ' + self.analysis.versions['bedtools'] + ').'
self.methods[self.reference_methods_title] = self.methods[
self.reference_methods_title].append(pd.Series(method))
def add_plasmids(self):
if not getattr(self.analysis, 'did_call_plasmids', False):
return
# Make sure we looked for mutations
plasmids = self.analysis.plasmids
if plasmids is None:
return
plasmids = plasmids.copy()
self.doc.append(NewPage())
with self.doc.create(
Section(self.analysis.plasmid_title, numbering=False)):
if (plasmids.shape[0] == 0):
self.doc.append('None')
return
plasmids.iloc[:, 3] = plasmids.iloc[:, 3].apply(
lambda x: '{:,}'.format(x))
plasmids.iloc[:, 4] = plasmids.iloc[:, 4].apply(
lambda x: '{:,}'.format(x))
plasmids.iloc[:, 5] = plasmids.iloc[:, 5].apply(
lambda x: '{:,}'.format(x))
table_format = 'p{0.1\linewidth}p{0.3\linewidth}p{0.15\linewidth}p{0.08\linewidth}p{0.08\linewidth}p{0.08\linewidth}'
with self.doc.create(Tabular(table_format)) as table:
table.add_row(('Genome contig', 'Plasmid hit', 'Plasmid acc.',
'Contig size', 'Aliged', 'Plasmid size'))
table.add_hline()
for i in range(plasmids.shape[0]):
table.add_row(plasmids.iloc[i, 0:6].values.tolist())
method = ' '.join([
'The plasmid reference database was queried against the genome assembly using minimap2 (v',
self.analysis.versions['minimap2'], ').'
])
self.methods[self.plasmid_methods_title] = self.methods[
self.plasmid_methods_title].append(pd.Series(method))
method = 'The resulting SAM was converted to a PSL using a custom version of sam2psl.'
self.methods[self.plasmid_methods_title] = self.methods[
self.plasmid_methods_title].append(pd.Series(method))
method = 'Plasmid-to-genome hits were resolved using the pChunks algorithm.'
self.methods[self.plasmid_methods_title] = self.methods[
self.plasmid_methods_title].append(pd.Series(method))
def add_methods(self):
if len(self.methods) == 0:
return
self.doc.append(NewPage())
with self.doc.create(Section(self.methods_title, numbering=False)):
for methods_section in self.methods.index.tolist():
if len(self.methods[methods_section]) == 0:
continue
with self.doc.create(
Subsection(methods_section, numbering=False)):
self.doc.append(' '.join(self.methods[methods_section]))
def make_tex(self):
self.doc.generate_tex(self.analysis.report_prefix)
def make_report(self):
self.start_doc()
self.add_header()
self.add_summary()
self.add_contamination()
self.add_alignment()
self.add_features()
self.add_feature_plots()
self.add_mutations()
self.add_large_indels()
self.add_plasmids()
self.add_amr_matrix()
#self.add_snps()
self.add_methods()
self.make_tex()
def generate_report(main_title, name, title, email, payroll):
# For saving the report in the Desktop folder
dir_output=os.path.join(
'~',
'Desktop',
'absconbest_payroll',
'output'
)
dir_output=os.path.expanduser(dir_output)
geometry_options = {
"head": "40pt",
"margin": "0.5in",
"bottom": "0.6in",
"includeheadfoot": True
}
doc = Document(geometry_options=geometry_options)
# Generating
# first page style
first_page = PageStyle("firstpage")
# Header image
with first_page.create(Head("L")) as header_left:
with header_left.create(
MiniPage(width=NoEscape(r"0.49\textwidth"), pos='c')
) as logo_wrapper:
logo_file = 'logo.png'
logo_wrapper.append(
StandAloneGraphic(
image_options="width=120px",
filename=logo_file
)
)
# Add document title
with first_page.create(Head("R")) as right_header:
with right_header.create(MiniPage(
width=NoEscape(r"0.49\textwidth"),
pos='c',
align='r')
) as title_wrapper:
title_wrapper.append(LargeText(bold('Payroll Report')))
title_wrapper.append(LineBreak())
title_wrapper.append(MediumText(bold(main_title)))
# Add footer
with first_page.create(Foot("C")):
first_page.append(simple_page_number())
doc.preamble.append(first_page)
#Add employee information
with doc.create(Tabu("X[l] X[r]")) as first_page_table:
employee = MiniPage(width=NoEscape(r"0.49\textwidth"), pos='h')
employee.append(name)
employee.append("\n")
employee.append(title)
employee.append("\n")
employee.append(email)
#Dummy table
branch = MiniPage(width=NoEscape(r"0.49\textwidth"), pos='t!',
align='r')
# branch.append(bold("1181..."))
# branch.append(LineBreak())
# branch.append(bold("TIB Cheque"))
first_page_table.add_row([employee, branch])
first_page_table.add_empty_row()
doc.change_document_style("firstpage")
doc.add_color(name="lightgray", model="gray", description="0.80")
#Add payroll table
with doc.create(LongTabu("X[l] X[c] X[c] X[c] X[r]",
row_height=1.5)) as data_table:
data_table.add_row(['Work',
'Rate Per Hour ($)',
'Time in Minutes',
'Time in Hours',
'Wage ($)'],
mapper=bold,
color="lightgray")
data_table.add_empty_row()
data_table.add_hline()
#Following Pandas' API
payroll=payroll.reset_index()
for i in range(len(payroll.index)):
try:
row = [payroll['Work'][i],
round(payroll['Rate Per Hour'][i],0),
round(payroll['TIM'][i],0),
round(payroll['TIH'][i],3),
round(payroll['Wage'][i],1)]
except TypeError:
row = [payroll['Work'][i],
'n/a',
round(payroll['TIM'][i],0),
round(payroll['TIH'][i],3),
round(payroll['Wage'][i],1)]
if (i%2)==0:
data_table.add_row(row, color="lightgray")
else:
data_table.add_row(row)
# data_table.add_row([payroll['Work'][l_p],
# round(payroll['TIM'][l_p],0),
# round(payroll['TIH'][l_p],3),
# '',
# round(payroll['Wage'][l_p],1)]
# )
doc.append(NewPage())
doc.generate_pdf(
filepath=os.path.join(
dir_output,
main_title.lower().replace(" ","_").replace(",",""),
),
clean_tex=True,
clean=True,
)
def create(self):
try:
self.status['text'] = 'Загрузка, подождите'
self.root.update()
# Настройки отступов, языка
geometry_options = {
"tmargin": "2cm",
"lmargin": "3cm",
"rmargin": "1.5cm",
"bmargin": "2cm"
}
doc = Document(geometry_options=geometry_options)
doc.packages.add(
Package('grffile',
options=['encoding', 'filenameencoding=utf8']))
doc.packages.add(Package('babel', options=['russian']))
# Вставляем логотип МИРЭА
image_filename = os.path.join(os.path.dirname(__file__),
'логотип.png')
with doc.create(Figure(position='h!')) as logo:
logo.add_image(image_filename, width='80px')
# Обложка
doc.change_length(r"\TPHorizModule", "1mm")
doc.change_length(r"\TPVertModule", "1mm")
with doc.create(MiniPage(width=r"\textwidth")) as page:
# Центральная часть обложки
with page.create(TextBlock(180, 0, 0)):
page.append(Command('centering'))
page.append('МИНОБРНАУКИ РОССИИ\n')
page.append(
'Федеральное государственное бюджетное образовательное учреждение высшего образования\n'
)
page.append(
MediumText(
bold(
'«МИРЭА - Российский Технологический Университет»\n'
)))
page.append(LargeText(bold('РТУ МИРЭА\n')))
page.append(LineBreak())
page.append(
MediumText(
bold(
'Институт комплексной безопасности и специального приборостроения\n'
)))
page.append(LineBreak())
page.append(
'Кафедра КБ-8 «Информационное Противоборство»\n')
page.append(LineBreak())
page.append(LineBreak())
page.append(LineBreak())
page.append(LargeText('Отчёт\n'))
page.append(f'{str(self.entry1.get())}\n')
# Правая часть обложки
with page.create(TextBlock(80, 88, 120)):
if self.your_var.get() == 0:
page.append('Выполнил:\n')
page.append(
f'Студент {str(self.entry2.get())} курса\n')
else:
page.append('Выполнила:\n')
page.append(
f'Студентка {str(self.entry2.get())} курса\n')
page.append(f'Группа {str(self.entry3.get())}\n')
page.append(f'Шифр {str(self.entry4.get())}\n')
page.append(f'{str(self.entry5.get())}\n')
page.append(LineBreak())
page.append(LineBreak())
if self.var.get() == 0:
page.append('Проверил:\n')
else:
page.append('Проверила:\n')
page.append(f'{str(self.entry6.get())}\n')
# Нижний колонтитул
header = PageStyle("header")
with header.create(Foot("C")):
header.append(f'Москва, {time.now().timetuple().tm_year}\n')
doc.preamble.append(header)
doc.change_document_style("header")
doc.generate_pdf("title", clean_tex=False)
self.status['text'] = 'Готово!'
except FileNotFoundError as e:
self.status['text'] = str(e)
def report(context, json_report, json_varreport, rulegraph_img):
config = json_report
sample_config = json.load(open(json_report))
var_config = json.load(open(get_config(json_varreport)))
tex_path = os.path.abspath(
os.path.join(sample_config["analysis"]["analysis_dir"],
"delivery_report"))
if not rulegraph_img:
rulegraph_img = sample_config['analysis']['dag']
os.makedirs(tex_path, exist_ok=True)
geometry_options = {
"head": "40pt",
"headheight": "130pt",
"headsep": "1cm",
"margin": "1.5cm",
"bottom": "1.5cm",
"includeheadfoot": True
}
doc = Document(geometry_options=geometry_options)
doc.packages.append(Package('lscape'))
doc.packages.append(Package('longtable'))
doc.packages.append(Package('float'))
doc.packages.append(Package('caption', options='labelfont=bf'))
doc.append(
NoEscape(
r'\captionsetup[table]{labelsep=space, justification=raggedright, singlelinecheck=off}'
))
#Add first page style
first_page = PageStyle("header", header_thickness=1)
#Add Header
with first_page.create(Head("C")) as mid_header:
with mid_header.create(
MiniPage(width=NoEscape(r"0.2\textwidth"),
pos='c')) as logo_wrapper:
logo_file = os.path.join(os.path.dirname(__file__), '..',
'assests/cg.png')
logo_wrapper.append(
StandAloneGraphic(image_options="width=50px",
filename=logo_file))
with mid_header.create(
Tabularx(
"p{3cm} p{2cm} X X p{4cm} p{3cm}",
width_argument=NoEscape(r"0.8\textwidth"))) as mid_table:
mid_table.add_row(
[MultiColumn(6, align='r', data=simple_page_number())])
mid_table.add_row([
MultiColumn(6,
align='c',
data=MediumText("Molecular report on"))
])
mid_table.add_row([
MultiColumn(6,
align='c',
data=MediumText(get_sample_name(config)))
])
mid_table.add_empty_row()
mid_table.add_row([
'gender', "NA", " ", " ", 'Sample recieved:',
sample_config['analysis']['date']['sample_received']
])
mid_table.add_row([
'tumor type', "NA", " ", " ", 'Analysis completion:',
sample_config['analysis']['date']['analysis_finish']
])
mid_table.add_row([
'analysis type', "NA", " ", " ", 'PDF Report date:',
datetime.now().strftime("%Y-%m-%d %H:%M")
])
mid_table.add_row(
['sample type', "NA", " ", " ", 'Delivery date', "NA"])
mid_table.add_row([
'sample origin', "NA", " ", " ", 'Analysis:',
r'BALSAMIC v' + sample_config['analysis']['BALSAMIC']
])
doc.preamble.append(first_page)
#End First page
# doc.preamble.append(
# Command(
# 'title',
# NoEscape(r'BALSAMIC v' + sample_config["analysis"]["BALSAMIC"] +
# r'\\ \large Developer Report')))
# doc.preamble.append(
# Command('author', 'Patient ID: ' + get_sample_name(config)))
# doc.preamble.append(Command('date', NoEscape(r'\today')))
# doc.append(NoEscape(r'\maketitle'))
doc.change_document_style("header")
with doc.create(Section(title='Analysis report', numbering=True)):
with doc.create(
Subsection('Summary of variants and variant callers',
numbering=True)):
doc.append(
"Placeholder for text about BAM alignment metrics and variant callers. Here comes the info on reads, "
+
"QC metrics, align metrics, and general sample information. preferabily in table format."
)
doc.append("\n")
summary_tables = ["TMB", "VarClass", "VarCaller", "VarCallerClass"]
for i in summary_tables:
shellcmd = [
os.path.join(os.path.dirname(os.path.abspath(__file__)),
"..", "..", "scripts/VariantReport.R")
]
shellcmd.extend([
"--infile", sample_config["vcf"]["merged"]["SNV"],
"--genomeSize", sample_config["bed"]["genome_size"],
"--type", "latex", "--mode", i, "--outfile",
os.path.join(tex_path,
sample_config['analysis']['sample_id'])
])
print(" ".join(shellcmd))
outTab = subprocess.check_output(shellcmd)
doc.append(
NoEscape(
outTab.decode('utf-8').replace("\\centering",
"\\small")))
doc.append(NoEscape(r'\normalsize'))
doc.append(NewPage())
with doc.create(Subsection("Summary of MVL report", numbering=True)):
doc.append(
"Placeholder for general description of MVL settings. A mention to summary "
+
"pipeline, summary of MVL settings. Gene coverage for identified genes should go here. Figures!"
)
outCov = dict()
cmd_param = defaultdict(list)
J = defaultdict(list)
for i in var_config["filters"]:
cmd_param["TUMOR_DP"].append(
var_config["filters"][i]["TUMOR"]["DP"])
cmd_param["TUMOR_AD"].append(
var_config["filters"][i]["TUMOR"]["AD"])
cmd_param["TUMOR_AFmax"].append(
var_config["filters"][i]["TUMOR"]["AF_max"])
cmd_param["TUMOR_AFmin"].append(
var_config["filters"][i]["TUMOR"]["AF_min"])
cmd_param["TUMOR_inMVL"].append(
var_config["filters"][i]["in_mvl"])
cmd_param["var_type"].append(",".join(
["SNP", "INDEL", "MNP", "OTHER"]))
cmd_param["varcaller"].append(",".join(
var_config["filters"][i]["variantcaller"]))
cmd_param["ann"].append(
",".join(var_config["filters"][i]["annotation"]["SNV"]) +
"," +
",".join(var_config["filters"][i]["annotation"]["INDEL"]))
cmd_param["name"].append(i.replace("_", "\_"))
cmd_param["outfile_tex"].append(tex_path + "/" + i + ".tex")
cmd_param["outfile_gene"].append(tex_path + "/" + i +
".genelist")
for i in cmd_param:
J[i] = ";".join(cmd_param[i])
shellcmd = [
os.path.join(os.path.dirname(os.path.abspath(__file__)), "..",
"..", "scripts/VariantReport.R")
]
shellcmd.extend([
"--infile", "'" + sample_config["vcf"]["merged"]["SNV"] + "'",
"--dp", "'" + J["TUMOR_DP"] + "'", "--tumorad",
"'" + J["TUMOR_AD"] + "'", "--afmax",
"'" + J["TUMOR_AFmax"] + "'", "--afmin",
"'" + J["TUMOR_AFmin"] + "'", "--inMVL",
"'" + J["TUMOR_inMVL"] + "'", "--exclusiveSets", "TRUE",
"--vartype", "'" + J["var_type"] + "'", "--varcaller",
"'" + J["varcaller"] + "'", "--ann", "'" + J["ann"] + "'",
"--name", "'" + J["name"] + "'", "--type", "latex"
])
subprocess.check_output(
" ".join(shellcmd +
["--outfile", "'" + J["outfile_tex"] + "'"]),
shell=True)
print(" ".join(shellcmd +
["--outfile", "'" + J["outfile_tex"] + "'"]))
subprocess.check_output(" ".join(shellcmd + [
"--outfile", "'" + J["outfile_gene"] + "'", "--exportGene", "T"
]),
shell=True)
for c, i in enumerate(var_config["filters"]):
with doc.create(
Subsubsection(var_config["filters"][i]["name"],
numbering=True)):
print(cmd_param["outfile_tex"])
fname = cmd_param["outfile_tex"][c]
if os.stat(fname).st_size > 10:
#get gene list
with open(cmd_param["outfile_gene"][c]) as myfile:
genes = myfile.read().replace('\n', '')
with open(fname, 'r') as myfile:
data = myfile.read() #.replace('\n', '')
#doc.append(NoEscape(r'\begin{landscape}'))
#longtable instead of tabular makes the table span multiple pages, but the header doesn't span. Occasionally
#the alignment also is messed up. There must be a hidden package conflict OR general alignment issues.
#doc.append(NoEscape(varreport.replace("{tabular}","{longtable}")))
doc.append(
NoEscape(
data.replace("\\centering", "\\scriptsize")))
for s in sample_config["bed"]["exon_cov"]:
shellcmd = [
os.path.join(
os.path.dirname(os.path.abspath(__file__)),
"..", "scripts/CoverageRep.R")
]
shellcmd.extend([
"--infile",
sample_config["bed"]["exon_cov"][s],
"--genename", genes, "--name",
s.replace("_", "\_"), "--type", "latex"
])
outCov = subprocess.check_output(shellcmd)
doc.append(
NoEscape(
outCov.decode('utf-8').replace(
"\\centering", "\\scriptsize")))
#doc.append(NoEscape(r'\end{landscape}'))
else:
doc.append("No variants were found for this filter")
# doc.append(NoEscape(r'\normalsize'))
doc.append(NewPage())
with doc.create(Subsection('Coverage report')):
for s in sample_config["bed"]["target_cov"]:
with doc.create(Figure(position='h!')) as cov_img:
covplot = ".".join(
[os.path.join(tex_path, s), "Coverage.pdf"])
shellcmd = [
os.path.join(
os.path.dirname(os.path.abspath(__file__)), "..",
"..", "scripts/CoveragePlot.R")
]
shellcmd.extend([
"--infile", sample_config["bed"]["target_cov"][s],
"--outfile", covplot, "--title",
s.replace("_", "\_")
])
subprocess.check_output(shellcmd)
cov_img.add_image(covplot, width='450px')
cov_img.add_caption('Coverage report for sample ' +
s.replace("_", "\_"))
doc.append(NewPage())
with doc.create(Subsection('Analysis pipeline')):
with doc.create(Figure(position='h!')) as pipeline_img:
pipeline_img.add_image(rulegraph_img, width='450px')
pipeline_img.add_caption('BALSAMIC pipeline')
doc.append(NewPage())
with doc.create(Section(title="Appendix", numbering=True)):
with doc.create(Subsection("MVL settings", numbering=True)):
fmt = "p{3cm}" * (len(var_config["filters"]) + 1)
with doc.create(Tabular(fmt)) as data_table:
header_row1 = [""]
for i in var_config["filters"]:
header_row1.append(var_config["filters"][i]["name"])
data_table.add_hline()
data_table.add_row(header_row1,
mapper=[bold],
color="lightgray")
data_table.add_hline()
data_table.add_empty_row()
column = list(var_config["filters"][next(
iter(var_config["filters"]))]["TUMOR"].keys())
for i in column:
row = [i]
for j in var_config["filters"]:
row.append(var_config["filters"][j]["TUMOR"][i])
data_table.add_row(row)
row = ["MVL"]
for i in var_config["filters"]:
row.append(var_config["filters"][i]["in_mvl"])
row = ["Variantcallers"]
for i in var_config["filters"]:
row.append("\n".join(
var_config["filters"][i]["variantcaller"]))
data_table.add_row(row)
data_table.add_hline()
with doc.create(
Subsection("Bioinformatic tool in pipeline", numbering=True)):
doc.append(
"The following Bioinformatic tools were used in the analysis:\n\n"
)
with doc.create(Tabular("p{4cm}p{4cm}")) as data_table:
data_table.add_hline()
conda_env = glob.glob(
os.path.join(os.path.dirname(os.path.abspath(__file__)),
"..", "..", "conda_yaml/*.yaml"))
pkgs = get_package_split(conda_env)
data_table.add_row(["Package", "Version"], color="lightgray")
data_table.add_hline()
data_table.add_row(
["BALSAMIC", sample_config['analysis']['BALSAMIC']])
for k, v in pkgs.items():
data_table.add_row([k, v])
doc.append(NewPage())
print(tex_path)
doc.generate_tex(os.path.join(tex_path, get_sample_name(config)))
# doc.generate_pdf(
# os.path.join(tex_path, get_sample_name(config)), clean_tex=False)
shellcmd = [
"pdflatex", "-output-directory=" + tex_path,
os.path.join(tex_path, get_sample_name(config)) + ".tex", "1>",
"/dev/null"
]
#generate_pdf doesn't run AUX files properly and ends up with incorrect total page numbers. So subprocess for
#pdflatex is called twice instead.
print(" ".join(shellcmd))
subprocess.run(" ".join(shellcmd), shell=True)
subprocess.run(" ".join(shellcmd), shell=True)
def generate_unique():
geometry_options = {
"head": "40pt",
"margin": "0.5in",
"bottom": "0.6in",
"includeheadfoot": True
}
doc = Document(geometry_options=geometry_options)
# Generating first page style
first_page = PageStyle("firstpage")
# Header image
with first_page.create(Head("L")) as header_left:
with header_left.create(
MiniPage(width=NoEscape(r"0.49\textwidth"),
pos='c')) as logo_wrapper:
logo_file = os.path.join(os.path.dirname(__file__),
'sample-logo.png')
logo_wrapper.append(
StandAloneGraphic(image_options="width=120px",
filename=logo_file))
# Add document title
with first_page.create(Head("R")) as right_header:
with right_header.create(
MiniPage(width=NoEscape(r"0.49\textwidth"), pos='c',
align='r')) as title_wrapper:
title_wrapper.append(LargeText(bold("Bank Account Statement")))
title_wrapper.append(LineBreak())
title_wrapper.append(MediumText(bold("Date")))
# Add footer
with first_page.create(Foot("C")) as footer:
message = "Important message please read"
with footer.create(
Tabularx(
"X X X X",
width_argument=NoEscape(r"\textwidth"))) as footer_table:
footer_table.add_row(
[MultiColumn(4, align='l', data=TextColor("blue", message))])
footer_table.add_hline(color="blue")
footer_table.add_empty_row()
branch_address = MiniPage(width=NoEscape(r"0.25\textwidth"),
pos='t')
branch_address.append("960 - 22nd street east")
branch_address.append("\n")
branch_address.append("Saskatoon, SK")
document_details = MiniPage(width=NoEscape(r"0.25\textwidth"),
pos='t',
align='r')
document_details.append("1000")
document_details.append(LineBreak())
document_details.append(simple_page_number())
footer_table.add_row([
branch_address, branch_address, branch_address,
document_details
])
doc.preamble.append(first_page)
# End first page style
# Add customer information
with doc.create(Tabu("X[l] X[r]")) as first_page_table:
customer = MiniPage(width=NoEscape(r"0.49\textwidth"), pos='h')
customer.append("Verna Volcano")
customer.append("\n")
customer.append("For some Person")
customer.append("\n")
customer.append("Address1")
customer.append("\n")
customer.append("Address2")
customer.append("\n")
customer.append("Address3")
# Add branch information
branch = MiniPage(width=NoEscape(r"0.49\textwidth"),
pos='t!',
align='r')
branch.append("Branch no.")
branch.append(LineBreak())
branch.append(bold("1181..."))
branch.append(LineBreak())
branch.append(bold("TIB Cheque"))
first_page_table.add_row([customer, branch])
first_page_table.add_empty_row()
doc.change_document_style("firstpage")
doc.add_color(name="lightgray", model="gray", description="0.80")
# Add statement table
with doc.create(LongTabu("X[l] X[2l] X[r] X[r] X[r]",
row_height=1.5)) as data_table:
data_table.add_row(
["date", "description", "debits($)", "credits($)", "balance($)"],
mapper=bold,
color="lightgray")
data_table.add_empty_row()
data_table.add_hline()
row = ["2016-JUN-01", "Test", "$100", "$1000", "-$900"]
for i in range(30):
if (i % 2) == 0:
data_table.add_row(row, color="lightgray")
else:
data_table.add_row(row)
doc.append(NewPage())
# Add cheque images
with doc.create(LongTabu("X[c] X[c]")) as cheque_table:
cheque_file = os.path.join(os.path.dirname(__file__),
'chequeexample.png')
cheque = StandAloneGraphic(cheque_file, image_options="width=200px")
for i in range(0, 20):
cheque_table.add_row([cheque, cheque])
doc.generate_pdf("complex_report", clean_tex=False)
def generate_unique(sectors_notirradiated, hv_notirradiated, spark_notirradiated, irradatgif):
geometry_options = {
"head": "40pt",
"margin": "0.5in",
"bottom": "1.0in",
"includeheadfoot": True
}
doc = Document(indent=False,geometry_options=geometry_options)
# Generating first page style
first_page = PageStyle("firstpage")
# Header image
with first_page.create(Head("L")) as header_left:
with header_left.create(MiniPage(width=NoEscape(r"0.49\textwidth"),
pos='c')) as logo_wrapper:
logo_file = os.path.join(os.path.dirname(__file__),
'../cernlogo.png')
logo_wrapper.append(StandAloneGraphic(image_options="width=80px",
filename=logo_file))
# Add document title
with first_page.create(Head("R")) as right_header:
with right_header.create(MiniPage(width=NoEscape(r"0.49\textwidth"),
pos='c', align='r')) as title_wrapper:
title_wrapper.append(LargeText(bold("ATLAS New Small Wheel")))
title_wrapper.append(LineBreak())
title_wrapper.append(bold("Integration Tests"))
title_wrapper.append(LineBreak())
title_wrapper.append(bold(now.strftime("%d-%m-%Y")))
title_wrapper.append(LineBreak())
title_wrapper.append("\n")
title_wrapper.append(LargeText(bold("Chamber: "+str(chambername))))
title_wrapper.append(LineBreak())
title_wrapper.append("ID: "+str(ID))
title_wrapper.append(LineBreak())
# Add footer
with first_page.create(Foot("C")) as footer:
with footer.create(Tabularx(
"X X X ",
width_argument=NoEscape(r"\textwidth"))) as footer_table:
footer_table.add_empty_row()
footer_table.add_hline(color="blue")
branch_address1 = MiniPage(
width=NoEscape(r"0.25\textwidth"),
pos='t')
branch_address1.append("Lorenzo Pezzotti")
branch_address1.append("\n")
branch_address1.append("*****@*****.**")
branch_address2 = MiniPage(
width=NoEscape(r"0.25\textwidth"),
pos='t')
branch_address2.append("Alan Peyaud")
branch_address2.append("\n")
branch_address2.append("*****@*****.**")
branch_address3 = MiniPage(
width=NoEscape(r"0.25\textwidth"),
pos='t')
branch_address3.append("Ivan Gnesi")
branch_address3.append("\n")
branch_address3.append("*****@*****.**")
document_details = MiniPage(width=NoEscape(r"0.2\textwidth"),
pos='t', align='r')
document_details.append(" ")
document_details.append(LineBreak())
document_details.append(simple_page_number())
footer_table.add_row([branch_address1, branch_address2,
branch_address3])
doc.append(first_page)
# End first page style
redcircle = glob.glob("redcircle.png")
redcircle = StandAloneGraphic(redcircle, image_options="width=220px")
# Add customer information
with doc.create(Tabu("X[r]")) as first_page_table:
'''
# Add branch information
branch = MiniPage(width=NoEscape(r"0.49\textwidth"), pos='t!',
align='r')
branch.append("Chamber name: ")
branch.append(LineBreak())
branch.append("ID: ")
branch.append(LineBreak())
first_page_table.add_row([branch])
'''
first_page_table.add_empty_row()
doc.change_document_style("firstpage")
doc.add_color(name="lightgray", model="gray", description="0.85")
doc.add_color(name="lightgray2", model="gray", description="0.6")
if irradatgif == "y":
title = "HV irradiated"
else:
title = "HV not irradiated"
with doc.create(Section(title, numbering=False)):
# Add statement table
doc.append("\n")
doc.append(timeslot)
doc.append(LineBreak())
doc.append(str(deltatime/60)+str("_min"))
doc.append(LineBreak())
doc.append("Spike_treshold_0.2_uA")
doc.append(LineBreak())
with doc.create(LongTabu("|X[l]|X[r]|X[r]|X[r]|X[r]|",
row_height=1.5)) as data_table:
data_table.add_hline()
data_table.add_row(["Sector",
"HV",
"spark/min",
"Efficiency",
"Flag"],
mapper=bold,
color="lightgray2")
data_table.add_hline()
data_table.end_table_header()
data_table.add_hline()
row = ["sector", "hv","spark", "efficiency", "0 or 1"]
acceptedlist = []
not_acc_counter = 0
pscolor = "blue"
for i in range(len(hv_notirradiated)):
if (i % 2) == 0:
'''
if int(hv_notirradiated[i]) > 567.9 and spark_notirradiated[i]<1.0:
accepted = 1
acceptedlist.append(accepted)
else:
accepted = 0
acceptedlist.append(accepted)
'''
if int(hv_notirradiated[i]) > 567.9:
hvcolor = "black"
if 548.0 < int(hv_notirradiated[i]) < 567.9:
hvcolor = "orange"
if int(hv_notirradiated[i])< 548.0:
hvcolor = "red"
if spark_notirradiated[i] > 6.0:
sparkcolor = "red"
if spark_notirradiated[i] == 6.0:
sparkcolor = "orange"
if spark_notirradiated[i] < 6.0:
sparkcolor = "black"
if efficiency[i] < 80.0:
effcolor = "red"
if efficiency[i] > 80.0:
effcolor = "black"
if efficiency == 80.0:
effcolor = "orange"
if sparkcolor == "red" or hvcolor == "red" or effcolor == "red":
acceptedcolor = "red"
accepted = 0
acceptedlist.append(accepted)
not_acc_counter = not_acc_counter+1
else:
acceptedcolor = "black"
accepted = 1
acceptedlist.append(accepted)
data_table.add_row([str(sectors_notirradiated[i]), TextColor(hvcolor,str(int(hv_notirradiated[i]))),
TextColor(sparkcolor, str(round(spark_notirradiated[i],2))), TextColor(effcolor, str(round(efficiency[i],1))),
TextColor(acceptedcolor, "V")])
data_table.add_hline()
else:
'''
if int(hv_notirradiated[i]) > 567.9 and spark_notirradiated[i]<1.0:
accepted = 1
acceptedlist.append(accepted)
else:
accepted = 0
acceptedlist.append(accepted)
'''
if int(hv_notirradiated[i]) > 567.9:
hvcolor = "black"
if 548.0 < int(hv_notirradiated[i]) < 567.9:
hvcolor = "orange"
if int(hv_notirradiated[i])< 548.0:
hvcolor = "red"
if spark_notirradiated[i] > 6.0:
sparkcolor = "red"
if spark_notirradiated[i] == 6.0:
sparkcolor = "orange"
if spark_notirradiated[i] < 6.0:
sparkcolor = "black"
if efficiency[i] < 80.0:
effcolor = "red"
if efficiency[i] > 80.0:
effcolor = "black"
if efficiency == 80.0:
effcolor = "orange"
if sparkcolor == "red" or hvcolor == "red" or effcolor == "red":
acceptedcolor = "red"
accepted = 0
acceptedlist.append(accepted)
not_acc_counter = not_acc_counter+1
else:
acceptedcolor = "black"
accepted = 1
acceptedlist.append(accepted)
data_table.add_row([str(sectors_notirradiated[i]), TextColor(hvcolor,str(int(hv_notirradiated[i]))),
TextColor(sparkcolor, str(round(spark_notirradiated[i],2))), TextColor(effcolor, str(round(efficiency[i],1))),
TextColor(acceptedcolor, "V")], color="lightgray")
data_table.add_hline()
data_table.add_hline()
data_table.add_row("Out of spec", str(len([x for x in hv_notirradiated if x < 548.0])), str(len([x for x in spark_notirradiated if x > 6.0])), str(len([x for x in efficiency if x < 80.0])), str(not_acc_counter))
data_table.add_empty_row()
data_table.add_hline()
data_table.add_row("Chamber efficiency", "","", "", str(round(total_efficiency)))
data_table.add_hline()
if "LM2" in chambername:
newefficiency = efficiency
newefficiency.pop(4)
newefficiency.pop(4)
newefficiency.pop(8)
newefficiency.pop(8)
data_table.add_row("Efficiency no LE8", "","", "", str(round(np.mean(newefficiency))))
data_table.add_hline()
doc.append(NoEscape('\\clearpage'))
with doc.create(Section('Summary', numbering=False)):
piecart.create_pie([acceptedlist.count(1), acceptedlist.count(0)], "piechart.pdf")
# Add cheque images
with doc.create(LongTabu("X[c]")) as summary1_table:
pie = glob.iglob("piechart.pdf")
#png_list = [StandAloneGraphic(x, image_options="width=120px") for x in png_list]
pienew = [StandAloneGraphic(x, image_options="width=220px") for x in pie]
summary1_table.add_row([pienew[0]])
#here I have sectors_notirradiated, hv_notirradiated, spark_notirradiated, acceptedlist
SM1channels = ["L1","R1","L2","R2","L3","R3","L4","R4","L5","R5"]
SM2channels = ["L6","R6","L7","R7","L8","R8"]
badresultsall = []
badresultseta = []
badresultsstereo = []
if chambername[0:3] == "SM1":
channels = SM1channels
if chambername[0:3] == "SM2":
channels = SM2channels
if chambername[0:3] == "LM1":
channels = SM1channels
if chambername[0:3] == "LM2":
channels = SM2channels
for channel in channels:
cntall = sum(1 for x, sector in enumerate(sectors_notirradiated) if sector[2:4] == channel and acceptedlist[x] == 1)
cnteta = sum(1 for x, sector in enumerate(sectors_notirradiated) if sector[2:4] == channel and (sector[1:2] == "1" or sector[1:2] == "2") and acceptedlist[x] == 1)
cntstereo = sum(1 for x, sector in enumerate(sectors_notirradiated) if sector[2:4] == channel and (sector[1:2] == "3" or sector[1:2] == "4") and acceptedlist[x] == 1)
badresultsall.append(4-int(cntall))
badresultseta.append(2-int(cnteta))
badresultsstereo.append(2-int(cntstereo))
#doc.append(NewPage())
with doc.create(LongTabu("X[l] X[r] X[r] X[r]",
row_height=1.5)) as data_table2:
data_table2.add_row(["Sector overimposed (from eta side)",
"Eta",
"Stereo",
"Eta+Stereo"],
mapper=bold,
color="lightgray2")
data_table2.add_empty_row()
data_table2.add_hline()
row = ["Sector (all layers)", "Out of spec (Eta)", "Out of spec (Stereo)", "Out of spec (E+S)"]
for i in range(len(channels)):
if (i % 2) == 0:
data_table2.add_row([str(channels[i]), str(int(badresultseta[i])), str(badresultsstereo[i]), badresultsall[i]], color="lightgray")
else:
data_table2.add_row([str(channels[i]), str(int(badresultseta[i])), str(badresultsstereo[i]), badresultsall[i]])
with doc.create(LongTabu("X[l] X[r]",
row_height=1.5)) as data_table3:
data_table3.add_row(["Layer",
"Mean Efficiency"],
mapper=bold,
color="lightgray2")
data_table3.add_empty_row()
data_table3.add_hline()
row = ["layers", "efficiency"]
channelsT3 = ["L1", "L2", "L3", "L4"]
for i in range(len(layers_efficiency)):
if (i % 2) == 0:
data_table3.add_row([str(channelsT3[i]), str(round(layers_efficiency[i],1))], color="lightgray")
else:
data_table3.add_row([str(channelsT3[i]), str(round(layers_efficiency[i],1))])
doc.append(NewPage())
if irradatgif == "y":
title = "Current with irradiation"
else:
title = "Current with no irradiation"
with doc.create(Section(title, numbering=False)):
# Add cheque images
with doc.create(LongTabu("X[c] X[c] X[c] X[c]")) as cheque_table:
png_list = glob.glob('BB5-i*.pdf')
png_list.sort(key=os.path.getmtime)
png_list = [StandAloneGraphic(x, image_options="width=120px") for x in png_list]
print len(png_list)
row_image = []
i = 0
for image in png_list:
row_image.append(image)
i = i +1
if i==4:
cheque_table.add_row([row_image[0], row_image[1], row_image[2], row_image[3]])
row_image = []
i=0
png_list = []
doc.generate_pdf("complex_report", clean_tex=False, compiler='pdflatex')
def generate_unique_dw(final_hvs1, final_hvs2, hl1_ch1, hl2_ch1, hl1_ch2,
hl2_ch2, sectors):
geometry_options = {
"head": "40pt",
"margin": "0.5in",
"bottom": "1.0in",
"includeheadfoot": True
}
doc = Document(indent=False, geometry_options=geometry_options)
# Generating first page style
first_page = PageStyle("firstpage")
# Header image
with first_page.create(Head("L")) as header_left:
with header_left.create(
MiniPage(width=NoEscape(r"0.49\textwidth"),
pos='c')) as logo_wrapper:
logo_file = os.path.join(os.path.dirname(__file__),
'../cernlogo.png')
logo_wrapper.append(
StandAloneGraphic(image_options="width=80px",
filename=logo_file))
# Add document title
with first_page.create(Head("R")) as right_header:
with right_header.create(
MiniPage(width=NoEscape(r"0.49\textwidth"), pos='c',
align='r')) as title_wrapper:
title_wrapper.append(LargeText(bold("ATLAS New Small Wheel")))
title_wrapper.append(LineBreak())
title_wrapper.append(bold("Integration Tests"))
title_wrapper.append(LineBreak())
title_wrapper.append(bold(now.strftime("%d-%m-%Y")))
title_wrapper.append(LineBreak())
title_wrapper.append("\n")
title_wrapper.append(
LargeText(bold("Double Wedge: " + str(DW_name))))
title_wrapper.append(LineBreak())
# Add footer
with first_page.create(Foot("C")) as footer:
with footer.create(
Tabularx(
"X X X ",
width_argument=NoEscape(r"\textwidth"))) as footer_table:
footer_table.add_empty_row()
footer_table.add_hline(color="blue")
branch_address1 = MiniPage(width=NoEscape(r"0.25\textwidth"),
pos='t')
branch_address1.append("Lorenzo Pezzotti")
branch_address1.append("\n")
branch_address1.append("*****@*****.**")
branch_address2 = MiniPage(width=NoEscape(r"0.25\textwidth"),
pos='t')
branch_address2.append("Alan Peyaud")
branch_address2.append("\n")
branch_address2.append("*****@*****.**")
branch_address3 = MiniPage(width=NoEscape(r"0.25\textwidth"),
pos='t')
branch_address3.append("Ivan Gnesi")
branch_address3.append("\n")
branch_address3.append("*****@*****.**")
document_details = MiniPage(width=NoEscape(r"0.2\textwidth"),
pos='t',
align='r')
document_details.append(" ")
document_details.append(LineBreak())
document_details.append(simple_page_number())
footer_table.add_row(
[branch_address1, branch_address2, branch_address3])
doc.append(first_page)
# End first page style
redcircle = glob.glob("redcircle.png")
redcircle = StandAloneGraphic(redcircle, image_options="width=220px")
# Add customer information
with doc.create(Tabu("X[r]")) as first_page_table:
first_page_table.add_empty_row()
doc.change_document_style("firstpage")
doc.add_color(name="lightgray", model="gray", description="0.80")
doc.append("\n")
doc.append(timeslot)
doc.append(LineBreak())
# IP
with doc.create(Section('IP SIDE', numbering=False)):
# first chamber
# Verify if its SM1, LM1, SM1 or LM2
if chambername1IP[0:3] == "SM1" or chambername2HO[0:3] == "LM1":
limit = 10
else:
limit = 6
with doc.create(
Subsection("Chambers: " + chambername1IP + " + " +
chambername2IP,
numbering=False)):
with doc.create(Subsection(chambername1IP, numbering=False)):
with doc.create(
LongTabu("|X[l]|X[r]|X[r]|X[r]|X[r]|X[r]|X[r]|",
row_height=1.5)) as data_table:
data_table.add_hline()
data_table.add_row(
["Sector", "L1", "L2", "L3", "L4", "HL1", "HL2"],
mapper=bold,
color="lightgray")
data_table.add_hline()
row = ["blank", "l1", "l2", "l3", "l4", "hl1", "hl2"]
for i, hv in enumerate(final_hvs1[0]):
hl1_str = ""
hl2_str = ""
l1 = ""
l2 = ""
l3 = ""
l4 = ""
# assign each sector to a line
if hv == hl1_ch1:
hl1_str = str(hl1_ch1)
elif hv == hl2_ch1:
hl2_str = str(hl2_ch1)
elif i > limit - 1 + limit * 2:
l4 = "570"
elif i > limit - 1 + limit:
l3 = "570"
elif i > limit - 1:
l2 = "570"
else:
l1 = "570"
if (i % 2) == 0:
data_table.add_row([
str(sectors[0][i]), l1, l2, l3, l4, hl1_str,
hl2_str
])
else:
data_table.add_row([
str(sectors[0][i]), l1, l2, l3, l4, hl1_str,
hl2_str
],
color="lightgray")
data_table.add_hline()
# second chamber
if chambername2IP[0:3] == "SM1" or chambername2HO[0:3] == "LM1":
limit = 10
else:
limit = 6
with doc.create(Subsection(chambername2IP, numbering=False)):
with doc.create(
LongTabu("|X[l]|X[r]|X[r]|X[r]|X[r]|X[r]|X[r]|",
row_height=1.5)) as data_table2:
data_table2.add_hline()
data_table2.add_row(
["Sector", "L1", "L2", "L3", "L4", "HL1", "HL2"],
mapper=bold,
color="lightgray")
data_table2.add_hline()
row = ["blank", "l1", "l2", "l3", "l4", "hl1", "hl2"]
for i, hv in enumerate(final_hvs1[1]):
hl1_str = ""
hl2_str = ""
l1 = ""
l2 = ""
l3 = ""
l4 = ""
# assign each sector to a line
if hv == hl1_ch1:
hl1_str = str(hl1_ch1)
elif hv == hl2_ch1:
hl2_str = str(hl2_ch1)
elif i > limit - 1 + limit * 2:
l4 = "570"
elif i > limit - 1 + limit:
l3 = "570"
elif i > limit - 1:
l2 = "570"
else:
l1 = "570"
if (i % 2) == 0:
data_table2.add_row([
str(sectors[1][i]), l1, l2, l3, l4, hl1_str,
hl2_str
])
else:
data_table2.add_row([
str(sectors[1][i]), l1, l2, l3, l4, hl1_str,
hl2_str
],
color="lightgray")
data_table2.add_hline()
# HO
# Swap R an L
final_hvs2[0] = swap(final_hvs2[0])
final_hvs2[1] = swap(final_hvs2[1])
if chambername1HO[0:3] == "SM1" or chambername2HO[0:3] == "LM1":
limit = 10
else:
limit = 6
doc.append(NewPage())
with doc.create(Section('HO SIDE', numbering=False)):
# first chamber
with doc.create(
Subsection("Chambers: " + chambername1HO + " + " +
chambername2HO,
numbering=False)):
with doc.create(Subsection(chambername1HO, numbering=False)):
with doc.create(
LongTabu("|X[l]|X[r]|X[r]|X[r]|X[r]|X[r]|X[r]|",
row_height=1.5)) as data_table3:
data_table3.add_hline()
data_table3.add_row(
["Sector", "L1", "L2", "L3", "L4", "HL1", "HL2"],
mapper=bold,
color="lightgray")
data_table3.add_hline()
row = ["blank", "l1", "l2", "l3", "l4", "hl1", "hl2"]
for i, hv in enumerate(final_hvs2[0]):
hl1_str = ""
hl2_str = ""
l1 = ""
l2 = ""
l3 = ""
l4 = ""
# assign each sector to a line
if hv == hl1_ch2:
hl1_str = str(hl1_ch2)
elif hv == hl2_ch2:
hl2_str = str(hl2_ch2)
elif i > limit - 1 + limit * 2:
l4 = "570"
elif i > limit - 1 + limit:
l3 = "570"
elif i > limit - 1:
l2 = "570"
else:
l1 = "570"
if (i % 2) == 0:
data_table3.add_row([
str(sectors[2][i]), l1, l2, l3, l4, hl1_str,
hl2_str
])
else:
data_table3.add_row([
str(sectors[2][i]), l1, l2, l3, l4, hl1_str,
hl2_str
],
color="lightgray")
data_table3.add_hline()
# second chamber
if chambername2HO[0:3] == "SM1" or chambername2HO[0:3] == "LM1":
limit = 10
else:
limit = 6
with doc.create(Subsection(chambername2HO, numbering=False)):
with doc.create(
LongTabu("|X[l]|X[r]|X[r]|X[r]|X[r]|X[r]|X[r]|",
row_height=1.5)) as data_table4:
data_table4.add_hline()
data_table4.add_row(
["Sector", "L1", "L2", "L3", "L4", "HL1", "HL2"],
mapper=bold,
color="lightgray")
data_table4.add_hline()
row = ["blank", "l1", "l2", "l3", "l4", "hl1", "hl2"]
for i, hv in enumerate(final_hvs2[1]):
hl1_str = ""
hl2_str = ""
l1 = ""
l2 = ""
l3 = ""
l4 = ""
# assign each sector to a line
if hv == hl1_ch2:
hl1_str = str(hl1_ch2)
elif hv == hl2_ch2:
hl2_str = str(hl2_ch2)
elif i > limit - 1 + limit * 2:
l4 = "570"
elif i > limit - 1 + limit:
l3 = "570"
elif i > limit - 1:
l2 = "570"
else:
l1 = "570"
if (i % 2) == 0:
data_table4.add_row([
str(sectors[3][i]), l1, l2, l3, l4, hl1_str,
hl2_str
])
else:
data_table4.add_row([
str(sectors[3][i]), l1, l2, l3, l4, hl1_str,
hl2_str
],
color="lightgray")
data_table4.add_hline()
doc.generate_pdf("complex_report_DW", clean_tex=False, compiler='pdflatex')
def generate_unique():
geometry_options = {
"head": "40pt",
"margin": "0.5in",
"bottom": "0.6in",
"includeheadfoot": True
}
doc = Document(geometry_options=geometry_options)
# Generating first page style
first_page = PageStyle("firstpage")
# Header image
with first_page.create(Head("C")) as header_center:
with header_center.create(
MiniPage(width=NoEscape(r"0.50\textwidth"),
pos='c')) as logo_wrapper:
logo_file = os.path.join(os.path.dirname(__file__),
'sample-logo.png')
logo_wrapper.append(
StandAloneGraphic(image_options="width=300px",
filename=logo_file))
# Add document title
# Add footer
with first_page.create(Foot("C")) as footer:
message = "Important message please read"
with footer.create(
Tabularx(
"X X X X",
width_argument=NoEscape(r"\textwidth"))) as footer_table:
branch_address = MiniPage(width=NoEscape(r"0.25\textwidth"),
pos='t')
document_details = MiniPage(width=NoEscape(r"0.25\textwidth"),
pos='t',
align='r')
document_details.append(LineBreak())
document_details.append(simple_page_number())
footer_table.add_row([
branch_address, branch_address, branch_address,
document_details
])
doc.preamble.append(first_page)
# End first page style
# Add customer information
with doc.create(Tabu("X[l] X[r]")) as first_page_table:
customer = MiniPage(width=NoEscape(r"0.49\textwidth"), pos='h')
# Add branch information
branch = MiniPage(width=NoEscape(r"0.49\textwidth"),
pos='t!',
align='r')
first_page_table.add_row([customer, branch])
first_page_table.add_empty_row()
doc.change_document_style("firstpage")
doc.add_color(name="lightgray", model="gray", description="0.80")
print("Enter the Region")
R = input(str)
with doc.create(MiniPage(align='c')):
doc.append(LargeText(bold("\n\n\n\n\n\n" + R)))
doc.append(LineBreak())
print("Enter the adress of home ")
A = input(str)
image_filename = os.path.join(os.path.dirname(__file__), 'home.jpg')
with doc.create(Section('Example : ' + A)):
with doc.create(Figure(position='h!')) as home_pic:
home_pic.add_image(image_filename, width='490px')
with doc.create(Section('Property information :')):
with doc.create(Itemize()) as itemize:
print("enter property type")
x = input(str)
itemize.add_item(bold("Property type : " + x))
print("How many bedrooms ?")
y = input(int)
itemize.add_item(bold("Bedroom : " + y))
print("How many bathrooms?")
z = input(float)
itemize.add_item(bold("Bathroom : " + z))
print('Enter the year of built please:')
a = input(int)
itemize.add_item(bold("Year built : " + a))
print('Enter the finished sqft :')
b = input(int)
itemize.add_item(bold("Finished sqft : " + b))
print("Enter the estimate price")
p1 = input(float)
print('enter the estimate rent')
p2 = input(float)
doc.append(LineBreak())
table1 = Tabular('|c|c|')
table1.add_hline()
table1.add_row(('Estimate price', 'Estimate rent'))
table1.add_hline()
table1.add_row((p1 + '$', p2 + '$'))
table1.add_hline()
doc.append(table1)
with doc.create(Section('Financing')):
with doc.create(Itemize()) as itemize:
print('Enter type of loan')
lo = input(str)
itemize.add_item(bold("Loan Type: " + lo))
print("Enter loan amount")
la = input(float)
itemize.add_item(bold("Loan Amount: " + la))
print("enter the interest rate with %")
IR = input(float)
itemize.add_item(bold("Interest Rate: " + IR + "%"))
print("enter LTV")
LTV = input(float)
itemize.add_item(bold("Loan to Value (LTV): " + LTV + "%"))
print("enter loan term")
LT = input(int)
itemize.add_item(bold("Loan Term: " + LT + "years"))
print("enter loan payment monthly")
LPM = input(int)
print("enter loan payment yearly")
LPY = input(int)
itemize.add_item(
bold("Loan Payment: " + LPM + "(monthly), " + LPY +
"(yearly)"))
with doc.create(Section('Assumptions')):
with doc.create(Itemize()) as itemize:
print("enter vacancy rate")
vr = input(float)
itemize.add_item(bold('Vacancy Rate' + vr))
print("property managment")
pr = input(float)
itemize.add_item(bold('Property Managment' + pr))
print("yearly expense")
yex = input(float)
itemize.add_item(bold('Yearly Expense incr' + yex))
print("yearly rent")
yr = input(float)
itemize.add_item(bold('Yearly Rent incr' + yr))
print("yearly equity")
ye = input(float)
itemize.add_item(bold('Yearly Equity incr' + ye))
print("land value")
lv = input(float)
itemize.add_item(bold('Land Value' + lv))
section = Section('Financial projection and expences analysis')
test1 = Subsection(bold('Financial Projection'))
test2 = Subsection(bold('Expences'))
table2 = Tabular('|c|c|c|c|c|c|c|c|c|c|')
table2.add_hline()
table2.add_row(("Type", "Year 1", "Year 2", "Year 3", "Year 4",
"Year 5", "Year 10", "Year 15", "Year 20", "Year 30"))
table2.add_hline()
table2.add_row(("Total Annuel Income", 6, 7, 8, 8, 8, 8, 8, 8, 8))
table2.add_hline()
table2.add_row(("Total Annuel Expenses", 6, 7, 8, 8, 8, 8, 8, 8, 8))
table2.add_hline()
table2.add_row(
("Total Annuel Operating Expenses", 6, 7, 8, 8, 8, 8, 8, 8, 8))
table2.add_hline()
table2.add_row(("Total Annual Cash Flow", 6, 7, 8, 8, 8, 8, 8, 8, 8))
table2.add_hline()
table2.add_row(("Property Value", 6, 7, 8, 8, 8, 8, 8, 8, 8))
table2.add_hline()
table2.add_row(("Cash on Cash ROI", 6, 7, 8, 8, 8, 8, 8, 8, 8))
table2.add_hline()
table2.add_row(("Loan Balance", 6, 7, 8, 8, 8, 8, 8, 8, 8))
table2.add_hline()
table2.add_row(("Cumulative Cash Flow", 6, 7, 8, 8, 8, 8, 8, 8, 8))
table2.add_hline()
table2.add_row(("Equity", 6, 7, 8, 8, 8, 8, 8, 8, 8))
table2.add_hline()
table3 = Tabular('|c|c|c|')
table3.add_hline()
table3.add_row((" ", "Monthly", "Annually"))
table3.add_hline()
table3.add_row(("Repair Cost", 6, 7))
table3.add_hline()
table3.add_row(("Vacancy", 6, 7))
table3.add_hline()
table3.add_row(("Insurance", 6, 7))
table3.add_hline()
table3.add_row(("Taxes", 6, 7))
table3.add_hline()
table3.add_row(("hoe", 6, 7))
table3.add_hline()
table3.add_row(("Capital Expenditures", 6, 7))
table3.add_hline()
table3.add_row(("Property Managment", 6, 7))
table3.add_hline()
table3.add_row(("Other Expences", 6, 7))
table3.add_hline()
table3.add_row((LargeText(bold("Total")), 6, 7))
table3.add_hline()
test1.append(table2)
test2.append(table3)
section.append(test1)
section.append(test2)
doc.append(section)
doc.append(LineBreak)
print('Cap Rate')
cap = input()
print('Cash on Cash Return')
cac = input()
print('Retur on investment')
roi = input()
doc.append(
LargeText(
bold('Cap Rate :' + cap + '\n\n' + "Cash on Cash Return" + cac +
"\n\n" + "Return on Investment" + roi)))
doc.generate_pdf("complex_report", clean_tex=False)
