def download_hpo_genes(institute_id, case_name, category):
"""Download the genes contained in a case dynamic gene list
Args:
institute_id(str): id for current institute
case_name(str): name for current case
category(str): variant category - "clinical" or "research"
"research" retrieves all gene symbols for each HPO term on the dynamic phenotype panel
"clinical" limits dynamic phenotype panel retrieval to genes present on case clinical genes
"""
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
# Create export object consisting of dynamic phenotypes with associated genes as a dictionary
is_clinical = category != "research"
phenotype_terms_with_genes = controllers.phenotypes_genes(
store, case_obj, is_clinical)
html_content = ""
for term_id, term in phenotype_terms_with_genes.items():
html_content += f"<hr><strong>{term_id} - {term.get('description')}</strong><br><br><font style='font-size:16px;'><i>{term.get('genes')}</i></font><br><br>"
bytes_file = html_to_pdf_file(html_content, "portrait", 300)
file_name = "_".join([
case_obj["display_name"],
datetime.datetime.now().strftime("%Y-%m-%d"),
category,
"dynamic_phenotypes.pdf",
])
return send_file(
bytes_file,
download_name=file_name,
mimetype="application/pdf",
as_attachment=True,
)
def delivery_report(institute_id, case_name):
"""Display delivery report."""
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
if case_obj.get("delivery_report") is None:
return abort(404)
date_str = request.args.get("date")
if date_str is not None:
delivery_report = None
for analysis_data in case_obj.get("analyses", []):
if str(analysis_data["date"].date()) == date_str:
delivery_report = analysis_data["delivery_report"]
if delivery_report is None:
return abort(404)
else:
delivery_report = case_obj["delivery_report"]
out_dir = os.path.abspath(os.path.dirname(delivery_report))
filename = os.path.basename(delivery_report)
report_format = request.args.get("format", "html")
if report_format == "pdf":
try: # file could not be available
html_file = open(delivery_report, "r")
source_code = html_file.read()
bytes_file = html_to_pdf_file(source_code, "portrait", 300)
file_name = "_".join([
case_obj["display_name"],
datetime.datetime.now().strftime("%Y-%m-%d"),
"scout_delivery.pdf",
])
return send_file(
bytes_file,
download_name=file_name,
mimetype="application/pdf",
as_attachment=True,
)
except Exception as ex:
flash(
"An error occurred while downloading delivery report {} -- {}".
format(delivery_report, ex),
"warning",
)
LOG.error(
f"An error occurred while downloading delivery report {delivery_report} -- {ex}"
)
return send_from_directory(out_dir, filename)
def pdf_case_report(institute_id, case_name):
"""Download a pdf report for a case"""
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
data = controllers.case_report_content(store, institute_id, case_name)
# add coverage report on the bottom of this report
if (current_app.config.get("SQLALCHEMY_DATABASE_URI")
and case_obj.get("track", "rare") != "cancer"):
data["coverage_report"] = controllers.coverage_report_contents(
request.url_root, institute_obj, case_obj)
# Workaround to be able to print the case pedigree to pdf
if case_obj.get("madeline_info") and case_obj.get("madeline_info") != "":
try:
write_to = os.path.join(cases_bp.static_folder, "madeline.png")
svg2png(
bytestring=case_obj["madeline_info"],
write_to=write_to,
) # Transform to png, since PDFkit can't render svg images
data["case"]["madeline_path"] = write_to
except Exception as ex:
LOG.error(
f"Could not convert SVG pedigree figure {case_obj['madeline_info']} to PNG: {ex}"
)
html_report = render_template("cases/case_report.html",
format="pdf",
**data)
bytes_file = html_to_pdf_file(html_string=html_report,
orientation="portrait",
dpi=300,
zoom=0.6)
file_name = "_".join([
case_obj["display_name"],
datetime.datetime.now().strftime("%Y-%m-%d"),
"scout_report.pdf",
])
return send_file(
bytes_file,
download_name=file_name,
mimetype="application/pdf",
as_attachment=True,
)
def test_html_to_pdf_file():
"""Test function that converts HTML file into pdf file using PDFKit"""
test_content = """
<!DOCTYPE html>
<html>
<head>
<title>A demo html page</title>
</head>
<body>
<p>Hello world!</p>
</body>
</html>
"""
# GIVEN an HTML report to be converted to PDF:
bytes_file = html_to_pdf_file(test_content, "landscape", 300)
assert isinstance(bytes_file, BytesIO)
def panel_export(panel_id):
"""Export panel to PDF file"""
panel_obj = store.panel(panel_id)
data = controllers.panel_export(store, panel_obj)
data["report_created_at"] = datetime.datetime.now().strftime("%Y-%m-%d")
html_report = render_template("panels/panel_pdf_simple.html", **data)
bytes_file = html_to_pdf_file(html_report, "portrait", 300)
file_name = "_".join([
data["panel"]["panel_name"],
str(data["panel"]["version"]),
datetime.datetime.now().strftime("%Y-%m-%d"),
"scout.pdf",
])
return send_file(
bytes_file,
download_name=file_name,
mimetype="application/pdf",
as_attachment=True,
)
def coverage_qc_report(institute_id, case_name):
"""Display coverage and qc report."""
_, case_obj = institute_and_case(store, institute_id, case_name)
coverage_qc_report = case_obj.get("coverage_qc_report")
if coverage_qc_report is None:
return abort(404)
report_format = request.args.get("format", "html")
out_dir = os.path.abspath(os.path.dirname(coverage_qc_report))
filename = os.path.basename(coverage_qc_report)
if report_format == "pdf":
try:
with open(os.path.abspath(coverage_qc_report), "r") as html_file:
source_code = html_file.read()
bytes_file = html_to_pdf_file(source_code, "landscape", 300)
file_name = "_".join([
case_obj["display_name"],
datetime.datetime.now().strftime("%Y-%m-%d"),
"coverage_qc_report.pdf",
])
return send_file(
bytes_file,
download_name=file_name,
mimetype="application/pdf",
as_attachment=True,
)
except Exception as ex:
flash(
"An error occurred while converting report to PDF: {} -- {}".
format(coverage_qc_report, ex),
"warning",
)
LOG.error(ex)
return send_from_directory(out_dir, filename)