def test_set_logo(mock_reports):
from onecodex.notebooks import report
myurl = "file:///path/to/logo.png"
mystyle = "text-align: center"
obj = report.set_logo(myurl, style=mystyle)
bundle = obj._repr_mimebundle_()
assert len(bundle) == 1
assert myurl in bundle["text/html"]
assert mystyle in bundle["text/html"]
assert "logo-left" in bundle["text/html"]
ET.fromstring(bundle["text/html"])
obj.display()
report.set_logo(myurl, position="left")
report.set_logo(myurl, position="right")
report.set_logo(myurl, position="center")
with pytest.raises(OneCodexException) as e:
report.set_logo(myurl, position="bottom")
assert "position must be one of" in str(e.value)
def test_set_logo(mock_reports):
from onecodex.notebooks import report
myurl = "file:///path/to/logo.png"
mystyle = "text-align: center"
obj = report.set_logo(myurl, style=mystyle)
bundle = obj._repr_mimebundle_()
assert len(bundle) == 1
assert myurl in bundle["text/html"]
assert mystyle in bundle["text/html"]
assert "logo-left" in bundle["text/html"]
ET.fromstring(bundle["text/html"])
obj.display()
report.set_logo(myurl, position="left")
report.set_logo(myurl, position="right")
report.set_logo(myurl, position="center")
with pytest.raises(OneCodexException) as e:
report.set_logo(myurl, position="bottom")
assert "position must be one of" in str(e.value)
def from_notebook_node(self, nb, resources=None, **kw):
"""Uses nbconvert's HTMLExporter to generate HTML, with slight modifications.
Notes
-----
This exporter will only save cells generated with Altair/Vega if they have an SVG image type
stored with them. This data is only stored if our fork of `ipyvega` is installed or the onecodex
# renderer is used--otherwise, they will be low-resolution PNGs, which will not be exported.
"""
nb = copy.deepcopy(nb)
# setup our dictionary that's accessible from within jinja templates
if resources is None:
resources = {"metadata": {}}
elif "metadata" not in resources:
resources["metadata"] = {}
# iterate over cells in the notebook and transform data as necessary
do_not_insert_date = False
# add one codex logo unless told not to
if not os.environ.get("ONE_CODEX_REPORT_NO_LOGO", False):
img = b64encode(
bytes(open(os.path.join(ASSETS_PATH, "one_codex_logo.png"), "rb").read())
).decode()
img = "data:image/png;charset=utf-8;base64,%s" % (img,)
logo_html = report.set_logo(img, position="right")._repr_mimebundle_()["text/html"]
head_block = resources["metadata"].get("head_block", "") + logo_html
resources["metadata"]["head_block"] = head_block
# add today's date unless told not to (i.e. a custom date was specified)
if not do_not_insert_date:
date_div = report.set_date()._repr_mimebundle_()[0]["text/html"]
head_block = resources["metadata"].get("head_block", "") + date_div
resources["metadata"]["head_block"] = head_block
# add the report ID and not for diagnostic use footer
report_info_div = '<div id="reportinfo">{}</div>'.format(
"{} - NOT FOR DIAGNOSTIC USE".format(os.environ["ONE_CODEX_REPORT_UUID"])
if os.environ.get("ONE_CODEX_REPORT_UUID")
else "NOT FOR DIAGNOSTIC USE"
)
head_block = resources["metadata"].get("head_block", "") + report_info_div
resources["metadata"]["head_block"] = head_block
# embed the default CSS
css = open(os.path.join(ASSETS_PATH, CSS_TEMPLATE_FILE), "r").read()
css = '<style type="text/css">{}</style>'.format(css)
head_block = resources["metadata"].get("head_block", "") + css
resources["metadata"]["head_block"] = head_block
# tag this report for traceability, if run from notebook service. these will be transferred
# to PDF metadata if the HTML output of this function is used as input for PDF generation
meta_tags = [("dcterms.created", datetime.datetime.now(pytz.utc).isoformat())]
user_uuid = os.environ.get("ONE_CODEX_USER_UUID")
if user_uuid is not None:
meta_tags.append(("author", "one_codex_user_uuid_{}".format(user_uuid)))
nb_uuid = os.environ.get("ONE_CODEX_NOTEBOOK_UUID")
if nb_uuid is not None:
meta_tags.append(("author", "one_codex_notebook_uuid_{}".format(nb_uuid)))
meta_html = ""
for meta_name, meta_val in meta_tags:
meta_html += '<meta name="{}" content="{}" />\n'.format(meta_name, meta_val)
head_block = resources["metadata"].get("head_block", "") + meta_html
resources["metadata"]["head_block"] = head_block
output, resources = super(OneCodexHTMLExporter, self).from_notebook_node(
nb, resources=resources, **kw
)
return output, resources
def from_notebook_node(self, nb, resources=None, **kw):
"""Uses nbconvert's HTMLExporter to generate HTML, with slight modifications.
Notes
-----
This exporter will only save cells generated with Altair/Vega if they have an SVG image type
stored with them. This data is only stored if our fork of `ipyvega` is installed or the onecodex
# renderer is used--otherwise, they will be low-resolution PNGs, which will not be exported.
"""
nb = copy.deepcopy(nb)
# setup our dictionary that's accessible from within jinja templates
if resources is None:
resources = {"metadata": {}}
elif "metadata" not in resources:
resources["metadata"] = {}
# iterate over cells in the notebook and transform data as necessary
do_not_insert_date = False
for cell in nb.cells:
if cell["cell_type"] == "code":
for out in cell["outputs"]:
# handle transforming images into a format Weasyprint can render. prefer SVGs
# over PNGs. SVGs must be base64 encoded, while PNGs come encoded already. drop
# other Vega output cells (like JavaScript)
if out.get("metadata") and out["metadata"].get(
"jupyter-vega"):
data = out.get("data", [])
if "image/svg+xml" in data:
img = b64encode(
bytes(data["image/svg+xml"],
encoding="UTF-8")).decode()
out["data"] = {
"text/html":
'<img src="data:image/svg+xml;charset=utf-8;base64,{}">'
.format(img)
}
elif "image/png" in data:
out["data"] = {
"text/html":
'<img src="{}"'.format(data["image/png"])
}
elif "application/vnd.vegalite.v2+json" in data:
vega_svg = render_vega_with_node(
data["application/vnd.vegalite.v2+json"])
if vega_svg:
img = b64encode(vega_svg).decode()
out["data"] = {
"text/html":
'<img src="data:image/svg+xml;charset=utf-8;base64,{}">'
.format(img)
}
else:
out["data"] = {}
# transfer text/css blocks to HTML <head> tag
elif out.get("metadata") and out["metadata"].get(
"onecodex") == "head.style":
for mimetype in out.get("data", []):
if mimetype == "text/css":
style_block = '<style type="text/css">{}</style>'.format(
out["data"]["text/css"])
head_block = (resources["metadata"].get(
"head_block", "") + style_block)
resources["metadata"][
"head_block"] = head_block
break
# we don't want this to be output as text, so clear it
out["data"] = {"text/plain": ""}
# if there's a custom date specified, don't insert it
elif out.get("metadata") and out["metadata"].get(
"onecodex") == "customdate":
do_not_insert_date = True
# add one codex logo unless told not to
if not os.environ.get("ONE_CODEX_REPORT_NO_LOGO", False):
img = b64encode(
bytes(
open(os.path.join(ASSETS_PATH, "one_codex_logo.png"),
"rb").read())).decode()
img = "data:image/png;charset=utf-8;base64,%s" % (img, )
logo_html = report.set_logo(
img, position="right")._repr_mimebundle_()["text/html"]
head_block = resources["metadata"].get("head_block",
"") + logo_html
resources["metadata"]["head_block"] = head_block
# add today's date unless told not to (i.e. a custom date was specified)
if not do_not_insert_date:
date_div = report.set_date()._repr_mimebundle_()[0]["text/html"]
head_block = resources["metadata"].get("head_block", "") + date_div
resources["metadata"]["head_block"] = head_block
# embed the default CSS
css = open(os.path.join(ASSETS_PATH, CSS_TEMPLATE_FILE), "r").read()
css = '<style type="text/css">{}</style>'.format(css)
head_block = resources["metadata"].get("head_block", "") + css
resources["metadata"]["head_block"] = head_block
# tag this report for traceability, if run from notebook service. these will be transferred
# to PDF metadata if the HTML output of this function is used as input for PDF generation
meta_tags = [("dcterms.created",
datetime.datetime.now(pytz.utc).isoformat())]
user_uuid = os.environ.get("ONE_CODEX_USER_UUID")
if user_uuid is not None:
meta_tags.append(
("author", "one_codex_user_uuid_{}".format(user_uuid)))
nb_uuid = os.environ.get("ONE_CODEX_NOTEBOOK_UUID")
if nb_uuid is not None:
meta_tags.append(
("author", "one_codex_notebook_uuid_{}".format(nb_uuid)))
meta_html = ""
for meta_name, meta_val in meta_tags:
meta_html += '<meta name="{}" content="{}" />\n'.format(
meta_name, meta_val)
head_block = resources["metadata"].get("head_block", "") + meta_html
resources["metadata"]["head_block"] = head_block
output, resources = super(OneCodexHTMLExporter,
self).from_notebook_node(nb,
resources=resources,
**kw)
return output, resources