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Add test for reports.py
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@polyatail
polyatail committed Jan 31, 2019
1 parent cff7db6 commit 76108d7
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Showing 3 changed files with 417 additions and 31 deletions.
67 changes: 38 additions & 29 deletions onecodex/reports.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,6 @@
import os
import pytz
from traitlets import default
from weasyprint import HTML, CSS

from onecodex.exceptions import OneCodexException

Expand Down Expand Up @@ -100,12 +99,12 @@ def display(self):
display(self)

def _repr_mimebundle_(self, include=None, exclude=None):
return {'text/html': '<img src="{}" width="120px" class="logo {}" style="{}">'.format(self.url, self.classes, self.style)}
return {'text/html': '<img src="{}" width="120px" class="logo {}" style="{}" />'.format(self.url, self.classes, self.style)}


class legend(object):
def __init__(self, text, heading=None, fignum=None, style=None):
self.heading = '' if heading is None else '{}&nbsp;'.format(heading)
self.heading = '' if heading is None else '{} '.format(heading)
self.text = text
self.style = '' if style is None else style

Expand All @@ -126,7 +125,7 @@ def display(self):

def _repr_mimebundle_(self, include=None, exclude=None):
return {
'text/html': '<div class="figurelegend" style="{}"><b>Figure {}.&nbsp;{}</b>{}</div>'.format(
'text/html': '<div class="figurelegend" style="{}"><b>Figure {}. {}</b>{}</div>'.format(
self.style, self.fignum, self.heading, self.text
)
}
Expand Down Expand Up @@ -182,6 +181,8 @@ def to_html(ref_num):

class bibliography(object):
def __init__(self, style=None):
self.style = '' if style is None else style

try:
ipy = get_ipython()
ref_list = ipy.meta.get('references', {})
Expand All @@ -195,13 +196,18 @@ def display(self):
display(self)

def _repr_mimebundle_(self, include=None, exclude=None):
cites = ['<h4>References</h4>', '<dl class="bibliography">']
cites = [
'<div>'
'<h4>References</h4>',
'<dl class="bibliography" style="{}">'.format(self.style)
]

for ref_label, (ref_num, ref_text) in self.ref_list.items():
cites.append('<dt>{}</dt>'.format(ref_num))
cites.append('<dd>{}</dd>'.format(ref_text))

cites.append('</dl>')
cites.append('</div>')

return {'text/html': '\n'.join(cites)}

Expand All @@ -212,15 +218,15 @@ def display(self):
display(self)

def _repr_mimebundle_(self, include=None, exclude=None):
return {'text/html': '<div class="pagebreak">'}
return {'text/html': '<div class="pagebreak"></div>'}


class coversheet(object):
def __init__(self, title, prepared_for, prepared_by, project_details, add_br=True):
if add_br:
title = title.replace('\n', '<br>')
prepared_for = prepared_for.replace('\n', '<br>')
prepared_by = prepared_by.replace('\n', '<br>')
title = title.replace('\n', '<br />')
prepared_for = prepared_for.replace('\n', '<br />')
prepared_by = prepared_by.replace('\n', '<br />')

self.title = title
self.prepared_for = prepared_for
Expand All @@ -238,7 +244,7 @@ def __init__(self, title, prepared_for, prepared_by, project_details, add_br=Tru
self.project_details = '\n'.join(deets)
else:
if add_br:
project_details = project_details.replace('\n', '<br>')
project_details = project_details.replace('\n', '<br />')

self.project_details = project_details

Expand All @@ -259,16 +265,18 @@ def display(self):

def _repr_mimebundle_(self, include=None, exclude=None):
body = """
<h2 class="coverpage-title">{}</h2>
<div class="coverpage-date">{}</div>
<h4>PREPARED FOR</h4>
{}
<br>
<h4>PREPARED BY</h4>
{}
<br>
<h4>PROJECT DETAILS</h4>
{}
<div class="pagebreak">
<h2 class="coverpage-title">{}</h2>
<div class="coverpage-date">{}</div>
<h4>PREPARED FOR</h4>
{}
<br />
<h4>PREPARED BY</h4>
{}
<br />
<h4>PROJECT DETAILS</h4>
{}
</div>
""".format(
self.title,
self.proj_date,
Expand All @@ -277,9 +285,7 @@ def _repr_mimebundle_(self, include=None, exclude=None):
self.project_details,
)

pagebreak_html = pagebreak()._repr_mimebundle_()['text/html']

return {'text/html': body + pagebreak_html}
return {'text/html': body}


class OneCodexHTMLExporter(HTMLExporter):
Expand Down Expand Up @@ -324,7 +330,8 @@ def from_notebook_node(self, nb, resources=None, **kw):
elif out.get('metadata') and out['metadata'].get('onecodex') == 'head.style':
for mimetype in out.get('data', []):
if mimetype == 'text/css':
head_block = resources['metadata'].get('head_block', '') + out['data']['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

Expand Down Expand Up @@ -356,7 +363,7 @@ def from_notebook_node(self, nb, resources=None, **kw):

# add link to our custom CSS using system path
css_path = 'file:///' + os.path.join(ASSETS_PATH, CSS_TEMPLATE_FILE).replace('\\', '/')
css_link = '<link rel="stylesheet" href="{}">'.format(css_path)
css_link = '<link rel="stylesheet" href="{}" />'.format(css_path)
head_block = resources['metadata'].get('head_block', '') + css_link
resources['metadata']['head_block'] = head_block

Expand Down Expand Up @@ -400,15 +407,17 @@ def _file_extension_default(self):
return '.html'


class PDFExporter(OneCodexHTMLExporter):
class OneCodexPDFExporter(OneCodexHTMLExporter):
export_from_notebook = 'One Codex PDF Report'
template_path = [ASSETS_PATH]

def from_notebook_node(self, nb, resources=None, **kw):
"""Takes output of OneCodexHTMLExporter and runs Weasyprint to get a PDF."""
from weasyprint import HTML, CSS

nb = copy.deepcopy(nb)

output, resources = super(PDFExporter, self).from_notebook_node(nb, resources=resources, **kw)
output, resources = super(OneCodexPDFExporter, self).from_notebook_node(nb, resources=resources, **kw)
buf = BytesIO()
HTML(string=output).write_pdf(
buf, stylesheets=[CSS(os.path.join(ASSETS_PATH, CSS_TEMPLATE_FILE))]
Expand All @@ -421,13 +430,13 @@ def _file_extension_default(self):
return '.pdf'


class DocumentExporter(PDFExporter):
class OneCodexDocumentExporter(OneCodexPDFExporter):
export_from_notebook = 'Export to One Codex Document Portal'

def from_notebook_node(self, nb, resources=None, **kw):
"""Takes PDF output from PDFExporter and uploads to One Codex Documents portal.
"""
output, resources = super(DocumentExporter, self).from_notebook_node(nb, resources=resources, **kw)
output, resources = super(OneCodexDocumentExporter, self).from_notebook_node(nb, resources=resources, **kw)

# TODO: implement storage of PDF in Documents portal

Expand Down
4 changes: 2 additions & 2 deletions setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -107,8 +107,8 @@ def run(self):
entry_points={
'console_scripts': ['onecodex = onecodex.cli:onecodex'],
'nbconvert.exporters': [
'onecodex_pdf = onecodex.reports:PDFExporter',
'onecodex_doc = onecodex.reports:DocumentExporter',
'onecodex_pdf = onecodex.reports:OneCodexPDFExporter',
# 'onecodex_doc = onecodex.reports:OneCodexDocumentExporter',
],
},
test_suite='tests'
Expand Down
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