19136907997

Committed 06 Nov 2025 12:56PM UTC coverage: 68.835% (-0.4%) from 69.186%

Build # 19136907997

Build Type

push

github

Committed by

web-flow

Commit Message

Merge pull request #875 from cokelaer/dev

update HTML variant calling + others

Run Details

157 of 332 new or added lines in 14 files covered. (47.29%)

5 existing lines in 3 files now uncovered.

14551 of 21139 relevant lines covered (68.83%)

2.07 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

73.94

/sequana/modules_report/base_module.py

# coding: utf-8
#
#  This file is part of Sequana software
#
#  Copyright (c) 2016 - Sequana Development Team
#
#  File author(s):
#      Dimitri Desvillechabrol <dimitri.desvillechabrol@pasteur.fr>,
#          <d.desvillechabrol@gmail.com>
#
#  Distributed under the terms of the 3-clause BSD license.
#  The full license is in the LICENSE file, distributed with this software.
#
#  website: https://github.com/sequana/sequana
#  documentation: http://sequana.readthedocs.io
#
##############################################################################
"""Generic module is the parent module of all other module"""
import base64
import io
import os
import shutil

import colorlog
from jinja2 import Environment, PackageLoader

# from reports import HTMLTable
from sequana.utils import config

logger = colorlog.getLogger(__name__)


__all__ = ["SequanaBaseModule"]


class SequanaBaseModule(object):
    """Generic Module to write HTML reports.


    # to add a TOC, add this code::

        <div id="tocDiv">
        <ul id="tocList"> </ul>
        </div>


    """

    def __init__(self, template_fn="standard.html", required_dir=None):
        if required_dir is None:
            self.required_dir = ("css", "js", "images")
        else:
            self.required_dir = required_dir

        self.output_dir = config.output_dir
        self.path = "./"
        # Initiate jinja template
        env = Environment(loader=PackageLoader("sequana", "resources/templates/"))
        self.template = env.get_template(template_fn)
        self._init_report()
        self._fotorama_js_added = False

    def _init_report(self):
        """Create the report directory. All necessary directories are copied
        in working directory.
        """
        # Be aware of #465 issue. We need to check that the target file is
        # valid, in which case there is no need to copy the files.

        # Create report directory
        if os.path.isdir(config.output_dir) is False:
            os.mkdir(self.output_dir)

        for directory in self.required_dir:
            complete_directory = os.sep.join([self.output_dir, directory])
            if os.path.isdir(complete_directory) is False:
                os.mkdir(complete_directory)

        # Copy css/js necessary files
        for filename in config.css_list:
            target = os.sep.join([self.output_dir, "css"])
            if os.path.isfile(target) is False:
                try:
                    shutil.copy(filename, target)
                except PermissionError:
                    pass

        for filename in config.js_list:
            target = os.sep.join([self.output_dir, "js"])
            if os.path.isfile(target) is False:
                try:
                    shutil.copy(filename, target)
                except PermissionError:
                    pass

        target = os.sep.join([self.output_dir, "images"])
        os.makedirs(target, exist_ok=True)
        if os.path.isfile(target) is False:
            try:
               shutil.copy(config.logo, target)
            except PermissionError:
                pass

    def create_html(self, output_filename):
        """Create HTML file with Jinja2.

        :param str output_filename: HTML output filename
        """
        if output_filename is None:
            return
        report_output = self.template.render(config=config, module=self)
        with open(os.sep.join([config.output_dir, output_filename]), "w") as fp:
            print(report_output, file=fp)

    def create_link(self, name, target, newtab=True, download=False):
        """Create an HTML hyperlink with name and target.

        :param str target: the target url.
        :param bool newtab: open html page in a new tab.
        :param bool download: download the target.

        Return as string the HTML hyperlink to the target.
        """
        link = '<a href="{0}" '
        if newtab:
            link += 'target="_blank" '
        if download:
            link += 'download="{0}" '
        link += ">{1}</a>"
        return link.format(target, name)

    def create_hide_section(self, html_id, name, content, hide=False):
        """Create an hideable section.

        :param str html_id: add short id to connect all elements.
        :param str name: name of the hyperlink to hide or display the content.
        :param str content: hideable HTML content.
        :param bool hide: set if the first state is hiding or not.

        Return tuple that contains HTML hyperlink and hideable section.
        """
        link = "<a href='#1' class='show_hide{0}'>{1}</a>".format(html_id, name)
        content = "<div class='slidingDiv{0}'>\n{1}\n</div>".format(html_id, content)
        hidden = ""
        if hide:
            hidden = '\n$(".slidingDiv{0}").hide();'.format(html_id)
        js = """
<script type="text/javascript">
    $(document).ready(function(){{{1}
        $(".show_hide{0}").click(function(){{
            $(".slidingDiv{0}").slideToggle();
        }});
    }});
</script>
        """.format(
            html_id, hidden
        )
        content = js + content
        return link, content

    def copy_file(self, filename, target_dir):
        """Copy a file to a target directory in report dir. Return the
        relative path of your file.

        :param str filename: file to copy.
        :param str target_dir: directory where to copy.

        Return relative path of the new file location.
        """
        directory = config.output_dir + os.sep + target_dir
        try:
            os.makedirs(directory)
        except FileExistsError:
            if os.path.isdir(directory):
                pass
            else:
                msg = "{0} exist and it is not a directory".format(directory)
                logger.error(msg)
                raise FileExistsError
        try:
            shutil.copy(filename, directory)
        except FileNotFoundError:
            msg = "{0} doesn't exist".format(filename)
            raise FileNotFoundError(msg)
        return target_dir + os.sep + os.path.basename(filename)

    def add_float_right(self, content):
        """Align a content to right."""
        return '<div style="float:right">{0}</div>'.format(content)

    def add_code_section(self, content, language):
        """Add code in your html."""
        html = '<div class="code"><pre><code class="{0}">{1}' "</code></pre></div>"
        return html.format(language, content)

    def include_svg_image(self, filename, alt="undefined"):
        """Include SVG image in the html."""
        html = '<object data="{0}" type="image/svg+xml">\n' '<img src="{0}" alt={1}></object>'
        return html.format(filename, alt)

    def png_to_embedded_png(self, png, style=None, alt="", title=""):
        """Include a PNG file as embedded file."""
        import base64

        with open(png, "rb") as fp:
            png = base64.b64encode(fp.read()).decode()
        if style:
            html = '<img style="{0}" alt="{1}" title="{2}"'.format(style, alt, title)
        else:
            html = '<img alt="{}" title="{}"'.format(alt, title)
        return '{0} src="data:image/png;base64,{1}">'.format(html, png)

    def create_embedded_png(self, plot_function, input_arg, style=None, **kwargs):
        """Take as a plot function as input and create a html embedded png
        image. You must set the arguments name for the output to connect
        buffer.
        """
        buf = io.BytesIO()
        # add buffer as output of the plot function
        kwargs = dict({input_arg: buf}, **kwargs)
        try:
            plot_function(**kwargs)
            html = "<img "
            if style:
                html += 'style="{0}"'.format(style)
            html += 'src="data:image/png;base64,{0}"/>'.format(base64.b64encode(buf.getvalue()).decode("utf-8"))
            buf.close()
        except Exception as err:
            print(err)
            html = "image not created"
        return html

    def create_combobox(self, path_list, html_id, newtab=True):
        """Create a dropdown menu with QueryJS.

        :param list path_list: list of links.

        return html div and js script as string.
        """
        option_list = (
            "<li>{0}</li>\n".format(self.create_link(os.path.basename(path), path, newtab)) for path in path_list
        )
        html = """
<div id="jq-dropdown-{1}" class="jq-dropdown jq-dropdown-tip jq-dropdown-scroll">
    <ul class="jq-dropdown-menu">
        {0}
    </ul>
</div>
<a href="#" data-jq-dropdown="#jq-dropdown-{1}">Subchromosome</a>
        """.format(
            "\n".join(option_list), html_id
        )
        return html

    def add_fotorama(
        self,
        files,
        width=600,
        height=800,
        loop=True,
        thumbnails=True,
        file_thumbnails=None,
        captions=None,
    ):
        if self._fotorama_js_added is False:
            script = """
        <!-- jQuery 1.8 or later, 33 KB -->
        <!--<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.11.1/jquery.min.js"></script>-->
        <!-- Fotorama from CDNJS, 19 KB -->
        <link  href="https://cdnjs.cloudflare.com/ajax/libs/fotorama/4.6.4/fotorama.css" rel="stylesheet">
        <script src="https://cdnjs.cloudflare.com/ajax/libs/fotorama/4.6.4/fotorama.js"></script>
        """
            self._fotorama_js_added = True
        else:
            script = ""

        if captions:
            if len(files) != len(captions):
                raise ValueError("captions and files must be of same length with 1-to-1 mapping")
        else:
            captions = [filename.name for filename in files]

        script += '<div class="fotorama" fzyz-keyboard="true" '
        if thumbnails is True:
            script += ' data-nav="thumbs"'
        if loop is True:
            script += ' data-loop="true"'
        script += ' data-width="{}"  data-height="{}"'.format(width, height)
        script += ">"
        for filename, caption in zip(files, captions):
            script += '<img src="{}" data-caption="{}">'.format(filename, caption)
        script += "</div>"
        return script

1	# coding: utf-8
2	#
3	# This file is part of Sequana software
4	#
5	# Copyright (c) 2016 - Sequana Development Team
6	#
7	# File author(s):
8	# Dimitri Desvillechabrol <dimitri.desvillechabrol@pasteur.fr>,
9	# <d.desvillechabrol@gmail.com>
10	#
11	# Distributed under the terms of the 3-clause BSD license.
12	# The full license is in the LICENSE file, distributed with this software.
13	#
14	# website: https://github.com/sequana/sequana
15	# documentation: http://sequana.readthedocs.io
16	#
17	##############################################################################
18	"""Generic module is the parent module of all other module"""	3✔
19	import base64	3✔
20	import io	3✔
21	import os	3✔
22	import shutil	3✔
23
24	import colorlog	3✔
25	from jinja2 import Environment, PackageLoader	3✔
26
27	# from reports import HTMLTable
28	from sequana.utils import config	3✔
29
30	logger = colorlog.getLogger(__name__)	3✔
31
32
33	__all__ = ["SequanaBaseModule"]	3✔
34
35
36	class SequanaBaseModule(object):	3✔
37	"""Generic Module to write HTML reports.
38
39
40	# to add a TOC, add this code::
41
42	<div id="tocDiv">
43	<ul id="tocList"> </ul>
44	</div>
45
46
47	"""
48
49	def __init__(self, template_fn="standard.html", required_dir=None):	3✔
50	if required_dir is None:	3✔
51	self.required_dir = ("css", "js", "images")	3✔
52	else:
53	self.required_dir = required_dir	×
54
55	self.output_dir = config.output_dir	3✔
56	self.path = "./"	3✔
57	# Initiate jinja template
58	env = Environment(loader=PackageLoader("sequana", "resources/templates/"))	3✔
59	self.template = env.get_template(template_fn)	3✔
60	self._init_report()	3✔
61	self._fotorama_js_added = False	3✔
62
63	def _init_report(self):	3✔
64	"""Create the report directory. All necessary directories are copied
65	in working directory.
66	"""
67	# Be aware of #465 issue. We need to check that the target file is
68	# valid, in which case there is no need to copy the files.
69
70	# Create report directory
71	if os.path.isdir(config.output_dir) is False:	3✔
72	os.mkdir(self.output_dir)	×
73
74	for directory in self.required_dir:	3✔
75	complete_directory = os.sep.join([self.output_dir, directory])	3✔
76	if os.path.isdir(complete_directory) is False:	3✔
77	os.mkdir(complete_directory)	3✔
78
79	# Copy css/js necessary files
80	for filename in config.css_list:	3✔
81	target = os.sep.join([self.output_dir, "css"])	3✔
82	if os.path.isfile(target) is False:	3✔
83	try:	3✔
84	shutil.copy(filename, target)	3✔
85	except PermissionError:	×
86	pass	×
87
88	for filename in config.js_list:	3✔
89	target = os.sep.join([self.output_dir, "js"])	3✔
90	if os.path.isfile(target) is False:	3✔
91	try:	3✔
92	shutil.copy(filename, target)	3✔
93	except PermissionError:	×
94	pass	×
95
96	target = os.sep.join([self.output_dir, "images"])	3✔
97	os.makedirs(target, exist_ok=True)	3✔
98	if os.path.isfile(target) is False:	3✔
99	try:	3✔
100	shutil.copy(config.logo, target)	3✔
101	except PermissionError:	×
102	pass	×
103
104	def create_html(self, output_filename):	3✔
105	"""Create HTML file with Jinja2.
106
107	:param str output_filename: HTML output filename
108	"""
109	if output_filename is None:	3✔
110	return	3✔
111	report_output = self.template.render(config=config, module=self)	3✔
112	with open(os.sep.join([config.output_dir, output_filename]), "w") as fp:	3✔
113	print(report_output, file=fp)	3✔
114
115	def create_link(self, name, target, newtab=True, download=False):	3✔
116	"""Create an HTML hyperlink with name and target.
117
118	:param str target: the target url.
119	:param bool newtab: open html page in a new tab.
120	:param bool download: download the target.
121
122	Return as string the HTML hyperlink to the target.
123	"""
124	link = '<a href="{0}" '	3✔
125	if newtab:	3✔
126	link += 'target="_blank" '	3✔
127	if download:	3✔
128	link += 'download="{0}" '	3✔
129	link += ">{1}</a>"	3✔
130	return link.format(target, name)	3✔
131
132	def create_hide_section(self, html_id, name, content, hide=False):	3✔
133	"""Create an hideable section.
134
135	:param str html_id: add short id to connect all elements.
136	:param str name: name of the hyperlink to hide or display the content.
137	:param str content: hideable HTML content.
138	:param bool hide: set if the first state is hiding or not.
139
140	Return tuple that contains HTML hyperlink and hideable section.
141	"""
142	link = "<a href='#1' class='show_hide{0}'>{1}</a>".format(html_id, name)	3✔
143	content = "<div class='slidingDiv{0}'>\n{1}\n</div>".format(html_id, content)	3✔
144	hidden = ""	3✔
145	if hide:	3✔
146	hidden = '\n$(".slidingDiv{0}").hide();'.format(html_id)	3✔
147	js = """	3✔
148	<script type="text/javascript">
149	$(document).ready(function(){{{1}
150	$(".show_hide{0}").click(function(){{
151	$(".slidingDiv{0}").slideToggle();
152	}});
153	}});
154	</script>
155	""".format(
156	html_id, hidden
157	)
158	content = js + content	3✔
159	return link, content	3✔
160
161	def copy_file(self, filename, target_dir):	3✔
162	"""Copy a file to a target directory in report dir. Return the
163	relative path of your file.
164
165	:param str filename: file to copy.
166	:param str target_dir: directory where to copy.
167
168	Return relative path of the new file location.
169	"""
170	directory = config.output_dir + os.sep + target_dir	3✔
171	try:	3✔
172	os.makedirs(directory)	3✔
173	except FileExistsError:	3✔
174	if os.path.isdir(directory):	3✔
175	pass	3✔
176	else:
177	msg = "{0} exist and it is not a directory".format(directory)	×
178	logger.error(msg)	×
179	raise FileExistsError	×
180	try:	3✔
181	shutil.copy(filename, directory)	3✔
182	except FileNotFoundError:	×
183	msg = "{0} doesn't exist".format(filename)	×
184	raise FileNotFoundError(msg)	×
185	return target_dir + os.sep + os.path.basename(filename)	3✔
186
187	def add_float_right(self, content):	3✔
188	"""Align a content to right."""
189	return '<div style="float:right">{0}</div>'.format(content)	3✔
190
191	def add_code_section(self, content, language):	3✔
192	"""Add code in your html."""
193	html = '<div class="code"><pre><code class="{0}">{1}' "</code></pre></div>"	3✔
194	return html.format(language, content)	3✔
195
196	def include_svg_image(self, filename, alt="undefined"):	3✔
197	"""Include SVG image in the html."""
198	html = '<object data="{0}" type="image/svg+xml">\n' '<img src="{0}" alt={1}></object>'	3✔
199	return html.format(filename, alt)	3✔
200
201	def png_to_embedded_png(self, png, style=None, alt="", title=""):	3✔
202	"""Include a PNG file as embedded file."""
203	import base64	3✔
204
205	with open(png, "rb") as fp:	3✔
206	png = base64.b64encode(fp.read()).decode()	3✔
207	if style:	3✔
208	html = '<img style="{0}" alt="{1}" title="{2}"'.format(style, alt, title)	×
209	else:
210	html = '<img alt="{}" title="{}"'.format(alt, title)	3✔
211	return '{0} src="data:image/png;base64,{1}">'.format(html, png)	3✔
212
213	def create_embedded_png(self, plot_function, input_arg, style=None, **kwargs):	3✔
214	"""Take as a plot function as input and create a html embedded png
215	image. You must set the arguments name for the output to connect
216	buffer.
217	"""
218	buf = io.BytesIO()	3✔
219	# add buffer as output of the plot function
220	kwargs = dict({input_arg: buf}, **kwargs)	3✔
221	try:	3✔
222	plot_function(**kwargs)	3✔
223	html = "<img "	3✔
224	if style:	3✔
225	html += 'style="{0}"'.format(style)	3✔
226	html += 'src="data:image/png;base64,{0}"/>'.format(base64.b64encode(buf.getvalue()).decode("utf-8"))	3✔
227	buf.close()	3✔
UNCOV 228	except Exception as err:	×
UNCOV 229	print(err)	×
UNCOV 230	html = "image not created"	×
231	return html	3✔
232
233	def create_combobox(self, path_list, html_id, newtab=True):	3✔
234	"""Create a dropdown menu with QueryJS.
235
236	:param list path_list: list of links.
237
238	return html div and js script as string.
239	"""
240	option_list = (	3✔
241	"<li>{0}</li>\n".format(self.create_link(os.path.basename(path), path, newtab)) for path in path_list
242	)
243	html = """	3✔
244	<div id="jq-dropdown-{1}" class="jq-dropdown jq-dropdown-tip jq-dropdown-scroll">
245	<ul class="jq-dropdown-menu">
246	{0}
247	</ul>
248	</div>
249	<a href="#" data-jq-dropdown="#jq-dropdown-{1}">Subchromosome</a>
250	""".format(
251	"\n".join(option_list), html_id
252	)
253	return html	3✔
254
255	def add_fotorama(	3✔
256	self,
257	files,
258	width=600,
259	height=800,
260	loop=True,
261	thumbnails=True,
262	file_thumbnails=None,
263	captions=None,
264	):
265	if self._fotorama_js_added is False:	×
266	script = """	×
267	<!-- jQuery 1.8 or later, 33 KB -->
268	<!--<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.11.1/jquery.min.js"></script>-->
269	<!-- Fotorama from CDNJS, 19 KB -->
270	<link href="https://cdnjs.cloudflare.com/ajax/libs/fotorama/4.6.4/fotorama.css" rel="stylesheet">
271	<script src="https://cdnjs.cloudflare.com/ajax/libs/fotorama/4.6.4/fotorama.js"></script>
272	"""
273	self._fotorama_js_added = True	×
274	else:
275	script = ""	×
276
277	if captions:	×
278	if len(files) != len(captions):	×
279	raise ValueError("captions and files must be of same length with 1-to-1 mapping")	×
280	else:
281	captions = [filename.name for filename in files]	×
282
283	script += '<div class="fotorama" fzyz-keyboard="true" '	×
284	if thumbnails is True:	×
285	script += ' data-nav="thumbs"'	×
286	if loop is True:	×
287	script += ' data-loop="true"'	×
288	script += ' data-width="{}" data-height="{}"'.format(width, height)	×
289	script += ">"	×
290	for filename, caption in zip(files, captions):	×
291	script += '<img src="{}" data-caption="{}">'.format(filename, caption)	×
292	script += "</div>"	×
293	return script	×

sequana / sequana / 19136907997

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous