def _alertAboutAssemblerWebsite(assembler):
link = ASSEMBLER_LINKS[assembler]
with h.div(id="alertUser", class_="row-fluid"):
with h.div(class_="span12"):
with h.div(class_="alert alert-info"):
h.button("x", class_="close", data_dismiss="alert",
type="button")
h.UNESCAPED(("Assemblies were performed using %s. If you have "
"questions on the quality of the assembly please "
"refer to the %s site.") % (link, link))
def _alertAboutAssemblerWebsite(assembler):
link = ASSEMBLER_LINKS[assembler]
with h.div(id="alertUser", class_="row-fluid"):
with h.div(class_="span12"):
with h.div(class_="alert alert-info"):
h.button("x", class_="close", data_dismiss="alert",
type="button")
h.UNESCAPED(("Assemblies were performed using %s. If you have "
"questions on the quality of the assembly please "
"refer to the %s site.") % (link, link))
def _linksToDownloads(sample, assembler):
div_id = "collapseDownload" + sample.name()
with h.div(class_="accordion-group"):
with h.div(class_="accordion-heading"):
h.a("Downloads", href="#"+div_id, class_="accordion-toggle",
data_toggle="collapse")
with h.div(class_="accordion-body collapse in", id=div_id):
with h.div(class_="accordion-inner"):
with h.div(class_="row-fluid", id="downloadPane"):
with h.div(class_="row-fluid"):
with h.div(class_="span12"):
h.p("Download all your assembly result files.")
with h.div(style="padding-top:5px"):
with h.p():
index = 0
downloads = sample.downloads(assembler)
for descr, url in downloads.items():
rurl = os.path.relpath(url, DIRNAME)
index += 1
if index % 5 != 1:
h.UNESCAPED((" |"
" "))
h.UNESCAPED("<a target='_blank' "
"href='%s'>"
"<i class='icon-download'>"
"</i>%s</a>" % (rurl, descr))
if index % 5 == 0:
h.br()
def _sampleSelector(samples):
with h.div(class_="row-fluid"):
with h.div(class_="span12", style="padding-top:20px"):
with h.div(class_="pull-left"):
h.strong("View Results")
h.TEXT(":")
with h.select(style="width:400px",
onchange="showSample(this.value)"):
for i, sample in enumerate(samples):
if i == 0:
h.option(sample.name(),
value=sample.name(), selected="selected")
else:
h.option(sample.name(), value=sample.name())
def _linksToDownloads(sample, assembler):
div_id = "collapseDownload" + sample.name()
with h.div(class_="accordion-group"):
with h.div(class_="accordion-heading"):
h.a("Downloads",
href="#" + div_id,
class_="accordion-toggle",
data_toggle="collapse")
with h.div(class_="accordion-body collapse in", id=div_id):
with h.div(class_="accordion-inner"):
with h.div(class_="row-fluid", id="downloadPane"):
with h.div(class_="row-fluid"):
with h.div(class_="span12"):
h.p("Download all your assembly result files.")
with h.div(style="padding-top:5px"):
with h.p():
index = 0
downloads = sample.downloads(assembler)
for descr, url in downloads.items():
rurl = os.path.relpath(url, DIRNAME)
index += 1
if index % 5 != 1:
h.UNESCAPED((" |"
" "))
h.UNESCAPED("<a target='_blank' "
"href='%s'>"
"<i class='icon-download'>"
"</i>%s</a>" %
(rurl, descr))
if index % 5 == 0:
h.br()
def _sampleSelector(samples):
with h.div(class_="row-fluid"):
with h.div(class_="span12", style="padding-top:20px"):
with h.div(class_="pull-left"):
h.strong("View Results")
h.TEXT(":")
with h.select(style="width:400px",
onchange="showSample(this.value)"):
for i, sample in enumerate(samples):
if i == 0:
h.option(sample.name(),
value=sample.name(), selected="selected")
else:
h.option(sample.name(), value=sample.name())
def _assemblyStats(sample, assembler):
def _assemblySettingsTable():
with h.table(class_="table table-condensed"):
h.tr(h.th("Parameter"), h.th("Value"))
for param, value in sample.assemblySettings(assembler).items():
h.tr(h.td(param), h.td(value))
def _assemblyMetricsTable(kind):
with h.table(class_="table table-condensed"):
with h.tr():
h.th("Metric")
with h.th():
h.UNESCAPED("Large " + kind + "s (≥ 500bp)")
h.th("All " + kind + 's')
for metric, value in sample.metrics(assembler, kind).items():
if len(value) == 1:
h.tr(h.td(metric), h.td(value[0], colspan='2'))
else:
h.tr(h.td(metric), h.td(value[0]), h.td(value[1]))
div_id = "collapseStats" + sample.name()
with h.div(class_="accordion-group"):
with h.div(class_="accordion-heading"):
h.a("Assembly Statistics",
href="#" + div_id,
class_="accordion-toggle",
data_toggle="collapse")
with h.div(id=div_id, class_="accordion-body collapse in"):
with h.div(class_="accordion-inner"):
with h.div(class_="row-fluid", id="statPane"):
with h.div(class_="row-fluid"):
with h.div(class_="span12"):
if sample.name() != '.':
h.p("Assembly summary statistics for ",
sample.name() + ".")
with h.div(style="padding-top:5px"):
_assemblySettingsTable()
with h.div(style="padding-top:10px"):
_assemblyMetricsTable("Contig")
if sample.hasScaffolds(assembler):
with h.div(style="padding-top:10px"):
_assemblyMetricsTable("Scaffold")
def generateReport(samples, assembler):
css_path = "/pluginMedia/AssemblerSPAdes/css/"
css = [
"kendo.common.min.css", "kendo.default.min.css", "kendo.ir.css",
"ir.css", "app.css", "bootstrap.css", "bootstrap-custom.css",
"bootstrap-select.css"
]
less = ["app.less"]
js_path = "/pluginMedia/AssemblerSPAdes/js/"
js = [
"less-1.4.1.min.js", "jquery-1.8.2.min.js", "bootstrap-select.min.js",
"bootstrap.min.js"
]
with h.html5() as root:
with h.head():
h.title("AssemblerSPAdes Plugin")
h.meta(name="viewport",
content="width=device-width, initial-scale=1.0")
for css_fn in css:
h.link(href=css_path + css_fn, rel="stylesheet")
for less_fn in less:
h.link(href=css_path + less_fn, rel="stylesheet/less")
with h.body():
for js_fn in js:
h.script('', src=js_path + js_fn)
with h.script():
h.UNESCAPED("function showSample(sample) { \n"
" var str = sample.replace(/\./g, '\\\\.') \n"
" $('div.row-fluid.sample').hide() \n"
" $('div#'+str+'.row-fluid.sample').show() \n"
"}")
with h.div(class_="main"):
with h.div(class_="main-content clearfix"):
with h.div(class_="container-fluid"):
_alertAboutAssemblerWebsite(assembler)
if len(samples) > 1:
_sampleSelector(samples)
for i, sample in enumerate(samples):
display = "display:" + ("none"
if i > 0 else "block")
if sample._info.get('spades'):
with h.div(name=sample.name(),
id=sample.name(),
class_="row-fluid sample",
style=display):
with h.div(class_="span12"):
with h.div(style="padding:0 19px"):
_linksToDownloads(
sample, assembler)
with h.div(
style="padding-top:10px"):
_assemblyStats(
sample, assembler)
return str(root)
def _assemblyStats(sample, assembler):
def _assemblySettingsTable():
with h.table(class_="table table-condensed"):
h.tr(h.th("Parameter"), h.th("Value"))
for param, value in sample.assemblySettings(assembler).items():
h.tr(h.td(param), h.td(value))
def _assemblyMetricsTable(kind):
with h.table(class_="table table-condensed"):
with h.tr():
h.th("Metric")
with h.th():
h.UNESCAPED("Large " + kind + "s (≥ 500bp)")
h.th("All " + kind + 's')
for metric, value in sample.metrics(assembler, kind).items():
if len(value) == 1:
h.tr(h.td(metric), h.td(value[0], colspan='2'))
else:
h.tr(h.td(metric), h.td(value[0]), h.td(value[1]))
div_id = "collapseStats" + sample.name()
with h.div(class_="accordion-group"):
with h.div(class_="accordion-heading"):
h.a("Assembly Statistics", href="#"+div_id,
class_="accordion-toggle", data_toggle="collapse")
with h.div(id=div_id, class_="accordion-body collapse in"):
with h.div(class_="accordion-inner"):
with h.div(class_="row-fluid", id="statPane"):
with h.div(class_="row-fluid"):
with h.div(class_="span12"):
if sample.name() != '.':
h.p("Assembly summary statistics for ",
sample.name() + ".")
with h.div(style="padding-top:5px"):
_assemblySettingsTable()
with h.div(style="padding-top:10px"):
_assemblyMetricsTable("Contig")
if sample.hasScaffolds(assembler):
with h.div(style="padding-top:10px"):
_assemblyMetricsTable("Scaffold")
def generateReport(samples, assembler):
css_path = "/pluginMedia/AssemblerPlus/css/"
css = ["kendo.common.min.css", "kendo.default.min.css", "kendo.ir.css",
"ir.css", "app.css", "bootstrap.css", "bootstrap-custom.css",
"bootstrap-select.css"]
less = ["app.less"]
js_path = "/pluginMedia/AssemblerPlus/js/"
js = ["less-1.4.1.min.js", "jquery-1.8.2.min.js",
"bootstrap-select.min.js", "bootstrap.min.js"]
with h.html5() as root:
with h.head():
h.title("AssemblerPlus Plugin")
h.meta(name="viewport",
content="width=device-width, initial-scale=1.0")
for css_fn in css:
h.link(href=css_path+css_fn, rel="stylesheet")
for less_fn in less:
h.link(href=css_path+less_fn, rel="stylesheet/less")
with h.body():
for js_fn in js:
h.script('', src=js_path+js_fn)
with h.script():
h.UNESCAPED("function showSample(sample) { \n"
" var str = sample.replace(/\./g, '\\\\.') \n"
" $('div.row-fluid.sample').hide() \n"
" $('div#'+str+'.row-fluid.sample').show() \n"
"}")
with h.div(class_="main"):
with h.div(class_="main-content clearfix"):
with h.div(class_="container-fluid"):
_alertAboutAssemblerWebsite(assembler)
if len(samples) > 1:
_sampleSelector(samples)
for i, sample in enumerate(samples):
display = "display:" + ("none" if i > 0 else "block")
if sample._info.get('spades'):
with h.div(name=sample.name(), id=sample.name(),
class_="row-fluid sample", style=display):
with h.div(class_="span12"):
with h.div(style="padding:0 19px"):
_linksToDownloads(sample, assembler)
with h.div(style="padding-top:10px"):
_assemblyStats(sample, assembler)
return str(root)