def html(
self, # Provenance instance
name, # Component name qualified by branch indices
):
'''Add to html view of self.
'''
from markup import oneliner
import os.path
# Start with a description list key
return_value = oneliner.dt(name,id=name)+'\n'
# Construct text for inclusion as description list value
href = 'file://'+self.file # EG, "file:///absolute_path/calc.py"
text = '{0}\n line {1:d}: {2}\n'.format(
oneliner.a(os.path.basename(self.file),href=href),
self.line_num,
self.line)
if self.text != '':
text += oneliner.p(self.text)+'\n'
if len(self.branches) == 0:
text += oneliner.p('No more provenance of {0}'.format(name))+'\n'
else:
text += 'Parent Components: '
for i,branch in enumerate(self.branches):
name_ = '{0}.{1}'.format(name,i)
text += oneliner.a(name_,href='#{0}'.format(name_))+', '
# Insert description list value
return_value += oneliner.dd(text.rstrip(' ,'))
# Recursion on branches
for i,branch in enumerate(self.branches):
return_value += branch.html('{0}.{1}'.format(name,i))
return return_value
def putResultsTable(p, b, data, id):
# p -> page
# data -> html_filename, pathwayName, summary dictionary (one row per pathway)
r = data[0]
summaryVals = r[2]
header = summaryVals["order"]
p.table(border=b, id=id, class_='tablesorter')
p.thead()
p.tr()
p.th("Image")
p.th("Name")
p.th(header, class_="{sorter:'digit'}")
p.tr.close()
p.thead.close()
p.tbody()
rowCount = 0
rowSum = [0 for h in header]
for r in data:
htmlFile = r[0]
pathwayName = r[1]
summaryVals = r[2]
p.tr()
base = os.path.basename(htmlFile)
#plot of ipls
p.td(o.a(o.img(src=pngBase + base[:-5] + ".png", width=100),
href=base))
#link to pathway details page
p.td(o.a(pathwayName, href=base))
vals = [round(summaryVals[h], 3) for h in header]
#additional columns of data
p.td(vals)
i = 0
#add data to totals for bottom of page
for h in header:
rowSum[i] += summaryVals[h]
i += 1
#end of row
p.tr.close()
p.tbody.close()
p.tbody()
p.tr()
p.td('')
p.td('Total')
# last row in table is sums
p.td(rowSum)
p.tr.close()
p.tbody.close()
p.table.close()
def mk_nav(self):
self.page.div(class_='col-md-3 blog-sidebar text-muted')
self.page.div(id_='sticky-anchor') # sticky nav from here: jsfiddle.net/livibetter/HV9HM
self.page.div.close()
self.page.div(class_='nav sidebar-module',id_='sticky')
self.page.h4('Navigation')
self.page.ul(class_='list-unstyled',role='navigation',style='font-size:90%')
for sec in self.sections:
self.page.li( e.a( sec['title'], href='#{:}'.format(sec['id']) ), style="border-bottom: 1px solid #eee; margin-top:8px;")
for subsec in sec['subsections']:
self.page.li( e.a( subsec['title'], href='#{:}'.format(subsec['id']) ) )
self.page.ul.close()
self.page.div.close()
self.page.div.close()
def __init__(
self, # GUN instance
C=Float(2.56e10, # dynes (cm)^3
'Constant in nominal equation of state: F = C/x^3 dynes', max_hist=10),
xi=Float(0.4, 'Initial position of projectile / cm'),
xf=Float(4.0, 'Final/muzzle position of projectile /cm'),
m=Float(
100.0,
'{0} of projectile / g'.format(
oneliner.a('Mass', href='http://en.wikipedia.org/wiki/Mass')
)),
N=400, # Number of intervals between xi and xf
sigma_sq_v=1.0e5, # Variance attributed to v measurements
):
x = Float(1e10,'Just for exercising Float operations')
C = C + x
C = C - x
C = C/x
C = C*x
C = -C
C = -C
self.C = C + 0.0 # Vacuous demonstration of Float + float
self.xi = xi
self.xf = xf
self.m = m
self._set_N(N)
self.sigma_sq_v = sigma_sq_v
self.components = set(('C','xi','xf','m'))#Component instance names
return
def putSummaryTable(p, b, data, id, tsv):
labels = data["sample"]["labels"]
p.table(border=b, id=id, class_='tablesorter')
p.thead()
p.tr()
p.th("Entity - Gene or Complex or Molecule")
p.th(labels, class_="{sorter:'digit'}")
p.tr.close()
p.thead.close()
p.tbody()
for d in data["sample"]:
if d == "labels":
continue
vals = data["sample"][d]
p.tr()
#name of gene
geneUrl = 'http://www.genecards.org/cgi-bin/carddisp.pl?gene=' + d
tsv.write('<a href=%s target="_blank">%s</a>\t' % (geneUrl, d))
p.td(o.a(d, href=geneUrl, target="_blank"))
tmp = [round(v, 3) for v in vals]
p.td(tmp)
tsv.write('%s\n' % tmp)
p.tr.close()
p.tbody.close()
tsv.close()
p.table.close()
def __str__(self):
page = markup.page( )
page.init(
title=self.title,
css=self.css,
header=self.header,
footer=self.footer
)
page.h1(self.title)
if len(self.subdirs):
links = []
for s in sorted(self.subdirs, key=operator.attrgetter('path')):
print s.path
base = os.path.basename(s.path)
link = e.a(base,
href='/'.join([base, 'index.html']))
links.append(link)
page.h2('Subdirectories:')
page.ul( class_='mylist' )
page.li( links, class_='myitem' )
page.ul.close()
size = 100/self.nimagesperrow - 1
if len(self.images):
for rimgs in split(sorted(self.images), self.nimagesperrow):
page.img( src=rimgs, width='{size}%'.format(size=size),
alt=rimgs)
page.br()
return str(page)
def start_subblock(self, title, id=None, doc=None, hidden=False, **kwargs):
if not id:
id = re.sub('-|:|\.| ','_', title)
if isinstance(doc, list):
#self.page.p('<pre>')
for p in doc:
self.page.p(p)
#self.page.p('</pre>')
elif doc:
self.page.p(doc)
#self.page.p('<pre>'+doc+'</pre>')
if hidden:
self.page.p(e.a(title, class_='btn btn-sm btn-default',
onclick="toggler('{:}extra');".format(id)),
class_="text-center")
self.page.div(id='{:}extra'.format(id), class_="myhidden")
self.page.div()
else:
self.page.a('',id=id,class_='anchor')
self.page.div()
self.page.h4(title)
self.sections[-1]['subsections'].append({})
self.sections[-1]['subsections'][-1]['title'] = title
self.sections[-1]['subsections'][-1]['id'] = id
return
def __str__(self):
page = markup.page()
page.init(title=self.title,
css=self.css,
header=self.header,
footer=self.footer)
page.h1(self.title)
if len(self.subdirs):
links = []
for s in sorted(self.subdirs, key=operator.attrgetter('path')):
print s.path
base = os.path.basename(s.path)
link = e.a(base, href='/'.join([base, 'index.html']))
links.append(link)
page.h2('Subdirectories:')
page.ul(class_='mylist')
page.li(links, class_='myitem')
page.ul.close()
size = 100 / self.nimagesperrow - 1
if len(self.images):
for rimgs in split(sorted(self.images), self.nimagesperrow):
page.img(src=rimgs,
width='{size}%'.format(size=size),
alt=rimgs)
page.br()
return str(page)
def putResultsTable(p, b, data, id):
r = data[0]
summaryVals = r[2]
header = summaryVals["order"]
p.table(border=b, id=id, class_='tablesorter')
p.thead()
p.tr()
p.th("Image")
p.th("Name")
p.th(header, class_="{sorter:'digit'}")
p.tr.close()
p.thead.close()
p.tbody()
rowCount = 0
rowSum = [0 for h in header]
for r in data:
htmlFile = r[0]
pathwayName = r[1]
summaryVals = r[2]
p.tr()
base = os.path.basename(htmlFile)
p.td(o.a(o.img(src=pngDir + base[:-5] + ".png", width=100), href=base))
p.td(o.a(pathwayName, href=base))
vals = [round(summaryVals[h], 3) for h in header]
p.td(vals)
i = 0
for h in header:
rowSum[i] += summaryVals[h]
i += 1
p.tr.close()
p.tbody.close()
p.tbody()
p.tr()
p.td('')
p.td('Total')
p.td(rowSum)
p.tr.close()
p.tbody.close()
p.table.close()
def inputPage(amrString, errors):
page = markup.page(mode='html')
page.init(lang="en",
charset='utf-8',
doctype=markup.doctype.strict,
title="GoPhiPy: an AMR Verbalizer",
script=('http://code.jquery.com/jquery-latest.min.js',
'../gophi-web/ace/ace.js', '../gophi-web/amr-verb.js'),
css=('../gophi-web/amr-verb.css'))
page.form(action="", method="POST", id='form')
page.h1(
e.a('Γω-Φ-∏', href="https://github.com/rali-udem/gophipy") +
': an AMR verbalizer')
page.p(
'AMR Color coding: ' + e.span('variable', class_='ace_variable') +
", " + e.span('concept', class_='ace_concept') + ", " +
e.span('role', class_='ace_role') + e.span(e.a(
"Editor help",
target="_blank",
href='https://github.com/ajaxorg/ace/wiki/Default-Keyboard-Shortcuts'
) + " " + e.a('Drag bottom border to resize editor', class_='resize'),
class_="help"))
page.div(
e.div("", id="amr", style="height:" + editorHeight + "px") +
e.div("", id="amr_dragbar", class_="app_editor_dragbar"))
page.div(amrString, id="inputAMR", name="amr")
page.textarea("", name="amr")
if len(errors) > 0:
page.pre(e.code(errors))
m = re.match(r"line +(\d+),(\d+) :", errors)
if m != None:
page.script(
'$(document).ready(function() {ace.edit("amr").gotoLine(%s,%s,true);})'
% m.groups())
page.input(id="indent", type="button", value="Indent")
page.input(name="submit", type="submit", value="Verbalize")
page.input(name="editorHeight", type="hidden", value="editorHeigth")
page.fieldset(
e.legend("Show Representations") + e.label("Semantic", for_="semR") +
makeCB("semR") + e.label("Syntactic", for_="syntR") + makeCB("syntR"))
page.input(name="mode", type="hidden", value="reply")
page.form.close()
return page
def html(
self, # Component instance
name, # Component name
):
'''Return tuple containing:
1. html description of self suitable for page.li()
2. html description of provenance sutible for page.add
inside of page.dl(), page.dl.close() pair
'''
from markup import oneliner
if self.display == False:
return '{0}: value={1}, {2}'.format(
name,
self.value,
oneliner.a('provenance',href='#{0}'.format(name))
)
return '{0}: {1}, {2}'.format(
name,
oneliner.a('value_link', href='#value of {0}'.format(name)),
oneliner.a('provenance',href='#{0}'.format(name))
)
def _build_header(self,*args,**kwargs):
self.page.div(class_='header')
self.page.nav(class_='navigation')
self.page.ul(class_='nav nav-pills pull-right')
self.page.li(e.a('Top',href='#top'),class_='active')
self.page.ul.close()
self.page.nav.close()
hutch = args[0].split('/')[0]
self.page.h3('{:} Data Summary '.format(hutch) +e.small('{:}, {:}'.format(*args),style='font-family:monospace;')
,class_='text-muted',style='color: {:};'.format( hutchcolor.get(hutch, 'gray') ))
self.page.div.close()
def link_to_single(page, singles, panel):
# Produce link to single plots
page.p("Individual model plots:", style='padding-top:100px;')
page.ul()
if panel.descr == 'JJAS-rp-timelat':
use_these = singles
else:
use_these = [ss for ss in singles if ss.descr == re.sub("(?:-diff)?(?:-page)?[0-9]?", "", panel.descr)]
#remove_rp_timelon = [ss for ss in singles if re.sub("-rp-timelon", "", ss.descr) == panel.descr]
#diff_removed = [ss for ss in remove_rp_timelon if ss.descr == re.sub("-diff", "", panel.descr)]
# if panel.descr == 'JJAS-rp-timelat':
# pdb.set_trace()
for s in sorted(use_these, key=lambda name:name.name):
single_html = s.fig + panel.fig + '.html'
page.li(e.a(s.name, href=single_html))
page.ul.close()
def createPage(droneurl):
req = Request(droneurl, headers={"X-Api-Key": apikey})
try:
response = urlopen(req)
except HTTPError as e:
page.div('HTTPError:' + str(e.code), class_="show")
writeout(config.get('output', 'filename') + '.html', str(page))
except URLError as e:
page.div('URLError: ' + str(e.reason), class_="show")
writeout(config.get('output', 'filename') + '.html', str(page))
else:
try:
data = loads(response.read())
except ValueError as e:
page.div('ValueError: ' + str(e), class_="show")
writeout(config.get('output', 'filename') + '.html', str(page))
else:
if len(data) == 0:
page.div(
"Uh oh! Doesn't look like you have any shows today! :(\nAdd more "
+ nest.a("here!", href=ndbaseurl),
class_="show")
writeout(config.get('output', 'filename') + '.html', str(page))
else:
page.div(config.get('output', 'head'), id="head")
for x in range(len(data)):
title = data[x]['title'].encode('utf-8')
series = data[x]['series']['title'].encode('utf-8')
airtime = data[x]['series']['airTime'].encode('utf-8')
overview = data[x]['overview'].encode('utf-8')
banner = data[x]['series']['images'][0]['url'].encode(
'utf-8')
if overview:
page.div(
nest.img(src=banner, class_="roundimg") +
nest.div(series + ": " + title, class_="title") +
nest.div(airtime, class_="airtime") +
nest.div(overview, class_="overview"),
class_="show")
else:
page.div(
nest.img(src=banner, class_="roundimg") +
nest.div(series + ": " + title, class_="title") +
nest.div(airtime, class_="airtime"),
class_="show")
writeout(config.get('output', 'filename') + '.html', str(page))
def replyPage(amrString, semR, syntR, semErrors):
page = markup.page(mode='html')
page.init(lang="en",
charset='utf-8',
doctype=markup.doctype.strict,
title="AMR verbalized by Γω-Φ-∏",
script=('http://code.jquery.com/jquery-latest.min.js',
'../gophi-web/jsRealB.min.js',
'../gophi-web/addLexicon-dme.js',
'../gophi-web/realize.js'))
page.style(
'.sent {font-weight:bold} textarea {font-family:monospace;font-size:large}'
)
page.h1('AMR verbalized by ' +
e.a('Γω-Φ-∏', href="https://github.com/rali-udem/gophipy"))
page.h2("AMR")
page.form(action="", method="POST", id='form')
page.pre(e.code(amrString))
if semRflag != "off":
page.h2("Semantic Representation")
page.pre(semR.prettyStr())
if len(semErrors) > 0:
page.h3(
"Errors in semantic to syntactic representation transformation")
page.pre(semErrors)
if syntRflag != "off":
page.h2("Syntactic Representation")
page.pre(syntR)
page.h2("English Sentence")
## HACK: combined uses of multiline strings in both Python and Javascript, this is "delicate"
page.script(f'''var syntR=`{syntR}`; '''
) # syntR must be quoted to prevent immediate evaluation
page.p('', id="realization")
page.input(name="amr", type="hidden", value=amrString)
page.input(name="editorHeight", type="hidden", value=editorHeight)
page.input(name="semR", type="hidden", value=semRflag)
page.input(name="syntR", type="hidden", value=syntRflag)
page.input(name="submit", type="submit", value="Edit the AMR")
page.input(name="mode", type="hidden", value="input")
page.form.close()
return page
def createTraitListingsHTML(traitListDir):
traitSet = set(gwasDB.__studyByTrait.keys())
for trait in traitSet:
if trait not in __traitMetaAnalysis:
continue
traitMetadata = __traitMetaAnalysis[trait]
RE_proteins = traitMetadata['RE']
drug_proteins = traitMetadata['drugbank']
other_proteins = traitMetadata['other']
chi_RE = traitMetadata['RE_chi']
chi_Drugbank = traitMetadata['drugbank_chi']
traitListFilename = os.sep.join([traitListDir, trait.replace(" ","_").replace("/", " or ").replace("\\", " or ") + ".html"])
traitpage = htmltools.createPage("Trait Summary: " + trait, css_file='../genereport.css')
htmltools.pageDescription(traitpage, "Gene list overlap summary for trait: %s" % (trait))
# two of these
htmltools.createContingencyTable(traitpage, "Overlap with rapidly evolving genes:", "RE", "trait", chi_RE[0], chi_RE[1], chi_RE[2],
chi_RE[3], chi_RE[4], chi_RE[5], chi_RE[6], chi_RE[7] )
htmltools.createContingencyTable(traitpage, "Overlap with drugbank genes:",
"Drugbank", "trait", chi_Drugbank[0], chi_Drugbank[1],
chi_Drugbank[2], chi_Drugbank[3], chi_Drugbank[4],
chi_Drugbank[5], chi_Drugbank[6], chi_Drugbank[7])
chi_drugs = traitMetadata['drugchi']
htmltools.createContingencyTable(traitpage, "Drug contingency for targeting disease vs targeting rapidly evolving proteins:",
"Targets Disease Genes", "Targets RE Genes", chi_drugs[0], chi_drugs[1],
chi_drugs[2], chi_drugs[3], chi_drugs[4],
chi_drugs[5], chi_drugs[6], chi_drugs[7])
traitpage.table.open(class_="invisible")
traitpage.tr.open()
traitpage.td.open()
traitpage.div("Gene Lists:", class_="header")
traitpage.div("Trait genes indicated as rapidly evolving: ", class_="description")
createGeneListTable(traitpage, RE_proteins)
traitpage.div("Trait genes associated with Drugbank targets: ", class_="description")
createGeneListTable(traitpage, drug_proteins)
traitpage.div("Other trait genes: ", class_="description")
createGeneListTable(traitpage, other_proteins)
traitpage.td.close()
traitpage.td.open()
traitpage.div("Drug Lists:", class_="header")
druglistlen = len(__traitMetaAnalysis[trait]['RE_drugs'])
traitpage.div("%d drugs targeting associated rapidly evolving proteins" % (druglistlen), class_="description")
traitpage.div.open(class_="druglist")
traitpage.ul.open()
for drug in __traitMetaAnalysis[trait]['RE_drugs']:
link = "http://www.drugbank.ca/drugs/%s" % (drug)
if drug not in drugDB.__drugs:
traitpage.li(oneliner.a(drug, href=link))
else:
traitpage.li(oneliner.a(drugDB.__drugs[drug]['name'], href=link))
traitpage.ul.close()
traitpage.div.close()
druglistlen = len(__traitMetaAnalysis[trait]['other_drugs'])
traitpage.div("%d Drugs targeting other proteins" % (druglistlen), class_="description")
traitpage.div.open(class_="druglist")
traitpage.ul.open()
for drug in __traitMetaAnalysis[trait]['other_drugs']:
link = "http://www.drugbank.ca/drugs/%s" % (drug)
if drug not in drugDB.__drugs:
traitpage.li(oneliner.a(drug, href=link))
else:
traitpage.li(oneliner.a(drugDB.__drugs[drug]['name'], href=link))
traitpage.ul.close()
traitpage.div.close()
traitpage.td.close()
traitpage.tr.close()
traitpage.table.close()
htmltools.savePage(traitpage, traitListFilename)
def createGeneListingsHTML(geneListDir):
pbar = ProgressBar()
pbar.setMaximum(len(gwasDB.__geneSet))
pbar.updateProgress(0)
i=0
for gene in gwasDB.__geneSet:
if i % 10 == 0:
pbar.updateProgress(i)
i+=1
genePage = htmltools.createPage("Gene Summary: " +
geneDB.__original_names[gene], css_file='../genereport.css',
scripts = {'../sorttable.js':'javascript'})
# Create the disease trait tables
traits = []
for trait in gwasDB.__traitDict[gene]:
traits.append(trait)
traits = sorted(traits, key=lambda trait: -__traitMetaAnalysis[trait]['RE_chi'][0])
traitTable = []
for trait in traits:
cnt = len(__traitMetaAnalysis[trait]['RE'])
oddsratio = __traitMetaAnalysis[trait]['RE_chi'][4]
kappa = __traitMetaAnalysis[trait]['RE_chi'][5]
fisher_exact = __traitMetaAnalysis[trait]['RE_chi'][6]
fisherp = __traitMetaAnalysis[trait]['RE_chi'][7]
numgenes = __traitMetaAnalysis[trait]['geneset_size']
translate = trait.replace(" ","_").replace("/", " or ").replace("\\", " or ")
if len(trait) > 38:
trait = trait[:35] + "..."
traitTable.append(["<a href=\"../traitlists/%s.html\">%s</a>" %
(translate,trait), cnt, numgenes, "%.7f" % (fisher_exact),
"%.7f" % (fisherp), "%.1f" % (oddsratio), "%.4f" % (kappa), ])
genePage.div("Gene %s, total traits: %d" % (geneDB.__original_names[gene],len(traitTable)), class_="header")
htmltools.createTable(genePage, traitTable, ["Disease/Trait", "#RE Genes",
"#Trait Genes", "fisher exact", "P-value",
"oddsratio", "kappa"], "traitlisthead", None,
["traitcol","recol",
"genecol","fishercol","pcol",
"oddscol","kappacol"], "sortable", None)
# Create drug bank links
if gene not in drugDB.__drugDict:
genePage.div("No drugs target gene %s" % (geneDB.__original_names[gene]), class_="header")
else:
drugbank_size = len(drugDB.__drugDict[gene])
genePage.div("%d drugs targeting gene %s" % (drugbank_size, geneDB.__original_names[gene]), class_="header")
genePage.div.open(class_="druglist")
genePage.ul.open()
for drug in drugDB.__drugDict[gene]:
link = "http://www.drugbank.ca/drugs/%s" % (drug)
if drug not in drugDB.__drugs:
genePage.li(oneliner.a(drug, href=link))
else:
genePage.li(oneliner.a(drugDB.__drugs[drug]['name'], href=link))
genePage.ul.close()
genePage.div.close()
htmltools.savePage(genePage, os.sep.join([geneListDir, gene + ".html"]))
pbar.finalize()
plots.append(htmlify.Diags(root_path, diag, panels, singles))
page = markup.page(mode='strict_html')
shutil.copy(os.path.join(run_path, 'htmlify.css'), options.target_folder)
page.init(css=os.path.join("..", 'htmlify.css'))
# Sort plots
plots = sorted(plots, key=attrgetter('diag'))
for plot in plots:
plot.panels.sort('descr')
# Write html with figures
page.h1("Diagnostics", id="the_top")
for diag in plots:
page.ul()
page.li(e.a(diag.diag, href='#' + diag.diag))
page.ul.close()
for diag in plots:
# Work with panel plots
for panel in diag.panels.files:
page.div(class_='diag', id=diag.diag)
page.img(src=os.path.join("..", fig_path, diag.diag, panel.fig),
id=panel.fig,
class_="figure")
# Create single plots
single_page = markup.page(mode='strict_html')
single_page.init(css=os.path.join(fig_path, 'htmlify.css'))
remove_err_vars = [s for s in diag.singles.files if s.var == panel.var]
htmlify.write_single(options.target_folder, options.link_folder,
def main(initfile, ntop):
# read configuration options and process
par = Parameters(initfile)
gpsb = par.res_param['gpsb']
gpse = par.res_param['gpse']
pdir = par.res_param['pdir']
hdir = par.res_param['hdir']
data = Data(hdir + 'post_proc_data.dat')
# relative paths of the stilesheets and javascripts for the results page
stylesheets = ('general.css', 'table.css', 'modal.css')
script = 'scripts.js'
# copy them in the results folder (that should already exist)
for sheet in stylesheets:
copy2(os.path.dirname(os.path.abspath(__file__)) + '/' + sheet, hdir)
copy2(os.path.dirname(os.path.abspath(__file__)) + '/' + script, hdir)
# Create summary web page
print "Generating Web Page..."
page = markup.page()
page.init(title="NonStatMoni",
css=stylesheets,
footer="(2017)" +
ol.a("Michele Valentini", href='mailto:[email protected]'))
# best coherences and ccfs summary table generation
page.button("Auxillary channels summary table", class_="accordion")
page.div(class_="panel")
page.input(type="text",
id="myInput",
onkeyup="myFunction()",
placeholder="Search for aux_channel names..")
page.table(id="t01")
for aux_name, aux_groups in data.aux_dict.iteritems():
page.tr()
page.td()
page.h4(aux_name)
page.td.close()
# Sort the dictionary according to the abs of the values,
# from highest to lowest
ccf_sorted = OrderedDict(
sorted(data.ccfs[aux_name].iteritems(),
key=lambda x: abs(x[1]),
reverse=True))
mean_coh_sorted = OrderedDict(
sorted(data.mean_cohs[aux_name].iteritems(),
key=lambda x: x[1],
reverse=True))
for chan_band, ccf in ccf_sorted.items()[0:4]:
pagename = 'cohe_{}.html'.format(chan_band.split('_')[0])
page.td(style="width:10%; font-size :11px;")
page.add(
"<a target=_blank href={}#{}>{}</a><br>(ccf={:3f})".format(
pagename,
aux_name.split(':')[1], chan_band, ccf))
page.td.close()
page.td()
page.add('<a> ******** </a>')
page.td.close()
for chan_band, coh in mean_coh_sorted.items()[0:4]:
pagename = 'cohe_{}.html'.format(chan_band.split('_')[0])
page.td(style="width:10%; font-size:11px;")
page.add(
'<a target=_blank href={}#{}>{}</a><br>(mncoh={:3f})'.format(
pagename,
aux_name.split(':')[1], chan_band, coh))
page.td.close()
page.tr.close()
page.table.close()
page.div.close()
# build the page menu
onclick_gen = ("openGroup(event, '{}')".format(group)
for group in data.group_dict.keys())
page.div(ol.button(data.group_dict.keys(),
class_='tablinks',
onclick=onclick_gen),
class_='tab')
# build each group subpage
for group, g_dict in data.group_dict.iteritems():
# Build the highest ccf and coherence for this group table
ccftab = {group: np.zeros(ntop)}
cohtab = {group: np.zeros(ntop)}
ccftab_names = {group: np.zeros(ntop, dtype='string')}
cohtab_names = {group: np.zeros(ntop, dtype='string')}
cohe_page_name = 'cohe_{}.html'.format(group)
for aux_n, (aux_name,
aux_groups) in enumerate(data.aux_dict.iteritems()):
if group in aux_groups:
for band in g_dict['band_list']:
if aux_n == 0:
ccftab[band] = np.zeros(ntop)
cohtab[band] = np.zeros(ntop)
ccftab_names[band] = np.zeros(ntop, dtype='string')
cohtab_names[band] = np.zeros(ntop, dtype='string')
ccf = data.ccfs[aux_name][group + '_' + band]
coh = data.mean_cohs[aux_name][group + '_' + band]
# todo: build single band tables too
if abs(ccf) > min(np.abs(ccftab[band])):
ccftab[band] = np.concatenate((ccftab[band], [ccf]))
ccftab_names[band] = np.concatenate(
(ccftab_names[band], [aux_name]))
best_indexes = np.abs(ccftab[band]).argsort()[1:][::-1]
ccftab[band] = ccftab[band][best_indexes]
ccftab_names[band] = ccftab_names[band][best_indexes]
if coh > min(cohtab[band]):
cohtab[band] = np.concatenate((cohtab[band], [coh]))
cohtab_names[band] = np.concatenate(
(cohtab_names[band], [aux_name]))
best_indexes = cohtab[band].argsort()[1:][::-1]
cohtab[band] = cohtab[band][best_indexes]
cohtab_names[band] = cohtab_names[band][best_indexes]
# Build the full group best tabs
if abs(ccf) > min(np.abs(ccftab[group])):
ccftab[group] = np.concatenate((ccftab[group], [ccf]))
ccftab_names[group] = np.concatenate(
(ccftab_names[group], [aux_name + ' with ' + band
]))
best_indexes = np.abs(
ccftab[group]).argsort()[1:][::-1]
ccftab[group] = ccftab[group][best_indexes]
ccftab_names[group] = ccftab_names[group][best_indexes]
if coh > min(cohtab[group]):
cohtab[group] = np.concatenate((cohtab[group], [coh]))
cohtab_names[group] = np.concatenate(
(cohtab_names[group], [aux_name + ' with ' + band
]))
best_indexes = cohtab[group].argsort()[1:][::-1]
cohtab[group] = cohtab[group][best_indexes]
cohtab_names[group] = cohtab_names[group][best_indexes]
tab = [[" CCF ", "Coherence"]]
for i in xrange(ntop):
row = [
"<a target=_blank href={0}#{1}>{2}</a><br>CCFs = {3:.2f}".
format(cohe_page_name,
ccftab_names[group][i].split(' ')[0].split(':')[1],
ccftab_names[group][i], ccftab[group][i]),
"<a target=_blank href={0}#{1}>{2}</a>"
"<br>Mean Coher. = {3:.3f}".format(
cohe_page_name,
cohtab_names[group][i].split(' ')[0].split(':')[1],
cohtab_names[group][i], cohtab[group][i])
]
tab.append(row)
tab_str = OrderedDict({group: tb.tabmaker(tab, True, False)})
for band in g_dict['band_list']:
tab = [[" CCF ", "Coherence"]]
for i in xrange(ntop):
row = [
"<a target=_blank href={0}#{1}>{2}</a><br>CCFs = {3:.2f}".
format(cohe_page_name, ccftab_names[band][i].split(':')[1],
ccftab_names[band][i], ccftab[band][i]),
"<a target=_blank href={0}#{1}>{2}</a>"
"<br>Mean Coher. = {3:.3f}".format(
cohe_page_name, cohtab_names[band][i].split(':')[1],
cohtab_names[band][i], cohtab[band][i])
]
tab.append(row)
tab_str[band] = tb.tabmaker(tab, True, False)
# build the rest of the frame
frame = ol.div(
ol.h1("NonStatMoni BRMS for {} GPS {:d} - {:d}".format(
g_dict['channel'], gpsb, gpse),
style="display:inline") +
ol.h3(ol.a("Coherences with slow channels",
target='_blank',
href=cohe_page_name),
style="display:inline"))
# todo: normalized by what?
time_title = ol.h2("Normalized BRMS time series")
time_img = ol.img(class_="myImg",
src=pdir + group + "_time.png",
alt=group + "Time plot",
width="400")
spec_title = ol.h2("Spectrum of BRMS time series")
spec_img = ol.img(class_="myImg",
src=pdir + group + "_psd.png",
alt=group + "PSD plot",
width="400")
frame += ol.div(time_title + time_img + spec_title + spec_img,
style="float:left")
tab_title_gen = (ol.h2("Best Correlations"
" and best Coherences for {}".format(c))
for c in ([group] + g_dict['band_list']))
frame += ol.div(
(title + tbl
for title, tbl in zip(tab_title_gen, tab_str.values())),
class_="v_tabcontent",
id=(['v_' + group] + g_dict['band_list']))
onclick_gen = ("openBand(event, '{}')".format(band)
for band in (['v_' + group] + g_dict['band_list']))
frame += ol.div(ol.button([group] + g_dict['band_list'],
class_='v_tablinks',
onclick=onclick_gen,
id=['defaultOpen', '']),
class_='vertical_tab')
page.div(frame, id=group, class_='tabcontent')
# create coherence subpage
page2 = markup.page()
page2.init(title="NonStatMoni", css='../style/style.css')
page2.h1("Coherences with slow channels")
for aux_name, aux_groups in data.aux_dict.iteritems():
if group in aux_groups:
page2.div(ol.img(src=(pdir + group + '_' + 'cohe_' +
aux_name.split(':')[1] + '.png'),
alt=(" No plots for" + aux_name)),
id=aux_name.split(':')[1])
page2.savehtml(hdir + cohe_page_name)
# create the modal for the plot images
modal = ol.span("×", class_="close")
modal += ol.img(class_="modal-content", id="img01")
modal += ol.div('', id="caption")
page.div(modal, id='myModal', class_="modal")
page.br()
page.h2("Contacts")
page.scripts({script: 'javascript'})
page.savehtml(hdir + 'index.html')
def putResultsTable(p, b, data, id):
# p -> page
# data -> html_filename, pathwayName, summary dictionary (one row per pathway)
r = data[0]
summaryVals = r[2]
header = summaryVals["order"]
p.table(border=b, id=id, class_='tablesorter')
p.thead()
p.tr()
p.th("Image")
p.th("Name")
p.th(header, class_="{sorter:'digit'}")
p.tr.close()
p.thead.close()
summary_tsv = open(rootDir + '/summary.tsv', 'wb')
summary_tsv.write(
"Pathway\tAvg num Alterations\tTotal alterations\tnum genes\tmin mean truth\tmax mean truth\tmin mean any\tmax mean any\tnormalized activity\n"
)
p.tbody()
rowCount = 0
rowSum = [0 for h in header]
for r in data:
htmlFile = r[0]
pathwayName = r[1]
summaryVals = r[2]
p.tr()
base = os.path.basename(htmlFile)
#plot of ipls
p.td(o.a(o.img(src=pngBase + base[:-5] + ".png", width=100),
href=base))
#link to pathway details page
p.td(o.a(pathwayName, href=base))
summary_tsv.write(pathwayName + '\t')
vals = [round(summaryVals[h], 3) for h in header]
for v in vals:
summary_tsv.write(str(v) + '\t')
#additional columns of data
p.td(vals)
i = 0
#add data to totals for bottom of page
for h in header:
rowSum[i] += summaryVals[h]
i += 1
#end of row
summary_tsv.write('\n')
p.tr.close()
summary_tsv.close()
p.tbody.close()
p.tbody()
p.tr()
p.td('')
p.td('Total')
# last row in table is sums
p.td(rowSum)
p.tr.close()
p.tbody.close()
p.table.close()
def generate(nims, no_quiz_feedback="False", test_time=300):
"""
Generate the HTML page based on the list of `nims` to be passed to `treatment`.
NOTE: Must be called within directory containing materials! This is done
by `generate_study.py`. Probably should rewrite to take paths as
arguments.
:param nims: list containing {t,e,f}
:param test_time: time for a single test fault scenario
:param no_quiz_feedback: turn off showing quiz scores
:return: HTML page as markup object
"""
test_time_minutes = format(test_time / 60.0, ".1f")
page = markup.page()
title = "Automated Student Benchmark Study"
page.init(title=title)
page.h1(title)
page.p(
"""Please follow the instructions on this page. The first few
linked documents (under the heading 'Reference Material') you may have
already seen; they are provided for your reference."""
)
page.p(
"""REMEMBER: You may refer to the material under 'Reference' at any
time, but you may <b>not</b> refer to the 'Curriculum' material during
quizzes or tests."""
)
page.h2("Reference Material")
page.ul()
page.li(e.a("Cover Letter", href=path.join("reference", "cover-letter.pdf"), target="blank"))
page.li(e.a("Student Instructions", href=path.join("reference", "student-instructions.pdf"), target="blank"))
page.li(e.a("Background Knowledge", href=path.join("reference", "background-knowledge.pdf"), target="blank"))
page.ul.close()
page.h2("Pre-Test")
page.p(
"In this pre-test you will be given "
+ test_time_minutes
+ " minutes to diagnose and fix the satellite tracking rig."
)
page.p(
""" Please begin by double-clicking the 'Pre-Test' link in the main
study folder to open the pre-test simulator. Click 'Start Simulation' when
you are ready to begin the timed test. After the timer runs out and the
simulation ends, please close the simulator and return to this page."""
)
# Get the rung info
curriculum_path = "curriculum"
rung_paths = glob(path.join(curriculum_path, "*"))
rung_paths.sort()
rung_names = [path.split(rung)[1] for rung in rung_paths]
# Glob the paths to the T, E, and BF slides by their names
slides_path = {}
for nim in ["T", "E", "BF"]:
slide_path = glob(path.join(curriculum_path, "*", "*", "*" + nim + "_slides*.pdf"))
slides_path[nim] = sorted(slide_path)
# Glob the quiz files
if no_quiz_feedback:
quiz_paths = glob(path.join("quizzes", "Rung*no_feedback.html"))
else:
quiz_paths = glob(path.join("quizzes", "Rung*yes_feedback.html"))
quiz_paths.sort()
quiz_full_names = [path.splitext(path.split(filename)[1])[0] for filename in quiz_paths]
pattern = "(Rung_\d(-\d)?_\d)_.+_feedback"
quiz_names = [re.search(pattern, full_name).groups()[0] for full_name in quiz_full_names]
quiz_dict = dict(zip(quiz_names, quiz_paths))
page.h2("Curriculum")
page.p(
"""Please complete the following lessons and quizzes in order. When
you have finished with one document, close the window or tab and move on to
the next. You are allowed to take notes, either on the scratch paper
provided or in Notepad."""
)
page.p(
"""Feedback lessons require you to interact with the simulator. To
launch the simulator for practice, double-click the shortcut labeled
'Simulator' in the main study folder."""
)
# """For Rung 6_4 only, instead double-click the shortcut labeled
#'Realtime-Simulator'.""")
nim_names = translate_treatment(nims)
nim_tuples = zip(*[slides_path[x] for x in nim_names])
for (rung_name, nim_set) in zip(rung_names, nim_tuples):
page.h3(rung_name)
page.ul()
for nim in nim_set:
file_name = path.split(nim)[1]
# pull out the descriptive rung name
match = re.search("(Rung_\d(-\d)?_\d_)?(.+)_slides", file_name)
desc_name = match.groups()[-1] # we want the last group
page.li(e.a(desc_name, href=nim, target="blank"))
page.ul.close()
if rung_name in quiz_names:
page.a(e.h3("Quiz"), href=quiz_dict[rung_name], target="blank")
page.h2("Post-Test 1")
page.p(
"In this post-test you will be given "
+ test_time_minutes
+ """ minutes per scenario to diagnose and fix any faults in the satellite
tracking rig (if any exist), for each of five scenarios."""
)
page.p(
"""Please begin by double-clicking the 'Post-Test-1' link in the main
study folder to open the post-test simulator. Click 'Start Simulation'
when you are ready to begin a scenario. After the timer runs out and the
simulation ends, please click 'Start Simulation' again to begin the next
scenario. After you have completed five scenarios, please close the
simulator and return to this page."""
)
page.h2("Post-Test 2")
page.p(
"In this post-test you will be given "
+ test_time_minutes
+ """ minutes to diagnose and fix any faults in the satellite tracking rig
(if any exist) for a single scenario."""
)
page.p(
"""Please begin by double-clicking the 'Post-Test-2' link in the
main study folder to open the post-test simulator. Click 'Start
Simulation' when you are ready to begin the scenario. After the timer runs
out and the simulation ends, please close the simulator and return to this
page."""
)
# give the all-fault case with a certain probability
if random.uniform(0, 1) < ALLFAULT_PROBABILITY:
page.h2("Final Test")
page.p(
"In this final test you will be given "
+ test_time_minutes
+ """ minutes to diagnose and fix the satellite tracking rig."""
)
page.p(
""" Please begin by double-clicking the 'Final-Test' link
in the main study folder to open the additional-test simulator. Click
'Start Simulation' when you are ready to begin the timed test. After
the timer runs out and the simulation ends, please close the simulator
and return to this page."""
)
page.p(
"""You are finished. Please raise your hand to alert the study
supervisor."""
)
return page
def createPage(droneurl):
req = Request(droneurl, headers={"X-Api-Key" : apikey})
try:
response = urlopen(req)
except HTTPError as e:
page.div('HTTPError:' + str(e.code),class_="show")
writeout(config.get('output', 'filename') + '.html',str(page))
except URLError as e:
page.div('URLError: ' + str(e.reason),class_="show")
writeout(config.get('output', 'filename') + '.html',str(page))
else:
try:
data = loads(response.read())
except ValueError as e:
page.div('ValueError: ' + str(e),class_="show")
writeout(config.get('output', 'filename') + '.html',str(page))
else:
if len(data) == 0:
page.div("Uh oh! Doesn't look like you have any shows today! :(\nAdd more " + nest.a("here!",href=ndbaseurl),class_="show")
writeout(config.get('output', 'filename') + '.html',str(page))
else:
page.div(config.get('output', 'head'),id="head")
for x in range(len(data)):
title = data[x]['title'].encode('utf-8')
series = data[x]['series']['title'].encode('utf-8')
airtime = data[x]['series']['airTime'].encode('utf-8')
overview = data[x]['overview'].encode('utf-8')
banner = data[x]['series']['images'][0]['url'].encode('utf-8')
if overview:
page.div(nest.img(src=banner,class_="roundimg") + nest.div(series + ": " + title, class_="title") + nest.div(airtime, class_="airtime") + nest.div(overview, class_="overview"), class_="show")
else:
page.div(nest.img(src=banner,class_="roundimg") + nest.div(series + ": " + title, class_="title") + nest.div(airtime, class_="airtime"), class_="show")
writeout(config.get('output', 'filename') + '.html',str(page))
def theme_header(title, image=None, help=None, config=None, nomodule=None, nowebmin=None,
rightside="", header=None, body=None, below=None):
acl = read_acl()
for l in list_languages():
if l["lang"] == current_lang:
lang = l
if force_charset:
charset = force_charset
elif lang.has_key("charset"):
charset = lang["charset"]
else:
charset = "iso-8859-1"
print "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\"\n\"http://www.w3.org/TR/REC-html40/loose.dtd\">"
if gconfig.has_key("real_os_type"):
os_type = gconfig["real_os_type"]
else:
os_type = gconfig["os_type"]
if gconfig.has_key("real_os_version"):
os_version = gconfig["real_os_version"]
else:
os_version = gconfig["os_version"]
print "<html>\n<head>"
if (charset):
print "<meta http-equiv=\"Content-Type\" "\
"content=\"text/html; charset=%s\">" % charset
print "<link rel='icon' href='images/webmin_icon.png' type='image/png'>"
if gconfig.get("sysinfo") == 1:
print "<title>%s : %s on %s (%s %s)</title>" % \
(title, remote_user, get_system_hostname(), os_type, os_version)
else:
print "<title>%s</title>" % title
if header:
print header
# Where does gconfig["sysinfo"] come from?
if gconfig.get("sysinfo") == 0 and remote_user:
print "<SCRIPT LANGUAGE=\"JavaScript\">"
if os.environ.has_key("SSL_USER"):
userstring = " (SSL certified)"
elif os.environ.has_key("LOCAL_USER"):
userstring = " (Local user)"
else:
userstring = ""
print "defaultStatus=\"%s%s logged into %s %s on %s (%s %s)\";" % \
(remote_user, userstring, text["programname"], get_webmin_version(),
get_system_hostname(), os_type, os_version)
print "</SCRIPT>"
msc_modules = get_all_module_infos(module_infos_access)
print "</head>"
if theme_no_table:
print '<body bgcolor="#6696bc" link="#000000" vlink="#000000" text="#000000" leftmargin="0" topmargin="0" marginwidth="0" marginheight="0" ', body, '>'
else:
print '<body bgcolor="#6696bc" link="#000000" vlink="#000000" text="#000000" leftmargin="0" topmargin="0" marginwidth="0" marginheight="0" ', body, '>'
if None != session_id:
logout = "/session_login.cgi?logout=1"
loicon = "logout.jpg"
lowidth = 84
lotext = text["main_logout"]
else:
logout = "switch_user.cgi"
loicon = "switch.jpg"
lowidth = 27
lotext = text["main_switch"]
hpage = markup.page()
## top_table = TableLite(width="100%", border="0", cellspacing="0",
## cellpadding="0", background="/images/top_bar/bg.jpg",
## height="32")
## t_body = TR()
hpage.table(width="100%", border="0", cellspacing="0",
cellpadding="0", background="/images/top_bar/bg.jpg",
height="32")
hpage.tr()
## TDList = [TD(IMG("/images/top_bar/left.jpg", height=32),
## width=4, nowrap="nowrap"),
## TD(Href(pytheme_logo_link,
## IMG(pytheme_logo, width=99,
## height=32,
## border="0", alt=pytheme_logo_alt)),
## width="100%", nowrap="nowrap")]
# TODO (Carsten) : missig auto alt tags for images (really needed ?)
hpage.td(e.img(src="/images/top_bar/left.jpg", height="32"),width="4", nowrap="nowrap")
hpage.td(width="100%", nowrap="nowrap")
hpage.a(e.img(src=pytheme_logo,width=99, height=32,alt=pytheme_logo_alt,border=0),href=pytheme_logo_link)
hpage.td.close()
if not os.environ.has_key("ANONYMOUS_USER"):
# XXX: acl.get("feedback") might not be correct
if gconfig.get("nofeedbackcc") != 2 and acl.get("feedback"):
## TDList.append(TD(Href("/feedback_form.cgi?module=%s" % module_name,
## IMG("/images/top_bar/feedback.jpg", width=97,
## height=32,
## border="0", alt=text["feedback"]))))
hpage.td()
hpage.a(e.img(src="/images/top_bar/feedback.jpg",width=97,height=32,border=0,
alt=text["feedback"]),href="/feedback_form.cgi?module=%s" % module_name)
hpage.td.close()
## TDList.append(TD(IMG("/images/top_bar/top_sep.jpg", width=12,
## height=32)))
hpage.td(e.img(src="/images/top_bar/top_sep.jpg", width=12, height=32))
## TDList.append(TD(Href(logout,
## IMG("/images/top_bar/"+loicon, width=lowidth,
## height=32,
## alt=lotext, border="0"))))
hpage.td()
hpage.a(e.img(src="/images/top_bar/"+loicon,width=lowidth ,height=32,border=0,alt=lotext),href=logout)
hpage.td.close()
## TDList.append(TD(Div(IMG("/images/top_bar/right.jpg", width=3, height=32)),
## width="3"))
hpage.td(e.div(e.img(src="/images/top_bar/right.jpg", width="3", height="32")),width=3)
## top_table.append(t_body + TDList)
hpage.tr.close()
hpage.table.close()
# print top_table
## cat_top_table = TableLite(width="100%", border="0", cellspacing="0",
## cellpadding="0", height="7")
##
##
## cat_top_table.append(TR(TD(IMG("/images/top_bar/shadow.jpg",width=8, height=7),
## background="/images/top_bar/shadow_bg.jpg",
## nowrap="nowrap")))
hpage.table(width="100%", border="0", cellspacing="0",
cellpadding="0", height="7")
hpage.tr()
hpage.td(e.img(src="/images/top_bar/shadow.jpg",width=8, height=7),
background="/images/top_bar/shadow_bg.jpg",nowrap="nowrap")
hpage.tr.close()
hpage.table.close()
# print cat_top_table
print hpage
catnames = read_file(os.path.join(config_directory, "webmin.catnames"))
cats = {}
for module in msc_modules:
c = module.get("category", "")
if cats.has_key(c):
continue
if catnames.has_key(c):
cats[c] = catnames[c]
elif text.has_key("category_%s" % c):
cats[c] = text["category_%s" % c]
else:
mtext = load_language(module["dir"])
if mtext.has_key("category_%s" % c):
cats[c] = mtext["category_%s" % c]
else:
c = ""
module["category"] = ""
cats[c] = text["category_%s" % c]
sorted_cats = cats.keys()
sorted_cats.sort()
sorted_cats.reverse()
if 0 == len(cats):
per = 100
else:
per = 100.0 / float(len(cats))
## Navigation Bar START ##
# (Carsten) Mode loose_html for the center tag
nav_page = markup.page(mode='loose_html')
## nav_table = TableLite(width="100%", border="0", cellspacing="0",
## cellpadding="0", height="57",
## background="/images/nav/bg.jpg")
# (Carsten) The background attribute is not in the final html code with HTMLgen
## nav_table_body = TR(background="/images/nav/bg.jpg")
nav_page.table(width="100%", border="0", cellspacing="0",
cellpadding="0", height="57",
background="/images/nav/bg.jpg")
nav_page.tr(background="/images/nav/bg.jpg")
## TDList = [TD(IMG("/images/nav/left.jpg", width=3, height=57),
## width="6", nowrap="nowrap")]
nav_page.td(e.img(src="/images/nav/left.jpg", width="3", height="57"),width="6", nowrap="nowrap")
for cat in sorted_cats:
uri = "/?cat=%s" % cat
## cont = Container()
nav_page.td(nowrap="nowrap")
nav_page.center()
nav_page.a(href=uri)
if cat in available:
if "" == cat:
## cont.append(IMG("/images/cats/others.jpg", width=43, height=44,
## border="0", alt=cat))
nav_page.img(src="/images/cats/others.jpg",width=43, height=44,
border="0", alt=cat)
else:
## cont.append(IMG("/images/cats/%s.jpg" % cat, width=43, height=44,
## border="0", alt=cat))
nav_page.img(src="/images/cats/%s.jpg" % cat, width=43, height=44,
border="0", alt=cat)
else:
## cont.append(IMG("/images/cats/unknown.jpg", width=43, height=44,
## border="0", alt=cat))
nav_page.img(src="/images/cats/unknown.jpg", width=43, height=44,
border="0", alt=cat)
## cont.append(BR())
## cont.append(chop_font(cats[cat]))
nav_page.br()
# (carsten) : str is needed becaus chop_font might return a HTMLgen/markup instance
nav_page.add(str(chop_font(cats[cat])))
## TDList.append(TD(Center(Href(uri, cont)), nowrap="nowrap"))
nav_page.a.close()
nav_page.center.close()
nav_page.td.close()
## TDList.append(TD(IMG("/images/nav/sep.jpg", width=17, height=57),
## width=17))
nav_page.td(e.img(src="/images/nav/sep.jpg", width=17, height=57),width=17)
## TDList.append(TD(Container(' '), nowrap="nowrap", width="100%"))
nav_page.td(" ",nowrap="nowrap", width="100%")
## nav_table.append(nav_table_body + TDList)
nav_page.tr.close()
nav_page.table.close()
# UGLY!
# The reason we replace all "\n" with "" is that Mozilla
# won't render the menu correctly otherwise. GAAAAH!
# Note (Carsten) : could be done by a simple change in page class
# print str(nav_table).replace("\n", "")
print str(nav_page).replace("\n", "")
## nav_under_table = TableLite(width="100%", border="0", cellspacing="0",
## cellpadding="0",
## background="/images/nav/bottom_bg.jpg",
## height="4")
##
## nav_under_table.append(TR()+[TD(IMG("/images/nav/bottom_left.jpg",
## width=3, height=4), width="100%")])
## print nav_under_table
nav_under_page = markup.page()
nav_under_page.table(width="100%", border="0", cellspacing="0",cellpadding="0",
background="/images/nav/bottom_bg.jpg",height="4")
nav_under_page.tr()
nav_under_page.td(e.img(src="/images/nav/bottom_left.jpg",width=3, height=4),width="100%")
nav_under_page.tr.close()
nav_under_page.table.close()
## tab_under_modcats = TableLite(width="100%", border="0",
## cellspacing="0", cellpadding="0",
## background="/images/nav/bottom_shadow2.jpg")
nav_under_page.table(width="100%", border="0",cellspacing="0",
cellpadding="0",background="/images/nav/bottom_shadow2.jpg")
# ---new/changed display (user) preference tab
## tab_under_modcats_prefs=None
## tab_under_modcats_help=None
ptab_under_modcats_prefs=None
ptab_under_modcats_help=None
# woraround because "if ptab_under_modcats_help" causes an error when it is actually not None
isptab_under_modcats_prefs=False
isptab_under_modcats_help=False
if help:
if type(help) == types.ListType:
helplink = hlink(text["header_help"], help[0], help[1])
else:
helplink = hlink(text["header_help"], help)
## tab_under_modcats_help = TableLite(border="0",cellspacing="0", cellpadding="0")
## tab_under_modcats_help.append(TR() + [TD(IMG("/images/tabs/left.jpg", width=12, height="21"),background="/images/tabs/bg.jpg")]+\
## [TD(Code(helplink),background="/images/tabs/bg.jpg")]+\
## [TD(IMG("/images/tabs/right.jpg", width=15, height="21"),background="/images/tabs/bg.jpg")])
## tab_under_modcats_help.append(TR() + [TD(IMG("/images/tabs/right_bottom.jpg", width=12, height="4"))]+\
## [TD(IMG("/images/tabs/bottom.jpg", width=17, height="4"),background="/images/tabs/bottom.jpg")]+\
## [TD(IMG("/images/tabs/left_bottom.jpg", width=15, height="4"))])
ptab_under_modcats_help = markup.page()
ptab_under_modcats_help.table(border="0",cellspacing="0", cellpadding="0")
ptab_under_modcats_help.tr()
ptab_under_modcats_help.td(e.img(src="/images/tabs/left.jpg", width=12, height="21"),
background="/images/tabs/bg.jpg")
# TODO (carsten) : Check what HTMLgen Code(helplink) does - Update: already done?
ptab_under_modcats_help.td(background="/images/tabs/bg.jpg")
ptab_under_modcats_help.code(helplink)
ptab_under_modcats_help.td.close()
ptab_under_modcats_help.td(e.img(src="/images/tabs/right.jpg", width=15, height="21"),
background="/images/tabs/bg.jpg")
ptab_under_modcats_help.tr.close()
ptab_under_modcats_help.tr()
ptab_under_modcats_help.td(e.img(src="/images/tabs/right_bottom.jpg", width=12, height="4"))
ptab_under_modcats_help.td(e.img(src="/images/tabs/bottom.jpg", width=17, height="4"),
background="/images/tabs/bottom.jpg")
ptab_under_modcats_help.td(e.img(src="/images/tabs/left_bottom.jpg", width=15, height="4"))
ptab_under_modcats_help.tr.close()
ptab_under_modcats_help.table.close()
isptab_under_modcats_help = True
if config:
access = get_module_acl();
if not access.get("noconfig") and not noprefs:
if user_module_config_directory:
cprog = "uconfig.cgi"
else:
cprog = "config.cgi"
uri='%s/%s?%s' % (gconfig.get("webprefix", ""), cprog, module_name)
## tab_under_modcats_prefs = TableLite(border="0",cellspacing="0", cellpadding="0")
## tab_under_modcats_prefs.append(TR() + [TD(IMG("/images/tabs/left.jpg", width=12, height="21"),background="/images/tabs/bg.jpg")]+\
## [TD(Href(uri,text["header_config"]),background="/images/tabs/bg.jpg")]+\
## [TD(IMG("/images/tabs/right.jpg", width=15, height="21"),background="/images/tabs/bg.jpg")])
## tab_under_modcats_prefs.append(TR() + [TD(IMG("/images/tabs/right_bottom.jpg", width=12, height="4"))]+\
## [TD(IMG("/images/tabs/bottom.jpg", width=17, height="4"),background="/images/tabs/bottom.jpg")]+\
## [TD(IMG("/images/tabs/left_bottom.jpg", width=15, height="4"))])
ptab_under_modcats_prefs = markup.page()
ptab_under_modcats_prefs.table(border="0",cellspacing="0", cellpadding="0")
ptab_under_modcats_prefs.tr()
ptab_under_modcats_prefs.td(e.img(src="/images/tabs/left.jpg", width=12, height="21"),
background="/images/tabs/bg.jpg")
ptab_under_modcats_prefs.td(e.a(text["header_config"],href=uri),background="/images/tabs/bg.jpg")
ptab_under_modcats_prefs.td(e.img(src="/images/tabs/right.jpg",width=15, height="21"),
background="/images/tabs/bg.jpg")
ptab_under_modcats_prefs.tr.close()
ptab_under_modcats_prefs.tr()
ptab_under_modcats_prefs.td(e.img(src="/images/tabs/right_bottom.jpg", width=12, height="4"))
ptab_under_modcats_prefs.td(e.img(src="/images/tabs/bottom.jpg", width=17, height="4"),
background="/images/tabs/bottom.jpg")
ptab_under_modcats_prefs.td(e.img(src="/images/tabs/left_bottom.jpg", width=15, height="4"))
ptab_under_modcats_prefs.tr.close()
ptab_under_modcats_prefs.table.close()
isptab_under_modcats_prefs=True
## tab_under_modcats_inner = TableLite(width="100%", border="0",
## cellspacing="0", cellpadding="0",
## background="/images/nav/bottom_shadow2.jpg")
## tab_under_modcats_inner.append(TR() + [TD(IMG("/images/nav/bottom_shadow.jpg", width=43, height="9"))])
# workariund, see above
# if ptab_under_modcats_prefs or ptab_under_modcats_help:
if isptab_under_modcats_prefs or isptab_under_modcats_help:
## tabTR = TR()
nav_under_page.tr()
if isptab_under_modcats_help==True:
## tabTR = tabTR + [TD(tab_under_modcats_help)]
nav_under_page.td(str(ptab_under_modcats_help))
if isptab_under_modcats_prefs==True:
## tabTR = tabTR + [TD(tab_under_modcats_prefs)]
nav_under_page.td(str(ptab_under_modcats_prefs))
## tabTR = tabTR + [TD(tab_under_modcats_inner,background="/images/nav/bottom_shadow2.jpg",width="100%",nowrap="nowarp",valign="top")]
nav_under_page.td(background="/images/nav/bottom_shadow2.jpg",width="100%",nowrap="nowarp",valign="top")
# tab_under_modcats_inner
nav_under_page.table(width="100%", border="0",cellspacing="0", cellpadding="0",
background="/images/nav/bottom_shadow2.jpg")
nav_under_page.tr()
nav_under_page.td(e.img(src="/images/nav/bottom_shadow.jpg", width=43, height="9"))
nav_under_page.tr.close()
nav_under_page.table.close()
# end tab_under_modcats_inner
nav_under_page.td.close()
nav_under_page.tr.close()
## tab_under_modcats(tabTR)
# tab_under_modcats.append(TR() + [TD(tab_under_modcats_prefs)]+ [TD(tab_under_modcats_inner,background="/images/nav/bottom_shadow2.jpg",width="100%",nowrap="nowarp",valign="top")])
else:
## tab_under_modcats.append(TR() + [TD(IMG("/images/nav/bottom_shadow.jpg", width=43, height="9"))])
nav_under_page.tr()
nav_under_page.td(e.img(src="/images/nav/bottom_shadow.jpg", width=43, height="9"))
nav_under_page.tr.close()
nav_under_page.table.close()
## print tab_under_modcats
## print "<br>"
nav_under_page.br()
print nav_under_page
# ----end new display (user) preference tab
if not nowebmin:
title = title.replace("ä", "ä")
title = title.replace("ö", "ö")
title = title.replace("ü", "ü")
title = title.replace(" ", " ")
print "<!-- ================== New Markup code =================== -->"
## title_table = TableLite(border=0, cellpadding=0, cellspacing=0,
## width="95%", align="center")
## inr_tt = TableLite(border=0, cellpadding=0, cellspacing=0, height=20)
## inr_tt_body = TR()
## inr_tt_TDList = [TD(IMG("/images/tabs/blue_left.jpg", width=13,
## height=22), bgcolor="#bae3ff"),
## TD(Strong(title), bgcolor="#bae3ff"),
## TD(IMG("/images/tabs/blue_right.jpg", width=13,
## height=22), bgcolor="#bae3ff")]
## inr_tt.append(inr_tt_body + inr_tt_TDList)
## title_table.append(TR(TD(inr_tt)))
ptitle_table = markup.page()
ptitle_table.table(border=0, cellpadding=0, cellspacing=0,
width="95%", align="center")
ptitle_table.tr()
ptitle_table.td()
ptitle_table.table(border=0, cellpadding=0, cellspacing=0, height=20)
ptitle_table.tr()
ptitle_table.td(e.img(src="/images/tabs/blue_left.jpg", width=13,height=22),bgcolor="#bae3ff")
ptitle_table.td(e.strong(title),bgcolor="#bae3ff")
ptitle_table.td(e.img(src="/images/tabs/blue_right.jpg", width=13,height=22),bgcolor="#bae3ff")
ptitle_table.tr.close()
ptitle_table.table.close()
ptitle_table.td.close()
ptitle_table.tr.close()
ptitle_table.table.close()
## print title_table
print ptitle_table
print "<!-- ================== New Markup code end =================== -->"
theme_prebody()
def main():
path = os.getcwd()
use_count
print('-' * 80)
NSX_Version = get_nsx_version(path)
print 'NSX version is %s \n' %NSX_Version
NSX_IP = get_nsx_ip(path)
print 'NSX manager IP is %s \n' %NSX_IP
vpxa_cfg_list = get_file_list(path,"vpxa.cfg")
vpxa_cfg = vpxa_cfg_list[0]
VC_ip = get_vc_ip(vpxa_cfg)
VC_version = get_vc_version(path)
print 'vCenter IP is %s \n' %VC_ip
print 'vCenter version is %s \n' %VC_version
print 'Please check product matrix \n'
print 'https://www.vmware.com/resources/compatibility/sim/interop_matrix.php \n'
vdr_info_list = get_file_list(path,"dump-vdr-info.sh.txt")
vxlan_info_list = get_file_list(path,"dump-vxlan-info.py.txt")
vmk_info_list = get_file_list(path,"esxcfg-vmknic_-l.txt")
## Get VC IP from esxi bundle
vpxa_cfg_list = get_file_list(path,"vpxa.cfg")
if len(vpxa_cfg_list) > 0:
get_vc_ip(vpxa_cfg_list[0])
num_file = len(vdr_info_list)
for i in range(num_file):
page = markup.page( )
page.init( title="NSX log ",
header="NSX vxlan info ",
footer="I will develop more ....." )
page.style("""
body {
background-color: AliceBlue ;
}
table {
font-family: arial, sans-serif;
border-collapse: collapse;
width: 70%;
}
td, th {
border: 1px solid #dddddd;
text-align: left;
padding: 8px;
}
tr:nth-child(even) {
background-color: #dddddd;
}
p {
font-family: verdana;
font-size: 20px;
}
""")
page.h1
esx_info = get_vmk_info(vmk_info_list[i]) # esxi_info is a list [hostname,vmk0,vxlan_vmk]
page.br()
page.p(esx_info)
page.br()
controller_mapping_dict = get_vxlan_info(vxlan_info_list[i]) # this is a dict
for vxlan,controller in controller_mapping_dict.items():
print('{} {}'.format(vxlan,controller))
print('-' * 80)
# create table for vxlan mapping to controller
page.div(style="overflow-x:auto;")
page.table(border="1")
page.tr()
page.th('vxlan')
page.th('controller')
page.th('status')
page.tr.close()
for vxlan,controller in controller_mapping_dict.items():
page.tr()
page.td(vxlan)
page.td(controller)
page.tr.close()
page.table.close()
vxlan_list = controller_mapping_dict.keys() # this a vlxan list
# create vxlan link table
page.br()
page.table(border="1")
page.tr()
page.th('vxlan')
page.th('vtep')
page.th('arp')
page.th('mac')
page.tr.close()
for vxlan in vxlan_list:
page.tr()
page.td(vxlan)
page.td(e.a(vxlan+'_vtep',href='#'+vxlan+'_vtep'))
page.td(e.a(vxlan+'_arp',href='#'+vxlan+'_arp'))
page.td(e.a(vxlan+'_mac',href='#'+vxlan+'_mac'))
page.tr.close()
page.table.close()
vds_name = get_vds_name(vxlan_info_list[i])
for vxlan_num in vxlan_list:
VTEP = get_vtep_table(vxlan_info_list[i],vds_name,vxlan_num) # this is a list
ARP = get_arp_table(vxlan_info_list[i],vds_name,vxlan_num)
MAC = get_mac_table(vxlan_info_list[i],vds_name,vxlan_num)
#create vtep,arp,mac
name_vtep = vxlan_num + '_vtep'
page.br()
page.h2(e.a(id=name_vtep))
page.p(VTEP)
page.br()
page.h2(e.a(id=vxlan_num+'_arp'))
page.p(ARP)
page.br()
page.h2(e.a(id=vxlan_num+'_mac'))
page.p(MAC)
page.br()
filename = esx_info[0] +'.html'
h = open(filename,'w')
h.write(str(page))
h.close()