def indexPage(form):
tl = twolocus.TwoLocus('/csbiodata/public/www.csbio.unc.edu/htdocs/sgreens/pairwise_origins/')
panel = markup.page()
helper.link_css_and_js(panel)
panel.div(style="padding:20px 20px;")
user, permissionLevel, date, time, elapsed = cgAdmin.getCompgenCookie(form)
editFlag = (form.getvalue("edit") == "True")
if permissionLevel >= 80:
panel.add(WikiApp.editTag("%s" % this_file, not editFlag))
panel.add(WikiApp.getWikiContent("%s" % this_file, editInPlace=(permissionLevel >= 80) and editFlag,
returnPage="./?run=%s" % this_file))
panel.br()
panel.form(_class="form-horizontal", action="", method="POST", enctype="multipart/form-data")
panel.div(_class="control-group")
panel.h3('Background Samples')
has_bg_strains = helper.strain_set_selector(panel, tl, 'background')
panel.h3('Foreground Samples')
has_fg_strains = helper.strain_set_selector(panel, tl, 'foreground')
panel.script("""$(".chosen").chosen()""", type="text/javascript")
panel.script('''$("form").submit(function () {return %s() && %s();});''' % (has_bg_strains, has_fg_strains),
type="text/javascript")
helper.select_all_buttons(panel)
panel.br()
panel.input(type="hidden", name="target", value="%s.visualization" % this_file)
panel.input(type="submit", name="submit", value="Submit")
panel.div.close() # control group
panel.form.close()
panel.div.close()
return panel
def indexPage(form):
tl = twolocus.TwoLocus('/csbiodata/public/www.csbio.unc.edu/htdocs/sgreens/pairwise_origins/')
panel = markup.page()
helper.link_css_and_js(panel)
panel.div(style="padding:20px 20px;")
user, permissionLevel, date, time, elapsed = cgAdmin.getCompgenCookie(form)
editFlag = (form.getvalue("edit") == "True")
if permissionLevel >= 80:
panel.add(WikiApp.editTag("%s" % this_file, not editFlag))
panel.add(WikiApp.getWikiContent("%s" % this_file, editInPlace=(permissionLevel >= 80) and editFlag,
returnPage="./?run=%s" % this_file))
panel.br()
panel.form(_class="form-horizontal", action="", method="POST", enctype="multipart/form-data")
panel.div(_class="control-group")
panel.h3('Set of Samples')
has_strains = helper.strain_set_selector(panel, tl)
for pos_num in ('1', '2'):
panel.h3('Position ' + pos_num)
helper.open_control(panel, 'Chromosome')
panel.select(_class="medium", name="chrom" + pos_num)
for chrom_num in xrange(1, 19):
panel.option(chrom_num)
panel.option('X', value='X')
panel.select.close()
helper.close_control(panel)
helper.open_control(panel, 'Position')
panel.add('''<input class="input-medium" name="pos%s" required pattern="\d+[\d,]*\.?\d*[mMkK]*">'''
% pos_num)
panel.add("""<p class="help-block">3000000 = 3,000,000 = 3m = 3M = 3000k = 3KK</p>""")
helper.close_control(panel)
panel.script(type="text/javascript")
panel.add("""$(".chosen").chosen()""")
panel.script.close()
helper.select_all_buttons(panel)
panel.br()
panel.input(type="hidden", name="target", value="%s.countMatrix" % this_file)
panel.input(type="submit", name="submit", value="Submit")
panel.div.close() # control group
panel.form.close()
panel.div.close()
chromo_sizes = {}
for string, integer in twolocus.CHROMO_TO_INT.iteritems():
chromo_sizes[string] = tl.sizes[integer-1]
panel.script('''
var chromoSizes = %s;
''' % json.dumps(chromo_sizes), type="text/javascript")
panel.script('''
function parsePosition(string) {
string = string.replace(',','').toLowerCase();
var pos = parseFloat(string);
var units = '';
var char
for (var i = 0; i < string.length; i++) {
char = string[i];
if (char == 'm' || char == 'k') {
pos = parseFloat(string.substring(0, i));
units = string.substring(i);
break;
}
}
for (i = 0; i < units.length; i++) {
char = units[i];
if (char == 'k') {
pos *= 1000;
}
if (char == 'm') {
pos *= 1000000;
}
}
return Math.floor(pos);
}
function isValidIndex(chromosome, position) {
return (chromosome in chromoSizes) && (0 <= position) && (position <= chromoSizes[chromosome]);
}
$("form").submit(function(event) {
var chrom, pos;
isValidInput = true;
for (var i = 1; i <= 2; i++) {
chrom = document.getElementsByName('chrom' + i)[0].value;
pos = parsePosition(document.getElementsByName('pos' + i)[0].value);
if (!isValidIndex(chrom, pos)) {
alert("Position " + i + " exceeds chromosome length");
isValidInput = false;
}
}
return %s(event) && isValidInput;
});
''' % has_strains, type="text/javascript")
return panel
def buildRadioSelect(form, panel, includeFormStart):
user, permissionLevel, date, time, elapsed = cgAdmin.getCompgenCookie(form)
citationDict = {}
citOrder = []
citCount = 1
tableOrdering = [
"Species", "Strain", "Data Type", "Sequence Method", "Number of Reads",
"Size of BWT", "Publication"
]
panel.h3("Select Dataset:")
if includeFormStart:
panel.form(action="", method="POST", enctype="multipart/form-data")
panel.ul(id='mainList')
for j, msdir in enumerate(MSBWTdirs):
if permissionLevel < minPermission[j]:
continue
available = sorted(glob.glob("%s/*/*msbwt.npy" % msdir))
panel.li()
#panel.input(type="checkbox", name="", value="")
panel.add(dirLabels[j])
panel.ul()
panel.table(border='1')
panel.tr()
panel.th("")
panel.th("Dataset")
for l in tableOrdering:
panel.th(l)
panel.tr.close()
for i, dataset in enumerate(available):
end = dataset.rfind('/')
start = dataset.rfind('/', 0, end - 1) + 1
shorten = dataset[start:end]
metadata = loadMetadata(dataset[0:end])
#panel.li()
panel.tr()
panel.td()
if i == 0 and j == 0:
panel.input(type="radio",
name="dataset",
value=str(j) + '-' + shorten,
checked="Y")
else:
panel.input(type="radio",
name="dataset",
value=str(j) + '-' + shorten)
panel.td.close()
panel.td()
panel.add(metadata.get("Name", shorten))
panel.td.close()
for l in tableOrdering:
if l == "Publication":
citation = metadata.get(l, "Not available")
if citation == "Not available":
panel.td("Not available", style="text-align:right;")
else:
if citationDict.has_key(citation):
citLink, citID = citationDict[citation]
else:
citLink = 'citation' + str(citCount)
citationDict[citation] = (citLink, citCount)
citOrder.append(citation)
citID = citCount
citCount += 1
panel.td()
panel.a('Pub ' + str(citID), href='#' + citLink)
panel.td.close()
else:
panel.td(metadata.get(l, "Not available"),
style="text-align:right;")
panel.tr.close()
#panel.li.close()
#panel.br()
panel.table.close()
panel.br()
panel.ul.close()
panel.li.close()
panel.ul.close() #this one closes the mainList
return citOrder, citationDict
