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Commit d5f1e49d authored by Vermaat's avatar Vermaat
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Refactor name checker to accept GET requests 

Until now, the name checker form used POST requests. As a special case for
linking from LOVD, GET requests were handled by showing results without the
full interface (header, menu, etc). Ordinary linking was done to a separate
checkForward location which then set a cookie with the variant name and a
redirect to the name checker results. This was all very hackish and somewhat
broken (see Track issue #94).

This commit refactors the name checker to use GET requests, so ordinary
bookmarking of result pages is possible. All old entrypoints are handled with
a redirect for backwards compatibility.

Worth mentioning is that variant descriptions in the name checker are now
limited in length by the maximum query string length. However, this maximum
is several thousand characters with Internet Explorer having the lowest
maximum of just over 2000. Longer descriptions are not practically checked
with the name checker web interface anyway, so this should not be a problem.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@521 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
parent 84d5de3c
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mutalyzer/templates/base/js/generator.js
+ 17
− 19
View file @ d5f1e49d
......@@ -10,7 +10,7 @@ function isNumber(x){
return re.test(x);
}
function isTranscript(x){
function isTranscript(x){
return isNumber(x);
}
......@@ -65,7 +65,7 @@ function isGeneSymbol(s){
/* Reference Object
* ----------------
* Holds the information of five fields.
* Holds the information of five fields.
* Reference
* Seqeuente Type
* Gene Symbol
......@@ -121,7 +121,7 @@ var reference = {
'errStr' : "must be a postive integer"},
'tlc' : 1,
'number': "",
getType : function(){
var translate = {'c':'cod', 'g':'gen','n':'non','r':'rna',
'm':'mit', 'e':'est','p1':'pr1','p3':'pr3'};
......@@ -158,7 +158,7 @@ var reference = {
/* seqTypes Object
* ---------------
* Holds the references to the different field checks depending on
* Holds the references to the different field checks depending on
* the type of sequence that is selected.
*
* Each key has three members
......@@ -186,7 +186,7 @@ var seqTypes = {
'non' : { 'pCheck' : isPosition,
'sCheck' : isDNASequence,
'errorStr' : "must consist of nucleotides [ACTG]"},
'est' : { 'pCheck' : isPosition,
'sCheck' : isDNASequence,
'errorStr' : "must consist of nucleotides [ACTG]"},
......@@ -202,7 +202,7 @@ var seqTypes = {
/* mutTypes Object
* ---------------
* Holds the information needed to display and check
* Holds the information needed to display and check
* the fields of selected mutation.
*
* Each key has three members:
......@@ -212,7 +212,7 @@ var seqTypes = {
* P1 = Position 1
* P2 = Position 2
*
* The usage of the 0, 1, + and * is identical to
* The usage of the 0, 1, + and * is identical to
* that of the reference object
* S1 - The partial name to display for the selected mutation
* in front of the first sequence field
......@@ -263,16 +263,16 @@ var variants = new Array(); //global storage of the variants
/* VariantField Object
* -------------------
* Holds the boilerplate for setting up a new variant and storing the
* Holds the boilerplate for setting up a new variant and storing the
* values associated with that variant. The five fields that are stored
* include Position 1 & 2, Sequence 1 & 2 and the mutation type.
*
* Each key has four members:
* value - The form value
* ok - boolean to store if check & len are both met
* check - placeholder to make this object checkable by the
* check - placeholder to make this object checkable by the
* main CheckElement function
* index - int to fetch the correct len setings of a field,
* index - int to fetch the correct len setings of a field,
* which depends on the type of mutation that is set
*
* This is a dynamic object, which means that the values of the members
......@@ -350,7 +350,7 @@ var VariantField = {
function clone(obj){
if(obj == null || typeof(obj) != 'object')
return obj;
var temp = new obj.constructor();
var temp = new obj.constructor();
for(var tkey in obj)
temp[tkey] = clone(obj[tkey]);
return temp;
......@@ -382,7 +382,7 @@ function checkElement(elem){
//check if obj is checkable
if (obj.check==undefined) continue;
//Get the value from the form
var IDt = elem["number"];
if(IDt === "")
......@@ -396,7 +396,7 @@ function checkElement(elem){
var name = elem.getName(key)+optional;
var check = elem.getCheck(key);
var errStr = elem.getErr(key);
//check if the value is ok
obj.ok = check(obj.value);
......@@ -447,9 +447,9 @@ function update(){
var hgvs = generateHGVS();
var ref = hgvs[0];
var vari = hgvs[1];
var encVar = encodeURIComponent(vari);
var url = "checkForward?mutationName="+ref+encVar;
var url = "check?name="+ref+encVar;
var link = ref+vari;
var Output = "<a href=\""+url+"\">"+link+"</a>";
......@@ -488,7 +488,7 @@ function updateVariant(variant){
"Interbase positions must be consecutive positions. <br />";
}
}
}
}
}
function updateReference(){
......@@ -502,7 +502,7 @@ function updateReference(){
hide("tVar");
else
show("tVar");
if(reference.seqT.value == "g"){
hide("gSym");
reference.gSym.value = "";
......@@ -648,5 +648,3 @@ function removeVariant(nmbr){
variants[nmbr].removed = true;
update();
}
mutalyzer/templates/check.html
+ 8
− 8
View file @ d5f1e49d
......@@ -23,16 +23,16 @@
</div><br>
Example: AB026906.1:c.274G&gt;T<br>
<br>
<form action = "" method = "post">
<form action = "" method = "get">
<input
type = "text"
name = "mutationName"
tal:attributes = "value lastpost"
name = "name"
tal:attributes = "value name"
style = "width:100%"
><br>
<input type="submit" value="Submit">
<input type="button" value="Clear field"
onClick = "clearForm(this.form, 'mutationName');">
onClick = "clearForm(this.form, 'name');">
</form>
</div>
<div tal:condition = "visualisation">
......@@ -52,7 +52,7 @@
<a tal:condition = "browserLink" tal:attributes = "href browserLink">View original variant in UCSC Genome Browser</a>
</div> <!-- form area -->
<br>
<div tal:condition = "lastpost">
<div tal:condition = "name">
<h3>Name checker results:</h3>
<div class="messages">
<p tal:repeat = "m messages" tal:content = "m/description"
......@@ -80,7 +80,7 @@
<tt>
<a tal:content = "genomicDescription/0"
tal:attributes = "href
string:checkForward?mutationName=${genomicDescription/1}">
string:check?name=${genomicDescription/1}">
</a><br>
</tt>
<br>
......@@ -99,7 +99,7 @@
<tt tal:repeat = "i descriptions">
<a tal:condition = "i/1" tal:content = "i/0"
tal:attributes =
"href string:checkForward?mutationName=${i/1}"></a><tal
"href string:check?name=${i/1}"></a><tal
tal:condition = "not:i/1" tal:replace = "i/0"></tal><br>
</tt>
<br>
......@@ -269,7 +269,7 @@
<br>
</div> <!-- interactive -->
</div> <!-- reference -->
</div> <!-- lastpost -->
</div> <!-- name -->
</div>
</body>
</html>
mutalyzer/website.py
+ 86
− 134
View file @ d5f1e49d
......@@ -65,11 +65,11 @@ urls = (
'/positionConverter', 'PositionConverter',
'/Variant_info', 'VariantInfo',
'/getGS', 'GetGS',
'/checkForward', 'CheckForward',
'/check', 'Check',
'/descriptionExtract', 'DescriptionExtractor',
'/bed', 'Bed',
'/syntaxCheck', 'SyntaxCheck',
'/checkForward', 'CheckForward',
'/batch([a-zA-Z]+)?', 'BatchChecker',
'/progress', 'BatchProgress',
'/Results_(\d+)\.txt', 'BatchResult',
......@@ -80,7 +80,7 @@ urls = (
)
class render_tal :
class render_tal:
"""
Render interface to TAL templates.
......@@ -89,28 +89,26 @@ class render_tal :
>>> render = render_tal('templates')
>>> render.hello('alice')
"""
def __init__(self, path, globals = {}) :
def __init__(self, path, globals={}):
"""
@arg path: Path to templates directory.
@kwarg globals: Dictionary of global template variables.
"""
self.path = path
self.globals = globals
#__init__
def __getattr__(self, name) :
def __getattr__(self, name):
"""
Returns a template. Call the template to get a render.
@arg name: Template name (usually a HTML filename without '.html').
@return: Template render function.
"""
filename = name
def template(args = {}, scheme = 'html', standalone = False) :
def template(args={}, scheme='html', standalone=False,
prevent_caching=False):
"""
Template render function.
......@@ -127,20 +125,19 @@ class render_tal :
argument for template.
@return: Render of template.
"""
file = filename
if scheme == 'html' :
if scheme == 'html':
file += '.html'
path = os.path.join(self.path, file)
context = simpleTALES.Context()
context.addGlobal("interactive", not standalone)
context.addGlobal('interactive', not standalone)
for name, value in self.globals.items() :
for name, value in self.globals.items():
context.addGlobal(name, value)
for name, value in args.items() :
for name, value in args.items():
context.addGlobal(name, value)
templateFile = open(path, 'r')
......@@ -148,16 +145,19 @@ class render_tal :
templateFile.close()
# Wrap in site layout with menu
if scheme == 'html' and not standalone :
if scheme == 'html' and not standalone:
context.addGlobal('sitemacros', template)
templateFile = open(os.path.join(self.path, 'menu.html'), 'r')
template = simpleTAL.compileHTMLTemplate(templateFile)
templateFile.close()
#if
if scheme == 'html' :
if scheme == 'html':
web.header('Content-Type', 'text/html')
if prevent_caching:
web.header('Cache-Control', 'no-cache')
web.header('Expires', '-1')
io = StringIO()
template.expand(context, io)
......@@ -396,7 +396,7 @@ class GetGS :
if i.forward :
p, a = i.mutationName.split(':')
return Check.check(p+'('+l[0]+'):'+a, interactive = False)
return Check.check(p+'('+l[0]+'):'+a, standalone=True)
#if
else :
web.header('Content-Type', 'text/plain')
......@@ -749,57 +749,59 @@ class VariantInfo :
#GET
#VariantInfo
class Check :
class CheckForward:
"""
The variant checker.
Old entrypoint to the namechecker. We keep it to not break existing
bookmarks (but this could also be done with an Apache rewrite rule).
"""
def GET(self) :
def GET(self):
"""
Render the variant checker HTML form.
There are two modes of invoking the checker with a GET request:
1. Provide the 'mutationName' parameter. In this case, the checker is
called non-interactively, meaning the result is rendered without
the HTML form, site layout, and menu.
2. By having a 'variant' value in the cookie. The value is removed.
Permanently redirect to the name checker.
Parameters:
- mutationName: Variant to check.
"""
interactive = True
i = web.input(mutationName = None)
if i.mutationName :
# Run checker non-interactively
interactive = False
variant = i.mutationName
#if
else :
# Run checker if cookie variant is not None
variant = web.cookies().get('variant')
web.setcookie('variant', '', 60)
#else
return self.check(variant, interactive = interactive)
i = web.input(mutationName=None)
raise web.redirect('/check?name=' + urllib.quote(i.mutationName))
#GET
#CheckForward
def POST(self) :
class Check:
"""
The variant checker.
"""
def GET(self):
"""
Run the name checker and render the variant checker HTML form.
Render the variant checker HTML form.
For backwards compatibility with older LOVD versions, we support the
'mutationName' argument. If present, we redirect and add standalone=1.
Parameters:
- mutationName: Variant to check.
- name: Variant to check.
"""
i = web.input(name=None, mutationName=None, standalone=False)
i = web.input(mutationName = None)
if i.mutationName:
raise web.redirect('/check?name=%s&standalone=1'
% urllib.quote(i.mutationName))
return self.check(i.name, standalone=bool(i.standalone))
#GET
return self.check(i.mutationName)
def POST(self):
"""
For now we also accept POST requests with a permanent redirect.
"""
i = web.input(name=None, mutationName=None, standalone=False)
raise web.redirect('/check?name=%s'
% urllib.quote(i.name or i.mutationName))
#POST
@staticmethod
def check(name = None, interactive = True) :
def check(name=None, standalone=False):
"""
Render the variant checker HTML form. If the name argument is given,
run the name checker.
......@@ -808,19 +810,12 @@ class Check :
@kwarg interactive: Run interactively, meaning we wrap the result in
the site layout and include the HTML form.
"""
if not name:
return render.check(dict(name=None), standalone=standalone)
output = Output(__file__)
IP = web.ctx["ip"]
args = {
'lastpost' : name
}
if not name :
return render.check(args, standalone = not interactive)
output.addMessage(__file__, -1, 'INFO',
'Received variant %s from %s' % (name, IP))
output.addMessage(__file__, -1, 'INFO', 'Received variant %s from %s'
% (name, web.ctx['ip']))
# Todo: The following is probably a problem elsewhere too.
# We stringify the variant, because a unicode string crashes
......@@ -831,73 +826,60 @@ class Check :
record_type = output.getIndexedOutput('recordType', 0, '')
reference = output.getIndexedOutput('reference', 0, '')
if reference :
if record_type == 'LRG' :
if reference:
if record_type == 'LRG':
reference = reference + '.xml'
else :
reference = reference + '.gb'
#if
# This is a tuple (variant, position)
# This is a tuple (variant, position) if we have a parse error
parse_error = output.getOutput('parseError')
if parse_error :
if parse_error:
parse_error[0] = parse_error[0].replace('<', '&lt;')
genomic_dna = output.getIndexedOutput('molType', 0) != 'n'
genomic_description = output.getIndexedOutput('genomicDescription', 0,
'')
genomic_description = output.getIndexedOutput('genomicDescription', 0, '')
# Create a tuple (description, link) from a description
def description_to_link(description) :
def description_to_link(description):
link = None
if description[-1] != '?' :
if description[-1] != '?':
link = urllib.quote(description)
return description, link
#description_to_link
# Create a link to the UCSC Genome Browser
browser_link = None
raw_variants = output.getIndexedOutput('rawVariantsChromosomal', 0)
if raw_variants :
if raw_variants:
positions = [pos
for descr, (first, last) in raw_variants[2]
for pos in (first, last)]
bed_url = web.ctx.homedomain + web.ctx.homepath + \
'/bed?variant=' + urllib.quote(name)
'/bed?name=' + urllib.quote(name)
browser_link = GENOME_BROWSER_URL.format(
chromosome = raw_variants[0], start = min(positions) - 10,
stop = max(positions) + 10, bed_file = urllib.quote(bed_url))
#if
chromosome=raw_variants[0], start=min(positions) - 10,
stop=max(positions) + 10, bed_file=urllib.quote(bed_url))
# Todo: Generate the fancy HTML views for the proteins here instead
# of in mutalyzer/variantchecker.py.
args = {
'lastpost' : name,
'messages' : map(util.message_info,
output.getMessages()),
'name' : name,
'messages' : map(util.message_info, output.getMessages()),
'summary' : summary,
'parseError' : parse_error,
'errors' : errors,
'genomicDescription' : (genomic_description,
urllib.quote(genomic_description)),
'chromDescription' : output.getIndexedOutput(
'genomicChromDescription', 0),
'genomicDescription' : (genomic_description, urllib.quote(genomic_description)),
'chromDescription' : output.getIndexedOutput('genomicChromDescription', 0),
'genomicDNA' : genomic_dna,
'visualisation' : output.getOutput('visualisation'),
'descriptions' : map(description_to_link,
output.getOutput('descriptions')),
'descriptions' : map(description_to_link, output.getOutput('descriptions')),
'protDescriptions' : output.getOutput('protDescriptions'),
'oldProtein' : output.getOutput('oldProteinFancy'),
'altStart' : output.getIndexedOutput('altStart', 0),
'altProtein' : output.getOutput('altProteinFancy'),
'newProtein' : output.getOutput('newProteinFancy'),
'transcriptInfo' : output.getIndexedOutput('hasTranscriptInfo',
0, False),
'transcriptCoding' : output.getIndexedOutput('transcriptCoding',
0, False),
'transcriptInfo' : output.getIndexedOutput('hasTranscriptInfo', 0, False),
'transcriptCoding' : output.getIndexedOutput('transcriptCoding', 0, False),
'exonInfo' : output.getOutput('exonInfo'),
'cdsStart_g' : output.getIndexedOutput('cdsStart_g', 0),
'cdsStart_c' : output.getIndexedOutput('cdsStart_c', 0),
......@@ -911,7 +893,7 @@ class Check :
output.addMessage(__file__, -1, 'INFO', 'Finished variant %s' % name)
return render.check(args, standalone = not interactive)
return render.check(args, standalone=standalone, prevent_caching=True)
#check
#Check
......@@ -1006,58 +988,52 @@ class DescriptionExtractor :
#DescriptionExtract
class Bed :
class Bed:
"""
Create BED track.
"""
def GET(self) :
def GET(self):
"""
Create a BED track for the given variant, listing the positioning of
its raw variants. E.g. for use in the UCSC Genome Browser.
Parameters:
- mutationName: Variant to create BED track for.
- name: Variant to create BED track for.
This basically just runs the variant checker and extracts the raw
variants with positions.
"""
web.header('Content-Type', 'text/plain')
i = web.input(variant = None)
variant = i.variant
i = web.input(name=None)
name = i.name
if not variant :
if not name:
web.ctx.status = '404 Not Found'
return 'Sorry, we have not BED track for this variant.'
#if
output = Output(__file__)
variantchecker.check_variant(str(variant), output)
variantchecker.check_variant(str(name), output)
raw_variants = output.getIndexedOutput('rawVariantsChromosomal', 0)
if not raw_variants :
if not raw_variants:
web.ctx.status = '404 Not Found'
return 'Sorry, we have no BED track for this variant.'
#if
fields = {
'name' : 'Mutalyzer',
'description': 'Mutalyzer track for ' + variant,
'description': 'Mutalyzer track for ' + name,
'visibility' : 'pack',
'db' : 'hg19',
'url' : web.ctx.homedomain + web.ctx.homepath +
'/checkForward?mutationName=' + urllib.quote(variant),
'/check?name=' + urllib.quote(name),
'color': '255,0,0'}
bed = ' '.join(['track'] + [
'%s="%s"' % field for field in fields.items()]) + '\n'
for description, positions in raw_variants[2] :
for description, positions in raw_variants[2]:
bed += '\t'.join([raw_variants[0], str(min(positions) - 1),
str(max(positions)), description, '0', raw_variants[1]]) + '\n'
......@@ -1066,30 +1042,6 @@ class Bed :
#Bed
class CheckForward :
"""
Set the given variant in the cookie and redirect to the name checker.
@todo: Cleaner solution (one without using a cookie).
"""
def GET(self) :
"""
Set the 'variant' cookie value to the given variant and redirect
to the name checker (where we will arrive by a GET request).
Parameters:
- mutationName: Variant to set in the cookie.
"""
i = web.input(mutationName = None)
web.setcookie('variant', i.mutationName, 5 * 60) # Five minutes
raise web.seeother('check')
#GET
#CheckForward
class BatchProgress :
"""
Batch jobs progress viewer.
......
tests/test_mapping.py
+ 4
− 0
View file @ d5f1e49d
......@@ -67,6 +67,10 @@ class TestConverter():
is exactly on the border of an exon.
Bug reported February 24, 2012 by S Venkata Suresh Kumar.
Note: You need the full hg18 and hg19 databases for these tests to
pass (i.e. the one used on the production server, possibly
updated with newer mappings from the NCBI).
"""
converter = self._converter('hg19')
coding = converter.chrom2c('NC_000001.10:g.115259837_115259837delT', 'list')
......
tests/test_website.py
+ 61
− 21
View file @ d5f1e49d
......@@ -156,32 +156,61 @@ class TestWSGI():
"""
r = self.app.get('/check')
form = r.forms[0]
form['mutationName'] = 'NM_002001.2:g.1del'
form['name'] = 'NM_002001.2:g.1del'
r = form.submit()
r.mustcontain('0 Errors',
'0 Warnings',
'Raw variant 1: deletion of 1',
'<a href="#bottom" class="hornav">go to bottom</a>',
'<input value="NM_002001.2:g.1del" type="text" name="mutationName" style="width:100%">')
'<input value="NM_002001.2:g.1del" type="text" name="name" style="width:100%">')
def test_check_more_valid(self):
"""
Test the name checker for some more variants.
"""
def check_name(name):
r = self.app.post('/check', {'mutationName': name})
r = self.app.get('/check?name=%s' % name)
r.mustcontain('0 Errors')
names = ['NG_012337.1:g.7055C>T']
for name in names:
check_name(name)
def test_check_post(self):
"""
Test the name checker for a POST request.
We accept POST requests for backwards compatibility.
"""
def check_name(name):
r = self.app.post('/check', {'name': name})
assert_equal(r.status, '301 Moved Permanently')
assert r.location.endswith('/check?name=%s' % urllib.quote(name))
names = ['NG_012337.1:g.7055C>T']
for name in names:
check_name(name)
def test_check_post_old(self):
"""
Test the name checker for a POST request with the old parameter
name.
We accept POST requests for backwards compatibility.
"""
def check_name(name):
r = self.app.post('/check', {'mutationName': name})
assert_equal(r.status, '301 Moved Permanently')
assert r.location.endswith('/check?name=%s' % urllib.quote(name))
names = ['NG_012337.1:g.7055C>T']
for name in names:
check_name(name)
def test_check_invalid(self):
"""
Submit the name checker form with an invalid variant.
"""
r = self.app.get('/check')
form = r.forms[0]
form['mutationName'] = 'NM_002001.2'
form['name'] = 'NM_002001.2'
r = form.submit()
r.mustcontain('1 Error',
'0 Warnings',
......@@ -194,7 +223,7 @@ class TestWSGI():
"""
r = self.app.get('/check')
form = r.forms[0]
form['mutationName'] = 'BAA81889.1:c.274G>T'
form['name'] = 'BAA81889.1:c.274G>T'
r = form.submit()
r.mustcontain('1 Error',
'0 Warnings',
......@@ -205,15 +234,24 @@ class TestWSGI():
Submit the name checker form non-interactively.
Should not include form and main layout HTML.
"""
r = self.app.get('/check?mutationName=NM_002001.2:g.1del')
r = self.app.get('/check?name=NM_002001.2:g.1del&standalone=1')
assert_false('<a href="#bottom" class="hornav">go to bottom</a>' in r)
assert_false('<input value="NM_002001.2:g.1del" type="text" name="mutationName" style="width:100%">' in r)
assert_false('<input value="NM_002001.2:g.1del" type="text" name="name" style="width:100%">' in r)
r.mustcontain('0 Errors',
'0 Warnings',
'Raw variant 1: deletion of 1',
'<html>',
'</html>')
def test_check_noninteractive_old(self):
"""
Submit the name checker form non-interactively in the old style.
Should redirect to new style.
"""
r = self.app.get('/check?mutationName=NM_002001.2:g.1del')
assert_equal(r.status, '301 Moved Permanently')
assert r.location.endswith('/check?name=%s&standalone=1' % urllib.quote('NM_002001.2:g.1del'))
def test_check_browser_link(self):
"""
Submit the name checker form with a coding variant on a transcript.
......@@ -221,25 +259,27 @@ class TestWSGI():
"""
r = self.app.get('/check')
form = r.forms[0]
form['mutationName'] = 'NM_003002.2:c.274G>T'
form['name'] = 'NM_003002.2:c.274G>T'
r = form.submit()
bed_track = urllib.quote(r.environ['wsgi.url_scheme'] + '://' + r.environ['HTTP_HOST'] + '/bed?variant=' + urllib.quote('NM_003002.2:c.274G>T'))
# Note: the r.environ does not work in versions higher than webob 1.1.1
bed_track = urllib.quote(r.environ['wsgi.url_scheme'] + '://' + r.environ['HTTP_HOST'] + '/bed?name=' + urllib.quote('NM_003002.2:c.274G>T'))
r.mustcontain('<a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&amp;position=chr11:111959685-111959705&amp;hgt.customText=%s">View original variant in UCSC Genome Browser</a>' % bed_track)
def test_checkforward(self):
"""
A checkForward request should set the given variant in the session and
redirect to the name checker.
A checkForward request should redirect to the name checker.
This is for backwards compatibility with old bookmarks.
"""
r = self.app.get('/checkForward?mutationName=NM_002001.2:g.1del')
assert_equal(r.status, '303 See Other')
assert r.location.endswith('/check')
r = self.app.get('/checkForward?mutationName=%s' % urllib.quote('NM_002001.2:g.1del'))
assert_equal(r.status, '301 Moved Permanently')
assert r.location.endswith('/check?name=%s' % urllib.quote('NM_002001.2:g.1del'))
r = r.follow()
r.mustcontain('0 Errors',
'0 Warnings',
'Raw variant 1: deletion of 1',
'<a href="#bottom" class="hornav">go to bottom</a>',
'<input value="NM_002001.2:g.1del" type="text" name="mutationName" style="width:100%">')
'<input value="NM_002001.2:g.1del" type="text" name="name" style="width:100%">')
def test_snp_converter_valid(self):
"""
......@@ -695,13 +735,13 @@ facilisi."""
"""
r = self.app.get('/check')
form = r.forms[0]
form['mutationName'] = 'AB026906.1:c.274G>T'
form['name'] = 'AB026906.1:c.274G>T'
r = form.submit()
r.mustcontain('0 Errors',
'1 Warning',
'Raw variant 1: substitution at 7872',
'<a href="#bottom" class="hornav">go to bottom</a>',
'<input value="AB026906.1:c.274G&gt;T" type="text" name="mutationName" style="width:100%">')
'<input value="AB026906.1:c.274G&gt;T" type="text" name="name" style="width:100%">')
r = self.app.get('/Reference/AB026906.1.gb')
assert_equal(r.content_type, 'text/plain')
assert_equal(r.content_length, 26427)
......@@ -716,13 +756,13 @@ facilisi."""
"""
r = self.app.get('/check')
form = r.forms[0]
form['mutationName'] = 'AB026906.1:c.274G>T'
form['name'] = 'AB026906.1:c.274G>T'
r = form.submit()
r.mustcontain('0 Errors',
'1 Warning',
'Raw variant 1: substitution at 7872',
'<a href="#bottom" class="hornav">go to bottom</a>',
'<input value="AB026906.1:c.274G&gt;T" type="text" name="mutationName" style="width:100%">')
'<input value="AB026906.1:c.274G&gt;T" type="text" name="name" style="width:100%">')
r = self.app.head('/Reference/AB026906.1.gb')
assert_equal(r.content_type, 'text/plain')
......@@ -736,7 +776,7 @@ facilisi."""
"""
BED track for variant.
"""
r = self.app.get('/bed?variant=NM_003002.2%3Ac.274G%3ET')
r = self.app.get('/bed?name=NM_003002.2%3Ac.274G%3ET')
assert_equal(r.content_type, 'text/plain')
r.mustcontain('\t'.join(['chr11', '111959694', '111959695', '274G>T', '0', '+']))
......@@ -744,7 +784,7 @@ facilisi."""
"""
BED track for variant on reverse strand.
"""
r = self.app.get('/bed?variant=NM_000132.3%3Ac.%5B4374A%3ET%3B4380_4381del%5D')
r = self.app.get('/bed?name=NM_000132.3%3Ac.%5B4374A%3ET%3B4380_4381del%5D')
assert_equal(r.content_type, 'text/plain')
r.mustcontain('\t'.join(['chrX', '154157690', '154157691', '4374A>T', '0', '-']))
r.mustcontain('\t'.join(['chrX', '154157683', '154157685', '4380_4381del', '0', '-']))
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