diff --git a/mutalyzer/templates/base/js/generator.js b/mutalyzer/templates/base/js/generator.js
index 41612ede8f4d5fd6b0f814c97552f223a1c81dc0..ceeecdd6071a9bd07f22d61ed2c12ab1fa773cee 100644
--- a/mutalyzer/templates/base/js/generator.js
+++ b/mutalyzer/templates/base/js/generator.js
@@ -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();
}
-
-
diff --git a/mutalyzer/templates/check.html b/mutalyzer/templates/check.html
index 0adef757e7d1b3d90f63f78c91a78a5312693207..758a9a4d50afd275de45b058b6b892fea95d2721 100644
--- a/mutalyzer/templates/check.html
+++ b/mutalyzer/templates/check.html
@@ -23,16 +23,16 @@
</div><br>
Example: AB026906.1:c.274G>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>
diff --git a/mutalyzer/website.py b/mutalyzer/website.py
index 4ba7962503c7133dbe2c427c1146da0c7a13ad0c..d44480a97a7ee0149c6691fd1656edbfb39aa3e9 100644
--- a/mutalyzer/website.py
+++ b/mutalyzer/website.py
@@ -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('<', '<')
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.
diff --git a/tests/test_mapping.py b/tests/test_mapping.py
index 71c2e458c0b0eec35dc30af6c069b7f17170a749..12e5608431ff913e8e4f6a2a35e29678bbf07a04 100644
--- a/tests/test_mapping.py
+++ b/tests/test_mapping.py
@@ -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')
diff --git a/tests/test_website.py b/tests/test_website.py
index 77ffac5dbafccb50fb41b1a1fd9b3fd57d77ff67..898074d01698008ebd9e99b9e5be28d1f0a342c4 100644
--- a/tests/test_website.py
+++ b/tests/test_website.py
@@ -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&position=chr11:111959685-111959705&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>T" type="text" name="mutationName" style="width:100%">')
+ '<input value="AB026906.1:c.274G>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>T" type="text" name="mutationName" style="width:100%">')
+ '<input value="AB026906.1:c.274G>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', '-']))