From 70c603e29e43ea08d871791c4110118ecd70ac8e Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Wed, 26 Jan 2011 09:03:36 +0000
Subject: [PATCH] templates/menu.html: - Link to bugtracker is now absolute. -
Header for external links is no longer a link.
src/Modules/File.py:
- Bugfix for previous commit (transparent support for different types of
line endings in batch input files).
src/tests/test_wsgi.py:
- Added batch tests with big input files. Added batch tests for different
types of line endings in input files.
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@166 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
src/Modules/File.py | 42 ++++++++++--
src/tests/test_wsgi.py | 126 ++++++++++++++++++++++++++++++-----
src/webservice.py | 10 +--
templates/base/css/style.css | 4 ++
templates/menu.html | 11 +--
5 files changed, 158 insertions(+), 35 deletions(-)
diff --git a/src/Modules/File.py b/src/Modules/File.py
index ab9b37fe..79cb81af 100644
--- a/src/Modules/File.py
+++ b/src/Modules/File.py
@@ -24,6 +24,7 @@ import zipfile # ZipFile()
import xml.dom.minidom # parseString()
import os # remove()
import types # UnicodeType
+from cStringIO import StringIO
from Modules import Misc
@@ -137,11 +138,41 @@ class File() :
#
# The fix is to get the handle's file descriptor and create a new
# handle for it, using 'U' mode.
- handle = os.fdopen(handle.fileno(), 'rU')
+ #
+ # However, sometimes our handler has no .fileno(), for example when
+ # the input file is quite small (< 1kb). In that case, the cgi
+ # module seems to optimize things and use a StringIO for the file,
+ # which of course has no .fileno().
+ #
+ # So our solution is:
+ # - We have .fileno(): Create a new handle, using 'U' mode.
+ # - We have no .fileno(): Replace all newlines by \n (in-memory)
+ # and wrap the result in a new StringIO.
+
+ if hasattr(handle, 'fileno'):
+ # Todo: We get the following error in our logs (exact origin
+ # unknown):
+ #
+ # close failed in file object destructor:
+ # IOError: [Errno 9] Bad file descriptor
+ #
+ # I am unable to find the reason for this. Everything seems to
+ # be working though.
+ new_handle = os.fdopen(handle.fileno(), 'rU')
+ elif hasattr(handle, 'getvalue'):
+ data = handle.getvalue()
+ data = data.replace('\r\n', '\n').replace('\r', '\n')
+ new_handle = StringIO(data)
+ else:
+ self.__output.addMessage(__file__, 4, "EBPARSE",
+ "Fatal error parsing input file, please"
+ " report this as a bug including the"
+ " input file.")
+ return None
# I don't think the .seek(0) is needed now we created a new handle
- handle.seek(0)
- buf = handle.read(self.__config.bufSize)
+ new_handle.seek(0)
+ buf = new_handle.read(self.__config.bufSize)
# Default dialect
dialect = 'excel'
@@ -162,13 +193,14 @@ class File() :
# if dialect.delimiter == ":":
# dialect.delimiter = "\t"
- handle.seek(0)
- reader = csv.reader(handle, dialect)
+ new_handle.seek(0)
+ reader = csv.reader(new_handle, dialect)
ret = []
for i in reader :
ret.append(i)
+ new_handle.close()
return ret
#__parseCsvFile
diff --git a/src/tests/test_wsgi.py b/src/tests/test_wsgi.py
index 759a1378..559cd0c9 100755
--- a/src/tests/test_wsgi.py
+++ b/src/tests/test_wsgi.py
@@ -12,6 +12,7 @@ I just installed webtest by 'easy_install webtest'.
@todo: Tests for /upload, /getGS, and /Variant_info.
"""
+#import logging; logging.basicConfig()
import re
import time
import unittest
@@ -54,8 +55,7 @@ class TestWSGI(unittest.TestCase):
"""
Test all links in the main menu.
"""
- ignore = ['external', # Todo: should not be a link
- 'bugtracker']
+ ignore = [] # This could contain relative links we want to skip
r = self.app.get('/')
for link in r.lxml.cssselect('#menu a'):
href = link.get('href')
@@ -202,7 +202,7 @@ class TestWSGI(unittest.TestCase):
r = form.submit()
r.mustcontain('NM_003002.2:c.204C>T')
- def _batch(self, batch_type='NameChecker', arg1=None, variants=[],
+ def _batch(self, batch_type='NameChecker', arg1=None, file="", size=0,
header=''):
"""
Submit a batch form.
@@ -210,7 +210,8 @@ class TestWSGI(unittest.TestCase):
@kwarg batch_type: Type of batch job to test. One of NameChecker,
SyntaxChecker, PositionConverter.
@kwarg arg1: Optional extra argument for the batch job.
- @kwarg variants: Variants to use as input for the batch job.
+ @kwarg file: String with variants to use as input for the batch job.
+ @kwarg size: Number of variants in input.
@kwarg header: Message that must be found in the batch job result.
"""
r = self.app.get('/batch')
@@ -220,53 +221,146 @@ class TestWSGI(unittest.TestCase):
form['batchType'] = batch_type
form['batchEmail'] = 'm.vermaat.hg@lumc.nl'
form.set('batchFile', ('test_%s.txt' % batch_type,
- '\n'.join(variants)))
+ file))
r = form.submit()
id = r.lxml.cssselect('#jobID')[0].get('value')
max_tries = 60
for i in range(max_tries):
- r = self.app.get('/progress?jobID=' + id + '&totalJobs=3&ajax=1')
+ r = self.app.get('/progress?jobID=' + id + '&totalJobs=' + str(size) + '&ajax=1')
self.assertEqual(r.content_type, 'text/plain')
#print '%s: %s' % (batch_type, r.body)
if r.body == 'OK': break
self.assertTrue(re.match('[0-9]+', r.body))
- time.sleep(5)
+ time.sleep(2)
self.assertEqual(r.body, 'OK')
r = self.app.get('/Results_' + id + '.txt')
self.assertEqual(r.content_type, 'text/plain')
r.mustcontain(header)
- self.assertTrue(len(r.body.strip().split('\n')) == len(variants) + 1)
+ self.assertTrue(len(r.body.strip().split('\n')) == size + 1)
def test_batch_namechecker(self):
"""
Submit the batch name checker form.
"""
+ variants=['AB026906.1(SDHD):g.7872G>T',
+ 'NM_003002.1:c.3_4insG',
+ 'AL449423.14(CDKN2A_v002):c.5_400del']
self._batch('NameChecker',
- variants=['AB026906.1(SDHD):g.7872G>T',
- 'NM_003002.1:c.3_4insG',
- 'AL449423.14(CDKN2A_v002):c.5_400del'],
+ file='\n'.join(variants),
+ size=len(variants),
header='Input\tErrors | Messages')
def test_batch_syntaxchecker(self):
"""
Submit the batch syntax checker form.
"""
+ variants = ['AB026906.1(SDHD):g.7872G>T',
+ 'NM_003002.1:c.3_4insG',
+ 'AL449423.14(CDKN2A_v002):c.5_400del']
self._batch('SyntaxChecker',
- variants = ['AB026906.1(SDHD):g.7872G>T',
- 'NM_003002.1:c.3_4insG',
- 'AL449423.14(CDKN2A_v002):c.5_400del'],
+ file='\n'.join(variants),
+ size=len(variants),
header='Input\tStatus')
def test_batch_positionconverter(self):
"""
Submit the batch position converter form.
"""
+ variants = ['NM_003002.2:c.204C>T',
+ 'NC_000011.9:g.111959625C>T']
self._batch('PositionConverter',
arg1='hg19',
- variants = ['NM_003002.2:c.204C>T',
- 'NC_000011.9:g.111959625C>T'],
+ file='\n'.join(variants),
+ size=len(variants),
header='Input Variant')
+ def test_batch_syntaxchecker_newlines_unix(self):
+ """
+ Submit the batch syntax checker form with unix line endings.
+ """
+ variants = ['AB026906.1(SDHD):g.7872G>T',
+ 'NM_003002.1:c.3_4insG',
+ 'AL449423.14(CDKN2A_v002):c.5_400del']
+ self._batch('SyntaxChecker',
+ file='\n'.join(variants),
+ size=len(variants),
+ header='Input\tStatus')
+
+ def test_batch_syntaxchecker_newlines_mac(self):
+ """
+ Submit the batch syntax checker form with mac line endings.
+ """
+ variants = ['AB026906.1(SDHD):g.7872G>T',
+ 'NM_003002.1:c.3_4insG',
+ 'AL449423.14(CDKN2A_v002):c.5_400del']
+ self._batch('SyntaxChecker',
+ file='\r'.join(variants),
+ size=len(variants),
+ header='Input\tStatus')
+
+ def test_batch_syntaxchecker_newlines_windows(self):
+ """
+ Submit the batch syntax checker form with windows line endings.
+ """
+ variants = ['AB026906.1(SDHD):g.7872G>T',
+ 'NM_003002.1:c.3_4insG',
+ 'AL449423.14(CDKN2A_v002):c.5_400del']
+ self._batch('SyntaxChecker',
+ file='\r\n'.join(variants),
+ size=len(variants),
+ header='Input\tStatus')
+
+ def test_batch_syntaxchecker_newlines_big_unix(self):
+ """
+ Submit the batch syntax checker form with unix line ending
+ styles and a big input file.
+ """
+ samples = ['AB026906.1(SDHD):g.7872G>T',
+ 'NM_003002.1:c.3_4insG',
+ 'AL449423.14(CDKN2A_v002):c.5_400del']
+ variants = []
+ # Create 240 variants out of 3 samples
+ for i in range(80):
+ variants.extend(samples)
+ self._batch('SyntaxChecker',
+ file='\n'.join(variants),
+ size=len(variants),
+ header='Input\tStatus')
+
+ def test_batch_syntaxchecker_newlines_big_mac(self):
+ """
+ Submit the batch syntax checker form with mac line ending
+ styles and a big input file.
+ """
+ samples = ['AB026906.1(SDHD):g.7872G>T',
+ 'NM_003002.1:c.3_4insG',
+ 'AL449423.14(CDKN2A_v002):c.5_400del']
+ variants = []
+ # Create 240 variants out of 3 samples
+ for i in range(80):
+ variants.extend(samples)
+ self._batch('SyntaxChecker',
+ file='\r'.join(variants),
+ size=len(variants),
+ header='Input\tStatus')
+
+ def test_batch_syntaxchecker_newlines_big_windows(self):
+ """
+ Submit the batch syntax checker form with windows line ending
+ styles and a big input file.
+ """
+ samples = ['AB026906.1(SDHD):g.7872G>T',
+ 'NM_003002.1:c.3_4insG',
+ 'AL449423.14(CDKN2A_v002):c.5_400del']
+ variants = []
+ # Create 240 variants out of 3 samples
+ for i in range(80):
+ variants.extend(samples)
+ self._batch('SyntaxChecker',
+ file='\r\n'.join(variants),
+ size=len(variants),
+ header='Input\tStatus')
+
def test_download_py(self):
"""
Download a Python example client for the webservice.
diff --git a/src/webservice.py b/src/webservice.py
index 445eaa49..bde27999 100644
--- a/src/webservice.py
+++ b/src/webservice.py
@@ -149,7 +149,7 @@ class MutalyzerService(DefinitionBase) :
#if
#__checkVariant
- @soap(Mandatory.String, Mandatory.String, Mandatory.Integer,
+ @soap(Mandatory.String, Mandatory.String, Mandatory.Integer,
_returns = List.String)
def getTranscripts(self, build, chrom, pos) :
"""Get all the transcripts that overlap with a chromosomal position.
@@ -360,7 +360,7 @@ class MutalyzerService(DefinitionBase) :
return result
#mappingInfo
- @soap(Mandatory.String, Mandatory.String, Mandatory.String,
+ @soap(Mandatory.String, Mandatory.String, Mandatory.String,
_returns = Transcript)
def transcriptInfo(self, LOVD_ver, build, accNo) :
"""Search for an NM number in the MySQL database, if the version
@@ -640,10 +640,10 @@ class MutalyzerService(DefinitionBase) :
@soap(Mandatory.String, Mandatory.String, Mandatory.Integer,
Mandatory.Integer, _returns = Mandatory.String)
- def sliceChromosomeByGene(self, geneSymbol, organism, upStream,
+ def sliceChromosomeByGene(self, geneSymbol, organism, upStream,
downStream) :
"""
- Todo: documentation, error handling, argument checking.
+ Todo: documentation, error handling, argument checking, tests.
"""
C = Config.Config()
@@ -654,7 +654,7 @@ class MutalyzerService(DefinitionBase) :
O.addMessage(__file__, -1, "INFO",
"Received request sliceChromosomeByGene(%s, %s, %s, %s)" % (
geneSymbol, organism, upStream, downStream))
-
+
UD = retriever.retrievegene(geneSymbol, organism, upStream, downStream)
O.addMessage(__file__, -1, "INFO",
diff --git a/templates/base/css/style.css b/templates/base/css/style.css
index e987b826..ddc3c662 100644
--- a/templates/base/css/style.css
+++ b/templates/base/css/style.css
@@ -263,6 +263,10 @@ ul {
z-index : 10;
}
+#menu td {
+ color : #002E65;
+}
+
.Interface {
color : #FFCC00;
background-color : #333333;
diff --git a/templates/menu.html b/templates/menu.html
index 4b48bc7b..3f1c02c3 100644
--- a/templates/menu.html
+++ b/templates/menu.html
@@ -391,7 +391,7 @@
<td colspan="3">
<a id="page_bugTrack"
onclick="swapActive('bugTrack');"
- href="bugtracker"
+ href="http://www.mutalyzer.nl/2.0/bugtracker"
onmouseover="navAct('base/images/bullitlicht1.gif',
'bugTrack');"
onmouseout="navDeAct('base/images/bullitdonker.gif',
@@ -407,14 +407,7 @@
<img src="base/images/bullitdonker.gif" id="b_external">
</td>
<td colspan="3">
- <a id="page_external"
- onclick="swapActive('external');"
- href="external"
- onmouseover="navAct('base/images/bullitlicht1.gif',
- 'external');"
- onmouseout="navDeAct('base/images/bullitdonker.gif',
- 'external');"
- class="vertnavsub">External Links</a>
+ External Links
</td>
</tr>
--
GitLab