diff --git a/README b/README
index fe53fef82e17ab55c0066f5481f2a13a821f0765..f345af367d61e6d2b71caf238eef0ee78fe8c492 100644
--- a/README
+++ b/README
@@ -25,7 +25,11 @@ The unit tests depend on a running batch daemon and SOAP webservice:
Now run the tests with:
- $ MUTALYZER_ENV=test nosetests
+ $ MUTALYZER_ENV=test nosetests -v
+
+Or, if you are in a hurry, skip the long-running tests with:
+
+ $ MUTALYZER_ENV=test MUTALYZER_QUICK_TEST=1 nosetests -v
Development Notes
diff --git a/mutalyzer/Retriever.py b/mutalyzer/Retriever.py
index 7dc6e160f1980c0b46860741a5e86ddb77597c5e..d3dd78a8d7767b96803e919f97088222e7f1ba05 100644
--- a/mutalyzer/Retriever.py
+++ b/mutalyzer/Retriever.py
@@ -271,8 +271,17 @@ class Retriever(object) :
return []
# Query dbSNP for the SNP.
- response = Entrez.efetch(db='SNP', id=id, rettype='flt',
- retmode='xml')
+ try:
+ response = Entrez.efetch(db='SNP', id=id, rettype='flt',
+ retmode='xml')
+ except IOError:
+ # Could not parse XML.
+ self._output.addMessage(__file__, 4, 'EENTREZ',
+ 'Error connecting to dbSNP.')
+ self._output.addMessage(__file__, -1, 'INFO',
+ 'IOError: %s' % str(e))
+ return []
+
response_text = response.read()
try:
diff --git a/mutalyzer/templates/check.html b/mutalyzer/templates/check.html
index 2496fd3a8d1093cce39e1f0acd5549c4053e7aef..271293e2bff8feb9fa951c69f396e97ee5e51958 100644
--- a/mutalyzer/templates/check.html
+++ b/mutalyzer/templates/check.html
@@ -10,7 +10,7 @@
<center>
<h3>Name checker</h3>
</center>
- <div style="border: 1px solid grey; background: #ccffff; padding: 20px;">
+ <div style="border: 1px solid grey; background-color: aliceblue; padding: 20px;">
<div id = "output" tal:condition = "interactive">
<div>
Please insert the mutation name using the
@@ -116,7 +116,7 @@
<div tal:condition = "transcriptInfo">
<b>Detailed information about the selected transcript:</b><br>
<br>
- <div style = "background-color : #ccffff; padding : 20px; border: 1px solid grey">
+ <div style = "background-color : aliceblue; padding : 20px; border: 1px solid grey">
<div tal:condition = "oldProtein">
<b>Reference protein:</b><br>
<pre><div tal:repeat = "i oldProtein"
diff --git a/mutalyzer/util.py b/mutalyzer/util.py
index af4b092a65a8b5e423dcbcf651a5d09fa088aa3c..892bde65f623843bdff3b2354b333b62f1734944 100644
--- a/mutalyzer/util.py
+++ b/mutalyzer/util.py
@@ -19,6 +19,7 @@ General utility functions.
"""
+import os
import math
import time
from itertools import izip_longest
@@ -719,3 +720,22 @@ def message_info(message):
'class': classes[message.level],
'description': message.description}
#message_info
+
+
+def slow(f):
+ """
+ Decorator for slow tests. This makes them to pass immediately, without
+ running them. But only if the environment variable MUTALYZER_QUICK_TEST
+ is 1.
+
+ @todo: I don't think this actually belongs here (a separate util module
+ for the unit tests?).
+ """
+ def slow_f(*args, **kwargs):
+ if 'MUTALYZER_QUICK_TEST' in os.environ \
+ and os.environ['MUTALYZER_QUICK_TEST'] == '1':
+ return
+ else:
+ f(*args, **kwargs)
+ return slow_f
+#slow
diff --git a/mutalyzer/webservice.py b/mutalyzer/webservice.py
index 2787ecb215a1c184414d33b53b2a2698823e6f2a..952063164eb8ae1d69cec46c1990129d5904c757 100644
--- a/mutalyzer/webservice.py
+++ b/mutalyzer/webservice.py
@@ -55,14 +55,18 @@ from mutalyzer import GenRecord
from mutalyzer.models import *
-class MutalyzerService(DefinitionBase) :
+class MutalyzerService(DefinitionBase):
"""
Mutalyzer webservices.
These methods are made public via a SOAP interface.
"""
+ def __init__(self, environ=None):
+ self._config = Config()
+ super(MutalyzerService, self).__init__(environ)
+ #__init__
- def __checkBuild(self, L, build, config) :
+ def __checkBuild(self, L, build) :
"""
Check if the build is supported (hg18 or hg19).
@@ -73,11 +77,9 @@ class MutalyzerService(DefinitionBase) :
@type L: object
@arg build: The human genome build name that needs to be checked.
@type build: string
- @arg config: Configuration object of the Db module.
- @type config: object
"""
- if not build in config.dbNames :
+ if not build in self._config.Db.dbNames :
L.addMessage(__file__, 4, "EARG", "EARG %s" % build)
raise Fault("EARG",
"The build argument (%s) was not a valid " \
@@ -169,16 +171,14 @@ class MutalyzerService(DefinitionBase) :
@return: A list of transcripts.
@rtype: list
"""
-
- C = Config()
- L = Output(__file__, C.Output)
+ L = Output(__file__, self._config.Output)
L.addMessage(__file__, -1, "INFO",
"Received request getTranscripts(%s %s %s)" % (build,
chrom, pos))
- self.__checkBuild(L, build, C.Db)
- D = Db.Mapping(build, C.Db)
+ self.__checkBuild(L, build)
+ D = Db.Mapping(build, self._config.Db)
self.__checkChrom(L, D, chrom)
self.__checkPos(L, pos)
@@ -196,25 +196,23 @@ class MutalyzerService(DefinitionBase) :
L.addMessage(__file__, -1, "INFO",
"We return %s" % ret)
- del D, L, C
+ del D, L
return ret
#getTranscripts
@soap(Mandatory.String, Mandatory.String, _returns = Array(Mandatory.String))
- def getTranscriptsByGeneName(self, build, name) :
+ def getTranscriptsByGeneName(self, build, name):
"""
Todo: documentation.
"""
-
- C = Config()
- L = Output(__file__, C.Output)
+ L = Output(__file__, self._config.Output)
L.addMessage(__file__, -1, "INFO",
"Received request getTranscriptsByGene(%s %s)" % (build,
name))
- self.__checkBuild(L, build, C.Db)
- D = Db.Mapping(build, C.Db)
+ self.__checkBuild(L, build)
+ D = Db.Mapping(build, self._config.Db)
ret = D.get_TranscriptsByGeneName(name)
@@ -247,16 +245,14 @@ class MutalyzerService(DefinitionBase) :
@return: A list of transcripts.
@rtype: list
"""
-
- C = Config()
- L = Output(__file__, C.Output)
+ L = Output(__file__, self._config.Output)
L.addMessage(__file__, -1, "INFO",
"Received request getTranscriptsRange(%s %s %s %s %s)" % (build,
chrom, pos1, pos2, method))
- D = Db.Mapping(build, C.Db)
- self.__checkBuild(L, build, C.Db)
+ D = Db.Mapping(build, self._config.Db)
+ self.__checkBuild(L, build)
ret = D.get_Transcripts(chrom, pos1, pos2, method)
@@ -267,7 +263,7 @@ class MutalyzerService(DefinitionBase) :
"Finished processing getTranscriptsRange(%s %s %s %s %s)" % (
build, chrom, pos1, pos2, method))
- del D, L, C
+ del D, L
return ret
#getTranscriptsRange
@@ -284,22 +280,20 @@ class MutalyzerService(DefinitionBase) :
@return: The name of the associated gene.
@rtype: string
"""
-
- C = Config()
- L = Output(__file__, C.Output)
+ L = Output(__file__, self._config.Output)
L.addMessage(__file__, -1, "INFO",
"Received request getGeneName(%s %s)" % (build, accno))
- D = Db.Mapping(build, C.Db)
- self.__checkBuild(L, build, C.Db)
+ D = Db.Mapping(build, self._config.Db)
+ self.__checkBuild(L, build)
ret = D.get_GeneName(accno.split('.')[0])
L.addMessage(__file__, -1, "INFO",
"Finished processing getGeneName(%s %s)" % (build, accno))
- del D, L, C
+ del D, L
return ret
#getGeneName
@@ -345,22 +339,20 @@ class MutalyzerService(DefinitionBase) :
- type ; The mutation type.
@rtype: object
"""
-
- C = Config()
- L = Output(__file__, C.Output)
+ L = Output(__file__, self._config.Output)
L.addMessage(__file__, -1, "INFO",
"Reveived request mappingInfo(%s %s %s %s)" % (
LOVD_ver, build, accNo, variant))
- conv = Mapper.Converter(build, C, L)
+ conv = Mapper.Converter(build, self._config, L)
result = conv.mainMapping(accNo, variant)
L.addMessage(__file__, -1, "INFO",
"Finished processing mappingInfo(%s %s %s %s)" % (
LOVD_ver, build, accNo, variant))
- del L, C
+ del L
return result
#mappingInfo
@@ -385,15 +377,13 @@ class MutalyzerService(DefinitionBase) :
- CDS_stop ; CDS stop in I{c.} notation.
@rtype: object
"""
-
- C = Config()
- O = Output(__file__, C.Output)
+ O = Output(__file__, self._config.Output)
O.addMessage(__file__, -1, "INFO",
"Received request transcriptInfo(%s %s %s)" % (LOVD_ver,
build, accNo))
- converter = Mapper.Converter(build, C, O)
+ converter = Mapper.Converter(build, self._config, O)
T = converter.mainTranscript(accNo)
O.addMessage(__file__, -1, "INFO",
@@ -415,14 +405,13 @@ class MutalyzerService(DefinitionBase) :
@return: The accession number of a chromosome.
@rtype: string
"""
- C = Config() # Read the configuration file.
- D = Db.Mapping(build, C.Db)
- L = Output(__file__, C.Output)
+ D = Db.Mapping(build, self._config.Db)
+ L = Output(__file__, self._config.Output)
L.addMessage(__file__, -1, "INFO",
"Received request chromAccession(%s %s)" % (build, name))
- self.__checkBuild(L, build, C.Db)
+ self.__checkBuild(L, build)
self.__checkChrom(L, D, name)
result = D.chromAcc(name)
@@ -431,7 +420,7 @@ class MutalyzerService(DefinitionBase) :
"Finished processing chromAccession(%s %s)" % (build,
name))
- del D,L,C
+ del D,L
return result
#chromAccession
@@ -448,14 +437,13 @@ class MutalyzerService(DefinitionBase) :
@return: The name of a chromosome.
@rtype: string
"""
- C = Config() # Read the configuration file.
- D = Db.Mapping(build, C.Db)
- L = Output(__file__, C.Output)
+ D = Db.Mapping(build, self._config.Db)
+ L = Output(__file__, self._config.Output)
L.addMessage(__file__, -1, "INFO",
"Received request chromName(%s %s)" % (build, accNo))
- self.__checkBuild(L, build, C.Db)
+ self.__checkBuild(L, build)
# self.__checkChrom(L, D, name)
result = D.chromName(accNo)
@@ -464,7 +452,7 @@ class MutalyzerService(DefinitionBase) :
"Finished processing chromName(%s %s)" % (build,
accNo))
- del D,L,C
+ del D,L
return result
#chromosomeName
@@ -481,14 +469,13 @@ class MutalyzerService(DefinitionBase) :
@return: The name of a chromosome.
@rtype: string
"""
- C = Config() # Read the configuration file.
- D = Db.Mapping(build, C.Db)
- L = Output(__file__, C.Output)
+ D = Db.Mapping(build, self._config.Db)
+ L = Output(__file__, self._config.Output)
L.addMessage(__file__, -1, "INFO",
"Received request getchromName(%s %s)" % (build, acc))
- self.__checkBuild(L, build, C.Db)
+ self.__checkBuild(L, build)
# self.__checkChrom(L, D, name)
result = D.get_chromName(acc)
@@ -497,7 +484,7 @@ class MutalyzerService(DefinitionBase) :
"Finished processing getchromName(%s %s)" % (build,
acc))
- del D,L,C
+ del D,L
return result
#chromosomeName
@@ -516,14 +503,12 @@ class MutalyzerService(DefinitionBase) :
@return: The variant(s) in either I{g.} or I{c.} notation.
@rtype: list
"""
-
- C = Config() # Read the configuration file.
- D = Db.Mapping(build, C.Db)
- O = Output(__file__, C.Output)
+ D = Db.Mapping(build, self._config.Db)
+ O = Output(__file__, self._config.Output)
O.addMessage(__file__, -1, "INFO",
"Received request cTogConversion(%s %s)" % (
build, variant))
- converter = Mapper.Converter(build, C, O)
+ converter = Mapper.Converter(build, self._config, O)
variant = converter.correctChrVariant(variant)
if "c." in variant :
@@ -553,8 +538,7 @@ class MutalyzerService(DefinitionBase) :
- messages: List of (error) messages as strings.
@rtype: object
"""
- C = Config() # Read the configuration file.
- output = Output(__file__, C.Output)
+ output = Output(__file__, self._config.Output)
output.addMessage(__file__, -1, "INFO",
"Received request checkSyntax(%s)" % (variant))
@@ -584,12 +568,10 @@ class MutalyzerService(DefinitionBase) :
"""
Todo: documentation.
"""
- C = Config() # Read the configuration file.
- O = Output(__file__, C.Output)
+ O = Output(__file__, self._config.Output)
O.addMessage(__file__, -1, "INFO",
"Received request runMutalyzer(%s)" % (variant))
- #Mutalyzer.process(variant, C, O)
- variantchecker.check_variant(variant, C, O)
+ variantchecker.check_variant(variant, self._config, O)
result = MutalyzerOutput()
@@ -647,17 +629,16 @@ class MutalyzerService(DefinitionBase) :
"""
Todo: documentation.
"""
- C = Config()
- O = Output(__file__, C.Output)
- D = Db.Cache(C.Db)
+ O = Output(__file__, self._config.Output)
+ D = Db.Cache(self._config.Db)
O.addMessage(__file__, -1, "INFO",
"Received request getGeneAndTranscript(%s, %s)" % (genomicReference,
transcriptReference))
- retriever = Retriever.GenBankRetriever(C.Retriever, O, D)
+ retriever = Retriever.GenBankRetriever(self._config.Retriever, O, D)
record = retriever.loadrecord(genomicReference)
- GenRecordInstance = GenRecord.GenRecord(O, C.GenRecord)
+ GenRecordInstance = GenRecord.GenRecord(O, self._config.GenRecord)
GenRecordInstance.record = record
GenRecordInstance.checkRecord()
@@ -714,17 +695,16 @@ class MutalyzerService(DefinitionBase) :
- id
- product
"""
- C = Config()
- O = Output(__file__, C.Output)
- D = Db.Cache(C.Db)
+ O = Output(__file__, self._config.Output)
+ D = Db.Cache(self._config.Db)
O.addMessage(__file__, -1, "INFO",
"Received request getTranscriptsAndInfo(%s)" % genomicReference)
- retriever = Retriever.GenBankRetriever(C.Retriever, O, D)
+ retriever = Retriever.GenBankRetriever(self._config.Retriever, O, D)
record = retriever.loadrecord(genomicReference)
# Todo: If loadRecord failed (e.g. DTD missing), we should abort here.
- GenRecordInstance = GenRecord.GenRecord(O, C.GenRecord)
+ GenRecordInstance = GenRecord.GenRecord(O, self._config.GenRecord)
GenRecordInstance.record = record
GenRecordInstance.checkRecord()
@@ -829,11 +809,9 @@ class MutalyzerService(DefinitionBase) :
"""
Todo: documentation, error handling, argument checking, tests.
"""
-
- C = Config()
- O = Output(__file__, C.Output)
- D = Db.Cache(C.Db)
- retriever = Retriever.GenBankRetriever(C.Retriever, O, D)
+ O = Output(__file__, self._config.Output)
+ D = Db.Cache(self._config.Db)
+ retriever = Retriever.GenBankRetriever(self._config.Retriever, O, D)
O.addMessage(__file__, -1, "INFO",
"Received request sliceChromosomeByGene(%s, %s, %s, %s)" % (
@@ -860,10 +838,9 @@ class MutalyzerService(DefinitionBase) :
"""
Todo: documentation, error handling, argument checking, tests.
"""
- C = Config()
- O = Output(__file__, C.Output)
- D = Db.Cache(C.Db)
- retriever = Retriever.GenBankRetriever(C.Retriever, O, D)
+ O = Output(__file__, self._config.Output)
+ D = Db.Cache(self._config.Db)
+ retriever = Retriever.GenBankRetriever(self._config.Retriever, O, D)
O.addMessage(__file__, -1, "INFO",
"Received request sliceChromosome(%s, %s, %s, %s)" % (
diff --git a/tests/test_mutalyzer.py b/tests/test_mutalyzer.py
index 68fd7cc5b672a949b157186c0a960d367444ee05..ddbaf0c326b845ded3f2e11aab8d105e140cfc07 100644
--- a/tests/test_mutalyzer.py
+++ b/tests/test_mutalyzer.py
@@ -105,7 +105,6 @@ class TestMutalyzer():
assert 'AL449423.14(CDKN2A_v001):c.99_100insTAG' in self.output.getOutput('descriptions')
assert_equal ('AL449423.14:g.65471_65472insACT', self.output.getIndexedOutput('genomicDescription', 0, ''))
assert len(self.output.getMessagesWithErrorCode('WROLLFORWARD')) == 1
- assert len(self.output.getMessagesWithErrorCode('WROLLREVERSE')) == 1
def test_roll_reverse_ins(self):
"""
@@ -116,6 +115,23 @@ class TestMutalyzer():
assert 'AL449423.14(CDKN2A_v001):c.99_100insTAG' in self.output.getOutput('descriptions')
assert_equal ('AL449423.14:g.65471_65472insACT', self.output.getIndexedOutput('genomicDescription', 0, ''))
assert len(self.output.getMessagesWithErrorCode('WROLLFORWARD')) == 0
+
+ def test_roll_message_forward(self):
+ """
+ Roll warning message should only be shown for currently selected
+ strand (forward).
+ """
+ check_variant('AL449423.14:g.65470_65471insTAC', self.config, self.output)
+ assert len(self.output.getMessagesWithErrorCode('WROLLFORWARD')) == 1
+ assert len(self.output.getMessagesWithErrorCode('WROLLREVERSE')) == 0
+
+ def test_roll_message_reverse(self):
+ """
+ Roll warning message should only be shown for currently selected
+ strand (reverse).
+ """
+ check_variant('AL449423.14(CDKN2A_v001):c.98_99insGTA', self.config, self.output)
+ assert len(self.output.getMessagesWithErrorCode('WROLLFORWARD')) == 0
assert len(self.output.getMessagesWithErrorCode('WROLLREVERSE')) == 1
def test_ins_cds_start(self):
diff --git a/tests/test_webservice.py b/tests/test_webservice.py
index 05e29713066666703a7197d8a1fd4c557f314952..5d9e08ff6af240924f0ba65afc13ed94f3286032 100644
--- a/tests/test_webservice.py
+++ b/tests/test_webservice.py
@@ -3,6 +3,19 @@ Tests for the SOAP interface to Mutalyzer.
"""
+# Monkey patch suds, because for some weird reason the location
+# http://www.w3.org/2001/xml.xsd is used for the XML namespace, but the W3C
+# seems to respond too slow on that url. We use therefore use
+# http://www.w3.org/2009/01/xml.xsd which fixes this.
+from suds.xsd.sxbasic import Import
+_import_open = Import.open
+def _import_open_patched(self, *args, **kwargs):
+ if self.location == 'http://www.w3.org/2001/xml.xsd':
+ self.location = 'http://www.w3.org/2009/01/xml.xsd'
+ return _import_open(self, *args, **kwargs)
+Import.open = _import_open_patched
+
+
import os
import logging; logging.raiseExceptions = 0
import urllib2
diff --git a/tests/test_wsgi.py b/tests/test_wsgi.py
index 5feea15704bd04ac4e78ce84acaf158e3be5e6ab..7ab668c847dd3d2d5271e2ff97fe8365bac12aee 100644
--- a/tests/test_wsgi.py
+++ b/tests/test_wsgi.py
@@ -20,6 +20,7 @@ from webtest import TestApp
import mutalyzer
from mutalyzer.wsgi import application
+from mutalyzer.util import slow
class TestWSGI():
@@ -235,6 +236,7 @@ class TestWSGI():
r = form.submit()
r.mustcontain('NM_003002.2:c.204C>T')
+ @slow
def _batch(self, batch_type='NameChecker', arg1=None, file="", size=0,
header='', lines=None):
"""
@@ -414,6 +416,7 @@ class TestWSGI():
size=len(variants)-1,
header='Input\tStatus')
+ @slow
def test_batch_syntaxchecker_toobig(self):
"""
Submit the batch syntax checker with a too big input file.
@@ -440,6 +443,7 @@ facilisi."""
r = form.submit(status=413)
assert_equal(r.content_type, 'text/plain')
+ @slow
def test_batch_multicolumn(self):
"""
Submit the batch syntax checker with a multiple-colums input file.