diff --git a/bin/mutalyzer b/bin/mutalyzer
index 68345947cd5c43c2f108c842ea6b7d96d32a2800..9013cd39154aeefdad383baa1278ae185cd2d8af 100755
--- a/bin/mutalyzer
+++ b/bin/mutalyzer
@@ -17,7 +17,6 @@ import os
from mutalyzer import variantchecker
from mutalyzer.output import Output
-from mutalyzer.config import Config
from mutalyzer.util import format_usage
@@ -27,12 +26,11 @@ def main(cmd):
@todo: documentation
"""
- C = Config()
- O = Output(__file__, C.Output)
+ O = Output(__file__)
O.addMessage(__file__, -1, "INFO", "Received variant " + cmd)
- RD = variantchecker.check_variant(cmd, C, O)
+ RD = variantchecker.check_variant(cmd, O)
O.addMessage(__file__, -1, "INFO", "Finished processing variant " + cmd)
diff --git a/bin/mutalyzer-batchd b/bin/mutalyzer-batchd
index 868eafa933fe36a3e7681c2d9641c6d7840fb0f5..2753d8a0032f2528e6c32d80e82e7bcbf93c75cb 100755
--- a/bin/mutalyzer-batchd
+++ b/bin/mutalyzer-batchd
@@ -23,7 +23,7 @@ import signal
import time
import traceback
-from mutalyzer.config import Config
+from mutalyzer import config
from mutalyzer.Db import Batch
from mutalyzer.Scheduler import Scheduler
@@ -40,10 +40,7 @@ def daemonize():
Write PID file when it is not locked and daemonize a loop processing
scheduled batch jobs.
"""
- config = Config()
- batch_config = config.Batch
-
- pidfile = os.path.realpath(batch_config.PIDfile)
+ pidfile = os.path.realpath(config.get('PIDfile'))
lockfile = pidlockfile.TimeoutPIDLockFile(pidfile, acquire_timeout=1,
threaded=False)
@@ -68,10 +65,10 @@ def daemonize():
with context:
# Note that any opened files are now closed. This is not a problem for
- # the Config instance, since it does not read its file again after
+ # the config module, since it does not read its file again after
# initialisation.
- database = Batch(config.Db)
- scheduler = Scheduler(config.Scheduler, database)
+ database = Batch()
+ scheduler = Scheduler(database)
def stop_scheduler(signum, stack_frame):
scheduler.stop()
diff --git a/bin/mutalyzer-cache-sync b/bin/mutalyzer-cache-sync
index 405084ea16b373b3e0e161a1cc35cb03cb55432b..5e012949ddff2661c4a9a61a42a0639af8e60a58 100755
--- a/bin/mutalyzer-cache-sync
+++ b/bin/mutalyzer-cache-sync
@@ -20,7 +20,6 @@ This program is intended to be run daily from cron. Example:
import sys
-from mutalyzer.config import Config
from mutalyzer.output import Output
from mutalyzer.sync import CacheSync
from mutalyzer import Db
@@ -31,11 +30,10 @@ def cache_sync(remote_wsdl, url_template, days):
"""
Synchronize the database cache with other Mutalyzer instances.
"""
- config = Config()
- output = Output(__file__, config.Output)
- database = Db.Cache(config.Db)
+ output = Output(__file__)
+ database = Db.Cache()
- sync = CacheSync(config.Retriever, output, database)
+ sync = CacheSync(output, database)
sync.sync_with_remote(remote_wsdl, url_template, days)
diff --git a/bin/mutalyzer-mapping-update b/bin/mutalyzer-mapping-update
index cbc88ef27dab3c6f81854a91424605748df7e1dd..8fe6bb3500b289fbe0d69434eabe2e6b85c6e6d5 100755
--- a/bin/mutalyzer-mapping-update
+++ b/bin/mutalyzer-mapping-update
@@ -19,7 +19,6 @@ This program is intended to be run daily from cron. Example:
import sys
-from mutalyzer.config import Config
from mutalyzer.output import Output
from mutalyzer.mapping import NCBIUpdater
from mutalyzer.util import format_usage
@@ -39,12 +38,11 @@ def main(database, mapping_file, assembly):
@todo: Also report how much was added/updated.
"""
- config = Config()
- output = Output(__file__, config.Output)
+ output = Output(__file__)
output.addMessage(__file__, -1, 'INFO',
'Starting NCBI mapping data update')
- updater = NCBIUpdater(database, config)
+ updater = NCBIUpdater(database)
updater.load(mapping_file, assembly)
updater.merge()
diff --git a/bin/mutalyzer-webservice.wsgi b/bin/mutalyzer-webservice.wsgi
index bc624da31f7e733ff61b899860ca67f6c2fafb2b..5a01545e2e705cf9b04bc26b14da521c24e8c3d9 100755
--- a/bin/mutalyzer-webservice.wsgi
+++ b/bin/mutalyzer-webservice.wsgi
@@ -25,8 +25,6 @@ To start the built-in HTTP server on port 8081:
kind of strictness checks on the input. For example, in
transcriptInfo, the build argument must really be present. (Hint:
use __checkBuild.)
-@todo: The mutalyzer.config.Config object can just be instantiated once
- and we should not create it on every request.
"""
diff --git a/extras/log-tools/find-crashes.py b/extras/log-tools/find-crashes.py
index cea38c2e667cb8ebf0fa3abd5fcf69845b6923d7..0e6d791ef19995d3708a982573b40861822ca71f 100755
--- a/extras/log-tools/find-crashes.py
+++ b/extras/log-tools/find-crashes.py
@@ -10,11 +10,10 @@ crashed.
import os
-from mutalyzer.config import Config
+from mutalyzer import config
-config = Config()
-handle = open(config.Output.log, 'r')
+handle = open(config.get('log'), 'r')
scanning = False
line = handle.readline()
diff --git a/mutalyzer/Db.py b/mutalyzer/Db.py
index 5bd25f3396680cd42ad2eeeb19f42ed23706bffe..60d61a183b9bbdf71fa7d718b3924be9c6e9fd94 100644
--- a/mutalyzer/Db.py
+++ b/mutalyzer/Db.py
@@ -25,6 +25,7 @@ import warnings
import MySQLdb
from mutalyzer import util
+from mutalyzer import config
#
@@ -115,7 +116,7 @@ class Mapping(Db) :
Database functions for mapping of transcripts and genes.
Special methods:
- - __init__(build, config) ; Initialise the class.
+ - __init__(build) ; Initialise the class.
Public methods:
- get_protAcc(mrnaAcc) ; Query the database for a protein ID.
@@ -135,18 +136,15 @@ class Mapping(Db) :
- Mapping; Accumulated mapping info.
"""
- def __init__(self, build, config) :
+ def __init__(self, build) :
"""
Initialise the Db parent class. Use the local database for a certain
build.
@arg build: The version of the mapping database
@type build: string
- @arg config: Configuration variables
- @type config: class instance
"""
-
- Db.__init__(self, build, config.LocalMySQLuser, config.LocalMySQLhost)
+ Db.__init__(self, build, config.get('LocalMySQLuser'), config.get('LocalMySQLhost'))
#__init__
def get_NM_version(self, mrnaAcc) :
@@ -660,7 +658,7 @@ class Cache(Db) :
Database functions for cache administration.
Special methods:
- - __init__(config) ; Initialise the class.
+ - __init__() ; Initialise the class.
Public methods:
- insertGB(accNo, GI, fileHash, ChrAccVer, ChrStart, ChrStop,
@@ -683,16 +681,12 @@ class Cache(Db) :
- GBInfo ; Information about cached and uploaded GenBank files.
"""
- def __init__(self, config) :
+ def __init__(self) :
"""
Initialise the Db parent class. Use the internalDb.
-
- @arg config: Configuration variables
- @type config: class instance
"""
-
- Db.__init__(self, config.internalDb, config.LocalMySQLuser,
- config.LocalMySQLhost)
+ Db.__init__(self, config.get('internalDb'),
+ config.get('LocalMySQLuser'), config.get('LocalMySQLhost'))
#__init__
def insertGB(self, accNo, GI, fileHash, ChrAccVer, ChrStart,
@@ -1099,7 +1093,7 @@ class Batch(Db) :
Database functions for the batch checker.
Special methods:
- - __init__(config) ; Initialise the class.
+ - __init__() ; Initialise the class.
Public methods:
- isJobListEmpty() ; See if there are active jobs.
@@ -1121,16 +1115,13 @@ class Batch(Db) :
- BatchQueue ; Requests.
"""
- def __init__(self, config) :
+ def __init__(self) :
"""
Initialise the Db parent class. Use the internalDb.
-
- @arg config: Configuration variables
- @type config: class instance
"""
-
- Db.__init__(self, config.internalDb, config.LocalMySQLuser,
- config.LocalMySQLhost)
+ Db.__init__(self, config.get('internalDb'),
+ config.get('LocalMySQLuser'),
+ config.get('LocalMySQLhost'))
#__init__
def isJobListEmpty(self) :
diff --git a/mutalyzer/File.py b/mutalyzer/File.py
index a03a1b3af460e35b51057b900348edb8f70a0279..561503d7bd605b968f1af779067bc7c4ea4427e5 100644
--- a/mutalyzer/File.py
+++ b/mutalyzer/File.py
@@ -27,13 +27,14 @@ import types # UnicodeType
from cStringIO import StringIO
from mutalyzer import util
+from mutalyzer import config
+
class File() :
"""
Parse CSV files and spreadsheets.
Private variables:
- - __config ; Configuration variables.
- __output ; The Output object.
Special methods:
@@ -53,21 +54,16 @@ class File() :
and sanitize the output.
"""
- def __init__(self, config, output) :
+ def __init__(self, output) :
"""
Initialise the class.
Private variables (altered):
- - __config ; Initialised with configuration variables.
- __output ; Set to the Output object.
- @arg config: Configuration variables
- @type config: class instance
@arg output: Output object
@type output: class instance
"""
-
- self.__config = config
self.__output = output #: The Output object
#__init__
@@ -106,9 +102,6 @@ class File() :
Parse a CSV file.
The stream is not rewinded after use.
- Private variables:
- - __config ; The bufSize configuration variables.
-
@arg handle: A handle to a stream
@type handle: stream
@@ -167,7 +160,7 @@ class File() :
# I don't think the .seek(0) is needed now we created a new handle
new_handle.seek(0)
- buf = new_handle.read(self.__config.bufSize)
+ buf = new_handle.read(config.get('bufSize'))
# Default dialect
dialect = 'excel'
@@ -270,9 +263,6 @@ class File() :
- The first and the last element should be non-empty.
- The first line should be the header defined in the config file.
- Private variables:
- - __config ; The header configuration variable.
-
@todo: Add more new style old style logic
@todo: if not inputl: try to make something out of it
@@ -289,7 +279,7 @@ class File() :
jobl = [(l+1, row) for l, row in enumerate(job)]
#TODO: Add more new style old style logic
- if jobl[0][1] == self.__config.header : #Old style NameCheckBatch job
+ if jobl[0][1] == config.get('header') : #Old style NameCheckBatch job
ret = []
notthree = []
emptyfield = []
@@ -374,7 +364,7 @@ class File() :
err = float(len(errlist))/len(ret)
if err == 0:
return (ret, columns)
- elif err < self.__config.threshold:
+ elif err < config.get('threshold'):
#allow a 5 (default) percent threshold for errors in batchfiles
self.__output.addMessage(__file__, 3, "EBPARSE",
"There were errors in your batch entry file, they are "
@@ -391,19 +381,14 @@ class File() :
Get the mime type of a stream by inspecting a fixed number of bytes.
The stream is rewinded after use.
- Private variables:
- - __config: The bufSize configuration variables.
-
@arg handle: A handle to a stream
@type handle: stream
@return: The mime type of a file
@rtype: string
"""
-
handle.seek(0)
- buf = handle.read(self.__config.bufSize) #: The bufSize configuration variables.
-
+ buf = handle.read(config.get('bufSize')) #: The bufSize configuration variables.
MagicInstance = magic.open(magic.MAGIC_MIME)
MagicInstance.load()
diff --git a/mutalyzer/GenRecord.py b/mutalyzer/GenRecord.py
index 3c96487220f582f3f076ed45151dda011194faf4..90d50c0f16a67764cc83e49944b9fc8bf04e976d 100644
--- a/mutalyzer/GenRecord.py
+++ b/mutalyzer/GenRecord.py
@@ -19,6 +19,7 @@ search for them each time.
import Bio
from mutalyzer import util
+from mutalyzer import config
from mutalyzer import Crossmap
from mutalyzer import Db
@@ -379,7 +380,7 @@ class GenRecord() :
- checkRecord() ; Check and repair self.record.
"""
- def __init__(self, output, config) :
+ def __init__(self, output) :
"""
Initialise the class.
@@ -388,12 +389,8 @@ class GenRecord() :
@arg output: an output object
@type output: object
- @arg config: a config object
- @type config: object
"""
-
self.__output = output
- self.__config = config
self.record = None
#__init__
@@ -807,13 +804,13 @@ class GenRecord() :
# TODO Also check a range properly.
intronPos = abs(transcript.CM.g2x(position)[1])
if intronPos :
- if intronPos <= self.__config.spliceAlarm :
+ if intronPos <= config.get('spliceAlarm'):
self.__output.addMessage(__file__, 2, "WSPLICE",
"Mutation on splice site in gene %s transcript %s." % (
gene.name, transcript.name))
return
#if
- if intronPos <= self.__config.spliceWarn :
+ if intronPos <= config.get('spliceWarn'):
self.__output.addMessage(__file__, 2, "WSPLICE",
"Mutation near splice site in gene %s transcript %s." % (
gene.name, transcript.name))
diff --git a/mutalyzer/Retriever.py b/mutalyzer/Retriever.py
index ded70bcc034d797cbe7a16ff5f2e6b87c706f288..4f5f624cbde53e18456ebcaddd6a5fcf9faef6c5 100644
--- a/mutalyzer/Retriever.py
+++ b/mutalyzer/Retriever.py
@@ -24,6 +24,7 @@ from xml.dom import DOMException, minidom
from xml.parsers import expat
from mutalyzer import util
+from mutalyzer import config
from mutalyzer.parsers import lrg
from mutalyzer.parsers import genbank
@@ -32,17 +33,10 @@ class Retriever(object) :
"""
Retrieve a record from either the cache or the NCBI.
- Inherited variables from Db.Output.Config:
- - email ; The email address which we give to the NCBI.
- - cache ; The directory where the records are stored.
- - cachesize ; Maximum size of the cache.
-
Special methods:
- - __init__(config, output, database) ; Use variables from the
+ - __init__(output, database) ; Use variables from the
configuration file to initialise the class private variables.
-
-
Private methods:
- _foldersize(folder) ; Return the size of a folder.
- _cleancache() ; Keep the cache at a maximum size.
@@ -67,29 +61,21 @@ class Retriever(object) :
- LogMsg(filename, message) ; Log a message.
"""
- def __init__(self, config, output, database) :
+ def __init__(self, output, database) :
"""
Use variables from the configuration file for some simple
settings. Make the cache directory if it does not exist yet.
- Inherited variables from Db.Output.Config:
- - email ; The email address which we give to the NCBI.
- - cache ; The directory where the records are stored.
-
- @arg config:
- @type config:
@arg output:
@type output:
@arg database:
@type database:
"""
-
- self._config = config
self._output = output
self._database = database
- if not os.path.isdir(self._config.cache) :
- os.mkdir(self._config.cache)
- Entrez.email = self._config.email
+ if not os.path.isdir(config.get('cache')) :
+ os.mkdir(config.get('cache'))
+ Entrez.email = config.get('email')
self.fileType = None
#__init__
@@ -119,18 +105,13 @@ class Retriever(object) :
First, the cache checked for its size, if it exceeds the maximum
size the ``oldest'' files are deleted. Note that accessing a file
makes it ``new''.
-
- Inherited variables from Db.Output.Config:
- - cache ; Directory under scrutiny.
- - cachesize ; Maximum size of the cache.
"""
-
- if self._foldersize(self._config.cache) < self._config.cachesize:
+ if self._foldersize(config.get('cache')) < config.get('cachesize'):
return
# Build a list of files sorted by access time.
cachelist = []
- for (path, dirs, files) in os.walk(self._config.cache) :
+ for (path, dirs, files) in os.walk(config.get('cache')) :
for filename in files :
filepath = os.path.join(path, filename)
cachelist.append(
@@ -141,7 +122,7 @@ class Retriever(object) :
# small enough (or until the list is exhausted).
for i in range(0, len(cachelist)) :
os.remove(cachelist[i][1])
- if self._foldersize(self._config.cache) < self._config.cachesize:
+ if self._foldersize(config.get('cache')) < config.get('cachesize'):
break;
#for
#_cleancache
@@ -150,17 +131,13 @@ class Retriever(object) :
"""
Convert an accession number to a filename.
- Inherited variables from Db.Output.Config:
- - cache ; Name of the cache directory.
-
@arg name: The accession number
@type name: string
@return: A filename
@rtype: string
"""
-
- return self._config.cache + '/' + name + "." + self.fileType + ".bz2"
+ return config.get('cache') + '/' + name + "." + self.fileType + ".bz2"
#_nametofile
def _write(self, raw_data, filename) :
@@ -339,13 +316,12 @@ class GenBankRetriever(Retriever):
"""
"""
- def __init__(self, config, output, database):
- # TODO documentation
+ def __init__(self, output, database):
"""
+ @todo: Documentation.
"""
-
# Recall init of parent
- Retriever.__init__(self, config, output, database)
+ Retriever.__init__(self, output, database)
self.fileType = "gb"
# Child specific init
#__init__
@@ -466,9 +442,6 @@ class GenBankRetriever(Retriever):
The content of the slice is placed in the cache with the UD number
as filename.
- Inherited variables from Db.Output.Config:
- - maxDldSize ; Maximum size of the slice.
-
@arg accno: The accession number of the chromosome
@type accno: string
@arg start: Start position of the slice
@@ -490,7 +463,7 @@ class GenBankRetriever(Retriever):
return None
# The slice can not be too big.
- if stop - start > self._config.maxDldSize :
+ if stop - start > config.get('maxDldSize'):
return None
# Check whether we have seen this slice before.
@@ -610,23 +583,18 @@ class GenBankRetriever(Retriever):
If the downloaded file is recognised by its hash, the old UD number
is used.
- Inherited variables from Db.Output.Config:
- - maxDldSize ; Maximum size of the file.
- - minDldSize ; Minimum size of the file.
-
@arg url: Location of a GenBank record
@type url: string
@return: UD or None
@rtype: string
"""
-
handle = urllib2.urlopen(url)
info = handle.info()
if info["Content-Type"] == "text/plain" :
length = int(info["Content-Length"])
- if length > self._config.minDldSize and \
- length < self._config.maxDldSize :
+ if length > config.get('minDldSize') and \
+ length < config.get('maxDldSize'):
raw_data = handle.read()
md5sum = self._calcHash(raw_data)
UD = self._database.getGBFromHash(md5sum)
@@ -756,22 +724,19 @@ class LRGRetriever(Retriever):
the cache and return the record.
"""
- def __init__(self, config, output, database):
+ def __init__(self, output, database):
#TODO documentation
"""
Initialize the class.
@todo: documentation
- @arg config:
- @type config:
@arg output:
@type output:
@arg database:
@type database:
"""
-
# Recall init of parent
- Retriever.__init__(self, config, output, database)
+ Retriever.__init__(self, output, database)
self.fileType = "xml"
# Child specific init
#__init__
@@ -815,9 +780,6 @@ class LRGRetriever(Retriever):
grab the file from the confirmed section, if this fails, get it
from the pending section.
- Inherited variables from Config.Retriever
- - lrgURL ; The base url from where LRG files are fetched
-
@arg name: The name of the LRG file to fetch
@type name: string
@@ -825,7 +787,7 @@ class LRGRetriever(Retriever):
@rtype: string
"""
- prefix = self._config.lrgURL
+ prefix = config.get('lrgURL')
url = prefix + "%s.xml" % name
pendingurl = prefix + "pending/%s.xml" % name
@@ -849,10 +811,6 @@ class LRGRetriever(Retriever):
"""
Download an LRG record from an URL.
- Inherited variables from Db.Output.Config:
- - maxDldSize ; Maximum size of the file.
- - minDldSize ; Minimum size of the file.
-
@arg url: Location of the LRG record
@type url: string
@@ -872,7 +830,7 @@ class LRGRetriever(Retriever):
if info["Content-Type"] == "application/xml" and info.has_key("Content-length"):
length = int(info["Content-Length"])
- if self._config.minDldSize < length < self._config.maxDldSize:
+ if config.get('minDldSize') < length < config.get('maxDldSize'):
raw_data = handle.read()
handle.close()
diff --git a/mutalyzer/Scheduler.py b/mutalyzer/Scheduler.py
index cc10261d93cce18730550b3ae823ff1e177ffadf..ca30875f3fb979e7fcbe948b33cb0d760a2f1a2a 100644
--- a/mutalyzer/Scheduler.py
+++ b/mutalyzer/Scheduler.py
@@ -20,9 +20,9 @@ import smtplib # smtplib.STMP
from email.mime.text import MIMEText # MIMEText
import mutalyzer
+from mutalyzer import config
from mutalyzer import variantchecker
from mutalyzer.grammar import Grammar
-from mutalyzer.config import Config
from mutalyzer.output import Output
from mutalyzer.mapping import Converter
from mutalyzer import Retriever # Retriever.Retriever
@@ -34,7 +34,7 @@ __all__ = ["Scheduler"]
class Scheduler() :
"""
Special methods:
- - __init__(config, database) ;
+ - __init__(database) ;
Public methods:
- addJob(outputFilter, eMail, queue, fromHost, jobType, Arg1) ; Add a
@@ -47,21 +47,16 @@ class Scheduler() :
- Batch Position Converter
"""
- def __init__(self, config, database) :
+ def __init__(self, database) :
#TODO: documentation
"""
- Initialize the Scheduler, which requires a config object
- and a database connection.
+ Initialize the Scheduler, which requires a database connection.
@todo: documentation
- @arg config: Config object
- @type config: object
@arg database:
@type database:
"""
-
- self.__config = config
self.__database = database
self.__run = True
#__init__
@@ -89,10 +84,6 @@ class Scheduler() :
"""
Send an e-mail containing an url to a batch job submitter.
- Private variables:
- - __config ; The variables mailSubject and mailFrom
- are used.
-
@todo: Handle Connection errors in a try, except clause
@arg mailTo: The batch job submitter
@@ -127,13 +118,13 @@ Thanks for using Mutalyzer.
With kind regards,
Mutalyzer batch checker.""" % url)
- message["Subject"] = self.__config.mailSubject
- message["From"] = self.__config.mailFrom
+ message["Subject"] = config.get('mailSubject')
+ message["From"] = config.get('mailFrom')
message["To"] = mailTo
smtpInstance = smtplib.SMTP()
smtpInstance.connect()
- smtpInstance.sendmail(self.__config.mailFrom, mailTo,
+ smtpInstance.sendmail(config.get('mailFrom'), mailTo,
message.as_string())
smtpInstance.quit()
#__sendMail
@@ -364,9 +355,7 @@ Mutalyzer batch checker.""" % url)
@arg flags: Flags of the current entry
@type flags:
"""
-
- C = Config()
- O = Output(__file__, C.Output)
+ O = Output(__file__)
O.addMessage(__file__, -1, "INFO",
"Received NameChecker batchvariant " + cmd)
@@ -398,12 +387,12 @@ Mutalyzer batch checker.""" % url)
outputline += batchOutput[0]
#Output
- filename = "%s/Results_%s.txt" % (self.__config.resultsDir, i)
+ filename = "%s/Results_%s.txt" % (config.get('resultsDir'), i)
if not os.path.exists(filename) :
# If the file does not yet exist, create it with the correct
# header above it. The header is read from the config file as
# a list. We need a tab delimited string.
- header = self.__config.nameCheckOutHeader
+ header = config.get('nameCheckOutHeader')
handle = open(filename, 'a')
handle.write("%s\n" % "\t".join(header))
#if
@@ -436,9 +425,7 @@ Mutalyzer batch checker.""" % url)
@arg flags: Flags of the current entry
@type flags:
"""
-
- C = Config()
- output = Output(__file__, C.Output)
+ output = Output(__file__)
grammar = Grammar(output)
output.addMessage(__file__, -1, "INFO",
@@ -457,12 +444,12 @@ Mutalyzer batch checker.""" % url)
result = "|".join(output.getBatchMessages(3))
#Output
- filename = "%s/Results_%s.txt" % (self.__config.resultsDir, i)
+ filename = "%s/Results_%s.txt" % (config.get('resultsDir'), i)
if not os.path.exists(filename) :
# If the file does not yet exist, create it with the correct
# header above it. The header is read from the config file as
# a list. We need a tab delimited string.
- header = self.__config.syntaxCheckOutHeader
+ header = config.get('syntaxCheckOutHeader')
handle = open(filename, 'a')
handle.write("%s\n" % "\t".join(header))
#if
@@ -499,9 +486,7 @@ Mutalyzer batch checker.""" % url)
@arg flags: Flags of the current entry
@type flags:
"""
-
- C = Config()
- O = Output(__file__, C.Output)
+ O = Output(__file__)
variant = cmd
variants = None
gName = ""
@@ -559,12 +544,12 @@ Mutalyzer batch checker.""" % url)
error = "%s" % "|".join(O.getBatchMessages(3))
#Output
- filename = "%s/Results_%s.txt" % (self.__config.resultsDir, i)
+ filename = "%s/Results_%s.txt" % (config.get('resultsDir'), i)
if not os.path.exists(filename) :
# If the file does not yet exist, create it with the correct
# header above it. The header is read from the config file as
# a list. We need a tab delimited string.
- header = self.__config.positionConverterOutHeader
+ header = config.get('positionConverterOutHeader')
handle = open(filename, 'a')
handle.write("%s\n" % "\t".join(header))
#if
@@ -598,9 +583,7 @@ Mutalyzer batch checker.""" % url)
@arg flags: Flags of the current entry
@type flags:
"""
-
- C = Config()
- O = Output(__file__, C.Output)
+ O = Output(__file__)
O.addMessage(__file__, -1, "INFO",
"Received SNP converter batch rs" + cmd)
@@ -610,7 +593,7 @@ Mutalyzer batch checker.""" % url)
descriptions = []
if not skip :
- R = Retriever.Retriever(C.Retriever, O, None)
+ R = Retriever.Retriever(O, None)
descriptions = R.snpConvert(cmd)
# Todo: Is output ok?
@@ -619,12 +602,12 @@ Mutalyzer batch checker.""" % url)
outputline += "%s\t" % "|".join(O.getBatchMessages(3))
#Output
- filename = "%s/Results_%s.txt" % (self.__config.resultsDir, i)
+ filename = "%s/Results_%s.txt" % (config.get('resultsDir'), i)
if not os.path.exists(filename) :
# If the file does not yet exist, create it with the correct
# header above it. The header is read from the config file as
# a list. We need a tab delimited string.
- header = self.__config.snpConverterOutHeader
+ header = config.get('snpConverterOutHeader')
handle = open(filename, 'a')
handle.write("%s\n" % "\t".join(header))
#if
diff --git a/mutalyzer/config.py b/mutalyzer/config.py
index cb98f726eaf8cc761243400b8d3bb571fdeda4c9..ae7f8cb0d6520485bf185b0fe07a00dc11c08d58 100644
--- a/mutalyzer/config.py
+++ b/mutalyzer/config.py
@@ -1,13 +1,26 @@
"""
-Module for reading the config file and splitting up the variables into
-subclasses. Each of these subclasses are used to configure a specific
-module.
+Module for reading the configuration values from configuration files.
+
+All communication with this module should be done by using the get function
+which returns a configuration value, given a name.
+
+Reading the configuration file is implemented lazily and as such done upon the
+first call to the get function.
+
+Configuration values are read from two locations, in this order:
+1) /etc/mutalyzer/config
+2) $XDG_CONFIG_HOME/mutalyzer/config
+
+If both files exist, values defined in the second overwrite values defined in
+the first.
"""
import os
from configobj import ConfigObj
+from mutalyzer.util import singleton
+
SYSTEM_CONFIGURATION = '/etc/mutalyzer/config'
USER_CONFIGURATION = os.path.join(
@@ -17,22 +30,36 @@ USER_CONFIGURATION = os.path.join(
class ConfigurationError(Exception):
+ """
+ Raised when a configuration file cannot be read.
+ """
pass
-class Config():
+def get(name):
+ """
+ Get a configuration value by name.
+
+ @arg name: Name for the configuration value.
+ @type name: string
+
+ @raise ConfigurationError: If configuration value could not be read.
+ Reasons are:
+ - Configuration file could not be parsed.
+ - Not all variables are present in configuration file.
+ - Given configuration value name does not exist.
"""
- Read the configuration file and store the data in subclasses.
+ return _Config().get(name)
+
+
+@singleton
+class _Config():
"""
- class Retriever(): pass
- class Db(): pass
- class Output(): pass
- class Mutator(): pass
- class Scheduler(): pass
- class Batch(): pass
- class File(): pass
- class GenRecord(): pass
+ Read the configuration file and provide access to its values.
+ Please note the limitations from the use of the @singleton decorator as
+ described in its docstring.
+ """
def __init__(self, filename=None):
"""
Initialise the class with variables read from the configuration
@@ -51,10 +78,6 @@ class Config():
is set. In that case, the locations listed above are ignored and the
configuration is read from {filename}.
- By the DRY-principle, we don't enumerate the configuration variables
- for each class in documentation. Instead, what variables are used by
- each class is easy to see from the code below.
-
@kwarg filename: Optional filename to read configuration from. If
present, this overrides automatic detection of configuration file
location.
@@ -85,58 +108,53 @@ class Config():
try:
- # Set the variables needed by the Retriever module.
- self.Retriever.email = config["email"]
- self.Retriever.cache = config["cache"]
- self.Retriever.cachesize = int(config["cachesize"]) * 1048576
- self.Retriever.maxDldSize = int(config["maxDldSize"]) * 1048576
- self.Retriever.minDldSize = int(config["minDldSize"])
- self.Retriever.lrgURL = config["lrgurl"]
-
- # Set the variables needed by the Db module.
- self.Db.internalDb = config["internalDb"]
- self.Db.dbNames = config["dbNames"]
- self.Db.LocalMySQLuser = config["LocalMySQLuser"]
- self.Db.LocalMySQLhost = config["LocalMySQLhost"]
-
- # Set the variables needed by the Output module.
- self.Output.log = config["log"]
- self.Output.datestring = config["datestring"]
- self.Output.loglevel = int(config["loglevel"])
- self.Output.outputlevel = int(config["outputlevel"])
- self.Output.debug = config.as_bool('debug')
-
- # Set the variables needed by the Mutator module.
- self.Mutator.flanksize = int(config["flanksize"])
- self.Mutator.maxvissize = int(config["maxvissize"])
- self.Mutator.flankclipsize = int(config["flankclipsize"])
-
- # Set the variables needed by the Scheduler module.
- self.Scheduler.mailFrom = config["mailFrom"]
- self.Scheduler.mailSubject = config["mailSubject"]
- self.Scheduler.resultsDir = config["resultsDir"]
- self.Scheduler.nameCheckOutHeader = config["nameCheckOutHeader"]
- self.Scheduler.syntaxCheckOutHeader = config["syntaxCheckOutHeader"]
- self.Scheduler.positionConverterOutHeader = config["positionConverterOutHeader"]
- self.Scheduler.snpConverterOutHeader = config["snpConverterOutHeader"]
-
- # Set thte variables neede for the Batch module.
- self.Batch.PIDfile = config["PIDfile"]
- self.Batch.batchInputMaxSize = int(config["batchInputMaxSize"]) * 1048576
-
- # Set the variables needed by the File module.
- self.File.bufSize = int(config["bufSize"])
- self.File.header = config["header"]
- self.File.threshold = float(config["threshold"])
-
- # Set the variables needed by the File module.
- self.GenRecord.spliceAlarm = int(config["spliceAlarm"])
- self.GenRecord.spliceWarn = int(config["spliceWarn"])
+ # We explicitely read all configuration values ad store them in
+ # our own dictionary. This makes sure we notice missing or
+ # incorrect values upon instantiation.
+
+ # A few 'special' values.
+ self._values = {'debug': config.as_bool('debug'),
+ 'threshold': float(config['threshold'])}
+
+ # Simple string values.
+ for name in ('email', 'cache', 'lrgurl', 'internalDb', 'dbNames',
+ 'LocalMySQLuser', 'LocalMySQLhost', 'log',
+ 'datestring', 'mailFrom', 'mailSubject',
+ 'resultsDir', 'nameCheckOutHeader',
+ 'syntaxCheckOutHeader', 'positionConverterOutHeader',
+ 'snpConverterOutHeader', 'PIDfile', 'header'):
+ self._values[name] = config[name]
+
+ # Simple integer values.
+ for name in ('minDldSize', 'loglevel', 'outputlevel', 'flanksize',
+ 'maxvissize', 'flankclipsize', 'bufSize',
+ 'spliceAlarm', 'spliceWarn'):
+ self._values[name] = int(config[name])
+
+ # File sizes (given in megabytes, stored in bytes).
+ for name in ('cachesize', 'maxDldSize', 'batchInputMaxSize'):
+ self._values[name] = int(config[name]) * 1048576
except KeyError as e:
raise ConfigurationError('Missing configuration value: %s' % e)
#__init__
+ def get(self, name):
+ """
+ Get a configuration value by name.
+
+ @arg name: Name for the configuration value.
+ @type name: string
+
+ @raise ConfigurationError: If given configuration value name does not
+ exist.
+ """
+ try:
+ return self._values[name]
+ except KeyError:
+ raise ConfigurationError('No such configuration value: %s' % name)
+ #get
+
def _load_config(self, filename):
"""
Create a ConfigObj from the configuration in {filename}.
@@ -150,4 +168,4 @@ class Config():
raise ConfigurationError('Could not parse configuration file: %s' \
% filename)
#_load_config
-#Config
+#_Config
diff --git a/mutalyzer/mapping.py b/mutalyzer/mapping.py
index 28dc5406e9d6760eca3cb98b16e4d215516c063d..584541f5aa993d315eaeef7cf52b8901f3416d80 100644
--- a/mutalyzer/mapping.py
+++ b/mutalyzer/mapping.py
@@ -41,22 +41,19 @@ class Converter(object) :
@todo: Refactor anything using {mutalyzer.models} into the {webservice}
module.
"""
- def __init__(self, build, C, O) :
+ def __init__(self, build, O) :
"""
Initialise the class.
@arg build: the genome build version of the organism (e.g. hg19 for
human genome build version 19)
@type build: string
- @arg C: crossmapper object
- @type C: object
@arg O: output object
@type O: object
"""
self.build = None
self.__output = O
- self.__config = C
- self.__database = Db.Mapping(build, C.Db)
+ self.__database = Db.Mapping(build)
# Populated arguments
self.parseTree = None
@@ -609,17 +606,14 @@ class Updater(object):
information into the 'MappingTemp' table. The {merge} method merges this
table into the real 'Mapping' table.
"""
- def __init__(self, build, config):
+ def __init__(self, build):
"""
@arg build: Human genome build (or database name), i.e. 'hg18' or
'hg19'.
@type build: string
- @arg config: A configuration object.
- @type config: mutalyzer.config.Config
"""
self.build = build
- self.config = config
- self.db = Db.Mapping(build, config.Db)
+ self.db = Db.Mapping(build)
#__init__
def load(self, *args, **kwargs):
@@ -649,7 +643,7 @@ class NCBIUpdater(Updater):
Example usage:
- >>> updater = NCBIUpdater('hg19', mutalyzer.config.Config())
+ >>> updater = NCBIUpdater('hg19')
>>> updater.load('/tmp/seq_gene.md', 'GRCh37.p2-Primary Assembly')
>>> updater.merge()
@@ -659,16 +653,14 @@ class NCBIUpdater(Updater):
'feature_name', 'feature_id', 'feature_type', 'group_label',
'transcript', 'evidence_code']
- def __init__(self, build, config):
+ def __init__(self, build):
"""
@arg build: Human genome build (or database name), i.e. 'hg18' or
'hg19'.
@type build: string
- @arg config: A configuration object.
- @type config: mutalyzer.config.Config
"""
self.exon_backlog = {}
- super(NCBIUpdater, self).__init__(build, config)
+ super(NCBIUpdater, self).__init__(build)
#__init__
def load(self, mapping_file, assembly):
diff --git a/mutalyzer/mutator.py b/mutalyzer/mutator.py
index 9065205016dfb634fd5c24f3d115f0a5285ba491..2a59c8b7db5ed6bfa360963ce302e07a4cceaa4c 100644
--- a/mutalyzer/mutator.py
+++ b/mutalyzer/mutator.py
@@ -12,12 +12,14 @@ The original as well as the mutated string are stored here.
"""
-from mutalyzer import util
from Bio import Restriction
from Bio.Seq import Seq
from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
from Bio.Seq import reverse_complement
+from mutalyzer import util
+from mutalyzer import config
+
class Mutator() :
"""
@@ -28,7 +30,6 @@ class Mutator() :
'addedRestrictionSites' respectively.
Private variables:
- - __config ; Configuration variables of this class.
- __output ; The output object.
- __shift ; A sorted list of tuples (position, shiftsize)
where the modifications in length are stored.
@@ -72,13 +73,11 @@ class Mutator() :
position pos1 to pos2.
"""
- def __init__(self, orig, config, output) :
+ def __init__(self, orig, output) :
"""
Initialise the class with the original string.
Private variables (altered):
- - __config ; Initialised with the configuration
- variables.
- __output ; Initialised with the output object.
- __shift ; Initialised to the empty list.
- __restrictionBatch ; Initialised to a default set of
@@ -90,13 +89,9 @@ class Mutator() :
@arg orig: The original string before mutation
@type orig: string
- @arg config: Configuration variables
- @type config: object
@arg output: The output object
@type output: object
"""
-
- self.__config = config
self.__output = output
self.__shift = []
self.__removed_sites = set()
@@ -214,8 +209,6 @@ class Mutator() :
we perform the alteration.
Private variables:
- - __config ; The variables maxvissize, flanksize and flankclipsize
- are used in the visualisation.
- __output ; Visualisation information is added.
Public variables (altered):
@@ -237,8 +230,8 @@ class Mutator() :
# This part is for visualisation.
#
- loflank = self.orig[max(pos1 - self.__config.flanksize, 0):pos1]
- roflank = self.orig[pos2:pos2 + self.__config.flanksize]
+ loflank = self.orig[max(pos1 - config.get('flanksize'), 0):pos1]
+ roflank = self.orig[pos2:pos2 + config.get('flanksize')]
delPart = self.orig[pos1:pos2]
#odel = delPart
#if len(odel) > self.__config.maxvissize :
@@ -249,8 +242,8 @@ class Mutator() :
bp1 = self.shiftpos(pos1)
bp2 = self.shiftpos(pos2)
- lmflank = self.mutated[max(bp1 - self.__config.flanksize, 0):bp1]
- rmflank = self.mutated[bp2:bp2 + self.__config.flanksize]
+ lmflank = self.mutated[max(bp1 - config.get('flanksize'), 0):bp1]
+ rmflank = self.mutated[bp2:bp2 + config.get('flanksize')]
#insvis = ins
#if len(ins) > self.__config.maxvissize :
@@ -304,10 +297,10 @@ class Mutator() :
@rtype: string
"""
- if len(string) > self.__config.maxvissize :
- return "%s [%ibp] %s" % (string[:self.__config.flankclipsize],
- len(string) - self.__config.flankclipsize * 2,
- string[-self.__config.flankclipsize:])
+ if len(string) > config.get('maxvissize'):
+ return "%s [%ibp] %s" % (string[:config.get('flankclipsize')],
+ len(string) - config.get('flankclipsize') * 2,
+ string[-config.get('flankclipsize'):])
return string
#visualiseIns
diff --git a/mutalyzer/output.py b/mutalyzer/output.py
index 53bedeed5aa127318bfdfdb3f41535e2b011effd..04d552b1d0bdc8186183785319a68544bee8676f 100644
--- a/mutalyzer/output.py
+++ b/mutalyzer/output.py
@@ -26,6 +26,7 @@ Public classes:
import time
from mutalyzer import util
+from mutalyzer import config
from mutalyzer.models import SoapMessage
@@ -34,7 +35,6 @@ class Output() :
Provide an output interface for errors, warnings and logging purposes.
Private variables:
- - __config ; Configuration variables.
- __outputdata ; The output dictionary.
- __messages ; The messages list.
- __instance ; The name of the module that made this object.
@@ -43,10 +43,9 @@ class Output() :
- __warnings ; The number of warnings that have been processed.
Special methods:
- - __init__(instance, config) ; Initialise the class with variables
- from the config file and the calling
- module.
- - __del__() ; Close the logfile and clean up.
+ - __init__(instance) ; Initialise the class with the calling
+ module.
+ - __del__() ; Close the logfile and clean up.
Public methods:
- addMessage(filename, level, code, description) ; Add a message to
@@ -59,13 +58,11 @@ class Output() :
and warnings.
"""
- def __init__(self, instance, config) :
+ def __init__(self, instance):
"""
- Initialise the class private variables with variables from the
- config file and the calling module.
+ Initialise the class with the calling module.
Private variables (altered):
- - __config ; Configuration variables.
- __outputdata ; The output dictionary.
- __messages ; The messages list.
- __instance ; Initialised with the name of the module that
@@ -77,15 +74,11 @@ class Output() :
@arg instance: The filename of the module that created this object
@type instance: string
- @arg config: The configuration object
- @type config: object
"""
-
- self.__config = config
self.__outputData = {}
self.__messages = []
self.__instance = util.nice_filename(instance)
- self.__loghandle = open(self.__config.log, "a+")
+ self.__loghandle = open(config.get('log'), "a+")
self.__errors = 0
self.__warnings = 0
#__init__
@@ -120,7 +113,6 @@ class Output() :
Private variables:
- __messages ; The messages list.
- __instance ; Module that created the Output object.
- - __config ; The variables loglevel and datestring are used.
- __loghandle ; Handle to the log file.
Private variables (altered):
@@ -145,9 +137,9 @@ class Output() :
# Log the message if the message is important enough, or if it is only
# meant to be logged (level -1).
- if level >= self.__config.loglevel or level == -1 :
+ if level >= config.get('loglevel') or level == -1 :
self.__loghandle.write(time.strftime(
- self.__config.datestring + ' ') + "%s (%s) %s: %s: %s\n" % (
+ config.get('datestring') + ' ') + "%s (%s) %s: %s: %s\n" % (
self.__instance, nice_name, code, message.named_level(),
description))
self.__loghandle.flush()
@@ -160,12 +152,11 @@ class Output() :
Private variables:
- __messages ; The messages list.
- - __config ; The variable outputlevel is used.
@return: A list of messages
@rtype: list
"""
- return filter(lambda m: m.level >= self.__config.outputlevel,
+ return filter(lambda m: m.level >= config.get('outputlevel'),
self.__messages)
#getMessages
diff --git a/mutalyzer/parsers/genbank.py b/mutalyzer/parsers/genbank.py
index 060e9a5277c5e35c02cf5667f2daf9366e2de725..8f640f618c72b37bd16c1f513cc626943c8e6651 100644
--- a/mutalyzer/parsers/genbank.py
+++ b/mutalyzer/parsers/genbank.py
@@ -8,7 +8,7 @@ import bz2
from Bio import SeqIO, Entrez
from Bio.Alphabet import ProteinAlphabet
-from mutalyzer.config import Config
+from mutalyzer import config
from mutalyzer import Db
from mutalyzer.GenRecord import PList, Locus, Gene, Record, GenRecord
@@ -52,17 +52,11 @@ class GBparser():
"""
Initialise the class
- Public variables:
- - config ; Config object.
-
Private variables:
- __database ; Db.Cache object
-
- @requires: Config
"""
- config = Config()
- Entrez.email = config.Retriever.email
- self.__database = Db.Cache(config.Db)
+ Entrez.email = config.get('email')
+ self.__database = Db.Cache()
#__init__
def __location2pos(self, location):
diff --git a/mutalyzer/sync.py b/mutalyzer/sync.py
index 2a96446bf2b268e284c1a9b0db6dca4349c20d27..ae3622b33732386cf196e3bbf4174920903246d0 100644
--- a/mutalyzer/sync.py
+++ b/mutalyzer/sync.py
@@ -11,6 +11,7 @@ from datetime import datetime, timedelta
import urllib2
from suds.client import Client
+from mutalyzer import config
from mutalyzer import Retriever
@@ -21,18 +22,15 @@ class CacheSync(object):
"""
Synchronize the database cache with other Mutalyzer instances.
"""
- def __init__(self, config, output, database):
+ def __init__(self, output, database):
"""
Instantiate the object.
- @arg config: A configuration object.
- @type config: mutalyzer.config.Config.Retriever
@arg output: An output object.
@type output: mutalyzer.output.Output
@arg database: A database object.
@type database: mutalyzer.Db.Cache
"""
- self._config = config
self._output = output
self._database = database
@@ -60,7 +58,7 @@ class CacheSync(object):
for entry in entries:
# Note that this way we only include Genbank files, not LRG files.
cached = None
- if os.path.isfile(os.path.join(self._config.cache,
+ if os.path.isfile(os.path.join(config.get('cache'),
'%s.gb.bz2' % entry[0])):
cached = '%s.gb' % entry[0]
cache.append({'name': entry[0],
@@ -135,9 +133,7 @@ class CacheSync(object):
handle.close()
# Store remote data
- retriever = Retriever.GenBankRetriever(self._config,
- self._output,
- self._database)
+ retriever = Retriever.GenBankRetriever(self._output, self.database)
retriever.write(data, name, 0)
def sync_with_remote(self, remote_wsdl, url_template,
diff --git a/mutalyzer/util.py b/mutalyzer/util.py
index 0918d4c2af139fba75c0a71d2d12c5fc8e9aed31..8738bbca0ee1650fb0ea9517a45be36c117d5b3a 100644
--- a/mutalyzer/util.py
+++ b/mutalyzer/util.py
@@ -1,20 +1,20 @@
"""
General utility functions.
-@todo: All these functions come from the old Mutalyzer.py file. Try to find
- general utility functions in other modules too.
+@todo: Most of these functions come from the old Mutalyzer.py file. Try to
+ find general utility functions in other modules too.
@todo: Use exceptions for failure handling.
@todo: End vs stop. I guess we should use start/stop (end goes with beginning).
- Or first/last, or acceptor/donor. Anyway, CDS is always denoted with
- start/stop. Important thing is that the semantics should be clear.
- Idea:
- * CDS -> use start/stop
- * splice sites or exons -> acceptor/donor
- * translation -> begin/end
- * any range of bases -> first/last
- * interbase position (if two numbers are used) -> before/after
+ Or first/last, or acceptor/donor. Anyway, CDS is always denoted with
+ start/stop. Important thing is that the semantics should be clear.
+ Idea:
+ * CDS -> use start/stop
+ * splice sites or exons -> acceptor/donor
+ * translation -> begin/end
+ * any range of bases -> first/last
+ * interbase position (if two numbers are used) -> before/after
@todo: We can also group this in separate files in a util/ directory, according
- to function (e.g. util/sequences.py, util/positioning.py, etc).
+ to function (e.g. util/sequences.py, util/positioning.py, etc).
@todo: Unit tests (some can directly be extracted from the docstring).
"""
@@ -788,6 +788,27 @@ def skip(f):
#skip
+def singleton(cls):
+ """
+ Decorator to define a class with a singleton instance.
+
+ Note that this decorator makes cls a function instead of a class and
+ things like super() and classmethods won't work anymore. So be carefull
+ with this and certainly don't use it with subclassing.
+
+ By Shane Hathaway, taken from PEP318 [1].
+
+ [1] http://www.python.org/dev/peps/pep-0318/#examples
+ """
+ instances = {}
+ def getinstance():
+ if cls not in instances:
+ instances[cls] = cls()
+ return instances[cls]
+ return getinstance
+#singleton
+
+
def monkey_patch_suds():
"""
Apply our monkey-patch for the suds package.
diff --git a/mutalyzer/variantchecker.py b/mutalyzer/variantchecker.py
index 8b7eb9e7091513288f413a604fc14a70df517a64..7ece5cbe3c72d025b7506077baba375742296937 100644
--- a/mutalyzer/variantchecker.py
+++ b/mutalyzer/variantchecker.py
@@ -1432,7 +1432,7 @@ def process_variant(mutator, description, record, output):
#process_variant
-def check_variant(description, config, output):
+def check_variant(description, output):
"""
Check the variant described by {description} according to the HGVS variant
nomenclature and populate the {output} object with various information
@@ -1440,8 +1440,6 @@ def check_variant(description, config, output):
@arg description: Variant description in HGVS notation.
@type description: string
- @arg config: A configuration object.
- @type config: Modules.Config.Config
@arg output: An output object.
@type output: Modules.Output.Output
@@ -1471,12 +1469,12 @@ def check_variant(description, config, output):
gene_symbol = transcript_id = ''
- database = Db.Cache(config.Db)
+ database = Db.Cache()
if parsed_description.LrgAcc:
filetype = 'LRG'
record_id = parsed_description.LrgAcc
transcript_id = parsed_description.LRGTranscriptID
- retriever = Retriever.LRGRetriever(config.Retriever, output, database)
+ retriever = Retriever.LRGRetriever(output, database)
else:
filetype = 'GB'
if parsed_description.Gene:
@@ -1485,8 +1483,7 @@ def check_variant(description, config, output):
if parsed_description.Gene.ProtIso:
output.addMessage(__file__, 4, 'EPROT', 'Indexing by ' \
'protein isoform is not supported.')
- retriever = Retriever.GenBankRetriever(config.Retriever, output,
- database)
+ retriever = Retriever.GenBankRetriever(output, database)
retrieved_record = retriever.loadrecord(record_id)
@@ -1506,7 +1503,7 @@ def check_variant(description, config, output):
output.addOutput('preColon', description.split(':')[0])
output.addOutput('variant', description.split(':')[-1])
- record = GenRecord.GenRecord(output, config.GenRecord)
+ record = GenRecord.GenRecord(output)
record.record = retrieved_record
record.checkRecord()
@@ -1530,7 +1527,7 @@ def check_variant(description, config, output):
# Note: The GenRecord instance is carrying the sequence in .record.seq.
# So is the Mutator instance in .mutator.orig.
- mutator = Mutator(record.record.seq, config.Mutator, output)
+ mutator = Mutator(record.record.seq, output)
# Todo: If processing of the variant fails, we might still want to show
# information about the record, gene, transcript.
diff --git a/mutalyzer/webservice.py b/mutalyzer/webservice.py
index e969c04249cd6a823e57662a28edc77808a3ebe8..4c87b5e901a0fe994b00ad9537c77f84a31fc1e5 100644
--- a/mutalyzer/webservice.py
+++ b/mutalyzer/webservice.py
@@ -32,7 +32,7 @@ import socket
from operator import itemgetter, attrgetter
import mutalyzer
-from mutalyzer.config import Config
+from mutalyzer import config
from mutalyzer.output import Output
from mutalyzer.grammar import Grammar
from mutalyzer.sync import CacheSync
@@ -51,7 +51,6 @@ class MutalyzerService(DefinitionBase):
These methods are made public via a SOAP interface.
"""
def __init__(self, environ=None):
- self._config = Config()
super(MutalyzerService, self).__init__(environ)
#__init__
@@ -68,7 +67,7 @@ class MutalyzerService(DefinitionBase):
@type build: string
"""
- if not build in self._config.Db.dbNames :
+ if not build in config.get('dbNames'):
L.addMessage(__file__, 4, "EARG", "EARG %s" % build)
raise Fault("EARG",
"The build argument (%s) was not a valid " \
@@ -162,14 +161,14 @@ class MutalyzerService(DefinitionBase):
@return: A list of transcripts.
@rtype: list
"""
- L = Output(__file__, self._config.Output)
+ L = Output(__file__)
L.addMessage(__file__, -1, "INFO",
"Received request getTranscripts(%s %s %s %s)" % (build,
chrom, pos, versions))
self.__checkBuild(L, build)
- D = Db.Mapping(build, self._config.Db)
+ D = Db.Mapping(build)
self.__checkChrom(L, D, chrom)
self.__checkPos(L, pos)
@@ -198,14 +197,14 @@ class MutalyzerService(DefinitionBase):
"""
Todo: documentation.
"""
- L = Output(__file__, self._config.Output)
+ L = Output(__file__)
L.addMessage(__file__, -1, "INFO",
"Received request getTranscriptsByGene(%s %s)" % (build,
name))
self.__checkBuild(L, build)
- D = Db.Mapping(build, self._config.Db)
+ D = Db.Mapping(build)
ret = D.get_TranscriptsByGeneName(name)
@@ -244,13 +243,13 @@ class MutalyzerService(DefinitionBase):
@return: A list of transcripts.
@rtype: list
"""
- L = Output(__file__, self._config.Output)
+ L = Output(__file__)
L.addMessage(__file__, -1, "INFO",
"Received request getTranscriptsRange(%s %s %s %s %s)" % (build,
chrom, pos1, pos2, method))
- D = Db.Mapping(build, self._config.Db)
+ D = Db.Mapping(build)
self.__checkBuild(L, build)
ret = D.get_Transcripts(chrom, pos1, pos2, method)
@@ -279,12 +278,12 @@ class MutalyzerService(DefinitionBase):
@return: The name of the associated gene.
@rtype: string
"""
- L = Output(__file__, self._config.Output)
+ L = Output(__file__)
L.addMessage(__file__, -1, "INFO",
"Received request getGeneName(%s %s)" % (build, accno))
- D = Db.Mapping(build, self._config.Db)
+ D = Db.Mapping(build)
self.__checkBuild(L, build)
ret = D.get_GeneName(accno.split('.')[0])
@@ -338,13 +337,13 @@ class MutalyzerService(DefinitionBase):
- type ; The mutation type.
@rtype: object
"""
- L = Output(__file__, self._config.Output)
+ L = Output(__file__)
L.addMessage(__file__, -1, "INFO",
"Reveived request mappingInfo(%s %s %s %s)" % (
LOVD_ver, build, accNo, variant))
- conv = Converter(build, self._config, L)
+ conv = Converter(build, L)
result = conv.mainMapping(accNo, variant)
L.addMessage(__file__, -1, "INFO",
@@ -376,13 +375,13 @@ class MutalyzerService(DefinitionBase):
- CDS_stop ; CDS stop in I{c.} notation.
@rtype: object
"""
- O = Output(__file__, self._config.Output)
+ O = Output(__file__)
O.addMessage(__file__, -1, "INFO",
"Received request transcriptInfo(%s %s %s)" % (LOVD_ver,
build, accNo))
- converter = Converter(build, self._config, O)
+ converter = Converter(build, O)
T = converter.mainTranscript(accNo)
O.addMessage(__file__, -1, "INFO",
@@ -404,8 +403,8 @@ class MutalyzerService(DefinitionBase):
@return: The accession number of a chromosome.
@rtype: string
"""
- D = Db.Mapping(build, self._config.Db)
- L = Output(__file__, self._config.Output)
+ D = Db.Mapping(build)
+ L = Output(__file__)
L.addMessage(__file__, -1, "INFO",
"Received request chromAccession(%s %s)" % (build, name))
@@ -436,8 +435,8 @@ class MutalyzerService(DefinitionBase):
@return: The name of a chromosome.
@rtype: string
"""
- D = Db.Mapping(build, self._config.Db)
- L = Output(__file__, self._config.Output)
+ D = Db.Mapping(build)
+ L = Output(__file__)
L.addMessage(__file__, -1, "INFO",
"Received request chromName(%s %s)" % (build, accNo))
@@ -468,8 +467,8 @@ class MutalyzerService(DefinitionBase):
@return: The name of a chromosome.
@rtype: string
"""
- D = Db.Mapping(build, self._config.Db)
- L = Output(__file__, self._config.Output)
+ D = Db.Mapping(build)
+ L = Output(__file__)
L.addMessage(__file__, -1, "INFO",
"Received request getchromName(%s %s)" % (build, acc))
@@ -504,12 +503,12 @@ class MutalyzerService(DefinitionBase):
@return: The variant(s) in either I{g.} or I{c.} notation.
@rtype: list
"""
- D = Db.Mapping(build, self._config.Db)
- O = Output(__file__, self._config.Output)
+ D = Db.Mapping(build)
+ O = Output(__file__)
O.addMessage(__file__, -1, "INFO",
"Received request cTogConversion(%s %s)" % (
build, variant))
- converter = Converter(build, self._config, O)
+ converter = Converter(build, O)
variant = converter.correctChrVariant(variant)
if "c." in variant :
@@ -539,7 +538,7 @@ class MutalyzerService(DefinitionBase):
- messages: List of (error) messages as strings.
@rtype: object
"""
- output = Output(__file__, self._config.Output)
+ output = Output(__file__)
output.addMessage(__file__, -1, "INFO",
"Received request checkSyntax(%s)" % (variant))
@@ -569,10 +568,10 @@ class MutalyzerService(DefinitionBase):
"""
Todo: documentation.
"""
- O = Output(__file__, self._config.Output)
+ O = Output(__file__)
O.addMessage(__file__, -1, "INFO",
"Received request runMutalyzer(%s)" % (variant))
- variantchecker.check_variant(variant, self._config, O)
+ variantchecker.check_variant(variant, O)
result = MutalyzerOutput()
@@ -630,16 +629,16 @@ class MutalyzerService(DefinitionBase):
"""
Todo: documentation.
"""
- O = Output(__file__, self._config.Output)
- D = Db.Cache(self._config.Db)
+ O = Output(__file__)
+ D = Db.Cache()
O.addMessage(__file__, -1, "INFO",
"Received request getGeneAndTranscript(%s, %s)" % (genomicReference,
transcriptReference))
- retriever = Retriever.GenBankRetriever(self._config.Retriever, O, D)
+ retriever = Retriever.GenBankRetriever(O, D)
record = retriever.loadrecord(genomicReference)
- GenRecordInstance = GenRecord.GenRecord(O, self._config.GenRecord)
+ GenRecordInstance = GenRecord.GenRecord(O)
GenRecordInstance.record = record
GenRecordInstance.checkRecord()
@@ -696,16 +695,16 @@ class MutalyzerService(DefinitionBase):
- id
- product
"""
- O = Output(__file__, self._config.Output)
- D = Db.Cache(self._config.Db)
+ O = Output(__file__)
+ D = Db.Cache()
O.addMessage(__file__, -1, "INFO",
"Received request getTranscriptsAndInfo(%s)" % genomicReference)
- retriever = Retriever.GenBankRetriever(self._config.Retriever, O, D)
+ retriever = Retriever.GenBankRetriever(O, D)
record = retriever.loadrecord(genomicReference)
# Todo: If loadRecord failed (e.g. DTD missing), we should abort here.
- GenRecordInstance = GenRecord.GenRecord(O, self._config.GenRecord)
+ GenRecordInstance = GenRecord.GenRecord(O)
GenRecordInstance.record = record
GenRecordInstance.checkRecord()
@@ -810,9 +809,9 @@ class MutalyzerService(DefinitionBase):
"""
Todo: documentation, error handling, argument checking, tests.
"""
- O = Output(__file__, self._config.Output)
- D = Db.Cache(self._config.Db)
- retriever = Retriever.GenBankRetriever(self._config.Retriever, O, D)
+ O = Output(__file__)
+ D = Db.Cache()
+ retriever = Retriever.GenBankRetriever(O, D)
O.addMessage(__file__, -1, "INFO",
"Received request sliceChromosomeByGene(%s, %s, %s, %s)" % (
@@ -839,9 +838,9 @@ class MutalyzerService(DefinitionBase):
"""
Todo: documentation, error handling, argument checking, tests.
"""
- O = Output(__file__, self._config.Output)
- D = Db.Cache(self._config.Db)
- retriever = Retriever.GenBankRetriever(self._config.Retriever, O, D)
+ O = Output(__file__)
+ D = Db.Cache()
+ retriever = Retriever.GenBankRetriever(O, D)
O.addMessage(__file__, -1, "INFO",
"Received request sliceChromosome(%s, %s, %s, %s)" % (
@@ -875,7 +874,7 @@ class MutalyzerService(DefinitionBase):
- contactEmail: The email address to contact for more information.
@rtype: object
"""
- output = Output(__file__, self._config.Output)
+ output = Output(__file__)
output.addMessage(__file__, -1, 'INFO', 'Received request info')
result = InfoOutput()
@@ -913,13 +912,13 @@ class MutalyzerService(DefinitionBase):
This method is intended to be used by Mutalyzer itself to synchronize
the cache between installations on different servers.
"""
- output = Output(__file__, self._config.Output)
+ output = Output(__file__)
output.addMessage(__file__, -1, 'INFO',
'Received request getCache')
- database = Db.Cache(self._config.Db)
- sync = CacheSync(self._config.Retriever, output, database)
+ database = Db.Cache()
+ sync = CacheSync(output, database)
cache = sync.local_cache(created_since)
@@ -948,12 +947,12 @@ class MutalyzerService(DefinitionBase):
@return: List of HGVS descriptions.
@rtype: list(string)
"""
- output = Output(__file__, self._config.Output)
+ output = Output(__file__)
output.addMessage(__file__, -1, 'INFO',
'Received request getdbSNPDescription(%s)' % rs_id)
- retriever = Retriever.Retriever(self._config.Retriever, output, None)
+ retriever = Retriever.Retriever(output, None)
descriptions = retriever.snpConvert(rs_id)
output.addMessage(__file__, -1, 'INFO',
diff --git a/mutalyzer/website.py b/mutalyzer/website.py
index 03e946a009d4f57862e9102551c3e537b4bf63e5..bd3328a01236949ddf6b0692404876d96c0a3248 100644
--- a/mutalyzer/website.py
+++ b/mutalyzer/website.py
@@ -30,7 +30,7 @@ from simpletal import simpleTAL
import mutalyzer
from mutalyzer import util
-from mutalyzer.config import Config
+from mutalyzer import config
from mutalyzer.grammar import Grammar
from mutalyzer import webservice
from mutalyzer import variantchecker
@@ -42,12 +42,8 @@ from mutalyzer import Retriever
from mutalyzer import File
-# Load configuration from configuration file
-config = Config()
-
-
# Show web.py debugging information.
-web.config.debug = config.Output.debug
+web.config.debug = config.get('debug')
# URL dispatch table
@@ -167,7 +163,7 @@ render = render_tal(os.path.join(mutalyzer.package_root(), 'templates'),
'nomenclatureVersion': mutalyzer.NOMENCLATURE_VERSION,
'releaseDate': mutalyzer.__date__,
'release': mutalyzer.RELEASE,
- 'contactEmail': config.Retriever.email})
+ 'contactEmail': config.get('email')})
# web.py application
app = web.application(urls, globals(), autoreload=False)
@@ -240,7 +236,7 @@ class Downloads:
if not os.path.isfile(file_path):
raise web.notfound()
handle = open(file_path)
- F = File.File(config.File, None)
+ F = File.File(None)
web.header('Content-Type', F.getMimeType(handle)[0])
web.header('Content-Disposition', 'attachment; filename="%s"' % file)
return handle.read()
@@ -263,7 +259,7 @@ class Reference:
The url routing currently makes sure to only call this with filenames
of the form [a-zA-Z\._-]+.
"""
- file_path = os.path.join(config.Retriever.cache, '%s.bz2' % file)
+ file_path = os.path.join(config.get('cache'), '%s.bz2' % file)
if not os.path.isfile(file_path):
raise web.notfound()
handle = bz2.BZ2File(file_path, 'r')
@@ -286,7 +282,7 @@ class Reference:
reconstructed from the information in the database. Because if the
latter is the case, Mutalyzer will add it to the cache on the fly.
"""
- file_path = os.path.join(config.Retriever.cache, '%s.bz2' % file)
+ file_path = os.path.join(config.get('cache'), '%s.bz2' % file)
if not os.path.isfile(file_path):
# The following is a hack to return a 404 not found status with
# empty body (as is checked by our unit test framework, WebTest).
@@ -325,7 +321,7 @@ class GetGS:
@return: Output of name checker if forward is set, otherwise the
GeneSymbol with the variant notation as string.
"""
- O = Output(__file__, config.Output)
+ output = Output(__file__)
i = web.input(mutationName=None, variantRecord=None, forward=None)
@@ -333,11 +329,9 @@ class GetGS:
# We stringify the variant, because a unicode string crashes
# Bio.Seq.reverse_complement in mapping.py:607.
- # We are only interested in the legend
- #Mutalyzer.process(str(i.mutationName), config, O)
- variantchecker.check_variant(str(i.mutationName), config, O)
+ variantchecker.check_variant(str(i.mutationName), output)
- legends = O.getOutput("legends")
+ legends = output.getOutput("legends")
# Filter the transcript from the legend
legends = [l for l in legends if "_v" in l[0]]
@@ -378,7 +372,7 @@ class SyntaxCheck:
Parameters:
- variant: Variant name to check.
"""
- output = Output(__file__, config.Output)
+ output = Output(__file__)
i = web.input()
variant = i.variant
if variant.find(',') >= 0:
@@ -431,13 +425,13 @@ class Snp:
@kwarg rs_id: The dbSNP rs number (including 'rs' prefix).
@type rs_id: string
"""
- output = Output(__file__, config.Output)
+ output = Output(__file__)
descriptions = []
if rs_id:
output.addMessage(__file__, -1, 'INFO', 'Received %s' % rs_id)
- retriever = Retriever.Retriever(config.Retriever, output, None)
+ retriever = Retriever.Retriever(output, None)
descriptions = retriever.snpConvert(rs_id)
output.addMessage(__file__, -1, 'INFO',
'Finished processing %s' % rs_id)
@@ -484,9 +478,9 @@ class PositionConverter:
@kwarg build: Human genome build (currently 'hg18' or 'hg19').
@kwarg variant: Variant to convert.
"""
- output = Output(__file__, config.Output)
+ output = Output(__file__)
- avail_builds = config.Db.dbNames[::-1]
+ avail_builds = config.get('dbNames')[::-1]
if build :
avail_builds.remove(build)
@@ -503,7 +497,7 @@ class PositionConverter:
}
if build and variant:
- converter = Converter(build, config, output)
+ converter = Converter(build, output)
#Convert chr accNo to NC number
variant = converter.correctChrVariant(variant)
@@ -589,13 +583,13 @@ class VariantInfo:
acc = i.acc
var = i.var
- output = Output(__file__, config.Output)
+ output = Output(__file__)
output.addMessage(__file__, -1, 'INFO',
'Received %s:%s (LOVD_ver %s, build %s)' \
% (acc, var, LOVD_ver, build))
- converter = Converter(build, config, output)
+ converter = Converter(build, output)
result = ''
@@ -682,7 +676,7 @@ class Check:
@kwarg interactive: Run interactively, meaning we wrap the result in
the site layout and include the HTML form.
"""
- output = Output(__file__, config.Output)
+ output = Output(__file__)
args = {
'lastpost' : name
@@ -695,7 +689,7 @@ class Check:
# Todo: The following is probably a problem elsewhere too.
# We stringify the variant, because a unicode string crashes
# Bio.Seq.reverse_complement in mapping.py:607.
- variantchecker.check_variant(str(name), config, output)
+ variantchecker.check_variant(str(name), output)
output.addMessage(__file__, -1, 'INFO',
'Finished processing variant %s' % name)
@@ -814,7 +808,7 @@ class BatchProgress:
total = int(i.totalJobs)
except ValueError:
return
- D = Db.Batch(config.Db)
+ D = Db.Batch()
left = D.entriesLeftForJob(jobID)
percentage = int(100 - (100 * left / float(total)))
if i.ajax:
@@ -876,9 +870,9 @@ class BatchChecker:
(default), 'SyntaxChecker', 'PositionConverter', or
'SnpConverter'.
"""
- O = Output(__file__, config.Output)
+ O = Output(__file__)
- maxUploadSize = config.Batch.batchInputMaxSize
+ maxUploadSize = config.get('batchInputMaxSize')
attr = {"messages" : [],
"errors" : [],
@@ -891,7 +885,7 @@ class BatchChecker:
"hideTypes" : batchType and 'none' or '',
"selected" : "0",
"batchType" : batchType or "",
- "avail_builds" : config.Db.dbNames[::-1],
+ "avail_builds" : config.get('dbNames')[::-1],
"jobID" : None,
"totalJobs" : None
}
@@ -923,9 +917,9 @@ class BatchChecker:
web.ctx.status = '413 Request entity too large'
return 'Sorry, only files up to %s megabytes are accepted.' % (float(maxUploadSize) / 1048576)
- D = Db.Batch(config.Db)
- S = Scheduler.Scheduler(config.Scheduler, D)
- FileInstance = File.File(config.File, O)
+ D = Db.Batch()
+ S = Scheduler.Scheduler(D)
+ FileInstance = File.File(O)
# Generate the fromhost URL from which the results can be fetched
fromHost = web.ctx.homedomain + web.ctx.homepath + '/'
@@ -970,7 +964,7 @@ class BatchResult:
of the form \d+.
"""
filename = 'Results_%s.txt' % result
- handle = open(os.path.join(config.Scheduler.resultsDir, filename))
+ handle = open(os.path.join(config.get('resultsDir'), filename))
web.header('Content-Type', 'text/plain')
web.header('Content-Disposition',
'attachment; filename="%s"' % filename)
@@ -1020,7 +1014,7 @@ class Uploader:
"""
Render reference sequence uploader form.
"""
- maxUploadSize = config.Retriever.maxDldSize
+ maxUploadSize = config.get('maxDldSize')
UD, errors = "", []
args = {
"UD" : UD,
@@ -1063,11 +1057,11 @@ class Uploader:
- stop: Stop position.
- orientation: Orientation.
"""
- maxUploadSize = config.Retriever.maxDldSize
+ maxUploadSize = config.get('maxDldSize')
- O = Output(__file__, config.Output)
- D = Db.Cache(config.Db)
- R = Retriever.GenBankRetriever(config.Retriever, O, D)
+ O = Output(__file__)
+ D = Db.Cache()
+ R = Retriever.GenBankRetriever(O, D)
UD, errors = "", []
diff --git a/tests/test_grammar.py b/tests/test_grammar.py
index 8aadc2a0c3a296736684d4550c01e3f190fdb9a8..3cc5c4255d432f3a549a7729e256748f7445bd3d 100644
--- a/tests/test_grammar.py
+++ b/tests/test_grammar.py
@@ -8,7 +8,6 @@ import os
from nose.tools import *
import mutalyzer
-from mutalyzer.config import Config
from mutalyzer.grammar import Grammar
from mutalyzer.output import Output
@@ -22,8 +21,7 @@ class TestGrammar():
"""
Initialize test Grammar instance.
"""
- self.config = Config()
- self.output = Output(__file__, self.config.Output)
+ self.output = Output(__file__)
self.grammar = Grammar(self.output)
def test_some_variants(self):
diff --git a/tests/test_mapping.py b/tests/test_mapping.py
index 036b46f6c7aadc2ca26629cc123fa7b01c9a4869..5c7b38c69e77fce9965841c189f52c58c076812d 100644
--- a/tests/test_mapping.py
+++ b/tests/test_mapping.py
@@ -6,7 +6,6 @@ Tests for the mapping module.
#import logging; logging.basicConfig()
from nose.tools import *
-from mutalyzer.config import Config
from mutalyzer.output import Output
from mutalyzer.mapping import Converter
@@ -19,14 +18,13 @@ class TestConverter():
"""
Initialize test converter module.
"""
- self.config = Config()
- self.output = Output(__file__, self.config.Output)
+ self.output = Output(__file__)
def _converter(self, build):
"""
Create a Converter instance for a given build.
"""
- return Converter(build, self.config, self.output)
+ return Converter(build, self.output)
def test_converter(self):
"""
diff --git a/tests/test_mutator.py b/tests/test_mutator.py
index ee01cf2a1f0a0ea04af396d5d458511159cfd932..89579e70b049dc253e94604d85bd6e1f28b9b059 100644
--- a/tests/test_mutator.py
+++ b/tests/test_mutator.py
@@ -12,7 +12,6 @@ from Bio.Seq import Seq
import mutalyzer
from mutalyzer.util import skip
-from mutalyzer.config import Config
from mutalyzer.output import Output
from mutalyzer import mutator
@@ -36,16 +35,13 @@ class TestMutator():
"""
Initialize test mutator module.
"""
- self.config = Config()
- self.output = Output(__file__, self.config.Output)
+ self.output = Output(__file__)
def _mutator(self, sequence):
"""
Create a Mutator instance for a given sequence.
"""
- return mutator.Mutator(sequence,
- self.config.Mutator,
- self.output)
+ return mutator.Mutator(sequence, self.output)
def test_shiftpos_no_change(self):
"""
diff --git a/tests/test_variantchecker.py b/tests/test_variantchecker.py
index 74bbae733b93b4caadcb097559de70ffa3b211fc..c665150dd10bffe948fe45d0c3fee48798d836ec 100644
--- a/tests/test_variantchecker.py
+++ b/tests/test_variantchecker.py
@@ -6,7 +6,6 @@ Tests for the variantchecker module.
#import logging; logging.basicConfig()
from nose.tools import *
-from mutalyzer.config import Config
from mutalyzer.output import Output
from mutalyzer.variantchecker import check_variant
@@ -19,16 +18,14 @@ class TestVariantchecker():
"""
Initialize test variantchecker module.
"""
- self.config = Config()
- self.output = Output(__file__, self.config.Output)
+ self.output = Output(__file__)
def test_deletion_in_frame(self):
"""
Simple in-frame deletion should give a simple description on protein
level.
"""
- check_variant('AL449423.14(CDKN2A_v001):c.161_163del',
- self.config, self.output)
+ check_variant('AL449423.14(CDKN2A_v001):c.161_163del', self.output)
assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
'AL449423.14:g.61937_61939del')
assert 'AL449423.14(CDKN2A_v001):c.161_163del' \
@@ -42,8 +39,7 @@ class TestVariantchecker():
Simple in-frame insertion should give a simple description on protein
level.
"""
- check_variant('AL449423.14(CDKN2A_v001):c.161_162insATC',
- self.config, self.output)
+ check_variant('AL449423.14(CDKN2A_v001):c.161_162insATC', self.output)
assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
'AL449423.14:g.61938_61939insGAT')
assert 'AL449423.14(CDKN2A_v001):c.161_162insATC' \
@@ -58,7 +54,7 @@ class TestVariantchecker():
protein level.
"""
check_variant('AL449423.14(CDKN2A_v001):c.161_162delinsATCCC',
- self.config, self.output)
+ self.output)
assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
'AL449423.14:g.61938_61939delinsGGGAT')
assert 'AL449423.14(CDKN2A_v001):c.161_162delinsATCCC' \
@@ -73,7 +69,7 @@ class TestVariantchecker():
protein level, also with the optional deleted sequence argument.
"""
check_variant('AL449423.14(CDKN2A_v001):c.161_162delTGinsATCCC',
- self.config, self.output)
+ self.output)
assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
'AL449423.14:g.61938_61939delinsGGGAT')
assert 'AL449423.14(CDKN2A_v001):c.161_162delinsATCCC' \
@@ -86,7 +82,7 @@ class TestVariantchecker():
"""
Just a variant where we should roll.
"""
- check_variant('NM_003002.2:c.273del', self.config, self.output)
+ check_variant('NM_003002.2:c.273del', self.output)
wroll = self.output.getMessagesWithErrorCode('WROLLFORWARD')
assert len(wroll) > 0
@@ -94,7 +90,7 @@ class TestVariantchecker():
"""
Just a variant where we cannot roll.
"""
- check_variant('NM_003002.2:c.274del', self.config, self.output)
+ check_variant('NM_003002.2:c.274del', self.output)
wroll = self.output.getMessagesWithErrorCode('WROLLFORWARD')
assert_equal(len(wroll), 0)
@@ -102,7 +98,7 @@ class TestVariantchecker():
"""
Here we can roll but should not, because it is over a splice site.
"""
- check_variant('NM_000088.3:g.459del', self.config, self.output)
+ check_variant('NM_000088.3:g.459del', self.output)
wrollback = self.output.getMessagesWithErrorCode('IROLLBACK')
assert len(wrollback) > 0
wroll = self.output.getMessagesWithErrorCode('WROLLFORWARD')
@@ -113,7 +109,7 @@ class TestVariantchecker():
Here we can roll two positions, but should roll only one because
otherwise it is over a splice site.
"""
- check_variant('NM_000088.3:g.494del', self.config, self.output)
+ check_variant('NM_000088.3:g.494del', self.output)
wrollback = self.output.getMessagesWithErrorCode('IROLLBACK')
assert len(wrollback) > 0
wroll = self.output.getMessagesWithErrorCode('WROLLFORWARD')
@@ -123,7 +119,7 @@ class TestVariantchecker():
"""
Here we can roll and should, we stay in the same exon.
"""
- check_variant('NM_000088.3:g.460del', self.config, self.output)
+ check_variant('NM_000088.3:g.460del', self.output)
wroll = self.output.getMessagesWithErrorCode('WROLLFORWARD')
assert len(wroll) > 0
@@ -155,7 +151,7 @@ class TestVariantchecker():
of AL449423.14:g.65471_65472insACT, where only the reverse roll should
be done.
"""
- check_variant('AL449423.14:g.65470_65471insTAC', self.config, self.output)
+ check_variant('AL449423.14:g.65470_65471insTAC', self.output)
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_equal(len(self.output.getMessagesWithErrorCode('WROLLFORWARD')), 1)
@@ -165,7 +161,7 @@ class TestVariantchecker():
Insertion that rolls on the reverse strand should not use the same
inserted sequence in descriptions on forward and reverse strands.
"""
- check_variant('AL449423.14:g.65471_65472insACT', self.config, self.output)
+ check_variant('AL449423.14:g.65471_65472insACT', self.output)
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_equal(len(self.output.getMessagesWithErrorCode('WROLLFORWARD')), 0)
@@ -175,7 +171,7 @@ class TestVariantchecker():
Roll warning message should only be shown for currently selected
strand (forward).
"""
- check_variant('AL449423.14:g.65470_65471insTAC', self.config, self.output)
+ check_variant('AL449423.14:g.65470_65471insTAC', self.output)
assert_equal(len(self.output.getMessagesWithErrorCode('WROLLFORWARD')), 1)
assert_equal(len(self.output.getMessagesWithErrorCode('WROLLREVERSE')), 0)
@@ -184,7 +180,7 @@ class TestVariantchecker():
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)
+ check_variant('AL449423.14(CDKN2A_v001):c.98_99insGTA', self.output)
assert_equal(len(self.output.getMessagesWithErrorCode('WROLLFORWARD')), 0)
assert_equal(len(self.output.getMessagesWithErrorCode('WROLLREVERSE')), 1)
@@ -192,7 +188,7 @@ class TestVariantchecker():
"""
Insertion on CDS start boundary should not be included in CDS.
"""
- check_variant('NM_000143.3:c.-1_1insCAT', self.config, self.output)
+ check_variant('NM_000143.3:c.-1_1insCAT', self.output)
assert_equal(self.output.getIndexedOutput("newprotein", 0), None)
# Todo: Is this a good test?
@@ -200,7 +196,7 @@ class TestVariantchecker():
"""
Insertion after CDS start boundary should be included in CDS.
"""
- check_variant('NM_000143.3:c.1_2insCAT', self.config, self.output)
+ check_variant('NM_000143.3:c.1_2insCAT', self.output)
assert_equal(self.output.getIndexedOutput("newprotein", 0), '?')
# Todo: Is this a good test?
@@ -208,8 +204,7 @@ class TestVariantchecker():
"""
Deletion hitting one splice site should not do a protein prediction.
"""
- check_variant('NG_012772.1(BRCA2_v001):c.632-5_670del',
- self.config, self.output)
+ check_variant('NG_012772.1(BRCA2_v001):c.632-5_670del', self.output)
assert len(self.output.getMessagesWithErrorCode('WOVERSPLICE')) > 0
assert_equal(self.output.getOutput('removedSpliceSites'), [])
# Todo: For now, the following is how to check if no protein
@@ -220,8 +215,7 @@ class TestVariantchecker():
"""
Deletion of an entire exon should be possible.
"""
- check_variant('NG_012772.1(BRCA2_v001):c.632-5_681+7del',
- self.config, self.output)
+ check_variant('NG_012772.1(BRCA2_v001):c.632-5_681+7del', self.output)
assert len(self.output.getMessagesWithErrorCode('WOVERSPLICE')) > 0
assert_equal(self.output.getOutput('removedSpliceSites'), [2])
# Todo: For now, the following is how to check if protein
@@ -232,8 +226,7 @@ class TestVariantchecker():
"""
Deletion of exactly an exon should be possible.
"""
- check_variant('NG_012772.1(BRCA2_v001):c.632_681del',
- self.config, self.output)
+ check_variant('NG_012772.1(BRCA2_v001):c.632_681del', self.output)
assert_equal(len(self.output.getMessagesWithErrorCode('WOVERSPLICE')), 0)
assert_equal(self.output.getOutput('removedSpliceSites'), [2])
# Todo: For now, the following is how to check if protein
@@ -249,8 +242,7 @@ class TestVariantchecker():
NG_012772.1(BRCA2_v001):c.68-7_316+7del is such a variant, since
positions 68 through 316 are exactly one exon and (316-68+1)/3 = 83.
"""
- check_variant('NG_012772.1(BRCA2_v001):c.68-7_316+7del',
- self.config, self.output)
+ check_variant('NG_012772.1(BRCA2_v001):c.68-7_316+7del', self.output)
assert len(self.output.getMessagesWithErrorCode('WOVERSPLICE')) > 0
assert_equal(self.output.getOutput('removedSpliceSites'), [2])
# Todo: For now, the following is how to check if protein
@@ -262,8 +254,7 @@ class TestVariantchecker():
"""
Deletion of two entire exons should be possible.
"""
- check_variant('NG_012772.1(BRCA2_v001):c.632-5_793+7del',
- self.config, self.output)
+ check_variant('NG_012772.1(BRCA2_v001):c.632-5_793+7del', self.output)
assert len(self.output.getMessagesWithErrorCode('WOVERSPLICE')) > 0
assert_equal(self.output.getOutput('removedSpliceSites'), [4])
# Todo: For now, the following is how to check if protein
@@ -275,8 +266,7 @@ class TestVariantchecker():
Deletion of an entire intron should be possible (fusion of remaining
exonic parts).
"""
- check_variant('NG_012772.1(BRCA2_v001):c.622_674del',
- self.config, self.output)
+ check_variant('NG_012772.1(BRCA2_v001):c.622_674del', self.output)
assert len(self.output.getMessagesWithErrorCode('WOVERSPLICE')) > 0
assert_equal(self.output.getOutput('removedSpliceSites'), [2])
# Todo: For now, the following is how to check if protein
@@ -288,8 +278,7 @@ class TestVariantchecker():
Deletion of exactly an intron should be possible (fusion of flanking
exons).
"""
- check_variant('NG_012772.1(BRCA2_v001):c.681+1_682-1del',
- self.config, self.output)
+ check_variant('NG_012772.1(BRCA2_v001):c.681+1_682-1del', self.output)
assert_equal(self.output.getMessagesWithErrorCode('WOVERSPLICE'), [])
assert_equal(self.output.getOutput('removedSpliceSites'), [2])
# Note: The protein prediction is done, but 'newprotein' is not set
@@ -304,8 +293,7 @@ class TestVariantchecker():
Deletion of an entire intron should be possible (fusion of remaining
exonic parts).
"""
- check_variant('NG_012772.1(BRCA2_v001):c.622_672del',
- self.config, self.output)
+ check_variant('NG_012772.1(BRCA2_v001):c.622_672del', self.output)
assert len(self.output.getMessagesWithErrorCode('WOVERSPLICE')) > 0
assert_equal(self.output.getOutput('removedSpliceSites'), [2])
# Todo: For now, the following is how to check if protein
@@ -317,8 +305,7 @@ class TestVariantchecker():
"""
Deletion of an entire exon with unknown offsets should be possible.
"""
- check_variant('NG_012772.1(BRCA2_v001):c.632-?_681+?del',
- self.config, self.output)
+ check_variant('NG_012772.1(BRCA2_v001):c.632-?_681+?del', self.output)
assert len(self.output.getMessagesWithErrorCode('WOVERSPLICE')) > 0
assert len(self.output.getMessagesWithErrorCode('IDELSPLICE')) > 0
# Todo: For now, the following is how to check if protein
@@ -343,8 +330,7 @@ class TestVariantchecker():
NG_012772.1(BRCA2_v001):c.68-?_316+?del is such a variant, since
positions 68 through 316 are exactly one exon and (316-68+1)/3 = 83.
"""
- check_variant('NG_012772.1(BRCA2_v001):c.68-?_316+?del',
- self.config, self.output)
+ check_variant('NG_012772.1(BRCA2_v001):c.68-?_316+?del', self.output)
assert len(self.output.getMessagesWithErrorCode('WOVERSPLICE')) > 0
assert len(self.output.getMessagesWithErrorCode('IDELSPLICE')) > 0
# Todo: For now, the following is how to check if protein
@@ -364,7 +350,7 @@ class TestVariantchecker():
variant with exact positioning should be possible.
"""
check_variant('NG_012772.1(BRCA2_v001):c.[632-?_681+?del;681+4del]',
- self.config, self.output)
+ self.output)
assert len(self.output.getMessagesWithErrorCode('WOVERSPLICE')) > 0
assert len(self.output.getMessagesWithErrorCode('IDELSPLICE')) > 0
# Todo: For now, the following is how to check if protein
@@ -384,7 +370,7 @@ class TestVariantchecker():
also on the reverse strand.
"""
check_variant('AL449423.14(CDKN2A_v001):c.151-?_457+?del',
- self.config, self.output)
+ self.output)
assert len(self.output.getMessagesWithErrorCode('WOVERSPLICE')) > 0
assert len(self.output.getMessagesWithErrorCode('IDELSPLICE')) > 0
# Todo: For now, the following is how to check if protein
@@ -405,7 +391,7 @@ class TestVariantchecker():
of the flanking exons (as would happen using the mechanism for genomic
references).
"""
- check_variant('NM_018723.3:c.758_890del', self.config, self.output)
+ check_variant('NM_018723.3:c.758_890del', self.output)
assert_equal(len(self.output.getMessagesWithErrorCode('WOVERSPLICE')), 0)
assert_equal(self.output.getOutput('removedSpliceSites'), [2])
# Todo: For now, the following is how to check if protein
@@ -416,12 +402,12 @@ class TestVariantchecker():
"""
Insertion of a range is not implemented yet.
"""
- check_variant('AB026906.1:c.274_275ins262_268', self.config, self.output)
+ check_variant('AB026906.1:c.274_275ins262_268', self.output)
assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 1)
def test_delins_range(self):
"""
Deletion/insertion of a range is not implemented yet.
"""
- check_variant('AB026906.1:c.274delins262_268', self.config, self.output)
+ check_variant('AB026906.1:c.274delins262_268', self.output)
assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 1)
diff --git a/tests/test_webservice.py b/tests/test_webservice.py
index 5c7437843943c9473338402ce4db0825391a091c..3e5f99d996d9bcee0e845ba45e6451e0c7dada15 100644
--- a/tests/test_webservice.py
+++ b/tests/test_webservice.py
@@ -8,7 +8,6 @@ from mutalyzer.util import monkey_patch_suds; monkey_patch_suds()
import os
from datetime import datetime, timedelta
import mutalyzer
-from mutalyzer.config import Config
from mutalyzer.output import Output
from mutalyzer.sync import CacheSync
from mutalyzer import Db
@@ -226,10 +225,9 @@ class TestWebservice():
"""
created_since = datetime.today() - timedelta(days=14)
- config = Config()
- database = Db.Cache(config.Db)
- output = Output(__file__, config.Output)
- sync = CacheSync(config.Retriever, output, database)
+ database = Db.Cache()
+ output = Output(__file__)
+ sync = CacheSync(output, database)
cache = sync.local_cache(created_since)
r = self.client.service.getCache(created_since)