diff --git a/.gitignore b/.gitignore
index b59df5c30a75add3fb5155c1e392d91c87ae7149..3c4834e999090b3648e7c46d1d921fd651cd82a9 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,4 +3,4 @@
/dist
/mutalyzer.egg-info
/static
-/mutalyzer.conf
+/settings.py
diff --git a/mutalyzer/Db.py b/mutalyzer/Db.py
index 9410e3b0b97fe37fba3cb3b1382b8119dc22429e..90b6d4f5ad8196cfc3ced73e3b33e76f483f266e 100644
--- a/mutalyzer/Db.py
+++ b/mutalyzer/Db.py
@@ -25,7 +25,7 @@ import warnings
import MySQLdb
from mutalyzer import util
-from mutalyzer import config
+from mutalyzer.config import settings
#
@@ -74,14 +74,11 @@ class Db():
is unfortunately not implemented in (most versions of) the Python
MySQLdb module.
Therefore we manually implement automatic reconnects in the query
- method, but also optionally use the reconnect option from MySQLdb
- if specified in the Mutalyzer configuration.
+ method.
Also see Trac ticket #91.
"""
- kwargs = dict(user=self._user, db=self._database, host=self._host)
- if config.get('autoReconnect'):
- kwargs.update(reconnect=True)
- self._connection = MySQLdb.connect(**kwargs)
+ self._connection = MySQLdb.connect(
+ user=self._user, db=self._database, host=self._host)
#_connect
def query(self, statement):
@@ -209,7 +206,7 @@ class Mapping(Db) :
@arg build: The version of the mapping database
@type build: string
"""
- Db.__init__(self, build, config.get('LocalMySQLuser'), config.get('LocalMySQLhost'))
+ Db.__init__(self, build, settings.MYSQL_USER, settings.MYSQL_HOST)
#__init__
def get_NM_version(self, mrnaAcc) :
@@ -873,8 +870,8 @@ class Cache(Db) :
"""
Initialise the Db parent class. Use the internalDb.
"""
- Db.__init__(self, config.get('internalDb'),
- config.get('LocalMySQLuser'), config.get('LocalMySQLhost'))
+ Db.__init__(self, settings.MYSQL_DATABASE,
+ settings.MYSQL_USER, settings.MYSQL_HOST)
#__init__
def insertGB(self, accNo, GI, fileHash, ChrAccVer, ChrStart,
@@ -1228,8 +1225,8 @@ class Cache(Db) :
created >= DATE_SUB(CURDATE(), INTERVAL %s DAY))
);
""", (mrnaAcc,
- config.get('proteinLinkNoneLifetime'),
- config.get('proteinLinkLifetime'))
+ settings.PROTEIN_LINK_NONE_LIFETIME,
+ settings.PROTEIN_LINK_LIFETIME)
ret = self.query(statement)
return ret[0][0]
@@ -1263,8 +1260,8 @@ class Cache(Db) :
created >= DATE_SUB(CURDATE(), INTERVAL %s DAY))
);
""", (protAcc,
- config.get('proteinLinkNoneLifetime'),
- config.get('proteinLinkLifetime'))
+ settings.PROTEIN_LINK_NONE_LIFETIME,
+ settings.PROTEIN_LINK_LIFETIME)
ret = self.query(statement)
return ret[0][0]
@@ -1325,9 +1322,9 @@ class Batch(Db) :
"""
Initialise the Db parent class. Use the internalDb.
"""
- Db.__init__(self, config.get('internalDb'),
- config.get('LocalMySQLuser'),
- config.get('LocalMySQLhost'))
+ Db.__init__(self, settings.MYSQL_DATABASE,
+ settings.MYSQL_USER,
+ settings.MYSQL_HOST)
#__init__
def isJobListEmpty(self) :
@@ -1612,9 +1609,9 @@ class Counter(Db):
"""
Initialise the Db parent class. Use the internalDb.
"""
- Db.__init__(self, config.get('internalDb'),
- config.get('LocalMySQLuser'),
- config.get('LocalMySQLhost'))
+ Db.__init__(self, settings.MYSQL_DATABASE,
+ settings.MYSQL_USER,
+ settings.MYSQL_HOST)
def increment(self, service, interface):
"""
diff --git a/mutalyzer/File.py b/mutalyzer/File.py
index 0261999eff3d7ef734b11b24466c0fb502632bb0..cce718c34fb8dab59317df7c3888c7ed533e9c3d 100644
--- a/mutalyzer/File.py
+++ b/mutalyzer/File.py
@@ -27,7 +27,11 @@ import types # UnicodeType
from cStringIO import StringIO
from mutalyzer import util
-from mutalyzer import config
+from mutalyzer.config import settings
+
+
+# Amount of bytes to be read for determining the file type.
+BUFFER_SIZE = 32768
class File() :
@@ -160,7 +164,7 @@ 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(config.get('bufSize'))
+ buf = new_handle.read(BUFFER_SIZE)
# Default dialect
dialect = 'excel'
@@ -280,7 +284,7 @@ class File() :
jobl = [(l+1, row) for l, row in enumerate(job)]
#TODO: Add more new style old style logic
- if jobl[0][1] == config.get('header') : #Old style NameCheckBatch job
+ if jobl[0][1] == ['AccNo', 'Genesymbol', 'Mutation']: #Old style NameCheckBatch job
ret = []
notthree = []
emptyfield = []
@@ -365,7 +369,7 @@ class File() :
err = float(len(errlist))/len(ret)
if err == 0:
return (ret, columns)
- elif err < config.get('threshold'):
+ elif err < settings.BATCH_JOBS_ERROR_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 "
@@ -389,7 +393,7 @@ class File() :
@rtype: string
"""
handle.seek(0)
- buf = handle.read(config.get('bufSize')) #: The bufSize configuration variables.
+ buf = handle.read(BUFFER_SIZE)
MagicInstance = magic.open(magic.MAGIC_MIME)
MagicInstance.load()
diff --git a/mutalyzer/GenRecord.py b/mutalyzer/GenRecord.py
index 05f40be534875e36fdb3dc6f3fe9dee975996d02..917d056c5aa71d652217008b4c4042cf061d4ff8 100644
--- a/mutalyzer/GenRecord.py
+++ b/mutalyzer/GenRecord.py
@@ -19,11 +19,14 @@ search for them each time.
import Bio
from mutalyzer import util
-from mutalyzer import config
from mutalyzer import Crossmap
from mutalyzer import Db
+SPLICE_ALARM = 2
+SPLICE_WARN = 5
+
+
class PList(object) :
"""
A position list object, to store a general location and a list of
@@ -841,11 +844,11 @@ class GenRecord() :
warning = 'WSPLICE_OTHER'
str_transcript = 'transcript %s' % transcript.name
- if intronPos <= config.get('spliceAlarm'):
+ if intronPos <= SPLICE_ALARM:
self.__output.addMessage(__file__, 2, warning,
"Mutation on splice site in gene %s %s." % (
gene.name, str_transcript))
- elif intronPos <= config.get('spliceWarn'):
+ elif intronPos <= SPLICE_WARN:
self.__output.addMessage(__file__, 2, warning,
"Mutation near splice site in gene %s %s." % (
gene.name, str_transcript))
diff --git a/mutalyzer/Retriever.py b/mutalyzer/Retriever.py
index 38e7140fb0c8dd75a623171ff2d6a0f1379cd6f7..7a80c1d916fcd4a9d9f70a722475c699c847d656 100644
--- a/mutalyzer/Retriever.py
+++ b/mutalyzer/Retriever.py
@@ -26,7 +26,7 @@ from xml.parsers import expat
from httplib import HTTPException, IncompleteRead
from mutalyzer import util
-from mutalyzer import config
+from mutalyzer.config import settings
from mutalyzer.parsers import lrg
from mutalyzer.parsers import genbank
@@ -79,9 +79,9 @@ class Retriever(object) :
"""
self._output = output
self._database = database
- if not os.path.isdir(config.get('cache')) :
- os.mkdir(config.get('cache'))
- Entrez.email = config.get('email')
+ if not os.path.isdir(settings.CACHE_DIR) :
+ os.mkdir(settings.CACHE_DIR)
+ Entrez.email = settings.EMAIL
self.fileType = None
#__init__
@@ -112,12 +112,12 @@ class Retriever(object) :
size the ``oldest'' files are deleted. Note that accessing a file
makes it ``new''.
"""
- if self._foldersize(config.get('cache')) < config.get('cachesize'):
+ if self._foldersize(settings.CACHE_DIR) < settings.MAX_CACHE_SIZE:
return
# Build a list of files sorted by access time.
cachelist = []
- for (path, dirs, files) in os.walk(config.get('cache')) :
+ for (path, dirs, files) in os.walk(settings.CACHE_DIR) :
for filename in files :
filepath = os.path.join(path, filename)
cachelist.append(
@@ -128,7 +128,7 @@ 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(config.get('cache')) < config.get('cachesize'):
+ if self._foldersize(settings.CACHE_DIR) < settings.MAX_CACHE_SIZE:
break;
#for
#_cleancache
@@ -143,7 +143,7 @@ class Retriever(object) :
@return: A filename
@rtype: string
"""
- return config.get('cache') + '/' + name + "." + self.fileType + ".bz2"
+ return os.path.join(settings.CACHE_DIR, name + "." + self.fileType + ".bz2")
#_nametofile
def _write(self, raw_data, filename) :
@@ -449,7 +449,7 @@ class GenBankRetriever(Retriever):
self._output.addMessage(__file__, 4, 'ERETR',
'Could not retrieve %s.' % name)
return None
- if length > config.get('maxDldSize'):
+ if length > settings.MAX_FILE_SIZE:
self._output.addMessage(__file__, 4, 'ERETR',
'Could not retrieve %s.' % name)
return None
@@ -508,7 +508,7 @@ class GenBankRetriever(Retriever):
return None
# The slice can not be too big.
- if stop - start > config.get('maxDldSize'):
+ if stop - start > settings.MAX_FILE_SIZE:
return None
# Check whether we have seen this slice before.
@@ -660,8 +660,7 @@ class GenBankRetriever(Retriever):
info = handle.info()
if info["Content-Type"] == "text/plain" :
length = int(info["Content-Length"])
- if length > config.get('minDldSize') and \
- length < config.get('maxDldSize'):
+ if 512 < length < settings.MAX_FILE_SIZE:
raw_data = handle.read()
md5sum = self._calcHash(raw_data)
UD = self._database.getGBFromHash(md5sum)
@@ -864,7 +863,7 @@ class LRGRetriever(Retriever):
@rtype: string
"""
- prefix = config.get('lrgurl')
+ prefix = settings.LRG_PREFIX_URL
url = prefix + "%s.xml" % name
pendingurl = prefix + "pending/%s.xml" % name
@@ -907,7 +906,7 @@ class LRGRetriever(Retriever):
if info["Content-Type"] == "application/xml" and info.has_key("Content-length"):
length = int(info["Content-Length"])
- if config.get('minDldSize') < length < config.get('maxDldSize'):
+ if 512 < length < settings.MAX_FILE_SIZE:
raw_data = handle.read()
handle.close()
diff --git a/mutalyzer/Scheduler.py b/mutalyzer/Scheduler.py
index 39494f5b416355307f5347492455fb7933f504a8..62d50a8a5d0724fec6a6c27ad56ce8f769121605 100644
--- a/mutalyzer/Scheduler.py
+++ b/mutalyzer/Scheduler.py
@@ -20,7 +20,7 @@ import smtplib # smtplib.STMP
from email.mime.text import MIMEText # MIMEText
import mutalyzer
-from mutalyzer import config
+from mutalyzer.config import settings
from mutalyzer import variantchecker
from mutalyzer.grammar import Grammar
from mutalyzer.output import Output
@@ -115,16 +115,15 @@ Thanks for using Mutalyzer.
With kind regards,
-Mutalyzer batch checker.""" % url)
+Mutalyzer batch scheduler""" % url)
- message["Subject"] = config.get('mailSubject')
- message["From"] = config.get('mailFrom')
+ message["Subject"] = "Result of your Mutalyzer batch job"
+ message["From"] = settings.EMAIL
message["To"] = mailTo
smtpInstance = smtplib.SMTP()
smtpInstance.connect()
- smtpInstance.sendmail(config.get('mailFrom'), mailTo,
- message.as_string())
+ smtpInstance.sendmail(settings.EMAIL, mailTo, message.as_string())
smtpInstance.quit()
#__sendMail
@@ -388,12 +387,28 @@ Mutalyzer batch checker.""" % url)
outputline += batchOutput[0]
#Output
- filename = "%s/Results_%s.txt" % (config.get('resultsDir'), i)
+ filename = "%s/Results_%s.txt" % (settings.CACHE_DIR, 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 = config.get('nameCheckOutHeader')
+ header = ['Input',
+ 'Errors | Messages',
+ 'AccNo',
+ 'Genesymbol',
+ 'Variant',
+ 'Reference Sequence Start Descr.',
+ 'Coding DNA Descr.',
+ 'Protein Descr.',
+ 'GeneSymbol Coding DNA Descr.',
+ 'GeneSymbol Protein Descr.',
+ 'Genomic Reference',
+ 'Coding Reference',
+ 'Protein Reference',
+ 'Affected Transcripts',
+ 'Affected Proteins',
+ 'Restriction Sites Created',
+ 'Restriction Sites Deleted']
handle = open(filename, 'a')
handle.write("%s\n" % "\t".join(header))
#if
@@ -447,12 +462,12 @@ Mutalyzer batch checker.""" % url)
result = "|".join(output.getBatchMessages(3))
#Output
- filename = "%s/Results_%s.txt" % (config.get('resultsDir'), i)
+ filename = "%s/Results_%s.txt" % (settings.CACHE_DIR, 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 = config.get('syntaxCheckOutHeader')
+ header = ['Input', 'Status']
handle = open(filename, 'a')
handle.write("%s\n" % "\t".join(header))
#if
@@ -549,12 +564,15 @@ Mutalyzer batch checker.""" % url)
error = "%s" % "|".join(O.getBatchMessages(3))
#Output
- filename = "%s/Results_%s.txt" % (config.get('resultsDir'), i)
+ filename = "%s/Results_%s.txt" % (settings.CACHE_DIR, 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 = config.get('positionConverterOutHeader')
+ header = ['Input Variant',
+ 'Errors',
+ 'Chromosomal Variant',
+ 'Coding Variant(s)']
handle = open(filename, 'a')
handle.write("%s\n" % "\t".join(header))
#if
@@ -609,12 +627,14 @@ Mutalyzer batch checker.""" % url)
outputline += "%s\t" % "|".join(O.getBatchMessages(3))
#Output
- filename = "%s/Results_%s.txt" % (config.get('resultsDir'), i)
+ filename = "%s/Results_%s.txt" % (settings.CACHE_DIR, 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 = config.get('snpConverterOutHeader')
+ header = ['Input Variant',
+ 'HGVS description(s)',
+ 'Errors | Messages']
handle = open(filename, 'a')
handle.write("%s\n" % "\t".join(header))
#if
diff --git a/mutalyzer/config.py b/mutalyzer/config.py
deleted file mode 100644
index dc8b5a83ebf14e62110050b9cad3af6806657eef..0000000000000000000000000000000000000000
--- a/mutalyzer/config.py
+++ /dev/null
@@ -1,176 +0,0 @@
-"""
-Module for reading the configuration values from a configuration file.
-
-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 is read from the file specified by the `MUTALYZER_SETTINGS`
-environment variable, or `mutalyzer.conf` in the current directory if it is
-not set.
-"""
-
-
-import os
-
-from configobj import ConfigObj
-
-from mutalyzer.util import singleton
-
-
-class ConfigurationError(Exception):
- """
- Raised when a configuration file cannot be read.
- """
- pass
-
-
-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.
- """
- return _Config().get(name)
-
-
-@singleton
-class _Config():
- """
- 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):
- """
- Initialise the class with variables read from the configuration
- file.
-
- Configuration values are read from the file specified by the
- `MUTALYZER_SETTINGS` environment variable, or `mutalyzer.conf` in the
- current directory if it is not set.
-
- :raises ConfigurationError: If configuration could not be read.
- """
- filename = os.environ.get('MUTALYZER_SETTINGS', 'mutalyzer.conf')
- config = self._load_config(filename)
-
- # We define default values for many configuration settings (except for
- # some that are mandatory for the user to define, i.e. those in the
- # extras/config.user.example file).
- # Todo: Do not duplicate default values here and in the example config
- # file template.
- config.setdefault('cachesize', 50)
- config.setdefault('maxDldSize', 10)
- config.setdefault('minDldSize', 512)
- config.setdefault('lrgurl', 'ftp://ftp.ebi.ac.uk/pub/databases/lrgex/')
- config.setdefault('internalDb', 'mutalyzer')
- config.setdefault('dbNames', ['hg18', 'hg19', 'mm10'])
- config.setdefault('defaultDb', 'hg19')
- config.setdefault('LocalMySQLuser', 'mutalyzer')
- config.setdefault('LocalMySQLhost', 'localhost')
- config.setdefault('autoReconnect', False)
- config.setdefault('proteinLinkLifetime', 30)
- config.setdefault('proteinLinkNoneLifetime', 5)
- config.setdefault('datestring', '%Y-%m-%d %H:%M:%S')
- config.setdefault('loglevel', 3)
- config.setdefault('outputlevel', 1)
- config.setdefault('debug', True)
- config.setdefault('flanksize', 25)
- config.setdefault('maxvissize', 25)
- config.setdefault('flankclipsize', 6)
- config.setdefault('mailFrom', 'noreply@humgen.nl')
- config.setdefault('mailSubject', 'Result of Mutalyzer batch check.')
- config.setdefault('resultsDir', config['cache'])
- config.setdefault('PIDfile', '/var/run/mutalyzer/mutalyzer-batchd.pid')
- config.setdefault('batchInputMaxSize', 5)
- config.setdefault('nameCheckOutHeader',
- ['Input', 'Errors | Messages', 'AccNo', 'Genesymbol', 'Variant',
- 'Reference Sequence Start Descr.', 'Coding DNA Descr.',
- 'Protein Descr.', 'GeneSymbol Coding DNA Descr.',
- 'GeneSymbol Protein Descr.', 'Genomic Reference',
- 'Coding Reference', 'Protein Reference', 'Affected Transcripts',
- 'Affected Proteins', 'Restriction Sites Created',
- 'Restriction Sites Deleted'])
- config.setdefault('syntaxCheckOutHeader', ['Input', 'Status'])
- config.setdefault('positionConverterOutHeader',
- ['Input Variant', 'Errors', 'Chromosomal Variant', 'Coding Variant(s)'])
- config.setdefault('snpConverterOutHeader',
- ['Input Variant', 'HGVS description(s)', 'Errors | Messages'])
- config.setdefault('bufSize', 32768)
- config.setdefault('header', ['AccNo', 'Genesymbol', 'Mutation'])
- config.setdefault('threshold', 0.05)
- config.setdefault('spliceAlarm', 2)
- config.setdefault('spliceWarn', 5)
- config.setdefault('piwik', False)
- config.setdefault('piwikBase', 'https://piwik.example.com')
- config.setdefault('piwikSite', 1)
-
- try:
- # 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 = {'autoReconnect': config.as_bool('autoReconnect'),
- 'debug': config.as_bool('debug'),
- 'piwik': config.as_bool('piwik'),
- 'threshold': config.as_float('threshold')}
-
- # Simple string values.
- for name in ('email', 'cache', 'lrgurl', 'internalDb', 'dbNames',
- 'LocalMySQLuser', 'LocalMySQLhost', 'log',
- 'datestring', 'mailFrom', 'mailSubject',
- 'resultsDir', 'nameCheckOutHeader', 'defaultDb',
- 'syntaxCheckOutHeader', 'positionConverterOutHeader',
- 'snpConverterOutHeader', 'PIDfile', 'header',
- 'piwikBase'):
- self._values[name] = config[name]
-
- # Simple integer values.
- for name in ('minDldSize', 'loglevel', 'outputlevel', 'flanksize',
- 'maxvissize', 'flankclipsize', 'bufSize',
- 'spliceAlarm', 'spliceWarn', 'piwikSite',
- 'proteinLinkLifetime', 'proteinLinkNoneLifetime'):
- self._values[name] = config.as_int(name)
-
- # File sizes (given in megabytes, stored in bytes).
- for name in ('cachesize', 'maxDldSize', 'batchInputMaxSize'):
- self._values[name] = config.as_int(name) * 1048576
-
- except KeyError as e:
- raise ConfigurationError('Missing configuration value: %s' % e)
-
- def get(self, name):
- """
- Get a configuration value by name.
-
- :arg name: Name for the configuration value.
- :type name: string
-
- :raises ConfigurationError: If given configuration value name does not
- exist.
- """
- try:
- return self._values[name]
- except KeyError:
- raise ConfigurationError('No such configuration value: %s' % name)
-
- def _load_config(self, filename):
- """
- Create a `ConfigObj` from the configuration in `filename`.
- """
- try:
- return ConfigObj(filename)
- except IOError:
- raise ConfigurationError('Could not open configuration file: %s'
- % filename)
- except SyntaxError:
- raise ConfigurationError('Could not parse configuration file: %s'
- % filename)
diff --git a/mutalyzer/config/__init__.py b/mutalyzer/config/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..6956473134c8ee44bcbcecf1dd8522d95e9ab0ee
--- /dev/null
+++ b/mutalyzer/config/__init__.py
@@ -0,0 +1,74 @@
+"""
+Module for reading the configuration values from a configuration file.
+
+Default values will be read from the :mod:`mutalyzer.config.default_settings`
+module and overridden by any values from the module specified by the
+`MUTALYZER_SETTINGS`.
+
+Alternatively, the default values can be overridden manually using the
+:meth:`settings.configure` method, in which case the `MUTALYZER_SETTINGS`
+environment variable will not be used.
+"""
+
+
+import flask.config
+import os
+
+from mutalyzer import util
+
+
+ENVIRONMENT_VARIABLE = 'MUTALYZER_SETTINGS'
+
+
+class Settings(flask.config.Config, util.AttributeDictMixin):
+ """
+ Dictionary with some extra ways to fill it from files or special
+ dictionaries (see `flask.config.Config`) and attribute access.
+ """
+ def __init__(self):
+ # We fix the root_path argument to the current working directory.
+ super(Settings, self).__init__(os.getcwd())
+
+
+class LazySettings(util.LazyObject):
+ """
+ A lazy proxy for a settings object.
+
+ Taken from `Django <https://www.djangoproject.com/>`_
+ (`django.conf.LazySettings`).
+
+ .. note:: Django also does some logging config magic here, we did not copy
+ that.
+ """
+ def _setup(self, settings=None):
+ """
+ Load the settings module pointed to by the environment variable. This
+ is used the first time we need any settings at all, if the user has not
+ previously configured the settings manually.
+ """
+ self._wrapped = Settings()
+ self._wrapped.from_object('mutalyzer.config.default_settings')
+ if settings is None:
+ self._wrapped.from_envvar(ENVIRONMENT_VARIABLE)
+ else:
+ self._wrapped.update(settings)
+
+ def configure(self, settings):
+ """
+ Called to manually configure the settings. The 'default_settings'
+ parameter sets where to retrieve any unspecified values from (its
+ argument must support attribute access (__getattr__)).
+ """
+ if self._wrapped is not None:
+ raise RuntimeError('settings already configured')
+ self._setup(settings)
+
+ @property
+ def configured(self):
+ """
+ Returns True if the settings have already been configured.
+ """
+ return self._wrapped is not None
+
+
+settings = LazySettings()
diff --git a/mutalyzer/config/default_settings.py b/mutalyzer/config/default_settings.py
new file mode 100644
index 0000000000000000000000000000000000000000..bc4b12cf9ab2d0d9298b888bb58f848422e3045a
--- /dev/null
+++ b/mutalyzer/config/default_settings.py
@@ -0,0 +1,80 @@
+"""
+Default Mutalyzer settings. Override these with settings in the module
+pointed-to by the `MUTALYZER_SETTINGS` environment variable.
+"""
+
+
+# Use Mutalyzer in debug mode.
+DEBUG = True
+
+# This address is used in contact information on the website, as sender in
+# batch job notifications, and with retrieval of records at the NCBI using
+# Entrez.
+EMAIL = 'mutalyzer@humgen.nl'
+
+# The cache directory. Used to store uploaded and downloaded files (e.g.,
+# reference files from NCBI or user) and batch job results.
+import tempfile
+CACHE_DIR = tempfile.mkdtemp()
+
+# Maximum size of the cache directory (in bytes).
+MAX_CACHE_SIZE = 50 * 1048576 # 50 MB
+
+# Maximum size for uploaded and downloaded files (in bytes).
+MAX_FILE_SIZE = 10 * 1048576 # 10 MB
+
+# Host name for local MySQL databases.
+MYSQL_HOST = 'localhost'
+
+# User for local MySQL databases.
+MYSQL_USER = 'mutalyzer'
+
+# Local MySQL database name.
+MYSQL_DATABASE = 'mutalyzer'
+
+# Available databases with mapping information.
+DB_NAMES = ['hg18', 'hg19', 'mm10']
+
+# Default database for mapping information.
+DEFAULT_DB = 'hg19'
+
+# Name and location of the log file.
+import os
+import tempfile
+log_handle, log_filename = tempfile.mkstemp()
+os.close(log_handle)
+LOG_FILE = log_filename
+
+# Level of logged messages.
+LOG_LEVEL = 3
+
+# Level of output messages.
+OUTPUT_LEVEL = 1
+
+# Format of time prefix for log messages. Can be anything that is accepted as
+# the format argument of time.strftime.
+# http://docs.python.org/2/library/time.html#time.strftime
+LOG_TIME_FORMAT = "%Y-%m-%d %H:%M:%S"
+
+# Prefix URL from where LRG files are fetched.
+LRG_PREFIX_URL = 'ftp://ftp.ebi.ac.uk/pub/databases/lrgex/'
+
+# Allow for this fraction of errors in batch jobs.
+BATCH_JOBS_ERROR_THRESHOLD = 0.05
+
+# Number of days a cached transcript->protein link from the NCBI is considered
+# valid.
+PROTEIN_LINK_LIFETIME = 30
+
+# Number of days a cached nonexisting transcript->protein link from the NCBI
+# is considered valid.
+PROTEIN_LINK_NONE_LIFETIME = 5
+
+# Is Piwik enabled?
+PIWIK = False
+
+# Base URL for the Piwik server.
+PIWIK_BASE_URL = 'https://piwik.example.com'
+
+# Piwik site ID for Mutalyzer.
+PIWIK_SITE_ID = 1
diff --git a/mutalyzer/mutator.py b/mutalyzer/mutator.py
index 55750bd92605e05f6cf6b7d7eda50763a24c7d20..8047d932d4bab1ca4fa66b2020e2d69428d97853 100644
--- a/mutalyzer/mutator.py
+++ b/mutalyzer/mutator.py
@@ -20,7 +20,17 @@ from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
from Bio.Seq import reverse_complement
from mutalyzer import util
-from mutalyzer import config
+
+
+# Length of the flanking sequences used in the visualisation of mutations.
+VIS_FLANK_LENGTH = 25
+
+# Maximum length of visualised mutations.
+VIS_MAX_LENGTH = 25
+
+# Length of the flanking sequences used if the visualised mutation is clipped
+# (because it exceeds VIS_MAX_LENGTH).
+VIS_CLIP_FLANK_LENGTH = 6
class Mutator():
@@ -104,19 +114,19 @@ class Mutator():
@return: Visualisation.
@rtype: str
"""
- loflank = self.orig[max(pos1 - config.get('flanksize'), 0):pos1]
- roflank = self.orig[pos2:pos2 + config.get('flanksize')]
+ loflank = self.orig[max(pos1 - VIS_FLANK_LENGTH, 0):pos1]
+ roflank = self.orig[pos2:pos2 + VIS_FLANK_LENGTH]
delPart = self.orig[pos1:pos2]
- odel = util.visualise_sequence(delPart, config.get('maxvissize'),
- config.get('flankclipsize'))
+ odel = util.visualise_sequence(delPart, VIS_MAX_LENGTH,
+ VIS_CLIP_FLANK_LENGTH)
bp1 = self.shift(pos1)
bp2 = self.shift(pos2)
- lmflank = self.mutated[max(bp1 - config.get('flanksize'), 0):bp1]
- rmflank = self.mutated[bp2:bp2 + config.get('flanksize')]
+ lmflank = self.mutated[max(bp1 - VIS_FLANK_LENGTH, 0):bp1]
+ rmflank = self.mutated[bp2:bp2 + VIS_FLANK_LENGTH]
- insvis = util.visualise_sequence(ins, config.get('maxvissize'),
- config.get('flankclipsize'))
+ insvis = util.visualise_sequence(ins, VIS_MAX_LENGTH,
+ VIS_CLIP_FLANK_LENGTH)
fill = abs(len(odel) - len(insvis))
if len(odel) > len(ins):
visualisation = ['%s %s %s' % (loflank, odel, roflank),
diff --git a/mutalyzer/output.py b/mutalyzer/output.py
index 97c96ea08cd0a41a8d97b12c9efa3281d514a713..3f720ea03c88791417917a465cc0f7941ed69e8b 100644
--- a/mutalyzer/output.py
+++ b/mutalyzer/output.py
@@ -26,7 +26,7 @@ Public classes:
import time
from mutalyzer import util
-from mutalyzer import config
+from mutalyzer.config import settings
from mutalyzer.models import SoapMessage
@@ -77,7 +77,7 @@ class Output() :
self._outputData = {}
self._messages = []
self._instance = util.nice_filename(instance)
- self._loghandle = open(config.get('log'), "a+")
+ self._loghandle = open(settings.LOG_FILE, "a+")
self._errors = 0
self._warnings = 0
#__init__
@@ -117,9 +117,9 @@ class Output() :
# Log the message if the message is important enough, or if it is only
# meant to be logged (level -1).
- if level >= config.get('loglevel') or level == -1 :
+ if level >= settings.LOG_LEVEL or level == -1 :
self._loghandle.write(time.strftime(
- config.get('datestring') + ' ') + "%s (%s) %s: %s: %s\n" % (
+ settings.LOG_TIME_FORMAT + ' ') + "%s (%s) %s: %s: %s\n" % (
self._instance, nice_name, code, message.named_level(),
description))
self._loghandle.flush()
@@ -136,7 +136,7 @@ class Output() :
@return: A list of messages
@rtype: list
"""
- return filter(lambda m: m.level >= config.get('outputlevel'),
+ return filter(lambda m: m.level >= settings.OUTPUT_LEVEL,
self._messages)
#getMessages
diff --git a/mutalyzer/parsers/genbank.py b/mutalyzer/parsers/genbank.py
index 5564d8f01ba78a8488816835185c55ca3b969d03..2e6c1338e3dbfea10699e9aa9072613d4fcbfa3a 100644
--- a/mutalyzer/parsers/genbank.py
+++ b/mutalyzer/parsers/genbank.py
@@ -11,7 +11,7 @@ from itertools import izip_longest
from Bio import SeqIO, Entrez
from Bio.Alphabet import ProteinAlphabet
-from mutalyzer import config
+from mutalyzer.config import settings
from mutalyzer import Db
from mutalyzer.GenRecord import PList, Locus, Gene, Record, GenRecord
@@ -62,7 +62,7 @@ class GBparser():
Private variables:
- __database ; Db.Cache object
"""
- Entrez.email = config.get('email')
+ Entrez.email = settings.EMAIL
self.__database = Db.Cache()
#__init__
diff --git a/mutalyzer/services/rpc.py b/mutalyzer/services/rpc.py
index 3a8b701adfa939cb78b9968447af41c0ac79a956..231d4862974323ea79acaeafd4359cdd597fa128 100644
--- a/mutalyzer/services/rpc.py
+++ b/mutalyzer/services/rpc.py
@@ -21,7 +21,7 @@ import tempfile
from operator import itemgetter, attrgetter
import mutalyzer
-from mutalyzer import config
+from mutalyzer.config import settings
from mutalyzer.output import Output
from mutalyzer.grammar import Grammar
from mutalyzer.sync import CacheSync
@@ -49,7 +49,7 @@ def _checkBuild(L, build) :
@type build: string
"""
- if not build in config.get('dbNames'):
+ if not build in settings.DB_NAMES:
L.addMessage(__file__, 4, "EARG", "EARG %s" % build)
raise Fault("EARG",
"The build argument (%s) was not a valid " \
@@ -171,7 +171,7 @@ class MutalyzerService(ServiceBase):
# argument for spyne.server.wsgi.WsgiApplication in all webservice
# instantiations.
- max_size = config.get('batchInputMaxSize')
+ max_size = settings.MAX_FILE_SIZE
batch_file = tempfile.TemporaryFile()
size = 0
@@ -236,7 +236,7 @@ class MutalyzerService(ServiceBase):
raise Fault('EBATCHNOTREADY', 'Batch job result is not yet ready.')
filename = 'Results_%s.txt' % job_id
- handle = open(os.path.join(config.get('resultsDir'), filename))
+ handle = open(os.path.join(settings.CACHE_DIR, filename))
return handle
@srpc(Mandatory.String, Mandatory.String, Mandatory.Integer, Boolean,
diff --git a/mutalyzer/sync.py b/mutalyzer/sync.py
index 48710f7e3af1f7d9fd1af6aa931c556dc470e85f..2438096f70c5e725c3a4facb32ec2091ff622639 100644
--- a/mutalyzer/sync.py
+++ b/mutalyzer/sync.py
@@ -11,7 +11,7 @@ from datetime import datetime, timedelta
import urllib2
from suds.client import Client
-from mutalyzer import config
+from mutalyzer.config import settings
from mutalyzer import Retriever
@@ -58,7 +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(config.get('cache'),
+ if os.path.isfile(os.path.join(settings.CACHE_DIR,
'%s.gb.bz2' % entry[0])):
cached = '%s.gb' % entry[0]
cache.append({'name': entry[0],
diff --git a/mutalyzer/util.py b/mutalyzer/util.py
index 446ec9c8e261218a2fe37b362ddc8c2352d92401..a367f31b6e8798af747a24bc2df56ee1ae018391 100644
--- a/mutalyzer/util.py
+++ b/mutalyzer/util.py
@@ -19,16 +19,17 @@ General utility functions.
"""
-import sys
-import os
-import math
-import time
+from functools import wraps
import inspect
from itertools import izip_longest
-from functools import wraps
+import math
+import operator
+import os
+import sys
+import time
-import Bio.Seq
from Bio.Alphabet import IUPAC
+import Bio.Seq
from Bio.SeqUtils import seq3
@@ -895,3 +896,81 @@ def monkey_patch_suds():
Import.open = _import_open_patched
Import.MUTALYZER_MONKEY_PATCHED = True
#monkey_patch_suds
+
+
+class AttributeDictMixin(object):
+ """
+ Augment classes with a Mapping interface by adding attribute access.
+
+ Taken from `Celery <http://www.celeryproject.org/>`_
+ (`celery.datastructures.AttributeDictMixin`).
+ """
+ def __getattr__(self, k):
+ try:
+ return self[k]
+ except KeyError:
+ raise AttributeError(
+ '{0!r} object has no attribute {1!r}'.format(
+ type(self).__name__, k))
+
+ def __setattr__(self, key, value):
+ self[key] = value
+
+
+# Helper for LazyObject.
+def _new_method_proxy(func):
+ def inner(self, *args):
+ if self._wrapped is None:
+ self._setup()
+ return func(self._wrapped, *args)
+ return inner
+
+
+class LazyObject(object):
+ """
+ A wrapper for another class that can be used to delay instantiation of the
+ wrapped class.
+
+ Taken from `Django <https://www.djangoproject.com/>`_
+ (`django.utils.functional.LazyObject`).
+ """
+ _wrapped = None
+
+ def __init__(self):
+ self._wrapped = None
+
+ __getattr__ = _new_method_proxy(getattr)
+
+ def __setattr__(self, name, value):
+ if name == '_wrapped':
+ # Assign to __dict__ to avoid infinite __setattr__ loops.
+ self.__dict__['_wrapped'] = value
+ else:
+ if self._wrapped is None:
+ self._setup()
+ setattr(self._wrapped, name, value)
+
+ def __delattr__(self, name):
+ if name == '_wrapped':
+ raise TypeError('can\'t delete _wrapped.')
+ if self._wrapped is None:
+ self._setup()
+ delattr(self._wrapped, name)
+
+ def _setup(self):
+ """
+ Must be implemented by subclasses to initialize the wrapped object.
+ """
+ raise NotImplementedError('subclasses of LazyObject must provide a '
+ '_setup() method')
+
+ # Introspection support
+ __dir__ = _new_method_proxy(dir)
+
+ # Dictionary methods support
+ __getitem__ = _new_method_proxy(operator.getitem)
+ __setitem__ = _new_method_proxy(operator.setitem)
+ __delitem__ = _new_method_proxy(operator.delitem)
+
+ __len__ = _new_method_proxy(len)
+ __contains__ = _new_method_proxy(operator.contains)
diff --git a/mutalyzer/variantchecker.py b/mutalyzer/variantchecker.py
index ce41a4aaebe0f7d0cba83288180523d03a6f131a..67ef0a63c6d9a0e4e11e4aaaaa113de8af881937 100644
--- a/mutalyzer/variantchecker.py
+++ b/mutalyzer/variantchecker.py
@@ -21,7 +21,6 @@ from Bio.Alphabet import IUPAC
from Bio.Alphabet import DNAAlphabet
from Bio.Alphabet import ProteinAlphabet
-from mutalyzer import config
from mutalyzer import util
from mutalyzer.grammar import Grammar
from mutalyzer.mutator import Mutator
@@ -377,13 +376,9 @@ def apply_deletion_duplication(first, last, type, mutator, record, O,
'Sequence "%s" at position %s was given, however, ' \
'the HGVS notation prescribes that on the forward strand ' \
'it should be "%s" at position %s.' % (
- util.visualise_sequence(str(mutator.orig[first - 1:last]),
- config.get('maxvissize'),
- config.get('flankclipsize')),
+ util.visualise_sequence(str(mutator.orig[first - 1:last])),
util.format_range(first, last),
- util.visualise_sequence(str(mutator.orig[new_first - 1:new_stop]),
- config.get('maxvissize'),
- config.get('flankclipsize')),
+ util.visualise_sequence(str(mutator.orig[new_first - 1:new_stop])),
util.format_range(new_first, new_stop)))
if forward_roll != original_forward_roll and not reverse_strand:
@@ -393,13 +388,9 @@ def apply_deletion_duplication(first, last, type, mutator, record, O,
O.addMessage(__file__, 1, 'IROLLBACK',
'Sequence "%s" at position %s was not corrected to "%s" at ' \
'position %s, since they reside in different exons.' % (
- util.visualise_sequence(str(mutator.orig[first - 1:last]),
- config.get('maxvissize'),
- config.get('flankclipsize')),
+ util.visualise_sequence(str(mutator.orig[first - 1:last])),
util.format_range(first, last),
- util.visualise_sequence(str(mutator.orig[incorrect_first - 1:incorrect_stop]),
- config.get('maxvissize'),
- config.get('flankclipsize')),
+ util.visualise_sequence(str(mutator.orig[incorrect_first - 1:incorrect_stop])),
util.format_range(incorrect_first, incorrect_stop)))
if reverse_roll and reverse_strand:
@@ -409,13 +400,9 @@ def apply_deletion_duplication(first, last, type, mutator, record, O,
'Sequence "%s" at position %s was given, however, ' \
'the HGVS notation prescribes that on the reverse strand ' \
'it should be "%s" at position %s.' % (
- util.visualise_sequence(str(mutator.orig[first - 1:last]),
- config.get('maxvissize'),
- config.get('flankclipsize')),
+ util.visualise_sequence(str(mutator.orig[first - 1:last])),
util.format_range(first, last),
- util.visualise_sequence(str(mutator.orig[new_first - 1:new_stop]),
- config.get('maxvissize'),
- config.get('flankclipsize')),
+ util.visualise_sequence(str(mutator.orig[new_first - 1:new_stop])),
util.format_range(new_first, new_stop)))
# We don't go through the trouble of visualising the *corrected* variant
@@ -457,9 +444,7 @@ def apply_inversion(first, last, mutator, record, O):
O.addMessage(__file__, 2, 'WNOCHANGE',
'Sequence "%s" at position %i_%i is a palindrome ' \
'(its own reverse complement).' % (
- util.visualise_sequence(str(mutator.orig[first - 1:last]),
- config.get('maxvissize'),
- config.get('flankclipsize')),
+ util.visualise_sequence(str(mutator.orig[first - 1:last])),
first, last))
return
else:
@@ -468,13 +453,10 @@ def apply_inversion(first, last, mutator, record, O):
'palindrome (the first %i nucleotide(s) are the reverse ' \
'complement of the last one(s)), the HGVS notation ' \
'prescribes that it should be "%s" at position %i_%i.' % (
- util.visualise_sequence(str(mutator.orig[first - 1:last]),
- config.get('maxvissize'),
- config.get('flankclipsize')),
+ util.visualise_sequence(str(mutator.orig[first - 1:last])),
first, last, snoop,
util.visualise_sequence(
- str(mutator.orig[first + snoop - 1: last - snoop]),
- config.get('maxvissize'), config.get('flankclipsize')),
+ str(mutator.orig[first + snoop - 1: last - snoop])),
first + snoop, last - snoop))
first += snoop
last -= snoop
@@ -637,9 +619,7 @@ def apply_delins(first, last, insert, mutator, record, output):
output.addMessage(__file__, 2, 'WNOCHANGE',
'Sequence "%s" at position %i_%i is identical to ' \
'the variant.' % (
- util.visualise_sequence(str(mutator.orig[first - 1:last]),
- config.get('maxvissize'),
- config.get('flankclipsize')),
+ util.visualise_sequence(str(mutator.orig[first - 1:last])),
first, last))
return
@@ -678,9 +658,7 @@ def apply_delins(first, last, insert, mutator, record, output):
'Sequence "%s" at position %i_%i has the same prefix or ' \
'suffix as the inserted sequence "%s". The HGVS notation ' \
'prescribes that it should be "%s" at position %i_%i.' % (
- util.visualise_sequence(str(mutator.orig[first - 1:last]),
- config.get('maxvissize'),
- config.get('flankclipsize')),
+ util.visualise_sequence(str(mutator.orig[first - 1:last])),
first, last, insert, insert_trimmed, first + lcp, last - lcs))
mutator.delins(first + lcp, last - lcs, insert_trimmed)
diff --git a/mutalyzer/website.py b/mutalyzer/website.py
index 651642f20fd4c024889bb691461697962e2579e5..af9b3ac453e7b426f70d0dccc975dafb6ac452fd 100644
--- a/mutalyzer/website.py
+++ b/mutalyzer/website.py
@@ -33,7 +33,7 @@ from spyne.server.http import HttpBase
import mutalyzer
from mutalyzer import util
-from mutalyzer import config
+from mutalyzer.config import settings
from mutalyzer.grammar import Grammar
from mutalyzer.services import soap
from mutalyzer import variantchecker
@@ -47,7 +47,7 @@ from mutalyzer import describe
# Show web.py debugging information.
-web.config.debug = config.get('debug')
+web.config.debug = settings.DEBUG
# URL dispatch table
@@ -88,12 +88,12 @@ render = render_jinja(pkg_resources.resource_filename('mutalyzer', 'templates'),
'releaseDate' : mutalyzer.__date__,
'release' : mutalyzer.RELEASE,
'copyrightYears' : mutalyzer.COPYRIGHT_YEARS,
- 'contactEmail' : config.get('email'),
+ 'contactEmail' : settings.EMAIL,
'serviceSoapLocation' : SERVICE_SOAP_LOCATION,
'serviceJsonLocation' : SERVICE_JSON_LOCATION,
- 'piwik' : config.get('piwik'),
- 'piwikBase' : config.get('piwikBase'),
- 'piwikSite' : config.get('piwikSite')})
+ 'piwik' : settings.PIWIK,
+ 'piwikBase' : settings.PIWIK_BASE_URL,
+ 'piwikSite' : settings.PIWIK_SITE_ID})
# web.py application
app = web.application(urls, globals(), autoreload=False)
@@ -202,7 +202,7 @@ 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.get('cache'), '%s.bz2' % file)
+ file_path = os.path.join(settings.CACHE_DIR, '%s.bz2' % file)
if not os.path.isfile(file_path):
raise web.notfound()
@@ -229,7 +229,7 @@ class Reference:
can be 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.get('cache'), '%s.bz2' % file)
+ file_path = os.path.join(settings.CACHE_DIR, '%s.bz2' % file)
if not os.path.isfile(file_path):
# The following is a hack to return a 404 not found status with
@@ -476,7 +476,7 @@ class PositionConverter:
output = Output(__file__)
IP = web.ctx["ip"]
- avail_builds = config.get('dbNames')
+ avail_builds = settings.DB_NAMES
# We have to put up with this crap just to get a certain <option>
# selected in our TAL template.
@@ -484,7 +484,7 @@ class PositionConverter:
if build in avail_builds:
selected_build = build
else:
- selected_build = config.get('defaultDb')
+ selected_build = settings.DEFAULT_DB
unselected_builds = sorted(b for b in avail_builds
if b != selected_build)
@@ -1050,9 +1050,9 @@ class BatchChecker:
"""
O = Output(__file__)
- maxUploadSize = config.get('batchInputMaxSize')
+ maxUploadSize = settings.MAX_FILE_SIZE
- avail_builds = config.get('dbNames')
+ avail_builds = settings.DB_NAMES
# We have to put up with this crap just to get a certain <option>
# selected in our TAL template.
@@ -1060,7 +1060,7 @@ class BatchChecker:
if arg1 in avail_builds:
selected_build = arg1
else:
- selected_build = config.get('defaultDb')
+ selected_build = settings.DEFAULT_DB
unselected_builds = sorted(b for b in avail_builds
if b != selected_build)
@@ -1163,7 +1163,7 @@ class BatchResult:
"""
# Todo: Check if batch job is ready (we have the job id).
filename = 'Results_%s.txt' % result
- handle = open(os.path.join(config.get('resultsDir'), filename))
+ handle = open(os.path.join(settings.CACHE_DIR, filename))
web.header('Content-Type', 'text/plain')
web.header('Content-Disposition',
'attachment; filename="%s"' % filename)
@@ -1216,13 +1216,13 @@ class Uploader:
"""
Render reference sequence uploader form.
"""
- maxUploadSize = config.get('maxDldSize')
- available_assemblies = config.get('dbNames')
+ maxUploadSize = settings.MAX_FILE_SIZE
+ available_assemblies = settings.DB_NAMES
# We have to put up with this crap just to get a certain <option>
# selected in our TAL template.
# Todo: Now we switched to Jinja2, we can make this sane.
- selected_assembly = config.get('defaultDb')
+ selected_assembly = settings.DEFAULT_DB
unselected_assemblies = sorted(b for b in available_assemblies
if b != selected_assembly)
@@ -1281,9 +1281,9 @@ class Uploader:
- chrnamestop: Stop position.
- chrnameorientation: Orientation.
"""
- maxUploadSize = config.get('maxDldSize')
+ maxUploadSize = settings.MAX_FILE_SIZE
- available_assemblies = config.get('dbNames')
+ available_assemblies = settings.DB_NAMES
O = Output(__file__)
IP = web.ctx["ip"]
@@ -1304,7 +1304,7 @@ class Uploader:
if i.chrnameassembly in available_assemblies:
selected_assembly = i.chrnameassembly
else:
- selected_assembly = config.get('defaultDb')
+ selected_assembly = settings.DEFAULT_DB
unselected_assemblies = sorted(b for b in available_assemblies
if b != selected_assembly)
diff --git a/requirements.txt b/requirements.txt
index 34b0cc02ba4f9031f0d5bd9820bf8f1a606251c1..e8b0fd5876c92abed8477e6676eb80074b5ca1eb 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,6 +1,5 @@
MySQL-python==1.2.4
biopython==1.63b
-configobj==4.7.2
lxml==3.2.4
nose==1.3.0
pyparsing==2.0.1
@@ -17,3 +16,4 @@ WebTest==1.4.2
cssselect==0.9.1
Jinja2==2.7.1
-e git+https://github.com/mammadori/magic-python.git#egg=Magic_file_extensions
+Flask==0.10.1
diff --git a/setup.py b/setup.py
index d7f16f16f8b3854a4dfa1704ffbaa49dd1245dd3..5fc25f3547340e761448398ab4b19f1b3bd3488c 100644
--- a/setup.py
+++ b/setup.py
@@ -41,6 +41,7 @@ setup(
platforms=['any'],
install_requires=install_requires,
packages=['mutalyzer',
+ 'mutalyzer.config',
'mutalyzer.entrypoints',
'mutalyzer.parsers',
'mutalyzer.services'],