From 581cac3fd54fad82495da0edf53b29aba149f4a1 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Thu, 5 Dec 2013 16:53:37 +0100
Subject: [PATCH] Define default values for most configuration settings
---
extras/config.example | 1 -
extras/config.user.example | 3 ++
mutalyzer/config.py | 58 +++++++++++++++++++++++++++++++++++---
3 files changed, 57 insertions(+), 5 deletions(-)
diff --git a/extras/config.example b/extras/config.example
index 33ebc4c3..62bf3ce3 100644
--- a/extras/config.example
+++ b/extras/config.example
@@ -122,7 +122,6 @@ PIDfile = "/var/run/mutalyzer/mutalyzer-batchd.pid"
batchInputMaxSize = 5
# The output header for NameChecking
-# Todo: migration for restriction sites
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"
# The output header for SyntaxChecking
diff --git a/extras/config.user.example b/extras/config.user.example
index 92dd1d4b..fe0887d7 100644
--- a/extras/config.user.example
+++ b/extras/config.user.example
@@ -4,6 +4,9 @@
# Copy this file to ~/.config/mutalyzer/config to overwrite definitions from
# /etc/mutalyzer.config.
+# Use this email address for retrieval of records at the NCBI.
+email = "mutalyzer@humgen.nl"
+
# The cache directory.
cache = "/home/<USERNAME>/.cache/mutalyzer"
diff --git a/mutalyzer/config.py b/mutalyzer/config.py
index 29ea9e07..0627927c 100644
--- a/mutalyzer/config.py
+++ b/mutalyzer/config.py
@@ -106,8 +106,58 @@ class _Config():
if not config:
raise ConfigurationError('Could not locate configuration.')
- try:
+ # 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.
@@ -116,7 +166,7 @@ class _Config():
self._values = {'autoReconnect': config.as_bool('autoReconnect'),
'debug': config.as_bool('debug'),
'piwik': config.as_bool('piwik'),
- 'threshold': float(config['threshold'])}
+ 'threshold': config.as_float('threshold')}
# Simple string values.
for name in ('email', 'cache', 'lrgurl', 'internalDb', 'dbNames',
@@ -133,11 +183,11 @@ class _Config():
'maxvissize', 'flankclipsize', 'bufSize',
'spliceAlarm', 'spliceWarn', 'piwikSite',
'proteinLinkLifetime', 'proteinLinkNoneLifetime'):
- self._values[name] = int(config[name])
+ self._values[name] = config.as_int(name)
# File sizes (given in megabytes, stored in bytes).
for name in ('cachesize', 'maxDldSize', 'batchInputMaxSize'):
- self._values[name] = int(config[name]) * 1048576
+ self._values[name] = config.as_int(name) * 1048576
except KeyError as e:
raise ConfigurationError('Missing configuration value: %s' % e)
--
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