Define default values for most configuration settings

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

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"
 

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)