From eb1513840ec08a7569031ec6227d0cbad5410f16 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Fri, 27 Jan 2012 14:02:52 +0000
Subject: [PATCH] Add logging to all website entry points (#84)
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@462 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
mutalyzer/website.py | 43 +++++++++++++++++++++++++++++++++++++++++--
1 file changed, 41 insertions(+), 2 deletions(-)
diff --git a/mutalyzer/website.py b/mutalyzer/website.py
index 1d154ca7..c20e481d 100644
--- a/mutalyzer/website.py
+++ b/mutalyzer/website.py
@@ -327,12 +327,20 @@ class GetGS:
i = web.input(mutationName=None, variantRecord=None, forward=None)
+ output.addMessage(__file__, -1, 'INFO',
+ 'Started request getGS(%s, %s, %s)' % \
+ (i.mutationName, i.variantRecord, i.forward))
+
# 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(i.mutationName), output)
+ output.addMessage(__file__, -1, 'INFO',
+ 'Finished request getGS(%s, %s, %s)' % \
+ (i.mutationName, i.variantRecord, i.forward))
+
legends = output.getOutput("legends")
# Filter the transcript from the legend
@@ -376,6 +384,10 @@ class SyntaxCheck:
"""
output = Output(__file__)
i = web.input()
+
+ output.addMessage(__file__, -1, 'INFO',
+ 'Started request syntaxCheck(%s)' % i.variant)
+
variant = i.variant
if variant.find(',') >= 0:
output.addMessage(__file__, 2, "WCOMMASYNTAX",
@@ -392,6 +404,10 @@ class SyntaxCheck:
"parseError" : pe,
"debug" : ""
}
+
+ output.addMessage(__file__, -1, 'INFO',
+ 'Finished request syntaxCheck(%s)' % i.variant)
+
return render.parse(args)
#SyntaxCheck
@@ -499,6 +515,11 @@ class PositionConverter:
}
if build and variant:
+
+ output.addMessage(__file__, -1, 'INFO',
+ 'Started request positionConverter(%s, %s)' % \
+ (build, variant))
+
converter = Converter(build, output)
#Convert chr accNo to NC number
@@ -529,6 +550,11 @@ class PositionConverter:
#if
attr['messages'] = map(util.message_info, output.getMessages())
+
+ output.addMessage(__file__, -1, 'INFO',
+ 'Finished request positionConverter(%s, %s)' % \
+ (build, variant))
+
return render.converter(attr)
#PositionConverter
@@ -688,12 +714,11 @@ class Check:
return render.check(args, standalone=not interactive)
output.addMessage(__file__, -1, 'INFO', 'Received variant %s' % name)
+
# 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), output)
- output.addMessage(__file__, -1, 'INFO',
- 'Finished processing variant %s' % name)
errors, warnings, summary = output.Summary()
record_type = output.getIndexedOutput('recordType', 0, '')
@@ -765,6 +790,9 @@ class Check:
'browserLink' : browser_link
}
+ output.addMessage(__file__, -1, 'INFO',
+ 'Finished processing variant %s' % name)
+
return render.check(args, standalone=not interactive)
#Check
@@ -1133,6 +1161,11 @@ class Uploader:
genesymbol='', organism='', fiveutr='', threeutr='',
chracc='', start='', stop='', orientation='')
+ O.addMessage(__file__, -1, 'INFO',
+ 'Started request upload(%s, %s, %s, %s, %s, %s, %s, %s, %s, %s)' % \
+ (i.invoermethode, i.urlveld, i.genesymbol, i.organism,
+ i.fiveutr, i.threeutr, i.chracc, i.start, i.stop, i.orientation))
+
try:
if i.invoermethode == "file" :
if not 'CONTENT_LENGTH' in web.ctx.environ.keys():
@@ -1196,6 +1229,12 @@ class Uploader:
"maxSize" : float(maxUploadSize) / 1048576,
"errors" : errors
}
+
+ O.addMessage(__file__, -1, 'INFO',
+ 'Finished request upload(%s, %s, %s, %s, %s, %s, %s, %s, %s, %s)' % \
+ (i.invoermethode, i.urlveld, i.genesymbol, i.organism,
+ i.fiveutr, i.threeutr, i.chracc, i.start, i.stop, i.orientation))
+
return render.gbupload(args)
#Uploader
--
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