From ffc9adab4456dc320b02e6f26bdbd0c0da77ec3c Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Wed, 26 Jan 2011 13:48:49 +0000
Subject: [PATCH] Fixed maximum size for uploaded genbank files. Added maximum
size for batch checker input files (5MB).
mutalyzer.conf:
src/Modules/Config.py:
- Add maximum size for batch checker input files.
src/wsgi.py:
templates/batch.html:
- Fixed maximum size for uploaded genbank files. Added maximum size for
batch checker input files (5MB).
tests/test_wsgi.py:
- Added test for a too big batch input file.
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@167 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
mutalyzer.conf | 3 +++
src/Modules/Config.py | 2 ++
src/tests/test_wsgi.py | 39 +++++++++++++++++++++++++++++++++++++++
src/wsgi.py | 20 ++++++++++++++++++--
templates/batch.html | 1 +
5 files changed, 63 insertions(+), 2 deletions(-)
diff --git a/mutalyzer.conf b/mutalyzer.conf
index 2a35880d..1cd39d23 100644
--- a/mutalyzer.conf
+++ b/mutalyzer.conf
@@ -117,6 +117,9 @@ resultsDir = "./var/cache"
# Location of the PID file.
PIDfile = "./var/batch.pid"
+# Maximum size for uploaded batch input files in megabytes.
+batchInputMaxSize = 5
+
# The output header for NameChecking
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"
diff --git a/src/Modules/Config.py b/src/Modules/Config.py
index f0662721..62f329c4 100644
--- a/src/Modules/Config.py
+++ b/src/Modules/Config.py
@@ -108,6 +108,7 @@ class Config() :
Public variables:
- PIDfile ; Location of the PID file.
+ - batchInputMaxSize ; Max size for batch input files in bytes.
"""
pass
@@ -208,6 +209,7 @@ class Config() :
# 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"])
diff --git a/src/tests/test_wsgi.py b/src/tests/test_wsgi.py
index 559cd0c9..759ffc23 100755
--- a/src/tests/test_wsgi.py
+++ b/src/tests/test_wsgi.py
@@ -361,6 +361,45 @@ class TestWSGI(unittest.TestCase):
size=len(variants),
header='Input\tStatus')
+ def test_batch_syntaxchecker_oldstyle(self):
+ """
+ Submit the batch syntax checker form with old style input file.
+ """
+ variants = ['AccNo\tGenesymbol\tMutation',
+ 'AB026906.1\tSDHD\tg.7872G>T',
+ 'NM_003002.1\t\tc.3_4insG',
+ 'AL449423.14\tCDKN2A_v002\tc.5_400del']
+ self._batch('SyntaxChecker',
+ file='\n'.join(variants),
+ size=len(variants)-1,
+ header='Input\tStatus')
+
+ def test_batch_syntaxchecker_toobig(self):
+ """
+ Submit the batch syntax checker with a too big input file.
+ """
+ seed = """
+Lorem ipsum dolor sit amet, consectetuer adipiscing elit, sed diam nonummy
+nibh euismod tincidunt ut laoreet dolore magna aliquam erat volutpat. Ut wisi
+enim ad minim veniam, quis nostrud exerci tation ullamcorper suscipit lobortis
+nisl ut aliquip ex ea commodo consequat. Duis autem vel eum iriure dolor in
+hendrerit in vulputate velit esse molestie consequat, vel illum dolore eu
+feugiat nulla facilisis at vero eros et accumsan et iusto odio dignissim qui
+blandit praesent luptatum zzril delenit augue duis dolore te feugait nulla
+facilisi."""
+ file = seed
+ # Very crude way of creating something at least 6MB in size
+ while len(file) < 6000000:
+ file += file
+ r = self.app.get('/batch')
+ form = r.forms[0]
+ form['batchType'] = 'SyntaxChecker'
+ form['batchEmail'] = 'm.vermaat.hg@lumc.nl'
+ form.set('batchFile', ('test_batch_toobig.txt',
+ file))
+ r = form.submit(status=413)
+ self.assertEqual(r.content_type, 'text/plain')
+
def test_download_py(self):
"""
Download a Python example client for the webservice.
diff --git a/src/wsgi.py b/src/wsgi.py
index 3bac3d00..cb5059bb 100644
--- a/src/wsgi.py
+++ b/src/wsgi.py
@@ -792,9 +792,12 @@ class BatchChecker:
"""
O = Output.Output(__file__, C.Output)
+ maxUploadSize = C.Batch.batchInputMaxSize
+
attr = {"messages" : [],
"errors" : [],
"debug" : [],
+ "maxSize" : float(maxUploadSize) / 1048576,
"batchTypes" : ["NameChecker",
"SyntaxChecker",
"PositionConverter",
@@ -823,6 +826,17 @@ class BatchChecker:
# to the truth value False, so 'if inFile: ...' is not useful.
if email and isEMail(email) and not inFile == None and inFile.file:
+
+ # Todo: These error messages could be delivered trough a template
+ if not 'CONTENT_LENGTH' in web.ctx.environ.keys():
+ web.header('Content-Type', 'text/plain')
+ web.ctx.status = '411 Length required'
+ return 'Content length required'
+ if int(web.ctx.environ.get('CONTENT_LENGTH')) > maxUploadSize:
+ web.header('Content-Type', 'text/plain')
+ web.ctx.status = '413 Request entity too large'
+ return 'Sorry, only files up to %s megabytes are accepted.' % (float(maxUploadSize) / 1048576)
+
D = Db.Batch(C.Db)
S = Scheduler.Scheduler(C.Scheduler, D)
FileInstance = File.File(C.File, O)
@@ -976,11 +990,13 @@ class Uploader:
try:
if i.invoermethode == "file" :
- if not 'Content-Length' in web.ctx.environ:
+ if not 'CONTENT_LENGTH' in web.ctx.environ.keys():
+ web.header('Content-Type', 'text/plain')
web.ctx.status = '411 Length required'
return 'Content length required.'
#if
- if int(web.ctx.environ['Content-Length']) > maxUploadSize :
+ if int(web.ctx.environ.get('CONTENT_LENGTH')) > maxUploadSize :
+ web.header('Content-Type', 'text/plain')
web.ctx.status = '413 Request entity too large'
return 'Upload limit exceeded.'
#if
diff --git a/templates/batch.html b/templates/batch.html
index a83ef982..2143f8c5 100644
--- a/templates/batch.html
+++ b/templates/batch.html
@@ -16,6 +16,7 @@
<li>Microsoft Excel file</li>
<li>OpenOffice ODS file</li>
</ul>
+ and the maximum size is <span tal:content = "maxSize"></span> megabytes.
</p>
<h5>We accept two types of input files, you can download examples below</h5>
<h5>Old Style:
--
GitLab