From b7c8fddd3339ec65e953a569055f81ea7498b79e Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Mon, 24 Nov 2014 12:05:11 +0100
Subject: [PATCH] Check batch job input field length
---
mutalyzer/File.py | 29 ++++++++++++++++++---
mutalyzer/website/templates/batch-jobs.html | 5 ++--
tests/test_scheduler.py | 17 ++++++++++++
3 files changed, 45 insertions(+), 6 deletions(-)
diff --git a/mutalyzer/File.py b/mutalyzer/File.py
index 1212d310..bbe3c2c4 100644
--- a/mutalyzer/File.py
+++ b/mutalyzer/File.py
@@ -292,6 +292,7 @@ class File() :
ret = []
notthree = []
emptyfield = []
+ toolong = []
for line, job in jobl[1:]:
#Empty line
@@ -319,7 +320,10 @@ class File() :
inputl = "~!InputFields: " #start with the skip flag
inputl+= "|".join(job)
- ret.append(inputl)
+ if len(inputl) > 200:
+ toolong.append(line)
+ else:
+ ret.append(inputl)
#for
#Create output Message for incompatible fields
@@ -335,7 +339,13 @@ class File() :
"The first and last column can't be left empty in "
"%i line(s): %s.\n" % (len(emptyfield), lines))
- errlist = notthree + emptyfield
+ if any(toolong):
+ lines = makeList(toolong, 10)
+ self.__output.addMessage(__file__, 3, "EBPARSE",
+ "Batch input field too long in %i line(s): %s.\n" %
+ (len(toolong), lines))
+
+ errlist = notthree + emptyfield + toolong
#if
else: #No Header, possibly a new BatchType
@@ -353,12 +363,23 @@ class File() :
"line(s): %s" %
(len(errlist), makeList(errlist)))
+ toolong = [line for line, row in jobl
+ if any(len(col) > 200 for col in row)]
+ if any(toolong):
+ self.__output.addMessage(__file__, 3, "EBPARSE",
+ "Batch input field too long in %i line(s): %s" %
+ (len(toolong), makeList(toolong)))
+
ret = []
for line, job in jobl:
if not any(job): #Empty line
ret.extend(['~!' for _ in range(columns)])
continue
- if line in errlist:
+ if line in toolong:
+ #Trim too long
+ ret.append("~!InputFields: " + ('|'.join(job))[:180] + '...')
+ ret.extend(['~!' for _ in range(columns - 1)])
+ elif line in errlist:
#Dirty Escape BatchEntries
ret.append("~!InputFields: " + '|'.join(job))
ret.extend(['~!' for _ in range(columns - 1)])
@@ -476,7 +497,7 @@ def makeList(l, maxlen=10):
@return: a list converted to a string with comma's and spaces
@rtype: unicode
"""
- ret = ", ".join(i for i in l[:maxlen])
+ ret = ", ".join(str(i) for i in l[:maxlen])
if len(l)>maxlen:
return ret+", ..."
else:
diff --git a/mutalyzer/website/templates/batch-jobs.html b/mutalyzer/website/templates/batch-jobs.html
index 0702c382..2029a828 100644
--- a/mutalyzer/website/templates/batch-jobs.html
+++ b/mutalyzer/website/templates/batch-jobs.html
@@ -15,13 +15,14 @@
</p>
<div id='help' style="display:none">
- <p>The mutalyzer batch checker accepts the following file formats
+ <p>The mutalyzer batch checker accepts the following file formats:
<ul>
<li>Tab delimited text file / CSV file</li>
<li>Microsoft Excel file</li>
<li>OpenOffice ODS file</li>
</ul>
- and the maximum size is <span tal:content = "maxSize"></span> megabytes.
+ The maximum file size is {{ max_file_size }} megabytes, and the maximum
+ length per entry (variant description) is 200 characters.
</p>
<h5>We accept two types of input files, you can download examples below</h5>
<h5>New Style <a href="{{ url_for('.downloads', filename='batchtestnew.txt') }}">Download Example File</a></h5>
diff --git a/tests/test_scheduler.py b/tests/test_scheduler.py
index 791f867d..c118bfd7 100644
--- a/tests/test_scheduler.py
+++ b/tests/test_scheduler.py
@@ -71,6 +71,23 @@ class TestScheduler(MutalyzerTest):
'OK']]
self._batch_job_plain_text(variants, expected, 'syntax-checker')
+ def test_large_input(self):
+ """
+ Simple batch job with large input.
+ """
+ variants = ['chr13:g.114503915delCACCTGCGGGAGGTGAGGGGCGCTGGGGACCCCCG'
+ 'TATCTACACCTGCGGGAGGTGAGGGGCGCTGGGGACCCCTATATCTACACCTGAG'
+ 'GGAGGTGinsTGCCTGCGGGAGGTGAGGGGCGCTGGGGACCCCCGTATCTACACC'
+ 'TGCGGGAGGTGAGGGGCGCTGGGGACCCCTATATCTACACCTGAGGGAGGTG']
+
+ expected = [['InputFields: chr13:g.114503915delCACCTGCGGGAGGTGAGGGGC'
+ 'GCTGGGGACCCCCGTATCTACACCTGCGGGAGGTGAGGGGCGCTGGGGACCCCT'
+ 'ATATCTACACCTGAGGGAGGTGinsTGCCTGCGGGAGGTGAGGGGCGCTGGGGA'
+ 'CCCCCGTATCTACACCTGCGGGAGGTGAGGG...',
+ '(Scheduler): Entry could not be formatted correctly, '
+ 'check batch input file help for details']]
+ self._batch_job_plain_text(variants, expected, 'syntax-checker')
+
@fix(cache('AB026906.1', 'NM_000059.3'))
def test_name_checker(self):
"""
--
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