From 54188c596af5aaee9b782fedf3596d0e2d46e197 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Mon, 18 May 2015 14:31:39 +0200
Subject: [PATCH] Limit input sequence length for description extractor
This is hopefully a temporary measure. At the moment we cannot accurately
predict the running time of the extractor, so we have to aggressively
limit the input based on the worst-case expectation.
As a worst-case scenario, we currently use random input sequences, where
length 1000bp yields about 500ms of running time.
In the future we hope to either:
1. Predict the running time and abort if needed.
2. Keep track of the running time and abort if needed.
3. Run the extractor in a task scheduler with a running time limit.
---
mutalyzer/services/rpc.py | 5 +++++
mutalyzer/website/templates/description-extractor.html | 9 ++++++---
mutalyzer/website/views.py | 6 +++++-
3 files changed, 16 insertions(+), 4 deletions(-)
diff --git a/mutalyzer/services/rpc.py b/mutalyzer/services/rpc.py
index 77027112..3e326417 100644
--- a/mutalyzer/services/rpc.py
+++ b/mutalyzer/services/rpc.py
@@ -1240,6 +1240,11 @@ class MutalyzerService(ServiceBase):
output.addMessage(__file__, -1, 'INFO',
'Received request descriptionExtract')
+ if not settings.TESTING and (len(reference) > 1000 or
+ len(observed) > 1000):
+ raise Fault('EMAXSIZE',
+ 'Input sequences are restricted to 1000bp.')
+
allele = extractor.describe_dna(reference, observed)
result = Allele()
diff --git a/mutalyzer/website/templates/description-extractor.html b/mutalyzer/website/templates/description-extractor.html
index ebf8ef51..5927bf3e 100644
--- a/mutalyzer/website/templates/description-extractor.html
+++ b/mutalyzer/website/templates/description-extractor.html
@@ -5,7 +5,10 @@
{% block content %}
-<p class="alert alert-warning">Note that this is an experimental service.</p>
+<p class="alert alert-warning">
+Please note that this is an experimental service and we are currently limiting
+input sequences to 1000bp.
+</p>
<p>
Extract the HGVS variant description from a reference sequence and an observed
@@ -85,7 +88,7 @@ Please supply a reference sequence and an observed sequence.
<div class="form-group">
<label for="reference_accession_number">Reference accession number</label>
<input type="text" name="reference_accession_number" id="reference_accession_number" value="{{ reference_accession_number }}" class="form-control form-pre example-target" placeholder="Reference accession number">
- <p>Example: <code class="example-input" data-for="reference_accession_number">NM_004006.1</code></p>
+ <p>Example: <code class="example-input" data-for="reference_accession_number">NM_198697.1</code></p>
</div>
</div>
</div>
@@ -140,7 +143,7 @@ Please supply a reference sequence and an observed sequence.
<div class="form-group">
<label for="sample_accession_number">Sample accession number</label>
<input type="text" name="sample_accession_number" id="sample_accession_number" value="{{ sample_accession_number }}" class="form-control form-pre example-target-2" placeholder="Sample accession number">
- <p>Example: <code class="example-input" data-for="sample_accession_number">NM_004006.2</code></p>
+ <p>Example: <code class="example-input" data-for="sample_accession_number">NM_198697.2</code></p>
</div>
</div>
</div>
diff --git a/mutalyzer/website/views.py b/mutalyzer/website/views.py
index b3b63e9b..fffb8bb6 100644
--- a/mutalyzer/website/views.py
+++ b/mutalyzer/website/views.py
@@ -783,7 +783,11 @@ def description_extractor_submit():
raw_vars = None
if r and s:
- raw_vars = extractor.describe_dna(r, s)
+ if not settings.TESTING and (len(r) > 1000 or len(s) > 1000):
+ output.addMessage(__file__, 3, 'EMAXSIZE',
+ 'Input sequences are restricted to 1000bp.')
+ else:
+ raw_vars = extractor.describe_dna(r, s)
errors, warnings, summary = output.Summary()
messages = map(util.message_info, output.getMessages())
--
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