From 690bf53d592d9d722b459228902dc4f42783b27f Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Mon, 20 Aug 2012 12:48:29 +0000
Subject: [PATCH] Fix descriptionExtract RPC method (for r595)
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@600 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
extras/soap-tools/descriptionExtract.py | 46 +++++++++++++++++++++++++
mutalyzer/services/rpc.py | 6 ++--
2 files changed, 50 insertions(+), 2 deletions(-)
create mode 100755 extras/soap-tools/descriptionExtract.py
diff --git a/extras/soap-tools/descriptionExtract.py b/extras/soap-tools/descriptionExtract.py
new file mode 100755
index 00000000..d1ff2b90
--- /dev/null
+++ b/extras/soap-tools/descriptionExtract.py
@@ -0,0 +1,46 @@
+#!/usr/bin/env python
+"""
+Extract the HGVS variant description from a reference sequence and an observed
+sequence.
+
+Usage:
+ {command} reference observed
+
+ reference: Reference DNA sequence.
+ observed: Observed DNA sequence.
+
+The extracted HGVS description is retrieved from the Mutalyzer SOAP webservice
+and printed to standard output.
+"""
+
+
+from mutalyzer.util import monkey_patch_suds; monkey_patch_suds()
+
+import sys
+from suds.client import Client
+
+from mutalyzer.util import format_usage
+
+
+WSDL_LOCATION = 'http://localhost/mutalyzer/services/?wsdl'
+
+
+def main(reference, observed):
+ """
+ Extract the HGVS variant description from a reference sequence and an
+ observed sequence.
+ """
+ service = Client(WSDL_LOCATION, cache=None).service
+ result = service.descriptionExtract(reference, observed)
+
+ if result:
+ print result.description
+ else:
+ print 'No description returned.'
+
+
+if __name__ == '__main__':
+ if len(sys.argv) != 3:
+ print format_usage()
+ sys.exit(1)
+ main(*sys.argv[1:])
diff --git a/mutalyzer/services/rpc.py b/mutalyzer/services/rpc.py
index 6551e3df..0270a194 100644
--- a/mutalyzer/services/rpc.py
+++ b/mutalyzer/services/rpc.py
@@ -539,7 +539,7 @@ class MutalyzerService(ServiceBase):
return result
#chromosomeName
- @srpc(Mandatory.String, Mandatory.String, String,
+ @srpc(Mandatory.String, Mandatory.String, String,
_returns=Array(Mandatory.String))
def numberConversion(build, variant, gene=None):
"""
@@ -1029,6 +1029,8 @@ class MutalyzerService(ServiceBase):
"""
Extract the HGVS variant description from a reference sequence and an
observed sequence.
+
+ Note that this only works on DNA sequences for now.
"""
output = Output(__file__)
@@ -1036,7 +1038,7 @@ class MutalyzerService(ServiceBase):
'Received request descriptionExtract')
result = Allele()
- result.allele = describe.describeDNA(reference, observed)
+ result.allele = describe.describe(reference, observed)
result.description = describe.alleleDescription(result.allele)
output.addMessage(__file__, -1, 'INFO',
--
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