Updated SOAP client examples and documentation.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/soaplib-branch@120 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

src/handler.py

@@ -34,7 +34,7 @@ def handler(req):
         - ".js"      ; Return the raw content of the file (to include JavaScript
                        from an HTML file).
         - ".py"      ; Return the content as a downloadable file after it has
-                       been processed by TAL (to generate webservice client
+          ".cs"        been processed by TAL (to generate webservice client
                        files).
 
     By default, the HTML publisher is used for normal HTML files and other
@@ -98,7 +98,7 @@ def handler(req):
     #if
 
     # Process the file with TAL and return the content as a downloadable file.
-    if req.uri.endswith(".py") :
+    if req.uri.endswith(".py") or req.uri.endswith(".cs") :
         reqFile = req.uri.split('/')[-1]
         #req.content_type = 'application/octet-stream'
         req.headers_out["Content-Disposition"] = \

templates/client-mono.cs

+/*
+Compilation instructions:
+
+wsdl 'http://<tal tal:replace = "path"></tal>/service/?wsdl'
+gmcs /target:library MutalyzerService.cs -r:System.Web.Services
+gmcs /r:MutalyzerService.dll client-mono.cs
+*/
+
+using System;
+
+class Mutalyzer {
+
+    public static void Main(string [] args) {
+
+        checkSyntax c = new checkSyntax();
+        c.variant = args[0];
+
+        Console.WriteLine("Checking " + c.variant);
+
+        MutalyzerService mutalyzer = new MutalyzerService();
+
+        checkSyntaxResponse result = mutalyzer.checkSyntax(c);
+
+        if (result == null)
+            Console.WriteLine("[No result]");
+        else
+            Console.WriteLine(result.checkSyntaxResult);
+
+    }
+
+}

templates/client-soappy.py

+#!/usr/bin/python
+
+import logging; logging.basicConfig()
+from SOAPpy import WSDL
+
+url = 'http://<tal tal:replace = "path"></tal>/service/?wsdl'
+o = WSDL.Proxy(url)
+
+# Get all transcripts that are hit when we look at position 159272155 on
+# chromosome 1.
+print "hg19", "chr1", 159272155
+transcripts = o.getTranscripts(build = "hg19", chrom = "chr1",
+                               pos = 159272155)
+if not type(transcripts) == list: transcripts = [transcripts]
+for i in transcripts :
+    print i, o.getGeneName(build = "hg19", accno = i)
+
+# Get all transcripts and genes that have (part of) a transcript in the range
+# 159272155-159372155 on chromosome 1
+print "\n", "hg19", "chr1", 159272155, 159372155, 1
+transcripts = o.getTranscriptsRange(build = "hg19", chrom = "chr1",
+                                    pos1 = 159272155, pos2 = 159372155, method = 1)
+if not type(transcripts) == list: transcripts = [transcripts]
+for i in transcripts :
+    print i, o.getGeneName(build = "hg19", accno = i)
+
+# Get all transcripts and genes that have the entire transcript in the range
+# 159272155-159372155 on chromosome 1
+print "\n", "hg19", "chr1", 159272155, 159372155, 0
+transcripts = o.getTranscriptsRange(build = "hg19", chrom = "chr1",
+                                    pos1 = 159272155, pos2 = 159372155, method = 0)
+if not type(transcripts) == list: transcripts = [transcripts]
+for i in transcripts :
+    print i, o.getGeneName(build = "hg19", accno = i)
+
+print "\n"
+print o.mappingInfo(LOVD_ver = "123", build = "hg19", accNo = "NM_002001.2",
+                    variant = "c.1del")
+
+print "\n"
+print o.transcriptInfo(LOVD_ver = "123", build = "hg19", accNo = "NM_002001.2")
+
+print "\n"
+print o.numberConversion(build = "hg19", variant = "NM_002001.2:c.1del")
+
+m = o.transcriptInfo(LOVD_ver = "123", build = "hg19", accNo = "NM_002001.2")
+print m.CDS_stop
+
+transcripts = o.getTranscriptsByGeneName(build = "hg19", name = "DMD")
+if not type(transcripts) == list: transcripts = [transcripts]
+for i in transcripts :
+    print i
+
+mutalyzerOutput = o.runMutalyzer(variant = "NM_002001.2:g.1del")
+print mutalyzerOutput.original
+print mutalyzerOutput.mutated
+print mutalyzerOutput.origMRNA
+print mutalyzerOutput.mutatedMRNA
+print mutalyzerOutput.origCDS
+print mutalyzerOutput.newCDS
+print mutalyzerOutput.origProtein
+print mutalyzerOutput.newProtein
+print mutalyzerOutput.altProtein
+print mutalyzerOutput.errors
+print mutalyzerOutput.warnings
+print mutalyzerOutput.summary

templates/sp.py → templates/client-suds.py

 #!/usr/bin/python
 
-from SOAPpy import WSDL
+import logging; logging.basicConfig()
+from suds.client import Client
 
-o = WSDL.Proxy("http://<tal tal:replace = "path"></tal>/service.wsdl")
+url = 'http://<tal tal:replace = "path"></tal>/service/?wsdl'
+c = Client(url)
+o = c.service
 
-# Get all transcripts that are hit when we look at position 159272155 on 
+# Get all transcripts that are hit when we look at position 159272155 on
 # chromosome 1.
 print "hg19", "chr1", 159272155
-for i in o.getTranscripts(build = "hg19", chrom = "chr1", 
+for i in o.getTranscripts(build = "hg19", chrom = "chr1",
               pos = 159272155) :
     print i, o.getGeneName(build = "hg19", accno = i)
 
-# Get all transcripts and genes that have (part of) a transcript in the range 
+# Get all transcripts and genes that have (part of) a transcript in the range
 # 159272155-159372155 on chromosome 1
 print "\n", "hg19", "chr1", 159272155, 159372155, 1
-for i in o.getTranscriptsRange(build = "hg19", chrom = "chr1", 
+for i in o.getTranscriptsRange(build = "hg19", chrom = "chr1",
               pos1 = 159272155, pos2 = 159372155, method = 1) :
     print i, o.getGeneName(build = "hg19", accno = i)
 
-# Get all transcripts and genes that have the entire transcript in the range 
+# Get all transcripts and genes that have the entire transcript in the range
 # 159272155-159372155 on chromosome 1
 print "\n", "hg19", "chr1", 159272155, 159372155, 0
-for i in o.getTranscriptsRange(build = "hg19", chrom = "chr1", 
+for i in o.getTranscriptsRange(build = "hg19", chrom = "chr1",
               pos1 = 159272155, pos2 = 159372155, method = 0) :
     print i, o.getGeneName(build = "hg19", accno = i)
 
 print "\n"
-print o.mappingInfo(LOVD_ver = "123", build = "hg19", accNo = "NM_002001.2", 
+print o.mappingInfo(LOVD_ver = "123", build = "hg19", accNo = "NM_002001.2",
                     variant = "c.1del")
 
 print "\n"
@@ -41,7 +44,7 @@ print m.CDS_stop
 for i in o.getTranscriptsByGeneName(build = "hg19", name = "DMD") :
     print i
 
-mutalyzerOutput = o.runMutalyzer(variant = "NM_002001.2:g.1del")
+mutalyzerOutput = o.runMutalyzer("NM_002001.2:g.1del")
 print mutalyzerOutput.original
 print mutalyzerOutput.mutated
 print mutalyzerOutput.origMRNA

templates/webservices.html

@@ -8,16 +8,18 @@
       <h3>Webservices page</h3>
     </center>
     <br>
-    The following programs are example scripts for the webservice. In order
-    for them to function, you need to have <tt>python-soappy</tt> installed.<br>
-    All these scripts use the following 
-    <tt><a href = "service.wsdl">service.wsdl</a></tt> file.<br>
-    <br>
-    The <tt><a href = "sp.py">sp.py</a></tt> test client. This client retrieves
-    a list of transcripts, given a chromosome and a genomic position. Of each
-    of these transcripts, the corresponding gene name is given.<br>
-    <br>
-    Also see the <a href = "documentation">documentation</a> page for a full 
+    Most Mutalyzer functionality is available trough a SOAP webservice.
+    A <a href="service/?wsdl">WSDL description</a> is available
+    for easy generation of client programs in many languages.
+    <h3>Example clients</h3>
+    The following are some example client programs for the webservice.
+    <ul>
+      <li>Python client using the suds library: <a href="client-suds.py"><tt>client-suds.py</tt></a>
+      <li>Python client using the soappy library: <a href="client-soappy.py"><tt>client-soappy.py</tt></a>
+      <li>Mono client in C#: <a href="client-mono.cs"><tt>client-mono.cs</tt></a>
+    </ul>
+    <h3>Documentation</h3>
+    Also see the <a href = "documentation">documentation</a> page for a full
     description of the webservice.
   </div>
   </body>