annotate nist_controller.py @ 12:3a69874edaf7

small fix
author pieter.lukasse@wur.nl
date Fri, 23 Jan 2015 10:48:21 +0100
parents cce6989ed423
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
1 """
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
2 Controller for integration with NIST data.
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
3
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
4 Place this in: <galaxy_home>/lib/galaxy/webapps/galaxy/controllers
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
5 and then it can be accessed via URL:
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
6
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
7 http://<galaxy_url>/nist_controller/get_nistdata
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
8 e.g.
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
9 http://dev1.ab.wurnet.nl:8088/nist_controller/get_nistdata
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
10
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
11 """
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
12
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
13 import urllib2
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
14 from galaxy.web.base.controller import BaseUIController, url_for, error, web
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
15
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
16
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
17 class NistController( BaseUIController ):
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
18 """
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
19 Provides some services for the NIST html report
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
20 """
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
21
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
22 @web.expose
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
23 def get_nistdata( self, trans, casnr=None ):
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
24 """
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
25 Generate a redirect to NIST webbook web app
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
26 casNr example: "C537268"
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
27
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
28 """
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
29
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
30 nist_response = _fire_query_and_return_content("http://webbook.nist.gov/cgi/cbook.cgi?JCAMP="+ casnr + "&Index=0&Type=Mass")
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
31 peak_table = nist_response.split("##PEAK TABLE=(XY..XY)")[1].split("##END=")[0]
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
32 peak_table = peak_table.replace("\n", " ").strip()
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
33 return peak_table
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
34
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
35
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
36
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
37
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
38
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
39 def _fire_query_and_return_content(url):
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
40 '''
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
41 This method will fire the HTTP call and
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
42 return the results
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
43 '''
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
44
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
45 try:
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
46 data = urllib2.urlopen(url).read()
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
47
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
48 return data
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
49
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
50 except urllib2.HTTPError, e:
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
51 raise Exception( "HTTP error for URL: " + url + " : %s - " % e.code + e.reason)
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
52 except urllib2.URLError, e:
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
53 raise Exception( "Network error: %s" % e.reason.args[1] + ". Error accessing remote service [" + url + "] ")
cce6989ed423 new NIST wrapper demo tools
pieter.lukasse@wur.nl
parents:
diff changeset
54