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