/lib/galaxy/webapps/demo_sequencer/controllers/common.py
Python | 227 lines | 192 code | 2 blank | 33 comment | 40 complexity | d87a546a2b37d1088848e68bc5ce5c0a MD5 | raw file
1from galaxy.web.base.controller import * 2from galaxy.web.framework.helpers import time_ago 3from galaxy import util 4import time, socket, urllib, urllib2, base64, copy 5from galaxy.util.json import * 6from urllib import quote_plus, unquote_plus 7 8import logging 9log = logging.getLogger( __name__ ) 10 11class CommonController( BaseUIController ): 12 @web.expose 13 def index( self, trans, **kwd ): 14 redirect_action = util.restore_text( kwd.get( 'redirect_action', '' ) ) 15 titles = util.restore_text( kwd.get( 'titles', '' ) ) 16 titles = util.listify( titles ) 17 JobId = util.restore_text( kwd.get( 'JobId', '' ) ) 18 sample_id = util.restore_text( kwd.get( 'sample_id', '' ) ) 19 message = util.restore_text( kwd.get( 'message', '' ) ) 20 status = kwd.get( 'status', 'done' ) 21 redirect_delay = trans.app.sequencer_actions_registry.redirect_delay 22 sequencer_redirects = copy.deepcopy( trans.app.sequencer_actions_registry.sequencer_redirects ) 23 sequencer_requests = copy.deepcopy( trans.app.sequencer_actions_registry.sequencer_requests ) 24 requests = [] 25 if redirect_action == 'stop': 26 # Handle any additional requests 27 for request_tup in sequencer_requests: 28 url, http_method, request_params, response_type = self.parse_request_tup( request_tup, **kwd ) 29 response = self.handle_request( trans, url, http_method, **request_params ) 30 # Handle response, currently only handles json 31 if response_type == 'json': 32 response = from_json_string( response ) 33 # Handle response that is an error, for example: 34 # { "Success":false, "Message":"some error string" } 35 if 'Success' in response and response[ 'Success' ] == 'false': 36 message = response[ 'Message' ] 37 return self.handle_failure( trans, url, message ) 38 if 'JobId' in response: 39 JobId = str( response[ 'JobId' ] ) 40 kwd[ 'JobId' ] = JobId 41 # Handle the final redirect, if any ( should only be 0 or 1 ). 42 for request_tup in trans.app.sequencer_actions_registry.final_redirect: 43 url, http_method, request_params, response_type = self.parse_request_tup( request_tup, **kwd ) 44 return trans.fill_template( 'webapps/demo_sequencer/redirect.mako', redirect_url=url ) 45 # Exit if we have no redirection 46 redirect_action = 'exit' 47 elif not redirect_action: 48 # Specially handle the initial request to the demo sequencer by starting with the first defined redirect. 49 redirect_action, action_dict = sequencer_redirects.items()[0] 50 titles = [ action_dict[ 'title' ] ] 51 if 'requests' in action_dict: 52 requests = action_dict[ 'requests' ] 53 else: 54 for index, key in enumerate( sequencer_redirects.iterkeys() ): 55 if redirect_action == key: 56 try: 57 # Move to the next action, if there is one. 58 redirect_action = sequencer_redirects.keys()[ index + 1 ] 59 action_dict = sequencer_redirects[ redirect_action ] 60 titles.append( action_dict[ 'title' ] ) 61 except: 62 # If we're done redirecting, stop. 63 redirect_action = 'stop' 64 break 65 if not trans.app.sequencer_actions_registry.authenticated: 66 # Support various types of authentication 67 if trans.app.sequencer_actions_registry.browser_login: 68 # We'll just build the URL here since authentication will be handled in the browser 69 url = trans.app.sequencer_actions_registry.browser_login[ 'url' ] 70 params = trans.app.sequencer_actions_registry.browser_login[ 'params' ] 71 trans.app.sequencer_actions_registry.browser_login = '%s?%s' %( url, urllib.urlencode( params ) ) 72 if not trans.app.sequencer_actions_registry.final_redirect: 73 # If we don't have a final_redirect tag, but we want our browser to authenticate, 74 # do it ow. If we have a final_redirect tag, browser authentication will happen there. 75 url = web.url_for( controller='common', action='index', **kwd ) 76 return trans.fill_template( 'webapps/demo_sequencer/redirect.mako', redirect_url=url ) 77 if trans.app.sequencer_actions_registry.basic_http_authentication: 78 # Example tag: 79 # <basic_http_authentication user="administrator" password="galaxy" url="http://127.0.0.1" realm="" /> 80 user, password, url, realm = trans.app.sequencer_actions_registry.basic_http_authentication 81 # Create a password manager 82 password_mgr = urllib2.HTTPPasswordMgrWithDefaultRealm() 83 # Add the username, password and realm. 84 if not realm: 85 realm = None 86 password_mgr.add_password( realm, url, user, password ) 87 handler = urllib2.HTTPBasicAuthHandler( password_mgr ) 88 # Create "opener" (OpenerDirector instance) 89 opener = urllib2.build_opener( handler ) 90 # Install the opener, now all calls to urllib2.urlopen use our opener. 91 urllib2.install_opener( opener ) 92 trans.app.sequencer_actions_registry.authenticated = True 93 if trans.app.sequencer_actions_registry.http_headers_authorization: 94 # Example tag: 95 # <http_headers_authorization credentials="administrator:galaxy" url="http://127.0.0.1" /> 96 url, credentials = trans.app.sequencer_actions_registry.http_headers_authorization 97 req = urllib2.Request( url ) 98 req.add_header( 'Authorization', 'Basic %s' % base64.b64encode( credentials ) ) 99 trans.app.sequencer_actions_registry.authenticated = True 100 if trans.app.sequencer_actions_registry.http_cookie_processor_authentication: 101 # Example tag: 102 # <http_cookie_processor_authentication url="http://127.0.0.1/login"> 103 # <param name="user" value="administrator"/> 104 # <param name="password" value="galaxy"/> 105 # </http_cookie_processor_authentication> 106 url = trans.app.sequencer_actions_registry.http_cookie_processor_authentication[ 'url' ] 107 params = trans.app.sequencer_actions_registry.http_cookie_processor_authentication[ 'params' ] 108 # Build opener with HTTPCookieProcessor 109 opener = urllib2.build_opener( urllib2.HTTPCookieProcessor() ) 110 urllib2.install_opener( opener ) 111 # Perform login with params 112 page = opener.open( url, urllib.urlencode( params ) ) 113 response = page.read() 114 page.close() 115 # Any additional requests should automatically pass back any 116 # cookies received during login, thanks to the HTTPCookieProcessor 117 trans.app.sequencer_actions_registry.authenticated = True 118 # Handle requests, if there are any 119 for request_tup in requests: 120 url, http_method, request_params, response_type = self.parse_request_tup( request_tup, **kwd ) 121 response = self.handle_request( trans, url, http_method, **request_params ) 122 # Handle response, currently only handles json 123 if response_type == 'json': 124 response = from_json_string( response ) 125 # Handle response that is an error, for example: 126 # { "Success":false, "Message":"some error string" } 127 if 'Success' in response and response[ 'Success' ] == 'false': 128 message = response[ 'Message' ] 129 return self.handle_failure( trans, url, message ) 130 if 'JobId' in response: 131 JobId = str( response[ 'JobId' ] ) 132 kwd[ 'JobId' ] = JobId 133 titles = ','.join( titles ) 134 return trans.fill_template( "webapps/demo_sequencer/index.mako", 135 redirect_action=redirect_action, 136 redirect_delay=redirect_delay, 137 titles=titles, 138 sample_id=sample_id, 139 JobId=JobId, 140 message=message, 141 status=status ) 142 def parse_request_tup( self, request_tup, **kwd ): 143 redirect_action = util.restore_text( kwd.get( 'redirect_action', '' ) ) 144 titles = util.restore_text( kwd.get( 'titles', '' ) ) 145 JobId = util.restore_text( kwd.get( 'JobId', '' ) ) 146 sample_id = util.restore_text( kwd.get( 'sample_id', '' ) ) 147 message = util.restore_text( kwd.get( 'message', '' ) ) 148 status = kwd.get( 'status', 'done' ) 149 url, http_method, request_params, response_type = request_tup 150 url = unquote_plus( url ) 151 # Handle URLs in which we replace param values, which will look something like: 152 # http://127.0.0.1/getinfo/{id}. 153 replace_with_param = url.find( '{' ) > 0 154 if replace_with_param: 155 # Handle the special-case {JobId} param. 156 if url.find( '{JobId}' ) > 0: 157 if JobId: 158 url = url.replace( '{JobId}', str( JobId ) ) 159 for key, value in kwd.items(): 160 # Don't attempt to replace if there is nothing with which to do it 161 # or if the value itself should be replaced with something. 162 if value and not value.startswith( '{' ): 163 replace_str = '{%s}' % key 164 if url.find( replace_str ) > 0: 165 url = url.replace( replace_str, value ) 166 # Handle request parameters in which we replace param values. 167 for key, val in request_params.items(): 168 if val and val.startswith( '{' ): 169 replace_key = val.lstrip( '{' ).rstrip( '}' ) 170 if replace_key in kwd: 171 request_params[ key ] = kwd[ replace_key ] 172 return url, http_method, request_params, response_type 173 def handle_request( self, trans, url, http_method=None, **kwd ): 174 if 'Name' in kwd and not kwd[ 'Name' ]: 175 # Hack: specially handle parameters named "Name" if no param_value is given 176 # by providing a date / time string - guarantees uniqueness, if required. 177 kwd[ 'Name' ] = time.strftime( "%a, %d %b %Y %H:%M:%S", time.gmtime() ) 178 if 'Comments' in kwd and not kwd[ 'Comments' ]: 179 # Hack: specially handle parameters named "Comments" if no param_value is given 180 # by providing a date / time string. 181 kwd[ 'Comments' ] = time.strftime( "%a, %d %b %Y %H:%M:%S", time.gmtime() ) 182 socket.setdefaulttimeout( 600 ) 183 # The following calls to urllib2.urlopen() will use the above default timeout. 184 try: 185 if not http_method or http_method == 'get': 186 page = urllib2.urlopen( url ) 187 response = page.read() 188 page.close() 189 return response 190 elif http_method == 'post': 191 page = urllib2.urlopen( url, urllib.urlencode( kwd ) ) 192 response = page.read() 193 page.close() 194 return response 195 elif http_method == 'put': 196 url += '/' + str( kwd.pop( 'id' ) ) + '?key=' + kwd.pop( 'key' ) 197 output = self.put( url, **kwd ) 198 except Exception, e: 199 raise 200 message = 'Problem sending request to the web application: %s. URL: %s. kwd: %s. Http method: %s' % \ 201 ( str( e ), str( url ), str( kwd ), str( http_method ) ) 202 return self.handle_failure( trans, url, message ) 203 def handle_failure( self, trans, url, message ): 204 message = '%s, URL: %s' % ( message, url ) 205 params = dict( message = message, 206 status = 'error', 207 redirect_action = 'exit', 208 titles = 'Error' ) 209 return trans.response.send_redirect( web.url_for( controller='common', 210 action='index', 211 **params ) ) 212 def put( self, url, **kwd ): 213 opener = urllib2.build_opener( urllib2.HTTPHandler ) 214 request = urllib2.Request( url, data=to_json_string( kwd ) ) 215 request.add_header( 'Content-Type', 'application/json' ) 216 request.get_method = lambda: 'PUT' 217 url = opener.open( request ) 218 output = url.read() 219 return from_json_string( output ) 220 @web.expose 221 def login( self, trans, **kwd ): 222 trans.app.sequencer_actions_registry.authenticated = True 223 return trans.fill_template( "webapps/demo_sequencer/login.mako" ) 224 @web.expose 225 def empty_page( self, trans, **kwd ): 226 # Hack to not display responses in the browser - src for a hidden iframe. 227 return trans.fill_template( "webapps/demo_sequencer/empty.mako" )