[2] | 1 | """ |
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| 2 | Upload class |
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| 3 | """ |
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| 4 | |
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| 5 | from galaxy.web.base.controller import * |
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| 6 | |
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| 7 | from galaxy import jobs, util, datatypes, web |
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| 8 | |
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| 9 | import logging, urllib, sys |
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| 10 | from galaxy.util.hash_util import * |
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| 11 | |
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| 12 | log = logging.getLogger( __name__ ) |
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| 13 | |
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| 14 | class ASync( BaseController ): |
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| 15 | |
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| 16 | @web.expose |
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| 17 | def default(self, trans, tool_id=None, data_id=None, data_secret=None, **kwd): |
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| 18 | """Catches the tool id and redirects as needed""" |
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| 19 | return self.index( trans, tool_id=tool_id, data_id=data_id, data_secret=data_secret, **kwd) |
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| 20 | |
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| 21 | @web.expose |
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| 22 | def index(self, trans, tool_id=None, data_secret=None, **kwd): |
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| 23 | """Manages ascynchronous connections""" |
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| 24 | |
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| 25 | if tool_id is None: |
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| 26 | return "tool_id argument is required" |
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| 27 | tool_id=str(tool_id) |
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| 28 | #log.debug('async params -> %s' % kwd) |
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| 29 | |
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| 30 | # redirect to main when getting no parameters |
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| 31 | if not kwd: |
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| 32 | return trans.response.send_redirect( "/index" ) |
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| 33 | |
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| 34 | history = trans.get_history( create=True ) |
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| 35 | params = util.Params(kwd, sanitize=False) |
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| 36 | STATUS = params.STATUS |
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| 37 | URL = params.URL |
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| 38 | data_id = params.data_id |
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| 39 | |
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| 40 | log.debug('async dataid -> %s' % data_id) |
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| 41 | trans.log_event( 'Async dataid -> %s' % str(data_id) ) |
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| 42 | |
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| 43 | # initialize the tool |
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| 44 | toolbox = self.get_toolbox() |
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| 45 | tool = toolbox.tools_by_id.get(tool_id, '') |
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| 46 | if not tool: |
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| 47 | return "Tool with id %s not found" % tool_id |
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| 48 | |
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| 49 | # |
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| 50 | # we have an incoming data_id |
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| 51 | # |
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| 52 | if data_id: |
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| 53 | if not URL: |
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| 54 | return "No URL parameter was submitted for data %s" % data_id |
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| 55 | data = trans.sa_session.query( trans.model.HistoryDatasetAssociation ).get( data_id ) |
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| 56 | |
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| 57 | if not data: |
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| 58 | return "Data %s does not exist or has already been deleted" % data_id |
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| 59 | |
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| 60 | if STATUS == 'OK': |
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| 61 | key = hmac_new( trans.app.config.tool_secret, "%d:%d" % ( data.id, data.history_id ) ) |
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| 62 | if key != data_secret: |
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| 63 | return "You do not have permission to alter data %s." % data_id |
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| 64 | # push the job into the queue |
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| 65 | data.state = data.blurb = data.states.RUNNING |
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| 66 | log.debug('executing tool %s' % tool.id) |
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| 67 | trans.log_event( 'Async executing tool %s' % tool.id, tool_id=tool.id ) |
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| 68 | galaxy_url = trans.request.base + '/async/%s/%s/%s' % ( tool_id, data.id, key ) |
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| 69 | galaxy_url = params.get("GALAXY_URL",galaxy_url) |
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| 70 | params = dict( url=URL, GALAXY_URL=galaxy_url ) |
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| 71 | # Assume there is exactly one output file possible |
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| 72 | params[tool.outputs.keys()[0]] = data.id |
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| 73 | tool.execute( trans, incoming=params ) |
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| 74 | else: |
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| 75 | log.debug('async error -> %s' % STATUS) |
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| 76 | trans.log_event( 'Async error -> %s' % STATUS ) |
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| 77 | data.state = data.blurb = jobs.JOB_ERROR |
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| 78 | data.info = "Error -> %s" % STATUS |
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| 79 | |
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| 80 | trans.sa_session.flush() |
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| 81 | |
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| 82 | return "Data %s with status %s received. OK" % (data_id, STATUS) |
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| 83 | |
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| 84 | # |
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| 85 | # no data_id must be parameter submission |
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| 86 | # |
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| 87 | if not data_id and len(params)>3: |
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| 88 | |
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| 89 | if params.galaxyFileFormat == 'wig': |
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| 90 | GALAXY_TYPE = 'wig' |
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| 91 | else: |
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| 92 | GALAXY_TYPE = params.GALAXY_TYPE or 'interval' |
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| 93 | |
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| 94 | GALAXY_NAME = params.GALAXY_NAME or '%s query' % tool.name |
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| 95 | GALAXY_INFO = params.GALAXY_INFO or params.galaxyDescription or '' |
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| 96 | GALAXY_BUILD = params.GALAXY_BUILD or params.galaxyFreeze or 'hg17' |
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| 97 | |
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| 98 | #data = datatypes.factory(ext=GALAXY_TYPE)() |
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| 99 | #data.ext = GALAXY_TYPE |
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| 100 | #data.name = GALAXY_NAME |
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| 101 | #data.info = GALAXY_INFO |
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| 102 | #data.dbkey = GALAXY_BUILD |
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| 103 | #data.state = jobs.JOB_OK |
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| 104 | #history.datasets.add_dataset( data ) |
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| 105 | |
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| 106 | data = trans.app.model.HistoryDatasetAssociation( create_dataset=True, sa_session=trans.sa_session, extension=GALAXY_TYPE ) |
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| 107 | trans.app.security_agent.set_all_dataset_permissions( data.dataset, trans.app.security_agent.history_get_default_permissions( trans.history ) ) |
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| 108 | data.name = GALAXY_NAME |
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| 109 | data.dbkey = GALAXY_BUILD |
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| 110 | data.info = GALAXY_INFO |
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| 111 | trans.sa_session.add( data ) #Need to add data to session before setting state (setting state requires that the data object is in the session, but this may change) |
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| 112 | data.state = data.states.NEW |
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| 113 | open( data.file_name, 'wb' ).close() #create the file |
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| 114 | trans.history.add_dataset( data, genome_build=GALAXY_BUILD ) |
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| 115 | trans.sa_session.add( trans.history ) |
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| 116 | trans.sa_session.flush() |
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| 117 | trans.log_event( "Added dataset %d to history %d" %(data.id, trans.history.id ), tool_id=tool_id ) |
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| 118 | |
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| 119 | try: |
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| 120 | key = hmac_new( trans.app.config.tool_secret, "%d:%d" % ( data.id, data.history_id ) ) |
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| 121 | galaxy_url = trans.request.base + '/async/%s/%s/%s' % ( tool_id, data.id, key ) |
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| 122 | params.update( { 'GALAXY_URL' :galaxy_url } ) |
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| 123 | params.update( { 'data_id' :data.id } ) |
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| 124 | url = tool.action + '?' + urllib.urlencode( params.flatten() ) |
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| 125 | log.debug("connecting to -> %s" % url) |
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| 126 | trans.log_event( "Async connecting to -> %s" % url ) |
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| 127 | text = urllib.urlopen(url).read(-1) |
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| 128 | text = text.strip() |
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| 129 | if not text.endswith('OK'): |
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| 130 | raise Exception, text |
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| 131 | data.state = data.blurb = data.states.RUNNING |
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| 132 | except Exception, e: |
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| 133 | data.info = str(e) |
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| 134 | data.state = data.blurb = data.states.ERROR |
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| 135 | |
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| 136 | trans.sa_session.flush() |
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| 137 | |
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| 138 | return trans.fill_template( 'tool_executed.mako', history=history, toolbox=toolbox, tool=tool, util=util, out_data={} ) |
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