- galaxy-commits - lists.galaxyproject.org

galaxy-dist commit af2d04e35680: Radio boxes in tool forms now have clickable labels as well. Update unit tests to reflect changes
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1288137500 14400 # Node ID af2d04e3568078d8d7ad94e229a17983f8282e20 # Parent 6a1ea9b6029416945caba087f2696c64a9a06621 Radio boxes in tool forms now have clickable labels as well. Update unit tests to reflect changes --- a/lib/galaxy/web/form_builder.py +++ b/lib/galaxy/web/form_builder.py @@ -184,16 +184,16 @@ class SelectField(BaseField): >>> t.add_option( "tuti", 1 ) >>> t.add_option( "fruity", "x" ) >>> print t.get_html() - <div><input type="radio" name="foo" value="1">tuti</div> - <div><input type="radio" name="foo" value="x">fruity</div> + <div><input type="radio" name="foo" value="1" id="foo|1"><label for="foo|1">tuti</label></div> + <div><input type="radio" name="foo" value="x" id="foo|x"><label for="foo|x">fruity</label></div> >>> t = SelectField( "bar", multiple=True, display="checkboxes" ) >>> t.add_option( "automatic", 3 ) >>> t.add_option( "bazooty", 4, selected=True ) >>> print t.get_html() <div class="checkUncheckAllPlaceholder" checkbox_name="bar"></div> - <div><input type="checkbox" name="bar" value="3">automatic</div> - <div><input type="checkbox" name="bar" value="4" checked>bazooty</div> + <div><input type="checkbox" name="bar" value="3" id="bar|3"><label for="bar|3">automatic</label></div> + <div><input type="checkbox" name="bar" value="4" id="bar|4" checked='checked'><label for="bar|4">bazooty</label></div> """ def __init__( self, name, multiple=None, display=None, refresh_on_change=False, refresh_on_change_values=[], size=None ): self.name = name @@ -232,13 +232,14 @@ class SelectField(BaseField): for text, value, selected in self.options: style = "" escaped_value = escape( str( value ), quote=True ) + uniq_id = "%s%s|%s" % (prefix, self.name, escaped_value) if len(self.options) > 2 and ctr % 2 == 1: style = " class=\"odd_row\"" selected_text = "" if selected: - selected_text = "checked='checked'" - rval.append( '<div%s><input type="checkbox" name="%s%s" value="%s" id="%s" %s%s><label for="%s">%s</label></div>' % \ - ( style, prefix, self.name, escaped_value, escaped_value, selected_text, self.get_disabled_str( disabled ), escaped_value, text ) ) + selected_text = " checked='checked'" + rval.append( '<div%s><input type="checkbox" name="%s%s" value="%s" id="%s"%s%s><label for="%s">%s</label></div>' % \ + ( style, prefix, self.name, escaped_value, uniq_id, selected_text, self.get_disabled_str( disabled ), uniq_id, text ) ) ctr += 1 return "\n".join( rval ) def get_html_radio( self, prefix="", disabled=False ): @@ -246,18 +247,23 @@ class SelectField(BaseField): ctr = 0 for text, value, selected in self.options: style = "" + escaped_value = escape( str( value ), quote=True ) + uniq_id = "%s%s|%s" % (prefix, self.name, escaped_value) if len(self.options) > 2 and ctr % 2 == 1: style = " class=\"odd_row\"" - if selected: selected_text = " checked" - else: selected_text = "" - rval.append( '<div%s><input type="radio" name="%s%s"%s value="%s"%s%s>%s</div>' % \ + selected_text = "" + if selected: + selected_text = " checked='checked'" + rval.append( '<div%s><input type="radio" name="%s%s"%s value="%s" id="%s"%s%s><label for="%s">%s</label></div>' % \ ( style, prefix, self.name, self.refresh_on_change_text, - escape( str( value ), quote=True ), + escaped_value, + uniq_id, selected_text, self.get_disabled_str( disabled ), + uniq_id, text ) ) ctr += 1 return "\n".join( rval ) --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -474,14 +474,14 @@ class SelectToolParameter( ToolParameter blah >>> print p.get_html() <div class="checkUncheckAllPlaceholder" checkbox_name="blah"></div> - <div><input type="checkbox" name="blah" value="x">I am X</div> - <div class="odd_row"><input type="checkbox" name="blah" value="y" checked>I am Y</div> - <div><input type="checkbox" name="blah" value="z" checked>I am Z</div> + <div><input type="checkbox" name="blah" value="x" id="blah|x"><label for="blah|x">I am X</label></div> + <div class="odd_row"><input type="checkbox" name="blah" value="y" id="blah|y" checked='checked'><label for="blah|y">I am Y</label></div> + <div><input type="checkbox" name="blah" value="z" id="blah|z" checked='checked'><label for="blah|z">I am Z</label></div> >>> print p.get_html( value=["x","y"]) <div class="checkUncheckAllPlaceholder" checkbox_name="blah"></div> - <div><input type="checkbox" name="blah" value="x" checked>I am X</div> - <div class="odd_row"><input type="checkbox" name="blah" value="y" checked>I am Y</div> - <div><input type="checkbox" name="blah" value="z">I am Z</div> + <div><input type="checkbox" name="blah" value="x" id="blah|x" checked='checked'><label for="blah|x">I am X</label></div> + <div class="odd_row"><input type="checkbox" name="blah" value="y" id="blah|y" checked='checked'><label for="blah|y">I am Y</label></div> + <div><input type="checkbox" name="blah" value="z" id="blah|z"><label for="blah|z">I am Z</label></div> >>> print p.to_param_dict_string( ["y", "z"] ) y,z """

1 0

galaxy-dist commit 49c7938d5827: sample tracking web api cleaned up
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1288122647 14400 # Node ID 49c7938d582799125a89f0d6ba38be0ddc6f4b4f # Parent d73fa5f14b013333b2e49bfbf775db8dd0197e2b sample tracking web api cleaned up - added a samples controller --- /dev/null +++ b/lib/galaxy/web/api/samples.py @@ -0,0 +1,44 @@ +""" +API operations on a sample tracking system. +""" +import logging, os, string, shutil, urllib, re, socket +from cgi import escape, FieldStorage +from galaxy import util, datatypes, jobs, web, util +from galaxy.web.base.controller import * +from galaxy.util.sanitize_html import sanitize_html +from galaxy.model.orm import * +from galaxy.util.bunch import Bunch + +log = logging.getLogger( __name__ ) + +class SamplesController( BaseController ): + + @web.expose_api + def index( self, trans, **kwd ): + """ + GET /api/requests/{encoded_request_id}/samples + Displays a collection (list) of sample of a sequencing request. + """ + try: + request_id = trans.security.decode_id( kwd[ 'request_id' ] ) + except TypeError: + trans.response.status = 400 + return "Malformed request id ( %s ) specified, unable to decode." % str( encoded_request_id ) + try: + request = trans.sa_session.query( trans.app.model.Request ).get( request_id ) + except: + request = None + if not request or not ( trans.user_is_admin() or request.user.id == trans.user.id ): + trans.response.status = 400 + return "Invalid request id ( %s ) specified." % str( request_id ) + rval = [] + for sample in request.samples: + item = sample.get_api_value() + item['url'] = url_for( 'samples', + request_id=trans.security.encode_id( request_id ), + id=trans.security.encode_id( sample.id ) ) + item['id'] = trans.security.encode_id( item['id'] ) + rval.append( item ) + return rval + + --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1767,6 +1767,7 @@ class RequestTypePermissions( object ): class Sample( object ): bulk_operations = Bunch( CHANGE_STATE = 'Change state', SELECT_LIBRARY = 'Select data library and folder' ) + api_collection_visible_keys = ( 'id', 'name' ) def __init__(self, name=None, desc=None, request=None, form_values=None, bar_code=None, library=None, folder=None): self.name = name self.desc = desc @@ -1818,6 +1819,18 @@ class Sample( object ): pexpect.TIMEOUT:print_ticks}, timeout=10) return output.replace(filepath, '').strip() + def get_api_value( self, view='collection' ): + rval = {} + try: + visible_keys = self.__getattribute__( 'api_' + view + '_visible_keys' ) + except AttributeError: + raise Exception( 'Unknown API view: %s' % view ) + for key in visible_keys: + try: + rval[key] = self.__getattribute__( key ) + except AttributeError: + rval[key] = None + return rval class SampleState( object ): def __init__(self, name=None, desc=None, request_type=None): --- a/lib/galaxy/web/buildapp.py +++ b/lib/galaxy/web/buildapp.py @@ -104,8 +104,15 @@ def app_factory( global_conf, **kwargs ) # If enabled, add the web API if asbool( kwargs.get( 'enable_api', False ) ): add_api_controllers( webapp, app ) - webapp.api_mapper.resource( 'content', 'contents', path_prefix='/api/libraries/:library_id', parent_resources=dict( member_name='library', collection_name='libraries' ) ) + webapp.api_mapper.resource( 'content', + 'contents', + path_prefix='/api/libraries/:library_id', + parent_resources=dict( member_name='library', collection_name='libraries' ) ) webapp.api_mapper.resource( 'library', 'libraries', path_prefix='/api' ) + webapp.api_mapper.resource( 'sample', + 'samples', + path_prefix='/api/requests/:request_id', + parent_resources=dict( member_name='request', collection_name='requests' ) ) webapp.api_mapper.resource( 'request', 'requests', path_prefix='/api' ) webapp.finalize_config() # Wrap the webapp in some useful middleware --- a/lib/galaxy/web/api/requests.py +++ b/lib/galaxy/web/api/requests.py @@ -22,23 +22,57 @@ class RequestsController( BaseController GET /api/requests Displays a collection (list) of sequencing requests. """ - query = trans.sa_session.query( trans.app.model.Request )\ - .filter( and_( trans.app.model.Request.table.c.user_id == trans.user.id \ - and trans.app.model.Request.table.c.deleted == False ) ) \ - .all() + # if admin user then return all requests + if trans.user_is_admin(): + query = trans.sa_session.query( trans.app.model.Request )\ + .filter( trans.app.model.Request.table.c.deleted == False )\ + .all() + else: + query = trans.sa_session.query( trans.app.model.Request )\ + .filter( and_( trans.app.model.Request.table.c.user_id == trans.user.id \ + and trans.app.model.Request.table.c.deleted == False ) ) \ + .all() rval = [] for request in query: item = request.get_api_value() item['url'] = url_for( 'requests', id=trans.security.encode_id( request.id ) ) item['id'] = trans.security.encode_id( item['id'] ) + if trans.user_is_admin(): + item['user'] = request.user.email rval.append( item ) return rval - + + @web.expose_api + def show( self, trans, id, **kwd ): + """ + GET /api/requests/{encoded_request_id} + Displays details of a sequencing request. + """ + try: + request_id = trans.security.decode_id( id ) + except TypeError: + trans.response.status = 400 + return "Malformed %s id ( %s ) specified, unable to decode." % ( update_type, str( id ) ) + try: + request = trans.sa_session.query( trans.app.model.Request ).get( request_id ) + except: + request = None + if not request or not ( trans.user_is_admin() or request.user.id == trans.user.id ): + trans.response.status = 400 + return "Invalid request id ( %s ) specified." % str( request_id ) + item = request.get_api_value() + item['url'] = url_for( 'requests', id=trans.security.encode_id( request.id ) ) + item['id'] = trans.security.encode_id( item['id'] ) + item['user'] = request.user.email + item['num_of_samples'] = len(request.samples) + return item + @web.expose_api def update( self, trans, id, key, payload, **kwd ): """ PUT /api/requests/{encoded_request_id} - Displays information about a sequencing request. + Updates a request state, sample state or sample dataset transfer status + depending on the update_type """ params = util.Params( kwd ) update_type = None @@ -124,7 +158,3 @@ class RequestsController( BaseController new_status=new_status, error_msg=error_msg ) return status, output - - - -

1 0

galaxy-dist commit e5f90080a2db: Merge with 29157e97e95453c5f9022d9c571527a6de4032e1
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1288149696 14400 # Node ID e5f90080a2db9c16bad2300c5ef0b5c49a558638 # Parent 61c786bd2efb6f9cc4d5fa4d43dfb056ed99b909 # Parent 29157e97e95453c5f9022d9c571527a6de4032e1 Merge with 29157e97e95453c5f9022d9c571527a6de4032e1

1 0

galaxy-dist commit 29157e97e954: Added setup script to configure RabbitMQ
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1288148662 14400 # Node ID 29157e97e95453c5f9022d9c571527a6de4032e1 # Parent af2d04e3568078d8d7ad94e229a17983f8282e20 Added setup script to configure RabbitMQ --- a/transfer_datasets.ini.sample +++ b/transfer_datasets.ini.sample @@ -3,13 +3,8 @@ [data_transfer_user_login_info] #email = datatx(a)bx.psu.edu #password = datatx - -# The following section contains 4 config variables neede for the data transfer. -# Please copy the exact values for each of these variables from the universe_wsgi.ini -# configuration file for this installation +#api_key = Generate it from the User menu in Galaxy [universe_wsgi_config] -#host = 127.0.0.1 -#port = -#database_connection = -#library_import_dir = +# The http server section name in the Galaxy config file (universe_wsgi.ini) +#http_server_section = server:main --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -420,4 +420,4 @@ upload1 = local:/// #queue = galaxy_queue #exchange = galaxy_exchange #routing_key = bar_code_scanner - +#rabbitmqctl_path = /path/to/rabbitmqctl --- /dev/null +++ b/scripts/galaxy_messaging/server/setup_rabbitmq.py @@ -0,0 +1,34 @@ +# +# Configuration script for RabbitMQ in Galaxy +# +# Requirements: +# - set the rabbitmqctl_path variable in the 'galaxy_amqp' section in Galaxy config file +# +# Usage: +# $ python setup_rabbitmq.py <Galaxy config file> +# + +import os, sys, csv, ConfigParser + +def main( config_file ): + config = ConfigParser.ConfigParser() + config.read( config_file ) + rabbitmqctl_path = config.get( 'galaxy_amqp', 'rabbitmqctl_path' ) + username = config.get( 'galaxy_amqp', 'userid' ) + password = config.get( 'galaxy_amqp', 'password' ) + virtual_host = config.get( 'galaxy_amqp', 'virtual_host' ) + + cmd_list = [ + 'add_user %s %s' % ( username, password ), + 'add_vhost %s' % config.get( 'galaxy_amqp', 'virtual_host' ), + 'set_permissions -p %s %s "%s.*" ".*" ".*"' % ( virtual_host, username, username ) + ] + + for cmd in cmd_list: + retval = os.system( rabbitmqctl_path + ' ' + cmd ) + if retval: + print "Failed command: %s" % cmd + sys.exit(1) + +if __name__ == '__main__': + main( sys.argv[1] )

1 0

galaxy-dist commit c22562b86d0f: Make the production buildbot use Main's tool conf
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1288123416 14400 # Node ID c22562b86d0f62d361fd2531d22d42cfd6bf07c1 # Parent 49c7938d582799125a89f0d6ba38be0ddc6f4b4f Make the production buildbot use Main's tool conf --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -54,6 +54,7 @@ def main(): galaxy_test_file_dir = os.path.join( os.getcwd(), galaxy_test_file_dir ) start_server = 'GALAXY_TEST_EXTERNAL' not in os.environ tool_path = os.environ.get( 'GALAXY_TEST_TOOL_PATH', 'tools' ) + tool_config_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', 'tool_conf.xml.sample' ) if start_server: psu_production = False galaxy_test_proxy_port = None @@ -75,6 +76,7 @@ def main(): nginx_upload_store = os.environ.get( 'GALAXY_TEST_NGINX_UPLOAD_STORE', None ) if not nginx_upload_store: raise Exception( 'Please set GALAXY_TEST_NGINX_UPLOAD_STORE to the path where the nginx upload module places uploaded files' ) + tool_config_file = 'tool_conf.xml.main' default_cluster_job_runner = os.environ.get( 'GALAXY_TEST_DEFAULT_CLUSTER_JOB_RUNNER', 'pbs:///' ) file_path = tempfile.mkdtemp( dir=base_file_path ) new_file_path = tempfile.mkdtemp( dir=base_new_file_path ) @@ -142,7 +144,7 @@ def main(): file_path = file_path, new_file_path = new_file_path, tool_path = tool_path, - tool_config_file = "tool_conf.xml.sample", + tool_config_file = tool_config_file, datatype_converters_config_file = "datatype_converters_conf.xml.sample", tool_parse_help = False, test_conf = "test.conf",

1 0

galaxy-dist commit 314f8a5d3823: Complete functional test for cuffcompare.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1288119881 14400 # Node ID 314f8a5d38237c3f1fafccb522ee45aebfa8464f # Parent 379d0701f198964fb964c3834cce7414cbc8f888 Complete functional test for cuffcompare. --- /dev/null +++ b/test-data/cuffcompare_out1.tmap @@ -0,0 +1,51 @@ +ref_gene_id ref_id class_code cuff_gene_id cuff_id FMI FPKM FPKM_conf_lo FPKM_conf_hi cov len major_iso_id +- - u CUFF.1 CUFF.1.1 100 20.607936 0.000000 49.751960 1.317073 41 CUFF.1.1 +- - u CUFF.3 CUFF.3.1 100 27.255658 0.000000 65.800979 1.741935 31 CUFF.3.1 +- - u CUFF.5 CUFF.5.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.5.1 +- - u CUFF.7 CUFF.7.1 100 9.999117 0.000000 19.998234 0.639053 169 CUFF.7.1 +- - u CUFF.9 CUFF.9.1 100 17.776896 9.153835 26.399957 1.136139 404 CUFF.9.1 +- - u CUFF.11 CUFF.11.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.11.1 +Xkr4 Xkr4 c CUFF.13 CUFF.13.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.13.1 +Xkr4 Xkr4 i CUFF.15 CUFF.15.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.15.1 +Xkr4 Xkr4 i CUFF.17 CUFF.17.1 100 8.710571 0.000000 21.029179 0.556701 97 CUFF.17.1 +Xkr4 Xkr4 i CUFF.19 CUFF.19.1 100 29.337687 3.097262 55.578113 1.875000 72 CUFF.19.1 +Xkr4 Xkr4 i CUFF.21 CUFF.21.1 100 13.851236 0.000000 33.439842 0.885246 61 CUFF.21.1 +Xkr4 Xkr4 i CUFF.23 CUFF.23.1 100 23.470150 0.000000 50.571145 1.500000 54 CUFF.23.1 +Xkr4 Xkr4 i CUFF.25 CUFF.25.1 100 14.567679 5.354270 23.781089 0.931034 290 CUFF.25.1 +Xkr4 Xkr4 i CUFF.27 CUFF.27.1 100 34.253732 0.000000 73.806535 2.189189 37 CUFF.27.1 +- - u CUFF.29 CUFF.29.1 100 107.103219 71.402146 142.804292 6.845070 142 CUFF.29.1 +- - u CUFF.31 CUFF.31.1 100 122.650461 40.883487 204.417435 7.838710 31 CUFF.31.1 +- - u CUFF.33 CUFF.33.1 100 109.527366 26.732460 192.322273 7.000000 27 CUFF.33.1 +- - u CUFF.35 CUFF.35.1 100 96.747183 61.420107 132.074259 6.183206 131 CUFF.35.1 +- - u CUFF.37 CUFF.37.1 100 104.085013 53.596365 154.573660 6.652174 69 CUFF.37.1 +- - u CUFF.39 CUFF.39.1 100 23.912983 0.000000 51.525317 1.528302 53 CUFF.39.1 +- - u CUFF.41 CUFF.41.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.41.1 +- - u CUFF.43 CUFF.43.1 100 10.561567 0.000000 25.497879 0.675000 80 CUFF.43.1 +- - u CUFF.45 CUFF.45.1 100 20.708956 2.186303 39.231609 1.323529 102 CUFF.45.1 +- - u CUFF.47 CUFF.47.1 100 20.607936 0.000000 49.751960 1.317073 41 CUFF.47.1 +- - u CUFF.49 CUFF.49.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.49.1 +- - u CUFF.51 CUFF.51.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.51.1 +- - u CUFF.53 CUFF.53.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.53.1 +- - u CUFF.55 CUFF.55.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.55.1 +- - u CUFF.57 CUFF.57.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.57.1 +- - u CUFF.59 CUFF.59.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.59.1 +Xkr4 Xkr4 i CUFF.61 CUFF.61.1 100 45.263860 0.000000 97.530065 2.892857 28 CUFF.61.1 +Xkr4 Xkr4 i CUFF.63 CUFF.63.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.63.1 +Xkr4 Xkr4 i CUFF.65 CUFF.65.1 100 15.362280 0.000000 37.087825 0.981818 55 CUFF.65.1 +Xkr4 Xkr4 i CUFF.67 CUFF.67.1 100 12.998852 0.000000 31.382005 0.830769 65 CUFF.67.1 +Xkr4 Xkr4 i CUFF.69 CUFF.69.1 100 10.058636 0.000000 24.283695 0.642857 84 CUFF.69.1 +Xkr4 Xkr4 i CUFF.71 CUFF.71.1 100 8.621688 0.000000 20.814595 0.551020 98 CUFF.71.1 +Xkr4 Xkr4 i CUFF.73 CUFF.73.1 100 15.362280 0.000000 37.087825 0.981818 55 CUFF.73.1 +Xkr4 Xkr4 i CUFF.75 CUFF.75.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.75.1 +Xkr4 Xkr4 i CUFF.77 CUFF.77.1 100 16.248565 0.000000 39.227507 1.038462 52 CUFF.77.1 +Xkr4 Xkr4 i CUFF.79 CUFF.79.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.79.1 +Xkr4 Xkr4 i CUFF.81 CUFF.81.1 100 13.201959 0.000000 31.872349 0.843750 64 CUFF.81.1 +Xkr4 Xkr4 i CUFF.83 CUFF.83.1 100 13.201959 0.000000 28.446269 0.843750 96 CUFF.83.1 +Xkr4 Xkr4 i CUFF.85 CUFF.85.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.85.1 +Xkr4 Xkr4 i CUFF.87 CUFF.87.1 100 17.243375 0.000000 41.629191 1.102041 49 CUFF.87.1 +Xkr4 Xkr4 i CUFF.89 CUFF.89.1 100 16.567165 0.000000 39.996674 1.058824 51 CUFF.89.1 +Xkr4 Xkr4 i CUFF.91 CUFF.91.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.91.1 +Xkr4 Xkr4 i CUFF.93 CUFF.93.1 100 21.664754 0.000000 52.303342 1.384615 39 CUFF.93.1 +Xkr4 Xkr4 i CUFF.95 CUFF.95.1 100 46.940300 0.000000 101.142289 3.000000 27 CUFF.95.1 +Xkr4 Xkr4 i CUFF.97 CUFF.97.1 100 21.481154 0.000000 46.285454 1.372881 59 CUFF.97.1 +Xkr4 Xkr4 i CUFF.99 CUFF.99.1 100 14.567679 0.000000 35.169489 0.931034 58 CUFF.99.1 --- /dev/null +++ b/test-data/cuffcompare_out2.refmap @@ -0,0 +1,2 @@ +ref_gene_id ref_id class_code cuff_id_list +Xkr4 Xkr4 c CUFF.13|CUFF.13.1 --- a/tools/ngs_rna/cuffcompare_wrapper.xml +++ b/tools/ngs_rna/cuffcompare_wrapper.xml @@ -81,16 +81,15 @@ <param name="use_ref_annotation" value="Yes"/><param name="reference_annotation" value="cuffcompare_in3.gtf" ftype="gtf"/><param name="ignore_nonoverlapping_reference" value="Yes"/> - ## HACK: need to specify output name and it needs to work (right now it uses the final output file) - <output name="XXXX" file="cuffcompare_out6.tracking"/> -  + <output name="transcripts_accuracy" file="cuffcompare_out7.txt" lines_diff="6"/><output name="input1_tmap" file="cuffcompare_out1.tmap"/><output name="input1_refmap" file="cuffcompare_out2.refmap"/><output name="input2_tmap" file="cuffcompare_out3.tmap"/><output name="input2_refmap" file="cuffcompare_out4.refmap"/> - <output name="transcripts_accuracy" file="cuffcompare_out7.txt"/> - --> + <output name="transcripts_combined" file="cuffcompare_out5.gtf"/> + <output name="transcripts_tracking" file="cuffcompare_out6.tracking"/></test></tests> --- /dev/null +++ b/test-data/cuffcompare_out4.refmap @@ -0,0 +1,1 @@ +ref_gene_id ref_id class_code cuff_id_list --- /dev/null +++ b/test-data/cuffcompare_out3.tmap @@ -0,0 +1,51 @@ +ref_gene_id ref_id class_code cuff_gene_id cuff_id FMI FPKM FPKM_conf_lo FPKM_conf_hi cov len major_iso_id +- - u CUFF.1 CUFF.1.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.1.1 +- - u CUFF.3 CUFF.3.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.3.1 +- - u CUFF.5 CUFF.5.1 100 21.226627 0.000000 59.889707 1.205672 27 CUFF.5.1 +- - u CUFF.7 CUFF.7.1 100 29.709524 19.806349 39.612698 1.687500 576 CUFF.7.1 +- - u CUFF.9 CUFF.9.1 100 34.072933 23.364686 44.781179 1.935341 565 CUFF.9.1 +- - u CUFF.11 CUFF.11.1 100 32.531777 24.582998 40.480555 1.847804 979 CUFF.11.1 +- - u CUFF.13 CUFF.13.1 100 16.582060 0.000000 35.729373 0.941860 86 CUFF.13.1 +- - u CUFF.15 CUFF.15.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.15.1 +- - u CUFF.17 CUFF.17.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.17.1 +- - u CUFF.19 CUFF.19.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.19.1 +- - u CUFF.21 CUFF.21.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.21.1 +- - u CUFF.23 CUFF.23.1 100 16.205195 0.000000 34.917342 0.920455 88 CUFF.23.1 +- - u CUFF.25 CUFF.25.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.25.1 +- - u CUFF.26 CUFF.26.1 100 29.709524 0.000000 71.725135 1.687500 32 CUFF.26.1 +- - u CUFF.29 CUFF.29.1 100 13.581496 0.000000 32.788633 0.771429 70 CUFF.29.1 +- - u CUFF.31 CUFF.31.1 100 22.635827 0.000000 45.271655 1.285714 84 CUFF.31.1 +Xkr4 Xkr4 i CUFF.33 CUFF.33.1 100 23.767619 0.000000 57.380108 1.350000 40 CUFF.33.1 +Xkr4 Xkr4 i CUFF.35 CUFF.35.1 100 11.317914 0.000000 27.323861 0.642857 84 CUFF.35.1 +Xkr4 Xkr4 i CUFF.37 CUFF.37.1 100 11.500461 0.000000 24.780049 0.653226 124 CUFF.37.1 +Xkr4 Xkr4 i CUFF.39 CUFF.39.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.39.1 +Xkr4 Xkr4 i CUFF.41 CUFF.41.1 100 43.213852 0.000000 93.112911 2.454545 33 CUFF.41.1 +Xkr4 Xkr4 i CUFF.43 CUFF.43.1 100 23.474191 0.000000 46.948383 1.333333 81 CUFF.43.1 +Xkr4 Xkr4 i CUFF.45 CUFF.45.1 100 20.667495 0.000000 49.895746 1.173913 46 CUFF.45.1 +Xkr4 Xkr4 i CUFF.47 CUFF.47.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.47.1 +Xkr4 Xkr4 i CUFF.49 CUFF.49.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.49.1 +Xkr4 Xkr4 i CUFF.51 CUFF.51.1 100 14.948188 7.228977 22.667399 0.849057 477 CUFF.51.1 +Xkr4 Xkr4 i CUFF.53 CUFF.53.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.53.1 +Xkr4 Xkr4 i CUFF.55 CUFF.55.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.55.1 +Xkr4 Xkr4 i CUFF.57 CUFF.57.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.57.1 +Xkr4 Xkr4 i CUFF.59 CUFF.59.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.59.1 +Xkr4 Xkr4 i CUFF.61 CUFF.61.1 100 13.204233 0.000000 31.877838 0.750000 72 CUFF.61.1 +Xkr4 Xkr4 i CUFF.63 CUFF.63.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.63.1 +Xkr4 Xkr4 i CUFF.65 CUFF.65.1 100 31.170648 0.000000 62.341295 1.770492 61 CUFF.65.1 +Xkr4 Xkr4 i CUFF.67 CUFF.67.1 100 15.681351 3.378764 27.983938 0.890700 197 CUFF.67.1 +Xkr4 Xkr4 i CUFF.69 CUFF.69.1 100 18.799247 8.750627 28.847866 1.067797 354 CUFF.69.1 +Xkr4 Xkr4 i CUFF.71 CUFF.71.1 100 22.635827 0.000000 54.647722 1.285714 42 CUFF.71.1 +Xkr4 Xkr4 i CUFF.73 CUFF.73.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.73.1 +Xkr4 Xkr4 i CUFF.75 CUFF.75.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.75.1 +Xkr4 Xkr4 i CUFF.77 CUFF.77.1 100 17.605644 0.000000 52.816931 1.000000 27 CUFF.77.1 +Xkr4 Xkr4 i CUFF.79 CUFF.79.1 100 13.390208 0.000000 32.326821 0.760563 71 CUFF.79.1 +Xkr4 Xkr4 i CUFF.81 CUFF.81.1 100 11.211141 1.183592 21.238690 0.636792 212 CUFF.81.1 +Xkr4 Xkr4 i CUFF.83 CUFF.83.1 100 21.126772 0.000000 51.004540 1.200000 45 CUFF.83.1 +Xkr4 Xkr4 i CUFF.85 CUFF.85.1 100 19.014095 0.000000 38.028190 1.080000 100 CUFF.85.1 +Xkr4 Xkr4 i CUFF.87 CUFF.87.1 100 24.170460 0.000000 52.080103 1.372881 59 CUFF.87.1 +Xkr4 Xkr4 i CUFF.89 CUFF.89.1 100 29.709524 0.000000 64.015126 1.687500 48 CUFF.89.1 +Xkr4 Xkr4 i CUFF.91 CUFF.91.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.91.1 +Xkr4 Xkr4 i CUFF.93 CUFF.93.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.93.1 +Xkr4 Xkr4 i CUFF.95 CUFF.95.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.95.1 +Xkr4 Xkr4 i CUFF.97 CUFF.97.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.97.1 +Xkr4 Xkr4 i CUFF.99 CUFF.99.1 100 19.602160 0.000000 39.204320 1.113402 97 CUFF.99.1 --- /dev/null +++ b/test-data/cuffcompare_out7.txt @@ -0,0 +1,50 @@ +# Cuffcompare v0.9.1 | Command line was: +#cuffcompare -r cuffcompare_in3.gtf -R cuffcompare_in1.gtf cuffcompare_in2.gtf +# +#> Genomic sequence: chr1 +# Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) +# (0 multi-transcript loci, ~1.0 transcripts per locus) +# Reference mRNAs : 1 in 1 loci (1 multi-exon) +# Corresponding super-loci: 1 +#--------------------| Sn | Sp | fSn | fSp + Base level: 2.2 2.3 - - + Exon level: 0.0 0.0 0.0 0.0 + Intron level: 0.0 nan 0.0 100.0 +Intron chain level: 0.0 100.0 0.0 100.0 + Transcript level: 0.0 0.0 0.0 0.0 + Locus level: 0.0 0.0 0.0 0.0 + Missed exons: 2/3 ( 66.7%) + Wrong exons: 49/50 ( 98.0%) + Missed introns: 2/2 (100.0%) + Missed loci: 0/1 ( 0.0%) + Wrong loci: 49/50 ( 98.0%) + +#= Summary for dataset: cuffcompare_in1.gtf : +# Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) +# (0 multi-transcript loci, ~1.0 transcripts per locus) +# Reference mRNAs : 1 in 1 loci (1 multi-exon) +# Corresponding super-loci: 1 +#--------------------| Sn | Sp | fSn | fSp + Base level: 2.2 2.3 - - + Exon level: 0.0 0.0 0.0 0.0 + Intron level: 0.0 nan 0.0 100.0 +Intron chain level: 0.0 100.0 0.0 100.0 + Transcript level: 0.0 0.0 0.0 0.0 + Locus level: 0.0 0.0 0.0 0.0 + Missed exons: 2/3 ( 66.7%) + Wrong exons: 49/50 ( 98.0%) + Missed introns: 2/2 (100.0%) + Missed loci: 0/1 ( 0.0%) + Wrong loci: 49/50 ( 98.0%) +#> Genomic sequence: chr1 +# Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) +# (0 multi-transcript loci, ~1.0 transcripts per locus) +# Reference mRNAs : 0 in 0 loci (0 multi-exon) + +#= Summary for dataset: cuffcompare_in2.gtf : +# Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) +# (0 multi-transcript loci, ~1.0 transcripts per locus) +# Reference mRNAs : 0 in 0 loci (0 multi-exon) + + Total union super-loci across all input datasets: 87 + (0 multi-transcript, ~1.1 transcripts per locus)

1 0

galaxy-dist commit e6e68c67dd97: Use a job to import a history from an archive. This makes it possible to move a history from one Galaxy instance to another, subject to the limitations below. The job itself unpacks the archive, and the job's cleanup creates a history from the archive. A history imported via an archive is only visible to the user when it has finished being imported.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1288106620 14400 # Node ID e6e68c67dd9759154876546662f59ee280b78a34 # Parent 677bcc65f74f5a460277f089d0cdebf170f02831 Use a job to import a history from an archive. This makes it possible to move a history from one Galaxy instance to another, subject to the limitations below. The job itself unpacks the archive, and the job's cleanup creates a history from the archive. A history imported via an archive is only visible to the user when it has finished being imported. Currently, there are limitations to this functionality; these will be fixed going forward. These limitations are: -history archives can be imported only via URL, not file; -histories must be shared in order for them to be importable via archive; -tags are not currently imported; -reproducibility is limited as parameters for imported jobs are not always recovered and set. --- a/lib/galaxy/web/controllers/history.py +++ b/lib/galaxy/web/controllers/history.py @@ -79,7 +79,7 @@ class HistoryListGrid( grids.Grid ): def get_current_item( self, trans, **kwargs ): return trans.get_history() def apply_query_filter( self, trans, query, **kwargs ): - return query.filter_by( user=trans.user, purged=False ) + return query.filter_by( user=trans.user, purged=False, importing=False ) class SharedHistoryListGrid( grids.Grid ): # Custom column types @@ -465,212 +465,40 @@ class HistoryController( BaseController, trans.sa_session.flush() return new_annotation - def import_archive( self, trans, archived_history=None, gzip=True ): - """ Import a history. """ + @web.expose + # TODO: Remove require_login when users are warned that, if they are not + # logged in, this will remove their current history. + @web.require_login( "use Galaxy histories" ) + def import_archive( self, trans, **kwargs ): + """ Import a history from a file archive. """ - def file_in_dir( file_path, a_dir ): - """ Returns true if file is in directory. """ - abs_file_path = os.path.abspath( file_path ) - return os.path.split( abs_file_path )[0] == a_dir + # Set archive source and type. + archive_file = kwargs.get( 'archive_file', None ) + archive_url = kwargs.get( 'archive_url', None ) + archive_source = None + if archive_file: + archive_source = archive_file + archive_type = 'file' + elif archive_url: + archive_source = archive_url + archive_type = 'url' - if archived_history is not None: - try: - history_archive_file = tarfile.open( archived_history.file.name ) - - # Unpack archive in temporary directory. - temp_output_dir = tempfile.mkdtemp() - history_archive_file.extractall( path=temp_output_dir ) - history_archive_file.close() - - # - # Create history. - # - history_attr_file_name = os.path.join( temp_output_dir, 'history_attrs.txt') - if not file_in_dir( history_attr_file_name, temp_output_dir ): - raise Exception( "Invalid location for history attributes file: %s" % history_attr_file_name ) - history_attr_in = open( history_attr_file_name, 'rb' ) - history_attr_str = '' - buffsize = 1048576 - try: - while True: - history_attr_str += history_attr_in.read( buffsize ) - if not history_attr_str or len( history_attr_str ) % buffsize != 0: - break - except OverflowError: - pass - history_attr_in.close() - history_attrs = from_json_string( history_attr_str ) - - # Create history. - new_history = model.History( name='imported from archive: %s' % history_attrs['name'].encode( 'utf-8' ), user=trans.user ) - trans.sa_session.add( new_history ) - - new_history.hid_counter = history_attrs['hid_counter'] - new_history.genome_build = history_attrs['genome_build'] - trans.sa_session.flush() - - # Builds a tag string for a tag, value pair. - def get_tag_str( tag, value ): - if not value: - return tag - else: - return tag + ":" + value - - # Add annotation, tags. - if trans.user: - self.add_item_annotation( trans.sa_session, trans.get_user(), new_history, history_attrs[ 'annotation' ] ) - for tag, value in history_attrs[ 'tags' ].items(): - trans.app.tag_handler.apply_item_tags( trans, trans.user, new_history, get_tag_str( tag, value ) ) - - # - # Create datasets. - # - datasets_attrs_file_name = os.path.join( temp_output_dir, 'datasets_attrs.txt') - if not file_in_dir( datasets_attrs_file_name, temp_output_dir ): - raise Exception( "Invalid location for dataset attributes file: %s" % datasets_attrs_file_name ) - datasets_attr_in = open( datasets_attrs_file_name, 'rb' ) - datasets_attr_str = '' - buffsize = 1048576 - try: - while True: - datasets_attr_str += datasets_attr_in.read( buffsize ) - if not datasets_attr_str or len( datasets_attr_str ) % buffsize != 0: - break - except OverflowError: - pass - datasets_attr_in.close() - datasets_attrs = from_json_string( datasets_attr_str ) - - # Create datasets. - for dataset_attrs in datasets_attrs: - metadata = dataset_attrs['metadata'] - - # Create dataset and HDA. - hda = model.HistoryDatasetAssociation( name = dataset_attrs['name'].encode( 'utf-8' ), - extension = dataset_attrs['extension'], - info = dataset_attrs['info'].encode( 'utf-8' ), - blurb = dataset_attrs['blurb'], - peek = dataset_attrs['peek'], - designation = dataset_attrs['designation'], - visible = dataset_attrs['visible'], - dbkey = metadata['dbkey'], - metadata = metadata, - history = new_history, - create_dataset = True, - sa_session = trans.sa_session ) - hda.state = hda.states.OK - trans.sa_session.add( hda ) - trans.sa_session.flush() - new_history.add_dataset( hda, genome_build = None ) - hda.hid = dataset_attrs['hid'] # Overwrite default hid set when HDA added to history. - permissions = trans.app.security_agent.history_get_default_permissions( new_history ) - trans.app.security_agent.set_all_dataset_permissions( hda.dataset, permissions ) - trans.sa_session.flush() - - # Do security check and copy dataset data. - temp_dataset_file_name = os.path.join( temp_output_dir, dataset_attrs['file_name'] ) - if not file_in_dir( temp_dataset_file_name, os.path.join( temp_output_dir, "datasets" ) ): - raise Exception( "Invalid dataset path: %s" % temp_dataset_file_name ) - shutil.move( temp_dataset_file_name, hda.file_name ) - - # Set tags, annotations. - if trans.user: - self.add_item_annotation( trans.sa_session, trans.get_user(), hda, dataset_attrs[ 'annotation' ] ) - for tag, value in dataset_attrs[ 'tags' ].items(): - trans.app.tag_handler.apply_item_tags( trans, trans.user, hda, get_tag_str( tag, value ) ) - trans.sa_session.flush() - - # - # Create jobs. - # - - # Read jobs attributes. - jobs_attr_file_name = os.path.join( temp_output_dir, 'jobs_attrs.txt') - if not file_in_dir( jobs_attr_file_name, temp_output_dir ): - raise Exception( "Invalid location for jobs' attributes file: %s" % jobs_attr_file_name ) - jobs_attr_in = open( jobs_attr_file_name, 'rb' ) - jobs_attr_str = '' - buffsize = 1048576 - try: - while True: - jobs_attr_str += jobs_attr_in.read( buffsize ) - if not jobs_attr_str or len( jobs_attr_str ) % buffsize != 0: - break - except OverflowError: - pass - jobs_attr_in.close() - - # Decode jobs attributes. - def as_hda( obj_dct ): - """ Hook to 'decode' an HDA; method uses history and HID to get the HDA represented by - the encoded object. This only works because HDAs are created above. """ - if obj_dct.get( '__HistoryDatasetAssociation__', False ): - return trans.sa_session.query( model.HistoryDatasetAssociation ) \ - .filter_by( history=new_history, hid=obj_dct['hid'] ).first() - return obj_dct - jobs_attrs = from_json_string( jobs_attr_str, object_hook=as_hda ) - - # Create each job. - for job_attrs in jobs_attrs: - imported_job = model.Job() - imported_job.user = trans.user - imported_job.session = trans.get_galaxy_session().id - imported_job.history = new_history - imported_job.tool_id = job_attrs[ 'tool_id' ] - imported_job.tool_version = job_attrs[ 'tool_version' ] - imported_job.set_state( job_attrs[ 'state' ] ) - imported_job.imported = True - trans.sa_session.add( imported_job ) - trans.sa_session.flush() - - class HistoryDatasetAssociationIDEncoder( simplejson.JSONEncoder ): - """ Custom JSONEncoder for a HistoryDatasetAssociation that encodes an HDA as its ID. """ - def default( self, obj ): - """ Encode an HDA, default encoding for everything else. """ - if isinstance( obj, model.HistoryDatasetAssociation ): - return obj.id - return simplejson.JSONEncoder.default( self, obj ) + # If no source to create archive from, show form to upload archive or specify URL. + if not archive_source: + return trans.show_form( + web.FormBuilder( web.url_for(), "Import a History from an Archive", submit_text="Submit" ) \ + .add_input( "text", "Archived History URL", "archive_url", value="", error=None ) + # TODO: add support for importing via a file. + #.add_input( "file", "Archived History File", "archive_file", value=None, error=None ) + ) - # Set parameters. May be useful to look at metadata.py for creating parameters. - # TODO: there may be a better way to set parameters, e.g.: - # for name, value in tool.params_to_strings( incoming, trans.app ).iteritems(): - # job.add_parameter( name, value ) - # to make this work, we'd need to flesh out the HDA objects. The code below is - # relatively similar. - for name, value in job_attrs[ 'params' ].items(): - # Transform parameter values when necessary. - if isinstance( value, model.HistoryDatasetAssociation ): - # HDA input: use hid to find input. - input_hda = trans.sa_session.query( model.HistoryDatasetAssociation ) \ - .filter_by( history=new_history, hid=value.hid ).first() - value = input_hda.id - #print "added parameter %s-->%s to job %i" % ( name, value, imported_job.id ) - imported_job.add_parameter( name, to_json_string( value, cls=HistoryDatasetAssociationIDEncoder ) ) - - # TODO: Connect jobs to input datasets. - - # Connect jobs to output datasets. - for output_hid in job_attrs[ 'output_datasets' ]: - #print "%s job has output dataset %i" % (imported_job.id, output_hid) - output_hda = trans.sa_session.query( model.HistoryDatasetAssociation ) \ - .filter_by( history=new_history, hid=output_hid ).first() - if output_hda: - imported_job.add_output_dataset( output_hda.name, output_hda ) - trans.sa_session.flush() - - # Cleanup. - if os.path.exists( temp_output_dir ): - shutil.rmtree( temp_output_dir ) - - return trans.show_ok_message( message="History '%s' has been imported. " % history_attrs['name'] ) - except Exception, e: - return trans.show_error_message( 'Error importing history archive. ' + str( e ) ) - - return trans.show_form( - web.FormBuilder( web.url_for(), "Import a History from an Archive", submit_text="Submit" ) - .add_input( "file", "Archived History File", "archived_history", value=None, error=None ) - ) - + # Run job to do import. + history_imp_tool = trans.app.toolbox.tools_by_id[ '__IMPORT_HISTORY__' ] + incoming = { '__ARCHIVE_SOURCE__' : archive_source, '__ARCHIVE_TYPE__' : archive_type } + history_imp_tool.execute( trans, incoming=incoming ) + return trans.show_message( "Importing history from '%s'. \ + This history will be visible when the import is complete" % archive_source ) + @web.expose def export_archive( self, trans, id=None, gzip=True, include_hidden=False, include_deleted=False ): """ Export a history to an archive. """ --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -608,6 +608,7 @@ class JobWrapper( object ): if self.app.config.set_metadata_externally: self.external_output_metadata.cleanup_external_metadata( self.sa_session ) galaxy.tools.imp_exp.JobExportHistoryArchiveWrapper( self.job_id ).cleanup_after_job( self.sa_session ) + galaxy.tools.imp_exp.JobImportHistoryArchiveWrapper( self.job_id ).cleanup_after_job( self.sa_session ) except: log.exception( "Unable to cleanup job %d" % self.job_id ) --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -227,7 +227,13 @@ class JobExportHistoryArchive( object ): self.history_attrs_filename = history_attrs_filename self.datasets_attrs_filename = datasets_attrs_filename self.jobs_attrs_filename = jobs_attrs_filename - + +class JobImportHistoryArchive( object ): + def __init__( self, job=None, history=None, archive_dir=None ): + self.job = job + self.history = history + self.archive_dir=archive_dir + class Group( object ): def __init__( self, name = None ): self.name = name @@ -244,6 +250,7 @@ class History( object, UsesAnnotations ) self.name = name or "Unnamed history" self.deleted = False self.purged = False + self.importing = False self.genome_build = None self.published = False # Relationships --- a/lib/galaxy/tools/imp_exp/__init__.py +++ b/lib/galaxy/tools/imp_exp/__init__.py @@ -2,7 +2,7 @@ import os, shutil, logging, tempfile, si from galaxy import model from galaxy.web.framework.helpers import to_unicode from galaxy.model.item_attrs import UsesAnnotations -from galaxy.util.json import to_json_string +from galaxy.util.json import * from galaxy.web.base.controller import UsesHistory log = logging.getLogger(__name__) @@ -26,21 +26,252 @@ def load_history_imp_exp_tools( toolbox </outputs></tool> """ + + # Load export tool. tmp_name = tempfile.NamedTemporaryFile() tmp_name.write( tool_xml_text ) tmp_name.flush() history_exp_tool = toolbox.load_tool( tmp_name.name ) toolbox.tools_by_id[ history_exp_tool.id ] = history_exp_tool log.debug( "Loaded history export tool: %s", history_exp_tool.id ) + + # Load import tool. + tool_xml = os.path.join( os.getcwd(), "lib/galaxy/tools/imp_exp/imp_history_from_archive.xml" ) + history_imp_tool = toolbox.load_tool( tool_xml ) + toolbox.tools_by_id[ history_imp_tool.id ] = history_imp_tool + log.debug( "Loaded history import tool: %s", history_imp_tool.id ) + +class JobImportHistoryArchiveWrapper( object, UsesHistory, UsesAnnotations ): + """ + Class provides support for performing jobs that import a history from + an archive. + """ + def __init__( self, job_id ): + self.job_id = job_id + + def cleanup_after_job( self, db_session ): + """ Set history, datasets, and jobs' attributes and clean up archive directory. """ + + # + # Helper methods. + # + + def file_in_dir( file_path, a_dir ): + """ Returns true if file is in directory. """ + abs_file_path = os.path.abspath( file_path ) + return os.path.split( abs_file_path )[0] == a_dir + + def read_file_contents( file_path ): + """ Read contents of a file. """ + fp = open( file_path, 'rb' ) + buffsize = 1048576 + file_contents = '' + try: + while True: + file_contents += fp.read( buffsize ) + if not file_contents or len( file_contents ) % buffsize != 0: + break + except OverflowError: + pass + fp.close() + return file_contents + + def get_tag_str( tag, value ): + """ Builds a tag string for a tag, value pair. """ + if not value: + return tag + else: + return tag + ":" + value + + # + # Import history. + # + + jiha = db_session.query( model.JobImportHistoryArchive ).filter_by( job_id=self.job_id ).first() + if jiha: + try: + archive_dir = jiha.archive_dir + user = jiha.job.user + + # + # Create history. + # + history_attr_file_name = os.path.join( archive_dir, 'history_attrs.txt') + history_attr_str = read_file_contents( history_attr_file_name ) + history_attrs = from_json_string( history_attr_str ) + + # Create history. + new_history = model.History( name='imported from archive: %s' % history_attrs['name'].encode( 'utf-8' ), \ + user=user ) + new_history.importing = True + new_history.hid_counter = history_attrs['hid_counter'] + new_history.genome_build = history_attrs['genome_build'] + db_session.add( new_history ) + jiha.history = new_history + db_session.flush() + + # Add annotation, tags. + if user: + self.add_item_annotation( db_session, user, new_history, history_attrs[ 'annotation' ] ) + """ + TODO: figure out to how add tags to item. + for tag, value in history_attrs[ 'tags' ].items(): + trans.app.tag_handler.apply_item_tags( trans, trans.user, new_history, get_tag_str( tag, value ) ) + """ + + # + # Create datasets. + # + datasets_attrs_file_name = os.path.join( archive_dir, 'datasets_attrs.txt') + datasets_attr_str = read_file_contents( datasets_attrs_file_name ) + datasets_attrs = from_json_string( datasets_attr_str ) + + # Get counts of how often each dataset file is used; a file can + # be linked to multiple dataset objects (HDAs). + datasets_usage_counts = {} + for dataset_attrs in datasets_attrs: + temp_dataset_file_name = \ + os.path.abspath( os.path.join( archive_dir, dataset_attrs['file_name'] ) ) + if ( temp_dataset_file_name not in datasets_usage_counts ): + datasets_usage_counts[ temp_dataset_file_name ] = 0 + datasets_usage_counts[ temp_dataset_file_name ] += 1 + + # Create datasets. + for dataset_attrs in datasets_attrs: + metadata = dataset_attrs['metadata'] + + # Create dataset and HDA. + hda = model.HistoryDatasetAssociation( name = dataset_attrs['name'].encode( 'utf-8' ), + extension = dataset_attrs['extension'], + info = dataset_attrs['info'].encode( 'utf-8' ), + blurb = dataset_attrs['blurb'], + peek = dataset_attrs['peek'], + designation = dataset_attrs['designation'], + visible = dataset_attrs['visible'], + dbkey = metadata['dbkey'], + metadata = metadata, + history = new_history, + create_dataset = True, + sa_session = db_session ) + hda.state = hda.states.OK + db_session.add( hda ) + db_session.flush() + new_history.add_dataset( hda, genome_build = None ) + hda.hid = dataset_attrs['hid'] # Overwrite default hid set when HDA added to history. + # TODO: Is there a way to recover permissions? Is this needed? + #permissions = trans.app.security_agent.history_get_default_permissions( new_history ) + #trans.app.security_agent.set_all_dataset_permissions( hda.dataset, permissions ) + db_session.flush() + + # Do security check and move/copy dataset data. + temp_dataset_file_name = \ + os.path.abspath( os.path.join( archive_dir, dataset_attrs['file_name'] ) ) + if not file_in_dir( temp_dataset_file_name, os.path.join( archive_dir, "datasets" ) ): + raise Exception( "Invalid dataset path: %s" % temp_dataset_file_name ) + if datasets_usage_counts[ temp_dataset_file_name ] == 1: + shutil.move( temp_dataset_file_name, hda.file_name ) + else: + datasets_usage_counts[ temp_dataset_file_name ] -= 1 + shutil.copyfile( temp_dataset_file_name, hda.file_name ) + + # Set tags, annotations. + if user: + self.add_item_annotation( db_session, user, hda, dataset_attrs[ 'annotation' ] ) + # TODO: Set tags. + """ + for tag, value in dataset_attrs[ 'tags' ].items(): + trans.app.tag_handler.apply_item_tags( trans, trans.user, hda, get_tag_str( tag, value ) ) + db_session.flush() + """ + + # + # Create jobs. + # + + # Read jobs attributes. + jobs_attr_file_name = os.path.join( archive_dir, 'jobs_attrs.txt') + jobs_attr_str = read_file_contents( jobs_attr_file_name ) + + # Decode jobs attributes. + def as_hda( obj_dct ): + """ Hook to 'decode' an HDA; method uses history and HID to get the HDA represented by + the encoded object. This only works because HDAs are created above. """ + if obj_dct.get( '__HistoryDatasetAssociation__', False ): + return db_session.query( model.HistoryDatasetAssociation ) \ + .filter_by( history=new_history, hid=obj_dct['hid'] ).first() + return obj_dct + jobs_attrs = from_json_string( jobs_attr_str, object_hook=as_hda ) + + # Create each job. + for job_attrs in jobs_attrs: + imported_job = model.Job() + imported_job.user = user + # TODO: set session? + # imported_job.session = trans.get_galaxy_session().id + imported_job.history = new_history + imported_job.tool_id = job_attrs[ 'tool_id' ] + imported_job.tool_version = job_attrs[ 'tool_version' ] + imported_job.set_state( job_attrs[ 'state' ] ) + imported_job.imported = True + db_session.add( imported_job ) + db_session.flush() + + class HistoryDatasetAssociationIDEncoder( simplejson.JSONEncoder ): + """ Custom JSONEncoder for a HistoryDatasetAssociation that encodes an HDA as its ID. """ + def default( self, obj ): + """ Encode an HDA, default encoding for everything else. """ + if isinstance( obj, model.HistoryDatasetAssociation ): + return obj.id + return simplejson.JSONEncoder.default( self, obj ) + + # Set parameters. May be useful to look at metadata.py for creating parameters. + # TODO: there may be a better way to set parameters, e.g.: + # for name, value in tool.params_to_strings( incoming, trans.app ).iteritems(): + # job.add_parameter( name, value ) + # to make this work, we'd need to flesh out the HDA objects. The code below is + # relatively similar. + for name, value in job_attrs[ 'params' ].items(): + # Transform parameter values when necessary. + if isinstance( value, model.HistoryDatasetAssociation ): + # HDA input: use hid to find input. + input_hda = db_session.query( model.HistoryDatasetAssociation ) \ + .filter_by( history=new_history, hid=value.hid ).first() + value = input_hda.id + #print "added parameter %s-->%s to job %i" % ( name, value, imported_job.id ) + imported_job.add_parameter( name, to_json_string( value, cls=HistoryDatasetAssociationIDEncoder ) ) + + # TODO: Connect jobs to input datasets. + + # Connect jobs to output datasets. + for output_hid in job_attrs[ 'output_datasets' ]: + #print "%s job has output dataset %i" % (imported_job.id, output_hid) + output_hda = db_session.query( model.HistoryDatasetAssociation ) \ + .filter_by( history=new_history, hid=output_hid ).first() + if output_hda: + imported_job.add_output_dataset( output_hda.name, output_hda ) + + # Done importing. + new_history.importing = False + + db_session.flush() + + # Cleanup. + if os.path.exists( archive_dir ): + shutil.rmtree( archive_dir ) + except Exception, e: + jiha.job.stderr += "Error cleaning up history import job: %s" % e + db_session.flush() class JobExportHistoryArchiveWrapper( object, UsesHistory, UsesAnnotations ): - """ Class provides support for performing jobs that export a history to an archive. """ + """ + Class provides support for performing jobs that export a history to an + archive. + """ def __init__( self, job_id ): self.job_id = job_id # TODO: should use db_session rather than trans in this method. def setup_job( self, trans, jeha, include_hidden=False, include_deleted=False ): - # jeha = job_export_history_archive for the job. """ Perform setup for job to export a history into an archive. Method generates attribute files for export, sets the corresponding attributes in the jeha object, and returns a command line for running the job. The command line --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1904,6 +1904,9 @@ class SetMetadataTool( Tool ): class ExportHistoryTool( Tool ): tool_type = 'export_history' + +class ImportHistoryTool( Tool ): + tool_type = 'import_history' # Populate tool_type to ToolClass mappings tool_types = {} --- a/lib/galaxy/tools/actions/history_imp_exp.py +++ b/lib/galaxy/tools/actions/history_imp_exp.py @@ -1,10 +1,56 @@ +import tempfile from __init__ import ToolAction from galaxy.util.odict import odict -from galaxy.tools.imp_exp import JobExportHistoryArchiveWrapper +from galaxy.tools.imp_exp import * import logging log = logging.getLogger( __name__ ) +class ImportHistoryToolAction( ToolAction ): + """Tool action used for importing a history to an archive. """ + + def execute( self, tool, trans, incoming = {}, set_output_hid = False, overwrite = True ): + # + # Create job. + # + job = trans.app.model.Job() + job.session_id = trans.get_galaxy_session().id + job.history_id = trans.history.id + job.tool_id = tool.id + job.user_id = trans.user.id + start_job_state = job.state #should be job.states.NEW + job.state = job.states.WAITING #we need to set job state to something other than NEW, or else when tracking jobs in db it will be picked up before we have added input / output parameters + trans.sa_session.add( job ) + trans.sa_session.flush() #ensure job.id are available + + # + # Setup job and job wrapper. + # + + # Add association for keeping track of job, history relationship. + archive_dir = tempfile.mkdtemp() + jiha = trans.app.model.JobImportHistoryArchive( job=job, archive_dir=archive_dir ) + trans.sa_session.add( jiha ) + job_wrapper = JobImportHistoryArchiveWrapper( job ) + + # + # Add parameters to job_parameter table. + # + + # Set additional parameters. + incoming[ '__DEST_DIR__' ] = jiha.archive_dir + for name, value in tool.params_to_strings( incoming, trans.app ).iteritems(): + job.add_parameter( name, value ) + + job.state = start_job_state #job inputs have been configured, restore initial job state + trans.sa_session.flush() + + # Queue the job for execution + trans.app.job_queue.put( job.id, tool ) + trans.log_event( "Added import history job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id ) + + return job, odict() + class ExportHistoryToolAction( ToolAction ): """Tool action used for exporting a history to an archive. """ @@ -30,6 +76,7 @@ class ExportHistoryToolAction( ToolActio job.session_id = trans.get_galaxy_session().id job.history_id = trans.history.id job.tool_id = tool.id + job.user_id = trans.user.id start_job_state = job.state #should be job.states.NEW job.state = job.states.WAITING #we need to set job state to something other than NEW, or else when tracking jobs in db it will be picked up before we have added input / output parameters trans.sa_session.add( job ) --- /dev/null +++ b/lib/galaxy/tools/imp_exp/imp_history_from_archive.xml @@ -0,0 +1,10 @@ +<tool id="__IMPORT_HISTORY__" name="Import History" version="0.1" tool_type="import_history"> + <type class="ImportHistoryTool" module="galaxy.tools"/> + <action module="galaxy.tools.actions.history_imp_exp" class="ImportHistoryToolAction"/> + <command interpreter="python">unpack_tar_gz_archive.py $__ARCHIVE_SOURCE__ $__DEST_DIR__ --$__ARCHIVE_TYPE__</command> + <inputs> + <param name="__ARCHIVE_SOURCE__" type="text"/> + <param name="__ARCHIVE_TYPE__" type="text"/> + <param name="__DEST_DIR__" type="text"/> + </inputs> +</tool> --- a/templates/root/index.mako +++ b/templates/root/index.mako @@ -53,10 +53,10 @@ galaxy_main.location = "${h.url_for( controller='history', action='delete_current' )}"; } }, - ##"Other Actions": null, - ##"Import from File": function() { - ## galaxy_main.location = "${h.url_for( controller='history', action='import_archive' )}"; - ##} + "Other Actions": null, + "Import from File": function() { + galaxy_main.location = "${h.url_for( controller='history', action='import_archive' )}"; + } }); // Init tool options. --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -77,6 +77,7 @@ History.table = Table( "history", metada Column( "hid_counter", Integer, default=1 ), Column( "deleted", Boolean, index=True, default=False ), Column( "purged", Boolean, index=True, default=False ), + Column( "importing", Boolean, index=True, default=False ), Column( "genome_build", TrimmedString( 40 ) ), Column( "importable", Boolean, default=False ), Column( "slug", TEXT, index=True ), @@ -384,6 +385,13 @@ JobExportHistoryArchive.table = Table( " Column( "jobs_attrs_filename", TEXT ) ) +JobImportHistoryArchive.table = Table( "job_import_history_archive", metadata, + Column( "id", Integer, primary_key=True ), + Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), + Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), + Column( "archive_dir", TEXT ) + ) + PostJobAction.table = Table("post_job_action", metadata, Column("id", Integer, primary_key=True), Column("workflow_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True, nullable=False), @@ -1220,6 +1228,9 @@ assign_mapper( context, JobExportHistory properties=dict( job = relation( Job ), history = relation( History ), dataset = relation( Dataset ) ) ) + +assign_mapper( context, JobImportHistoryArchive, JobImportHistoryArchive.table, + properties=dict( job = relation( Job ), history = relation( History ) ) ) assign_mapper( context, PostJobAction, PostJobAction.table, properties=dict(workflow_step = relation( WorkflowStep, backref='post_job_actions', primaryjoin=(WorkflowStep.table.c.id == PostJobAction.table.c.workflow_step_id)))) --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0060_history_archive_import.py @@ -0,0 +1,72 @@ +""" +Migration script to create column and table for importing histories from +file archives. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + +# Columns to add. + +importing_col = Column( "importing", Boolean, index=True, default=False ) +ldda_parent_col = Column( "ldda_parent_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True ) + +# Table to add. + +JobImportHistoryArchive_table = Table( "job_import_history_archive", metadata, + Column( "id", Integer, primary_key=True ), + Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), + Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), + Column( "archive_dir", TEXT ) + ) + +def upgrade(): + print __doc__ + metadata.reflect() + + # Add column to history table and initialize. + try: + History_table = Table( "history", metadata, autoload=True ) + importing_col.create( History_table ) + assert importing_col is History_table.c.importing + + # Initialize column to false. + if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': + default_false = "0" + elif migrate_engine.name == 'postgres': + default_false = "false" + db_session.execute( "UPDATE history SET importing=%s" % default_false ) + except Exception, e: + print str(e) + log.debug( "Adding column 'importing' to history table failed: %s" % str( e ) ) + + # Create job_import_history_archive table. + try: + JobImportHistoryArchive_table.create() + except Exception, e: + log.debug( "Creating job_import_history_archive table failed: %s" % str( e ) ) + +def downgrade(): + metadata.reflect() + + # Drop 'importing' column from history table. + try: + History_table = Table( "history", metadata, autoload=True ) + importing_col = History_table.c.importing + importing_col.drop() + except Exception, e: + log.debug( "Dropping column 'importing' from history table failed: %s" % ( str( e ) ) ) + + # Drop job_import_history_archive table. + try: + JobImportHistoryArchive_table.drop() + except Exception, e: + log.debug( "Dropping job_import_history_archive table failed: %s" % str( e ) ) --- /dev/null +++ b/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py @@ -0,0 +1,66 @@ +#!/usr/bin/env python +""" +Unpack a tar or tar.gz archive into a directory. + +usage: %prog archive_source dest_dir + --[url|file] source type, either a URL or a file. +""" + +import sys, optparse, tarfile, tempfile, urllib2, math + +# Set max size of archive/file that will be handled to be 100 GB. This is +# arbitrary and should be adjusted as needed. +MAX_SIZE = 100 * math.pow( 2, 30 ) + +def url_to_file( url, dest_file ): + """ + Transfer a file from a remote URL to a temporary file. + """ + try: + url_reader = urllib2.urlopen( url ) + CHUNK = 10 * 1024 # 10k + total = 0 + fp = open( dest_file, 'wb') + while True: + chunk = url_reader.read( CHUNK ) + if not chunk: + break + fp.write( chunk ) + total += CHUNK + if total > MAX_SIZE: + break + fp.close() + return dest_file + except Exception, e: + print "Exception getting file from URL: %s" % e, sys.stderr + return None + +def unpack_archive( archive_file, dest_dir ): + """ + Unpack a tar and/or gzipped archive into a destination directory. + """ + archive_fp = tarfile.open( archive_file, mode='r:gz' ) + archive_fp.extractall( path=dest_dir ) + archive_fp.close() + +if __name__ == "__main__": + # Parse command line. + parser = optparse.OptionParser() + parser.add_option( '-U', '--url', dest='is_url', action="store_true", help='Source is a URL.' ) + parser.add_option( '-F', '--file', dest='is_file', action="store_true", help='Source is a URL.' ) + (options, args) = parser.parse_args() + is_url = bool( options.is_url ) + is_file = bool( options.is_file ) + archive_source, dest_dir = args + + try: + # Get archive from URL. + if is_url: + archive_file = url_to_file( archive_source, tempfile.NamedTemporaryFile( dir=dest_dir ).name ) + elif is_file: + archive_file = archive_source + + # Unpack archive. + unpack_archive( archive_file, dest_dir ) + except Exception, e: + print "Error unpacking tar/gz archive: %s" % e, sys.stderr

1 0

galaxy-dist commit d73fa5f14b01: fixed select all checkbox in grid. the footer now updates when all items are selected
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1288121253 14400 # Node ID d73fa5f14b013333b2e49bfbf775db8dd0197e2b # Parent 314f8a5d38237c3f1fafccb522ee45aebfa8464f fixed select all checkbox in grid. the footer now updates when all items are selected --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -611,34 +611,27 @@ }); } - function check_all_items() - { + function check_all_items() { var chk_all = document.getElementById('check_all'); var checks = document.getElementsByTagName('input'); //var boxLength = checks.length; var total = 0; - if ( chk_all.checked == true ) - { - for ( i=0; i < checks.length; i++ ) - { - if ( checks[i].name.indexOf( 'id' ) != -1) - { + if ( chk_all.checked == true ) { + for ( i=0; i < checks.length; i++ ) { + if ( checks[i].name.indexOf( 'id' ) != -1) { checks[i].checked = true; total++; } } } - else - { - for ( i=0; i < checks.length; i++ ) - { - if ( checks[i].name.indexOf( 'id' ) != -1) - { + else { + for ( i=0; i < checks.length; i++ ) { + if ( checks[i].name.indexOf( 'id' ) != -1) { checks[i].checked = false } } } - + init_grid_elements(); } </script></%def>

1 0

galaxy-dist commit 87a6d4a29eee: fixed mutation viz functional tests
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1288111817 14400 # Node ID 87a6d4a29eeea038c669f086d254aaa4140a15bb # Parent e6e68c67dd9759154876546662f59ee280b78a34 fixed mutation viz functional tests --- a/test-data/mutation_data1_zoom3x.svg +++ b/test-data/mutation_data1_zoom3x.svg @@ -5,21 +5,21 @@ <g id="viewport"> -<text y="4" x="12" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">A</tspan></text> +<text y="3" x="12" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">A</tspan></text> -<rect fill-opacity="0.5" height="3" width="4" stroke="none" y="1" x="14" fill="blue" /> +<rect fill-opacity="0.5" height="3" width="4" stroke="none" y="0" x="14" fill="blue" /> -<text y="4" x="22" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">C</tspan></text> +<text y="3" x="22" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">C</tspan></text> -<rect fill-opacity="0.5" height="3" width="4" stroke="none" y="1" x="24" fill="green" /> +<rect fill-opacity="0.5" height="3" width="4" stroke="none" y="0" x="24" fill="green" /> -<text y="4" x="32" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">G</tspan></text> +<text y="3" x="32" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">G</tspan></text> -<rect fill-opacity="0.5" height="3" width="4" stroke="none" y="1" x="34" fill="orange" /> +<rect fill-opacity="0.5" height="3" width="4" stroke="none" y="0" x="34" fill="orange" /> -<text y="4" x="42" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">T</tspan></text> +<text y="3" x="42" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">T</tspan></text> -<rect fill-opacity="0.5" height="3" width="4" stroke="none" y="1" x="44" fill="red" /> +<rect fill-opacity="0.5" height="3" width="4" stroke="none" y="0" x="44" fill="red" /><text y="25" x="23" stroke="none" transform="rotate(-90 23,25)" fill="black"><tspan style="font-family:Verdana;font-size:25%">s1</tspan></text> --- a/test-data/mutation_data1_interactive.svg +++ b/test-data/mutation_data1_interactive.svg @@ -234,21 +234,21 @@ function handleMouseUp(evt) { <g id="viewport"> -<text y="4" x="12" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">A</tspan></text> +<text y="3" x="12" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">A</tspan></text> -<rect fill-opacity="0.5" height="3" width="4" stroke="none" y="1" x="14" fill="blue" /> +<rect fill-opacity="0.5" height="3" width="4" stroke="none" y="0" x="14" fill="blue" /> -<text y="4" x="22" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">C</tspan></text> +<text y="3" x="22" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">C</tspan></text> -<rect fill-opacity="0.5" height="3" width="4" stroke="none" y="1" x="24" fill="green" /> +<rect fill-opacity="0.5" height="3" width="4" stroke="none" y="0" x="24" fill="green" /> -<text y="4" x="32" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">G</tspan></text> +<text y="3" x="32" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">G</tspan></text> -<rect fill-opacity="0.5" height="3" width="4" stroke="none" y="1" x="34" fill="orange" /> +<rect fill-opacity="0.5" height="3" width="4" stroke="none" y="0" x="34" fill="orange" /> -<text y="4" x="42" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">T</tspan></text> +<text y="3" x="42" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">T</tspan></text> -<rect fill-opacity="0.5" height="3" width="4" stroke="none" y="1" x="44" fill="red" /> +<rect fill-opacity="0.5" height="3" width="4" stroke="none" y="0" x="44" fill="red" /><text y="35" x="23" stroke="none" transform="rotate(-90 23,35)" fill="black"><tspan style="font-family:Verdana;font-size:25%">s1</tspan></text>

1 0

galaxy-dist commit 677bcc65f74f: sample_tracking:
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1288101623 14400 # Node ID 677bcc65f74f5a460277f089d0cdebf170f02831 # Parent 9e27a8ad881dc4451add6d518468a73dbc9028bc sample_tracking: - added web api methods to update requests, samples using restful api - removed the old ad-doc web api - modified the data transfer code to use this api - code cleanup --- a/scripts/galaxy_messaging/server/galaxyweb_interface.py +++ /dev/null @@ -1,122 +0,0 @@ -import ConfigParser -import sys, os -import array -import time -import optparse,array -import shutil, traceback -import urllib,urllib2, cookielib - -assert sys.version_info[:2] >= ( 2, 4 ) -new_path = [ os.path.join( os.getcwd(), "lib" ) ] -new_path.extend( sys.path[1:] ) # remove scripts/ from the path -sys.path = new_path - -from galaxy import eggs -import pkg_resources - -import pkg_resources -pkg_resources.require( "pycrypto" ) - -from Crypto.Cipher import Blowfish -from Crypto.Util.randpool import RandomPool -from Crypto.Util import number - - -class GalaxyWebInterface(object): - def __init__(self, server_host, server_port, datatx_email, datatx_password, config_id_secret): - self.server_host = server_host - self.server_port = server_port - self.datatx_email = datatx_email - self.datatx_password = datatx_password - self.config_id_secret = config_id_secret - # create url - self.base_url = "http://%s:%s" % (self.server_host, self.server_port) - # login - url = "%s/user/login?email=%s&password=%s&login_button=Login" % (self.base_url, self.datatx_email, self.datatx_password) - cj = cookielib.CookieJar() - self.opener = urllib2.build_opener(urllib2.HTTPCookieProcessor(cj)) - #print url - f = self.opener.open(url) - if f.read().find("ogged in as "+self.datatx_email) == -1: - # if the user doesnt exist, create the user - url = "%s/user/create?email=%s&username=%s&password=%s&confirm=%s&create_user_button=Submit" % ( self.base_url, self.datatx_email, self.datatx_email, self.datatx_password, self.datatx_password ) - f = self.opener.open(url) - if f.read().find("ogged in as "+self.datatx_email) == -1: - raise Exception("The "+self.datatx_email+" user could not login to Galaxy") - - def add_to_library(self, server_dir, library_id, folder_id, dbkey=''): - ''' - This method adds the dataset file to the target data library & folder - by opening the corresponding url in Galaxy server running. - ''' - params = urllib.urlencode(dict( cntrller='library_admin', - tool_id='upload1', - tool_state='None', - library_id=self.encode_id(library_id), - folder_id=self.encode_id(folder_id), - upload_option='upload_directory', - file_type='auto', - server_dir=os.path.basename(server_dir), - dbkey=dbkey, - show_dataset_id='True', - runtool_btn='Upload to library')) - url = self.base_url+"/library_common/upload_library_dataset" - print url - print params - try: - f = self.opener.open(url, params) - if f.read().find("Data Library") == -1: - raise Exception("Dataset could not be uploaded to the data library. URL: %s, PARAMS=%s" % (url, params)) - except: - return 'ERROR', url, params - - def import_to_history(self, ldda_id, library_id, folder_id): - params = urllib.urlencode(dict( cntrller='library_admin', - show_deleted='False', - library_id=self.encode_id(library_id), - folder_id=self.encode_id(folder_id), - ldda_ids=self.encode_id(ldda_id), - do_action='import_to_history', - use_panels='False')) - #url = "http://lion.bx.psu.edu:8080/library_common/act_on_multiple_datasets?library…" - url = self.base_url+"/library_common/act_on_multiple_datasets" - f = self.opener.open(url, params) - x = f.read() - if x.find("1 dataset(s) have been imported into your history.") == -1: - raise Exception("Dataset could not be imported into history") - - def run_workflow(self, workflow_id, hid, workflow_step): - input = str(workflow_step)+'|input' - params = urllib.urlencode({'id':self.encode_id(workflow_id), - 'run_workflow': 'Run workflow', - input: hid}) - url = self.base_url+"/workflow/run" - f = self.opener.open(url, params) - - def logout(self): - # finally logout - f = self.opener.open(self.base_url+'/user/logout') - - def encode_id(self, obj_id ): - id_cipher = Blowfish.new( self.config_id_secret ) - # Convert to string - s = str( obj_id ) - # Pad to a multiple of 8 with leading "!" - s = ( "!" * ( 8 - len(s) % 8 ) ) + s - # Encrypt - return id_cipher.encrypt( s ).encode( 'hex' ) - - def update_request_state(self, request_id): - params = urllib.urlencode(dict( cntrller='requests_admin', - request_id=request_id)) - url = self.base_url + "/requests_common/update_request_state" - f = self.opener.open(url, params) - print url - print params - x = f.read() - - - - - - --- /dev/null +++ b/scripts/api/requests_update_state.py @@ -0,0 +1,16 @@ +#!/usr/bin/env python + + +import os, sys, traceback +sys.path.insert( 0, os.path.dirname( __file__ ) ) +from common import update + +try: + data = {} + data[ 'update_type' ] = 'request_state' +except IndexError: + print 'usage: %s key url' % os.path.basename( sys.argv[0] ) + sys.exit( 1 ) + +update( sys.argv[1], sys.argv[2], data, return_formatted=True ) + --- a/lib/galaxy/web/buildapp.py +++ b/lib/galaxy/web/buildapp.py @@ -106,6 +106,7 @@ def app_factory( global_conf, **kwargs ) add_api_controllers( webapp, app ) webapp.api_mapper.resource( 'content', 'contents', path_prefix='/api/libraries/:library_id', parent_resources=dict( member_name='library', collection_name='libraries' ) ) webapp.api_mapper.resource( 'library', 'libraries', path_prefix='/api' ) + webapp.api_mapper.resource( 'request', 'requests', path_prefix='/api' ) webapp.finalize_config() # Wrap the webapp in some useful middleware if kwargs.get( 'middleware', True ): --- /dev/null +++ b/scripts/api/sample_dataset_update_status.py @@ -0,0 +1,22 @@ +#!/usr/bin/env python + + +import os, sys, traceback +sys.path.insert( 0, os.path.dirname( __file__ ) ) +from common import display +from common import submit +from common import update +try: + data = {} + data[ 'update_type' ] = 'sample_dataset_transfer_status' + data[ 'sample_dataset_ids' ] = sys.argv[3].split(',') + data[ 'new_status' ] = sys.argv[4] +except IndexError: + print 'usage: %s key url sample_dataset_ids new_state [error msg]' % os.path.basename( sys.argv[0] ) + sys.exit( 1 ) +try: + data[ 'error_msg' ] = sys.argv[5] +except IndexError: + data[ 'error_msg' ] = '' +print data +update( sys.argv[1], sys.argv[2], data, return_formatted=True ) --- a/scripts/galaxy_messaging/server/amqp_consumer.py +++ b/scripts/galaxy_messaging/server/amqp_consumer.py @@ -14,24 +14,22 @@ import sys, os import optparse import xml.dom.minidom import subprocess +import urllib2 from galaxydb_interface import GalaxyDbInterface -new_path = [ os.path.join( os.getcwd(), "scripts/galaxy_messaging/server" ) ] -new_path.extend( sys.path[1:] ) # remove scripts/ from the path -sys.path = new_path -from galaxyweb_interface import GalaxyWebInterface +api_path = [ os.path.join( os.getcwd(), "scripts/api" ) ] +sys.path.extend( api_path ) +import common as api assert sys.version_info[:2] >= ( 2, 4 ) new_path = [ os.path.join( os.getcwd(), "lib" ) ] new_path.extend( sys.path[1:] ) # remove scripts/ from the path sys.path = new_path - - from galaxy import eggs +from galaxy.web.api.requests import RequestsController import pkg_resources pkg_resources.require( "amqplib" ) - from amqplib import client_0_8 as amqp import logging @@ -43,7 +41,12 @@ formatter = logging.Formatter("%(asctime fh.setFormatter(formatter) log.addHandler(fh) +# data transfer script +data_transfer_script = os.path.join( os.getcwd(), + "scripts/galaxy_messaging/server/data_transfer.py" ) + global dbconnstr +global webconfig global config def get_value(dom, tag_name): @@ -71,84 +74,98 @@ def get_value_index(dom, tag_name, index rc = rc + node.data return rc -def recv_callback(msg): - global config - global webconfig +def start_data_transfer(message): + # fork a new process to transfer datasets + cmd = '%s "%s" "%s" "%s"' % ( "python", + data_transfer_script, + message.body, + sys.argv[1] ) # Galaxy config file name + pid = subprocess.Popen(cmd, shell=True).pid + log.debug('Started process (%i): %s' % (pid, str(cmd))) + +def update_sample_state(message): + dom = xml.dom.minidom.parseString(message.body) + barcode = get_value(dom, 'barcode') + state = get_value(dom, 'state') + log.debug('Barcode: ' + barcode) + log.debug('State: ' + state) + # update the sample state in Galaxy db + galaxydb = GalaxyDbInterface(dbconnstr) + sample_id = galaxydb.get_sample_id(field_name='bar_code', value=barcode) + if sample_id == -1: + log.debug('Invalid barcode.') + return + galaxydb.change_state(sample_id, state) + # after updating the sample state, update request status + request_id = galaxydb.get_request_id(sample_id) + update_request( request_id ) + +def update_request( request_id ): + http_server_section = webconfig.get( "universe_wsgi_config", "http_server_section" ) + encoded_request_id = api.encode_id( config.get( "app:main", "id_secret" ), request_id ) + api_key = webconfig.get( "data_transfer_user_login_info", "api_key" ) + data = dict( update_type=RequestsController.update_types.REQUEST ) + url = "http://%s:%s/api/requests/%s" % ( config.get(http_server_section, "host"), + config.get(http_server_section, "port"), + encoded_request_id ) + log.debug( 'Updating request %i' % request_id ) + try: + api.update( api_key, url, data, return_formatted=False ) + except urllib2.URLError, e: + log.debug( 'ERROR(update_request (%s)): %s' % ( str((self.api_key, url, data)), str(e) ) ) + +def recv_callback(message): # check the meesage type. - msg_type = msg.properties['application_headers'].get('msg_type') - log.debug('\nMESSAGE RECVD: '+str(msg_type)) + msg_type = message.properties['application_headers'].get('msg_type') + log.debug( 'MESSAGE RECVD: ' + str( msg_type ) ) if msg_type == 'data_transfer': - log.debug('DATA TRANSFER') - # fork a new process to transfer datasets - transfer_script = os.path.join(os.getcwd(), - "scripts/galaxy_messaging/server/data_transfer.py") - cmd = '%s "%s" "%s" "%s"' % ("python", - transfer_script, - msg.body, - config.get("app:main", "id_secret") ) - pid = subprocess.Popen(cmd, shell=True).pid - log.debug('Started process (%i): %s' % (pid, str(cmd))) + log.debug( 'DATA TRANSFER' ) + start_data_transfer( message ) elif msg_type == 'sample_state_update': - log.debug('SAMPLE STATE UPDATE') - dom = xml.dom.minidom.parseString(msg.body) - barcode = get_value(dom, 'barcode') - state = get_value(dom, 'state') - log.debug('Barcode: '+barcode) - log.debug('State: '+state) - # update the galaxy db - galaxydb = GalaxyDbInterface(dbconnstr) - sample_id = galaxydb.get_sample_id(field_name='bar_code', value=barcode) - if sample_id == -1: - log.debug('Invalid barcode.') - return - galaxydb.change_state(sample_id, state) - # update the request state - galaxyweb = GalaxyWebInterface(webconfig.get("universe_wsgi_config", "host"), - webconfig.get("universe_wsgi_config", "port"), - webconfig.get("data_transfer_user_login_info", "email"), - webconfig.get("data_transfer_user_login_info", "password"), - config.get("app:main", "id_secret")) - galaxyweb.update_request_state(galaxydb.get_request_id(sample_id)) - galaxyweb.logout() + log.debug( 'SAMPLE STATE UPDATE' ) + update_sample_state( message ) def main(): if len(sys.argv) < 2: - print 'Usage: python amqp_consumer.py <Galaxy config file>' + print 'Usage: python amqp_consumer.py <Galaxy configuration file>' return global config config = ConfigParser.ConfigParser() - config.read(sys.argv[1]) + config.read( sys.argv[1] ) global dbconnstr dbconnstr = config.get("app:main", "database_connection") amqp_config = {} for option in config.options("galaxy_amqp"): amqp_config[option] = config.get("galaxy_amqp", option) - log.debug(str(amqp_config)) + log.debug("PID: " + str(os.getpid()) + ", " + str(amqp_config)) # web server config global webconfig webconfig = ConfigParser.ConfigParser() webconfig.read('transfer_datasets.ini') - - - - - + # connect conn = amqp.Connection(host=amqp_config['host']+":"+amqp_config['port'], userid=amqp_config['userid'], password=amqp_config['password'], virtual_host=amqp_config['virtual_host'], insist=False) chan = conn.channel() - chan.queue_declare(queue=amqp_config['queue'], durable=True, exclusive=True, auto_delete=False) - chan.exchange_declare(exchange=amqp_config['exchange'], type="direct", durable=True, auto_delete=False,) - chan.queue_bind(queue=amqp_config['queue'], - exchange=amqp_config['exchange'], - routing_key=amqp_config['routing_key']) + chan.queue_declare( queue=amqp_config['queue'], + durable=True, + exclusive=True, + auto_delete=False) + chan.exchange_declare( exchange=amqp_config['exchange'], + type="direct", + durable=True, + auto_delete=False,) + chan.queue_bind( queue=amqp_config['queue'], + exchange=amqp_config['exchange'], + routing_key=amqp_config['routing_key']) - chan.basic_consume(queue=amqp_config['queue'], - no_ack=True, - callback=recv_callback, - consumer_tag="testtag") + chan.basic_consume( queue=amqp_config['queue'], + no_ack=True, + callback=recv_callback, + consumer_tag="testtag") + log.debug('Connected to rabbitmq server - '+amqp_config['host']+":"+amqp_config['port']) while True: chan.wait() chan.basic_cancel("testtag") @@ -157,3 +174,5 @@ def main(): if __name__ == '__main__': main() + + --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1584,6 +1584,7 @@ class Request( object ): SUBMITTED = 'In Progress', REJECTED = 'Rejected', COMPLETE = 'Complete' ) + api_collection_visible_keys = ( 'id', 'name', 'state' ) def __init__( self, name=None, desc=None, request_type=None, user=None, form_values=None, notification=None ): self.name = name self.desc = desc @@ -1663,7 +1664,7 @@ class Request( object ): # Send email if trans.app.config.smtp_server is not None and self.notification and self.notification[ 'email' ]: host = trans.request.host.split( ':' )[0] - if host in [ 'localhost', '127.0.0.1' ]: + if host in [ 'localhost', '127.0.0.1', '0.0.0.0' ]: host = socket.getfqdn() body = """ Galaxy Sample Tracking Notification @@ -1704,8 +1705,8 @@ All samples in state: %(sample_state s.sendmail( frm, to, message ) s.quit() comments = "Email notification sent to %s." % ", ".join( to ).strip().strip( ',' ) - except: - comments = "Email notification failed." + except Exception,e: + comments = "Email notification failed. (%s)" % str(e) # update the request history with the email notification event elif not trans.app.config.smtp_server: comments = "Email notification failed as SMTP server not set in config file" @@ -1714,6 +1715,18 @@ All samples in state: %(sample_state trans.sa_session.add( event ) trans.sa_session.flush() return comments + def get_api_value( self, view='collection' ): + rval = {} + try: + visible_keys = self.__getattribute__( 'api_' + view + '_visible_keys' ) + except AttributeError: + raise Exception( 'Unknown API view: %s' % view ) + for key in visible_keys: + try: + rval[key] = self.__getattribute__( key ) + except AttributeError: + rval[key] = None + return rval class RequestEvent( object ): def __init__(self, request=None, request_state=None, comment=''): @@ -1734,7 +1747,7 @@ class RequestType( object ): self.sample_form = sample_form self.datatx_info = datatx_info @property - def state( self ): + def final_sample_state( self ): # The states mapper for this object orders ascending return self.states[-1] @@ -1747,12 +1760,6 @@ class RequestTypePermissions( object ): class Sample( object ): bulk_operations = Bunch( CHANGE_STATE = 'Change state', SELECT_LIBRARY = 'Select data library and folder' ) - transfer_status = Bunch( NOT_STARTED = 'Not started', - IN_QUEUE = 'In queue', - TRANSFERRING = 'Transferring dataset', - ADD_TO_LIBRARY = 'Adding to data library', - COMPLETE = 'Complete', - ERROR = 'Error' ) def __init__(self, name=None, desc=None, request=None, form_values=None, bar_code=None, library=None, folder=None): self.name = name self.desc = desc @@ -1776,21 +1783,21 @@ class Sample( object ): def untransferred_dataset_files( self ): untransferred_datasets = [] for dataset in self.datasets: - if dataset.status == self.transfer_status.NOT_STARTED: + if dataset.status == SampleDataset.transfer_status.NOT_STARTED: untransferred_datasets.append( dataset ) return untransferred_datasets @property def inprogress_dataset_files( self ): inprogress_datasets = [] for dataset in self.datasets: - if dataset.status not in [ self.transfer_status.NOT_STARTED, self.transfer_status.COMPLETE ]: + if dataset.status not in [ SampleDataset.transfer_status.NOT_STARTED, SampleDataset.transfer_status.COMPLETE ]: inprogress_datasets.append( dataset ) return inprogress_datasets @property def transferred_dataset_files( self ): transferred_datasets = [] for dataset in self.datasets: - if dataset.status == self.transfer_status.COMPLETE: + if dataset.status == SampleDataset.transfer_status.COMPLETE: transferred_datasets.append( dataset ) return transferred_datasets def dataset_size( self, filepath ): @@ -1818,6 +1825,12 @@ class SampleEvent( object ): self.comment = comment class SampleDataset( object ): + transfer_status = Bunch( NOT_STARTED = 'Not started', + IN_QUEUE = 'In queue', + TRANSFERRING = 'Transferring dataset', + ADD_TO_LIBRARY = 'Adding to data library', + COMPLETE = 'Complete', + ERROR = 'Error' ) def __init__(self, sample=None, name=None, file_path=None, status=None, error_msg=None, size=None): self.sample = sample --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -275,7 +275,7 @@ class RequestsCommon( BaseController, Us request_type = request.type name = util.restore_text( params.get( 'name', '' ) ) desc = util.restore_text( params.get( 'desc', '' ) ) - notification = dict( email=[ user.email ], sample_states=[ request_type.state.id ], body='', subject='' ) + notification = dict( email=[ user.email ], sample_states=[ request_type.final_sample_state.id ], body='', subject='' ) values = [] for index, field in enumerate( request_type.request_form.fields ): field_type = field[ 'type' ] @@ -416,11 +416,7 @@ class RequestsCommon( BaseController, Us elif params.get( 'change_state_button', False ): sample_event_comment = util.restore_text( params.get( 'sample_event_comment', '' ) ) new_state = trans.sa_session.query( trans.model.SampleState ).get( trans.security.decode_id( sample_state_id ) ) - for sample_id in selected_samples: - sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) ) - event = trans.model.SampleEvent( sample, new_state, sample_event_comment ) - trans.sa_session.add( event ) - trans.sa_session.flush() + self.update_sample_state(trans, cntrller, selected_samples, new_state, comment=sample_event_comment ) return trans.response.send_redirect( web.url_for( controller='requests_common', cntrller=cntrller, action='update_request_state', @@ -486,6 +482,22 @@ class RequestsCommon( BaseController, Us status=status, message=message ) @web.expose + def update_sample_state(self, trans, cntrller, sample_ids, new_state, comment=None ): + for sample_id in sample_ids: + try: + sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) ) + except: + if cntrller == 'api': + trans.response.status = 400 + return "Malformed sample id ( %s ) specified, unable to decode." % str( sample_id ) + else: + return invalid_id_redirect( trans, cntrller, sample_id ) + event = trans.model.SampleEvent( sample, new_state, comment ) + trans.sa_session.add( event ) + trans.sa_session.flush() + if cntrller == 'api': + return 200, 'Done' + @web.expose @web.require_login( "delete sequencing requests" ) def delete_request( self, trans, cntrller, **kwd ): params = util.Params( kwd ) @@ -640,6 +652,8 @@ class RequestsCommon( BaseController, Us event = trans.model.RequestEvent( request, request.states.SUBMITTED, message ) trans.sa_session.add( event ) trans.sa_session.flush() + if cntrller == 'api': + return 200, message return trans.response.send_redirect( web.url_for( controller='requests_common', action='manage_request', cntrller=cntrller, @@ -647,7 +661,7 @@ class RequestsCommon( BaseController, Us status=status, message=message ) ) final_state = False - request_type_state = request.type.state + request_type_state = request.type.final_sample_state if common_state.id == request_type_state.id: # since all the samples are in the final state, change the request state to 'Complete' comments = "All samples of this request are in the last sample state (%s). " % request_type_state.name @@ -656,7 +670,7 @@ class RequestsCommon( BaseController, Us else: comments = "All samples are in %s state. " % common_state.name state = request.states.SUBMITTED - event = trans.model.RequestEvent(request, state, comments) + event = trans.model.RequestEvent( request, state, comments ) trans.sa_session.add( event ) trans.sa_session.flush() # check if an email notification is configured to be sent when the samples @@ -666,6 +680,8 @@ class RequestsCommon( BaseController, Us message = comments + retval else: message = comments + if cntrller == 'api': + return 200, message return trans.response.send_redirect( web.url_for( controller='requests_common', action='manage_request', cntrller=cntrller, --- a/scripts/galaxy_messaging/server/data_transfer.py +++ b/scripts/galaxy_messaging/server/data_transfer.py @@ -19,25 +19,26 @@ import urllib,urllib2, cookielib, shutil import logging, time, datetime import xml.dom.minidom -sp = sys.path[0] +log = logging.getLogger("datatx_"+str(os.getpid())) +log.setLevel(logging.DEBUG) +fh = logging.FileHandler("data_transfer.log") +fh.setLevel(logging.DEBUG) +formatter = logging.Formatter("%(asctime)s - %(name)s - %(message)s") +fh.setFormatter(formatter) +log.addHandler(fh) -from galaxydb_interface import GalaxyDbInterface - -assert sys.version_info[:2] >= ( 2, 4 ) -new_path = [ sp ] -new_path.extend( sys.path ) -sys.path = new_path - -from galaxyweb_interface import GalaxyWebInterface +api_path = [ os.path.join( os.getcwd(), "scripts/api" ) ] +sys.path.extend( api_path ) +import common as api assert sys.version_info[:2] >= ( 2, 4 ) new_path = [ os.path.join( os.getcwd(), "lib" ) ] new_path.extend( sys.path[1:] ) # remove scripts/ from the path sys.path = new_path - from galaxy.util.json import from_json_string, to_json_string -from galaxy.model import Sample +from galaxy.model import SampleDataset +from galaxy.web.api.requests import RequestsController from galaxy import eggs import pkg_resources pkg_resources.require( "pexpect" ) @@ -46,28 +47,19 @@ import pexpect pkg_resources.require( "simplejson" ) import simplejson -log = logging.getLogger("datatx_"+str(os.getpid())) -log.setLevel(logging.DEBUG) -fh = logging.FileHandler("data_transfer.log") -fh.setLevel(logging.DEBUG) -formatter = logging.Formatter("%(asctime)s - %(name)s - %(message)s") -fh.setFormatter(formatter) -log.addHandler(fh) - - class DataTransfer(object): - def __init__(self, msg, config_id_secret): + def __init__(self, msg, config_file): log.info(msg) self.dom = xml.dom.minidom.parseString(msg) - self.host = self.get_value(self.dom, 'data_host') - self.username = self.get_value(self.dom, 'data_user') - self.password = self.get_value(self.dom, 'data_password') + self.sequencer_host = self.get_value(self.dom, 'data_host') + self.sequencer_username = self.get_value(self.dom, 'data_user') + self.sequencer_password = self.get_value(self.dom, 'data_password') + self.request_id = self.get_value(self.dom, 'request_id') self.sample_id = self.get_value(self.dom, 'sample_id') self.library_id = self.get_value(self.dom, 'library_id') self.folder_id = self.get_value(self.dom, 'folder_id') self.dataset_files = [] - self.config_id_secret = config_id_secret count=0 while True: dataset_id = self.get_value_index(self.dom, 'dataset_id', count) @@ -82,21 +74,25 @@ class DataTransfer(object): count=count+1 try: # Retrieve the upload user login information from the config file + transfer_datasets_config = ConfigParser.ConfigParser() + transfer_datasets_config.read('transfer_datasets.ini') + self.data_transfer_user_email = transfer_datasets_config.get("data_transfer_user_login_info", "email") + self.data_transfer_user_password = transfer_datasets_config.get("data_transfer_user_login_info", "password") + self.api_key = transfer_datasets_config.get("data_transfer_user_login_info", "api_key") + self.http_server_section = transfer_datasets_config.get("universe_wsgi_config", "http_server_section") config = ConfigParser.ConfigParser() - config.read('transfer_datasets.ini') - self.datatx_email = config.get("data_transfer_user_login_info", "email") - self.datatx_password = config.get("data_transfer_user_login_info", "password") - self.server_host = config.get("universe_wsgi_config", "host") - self.server_port = config.get("universe_wsgi_config", "port") - self.database_connection = config.get("universe_wsgi_config", "database_connection") - self.import_dir = config.get("universe_wsgi_config", "library_import_dir") + config.read( config_file ) + self.server_host = config.get(self.http_server_section, "host") + self.server_port = config.get(self.http_server_section, "port") + self.database_connection = config.get("app:main", "database_connection") + self.import_dir = config.get("app:main", "library_import_dir") + self.config_id_secret = config.get("app:main", "id_secret") + # create the destination directory within the import directory self.server_dir = os.path.join( self.import_dir, 'datatx_'+str(os.getpid())+'_'+datetime.date.today().strftime("%d%b%Y") ) os.mkdir(self.server_dir) if not os.path.exists(self.server_dir): raise Exception - # connect to db - self.galaxydb = GalaxyDbInterface(self.database_connection) except: log.error(traceback.format_exc()) log.error('FATAL ERROR') @@ -114,7 +110,7 @@ class DataTransfer(object): # add the dataset to the given library self.add_to_library() # update the data transfer status in the db - self.update_status(Sample.transfer_status.COMPLETE) + self.update_status(SampleDataset.transfer_status.COMPLETE) # cleanup #self.cleanup() sys.exit(0) @@ -149,15 +145,15 @@ class DataTransfer(object): def print_ticks(d): pass for i, df in enumerate(self.dataset_files): - self.update_status(Sample.transfer_status.TRANSFERRING, df['dataset_id']) + self.update_status(SampleDataset.transfer_status.TRANSFERRING, df['dataset_id']) try: - cmd = "scp %s@%s:'%s' '%s/%s'" % ( self.username, - self.host, - df['file'].replace(' ', '\ '), - self.server_dir.replace(' ', '\ '), - df['name'].replace(' ', '\ ')) + cmd = "scp %s@%s:'%s' '%s/%s'" % ( self.sequencer_username, + self.sequencer_host, + df['file'].replace(' ', '\ '), + self.server_dir.replace(' ', '\ '), + df['name'].replace(' ', '\ ') ) log.debug(cmd) - output = pexpect.run(cmd, events={'.ssword:*': self.password+'\r\n', + output = pexpect.run(cmd, events={'.ssword:*': self.sequencer_password+'\r\n', pexpect.TIMEOUT:print_ticks}, timeout=10) log.debug(output) @@ -176,17 +172,21 @@ class DataTransfer(object): This method adds the dataset file to the target data library & folder by opening the corresponding url in Galaxy server running. ''' + self.update_status(SampleDataset.transfer_status.ADD_TO_LIBRARY) try: - self.update_status(Sample.transfer_status.ADD_TO_LIBRARY) - log.debug("dir:%s, lib:%s, folder:%s" % (self.server_dir, str(self.library_id), str(self.folder_id))) - galaxyweb = GalaxyWebInterface(self.server_host, self.server_port, - self.datatx_email, self.datatx_password, - self.config_id_secret) - retval = galaxyweb.add_to_library(self.server_dir, self.library_id, self.folder_id) - log.debug(str(retval)) - galaxyweb.logout() - except Exception, e: - log.debug(e) + data = {} + data[ 'folder_id' ] = api.encode_id( self.config_id_secret, '%s.%s' % ( 'folder', self.folder_id ) ) + data[ 'file_type' ] = 'auto' + data[ 'server_dir' ] = self.server_dir + data[ 'dbkey' ] = '' + data[ 'upload_option' ] = 'upload_directory' + data[ 'create_type' ] = 'file' + url = "http://%s:%s/api/libraries/%s/contents" % ( self.server_host, + self.server_port, + api.encode_id( self.config_id_secret, self.library_id ) ) + log.debug(str((self.api_key, url, data))) + retval = api.submit( self.api_key, url, data, return_formatted=False ) + except: self.error_and_exit(str(e)) def update_status(self, status, dataset_id='All', msg=''): @@ -195,12 +195,27 @@ class DataTransfer(object): ''' try: log.debug('Setting status "%s" for dataset "%s" of sample "%s"' % ( status, str(dataset_id), str(self.sample_id) ) ) + sample_dataset_ids = [] if dataset_id == 'All': for dataset in self.dataset_files: - self.galaxydb.set_sample_dataset_status(dataset['dataset_id'], status, msg) + sample_dataset_ids.append( api.encode_id( self.config_id_secret, dataset['dataset_id'] ) ) else: - self.galaxydb.set_sample_dataset_status(dataset_id, status, msg) + sample_dataset_ids.append( api.encode_id( self.config_id_secret, dataset_id ) ) + # update the transfer status + data = {} + data[ 'update_type' ] = RequestsController.update_types.SAMPLE_DATASET + data[ 'sample_dataset_ids' ] = sample_dataset_ids + data[ 'new_status' ] = status + data[ 'error_msg' ] = msg + url = "http://%s:%s/api/requests/%s" % ( self.server_host, + self.server_port, + api.encode_id( self.config_id_secret, self.request_id ) ) + log.debug(str((self.api_key, url, data))) + retval = api.update( self.api_key, url, data, return_formatted=False ) log.debug('done.') + except urllib2.URLError, e: + log.debug( 'ERROR(sample_dataset_transfer_status (%s)): %s' % ( url, str(e) ) ) + log.error(traceback.format_exc()) except: log.error(traceback.format_exc()) log.error('FATAL ERROR') --- a/templates/admin/requests/rename_datasets.mako +++ b/templates/admin/requests/rename_datasets.mako @@ -32,7 +32,7 @@ <tbody> %for id in id_list: <% sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( id ) ) %> - %if sample_dataset.status == trans.app.model.Sample.transfer_status.NOT_STARTED: + %if sample_dataset.status == trans.app.model.SampleDataset.transfer_status.NOT_STARTED: <tr><td><% rename_datasets_for_sample_select_field = build_rename_datasets_for_sample_select_field( trans, sample_dataset ) %> --- a/scripts/api/common.py +++ b/scripts/api/common.py @@ -10,6 +10,11 @@ import pkg_resources pkg_resources.require( "simplejson" ) import simplejson +pkg_resources.require( "pycrypto" ) +from Crypto.Cipher import Blowfish +from Crypto.Util.randpool import RandomPool +from Crypto.Util import number + def make_url( api_key, url, args=None ): # Adds the API Key to the URL if it's not already there. if args is None: @@ -36,7 +41,15 @@ def post( api_key, url, data ): req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = simplejson.dumps( data ) ) return simplejson.loads( urllib2.urlopen( req ).read() ) -def display( api_key, url ): +def put( api_key, url, data ): + # Do the actual PUT + url = make_url( api_key, url ) + req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = simplejson.dumps( data )) + req.get_method = lambda: 'PUT' + return simplejson.loads( urllib2.urlopen( req ).read() ) + + +def display( api_key, url, return_formatted=True ): # Sends an API GET request and acts as a generic formatter for the JSON response. try: r = get( api_key, url ) @@ -47,6 +60,8 @@ def display( api_key, url ): if type( r ) == unicode: print 'error: %s' % r return None + if not return_formatted: + return r elif type( r ) == list: # Response is a collection as defined in the REST style. print 'Collection Members' @@ -68,7 +83,7 @@ def display( api_key, url ): else: print 'response is unknown type: %s' % type( r ) -def submit( api_key, url, data ): +def submit( api_key, url, data, return_formatted=True ): # Sends an API POST request and acts as a generic formatter for the JSON response. # 'data' will become the JSON payload read by Galaxy. try: @@ -77,6 +92,8 @@ def submit( api_key, url, data ): print e print e.read( 1024 ) sys.exit( 1 ) + if not return_formatted: + return r print 'Response' print '--------' if type( r ) == list: @@ -96,3 +113,45 @@ def submit( api_key, url, data ): print i else: print r + +def update( api_key, url, data, return_formatted=True ): + # Sends an API PUT request and acts as a generic formatter for the JSON response. + # 'data' will become the JSON payload read by Galaxy. + try: + r = put( api_key, url, data ) + except urllib2.HTTPError, e: + print e + print e.read( 1024 ) + sys.exit( 1 ) + if not return_formatted: + return r + print 'Response' + print '--------' + if type( r ) == list: + # Currently the only implemented responses are lists of dicts, because + # submission creates some number of collection elements. + for i in r: + if type( i ) == dict: + if 'url' in i: + print i.pop( 'url' ) + else: + print '----' + if 'name' in i: + print ' name: %s' % i.pop( 'name' ) + for k, v in i.items(): + print ' %s: %s' % ( k, v ) + else: + print i + else: + print r + +# utility method to encode ID's +def encode_id( config_id_secret, obj_id ): + id_cipher = Blowfish.new( config_id_secret ) + # Convert to string + s = str( obj_id ) + # Pad to a multiple of 8 with leading "!" + s = ( "!" * ( 8 - len(s) % 8 ) ) + s + # Encrypt + return id_cipher.encrypt( s ).encode( 'hex' ) + --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -129,9 +129,9 @@ class DataTransferGrid( grids.Grid ): visible=False, filterable="standard" ) ) operations = [ - grids.GridOperation( "Start Transfer", allow_multiple=True, condition=( lambda item: item.status in [ model.Sample.transfer_status.NOT_STARTED ] ) ), - grids.GridOperation( "Rename", allow_multiple=True, allow_popup=False, condition=( lambda item: item.status in [ model.Sample.transfer_status.NOT_STARTED ] ) ), - grids.GridOperation( "Delete", allow_multiple=True, condition=( lambda item: item.status in [ model.Sample.transfer_status.NOT_STARTED ] ) ), + grids.GridOperation( "Start Transfer", allow_multiple=True, condition=( lambda item: item.status in [ model.SampleDataset.transfer_status.NOT_STARTED ] ) ), + grids.GridOperation( "Rename", allow_multiple=True, allow_popup=False, condition=( lambda item: item.status in [ model.SampleDataset.transfer_status.NOT_STARTED ] ) ), + grids.GridOperation( "Delete", allow_multiple=True, condition=( lambda item: item.status in [ model.SampleDataset.transfer_status.NOT_STARTED ] ) ), ] def apply_query_filter( self, trans, query, **kwd ): sample_id = kwd.get( 'sample_id', None ) @@ -506,7 +506,7 @@ class RequestsAdmin( BaseController, Use name = self.__dataset_name( sample, filepath.split( '/' )[-1] ) sample_dataset = trans.model.SampleDataset( sample=sample, file_path=filepath, - status=sample.transfer_status.NOT_STARTED, + status=trans.app.model.SampleDataset.transfer_status.NOT_STARTED, name=name, error_msg='', size=sample.dataset_size( filepath ) ) @@ -575,6 +575,7 @@ class RequestsAdmin( BaseController, Use <data_host>%(DATA_HOST)s</data_host><data_user>%(DATA_USER)s</data_user><data_password>%(DATA_PASSWORD)s</data_password> + <request_id>%(REQUEST_ID)s</request_id><sample_id>%(SAMPLE_ID)s</sample_id><library_id>%(LIBRARY_ID)s</library_id><folder_id>%(FOLDER_ID)s</folder_id> @@ -588,16 +589,17 @@ class RequestsAdmin( BaseController, Use </dataset>''' datasets = '' for sample_dataset in selected_sample_datasets: - if sample_dataset.status == sample.transfer_status.NOT_STARTED: + if sample_dataset.status == trans.app.model.SampleDataset.transfer_status.NOT_STARTED: datasets = datasets + dataset_xml % dict( ID=str( sample_dataset.id ), NAME=sample_dataset.name, FILE=sample_dataset.file_path ) - sample_dataset.status = sample.transfer_status.IN_QUEUE + sample_dataset.status = trans.app.model.SampleDataset.transfer_status.IN_QUEUE trans.sa_session.add( sample_dataset ) trans.sa_session.flush() data = xml % dict( DATA_HOST=datatx_info['host'], DATA_USER=datatx_info['username'], DATA_PASSWORD=datatx_info['password'], + REQUEST_ID=str(sample.request.id), SAMPLE_ID=str(sample.id), LIBRARY_ID=str(sample.library.id), FOLDER_ID=str(sample.folder.id), @@ -644,6 +646,25 @@ class RequestsAdmin( BaseController, Use sample_id=trans.security.encode_id( sample.id ), status=status, message=message) ) + @web.expose + def update_sample_dataset_status(self, trans, cntrller, sample_dataset_ids, new_status, error_msg=None ): + # check if the new status is a valid transfer status + possible_status_list = [v[1] for v in trans.app.model.SampleDataset.transfer_status.items()] + if new_status not in possible_status_list: + trans.response.status = 400 + return "The requested transfer status ( %s ) is not a valid transfer status." % new_status + for id in util.listify( sample_dataset_ids ): + try: + sd_id = trans.security.decode_id( id ) + sample_dataset = trans.sa_session.query( trans.app.model.SampleDataset ).get( sd_id ) + except: + trans.response.status = 400 + return "Invalid sample dataset id ( %s ) specified." % str( id ) + sample_dataset.status = new_status + sample_dataset.error_msg = error_msg + trans.sa_session.add( sample_dataset ) + trans.sa_session.flush() + return 200, 'Done' # Request Type Stuff @web.expose @web.require_admin --- a/scripts/galaxy_messaging/server/galaxydb_interface.py +++ b/scripts/galaxy_messaging/server/galaxydb_interface.py @@ -28,7 +28,7 @@ class GalaxyDbInterface(object): def __init__(self, dbstr): self.dbstr = dbstr self.db_engine = create_engine(self.dbstr) - self.db_engine.echo = True + self.db_engine.echo = False self.metadata = MetaData(self.db_engine) self.session = sessionmaker(bind=self.db_engine) self.event_table = Table('sample_event', self.metadata, autoload=True ) --- /dev/null +++ b/scripts/api/sample_update_state.py @@ -0,0 +1,23 @@ +#!/usr/bin/env python + + +import os, sys, traceback +sys.path.insert( 0, os.path.dirname( __file__ ) ) +from common import display +from common import submit +from common import update + +try: + data = {} + data[ 'update_type' ] = 'sample_state' + data[ 'sample_ids' ] = sys.argv[3].split(',') + data[ 'new_state' ] = sys.argv[4] +except IndexError: + print 'usage: %s key url sample_ids new_state [comment]' % os.path.basename( sys.argv[0] ) + sys.exit( 1 ) +try: + data[ 'comment' ] = sys.argv[5] +except IndexError: + data[ 'comment' ] = '' + +update( sys.argv[1], sys.argv[2], data, return_formatted=True ) --- /dev/null +++ b/lib/galaxy/web/api/requests.py @@ -0,0 +1,130 @@ +""" +API operations on a sample tracking system. +""" +import logging, os, string, shutil, urllib, re, socket +from cgi import escape, FieldStorage +from galaxy import util, datatypes, jobs, web, util +from galaxy.web.base.controller import * +from galaxy.util.sanitize_html import sanitize_html +from galaxy.model.orm import * +from galaxy.util.bunch import Bunch + +log = logging.getLogger( __name__ ) + +class RequestsController( BaseController ): + update_types = Bunch( REQUEST = 'request_state', + SAMPLE = 'sample_state', + SAMPLE_DATASET = 'sample_dataset_transfer_status' ) + update_type_values = [v[1] for v in update_types.items()] + @web.expose_api + def index( self, trans, **kwd ): + """ + GET /api/requests + Displays a collection (list) of sequencing requests. + """ + query = trans.sa_session.query( trans.app.model.Request )\ + .filter( and_( trans.app.model.Request.table.c.user_id == trans.user.id \ + and trans.app.model.Request.table.c.deleted == False ) ) \ + .all() + rval = [] + for request in query: + item = request.get_api_value() + item['url'] = url_for( 'requests', id=trans.security.encode_id( request.id ) ) + item['id'] = trans.security.encode_id( item['id'] ) + rval.append( item ) + return rval + + @web.expose_api + def update( self, trans, id, key, payload, **kwd ): + """ + PUT /api/requests/{encoded_request_id} + Displays information about a sequencing request. + """ + params = util.Params( kwd ) + update_type = None + if 'update_type' not in payload: + trans.response.status = 400 + return "Missing required 'update_type' parameter. Please consult the API documentation for help." + else: + update_type = payload.pop( 'update_type' ) + if update_type not in self.update_type_values: + trans.response.status = 400 + return "Invalid value for 'update_type' parameter ( %s ) specified. Please consult the API documentation for help." % update_type + try: + request_id = trans.security.decode_id( id ) + except TypeError: + trans.response.status = 400 + return "Malformed %s id ( %s ) specified, unable to decode." % ( update_type, str( id ) ) + try: + request = trans.sa_session.query( trans.app.model.Request ).get( request_id ) + except: + request = None + if not request or not ( trans.user_is_admin() or request.user.id == trans.user.id ): + trans.response.status = 400 + return "Invalid request id ( %s ) specified." % str( request_id ) + # check update type + if update_type == 'request_state': + return self.__update_request_state( trans, encoded_request_id=id ) + elif update_type == 'sample_state': + return self.__update_sample_state( trans, request.type, **payload ) + elif update_type == 'sample_dataset_transfer_status': + # update sample_dataset transfer status + return self.__update_sample_dataset_status( trans, **payload ) + + + def __update_request_state( self, trans, encoded_request_id ): + requests_common_cntrller = trans.webapp.controllers['requests_common'] + status, output = requests_common_cntrller.update_request_state( trans, + cntrller='api', + request_id=encoded_request_id ) + return status, output + def __update_sample_state( self, trans, request_type, **payload ): + # only admin user may update sample state in Galaxy sample tracking + if not trans.user_is_admin(): + trans.response.status = 400 + return "only an admin user may update sample state in Galaxy sample tracking." + if 'sample_ids' not in payload or 'new_state' not in payload: + trans.response.status = 400 + return "Missing one or more required parameters: 'sample_ids' and 'new_state'." + sample_ids = payload.pop( 'sample_ids' ) + new_state_name = payload.pop( 'new_state' ) + comment = payload.get( 'comment', '' ) + # check if the new state is a valid sample state + possible_states = request_type.states + new_state = None + for state in possible_states: + if state.name == new_state_name: + new_state = state + if not new_state: + trans.response.status = 400 + return "Invalid sample state requested ( %s )." % new_state + requests_common_cntrller = trans.webapp.controllers['requests_common'] + status, output = requests_common_cntrller.update_sample_state( trans, + cntrller='api', + sample_ids=sample_ids, + new_state=new_state, + comment=comment ) + return status, output + + def __update_sample_dataset_status( self, trans, **payload ): + # only admin user may transfer sample datasets in Galaxy sample tracking + if not trans.user_is_admin(): + trans.response.status = 400 + return "Only an admin user may transfer sample datasets in Galaxy sample tracking and thus update transfer status." + if 'sample_dataset_ids' not in payload or 'new_status' not in payload: + trans.response.status = 400 + return "Missing one or more required parameters: 'sample_dataset_ids' and 'new_status'." + sample_dataset_ids = payload.pop( 'sample_dataset_ids' ) + new_status = payload.pop( 'new_status' ) + error_msg = payload.get( 'error_msg', '' ) + requests_admin_cntrller = trans.webapp.controllers['requests_admin'] + status, output = requests_admin_cntrller.update_sample_dataset_status( trans, + cntrller='api', + sample_dataset_ids=sample_dataset_ids, + new_status=new_status, + error_msg=error_msg ) + return status, output + + + + --- a/templates/admin/requests/dataset.mako +++ b/templates/admin/requests/dataset.mako @@ -58,7 +58,7 @@ <label>Transfer status:</label><div style="float: left; width: 250px; margin-right: 10px;"> ${sample_dataset.status} - %if sample_dataset.status == sample.transfer_status.ERROR: + %if sample_dataset.status == trans.app.model.SampleDataset.transfer_status.ERROR: <br/> ${sample_dataset.error_msg} %endif --- a/scripts/api/display.py +++ b/scripts/api/display.py @@ -1,6 +1,6 @@ #!/usr/bin/env python -import os, sys +import os, sys, urllib2 sys.path.insert( 0, os.path.dirname( __file__ ) ) from common import display @@ -9,3 +9,6 @@ try: except TypeError: print 'usage: %s key url' % os.path.basename( sys.argv[0] ) sys.exit( 1 ) +except urllib2.URLError, e: + print str(e) + sys.exit( 1 )

1 0