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[hg] galaxy 3017: Added sff datatype
by Greg Von Kuster 12 Nov '09

12 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/18586d1194f9 changeset: 3017:18586d1194f9 user: rc date: Wed Nov 11 17:55:08 2009 -0500 description: Added sff datatype Also, made changes to upload.py to sniff sff binary files diffstat: lib/galaxy/datatypes/data.py | 34 ++++++++++++++++- lib/galaxy/datatypes/registry.py | 3 + lib/galaxy/datatypes/sniff.py | 3 + lib/galaxy/datatypes/test/1.sff | test-data/1.sff | test/functional/test_sniffing_and_metadata_settings.py | 11 +++++ tools/data_source/upload.py | 4 ++ 7 files changed, 54 insertions(+), 1 deletions(-) diffs (124 lines): diff -r 9b9c3603fd09 -r 18586d1194f9 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py Wed Nov 11 16:52:18 2009 -0500 +++ b/lib/galaxy/datatypes/data.py Wed Nov 11 17:55:08 2009 -0500 @@ -1,4 +1,4 @@ -import logging, os, sys, time, tempfile +import logging, os, sys, time, tempfile, binascii from galaxy import util from galaxy.util.odict import odict from galaxy.util.bunch import Bunch @@ -455,3 +455,35 @@ class Newick( Text ): pass + +class Sff( Binary ): + """ Standard Flowgram Format (SFF) """ + file_ext = "sff" + def __init__( self, **kwd ): + Binary.__init__(self, **kwd) + def init_meta( self, dataset, copy_from=None ): + Binary.init_meta( self, dataset, copy_from=copy_from ) + def sniff( self, filename ): + ''' + The first 4 bytes of any sff file is '.sff' + + >>> fname = get_test_fname( '1.sff' ) + >>> Sff().sniff( fname ) + True + ''' + header = open( filename ).read(4) + if binascii.b2a_hex( header ) == binascii.hexlify( '.sff' ): + return True + return False + def set_peek( self, dataset ): + if not dataset.dataset.purged: + dataset.peek = "Binary sff file" + dataset.blurb = nice_size( dataset.get_size() ) + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disk' + def display_peek(self, dataset): + try: + return dataset.peek + except: + return "sff file (%s)" % ( nice_size( dataset.get_size() ) ) diff -r 9b9c3603fd09 -r 18586d1194f9 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py Wed Nov 11 16:52:18 2009 -0500 +++ b/lib/galaxy/datatypes/registry.py Wed Nov 11 17:55:08 2009 -0500 @@ -133,6 +133,7 @@ 'qual454' : qualityscore.QualityScore454(), 'sam' : tabular.Sam(), 'scf' : images.Scf(), + 'sff' : data.Sff(), 'tabular' : tabular.Tabular(), 'taxonomy' : tabular.Taxonomy(), 'txt' : data.Text(), @@ -162,6 +163,7 @@ 'qual454' : 'text/plain', 'sam' : 'text/plain', 'scf' : 'application/octet-stream', + 'sff' : 'application/octet-stream', 'tabular' : 'text/plain', 'taxonomy' : 'text/plain', 'txt' : 'text/plain', @@ -172,6 +174,7 @@ # because some formats are much more flexibly defined than others. if len(self.sniff_order) < 1: self.sniff_order = [ + data.Sff(), xml.BlastXml(), sequence.Maf(), sequence.Lav(), diff -r 9b9c3603fd09 -r 18586d1194f9 lib/galaxy/datatypes/sniff.py --- a/lib/galaxy/datatypes/sniff.py Wed Nov 11 16:52:18 2009 -0500 +++ b/lib/galaxy/datatypes/sniff.py Wed Nov 11 17:55:08 2009 -0500 @@ -249,6 +249,9 @@ >>> fname = get_test_fname('alignment.lav') >>> guess_ext(fname) 'lav' + >>> fname = get_test_fname('1.sff') + >>> guess_ext(fname) + 'sff' """ if sniff_order is None: datatypes_registry = registry.Registry() diff -r 9b9c3603fd09 -r 18586d1194f9 lib/galaxy/datatypes/test/1.sff Binary file lib/galaxy/datatypes/test/1.sff has changed diff -r 9b9c3603fd09 -r 18586d1194f9 test-data/1.sff Binary file test-data/1.sff has changed diff -r 9b9c3603fd09 -r 18586d1194f9 test/functional/test_sniffing_and_metadata_settings.py --- a/test/functional/test_sniffing_and_metadata_settings.py Wed Nov 11 16:52:18 2009 -0500 +++ b/test/functional/test_sniffing_and_metadata_settings.py Wed Nov 11 17:55:08 2009 -0500 @@ -246,6 +246,17 @@ assert latest_hda is not None, "Problem retrieving fastq hda from the database" if not latest_hda.name == '2gen.fastq' and not latest_hda.extension == 'fastq': raise AssertionError, "fastq data type was not correctly sniffed." + def test_0100_sff_datatype( self ): + """Testing correctly sniffing sff format upon upload""" + self.upload_file( '1.sff' ) + self.verify_dataset_correctness( '1.sff' ) + self.check_history_for_string( 'format: <span class="sff">sff' ) + latest_hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \ + .first() + assert latest_hda is not None, "Problem retrieving sff hda from the database" + if not latest_hda.name == '1.sff' and not latest_hda.extension == 'sff': + raise AssertionError, "sff data type was not correctly sniffed." def test_9999_clean_up( self ): self.delete_history( id=self.security.encode_id( history1.id ) ) self.logout() diff -r 9b9c3603fd09 -r 18586d1194f9 tools/data_source/upload.py --- a/tools/data_source/upload.py Wed Nov 11 16:52:18 2009 -0500 +++ b/tools/data_source/upload.py Wed Nov 11 17:55:08 2009 -0500 @@ -234,6 +234,10 @@ else: ext = dataset.file_type data_type = ext + elif data_type == 'binary' and ext == 'auto': + # currently we are only sniffing sff binary files + ext = sniff.guess_ext( dataset.path ) + data_type = ext # Save job info for the framework if ext == 'auto' and dataset.ext: ext = dataset.ext

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[hg] galaxy 3014: The job working directory was not being used f...
by Greg Von Kuster 12 Nov '09

12 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/0edb42925161 changeset: 3014:0edb42925161 user: Nate Coraor <nate(a)bx.psu.edu> date: Wed Nov 11 15:13:12 2009 -0500 description: The job working directory was not being used for _any_ cluster jobs. No idea how this was missed for so long. Data source jobs should now work on the cluster. diffstat: lib/galaxy/jobs/runners/pbs.py | 4 ++-- lib/galaxy/jobs/runners/sge.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diffs (33 lines): diff -r 120a34362c82 -r 0edb42925161 lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py Wed Nov 11 14:57:34 2009 -0500 +++ b/lib/galaxy/jobs/runners/pbs.py Wed Nov 11 15:13:12 2009 -0500 @@ -205,7 +205,7 @@ job_attrs[3].value = stageout job_attrs[4].name = pbs.ATTR_N job_attrs[4].value = "%s_%s" % ( job_wrapper.job_id, job_wrapper.tool.id ) - exec_dir = os.path.abspath( os.getcwd() ) + exec_dir = os.path.abspath( job_wrapper.working_directory ) # If not, we're using NFS else: job_attrs = pbs.new_attropl(3) @@ -215,7 +215,7 @@ job_attrs[1].value = efile job_attrs[2].name = pbs.ATTR_N job_attrs[2].value = "%s_%s" % ( job_wrapper.job_id, job_wrapper.tool.id ) - exec_dir = os.getcwd() + exec_dir = os.path.abspath( job_wrapper.working_directory ) # write the job script if self.app.config.pbs_stage_path != '': diff -r 120a34362c82 -r 0edb42925161 lib/galaxy/jobs/runners/sge.py --- a/lib/galaxy/jobs/runners/sge.py Wed Nov 11 14:57:34 2009 -0500 +++ b/lib/galaxy/jobs/runners/sge.py Wed Nov 11 15:13:12 2009 -0500 @@ -143,7 +143,7 @@ if sge_queue_name is not None: jt.setNativeSpecification( "-q %s" % sge_queue_name ) - script = sge_template % (job_wrapper.galaxy_lib_dir, os.getcwd(), command_line) + script = sge_template % (job_wrapper.galaxy_lib_dir, os.path.abspath( job_wrapper.working_directory ), command_line) fh = file( jt.remoteCommand, "w" ) fh.write( script ) fh.close()

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[hg] galaxy 3013: Include the tool name in the job name too
by Greg Von Kuster 12 Nov '09

12 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/120a34362c82 changeset: 3013:120a34362c82 user: Nate Coraor <nate(a)bx.psu.edu> date: Wed Nov 11 14:57:34 2009 -0500 description: Include the tool name in the job name too diffstat: lib/galaxy/jobs/runners/pbs.py | 4 ++-- 1 files changed, 2 insertions(+), 2 deletions(-) diffs (21 lines): diff -r dc9b5a47754c -r 120a34362c82 lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py Wed Nov 11 14:41:32 2009 -0500 +++ b/lib/galaxy/jobs/runners/pbs.py Wed Nov 11 14:57:34 2009 -0500 @@ -204,7 +204,7 @@ job_attrs[3].name = pbs.ATTR_stageout job_attrs[3].value = stageout job_attrs[4].name = pbs.ATTR_N - job_attrs[4].value = "%s" % job_wrapper.job_id + job_attrs[4].value = "%s_%s" % ( job_wrapper.job_id, job_wrapper.tool.id ) exec_dir = os.path.abspath( os.getcwd() ) # If not, we're using NFS else: @@ -214,7 +214,7 @@ job_attrs[1].name = pbs.ATTR_e job_attrs[1].value = efile job_attrs[2].name = pbs.ATTR_N - job_attrs[2].value = "%s" % job_wrapper.job_id + job_attrs[2].value = "%s_%s" % ( job_wrapper.job_id, job_wrapper.tool.id ) exec_dir = os.getcwd() # write the job script

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[hg] galaxy 3012: Fix for issue #210, redirect to the proper pat...
by Greg Von Kuster 12 Nov '09

12 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/dc9b5a47754c changeset: 3012:dc9b5a47754c user: Nate Coraor <nate(a)bx.psu.edu> date: Wed Nov 11 14:41:32 2009 -0500 description: Fix for issue #210, redirect to the proper path when the tool executed form is instructed to redirect. diffstat: templates/tool_executed.mako | 6 +++--- 1 files changed, 3 insertions(+), 3 deletions(-) diffs (27 lines): diff -r d36d08cc4abb -r dc9b5a47754c templates/tool_executed.mako --- a/templates/tool_executed.mako Wed Nov 11 13:53:48 2009 -0500 +++ b/templates/tool_executed.mako Wed Nov 11 14:41:32 2009 -0500 @@ -28,7 +28,7 @@ } function refresh() { - top.location.href = '${request.base}'; + top.location.href = '${h.url_for( "/" )}'; } </script> @@ -53,11 +53,11 @@ </p> %if tool.options.refresh: -<p id="refresh_message" style="display: none;">You are now being redirected back to <a href="${request.base}">Galaxy</a></div> +<p id="refresh_message" style="display: none;">You are now being redirected back to <a href="${h.url_for( '/' )}">Galaxy</a></div> %endif </div> </body> -</html> \ No newline at end of file +</html>

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[hg] galaxy 3011: Changed sam-to-bam test by removing nonexisten...
by Greg Von Kuster 12 Nov '09

12 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/d36d08cc4abb changeset: 3011:d36d08cc4abb user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Wed Nov 11 13:53:48 2009 -0500 description: Changed sam-to-bam test by removing nonexistent dbkey from test input specification. diffstat: tools/samtools/sam_to_bam.xml | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r 68c3b25ea133 -r d36d08cc4abb tools/samtools/sam_to_bam.xml --- a/tools/samtools/sam_to_bam.xml Wed Nov 11 13:08:11 2009 -0500 +++ b/tools/samtools/sam_to_bam.xml Wed Nov 11 13:53:48 2009 -0500 @@ -36,7 +36,7 @@ <tests> <test> <param name="indexSource" value="history" /> - <param name="input1" value="sam_to_bam_in1.sam" ftype="sam" dbkey="chrM" /> + <param name="input1" value="sam_to_bam_in1.sam" ftype="sam" /> <param name="ref_file" value="chrM.fa" ftype="fasta" /> <output name="output1" file="sam_to_bam_out1.bam" /> </test>

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[hg] galaxy 3007: Changes system call method from subprocess.che...
by Greg Von Kuster 12 Nov '09

12 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/f9bd28601cba changeset: 3007:f9bd28601cba user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Tue Nov 10 17:09:02 2009 -0500 description: Changes system call method from subprocess.check_call to os.system in Bam set_meta in images.py. Change to sam_to_bam_out1.bam should fix sam-to-bam functional test. diffstat: lib/galaxy/datatypes/images.py | 12 ++++++------ test-data/sam_to_bam_out1.bam | 2 files changed, 6 insertions(+), 6 deletions(-) diffs (24 lines): diff -r 4fdf952e413e -r f9bd28601cba lib/galaxy/datatypes/images.py --- a/lib/galaxy/datatypes/images.py Tue Nov 10 16:49:05 2009 -0500 +++ b/lib/galaxy/datatypes/images.py Tue Nov 10 17:09:02 2009 -0500 @@ -254,12 +254,12 @@ tmpf1 = tempfile.NamedTemporaryFile(dir=tmp_dir) tmpf1bai = '%s.bai' % tmpf1.name try: - subprocess.check_call(['cd', tmp_dir], shell=True) - subprocess.check_call('cp %s %s' % (dataset.file_name, tmpf1.name), shell=True) - subprocess.check_call('samtools index %s' % tmpf1.name, shell=True) - subprocess.check_call('cp %s %s' % (tmpf1bai, index_file.file_name), shell=True) - except subprocess.CalledProcessError: - sys.stderr.write('There was a problem creating the index for the BAM file\n') + os.system('cd %s' % tmp_dir) + os.system('cp %s %s' % (dataset.file_name, tmpf1.name)) + os.system('samtools index %s' % tmpf1.name) + os.system('cp %s %s' % (tmpf1bai, index_file.file_name)) + except Exception, ex: + sys.stderr.write('There was a problem creating the index for the BAM file\n%s\n' + str(ex)) tmpf1.close() if os.path.exists(tmpf1bai): os.remove(tmpf1bai) diff -r 4fdf952e413e -r f9bd28601cba test-data/sam_to_bam_out1.bam Binary file test-data/sam_to_bam_out1.bam has changed

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[hg] galaxy 3009: HostAgent needs an sa_session
by Greg Von Kuster 12 Nov '09

12 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/6b23bba26001 changeset: 3009:6b23bba26001 user: Nate Coraor <nate(a)bx.psu.edu> date: Wed Nov 11 11:49:08 2009 -0500 description: HostAgent needs an sa_session diffstat: lib/galaxy/security/__init__.py | 3 +++ 1 files changed, 3 insertions(+), 0 deletions(-) diffs (13 lines): diff -r ba4ad1b7a746 -r 6b23bba26001 lib/galaxy/security/__init__.py --- a/lib/galaxy/security/__init__.py Wed Nov 11 11:38:48 2009 -0500 +++ b/lib/galaxy/security/__init__.py Wed Nov 11 11:49:08 2009 -0500 @@ -569,6 +569,9 @@ self.model = model if permitted_actions: self.permitted_actions = permitted_actions + @property + def sa_session( self ): + return self.model.context.current def allow_action( self, addr, action, **kwd ): if 'dataset' in kwd and action == self.permitted_actions.DATASET_ACCESS: hda = kwd['dataset']

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[hg] galaxy 3006: Add Paste#gzip and visualization module option...
by Greg Von Kuster 12 Nov '09

12 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/4fdf952e413e changeset: 3006:4fdf952e413e user: Kanwei Li <kanwei(a)gmail.com> date: Tue Nov 10 16:49:05 2009 -0500 description: Add Paste#gzip and visualization module options to universe_wsgi.ini.sample diffstat: universe_wsgi.ini.sample | 17 ++++++++++++++++- 1 files changed, 16 insertions(+), 1 deletions(-) diffs (29 lines): diff -r 6eddc13b1d3b -r 4fdf952e413e universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample Tue Nov 10 16:02:49 2009 -0500 +++ b/universe_wsgi.ini.sample Tue Nov 10 16:49:05 2009 -0500 @@ -8,9 +8,24 @@ use_threadpool = true threadpool_workers = 10 +# ---- HTTP gzip compression ---- +# If planning to run Galaxy as a production service, we recommend running Galaxy +# through a proxy and enabling gzip compression there (instructions at +# http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer ) +# but you may also turn on Paste's built-in gzip compressor by uncommenting the following lines +# and also the 'filter-with = gzip' line under [app:main]. This will reduce network traffic +# and should speed up the interface, especially the visualization module. +# [filter:gzip] +# use = egg:Paste#gzip + # ---- Galaxy Web Interface ------------------------------------------------- +[app:main] -[app:main] +# Uncomment following line to enable Paste gzip compression +# filter-with = gzip + +# Uncomment following line below to enable visualization module +# enable_tracks = True # Specifies the factory for the universe WSGI application paste.app_factory = galaxy.web.buildapp:app_factory

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[hg] galaxy 3008: Convert lib/galaxy/security/__init__.py from D...
by Greg Von Kuster 12 Nov '09

12 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/ba4ad1b7a746 changeset: 3008:ba4ad1b7a746 user: Nate Coraor <nate(a)bx.psu.edu> date: Wed Nov 11 11:38:48 2009 -0500 description: Convert lib/galaxy/security/__init__.py from DOS to UNIX line endings (no other changes) diffstat: lib/galaxy/security/__init__.py | 1236 ++++++++++++++++++++++---------------------- 1 files changed, 618 insertions(+), 618 deletions(-) diffs (1244 lines): diff -r f9bd28601cba -r ba4ad1b7a746 lib/galaxy/security/__init__.py --- a/lib/galaxy/security/__init__.py Tue Nov 10 17:09:02 2009 -0500 +++ b/lib/galaxy/security/__init__.py Wed Nov 11 11:38:48 2009 -0500 @@ -1,622 +1,622 @@ -""" -Galaxy Security - -""" -import logging, socket -from datetime import datetime, timedelta -from galaxy.util.bunch import Bunch -from galaxy.model.orm import * - -log = logging.getLogger(__name__) - -class Action( object ): - def __init__( self, action, description, model ): - self.action = action - self.description = description - self.model = model - -class RBACAgent: - """Class that handles galaxy security""" - permitted_actions = Bunch( - DATASET_MANAGE_PERMISSIONS = Action( "manage permissions", "Role members can manage the roles associated with this dataset", "grant" ), - DATASET_ACCESS = Action( "access", "Role members can import this dataset into their history for analysis", "restrict" ), - LIBRARY_ADD = Action( "add library item", "Role members can add library items to this library item", "grant" ), - LIBRARY_MODIFY = Action( "modify library item", "Role members can modify this library item", "grant" ), - LIBRARY_MANAGE = Action( "manage library permissions", "Role members can manage roles associated with this library item", "grant" ) - ) - def get_action( self, name, default=None ): - """Get a permitted action by its dict key or action name""" - for k, v in self.permitted_actions.items(): - if k == name or v.action == name: - return v - return default - def get_actions( self ): - """Get all permitted actions as a list of Action objects""" - return self.permitted_actions.__dict__.values() - def get_item_actions( self, action, item ): - raise 'No valid method of retrieving action (%s) for item %s.' % ( action, item ) - def guess_derived_permissions_for_datasets( self, datasets = [] ): - raise "Unimplemented Method" - def can_access_dataset( self, roles, dataset ): - raise "Unimplemented Method" - def can_manage_dataset( self, roles, dataset ): - raise "Unimplemented Method" - def can_add_library_item( self, user, roles, item ): - raise "Unimplemented Method" - def can_modify_library_item( self, user, roles, item ): - raise "Unimplemented Method" - def can_manage_library_item( self, user, roles, item ): - raise "Unimplemented Method" - def associate_components( self, **kwd ): - raise 'No valid method of associating provided components: %s' % kwd - def create_private_user_role( self, user ): - raise "Unimplemented Method" - def get_private_user_role( self, user ): - raise "Unimplemented Method" - def user_set_default_permissions( self, user, permissions={}, history=False, dataset=False ): - raise "Unimplemented Method" - def history_set_default_permissions( self, history, permissions=None, dataset=False, bypass_manage_permission=False ): - raise "Unimplemented Method" - def set_all_dataset_permissions( self, dataset, permissions ): - raise "Unimplemented Method" - def set_dataset_permission( self, dataset, permission ): - raise "Unimplemented Method" - def set_all_library_permissions( self, dataset, permissions ): - raise "Unimplemented Method" - def dataset_is_public( self, dataset ): - raise "Unimplemented Method" - def make_dataset_public( self, dataset ): - raise "Unimplemented Method" - def get_component_associations( self, **kwd ): - raise "Unimplemented Method" - def components_are_associated( self, **kwd ): - return bool( self.get_component_associations( **kwd ) ) - def convert_permitted_action_strings( self, permitted_action_strings ): - """ - When getting permitted actions from an untrusted source like a - form, ensure that they match our actual permitted actions. - """ - return filter( lambda x: x is not None, [ self.permitted_actions.get( action_string ) for action_string in permitted_action_strings ] ) - -class GalaxyRBACAgent( RBACAgent ): - def __init__( self, model, permitted_actions=None ): - self.model = model - if permitted_actions: - self.permitted_actions = permitted_actions - # List of "library_item" objects and their associated permissions and info template objects - self.library_item_assocs = ( - ( self.model.Library, self.model.LibraryPermissions ), - ( self.model.LibraryFolder, self.model.LibraryFolderPermissions ), - ( self.model.LibraryDataset, self.model.LibraryDatasetPermissions ), - ( self.model.LibraryDatasetDatasetAssociation, self.model.LibraryDatasetDatasetAssociationPermissions ) ) - @property - def sa_session( self ): - """ - Returns a SQLAlchemy session -- currently just gets the current - session from the threadlocal session context, but this is provided - to allow migration toward a more SQLAlchemy 0.4 style of use. - """ - return self.model.context.current - def allow_dataset_action( self, roles, action, dataset ): - """ - Returns true when user has permission to perform an action on an - instance of Dataset. - """ - dataset_actions = self.get_item_actions( action, dataset ) - if not dataset_actions: - return action.model == 'restrict' - ret_val = False - for dataset_action in dataset_actions: - if dataset_action.role in roles: - ret_val = True - break - return ret_val - def can_access_dataset( self, roles, dataset ): - return self.allow_dataset_action( roles, self.permitted_actions.DATASET_ACCESS, dataset ) - def can_manage_dataset( self, roles, dataset ): - return self.allow_dataset_action( roles, self.permitted_actions.DATASET_MANAGE_PERMISSIONS, dataset ) - def allow_library_item_action( self, user, roles, action, item ): - """ - Method for checking a permission for the current user to perform a - specific library action on a library item, which must be one of: - Library, LibraryFolder, LibraryDataset, LibraryDatasetDatasetAssociation - """ - if user is None: - # All permissions are granted, so non-users cannot have permissions - return False - # Check to see if user has access to any of the roles associated with action - item_actions = self.get_item_actions( action, item ) - if not item_actions: - # All permissions are granted, so item must have action - return False - ret_val = False - for item_action in item_actions: - if item_action.role in roles: - ret_val = True - break - return ret_val - def can_add_library_item( self, user, roles, item ): - return self.allow_library_item_action( user, roles, self.permitted_actions.LIBRARY_ADD, item ) - def can_modify_library_item( self, user, roles, item ): - return self.allow_library_item_action( user, roles, self.permitted_actions.LIBRARY_MODIFY, item ) - def can_manage_library_item( self, user, roles, item ): - return self.allow_library_item_action( user, roles, self.permitted_actions.LIBRARY_MANAGE, item ) - def get_item_actions( self, action, item ): - # item must be one of: Dataset, Library, LibraryFolder, LibraryDataset, LibraryDatasetDatasetAssociation - return [ permission for permission in item.actions if permission.action == action.action ] - def guess_derived_permissions_for_datasets( self, datasets=[] ): - """Returns a dict of { action : [ role, role, ... ] } for the output dataset based upon provided datasets""" - perms = {} - for dataset in datasets: - if not isinstance( dataset, self.model.Dataset ): - dataset = dataset.dataset - these_perms = {} - # initialize blank perms - for action in self.get_actions(): - these_perms[ action ] = [] - # collect this dataset's perms - these_perms = self.get_dataset_permissions( dataset ) - # join or intersect this dataset's permissions with others - for action, roles in these_perms.items(): - if action not in perms.keys(): - perms[ action ] = roles - else: - if action.model == 'grant': - # intersect existing roles with new roles - perms[ action ] = filter( lambda x: x in perms[ action ], roles ) - elif action.model == 'restrict': - # join existing roles with new roles - perms[ action ].extend( filter( lambda x: x not in perms[ action ], roles ) ) - return perms - def associate_components( self, **kwd ): - if 'user' in kwd: - if 'group' in kwd: - return self.associate_user_group( kwd['user'], kwd['group'] ) - elif 'role' in kwd: - return self.associate_user_role( kwd['user'], kwd['role'] ) - elif 'role' in kwd: - if 'group' in kwd: - return self.associate_group_role( kwd['group'], kwd['role'] ) - if 'action' in kwd: - if 'dataset' in kwd and 'role' in kwd: - return self.associate_action_dataset_role( kwd['action'], kwd['dataset'], kwd['role'] ) - raise 'No valid method of associating provided components: %s' % kwd - def associate_user_group( self, user, group ): - assoc = self.model.UserGroupAssociation( user, group ) - assoc.flush() - return assoc - def associate_user_role( self, user, role ): - assoc = self.model.UserRoleAssociation( user, role ) - assoc.flush() - return assoc - def associate_group_role( self, group, role ): - assoc = self.model.GroupRoleAssociation( group, role ) - assoc.flush() - return assoc - def associate_action_dataset_role( self, action, dataset, role ): - assoc = self.model.DatasetPermissions( action, dataset, role ) - assoc.flush() - return assoc - def create_private_user_role( self, user ): - # Create private role - role = self.model.Role( name=user.email, description='Private Role for ' + user.email, type=self.model.Role.types.PRIVATE ) - role.flush() - # Add user to role - self.associate_components( role=role, user=user ) - return role - def get_private_user_role( self, user, auto_create=False ): - role = self.sa_session.query( self.model.Role ) \ - .filter( and_( self.model.Role.table.c.name == user.email, - self.model.Role.table.c.type == self.model.Role.types.PRIVATE ) ) \ - .first() - if not role: - if auto_create: - return self.create_private_user_role( user ) - else: - return None - return role - def user_set_default_permissions( self, user, permissions={}, history=False, dataset=False, bypass_manage_permission=False, default_access_private = False ): - # bypass_manage_permission is used to change permissions of datasets in a userless history when logging in - if user is None: - return None - if not permissions: +""" +Galaxy Security + +""" +import logging, socket +from datetime import datetime, timedelta +from galaxy.util.bunch import Bunch +from galaxy.model.orm import * + +log = logging.getLogger(__name__) + +class Action( object ): + def __init__( self, action, description, model ): + self.action = action + self.description = description + self.model = model + +class RBACAgent: + """Class that handles galaxy security""" + permitted_actions = Bunch( + DATASET_MANAGE_PERMISSIONS = Action( "manage permissions", "Role members can manage the roles associated with this dataset", "grant" ), + DATASET_ACCESS = Action( "access", "Role members can import this dataset into their history for analysis", "restrict" ), + LIBRARY_ADD = Action( "add library item", "Role members can add library items to this library item", "grant" ), + LIBRARY_MODIFY = Action( "modify library item", "Role members can modify this library item", "grant" ), + LIBRARY_MANAGE = Action( "manage library permissions", "Role members can manage roles associated with this library item", "grant" ) + ) + def get_action( self, name, default=None ): + """Get a permitted action by its dict key or action name""" + for k, v in self.permitted_actions.items(): + if k == name or v.action == name: + return v + return default + def get_actions( self ): + """Get all permitted actions as a list of Action objects""" + return self.permitted_actions.__dict__.values() + def get_item_actions( self, action, item ): + raise 'No valid method of retrieving action (%s) for item %s.' % ( action, item ) + def guess_derived_permissions_for_datasets( self, datasets = [] ): + raise "Unimplemented Method" + def can_access_dataset( self, roles, dataset ): + raise "Unimplemented Method" + def can_manage_dataset( self, roles, dataset ): + raise "Unimplemented Method" + def can_add_library_item( self, user, roles, item ): + raise "Unimplemented Method" + def can_modify_library_item( self, user, roles, item ): + raise "Unimplemented Method" + def can_manage_library_item( self, user, roles, item ): + raise "Unimplemented Method" + def associate_components( self, **kwd ): + raise 'No valid method of associating provided components: %s' % kwd + def create_private_user_role( self, user ): + raise "Unimplemented Method" + def get_private_user_role( self, user ): + raise "Unimplemented Method" + def user_set_default_permissions( self, user, permissions={}, history=False, dataset=False ): + raise "Unimplemented Method" + def history_set_default_permissions( self, history, permissions=None, dataset=False, bypass_manage_permission=False ): + raise "Unimplemented Method" + def set_all_dataset_permissions( self, dataset, permissions ): + raise "Unimplemented Method" + def set_dataset_permission( self, dataset, permission ): + raise "Unimplemented Method" + def set_all_library_permissions( self, dataset, permissions ): + raise "Unimplemented Method" + def dataset_is_public( self, dataset ): + raise "Unimplemented Method" + def make_dataset_public( self, dataset ): + raise "Unimplemented Method" + def get_component_associations( self, **kwd ): + raise "Unimplemented Method" + def components_are_associated( self, **kwd ): + return bool( self.get_component_associations( **kwd ) ) + def convert_permitted_action_strings( self, permitted_action_strings ): + """ + When getting permitted actions from an untrusted source like a + form, ensure that they match our actual permitted actions. + """ + return filter( lambda x: x is not None, [ self.permitted_actions.get( action_string ) for action_string in permitted_action_strings ] ) + +class GalaxyRBACAgent( RBACAgent ): + def __init__( self, model, permitted_actions=None ): + self.model = model + if permitted_actions: + self.permitted_actions = permitted_actions + # List of "library_item" objects and their associated permissions and info template objects + self.library_item_assocs = ( + ( self.model.Library, self.model.LibraryPermissions ), + ( self.model.LibraryFolder, self.model.LibraryFolderPermissions ), + ( self.model.LibraryDataset, self.model.LibraryDatasetPermissions ), + ( self.model.LibraryDatasetDatasetAssociation, self.model.LibraryDatasetDatasetAssociationPermissions ) ) + @property + def sa_session( self ): + """ + Returns a SQLAlchemy session -- currently just gets the current + session from the threadlocal session context, but this is provided + to allow migration toward a more SQLAlchemy 0.4 style of use. + """ + return self.model.context.current + def allow_dataset_action( self, roles, action, dataset ): + """ + Returns true when user has permission to perform an action on an + instance of Dataset. + """ + dataset_actions = self.get_item_actions( action, dataset ) + if not dataset_actions: + return action.model == 'restrict' + ret_val = False + for dataset_action in dataset_actions: + if dataset_action.role in roles: + ret_val = True + break + return ret_val + def can_access_dataset( self, roles, dataset ): + return self.allow_dataset_action( roles, self.permitted_actions.DATASET_ACCESS, dataset ) + def can_manage_dataset( self, roles, dataset ): + return self.allow_dataset_action( roles, self.permitted_actions.DATASET_MANAGE_PERMISSIONS, dataset ) + def allow_library_item_action( self, user, roles, action, item ): + """ + Method for checking a permission for the current user to perform a + specific library action on a library item, which must be one of: + Library, LibraryFolder, LibraryDataset, LibraryDatasetDatasetAssociation + """ + if user is None: + # All permissions are granted, so non-users cannot have permissions + return False + # Check to see if user has access to any of the roles associated with action + item_actions = self.get_item_actions( action, item ) + if not item_actions: + # All permissions are granted, so item must have action + return False + ret_val = False + for item_action in item_actions: + if item_action.role in roles: + ret_val = True + break + return ret_val + def can_add_library_item( self, user, roles, item ): + return self.allow_library_item_action( user, roles, self.permitted_actions.LIBRARY_ADD, item ) + def can_modify_library_item( self, user, roles, item ): + return self.allow_library_item_action( user, roles, self.permitted_actions.LIBRARY_MODIFY, item ) + def can_manage_library_item( self, user, roles, item ): + return self.allow_library_item_action( user, roles, self.permitted_actions.LIBRARY_MANAGE, item ) + def get_item_actions( self, action, item ): + # item must be one of: Dataset, Library, LibraryFolder, LibraryDataset, LibraryDatasetDatasetAssociation + return [ permission for permission in item.actions if permission.action == action.action ] + def guess_derived_permissions_for_datasets( self, datasets=[] ): + """Returns a dict of { action : [ role, role, ... ] } for the output dataset based upon provided datasets""" + perms = {} + for dataset in datasets: + if not isinstance( dataset, self.model.Dataset ): + dataset = dataset.dataset + these_perms = {} + # initialize blank perms + for action in self.get_actions(): + these_perms[ action ] = [] + # collect this dataset's perms + these_perms = self.get_dataset_permissions( dataset ) + # join or intersect this dataset's permissions with others + for action, roles in these_perms.items(): + if action not in perms.keys(): + perms[ action ] = roles + else: + if action.model == 'grant': + # intersect existing roles with new roles + perms[ action ] = filter( lambda x: x in perms[ action ], roles ) + elif action.model == 'restrict': + # join existing roles with new roles + perms[ action ].extend( filter( lambda x: x not in perms[ action ], roles ) ) + return perms + def associate_components( self, **kwd ): + if 'user' in kwd: + if 'group' in kwd: + return self.associate_user_group( kwd['user'], kwd['group'] ) + elif 'role' in kwd: + return self.associate_user_role( kwd['user'], kwd['role'] ) + elif 'role' in kwd: + if 'group' in kwd: + return self.associate_group_role( kwd['group'], kwd['role'] ) + if 'action' in kwd: + if 'dataset' in kwd and 'role' in kwd: + return self.associate_action_dataset_role( kwd['action'], kwd['dataset'], kwd['role'] ) + raise 'No valid method of associating provided components: %s' % kwd + def associate_user_group( self, user, group ): + assoc = self.model.UserGroupAssociation( user, group ) + assoc.flush() + return assoc + def associate_user_role( self, user, role ): + assoc = self.model.UserRoleAssociation( user, role ) + assoc.flush() + return assoc + def associate_group_role( self, group, role ): + assoc = self.model.GroupRoleAssociation( group, role ) + assoc.flush() + return assoc + def associate_action_dataset_role( self, action, dataset, role ): + assoc = self.model.DatasetPermissions( action, dataset, role ) + assoc.flush() + return assoc + def create_private_user_role( self, user ): + # Create private role + role = self.model.Role( name=user.email, description='Private Role for ' + user.email, type=self.model.Role.types.PRIVATE ) + role.flush() + # Add user to role + self.associate_components( role=role, user=user ) + return role + def get_private_user_role( self, user, auto_create=False ): + role = self.sa_session.query( self.model.Role ) \ + .filter( and_( self.model.Role.table.c.name == user.email, + self.model.Role.table.c.type == self.model.Role.types.PRIVATE ) ) \ + .first() + if not role: + if auto_create: + return self.create_private_user_role( user ) + else: + return None + return role + def user_set_default_permissions( self, user, permissions={}, history=False, dataset=False, bypass_manage_permission=False, default_access_private = False ): + # bypass_manage_permission is used to change permissions of datasets in a userless history when logging in + if user is None: + return None + if not permissions: #default permissions permissions = { self.permitted_actions.DATASET_MANAGE_PERMISSIONS : [ self.get_private_user_role( user, auto_create=True ) ] } #new_user_dataset_access_role_default_private is set as True in config file if default_access_private: - permissions[ self.permitted_actions.DATASET_ACCESS ] = permissions.values()[ 0 ] - # Delete all of the current default permissions for the user - for dup in user.default_permissions: - self.sa_session.delete( dup ) - dup.flush() - # Add the new default permissions for the user - for action, roles in permissions.items(): - if isinstance( action, Action ): - action = action.action - for dup in [ self.model.DefaultUserPermissions( user, action, role ) for role in roles ]: - dup.flush() - if history: - for history in user.active_histories: - self.history_set_default_permissions( history, permissions=permissions, dataset=dataset, bypass_manage_permission=bypass_manage_permission ) - def user_get_default_permissions( self, user ): - permissions = {} - for dup in user.default_permissions: - action = self.get_action( dup.action ) - if action in permissions: - permissions[ action ].append( dup.role ) - else: - permissions[ action ] = [ dup.role ] - return permissions - def history_set_default_permissions( self, history, permissions={}, dataset=False, bypass_manage_permission=False ): - # bypass_manage_permission is used to change permissions of datasets in a user-less history when logging in - user = history.user - if not user: - # default permissions on a user-less history are None - return None - if not permissions: - permissions = self.user_get_default_permissions( user ) - # Delete all of the current default permission for the history - for dhp in history.default_permissions: - self.sa_session.delete( dhp ) - dhp.flush() - # Add the new default permissions for the history - for action, roles in permissions.items(): - if isinstance( action, Action ): - action = action.action - for dhp in [ self.model.DefaultHistoryPermissions( history, action, role ) for role in roles ]: - dhp.flush() - if dataset: - # Only deal with datasets that are not purged - for hda in history.activatable_datasets: - dataset = hda.dataset - if dataset.library_associations: - # Don't change permissions on a dataset associated with a library - continue - if [ assoc for assoc in dataset.history_associations if assoc.history not in user.histories ]: - # Don't change permissions on a dataset associated with a history not owned by the user - continue - if bypass_manage_permission or self.can_manage_dataset( user.all_roles(), dataset ): - self.set_all_dataset_permissions( dataset, permissions ) - def history_get_default_permissions( self, history ): - permissions = {} - for dhp in history.default_permissions: - action = self.get_action( dhp.action ) - if action in permissions: - permissions[ action ].append( dhp.role ) - else: - permissions[ action ] = [ dhp.role ] - return permissions - def set_all_dataset_permissions( self, dataset, permissions={} ): - """ - Set new permissions on a dataset, eliminating all current permissions - permissions looks like: { Action : [ Role, Role ] } - """ - # Delete all of the current permissions on the dataset - # TODO: If setting ACCESS permission, at least 1 user must have every role associated with this dataset, - # or the dataset is inaccessible. See admin/library_dataset_dataset_association() - for dp in dataset.actions: - self.sa_session.delete( dp ) - dp.flush() - # Add the new permissions on the dataset - for action, roles in permissions.items(): - if isinstance( action, Action ): - action = action.action - for dp in [ self.model.DatasetPermissions( action, dataset, role ) for role in roles ]: - dp.flush() - def set_dataset_permission( self, dataset, permission={} ): - """ - Set a specific permission on a dataset, leaving all other current permissions on the dataset alone - permissions looks like: { Action : [ Role, Role ] } - """ - # TODO: If setting ACCESS permission, at least 1 user must have every role associated with this dataset, - # or the dataset is inaccessible. See admin/library_dataset_dataset_association() - for action, roles in permission.items(): - if isinstance( action, Action ): - action = action.action - # Delete the current specific permission on the dataset if one exists - for dp in dataset.actions: - if dp.action == action: - self.sa_session.delete( dp ) - dp.flush() - # Add the new specific permission on the dataset - for dp in [ self.model.DatasetPermissions( action, dataset, role ) for role in roles ]: - dp.flush() - def dataset_is_public( self, dataset ): - # A dataset is considered public if there are no "access" actions associated with it. Any - # other actions ( 'manage permissions', 'edit metadata' ) are irrelevant. - return self.permitted_actions.DATASET_ACCESS.action not in [ a.action for a in dataset.actions ] - def make_dataset_public( self, dataset ): - # A dataset is considered public if there are no "access" actions associated with it. Any - # other actions ( 'manage permissions', 'edit metadata' ) are irrelevant. - for dp in dataset.actions: - if dp.action == self.permitted_actions.DATASET_ACCESS.action: - self.sa_session.delete( dp ) - dp.flush() - def get_dataset_permissions( self, dataset ): - """ - Return a dictionary containing the actions and associated roles on dataset. - The dictionary looks like: { Action : [ Role, Role ] } - dataset must be an instance of Dataset() - """ - permissions = {} - for dp in dataset.actions: - action = self.get_action( dp.action ) - if action in permissions: - permissions[ action ].append( dp.role ) - else: - permissions[ action ] = [ dp.role ] - return permissions - def copy_dataset_permissions( self, src, dst ): - if not isinstance( src, self.model.Dataset ): - src = src.dataset - if not isinstance( dst, self.model.Dataset ): - dst = dst.dataset - self.set_all_dataset_permissions( dst, self.get_dataset_permissions( src ) ) - def privately_share_dataset( self, dataset, users = [] ): - intersect = None - for user in users: - roles = [ ura.role for ura in user.roles if ura.role.type == self.model.Role.types.SHARING ] - if intersect is None: - intersect = roles - else: - new_intersect = [] - for role in roles: - if role in intersect: - new_intersect.append( role ) - intersect = new_intersect - sharing_role = None - if intersect: - for role in intersect: - if not filter( lambda x: x not in users, [ ura.user for ura in role.users ] ): - # only use a role if it contains ONLY the users we're sharing with - sharing_role = role - break - if sharing_role is None: - sharing_role = self.model.Role( name = "Sharing role for: " + ", ".join( [ u.email for u in users ] ), - type = self.model.Role.types.SHARING ) - sharing_role.flush() - for user in users: - self.associate_components( user=user, role=sharing_role ) - self.set_dataset_permission( dataset, { self.permitted_actions.DATASET_ACCESS : [ sharing_role ] } ) - def set_all_library_permissions( self, library_item, permissions={} ): - # Set new permissions on library_item, eliminating all current permissions - for role_assoc in library_item.actions: - self.sa_session.delete( role_assoc ) - role_assoc.flush() - # Add the new permissions on library_item - for item_class, permission_class in self.library_item_assocs: - if isinstance( library_item, item_class ): - for action, roles in permissions.items(): - if isinstance( action, Action ): - action = action.action - for role_assoc in [ permission_class( action, library_item, role ) for role in roles ]: - role_assoc.flush() - def get_library_dataset_permissions( self, library_dataset ): - # Permissions will always be the same for LibraryDatasets and associated - # LibraryDatasetDatasetAssociations - if isinstance( library_dataset, self.model.LibraryDatasetDatasetAssociation ): - library_dataset = library_dataset.library_dataset - permissions = {} - for library_dataset_permission in library_dataset.actions: - action = self.get_action( library_dataset_permission.action ) - if action in permissions: - permissions[ action ].append( library_dataset_permission.role ) - else: - permissions[ action ] = [ library_dataset_permission.role ] - return permissions - def copy_library_permissions( self, source_library_item, target_library_item, user=None ): - # Copy all permissions from source - permissions = {} - for role_assoc in source_library_item.actions: - if role_assoc.action in permissions: - permissions[role_assoc.action].append( role_assoc.role ) - else: - permissions[role_assoc.action] = [ role_assoc.role ] - self.set_all_library_permissions( target_library_item, permissions ) - if user: - item_class = None - for item_class, permission_class in self.library_item_assocs: - if isinstance( target_library_item, item_class ): - break - if item_class: - # Make sure user's private role is included - private_role = self.model.security_agent.get_private_user_role( user ) - for name, action in self.permitted_actions.items(): - if not permission_class.filter_by( role_id = private_role.id, action = action.action ).first(): - lp = permission_class( action.action, target_library_item, private_role ) - lp.flush() - else: - raise 'Invalid class (%s) specified for target_library_item (%s)' % \ - ( target_library_item.__class__, target_library_item.__class__.__name__ ) - def show_library_item( self, user, roles, library_item, actions_to_check, hidden_folder_ids='' ): - """ - This method must be sent an instance of Library() or LibraryFolder(). Recursive execution produces a - comma-separated string of folder ids whose folders do NOT meet the criteria for showing. Along with - the string, True is returned if the current user has permission to perform any 1 of actions_to_check - on library_item. Otherwise, cycle through all sub-folders in library_item until one is found that meets - this criteria, if it exists. This method does not necessarily scan the entire library as it returns - when it finds the first library_item that allows user to perform any one action in actions_to_check. - """ - for action in actions_to_check: - if self.allow_library_item_action( user, roles, action, library_item ): - return True, hidden_folder_ids - if isinstance( library_item, self.model.Library ): - return self.show_library_item( user, roles, library_item.root_folder, actions_to_check, hidden_folder_ids='' ) - if isinstance( library_item, self.model.LibraryFolder ): - for folder in library_item.active_folders: - can_show, hidden_folder_ids = self.show_library_item( user, roles, folder, actions_to_check, hidden_folder_ids=hidden_folder_ids ) - if can_show: - return True, hidden_folder_ids - if hidden_folder_ids: - hidden_folder_ids = '%s,%d' % ( hidden_folder_ids, folder.id ) - else: - hidden_folder_ids = '%d' % folder.id - return False, hidden_folder_ids - def get_showable_folders( self, user, roles, library_item, actions_to_check, hidden_folder_ids=[], showable_folders=[] ): - """ - This method must be sent an instance of Library(), all the folders of which are scanned to determine if - user is allowed to perform any action in actions_to_check. The param hidden_folder_ids, if passed, should - contain a list of folder IDs which was generated when the library was previously scanned - using the same actions_to_check. A list of showable folders is generated. This method scans the entire library. - """ - if isinstance( library_item, self.model.Library ): - return self.get_showable_folders( user, roles, library_item.root_folder, actions_to_check, showable_folders=[] ) - if isinstance( library_item, self.model.LibraryFolder ): - if library_item.id not in hidden_folder_ids: - for action in actions_to_check: - if self.allow_library_item_action( user, roles, action, library_item ): - showable_folders.append( library_item ) - break - for folder in library_item.active_folders: - self.get_showable_folders( user, roles, folder, actions_to_check, showable_folders=showable_folders ) - return showable_folders - def set_entity_user_associations( self, users=[], roles=[], groups=[], delete_existing_assocs=True ): - for user in users: - if delete_existing_assocs: - for a in user.non_private_roles + user.groups: - self.sa_session.delete( a ) - a.flush() - self.sa_session.refresh( user ) - for role in roles: - # Make sure we are not creating an additional association with a PRIVATE role - if role not in user.roles: - self.associate_components( user=user, role=role ) - for group in groups: - self.associate_components( user=user, group=group ) - def set_entity_group_associations( self, groups=[], users=[], roles=[], delete_existing_assocs=True ): - for group in groups: - if delete_existing_assocs: - for a in group.roles + group.users: - self.sa_session.delete( a ) - a.flush() - for role in roles: - self.associate_components( group=group, role=role ) - for user in users: - self.associate_components( group=group, user=user ) - def set_entity_role_associations( self, roles=[], users=[], groups=[], delete_existing_assocs=True ): - for role in roles: - if delete_existing_assocs: - for a in role.users + role.groups: - self.sa_session.delete( a ) - a.flush() - for user in users: - self.associate_components( user=user, role=role ) - for group in groups: - self.associate_components( group=group, role=role ) - def get_component_associations( self, **kwd ): - assert len( kwd ) == 2, 'You must specify exactly 2 Galaxy security components to check for associations.' - if 'dataset' in kwd: - if 'action' in kwd: - return self.sa_session.query( self.model.DatasetPermissions ).filter_by( action = kwd['action'].action, dataset_id = kwd['dataset'].id ).first() - elif 'user' in kwd: - if 'group' in kwd: - return self.sa_session.query( self.model.UserGroupAssociation ).filter_by( group_id = kwd['group'].id, user_id = kwd['user'].id ).first() - elif 'role' in kwd: - return self.sa_session.query( self.model.UserRoleAssociation ).filter_by( role_id = kwd['role'].id, user_id = kwd['user'].id ).first() - elif 'group' in kwd: - if 'role' in kwd: - return self.sa_session.query( self.model.GroupRoleAssociation ).filter_by( role_id = kwd['role'].id, group_id = kwd['group'].id ).first() - raise 'No valid method of associating provided components: %s' % kwd - def check_folder_contents( self, user, roles, folder, hidden_folder_ids='' ): - """ - This method must always be sent an instance of LibraryFolder(). Recursive execution produces a - comma-separated string of folder ids whose folders do NOT meet the criteria for showing. Along - with the string, True is returned if the current user has permission to access folder. Otherwise, - cycle through all sub-folders in folder until one is found that meets this criteria, if it exists. - This method does not necessarily scan the entire library as it returns when it finds the first - folder that is accessible to user. - """ - action = self.permitted_actions.DATASET_ACCESS - lddas = self.sa_session.query( self.model.LibraryDatasetDatasetAssociation ) \ - .join( "library_dataset" ) \ - .filter( self.model.LibraryDataset.folder == folder ) \ - .join( "dataset" ) \ - .options( eagerload_all( "dataset.actions" ) ) \ - .all() - for ldda in lddas: - ldda_access_permissions = self.get_item_actions( action, ldda.dataset ) - if not ldda_access_permissions: - # Dataset is public - return True, hidden_folder_ids - for ldda_access_permission in ldda_access_permissions: - if ldda_access_permission.role in roles: - # The current user has access permission on the dataset - return True, hidden_folder_ids - for sub_folder in folder.active_folders: - can_access, hidden_folder_ids = self.check_folder_contents( user, roles, sub_folder, hidden_folder_ids=hidden_folder_ids ) - if can_access: - return True, hidden_folder_ids - if hidden_folder_ids: - hidden_folder_ids = '%s,%d' % ( hidden_folder_ids, sub_folder.id ) - else: - hidden_folder_ids = '%d' % sub_folder.id - return False, hidden_folder_ids - -class HostAgent( RBACAgent ): - """ - A simple security agent which allows access to datasets based on host. - This exists so that externals sites such as UCSC can gain access to - datasets which have permissions which would normally prevent such access. - """ - # TODO: Make sites user configurable - sites = Bunch( - ucsc_main = ( 'hgw1.cse.ucsc.edu', 'hgw2.cse.ucsc.edu', 'hgw3.cse.ucsc.edu', 'hgw4.cse.ucsc.edu', - 'hgw5.cse.ucsc.edu', 'hgw6.cse.ucsc.edu', 'hgw7.cse.ucsc.edu', 'hgw8.cse.ucsc.edu' ), - ucsc_test = ( 'hgwdev.cse.ucsc.edu', ), - ucsc_archaea = ( 'lowepub.cse.ucsc.edu', ) - ) - def __init__( self, model, permitted_actions=None ): - self.model = model - if permitted_actions: - self.permitted_actions = permitted_actions - def allow_action( self, addr, action, **kwd ): - if 'dataset' in kwd and action == self.permitted_actions.DATASET_ACCESS: - hda = kwd['dataset'] - if action == self.permitted_actions.DATASET_ACCESS and action.action not in [ dp.action for dp in hda.dataset.actions ]: - log.debug( 'Allowing access to public dataset with hda: %i.' % hda.id ) - return True # dataset has no roles associated with the access permission, thus is already public - hdadaa = self.sa_session.query( self.model.HistoryDatasetAssociationDisplayAtAuthorization ) \ - .filter_by( history_dataset_association_id = hda.id ).first() - if not hdadaa: - log.debug( 'Denying access to private dataset with hda: %i. No hdadaa record for this dataset.' % hda.id ) - return False # no auth - # We could just look up the reverse of addr, but then we'd also - # have to verify it with the forward address and special case any - # IPs (instead of hosts) in the server list. - # - # This would be improved by caching, but that's what the OS's name - # service cache daemon is for (you ARE running nscd, right?). - for server in HostAgent.sites.get( hdadaa.site, [] ): - # We're going to search in order, but if the remote site is load - # balancing their connections (as UCSC does), this is okay. - try: - if socket.gethostbyname( server ) == addr: - break # remote host is in the server list - except ( socket.error, socket.gaierror ): - pass # can't resolve, try next - else: - log.debug( 'Denying access to private dataset with hda: %i. Remote addr is not a valid server for site: %s.' % ( hda.id, hdadaa.site ) ) - return False # remote addr is not in the server list - if ( datetime.utcnow() - hdadaa.update_time ) > timedelta( seconds=60 ): - log.debug( 'Denying access to private dataset with hda: %i. Authorization was granted, but has expired.' % hda.id ) - return False # not authz'd in the last 60 seconds - log.debug( 'Allowing access to private dataset with hda: %i. Remote server is: %s.' % ( hda.id, server ) ) - return True - else: - raise 'The dataset access permission is the only valid permission in the host security agent.' - def set_dataset_permissions( self, hda, user, site ): - hdadaa = self.sa_session.query( self.model.HistoryDatasetAssociationDisplayAtAuthorization ) \ - .filter_by( history_dataset_association_id = hda.id ).first() - if hdadaa: - hdadaa.update_time = datetime.utcnow() - else: - hdadaa = self.model.HistoryDatasetAssociationDisplayAtAuthorization( hda=hda, user=user, site=site ) - hdadaa.flush() - -def get_permitted_actions( filter=None ): - '''Utility method to return a subset of RBACAgent's permitted actions''' - if filter is None: - return RBACAgent.permitted_actions - tmp_bunch = Bunch() - [ tmp_bunch.__dict__.__setitem__(k, v) for k, v in RBACAgent.permitted_actions.items() if k.startswith( filter ) ] - return tmp_bunch + permissions[ self.permitted_actions.DATASET_ACCESS ] = permissions.values()[ 0 ] + # Delete all of the current default permissions for the user + for dup in user.default_permissions: + self.sa_session.delete( dup ) + dup.flush() + # Add the new default permissions for the user + for action, roles in permissions.items(): + if isinstance( action, Action ): + action = action.action + for dup in [ self.model.DefaultUserPermissions( user, action, role ) for role in roles ]: + dup.flush() + if history: + for history in user.active_histories: + self.history_set_default_permissions( history, permissions=permissions, dataset=dataset, bypass_manage_permission=bypass_manage_permission ) + def user_get_default_permissions( self, user ): + permissions = {} + for dup in user.default_permissions: + action = self.get_action( dup.action ) + if action in permissions: + permissions[ action ].append( dup.role ) + else: + permissions[ action ] = [ dup.role ] + return permissions + def history_set_default_permissions( self, history, permissions={}, dataset=False, bypass_manage_permission=False ): + # bypass_manage_permission is used to change permissions of datasets in a user-less history when logging in + user = history.user + if not user: + # default permissions on a user-less history are None + return None + if not permissions: + permissions = self.user_get_default_permissions( user ) + # Delete all of the current default permission for the history + for dhp in history.default_permissions: + self.sa_session.delete( dhp ) + dhp.flush() + # Add the new default permissions for the history + for action, roles in permissions.items(): + if isinstance( action, Action ): + action = action.action + for dhp in [ self.model.DefaultHistoryPermissions( history, action, role ) for role in roles ]: + dhp.flush() + if dataset: + # Only deal with datasets that are not purged + for hda in history.activatable_datasets: + dataset = hda.dataset + if dataset.library_associations: + # Don't change permissions on a dataset associated with a library + continue + if [ assoc for assoc in dataset.history_associations if assoc.history not in user.histories ]: + # Don't change permissions on a dataset associated with a history not owned by the user + continue + if bypass_manage_permission or self.can_manage_dataset( user.all_roles(), dataset ): + self.set_all_dataset_permissions( dataset, permissions ) + def history_get_default_permissions( self, history ): + permissions = {} + for dhp in history.default_permissions: + action = self.get_action( dhp.action ) + if action in permissions: + permissions[ action ].append( dhp.role ) + else: + permissions[ action ] = [ dhp.role ] + return permissions + def set_all_dataset_permissions( self, dataset, permissions={} ): + """ + Set new permissions on a dataset, eliminating all current permissions + permissions looks like: { Action : [ Role, Role ] } + """ + # Delete all of the current permissions on the dataset + # TODO: If setting ACCESS permission, at least 1 user must have every role associated with this dataset, + # or the dataset is inaccessible. See admin/library_dataset_dataset_association() + for dp in dataset.actions: + self.sa_session.delete( dp ) + dp.flush() + # Add the new permissions on the dataset + for action, roles in permissions.items(): + if isinstance( action, Action ): + action = action.action + for dp in [ self.model.DatasetPermissions( action, dataset, role ) for role in roles ]: + dp.flush() + def set_dataset_permission( self, dataset, permission={} ): + """ + Set a specific permission on a dataset, leaving all other current permissions on the dataset alone + permissions looks like: { Action : [ Role, Role ] } + """ + # TODO: If setting ACCESS permission, at least 1 user must have every role associated with this dataset, + # or the dataset is inaccessible. See admin/library_dataset_dataset_association() + for action, roles in permission.items(): + if isinstance( action, Action ): + action = action.action + # Delete the current specific permission on the dataset if one exists + for dp in dataset.actions: + if dp.action == action: + self.sa_session.delete( dp ) + dp.flush() + # Add the new specific permission on the dataset + for dp in [ self.model.DatasetPermissions( action, dataset, role ) for role in roles ]: + dp.flush() + def dataset_is_public( self, dataset ): + # A dataset is considered public if there are no "access" actions associated with it. Any + # other actions ( 'manage permissions', 'edit metadata' ) are irrelevant. + return self.permitted_actions.DATASET_ACCESS.action not in [ a.action for a in dataset.actions ] + def make_dataset_public( self, dataset ): + # A dataset is considered public if there are no "access" actions associated with it. Any + # other actions ( 'manage permissions', 'edit metadata' ) are irrelevant. + for dp in dataset.actions: + if dp.action == self.permitted_actions.DATASET_ACCESS.action: + self.sa_session.delete( dp ) + dp.flush() + def get_dataset_permissions( self, dataset ): + """ + Return a dictionary containing the actions and associated roles on dataset. + The dictionary looks like: { Action : [ Role, Role ] } + dataset must be an instance of Dataset() + """ + permissions = {} + for dp in dataset.actions: + action = self.get_action( dp.action ) + if action in permissions: + permissions[ action ].append( dp.role ) + else: + permissions[ action ] = [ dp.role ] + return permissions + def copy_dataset_permissions( self, src, dst ): + if not isinstance( src, self.model.Dataset ): + src = src.dataset + if not isinstance( dst, self.model.Dataset ): + dst = dst.dataset + self.set_all_dataset_permissions( dst, self.get_dataset_permissions( src ) ) + def privately_share_dataset( self, dataset, users = [] ): + intersect = None + for user in users: + roles = [ ura.role for ura in user.roles if ura.role.type == self.model.Role.types.SHARING ] + if intersect is None: + intersect = roles + else: + new_intersect = [] + for role in roles: + if role in intersect: + new_intersect.append( role ) + intersect = new_intersect + sharing_role = None + if intersect: + for role in intersect: + if not filter( lambda x: x not in users, [ ura.user for ura in role.users ] ): + # only use a role if it contains ONLY the users we're sharing with + sharing_role = role + break + if sharing_role is None: + sharing_role = self.model.Role( name = "Sharing role for: " + ", ".join( [ u.email for u in users ] ), + type = self.model.Role.types.SHARING ) + sharing_role.flush() + for user in users: + self.associate_components( user=user, role=sharing_role ) + self.set_dataset_permission( dataset, { self.permitted_actions.DATASET_ACCESS : [ sharing_role ] } ) + def set_all_library_permissions( self, library_item, permissions={} ): + # Set new permissions on library_item, eliminating all current permissions + for role_assoc in library_item.actions: + self.sa_session.delete( role_assoc ) + role_assoc.flush() + # Add the new permissions on library_item + for item_class, permission_class in self.library_item_assocs: + if isinstance( library_item, item_class ): + for action, roles in permissions.items(): + if isinstance( action, Action ): + action = action.action + for role_assoc in [ permission_class( action, library_item, role ) for role in roles ]: + role_assoc.flush() + def get_library_dataset_permissions( self, library_dataset ): + # Permissions will always be the same for LibraryDatasets and associated + # LibraryDatasetDatasetAssociations + if isinstance( library_dataset, self.model.LibraryDatasetDatasetAssociation ): + library_dataset = library_dataset.library_dataset + permissions = {} + for library_dataset_permission in library_dataset.actions: + action = self.get_action( library_dataset_permission.action ) + if action in permissions: + permissions[ action ].append( library_dataset_permission.role ) + else: + permissions[ action ] = [ library_dataset_permission.role ] + return permissions + def copy_library_permissions( self, source_library_item, target_library_item, user=None ): + # Copy all permissions from source + permissions = {} + for role_assoc in source_library_item.actions: + if role_assoc.action in permissions: + permissions[role_assoc.action].append( role_assoc.role ) + else: + permissions[role_assoc.action] = [ role_assoc.role ] + self.set_all_library_permissions( target_library_item, permissions ) + if user: + item_class = None + for item_class, permission_class in self.library_item_assocs: + if isinstance( target_library_item, item_class ): + break + if item_class: + # Make sure user's private role is included + private_role = self.model.security_agent.get_private_user_role( user ) + for name, action in self.permitted_actions.items(): + if not permission_class.filter_by( role_id = private_role.id, action = action.action ).first(): + lp = permission_class( action.action, target_library_item, private_role ) + lp.flush() + else: + raise 'Invalid class (%s) specified for target_library_item (%s)' % \ + ( target_library_item.__class__, target_library_item.__class__.__name__ ) + def show_library_item( self, user, roles, library_item, actions_to_check, hidden_folder_ids='' ): + """ + This method must be sent an instance of Library() or LibraryFolder(). Recursive execution produces a + comma-separated string of folder ids whose folders do NOT meet the criteria for showing. Along with + the string, True is returned if the current user has permission to perform any 1 of actions_to_check + on library_item. Otherwise, cycle through all sub-folders in library_item until one is found that meets + this criteria, if it exists. This method does not necessarily scan the entire library as it returns + when it finds the first library_item that allows user to perform any one action in actions_to_check. + """ + for action in actions_to_check: + if self.allow_library_item_action( user, roles, action, library_item ): + return True, hidden_folder_ids + if isinstance( library_item, self.model.Library ): + return self.show_library_item( user, roles, library_item.root_folder, actions_to_check, hidden_folder_ids='' ) + if isinstance( library_item, self.model.LibraryFolder ): + for folder in library_item.active_folders: + can_show, hidden_folder_ids = self.show_library_item( user, roles, folder, actions_to_check, hidden_folder_ids=hidden_folder_ids ) + if can_show: + return True, hidden_folder_ids + if hidden_folder_ids: + hidden_folder_ids = '%s,%d' % ( hidden_folder_ids, folder.id ) + else: + hidden_folder_ids = '%d' % folder.id + return False, hidden_folder_ids + def get_showable_folders( self, user, roles, library_item, actions_to_check, hidden_folder_ids=[], showable_folders=[] ): + """ + This method must be sent an instance of Library(), all the folders of which are scanned to determine if + user is allowed to perform any action in actions_to_check. The param hidden_folder_ids, if passed, should + contain a list of folder IDs which was generated when the library was previously scanned + using the same actions_to_check. A list of showable folders is generated. This method scans the entire library. + """ + if isinstance( library_item, self.model.Library ): + return self.get_showable_folders( user, roles, library_item.root_folder, actions_to_check, showable_folders=[] ) + if isinstance( library_item, self.model.LibraryFolder ): + if library_item.id not in hidden_folder_ids: + for action in actions_to_check: + if self.allow_library_item_action( user, roles, action, library_item ): + showable_folders.append( library_item ) + break + for folder in library_item.active_folders: + self.get_showable_folders( user, roles, folder, actions_to_check, showable_folders=showable_folders ) + return showable_folders + def set_entity_user_associations( self, users=[], roles=[], groups=[], delete_existing_assocs=True ): + for user in users: + if delete_existing_assocs: + for a in user.non_private_roles + user.groups: + self.sa_session.delete( a ) + a.flush() + self.sa_session.refresh( user ) + for role in roles: + # Make sure we are not creating an additional association with a PRIVATE role + if role not in user.roles: + self.associate_components( user=user, role=role ) + for group in groups: + self.associate_components( user=user, group=group ) + def set_entity_group_associations( self, groups=[], users=[], roles=[], delete_existing_assocs=True ): + for group in groups: + if delete_existing_assocs: + for a in group.roles + group.users: + self.sa_session.delete( a ) + a.flush() + for role in roles: + self.associate_components( group=group, role=role ) + for user in users: + self.associate_components( group=group, user=user ) + def set_entity_role_associations( self, roles=[], users=[], groups=[], delete_existing_assocs=True ): + for role in roles: + if delete_existing_assocs: + for a in role.users + role.groups: + self.sa_session.delete( a ) + a.flush() + for user in users: + self.associate_components( user=user, role=role ) + for group in groups: + self.associate_components( group=group, role=role ) + def get_component_associations( self, **kwd ): + assert len( kwd ) == 2, 'You must specify exactly 2 Galaxy security components to check for associations.' + if 'dataset' in kwd: + if 'action' in kwd: + return self.sa_session.query( self.model.DatasetPermissions ).filter_by( action = kwd['action'].action, dataset_id = kwd['dataset'].id ).first() + elif 'user' in kwd: + if 'group' in kwd: + return self.sa_session.query( self.model.UserGroupAssociation ).filter_by( group_id = kwd['group'].id, user_id = kwd['user'].id ).first() + elif 'role' in kwd: + return self.sa_session.query( self.model.UserRoleAssociation ).filter_by( role_id = kwd['role'].id, user_id = kwd['user'].id ).first() + elif 'group' in kwd: + if 'role' in kwd: + return self.sa_session.query( self.model.GroupRoleAssociation ).filter_by( role_id = kwd['role'].id, group_id = kwd['group'].id ).first() + raise 'No valid method of associating provided components: %s' % kwd + def check_folder_contents( self, user, roles, folder, hidden_folder_ids='' ): + """ + This method must always be sent an instance of LibraryFolder(). Recursive execution produces a + comma-separated string of folder ids whose folders do NOT meet the criteria for showing. Along + with the string, True is returned if the current user has permission to access folder. Otherwise, + cycle through all sub-folders in folder until one is found that meets this criteria, if it exists. + This method does not necessarily scan the entire library as it returns when it finds the first + folder that is accessible to user. + """ + action = self.permitted_actions.DATASET_ACCESS + lddas = self.sa_session.query( self.model.LibraryDatasetDatasetAssociation ) \ + .join( "library_dataset" ) \ + .filter( self.model.LibraryDataset.folder == folder ) \ + .join( "dataset" ) \ + .options( eagerload_all( "dataset.actions" ) ) \ + .all() + for ldda in lddas: + ldda_access_permissions = self.get_item_actions( action, ldda.dataset ) + if not ldda_access_permissions: + # Dataset is public + return True, hidden_folder_ids + for ldda_access_permission in ldda_access_permissions: + if ldda_access_permission.role in roles: + # The current user has access permission on the dataset + return True, hidden_folder_ids + for sub_folder in folder.active_folders: + can_access, hidden_folder_ids = self.check_folder_contents( user, roles, sub_folder, hidden_folder_ids=hidden_folder_ids ) + if can_access: + return True, hidden_folder_ids + if hidden_folder_ids: + hidden_folder_ids = '%s,%d' % ( hidden_folder_ids, sub_folder.id ) + else: + hidden_folder_ids = '%d' % sub_folder.id + return False, hidden_folder_ids + +class HostAgent( RBACAgent ): + """ + A simple security agent which allows access to datasets based on host. + This exists so that externals sites such as UCSC can gain access to + datasets which have permissions which would normally prevent such access. + """ + # TODO: Make sites user configurable + sites = Bunch( + ucsc_main = ( 'hgw1.cse.ucsc.edu', 'hgw2.cse.ucsc.edu', 'hgw3.cse.ucsc.edu', 'hgw4.cse.ucsc.edu', + 'hgw5.cse.ucsc.edu', 'hgw6.cse.ucsc.edu', 'hgw7.cse.ucsc.edu', 'hgw8.cse.ucsc.edu' ), + ucsc_test = ( 'hgwdev.cse.ucsc.edu', ), + ucsc_archaea = ( 'lowepub.cse.ucsc.edu', ) + ) + def __init__( self, model, permitted_actions=None ): + self.model = model + if permitted_actions: + self.permitted_actions = permitted_actions + def allow_action( self, addr, action, **kwd ): + if 'dataset' in kwd and action == self.permitted_actions.DATASET_ACCESS: + hda = kwd['dataset'] + if action == self.permitted_actions.DATASET_ACCESS and action.action not in [ dp.action for dp in hda.dataset.actions ]: + log.debug( 'Allowing access to public dataset with hda: %i.' % hda.id ) + return True # dataset has no roles associated with the access permission, thus is already public + hdadaa = self.sa_session.query( self.model.HistoryDatasetAssociationDisplayAtAuthorization ) \ + .filter_by( history_dataset_association_id = hda.id ).first() + if not hdadaa: + log.debug( 'Denying access to private dataset with hda: %i. No hdadaa record for this dataset.' % hda.id ) + return False # no auth + # We could just look up the reverse of addr, but then we'd also + # have to verify it with the forward address and special case any + # IPs (instead of hosts) in the server list. + # + # This would be improved by caching, but that's what the OS's name + # service cache daemon is for (you ARE running nscd, right?). + for server in HostAgent.sites.get( hdadaa.site, [] ): + # We're going to search in order, but if the remote site is load + # balancing their connections (as UCSC does), this is okay. + try: + if socket.gethostbyname( server ) == addr: + break # remote host is in the server list + except ( socket.error, socket.gaierror ): + pass # can't resolve, try next + else: + log.debug( 'Denying access to private dataset with hda: %i. Remote addr is not a valid server for site: %s.' % ( hda.id, hdadaa.site ) ) + return False # remote addr is not in the server list + if ( datetime.utcnow() - hdadaa.update_time ) > timedelta( seconds=60 ): + log.debug( 'Denying access to private dataset with hda: %i. Authorization was granted, but has expired.' % hda.id ) + return False # not authz'd in the last 60 seconds + log.debug( 'Allowing access to private dataset with hda: %i. Remote server is: %s.' % ( hda.id, server ) ) + return True + else: + raise 'The dataset access permission is the only valid permission in the host security agent.' + def set_dataset_permissions( self, hda, user, site ): + hdadaa = self.sa_session.query( self.model.HistoryDatasetAssociationDisplayAtAuthorization ) \ + .filter_by( history_dataset_association_id = hda.id ).first() + if hdadaa: + hdadaa.update_time = datetime.utcnow() + else: + hdadaa = self.model.HistoryDatasetAssociationDisplayAtAuthorization( hda=hda, user=user, site=site ) + hdadaa.flush() + +def get_permitted_actions( filter=None ): + '''Utility method to return a subset of RBACAgent's permitted actions''' + if filter is None: + return RBACAgent.permitted_actions + tmp_bunch = Bunch() + [ tmp_bunch.__dict__.__setitem__(k, v) for k, v in RBACAgent.permitted_actions.items() if k.startswith( filter ) ] + return tmp_bunch

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[hg] galaxy 3010: Properly set the PBS job name when not using s...
by Greg Von Kuster 12 Nov '09

12 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/68c3b25ea133 changeset: 3010:68c3b25ea133 user: Nate Coraor <nate(a)bx.psu.edu> date: Wed Nov 11 13:08:11 2009 -0500 description: Properly set the PBS job name when not using staging diffstat: lib/galaxy/jobs/runners/pbs.py | 4 +++- 1 files changed, 3 insertions(+), 1 deletions(-) diffs (18 lines): diff -r 6b23bba26001 -r 68c3b25ea133 lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py Wed Nov 11 11:49:08 2009 -0500 +++ b/lib/galaxy/jobs/runners/pbs.py Wed Nov 11 13:08:11 2009 -0500 @@ -208,11 +208,13 @@ exec_dir = os.path.abspath( os.getcwd() ) # If not, we're using NFS else: - job_attrs = pbs.new_attropl(2) + job_attrs = pbs.new_attropl(3) job_attrs[0].name = pbs.ATTR_o job_attrs[0].value = ofile job_attrs[1].name = pbs.ATTR_e job_attrs[1].value = efile + job_attrs[2].name = pbs.ATTR_N + job_attrs[2].value = "%s" % job_wrapper.job_id exec_dir = os.getcwd() # write the job script

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