July 2014 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: davebgx: When executing a download_file action, take into account that the current working directory may have been modified by previous steps.
by commits-noreply＠bitbucket.org 14 Jul '14

14 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/deba1986ea22/ Changeset: deba1986ea22 Branch: stable User: davebgx Date: 2014-07-09 16:39:01 Summary: When executing a download_file action, take into account that the current working directory may have been modified by previous steps. Affected #: 1 file diff -r b1441a96b8401fd14ab3364c5d6dfa0733df263e -r deba1986ea22e42fb1f290f50a62b51d4cfad762 lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py @@ -447,7 +447,9 @@ filename = action_dict[ 'target_filename' ] else: filename = url.split( '/' )[ -1 ] - td_common_util.url_download( work_dir, filename, url ) + if current_dir is not None: + work_dir = current_dir + td_common_util.url_download( work_dir, filename, url, extract=action_dict[ 'extract' ] ) if initial_download: dir = os.path.curdir return tool_dependency, filtered_actions, dir Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Fix bug in visualization data provider: correctly hash identifier.
by commits-noreply＠bitbucket.org 12 Jul '14

12 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5b7e495d6f2f/ Changeset: 5b7e495d6f2f User: jgoecks Date: 2014-07-13 01:41:55 Summary: Fix bug in visualization data provider: correctly hash identifier. Affected #: 1 file diff -r 20094b0c186b6231251838d96662ad202622ef22 -r 5b7e495d6f2fefe2b51da8bc438e4053b2a7a6af lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -1057,7 +1057,7 @@ r1 = [ read['start'], read['end'], read['cigar'], read['strand'], read['seq'] ] r2 = [ read['mate_start'], read['mate_start'] ] - results.append( [ "%i_%s" % ( read_start, qname ), read_start, read_end, qname, r1, r2, [read[ 'mapq' ], 125] ] ) + results.append( [ hash( "%i_%s" % ( read_start, qname ) ), read_start, read_end, qname, r1, r2, [read[ 'mapq' ], 125] ] ) # Clean up. TODO: is this needed? If so, we'll need a cleanup function after processing the data. # bamfile.close() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Visualization genome data providers: readd require numpy because it is a dependency of bx-python.
by commits-noreply＠bitbucket.org 11 Jul '14

11 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/20094b0c186b/ Changeset: 20094b0c186b User: jgoecks Date: 2014-07-11 19:53:04 Summary: Visualization genome data providers: readd require numpy because it is a dependency of bx-python. Affected #: 1 file diff -r b74c56d994efbb0e8330d9dd75c682358c963497 -r 20094b0c186b6231251838d96662ad202622ef22 lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -8,6 +8,7 @@ import random import math +pkg_resources.require( "numpy" ) pkg_resources.require( "bx-python" ) pkg_resources.require( "pysam" ) from bx.interval_index_file import Indexes Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Visualization genome data providers: remove dependency on numpy.
by commits-noreply＠bitbucket.org 11 Jul '14

11 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b74c56d994ef/ Changeset: b74c56d994ef User: jgoecks Date: 2014-07-11 18:20:40 Summary: Visualization genome data providers: remove dependency on numpy. Affected #: 1 file diff -r 154429911adcedfefb26776670805f4591baf502 -r b74c56d994efbb0e8330d9dd75c682358c963497 lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -6,11 +6,10 @@ import pkg_resources import itertools import random +import math pkg_resources.require( "bx-python" ) pkg_resources.require( "pysam" ) -pkg_resources.require( "numpy" ) -import numpy from bx.interval_index_file import Indexes from bx.bbi.bigwig_file import BigWigFile from bx.bbi.bigbed_file import BigBedFile @@ -1179,7 +1178,7 @@ var = summary.sum_squares[0] - mean if valid_count > 1: var /= valid_count - 1 - sd = numpy.sqrt( var ) + sd = math.sqrt( var ) min_val = summary.min_val[0] max_val = summary.max_val[0] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Migration 104 was using a Session() object that conflicts with the threadlocal strategy, which has been causing the '103 is not 105' migration errors we've seen. scoped_session works, but the threadlocal should probably be completely deprecated moving forward (removed from universe_wsgi.ini.sample by nate just now). See http://docs.sqlalchemy.org/en/rel_0_9/core/connections.html#threadlocal-strategy
by commits-noreply＠bitbucket.org 11 Jul '14

11 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/154429911adc/ Changeset: 154429911adc User: dannon Date: 2014-07-11 17:54:27 Summary: Migration 104 was using a Session() object that conflicts with the threadlocal strategy, which has been causing the '103 is not 105' migration errors we've seen. scoped_session works, but the threadlocal should probably be completely deprecated moving forward (removed from universe_wsgi.ini.sample by nate just now). See http://docs.sqlalchemy.org/en/rel_0_9/core/connections.html#threadlocal-str… Affected #: 1 file diff -r 6968401b626be099ac96a4b41c51ee6c5bdcea58 -r 154429911adcedfefb26776670805f4591baf502 lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py --- a/lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py +++ b/lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py @@ -23,6 +23,8 @@ handler.setFormatter( formatter ) log.addHandler( handler ) +metadata = MetaData() +context = scoped_session( sessionmaker( autoflush=False, autocommit=True ) ) class DeferredJob( object ): states = Bunch( NEW = 'new', @@ -37,12 +39,8 @@ self.params = params def upgrade(migrate_engine): - metadata = MetaData() metadata.bind = migrate_engine - Session = sessionmaker( bind=migrate_engine) - context = Session() - DeferredJob.table = Table( "deferred_job", metadata, Column( "id", Integer, primary_key=True ), Column( "create_time", DateTime, default=now ), @@ -70,12 +68,8 @@ context.flush() def downgrade(migrate_engine): - metadata = MetaData() metadata.bind = migrate_engine - Session = sessionmaker( bind=migrate_engine) - context = Session() - jobs = context.query( DeferredJob ).filter_by( plugin='GenomeTransferPlugin' ).all() for job in jobs: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Remove deprecated threadlocal engine strategy from sample config.
by commits-noreply＠bitbucket.org 11 Jul '14

11 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6968401b626b/ Changeset: 6968401b626b User: natefoo Date: 2014-07-11 17:38:30 Summary: Remove deprecated threadlocal engine strategy from sample config. Affected #: 1 file diff -r bde270ca78de3a6c380250e8f594c31a4a4ce73c -r 6968401b626be099ac96a4b41c51ee6c5bdcea58 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -109,10 +109,6 @@ # only available for PostgreSQL and is highly recommended. #database_engine_option_server_side_cursors = False -# Create only one connection to the database per thread, to reduce the -# connection overhead. Recommended when not using SQLite: -#database_engine_option_strategy = threadlocal - # Log all database transactions, can be useful for debugging and performance # profiling. Logging is done via Python's 'logging' module under the qualname # 'galaxy.model.orm.logging_connection_proxy' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Automatically use a virtualenv in galaxy_root/.venv/ if it exists (a la Pulsar).
by commits-noreply＠bitbucket.org 11 Jul '14

11 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bde270ca78de/ Changeset: bde270ca78de User: natefoo Date: 2014-07-11 15:58:08 Summary: Automatically use a virtualenv in galaxy_root/.venv/ if it exists (a la Pulsar). Affected #: 2 files diff -r 82a80300b9a101072ea614de5424ec76ebae9340 -r bde270ca78de3a6c380250e8f594c31a4a4ce73c .hgignore --- a/.hgignore +++ b/.hgignore @@ -11,6 +11,9 @@ scripts/scramble/lib scripts/scramble/archives +# Python virtualenv +.venv + # Database stuff database/beaker_sessions database/community_files diff -r 82a80300b9a101072ea614de5424ec76ebae9340 -r bde270ca78de3a6c380250e8f594c31a4a4ce73c run.sh --- a/run.sh +++ b/run.sh @@ -11,6 +11,13 @@ python ./scripts/build_universe_config.py "$GALAXY_UNIVERSE_CONFIG_DIR" fi +# If there is a .venv/ directory, assume it contains a virtualenv that we +# should run this instance in. +if [ -d .venv ]; +then + . .venv/bin/activate +fi + if [ -n "$GALAXY_RUN_ALL" ]; then servers=`sed -n 's/^\[server:$.*$\]/\1/ p' universe_wsgi.ini | xargs echo` daemon=`echo "$@" | grep -q daemon` Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 10 Jul '14

10 Jul '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2dc7164b613f/ Changeset: 2dc7164b613f User: dannon Date: 2014-07-10 23:03:11 Summary: Include annotations (toplevel workflow and step) in workflow show via API. Affected #: 1 file diff -r 2d31b83e2a412cbd07d32a842fa1e51d1a8dc033 -r 2dc7164b613f9d9a01c2017fa57d3f6f83ebff9e lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -9,6 +9,7 @@ from galaxy import exceptions from galaxy import util from galaxy import web +from galaxy.model.item_attrs import UsesAnnotations from galaxy.web import _future_expose_api as expose_api from galaxy.web.base.controller import BaseAPIController, url_for, UsesStoredWorkflowMixin from galaxy.web.base.controller import UsesHistoryMixin @@ -20,7 +21,7 @@ log = logging.getLogger(__name__) -class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesHistoryMixin): +class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesHistoryMixin, UsesAnnotations): @web.expose_api def index(self, trans, **kwd): @@ -94,12 +95,14 @@ # Eventually, allow regular tool parameters to be inserted and modified at runtime. # p = step.get_required_parameters() item['inputs'] = inputs + item['annotation'] = self.get_item_annotation_str( trans.sa_session, stored_workflow.user, stored_workflow ) steps = {} for step in latest_workflow.steps: steps[step.id] = {'id': step.id, 'type': step.type, 'tool_id': step.tool_id, 'tool_version': step.tool_version, + 'annotation': self.get_item_annotation_str( trans.sa_session, stored_workflow.user, step ), 'tool_inputs': step.tool_inputs, 'input_steps': {}} for conn in step.input_connections: https://bitbucket.org/galaxy/galaxy-central/commits/50f84f60b60b/ Changeset: 50f84f60b60b User: dannon Date: 2014-07-10 23:11:01 Summary: pep8/cleanup in api/workflows Affected #: 1 file diff -r 2dc7164b613f9d9a01c2017fa57d3f6f83ebff9e -r 50f84f60b60b8bfe307994431676a56ae2e97582 lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -6,17 +6,14 @@ import logging from sqlalchemy import desc, or_ -from galaxy import exceptions -from galaxy import util -from galaxy import web +from galaxy import exceptions, util, web from galaxy.model.item_attrs import UsesAnnotations from galaxy.web import _future_expose_api as expose_api from galaxy.web.base.controller import BaseAPIController, url_for, UsesStoredWorkflowMixin from galaxy.web.base.controller import UsesHistoryMixin +from galaxy.workflow.extract import extract_workflow from galaxy.workflow.run import invoke from galaxy.workflow.run import WorkflowRunConfig -from galaxy.workflow.extract import extract_workflow - log = logging.getLogger(__name__) @@ -37,9 +34,9 @@ rval = [] filter1 = ( trans.app.model.StoredWorkflow.user == trans.user ) if show_published: - filter1 = or_( filter1, ( trans.app.model.StoredWorkflow.published == True ) ) + filter1 = or_( filter1, ( trans.app.model.StoredWorkflow.published == True ) ) #noqa -- sqlalchemy comparison for wf in trans.sa_session.query( trans.app.model.StoredWorkflow ).filter( - filter1, trans.app.model.StoredWorkflow.table.c.deleted == False ).order_by( + filter1, trans.app.model.StoredWorkflow.table.c.deleted == False ).order_by( #noqa -- sqlalchemy comparison desc( trans.app.model.StoredWorkflow.table.c.update_time ) ).all(): item = wf.to_dict( value_mapper={ 'id': trans.security.encode_id } ) encoded_id = trans.security.encode_id(wf.id) @@ -48,7 +45,7 @@ rval.append(item) for wf_sa in trans.sa_session.query( trans.app.model.StoredWorkflowUserShareAssociation ).filter_by( user=trans.user ).join( 'stored_workflow' ).filter( - trans.app.model.StoredWorkflow.deleted == False ).order_by( + trans.app.model.StoredWorkflow.deleted == False ).order_by( #noqa -- sqlalchemy comparison desc( trans.app.model.StoredWorkflow.update_time ) ).all(): item = wf_sa.stored_workflow.to_dict( value_mapper={ 'id': trans.security.encode_id } ) encoded_id = trans.security.encode_id(wf_sa.stored_workflow.id) @@ -72,7 +69,7 @@ return "Malformed workflow id ( %s ) specified, unable to decode." % str(workflow_id) try: stored_workflow = trans.sa_session.query(trans.app.model.StoredWorkflow).get(decoded_workflow_id) - if stored_workflow.importable == False and stored_workflow.user != trans.user and not trans.user_is_admin(): + if stored_workflow.importable is False and stored_workflow.user != trans.user and not trans.user_is_admin(): if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: trans.response.status = 400 return("Workflow is neither importable, nor owned by or shared with current user") @@ -202,8 +199,7 @@ history_param = payload.get('history', '') # Get workflow + accessibility check. - stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get( - trans.security.decode_id(workflow_id)) + stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get(trans.security.decode_id(workflow_id)) if stored_workflow.user != trans.user and not trans.user_is_admin(): if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: trans.response.status = 400 @@ -226,9 +222,8 @@ # Get target history. if history_param.startswith('hist_id='): - #Passing an existing history to use. - history = trans.sa_session.query(self.app.model.History).get( - trans.security.decode_id(history_param[8:])) + # Passing an existing history to use. + history = trans.sa_session.query(self.app.model.History).get(trans.security.decode_id(history_param[8:])) if history.user != trans.user and not trans.user_is_admin(): trans.response.status = 400 return "Invalid History specified." @@ -314,7 +309,7 @@ ret_dict = self._workflow_to_dict( trans, stored_workflow ) if not ret_dict: - #This workflow has a tool that's missing from the distribution + # This workflow has a tool that's missing from the distribution trans.response.status = 400 return "Workflow cannot be exported due to missing tools." return ret_dict @@ -341,12 +336,11 @@ trans.response.status = 403 return("Workflow is not owned by current user") - #Mark a workflow as deleted + # Mark a workflow as deleted stored_workflow.deleted = True trans.sa_session.flush() # TODO: Unsure of response message to let api know that a workflow was successfully deleted - #return 'OK' return ( "Workflow '%s' successfully deleted" % stored_workflow.name ) @web.expose_api @@ -397,7 +391,7 @@ stored_workflow = self.get_stored_workflow( trans, workflow_id, check_ownership=False ) except: raise exceptions.ObjectNotFound( "Malformed workflow id ( %s ) specified." % workflow_id ) - if stored_workflow.importable == False: + if stored_workflow.importable is False: raise exceptions.MessageException( 'The owner of this workflow has disabled imports via this link.' ) elif stored_workflow.deleted: raise exceptions.MessageException( "You can't import this workflow because it has been deleted." ) @@ -420,13 +414,13 @@ """ try: stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get(trans.security.decode_id(workflow_id)) - except Exception, e: + except Exception: raise exceptions.ObjectNotFound() # check to see if user has permissions to selected workflow if stored_workflow.user != trans.user and not trans.user_is_admin(): if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: raise exceptions.ItemOwnershipException() - results = trans.sa_session.query(self.app.model.WorkflowInvocation).filter(self.app.model.WorkflowInvocation.workflow_id==stored_workflow.latest_workflow_id) + results = trans.sa_session.query(self.app.model.WorkflowInvocation).filter(self.app.model.WorkflowInvocation.workflow_id == stored_workflow.latest_workflow_id) out = [] for r in results: out.append( self.encode_all_ids( trans, r.to_dict(), True) ) @@ -449,13 +443,13 @@ try: stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get(trans.security.decode_id(workflow_id)) - except Exception, e: + except Exception: raise exceptions.ObjectNotFound() # check to see if user has permissions to selected workflow if stored_workflow.user != trans.user and not trans.user_is_admin(): if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: raise exceptions.ItemOwnershipException() - results = trans.sa_session.query(self.app.model.WorkflowInvocation).filter(self.app.model.WorkflowInvocation.workflow_id==stored_workflow.latest_workflow_id) + results = trans.sa_session.query(self.app.model.WorkflowInvocation).filter(self.app.model.WorkflowInvocation.workflow_id == stored_workflow.latest_workflow_id) results = results.filter(self.app.model.WorkflowInvocation.id == trans.security.decode_id(usage_id)) out = results.first() if out is not None: https://bitbucket.org/galaxy/galaxy-central/commits/82a80300b9a1/ Changeset: 82a80300b9a1 User: dannon Date: 2014-07-10 23:22:01 Summary: Update simple filters in workflows api to use filter_by where appropriate, instead of the heavier weight filter. Affected #: 1 file diff -r 50f84f60b60b8bfe307994431676a56ae2e97582 -r 82a80300b9a101072ea614de5424ec76ebae9340 lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -420,7 +420,7 @@ if stored_workflow.user != trans.user and not trans.user_is_admin(): if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: raise exceptions.ItemOwnershipException() - results = trans.sa_session.query(self.app.model.WorkflowInvocation).filter(self.app.model.WorkflowInvocation.workflow_id == stored_workflow.latest_workflow_id) + results = trans.sa_session.query(self.app.model.WorkflowInvocation).filter_by(workflow_id=stored_workflow.latest_workflow_id) out = [] for r in results: out.append( self.encode_all_ids( trans, r.to_dict(), True) ) @@ -449,8 +449,8 @@ if stored_workflow.user != trans.user and not trans.user_is_admin(): if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: raise exceptions.ItemOwnershipException() - results = trans.sa_session.query(self.app.model.WorkflowInvocation).filter(self.app.model.WorkflowInvocation.workflow_id == stored_workflow.latest_workflow_id) - results = results.filter(self.app.model.WorkflowInvocation.id == trans.security.decode_id(usage_id)) + results = trans.sa_session.query(self.app.model.WorkflowInvocation).filter_by(workflow_id=stored_workflow.latest_workflow_id) + results = results.filter_by(id=trans.security.decode_id(usage_id)) out = results.first() if out is not None: return self.encode_all_ids( trans, out.to_dict('element'), True) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Fix style of previous remote user change.
by commits-noreply＠bitbucket.org 10 Jul '14

10 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2d31b83e2a41/ Changeset: 2d31b83e2a41 User: dannon Date: 2014-07-10 22:30:11 Summary: Fix style of previous remote user change. Affected #: 1 file diff -r a3fef3c3f644d87ab00bdf3e1962376f405e31c0 -r 2d31b83e2a412cbd07d32a842fa1e51d1a8dc033 lib/galaxy/web/framework/middleware/remoteuser.py --- a/lib/galaxy/web/framework/middleware/remoteuser.py +++ b/lib/galaxy/web/framework/middleware/remoteuser.py @@ -94,8 +94,8 @@ pass # toolbox filters can be managed when remote_user is in use elif path_info.startswith( '/user/set_default_permissions' ): pass # default permissions can be managed when remote_user is in use - elif path_info == '/user' or path_info =='/user/': - pass # We do allow access to the root user preferences page. + elif path_info == '/user' or path_info == '/user/': + pass # We do allow access to the root user preferences page. elif path_info.startswith( '/user' ): # Any other endpoint in the user controller is off limits title = "Access to Galaxy user controls is disabled" Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: External Auth: this change allows users when use_remote_user is in action to
by commits-noreply＠bitbucket.org 10 Jul '14

10 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a3fef3c3f644/ Changeset: a3fef3c3f644 User: dannon Date: 2014-07-10 22:24:29 Summary: External Auth: this change allows users when use_remote_user is in action to navigate to the user preferences page. This specifically allows use of toolbox filters, and default permission setting on new histories as new functionality w/ external auth. Also added shortcut for whitelist comparison for non-user-controller requests. Affected #: 2 files diff -r a129d77f8d203d4db7940dbd0b9fdc8c48436781 -r a3fef3c3f644d87ab00bdf3e1962376f405e31c0 lib/galaxy/web/framework/middleware/remoteuser.py --- a/lib/galaxy/web/framework/middleware/remoteuser.py +++ b/lib/galaxy/web/framework/middleware/remoteuser.py @@ -76,7 +76,11 @@ before you may access Galaxy. """ return self.error( start_response, title, message ) - if path_info.startswith( '/user/create' ) and environ[ self.remote_user_header ] in self.admin_users: + if not path_info.startswith('/user'): + # shortcut the following whitelist for non-user-controller + # requests. + pass + elif path_info.startswith( '/user/create' ) and environ[ self.remote_user_header ] in self.admin_users: pass # admins can create users elif path_info.startswith( '/user/logout' ) and environ[ self.remote_user_header ] in self.admin_users: pass # Admin users may be impersonating, allow logout. @@ -86,7 +90,14 @@ pass # username can be managed when remote_user is in use elif path_info.startswith( '/user/dbkeys' ): pass # dbkeys can be managed when remote_user is in use + elif path_info.startswith( '/user/toolbox_filters' ): + pass # toolbox filters can be managed when remote_user is in use + elif path_info.startswith( '/user/set_default_permissions' ): + pass # default permissions can be managed when remote_user is in use + elif path_info == '/user' or path_info =='/user/': + pass # We do allow access to the root user preferences page. elif path_info.startswith( '/user' ): + # Any other endpoint in the user controller is off limits title = "Access to Galaxy user controls is disabled" message = """ User controls are disabled when Galaxy is configured diff -r a129d77f8d203d4db7940dbd0b9fdc8c48436781 -r a3fef3c3f644d87ab00bdf3e1962376f405e31c0 templates/user/index.mako --- a/templates/user/index.mako +++ b/templates/user/index.mako @@ -10,11 +10,13 @@ <p>You are currently logged in as ${trans.user.email}.</p><ul> %if t.webapp.name == 'galaxy': - <li><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller )}">${_('Manage your information')}</a></li> + %if not trans.app.config.use_remote_user: + <li><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller )}">${_('Manage your information')}</a></li> + %endif <li><a href="${h.url_for( controller='user', action='set_default_permissions', cntrller=cntrller )}">${_('Change default permissions')}</a> for new histories</li><li><a href="${h.url_for( controller='user', action='api_keys', cntrller=cntrller )}">${_('Manage your API keys')}</a></li><li><a href="${h.url_for( controller='user', action='toolbox_filters', cntrller=cntrller )}">${_('Manage your ToolBox filters')}</a></li> - %if trans.app.config.enable_openid: + %if trans.app.config.enable_openid and not trans.app.config.use_remote_user: <li><a href="${h.url_for( controller='user', action='openid_manage', cntrller=cntrller )}">${_('Manage OpenIDs')}</a> linked to your account</li> %endif %if trans.app.config.use_remote_user: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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