galaxy-commits February 2015

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commit/galaxy-central: carlfeberhard: API, users: use _future_expose_api and minor clean up
by commits-noreply＠bitbucket.org 03 Feb '15

03 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1d57664c6d9c/ Changeset: 1d57664c6d9c User: carlfeberhard Date: 2015-02-02 22:48:31+00:00 Summary: API, users: use _future_expose_api and minor clean up Affected #: 1 file diff -r 83414d1a3943a6902fe63509b07ed46cba874951 -r 1d57664c6d9c4875e5c818220fa8199cf3967de0 lib/galaxy/webapps/galaxy/api/users.py --- a/lib/galaxy/webapps/galaxy/api/users.py +++ b/lib/galaxy/webapps/galaxy/api/users.py @@ -1,23 +1,29 @@ """ API operations on User objects. """ -import logging -from paste.httpexceptions import HTTPBadRequest, HTTPNotImplemented -from galaxy import util, web, exceptions +from galaxy.web.base.controller import BaseAPIController +from galaxy.web.base.controller import UsesTagsMixin +from galaxy.web.base.controller import CreatesApiKeysMixin +from galaxy.web.base.controller import CreatesUsersMixin + from galaxy.security.validate_user_input import validate_email from galaxy.security.validate_user_input import validate_password from galaxy.security.validate_user_input import validate_publicname -from galaxy.web.base.controller import BaseAPIController, UsesTagsMixin -from galaxy.web.base.controller import CreatesApiKeysMixin -from galaxy.web.base.controller import CreatesUsersMixin +from galaxy.web import _future_expose_api as expose_api +from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous +from galaxy import web +from galaxy import util +from galaxy import exceptions + +import logging log = logging.getLogger( __name__ ) class UserAPIController( BaseAPIController, UsesTagsMixin, CreatesUsersMixin, CreatesApiKeysMixin ): - @web.expose_api + @expose_api def index( self, trans, deleted='False', f_email=None, **kwd ): """ GET /api/users @@ -46,7 +52,7 @@ rval.append( item ) return rval - @web.expose_api_anonymous + @expose_api_anonymous def show( self, trans, id, deleted='False', **kwd ): """ GET /api/users/{encoded_user_id} @@ -73,30 +79,28 @@ assert trans.user == user assert not user.deleted except: - if trans.user_is_admin(): - raise - else: - raise HTTPBadRequest( detail='Invalid user id ( %s ) specified' % id ) + raise exceptions.RequestParameterInvalidException( 'Invalid user id specified', id=id ) + item = user.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id, 'total_disk_usage': float } ) # add a list of tags used by the user (as strings) item[ 'tags_used' ] = self.get_user_tags_used( trans, user=user ) # TODO: move into api_values (needs trans, tho - can we do that with api_keys/@property??) # TODO: works with other users (from admin)?? - item['quota_percent'] = trans.app.quota_agent.get_percent( trans=trans ) - item['is_admin'] = trans.user_is_admin() + item[ 'quota_percent' ] = trans.app.quota_agent.get_percent( trans=trans ) + item[ 'is_admin' ] = trans.user_is_admin() return item - @web.expose_api + @expose_api def create( self, trans, payload, **kwd ): """ POST /api/users Creates a new Galaxy user. """ if not trans.app.config.allow_user_creation: - raise HTTPNotImplemented( detail='User creation is not allowed in this Galaxy instance' ) + raise exceptions.ConfigDoesNotAllowException( 'User creation is not allowed in this Galaxy instance' ) if trans.app.config.use_remote_user and trans.user_is_admin(): - user = trans.get_or_create_remote_user(remote_user_email=payload['remote_user_email']) + user = trans.get_or_create_remote_user( remote_user_email=payload['remote_user_email'] ) elif trans.user_is_admin(): username = payload[ 'username' ] email = payload[ 'email' ] @@ -109,12 +113,12 @@ else: user = self.create_user( trans=trans, email=email, username=username, password=password ) else: - raise HTTPNotImplemented() + raise exceptions.NotImplemented() item = user.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id, 'total_disk_usage': float } ) return item - @web.expose_api + @expose_api @web.require_admin def api_key( self, trans, user_id, **kwd ): """ @@ -125,17 +129,17 @@ key = self.create_api_key( trans, user ) return key - @web.expose_api + @expose_api def update( self, trans, **kwd ): - raise HTTPNotImplemented() + raise exceptions.NotImplemented() - @web.expose_api + @expose_api def delete( self, trans, **kwd ): - raise HTTPNotImplemented() + raise exceptions.NotImplemented() - @web.expose_api + @expose_api def undelete( self, trans, **kwd ): - raise HTTPNotImplemented() + raise exceptions.NotImplemented() # TODO: move to more basal, common resource than this def anon_user_api_value( self, trans ): 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: 2 new changesets
by commits-noreply＠bitbucket.org 03 Feb '15

03 Feb '15

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/119898e03506/ Changeset: 119898e03506 User: carlfeberhard Date: 2015-02-02 22:08:17+00:00 Summary: API, tags & annotations: use _future_expose_api and minor clean up Affected #: 2 files diff -r 117db343f853b815b6f584679c23d0f44277c07b -r 119898e035065e3ffd1ca9b3e84f23f380faf023 lib/galaxy/webapps/galaxy/api/annotations.py --- a/lib/galaxy/webapps/galaxy/api/annotations.py +++ b/lib/galaxy/webapps/galaxy/api/annotations.py @@ -1,27 +1,31 @@ """ API operations on annotations. """ -import logging -from galaxy import web + +from galaxy.web.base.controller import BaseAPIController +from galaxy.web.base.controller import UsesStoredWorkflowMixin from galaxy.model.item_attrs import UsesAnnotations -from galaxy.util.sanitize_html import sanitize_html -from galaxy.web.base.controller import BaseAPIController, HTTPNotImplemented, UsesStoredWorkflowMixin from galaxy import managers +from galaxy import exceptions +from galaxy.web import _future_expose_api as expose_api +from galaxy.util import sanitize_html + +import logging log = logging.getLogger( __name__ ) class BaseAnnotationsController( BaseAPIController, UsesStoredWorkflowMixin, UsesAnnotations ): - @web.expose_api + @expose_api def index( self, trans, **kwd ): idnum = kwd[self.tagged_item_id] item = self._get_item_from_id(trans, idnum) if item is not None: return self.get_item_annotation_str( trans.sa_session, trans.get_user(), item ) - @web.expose_api + @expose_api def create( self, trans, payload, **kwd ): if "text" not in payload: return "" @@ -29,24 +33,24 @@ item = self._get_item_from_id(trans, idnum) if item is not None: new_annotation = payload.get("text") - # Sanitize annotation before adding it. - new_annotation = sanitize_html( new_annotation, 'utf-8', 'text/html' ) + #TODO: sanitize on display not entry + new_annotation = sanitize_html.sanitize_html( new_annotation, 'utf-8', 'text/html' ) self.add_item_annotation( trans.sa_session, trans.get_user(), item, new_annotation ) trans.sa_session.flush() return new_annotation return "" - @web.expose_api + @expose_api def delete( self, trans, **kwd ): idnum = kwd[self.tagged_item_id] item = self._get_item_from_id(trans, idnum) if item is not None: return self.delete_item_annotation( trans.sa_session, trans.get_user(), item ) - @web.expose_api + @expose_api def undelete( self, trans, **kwd ): - raise HTTPNotImplemented() + raise exceptions.NotImplemented() class HistoryAnnotationsController(BaseAnnotationsController): @@ -63,7 +67,7 @@ return history -class HistoryContentAnnotationsController(BaseAnnotationsController): +class HistoryContentAnnotationsController( BaseAnnotationsController ): controller_name = "history_content_annotations" tagged_item_id = "history_content_id" @@ -78,10 +82,10 @@ return hda -class WorkflowAnnotationsController(BaseAnnotationsController): +class WorkflowAnnotationsController( BaseAnnotationsController ): controller_name = "workflow_annotations" tagged_item_id = "workflow_id" def _get_item_from_id(self, trans, idstr): - hda = self.get_stored_workflow(trans, idstr) + hda = self.get_stored_workflow( trans, idstr ) return hda diff -r 117db343f853b815b6f584679c23d0f44277c07b -r 119898e035065e3ffd1ca9b3e84f23f380faf023 lib/galaxy/webapps/galaxy/api/item_tags.py --- a/lib/galaxy/webapps/galaxy/api/item_tags.py +++ b/lib/galaxy/webapps/galaxy/api/item_tags.py @@ -1,52 +1,55 @@ """ API operations related to tagging items. """ +from galaxy.web.base.controller import BaseAPIController +from galaxy.web.base.controller import UsesTagsMixin + +from galaxy.web import _future_expose_api as expose_api +from galaxy import exceptions + import logging -from galaxy import web -from galaxy.web.base.controller import BaseAPIController, UsesTagsMixin -from paste.httpexceptions import HTTPBadRequest - log = logging.getLogger( __name__ ) class BaseItemTagsController( BaseAPIController, UsesTagsMixin ): """ """ - @web.expose_api + @expose_api def index( self, trans, **kwd ): """ """ - tags = self._get_user_tags(trans, self.tagged_item_class, kwd[self.tagged_item_id]) + tags = self._get_user_tags(trans, self.tagged_item_class, kwd[ self.tagged_item_id ]) return [ self._api_value( tag, trans, view='collection' ) for tag in tags ] - @web.expose_api + @expose_api def show( self, trans, tag_name, **kwd ): """ """ - tag = self._get_item_tag_assoc( trans, self.tagged_item_class, kwd[self.tagged_item_id], tag_name ) + tag = self._get_item_tag_assoc( trans, self.tagged_item_class, kwd[ self.tagged_item_id ], tag_name ) if not tag: - raise HTTPBadRequest("Failed to retrieve specified tag.") + raise exceptions.ObjectNotFound( "Failed to retrieve specified tag." ) return self._api_value( tag, trans ) - @web.expose_api + @expose_api def create( self, trans, tag_name, payload=None, **kwd ): """ """ payload = payload or {} - value = payload.get("value", None) - tag = self._apply_item_tag( trans, self.tagged_item_class, kwd[self.tagged_item_id], tag_name, value ) + value = payload.get( "value", None ) + tag = self._apply_item_tag( trans, self.tagged_item_class, kwd[ self.tagged_item_id ], tag_name, value ) return self._api_value( tag, trans ) # Not handling these differently at this time update = create - @web.expose_api + @expose_api def delete( self, trans, tag_name, **kwd ): """ """ - deleted = self._remove_items_tag( trans, self.tagged_item_class, kwd[self.tagged_item_id], tag_name ) + deleted = self._remove_items_tag( trans, self.tagged_item_class, kwd[ self.tagged_item_id ], tag_name ) if not deleted: - raise HTTPBadRequest("Failed to delete specified tag.") + raise exceptions.RequestParameterInvalidException( "Failed to delete specified tag." ) + #TODO: ugh - 204 would be better return 'OK' def _api_value( self, tag, trans, view='element' ): https://bitbucket.org/galaxy/galaxy-central/commits/83414d1a3943/ Changeset: 83414d1a3943 User: carlfeberhard Date: 2015-02-02 22:09:12+00:00 Summary: Core, startup: add deprecation log.warn if using 'pack_scripts' option Affected #: 1 file diff -r 119898e035065e3ffd1ca9b3e84f23f380faf023 -r 83414d1a3943a6902fe63509b07ed46cba874951 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -90,6 +90,7 @@ webapp = wrap_in_static( webapp, global_conf, plugin_frameworks=[ app.visualizations_registry ], **kwargs ) #webapp = wrap_in_static( webapp, global_conf, plugin_frameworks=None, **kwargs ) if asbool(kwargs.get('pack_scripts', False)): + log.warn( "The 'pack_scripts' option is deprecated" ) pack_scripts() # Close any pooled database connections before forking try: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: API, visualizations: use _future_expose_api, some clean-up
by commits-noreply＠bitbucket.org 03 Feb '15

03 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/117db343f853/ Changeset: 117db343f853 User: carlfeberhard Date: 2015-02-02 21:38:30+00:00 Summary: API, visualizations: use _future_expose_api, some clean-up Affected #: 1 file diff -r b9ec027d4b1e1b67f26632a55076dbf53e3225bd -r 117db343f853b815b6f584679c23d0f44277c07b lib/galaxy/webapps/galaxy/api/visualizations.py --- a/lib/galaxy/webapps/galaxy/api/visualizations.py +++ b/lib/galaxy/webapps/galaxy/api/visualizations.py @@ -5,68 +5,52 @@ may change often. """ -import pkg_resources -pkg_resources.require( 'SQLAlchemy >= 0.4' ) -from sqlalchemy import or_ +from galaxy.web.base.controller import BaseAPIController +from galaxy.web.base.controller import UsesVisualizationMixin +from galaxy.web.base.controller import SharableMixin +from galaxy.model.item_attrs import UsesAnnotations -from galaxy import web, util -from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin, SharableMixin -from galaxy.model.item_attrs import UsesAnnotations -from galaxy.exceptions import ( ItemAccessibilityException, ItemDeletionException, ItemOwnershipException, - MessageException ) - -from galaxy.web import url_for +from galaxy.web import _future_expose_api as expose_api +from galaxy import web +from galaxy import util +from galaxy import exceptions import logging log = logging.getLogger( __name__ ) + class VisualizationsController( BaseAPIController, UsesVisualizationMixin, SharableMixin, UsesAnnotations ): """ RESTful controller for interactions with visualizations. """ - @web.expose_api + @expose_api def index( self, trans, **kwargs ): """ GET /api/visualizations: """ - #TODO: search for vizsesses that apply to an object (sending model class and id? - how to do this?) rval = [] - try: - if not trans.user: - raise ItemAccessibilityException( 'You must be logged in to access visualizations' ) - user = trans.user + user = trans.user - #TODO: search for: title, made by user, creation time range, type (vis name), dbkey, etc. - #TODO: limit, offset, order_by - #TODO: deleted + #TODO: search for: title, made by user, creation time range, type (vis name), dbkey, etc. + #TODO: limit, offset, order_by + #TODO: deleted - # this is the default search - user's vis, vis shared with user, published vis - visualizations = self.get_visualizations_by_user( trans, user ) - visualizations += self.get_visualizations_shared_with_user( trans, user ) - visualizations += self.get_published_visualizations( trans, exclude_user=user ) - #TODO: the admin case - everything + # this is the default search - user's vis, vis shared with user, published vis + visualizations = self.get_visualizations_by_user( trans, user ) + visualizations += self.get_visualizations_shared_with_user( trans, user ) + visualizations += self.get_published_visualizations( trans, exclude_user=user ) + #TODO: the admin case - everything - for visualization in visualizations: - item = self.get_visualization_summary_dict( visualization ) - item = trans.security.encode_dict_ids( item ) - item[ 'url' ] = web.url_for( 'visualization', id=item[ 'id' ] ) - rval.append( item ) - - except ItemAccessibilityException, exception: - trans.response.status = 403 - rval = { 'error': str( exception ) } - if trans.debug: - log.exception( str( exception ) ) - - except Exception, exception: - trans.response.status = 500 - rval = { 'error': str( exception ) } - log.exception( 'visualizations index failed: %s' %( str( exception ) ) ) + for visualization in visualizations: + item = self.get_visualization_summary_dict( visualization ) + item = trans.security.encode_dict_ids( item ) + item[ 'url' ] = web.url_for( 'visualization', id=item[ 'id' ] ) + rval.append( item ) return rval - @web.json + @expose_api def show( self, trans, id, **kwargs ): """ GET /api/visualizations/{viz_id} @@ -75,37 +59,25 @@ # the important thing is the config rval = {} #TODO:?? /api/visualizations/registry -> json of registry.listings? - try: - visualization = self.get_visualization( trans, id, check_ownership=False, check_accessible=True ) - dictionary = trans.security.encode_dict_ids( self.get_visualization_dict( visualization ) ) - dictionary[ 'url' ] = url_for( controller='visualization', - action="display_by_username_and_slug", username=visualization.user.username, slug=visualization.slug ) - dictionary[ 'annotation' ] = self.get_item_annotation_str( trans.sa_session, trans.user, visualization ) - # need to encode ids in revisions as well - encoded_revisions = [] - for revision in dictionary[ 'revisions' ]: - #NOTE: does not encode ids inside the configs - encoded_revisions.append( trans.security.encode_id( revision ) ) - dictionary[ 'revisions' ] = encoded_revisions - dictionary[ 'latest_revision' ] = trans.security.encode_dict_ids( dictionary[ 'latest_revision' ] ) + visualization = self.get_visualization( trans, id, check_ownership=False, check_accessible=True ) + dictionary = trans.security.encode_dict_ids( self.get_visualization_dict( visualization ) ) + dictionary[ 'url' ] = web.url_for( controller='visualization', + action="display_by_username_and_slug", username=visualization.user.username, slug=visualization.slug ) + dictionary[ 'annotation' ] = self.get_item_annotation_str( trans.sa_session, trans.user, visualization ) - rval = dictionary + # need to encode ids in revisions as well + encoded_revisions = [] + for revision in dictionary[ 'revisions' ]: + #NOTE: does not encode ids inside the configs + encoded_revisions.append( trans.security.encode_id( revision ) ) + dictionary[ 'revisions' ] = encoded_revisions + dictionary[ 'latest_revision' ] = trans.security.encode_dict_ids( dictionary[ 'latest_revision' ] ) - except ( ItemAccessibilityException, ItemDeletionException ), exception: - trans.response.status = 403 - rval = { 'error': str( exception ) } - if trans.debug: - log.exception( 'visualization show forbidden (%s): %s' %( id, str( exception ) ) ) - - except Exception, exception: - trans.response.status = 500 - rval = { 'error': str( exception ) } - log.exception( 'visualization show failed (%s): %s' %( id, str( exception ) ) ) - + rval = dictionary return rval - @web.expose_api + @expose_api def create( self, trans, payload, **kwargs ): """ POST /api/visualizations @@ -115,93 +87,61 @@ imports a copy of an existing visualization into the user's workspace """ rval = None - try: - if 'import_id' in payload: - import_id = payload( 'import_id' ) - visualization = self.import_visualization( trans, import_id, user=trans.user ) - else: - payload = self._validate_and_parse_payload( payload ) - # must have a type (I've taken this to be the visualization name) - if 'type' not in payload: - raise ValueError( "key/value 'type' is required" ) - vis_type = payload.pop( 'type', False ) + if 'import_id' in payload: + import_id = payload( 'import_id' ) + visualization = self.import_visualization( trans, import_id, user=trans.user ) - payload[ 'save' ] = True + else: + payload = self._validate_and_parse_payload( payload ) + # must have a type (I've taken this to be the visualization name) + if 'type' not in payload: + raise exceptions.RequestParameterMissingException( "key/value 'type' is required" ) + vis_type = payload.pop( 'type', False ) + + payload[ 'save' ] = True + try: # generate defaults - this will err if given a weird key? visualization = self.create_visualization( trans, vis_type, **payload ) + except ValueError, val_err: + raise exceptions.RequestParameterMissingException( str( val_err ) ) - rval = { 'id' : trans.security.encode_id( visualization.id ) } - - #TODO: exception boilerplate - except ( ItemAccessibilityException, ItemDeletionException ), exception: - trans.response.status = 403 - rval = { 'error': str( exception ) } - if trans.debug: - log.exception( str( exception ) ) - - except ( ValueError, AttributeError ), exception: - trans.response.status = 400 - rval = { 'error': str( exception ) } - if trans.debug: - log.exception( str( exception ) ) - - except Exception, exception: - trans.response.status = 500 - rval = { 'error': str( exception ) } - log.exception( 'creation of visualization failed: %s' %( str( exception ) ) ) + rval = { 'id' : trans.security.encode_id( visualization.id ) } return rval - @web.expose_api + @expose_api def update( self, trans, id, payload, **kwargs ): """ PUT /api/visualizations/{encoded_visualization_id} """ rval = None - try: - payload = self._validate_and_parse_payload( payload ) - # there's a differentiation here between updating the visualiztion and creating a new revision - # that needs to be handled clearly here - # or alternately, using a different controller like PUT /api/visualizations/{id}/r/{id} + payload = self._validate_and_parse_payload( payload ) - #TODO: consider allowing direct alteration of revisions title (without a new revision) - # only create a new revsion on a different config + # there's a differentiation here between updating the visualiztion and creating a new revision + # that needs to be handled clearly here + # or alternately, using a different controller like PUT /api/visualizations/{id}/r/{id} - # only update owned visualizations - visualization = self.get_visualization( trans, id, check_ownership=True ) - title = payload.get( 'title', visualization.latest_revision.title ) - dbkey = payload.get( 'dbkey', visualization.latest_revision.dbkey ) - config = payload.get( 'config', visualization.latest_revision.config ) + #TODO: consider allowing direct alteration of revisions title (without a new revision) + # only create a new revsion on a different config - latest_config = visualization.latest_revision.config - if( ( title != visualization.latest_revision.title ) - or ( dbkey != visualization.latest_revision.dbkey ) - or ( util.json.dumps( config ) != util.json.dumps( latest_config ) ) ): - revision = self.add_visualization_revision( trans, visualization, config, title, dbkey ) - rval = { 'id' : id, 'revision' : revision.id } + # only update owned visualizations + visualization = self.get_visualization( trans, id, check_ownership=True ) + title = payload.get( 'title', visualization.latest_revision.title ) + dbkey = payload.get( 'dbkey', visualization.latest_revision.dbkey ) + config = payload.get( 'config', visualization.latest_revision.config ) - # allow updating vis title - visualization.title = title - trans.sa_session.flush() + latest_config = visualization.latest_revision.config + if( ( title != visualization.latest_revision.title ) + or ( dbkey != visualization.latest_revision.dbkey ) + or ( util.json.dumps( config ) != util.json.dumps( latest_config ) ) ): + revision = self.add_visualization_revision( trans, visualization, config, title, dbkey ) + rval = { 'id' : id, 'revision' : revision.id } - except ( ItemAccessibilityException, ItemDeletionException ), exception: - trans.response.status = 403 - rval = { 'error': str( exception ) } - if trans.debug: - log.exception( str( exception ) ) - - except ( ValueError, AttributeError ), exception: - trans.response.status = 400 - rval = { 'error': str( exception ) } - if trans.debug: - log.exception( str( exception ) ) - - except Exception, exception: - trans.response.status = 500 - rval = { 'error': str( exception ) } - log.exception( 'update of visualization (%s) failed: %s' %( id, str( exception ) ) ) + # allow updating vis title + visualization.title = title + trans.sa_session.flush() return rval @@ -224,36 +164,37 @@ ) #TODO: deleted #TODO: importable + ValidationError = exceptions.RequestParameterInvalidException validated_payload = {} for key, val in payload.items(): #TODO: validate types in VALID_TYPES/registry names at the mixin/model level? if key == 'type': if not ( isinstance( val, str ) or isinstance( val, unicode ) ): - raise ValueError( '%s must be a string or unicode: %s' %( key, str( type( val ) ) ) ) + raise ValidationError( '%s must be a string or unicode: %s' %( key, str( type( val ) ) ) ) val = util.sanitize_html.sanitize_html( val, 'utf-8' ) elif key == 'config': if not isinstance( val, dict ): - raise ValueError( '%s must be a dictionary: %s' %( key, str( type( val ) ) ) ) + raise ValidationError( '%s must be a dictionary: %s' %( key, str( type( val ) ) ) ) elif key == 'annotation': if not ( isinstance( val, str ) or isinstance( val, unicode ) ): - raise ValueError( '%s must be a string or unicode: %s' %( key, str( type( val ) ) ) ) + raise ValidationError( '%s must be a string or unicode: %s' %( key, str( type( val ) ) ) ) val = util.sanitize_html.sanitize_html( val, 'utf-8' ) # these are keys that actually only be *updated* at the revision level and not here # (they are still valid for create, tho) elif key == 'title': if not ( isinstance( val, str ) or isinstance( val, unicode ) ): - raise ValueError( '%s must be a string or unicode: %s' %( key, str( type( val ) ) ) ) + raise ValidationError( '%s must be a string or unicode: %s' %( key, str( type( val ) ) ) ) val = util.sanitize_html.sanitize_html( val, 'utf-8' ) elif key == 'slug': if not ( isinstance( val, str ) or isinstance( val, unicode ) ): - raise ValueError( '%s must be a string: %s' %( key, str( type( val ) ) ) ) + raise ValidationError( '%s must be a string: %s' %( key, str( type( val ) ) ) ) val = util.sanitize_html.sanitize_html( val, 'utf-8' ) elif key == 'dbkey': if not ( isinstance( val, str ) or isinstance( val, unicode ) ): - raise ValueError( '%s must be a string or unicode: %s' %( key, str( type( val ) ) ) ) + raise ValidationError( '%s must be a string or unicode: %s' %( key, str( type( val ) ) ) ) val = util.sanitize_html.sanitize_html( val, 'utf-8' ) elif key not in valid_but_uneditable_keys: @@ -262,11 +203,3 @@ validated_payload[ key ] = val return validated_payload - - #(a)web.expose_api - #def delete( self, trans, id, **kwd ): - # """ - # DELETE /api/visualizations/{encoded_history_id} - # Deletes a visualization from the database - # """ - # pass Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Merged in dan/galaxy-central-prs/stable (pull request #657)
by commits-noreply＠bitbucket.org 03 Feb '15

03 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5e4060f5ac7a/ Changeset: 5e4060f5ac7a Branch: stable User: jmchilton Date: 2015-02-02 21:30:49+00:00 Summary: Merged in dan/galaxy-central-prs/stable (pull request #657) [STABLE] Fix for preventing non-admins from running data managers via the api. Affected #: 4 files diff -r 96aabc4e66f193d4bb3b7b37d8ad4dce671f1b04 -r 5e4060f5ac7a3c11d4681bc80f94c620df9d0479 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1388,6 +1388,12 @@ return section_id, section_name return None, None + def allow_user_access( self, user ): + """ + :returns: bool -- Whether the user is allowed to access the tool. + """ + return True + def parse( self, root, guid=None ): """ Read tool configuration from the element `root` and fill in `self`. @@ -3392,6 +3398,7 @@ self.data_manager_id = self.id def exec_after_process( self, app, inp_data, out_data, param_dict, job=None, **kwds ): + assert self.allow_user_access( job.user ), "You must be an admin to access this tool." #run original exec_after_process super( DataManagerTool, self ).exec_after_process( app, inp_data, out_data, param_dict, job=job, **kwds ) #process results of tool @@ -3415,6 +3422,7 @@ return history user = trans.user assert user, 'You must be logged in to use this tool.' + assert self.allow_user_access( user ), "You must be an admin to access this tool." history = user.data_manager_histories if not history: #create @@ -3434,6 +3442,17 @@ history = None return history + def allow_user_access( self, user ): + """ + :returns: bool -- Whether the user is allowed to access the tool. + Data Manager tools are only accessible to admins. + """ + if super( DataManagerTool, self ).allow_user_access( user ) and self.app.config.is_admin_user( user ): + return True + if user: + user = user.id + log.debug( "User (%s) attempted to access a data manager tool (%s), but is not an admin.", user, self.id ) + return False # Populate tool_type to ToolClass mappings tool_types = {} diff -r 96aabc4e66f193d4bb3b7b37d8ad4dce671f1b04 -r 5e4060f5ac7a3c11d4681bc80f94c620df9d0479 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -155,6 +155,7 @@ submitting the job to the job queue. If history is not specified, use trans.history as destination for tool's output datasets. """ + assert tool.allow_user_access( trans.user ), "User (%s) is not allowed to access this tool." % ( trans.user ) # Set history. if not history: history = tool.get_default_history_by_trans( trans, create=True ) diff -r 96aabc4e66f193d4bb3b7b37d8ad4dce671f1b04 -r 5e4060f5ac7a3c11d4681bc80f94c620df9d0479 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -63,7 +63,7 @@ """ io_details = util.string_as_bool( kwd.get( 'io_details', False ) ) link_details = util.string_as_bool( kwd.get( 'link_details', False ) ) - tool = self._get_tool( id ) + tool = self._get_tool( id, user=trans.user ) return tool.to_dict( trans, io_details=io_details, link_details=link_details ) @_future_expose_api_anonymous @@ -89,7 +89,7 @@ @_future_expose_api_anonymous def citations( self, trans, id, **kwds ): - tool = self._get_tool( id ) + tool = self._get_tool( id, user=trans.user ) rval = [] for citation in tool.citations: rval.append( citation.to_dict( 'bibtex' ) ) @@ -122,7 +122,7 @@ # Get tool. tool = trans.app.toolbox.get_tool( payload[ 'tool_id' ] ) if 'tool_id' in payload else None - if not tool: + if not tool or not tool.allow_user_access( trans.user ): trans.response.status = 404 return { "message": { "type": "error", "text" : trans.app.model.Dataset.conversion_messages.NO_TOOL } } @@ -212,10 +212,10 @@ # # -- Helper methods -- # - def _get_tool( self, id ): + def _get_tool( self, id, user=None ): id = urllib.unquote_plus( id ) tool = self.app.toolbox.get_tool( id ) - if not tool: + if not tool or not tool.allow_user_access( user ): raise exceptions.ObjectNotFound("Could not find tool with id '%s'" % id) return tool @@ -281,7 +281,7 @@ # original_job = self.get_hda_job( original_dataset ) tool = trans.app.toolbox.get_tool( original_job.tool_id ) - if not tool: + if not tool or not tool.allow_user_access( trans.user ): return trans.app.model.Dataset.conversion_messages.NO_TOOL tool_params = dict( [ ( p.name, p.value ) for p in original_job.parameters ] ) diff -r 96aabc4e66f193d4bb3b7b37d8ad4dce671f1b04 -r 5e4060f5ac7a3c11d4681bc80f94c620df9d0479 lib/galaxy/webapps/galaxy/controllers/tool_runner.py --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -65,7 +65,7 @@ get_loaded_tools_by_lineage=False, set_selected=refreshed_on_change ) # No tool matching the tool id, display an error (shouldn't happen) - if not tool: + if not tool or not tool.allow_user_access( trans.user ): log.error( "index called with tool id '%s' but no such tool exists", tool_id ) trans.log_event( "Tool id '%s' does not exist" % tool_id ) trans.response.status = 404 @@ -191,6 +191,8 @@ # This is expected so not an exception. tool_id_version_message = '' error( "This dataset was created by an obsolete tool (%s). Can't re-run." % tool_id ) + if not tool.allow_user_access( trans.user ): + error( "The requested tool is unknown." ) # Can't rerun upload, external data sources, et cetera. Workflow compatible will proxy this for now if not tool.is_workflow_compatible: error( "The '%s' tool does not currently support rerunning." % tool.name ) 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.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 03 Feb '15

03 Feb '15

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0b9127ab708d/ Changeset: 0b9127ab708d Branch: stable User: dan Date: 2015-02-02 21:21:00+00:00 Summary: Fix for preventing non-admins from running data managers via the api. Affected #: 4 files diff -r 1b96d3a4ff28da2bd547b65ad86c5ad5a9bbfb90 -r 0b9127ab708d7d8497e80169a3b8636aea1e37c6 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1388,6 +1388,12 @@ return section_id, section_name return None, None + def allow_user_access( self, user ): + """ + :returns: bool -- Whether the user is allowed to access the tool. + """ + return True + def parse( self, root, guid=None ): """ Read tool configuration from the element `root` and fill in `self`. @@ -3392,6 +3398,7 @@ self.data_manager_id = self.id def exec_after_process( self, app, inp_data, out_data, param_dict, job=None, **kwds ): + assert self.allow_user_access( job.user ), "You must be an admin to access this tool." #run original exec_after_process super( DataManagerTool, self ).exec_after_process( app, inp_data, out_data, param_dict, job=job, **kwds ) #process results of tool @@ -3415,6 +3422,7 @@ return history user = trans.user assert user, 'You must be logged in to use this tool.' + assert self.allow_user_access( user ), "You must be an admin to access this tool." history = user.data_manager_histories if not history: #create @@ -3434,6 +3442,17 @@ history = None return history + def allow_user_access( self, user ): + """ + :returns: bool -- Whether the user is allowed to access the tool. + Data Manager tools are only accessible to admins. + """ + if super( DataManagerTool, self ).allow_user_access( user ) and self.app.config.is_admin_user( user ): + return True + if user: + user = user.id + log.debug( "User (%s) attempted to access a data manager tool (%s), but is not an admin.", user, self.id ) + return False # Populate tool_type to ToolClass mappings tool_types = {} diff -r 1b96d3a4ff28da2bd547b65ad86c5ad5a9bbfb90 -r 0b9127ab708d7d8497e80169a3b8636aea1e37c6 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -155,6 +155,7 @@ submitting the job to the job queue. If history is not specified, use trans.history as destination for tool's output datasets. """ + assert tool.allow_user_access( trans.user ), "User (%s) is not allowed to access this tool." % ( trans.user ) # Set history. if not history: history = tool.get_default_history_by_trans( trans, create=True ) diff -r 1b96d3a4ff28da2bd547b65ad86c5ad5a9bbfb90 -r 0b9127ab708d7d8497e80169a3b8636aea1e37c6 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -63,7 +63,7 @@ """ io_details = util.string_as_bool( kwd.get( 'io_details', False ) ) link_details = util.string_as_bool( kwd.get( 'link_details', False ) ) - tool = self._get_tool( id ) + tool = self._get_tool( id, user=trans.user ) return tool.to_dict( trans, io_details=io_details, link_details=link_details ) @_future_expose_api_anonymous @@ -89,7 +89,7 @@ @_future_expose_api_anonymous def citations( self, trans, id, **kwds ): - tool = self._get_tool( id ) + tool = self._get_tool( id, user=trans.user ) rval = [] for citation in tool.citations: rval.append( citation.to_dict( 'bibtex' ) ) @@ -122,7 +122,7 @@ # Get tool. tool = trans.app.toolbox.get_tool( payload[ 'tool_id' ] ) if 'tool_id' in payload else None - if not tool: + if not tool or not tool.allow_user_access( trans.user ): trans.response.status = 404 return { "message": { "type": "error", "text" : trans.app.model.Dataset.conversion_messages.NO_TOOL } } @@ -212,10 +212,10 @@ # # -- Helper methods -- # - def _get_tool( self, id ): + def _get_tool( self, id, user=None ): id = urllib.unquote_plus( id ) tool = self.app.toolbox.get_tool( id ) - if not tool: + if not tool or not tool.allow_user_access( user ): raise exceptions.ObjectNotFound("Could not find tool with id '%s'" % id) return tool @@ -281,7 +281,7 @@ # original_job = self.get_hda_job( original_dataset ) tool = trans.app.toolbox.get_tool( original_job.tool_id ) - if not tool: + if not tool or not tool.allow_user_access( trans.user ): return trans.app.model.Dataset.conversion_messages.NO_TOOL tool_params = dict( [ ( p.name, p.value ) for p in original_job.parameters ] ) diff -r 1b96d3a4ff28da2bd547b65ad86c5ad5a9bbfb90 -r 0b9127ab708d7d8497e80169a3b8636aea1e37c6 lib/galaxy/webapps/galaxy/controllers/tool_runner.py --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -65,7 +65,7 @@ get_loaded_tools_by_lineage=False, set_selected=refreshed_on_change ) # No tool matching the tool id, display an error (shouldn't happen) - if not tool: + if not tool or not tool.allow_user_access( trans.user ): log.error( "index called with tool id '%s' but no such tool exists", tool_id ) trans.log_event( "Tool id '%s' does not exist" % tool_id ) trans.response.status = 404 @@ -191,6 +191,8 @@ # This is expected so not an exception. tool_id_version_message = '' error( "This dataset was created by an obsolete tool (%s). Can't re-run." % tool_id ) + if not tool.allow_user_access( trans.user ): + error( "The requested tool is unknown." ) # Can't rerun upload, external data sources, et cetera. Workflow compatible will proxy this for now if not tool.is_workflow_compatible: error( "The '%s' tool does not currently support rerunning." % tool.name ) https://bitbucket.org/galaxy/galaxy-central/commits/5e4060f5ac7a/ Changeset: 5e4060f5ac7a Branch: stable User: jmchilton Date: 2015-02-02 21:30:49+00:00 Summary: Merged in dan/galaxy-central-prs/stable (pull request #657) [STABLE] Fix for preventing non-admins from running data managers via the api. Affected #: 4 files diff -r 96aabc4e66f193d4bb3b7b37d8ad4dce671f1b04 -r 5e4060f5ac7a3c11d4681bc80f94c620df9d0479 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1388,6 +1388,12 @@ return section_id, section_name return None, None + def allow_user_access( self, user ): + """ + :returns: bool -- Whether the user is allowed to access the tool. + """ + return True + def parse( self, root, guid=None ): """ Read tool configuration from the element `root` and fill in `self`. @@ -3392,6 +3398,7 @@ self.data_manager_id = self.id def exec_after_process( self, app, inp_data, out_data, param_dict, job=None, **kwds ): + assert self.allow_user_access( job.user ), "You must be an admin to access this tool." #run original exec_after_process super( DataManagerTool, self ).exec_after_process( app, inp_data, out_data, param_dict, job=job, **kwds ) #process results of tool @@ -3415,6 +3422,7 @@ return history user = trans.user assert user, 'You must be logged in to use this tool.' + assert self.allow_user_access( user ), "You must be an admin to access this tool." history = user.data_manager_histories if not history: #create @@ -3434,6 +3442,17 @@ history = None return history + def allow_user_access( self, user ): + """ + :returns: bool -- Whether the user is allowed to access the tool. + Data Manager tools are only accessible to admins. + """ + if super( DataManagerTool, self ).allow_user_access( user ) and self.app.config.is_admin_user( user ): + return True + if user: + user = user.id + log.debug( "User (%s) attempted to access a data manager tool (%s), but is not an admin.", user, self.id ) + return False # Populate tool_type to ToolClass mappings tool_types = {} diff -r 96aabc4e66f193d4bb3b7b37d8ad4dce671f1b04 -r 5e4060f5ac7a3c11d4681bc80f94c620df9d0479 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -155,6 +155,7 @@ submitting the job to the job queue. If history is not specified, use trans.history as destination for tool's output datasets. """ + assert tool.allow_user_access( trans.user ), "User (%s) is not allowed to access this tool." % ( trans.user ) # Set history. if not history: history = tool.get_default_history_by_trans( trans, create=True ) diff -r 96aabc4e66f193d4bb3b7b37d8ad4dce671f1b04 -r 5e4060f5ac7a3c11d4681bc80f94c620df9d0479 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -63,7 +63,7 @@ """ io_details = util.string_as_bool( kwd.get( 'io_details', False ) ) link_details = util.string_as_bool( kwd.get( 'link_details', False ) ) - tool = self._get_tool( id ) + tool = self._get_tool( id, user=trans.user ) return tool.to_dict( trans, io_details=io_details, link_details=link_details ) @_future_expose_api_anonymous @@ -89,7 +89,7 @@ @_future_expose_api_anonymous def citations( self, trans, id, **kwds ): - tool = self._get_tool( id ) + tool = self._get_tool( id, user=trans.user ) rval = [] for citation in tool.citations: rval.append( citation.to_dict( 'bibtex' ) ) @@ -122,7 +122,7 @@ # Get tool. tool = trans.app.toolbox.get_tool( payload[ 'tool_id' ] ) if 'tool_id' in payload else None - if not tool: + if not tool or not tool.allow_user_access( trans.user ): trans.response.status = 404 return { "message": { "type": "error", "text" : trans.app.model.Dataset.conversion_messages.NO_TOOL } } @@ -212,10 +212,10 @@ # # -- Helper methods -- # - def _get_tool( self, id ): + def _get_tool( self, id, user=None ): id = urllib.unquote_plus( id ) tool = self.app.toolbox.get_tool( id ) - if not tool: + if not tool or not tool.allow_user_access( user ): raise exceptions.ObjectNotFound("Could not find tool with id '%s'" % id) return tool @@ -281,7 +281,7 @@ # original_job = self.get_hda_job( original_dataset ) tool = trans.app.toolbox.get_tool( original_job.tool_id ) - if not tool: + if not tool or not tool.allow_user_access( trans.user ): return trans.app.model.Dataset.conversion_messages.NO_TOOL tool_params = dict( [ ( p.name, p.value ) for p in original_job.parameters ] ) diff -r 96aabc4e66f193d4bb3b7b37d8ad4dce671f1b04 -r 5e4060f5ac7a3c11d4681bc80f94c620df9d0479 lib/galaxy/webapps/galaxy/controllers/tool_runner.py --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -65,7 +65,7 @@ get_loaded_tools_by_lineage=False, set_selected=refreshed_on_change ) # No tool matching the tool id, display an error (shouldn't happen) - if not tool: + if not tool or not tool.allow_user_access( trans.user ): log.error( "index called with tool id '%s' but no such tool exists", tool_id ) trans.log_event( "Tool id '%s' does not exist" % tool_id ) trans.response.status = 404 @@ -191,6 +191,8 @@ # This is expected so not an exception. tool_id_version_message = '' error( "This dataset was created by an obsolete tool (%s). Can't re-run." % tool_id ) + if not tool.allow_user_access( trans.user ): + error( "The requested tool is unknown." ) # Can't rerun upload, external data sources, et cetera. Workflow compatible will proxy this for now if not tool.is_workflow_compatible: error( "The '%s' tool does not currently support rerunning." % tool.name ) 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: jmchilton: Expose improved sample tracking to tools for implicit map/reduce ops.
by commits-noreply＠bitbucket.org 03 Feb '15

03 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b9ec027d4b1e/ Changeset: b9ec027d4b1e User: jmchilton Date: 2015-02-02 21:29:42+00:00 Summary: Expose improved sample tracking to tools for implicit map/reduce ops. Tools may now use $input.element_identifier during tool evalution for input 'data' parameters with the following semantics: - If the input was specified as a single dataset by the user - this just fallbacks to providing the $input.name. - If the input was mapped over a collection (to produce many jobs) or if the input is a 'multiple="true"' input that was provided a collection - the $input.element_identifier will be the element identifier for the corresponding collection item (generally much more useful the dataset name - since if preserved throughout workflows). 'data_collection' parameters already can access this kind of information - but it is something of a best practice to use simple 'data' parameters since they are compatible with more traditional un-collected datasets. This commit really needs more comments - but Philip Mabon has been patiently waiting for this functionality for a long time. Affected #: 9 files diff -r ff3c5721f74857cf689966abfdeb0dc9390bf605 -r b9ec027d4b1e1b67f26632a55076dbf53e3225bd lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -2685,6 +2685,16 @@ return instances @property + def dataset_elements( self ): + elements = [] + for element in self.elements: + if element.is_collection: + elements.extend( element.child_collection.dataset_elements ) + else: + elements.append( element ) + return elements + + @property def state( self ): # TODO: DatasetCollection state handling... return 'ok' diff -r ff3c5721f74857cf689966abfdeb0dc9390bf605 -r b9ec027d4b1e1b67f26632a55076dbf53e3225bd lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -191,6 +191,10 @@ if data.dbkey not in [None, '?']: input_dbkey = data.dbkey + identifier = getattr( data, "element_identifier", None ) + if identifier is not None: + incoming[ "%s|__identifier__" % name ] = identifier + # Collect chromInfo dataset and add as parameters to incoming ( chrom_info, db_dataset ) = trans.app.genome_builds.get_chrom_info( input_dbkey, trans=trans, custom_build_hack_get_len_from_fasta_conversion=tool.id != 'CONVERTER_fasta_to_len' ) if db_dataset: diff -r ff3c5721f74857cf689966abfdeb0dc9390bf605 -r b9ec027d4b1e1b67f26632a55076dbf53e3225bd lib/galaxy/tools/evaluation.py --- a/lib/galaxy/tools/evaluation.py +++ b/lib/galaxy/tools/evaluation.py @@ -154,7 +154,7 @@ if isinstance( input, DataToolParameter ) and input.multiple: dataset_instances = input_values[ input.name ] if isinstance( dataset_instances, model.HistoryDatasetCollectionAssociation ): - dataset_instances = dataset_instances.collection.dataset_instances[:] + dataset_instances = dataset_instances.collection.dataset_elements[:] input_values[ input.name ] = \ DatasetListWrapper( dataset_instances, dataset_paths=input_dataset_paths, @@ -199,6 +199,9 @@ tool=self, name=input.name ) + identifier_key = "%s|__identifier__" % input.name + if identifier_key in param_dict: + wrapper_kwds["identifier"] = param_dict[identifier_key] if dataset: #A None dataset does not have a filename real_path = dataset.file_name diff -r ff3c5721f74857cf689966abfdeb0dc9390bf605 -r b9ec027d4b1e1b67f26632a55076dbf53e3225bd lib/galaxy/tools/parameters/meta.py --- a/lib/galaxy/tools/parameters/meta.py +++ b/lib/galaxy/tools/parameters/meta.py @@ -14,6 +14,13 @@ execution). """ + to_remove = [] + for key in incoming.keys(): + if key.endswith("|__identifier__"): + to_remove.append(key) + for key in to_remove: + incoming.pop(key) + def classify_unmodified_parameter( input_key ): value = incoming[ input_key ] if isinstance( value, dict ) and 'values' in value: @@ -118,7 +125,11 @@ subcollection_elements = subcollections.split_dataset_collection_instance( hdc, subcollection_type ) return subcollection_elements else: - hdas = hdc.collection.dataset_instances + hdas = [] + for element in hdc.collection.dataset_elements: + hda = element.dataset_instance + hda.element_identifier = element.element_identifier + hdas.append( hda ) return hdas diff -r ff3c5721f74857cf689966abfdeb0dc9390bf605 -r b9ec027d4b1e1b67f26632a55076dbf53e3225bd lib/galaxy/tools/wrappers.py --- a/lib/galaxy/tools/wrappers.py +++ b/lib/galaxy/tools/wrappers.py @@ -187,7 +187,7 @@ def items( self ): return iter( [ ( k, self.get( k ) ) for k, v in self.metadata.items() ] ) - def __init__( self, dataset, datatypes_registry=None, tool=None, name=None, dataset_path=None ): + def __init__( self, dataset, datatypes_registry=None, tool=None, name=None, dataset_path=None, identifier=None ): if not dataset: try: # TODO: allow this to work when working with grouping @@ -205,6 +205,14 @@ self.datatypes_registry = datatypes_registry self.false_path = getattr( dataset_path, "false_path", None ) self.false_extra_files_path = getattr( dataset_path, "false_extra_files_path", None ) + self._element_identifier = identifier + + @property + def element_identifier( self ): + identifier = self._element_identifier + if identifier is None: + identifier = self.name + return identifier @property def is_collection( self ): @@ -270,6 +278,10 @@ datasets = [datasets] def to_wrapper( dataset ): + if hasattr(dataset, "element_identifier"): + element = dataset + dataset = element.dataset_instance + kwargs["identifier"] = element.element_identifier return self._dataset_wrapper( dataset, dataset_paths, **kwargs ) list.__init__( self, map( to_wrapper, datasets ) ) diff -r ff3c5721f74857cf689966abfdeb0dc9390bf605 -r b9ec027d4b1e1b67f26632a55076dbf53e3225bd test/api/test_tools.py --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -553,6 +553,93 @@ self.assertEquals( output1_content.strip(), "123" ) self.assertEquals( output2_content.strip(), "456" ) + @skip_without_tool( "identifier_single" ) + def test_identifier_in_map( self ): + history_id = self.dataset_populator.new_history() + hdca_id = self.__build_pair( history_id, [ "123", "456" ] ) + inputs = { + "input1": { 'batch': True, 'values': [ { 'src': 'hdca', 'id': hdca_id } ] }, + } + create_response = self._run( "identifier_single", history_id, inputs ) + self._assert_status_code_is( create_response, 200 ) + create = create_response.json() + outputs = create[ 'outputs' ] + jobs = create[ 'jobs' ] + implicit_collections = create[ 'implicit_collections' ] + self.assertEquals( len( jobs ), 2 ) + self.assertEquals( len( outputs ), 2 ) + self.assertEquals( len( implicit_collections ), 1 ) + output1 = outputs[ 0 ] + output2 = outputs[ 1 ] + output1_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output1 ) + output2_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output2 ) + self.assertEquals( output1_content.strip(), "forward" ) + self.assertEquals( output2_content.strip(), "reverse" ) + + @skip_without_tool( "identifier_single" ) + def test_identifier_outside_map( self ): + history_id = self.dataset_populator.new_history() + new_dataset1 = self.dataset_populator.new_dataset( history_id, content='123' ) + inputs = { + "input1": { 'src': 'hda', 'id': new_dataset1["id"] }, + } + create_response = self._run( "identifier_single", history_id, inputs ) + self._assert_status_code_is( create_response, 200 ) + create = create_response.json() + outputs = create[ 'outputs' ] + jobs = create[ 'jobs' ] + implicit_collections = create[ 'implicit_collections' ] + self.assertEquals( len( jobs ), 1 ) + self.assertEquals( len( outputs ), 1 ) + self.assertEquals( len( implicit_collections ), 0 ) + output1 = outputs[ 0 ] + output1_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output1 ) + self.assertEquals( output1_content.strip(), "Pasted Entry" ) + + @skip_without_tool( "identifier_multiple" ) + def test_identifier_in_multiple_reduce( self ): + history_id = self.dataset_populator.new_history() + hdca_id = self.__build_pair( history_id, [ "123", "456" ] ) + inputs = { + "input1": { 'src': 'hdca', 'id': hdca_id }, + } + create_response = self._run( "identifier_multiple", history_id, inputs ) + self._assert_status_code_is( create_response, 200 ) + create = create_response.json() + outputs = create[ 'outputs' ] + jobs = create[ 'jobs' ] + implicit_collections = create[ 'implicit_collections' ] + self.assertEquals( len( jobs ), 1 ) + self.assertEquals( len( outputs ), 1 ) + self.assertEquals( len( implicit_collections ), 0 ) + output1 = outputs[ 0 ] + output1_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output1 ) + self.assertEquals( output1_content.strip(), "forward\nreverse" ) + + @skip_without_tool( "identifier_multiple" ) + def test_identifier_with_multiple_normal_datasets( self ): + history_id = self.dataset_populator.new_history() + new_dataset1 = self.dataset_populator.new_dataset( history_id, content='123' ) + new_dataset2 = self.dataset_populator.new_dataset( history_id, content='456' ) + inputs = { + "input1": [ + { 'src': 'hda', 'id': new_dataset1["id"] }, + { 'src': 'hda', 'id': new_dataset2["id"] } + ] + } + create_response = self._run( "identifier_multiple", history_id, inputs ) + self._assert_status_code_is( create_response, 200 ) + create = create_response.json() + outputs = create[ 'outputs' ] + jobs = create[ 'jobs' ] + implicit_collections = create[ 'implicit_collections' ] + self.assertEquals( len( jobs ), 1 ) + self.assertEquals( len( outputs ), 1 ) + self.assertEquals( len( implicit_collections ), 0 ) + output1 = outputs[ 0 ] + output1_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output1 ) + self.assertEquals( output1_content.strip(), "Pasted Entry\nPasted Entry" ) + @skip_without_tool( "cat1" ) def test_map_over_nested_collections_legacy( self ): history_id = self.dataset_populator.new_history() diff -r ff3c5721f74857cf689966abfdeb0dc9390bf605 -r b9ec027d4b1e1b67f26632a55076dbf53e3225bd test/functional/tools/identifier_multiple.xml --- /dev/null +++ b/test/functional/tools/identifier_multiple.xml @@ -0,0 +1,15 @@ +<tool id="identifier_multiple" name="identifier_multiple"> + <command> + #for $input in $input1# + echo '$input.element_identifier' >> 'output1'; + #end for# + </command> + <inputs> + <param type="data" name="input1" label="Input 1" multiple="true" /> + </inputs> + <outputs> + <data name="output1" type="tabular" from_work_dir="output1" /> + </outputs> + <tests> + </tests> +</tool> diff -r ff3c5721f74857cf689966abfdeb0dc9390bf605 -r b9ec027d4b1e1b67f26632a55076dbf53e3225bd test/functional/tools/identifier_single.xml --- /dev/null +++ b/test/functional/tools/identifier_single.xml @@ -0,0 +1,13 @@ +<tool id="identifier_single" name="identifier_single"> + <command> + echo '$input1.element_identifier' > 'output1' + </command> + <inputs> + <param type="data" name="input1" label="Input 1" /> + </inputs> + <outputs> + <data name="output1" type="tabular" from_work_dir="output1" /> + </outputs> + <tests> + </tests> +</tool> diff -r ff3c5721f74857cf689966abfdeb0dc9390bf605 -r b9ec027d4b1e1b67f26632a55076dbf53e3225bd test/functional/tools/samples_tool_conf.xml --- a/test/functional/tools/samples_tool_conf.xml +++ b/test/functional/tools/samples_tool_conf.xml @@ -30,6 +30,8 @@ <tool file="validation_default.xml" /><tool file="validation_sanitizer.xml" /><tool file="validation_repeat.xml" /> + <tool file="identifier_single.xml" /> + <tool file="identifier_multiple.xml" /><tool file="collection_paired_test.xml" /><tool file="collection_nested_test.xml" /><tool file="collection_mixed_param.xml" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Fix for preventing non-admins from running data managers via the api.
by commits-noreply＠bitbucket.org 03 Feb '15

03 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ff3c5721f748/ Changeset: ff3c5721f748 User: dan Date: 2015-02-02 20:57:18+00:00 Summary: Fix for preventing non-admins from running data managers via the api. Affected #: 4 files diff -r 8e5b9caba8ff493c25684ebdb6f69b819c34dca6 -r ff3c5721f74857cf689966abfdeb0dc9390bf605 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -550,6 +550,12 @@ def get_panel_section( self ): return self.app.toolbox.get_integrated_section_for_tool( self ) + def allow_user_access( self, user ): + """ + :returns: bool -- Whether the user is allowed to access the tool. + """ + return True + def parse( self, tool_source, guid=None ): """ Read tool configuration from the element `root` and fill in `self`. @@ -2799,6 +2805,7 @@ self.data_manager_id = self.id def exec_after_process( self, app, inp_data, out_data, param_dict, job=None, **kwds ): + assert self.allow_user_access( job.user ), "You must be an admin to access this tool." #run original exec_after_process super( DataManagerTool, self ).exec_after_process( app, inp_data, out_data, param_dict, job=job, **kwds ) #process results of tool @@ -2822,6 +2829,7 @@ return history user = trans.user assert user, 'You must be logged in to use this tool.' + assert self.allow_user_access( user ), "You must be an admin to access this tool." history = user.data_manager_histories if not history: #create @@ -2841,6 +2849,17 @@ history = None return history + def allow_user_access( self, user ): + """ + :returns: bool -- Whether the user is allowed to access the tool. + Data Manager tools are only accessible to admins. + """ + if super( DataManagerTool, self ).allow_user_access( user ) and self.app.config.is_admin_user( user ): + return True + if user: + user = user.id + log.debug( "User (%s) attempted to access a data manager tool (%s), but is not an admin.", user, self.id ) + return False # Populate tool_type to ToolClass mappings tool_types = {} diff -r 8e5b9caba8ff493c25684ebdb6f69b819c34dca6 -r ff3c5721f74857cf689966abfdeb0dc9390bf605 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -155,6 +155,7 @@ submitting the job to the job queue. If history is not specified, use trans.history as destination for tool's output datasets. """ + assert tool.allow_user_access( trans.user ), "User (%s) is not allowed to access this tool." % ( trans.user ) # Set history. if not history: history = tool.get_default_history_by_trans( trans, create=True ) diff -r 8e5b9caba8ff493c25684ebdb6f69b819c34dca6 -r ff3c5721f74857cf689966abfdeb0dc9390bf605 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -67,7 +67,7 @@ """ io_details = util.string_as_bool( kwd.get( 'io_details', False ) ) link_details = util.string_as_bool( kwd.get( 'link_details', False ) ) - tool = self._get_tool( id ) + tool = self._get_tool( id, user=trans.user ) return tool.to_dict( trans, io_details=io_details, link_details=link_details ) @_future_expose_api_anonymous @@ -98,7 +98,7 @@ @_future_expose_api_anonymous def citations( self, trans, id, **kwds ): - tool = self._get_tool( id ) + tool = self._get_tool( id, user=trans.user ) rval = [] for citation in tool.citations: rval.append( citation.to_dict( 'bibtex' ) ) @@ -132,7 +132,7 @@ # Get tool. tool_version = payload.get( 'tool_version', None ) tool = trans.app.toolbox.get_tool( payload[ 'tool_id' ] , tool_version ) if 'tool_id' in payload else None - if not tool: + if not tool or not tool.allow_user_access( trans.user ): trans.response.status = 404 return { "message": { "type": "error", "text" : trans.app.model.Dataset.conversion_messages.NO_TOOL } } @@ -230,10 +230,10 @@ # # -- Helper methods -- # - def _get_tool( self, id, tool_version=None ): + def _get_tool( self, id, tool_version=None, user=None ): id = urllib.unquote_plus( id ) tool = self.app.toolbox.get_tool( id, tool_version ) - if not tool: + if not tool or not tool.allow_user_access( user ): raise exceptions.ObjectNotFound("Could not find tool with id '%s'" % id) return tool @@ -300,7 +300,7 @@ # original_job = self.hda_manager.creating_job( original_dataset ) tool = trans.app.toolbox.get_tool( original_job.tool_id ) - if not tool: + if not tool or not tool.allow_user_access( trans.user ): return trans.app.model.Dataset.conversion_messages.NO_TOOL tool_params = dict( [ ( p.name, p.value ) for p in original_job.parameters ] ) diff -r 8e5b9caba8ff493c25684ebdb6f69b819c34dca6 -r ff3c5721f74857cf689966abfdeb0dc9390bf605 lib/galaxy/webapps/galaxy/controllers/tool_runner.py --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -65,7 +65,7 @@ get_loaded_tools_by_lineage=False, set_selected=refreshed_on_change ) # No tool matching the tool id, display an error (shouldn't happen) - if not tool: + if not tool or not tool.allow_user_access( trans.user ): log.error( "index called with tool id '%s' but no such tool exists", tool_id ) trans.log_event( "Tool id '%s' does not exist" % tool_id ) trans.response.status = 404 @@ -191,6 +191,8 @@ # This is expected so not an exception. tool_id_version_message = '' error( "This dataset was created by an obsolete tool (%s). Can't re-run." % tool_id ) + if not tool.allow_user_access( trans.user ): + error( "The requested tool is unknown." ) # Can't rerun upload, external data sources, et cetera. Workflow compatible will proxy this for now if not tool.is_workflow_compatible: error( "The '%s' tool does not currently support rerunning." % tool.name ) 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: carlfeberhard: Core: error with 403 if user is not logged in *and* there is no session (gen. api call with no api key)
by commits-noreply＠bitbucket.org 03 Feb '15

03 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8e5b9caba8ff/ Changeset: 8e5b9caba8ff User: carlfeberhard Date: 2015-02-02 20:37:34+00:00 Summary: Core: error with 403 if user is not logged in *and* there is no session (gen. api call with no api key) Affected #: 1 file diff -r e56a78608c79097a6227f8c06cba8a45580a2a7d -r 8e5b9caba8ff493c25684ebdb6f69b819c34dca6 lib/galaxy/web/framework/decorators.py --- a/lib/galaxy/web/framework/decorators.py +++ b/lib/galaxy/web/framework/decorators.py @@ -206,7 +206,10 @@ # TODO: Document this branch, when can this happen, # I don't understand it. return __api_error_response( trans, err_msg=trans.error_message ) - if user_required and trans.anonymous: + # error if user required and anon + # error if anon and no session + if ( ( trans.anonymous and user_required ) + or ( trans.anonymous and not trans.galaxy_session ) ): error_code = error_codes.USER_NO_API_KEY # Use error codes default error message. err_msg = "API authentication required for this request" @@ -219,8 +222,10 @@ return __api_error_response( trans, status_code=400, err_code=error_code ) trans.response.set_content_type( JSON_CONTENT_TYPE ) + # send 'do not cache' headers to handle IE's caching of ajax get responses trans.response.headers[ 'Cache-Control' ] = "max-age=0,no-cache,no-store" + # TODO: Refactor next block out into a helper procedure. # Perform api_run_as processing, possibly changing identity if 'payload' in kwargs and 'run_as' in kwargs['payload']: 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: Merged in nsoranzo/galaxy-central (pull request #656)
by commits-noreply＠bitbucket.org 03 Feb '15

03 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e56a78608c79/ Changeset: e56a78608c79 User: dannon Date: 2015-02-02 20:22:32+00:00 Summary: Merged in nsoranzo/galaxy-central (pull request #656) Merge rolling_restart.sh in run.sh by adding --wait parameter. Affected #: 2 files diff -r 8d74daa932a06f7bbd3e357f8216c8f58ae55965 -r e56a78608c79097a6227f8c06cba8a45580a2a7d rolling_restart.sh --- a/rolling_restart.sh +++ b/rolling_restart.sh @@ -2,60 +2,4 @@ cd `dirname $0` -# 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 - -python ./scripts/check_python.py -[ $? -ne 0 ] && exit 1 - -./scripts/common_startup.sh - -if [ -n "$GALAXY_UNIVERSE_CONFIG_DIR" ]; then - python ./scripts/build_universe_config.py "$GALAXY_UNIVERSE_CONFIG_DIR" -fi - -if [ -z "$GALAXY_CONFIG_FILE" ]; then - if [ -f universe_wsgi.ini ]; then - GALAXY_CONFIG_FILE=universe_wsgi.ini - elif [ -f config/galaxy.ini ]; then - GALAXY_CONFIG_FILE=config/galaxy.ini - else - GALAXY_CONFIG_FILE=config/galaxy.ini.sample - fi - export GALAXY_CONFIG_FILE -fi - -servers=`sed -n 's/^\[server:$.*$\]/\1/ p' $GALAXY_CONFIG_FILE | xargs echo` -for server in $servers; do - # If there's a pid - if [ -e $server.pid ]; then - # Then kill it - echo "Killing $server" - pid=`cat $server.pid` - kill $pid - else - # Otherwise just continue - echo "$server not running" - fi - # Start the server (and background) (should this be nohup'd?) - python ./scripts/paster.py serve $GALAXY_CONFIG_FILE --server-name=$server --pid-file=$server.pid --log-file=$server.log --daemon $@ - while true; do - sleep 1 - printf "." - # Grab the current pid from the pid file - if ! current_pid_in_file=$(cat $server.pid); then - echo "A Galaxy process died, interrupting" >&2 - exit 1 - fi - # Search for all pids in the logs and tail for the last one - latest_pid=`egrep '^Starting server in PID [0-9]+\.$' $server.log -o | sed 's/Starting server in PID //g;s/\.$//g' | tail -n 1` - # If they're equivalent, then the current pid file agrees with our logs - # and we've succesfully started - [ -n "$latest_pid" ] && [ $latest_pid -eq $current_pid_in_file ] && break - done - echo -done +GALAXY_RUN_ALL=1 ./run.sh restart --wait diff -r 8d74daa932a06f7bbd3e357f8216c8f58ae55965 -r e56a78608c79097a6227f8c06cba8a45580a2a7d run.sh --- a/run.sh +++ b/run.sh @@ -44,15 +44,38 @@ if [ -n "$GALAXY_RUN_ALL" ]; then servers=`sed -n 's/^\[server:$.*$\]/\1/ p' $GALAXY_CONFIG_FILE | xargs echo` - daemon=`echo "$@" | grep -q daemon` + echo "$@" | grep -q 'daemon\|restart' if [ $? -ne 0 ]; then - echo 'ERROR: $GALAXY_RUN_ALL cannot be used without the `--daemon` or `--stop-daemon` arguments to run.sh' + echo 'ERROR: $GALAXY_RUN_ALL cannot be used without the `--daemon`, `--stop-daemon` or `restart` arguments to run.sh' exit 1 fi + (echo "$@" | grep -q -e '--daemon\|restart') && (echo "$@" | grep -q -e '--wait') + WAIT=$? + ARGS=`echo "$@" | sed 's/--wait//'` for server in $servers; do - echo "Handling $server with log file $server.log..." - python ./scripts/paster.py serve $GALAXY_CONFIG_FILE --server-name=$server --pid-file=$server.pid --log-file=$server.log $@ + if [ $WAIT -eq 0 ]; then + python ./scripts/paster.py serve $GALAXY_CONFIG_FILE --server-name=$server --pid-file=$server.pid --log-file=$server.log $ARGS + while true; do + sleep 1 + printf "." + # Grab the current pid from the pid file + if ! current_pid_in_file=$(cat $server.pid); then + echo "A Galaxy process died, interrupting" >&2 + exit 1 + fi + # Search for all pids in the logs and tail for the last one + latest_pid=`egrep '^Starting server in PID [0-9]+\.$' $server.log -o | sed 's/Starting server in PID //g;s/\.$//g' | tail -n 1` + # If they're equivalent, then the current pid file agrees with our logs + # and we've succesfully started + [ -n "$latest_pid" ] && [ $latest_pid -eq $current_pid_in_file ] && break + done + echo + else + echo "Handling $server with log file $server.log..." + python ./scripts/paster.py serve $GALAXY_CONFIG_FILE --server-name=$server --pid-file=$server.pid --log-file=$server.log $@ + fi done else + # Handle only 1 server, whose name can be specified with --server-name parameter (defaults to "main") python ./scripts/paster.py serve $GALAXY_CONFIG_FILE $@ fi 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: 4 new changesets
by commits-noreply＠bitbucket.org 03 Feb '15

03 Feb '15

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1333f32a5063/ Changeset: 1333f32a5063 User: nsoranzo Date: 2015-02-02 15:46:48+00:00 Summary: Allow "GALAXY_RUN_ALL=1 ./run.sh restart" since --daemon is implied. Affected #: 1 file diff -r 5aca28ab8cfbbc1769f68fcfacf3dfbf9352ccde -r 1333f32a50639a2d2dfaca327b20520da358721c run.sh --- a/run.sh +++ b/run.sh @@ -44,9 +44,9 @@ if [ -n "$GALAXY_RUN_ALL" ]; then servers=`sed -n 's/^\[server:$.*$\]/\1/ p' $GALAXY_CONFIG_FILE | xargs echo` - daemon=`echo "$@" | grep -q daemon` + echo "$@" | grep -q 'daemon\|restart' if [ $? -ne 0 ]; then - echo 'ERROR: $GALAXY_RUN_ALL cannot be used without the `--daemon` or `--stop-daemon` arguments to run.sh' + echo 'ERROR: $GALAXY_RUN_ALL cannot be used without the `--daemon`, `--stop-daemon` or `restart` arguments to run.sh' exit 1 fi for server in $servers; do @@ -54,5 +54,6 @@ python ./scripts/paster.py serve $GALAXY_CONFIG_FILE --server-name=$server --pid-file=$server.pid --log-file=$server.log $@ done else + # Handle only 1 server, whose name can be specified with --server-name parameter (defaults to "main") python ./scripts/paster.py serve $GALAXY_CONFIG_FILE $@ fi https://bitbucket.org/galaxy/galaxy-central/commits/6d11484ceb7d/ Changeset: 6d11484ceb7d User: nsoranzo Date: 2015-02-02 16:08:13+00:00 Summary: Merge rolling_restart.sh in run.sh by adding --wait parameter. Also add the following combination: GALAXY_RUN_ALL=1 ./run.sh --daemon --wait which, by preventing servers from starting simultaneously, is useful when multiple servers are configured before creating the database, or when updating to a new Galaxy release containing a database upgrade. Affected #: 2 files diff -r 1333f32a50639a2d2dfaca327b20520da358721c -r 6d11484ceb7d797f5571df24a147d3f59f8ee553 rolling_restart.sh --- a/rolling_restart.sh +++ b/rolling_restart.sh @@ -1,61 +1,3 @@ #!/bin/sh -cd `dirname $0` - -# 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 - -python ./scripts/check_python.py -[ $? -ne 0 ] && exit 1 - -./scripts/common_startup.sh - -if [ -n "$GALAXY_UNIVERSE_CONFIG_DIR" ]; then - python ./scripts/build_universe_config.py "$GALAXY_UNIVERSE_CONFIG_DIR" -fi - -if [ -z "$GALAXY_CONFIG_FILE" ]; then - if [ -f universe_wsgi.ini ]; then - GALAXY_CONFIG_FILE=universe_wsgi.ini - elif [ -f config/galaxy.ini ]; then - GALAXY_CONFIG_FILE=config/galaxy.ini - else - GALAXY_CONFIG_FILE=config/galaxy.ini.sample - fi - export GALAXY_CONFIG_FILE -fi - -servers=`sed -n 's/^\[server:$.*$\]/\1/ p' $GALAXY_CONFIG_FILE | xargs echo` -for server in $servers; do - # If there's a pid - if [ -e $server.pid ]; then - # Then kill it - echo "Killing $server" - pid=`cat $server.pid` - kill $pid - else - # Otherwise just continue - echo "$server not running" - fi - # Start the server (and background) (should this be nohup'd?) - python ./scripts/paster.py serve $GALAXY_CONFIG_FILE --server-name=$server --pid-file=$server.pid --log-file=$server.log --daemon $@ - while true; do - sleep 1 - printf "." - # Grab the current pid from the pid file - if ! current_pid_in_file=$(cat $server.pid); then - echo "A Galaxy process died, interrupting" >&2 - exit 1 - fi - # Search for all pids in the logs and tail for the last one - latest_pid=`egrep '^Starting server in PID [0-9]+\.$' $server.log -o | sed 's/Starting server in PID //g;s/\.$//g' | tail -n 1` - # If they're equivalent, then the current pid file agrees with our logs - # and we've succesfully started - [ -n "$latest_pid" ] && [ $latest_pid -eq $current_pid_in_file ] && break - done - echo -done +GALAXY_RUN_ALL=1 ./run.sh restart --wait diff -r 1333f32a50639a2d2dfaca327b20520da358721c -r 6d11484ceb7d797f5571df24a147d3f59f8ee553 run.sh --- a/run.sh +++ b/run.sh @@ -49,9 +49,31 @@ echo 'ERROR: $GALAXY_RUN_ALL cannot be used without the `--daemon`, `--stop-daemon` or `restart` arguments to run.sh' exit 1 fi + (echo "$@" | grep -q -e '--daemon\|restart') && (echo "$@" | grep -q -e '--wait') + WAIT=$? + ARGS=`echo "$@" | sed 's/--wait//'` for server in $servers; do - echo "Handling $server with log file $server.log..." - python ./scripts/paster.py serve $GALAXY_CONFIG_FILE --server-name=$server --pid-file=$server.pid --log-file=$server.log $@ + if [ $WAIT -eq 0 ]; then + python ./scripts/paster.py serve $GALAXY_CONFIG_FILE --server-name=$server --pid-file=$server.pid --log-file=$server.log $ARGS + while true; do + sleep 1 + printf "." + # Grab the current pid from the pid file + if ! current_pid_in_file=$(cat $server.pid); then + echo "A Galaxy process died, interrupting" >&2 + exit 1 + fi + # Search for all pids in the logs and tail for the last one + latest_pid=`egrep '^Starting server in PID [0-9]+\.$' $server.log -o | sed 's/Starting server in PID //g;s/\.$//g' | tail -n 1` + # If they're equivalent, then the current pid file agrees with our logs + # and we've succesfully started + [ -n "$latest_pid" ] && [ $latest_pid -eq $current_pid_in_file ] && break + done + echo + else + echo "Handling $server with log file $server.log..." + python ./scripts/paster.py serve $GALAXY_CONFIG_FILE --server-name=$server --pid-file=$server.pid --log-file=$server.log $@ + fi done else # Handle only 1 server, whose name can be specified with --server-name parameter (defaults to "main") https://bitbucket.org/galaxy/galaxy-central/commits/d9c2dce96ec4/ Changeset: d9c2dce96ec4 User: nsoranzo Date: 2015-02-02 17:30:03+00:00 Summary: Restore a line deleted by mistake. Thanks John. Affected #: 1 file diff -r 6d11484ceb7d797f5571df24a147d3f59f8ee553 -r d9c2dce96ec4376816a0bf23b4ba956616b63a48 rolling_restart.sh --- a/rolling_restart.sh +++ b/rolling_restart.sh @@ -1,3 +1,5 @@ #!/bin/sh +cd `dirname $0` + GALAXY_RUN_ALL=1 ./run.sh restart --wait https://bitbucket.org/galaxy/galaxy-central/commits/e56a78608c79/ Changeset: e56a78608c79 User: dannon Date: 2015-02-02 20:22:32+00:00 Summary: Merged in nsoranzo/galaxy-central (pull request #656) Merge rolling_restart.sh in run.sh by adding --wait parameter. Affected #: 2 files diff -r 8d74daa932a06f7bbd3e357f8216c8f58ae55965 -r e56a78608c79097a6227f8c06cba8a45580a2a7d rolling_restart.sh --- a/rolling_restart.sh +++ b/rolling_restart.sh @@ -2,60 +2,4 @@ cd `dirname $0` -# 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 - -python ./scripts/check_python.py -[ $? -ne 0 ] && exit 1 - -./scripts/common_startup.sh - -if [ -n "$GALAXY_UNIVERSE_CONFIG_DIR" ]; then - python ./scripts/build_universe_config.py "$GALAXY_UNIVERSE_CONFIG_DIR" -fi - -if [ -z "$GALAXY_CONFIG_FILE" ]; then - if [ -f universe_wsgi.ini ]; then - GALAXY_CONFIG_FILE=universe_wsgi.ini - elif [ -f config/galaxy.ini ]; then - GALAXY_CONFIG_FILE=config/galaxy.ini - else - GALAXY_CONFIG_FILE=config/galaxy.ini.sample - fi - export GALAXY_CONFIG_FILE -fi - -servers=`sed -n 's/^\[server:$.*$\]/\1/ p' $GALAXY_CONFIG_FILE | xargs echo` -for server in $servers; do - # If there's a pid - if [ -e $server.pid ]; then - # Then kill it - echo "Killing $server" - pid=`cat $server.pid` - kill $pid - else - # Otherwise just continue - echo "$server not running" - fi - # Start the server (and background) (should this be nohup'd?) - python ./scripts/paster.py serve $GALAXY_CONFIG_FILE --server-name=$server --pid-file=$server.pid --log-file=$server.log --daemon $@ - while true; do - sleep 1 - printf "." - # Grab the current pid from the pid file - if ! current_pid_in_file=$(cat $server.pid); then - echo "A Galaxy process died, interrupting" >&2 - exit 1 - fi - # Search for all pids in the logs and tail for the last one - latest_pid=`egrep '^Starting server in PID [0-9]+\.$' $server.log -o | sed 's/Starting server in PID //g;s/\.$//g' | tail -n 1` - # If they're equivalent, then the current pid file agrees with our logs - # and we've succesfully started - [ -n "$latest_pid" ] && [ $latest_pid -eq $current_pid_in_file ] && break - done - echo -done +GALAXY_RUN_ALL=1 ./run.sh restart --wait diff -r 8d74daa932a06f7bbd3e357f8216c8f58ae55965 -r e56a78608c79097a6227f8c06cba8a45580a2a7d run.sh --- a/run.sh +++ b/run.sh @@ -44,15 +44,38 @@ if [ -n "$GALAXY_RUN_ALL" ]; then servers=`sed -n 's/^\[server:$.*$\]/\1/ p' $GALAXY_CONFIG_FILE | xargs echo` - daemon=`echo "$@" | grep -q daemon` + echo "$@" | grep -q 'daemon\|restart' if [ $? -ne 0 ]; then - echo 'ERROR: $GALAXY_RUN_ALL cannot be used without the `--daemon` or `--stop-daemon` arguments to run.sh' + echo 'ERROR: $GALAXY_RUN_ALL cannot be used without the `--daemon`, `--stop-daemon` or `restart` arguments to run.sh' exit 1 fi + (echo "$@" | grep -q -e '--daemon\|restart') && (echo "$@" | grep -q -e '--wait') + WAIT=$? + ARGS=`echo "$@" | sed 's/--wait//'` for server in $servers; do - echo "Handling $server with log file $server.log..." - python ./scripts/paster.py serve $GALAXY_CONFIG_FILE --server-name=$server --pid-file=$server.pid --log-file=$server.log $@ + if [ $WAIT -eq 0 ]; then + python ./scripts/paster.py serve $GALAXY_CONFIG_FILE --server-name=$server --pid-file=$server.pid --log-file=$server.log $ARGS + while true; do + sleep 1 + printf "." + # Grab the current pid from the pid file + if ! current_pid_in_file=$(cat $server.pid); then + echo "A Galaxy process died, interrupting" >&2 + exit 1 + fi + # Search for all pids in the logs and tail for the last one + latest_pid=`egrep '^Starting server in PID [0-9]+\.$' $server.log -o | sed 's/Starting server in PID //g;s/\.$//g' | tail -n 1` + # If they're equivalent, then the current pid file agrees with our logs + # and we've succesfully started + [ -n "$latest_pid" ] && [ $latest_pid -eq $current_pid_in_file ] && break + done + echo + else + echo "Handling $server with log file $server.log..." + python ./scripts/paster.py serve $GALAXY_CONFIG_FILE --server-name=$server --pid-file=$server.pid --log-file=$server.log $@ + fi done else + # Handle only 1 server, whose name can be specified with --server-name parameter (defaults to "main") python ./scripts/paster.py serve $GALAXY_CONFIG_FILE $@ fi Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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galaxy-commits February 2015