October 2012 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: greg: Handle weak Python 2.5 unicode string handling in the tool shed.
by Bitbucket 23 Oct '12

23 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/33db1925e701/ changeset: 33db1925e701 user: greg date: 2012-10-23 22:52:25 summary: Handle weak Python 2.5 unicode string handling in the tool shed. affected #: 2 files diff -r 70ae646e6892e7bb5a05500c99b4cfcc22495a37 -r 33db1925e701664785735160f3738dfde97fc2e6 lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -50,7 +50,7 @@ break if found: break - full_path = os.path.abspath( os.path.join( root, name ) ) + full_path = str( os.path.abspath( os.path.join( root, name ) ) ) tool = self.toolbox.load_tool( full_path ) return generate_tool_guid( repository_clone_url, tool ) def get_proprietary_tool_panel_elems( self, latest_tool_migration_script_number ): diff -r 70ae646e6892e7bb5a05500c99b4cfcc22495a37 -r 33db1925e701664785735160f3738dfde97fc2e6 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -685,7 +685,7 @@ metadata_dict[ 'readme' ] = relative_path_to_readme # See if we have a tool config. elif name not in NOT_TOOL_CONFIGS and name.endswith( '.xml' ): - full_path = os.path.abspath( os.path.join( root, name ) ) + full_path = str( os.path.abspath( os.path.join( root, name ) ) ) if os.path.getsize( full_path ) > 0: if not ( check_binary( full_path ) or check_image( full_path ) or check_gzip( full_path )[ 0 ] or check_bz2( full_path )[ 0 ] or check_zip( full_path ) ): 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: greg: Eliminate the problematic Repository.ReviewedRevisions mapper from the tool shed model.
by Bitbucket 23 Oct '12

23 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/70ae646e6892/ changeset: 70ae646e6892 user: greg date: 2012-10-23 22:20:05 summary: Eliminate the problematic Repository.ReviewedRevisions mapper from the tool shed model. affected #: 3 files diff -r d6ce5e2a1cdb8645f3490043b151f2b271f4b2b4 -r 70ae646e6892e7bb5a05500c99b4cfcc22495a37 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -156,11 +156,9 @@ def changeset_revision_reviewed_by_user( trans, user, repository, changeset_revision ): """Determine if the current changeset revision has been reviewed by the current user.""" changeset_revision_reviewed_by_user = False - for reviewed_revision in repository.reviewed_revisions: - if reviewed_revision.changeset_revision == changeset_revision: - for review in repository.reviews: - if review.changeset_revision == changeset_revision and review.user == user: - return True + for review in repository.reviews: + if review.changeset_revision == changeset_revision and review.user == user: + return True return False def check_file_contents( trans ): # See if any admin users have chosen to receive email alerts when a repository is updated. @@ -505,13 +503,15 @@ def get_previous_repository_reviews( trans, repository, changeset_revision ): """Return an ordered dictionary of repository reviews up to and including the received changeset revision.""" repo = hg.repository( get_configured_ui(), repository.repo_path ) - reviewed_revision_hashes = [ reviewed_revisions.changeset_revision for reviewed_revisions in repository.reviewed_revisions ] + reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ] previous_reviews_dict = odict() for changeset in reversed_upper_bounded_changelog( repo, changeset_revision ): previous_changeset_revision = str( repo.changectx( changeset ) ) if previous_changeset_revision in reviewed_revision_hashes: previous_rev, previous_changeset_revision_label = get_rev_label_from_changeset_revision( repo, previous_changeset_revision ) - revision_reviews = get_reviews_by_repository_id_changeset_revision( trans, trans.security.encode_id( repository.id ), previous_changeset_revision ) + revision_reviews = get_reviews_by_repository_id_changeset_revision( trans, + trans.security.encode_id( repository.id ), + previous_changeset_revision ) previous_reviews_dict[ previous_changeset_revision ] = dict( changeset_revision_label=previous_changeset_revision_label, reviews=revision_reviews ) return previous_reviews_dict @@ -701,7 +701,7 @@ def has_previous_repository_reviews( trans, repository, changeset_revision ): """Determine if a repository has a changeset revision review prior to the received changeset revision.""" repo = hg.repository( get_configured_ui(), repository.repo_path ) - reviewed_revision_hashes = [ reviewed_revisions.changeset_revision for reviewed_revisions in repository.reviewed_revisions ] + reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ] for changeset in reversed_upper_bounded_changelog( repo, changeset_revision ): previous_changeset_revision = str( repo.changectx( changeset ) ) if previous_changeset_revision in reviewed_revision_hashes: diff -r d6ce5e2a1cdb8645f3490043b151f2b271f4b2b4 -r 70ae646e6892e7bb5a05500c99b4cfcc22495a37 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1530,7 +1530,7 @@ if current_user: # See if the current user owns any repositories that have been reviewed. for repository in current_user.active_repositories: - if repository.reviewed_revisions: + if repository.reviews: has_reviewed_repositories = True break # See if the current user has any repositories that have been marked as deprecated. diff -r d6ce5e2a1cdb8645f3490043b151f2b271f4b2b4 -r 70ae646e6892e7bb5a05500c99b4cfcc22495a37 lib/galaxy/webapps/community/model/mapping.py --- a/lib/galaxy/webapps/community/model/mapping.py +++ b/lib/galaxy/webapps/community/model/mapping.py @@ -239,12 +239,7 @@ reviewers=relation( User, secondary=RepositoryReview.table, primaryjoin=( Repository.table.c.id == RepositoryReview.table.c.repository_id ), - secondaryjoin=( RepositoryReview.table.c.user_id == User.table.c.id ) ), - reviewed_revisions=relation( RepositoryMetadata, - secondary=RepositoryReview.table, - foreign_keys=[ RepositoryMetadata.table.c.repository_id, RepositoryMetadata.table.c.changeset_revision ], - primaryjoin=( Repository.table.c.id == RepositoryMetadata.table.c.repository_id ), - secondaryjoin=( ( RepositoryMetadata.table.c.repository_id == RepositoryReview.table.c.repository_id ) & ( RepositoryMetadata.table.c.changeset_revision == RepositoryReview.table.c.changeset_revision ) ) ) ) ) + secondaryjoin=( RepositoryReview.table.c.user_id == User.table.c.id ) ) ) ) assign_mapper( context, RepositoryMetadata, RepositoryMetadata.table, properties=dict( repository=relation( Repository ), Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Circster, enhancements for chords: (a) adjust chords when datasets added/removed from visualization; (b) use config to color; and (c) enable dynamic addition of chord/interaction datasets.
by Bitbucket 23 Oct '12

23 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d6ce5e2a1cdb/ changeset: d6ce5e2a1cdb user: jgoecks date: 2012-10-23 21:41:48 summary: Circster, enhancements for chords: (a) adjust chords when datasets added/removed from visualization; (b) use config to color; and (c) enable dynamic addition of chord/interaction datasets. affected #: 3 files diff -r f23c2b0ef005f1e44299d11fd8fbe5077fe850f0 -r d6ce5e2a1cdb8645f3490043b151f2b271f4b2b4 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -19,6 +19,7 @@ from paste.httpexceptions import * from galaxy.exceptions import * from galaxy.model import NoConverterException, ConverterDependencyException +from galaxy.datatypes.interval import ChromatinInteractions from Cheetah.Template import Template @@ -602,7 +603,7 @@ return visualization - def _get_genome_data( self, trans, dataset, dbkey=None, source='index' ): + def _get_genome_data( self, trans, dataset, dbkey=None ): """ Returns genome-wide data for dataset if available; if not, message is returned. """ @@ -621,6 +622,11 @@ if message: rval = message else: + # HACK: chromatin interactions tracks use data as source. + source = 'index' + if isinstance( dataset.datatype, ChromatinInteractions ): + source = 'data' + data_provider = trans.app.data_provider_registry.get_data_provider( trans, original_dataset=dataset, source=source ) diff -r f23c2b0ef005f1e44299d11fd8fbe5077fe850f0 -r d6ce5e2a1cdb8645f3490043b151f2b271f4b2b4 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -8,7 +8,6 @@ from galaxy.visualization.genomes import decode_dbkey from galaxy.visualization.genome.visual_analytics import get_dataset_job from galaxy.visualization.data_providers.phyloviz import PhylovizDataProvider -from galaxy.datatypes.interval import ChromatinInteractions from .library import LibraryListGrid @@ -753,12 +752,8 @@ tracks = viz_config.get( 'tracks', [] ) for track in tracks: dataset = self.get_hda_or_ldda( trans, track[ 'hda_ldda'], track[ 'dataset_id' ] ) - # HACK: chromatin interactions tracks use data as source. - source = 'index' - if isinstance( dataset.datatype, ChromatinInteractions ): - source = 'data' - genome_data = self._get_genome_data( trans, dataset, dbkey, source=source ) + genome_data = self._get_genome_data( trans, dataset, dbkey ) if not isinstance( genome_data, str ): track[ 'preloaded_data' ] = genome_data diff -r f23c2b0ef005f1e44299d11fd8fbe5077fe850f0 -r d6ce5e2a1cdb8645f3490043b151f2b271f4b2b4 static/scripts/viz/circster.js --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -200,31 +200,53 @@ * Render a single track on the outside of the current visualization. */ add_track: function(new_track) { - // Recompute and update track bounds. - var new_track_bounds = this.get_tracks_bounds(); - _.each(this.circular_views, function(track_view, i) { - track_view.update_radius_bounds(new_track_bounds[i]); - }); + if (new_track.get('track_type') === 'DiagonalHeatmapTrack') { + // Added chords track. + var innermost_radius_bounds = this.circular_views[0].radius_bounds, + new_view = new CircsterChromInteractionsTrackView({ + el: d3.select('g.tracks').append('g')[0], + track: new_track, + radius_bounds: innermost_radius_bounds, + genome: this.genome, + total_gap: this.total_gap + }); + new_view.render(); + this.chords_views.push(new_view); + } + else { + // Added circular track. - // Render new track. - var track_index = this.circular_views.length, - track_view_class = (new_track.get('track_type') === 'LineTrack' ? - CircsterBigWigTrackView : - CircsterSummaryTreeTrackView ), - track_view = new track_view_class({ - el: d3.select('g.tracks').append('g')[0], - track: new_track, - radius_bounds: new_track_bounds[track_index], - genome: this.genome, - total_gap: this.total_gap + // Recompute and update track bounds. + var new_track_bounds = this.get_tracks_bounds(); + _.each(this.circular_views, function(track_view, i) { + track_view.update_radius_bounds(new_track_bounds[i]); }); - track_view.render(); - this.circular_views.push(track_view); - // Update label track. - var track_bounds = new_track_bounds[ new_track_bounds.length-1 ]; - track_bounds[1] = track_bounds[0]; - this.label_track_view.update_radius_bounds(track_bounds); + // Update chords tracks. + _.each(this.chords_views, function(track_view) { + track_view.update_radius_bounds(new_track_bounds[0]); + }); + + // Render new track. + var track_index = this.circular_views.length, + track_view_class = (new_track.get('track_type') === 'LineTrack' ? + CircsterBigWigTrackView : + CircsterSummaryTreeTrackView ), + track_view = new track_view_class({ + el: d3.select('g.tracks').append('g')[0], + track: new_track, + radius_bounds: new_track_bounds[track_index], + genome: this.genome, + total_gap: this.total_gap + }); + track_view.render(); + this.circular_views.push(track_view); + + // Update label track. + var track_bounds = new_track_bounds[ new_track_bounds.length-1 ]; + track_bounds[1] = track_bounds[0]; + this.label_track_view.update_radius_bounds(track_bounds); + } }, /** @@ -269,6 +291,15 @@ }, /** + * Get fill color from config. + */ + get_fill_color: function() { + var color = this.track.get('config').get_value('block_color'); + if (!color) { color = this.track.get('config').get_value('color'); } + return color; + }, + + /** * Render track's data by adding SVG elements to parent. */ render: function() { @@ -382,10 +413,8 @@ }); // Add new data path and apply preferences. - var prefs = self.track.get('prefs'), - block_color = prefs.block_color; - if (!block_color) { block_color = prefs.color; } - self._render_chrom_data(self.parent_elt, chrom_arc, data).style('stroke', block_color).style('fill', block_color); + var color = self.get_fill_color(); + self._render_chrom_data(self.parent_elt, chrom_arc, data).style('stroke', color).style('fill', color); }); }); @@ -463,10 +492,8 @@ }); // Apply prefs to all track data. - var config = track.get('config'), - block_color = config.get_value('block_color'); - if (!block_color) { block_color = config.get_value('color'); } - self.parent_elt.selectAll('path.chrom-data').style('stroke', block_color).style('fill', block_color); + var color = self.get_fill_color(); + self.parent_elt.selectAll('path.chrom-data').style('stroke', color).style('fill', color); rendered_deferred.resolve(svg); }); @@ -653,7 +680,7 @@ // When data is ready, render track. $.when(self.track.get('data_manager').data_is_ready()).then(function() { - // Convert genome-wide data in chord data. + // When data has been fetched, render track. $.when(self.track.get('data_manager').get_genome_wide_data(self.genome)).then(function(genome_wide_data) { var chord_data = [], chroms_info = self.genome.get_chroms_info(); @@ -685,13 +712,18 @@ .selectAll("path") .data(chord_data) .enter().append("path") - .style("fill", '000') + .style("fill", self.get_fill_color()) .attr("d", d3.svg.chord().radius(self.radius_bounds[0])) .style("opacity", 1); }); }); }, + update_radius_bounds: function(radius_bounds) { + this.radius_bounds = radius_bounds; + this.parent_elt.selectAll("path").transition().attr("d", d3.svg.chord().radius(this.radius_bounds[0])); + }, + /** * Returns radians for a genomic position. */ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Clarify the various url protocols that are supported by the tool shed repository upload component.
by Bitbucket 23 Oct '12

23 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f23c2b0ef005/ changeset: f23c2b0ef005 user: greg date: 2012-10-23 21:23:51 summary: Clarify the various url protocols that are supported by the tool shed repository upload component. affected #: 1 file diff -r bad5602cdf998dff9c2aecf478dc4ed1a797a023 -r f23c2b0ef005f1e44299d11fd8fbe5077fe850f0 templates/webapps/community/repository/upload.mako --- a/templates/webapps/community/repository/upload.mako +++ b/templates/webapps/community/repository/upload.mako @@ -85,10 +85,10 @@ <input name="url" type="textfield" value="${url | h}" size="40"/></div><div class="toolParamHelp" style="clear: both;"> - Enter a URL to upload your files via http. URLs that point to mercurial repositories (URLs that start with hg:// or hgs://) - are allowed. This mechanism results in the tip revision of an external mercurial repository being added to the tool shed - repository as a single new changeset. The revision history of the originating external mercurial repository is not uploaded - to the tool shed repository. + Enter a url to upload your files. In addition to http and ftp urls, urls that point to mercurial repositories (urls that start + with hg:// or hgs://) are allowed. This mechanism results in the tip revision of an external mercurial repository being added + to the tool shed repository as a single new changeset. The revision history of the originating external mercurial repository is + not uploaded to the tool shed repository. </div><div style="clear: both"></div></div> 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: greg: Add help text to the tool shed repository upload form to advertise John Chilton's recent enhancement allowing for mercurial repository urls staring with hg:// or hgs://.
by Bitbucket 23 Oct '12

23 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/bad5602cdf99/ changeset: bad5602cdf99 user: greg date: 2012-10-23 20:59:31 summary: Add help text to the tool shed repository upload form to advertise John Chilton's recent enhancement allowing for mercurial repository urls staring with hg:// or hgs://. affected #: 2 files diff -r 5ae989999225b9edf884de6dfe23a2e82f9de403 -r bad5602cdf998dff9c2aecf478dc4ed1a797a023 lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -48,13 +48,12 @@ message = 'No files were entered on the upload form.' status = 'error' uploaded_file = None - elif url and url.startswith("hg"): - # Use mercurial clone to fetch repository, contents will then - # be copied over. + elif url and url.startswith( 'hg' ): + # Use mercurial clone to fetch repository, contents will then be copied over. uploaded_directory = tempfile.mkdtemp() - repo_url = "http%s" % url[len("hg"):] - repo_url = repo_url.encode('ascii', 'replace') - commands.clone(get_configured_ui(), repo_url, uploaded_directory) + repo_url = 'http%s' % url[ len( 'hg' ): ] + repo_url = repo_url.encode( 'ascii', 'replace' ) + commands.clone( get_configured_ui(), repo_url, uploaded_directory ) elif url: valid_url = True try: diff -r 5ae989999225b9edf884de6dfe23a2e82f9de403 -r bad5602cdf998dff9c2aecf478dc4ed1a797a023 templates/webapps/community/repository/upload.mako --- a/templates/webapps/community/repository/upload.mako +++ b/templates/webapps/community/repository/upload.mako @@ -85,7 +85,10 @@ <input name="url" type="textfield" value="${url | h}" size="40"/></div><div class="toolParamHelp" style="clear: both;"> - Enter a URL to upload your files via http. + Enter a URL to upload your files via http. URLs that point to mercurial repositories (URLs that start with hg:// or hgs://) + are allowed. This mechanism results in the tip revision of an external mercurial repository being added to the tool shed + repository as a single new changeset. The revision history of the originating external mercurial repository is not uploaded + to the tool shed repository. </div><div style="clear: both"></div></div> 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: greg: Fix for managing tool shed repository reviews.
by Bitbucket 23 Oct '12

23 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5ae989999225/ changeset: 5ae989999225 user: greg date: 2012-10-23 20:38:38 summary: Fix for managing tool shed repository reviews. affected #: 1 file diff -r 1d8578333bd37d7fd84f276d115f414bbde0b607 -r 5ae989999225b9edf884de6dfe23a2e82f9de403 lib/galaxy/webapps/community/controllers/repository_review.py --- a/lib/galaxy/webapps/community/controllers/repository_review.py +++ b/lib/galaxy/webapps/community/controllers/repository_review.py @@ -654,7 +654,7 @@ repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) metadata_revision_hashes = [ metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions ] - reviewed_revision_hashes = [ reviewed_revisions.changeset_revision for reviewed_revisions in repository.reviewed_revisions ] + reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ] reviews_dict = odict() for changeset in get_reversed_changelog_changesets( repo ): ctx = repo.changectx( changeset ) @@ -667,7 +667,10 @@ # Determine if the current user can add a review to this revision. can_add_review = trans.user not in [ repository_review.user for repository_review in repository_reviews ] repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) - repository_metadata_reviews = util.listify( repository_metadata.reviews ) + if repository_metadata: + repository_metadata_reviews = util.listify( repository_metadata.reviews ) + else: + repository_metadata_reviews = [] else: repository_reviews = [] repository_metadata_reviews = [] 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: greg: Fix for RepositoriesWithReviewsGrid columns.
by Bitbucket 23 Oct '12

23 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1d8578333bd3/ changeset: 1d8578333bd3 user: greg date: 2012-10-23 19:43:08 summary: Fix for RepositoriesWithReviewsGrid columns. affected #: 2 files diff -r 7a0c93ca036bcd7a8ed33ed15dec95205974f46e -r 1d8578333bd37d7fd84f276d115f414bbde0b607 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -120,20 +120,6 @@ elif len( select_field.options ) == 1: return select_field.options[ 0 ][ 0 ] return '' - class WithoutReviewsRevisionColumn( grids.GridColumn ): - def __init__( self, col_name ): - grids.GridColumn.__init__( self, col_name ) - def get_value( self, trans, grid, repository ): - # Restrict the options to revisions that have not yet been reviewed. - repository_metadata_revisions = get_repository_metadata_revisions_for_review( repository, reviewed=False ) - if repository_metadata_revisions: - rval = '' - for repository_metadata in repository_metadata_revisions: - rev, label, changeset_revision = get_rev_label_changeset_revision_from_repository_metadata( repository_metadata, repository=repository ) - rval += '<a href="manage_repository_reviews_of_revision' - rval += '?id=%s&changeset_revision=%s">%s</a><br/>' % ( trans.security.encode_id( repository.id ), changeset_revision, label ) - return rval - return '' class TipRevisionColumn( grids.GridColumn ): def __init__( self, col_name ): grids.GridColumn.__init__( self, col_name ) diff -r 7a0c93ca036bcd7a8ed33ed15dec95205974f46e -r 1d8578333bd37d7fd84f276d115f414bbde0b607 lib/galaxy/webapps/community/controllers/repository_review.py --- a/lib/galaxy/webapps/community/controllers/repository_review.py +++ b/lib/galaxy/webapps/community/controllers/repository_review.py @@ -51,8 +51,6 @@ class RepositoriesWithReviewsGrid( RepositoryGrid ): # This grid filters out repositories that have been marked as deprecated. class WithReviewsRevisionColumn( grids.GridColumn ): - def __init__( self, col_name ): - grids.GridColumn.__init__( self, col_name ) def get_value( self, trans, grid, repository ): # Restrict to revisions that have been reviewed. if repository.reviews: @@ -65,6 +63,18 @@ rval += '?id=%s&changeset_revision=%s">%s</a><br/>' % ( trans.security.encode_id( repository.id ), changeset_revision, label ) return rval return '' + class WithoutReviewsRevisionColumn( grids.GridColumn ): + def get_value( self, trans, grid, repository ): + # Restrict the options to revisions that have not yet been reviewed. + repository_metadata_revisions = get_repository_metadata_revisions_for_review( repository, reviewed=False ) + if repository_metadata_revisions: + rval = '' + for repository_metadata in repository_metadata_revisions: + rev, label, changeset_revision = get_rev_label_changeset_revision_from_repository_metadata( repository_metadata, repository=repository ) + rval += '<a href="manage_repository_reviews_of_revision' + rval += '?id=%s&changeset_revision=%s">%s</a><br/>' % ( trans.security.encode_id( repository.id ), changeset_revision, label ) + return rval + return '' class ReviewersColumn( grids.TextColumn ): def get_value( self, trans, grid, repository ): rval = '' @@ -84,7 +94,7 @@ link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=True ), WithReviewsRevisionColumn( "Reviewed revisions" ), - RepositoryGrid.WithoutReviewsRevisionColumn( "Revisions for review" ), + WithoutReviewsRevisionColumn( "Revisions for review" ), RepositoryGrid.UserColumn( "Owner", attach_popup=False ), ReviewersColumn( "Reviewers", attach_popup=False ) ] 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: greg: Alllow non-admin users to see metadata revisions when viewing a repository changelog in the tool shed.
by Bitbucket 23 Oct '12

23 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7a0c93ca036b/ changeset: 7a0c93ca036b user: greg date: 2012-10-23 19:38:34 summary: Alllow non-admin users to see metadata revisions when viewing a repository changelog in the tool shed. affected #: 1 file diff -r 26017976e4e9d5de317e0b1ef29423effdbe5e24 -r 7a0c93ca036bcd7a8ed33ed15dec95205974f46e templates/webapps/community/repository/view_changelog.mako --- a/templates/webapps/community/repository/view_changelog.mako +++ b/templates/webapps/community/repository/view_changelog.mako @@ -114,14 +114,14 @@ has_metadata_str = '<table border="0"><tr><td bgcolor="#D8D8D8">Repository metadata is associated with this change set.</td></tr></table>' else: has_metadata_str = '' + display_date = changeset[ 'display_date' ] %> - <% display_date = changeset[ 'display_date' ] %> %if test_date != display_date: <tr colspan="2"><td bgcolor="#D8D8D8">${display_date}</td></tr> %endif <tr><td> - %if is_admin and has_metadata_str: + %if has_metadata_str: <div class="form-row"> ${has_metadata_str} </div> 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 Bitbucket 23 Oct '12

23 Oct '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/283776e0ad29/ changeset: 283776e0ad29 user: jgoecks date: 2012-10-23 19:30:26 summary: Make DiagonalHeatMapTrack compatible with recent refactoring. affected #: 1 file diff -r 6b0cc1c4f105f9562066bcbad46ed00858e9372a -r 283776e0ad29cd9638d5be726fe051d985922c48 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -3686,17 +3686,14 @@ /** * Draw LineTrack tile. */ - draw_tile: function(result, ctx, mode, resolution, tile_index, w_scale) { + draw_tile: function(result, ctx, mode, resolution, region, w_scale) { // Paint onto canvas. var canvas = ctx.canvas, - tile_bounds = this._get_tile_bounds(tile_index, resolution), - tile_low = tile_bounds[0], - tile_high = tile_bounds[1], - painter = new painters.DiagonalHeatmapPainter(result.data, tile_low, tile_high, this.prefs, mode); + painter = new painters.DiagonalHeatmapPainter(result.data, region.get('start'), region.get('end'), this.prefs, mode); painter.draw(ctx, canvas.width, canvas.height, w_scale); - return new Tile(this, tile_index, resolution, canvas, result.data); + return new Tile(this, region, resolution, canvas, result.data); } }); https://bitbucket.org/galaxy/galaxy-central/changeset/26017976e4e9/ changeset: 26017976e4e9 user: jgoecks date: 2012-10-23 19:30:56 summary: Automated Merge affected #: 3 files diff -r 283776e0ad29cd9638d5be726fe051d985922c48 -r 26017976e4e9d5de317e0b1ef29423effdbe5e24 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -20,6 +20,8 @@ from galaxy import eggs eggs.require('mercurial') from mercurial import hg, ui, patch, commands +eggs.require('markupsafe') +from markupsafe import escape as escape_html log = logging.getLogger( __name__ ) @@ -105,7 +107,7 @@ class RepositoryGrid( grids.Grid ): class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, repository ): - return repository.name + return escape_html( repository.name ) class MetadataRevisionColumn( grids.GridColumn ): def __init__( self, col_name ): grids.GridColumn.__init__( self, col_name ) @@ -137,10 +139,10 @@ grids.GridColumn.__init__( self, col_name ) def get_value( self, trans, grid, repository ): """Display the repository tip revision label.""" - return repository.revision + return escape_html( repository.revision ) class DescriptionColumn( grids.TextColumn ): def get_value( self, trans, grid, repository ): - return repository.description + return escape_html( repository.description ) class CategoryColumn( grids.TextColumn ): def get_value( self, trans, grid, repository ): rval = '<ul>' @@ -161,7 +163,7 @@ class UserColumn( grids.TextColumn ): def get_value( self, trans, grid, repository ): if repository.user: - return repository.user.username + return escape_html( repository.user.username ) return 'no user' class EmailColumn( grids.TextColumn ): def filter( self, trans, user, query, column_filter ): diff -r 283776e0ad29cd9638d5be726fe051d985922c48 -r 26017976e4e9d5de317e0b1ef29423effdbe5e24 templates/webapps/community/common/common.mako --- a/templates/webapps/community/common/common.mako +++ b/templates/webapps/community/common/common.mako @@ -1,5 +1,7 @@ <%def name="escape_html_add_breaks( value )"><% + from galaxy import eggs + eggs.require('markupsafe') import markupsafe value = str( markupsafe.escape( value ) ).replace( '\n', '<br/>' ) %> diff -r 283776e0ad29cd9638d5be726fe051d985922c48 -r 26017976e4e9d5de317e0b1ef29423effdbe5e24 test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -746,9 +746,9 @@ temp_local = tempfile.NamedTemporaryFile( suffix='.sam', prefix='local_bam_converted_to_sam_' ) fd, temp_temp = tempfile.mkstemp( suffix='.sam', prefix='history_bam_converted_to_sam_' ) os.close( fd ) - p = subprocess.Popen( args="samtools view -h %s -o %s" % ( local_name, temp_local.name ), shell=True ) + p = subprocess.Popen( args='samtools view -h -o "%s" "%s"' % ( temp_local.name, local_name ), shell=True ) assert not p.wait(), 'Converting local (test-data) bam to sam failed' - p = subprocess.Popen( args="samtools view -h %s -o %s" % ( temp_name, temp_temp ), shell=True ) + p = subprocess.Popen( args='samtools view -h -o "%s" "%s"' % ( temp_temp, temp_name ), shell=True ) assert not p.wait(), 'Converting history bam to sam failed' os.remove( temp_name ) return temp_local, temp_temp 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: dan: Tweak for functional tests of BAM outputs on Macs.
by Bitbucket 23 Oct '12

23 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/72484a95b873/ changeset: 72484a95b873 user: dan date: 2012-10-23 18:28:22 summary: Tweak for functional tests of BAM outputs on Macs. affected #: 1 file diff -r 8f82e2c36ec3da564aa0cdc507adad19e295b317 -r 72484a95b8732bf391ded562d9c26f4b61f51b43 test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -746,9 +746,9 @@ temp_local = tempfile.NamedTemporaryFile( suffix='.sam', prefix='local_bam_converted_to_sam_' ) fd, temp_temp = tempfile.mkstemp( suffix='.sam', prefix='history_bam_converted_to_sam_' ) os.close( fd ) - p = subprocess.Popen( args="samtools view -h %s -o %s" % ( local_name, temp_local.name ), shell=True ) + p = subprocess.Popen( args='samtools view -h -o "%s" "%s"' % ( temp_local.name, local_name ), shell=True ) assert not p.wait(), 'Converting local (test-data) bam to sam failed' - p = subprocess.Popen( args="samtools view -h %s -o %s" % ( temp_name, temp_temp ), shell=True ) + p = subprocess.Popen( args='samtools view -h -o "%s" "%s"' % ( temp_temp, temp_name ), shell=True ) assert not p.wait(), 'Converting history bam to sam failed' os.remove( temp_name ) return temp_local, temp_temp 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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