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commit/galaxy-central: jgoecks: Trackster documentation.
by Bitbucket 22 Jul '11

22 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4e6d4f51bff9/ changeset: 4e6d4f51bff9 user: jgoecks date: 2011-07-22 16:15:37 summary: Trackster documentation. affected #: 2 files (100 bytes) --- a/lib/galaxy/web/controllers/tracks.py Fri Jul 22 10:03:41 2011 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Fri Jul 22 10:15:37 2011 -0400 @@ -90,7 +90,7 @@ class DbKeyColumn( grids.GridColumn ): """ Column for filtering by and displaying dataset dbkey. """ def filter( self, trans, user, query, dbkey ): - """ Filter by dbkey. """ + """ Filter by dbkey; datasets without a dbkey are returned as well. """ # use raw SQL b/c metadata is a BLOB dbkey = dbkey.replace("'", "\\'") return query.filter( or_( \ --- a/static/scripts/trackster.js Fri Jul 22 10:03:41 2011 -0400 +++ b/static/scripts/trackster.js Fri Jul 22 10:15:37 2011 -0400 @@ -825,6 +825,9 @@ label_track.view = this; this.label_tracks.push(label_track); }, + /** + * Remove a track from the view. + */ remove_track: function(track) { this.has_changes = true; delete this.tracks[this.tracks.indexOf(track)]; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: enable datasets without a set dbkey to be added to a visualization.
by Bitbucket 22 Jul '11

22 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/e35c7bb3f7ed/ changeset: e35c7bb3f7ed user: jgoecks date: 2011-07-22 16:03:41 summary: Trackster: enable datasets without a set dbkey to be added to a visualization. affected #: 3 files (275 bytes) --- a/lib/galaxy/web/controllers/tracks.py Thu Jul 21 16:19:52 2011 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Fri Jul 22 10:03:41 2011 -0400 @@ -93,7 +93,11 @@ """ Filter by dbkey. """ # use raw SQL b/c metadata is a BLOB dbkey = dbkey.replace("'", "\\'") - return query.filter( or_( "metadata like '%%\"dbkey\": [\"%s\"]%%'" % dbkey, "metadata like '%%\"dbkey\": \"%s\"%%'" % dbkey ) ) + return query.filter( or_( \ + or_( "metadata like '%%\"dbkey\": [\"%s\"]%%'" % dbkey, "metadata like '%%\"dbkey\": \"%s\"%%'" % dbkey ), \ + or_( "metadata like '%%\"dbkey\": [\"?\"]%%'", "metadata like '%%\"dbkey\": \"?\"%%'" ) \ + ) + ) class HistoryColumn( grids.GridColumn ): """ Column for filtering by history id. """ --- a/static/scripts/trackster.js Thu Jul 21 16:19:52 2011 -0400 +++ b/static/scripts/trackster.js Fri Jul 22 10:03:41 2011 -0400 @@ -807,6 +807,9 @@ } view.redraw(); }, + /** + * Add a track to the view. + */ add_track: function(track) { track.view = this; track.track_id = this.track_id_counter; --- a/templates/tracks/browser.mako Thu Jul 21 16:19:52 2011 -0400 +++ b/templates/tracks/browser.mako Fri Jul 22 10:03:41 2011 -0400 @@ -273,7 +273,7 @@ } // Add track. - tracks.push( { + tracks.push({ "track_type": track.get_type(), "name": track.name, "hda_ldda": track.hda_ldda, 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 the ability to view all stored metadata for each tool in a tool shed repository, as well as some tool attributes that are not stored as metadata (e.g., tool.command, etc ).
by Bitbucket 21 Jul '11

21 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/7702f72354f2/ changeset: 7702f72354f2 user: greg date: 2011-07-21 22:19:52 summary: Add the ability to view all stored metadata for each tool in a tool shed repository, as well as some tool attributes that are not stored as metadata (e.g., tool.command, etc ). affected #: 4 files (3.3 KB) --- a/lib/galaxy/webapps/community/controllers/repository.py Thu Jul 21 14:37:25 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Thu Jul 21 16:19:52 2011 -0400 @@ -935,14 +935,22 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) repository = get_repository( trans, repository_id ) - tool = load_tool( trans, os.path.abspath( tool_config ) ) - tool_state = self.__new_state( trans ) - return trans.fill_template( "/webapps/community/repository/tool_form.mako", - repository=repository, - tool=tool, - tool_state=tool_state, - message=message, - status=status ) + try: + tool = load_tool( trans, os.path.abspath( tool_config ) ) + tool_state = self.__new_state( trans ) + return trans.fill_template( "/webapps/community/repository/tool_form.mako", + repository=repository, + tool=tool, + tool_state=tool_state, + message=message, + status=status ) + except Exception, e: + message = 'Error loading tool: %s. Click <b>Reset metadata</b> to correct this error.' % str( e ) + return trans.response.send_redirect( web.url_for( controller='repository', + action='manage_repository', + id=repository_id, + message=message, + status='error' ) ) def __new_state( self, trans, all_pages=False ): """ Create a new `DefaultToolState` for this tool. It will not be initialized @@ -955,6 +963,27 @@ state.inputs = {} return state @web.expose + def view_tool_metadata( self, trans, repository_id, changeset_revision, tool_id, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + repository = get_repository( trans, repository_id ) + metadata = {} + tool = None + repository_metadata = get_repository_metadata( trans, repository_id, changeset_revision ).metadata + if 'tools' in repository_metadata: + for tool_metadata_dict in repository_metadata[ 'tools' ]: + if tool_metadata_dict[ 'id' ] == tool_id: + metadata = tool_metadata_dict + tool = load_tool( trans, os.path.abspath( metadata[ 'tool_config' ] ) ) + break + return trans.fill_template( "/webapps/community/repository/view_tool_metadata.mako", + repository=repository, + tool=tool, + metadata=metadata, + message=message, + status=status ) + @web.expose def download( self, trans, repository_id, file_type, **kwd ): # Download an archive of the repository files compressed as zip, gz or bz2. params = util.Params( kwd ) --- a/templates/webapps/community/repository/manage_repository.mako Thu Jul 21 14:37:25 2011 -0400 +++ b/templates/webapps/community/repository/manage_repository.mako Thu Jul 21 16:19:52 2011 -0400 @@ -120,7 +120,7 @@ <div style="clear: both"></div></div><div class="form-row"> - <label>Version:</label> + <label>Revision:</label> %if can_view_change_log: <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${repository.revision}</a> %else: @@ -151,34 +151,6 @@ </form></div></div> -<p/> -<div class="toolForm"> - <div class="toolFormTitle">Manage categories</div> - <div class="toolFormBody"> - <form name="categories" id="categories" action="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ) )}" method="post" > - <div class="form-row"> - <label>Categories</label> - <select name="category_id" multiple> - %for category in categories: - %if category.id in selected_categories: - <option value="${trans.security.encode_id( category.id )}" selected>${category.name}</option> - %else: - <option value="${trans.security.encode_id( category.id )}">${category.name}</option> - %endif - %endfor - </select> - <div class="toolParamHelp" style="clear: both;"> - Multi-select list - hold the appropriate key while clicking to select multiple categories. - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <input type="submit" name="manage_categories_button" value="Save"/> - </div> - </form> - </div> -</div> -<p/> %if can_set_metadata: <p/><div class="toolForm"> @@ -204,7 +176,16 @@ </tr> %for tool_dict in tool_dicts: <tr> - <td><a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ] )}">${tool_dict[ 'name' ]}</a></td> + <td> + <div style="float: left; margin-left: 1px;" class="menubutton split popup" id="tool-${tool_dict[ 'id' ]}-popup"> + <a class="view-info" href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ] )}"> + ${tool_dict[ 'name' ]} + </a> + </div> + <div popupmenu="tool-${tool_dict[ 'id' ]}-popup"> + <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip, tool_id=tool_dict[ 'id' ] )}">View all metadata for this tool</a> + </div> + </td><td>${tool_dict[ 'description' ]}</td><td>${tool_dict[ 'version' ]}</td><td> @@ -274,6 +255,33 @@ </div></div> %endif +<p/> +<div class="toolForm"> + <div class="toolFormTitle">Manage categories</div> + <div class="toolFormBody"> + <form name="categories" id="categories" action="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ) )}" method="post" > + <div class="form-row"> + <label>Categories</label> + <select name="category_id" multiple> + %for category in categories: + %if category.id in selected_categories: + <option value="${trans.security.encode_id( category.id )}" selected>${category.name}</option> + %else: + <option value="${trans.security.encode_id( category.id )}">${category.name}</option> + %endif + %endfor + </select> + <div class="toolParamHelp" style="clear: both;"> + Multi-select list - hold the appropriate key while clicking to select multiple categories. + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <input type="submit" name="manage_categories_button" value="Save"/> + </div> + </form> + </div> +</div> %if trans.app.config.smtp_server: <p/><div class="toolForm"> @@ -330,8 +338,8 @@ </form></div></div> -<p/> %if repository.ratings: + <p/><div class="toolForm"><div class="toolFormTitle">Rating</div><div class="toolFormBody"> --- a/templates/webapps/community/repository/view_repository.mako Thu Jul 21 14:37:25 2011 -0400 +++ b/templates/webapps/community/repository/view_repository.mako Thu Jul 21 16:19:52 2011 -0400 @@ -118,7 +118,7 @@ </div> %endif <div class="form-row"> - <label>Version:</label> + <label>Revision:</label> %if can_view_change_log: <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${repository.revision}</a> %else: @@ -145,20 +145,6 @@ %endif </div></div> -%if repository.categories: - <p/> - <div class="toolForm"> - <div class="toolFormTitle">Categories</div> - <div class="toolFormBody"> - %for rca in repository.categories: - <div class="form-row"> - ${rca.category.name} - </div> - %endfor - <div style="clear: both"></div> - </div> - </div> -%endif %if metadata: <p/><div class="toolForm"> @@ -183,9 +169,18 @@ </tr> %for tool_dict in tool_dicts: <tr> - <td><a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ] )}">${tool_dict[ 'name' ]}</a></td> + <td> + <div style="float: left; margin-left: 1px;" class="menubutton split popup" id="tool-${repository.id}-popup"> + <a class="view-info" href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ] )}"> + ${tool_dict[ 'name' ]} + </a> + </div> + <div popupmenu="tool-${repository.id}-popup"> + <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip, tool_id=tool_dict[ 'id' ] )}">View all metadata for this tool</a> + </div> + </td><td>${tool_dict[ 'description' ]}</td> - <td>version: ${tool_dict[ 'version' ]}</td> + <td>${tool_dict[ 'version' ]}</td><td><% if 'requirements' in tool_dict: @@ -242,6 +237,20 @@ </div></div> %endif +%if repository.categories: + <p/> + <div class="toolForm"> + <div class="toolFormTitle">Categories</div> + <div class="toolFormBody"> + %for rca in repository.categories: + <div class="form-row"> + ${rca.category.name} + </div> + %endfor + <div style="clear: both"></div> + </div> + </div> +%endif %if trans.user and trans.app.config.smtp_server: <p/><div class="toolForm"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Prevent keyboard navigation from within input elements in shared visualizations.
by Bitbucket 21 Jul '11

21 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/c360836d2c56/ changeset: c360836d2c56 user: jgoecks date: 2011-07-21 20:37:25 summary: Prevent keyboard navigation from within input elements in shared visualizations. affected #: 1 file (187 bytes) --- a/templates/visualization/display.mako Thu Jul 21 14:22:33 2011 -0400 +++ b/templates/visualization/display.mako Thu Jul 21 14:37:25 2011 -0400 @@ -122,6 +122,11 @@ // Keyboard navigation. Scroll ~7% of height when scrolling up/down. // $(document).keydown(function(e) { + // Do not navigate if arrow keys used in input element. + if ($(e.srcElement).is(':input')) { + return; + } + // Key codes: left == 37, up == 38, right == 39, down == 40 switch(e.which) { case 37: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: save data in Tile object and use to determine if filters are available.
by Bitbucket 21 Jul '11

21 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a7b8b0f49b48/ changeset: a7b8b0f49b48 user: jgoecks date: 2011-07-21 20:22:33 summary: Trackster: save data in Tile object and use to determine if filters are available. affected #: 1 file (58 bytes) --- a/static/scripts/trackster.js Thu Jul 21 13:55:24 2011 -0400 +++ b/static/scripts/trackster.js Thu Jul 21 14:22:33 2011 -0400 @@ -1588,23 +1588,24 @@ /** * Tiles drawn by tracks. */ -var Tile = function(index, resolution, canvas) { +var Tile = function(index, resolution, canvas, data) { this.index = index; this.low = index * DENSITY * resolution; this.high = (index + 1) * DENSITY * resolution; this.resolution = resolution; // Wrap element in div for background. this.canvas = $("<div class='track-tile'/>").append(canvas); + this.data = data; this.stale = false; }; -var SummaryTreeTile = function(index, resolution, canvas, max_val) { - Tile.call(this, index, resolution, canvas); +var SummaryTreeTile = function(index, resolution, canvas, data, max_val) { + Tile.call(this, index, resolution, canvas, data); this.max_val = max_val; }; -var FeatureTrackTile = function(index, resolution, canvas, message) { - Tile.call(this, index, resolution, canvas); +var FeatureTrackTile = function(index, resolution, canvas, data, message) { + Tile.call(this, index, resolution, canvas, data); this.message = message; }; @@ -2096,13 +2097,17 @@ filters[f].update_ui_elt(); } - // Determine if filters are available; this is based on the example feature. - var filters_available = false; - if (track.example_feature) { - for (var f = 0; f < filters.length; f++) { - if (filters[f].applies_to(track.example_feature)) { - filters_available = true; - break; + // Determine if filters are available; this is based on the tiles' data. + var filters_available = false, + example_feature; + for (var i = 0; i < drawn_tiles.length; i++) { + if (drawn_tiles[i].data.length) { + example_feature = drawn_tiles[i].data[0]; + for (var f = 0; f < filters.length; f++) { + if (filters[f].applies_to(example_feature)) { + filters_available = true; + break; + } } } } @@ -2385,7 +2390,7 @@ var c_start = Math.round(c * w_scale); ctx.fillText(seq[c], c_start + track.left_offset, 10); } - return new Tile(tile_index, resolution, canvas); + return new Tile(tile_index, resolution, canvas, seq); } this.content_div.css("height", "0px"); } @@ -2523,7 +2528,7 @@ var painter = new painters.LinePainter(result.data, tile_low, tile_low + tile_length, this.prefs, this.mode); painter.draw(ctx, width, height); - return new Tile(tile_index, resolution, canvas); + return new Tile(tile_index, resolution, canvas, result.data); } }); @@ -2737,7 +2742,7 @@ // TODO: this shouldn't be done at the tile level this.container_div.find(".yaxislabel").remove(); var max_label = $("<div />").addClass('yaxislabel'); - max_label.text( result.max ); + max_label.text(result.max); max_label.css({ position: "absolute", top: "24px", left: "10px", color: this.prefs.label_color }); max_label.prependTo(this.container_div); // Create canvas @@ -2760,7 +2765,7 @@ // Deal with left_offset by translating ctx.translate(left_offset, SUMMARY_TREE_TOP_PADDING); painter.draw(ctx, width, required_height); - return new SummaryTreeTile(tile_index, resolution, canvas, result.max); + return new SummaryTreeTile(tile_index, resolution, canvas, result.data, result.max); } // Start dealing with row-by-row tracks @@ -2811,16 +2816,12 @@ this.container_div.find(".yaxislabel").remove(); if (result.data) { - // Set example feature. This is needed so that track can update its UI based on feature attributes. - // TODO: use tile data rather than example feature? - this.example_feature = (result.data.length ? result.data[0] : undefined); - // Draw features. ctx.translate(left_offset, 0); painter.draw(ctx, width, required_height, slots); } - return new FeatureTrackTile(tile_index, resolution, canvas, result.message); + return new FeatureTrackTile(tile_index, resolution, canvas, result.data, result.message); } }); 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 Assaf Gordon's collect_job_timings.sh script.
by Bitbucket 21 Jul '11

21 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/c609c2574c66/ changeset: c609c2574c66 user: greg date: 2011-07-21 19:55:24 summary: Add Assaf Gordon's collect_job_timings.sh script. This shell script produces the report, combining information from SGE's QACCT with the galaxy job/dataset information. The output contains: job, user, tool name, dbkey, total input size in bytes, waiting time in SGE queue, actual SGE executiong running time, and some other tidbits. This allows finding how much running time each user had on the cluster, how much time each tool/user spend idly waiting, and some possible correlations between tools, dbkeys, input size and running time. The script is tightly coupled with SGE and PostgreSQL, but can probably be adapted to PBS/MySQL. affected #: 1 file (0 bytes) 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 tool configs that do not include a command tag.
by Bitbucket 21 Jul '11

21 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0f15591f2acd/ changeset: 0f15591f2acd user: greg date: 2011-07-21 19:44:45 summary: Fix for tool configs that do not include a command tag. affected #: 1 file (35 bytes) --- a/lib/galaxy/tools/__init__.py Thu Jul 21 13:14:13 2011 -0400 +++ b/lib/galaxy/tools/__init__.py Thu Jul 21 13:44:45 2011 -0400 @@ -374,15 +374,15 @@ self.input_translator = root.find( "request_param_translation" ) if self.input_translator: self.input_translator = ToolInputTranslator.from_element( self.input_translator ) - # Command line (template). Optional for tools that do not invoke a - # local program + # Command line (template). Optional for tools that do not invoke a local program command = root.find("command") if command is not None and command.text is not None: self.command = command.text.lstrip() # get rid of leading whitespace + # Must pre-pend this AFTER processing the cheetah command template + self.interpreter = command.get( "interpreter", None ) else: self.command = '' - # Must pre-pend this AFTER processing the cheetah command template - self.interpreter = command.get("interpreter", None) + self.interpreter = None # Parameters used to build URL for redirection to external app redirect_url_params = root.find( "redirect_url_params" ) if redirect_url_params is not None and redirect_url_params.text is not None: 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 21 Jul '11

21 Jul '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0ff5ad458dea/ changeset: 0ff5ad458dea user: kanwei date: 2011-07-21 19:13:48 summary: Return JSON for LibraryDatasetToolParam metadata affected #: 1 file (75 bytes) --- a/lib/galaxy/tools/__init__.py Thu Jul 21 13:03:04 2011 -0400 +++ b/lib/galaxy/tools/__init__.py Thu Jul 21 13:13:48 2011 -0400 @@ -2029,6 +2029,7 @@ def __str__( self ): return self.value.name def templates( self ): + """ Returns JSON dict of templates => data """ if not self.value: return None template_data = {} @@ -2039,7 +2040,7 @@ for field in template.fields: tmp_dict[field['label']] = content[field['name']] template_data[template.name] = tmp_dict - return template_data + return simplejson.dumps( template_data ) def __getattr__( self, key ): return getattr( self.value, key ) http://bitbucket.org/galaxy/galaxy-central/changeset/448490d701fa/ changeset: 448490d701fa user: kanwei date: 2011-07-21 19:14:13 summary: Fix workflow overlay error introduced in recent commit affected #: 1 file (35 bytes) --- a/templates/workflow/editor.mako Thu Jul 21 13:13:48 2011 -0400 +++ b/templates/workflow/editor.mako Thu Jul 21 13:14:13 2011 -0400 @@ -931,9 +931,9 @@ </div></%def> -<%def name="overlay()"> +<%def name="overlay(visible=False)"> ${parent.overlay( "Loading workflow editor...", - "<img src='" + h.url_for('/static/images/yui/rel_interstitial_loading.gif') + "'/>" )} + "<img src='" + h.url_for('/static/images/yui/rel_interstitial_loading.gif') + "'/>", self.overlay_visible )} </%def><%def name="left_panel()"> 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: Remove tool shed repository files from disk that become untracked because they were removed from the repository within an exception block (only occurs in the tool shed test / production environments ).
by Bitbucket 21 Jul '11

21 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/bdb3436ff22f/ changeset: bdb3436ff22f user: greg date: 2011-07-21 19:03:04 summary: Remove tool shed repository files from disk that become untracked because they were removed from the repository within an exception block (only occurs in the tool shed test / production environments ). affected #: 2 files (1.6 KB) --- a/lib/galaxy/webapps/community/controllers/repository.py Thu Jul 21 12:46:27 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Thu Jul 21 13:03:04 2011 -0400 @@ -459,6 +459,21 @@ relative_selected_file = selected_file.split( 'repo_%d' % repository.id )[1].lstrip( '/' ) repo.dirstate.remove( relative_selected_file ) repo.dirstate.write() + absolute_selected_file = os.path.abspath( selected_file ) + if os.path.isdir( absolute_selected_file ): + try: + os.rmdir( absolute_selected_file ) + except OSError, e: + # The directory is not empty + pass + elif os.path.isfile( absolute_selected_file ): + os.remove( absolute_selected_file ) + dir = os.path.split( absolute_selected_file )[0] + try: + os.rmdir( dir ) + except OSError, e: + # The directory is not empty + pass # Commit the change set. if not commit_message: commit_message = 'Deleted selected files' --- a/lib/galaxy/webapps/community/controllers/upload.py Thu Jul 21 12:46:27 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/upload.py Thu Jul 21 13:03:04 2011 -0400 @@ -191,6 +191,21 @@ relative_selected_file = selected_file.split( 'repo_%d' % repository.id )[1].lstrip( '/' ) repo.dirstate.remove( relative_selected_file ) repo.dirstate.write() + absolute_selected_file = os.path.abspath( selected_file ) + if os.path.isdir( absolute_selected_file ): + try: + os.rmdir( absolute_selected_file ) + except OSError, e: + # The directory is not empty + pass + elif os.path.isfile( absolute_selected_file ): + os.remove( absolute_selected_file ) + dir = os.path.split( absolute_selected_file )[0] + try: + os.rmdir( dir ) + except OSError, e: + # The directory is not empty + pass for filename_in_archive in filenames_in_archive: commands.add( repo.ui, repo, filename_in_archive ) if filename_in_archive.endswith( '.loc.sample' ): 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 exception handling for mercurial commands that break in the test / production tool shed environment, but not elsewhere.
by Bitbucket 21 Jul '11

21 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/86bdb4a9db48/ changeset: 86bdb4a9db48 user: greg date: 2011-07-21 18:46:27 summary: Add exception handling for mercurial commands that break in the test / production tool shed environment, but not elsewhere. affected #: 2 files (1.1 KB) --- a/lib/galaxy/webapps/community/controllers/repository.py Thu Jul 21 10:43:16 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Thu Jul 21 12:46:27 2011 -0400 @@ -450,8 +450,15 @@ # Get the current repository tip. tip = repository.tip for selected_file in selected_files_to_delete: - repo_file = os.path.abspath( selected_file ) - commands.remove( repo.ui, repo, repo_file, force=True ) + try: + commands.remove( repo.ui, repo, repo_file, force=True ) + except Exception, e: + # I never have a problem with commands.remove on a Mac, but in the test/production + # tool shed environment, it throws an exception whenever I delete all files from a + # repository. If this happens, we'll try the following. + relative_selected_file = selected_file.split( 'repo_%d' % repository.id )[1].lstrip( '/' ) + repo.dirstate.remove( relative_selected_file ) + repo.dirstate.write() # Commit the change set. if not commit_message: commit_message = 'Deleted selected files' --- a/lib/galaxy/webapps/community/controllers/upload.py Thu Jul 21 10:43:16 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/upload.py Thu Jul 21 12:46:27 2011 -0400 @@ -182,7 +182,15 @@ for repo_file in files_to_remove: # Remove files in the repository (relative to the upload point) # that are not in the uploaded archive. - commands.remove( repo.ui, repo, repo_file, force=True ) + try: + commands.remove( repo.ui, repo, repo_file, force=True ) + except Exception, e: + # I never have a problem with commands.remove on a Mac, but in the test/production + # tool shed environment, it throws an exception whenever I delete all files from a + # repository. If this happens, we'll try the following. + relative_selected_file = selected_file.split( 'repo_%d' % repository.id )[1].lstrip( '/' ) + repo.dirstate.remove( relative_selected_file ) + repo.dirstate.write() for filename_in_archive in filenames_in_archive: commands.add( repo.ui, repo, filename_in_archive ) if filename_in_archive.endswith( '.loc.sample' ): 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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