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commit/galaxy-central: jgoecks: Trackster: do not use child tracks for now because they do not work with new request_redraw structure.
by Bitbucket 19 Sep '11

19 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5344a6864d47/ changeset: 5344a6864d47 user: jgoecks date: 2011-09-19 06:07:24 summary: Trackster: do not use child tracks for now because they do not work with new request_redraw structure. affected #: 1 file (-1 bytes) --- a/static/scripts/trackster.js Thu Sep 15 17:10:39 2011 -0400 +++ b/static/scripts/trackster.js Mon Sep 19 00:07:24 2011 -0400 @@ -1228,7 +1228,7 @@ new_track = new ToolDataFeatureTrack(track_name, view, current_track.hda_ldda, undefined, {}, {}, current_track); new_track.change_mode(current_track.mode); } - this.track.add_track(new_track); + this.track.view.add_track(new_track); new_track.content_div.text("Starting job."); // Run tool. 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: Comment the Trinity assembler out of the sample tool conf so that it must be explicitly enabled.
by Bitbucket 15 Sep '11

15 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/32b3ed6d5255/ changeset: 32b3ed6d5255 user: jgoecks date: 2011-09-15 23:10:39 summary: Comment the Trinity assembler out of the sample tool conf so that it must be explicitly enabled. affected #: 1 file (-1 bytes) --- a/tool_conf.xml.sample Wed Sep 14 14:41:19 2011 -0400 +++ b/tool_conf.xml.sample Thu Sep 15 17:10:39 2011 -0400 @@ -338,8 +338,11 @@ <tool file="ngs_rna/cufflinks_wrapper.xml" /><tool file="ngs_rna/cuffcompare_wrapper.xml" /><tool file="ngs_rna/cuffdiff_wrapper.xml" /> + <label text="Filtering" id="filtering" /><tool file="ngs_rna/filter_transcripts_via_tracking.xml" /></section> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: New API scripts to do POST/PUT/DELETE without any guidance. Use like:
by Bitbucket 14 Sep '11

14 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0540dedaaca0/ changeset: 0540dedaaca0 user: natefoo date: 2011-09-14 20:40:38 summary: New API scripts to do POST/PUT/DELETE without any guidance. Use like: ./update.py key url param1=val param2=val affected #: 3 files (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: natefoo: New API features:
by Bitbucket 14 Sep '11

14 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/ca6db8f67477/ changeset: ca6db8f67477 user: natefoo date: 2011-09-14 20:36:38 summary: New API features: * The @web.require_admin decorator can now be used on API methods * When using model.model_class.get_api_value(), api_*_visible_keys can now be mapper attributes to other model classes (get_api_value() recursion) * Monkeypatch the route mapper to contain a resource_with_deleted() method. This works just like the existing mapper.resource() method but adds extra routes. The following is a supplement to the Routes RESTful services documentation at: https://routes.groovie.org/restful.html Using: mapper.resources_with_deleted( "message", "items" ) Would result in the same routes as in the use of resource(), with the addition of: map.connect("deleted_messages", "/messages/deleted", controller=messages, action="index", deleted=True, conditions=dict(method=["GET"]) map.connect("deleted_message", "/messages/deleted/{id}", controller=messages, action="show", deleted=True, conditions=dict(method=["GET"]) map.connect("undelete_deleted_message", "/messages/deleted/{id}/undelete", controller=messages, action="index", conditions=dict(method=["POST"]) Which adds to the convention: GET /messages/deleted => messages.index(deleted=True) => url("deleted_messages") GET /messages/deleted/1 => messages.show(id, deleted=True) => url("deleted_message", id=1) POST /messages/deleted/1/undelete => messages.undelete(id) => url("undelete_deleted_message", id=1) affected #: 3 files (1.7 KB) --- a/lib/galaxy/model/item_attrs.py Tue Sep 13 16:55:17 2011 -0400 +++ b/lib/galaxy/model/item_attrs.py Wed Sep 14 14:36:38 2011 -0400 @@ -1,4 +1,5 @@ from sqlalchemy.sql.expression import func +from sqlalchemy.orm.collections import InstrumentedList # Cannot import galaxy.model b/c it creates a circular import graph. import galaxy import logging @@ -156,6 +157,13 @@ #api_collection_visible_keys = ( 'id' ) #api_element_visible_keys = ( 'id' ) def get_api_value( self, view='collection', value_mapper = None ): + def get_value( key, item ): + try: + return item.get_api_value( view=view, value_mapper=value_mapper ) + except: + if key in value_mapper: + return value_mapper.get( key )( item ) + return item if value_mapper is None: value_mapper = {} rval = {} @@ -165,9 +173,13 @@ raise Exception( 'Unknown API view: %s' % view ) for key in visible_keys: try: - rval[key] = self.__getattribute__( key ) - if key in value_mapper: - rval[key] = value_mapper.get( key )( rval[key] ) + item = self.__getattribute__( key ) + if type( item ) == InstrumentedList: + rval[key] = [] + for i in item: + rval[key].append( get_value( key, i ) ) + else: + rval[key] = get_value( key, item ) except AttributeError: rval[key] = None return rval --- a/lib/galaxy/web/framework/__init__.py Tue Sep 13 16:55:17 2011 -0400 +++ b/lib/galaxy/web/framework/__init__.py Wed Sep 14 14:36:38 2011 -0400 @@ -117,7 +117,7 @@ return error trans.response.set_content_type( "application/json" ) trans.set_user( provided_key.user ) -# Perform api_run_as processing, possibly changing identity + # Perform api_run_as processing, possibly changing identity if 'run_as' in kwargs: if not trans.user_can_do_run_as(): error_message = 'User does not have permissions to run jobs as another user' @@ -147,13 +147,18 @@ def require_admin( func ): def decorator( self, trans, *args, **kwargs ): if not trans.user_is_admin(): + msg = "You must be an administrator to access this feature." admin_users = trans.app.config.get( "admin_users", "" ).split( "," ) + user = trans.get_user() if not admin_users: - return trans.show_error_message( "You must be logged in as an administrator to access this feature, but no administrators are set in the Galaxy configuration." ) - user = trans.get_user() - if not user: - return trans.show_error_message( "You must be logged in as an administrator to access this feature." ) - return trans.show_error_message( "You must be an administrator to access this feature." ) + msg = "You must be logged in as an administrator to access this feature, but no administrators are set in the Galaxy configuration." + elif not user: + msg = "You must be logged in as an administrator to access this feature." + trans.response.status = 403 + if trans.response.get_content_type() == 'application/json': + return msg + else: + return trans.show_error_message( msg ) return func( self, trans, *args, **kwargs ) return decorator --- a/lib/galaxy/web/framework/base.py Tue Sep 13 16:55:17 2011 -0400 +++ b/lib/galaxy/web/framework/base.py Wed Sep 14 14:36:38 2011 -0400 @@ -29,6 +29,21 @@ log = logging.getLogger( __name__ ) +def __resource_with_deleted( self, member_name, collection_name, **kwargs ): + """ + Method to monkeypatch on to routes.mapper.Mapper which does the same thing + as resource() with the addition of standardized routes for handling + elements in Galaxy's "deleted but not really deleted" fashion. + """ + collection_path = kwargs.get( 'path_prefix', '' ) + '/' + collection_name + '/deleted' + member_path = collection_path + '/:id' + self.connect( 'deleted_' + collection_name, collection_path, controller=collection_name, action='index', deleted=True ) + self.connect( 'deleted_' + member_name, member_path, controller=collection_name, action='show', deleted=True ) + self.connect( 'undelete_deleted_' + member_name, member_path + '/undelete', controller=collection_name, action='undelete', + conditions=dict( method=['POST'] ) ) + self.resource( member_name, collection_name, **kwargs ) +routes.Mapper.resource_with_deleted = __resource_with_deleted + class WebApplication( object ): """ A simple web application which maps requests to objects using routes, @@ -320,6 +335,8 @@ Sets the Content-Type header """ self.headers[ "content-type" ] = type + def get_content_type( self ): + return self.headers[ "content-type" ] def send_redirect( self, url ): """ Send an HTTP redirect response to (target `url`) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Trackster: improve method for fetching additional data and simply data fetching.
by Bitbucket 13 Sep '11

13 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/c6452f6558ee/ changeset: c6452f6558ee user: jgoecks date: 2011-09-13 22:55:17 summary: Trackster: improve method for fetching additional data and simply data fetching. affected #: 3 files (1.4 KB) --- a/lib/galaxy/visualization/tracks/data_providers.py Mon Sep 12 14:51:26 2011 -0400 +++ b/lib/galaxy/visualization/tracks/data_providers.py Tue Sep 13 16:55:17 2011 -0400 @@ -3,7 +3,7 @@ """ import sys -from math import floor, ceil, log, pow +from math import ceil, log import pkg_resources pkg_resources.require( "bx-python" ) if sys.version_info[:2] == (2, 4): @@ -13,14 +13,12 @@ from galaxy.datatypes.util.gff_util import * from galaxy.util.json import from_json_string from bx.interval_index_file import Indexes -from bx.arrays.array_tree import FileArrayTreeDict from bx.bbi.bigwig_file import BigWigFile from galaxy.util.lrucache import LRUCache from galaxy.visualization.tracks.summary import * import galaxy_utils.sequence.vcf from galaxy.datatypes.tabular import Vcf from galaxy.datatypes.interval import Bed, Gff, Gtf -from galaxy.datatypes.util.gff_util import parse_gff_attributes from pysam import csamtools, ctabix @@ -32,7 +30,20 @@ return None else: return float(n) - + +def get_bounds( reads, start_pos_index, end_pos_index ): + """ + Returns the minimum and maximum position for a set of reads. + """ + max_low = sys.maxint + max_high = -sys.maxint + for read in reads: + if read[ start_pos_index ] < max_low: + max_low = read[ start_pos_index ] + if read[ end_pos_index ] > max_high: + max_high = read[ end_pos_index ] + return max_low, max_high + class TracksDataProvider( object ): """ Base class for tracks data providers. """ @@ -75,8 +86,11 @@ def get_data( self, chrom, start, end, start_val=0, max_vals=None, **kwargs ): """ Returns data in region defined by chrom, start, and end. start_val and - max_vals are used to denote the data to return: start_val is the first value to + max_vals are used to denote the data to return: start_val is the first element to return and max_vals indicates the number of values to return. + + Return value must be a dictionary with the following attributes: + dataset_type, data """ # Override. pass @@ -218,18 +232,23 @@ def get_data( self, chrom, start, end, start_val=0, max_vals=sys.maxint, **kwargs ): """ - Fetch reads in the region. + Fetch reads in the region and additional metadata. - Each read is a list with the format - [<guid>, <start>, <end>, <name>, <read_1>, <read_2>] - where <read_1> has the format - [<start>, <end>, <cigar>, ?<read_seq>?] - and <read_2> has the format - [<start>, <end>, <cigar>, ?<read_seq>?] - For single-end reads, read has format: - [<guid>, <start>, <end>, <name>, cigar, seq] - NOTE: read end and sequence data are not valid for reads outside of - requested region and should not be used. + Returns a dict with the following attributes: + data - a list of reads with the format + [<guid>, <start>, <end>, <name>, <read_1>, <read_2>] + where <read_1> has the format + [<start>, <end>, <cigar>, ?<read_seq>?] + and <read_2> has the format + [<start>, <end>, <cigar>, ?<read_seq>?] + For single-end reads, read has format: + [<guid>, <start>, <end>, <name>, cigar, seq] + NOTE: read end and sequence data are not valid for reads outside of + requested region and should not be used. + + max_low - lowest coordinate for the returned reads + max_high - highest coordinate for the returned reads + message - error/informative message """ start, end = int(start), int(end) orig_data_filename = self.original_dataset.file_name @@ -304,9 +323,13 @@ r2 = [ read['mate_start'], read['mate_start'] ] results.append( [ "%i_%s" % ( read_start, qname ), read_start, read_end, qname, r1, r2 ] ) - + + # Clean up. bamfile.close() - return { 'data': results, 'message': message } + + max_low, max_high = get_bounds( results, 1, 2 ) + + return { 'data': results, 'message': message, 'max_low': max_low, 'max_high': max_high } class BBIDataProvider( TracksDataProvider ): """ @@ -334,9 +357,10 @@ return None all_dat = all_dat[0] # only 1 summary - return { 'max': float( all_dat['max'] ), \ - 'min': float( all_dat['min'] ), \ - 'total_frequency': float( all_dat['coverage'] ) } + return { 'data' : { 'max': float( all_dat['max'] ), \ + 'min': float( all_dat['min'] ), \ + 'total_frequency': float( all_dat['coverage'] ) } \ + } start = int(start) end = int(end) @@ -361,7 +385,7 @@ result.append( (pos, float_nan(dat_dict['mean']) ) ) pos += step_size - return result + return { 'data': result } class BigBedDataProvider( BBIDataProvider ): def _get_dataset( self ): @@ -654,7 +678,7 @@ float( feature[5] )] rval.append(payload) - return { 'data_type' : 'vcf', 'data': rval, 'message': message } + return { 'data': rval, 'message': message } class GFFDataProvider( TracksDataProvider ): """ --- a/lib/galaxy/web/controllers/tracks.py Mon Sep 12 14:51:26 2011 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Tue Sep 13 16:55:17 2011 -0400 @@ -530,15 +530,9 @@ data_provider = data_provider_class( converted_dataset=converted_dataset, original_dataset=dataset, dependencies=deps ) # Get and return data from data_provider. - data = data_provider.get_data( chrom, low, high, int(start_val), int(max_vals), **kwargs ) - message = None - if isinstance(data, dict) and 'message' in data: - message = data['message'] - tracks_dataset_type = data.get( 'data_type', tracks_dataset_type ) - track_data = data['data'] - else: - track_data = data - return { 'dataset_type': tracks_dataset_type, 'extra_info': extra_info, 'data': track_data, 'message': message } + result = data_provider.get_data( chrom, low, high, int(start_val), int(max_vals), **kwargs ) + result.update( { 'dataset_type': tracks_dataset_type, 'extra_info': extra_info } ) + return result @web.json def save( self, trans, **kwargs ): --- a/static/scripts/trackster.js Mon Sep 12 14:51:26 2011 -0400 +++ b/static/scripts/trackster.js Tue Sep 13 16:55:17 2011 -0400 @@ -443,9 +443,9 @@ $.extend(extra_params, {start_val: cur_data.data.length + 1}); } else if (req_type === this.BROAD_DATA_REQ) { - // Set query low to be past the last feature returned so that an area of extreme feature depth - // is bypassed. - query_low = cur_data.data[cur_data.data.length - 1][2] + 1; + // To get past an area of extreme feature depth, set query low to be after either + // (a) the maximum high or HACK/FIXME (b) the end of the last feature returned. + query_low = (cur_data.max_high ? cur_data.max_high : cur_data.data[cur_data.data.length - 1][2]) + 1; } // @@ -463,6 +463,9 @@ // Update data and message. if (result.data) { result.data = cur_data.data.concat(result.data); + if (result.max_low) { + result.max_low = cur_data.max_low; + } if (result.message) { // HACK: replace number in message with current data length. Works but is ugly. result.message = result.message.replace(/[0-9]+/, result.data.length); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Fix trackster bug in determining tile bounds and in documentation.
by Bitbucket 12 Sep '11

12 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/cafb70f10379/ changeset: cafb70f10379 user: jgoecks date: 2011-09-12 20:51:26 summary: Fix trackster bug in determining tile bounds and in documentation. affected #: 1 file (0 bytes) --- a/static/scripts/trackster.js Fri Sep 09 16:05:52 2011 -0400 +++ b/static/scripts/trackster.js Mon Sep 12 14:51:26 2011 -0400 @@ -2495,7 +2495,7 @@ var tile_low = tile_index * DENSITY * resolution, tile_length = DENSITY * resolution, // Tile high cannot be larger than view.max_high, which the chromosome length. - tile_high = (tile_low + tile_length <= this.view.max ? tile_low + tile_length : this.view.max_high); + tile_high = (tile_low + tile_length <= this.view.max_high ? tile_low + tile_length : this.view.max_high); return [tile_low, tile_high]; }, /** @@ -2998,7 +2998,7 @@ * @param mode mode to draw in * @param resolution view resolution * @param tile_index index of tile to be drawn - * @param w_scale base pairs per pixel + * @param w_scale pixels per base * @param ref_seq reference sequence data */ draw_tile: function(result, mode, resolution, tile_index, w_scale, ref_seq) { 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: Two minor but important bug fixes in searching for and displaying tool shed repositories.
by Bitbucket 09 Sep '11

09 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/35063fa0b2cb/ changeset: 35063fa0b2cb user: greg date: 2011-09-09 22:05:52 summary: Two minor but important bug fixes in searching for and displaying tool shed repositories. affected #: 2 files (513 bytes) --- a/lib/galaxy/webapps/community/controllers/common.py Fri Sep 09 12:15:27 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Fri Sep 09 16:05:52 2011 -0400 @@ -380,7 +380,7 @@ return message, status def get_repository_by_name( trans, name ): """Get a repository from the database via name""" - return trans.sa_session.query( app.model.Repository ).filter_by( name=name ).one() + return trans.sa_session.query( trans.model.Repository ).filter_by( name=name ).one() def get_changectx_for_changeset( trans, repo, changeset_revision, **kwd ): """Retrieve a specified changectx from a repository""" for changeset in repo.changelog: --- a/lib/galaxy/webapps/community/controllers/repository.py Fri Sep 09 12:15:27 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Fri Sep 09 16:05:52 2011 -0400 @@ -241,6 +241,14 @@ # What we've done is rendered the search box for the RepositoryListGrid on the grid.mako # template for the CategoryListGrid. See ~/templates/webapps/community/category/grid.mako. # Since we are searching repositories and not categories, redirect to browse_repositories(). + if 'id' in kwd and 'f-free-text-search' in kwd and kwd[ 'id' ] == kwd[ 'f-free-text-search' ]: + # The value of 'id' has been set to the search string, which is a repository name. + # We'll try to get the desired encoded repository id to pass on. + try: + repository = get_repository_by_name( trans, kwd[ 'id' ] ) + kwd[ 'id' ] = trans.security.encode_id( repository.id ) + except: + pass return self.browse_repositories( trans, **kwd ) if 'operation' in kwd: operation = kwd['operation'].lower() 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: Fix tabs in secure_hash_message_digest.xml.
by Bitbucket 09 Sep '11

09 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a0a77ce93344/ changeset: a0a77ce93344 user: dan date: 2011-09-09 18:15:27 summary: Fix tabs in secure_hash_message_digest.xml. affected #: 1 file (12 bytes) --- a/tools/filters/secure_hash_message_digest.xml Fri Sep 09 12:01:43 2011 -0400 +++ b/tools/filters/secure_hash_message_digest.xml Fri Sep 09 12:15:27 2011 -0400 @@ -2,10 +2,10 @@ <description>on a dataset</description><command interpreter="python">secure_hash_message_digest.py --input "${input1}" --output "${out_file1}" #if $algorithms.value: - #for $algorithm in str( $algorithms ).split( "," ): - --algorithm "${algorithm}" - #end for - #end if + #for $algorithm in str( $algorithms ).split( "," ): + --algorithm "${algorithm}" + #end for + #end if </command><inputs><param format="data" name="input1" type="data" label="Text file"/> 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: Add tool for calculating Secure Hashes / Message Digests of a dataset using the user selected algorithms.
by Bitbucket 09 Sep '11

09 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/ea163dae4490/ changeset: ea163dae4490 user: dan date: 2011-09-09 18:01:43 summary: Add tool for calculating Secure Hashes / Message Digests of a dataset using the user selected algorithms. affected #: 4 files (59 bytes) --- a/tool_conf.xml.sample Fri Sep 09 11:18:05 2011 -0400 +++ b/tool_conf.xml.sample Fri Sep 09 12:01:43 2011 -0400 @@ -56,6 +56,7 @@ <tool file="filters/tailWrapper.xml" /><tool file="filters/trimmer.xml" /><tool file="filters/wc_gnu.xml" /> + <tool file="filters/secure_hash_message_digest.xml" /><tool file="stats/dna_filtering.xml" /><tool file="new_operations/tables_arithmetic_operations.xml" /></section> 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 for a tool shed repository owner to reset the repository metadata for any change set revision that has associated repository metadata (previously could only be reset for repository tip)
by Bitbucket 09 Sep '11

09 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/7547a3131862/ changeset: 7547a3131862 user: greg date: 2011-09-09 17:18:05 summary: Add the ability for a tool shed repository owner to reset the repository metadata for any change set revision that has associated repository metadata (previously could only be reset for repository tip) affected #: 5 files (3.1 KB) --- a/lib/galaxy/webapps/community/controllers/common.py Fri Sep 09 10:16:48 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Fri Sep 09 11:18:05 2011 -0400 @@ -110,7 +110,7 @@ """Get last metadata defined for a specified repository from the database""" return trans.sa_session.query( trans.model.RepositoryMetadata ) \ .filter( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ) ) \ - .order_by( trans.model.RepositoryMetadata.table.c.update_time.desc() ) \ + .order_by( trans.model.RepositoryMetadata.table.c.id.desc() ) \ .first() def generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict ): """ @@ -163,7 +163,7 @@ repository.name, tool.id, tool.version ) -def generate_tool_metadata( trans, id, changeset_revision, root, name, tool, metadata_dict ): +def generate_tool_metadata( trans, id, changeset_revision, tool_config, tool, metadata_dict ): """ Update the received metadata_dict with changes that have been applied to the received tool. @@ -189,7 +189,7 @@ version=tool.version, description=tool.description, version_string_cmd = tool.version_string_cmd, - tool_config=os.path.join( root, name ), + tool_config=tool_config, requirements=tool_requirements, tests=tool_tests ) if 'tools' in metadata_dict: @@ -249,49 +249,87 @@ ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) if ctx is not None: metadata_dict = {} - for root, dirs, files in os.walk( repo_dir ): - if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0: - if '.hg' in dirs: - # Don't visit .hg directories - should be impossible since we don't - # allow uploaded archives that contain .hg dirs, but just in case... - dirs.remove( '.hg' ) - if 'hgrc' in files: - # Don't include hgrc files in commit. - files.remove( 'hgrc' ) - for name in files: - # Find all tool configs. - if name.endswith( '.xml' ): - try: - full_path = os.path.abspath( os.path.join( root, name ) ) - tool = load_tool( trans, full_path ) - if tool is not None: - # Update the list metadata dictionaries for tools in metadata_dict. - metadata_dict = generate_tool_metadata( trans, id, changeset_revision, root, name, tool, metadata_dict ) - except Exception, e: - invalid_files.append( ( name, str( e ) ) ) - # Find all exported workflows - elif name.endswith( '.ga' ): - try: - full_path = os.path.abspath( os.path.join( root, name ) ) - # Convert workflow data from json - fp = open( full_path, 'rb' ) - workflow_text = fp.read() - fp.close() - exported_workflow_dict = from_json_string( workflow_text ) - # Update the list of metadata dictionaries for workflows in metadata_dict. - metadata_dict = generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict ) - except Exception, e: - invalid_files.append( ( name, str( e ) ) ) + if changeset_revision == repository.tip: + for root, dirs, files in os.walk( repo_dir ): + if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0: + if '.hg' in dirs: + # Don't visit .hg directories - should be impossible since we don't + # allow uploaded archives that contain .hg dirs, but just in case... + dirs.remove( '.hg' ) + if 'hgrc' in files: + # Don't include hgrc files in commit. + files.remove( 'hgrc' ) + for name in files: + # Find all tool configs. + if name.endswith( '.xml' ): + try: + full_path = os.path.abspath( os.path.join( root, name ) ) + tool = load_tool( trans, full_path ) + if tool is not None: + # Update the list metadata dictionaries for tools in metadata_dict. + tool_config = os.path.join( root, name ) + metadata_dict = generate_tool_metadata( trans, id, changeset_revision, tool_config, tool, metadata_dict ) + except Exception, e: + invalid_files.append( ( name, str( e ) ) ) + # Find all exported workflows + elif name.endswith( '.ga' ): + try: + full_path = os.path.abspath( os.path.join( root, name ) ) + # Convert workflow data from json + fp = open( full_path, 'rb' ) + workflow_text = fp.read() + fp.close() + exported_workflow_dict = from_json_string( workflow_text ) + # Update the list of metadata dictionaries for workflows in metadata_dict. + metadata_dict = generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict ) + except Exception, e: + invalid_files.append( ( name, str( e ) ) ) + else: + # Get all tool config file names from the hgweb url, something like: + # /repos/test/convert_chars1/file/e58dcf0026c7/convert_characters.xml + for filename in ctx: + # Find all tool configs - should not have to update metadata for workflows. + if filename.endswith( '.xml' ): + fctx = ctx[ filename ] + # Write the contents of the old tool config to a temporary file. + fh = tempfile.NamedTemporaryFile( 'w' ) + tmp_filename = fh.name + fh.close() + fh = open( tmp_filename, 'w' ) + fh.write( fctx.data() ) + fh.close() + try: + tool = load_tool( trans, tmp_filename ) + if tool is not None: + # Update the list metadata dictionaries for tools in metadata_dict. Note that filename + # here is the relative path to the config file within the change set context, something + # like filtering.xml, but when the change set was the repository tip, the value was + # something like database/community_files/000/repo_1/filtering.xml. This shouldn't break + # anything, but may result in a bit of confusion when maintaining the code / data over time. + metadata_dict = generate_tool_metadata( trans, id, changeset_revision, filename, tool, metadata_dict ) + except Exception, e: + invalid_files.append( ( name, str( e ) ) ) + try: + os.unlink( tmp_filename ) + except: + pass if metadata_dict: - if new_tool_metadata_required( trans, id, metadata_dict ) or new_workflow_metadata_required( trans, id, metadata_dict ): - # Create a new repository_metadata table row. - repository_metadata = trans.model.RepositoryMetadata( repository.id, changeset_revision, metadata_dict ) - trans.sa_session.add( repository_metadata ) - trans.sa_session.flush() + if changeset_revision == repository.tip: + if new_tool_metadata_required( trans, id, metadata_dict ) or new_workflow_metadata_required( trans, id, metadata_dict ): + # Create a new repository_metadata table row. + repository_metadata = trans.model.RepositoryMetadata( repository.id, changeset_revision, metadata_dict ) + trans.sa_session.add( repository_metadata ) + trans.sa_session.flush() + else: + # Update the last saved repository_metadata table row. + repository_metadata = get_latest_repository_metadata( trans, id ) + repository_metadata.changeset_revision = changeset_revision + repository_metadata.metadata = metadata_dict + trans.sa_session.add( repository_metadata ) + trans.sa_session.flush() else: - # Update the last saved repository_metadata table row. - repository_metadata = get_latest_repository_metadata( trans, id ) - repository_metadata.changeset_revision = changeset_revision + # We're re-generating metadata for an old repository revision. + repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) repository_metadata.metadata = metadata_dict trans.sa_session.add( repository_metadata ) trans.sa_session.flush() --- a/lib/galaxy/webapps/community/controllers/repository.py Fri Sep 09 10:16:48 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Fri Sep 09 11:18:05 2011 -0400 @@ -1237,22 +1237,26 @@ # /repos/test/convert_chars1/file/e58dcf0026c7/convert_characters.xml old_tool_config_file_name = tool_config.split( '/' )[ -1 ] ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) + fctx = None for filename in ctx: if filename == old_tool_config_file_name: fctx = ctx[ filename ] break - # Write the contents of the old tool config to a temporary file. - fh = tempfile.NamedTemporaryFile( 'w' ) - tmp_filename = fh.name - fh.close() - fh = open( tmp_filename, 'w' ) - fh.write( fctx.data() ) - fh.close() - tool = load_tool( trans, tmp_filename ) - try: - os.unlink( tmp_filename ) - except: - pass + if fctx: + # Write the contents of the old tool config to a temporary file. + fh = tempfile.NamedTemporaryFile( 'w' ) + tmp_filename = fh.name + fh.close() + fh = open( tmp_filename, 'w' ) + fh.write( fctx.data() ) + fh.close() + tool = load_tool( trans, tmp_filename ) + try: + os.unlink( tmp_filename ) + except: + pass + else: + tool = None tool_state = self.__new_state( trans ) is_malicious = change_set_is_malicious( trans, repository_id, repository.tip ) return trans.fill_template( "/webapps/community/repository/tool_form.mako", --- a/lib/galaxy/webapps/community/model/mapping.py Fri Sep 09 10:16:48 2011 -0400 +++ b/lib/galaxy/webapps/community/model/mapping.py Fri Sep 09 11:18:05 2011 -0400 @@ -194,7 +194,7 @@ categories=relation( RepositoryCategoryAssociation ), ratings=relation( RepositoryRatingAssociation, order_by=desc( RepositoryRatingAssociation.table.c.update_time ), backref="repositories" ), user=relation( User.mapper ), - downloadable_revisions=relation( RepositoryMetadata, order_by=desc( RepositoryMetadata.table.c.update_time ) ) ) ) + downloadable_revisions=relation( RepositoryMetadata, order_by=desc( RepositoryMetadata.table.c.id ) ) ) ) assign_mapper( context, RepositoryMetadata, RepositoryMetadata.table, properties=dict( repository=relation( Repository ) ) ) --- a/templates/webapps/community/repository/common.mako Fri Sep 09 10:16:48 2011 -0400 +++ b/templates/webapps/community/repository/common.mako Fri Sep 09 11:18:05 2011 -0400 @@ -176,20 +176,16 @@ %endif %endif %if can_set_metadata: - %if repository.tip == changeset_revision: - ## TODO: when we support previewing older versions of tools, we - ## should allow resetting metadata on the older versions as well. - <form name="set_metadata" action="${h.url_for( controller='repository', action='set_metadata', id=trans.security.encode_id( repository.id ), ctx_str=changeset_revision )}" method="post"> - <div class="form-row"> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="submit" name="set_metadata_button" value="Reset metadata"/> - </div> - <div class="toolParamHelp" style="clear: both;"> - Inspect the repository and reset the above attributes for the repository tip. - </div> + <form name="set_metadata" action="${h.url_for( controller='repository', action='set_metadata', id=trans.security.encode_id( repository.id ), ctx_str=changeset_revision )}" method="post"> + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="submit" name="set_metadata_button" value="Reset metadata"/></div> - </form> - %endif + <div class="toolParamHelp" style="clear: both;"> + Inspect the repository and reset the above attributes for the repository tip. + </div> + </div> + </form> %endif </div></div> --- a/templates/webapps/community/repository/tool_form.mako Fri Sep 09 10:16:48 2011 -0400 +++ b/templates/webapps/community/repository/tool_form.mako Fri Sep 09 11:18:05 2011 -0400 @@ -152,26 +152,30 @@ ${render_msg( message, status )} %endif - <div class="toolForm" id="${tool.id}"> - <div class="toolFormTitle">${tool.name} (version ${tool.version})</div> - <div class="toolFormBody"> - <form id="tool_form" name="tool_form" action="" method="get"> - <input type="hidden" name="tool_state" value="${util.object_to_string( tool_state.encode( tool, app ) )}"> - ${do_inputs( tool.inputs_by_page[ tool_state.page ], tool_state.inputs, "" )} - </form> + %if tool: + <div class="toolForm" id="${tool.id}"> + <div class="toolFormTitle">${tool.name} (version ${tool.version})</div> + <div class="toolFormBody"> + <form id="tool_form" name="tool_form" action="" method="get"> + <input type="hidden" name="tool_state" value="${util.object_to_string( tool_state.encode( tool, app ) )}"> + ${do_inputs( tool.inputs_by_page[ tool_state.page ], tool_state.inputs, "" )} + </form> + </div></div> - </div> - %if tool.help: - <div class="toolHelp"> - <div class="toolHelpBody"> - <% - # Convert to unicode to display non-ascii characters. - if type( tool.help ) is not unicode: - tool.help = unicode( tool.help, 'utf-8') - %> - ${tool.help} - </div> - </div> + %if tool.help: + <div class="toolHelp"> + <div class="toolHelpBody"> + <% + # Convert to unicode to display non-ascii characters. + if type( tool.help ) is not unicode: + tool.help = unicode( tool.help, 'utf-8') + %> + ${tool.help} + </div> + </div> + %endif + %else: + Tool not properly loaded. %endif </body></html> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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