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

commit/galaxy-central: jgoecks: Enable function to be used for generating a grid operation link; use this functionality to generate link for viewing/editing visualization.
by Bitbucket 24 Aug '12

24 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3d32fa091951/ changeset: 3d32fa091951 user: jgoecks date: 2012-08-25 00:15:29 summary: Enable function to be used for generating a grid operation link; use this functionality to generate link for viewing/editing visualization. affected #: 2 files diff -r df99df26d92fa8a5e3eaef4fd1eef4b6ee18f86d -r 3d32fa091951e9aa72f3c69272960b3f6b648722 lib/galaxy/web/controllers/visualization.py --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -5,7 +5,7 @@ from galaxy.util.sanitize_html import sanitize_html class VisualizationListGrid( grids.Grid ): - def get_link( item ): + def get_url_args( item ): """ Returns dictionary used to create item link. """ @@ -24,7 +24,7 @@ default_sort_key = "-update_time" default_filter = dict( title="All", deleted="False", tags="All", sharing="All" ) columns = [ - grids.TextColumn( "Title", key="title", attach_popup=True, link=get_link ), + grids.TextColumn( "Title", key="title", attach_popup=True, link=get_url_args ), grids.TextColumn( "Type", key="type" ), grids.TextColumn( "Dbkey", key="dbkey" ), grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ), @@ -42,7 +42,7 @@ grids.GridAction( "Create new visualization", dict( action='create' ) ) ] operations = [ - grids.GridOperation( "View/Edit", allow_multiple=False, url_args=dict( controller='tracks', action='browser' ) ), + grids.GridOperation( "View/Edit", allow_multiple=False, url_args=get_url_args ), grids.GridOperation( "Edit Attributes", allow_multiple=False, url_args=dict( action='edit') ), grids.GridOperation( "Copy", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False, url_args=dict( action='clone') ), grids.GridOperation( "Share or Publish", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ), diff -r df99df26d92fa8a5e3eaef4fd1eef4b6ee18f86d -r 3d32fa091951e9aa72f3c69272960b3f6b648722 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py +++ b/lib/galaxy/web/framework/helpers/grids.py @@ -728,9 +728,12 @@ self.global_operation = global_operation def get_url_args( self, item ): if self.url_args: - temp = dict( self.url_args ) - temp['id'] = item.id - return temp + if hasattr( self.url_args, '__call__' ): + url_args = self.url_args( item ) + else: + url_args = dict( self.url_args ) + url_args['id'] = item.id + return url_args else: return dict( operation=self.label, id=item.id ) def allowed( self, item ): 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: inithello: Added script to update NCBI builds list, replaced Broad data source with direct URL, cleaned up help text.
by Bitbucket 23 Aug '12

23 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/df99df26d92f/ changeset: df99df26d92f user: inithello date: 2012-08-23 22:36:58 summary: Added script to update NCBI builds list, replaced Broad data source with direct URL, cleaned up help text. affected #: 4 files diff -r 429c1054c13e9c2206ccd4bc3dfd1ca1fa75973c -r df99df26d92fa8a5e3eaef4fd1eef4b6ee18f86d cron/get_ncbi.py --- /dev/null +++ b/cron/get_ncbi.py @@ -0,0 +1,93 @@ +import urllib, pkg_resources, os +pkg_resources.require( 'elementtree' ) +from elementtree import ElementTree, ElementInclude +from xml.parsers.expat import ExpatError as XMLParseErrorThing +import sys + +import pkg_resources + +class GetListing: + def __init__( self, data ): + self.tree = ElementTree.parse( data ) + self.root = self.tree.getroot() + ElementInclude.include(self.root) + + def xml_text(self, name=None): + """Returns the text inside an element""" + root = self.root + if name is not None: + # Try attribute first + val = root.get(name) + if val: + return val + # Then try as element + elem = root.find(name) + else: + elem = root + if elem is not None and elem.text: + text = ''.join(elem.text.splitlines()) + return text.strip() + # No luck, return empty string + return '' + +def dlcachefile( webenv, querykey, i, results ): + url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nuccore&usehis…' + fp = urllib.urlopen( url ) + search = GetListing( fp ) + fp.close() + webenv = search.xml_text( 'WebEnv' ) + querykey = search.xml_text( 'QueryKey' ) + url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=nuccore&WebEn…' % ( webenv, querykey, i, results ) + fp = urllib.urlopen( url ) + cachefile = os.tmpfile() + for line in fp: + cachefile.write( line ) + fp.close() + cachefile.flush() + cachefile.seek(0) + return cachefile + + +url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nuccore&usehis…' +fp = urllib.urlopen( url ) +results = GetListing( fp ) +fp.close() + +webenv = results.xml_text( 'WebEnv' ) +querykey = results.xml_text( 'QueryKey' ) +counts = int( results.xml_text( 'Count' ) ) +results = 10000 +found = 0 + +for i in range(0, counts + results, results): + rets = dict() + cache = dlcachefile( webenv, querykey, i, results ) + try: + xmldoc = GetListing( cache ) + except (IOError, XMLParseErrorThing): + cache = dlcachefile( webenv, querykey, i, results ) + try: + xmldoc = GetListing( cache ) + except (IOError, XMLParseErrorThing): + cache.close() + exit() + pass + finally: + cache.close() + entries = xmldoc.root.findall( 'DocSum' ) + for entry in entries: + dbkey = None + children = entry.findall('Item') + for item in children: + rets[ item.get('Name') ] = item.text + if not rets['Caption'].startswith('NC_'): + continue + + for ret in rets['Extra'].split('|'): + if not ret.startswith('NC_'): + continue + else: + dbkey = ret + break + if dbkey is not None: + print '\t'.join( [ dbkey, rets['Title'] ] ) diff -r 429c1054c13e9c2206ccd4bc3dfd1ca1fa75973c -r df99df26d92fa8a5e3eaef4fd1eef4b6ee18f86d cron/updatencbi.sh.sample --- /dev/null +++ b/cron/updatencbi.sh.sample @@ -0,0 +1,42 @@ +#!/bin/sh +# +# Script to update NCBI shared data tables. The idea is to update, but if +# the update fails, not replace current data/tables with error +# messages. + +# Edit this line to refer to galaxy's path: +GALAXY=/path/to/galaxy +PYTHONPATH=${GALAXY}/lib +export PYTHONPATH + +# setup directories +echo "Creating required directories." +DIRS=" +${GALAXY}/tool-data/shared/ncbi +${GALAXY}/tool-data/shared/ncbi/new +" +for dir in $DIRS; do + if [ ! -d $dir ]; then + echo "Creating $dir" + mkdir $dir + else + echo "$dir already exists, continuing." + fi +done + +date +echo "Updating NCBI shared data tables." + +# Try to build "builds.txt" +echo "Updating builds.txt" +python ${GALAXY}/cron/get_ncbi.py > ${GALAXY}/tool-data/shared/ncbi/new/builds.txt +if [ $? -eq 0 ] +then + diff ${GALAXY}/tool-data/shared/ncbi/new/builds.txt ${GALAXY}/tool-data/shared/ncbi/builds.txt > /dev/null 2>&1 + if [ $? -ne 0 ] + then + cp -f ${GALAXY}/tool-data/shared/ncbi/new/builds.txt ${GALAXY}/tool-data/shared/ncbi/builds.txt + fi +else + echo "Failed to update builds.txt" >&2 +fi diff -r 429c1054c13e9c2206ccd4bc3dfd1ca1fa75973c -r df99df26d92fa8a5e3eaef4fd1eef4b6ee18f86d lib/galaxy/web/controllers/data_admin.py --- a/lib/galaxy/web/controllers/data_admin.py +++ b/lib/galaxy/web/controllers/data_admin.py @@ -75,7 +75,7 @@ @web.require_admin def add_genome( self, trans, **kwd ): if trans.app.config.get_bool( 'enable_beta_job_managers', False ) == False: - return trans.fill_template( '/admin/data_admin/betajob.mako' ) + return trans.fill_template( '/admin/data_admin/generic_error.mako', message='This feature requires that enable_beta_job_managers be set to True in your Galaxy configuration.' ) dbkeys = trans.ucsc_builds ensemblkeys = trans.ensembl_builds ncbikeys = trans.ncbi_builds @@ -137,9 +137,10 @@ dbkey = build.split( ': ' )[0] longname = build.split( ': ' )[-1] url = 'http://togows.dbcls.jp/entry/ncbi-nucleotide/%s.fasta' % dbkey - elif source == 'Broad': - dbkey = params.get('broad_dbkey', '')[0] - url = 'ftp://ftp.broadinstitute.org/pub/seq/references/%s.fasta' % dbkey + elif source == 'URL': + dbkey = params.get( 'url_dbkey', '' ) + url = params.get( 'url', None ) + longname = params.get( 'longname', None ) elif source == 'UCSC': longname = None for build in trans.ucsc_builds: @@ -198,7 +199,9 @@ break url = 'ftp://ftp.ensembl.org/pub/release-%s/fasta/%s/dna/%s.%s.%s.dna.toplevel.fa.…' % ( release, pathname.lower(), pathname, dbkey, release ) else: - raise ValueError, 'Somehow an invalid data source was specified.' + return trans.fill_template( '/admin/data_admin/generic_error.mako', message='Somehow an invalid data source was specified.' ) + if url is None: + return trans.fill_template( '/admin/data_admin/generic_error.mako', message='Unable to generate a valid URL with the specified parameters.' ) params = dict( protocol='http', name=dbkey, datatype='fasta', url=url, user=trans.user.id ) jobid = trans.app.job_manager.deferred_job_queue.plugins['GenomeTransferPlugin'].create_job( trans, url, dbkey, longname, indexers ) chainjob = [] diff -r 429c1054c13e9c2206ccd4bc3dfd1ca1fa75973c -r df99df26d92fa8a5e3eaef4fd1eef4b6ee18f86d templates/admin/data_admin/data_form.mako --- a/templates/admin/data_admin/data_form.mako +++ b/templates/admin/data_admin/data_form.mako @@ -53,7 +53,7 @@ <label for="source">Data Source</label><select id="datasource" name="source" label="Data Source"><option value="UCSC">UCSC</option> - <option value="Broad">Broad Institute</option> + <option value="URL">Direct Link</option><option value="NCBI">NCBI</option><option value="Ensembl">EnsemblGenome</option></select> @@ -75,22 +75,31 @@ </div></div><h2>Parameters</h2> - <div id="params_Broad" class="params-block"> + <div id="params_URL" class="params-block"><div class="form-row"> - <label for="longname">Internal Name</label> - <input name="longname" type="text" label="Internal Name" /> + <label for="longname">Long Name</label> + <input name="longname" type="text" label="Long Name" /><div style="clear: both;"> </div> + <div class="toolParamHelp" style="clear: both;"> + A descriptive name for this build. + </div></div><div class="form-row"> - <label for="uniqid">Internal Unique Identifier</label> - <input name="uniqid" type="text" label="Internal Identifier" /> + <label for="url_dbkey">DB Key</label> + <input name="url_dbkey" type="text" label="DB Key" /><div style="clear: both;"> </div> + <div class="toolParamHelp" style="clear: both;"> + The internal DB key for this build. WARNING: Using a value that already exists in one or more .loc files may have unpredictable results. + </div></div><div id="dlparams"><div class="form-row"> - <label for="broad_dbkey">External Name</label> - <input name="broad_dbkey" type="text" label="Genome Unique Name" /> + <label for="url">URL</label> + <input name="url" type="text" label="URL" /><div style="clear: both;"> </div> + <div class="toolParamHelp" style="clear: both;"> + The URL to download this build from. + </div></div></div></div> @@ -101,7 +110,9 @@ <input type="text" class="text-and-autocomplete-select ac_input" size="40" name="ncbi_name" id="ncbi_name" value="" /></div><div class="toolParamHelp" style="clear: both;"> - If you can't find the build you want in this list, <insert link to instructions here> + If you can't find the build you want in this list, open a terminal and execute + <pre>sh cron/updatencbi.sh</pre> + in your galaxy root directory. </div></div></div> @@ -116,7 +127,9 @@ </select></div><div class="toolParamHelp" style="clear: both;"> - If you can't find the build you want in this list, <insert link to instructions here> + If you can't find the build you want in this list, open a terminal and execute + <pre>sh cron/updateensembl.sh</pre> + in your galaxy root directory. </div></div></div> @@ -135,7 +148,9 @@ </select></div><div class="toolParamHelp" style="clear: both;"> - If you can't find the build you want in this list, <insert link to instructions here> + If you can't find the build you want in this list, open a terminal and execute + <pre>sh cron/updateucsc.sh</pre> + in your galaxy root directory. </div></div></div> @@ -145,7 +160,6 @@ <script type="text/javascript"> $(document).ready(function() { checkDataSource(); - // Replace dbkey select with search+select. }); $('#datasource').change(function() { checkDataSource(); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Require pileup format as input to pileup parser tool.
by Bitbucket 23 Aug '12

23 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/429c1054c13e/ changeset: 429c1054c13e user: jgoecks date: 2012-08-23 21:58:11 summary: Require pileup format as input to pileup parser tool. affected #: 1 file diff -r 3bd47802bff7946958b0a616e3d42aef50c63277 -r 429c1054c13e9c2206ccd4bc3dfd1ca1fa75973c tools/samtools/pileup_parser.xml --- a/tools/samtools/pileup_parser.xml +++ b/tools/samtools/pileup_parser.xml @@ -7,7 +7,7 @@ #end if# </command><inputs> - <param name="input" type="data" format="tabular" label="Select dataset"/> + <param name="input" type="data" format="pileup" label="Select dataset"/><conditional name="pileup_type"><param name="type_select" type="select" label="which contains" help="See "Types of pileup datasets" below for examples"><option value="six" selected="true">Pileup with six columns (simple)</option> 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: for feature tracks, only draw name if available.
by Bitbucket 23 Aug '12

23 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3bd47802bff7/ changeset: 3bd47802bff7 user: jgoecks date: 2012-08-23 19:56:34 summary: Trackster: for feature tracks, only draw name if available. affected #: 1 file diff -r c06d0ea23c902e13a5d38ed56ab8cad53130fea5 -r 3bd47802bff7946958b0a616e3d42aef50c63277 static/scripts/viz/trackster.js --- a/static/scripts/viz/trackster.js +++ b/static/scripts/viz/trackster.js @@ -5690,7 +5690,7 @@ ctx.globalAlpha = 1; // Draw label for Pack mode. - if (mode === "Pack" && feature_start > tile_low) { + if (feature_name && mode === "Pack" && feature_start > tile_low) { ctx.fillStyle = label_color; // FIXME: assumption here that the entire view starts at 0 if (tile_low === 0 && f_start - ctx.measureText(feature_name).width < 0) { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 5 new changesets
by Bitbucket 23 Aug '12

23 Aug '12

5 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5e12fae63066/ changeset: 5e12fae63066 user: jmchilton date: 2012-08-22 04:05:53 summary: Roles API bug fixes. affected #: 1 file diff -r e27c236c05e5d65f3ce92f271a712419e7fd73a5 -r 5e12fae63066b12cf3f7f4342ad0ebecb5407a72 lib/galaxy/web/api/roles.py --- a/lib/galaxy/web/api/roles.py +++ b/lib/galaxy/web/api/roles.py @@ -17,7 +17,7 @@ """ rval = [] for role in trans.sa_session.query( trans.app.model.Role ).filter( trans.app.model.Role.table.c.deleted == False ): - if trans.app.security_agent.ok_to_display( trans.user, role ): + if trans.user_is_admin() or trans.app.security_agent.ok_to_display( trans.user, role ): item = role.get_api_value( value_mapper={ 'id': trans.security.encode_id } ) encoded_id = trans.security.encode_id( role.id ) item['url'] = url_for( 'role', id=encoded_id ) @@ -32,7 +32,7 @@ """ role_id = id try: - role_id = trans.security.decode_id( role_id ) + decoded_role_id = trans.security.decode_id( role_id ) except TypeError: trans.response.status = 400 return "Malformed role id ( %s ) specified, unable to decode." % str( role_id ) @@ -40,7 +40,7 @@ role = trans.sa_session.query( trans.app.model.Role ).get( decoded_role_id ) except: role = None - if not role or not trans.app.security_agent.ok_to_display( trans.user, role ): + if not role or not (trans.user_is_admin() or trans.app.security_agent.ok_to_display( trans.user, role )): trans.response.status = 400 return "Invalid role id ( %s ) specified." % str( role_id ) item = role.get_api_value( view='element', value_mapper={ 'id': trans.security.encode_id } ) https://bitbucket.org/galaxy/galaxy-central/changeset/558547d5329f/ changeset: 558547d5329f user: jmchilton date: 2012-08-22 06:05:05 summary: Fix library permissions API which has been broken since security API changes in 8731db1b2bfb (June 2011). affected #: 1 file diff -r 5e12fae63066b12cf3f7f4342ad0ebecb5407a72 -r 558547d5329f49cad685056cd4284e8e7661cffc lib/galaxy/web/api/permissions.py --- a/lib/galaxy/web/api/permissions.py +++ b/lib/galaxy/web/api/permissions.py @@ -40,10 +40,10 @@ role_params = params.get( k + '_in', [] ) in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( trans.security.decode_id( x ) ) for x in util.listify( role_params ) ] permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles - trans.app.security_agent.set_all_library_permissions( library, permissions ) + trans.app.security_agent.set_all_library_permissions( trans, library, permissions ) trans.sa_session.refresh( library ) # Copy the permissions to the root folder - trans.app.security_agent.copy_library_permissions( library, library.root_folder ) + trans.app.security_agent.copy_library_permissions( trans, library, library.root_folder ) message = "Permissions updated for library '%s'." % library.name item = library.get_api_value( view='element' ) https://bitbucket.org/galaxy/galaxy-central/changeset/a186a4bd7bae/ changeset: a186a4bd7bae user: jmchilton date: 2012-08-22 23:57:04 summary: Create method in libraries API should return the created library not an array containing only the created library. This was confirmed by dannon in the comments on issue 802. affected #: 1 file diff -r 558547d5329f49cad685056cd4284e8e7661cffc -r a186a4bd7bae84459de066b22d49e226e2112ce1 lib/galaxy/web/api/libraries.py --- a/lib/galaxy/web/api/libraries.py +++ b/lib/galaxy/web/api/libraries.py @@ -98,7 +98,7 @@ rval['url'] = url_for( 'library', id=encoded_id ) rval['name'] = name rval['id'] = encoded_id - return [ rval ] + return rval @web.expose_api def delete( self, trans, id, **kwd ): https://bitbucket.org/galaxy/galaxy-central/changeset/bec712216582/ changeset: bec712216582 user: jmchilton date: 2012-08-23 00:05:53 summary: Include created history url in json rendered by histories API on successful history creation. Dannon verified this is the desired behvaior in the comments on issue 802 in bitbucket. affected #: 1 file diff -r a186a4bd7bae84459de066b22d49e226e2112ce1 -r bec712216582134338a733ccd85bc4dac25353c4 lib/galaxy/web/api/histories.py --- a/lib/galaxy/web/api/histories.py +++ b/lib/galaxy/web/api/histories.py @@ -109,6 +109,7 @@ trans.sa_session.add( new_history ) trans.sa_session.flush() item = new_history.get_api_value(view='element', value_mapper={'id':trans.security.encode_id}) + item['url'] = url_for( 'history', id=item['id'] ) return item @web.expose_api https://bitbucket.org/galaxy/galaxy-central/changeset/c06d0ea23c90/ changeset: c06d0ea23c90 user: dannon date: 2012-08-23 15:34:43 summary: Merged in jmchilton/galaxy-central-roles-api-fixes (pull request #62) affected #: 4 files diff -r 146d0f4c29decefb441a7133b4aa16442afdacb1 -r c06d0ea23c902e13a5d38ed56ab8cad53130fea5 lib/galaxy/web/api/histories.py --- a/lib/galaxy/web/api/histories.py +++ b/lib/galaxy/web/api/histories.py @@ -109,6 +109,7 @@ trans.sa_session.add( new_history ) trans.sa_session.flush() item = new_history.get_api_value(view='element', value_mapper={'id':trans.security.encode_id}) + item['url'] = url_for( 'history', id=item['id'] ) return item @web.expose_api diff -r 146d0f4c29decefb441a7133b4aa16442afdacb1 -r c06d0ea23c902e13a5d38ed56ab8cad53130fea5 lib/galaxy/web/api/libraries.py --- a/lib/galaxy/web/api/libraries.py +++ b/lib/galaxy/web/api/libraries.py @@ -98,7 +98,7 @@ rval['url'] = url_for( 'library', id=encoded_id ) rval['name'] = name rval['id'] = encoded_id - return [ rval ] + return rval @web.expose_api def delete( self, trans, id, **kwd ): diff -r 146d0f4c29decefb441a7133b4aa16442afdacb1 -r c06d0ea23c902e13a5d38ed56ab8cad53130fea5 lib/galaxy/web/api/permissions.py --- a/lib/galaxy/web/api/permissions.py +++ b/lib/galaxy/web/api/permissions.py @@ -40,10 +40,10 @@ role_params = params.get( k + '_in', [] ) in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( trans.security.decode_id( x ) ) for x in util.listify( role_params ) ] permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles - trans.app.security_agent.set_all_library_permissions( library, permissions ) + trans.app.security_agent.set_all_library_permissions( trans, library, permissions ) trans.sa_session.refresh( library ) # Copy the permissions to the root folder - trans.app.security_agent.copy_library_permissions( library, library.root_folder ) + trans.app.security_agent.copy_library_permissions( trans, library, library.root_folder ) message = "Permissions updated for library '%s'." % library.name item = library.get_api_value( view='element' ) diff -r 146d0f4c29decefb441a7133b4aa16442afdacb1 -r c06d0ea23c902e13a5d38ed56ab8cad53130fea5 lib/galaxy/web/api/roles.py --- a/lib/galaxy/web/api/roles.py +++ b/lib/galaxy/web/api/roles.py @@ -17,7 +17,7 @@ """ rval = [] for role in trans.sa_session.query( trans.app.model.Role ).filter( trans.app.model.Role.table.c.deleted == False ): - if trans.app.security_agent.ok_to_display( trans.user, role ): + if trans.user_is_admin() or trans.app.security_agent.ok_to_display( trans.user, role ): item = role.get_api_value( value_mapper={ 'id': trans.security.encode_id } ) encoded_id = trans.security.encode_id( role.id ) item['url'] = url_for( 'role', id=encoded_id ) @@ -32,7 +32,7 @@ """ role_id = id try: - role_id = trans.security.decode_id( role_id ) + decoded_role_id = trans.security.decode_id( role_id ) except TypeError: trans.response.status = 400 return "Malformed role id ( %s ) specified, unable to decode." % str( role_id ) @@ -40,7 +40,7 @@ role = trans.sa_session.query( trans.app.model.Role ).get( decoded_role_id ) except: role = None - if not role or not trans.app.security_agent.ok_to_display( trans.user, role ): + if not role or not (trans.user_is_admin() or trans.app.security_agent.ok_to_display( trans.user, role )): trans.response.status = 400 return "Invalid role id ( %s ) specified." % str( role_id ) item = role.get_api_value( view='element', value_mapper={ 'id': trans.security.encode_id } ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Fix for handling missing quality values in VCF data provider + some whitespace. Thanks to Jim Johnson for fix.
by Bitbucket 23 Aug '12

23 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/146d0f4c29de/ changeset: 146d0f4c29de user: jgoecks date: 2012-08-23 15:04:08 summary: Fix for handling missing quality values in VCF data provider + some whitespace. Thanks to Jim Johnson for fix. affected #: 1 file diff -r dd8a939cf0a26ea9e3cb969297bbfe7d749e88f7 -r 146d0f4c29decefb441a7133b4aa16442afdacb1 lib/galaxy/visualization/tracks/data_providers.py --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -625,7 +625,8 @@ end = start + len( new_seq ) # Pack line. - payload = [ hash( line ), + payload = [ + hash( line ), start, end, # ID: @@ -634,7 +635,8 @@ # TODO? VCF does not have strand, so default to positive. "+", new_seq, - float( feature[5] ) ] + None if feature[5] == '.' else float( feature[5] ) + ] rval.append(payload) return { 'data': rval, 'message': 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: jgoecks: Update datatypes conf sample to include bedgraph to bigwig converter.
by Bitbucket 22 Aug '12

22 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/dd8a939cf0a2/ changeset: dd8a939cf0a2 user: jgoecks date: 2012-08-23 04:54:54 summary: Update datatypes conf sample to include bedgraph to bigwig converter. affected #: 1 file diff -r f0e26a4f7dd91d9a632913ae450e285e37a9a302 -r dd8a939cf0a26ea9e3cb969297bbfe7d749e88f7 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -23,7 +23,9 @@ <display file="genetrack.xml" /><display file="igb/bed.xml" /></datatype> - <datatype extension="bedgraph" type="galaxy.datatypes.interval:BedGraph" display_in_upload="true" /> + <datatype extension="bedgraph" type="galaxy.datatypes.interval:BedGraph" display_in_upload="true"> + <converter file="bedgraph_to_bigwig_converter.xml" target_datatype="bigwig"/> + </datatype><datatype extension="bedstrict" type="galaxy.datatypes.interval:BedStrict" /><datatype extension="bed6" type="galaxy.datatypes.interval:Bed6"><converter file="bed_to_genetrack_converter.xml" target_datatype="genetrack"/> 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: Output sorted BAM from Bowtie2.
by Bitbucket 22 Aug '12

22 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f0e26a4f7dd9/ changeset: f0e26a4f7dd9 user: jgoecks date: 2012-08-22 22:49:12 summary: Output sorted BAM from Bowtie2. affected #: 1 file diff -r 695159af542b44ac5038d1b3cc401b3f4b98d2e3 -r f0e26a4f7dd91d9a632913ae450e285e37a9a302 tools/sr_mapping/bowtie2_wrapper.py --- a/tools/sr_mapping/bowtie2_wrapper.py +++ b/tools/sr_mapping/bowtie2_wrapper.py @@ -64,8 +64,8 @@ else: index_path = options.index_path - # Build bowtie command. - cmd = 'bowtie2 %s -x %s %s | samtools view -Sb - > %s' + # Build bowtie command; use view and sort to create sorted bam. + cmd = 'bowtie2 %s -x %s %s | samtools view -Su - | samtools sort -o - sorted > %s' # Set up reads. if options.single_paired == 'paired': Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Remove blast tools and test data from the distribution, update tool_conf.xml.sample to reflect this.
by Bitbucket 22 Aug '12

22 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/695159af542b/ changeset: 695159af542b user: dannon date: 2012-08-22 22:12:59 summary: Remove blast tools and test data from the distribution, update tool_conf.xml.sample to reflect this. affected #: 36 files Diff too large to display. 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: richard_burhans: name change: _BX main_ browser -> _BX_ table browser
by Bitbucket 22 Aug '12

22 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/bf6517b2b336/ changeset: bf6517b2b336 user: richard_burhans date: 2012-08-22 21:31:23 summary: name change: _BX main_ browser -> _BX_ table browser affected #: 1 file diff -r 863e1150c85b7383a1b136c9b3c9376da81bc16b -r bf6517b2b336113964fe90ef74b6db333ee97f63 tools/data_source/bx_browser.xml --- a/tools/data_source/bx_browser.xml +++ b/tools/data_source/bx_browser.xml @@ -4,8 +4,8 @@ the initial response. If value of 'URL_method' is 'post', any additional params coming back in the initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed. --> -<tool name="BX main" id="bx_browser" tool_type="data_source"> - <description>browser</description> +<tool name="BX" id="bx_browser" tool_type="data_source"> + <description>table browser</description><command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command><inputs action="http://main.genome-browser.bx.psu.edu/cgi-bin/hgTables" check_values="false" method="get"><display>go to BX Browser $GALAXY_URL</display> 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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