- galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: 2 new changesets
by Bitbucket 03 May '12

03 May '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/81e6e2f44d32/ changeset: 81e6e2f44d32 user: cjav date: 2012-05-03 01:30:11 summary: expose dataset full path through the API affected #: 1 file diff -r c5f3e218266e8b82cd509b9177461839c74971c3 -r 81e6e2f44d32845b8d48459ea779030d596c7c48 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1167,6 +1167,7 @@ deleted = hda.deleted, visible = hda.visible, state = hda.state, + file_name = hda.file_name, file_size = int( hda.get_size() ), data_type = hda.ext, genome_build = hda.dbkey, https://bitbucket.org/galaxy/galaxy-central/changeset/4d7077d8d2b8/ changeset: 4d7077d8d2b8 user: dannon date: 2012-05-03 16:18:38 summary: Incorporation and slight update to pull request #43. The original contribution allowed access to file_path regardless of admin status and config setting. affected #: 2 files diff -r 81e6e2f44d32845b8d48459ea779030d596c7c48 -r 4d7077d8d2b875feed71fa8c9ab7bd701957b909 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1167,7 +1167,6 @@ deleted = hda.deleted, visible = hda.visible, state = hda.state, - file_name = hda.file_name, file_size = int( hda.get_size() ), data_type = hda.ext, genome_build = hda.dbkey, diff -r 81e6e2f44d32845b8d48459ea779030d596c7c48 -r 4d7077d8d2b875feed71fa8c9ab7bd701957b909 lib/galaxy/web/api/history_contents.py --- a/lib/galaxy/web/api/history_contents.py +++ b/lib/galaxy/web/api/history_contents.py @@ -1,11 +1,9 @@ """ API operations on the contents of a history. """ -import logging, os, string, shutil, urllib, re, socket -from cgi import escape, FieldStorage -from galaxy import util, datatypes, jobs, web, util +import logging +from galaxy import web from galaxy.web.base.controller import * -from galaxy.util.sanitize_html import sanitize_html from galaxy.model.orm import * import pkg_resources @@ -56,6 +54,8 @@ return str( e ) try: item = content.get_api_value( view='element' ) + if trans.user_is_admin() or trans.app.config.expose_dataset_path: + item['file_name'] = hda.file_name if not item['deleted']: # Problem: Method url_for cannot use the dataset controller # Get the environment from DefaultWebTransaction and use default webapp mapper instead of webapp API mapper @@ -76,7 +76,6 @@ POST /api/libraries/{encoded_history_id}/contents Creates a new history content item (file, aka HistoryDatasetAssociation). """ - params = util.Params( payload ) from_ld_id = payload.get( 'from_ld_id', None ) try: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dan: Update WormBase datasource tool to use WormBase 2.
by Bitbucket 02 May '12

02 May '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c5f3e218266e/ changeset: c5f3e218266e user: dan date: 2012-05-02 23:04:33 summary: Update WormBase datasource tool to use WormBase 2. affected #: 1 file diff -r a781f132e259b60c417c674047535ac0a688b69d -r c5f3e218266e8b82cd509b9177461839c74971c3 tools/data_source/wormbase.xml --- a/tools/data_source/wormbase.xml +++ b/tools/data_source/wormbase.xml @@ -1,8 +1,8 @@ <?xml version="1.0"?> -<tool name="Wormbase" id="wormbase" tool_type="data_source"> +<tool name="WormBase" id="wormbase" tool_type="data_source" version="1.0.1"><description>server</description><command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> - <inputs action="http://www.wormbase.org/db/seq/gbgff/c_elegans/" check_values="false" target="_top"> + <inputs action="http://www.wormbase.org/tools/genome/gbrowse/c_elegans/" check_values="false" target="_top"><display>go to Wormbase server $GALAXY_URL</display><param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=wormbase" /></inputs> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dan: Fix typo in BAM slice tool.
by Bitbucket 02 May '12

02 May '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a781f132e259/ changeset: a781f132e259 user: dan date: 2012-05-02 17:47:04 summary: Fix typo in BAM slice tool. affected #: 1 file diff -r 926c93b412beaaff5579e6faa2d052768e9408d1 -r a781f132e259b60c417c674047535ac0a688b69d tools/samtools/samtools_slice_bam.xml --- a/tools/samtools/samtools_slice_bam.xml +++ b/tools/samtools/samtools_slice_bam.xml @@ -20,7 +20,7 @@ <test><param name="input_bam" value="gatk/fake_phiX_reads_1.bam" ftype="bam" /><param name="input_interval" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" /> - <output name="output_log" file="gatk/fake_phiX_reads_1.bam" ftype="bam" /> + <output name="output_bam" file="gatk/fake_phiX_reads_1.bam" ftype="bam" /></test></tests><help> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dan: Add Slice BAM by regions tool.
by Bitbucket 02 May '12

02 May '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/926c93b412be/ changeset: 926c93b412be user: dan date: 2012-05-02 17:32:19 summary: Add Slice BAM by regions tool. affected #: 3 files diff -r 5e53e5d824009984629a269b9d768b99b5683310 -r 926c93b412beaaff5579e6faa2d052768e9408d1 tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -384,6 +384,7 @@ <tool file="samtools/pileup_interval.xml" /><tool file="samtools/samtools_flagstat.xml" /><tool file="samtools/samtools_rmdup.xml" /> + <tool file="samtools/samtools_slice_bam.xml" /></section><section name="NGS: GATK Tools (beta)" id="gatk"><label text="Alignment Utilities" id="gatk_bam_utilities"/> diff -r 5e53e5d824009984629a269b9d768b99b5683310 -r 926c93b412beaaff5579e6faa2d052768e9408d1 tools/samtools/samtools_slice_bam.py --- /dev/null +++ b/tools/samtools/samtools_slice_bam.py @@ -0,0 +1,75 @@ +#!/usr/bin/env python +#Dan Blankenberg + +""" +A wrapper script for slicing a BAM file by provided BED file using SAMTools. +%prog input_filename.sam output_filename.bam +""" +#TODO: Confirm that the sort is necessary e.g. if input regions are out of order + + +import sys, optparse, os, tempfile, subprocess, shutil + +CHUNK_SIZE = 2**20 #1mb + +def cleanup_before_exit( tmp_dir ): + if tmp_dir and os.path.exists( tmp_dir ): + shutil.rmtree( tmp_dir ) + +def __main__(): + #Parse Command Line + parser = optparse.OptionParser() + (options, args) = parser.parse_args() + + assert len( args ) == 4, "Invalid command line: samtools_slice_bam.py input.bam input.bam.bai input.interval output.bam" + input_bam_filename, input_index_filename, input_interval_filename, output_bam_filename = args + + tmp_dir = tempfile.mkdtemp( prefix='tmp-samtools_slice_bam-' ) + + tmp_input_bam_filename = os.path.join( tmp_dir, 'input_bam.bam' ) + os.symlink( input_bam_filename, tmp_input_bam_filename ) + os.symlink( input_index_filename, "%s.bai" % tmp_input_bam_filename ) + + #Slice BAM + unsorted_bam_filename = os.path.join( tmp_dir, 'unsorted.bam' ) + unsorted_stderr_filename = os.path.join( tmp_dir, 'unsorted.stderr' ) + cmd = 'samtools view -b -L "%s" "%s" > "%s"' % ( input_interval_filename, tmp_input_bam_filename, unsorted_bam_filename ) + proc = subprocess.Popen( args=cmd, stderr=open( unsorted_stderr_filename, 'wb' ), shell=True, cwd=tmp_dir ) + return_code = proc.wait() + if return_code: + stderr_target = sys.stderr + else: + stderr_target = sys.stdout + stderr = open( unsorted_stderr_filename ) + while True: + chunk = stderr.read( CHUNK_SIZE ) + if chunk: + stderr_target.write( chunk ) + else: + break + stderr.close() + + #sort sam, so indexing will not fail + #TODO: confirm if sorting is necessary (is original BAM order maintained, or does the output follow the order of input intervals?) + sorted_stderr_filename = os.path.join( tmp_dir, 'sorted.stderr' ) + sorting_prefix = os.path.join( tmp_dir, 'sorted_bam' ) + cmd = 'samtools sort -o "%s" "%s" > "%s"' % ( unsorted_bam_filename, sorting_prefix, output_bam_filename ) + proc = subprocess.Popen( args=cmd, stderr=open( sorted_stderr_filename, 'wb' ), shell=True, cwd=tmp_dir ) + return_code = proc.wait() + + if return_code: + stderr_target = sys.stderr + else: + stderr_target = sys.stdout + stderr = open( sorted_stderr_filename ) + while True: + chunk = stderr.read( CHUNK_SIZE ) + if chunk: + stderr_target.write( chunk ) + else: + break + stderr.close() + + cleanup_before_exit( tmp_dir ) + +if __name__=="__main__": __main__() diff -r 5e53e5d824009984629a269b9d768b99b5683310 -r 926c93b412beaaff5579e6faa2d052768e9408d1 tools/samtools/samtools_slice_bam.xml --- /dev/null +++ b/tools/samtools/samtools_slice_bam.xml @@ -0,0 +1,40 @@ +<tool id="samtools_slice_bam" name="Slice BAM" version="0.0.1"> + <description>by provided regions</description> + <requirements> + <requirement type="package">samtools</requirement> + </requirements> + <command interpreter="python">samtools_slice_bam.py + "${input_bam}" + "${input_bam.metadata.bam_index}" + "${input_interval}" + "${output_bam}" + </command> + <inputs> + <param name="input_bam" type="data" format="bam" label="BAM file" /> + <param name="input_interval" type="data" format="bed" label="BED file" /> + </inputs> + <outputs> + <data format="bam" name="output_bam"/> + </outputs> + <tests> + <test> + <param name="input_bam" value="gatk/fake_phiX_reads_1.bam" ftype="bam" /> + <param name="input_interval" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" /> + <output name="output_log" file="gatk/fake_phiX_reads_1.bam" ftype="bam" /> + </test> + </tests> + <help> +**What it does** + + Accepts an input BAM file and an input BED file and creates an output BAM file containing only those alignments that overlap the provided BED intervals. + +------ + +**Citation** + +For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ + +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + + </help> +</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.

1 0

commit/galaxy-central: greg: Fix popup menu for viewing tool metadata in a tool shed repository to be compatible with new styles.
by Bitbucket 01 May '12

01 May '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5e53e5d82400/ changeset: 5e53e5d82400 user: greg date: 2012-05-01 18:17:07 summary: Fix popup menu for viewing tool metadata in a tool shed repository to be compatible with new styles. affected #: 1 file diff -r 49b5dc00dfb6ef3bf0f4bb1f611db33042469181 -r 5e53e5d824009984629a269b9d768b99b5683310 templates/webapps/community/repository/common.mako --- a/templates/webapps/community/repository/common.mako +++ b/templates/webapps/community/repository/common.mako @@ -108,15 +108,13 @@ <td><b>version</b></td><td><b>requirements</b></td></tr> - %for tool_dict in tool_dicts: + %for index, tool_dict in enumerate( tool_dicts ): <tr><td> - <div style="float: left; margin-left: 1px;" class="menubutton split popup" id="tool-${tool_dict[ 'id' ].replace( ' ', '_' )}-popup"> - <a class="view-info" href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ], changeset_revision=changeset_revision, webapp=webapp )}"> - ${tool_dict[ 'name' ]} - </a> + <div style="float:left;" class="menubutton split popup" id="tool-${index}-popup"> + <a class="view-info" href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ], changeset_revision=changeset_revision, webapp=webapp )}">${tool_dict[ 'name' ]}</a></div> - <div popupmenu="tool-${tool_dict[ 'id' ].replace( ' ', '_' )}-popup"> + <div popupmenu="tool-${index}-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=changeset_revision, tool_id=tool_dict[ 'id' ], webapp=webapp )}">View tool metadata</a></div></td> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Eliminate the fabfile/method type from ToolRequirement.
by Bitbucket 01 May '12

01 May '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/49b5dc00dfb6/ changeset: 49b5dc00dfb6 user: greg date: 2012-05-01 15:15:59 summary: Eliminate the fabfile/method type from ToolRequirement. affected #: 1 file diff -r 0090f9df64fd84a9fda73d12b816a7d4d044b822 -r 49b5dc00dfb6ef3bf0f4bb1f611db33042469181 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -702,19 +702,13 @@ class ToolRequirement( object ): """ - Represents an external requirement that must be available for the tool to - run (for example, a program, package, or library). Requirements can - optionally assert a specific version, or reference a command to execute a - fabric script. If fabric is used, the type is 'fabfile' and the version - attribute is not used since the fabric script includes all necessary - information for automatic dependency installation. + Represents an external requirement that must be available for the tool to run (for example, a program, package, or library). + Requirements can optionally assert a specific version. """ - def __init__( self, name=None, type=None, version=None, fabfile=None, method=None ): + def __init__( self, name=None, type=None, version=None ): self.name = name self.type = type self.version = version - self.fabfile = fabfile - self.method = method class ToolParallelismInfo(object): """ @@ -1339,19 +1333,8 @@ for requirement_elem in requirements_elem.findall( 'requirement' ): name = util.xml_text( requirement_elem ) type = requirement_elem.get( "type", "package" ) - if type == 'fabfile': - # The fabric script will include all necessary information for - # automatically installing the tool dependencies. - fabfile = requirement_elem.get( "fabfile" ) - method = requirement_elem.get( "method" ) - version = None - else: - # For backward compatibility, requirements tag sets should not require the - # use of a fabric script. - version = requirement_elem.get( "version" ) - fabfile = None - method = None - requirement = ToolRequirement( name=name, type=type, version=version, fabfile=fabfile, method=method ) + version = requirement_elem.get( "version", None ) + requirement = ToolRequirement( name=name, type=type, version=version ) self.requirements.append( requirement ) def check_workflow_compatible( self ): """ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Fix the instructions on the veiw request type page.
by Bitbucket 01 May '12

01 May '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0090f9df64fd/ changeset: 0090f9df64fd user: greg date: 2012-05-01 15:11:07 summary: Fix the instructions on the veiw request type page. affected #: 1 file diff -r 1640cbaafd09a3cb4bcdea55d95c43d619a0471f -r 0090f9df64fd84a9fda73d12b816a7d4d044b822 templates/admin/request_type/view_request_type.mako --- a/templates/admin/request_type/view_request_type.mako +++ b/templates/admin/request_type/view_request_type.mako @@ -73,7 +73,7 @@ %endfor %else: <div class="form-row"> - External service login information is not set. Select the <b>Edit request type</b> option in the <b>Configuration options</b> menu. + External service login information is not set. Select the <b>Edit request type</b> option in the <b>Request type actions</b> menu. </div> %endif </div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: natefoo: Allow for library deletion from the API (admins only).
by Bitbucket 30 Apr '12

30 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1640cbaafd09/ changeset: 1640cbaafd09 user: natefoo date: 2012-04-30 22:27:55 summary: Allow for library deletion from the API (admins only). affected #: 2 files diff -r 4ff0dd2aa475275a13c65f183c4bb2595f001941 -r 1640cbaafd09a3cb4bcdea55d95c43d619a0471f lib/galaxy/web/api/libraries.py --- a/lib/galaxy/web/api/libraries.py +++ b/lib/galaxy/web/api/libraries.py @@ -7,18 +7,27 @@ from galaxy.web.base.controller import * from galaxy.util.sanitize_html import sanitize_html from galaxy.model.orm import * +from paste.httpexceptions import * log = logging.getLogger( __name__ ) class LibrariesController( BaseAPIController ): @web.expose_api - def index( self, trans, **kwd ): + def index( self, trans, deleted='False', **kwd ): """ GET /api/libraries + GET /api/libraries/deleted Displays a collection (list) of libraries. """ - query = trans.sa_session.query( trans.app.model.Library ).filter( trans.app.model.Library.table.c.deleted == False ) + query = trans.sa_session.query( trans.app.model.Library ) + deleted = util.string_as_bool( deleted ) + if deleted: + route = 'deleted_library' + query = query.filter( trans.app.model.Library.table.c.deleted == True ) + else: + route = 'library' + query = query.filter( trans.app.model.Library.table.c.deleted == False ) current_user_role_ids = [ role.id for role in trans.get_current_user_roles() ] library_access_action = trans.app.security_agent.permitted_actions.LIBRARY_ACCESS.action restricted_library_ids = [ lp.library_id for lp in trans.sa_session.query( trans.model.LibraryPermissions ) \ @@ -32,31 +41,32 @@ rval = [] for library in query: item = library.get_api_value() - item['url'] = url_for( 'library', id=trans.security.encode_id( library.id ) ) + item['url'] = url_for( route, id=trans.security.encode_id( library.id ) ) item['id'] = trans.security.encode_id( item['id'] ) rval.append( item ) return rval @web.expose_api - def show( self, trans, id, **kwd ): + def show( self, trans, id, deleted='False', **kwd ): """ GET /api/libraries/{encoded_library_id} + GET /api/libraries/deleted/{encoded_library_id} Displays information about a library. """ library_id = id + deleted = util.string_as_bool( deleted ) params = util.Params( kwd ) try: decoded_library_id = trans.security.decode_id( library_id ) except TypeError: - trans.response.status = 400 - return "Malformed library id ( %s ) specified, unable to decode." % str( library_id ) + raise HTTPBadRequest( detail='Malformed library id ( %s ) specified, unable to decode.' % id ) try: library = trans.sa_session.query( trans.app.model.Library ).get( decoded_library_id ) + assert library.deleted == deleted except: library = None if not library or not ( trans.user_is_admin() or trans.app.security_agent.can_access_library( trans.get_current_user_roles(), library ) ): - trans.response.status = 400 - return "Invalid library id ( %s ) specified." % str( library_id ) + raise HTTPBadRequest( detail='Invalid library id ( %s ) specified.' % id ) item = library.get_api_value( view='element' ) #item['contents_url'] = url_for( 'contents', library_id=library_id ) item['contents_url'] = url_for( 'library_contents', library_id=library_id ) @@ -69,13 +79,11 @@ Creates a new library. """ if not trans.user_is_admin(): - trans.response.status = 403 - return "You are not authorized to create a new library." + raise HTTPForbidden( detail='You are not authorized to create a new library.' ) params = util.Params( payload ) name = util.restore_text( params.get( 'name', None ) ) if not name: - trans.response.status = 400 - return "Missing required parameter 'name'." + raise HTTPBadRequest( detail="Missing required parameter 'name'." ) description = util.restore_text( params.get( 'description', '' ) ) synopsis = util.restore_text( params.get( 'synopsis', '' ) ) if synopsis in [ 'None', None ]: @@ -91,3 +99,22 @@ rval['name'] = name rval['id'] = encoded_id return [ rval ] + + @web.expose_api + def delete( self, trans, id, **kwd ): + if not trans.user_is_admin(): + raise HTTPForbidden( detail='You are not authorized to delete libraries.' ) + try: + decoded_id = trans.security.decode_id( id ) + except TypeError: + raise HTTPBadRequest( detail='Malformed library id ( %s ) specified, unable to decode.' % id ) + try: + library = trans.sa_session.query( trans.app.model.Library ).get( decoded_id ) + except: + library = None + if not library: + raise HTTPBadRequest( detail='Invalid library id ( %s ) specified.' % id ) + library.deleted = True + trans.sa_session.add( library ) + trans.sa_session.flush() + return library.get_api_value( view='element', value_mapper={ 'id' : trans.security.encode_id } ) diff -r 4ff0dd2aa475275a13c65f183c4bb2595f001941 -r 1640cbaafd09a3cb4bcdea55d95c43d619a0471f lib/galaxy/web/buildapp.py --- a/lib/galaxy/web/buildapp.py +++ b/lib/galaxy/web/buildapp.py @@ -123,7 +123,7 @@ path_prefix='/api/libraries/:library_id', parent_resources=dict( member_name='library', collection_name='libraries' ) ) webapp.api_mapper.resource( 'dataset', 'datasets', path_prefix='/api' ) - webapp.api_mapper.resource( 'library', 'libraries', path_prefix='/api' ) + webapp.api_mapper.resource_with_deleted( 'library', 'libraries', path_prefix='/api' ) webapp.api_mapper.resource( 'sample', 'samples', path_prefix='/api' ) webapp.api_mapper.resource( 'request', 'requests', path_prefix='/api' ) webapp.api_mapper.resource( 'form', 'forms', path_prefix='/api' ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Eliminate resetting all repository metadata on a tool shed repostiory when its not necessary.
by Bitbucket 30 Apr '12

30 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4ff0dd2aa475/ changeset: 4ff0dd2aa475 user: greg date: 2012-04-30 20:42:39 summary: Eliminate resetting all repository metadata on a tool shed repostiory when its not necessary. affected #: 4 files diff -r 559105c554d540d8137d6583c58b2e237fe1eff4 -r 4ff0dd2aa475275a13c65f183c4bb2595f001941 lib/galaxy/tool_shed/update_manager.py --- a/lib/galaxy/tool_shed/update_manager.py +++ b/lib/galaxy/tool_shed/update_manager.py @@ -34,7 +34,7 @@ log.info( 'Transfer job restarter shutting down...' ) def check_for_update( self, repository ): tool_shed_url = get_url_from_repository_tool_shed( self.app, repository ) - url = '%s/repository/check_for_updates?name=%s&owner=%s&changeset_revision=%s&webapp=update_manager' % \ + url = '%s/repository/check_for_updates?name=%s&owner=%s&changeset_revision=%s&webapp=update_manager&no_reset=true' % \ ( tool_shed_url, repository.name, repository.owner, repository.changeset_revision ) response = urllib2.urlopen( url ) text = response.read() diff -r 559105c554d540d8137d6583c58b2e237fe1eff4 -r 4ff0dd2aa475275a13c65f183c4bb2595f001941 lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -149,7 +149,7 @@ def browse_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] galaxy_url = url_for( '/', qualified=True ) - url = '%srepository/browse_valid_repositories?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url ) + url = '%srepository/browse_valid_repositories?galaxy_url=%s&webapp=galaxy&no_reset=true' % ( tool_shed_url, galaxy_url ) return trans.response.send_redirect( url ) @web.expose @web.require_admin @@ -167,7 +167,7 @@ # Send a request to the relevant tool shed to see if there are any updates. repository = get_repository( trans, kwd[ 'id' ] ) tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) - url = '%s/repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + url = '%s/repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy&no_reset=true' % \ ( tool_shed_url, url_for( '/', qualified=True ), repository.name, repository.owner, repository.changeset_revision ) return trans.response.send_redirect( url ) @web.expose @@ -218,14 +218,14 @@ def find_tools_in_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] galaxy_url = url_for( '/', qualified=True ) - url = '%srepository/find_tools?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url ) + url = '%srepository/find_tools?galaxy_url=%s&webapp=galaxy&no_reset=true' % ( tool_shed_url, galaxy_url ) return trans.response.send_redirect( url ) @web.expose @web.require_admin def find_workflows_in_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] galaxy_url = url_for( '/', qualified=True ) - url = '%srepository/find_workflows?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url ) + url = '%srepository/find_workflows?galaxy_url=%s&webapp=galaxy&no_reset=true' % ( tool_shed_url, galaxy_url ) return trans.response.send_redirect( url ) @web.expose @web.require_admin @@ -318,7 +318,7 @@ shed_tool_conf=shed_tool_conf ) if 'tools' in metadata_dict: # Get the tool_versions from the tool shed for each tool in the installed change set. - url = '%srepository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + url = '%srepository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy&no_reset=true' % \ ( tool_shed_url, name, owner, changeset_revision ) response = urllib2.urlopen( url ) text = response.read() @@ -367,7 +367,7 @@ repo_info_tuple = decoded_repo_info_dict[ name ] description, repository_clone_url, changeset_revision, ctx_rev = repo_info_tuple owner = get_repository_owner( clean_repository_clone_url( repository_clone_url ) ) - url = '%srepository/get_readme?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % ( tool_shed_url, name, owner, changeset_revision ) + url = '%srepository/get_readme?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy&no_reset=true' % ( tool_shed_url, name, owner, changeset_revision ) response = urllib2.urlopen( url ) raw_text = response.read() response.close() @@ -564,7 +564,7 @@ # Get the tool_versions from the tool shed for each tool in the installed change set. repository = get_repository( trans, kwd[ 'id' ] ) tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) - url = '%s/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + url = '%s/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy&no_reset=true' % \ ( tool_shed_url, repository.name, repository.owner, repository.changeset_revision ) response = urllib2.urlopen( url ) text = response.read() diff -r 559105c554d540d8137d6583c58b2e237fe1eff4 -r 4ff0dd2aa475275a13c65f183c4bb2595f001941 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -1145,7 +1145,7 @@ import_button = True if tool_shed_url and not import_button: # Use urllib (send another request to the tool shed) to retrieve the workflow. - workflow_url = '%s/workflow/import_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&open_for_url=true' % \ + workflow_url = '%s/workflow/import_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&open_for_url=true&no_reset=true' % \ ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ), webapp ) response = urllib2.urlopen( workflow_url ) workflow_text = response.read() diff -r 559105c554d540d8137d6583c58b2e237fe1eff4 -r 4ff0dd2aa475275a13c65f183c4bb2595f001941 lib/galaxy/webapps/community/controllers/hg.py --- a/lib/galaxy/webapps/community/controllers/hg.py +++ b/lib/galaxy/webapps/community/controllers/hg.py @@ -16,8 +16,10 @@ # hg clone http://test@127.0.0.1:9009/repos/test/convert_characters1 cmd = kwd.get( 'cmd', None ) wsgi_app = wsgiapplication( make_web_app ) - if cmd == 'listkeys': - # This results from an "hg push" from the command line. When doing this, the following 7 commands, in order, + # Hack: Add a parameter to requests for which we do not want all repository metadata reset. + reset_metadata = not ( kwd.get( 'no_reset', False ) ) + if cmd == 'listkeys' and reset_metadata: + # This possibly results from an "hg push" from the command line. When doing this, the following 7 commands, in order, # will be retrieved from environ: between -> capabilities -> heads -> branchmap -> unbundle -> unbundle -> listkeys path_info = kwd.get( 'path_info', None ) if path_info: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dannon: Extract workflow - fix nested dataset input mapping.
by Bitbucket 30 Apr '12

30 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/559105c554d5/ changeset: 559105c554d5 user: dannon date: 2012-04-30 18:16:09 summary: Extract workflow - fix nested dataset input mapping. affected #: 1 file diff -r c542aecc608617645d31c6ce9775f31a93c10bef -r 559105c554d540d8137d6583c58b2e237fe1eff4 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -1338,11 +1338,6 @@ tool = trans.app.toolbox.get_tool( job.tool_id ) param_values = job.get_param_values( trans.app ) associations = cleanup_param_values( tool.inputs, param_values ) - # Doing it this way breaks dynamic parameters, backed out temporarily. - # def extract_callback( input, value, prefixed_name, prefixed_label ): - # if isinstance( value, UnvalidatedValue ): - # return str( value ) - # visit_input_values( tool.inputs, param_values, extract_callback ) step = model.WorkflowStep() step.type = 'tool' step.tool_id = job.tool_id @@ -2043,13 +2038,11 @@ group_values = values[key] for i, rep_values in enumerate( group_values ): rep_index = rep_values['__index__'] - prefix = "%s_%d|" % ( key, rep_index ) - cleanup( prefix, input.inputs, group_values[i] ) + cleanup( "%s%s_%d|" % (prefix, key, rep_index ), input.inputs, group_values[i] ) elif isinstance( input, Conditional ): group_values = values[input.name] current_case = group_values['__current_case__'] - prefix = "%s|" % ( key ) - cleanup( prefix, input.cases[current_case].inputs, group_values ) + cleanup( "%s%s|" % ( prefix, key ), input.cases[current_case].inputs, group_values ) cleanup( "", inputs, values ) return associations Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0