June 2011 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: dan: Fix for Select All / Unselect All functionality when more than one set of checkboxes is present on a page.
by Bitbucket 07 Jun '11

07 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/9d268e6d85f3/ changeset: 9d268e6d85f3 branches: user: dan date: 2011-06-07 16:46:52 summary: Fix for Select All / Unselect All functionality when more than one set of checkboxes is present on a page. affected #: 1 file (2 bytes) --- a/templates/tool_form.mako Tue Jun 07 09:04:55 2011 -0400 +++ b/templates/tool_form.mako Tue Jun 07 10:46:52 2011 -0400 @@ -51,7 +51,7 @@ }); function checkUncheckAll( name, check ) { - $("input[name=" + name + "][type='checkbox']").attr('checked', !!check); + $("input[name='" + name + "'][type='checkbox']").attr('checked', !!check); } // Inserts the Select All / Unselect All buttons for checkboxes 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 for incorrect variable name reuse ('roles'), occurring when importing multiple datasets from a history into a library.
by Bitbucket 07 Jun '11

07 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/eeb9fdfcbe00/ changeset: eeb9fdfcbe00 branches: user: dan date: 2011-06-07 15:04:55 summary: Fix for incorrect variable name reuse ('roles'), occurring when importing multiple datasets from a history into a library. affected #: 1 file (40 bytes) --- a/lib/galaxy/web/controllers/library_common.py Mon Jun 06 16:17:09 2011 -0400 +++ b/lib/galaxy/web/controllers/library_common.py Tue Jun 07 09:04:55 2011 -0400 @@ -1221,7 +1221,7 @@ # it exists, then we need to apply the LIBRARY_MANAGE permission to the library dataset. dataset_manage_permissions_action = trans.app.security_agent.get_action( 'DATASET_MANAGE_PERMISSIONS' ).action flush_needed = False - for action, roles in dataset_permissions_dict.items(): + for action, dataset_permissions_roles in dataset_permissions_dict.items(): if isinstance( action, Action ): action = action.action if action == dataset_manage_permissions_action: @@ -1229,7 +1229,7 @@ action = trans.app.security_agent.get_action( 'LIBRARY_MANAGE' ).action # Allow the permissions inherited from the folder to over-ride the same permissions on the dataset. if action not in current_library_dataset_actions: - for ldp in [ trans.model.LibraryDatasetPermissions( action, ldda.library_dataset, role ) for role in roles ]: + for ldp in [ trans.model.LibraryDatasetPermissions( action, ldda.library_dataset, role ) for role in dataset_permissions_roles ]: trans.sa_session.add( ldp ) flush_needed = True if flush_needed: 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: jgoecks: Fix GFF3 reader bug.
by Bitbucket 06 Jun '11

06 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/1f9173561795/ changeset: 1f9173561795 branches: user: jgoecks date: 2011-06-06 22:17:09 summary: Fix GFF3 reader bug. affected #: 1 file (10 bytes) --- a/lib/galaxy/datatypes/util/gff_util.py Mon Jun 06 15:45:16 2011 -0400 +++ b/lib/galaxy/datatypes/util/gff_util.py Mon Jun 06 16:17:09 2011 -0400 @@ -217,7 +217,7 @@ # GFF3 test: parent_id = interval.attributes.get( 'Parent', None ) cur_id = interval.attributes.get( 'ID', None ) - if feature_id and parent_id != feature_parent_id and feature_id != cur_id: + if ( cur_id and cur_id != feature_id ) or ( parent_id and parent_id != feature_id ): break # GTF test: gene_id = interval.attributes.get( 'gene_id', None ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Code cleanup for uploading files to a repo in the tool shed.
by Bitbucket 06 Jun '11

06 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/e0de7ec40a80/ changeset: e0de7ec40a80 branches: user: greg date: 2011-06-06 21:45:16 summary: Code cleanup for uploading files to a repo in the tool shed. affected #: 3 files (8.8 KB) --- a/lib/galaxy/webapps/community/controllers/repository.py Mon Jun 06 15:30:02 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Mon Jun 06 15:45:16 2011 -0400 @@ -16,9 +16,12 @@ # Characters that must be html escaped MAPPED_CHARS = { '>' :'>', - '<' :'<' } + '<' :'<', + '"' : '"', + '&' : '&', + '\'' : ''' } MAX_CONTENT_SIZE = 32768 -VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;" ) +VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;{}" ) VALID_REPOSITORYNAME_RE = re.compile( "^[a-z0-9\_]+$" ) class CategoryListGrid( grids.Grid ): @@ -673,7 +676,7 @@ for i, line in enumerate( open( file_path ) ): to_html = '%s%s' % ( to_html, self.to_html_str( line ) ) if len( to_html ) > MAX_CONTENT_SIZE: - large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %d\n' % MAX_CONTENT_SIZE + large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %s\n' % util.nice_size( MAX_CONTENT_SIZE ) to_html = '%s%s' % ( to_html, self.to_html_str( large_str ) ) break return to_html @@ -706,9 +709,9 @@ translated.append( ' ' ) elif c == '\t': translated.append( '    ' ) - elif c in [ '\r\n', '\n' ]: + elif c == '\n': translated.append( '<br/>' ) - else: + elif c not in [ '\r' ]: translated.append( 'X' ) return ''.join( translated ) def __build_allow_push_select_field( self, trans, current_push_list, selected_value='none' ): --- a/lib/galaxy/webapps/community/controllers/upload.py Mon Jun 06 15:30:02 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/upload.py Mon Jun 06 15:45:16 2011 -0400 @@ -60,12 +60,9 @@ elif file_data not in ( '', None ): uploaded_file = file_data.file if uploaded_file: - # TODO: our current support for browsing repo contents requires a copy - # of the repository files in the repo root directory. To produce these - # copies, we update without passing the -r null flag (see below). When - # we're uploading more files, we have to clean out the repo root directory - # so we can move them into it. We need to eliminate all this when we figure - # out how to browse the repository files. + # Our current support for browsing repo contents requires a copy of the + # repository files in the repo root directory. To produce these copies, + # we update without passing the "-r null" flag. os.chdir( repo_dir ) os.system( 'hg update -r null > /dev/null 2>&1' ) os.chdir( current_working_dir ) @@ -76,16 +73,16 @@ tar = tarfile.open( uploaded_file.name ) istar = True except tarfile.ReadError, e: + tar = None istar = False - if istar: - ok, message = self.__check_archive( tar ) - if ok: - if repository.is_new: + if repository.is_new: + if istar: + # We have an archive ( a tarball ) + ok, message = self.__check_archive( tar ) + if ok: tar.extractall( path=repo_dir ) tar.close() uploaded_file.close() - # TODO: The following will only work on new, empty repos, - # need to also handle repos with existing contents for root, dirs, files in os.walk( repo_dir, topdown=False ): # Don't visit .hg directories and don't include hgrc files in commit. if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0: @@ -109,78 +106,9 @@ repo.dirstate.add( file_path ) files_to_commit.append( file_path ) else: - # The repo already contains the file, so we need to make sure the file being - # uploaded is different from the file in the repo. This is a temporary brute- - # force method. - # Make a clone of the repository in a temporary location - tmp_dir = tempfile.mkdtemp() - tmp_archive_dir = os.path.join( tmp_dir, 'tmp_archive_dir' ) - if not os.path.exists( tmp_archive_dir ): - os.makedirs( tmp_archive_dir ) - cmd = "hg clone %s > /dev/null 2>&1" % os.path.abspath( repo_dir ) - os.chdir( tmp_archive_dir ) - os.system( cmd ) - os.chdir( current_working_dir ) - cloned_repo_dir = os.path.join( tmp_archive_dir, 'repo_%d' % repository.id ) - if upload_point is not None: - full_path = os.path.abspath( os.path.join( cloned_repo_dir, upload_point, file_data.filename ) ) - else: - full_path = os.path.abspath( os.path.join( cloned_repo_dir, file_data.filename ) ) - # Extract the uploaded tarball to the load_point within the cloned repository hierarchy - tar.extractall( path=full_path ) tar.close() - uploaded_file.close() - # We want these change sets to be associated with the owner of the repository, so we'll - # set the HGUSER environment variable accordingly. - os.environ[ 'HGUSER' ] = trans.user.username - # Add the file to the cloned repository. If it's already tracked, this should do nothing. - os.chdir( cloned_repo_dir ) - os.system( 'hg add > /dev/null 2>&1' ) - os.chdir( current_working_dir ) - os.chdir( cloned_repo_dir ) - # Commit the change set to the cloned repository - os.system( "hg commit -m '%s' > /dev/null 2>&1" % commit_message ) - os.chdir( current_working_dir ) - # Push the change set to the master repository - cmd = "hg push %s > /dev/null 2>&1" % os.path.abspath( repo_dir ) - os.chdir( cloned_repo_dir ) - os.system( cmd ) - # Change the current working directory to the original - os.chdir( current_working_dir ) - # Since we extracted the archive into repo_dir, a copy of the archive's - # files remains there. The following will remove them. It would be - # more ideal if we could use the mercurial api to do this, but I haven't - # yet discovered a way to pass the -r null flag to repo.update(). - # TODO: our current support for browsing repo contents requires a copy - # of the repository files in the repo root directory. To produce these - # copies, we'll update without passing the -r null flag. When we figure - # out how to browse the repository files, uncomment the -r flag below. - os.chdir( repo_dir ) - os.system( 'hg update > /dev/null 2>&1' ) - os.chdir( current_working_dir ) - # Remove tmp directory - shutil.rmtree( tmp_dir ) - message = "The file '%s' has been successfully uploaded to the repository." % file_data.filename - trans.response.send_redirect( web.url_for( controller='repository', - action='browse_repository', - message=message, - id=trans.security.encode_id( repository.id ) ) ) - - else: - tar.close() - else: - """ - # TODO: This segment uses the mercurial api (and works), but we need the - # api section below to be functional in order for this segment to be used. - # In the meantime, we use the repository.is_new check below... - repo_contains = file_path in [ i for i in ctx.manifest() ] - if not repo_contains: - repo.dirstate.add( file_path ) - files_to_commit.append( file_path ) - """ - if repository.is_new: - # We're uploading a single file + # We have a single file if upload_point is not None: full_path = os.path.abspath( os.path.join( upload_point, file_data.filename ) ) file_path = os.path.join( upload_point, file_data.filename ) @@ -190,98 +118,18 @@ shutil.move( uploaded_file.name, full_path ) repo.dirstate.add( file_path ) files_to_commit.append( file_path ) - else: - """ - # TODO: This segment attempts to use the mercurial api, but is not functional. - # Until we get it working, we're using the brute force method below it. - fctx = None - for changeset in repo.changelog: - ctx = repo.changectx( changeset ) - if file_path not in ctx.files(): - continue - fctx = ctx[ file_path ] - break - # We now have the parent version of the upload file. - if fctx: - data = fctx.data() - # TODO: obviously very bad way of comparing files... - file_path_data = open( full_path ).read() - different = data != file_path_data - if different: - # TODO: how do you insert a new version of an existing file using the mercurial api??? - # the follwoin gis not correct! - #repo.dirstate.normallookup( file_path ) - #files_to_commit.append( file_path ) - pass - """ - # The repo already contains the file, so we need to make sure the file being - # uploaded is different from the file in the repo. This is a temporary brute- - # force method. - # Make a clone of the repository in a temporary location - tmp_dir = tempfile.mkdtemp() - tmp_archive_dir = os.path.join( tmp_dir, 'tmp_archive_dir' ) - if not os.path.exists( tmp_archive_dir ): - os.makedirs( tmp_archive_dir ) - cmd = "hg clone %s > /dev/null 2>&1" % os.path.abspath( repo_dir ) - os.chdir( tmp_archive_dir ) - os.system( cmd ) - os.chdir( current_working_dir ) - cloned_repo_dir = os.path.join( tmp_archive_dir, 'repo_%d' % repository.id ) - if upload_point is not None: - full_path = os.path.abspath( os.path.join( cloned_repo_dir, upload_point, file_data.filename ) ) - else: - full_path = os.path.abspath( os.path.join( cloned_repo_dir, file_data.filename ) ) - # Move the uploaded file to the load_point within the cloned repository hierarchy - shutil.move( uploaded_file.name, full_path ) - # We want these change sets to be associated with the owner of the repository, so we'll - # set the HGUSER environment variable accordingly. - os.environ[ 'HGUSER' ] = trans.user.username - # Add the file to the cloned repository. If it's already tracked, this should do nothing. - os.chdir( cloned_repo_dir ) - os.system( 'hg add > /dev/null 2>&1' ) - os.chdir( current_working_dir ) - os.chdir( cloned_repo_dir ) - # Commit the change set to the cloned repository - os.system( "hg commit -m '%s' > /dev/null 2>&1" % commit_message ) - os.chdir( current_working_dir ) - # Push the change set to the master repository - cmd = "hg push %s > /dev/null 2>&1" % os.path.abspath( repo_dir ) - os.chdir( cloned_repo_dir ) - os.system( cmd ) - os.chdir( current_working_dir ) - # Since we extracted the archive into repo_dir, a copy of the archive's - # files remains there. The following will remove them. It would be - # more ideal if we could use the mercurial api to do this, but I haven't - # yet discovered a way to pass the -r null flag to repo.update(). - # TODO: our current support for browsing repo contents requires a copy - # of the repository files in the repo root directory. To produce these - # copies, we'll update without passing the -r null flag. When we figure - # out how to browse the repository files, uncomment the -r flag below. - os.chdir( repo_dir ) - os.system( 'hg update > /dev/null 2>&1' ) - os.chdir( current_working_dir ) - # Remove tmp directory - shutil.rmtree( tmp_dir ) - message = "The file '%s' has been successfully uploaded to the repository." % file_data.filename - trans.response.send_redirect( web.url_for( controller='repository', - action='browse_repository', - message=message, - id=trans.security.encode_id( repository.id ) ) ) + else: + # We're uploading files to a repository with existing + # contents, so clone the repository to a temporary location. + tmp_dir, cloned_repo_dir = self.__handle_hg_clone( trans, repository, upload_point, uploaded_file, file_data, repo_dir, current_working_dir, istar, tar=tar ) + # Commit and push the changes from the cloned repo to the master repo. + self.__handle_hg_push( trans, repository, file_data, commit_message, current_working_dir, cloned_repo_dir, repo_dir, tmp_dir ) if ok: if files_to_commit: repo.dirstate.write() repo.commit( text=commit_message ) - # Since we extracted the archive into repo_dir, a copy of the archive's - # files remains there. The following will remove them. It would be - # more ideal if we could use the mercurial api to do this, but I haven't - # yet discovered a way to pass the -r null flag to repo.update(). - # TODO: our current support for browsing repo contents requires a copy - # of the repository files in the repo root directory. To produce these - # copies, we'll update without passing the -r null flag. When we figure - # out how to browse the repository files, uncomment the -r flag below. os.chdir( repo_dir ) os.system( 'hg update > /dev/null 2>&1' ) - #os.system( 'hg update -r null' ) os.chdir( current_working_dir ) message = "The file '%s' has been successfully uploaded to the repository." % file_data.filename trans.response.send_redirect( web.url_for( controller='repository', @@ -290,17 +138,8 @@ id=trans.security.encode_id( repository.id ) ) ) else: status = 'error' - # Since we extracted the archive into repo_dir, a copy of the archive's - # files remains there. The following will remove them. It would be - # more ideal if we could use the mercurial api to do this, but I haven't - # yet discovered a way to pass the -r null flag to repo.update(). - # TODO: our current support for browsing repo contents requires a copy - # of the repository files in the repo root directory. To produce these - # copies, we'll update without passing the -r null flag. When we figure - # out how to browse the repository files, uncomment the -r flag below. os.chdir( repo_dir ) os.system( 'hg update > /dev/null 2>&1' ) - #os.system( 'hg update -r null' ) os.chdir( current_working_dir ) selected_categories = [ trans.security.decode_id( id ) for id in category_ids ] return trans.fill_template( '/webapps/community/repository/upload.mako', @@ -308,6 +147,57 @@ commit_message=commit_message, message=message, status=status ) + def __handle_hg_clone( self, trans, repository, upload_point, uploaded_file, file_data, repo_dir, current_working_dir, istar, tar=None ): + tmp_dir = tempfile.mkdtemp() + tmp_archive_dir = os.path.join( tmp_dir, 'tmp_archive_dir' ) + if not os.path.exists( tmp_archive_dir ): + os.makedirs( tmp_archive_dir ) + # Make a clone of the repository in a temporary location + cmd = "hg clone %s > /dev/null 2>&1" % os.path.abspath( repo_dir ) + os.chdir( tmp_archive_dir ) + os.system( cmd ) + os.chdir( current_working_dir ) + cloned_repo_dir = os.path.join( tmp_archive_dir, 'repo_%d' % repository.id ) + if upload_point is not None: + full_path = os.path.abspath( os.path.join( cloned_repo_dir, upload_point, file_data.filename ) ) + else: + full_path = os.path.abspath( os.path.join( cloned_repo_dir, file_data.filename ) ) + if istar: + # Extract the uploaded tarball to the load_point within the cloned repository hierarchy + tar.extractall( path=full_path ) + tar.close() + uploaded_file.close() + else: + # Move the uploaded file to the load_point within the cloned repository hierarchy + shutil.move( uploaded_file.name, full_path ) + return tmp_dir, cloned_repo_dir + def __handle_hg_push( self, trans, repository, file_data, commit_message, current_working_dir, cloned_repo_dir, repo_dir, tmp_dir ): + # We want these change sets to be associated with the owner of the repository, so we'll + # set the HGUSER environment variable accordingly. + os.environ[ 'HGUSER' ] = trans.user.username + # Add the file to the cloned repository. If it's already tracked, this should do nothing. + os.chdir( cloned_repo_dir ) + os.system( 'hg add > /dev/null 2>&1' ) + os.chdir( current_working_dir ) + os.chdir( cloned_repo_dir ) + # Commit the change set to the cloned repository + os.system( "hg commit -m '%s' > /dev/null 2>&1" % commit_message ) + os.chdir( current_working_dir ) + # Push the change set to the master repository + cmd = "hg push %s > /dev/null 2>&1" % os.path.abspath( repo_dir ) + os.chdir( cloned_repo_dir ) + os.system( cmd ) + os.chdir( current_working_dir ) + # Make a copy of the updated repository files for browsing. + os.chdir( repo_dir ) + os.system( 'hg update > /dev/null 2>&1' ) + os.chdir( current_working_dir ) + shutil.rmtree( tmp_dir ) + message = "The file '%s' has been successfully uploaded to the repository." % file_data.filename + trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repository', + message=message, + id=trans.security.encode_id( repository.id ) ) ) def __check_archive( self, archive ): for member in archive.getmembers(): # Allow regular files and directories only --- a/templates/webapps/community/upload/upload.mako Mon Jun 06 15:30:02 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,242 +0,0 @@ -<%namespace file="/message.mako" import="render_msg" /> - -<%! - def inherit(context): - if context.get('use_panels'): - return '/webapps/community/base_panels.mako' - else: - return '/base.mako' -%> - -<%inherit file="${inherit(context)}"/> - -<% - if selected_upload_type == 'tool': - title = 'Upload a tool archive' - type_label = 'tool' - elif selected_upload_type == 'toolsuite': - title = 'Upload a tool suite archive' - type_label = 'tool suite' -%> - -<%def name="title()"> - ${title} -</%def> - -<%def name="javascripts()"> - ${parent.javascripts()} - <script type="text/javascript"> - $( function() { - $( "select[refresh_on_change='true']").change( function() { - $( "#upload_form" ).submit(); - }); - }); - </script> -</%def> - -<h2>${title}</h2> - -%if message: - ${render_msg( message, status )} -%endif - -<div class="toolForm"> - <div class="toolFormTitle">${title}</div> - <div class="toolFormBody"> - ## TODO: nginx - <form id="upload_form" name="upload_form" action="${h.url_for( controller='tool_upload', action='upload' )}" enctype="multipart/form-data" method="post"> - %if replace_id is not None: - <input type='hidden' name="replace_id" value="${replace_id}"/> - %endif - <div class="form-row"> - <label>Upload Type</label> - <div class="form-row-input"> - ${upload_type_select_list.get_html()} - </div> - <div class="toolParamHelp" style="clear: both;"> - Need help creating a ${type_label} archive? See details below. - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>File:</label> - <div class="form-row-input"><input type="file" name="file_data"/></div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>Category</label> - <div class="form-row-input"> - <select name="category_id" multiple> - %for category in categories: - %if category.id in selected_categories: - <option value="${trans.security.encode_id( category.id )}" selected>${category.name}</option> - %else: - <option value="${trans.security.encode_id( category.id )}">${category.name}</option> - %endif - %endfor - </select> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>URL:</label> - <div class="form-row-input"><input type="text" name="url" style="width: 100%;"/></div> - <div class="toolParamHelp" style="clear: both;"> - Instead of uploading directly from your computer, you may instruct Galaxy to download the file from a Web or FTP address. - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <input type="submit" class="primary-button" name="upload_button" value="Upload"> - </div> - </form> - </div> -</div> -<p/> -<div class="toolFormTitle">Creating an archive containing a tool or a suite of tools</div> -<p> - A tool or tool suite archive is a tar-format file (bzipped or gzipped tar are valid) - containing all the files necessary to load the tool(s) into a Galaxy instance. -</p> -%if selected_upload_type == 'toolsuite': - <h3>Tool Suite Archive</h3> - <p> - A tools suite must include a file named <code>suite_config.xml</code> which provides information about the id, name, - version and description of the tool suite, as well as the id, name, version and description of each tool - in the suite. Here is an example <code>suite_config.xml</code> file. - </p> - <p> -<pre> - <suite id="lastz_toolsuite" name="Suite of Lastz tools" version="1.0.0"> - <description>This suite contains all of my Lastz tools for Galaxy</description> - <tool id="lastz_wrapper_2" name="Lastz" version="1.1.0"> - <description> map short reads against reference sequence</description> - </tool> - <tool id="lastz_paired_reads_wrapper" name="Lastz paired reads" version="1.0.0"> - <description> map short paired reads against reference sequence</description> - </tool> - </suite> -</pre> - </p> - </p> - <p> - New versions of the suite can be uploaded, replacing an older version of the suite, but the version attribute - of the <suite> tag must be altered the same way that the version attribute of a single tool config must be altered - if uploading a new version of a tool. - </p> - <p> - The id, name and version attributes of each <tool> tag in the <code>suite_config.xml</code> file must exactly match the same - attributes in each associated tool config in the archive or you will not be allowed to upload the archive. - </p> - <p> - In addition to the <code>suite_config.xml</code> file, the archive must include all - <a href="http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax" target="_blank">tool config files</a>, - executables, functional test data (if your tool config includes functional tests) and other files needed for each - of the tools in your suite to function within Galaxy. See the information about single tool archives below for - additional hints to enable ease-of-use when others download your suite of tools. - </p> - <p> - For example, to package the above Lastz suite of tools: -<pre> - user@host:~% tar jcvf ~/Desktop/galaxy_lastz_toolsuite.tar.bz2 lastzsuite - lastzsuite/ - lastzsuite/README - lastzsuite/suite_config.xml - lastzsuite/lastz_paired_reads_wrapper.py - lastzsuite/lastz_paired_reads_wrapper.xml - lastzsuite/lastz_wrapper.py - lastzsuite/lastz_wrapper.xml - lastzsuite/lastz-distrib-1.02.00/ - lastzsuite/lastz-distrib-1.02.00/src/ - lastzsuite/lastz-distrib-1.02.00/src/Makefile - lastzsuite/lastz-distrib-1.02.00/src/version.mak - lastzsuite/lastz-distrib-1.02.00/src/lastz.c - lastzsuite/lastz-distrib-1.02.00/src/lastz.h - ... -</pre> - ~/Desktop/galaxy_lastz_tool.tar.bz2 is now ready to be uploaded. - </p> -%endif -<h3>Single Tool Archive</h3> -<p> - A single tool archive must include a - <a href="http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax" target="_blank">tool config file</a> - and will probably also include a tool script. If any steps are necessary to install your tool beyond the basic - instructions below, include a README file to provide details. If the tool (or parts of it) are written in C, - the source code can be included (or put links to the source in the README). Do not include pre-compiled binaries - without source since Galaxy is run on a wide variety of platforms. Also, if you are only wrapping or providing a - Galaxy config for a tool that is not your own, be sure the license allows for redistribution before including any - part of that tool in the archive. -</p> -<p> - There are no requirements about the directory structure inside the archive, but for ease of use it's generally - a good idea to put everything inside a sub-directory, instead of directly at the top level. -</p> -<p> - For example, to package the Lastz tool's config file, Galaxy wrapper, and the C source: -<pre> - user@host:~% tar jcvf ~/Desktop/galaxy_lastz_tool.tar.bz2 lastz - lastz/ - lastz/README - lastz/lastz_wrapper.py - lastz/lastz_wrapper.xml - lastz/lastz-distrib-1.02.00/ - lastz/lastz-distrib-1.02.00/src/ - lastz/lastz-distrib-1.02.00/src/Makefile - lastz/lastz-distrib-1.02.00/src/version.mak - lastz/lastz-distrib-1.02.00/src/lastz.c - lastz/lastz-distrib-1.02.00/src/lastz.h - ... -</pre> - ~/Desktop/galaxy_lastz_tool.tar.bz2 is now ready to be uploaded. -</p> -<h3>Editing Information, Categories, and Submitting For Approval</h3> -<p> - Simply uploading a tool to the Galaxy too shed will not allow other users to find and download your tool. It will - need to be approved by an administrator before it appears in the tool list. -</p> -<p> - After your archive has successfully uploaded, you will be redirected to the Edit Tool page. Provide a detailed - description of what the tool does - this will be used by administrators to understand the tool before approving it - for display on the site. Once approved, this information will be displayed to users who view your tool. In addition, - the site administrators will have configured a number of categories with which you can associate your tool to make it - easy to find by users looking to solve specific problems. Associate as many categories as are relevant to your tool. - You may change the description and associated categories as often as you'd like until you click the "<strong>Submit for - approval</strong>" button. Once submitted, the tool will be approved or rejected by an administrator. If the tool is - rejected, you will see information about why it was rejected, and you can make appropriate changes to the archive and - re-submit it for approval. When it is approved, your archive will be visible to everyone. At that point, the description - and associated categories can only be changed by an administrator. -</p> -<p> - When the tool has been approved or rejected, you may upload a new version by browsing to the tool's "View Tool" page, - clicking the "Tool actions" menu in the upper right corner of the page, and selecting "Upload a new version" from the - menu. -</p> -<hr/> -<h3>Downloading and Installing Tools</h3> -<p> - A tool's download link will send you the tool archive. Once downloaded, unpack the tool on your local Galaxy instance's server: -<pre> - user@host:~% tar xvf galaxy_lastz_tool.tar - ... - user@host:~% tar zxvf galaxy_lastz_tool.tar.gz - ... - user@host:~% tar jxvf galaxy_lastz_tool.tar.bz2 - ... -</pre> - If the archive includes a README file, consult it for installation instructions. If not, follow these basic steps: - <ol> - <li>Create a directory under <code>galaxy_dist/tools/</code> to house downloaded tool(s).</li> - <li>In the new directory, place the XML and any script file(s) which were contained in the archive.</li> - <li> - If the tool includes binaries, you'll need to copy them to a directory on your <code>$PATH</code>. If the tool depends on - C binaries but does not come with them (only source), you'll need to compile the source first. - </li> - <li>Add the tool to <code>galaxy_dist/tool_conf.xml</code>.</li> - <li>Restart your Galaxy server process.</li> - </ol> -</p> -<p> - In the near future, we plan to implement a more direct method to install tools via the Galaxy administrator user interface instead - of placing files on the filesystem and manually managing the <code>tool_conf.xml</code> file. -</p> 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: kanwei: Improve docs for Grouping tool. Closes #576
by Bitbucket 06 Jun '11

06 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/d34c83a1301e/ changeset: d34c83a1301e branches: user: kanwei date: 2011-06-06 21:30:02 summary: Improve docs for Grouping tool. Closes #576 affected #: 1 file (364 bytes) --- a/tools/stats/grouping.xml Mon Jun 06 13:17:18 2011 -0400 +++ b/tools/stats/grouping.xml Mon Jun 06 15:30:02 2011 -0400 @@ -88,7 +88,11 @@ **Syntax** -This tool allows you to group the input dataset by a particular column and perform aggregate functions: Mean, Median, Mode, Sum, Max, Min, Count, Randomly pick, and Concatenate on any column. +This tool allows you to group the input dataset by a particular column and perform aggregate functions: Mean, Median, Mode, Sum, Max, Min, Count, Concatenate, and Randomly pick on any column(s). + +The Concatenate function will take, for each group, each item in the specified column and build a comma delimited list. Concatenate Unique will do the same but will build a list of unique items with no repetition. + +Count and Count Unique are equivalent to Concatenate and Concatenate Unique, but will only count the number of items and will return an integer. - If multiple modes are present, all are reported. 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: kanwei: trackster: Fix VCF data provider
by Bitbucket 06 Jun '11

06 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/346ad6f83be1/ changeset: 346ad6f83be1 branches: user: kanwei date: 2011-06-06 19:17:18 summary: trackster: Fix VCF data provider affected #: 1 file (62 bytes) --- a/lib/galaxy/visualization/tracks/data_providers.py Mon Jun 06 11:17:31 2011 -0400 +++ b/lib/galaxy/visualization/tracks/data_providers.py Mon Jun 06 13:17:18 2011 -0400 @@ -607,12 +607,12 @@ out.write( line ) out.close() -class VcfDataProvider( TracksDataProvider ): +class VcfDataProvider( TabixDataProvider ): """ VCF data provider for the Galaxy track browser. Payload format: - [ uid (offset), start, end, ID, reference base(s), alternate base(s), quality score] + [ uid (offset), start, end, ID, reference base(s), alternate base(s), quality score ] """ col_name_data_attr_mapping = { 'Qual' : { 'index': 6 , 'name' : 'Qual' } } @@ -622,21 +622,20 @@ count = 0 message = None - reader = galaxy_utils.sequence.vcf.Reader( iterator ) - for line in reader: + for line in iterator: if count >= MAX_VALS: message = ERROR_MAX_VALS % "features" break count += 1 feature = line.split() - payload = [ hash(line), vcf_line.pos-1, vcf_line.pos, \ + payload = [ hash(line), int(feature[1])-1, int(feature[1]), # ID: - feature[2], \ + feature[2], # reference base(s): - feature[3], \ + feature[3], # alternative base(s) - feature[4], \ + feature[4], # phred quality score int( feature[5] )] rval.append(payload) 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: jgoecks: Trackster: use error padding only when needed by placing error messages in div above tiles rather than in tiles.
by Bitbucket 06 Jun '11

06 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b7c4c1bcf03d/ changeset: b7c4c1bcf03d branches: user: jgoecks date: 2011-06-06 17:17:31 summary: Trackster: use error padding only when needed by placing error messages in div above tiles rather than in tiles. affected #: 3 files (966 bytes) --- a/static/june_2007_style/blue/trackster.css Mon Jun 06 11:12:04 2011 -0400 +++ b/static/june_2007_style/blue/trackster.css Mon Jun 06 11:17:31 2011 -0400 @@ -26,6 +26,7 @@ .label-track .track-content{background:white;} .track-tile{background:white;} .track-tile canvas{position:relative;z-index:100;border:solid white;border-width:2px 0px 0px 0px;} +.tile-message {border-bottom:solid 1px red;text-align:center;color:red;background-color:white;} .track.error .track-content{background-color:#ECB4AF;background-image:none;} .track.nodata .track-content{background-color:#eee;background-image:none;} .track.pending .track-content{background-color:white;background-image:none;} --- a/static/june_2007_style/trackster.css.tmpl Mon Jun 06 11:12:04 2011 -0400 +++ b/static/june_2007_style/trackster.css.tmpl Mon Jun 06 11:17:31 2011 -0400 @@ -167,6 +167,13 @@ border-width: 2px 0px 0px 0px; } +.tile-message { + border-bottom: solid 1px red; + text-align: center; + color: red; + background-color: white; +} + .track.error .track-content { background-color: #ECB4AF; background-image: none; --- a/static/scripts/trackster.js Mon Jun 06 11:12:04 2011 -0400 +++ b/static/scripts/trackster.js Mon Jun 06 11:17:31 2011 -0400 @@ -172,7 +172,7 @@ // height of individual features within tracks. Feature height, then, should always be less // than track height. CHAR_HEIGHT_PX = 9, // FIXME: font size may not be static - ERROR_PADDING = 10, // Padding at the top of tracks for error messages + ERROR_PADDING = 15, // Padding at the top of tracks for error messages SUMMARY_TREE_TOP_PADDING = CHAR_HEIGHT_PX + 2, // Maximum number of rows un a slotted track MAX_FEATURE_DEPTH = 100, @@ -1507,8 +1507,9 @@ this.max_val = max_val; }; -var FeatureTrackTile = function(index, resolution, canvas) { +var FeatureTrackTile = function(index, resolution, canvas, message) { Tile.call(this, index, resolution, canvas); + this.message = message; }; /** @@ -1993,6 +1994,27 @@ } } + // + // If some tiles have messages, set padding of tiles without messages + // so features and rows align. + // + var messages_to_show = false; + for (var tile_index = 0; tile_index < drawn_tiles.length; tile_index++) { + if (drawn_tiles[tile_index].message) { + messages_to_show = true; + break; + } + } + if (messages_to_show) { + for (var tile_index = 0; tile_index < drawn_tiles.length; tile_index++) { + tile = drawn_tiles[tile_index]; + if (!tile.message) { + // Need to align with other tile(s) that have message(s). + tile.canvas.css("padding-top", ERROR_PADDING); + } + } + } + // Store initial canvas in case we need to use it for overview /* This is completely broken, just saves the first tile it sees regardless of if it should be the overview @@ -2620,8 +2642,7 @@ // Create painter, and canvas of sufficient size to contain all features // HACK: ref_seq will only be defined for ReadTracks, and only the ReadPainter accepts that argument var painter = new (this.painter)( filtered, tile_low, tile_high, this.prefs, mode, ref_seq ); - // FIXME: ERROR_PADDING is an ugly gap most of the time - var required_height = painter.get_required_height( slots_required ) + ERROR_PADDING; + var required_height = painter.get_required_height(slots_required); var canvas = this.view.canvas_manager.new_canvas(); canvas.width = width + left_offset; @@ -2634,31 +2655,26 @@ ctx.textAlign = "right"; this.container_div.find(".yaxislabel").remove(); - // If there is a message, draw it on canvas so that it moves around with canvas, and make the border red - // to indicate region where message is applicable + if (result.data) { + // Set example feature. This is needed so that track can update its UI based on feature attributes. + this.example_feature = (result.data.length ? result.data[0] : undefined); + + // Draw features. + painter.draw(ctx, width, required_height, slots); + } + + // If tile has a message, create container div with both a message div and the canvas. if (result.message) { - ctx.fillStyle = "red"; - ctx.textAlign = "left"; - var old_base = ctx.textBaseline; - ctx.textBaseline = "top"; - ctx.fillRect(left_offset, 0, canvas.width - left_offset, 1); - ctx.fillText(result.message, left_offset, 2); - ctx.textBaseline = old_base; - - // If there's no data, return. - if (!result.data) { - return new Tile(tile_index, resolution, canvas, required_height); - } + var container_div = $("<div/>"); + var message_div = $("<div/>").addClass("tile-message").text(result.message).css('width', canvas.width); + message_div.css({position: 'absolute', top: 0}); + $(canvas).css("top", 15); + container_div.append(message_div); + container_div.append(canvas); + canvas = container_div; } - // Set example feature. This is needed so that track can update its UI based on feature attributes. - this.example_feature = (result.data.length ? result.data[0] : undefined); - - // Draw features - ctx.translate(left_offset, ERROR_PADDING); - painter.draw(ctx, width, required_height, slots); - - return new FeatureTrackTile(tile_index, resolution, canvas); + return new FeatureTrackTile(tile_index, resolution, canvas, result.message); } }); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: kanwei: Restore error icon for color-blindness; needs further testing
by Bitbucket 06 Jun '11

06 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/e4ef73d003f6/ changeset: e4ef73d003f6 branches: user: kanwei date: 2011-06-06 17:12:04 summary: Restore error icon for color-blindness; needs further testing affected #: 1 file (41 bytes) --- a/templates/root/history_common.mako Mon Jun 06 09:37:06 2011 -0400 +++ b/templates/root/history_common.mako Mon Jun 06 11:12:04 2011 -0400 @@ -69,6 +69,7 @@ <a class="icon-button delete tooltip" title="Delete" href="${h.url_for( action='delete', id=data.id, show_deleted_on_refresh=show_deleted_on_refresh )}" id="historyItemDeleter-${data.id}"></a> %endif </div> + <span class="state-icon"></span><span class="historyItemTitle">${hid}: ${data.display_name()}</span></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: jgoecks: Disable update check in cuffdiff wrapper.
by Bitbucket 06 Jun '11

06 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/1ab3dfb5d929/ changeset: 1ab3dfb5d929 branches: user: jgoecks date: 2011-06-06 15:37:06 summary: Disable update check in cuffdiff wrapper. affected #: 1 file (36 bytes) --- a/tools/ngs_rna/cuffdiff_wrapper.py Mon Jun 06 09:08:59 2011 -0400 +++ b/tools/ngs_rna/cuffdiff_wrapper.py Mon Jun 06 09:37:06 2011 -0400 @@ -101,7 +101,7 @@ try: tmp = tempfile.NamedTemporaryFile().name tmp_stdout = open( tmp, 'wb' ) - proc = subprocess.Popen( args='cuffdiff 2>&1', shell=True, stdout=tmp_stdout ) + proc = subprocess.Popen( args='cuffdiff --no-update-check 2>&1', shell=True, stdout=tmp_stdout ) tmp_stdout.close() returncode = proc.wait() stdout = None @@ -135,7 +135,7 @@ # Build command. # Base; always use quiet mode to avoid problems with storing log output. - cmd = "cuffdiff -q" + cmd = "cuffdiff --no-update-check -q" # Add options. if options.inner_dist_std_dev: 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: jgoecks: Removed unspecified build validators from Cufflinks/compare/diff tools as these cause trouble when running tools on custom genomes.
by Bitbucket 06 Jun '11

06 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/058a5d7a4f84/ changeset: 058a5d7a4f84 branches: user: jgoecks date: 2011-06-06 15:08:59 summary: Removed unspecified build validators from Cufflinks/compare/diff tools as these cause trouble when running tools on custom genomes. affected #: 3 files (205 bytes) --- a/tools/ngs_rna/cuffcompare_wrapper.xml Fri Jun 03 17:00:20 2011 -0400 +++ b/tools/ngs_rna/cuffcompare_wrapper.xml Mon Jun 06 09:08:59 2011 -0400 @@ -33,9 +33,7 @@ #end for </command><inputs> - <param format="gtf" name="first_input" type="data" label="GTF file produced by Cufflinks" help=""> - <validator type="unspecified_build" /> - </param> + <param format="gtf" name="first_input" type="data" label="GTF file produced by Cufflinks" help=""/><repeat name="input_files" title="Additional GTF Input Files"><param format="gtf" name="additional_input" type="data" label="GTF file produced by Cufflinks" help=""><validator type="unspecified_build" /> --- a/tools/ngs_rna/cuffdiff_wrapper.xml Fri Jun 03 17:00:20 2011 -0400 +++ b/tools/ngs_rna/cuffdiff_wrapper.xml Mon Jun 06 09:08:59 2011 -0400 @@ -67,9 +67,7 @@ </command><inputs> - <param format="gtf" name="gtf_input" type="data" label="Transcripts" help="A transcript GTF file produced by cufflinks, cuffcompare, or other source."> - <validator type="unspecified_build" /> - </param> + <param format="gtf" name="gtf_input" type="data" label="Transcripts" help="A transcript GTF file produced by cufflinks, cuffcompare, or other source."/><conditional name="group_analysis"><param name="do_groups" type="select" label="Perform replicate analysis" help="Perform cuffdiff with replicates in each group."><option value="No">No</option> --- a/tools/ngs_rna/cufflinks_wrapper.xml Fri Jun 03 17:00:20 2011 -0400 +++ b/tools/ngs_rna/cufflinks_wrapper.xml Mon Jun 06 09:08:59 2011 -0400 @@ -41,9 +41,7 @@ #end if </command><inputs> - <param format="sam,bam" name="input" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""> - <validator type="unspecified_build" /> - </param> + <param format="sam,bam" name="input" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/><param name="max_intron_len" type="integer" value="300000" min="1" max="600000" label="Max Intron Length" help=""/><param name="min_isoform_fraction" type="float" value="0.05" min="0" max="1" label="Min Isoform Fraction" help=""/><param name="pre_mrna_fraction" type="float" value="0.05" min="0" max="1" label="Pre MRNA Fraction" 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