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commit/galaxy-central: kanwei: Improve BLAST parser tool error handling, and improve elementtree import as well.
by Bitbucket 13 Jul '11

13 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/26bffb1b7d57/ changeset: 26bffb1b7d57 user: kanwei date: 2011-07-13 00:14:56 summary: Improve BLAST parser tool error handling, and improve elementtree import as well. affected #: 3 files (260 bytes) --- a/tools/metag_tools/megablast_xml_parser.py Tue Jul 12 17:04:16 2011 -0400 +++ b/tools/metag_tools/megablast_xml_parser.py Tue Jul 12 18:14:56 2011 -0400 @@ -2,12 +2,12 @@ import sys, os, re -assert sys.version_info[:2] >= ( 2, 4 ) - if sys.version_info[:2] >= ( 2, 5 ): - import xml.etree.cElementTree as cElementTree + import xml.etree.cElementTree as ElementTree else: - import cElementTree + from galaxy import eggs + import pkg_resources; pkg_resources.require( "elementtree" ) + from elementtree import ElementTree def stop_err( msg ): sys.stderr.write( "%s\n" % msg ) @@ -34,7 +34,7 @@ # get an iterable try: - context = cElementTree.iterparse( source, events=( "start", "end" ) ) + context = ElementTree.iterparse( source, events=( "start", "end" ) ) except: stop_err( "Invalid data format." ) # turn it into an iterator @@ -46,7 +46,7 @@ stop_err( "Invalid data format." ) outfile = open( sys.argv[2], 'w' ) - try: + try: for event, elem in context: # for every <Iteration> tag if event == "end" and elem.tag == "Iteration": @@ -71,7 +71,7 @@ elem.clear() except: outfile.close() - stop_err( "The input data contains tags that are not recognizable by the tool." ) + stop_err( "The input data is malformed, or there is more than one dataset in the input file. Error: %s" % sys.exc_info()[1] ) outfile.close() --- a/tools/metag_tools/megablast_xml_parser.xml Tue Jul 12 17:04:16 2011 -0400 +++ b/tools/metag_tools/megablast_xml_parser.xml Tue Jul 12 18:14:56 2011 -0400 @@ -2,26 +2,23 @@ <description></description><command interpreter="python">megablast_xml_parser.py $input1 $output1</command><inputs> - <param name="input1" type="data" format="blastxml" label="Megablast XML output" /> + <param name="input1" type="data" format="blastxml" label="Megablast XML output" /></inputs><outputs> - <data name="output1" format="tabular"/> + <data name="output1" format="tabular"/></outputs> -<requirements> - <requirement type="python-module">cElementTree</requirement> -</requirements><tests> - <test> - <param name="input1" value="megablast_xml_parser_test1.gz" ftype="blastxml" /> - <output name="output1" file="megablast_xml_parser_test1_out.tabular" ftype="tabular" /> - </test> + <test> + <param name="input1" value="megablast_xml_parser_test1.gz" ftype="blastxml" /> + <output name="output1" file="megablast_xml_parser_test1_out.tabular" ftype="tabular" /> + </test></tests><help> **What it does** This tool processes the XML output of any NCBI blast tool (if you run your own blast jobs, the XML output can be generated with **-m 7** option). - + ----- **Output fields** --- a/tools/ncbi_blast_plus/blastxml_to_tabular.py Tue Jul 12 17:04:16 2011 -0400 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.py Tue Jul 12 18:14:56 2011 -0400 @@ -5,7 +5,7 @@ BLAST filename, output format (std for standard 12 columns, or ext for the extended 24 columns offered in the BLAST+ wrappers). -The 12 colums output are 'qseqid sseqid pident length mismatch gapopen qstart +The 12 columns output are 'qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore' or 'std' at the BLAST+ command line, which mean: @@ -51,22 +51,23 @@ Be aware that the sequence in the extended tabular output or XML direct from BLAST+ may or may not use XXXX masking on regions of low complexity. This can throw the off the calculation of percentage identity and gap openings. -[In fact, both BLAST 2.2.24+ and 2.2.25+ have a sutle bug in this regard, +[In fact, both BLAST 2.2.24+ and 2.2.25+ have a subtle bug in this regard, with these numbers changing depending on whether or not the low complexity filter is used.] -This script attempts to produce idential output to what BLAST+ would have done. +This script attempts to produce identical output to what BLAST+ would have done. However, check this with "diff -b ..." since BLAST+ sometimes includes an extra space character (probably a bug). """ import sys import re -assert sys.version_info[:2] >= ( 2, 4 ) if sys.version_info[:2] >= ( 2, 5 ): - import xml.etree.cElementTree as cElementTree + import xml.etree.cElementTree as ElementTree else: - import cElementTree + from galaxy import eggs + import pkg_resources; pkg_resources.require( "elementtree" ) + from elementtree import ElementTree def stop_err( msg ): sys.stderr.write("%s\n" % msg) @@ -90,7 +91,7 @@ # get an iterable try: - context = cElementTree.iterparse(in_file, events=("start", "end")) + context = ElementTree.iterparse(in_file, events=("start", "end")) except: stop_err("Invalid data format.") # turn it into an iterator 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: kanwei: Rename version_string -> version_command, update wrappers
by Bitbucket 12 Jul '11

12 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/12cb939a8147/ changeset: 12cb939a8147 user: kanwei date: 2011-07-12 23:04:16 summary: Rename version_string -> version_command, update wrappers affected #: 7 files (31 bytes) --- a/lib/galaxy/tools/__init__.py Thu Jul 07 11:19:33 2011 +0100 +++ b/lib/galaxy/tools/__init__.py Tue Jul 12 17:04:16 2011 -0400 @@ -397,8 +397,9 @@ self.description = util.xml_text(root, "description") # Versioning for tools self.version_string_cmd = None - if root.find("version_string") is not None: - self.version_string_cmd = root.find("version_string").text + version_cmd = root.find("version_command") + if version_cmd is not None: + self.version_string_cmd = version_cmd.text # Parallelism for tasks, read from tool config. parallelism = root.find("parallelism") if parallelism is not None and parallelism.get("method"): --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Tue Jul 12 17:04:16 2011 -0400 @@ -1,6 +1,6 @@ <tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.11"><description>Search nucleotide database with nucleotide query sequence(s)</description> - <version_string>blastn -version</version_string> + <version_command>blastn -version</version_command><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Tue Jul 12 17:04:16 2011 -0400 @@ -1,6 +1,6 @@ <tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.11"><description>Search protein database with protein query sequence(s)</description> - <version_string>blastp -version</version_string> + <version_command>blastp -version</version_command><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Tue Jul 12 17:04:16 2011 -0400 @@ -1,6 +1,6 @@ <tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.11"><description>Search protein database with translated nucleotide query sequence(s)</description> - <version_string>blastx -version</version_string> + <version_command>blastx -version</version_command><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Tue Jul 12 17:04:16 2011 -0400 @@ -1,6 +1,6 @@ <tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.11"><description>Search translated nucleotide database with protein query sequence(s)</description> - <version_string>tblastn -version</version_string> + <version_command>tblastn -version</version_command><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Tue Jul 12 17:04:16 2011 -0400 @@ -1,6 +1,6 @@ <tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.11"><description>Search translated nucleotide database with translated nucleotide query sequence(s)</description> - <version_string>tblastx -version</version_string> + <version_command>tblastx -version</version_command><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces --- a/tools/ngs_rna/tophat_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 +++ b/tools/ngs_rna/tophat_wrapper.xml Tue Jul 12 17:04:16 2011 -0400 @@ -1,6 +1,6 @@ <tool id="tophat" name="Tophat for Illumina" version="1.5.0"><description>Find splice junctions using RNA-seq data</description> - <version_string>tophat --version</version_string> + <version_command>tophat --version</version_command><requirements><requirement type="package">tophat</requirement></requirements> 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: peterjc: Support new tool version tag in NCBI BLAST+ wrappers
by Bitbucket 12 Jul '11

12 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/632d4c48d97c/ changeset: 632d4c48d97c user: peterjc date: 2011-07-07 12:19:33 summary: Support new tool version tag in NCBI BLAST+ wrappers affected #: 5 files (267 bytes) --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Tue Jul 12 15:02:37 2011 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 @@ -1,5 +1,6 @@ -<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.10"> +<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.11"><description>Search nucleotide database with nucleotide query sequence(s)</description> + <version_string>blastn -version</version_string><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Tue Jul 12 15:02:37 2011 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 @@ -1,5 +1,6 @@ -<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.10"> +<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.11"><description>Search protein database with protein query sequence(s)</description> + <version_string>blastp -version</version_string><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Tue Jul 12 15:02:37 2011 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 @@ -1,5 +1,6 @@ -<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.10"> +<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.11"><description>Search protein database with translated nucleotide query sequence(s)</description> + <version_string>blastx -version</version_string><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Tue Jul 12 15:02:37 2011 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 @@ -1,5 +1,6 @@ -<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.10"> +<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.11"><description>Search translated nucleotide database with protein query sequence(s)</description> + <version_string>tblastn -version</version_string><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Tue Jul 12 15:02:37 2011 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 @@ -1,5 +1,6 @@ -<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.10"> +<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.11"><description>Search translated nucleotide database with translated nucleotide query sequence(s)</description> + <version_string>tblastx -version</version_string><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix for displaying tools.
by Bitbucket 12 Jul '11

12 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/661aca672402/ changeset: 661aca672402 user: greg date: 2011-07-12 21:02:37 summary: Fix for displaying tools. affected #: 1 file (14 bytes) --- a/templates/webapps/community/repository/tool_form.mako Tue Jul 12 13:51:28 2011 -0400 +++ b/templates/webapps/community/repository/tool_form.mako Tue Jul 12 15:02:37 2011 -0400 @@ -84,7 +84,7 @@ field = SelectField( param.name ) field.add_option( param.name, param.name ) field_html = field.get_html() - elif isinstance( param, SelectToolParameter ) and param.data_ref: + elif isinstance( param, SelectToolParameter ) and hasattr( param, 'data_ref' ): field = SelectField( param.name, display=param.display ) field.add_option( param.data_ref, param.data_ref ) field_html = field.get_html( prefix ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Make a backup copy of the tool shed's hgweb.config file just before changes are made to it. Add the ability for a repository owner to change categories associated with their repository.
by Bitbucket 12 Jul '11

12 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/af9b19b57969/ changeset: af9b19b57969 user: greg date: 2011-07-12 19:51:28 summary: Make a backup copy of the tool shed's hgweb.config file just before changes are made to it. Add the ability for a repository owner to change categories associated with their repository. affected #: 4 files (3.8 KB) --- a/lib/galaxy/webapps/community/controllers/repository.py Tue Jul 12 10:07:15 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Tue Jul 12 13:51:28 2011 -0400 @@ -356,11 +356,19 @@ if not( VALID_REPOSITORYNAME_RE.match( name ) ): return "Repository names must contain only lower-case letters, numbers and underscore '_'." return '' + def __make_hgweb_config_copy( self, trans, hgweb_config ): + # Make a backup of the hgweb.config file + today = date.today() + backup_date = today.strftime( "%Y_%m_%d" ) + hgweb_config_copy = '%s/hgweb.config_%s_backup' % ( trans.app.config.root, backup_date ) + shutil.copy( os.path.abspath( hgweb_config ), os.path.abspath( hgweb_config_copy ) ) def __add_hgweb_config_entry( self, trans, repository, repository_path ): # Add an entry in the hgweb.config file for a new repository. # An entry looks something like: # repos/test/mira_assembler = database/community_files/000/repo_123. hgweb_config = "%s/hgweb.config" % trans.app.config.root + # Make a backup of the hgweb.config file since we're going to be changing it. + self.__make_hgweb_config_copy( trans, hgweb_config ) entry = "repos/%s/%s = %s" % ( repository.user.username, repository.name, repository_path.lstrip( './' ) ) if os.path.exists( hgweb_config ): output = open( hgweb_config, 'a' ) @@ -374,6 +382,8 @@ # the owner changes the name of the repository. An entry looks something like: # repos/test/mira_assembler = database/community_files/000/repo_123. hgweb_config = "%s/hgweb.config" % trans.app.config.root + # Make a backup of the hgweb.config file since we're going to be changing it. + self.__make_hgweb_config_copy( trans, hgweb_config ) repo_dir = repository.repo_path old_lhs = "repos/%s/%s" % ( repository.user.username, old_repository_name ) old_entry = "%s = %s" % ( old_lhs, repo_dir ) @@ -537,6 +547,7 @@ display_reviews = util.string_as_bool( params.get( 'display_reviews', False ) ) alerts = params.get( 'alerts', '' ) alerts_checked = CheckboxField.is_checked( alerts ) + category_ids = util.listify( params.get( 'category_id', '' ) ) if repository.email_alerts: email_alerts = from_json_string( repository.email_alerts ) else: @@ -572,7 +583,21 @@ if flush_needed: trans.sa_session.add( repository ) trans.sa_session.flush() - message = "The repository information has been updated." + message = "The repository information has been updated." + elif params.get( 'manage_categories_button', False ): + flush_needed = False + # Delete all currently existing categories. + for rca in repository.categories: + trans.sa_session.delete( rca ) + trans.sa_session.flush() + if category_ids: + # Create category associations + for category_id in category_ids: + category = trans.app.model.Category.get( trans.security.decode_id( category_id ) ) + rca = trans.app.model.RepositoryCategoryAssociation( repository, category ) + trans.sa_session.add( rca ) + trans.sa_session.flush() + message = "The repository information has been updated." elif params.get( 'user_access_button', False ): if allow_push not in [ 'none' ]: remove_auth = params.get( 'remove_auth', '' ) @@ -586,6 +611,7 @@ usernames.append( user.username ) usernames = ','.join( usernames ) repository.set_allow_push( usernames, remove_auth=remove_auth ) + message = "The repository information has been updated." elif params.get( 'receive_email_alerts_button', False ): flush_needed = False if alerts_checked: @@ -601,6 +627,7 @@ if flush_needed: trans.sa_session.add( repository ) trans.sa_session.flush() + message = "The repository information has been updated." if error: status = 'error' if repository.allow_push: @@ -615,6 +642,8 @@ metadata = repository_metadata.metadata else: metadata = None + categories = get_categories( trans ) + selected_categories = [ rca.category_id for rca in repository.categories ] return trans.fill_template( '/webapps/community/repository/manage_repository.mako', repo_name=repo_name, description=description, @@ -623,6 +652,8 @@ allow_push_select_field=allow_push_select_field, repo=repo, repository=repository, + selected_categories=selected_categories, + categories=categories, metadata=metadata, avg_rating=avg_rating, display_reviews=display_reviews, --- a/templates/webapps/community/repository/create_repository.mako Tue Jul 12 10:07:15 2011 -0400 +++ b/templates/webapps/community/repository/create_repository.mako Tue Jul 12 13:51:28 2011 -0400 @@ -38,7 +38,7 @@ <div style="clear: both"></div></div><div class="form-row"> - <label>Category</label> + <label>Categories</label><div class="form-row"><select name="category_id" multiple> %for category in categories: @@ -50,6 +50,9 @@ %endfor </select></div> + <div class="toolParamHelp" style="clear: both;"> + Multi-select list - hold the appropriate key while clicking to select multiple categories. + </div><div style="clear: both"></div></div><div class="form-row"> --- a/templates/webapps/community/repository/manage_repository.mako Tue Jul 12 10:07:15 2011 -0400 +++ b/templates/webapps/community/repository/manage_repository.mako Tue Jul 12 13:51:28 2011 -0400 @@ -151,6 +151,34 @@ </form></div></div> +<p/> +<div class="toolForm"> + <div class="toolFormTitle">Manage categories</div> + <div class="toolFormBody"> + <form name="categories" id="categories" action="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ) )}" method="post" > + <div class="form-row"> + <label>Categories</label> + <select name="category_id" multiple> + %for category in categories: + %if category.id in selected_categories: + <option value="${trans.security.encode_id( category.id )}" selected>${category.name}</option> + %else: + <option value="${trans.security.encode_id( category.id )}">${category.name}</option> + %endif + %endfor + </select> + <div class="toolParamHelp" style="clear: both;"> + Multi-select list - hold the appropriate key while clicking to select multiple categories. + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <input type="submit" name="manage_categories_button" value="Save"/> + </div> + </form> + </div> +</div> +<p/> %if can_set_metadata: <p/><div class="toolForm"> @@ -215,7 +243,7 @@ %if trans.app.config.smtp_server: <p/><div class="toolForm"> - <div class="toolFormTitle">${repository.name}</div> + <div class="toolFormTitle">Notification on update</div><div class="toolFormBody"><form name="receive_email_alerts" id="receive_email_alerts" action="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ) )}" method="post" ><div class="form-row"> --- a/templates/webapps/community/repository/view_repository.mako Tue Jul 12 10:07:15 2011 -0400 +++ b/templates/webapps/community/repository/view_repository.mako Tue Jul 12 13:51:28 2011 -0400 @@ -145,6 +145,20 @@ %endif </div></div> +%if repository.categories: + <p/> + <div class="toolForm"> + <div class="toolFormTitle">Categories</div> + <div class="toolFormBody"> + %for rca in repository.categories: + <div class="form-row"> + ${rca.category.name} + </div> + %endfor + <div style="clear: both"></div> + </div> + </div> +%endif %if metadata: <p/><div class="toolForm"> @@ -197,7 +211,7 @@ %if trans.user and trans.app.config.smtp_server: <p/><div class="toolForm"> - <div class="toolFormTitle">${repository.name}</div> + <div class="toolFormTitle">Notification on update</div><div class="toolFormBody"><form name="receive_email_alerts" id="receive_email_alerts" action="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ) )}" method="post" ><div class="form-row"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fix for renaming a tool shed repository, and aother fix for displaying a tool that includes a SelectToolParameter with a data_ref.
by Bitbucket 12 Jul '11

12 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/7c7d01c511d0/ changeset: 7c7d01c511d0 user: greg date: 2011-07-12 16:07:15 summary: Fix for renaming a tool shed repository, and aother fix for displaying a tool that includes a SelectToolParameter with a data_ref. affected #: 5 files (2.0 KB) --- a/lib/galaxy/webapps/community/controllers/repository.py Mon Jul 11 14:48:12 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Tue Jul 12 10:07:15 2011 -0400 @@ -369,6 +369,23 @@ output.write( '[paths]\n' ) output.write( "%s\n" % entry ) output.close() + def __change_hgweb_config_entry( self, trans, repository, old_repository_name, new_repository_name ): + # Change an entry in the hgweb.config file for a repository. This only happens when + # the owner changes the name of the repository. An entry looks something like: + # repos/test/mira_assembler = database/community_files/000/repo_123. + hgweb_config = "%s/hgweb.config" % trans.app.config.root + repo_dir = repository.repo_path + old_lhs = "repos/%s/%s" % ( repository.user.username, old_repository_name ) + old_entry = "%s = %s" % ( old_lhs, repo_dir ) + new_entry = "repos/%s/%s = %s\n" % ( repository.user.username, new_repository_name, repo_dir ) + tmp_fd, tmp_fname = tempfile.mkstemp() + new_hgweb_config = open( tmp_fname, 'wb' ) + for i, line in enumerate( open( hgweb_config ) ): + if line.startswith( old_lhs ): + new_hgweb_config.write( new_entry ) + else: + new_hgweb_config.write( line ) + shutil.move( tmp_fname, os.path.abspath( hgweb_config ) ) def __create_hgrc_file( self, repository ): # At this point, an entry for the repository is required to be in the hgweb.config # file so we can call repository.repo_path. @@ -511,7 +528,8 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) repository = get_repository( trans, id ) - repo = hg.repository( ui.ui(), repository.repo_path ) + repo_dir = repository.repo_path + repo = hg.repository( ui.ui(), repo_dir ) repo_name = util.restore_text( params.get( 'repo_name', repository.name ) ) description = util.restore_text( params.get( 'description', repository.description ) ) long_description = util.restore_text( params.get( 'long_description', repository.long_description ) ) @@ -528,6 +546,7 @@ user = trans.user if params.get( 'edit_repository_button', False ): flush_needed = False + # TODO: add a can_manage in the security agent. if user != repository.user: message = "You are not the owner of this repository, so you cannot manage it." status = error @@ -541,6 +560,7 @@ if message: error = True else: + self.__change_hgweb_config_entry( trans, repository, repository.name, repo_name ) repository.name = repo_name flush_needed = True if description != repository.description: @@ -552,6 +572,7 @@ if flush_needed: trans.sa_session.add( repository ) trans.sa_session.flush() + message = "The repository information has been updated." elif params.get( 'user_access_button', False ): if allow_push not in [ 'none' ]: remove_auth = params.get( 'remove_auth', '' ) --- a/lib/galaxy/webapps/community/model/__init__.py Mon Jul 11 14:48:12 2011 -0400 +++ b/lib/galaxy/webapps/community/model/__init__.py Tue Jul 12 10:07:15 2011 -0400 @@ -4,7 +4,7 @@ Naming: try to use class names that have a distinct plural form so that the relationship cardinalities are obvious (e.g. prefer Dataset to Data) """ -import os.path, os, errno, sys, codecs, operator, tempfile, logging, tarfile, mimetypes, ConfigParser +import os.path, os, errno, sys, codecs, operator, logging, tarfile, mimetypes, ConfigParser from galaxy import util from galaxy.util.bunch import Bunch from galaxy.util.hash_util import * --- a/templates/webapps/community/repository/manage_repository.mako Mon Jul 11 14:48:12 2011 -0400 +++ b/templates/webapps/community/repository/manage_repository.mako Tue Jul 12 10:07:15 2011 -0400 @@ -9,6 +9,7 @@ can_push = trans.app.security_agent.can_push( trans.user, repository ) can_upload = can_push can_browse_contents = not is_new + can_set_metadata = not is_new can_rate = not is_new and trans.user and repository.user != trans.user can_view_change_log = not is_new if can_push: @@ -79,10 +80,10 @@ %endif %if can_browse_contents: <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> %endif - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a></div> %endif </ul> @@ -150,65 +151,67 @@ </form></div></div> -<p/> -<div class="toolForm"> - <div class="toolFormTitle">Repository metadata</div> - <div class="toolFormBody"> - %if metadata: - %if 'tools' in metadata: +%if can_set_metadata: + <p/> + <div class="toolForm"> + <div class="toolFormTitle">Repository metadata</div> + <div class="toolFormBody"> + %if metadata: + %if 'tools' in metadata: + <div class="form-row"> + <label>Tools:</label> + <% tool_dicts = metadata[ 'tools' ] %> + <table class="grid"> + <tr> + <td><b>name</b></td> + <td><b>description</b></td> + <td><b>version</b></td> + <td><b>requirements</b></td> + </tr> + %for tool_dict in tool_dicts: + <tr> + <td><a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ] )}">${tool_dict[ 'name' ]}</a></td> + <td>${tool_dict[ 'description' ]}</td> + <td>${tool_dict[ 'version' ]}</td> + <td> + <% + if 'requirements' in tool_dict: + requirements = tool_dict[ 'requirements' ] + else: + requirements = None + %> + %if requirements: + <% + requirements_str = '' + for requirement_dict in tool_dict[ 'requirements' ]: + requirements_str += '%s (%s), ' % ( requirement_dict[ 'name' ], requirement_dict[ 'type' ] ) + requirements_str = requirements_str.rstrip( ', ' ) + %> + ${requirements_str} + %else: + none + %endif + </td> + </tr> + %endfor + </table> + </div> + <div style="clear: both"></div> + %endif + %endif + <form name="set_metadata" action="${h.url_for( controller='repository', action='set_metadata', id=trans.security.encode_id( repository.id ), ctx_str=repository.tip )}" method="post"><div class="form-row"> - <label>Tools:</label> - <% tool_dicts = metadata[ 'tools' ] %> - <table class="grid"> - <tr> - <td><b>name</b></td> - <td><b>description</b></td> - <td><b>version</b></td> - <td><b>requirements</b></td> - </tr> - %for tool_dict in tool_dicts: - <tr> - <td><a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ] )}">${tool_dict[ 'name' ]}</a></td> - <td>${tool_dict[ 'description' ]}</td> - <td>${tool_dict[ 'version' ]}</td> - <td> - <% - if 'requirements' in tool_dict: - requirements = tool_dict[ 'requirements' ] - else: - requirements = None - %> - %if requirements: - <% - requirements_str = '' - for requirement_dict in tool_dict[ 'requirements' ]: - requirements_str += '%s (%s), ' % ( requirement_dict[ 'name' ], requirement_dict[ 'type' ] ) - requirements_str = requirements_str.rstrip( ', ' ) - %> - ${requirements_str} - %else: - none - %endif - </td> - </tr> - %endfor - </table> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="submit" name="set_metadata_button" value="Reset metadata"/> + </div> + <div class="toolParamHelp" style="clear: both;"> + Inspect the repository and reset the above attributes for the repository tip. + </div></div> - <div style="clear: both"></div> - %endif - %endif - <form name="set_metadata" action="${h.url_for( controller='repository', action='set_metadata', id=trans.security.encode_id( repository.id ), ctx_str=repository.tip )}" method="post"> - <div class="form-row"> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="submit" name="set_metadata_button" value="Reset metadata"/> - </div> - <div class="toolParamHelp" style="clear: both;"> - Inspect the repository and reset the above attributes for the repository tip. - </div> - </div> - </form> + </form> + </div></div> -</div> +%endif %if trans.app.config.smtp_server: <p/><div class="toolForm"> --- a/templates/webapps/community/repository/tool_form.mako Mon Jul 11 14:48:12 2011 -0400 +++ b/templates/webapps/community/repository/tool_form.mako Tue Jul 12 10:07:15 2011 -0400 @@ -4,7 +4,7 @@ <% from galaxy.util.expressions import ExpressionContext from galaxy import util - from galaxy.tools.parameters.basic import DataToolParameter, ColumnListParameter + from galaxy.tools.parameters.basic import DataToolParameter, ColumnListParameter, SelectToolParameter from galaxy.web.form_builder import SelectField is_admin = trans.user_is_admin() @@ -84,6 +84,10 @@ field = SelectField( param.name ) field.add_option( param.name, param.name ) field_html = field.get_html() + elif isinstance( param, SelectToolParameter ) and param.data_ref: + field = SelectField( param.name, display=param.display ) + field.add_option( param.data_ref, param.data_ref ) + field_html = field.get_html( prefix ) else: field = param.get_html_field( trans, None, other_values ) field_html = field.get_html( prefix ) --- a/templates/webapps/community/repository/view_repository.mako Mon Jul 11 14:48:12 2011 -0400 +++ b/templates/webapps/community/repository/view_repository.mako Tue Jul 12 10:07:15 2011 -0400 @@ -79,10 +79,10 @@ %endif %if can_browse_contents: <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> %endif - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a></div> %endif </ul> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fix for setting tool shed repository etadata multiple times when nothing in the repository has changed.
by Bitbucket 11 Jul '11

11 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/38899d79629b/ changeset: 38899d79629b user: greg date: 2011-07-11 20:48:12 summary: Fix for setting tool shed repository etadata multiple times when nothing in the repository has changed. affected #: 1 file (178 bytes) --- a/lib/galaxy/webapps/community/controllers/common.py Mon Jul 11 14:10:56 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Mon Jul 11 14:48:12 2011 -0400 @@ -146,10 +146,13 @@ metadata_dict[ 'tools' ] = [ tool_dict ] except Exception, e: invalid_tool_configs.append( ( name, str( e ) ) ) - repository_metadata = trans.model.RepositoryMetadata( repository.id, repository.tip, metadata_dict ) - trans.sa_session.add( repository_metadata ) - if not flush_needed: - flush_needed = True + if metadata_dict: + # The metadata_dict dictionary will contain items only + # if the repository did not already have metadata set. + repository_metadata = trans.model.RepositoryMetadata( repository.id, repository.tip, metadata_dict ) + trans.sa_session.add( repository_metadata ) + if not flush_needed: + flush_needed = True else: message = "Repository does not include changeset revision '%s'." % str( ctx_str ) status = 'error' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Bug fix for setting tool shed repository metadata on repositories containing more than 1 tool.
by Bitbucket 11 Jul '11

11 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/6e9fca39e3f4/ changeset: 6e9fca39e3f4 user: greg date: 2011-07-11 20:10:56 summary: Bug fix for setting tool shed repository metadata on repositories containing more than 1 tool. affected #: 1 file (106 bytes) --- a/lib/galaxy/webapps/community/controllers/common.py Mon Jul 11 13:45:57 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Mon Jul 11 14:10:56 2011 -0400 @@ -86,6 +86,7 @@ invalid_tool_configs = [] flush_needed = False if change_set is not None: + metadata_dict = {} for root, dirs, files in os.walk( repo_dir ): if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0: if '.hg' in dirs: @@ -139,13 +140,16 @@ if not flush_needed: flush_needed = True else: - metadata_dict = dict( tools = [ tool_dict ] ) - repository_metadata = trans.model.RepositoryMetadata( repository.id, repository.tip, metadata_dict ) - trans.sa_session.add( repository_metadata ) - if not flush_needed: - flush_needed = True + if 'tools' in metadata_dict: + metadata_dict[ 'tools' ].append( tool_dict ) + else: + metadata_dict[ 'tools' ] = [ tool_dict ] except Exception, e: invalid_tool_configs.append( ( name, str( e ) ) ) + repository_metadata = trans.model.RepositoryMetadata( repository.id, repository.tip, metadata_dict ) + trans.sa_session.add( repository_metadata ) + if not flush_needed: + flush_needed = True else: message = "Repository does not include changeset revision '%s'." % str( ctx_str ) status = 'error' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Allow an admin user to manage repositories they do not own.
by Bitbucket 11 Jul '11

11 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0007cf69d1dc/ changeset: 0007cf69d1dc user: greg date: 2011-07-11 19:45:57 summary: Allow an admin user to manage repositories they do not own. affected #: 1 file (61 bytes) --- a/lib/galaxy/webapps/community/controllers/repository.py Mon Jul 11 13:34:23 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Mon Jul 11 13:45:57 2011 -0400 @@ -214,7 +214,8 @@ if operation == "view_or_manage_repository": repository_id = kwd.get( 'id', None ) repository = get_repository( trans, repository_id ) - if repository.user == trans.user: + is_admin = trans.user_is_admin() + if is_admin or repository.user == trans.user: return trans.response.send_redirect( web.url_for( controller='repository', action='manage_repository', **kwd ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Do not set tool shed repository metadata if tool does not load. Add tool config <requirements> settings to tool shed repository metadata.
by Bitbucket 11 Jul '11

11 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/34c190323b36/ changeset: 34c190323b36 user: greg date: 2011-07-11 19:34:23 summary: Do not set tool shed repository metadata if tool does not load. Add tool config <requirements> settings to tool shed repository metadata. affected #: 5 files (4.3 KB) --- a/lib/galaxy/webapps/community/controllers/common.py Fri Jul 08 16:11:28 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Mon Jul 11 13:34:23 2011 -0400 @@ -75,9 +75,100 @@ .filter( and_( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ), trans.model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) ) \ .first() +def set_repository_metadata( trans, id, ctx_str, **kwd ): + """Set repository metadata""" + message = '' + status = 'done' + repository = get_repository( trans, id ) + repo_dir = repository.repo_path + repo = hg.repository( ui.ui(), repo_dir ) + change_set = get_change_set( trans, repo, ctx_str ) + invalid_tool_configs = [] + flush_needed = False + if change_set is not None: + for root, dirs, files in os.walk( repo_dir ): + if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0: + if '.hg' in dirs: + # Don't visit .hg directories - should be impossible since we don't + # allow uploaded archives that contain .hg dirs, but just in case... + dirs.remove( '.hg' ) + if 'hgrc' in files: + # Don't include hgrc files in commit. + files.remove( 'hgrc' ) + for name in files: + # Find all tool configs. + if name.endswith( '.xml' ): + try: + full_path = os.path.abspath( os.path.join( root, name ) ) + tool = load_tool( trans, full_path ) + if tool is not None: + repository_metadata = get_repository_metadata( trans, id, repository.tip ) + tool_requirements = [] + for tr in tool.requirements: + requirement_dict = dict( name=tr.name, + type=tr.type, + version=tr.version ) + tool_requirements.append( requirement_dict ) + tool_dict = dict( id = tool.id, + name = tool.name, + version = tool.version, + description = tool.description, + tool_config = os.path.join( root, name ), + requirements = tool_requirements ) + if repository_metadata: + metadata = repository_metadata.metadata + if metadata and 'tools' in metadata: + metadata_tools = metadata[ 'tools' ] + found = False + for tool_metadata_dict in metadata_tools: + if 'id' in tool_metadata_dict and tool_metadata_dict[ 'id' ] == tool.id and \ + 'version' in tool_metadata_dict and tool_metadata_dict[ 'version' ] == tool.version: + found = True + tool_metadata_dict[ 'name' ] = tool.name + tool_metadata_dict[ 'description' ] = tool.description + tool_metadata_dict[ 'tool_config' ] = os.path.join( root, name ) + tool_metadata_dict[ 'requirements' ] = tool_requirements + flush_needed = True + if not found: + metadata_tools.append( tool_dict ) + else: + if metadata is None: + repository_metadata.metadata = {} + repository_metadata.metadata[ 'tools' ] = [ tool_dict ] + trans.sa_session.add( repository_metadata ) + if not flush_needed: + flush_needed = True + else: + metadata_dict = dict( tools = [ tool_dict ] ) + repository_metadata = trans.model.RepositoryMetadata( repository.id, repository.tip, metadata_dict ) + trans.sa_session.add( repository_metadata ) + if not flush_needed: + flush_needed = True + except Exception, e: + invalid_tool_configs.append( ( name, str( e ) ) ) + else: + message = "Repository does not include changeset revision '%s'." % str( ctx_str ) + status = 'error' + if invalid_tool_configs: + message = "Metadata cannot be defined for change set revision '%s'. Correct the following problems and reset metadata.<br/>" % str( ctx_str ) + for itc_tup in invalid_tool_configs: + message += "<b>%s</b> - %s<br/>" % ( itc_tup[0], itc_tup[1] ) + status = 'error' + elif flush_needed: + # We only flush if there are no tool config errors, so change sets will only have metadata + # if everything in them is valid. + trans.sa_session.flush() + return message, status def get_repository_by_name( trans, name ): """Get a repository from the database via name""" return trans.sa_session.query( app.model.Repository ).filter_by( name=name ).one() +def get_change_set( trans, repo, ctx_str, **kwd ): + """Retrieve a specified change set from a repository""" + for changeset in repo.changelog: + ctx = repo.changectx( changeset ) + if str( ctx ) == ctx_str: + return ctx + return None def get_user( trans, id ): """Get a user from the database""" return trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( id ) ) @@ -184,77 +275,3 @@ ToolClass = Tool return ToolClass( config_file, root, trans.app ) return None -def set_repository_metadata( trans, id, ctx_str, **kwd ): - """Set repository metadata""" - message = '' - status = 'done' - repository = get_repository( trans, id ) - repo_dir = repository.repo_path - repo = hg.repository( ui.ui(), repo_dir ) - found = False - invalid_tool_configs = [] - for changeset in repo.changelog: - ctx = repo.changectx( changeset ) - if str( ctx ) == ctx_str: - found = True - break - if found: - for root, dirs, files in os.walk( repo_dir ): - if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0: - if '.hg' in dirs: - # Don't visit .hg directories - should be impossible since we don't - # allow uploaded archives that contain .hg dirs, but just in case... - dirs.remove( '.hg' ) - if 'hgrc' in files: - # Don't include hgrc files in commit. - files.remove( 'hgrc' ) - for name in files: - # Find all tool configs. - if name.endswith( '.xml' ): - try: - full_path = os.path.abspath( os.path.join( root, name ) ) - tool = load_tool( trans, full_path ) - if tool is not None: - repository_metadata = get_repository_metadata( trans, id, repository.tip ) - # TODO: add more stuff, like requirements - tool_dict = dict( id = tool.id, - name = tool.name, - version = tool.version, - description = tool.description, - tool_config = full_path ) - if repository_metadata: - metadata = repository_metadata.metadata - if metadata and 'tools' in metadata: - metadata_tools = metadata[ 'tools' ] - found = False - for tool_metadata_dict in metadata_tools: - if 'id' in tool_metadata_dict and tool_metadata_dict[ 'id' ] == tool.id and \ - 'version' in tool_metadata_dict and tool_metadata_dict[ 'version' ] == tool.version: - found = True - tool_metadata_dict[ 'name' ] = tool.name - tool_metadata_dict[ 'description' ] = tool.description - tool_metadata_dict[ 'tool_config' ] = os.path.join( root, name ) - # TODO: add more stuff, like tool requirements, code files, etc - if not found: - metadata_tools.append( tool_dict ) - else: - if metadata is None: - repository_metadata.metadata = {} - repository_metadata.metadata[ 'tools' ] = [ tool_dict ] - trans.sa_session.add( repository_metadata ) - else: - metadata_dict = dict( tools = [ tool_dict ] ) - repository_metadata = trans.model.RepositoryMetadata( repository.id, repository.tip, metadata_dict ) - trans.sa_session.add( repository_metadata ) - trans.sa_session.flush() - except Exception, e: - invalid_tool_configs.append( ( name, str( e ) ) ) - else: - message = "Repository does not include changeset revision '%s'." % str( ctx_str ) - status = 'error' - if invalid_tool_configs: - message = "The following tool configs are invalid and were not added to the repository metadata:<br/>" - for itc_tup in invalid_tool_configs: - message += "<b>%s</b> - %s<br/>" % ( itc_tup[0], itc_tup[1] ) - status = 'error' - return message, status --- a/lib/galaxy/webapps/community/controllers/repository.py Fri Jul 08 16:11:28 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Mon Jul 11 13:34:23 2011 -0400 @@ -643,13 +643,8 @@ status = params.get( 'status', 'done' ) repository = get_repository( trans, id ) repo = hg.repository( ui.ui(), repository.repo_path ) - found = False - for changeset in repo.changelog: - ctx = repo.changectx( changeset ) - if str( ctx ) == ctx_str: - found = True - break - if not found: + ctx = get_change_set( trans, repo, ctx_str ) + if ctx is None: message = "Repository does not include changeset revision '%s'." % str( ctx_str ) status = 'error' return trans.response.send_redirect( web.url_for( controller='repository', @@ -753,6 +748,8 @@ @web.require_login( "set repository metadata" ) def set_metadata( self, trans, id, ctx_str, **kwd ): message, status = set_repository_metadata( trans, id, ctx_str, **kwd ) + if not message: + message = "Metadata for change set revision '%s' has been reset." % str( ctx_str ) return trans.response.send_redirect( web.url_for( controller='repository', action='manage_repository', id=id, --- a/templates/webapps/community/repository/manage_repository.mako Fri Jul 08 16:11:28 2011 -0400 +++ b/templates/webapps/community/repository/manage_repository.mako Mon Jul 11 13:34:23 2011 -0400 @@ -160,11 +160,36 @@ <label>Tools:</label><% tool_dicts = metadata[ 'tools' ] %><table class="grid"> + <tr> + <td><b>name</b></td> + <td><b>description</b></td> + <td><b>version</b></td> + <td><b>requirements</b></td> + </tr> %for tool_dict in tool_dicts: <tr><td><a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ] )}">${tool_dict[ 'name' ]}</a></td><td>${tool_dict[ 'description' ]}</td> - <td>version: ${tool_dict[ 'version' ]}</td> + <td>${tool_dict[ 'version' ]}</td> + <td> + <% + if 'requirements' in tool_dict: + requirements = tool_dict[ 'requirements' ] + else: + requirements = None + %> + %if requirements: + <% + requirements_str = '' + for requirement_dict in tool_dict[ 'requirements' ]: + requirements_str += '%s (%s), ' % ( requirement_dict[ 'name' ], requirement_dict[ 'type' ] ) + requirements_str = requirements_str.rstrip( ', ' ) + %> + ${requirements_str} + %else: + none + %endif + </td></tr> %endfor </table> --- a/templates/webapps/community/repository/tool_form.mako Fri Jul 08 16:11:28 2011 -0400 +++ b/templates/webapps/community/repository/tool_form.mako Mon Jul 11 13:34:23 2011 -0400 @@ -15,6 +15,10 @@ can_rate = trans.user and repository.user != trans.user can_manage = is_admin or repository.user == trans.user can_view_change_log = not is_new + if can_push: + browse_label = 'Browse or delete repository files' + else: + browse_label = 'Browse repository files' %><html> @@ -116,6 +120,9 @@ %if can_view_change_log: <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif + %if can_browse_contents: + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> + %endif %if can_rate: <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif --- a/templates/webapps/community/repository/view_repository.mako Fri Jul 08 16:11:28 2011 -0400 +++ b/templates/webapps/community/repository/view_repository.mako Mon Jul 11 13:34:23 2011 -0400 @@ -155,11 +155,36 @@ <label>Tools:</label><% tool_dicts = metadata[ 'tools' ] %><table class="grid"> + <tr> + <td><b>name</b></td> + <td><b>description</b></td> + <td><b>version</b></td> + <td><b>requirements</b></td> + </tr> %for tool_dict in tool_dicts: <tr><td><a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ] )}">${tool_dict[ 'name' ]}</a></td><td>${tool_dict[ 'description' ]}</td><td>version: ${tool_dict[ 'version' ]}</td> + <td> + <% + if 'requirements' in tool_dict: + requirements = tool_dict[ 'requirements' ] + else: + requirements = None + %> + %if requirements: + <% + requirements_str = '' + for requirement_dict in tool_dict[ 'requirements' ]: + requirements_str += '%s (%s), ' % ( requirement_dict[ 'name' ], requirement_dict[ 'type' ] ) + requirements_str = requirements_str.rstrip( ', ' ) + %> + ${requirements_str} + %else: + none + %endif + </td></tr> %endfor </table> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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