# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster greg@bx.psu.edu # Date 1279831412 14400 # Node ID cecc290755014c02aa21906d433a3d39f2d657d5 # Parent db1ae0bc8995cb30deef73ce9d14ef175c512f90 Galaxy Tool Shed enhancements 1. Rename Galaxy Community Space to Galaxy Tool Shed 2. Add the ability to upload an archive consisting of a suite of tools in addition to a single tool archive. 3. Miscellaneous code cleanup including elimination of all sniffer related code.
--- a/templates/webapps/community/tool/edit_tool.mako +++ b/templates/webapps/community/tool/edit_tool.mako @@ -93,7 +93,7 @@
%if can_edit: <form id="edit_tool" name="edit_tool" action="${h.url_for( controller='common', action='edit_tool' )}" method="post"> - %if tool.is_rejected(): + %if tool.is_rejected: <div class="toolForm"><div class="toolFormTitle">Reason for rejection</div><div class="toolFormBody"> @@ -169,7 +169,7 @@ </div></div><p/> - %if tool.is_new() or tool.is_rejected(): + %if tool.is_new or tool.is_rejected: <div class="toolForm"><div class="toolFormTitle">Get approval for publishing</div><div class="toolFormBody">
--- a/lib/galaxy/webapps/community/security/__init__.py +++ b/lib/galaxy/webapps/community/security/__init__.py @@ -1,5 +1,5 @@ """ -Galaxy Community Space Security +Galaxy Tool Shed Security """ import logging, socket, operator from datetime import datetime, timedelta @@ -167,14 +167,14 @@ class CommunityRBACAgent( RBACAgent ): def can_approve_or_reject( self, user, user_is_admin, cntrller, item ): # The current user can approve or reject the item if the user # is an admin, and the item's state is WAITING. - return user and user_is_admin and cntrller=='admin' and item.is_waiting() + return user and user_is_admin and cntrller=='admin' and item.is_waiting def can_delete( self, user, user_is_admin, cntrller, item ): # The current user can delete the item if they are an admin or if they uploaded the # item and in either case the item's state is not DELETED. if user and user_is_admin and cntrller == 'admin': - can_delete = not item.is_deleted() + can_delete = not item.is_deleted elif cntrller in [ 'tool' ]: - can_delete = user==item.user and not item.is_deleted() + can_delete = user==item.user and not item.is_deleted else: can_delete = False return can_delete @@ -184,7 +184,7 @@ class CommunityRBACAgent( RBACAgent ): if user and user_is_admin and cntrller == 'admin': return True elif cntrller in [ 'tool' ]: - can_download = not( item.is_new() or item.is_waiting() ) + can_download = not( item.is_new or item.is_waiting ) else: can_download = False return can_download @@ -194,7 +194,7 @@ class CommunityRBACAgent( RBACAgent ): if user and user_is_admin and cntrller == 'admin': return True if cntrller in [ 'tool' ]: - return user and user==item.user and ( item.is_new() or item.is_rejected() ) + return user and user==item.user and ( item.is_new or item.is_rejected ) return False def can_purge( self, user, user_is_admin, cntrller ): # The current user can purge the item if they are an admin. @@ -206,7 +206,7 @@ class CommunityRBACAgent( RBACAgent ): versions = get_versions( item ) state_ok = True for version in versions: - if version.is_new() or version.is_waiting(): + if version.is_new or version.is_waiting: state_ok = False break return state_ok @@ -215,7 +215,7 @@ class CommunityRBACAgent( RBACAgent ): # or if the item's state is APPROVED. if user and user_is_admin and cntrller == 'admin': return True - if cntrller in [ 'tool' ] and item.is_approved(): + if cntrller in [ 'tool' ] and item.is_approved: return True return user and user==item.user def get_all_action_permissions( self, user, user_is_admin, cntrller, item ): @@ -236,7 +236,7 @@ class CommunityRBACAgent( RBACAgent ): elif cntrller in [ 'tool' ]: visible_versions = [] for version in get_versions( item ): - if version.is_approved() or version.is_archived() or version.user == user: + if version.is_approved or version.is_archived or version.user == user: visible_versions.append( version ) else: visible_versions = []
--- a/templates/webapps/community/tool/view_tool.mako +++ b/templates/webapps/community/tool/view_tool.mako @@ -85,7 +85,7 @@ %endif
%if can_view: - %if tool.is_rejected(): + %if tool.is_rejected: <div class="toolForm"><div class="toolFormTitle">Reason for rejection</div><div class="toolFormBody"> @@ -168,7 +168,7 @@ <div class="toolFormBody"><div class="form-row"><ul class="toolFile"> - <li><a href="${h.url_for( controller='tool', action='download_tool', id=trans.app.security.encode_id( tool.id ) )}">${tool.download_file_name}</a></li> + <li><a href="${h.url_for( controller='common', action='download_tool', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">${tool.download_file_name}</a></li><ul class="fileBrowser"> %for name in tool_file_contents: <li><a href="${h.url_for( controller='tool', action='view_tool_file', id=trans.app.security.encode_id( tool.id ), file_name=quote_plus( name ) )}">${name}</a></li>
--- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -14,6 +14,11 @@ class ToolListGrid( grids.Grid ): class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): return tool.name + class TypeColumn( grids.GridColumn ): + def get_value( self, trans, grid, tool ): + if tool.is_suite: + return 'Suite' + return 'Tool' class VersionColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): return tool.version @@ -60,6 +65,10 @@ class ToolListGrid( grids.Grid ): model_class=model.Tool, attach_popup=False ), + TypeColumn( "Type", + key="suite", + model_class=model.Tool, + attach_popup=False ), VersionColumn( "Version", key="version", model_class=model.Tool, @@ -229,7 +238,7 @@ class CommonController( BaseController ) in_categories.append( ( category.id, category.name ) ) else: out_categories.append( ( category.id, category.name ) ) - if tool.is_rejected(): + if tool.is_rejected: # Include the comments regarding the reason for rejection reason_for_rejection = get_most_recent_event( tool ).comment else: @@ -283,7 +292,7 @@ class CommonController( BaseController ) visible_versions = trans.app.security_agent.get_visible_versions( trans.user, trans.user_is_admin(), cntrller, tool ) categories = [ tca.category for tca in tool.categories ] tool_file_contents = tarfile.open( tool.file_name, 'r' ).getnames() - if tool.is_rejected(): + if tool.is_rejected: # Include the comments regarding the reason for rejection reason_for_rejection = get_most_recent_event( tool ).comment else:
--- /dev/null +++ b/lib/galaxy/webapps/community/model/migrate/versions/0002_add_tool_suite_column.py @@ -0,0 +1,48 @@ +""" +Migration script to add the suite column to the tool table. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + +def upgrade(): + print __doc__ + metadata.reflect() + + # Create and initialize imported column in job table. + Tool_table = Table( "tool", metadata, autoload=True ) + c = Column( "suite", Boolean, default=False, index=True ) + try: + # Create + c.create( Tool_table ) + assert c is Tool_table.c.suite + + # Initialize. + if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': + default_false = "0" + elif migrate_engine.name == 'postgres': + default_false = "false" + db_session.execute( "UPDATE tool SET suite=%s" % default_false ) + + except Exception, e: + print "Adding suite column to the tool table failed: %s" % str( e ) + log.debug( "Adding suite column to the tool table failed: %s" % str( e ) ) + +def downgrade(): + metadata.reflect() + + # Drop imported column from job table. + Tool_table = Table( "tool", metadata, autoload=True ) + try: + Tool_table.c.suite.drop() + except Exception, e: + print "Dropping column suite from the tool table failed: %s" % str( e ) + log.debug( "Dropping column suite from the tool table failed: %s" % str( e ) )
--- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -2,6 +2,7 @@ import sys, os, shutil, logging, urllib2 from galaxy.web.base.controller import * from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.model.orm import * +from galaxy.web.form_builder import SelectField from galaxy.webapps.community import datatypes from common import get_categories, get_category, get_versions
@@ -25,12 +26,13 @@ class UploadController( BaseController ) replace_id = params.get( 'replace_id', None ) replace_version = None uploaded_file = None + upload_type = params.get( 'upload_type', 'tool' ) categories = get_categories( trans ) if not categories: return trans.response.send_redirect( web.url_for( controller='tool', action='browse_tools', cntrller='tool', - message='No categories have been configured in this instance of the Galaxy Community. An administrator needs to create some via the Administrator control panel before anything can be uploaded', + message='No categories have been configured in this instance of the Galaxy Tool Shed. An administrator needs to create some via the Administrator control panel before anything can be uploaded', status='error' ) ) if params.get( 'upload_button', False ): url_paste = params.get( 'url', '' ).strip() @@ -50,8 +52,6 @@ class UploadController( BaseController ) elif file_data not in ( '', None ): uploaded_file = file_data.file if uploaded_file: - # TODO: tool should no longer be the default when we upload histories and workflows - upload_type = params.get( 'upload_type', 'tool' ) datatype = trans.app.datatypes_registry.get_datatype_by_extension( upload_type ) if datatype is None: message = 'An unknown file type was selected. This should not be possible, please report the error.' @@ -62,6 +62,7 @@ class UploadController( BaseController ) meta = datatype.verify( uploaded_file ) meta.user = trans.user meta.guid = trans.app.security.get_new_guid() + meta.suite = upload_type == 'toolsuite' obj = datatype.create_model_object( meta ) trans.sa_session.add( obj ) if isinstance( obj, trans.app.model.Tool ): @@ -71,25 +72,32 @@ class UploadController( BaseController ) if replace_id: replace_version = trans.sa_session.query( trans.app.model.Tool ).get( trans.security.decode_id( replace_id ) ) if existing and not replace_id: - raise UploadError( 'A tool with the same ID already exists. If you are trying to update this tool to a new version, please use the upload form on the "Edit Tool" page. Otherwise, please choose a new ID.' ) + raise UploadError( 'A %s with the same Id already exists. If you are trying to update this %s to a new version, use the upload form on the "Edit Tool" page. Otherwise, change the Id in the %s config.' % \ + ( obj.label, obj.label, obj.label ) ) elif replace_id and not existing: - raise UploadError( 'Tool ids must match when uploading a new version of a tool. The new tool id does not match the old tool id (%s). Check the tool XML files.' % str( replace_version.tool_id ) ) + raise UploadError( 'The new %s id (%s) does not match the old %s id (%s). Check the %s config files.' % \ + ( obj.label, str( meta.id ), obj.label, str( replace_version.tool_id ), obj.label ) ) elif existing and replace_id: if replace_version.newer_version: # If the user has picked an old version, switch to the newest version replace_version = get_versions( replace_version )[0] if replace_version.tool_id != meta.id: - raise UploadError( 'Tool ids must match when uploading a new version of a tool. The new tool id (%s) does not match the old tool id (%s). Check the tool XML files.' % ( str( meta.id ), str( replace_version.tool_id ) ) ) + raise UploadError( 'The new %s id (%s) does not match the old %s id (%s). Check the %s config files.' % \ + ( obj.label, str( meta.id ), obj.label, str( replace_version.tool_id ), obj.label ) ) for old_version in get_versions( replace_version ): if old_version.version == meta.version: - raise UploadError( 'The new version (%s) matches an old version. Check your version in the tool XML file.' % str( meta.version ) ) - if old_version.is_new(): - raise UploadError( 'There is an existing version of this tool which has not yet been submitted for approval, so either <a href="%s">submit or delete it</a> before uploading a new version.' % url_for( controller='common', - action='view_tool', - cntrller='tool', - id=trans.security.encode_id( old_version.id ) ) ) - if old_version.is_waiting(): - raise UploadError( 'There is an existing version of this tool which is waiting for administrative approval, so contact an administrator for help.' ) + raise UploadError( 'The new version (%s) matches an old version. Check your version in the %s config file.' % \ + ( str( meta.version ), obj.label ) ) + if old_version.is_new: + raise UploadError( 'There is an existing version of this %s which has not yet been submitted for approval, so either <a href="%s">submit it or delete it</a> before uploading a new version.' % \ + ( obj.label, + url_for( controller='common', + action='view_tool', + cntrller='tool', + id=trans.security.encode_id( old_version.id ) ) ) ) + if old_version.is_waiting: + raise UploadError( 'There is an existing version of this %s which is waiting for administrative approval, so contact an administrator for help.' % \ + obj.label ) # Defer setting the id since the newer version id doesn't exist until the new Tool object is flushed if category_ids: for category_id in category_ids: @@ -128,10 +136,10 @@ class UploadController( BaseController ) replace_version = trans.sa_session.query( trans.app.model.Tool ).get( int( trans.app.security.decode_id( replace_id ) ) ) old_version = None for old_version in get_versions( replace_version ): - if old_version.is_new(): + if old_version.is_new: message = 'There is an existing version of this tool which has not been submitted for approval, so either submit or delete it before uploading a new version.' break - if old_version.is_waiting(): + if old_version.is_waiting: message = 'There is an existing version of this tool which is waiting for administrative approval, so contact an administrator for help.' break else: @@ -143,13 +151,23 @@ class UploadController( BaseController ) id=trans.app.security.encode_id( old_version.id ), message=message, status='error' ) ) - selected_upload_type = params.get( 'type', 'tool' ) selected_categories = [ trans.security.decode_id( id ) for id in category_ids ] + datatype_labels=trans.app.datatypes_registry.get_datatype_labels() + type_ids = [ tup[0] for tup in datatype_labels ] + upload_type_select_list = SelectField( 'upload_type', + refresh_on_change=True, + refresh_on_change_values=type_ids ) + for type_id, type_label in datatype_labels: + if type_id == upload_type: + upload_type_select_list.add_option( type_label, type_id, selected = True ) + else: + upload_type_select_list.add_option( type_label, type_id, selected = False ) return trans.fill_template( '/webapps/community/upload/upload.mako', message=message, status=status, - selected_upload_type=selected_upload_type, - upload_types=trans.app.datatypes_registry.get_datatypes_for_select_list(), + selected_upload_type=upload_type, + upload_type_select_list=upload_type_select_list, + datatype_labels=trans.app.datatypes_registry.get_datatype_labels(), replace_id=replace_id, selected_categories=selected_categories, categories=get_categories( trans ) )
--- a/community_datatypes_conf.xml.sample +++ b/community_datatypes_conf.xml.sample @@ -2,8 +2,6 @@ <datatypes><registration><datatype extension="tool" type="galaxy.webapps.community.datatypes:Tool" model="galaxy.webapps.community.model:Tool"/> + <datatype extension="toolsuite" type="galaxy.webapps.community.datatypes:ToolSuite" model="galaxy.webapps.community.model:Tool"/></registration> - <sniffers> - <sniffer type="galaxy.webapps.community.datatypes:Tool"/> - </sniffers></datatypes>
--- a/templates/webapps/community/upload/upload.mako +++ b/templates/webapps/community/upload/upload.mako @@ -9,16 +9,43 @@ %><%inherit file="${inherit(context)}"/>
-<%def name="title()">Upload</%def> +<%def name="javascripts()"> + ${parent.javascripts()} + <script type="text/javascript"> + $( function() { + $( "select[refresh_on_change='true']").change( function() { + $( "#upload_form" ).submit(); + }); + }); + </script> +</%def>
-<h2>Upload</h2> +<%def name="title()"> + %if selected_upload_type == 'tool': + Upload a tool archive + %elif selected_upload_type == 'toolsuite': + Upload a tool suite archive + %endif +</%def> + +<h2> + %if selected_upload_type == 'tool': + Upload a tool archive + %elif selected_upload_type == 'toolsuite': + Upload a tool suite archive + %endif +</h2>
%if message: ${render_msg( message, status )} %endif
<div class="toolForm"> - <div class="toolFormTitle">Upload</div> + %if selected_upload_type == 'tool': + <div class="toolFormTitle">Upload a single tool archive</div> + %else: + <div class="toolFormTitle">Upload a tool suite archive</div> + %endif <div class="toolFormBody"> ## TODO: nginx <form id="upload_form" name="upload_form" action="${h.url_for( controller='upload', action='upload' )}" enctype="multipart/form-data" method="post"> @@ -28,18 +55,14 @@ <div class="form-row"><label>Upload Type</label><div class="form-row-input"> - <select name="upload_type"> - %for type_id, type_name in upload_types: - %if type_id == selected_upload_type: - <option value="${type_id}" selected>${type_name}</option> - %else: - <option value="${type_id}">${type_name}</option> - %endif - %endfor - </select> + ${upload_type_select_list.get_html()} </div><div class="toolParamHelp" style="clear: both;"> - Need help creating a tool file? See the <a href="${h.url_for( controller='tool', action='help' )}">Tool Help</a> page. + %if selected_upload_type == 'tool': + Need help creating a single tool archive? See details below. + %elif selected_upload_type == 'toolsuite': + Need help creating a tool suite archive? See details below. + %endif </div><div style="clear: both"></div></div> @@ -77,3 +100,151 @@ </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>
--- a/templates/webapps/community/admin/index.mako +++ b/templates/webapps/community/admin/index.mako @@ -1,7 +1,7 @@ <%inherit file="/webapps/community/base_panels.mako"/>
## Default title -<%def name="title()">Galaxy Community Space Administration</%def> +<%def name="title()">Galaxy Tool Shed Administration</%def><%def name="stylesheets()"> ${parent.stylesheets()}
--- a/templates/webapps/community/tool/help.mako +++ b/templates/webapps/community/tool/help.mako @@ -17,35 +17,87 @@ ${render_msg( message, status )} %endif
-<h3>Uploading Tools</h3> - -<p><strong>Tool File Format</strong></p> +<p/> +<div class="toolFormTitle">Creating an archive containing a tool or a suite of tools</div><p> - - A tool file is a tar-format (bzipped or gzipped tar are valid) archive - containing all the files necessary to load the tool in Galaxy. At the very - least, it must contain a - <a href="http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax" target="_blank">Tool XML File</a>, - and will probably also include a tool script. If any steps are necessary - to install your tool beyond the basic instructions below, please include a - README file which details these steps. 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). Please do not include precompiled 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, - please be sure the license allows for redistribution before including any - part of that tool in the tar archive! + 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> +<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> - There are no requirements about the directory structure inside the tar - archive, but for ease of use, it's generally a good idea to put everything - inside of a subdirectory, instead of directly at the top level. +<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><strong>Tool File Example</strong></p> +</p><p> - To package up the LASTZ tool's config file, Galaxy wrapper, and the C source: - <pre> + 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> +<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 @@ -58,68 +110,57 @@ lastz/lastz-distrib-1.02.00/src/lastz.c lastz/lastz-distrib-1.02.00/src/lastz.h ... - </pre> - <code>~/Desktop/galaxy_lastz_tool.tar.bz2</code> is now ready to be uploaded. +</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>
-<p><strong>Editing Information, Categories, and Submitting For Approval</strong></p> - -<p> - Simply uploading a tool to the Community 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 the tool has successfully uploaded, you will be redirected to the - Edit Tool page. Please 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 easily findable by users looking to - solve specific problems. Please 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. Once approved, it will be visible to - everyone. At that point, the description and associated categories can - only be changed by an administrator. -</p> -<p> - Once the tool has been approved or rejected, you may upload a new version - by browsing to the tool's "View Tool" page, clicking the context menu to - the right of the tool's name, and selecting "Upload a new version." -</p> - -<hr/> - -<h3>Downloading and Installing Tools</h3> - -<p> - A tool's download link will send you the tool tar archive. Once - downloaded, unpack the tool on your local Galaxy instance's server: - <pre> - user@host:~% tar xvf galaxy_tool.tar - ... - user@host:~% tar zxvf galaxy_tool.tar.gz - ... - user@host:~% tar jxvf galaxy_tool.tar.bz2 - ... - </pre> - If the tar 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 tar 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 the Galaxy server process.</li> - </ol> -</p> - -<p> - 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 - managing the <code>tool_conf.xml</code> file by hand. In the meantime, - this is the process. -</p>
--- a/lib/galaxy/webapps/community/model/__init__.py +++ b/lib/galaxy/webapps/community/model/__init__.py @@ -1,5 +1,5 @@ """ -Galaxy Community Space data model classes +Galaxy Tool Shed data model classes
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) @@ -95,7 +95,7 @@ class Tool( object ): REJECTED = 'rejected', ARCHIVED = 'archived' ) def __init__( self, guid=None, tool_id=None, name=None, description=None, user_description=None, - category=None, version=None, user_id=None, external_filename=None ): + category=None, version=None, user_id=None, external_filename=None, suite=False ): self.guid = guid self.tool_id = tool_id self.name = name or "Unnamed tool" @@ -106,6 +106,7 @@ class Tool( object ): self.external_filename = external_filename self.deleted = False self.__extension = None + self.suite = suite def get_file_name( self ): if not self.external_filename: assert self.id is not None, "ID must be set before filename used (commit the object)" @@ -133,6 +134,8 @@ class Tool( object ): self.description = datatype_bunch.description self.version = datatype_bunch.version self.user_id = datatype_bunch.user.id + self.suite = datatype_bunch.suite + @property def state( self ): if self.events: # Sort the events in ascending order by update_time @@ -150,35 +153,47 @@ class Tool( object ): else: return '' return 'No comment' + # Tool states + @property def is_new( self ): - return self.state() == self.states.NEW + return self.state == self.states.NEW + @property def is_error( self ): - return self.state() == self.states.ERROR + return self.state == self.states.ERROR + @property def is_deleted( self ): - return self.state() == self.states.DELETED + return self.state == self.states.DELETED + @property def is_waiting( self ): - return self.state() == self.states.WAITING + return self.state == self.states.WAITING + @property def is_approved( self ): - return self.state() == self.states.APPROVED + return self.state == self.states.APPROVED + @property def is_rejected( self ): - return self.state() == self.states.REJECTED + return self.state == self.states.REJECTED + @property def is_archived( self ): - return self.state() == self.states.ARCHIVED + return self.state == self.states.ARCHIVED def get_state_message( self ): - if self.is_new(): - return '<font color="red"><b><i>This is an unsubmitted version of this tool</i></b></font>' - if self.is_error(): - return '<font color="red"><b><i>This tool is in an error state</i></b></font>' - if self.is_deleted(): - return '<font color="red"><b><i>This is a deleted version of this tool</i></b></font>' - if self.is_waiting(): - return '<font color="red"><b><i>This version of this tool is awaiting administrative approval</i></b></font>' - if self.is_approved(): - return '<b><i>This is the latest approved version of this tool</i></b>' - if self.is_rejected(): - return '<font color="red"><b><i>This version of this tool has been rejected by an administrator</i></b></font>' - if self.is_archived(): - return '<font color="red"><b><i>This is an archived version of this tool</i></b></font>' + if self.is_suite: + label = 'tool suite' + else: + label = 'tool' + if self.is_new: + return '<font color="red"><b><i>This is an unsubmitted version of this %s</i></b></font>' % label + if self.is_error: + return '<font color="red"><b><i>This %s is in an error state</i></b></font>' % label + if self.is_deleted: + return '<font color="red"><b><i>This is a deleted version of this %s</i></b></font>' % label + if self.is_waiting: + return '<font color="red"><b><i>This version of this %s is awaiting administrative approval</i></b></font>' % label + if self.is_approved: + return '<b><i>This is the latest approved version of this %s</i></b>' % label + if self.is_rejected: + return '<font color="red"><b><i>This version of this %s has been rejected by an administrator</i></b></font>' % label + if self.is_archived: + return '<font color="red"><b><i>This is an archived version of this %s</i></b></font>' % label @property def extension( self ): # if instantiated via a query, this unmapped property won't exist @@ -202,6 +217,15 @@ class Tool( object ): self.__extension = 'tar' return self.__extension @property + def is_suite( self ): + return self.suite + @property + def label( self ): + if self.is_suite: + return 'tool suite' + else: + return 'tool' + @property def download_file_name( self ): return '%s_%s.%s' % ( self.tool_id, self.version, self.extension ) @property
--- a/templates/webapps/community/base_panels.mako +++ b/templates/webapps/community/base_panels.mako @@ -1,7 +1,7 @@ <%inherit file="/base_panels.mako"/>
## Default title -<%def name="title()">Galaxy Community Space</%def> +<%def name="title()">Galaxy Tool Shed</%def>
## Masthead <%def name="masthead()"> @@ -94,7 +94,7 @@ <div class="title" style="position: absolute; top: 0; left: 0;"><a href="${app.config.get( 'logo_url', '/' )}"><img border="0" src="${h.url_for('/static/images/galaxyIcon_noText.png')}" style="width: 26px; vertical-align: top;"> - Galaxy Community + Galaxy Tool Shed %if app.config.brand: <span class='brand'>/ ${app.config.brand}</span> %endif
--- a/lib/galaxy/webapps/community/model/mapping.py +++ b/lib/galaxy/webapps/community/model/mapping.py @@ -113,7 +113,8 @@ Tool.table = Table( "tool", metadata, Column( "version", TrimmedString( 255 ) ), Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), Column( "external_filename" , TEXT ), - Column( "deleted", Boolean, index=True, default=False ) ) + Column( "deleted", Boolean, index=True, default=False ), + Column( "suite", Boolean, default=False, index=True ) )
Category.table = Table( "category", metadata, Column( "id", Integer, primary_key=True ),
--- a/lib/galaxy/webapps/community/controllers/tool.py +++ b/lib/galaxy/webapps/community/controllers/tool.py @@ -15,7 +15,7 @@ class ApprovedToolListGrid( ToolListGrid class MyToolsListGrid( ToolListGrid ): class StateColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): - state = tool.state() + state = tool.state if state == 'approved': state_color = 'ok' elif state == 'rejected': @@ -64,7 +64,7 @@ class ToolCategoryListGrid( CategoryList viewable_tools = 0 for tca in category.tools: tool = tca.tool - if tool.is_approved(): + if tool.is_approved: viewable_tools += 1 return viewable_tools return 0
--- a/lib/galaxy/webapps/community/datatypes/__init__.py +++ b/lib/galaxy/webapps/community/datatypes/__init__.py @@ -17,7 +17,6 @@ class DatatypeVerificationError( Excepti class Registry( object ): def __init__( self, root_dir=None, config=None ): self.datatypes_by_extension = {} - self.sniff_order = [] if root_dir and config: # Parse datatypes_conf.xml tree = galaxy.util.parse_xml( config ) @@ -50,98 +49,143 @@ class Registry( object ): log.debug( 'Added model class: %s to datatype: %s' % ( model_class, dtype ) ) except Exception, e: log.warning( 'Error loading datatype "%s", problem: %s' % ( extension, str( e ) ) ) - # Load datatype sniffers from the config - sniff_order = [] - sniffers = root.find( 'sniffers' ) - for elem in sniffers.findall( 'sniffer' ): - dtype = elem.get( 'type', None ) - if dtype: - sniff_order.append( dtype ) - for dtype in sniff_order: - try: - fields = dtype.split( ":" ) - datatype_module = fields[0] - datatype_class = fields[1] - fields = datatype_module.split( "." ) - module = __import__( fields.pop(0) ) - for mod in fields: - module = getattr( module, mod ) - aclass = getattr( module, datatype_class )() - included = False - for atype in self.sniff_order: - if not issubclass( atype.__class__, aclass.__class__ ) and isinstance( atype, aclass.__class__ ): - included = True - break - if not included: - self.sniff_order.append( aclass ) - log.debug( 'Loaded sniffer for datatype: %s' % dtype ) - except Exception, exc: - log.warning( 'Error appending datatype %s to sniff_order, problem: %s' % ( dtype, str( exc ) ) ) def get_datatype_by_extension( self, ext ): return self.datatypes_by_extension.get( ext, None ) - def get_datatypes_for_select_list( self ): + def get_datatype_labels( self ): rval = [] for ext, datatype in self.datatypes_by_extension.items(): - rval.append( ( ext, datatype.select_name ) ) + rval.append( ( ext, datatype.label ) ) return rval - def sniff( self, fname ): - for datatype in sniff_order: - try: - datatype.sniff( fname ) - return datatype.file_ext - except: - pass
class Tool( object ): - select_name = 'Tool' def __init__( self, model_object=None ): self.model_object = model_object - def verify( self, file ): - msg = '' + self.label = 'Tool' + def verify( self, f, xml_files=[], tool_tags={} ): + # xml_files and tool_tags will only be received if we're called from the ToolSuite.verify() method. try: - tar = tarfile.open( file.name ) + tar = tarfile.open( f.name ) except tarfile.ReadError: - raise DatatypeVerificationError( 'The tool file is not a readable tar file' ) - xml_names = filter( lambda x: x.lower().endswith( '.xml' ), tar.getnames() ) - if not xml_names: - raise DatatypeVerificationError( 'The tool file does not contain an XML file' ) - for xml_name in xml_names: + raise DatatypeVerificationError( 'The archive is not a readable tar file.' ) + if not xml_files: + # Make sure we're not uploading a tool suite + if filter( lambda x: x.lower() == 'tool_suite.xml', tar.getnames() ): + raise DatatypeVerificationError( 'The archive includes a tool_suite.xml file, so set the upload type to "Tool Suite".' ) + xml_files = filter( lambda x: x.lower().endswith( '.xml' ), tar.getnames() ) + if not xml_files: + raise DatatypeVerificationError( 'The archive does not contain any xml config files.' ) + for xml_file in xml_files: try: - tree = ElementTree.parse( tar.extractfile( xml_name ) ) + tree = ElementTree.parse( tar.extractfile( xml_file ) ) root = tree.getroot() except: log.exception( 'fail:' ) continue if root.tag == 'tool': - rval = Bunch() - try: - rval.id = root.attrib['id'] - rval.name = root.attrib['name'] - rval.version = root.attrib['version'] - except KeyError, e: - raise DatatypeVerificationError( 'Tool XML file does not conform to the specification. Missing required <tool> tag attribute: %s' % e ) - rval.description = '' - desc_tag = root.find( 'description' ) - if desc_tag is not None: - description = desc_tag.text - if description: - rval.description = description.strip() - rval.message = 'Tool: %s %s, Version: %s, ID: %s' % ( str( rval.name ), str( rval.description ), str( rval.version ), str( rval.id ) ) - return rval - else: - raise DatatypeVerificationError( 'Unable to find a properly formatted tool XML file' ) + if tool_tags: + # We are verifying the tools inside a tool suite, so the current tag should have been found in the suite_config.xml + # file parsed in the ToolSuite verify() method. The tool_tags dictionary should include a key matching the current + # tool Id, and a tuple value matching the tool name and version. + if root.attrib[ 'id' ] not in tool_tags: + raise DatatypeVerificationError( 'Tool Id (%s) is not included in the suite_config.xml file.' % \ + ( str( root.attrib[ 'id' ] ) ) ) + tup = tool_tags[ root.attrib[ 'id' ] ] + if root.attrib[ 'name' ] != tup[ 0 ]: + raise DatatypeVerificationError( 'Tool name (%s) differs between suite_config.xml and the tool config file for tool Id (%s).' % \ + ( str( root.attrib[ 'name' ] ), str( root.attrib[ 'id' ] ) ) ) + if root.attrib[ 'version' ] != tup[ 1 ]: + raise DatatypeVerificationError( 'Tool version (%s) differs between suite_config.xml and the tool config file for tool Id (%s).' % \ + ( str( root.attrib[ 'version' ] ), str( root.attrib[ 'id' ] ) ) ) + else: + # We are not verifying a tool suite, so we'll create a bunch for returning to the caller. + tool_bunch = Bunch() + try: + tool_bunch.id = root.attrib['id'] + tool_bunch.name = root.attrib['name'] + tool_bunch.version = root.attrib['version'] + except KeyError, e: + raise DatatypeVerificationError( 'Tool XML file does not conform to the specification. Missing required <tool> tag attribute: %s' % str( e ) ) + tool_bunch.description = '' + desc_tag = root.find( 'description' ) + if desc_tag is not None: + description = desc_tag.text + if description: + tool_bunch.description = description.strip() + tool_bunch.message = 'Tool: %s %s, Version: %s, Id: %s' % \ + ( str( tool_bunch.name ), str( tool_bunch.description ), str( tool_bunch.version ), str( tool_bunch.id ) ) + return tool_bunch + else: + # TODO: should we verify files that are not tool configs? + log.debug( "The file named (%s) is not a tool config, so skipping verification." % str( xml_file ) ) def create_model_object( self, datatype_bunch ): if self.model_object is None: - raise Exception( 'No model object configured for %s, please check the datatype configuration file' % self.__class__.__name__ ) + raise Exception( 'No model object configured for %s, check the datatype configuration file' % self.__class__.__name__ ) if datatype_bunch is None: # TODO: do it automatically raise Exception( 'Unable to create %s model object without passing in data' % self.__class__.__name__ ) o = self.model_object() o.create_from_datatype( datatype_bunch ) return o - def sniff( self, fname ): + +class ToolSuite( Tool ): + def __init__( self, model_object=None ): + self.model_object = model_object + self.label = 'Tool Suite' + def verify( self, f ): + """ + A sample tool suite config: + <suite id="onto_toolkit" name="ONTO Toolkit" version="1.0"> + <description>ONTO-Toolkit is a collection of Galaxy tools which support the manipulation of bio-ontologies.</description> + <tool id="get_ancestor_terms" name="Get the ancestor terms of a given OBO term" version="1.0.0"> + <description>Collects the ancestor terms from a given term in the given OBO ontology</description> + </tool> + <tool id="get_child_terms" name="Get the child terms of a given OBO term" version="1.0.0"> + <description>Collects the child terms from a given term in the given OBO ontology</description> + </tool> + </suite> + """ try: - self.verify( open( fname, 'r' ) ) - return True + tar = tarfile.open( f.name ) + except tarfile.ReadError: + raise DatatypeVerificationError( 'The archive is not a readable tar file.' ) + suite_config = filter( lambda x: x.lower() == 'tool_suite.xml', tar.getnames() ) + if not suite_config: + raise DatatypeVerificationError( 'The archive does not contain the required tool_suite.xml config file. If you are uploading a single tool archive, set the upload type to "Tool".' ) + suite_config = suite_config[ 0 ] + # Parse and verify suite_config + archive_ok = False + try: + tree = ElementTree.parse( tar.extractfile( suite_config ) ) + root = tree.getroot() + archive_ok = True except: - return False + log.exception( 'fail:' ) + if archive_ok and root.tag == 'suite': + suite_bunch = Bunch() + try: + suite_bunch.id = root.attrib['id'] + suite_bunch.name = root.attrib['name'] + suite_bunch.version = root.attrib['version'] + except KeyError, e: + raise DatatypeVerificationError( 'The file named tool-suite.xml does not conform to the specification. Missing required <suite> tag attribute: %s' % str( e ) ) + suite_bunch.description = '' + desc_tag = root.find( 'description' ) + if desc_tag is not None: + description = desc_tag.text + if description: + suite_bunch.description = description.strip() + suite_bunch.message = 'Tool suite: %s %s, Version: %s, Id: %s' % \ + ( str( suite_bunch.name ), str( suite_bunch.description ), str( suite_bunch.version ), str( suite_bunch.id ) ) + # Create a dictionary of the tools in the suite where the keys are tool_ids and the + # values are tuples of tool name and version + tool_tags = {} + for elem in root.findall( 'tool' ): + tool_tags[ elem.attrib['id'] ] = ( elem.attrib['name'], elem.attrib['version'] ) + else: + raise DatatypeVerificationError( "The file named %s is not a valid tool suite config." % str( suite_config ) ) + # Verify all included tool config files + xml_files = filter( lambda x: x.lower().endswith( '.xml' ) and x.lower() != 'tool_suite.xml', tar.getnames() ) + if not xml_files: + raise DatatypeVerificationError( 'The archive does not contain any tool config (xml) files.' ) + Tool.verify( self, f, xml_files=xml_files, tool_tags=tool_tags ) + return suite_bunch
--- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -299,7 +299,7 @@ class GroupListGrid( grids.Grid ): class AdminToolListGrid( ToolListGrid ): class StateColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): - state = tool.state() + state = tool.state if state == 'approved': state_color = 'ok' elif state == 'rejected': @@ -441,7 +441,7 @@ class AdminController( BaseController, A # Called from the ToolStateColumn link tool_id = kwd.get( 'id', None ) tool = get_tool( trans, tool_id ) - kwd[ 'f-state' ] = tool.state() + kwd[ 'f-state' ] = tool.state elif operation == "tools_by_category": # Eliminate the current filters if any exist. for k, v in kwd.items(): @@ -547,7 +547,7 @@ class AdminController( BaseController, A # If we're approving a tool, all previously approved versions must be set to archived for version in get_versions( tool ): # TODO: get latest approved version instead of all versions - if version != tool and version.is_approved(): + if version != tool and version.is_approved: # Create an event with state ARCHIVED for the previously approved version of this tool self.__create_tool_event( trans, version, @@ -799,30 +799,30 @@ def get_tools_by_state( trans, state ): ids = [] if state == trans.model.Tool.states.NEW: for tool in get_tools( trans ): - if tool.is_new(): + if tool.is_new: ids.append( tool.id ) elif state == trans.model.Tool.states.ERROR: for tool in get_tools( trans ): - if tool.is_error(): + if tool.is_error: ids.append( tool.id ) elif state == trans.model.Tool.states.DELETED: for tool in get_tools( trans ): - if tool.is_deleted(): + if tool.is_deleted: ids.append( tool.id ) elif state == trans.model.Tool.states.WAITING: for tool in get_tools( trans ): - if tool.is_waiting(): + if tool.is_waiting: ids.append( tool.id ) elif state == trans.model.Tool.states.APPROVED: for tool in get_tools( trans ): - if tool.is_approved(): + if tool.is_approved: ids.append( tool.id ) elif state == trans.model.Tool.states.REJECTED: for tool in get_tools( trans ): - if tool.is_rejected(): + if tool.is_rejected: ids.append( tool.id ) elif state == trans.model.Tool.states.ARCHIVED: for tool in get_tools( trans ): - if tool.is_archived(): + if tool.is_archived: ids.append( tool.id ) return ids