[galaxy-commits] commit/galaxy-central: greg: Add the ability to browse the installation directory of tool dependencies for installed tool shed repositories.

14 Jun 2012

1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/bef69fd3fcc1/
changeset:   bef69fd3fcc1
user:        greg
date:        2012-06-14 16:00:51
summary:     Add the ability to browse the installation directory of tool dependencies for installed tool shed repositories.
affected #:  10 files
diff -r b1f35669f93c4163cf803d64beb37a1cb0d5381c -r bef69fd3fcc191b9a9a4d140876a6ee932e9fc3e lib/galaxy/model/__init__.py

--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -2740,7 +2740,13 @@
         self.version = version
         self.type = type
         self.uninstalled = uninstalled
-
+    def installation_directory( self, app ):
+        return os.path.join( app.config.tool_dependency_dir,
+                             self.name,
+                             self.version,
+                             self.tool_shed_repository.owner,
+                             self.tool_shed_repository.name,
+                             self.installed_changeset_revision )
 class ToolVersion( object ):
     def __init__( self, id=None, create_time=None, tool_id=None, tool_shed_repository=None ):
         self.id = id
diff -r b1f35669f93c4163cf803d64beb37a1cb0d5381c -r bef69fd3fcc191b9a9a4d140876a6ee932e9fc3e lib/galaxy/tool_shed/tool_dependencies/install_util.py
--- a/lib/galaxy/tool_shed/tool_dependencies/install_util.py
+++ b/lib/galaxy/tool_shed/tool_dependencies/install_util.py
@@ -41,7 +41,7 @@
     sa_session.add( tool_dependency )
     sa_session.flush()
     return tool_dependency
-def get_install_dir( app, repository, installed_changeset_revision, package_name, package_version ):
+def get_tool_dependency_install_dir( app, repository, installed_changeset_revision, package_name, package_version ):
     return os.path.abspath( os.path.join( app.config.tool_dependency_dir,
                                           package_name,
                                           package_version,
diff -r b1f35669f93c4163cf803d64beb37a1cb0d5381c -r bef69fd3fcc191b9a9a4d140876a6ee932e9fc3e lib/galaxy/tools/deps/__init__.py
--- a/lib/galaxy/tools/deps/__init__.py
+++ b/lib/galaxy/tools/deps/__init__.py
@@ -46,7 +46,7 @@
         if installed_tool_dependencies:
             for installed_dependency in installed_tool_dependencies:
                 if not installed_dependency.uninstalled:
-                    if installed_dependency.name == name and installed_dependency.version == version and installed_dependency.type == type:
+                    if installed_dependency.name==name and installed_dependency.version==version and installed_dependency.type==type:
                         break
         for base_path in self.base_paths:
             if installed_dependency:
diff -r b1f35669f93c4163cf803d64beb37a1cb0d5381c -r bef69fd3fcc191b9a9a4d140876a6ee932e9fc3e lib/galaxy/util/shed_util.py
--- a/lib/galaxy/util/shed_util.py
+++ b/lib/galaxy/util/shed_util.py
@@ -956,6 +956,9 @@
             file_name = strip_path( shed_tool_conf_dict[ 'config_filename' ] )
             if shed_tool_conf == file_name:
                 return index, shed_tool_conf_dict
+def get_tool_dependency( trans, id ):
+    """Get a tool_dependency from the database via id"""
+    return trans.sa_session.query( trans.model.ToolDependency ).get( trans.security.decode_id( id ) )
 def get_tool_panel_config_tool_path_install_dir( app, repository ):
     # Return shed-related tool panel config, the tool_path configured in it, and the relative path to the directory where the
     # repository is installed.  This method assumes all repository tools are defined in a single shed-related tool panel config.
diff -r b1f35669f93c4163cf803d64beb37a1cb0d5381c -r bef69fd3fcc191b9a9a4d140876a6ee932e9fc3e lib/galaxy/web/controllers/admin_toolshed.py
--- a/lib/galaxy/web/controllers/admin_toolshed.py
+++ b/lib/galaxy/web/controllers/admin_toolshed.py
@@ -2,7 +2,7 @@
 from galaxy.web.controllers.admin import *
 from galaxy.util.json import from_json_string, to_json_string
 from galaxy.util.shed_util import *
-from galaxy.tool_shed.tool_dependencies.install_util import get_install_dir, not_installed
+from galaxy.tool_shed.tool_dependencies.install_util import get_tool_dependency_install_dir, not_installed
 from galaxy.tool_shed.encoding_util import *
 from galaxy import eggs, tools
@@ -148,6 +148,19 @@
         return self.repository_list_grid( trans, **kwd )
     @web.expose
     @web.require_admin
+    def browse_tool_dependency( self, trans, **kwd ):
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
+        tool_dependency = get_tool_dependency( trans, kwd[ 'id' ] )
+        repository = get_repository( trans, kwd[ 'repository_id' ] )
+        return trans.fill_template( '/admin/tool_shed_repository/browse_tool_dependency.mako',
+                                    repository=repository,
+                                    tool_dependency=tool_dependency,
+                                    message=message,
+                                    status=status )
+    @web.expose
+    @web.require_admin
     def browse_tool_shed( self, trans, **kwd ):
         tool_shed_url = kwd[ 'tool_shed_url' ]
         galaxy_url = url_for( '/', qualified=True )
@@ -256,6 +269,7 @@
         url = '%srepository/find_workflows?galaxy_url=%s&webapp=galaxy&no_reset=true' % ( tool_shed_url, galaxy_url )
         return trans.response.send_redirect( url )
     @web.json
+    @web.require_admin
     def get_file_contents( self, trans, file_path ):
         # Avoid caching
         trans.response.headers['Pragma'] = 'no-cache'
@@ -341,7 +355,7 @@
             for dependency_key, requirements_dict in tool_dependencies.items():
                 name = requirements_dict[ 'name' ]
                 version = requirements_dict[ 'version' ]
-                install_dir = get_install_dir( trans.app, repository, repository.changeset_revision, name, version )
+                install_dir = get_tool_dependency_install_dir( trans.app, repository, repository.changeset_revision, name, version )
                 if not_installed( install_dir ):
                     filtered_tool_dependencies[ dependency_key ] = requirements_dict
             tool_dependencies = filtered_tool_dependencies
@@ -585,6 +599,7 @@
                                     message=message,
                                     status=status )
     @web.json
+    @web.require_admin
     def open_folder( self, trans, folder_path ):
         # Avoid caching
         trans.response.headers['Pragma'] = 'no-cache'
diff -r b1f35669f93c4163cf803d64beb37a1cb0d5381c -r bef69fd3fcc191b9a9a4d140876a6ee932e9fc3e templates/admin/tool_shed_repository/browse_repository.mako
--- a/templates/admin/tool_shed_repository/browse_repository.mako
+++ b/templates/admin/tool_shed_repository/browse_repository.mako
@@ -10,7 +10,7 @@
 <%def name="javascripts()">
     ${parent.javascripts()}
     ${h.js( "ui.core", "jquery.dynatree" )}
-    ${common_javascripts(repository)}
+    ${common_javascripts(repository.name, repository.repo_files_directory(trans.app))}
 </%def><br/><br/>
diff -r b1f35669f93c4163cf803d64beb37a1cb0d5381c -r bef69fd3fcc191b9a9a4d140876a6ee932e9fc3e templates/admin/tool_shed_repository/browse_tool_dependency.mako
--- /dev/null
+++ b/templates/admin/tool_shed_repository/browse_tool_dependency.mako
@@ -0,0 +1,62 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+<%namespace file="/admin/tool_shed_repository/common.mako" import="*" />
+
+<%def name="stylesheets()">
+    ${parent.stylesheets()}
+    ${h.css( "dynatree_skin/ui.dynatree" )}
+</%def>
+
+<%def name="javascripts()">
+    ${parent.javascripts()}
+    ${h.js( "ui.core", "jquery.dynatree" )}
+    ${common_javascripts(tool_dependency.name, tool_dependency.installation_directory( trans.app ))}
+</%def>
+
+<br/><br/>
+<ul class="manage-table-actions">
+    <li><a class="action-button" id="tool_dependency-${tool_dependency.id}-popup" class="menubutton">Repository Actions</a></li>
+    <div popupmenu="tool_dependency-${tool_dependency.id}-popup">
+        <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ) )}">Manage repository</a>
+        <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get updates</a>
+        <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) )}">Deactivate or Uninstall</a>
+        %if repository.tool_dependencies:
+            <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', id=trans.security.encode_id( repository.id ) )}">Manage tool dependencies</a>
+        %endif
+    </div>
+</ul>
+
+%if message:
+    ${render_msg( message, status )}
+%endif
+
+<div class="toolForm">
+    <div class="toolFormTitle">Browse tool dependency ${tool_dependency.name} installation directory</div>
+    <div class="toolFormBody">
+        <div class="form-row" >
+            <label>Tool shed repository:</label>
+            ${repository.name}
+            <div style="clear: both"></div>
+        </div>
+        <div class="form-row" >
+            <label>Tool shed repository changeset revision:</label>
+            ${repository.changeset_revision}
+            <div style="clear: both"></div>
+        </div>
+        <div class="form-row" >
+            <label>Tool dependency installation directory:</label>
+            ${tool_dependency.installation_directory( trans.app )}
+            <div style="clear: both"></div>
+        </div>
+        <div class="form-row" >
+            <label>Contents:</label>
+            <div id="tree" >
+                Loading...
+            </div>
+            <div style="clear: both"></div>
+        </div>
+        <div class="form-row">
+            <div id="file_contents" class="toolParamHelp" style="clear: both;background-color:#FAFAFA;"></div>
+        </div>
+    </div>
+</div>
diff -r b1f35669f93c4163cf803d64beb37a1cb0d5381c -r bef69fd3fcc191b9a9a4d140876a6ee932e9fc3e templates/admin/tool_shed_repository/common.mako
--- a/templates/admin/tool_shed_repository/common.mako
+++ b/templates/admin/tool_shed_repository/common.mako
@@ -1,4 +1,4 @@
-<%def name="common_javascripts(repository)">
+<%def name="common_javascripts(title_text, directory_path)"><script type="text/javascript">
         $(function(){
             $("#tree").ajaxComplete(function(event, XMLHttpRequest, ajaxOptions) {
@@ -6,7 +6,7 @@
             });
             // --- Initialize sample trees
             $("#tree").dynatree({
-                title: "${repository.name}",
+                title: "${title_text}",
                 rootVisible: true,
                 minExpandLevel: 0, // 1: root node is not collapsible
                 persist: false,
@@ -22,7 +22,7 @@
                 // initAjax is hard to fake, so we pass the children as object array:
                 initAjax: {url: "${h.url_for( controller='admin_toolshed', action='open_folder' )}",
                            dataType: "json", 
-                           data: { folder_path: "${repository.repo_files_directory(trans.app)}" },
+                           data: { folder_path: "${directory_path}" },
                 },
                 onLazyRead: function(dtnode){
                     dtnode.appendAjax({
@@ -43,7 +43,7 @@
                     var cell = $("#file_contents");
                     var selected_value;
                      if (dtnode.data.key == 'root') {
-                        selected_value = "${repository.repo_files_directory(trans.app)}/";
+                        selected_value = "${directory_path}/";
                     } else {
                         selected_value = dtnode.data.key;
                     };
@@ -66,221 +66,3 @@
         });
     </script></%def>
-
-<%def name="render_repository_contents( repository, can_reset_metadata=False )">
-    <div class="toolForm">
-        <div class="toolFormTitle">${repository.name}</div>
-        <div class="toolFormBody">
-            <%
-                metadata = repository.metadata
-                missing_tool_dependencies = repository.missing_tool_dependencies
-                installed_tool_dependencies = repository.installed_tool_dependencies
-            %>
-            %if missing_tool_dependencies:
-                <div class="form-row">
-                    <table width="100%">
-                        <tr bgcolor="#D8D8D8" width="100%">
-                            <td><b>Missing tool dependencies</i></td>
-                        </tr>
-                    </table>
-                </div>
-                <div style="clear: both"></div>
-                <div class="form-row">
-                    <table class="grid">
-                        <tr>
-                            <td><b>name</b></td>
-                            <td><b>type</b></td>
-                            <td><b>version</b></td>
-                        </tr>
-                        %for name, requirements_dict in missing_tool_dependencies.items():
-                            <tr>
-                                <td>${requirements_dict[ 'name' ]}</td>
-                                <td>${requirements_dict[ 'type' ]}</td>
-                                <td>${requirements_dict[ 'version' ]}</td>
-                            </tr>
-                        %endfor
-                    </table>
-                </div>
-                <div style="clear: both"></div>
-            %endif
-            %if installed_tool_dependencies:
-                <div class="form-row">
-                    <table width="100%">
-                        <tr bgcolor="#D8D8D8" width="100%">
-                            <td><b>Installed tool dependencies</i></td>
-                        </tr>
-                    </table>
-                </div>
-                <div style="clear: both"></div>
-                <div class="form-row">
-                    <table class="grid">
-                        <tr>
-                            <td><b>name</b></td>
-                            <td><b>type</b></td>
-                            <td><b>version</b></td>
-                        </tr>
-                        %for installed_tool_dependency in installed_tool_dependencies:
-                            <tr>
-                                <td>${installed_tool_dependency.name}</td>
-                                <td>${installed_tool_dependency.type}</td>
-                                <td>${installed_tool_dependency.version}</td>
-                            </tr>
-                        %endfor
-                    </table>
-                </div>
-                <div style="clear: both"></div>
-            %endif
-            %if 'tools' in metadata:
-                <div class="form-row">
-                    <table width="100%">
-                        <tr bgcolor="#D8D8D8" width="100%">
-                            <td><b>Tools</b><i> - click the name to view information about the tool</i></td>
-                        </tr>
-                    </table>
-                </div>
-                <div class="form-row">
-                    <% 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 class="view-info" href="${h.url_for( controller='admin_toolshed', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), tool_id=tool_dict[ 'id' ] )}">
-                                        ${tool_dict[ 'name' ]}
-                                    </a>
-                                </td>
-                                <td>${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
-            %if 'workflows' in metadata:
-                ## metadata[ 'workflows' ] is a list of tuples where each contained tuple is
-                ## [ <relative path to the .ga file in the repository>, <exported workflow dict> ]
-                <div class="form-row">
-                    <table width="100%">
-                        <tr bgcolor="#D8D8D8" width="100%">
-                            <td><b>Workflows</b><i> - click the name to import</i></td>
-                        </tr>
-                    </table>
-                </div>
-                <div style="clear: both"></div>
-                <div class="form-row">
-                    <% workflow_tups = metadata[ 'workflows' ] %>
-                    <table class="grid">
-                        <tr>
-                            <td><b>name</b></td>
-                            <td><b>steps</b></td>
-                            <td><b>format-version</b></td>
-                            <td><b>annotation</b></td>
-                        </tr>
-                        <% index = 0 %>
-                        %for workflow_tup in workflow_tups:
-                            <%
-                                import os.path
-                                relative_path = workflow_tup[ 0 ]
-                                full_path = os.path.abspath( relative_path )
-                                workflow_dict = workflow_tup[ 1 ]
-                                workflow_name = workflow_dict[ 'name' ]
-                                ## Initially steps were not stored in the metadata record.
-                                steps = workflow_dict.get( 'steps', [] )
-                                format_version = workflow_dict[ 'format-version' ]
-                                annotation = workflow_dict[ 'annotation' ]
-                            %>
-                            <tr>
-                                <td>
-                                    <div class="menubutton" style="float: left;" id="workflow-${index}-popup">
-                                        ${workflow_name}
-                                        <div popupmenu="workflow-${index}-popup">
-                                            <a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', installed_repository_file=full_path, repository_id=trans.security.encode_id( repository.id ) )}">Import to Galaxy</a>
-                                        </div>
-                                    </div>
-                                </td>
-                                <td>
-                                    %if steps:
-                                        ${len( steps )}
-                                    %else:
-                                        unknown
-                                    %endif
-                                </td>
-                                <td>${format_version}</td>
-                                <td>${annotation}</td>
-                            </tr>
-                            <% index += 1 %>
-                        %endfor
-                    </table>
-                </div>
-                <div style="clear: both"></div>
-            %endif
-            %if 'datatypes' in metadata:
-                <div class="form-row">
-                    <table width="100%">
-                        <tr bgcolor="#D8D8D8" width="100%">
-                            <td><b>Data types</b></td>
-                        </tr>
-                    </table>
-                </div>
-                <div style="clear: both"></div>
-                <div class="form-row">
-                    <% datatypes_dicts = metadata[ 'datatypes' ] %>
-                    <table class="grid">
-                        <tr>
-                            <td><b>extension</b></td>
-                            <td><b>type</b></td>
-                            <td><b>mimetype</b></td>
-                            <td><b>subclass</b></td>
-                        </tr>
-                        %for datatypes_dict in datatypes_dicts:
-                            <tr>
-                                <td>${datatypes_dict.get( 'extension', '&nbsp;' )}</td>
-                                <td>${datatypes_dict.get( 'dtype', '&nbsp;' )}</td>
-                                <td>${datatypes_dict.get( 'mimetype', '&nbsp;' )}</td>
-                                <td>${datatypes_dict.get( 'subclass', '&nbsp;' )}</td>
-                            </tr>
-                        %endfor
-                    </table>
-                </div>
-                <div style="clear: both"></div>
-            %endif
-            %if can_reset_metadata:
-                <form name="set_metadata" action="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ) )}" 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.
-                        </div>
-                    </div>
-                </form>
-            %endif
-        </div>
-    </div>
-</%def>
diff -r b1f35669f93c4163cf803d64beb37a1cb0d5381c -r bef69fd3fcc191b9a9a4d140876a6ee932e9fc3e templates/admin/tool_shed_repository/manage_repository.mako
--- a/templates/admin/tool_shed_repository/manage_repository.mako
+++ b/templates/admin/tool_shed_repository/manage_repository.mako
@@ -64,5 +64,223 @@
     </div></div><p/>
-${render_repository_contents( repository, can_reset_metadata=True )}
+<div class="toolForm">
+    <div class="toolFormTitle">${repository.name}</div>
+    <div class="toolFormBody">
+        <%
+            metadata = repository.metadata
+            missing_tool_dependencies = repository.missing_tool_dependencies
+            installed_tool_dependencies = repository.installed_tool_dependencies
+        %>
+        %if missing_tool_dependencies:
+            <div class="form-row">
+                <table width="100%">
+                    <tr bgcolor="#D8D8D8" width="100%">
+                        <td><b>Missing tool dependencies</i></td>
+                    </tr>
+                </table>
+            </div>
+            <div style="clear: both"></div>
+            <div class="form-row">
+                <table class="grid">
+                    <tr>
+                        <td><b>name</b></td>
+                        <td><b>type</b></td>
+                        <td><b>version</b></td>
+                    </tr>
+                    %for name, requirements_dict in missing_tool_dependencies.items():
+                        <tr>
+                            <td>${requirements_dict[ 'name' ]}</td>
+                            <td>${requirements_dict[ 'type' ]}</td>
+                            <td>${requirements_dict[ 'version' ]}</td>
+                        </tr>
+                    %endfor
+                </table>
+            </div>
+            <div style="clear: both"></div>
+        %endif
+        %if installed_tool_dependencies:
+            <div class="form-row">
+                <table width="100%">
+                    <tr bgcolor="#D8D8D8" width="100%">
+                        <td><b>Installed tool dependencies<i> - click the name to browse the dependency installation directory</i></td>
+                    </tr>
+                </table>
+            </div>
+            <div style="clear: both"></div>
+            <div class="form-row">
+                <table class="grid">
+                    <tr>
+                        <td><b>name</b></td>
+                        <td><b>type</b></td>
+                        <td><b>version</b></td>
+                    </tr>
+                    %for installed_tool_dependency in installed_tool_dependencies:
+                        <tr>
+                            <td>
+                                <a class="view-info" href="${h.url_for( controller='admin_toolshed', action='browse_tool_dependency', id=trans.security.encode_id( installed_tool_dependency.id ), repository_id=trans.security.encode_id( repository.id ) )}">
+                                    ${installed_tool_dependency.name}
+                                </a>
+                            </td>
+                            <td>${installed_tool_dependency.type}</td>
+                            <td>${installed_tool_dependency.version}</td>
+                        </tr>
+                    %endfor
+                </table>
+            </div>
+            <div style="clear: both"></div>
+        %endif
+        %if 'tools' in metadata:
+            <div class="form-row">
+                <table width="100%">
+                    <tr bgcolor="#D8D8D8" width="100%">
+                        <td><b>Tools</b><i> - click the name to view information about the tool</i></td>
+                    </tr>
+                </table>
+            </div>
+            <div class="form-row">
+                <% tool_dicts = metadata[ 'tools' ] %>
+                <table class="grid">
+                    <tr>
+                        <td><b>name</b></td>
+                        <td><b>description</b></td>
+                        <td><b>version</b></td>
+                        <td><b>requirements</b></td>
+                    </tr>
+                    %for tool_dict in tool_dicts:
+                        <tr>
+                            <td>
+                                <a class="view-info" href="${h.url_for( controller='admin_toolshed', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), tool_id=tool_dict[ 'id' ] )}">
+                                    ${tool_dict[ 'name' ]}
+                                </a>
+                            </td>
+                            <td>${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
+        %if 'workflows' in metadata:
+            ## metadata[ 'workflows' ] is a list of tuples where each contained tuple is
+            ## [ <relative path to the .ga file in the repository>, <exported workflow dict> ]
+            <div class="form-row">
+                <table width="100%">
+                    <tr bgcolor="#D8D8D8" width="100%">
+                        <td><b>Workflows</b><i> - click the name to import</i></td>
+                    </tr>
+                </table>
+            </div>
+            <div style="clear: both"></div>
+            <div class="form-row">
+                <% workflow_tups = metadata[ 'workflows' ] %>
+                <table class="grid">
+                    <tr>
+                        <td><b>name</b></td>
+                        <td><b>steps</b></td>
+                        <td><b>format-version</b></td>
+                        <td><b>annotation</b></td>
+                    </tr>
+                    <% index = 0 %>
+                    %for workflow_tup in workflow_tups:
+                        <%
+                            import os.path
+                            relative_path = workflow_tup[ 0 ]
+                            full_path = os.path.abspath( relative_path )
+                            workflow_dict = workflow_tup[ 1 ]
+                            workflow_name = workflow_dict[ 'name' ]
+                            ## Initially steps were not stored in the metadata record.
+                            steps = workflow_dict.get( 'steps', [] )
+                            format_version = workflow_dict[ 'format-version' ]
+                            annotation = workflow_dict[ 'annotation' ]
+                        %>
+                        <tr>
+                            <td>
+                                <div class="menubutton" style="float: left;" id="workflow-${index}-popup">
+                                    ${workflow_name}
+                                    <div popupmenu="workflow-${index}-popup">
+                                        <a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', installed_repository_file=full_path, repository_id=trans.security.encode_id( repository.id ) )}">Import to Galaxy</a>
+                                    </div>
+                                </div>
+                            </td>
+                            <td>
+                                %if steps:
+                                    ${len( steps )}
+                                %else:
+                                    unknown
+                                %endif
+                            </td>
+                            <td>${format_version}</td>
+                            <td>${annotation}</td>
+                        </tr>
+                        <% index += 1 %>
+                    %endfor
+                </table>
+            </div>
+            <div style="clear: both"></div>
+        %endif
+        %if 'datatypes' in metadata:
+            <div class="form-row">
+                <table width="100%">
+                    <tr bgcolor="#D8D8D8" width="100%">
+                        <td><b>Data types</b></td>
+                    </tr>
+                </table>
+            </div>
+            <div style="clear: both"></div>
+            <div class="form-row">
+                <% datatypes_dicts = metadata[ 'datatypes' ] %>
+                <table class="grid">
+                    <tr>
+                        <td><b>extension</b></td>
+                        <td><b>type</b></td>
+                        <td><b>mimetype</b></td>
+                        <td><b>subclass</b></td>
+                    </tr>
+                    %for datatypes_dict in datatypes_dicts:
+                        <tr>
+                            <td>${datatypes_dict.get( 'extension', '&nbsp;' )}</td>
+                            <td>${datatypes_dict.get( 'dtype', '&nbsp;' )}</td>
+                            <td>${datatypes_dict.get( 'mimetype', '&nbsp;' )}</td>
+                            <td>${datatypes_dict.get( 'subclass', '&nbsp;' )}</td>
+                        </tr>
+                    %endfor
+                </table>
+            </div>
+            <div style="clear: both"></div>
+        %endif
+        %if can_reset_metadata:
+            <form name="set_metadata" action="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ) )}" 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.
+                    </div>
+                </div>
+            </form>
+        %endif
+    </div>
+</div><p/>
diff -r b1f35669f93c4163cf803d64beb37a1cb0d5381c -r bef69fd3fcc191b9a9a4d140876a6ee932e9fc3e templates/admin/tool_shed_repository/manage_tool_dependencies.mako
--- a/templates/admin/tool_shed_repository/manage_tool_dependencies.mako
+++ b/templates/admin/tool_shed_repository/manage_tool_dependencies.mako
@@ -24,7 +24,7 @@
 %endif
<div class="toolForm">
-    <div class="toolFormTitle">${repository.name} repository's installed tool dependencies</div>
+    <div class="toolFormTitle">${repository.name} repository's tool dependencies</div><div class="toolFormBody"><div class="form-row"><table class="grid">
@@ -45,7 +45,18 @@
                         <tr><td bgcolor="#D8D8D8"><b>Name</b></td><td bgcolor="#D8D8D8">${name}</td></tr><tr><th>Version</th><td>${version}</td></tr><tr><th>Type</th><td>${type}</td></tr>
-                        <tr><th>Install directory</th><td>${install_dir}</td></tr>
+                        <tr>
+                            <th>Install directory</th>
+                            <td>
+                                %if uninstalled:
+                                    This dependency is not currently installed
+                                %else:
+                                    <a class="view-info" href="${h.url_for( controller='admin_toolshed', action='browse_tool_dependency', id=trans.security.encode_id( tool_dependency.id ), repository_id=trans.security.encode_id( repository.id ) )}">
+                                        ${install_dir}
+                                    </a>
+                                %endif
+                            </td>
+                        </tr><tr><th>Installed changeset revision</th><td>${installed_changeset_revision}</td></tr><tr><th>Uninstalled</th><td>${uninstalled}</td></tr>
                 %endfor
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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[galaxy-commits] commit/galaxy-central: greg: Add the ability to browse the installation directory of tool dependencies for installed tool shed repositories.