Add a simple UI to manage tool dependencies

This page simply lists all loaded tools and their dependency status. On the left are checkboxes to select multiple tools, and at the bottom is a button to install the selected tool dependencies.
galaxyproject · Mar 8, 2017 · aa0af35 · aa0af35
1 parent b9c1abd
commit aa0af35
Show file tree

Hide file tree

Showing 4 changed files with 109 additions and 30 deletions.
diff --git a/lib/galaxy/web/base/controllers/admin.py b/lib/galaxy/web/base/controllers/admin.py
@@ -1123,6 +1123,18 @@ def job_info( self, trans, jobid=None ):
                                     job=job,
                                     message="<a href='jobs'>Back</a>" )
 
+    @web.expose
+    @web.require_admin
+    def manage_tool_dependencies( self, trans, install_dependencies=False, install_for_tools=[]):
+        if install_dependencies:
+            # install the dependencies for the tools in the install_for_tools list
+            if not isinstance(install_for_tools, list):
+                install_for_tools = [install_for_tools]
+            requirements = set([trans.app.toolbox.tools_by_id[tid].tool_requirements for tid in install_for_tools])
+            [trans.app.toolbox.tools_by_id[install_for_tools[0]]._view.install_dependencies(r) for r in requirements]
+        return trans.fill_template( '/webapps/galaxy/admin/manage_dependencies.mako',
+                                    tools=trans.app.toolbox.tools_by_id )
+
     @web.expose
     @web.require_admin
     def sanitize_whitelist( self, trans, submit_whitelist=False, tools_to_whitelist=[]):

diff --git a/templates/webapps/galaxy/admin/index.mako b/templates/webapps/galaxy/admin/index.mako
@@ -78,6 +78,7 @@
                         <div class="toolTitle"><a href="${h.url_for( controller='admin', action='review_tool_migration_stages' )}" target="galaxy_main">Review tool migration stages</a></div>
                         <div class="toolTitle"><a href="${h.url_for( controller='admin', action='tool_errors' )}" target="galaxy_main">View Tool Error Logs</a></div>
                         <div class="toolTitle"><a href="${h.url_for( controller='admin', action='sanitize_whitelist' )}" target="galaxy_main">Manage Display Whitelist</a></div>
+                        <div class="toolTitle"><a href="${h.url_for( controller='admin', action='manage_tool_dependencies' )}" target="galaxy_main">Manage Tool Dependencies</a></div>
                     </div>
                 </div>
                 <div class="toolSectionPad"></div>

diff --git a/templates/webapps/galaxy/admin/manage_dependencies.mako b/templates/webapps/galaxy/admin/manage_dependencies.mako
@@ -0,0 +1,63 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/webapps/tool_shed/repository/common.mako" import="render_dependency_status"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+<%def name="render_tool_dependencies( requirements_status, ctr=False )">
+    %for i, dependency in enumerate(requirements_status):
+        %if i != 0:
+            </tr>
+            %if ctr % 2 == 1:
+                <tr class="odd_row">
+            %else:
+                <tr class="tr">
+            %endif
+            <td></td>
+            <td></td>
+            <td></td>
+        %endif
+        ${render_dependency_status(dependency)}
+    %endfor
+</%def>
+
+%if message:
+    ${render_msg( message, status )}
+%endif
+
+    <form name="manage_tool_dependencies" action="${h.url_for( controller='admin', action='manage_tool_dependencies' )}">
+    <div class="toolForm">
+        <div class="toolFormTitle">Manage dependencies for loaded tools</div>
+        <div class="toolFormBody">
+            <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%">
+                <tr>
+                    <th bgcolor="#D8D8D8">Install</th>
+                    <th bgcolor="#D8D8D8">Name</th>
+                    <th bgcolor="#D8D8D8">ID</th>
+                    <th bgcolor="#D8D8D8">Requirement</th>
+                    <th bgcolor="#D8D8D8">Version</th>
+                    <th bgcolor="#D8D8D8">Resolver</th>
+                    <th bgcolor="#D8D8D8">Exact</th>
+                    <th bgcolor="#D8D8D8"></th>
+                </tr>
+                <% ctr = 0 %>
+                %for tool in tools.values():
+                    %if tool.tool_requirements:
+                        %if ctr % 2 == 1:
+                            <tr class="odd_row">
+                        %else:
+                            <tr class="tr">
+                        %endif
+                        <td>
+                            <input type="checkbox" name="install_for_tools" value="${tool.id}"/>
+                        </td>
+                        <td>${ tool.name | h }</td>
+                        <td>${ tool.id | h }</td>
+                        ${render_tool_dependencies( tool._view.get_requirements_status({tool.id: tool.tool_requirements}, tool.installed_tool_dependencies), ctr=ctr) }
+                        </tr>
+                    <% ctr += 1 %>
+                    %endif
+                %endfor
+            </table>
+        </div>
+    </div>
+    <input type="submit" name="install_dependencies" value="Install checked dependencies using Conda"/>
+    </form>
diff --git a/templates/webapps/tool_shed/repository/common.mako b/templates/webapps/tool_shed/repository/common.mako
@@ -1026,6 +1026,38 @@
     %>
 </%def>
 
+<%def name="render_dependency_status( dependency, prepare_for_install=False)">
+    <td>${dependency['name'] | h}</td>
+    <td>${dependency['version'] | h}</td>
+    %if not prepare_for_install:
+        %if dependency['dependency_type']:
+            <td>${dependency['dependency_type'].title() | h}</td>
+        %else:
+            <td>${dependency['dependency_type'] | h}</td>
+        %endif
+        <td>${dependency['exact'] | h}</td>
+    %endif
+    %if dependency['dependency_type'] == None:
+        <td>
+           <img src="${h.url_for('/static')}/images/icon_error_sml.gif" title='Dependency not resolved'/>
+           %if prepare_for_install:
+               Not Installed
+           %endif
+        </td>
+    %elif not dependency['exact']:
+        <td>
+            <img src="${h.url_for('/static')}/images/icon_warning_sml.gif" title='Dependency resolved, but version ${dependency['version']} not found'/>
+        </td>
+    %else:
+        <td>
+            <img src="${h.url_for('/static')}/june_2007_style/blue/ok_small.png"/>
+            %if prepare_for_install:
+                Installed through ${dependency['dependency_type'].title() | h}
+            %endif
+        </td>
+    %endif
+</%def>
+
 <%def name="render_tool_dependency_resolver( requirements_status, prepare_for_install=False )">
     <tr class="datasetRow">
         <td style="padding-left: 20 px;">
@@ -1043,37 +1075,8 @@
                 </head>
                 <body>
                     %for dependency in requirements_status:
+                        ${render_dependency_status(dependency, prepare_for_install)}
                         <tr>
-                            <td>${dependency['name'] | h}</td>
-                            <td>${dependency['version'] | h}</td>
-                            %if not prepare_for_install:
-                                %if dependency['dependency_type']:
-                                    <td>${dependency['dependency_type'].title() | h}</td>
-                                %else:
-                                    <td>${dependency['dependency_type'] | h}</td>
-                                %endif
-                                <td>${dependency['exact'] | h}</td>
-                            %endif
-                        %if dependency['dependency_type'] == None:
-                            <td>
-                               <img src="${h.url_for('/static')}/images/icon_error_sml.gif" title='Dependency not resolved'/>
-                               %if prepare_for_install:
-                                   Not Installed
-                               %endif
-                            </td>
-                        %elif not dependency['exact']:
-                            <td>
-                                <img src="${h.url_for('/static')}/images/icon_warning_sml.gif" title='Dependency resolved, but version ${dependency['version']} not found'/>
-                            </td>
-                        %else:
-                            <td>
-                                <img src="${h.url_for('/static')}/june_2007_style/blue/ok_small.png"/>
-                                %if prepare_for_install:
-                                    Installed through ${dependency['dependency_type'].title() | h}
-                                %endif
-                            </td>
-                        %endif
-                        </tr>
                     %endfor
                 </body>
             </table>