Merge pull request #3479 from mvdbeek/manage_tool_dependencies

Add a simple UI to manage tool dependencies

lib/galaxy/tools/deps/resolvers/conda.py

@@ -232,7 +232,7 @@ class CondaDependencyResolver(DependencyResolver, MultipleDependencyResolver, Li
         if job_directory:
             conda_environment = os.path.join(job_directory, conda_env)
         else:
-            conda_environment = None
+            conda_environment = self.conda_context.env_path(conda_target.install_environment)
 
         return CondaDependency(
             self.conda_context,

lib/galaxy/web/base/controllers/admin.py

@@ -1,7 +1,7 @@
 import logging
 import os
 from datetime import datetime, timedelta
-from six import string_types
+import six
 from string import punctuation as PUNCTUATION
 
 from sqlalchemy import and_, false, func, or_
@@ -1123,6 +1123,30 @@ class Admin( object ):
                                     job=job,
                                     message="<a href='jobs'>Back</a>" )
 
+    @web.expose
+    @web.require_admin
+    def manage_tool_dependencies( self, trans, install_dependencies=False, build_cache=False, install_for_tools=[], viewkey='View tool-centric dependencies'):
+        tools_by_id = trans.app.toolbox.tools_by_id
+        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([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]
+        view = six.next(six.itervalues(trans.app.toolbox.tools_by_id))._view
+        tool_ids_by_requirements = {}
+        for tid, tool in trans.app.toolbox.tools_by_id.items():
+            if tool.tool_requirements not in tool_ids_by_requirements:
+                tool_ids_by_requirements[tool.tool_requirements] = [tid]
+            else:
+                tool_ids_by_requirements[tool.tool_requirements].append(tid)
+        requirements_status = {r: view.get_requirements_status({tid: r}, tools_by_id[tids[0]].installed_tool_dependencies) for r, tids in tool_ids_by_requirements.items()}
+        return trans.fill_template( '/webapps/galaxy/admin/manage_dependencies.mako',
+                                    tools=tools_by_id,
+                                    requirements_status=requirements_status,
+                                    tool_ids_by_requirements=tool_ids_by_requirements,
+                                    viewkey=viewkey )
+
     @web.expose
     @web.require_admin
     def sanitize_whitelist( self, trans, submit_whitelist=False, tools_to_whitelist=[]):
@@ -1130,7 +1154,7 @@ class Admin( object ):
             # write the configured sanitize_whitelist_file with new whitelist
             # and update in-memory list.
             with open(trans.app.config.sanitize_whitelist_file, 'wt') as f:
-                if isinstance(tools_to_whitelist, string_types):
+                if isinstance(tools_to_whitelist, six.string_types):
                     tools_to_whitelist = [tools_to_whitelist]
                 new_whitelist = sorted([tid for tid in tools_to_whitelist if tid in trans.app.toolbox.tools_by_id])
                 f.write("\n".join(new_whitelist))

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>

templates/webapps/galaxy/admin/manage_dependencies.mako

@@ -0,0 +1,114 @@
+<%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, ncols_extra=4, show_environment_path=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
+            %for i in range(ncols_extra-1):
+                <td></td>
+            %endfor
+        %endif
+        %if show_environment_path:
+            <td>${dependency.get('environment_path', '') | h}</td>
+        %endif
+        ${render_dependency_status(dependency)}
+    %endfor
+</%def>
+
+<%def name="render_tool_centric_table( tools, requirements_status)">
+    <tr>
+        <th bgcolor="#D8D8D8">Install</th>
+        <th bgcolor="#D8D8D8">Name</th>
+        <th bgcolor="#D8D8D8">ID</th>
+        <th bgcolor="#D8D8D8">Requirement</th>
+        <th bgcolor="#D8D8D8">Version</th>
+        <th bgcolor="#D8D8D8">Resolver</th>
+        <th bgcolor="#D8D8D8">Exact</th>
+        <th bgcolor="#D8D8D8"></th>
+    </tr>
+    <% ctr = 0 %>
+    %for tool in tools.values():
+        %if tool.tool_requirements:
+            %if ctr % 2 == 1:
+                <tr class="odd_row">
+            %else:
+                <tr class="tr">
+            %endif
+            <td>
+                <input type="checkbox" name="install_for_tools" value="${tool.id}"/>
+            </td>
+            <td>${ tool.name | h }</td>
+            <td>${ tool.id | h }</td>
+            ${render_tool_dependencies( requirements_status[tool.tool_requirements], ctr=ctr) }
+            </tr>
+        <% ctr += 1 %>
+        %endif
+    %endfor
+</%def>
+
+<%def name="render_dependencies_details( tools, requirements_status, tool_ids_by_requirements)">
+    <tr>
+        <th bgcolor="#D8D8D8">Install</th>
+        <th bgcolor="#D8D8D8">Used by</th>
+        <th bgcolor="#D8D8D8">Environment Path</th>
+        <th bgcolor="#D8D8D8">Requirement</th>
+        <th bgcolor="#D8D8D8">Version</th>
+        <th bgcolor="#D8D8D8">Resolver</th>
+        <th bgcolor="#D8D8D8">Exact</th>
+        <th bgcolor="#D8D8D8"></th>
+    </tr>
+    <% ctr = 0 %>
+    %for requirements, r_status in requirements_status.items():
+        %if requirements:
+            <% tool_ids = tool_ids_by_requirements[requirements] %>
+            %if ctr % 2 == 1:
+                <tr class="odd_row">
+            %else:
+                <tr class="tr">
+            %endif
+            <td>
+                <input type="checkbox" name="install_for_tools" value="${tool_ids[0]}"/>
+            </td>
+            <td>${ ", ".join([tools[tid].name for tid in tool_ids]) | h }</td>
+            ${render_tool_dependencies( r_status, ctr=ctr, show_environment_path=True, ncols_extra=3) }
+            </tr>
+        %endif
+        <% ctr += 1 %>
+    %endfor
+</%def>
+
+%if message:
+    ${render_msg( message, status )}
+%endif
+
+<h2>Manage Tool Dependencies</h2>
+<p>This page gives an overview of all tool dependencies required by all tools currently loaded, including tools not installed through the Tool Shed.</p>
+
+<form name="manage_tool_dependencies" action="${h.url_for( controller='admin', action='manage_tool_dependencies' )}">
+%if viewkey == "Switch to tool-centric view":
+    <input type="submit" name="viewkey" value="Switch to details view"/>
+    <div class="toolForm">
+        <div class="toolFormTitle">Tool-centric dependencies</div>
+        <div class="toolFormBody">
+            <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%">
+                ${render_tool_centric_table(tools, requirements_status)}
+%else:
+    <input type="submit" name="viewkey" value="Switch to tool-centric view"/>
+    <div class="toolForm">
+        <div class="toolFormTitle">Dependency details</div>
+        <div class="toolFormBody">
+            <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%">
+                    ${render_dependencies_details(tools, requirements_status, tool_ids_by_requirements)}
+%endif
+            </table>
+        </div>
+    </div>
+    <input type="submit" name="install_dependencies" value="Install checked dependencies using Conda"/>
+</form>

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>