From a146ac6df0633f51ec12f4dae3c1c556527ef8f5 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Wed, 4 Apr 2012 13:36:37 -0400
Subject: [PATCH] Add the ability to browse invalid tools in the tool shed -
 current user is restricted to seeing only their invalid tools if not an
 admin.  Also a bit of cleanup in tool shed statistics.

---
 lib/galaxy/util/shed_util.py                  |  9 +++-
 .../webapps/community/controllers/admin.py    | 41 +++++++++++--------
 .../community/controllers/repository.py       | 32 +++++++++++++++
 templates/webapps/community/admin/index.mako  |  3 ++
 .../admin/reset_all_repository_metadata.mako  | 19 +++++++++
 .../webapps/community/admin/statistics.mako   |  2 +-
 templates/webapps/community/index.mako        |  3 ++
 .../repository/browse_invalid_tools.mako      | 38 +++++++++++++++++
 8 files changed, 127 insertions(+), 20 deletions(-)
 create mode 100644 templates/webapps/community/admin/reset_all_repository_metadata.mako
 create mode 100644 templates/webapps/community/repository/browse_invalid_tools.mako

diff --git a/lib/galaxy/util/shed_util.py b/lib/galaxy/util/shed_util.py
index f023dc12f73..b794bbc9fec 100644
--- a/lib/galaxy/util/shed_util.py
+++ b/lib/galaxy/util/shed_util.py
@@ -50,9 +50,14 @@ class ShedCounter( object ):
         for repository in self.sa_session.query( self.model.Repository ):
             self.repositories += 1
             self.total_clones += repository.times_downloaded
-            if repository.deleted:
+            is_deleted = repository.deleted
+            is_new = repository.is_new
+            if is_deleted and is_new:
                 self.deleted_repositories += 1
-            elif repository.is_new:
+                self.new_repositories += 1
+            elif is_deleted:
+                self.deleted_repositories += 1
+            elif is_new:
                 self.new_repositories += 1
             else:
                 processed_guids = []
diff --git a/lib/galaxy/webapps/community/controllers/admin.py b/lib/galaxy/webapps/community/controllers/admin.py
index 41f1c9efd8b..6168f4e0ddd 100644
--- a/lib/galaxy/webapps/community/controllers/admin.py
+++ b/lib/galaxy/webapps/community/controllers/admin.py
@@ -461,21 +461,25 @@ class AdminController( BaseUIController, Admin ):
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
-        count = 0
-        for repository in trans.sa_session.query( trans.model.Repository ) \
-                                          .filter( trans.model.Repository.table.c.deleted == False ):
-            try:
-                reset_all_repository_metadata( trans, trans.security.encode_id( repository.id ) )
-                log.debug( "Reset metadata on repository %s" % repository.name )
-                count += 1
-            except Exception, e:
-                log.debug( "Error attempting to reset metadata on repository %s: %s" % ( repository.name, str( e ) ) )
-        message = "Reset metadata on %d repositories" % count
-        trans.response.send_redirect( web.url_for( controller='admin',
-                                                   action='browse_repository_metadata',
-                                                   webapp='community',
-                                                   message=util.sanitize_text( message ),
-                                                   status=status ) )
+        if 'reset_all_repository_metadata_button' in kwd:
+            count = 0
+            for repository in trans.sa_session.query( trans.model.Repository ) \
+                                              .filter( trans.model.Repository.table.c.deleted == False ):
+                try:
+                    reset_all_repository_metadata( trans, trans.security.encode_id( repository.id ) )
+                    log.debug( "Reset metadata on repository %s" % repository.name )
+                    count += 1
+                except Exception, e:
+                    log.debug( "Error attempting to reset metadata on repository %s: %s" % ( repository.name, str( e ) ) )
+            message = "Reset metadata on %d repositories" % count
+            trans.response.send_redirect( web.url_for( controller='admin',
+                                                       action='browse_repository_metadata',
+                                                       webapp='community',
+                                                       message=util.sanitize_text( message ),
+                                                       status=status ) )
+        return trans.fill_template( '/webapps/community/admin/reset_all_repository_metadata.mako',
+                                    message=message,
+                                    status=status )
     @web.expose
     @web.require_admin
     def browse_repositories( self, trans, **kwd ):
@@ -549,12 +553,15 @@ class AdminController( BaseUIController, Admin ):
     @web.expose
     @web.require_admin
     def regenerate_statistics( self, trans, **kwd ):
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
         if 'regenerate_statistics_button' in kwd:
             trans.app.shed_counter.generate_statistics()
-        message = "Successfully regenerated statistics"
+            message = "Successfully regenerated statistics"
         return trans.fill_template( '/webapps/community/admin/statistics.mako',
                                     message=message,
-                                    status='done' )
+                                    status=status )
     @web.expose
     @web.require_admin
     def delete_repository( self, trans, **kwd ):
diff --git a/lib/galaxy/webapps/community/controllers/repository.py b/lib/galaxy/webapps/community/controllers/repository.py
index 20ecc6daad5..72a9857fe30 100644
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -400,6 +400,38 @@ class RepositoryController( BaseUIController, ItemRatings ):
         # Render the list view
         return self.valid_repository_list_grid( trans, **kwd )
     @web.expose
+    def browse_invalid_tools( self, trans, **kwd ):
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
+        webapp = params.get( 'webapp', 'community' )
+        is_admin = trans.user_is_admin()
+        invalid_tools_dict = odict()
+        if is_admin:
+            for repository in trans.sa_session.query( trans.model.Repository ) \
+                                              .filter( trans.model.Repository.table.c.deleted == False ) \
+                                              .order_by( trans.model.Repository.table.c.name ):
+                for downloadable_revision in repository.downloadable_revisions:
+                    metadata = downloadable_revision.metadata
+                    invalid_tools = metadata.get( 'invalid_tools', [] )
+                    for invalid_tool_config in invalid_tools:
+                        invalid_tools_dict[ invalid_tool_config ] = ( repository.id, repository.name, downloadable_revision.changeset_revision )
+        else:
+            for repository in trans.sa_session.query( trans.model.Repository ) \
+                                              .filter( and_( trans.model.Repository.table.c.deleted == False,
+                                                             trans.model.Repository.table.c.user_id == trans.user.id ) ) \
+                                              .order_by( trans.model.Repository.table.c.name ):
+                for downloadable_revision in repository.downloadable_revisions:
+                    metadata = downloadable_revision.metadata
+                    invalid_tools = metadata.get( 'invalid_tools', [] )
+                    for invalid_tool_config in invalid_tools:
+                        invalid_tools_dict[ invalid_tool_config ] = ( repository.id, repository.name, downloadable_revision.changeset_revision )
+        return trans.fill_template( '/webapps/community/repository/browse_invalid_tools.mako',
+                                    invalid_tools_dict=invalid_tools_dict,
+                                    webapp=webapp,
+                                    message=message,
+                                    status=status )     
+    @web.expose
     def find_workflows( self, trans, **kwd ):
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', '' ) )
diff --git a/templates/webapps/community/admin/index.mako b/templates/webapps/community/admin/index.mako
index 84c3300a539..06763c0d9c2 100644
--- a/templates/webapps/community/admin/index.mako
+++ b/templates/webapps/community/admin/index.mako
@@ -60,6 +60,9 @@
                         <div class="toolTitle">
                             <a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repository_metadata', webapp='community' )}">Browse metadata</a>
                         </div>
+                        <div class="toolTitle">
+                            <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_invalid_tools', webapp='community' )}">Browse invalid tools</a>
+                        </div>
                     </div>
                 </div>
                 <div class="toolSectionTitle">
diff --git a/templates/webapps/community/admin/reset_all_repository_metadata.mako b/templates/webapps/community/admin/reset_all_repository_metadata.mako
new file mode 100644
index 00000000000..ba1c6c2e044
--- /dev/null
+++ b/templates/webapps/community/admin/reset_all_repository_metadata.mako
@@ -0,0 +1,19 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+%if message:
+    ${render_msg( message, status )}
+%endif
+
+<div class="toolForm">
+    <div class="toolFormTitle">Reset metadata on each change set of the repositories in this tool shed</div>
+        <form name="reset_all_repository_metadata" id="reset_all_repository_metadata" action="${h.url_for( controller='admin', action='reset_all_repository_metadata' )}" method="post" >
+            <div class="form-row">
+                Click the button below to reset metadata on each change set of the repositories in this tool shed.
+            </div>
+            <div class="form-row">
+                <input type="submit" name="reset_all_repository_metadata_button" value="Reset all repository metadata"/>
+            </div>
+        </form>
+    </div>
+</div>
diff --git a/templates/webapps/community/admin/statistics.mako b/templates/webapps/community/admin/statistics.mako
index b68a64846a1..e9a266a0877 100644
--- a/templates/webapps/community/admin/statistics.mako
+++ b/templates/webapps/community/admin/statistics.mako
@@ -19,7 +19,7 @@
                         <td>${trans.app.shed_counter.repositories}</td>
                     </tr>
                     <tr>
-                        <td>New repositories</td>
+                        <td>Empty repositories</td>
                         <td>${trans.app.shed_counter.new_repositories}</td>
                     </tr>
                     <tr>
diff --git a/templates/webapps/community/index.mako b/templates/webapps/community/index.mako
index 65a984e946d..2eaf1d94691 100644
--- a/templates/webapps/community/index.mako
+++ b/templates/webapps/community/index.mako
@@ -71,6 +71,9 @@
                             <div class="toolTitle">
                                 <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='my_repositories', webapp='community' )}">Browse my repositories</a>
                             </div>
+                            <div class="toolTitle">
+                                <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_invalid_tools', webapp='community' )}">Browse my invalid tools</a>
+                            </div>
                         %endif
                     </div>
                 </div>
diff --git a/templates/webapps/community/repository/browse_invalid_tools.mako b/templates/webapps/community/repository/browse_invalid_tools.mako
new file mode 100644
index 00000000000..e0ccf159324
--- /dev/null
+++ b/templates/webapps/community/repository/browse_invalid_tools.mako
@@ -0,0 +1,38 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+%if message:
+    ${render_msg( message, status )}
+%endif
+
+<div class="toolForm">
+    %if invalid_tools_dict:
+        <div class="toolFormTitle">Invalid tools<i> - click the tool config file name to see why the tool is invalid</i></div>
+            <div class="form-row">
+                <table class="grid">
+                    <tr>
+                        <th>Tool config</th>
+                        <th>Repository name</th>
+                        <th>Changeset revision</th>
+                    </tr>
+                    %for invalid_tool_config, repository_tup in invalid_tools_dict.items():
+                        <% repository_id, repository_name, changeset_revision = repository_tup %>
+                        <tr>
+                            <td>
+                                <a class="view-info" href="${h.url_for( controller='repository', action='load_invalid_tool', repository_id=trans.security.encode_id( repository_id ), tool_config=invalid_tool_config, changeset_revision=changeset_revision, webapp=webapp )}">
+                                    ${invalid_tool_config}
+                                </a>
+                            </td>
+                            <td>${repository_name}</td>
+                            <td>${changeset_revision}</td>
+                        </tr>
+                    %endfor
+                </table>
+            </div>
+        </div>
+    %else:
+        <div class="form-row">
+            You do not own any repositories that contain invalid tools.
+        </div>
+    %endif
+</div>