[galaxy-commits] commit/galaxy-central: greg: Add grids for tool shed repositories that are ready for review or have tools with invalid functional tests.

12 Mar 2013

1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/01e294adf7ac/
changeset:   01e294adf7ac
user:        greg
date:        2013-03-12 19:29:19
summary:     Add grids for tool shed repositories that are ready for review or have tools with invalid functional tests.
affected #:  4 files
diff -r f6bc826d0ec20da52746e0703774175e835aee94 -r 01e294adf7ac8715039d0baed1d44417e338c1a4 lib/galaxy/webapps/tool_shed/controllers/repository_review.py

--- a/lib/galaxy/webapps/tool_shed/controllers/repository_review.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/repository_review.py
@@ -20,11 +20,13 @@
 class RepositoryReviewController( BaseUIController, common_util.ItemRatings ):
component_grid = repository_review_grids.ComponentGrid()
+    repositories_ready_for_review_grid = repository_review_grids.RepositoriesReadyForReviewGrid()
     repositories_reviewed_by_me_grid = repository_review_grids.RepositoriesReviewedByMeGrid()
     repositories_with_reviews_grid = repository_review_grids.RepositoriesWithReviewsGrid()
     repositories_without_reviews_grid = repository_review_grids.RepositoriesWithoutReviewsGrid()
     repository_reviews_by_user_grid = repository_review_grids.RepositoryReviewsByUserGrid()
     reviewed_repositories_i_own_grid = repository_review_grids.ReviewedRepositoriesIOwnGrid()
+    repositories_with_invalid_tests_grid = repository_review_grids.RepositoriesWithInvalidTestsGrid()
@web.expose
     @web.require_login( "approve repository review" )
@@ -368,6 +370,31 @@
         return self.component_grid( trans, **kwd )
@web.expose
+    @web.require_login( "manage repositories ready for review" )
+    def manage_repositories_ready_for_review( self, trans, **kwd ):
+        """
+        A repository is ready to be reviewed if one of the following conditions is met:
+        1) It contains no tools
+        2) It contains tools the tools_functionally_correct flag is set to True.  This implies that the repository metadata revision was installed and tested
+           by the Tool Shed's install and test framework.
+        """
+        if 'operation' in kwd:
+            operation = kwd['operation'].lower()
+            if operation == "inspect repository revisions":
+                return trans.response.send_redirect( web.url_for( controller='repository_review',
+                                                                  action='create_review',
+                                                                  **kwd ) )
+            if operation == "view_or_manage_repository":
+                return trans.response.send_redirect( web.url_for( controller='repository_review',
+                                                                  action='view_or_manage_repository',
+                                                                  **kwd ) )
+        message = 'Any of these repositories that contain tools have been installed into Galaxy and proven to be functionally correct by executing the tests defined '
+        message += 'for each tool.  Repositories that do not contain tools have not been installed into Galaxy. '
+        kwd[ 'message' ] = message
+        kwd[ 'status' ] = 'warning'
+        return self.repositories_ready_for_review_grid( trans, **kwd )
+
+    @web.expose
     @web.require_login( "manage repositories reviewed by me" )
     def manage_repositories_reviewed_by_me( self, trans, **kwd ):
         # The value of the received id is the encoded repository id.
@@ -383,6 +410,25 @@
         return self.repositories_reviewed_by_me_grid( trans, **kwd )
@web.expose
+    @web.require_login( "manage repositories with invalid tests" )
+    def manage_repositories_with_invalid_tests( self, trans, **kwd ):
+        """Display a list of repositories that contain tools, have not yet been reviewed, and have invalid functional tests."""
+        if 'operation' in kwd:
+            operation = kwd['operation'].lower()
+            if operation == "inspect repository revisions":
+                return trans.response.send_redirect( web.url_for( controller='repository_review',
+                                                                  action='create_review',
+                                                                  **kwd ) )
+            if operation == "view_or_manage_repository":
+                return trans.response.send_redirect( web.url_for( controller='repository_review',
+                                                                  action='view_or_manage_repository',
+                                                                  **kwd ) )
+        message = 'These repositories contain tools with invalid functional tests (they have not yet been reviewed).  '
+        kwd[ 'message' ] = message
+        kwd[ 'status' ] = 'warning'
+        return self.repositories_with_invalid_tests_grid( trans, **kwd )
+
+    @web.expose
     @web.require_login( "manage repositories with reviews" )
     def manage_repositories_with_reviews( self, trans, **kwd ):
         # The value of the received id is the encoded repository id.
diff -r f6bc826d0ec20da52746e0703774175e835aee94 -r 01e294adf7ac8715039d0baed1d44417e338c1a4 lib/tool_shed/grids/repository_review_grids.py
--- a/lib/tool_shed/grids/repository_review_grids.py
+++ b/lib/tool_shed/grids/repository_review_grids.py
@@ -1,7 +1,7 @@
 import os, logging
 from galaxy.webapps.tool_shed import model
 from galaxy.web.framework.helpers import grids
-from galaxy.model.orm import and_
+from galaxy.model.orm import and_, or_
 from tool_shed.grids.repository_grids import RepositoryGrid
 import tool_shed.util.shed_util_common as suc
@@ -11,13 +11,21 @@
log = logging.getLogger( __name__ )
+
 class ComponentGrid( grids.Grid ):
+
+
     class NameColumn( grids.TextColumn ):
+
         def get_value( self, trans, grid, component ):
             return component.name
+
+
     class DescriptionColumn( grids.TextColumn ):
+
         def get_value( self, trans, grid, component ):
             return component.description
+
     title = "Repository review components"
     model_class = model.Component
     template='/webapps/tool_shed/repository_review/grid.mako'
@@ -44,6 +52,8 @@
class RepositoriesWithReviewsGrid( RepositoryGrid ):
     # This grid filters out repositories that have been marked as either deprecated or deleted.
+
+
     class WithReviewsRevisionColumn( grids.GridColumn ):
         def get_value( self, trans, grid, repository ):
             # Restrict to revisions that have been reviewed.
@@ -53,10 +63,12 @@
                 for review in repository.reviews:
                     changeset_revision = review.changeset_revision
                     rev, label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision )
-                    rval += '<a href="manage_repository_reviews_of_revision'
-                    rval += '?id=%s&changeset_revision=%s">%s</a><br/>' % ( trans.security.encode_id( repository.id ), changeset_revision, label )
+                    rval += '<a href="manage_repository_reviews_of_revision?id=%s&changeset_revision=%s">%s</a><br/>' % \
+                        ( trans.security.encode_id( repository.id ), changeset_revision, label )
                 return rval
             return ''
+
+
     class WithoutReviewsRevisionColumn( grids.GridColumn ):
         def get_value( self, trans, grid, repository ):
             # Restrict the options to revisions that have not yet been reviewed.
@@ -67,11 +79,14 @@
                     rev, label, changeset_revision = suc.get_rev_label_changeset_revision_from_repository_metadata( trans,
                                                                                                                     repository_metadata,
                                                                                                                     repository=repository )
-                    rval += '<a href="manage_repository_reviews_of_revision'
-                    rval += '?id=%s&changeset_revision=%s">%s</a><br/>' % ( trans.security.encode_id( repository.id ), changeset_revision, label )
+                    rval += '<a href="manage_repository_reviews_of_revision?id=%s&changeset_revision=%s">%s</a><br/>' % \
+                        ( trans.security.encode_id( repository.id ), changeset_revision, label )
                 return rval
             return ''
+
+
     class ReviewersColumn( grids.TextColumn ):
+
         def get_value( self, trans, grid, repository ):
             rval = ''
             if repository.reviewers:
@@ -95,7 +110,7 @@
         ReviewersColumn( "Reviewers", attach_popup=False )
     ]
     columns.append( grids.MulticolFilterColumn( "Search repository name", 
-                                                cols_to_filter=[ columns[0] ],
+                                                cols_to_filter=[ columns[ 0 ] ],
                                                 key="free-text-search",
                                                 visible=False,
                                                 filterable="standard" ) )
@@ -105,6 +120,7 @@
                              condition=( lambda item: not item.deleted ),
                              async_compatible=False )
     ]
+
     def build_initial_query( self, trans, **kwd ):
         return trans.sa_session.query( model.Repository ) \
                                .filter( and_( model.Repository.table.c.deleted == False,
@@ -114,6 +130,7 @@
                                .outerjoin( ( model.ComponentReview.table, model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id ) ) \
                                .outerjoin( ( model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id ) )
+
 class RepositoriesWithoutReviewsGrid( RepositoriesWithReviewsGrid ):
     # This grid filters out repositories that have been marked as either deprecated or deleted.
     title = "Repositories with no reviews"
@@ -123,14 +140,14 @@
                                                 link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ),
                                                 attach_popup=True ),
         RepositoriesWithReviewsGrid.DescriptionColumn( "Synopsis",
-                                                        key="description",
-                                                        attach_popup=False ),
+                                                       key="description",
+                                                       attach_popup=False ),
         RepositoriesWithReviewsGrid.WithoutReviewsRevisionColumn( "Revisions for review" ),
         RepositoriesWithReviewsGrid.UserColumn( "Owner",
                                                 attach_popup=False )
     ]
     columns.append( grids.MulticolFilterColumn( "Search repository name, description", 
-                                                cols_to_filter=[ columns[0], columns[1] ],
+                                                cols_to_filter=[ columns[ 0 ], columns[ 1 ] ],
                                                 key="free-text-search",
                                                 visible=False,
                                                 filterable="standard" ) )
@@ -138,6 +155,7 @@
                                         allow_multiple=False,
                                         condition=( lambda item: not item.deleted ),
                                         async_compatible=False ) ]
+
     def build_initial_query( self, trans, **kwd ):
         return trans.sa_session.query( model.Repository ) \
                                .filter( and_( model.Repository.table.c.deleted == False,
@@ -145,8 +163,51 @@
                                               model.Repository.reviews == None ) ) \
                                .join( model.User.table )
+
+class RepositoriesReadyForReviewGrid( RepositoriesWithoutReviewsGrid ):
+    # Repositories that are ready for human review are those that either:
+    # 1) Have no tools
+    # 2) Have tools that have been proven to be functionally correct within Galaxy.
+    # This grid filters out repositories that have been marked as either deprecated or deleted.
+    title = "Repositories ready for review"
+    columns = [
+        RepositoriesWithoutReviewsGrid.NameColumn( "Repository name",
+                                                   key="name",
+                                                   link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ),
+                                                   attach_popup=True ),
+        RepositoriesWithoutReviewsGrid.DescriptionColumn( "Synopsis",
+                                                          key="description",
+                                                          attach_popup=False ),
+        RepositoriesWithoutReviewsGrid.WithoutReviewsRevisionColumn( "Revisions for review" ),
+        RepositoriesWithoutReviewsGrid.UserColumn( "Owner",
+                                                   attach_popup=False )
+    ]
+    columns.append( grids.MulticolFilterColumn( "Search repository name, description", 
+                                                cols_to_filter=[ columns[ 0 ], columns[ 1 ] ],
+                                                key="free-text-search",
+                                                visible=False,
+                                                filterable="standard" ) )
+    operations = [ grids.GridOperation( "Inspect repository revisions",
+                                        allow_multiple=False,
+                                        condition=( lambda item: not item.deleted ),
+                                        async_compatible=False ) ]
+
+    def build_initial_query( self, trans, **kwd ):
+        return trans.sa_session.query( model.Repository ) \
+                               .filter( and_( model.Repository.table.c.deleted == False,
+                                              model.Repository.table.c.deprecated == False,
+                                              model.Repository.reviews == None ) ) \
+                               .join( model.RepositoryMetadata.table ) \
+                               .filter( and_( model.RepositoryMetadata.table.c.downloadable == True,
+                                              or_( model.RepositoryMetadata.table.c.includes_tools == False,
+                                                   and_( model.RepositoryMetadata.table.c.includes_tools == True,
+                                                         model.RepositoryMetadata.table.c.tools_functionally_correct == True ) ) ) ) \
+                               .join( model.User.table )
+
+
 class RepositoriesReviewedByMeGrid( RepositoriesWithReviewsGrid ):
     # This grid filters out repositories that have been marked as either deprecated or deleted.
+
     def build_initial_query( self, trans, **kwd ):
         return trans.sa_session.query( model.Repository ) \
                                .filter( and_( model.Repository.table.c.deleted == False,
@@ -157,15 +218,25 @@
                                .outerjoin( ( model.ComponentReview.table, model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id ) ) \
                                .outerjoin( ( model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id ) )
+
 class RepositoryReviewsByUserGrid( grids.Grid ):
     # This grid filters out repositories that have been marked as deprecated.
+
+
     class RepositoryNameColumn( grids.TextColumn ):
+
         def get_value( self, trans, grid, review ):
             return review.repository.name
+
+
     class RepositoryDescriptionColumn( grids.TextColumn ):
+
         def get_value( self, trans, grid, review ):
             return review.repository.description
+
+
     class RevisionColumn( grids.TextColumn ):
+
         def get_value( self, trans, grid, review ):
             encoded_review_id = trans.security.encode_id( review.id )
             rval = '<a class="action-button" href="'
@@ -175,7 +246,10 @@
                 rval +='browse_review'
             rval += '?id=%s">%s</a>' % ( encoded_review_id, suc.get_revision_label( trans, review.repository, review.changeset_revision ) )
             return rval
+
+
     class RatingColumn( grids.TextColumn ):
+
         def get_value( self, trans, grid, review ):
             if review.rating:
                 rval = '<input '
@@ -187,6 +261,7 @@
                 rval += '/>'
                 return rval
             return ''
+
     title = "Reviews by user"
     model_class = model.RepositoryReview
     template='/webapps/tool_shed/repository_review/grid.mako'
@@ -217,6 +292,7 @@
     num_rows_per_page = 50
     preserve_state = False
     use_paging = True
+
     def build_initial_query( self, trans, **kwd ):
         user_id = trans.security.decode_id( kwd[ 'id' ] )
         return trans.sa_session.query( model.RepositoryReview ) \
@@ -225,6 +301,7 @@
                                .join( ( model.Repository.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id ) ) \
                                .filter( model.Repository.table.c.deprecated == False )
+
 class ReviewedRepositoriesIOwnGrid( RepositoriesWithReviewsGrid ):
     title = "Reviewed repositories I own"
     columns = [
@@ -248,6 +325,7 @@
                              condition=( lambda item: not item.deleted ),
                              async_compatible=False )
     ]
+
     def build_initial_query( self, trans, **kwd ):
         return trans.sa_session.query( model.Repository ) \
                                .join( ( model.RepositoryReview.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id ) ) \
@@ -255,4 +333,43 @@
                                .join( ( model.User.table, model.User.table.c.id == model.RepositoryReview.table.c.user_id ) ) \
                                .outerjoin( ( model.ComponentReview.table, model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id ) ) \
                                .outerjoin( ( model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id ) )
-                        
\ No newline at end of file
+
+
+class RepositoriesWithInvalidTestsGrid( RepositoriesWithoutReviewsGrid ):
+    # Repositories that are ready for human review are those that either:
+    # 1) Have no tools
+    # 2) Have tools that have been proven to be functionally correct within Galaxy.
+    # This grid filters out repositories that have been marked as either deprecated or deleted.
+    title = "Repositories that contain tools with invalid functional tests"
+    columns = [
+        RepositoriesWithoutReviewsGrid.NameColumn( "Repository name",
+                                                   key="name",
+                                                   link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ),
+                                                   attach_popup=True ),
+        RepositoriesWithoutReviewsGrid.DescriptionColumn( "Synopsis",
+                                                          key="description",
+                                                          attach_popup=False ),
+        RepositoriesWithoutReviewsGrid.WithoutReviewsRevisionColumn( "Revisions for review" ),
+        RepositoriesWithoutReviewsGrid.UserColumn( "Owner",
+                                                   attach_popup=False )
+    ]
+    columns.append( grids.MulticolFilterColumn( "Search repository name, description", 
+                                                cols_to_filter=[ columns[ 0 ], columns[ 1 ] ],
+                                                key="free-text-search",
+                                                visible=False,
+                                                filterable="standard" ) )
+    operations = [ grids.GridOperation( "Inspect repository revisions",
+                                        allow_multiple=False,
+                                        condition=( lambda item: not item.deleted ),
+                                        async_compatible=False ) ]
+
+    def build_initial_query( self, trans, **kwd ):
+        return trans.sa_session.query( model.Repository ) \
+                               .filter( and_( model.Repository.table.c.deleted == False,
+                                              model.Repository.table.c.deprecated == False,
+                                              model.Repository.reviews == None ) ) \
+                               .join( model.RepositoryMetadata.table ) \
+                               .filter( and_( model.RepositoryMetadata.table.c.downloadable == True,
+                                              model.RepositoryMetadata.table.c.includes_tools == True,
+                                              model.RepositoryMetadata.table.c.tools_functionally_correct == False ) ) \
+                               .join( model.User.table )
diff -r f6bc826d0ec20da52746e0703774175e835aee94 -r 01e294adf7ac8715039d0baed1d44417e338c1a4 templates/webapps/tool_shed/admin/index.mako
--- a/templates/webapps/tool_shed/admin/index.mako
+++ b/templates/webapps/tool_shed/admin/index.mako
@@ -72,6 +72,15 @@
                     </div><div class="toolSectionBody"><div class="toolSectionBg">
+                            <div class="toolTitle">
+                                <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_repositories_ready_for_review' )}">Repositories ready for review</a>
+                            </div>
+                            <div class="toolTitle">
+                                <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_repositories_with_invalid_tests' )}">Repositories with invalid tests</a>
+                            </div>
+                            <div class="toolTitle">
+                                <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_repositories_without_reviews' )}">All repositories with no reviews</a>
+                            </div>
                             %if trans.user.repository_reviews:
                                 <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_repositories_reviewed_by_me' )}">Repositories reviewed by me</a>
@@ -81,9 +90,6 @@
                                 <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_repositories_with_reviews' )}">All reviewed repositories</a></div><div class="toolTitle">
-                                <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_repositories_without_reviews' )}">Repositories with no reviews</a>
-                            </div>
-                            <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_components' )}">Manage review components</a></div></div>
diff -r f6bc826d0ec20da52746e0703774175e835aee94 -r 01e294adf7ac8715039d0baed1d44417e338c1a4 templates/webapps/tool_shed/index.mako
--- a/templates/webapps/tool_shed/index.mako
+++ b/templates/webapps/tool_shed/index.mako
@@ -129,6 +129,15 @@
                             </div><div class="toolSectionBody"><div class="toolSectionBg">
+                                    <div class="toolTitle">
+                                        <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_repositories_ready_for_review' )}">Repositories ready for review</a>
+                                    </div>
+                                    <div class="toolTitle">
+                                        <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_repositories_with_invalid_tests' )}">Repositories with invalid tests</a>
+                                    </div>
+                                    <div class="toolTitle">
+                                        <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_repositories_without_reviews' )}">All repositories with no reviews</a>
+                                    </div>
                                     %if trans.user.repository_reviews:
                                         <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_repositories_reviewed_by_me' )}">Repositories reviewed by me</a>
@@ -138,9 +147,6 @@
                                         <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_repositories_with_reviews' )}">All reviewed repositories</a></div><div class="toolTitle">
-                                        <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_repositories_without_reviews' )}">Repositories with no reviews</a>
-                                    </div>
-                                    <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_components' )}">Manage review components</a></div></div>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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[galaxy-commits] commit/galaxy-central: greg: Add grids for tool shed repositories that are ready for review or have tools with invalid functional tests.