import logging
import os
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 or_
from tool_shed.grids.repository_grids import RepositoryGrid
import tool_shed.util.shed_util_common as suc
from tool_shed.util import hg_util
from tool_shed.util import metadata_util
log = logging.getLogger( __name__ )
[docs]class ComponentGrid( grids.Grid ):
[docs] class NameColumn( grids.TextColumn ):
[docs] def get_value( self, trans, grid, component ):
return component.name
[docs] class DescriptionColumn( grids.TextColumn ):
[docs] 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'
default_sort_key = "name"
use_hide_message = False
columns = [
NameColumn( "Name",
key="Component.name",
link=( lambda item: dict( operation="edit", id=item.id ) ),
attach_popup=False ),
DescriptionColumn( "Description",
key="Component.description",
attach_popup=False )
]
default_filter = {}
global_actions = [
grids.GridAction( "Add new component",
dict( controller='repository_review', action='manage_components', operation='create' ) )
]
operations = []
standard_filters = []
num_rows_per_page = 50
preserve_state = False
use_paging = False
[docs]class RepositoriesWithReviewsGrid( RepositoryGrid ):
# This grid filters out repositories that have been marked as either deprecated or deleted.
[docs] class WithReviewsRevisionColumn( grids.GridColumn ):
[docs] def get_value( self, trans, grid, repository ):
# Restrict to revisions that have been reviewed.
if repository.reviews:
rval = ''
repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
for review in repository.reviews:
changeset_revision = review.changeset_revision
rev, label = hg_util.get_rev_label_from_changeset_revision( repo, changeset_revision )
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 ''
[docs] class WithoutReviewsRevisionColumn( grids.GridColumn ):
[docs] def get_value( self, trans, grid, repository ):
# Restrict the options to revisions that have not yet been reviewed.
repository_metadata_revisions = metadata_util.get_repository_metadata_revisions_for_review( repository, reviewed=False )
if repository_metadata_revisions:
rval = ''
for repository_metadata in repository_metadata_revisions:
rev, label, changeset_revision = \
hg_util.get_rev_label_changeset_revision_from_repository_metadata( trans.app,
repository_metadata,
repository=repository,
include_date=True,
include_hash=False )
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 ''
[docs] class ReviewersColumn( grids.TextColumn ):
[docs] def get_value( self, trans, grid, repository ):
rval = ''
if repository.reviewers:
for user in repository.reviewers:
rval += '<a class="view-info" href="repository_reviews_by_user?id=%s">' % trans.security.encode_id( user.id )
rval += '%s</a> | ' % user.username
rval = rval.rstrip( ' | ' )
return rval
[docs] class RatingColumn( grids.TextColumn ):
[docs] def get_value( self, trans, grid, repository ):
rval = ''
for review in repository.reviews:
if review.rating:
for index in range( 1, 6 ):
rval += '<input '
rval += 'name="star1-%s" ' % trans.security.encode_id( review.id )
rval += 'type="radio" '
rval += 'class="community_rating_star star" '
rval += 'disabled="disabled" '
rval += 'value="%s" ' % str( review.rating )
if review.rating > ( index - 0.5 ) and review.rating < ( index + 0.5 ):
rval += 'checked="checked" '
rval += '/>'
rval += '<br/>'
return rval
[docs] class ApprovedColumn( grids.TextColumn ):
[docs] def get_value( self, trans, grid, repository ):
rval = ''
for review in repository.reviews:
if review.approved:
rval += '%s<br/>' % review.approved
return rval
title = "All reviewed repositories"
model_class = model.Repository
template='/webapps/tool_shed/repository_review/grid.mako'
default_sort_key = "Repository.name"
columns = [
RepositoryGrid.NameColumn( "Repository name",
key="name",
link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ),
attach_popup=True ),
RepositoryGrid.UserColumn( "Owner",
model_class=model.User,
attach_popup=False,
key="User.username" ),
WithReviewsRevisionColumn( "Reviewed revisions" ),
ReviewersColumn( "Reviewers", attach_popup=False ),
RatingColumn( "Rating", attach_popup=False ),
ApprovedColumn( "Approved", attach_popup=False )
]
columns.append( grids.MulticolFilterColumn( "Search repository name",
cols_to_filter=[ columns[ 0 ] ],
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 )
]
[docs] 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 ) ) \
.join( ( model.RepositoryReview.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id ) ) \
.join( ( model.User.table, model.User.table.c.id == model.Repository.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 ) )
[docs]class RepositoriesWithoutReviewsGrid( RepositoriesWithReviewsGrid ):
# This grid filters out repositories that have been marked as either deprecated or deleted.
title = "Repositories with no reviews"
columns = [
RepositoriesWithReviewsGrid.NameColumn( "Repository name",
key="name",
link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ),
attach_popup=True ),
RepositoriesWithReviewsGrid.DescriptionColumn( "Synopsis",
key="description",
attach_popup=False ),
RepositoriesWithReviewsGrid.WithoutReviewsRevisionColumn( "Revisions for review" ),
RepositoriesWithReviewsGrid.UserColumn( "Owner",
model_class=model.User,
attach_popup=False,
key="User.username" )
]
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 ) ]
[docs] 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.User.table )
[docs]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",
model_class=model.User,
attach_popup=False,
key="User.username" )
]
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 ) ]
[docs] 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 )
[docs]class RepositoriesReviewedByMeGrid( RepositoriesWithReviewsGrid ):
# This grid filters out repositories that have been marked as either deprecated or deleted.
columns = [
RepositoriesWithReviewsGrid.NameColumn( "Repository name",
key="name",
link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ),
attach_popup=True ),
RepositoriesWithReviewsGrid.UserColumn( "Owner", attach_popup=False ),
RepositoriesWithReviewsGrid.WithReviewsRevisionColumn( "Reviewed revisions" ),
RepositoriesWithReviewsGrid.ReviewersColumn( "Reviewers", attach_popup=False ),
RepositoriesWithReviewsGrid.RatingColumn( "Rating", attach_popup=False ),
RepositoriesWithReviewsGrid.ApprovedColumn( "Approved", attach_popup=False )
]
columns.append( grids.MulticolFilterColumn( "Search repository name",
cols_to_filter=[ columns[ 0 ] ],
key="free-text-search",
visible=False,
filterable="standard" ) )
[docs] 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 ) ) \
.join( ( model.RepositoryReview.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id ) ) \
.filter( model.RepositoryReview.table.c.user_id == trans.user.id ) \
.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 ) )
[docs]class RepositoryReviewsByUserGrid( grids.Grid ):
# This grid filters out repositories that have been marked as deprecated.
[docs] class RepositoryNameColumn( grids.TextColumn ):
[docs] def get_value( self, trans, grid, review ):
return review.repository.name
[docs] class RepositoryDescriptionColumn( grids.TextColumn ):
[docs] def get_value( self, trans, grid, review ):
return review.repository.description
[docs] class RevisionColumn( grids.TextColumn ):
[docs] def get_value( self, trans, grid, review ):
encoded_review_id = trans.security.encode_id( review.id )
rval = '<a class="action-button" href="'
if review.user == trans.user:
rval += 'edit_review'
else:
rval +='browse_review'
revision_label = hg_util.get_revision_label( trans.app,
review.repository,
review.changeset_revision,
include_date=True,
include_hash=False )
rval += '?id=%s">%s</a>' % ( encoded_review_id, revision_label )
return rval
[docs] class RatingColumn( grids.TextColumn ):
[docs] def get_value( self, trans, grid, review ):
if review.rating:
for index in range( 1, 6 ):
rval = '<input '
rval += 'name="star1-%s" ' % trans.security.encode_id( review.id )
rval += 'type="radio" '
rval += 'class="community_rating_star star" '
rval += 'disabled="disabled" '
rval += 'value="%s" ' % str( review.rating )
if review.rating > ( index - 0.5 ) and review.rating < ( index + 0.5 ):
rval += 'checked="checked" '
rval += '/>'
return rval
return ''
title = "Reviews by user"
model_class = model.RepositoryReview
template='/webapps/tool_shed/repository_review/grid.mako'
default_sort_key = 'repository_id'
use_hide_message = False
columns = [
RepositoryNameColumn( "Repository Name",
model_class=model.Repository,
key="Repository.name",
link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ),
attach_popup=True ),
RepositoryDescriptionColumn( "Description",
model_class=model.Repository,
key="Repository.description",
attach_popup=False ),
RevisionColumn( "Revision", attach_popup=False ),
RatingColumn( "Rating", attach_popup=False ),
]
# Override these
default_filter = {}
global_actions = []
operations = [
grids.GridOperation( "Inspect repository revisions",
allow_multiple=False,
condition=( lambda item: not item.deleted ),
async_compatible=False )
]
standard_filters = []
num_rows_per_page = 50
preserve_state = False
use_paging = False
[docs] def build_initial_query( self, trans, **kwd ):
user_id = trans.security.decode_id( kwd[ 'id' ] )
return trans.sa_session.query( model.RepositoryReview ) \
.filter( and_( model.RepositoryReview.table.c.deleted == False, \
model.RepositoryReview.table.c.user_id == user_id ) ) \
.join( ( model.Repository.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id ) ) \
.filter( model.Repository.table.c.deprecated == False )
[docs]class ReviewedRepositoriesIOwnGrid( RepositoriesWithReviewsGrid ):
title = "Reviewed repositories I own"
columns = [
RepositoriesWithReviewsGrid.NameColumn( "Repository name",
key="name",
link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ),
attach_popup=True ),
RepositoriesWithReviewsGrid.WithReviewsRevisionColumn( "Reviewed revisions" ),
RepositoriesWithReviewsGrid.WithoutReviewsRevisionColumn( "Revisions for review" ),
RepositoriesWithReviewsGrid.ReviewersColumn( "Reviewers", attach_popup=False ),
RepositoryGrid.DeprecatedColumn( "Deprecated" )
]
columns.append( grids.MulticolFilterColumn( "Search repository name",
cols_to_filter=[ columns[0] ],
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 )
]
[docs] 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 ) ) \
.filter( model.Repository.table.c.user_id == trans.user.id ) \
.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 ) )