Warning
This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.
Source code for tool_shed.grids.repository_review_grids
import logging
from markupsafe import escape
from sqlalchemy import and_, false, null, or_, true
from galaxy.webapps.reports.framework import grids
from galaxy.webapps.tool_shed import model
from tool_shed.grids.repository_grids import RepositoryGrid
from tool_shed.util import hg_util, metadata_util
log = logging.getLogger(__name__)
[docs]class ComponentGrid(grids.Grid):
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
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)
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 == null())) \
.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 == null())) \
.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 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
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))
[docs]class RepositoriesWithNoToolTestsGrid(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 no tests or test data"
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())) \
.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)