Warning
This document is for an old release 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, 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 == 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)