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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.web.framework.helpers 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):
[docs] class NameColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, component): return escape(component.name)
[docs] class DescriptionColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, component): return escape(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 == 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 RepositoryNameColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, review): return escape(review.repository.name)
[docs] class RepositoryDescriptionColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, review): return escape(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))
[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)