From 44d6a34178f6c8ae93834ae69f3dcf14b7557cfe Mon Sep 17 00:00:00 2001 From: John Chilton Date: Fri, 16 Sep 2022 19:26:50 -0400 Subject: [PATCH] Remove repository review functionality from tool shed. --- .../grids/repository_review_grids.py | 535 -------------- lib/tool_shed/grids/util.py | 40 +- lib/tool_shed/test/base/test_db_util.py | 65 -- lib/tool_shed/test/base/twilltestcase.py | 110 --- .../test_0400_repository_component_reviews.py | 666 ----------------- ...ository_component_review_access_control.py | 246 ------- lib/tool_shed/util/metadata_util.py | 21 - lib/tool_shed/util/review_util.py | 143 ---- lib/tool_shed/util/shed_index.py | 8 +- lib/tool_shed/webapp/api/groups.py | 10 - .../webapp/controllers/repository.py | 24 - .../webapp/controllers/repository_review.py | 670 ------------------ lib/tool_shed/webapp/model/__init__.py | 124 +--- lib/tool_shed/webapp/security/__init__.py | 32 - .../webapps/tool_shed/admin/index.mako | 1 - .../webapps/tool_shed/common/common.mako | 16 - .../common/repository_actions_menu.mako | 38 - .../templates/webapps/tool_shed/index.mako | 59 -- .../repository/manage_repository.mako | 52 +- .../tool_shed/repository/rate_repository.mako | 51 -- .../tool_shed/repository/view_repository.mako | 42 -- .../repository_review/browse_review.mako | 118 --- .../repository_review/create_component.mako | 34 - .../repository_review/edit_component.mako | 37 - .../repository_review/edit_review.mako | 162 ----- .../tool_shed/repository_review/grid.mako | 1 - .../reviews_of_changeset_revision.mako | 112 --- .../reviews_of_repository.mako | 87 --- .../select_previous_review.mako | 89 --- test/unit/shed_unit/model/test_mapping.py | 244 +------ 30 files changed, 9 insertions(+), 3828 deletions(-) delete mode 100644 lib/tool_shed/grids/repository_review_grids.py delete mode 100644 lib/tool_shed/test/functional/test_0400_repository_component_reviews.py delete mode 100644 lib/tool_shed/test/functional/test_0410_repository_component_review_access_control.py delete mode 100644 lib/tool_shed/util/review_util.py delete mode 100644 lib/tool_shed/webapp/controllers/repository_review.py delete mode 100644 lib/tool_shed/webapp/templates/webapps/tool_shed/repository_review/browse_review.mako delete mode 100644 lib/tool_shed/webapp/templates/webapps/tool_shed/repository_review/create_component.mako delete mode 100644 lib/tool_shed/webapp/templates/webapps/tool_shed/repository_review/edit_component.mako delete mode 100644 lib/tool_shed/webapp/templates/webapps/tool_shed/repository_review/edit_review.mako delete mode 100644 lib/tool_shed/webapp/templates/webapps/tool_shed/repository_review/grid.mako delete mode 100644 lib/tool_shed/webapp/templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako delete mode 100644 lib/tool_shed/webapp/templates/webapps/tool_shed/repository_review/reviews_of_repository.mako delete mode 100644 lib/tool_shed/webapp/templates/webapps/tool_shed/repository_review/select_previous_review.mako diff --git a/lib/tool_shed/grids/repository_review_grids.py b/lib/tool_shed/grids/repository_review_grids.py deleted file mode 100644 index f228efd9e5e..00000000000 --- a/lib/tool_shed/grids/repository_review_grids.py +++ /dev/null @@ -1,535 +0,0 @@ -import logging - -from markupsafe import escape -from sqlalchemy import ( - and_, - false, - null, - or_, - true, -) - -from galaxy.web.legacy_framework import grids -from tool_shed.grids.repository_grids import RepositoryGrid -from tool_shed.util import ( - hg_util, - metadata_util, -) -from tool_shed.webapp import model - -log = logging.getLogger(__name__) - - -class ComponentGrid(grids.Grid): - class NameColumn(grids.TextColumn): - def get_value(self, trans, grid, component): - return escape(component.name) - - class DescriptionColumn(grids.TextColumn): - 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), - ] - global_actions = [ - grids.GridAction( - "Add new component", dict(controller="repository_review", action="manage_components", operation="create") - ) - ] - num_rows_per_page = 50 - - -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. - if repository.reviews: - rval = "" - repo = repository.hg_repo - for review in repository.reviews: - changeset_revision = review.changeset_revision - rev, label = hg_util.get_rev_label_from_changeset_revision(repo, changeset_revision) - rval += ( - '%s
' - % (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. - 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 += ( - '%s
' - % (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: - for user in repository.reviewers: - rval += f'' - rval += f"{user.username} | " - if rval[-3:] == " | ": - rval = rval[:-3] - return rval - - class RatingColumn(grids.TextColumn): - def get_value(self, trans, grid, repository): - rval = "" - for review in repository.reviews: - if review.rating: - for index in range(1, 6): - rval += " (index - 0.5) and review.rating < (index + 0.5): - rval += 'checked="checked" ' - rval += "/>" - rval += "
" - return rval - - class ApprovedColumn(grids.TextColumn): - def get_value(self, trans, grid, repository): - rval = "" - for review in repository.reviews: - if review.approved: - rval += f"{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, - ) - ] - - 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) - ) - ) - - -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, - ) - ] - - 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) - ) - - -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, - ) - ] - - 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) - ) - - -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", - ) - ) - - 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) - ) - ) - - -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 escape(review.repository.name) - - class RepositoryDescriptionColumn(grids.TextColumn): - def get_value(self, trans, grid, review): - return escape(review.repository.description) - - class RevisionColumn(grids.TextColumn): - def get_value(self, trans, grid, review): - encoded_review_id = trans.security.encode_id(review.id) - rval = '{revision_label}' - return rval - - class RatingColumn(grids.TextColumn): - def get_value(self, trans, grid, review): - if review.rating: - for index in range(1, 6): - rval = " (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), - ] - operations = [ - grids.GridOperation( - "Inspect repository revisions", - allow_multiple=False, - condition=(lambda item: not item.deleted), - async_compatible=False, - ) - ] - num_rows_per_page = 50 - - 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()) - ) - - -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, - ) - ] - - 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) - ) - ) - - -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, - ) - ] - - 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) - ) diff --git a/lib/tool_shed/grids/util.py b/lib/tool_shed/grids/util.py index e80dc717f77..06c500d4b30 100644 --- a/lib/tool_shed/grids/util.py +++ b/lib/tool_shed/grids/util.py @@ -9,24 +9,12 @@ from tool_shed.util import ( log = logging.getLogger(__name__) -def build_approved_select_field(trans, name, selected_value=None, for_component=True): - options = [ - ("No", trans.model.ComponentReview.approved_states.NO), - ("Yes", trans.model.ComponentReview.approved_states.YES), - ] - if for_component: - options.append(("Not applicable", trans.model.ComponentReview.approved_states.NA)) - if selected_value is None: - selected_value = trans.model.ComponentReview.approved_states.NA - select_field = SelectField(name=name) - for option_tup in options: - selected = selected_value and option_tup[1] == selected_value - select_field.add_option(option_tup[0], option_tup[1], selected=selected) - return select_field - - def build_changeset_revision_select_field( - trans, repository, selected_value=None, add_id_to_name=True, downloadable=False, reviewed=False, not_reviewed=False + trans, + repository, + selected_value=None, + add_id_to_name=True, + downloadable=False, ): """ Build a SelectField whose options are the changeset_rev strings of certain revisions of the @@ -38,24 +26,6 @@ def build_changeset_revision_select_field( if downloadable: # Restrict the options to downloadable revisions. repository_metadata_revisions = repository.downloadable_revisions - elif reviewed: - # Restrict the options to revisions that have been reviewed. - repository_metadata_revisions = [] - metadata_changeset_revision_hashes = [] - for metadata_revision in repository.metadata_revisions: - metadata_changeset_revision_hashes.append(metadata_revision.changeset_revision) - for review in repository.reviews: - if review.changeset_revision in metadata_changeset_revision_hashes: - repository_metadata_revisions.append(review.repository_metadata) - elif not_reviewed: - # Restrict the options to revisions that have not yet been reviewed. - repository_metadata_revisions = [] - reviewed_metadata_changeset_revision_hashes = [] - for review in repository.reviews: - reviewed_metadata_changeset_revision_hashes.append(review.changeset_revision) - for metadata_revision in repository.metadata_revisions: - if metadata_revision.changeset_revision not in reviewed_metadata_changeset_revision_hashes: - repository_metadata_revisions.append(metadata_revision) else: # Restrict the options to all revisions that have associated metadata. repository_metadata_revisions = repository.metadata_revisions diff --git a/lib/tool_shed/test/base/test_db_util.py b/lib/tool_shed/test/base/test_db_util.py index 0fe066ab082..7c02906476b 100644 --- a/lib/tool_shed/test/base/test_db_util.py +++ b/lib/tool_shed/test/base/test_db_util.py @@ -138,56 +138,6 @@ def get_repository_role_association(repository_id, role_id): return rra -def get_repository_reviews(repository_id, reviewer_user_id=None, changeset_revision=None): - if reviewer_user_id and changeset_revision: - reviews = ( - sa_session.query(model.RepositoryReview) - .filter( - and_( - model.RepositoryReview.table.c.repository_id == repository_id, - model.RepositoryReview.table.c.deleted == false(), - model.RepositoryReview.table.c.changeset_revision == changeset_revision, - model.RepositoryReview.table.c.user_id == reviewer_user_id, - ) - ) - .all() - ) - elif reviewer_user_id: - reviews = ( - sa_session.query(model.RepositoryReview) - .filter( - and_( - model.RepositoryReview.table.c.repository_id == repository_id, - model.RepositoryReview.table.c.deleted == false(), - model.RepositoryReview.table.c.user_id == reviewer_user_id, - ) - ) - .all() - ) - else: - reviews = ( - sa_session.query(model.RepositoryReview) - .filter( - and_( - model.RepositoryReview.table.c.repository_id == repository_id, - model.RepositoryReview.table.c.deleted == false(), - ) - ) - .all() - ) - return reviews - - -def get_reviews_ordered_by_changeset_revision(repository_id, changelog_tuples, reviewer_user_id=None): - reviews = get_repository_reviews(repository_id, reviewer_user_id=reviewer_user_id) - ordered_reviews = [] - for _ctx_rev, changeset_hash in changelog_tuples: - for review in reviews: - if str(review.changeset_revision) == str(changeset_hash): - ordered_reviews.append(review) - return ordered_reviews - - def get_repository_by_id(repository_id): return sa_session.query(model.Repository).filter(model.Repository.table.c.id == repository_id).first() @@ -220,21 +170,6 @@ def get_repository_metadata_for_changeset_revision(repository_id, changeset_revi return repository_metadata -def get_repository_review_by_user_id_changeset_revision(user_id, repository_id, changeset_revision): - review = ( - sa_session.query(model.RepositoryReview) - .filter( - and_( - model.RepositoryReview.table.c.user_id == user_id, - model.RepositoryReview.table.c.repository_id == repository_id, - model.RepositoryReview.table.c.changeset_revision == changeset_revision, - ) - ) - .first() - ) - return review - - def get_role_by_name(role_name): return sa_session.query(model.Role).filter(model.Role.table.c.name == role_name).first() diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py index 7a61e5045ae..05b01f38ea6 100644 --- a/lib/tool_shed/test/base/twilltestcase.py +++ b/lib/tool_shed/test/base/twilltestcase.py @@ -237,11 +237,6 @@ class ShedTwillTestCase(ShedBaseTestCase): fh.write(smart_str(content)) return fh.name - def add_repository_review_component(self, **kwd): - params = {"operation": "create"} - self.visit_url("/repository_review/create_component", params=params) - self.submit_form(button="create_component_button", **kwd) - def assign_admin_role(self, repository, user): # As elsewhere, twill limits the possibility of submitting the form, this time due to not executing the javascript # attached to the role selection form. Visit the action url directly with the necessary parameters. @@ -262,11 +257,6 @@ class ShedTwillTestCase(ShedBaseTestCase): self.visit_url("/repository/browse_valid_categories", params=params) self.check_for_strings(strings_displayed, strings_not_displayed) - def browse_component_review(self, review, strings_displayed=None, strings_not_displayed=None): - params = {"id": self.security.encode_id(review.id)} - self.visit_url("/repository_review/browse_review", params=params) - self.check_for_strings(strings_displayed, strings_not_displayed) - def browse_custom_datatypes(self, strings_displayed=None, strings_not_displayed=None): url = "/repository/browse_datatypes" self.visit_url(url) @@ -517,34 +507,6 @@ class ShedTwillTestCase(ShedBaseTestCase): strings_not_displayed=None, ) - def create_repository_review(self, repository, review_contents_dict, changeset_revision=None, copy_from=None): - strings_displayed = [] - if not copy_from: - strings_displayed.append("Begin your review") - strings_not_displayed = [] - if not changeset_revision: - changeset_revision = self.get_repository_tip(repository) - params = {"changeset_revision": changeset_revision, "id": self.security.encode_id(repository.id)} - self.visit_url("/repository_review/create_review", params=params) - self.check_for_strings(strings_displayed, strings_not_displayed) - strings_displayed = [] - if copy_from: - old_changeset_revision, review_id = copy_from - strings_displayed = [ - "You have elected to create a new review", - "Select previous revision", - changeset_revision, - ] - self.check_for_strings(strings_displayed) - strings_displayed = [] - params = { - "changeset_revision": self.get_repository_tip(repository), - "id": self.security.encode_id(repository.id), - "previous_review_id": self.security.encode_id(review_id), - } - self.visit_url("/repository_review/create_review", params=params) - self.fill_review_form(review_contents_dict, strings_displayed, strings_not_displayed) - def create_user_in_galaxy( self, cntrller="user", email="test@bx.psu.edu", password="testuser", username="admin-user", redirect="" ): @@ -668,16 +630,6 @@ class ShedTwillTestCase(ShedBaseTestCase): self.visit_url(url, params=params) self.check_for_strings(strings_displayed, strings_not_displayed) - def display_reviewed_repositories_owned_by_user(self, strings_displayed=None, strings_not_displayed=None): - url = "/repository_review/reviewed_repositories_i_own" - self.visit_url(url) - self.check_for_strings(strings_displayed, strings_not_displayed) - - def display_repository_reviews_by_user(self, user, strings_displayed=None, strings_not_displayed=None): - params = {"id": self.security.encode_id(user.id)} - self.visit_url("/repository_review/repository_reviews_by_user", params=params) - self.check_for_strings(strings_displayed, strings_not_displayed) - def edit_repository_categories( self, repository, categories_to_add=None, categories_to_remove=None, restore_original=True ): @@ -754,25 +706,6 @@ class ShedTwillTestCase(ShedBaseTestCase): self.visit_url(url) self.check_for_strings(strings_displayed, strings_not_displayed) - def fill_review_form(self, review_contents_dict, strings_displayed=None, strings_not_displayed=None): - kwd = dict() - changed = False - for label, contents in review_contents_dict.items(): - if contents: - changed = True - kwd[f"{label}__ESEP__comment"] = contents["comment"] - kwd[f"{label}__ESEP__rating"] = contents["rating"] - if "private" in contents: - kwd[f"{label}__ESEP__private"] = contents["private"] - kwd[f"{label}__ESEP__approved"] = contents["approved"] - else: - kwd[f"{label}__ESEP__approved"] = "not_applicable" - self.check_for_strings(strings_displayed, strings_not_displayed) - self.submit_form(button="Workflows__ESEP__review_button", **kwd) - if changed: - strings_displayed.append("Reviews were saved") - self.check_for_strings(strings_displayed, strings_not_displayed) - def galaxy_token(self): self.visit_galaxy_url("/") html = self.last_page() @@ -882,17 +815,6 @@ class ShedTwillTestCase(ShedBaseTestCase): def get_hg_repo(self, path): return hg.repository(ui.ui(), path.encode("utf-8")) - def get_last_reviewed_revision_by_user(self, user, repository): - changelog_tuples = self.get_repository_changelog_tuples(repository) - reviews = test_db_util.get_reviews_ordered_by_changeset_revision( - repository.id, changelog_tuples, reviewer_user_id=user.id - ) - if reviews: - last_review = reviews[-1] - else: - last_review = None - return last_review - def get_repositories_category_api(self, categories, strings_displayed=None, strings_not_displayed=None): for category in categories: url = f"/api/categories/{self.security.encode_id(category.id)}/repositories" @@ -1261,11 +1183,6 @@ class ShedTwillTestCase(ShedBaseTestCase): self.visit_galaxy_url("/tool_runner", params=params) self.check_for_strings(strings_displayed, strings_not_displayed) - def manage_review_components(self, strings_displayed=None, strings_not_displayed=None): - url = "/repository_review/manage_components" - self.visit_url(url) - self.check_for_strings(strings_displayed, strings_not_displayed) - def preview_repository_in_tool_shed( self, name, owner, changeset_revision=None, strings_displayed=None, strings_not_displayed=None ): @@ -1355,19 +1272,6 @@ class ShedTwillTestCase(ShedBaseTestCase): self.visit_url("/repository/reset_all_metadata", params=params) self.check_for_strings(["All repository metadata has been reset."]) - def review_repository(self, repository, review_contents_dict, user=None, changeset_revision=None): - strings_displayed = [] - strings_not_displayed = [] - if not changeset_revision: - changeset_revision = self.get_repository_tip(repository) - if user: - review = test_db_util.get_repository_review_by_user_id_changeset_revision( - user.id, repository.id, changeset_revision - ) - params = {"id": self.security.encode_id(review.id)} - self.visit_url("/repository_review/edit_review", params=params) - self.fill_review_form(review_contents_dict, strings_displayed, strings_not_displayed) - def revoke_write_access(self, repository, username): params = {"user_access_button": "Remove", "id": self.security.encode_id(repository.id), "remove_auth": username} self.visit_url("/repository/manage_repository", params=params) @@ -1651,20 +1555,6 @@ class ShedTwillTestCase(ShedBaseTestCase): # or we know that the repository was not correctly installed! assert found, f"No entry for {required_data_table_entry} in {self.shed_tool_data_table_conf}." - def verify_repository_reviews(self, repository, reviewer=None, strings_displayed=None, strings_not_displayed=None): - changeset_revision = self.get_repository_tip(repository) - # Verify that the currently logged in user has a repository review for the specified repository, reviewer, and changeset revision. - strings_displayed = [repository.name, reviewer.username] - self.display_reviewed_repositories_owned_by_user(strings_displayed=strings_displayed) - # Verify that the reviewer has reviewed the specified repository's changeset revision. - strings_displayed = [repository.name, repository.description] - self.display_repository_reviews_by_user(reviewer, strings_displayed=strings_displayed) - # Load the review and check for the components passed in strings_displayed. - review = test_db_util.get_repository_review_by_user_id_changeset_revision( - reviewer.id, repository.id, changeset_revision - ) - self.browse_component_review(review, strings_displayed=strings_displayed) - def verify_tool_metadata_for_installed_repository( self, installed_repository, strings_displayed=None, strings_not_displayed=None ): diff --git a/lib/tool_shed/test/functional/test_0400_repository_component_reviews.py b/lib/tool_shed/test/functional/test_0400_repository_component_reviews.py deleted file mode 100644 index aceeee96779..00000000000 --- a/lib/tool_shed/test/functional/test_0400_repository_component_reviews.py +++ /dev/null @@ -1,666 +0,0 @@ -from ..base.twilltestcase import ( - common, - ShedTwillTestCase, -) - -repository_name = "filtering_0400" -repository_description = "Galaxy filtering tool for test 0400" -repository_long_description = "Long description of Galaxy filtering tool for test 0400" - -""" -1. Create users. -2. Grant reviewer role to test_user_2. -3. Check that the review components that are to be tested are defined in this tool shed instance. -4. Create a repository, owned by test_user_1, to be reviewed by test_user_2. -5. Review the datatypes component on the repository. -6. Check that no other components besides datatypes display as reviewed. -7. Review the functional tests component on the repository. -8. Check that only functional tests and datatypes display as reviewed. -9. Review the readme component on the repository. -10. Check that only functional tests, datatypes, and readme display as reviewed. -11. Review the repository dependencies component. -12. Check that only repository dependencies, functional tests, datatypes, and readme display as reviewed. -13. Review the tool dependencies component. -14. Check that only tool dependencies, repository dependencies, functional tests, datatypes, and readme display as reviewed. -15. Review the tools component. -16. Check that only tools, tool dependencies, repository dependencies, functional tests, datatypes, and readme display as reviewed. -17. Review the workflows component. -18. Check that all components display as reviewed. -19. Upload readme.txt to the repository. -20. Copy the previous review, and update the readme component review to reflect the existence of a readme file. -21. Check that the readme component review has been updated, and the other component reviews are present. -22. Upload test data to the repository. This will also create a new changeset revision. -23. Review the functional tests component on the repository, copying the other components from the previous review. -24. Verify that the functional tests component review has been updated, and as in step 21, the other reviews are unchanged. -25. Upload a new version of the tool. -26. Review the new revision's functional tests component. -27. Verify that the functional tests component review displays correctly. -""" - - -class TestRepositoryComponentReviews(ShedTwillTestCase): - """Test repository component review features.""" - - def test_0000_initiate_users(self): - """Create necessary user accounts and login as an admin user. - - We are at step 1. - Create all the user accounts that are needed for this test script to run independently of other test. - Previously created accounts will not be re-created. - """ - self.login(email=common.test_user_1_email, username=common.test_user_1_name) - test_user_1 = self.test_db_util.get_user(common.test_user_1_email) - assert ( - test_user_1 is not None - ), f"Problem retrieving user with email {common.test_user_1_email} from the database" - self.test_db_util.get_private_role(test_user_1) - self.login(email=common.test_user_2_email, username=common.test_user_2_name) - test_user_2 = self.test_db_util.get_user(common.test_user_2_email) - assert ( - test_user_2 is not None - ), f"Problem retrieving user with email {common.test_user_2_email} from the database" - self.test_db_util.get_private_role(test_user_2) - self.login(email=common.admin_email, username=common.admin_username) - admin_user = self.test_db_util.get_user(common.admin_email) - assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database" - self.test_db_util.get_private_role(admin_user) - - def test_0005_grant_reviewer_role(self): - """Grant the repository reviewer role to test_user_2. - - We are at step 2. - We now have an admin user (admin_user) and two non-admin users (test_user_1 and test_user_2). Grant the repository - reviewer role to test_user_2, who will not be the owner of the reviewed repositories. - """ - reviewer_role = self.test_db_util.get_role_by_name("Repository Reviewer") - test_user_2 = self.test_db_util.get_user(common.test_user_2_email) - self.grant_role_to_user(test_user_2, reviewer_role) - - def test_0010_verify_repository_review_components(self): - """Ensure that the required review components exist. - - We are at step 3. - We now have an admin user (admin_user) and two non-admin users (test_user_1 and test_user_2). Grant the repository - reviewer role to test_user_2, who will not be the owner of the reviewed repositories. - """ - strings_not_displayed = ["Repository dependencies"] - self.manage_review_components(strings_not_displayed=strings_not_displayed) - self.add_repository_review_component( - name="Repository dependencies", - description="Repository dependencies defined in a file named repository_dependencies.xml included in the repository", - ) - strings_displayed = [ - "Data types", - "Functional tests", - "README", - "Repository dependencies", - "Tool dependencies", - "Tools", - "Workflows", - ] - self.manage_review_components(strings_displayed=strings_displayed) - - def test_0015_create_repository(self): - """Create and populate the filtering repository - - We are at step 4. - Log in as test_user_1 and create the filtering repository, then upload a basic set of - components to be reviewed in subsequent tests. - """ - category = self.create_category( - name="Test 0400 Repository Component Reviews", description="Test 0400 Repository Component Reviews" - ) - self.login(email=common.test_user_1_email, username=common.test_user_1_name) - strings_displayed = self.expect_repo_created_strings(repository_name) - repository = self.get_or_create_repository( - name=repository_name, - description=repository_description, - long_description=repository_long_description, - owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), - strings_displayed=strings_displayed, - ) - self.upload_file( - repository, - filename="filtering/filtering_1.1.0.tar", - filepath=None, - valid_tools_only=True, - uncompress_file=True, - remove_repo_files_not_in_tar=False, - commit_message="Uploaded filtering 1.1.0 tarball.", - strings_displayed=[], - strings_not_displayed=[], - ) - - def test_0020_review_initial_revision_data_types(self): - """Review the datatypes component for the current tip revision. - - We are at step 5. - Log in as test_user_2 and review the data types component of the filtering repository owned by test_user_1. - # Review this revision: - # Data types (N/A) - """ - self.login(email=common.test_user_2_email, username=common.test_user_2_name) - repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name) - # The create_repository_review method takes a dict( component label=review contents ). - # If review_contents is empty, it marks that component as not applicable. The review - # contents dict should have the structure: - # { - # rating: 1-5, - # comment: - # approved: yes/no - # private: yes/no - # } - review_contents_dict = {"Data types": dict()} - self.create_repository_review(repository, review_contents_dict) - - def test_0025_verify_datatype_review(self): - """Verify that the datatypes component review displays correctly. - - We are at step 6. - Log in as test_user_1 and check that the filtering repository only has a review for the data types component. - """ - self.login(email=common.test_user_1_email, username=common.test_user_1_name) - repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name) - user = self.test_db_util.get_user(common.test_user_2_email) - strings_displayed = ["Data types", "not_applicable"] - strings_not_displayed = [ - "Functional tests", - "README", - "Repository dependencies", - "Tool dependencies", - "Tools", - "Workflows", - ] - self.verify_repository_reviews( - repository, reviewer=user, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed - ) - - def test_0030_review_initial_revision_functional_tests(self): - """Review the functional tests component for the current tip revision. - - We are at step 7. - Log in as test_user_2 and review the functional tests component for this repository. Since the repository - has not been altered, this will update the existing review to add a component. - # Review this revision: - # Data types (N/A) - # Functional tests (One star, comment 'functional tests missing') - """ - self.login(email=common.test_user_2_email, username=common.test_user_2_name) - repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name) - user = self.test_db_util.get_user(common.test_user_2_email) - # The create_repository_review method takes a dict( component label=review contents ). - # If review_contents is empty, it marks that component as not applicable. The review - # contents dict should have the structure: - # { - # rating: 1-5, - # comment: - # approved: yes/no - # private: yes/no - # } - review_contents_dict = { - "Functional tests": dict(rating=1, comment="Functional tests missing", approved="no", private="yes") - } - self.review_repository(repository, review_contents_dict, user) - - # def test_0030_verify_review_display( self ): - # """Verify that private reviews are restricted to owner and reviewer, and non-private views are viewable by others.""" - # # Currently not implemented because third parties cannot view reviews whether they are private or not. - # self.login( email=common.test_user_3_email, username=common.test_user_3_name ) - - def test_0035_verify_functional_test_review(self): - """Verify that the functional tests component review displays correctly. - - We are at step 8. - Log in as test_user_1 and check that the filtering repository now has reviews - for the data types and functional tests components. Since the functional tests component was not marked as 'Not applicable', - also check for the review comment. - """ - self.login(email=common.test_user_1_email, username=common.test_user_1_name) - repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name) - user = self.test_db_util.get_user(common.test_user_2_email) - strings_displayed = ["Functional tests", "Functional tests missing", "no"] - strings_not_displayed = ["README", "Repository dependencies", "Tool dependencies", "Tools", "Workflows"] - self.verify_repository_reviews( - repository, reviewer=user, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed - ) - - def test_0040_review_readme(self): - """Review the readme component for the current tip revision. - - We are at step 9. - Log in as test_user_2 and update the review with the readme component marked as 'Not applicable'. - # Review this revision: - # Data types (N/A) - # Functional tests (One star, comment 'functional tests missing') - # README (N/A) - """ - self.login(email=common.test_user_2_email, username=common.test_user_2_name) - repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name) - user = self.test_db_util.get_user(common.test_user_2_email) - # The create_repository_review method takes a dict( component label=review contents ). - # If review_contents is empty, it marks that component as not applicable. The review - # contents dict should have the structure: - # { - # rating: 1-5, - # comment: - # approved: yes/no - # private: yes/no - # } - review_contents_dict = {"README": dict()} - self.review_repository(repository, review_contents_dict, user) - - def test_0045_verify_readme_review(self): - """Verify that the readme component review displays correctly. - - We are at step 10. - Log in as test_user_1 and verify that the repository component reviews now include a review for the readme component. - """ - self.login(email=common.test_user_1_email, username=common.test_user_1_name) - repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name) - user = self.test_db_util.get_user(common.test_user_2_email) - strings_displayed = ["README", "not_applicable"] - strings_not_displayed = ["Repository dependencies", "Tool dependencies", "Tools", "Workflows"] - self.verify_repository_reviews( - repository, reviewer=user, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed - ) - - def test_0050_review_repository_dependencies(self): - """Review the repository dependencies component for the current tip revision. - - We are at step 11. - Log in as test_user_2 and update the review with the repository dependencies component marked as 'Not applicable'. - # Review this revision: - # Data types (N/A) - # Functional tests (One star, comment 'functional tests missing') - # README (N/A) - # Repository dependencies (N/A) - """ - self.login(email=common.test_user_2_email, username=common.test_user_2_name) - repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name) - user = self.test_db_util.get_user(common.test_user_2_email) - # The create_repository_review method takes a dict( component label=review contents ). - # If review_contents is empty, it marks that component as not applicable. The review - # contents dict should have the structure: - # { - # rating: 1-5, - # comment: - # approved: yes/no - # private: yes/no - # } - review_contents_dict = {"Repository dependencies": dict()} - self.review_repository(repository, review_contents_dict, user) - - def test_0055_verify_repository_dependency_review(self): - """Verify that the repository dependencies component review displays correctly. - - We are at step 12. - Log in as test_user_1 and verify that the repository component reviews now include a review - for the repository dependencies component. - """ - self.login(email=common.test_user_1_email, username=common.test_user_1_name) - repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name) - user = self.test_db_util.get_user(common.test_user_2_email) - strings_displayed = ["Repository dependencies", "not_applicable"] - strings_not_displayed = ["Tool dependencies", "Tools", "Workflows"] - self.verify_repository_reviews( - repository, reviewer=user, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed - ) - - def test_0060_review_tool_dependencies(self): - """Review the tool dependencies component for the current tip revision. - - We are at step 13. - Log in as test_user_2 and update the review with the tool dependencies component marked as 'Not applicable'. - # Review this revision: - # Data types (N/A) - # Functional tests (One star, comment 'functional tests missing') - # README (N/A) - # Repository dependencies (N/A) - # Tool dependencies (N/A) - """ - self.login(email=common.test_user_2_email, username=common.test_user_2_name) - repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name) - user = self.test_db_util.get_user(common.test_user_2_email) - # The create_repository_review method takes a dict( component label=review contents ). - # If review_contents is empty, it marks that component as not applicable. The review - # contents dict should have the structure: - # { - # rating: 1-5, - # comment: - # approved: yes/no - # private: yes/no - # } - review_contents_dict = {"Tool dependencies": dict()} - self.review_repository(repository, review_contents_dict, user) - - def test_0065_verify_tool_dependency_review(self): - """Verify that the tool dependencies component review displays correctly. - - We are at step 14. - Log in as test_user_1 and verify that the repository component reviews now include a review - for the tool dependencies component. - """ - self.login(email=common.test_user_1_email, username=common.test_user_1_name) - repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name) - user = self.test_db_util.get_user(common.test_user_2_email) - strings_displayed = ["Tool dependencies", "not_applicable"] - strings_not_displayed = ["Tools", "Workflows"] - self.verify_repository_reviews( - repository, reviewer=user, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed - ) - - def test_0070_review_tools(self): - """Review the tools component for the current tip revision. - - We are at step 15. - Log in as test_user_2 and update the review with the tools component given - a favorable review, with 5 stars, and approved status. - # Review this revision: - # Data types (N/A) - # Functional tests (One star, comment 'functional tests missing') - # README (N/A) - # Repository dependencies (N/A) - # Tool dependencies (N/A) - # Tools (5 stars, good review) - """ - self.login(email=common.test_user_2_email, username=common.test_user_2_name) - repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name) - user = self.test_db_util.get_user(common.test_user_2_email) - # The create_repository_review method takes a dict( component label=review contents ). - # If review_contents is empty, it marks that component as not applicable. The review - # contents dict should have the structure: - # { - # rating: 1-5, - # comment: - # approved: yes/no - # private: yes/no - # } - review_contents_dict = { - "Tools": dict(rating=5, comment="Excellent tool, easy to use.", approved="yes", private="no") - } - self.review_repository(repository, review_contents_dict, user) - - def test_0075_verify_tools_review(self): - """Verify that the tools component review displays correctly. - - We are at step 16. - Log in as test_user_1 and verify that the repository component reviews now include a review - for the tools component. As before, check for the presence of the comment on this review. - """ - self.login(email=common.test_user_1_email, username=common.test_user_1_name) - repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name) - user = self.test_db_util.get_user(common.test_user_2_email) - strings_displayed = ["Tools", "yes", "Excellent tool, easy to use."] - strings_not_displayed = ["Workflows"] - self.verify_repository_reviews( - repository, reviewer=user, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed - ) - - def test_0080_review_workflows(self): - """Review the workflows component for the current tip revision. - - We are at step 17. - Log in as test_user_2 and update the review with the workflows component marked as 'Not applicable'. - # Review this revision: - # Data types (N/A) - # Functional tests (One star, comment 'functional tests missing') - # README (N/A) - # Repository dependencies (N/A) - # Tool dependencies (N/A) - # Tools (5 stars, good review) - # Workflows (N/A) - """ - self.login(email=common.test_user_2_email, username=common.test_user_2_name) - repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name) - user = self.test_db_util.get_user(common.test_user_2_email) - # The create_repository_review method takes a dict( component label=review contents ). - # If review_contents is empty, it marks that component as not applicable. The review - # contents dict should have the structure: - # { - # rating: 1-5, - # comment: - # approved: yes/no - # private: yes/no - # } - review_contents_dict = {"Workflows": dict()} - self.review_repository(repository, review_contents_dict, user) - - def test_0085_verify_workflows_review(self): - """Verify that the workflows component review displays correctly. - - We are at step 18. - Log in as test_user_1 and verify that the repository component reviews now include a review - for the workflows component. - """ - self.login(email=common.test_user_1_email, username=common.test_user_1_name) - repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name) - user = self.test_db_util.get_user(common.test_user_2_email) - strings_displayed = ["Workflows", "not_applicable"] - self.verify_repository_reviews(repository, reviewer=user, strings_displayed=strings_displayed) - - def test_0090_upload_readme_file(self): - """Upload a readme file to the filtering repository. - - We are at step 19. - Log in as test_user_1, the repository owner, and upload readme.txt to the repository. This will create - a new changeset revision for this repository, which will need to be reviewed. - """ - self.login(email=common.test_user_1_email, username=common.test_user_1_name) - repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name) - self.upload_file( - repository, - filename="readme.txt", - filepath=None, - valid_tools_only=True, - uncompress_file=False, - remove_repo_files_not_in_tar=False, - commit_message="Uploaded readme.txt.", - strings_displayed=[], - strings_not_displayed=[], - ) - - def test_0095_review_new_changeset_readme_component(self): - """Update the filtering repository's readme component review to reflect the presence of the readme file. - - We are at step 20. - There is now a new changeset revision in the repository's changelog, but it has no review associated with it. - Get the previously reviewed changeset hash, and pass that and the review id to the create_repository_review - method, in order to copy the previous review's contents. Then update the new review to reflect the presence of - a readme file. - """ - self.login(email=common.test_user_2_email, username=common.test_user_2_name) - repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name) - user = self.test_db_util.get_user(common.test_user_2_email) - # Get the last changeset revision that has a review associated with it. - last_review = self.get_last_reviewed_revision_by_user(user, repository) - if last_review is None: - raise AssertionError("Previous review expected, none found.") - # The create_repository_review method takes a dict( component label=review contents ). - # If review_contents is empty, it marks that component as not applicable. The review - # contents dict should have the structure: - # { - # rating: 1-5, - # comment: - # approved: yes/no - # private: yes/no - # } - review_contents_dict = { - "README": dict( - rating=5, - comment="Clear and concise readme file, a true pleasure to read.", - approved="yes", - private="no", - ) - } - self.create_repository_review( - repository, - review_contents_dict, - changeset_revision=self.get_repository_tip(repository), - copy_from=(str(last_review.changeset_revision), last_review.id), - ) - - def test_0100_verify_readme_review(self): - """Verify that the readme component review displays correctly. - - We are at step 21. - Log in as the repository owner (test_user_1) and check the repository component reviews to - verify that the readme component is now reviewed and approved. - """ - self.login(email=common.test_user_1_email, username=common.test_user_1_name) - repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name) - user = self.test_db_util.get_user(common.test_user_2_email) - strings_displayed = ["README", "yes", "Clear and concise readme file, a true pleasure to read."] - self.verify_repository_reviews(repository, reviewer=user, strings_displayed=strings_displayed) - - def test_0105_upload_test_data(self): - """Upload the missing test data to the filtering repository. - - We are at step 22. - Remain logged in as test_user_1 and upload test data to the repository. This will also create a - new changeset revision that needs to be reviewed. This will replace the changeset hash associated with - the last dowloadable revision, but the last repository review will still be associated with the - last dowloadable revision hash. - """ - repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name) - self.upload_file( - repository, - filename="filtering/filtering_test_data.tar", - filepath=None, - valid_tools_only=True, - uncompress_file=True, - remove_repo_files_not_in_tar=False, - commit_message="Uploaded filtering test data.", - strings_displayed=[], - strings_not_displayed=[], - ) - - def test_0110_review_new_changeset_functional_tests(self): - """Update the filtering repository's readme component review to reflect the presence of the readme file. - - We are at step 23. - Log in as test_user_2 and get the last reviewed changeset hash, and pass that and the review id to - the create_repository_review method, then update the copied review to approve the functional tests - component. - """ - self.login(email=common.test_user_2_email, username=common.test_user_2_name) - repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name) - user = self.test_db_util.get_user(common.test_user_2_email) - # Get the changeset immediately prior to the tip, and pass it to the create review method. - last_review = self.get_last_reviewed_revision_by_user(user, repository) - # The create_repository_review method takes a dict( component label=review contents ). - # If review_contents is empty, it marks that component as not applicable. The review - # contents dict should have the structure: - # { - # rating: 1-5, - # comment: - # approved: yes/no - # private: yes/no - # } - review_contents_dict = { - "Functional tests": dict(rating=5, comment="A good set of functional tests.", approved="yes", private="no") - } - self.create_repository_review( - repository, - review_contents_dict, - changeset_revision=self.get_repository_tip(repository), - copy_from=(str(last_review.changeset_revision), last_review.id), - ) - - def test_0115_verify_functional_tests_review(self): - """Verify that the functional tests component review displays correctly. - - We are at step 24. - Log in as the repository owner, test_user_1, and verify that the new revision's functional tests component - review has been updated with an approved status and favorable comment. - """ - self.login(email=common.test_user_1_email, username=common.test_user_1_name) - repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name) - user = self.test_db_util.get_user(common.test_user_2_email) - strings_displayed = ["Functional tests", "yes", "A good set of functional tests."] - self.verify_repository_reviews(repository, reviewer=user, strings_displayed=strings_displayed) - - def test_0120_upload_new_tool_version(self): - """Upload filtering 2.2.0 to the filtering repository. - - We are at step 25. - Log in as test_user_1 and upload a new version of the tool to the filtering repository. This will create - a new downloadable revision, with no associated repository component reviews. - """ - self.login(email=common.test_user_1_email, username=common.test_user_1_name) - repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name) - self.upload_file( - repository, - filename="filtering/filtering_2.2.0.tar", - filepath=None, - valid_tools_only=True, - uncompress_file=True, - remove_repo_files_not_in_tar=False, - commit_message="Uploaded filtering 2.2.0 tarball.", - strings_displayed=[], - strings_not_displayed=[], - ) - - def test_0125_review_new_changeset_functional_tests(self): - """Update the filtering repository's review to apply to the new changeset with filtering 2.2.0. - - We are at step 26. - Log in as test_user_2 and copy the last review for this repository to the new changeset. Then - update the tools component review to refer to the new tool version. - """ - self.login(email=common.test_user_2_email, username=common.test_user_2_name) - repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name) - user = self.test_db_util.get_user(common.test_user_2_email) - last_review = self.get_last_reviewed_revision_by_user(user, repository) - # Something needs to change so that the review will save. - # The create_repository_review method takes a dict( component label=review contents ). - # If review_contents is empty, it marks that component as not applicable. The review - # contents dict should have the structure: - # { - # rating: 1-5, - # comment: - # approved: yes/no - # private: yes/no - # } - review_contents_dict = { - "Tools": dict( - rating=5, - comment="Version 2.2.0 does the impossible and improves this tool.", - approved="yes", - private="yes", - ) - } - self.create_repository_review( - repository, - review_contents_dict, - changeset_revision=self.get_repository_tip(repository), - copy_from=(str(last_review.changeset_revision), last_review.id), - ) - - def test_0135_verify_review_for_new_version(self): - """Verify that the reviews display correctly for this changeset revision. - - We are at step 27. - Log in as test_user_1 and check that the tools component review is for filtering 2.2.0, but that the other component - reviews had their contents copied from the last reviewed changeset. - """ - self.login(email=common.test_user_1_email, username=common.test_user_1_name) - repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name) - user = self.test_db_util.get_user(common.test_user_2_email) - strings_displayed = [ - "Data types", - "Functional tests", - "yes", - "A good set of functional tests.", - "README", - "yes", - "Workflows", - "Tools", - ] - strings_displayed.extend( - ["Clear and concise readme file, a true pleasure to read.", "Tool dependencies", "not_applicable"] - ) - strings_displayed.extend( - ["Repository dependencies", "Version 2.2.0 does the impossible and improves this tool."] - ) - self.verify_repository_reviews(repository, reviewer=user, strings_displayed=strings_displayed) diff --git a/lib/tool_shed/test/functional/test_0410_repository_component_review_access_control.py b/lib/tool_shed/test/functional/test_0410_repository_component_review_access_control.py deleted file mode 100644 index fc6bfa418bc..00000000000 --- a/lib/tool_shed/test/functional/test_0410_repository_component_review_access_control.py +++ /dev/null @@ -1,246 +0,0 @@ -from ..base.twilltestcase import ( - common, - ShedTwillTestCase, -) - -repository_name = "filtering_0410" -repository_description = "Galaxy filtering tool for test 0410" -repository_long_description = "Long description of Galaxy filtering tool for test 0410" - -""" -1. Create a repository in the tool shed owned by test_user_1. -2. Have test_user_2 complete a review of the repository. -3. Have test_user_1 browse the review. -4. Have test_user_3 browse the repository and make sure they are not allowed to browse the review. -5. Have test_user_1 give write permission on the repository to the test_user_3. -6. Have test_user_3 browse the repository again and they should now have the ability to browse the review. -7. Have test_user_3 browse the review. -""" - - -class TestRepositoryComponentReviews(ShedTwillTestCase): - """Test repository component review features.""" - - def test_0000_initiate_users(self): - """Create necessary user accounts and login as an admin user. - - Create all the user accounts that are needed for this test script to run independently of other test. - Previously created accounts will not be re-created. - """ - self.login(email=common.test_user_1_email, username=common.test_user_1_name) - test_user_1 = self.test_db_util.get_user(common.test_user_1_email) - assert ( - test_user_1 is not None - ), f"Problem retrieving user with email {common.test_user_1_email} from the database" - self.test_db_util.get_private_role(test_user_1) - self.login(email=common.test_user_2_email, username=common.test_user_2_name) - test_user_2 = self.test_db_util.get_user(common.test_user_2_email) - assert ( - test_user_2 is not None - ), f"Problem retrieving user with email {common.test_user_2_email} from the database" - self.test_db_util.get_private_role(test_user_2) - self.login(email=common.test_user_3_email, username=common.test_user_3_name) - test_user_3 = self.test_db_util.get_user(common.test_user_3_email) - assert ( - test_user_3 is not None - ), f"Problem retrieving user with email {common.test_user_3_email} from the database" - self.test_db_util.get_private_role(test_user_3) - self.login(email=common.admin_email, username=common.admin_username) - admin_user = self.test_db_util.get_user(common.admin_email) - assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database" - self.test_db_util.get_private_role(admin_user) - - def test_0005_grant_reviewer_role(self): - """Grant the repository reviewer role to test_user_2. - - We now have an admin user (admin_user) and three non-admin users (test_user_1, test_user_2, and test_user_3). Grant the repository - reviewer role to test_user_2, who will not be the owner of the reviewed repositories, and do not grant any roles to test_user_3 yet. - """ - reviewer_role = self.test_db_util.get_role_by_name("Repository Reviewer") - test_user_2 = self.test_db_util.get_user(common.test_user_2_email) - self.grant_role_to_user(test_user_2, reviewer_role) - - def test_0010_verify_repository_review_components(self): - """Ensure that the required review components exist. - - Make sure all the components we are to review are recorded in the database. - """ - self.add_repository_review_component( - name="Repository dependencies", - description="Repository dependencies defined in a file named repository_dependencies.xml included in the repository", - ) - strings_displayed = [ - "Data types", - "Functional tests", - "README", - "Repository dependencies", - "Tool dependencies", - "Tools", - "Workflows", - ] - self.manage_review_components(strings_displayed=strings_displayed) - - def test_0015_create_repository(self): - """Create and populate the filtering repository - - We are at step 1. - Log in as test_user_1 and create the filtering repository, then upload a basic set of - components to be reviewed in subsequent tests. - """ - category = self.create_category( - name="Test 0400 Repository Component Reviews", description="Test 0400 Repository Component Reviews" - ) - self.login(email=common.test_user_1_email, username=common.test_user_1_name) - strings_displayed = self.expect_repo_created_strings(repository_name) - repository = self.get_or_create_repository( - name=repository_name, - description=repository_description, - long_description=repository_long_description, - owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), - strings_displayed=strings_displayed, - ) - self.upload_file( - repository, - filename="filtering/filtering_1.1.0.tar", - filepath=None, - valid_tools_only=True, - uncompress_file=True, - remove_repo_files_not_in_tar=False, - commit_message="Uploaded filtering 1.1.0 tarball.", - strings_displayed=[], - strings_not_displayed=[], - ) - self.upload_file( - repository, - filename="filtering/filtering_test_data.tar", - filepath=None, - valid_tools_only=True, - uncompress_file=True, - remove_repo_files_not_in_tar=False, - commit_message="Uploaded filtering test data.", - strings_displayed=[], - strings_not_displayed=[], - ) - self.upload_file( - repository, - filename="readme.txt", - filepath=None, - valid_tools_only=True, - uncompress_file=True, - remove_repo_files_not_in_tar=False, - commit_message="Uploaded readme.txt.", - strings_displayed=[], - strings_not_displayed=[], - ) - - def test_0020_review_repository(self): - """Complete a review of the filtering repository. - - We are at step 2 - Have test_user_2 complete a review of the repository. - Review all components of the filtering repository, with the appropriate contents and approved/not approved/not applicable status. - """ - self.login(email=common.test_user_2_email, username=common.test_user_2_name) - repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name) - review_contents_dict = { - "Data types": dict(), - "README": dict( - rating=5, - comment="Clear and concise readme file, a true pleasure to read.", - approved="yes", - private="no", - ), - "Functional tests": dict(rating=5, comment="A good set of functional tests.", approved="yes", private="no"), - "Repository dependencies": dict(), - "Tool dependencies": dict(), - "Tools": dict(rating=5, comment="Excellent tool, easy to use.", approved="yes", private="no"), - "Workflows": dict(), - } - self.create_repository_review(repository, review_contents_dict) - - def test_0025_verify_repository_review(self): - """Verify that the review was completed and displays properly. - - We are at step 3 - Have test_user_1 browse the review. - Verify that all the review components were submitted, and that the repository owner can see the review. - """ - self.login(email=common.test_user_1_email, username=common.test_user_1_name) - repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name) - user = self.test_db_util.get_user(common.test_user_2_email) - strings_displayed = [ - "Data types", - "Functional tests", - "yes", - "A good set of functional tests.", - "README", - "yes", - "Workflows", - "Tools", - ] - strings_displayed.extend( - ["Clear and concise readme file, a true pleasure to read.", "Tool dependencies", "not_applicable"] - ) - strings_displayed.extend(["Repository dependencies", "Excellent tool, easy to use."]) - strings_displayed = ["Browse reviews of this repository"] - self.display_manage_repository_page(repository, strings_displayed=strings_displayed) - self.verify_repository_reviews(repository, reviewer=user, strings_displayed=strings_displayed) - - def test_0030_browse_with_other_user(self): - """Verify that test_user_3 is blocked from browsing the review. - - We are at step 4 - Have test_user_3 browse the repository and make sure they are not allowed to browse the review. - """ - self.login(email=common.test_user_3_email, username=common.test_user_3_name) - repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name) - user = self.test_db_util.get_user(common.test_user_2_email) - strings_not_displayed = ["Browse reviews of this repository"] - self.display_manage_repository_page(repository, strings_not_displayed=strings_not_displayed) - strings_not_displayed = [ - "A good set of functional tests.", - "Clear and concise readme file, a true pleasure to read.", - ] - strings_not_displayed.append("Excellent tool, easy to use.") - changeset_revision = self.get_repository_tip(repository) - review = self.test_db_util.get_repository_review_by_user_id_changeset_revision( - user.id, repository.id, changeset_revision - ) - self.browse_component_review(review, strings_not_displayed=strings_not_displayed) - - def test_0035_grant_write_access_to_other_user(self): - """Grant write access on the filtering_0410 repository to test_user_3. - - We are at step 5 - Have test_user_1 give write permission on the repository to the test_user_3. - """ - self.login(email=common.test_user_1_email, username=common.test_user_1_name) - repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name) - self.grant_write_access(repository, usernames=[common.test_user_3_name]) - - def test_0040_verify_test_user_3_can_browse_reviews(self): - """Check that test_user_3 can now browse reviews. - - We are at step 6 - Have test_user_3 browse the repository again and they should now have the ability to browse the review. - """ - self.login(email=common.test_user_3_email, username=common.test_user_3_name) - repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name) - strings_displayed = ["Browse reviews of this repository"] - self.display_manage_repository_page(repository, strings_displayed=strings_displayed) - - def test_0045_verify_browse_review_with_write_access(self): - """Check that test_user_3 can now display reviews. - - We are at step 7 - Have test_user_3 browse the review. - """ - self.login(email=common.test_user_3_email, username=common.test_user_3_name) - repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name) - user = self.test_db_util.get_user(common.test_user_2_email) - strings_displayed = [ - "A good set of functional tests.", - "Clear and concise readme file", - "a true pleasure to read.", - "Excellent tool, easy to use.", - ] - changeset_revision = self.get_repository_tip(repository) - review = self.test_db_util.get_repository_review_by_user_id_changeset_revision( - user.id, repository.id, changeset_revision - ) - self.browse_component_review(review, strings_displayed=strings_displayed) diff --git a/lib/tool_shed/util/metadata_util.py b/lib/tool_shed/util/metadata_util.py index e6f77309836..629ee0ff0ae 100644 --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -272,27 +272,6 @@ def get_repository_metadata_by_repository_id_changeset_revision(app, id, changes return get_repository_metadata_by_changeset_revision(app, id, changeset_revision) -def get_repository_metadata_revisions_for_review(repository, reviewed=True): - repository_metadata_revisions = [] - metadata_changeset_revision_hashes = [] - if reviewed: - for metadata_revision in repository.metadata_revisions: - metadata_changeset_revision_hashes.append(metadata_revision.changeset_revision) - for review in repository.reviews: - if review.changeset_revision in metadata_changeset_revision_hashes: - rmcr_hashes = [rmr.changeset_revision for rmr in repository_metadata_revisions] - if review.changeset_revision not in rmcr_hashes: - repository_metadata_revisions.append(review.repository_metadata) - else: - for review in repository.reviews: - if review.changeset_revision not in metadata_changeset_revision_hashes: - metadata_changeset_revision_hashes.append(review.changeset_revision) - for metadata_revision in repository.metadata_revisions: - if metadata_revision.changeset_revision not in metadata_changeset_revision_hashes: - repository_metadata_revisions.append(metadata_revision) - return repository_metadata_revisions - - def get_updated_changeset_revisions(app, name, owner, changeset_revision): """ Return a string of comma-separated changeset revision hashes for all available updates to the received changeset diff --git a/lib/tool_shed/util/review_util.py b/lib/tool_shed/util/review_util.py deleted file mode 100644 index 7c745620aa7..00000000000 --- a/lib/tool_shed/util/review_util.py +++ /dev/null @@ -1,143 +0,0 @@ -import logging - -from sqlalchemy import and_ - -from tool_shed.util import hg_util - -log = logging.getLogger(__name__) - - -def can_browse_repository_reviews(app, user, repository): - """ - Determine if there are any reviews of the received repository for which the - current user has permission to browse any component reviews. - """ - if user: - for review in repository.reviews: - for component_review in review.component_reviews: - if app.security_agent.user_can_browse_component_review(app, repository, component_review, user): - return True - return False - - -def changeset_revision_reviewed_by_user(user, repository, changeset_revision): - """Determine if the current changeset revision has been reviewed by the current user.""" - for review in repository.reviews: - if review.changeset_revision == changeset_revision and review.user == user: - return True - return False - - -def get_component(app, id): - """Get a component from the database.""" - sa_session = app.model.session - return sa_session.query(app.model.Component).get(app.security.decode_id(id)) - - -def get_component_review(app, id): - """Get a component_review from the database""" - sa_session = app.model.session - return sa_session.query(app.model.ComponentReview).get(app.security.decode_id(id)) - - -def get_component_by_name(app, name): - """Get a component from the database via a name.""" - sa_session = app.model.session - return sa_session.query(app.model.Component).filter(app.model.Component.table.c.name == name).first() - - -def get_component_review_by_repository_review_id_component_id(app, repository_review_id, component_id): - """Get a component_review from the database via repository_review_id and component_id.""" - sa_session = app.model.session - return ( - sa_session.query(app.model.ComponentReview) - .filter( - and_( - app.model.ComponentReview.table.c.repository_review_id == app.security.decode_id(repository_review_id), - app.model.ComponentReview.table.c.component_id == app.security.decode_id(component_id), - ) - ) - .first() - ) - - -def get_components(app): - sa_session = app.model.session - return sa_session.query(app.model.Component).order_by(app.model.Component.name).all() - - -def get_previous_repository_reviews(app, repository, changeset_revision): - """ - Return an ordered dictionary of repository reviews up to and including the - received changeset revision. - """ - repo = repository.hg_repo - reviewed_revision_hashes = [review.changeset_revision for review in repository.reviews] - previous_reviews_dict = {} - for changeset in hg_util.reversed_upper_bounded_changelog(repo, changeset_revision): - previous_changeset_revision = str(repo[changeset]) - if previous_changeset_revision in reviewed_revision_hashes: - previous_rev, previous_changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( - repo, previous_changeset_revision - ) - revision_reviews = get_reviews_by_repository_id_changeset_revision( - app, app.security.encode_id(repository.id), previous_changeset_revision - ) - previous_reviews_dict[previous_changeset_revision] = dict( - changeset_revision_label=previous_changeset_revision_label, reviews=revision_reviews - ) - return previous_reviews_dict - - -def get_review(app, id): - """Get a repository_review from the database via id.""" - sa_session = app.model.session - return sa_session.query(app.model.RepositoryReview).get(app.security.decode_id(id)) - - -def get_review_by_repository_id_changeset_revision_user_id(app, repository_id, changeset_revision, user_id): - """ - Get a repository_review from the database via repository id, changeset_revision - and user_id. - """ - sa_session = app.model.session - return ( - sa_session.query(app.model.RepositoryReview) - .filter( - and_( - app.model.RepositoryReview.repository_id == app.security.decode_id(repository_id), - app.model.RepositoryReview.changeset_revision == changeset_revision, - app.model.RepositoryReview.user_id == app.security.decode_id(user_id), - ) - ) - .first() - ) - - -def get_reviews_by_repository_id_changeset_revision(app, repository_id, changeset_revision): - """Get all repository_reviews from the database via repository id and changeset_revision.""" - sa_session = app.model.session - return ( - sa_session.query(app.model.RepositoryReview) - .filter( - and_( - app.model.RepositoryReview.repository_id == app.security.decode_id(repository_id), - app.model.RepositoryReview.changeset_revision == changeset_revision, - ) - ) - .all() - ) - - -def has_previous_repository_reviews(app, repository, changeset_revision): - """ - Determine if a repository has a changeset revision review prior to the - received changeset revision. - """ - repo = repository.hg_repo - reviewed_revision_hashes = [review.changeset_revision for review in repository.reviews] - for changeset in hg_util.reversed_upper_bounded_changelog(repo, changeset_revision): - previous_changeset_revision = str(repo[changeset]) - if previous_changeset_revision in reviewed_revision_hashes: - return True - return False diff --git a/lib/tool_shed/util/shed_index.py b/lib/tool_shed/util/shed_index.py index e0229583d83..5c14db7e566 100644 --- a/lib/tool_shed/util/shed_index.py +++ b/lib/tool_shed/util/shed_index.py @@ -123,12 +123,6 @@ def get_repos(sa_session, file_path, hgweb_config_dir, **kwargs): user = sa_session.query(model.User).filter(model.User.id == repo.user_id).one() repo_owner_username = user.username.lower() - approved = "no" - for review in repo.reviews: - if review.approved == "yes": - approved = "yes" - break - last_updated = pretty_print_time_interval(repo.update_time) full_last_updated = repo.update_time.strftime("%Y-%m-%d %I:%M %p") @@ -165,7 +159,7 @@ def get_repos(sa_session, file_path, hgweb_config_dir, **kwargs): remote_repository_url=unicodify(remote_repository_url), repo_owner_username=unicodify(repo_owner_username), times_downloaded=unicodify(times_downloaded), - approved=unicodify(approved), + approved=unicodify("no"), last_updated=unicodify(last_updated), full_last_updated=unicodify(full_last_updated), tools_list=tools_list, diff --git a/lib/tool_shed/webapp/api/groups.py b/lib/tool_shed/webapp/api/groups.py index 82ecb5fb6ef..512b542979b 100644 --- a/lib/tool_shed/webapp/api/groups.py +++ b/lib/tool_shed/webapp/api/groups.py @@ -125,15 +125,7 @@ class GroupsController(BaseAPIController): time_repo_updated_full = repo.update_time.strftime("%Y-%m-%d %I:%M %p") time_repo_created = pretty_print_time_interval(repo.create_time, True) time_repo_updated = pretty_print_time_interval(repo.update_time, True) - approved = "" - ratings = [] - for review in repo.reviews: - if review.rating: - ratings.append(review.rating) - if review.approved == "yes": - approved = "yes" # TODO add user ratings - ratings_mean = str(float(sum(ratings)) / len(ratings)) if len(ratings) > 0 else "" total_downloads += repo.times_downloaded group_repos.append( { @@ -145,8 +137,6 @@ class GroupsController(BaseAPIController): "time_updated_full": time_repo_updated_full, "time_updated": time_repo_updated, "description": repo.description, - "approved": approved, - "ratings_mean": ratings_mean, "categories": categories, } ) diff --git a/lib/tool_shed/webapp/controllers/repository.py b/lib/tool_shed/webapp/controllers/repository.py index 314c4447de0..5846a8a6f6a 100644 --- a/lib/tool_shed/webapp/controllers/repository.py +++ b/lib/tool_shed/webapp/controllers/repository.py @@ -263,10 +263,6 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings): return trans.response.send_redirect( web.url_for(controller="repository", action="browse_repositories_by_user", **kwd) ) - elif operation == "reviewed_repositories_i_own": - return trans.response.send_redirect( - web.url_for(controller="repository_review", action="reviewed_repositories_i_own") - ) elif operation == "repositories_by_category": category_id = kwd.get("id", None) message = escape(kwd.get("message", "")) @@ -1632,14 +1628,8 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings): # TODO: move the following to some in-memory register so these queries can be done once # at startup. The in-memory register can then be managed during the current session. can_administer_repositories = False - has_reviewed_repositories = False has_deprecated_repositories = False if current_user: - # See if the current user owns any repositories that have been reviewed. - for repository in current_user.active_repositories: - if repository.reviews: - has_reviewed_repositories = True - break # See if the current user has any repositories that have been marked as deprecated. for repository in current_user.active_repositories: if repository.deprecated: @@ -1666,7 +1656,6 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings): "/webapps/tool_shed/index.mako", repository_metadata=repository_metadata, can_administer_repositories=can_administer_repositories, - has_reviewed_repositories=has_reviewed_repositories, has_deprecated_repositories=has_deprecated_repositories, user_id=user_id, repository_id=repository_id, @@ -1822,7 +1811,6 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings): description = kwd.get("description", repository.description) long_description = kwd.get("long_description", repository.long_description) avg_rating, num_ratings = self.get_ave_item_rating_data(trans.sa_session, repository, webapp_model=trans.model) - display_reviews = util.string_as_bool(kwd.get("display_reviews", False)) alerts = kwd.get("alerts", "") alerts_checked = CheckboxField.is_checked(alerts) category_ids = util.listify(kwd.get("category_id", "")) @@ -2016,7 +2004,6 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings): categories=categories, metadata=metadata, avg_rating=avg_rating, - display_reviews=display_reviews, num_ratings=num_ratings, alerts_check_box=alerts_check_box, malicious_check_box=malicious_check_box, @@ -2074,13 +2061,6 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings): status=status, ) - @web.expose - @require_login("review repository revision") - def manage_repository_reviews_of_revision(self, trans, **kwd): - return trans.response.send_redirect( - web.url_for(controller="repository_review", action="manage_repository_reviews_of_revision", **kwd) - ) - @web.expose @require_login("multi select email alerts") def multi_select_email_alerts(self, trans, **kwd): @@ -2268,7 +2248,6 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings): comment = kwd.get("comment", "") rating = self.rate_item(trans, trans.user, repository, rating, comment) avg_rating, num_ratings = self.get_ave_item_rating_data(trans.sa_session, repository, webapp_model=trans.model) - display_reviews = util.string_as_bool(kwd.get("display_reviews", False)) rra = self.get_user_item_rating(trans.sa_session, trans.user, repository, webapp_model=trans.model) metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans.app, id, changeset_revision, metadata_only=True @@ -2281,7 +2260,6 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings): metadata=metadata, revision_label=revision_label, avg_rating=avg_rating, - display_reviews=display_reviews, num_ratings=num_ratings, rra=rra, repository_type_select_field=repository_type_select_field, @@ -2763,7 +2741,6 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings): repository, changeset_revision=changeset_revision ) repository.clone_url = common_util.generate_clone_url_for_repository_in_tool_shed(trans.user, repository) - display_reviews = kwd.get("display_reviews", False) alerts = kwd.get("alerts", "") alerts_checked = CheckboxField.is_checked(alerts) if repository.email_alerts: @@ -2833,7 +2810,6 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings): metadata=metadata, containers_dict=containers_dict, avg_rating=avg_rating, - display_reviews=display_reviews, num_ratings=num_ratings, alerts_check_box=alerts_check_box, changeset_revision=changeset_revision, diff --git a/lib/tool_shed/webapp/controllers/repository_review.py b/lib/tool_shed/webapp/controllers/repository_review.py deleted file mode 100644 index 7338dc6b7bc..00000000000 --- a/lib/tool_shed/webapp/controllers/repository_review.py +++ /dev/null @@ -1,670 +0,0 @@ -import logging - -from sqlalchemy import ( - and_, - false, - func, -) - -import tool_shed.grids.repository_review_grids as repository_review_grids -import tool_shed.grids.util as grids_util -from galaxy import ( - util, - web, -) -from galaxy.web.form_builder import CheckboxField -from galaxy.webapps.base.controller import BaseUIController -from tool_shed.util import ( - hg_util, - metadata_util, - repository_util, - review_util, - shed_util_common as suc, -) -from tool_shed.util.container_util import STRSEP -from tool_shed.util.web_util import escape -from tool_shed.webapp.framework.decorators import require_login -from tool_shed.webapp.util import ratings_util - -log = logging.getLogger(__name__) - - -class RepositoryReviewController(BaseUIController, ratings_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_no_tool_tests_grid = repository_review_grids.RepositoriesWithNoToolTestsGrid() - - @web.expose - @require_login("approve repository review") - def approve_repository_review(self, trans, **kwd): - # The value of the received id is the encoded review id. - message = escape(kwd.get("message", "")) - status = kwd.get("status", "done") - encoded_review_id = kwd["id"] - review = review_util.get_review(trans.app, encoded_review_id) - if kwd.get("approve_repository_review_button", False): - approved_select_field_name = f"{encoded_review_id}{STRSEP}approved" - approved_select_field_value = str(kwd[approved_select_field_name]) - review.approved = approved_select_field_value - trans.sa_session.add(review) - trans.sa_session.flush() - message = f"Approved value {escape(approved_select_field_value)} saved for this revision." - repository_id = trans.security.encode_id(review.repository_id) - changeset_revision = review.changeset_revision - return trans.response.send_redirect( - web.url_for( - controller="repository_review", - action="manage_repository_reviews_of_revision", - id=repository_id, - changeset_revision=changeset_revision, - message=message, - status=status, - ) - ) - - @web.expose - @require_login("browse components") - def browse_components(self, trans, **kwd): - if "operation" in kwd: - operation = kwd["operation"].lower() - if operation == "create": - return trans.response.send_redirect( - web.url_for(controller="repository_review", action="create_component", **kwd) - ) - return self.component_grid(trans, **kwd) - - @web.expose - @require_login("browse review") - def browse_review(self, trans, **kwd): - message = escape(kwd.get("message", "")) - status = kwd.get("status", "done") - review = review_util.get_review(trans.app, kwd["id"]) - repository = review.repository - repo = repository.hg_repo - rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision(repo, review.changeset_revision) - return trans.fill_template( - "/webapps/tool_shed/repository_review/browse_review.mako", - repository=repository, - changeset_revision_label=changeset_revision_label, - review=review, - message=message, - status=status, - ) - - def copy_review(self, trans, review_to_copy, review): - for component_review in review_to_copy.component_reviews: - copied_component_review = trans.model.ComponentReview( - repository_review_id=review.id, - component_id=component_review.component.id, - comment=component_review.comment, - private=component_review.private, - approved=component_review.approved, - rating=component_review.rating, - ) - trans.sa_session.add(copied_component_review) - trans.sa_session.flush() - review.approved = review_to_copy.approved - review.rating = review_to_copy.rating - trans.sa_session.add(review) - trans.sa_session.flush() - - @web.expose - @require_login("create component") - def create_component(self, trans, **kwd): - message = escape(kwd.get("message", "")) - status = kwd.get("status", "done") - name = kwd.get("name", "") - description = kwd.get("description", "") - if kwd.get("create_component_button", False): - if not name or not description: - message = "Enter a valid name and a description" - status = "error" - elif review_util.get_component_by_name(trans.app, name): - message = "A component with that name already exists" - status = "error" - else: - component = trans.app.model.Component(name=name, description=description) - trans.sa_session.add(component) - trans.sa_session.flush() - message = f"Component '{escape(component.name)}' has been created" - status = "done" - trans.response.send_redirect( - web.url_for( - controller="repository_review", action="manage_components", message=message, status=status - ) - ) - return trans.fill_template( - "/webapps/tool_shed/repository_review/create_component.mako", - name=name, - description=description, - message=message, - status=status, - ) - - @web.expose - @require_login("create review") - def create_review(self, trans, **kwd): - # The value of the received id is the encoded repository id. - message = escape(kwd.get("message", "")) - status = kwd.get("status", "done") - repository_id = kwd.get("id", None) - changeset_revision = kwd.get("changeset_revision", None) - previous_review_id = kwd.get("previous_review_id", None) - create_without_copying = "create_without_copying" in kwd - if repository_id: - if changeset_revision: - # Make sure there is not already a review of the revision by the user. - repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id) - if review_util.get_review_by_repository_id_changeset_revision_user_id( - app=trans.app, - repository_id=repository_id, - changeset_revision=changeset_revision, - user_id=trans.security.encode_id(trans.user.id), - ): - message = f"You have already created a review for revision {changeset_revision} of repository {escape(repository.name)}." - status = "error" - else: - # See if there are any reviews for previous changeset revisions that the user can copy. - if ( - not create_without_copying - and not previous_review_id - and review_util.has_previous_repository_reviews(trans.app, repository, changeset_revision) - ): - return trans.response.send_redirect( - web.url_for(controller="repository_review", action="select_previous_review", **kwd) - ) - # A review can be initially performed only on an installable revision of a repository, so make sure we have metadata associated - # with the received changeset_revision. - repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( - trans.app, repository_id, changeset_revision - ) - if repository_metadata: - metadata = repository_metadata.metadata - if metadata: - review = trans.app.model.RepositoryReview( - repository_id=repository_metadata.repository_id, - changeset_revision=changeset_revision, - user_id=trans.user.id, - rating=None, - deleted=False, - ) - trans.sa_session.add(review) - trans.sa_session.flush() - if previous_review_id: - review_to_copy = review_util.get_review(trans.app, previous_review_id) - self.copy_review(trans, review_to_copy, review) - review_id = trans.security.encode_id(review.id) - message = f"Begin your review of revision {changeset_revision} of repository {repository.name}." - status = "done" - trans.response.send_redirect( - web.url_for( - controller="repository_review", - action="edit_review", - id=review_id, - message=message, - status=status, - ) - ) - else: - message = ( - "A new review cannot be created for revision %s of repository %s. Select a valid revision and try again." - % (changeset_revision, escape(repository.name)) - ) - kwd["message"] = message - kwd["status"] = "error" - else: - return trans.response.send_redirect( - web.url_for(controller="repository_review", action="manage_repository_reviews", **kwd) - ) - return trans.response.send_redirect( - web.url_for(controller="repository_review", action="view_or_manage_repository", **kwd) - ) - - @web.expose - @require_login("edit component") - def edit_component(self, trans, **kwd): - message = escape(kwd.get("message", "")) - status = kwd.get("status", "done") - id = kwd.get("id", None) - if not id: - message = "No component ids received for editing" - trans.response.send_redirect( - web.url_for(controller="admin", action="manage_categories", message=message, status="error") - ) - component = review_util.get_component(trans.app, id) - if kwd.get("edit_component_button", False): - new_description = kwd.get("description", "").strip() - if component.description != new_description: - component.description = new_description - trans.sa_session.add(component) - trans.sa_session.flush() - message = f"The information has been saved for the component named {escape(component.name)}" - status = "done" - return trans.response.send_redirect( - web.url_for( - controller="repository_review", action="manage_components", message=message, status=status - ) - ) - return trans.fill_template( - "/webapps/tool_shed/repository_review/edit_component.mako", - component=component, - message=message, - status=status, - ) - - @web.expose - @require_login("edit review") - def edit_review(self, trans, **kwd): - # The value of the received id is the encoded review id. - message = escape(kwd.get("message", "")) - status = kwd.get("status", "done") - review_id = kwd.get("id", None) - review = review_util.get_review(trans.app, review_id) - components_dict = {} - for component in review_util.get_components(trans.app): - components_dict[component.name] = dict(component=component, component_review=None) - repository = review.repository - repo = repository.hg_repo - for component_review in review.component_reviews: - if component_review and component_review.component: - component_name = component_review.component.name - if component_name in components_dict: - component_review_dict = components_dict[component_name] - component_review_dict["component_review"] = component_review - components_dict[component_name] = component_review_dict - # Handle a Save button click. - save_button_clicked = False - save_buttons = [f"{comp_name}{STRSEP}review_button" for comp_name in components_dict.keys()] - save_buttons.append("revision_approved_button") - for save_button in save_buttons: - if save_button in kwd: - save_button_clicked = True - break - if save_button_clicked: - # Handle the revision_approved_select_field value. - revision_approved = kwd.get("revision_approved", None) - revision_approved_setting_changed = False - if revision_approved: - revision_approved = str(revision_approved) - if review.approved != revision_approved: - revision_approved_setting_changed = True - review.approved = revision_approved - trans.sa_session.add(review) - trans.sa_session.flush() - saved_component_names = [] - for component_name in components_dict.keys(): - flushed = False - # Retrieve the review information from the form. - # The star rating form field is a radio button list, so it will not be received if it was not clicked in the form. - # Due to this behavior, default the value to 0. - rating = 0 - private = False - for k, v in kwd.items(): - if k.startswith(f"{component_name}{STRSEP}"): - component_review_attr = k.replace(f"{component_name}{STRSEP}", "") - if component_review_attr == "component_id": - component_id = str(v) - elif component_review_attr == "comment": - comment = str(v) - elif component_review_attr == "private": - private = CheckboxField.is_checked(v) - elif component_review_attr == "approved": - approved = str(v) - elif component_review_attr == "rating": - rating = int(str(v)) - component = review_util.get_component(trans.app, component_id) - component_review = review_util.get_component_review_by_repository_review_id_component_id( - trans.app, review_id, component_id - ) - if component_review: - # See if the existing component review should be updated. - if ( - component_review.comment != comment - or component_review.private != private - or component_review.approved != approved - or component_review.rating != rating - ): - component_review.comment = comment - component_review.private = private - component_review.approved = approved - component_review.rating = rating - trans.sa_session.add(component_review) - trans.sa_session.flush() - flushed = True - saved_component_names.append(component_name) - else: - # See if a new component_review should be created. - if comment or private or approved != trans.model.ComponentReview.approved_states.NO or rating: - component_review = trans.model.ComponentReview( - repository_review_id=review.id, - component_id=component.id, - comment=comment, - approved=approved, - rating=rating, - ) - trans.sa_session.add(component_review) - trans.sa_session.flush() - flushed = True - saved_component_names.append(component_name) - if flushed: - # Update the repository rating value to be the average of all component review ratings. - average_rating = ( - trans.sa_session.query(func.avg(trans.model.ComponentReview.table.c.rating)) - .filter( - and_( - trans.model.ComponentReview.table.c.repository_review_id == review.id, - trans.model.ComponentReview.table.c.deleted == false(), - trans.model.ComponentReview.table.c.approved - != trans.model.ComponentReview.approved_states.NA, - ) - ) - .scalar() - ) - if average_rating is not None: - review.rating = int(average_rating) - trans.sa_session.add(review) - trans.sa_session.flush() - # Update the information in components_dict. - if component_name in components_dict: - component_review_dict = components_dict[component_name] - component_review_dict["component_review"] = component_review - components_dict[component_name] = component_review_dict - if revision_approved_setting_changed: - message += f"Approved value {review.approved} saved for this revision.
" - if saved_component_names: - message += f"Reviews were saved for components: {', '.join(saved_component_names)}" - if not revision_approved_setting_changed and not saved_component_names: - message += "No changes were made to this review, so nothing was saved." - if review and review.approved: - selected_value = review.approved - else: - selected_value = trans.model.ComponentReview.approved_states.NO - revision_approved_select_field = grids_util.build_approved_select_field( - trans, name="revision_approved", selected_value=selected_value, for_component=False - ) - rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision(repo, review.changeset_revision) - return trans.fill_template( - "/webapps/tool_shed/repository_review/edit_review.mako", - repository=repository, - review=review, - changeset_revision_label=changeset_revision_label, - revision_approved_select_field=revision_approved_select_field, - components_dict=components_dict, - message=message, - status=status, - ) - - @web.expose - @require_login("manage components") - def manage_components(self, trans, **kwd): - if "operation" in kwd: - operation = kwd["operation"].lower() - if operation == "create": - return trans.response.send_redirect( - web.url_for(controller="repository_review", action="create_component", **kwd) - ) - elif operation == "edit": - return trans.response.send_redirect( - web.url_for(controller="repository_review", action="edit_component", **kwd) - ) - if "message" not in kwd: - message = "This is a list of repository components (features) that can be reviewed. You can add new components or change " - message += "the description of an existing component if appropriate. Click on the name link to change the description." - status = "warning" - kwd["message"] = message - kwd["status"] = status - return self.component_grid(trans, **kwd) - - @web.expose - @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 - @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. - if "operation" in kwd: - kwd["mine"] = True - return trans.response.send_redirect( - web.url_for(controller="repository_review", action="manage_repositories_with_reviews", **kwd) - ) - self.repositories_reviewed_by_me_grid.title = "Repositories reviewed by me" - return self.repositories_reviewed_by_me_grid(trans, **kwd) - - @web.expose - @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. Tests are defined as - invalid if they are missing from the tool config or if defined test data is not included in the repository. - """ - 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 missing functional tests or test data. " - kwd["message"] = message - kwd["status"] = "warning" - return self.repositories_with_no_tool_tests_grid(trans, **kwd) - - @web.expose - @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. - 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="manage_repository_reviews", **kwd) - ) - if operation == "view_or_manage_repository": - return trans.response.send_redirect( - web.url_for(controller="repository_review", action="view_or_manage_repository", **kwd) - ) - return self.repositories_with_reviews_grid(trans, **kwd) - - @web.expose - @require_login("manage repositories without reviews") - def manage_repositories_without_reviews(self, trans, **kwd): - 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) - ) - return self.repositories_without_reviews_grid(trans, **kwd) - - @web.expose - @require_login("manage repository reviews") - def manage_repository_reviews(self, trans, mine=False, **kwd): - # The value of the received id is the encoded repository id. - message = escape(kwd.get("message", "")) - status = kwd.get("status", "done") - repository_id = kwd.get("id", None) - if repository_id: - repository = suc.get_repository_in_tool_shed(trans.app, repository_id) - repo = repository.hg_repo - metadata_revision_hashes = [ - metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions - ] - reviewed_revision_hashes = [review.changeset_revision for review in repository.reviews] - reviews_dict = {} - for changeset in hg_util.get_reversed_changelog_changesets(repo): - changeset_revision = str(repo[changeset]) - if changeset_revision in metadata_revision_hashes or changeset_revision in reviewed_revision_hashes: - rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( - repo, changeset_revision - ) - if changeset_revision in reviewed_revision_hashes: - # Find the review for this changeset_revision - repository_reviews = review_util.get_reviews_by_repository_id_changeset_revision( - trans.app, repository_id, changeset_revision - ) - # Determine if the current user can add a review to this revision. - can_add_review = trans.user not in [ - repository_review.user for repository_review in repository_reviews - ] - repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( - trans.app, repository_id, changeset_revision - ) - if repository_metadata: - repository_metadata_reviews = util.listify(repository_metadata.reviews) - else: - repository_metadata_reviews = [] - else: - repository_reviews = [] - repository_metadata_reviews = [] - can_add_review = True - installable = changeset_revision in metadata_revision_hashes - revision_dict = dict( - changeset_revision_label=changeset_revision_label, - repository_reviews=repository_reviews, - repository_metadata_reviews=repository_metadata_reviews, - installable=installable, - can_add_review=can_add_review, - ) - reviews_dict[changeset_revision] = revision_dict - return trans.fill_template( - "/webapps/tool_shed/repository_review/reviews_of_repository.mako", - repository=repository, - reviews_dict=reviews_dict, - mine=mine, - message=message, - status=status, - ) - - @web.expose - @require_login("manage repository reviews of revision") - def manage_repository_reviews_of_revision(self, trans, **kwd): - # The value of the received id is the encoded repository id. - message = escape(kwd.get("message", "")) - status = kwd.get("status", "done") - repository_id = kwd.get("id", None) - changeset_revision = kwd.get("changeset_revision", None) - repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id) - repo = repository.hg_repo - installable = changeset_revision in [ - metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions - ] - rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision(repo, changeset_revision) - reviews = review_util.get_reviews_by_repository_id_changeset_revision( - trans.app, repository_id, changeset_revision - ) - return trans.fill_template( - "/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako", - repository=repository, - changeset_revision=changeset_revision, - changeset_revision_label=changeset_revision_label, - reviews=reviews, - installable=installable, - message=message, - status=status, - ) - - @web.expose - @require_login("repository reviews by user") - def repository_reviews_by_user(self, trans, **kwd): - - if "operation" in kwd: - operation = kwd["operation"].lower() - # The value of the received id is the encoded review id. - review = review_util.get_review(trans.app, kwd["id"]) - repository = review.repository - kwd["id"] = trans.security.encode_id(repository.id) - if operation == "inspect repository revisions": - return trans.response.send_redirect( - web.url_for(controller="repository_review", action="manage_repository_reviews", **kwd) - ) - if operation == "view_or_manage_repository": - kwd["changeset_revision"] = review.changeset_revision - return trans.response.send_redirect( - web.url_for(controller="repository_review", action="view_or_manage_repository", **kwd) - ) - # The user may not be the current user. The value of the received id is the encoded user id. - user = suc.get_user(trans.app, kwd["id"]) - self.repository_reviews_by_user_grid.title = f"All repository revision reviews for user '{user.username}'" - return self.repository_reviews_by_user_grid(trans, **kwd) - - @web.expose - @require_login("reviewed repositories i own") - def reviewed_repositories_i_own(self, trans, **kwd): - # The value of the received id is the encoded repository id. - 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="manage_repository_reviews", **kwd) - ) - if operation == "view_or_manage_repository": - return trans.response.send_redirect( - web.url_for(controller="repository_review", action="view_or_manage_repository", **kwd) - ) - return self.reviewed_repositories_i_own_grid(trans, **kwd) - - @web.expose - @require_login("select previous review") - def select_previous_review(self, trans, **kwd): - # The value of the received id is the encoded repository id. - message = escape(kwd.get("message", "")) - status = kwd.get("status", "done") - repository = repository_util.get_repository_in_tool_shed(trans.app, kwd["id"]) - changeset_revision = kwd.get("changeset_revision", None) - repo = repository.hg_repo - previous_reviews_dict = review_util.get_previous_repository_reviews(trans.app, repository, changeset_revision) - rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision(repo, changeset_revision) - return trans.fill_template( - "/webapps/tool_shed/repository_review/select_previous_review.mako", - repository=repository, - changeset_revision=changeset_revision, - changeset_revision_label=changeset_revision_label, - previous_reviews_dict=previous_reviews_dict, - message=message, - status=status, - ) - - @web.expose - @require_login("view or manage repository") - def view_or_manage_repository(self, trans, **kwd): - repository = repository_util.get_repository_in_tool_shed(trans.app, kwd["id"]) - if trans.user_is_admin or repository.user == trans.user: - return trans.response.send_redirect(web.url_for(controller="repository", action="manage_repository", **kwd)) - else: - return trans.response.send_redirect(web.url_for(controller="repository", action="view_repository", **kwd)) diff --git a/lib/tool_shed/webapp/model/__init__.py b/lib/tool_shed/webapp/model/__init__.py index 810665b404b..d246f373e0a 100644 --- a/lib/tool_shed/webapp/model/__init__.py +++ b/lib/tool_shed/webapp/model/__init__.py @@ -20,7 +20,6 @@ from sqlalchemy import ( Column, DateTime, desc, - false, ForeignKey, Integer, not_, @@ -132,7 +131,6 @@ class User(Base, Dictifiable, _HasTable): & not_(Role.name == User.email) # type: ignore[has-type] ), ) - repository_reviews = relationship("RepositoryReview", back_populates="user") def __init__(self, email=None, password=None): self.email = email @@ -375,8 +373,6 @@ class Repository(Base, Dictifiable, _HasTable): back_populates="repository", ) roles = relationship("RepositoryRoleAssociation", back_populates="repository") - reviews = relationship("RepositoryReview", back_populates="repository") - reviewers = relationship("User", secondary=lambda: RepositoryReview.__table__, viewonly=True) # type: ignore dict_collection_visible_keys = [ "id", @@ -541,114 +537,6 @@ class Repository(Base, Dictifiable, _HasTable): return rval -class RepositoryReview(Base, Dictifiable, _HasTable): - __tablename__ = "repository_review" - - id = Column(Integer, primary_key=True) - create_time = Column(DateTime, default=now) - update_time = Column(DateTime, default=now, onupdate=now) - repository_id = Column(ForeignKey("repository.id"), index=True) - changeset_revision = Column(TrimmedString(255), index=True) - user_id = Column(ForeignKey("galaxy_user.id"), index=True, nullable=False) - approved = Column(TrimmedString(255)) - rating = Column(Integer, index=True) - deleted = Column(Boolean, index=True, default=False) - repository = relationship("Repository", back_populates="reviews") - # Take care when using the mapper below! It should be used only when a new review is being created for a repository change set revision. - # Keep in mind that repository_metadata records can be removed from the database for certain change set revisions when metadata is being - # reset on a repository! - repository_metadata = relationship( - "RepositoryMetadata", - viewonly=True, - foreign_keys=lambda: [RepositoryReview.repository_id, RepositoryReview.changeset_revision], - primaryjoin=lambda: ( - (RepositoryReview.repository_id == RepositoryMetadata.repository_id) # type: ignore[has-type] - & (RepositoryReview.changeset_revision == RepositoryMetadata.changeset_revision) # type: ignore[has-type] - ), - back_populates="reviews", - ) - user = relationship("User", back_populates="repository_reviews") - - component_reviews = relationship( - "ComponentReview", - viewonly=True, - primaryjoin=lambda: ( - (RepositoryReview.id == ComponentReview.repository_review_id) # type: ignore[has-type] - & (ComponentReview.deleted == false()) # type: ignore[has-type] - ), - back_populates="repository_review", - ) - - private_component_reviews = relationship( - "ComponentReview", - viewonly=True, - primaryjoin=lambda: ( - (RepositoryReview.id == ComponentReview.repository_review_id) # type: ignore[has-type] - & (ComponentReview.deleted == false()) # type: ignore[has-type] - & (ComponentReview.private == true()) # type: ignore[has-type] - ), - ) - - dict_collection_visible_keys = ["id", "repository_id", "changeset_revision", "user_id", "rating", "deleted"] - dict_element_visible_keys = ["id", "repository_id", "changeset_revision", "user_id", "rating", "deleted"] - approved_states = Bunch(NO="no", YES="yes") - - def __init__(self, deleted=False, **kwd): - super().__init__(**kwd) - self.deleted = deleted - - -class ComponentReview(Base, Dictifiable, _HasTable): - __tablename__ = "component_review" - - id = Column(Integer, primary_key=True) - create_time = Column(DateTime, default=now) - update_time = Column(DateTime, default=now, onupdate=now) - repository_review_id = Column(ForeignKey("repository_review.id"), index=True) - component_id = Column(ForeignKey("component.id"), index=True) - comment = Column(TEXT) - private = Column(Boolean, default=False) - approved = Column(TrimmedString(255)) - rating = Column(Integer) - deleted = Column(Boolean, index=True, default=False) - repository_review = relationship("RepositoryReview", back_populates="component_reviews") - component = relationship("Component") - - dict_collection_visible_keys = [ - "id", - "repository_review_id", - "component_id", - "private", - "approved", - "rating", - "deleted", - ] - dict_element_visible_keys = [ - "id", - "repository_review_id", - "component_id", - "private", - "approved", - "rating", - "deleted", - ] - approved_states = Bunch(NO="no", YES="yes", NA="not_applicable") - - def __init__(self, private=False, approved=False, deleted=False, **kwd): - super().__init__(**kwd) - self.private = private - self.approved = approved - self.deleted = deleted - - -class Component(Base, _HasTable): - __tablename__ = "component" - - id = Column(Integer, primary_key=True) - name = Column(TrimmedString(255)) - description = Column(TEXT) - - class ItemRatingAssociation(_HasTable): def __init__(self, id=None, user=None, item=None, rating=0, comment=""): self.id = id @@ -841,23 +729,13 @@ class RepositoryMetadata(Dictifiable, _HasTable): # After the map_imperatively statement has been executed, the members of the -# properties dictionary (repository, reviews) will be available as instrumented +# properties dictionary (repository) will be available as instrumented # class attributes on RepositoryMetadata. mapper_registry.map_imperatively( RepositoryMetadata, RepositoryMetadata.table, properties=dict( repository=relationship(Repository, back_populates="metadata_revisions"), - reviews=relationship( - RepositoryReview, - viewonly=True, - foreign_keys=lambda: [RepositoryReview.repository_id, RepositoryReview.changeset_revision], - primaryjoin=lambda: ( - (RepositoryReview.repository_id == RepositoryMetadata.repository_id) - & (RepositoryReview.changeset_revision == RepositoryMetadata.changeset_revision) - ), - back_populates="repository_metadata", - ), ), ) diff --git a/lib/tool_shed/webapp/security/__init__.py b/lib/tool_shed/webapp/security/__init__.py index bd6c12acb82..29c15a7a57e 100644 --- a/lib/tool_shed/webapp/security/__init__.py +++ b/lib/tool_shed/webapp/security/__init__.py @@ -164,18 +164,6 @@ class CommunityRBACAgent(RBACAgent): return None return role - def get_repository_reviewer_role(self): - return ( - self.sa_session.query(self.model.Role) - .filter( - and_( - self.model.Role.table.c.name == "Repository Reviewer", - self.model.Role.table.c.type == self.model.Role.types.SYSTEM, - ) - ) - .first() - ) - def set_entity_group_associations(self, groups=None, users=None, roles=None, delete_existing_assocs=True): if groups is None: groups = [] @@ -283,26 +271,6 @@ class CommunityRBACAgent(RBACAgent): return True return False - def user_can_review_repositories(self, user): - if user: - roles = user.all_roles() - if roles: - repository_reviewer_role = self.get_repository_reviewer_role() - if repository_reviewer_role: - return repository_reviewer_role in roles - return False - - def user_can_browse_component_review(self, app, repository, component_review, user): - if component_review and user: - if self.can_push(app, user, repository): - # A user with write permission on the repository can access private/public component reviews. - return True - else: - if self.user_can_review_repositories(user): - # Reviewers can access private/public component reviews. - return True - return False - def get_permitted_actions(filter=None): """Utility method to return a subset of RBACAgent's permitted actions""" diff --git a/lib/tool_shed/webapp/templates/webapps/tool_shed/admin/index.mako b/lib/tool_shed/webapp/templates/webapps/tool_shed/admin/index.mako index b60ba1af1c1..fdd53b539f9 100644 --- a/lib/tool_shed/webapp/templates/webapps/tool_shed/admin/index.mako +++ b/lib/tool_shed/webapp/templates/webapps/tool_shed/admin/index.mako @@ -31,7 +31,6 @@ <%def name="left_panel()"> - <% can_review_repositories = trans.app.security_agent.user_can_review_repositories( trans.user ) %>
Administration
diff --git a/lib/tool_shed/webapp/templates/webapps/tool_shed/common/common.mako b/lib/tool_shed/webapp/templates/webapps/tool_shed/common/common.mako index 37b90a5b303..c1d43f10ea8 100644 --- a/lib/tool_shed/webapp/templates/webapps/tool_shed/common/common.mako +++ b/lib/tool_shed/webapp/templates/webapps/tool_shed/common/common.mako @@ -152,19 +152,3 @@ ${heads_str} - -<%def name="render_review_comment( comment_text )"> - - - -
${comment_text}
- diff --git a/lib/tool_shed/webapp/templates/webapps/tool_shed/common/repository_actions_menu.mako b/lib/tool_shed/webapp/templates/webapps/tool_shed/common/repository_actions_menu.mako index 008e9103a55..41c545eadb9 100644 --- a/lib/tool_shed/webapp/templates/webapps/tool_shed/common/repository_actions_menu.mako +++ b/lib/tool_shed/webapp/templates/webapps/tool_shed/common/repository_actions_menu.mako @@ -2,7 +2,6 @@ <%def name="render_tool_shed_repository_actions( repository, metadata=None, changeset_revision=None )"> <% - from tool_shed.util.review_util import can_browse_repository_reviews, changeset_revision_reviewed_by_user, get_review_by_repository_id_changeset_revision_user_id from tool_shed.util.metadata_util import is_malicious if repository.metadata_revisions: @@ -34,11 +33,6 @@ can_browse_contents = not is_new - if can_browse_repository_reviews( trans.app, trans.user, repository ): - can_browse_reviews = True - else: - can_browse_reviews = False - if trans.user and trans.user != repository.user: can_contact_owner = True else: @@ -73,28 +67,6 @@ can_rate = True else: can_rate = False - - if metadata is not None and changeset_revision is not None: - if has_metadata and not is_deprecated and trans.app.security_agent.user_can_review_repositories( trans.user ): - can_review_repository = True - else: - can_review_repository = False - if changeset_revision_reviewed_by_user( trans.user, repository, changeset_revision ): - reviewed_by_user = True - else: - reviewed_by_user = False - else: - can_review_repository = False - reviewed_by_user = False - - if reviewed_by_user: - review = get_review_by_repository_id_changeset_revision_user_id( app=trans.app, - repository_id=trans.security.encode_id( repository.id ), - changeset_revision=changeset_revision, - user_id=trans.security.encode_id( trans.user.id ) ) - review_id = trans.security.encode_id( review.id ) - else: - review_id = None if not is_new and not is_deprecated: can_set_metadata = True @@ -134,16 +106,6 @@ %else:
  • Repository Actions
    • - %if can_review_repository: - %if reviewed_by_user: - Manage my review of this revision - %else: - Add a review to this revision - %endif - %endif - %if can_browse_reviews: - Browse reviews of this repository - %endif %if can_upload: Upload files to repository %endif diff --git a/lib/tool_shed/webapp/templates/webapps/tool_shed/index.mako b/lib/tool_shed/webapp/templates/webapps/tool_shed/index.mako index ca554f96684..7b3d776af14 100644 --- a/lib/tool_shed/webapp/templates/webapps/tool_shed/index.mako +++ b/lib/tool_shed/webapp/templates/webapps/tool_shed/index.mako @@ -28,7 +28,6 @@ <%def name="left_panel()"> - <% can_review_repositories = trans.app.security_agent.user_can_review_repositories( trans.user ) %>
    ${trans.app.shed_counter.unique_valid_tools | h} valid tools on ${util.unicodify( trans.app.shed_counter.generation_time ) | h}
    @@ -93,11 +92,6 @@ Repositories I can administer
    %endif - %if has_reviewed_repositories: -
    - Reviewed repositories I own -
    - %endif %if has_deprecated_repositories:
    Deprecated repositories I own @@ -128,59 +122,6 @@ Create Galaxy Docker Image
    %endif - %if can_review_repositories: -
    -
    - Reviewing Repositories -
    -
    -
    -
    - Repositories ready for review -
    -
    - All repositories with no reviews -
    - %if trans.user.repository_reviews: -
    - Repositories reviewed by me -
    - %endif -
    - All reviewed repositories -
    -
    - Manage review components -
    -
    -
    -
    -
    - Reviewing Repositories With Tools -
    -
    -
    -
    - Latest revision: missing tool tests -
    -
    - Latest revision: installation errors -
    -
    - Latest revision: failing tool tests -
    -
    - Latest revision: skip tool tests -
    -
    - Latest revision: all tool tests pass -
    -
    - Latest revision: invalid tools -
    -
    -
    - %endif %else:
    diff --git a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/manage_repository.mako b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/manage_repository.mako index 66e19e6c2b6..5a9db98b8f2 100644 --- a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/manage_repository.mako +++ b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/manage_repository.mako @@ -38,11 +38,6 @@ else: can_download = False - if has_metadata and not is_deprecated and trans.app.security_agent.user_can_review_repositories( trans.user ): - can_review_repository = True - else: - can_review_repository = False - if not is_new and not is_deprecated: can_set_metadata = True else: @@ -132,11 +127,7 @@ ${render_tool_shed_repository_actions( repository, metadata=metadata, changeset_
    ${render_select(changeset_revision_select_field)} ${tip_str}
    - %if can_review_repository: - Select a revision to inspect for adding or managing a review or for download or installation. - %else: - Select a revision to inspect for download or installation. - %endif + Select a revision to inspect for download or installation.
    @@ -343,47 +334,6 @@ ${render_repository_items( metadata, containers_dict, can_set_metadata=True, ren

    -

    -
    - %if display_reviews: -
    - -
    -
    -
    - - - - - - - - - - <% count = 0 %> - %for review in repository.ratings: - <% - count += 1 - name = 'rating%d' % count - %> - - - - - - - %endfor -
    RatingCommentsReviewedUser
    ${render_star_rating( name, review.rating, disabled=True )}${render_review_comment( to_html_string( review.comment ) )}${time_ago( review.update_time )}${review.user.username | h}
    -
    -
    - %else: -
    - -
    -
    - %endif -
    -
    %endif

    %if can_set_malicious: diff --git a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/rate_repository.mako b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/rate_repository.mako index 72e49ca9535..925531628e7 100644 --- a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/rate_repository.mako +++ b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/rate_repository.mako @@ -92,19 +92,6 @@ ${render_tool_shed_repository_actions( repository, metadata=None, changeset_revi ${render_star_rating( 'rating', rating )}

    -
    - - %if rra and rra.comment: -
    -
    -
    - %else: -
    - -
    - %endif -
    -
    @@ -112,42 +99,4 @@ ${render_tool_shed_repository_actions( repository, metadata=None, changeset_revi

    - %if repository.ratings and ( len( repository.ratings ) > 1 or repository.ratings[0] != rra ): -

    -
    - %if display_reviews: -
    - -
    - - - - - - - - - - <% count = 0 %> - %for review in repository.ratings: - <% - count += 1 - name = 'rating%d' % count - %> - - - - - - - %endfor -
    RatingCommentsReviewedUser
    ${render_star_rating( name, review.rating, disabled=True )}
    ${review.comment | h}
    		${time_ago( review.update_time )}${review.user.username | h}
    - %else: -
    - -
    - %endif -
    -
    - %endif %endif diff --git a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/view_repository.mako b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/view_repository.mako index d07644ff0fa..9bcdda09f40 100644 --- a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/view_repository.mako +++ b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/view_repository.mako @@ -230,47 +230,5 @@ ${render_repository_items( metadata, containers_dict, can_set_metadata=False, re -

    -

    -
    - %if display_reviews: -
    - -
    -
    -
    - - - - - - - - - - <% count = 0 %> - %for review in repository.ratings: - <% - count += 1 - name = 'rating%d' % count - %> - - - - - - - %endfor -
    RatingCommentsReviewedUser
    ${render_star_rating( name, review.rating, disabled=True )}${render_review_comment( to_html_string( review.comment ) )}${time_ago( review.update_time )}${review.user.username}
    -
    -
    - %else: -
    - -
    -
    - %endif -
    -
    %endif

    diff --git a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository_review/browse_review.mako b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository_review/browse_review.mako deleted file mode 100644 index c338d56bb3a..00000000000 --- a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository_review/browse_review.mako +++ /dev/null @@ -1,118 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/webapps/tool_shed/common/common.mako" import="*" /> -<%namespace file="/webapps/tool_shed/common/repository_actions_menu.mako" import="render_tool_shed_repository_actions" /> - -<% - from galaxy.web.form_builder import CheckboxField - from tool_shed.util.container_util import STRSEP - from tool_shed.util.basic_util import to_html_string -%> - -<%def name="stylesheets()"> - ${h.css('base')} - - -<%def name="javascripts()"> - ${parent.javascripts()} - - -${render_tool_shed_repository_actions( repository=repository, changeset_revision=review.changeset_revision )} - -%if message: - ${render_msg( message, status )} -%endif - -

    -
    Review of repository '${repository.name | h}'
    -
    -
    - - ${review.user.username} -
    -
    -
    - - ${changeset_revision_label} -
    -
    -
    - - ${repository.user.username | h} -
    -
    -
    - - ${repository.description | h} -
    -
    -
    - %if review.component_reviews: - - %for component_review in review.component_reviews: - <% - can_browse = trans.app.security_agent.user_can_browse_component_review( trans.app, repository, component_review, trans.user ) - component = component_review.component - if can_browse: - # Initialize Private check box. - private_check_box_name = '%s%sprivate' % ( component.name, STRSEP ) - private_check_box = CheckboxField( name=private_check_box_name, value=component_review.private ) - - # Initialize star rating. - rating_name = '%s%srating' % ( component.name, STRSEP ) - %> - - - - - - - - %endfor -
    ${component.name | h}${component.description | h}
    - %if can_browse: - - - - - %if component_review.comment: - - - - %endif - - - - - - -
    - - ${render_checkbox(private_check_box, disabled=True)} -
    - A private review can be accessed only by the owner of the repository and authorized repository reviewers. -
    -
    -
    -
    - ${ to_html_string( component_review.comment ) } -
    -
    - - ${component_review.approved | h} -
    -
    - - ${render_star_rating( rating_name, component_review.rating, disabled=True )} -
    -
    - %else: - You are not authorized to access the review of this component since it has been marked private. - %endif -
    - %else: - This review has not yet been started. - %endif -
    -
    -
    diff --git a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository_review/create_component.mako b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository_review/create_component.mako deleted file mode 100644 index 263998921fd..00000000000 --- a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository_review/create_component.mako +++ /dev/null @@ -1,34 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -<%def name="javascripts()"> - ${parent.javascripts()} - - - -%if message: - ${render_msg( message, status )} -%endif - -
    -
    Create Component
    -
    -
    -
    - - -
    -
    - - -
    -
    - -
    -
    -
    -
    diff --git a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository_review/edit_component.mako b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository_review/edit_component.mako deleted file mode 100644 index 483f4024551..00000000000 --- a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository_review/edit_component.mako +++ /dev/null @@ -1,37 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -%if message: - ${render_msg( message, status )} -%endif - -
    -
    Change component description
    -
    -
    -
    - -
    - ${component.name | h} -
    -
    -
    -
    - -
    - -
    -
    -
    -
    -
    - -
    -
    -
    -
    - -
    -
    -
    -
    diff --git a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository_review/edit_review.mako b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository_review/edit_review.mako deleted file mode 100644 index 3734130b30c..00000000000 --- a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository_review/edit_review.mako +++ /dev/null @@ -1,162 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/webapps/tool_shed/common/common.mako" import="*" /> -<%namespace file="/webapps/tool_shed/common/repository_actions_menu.mako" import="render_tool_shed_repository_actions" /> - -<% - from galaxy.web.form_builder import CheckboxField - from tool_shed.grids.util import build_approved_select_field - from tool_shed.util.container_util import STRSEP -%> - -<%def name="stylesheets()"> - ${h.css('base')} - - -<%def name="javascripts()"> - ${parent.javascripts()} - - -${render_tool_shed_repository_actions( repository=repository, changeset_revision=review.changeset_revision )} - -%if message: - ${render_msg( message, status )} -%endif - -
    -
    My review of repository '${repository.name | h}'
    -
    -
    -
    - - ${changeset_revision_label} -
    -
    -
    - - ${repository.user.username | h} -
    -
    -
    - - ${repository.description | h} -
    -
    -
    - - ${render_select(revision_approved_select_field)} -
    - Individual components below may be approved without approving the repository revision. -
    -
    -
    -
    - -
    - All changes made on this page will be saved when any Save button is clicked. -
    -
    -
    -
    - - %for component_name, component_review_dict in components_dict.items(): - <% - component = component_review_dict[ 'component' ] - encoded_component_id = trans.security.encode_id( component.id ) - - component_review = component_review_dict[ 'component_review' ] - if component_review: - comment = component_review.comment or '' - rating = component_review.rating - approved_select_field_selected_value = component_review.approved - private = component_review.private - else: - comment = '' - rating = 0 - approved_select_field_selected_value = None - private = False - - # Initialize Approved select field. - approved_select_field_name = '%s%sapproved' % ( component_name, STRSEP ) - approved_select_field = build_approved_select_field( trans, name=approved_select_field_name, selected_value=approved_select_field_selected_value, for_component=True ) - - # Initialize Private check box. - private_check_box_name = '%s%sprivate' % ( component_name, STRSEP ) - private_check_box = CheckboxField( name=private_check_box_name, value=private ) - - # Initialize star rating. - rating_name = '%s%srating' % ( component_name, STRSEP ) - - # Initialize comment text area. - comment_name = '%s%scomment' % ( component_name, STRSEP ) - - # Initialize the component id form field name. - component_id_name = '%s%scomponent_id' % ( component_name, STRSEP ) - - # Initialize the Save button. - review_button_name = '%s%sreview_button' % ( component_name, STRSEP ) - %> - - - - - - - - %endfor -
    ${component.name | h}${component.description | h}
    - - - - - - - - - - - - - - - - -
    - - ${render_checkbox(private_check_box)} -
    - A private review can be accessed only by the owner of the repository and authorized repository reviewers. -
    -
    -
    - - %if component_review: -
    - %else: - - %endif -
    -
    - - ${render_select(approved_select_field)} -
    -
    - - ${render_star_rating( rating_name, rating )} -
    -
    - Rate this component only - the average of all component ratings defines the value of the repository rating. -
    -
    - - -
    -
    - All changes made on this page will be saved when any Save button is clicked. -
    -
    -
    -
    -
    -
    -
    diff --git a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository_review/grid.mako b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository_review/grid.mako deleted file mode 100644 index 2e645fe5a2e..00000000000 --- a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository_review/grid.mako +++ /dev/null @@ -1 +0,0 @@ -<%inherit file="/legacy/grid_base.mako"/> diff --git a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako deleted file mode 100644 index 54554e06797..00000000000 --- a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako +++ /dev/null @@ -1,112 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/webapps/tool_shed/common/common.mako" import="*" /> -<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" /> -<%namespace file="/webapps/tool_shed/common/repository_actions_menu.mako" import="render_tool_shed_repository_actions" /> - -<% - from tool_shed.grids.util import build_approved_select_field - from tool_shed.util.container_util import STRSEP - - if installable: - installable_str = 'yes' - else: - installable_str = 'no' - can_review_repositories = trans.app.security_agent.user_can_review_repositories( trans.user ) -%> - -<%! - def inherit(context): - if context.get('use_panels'): - return '/webapps/tool_shed/base_panels.mako' - else: - return '/base.mako' -%> -<%inherit file="${inherit(context)}"/> - -<%def name="stylesheets()"> - ${h.css('base')} - - -<%def name="javascripts()"> - ${parent.javascripts()} - ${common_javascripts(repository)} - - -${render_tool_shed_repository_actions( repository=repository, changeset_revision=changeset_revision )} - -%if message: - ${render_msg( message, status )} -%endif - -
    -
    Revision reviews of repository '${repository.name | h}'
    -
    -
    - - ${changeset_revision_label} -
    -
    -
    - - ${installable_str | h} -
    -
    -
    - %if reviews: - - - - - - - - %for review in reviews: - <% - encoded_review_id = trans.security.encode_id( review.id ) - approved_select_field_name = '%s%sapproved' % ( encoded_review_id, STRSEP ) - approved_select_field_selected_value = review.approved - approved_select_field = build_approved_select_field( trans, name=approved_select_field_name, selected_value=approved_select_field_selected_value, for_component=False ) - if review.approved not in [ None, 'None', 'none' ]: - approved_str = review.approved - else: - approved_str = '' - repository_rating_name = '%srepository_rating' % encoded_review_id - %> - - - - %if review.user == trans.user: - - - - - %else: - - - %endif - - %endfor -
    ReviewerRepository ratingApproved
    - -
    - %if review.user == trans.user: - Edit my review - %else: - Browse this review - %endif -
    -     		${render_star_rating( repository_rating_name, review.rating, disabled=True )}
    ${render_select(approved_select_field)}${approved_str | h}
    - %else: - - %if can_review_repositories: - Add a review to this revision -
    - %endif - %endif -
    -
    -
    -
    diff --git a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository_review/reviews_of_repository.mako b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository_review/reviews_of_repository.mako deleted file mode 100644 index 1116d16e64a..00000000000 --- a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository_review/reviews_of_repository.mako +++ /dev/null @@ -1,87 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/webapps/tool_shed/common/common.mako" import="*" /> -<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" /> -<%namespace file="/webapps/tool_shed/common/repository_actions_menu.mako" import="render_tool_shed_repository_actions" /> - -<% - if mine: - title = "My reviews of repository '%s'" % repository.name - else: - title = "All reviews of repository '%s'" % repository.name -%> - -<%! - def inherit(context): - if context.get('use_panels'): - return '/webapps/tool_shed/base_panels.mako' - else: - return '/base.mako' -%> -<%inherit file="${inherit(context)}"/> - -<%def name="javascripts()"> - ${parent.javascripts()} - ${common_javascripts(repository)} - - -${render_tool_shed_repository_actions( repository=repository )} - -%if message: - ${render_msg( message, status )} -%endif - -
    -
    ${title | h}
    -
    -
    - - - - - - - %for changeset_revision, revision_dict in reviews_dict.items(): - <% - changeset_revision_label = revision_dict[ 'changeset_revision_label' ] - repository_reviews = revision_dict[ 'repository_reviews' ] - repository_metadata_reviews = revision_dict[ 'repository_metadata_reviews' ] - reviewers_str = '' - if repository_reviews: - for repository_review in repository_reviews: - reviewers_str += '%s' % ( trans.security.encode_id( repository_review.id ), repository_review.user.username ) - reviewers_str += ' | ' - reviewers_str = reviewers_str.rstrip( '| ' ) - if revision_dict[ 'installable' ]: - installable_str = 'yes' - else: - installable_str = '' - can_add_review = revision_dict[ 'can_add_review' ] - %> - - - - - - %endfor -
    RevisionReviewersInstallable
    - -
    - %if repository_reviews: - Browse reviews of this revision - %elif can_add_review: - Add a review to this revision - %endif -
    -     		${reviewers_str}${installable_str | h}
    -
    -
    -
    -
    diff --git a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository_review/select_previous_review.mako b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository_review/select_previous_review.mako deleted file mode 100644 index 56383b51afe..00000000000 --- a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository_review/select_previous_review.mako +++ /dev/null @@ -1,89 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/webapps/tool_shed/common/common.mako" import="*" /> -<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" /> -<%namespace file="/webapps/tool_shed/common/repository_actions_menu.mako" import="render_tool_shed_repository_actions" /> - -<%! - def inherit(context): - if context.get('use_panels'): - return '/webapps/tool_shed/base_panels.mako' - else: - return '/base.mako' -%> -<%inherit file="${inherit(context)}"/> - -<%def name="stylesheets()"> - ${h.css('base')} - - -<%def name="javascripts()"> - ${parent.javascripts()} - ${common_javascripts(repository)} - - -${render_tool_shed_repository_actions( repository=repository )} - -%if message: - ${render_msg( message, status )} -%endif - -
    - You have elected to create a new review for revision ${changeset_revision_label}of this repository. Since previous revisions have been reviewed, - you can select a previous review to copy to your new review, or click the Create a review without copying button. -
    - -
    -
    Select previous revision review of repository '${repository.name | h}'
    -
    -
    - - ${changeset_revision_label} -
    -
    -
    - - - - - - - - - - - %for previous_changeset_revision, previous_changeset_revision_dict in previous_reviews_dict.items(): - <% - previous_changeset_revision_label = previous_changeset_revision_dict[ 'changeset_revision_label' ] - previous_reviews = previous_changeset_revision_dict[ 'reviews' ] - %> - %for review in previous_reviews: - <% - encoded_review_id = trans.security.encode_id( review.id ) - if review.approved not in [ None, 'None', 'none' ]: - approved_str = review.approved - else: - approved_str = '' - repository_rating_name = '%srepository_rating' % encoded_review_id - %> - - - - - - - %endfor - %endfor -
    Previous revision reviews of repository '${repository.name | h}' that can be copied to your new review
    ReviewerRevision reviewedRepository ratingApproved
    - - - ${previous_changeset_revision_label}${render_star_rating( repository_rating_name, review.rating, disabled=True )}${approved_str | h}
    -
    -
    - Create a review without copying -
    -
    diff --git a/test/unit/shed_unit/model/test_mapping.py b/test/unit/shed_unit/model/test_mapping.py index 3100bbeb940..85713806c46 100644 --- a/test/unit/shed_unit/model/test_mapping.py +++ b/test/unit/shed_unit/model/test_mapping.py @@ -94,69 +94,6 @@ class TestCategory(BaseTest): assert stored_obj.repositories == [repository_category_association] -class TestComponent(BaseTest): - def test_table(self, cls_): - assert cls_.__tablename__ == "component" - - def test_columns(self, session, cls_): - name, description = "a", "b" - obj = cls_(name=name, description=description) - - with dbcleanup(session, obj) as obj_id: - stored_obj = get_stored_obj(session, cls_, obj_id) - assert stored_obj.id == obj_id - assert stored_obj.name == name - assert stored_obj.description == description - - -class TestComponentReview(BaseTest): - def test_table(self, cls_): - assert cls_.__tablename__ == "component_review" - - def test_columns(self, session, cls_, repository_review, component): - create_time = datetime.now() - update_time = create_time + timedelta(hours=1) - comment = "a" - private = True - approved = "b" - rating = 1 - deleted = True - - obj = cls_() - obj.create_time = create_time - obj.update_time = update_time - obj.repository_review = repository_review - obj.component = component - obj.comment = comment - obj.private = private - obj.approved = approved - obj.rating = rating - obj.deleted = deleted - - with dbcleanup(session, obj) as obj_id: - stored_obj = get_stored_obj(session, cls_, obj_id) - assert stored_obj.id == obj_id - assert stored_obj.create_time == create_time - assert stored_obj.update_time == update_time - assert stored_obj.repository_review_id == repository_review.id - assert stored_obj.component_id == component.id - assert stored_obj.comment == comment - assert stored_obj.private == private - assert stored_obj.approved == approved - assert stored_obj.rating == rating - assert stored_obj.deleted == deleted - - def test_relationships(self, session, cls_, repository_review, component): - obj = cls_() - obj.repository_review = repository_review - obj.component = component - - with dbcleanup(session, obj) as obj_id: - stored_obj = get_stored_obj(session, cls_, obj_id) - assert stored_obj.repository_review.id == repository_review.id - assert stored_obj.component.id == component.id - - class TestGalaxySession(BaseTest): def test_table(self, cls_): assert cls_.__tablename__ == "galaxy_session" @@ -364,9 +301,7 @@ class TestRepository(BaseTest): repository_rating_association, repository_metadata_factory, repository_role_association, - repository_review_factory, user, - user_factory, ): obj = cls_() obj.user = user @@ -374,16 +309,6 @@ class TestRepository(BaseTest): obj.ratings.append(repository_rating_association) obj.roles.append(repository_role_association) - reviewer1 = user_factory() - review1 = repository_review_factory() - review1.user = reviewer1 - review1.repository = obj - - reviewer2 = user_factory() - review2 = repository_review_factory() - review2.user = reviewer2 - review2.repository = obj - metadata1 = repository_metadata_factory() metadata1.repository = obj metadata1.downloadable = False @@ -400,12 +325,10 @@ class TestRepository(BaseTest): assert stored_obj.categories == [repository_category_association] assert stored_obj.ratings == [repository_rating_association] assert stored_obj.roles == [repository_role_association] - assert collection_consists_of_objects(stored_obj.reviews, review1, review2) - assert collection_consists_of_objects(stored_obj.reviewers, reviewer1, reviewer2) assert collection_consists_of_objects(stored_obj.metadata_revisions, metadata1, metadata2) assert stored_obj.downloadable_revisions == [metadata2] - delete_from_database(session, [reviewer1, reviewer2, review1, review2, metadata1, metadata2]) + delete_from_database(session, [metadata1, metadata2]) class TestRepositoryCategoryAssociation(BaseTest): @@ -491,7 +414,6 @@ class TestRepositoryMetadata(BaseTest): session, cls_, repository, - repository_review_factory, user, ): @@ -499,38 +421,6 @@ class TestRepositoryMetadata(BaseTest): obj.repository = repository obj.changeset_revision = "nonempty" - # create 3 reviews - review1 = repository_review_factory() - review2 = repository_review_factory() - review3 = repository_review_factory() - - # set the same user for all reviews - review1.user = user - review2.user = user - review3.user = user - - # set the same repository for all reviews - review1.repository = obj.repository - review2.repository = obj.repository - review3.repository = obj.repository - - # set the same changeset for reviews 1,2 - review1.changeset_revision = obj.changeset_revision - review2.changeset_revision = obj.changeset_revision - review3.changeset_revision = "something else" # this won't be in reviews for this metadata - - # add to session - session.add(review1) - session.add(review2) - session.add(review3) - - with dbcleanup(session, obj) as obj_id: - stored_obj = get_stored_obj(session, cls_, obj_id) - assert stored_obj.repository.id == repository.id - assert collection_consists_of_objects(stored_obj.reviews, review1, review2) - - delete_from_database(session, [review1, review2, review3]) - class TestRepositoryRatingAssociation(BaseTest): def test_table(self, cls_): @@ -571,106 +461,6 @@ class TestRepositoryRatingAssociation(BaseTest): assert stored_obj.user.id == user.id -class TestRepositoryReview(BaseTest): - def test_table(self, cls_): - assert cls_.__tablename__ == "repository_review" - - def test_columns(self, session, cls_, repository, user): - create_time = datetime.now() - update_time = create_time + timedelta(hours=1) - changeset_revision = "a" - approved = "b" - rating = 1 - deleted = True - - obj = cls_() - obj.create_time = create_time - obj.update_time = update_time - obj.repository = repository - obj.changeset_revision = changeset_revision - obj.user = user - obj.approved = approved - obj.rating = rating - obj.deleted = deleted - - with dbcleanup(session, obj) as obj_id: - stored_obj = get_stored_obj(session, cls_, obj_id) - assert stored_obj.id == obj_id - assert stored_obj.create_time == create_time - assert stored_obj.update_time == update_time - assert stored_obj.repository_id == repository.id - assert stored_obj.changeset_revision == changeset_revision - assert stored_obj.user_id == user.id - assert stored_obj.approved == approved - assert stored_obj.rating == rating - assert stored_obj.deleted == deleted - - def test_relationships( - self, session, cls_, repository, user, repository_metadata_factory, component_review_factory - ): - obj = cls_() - changeset = "nonempty" - obj.changeset_revision = changeset - obj.repository = repository - obj.user = user - - metadata1 = repository_metadata_factory() - metadata2 = repository_metadata_factory() - metadata1.repository = repository - metadata2.repository = repository - metadata1.changeset_revision = changeset - metadata2.changeset_revision = "something else" - - component_review1 = component_review_factory() - component_review1.repository_review = obj - component_review1.deleted = False - - component_review2 = component_review_factory() - component_review2.repository_review = obj - component_review2.deleted = False - component_review2.private = True - - session.add_all([metadata1, metadata2, component_review1, component_review2]) - - with dbcleanup(session, obj) as obj_id: - stored_obj = get_stored_obj(session, cls_, obj_id) - assert stored_obj.repository.id == repository.id - assert stored_obj.user.id == user.id - assert stored_obj.repository_metadata == metadata1 - assert collection_consists_of_objects(stored_obj.component_reviews, component_review1, component_review2) - assert stored_obj.private_component_reviews == [component_review2] - - delete_from_database(session, [component_review1, component_review2, metadata1, metadata2]) - - -class TestRepositoryRoleAssociation(BaseTest): - def test_table(self, cls_): - assert cls_.__tablename__ == "repository_role_association" - - def test_columns(self, session, cls_, repository, role): - create_time = datetime.now() - update_time = create_time + timedelta(hours=1) - obj = cls_(repository, role) - obj.create_time = create_time - obj.update_time = update_time - - with dbcleanup(session, obj) as obj_id: - stored_obj = get_stored_obj(session, cls_, obj_id) - assert stored_obj.id == obj_id - assert stored_obj.repository_id == repository.id - assert stored_obj.role_id == role.id - assert stored_obj.create_time == create_time - assert stored_obj.update_time == update_time - - def test_relationships(self, session, cls_, repository, role): - obj = cls_(repository, role) - - with dbcleanup(session, obj) as obj_id: - stored_obj = get_stored_obj(session, cls_, obj_id) - assert stored_obj.repository.id == repository.id - assert stored_obj.role.id == role.id - - class TestRole(BaseTest): def test_table(self, cls_): assert cls_.__tablename__ == "role" @@ -808,7 +598,6 @@ class TestUser(BaseTest): repository, galaxy_session, api_keys, - repository_review, role, group, password_reset_token, @@ -825,7 +614,6 @@ class TestUser(BaseTest): obj.api_keys.append(api_keys) obj.reset_tokens.append(password_reset_token) obj.groups.append(user_group_association) - obj.repository_reviews.append(repository_review) _private_role = role_factory(name=obj.email) private_user_role = user_role_association_factory(obj, _private_role) @@ -842,7 +630,6 @@ class TestUser(BaseTest): assert stored_obj.api_keys == [api_keys] assert stored_obj.reset_tokens == [password_reset_token] assert stored_obj.groups == [user_group_association] - assert stored_obj.repository_reviews == [repository_review] assert collection_consists_of_objects(stored_obj.roles, private_user_role, non_private_user_role) assert stored_obj.non_private_roles == [non_private_user_role] @@ -948,12 +735,6 @@ def category(model, session): yield from dbcleanup_wrapper(session, instance) -@pytest.fixture -def component(model, session): - instance = model.Component() - yield from dbcleanup_wrapper(session, instance) - - @pytest.fixture def galaxy_session(model, session): instance = model.GalaxySession(session_key=get_unique_value()) @@ -992,13 +773,6 @@ def repository_metadata(model, session): yield from dbcleanup_wrapper(session, instance) -@pytest.fixture -def repository_review(model, session, user): - instance = model.RepositoryReview() - instance.user = user - yield from dbcleanup_wrapper(session, instance) - - @pytest.fixture def repository_category_association(model, session, repository, category): instance = model.RepositoryCategoryAssociation(repository, category) @@ -1044,14 +818,6 @@ def user_role_association(model, session, user, role): # Fixtures yielding factory functions. -@pytest.fixture -def component_review_factory(model): - def make_instance(*args, **kwds): - return model.ComponentReview(*args, **kwds) - - return make_instance - - @pytest.fixture def group_role_association_factory(model): def make_instance(*args, **kwds): @@ -1068,14 +834,6 @@ def repository_metadata_factory(model): return make_instance -@pytest.fixture -def repository_review_factory(model): - def make_instance(*args, **kwds): - return model.RepositoryReview(*args, **kwds) - - return make_instance - - @pytest.fixture def role_factory(model): def make_instance(*args, **kwds):