Source code for tool_shed.grids.repository_review_grids

import logging

from markupsafe import escape
from sqlalchemy import (
    and_,
    false,
    null,
    or_,
    true,
)

from galaxy.web.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__)


[docs]class ComponentGrid(grids.Grid):
[docs]    class NameColumn(grids.TextColumn):
[docs]        def get_value(self, trans, grid, component):
            return escape(component.name)

[docs]    class DescriptionColumn(grids.TextColumn):
[docs]        def get_value(self, trans, grid, component):
            return escape(component.description)

    title = "Repository review components"
    model_class = model.Component
    template = "/webapps/tool_shed/repository_review/grid.mako"
    default_sort_key = "name"
    use_hide_message = False
    columns = [
        NameColumn(
            "Name", key="Component.name", link=(lambda item: dict(operation="edit", id=item.id)), attach_popup=False
        ),
        DescriptionColumn("Description", key="Component.description", attach_popup=False),
    ]
    global_actions = [
        grids.GridAction(
            "Add new component", dict(controller="repository_review", action="manage_components", operation="create")
        )
    ]
    num_rows_per_page = 50


[docs]class RepositoriesWithReviewsGrid(RepositoryGrid):
    # This grid filters out repositories that have been marked as either deprecated or deleted.

[docs]    class WithReviewsRevisionColumn(grids.GridColumn):
[docs]        def get_value(self, trans, grid, repository):
            # Restrict to revisions that have been reviewed.
            if repository.reviews:
                rval = ""
                repo = 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 += (
                        '<a href="manage_repository_reviews_of_revision?id=%s&changeset_revision=%s">%s</a><br/>'
                        % (trans.security.encode_id(repository.id), changeset_revision, label)
                    )
                return rval
            return ""

[docs]    class WithoutReviewsRevisionColumn(grids.GridColumn):
[docs]        def get_value(self, trans, grid, repository):
            # Restrict the options to revisions that have not yet been reviewed.
            repository_metadata_revisions = metadata_util.get_repository_metadata_revisions_for_review(
                repository, reviewed=False
            )
            if repository_metadata_revisions:
                rval = ""
                for repository_metadata in repository_metadata_revisions:
                    rev, label, changeset_revision = hg_util.get_rev_label_changeset_revision_from_repository_metadata(
                        trans.app, repository_metadata, repository=repository, include_date=True, include_hash=False
                    )
                    rval += (
                        '<a href="manage_repository_reviews_of_revision?id=%s&changeset_revision=%s">%s</a><br/>'
                        % (trans.security.encode_id(repository.id), changeset_revision, label)
                    )
                return rval
            return ""

[docs]    class ReviewersColumn(grids.TextColumn):
[docs]        def get_value(self, trans, grid, repository):
            rval = ""
            if repository.reviewers:
                for user in repository.reviewers:
                    rval += f'<a class="view-info" href="repository_reviews_by_user?id={trans.security.encode_id(user.id)}">'
                    rval += f"{user.username}</a> | "
                if rval[-3:] == " | ":
                    rval = rval[:-3]
            return rval

[docs]    class RatingColumn(grids.TextColumn):
[docs]        def get_value(self, trans, grid, repository):
            rval = ""
            for review in repository.reviews:
                if review.rating:
                    for index in range(1, 6):
                        rval += "<input "
                        rval += f'name="star1-{trans.security.encode_id(review.id)}" '
                        rval += 'type="radio" '
                        rval += 'class="community_rating_star star" '
                        rval += 'disabled="disabled" '
                        rval += f'value="{str(review.rating)}" '
                        if review.rating > (index - 0.5) and review.rating < (index + 0.5):
                            rval += 'checked="checked" '
                        rval += "/>"
                rval += "<br/>"
            return rval

[docs]    class ApprovedColumn(grids.TextColumn):
[docs]        def get_value(self, trans, grid, repository):
            rval = ""
            for review in repository.reviews:
                if review.approved:
                    rval += f"{review.approved}<br/>"
            return rval

    title = "All reviewed repositories"
    model_class = model.Repository
    template = "/webapps/tool_shed/repository_review/grid.mako"
    default_sort_key = "Repository.name"
    columns = [
        RepositoryGrid.NameColumn(
            "Repository name",
            key="name",
            link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
            attach_popup=True,
        ),
        RepositoryGrid.UserColumn("Owner", model_class=model.User, attach_popup=False, key="User.username"),
        WithReviewsRevisionColumn("Reviewed revisions"),
        ReviewersColumn("Reviewers", attach_popup=False),
        RatingColumn("Rating", attach_popup=False),
        ApprovedColumn("Approved", attach_popup=False),
    ]
    columns.append(
        grids.MulticolFilterColumn(
            "Search repository name",
            cols_to_filter=[columns[0]],
            key="free-text-search",
            visible=False,
            filterable="standard",
        )
    )
    operations = [
        grids.GridOperation(
            "Inspect repository revisions",
            allow_multiple=False,
            condition=(lambda item: not item.deleted),
            async_compatible=False,
        )
    ]

[docs]    def build_initial_query(self, trans, **kwd):
        return (
            trans.sa_session.query(model.Repository)
            .filter(and_(model.Repository.table.c.deleted == false(), model.Repository.table.c.deprecated == false()))
            .join(
                (
                    model.RepositoryReview.table,
                    model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id,
                )
            )
            .join((model.User.table, model.User.table.c.id == model.Repository.table.c.user_id))
            .outerjoin(
                (
                    model.ComponentReview.table,
                    model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id,
                )
            )
            .outerjoin(
                (model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id)
            )
        )


[docs]class RepositoriesWithoutReviewsGrid(RepositoriesWithReviewsGrid):
    # This grid filters out repositories that have been marked as either deprecated or deleted.
    title = "Repositories with no reviews"
    columns = [
        RepositoriesWithReviewsGrid.NameColumn(
            "Repository name",
            key="name",
            link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
            attach_popup=True,
        ),
        RepositoriesWithReviewsGrid.DescriptionColumn("Synopsis", key="description", attach_popup=False),
        RepositoriesWithReviewsGrid.WithoutReviewsRevisionColumn("Revisions for review"),
        RepositoriesWithReviewsGrid.UserColumn(
            "Owner", model_class=model.User, attach_popup=False, key="User.username"
        ),
    ]
    columns.append(
        grids.MulticolFilterColumn(
            "Search repository name, description",
            cols_to_filter=[columns[0], columns[1]],
            key="free-text-search",
            visible=False,
            filterable="standard",
        )
    )
    operations = [
        grids.GridOperation(
            "Inspect repository revisions",
            allow_multiple=False,
            condition=(lambda item: not item.deleted),
            async_compatible=False,
        )
    ]

[docs]    def build_initial_query(self, trans, **kwd):
        return (
            trans.sa_session.query(model.Repository)
            .filter(
                and_(
                    model.Repository.table.c.deleted == false(),
                    model.Repository.table.c.deprecated == false(),
                    model.Repository.reviews == null(),
                )
            )
            .join(model.User.table)
        )


[docs]class RepositoriesReadyForReviewGrid(RepositoriesWithoutReviewsGrid):
    # Repositories that are ready for human review are those that either:
    # 1) Have no tools
    # 2) Have tools that have been proven to be functionally correct within Galaxy.
    # This grid filters out repositories that have been marked as either deprecated or deleted.
    title = "Repositories ready for review"
    columns = [
        RepositoriesWithoutReviewsGrid.NameColumn(
            "Repository name",
            key="name",
            link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
            attach_popup=True,
        ),
        RepositoriesWithoutReviewsGrid.DescriptionColumn("Synopsis", key="description", attach_popup=False),
        RepositoriesWithoutReviewsGrid.WithoutReviewsRevisionColumn("Revisions for review"),
        RepositoriesWithoutReviewsGrid.UserColumn(
            "Owner", model_class=model.User, attach_popup=False, key="User.username"
        ),
    ]
    columns.append(
        grids.MulticolFilterColumn(
            "Search repository name, description",
            cols_to_filter=[columns[0], columns[1]],
            key="free-text-search",
            visible=False,
            filterable="standard",
        )
    )
    operations = [
        grids.GridOperation(
            "Inspect repository revisions",
            allow_multiple=False,
            condition=(lambda item: not item.deleted),
            async_compatible=False,
        )
    ]

[docs]    def build_initial_query(self, trans, **kwd):
        return (
            trans.sa_session.query(model.Repository)
            .filter(
                and_(
                    model.Repository.table.c.deleted == false(),
                    model.Repository.table.c.deprecated == false(),
                    model.Repository.reviews == null(),
                )
            )
            .join(model.RepositoryMetadata.table)
            .filter(
                and_(
                    model.RepositoryMetadata.table.c.downloadable == true(),
                    or_(
                        model.RepositoryMetadata.table.c.includes_tools == false(),
                        and_(
                            model.RepositoryMetadata.table.c.includes_tools == true(),
                            model.RepositoryMetadata.table.c.tools_functionally_correct == true(),
                        ),
                    ),
                )
            )
            .join(model.User.table)
        )


[docs]class RepositoriesReviewedByMeGrid(RepositoriesWithReviewsGrid):
    # This grid filters out repositories that have been marked as either deprecated or deleted.

    columns = [
        RepositoriesWithReviewsGrid.NameColumn(
            "Repository name",
            key="name",
            link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
            attach_popup=True,
        ),
        RepositoriesWithReviewsGrid.UserColumn("Owner", attach_popup=False),
        RepositoriesWithReviewsGrid.WithReviewsRevisionColumn("Reviewed revisions"),
        RepositoriesWithReviewsGrid.ReviewersColumn("Reviewers", attach_popup=False),
        RepositoriesWithReviewsGrid.RatingColumn("Rating", attach_popup=False),
        RepositoriesWithReviewsGrid.ApprovedColumn("Approved", attach_popup=False),
    ]
    columns.append(
        grids.MulticolFilterColumn(
            "Search repository name",
            cols_to_filter=[columns[0]],
            key="free-text-search",
            visible=False,
            filterable="standard",
        )
    )

[docs]    def build_initial_query(self, trans, **kwd):
        return (
            trans.sa_session.query(model.Repository)
            .filter(and_(model.Repository.table.c.deleted == false(), model.Repository.table.c.deprecated == false()))
            .join(
                (
                    model.RepositoryReview.table,
                    model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id,
                )
            )
            .filter(model.RepositoryReview.table.c.user_id == trans.user.id)
            .join((model.User.table, model.User.table.c.id == model.RepositoryReview.table.c.user_id))
            .outerjoin(
                (
                    model.ComponentReview.table,
                    model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id,
                )
            )
            .outerjoin(
                (model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id)
            )
        )


[docs]class RepositoryReviewsByUserGrid(grids.Grid):
    # This grid filters out repositories that have been marked as deprecated.

[docs]    class RepositoryNameColumn(grids.TextColumn):
[docs]        def get_value(self, trans, grid, review):
            return escape(review.repository.name)

[docs]    class RepositoryDescriptionColumn(grids.TextColumn):
[docs]        def get_value(self, trans, grid, review):
            return escape(review.repository.description)

[docs]    class RevisionColumn(grids.TextColumn):
[docs]        def get_value(self, trans, grid, review):
            encoded_review_id = trans.security.encode_id(review.id)
            rval = '<a class="action-button" href="'
            if review.user == trans.user:
                rval += "edit_review"
            else:
                rval += "browse_review"
            revision_label = hg_util.get_revision_label(
                trans.app, review.repository, review.changeset_revision, include_date=True, include_hash=False
            )
            rval += f'?id={encoded_review_id}">{revision_label}</a>'
            return rval

[docs]    class RatingColumn(grids.TextColumn):
[docs]        def get_value(self, trans, grid, review):
            if review.rating:
                for index in range(1, 6):
                    rval = "<input "
                    rval += f'name="star1-{trans.security.encode_id(review.id)}" '
                    rval += 'type="radio" '
                    rval += 'class="community_rating_star star" '
                    rval += 'disabled="disabled" '
                    rval += f'value="{str(review.rating)}" '
                    if review.rating > (index - 0.5) and review.rating < (index + 0.5):
                        rval += 'checked="checked" '
                    rval += "/>"
                return rval
            return ""

    title = "Reviews by user"
    model_class = model.RepositoryReview
    template = "/webapps/tool_shed/repository_review/grid.mako"
    default_sort_key = "repository_id"
    use_hide_message = False
    columns = [
        RepositoryNameColumn(
            "Repository Name",
            model_class=model.Repository,
            key="Repository.name",
            link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
            attach_popup=True,
        ),
        RepositoryDescriptionColumn(
            "Description", model_class=model.Repository, key="Repository.description", attach_popup=False
        ),
        RevisionColumn("Revision", attach_popup=False),
        RatingColumn("Rating", attach_popup=False),
    ]
    operations = [
        grids.GridOperation(
            "Inspect repository revisions",
            allow_multiple=False,
            condition=(lambda item: not item.deleted),
            async_compatible=False,
        )
    ]
    num_rows_per_page = 50

[docs]    def build_initial_query(self, trans, **kwd):
        user_id = trans.security.decode_id(kwd["id"])
        return (
            trans.sa_session.query(model.RepositoryReview)
            .filter(
                and_(
                    model.RepositoryReview.table.c.deleted == false(), model.RepositoryReview.table.c.user_id == user_id
                )
            )
            .join((model.Repository.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id))
            .filter(model.Repository.table.c.deprecated == false())
        )


[docs]class ReviewedRepositoriesIOwnGrid(RepositoriesWithReviewsGrid):
    title = "Reviewed repositories I own"
    columns = [
        RepositoriesWithReviewsGrid.NameColumn(
            "Repository name",
            key="name",
            link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
            attach_popup=True,
        ),
        RepositoriesWithReviewsGrid.WithReviewsRevisionColumn("Reviewed revisions"),
        RepositoriesWithReviewsGrid.WithoutReviewsRevisionColumn("Revisions for review"),
        RepositoriesWithReviewsGrid.ReviewersColumn("Reviewers", attach_popup=False),
        RepositoryGrid.DeprecatedColumn("Deprecated"),
    ]
    columns.append(
        grids.MulticolFilterColumn(
            "Search repository name",
            cols_to_filter=[columns[0]],
            key="free-text-search",
            visible=False,
            filterable="standard",
        )
    )
    operations = [
        grids.GridOperation(
            "Inspect repository revisions",
            allow_multiple=False,
            condition=(lambda item: not item.deleted),
            async_compatible=False,
        )
    ]

[docs]    def build_initial_query(self, trans, **kwd):
        return (
            trans.sa_session.query(model.Repository)
            .join(
                (
                    model.RepositoryReview.table,
                    model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id,
                )
            )
            .filter(model.Repository.table.c.user_id == trans.user.id)
            .join((model.User.table, model.User.table.c.id == model.RepositoryReview.table.c.user_id))
            .outerjoin(
                (
                    model.ComponentReview.table,
                    model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id,
                )
            )
            .outerjoin(
                (model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id)
            )
        )


[docs]class RepositoriesWithNoToolTestsGrid(RepositoriesWithoutReviewsGrid):
    # Repositories that are ready for human review are those that either:
    # 1) Have no tools
    # 2) Have tools that have been proven to be functionally correct within Galaxy.
    # This grid filters out repositories that have been marked as either deprecated or deleted.
    title = "Repositories that contain tools with no tests or test data"
    columns = [
        RepositoriesWithoutReviewsGrid.NameColumn(
            "Repository name",
            key="name",
            link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
            attach_popup=True,
        ),
        RepositoriesWithoutReviewsGrid.DescriptionColumn("Synopsis", key="description", attach_popup=False),
        RepositoriesWithoutReviewsGrid.WithoutReviewsRevisionColumn("Revisions for review"),
        RepositoriesWithoutReviewsGrid.UserColumn(
            "Owner", model_class=model.User, attach_popup=False, key="User.username"
        ),
    ]
    columns.append(
        grids.MulticolFilterColumn(
            "Search repository name, description",
            cols_to_filter=[columns[0], columns[1]],
            key="free-text-search",
            visible=False,
            filterable="standard",
        )
    )
    operations = [
        grids.GridOperation(
            "Inspect repository revisions",
            allow_multiple=False,
            condition=(lambda item: not item.deleted),
            async_compatible=False,
        )
    ]

[docs]    def build_initial_query(self, trans, **kwd):
        return (
            trans.sa_session.query(model.Repository)
            .filter(and_(model.Repository.table.c.deleted == false(), model.Repository.table.c.deprecated == false()))
            .join(model.RepositoryMetadata.table)
            .filter(
                and_(
                    model.RepositoryMetadata.table.c.downloadable == true(),
                    model.RepositoryMetadata.table.c.includes_tools == true(),
                    model.RepositoryMetadata.table.c.tools_functionally_correct == false(),
                )
            )
            .join(model.User.table)
        )