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Source code for tool_shed.grids.util

import logging

from galaxy.web.form_builder import SelectField
from tool_shed.util import hg_util, metadata_util

log = logging.getLogger(__name__)


[docs]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
[docs]def build_changeset_revision_select_field(trans, repository, selected_value=None, add_id_to_name=True, downloadable=False, reviewed=False, not_reviewed=False): """ Build a SelectField whose options are the changeset_rev strings of certain revisions of the received repository. """ options = [] changeset_tups = [] refresh_on_change_values = [] 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 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) changeset_tups.append((rev, label, changeset_revision)) refresh_on_change_values.append(changeset_revision) # Sort options by the revision label. Even though the downloadable_revisions query sorts by update_time, # the changeset revisions may not be sorted correctly because setting metadata over time will reset update_time. for changeset_tup in sorted(changeset_tups): # Display the latest revision first. options.insert(0, (changeset_tup[1], changeset_tup[2])) if add_id_to_name: name = 'changeset_revision_%d' % repository.id else: name = 'changeset_revision' select_field = SelectField(name=name, refresh_on_change=True, refresh_on_change_values=refresh_on_change_values) 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
[docs]def filter_by_latest_downloadable_changeset_revision_that_has_missing_tool_test_components(trans, repository): """ Inspect the latest downloadable changeset revision for the received repository to see if it includes tools that are either missing functional tests or functional test data. If the changset revision includes tools but is missing tool test components, return the changeset revision hash. This will filter out repositories of type repository_suite_definition and tool_dependency_definition. """ repository_metadata = get_latest_downloadable_repository_metadata_if_it_includes_tools(trans, repository) if repository_metadata is not None \ and repository_metadata.missing_test_components: return repository_metadata.changeset_revision return None
[docs]def filter_by_latest_metadata_changeset_revision_that_has_invalid_tools(trans, repository): """ Inspect the latest changeset revision with associated metadata for the received repository to see if it has invalid tools. This will filter out repositories of type repository_suite_definition and tool_dependency_definition. """ repository_metadata = get_latest_repository_metadata_if_it_includes_invalid_tools(trans, repository) if repository_metadata is not None: return repository_metadata.changeset_revision return None
[docs]def get_latest_downloadable_repository_metadata(trans, repository): """ Return the latest downloadable repository_metadata record for the received repository. This will return repositories of type unrestricted as well as types repository_suite_definition and tool_dependency_definition. """ encoded_repository_id = trans.security.encode_id(repository.id) repo = hg_util.get_repo_for_repository(trans.app, repository=repository, repo_path=None, create=False) tip_ctx = str(repo.changectx(repo.changelog.tip())) repository_metadata = None try: repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app, encoded_repository_id, tip_ctx) if repository_metadata is not None and repository_metadata.downloadable: return repository_metadata return None except: latest_downloadable_revision = metadata_util.get_previous_metadata_changeset_revision(repository, repo, tip_ctx, downloadable=True) if latest_downloadable_revision == hg_util.INITIAL_CHANGELOG_HASH: return None repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app, encoded_repository_id, latest_downloadable_revision) if repository_metadata is not None and repository_metadata.downloadable: return repository_metadata return None
[docs]def get_latest_downloadable_repository_metadata_if_it_includes_tools(trans, repository): """ Return the latest downloadable repository_metadata record for the received repository if its includes_tools attribute is True. This will filter out repositories of type repository_suite_definition and tool_dependency_definition. """ repository_metadata = get_latest_downloadable_repository_metadata(trans, repository) if repository_metadata is not None and repository_metadata.includes_tools: return repository_metadata return None
[docs]def get_latest_repository_metadata(trans, repository): """ Return the latest repository_metadata record for the received repository if it exists. This will return repositories of type unrestricted as well as types repository_suite_definition and tool_dependency_definition. """ encoded_repository_id = trans.security.encode_id(repository.id) repo = hg_util.get_repo_for_repository(trans.app, repository=repository, repo_path=None, create=False) tip_ctx = str(repo.changectx(repo.changelog.tip())) try: repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app, encoded_repository_id, tip_ctx) return repository_metadata except: latest_downloadable_revision = metadata_util.get_previous_metadata_changeset_revision(repository, repo, tip_ctx, downloadable=False) if latest_downloadable_revision == hg_util.INITIAL_CHANGELOG_HASH: return None repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app, encoded_repository_id, latest_downloadable_revision) return repository_metadata
[docs]def get_latest_repository_metadata_if_it_includes_invalid_tools(trans, repository): """ Return the latest repository_metadata record for the received repository that contains invalid tools if one exists. This will filter out repositories of type repository_suite_definition and tool_dependency_definition. """ repository_metadata = get_latest_repository_metadata(trans, repository) if repository_metadata is not None: metadata = repository_metadata.metadata if metadata is not None and 'invalid_tools' in metadata: return repository_metadata return None