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Source code for galaxy.workflow.reports.generators

"""Module containing Galaxy workflow report generator plugins.
"""
from abc import (
    ABCMeta,
    abstractmethod
)

from galaxy.managers import workflows
from galaxy.managers.markdown_util import (
    internal_galaxy_markdown_to_pdf,
    ready_galaxy_markdown_for_export,
    resolve_invocation_markdown,
)
from galaxy.schema import PdfDocumentType


[docs]class WorkflowReportGeneratorPlugin(metaclass=ABCMeta): """ """ @property @abstractmethod def plugin_type(self): """Short string labelling this plugin."""
[docs] @abstractmethod def generate_report_json(self, trans, invocation, runtime_report_config_json=None): """ """
[docs] @abstractmethod def generate_report_pdf(self, trans, invocation, runtime_report_config_json=None): """ """
[docs]class WorkflowMarkdownGeneratorPlugin(WorkflowReportGeneratorPlugin, metaclass=ABCMeta): """WorkflowReportGeneratorPlugin that generates markdown as base report."""
[docs] def generate_report_json(self, trans, invocation, runtime_report_config_json=None): """ """ workflow_manager = workflows.WorkflowsManager(trans.app) workflow_encoded_id = trans.app.security.encode_id(invocation.workflow_id) workflow = workflow_manager.get_stored_accessible_workflow(trans, workflow_encoded_id, by_stored_id=False) internal_markdown = self._generate_internal_markdown(trans, invocation, runtime_report_config_json=runtime_report_config_json) export_markdown, extra_rendering_data = ready_galaxy_markdown_for_export(trans, internal_markdown) rval = { "render_format": "markdown", # Presumably the frontend could render things other ways. "markdown": export_markdown, "invocation_markdown": export_markdown, "model_class": "Report", "id": trans.app.security.encode_id(invocation.workflow_id), "username": trans.user.username, "title": workflow.name, } rval.update(extra_rendering_data) return rval
[docs] def generate_report_pdf(self, trans, invocation, runtime_report_config_json=None): internal_markdown = self._generate_internal_markdown(trans, invocation, runtime_report_config_json=runtime_report_config_json) return internal_galaxy_markdown_to_pdf(trans, internal_markdown, PdfDocumentType.invocation_report)
@abstractmethod def _generate_report_markdown(self, trans, invocation, runtime_report_config_json=None): """ """ def _generate_internal_markdown(self, trans, invocation, runtime_report_config_json=None): workflow_markdown = self._generate_report_markdown(trans, invocation, runtime_report_config_json=runtime_report_config_json) internal_markdown = resolve_invocation_markdown(trans, invocation, workflow_markdown) return internal_markdown