snakemake-interface-report-plugins

import os from pathlib import Path from snakemake_interface_report_plugins.api import ReportPluginBase, register_report_plugin @register_report_plugin class MyCustomReportPlugin(ReportPluginBase): """ A minimal Snakemake report plugin demonstrating the required interface. """ def __init__( self, report_dir: Path, report_paths: dict[str, Path], log_file: Path, **kwargs, ): super().__init__(report_dir, report_paths, log_file, **kwargs) self.plugin_id = kwargs.get("name", "my-custom-report") # Custom initialization logic here def get_report_name(self) -> str: """Returns the unique name for this report plugin.""" return self.plugin_id def get_report_css(self) -> list[Path]: """Returns a list of paths to CSS files for the report.""" # In a real plugin, these would typically be relative paths to files # within the plugin's package, resolved by pkg_resources or importlib.resources. return [] def get_report_js(self) -> list[Path]: """Returns a list of paths to JS files for the report.""" return [] def get_report_html(self, jobid: str) -> str: """ Generates the HTML content for a specific job ID. This content will be embedded into the final Snakemake report. """ return f""" <div class="custom-report-section"> <h3>Report for job: <code>{jobid}</code> from {self.plugin_id}</h3> <p>Report directory: {self.report_dir}</p> <p>Log file: {self.log_file}</p> <p>Timestamp: {os.path.getmtime(self.log_file) if self.log_file.exists() else 'N/A'}</p> </div> """ # To demonstrate, a plugin needs to be discovered by Snakemake. # This example code does not run a Snakemake workflow, but shows # the structure of a plugin Python file. # In a real scenario, Snakemake would import and instantiate this class. if __name__ == "__main__": # Simulate Snakemake's environment for instantiation temp_dir = Path("./temp_plugin_test").resolve() temp_dir.mkdir(exist_ok=True) sample_log_file = temp_dir / "sample_log.txt" sample_log_file.write_text("Log content here.") # Snakemake would instantiate your plugin like this: mock_report_paths = {"summary": temp_dir / "summary.html"} plugin_instance = MyCustomReportPlugin( report_dir=temp_dir, report_paths=mock_report_paths, log_file=sample_log_file, name="demo-plugin-instance" ) print(f"Plugin registered: {plugin_instance.get_report_name()}") print(f"Example HTML output for 'job_A':\n{plugin_instance.get_report_html('job_A')}") # Cleanup sample_log_file.unlink() temp_dir.rmdir()