from modules.software_base import WorkflowRunnerBase
import os

class ControlSimpleRunner(WorkflowRunnerBase):
    def __init__(self, logger, manifest_list, input_path, output_path="", additional_args="", threads=2, stepname="", mode=None):
        super().__init__(
            logger=logger,
            manifest_list=manifest_list,
            input_path=input_path,
            output_path=output_path,
            additional_args=additional_args,
            threads=threads,
            stepname=stepname,
            software_name="controlSimple.py",
            unneeded_args=["-i", "-o", "-t", "--input_dir", "--output_dir", "--threads"],
            output_type="bam",
            rescan_output=True,
            mode=mode
        )

    def find_input_files(self,prev_step_files):
        self.logger.info(prev_step_files, self.input_path, self.output_path, self.manifest_list)  
        for line in prev_step_files:

            self.input_file_list.append({
                "id": line['id'],
                "input1": self.input_path,
                "input2": None,
                "output1": f"{os.path.join(self.output_path, line['id'])}.{self.output_type}",
                "output2": None,
            })
        if self.leaf:
            return prev_step_files
        else:
            return None

    def build_command_queue(self):
        for item in self.input_file_list:
            
            file_manifest = [mandata for mandata in self.manifest_list if mandata['id'] == item['id']][0]

            if file_manifest['ctrl_id'] != "":
                cmd = [
                    self.software_name,
                    f"--input_path {item['input1']}",
                    f"--input_id {item['id']}",
                    f"--output_file {item['output1']}"
                ]
                
                for ctrl_id in file_manifest['ctrl_id'].strip('[]').split(', '):
                    cmd.append(f"--control_id {ctrl_id}")

                cmd.append(f"{self.additional_args}")
                
                self.command_queue.append(" ".join(cmd))