diff --git a/cg_lims/EPPs/files/smrt_link/models.py b/cg_lims/EPPs/files/smrt_link/models.py index 0a574fba..62b57ac9 100644 --- a/cg_lims/EPPs/files/smrt_link/models.py +++ b/cg_lims/EPPs/files/smrt_link/models.py @@ -191,8 +191,8 @@ class RevioRun: pools: List[Artifact] run_name: str instrument_type: str - plate_1: str - plate_2: Optional[str] + plate_1_type: str + plate_2_type: Optional[str] file_version: int = 1 run_comments: Optional[str] movie_acquisition_time: int @@ -207,17 +207,21 @@ def __init__(self, process: Process): self.pools: List[Artifact] = get_artifacts(process=process) self.run_name: str = process.udf.get("Run Name") self.instrument_type: str = process.udf.get("Instrument Type") - self.run_comments: str = "Generated by automation in cg-lims.sys.scilifelab.se" + self.run_comments: str = ( + f"Generated by automation in https://cg-lims-stage.sys.scilifelab.se/clarity/work-details/{process.id.split('-')[1]}" + ) self.movie_acquisition_time: str = process.udf.get("Movie Acquisition Time (hours)") self.adaptive_loading: bool = process.udf.get("Adaptive Loading") self.base_kinetics: bool = process.udf.get("Include Base Kinetics") self.consensus_mode: bool = process.udf.get("Consensus Mode") + self.plate_1_type: str = process.udf.get("Plate 1 Type") + self.plate_2_type: str = process.udf.get("Plate 2 Type") def _create_run_settings(self) -> str: """Return the [Run Settings] section of the run design.""" - plate_rows: str = f"Plate 1,{self.plates[1]}\n" + plate_rows: str = f"Plate 1,{PLATE_PART_NUMBERS[self.plate_1_type]}\n" if self.plates[2]: - plate_rows += f"Plate 2,{self.plates[2]}\n" + plate_rows += f"Plate 2,{PLATE_PART_NUMBERS[self.plate_2_type]}\n" return ( f"{RunDesignHeader.RUN_SETTINGS}\n" f"Instrument Type,{self.instrument_type}\n"