diff --git a/cg_lims/EPPs/udf/calculate/base.py b/cg_lims/EPPs/udf/calculate/base.py index 5f4edd97..27030625 100644 --- a/cg_lims/EPPs/udf/calculate/base.py +++ b/cg_lims/EPPs/udf/calculate/base.py @@ -9,6 +9,7 @@ calculate_average_size_and_set_qc, ) from cg_lims.EPPs.udf.calculate.calculate_beads import calculate_beads +from cg_lims.EPPs.udf.calculate.calculate_buffer import volume_buffer from cg_lims.EPPs.udf.calculate.calculate_microbial_aliquot_volumes import ( calculate_microbial_aliquot_volumes, ) @@ -16,7 +17,6 @@ calculate_resuspension_buffer_volume, ) from cg_lims.EPPs.udf.calculate.calculate_saphyr_concentration import calculate_saphyr_concentration -from cg_lims.EPPs.udf.calculate.calculate_buffer import volume_buffer from cg_lims.EPPs.udf.calculate.calculate_water_volume_rna import calculate_water_volume_rna from cg_lims.EPPs.udf.calculate.get_missing_reads import get_missing_reads from cg_lims.EPPs.udf.calculate.library_normalization import library_normalization diff --git a/cg_lims/EPPs/udf/calculate/calculate_buffer.py b/cg_lims/EPPs/udf/calculate/calculate_buffer.py index d0364754..7e524e08 100644 --- a/cg_lims/EPPs/udf/calculate/calculate_buffer.py +++ b/cg_lims/EPPs/udf/calculate/calculate_buffer.py @@ -1,14 +1,14 @@ """CLI module for calculating beads volumes""" + import logging import sys from typing import List import click -from genologics.entities import Artifact - from cg_lims import options from cg_lims.exceptions import LimsError, MissingUDFsError from cg_lims.get.artifacts import get_artifacts +from genologics.entities import Artifact LOG = logging.getLogger(__name__) @@ -18,8 +18,13 @@ def calculate_buffer_volume(sample_volume: float, sample_volume_limit: float) -> return sample_volume_limit - sample_volume if sample_volume < sample_volume_limit else 0.0 -def calculate_volumes(artifacts: List[Artifact], total_volume_udf: str, - volume_udf: str, buffer_udf: str, sample_volume_limit: float): +def calculate_volumes( + artifacts: List[Artifact], + total_volume_udf: str, + volume_udf: str, + buffer_udf: str, + sample_volume_limit: float, +): """Calculates buffer volume and total volume""" missing_udfs = 0 @@ -56,7 +61,13 @@ def calculate_volumes(artifacts: List[Artifact], total_volume_udf: str, @options.buffer_udf() @options.sample_volume_limit() @click.pass_context -def volume_buffer(context: click.Context, total_volume_udf: str, volume_udf: str, buffer_udf: str, sample_volume_limit: float): +def volume_buffer( + context: click.Context, + total_volume_udf: str, + volume_udf: str, + buffer_udf: str, + sample_volume_limit: float, +): """Buffer volume calculation.""" LOG.info(f"Running {context.command_path} with params: {context.params}") @@ -65,8 +76,13 @@ def volume_buffer(context: click.Context, total_volume_udf: str, volume_udf: str try: artifacts: List[Artifact] = get_artifacts(process=process, input=False) - calculate_volumes(artifacts=artifacts, total_volume_udf=total_volume_udf, - volume_udf=volume_udf, buffer_udf=buffer_udf, sample_volume_limit=sample_volume_limit) + calculate_volumes( + artifacts=artifacts, + total_volume_udf=total_volume_udf, + volume_udf=volume_udf, + buffer_udf=buffer_udf, + sample_volume_limit=sample_volume_limit, + ) message = "Volumes have been calculated." LOG.info(message) click.echo(message) diff --git a/cg_lims/models/arnold/prep/twist/aliquot_samples_for_enzymatic_fragmentation_twist.py b/cg_lims/models/arnold/prep/twist/aliquot_samples_for_enzymatic_fragmentation_twist.py index 194be46a..d9f7d208 100644 --- a/cg_lims/models/arnold/prep/twist/aliquot_samples_for_enzymatic_fragmentation_twist.py +++ b/cg_lims/models/arnold/prep/twist/aliquot_samples_for_enzymatic_fragmentation_twist.py @@ -13,6 +13,7 @@ class ProcessUDFs(BaseModel): GMSlymphoid_HD829: Optional[str] = Field(None, alias="Batch no GMSlymphoid-HD829") GMSmyeloid_HD829: Optional[str] = Field(None, alias="Batch no GMSmyeloid-HD829") GMSsolid_HD832: Optional[str] = Field(None, alias="Batch no GMSsolid-HD832") + hamilton_instrument: Optional[str] = Field(None, alias="Hamilton instrument") aliquot_samples_library_preparation_method_2: Optional[str] = Field( None, alias="Method document 2" )