Update Saphyr concentration inputs (#491)(patch)

### Changed
- Made the number of concentration replicates flexible
- Added a new click option

cg_lims/EPPs/udf/calculate/calculate_saphyr_concentration.py

@@ -4,17 +4,16 @@
 
 import click
 import numpy as np
+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__)
 
 
-def get_concentrations(artifact: Artifact) -> List[float]:
-    """Returns a list of all concentration replicates called
-    Concentration 1 (ng/ul), Concentration 2 (ng/ul) and Concentration 3 (ng/ul) of an artifact."""
-    udf_names = ["Concentration 1 (ng/ul)", "Concentration 2 (ng/ul)", "Concentration 3 (ng/ul)"]
+def get_concentrations(artifact: Artifact, udf_names: List[str]) -> List[float]:
+    """Returns a list of all concentration replicates of an artifact."""
     concentrations = []
     for name in udf_names:
         concentrations.append(artifact.udf.get(name))
@@ -35,11 +34,11 @@ def calculate_cv(concentrations: List[float]) -> float:
     return coefficient_variation
 
 
-def set_average_and_cv(artifact: Artifact) -> None:
+def set_average_and_cv(artifact: Artifact, udf_names: List[str]) -> None:
     """Calls on the previous functions get_concentration, calculate_average_concentration and calculate_cv
     and updates the UDFs Average concentration (ng/ul) and Coefficient of variation (CV) with the calculated values
     """
-    concentrations = get_concentrations(artifact=artifact)
+    concentrations = get_concentrations(artifact=artifact, udf_names=udf_names)
     average_concentration = calculate_average_concentration(concentrations=concentrations)
     coefficient_variation = calculate_cv(concentrations=concentrations)
 
@@ -48,10 +47,9 @@ def set_average_and_cv(artifact: Artifact) -> None:
     artifact.put()
 
 
-def validate_udf_values(artifact: Artifact) -> bool:
+def validate_udf_values(artifact: Artifact, udf_names: List[str]) -> bool:
     """A function checking whether a concentration in the list of concentrations for each artifact has a negative/no/zero value.
     Then the function returns the output as 'False' and logs all those sample IDs in the EPP log"""
-    udf_names = ["Concentration 1 (ng/ul)", "Concentration 2 (ng/ul)", "Concentration 3 (ng/ul)"]
     output = True
     for name in udf_names:
         if not artifact.udf.get(name) or artifact.udf.get(name) < 0:
@@ -63,8 +61,9 @@ def validate_udf_values(artifact: Artifact) -> bool:
 
 
 @click.command()
+@options.concentration_replicates()
 @click.pass_context
-def calculate_saphyr_concentration(ctx) -> None:
+def calculate_saphyr_concentration(ctx, concentration_udf: List[str]) -> None:
     """Calculates and sets the average concentration and coefficient of variance based on three given concentrations.
     Returns a message if this worked well, and if there were negative/no/zero concentration values, there's an error message for this
     """
@@ -76,10 +75,10 @@ def calculate_saphyr_concentration(ctx) -> None:
         artifacts: List[Artifact] = get_artifacts(process=process, measurement=True)
         failed_samples = 0
         for artifact in artifacts:
-            if not validate_udf_values(artifact=artifact):
+            if not validate_udf_values(artifact=artifact, udf_names=concentration_udf):
                 failed_samples += 1
                 continue
-            set_average_and_cv(artifact=artifact)
+            set_average_and_cv(artifact=artifact, udf_names=concentration_udf)
         if failed_samples:
             raise MissingUDFsError(
                 f"{failed_samples} samples have invalid concentration values (<= 0). See log for more information."

cg_lims/options.py

@@ -183,6 +183,16 @@ def artifact_udfs(help: str = "Artifact udfs.") -> click.option:
     )
 
 
+def concentration_replicates(help: str = "Udf name for concentration replicates.") -> click.option:
+    return click.option(
+        "-cr",
+        "--concentration-udf",
+        required=True,
+        multiple=True,
+        help=help,
+    )
+
+
 def source_artifact_udfs(help: str = "Artifact udfs.") -> click.option:
     return click.option(
         "-sau",