add more options to aliquot EPP, refactored some options (#490)

### Changed

- made the "Calculate Aliquot Volume" EPP more general by allowing for custom UDF names as CLI input
- refactored some click options

cg_lims/EPPs/udf/calculate/aliquot_volume.py

@@ -3,52 +3,91 @@
 from typing import List
 
 import click
+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, Process
 
 LOG = logging.getLogger(__name__)
 
 
-def calculate_volumes(artifacts: List[Artifact], process: Process):
+def calculate_volumes(
+    artifacts: List[Artifact],
+    process: Process,
+    concentration_udf: str,
+    sample_volume_udf: str,
+    buffer_volume_udf: str,
+    total_volume_udf: str,
+    amount_needed_udf: str,
+):
     """Calculates volumes for diluting samples. The total volume differ depending on
-    type of sample. It is given by the process udf 'Total Volume (ul)'."""
+    type of sample. It is given by the process udf <total_volume_udf>."""
 
-    max_volume = process.udf.get("Total Volume (ul)")
+    max_volume = process.udf.get(total_volume_udf)
     if not max_volume:
-        raise MissingUDFsError("Process udf missing: Total Volume (ul)")
+        raise MissingUDFsError(f"Process udf missing:{total_volume_udf}")
 
     missing_udfs = 0
 
     for art in artifacts:
-        concentration = art.udf.get("Concentration")
-        amount = art.udf.get("Amount needed (ng)")
+        concentration = art.udf.get(concentration_udf)
+        amount = art.udf.get(amount_needed_udf)
         if not amount or not concentration:
             missing_udfs += 1
             continue
 
-        art.udf["Sample Volume (ul)"] = amount / float(concentration)
-        art.udf["Volume H2O (ul)"] = max_volume - art.udf["Sample Volume (ul)"]
+        art.udf[sample_volume_udf] = amount / float(concentration)
+        art.udf[buffer_volume_udf] = max_volume - art.udf[sample_volume_udf]
         art.put()
 
     if missing_udfs:
         raise MissingUDFsError(
-            f"UDFs 'Concentration' and/or 'Amount needed (ng)' missing for {missing_udfs} samples"
+            f"UDFs '{concentration_udf}' and/or '{amount_needed_udf}' missing for {missing_udfs} samples"
         )
 
 
 @click.command()
+@options.concentration_udf(help="Name of the concentration (ng/ul) artifact UDF")
+@options.volume_udf(help="Name of the sample volume artifact UDF")
+@options.buffer_udf(help="Name of the buffer volume artifact UDF")
+@options.total_volume_udf(help="Name of the total volume process UDF")
+@options.amount_ng_udf(
+    help="Use if you want to overwrite the default UDF name 'Amount needed (ng)'"
+)
+@options.measurement(
+    help="UDFs will be calculated and set on measurement artifacts. Use in QC steps."
+)
+@options.input(
+    help="UDFs will be calculated ans set on input artifacts. Use non-output generating steps."
+)
 @click.pass_context
-def aliquot_volume(ctx):
+def aliquot_volume(
+    ctx: click.Context,
+    concentration_udf: str,
+    volume_udf: str,
+    buffer_udf: str,
+    total_volume_udf: str,
+    amount_ng_udf: str = "Amount needed (ng)",
+    measurement: bool = False,
+    input: bool = False,
+):
     """Calculates amount needed for samples."""
 
     LOG.info(f"Running {ctx.command_path} with params: {ctx.params}")
 
     process = ctx.obj["process"]
 
     try:
-        artifacts = get_artifacts(process=process, input=False)
-        calculate_volumes(artifacts=artifacts, process=process)
+        artifacts = get_artifacts(process=process, input=input, measurement=measurement)
+        calculate_volumes(
+            artifacts=artifacts,
+            process=process,
+            concentration_udf=concentration_udf,
+            sample_volume_udf=volume_udf,
+            buffer_volume_udf=buffer_udf,
+            total_volume_udf=total_volume_udf,
+            amount_needed_udf=amount_ng_udf,
+        )
         message = "Volumes have been calculated for all samples."
         LOG.info(message)
         click.echo(message)

cg_lims/EPPs/udf/calculate/calculate_amount_ng.py

@@ -12,7 +12,7 @@
 
 
 @click.command()
-@options.concentration_udf_option()
+@options.concentration_udf()
 @options.amount_udf_option()
 @options.volume_udf()
 @options.subtract_volume_option()

cg_lims/EPPs/udf/calculate/calculate_amount_ng_fmol.py

@@ -112,7 +112,7 @@ def set_amounts(
 
 @click.command()
 @options.process_types()
-@options.concentration_udf_option()
+@options.concentration_udf()
 @options.volume_udf_option()
 @options.preset_volume()
 @options.size_udf()

cg_lims/EPPs/udf/calculate/ont_aliquot_volume.py

@@ -93,7 +93,7 @@ def set_volumes(
 
 @click.command()
 @options.process_types()
-@options.concentration_udf_option()
+@options.concentration_udf()
 @options.size_udf()
 @options.volume_udf(help="Name of sample volume UDF")
 @options.buffer_udf()
@@ -115,7 +115,7 @@ def ont_aliquot_volume(
     volume_udf: str,
     buffer_udf: str,
     amount_fmol_udf: str = "Amount needed (fmol)",
-    amount_ng_udf: str = "Amount needed (fmol)",
+    amount_ng_udf: str = "Amount needed (ng)",
     total_volume_udf: Optional[str] = None,
     measurement: bool = False,
     input: bool = False,

cg_lims/options.py

@@ -279,7 +279,7 @@ def volume_udf_option(
     return click.option("--volume-udf", required=False, help=help)
 
 
-def concentration_udf_option(
+def concentration_udf(
     help: str = "String of UDF used to get concentration value",
 ) -> click.option:
     return click.option("--concentration-udf", required=True, help=help)

tests/EPPs/udf/calculate/test_aliquot_volume.py

@@ -38,7 +38,15 @@ def test_calculate_volumes(
     artifact_1.put()
 
     # WHEN calculating the aliquot sample and water volumes
-    calculate_volumes(artifacts=[artifact_1], process=process)
+    calculate_volumes(
+        artifacts=[artifact_1],
+        process=process,
+        concentration_udf="Concentration",
+        sample_volume_udf="Sample Volume (ul)",
+        buffer_volume_udf="Volume H2O (ul)",
+        total_volume_udf="Total Volume (ul)",
+        amount_needed_udf="Amount needed (ng)",
+    )
 
     # THEN the correct values are calculated for the artifact UDFs 'Volume H2O (ul)' and 'Sample Volume (ul)'
     assert artifact_1.udf["Sample Volume (ul)"] == sample_vol
@@ -73,7 +81,15 @@ def test_calculate_volumes_missing_artifact_udf(lims: Lims, udf_name: str):
     # WHEN calculating the aliquot sample and water volumes
     # THEN MissingUDFsError is being raised, while also correctly setting the values for artifact_2
     with pytest.raises(MissingUDFsError):
-        calculate_volumes(artifacts=[artifact_1, artifact_2], process=process)
+        calculate_volumes(
+            artifacts=[artifact_1, artifact_2],
+            process=process,
+            concentration_udf="Concentration",
+            sample_volume_udf="Sample Volume (ul)",
+            buffer_volume_udf="Volume H2O (ul)",
+            total_volume_udf="Total Volume (ul)",
+            amount_needed_udf="Amount needed (ng)",
+        )
     assert artifact_2.udf["Sample Volume (ul)"] == 20
     assert artifact_2.udf["Volume H2O (ul)"] == 30
 
@@ -94,4 +110,12 @@ def test_calculate_volumes_missing_process_udf(lims: Lims):
     # WHEN calculating the aliquot sample and water volumes
     # THEN MissingUDFsError is being raised
     with pytest.raises(MissingUDFsError):
-        calculate_volumes(artifacts=[artifact_1], process=process)
+        calculate_volumes(
+            artifacts=[artifact_1],
+            process=process,
+            concentration_udf="Concentration",
+            sample_volume_udf="Sample Volume (ul)",
+            buffer_volume_udf="Volume H2O (ul)",
+            total_volume_udf="Total Volume (ul)",
+            amount_needed_udf="Amount needed (ng)",
+        )