Generalize and rename buffer aliquotation script used in the Sample P…

…lacement step in several LIMS workflows (#534) (minor)

### Changed
- Re-named calculate-water to calculate-buffer
- Re-named main function from volume_water to volume_buffer
- Added new CLI flags for specifying UDF names for volumes

cg_lims/EPPs/udf/calculate/base.py

@@ -16,7 +16,7 @@
     calculate_resuspension_buffer_volume,
 )
 from cg_lims.EPPs.udf.calculate.calculate_saphyr_concentration import calculate_saphyr_concentration
-from cg_lims.EPPs.udf.calculate.calculate_water import volume_water
+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
@@ -51,7 +51,7 @@ def calculate(ctx):
 calculate.add_command(get_missing_reads)
 calculate.add_command(calculate_amount_ng)
 calculate.add_command(calculate_amount_ng_fmol)
-calculate.add_command(volume_water)
+calculate.add_command(volume_buffer)
 calculate.add_command(molar_concentration)
 calculate.add_command(calculate_beads)
 calculate.add_command(missing_reads_in_pool)

cg_lims/EPPs/udf/calculate/calculate_water.py → cg_lims/EPPs/udf/calculate/calculate_buffer.py

@@ -13,30 +13,31 @@
 LOG = logging.getLogger(__name__)
 
 
-def calculate_water_volume(sample_volume: float, sample_volume_limit: float) -> float:
-    """Calculates the H20 volume based on the sample volume"""
+def calculate_buffer_volume(sample_volume: float, sample_volume_limit: float) -> float:
+    """Calculates the buffer volume based on the sample volume"""
     return sample_volume_limit - sample_volume if sample_volume < sample_volume_limit else 0.0
 
 
-def calculate_volumes(artifacts: List[Artifact], sample_volume_limit: float):
-    """Calculates water volume and total volume"""
+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
     high_volume_warning = False
     warning_message = ""
     for artifact in artifacts:
-        sample_volume: float = artifact.udf.get("Sample Volume (ul)")
+        sample_volume: float = artifact.udf.get(volume_udf)
         if sample_volume is None:
             missing_udfs += 1
             continue
-        h2o_volume = calculate_water_volume(
+        buffer_volume = calculate_buffer_volume(
             sample_volume=sample_volume, sample_volume_limit=sample_volume_limit
         )
-        total_volume = h2o_volume + sample_volume
+        total_volume = buffer_volume + sample_volume
         if total_volume > 100:
             high_volume_warning = True
-        artifact.udf["Volume H2O (ul)"] = h2o_volume
-        artifact.udf["Total Volume (uL)"] = total_volume
+        artifact.udf[buffer_udf] = buffer_volume
+        artifact.udf[total_volume_udf] = total_volume
         artifact.put()
 
     if missing_udfs:
@@ -50,19 +51,23 @@ def calculate_volumes(artifacts: List[Artifact], sample_volume_limit: float):
 
 
 @click.command()
+@options.total_volume_udf()
+@options.volume_udf()
+@options.buffer_udf()
 @options.sample_volume_limit()
 @click.pass_context
-def volume_water(context: click.Context, sample_volume_limit: float):
-    """Water volume calculation."""
+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}")
 
     process = context.obj["process"]
 
     try:
         artifacts: List[Artifact] = get_artifacts(process=process, input=False)
-        calculate_volumes(artifacts=artifacts, sample_volume_limit=sample_volume_limit)
-        message = "Beads volumes have been calculated."
+        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)
     except LimsError as e:

tests/EPPs/udf/calculate/test_calculate_beads.py

@@ -5,7 +5,7 @@
     calculate_elution_volume,
     calculate_volumes,
 )
-from cg_lims.EPPs.udf.calculate.calculate_water import calculate_water_volume
+from cg_lims.EPPs.udf.calculate.calculate_buffer import calculate_buffer_volume
 from cg_lims.exceptions import MissingUDFsError
 from genologics.entities import Artifact
 from genologics.lims import Lims
@@ -36,11 +36,11 @@ def test_calculate_elution_volume():
         (SAMPLE_VOLUME_LIMIT + OFFSET, 0.0),
     ],
 )
-def test_calculate_water_volume(sample_volume: float, expected_return_value: float):
+def test_calculate_buffer_volume(sample_volume: float, expected_return_value: float):
     # GIVEN a sample volume less than, equal to, and greater than SAMPLE_VOLUME_LIMIT
 
     # WHEN calculating the water volume
-    result = calculate_water_volume(
+    result = calculate_buffer_volume(
         sample_volume=sample_volume, sample_volume_limit=SAMPLE_VOLUME_LIMIT
     )
 
@@ -106,19 +106,19 @@ def test_calculate_volumes_single_artifact_missing_sample_volume_udf(
 
 
 @mock.patch("cg_lims.EPPs.udf.calculate.calculate_beads.calculate_elution_volume")
-@mock.patch("cg_lims.EPPs.udf.calculate.calculate_water.calculate_water_volume")
+@mock.patch("cg_lims.EPPs.udf.calculate.calculate_buffer.calculate_buffer_volume")
 @mock.patch("cg_lims.EPPs.udf.calculate.calculate_beads.calculate_beads_volume")
 @pytest.mark.parametrize(
-    "sample_volume, elution_volume, water_volume, beads_volume",
+    "sample_volume, elution_volume, buffer_volume, beads_volume",
     [(20.0, 40.0, 30.0, 100.0)],
 )
 def test_calculate_volumes_multiple_artifacts_missing_sample_volume_udf(
     mock_beads_volume,
-    mock_water_volume,
+    mock_buffer_volume,
     mock_elution_volume,
     sample_volume: float,
     elution_volume: float,
-    water_volume: float,
+    buffer_volume: float,
     beads_volume: float,
     lims: Lims,
     artifact_1: Artifact,
@@ -132,7 +132,7 @@ def test_calculate_volumes_multiple_artifacts_missing_sample_volume_udf(
     artifacts = [artifact_1, artifact_2]
 
     mock_elution_volume.return_value = elution_volume
-    mock_water_volume.return_value = water_volume
+    mock_buffer_volume.return_value = buffer_volume
     mock_beads_volume.return_value = beads_volume
 
     # WHEN calculating the volumes