Update Calculate Amount scripts for more flexibility (#562)

Changes are needed for the new Pacbio Revio workflow but they also affect many other steps that have different types of calculate amount automations using the same script

### Changed

For script calculate_amount_ng.py:
- From options.py, "subtract_volume_option" was substituted with "subtract_volume" as it offers more flexibility
- From options.py, "preset_volume" was added so that a volume specified in the cli can be used in the calculation

For script twist_qc_amount.py:
- From options.py, "subtract_volume" was added and substitutes the hardcoded volume subtraction in the script - the value can be modified in the cli command instead.
- Its pytest test_twist_qc_amount.py was modified to reflect the added option mentioned above

cg_lims/EPPs/udf/calculate/calculate_amount_ng.py

@@ -15,7 +15,8 @@
 @options.concentration_udf()
 @options.amount_udf_option()
 @options.volume_udf()
-@options.subtract_volume_option()
+@options.subtract_volume()
+@options.preset_volume()
 @options.measurement()
 @options.input()
 @click.pass_context
@@ -25,12 +26,14 @@ def calculate_amount_ng(
     volume_udf: str,
     concentration_udf: str,
     subtract_volume: str,
+    preset_volume: float,
     measurement: bool = False,
     input: bool = False,
 ):
     """Calculates and auto-fills the quantities of DNA in sample from concentration and volume
-    measurements. The volume is subtracted by either 0 or 3 in the calculations. This is
-    because the lab uses 0 or 3 ul in the initial qc measurements."""
+    measurements. The volume can be subtracted by an optional specification in the cli. This is
+    because the lab uses some microliters of the sample in the qc measurements. A pre-set
+    volume can be set in the cli as well."""
 
     LOG.info(f"Running {ctx.command_path} with params: {ctx.params}")
 
@@ -43,13 +46,15 @@ def calculate_amount_ng(
         missing_udfs_count: int = 0
         artifacts_with_missing_udf: List = []
         for artifact in artifacts:
-            vol: float = artifact.udf.get(volume_udf)
+            if preset_volume:
+                vol = float(preset_volume)
+            elif volume_udf:
+                vol = artifact.udf.get(volume_udf)
             conc: float = artifact.udf.get(concentration_udf)
             if None in [conc, vol]:
                 missing_udfs_count += 1
                 artifacts_with_missing_udf.append(artifact.id)
                 continue
-
             artifact.udf[amount_udf] = conc * (vol - int(subtract_volume))
             artifact.put()
         if missing_udfs_count:

cg_lims/EPPs/udf/calculate/twist_qc_amount.py

@@ -3,6 +3,7 @@
 from typing import List
 
 import click
+from cg_lims import options
 from cg_lims.exceptions import FailingQCError, LimsError, MissingUDFsError
 from cg_lims.get.artifacts import get_artifacts
 from cg_lims.get.samples import get_one_sample_from_artifact
@@ -29,7 +30,7 @@ def get_qc(source: str, conc: float, amount: float, max_amount: float) -> str:
     return qc
 
 
-def calculate_amount_and_set_qc(artifacts: List[Artifact]) -> None:
+def calculate_amount_and_set_qc(artifacts: List[Artifact], subtract_volume: int) -> None:
     """Calculate amount and set qc for twist samples"""
 
     missing_udfs_count = 0
@@ -43,7 +44,7 @@ def calculate_amount_and_set_qc(artifacts: List[Artifact]) -> None:
             missing_udfs_count += 1
             continue
 
-        amount = conc * (vol - 3)
+        amount = conc * (vol - subtract_volume)
         artifact.udf["Amount (ng)"] = amount
         max_amount = get_maximum_amount(artifact=artifact, default_amount=MAXIMUM_SAMPLE_AMOUNT)
         qc = get_qc(source=source, conc=conc, amount=amount, max_amount=max_amount)
@@ -64,8 +65,12 @@ def calculate_amount_and_set_qc(artifacts: List[Artifact]) -> None:
 
 
 @click.command()
+@options.subtract_volume()
 @click.pass_context
-def twist_qc_amount(ctx):
+def twist_qc_amount(
+    ctx: click.Context,
+    subtract_volume: str,
+):
     """Calculates amount of samples for qc validation."""
 
     LOG.info(f"Running {ctx.command_path} with params: {ctx.params}")
@@ -74,7 +79,7 @@ def twist_qc_amount(ctx):
 
     try:
         artifacts = get_artifacts(process=process, measurement=True)
-        calculate_amount_and_set_qc(artifacts=artifacts)
+        calculate_amount_and_set_qc(artifacts=artifacts, subtract_volume=int(subtract_volume))
         message = "Amounts have been calculated and qc flags set for all samples."
         LOG.info(message)
         click.echo(message)

tests/EPPs/udf/calculate/test_twist_qc_amount.py

@@ -7,14 +7,15 @@
 
 
 @pytest.mark.parametrize(
-    "volume,concentration,source",
-    [(3, 1, "blood"), (10, 0.1, "cfDNA"), (50, 300, "blood"), (300, 2, "blood"), (10, 10, "blood")],
+    "volume,concentration,source,subtract",
+    [(3, 1, "blood",2), (10, 0.1, "cfDNA",2), (50, 300, "blood",2), (300, 2, "blood",2), (10, 10, "blood",2)],
 )
 def test_calculate_amount_and_set_qc_failing(
-    volume: int, concentration: float, source: int, artifact_1: Artifact, sample_1: Sample
+    volume: int, concentration: float, source: int, artifact_1: Artifact, sample_1: Sample, subtract: int
 ):
     # GIVEN: A sample with udf Source: <source>,
     # and a related Artifact with udfs: Concentration: <concentration> and  Volume (ul): <volume>
+    # and a subtraction volume
     server("flat_tests")
     artifact_1.udf["Volume (ul)"] = volume
     artifact_1.udf["Concentration"] = concentration
@@ -26,13 +27,13 @@ def test_calculate_amount_and_set_qc_failing(
 
     # THEN FailingQCError is being raised and the artifacts should be FAILED
     with pytest.raises(FailingQCError):
-        calculate_amount_and_set_qc(artifacts=[artifact_1])
+        calculate_amount_and_set_qc(artifacts=[artifact_1], subtract_volume=subtract)
     assert artifact_1.qc_flag == "FAILED"
 
 
-@pytest.mark.parametrize("volume,concentration,source", [(35, 10, "cfDNA"), (50, 50, "blood")])
+@pytest.mark.parametrize("volume,concentration,source,subtract", [(35, 10, "cfDNA",2), (50, 50, "blood",2)])
 def test_calculate_amount_and_set_qc_passing(
-    volume: int, concentration: float, source: int, artifact_1: Artifact, sample_1: Sample
+    volume: int, concentration: float, source: int, artifact_1: Artifact, sample_1: Sample, subtract: int
 ):
     # GIVEN: A sample with udf Source: <source>,
     # and a related Artifact with udfs: Concentration: <concentration> and  Volume (ul): <volume>
@@ -46,7 +47,7 @@ def test_calculate_amount_and_set_qc_passing(
     sample_1.put()
 
     # WHEN running calculate_amount_and_set_qc
-    calculate_amount_and_set_qc(artifacts=[artifact_1])
+    calculate_amount_and_set_qc(artifacts=[artifact_1], subtract_volume=subtract)
 
     # THEN the artifacts should be PASSED
     assert artifact_1.qc_flag == "PASSED"
@@ -67,4 +68,4 @@ def test_calculate_amount_and_set_qc_missing_udf(
     # WHEN running calculate_amount_and_set_qc
     # THEN MissingUDFsError is being raised
     with pytest.raises(MissingUDFsError):
-        calculate_amount_and_set_qc(artifacts=artifacts)
+        calculate_amount_and_set_qc(artifacts=artifacts, subtract_volume=2)