Patch TWIST EPPs to take new UDF "Maximum input amount (ng)" into con…

…sideration (#457)(patch)

### Added
- new functions to fetch the maximum input amount of samples

### Changed
- the threshold used when assessing input amounts

cg_lims/EPPs/udf/calculate/twist_aliquot_amount.py

@@ -7,6 +7,7 @@
 
 from cg_lims.exceptions import LimsError, MissingUDFsError
 from cg_lims.get.artifacts import get_artifacts
+from cg_lims.get.udfs import get_maximum_amount
 
 LOG = logging.getLogger(__name__)
 
@@ -21,16 +22,17 @@ def set_amount_needed(artifacts: List[Artifact]):
     Any amount below this can be used in the prep if the total amount is limited."""
 
     missing_udfs = 0
-    for art in artifacts:
-        amount = art.udf.get("Amount (ng)")
+    for artifact in artifacts:
+        amount = artifact.udf.get("Amount (ng)")
+        maximum_amount = get_maximum_amount(artifact=artifact, default_amount=MAXIMUM_SAMPLE_AMOUNT)
         if not amount:
             missing_udfs += 1
             continue
-        if amount >= MAXIMUM_SAMPLE_AMOUNT:
-            art.udf["Amount needed (ng)"] = MAXIMUM_SAMPLE_AMOUNT
+        if amount >= maximum_amount:
+            artifact.udf["Amount needed (ng)"] = maximum_amount
         else:
-            art.udf["Amount needed (ng)"] = amount
-        art.put()
+            artifact.udf["Amount needed (ng)"] = amount
+        artifact.put()
 
     if missing_udfs:
         raise MissingUDFsError(f"Udf missing for {missing_udfs} samples")

cg_lims/EPPs/udf/calculate/twist_qc_amount.py

@@ -8,24 +8,25 @@
 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
+from cg_lims.get.udfs import get_maximum_amount
 
 LOG = logging.getLogger(__name__)
 
+MAXIMUM_SAMPLE_AMOUNT = 250
 
-def get_qc(source: str, conc: float, amount: float) -> str:
+
+def get_qc(source: str, conc: float, amount: float, max_amount: float) -> str:
     """QC-criteria depends on sample source, total amount and sample concentration. See AMS doc 1117, 1993 and 2125.
-    The volume is subtracted by 3 in the calculations. This is beacause the lab uses 3 ul in the initial qc measurements.
+    The volume is subtracted by 3 in the calculations. This is because the lab uses 3 ul in the initial qc measurements.
     """
 
     qc = "FAILED"
-
     if source == "cell-free DNA" or source == "cfDNA":
-        if amount >= 10 and conc <= 250 and conc >= 0.2:
+        if amount >= 10 and 250 >= conc >= 0.2:
             qc = "PASSED"
     else:
-        if amount >= 250 and conc <= 250 and conc >= 8.33:
+        if amount >= max_amount and 250 >= conc >= 8.33:
             qc = "PASSED"
-
     return qc
 
 
@@ -35,7 +36,7 @@ def calculate_amount_and_set_qc(artifacts: List[Artifact]) -> None:
     missing_udfs_count = 0
     qc_fail_count = 0
     for artifact in artifacts:
-        sample = get_one_sample_from_artifact(artifact)
+        sample = get_one_sample_from_artifact(artifact=artifact)
         source = sample.udf.get("Source")
         vol = artifact.udf.get("Volume (ul)")
         conc = artifact.udf.get("Concentration")
@@ -45,7 +46,8 @@ def calculate_amount_and_set_qc(artifacts: List[Artifact]) -> None:
 
         amount = conc * (vol - 3)
         artifact.udf["Amount (ng)"] = amount
-        qc = get_qc(source, conc, 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)
         if qc == "FAILED":
             qc_fail_count += 1
             LOG.info(
@@ -70,11 +72,10 @@ def twist_qc_amount(ctx):
     LOG.info(f"Running {ctx.command_path} with params: {ctx.params}")
 
     process = ctx.obj["process"]
-    lims = ctx.obj["lims"]
 
     try:
         artifacts = get_artifacts(process=process, measurement=True)
-        calculate_amount_and_set_qc(artifacts)
+        calculate_amount_and_set_qc(artifacts=artifacts)
         message = "Amounts have been calculated and qc flags set for all samples."
         LOG.info(message)
         click.echo(message)

cg_lims/get/udfs.py

@@ -1,7 +1,7 @@
 from datetime import date
 from enum import Enum
 from typing import Optional
-from genologics.entities import Entity
+from genologics.entities import Entity, Artifact
 from genologics.lims import Lims
 
 from cg_lims.exceptions import MissingUDFsError
@@ -50,3 +50,12 @@ def get_q30_threshold(entity: Entity) -> Optional[str]:
         return get_udf(entity, UserDefinedFields.Q30_THRESHOLD.value)
     except MissingUDFsError:
         return None
+
+
+def get_maximum_amount(artifact: Artifact, default_amount: float) -> float:
+    """Return the maximum allowed input amount of an artifact. A default value is returned if no UDF has been set."""
+    sample = artifact.samples[0]
+    maximum_amount = sample.udf.get("Maximum input amount (ng)")
+    if maximum_amount:
+        return maximum_amount
+    return default_amount