type hints

cg_lims/EPPs/udf/calculate/calculate_amount_ng.py

@@ -1,10 +1,12 @@
 import logging
 import sys
+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__)
 
@@ -32,16 +34,17 @@ def calculate_amount_ng(
 
     LOG.info(f"Running {ctx.command_path} with params: {ctx.params}")
 
-    process = ctx.obj["process"]
-    lims = ctx.obj["lims"]
+    process: Process = ctx.obj["process"]
 
     try:
-        artifacts = get_artifacts(process=process, measurement=measurement, input=input)
-        missing_udfs_count = 0
-        artifacts_with_missing_udf = []
+        artifacts: List[Artifact] = get_artifacts(
+            process=process, measurement=measurement, input=input
+        )
+        missing_udfs_count: int = 0
+        artifacts_with_missing_udf: List = []
         for artifact in artifacts:
-            vol = artifact.udf.get(volume_udf)
-            conc = artifact.udf.get(concentration_udf)
+            vol: float = 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)
@@ -54,7 +57,7 @@ def calculate_amount_ng(
                 f"Udf missing for {missing_udfs_count} artifact(s): "
                 f"{','.join(artifacts_with_missing_udf)}. "
             )
-        message = "Amounts have been calculated for all artifacts."
+        message: str = "Amounts have been calculated for all artifacts."
         LOG.info(message)
         click.echo(message)
     except LimsError as e:

cg_lims/EPPs/udf/copy/sample_to_artifact.py

@@ -8,7 +8,7 @@
 from cg_lims.exceptions import LimsError, MissingUDFsError
 from cg_lims.get.artifacts import get_artifacts
 from cg_lims.get.udfs import get_udf_type
-from genologics.entities import Artifact, Process
+from genologics.entities import Artifact, Process, Sample
 from genologics.lims import Lims
 
 LOG = logging.getLogger(__name__)
@@ -35,15 +35,15 @@ def udf_copy_sample_to_artifact(
         sample_udf: sample udf to set
         lims: genologics Lims object connected to the database
         ignore_fail: bool option to mute warnings"""
-    failed_udfs = 0
-    passed_udfs = 0
+    failed_udfs: int = 0
+    passed_udfs: int = 0
     udf_type = get_udf_type(
         lims=lims, udf_name=artifact_udf, attach_to_name=artifacts[0].output_type
     )
     for artifact in artifacts:
         if len(artifact.samples) > 1:
             LOG.info("More than one sample per artifact, picking the first one")
-        sample = artifact.samples[0]
+        sample: Sample = artifact.samples[0]
         udf = sample.udf.get(sample_udf)
         if not isinstance(udf, udf_type):
             try: