Skip RC QC EPP updates (#470)(minor)

### Added
- new option to skip error messages to the copy EPP sample_to_artifact.py
- new measurement and input artifact flags for the calculate EPP calculate_amount_ng.py

cg_lims/EPPs/udf/calculate/calculate_amount_ng.py

@@ -1,11 +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__)
 
@@ -15,30 +16,35 @@
 @options.amount_udf_option()
 @options.volume_udf_option()
 @options.subtract_volume_option()
+@options.measurement()
+@options.input()
 @click.pass_context
 def calculate_amount_ng(
     ctx: click.Context,
     amount_udf: str,
     volume_udf: str,
     concentration_udf: str,
     subtract_volume: str,
+    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."""
 
     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=True)
-        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)
@@ -51,7 +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

@@ -1,75 +1,97 @@
 #!/usr/bin/env python
 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 cg_lims.get.udfs import get_udf_type
+from genologics.entities import Artifact, Process, Sample
+from genologics.lims import Lims
 
 LOG = logging.getLogger(__name__)
 
 
-def udf_copy_sample_to_artifact(artifacts: list, sample_udf: str, art_udf: str, lims) -> None:
+def udf_copy_sample_to_artifact(
+    artifacts: List[Artifact],
+    sample_udf: str,
+    artifact_udf: str,
+    lims: Lims,
+    ignore_fail: bool = False,
+) -> None:
     """Function to copy sample udf to artifact.
 
-    For each artifact in the artifacts list, picking the first sample in the art.samples list.
-    copying the samp_udf from the sample to the art_udf on the artifact.
+    For each artifact in the artifacts list, picking the first sample in the artifact.samples list.
+    copying the sample_udf from the sample to the art_udf on the artifact.
     Warns if sample_udf is missing on a sample.
     Logs if a the sample list of a artifact contains more than one sample.
 
 
     Arguments:
         artifacts: list of artifacts to copy from
-        art_udf: artifact udf to get
-        sample_udf: sample udf to set"""
-    failed_udfs = 0
-    passed_udfs = 0
-    udf_type = get_udf_type(lims=lims, udf_name=art_udf, attach_to_name=artifacts[0].output_type)
-    for art in artifacts:
-        if len(art.samples) > 1:
+        artifact_udf: artifact udf to get
+        sample_udf: sample udf to set
+        lims: genologics Lims object connected to the database
+        ignore_fail: bool option to mute warnings"""
+    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 = art.samples[0]
+        sample: Sample = artifact.samples[0]
         udf = sample.udf.get(sample_udf)
         if not isinstance(udf, udf_type):
             try:
                 udf = udf_type(udf)
             except:
                 failed_udfs += 1
                 LOG.error(
-                    f"Udf: {sample_udf} missing on sample {sample.id} or it could not be converted to type {udf_type}"
+                    f"UDF: {sample_udf} missing on sample {sample.id} or it could not be converted to type {udf_type}"
                 )
                 continue
 
-        art.udf[art_udf] = udf
-        art.put()
+        artifact.udf[artifact_udf] = udf
+        artifact.put()
         LOG.info(
-            f"copied udf {sample_udf} from sample {sample.id} to artifact: {art.id}, udf: {art_udf}"
+            f"copied UDF {sample_udf} from sample {sample.id} to artifact: {artifact.id}, UDF: {artifact_udf}"
         )
         passed_udfs += 1
 
-    if failed_udfs:
+    if failed_udfs and not ignore_fail:
         raise MissingUDFsError(
-            message=f"The udf '{sample_udf}' is missing for {failed_udfs} samples. Udfs were set on {passed_udfs} artifacts."
+            message=f"The UDF '{sample_udf}' is missing for {failed_udfs} samples. UDFs were set on {passed_udfs} artifacts."
         )
 
 
 @click.command()
-@options.sample_udf(help="Sample udf to set.")
-@options.artifact_udf(help="Artifact udf to get.")
-@options.measurement(help="Udfs will be set on measurements.")
-@options.input(help="Udfs will be set on input artifacts.")
+@options.sample_udf(help="Sample UDF to set.")
+@options.artifact_udf(help="Artifact UDF to get.")
+@options.measurement(help="UDFs will be set on measurements.")
+@options.input(help="UDFs will be set on input artifacts.")
+@options.ignore_fail(help="Script will not raise exception errors when not all UDFs are set.")
 @click.pass_context
-def sample_to_artifact(ctx, sample_udf, artifact_udf, measurement, input):
-    """Script to copy artifact udf to sample udf"""
+def sample_to_artifact(ctx, sample_udf, artifact_udf, measurement, input, ignore_fail):
+    """Script to copy artifact UDF to sample UDF"""
 
-    process = ctx.obj["process"]
-    lims = ctx.obj["lims"]
+    process: Process = ctx.obj["process"]
+    lims: Lims = ctx.obj["lims"]
 
     try:
-        artifacts = get_artifacts(process=process, input=input, measurement=measurement)
-        udf_copy_sample_to_artifact(artifacts, sample_udf, artifact_udf, lims)
-        click.echo("Udfs have been set on all samples.")
+        artifacts: List[Artifact] = get_artifacts(
+            process=process, input=input, measurement=measurement
+        )
+        udf_copy_sample_to_artifact(
+            artifacts=artifacts,
+            sample_udf=sample_udf,
+            artifact_udf=artifact_udf,
+            lims=lims,
+            ignore_fail=ignore_fail,
+        )
+        click.echo("UDFs have been set on all samples.")
     except LimsError as e:
         sys.exit(e.message)