New Femtopulse csv file EPP (#569) (minor)

### Added

- New EPP "Create Femtopulse Run File"

cg_lims/EPPs/files/base.py

@@ -2,8 +2,7 @@
 import click
 from cg_lims.EPPs.files.barcode_tubes import make_barcode_csv
 from cg_lims.EPPs.files.csv_for_kapa_truble_shooting.csv_for_kapa_debug import trouble_shoot_kapa
-
-# commands
+from cg_lims.EPPs.files.femtopulse_csv import make_femtopulse_csv
 from cg_lims.EPPs.files.file_to_udf import csv_well_to_udf
 from cg_lims.EPPs.files.hamilton.base import hamilton
 from cg_lims.EPPs.files.ont_json_to_udf import parse_ont_report
@@ -33,5 +32,6 @@ def files(ctx):
 files.add_command(create_sample_sheet)
 files.add_command(parse_run_parameters)
 files.add_command(parse_ont_report)
+files.add_command(make_femtopulse_csv)
 files.add_command(create_smrtlink_sample_setup)
 files.add_command(create_smrtlink_run_design)

cg_lims/EPPs/files/femtopulse_csv.py

@@ -0,0 +1,109 @@
+import logging
+import sys
+from pathlib import Path
+from typing import List
+
+import click
+import pandas as pd
+from cg_lims import options
+from cg_lims.exceptions import InvalidValueError, LimsError
+from cg_lims.get.artifacts import get_artifacts
+from cg_lims.get.fields import get_artifact_well
+from genologics.lims import Artifact
+
+LOG = logging.getLogger(__name__)
+
+
+WELL_POSITIONS = [f"A{i}" for i in range(1, 13)]  # List with well positions A1-A12
+SAMPLE_NAMES = [""] * len(WELL_POSITIONS)  # List with twelve empty positions for sample names
+DATAFRAME = pd.DataFrame(
+    {"well positions": WELL_POSITIONS, "sample names": SAMPLE_NAMES}
+)  # Dataframe with well positions and sample names
+
+
+def get_sample_artifact_name(artifact: Artifact):
+
+    artifact_name: str = artifact.samples[0].name
+
+    return artifact_name
+
+
+def get_data_and_write(artifacts: List[Artifact], file: str):
+    """Make a csv file for a Femtopulse run start with three columns:
+    one numbered 1-12, one with the sample position/well for the run and
+    a column with the sample name or ladder (in the 12th position)."""
+
+    failed_samples: list = []
+
+    for artifact in artifacts:
+
+        artifact_name: str = get_sample_artifact_name(artifact=artifact)
+
+        # Fetch sample well in format 'A1'
+        artifact_well: str = get_artifact_well(artifact=artifact)
+
+        # Checks that the sample well matches with one in the WELL_POSITIONS list (A1-A11)
+        # and adds the sample name to the SAMPLE_NAMES list for that position
+        if artifact_well in DATAFRAME["well positions"].values:
+            if artifact_well == DATAFRAME["well positions"].iloc[-1]:
+                failed_samples.append(
+                    {
+                        "artifact_name": artifact_name,
+                        "parsed_well": artifact_well,
+                        "error": "This position is reserved for the ladder.",
+                    }
+                )
+            else:
+                DATAFRAME.loc[DATAFRAME["well positions"] == artifact_well, "sample names"] = (
+                    artifact_name
+                )
+        else:
+            failed_samples.append(
+                {
+                    "artifact_name": artifact_name,
+                    "parsed_well": artifact_well,
+                    "error": "This position is not possible for the run.",
+                }
+            )
+
+    # Prints out error message(s)
+    if failed_samples:
+        all_errors = ""
+        for sample in failed_samples:
+            error_message: str = (
+                f"Sample {sample['artifact_name']} in position {sample['parsed_well']}: {sample['error']}"
+            )
+            all_errors = all_errors + " " + error_message
+        raise InvalidValueError(f"Errors found: {all_errors}")
+
+    # The ladder will always be in well A12
+    DATAFRAME["sample names"].iloc[-1] = "ladder"
+
+    # Create the csv file
+    DATAFRAME.index = range(1, len(DATAFRAME) + 1)
+    DATAFRAME.to_csv(Path(file), index=True, header=False)
+
+
+@click.command()
+@options.file_placeholder()
+@options.measurement()
+@click.pass_context
+def make_femtopulse_csv(
+    ctx: click.Context,
+    file: str,
+    measurement: bool,
+):
+    """Script to make a csv file for a Femtopulse run"""
+
+    LOG.info(f"Running {ctx.command_path} with params: {ctx.params}")
+    process = ctx.obj["process"]
+    artifacts = get_artifacts(process=process, measurement=measurement)
+
+    try:
+        get_data_and_write(
+            artifacts=artifacts,
+            file=f"{file}_femtopulse.csv",
+        )
+        click.echo("The file was successfully generated.")
+    except LimsError as e:
+        sys.exit(e.message)