From 187d09820d67b0751da420a2a35d5b454fd18cac Mon Sep 17 00:00:00 2001
From: idalindegaard <ida.lindegaard@scilifelab.se>
Date: Fri, 13 Dec 2024 14:55:32 +0100
Subject: [PATCH 01/25] New Femtopulse csv file script

---
 cg_lims/EPPs/files/base.py           |  2 +
 cg_lims/EPPs/files/femtopulse_csv.py | 90 ++++++++++++++++++++++++++++
 2 files changed, 92 insertions(+)
 create mode 100644 cg_lims/EPPs/files/femtopulse_csv.py

diff --git a/cg_lims/EPPs/files/base.py b/cg_lims/EPPs/files/base.py
index 94e1a27d..28aed224 100644
--- a/cg_lims/EPPs/files/base.py
+++ b/cg_lims/EPPs/files/base.py
@@ -12,6 +12,7 @@
 from cg_lims.EPPs.files.sample_sheet.create_ont_sample_sheet import create_ont_sample_sheet
 from cg_lims.EPPs.files.sample_sheet.create_sample_sheet import create_sample_sheet
 from cg_lims.EPPs.files.xml_to_udf import parse_run_parameters
+from cg_lims.EPPs.files.femtopulse_csv import make_femtopulse_csv
 
 
 @click.group(invoke_without_command=True)
@@ -31,3 +32,4 @@ 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)
diff --git a/cg_lims/EPPs/files/femtopulse_csv.py b/cg_lims/EPPs/files/femtopulse_csv.py
new file mode 100644
index 00000000..d463ec25
--- /dev/null
+++ b/cg_lims/EPPs/files/femtopulse_csv.py
@@ -0,0 +1,90 @@
+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 genologics.lims import Artifact
+
+LOG = logging.getLogger(__name__)
+
+ROWS = list(range(1,13)) # list numbered 1 to 12
+WELL_POSITIONS = [f"A{i}" for i in range(1,13)] # list with well positions A1-A12
+SAMPLE_NAMES = [""] * 12 # List with twelve empty positions for sample names
+
+
+def parse_well(artifact_position: str) -> str:
+    """Convert position from format 'A:1' to 'A1'."""
+    try:
+        row, col = artifact_position.split(":")
+        return f"{row}{col}"
+    except Exception:
+        return None
+
+
+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)."""
+
+    for artifact in artifacts:
+
+        artifact_name: str = artifact.samples[0].name
+        artifact_well: str = artifact.location[1]
+
+        # Convert sample well format from 'A:1' to 'A1'
+        parsed_well: str = parse_well(artifact_well)
+
+        # Checks that the sample well matches with one in the WELL_POSITIONS list and is A1-A11
+        if parsed_well in WELL_POSITIONS:
+            index: int = WELL_POSITIONS.index(parsed_well)
+            if index < 11:
+                SAMPLE_NAMES[index] = artifact_name
+            else:
+                raise InvalidValueError(f"Position {parsed_well} reserved for 'ladder', skipped.")
+        else:
+            raise InvalidValueError(f"Not possible position ({parsed_well}) for {artifact_name}, skipped.")
+
+    # The ladder will always be in well A12
+    SAMPLE_NAMES[-1] = "ladder"
+
+    # Create the csv file
+    df = pd.DataFrame({
+        0: ROWS,
+        1: WELL_POSITIONS,
+        2: SAMPLE_NAMES
+    })
+    print(df)
+    print(file)
+    df.to_csv(Path(file), index=False, 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"{process.id}-{file}.csv",
+        )
+        click.echo("The file was successfully generated.")
+    except LimsError as e:
+        sys.exit(e.message)
\ No newline at end of file

From a86a2cab79cbfcb74cb8b27d1f45496086e468c9 Mon Sep 17 00:00:00 2001
From: idalindegaard <ida.lindegaard@scilifelab.se>
Date: Fri, 13 Dec 2024 15:02:56 +0100
Subject: [PATCH 02/25] clean up the code a bit

---
 cg_lims/EPPs/files/femtopulse_csv.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/cg_lims/EPPs/files/femtopulse_csv.py b/cg_lims/EPPs/files/femtopulse_csv.py
index d463ec25..29b8e998 100644
--- a/cg_lims/EPPs/files/femtopulse_csv.py
+++ b/cg_lims/EPPs/files/femtopulse_csv.py
@@ -12,8 +12,8 @@
 
 LOG = logging.getLogger(__name__)
 
-ROWS = list(range(1,13)) # list numbered 1 to 12
-WELL_POSITIONS = [f"A{i}" for i in range(1,13)] # list with well positions A1-A12
+ROWS = list(range(1,13)) # List numbered 1 to 12
+WELL_POSITIONS = [f"A{i}" for i in range(1,13)] # List with well positions A1-A12
 SAMPLE_NAMES = [""] * 12 # List with twelve empty positions for sample names
 
 
@@ -61,8 +61,6 @@ def get_data_and_write(
         1: WELL_POSITIONS,
         2: SAMPLE_NAMES
     })
-    print(df)
-    print(file)
     df.to_csv(Path(file), index=False, header=False)
 
 @click.command()

From ed5d0cfc18ba2d898a0cd6fa0331fa14ab05259d Mon Sep 17 00:00:00 2001
From: idalindegaard <ida.lindegaard@scilifelab.se>
Date: Fri, 13 Dec 2024 15:27:07 +0100
Subject: [PATCH 03/25] updated file name

---
 cg_lims/EPPs/files/femtopulse_csv.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/cg_lims/EPPs/files/femtopulse_csv.py b/cg_lims/EPPs/files/femtopulse_csv.py
index 29b8e998..12838cb6 100644
--- a/cg_lims/EPPs/files/femtopulse_csv.py
+++ b/cg_lims/EPPs/files/femtopulse_csv.py
@@ -63,6 +63,7 @@ def get_data_and_write(
     })
     df.to_csv(Path(file), index=False, header=False)
 
+
 @click.command()
 @options.file_placeholder()
 @options.measurement()
@@ -81,7 +82,7 @@ def make_femtopulse_csv(
     try:
         get_data_and_write(
             artifacts=artifacts,
-            file=f"{process.id}-{file}.csv",
+            file=f"{file}.csv",
         )
         click.echo("The file was successfully generated.")
     except LimsError as e:

From 64c2956ede1fd4b6e40cf7c84db4bd75238537b1 Mon Sep 17 00:00:00 2001
From: idalindegaard <ida.lindegaard@scilifelab.se>
Date: Fri, 13 Dec 2024 15:29:09 +0100
Subject: [PATCH 04/25] updated file name again

---
 cg_lims/EPPs/files/femtopulse_csv.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cg_lims/EPPs/files/femtopulse_csv.py b/cg_lims/EPPs/files/femtopulse_csv.py
index 12838cb6..53368a33 100644
--- a/cg_lims/EPPs/files/femtopulse_csv.py
+++ b/cg_lims/EPPs/files/femtopulse_csv.py
@@ -82,7 +82,7 @@ def make_femtopulse_csv(
     try:
         get_data_and_write(
             artifacts=artifacts,
-            file=f"{file}.csv",
+            file=f"{file}_femtopulse.csv",
         )
         click.echo("The file was successfully generated.")
     except LimsError as e:

From 1a4a9c8764fc1d239766fd27d5bc8d0b6a21771c Mon Sep 17 00:00:00 2001
From: idalindegaard <ida.lindegaard@scilifelab.se>
Date: Fri, 13 Dec 2024 15:53:40 +0100
Subject: [PATCH 05/25] ran isort

---
 cg_lims/EPPs/files/femtopulse_csv.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/cg_lims/EPPs/files/femtopulse_csv.py b/cg_lims/EPPs/files/femtopulse_csv.py
index 53368a33..fe11c197 100644
--- a/cg_lims/EPPs/files/femtopulse_csv.py
+++ b/cg_lims/EPPs/files/femtopulse_csv.py
@@ -5,10 +5,11 @@
 
 import click
 import pandas as pd
+from genologics.lims import Artifact
+
 from cg_lims import options
 from cg_lims.exceptions import InvalidValueError, LimsError
 from cg_lims.get.artifacts import get_artifacts
-from genologics.lims import Artifact
 
 LOG = logging.getLogger(__name__)
 

From 1df87aff28c8c84a0e2f4ecd4f12ab3606eb90c7 Mon Sep 17 00:00:00 2001
From: idalindegaard <ida.lindegaard@scilifelab.se>
Date: Mon, 16 Dec 2024 13:56:36 +0100
Subject: [PATCH 06/25] updated error handling

---
 cg_lims/EPPs/files/femtopulse_csv.py | 17 +++++++++++++++--
 1 file changed, 15 insertions(+), 2 deletions(-)

diff --git a/cg_lims/EPPs/files/femtopulse_csv.py b/cg_lims/EPPs/files/femtopulse_csv.py
index fe11c197..bb346c3c 100644
--- a/cg_lims/EPPs/files/femtopulse_csv.py
+++ b/cg_lims/EPPs/files/femtopulse_csv.py
@@ -35,6 +35,8 @@ def get_data_and_write(
     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 = artifact.samples[0].name
@@ -49,9 +51,20 @@ def get_data_and_write(
             if index < 11:
                 SAMPLE_NAMES[index] = artifact_name
             else:
-                raise InvalidValueError(f"Position {parsed_well} reserved for 'ladder', skipped.")
+                failed_samples.append({"artifact_name": artifact_name, 
+                                       "parsed_well": parsed_well, 
+                                       "error": "This position is reserved for the ladder"})
         else:
-            raise InvalidValueError(f"Not possible position ({parsed_well}) for {artifact_name}, skipped.")
+            failed_samples.append({"artifact_name": artifact_name, 
+                                "parsed_well": parsed_well, 
+                                "error": "Position is not possible for the run"})
+
+    if failed_samples:
+        error_message: str = "\n".join(
+            f"Sample {sample['artifact_name']} in position {sample['parsed_well']}: {sample['error']}"
+        for sample in failed_samples
+        )
+        raise InvalidValueError(f"Errors found:\n{error_message}")
 
     # The ladder will always be in well A12
     SAMPLE_NAMES[-1] = "ladder"

From aa06f8ef6d3cfd16c44f13714c987de97a2099df Mon Sep 17 00:00:00 2001
From: idalindegaard <ida.lindegaard@scilifelab.se>
Date: Mon, 16 Dec 2024 14:34:53 +0100
Subject: [PATCH 07/25] updated error handling again

---
 cg_lims/EPPs/files/femtopulse_csv.py | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/cg_lims/EPPs/files/femtopulse_csv.py b/cg_lims/EPPs/files/femtopulse_csv.py
index bb346c3c..6897f63f 100644
--- a/cg_lims/EPPs/files/femtopulse_csv.py
+++ b/cg_lims/EPPs/files/femtopulse_csv.py
@@ -60,11 +60,15 @@ def get_data_and_write(
                                 "error": "Position is not possible for the run"})
 
     if failed_samples:
-        error_message: str = "\n".join(
-            f"Sample {sample['artifact_name']} in position {sample['parsed_well']}: {sample['error']}"
-        for sample in failed_samples
-        )
-        raise InvalidValueError(f"Errors found:\n{error_message}")
+        error_index: int = 0
+        for sample in failed_samples:
+            error_message: str = f"Sample {sample['artifact_name']} in position {sample['parsed_well']}: {sample['error']}"
+            if error_index < 1:
+                all_errors: str = error_message
+                error_index =+ 1
+            else:
+                all_errors = all_errors + '\n' + error_message
+        raise InvalidValueError(f"Errors found:\n{all_errors}")
 
     # The ladder will always be in well A12
     SAMPLE_NAMES[-1] = "ladder"

From b3ac98028923f81d0461bd44a9771fcd4a70619b Mon Sep 17 00:00:00 2001
From: idalindegaard <ida.lindegaard@scilifelab.se>
Date: Mon, 16 Dec 2024 16:12:59 +0100
Subject: [PATCH 08/25] finishing touches

---
 cg_lims/EPPs/files/femtopulse_csv.py | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/cg_lims/EPPs/files/femtopulse_csv.py b/cg_lims/EPPs/files/femtopulse_csv.py
index 6897f63f..0aa0e987 100644
--- a/cg_lims/EPPs/files/femtopulse_csv.py
+++ b/cg_lims/EPPs/files/femtopulse_csv.py
@@ -42,10 +42,11 @@ def get_data_and_write(
         artifact_name: str = artifact.samples[0].name
         artifact_well: str = artifact.location[1]
 
-        # Convert sample well format from 'A:1' to 'A1'
+        # Converts sample well format from 'A:1' to 'A1'
         parsed_well: str = parse_well(artifact_well)
 
-        # Checks that the sample well matches with one in the WELL_POSITIONS list and is A1-A11
+        # 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 parsed_well in WELL_POSITIONS:
             index: int = WELL_POSITIONS.index(parsed_well)
             if index < 11:
@@ -53,12 +54,13 @@ def get_data_and_write(
             else:
                 failed_samples.append({"artifact_name": artifact_name, 
                                        "parsed_well": parsed_well, 
-                                       "error": "This position is reserved for the ladder"})
+                                       "error": "This position is reserved for the ladder."})
         else:
             failed_samples.append({"artifact_name": artifact_name, 
                                 "parsed_well": parsed_well, 
-                                "error": "Position is not possible for the run"})
+                                "error": "Position is not possible for the run."})
 
+    # Prints out error message(s)
     if failed_samples:
         error_index: int = 0
         for sample in failed_samples:
@@ -67,8 +69,8 @@ def get_data_and_write(
                 all_errors: str = error_message
                 error_index =+ 1
             else:
-                all_errors = all_errors + '\n' + error_message
-        raise InvalidValueError(f"Errors found:\n{all_errors}")
+                all_errors = all_errors + ' ' + error_message
+        raise InvalidValueError(f"Errors found: {all_errors}")
 
     # The ladder will always be in well A12
     SAMPLE_NAMES[-1] = "ladder"

From dc9ebcdbc6484696390430e4f2ba1bdad9dea6b1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Karl=20Sv=C3=A4rd?= <karl.svard@scilifelab.se>
Date: Thu, 19 Dec 2024 17:56:18 +0100
Subject: [PATCH 09/25] black and isort

---
 cg_lims/EPPs/files/base.py           |  2 +-
 cg_lims/EPPs/files/femtopulse_csv.py | 54 ++++++++++++++--------------
 2 files changed, 29 insertions(+), 27 deletions(-)

diff --git a/cg_lims/EPPs/files/base.py b/cg_lims/EPPs/files/base.py
index a7909d12..6f0d142b 100644
--- a/cg_lims/EPPs/files/base.py
+++ b/cg_lims/EPPs/files/base.py
@@ -2,6 +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
+from cg_lims.EPPs.files.femtopulse_csv import make_femtopulse_csv
 
 # commands
 from cg_lims.EPPs.files.file_to_udf import csv_well_to_udf
@@ -14,7 +15,6 @@
 from cg_lims.EPPs.files.smrt_link.run_design import create_smrtlink_run_design
 from cg_lims.EPPs.files.smrt_link.sample_setup import create_smrtlink_sample_setup
 from cg_lims.EPPs.files.xml_to_udf import parse_run_parameters
-from cg_lims.EPPs.files.femtopulse_csv import make_femtopulse_csv
 
 
 @click.group(invoke_without_command=True)
diff --git a/cg_lims/EPPs/files/femtopulse_csv.py b/cg_lims/EPPs/files/femtopulse_csv.py
index 0aa0e987..6a0c34d4 100644
--- a/cg_lims/EPPs/files/femtopulse_csv.py
+++ b/cg_lims/EPPs/files/femtopulse_csv.py
@@ -5,17 +5,16 @@
 
 import click
 import pandas as pd
-from genologics.lims import Artifact
-
 from cg_lims import options
 from cg_lims.exceptions import InvalidValueError, LimsError
 from cg_lims.get.artifacts import get_artifacts
+from genologics.lims import Artifact
 
 LOG = logging.getLogger(__name__)
 
-ROWS = list(range(1,13)) # List numbered 1 to 12
-WELL_POSITIONS = [f"A{i}" for i in range(1,13)] # List with well positions A1-A12
-SAMPLE_NAMES = [""] * 12 # List with twelve empty positions for sample names
+ROWS = list(range(1, 13))  # List numbered 1 to 12
+WELL_POSITIONS = [f"A{i}" for i in range(1, 13)]  # List with well positions A1-A12
+SAMPLE_NAMES = [""] * 12  # List with twelve empty positions for sample names
 
 
 def parse_well(artifact_position: str) -> str:
@@ -27,12 +26,9 @@ def parse_well(artifact_position: str) -> str:
         return None
 
 
-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 
+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 = []
@@ -52,35 +48,41 @@ def get_data_and_write(
             if index < 11:
                 SAMPLE_NAMES[index] = artifact_name
             else:
-                failed_samples.append({"artifact_name": artifact_name, 
-                                       "parsed_well": parsed_well, 
-                                       "error": "This position is reserved for the ladder."})
+                failed_samples.append(
+                    {
+                        "artifact_name": artifact_name,
+                        "parsed_well": parsed_well,
+                        "error": "This position is reserved for the ladder.",
+                    }
+                )
         else:
-            failed_samples.append({"artifact_name": artifact_name, 
-                                "parsed_well": parsed_well, 
-                                "error": "Position is not possible for the run."})
+            failed_samples.append(
+                {
+                    "artifact_name": artifact_name,
+                    "parsed_well": parsed_well,
+                    "error": "Position is not possible for the run.",
+                }
+            )
 
     # Prints out error message(s)
     if failed_samples:
         error_index: int = 0
         for sample in failed_samples:
-            error_message: str = f"Sample {sample['artifact_name']} in position {sample['parsed_well']}: {sample['error']}"
+            error_message: str = (
+                f"Sample {sample['artifact_name']} in position {sample['parsed_well']}: {sample['error']}"
+            )
             if error_index < 1:
                 all_errors: str = error_message
-                error_index =+ 1
+                error_index = +1
             else:
-                all_errors = all_errors + ' ' + error_message
+                all_errors = all_errors + " " + error_message
         raise InvalidValueError(f"Errors found: {all_errors}")
 
     # The ladder will always be in well A12
     SAMPLE_NAMES[-1] = "ladder"
 
     # Create the csv file
-    df = pd.DataFrame({
-        0: ROWS,
-        1: WELL_POSITIONS,
-        2: SAMPLE_NAMES
-    })
+    df = pd.DataFrame({0: ROWS, 1: WELL_POSITIONS, 2: SAMPLE_NAMES})
     df.to_csv(Path(file), index=False, header=False)
 
 
@@ -106,4 +108,4 @@ def make_femtopulse_csv(
         )
         click.echo("The file was successfully generated.")
     except LimsError as e:
-        sys.exit(e.message)
\ No newline at end of file
+        sys.exit(e.message)

From 8b30f0bae224a297ee1e6b5e8bad9d5a1148f77a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Karl=20Sv=C3=A4rd?= <karl.svard@scilifelab.se>
Date: Thu, 19 Dec 2024 17:57:44 +0100
Subject: [PATCH 10/25] more isort for some reason

---
 cg_lims/EPPs/files/base.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/cg_lims/EPPs/files/base.py b/cg_lims/EPPs/files/base.py
index 6f0d142b..e5cbef56 100644
--- a/cg_lims/EPPs/files/base.py
+++ b/cg_lims/EPPs/files/base.py
@@ -3,8 +3,6 @@
 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
 from cg_lims.EPPs.files.femtopulse_csv import make_femtopulse_csv
-
-# commands
 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

From e2d805944bc636781203e40c2d11c4e522c0c677 Mon Sep 17 00:00:00 2001
From: idalindegaard <ida.lindegaard@scilifelab.se>
Date: Tue, 7 Jan 2025 16:15:24 +0100
Subject: [PATCH 11/25] several changes after feedback

---
 cg_lims/EPPs/files/femtopulse_csv.py | 62 ++++++++++++++--------------
 1 file changed, 32 insertions(+), 30 deletions(-)

diff --git a/cg_lims/EPPs/files/femtopulse_csv.py b/cg_lims/EPPs/files/femtopulse_csv.py
index 6a0c34d4..756d77a8 100644
--- a/cg_lims/EPPs/files/femtopulse_csv.py
+++ b/cg_lims/EPPs/files/femtopulse_csv.py
@@ -5,25 +5,30 @@
 
 import click
 import pandas as pd
+from genologics.lims import Artifact
+
 from cg_lims import options
 from cg_lims.exceptions import InvalidValueError, LimsError
 from cg_lims.get.artifacts import get_artifacts
-from genologics.lims import Artifact
+from cg_lims.get.fields import get_artifact_well
 
 LOG = logging.getLogger(__name__)
 
-ROWS = list(range(1, 13))  # List numbered 1 to 12
+
 WELL_POSITIONS = [f"A{i}" for i in range(1, 13)]  # List with well positions A1-A12
-SAMPLE_NAMES = [""] * 12  # List with twelve empty positions for sample names
+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 parse_well(artifact_position: str) -> str:
-    """Convert position from format 'A:1' to 'A1'."""
-    try:
-        row, col = artifact_position.split(":")
-        return f"{row}{col}"
-    except Exception:
-        return None
+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):
@@ -35,55 +40,52 @@ def get_data_and_write(artifacts: List[Artifact], file: str):
 
     for artifact in artifacts:
 
-        artifact_name: str = artifact.samples[0].name
-        artifact_well: str = artifact.location[1]
+        artifact_name: str = get_sample_artifact_name(artifact=artifact)
+        artifact_well: str = get_artifact_well(artifact=artifact)
 
         # Converts sample well format from 'A:1' to 'A1'
-        parsed_well: str = parse_well(artifact_well)
+        #parsed_well: str = parse_well(artifact_well)
 
         # 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 parsed_well in WELL_POSITIONS:
-            index: int = WELL_POSITIONS.index(parsed_well)
-            if index < 11:
-                SAMPLE_NAMES[index] = artifact_name
-            else:
+        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": parsed_well,
+                        "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": parsed_well,
-                    "error": "Position is not possible for the run.",
+                    "parsed_well": artifact_well,
+                    "error": "This position is not possible for the run.",
                 }
             )
 
     # Prints out error message(s)
     if failed_samples:
-        error_index: int = 0
+        all_errors = ""
         for sample in failed_samples:
             error_message: str = (
                 f"Sample {sample['artifact_name']} in position {sample['parsed_well']}: {sample['error']}"
             )
-            if error_index < 1:
-                all_errors: str = error_message
-                error_index = +1
-            else:
-                all_errors = all_errors + " " + error_message
+            all_errors = all_errors + " " + error_message
         raise InvalidValueError(f"Errors found: {all_errors}")
 
     # The ladder will always be in well A12
-    SAMPLE_NAMES[-1] = "ladder"
+    DATAFRAME["sample names"].iloc[-1] = "ladder"
 
     # Create the csv file
-    df = pd.DataFrame({0: ROWS, 1: WELL_POSITIONS, 2: SAMPLE_NAMES})
-    df.to_csv(Path(file), index=False, header=False)
+    DATAFRAME.to_csv(Path(file), index=True, header=False)
+    DATAFRAME.index = range(1, len(DATAFRAME) + 1)
 
 
 @click.command()

From edb580a1d59f96bb9aad7f4dfc8e5936a3cd8d3b Mon Sep 17 00:00:00 2001
From: idalindegaard <ida.lindegaard@scilifelab.se>
Date: Tue, 7 Jan 2025 16:28:13 +0100
Subject: [PATCH 12/25] index range fix

---
 cg_lims/EPPs/files/femtopulse_csv.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cg_lims/EPPs/files/femtopulse_csv.py b/cg_lims/EPPs/files/femtopulse_csv.py
index 756d77a8..b07cb198 100644
--- a/cg_lims/EPPs/files/femtopulse_csv.py
+++ b/cg_lims/EPPs/files/femtopulse_csv.py
@@ -84,8 +84,8 @@ def get_data_and_write(artifacts: List[Artifact], file: str):
     DATAFRAME["sample names"].iloc[-1] = "ladder"
 
     # Create the csv file
-    DATAFRAME.to_csv(Path(file), index=True, header=False)
     DATAFRAME.index = range(1, len(DATAFRAME) + 1)
+    DATAFRAME.to_csv(Path(file), index=True, header=False)
 
 
 @click.command()

From 7fa34cee47db5ef9a844829b63cbb2baedf2a456 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Karl=20Sv=C3=A4rd?= <karl.svard@scilifelab.se>
Date: Tue, 7 Jan 2025 17:00:04 +0100
Subject: [PATCH 13/25] sneak edits

---
 cg_lims/EPPs/files/femtopulse_csv.py | 18 +++++++-----------
 1 file changed, 7 insertions(+), 11 deletions(-)

diff --git a/cg_lims/EPPs/files/femtopulse_csv.py b/cg_lims/EPPs/files/femtopulse_csv.py
index b07cb198..437e0eec 100644
--- a/cg_lims/EPPs/files/femtopulse_csv.py
+++ b/cg_lims/EPPs/files/femtopulse_csv.py
@@ -5,20 +5,17 @@
 
 import click
 import pandas as pd
-from genologics.lims import Artifact
-
 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
+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
@@ -41,10 +38,9 @@ def get_data_and_write(artifacts: List[Artifact], file: str):
     for artifact in artifacts:
 
         artifact_name: str = get_sample_artifact_name(artifact=artifact)
-        artifact_well: str = get_artifact_well(artifact=artifact)
 
-        # Converts sample well format from 'A:1' to 'A1'
-        #parsed_well: str = parse_well(artifact_well)
+        # 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
@@ -58,9 +54,9 @@ def get_data_and_write(artifacts: List[Artifact], file: str):
                     }
                 )
             else:
-                DATAFRAME.loc[
-                    DATAFRAME["well positions"] == artifact_well, "sample names"
-                ] = artifact_name
+                DATAFRAME.loc[DATAFRAME["well positions"] == artifact_well, "sample names"] = (
+                    artifact_name
+                )
         else:
             failed_samples.append(
                 {

From d93460e8730a4a0f3b4a956656ea99ab6464475f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Karl=20Sv=C3=A4rd?= <karl.svard@scilifelab.se>
Date: Wed, 8 Jan 2025 09:39:34 +0100
Subject: [PATCH 14/25] renamed xml parser

---
 cg_lims/EPPs/files/base.py                                   | 2 +-
 cg_lims/EPPs/files/{xml_to_udf.py => illumina_xml_to_udf.py} | 0
 2 files changed, 1 insertion(+), 1 deletion(-)
 rename cg_lims/EPPs/files/{xml_to_udf.py => illumina_xml_to_udf.py} (100%)

diff --git a/cg_lims/EPPs/files/base.py b/cg_lims/EPPs/files/base.py
index e5cbef56..fd57065a 100644
--- a/cg_lims/EPPs/files/base.py
+++ b/cg_lims/EPPs/files/base.py
@@ -5,6 +5,7 @@
 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.illumina_xml_to_udf import parse_run_parameters
 from cg_lims.EPPs.files.ont_json_to_udf import parse_ont_report
 from cg_lims.EPPs.files.placement_map.make_96well_placement_map import placement_map
 from cg_lims.EPPs.files.pooling_map.make_pooling_map import pool_map
@@ -12,7 +13,6 @@
 from cg_lims.EPPs.files.sample_sheet.create_sample_sheet import create_sample_sheet
 from cg_lims.EPPs.files.smrt_link.run_design import create_smrtlink_run_design
 from cg_lims.EPPs.files.smrt_link.sample_setup import create_smrtlink_sample_setup
-from cg_lims.EPPs.files.xml_to_udf import parse_run_parameters
 
 
 @click.group(invoke_without_command=True)
diff --git a/cg_lims/EPPs/files/xml_to_udf.py b/cg_lims/EPPs/files/illumina_xml_to_udf.py
similarity index 100%
rename from cg_lims/EPPs/files/xml_to_udf.py
rename to cg_lims/EPPs/files/illumina_xml_to_udf.py

From 4cb6ce505ce52766721f96c00f6b50c842615dba Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Karl=20Sv=C3=A4rd?= <karl.svard@scilifelab.se>
Date: Wed, 8 Jan 2025 09:41:57 +0100
Subject: [PATCH 15/25] moved all parsers into new sub dir

---
 cg_lims/EPPs/files/base.py                              | 6 +++---
 cg_lims/EPPs/files/parsers/__init__.py                  | 0
 cg_lims/EPPs/files/{ => parsers}/file_to_udf.py         | 0
 cg_lims/EPPs/files/{ => parsers}/illumina_xml_to_udf.py | 0
 cg_lims/EPPs/files/{ => parsers}/ont_json_to_udf.py     | 0
 5 files changed, 3 insertions(+), 3 deletions(-)
 create mode 100644 cg_lims/EPPs/files/parsers/__init__.py
 rename cg_lims/EPPs/files/{ => parsers}/file_to_udf.py (100%)
 rename cg_lims/EPPs/files/{ => parsers}/illumina_xml_to_udf.py (100%)
 rename cg_lims/EPPs/files/{ => parsers}/ont_json_to_udf.py (100%)

diff --git a/cg_lims/EPPs/files/base.py b/cg_lims/EPPs/files/base.py
index fd57065a..15236771 100644
--- a/cg_lims/EPPs/files/base.py
+++ b/cg_lims/EPPs/files/base.py
@@ -3,10 +3,10 @@
 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
 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.illumina_xml_to_udf import parse_run_parameters
-from cg_lims.EPPs.files.ont_json_to_udf import parse_ont_report
+from cg_lims.EPPs.files.parsers.file_to_udf import csv_well_to_udf
+from cg_lims.EPPs.files.parsers.illumina_xml_to_udf import parse_run_parameters
+from cg_lims.EPPs.files.parsers.ont_json_to_udf import parse_ont_report
 from cg_lims.EPPs.files.placement_map.make_96well_placement_map import placement_map
 from cg_lims.EPPs.files.pooling_map.make_pooling_map import pool_map
 from cg_lims.EPPs.files.sample_sheet.create_ont_sample_sheet import create_ont_sample_sheet
diff --git a/cg_lims/EPPs/files/parsers/__init__.py b/cg_lims/EPPs/files/parsers/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/cg_lims/EPPs/files/file_to_udf.py b/cg_lims/EPPs/files/parsers/file_to_udf.py
similarity index 100%
rename from cg_lims/EPPs/files/file_to_udf.py
rename to cg_lims/EPPs/files/parsers/file_to_udf.py
diff --git a/cg_lims/EPPs/files/illumina_xml_to_udf.py b/cg_lims/EPPs/files/parsers/illumina_xml_to_udf.py
similarity index 100%
rename from cg_lims/EPPs/files/illumina_xml_to_udf.py
rename to cg_lims/EPPs/files/parsers/illumina_xml_to_udf.py
diff --git a/cg_lims/EPPs/files/ont_json_to_udf.py b/cg_lims/EPPs/files/parsers/ont_json_to_udf.py
similarity index 100%
rename from cg_lims/EPPs/files/ont_json_to_udf.py
rename to cg_lims/EPPs/files/parsers/ont_json_to_udf.py

From c07e94e770e9be7bcd24ae5ff42e0b70796c71dc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Karl=20Sv=C3=A4rd?= <karl.svard@scilifelab.se>
Date: Wed, 8 Jan 2025 11:16:39 +0100
Subject: [PATCH 16/25] add new common func for creating well/artifact dicts

---
 .../files/parsers/quantit_excel_to_udf.py     | 13 +++++++++
 cg_lims/get/artifacts.py                      | 29 +++++++++++++++++++
 2 files changed, 42 insertions(+)
 create mode 100644 cg_lims/EPPs/files/parsers/quantit_excel_to_udf.py

diff --git a/cg_lims/EPPs/files/parsers/quantit_excel_to_udf.py b/cg_lims/EPPs/files/parsers/quantit_excel_to_udf.py
new file mode 100644
index 00000000..61928321
--- /dev/null
+++ b/cg_lims/EPPs/files/parsers/quantit_excel_to_udf.py
@@ -0,0 +1,13 @@
+import csv
+import logging
+import sys
+from pathlib import Path
+
+import click
+from cg_lims import options
+from cg_lims.exceptions import LimsError, MissingArtifactError, MissingFileError
+from cg_lims.get.artifacts import create_well_dict, get_artifact_by_name
+from cg_lims.get.files import get_file_path
+from genologics.entities import Artifact
+
+LOG = logging.getLogger(__name__)
diff --git a/cg_lims/get/artifacts.py b/cg_lims/get/artifacts.py
index 2568b447..17a1eb42 100644
--- a/cg_lims/get/artifacts.py
+++ b/cg_lims/get/artifacts.py
@@ -245,3 +245,32 @@ def get_non_pooled_artifacts(artifact: Artifact) -> List[Artifact]:
     for artifact in artifact.input_artifact_list():
         artifacts.extend(get_non_pooled_artifacts(artifact))
     return artifacts
+
+
+def create_well_dict(
+    process: Process,
+    input_flag: bool = False,
+    native_well_format: bool = False,
+) -> Dict[str, Artifact]:
+    """Creates a well dict based on the input_output_map
+    keys: well of input artifact
+    values: input/output artifact depending on the input flag
+    """
+
+    well_dict: Dict[str, Artifact] = {}
+    lims: Lims = process.lims
+    for input, output in process.input_output_maps:
+        if output.get("output-generation-type") == "PerAllInputs":
+            continue
+        source_artifact: Artifact = (
+            Artifact(lims, id=input["limsid"])
+            if input_flag
+            else Artifact(lims, id=output["limsid"])
+        )
+        well: str = (
+            source_artifact.location[1].replace(":", "")
+            if not native_well_format
+            else source_artifact.location[1]
+        )
+        well_dict[well] = source_artifact
+    return well_dict

From bf2ff8a6939d8a914a7ce3e6195c9f77f5f09b6f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Karl=20Sv=C3=A4rd?= <karl.svard@scilifelab.se>
Date: Wed, 8 Jan 2025 11:27:59 +0100
Subject: [PATCH 17/25] add type hints and a bit of refactoring to file_to_udf

---
 cg_lims/EPPs/files/parsers/file_to_udf.py | 57 ++++++++---------------
 1 file changed, 19 insertions(+), 38 deletions(-)

diff --git a/cg_lims/EPPs/files/parsers/file_to_udf.py b/cg_lims/EPPs/files/parsers/file_to_udf.py
index 9e44396b..9513b610 100644
--- a/cg_lims/EPPs/files/parsers/file_to_udf.py
+++ b/cg_lims/EPPs/files/parsers/file_to_udf.py
@@ -4,46 +4,28 @@
 import logging
 import sys
 from pathlib import Path
+from typing import Any, Dict, List
 
 import click
 from cg_lims import options
 from cg_lims.exceptions import LimsError, MissingArtifactError, MissingFileError
-from cg_lims.get.artifacts import get_artifact_by_name
+from cg_lims.get.artifacts import create_well_dict, get_artifact_by_name
 from cg_lims.get.files import get_file_path
-from genologics.entities import Artifact
+from genologics.entities import Artifact, Process
 
 LOG = logging.getLogger(__name__)
 
 
-def make_well_dict(process, lims, input):
-    """Creates a well dict based on input_output_map
-    keys: well of input artifact
-    values: input/output artifact depending on the input flag
-    """
-
-    well_dict = {}
-    for inp, outp in process.input_output_maps:
-        if outp.get("output-generation-type") == "PerAllInputs":
-            continue
-        in_art = Artifact(lims, id=inp["limsid"])
-        out_art = Artifact(lims, id=outp["limsid"])
-        source_art = in_art if input == True else out_art
-        col, row = source_art.location[1].split(":")
-        well = col + row
-        well_dict[well] = out_art
-    return well_dict
-
-
 def set_udfs(well_field: str, value_field: str, udf: str, well_dict: dict, result_file: Path):
     """Reads the csv and sets the value for each sample"""
 
-    error_msg = []
-    passed_arts = 0
+    error_msg: List[str] = []
+    passed_arts: int = 0
     with open(result_file, newline="", encoding="latin1") as csvfile:
-        reader = csv.DictReader(csvfile)
+        reader: csv.DictReader = csv.DictReader(csvfile)
         for sample in reader:
-            well = sample.get(well_field)
-            value = sample.get(value_field)
+            well: str = sample.get(well_field)
+            value: Any = sample.get(value_field)
             if value is None:
                 error_msg.append("Some samples in the file had missing values.")
                 LOG.info(f"Missing value for sample {sample} in well {well}. Skipping!")
@@ -51,18 +33,18 @@ def set_udfs(well_field: str, value_field: str, udf: str, well_dict: dict, resul
             elif well not in well_dict:
                 LOG.info(f"Well {well} was not found in the step. Skipping!")
                 continue
-            art = well_dict[well]
+            artifact: Artifact = well_dict[well]
             try:
-                art.udf[udf] = str(value)
+                artifact.udf[udf] = str(value)
             except:
-                art.udf[udf] = float(value)
-            art.put()
+                artifact.udf[udf] = float(value)
+            artifact.put()
             passed_arts += 1
 
     if passed_arts < len(well_dict.keys()):
         error_msg.append("Some samples in the step were not represented in the file.")
 
-    error_string = " ".join(list(set(error_msg)))
+    error_string: str = " ".join(list(set(error_msg)))
     if error_msg:
         raise MissingArtifactError(error_string)
 
@@ -81,20 +63,19 @@ def csv_well_to_udf(
     """Script to copy data from file to udf based on well position"""
 
     LOG.info(f"Running {ctx.command_path} with params: {ctx.params}")
-    process = ctx.obj["process"]
-    lims = ctx.obj["lims"]
+    process: Process = ctx.obj["process"]
 
     if local_file:
-        file_path = local_file
+        file_path: str = local_file
     else:
-        file_art = get_artifact_by_name(process=process, name=file)
-        file_path = get_file_path(file_art)
+        file_art: Artifact = get_artifact_by_name(process=process, name=file)
+        file_path: str = get_file_path(file_art)
 
     try:
         if not Path(file_path).is_file():
             raise MissingFileError(f"No such file: {file_path}")
-        well_dict = make_well_dict(process, lims, input)
-        set_udfs(well_field, value_field, udf, well_dict, file_path)
+        well_dict: Dict[str, Artifact] = create_well_dict(process=process, input_flag=input)
+        set_udfs(well_field, value_field, udf, well_dict, Path(file_path))
         click.echo("The udfs were sucessfully populated.")
     except LimsError as e:
         sys.exit(e.message)

From 75f60dabbe345a06eca605a3f57a24e86cb15c7a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Karl=20Sv=C3=A4rd?= <karl.svard@scilifelab.se>
Date: Wed, 8 Jan 2025 15:14:17 +0100
Subject: [PATCH 18/25] adding more code

---
 cg_lims/EPPs/files/base.py                    |  2 +
 .../files/parsers/quantit_excel_to_udf.py     | 64 ++++++++++++++++++-
 2 files changed, 64 insertions(+), 2 deletions(-)

diff --git a/cg_lims/EPPs/files/base.py b/cg_lims/EPPs/files/base.py
index 15236771..54df436a 100644
--- a/cg_lims/EPPs/files/base.py
+++ b/cg_lims/EPPs/files/base.py
@@ -7,6 +7,7 @@
 from cg_lims.EPPs.files.parsers.file_to_udf import csv_well_to_udf
 from cg_lims.EPPs.files.parsers.illumina_xml_to_udf import parse_run_parameters
 from cg_lims.EPPs.files.parsers.ont_json_to_udf import parse_ont_report
+from cg_lims.EPPs.files.parsers.quantit_excel_to_udf import quantit_excel_to_udf
 from cg_lims.EPPs.files.placement_map.make_96well_placement_map import placement_map
 from cg_lims.EPPs.files.pooling_map.make_pooling_map import pool_map
 from cg_lims.EPPs.files.sample_sheet.create_ont_sample_sheet import create_ont_sample_sheet
@@ -35,3 +36,4 @@ def files(ctx):
 files.add_command(make_femtopulse_csv)
 files.add_command(create_smrtlink_sample_setup)
 files.add_command(create_smrtlink_run_design)
+files.add_command(quantit_excel_to_udf)
diff --git a/cg_lims/EPPs/files/parsers/quantit_excel_to_udf.py b/cg_lims/EPPs/files/parsers/quantit_excel_to_udf.py
index 61928321..fb151f58 100644
--- a/cg_lims/EPPs/files/parsers/quantit_excel_to_udf.py
+++ b/cg_lims/EPPs/files/parsers/quantit_excel_to_udf.py
@@ -1,13 +1,73 @@
-import csv
 import logging
 import sys
 from pathlib import Path
+from typing import Dict
 
 import click
+import pandas as pd
 from cg_lims import options
 from cg_lims.exceptions import LimsError, MissingArtifactError, MissingFileError
 from cg_lims.get.artifacts import create_well_dict, get_artifact_by_name
 from cg_lims.get.files import get_file_path
-from genologics.entities import Artifact
+from genologics.entities import Artifact, Process
 
 LOG = logging.getLogger(__name__)
+
+
+def set_udfs(udf: str, well_dict: dict, result_file: Path):
+    """Reads the Quant-iT Excel file and sets the value for each sample"""
+
+    failed_artifacts: int = 0
+    df: pd.DataFrame = pd.read_excel(result_file, skiprows=11, header=None)
+    for index, row in df.iterrows():
+        if row[0] not in well_dict.keys():
+            LOG.info(f"Well {row[0]} is not used by a sample in the step, skipping.")
+            continue
+        elif pd.isna(row[2]):
+            LOG.info(
+                f"Well {row[0]} does not have a valid concentration value ({row[2]}), skipping."
+            )
+            failed_artifacts += 1
+            continue
+        artifact: Artifact = well_dict[row[0]]
+        artifact.udf[udf] = row[2]
+        artifact.put()
+
+    if failed_artifacts:
+        raise MissingArtifactError(
+            f"Warning: Skipped {failed_artifacts} artifact(s) with wrong and/or blank values for some UDFs."
+        )
+
+
+@click.command()
+@options.file_placeholder(help="File placeholder name.")
+@options.local_file()
+@options.udf()
+@options.input()
+@click.pass_context
+def quantit_excel_to_udf(
+    ctx,
+    file: str,
+    local_file: str,
+    udf: str,
+    input: bool,
+):
+    """Script to copy data from a Quant-iT result Excel file to concentration UDFs based on well position"""
+
+    LOG.info(f"Running {ctx.command_path} with params: {ctx.params}")
+    process: Process = ctx.obj["process"]
+
+    if local_file:
+        file_path: str = local_file
+    else:
+        file_art: Artifact = get_artifact_by_name(process=process, name=file)
+        file_path: str = get_file_path(file_art)
+
+    try:
+        if not Path(file_path).is_file():
+            raise MissingFileError(f"No such file: {file_path}")
+        well_dict: Dict[str, Artifact] = create_well_dict(process=process, input_flag=input)
+        set_udfs(udf, well_dict, Path(file_path))
+        click.echo(f"Updated {len(well_dict.keys())} artifact(s) successfully.")
+    except LimsError as e:
+        sys.exit(e.message)

From f9b4c70ac1f2cda12ab3ed739445d8b9e5736d02 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Karl=20Sv=C3=A4rd?= <karl.svard@scilifelab.se>
Date: Wed, 8 Jan 2025 17:10:31 +0100
Subject: [PATCH 19/25] some fixes and additions

---
 .../files/parsers/quantit_excel_to_udf.py     |  6 ++--
 cg_lims/get/artifacts.py                      | 29 +++++++++++--------
 cg_lims/get/fields.py                         |  9 ++++++
 3 files changed, 30 insertions(+), 14 deletions(-)

diff --git a/cg_lims/EPPs/files/parsers/quantit_excel_to_udf.py b/cg_lims/EPPs/files/parsers/quantit_excel_to_udf.py
index fb151f58..9b7c35b2 100644
--- a/cg_lims/EPPs/files/parsers/quantit_excel_to_udf.py
+++ b/cg_lims/EPPs/files/parsers/quantit_excel_to_udf.py
@@ -66,8 +66,10 @@ def quantit_excel_to_udf(
     try:
         if not Path(file_path).is_file():
             raise MissingFileError(f"No such file: {file_path}")
-        well_dict: Dict[str, Artifact] = create_well_dict(process=process, input_flag=input)
-        set_udfs(udf, well_dict, Path(file_path))
+        well_dict: Dict[str, Artifact] = create_well_dict(
+            process=process, input_flag=input, quantit_well_format=True
+        )
+        set_udfs(udf=udf, well_dict=well_dict, result_file=Path(file_path))
         click.echo(f"Updated {len(well_dict.keys())} artifact(s) successfully.")
     except LimsError as e:
         sys.exit(e.message)
diff --git a/cg_lims/get/artifacts.py b/cg_lims/get/artifacts.py
index 17a1eb42..c05bb919 100644
--- a/cg_lims/get/artifacts.py
+++ b/cg_lims/get/artifacts.py
@@ -3,7 +3,8 @@
 from enum import Enum
 from typing import Dict, List, Literal, Optional, Set, Tuple
 
-from cg_lims.exceptions import FileError, MissingArtifactError
+from cg_lims.exceptions import FileError, InvalidValueError, MissingArtifactError
+from cg_lims.get.fields import get_artifact_well, get_quantit_artifact_well
 from genologics.entities import Artifact, Process, Sample
 from genologics.lims import Lims
 
@@ -251,6 +252,7 @@ def create_well_dict(
     process: Process,
     input_flag: bool = False,
     native_well_format: bool = False,
+    quantit_well_format: bool = False,
 ) -> Dict[str, Artifact]:
     """Creates a well dict based on the input_output_map
     keys: well of input artifact
@@ -262,15 +264,18 @@ def create_well_dict(
     for input, output in process.input_output_maps:
         if output.get("output-generation-type") == "PerAllInputs":
             continue
-        source_artifact: Artifact = (
-            Artifact(lims, id=input["limsid"])
-            if input_flag
-            else Artifact(lims, id=output["limsid"])
-        )
-        well: str = (
-            source_artifact.location[1].replace(":", "")
-            if not native_well_format
-            else source_artifact.location[1]
-        )
-        well_dict[well] = source_artifact
+        input_artifact = Artifact(lims, id=input["limsid"])
+        output_artifact = Artifact(lims, id=output["limsid"])
+        source_artifact: Artifact = input_artifact if input_flag else output_artifact
+        if native_well_format:
+            well: str = source_artifact.location[1]
+        elif quantit_well_format:
+            well: str = get_quantit_artifact_well(artifact=source_artifact)
+        else:
+            well: str = get_artifact_well(artifact=source_artifact)
+        if well in well_dict.keys():
+            raise InvalidValueError(
+                f"Can't create dictionary! Well {well} is already used by another artifact."
+            )
+        well_dict[well] = output_artifact
     return well_dict
diff --git a/cg_lims/get/fields.py b/cg_lims/get/fields.py
index 24f65442..b3fd6a9a 100644
--- a/cg_lims/get/fields.py
+++ b/cg_lims/get/fields.py
@@ -65,6 +65,15 @@ def get_artifact_well(artifact: Artifact) -> str:
     return location[1].replace(":", "")
 
 
+def get_quantit_artifact_well(artifact: Artifact) -> str:
+    """Parsing out the well position from LocationDescriptor"""
+
+    col, row = artifact.location[1].split(":")
+    if int(row) < 10:
+        row = "0" + row
+    return col + row
+
+
 def get_index_well(artifact: Artifact):
     """Parsing out the index well position from the reagent label string which
     typically looks like this: '44_A05 IDT_10nt_446 (AGCGTGACCT-CCATCCGAGT)'

From 89e1dd63dd86115fdfe5a4ea159e34c878c63b79 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Karl=20Sv=C3=A4rd?= <karl.svard@scilifelab.se>
Date: Thu, 9 Jan 2025 16:44:59 +0100
Subject: [PATCH 20/25] add more detailed error messages

---
 cg_lims/EPPs/files/parsers/quantit_excel_to_udf.py | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/cg_lims/EPPs/files/parsers/quantit_excel_to_udf.py b/cg_lims/EPPs/files/parsers/quantit_excel_to_udf.py
index 9b7c35b2..a344a275 100644
--- a/cg_lims/EPPs/files/parsers/quantit_excel_to_udf.py
+++ b/cg_lims/EPPs/files/parsers/quantit_excel_to_udf.py
@@ -18,10 +18,12 @@ def set_udfs(udf: str, well_dict: dict, result_file: Path):
     """Reads the Quant-iT Excel file and sets the value for each sample"""
 
     failed_artifacts: int = 0
+    skipped_artifacts: int = 0
     df: pd.DataFrame = pd.read_excel(result_file, skiprows=11, header=None)
     for index, row in df.iterrows():
         if row[0] not in well_dict.keys():
             LOG.info(f"Well {row[0]} is not used by a sample in the step, skipping.")
+            skipped_artifacts += 1
             continue
         elif pd.isna(row[2]):
             LOG.info(
@@ -33,10 +35,13 @@ def set_udfs(udf: str, well_dict: dict, result_file: Path):
         artifact.udf[udf] = row[2]
         artifact.put()
 
-    if failed_artifacts:
-        raise MissingArtifactError(
-            f"Warning: Skipped {failed_artifacts} artifact(s) with wrong and/or blank values for some UDFs."
-        )
+    if failed_artifacts or skipped_artifacts:
+        error_message = "Warning:"
+        if failed_artifacts:
+            error_message += f" Skipped {failed_artifacts} artifact(s) with wrong and/or blank values for some UDFs."
+        if skipped_artifacts:
+            error_message += f" Skipped {failed_artifacts} artifact(s) as they weren't represented in the result file."
+        raise MissingArtifactError(error_message)
 
 
 @click.command()

From 6b18bece9dab0ac1ec72aa9b9dbac7f7eabdd938 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Karl=20Sv=C3=A4rd?= <karl.svard@scilifelab.se>
Date: Fri, 10 Jan 2025 15:45:52 +0100
Subject: [PATCH 21/25] first set of changes to file2udf

---
 cg_lims/EPPs/files/parsers/file_to_udf.py | 148 ++++++++++++++++------
 cg_lims/options.py                        |  18 ++-
 2 files changed, 128 insertions(+), 38 deletions(-)

diff --git a/cg_lims/EPPs/files/parsers/file_to_udf.py b/cg_lims/EPPs/files/parsers/file_to_udf.py
index 9513b610..028eb87a 100644
--- a/cg_lims/EPPs/files/parsers/file_to_udf.py
+++ b/cg_lims/EPPs/files/parsers/file_to_udf.py
@@ -4,11 +4,11 @@
 import logging
 import sys
 from pathlib import Path
-from typing import Any, Dict, List
+from typing import Any, Dict, List, Optional, Tuple
 
 import click
 from cg_lims import options
-from cg_lims.exceptions import LimsError, MissingArtifactError, MissingFileError
+from cg_lims.exceptions import ArgumentError, LimsError, MissingArtifactError, MissingFileError
 from cg_lims.get.artifacts import create_well_dict, get_artifact_by_name
 from cg_lims.get.files import get_file_path
 from genologics.entities import Artifact, Process
@@ -16,66 +16,140 @@
 LOG = logging.getLogger(__name__)
 
 
-def set_udfs(well_field: str, value_field: str, udf: str, well_dict: dict, result_file: Path):
+def make_udf_dict(udfs: Tuple[str], value_fields: Tuple[str]) -> Dict[str, str]:
+    """"""
+    if len(udfs) != len(value_fields):
+        raise ArgumentError(
+            f"The number of artifact-udfs to update and file value fields must be the same."
+        )
+    udf_vf_dict: dict = {}
+    for i in range(len(udfs)):
+        udf_vf_dict[udfs[i]] = value_fields[i]
+    return udf_vf_dict
+
+
+def get_file_placeholder_paths(placeholder_names: List[str], process: Process) -> List[str]:
+    """"""
+    file_paths = []
+    for placeholder_name in placeholder_names:
+        file_artifact: Artifact = get_artifact_by_name(process=process, name=placeholder_name)
+        file_paths.append(get_file_path(file_artifact=file_artifact))
+    return file_paths
+
+
+def set_udfs_from_file(
+    well_field: str, udf_vf_dict: Dict[str, str], well_dict: dict, result_file: Path
+) -> List[str]:
     """Reads the csv and sets the value for each sample"""
 
     error_msg: List[str] = []
     passed_arts: int = 0
     with open(result_file, newline="", encoding="latin1") as csvfile:
         reader: csv.DictReader = csv.DictReader(csvfile)
-        for sample in reader:
-            well: str = sample.get(well_field)
-            value: Any = sample.get(value_field)
-            if value is None:
-                error_msg.append("Some samples in the file had missing values.")
-                LOG.info(f"Missing value for sample {sample} in well {well}. Skipping!")
+        for udf_name in list(udf_vf_dict.keys()):
+            if udf_vf_dict[udf_name] not in reader.fieldnames:
+                LOG.info(
+                    f"Value {udf_vf_dict[udf_name]} does not exist in file {result_file}, skipping."
+                )
                 continue
-            elif well not in well_dict:
-                LOG.info(f"Well {well} was not found in the step. Skipping!")
-                continue
-            artifact: Artifact = well_dict[well]
-            try:
-                artifact.udf[udf] = str(value)
-            except:
-                artifact.udf[udf] = float(value)
-            artifact.put()
-            passed_arts += 1
+            value_field: str = udf_vf_dict.pop(udf_name)
+
+            for sample in reader:
+                well: str = sample.get(well_field)
+                if well not in well_dict:
+                    LOG.info(f"Well {well} was not found in the step. Skipping!")
+                    continue
+                artifact: Artifact = well_dict[well]
+
+                value: Any = sample.get(value_field)
+                if value is None:
+                    error_msg.append("Some samples in the file had missing values.")
+                    LOG.info(f"Missing value for sample {sample} in well {well}. Skipping!")
+                    continue
+                try:
+                    artifact.udf[udf_name] = str(value)
+                except:
+                    artifact.udf[udf_name] = float(value)
+                artifact.put()
+                passed_arts += 1
 
     if passed_arts < len(well_dict.keys()):
         error_msg.append("Some samples in the step were not represented in the file.")
 
-    error_string: str = " ".join(list(set(error_msg)))
-    if error_msg:
+    return error_msg
+
+
+def set_udfs(
+    well_fields: List[str],
+    udf_vf_dict: Dict[str, str],
+    well_dict: dict,
+    file_placeholders: List[str],
+    local_files: Optional[List[str]],
+    process: Process,
+) -> None:
+    """"""
+    if local_files:
+        files: List[str] = local_files
+    else:
+        files: List[str] = get_file_placeholder_paths(
+            placeholder_names=file_placeholders, process=process
+        )
+    if len(well_fields) != len(files):
+        raise ArgumentError(f"The number of files to read  and file value fields must be the same.")
+
+    file_well_list: zip = zip(files, well_fields)
+    error_message: List[str] = []
+
+    for file_tuple in file_well_list:
+        file: str = file_tuple[0]
+        well_field: str = file_tuple[1]
+        if not Path(file).is_file():
+            raise MissingFileError(f"No such file: {file}")
+        error_message += set_udfs_from_file(
+            well_field=well_field,
+            udf_vf_dict=udf_vf_dict,
+            well_dict=well_dict,
+            result_file=Path(file),
+        )
+
+    if error_message:
+        error_string: str = " ".join(list(set(error_message)))
         raise MissingArtifactError(error_string)
 
 
 @click.command()
-@options.file_placeholder(help="File placeholder name.")
-@options.local_file()
-@options.udf()
-@options.well_field()
-@options.value_field()
+@options.file_placeholders(help="File placeholder name.")
+@options.local_files()
+@options.udf_values()
+@options.well_fields()
+@options.value_fields()
 @options.input()
 @click.pass_context
 def csv_well_to_udf(
-    ctx, file: str, well_field: str, value_field: str, udf: str, input: bool, local_file: str
+    ctx,
+    files: Tuple[str],
+    local_files: Tuple[str],
+    udf_values: Tuple[str],
+    well_fields: Tuple[str],
+    value_fields: Tuple[str],
+    input: bool,
 ):
     """Script to copy data from file to udf based on well position"""
 
     LOG.info(f"Running {ctx.command_path} with params: {ctx.params}")
     process: Process = ctx.obj["process"]
 
-    if local_file:
-        file_path: str = local_file
-    else:
-        file_art: Artifact = get_artifact_by_name(process=process, name=file)
-        file_path: str = get_file_path(file_art)
-
     try:
-        if not Path(file_path).is_file():
-            raise MissingFileError(f"No such file: {file_path}")
         well_dict: Dict[str, Artifact] = create_well_dict(process=process, input_flag=input)
-        set_udfs(well_field, value_field, udf, well_dict, Path(file_path))
-        click.echo("The udfs were sucessfully populated.")
+        udf_vf_dict: Dict[str, str] = make_udf_dict(udfs=udf_values, value_fields=value_fields)
+        set_udfs(
+            well_fields=list(well_fields),
+            udf_vf_dict=udf_vf_dict,
+            well_dict=well_dict,
+            file_placeholders=list(files),
+            local_files=list(local_files),
+            process=process,
+        )
+        click.echo("The UDFs were successfully populated.")
     except LimsError as e:
         sys.exit(e.message)
diff --git a/cg_lims/options.py b/cg_lims/options.py
index b1e3473e..874a01dc 100644
--- a/cg_lims/options.py
+++ b/cg_lims/options.py
@@ -47,6 +47,12 @@ def well_field(
     return click.option("-wf", "--well-field", required=True, help=help)
 
 
+def well_fields(
+    help: str = "Well field in file",
+) -> click.option:
+    return click.option("-wf", "--well-fields", required=True, multiple=True, help=help)
+
+
 def value_field(
     help: str = "Value field in file",
 ) -> click.option:
@@ -92,7 +98,7 @@ def file_placeholder(
 def file_placeholders(
     help: str = "File placeholder option used when multiple are possible.",
 ) -> click.option:
-    return click.option("-f", "--files", required=True, multiple=True, help=help)
+    return click.option("-f", "--files", required=False, multiple=True, help=help)
 
 
 def samples_file(help: str = "Txt file with sample ids") -> click.option:
@@ -107,6 +113,10 @@ def local_file(help="local file path for debug purposes.") -> click.option:
     return click.option("-lf", "--local_file", required=False, help=help)
 
 
+def local_files(help="local file paths for debug purposes.") -> click.option:
+    return click.option("-lf", "--local_files", required=False, multiple=True, help=help)
+
+
 def input(
     help: str = "Use this flag if you run the script from a QC step.",
 ) -> click.option:
@@ -741,3 +751,9 @@ def round_decimals(
     help: str = "The number of decimals you want to round to.",
 ) -> click.option:
     return click.option("-r", "--round-decimals", required=False, help=help)
+
+
+def value_fields(
+    help: str = "Value fields in file",
+) -> click.option:
+    return click.option("-vf", "--value-fields", required=True, multiple=True, help=help)

From 284390ccdab30e21010b576460eb0a4fa9b61ce7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Karl=20Sv=C3=A4rd?= <karl.svard@scilifelab.se>
Date: Fri, 10 Jan 2025 16:32:48 +0100
Subject: [PATCH 22/25] docstrings

---
 cg_lims/EPPs/files/parsers/file_to_udf.py | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

diff --git a/cg_lims/EPPs/files/parsers/file_to_udf.py b/cg_lims/EPPs/files/parsers/file_to_udf.py
index 028eb87a..a7b96f10 100644
--- a/cg_lims/EPPs/files/parsers/file_to_udf.py
+++ b/cg_lims/EPPs/files/parsers/file_to_udf.py
@@ -17,7 +17,7 @@
 
 
 def make_udf_dict(udfs: Tuple[str], value_fields: Tuple[str]) -> Dict[str, str]:
-    """"""
+    """Create dictionary containing UDF names and their corresponding value field names."""
     if len(udfs) != len(value_fields):
         raise ArgumentError(
             f"The number of artifact-udfs to update and file value fields must be the same."
@@ -29,8 +29,8 @@ def make_udf_dict(udfs: Tuple[str], value_fields: Tuple[str]) -> Dict[str, str]:
 
 
 def get_file_placeholder_paths(placeholder_names: List[str], process: Process) -> List[str]:
-    """"""
-    file_paths = []
+    """Convert a list of file placeholder names to complete file paths."""
+    file_paths: List[str] = []
     for placeholder_name in placeholder_names:
         file_artifact: Artifact = get_artifact_by_name(process=process, name=placeholder_name)
         file_paths.append(get_file_path(file_artifact=file_artifact))
@@ -40,8 +40,7 @@ def get_file_placeholder_paths(placeholder_names: List[str], process: Process) -
 def set_udfs_from_file(
     well_field: str, udf_vf_dict: Dict[str, str], well_dict: dict, result_file: Path
 ) -> List[str]:
-    """Reads the csv and sets the value for each sample"""
-
+    """Parse a CSV file and set the corresponding UDF values for each sample."""
     error_msg: List[str] = []
     passed_arts: int = 0
     with open(result_file, newline="", encoding="latin1") as csvfile:
@@ -60,7 +59,6 @@ def set_udfs_from_file(
                     LOG.info(f"Well {well} was not found in the step. Skipping!")
                     continue
                 artifact: Artifact = well_dict[well]
-
                 value: Any = sample.get(value_field)
                 if value is None:
                     error_msg.append("Some samples in the file had missing values.")
@@ -87,7 +85,7 @@ def set_udfs(
     local_files: Optional[List[str]],
     process: Process,
 ) -> None:
-    """"""
+    """Loop through each given file and parse out the given values which are then set to their corresponding UDFs."""
     if local_files:
         files: List[str] = local_files
     else:
@@ -134,7 +132,7 @@ def csv_well_to_udf(
     value_fields: Tuple[str],
     input: bool,
 ):
-    """Script to copy data from file to udf based on well position"""
+    """Script to copy data from files to UDFs based on well position."""
 
     LOG.info(f"Running {ctx.command_path} with params: {ctx.params}")
     process: Process = ctx.obj["process"]

From 8eabfdcb9122cdffb11b7441f1353dc6dad47e2f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Karl=20Sv=C3=A4rd?= <karl.svard@scilifelab.se>
Date: Mon, 13 Jan 2025 09:33:30 +0100
Subject: [PATCH 23/25] some more stuff

---
 cg_lims/EPPs/files/parsers/file_to_udf.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/cg_lims/EPPs/files/parsers/file_to_udf.py b/cg_lims/EPPs/files/parsers/file_to_udf.py
index a7b96f10..d0e8b841 100644
--- a/cg_lims/EPPs/files/parsers/file_to_udf.py
+++ b/cg_lims/EPPs/files/parsers/file_to_udf.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 import csv
 import logging
 import sys
@@ -60,7 +58,7 @@ def set_udfs_from_file(
                     continue
                 artifact: Artifact = well_dict[well]
                 value: Any = sample.get(value_field)
-                if value is None:
+                if not value:
                     error_msg.append("Some samples in the file had missing values.")
                     LOG.info(f"Missing value for sample {sample} in well {well}. Skipping!")
                     continue
@@ -112,7 +110,7 @@ def set_udfs(
 
     if error_message:
         error_string: str = " ".join(list(set(error_message)))
-        raise MissingArtifactError(error_string)
+        raise MissingArtifactError(error_string + " See the log for details.")
 
 
 @click.command()

From 936a8916b85e6c3af595bde9fa449024ffce04ec Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Karl=20Sv=C3=A4rd?= <karl.svard@scilifelab.se>
Date: Mon, 13 Jan 2025 10:53:19 +0100
Subject: [PATCH 24/25] add new udf option to not break existing configs

---
 cg_lims/EPPs/files/parsers/file_to_udf.py | 6 +++---
 cg_lims/options.py                        | 6 ++++++
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/cg_lims/EPPs/files/parsers/file_to_udf.py b/cg_lims/EPPs/files/parsers/file_to_udf.py
index d0e8b841..c925d2ec 100644
--- a/cg_lims/EPPs/files/parsers/file_to_udf.py
+++ b/cg_lims/EPPs/files/parsers/file_to_udf.py
@@ -116,7 +116,7 @@ def set_udfs(
 @click.command()
 @options.file_placeholders(help="File placeholder name.")
 @options.local_files()
-@options.udf_values()
+@options.udfs()
 @options.well_fields()
 @options.value_fields()
 @options.input()
@@ -125,7 +125,7 @@ def csv_well_to_udf(
     ctx,
     files: Tuple[str],
     local_files: Tuple[str],
-    udf_values: Tuple[str],
+    udfs: Tuple[str],
     well_fields: Tuple[str],
     value_fields: Tuple[str],
     input: bool,
@@ -137,7 +137,7 @@ def csv_well_to_udf(
 
     try:
         well_dict: Dict[str, Artifact] = create_well_dict(process=process, input_flag=input)
-        udf_vf_dict: Dict[str, str] = make_udf_dict(udfs=udf_values, value_fields=value_fields)
+        udf_vf_dict: Dict[str, str] = make_udf_dict(udfs=udfs, value_fields=value_fields)
         set_udfs(
             well_fields=list(well_fields),
             udf_vf_dict=udf_vf_dict,
diff --git a/cg_lims/options.py b/cg_lims/options.py
index 874a01dc..3c6d7319 100644
--- a/cg_lims/options.py
+++ b/cg_lims/options.py
@@ -29,6 +29,12 @@ def udf(
     return click.option("-u", "--udf", required=False, help=help)
 
 
+def udfs(
+    help: str = "UDF names",
+) -> click.option:
+    return click.option("-u", "--udfs", required=False, multiple=True, help=help)
+
+
 def buffer_udf(
     help: str = "UDF name",
 ) -> click.option:

From e142fc604c0aca5420762654287b90fa135b7b29 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Karl=20Sv=C3=A4rd?= <karl.svard@scilifelab.se>
Date: Mon, 13 Jan 2025 14:17:34 +0100
Subject: [PATCH 25/25] type hint

---
 cg_lims/EPPs/files/parsers/quantit_excel_to_udf.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cg_lims/EPPs/files/parsers/quantit_excel_to_udf.py b/cg_lims/EPPs/files/parsers/quantit_excel_to_udf.py
index a344a275..ee4c1a71 100644
--- a/cg_lims/EPPs/files/parsers/quantit_excel_to_udf.py
+++ b/cg_lims/EPPs/files/parsers/quantit_excel_to_udf.py
@@ -36,7 +36,7 @@ def set_udfs(udf: str, well_dict: dict, result_file: Path):
         artifact.put()
 
     if failed_artifacts or skipped_artifacts:
-        error_message = "Warning:"
+        error_message: str = "Warning:"
         if failed_artifacts:
             error_message += f" Skipped {failed_artifacts} artifact(s) with wrong and/or blank values for some UDFs."
         if skipped_artifacts: