ruff format

kedhammar · Dec 11, 2023 · 6899e33 · 6899e33
1 parent 548a3eb
commit 6899e33
Show file tree

Hide file tree

Showing 13 changed files with 44 additions and 119 deletions.
diff --git a/scilifelab_epps/epp.py b/scilifelab_epps/epp.py
@@ -89,9 +89,7 @@ def __enter__(self):
             )
         except DistributionNotFound as e:
             logging.error(e)
-            logging.error(
-                f"Make sure you have the {self.PACKAGE} " "package installed"
-            )
+            logging.error(f"Make sure you have the {self.PACKAGE} " "package installed")
             sys.exit(-1)
         return self
 

diff --git a/scripts/attach_caliper_files.py b/scripts/attach_caliper_files.py
@@ -75,24 +75,18 @@ def main(lims, args, epp_logger):
         fns = list(filter(im_file_r.match, file_list))
 
         if len(fns) == 0:
-            logging.warning(
-                f"No image file found for artifact with id {i_a.id}"
-            )
+            logging.warning(f"No image file found for artifact with id {i_a.id}")
             artifact_missing_file.append(i_a)
         elif len(fns) > 1:
             logging.warning(
-
-                    f"Multiple image files found for artifact with id {i_a.id}, "
-                    "please attach files manually"
-
+                f"Multiple image files found for artifact with id {i_a.id}, "
+                "please attach files manually"
             )
             artifact_multiple_file.append(i_a)
         else:
             fn = fns[0]
             found_files.append(fn)
-            logging.info(
-                f"Found image file {fn} for artifact with id {i_a.id}"
-            )
+            logging.info(f"Found image file {fn} for artifact with id {i_a.id}")
             fp = os.path.join(args.path, fn)
 
             # Attach file to the LIMS

diff --git a/scripts/bravo_csv.py b/scripts/bravo_csv.py
@@ -1248,9 +1248,7 @@ def calc_vol(art_tuple, logContext, checkTheLog):
             f"{total_volume:.2f}",
         )
     except KeyError as e:
-        logContext.write(
-            f"ERROR : The input artifact is lacking a field : {e}\n"
-        )
+        logContext.write(f"ERROR : The input artifact is lacking a field : {e}\n")
         checkTheLog[0] = True
     except AssertionError:
         logContext.write(

diff --git a/scripts/calculate_cell_nuclei_conc.py b/scripts/calculate_cell_nuclei_conc.py
@@ -38,9 +38,7 @@ def calculate_cell_nuclei_conc(pro):
             art.udf["Conc. Units"] = "count/ul"
             art.udf["Amount (ng)"] = 0
             art.put()
-            log.append(
-                f"Sample {sample} concentration set to {conc} count/ul."
-            )
+            log.append(f"Sample {sample} concentration set to {conc} count/ul.")
         # Throw error message when there is missing value
         else:
             for k, v in value_dict.items():

diff --git a/scripts/copy_frag_an.py b/scripts/copy_frag_an.py
@@ -176,13 +176,9 @@ def get_frag_an_csv_data(process):
                             if k == "concentration":
                                 target_file.udf["Conc. Units"] = "ng/ul"
                         else:
-                            log.append(
-                                f"NaN {k} value for Sample {file_sample}."
-                            )
+                            log.append(f"NaN {k} value for Sample {file_sample}.")
                     except ValueError:
-                        log.append(
-                            f"Bad {k} value format for Sample {file_sample}."
-                        )
+                        log.append(f"Bad {k} value format for Sample {file_sample}.")
             # actually set the data
             target_file.put()
             set_field(target_file)

diff --git a/scripts/illumina_run_parameter_parser.py b/scripts/illumina_run_parameter_parser.py
@@ -64,9 +64,7 @@ def fetch_rundir(fc_id, run_type):
         data_dir = "NovaSeqXPlus_data"
 
     metadata_dir = "ngi-nas-ns"
-    run_dir_path = os.path.join(
-        os.sep, "srv", metadata_dir, data_dir, f"*{fc_id}"
-    )
+    run_dir_path = os.path.join(os.sep, "srv", metadata_dir, data_dir, f"*{fc_id}")
 
     if len(glob.glob(run_dir_path)) == 1:
         run_dir = glob.glob(run_dir_path)[0]
@@ -82,13 +80,9 @@ def fetch_rundir(fc_id, run_type):
 def parse_run(run_dir):
     runParserObj = RunParser(run_dir)
     if os.path.exists(f"{run_dir}/RunParameters.xml"):
-        RunParametersParserObj = RunParametersParser(
-            f"{run_dir}/RunParameters.xml"
-        )
+        RunParametersParserObj = RunParametersParser(f"{run_dir}/RunParameters.xml")
     elif os.path.exists(f"{run_dir}/runParameters.xml"):
-        RunParametersParserObj = RunParametersParser(
-            f"{run_dir}/runParameters.xml"
-        )
+        RunParametersParserObj = RunParametersParser(f"{run_dir}/runParameters.xml")
     else:
         sys.stderr.write(f"No RunParameters.xml found in path {run_dir}")
         sys.exit(2)
@@ -212,13 +206,11 @@ def set_run_stats_in_lims(process, run_stats_summary):
             for i in list(run_stats_summary[lane_nbr].keys()):
                 lane_stats_for_read = run_stats_summary[lane_nbr][i]
                 if not math.isnan(lane_stats_for_read["density"]):
-                    art.udf[
-                        f"Cluster Density (K/mm^2) R{read}"
-                    ] = lane_stats_for_read["density"]
-                if not math.isnan(lane_stats_for_read["error_rate"]):
-                    art.udf[f"% Error Rate R{read}"] = lane_stats_for_read[
-                        "error_rate"
+                    art.udf[f"Cluster Density (K/mm^2) R{read}"] = lane_stats_for_read[
+                        "density"
                     ]
+                if not math.isnan(lane_stats_for_read["error_rate"]):
+                    art.udf[f"% Error Rate R{read}"] = lane_stats_for_read["error_rate"]
                 if not math.isnan(lane_stats_for_read["first_cycle_intensity"]):
                     art.udf[f"Intensity Cycle 1 R{read}"] = lane_stats_for_read[
                         "first_cycle_intensity"
@@ -234,21 +226,15 @@ def set_run_stats_in_lims(process, run_stats_summary):
                 if not math.isnan(lane_stats_for_read["percent_pf"]):
                     art.udf[f"%PF R{read}"] = lane_stats_for_read["percent_pf"]
                 if not math.isnan(lane_stats_for_read["phasing"]):
-                    art.udf[f"% Phasing R{read}"] = lane_stats_for_read[
-                        "phasing"
-                    ]
+                    art.udf[f"% Phasing R{read}"] = lane_stats_for_read["phasing"]
                 if not math.isnan(lane_stats_for_read["prephasing"]):
-                    art.udf[f"% Prephasing R{read}"] = lane_stats_for_read[
-                        "prephasing"
-                    ]
+                    art.udf[f"% Prephasing R{read}"] = lane_stats_for_read["prephasing"]
                 if not math.isnan(lane_stats_for_read["reads_pf"]):
                     art.udf[f"Reads PF (M) R{read}"] = (
                         lane_stats_for_read["reads_pf"] / 1000000
                     )
                 if not math.isnan(lane_stats_for_read["yield_g"]):
-                    art.udf[f"Yield PF (Gb) R{read}"] = lane_stats_for_read[
-                        "yield_g"
-                    ]
+                    art.udf[f"Yield PF (Gb) R{read}"] = lane_stats_for_read["yield_g"]
                 read += 1
             art.put()
     process.put()
@@ -271,13 +257,9 @@ def set_run_stats_in_lims_miseq(process, run_stats_summary):
                 "first_cycle_intensity"
             ]
         if not math.isnan(lane_stats_for_read["percent_aligned"]):
-            art.udf[f"% Aligned R{read}"] = lane_stats_for_read[
-                "percent_aligned"
-            ]
+            art.udf[f"% Aligned R{read}"] = lane_stats_for_read["percent_aligned"]
         if not math.isnan(lane_stats_for_read["percent_gt_q30"]):
-            art.udf[f"% Bases >=Q30 R{read}"] = lane_stats_for_read[
-                "percent_gt_q30"
-            ]
+            art.udf[f"% Bases >=Q30 R{read}"] = lane_stats_for_read["percent_gt_q30"]
         if not math.isnan(lane_stats_for_read["percent_pf"]):
             art.udf[f"%PF R{read}"] = lane_stats_for_read["percent_pf"]
         if not math.isnan(lane_stats_for_read["phasing"]):

diff --git a/scripts/index_distance_checker.py b/scripts/index_distance_checker.py
@@ -67,9 +67,7 @@ def verify_indexes(data):
                 )
             )
         if len(idx_length) > 1:
-            message.append(
-                f"INDEX WARNING: Multiple index lengths noticed in pool {p}"
-            )
+            message.append(f"INDEX WARNING: Multiple index lengths noticed in pool {p}")
     return message
 
 

diff --git a/scripts/make_running_note_from_pooling.py b/scripts/make_running_note_from_pooling.py
@@ -72,9 +72,7 @@ def main(lims, args):
         if out.name == "RNotes Log":
             attach_file(os.path.join(os.getcwd(), "EPP_Notes.log"), out)
 
-    sys.stderr.write(
-        f"Updated {len(list(datamap.keys()))} projects successfully"
-    )
+    sys.stderr.write(f"Updated {len(list(datamap.keys()))} projects successfully")
 
 
 if __name__ == "__main__":

diff --git a/scripts/make_running_note_from_workset.py b/scripts/make_running_note_from_workset.py
@@ -72,9 +72,7 @@ def main(lims, args):
         if out.name == "RNotes Log":
             attach_file(os.path.join(os.getcwd(), "EPP_Notes.log"), out)
 
-    sys.stderr.write(
-        f"Updated {len(list(datamap.keys()))} projects successfully"
-    )
+    sys.stderr.write(f"Updated {len(list(datamap.keys()))} projects successfully")
 
 
 if __name__ == "__main__":

diff --git a/scripts/manage_demux_stats.py b/scripts/manage_demux_stats.py
@@ -60,9 +60,7 @@ def get_process_stats(demux_process):
             inputartifactlimsid=demux_process.all_inputs()[0].id, type=seq_processes
         )[0]
     except Exception as e:
-        problem_handler(
-            "exit", f"Undefined prior workflow step (run type): {str(e)}"
-        )
+        problem_handler("exit", f"Undefined prior workflow step (run type): {str(e)}")
     # Copies LIMS sequencing step content
     proc_stats = dict(list(seq_process.udf.items()))
     # Instrument is denoted the way it is since it is also used to find
@@ -114,9 +112,7 @@ def get_process_stats(demux_process):
         try:
             proc_stats["Chemistry"] = seq_process.udf["Chemistry"]
         except Exception as e:
-            problem_handler(
-                "exit", f"No run type set in sequencing step: {str(e)}"
-            )
+            problem_handler("exit", f"No run type set in sequencing step: {str(e)}")
         proc_stats["Instrument"] = "NextSeq"
         proc_stats["Read Length"] = (
             max(seq_process.udf["Read 1 Cycles"], seq_process.udf["Read 2 Cycles"])
@@ -133,9 +129,7 @@ def get_process_stats(demux_process):
     try:
         proc_stats["Paired"] = proc_stats.get("Paired", False)
     except Exception as e:
-        problem_handler(
-            "exit", f"Unable to fetch workflow information: {str(e)}"
-        )
+        problem_handler("exit", f"Unable to fetch workflow information: {str(e)}")
     if "Read 2 Cycles" in proc_stats:
         proc_stats["Paired"] = True
     logger.info("Paired libraries: {}".format(proc_stats["Paired"]))
@@ -229,9 +223,7 @@ def fill_process_fields(demux_process, process_stats):
     try:
         demux_process.put()
     except Exception as e:
-        problem_handler(
-            "exit", f"Failed to apply process thresholds to LIMS: {str(e)}"
-        )
+        problem_handler("exit", f"Failed to apply process thresholds to LIMS: {str(e)}")
 
 
 def set_sample_values(demux_process, parser_struct, process_stats):
@@ -261,9 +253,7 @@ def set_sample_values(demux_process, parser_struct, process_stats):
             inputartifactlimsid=demux_process.all_inputs()[0].id, type=seq_processes
         )[0]
     except Exception as e:
-        problem_handler(
-            "exit", f"Undefined prior workflow step (run type): {str(e)}"
-        )
+        problem_handler("exit", f"Undefined prior workflow step (run type): {str(e)}")
 
     if "Lanes to include undetermined" in demux_process.udf:
         try:
@@ -286,9 +276,7 @@ def set_sample_values(demux_process, parser_struct, process_stats):
         try:
             outarts_per_lane = demux_process.outputs_per_input(pool.id, ResultFile=True)
         except Exception as e:
-            problem_handler(
-                "exit", f"Unable to fetch artifacts of process: {str(e)}"
-            )
+            problem_handler("exit", f"Unable to fetch artifacts of process: {str(e)}")
         if process_stats["Instrument"] == "miseq":
             lane_no = "1"
         else:
@@ -317,9 +305,7 @@ def set_sample_values(demux_process, parser_struct, process_stats):
                 "exit",
                 f"Faulty LIMS setup. Pool in lane {lane_no} has no samples: {e}",
             )
-        logger.info(
-            f"Expected sample clusters for this lane: {exp_smp_per_lne}"
-        )
+        logger.info(f"Expected sample clusters for this lane: {exp_smp_per_lne}")
 
         # Artifacts in each lane
         for target_file in outarts_per_lane:
@@ -735,9 +721,7 @@ def set_sample_values(demux_process, parser_struct, process_stats):
         problem_handler("warning", "Undetermined reads included in read count!")
 
     if failed_entries > 0:
-        problem_handler(
-            "warning", f"{failed_entries} entries failed automatic QC"
-        )
+        problem_handler("warning", f"{failed_entries} entries failed automatic QC")
 
 
 def write_demuxfile(process_stats, demux_id):

diff --git a/scripts/readscount.py b/scripts/readscount.py
@@ -195,9 +195,7 @@ def sumreads(sample, summary):
     except AttributeError as e:
         print(e)
         # base_art is still None because no arts were found
-        logging.info(
-            f"No demultiplexing processes found for sample {sample.name}"
-        )
+        logging.info(f"No demultiplexing processes found for sample {sample.name}")
 
     # total is displayed as millions
     tot /= 1000000