[pre-commit] fixes from hooks

backend/incoming_libraries/serializers.py

@@ -76,10 +76,7 @@ def get_library_protocol_name(self, obj):
 class LibrarySerializer(BaseSerializer):
     class Meta(BaseSerializer.Meta):
         model = Library
-        fields = BaseSerializer.Meta.fields + (
-            "measuring_unit",
-            "measured_value"
-        )
+        fields = BaseSerializer.Meta.fields + ("measuring_unit", "measured_value")
         extra_kwargs = {
             **BaseSerializer.Meta.extra_kwargs,
             **{
@@ -98,9 +95,8 @@ class Meta(BaseSerializer.Meta):
             "nucleic_acid_type",
             "nucleic_acid_type_name",
             "measuring_unit",
-            "measured_value"
-            "measuring_unit_facility",
-            "measured_value_facility"
+            "measured_value" "measuring_unit_facility",
+            "measured_value_facility",
         )
         extra_kwargs = {
             **BaseSerializer.Meta.extra_kwargs,

backend/library/migrations/0007_rename_amplification_cycles_library_removed_amplification_cycles_and_more.py

@@ -6,48 +6,48 @@
 class Migration(migrations.Migration):
 
     dependencies = [
-        ('library', '0006_rename_mean_fragment_size_library_measured_value'),
+        ("library", "0006_rename_mean_fragment_size_library_measured_value"),
     ]
 
     operations = [
         migrations.RenameField(
-            model_name='library',
-            old_name='amplification_cycles',
-            new_name='removed_amplification_cycles',
+            model_name="library",
+            old_name="amplification_cycles",
+            new_name="removed_amplification_cycles",
         ),
         migrations.RenameField(
-            model_name='library',
-            old_name='comments',
-            new_name='removed_comments',
+            model_name="library",
+            old_name="comments",
+            new_name="removed_comments",
         ),
         migrations.RenameField(
-            model_name='library',
-            old_name='comments_facility',
-            new_name='removed_comments_facility',
+            model_name="library",
+            old_name="comments_facility",
+            new_name="removed_comments_facility",
         ),
         migrations.RenameField(
-            model_name='library',
-            old_name='concentration_method',
-            new_name='removed_concentration_method',
+            model_name="library",
+            old_name="concentration_method",
+            new_name="removed_concentration_method",
         ),
         migrations.RenameField(
-            model_name='library',
-            old_name='concentration_method_facility',
-            new_name='removed_concentration_method_facility',
+            model_name="library",
+            old_name="concentration_method_facility",
+            new_name="removed_concentration_method_facility",
         ),
         migrations.RenameField(
-            model_name='library',
-            old_name='equal_representation_nucleotides',
-            new_name='removed_equal_representation_nucleotides',
+            model_name="library",
+            old_name="equal_representation_nucleotides",
+            new_name="removed_equal_representation_nucleotides",
         ),
         migrations.RenameField(
-            model_name='library',
-            old_name='qpcr_result',
-            new_name='removed_qpcr_result',
+            model_name="library",
+            old_name="qpcr_result",
+            new_name="removed_qpcr_result",
         ),
         migrations.RenameField(
-            model_name='library',
-            old_name='qpcr_result_facility',
-            new_name='removed_qpcr_result_facility',
+            model_name="library",
+            old_name="qpcr_result_facility",
+            new_name="removed_qpcr_result_facility",
         ),
     ]

backend/library/migrations/0008_alter_library_removed_equal_representation_nucleotides.py

@@ -6,13 +6,20 @@
 class Migration(migrations.Migration):
 
     dependencies = [
-        ('library', '0007_rename_amplification_cycles_library_removed_amplification_cycles_and_more'),
+        (
+            "library",
+            "0007_rename_amplification_cycles_library_removed_amplification_cycles_and_more",
+        ),
     ]
 
     operations = [
         migrations.AlterField(
-            model_name='library',
-            name='removed_equal_representation_nucleotides',
-            field=models.BooleanField(blank=True, default=False, verbose_name='Equal Representation of Nucleotides'),
+            model_name="library",
+            name="removed_equal_representation_nucleotides",
+            field=models.BooleanField(
+                blank=True,
+                default=False,
+                verbose_name="Equal Representation of Nucleotides",
+            ),
         ),
     ]

backend/library/migrations/0009_alter_library_removed_concentration_method.py

@@ -1,20 +1,31 @@
 # Generated by Django 4.2.15 on 2024-09-25 00:31
 
-from django.db import migrations, models
 import library_sample_shared.models
+from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
 
     dependencies = [
-        ('library_sample_shared', '0011_alter_indexi5_number_alter_indexi5_prefix_and_more'),
-        ('library', '0008_alter_library_removed_equal_representation_nucleotides'),
+        (
+            "library_sample_shared",
+            "0011_alter_indexi5_number_alter_indexi5_prefix_and_more",
+        ),
+        ("library", "0008_alter_library_removed_equal_representation_nucleotides"),
     ]
 
     operations = [
         migrations.AlterField(
-            model_name='library',
-            name='removed_concentration_method',
-            field=models.ForeignKey(blank=True, null=True, on_delete=models.SET(library_sample_shared.models.get_removed_concentrationmethod), to='library_sample_shared.concentrationmethod', verbose_name='Concentration Method'),
+            model_name="library",
+            name="removed_concentration_method",
+            field=models.ForeignKey(
+                blank=True,
+                null=True,
+                on_delete=models.SET(
+                    library_sample_shared.models.get_removed_concentrationmethod
+                ),
+                to="library_sample_shared.concentrationmethod",
+                verbose_name="Concentration Method",
+            ),
         ),
     ]

backend/library_preparation/migrations/0005_rename_qpcr_result_librarypreparation_removed_qpcr_result.py

@@ -6,13 +6,13 @@
 class Migration(migrations.Migration):
 
     dependencies = [
-        ('library_preparation', '0004_librarypreparation_smear_analysis'),
+        ("library_preparation", "0004_librarypreparation_smear_analysis"),
     ]
 
     operations = [
         migrations.RenameField(
-            model_name='librarypreparation',
-            old_name='qpcr_result',
-            new_name='removed_qpcr_result',
+            model_name="librarypreparation",
+            old_name="qpcr_result",
+            new_name="removed_qpcr_result",
         ),
     ]

backend/sample/migrations/0010_rename_amplification_cycles_sample_removed_amplification_cycles_and_more.py

@@ -7,48 +7,60 @@
 class Migration(migrations.Migration):
 
     dependencies = [
-        ('sample', '0009_alter_sample_measuring_unit'),
+        ("sample", "0009_alter_sample_measuring_unit"),
     ]
 
     operations = [
         migrations.RenameField(
-            model_name='sample',
-            old_name='amplification_cycles',
-            new_name='removed_amplification_cycles',
+            model_name="sample",
+            old_name="amplification_cycles",
+            new_name="removed_amplification_cycles",
         ),
         migrations.RenameField(
-            model_name='sample',
-            old_name='comments',
-            new_name='removed_comments',
+            model_name="sample",
+            old_name="comments",
+            new_name="removed_comments",
         ),
         migrations.RenameField(
-            model_name='sample',
-            old_name='comments_facility',
-            new_name='removed_comments_facility',
+            model_name="sample",
+            old_name="comments_facility",
+            new_name="removed_comments_facility",
         ),
         migrations.RenameField(
-            model_name='sample',
-            old_name='concentration_method',
-            new_name='removed_concentration_method',
+            model_name="sample",
+            old_name="concentration_method",
+            new_name="removed_concentration_method",
         ),
         migrations.RenameField(
-            model_name='sample',
-            old_name='concentration_method_facility',
-            new_name='removed_concentration_method_facility',
+            model_name="sample",
+            old_name="concentration_method_facility",
+            new_name="removed_concentration_method_facility",
         ),
         migrations.RenameField(
-            model_name='sample',
-            old_name='equal_representation_nucleotides',
-            new_name='removed_equal_representation_nucleotides',
+            model_name="sample",
+            old_name="equal_representation_nucleotides",
+            new_name="removed_equal_representation_nucleotides",
         ),
         migrations.RenameField(
-            model_name='sample',
-            old_name='rna_quality_facility',
-            new_name='measured_value_facility',
+            model_name="sample",
+            old_name="rna_quality_facility",
+            new_name="measured_value_facility",
         ),
         migrations.AddField(
-            model_name='sample',
-            name='measuring_unit_facility',
-            field=models.CharField(blank=True, choices=[('bp', 'bp (DNA)'), ('nt', 'nt (RNA)'), ('RQN', 'RQN (RNA (total))'), ('M', 'M (Cells)'), ('-', 'Measure for Me')], max_length=50, null=True, verbose_name='Measuring Unit (facility)'),
+            model_name="sample",
+            name="measuring_unit_facility",
+            field=models.CharField(
+                blank=True,
+                choices=[
+                    ("bp", "bp (DNA)"),
+                    ("nt", "nt (RNA)"),
+                    ("RQN", "RQN (RNA (total))"),
+                    ("M", "M (Cells)"),
+                    ("-", "Measure for Me"),
+                ],
+                max_length=50,
+                null=True,
+                verbose_name="Measuring Unit (facility)",
+            ),
         ),
     ]

backend/sample/migrations/0011_alter_sample_measured_value_facility.py

@@ -7,13 +7,21 @@
 class Migration(migrations.Migration):
 
     dependencies = [
-        ('sample', '0010_rename_amplification_cycles_sample_removed_amplification_cycles_and_more'),
+        (
+            "sample",
+            "0010_rename_amplification_cycles_sample_removed_amplification_cycles_and_more",
+        ),
     ]
 
     operations = [
         migrations.AlterField(
-            model_name='sample',
-            name='measured_value_facility',
-            field=models.FloatField(blank=True, null=True, validators=[django.core.validators.MinValueValidator(-1)], verbose_name='Measured Value (facility)'),
+            model_name="sample",
+            name="measured_value_facility",
+            field=models.FloatField(
+                blank=True,
+                null=True,
+                validators=[django.core.validators.MinValueValidator(-1)],
+                verbose_name="Measured Value (facility)",
+            ),
         ),
     ]

backend/sample/migrations/0012_alter_sample_removed_equal_representation_nucleotides.py

@@ -6,13 +6,17 @@
 class Migration(migrations.Migration):
 
     dependencies = [
-        ('sample', '0011_alter_sample_measured_value_facility'),
+        ("sample", "0011_alter_sample_measured_value_facility"),
     ]
 
     operations = [
         migrations.AlterField(
-            model_name='sample',
-            name='removed_equal_representation_nucleotides',
-            field=models.BooleanField(blank=True, default=False, verbose_name='Equal Representation of Nucleotides'),
+            model_name="sample",
+            name="removed_equal_representation_nucleotides",
+            field=models.BooleanField(
+                blank=True,
+                default=False,
+                verbose_name="Equal Representation of Nucleotides",
+            ),
         ),
     ]

backend/sample/migrations/0013_alter_sample_removed_concentration_method.py

@@ -1,20 +1,31 @@
 # Generated by Django 4.2.15 on 2024-09-25 00:31
 
-from django.db import migrations, models
 import library_sample_shared.models
+from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
 
     dependencies = [
-        ('library_sample_shared', '0011_alter_indexi5_number_alter_indexi5_prefix_and_more'),
-        ('sample', '0012_alter_sample_removed_equal_representation_nucleotides'),
+        (
+            "library_sample_shared",
+            "0011_alter_indexi5_number_alter_indexi5_prefix_and_more",
+        ),
+        ("sample", "0012_alter_sample_removed_equal_representation_nucleotides"),
     ]
 
     operations = [
         migrations.AlterField(
-            model_name='sample',
-            name='removed_concentration_method',
-            field=models.ForeignKey(blank=True, null=True, on_delete=models.SET(library_sample_shared.models.get_removed_concentrationmethod), to='library_sample_shared.concentrationmethod', verbose_name='Concentration Method'),
+            model_name="sample",
+            name="removed_concentration_method",
+            field=models.ForeignKey(
+                blank=True,
+                null=True,
+                on_delete=models.SET(
+                    library_sample_shared.models.get_removed_concentrationmethod
+                ),
+                to="library_sample_shared.concentrationmethod",
+                verbose_name="Concentration Method",
+            ),
         ),
     ]

backend/static/main-hub/app/model/libraries/BatchAdd/Library.js

@@ -47,7 +47,7 @@ Ext.define("MainHub.model.libraries.BatchAdd.Library", {
     {
       type: "string",
       name: "index_i5"
-    },
+    }
   ],
 
   validators: {

backend/static/main-hub/app/view/libraries/Libraries.js

@@ -488,12 +488,14 @@ Ext.define("MainHub.view.libraries.Libraries", {
             tooltip: "Starting Amount",
             dataIndex: "amount_facility",
             renderer: "gridCellTooltipRenderer"
-          },          {
+          },
+          {
             text: "PCR Cycles",
             tooltip: "PCR Cycles",
             dataIndex: "pcr_cycles",
             renderer: "gridCellTooltipRenderer"
-          },          {
+          },
+          {
             text: "ng/μl (Output)",
             tooltip: "ng/μl (Output)",
             dataIndex: "concentration_facility",
@@ -535,7 +537,7 @@ Ext.define("MainHub.view.libraries.Libraries", {
             text: "Depth (M)",
             tooltip: "Sequencing Depth",
             dataIndex: "sequencing_depth"
-          },
+          }
         ]
       }
     }