diff --git a/backend/flowcell/serializers.py b/backend/flowcell/serializers.py
index 25ec4b0a3..f54603dca 100644
--- a/backend/flowcell/serializers.py
+++ b/backend/flowcell/serializers.py
@@ -57,7 +57,6 @@ class LaneSerializer(ModelSerializer):
read_length_name = SerializerMethodField()
index_i7_show = SerializerMethodField()
index_i5_show = SerializerMethodField()
- equal_representation = SerializerMethodField()
quality_check = CharField(required=False)
request = SerializerMethodField()
protocol = SerializerMethodField()
@@ -73,7 +72,6 @@ class Meta:
"read_length_name",
"index_i7_show",
"index_i5_show",
- "equal_representation",
"loading_concentration",
"phix",
"quality_check",
@@ -168,13 +166,6 @@ def get_index_i5_show(self, obj):
return ""
# return None
- def get_equal_representation(self, obj):
- records = list(
- itertools.chain(obj.pool.libraries.all(), obj.pool.samples.all())
- )
- ern = [x.equal_representation_nucleotides for x in records].count(True)
- return len(records) == ern
-
class FlowcellListSerializer(ModelSerializer):
flowcell = SerializerMethodField()
diff --git a/backend/flowcell/views.py b/backend/flowcell/views.py
index 7659420f9..3de2d99cb 100644
--- a/backend/flowcell/views.py
+++ b/backend/flowcell/views.py
@@ -117,13 +117,13 @@ def get_queryset(self):
libraries_qs = (
Library.objects.filter(~Q(status=-1))
.prefetch_related("read_length", "index_type")
- .only("read_length", "index_type", "equal_representation_nucleotides")
+ .only("read_length", "index_type")
)
samples_qs = (
Sample.objects.filter(~Q(status=-1))
.prefetch_related("read_length", "index_type")
- .only("read_length", "index_type", "equal_representation_nucleotides")
+ .only("read_length", "index_type")
)
lanes_qs = (
diff --git a/backend/incoming_libraries/serializers.py b/backend/incoming_libraries/serializers.py
index 3fb6e723d..c59b5cd04 100644
--- a/backend/incoming_libraries/serializers.py
+++ b/backend/incoming_libraries/serializers.py
@@ -49,15 +49,12 @@ class Meta:
"record_type",
"library_protocol",
"concentration",
- "concentration_method",
"dilution_factor",
"concentration_facility",
- "concentration_method_facility",
"sample_volume_facility",
"amount_facility",
"quality_check",
"size_distribution_facility",
- "comments_facility",
"sequencing_depth",
"library_protocol_name",
)
@@ -66,7 +63,6 @@ class Meta:
"barcode": {"required": False},
"library_protocol": {"required": False},
"concentration": {"required": False},
- "concentration_method": {"required": False},
"sequencing_depth": {"required": False},
}
@@ -81,15 +77,14 @@ class LibrarySerializer(BaseSerializer):
class Meta(BaseSerializer.Meta):
model = Library
fields = BaseSerializer.Meta.fields + (
- "qpcr_result",
- "qpcr_result_facility",
- "mean_fragment_size",
+ "measuring_unit",
+ "measured_value"
)
extra_kwargs = {
**BaseSerializer.Meta.extra_kwargs,
**{
- "qpcr_result": {"required": False},
- "mean_fragment_size": {"required": False},
+ "measuring_unit": {"required": False},
+ "measured_value": {"required": False},
},
}
@@ -102,14 +97,17 @@ class Meta(BaseSerializer.Meta):
fields = BaseSerializer.Meta.fields + (
"nucleic_acid_type",
"nucleic_acid_type_name",
- "rna_quality",
- "rna_quality_facility",
+ "measuring_unit",
+ "measured_value"
+ "measuring_unit_facility",
+ "measured_value_facility"
)
extra_kwargs = {
**BaseSerializer.Meta.extra_kwargs,
**{
"nucleic_acid_type": {"required": False},
- "rna_quality": {"required": False},
+ "measuring_unit": {"required": False},
+ "measured_value": {"required": False},
},
}
diff --git a/backend/incoming_libraries/views.py b/backend/incoming_libraries/views.py
index 83a18691e..aa9840977 100644
--- a/backend/incoming_libraries/views.py
+++ b/backend/incoming_libraries/views.py
@@ -28,11 +28,9 @@ def list(self, request):
"""Get the list of all incoming libraries and samples."""
libraries_qs = Library.objects.select_related(
"library_protocol",
- "concentration_method",
).filter(status=1)
samples_qs = Sample.objects.select_related(
"library_protocol",
- "concentration_method",
"nucleic_acid_type",
).filter(status=1)
diff --git a/backend/library/admin.py b/backend/library/admin.py
index 755721b30..ff4f27150 100644
--- a/backend/library/admin.py
+++ b/backend/library/admin.py
@@ -77,12 +77,9 @@ class LibraryAdmin(admin.ModelAdmin):
"fields": (
"dilution_factor",
"concentration_facility",
- "concentration_method_facility",
"sample_volume_facility",
"amount_facility",
"size_distribution_facility",
- "qpcr_result_facility",
- "comments_facility",
),
},
),
diff --git a/backend/library/migrations/0008_alter_library_removed_equal_representation_nucleotides.py b/backend/library/migrations/0008_alter_library_removed_equal_representation_nucleotides.py
new file mode 100644
index 000000000..d019d3a59
--- /dev/null
+++ b/backend/library/migrations/0008_alter_library_removed_equal_representation_nucleotides.py
@@ -0,0 +1,18 @@
+# Generated by Django 4.2.15 on 2024-09-24 23:54
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('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'),
+ ),
+ ]
diff --git a/backend/library/migrations/max_migration.txt b/backend/library/migrations/max_migration.txt
index e491a3d70..a149037bf 100644
--- a/backend/library/migrations/max_migration.txt
+++ b/backend/library/migrations/max_migration.txt
@@ -1 +1 @@
-0007_rename_amplification_cycles_library_removed_amplification_cycles_and_more
+0008_alter_library_removed_equal_representation_nucleotides
diff --git a/backend/library/tests.py b/backend/library/tests.py
index ed7cdb1ae..0e80a34d9 100644
--- a/backend/library/tests.py
+++ b/backend/library/tests.py
@@ -25,9 +25,6 @@ def create_library(name, status=0, save=True, read_length=None, index_type=None)
organism = Organism(name="Organism")
organism.save()
- concentration_method = ConcentrationMethod(name="Concentration Method")
- concentration_method.save()
-
if read_length is None:
read_length = ReadLength(name="Read Length")
read_length.save()
@@ -56,12 +53,10 @@ def create_library(name, status=0, save=True, read_length=None, index_type=None)
status=status,
organism_id=organism.pk,
concentration=1.0,
- concentration_method_id=concentration_method.pk,
read_length_id=read_length.pk,
sequencing_depth=1,
library_protocol_id=library_protocol.pk,
library_type_id=library_type.pk,
- amplification_cycles=1,
index_type_id=index_type.pk,
index_reads=0,
mean_fragment_size=1,
@@ -214,12 +209,10 @@ def test_add_library(self):
"name": name,
"organism": library.organism.pk,
"concentration": 1.0,
- "concentration_method": library.concentration_method.pk,
"read_length": library.read_length.pk,
"sequencing_depth": 1,
"library_protocol": library.library_protocol.pk,
"library_type": library.library_type.pk,
- "amplification_cycles": 1,
"index_type": library.index_type.pk,
"index_reads": 0,
"mean_fragment_size": 1,
@@ -246,12 +239,10 @@ def test_add_library_contains_invalid(self):
"name": name,
"organism": self.library.organism.pk,
"concentration": 1.0,
- "concentration_method": self.library.concentration_method.pk,
"read_length": self.library.read_length.pk,
"sequencing_depth": 1,
"library_protocol": self.library.library_protocol.pk,
"library_type": self.library.library_type.pk,
- "amplification_cycles": 1,
"index_type": self.library.index_type.pk,
"index_reads": 0,
"mean_fragment_size": 1,
@@ -260,7 +251,6 @@ def test_add_library_contains_invalid(self):
"name": self._get_random_name(),
"concentration": 1.0,
"sequencing_depth": 1,
- "amplification_cycles": 1,
"index_reads": 0,
"mean_fragment_size": 1,
},
@@ -317,12 +307,10 @@ def test_update_library(self):
"name": new_name,
"organism": library.organism.pk,
"concentration": 1.0,
- "concentration_method": library.concentration_method.pk,
"read_length": library.read_length.pk,
"sequencing_depth": 1,
"library_protocol": library.library_protocol.pk,
"library_type": library.library_type.pk,
- "amplification_cycles": 1,
"index_type": library.index_type.pk,
"index_reads": 0,
"mean_fragment_size": 1,
@@ -352,12 +340,10 @@ def test_update_library_contains_invalid(self):
"name": new_name1,
"organism": library1.organism.pk,
"concentration": 1.0,
- "concentration_method": library1.concentration_method.pk,
"read_length": library1.read_length.pk,
"sequencing_depth": 1,
"library_protocol": library1.library_protocol.pk,
"library_type": library1.library_type.pk,
- "amplification_cycles": 1,
"index_type": library1.index_type.pk,
"index_reads": 0,
"mean_fragment_size": 1,
@@ -367,7 +353,6 @@ def test_update_library_contains_invalid(self):
"name": new_name2,
"concentration": 2.0,
"sequencing_depth": 2,
- "amplification_cycles": 2,
"index_reads": 0,
"mean_fragment_size": 2,
},
diff --git a/backend/library_preparation/migrations/0005_rename_qpcr_result_librarypreparation_removed_qpcr_result.py b/backend/library_preparation/migrations/0005_rename_qpcr_result_librarypreparation_removed_qpcr_result.py
new file mode 100644
index 000000000..7afc75706
--- /dev/null
+++ b/backend/library_preparation/migrations/0005_rename_qpcr_result_librarypreparation_removed_qpcr_result.py
@@ -0,0 +1,18 @@
+# Generated by Django 4.2.15 on 2024-09-24 23:54
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('library_preparation', '0004_librarypreparation_smear_analysis'),
+ ]
+
+ operations = [
+ migrations.RenameField(
+ model_name='librarypreparation',
+ old_name='qpcr_result',
+ new_name='removed_qpcr_result',
+ ),
+ ]
diff --git a/backend/library_preparation/migrations/max_migration.txt b/backend/library_preparation/migrations/max_migration.txt
index 9dfac2c79..0983993f8 100644
--- a/backend/library_preparation/migrations/max_migration.txt
+++ b/backend/library_preparation/migrations/max_migration.txt
@@ -1 +1 @@
-0004_librarypreparation_smear_analysis
+0005_rename_qpcr_result_librarypreparation_removed_qpcr_result
diff --git a/backend/library_preparation/models.py b/backend/library_preparation/models.py
index 95901a7cf..f81d8e4ea 100644
--- a/backend/library_preparation/models.py
+++ b/backend/library_preparation/models.py
@@ -51,11 +51,11 @@ class LibraryPreparation(DateTimeMixin):
blank=True,
)
- qpcr_result = models.FloatField(
+ removed_qpcr_result = models.FloatField(
"qPCR Result",
null=True,
blank=True,
- )
+ ) # This field is not in use
comments = models.TextField(
"Comments",
diff --git a/backend/library_sample_shared/models.py b/backend/library_sample_shared/models.py
index e9b697b06..58b246f1f 100644
--- a/backend/library_sample_shared/models.py
+++ b/backend/library_sample_shared/models.py
@@ -412,7 +412,8 @@ def index_i5_id(self):
removed_equal_representation_nucleotides = models.BooleanField(
"Equal Representation of Nucleotides",
- default=True,
+ blank=True,
+ default=False,
) # This field is not in use
removed_comments = models.TextField(
diff --git a/backend/library_sample_shared/tests.py b/backend/library_sample_shared/tests.py
index b10d83d77..3488827f4 100644
--- a/backend/library_sample_shared/tests.py
+++ b/backend/library_sample_shared/tests.py
@@ -66,15 +66,6 @@ def test_organism_name(self):
self.assertEqual(self.organism.__str__(), self.organism.name)
-class ConcentrationMethodTest(TestCase):
- def setUp(self):
- self.method = ConcentrationMethod(name=get_random_name())
-
- def test_concentration_method_name(self):
- self.assertTrue(isinstance(self.method, ConcentrationMethod))
- self.assertEqual(self.method.__str__(), self.method.name)
-
-
class ReadLengthTest(TestCase):
def setUp(self):
self.read_length = ReadLength(name=get_random_name())
@@ -229,23 +220,6 @@ def test_organisms_list(self):
self.assertIn(self.read_length.name, read_lengths)
-class TestConcentrationMethods(BaseTestCase):
- def setUp(self):
- self.create_user("foo@bar.io", "foo-foo")
- self.client.login(email="foo@bar.io", password="foo-foo")
-
- self.concentration_method = ConcentrationMethod(name=self._get_random_name())
- self.concentration_method.save()
-
- def test_organisms_list(self):
- """Ensure get concentration methods behaves correctly."""
- response = self.client.get(reverse("concentration-method-list"))
- data = response.json()
- concentration_methods = [x["name"] for x in data]
- self.assertEqual(response.status_code, 200)
- self.assertIn(self.concentration_method.name, concentration_methods)
-
-
class TestIndexTypes(BaseTestCase):
def setUp(self):
self.create_user("foo@bar.io", "foo-foo")
diff --git a/backend/request/views.py b/backend/request/views.py
index e7cf5115d..29165b733 100644
--- a/backend/request/views.py
+++ b/backend/request/views.py
@@ -1093,14 +1093,10 @@ def export_request(request):
dataset = Dataset()
dataset.headers = (
# The following are not submitted by user...
- # id barcode create_time update_time status concentration concentration_method
- # equal_representation_nucleotides comments is_pooled amplification_cycles
- # dilution_factor concentration_facility concentration_method_facility archived
+ # id barcode create_time update_time status concentration
+ # is_pooled dilution_factor concentration_facility archived
# sample_volume_facility amount_facility size_distribution_facility comments_facility
- ##libraries-exclusively:
- # qpcr_result qpcr_result_facility
- ##sample-exclusively:
- # is_converted
+ ## sample-exclusively: is_converted
"id",
"name",
"barcode",
diff --git a/backend/sample/admin.py b/backend/sample/admin.py
index 1d0ea9730..e2039750e 100644
--- a/backend/sample/admin.py
+++ b/backend/sample/admin.py
@@ -102,14 +102,13 @@ class SampleAdmin(admin.ModelAdmin):
"Determined by Facility",
{
"fields": (
+ "measuring_unit_facility",
+ "measured_value_facility",
"dilution_factor",
"concentration_facility",
- "concentration_method_facility",
"sample_volume_facility",
"amount_facility",
"size_distribution_facility",
- "rna_quality_facility",
- "comments_facility",
),
},
),
diff --git a/backend/sample/migrations/0012_alter_sample_removed_equal_representation_nucleotides.py b/backend/sample/migrations/0012_alter_sample_removed_equal_representation_nucleotides.py
new file mode 100644
index 000000000..bf965fa9b
--- /dev/null
+++ b/backend/sample/migrations/0012_alter_sample_removed_equal_representation_nucleotides.py
@@ -0,0 +1,18 @@
+# Generated by Django 4.2.15 on 2024-09-24 23:54
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('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'),
+ ),
+ ]
diff --git a/backend/sample/migrations/max_migration.txt b/backend/sample/migrations/max_migration.txt
index f3df05692..ba6aad436 100644
--- a/backend/sample/migrations/max_migration.txt
+++ b/backend/sample/migrations/max_migration.txt
@@ -1 +1 @@
-0011_alter_sample_measured_value_facility
+0012_alter_sample_removed_equal_representation_nucleotides
diff --git a/backend/sample/tests.py b/backend/sample/tests.py
index 93f025535..cc77c0a6d 100644
--- a/backend/sample/tests.py
+++ b/backend/sample/tests.py
@@ -25,9 +25,6 @@ def create_sample(name, status=0, save=True, read_length=None, index_type=None):
organism = Organism(name="Organism")
organism.save()
- concentration_method = ConcentrationMethod(name="Concentration Method")
- concentration_method.save()
-
if read_length is None:
read_length = ReadLength(name="Read Length")
read_length.save()
@@ -55,7 +52,6 @@ def create_sample(name, status=0, save=True, read_length=None, index_type=None):
status=status,
organism_id=organism.pk,
concentration=1.0,
- concentration_method_id=concentration_method.pk,
read_length_id=read_length.pk,
sequencing_depth=1,
library_protocol_id=library_protocol.pk,
@@ -216,7 +212,6 @@ def test_add_sample(self):
"name": name,
"organism": self.sample.organism.pk,
"concentration": 1.0,
- "concentration_method": self.sample.concentration_method.pk,
"read_length": self.sample.read_length.pk,
"sequencing_depth": 1,
"library_protocol": self.sample.library_protocol.pk,
@@ -245,7 +240,6 @@ def test_add_sample_contains_invalid(self):
"name": name,
"organism": self.sample.organism.pk,
"concentration": 1.0,
- "concentration_method": self.sample.concentration_method.pk,
"read_length": self.sample.read_length.pk,
"sequencing_depth": 1,
"library_protocol": self.sample.library_protocol.pk,
@@ -310,7 +304,6 @@ def test_update_sample(self):
"name": new_name,
"organism": sample.organism.pk,
"concentration": 1.0,
- "concentration_method": sample.concentration_method.pk,
"read_length": sample.read_length.pk,
"sequencing_depth": 1,
"library_protocol": sample.library_protocol.pk,
@@ -342,7 +335,6 @@ def test_update_sample_contains_invalid(self):
"name": new_name1,
"organism": sample1.organism.pk,
"concentration": 1.0,
- "concentration_method": sample1.concentration_method.pk,
"read_length": sample1.read_length.pk,
"sequencing_depth": 1,
"library_protocol": sample1.library_protocol.pk,
diff --git a/backend/static/main-hub/app/model/incominglibraries/IncomingLibraries.js b/backend/static/main-hub/app/model/incominglibraries/IncomingLibraries.js
index 00431ffc6..eda534f2e 100644
--- a/backend/static/main-hub/app/model/incominglibraries/IncomingLibraries.js
+++ b/backend/static/main-hub/app/model/incominglibraries/IncomingLibraries.js
@@ -14,10 +14,6 @@ Ext.define("MainHub.model.incominglibraries.IncomingLibraries", {
type: "float",
allowNull: true
},
- {
- name: "concentration_method_facility",
- type: "int"
- },
{
name: "sample_volume_facility",
type: "int",
@@ -34,20 +30,15 @@ Ext.define("MainHub.model.incominglibraries.IncomingLibraries", {
allowNull: true
},
{
- name: "qpcr_result_facility",
- type: "float",
- allowNull: true
+ name: "measuring_unit_facility",
+ type: "string"
},
{
- name: "rna_quality_facility",
+ name: "measured_value_facility",
type: "float",
allowNull: true,
defaultValue: null
},
- {
- name: "comments_facility",
- type: "string"
- },
{
name: "samples_submitted",
type: "bool"
diff --git a/backend/static/main-hub/app/model/libraries/BatchAdd/Common.js b/backend/static/main-hub/app/model/libraries/BatchAdd/Common.js
index 7700b70fe..fc9f8badb 100644
--- a/backend/static/main-hub/app/model/libraries/BatchAdd/Common.js
+++ b/backend/static/main-hub/app/model/libraries/BatchAdd/Common.js
@@ -78,21 +78,6 @@ Ext.define("MainHub.model.libraries.BatchAdd.Common", {
name: "concentration",
defaultValue: null
},
- {
- type: "int",
- name: "concentration_method",
- allowNull: true,
- defaultValue: null
- },
- {
- type: "int",
- name: "amplification_cycles",
- defaultValue: null
- },
- {
- type: "bool",
- name: "equal_representation_nucleotides"
- },
{
type: "int",
name: "read_length",
@@ -134,8 +119,6 @@ Ext.define("MainHub.model.libraries.BatchAdd.Common", {
volume: "greaterthanten",
read_length: "presence",
sequencing_depth: "greaterthanten",
- // amplification_cycles: 'presence',
- // concentration_method: 'presence',
organism: "presence"
}
});
diff --git a/backend/static/main-hub/app/model/libraries/BatchAdd/Library.js b/backend/static/main-hub/app/model/libraries/BatchAdd/Library.js
index a09876266..2740ffaa5 100644
--- a/backend/static/main-hub/app/model/libraries/BatchAdd/Library.js
+++ b/backend/static/main-hub/app/model/libraries/BatchAdd/Library.js
@@ -48,12 +48,6 @@ Ext.define("MainHub.model.libraries.BatchAdd.Library", {
type: "string",
name: "index_i5"
},
- {
- type: "int",
- name: "qpcr_result",
- allowNull: true,
- defaultValue: null
- }
],
validators: {
diff --git a/backend/static/main-hub/app/model/libraries/Library.js b/backend/static/main-hub/app/model/libraries/Library.js
index 99672d8d1..54689f95d 100644
--- a/backend/static/main-hub/app/model/libraries/Library.js
+++ b/backend/static/main-hub/app/model/libraries/Library.js
@@ -32,11 +32,6 @@ Ext.define("MainHub.model.libraries.Library", {
name: "library_type_name",
type: "string"
},
- {
- name: "amplification_cycles",
- type: "int",
- allowNull: true
- },
{
name: "organism",
type: "int"
@@ -66,24 +61,11 @@ Ext.define("MainHub.model.libraries.Library", {
name: "index_i5",
type: "string"
},
- {
- name: "equal_representation_nucleotides",
- type: "bool",
- allowNull: true
- },
{
name: "concentration",
type: "float",
allowNull: true
},
- {
- name: "concentration_method",
- type: "int"
- },
- {
- name: "concentration_method_name",
- type: "string"
- },
{
name: "measuring_unit",
type: "string"
@@ -94,11 +76,6 @@ Ext.define("MainHub.model.libraries.Library", {
allowNull: true,
defaultValue: null
},
- {
- name: "qpcr_result",
- type: "float",
- allowNull: true
- },
{
name: "read_length",
type: "int"
diff --git a/backend/static/main-hub/app/model/librarypreparation/LibraryPreparation.js b/backend/static/main-hub/app/model/librarypreparation/LibraryPreparation.js
index e176bf03f..1abbe967b 100644
--- a/backend/static/main-hub/app/model/librarypreparation/LibraryPreparation.js
+++ b/backend/static/main-hub/app/model/librarypreparation/LibraryPreparation.js
@@ -102,11 +102,6 @@ Ext.define("MainHub.model.librarypreparation.LibraryPreparation", {
type: "float",
allowNull: true
},
- {
- name: "qpcr_result",
- type: "float",
- allowNull: true
- },
{
name: "dilution_factor",
type: "int",
diff --git a/backend/static/main-hub/app/view/incominglibraries/IncomingLibraries.js b/backend/static/main-hub/app/view/incominglibraries/IncomingLibraries.js
index dd20c1bee..e982f09d9 100644
--- a/backend/static/main-hub/app/view/incominglibraries/IncomingLibraries.js
+++ b/backend/static/main-hub/app/view/incominglibraries/IncomingLibraries.js
@@ -141,28 +141,6 @@ Ext.define("MainHub.view.incominglibraries.IncomingLibraries", {
tdCls: "userEntry",
width: 70
},
- {
- text: "F/S",
- tooltip: "Concentration Determined by (user)",
- dataIndex: "concentration_method",
- tdCls: "userEntry",
- width: 50,
- renderer: function (value, meta) {
- var store = Ext.getStore("concentrationMethodsStore");
- var record = store.findRecord("id", value);
- meta.tdAttr = 'data-qtip="' + record.get("name") + '"';
- return record ? record.getShortName() : "";
- },
- hidden: true
- },
- {
- text: "qPCR (nM)",
- tooltip: "qPCR Result (user)",
- dataIndex: "qpcr_result",
- tdCls: "userEntry",
- width: 85,
- hidden: true
- },
{
text: "bp",
tooltip: "Mean Fragment Size (user)",
@@ -229,46 +207,6 @@ Ext.define("MainHub.view.incominglibraries.IncomingLibraries", {
minValue: 0
}
},
- {
- text: "F/S",
- tooltip: "Concentration Determined by (facility)",
- dataIndex: "concentration_method_facility",
- tdCls: "facilityEntry",
- width: 80,
- editor: {
- xtype: "combobox",
- queryMode: "local",
- displayField: "name",
- valueField: "id",
- store: "concentrationMethodsStore",
- matchFieldWidth: false,
- forceSelection: true
- },
- renderer: function (value, meta) {
- var store = Ext.getStore("concentrationMethodsStore");
- var record = store.findRecord("id", value);
-
- if (record) {
- meta.tdAttr = 'data-qtip="' + record.get("name") + '"';
- }
-
- return record ? record.getShortName() : "";
- },
- hidden: true
- },
- {
- text: "qPCR (nM)",
- tooltip: "qPCR Result (facility)",
- dataIndex: "qpcr_result_facility",
- tdCls: "facilityEntry",
- width: 85,
- editor: {
- xtype: "numberfield",
- id: "qPCRResultEditor",
- minValue: 0
- },
- hidden: true
- },
{
text: "bp",
tooltip: "Size Distribution (facility)",
diff --git a/backend/static/main-hub/app/view/incominglibraries/IncomingLibrariesController.js b/backend/static/main-hub/app/view/incominglibraries/IncomingLibrariesController.js
index 536f6cfd9..e29f32452 100644
--- a/backend/static/main-hub/app/view/incominglibraries/IncomingLibrariesController.js
+++ b/backend/static/main-hub/app/view/incominglibraries/IncomingLibrariesController.js
@@ -96,13 +96,11 @@ Ext.define("MainHub.view.incominglibraries.IncomingLibrariesController", {
var allowedColumns = [
"dilution_factor",
"concentration_facility",
- "concentration_method_facility",
"sample_volume_facility",
"amount_facility",
"size_distribution_facility",
- "comments_facility",
- "qpcr_result_facility",
- "rna_quality_facility"
+ "measuring_unit_facility",
+ "measured_value_facility"
];
var ngFormulaDataIndices = [
"dilution_factor",
diff --git a/backend/static/main-hub/app/view/libraries/BatchAddWindowController.js b/backend/static/main-hub/app/view/libraries/BatchAddWindowController.js
index e858e20ab..e4bb2ba10 100644
--- a/backend/static/main-hub/app/view/libraries/BatchAddWindowController.js
+++ b/backend/static/main-hub/app/view/libraries/BatchAddWindowController.js
@@ -1176,13 +1176,6 @@ Ext.define("MainHub.view.libraries.BatchAddWindowController", {
validateRecord: function (record, url) {
var grid = Ext.getCmp("batch-add-grid");
var store = grid.getStore();
-
- // Passing default values to the API for the removed variables which are still required in the request object
- record.data.amplification_cycles = 0;
- record.data.concentration_method = 4;
- record.data.equal_representation_nucleotides = false;
- if (url == "api/libraries/") record.data.qpcr_result = 0;
-
var validation = record.getValidation(true).data;
var invalid = false;
var errors = {};
diff --git a/backend/static/main-hub/app/view/libraries/Libraries.js b/backend/static/main-hub/app/view/libraries/Libraries.js
index 8ca3b6f38..6c63aacbf 100644
--- a/backend/static/main-hub/app/view/libraries/Libraries.js
+++ b/backend/static/main-hub/app/view/libraries/Libraries.js
@@ -509,53 +509,11 @@ Ext.define("MainHub.view.libraries.Libraries", {
tooltip: "Sequencing Depth",
dataIndex: "sequencing_depth"
},
- // {
- // text: 'Amplification',
- // tooltip: 'Amplification Cycles',
- // dataIndex: 'amplification_cycles'
- // },
- // {
- // text: 'Equal nucl.',
- // tooltip: 'Equal Representation of Nucleotides',
- // dataIndex: 'equal_representation_nucleotides',
- // width: 90,
- // renderer: function (value, meta) {
- // if (meta.record.get('leaf')) {
- // return value ? 'Yes' : 'No';
- // }
- // }
- // },
- // {
- // text: 'qPCR (nM)',
- // tooltip: 'qPCR Result',
- // dataIndex: 'qpcr_result'
- // },
- // {
- // text: 'F/S',
- // tooltip: 'Concentration Determined by',
- // dataIndex: 'concentration_method',
- // width: 50,
- // renderer: function (value, meta) {
- // if (meta.record.get('leaf')) {
- // var store = Ext.getStore('concentrationMethodsStore');
- // var record = store.findRecord('id', value);
- // var name = record.get('name');
- // meta.tdAttr = Ext.String.format('data-qtip="{0}"', name);
- // return name.charAt(0);
- // }
- // }
- // },
{
text: "Organism",
dataIndex: "organism_name",
width: 150
},
- {
- text: "Comments",
- dataIndex: "comments",
- renderer: "gridCellTooltipRenderer",
- width: 150
- }
]
}
}
diff --git a/backend/static/main-hub/app/view/libraries/LibraryWindow.js b/backend/static/main-hub/app/view/libraries/LibraryWindow.js
index b387b2fb3..5a93fe669 100644
--- a/backend/static/main-hub/app/view/libraries/LibraryWindow.js
+++ b/backend/static/main-hub/app/view/libraries/LibraryWindow.js
@@ -266,63 +266,6 @@ Ext.define("MainHub.view.libraries.LibraryWindow", {
minValue: 1,
allowDecimals: false
},
- {
- xtype: "numberfield",
- name: "amplification_cycles",
- fieldLabel:
- 'Number of amplification cycles [?]',
- emptyText: "Number of amplification cycles",
- allowDecimals: false,
- minValue: 0
- },
- {
- xtype: "fieldcontainer",
- id: "equalRepresentation",
- fieldLabel:
- 'Equal Representation of Nucleotides [?]',
- defaultType: "radiofield",
- defaults: {
- // flex: 1
- },
- layout: "hbox",
- items: [
- {
- boxLabel: "Yes",
- name: "equal_representation_nucleotides",
- inputValue: true,
- id: "equalRepresentationRadio1",
- checked: true,
- margin: "0 15px 0 0"
- },
- {
- boxLabel: "No",
- name: "equal_representation_nucleotides",
- inputValue: false,
- id: "equalRepresentationRadio2"
- }
- ]
- },
- {
- xtype: "numberfield",
- name: "qpcr_result",
- fieldLabel:
- 'qPCR Result (nM) [?]',
- emptyText: "qPCR Result (nM)",
- allowBlank: true,
- minValue: 1
- },
- {
- xtype: "combobox",
- id: "concentrationMethodField",
- queryMode: "local",
- displayField: "name",
- valueField: "id",
- name: "concentration_method",
- fieldLabel: "Concentration Determined by",
- emptyText: "Concentration Determined by",
- store: "concentrationMethodsStore",
- forceSelection: true
- },
{
xtype: "combobox",
id: "organismField",
@@ -336,14 +279,6 @@ Ext.define("MainHub.view.libraries.LibraryWindow", {
store: "organismsStore",
forceSelection: true
},
- {
- xtype: "textarea",
- name: "comments",
- fieldLabel: "Comments",
- emptyText: "Comments",
- allowBlank: true,
- height: 150
- }
]
}
]
@@ -491,52 +426,6 @@ Ext.define("MainHub.view.libraries.LibraryWindow", {
minValue: 1,
allowDecimals: false
},
- {
- xtype: "numberfield",
- name: "amplification_cycles",
- fieldLabel:
- 'Sample amplification (cycles) [?]',
- emptyText: "Sample amplification (cycles)",
- allowDecimals: false,
- minValue: 0,
- allowBlank: true
- },
- {
- xtype: "fieldcontainer",
- id: "equalRepresentationSample",
- fieldLabel:
- 'Equal Representation of Nucleotides [?]',
- defaultType: "radiofield",
- layout: "hbox",
- items: [
- {
- boxLabel: "Yes",
- name: "equal_representation_nucleotides",
- inputValue: true,
- id: "equalRepresentationRadio3",
- checked: true,
- margin: "0 15px 0 0"
- },
- {
- boxLabel: "No",
- name: "equal_representation_nucleotides",
- inputValue: false,
- id: "equalRepresentationRadio4"
- }
- ]
- },
- {
- xtype: "combobox",
- id: "concentrationSampleMethodField",
- queryMode: "local",
- displayField: "name",
- valueField: "id",
- name: "concentration_method",
- fieldLabel: "Concentration Determined by",
- emptyText: "Concentration Determined by",
- store: "concentrationMethodsStore",
- forceSelection: true
- },
{
xtype: "combobox",
id: "organismSampleField",
@@ -550,14 +439,6 @@ Ext.define("MainHub.view.libraries.LibraryWindow", {
store: "organismsStore",
forceSelection: true
},
- {
- xtype: "textarea",
- name: "comments",
- fieldLabel: "Comments",
- emptyText: "Comments",
- allowBlank: true,
- height: 150
- }
]
}
]
diff --git a/backend/static/main-hub/app/view/libraries/LibraryWindowController.js b/backend/static/main-hub/app/view/libraries/LibraryWindowController.js
index 723116390..855665c14 100644
--- a/backend/static/main-hub/app/view/libraries/LibraryWindowController.js
+++ b/backend/static/main-hub/app/view/libraries/LibraryWindowController.js
@@ -139,15 +139,6 @@ Ext.define("MainHub.view.libraries.LibraryWindowController", {
true
);
- // Set Concentration Method
- var concentrationMethodField = Ext.getCmp("concentrationMethodField");
- concentrationMethodField.select(record.concentration_method);
- concentrationMethodField.fireEvent(
- "select",
- concentrationMethodField,
- concentrationMethodField.findRecordByValue(record.concentration_method)
- );
-
// Set Read Length
var readLengthField = Ext.getCmp("readLengthField");
readLengthField.select(record.readLengthId);
@@ -337,19 +328,6 @@ Ext.define("MainHub.view.libraries.LibraryWindowController", {
organismSampleField.findRecordByValue(record.organism)
);
- // Set concentration method
- var concentrationSampleMethodField = Ext.getCmp(
- "concentrationSampleMethodField"
- );
- concentrationSampleMethodField.select(record.concentration_method);
- concentrationSampleMethodField.fireEvent(
- "select",
- concentrationSampleMethodField,
- concentrationSampleMethodField.findRecordByValue(
- record.concentration_method
- )
- );
-
// Set read length
var readLengthSampleField = Ext.getCmp("readLengthSampleField");
readLengthSampleField.select(record.readLengthId);
diff --git a/backend/static/main-hub/app/view/librarypreparation/LibraryPreparation.js b/backend/static/main-hub/app/view/librarypreparation/LibraryPreparation.js
index f8bef0dec..7dba54eee 100644
--- a/backend/static/main-hub/app/view/librarypreparation/LibraryPreparation.js
+++ b/backend/static/main-hub/app/view/librarypreparation/LibraryPreparation.js
@@ -186,16 +186,6 @@ Ext.define("MainHub.view.librarypreparation.LibraryPreparation", {
minValue: 0
}
},
- {
- text: "qPCR (nM)",
- tooltip: "qPCR Result (nM)",
- dataIndex: "qpcr_result",
- width: 100,
- editor: {
- xtype: "numberfield",
- minValue: 0
- }
- },
{
text: "bp",
tooltip: "Mean Fragment Size (bp)",
diff --git a/backend/static/main-hub/app/view/librarypreparation/LibraryPreparationController.js b/backend/static/main-hub/app/view/librarypreparation/LibraryPreparationController.js
index f69ca9b28..f0f3d8a05 100644
--- a/backend/static/main-hub/app/view/librarypreparation/LibraryPreparationController.js
+++ b/backend/static/main-hub/app/view/librarypreparation/LibraryPreparationController.js
@@ -83,7 +83,6 @@ Ext.define("MainHub.view.librarypreparation.LibraryPreparationController", {
"concentration_sample",
"comments_facility",
"comments",
- "qpcr_result"
];
var nMFormulaDataIndices = ["concentration_library", "mean_fragment_size"];