modules and filter tests passing

yeastregulatorydb/regulatory_data/api/filters/BindingFilter.py

@@ -8,13 +8,14 @@ class BindingFilter(django_filters.FilterSet):
     id = django_filters.NumberFilter()
     pk = django_filters.NumberFilter()
     regulator = django_filters.NumberFilter()
-    regulator_locus_tag = django_filters.CharFilter(field_name="regulator__locus_tag", lookup_expr="iexact")
-    regulator_symbol = django_filters.CharFilter(field_name="regulator__symbol", lookup_expr="iexact")
+    regulator_locus_tag = django_filters.CharFilter(field_name="regulator__regulator__locus_tag", lookup_expr="iexact")
+    regulator_symbol = django_filters.CharFilter(field_name="regulator__regulator__symbol", lookup_expr="iexact")
     batch = django_filters.CharFilter(lookup_expr="iexact")
     # pylint: enable=R0801
     replicate = django_filters.NumberFilter()
     source = django_filters.NumberFilter()
     source_orig_id = django_filters.CharFilter(lookup_expr="iexact")
+    strain = django_filters.CharFilter(lookup_expr="iexact")
     lab = django_filters.CharFilter(field_name="source__lab", lookup_expr="iexact")
     assay = django_filters.CharFilter(field_name="source__assay", lookup_expr="iexact")
     workflow = django_filters.CharFilter(field_name="source__workflow", lookup_expr="iexact")
@@ -32,6 +33,7 @@ class Meta:
             "replicate",
             "source",
             "source_orig_id",
+            "strain",
             "lab",
             "assay",
             "workflow",

yeastregulatorydb/regulatory_data/api/filters/ExpressionFilter.py

@@ -8,16 +8,16 @@ class ExpressionFilter(django_filters.FilterSet):
     id = django_filters.NumberFilter()
     pk = django_filters.NumberFilter()
     regulator = django_filters.NumberFilter()
-    regulator_locus_tag = django_filters.CharFilter(field_name="regulator__locus_tag", lookup_expr="iexact")
-    regulator_symbol = django_filters.CharFilter(field_name="regulator__symbol", lookup_expr="iexact")
+    regulator_locus_tag = django_filters.CharFilter(field_name="regulator__regulator__locus_tag", lookup_expr="iexact")
+    regulator_symbol = django_filters.CharFilter(field_name="regulator__regulator__symbol", lookup_expr="iexact")
     batch = django_filters.CharFilter(field_name="batch", lookup_expr="iexact")
     # pylint: enable=R0801
     replicate = django_filters.NumberFilter()
     control = django_filters.CharFilter(lookup_expr="iexact")
     mechanism = django_filters.CharFilter(lookup_expr="iexact")
     restriction = django_filters.CharFilter(lookup_expr="iexact")
     time = django_filters.NumberFilter(field_name="time")
-    source = django_filters.CharFilter(lookup_expr="iexact")
+    source = django_filters.NumberFilter()
     lab = django_filters.CharFilter(field_name="source__lab", lookup_expr="iexact")
     assay = django_filters.CharFilter(field_name="source__assay", lookup_expr="iexact")
     workflow = django_filters.CharFilter(field_name="source__workflow", lookup_expr="iexact")

yeastregulatorydb/regulatory_data/api/filters/ExpressionManualQCFilter.py

@@ -9,16 +9,18 @@ class ExpressionManualQCFilter(django_filters.FilterSet):
     expression = django_filters.NumberFilter()
     strain_verified = django_filters.ChoiceFilter(choices=[("yes", "yes"), ("no", "no"), ("unverified", "unverified")])
     regulator_locus_tag = django_filters.CharFilter(
-        field_name="expression__regulator__locus_tag", lookup_expr="iexact"
+        field_name="expression__regulator__regulator__locus_tag", lookup_expr="iexact"
+    )
+    regulator_symbol = django_filters.CharFilter(
+        field_name="expression__regulator__regulator__symbol", lookup_expr="iexact"
     )
-    regulator_symbol = django_filters.CharFilter(field_name="expression__regulator__symbol", lookup_expr="iexact")
     batch = django_filters.CharFilter(field_name="expression__batch", lookup_expr="iexact")
     replicate = django_filters.NumberFilter(field_name="expression__replicate")
     control = django_filters.CharFilter(field_name="expression__control", lookup_expr="iexact")
     mechanism = django_filters.CharFilter(field_name="expression__mechanism", lookup_expr="iexact")
     restriction = django_filters.CharFilter(field_name="expression__restriction", lookup_expr="iexact")
     time = django_filters.NumberFilter(field_name="expression__time")
-    source = django_filters.CharFilter(field_name="expression__source", lookup_expr="iexact")
+    source = django_filters.NumberFilter(field_name="expression__source__id")
     lab = django_filters.CharFilter(field_name="expression__source__lab", lookup_expr="iexact")
     assay = django_filters.CharFilter(field_name="expression__source__assay", lookup_expr="iexact")
     workflow = django_filters.CharFilter(field_name="expression__source__workflow", lookup_expr="iexact")

yeastregulatorydb/regulatory_data/api/filters/ExpressionSourceFilter.py

@@ -7,7 +7,7 @@ class ExpressionSourceFilter(django_filters.FilterSet):
     id = django_filters.NumberFilter()
     pk = django_filters.NumberFilter()
     fileformat_id = django_filters.NumberFilter()
-    fileformat = django_filters.CharFilter(field_name="fileformat_id__fileformat", lookup_expr="iexact")
+    fileformat = django_filters.CharFilter(field_name="fileformat__fileformat", lookup_expr="iexact")
     lab = django_filters.CharFilter(lookup_expr="iexact")
     assay = django_filters.CharFilter(lookup_expr="iexact")
     workflow = django_filters.CharFilter(lookup_expr="iexact")

yeastregulatorydb/regulatory_data/api/filters/GenomicFeatureFilter.py

@@ -9,9 +9,9 @@ class GenomicFeatureFilter(django_filters.FilterSet):
     end = django_filters.NumberFilter()
     strand = django_filters.CharFilter(lookup_expr="exact")
     type = django_filters.CharFilter(lookup_expr="iexact")
-    gene_biotype = django_filters.CharFilter(lookup_expr="iexact")
+    biotype = django_filters.CharFilter(lookup_expr="iexact")
     locus_tag = django_filters.CharFilter(lookup_expr="iexact")
-    gene = django_filters.CharFilter(lookup_expr="iexact")
+    symbol = django_filters.CharFilter(lookup_expr="iexact")
     source = django_filters.CharFilter(lookup_expr="iexact")
     alias = django_filters.CharFilter(lookup_expr="iexact")
     note = django_filters.CharFilter(lookup_expr="iexact")
@@ -24,9 +24,9 @@ class Meta:
             "end",
             "strand",
             "type",
-            "gene_biotype",
+            "biotype",
             "locus_tag",
-            "gene",
+            "symbol",
             "source",
             "alias",
             "note",

yeastregulatorydb/regulatory_data/api/filters/PromoterSetSigFilter.py

@@ -7,12 +7,16 @@ class PromoterSetSigFilter(django_filters.FilterSet):
     id = django_filters.NumberFilter()
     pk = django_filters.NumberFilter()
     binding = django_filters.NumberFilter()
-    promoter_id = django_filters.NumberFilter()
-    promoter_name = django_filters.CharFilter(field_name="promoter_id__name", lookup_expr="iexact")
-    background_id = django_filters.NumberFilter(field_name="background_id")
+    promoter = django_filters.NumberFilter()
+    promoter_name = django_filters.CharFilter(field_name="promoter__name", lookup_expr="iexact")
+    background = django_filters.NumberFilter()
     background_name = django_filters.CharFilter(field_name="background_id__name", lookup_expr="iexact")
-    regulator_locus_tag = django_filters.CharFilter(field_name="binding__regulator__locus_tag", lookup_expr="iexact")
-    regulator_symbol = django_filters.CharFilter(field_name="binding__regulator__symbol", lookup_expr="iexact")
+    regulator_locus_tag = django_filters.CharFilter(
+        field_name="binding__regulator__regulator__locus_tag", lookup_expr="iexact"
+    )
+    regulator_symbol = django_filters.CharFilter(
+        field_name="binding__regulator__regulator__symbol", lookup_expr="iexact"
+    )
     batch = django_filters.CharFilter(field_name="binding__batch", lookup_expr="iexact")
     replicate = django_filters.NumberFilter(field_name="binding__replicate")
     source = django_filters.NumberFilter(field_name="binding__source")

yeastregulatorydb/regulatory_data/api/filters/__init__.py

@@ -0,0 +1,12 @@
+from .BindingFilter import BindingFilter
+from .BindingManualQCFilter import BindingManualQCFilter
+from .BindingSourceFilter import BindingSourceFilter
+from .CallingCardsBackgroundFilter import CallingCardsBackgroundFilter
+from .ExpressionFilter import ExpressionFilter
+from .ExpressionManualQCFilter import ExpressionManualQCFilter
+from .ExpressionSourceFilter import ExpressionSourceFilter
+from .FileFormatFilter import FileFormatFilter
+from .GenomicFeatureFilter import GenomicFeatureFilter
+from .PromoterSetFilter import PromoterSetFilter
+from .PromoterSetSigFilter import PromoterSetSigFilter
+from .RegulatorFilter import RegulatorFilter

yeastregulatorydb/regulatory_data/api/serializers/PromoterSetSigSerializer.py

@@ -18,4 +18,4 @@ class Meta:
         fields = "__all__"
 
     def get_background_id(self, obj):
-        return obj.background_id.id if obj.background_id else "undefined"
+        return obj.background.id if obj.background else "undefined"

yeastregulatorydb/regulatory_data/migrations/0002_rename_fileformat_id_bindingsource_fileformat.py

@@ -0,0 +1,17 @@
+# Generated by Django 4.2.8 on 2023-12-12 18:50
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("regulatory_data", "0001_initial"),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name="bindingsource",
+            old_name="fileformat_id",
+            new_name="fileformat",
+        ),
+    ]

yeastregulatorydb/regulatory_data/migrations/0003_rename_fileformat_id_expressionsource_fileformat.py

@@ -0,0 +1,17 @@
+# Generated by Django 4.2.8 on 2023-12-12 18:53
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("regulatory_data", "0002_rename_fileformat_id_bindingsource_fileformat"),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name="expressionsource",
+            old_name="fileformat_id",
+            new_name="fileformat",
+        ),
+    ]

yeastregulatorydb/regulatory_data/migrations/0004_rename_background_id_promotersetsig_background_and_more.py

@@ -0,0 +1,31 @@
+# Generated by Django 4.2.8 on 2023-12-12 21:56
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("regulatory_data", "0003_rename_fileformat_id_expressionsource_fileformat"),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name="promotersetsig",
+            old_name="background_id",
+            new_name="background",
+        ),
+        migrations.RenameField(
+            model_name="promotersetsig",
+            old_name="promoter_id",
+            new_name="promoter",
+        ),
+        migrations.AlterField(
+            model_name="expression",
+            name="control",
+            field=models.CharField(
+                choices=[("undefined", "undefined"), ("wt", "wt"), ("wt_meta", "wt_meta")],
+                default="undefined",
+                help_text="Intended for micro-array data, this field records the control strain used to generate the relative intensity data",
+            ),
+        ),
+    ]

yeastregulatorydb/regulatory_data/models/BaseModel.py

@@ -46,6 +46,12 @@ class MyModel(BaseModel):
     class Meta:
         abstract = True
 
+    def save(self, *args, **kwargs):
+        # If the record is being created, set the modifier to the uploader
+        if self._state.adding:
+            self.modifier = self.uploader
+        super().save(*args, **kwargs)
+
 
 @receiver(pre_save, sender=BaseModel)
 def update_modified_date(sender, instance, **kwargs):  # pylint: disable=unused-argument

yeastregulatorydb/regulatory_data/models/BindingSource.py

@@ -15,7 +15,7 @@ class BindingSource(BaseModel):
     Store binding data source information
     """
 
-    fileformat_id = models.ForeignKey(
+    fileformat = models.ForeignKey(
         "FileFormat",
         on_delete=models.CASCADE,
         help_text="Foreign key to the FileFormat table",

yeastregulatorydb/regulatory_data/models/Expression.py

@@ -23,7 +23,7 @@ class Expression(BaseModel, FileUploadMixin):
     )
     replicate = models.PositiveIntegerField(default=1, help_text="Replicate number")
     control = models.CharField(
-        choices=[("undefined", "undefined"), ("wt", "wt"), ("wt_mata", "wt_mata")],
+        choices=[("undefined", "undefined"), ("wt", "wt"), ("wt_meta", "wt_meta")],
         default="undefined",
         help_text="Intended for micro-array data, this field records the "
         "control strain used to generate the relative intensity data",

yeastregulatorydb/regulatory_data/models/ExpressionSource.py

@@ -15,7 +15,7 @@ class ExpressionSource(BaseModel):
     Store expression data source information
     """
 
-    fileformat_id = models.ForeignKey(
+    fileformat = models.ForeignKey(
         "FileFormat", on_delete=models.CASCADE, help_text="foreign key to the fileformat table"
     )
     lab = models.CharField(

yeastregulatorydb/regulatory_data/models/PromoterSetSig.py

@@ -16,12 +16,12 @@ class PromoterSetSig(BaseModel, FileUploadMixin):
     """
 
     binding = models.ForeignKey("Binding", on_delete=models.CASCADE, help_text="foreign key to the 'Binding' table")
-    promoter_id = models.ForeignKey(
+    promoter = models.ForeignKey(
         "PromoterSet", on_delete=models.CASCADE, help_text="foreign key to the 'promoter' table"
     )
     # note: in the serializer, when a user makes a GET request, a null value
     # is transformed to the string 'undefined' prior to returning to client
-    background_id = models.ForeignKey(
+    background = models.ForeignKey(
         "CallingCardsBackground",
         on_delete=models.CASCADE,
         blank=True,
@@ -34,10 +34,7 @@ class PromoterSetSig(BaseModel, FileUploadMixin):
     file = models.FileField(upload_to="temp", help_text="A file which stores data on " "regulator/DNA interaction")
 
     def __str__(self):
-        return (
-            f"pk:{self.pk};binding:{self.binding};"
-            f"promoter_id:{self.promoter_id};background_id:{self.background_id}"
-        )
+        return f"pk:{self.pk};binding:{self.binding};" f"promoter_id:{self.promoter};background:{self.background}"
 
     class Meta:
         db_table = "promotersetsig"

yeastregulatorydb/regulatory_data/tests/factories.py

@@ -1,5 +1,5 @@
 import faker
-from factory import Faker, SubFactory
+from factory import Faker, LazyFunction, SubFactory
 from factory.django import DjangoModelFactory, FileField
 
 from yeastregulatorydb.users.tests.factories import UserFactory
@@ -23,6 +23,13 @@
 fake = faker.Faker()
 
 
+def sentence_with_max_chars(max_chars=100):
+    sentence = fake.sentence(nb_words=10)
+    if len(sentence) > max_chars:
+        sentence = sentence[:max_chars].rsplit(" ", 1)[0] + "."
+    return sentence
+
+
 class ChrMapFactory(DjangoModelFactory):
     uploader = SubFactory(UserFactory)
     modifier = SubFactory(UserFactory)
@@ -97,7 +104,7 @@ class Meta:
 class ExpressionSourceFactory(DjangoModelFactory):
     uploader = SubFactory(UserFactory)
     modifier = SubFactory(UserFactory)
-    fileformat_id = SubFactory(FileFormatFactory)
+    fileformat = SubFactory(FileFormatFactory)
     lab = Faker("word")
     assay = Faker("word")
     workflow = Faker("word")
@@ -107,7 +114,7 @@ class ExpressionSourceFactory(DjangoModelFactory):
 
     class Meta:
         model = ExpressionSource
-        django_get_or_create = ["fileformat_id"]
+        django_get_or_create = ["fileformat"]
 
 
 class ExpressionFactory(DjangoModelFactory):
@@ -158,7 +165,7 @@ class Meta:
 class BindingSourceFactory(DjangoModelFactory):
     uploader = SubFactory(UserFactory)
     modifier = SubFactory(UserFactory)
-    fileformat_id = SubFactory(FileFormatFactory)
+    fileformat = SubFactory(FileFormatFactory)
     lab = Faker("pystr", max_chars=20)
     assay = Faker("pystr", max_chars=20)
     workflow = Faker("pystr", max_chars=50)
@@ -168,7 +175,7 @@ class BindingSourceFactory(DjangoModelFactory):
 
     class Meta:
         model = BindingSource
-        django_get_or_create = ["fileformat_id", "lab", "assay", "workflow"]
+        django_get_or_create = ["fileformat", "lab", "assay", "workflow"]
 
 
 class BindingFactory(DjangoModelFactory):
@@ -211,7 +218,7 @@ class PromoterSetFactory(DjangoModelFactory):
     modifier = SubFactory(UserFactory)
     name = Faker("pystr", max_chars=10)
     file = FileField(filename="testfile.bed.gz")
-    notes = Faker("sentence", nb_words=10)
+    notes = LazyFunction(sentence_with_max_chars)
 
     class Meta:
         model = PromoterSet
@@ -222,11 +229,11 @@ class PromoterSetSigFactory(DjangoModelFactory):
     uploader = SubFactory(UserFactory)
     modifier = SubFactory(UserFactory)
     binding = SubFactory(BindingFactory)
-    promoter_id = SubFactory(PromoterSetFactory)
-    background_id = SubFactory(CallingCardsBackgroundFactory)
+    promoter = SubFactory(PromoterSetFactory)
+    background = SubFactory(CallingCardsBackgroundFactory)
     filetype = SubFactory(FileFormatFactory)
     file = FileField(filename="testfile.tsv.gz")
 
     class Meta:
         model = PromoterSetSig
-        django_get_or_create = ["binding", "promoter_id", "background_id"]
+        django_get_or_create = ["binding", "promoter", "background"]