regulatory_data parts seem to be functioning. all untested. no test d…

…ata yet

README.md

@@ -19,27 +19,45 @@ Moved to [settings](http://cookiecutter-django.readthedocs.io/en/latest/settings
 
 - To create a **superuser account**, use this command:
 
-      $ python manage.py createsuperuser
+```bash
+  python manage.py createsuperuser
+```
 
 For convenience, you can keep your normal user logged in on Chrome and your superuser logged in on Firefox (or similar), so that you can see how the site behaves for both kinds of users.
 
 ### Type checks
 
 Running type checks with mypy:
 
-    $ mypy yeastregulatorydb
+```bash
+  mypy yeastregulatorydb
+```
+
+#### mypy caveats
+
+- there is an issue accessing `Models.objects` that is unresolved. See
+  [issue 1684](https://github.com/typeddjango/django-stubs/issues/1684). I
+  choose to resolve this by ignoring the attr-defined error when accessing
+  `Model.objects` (see any viewset for an example). Note that in cases where
+  a custom manager is defined, I use _default_manager
+  ([see django docs](https://docs.djangoproject.com/en/4.2/topics/db/managers/#django.db.models.Model._default_manager)). This raises a "accessing private method" warning in pylint,
+  which is also ignored.
 
 ### Test coverage
 
 To run the tests, check your test coverage, and generate an HTML coverage report:
 
-    $ coverage run -m pytest
-    $ coverage html
-    $ open htmlcov/index.html
+```bash
+  coverage run -m pytest
+  coverage html
+  open htmlcov/index.html
+```
 
 #### Running tests with pytest
 
-    $ pytest
+```bash
+  pytest
+```
 
 ### Live reloading and Sass CSS compilation
 
@@ -161,4 +179,4 @@ it okay to delete and re-download it? [y/n] (y): y
     Choose from [1/2/3/4/5] (1): 4
   [26/27] keep_local_envs_in_vcs (y): n
   [27/27] debug (n): n
-```
+```

compose/local/django/Dockerfile

@@ -11,7 +11,11 @@ RUN apt-get update && apt-get install --no-install-recommends -y \
   # dependencies for building Python packages
   build-essential \
   # psycopg2 dependencies
-  libpq-dev
+  libpq-dev \
+  # HTSlib dependencies
+  zlib1g-dev \
+  libbz2-dev \
+  liblzma-dev
 
 # Requirements are installed here to ensure they will be cached.
 COPY ./requirements .

compose/local/docs/Dockerfile

@@ -12,6 +12,10 @@ RUN apt-get update && apt-get install --no-install-recommends -y \
   build-essential \
   # psycopg2 dependencies
   libpq-dev \
+  # HTSlib dependencies
+  zlib1g-dev \
+  libbz2-dev \
+  liblzma-dev \
   # cleaning up unused files
   && apt-get purge -y --auto-remove -o APT::AutoRemove::RecommendsImportant=false \
   && rm -rf /var/lib/apt/lists/*

compose/production/django/Dockerfile

@@ -12,7 +12,11 @@ RUN apt-get update && apt-get install --no-install-recommends -y \
   # dependencies for building Python packages
   build-essential \
   # psycopg2 dependencies
-  libpq-dev
+  libpq-dev \
+    # HTSlib dependencies
+  zlib1g-dev \
+  libbz2-dev \
+  liblzma-dev
 
 # Requirements are installed here to ensure they will be cached.
 COPY ./requirements .

config/api_router.py

@@ -1,6 +1,20 @@
 from django.conf import settings
 from rest_framework.routers import DefaultRouter, SimpleRouter
 
+from yeastregulatorydb.regulatory_data.api.views import (
+    BindingSourceViewSet,
+    BindingViewSet,
+    CallingCardsBackgroundViewSet,
+    ChrMapViewSet,
+    ExpressionManualQCViewSet,
+    ExpressionSourceViewSet,
+    ExpressionViewSet,
+    FileFormatViewSet,
+    GenomicFeatureViewSet,
+    PromoterSetSigViewSet,
+    PromoterSetViewSet,
+    RegulatorViewSet,
+)
 from yeastregulatorydb.users.api.views import UserViewSet
 
 if settings.DEBUG:
@@ -9,6 +23,18 @@
     router = SimpleRouter()
 
 router.register("users", UserViewSet)
+router.register("bindingsource", BindingSourceViewSet)
+router.register("binding", BindingViewSet)
+router.register("callingcardsbackground", CallingCardsBackgroundViewSet)
+router.register("chrmap", ChrMapViewSet)
+router.register("expressionmanualqc", ExpressionManualQCViewSet)
+router.register("expressionsource", ExpressionSourceViewSet)
+router.register("expression", ExpressionViewSet)
+router.register("fileformat", FileFormatViewSet)
+router.register("genomicfeature", GenomicFeatureViewSet)
+router.register("promotersetsig", PromoterSetSigViewSet)
+router.register("promoterset", PromoterSetViewSet)
+router.register("regulator", RegulatorViewSet)
 
 
 app_name = "api"

docs/api/yeastregulatorydb.regulatory_data.api.serializers.rst

@@ -100,10 +100,10 @@ yeastregulatorydb.regulatory\_data.api.serializers.PromoterSetSigSerializer modu
    :undoc-members:
    :show-inheritance:
 
-yeastregulatorydb.regulatory\_data.api.serializers.RegulatorSerializerSerializer module
+yeastregulatorydb.regulatory\_data.api.serializers.RegulatorSerializer module
 ---------------------------------------------------------------------------------------
 
-.. automodule:: yeastregulatorydb.regulatory_data.api.serializers.RegulatorSerializerSerializer
+.. automodule:: yeastregulatorydb.regulatory_data.api.serializers.RegulatorSerializer
    :members:
    :undoc-members:
    :show-inheritance:

docs/index.rst

@@ -12,7 +12,6 @@ Welcome to YeastRegulatoryDB's documentation!
 
    howto
    users
-   api
 
 
 

requirements/base.txt

@@ -24,3 +24,7 @@ django-cors-headers==4.3.1  # https://github.com/adamchainz/django-cors-headers
 # DRF-spectacular for api documentation
 drf-spectacular==0.26.5  # https://github.com/tfranzel/drf-spectacular
 django-filter==23.5  # https://github.com/carltongibson/django-filter
+
+# Third Party Software
+# ------------------------------------------------------------------------------
+callingcardstools==1.3.0 # https://github.com/cmatkhan/callingcardstools

yeastregulatorydb/contrib/sites/migrations/0001_initial.py

@@ -4,7 +4,6 @@
 
 
 class Migration(migrations.Migration):
-
     dependencies = []
 
     operations = [

yeastregulatorydb/contrib/sites/migrations/0002_alter_domain_unique.py

@@ -3,7 +3,6 @@
 
 
 class Migration(migrations.Migration):
-
     dependencies = [("sites", "0001_initial")]
 
     operations = [

yeastregulatorydb/contrib/sites/migrations/0003_set_site_domain_and_name.py

@@ -23,7 +23,7 @@ def _update_or_create_site_with_sequence(site_model, connection, domain, name):
         # site is created.
         # To avoid this, we need to manually update DB sequence and make sure it's
         # greater than the maximum value.
-        max_id = site_model.objects.order_by('-id').first().id
+        max_id = site_model.objects.order_by("-id").first().id
         with connection.cursor() as cursor:
             cursor.execute("SELECT last_value from django_site_id_seq")
             (current_id,) = cursor.fetchone()
@@ -57,7 +57,6 @@ def update_site_backward(apps, schema_editor):
 
 
 class Migration(migrations.Migration):
-
     dependencies = [("sites", "0002_alter_domain_unique")]
 
     operations = [migrations.RunPython(update_site_forward, update_site_backward)]

yeastregulatorydb/contrib/sites/migrations/0004_alter_options_ordering_domain.py

@@ -4,7 +4,6 @@
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("sites", "0003_set_site_domain_and_name"),
     ]

yeastregulatorydb/regulatory_data/admin.py

@@ -1,3 +1,5 @@
+# pylint: disable=unused-import
 from django.contrib import admin
 
 # Register your models here.
+from .models import *

yeastregulatorydb/regulatory_data/api/filters/BindingFilter.py

@@ -4,19 +4,22 @@
 
 
 class BindingFilter(django_filters.FilterSet):
+    # pylint: disable=R0801
     id = django_filters.NumberFilter()
     pk = django_filters.NumberFilter()
     regulator_id = 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")
     batch = django_filters.CharFilter(lookup_expr="iexact")
+    # pylint: enable=R0801
     replicate = django_filters.NumberFilter()
     source_id = django_filters.NumberFilter()
     source_orig_id = django_filters.CharFilter(lookup_expr="iexact")
     lab = django_filters.CharFilter(field_name="source_id__lab", lookup_expr="iexact")
     assay = django_filters.CharFilter(field_name="source_id__assay", lookup_expr="iexact")
     workflow = django_filters.CharFilter(field_name="source_id__workflow", lookup_expr="iexact")
 
+    # pylint: disable=R0801
     class Meta:
         model = Binding
         fields = [
@@ -33,3 +36,5 @@ class Meta:
             "assay",
             "workflow",
         ]
+
+    # pylint: enable=R0801

yeastregulatorydb/regulatory_data/api/filters/CallingCardsBackgroundFilter.py

@@ -3,7 +3,7 @@
 from ...models.CallingCardsBackground import CallingCardsBackground
 
 
-class CallingCardsBackgroundFilter(django_filters.filters.FilterSet):
+class CallingCardsBackgroundFilter(django_filters.FilterSet):
     class Meta:
         model = CallingCardsBackground
         fields = {"name": ["exact"]}

yeastregulatorydb/regulatory_data/api/filters/ExpressionFilter.py

@@ -4,12 +4,14 @@
 
 
 class ExpressionFilter(django_filters.FilterSet):
+    # pylint: disable=R0801
     id = django_filters.NumberFilter()
     pk = django_filters.NumberFilter()
     regulator_id = 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")
     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")
@@ -39,3 +41,5 @@ class Meta:
             "assay",
             "workflow",
         ]
+
+    # pylint: enable=R0801

yeastregulatorydb/regulatory_data/api/filters/ExpressionManualQCFilter.py

@@ -23,6 +23,7 @@ class ExpressionManualQCFilter(django_filters.FilterSet):
     assay = django_filters.CharFilter(field_name="expression_id__source_id__assay", lookup_expr="iexact")
     workflow = django_filters.CharFilter(field_name="expression_id__source_id__workflow", lookup_expr="iexact")
 
+    # pylint: disable=R0801
     class Meta:
         model = ExpressionManualQC
         fields = [
@@ -43,3 +44,5 @@ class Meta:
             "assay",
             "workflow",
         ]
+
+    # pylint: enable=R0801

yeastregulatorydb/regulatory_data/api/filters/FileFormatFilter.py

@@ -3,7 +3,7 @@
 from ...models.FileFormat import FileFormat
 
 
-class ExpressionManualQCFilter(django_filters.FilterSet):
+class FileFormatFilter(django_filters.FilterSet):
     class Meta:
         model = FileFormat
         fields = {"fileformat": ["exact"]}

yeastregulatorydb/regulatory_data/api/filters/GenomicFeatureFilter.py

@@ -7,7 +7,7 @@ class GenomicFeatureFilter(django_filters.FilterSet):
     chr = django_filters.CharFilter(field_name="chr__ucsc")
     start = django_filters.NumberFilter()
     end = django_filters.NumberFilter()
-    strand = django_filters.ChoiceFilter(choices=GenomicFeature.STRAND_CHOICES)
+    strand = django_filters.CharFilter(lookup_expr='exact')
     type = django_filters.CharFilter(lookup_expr="iexact")
     gene_biotype = django_filters.CharFilter(lookup_expr="iexact")
     locus_tag = django_filters.CharFilter(lookup_expr="iexact")

yeastregulatorydb/regulatory_data/api/filters/PromoterSetSigFilter.py

@@ -22,6 +22,7 @@ class PromoterSetSigFilter(django_filters.FilterSet):
     assay = django_filters.CharFilter(field_name="binding_id__source_id__assay", lookup_expr="iexact")
     workflow = django_filters.CharFilter(field_name="binding_id__source_id__workflow", lookup_expr="iexact")
 
+    # pylint: disable=R0801
     class Meta:
         model = PromoterSetSig
         fields = [
@@ -39,3 +40,5 @@ class Meta:
             "assay",
             "workflow",
         ]
+
+        # pylint: enable=R0801

yeastregulatorydb/regulatory_data/api/serializers/BindingManualQCSerializer.py

@@ -1,9 +1,10 @@
 from rest_framework import serializers
 
 from ...models.BindingManualQC import BindingManualQC
+from .mixins.CustomValidateMixin import CustomValidateMixin
 
 
-class BindingManualQCSerializer(serializers.ModelSerializer):
+class BindingManualQCSerializer(CustomValidateMixin, serializers.ModelSerializer):
     uploader = serializers.ReadOnlyField(source="uploader.username")
     modifiedBy = serializers.CharField(source="uploader.username", required=False)
 

yeastregulatorydb/regulatory_data/api/serializers/BindingSerializer.py

@@ -1,9 +1,10 @@
 from rest_framework import serializers
 
 from ...models.Binding import Binding
+from .mixins.CustomValidateMixin import CustomValidateMixin
 
 
-class BindingSerializer(serializers.ModelSerializer):
+class BindingSerializer(CustomValidateMixin, serializers.ModelSerializer):
     uploader = serializers.ReadOnlyField(source="uploader.username")
     modifiedBy = serializers.CharField(source="uploader.username", required=False)
 

yeastregulatorydb/regulatory_data/api/serializers/BindingSourceSerializer.py

@@ -1,9 +1,10 @@
 from rest_framework import serializers
 
 from ...models.BindingSource import BindingSource
+from .mixins.CustomValidateMixin import CustomValidateMixin
 
 
-class BindingSourceSerializer(serializers.ModelSerializer):
+class BindingSourceSerializer(CustomValidateMixin, serializers.ModelSerializer):
     uploader = serializers.ReadOnlyField(source="uploader.username")
     modifiedBy = serializers.CharField(source="uploader.username", required=False)
 

yeastregulatorydb/regulatory_data/api/serializers/CallingCardsBackgroundSerializer.py

@@ -1,9 +1,10 @@
 from rest_framework import serializers
 
 from ...models.CallingCardsBackground import CallingCardsBackground
+from .mixins.CustomValidateMixin import CustomValidateMixin
 
 
-class CallingCardsBackgroundSerializer(serializers.ModelSerializer):
+class CallingCardsBackgroundSerializer(CustomValidateMixin, serializers.ModelSerializer):
     uploader = serializers.ReadOnlyField(source="uploader.username")
     modifiedBy = serializers.CharField(source="uploader.username", required=False)
 

yeastregulatorydb/regulatory_data/api/serializers/ChrMapSerializer.py

@@ -1,9 +1,10 @@
 from rest_framework import serializers
 
 from ...models.ChrMap import ChrMap
+from .mixins.CustomValidateMixin import CustomValidateMixin
 
 
-class ChrMapSerializer(serializers.ModelSerializer):
+class ChrMapSerializer(CustomValidateMixin, serializers.ModelSerializer):
     uploader = serializers.ReadOnlyField(source="uploader.username")
     modifiedBy = serializers.CharField(source="uploader.username", required=False)
 

yeastregulatorydb/regulatory_data/api/serializers/ExpressionManualQCSerializer.py

@@ -1,9 +1,10 @@
 from rest_framework import serializers
 
 from ...models.ExpressionManualQC import ExpressionManualQC
+from .mixins.CustomValidateMixin import CustomValidateMixin
 
 
-class ExpressionManualQCSerializer(serializers.ModelSerializer):
+class ExpressionManualQCSerializer(CustomValidateMixin, serializers.ModelSerializer):
     uploader = serializers.ReadOnlyField(source="uploader.username")
     modifiedBy = serializers.CharField(source="uploader.username", required=False)