all basic functionality has minimal testing and passing

cmatKhan · Dec 20, 2023 · aa6ee05 · aa6ee05
1 parent 07c4c47
commit aa6ee05
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Showing 38 changed files with 556 additions and 205 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -41,11 +41,11 @@ jobs:
       - name: Checkout Code Repository
         uses: actions/checkout@v4
 
-      run: |
-        ENCODED=$(echo "${{ secrets.ENVS_FILE }}")
-        echo "Encoded length: ${#ENCODED}"
-        echo "$ENCODED" | base64 -d > envs.tar.gz
-        tar -xzvf envs.tar.gz
+        run: |
+          ENCODED=$(echo "${{ secrets.ENVS_FILE }}")
+          echo "Encoded length: ${#ENCODED}"
+          echo "$ENCODED" | base64 -d > envs.tar.gz
+          tar -xzvf envs.tar.gz
 
       - name: Build the Stack
         run: docker compose -f local.yml build

diff --git a/config/api_router.py b/config/api_router.py
@@ -13,6 +13,7 @@
     GenomicFeatureViewSet,
     PromoterSetSigViewSet,
     PromoterSetViewSet,
+    RankResponseViewSet,
     RegulatorViewSet,
 )
 from yeastregulatorydb.users.api.views import UserViewSet
@@ -34,6 +35,7 @@
 router.register("genomicfeature", GenomicFeatureViewSet)
 router.register("promotersetsig", PromoterSetSigViewSet)
 router.register("promoterset", PromoterSetViewSet)
+router.register("rankresponse", RankResponseViewSet)
 router.register("regulator", RegulatorViewSet)
 
 

diff --git a/setup.cfg b/setup.cfg
@@ -4,7 +4,7 @@
 [flake8]
 max-line-length = 119
 exclude = .tox,.git,*/migrations/*,*/static/CACHE/*,docs,node_modules,venv,.venv
-extend-ignore = E203
+extend-ignore = E203,E731
 
 [pycodestyle]
 max-line-length = 119

diff --git a/yeastregulatorydb/conftest.py b/yeastregulatorydb/conftest.py
@@ -23,14 +23,14 @@
     BindingFactory,
     BindingManualQCFactory,
     CallingCardsBackgroundFactory,
-    ChrMapFactory,
     DataSourceFactory,
     ExpressionFactory,
     ExpressionManualQCFactory,
     FileFormatFactory,
     GenomicFeatureFactory,
     PromoterSetFactory,
     PromoterSetSigFactory,
+    RankResponseFactory,
     RegulatorFactory,
 )
 from yeastregulatorydb.users.models import User
@@ -156,8 +156,16 @@ def datasource(db) -> DataSource:
 def fileformat(db) -> QuerySet:
     # harb, hu both csvs
     format_dict = {
-        "array": ({"gene_id": "int", "effect": "float", "pval": "float"}, ",", "effect", "pval"),
-        "qbed": ({"chr": "str", "start": "int", "end": "int", "depth": "int", "strand": "str"}, "\t", "none", "none"),
+        "array": ({"gene_id": "int", "effect": "float", "pval": "float"}, ",", "effect", 0.0, "pval", 1.0, "none"),
+        "qbed": (
+            {"chr": "str", "start": "int", "end": "int", "depth": "int", "strand": "str"},
+            "\t",
+            "none",
+            0.0,
+            "none",
+            1.0,
+            "none",
+        ),
         "chipexo_allevents": (
             {
                 "chr": "str",
@@ -170,7 +178,10 @@ def fileformat(db) -> QuerySet:
             },
             ",",
             "YPD_log2Fold",
+            0.0,
             "YPD_log2P",
+            1.0,
+            "none",
         ),
         "chipexo_promoter_sig": (
             {
@@ -188,6 +199,7 @@ def fileformat(db) -> QuerySet:
             0.0,
             "min_pval",
             1.0,
+            "name",
         ),
         "cc_promoter_sig": (
             {
@@ -209,6 +221,7 @@ def fileformat(db) -> QuerySet:
             0.0,
             "poisson_pval",
             1.0,
+            "name",
         ),
         "kemmeren": (
             {"gene_id": "int", "M": "float", "Madj": "float", "A": "float", "pval": "float"},
@@ -217,6 +230,7 @@ def fileformat(db) -> QuerySet:
             0.0,
             "pval",
             1.0,
+            "gene_id",
         ),
         "mcisaac": (
             {
@@ -233,6 +247,7 @@ def fileformat(db) -> QuerySet:
             0.0,
             "none",
             1.0,
+            "gene_id",
         ),
         "bed6": (
             {"chr": "str", "start": "int", "end": "int", "name": "str", "score": "float", "strand": "str"},
@@ -241,27 +256,31 @@ def fileformat(db) -> QuerySet:
             0.0,
             "none",
             1.0,
+            "name",
         ),
-        "rank_response_summary": (
+        "rankresponse": (
             {
                 "feature": "str",
-                "expression_effect": "int",
-                "expression_pvalue": "int",
-                "binding_effect": "str",
-                "binding_pvalue": "str",
+                "expression_effect": "float",
+                "expression_pvalue": "float",
+                "expression_source": "str",
+                "binding_effect": "float",
+                "binding_pvalue": "float",
+                "binding_source": "str",
                 "responsive": "int",
-                "ran_bin": "float",
+                "rank_bin": "int",
                 "random": "float",
             },
             ",",
             "none",
             0.0,
             "none",
             1.0,
+            "feature",
         ),
     }
     for key, value in format_dict.items():
-        fields, separator, effect, effect_thres, pval, pval_thres = value
+        fields, separator, effect, effect_thres, pval, pval_thres, feature_identifier_col = value
         FileFormatFactory.create(
             fileformat=key,
             fields=fields,
@@ -270,6 +289,7 @@ def fileformat(db) -> QuerySet:
             default_effect_threshold=effect_thres,
             pval_col=pval,
             default_pvalue_threshold=pval_thres,
+            feature_identifier_col=feature_identifier_col,
         )
     return FileFormat.objects.all()
 
@@ -318,6 +338,7 @@ def harbison_datasource(db, fileformat: QuerySet) -> DataSource:
 def hu_datasource(db, fileformat: QuerySet) -> DataSource:
     array = fileformat.filter(fileformat="array").first()
     content = {
+        "id": 101,
         "name": "hu_reimann_tfko",
         "fileformat": array,
         "lab": "hu",
@@ -344,12 +365,14 @@ def kemmeren_datasource(db, fileformat: QuerySet) -> DataSource:
 def mcisaac_datasource(db, fileformat: QuerySet) -> DataSource:
     mcisaac = fileformat.filter(fileformat="mcisaac").first()
     content = {
+        "id": 102,
         "name": "mcisaac_oe",
         "fileformat": mcisaac,
         "lab": "mcisaac",
         "assay": "overexpression",
         "workflow": "none",
     }
+    return DataSourceFactory(**content)
 
 
 @pytest.fixture
@@ -384,3 +407,11 @@ def promotersetsig(db) -> PromoterSetSig:
 def regulator(db) -> Regulator:
     hap5_genomic_feature = GenomicFeatureFactory(locus_tag="YOR358W", symbol="HAP5")
     return RegulatorFactory(id=1, regulator=hap5_genomic_feature)
+
+
+@pytest.fixture
+def rankresponse(db, regulator: Regulator) -> QuerySet:
+    binding = BindingFactory(regulator=regulator)
+    expression = ExpressionFactory(regulator=regulator)
+    promotersetsig = PromoterSetSigFactory(binding=binding)
+    return RankResponseFactory(promotersetsig=promotersetsig, expression=expression)
diff --git a/yeastregulatorydb/regulatory_data/api/filters/RankResponseFilter.py b/yeastregulatorydb/regulatory_data/api/filters/RankResponseFilter.py
@@ -13,12 +13,15 @@ class RankResponseFilter(django_filters.FilterSet):
     expression_id = django_filters.NumberFilter(field_name="expression__id")
     expression_source = django_filters.CharFilter(field_name="expression__source__name", lookup_expr="iexact")
     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")
     expression_effect_threshold = django_filters.NumberFilter()
     expression_pvalue_threshold = django_filters.NumberFilter()
     normalized = django_filters.BooleanFilter()
+    significant_response = django_filters.BooleanFilter()
 
     class Meta:
         model = RankResponse
@@ -34,4 +37,5 @@ class Meta:
             "expression_effect_threshold",
             "expression_pvalue_threshold",
             "normalized",
+            "significant_response",
         ]
diff --git a/yeastregulatorydb/regulatory_data/api/filters/__init__.py b/yeastregulatorydb/regulatory_data/api/filters/__init__.py
@@ -8,4 +8,20 @@
 from .GenomicFeatureFilter import GenomicFeatureFilter
 from .PromoterSetFilter import PromoterSetFilter
 from .PromoterSetSigFilter import PromoterSetSigFilter
+from .RankResponseFilter import RankResponseFilter
 from .RegulatorFilter import RegulatorFilter
+
+__all__ = [
+    "BindingFilter",
+    "BindingManualQCFilter",
+    "CallingCardsBackgroundFilter",
+    "DataSourceFilter",
+    "ExpressionFilter",
+    "ExpressionManualQCFilter",
+    "FileFormatFilter",
+    "GenomicFeatureFilter",
+    "PromoterSetFilter",
+    "PromoterSetSigFilter",
+    "RankResponseFilter",
+    "RegulatorFilter",
+]
diff --git a/yeastregulatorydb/regulatory_data/api/serializers/PromoterSetSerializer.py b/yeastregulatorydb/regulatory_data/api/serializers/PromoterSetSerializer.py
@@ -1,5 +1,3 @@
-import pandas as pd
-from django.conf import settings
 from rest_framework import serializers
 
 from ...models.PromoterSet import PromoterSet

diff --git a/yeastregulatorydb/regulatory_data/api/serializers/__init__.py b/yeastregulatorydb/regulatory_data/api/serializers/__init__.py
@@ -24,5 +24,6 @@
     "GenomicFeatureSerializer",
     "PromoterSetSerializer",
     "PromoterSetSigSerializer",
-    "RankResponseSerializer" "RegulatorSerializer",
+    "RankResponseSerializer",
+    "RegulatorSerializer",
 ]
diff --git a/yeastregulatorydb/regulatory_data/api/views/BindingViewSet.py b/yeastregulatorydb/regulatory_data/api/views/BindingViewSet.py
@@ -34,9 +34,9 @@ def perform_create(self, serializer):
             task_type = "callingcards_promoter_sig"
 
         if task_type:
-            lock_id = f"add_data_lock"
-            acquire_lock = lambda: cache.add(lock_id, True, timeout=60 * 60)
-            release_lock = lambda: cache.delete(lock_id)
+            lock_id = "add_data_lock"
+            acquire_lock = lambda: cache.add(lock_id, True, timeout=60 * 60)  # flake8: noqa: E731
+            release_lock = lambda: cache.delete(lock_id)  # flake8: noqa: E731
 
             if acquire_lock():
                 try:

diff --git a/yeastregulatorydb/regulatory_data/api/views/ExpressionViewSet.py b/yeastregulatorydb/regulatory_data/api/views/ExpressionViewSet.py
@@ -1,4 +1,3 @@
-from celery import chain
 from django.core.cache import cache
 from django_filters.rest_framework import DjangoFilterBackend
 from rest_framework import viewsets
@@ -32,9 +31,9 @@ def perform_create(self, serializer):
         ).values_list("id", flat=True)
 
         # Create a chain of tasks for each promotersetsig_id
-        lock_id = f"add_data_lock"
-        acquire_lock = lambda: cache.add(lock_id, True, timeout=60 * 60)
-        release_lock = lambda: cache.delete(lock_id)
+        lock_id = "add_data_lock"
+        acquire_lock = lambda: cache.add(lock_id, True, timeout=60 * 60)  # flake8: noqa: E731
+        release_lock = lambda: cache.delete(lock_id)  # flake8: noqa: E731
 
         if acquire_lock():
             try:

diff --git a/yeastregulatorydb/regulatory_data/api/views/PromoterSetViewSet.py b/yeastregulatorydb/regulatory_data/api/views/PromoterSetViewSet.py
@@ -28,7 +28,7 @@ class PromoterSetViewSet(UpdateModifiedMixin, viewsets.ModelViewSet):
 def perform_create(self, serializer):
     instance = serializer.save()
 
-    lock_id = f"add_data_lock"
+    lock_id = "add_data_lock"
     acquire_lock = lambda: cache.add(lock_id, True, timeout=60 * 60)
     release_lock = lambda: cache.delete(lock_id)
 

diff --git a/yeastregulatorydb/regulatory_data/api/views/__init__.py b/yeastregulatorydb/regulatory_data/api/views/__init__.py
@@ -9,6 +9,7 @@
 from .GenomicFeatureViewSet import GenomicFeatureViewSet
 from .PromoterSetSigViewSet import PromoterSetSigViewSet
 from .PromoterSetViewSet import PromoterSetViewSet
+from .RankResponseViewSet import RankResponseViewSet
 from .RegulatorViewSet import RegulatorViewSet
 
 __all__ = [
@@ -23,5 +24,6 @@
     "GenomicFeatureViewSet",
     "PromoterSetSigViewSet",
     "PromoterSetViewSet",
+    "RankResponseViewSet",
     "RegulatorViewSet",
 ]
diff --git a/yeastregulatorydb/regulatory_data/api/views/mixins/BulkUploadMixin.py b/yeastregulatorydb/regulatory_data/api/views/mixins/BulkUploadMixin.py
@@ -17,7 +17,7 @@ def bulk_upload(self, request):
             file_mapping = {file.name: file for file in files}
 
             df = pd.read_csv(csv_file)
-            if not "file" in df.columns:
+            if "file" not in df.columns:
                 return Response("Column 'file' not found in CSV", status=status.HTTP_400_BAD_REQUEST)
 
             serializer_list = []

diff --git a/yeastregulatorydb/regulatory_data/forms/__init__.py b/yeastregulatorydb/regulatory_data/forms/__init__.py
@@ -1 +1,5 @@
 from .BulkUploadForm import BulkUploadForm
+
+__all__ = [
+    "BulkUploadForm",
+]