Merge pull request #1733 from microbiomedata/issue-1731-executn-resource-nullable

Make `execution_resource` nullable

Author: naglepuff

nmdc_server/migrations/versions/43fc92514a16_nullable_execution_resource.py

@@ -0,0 +1,100 @@
+"""Make execution_resource nullable.
+
+Revision ID: 43fc92514a16
+Revises: 09a705b0bc00
+Create Date: 2025-08-12 18:10:18.144086
+
+"""
+
+from typing import Optional
+
+import sqlalchemy as sa
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision: str = "43fc92514a16"
+down_revision: Optional[str] = "09a705b0bc00"
+branch_labels: Optional[str] = None
+depends_on: Optional[str] = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.alter_column(
+        "mags_analysis", "execution_resource", existing_type=sa.VARCHAR(), nullable=True
+    )
+    op.alter_column(
+        "metabolomics_analysis", "execution_resource", existing_type=sa.VARCHAR(), nullable=True
+    )
+    op.alter_column(
+        "metagenome_annotation", "execution_resource", existing_type=sa.VARCHAR(), nullable=True
+    )
+    op.alter_column(
+        "metagenome_assembly", "execution_resource", existing_type=sa.VARCHAR(), nullable=True
+    )
+    op.alter_column(
+        "metaproteomic_analysis", "execution_resource", existing_type=sa.VARCHAR(), nullable=True
+    )
+    op.alter_column(
+        "metatranscriptome", "execution_resource", existing_type=sa.VARCHAR(), nullable=True
+    )
+    op.alter_column(
+        "metatranscriptome_annotation",
+        "execution_resource",
+        existing_type=sa.VARCHAR(),
+        nullable=True,
+    )
+    op.alter_column(
+        "metatranscriptome_assembly",
+        "execution_resource",
+        existing_type=sa.VARCHAR(),
+        nullable=True,
+    )
+    op.alter_column("nom_analysis", "execution_resource", existing_type=sa.VARCHAR(), nullable=True)
+    op.alter_column(
+        "read_based_analysis", "execution_resource", existing_type=sa.VARCHAR(), nullable=True
+    )
+    op.alter_column("reads_qc", "execution_resource", existing_type=sa.VARCHAR(), nullable=True)
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.alter_column("reads_qc", "execution_resource", existing_type=sa.VARCHAR(), nullable=False)
+    op.alter_column(
+        "read_based_analysis", "execution_resource", existing_type=sa.VARCHAR(), nullable=False
+    )
+    op.alter_column(
+        "nom_analysis", "execution_resource", existing_type=sa.VARCHAR(), nullable=False
+    )
+    op.alter_column(
+        "metatranscriptome_assembly",
+        "execution_resource",
+        existing_type=sa.VARCHAR(),
+        nullable=False,
+    )
+    op.alter_column(
+        "metatranscriptome_annotation",
+        "execution_resource",
+        existing_type=sa.VARCHAR(),
+        nullable=False,
+    )
+    op.alter_column(
+        "metatranscriptome", "execution_resource", existing_type=sa.VARCHAR(), nullable=False
+    )
+    op.alter_column(
+        "metaproteomic_analysis", "execution_resource", existing_type=sa.VARCHAR(), nullable=False
+    )
+    op.alter_column(
+        "metagenome_assembly", "execution_resource", existing_type=sa.VARCHAR(), nullable=False
+    )
+    op.alter_column(
+        "metagenome_annotation", "execution_resource", existing_type=sa.VARCHAR(), nullable=False
+    )
+    op.alter_column(
+        "metabolomics_analysis", "execution_resource", existing_type=sa.VARCHAR(), nullable=False
+    )
+    op.alter_column(
+        "mags_analysis", "execution_resource", existing_type=sa.VARCHAR(), nullable=False
+    )
+    # ### end Alembic commands ###

nmdc_server/models.py

@@ -448,7 +448,7 @@ class PipelineStep:
     git_url = Column(String, nullable=False)
     started_at_time = Column(DateTime, nullable=False)
     ended_at_time = Column(DateTime)
-    execution_resource = Column(String, nullable=False)
+    execution_resource = Column(String, nullable=True)
 
     has_inputs = association_proxy("inputs", "id")
     has_outputs = association_proxy("outputs", "id")

nmdc_server/schemas.py

@@ -428,7 +428,7 @@ class PipelineStepBase(BaseModel):
     git_url: str
     started_at_time: DateType
     ended_at_time: Optional[DateType] = None
-    execution_resource: str
+    execution_resource: Optional[str] = None
 
 
 class PipelineStep(PipelineStepBase):

web/src/data/api.ts

@@ -101,7 +101,7 @@ export interface DerivedDataResult extends BaseSearchResult {
   git_url: string;
   started_at_time: string;
   ended_at_time: string;
-  execution_resource: string;
+  execution_resource: string | null;
   was_informed_by: OmicsProcessingBaseResult[];
   outputs: DataObjectSearchResult[];
 }