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Make ended_at_time nullable
This is needed to support data from the JAWS rollout.
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-2
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3 files changed

+126
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‎nmdc_server/migrations/versions/9e6c9a57b893_make_ended_at_time_nullable.py

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"""Make ended_at_time nullable
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Revision ID: 9e6c9a57b893
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Revises: 8993ccbbb9e4
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Create Date: 2025-04-30 18:16:12.463808
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"""
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from typing import Optional
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from alembic import op
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from sqlalchemy.dialects import postgresql
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# revision identifiers, used by Alembic.
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revision: str = "9e6c9a57b893"
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down_revision: Optional[str] = "8993ccbbb9e4"
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branch_labels: Optional[str] = None
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depends_on: Optional[str] = None
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def upgrade():
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# ### commands auto generated by Alembic - please adjust! ###
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op.alter_column(
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"mags_analysis", "ended_at_time", existing_type=postgresql.TIMESTAMP(), nullable=True
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)
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op.alter_column(
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"metabolomics_analysis",
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"ended_at_time",
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existing_type=postgresql.TIMESTAMP(),
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nullable=True,
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)
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op.alter_column(
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"metagenome_annotation",
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"ended_at_time",
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existing_type=postgresql.TIMESTAMP(),
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nullable=True,
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)
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op.alter_column(
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"metagenome_assembly", "ended_at_time", existing_type=postgresql.TIMESTAMP(), nullable=True
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)
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op.alter_column(
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"metaproteomic_analysis",
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"ended_at_time",
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existing_type=postgresql.TIMESTAMP(),
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nullable=True,
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)
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op.alter_column(
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"metatranscriptome", "ended_at_time", existing_type=postgresql.TIMESTAMP(), nullable=True
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)
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op.alter_column(
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"metatranscriptome_annotation",
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"ended_at_time",
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existing_type=postgresql.TIMESTAMP(),
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nullable=True,
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)
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op.alter_column(
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"metatranscriptome_assembly",
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"ended_at_time",
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existing_type=postgresql.TIMESTAMP(),
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nullable=True,
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)
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op.alter_column(
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"nom_analysis", "ended_at_time", existing_type=postgresql.TIMESTAMP(), nullable=True
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)
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op.alter_column(
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"read_based_analysis", "ended_at_time", existing_type=postgresql.TIMESTAMP(), nullable=True
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)
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op.alter_column(
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"reads_qc", "ended_at_time", existing_type=postgresql.TIMESTAMP(), nullable=True
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)
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# ### end Alembic commands ###
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def downgrade():
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# ### commands auto generated by Alembic - please adjust! ###
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op.alter_column(
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"reads_qc", "ended_at_time", existing_type=postgresql.TIMESTAMP(), nullable=False
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)
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op.alter_column(
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"read_based_analysis", "ended_at_time", existing_type=postgresql.TIMESTAMP(), nullable=False
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)
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op.alter_column(
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"nom_analysis", "ended_at_time", existing_type=postgresql.TIMESTAMP(), nullable=False
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)
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op.alter_column(
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"metatranscriptome_assembly",
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"ended_at_time",
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existing_type=postgresql.TIMESTAMP(),
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nullable=False,
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)
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op.alter_column(
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"metatranscriptome_annotation",
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"ended_at_time",
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existing_type=postgresql.TIMESTAMP(),
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nullable=False,
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)
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op.alter_column(
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"metatranscriptome", "ended_at_time", existing_type=postgresql.TIMESTAMP(), nullable=False
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)
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op.alter_column(
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"metaproteomic_analysis",
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"ended_at_time",
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existing_type=postgresql.TIMESTAMP(),
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nullable=False,
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)
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op.alter_column(
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"metagenome_assembly", "ended_at_time", existing_type=postgresql.TIMESTAMP(), nullable=False
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)
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op.alter_column(
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"metagenome_annotation",
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"ended_at_time",
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existing_type=postgresql.TIMESTAMP(),
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nullable=False,
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)
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op.alter_column(
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"metabolomics_analysis",
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"ended_at_time",
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existing_type=postgresql.TIMESTAMP(),
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nullable=False,
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)
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op.alter_column(
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"mags_analysis", "ended_at_time", existing_type=postgresql.TIMESTAMP(), nullable=False
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)
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# ### end Alembic commands ###

‎nmdc_server/models.py

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@@ -496,7 +496,7 @@ class PipelineStep:
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type = Column(String, nullable=False)
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git_url = Column(String, nullable=False)
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started_at_time = Column(DateTime, nullable=False)
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ended_at_time = Column(DateTime, nullable=False)
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ended_at_time = Column(DateTime)
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execution_resource = Column(String, nullable=False)
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@declared_attr

‎nmdc_server/schemas.py

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@@ -417,7 +417,7 @@ class PipelineStepBase(BaseModel):
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type: str
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git_url: str
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started_at_time: DateType
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ended_at_time: DateType
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ended_at_time: Optional[DateType] = None
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execution_resource: str
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omics_processing_id: str
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