feat: update results reporting and assembly manifest generation

alembic/versions/0010_add_taxonomy_info.py

@@ -6,6 +6,7 @@
 """
 
 import sqlalchemy as sa
+
 from alembic import op
 
 revision = "0010_add_taxonomy_info"
@@ -30,9 +31,7 @@ def upgrade() -> None:
         sa.Column("augustus_dataset_name", sa.Text(), nullable=True),
         sa.Column("genetic_code_id", sa.Integer(), nullable=True),
         sa.PrimaryKeyConstraint("taxon_id"),
-        sa.ForeignKeyConstraint(
-            ["taxon_id"], ["organism.taxon_id"], ondelete="CASCADE"
-        ),
+        sa.ForeignKeyConstraint(["taxon_id"], ["organism.taxon_id"], ondelete="CASCADE"),
     )
 
     # 2. Migrate existing augustus_dataset_name values from organism into taxonomy_info

alembic/versions/0011_assembly_first_and_stages.py

@@ -0,0 +1,153 @@
+"""Assembly-first manifest flow: nullable fields, status, and stage reporting tables.
+
+Revision ID: 0011_assembly_first_and_stages
+Revises: 0010_add_taxonomy_info
+Create Date: 2026-05-05
+"""
+
+import sqlalchemy as sa
+from sqlalchemy.dialects.postgresql import JSONB, UUID
+
+from alembic import op
+
+revision = "0011_assembly_first_and_stages"
+down_revision = "0010_add_taxonomy_info"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ── 1. Make late-known assembly fields nullable ──────────────────────────
+    op.alter_column("assembly", "assembly_name", existing_type=sa.Text(), nullable=True)
+    op.alter_column("assembly", "coverage", existing_type=sa.Float(), nullable=True)
+    op.alter_column("assembly", "program", existing_type=sa.Text(), nullable=True)
+
+    # ── 2. Add lifecycle status to assembly ───────────────────────────────────
+    op.add_column(
+        "assembly",
+        sa.Column(
+            "status",
+            sa.Text(),
+            nullable=False,
+            server_default="requested",
+        ),
+    )
+    op.create_check_constraint(
+        "ck_assembly_status",
+        "assembly",
+        "status IN ('requested', 'running', 'curating', 'completed', 'failed', 'cancelled')",
+    )
+
+    # ── 3. assembly_stage catalog ─────────────────────────────────────────────
+    op.create_table(
+        "assembly_stage",
+        sa.Column("name", sa.Text(), primary_key=True),
+        sa.Column("category", sa.Text(), nullable=False),
+        sa.Column("is_active", sa.Boolean(), nullable=False, server_default=sa.true()),
+        sa.CheckConstraint("category IN ('pipeline', 'manual')", name="ck_assembly_stage_category"),
+    )
+
+    op.execute(
+        """
+        INSERT INTO assembly_stage (name, category) VALUES
+            ('genomeassembly', 'pipeline'),
+            ('ascc', 'pipeline'),
+            ('treeval', 'pipeline'),
+            ('curation-pretext', 'pipeline'),
+            ('manual-curation', 'manual')
+        """
+    )
+
+    # ── 4. assembly_stage_run ─────────────────────────────────────────────────
+    op.create_table(
+        "assembly_stage_run",
+        sa.Column(
+            "id",
+            UUID(as_uuid=True),
+            primary_key=True,
+            server_default=sa.text("uuid_generate_v4()"),
+        ),
+        sa.Column(
+            "assembly_id",
+            UUID(as_uuid=True),
+            sa.ForeignKey("assembly.id", ondelete="CASCADE"),
+            nullable=False,
+        ),
+        sa.Column(
+            "stage_name",
+            sa.Text(),
+            sa.ForeignKey("assembly_stage.name"),
+            nullable=False,
+        ),
+        sa.Column("status", sa.Text(), nullable=False),
+        sa.Column("external_run_id", sa.Text(), nullable=True),
+        sa.Column("attempt", sa.Integer(), nullable=False, server_default="1"),
+        sa.Column("stats", JSONB(), nullable=False, server_default="{}"),
+        sa.Column("started_at", sa.DateTime(timezone=True), nullable=True),
+        sa.Column("completed_at", sa.DateTime(timezone=True), nullable=True),
+        sa.Column(
+            "created_at",
+            sa.DateTime(timezone=True),
+            nullable=False,
+            server_default=sa.func.now(),
+        ),
+        sa.Column(
+            "updated_at",
+            sa.DateTime(timezone=True),
+            nullable=False,
+            server_default=sa.func.now(),
+        ),
+        sa.CheckConstraint(
+            "status IN ('running', 'succeeded', 'failed', 'cancelled')",
+            name="ck_assembly_stage_run_status",
+        ),
+        sa.UniqueConstraint(
+            "assembly_id", "stage_name", "attempt", name="uq_stage_run_assembly_stage_attempt"
+        ),
+    )
+    op.create_index("ix_assembly_stage_run_assembly_id", "assembly_stage_run", ["assembly_id"])
+
+    # ── 5. assembly_stage_run_file ────────────────────────────────────────────
+    op.create_table(
+        "assembly_stage_run_file",
+        sa.Column(
+            "id",
+            UUID(as_uuid=True),
+            primary_key=True,
+            server_default=sa.text("uuid_generate_v4()"),
+        ),
+        sa.Column(
+            "assembly_stage_run_id",
+            UUID(as_uuid=True),
+            sa.ForeignKey("assembly_stage_run.id", ondelete="CASCADE"),
+            nullable=False,
+        ),
+        sa.Column("storage_type", sa.Text(), nullable=False),
+        sa.Column("storage_uri", sa.Text(), nullable=False),
+        sa.Column("storage_details", JSONB(), nullable=False, server_default="{}"),
+        sa.Column("sha256sum", sa.Text(), nullable=False),
+        sa.Column(
+            "created_at",
+            sa.DateTime(timezone=True),
+            nullable=False,
+            server_default=sa.func.now(),
+        ),
+    )
+    op.create_index(
+        "ix_assembly_stage_run_file_run_id",
+        "assembly_stage_run_file",
+        ["assembly_stage_run_id"],
+    )
+
+
+def downgrade() -> None:
+    op.drop_table("assembly_stage_run_file")
+    op.drop_table("assembly_stage_run")
+    op.drop_table("assembly_stage")
+
+    op.drop_constraint("ck_assembly_status", "assembly", type_="check")
+    op.drop_column("assembly", "status")
+
+    op.alter_column("assembly", "program", existing_type=sa.Text(), nullable=False)
+    op.alter_column("assembly", "coverage", existing_type=sa.Float(), nullable=False)
+    op.alter_column("assembly", "assembly_name", existing_type=sa.Text(), nullable=False)

alembic/versions/0012_assembly_manifest_columns.py

@@ -0,0 +1,60 @@
+"""Add specimen sample IDs and manifest JSON to assembly.
+
+Revision ID: 0012_assembly_manifest_columns
+Revises: 0011_assembly_first_and_stages
+Create Date: 2026-05-08
+
+Adds three nullable columns to the assembly table:
+- long_read_specimen_sample_id: the specimen sample used for long reads (PacBio / ONT)
+- hic_specimen_sample_id: the specimen sample used for Hi-C reads (optional)
+- manifest_json: persisted JSON manifest generated at intent time
+
+All columns are nullable so existing rows are unaffected.
+"""
+
+import sqlalchemy as sa
+from sqlalchemy.dialects.postgresql import JSONB, UUID
+
+from alembic import op
+
+revision = "0012_assembly_manifest_columns"
+down_revision = "0011_assembly_first_and_stages"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    op.add_column(
+        "assembly",
+        sa.Column(
+            "long_read_specimen_sample_id",
+            UUID(as_uuid=True),
+            sa.ForeignKey("sample.id"),
+            nullable=True,
+        ),
+    )
+    op.add_column(
+        "assembly",
+        sa.Column(
+            "hic_specimen_sample_id",
+            UUID(as_uuid=True),
+            sa.ForeignKey("sample.id"),
+            nullable=True,
+        ),
+    )
+    op.add_column(
+        "assembly",
+        sa.Column("manifest_json", JSONB(), nullable=True),
+    )
+    op.create_index(
+        "idx_assembly_intent_version_key",
+        "assembly",
+        ["taxon_id", "long_read_specimen_sample_id"],
+    )
+
+
+def downgrade() -> None:
+    op.drop_index("idx_assembly_intent_version_key", table_name="assembly")
+    op.drop_column("assembly", "manifest_json")
+    op.drop_column("assembly", "hic_specimen_sample_id")
+    op.drop_column("assembly", "long_read_specimen_sample_id")

app/api/v1/api.py

@@ -47,9 +47,7 @@
 api_router.include_router(reads.router, prefix="/reads", tags=["reads"])
 api_router.include_router(qc_reads.router, prefix="/qc-reads", tags=["qc-reads"])
 api_router.include_router(genome_notes.router, prefix="/genome-notes", tags=["genome-notes"])
-api_router.include_router(
-    taxonomy_info.router, prefix="/taxonomy-info", tags=["taxonomy-info"]
-)
+api_router.include_router(taxonomy_info.router, prefix="/taxonomy-info", tags=["taxonomy-info"])
 
 # XML export endpoints
 api_router.include_router(xml_export.router, prefix="/xml-export", tags=["xml-export"])