added Analysis files functionality

bbconf/alembic/versions/c7f3a9e1b204_added_analysis_files_table.py

@@ -0,0 +1,99 @@
+"""Added analysis_files table
+
+Revision ID: c7f3a9e1b204
+Revises: 845d978eac7d
+Create Date: 2026-08-17 21:00:00.000000
+
+"""
+
+from typing import Sequence, Union
+
+import sqlalchemy as sa
+from alembic import op
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision: str = "c7f3a9e1b204"
+down_revision: Union[str, None] = "845d978eac7d"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    """Upgrade schema."""
+    op.create_table(
+        "analysis_files",
+        sa.Column("id", sa.Integer(), autoincrement=True, nullable=False),
+        sa.Column(
+            "name",
+            sa.String(),
+            nullable=False,
+            comment="Logical name/key, e.g. openSignalMatrix",
+        ),
+        sa.Column(
+            "file_path",
+            sa.String(),
+            nullable=False,
+            comment="S3 object key, relative to the bucket root",
+        ),
+        sa.Column(
+            "file_type",
+            sa.String(),
+            nullable=True,
+            comment="Category, e.g. openSignalMatrix | reference | model",
+        ),
+        sa.Column(
+            "genome",
+            sa.String(),
+            nullable=True,
+            comment="Genome/assembly, e.g. hg38 (optional)",
+        ),
+        sa.Column("description", sa.String(), nullable=True),
+        sa.Column(
+            "tags",
+            postgresql.ARRAY(sa.String()),
+            nullable=True,
+            comment="Free-form tags",
+        ),
+        sa.Column(
+            "file_size",
+            sa.Integer(),
+            nullable=True,
+            comment="Size of the file in bytes",
+        ),
+        sa.Column("checksum", sa.String(), nullable=True, comment="SHA256 of the file"),
+        sa.Column(
+            "creation_date",
+            sa.TIMESTAMP(timezone=True),
+            nullable=False,
+            comment="Upload date",
+        ),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_index(
+        op.f("ix_analysis_files_id"), "analysis_files", ["id"], unique=False
+    )
+    op.create_index(
+        op.f("ix_analysis_files_name"), "analysis_files", ["name"], unique=False
+    )
+    op.create_index(
+        op.f("ix_analysis_files_file_type"),
+        "analysis_files",
+        ["file_type"],
+        unique=False,
+    )
+    op.create_index(
+        op.f("ix_analysis_files_genome"),
+        "analysis_files",
+        ["genome"],
+        unique=False,
+    )
+
+
+def downgrade() -> None:
+    """Downgrade schema."""
+    op.drop_index(op.f("ix_analysis_files_genome"), table_name="analysis_files")
+    op.drop_index(op.f("ix_analysis_files_file_type"), table_name="analysis_files")
+    op.drop_index(op.f("ix_analysis_files_name"), table_name="analysis_files")
+    op.drop_index(op.f("ix_analysis_files_id"), table_name="analysis_files")
+    op.drop_table("analysis_files")

bbconf/bbagent.py

@@ -35,6 +35,7 @@
     UsageModel,
     UsageStats,
 )
+from bbconf.modules.analysis_files import BedAgentAnalysisFile
 from bbconf.modules.bedfiles import BedAgentBedFile
 from bbconf.modules.bedsets import BedAgentBedSet
 from bbconf.modules.objects import BBObjects
@@ -66,6 +67,7 @@ def __init__(
         self._bedset = BedAgentBedSet(self.config)
         self._objects = BBObjects(self.config)
         self._snapshot = BedAgentSnapshot(self.config)
+        self._analysis_files = BedAgentAnalysisFile(self.config)
 
         # get_stats() runs three uncached COUNT queries on the multi-hundred-
         # thousand-row bed table and is called on hot paths (the stats endpoint
@@ -91,6 +93,10 @@ def objects(self) -> BBObjects:
     def snapshot(self) -> BedAgentSnapshot:
         return self._snapshot
 
+    @property
+    def analysis_files(self) -> BedAgentAnalysisFile:
+        return self._analysis_files
+
     def __repr__(self) -> str:
         repr = f"BedBaseAgent(config={self.config})"
         repr += f"\n{self.bed}"

bbconf/db_utils.py

@@ -718,6 +718,48 @@ class BedSnapshot(Base):
     )
 
 
+class AnalysisFile(Base):
+    """
+    Registry of standalone analysis files (openSignalMatrix, models, other
+    analysis inputs) stored in S3. Not tied to any bed file or bedset.
+
+    Append-only: one row per uploaded file, so name-based lookups resolve the
+    newest matching row (same model as ``bed_snapshots``). This is a new table,
+    so ``Base.metadata.create_all()`` creates it on the next connection.
+    """
+
+    __tablename__ = "analysis_files"
+
+    id: Mapped[int] = mapped_column(primary_key=True, index=True, autoincrement=True)
+    name: Mapped[str] = mapped_column(
+        nullable=False, index=True, comment="Logical name/key, e.g. openSignalMatrix"
+    )
+    file_path: Mapped[str] = mapped_column(
+        nullable=False, comment="S3 object key, relative to the bucket root"
+    )
+    file_type: Mapped[Optional[str]] = mapped_column(
+        nullable=True,
+        index=True,
+        comment="Category, e.g. openSignalMatrix | reference | model",
+    )
+    genome: Mapped[Optional[str]] = mapped_column(
+        nullable=True, index=True, comment="Genome/assembly, e.g. hg38 (optional)"
+    )
+    description: Mapped[Optional[str]] = mapped_column(nullable=True)
+    tags: Mapped[Optional[list]] = mapped_column(
+        ARRAY(String), nullable=True, comment="Free-form tags"
+    )
+    file_size: Mapped[Optional[int]] = mapped_column(
+        nullable=True, comment="Size of the file in bytes"
+    )
+    checksum: Mapped[Optional[str]] = mapped_column(
+        nullable=True, comment="SHA256 of the file"
+    )
+    creation_date: Mapped[datetime.datetime] = mapped_column(
+        default=deliver_update_date, comment="Upload date"
+    )
+
+
 class BaseEngine:
     """
     A class with base methods, that are used in several classes.

bbconf/exceptions.py

@@ -77,6 +77,13 @@ class SnapshotNotFoundError(BedBaseConfError):
     pass
 
 
+class AnalysisFileNotFoundError(BedBaseConfError):
+    """
+    Error type for missing analysis file"""
+
+    pass
+
+
 class UniverseNotFoundError(BedBaseConfError):
     """
     Error type for missing universe"""

bbconf/models/base_models.py

@@ -131,3 +131,36 @@ class BedSnapshotResult(BaseModel):
 class BedSnapshotListResult(BaseModel):
     count: int
     results: list[BedSnapshotResult]
+
+
+class AnalysisFileArtifact(BaseModel):
+    """A standalone analysis file to publish (upload to S3 + record in the database)."""
+
+    path: str  # local file path to upload
+    name: str
+    file_type: str | None = None
+    genome: str | None = None
+    description: str | None = None
+    tags: list[str] | None = None
+    file_size: int | None = None
+    checksum: str | None = None
+
+
+class AnalysisFileResult(BaseModel):
+    """One registered standalone analysis file."""
+
+    id: int | None = None
+    name: str
+    file_path: str
+    file_type: str | None = None
+    genome: str | None = None
+    description: str | None = None
+    tags: list[str] | None = None
+    file_size: int | None = None
+    checksum: str | None = None
+    creation_date: datetime.datetime
+
+
+class AnalysisFileListResult(BaseModel):
+    count: int
+    results: list[AnalysisFileResult]