DB Files Support

alembic/env.py

@@ -8,9 +8,10 @@
 from core.config import get_settings
 
 # Import all models here so that they are registered with SQLModel metadata
-from api.samples.models import Sample, SampleAttribute
+from api.files.models import File
 from api.project.models import Project
 from api.runs.models import SequencingRun
+from api.samples.models import Sample, SampleAttribute
 from api.vendors.models import Vendor
 from api.workflow.models import Workflow, WorkflowAttribute
 
@@ -33,6 +34,7 @@
 # target_metadata = None
 target_metadata = SQLModel.metadata
 
+
 # other values from the config, defined by the needs of env.py,
 # can be acquired:
 # my_important_option = config.get_main_option("my_important_option")

alembic/versions/95817dee746c_add_files_table.py

@@ -0,0 +1,53 @@
+"""add_files_table
+
+Revision ID: 95817dee746c
+Revises: c955364e5391
+Create Date: 2025-09-20 14:28:45.987919
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+import sqlmodel
+
+
+# revision identifiers, used by Alembic.
+revision: str = '95817dee746c'
+down_revision: Union[str, Sequence[str], None] = '43c1f122cf7f'
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    """Upgrade schema."""
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table('file',
+    sa.Column('id', sa.Uuid(), nullable=False),
+    sa.Column('file_id', sqlmodel.sql.sqltypes.AutoString(length=100), nullable=False),
+    sa.Column('filename', sqlmodel.sql.sqltypes.AutoString(length=255), nullable=False),
+    sa.Column('original_filename', sqlmodel.sql.sqltypes.AutoString(length=255), nullable=False),
+    sa.Column('file_path', sqlmodel.sql.sqltypes.AutoString(length=1024), nullable=False),
+    sa.Column('file_size', sa.Integer(), nullable=True),
+    sa.Column('mime_type', sqlmodel.sql.sqltypes.AutoString(length=100), nullable=True),
+    sa.Column('checksum', sqlmodel.sql.sqltypes.AutoString(length=64), nullable=True),
+    sa.Column('description', sqlmodel.sql.sqltypes.AutoString(length=1024), nullable=True),
+    sa.Column('file_type', sa.Enum('FASTQ', 'BAM', 'VCF', 'SAMPLESHEET', 'METRICS', 'REPORT', 'LOG', 'IMAGE', 'DOCUMENT', 'OTHER', name='filetype'), nullable=False),
+    sa.Column('upload_date', sa.DateTime(), nullable=False),
+    sa.Column('created_by', sqlmodel.sql.sqltypes.AutoString(length=100), nullable=True),
+    sa.Column('entity_type', sa.Enum('PROJECT', 'RUN', name='entitytype'), nullable=False),
+    sa.Column('entity_id', sqlmodel.sql.sqltypes.AutoString(length=100), nullable=False),
+    sa.Column('storage_backend', sa.Enum('LOCAL', 'S3', 'AZURE', 'GCS', name='storagebackend'), nullable=False),
+    sa.Column('is_public', sa.Boolean(), nullable=False),
+    sa.Column('is_archived', sa.Boolean(), nullable=False),
+    sa.PrimaryKeyConstraint('id'),
+    sa.UniqueConstraint('file_id')
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    """Downgrade schema."""
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_table('file')
+    # ### end Alembic commands ###

api/files/models.py

@@ -1,7 +1,195 @@
 """
 Models for the Files API
 """
-from sqlmodel import SQLModel
+
+from typing import List
+import uuid
+from datetime import datetime
+from enum import Enum
+
+from sqlmodel import SQLModel, Field
+from pydantic import ConfigDict
+
+
+class FileType(str, Enum):
+    """File type categories"""
+
+    FASTQ = "fastq"
+    BAM = "bam"
+    VCF = "vcf"
+    SAMPLESHEET = "samplesheet"
+    METRICS = "metrics"
+    REPORT = "report"
+    LOG = "log"
+    IMAGE = "image"
+    DOCUMENT = "document"
+    OTHER = "other"
+
+
+class EntityType(str, Enum):
+    """Entity types that can have files"""
+
+    PROJECT = "project"
+    RUN = "run"
+
+
+class StorageBackend(str, Enum):
+    """Storage backend types"""
+
+    LOCAL = "local"
+    S3 = "s3"
+    AZURE = "azure"
+    GCS = "gcs"
+
+
+class File(SQLModel, table=True):
+    """Core file entity that can be associated with runs or projects"""
+
+    __searchable__ = ["filename", "description", "file_id"]
+
+    id: uuid.UUID | None = Field(default_factory=uuid.uuid4, primary_key=True)
+    file_id: str = Field(unique=True, max_length=100)  # Human-readable identifier
+    filename: str = Field(max_length=255)
+    original_filename: str = Field(max_length=255)
+    file_path: str = Field(max_length=1024)  # Storage path/URI
+    file_size: int | None = None  # Size in bytes
+    mime_type: str | None = Field(default=None, max_length=100)
+    checksum: str | None = Field(default=None, max_length=64)  # SHA-256 hash
+
+    # Metadata
+    description: str | None = Field(default=None, max_length=1024)
+    file_type: FileType = Field(default=FileType.OTHER)
+    upload_date: datetime = Field(default_factory=datetime.utcnow)
+    created_by: str | None = Field(default=None, max_length=100)  # User identifier
+
+    # Polymorphic associations
+    entity_type: EntityType  # "project" or "run"
+    entity_id: str = Field(max_length=100)  # project_id or run barcode
+
+    # Storage metadata
+    storage_backend: StorageBackend = Field(default=StorageBackend.LOCAL)
+    is_public: bool = Field(default=False)
+    is_archived: bool = Field(default=False)
+
+    model_config = ConfigDict(from_attributes=True)
+
+    def generate_file_id(self) -> str:
+        """Generate a unique file ID"""
+        import secrets
+        import string
+
+        alphabet = string.ascii_letters + string.digits
+        return "".join(secrets.choice(alphabet) for _ in range(12))
+
+
+class FileCreate(SQLModel):
+    """Request model for creating a file"""
+
+    filename: str
+    original_filename: str | None = None
+    description: str | None = None
+    file_type: FileType = FileType.OTHER
+    entity_type: EntityType
+    entity_id: str
+    is_public: bool = False
+    created_by: str | None = None
+
+    model_config = ConfigDict(extra="forbid")
+
+
+class FileUpdate(SQLModel):
+    """Request model for updating file metadata"""
+
+    filename: str | None = None
+    description: str | None = None
+    file_type: FileType | None = None
+    is_public: bool | None = None
+    is_archived: bool | None = None
+
+    model_config = ConfigDict(extra="forbid")
+
+
+class FilePublic(SQLModel):
+    """Public file representation"""
+
+    file_id: str
+    filename: str
+    original_filename: str
+    file_size: int | None
+    mime_type: str | None
+    description: str | None
+    file_type: FileType
+    upload_date: datetime
+    created_by: str | None
+    entity_type: EntityType
+    entity_id: str
+    is_public: bool
+    is_archived: bool
+    storage_backend: StorageBackend
+    checksum: str | None = None
+
+
+class FilesPublic(SQLModel):
+    """Paginated file listing"""
+
+    data: List[FilePublic]
+    total_items: int
+    total_pages: int
+    current_page: int
+    per_page: int
+    has_next: bool
+    has_prev: bool
+
+
+class FileUploadRequest(SQLModel):
+    """Request model for file upload"""
+
+    filename: str
+    description: str | None = None
+    file_type: FileType = FileType.OTHER
+    is_public: bool = False
+
+    model_config = ConfigDict(extra="forbid")
+
+
+class FileUploadResponse(SQLModel):
+    """Response model for file upload"""
+
+    file_id: str
+    filename: str
+    file_size: int | None = None
+    checksum: str | None = None
+    upload_date: datetime
+    message: str = "File uploaded successfully"
+
+
+class FileFilters(SQLModel):
+    """File filtering options"""
+
+    entity_type: EntityType | None = None
+    entity_id: str | None = None
+    file_type: FileType | None = None
+    mime_type: str | None = None
+    created_by: str | None = None
+    is_public: bool | None = None
+    is_archived: bool | None = None
+    search_query: str | None = None  # Search in filename/description
+
+    model_config = ConfigDict(extra="forbid")
+
+
+class PaginatedFileResponse(SQLModel):
+    """Paginated response for file listings"""
+
+    data: list[FilePublic]
+    total_items: int
+    total_pages: int
+    current_page: int
+    per_page: int
+    has_next: bool
+    has_prev: bool
+
+    model_config = ConfigDict(from_attributes=True)
 
 
 class FileBrowserFolder(SQLModel):