osa-py 0.8.0

OSA Python SDK — validators and transforms for the Open Scientific Archive

OSA Python SDK

The developer toolkit for the Open Science Archive — define metadata schemas, write validation hooks, build ingesters, and deploy conventions.

Pre-release — APIs will change without notice.

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Install

pip install osa-py

Quickstart

A convention defines what data your archive accepts. Here's an example that archives protein structures and runs analysis on the deposited files:

from datetime import date
import httpx
from pydantic import BaseModel
from osa import (
    Schema, Field, Record, Reject, hook, convention,
    IngesterContext, IngesterRecord,
)

# 1. Define the metadata schema
class PDBStructure(Schema):
    __schema_id__ = "pdb-structure"

    pdb_id: str
    title: str
    method: str
    resolution: float | None = Field(default=None, unit="Å")
    deposition_date: date
    molecular_weight: float = Field(unit="kDa")
    chain_count: int

# 2. Validate incoming records
@hook
def validate_structure(record: Record[PDBStructure]) -> None:
    if record.metadata.resolution and record.metadata.resolution > 4.0:
        raise Reject("Resolution too low for reliable analysis")
    if not record.files.glob("*.cif"):
        raise Reject("At least one CIF file is required")

# 3. Extract features from the data
class Pocket(BaseModel):
    pocket_id: int
    score: float
    volume: float

@hook
def find_pockets(record: Record[PDBStructure]) -> list[Pocket]:
    cif = record.files["structure.cif"]
    size_kb = cif.size / 1024
    return [Pocket(pocket_id=0, score=round(size_kb / 100, 2), volume=size_kb)]

# 4. Pull records from an external source
class PDBIngester:
    name = "pdb-rcsb"
    schedule = None
    initial_run = None
    max_file_mb = 50.0

    async def pull(self, *, ctx: IngesterContext, limit=None, **kwargs):
        for pdb_id in ["4TOS", "1TIM", "6LU7"][:limit]:
            entry = httpx.get(f"https://data.rcsb.org/rest/v1/core/entry/{pdb_id}").json()
            file_ref = await ctx.add_file(
                pdb_id, "structure.cif",
                url=f"https://files.rcsb.org/download/{pdb_id}.cif",
            )
            yield IngesterRecord(
                source_id=pdb_id,
                metadata={"pdb_id": pdb_id, "title": entry["struct"]["title"], ...},
                files=[file_ref],
            )

# 5. Register the convention
convention(
    title="Protein Structures",
    version="1.0.0",
    schema=PDBStructure,
    ingester=PDBIngester,
    hooks=[validate_structure, find_pockets],
    files={"accepted_types": [".cif", ".pdb"], "max_count": 5},
)

Register the convention as a setuptools entry point in pyproject.toml:

[project.entry-points."osa.conventions"]
my_convention = "my_package"

Testing

Test the full convention pipeline end-to-end — the ingester pulls real data, then every hook runs against each record:

osa test --limit 2

Running ingester pdb-rcsb...
  Fetched 2 record(s) (4TOS, 1TIM)

Running hooks...

  4TOS
    ✓ validate_structure
    ✓ find_pockets → 1 Pocket(s)

  1TIM
    ✓ validate_structure
    ✓ find_pockets → 1 Pocket(s)

2 record(s), 2 accepted, 0 rejected

You can also test individual hooks in-process with synthetic data:

from osa.testing import run_hook

run_hook(validate_structure, meta={"pdb_id": "TEST", ...}, files=tmp_path)

Local development

Run a full OSA stack locally with Docker:

osa init my-archive
cd my-archive
osa start

This scaffolds a project directory with osa.yaml, .env, and a Docker Compose stack (Postgres, OSA server, docker-socket-proxy). Authentication is handled automatically — osa start mints a dev JWT so osa deploy and osa ingestion start work immediately.

Deploy

Deploy conventions to a running archive:

osa deploy

This builds OCI images for your hooks and ingesters, pushes them to the server's registry, and registers the convention.

CLI

Local instance

Command	Description
osa init [dir]	Scaffold a new project (osa.yaml, .env, .gitignore)
osa start	Start the local OSA stack
osa stop	Stop the local stack
osa logs [-f] [service]	View container logs
osa status	Show running containers

Convention workflow

Command	Description
osa test [--limit N]	Test the full pipeline: ingester → hooks
osa deploy	Build OCI images and register conventions
osa meta	Print the convention manifest as JSON
osa ingestion start	Trigger an ingestion run

Authentication

Command	Description
osa login	Authenticate via ORCID device flow
osa logout	Remove stored credentials
osa link --server <url>	Link project to a remote archive

Concepts

Schema — a Pydantic model defining typed metadata fields. Each field can carry units and constraints. The schema is the contract between depositors, hooks, and the archive.

Hook — a pure function decorated with @hook that receives a Record[T] and returns structured results. Hooks run as OCI containers — the SDK builds the image, the server orchestrates execution.

Convention — a bundle of a schema, hooks, file requirements, and an optional ingester. Conventions are the unit of deployment.

Ingester — an async generator that pulls records from external systems (APIs, databases, file servers) into the archive on a schedule.

Record[T] — generic container binding a schema type T to its metadata, files, and SRN (Scientific Resource Name).

License

Apache 2.0