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Upload

This is the path a submitted file takes from the researcher’s machine into the TSD inbox. It is the only route by which data enters the system.

sequenceDiagram
    autonumber
    actor User as Submitter
    participant LC as lega-commander
    participant AAI as Life Science AAI
    participant Proxy as localega-tsd-proxy
    participant TSD as tsd-file-api
    participant Inbox as TSD inbox

    User->>AAI: authenticate
    AAI-->>User: GA4GH visa token
    Note over User: the file is encrypted to<br/>Crypt4GH beforehand, with a<br/>separate tool
    User->>LC: upload file.raw.enc
    LC->>LC: reject if not a<br/>Crypt4GH container

    loop each chunk
        LC->>Proxy: PATCH chunk<br/>Proxy-Authorization: Bearer visa<br/>Authorization: Basic CEGA
        Proxy->>Proxy: verify visa signature + expiry,<br/>and CEGA credentials
        alt credentials bad
            Proxy-->>LC: 403 (401 if token missing)
        else ok
            Proxy->>TSD: forward chunk
            TSD->>Inbox: append
        end
    end

    LC->>Proxy: finalize
    Proxy->>TSD: finalize upload
    TSD-->>Proxy: 201 Created
    Proxy-->>LC: upload complete
    Proxy->>Proxy: publish upload event<br/>so CEGA learns the file arrived

What matters here

Section titled “What matters here”

Two credentials are required, not one. The submitter presents a GA4GH visa in a Proxy-Authorization: Bearer header and CEGA credentials in a standard Authorization: Basic header. Both are enforced. Diagrams that show only the visa are incomplete, and a request carrying just the visa will not upload.

A bad or forged token is rejected with 403; a missing token gives 401.

There is no upload session handshake. The first PATCH both carries the first chunk and initialises the resumable upload on the TSD side, returning the upload id. There is no separate “request an upload slot” call, and every chunk request is independently authenticated, so authentication is per-request rather than once at the front.

The proxy is a pass-through, not a store. It never writes the file to disk. One nuance: each chunk is read fully into memory before being forwarded, so it streams at chunk granularity rather than byte by byte.

Encryption is not the client tool’s job either. lega-commander does not encrypt. It verifies the file is already a Crypt4GH container and refuses it otherwise. Encryption happens before lega-commander runs, with a separate Crypt4GH tool. The proxy could not decrypt the stream even if it wanted to.

Uploads are resumable. The chunked PATCH protocol comes from the TSD file API, which means an interrupted upload can continue rather than restart.

After the upload

Section titled “After the upload”

The file sits in the inbox: not archived, not downloadable.

Two things happen next, and it is worth separating them. On finalize the proxy automatically publishes an upload event, which is how Central EGA learns the file arrived. But ingestion itself does not start automatically; it waits for an explicit ingest message. That is covered in file ingestion.

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