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FlyWire access check

Not an analysis. It answers two questions before real work: does this machine have permission to query CAVE, and do the local census ids exist on the server? The public datastack is frozen at release 783 and has six tables; cell types are not one of them (they come from Codex, see collect).

check_btn = mo.ui.run_button(label="run checks against CAVE")
check_btn

class Inventory(NamedTuple):
    """What the server reports: the materialization versions, the
    version in use, and the table names."""

    versions: list
    version: int
    tables: list

def check_inventory(m) -> Inventory:
    """Materialization versions and table names the server reports."""
    return Inventory(
        versions=m.get_versions(), version=m.version, tables=m.get_tables()
    )

mo.stop(not check_btn.value)
m = cave_materialize()
check_inventory(m)

Sample the core tables

• nuclei_v1: one cell body. Its position is pt_position, and split_positions=True gives x, y, z.
• Sources.SYNAPSE_VIEW: one synapse. Every connection count comes from this view; it is a view, so get_tables does not list it.
• Sources.TRANSMITTER_TABLE: one synapse, with per-transmitter probabilities and no single nt_type column.

def sample_tables(m):
    """Three nuclei rows, one row of the synapse view, and one row of
    the transmitter table, to prove all three answer."""
    nuclei = m.query_table(
        "nuclei_v1",
        select_columns=["pt_root_id", "pt_position"],
        limit=3,
        split_positions=True,
    )
    view_row = m.query_view(Sources.SYNAPSE_VIEW, limit=1)
    synapse = m.query_table(Sources.TRANSMITTER_TABLE, limit=1)
    return nuclei, view_row, synapse

nuclei_rows, view_row, synapse_row = sample_tables(m)
nuclei_rows

ancestor-stopped: This cell wasn't run because an ancestor was stopped with `mo.stop`:

view_row.T

ancestor-stopped: This cell wasn't run because an ancestor was stopped with `mo.stop`:

synapse_row.T

ancestor-stopped: This cell wasn't run because an ancestor was stopped with `mo.stop`:

Do the census LC16 ids exist on the server?

The Codex census and the CAVE tables are separate products. Every census LC16 id is looked up in nuclei_v1; most should resolve, and zero means the two disagree on the release.

def lc16_in_nuclei(m, census) -> int:
    """Number of census LC16 root ids found in nuclei_v1."""
    ids = root_ids_of_type(census, "LC16")
    hit = m.query_table(
        "nuclei_v1",
        filter_in_dict={"pt_root_id": ids},
        select_columns=["pt_root_id"],
    )
    return int(hit["pt_root_id"].nunique())

_census = load_census()
_found = lc16_in_nuclei(m, _census)
_total = len(root_ids_of_type(_census, "LC16"))
mo.md(f"**{_found}** of {_total} census LC16 ids found in `nuclei_v1`.")

ancestor-stopped: This cell wasn't run because an ancestor was stopped with `mo.stop`:

On a login error

On 401, 403, or anything mentioning a token, create one at https://global.daf-apis.com/auth/api/v1/create_token, then save it with the global client, not the datastack client. A new token invalidates the old one.

from caveclient import CAVEclient

client = CAVEclient(server_address="https://global.daf-apis.com")
client.auth.save_token("<TOKEN>", overwrite=True)

def main() -> None:
    """Batch: run every check, printing results; exit 1 with token
    hints on failure."""
    try:
        m = cave_materialize()
        inventory = check_inventory(m)
        print(f"version {inventory.version}; tables {inventory.tables}")
        nuclei, view_row, synapse = sample_tables(m)
        print(
            f"nuclei_v1 ok ({len(nuclei)} rows); "
            f"{Sources.SYNAPSE_VIEW} columns {list(view_row.columns)}; "
            f"{Sources.TRANSMITTER_TABLE} columns {list(synapse.columns)}"
        )
        print(f"LC16 ids in nuclei_v1: {lc16_in_nuclei(m, load_census())}")
    except Exception as e:  # a smoke test reports any failure
        print(f"FAILED: {type(e).__name__}: {e}")
        if "401" in str(e) or "403" in str(e) or "token" in str(e).lower():
            print(
                "token missing or expired; "
                "see the last section of this notebook"
            )
        if "503" in str(e):
            print("materialize host is down")
        sys.exit(1)