app

MIAPPE Metadata Editor - Dash Web UI

A web-based UI to view, edit and bulk-fill the MIAPPE-aligned biological metadata (investigation / study / biologicalMaterial / observedVariable) of the scans of a local PlantDB (FSDB).

It offers two editing modes:

• a bulk editor to set a single field's value on a chosen subset of scans (all / matching a scan-ID regexp / matching a metadata field value / an explicit checklist), and
• a per-scan editor to inspect and edit the full tree of one scan.

Each field shows the MIAPPE definition as a tooltip on hover, and free-text fields suggest values already used across the database.

Usage example

metadata_app --db-path /data/ROMI/test_PI3_juillet_Alexis
# then open http://localhost:8050

main

main(db_path, port, debug)

Launch the MIAPPE metadata editor web UI.

Source code in plantdb/client/metadata_app/app.py

@click.command(context_settings=dict(help_option_names=["-h", "--help"]))
@click.option("--db-path", type=click.Path(exists=True, file_okay=False, dir_okay=True),
              help="Path to the local PlantDB (FSDB) to edit.")
@click.option("--port", type=int, default=8050, help="Port to run the web application on.")
@click.option("--debug", is_flag=True, help="Enable debug mode.")
def main(db_path: str | None, port: int, debug: bool) -> None:
    """Launch the MIAPPE metadata editor web UI."""
    # Pre-seed the store so the DB loads automatically without clicking Load.
    if db_path:
        DB_PATH_STORE.data = db_path

    app.run(host="0.0.0.0", port=port, debug=debug)

render_edit_form

render_edit_form(mode, scan_id, data)

Render the unified field form: values filled for a single scan, placeholders for bulk.

Source code in plantdb/client/metadata_app/app.py

@callback(
    Output("per-scan-form", "children"),
    [Input("edit-accordion", "active_item"),
     Input("scan-select", "value")],
    State("scans-store", "data"),
    prevent_initial_call=False
)
def render_edit_form(mode, scan_id, data):
    """Render the unified field form: values filled for a single scan, placeholders for bulk."""
    flat = {}
    if mode == "single" and scan_id and data and data.get("scans"):
        flat = data["scans"].get(scan_id, {})
    # One shared form is used for both edit modes: in "single" mode it is prefilled
    # with the scan's values, in "bulk" mode the fields stay empty as templates.
    section_accordion = dbc.Accordion([], id="field-accordion", always_open=True)
    for section in sections():
        specs = specs_for_section(section)
        if not specs:
            continue
        rows = []
        for spec in specs:
            path = spec["path"]
            value = flat.get(path)
            kind = {"type": "number"} if spec["type"] in ("int", "float") else {"type": "text"}
            rows.append(dbc.InputGroup([
                dbc.InputGroupText(html.Label(spec["label"]), className="align-self-center"),
                dbc.Input(id=_field_input_id(path), value="" if value is None else str(value), **kind),
                dbc.InputGroupText(html.I(className="bi bi-question-circle", title=_tooltip(spec)),
                                   className="align-self-center"),
            ], className="mb-1 field-group"))

        sec_acc = dbc.AccordionItem(rows,
                                    title=[html.I(className=f"{_SECTION_ICONS.get(section, 'bi-folder')} me-2"),
                                           section],
                                    className="mb-2")
        section_accordion.children.append(sec_acc)
    return section_accordion

scan_checklist

scan_checklist(scan_ids)

Build the scope checklist options for the given scan ids.

Parameters:

Name	Type	Description	Default
scan_ids	list[str]	The scan ids to turn into checklist entries.	required

Returns:

Type	Description
list[dict[str, str]]	{"label": id, "value": id} entries for a Dash checklist.

Source code in plantdb/client/metadata_app/app.py

def scan_checklist(scan_ids: list[str]) -> list[dict[str, str]]:
    """Build the scope checklist options for the given scan ids.

    Parameters
    ----------
    scan_ids : list[str]
        The scan ids to turn into checklist entries.

    Returns
    -------
    list[dict[str, str]]
        ``{"label": id, "value": id}`` entries for a Dash checklist.
    """
    return [{"label": s, "value": s} for s in scan_ids]

set_db_path_from_button

set_db_path_from_button(n_clicks, db_path)

Write the entered path into the store, which triggers loading.

Source code in plantdb/client/metadata_app/app.py

@callback(
    Output("db-path-store", "data"),
    Input("load-btn", "n_clicks"),
    State("db-path", "value"),
    prevent_initial_call=True
)
def set_db_path_from_button(n_clicks, db_path):
    """Write the entered path into the store, which triggers loading."""
    if n_clicks and db_path:
        return db_path
    return None

set_db_path_value

set_db_path_value(db_path)

Update the text input value from the store.

Source code in plantdb/client/metadata_app/app.py

@callback(
    Output("db-path", "value"),
    Input("db-path-store", "data"),
    prevent_initial_call=False
)
def set_db_path_value(db_path):
    """Update the text input value from the store."""
    return db_path or ""