Misc feedback on v1.b5

[0dey]

Some typos on the "Run the Quaero Explorer" documentation

• The data argument might be missing in the code block from the "What is the saved format?" part.
• There is a "return" without any function defined in the code block from the "Assemble everything" part.

Feature Request

• Once a factory is instantiated, we cannot overwrite this factory with other parameters. It might be interesting to add a boolean overwrite parameter to DatasetExplorerWidgetFactory. This could be useful for tests or even if we did a mistake in the data dict.
• It might be interesting to add the possibility to instantiate the scheme of entites annotation in the case where we don't want to pre-annotate texts
• In table cells, it might be interesting to add the possibility to have choices in a drop-down menu and the possibility to have multiple mutually exclusive boxes.

Bug

Description

The "scroll" feature works the first time, and once a button was clicked, it does not work any more.

How to reproduce the bug

def on_note_selected_in_table(
  row_id: str, row_idx: int, col: str, mode: str, cause: str
):
  if row_id is None:
      return
  top_level_state["note_id"] = row_id
  note_text_handle.current["set_doc_by_id"](row_id)
  note_form_handle.current["set_row_id"](row_id)

def on_patient_selected_in_table(
  row_id: str, row_idx: int, col: str, mode: str, cause: str
):
  if row_id is None:
      return
  top_level_state["person_id"] = row_id
  note_id = [note for note in notes if note["person_id"] == row_id][0]["note_id"]
  top_level_state["note_id"] = note_id
  notes_table_handle.current["set_filter"]("person_id", str(row_id))
  notes_table_handle.current["scroll_to_row_id"](note_id)
  notes_table_handle.current["scroll_to_row_idx"](note_id)
  notes_table_handle.current["set_highlighted"]([note_id])
  note_text_handle.current["set_doc_by_id"](note_id)
  note_form_handle.current["set_row_id"](note_id)

def on_pt_row_hovered(person_id: str, person_idx: int, mod_keys: List[str]):
  patients_table_handle.current["set_highlighted"]([str(person_id)])

@component
def NoteTextHeader():
  note_id = use_store_snapshot(top_level_state)["note_id"]
  return f"Note {note_id}" if note_id else "Note"

@component
def NotesHeader():
  person_id = use_store_snapshot(top_level_state)["person_id"]
  return f"Notes from patient {person_id}" if person_id else "Notes"

data = edsnlp.data.read_parquet(
  notes_path,
  span_setter="entities",
  notes_as_span_attribute="cui",
)

patients_dict = {}
notes = []
init_labels_dict = {label: False for label in labels}
for idx, doc in enumerate(data):
  notes.append(
      {
          "note_id": str(doc["note_id"]),
          "note_datetime": str(doc["note_datetime"]),
          "note_class_source_value": str(doc["note_class_source_value"]),
          "visit_occurrence_id": str(doc["visit_occurrence_id"]),
          "care_site_id": str(doc["care_site_id"]),
          "note_title": str(doc["note_title"]),
          "row_status_source_value": str(doc["row_status_source_value"]),
          "note_text": doc["note_text"],
          "person_id": str(doc["person_id"]),
          "interesting": False,
          "seen": False,
      }
  )

  if str(doc["person_id"]) not in patients_dict:
      d1 = {"person_id": str(doc["person_id"]), "seen": False}
      patients_dict[str(doc["person_id"])] = dict(
          chain.from_iterable(d.items() for d in (d1, init_labels_dict))
      )

patients = list(patients_dict.values())
notes = sorted(notes, key=lambda d: d["note_datetime"])

factory = DatasetExplorerWidgetFactory(
  {
      "notes": notes,
      "patients": patients,
  },
  sync=annotations_path,
)
data = factory.data

notes_table_handle: RefType[TableWidgetHandle] = use_ref()
patients_table_handle: RefType[TableWidgetHandle] = use_ref()
note_text_handle: RefType[TextWidgetHandle] = use_ref()
note_form_handle: RefType[FormWidgetHandle] = use_ref()

top_level_state = create_store(
  {
      "note_id": notes[0]["note_id"] if notes else None,
      "person_id": patients[0]["person_id"] if patients else None,
  }
)

notes_view = factory.create_table_widget(
  store_key="notes",
  primary_key="note_id",
  first_keys=[
      "note_id",
      "seen",
      "interesting",
      "note_datetime",
      "note_title",
      "note_class_source_value",
  ],
  id_keys=["note_id"],
  editable_keys=["seen", "interesting"],
  categorical_keys=["seen", "interesting"],
  hidden_keys=[],
  style={"--min-notebook-height": "300px"},
  handle=notes_table_handle,
  on_position_change=on_note_selected_in_table,
)

note_form_view = factory.create_form_widget(
  store_key="notes",
  primary_key="note_id",
  first_keys=[
      "note_id",
      "note_datetime",
      "note_title",
      "note_class_source_value",
  ],
  hidden_keys=["note_text", "seen", "interesting"],
  style={
      "--min-notebook-height": "300px",
      "margin": "10px",
      "alignItems": "flex-start",
  },
  handle=note_form_handle,
)

patients_view = factory.create_table_widget(
  store_key="patients",
  primary_key="person_id",
  first_keys=["person_id", "seen"] + labels,
  id_keys=["person_id"],
  editable_keys=["seen"] + labels,
  categorical_keys=["seen"] + labels,
  style={"--min-notebook-height": "300px"},
  handle=patients_table_handle,
  on_position_change=on_patient_selected_in_table,
  on_mouse_hover_row=on_pt_row_hovered,
)

note_text_view = factory.create_text_widget(
  store_text_key="notes",
  handle=note_text_handle,
  text_key="note_text",
  text_primary_key="note_id",
  spans_primary_key="ent_id",
  style={"--min-notebook-height": "300px"},
)

layout = div(
    Layout(
        Panel(patients_view, key="Patients"),
        Panel(notes_view, header=NotesHeader(), key="Notes"),
        Panel(note_form_view, header=NoteTextHeader(), key="Note Form"),
        Panel(note_text_view, header=NoteTextHeader(), key="Note Text"),
        default_config={
            "kind": "row",
            "children": [
                "Patients",
                ["Notes", "Note Form"],
                "Note Text",
            ],
        },
    ),
    style={
        "background": "var(--joy-palette-background-level2, #f0f0f0)",
        "width": "100%",
        "height": "100%",
        "minHeight": "300px",
        "--sd-background-color": "transparent",
    },
)