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editable table #7

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merged 4 commits into from
Nov 6, 2024
Merged

editable table #7

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8dc4198
run pre-commit hook
abhidg Nov 4, 2024
1fbe431
app: allow editing table and accepting rows for final mapping
abhidg Nov 4, 2024
9b312bb
app: add download mapping file support
abhidg Nov 5, 2024
b5441ca
app: fix highlighting using row_ids
abhidg Nov 5, 2024
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2 changes: 1 addition & 1 deletion PRD.md
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Original file line number Diff line number Diff line change
Expand Up @@ -90,4 +90,4 @@ notebook or Python interface.

Figma: https://www.figma.com/design/bpaumciR1DPhGejjCXER86/ISARIC-ARCmapper

![ARCmapper UX mockup](images/arcmapper-mockup.png)
![ARCmapper UX mockup](images/arcmapper-mockup.png)
243 changes: 86 additions & 157 deletions src/arcmapper/app.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,7 @@
from dash import dcc, html, ctx, callback, dash_table, Input, Output, State
import dash_bootstrap_components as dbc


from .components import select
from .components import arc_form, upload_form
from .util import read_upload_data
from .dictionary import read_data_dictionary
from .strategies import map as map_data_dictionary_to_arc
Expand All @@ -15,6 +14,10 @@
app = dash.Dash("arcmapper", external_stylesheets=[dbc.themes.BOOTSTRAP])
app.title = "ARCMapper"

PAGE_SIZE = 25
OK = "✅"
HIGHLIGHT_COLOR = "bisque"

navbar = dbc.Navbar(
dbc.Container(
[
Expand Down Expand Up @@ -43,159 +46,23 @@
dark=True,
)

upload_form = dbc.Container(
output_table = dbc.Container(
html.Div(
dbc.Form(
[
dbc.Row(
[
html.P(
[
html.Strong("SOURCE: "),
"ARCmapper supports data dictionaries in CSV, XLSX, JSON schema, or you can upload sample data.",
]
)
]
),
dbc.Row(
dbc.Col(
dbc.Switch(
id="upload-is-sample-data",
label="Uploaded file is sample data, not a data dictionary. Data will be sent to server, only use on local deployments",
disabled=True,
)
)
),
dbc.Row(
[
dbc.Label("Responses column", width="auto"),
dbc.Col(
dbc.Input(
id="upload-col-responses",
type="text",
value="Choices, Calculations, OR Slider Labels",
),
className="me-3",
),
dbc.Label("Description column", width="auto"),
dbc.Col(
dbc.Input(
id="upload-col-description",
type="text",
placeholder="Defaults to longest column",
value="Field Label",
),
className="me-3",
),
dbc.Col(
dcc.Upload(
id="upload-input-file",
children=html.Div(
"Drag and drop or select file",
style={
"border": "1px dashed silver",
"padding": "0.3em",
},
),
),
className="me-3",
),
dbc.Col(
dbc.Button(
"Upload", id="upload-btn", color="primary", n_clicks=0
)
),
dcc.Store(id="upload-data-dictionary"),
],
className="g-2",
),
dbc.Row(id="upload-status"),
]
),
style={
"border": "1px solid silver",
"border-radius": "0.4em",
"padding": "1em",
},
),
style={"margin-top": "1em"},
dbc.Row(id="output"),
style={"padding": "0.5em", "border": "1px solid silver", "borderRadius": "5px"},
)
)

arc_form = dbc.Container(
html.Div(
dbc.Form(
final_mapping_form = dbc.Container(
dbc.Row(
dbc.Col(
[
dbc.Row(
html.P(
[
html.Strong("TARGET: "),
"Choose the target ARC version and select method and method parameters",
]
)
),
dbc.Row(
[
dbc.Label("Target ARC version", width="auto"),
dbc.Col(
select("arc-version", ["1.0.0", "1.0.1"]),
className="me-3",
),
dbc.Label("Mapping method", width="auto"),
dbc.Col(
dbc.Select(
id="arc-mapping-method",
options=[
{"label": "TF-IDF", "value": "tf-idf"},
{
"label": "Sentence Transformers",
"value": "sbert",
},
],
value="tf-idf",
),
className="me-3",
),
dbc.Label("Number of matches", width="auto"),
dbc.Col(
dbc.Input(
id="arc-num-matches",
type="number",
min=2,
max=10,
step=1,
value=3,
),
),
dbc.Label("Threshold", width="auto"),
dbc.Col(
dbc.Input(
id="arc-threshold",
type="number",
min=0.1,
max=1,
step=0.1,
value=0.3,
),
),
dbc.Col(dbc.Button("Map to ARC", id="map-btn"), width="auto"),
],
className="g-2",
dcc.Download(id="download-mapping"),
dbc.Button(
"Download mapping", id="download-btn", style={"marginTop": "1em"}
),
]
),
style={
"border": "1px solid silver",
"border-radius": "0.4em",
"padding": "1em",
},
),
style={"margin-top": "1em"},
)

output_table = dbc.Container(
html.Div(
dbc.Row(id="output"),
style={"padding": "0.5em", "border": "1px solid silver", "borderRadius": "5px"},
)
)
)

Expand All @@ -217,9 +84,10 @@ def upload_data_dictionary(
col_responses,
col_description,
):
ok = dbc.Alert("Upload successful", color="success")
ok = dbc.Alert("Upload successful", color="success", style={"marginTop": "1em"})

def err(msg): return dbc.Alert(msg, color="danger")
def err(msg):
return dbc.Alert(msg, color="danger", style={"marginTop": "1em"})

if ctx.triggered_id == "upload-btn" and upload_contents is not None:
try:
Expand All @@ -231,7 +99,12 @@ def err(msg): return dbc.Alert(msg, color="danger")
return {}, err("Description column not found")
if col_responses not in df.columns:
return {}, err("Responses column not found")
data = read_data_dictionary(df, description_field=col_description, response_field=col_responses, response_func="redcap")
data = read_data_dictionary(
df,
description_field=col_description,
response_field=col_responses,
response_func="redcap",
)
return data.to_json(), ok

except Exception as e:
Expand All @@ -253,23 +126,79 @@ def invoke_map_arc(data, _, version, method, num_matches):
if ctx.triggered_id == "map-btn":
arc = read_arc_schema(version)
dictionary = pd.read_json(data)

mapped_data = map_data_dictionary_to_arc(method, dictionary, arc, num_matches)
data = mapped_data.to_dict("records")
for i, row in enumerate(data):
row["id"] = i
return (
dash_table.DataTable(
id="mapping",
data=mapped_data.to_dict("records"),
columns=[{"name": i, "id": i} for i in mapped_data.columns],
data=data,
columns=[
{"name": i, "id": i, "editable": i != "status"}
for i in mapped_data.columns
],
editable=True,
style_data={
"whiteSpace": "normal",
"height": "auto",
"fontSize": "90%",
},
style_table={"overflowX": "auto"},
page_size=25,
page_size=PAGE_SIZE,
),
)
return html.Span("No data to see here")
else:
return html.Span("No data to see here")


@callback(
Output("mapping", "data"),
Output("mapping", "style_data_conditional"),
Output("mapping", "active_cell"),
Input("mapping", "data"),
Input("mapping", "active_cell"),
prevent_initial_call=True,
)
def handle_status(data, active_cell):
if active_cell and active_cell.get("column_id") == "status":
i = active_cell.get("row_id")
row = data[i]
row["status"] = OK if row["status"] == "-" else "-"
else:
raise dash.exceptions.PreventUpdate
highlighted_rows = [i for i in range(len(data)) if data[i]["status"] == OK]
return (
data, # mapping data
[
{
"if": {
"filter_query": " || ".join(
f"{{id}} = {k}" for k in highlighted_rows
)
},
"backgroundColor": HIGHLIGHT_COLOR,
}
], # style_data_conditional
False, # unsets active cell, allowing the cell to be clicked immediately again
)


@callback(
Output("download-mapping", "data"),
Input("download-btn", "n_clicks"),
State("mapping", "data"),
prevent_initial_call=True,
)
def handle_download(_, data):
if ctx.triggered_id == "download-btn":
df = pd.DataFrame(data)
df = df[df.status == OK].drop(columns=["status", "rank"])
return dcc.send_data_frame(df.to_csv, "arcmapper-mapping-file.csv", index=False)
else:
raise dash.exceptions.PreventUpdate


app.layout = html.Div([navbar, upload_form, arc_form, output_table])
app.layout = html.Div([navbar, upload_form, arc_form, output_table, final_mapping_form])
server = app.server
1 change: 0 additions & 1 deletion src/arcmapper/arc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,6 @@ def arc_schema_url(arc_version: str) -> str:
return f"https://github.com/ISARICResearch/DataPlatform/raw/refs/heads/main/ARCH/ARCH{arc_version}/ARCH.csv"



def read_arc_schema(
arc_version_or_file: str, preset: str | None = None
) -> pd.DataFrame:
Expand Down
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