Spaces:
Running
Running
File size: 30,008 Bytes
7792455 ab14f8c 37f8669 1477c63 7792455 f50685c 7792455 314ce90 7792455 37f8669 1477c63 33b5fb3 62c31e6 7792455 2b49949 33b5fb3 1477c63 7792455 2187395 7792455 314ce90 1477c63 7792455 1477c63 1dbb331 7792455 ec99d66 6cea09c 314ce90 7792455 1477c63 d520b4f 314ce90 d520b4f 1477c63 d520b4f 7792455 2187395 4823b22 2187395 d520b4f b8b1f43 4823b22 7792455 84ff870 1477c63 84ff870 d520b4f b8b1f43 d520b4f b8b1f43 7792455 b8b1f43 314ce90 b8b1f43 314ce90 b8b1f43 314ce90 b8b1f43 314ce90 b8b1f43 314ce90 b8b1f43 314ce90 b8b1f43 314ce90 7792455 b8b1f43 7792455 d520b4f 1477c63 d520b4f 1477c63 d520b4f 84ff870 d520b4f b8b1f43 1477c63 b8b1f43 7792455 1477c63 d520b4f 1477c63 12e9fbb 49d41a8 12e9fbb 49d41a8 12e9fbb 49d41a8 12e9fbb 49d41a8 1477c63 e202c66 e9ef774 1477c63 7792455 1477c63 7792455 314ce90 7792455 1477c63 7792455 37f8669 7792455 314ce90 7792455 1477c63 7792455 62c31e6 7792455 1477c63 314ce90 7792455 314ce90 7792455 1477c63 7792455 37f8669 7792455 42cd864 7792455 1dbb331 7792455 1dbb331 7792455 42cd864 7792455 42cd864 7792455 42cd864 7792455 314ce90 15e5f4e 314ce90 42cd864 7792455 b8b1f43 42cd864 1477c63 42cd864 7792455 b8b1f43 42cd864 b8b1f43 42cd864 1477c63 42cd864 7792455 b8b1f43 1477c63 10b55c8 b8b1f43 d520b4f 1477c63 d520b4f 1477c63 d520b4f 7792455 b8b1f43 49d41a8 12e9fbb 49d41a8 1477c63 49d41a8 37f8669 b8b1f43 4823b22 b8b1f43 4823b22 1477c63 4823b22 ec99d66 b8b1f43 e9ef774 65b20cd e9ef774 8369f5c 1477c63 e9ef774 7792455 76345d2 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 |
import json
import os
from collections import defaultdict
from datetime import datetime, timezone
from pathlib import Path
import gradio as gr
import requests
import spaces
import torch
import yaml
from gradio_rangeslider import RangeSlider
from guidance import json as gen_json
from guidance.models import Transformers
from transformers import AutoTokenizer, GPT2LMHeadModel, set_seed
from schema import GDCCohortSchema # isort: skip
from scheduler import ParquetScheduler # isort: skip
EXAMPLE_INPUTS = [
"bam files for TCGA-BRCA",
"kidney or adrenal gland cancers with alcohol history",
"tumor samples from male patients with acute myeloid lymphoma",
]
GDC_CASES_API_ENDPOINT = "https://api.gdc.cancer.gov/cases"
MODEL_NAME = "uc-ctds/gdc-cohort-llm-gpt2-s1M"
TOKENIZER_NAME = MODEL_NAME
MODEL_READ_TOKEN = os.environ.get("MODEL_READ_TOKEN", None)
DATASET_WRITE_TOKEN = os.environ.get("DATASET_WRITE_TOKEN", None)
with open("config.yaml", "r") as f:
CONFIG = yaml.safe_load(f)
TAB_NAMES = [tab["name"] for tab in CONFIG["tabs"]]
CARD_NAMES = [card["name"] for tab in CONFIG["tabs"] for card in tab["cards"]]
CARD_FIELDS = [card["field"] for tab in CONFIG["tabs"] for card in tab["cards"]]
CARD_2_FIELD = dict(list(zip(CARD_NAMES, CARD_FIELDS)))
FIELD_2_CARD = dict(list(zip(CARD_FIELDS, CARD_NAMES)))
CARD_2_VALUES = {
card["name"]: card["values"] for tab in CONFIG["tabs"] for card in tab["cards"]
}
FACETS_STR = ",".join(
[
f.replace("cases.", "")
for f, n in zip(CARD_FIELDS, CARD_NAMES)
if not isinstance(CARD_2_VALUES[n], dict)
# ^ skip range facets in bin counts
]
)
PREF_DS = os.environ.get("PREF_DS", False)
if PREF_DS:
assert DATASET_WRITE_TOKEN is not None
scheduler = ParquetScheduler(
repo_id=PREF_DS,
token=DATASET_WRITE_TOKEN,
schema={
"prompt": {"_type": "Value", "dtype": "string"},
"cohort_filter": {"_type": "Value", "dtype": "string"},
"preference": {"_type": "Value", "dtype": "bool"},
"timestamp": {"_type": "Value", "dtype": "string"},
},
)
tok = AutoTokenizer.from_pretrained(TOKENIZER_NAME, token=MODEL_READ_TOKEN)
model = GPT2LMHeadModel.from_pretrained(MODEL_NAME, token=MODEL_READ_TOKEN)
model = model.to("cuda" if torch.cuda.is_available() else "cpu")
model = model.eval()
# Generate cohort filter JSON from free text
@spaces.GPU(duration=15)
def generate_filter(query: str) -> str:
"""
Converts a free text description of a cancer cohort into a GDC structured cohort filter.
Args:
query (str): The free text cohort description
Returns:
str: JSON structured GDC cohort filter
"""
set_seed(42)
lm = Transformers(
model=model,
tokenizer=tok,
# sampling_params=SamplingParams,
)
lm += query
lm += gen_json(
name="cohort", schema=GDCCohortSchema, temperature=0, max_tokens=1024
)
cohort_filter = lm["cohort"]
cohort_filter = json.dumps(json.loads(cohort_filter), indent=4)
return cohort_filter
def _prepare_value_count(value: str, count: int) -> str:
return f"{value} [{count}]"
def _get_base_value(value_count: str) -> str:
value = value_count
if " [" in value:
value = value[: value.rfind(" [")]
return value
def _patch_range_filters_for_facet_endpoint(cohort_filter: str) -> str:
# patch for range selectors which use nested `and`
# seems `facets` and nested `and` don't play well together
# so flatten direct nested `and` for query execution only
# this is equivalent since our top-level is always `and`
# keeping nested `and` for presentation and model generations though
temp = json.loads(cohort_filter)
ops = temp["content"]
new_ops = []
for op in ops:
# assumes no deeper than single level nesting
if op["op"] == "and":
for subop in op["content"]:
new_ops.append(subop)
else:
new_ops.append(op)
temp["content"] = new_ops
return json.dumps(temp)
def _convert_cohort_filter_to_lookup(cohort_filter: str) -> dict[str, int | list[str]]:
# Pre-flatten nested ops for easier mapping in next step
flattened_ops = []
for op in json.loads(cohort_filter)["content"]:
# nested `and` can only be 1 deep based on schema
if op["op"] == "and":
flattened_ops.extend(op["content"])
else:
flattened_ops.append(op)
# Prepare and validate generated filters
selected_field_2_values = dict()
for op in flattened_ops:
assert op["op"] in ["in", "=", "<", ">", "<=", ">="], f"Unknown handling for op: {op}" # fmt: skip
content = op["content"]
field, value = content["field"], content["value"]
if op["op"] == "=":
# convert = to <=,>= ops so it can be filled into card
# use flattened_ops as a queue, defer current op
flattened_ops.append(
{
"op": "<=",
"content": content,
}
)
flattened_ops.append(
{
"op": ">=",
"content": content,
}
)
continue # defer current op
elif op["op"] == "<":
# comparator values are ints so can convert to lte by sub 1
op["op"] = "<="
value -= 1
elif op["op"] == ">":
# comparator values are ints so can convert to gte by add 1
op["op"] = ">="
value += 1
# comp ops will duplicate name, disambiguate by appending comp
if op["op"] != "in":
field += "_" + op["op"]
# check that fields are not duplicated
if field in selected_field_2_values:
raise ValueError(f"{field} is ambiguously duplicated")
selected_field_2_values[field] = value
return selected_field_2_values
def _convert_cohort_filter_to_active_selections(cohort_filter: str) -> list[str]:
selected_field_2_values = _convert_cohort_filter_to_lookup(cohort_filter)
active_choices = []
for field, values in selected_field_2_values.items():
card_name = FIELD_2_CARD[
field.replace("_<=", "").replace("_>=", "") # from lookup conversion
]
default_values = CARD_2_VALUES[card_name]
if isinstance(default_values, list):
# checkbox
possible_values = set(default_values)
for value in values:
if value not in possible_values:
continue # model hallucination?
active_choices.append(f"{card_name.upper()}: {value}")
elif isinstance(default_values, dict):
# range-slider, maybe other options in the future?
assert default_values["type"] == "range", f"Expected range slider for card {card_name}" # fmt: skip
assert isinstance(values, int), "values should be integer for range op"
if ">=" in field:
if values != default_values["min"]:
active_choices.append(f"{card_name.upper()}: ≥{values}")
elif "<=" in field:
if values != default_values["max"]:
active_choices.append(f"{card_name.upper()}: ≤{values}")
else:
raise ValueError(f"Unclear how field is not l/gte: {field}")
else:
raise ValueError(f"Unknown values for card {card_name}")
return active_choices
def _convert_cohort_filter_to_cards(cohort_filter: str, api_data: dict) -> list[dict]:
# create lookup to use while iterating through filter card updates
selected_field_2_values = _convert_cohort_filter_to_lookup(cohort_filter)
# prepare card updates, use selected values to check boxes
# values are given by the union of selected values and bucket counts
# (some selected values may have 0 bucket counts)
card_updates = []
for card_name, card_field in zip(CARD_NAMES, CARD_FIELDS):
default_values = CARD_2_VALUES[card_name]
if isinstance(default_values, list):
# checkbox selector
updated_choices = [] # the possible checkboxes
updated_values = [] # the selected checkboxes
other_choices = [] # separate out for sorting
bucket_counts = api_data["aggregations"][card_field.replace("cases.", "")]["buckets"] # fmt: skip
bucket_counts = {x["key"]: x["doc_count"] for x in bucket_counts}
possible_values = set(default_values)
# selected values go first as both values and choices
if card_field in selected_field_2_values:
unmatched_values = []
selected_values = selected_field_2_values.pop(card_field)
for selected_value in selected_values:
if selected_value not in possible_values:
print(
f"{card_field} value {selected_value} is not in the "
"list of default values, is this a model hallucination?"
)
unmatched_values.append(selected_value)
continue # model hallucination? distinct from value with 0 count
count = bucket_counts.pop(selected_value, 0)
value_count = _prepare_value_count(selected_value, count)
updated_choices.append(value_count)
updated_values.append(value_count)
if len(unmatched_values) != 0:
# collect unmatched values back into selected_field_2_values
# which may otherwise be tracking unmatched fields
selected_field_2_values[card_field] = unmatched_values
# fill in remaining possible values from bucket counts
for other_choice, count in bucket_counts.items():
if other_choice not in possible_values:
continue # schema mistmatch? ie if values are added
other_choices.append(_prepare_value_count(other_choice, count))
update_obj = gr.update(
choices=sorted(updated_choices) + sorted(other_choices),
value=updated_values, # I think the order given here preserves selection order
)
elif isinstance(default_values, dict):
# range-slider, maybe other options in the future?
# nothing to do with bucket counts for range slider
assert (
default_values["type"] == "range"
), f"Expected range slider for card {card_name}"
# Need to handle if model outputs flat range or nested range
card_field_gte = card_field + "_>="
card_field_lte = card_field + "_<="
_min = default_values["min"]
_max = default_values["max"]
lo = selected_field_2_values.pop(card_field_gte, _min)
hi = selected_field_2_values.pop(card_field_lte, _max)
assert (
lo >= _min
), f"Generated lower bound ({lo}) less than minimum allowable value ({_min})"
assert (
hi <= _max
), f"Generated upper bound ({hi}) greater than maximum allowable value ({_max})"
update_obj = gr.update(value=(lo, hi))
else:
raise ValueError(f"Unknown card type {card_name}")
card_updates.append(update_obj)
# selected_field_2_values may now have remaining, unmatched values
# edit: updated json schema with enumerated fields should prevent unmatched fields
if len(selected_field_2_values) != 0:
print(f"Unmatched field/values in filter selections: {selected_field_2_values}")
return card_updates
def update_elements_from_filtered_api_call(cohort_filter: str) -> list[dict]:
# return updates for:
# - counter (text)
# - active selections (checkbox group)
# - upvote (enable button, reset text)
# - downvote (enable button, reset text)
# - cards (list of checkbox group)
# --- Execute API Call ---
patched_cohort_filter = _patch_range_filters_for_facet_endpoint(cohort_filter)
params = {
"filters": patched_cohort_filter,
"facets": FACETS_STR,
"pretty": "false",
"format": "JSON",
"size": 0,
}
response = requests.get(GDC_CASES_API_ENDPOINT, params=params)
if not response.ok:
raise Exception(f"API error: {response.status_code}\n{response.json()}")
api_data = response.json()["data"]
# --- Update Elements ---
case_count = api_data["pagination"]["total"]
active_choices = _convert_cohort_filter_to_active_selections(cohort_filter)
card_updates = _convert_cohort_filter_to_cards(cohort_filter, api_data)
return [
gr.update(value=f"{case_count} Cases"), # case counter
gr.update(choices=active_choices, value=active_choices), # actives
gr.update(interactive=True, value="⬆"),
gr.update(interactive=True, value="⬇"),
] + card_updates
def update_json_from_cards(*selected_filters_per_card: tuple[str]) -> str:
ops = []
for card_name, selected_filters in zip(CARD_NAMES, selected_filters_per_card):
# use the default values to determine card type (checkbox, range, etc)
default_values = CARD_2_VALUES[card_name]
if isinstance(default_values, list):
# checkbox
if len(selected_filters) > 0:
base_values = []
for selected_value in selected_filters:
base_value = _get_base_value(selected_value)
base_values.append(base_value)
content = {
"field": CARD_2_FIELD[card_name],
"value": base_values,
}
op = {
"op": "in",
"content": content,
}
ops.append(op)
elif isinstance(default_values, dict):
# range-slider, maybe other options in the future?
assert (
default_values["type"] == "range"
), f"Expected range slider for card {card_name}"
lo, hi = selected_filters
subops = []
for val, limit, comp in [
(lo, default_values["min"], ">="),
(hi, default_values["max"], "<="),
]:
# only add range filter if not default
if val == limit:
continue
subop = {
"op": comp,
"content": {
"field": CARD_2_FIELD[card_name],
"value": int(val),
},
}
subops.append(subop)
if len(subops) > 0:
ops.append({"op": "and", "content": subops})
else:
raise ValueError(f"Unknown values for card {card_name}")
cohort_filter = {
"op": "and",
"content": ops,
}
filter_json = json.dumps(cohort_filter, indent=4)
return gr.update(value=filter_json)
def update_json_from_active(active_selections: list[str]) -> str:
grouped_selections = defaultdict(list)
for k_v in active_selections:
idx = k_v.find(": ")
k, v = k_v[:idx], k_v[idx + 2 :]
grouped_selections[k].append(v)
# mock-up as card selections and defer to update_json_from_cards
selected_filters_per_card = []
for card_name in CARD_NAMES:
default_values = CARD_2_VALUES[card_name]
card_name = card_name.upper() # match active selections casing
if card_name not in grouped_selections:
if isinstance(default_values, list):
# mock-up for empty checkbox group
selected_filters_per_card.append([])
elif isinstance(default_values, dict):
# mock-up for default range selector
selected_filters_per_card.append(
(
default_values["min"],
default_values["max"],
)
)
else:
raise ValueError(f"Unknown card type for card: {card_name}")
else:
selected_values = grouped_selections[card_name]
if isinstance(default_values, list):
# mock-up for checkbox group selections
selected_filters_per_card.append(selected_values)
elif isinstance(default_values, dict):
# mock-up for range selector selections
assert (
len(selected_values) <= 2
), "Cannot do range op with more than 2 ops"
assert all(
[
"≥" in x or "≤" in x for x in selected_values
] # had to get fancy with the unicode symbols...
), "Unclear how ops besides l/gte are in active selection, did that logic change?"
selected_range = dict()
for x in selected_values:
comp = ">=" if "≥" in x else "<="
# if the active selection logic changes (s.t. there's other ops besides l/gte),
# make sure this shortcut to get the int is also checked
value = int(x[1:])
if comp in selected_range:
raise ValueError(
f"Duplicated comparator {comp} for {card_name}"
)
selected_range[comp] = value
selected_filters_per_card.append(
(
selected_range.get(">=", default_values["min"]),
selected_range.get("<=", default_values["max"]),
)
)
else:
raise ValueError(f"Unknown card type for card: {card_name}")
return update_json_from_cards(*selected_filters_per_card)
def get_default_filter() -> str:
gr.Warning(
message="GDC Cohort Copilot can make mistakes. Interactively refine your search using the checkboxes.",
duration=None,
title="GDC Cohort Copilot Should Be Used Interactively!",
)
return json.dumps({"op": "and", "content": []}, indent=4)
def set_active_tab(selected_tab: str) -> list[dict]:
visibles = [gr.update(visible=(tab == selected_tab)) for tab in TAB_NAMES]
elem_classes = [
gr.update(variant="primary" if tab == selected_tab else "secondary")
for tab in TAB_NAMES
]
return visibles + elem_classes
def save_user_preference(cohort_query: str, cohort_filter: str, preference: bool) -> list[dict]: # fmt: skip
timestamp = datetime.now(timezone.utc).isoformat()
data = {
"prompt": cohort_query,
"cohort_filter": json.dumps(json.loads(cohort_filter)), # remove whitespace
"preference": preference,
"timestamp": timestamp,
}
if PREF_DS:
scheduler.append(data)
print(f"Logged user preference data at {timestamp}")
else:
print(
f"No preference dataset configured, "
f"set PREF_DS env var to point to a HuggingFace Dataset Repo. "
f"Would have logged {data}"
)
# disable buttons
if preference:
upval = "✓"
downval = "--" # whitespace seems to be escaped by gradio
else:
upval = "--" # whitespace seems to be escaped by gradio
downval = "✗"
return [
gr.update(interactive=False, value=upval),
gr.update(interactive=False, value=downval),
]
DOWNLOAD_CASES_JS = f"""
function download_cases(filter_str) {{
const params = new URLSearchParams();
params.set('fields', 'case_id');
params.set('format', 'JSON');
params.set('size', 100000);
params.set('filters', filter_str);
const url = "{GDC_CASES_API_ENDPOINT}?" + params.toString();
const button = document.getElementById("download-btn");
button.innerHTML = '<div class="spinner"><\div>';
button.disabled = true;
fetch(url).then(resp => {{
if (!resp.ok) throw new Error("Failed to fetch TSV.");
return resp.json();
}})
.then(data => {{
const ids = data.data.hits.map(item => item.id);
const text = ids.join("\\n");
const blob = new Blob([text], {{type: "text/plain"}});
return blob;
}})
.then(blob => {{
const url = URL.createObjectURL(blob);
const a = document.createElement('a');
a.href = url;
a.download = "gdc_cohort_case_ids.tsv";
document.body.appendChild(a);
a.click();
document.body.removeChild(a);
URL.revokeObjectURL(url);
button.innerHTML = 'Export to GDC';
button.disabled = false;
}})
.catch(error => {{
alert("Download failed: " + error.message);
}});
}}
"""
with gr.Blocks(css_paths="style.css") as demo:
gr.Markdown("# GDC Cohort Copilot")
with gr.Row(equal_height=True):
with gr.Column(scale=7):
text_input = gr.Textbox(
label="Describe the cohort you're looking for:",
info=(
"Only provide the cohort characteristics. "
"Do not include extraneous text. "
"For example, write 'patients with X' "
"instead of 'I would like patients with X':"
),
submit_btn="Generate Cohort",
elem_id="description-input",
placeholder="Enter a cohort description to begin...",
)
with gr.Column(scale=1, min_width=150):
case_counter = gr.Text(
show_label=False,
interactive=False,
container=False,
elem_id="case-counter",
min_width=150,
)
case_download = gr.Button(
value="Export to GDC",
min_width=150,
elem_id="download-btn",
)
with gr.Row(equal_height=True):
with gr.Column(scale=2, min_width=250):
gr.Examples(
examples=EXAMPLE_INPUTS,
inputs=text_input,
)
with gr.Column(scale=7):
json_output = gr.Code(
label="Cohort Filter JSON",
language="json",
interactive=False,
show_label=True,
container=True,
elem_id="json-output",
)
with gr.Column(scale=1, min_width=50):
gr.Markdown(
"Is this correct?",
elem_id="vote-label",
)
upvote = gr.Button(
value="⬆",
min_width=50,
elem_id="upvote-btn",
)
downvote = gr.Button(
value="⬇",
min_width=50,
elem_id="download-btn",
)
with gr.Row():
gr.Markdown(
"The generated cohort filter will autopopulate into the filter cards below. "
"**<u>GDC Cohort Copilot can make mistakes!</u>** "
"Refine your search using the interactive checkboxes. "
"Note that many other options can be found by selecting the different tabs. "
"**<u>If you'd like to help us improve our model</u>**, you can use the up or down vote button to send us feedback. "
"We'll only save the current free text description, the cohort filter JSON, and your vote. "
"You can also show us what the right filter should have been by manually refining it using the checkboxes, before up voting."
)
with gr.Row(equal_height=True):
with gr.Column(scale=1, min_width=250):
gr.Markdown("## Currently Selected Filters")
with gr.Column(scale=4):
active_selections = gr.CheckboxGroup(
choices=[],
show_label=False,
interactive=True,
elem_id="active-selections",
)
with gr.Row():
# Tab selectors
tab_buttons = []
with gr.Column(scale=1, min_width=250):
for tab_name in TAB_NAMES:
tab_button = gr.Button(
value=tab_name,
variant="primary" if tab_name == TAB_NAMES[0] else "secondary",
)
tab_buttons.append(tab_button)
# Filter cards
tab_containers = []
filter_cards = []
for tab in CONFIG["tabs"]:
visible = tab["name"] == TAB_NAMES[0] # default first card
with gr.Column(scale=4, visible=visible) as tab_container:
tab_containers.append(tab_container)
with gr.Row(elem_classes=["card-group"]):
for card in tab["cards"]:
if isinstance(card["values"], list):
filter_card = gr.CheckboxGroup(
choices=[],
label=card["name"],
interactive=True,
elem_classes=["filter-card"],
)
else:
# values is a dictionary and defines some meta options
metaopts = card["values"]
assert (
"type" in metaopts
and metaopts["type"] == "range"
and all(
k in metaopts
for k in [
"min",
"max",
]
)
), f"Unknown meta options for {card['name']}"
info = "Inclusive range"
if "unit" in metaopts:
info += f", units in {metaopts['unit']}"
filter_card = RangeSlider(
label=card["name"],
info=info,
minimum=metaopts["min"],
maximum=metaopts["max"],
step=1, # assume integer
elem_classes=["filter-card", "filter-range"],
)
filter_cards.append(filter_card)
# Toggle card group (tab) visibility
for tab_button, name in zip(tab_buttons, TAB_NAMES):
tab_button.click(
fn=set_active_tab,
inputs=gr.State(name),
outputs=tab_containers + tab_buttons,
# api_name=False,
show_api=False,
)
# Callback for case download button
case_download.click(
fn=None, # apparently this isn't the same as not specifying it, even though the default is None?
js=DOWNLOAD_CASES_JS, # need custom JSON to execute browser side download
inputs=json_output,
# api_name=False,
show_api=False,
)
# Enable user preference logging
upvote.click(
fn=save_user_preference,
inputs=[text_input, json_output, gr.State(True)],
outputs=[upvote, downvote],
# api_name=False,
show_api=False,
)
downvote.click(
fn=save_user_preference,
inputs=[text_input, json_output, gr.State(False)],
outputs=[upvote, downvote],
# api_name=False,
show_api=False,
)
# Model generation should change the JSON filter
# All other element updates cascade
# This is the only API that should be exposed
text_input.submit(
fn=generate_filter,
inputs=text_input,
outputs=json_output,
)
# Changing the card selections should change the JSON filter
# All other element updates (including cards themselves) cascade
for filter_card in filter_cards:
if isinstance(filter_card, RangeSlider):
filter_card.release(
fn=update_json_from_cards,
inputs=filter_cards,
outputs=json_output,
# api_name=False,
show_api=False,
)
else:
filter_card.input(
fn=update_json_from_cards,
inputs=filter_cards,
outputs=json_output,
# api_name=False,
show_api=False,
)
# Changing the active selections should change the JSON filter
# All other element updates (including active selections itself) cascade
active_selections.input(
fn=update_json_from_active,
inputs=active_selections,
outputs=json_output,
# api_name=False,
show_api=False,
)
# JSON filter change executes API call and updates all elements
json_output.change(
fn=update_elements_from_filtered_api_call,
inputs=json_output,
outputs=[case_counter, active_selections, upvote, downvote] + filter_cards,
# api_name=False,
show_api=False,
)
# Trigger initial update
demo.load(
fn=get_default_filter,
inputs=None,
outputs=json_output,
# api_name=False, # this breaks the API functionality, not sure why
show_api=False, # so just hide the API endpoints instead, not ideal
# the weirdness with the API toggle seems true for all disabled API endpoints
)
if __name__ == "__main__":
demo.launch(mcp_server=True)
|