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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)