app.py.old

import json
import os
from collections import defaultdict

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

DEBUG = "DEBUG" in os.environ
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
AUTH_TOKEN = os.environ.get("HF_TOKEN", False)  # HF_TOKEN must be set to use auth

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)))
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
    ]
)

if not DEBUG:
    tok = AutoTokenizer.from_pretrained(TOKENIZER_NAME, token=AUTH_TOKEN)
    # for some reason, pre-invoking tokenizer prevents endless generation when using guidance
    # opened ticket here: https://github.com/guidance-ai/guidance/issues/1322
    tok("foobar")
    model = GPT2LMHeadModel.from_pretrained(MODEL_NAME, token=AUTH_TOKEN)
    model = model.to("cuda" if torch.cuda.is_available() else "cpu")
    model = model.eval()


DUMMY_FILTER = json.dumps(
    {
        "op": "and",
        "content": [
            {
                "op": "in",
                "content": {
                    "field": "cases.project.project_id",
                    "value": ["TCGA-BRCA"],
                },
            },
            {
                "op": "in",
                "content": {
                    "field": "cases.project.program.name",
                    "value": ["TCGA"],
                },
            },
            {
                "op": "and",
                "content": [
                    {
                        "op": ">=",
                        "content": {
                            "field": "cases.diagnoses.age_at_diagnosis",
                            "value": 7305,
                        },
                    },
                    {
                        "op": "<=",
                        "content": {
                            "field": "cases.diagnoses.age_at_diagnosis",
                            "value": 14610,
                        },
                    },
                ],
            },
        ],
    },
    indent=4,
)


# 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
    """
    if DEBUG:
        return DUMMY_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


# Transform query to filter to checkbox selections (and update json box)
def process_query(query):
    # Generate filter
    cohort_filter_str = generate_filter(query)
    cohort_filter = json.loads(cohort_filter_str)

    # Pre-flatten nested ops for easier mapping in next step
    flattened_ops = []
    for op in 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
    generated_field_2_values = dict()
    for op in flattened_ops:
        assert op["op"] in [
            "in",
            "=",
            "<",
            ">",
            "<=",
            ">=",
        ], f"Unknown handling for op: {op}"
        content = op["content"]
        field, value = content["field"], content["value"]
        # comparators are ints so can convert to g/lte by add/sub 1
        if op["op"] == "<":
            op["op"] = "<="
            value -= 1
        elif op["op"] == ">":
            op["op"] = ">="
            value += 1
        elif op["op"] == "=":
            # convert = to <=,>= ops so it can be filled into card
            flattened_ops.append(
                {
                    "op": "<=",
                    "content": content,
                }
            )
            flattened_ops.append(
                {
                    "op": ">=",
                    "content": content,
                }
            )
            continue

        if op["op"] != "in":
            # comp ops will duplicate name, disambiguate by appending comp
            field += "_" + op["op"]

        if field in generated_field_2_values:
            raise ValueError(f"{field} is ambiguously duplicated")
        generated_field_2_values[field] = value

    # Map filter selections to cards
    card_updates = []
    for card_name, card_field in zip(CARD_NAMES, CARD_FIELDS):
        # Need to update all cards so use all possible cards as ref
        default_values = CARD_2_VALUES[card_name]
        if isinstance(default_values, list):
            updated_values = []
            updated_choices = default_values  # reset value
            possible_values = set(updated_choices)
            if card_field in generated_field_2_values:
                # check ref against generated
                selected_values = generated_field_2_values.pop(card_field)
                unmatched_values = []
                for selected_value in selected_values:
                    if selected_value in possible_values:
                        updated_values.append(selected_value)
                    else:
                        # model hallucination?
                        unmatched_values.append(selected_value)
                if len(unmatched_values) > 0:
                    generated_field_2_values[card_field] = unmatched_values
            update_obj = gr.update(
                choices=updated_choices,
                value=updated_values,  # will override existing selections
            )
        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}"
            # 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 = generated_field_2_values.pop(card_field_gte, _min)
            hi = generated_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 values for card {card_name}")
        card_updates.append(update_obj)
    # generated_field_2_values will have remaining, unmatched values
    # edit: updated json schema with enumerated fields prevents unmatched fields
    print(f"Unmatched values in model generation: {generated_field_2_values}")
    return card_updates + [gr.update(value=cohort_filter_str)]


# Update JSON based on checkbox selections
def update_json_from_cards(*selected_filters_per_card):
    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)


# Execute GDC API query and prepare checkbox + case counter updates
# Preserve prior selections
def update_cards_with_counts(cohort_filter: str, *selected_filters_per_card):
    card_2_selections = dict(list(zip(CARD_NAMES, selected_filters_per_card)))

    # Execute GDC API query
    params = {
        "facets": FACETS_STR,
        "pretty": "false",
        "format": "JSON",
        "size": 0,
    }

    if cohort_filter:
        # 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
        cohort_filter = json.dumps(temp)
        params["filters"] = cohort_filter

    response = requests.get(GDC_CASES_API_ENDPOINT, params=params)
    if not response.ok:
        raise Exception(f"API error: {response.status_code}\n{response.json()}")
    temp = response.json()

    # Update checkboxes with bin counts
    card_updates = []
    all_counts = temp["data"]["aggregations"]
    for card_name in CARD_NAMES:
        card_field = CARD_2_FIELD[card_name]
        card_field = card_field.replace("cases.", "")
        card_values = CARD_2_VALUES[card_name]
        if isinstance(card_values, list):
            # value checkboxes
            choice_mapping = {}
            updated_choices = []
            card_counts = {
                x["key"]: x["doc_count"] for x in all_counts[card_field]["buckets"]
            }
            for value_name in card_values:
                if value_name in card_counts:
                    value_str = prepare_value_count(
                        value_name,
                        card_counts[value_name],
                    )
                    # track possible choices to use as values
                    choice_mapping[value_name] = value_str
                    updated_choices.append(value_str)

            # Align prior selections with new choices
            updated_values = []
            for selected_value in card_2_selections[card_name]:
                base_value = get_base_value(selected_value)
                if base_value not in choice_mapping:
                    # Re-add choices which now presumably have 0 counts
                    choice_mapping[base_value] = prepare_value_count(base_value, 0)
                updated_values.append(choice_mapping[base_value])

            update_obj = gr.update(
                choices=updated_choices,
                value=updated_values,
            )
        elif isinstance(card_values, dict):
            # range-slider, maybe other options in the future?
            assert (
                card_values["type"] == "range"
            ), f"Expected range slider for card {card_name}"
            # for range slider, nothing to actually do!
            update_obj = gr.update()
        else:
            raise ValueError(f"Unknown values for card {card_name}")

        card_updates.append(update_obj)

    case_count = temp["data"]["pagination"]["total"]

    return card_updates + [gr.update(value=f"{case_count} Cases")]


def update_active_selections(*selected_filters_per_card):
    choices = []
    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
            for selected_value in selected_filters:
                base_value = get_base_value(selected_value)
                choices.append(f"{card_name.upper()}: {base_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}"
            lo, hi = selected_filters
            if lo != default_values["min"] or hi != default_values["max"]:
                # only add range filter if not default
                lo, hi = int(lo), int(hi)
                choices.append(f"{card_name.upper()}: {lo}-{hi}")
        else:
            raise ValueError(f"Unknown values for card {card_name}")

    return gr.update(choices=choices, value=choices)


def update_cards_from_active(current_selections, *selected_filters_per_card):
    # active selector uses a flattened list so re-agg values under card groups
    grouped_selections = defaultdict(set)
    for k_v in current_selections:
        idx = k_v.find(": ")
        k, v = k_v[:idx], k_v[idx + 2 :]
        grouped_selections[k].add(v)

    card_updates = []
    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
            updated_values = []
            for selected_value in selected_filters:
                base_value = get_base_value(selected_value)
                if base_value in grouped_selections[card_name.upper()]:
                    updated_values.append(selected_value)
            update_obj = gr.update(value=updated_values)
        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}"
            # the active selector cannot change range values
            # so if present as an active selection, no action is needed
            # otherwise, reset entire range selector
            if card_name.upper() in grouped_selections:
                update_obj = gr.update()
            else:
                update_obj = gr.update(
                    value=(
                        default_values["min"],
                        default_values["max"],
                    )
                )
        else:
            raise ValueError(f"Unknown values for card {card_name}")

        card_updates.append(update_obj)

    # also remove unselected value as possible choice
    active_selection_update = gr.update(choices=current_selections)
    return [active_selection_update] + card_updates


def prepare_value_count(value, count):
    return f"{value} [{count}]"


def get_base_value(value):
    if " [" in value:
        value = value[: value.rfind(" [")]
    return value


# Tab selection helper
def set_active_tab(selected_tab):
    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


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=1, min_width=250):
            gr.Examples(
                examples=EXAMPLE_INPUTS,
                inputs=text_input,
            )
        with gr.Column(scale=4):
            json_output = gr.Code(
                label="Cohort Filter JSON",
                value=json.dumps({"op": "and", "content": []}, indent=4),
                language="json",
                interactive=False,
                show_label=True,
                container=True,
                elem_id="json-output",
            )

    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():
        gr.Markdown(
            "The generated cohort filter will autopopulate into the filter cards below. "
            "**GDC Cohort Copilot can make mistakes!** "
            "Refine your search using the interactive checkboxes. "
            "Note that many other options can be found by selecting the different tabs on the left."
        )

    with gr.Row():
        # Tab selectors
        tab_buttons = []
        with gr.Column(scale=1, min_width=250):
            for name in TAB_NAMES:
                tab_button = gr.Button(
                    value=name,
                    variant="primary" if 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)

    # Assign tab buttons to toggle 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,
        )

    # Enable case download
    case_download.click(
        fn=None,  # apparently this isn't the same as not specifying it
        js=DOWNLOAD_CASES_JS,
        inputs=json_output,
        api_name=False,
    )

    # Load initial counts on startup
    demo.load(
        fn=update_cards_with_counts,
        inputs=[gr.State("")] + filter_cards,
        outputs=filter_cards + [case_counter],
        api_name=False,
    )

    # Update checkboxes on filter generation
    # Also update JSON based on checkboxes
    # - relying on checkbox update to do this fires multiple times
    # - also propagates new model selections after json is updated
    # Also this way it shows the model generated JSON
    text_input.submit(
        fn=process_query,
        inputs=text_input,
        outputs=filter_cards + [json_output],
        api_name=False,
    ).success(
        fn=update_active_selections,
        inputs=filter_cards,
        outputs=[active_selections],
        api_name=False,
    )

    # Update JSON based on cards
    # Keep user `input` event listener (vs `change`) otherwise will fire multiple times
    # Seems like otherwise it should be cyclical, Gradio must have some logic to prevent infinite loops
    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,
            ).success(
                fn=update_active_selections,
                inputs=filter_cards,
                outputs=[active_selections],
                api_name=False,
            )
        else:
            filter_card.input(
                fn=update_json_from_cards,
                inputs=filter_cards,
                outputs=json_output,
                api_name=False,
            ).success(
                fn=update_active_selections,
                inputs=filter_cards,
                outputs=[active_selections],
                api_name=False,
            )

    # Enable functionality of the active filter selectors
    active_selections.input(
        fn=update_cards_from_active,
        inputs=[active_selections] + filter_cards,
        outputs=[active_selections] + filter_cards,
        api_name=False,
    ).success(
        fn=update_json_from_cards,
        inputs=filter_cards,
        outputs=json_output,
        api_name=False,
    )

    # Update checkboxes after executing filter query
    json_output.change(
        fn=update_cards_with_counts,
        inputs=[json_output] + filter_cards,
        outputs=filter_cards + [case_counter],
        api_name=False,
    )

    # gr.api(generate_filter, api_name="generate_filter")

if __name__ == "__main__":
    demo.launch(ssr_mode=False)