port cohort builder clone to gradio

.gitignore

@@ -0,0 +1,3 @@
+__pycache__
+dev.*
+

README.md

@@ -1,6 +1,6 @@
 ---
 title: GDC Cohort Copilot
-emoji: 🏆
+emoji: 🧬
 colorFrom: green
 colorTo: indigo
 sdk: gradio

app.py

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+import json
+
+import gradio as gr
+import requests
+import spaces
+import yaml
+from guidance import json as gen_json
+from guidance.models import Transformers
+from schema import GDCCohortSchema
+from transformers import AutoTokenizer, GPT2LMHeadModel, set_seed
+
+GDC_CASES_API_ENDPOINT = "https://api.gdc.cancer.gov/cases"
+MODEL_NAME = "/opt/gpudata/gdc-cohort-data/models/gpt2-1m"
+TOKENIZER_NAME = "openai-community/gpt2"
+
+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"]
+}
+
+tok = AutoTokenizer.from_pretrained(TOKENIZER_NAME)
+model = GPT2LMHeadModel.from_pretrained(MODEL_NAME)
+model = model.to("cuda")
+model = model.eval()
+
+
+# Generate cohort filter JSON from free text
+@spaces.GPU(duration=15)
+def generate_filter(query):
+    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)
+
+    # DUMMY FILTER
+    # cohort_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"]}}]})
+    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)
+
+    # Map filter selections to checkboxes
+    generated_field_2_values = {
+        op["content"]["field"]: op["content"]["value"]
+        for op in cohort_filter["content"]
+    }
+    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
+        updated_values = []
+        updated_choices = CARD_2_VALUES[card_name]  # 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
+        card_updates.append(
+            gr.update(
+                choices=updated_choices,
+                value=updated_values,  # will override existing selections
+            ),
+        )
+    # TODO generated_field_2_values will have remaining, unmatched fields or values
+    return card_updates + [gr.update(value=cohort_filter_str)]
+
+
+# Update JSON based on checkbox selections
+def update_json_from_checkboxes(*selected_filters_per_card):
+    ops = []
+    for card_name, selected_filters in zip(CARD_NAMES, selected_filters_per_card):
+        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)
+            card_field = CARD_2_FIELD[card_name]
+            content = {
+                "field": card_field,
+                "value": base_values,
+            }
+            op = {
+                "op": "in",
+                "content": content,
+            }
+            ops.append(op)
+    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 get_bin_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": ",".join([x.replace("cases.", "") for x in CARD_FIELDS]),
+        "pretty": "false",
+        "format": "JSON",
+        "size": 0,
+    }
+
+    if cohort_filter:
+        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}")
+    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.", "")
+        choice_mapping = {}
+        updated_choices = []
+        card_counts = {
+            x["key"]: x["doc_count"] for x in all_counts[card_field]["buckets"]
+        }
+        for value_name in CARD_2_VALUES[card_name]:
+            if value_name in card_counts:
+                value_str = prepare_value_count(value_name, card_counts[value_name])
+                choice_mapping[value_name] = (
+                    value_str  # track possible choices to use as values
+                )
+                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])
+
+        card_updates.append(
+            gr.update(
+                choices=updated_choices,
+                value=updated_values,
+            ),
+        )
+
+    case_count = temp["data"]["pagination"]["total"]
+
+    return card_updates + [gr.update(value=f"Case Count: {case_count}")]
+
+
+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 = 'Download Cases';
+        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:",
+                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="Download Cases",
+                min_width=150,
+                elem_id="download-btn",
+            )
+
+    with gr.Row(equal_height=True):
+        with gr.Column(scale=1, min_width=250):
+            gr.Examples(
+                examples=[
+                    "bam files for TCGA-BRCA",
+                    "kidney or adrenal gland cancers with alcohol history",
+                    "tumor samples from male patients acute myeloid lymphoma",
+                ],
+                inputs=text_input,
+            )
+        with gr.Column(scale=4):
+            json_output = gr.Textbox(
+                label="Cohort Filter JSON",
+                info="Use the button in the top right corner to copy the cohort filter JSON.",
+                value=json.dumps({"op": "and", "content": []}, indent=4),
+                interactive=False,
+                show_copy_button=True,
+                show_label=True,
+                container=True,
+                lines=5,
+                elem_id="json-output",
+            )
+
+    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"]:
+                        filter_card = gr.CheckboxGroup(
+                            choices=[],
+                            label=card["name"],
+                            interactive=True,
+                            elem_classes=["filter-card"],
+                        )
+                        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,
+        )
+
+    # 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,
+    )
+
+    # Load initial counts on startup
+    demo.load(
+        fn=get_bin_counts,
+        inputs=[gr.State("")] + filter_cards,
+        outputs=filter_cards + [case_counter],
+    )
+
+    # Update checkboxes on filter generation
+    # Also update JSON based on checkboxes (relying on checkbox update to do this fires multiple times)
+    # Also this way it shows the model generated JSON
+    text_input.submit(
+        fn=process_query,
+        inputs=text_input,
+        outputs=filter_cards + [json_output],
+    )
+
+    # Update JSON based on checkboxes
+    # Keep checkboxes to user input otherwise will fire multiple times
+    # Seems like it should be cyclical, Gradio must have some logic to prevent infinite loops
+    for filter_card in filter_cards:
+        filter_card.input(
+            fn=update_json_from_checkboxes,
+            inputs=filter_cards,
+            outputs=json_output,
+        )
+
+    # Update checkboxes after executing filter query
+    json_output.change(
+        fn=get_bin_counts,
+        inputs=[json_output] + filter_cards,
+        outputs=filter_cards + [case_counter],
+    )
+
+if __name__ == "__main__":
+    demo.launch()

config.yaml

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+tabs:
+- name: General
+  cards:
+  - name: Program
+    field: cases.project.program.name
+    values:
+    - APOLLO
+    - BEATAML1.0
+    - CDDP EAGLE
+    - CGCI
+    - CMI
+    - CPTAC
+    - CTSP
+    - EXCEPTIONAL RESPONDERS
+    - FM
+    - HCMI
+    - MATCH
+    - MMRF
+    - MP2PRT
+    - NCICCR
+    - OHSU
+    - ORGANOID
+    - REBC
+    - TARGET
+    - TCGA
+    - TRIO
+    - VAREPOP
+    - WCDT
+  - name: Project
+    field: cases.project.project_id
+    values:
+    - APOLLO-LUAD
+    - BEATAML1.0-COHORT
+    - BEATAML1.0-CRENOLANIB
+    - CDDP EAGLE-1
+    - CGCI-BLGSP
+    - CGCI-HTMCP-CC
+    - CGCI-HTMCP-DLBCL
+    - CGCI-HTMCP-LC
+    - CMI-ASC
+    - CMI-MBC
+    - CMI-MPC
+    - CPTAC-2
+    - CPTAC-3
+    - CTSP-DLBCL1
+    - EXCEPTIONAL RESPONDERS-ER
+    - FM-AD
+    - HCMI-CMDC
+    - MATCH-B
+    - MATCH-C1
+    - MATCH-H
+    - MATCH-I
+    - MATCH-N
+    - MATCH-P
+    - MATCH-Q
+    - MATCH-R
+    - MATCH-S1
+    - MATCH-S2
+    - MATCH-U
+    - MATCH-W
+    - MATCH-Y
+    - MATCH-Z1A
+    - MATCH-Z1B
+    - MATCH-Z1D
+    - MATCH-Z1I
+    - MMRF-COMMPASS
+    - MP2PRT-ALL
+    - MP2PRT-WT
+    - NCICCR-DLBCL
+    - OHSU-CNL
+    - ORGANOID-PANCREATIC
+    - REBC-THYR
+    - TARGET-ALL-P1
+    - TARGET-ALL-P2
+    - TARGET-ALL-P3
+    - TARGET-AML
+    - TARGET-CCSK
+    - TARGET-NBL
+    - TARGET-OS
+    - TARGET-RT
+    - TARGET-WT
+    - TCGA-ACC
+    - TCGA-BLCA
+    - TCGA-BRCA
+    - TCGA-CESC
+    - TCGA-CHOL
+    - TCGA-COAD
+    - TCGA-DLBC
+    - TCGA-ESCA
+    - TCGA-GBM
+    - TCGA-HNSC
+    - TCGA-KICH
+    - TCGA-KIRC
+    - TCGA-KIRP
+    - TCGA-LAML
+    - TCGA-LGG
+    - TCGA-LIHC
+    - TCGA-LUAD
+    - TCGA-LUSC
+    - TCGA-MESO
+    - TCGA-OV
+    - TCGA-PAAD
+    - TCGA-PCPG
+    - TCGA-PRAD
+    - TCGA-READ
+    - TCGA-SARC
+    - TCGA-SKCM
+    - TCGA-STAD
+    - TCGA-TGCT
+    - TCGA-THCA
+    - TCGA-THYM
+    - TCGA-UCEC
+    - TCGA-UCS
+    - TCGA-UVM
+    - TRIO-CRU
+    - VAREPOP-APOLLO
+    - WCDT-MCRPC
+  - name: Disease Type
+    field: cases.disease_type
+    values:
+    - acinar cell neoplasms
+    - acute lymphoblastic leukemia
+    - adenomas and adenocarcinomas
+    - adnexal and skin appendage neoplasms
+    - basal cell neoplasms
+    - blood vessel tumors
+    - chronic myeloproliferative disorders
+    - complex epithelial neoplasms
+    - complex mixed and stromal neoplasms
+    - cystic, mucinous and serous neoplasms
+    - ductal and lobular neoplasms
+    - epithelial neoplasms, nos
+    - fibroepithelial neoplasms
+    - fibromatous neoplasms
+    - germ cell neoplasms
+    - gliomas
+    - leukemias, nos
+    - lipomatous neoplasms
+    - lymphoid leukemias
+    - mature b-cell lymphomas
+    - mature t- and nk-cell lymphomas
+    - meningiomas
+    - mesothelial neoplasms
+    - miscellaneous bone tumors
+    - miscellaneous tumors
+    - mucoepidermoid neoplasms
+    - myelodysplastic syndromes
+    - myeloid leukemias
+    - myomatous neoplasms
+    - neoplasms, nos
+    - nerve sheath tumors
+    - neuroepitheliomatous neoplasms
+    - nevi and melanomas
+    - not applicable
+    - not reported
+    - osseous and chondromatous neoplasms
+    - paragangliomas and glomus tumors
+    - plasma cell tumors
+    - soft tissue tumors and sarcomas, nos
+    - specialized gonadal neoplasms
+    - squamous cell neoplasms
+    - synovial-like neoplasms
+    - thymic epithelial neoplasms
+    - transitional cell papillomas and carcinomas
+    - unknown
+  - name: Primary Diagnosis
+    field: cases.diagnoses.primary_diagnosis
+    values:
+    - acinar adenocarcinoma
+    - acinar cell carcinoma
+    - acinar cell tumor
+    - acute leukemia, nos
+    - acute lymphoblastic leukemia, nos
+    - acute lymphocytic leukemia
+    - acute monoblastic and monocytic leukemia
+    - acute monocytic leukemia
+    - acute myeloid leukemia with inv(3)(q21q26.2) or t(3;3)(q21;q26.2); rpn1-evi1
+    - acute myeloid leukemia with maturation
+    - acute myeloid leukemia with mutated cebpa
+    - acute myeloid leukemia with mutated npm1
+    - acute myeloid leukemia with myelodysplasia-related changes
+    - acute myeloid leukemia with t(8;21)(q22;q22); runx1-runx1t1
+    - acute myeloid leukemia with t(9;11)(p22;q23); mllt3-mll
+    - acute myeloid leukemia without maturation
+    - acute myeloid leukemia, cbf-beta/myh11
+    - acute myeloid leukemia, minimal differentiation
+    - acute myeloid leukemia, nos
+    - acute myelomonocytic leukemia
+    - acute promyelocytic leukaemia, pml-rar-alpha
+    - acute promyelocytic leukaemia, t(15;17)(q22;q11-12)
+    - adenocarcinoma in tubulovillous adenoma
+    - adenocarcinoma with mixed subtypes
+    - adenocarcinoma, diffuse type
+    - adenocarcinoma, endocervical type
+    - adenocarcinoma, intestinal type
+    - adenocarcinoma, metastatic, nos
+    - adenocarcinoma, nos
+    - adenoid cystic carcinoma
+    - adenosquamous carcinoma
+    - adnexal carcinoma
+    - adrenal cortical carcinoma
+    - amelanotic melanoma
+    - angiosarcoma
+    - astrocytoma, anaplastic
+    - astrocytoma, nos
+    - atypical carcinoid tumor
+    - atypical chronic myeloid leukemia, bcr/abl negative
+    - basal cell carcinoma, nos
+    - basaloid squamous cell carcinoma
+    - bronchio-alveolar carcinoma, mucinous
+    - bronchiolo-alveolar carcinoma, non-mucinous
+    - burkitt lymphoma, nos (includes all variants)
+    - burkitt-like lymphoma
+    - carcinoid tumor, nos
+    - carcinoma in situ, nos
+    - carcinoma, anaplastic, nos
+    - carcinoma, diffuse type
+    - carcinoma, nos
+    - carcinoma, undifferentiated, nos
+    - carcinosarcoma, nos
+    - cholangiocarcinoma
+    - chordoma, nos
+    - chronic myelomonocytic leukemia, nos
+    - chronic neutrophilic leukemia
+    - clear cell adenocarcinoma, nos
+    - clear cell carcinoma
+    - clear cell sarcoma of kidney
+    - collecting duct carcinoma
+    - combined hepatocellular carcinoma and cholangiocarcinoma
+    - combined small cell carcinoma
+    - common precursor b all
+    - dedifferentiated liposarcoma
+    - diffuse large b-cell lymphoma, nos
+    - duct adenocarcinoma, nos
+    - duct carcinoma, nos
+    - ductal carcinoma in situ, nos
+    - embryonal carcinoma, nos
+    - endometrioid adenocarcinoma, nos
+    - ependymoma, nos
+    - epithelial tumor, malignant
+    - epithelioid cell melanoma
+    - epithelioid mesothelioma, malignant
+    - esthesioneuroblastoma
+    - extra-adrenal paraganglioma, malignant
+    - extra-adrenal paraganglioma, nos
+    - fibromyxosarcoma
+    - follicular carcinoma, nos
+    - ganglioneuroblastoma
+    - gastrointestinal stromal tumor, nos
+    - germ cell tumor, nos
+    - glioblastoma
+    - glioblastoma multiforme
+    - glioma, malignant
+    - granulosa cell tumor, nos
+    - hepatocellular carcinoma, clear cell type
+    - hepatocellular carcinoma, fibrolamellar
+    - hepatocellular carcinoma, nos
+    - hodgkin lymphoma, nos
+    - infiltrating duct and lobular carcinoma
+    - infiltrating duct carcinoma, nos
+    - infiltrating duct mixed with other types of carcinoma
+    - infiltrating lobular carcinoma, nos
+    - infiltrating lobular mixed with other types of carcinoma
+    - inflammatory carcinoma
+    - intraductal carcinoma, noninfiltrating, nos
+    - invasive mammary carcinoma
+    - invasive micropapillary carcinoma
+    - large cell carcinoma, nos
+    - large cell neuroendocrine carcinoma
+    - leiomyosarcoma, nos
+    - leukemia, nos
+    - lobular carcinoma, nos
+    - malignant fibrous histiocytoma
+    - malignant lymphoma, non-hodgkin, nos
+    - malignant melanoma, nos
+    - malignant peripheral nerve sheath tumor
+    - malignant rhabdoid tumor
+    - medullary carcinoma, nos
+    - medulloblastoma, nos
+    - melanoma, nos
+    - meningioma, nos
+    - merkel cell carcinoma
+    - mesothelioma, biphasic, malignant
+    - mesothelioma, malignant
+    - mesothelioma, nos
+    - metaplastic carcinoma, nos
+    - mixed epithelioid and spindle cell melanoma
+    - mixed germ cell tumor
+    - mixed glioma
+    - mucinous adenocarcinoma
+    - mucinous adenocarcinoma, endocervical type
+    - mucinous carcinoma
+    - mucoepidermoid carcinoma
+    - mullerian mixed tumor
+    - multiple myeloma
+    - myelodysplastic syndrome, unclassifiable
+    - myelodysplastic/myeloproliferative neoplasm, unclassifiable
+    - myeloid sarcoma
+    - myloproliferative neoplasm, unclassifiable
+    - myoepithelial carcinoma
+    - myxoid leiomyosarcoma
+    - neoplasm, malignant
+    - neoplasm, nos
+    - nephroblastoma, nos
+    - neuroblastoma, nos
+    - neuroendocrine carcinoma, nos
+    - nodular melanoma
+    - non-small cell carcinoma
+    - not reported
+    - oligodendroglioma, anaplastic
+    - oligodendroglioma, nos
+    - oncocytoma
+    - osteosarcoma, nos
+    - papillary adenocarcinoma, nos
+    - papillary carcinoma, columnar cell
+    - papillary carcinoma, follicular variant
+    - papillary carcinoma, nos
+    - papillary renal cell carcinoma
+    - papillary serous adenocarcinoma
+    - papillary serous cystadenocarcinoma
+    - papillary squamous cell carcinoma
+    - papillary transitional cell carcinoma
+    - papillary transitional cell carcinoma, non-invasive
+    - paraganglioma, nos
+    - pheochromocytoma, malignant
+    - pheochromocytoma, nos
+    - pituitary adenoma, nos
+    - precursor b-cell lymphoblastic leukemia
+    - precursor cell lymphoblastic leukemia, nos
+    - precursor cell lymphoblastic leukemia, not phenotyped
+    - renal cell carcinoma, chromophobe type
+    - renal cell carcinoma, nos
+    - sarcomatoid carcinoma
+    - seminoma, nos
+    - serous adenocarcinoma, nos
+    - serous carcinoma, nos
+    - serous cystadenocarcinoma, nos
+    - serous surface papillary carcinoma
+    - sex cord tumor, nos
+    - signet ring cell carcinoma
+    - small cell carcinoma, nos
+    - solid carcinoma, nos
+    - spindle cell carcinoma, nos
+    - spindle cell melanoma, nos
+    - spindle cell melanoma, type b
+    - squamous cell carcinoma, keratinizing, nos
+    - squamous cell carcinoma, large cell, nonkeratinizing, nos
+    - squamous cell carcinoma, nonkeratinizing, nos
+    - squamous cell carcinoma, nos
+    - superficial spreading melanoma
+    - synovial sarcoma, spindle cell
+    - teratocarcinoma
+    - therapy related myeloid neoplasm
+    - thymic carcinoma, nos
+    - thymoma, nos
+    - thymoma, type a, malignant
+    - thymoma, type ab, malignant
+    - thymoma, type ab, nos
+    - thymoma, type b1, malignant
+    - thymoma, type b2, malignant
+    - thymoma, type b3, malignant
+    - transitional cell carcinoma
+    - tubular adenocarcinoma
+    - tumor, nos
+    - undifferentiated sarcoma
+    - unknown
+    - urothelial carcinoma, nos
+    - wilms tumor
+  - name: Primary Site
+    field: cases.primary_site
+    values:
+    - accessory sinuses
+    - adrenal gland
+    - anus and anal canal
+    - base of tongue
+    - bladder
+    - bones, joints and articular cartilage of limbs
+    - bones, joints and articular cartilage of other and unspecified sites
+    - brain
+    - breast
+    - bronchus and lung
+    - cervix uteri
+    - colon
+    - connective, subcutaneous and other soft tissues
+    - corpus uteri
+    - esophagus
+    - eye and adnexa
+    - floor of mouth
+    - gallbladder
+    - gum
+    - heart, mediastinum, and pleura
+    - hematopoietic and reticuloendothelial systems
+    - hypopharynx
+    - kidney
+    - larynx
+    - lip
+    - liver and intrahepatic bile ducts
+    - lymph nodes
+    - meninges
+    - nasal cavity and middle ear
+    - nasopharynx
+    - not reported
+    - oropharynx
+    - other and ill-defined digestive organs
+    - other and ill-defined sites
+    - other and ill-defined sites in lip, oral cavity and pharynx
+    - other and ill-defined sites within respiratory system and intrathoracic organs
+    - other and unspecified female genital organs
+    - other and unspecified major salivary glands
+    - other and unspecified male genital organs
+    - other and unspecified parts of biliary tract
+    - other and unspecified parts of mouth
+    - other and unspecified parts of tongue
+    - other and unspecified urinary organs
+    - other endocrine glands and related structures
+    - ovary
+    - palate
+    - pancreas
+    - parotid gland
+    - penis
+    - peripheral nerves and autonomic nervous system
+    - prostate gland
+    - rectosigmoid junction
+    - rectum
+    - renal pelvis
+    - retroperitoneum and peritoneum
+    - skin
+    - small intestine
+    - spinal cord, cranial nerves, and other parts of central nervous system
+    - stomach
+    - testis
+    - thymus
+    - thyroid gland
+    - tonsil
+    - trachea
+    - unknown
+    - ureter
+    - uterus, nos
+    - vagina
+    - vulva
+  - name: Tissue or Organ of Origin
+    field: cases.diagnoses.tissue_or_organ_of_origin
+    values:
+    - abdomen, nos
+    - adrenal gland, nos
+    - ampulla of vater
+    - anal canal
+    - anterior floor of mouth
+    - anterior mediastinum
+    - anterior wall of bladder
+    - anus, nos
+    - aortic body and other paraganglia
+    - appendix
+    - ascending colon
+    - autonomic nervous system, nos
+    - base of tongue, nos
+    - biliary tract, nos
+    - bladder neck
+    - bladder, nos
+    - blood
+    - body of pancreas
+    - body of stomach
+    - bone marrow
+    - bone, nos
+    - bones of skull and face and associated joints
+    - border of tongue
+    - brain stem
+    - brain, nos
+    - breast, nos
+    - cardia, nos
+    - carotid body
+    - cecum
+    - cerebellum, nos
+    - cerebrum
+    - cervix uteri
+    - cheek mucosa
+    - choroid
+    - ciliary body
+    - colon, nos
+    - connective, subcutaneous and other soft tissues of abdomen
+    - connective, subcutaneous and other soft tissues of head, face, and neck
+    - connective, subcutaneous and other soft tissues of lower limb and hip
+    - connective, subcutaneous and other soft tissues of pelvis
+    - connective, subcutaneous and other soft tissues of thorax
+    - connective, subcutaneous and other soft tissues of trunk, nos
+    - connective, subcutaneous and other soft tissues of upper limb and shoulder
+    - connective, subcutaneous and other soft tissues, nos
+    - corpus uteri
+    - cortex of adrenal gland
+    - descending colon
+    - dome of bladder
+    - duodenum
+    - endocervix
+    - endocrine gland, nos
+    - endometrium
+    - esophagus, nos
+    - exocervix
+    - external ear
+    - external upper lip
+    - extrahepatic bile duct
+    - eye, nos
+    - eyelid
+    - fallopian tube
+    - female genital tract, nos
+    - floor of mouth, nos
+    - frontal lobe
+    - fundus of stomach
+    - fundus uteri
+    - gallbladder
+    - gastric antrum
+    - gastrointestinal tract, nos
+    - gum, nos
+    - hard palate
+    - head of pancreas
+    - head, face or neck, nos
+    - heart
+    - hematopoietic system, nos
+    - hepatic flexure of colon
+    - hypopharynx, nos
+    - ileum
+    - intestinal tract, nos
+    - intra-abdominal lymph nodes
+    - intrahepatic bile duct
+    - intrathoracic lymph nodes
+    - isthmus uteri
+    - jejunum
+    - kidney, nos
+    - larynx, nos
+    - lateral wall of bladder
+    - lesser curvature of stomach, nos
+    - lip, nos
+    - liver
+    - long bones of lower limb and associated joints
+    - long bones of upper limb, scapula and associated joints
+    - lower gum
+    - lower limb, nos
+    - lower lobe, lung
+    - lower third of esophagus
+    - lower-inner quadrant of breast
+    - lower-outer quadrant of breast
+    - lung, nos
+    - lymph node, nos
+    - lymph nodes of axilla or arm
+    - lymph nodes of head, face and neck
+    - lymph nodes of inguinal region or leg
+    - lymph nodes of multiple regions
+    - main bronchus
+    - major salivary gland, nos
+    - mandible
+    - mediastinum, nos
+    - medulla of adrenal gland
+    - meninges, nos
+    - middle lobe, lung
+    - middle third of esophagus
+    - mouth, nos
+    - myometrium
+    - nasal cavity
+    - nasopharynx, nos
+    - nervous system, nos
+    - not reported
+    - occipital lobe
+    - orbit, nos
+    - oropharynx, nos
+    - other ill-defined sites
+    - ovary
+    - overlapping lesion of brain
+    - overlapping lesion of breast
+    - overlapping lesion of colon
+    - overlapping lesion of eye and adnexa
+    - overlapping lesion of lip, oral cavity and pharynx
+    - overlapping lesion of lung
+    - overlapping lesion of nasopharynx
+    - overlapping lesion of pancreas
+    - overlapping lesion of retroperitoneum and peritoneum
+    - pancreas, nos
+    - parietal lobe
+    - parotid gland
+    - pelvic bones, sacrum, coccyx and associated joints
+    - pelvic lymph nodes
+    - pelvis, nos
+    - penis, nos
+    - peripheral nerves and autonomic nervous system of abdomen
+    - peripheral nerves and autonomic nervous system of head, face, and neck
+    - peripheral nerves and autonomic nervous system of thorax
+    - peripheral nerves and autonomic nervous system of trunk, nos
+    - peripheral nerves and autonomic nervous system of upper limb and shoulder
+    - peritoneum, nos
+    - pharynx, nos
+    - pituitary gland
+    - pleura, nos
+    - posterior mediastinum
+    - posterior wall of bladder
+    - prostate gland
+    - rectosigmoid junction
+    - rectum, nos
+    - renal pelvis
+    - retromolar area
+    - retroperitoneum
+    - rib, sternum, clavicle and associated joints
+    - scrotum, nos
+    - short bones of lower limb and associated joints
+    - sigmoid colon
+    - skin of lower limb and hip
+    - skin of other and unspecified parts of face
+    - skin of scalp and neck
+    - skin of trunk
+    - skin of upper limb and shoulder
+    - skin, nos
+    - small intestine, nos
+    - specified parts of peritoneum
+    - spinal cord
+    - spinal meninges
+    - spleen
+    - splenic flexure of colon
+    - stomach, nos
+    - submandibular gland
+    - supraglottis
+    - tail of pancreas
+    - temporal lobe
+    - testis, nos
+    - thoracic esophagus
+    - thorax, nos
+    - thymus
+    - thyroid gland
+    - tongue, nos
+    - tonsil, nos
+    - trachea
+    - transverse colon
+    - trigone of bladder
+    - unknown
+    - unknown primary site
+    - upper limb, nos
+    - upper lobe, lung
+    - upper third of esophagus
+    - upper-inner quadrant of breast
+    - upper-outer quadrant of breast
+    - ureter
+    - urethra
+    - urinary system, nos
+    - uterus, nos
+    - vagina, nos
+    - vertebral column
+    - vulva, nos
+- name: Demographic
+  cards:
+  - name: Gender
+    field: cases.demographic.gender
+    values:
+    - female
+    - male
+    - not reported
+    - unknown
+    - unspecified
+  - name: Race
+    field: cases.demographic.race
+    values:
+    - american indian or alaska native
+    - asian
+    - black or african american
+    - native hawaiian or other pacific islander
+    - not allowed to collect
+    - not reported
+    - other
+    - unknown
+    - white
+  - name: Ethnicity
+    field: cases.demographic.ethnicity
+    values:
+    - hispanic or latino
+    - not hispanic or latino
+    - not reported
+    - unknown
+  # - name: Age at Diagnosis
+  #   field: cases.diagnoses.age_at_diagnosis
+  #   values:
+  #     type: range+checkboxes
+  #     min: 0
+  #     max: 32872
+  #     units: days
+  #     min_label: From
+  #     max_label: To
+  #     popular:
+  #     - label: "\u2265 18,263 to < 21,915 days"
+  #       min: 18263
+  #       max: 21915
+  #     - label: "\u2265 14,610 to < 18,263 days"
+  #       min: 14610
+  #       max: 18263
+  #     - label: "\u2265 10,958 to < 14,610 days"
+  #       min: 10958
+  #       max: 14610
+  #     - label: "\u2265 7,305 to < 10,958 days"
+  #       min: 7305
+  #       max: 10958
+  #     - label: "\u2265 3,653 to < 7,305 days"
+  #       min: 3653
+  #       max: 7305
+  #     - label: "\u2265 0 to < 3,653 days"
+  #       min: 0
+  #       max: 3653
+  - name: Vital Status
+    field: cases.demographic.vital_status
+    values:
+    - alive
+    - dead
+    - not reported
+    - unknown
+- name: General Diagnosis
+  cards:
+  - name: Ajcc Clinical Stage
+    field: cases.diagnoses.ajcc_clinical_stage
+    values:
+    - not reported
+    - stage 0
+    - stage i
+    - stage ia
+    - stage ia2
+    - stage ib
+    - stage ii
+    - stage iia
+    - stage iib
+    - stage iic
+    - stage iii
+    - stage iiia
+    - stage iiib
+    - stage iiic
+    - stage is
+    - stage iv
+    - stage iva
+    - stage ivb
+    - stage ivc
+    - stage x
+  - name: Ajcc Pathologic Stage
+    field: cases.diagnoses.ajcc_pathologic_stage
+    values:
+    - not reported
+    - stage 0
+    - stage 0a
+    - stage 0is
+    - stage i
+    - stage ia
+    - stage ia1
+    - stage ia2
+    - stage ia3
+    - stage ib
+    - stage ib1
+    - stage ic
+    - stage ii
+    - stage iia
+    - stage iib
+    - stage iic
+    - stage iii
+    - stage iiia
+    - stage iiia2
+    - stage iiib
+    - stage iiic
+    - stage iiic1
+    - stage iiic2
+    - stage is
+    - stage iv
+    - stage iva
+    - stage ivb
+    - stage ivc
+    - stage tis
+    - stage x
+    - unknown
+  - name: Uicc Clinical Stage
+    field: cases.diagnoses.uicc_clinical_stage
+    values:
+    - not reported
+    - stage 0
+    - stage i
+    - stage ia
+    - stage ib
+    - stage iia
+    - stage iib
+    - stage iic
+    - stage iii
+    - stage iiia
+    - stage iiib
+    - stage iiic
+    - stage iv
+    - stage iva
+  - name: Uicc Pathologic Stage
+    field: cases.diagnoses.uicc_pathologic_stage
+    values:
+    - not reported
+    - stage 0
+    - stage i
+    - stage ia
+    - stage ib
+    - stage iia
+    - stage iib
+    - stage iii
+    - stage iiia
+    - stage iiib
+    - stage iiic
+    - stage iv
+    - stage iva
+  - name: Tumor Grade
+    field: cases.diagnoses.tumor_grade
+    values:
+    - g1
+    - g2
+    - g3
+    - g4
+    - gb
+    - gx
+    - high grade
+    - low grade
+    - not reported
+    - unknown
+  - name: Morphology
+    field: cases.diagnoses.morphology
+    values:
+    - 8010/2
+    - 8010/3
+    - 8012/3
+    - 8013/3
+    - 8020/3
+    - 8021/3
+    - 8022/3
+    - 8032/3
+    - 8033/3
+    - 8041/3
+    - 8041/34
+    - 8045/3
+    - 8046/3
+    - 8050/3
+    - 8052/3
+    - 8070/2
+    - 8070/3
+    - 8071/3
+    - 8072/3
+    - 8083/3
+    - 8084/3
+    - 8090/3
+    - 8120/3
+    - 8123/3
+    - 8130/3
+    - 8140/3
+    - 8140/6
+    - 8144/3
+    - 8145/3
+    - 8160/3
+    - 8170/3
+    - 8171/3
+    - 8174/3
+    - 8180/3
+    - 8200/3
+    - 8211/3
+    - 8230/3
+    - 8240/3
+    - 8246/3
+    - 8247/3
+    - 8249/3
+    - 8250/3
+    - 8252/3
+    - 8253/3
+    - 8255/3
+    - 8260/3
+    - 8263/0
+    - 8263/3
+    - 8272/0
+    - 8290/0
+    - 8310/3
+    - 8312/3
+    - 8317/3
+    - 8319/3
+    - 8330/3
+    - 8340/3
+    - 8344/3
+    - 8350/3
+    - 8370/1
+    - 8370/3
+    - 8380/3
+    - 8384/3
+    - 8390/3
+    - 8430/3
+    - 8441/3
+    - 8452/1
+    - 8460/3
+    - 8461/3
+    - 8480/3
+    - 8482/3
+    - 8490/3
+    - 8500/2
+    - 8500/3
+    - 8500/6
+    - 8503/3
+    - 8507/3
+    - 8510/3
+    - 8520/2
+    - 8520/3
+    - 8522/3
+    - 8523/3
+    - 8524/3
+    - 8530/3
+    - 8541/3
+    - 8550/1
+    - 8550/3
+    - 8560/3
+    - 8575/3
+    - 8580/1
+    - 8581/1
+    - 8581/3
+    - 8582/1
+    - 8582/3
+    - 8583/1
+    - 8583/3
+    - 8584/1
+    - 8584/3
+    - 8585/3
+    - 8586/3
+    - 8590/1
+    - 8620/1
+    - 8680/1
+    - 8693/1
+    - 8693/3
+    - 8700/0
+    - 8700/3
+    - 8720/3
+    - 8720/6
+    - 8721/3
+    - 8730/3
+    - 8742/3
+    - 8743/3
+    - 8744/3
+    - 8770/3
+    - 8771/3
+    - 8772/3
+    - 8774/3
+    - 8800/3
+    - 8805/3
+    - 8811/3
+    - 8822/1
+    - 8830/3
+    - 8851/3
+    - 8858/3
+    - 8890/3
+    - 8896/3
+    - 8936/1
+    - 8950/3
+    - 8960/3
+    - 8963/3
+    - 8964/3
+    - 8980/3
+    - 8982/3
+    - 9020/3
+    - 9041/3
+    - 9050/3
+    - 9052/3
+    - 9053/3
+    - 9061/3
+    - 9064/3
+    - 9070/3
+    - 9071/3
+    - 9080/0
+    - 9080/3
+    - 9081/3
+    - 9085/3
+    - 9180/3
+    - 9370/3
+    - 9380/3
+    - 9382/3
+    - 9391/3
+    - 9400/3
+    - 9401/3
+    - 9440/3
+    - 9450/3
+    - 9451/3
+    - 9470/3
+    - 9490/3
+    - 9500/3
+    - 9522/3
+    - 9530/0
+    - 9540/3
+    - 9591/3
+    - 9650/3
+    - 9680/3
+    - 9687/3
+    - 9690/3
+    - 9728/3
+    - 9732/3
+    - 9800/3
+    - 9801/3
+    - 9809/3
+    - 9823/3
+    - 9835/3
+    - 9836/3
+    - 9840/3
+    - 9861/3
+    - 9865/3
+    - 9866/3
+    - 9867/3
+    - 9869/3
+    - 9871/3
+    - 9872/3
+    - 9873/3
+    - 9874/3
+    - 9876/3
+    - 9891/3
+    - 9895/3
+    - 9896/3
+    - 9897/3
+    - 9910/3
+    - 9920/3
+    - 9930/3
+    - 9945/3
+    - 9963/3
+    - 9975/3
+    - 9983/3
+    - 9989/3
+    - not reported
+    - unknown
+  # - name: Year Of Diagnosis
+  #   field: cases.diagnoses.year_of_diagnosis
+  #   values:
+  #     type: range+checkboxes
+  #     min: 1900
+  #     max: 2050
+  #     units: years
+  #     min_label: From
+  #     max_label: To
+  #     popular:
+  #     - label: "\u2265 2020 to < 2030"
+  #       min: 2020
+  #       max: 2030
+  #     - label: "\u2265 2010 to < 2020"
+  #       min: 2010
+  #       max: 2020
+  #     - label: "\u2265 2000 to < 2010"
+  #       min: 2000
+  #       max: 2010
+  #     - label: "\u2265 1990 to < 2000"
+  #       min: 1990
+  #       max: 2000
+  #     - label: "\u2265 1980 to < 1990"
+  #       min: 1980
+  #       max: 1990
+  #     - label: "\u2265 1970 to < 1980"
+  #       min: 1970
+  #       max: 1980
+  - name: Site Of Resection Or Biopsy
+    field: cases.diagnoses.site_of_resection_or_biopsy
+    values:
+    - abdomen, nos
+    - adrenal gland, nos
+    - ampulla of vater
+    - anal canal
+    - anterior mediastinum
+    - anus, nos
+    - aortic body and other paraganglia
+    - appendix
+    - ascending colon
+    - axillary tail of breast
+    - base of tongue, nos
+    - biliary tract, nos
+    - bladder, nos
+    - blood
+    - body of pancreas
+    - body of stomach
+    - bone marrow
+    - bone, nos
+    - bones of skull and face and associated joints
+    - border of tongue
+    - brain stem
+    - brain, nos
+    - breast, nos
+    - cardia, nos
+    - cecum
+    - cerebellum, nos
+    - cerebrum
+    - cervix uteri
+    - cheek mucosa
+    - choroid
+    - ciliary body
+    - colon, nos
+    - connective, subcutaneous and other soft tissues of abdomen
+    - connective, subcutaneous and other soft tissues of head, face, and neck
+    - connective, subcutaneous and other soft tissues of lower limb and hip
+    - connective, subcutaneous and other soft tissues of pelvis
+    - connective, subcutaneous and other soft tissues of thorax
+    - connective, subcutaneous and other soft tissues of trunk, nos
+    - connective, subcutaneous and other soft tissues of upper limb and shoulder
+    - connective, subcutaneous and other soft tissues, nos
+    - corpus uteri
+    - cortex of adrenal gland
+    - descending colon
+    - dome of bladder
+    - duodenum
+    - endometrium
+    - esophagus, nos
+    - external ear
+    - extrahepatic bile duct
+    - eye, nos
+    - fallopian tube
+    - floor of mouth, nos
+    - frontal lobe
+    - fundus uteri
+    - gallbladder
+    - gastric antrum
+    - gastrointestinal tract, nos
+    - glottis
+    - gum, nos
+    - head of pancreas
+    - head, face or neck, nos
+    - heart
+    - hematopoietic system, nos
+    - hepatic flexure of colon
+    - ileum
+    - intra-abdominal lymph nodes
+    - intrathoracic lymph nodes
+    - isthmus uteri
+    - jejunum
+    - kidney, nos
+    - larynx, nos
+    - lateral wall of bladder
+    - lip, nos
+    - liver
+    - long bones of lower limb and associated joints
+    - long bones of upper limb, scapula and associated joints
+    - lower gum
+    - lower lobe, lung
+    - lower third of esophagus
+    - lung, nos
+    - lymph node, nos
+    - lymph nodes of axilla or arm
+    - lymph nodes of head, face and neck
+    - lymph nodes of inguinal region or leg
+    - main bronchus
+    - major salivary gland, nos
+    - mandible
+    - mediastinum, nos
+    - medulla of adrenal gland
+    - middle lobe, lung
+    - middle third of esophagus
+    - mouth, nos
+    - myometrium
+    - nasal cavity
+    - nervous system, nos
+    - not reported
+    - occipital lobe
+    - orbit, nos
+    - oropharynx, nos
+    - other ill-defined sites
+    - ovary
+    - overlapping lesion of bladder
+    - overlapping lesion of colon
+    - overlapping lesion of connective, subcutaneous and other soft tissues
+    - overlapping lesion of digestive system
+    - overlapping lesion of eye and adnexa
+    - overlapping lesion of female genital organs
+    - overlapping lesion of ill-defined sites
+    - overlapping lesion of lip, oral cavity and pharynx
+    - overlapping lesion of rectum, anus and anal canal
+    - pancreas, nos
+    - pancreatic duct
+    - pancreatic neck
+    - parietal lobe
+    - parotid gland
+    - pelvic bones, sacrum, coccyx and associated joints
+    - pelvic lymph nodes
+    - pelvis, nos
+    - penis, nos
+    - peripheral nerves and autonomic nervous system of upper limb and shoulder
+    - peritoneum, nos
+    - pituitary gland
+    - pleura, nos
+    - prostate gland
+    - rectosigmoid junction
+    - rectum, nos
+    - retroperitoneum
+    - short bones of lower limb and associated joints
+    - sigmoid colon
+    - skin of lower limb and hip
+    - skin of other and unspecified parts of face
+    - skin of scalp and neck
+    - skin of trunk
+    - skin of upper limb and shoulder
+    - skin, nos
+    - small intestine, nos
+    - specified parts of peritoneum
+    - spermatic cord
+    - spinal cord
+    - spinal meninges
+    - spleen
+    - splenic flexure of colon
+    - stomach, nos
+    - submandibular gland
+    - tail of pancreas
+    - temporal lobe
+    - testis, nos
+    - thorax, nos
+    - thymus
+    - thyroid gland
+    - tongue, nos
+    - tonsil, nos
+    - trachea
+    - transverse colon
+    - unknown
+    - unknown primary site
+    - upper lobe, lung
+    - ureter
+    - urethra
+    - uterine adnexa
+    - uterus, nos
+    - vagina, nos
+    - vertebral column
+    - vestibule of mouth
+    - vulva, nos
+  - name: Sites Of Involvement
+    field: cases.diagnoses.sites_of_involvement
+    values:
+    - abdomen
+    - abdominal peritoneum
+    - adnexa
+    - adrenal gland, nos
+    - anus, nos
+    - appendix
+    - ascites
+    - bladder, nos
+    - bone marrow
+    - bone, nos
+    - brain, brain stem
+    - brain, cerebellum, nos
+    - brain, cerebrum
+    - brain, frontal lobe
+    - brain, nos
+    - brain, occipital lobe
+    - brain, parietal
+    - brain, temporal lobe
+    - breast, left lower inner
+    - breast, left lower outer
+    - breast, left upper inner
+    - breast, left upper outer
+    - breast, nos
+    - breast, right lower inner
+    - breast, right lower outer
+    - breast, right upper inner
+    - breast, right upper outer
+    - bronchus
+    - central lung
+    - central nervous system
+    - cerebrospinal fluid
+    - cervix
+    - chest wall
+    - colon, nos
+    - common or superficial femoral vein
+    - diaphragm
+    - distant nodes
+    - ear
+    - epididymis
+    - esophagus, lower third
+    - esophagus, middle third
+    - esophagus, nos
+    - esophagus, upper third
+    - eye
+    - eye, choroid
+    - eye, ciliary body
+    - eye, iris
+    - fallopian tube, left
+    - fallopian tube, nos
+    - fallopian tube, right
+    - gallbladder
+    - gastrointestinal tract
+    - great blood vessel
+    - groin
+    - heart
+    - hilar fat
+    - inferior vena cava
+    - kidney, nos
+    - kidney, upper pole
+    - liver
+    - lung, nos
+    - lymph node, axillary
+    - lymph node, cervical
+    - lymph node, femoral
+    - lymph node, hilar
+    - lymph node, iliac-common
+    - lymph node, iliac-external
+    - lymph node, inguinal
+    - lymph node, mediastinal
+    - lymph node, mesenteric
+    - lymph node, nos
+    - lymph node, para-aortic
+    - lymph node, regional
+    - lymph node, retroperitoneal
+    - lymph node, splenic
+    - lymph node, subcarinal
+    - lymph node, submandibular
+    - lymph node, supraclavicular
+    - mandible
+    - maxilla
+    - mediastinal soft tissue
+    - mesentery
+    - mouth
+    - nasopharynx
+    - neck
+    - not reported
+    - ocular orbits
+    - omentum
+    - oropharynx
+    - other
+    - ovary, left
+    - ovary, nos
+    - ovary, right
+    - pancreas body
+    - pancreas head
+    - pancreas tail
+    - pancreas, nos
+    - parametrium, left
+    - parametrium, right
+    - parotid gland
+    - pelvic lymph node(s)
+    - pelvic peritoneum
+    - pelvic vein, common, external or iliac
+    - pelvis
+    - peri-aortic lymph node(s)
+    - peri-orbital soft tissue
+    - pericardium
+    - perineum
+    - peripheral blood
+    - peripheral lung
+    - peripheral nervous system
+    - peritoneum, nos
+    - pleura
+    - prostate
+    - rectum
+    - renal vein
+    - rete testis
+    - retroperitoneum
+    - scalp
+    - sigmoid colon
+    - sinus
+    - skin
+    - skin, extremities
+    - skin, groin
+    - skin, head and neck
+    - skin, trunk
+    - small intestine
+    - soft tissue
+    - spermatic cord
+    - spleen
+    - stomach
+    - testes
+    - thyroid
+    - tongue
+    - tonsil
+    - transplanted kidney
+    - transverse colon
+    - tunica albuginea
+    - tunica vaginalis
+    - unknown
+    - uterus
+    - vagina
+    - vertebrae
+    - vulva, nos
+  - name: Laterality
+    field: cases.diagnoses.laterality
+    values:
+    - bilateral
+    - left
+    - midline
+    - not reported
+    - right
+    - unknown
+- name: Disease Status and History
+  cards:
+  - name: Prior Malignancy
+    field: cases.diagnoses.prior_malignancy
+    values:
+    - 'no'
+    - not reported
+    - unknown
+    - 'yes'
+  - name: Prior Treatment
+    field: cases.diagnoses.prior_treatment
+    values:
+    - 'no'
+    - not reported
+    - unknown
+    - 'yes'
+  - name: Synchronous Malignancy
+    field: cases.diagnoses.synchronous_malignancy
+    values:
+    - 'no'
+    - not reported
+    - unknown
+    - 'yes'
+  - name: Progression Or Recurrence
+    field: cases.diagnoses.progression_or_recurrence
+    values:
+    - 'no'
+    - not reported
+    - unknown
+    - 'yes'
+  - name: Residual Disease
+    field: cases.diagnoses.residual_disease
+    values:
+    - not reported
+    - r0
+    - r1
+    - r2
+    - rx
+    - unknown
+  - name: Child Pugh Classification
+    field: cases.diagnoses.child_pugh_classification
+    values:
+    - a
+    - b
+    - c
+    - unknown
+  - name: Ishak Fibrosis Score
+    field: cases.diagnoses.ishak_fibrosis_score
+    values:
+    - 0 - no fibrosis
+    - 1,2 - portal fibrosis
+    - 3,4 - fibrous septa
+    - 5 - nodular formation and incomplete cirrhosis
+    - 6 - established cirrhosis
+    - unknown
+- name: Disease Specific Classifications
+  cards:
+  - name: Ann Arbor Clinical Stage
+    field: cases.diagnoses.ann_arbor_clinical_stage
+    values:
+    - not reported
+    - stage i
+    - stage ii
+    - stage iii
+    - stage iv
+    - unknown
+  - name: Ann Arbor Pathologic Stage
+    field: cases.diagnoses.ann_arbor_pathologic_stage
+    values:
+    - not reported
+    - stage i
+    - stage ii
+    - stage iii
+    - stage iv
+  - name: Cog Renal Stage
+    field: cases.diagnoses.cog_renal_stage
+    values:
+    - stage i
+    - stage ii
+    - stage iii
+    - stage iv
+  - name: Figo Stage
+    field: cases.diagnoses.figo_stage
+    values:
+    - not reported
+    - stage i
+    - stage ia
+    - stage ia1
+    - stage ia2
+    - stage ib
+    - stage ib1
+    - stage ib2
+    - stage ic
+    - stage ic2
+    - stage ii
+    - stage iia
+    - stage iia1
+    - stage iia2
+    - stage iib
+    - stage iic
+    - stage iii
+    - stage iiia
+    - stage iiib
+    - stage iiic
+    - stage iiic1
+    - stage iiic2
+    - stage iv
+    - stage iva
+    - stage ivb
+  - name: Igcccg Stage
+    field: cases.diagnoses.igcccg_stage
+    values:
+    - good prognosis
+    - intermediate prognosis
+    - poor prognosis
+  - name: Inss Stage
+    field: cases.diagnoses.inss_stage
+    values:
+    - stage 1
+    - stage 2a
+    - stage 2b
+    - stage 3
+    - stage 4
+    - stage 4s
+    - unknown
+  - name: Iss Stage
+    field: cases.diagnoses.iss_stage
+    values:
+    - i
+    - ii
+    - iii
+    - unknown
+  - name: Masaoka Stage
+    field: cases.diagnoses.masaoka_stage
+    values:
+    - stage i
+    - stage iia
+    - stage iib
+    - stage iii
+    - stage iva
+    - stage ivb
+  - name: Inpc Grade
+    field: cases.diagnoses.inpc_grade
+    values:
+    - differentiating
+    - poorly differentiated
+    - undifferentiated or poorly differentiated
+    - unknown
+  - name: Who Cns Grade
+    field: cases.diagnoses.who_cns_grade
+    values:
+    - grade iv
+  - name: Cog Neuroblastoma Risk Group
+    field: cases.diagnoses.cog_neuroblastoma_risk_group
+    values:
+    - high risk
+    - intermediate risk
+    - low risk
+  - name: Cog Rhabdomyosarcoma Risk Group
+    field: cases.diagnoses.cog_rhabdomyosarcoma_risk_group
+    values:
+    - high risk
+  - name: Eln Risk Classification
+    field: cases.diagnoses.eln_risk_classification
+    values:
+    - adverse
+    - favorable
+    - intermediate
+    - not reported
+    - unknown
+  - name: International Prognostic Index
+    field: cases.diagnoses.international_prognostic_index
+    values:
+    - high risk
+    - high-intermediate risk
+    - low risk
+    - low-intermediate risk
+  - name: Wilms Tumor Histologic Subtype
+    field: cases.diagnoses.wilms_tumor_histologic_subtype
+    values:
+    - favorable
+    - unfavorable
+  - name: Weiss Assessment Score
+    field: cases.diagnoses.weiss_assessment_score
+    values:
+    - 2
+    - 3
+    - 4
+    - 5
+    - 6
+    - 7
+    - 8
+    - 9
+- name: Treatment
+  cards:
+  - name: Best Overall Response
+    field: cases.diagnoses.best_overall_response
+    values:
+    - cr-complete response
+    - cru-complete response unconfirmed
+    - nr-no response
+    - pr-partial response
+  - name: Therapeutic Agents
+    field: cases.diagnoses.treatments.therapeutic_agents
+    values:
+    - abiraterone
+    - ae37 peptide/gm-csf vaccine
+    - afatinib
+    - afatinib dimaleate
+    - aldesleukin
+    - altretamine
+    - amifostine
+    - aminocamptothecin
+    - anastrozole
+    - antineoplastic vaccine
+    - arsenic trioxide
+    - asparaginase
+    - axitinib
+    - azathioprine
+    - banoxantrone
+    - bcg solution
+    - bendamustine
+    - bevacizumab
+    - bicalutamide
+    - bleomycin
+    - bortezomib
+    - braf inhibitor
+    - cabazitaxel
+    - cabozantinib
+    - cabozantinib s-malate
+    - capecitabine
+    - carboplatin
+    - carfilzomib
+    - carmustine
+    - carmustine implant
+    - cediranib
+    - celecoxib
+    - cetuximab
+    - cilengitide
+    - cintredekin besudotox
+    - cisplatin
+    - clinical trial
+    - clinical trial agent
+    - clodronate disodium
+    - cositecan
+    - cyclophosphamide
+    - cytarabine
+    - dabrafenib
+    - dacarbazine
+    - dactinomycin
+    - daratumumab
+    - dasatinib
+    - daunorubicin
+    - degarelix
+    - dendritic cell vaccine
+    - denosumab
+    - dexamethasone
+    - didox
+    - docetaxel
+    - doxifluridine
+    - doxorubicin
+    - doxorubicin hydrochloride
+    - elotuzumab
+    - epirubicin
+    - epirubicin hydrochloride
+    - erlotinib
+    - erlotinib hydrochloride
+    - etoposide
+    - everolimus
+    - exemestane
+    - filgrastim
+    - floxuridine
+    - fluorouracil
+    - fotemustine
+    - fulvestrant
+    - gefitinib
+    - gemcitabine
+    - gemcitabine hydrochloride
+    - gemtuzumab ozogamicin
+    - gonadotropin-releasing hormone analog
+    - goserelin
+    - goserelin acetate
+    - gossypol
+    - halichondrin b
+    - hormone therapy
+    - hpph
+    - hydroxyurea
+    - ifosfamide
+    - imatinib
+    - imatinib mesylate
+    - iniparib
+    - interferon
+    - interferon alfa-2b
+    - iodine i 131 monoclonal antibody 81c6
+    - ipilimumab
+    - irinotecan
+    - irinotecan hydrochloride
+    - irofulven
+    - isotretinoin
+    - ixabepilone
+    - ixazomib
+    - ketoconazole
+    - lapatinib
+    - lenalidomide
+    - letrozole
+    - leucovorin
+    - leucovorin calcium
+    - leuprolide
+    - leuprolide acetate
+    - levetiracetam
+    - levothyroxine
+    - levothyroxine sodium
+    - liothyronine sodium
+    - lomustine
+    - lonafarnib
+    - mage-a3 peptide vaccine
+    - megestrol acetate
+    - melphalan
+    - mercaptopurine
+    - mesna
+    - methotrexate
+    - methylprednisolone
+    - mitomycin
+    - mitotane
+    - mitoxantrone
+    - mivobulin isethionate
+    - monoclonal antibody 81c6
+    - motesanib diphosphate
+    - motexafin gadolinium
+    - nab-paclitaxel
+    - nelipepimut-s
+    - nivolumab
+    - not otherwise specified
+    - not reported
+    - o6-benzylguanine
+    - oregovomab
+    - other
+    - oxaliplatin
+    - oxcarbazepine
+    - paclitaxel
+    - paclitaxel poliglumex
+    - palonosetron hydrochloride
+    - pamidronate disodium
+    - panitumumab
+    - panobinostat
+    - patupilone
+    - pazopanib
+    - pazopanib hydrochloride
+    - pegfilgrastim
+    - peginterferon alfa-2b
+    - pegylated liposomal doxorubicin hydrochloride
+    - pembrolizumab
+    - pemetrexed
+    - pemetrexed disodium
+    - pep-3-klh conjugate vaccine
+    - platinum
+    - polysaccharide-k
+    - pomalidomide
+    - porfimer sodium
+    - prednisone
+    - procarbazine
+    - ramucirumab
+    - recombinant interferon alfa
+    - recombinant interferon alfa-2b
+    - recombinant interleukin-12
+    - recombinant interleukin-2
+    - regorafenib
+    - rituximab
+    - sargramostim
+    - selumetinib
+    - sirolimus
+    - sorafenib
+    - sorafenib tosylate
+    - streptozocin
+    - sunitinib
+    - sunitinib malate
+    - tamoxifen
+    - tamoxifen citrate
+    - tegafur-gimeracil-oteracil potassium
+    - temozolomide
+    - temsirolimus
+    - tetrathiomolybdate
+    - thalidomide
+    - thioguanine
+    - tipifarnib
+    - topotecan
+    - topotecan hydrochloride
+    - toremifene citrate
+    - trabectedin
+    - trametinib
+    - trastuzumab
+    - tretinoin
+    - triptorelin
+    - unknown
+    - vandetanib
+    - veliparib
+    - vemurafenib
+    - vinblastine
+    - vincristine
+    - vinorelbine
+    - vinorelbine tartrate
+    - vitespen
+    - vorinostat
+    - ziv-aflibercept
+    - zoledronic acid
+  - name: Treatment Intent Type
+    field: cases.diagnoses.treatments.treatment_intent_type
+    values:
+    - adjuvant
+    - androgen deprivation therapy (adt)
+    - consolidation therapy
+    - cure
+    - first-line therapy
+    - induction
+    - maintenance therapy
+    - neoadjuvant
+    - not reported
+    - palliative
+    - prevention
+    - re-excision
+    - salvage
+    - unknown
+  - name: Treatment Outcome
+    field: cases.diagnoses.treatments.treatment_outcome
+    values:
+    - complete response
+    - no measurable disease
+    - no response
+    - not reported
+    - partial response
+    - persistent disease
+    - progressive disease
+    - stable disease
+    - treatment ongoing
+    - treatment stopped due to toxicity
+    - unknown
+  - name: Treatment Type
+    field: cases.diagnoses.treatments.treatment_type
+    values:
+    - ablation or embolization, nos
+    - ablation, cryo
+    - ablation, ethanol injection
+    - ablation, microwave
+    - ablation, nos
+    - ablation, radiofrequency
+    - ancillary treatment
+    - antiseizure treatment
+    - biopsy, excisional
+    - bisphosphonate therapy
+    - brachytherapy, high dose
+    - brachytherapy, low dose
+    - brachytherapy, nos
+    - chemoembolization
+    - chemotherapy
+    - distal pancreatectomy
+    - external beam radiation
+    - hormone therapy
+    - hysterectomy, nos
+    - i-131 radiation therapy
+    - immunotherapy (including vaccines)
+    - isolated limb perfusion (ilp)
+    - not reported
+    - organ transplantation
+    - peptide receptor radionuclide therapy (prrt)
+    - pharmaceutical therapy, nos
+    - pleurodesis, nos
+    - radiation therapy, nos
+    - radiation, 2d conventional
+    - radiation, 3d conformal
+    - radiation, combination
+    - radiation, cyberknife
+    - radiation, external beam
+    - radiation, implants
+    - radiation, intensity-modulated radiotherapy
+    - radiation, internal
+    - radiation, mixed photon beam
+    - radiation, proton beam
+    - radiation, radioisotope
+    - radiation, stereotactic/gamma knife/srs
+    - radiation, systemic
+    - radioembolization
+    - radiosensitizing agent
+    - stem cell transplantation, allogeneic
+    - stem cell transplantation, autologous
+    - stem cell transplantation, nos
+    - stereotactic radiosurgery
+    - steroid therapy
+    - surgery, minimally invasive
+    - surgery, nos
+    - surgery, open
+    - targeted molecular therapy
+    - total pancreatectomy
+    - unknown
+    - whipple
+- name: Exposure
+  cards:
+  - name: Alcohol History
+    field: cases.exposures.alcohol_history
+    values:
+    - 'no'
+    - not reported
+    - unknown
+    - 'yes'
+  - name: Alcohol Intensity
+    field: cases.exposures.alcohol_intensity
+    values:
+    - drinker
+    - heavy drinker
+    - lifelong non-drinker
+    - non-drinker
+    - occasional drinker
+    - social drinker
+    - unknown
+  - name: Tobacco Smoking Status
+    field: cases.exposures.tobacco_smoking_status
+    values:
+    - current reformed smoker for < or = 15 yrs
+    - current reformed smoker for > 15 yrs
+    - current reformed smoker, duration not specified
+    - current smoker
+    - lifelong non-smoker
+    - not reported
+    - smoking history not documented
+    - unknown
+  # - name: Cigarettes Per Day
+  #   field: cases.exposures.cigarettes_per_day
+  #   values:
+  #     type: range
+  #     min: 0
+  #     max: 99999
+  #     unit: days
+  #     min_label: From
+  #     max_label: To
+  # - name: Pack Years Smoked
+  #   field: cases.exposures.pack_years_smoked
+  #   values:
+  #     type: range
+  #     min: 0
+  #     max: 999999
+  #     unit: years
+  #     min_label: From
+  #     max_label: To
+  # - name: Tobacco Smoking Onset Year
+  #   field: cases.exposures.tobacco_smoking_onset_year
+  #   values:
+  #     type: range+checkboxes
+  #     min: 1950
+  #     max: 2050
+  #     min_label: From
+  #     max_label: To
+  #     popular:
+  #     - label: '>= 1970 to < 1980 yrs'
+  #       min: 1970
+  #       max: 1980
+  #     - label: '>= 1960 to < 1970 yrs'
+  #       min: 1960
+  #       max: 1970
+  #     - label: '>= 1950 to < 1960 yrs'
+  #       min: 1950
+  #       max: 1960
+  #     - label: '>= 1940 to < 1950 yrs'
+  #       min: 1940
+  #       max: 1950
+  #     - label: '>= 1930 to < 1940 yrs'
+  #       min: 1930
+  #       max: 1940
+  #     - label: '>= 1920 to < 1930 yrs'
+  #       min: 1920
+  #       max: 1930
+- name: Biospecimen
+  cards:
+  - name: Tissue Type
+    field: cases.samples.tissue_type
+    values:
+    - normal
+    - peritumoral
+    - tumor
+  - name: Biospecimen Anatomic Site
+    field: cases.samples.biospecimen_anatomic_site
+    values:
+    - abdomen
+    - abdominal wall
+    - adrenal
+    - anus
+    - appendix
+    - axilla
+    - back
+    - bladder
+    - blood
+    - bone
+    - bone marrow
+    - brain
+    - breast
+    - bronchus
+    - brow
+    - buccal mucosa
+    - cerebral cortex
+    - cerebrum
+    - cervical spine
+    - cervix
+    - chest
+    - chest wall
+    - chin
+    - colon
+    - esophagus
+    - fallopian tube
+    - forearm
+    - forehead
+    - frontal cortex
+    - frontal lobe
+    - gallbladder
+    - gastrointestinal tract
+    - groin
+    - gum
+    - head & neck
+    - head, face or neck, nos
+    - heart
+    - hepatic flexure
+    - ilium
+    - kidney
+    - large bowel
+    - leg
+    - leptomeninges
+    - liver
+    - lung
+    - lymph node
+    - lymph node(s) axilla
+    - lymph node(s) cervical
+    - lymph node(s) hilar
+    - lymph node(s) iliac-common
+    - lymph node(s) inguinal
+    - lymph node(s) mammary
+    - lymph node(s) mesenteric
+    - lymph node(s) paraaortic
+    - lymph node(s) pelvic
+    - lymph node(s) regional
+    - lymph node(s) retroperitoneal
+    - lymph node(s) splenic
+    - lymph node(s) submandibular
+    - lymph node(s) supraclavicular
+    - lymph nodes(s) mediastinal
+    - mandible
+    - maxilla
+    - mediastinal soft tissue
+    - mediastinum
+    - mesentery
+    - muscle
+    - neck
+    - not reported
+    - occipital cortex
+    - omentum
+    - oral cavity
+    - other
+    - ovary
+    - pancreas
+    - parotid gland
+    - pelvis
+    - peritoneal cavity
+    - peritoneum
+    - pleura
+    - prostate
+    - retroperitoneum
+    - rib
+    - scalp
+    - shoulder
+    - sigmoid colon
+    - sinus
+    - skeletal muscle
+    - skin
+    - skull
+    - small bowel
+    - soft tissue
+    - spinal column
+    - spleen
+    - stomach
+    - temporal cortex
+    - testis
+    - thorax
+    - thyroid
+    - tongue
+    - unknown
+    - uterus
+    - vagina
+    - vein
+    - vulva
+  - name: Specimen Type
+    field: cases.samples.specimen_type
+    values:
+    - 2d modified conditionally reprogrammed cells
+    - 3d air-liquid interface organoid
+    - 3d neurosphere
+    - 3d organoid
+    - adherent cell line
+    - bone marrow components nos
+    - bone marrow nos
+    - buccal cells
+    - buffy coat
+    - cell
+    - derived cell line
+    - fibroblasts from bone marrow
+    - granulocytes
+    - human original cells
+    - lymphocytes
+    - lymphoid
+    - mixed adherent suspension
+    - mononuclear cells from bone marrow
+    - peripheral blood components nos
+    - peripheral blood nos
+    - peripheral whole blood
+    - pleural effusion
+    - saliva
+    - solid tissue
+    - sorted cells
+    - unknown
+    - whole bone marrow
+  - name: Preservation Method
+    field: cases.samples.preservation_method
+    values:
+    - cryopreserved
+    - edta
+    - ffpe
+    - fresh
+    - frozen
+    - oct
+    - snap frozen
+    - unknown
+  - name: Tumor Descriptor
+    field: cases.samples.tumor_descriptor
+    values:
+    - metastatic
+    - new primary
+    - not applicable
+    - not reported
+    - premalignant
+    - primary
+    - recurrence
+    - unknown
+    - xenograft
+  - name: Analyte Type
+    field: cases.samples.portions.analytes.aliquots.analyte_type
+    values:
+    - cfdna
+    - dna
+    - ffpe dna
+    - ffpe rna
+    - nuclei rna
+    - rna
+    - total rna
+- name: Available Data
+  cards:
+  - name: Data Category
+    field: files.data_category
+    values:
+    - biospecimen
+    - clinical
+    - combined nucleotide variation
+    - copy number variation
+    - dna methylation
+    - proteome profiling
+    - sequencing reads
+    - simple nucleotide variation
+    - somatic structural variation
+    - structural variation
+    - transcriptome profiling
+  - name: Data Type
+    field: files.data_type
+    values:
+    - Aggregated Somatic Mutation
+    - Aligned Reads
+    - Allele-specific Copy Number Segment
+    - Annotated Somatic Mutation
+    - Biospecimen Supplement
+    - Clinical Supplement
+    - Copy Number Segment
+    - Differential Gene Expression
+    - Gene Expression Quantification
+    - Gene Level Copy Number
+    - Intermediate Analysis Archive
+    - Isoform Expression Quantification
+    - Masked Copy Number Segment
+    - Masked Intensities
+    - Masked Somatic Mutation
+    - Methylation Beta Value
+    - miRNA Expression Quantification
+    - Pathology Report
+    - Protein Expression Quantification
+    - Raw CGI Variant
+    - Raw Intensities
+    - Raw Simple Somatic Mutation
+    - Simple Germline Variation
+    - Single Cell Analysis
+    - Slide Image
+    - Splice Junction Quantification
+    - Structural Rearrangement
+    - Tissue Microarray Image
+    - Transcript Fusion
+  - name: Experimental Strategy
+    field: files.experimental_strategy
+    values:
+    - ATAC-Seq
+    - Diagnostic Slide
+    - Expression Array
+    - Genotyping Array
+    - Methylation Array
+    - miRNA-Seq
+    - Reverse Phase Protein Array
+    - RNA-Seq
+    - scRNA-Seq
+    - Targeted Sequencing
+    - Tissue Slide
+    - WGS
+    - WXS
+  - name: Workflow Type
+    field: files.analysis.workflow_type
+    values:
+    - ABSOLUTE LiftOver
+    - Aliquot Ensemble Somatic Variant Merging and Masking
+    - Arriba
+    - ASCAT2
+    - ASCAT3
+    - AscatNGS
+    - BCGSC miRNA Profiling
+    - Birdseed
+    - BRASS
+    - BWA
+    - BWA with BQSR
+    - BWA with Mark Duplicates and BQSR
+    - BWA-aln
+    - CaVEMan
+    - CellRanger - 10x Chromium
+    - CellRanger - 10x Filtered Counts
+    - CellRanger - 10x Raw Counts
+    - DNAcopy
+    - FM Simple Somatic Mutation
+    - FoundationOne Annotation
+    - FoundationOne Variant Aggregation and Masking
+    - GATK4 CNV
+    - GATK4 MuTect2
+    - GATK4 MuTect2 Annotation
+    - GATK4 MuTect2 Tumor-Only
+    - GATK4 MuTect2 Tumor-Only Annotation
+    - Manta
+    - MuSE
+    - MuSE Annotation
+    - MuTect2
+    - MuTect2 Annotation
+    - Pindel
+    - Pindel Annotation
+    - SeSAMe Methylation Beta Estimation
+    - Seurat - 10x Chromium
+    - STAR - Counts
+    - STAR 2-Pass Chimeric
+    - STAR 2-Pass Genome
+    - STAR 2-Pass Transcriptome
+    - STAR-Fusion
+    - SvABA
+    - SvABA Indel
+    - SvABA Indel Annotation
+    - Tumor-Only Somatic Variant Merging and Masking
+    - VarScan2
+    - VarScan2 Annotation
+    - VCF LiftOver
+  - name: Data Format
+    field: files.data_format
+    values:
+    - bam
+    - bcr auxiliary xml
+    - bcr biotab
+    - bcr omf xml
+    - bcr pps xml
+    - bcr ssf xml
+    - bcr xml
+    - bedpe
+    - cdc json
+    - cel
+    - hdf5
+    - idat
+    - jpeg 2000
+    - maf
+    - mex
+    - pdf
+    - svs
+    - tar
+    - tsv
+    - txt
+    - vcf
+    - xlsx
+  - name: Platform
+    field: files.platform
+    values:
+    - affymetrix snp 6.0
+    - complete genomics
+    - genechip u133 plus 2.0
+    - genechip u133a
+    - illumina
+    - illumina human methylation 27
+    - illumina human methylation 450
+    - illumina methylation epic
+    - illumina methylation epic v2
+    - rppa
+  - name: Access
+    field: files.access
+    values:
+    - controlled
+    - open

requirements.txt

@@ -0,0 +1,5 @@
+torch==2.5.1
+transformers==4.50.0
+gradio==5.35.0
+guidance==0.2.4
+spaces

schema.py

@@ -0,0 +1,73 @@
+from enum import Enum
+from typing import Annotated, Literal
+
+from pydantic import BaseModel, Field, StringConstraints
+
+
+class InnerOp(Enum):
+    IN = "in"
+    EQ = "="
+    LT = "<"
+    GT = ">"
+    LE = "<="
+    GE = ">="
+
+
+class MiddleOp(Enum):
+    AND = "and"
+
+
+class OuterOp(Enum):
+    AND = "and"
+
+
+class InnerStrContent(BaseModel):
+    field: Annotated[str, StringConstraints(min_length=1, max_length=64)]
+    value: list[Annotated[str, StringConstraints(min_length=1, max_length=128)]]
+
+
+class InnerAgeDxContent(BaseModel):
+    field: Literal["cases.diagnoses.age_at_diagnosis"]
+    value: Annotated[int, Field(ge=0, le=32872)]
+
+
+class InnerYearDxContent(BaseModel):
+    field: Literal["cases.diagnoses.year_of_diagnosis"]
+    value: Annotated[int, Field(ge=1900, le=2050)]
+
+
+class InnerCigDayContent(BaseModel):
+    field: Literal["cases.exposures.cigarettes_per_day"]
+    value: Annotated[int, Field(ge=0, le=999999)]
+
+
+class InnerPackYrContent(BaseModel):
+    field: Literal["cases.exposures.pack_years_smoked"]
+    value: Annotated[int, Field(ge=0, le=999999)]
+
+
+class InnerCigStrtContent(BaseModel):
+    field: Literal["cases.exposures.tobacco_smoking_onset_year"]
+    value: Annotated[int, Field(ge=1900, le=2050)]
+
+
+class Inner(BaseModel):
+    op: InnerOp
+    content: (
+        InnerStrContent
+        | InnerAgeDxContent
+        | InnerYearDxContent
+        | InnerCigDayContent
+        | InnerPackYrContent
+        | InnerCigStrtContent
+    )
+
+
+class Middle(BaseModel):
+    op: MiddleOp
+    content: list[Inner]
+
+
+class GDCCohortSchema(BaseModel):
+    op: OuterOp
+    content: list[Inner | Middle]

style.css

@@ -0,0 +1,105 @@
+:root {
+  --card-min-width: 300px;
+}
+
+#description-input button {
+    background-color: var(--button-primary-background-fill);
+    color: var(--button-primary-text-color);
+    font-weight: var(--button-large-text-weight);
+}
+
+#description-input button:hover {
+    background-color: var(--button-primary-background-fill-hover);
+    color: var(--button-primary-text-color-hover);
+}
+
+#case-counter textarea {
+    text-align: center;
+    font-weight: 800;
+    font-size: calc(var(--block-title-text-size) + 2px);
+}
+
+#json-output textarea {
+    height: 96px !important;
+}
+
+.card-group, .card-group > div {
+    background-color: transparent;
+    border: 0px;
+}
+
+.card-group > div {
+    display: grid !important;
+    /* grid-template-columns: repeat(3, minmax(var(--card-min-width), 1fr)); */
+    grid-auto-rows: auto !important;
+    gap: 12px !important;
+}
+
+@media (min-width: 768px) {
+    .card-group > div {
+        grid-template-columns: repeat(1, minmax(var(--card-min-width), 1fr));
+    }
+}
+
+@media (min-width: 1024px) {
+    .card-group > div {
+        grid-template-columns: repeat(2, minmax(var(--card-min-width), 1fr));
+    }
+}
+
+@media (min-width: 1420px) {
+    .card-group > div {
+        grid-template-columns: repeat(3, minmax(var(--card-min-width), 1fr));
+    }
+}
+
+.filter-card {
+    min-width: min(var(--card-min-width), 100%) !important;
+    height: 254px; /* this height clips the option text to help indicate the need to scroll */
+    border: var(--block-border-width) solid var(--block-border-color) !important;
+    border-radius: var(--block-radius) !important;
+    overflow-y: scroll;
+}
+
+/* target the span with the card title */
+.filter-card > span:first-of-type {
+    font-weight: 800;
+    font-size: calc(var(--block-title-text-size) + 2px);
+    text-decoration: underline;
+}
+
+/* target the div with the labels */
+.filter-card div:last-of-type {
+    display: block;
+}
+
+.filter-card label {
+    border: 0;
+}
+
+.filter-card::-webkit-scrollbar, #json-output textarea::-webkit-scrollbar {
+    -webkit-appearance: none;
+    width: 7px;
+}
+.filter-card::-webkit-scrollbar-thumb, #json-output textarea::-webkit-scrollbar-thumb {
+    border-radius: 4px;
+    background-color: rgba(150,150,150,.5);
+    -webkit-box-shadow: 0 0 1px rgba(255,255,255,.5);
+}
+
+@keyframes spin {
+  to {
+    transform: rotate(360deg);
+  }
+}
+
+.spinner {
+  width: 24px;
+  height: 24px;
+  border: 4px solid rgba(0, 0, 0, 0.1);
+  border-top-color: #3498db;
+  border-radius: 50%;
+  animation: spin 1s linear infinite;
+  display: inline-block;
+}
+