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Commit 7ad71679 authored by Severine Duvaud's avatar Severine Duvaud
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Hopefully resolves issue #1 + dataset retrieval from arraymap API (preliminary... 

Hopefully resolves issue #1 + dataset retrieval from arraymap API (preliminary - still issues with callbacks)
parent 0c03c9d8
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beacon-app/arraymap-beacon/v0.4/arraymap-beacon.js
View file @ 7ad71679
var beacon = {};
beacon.info = require('./beacon-info.js').info
beacon.info = require('./beacon-info.js').getDatasetsFromArrayMap;
beacon.checkResultAndGetResponse = require('./beacon-query.js').checkResultAndGetResponse
beacon.checkPreconditions = require('./beacon-query.js').checkPreconditions
beacon.buildMongoQuery = require('./beacon-query.js').buildMongoQuery
beacon.checkResultAndGetResponse = require('./beacon-query.js').checkResultAndGetResponse;
beacon.checkPreconditions = require('./beacon-query.js').checkPreconditions;
beacon.buildMongoQuery = require('./beacon-query.js').buildMongoQuery;
beacon.checkDatasetIdentifier = require('./beacon-dataset.js').checkDatasetIdentifier
beacon.buildMongoDatasetQuery = require('./beacon-dataset.js').buildMongoDatasetQuery
beacon.checkDatasetResultAndGetResponse = require('./beacon-dataset.js').checkDatasetResultAndGetResponse
beacon.checkDatasetIdentifier = require('./beacon-dataset.js').checkDatasetIdentifier;
beacon.getDatasets = require('./beacon-dataset.js').getDatasets;
module.exports = beacon;
\ No newline at end of file
beacon-app/arraymap-beacon/v0.4/beacon-dataset.js
View file @ 7ad71679
......@@ -2,17 +2,17 @@
* Created by sduvaud on 26/05/16.
*/
var info = require('./beacon-info.js').info;
var info = require('./beacon-info.js');
// store all the dataset identifiers
var allDatasetIds = [];
info['info']['info']['datasets'].forEach(function(dataset){
allDatasetIds.push(dataset.id);
info.getDatasetsFromArrayMap(function (callback){
infoObject = callback;
});
var infoObject = {};
function checkDatasetIdentifier(params) {
if (!params.id) {
if (!params.info && !params.id) {
return {
hasError: true,
msg: "No identifier specified"
......@@ -23,82 +23,44 @@ function checkDatasetIdentifier(params) {
};
}
function buildMongoDatasetQuery(params)
{
console.log("ID=" + params.id);
var groupCondition = {
$group: {
_id: "$ICDMORPHOLOGYCODE",
sampleCount: {$sum: 1},
name: { $first: "$ICDMORPHOLOGY"}
}
};
function getDatasets(params) {
if (params.info) {
return infoObject;
}
if (params.id == 'all') {
return [
groupCondition
];
return infoObject.info.info.datasets;
}
else {
var orConditions = [];
var found = {};
var datasets = infoObject.info.info.datasets;
var identifiers = params.id.split(','); // comma separated list of datasets
var output = [];
identifiers.forEach(function (id) {
orConditions.push({ICDMORPHOLOGYCODE: id});
});
return [
{
$match: {
$or: orConditions
found = {};
datasets.forEach(function (dataset) {
if (dataset.id == id) {
found = dataset;
}
},
groupCondition
];
}
}
function checkDatasetResultAndGetResponse(params, datasets) {
var matchedIdentifiers = [];
datasets.forEach(function(dataset){
matchedIdentifiers.push(dataset._id);
});
var submittedIdentifiers = allDatasetIds;
if (params.id != 'all') {
submittedIdentifiers = params.id.split(',');
}
if (submittedIdentifiers.length != matchedIdentifiers.length) {
var missingIdentifiers = [];
submittedIdentifiers.forEach(function(submitted) {
var found = false;
matchedIdentifiers.forEach(function(matched) {
if (matched == submitted) {
found = true;
}
}
);
if (!found) {
missingIdentifiers.push(submitted);
}
}
);
missingIdentifiers.forEach(function (missing) {
});
if (JSON.stringify(found)=='{}') {
var json = {
"_id": missing,
"sampleCount": 0,
"name": "Dataset not found"
"id": id,
"description": "Not found",
"reference": "reference genome",
"size": {
"variants": "-1",
"samples": 0
}
};
datasets.push(json);
output.push(json);
}
else {
output.push(found);
}
);
});
return output;
}
return datasets;
}
module.exports.checkDatasetIdentifier = checkDatasetIdentifier;
module.exports.buildMongoDatasetQuery = buildMongoDatasetQuery;
module.exports.checkDatasetResultAndGetResponse = checkDatasetResultAndGetResponse;
\ No newline at end of file
module.exports.getDatasets = getDatasets;
\ No newline at end of file
beacon-app/arraymap-beacon/v0.4/beacon-info.js
View file @ 7ad71679
var object = {
info: { "info": {
"id": "arraymap-beacon",
"name": "Beacon ArrayMap",
"organization": "SIB Swiss Institute of Bioinformatics",
"description": "First Prototype of a Beacon v0.4 implementation for arrayMap",
"api": "v0.4",
"homepage": "http://beacon.arraymap.org/",
"email": "SIB-Technology@isb-sib.ch",
"datasets": [
{"id": "8050/3", "description": "Papillary carcinoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "16"}},
{"id": "8586/3", "description": "Thymoma, type C [C37.9]", "reference": "reference genome", "size": { "variants": "-1", "samples": "65"}},
{"id": "8148/2", "description": "prostatic intraepithelial neoplasia, grade III", "reference": "reference genome", "size": { "variants": "-1", "samples": "14"}},
{"id": "8215/3", "description": "Adenocarcinoma of anal ducts [C21.1]", "reference": "reference genome", "size": { "variants": "-1", "samples": "3"}},
{"id": "8821/1", "description": "desmoid-type fibromatosis", "reference": "reference genome", "size": { "variants": "-1", "samples": "55"}},
{"id": "8330/3", "description": "follicular carcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "15"}},
{"id": "8825/1", "description": "Inflammatory myofibroblastic tumour", "reference": "reference genome", "size": { "variants": "-1", "samples": "1"}},
{"id": "8370/0", "description": "Adrenal cortical adenoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "2"}},
{"id": "8680/1", "description": "Paraganglioma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "31"}},
{"id": "8743/3", "description": "Superficial spreading melanoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "22"}},
{"id": "8082/3", "description": "Undifferentiated nasopharyngeal carcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "52"}},
{"id": "8201/3", "description": "Ductal carcinoma, cribriform type [C50._]", "reference": "reference genome", "size": { "variants": "-1", "samples": "7"}},
{"id": "8250/3", "description": "Bronchiolo-alveolar adenocarcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "23"}},
{"id": "9731/3", "description": "Multiple myeloma", "reference": "reference genome", "size": { "variants": "-1", "samples": "646"}},
{"id": "9698/3", "description": "Follicular lymphoma, grade 3", "reference": "reference genome", "size": { "variants": "-1", "samples": "1"}},
{"id": "9691/3", "description": "Follicular lymphoma, grade 2", "reference": "reference genome", "size": { "variants": "-1", "samples": "6"}},
{"id": "8507/3", "description": "Invasive micropapillary carcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "39"}},
{"id": "8260/8", "description": "Papillary adenocarcinoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "1"}},
{"id": "8430/3", "description": "Mucoepidermoid carcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "48"}},
{"id": "9931/3", "description": "Acute myelofibrosis", "reference": "reference genome", "size": { "variants": "-1", "samples": "1"}},
{"id": "8318/3", "description": "Renal cell carcinoma, spindle cell [C64.9]", "reference": "reference genome", "size": { "variants": "-1", "samples": "4"}},
{"id": "9678/3", "description": "Primary effusion lymphoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "37"}},
{"id": "9220/0", "description": "Chondroma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "18"}},
{"id": "9581/3", "description": "Alveolar soft part sarcoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "15"}},
{"id": "8830/0", "description": "Fibrous histiocytoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "1"}},
{"id": "8330/0", "description": "Follicular adenoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "1"}},
{"id": "8031/3", "description": "Giant cell carcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "4"}},
{"id": "9717/3", "description": "Enteropathy type T-cell lymphoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "31"}},
{"id": "8150/3", "description": "Islet cell carcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "1"}},
{"id": "9424/3", "description": "Pleomorphic xanthoastrocytoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "2"}},
{"id": "9805/3", "description": "Acute biphenotypic leukemia", "reference": "reference genome", "size": { "variants": "-1", "samples": "56"}},
{"id": "8440/3", "description": "Cystadenocarcinoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "2"}},
{"id": "8333/0", "description": "Fetal adenoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "3"}},
{"id": "8161/3", "description": "Bile duct cystadenocarcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "25"}},
{"id": "8910/3", "description": "Embryonal rhabdomyosarcoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "46"}},
{"id": "8890/0", "description": "Leiomyoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "52"}},
{"id": "8272/3", "description": "Pituitary carcinoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "13"}},
{"id": "9875/3", "description": "Chronic myelogenous leukemia", "reference": "reference genome", "size": { "variants": "-1", "samples": "1"}},
{"id": "8251/3", "description": "Alveolar adenocarcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "1"}},
{"id": "8335/3", "description": "Follicular carcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "3"}},
{"id": "8963/3", "description": "Rhabdoid tumor, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "2"}},
{"id": "9765/1", "description": "Monoclonal gammopathy", "reference": "reference genome", "size": { "variants": "-1", "samples": "6"}},
{"id": "9983/3", "description": "Refractory anemia with excess blasts [RAEB]", "reference": "reference genome", "size": { "variants": "-1", "samples": "3"}},
{"id": "8070/1", "description": "premalignant squamous epithelium, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "46"}},
{"id": "8382/3", "description": "Endometrioid adenocarcinoma, secretory variant", "reference": "reference genome", "size": { "variants": "-1", "samples": "6"}},
{"id": "8211/3", "description": "Tubular adenocarcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "5"}},
{"id": "8071/0", "description": "Squamous cell keratosis, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "11"}},
{"id": "9060/3", "description": "Dysgerminoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "1"}},
{"id": "8010/2", "description": "Carcinoma in situ, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "20"}},
{"id": "8441/3", "description": "Serous adenocarcinoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "542"}},
{"id": "9761/3", "description": "Waldenstrom macroglobulinemia", "reference": "reference genome", "size": { "variants": "-1", "samples": "42"}},
{"id": "8550/3", "description": "Acinar cell carcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "2"}},
{"id": "8503/2", "description": "Ductal carcinoma in situ, papillary [C50._]", "reference": "reference genome", "size": { "variants": "-1", "samples": "1"}},
{"id": "8310/3", "description": "Clear cell renal cell carcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "1095"}},
{"id": "8090/3", "description": "Basal cell carcinoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "28"}},
{"id": "8252/3", "description": "Bronchiolo-alveolar carcinoma, non-mucinous", "reference": "reference genome", "size": { "variants": "-1", "samples": "1"}},
{"id": "8560/3", "description": "Adenosquamous carcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "21"}},
{"id": "8805/3", "description": "Undifferentiated sarcoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "34"}},
{"id": "9362/3", "description": "Pineoblastoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "16"}},
{"id": "8010/0", "description": "Epithelial tumor, benign", "reference": "reference genome", "size": { "variants": "-1", "samples": "10"}},
{"id": "9382/3", "description": "Glioma, mixed", "reference": "reference genome", "size": { "variants": "-1", "samples": "56"}},
{"id": "9590/3", "description": "Malignant lymphoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "48"}},
{"id": "8312/3", "description": "Renal cell carcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "449"}},
{"id": "9530/3", "description": "Meningioma, malignant", "reference": "reference genome", "size": { "variants": "-1", "samples": "2"}},
{"id": "9823/3", "description": "B-cell chronic lymphocytic leukemia/small lymphocytic lymphoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "2109"}},
{"id": "9876/3", "description": "Atypical chronic myeloid leukemia, BCR/ABL negative", "reference": "reference genome", "size": { "variants": "-1", "samples": "61"}},
{"id": "8541/3", "description": "Paget disease and infiltrating duct carcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "1"}},
{"id": "9964/3", "description": "Hypereosinophilic syndrome", "reference": "reference genome", "size": { "variants": "-1", "samples": "3"}},
{"id": "9071/3", "description": "Yolk sac tumor", "reference": "reference genome", "size": { "variants": "-1", "samples": "18"}},
{"id": "8852/3", "description": "Liposarcoma, myxoid", "reference": "reference genome", "size": { "variants": "-1", "samples": "21"}},
{"id": "9508/3", "description": "Atypical teratoid/rhabdoid tumor", "reference": "reference genome", "size": { "variants": "-1", "samples": "2"}},
{"id": "8453/2", "description": "Intraductal papillary-mucinous carcinoma, non-invasive [C25._]", "reference": "reference genome", "size": { "variants": "-1", "samples": "5"}},
{"id": "8453/1", "description": "Intraductal papillary-mucinous tumor with moderate dysplasia [C25._]", "reference": "reference genome", "size": { "variants": "-1", "samples": "5"}},
{"id": "8453/0", "description": "Intraductal papillary-mucinous adenoma [C25._]", "reference": "reference genome", "size": { "variants": "-1", "samples": "7"}},
{"id": "9041/3", "description": "Synovial sarcoma, monophasic", "reference": "reference genome", "size": { "variants": "-1", "samples": "20"}},
{"id": "9110/3", "description": "Mesonephroma, malignant", "reference": "reference genome", "size": { "variants": "-1", "samples": "1"}},
{"id": "9050/3", "description": "Mesothelioma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "87"}},
{"id": "8823/0", "description": "Desmoplastic fibroma", "reference": "reference genome", "size": { "variants": "-1", "samples": "1"}},
{"id": "9053/3", "description": "Mesothelioma, biphasic, malignant", "reference": "reference genome", "size": { "variants": "-1", "samples": "3"}},
{"id": "9043/3", "description": "Synovial sarcoma, biphasic", "reference": "reference genome", "size": { "variants": "-1", "samples": "4"}},
{"id": "9867/3", "description": "Acute myelomonocytic leukemia [FAB type M4]", "reference": "reference genome", "size": { "variants": "-1", "samples": "2"}},
{"id": "9874/3", "description": "Acute myeloblastic leukemia with maturation [FAB M2]", "reference": "reference genome", "size": { "variants": "-1", "samples": "11"}},
{"id": "8077/2", "description": "Squamous intraepithelial neoplasia, grade III", "reference": "reference genome", "size": { "variants": "-1", "samples": "136"}},
{"id": "9080/0", "description": "Teratoma, benign", "reference": "reference genome", "size": { "variants": "-1", "samples": "12"}},
{"id": "9910/3", "description": "Acute megakaryoblastic leukemia [FAB M7]", "reference": "reference genome", "size": { "variants": "-1", "samples": "7"}},
{"id": "9985/3", "description": "Refractory cytopenia with multilineage dysplasia", "reference": "reference genome", "size": { "variants": "-1", "samples": "2"}},
{"id": "9982/3", "description": "Refractory anemia with ringed sideroblasts [RARS]", "reference": "reference genome", "size": { "variants": "-1", "samples": "11"}},
{"id": "8936/1", "description": "Gastrointestinal stromal tumor, uncertain malignant potential", "reference": "reference genome", "size": { "variants": "-1", "samples": "15"}},
{"id": "8700/0", "description": "Pheochromocytoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "104"}},
{"id": "9120/3", "description": "Angiosarcoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "11"}},
{"id": "9442/3", "description": "Gliosarcoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "3"}},
{"id": "8033/3", "description": "Sarcomatoid carcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "2"}},
{"id": "9836/3", "description": "Precursor B-cell lymphoblastic leukemia", "reference": "reference genome", "size": { "variants": "-1", "samples": "22"}},
{"id": "8041/3", "description": "Small cell carcinoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "132"}},
{"id": "9505/1", "description": "Ganglioglioma", "reference": "reference genome", "size": { "variants": "-1", "samples": "20"}},
{"id": "8240/3", "description": "Carcinoid tumor, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "2"}},
{"id": "8254/3", "description": "Bronchiolo-alveolar carcinoma, indeterminate type [C34._]", "reference": "reference genome", "size": { "variants": "-1", "samples": "4"}},
{"id": "8510/3", "description": "Medullary carcinoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "33"}},
{"id": "9827/3", "description": "Adult T-cell leukemia/lymphoma [HTLV1 pos.]", "reference": "reference genome", "size": { "variants": "-1", "samples": "179"}},
{"id": "9183/3", "description": "Osteosarcoma, telangiectatic", "reference": "reference genome", "size": { "variants": "-1", "samples": "3"}},
{"id": "8960/3", "description": "Nephroblastoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "31"}},
{"id": "8333/3", "description": "Fetal adenocarcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "1"}},
{"id": "8160/3", "description": "Cholangiocarcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "20"}},
{"id": "8973/3", "description": "pleuropulmonary blastoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "1"}},
{"id": "9370/3", "description": "Chordoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "51"}},
{"id": "9503/3", "description": "Neuroepithelioma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "3"}},
{"id": "9834/3", "description": "Prolymphocytic leukemia, T-cell type", "reference": "reference genome", "size": { "variants": "-1", "samples": "12"}},
{"id": "8210/3", "description": "Adenocarcinoma in adenomatous polyp", "reference": "reference genome", "size": { "variants": "-1", "samples": "1"}},
{"id": "9052/3", "description": "Epithelioid mesothelioma, malignant", "reference": "reference genome", "size": { "variants": "-1", "samples": "15"}},
{"id": "8290/0", "description": "Oncocytoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "23"}},
{"id": "9260/3", "description": "Ewing sarcoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "136"}},
{"id": "9380/3", "description": "Glioma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "337"}},
{"id": "8021/3", "description": "Carcinoma, anaplastic type, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "4"}},
{"id": "9980/3", "description": "Refractory anemia, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "18"}},
{"id": "8140/3", "description": "Adenocarcinoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "10473"}},
{"id": "8130/1", "description": "Urothelial papilloma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "184"}},
{"id": "8890/3", "description": "Leiomyosarcoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "119"}},
{"id": "9861/3", "description": "Acute myeloid leukemia, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "2793"}},
{"id": "9729/3", "description": "Precursor T-cell lymphoblastic lymphoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "30"}},
{"id": "8530/3", "description": "Inflammatory carcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "2"}},
{"id": "8453/3", "description": "Intraductal papillary-mucinous carcinoma, invasive [C25._]", "reference": "reference genome", "size": { "variants": "-1", "samples": "4"}},
{"id": "8523/3", "description": "Infiltrating duct mixed with other types of carcinoma [C50._]", "reference": "reference genome", "size": { "variants": "-1", "samples": "1"}},
{"id": "8858/3", "description": "Liposarcoma, dedifferentiated", "reference": "reference genome", "size": { "variants": "-1", "samples": "53"}},
{"id": "8145/3", "description": "Carcinoma, diffuse type", "reference": "reference genome", "size": { "variants": "-1", "samples": "7"}},
{"id": "9671/3", "description": "Malignant lymphoma, lymphoplasmacytic", "reference": "reference genome", "size": { "variants": "-1", "samples": "23"}},
{"id": "9699/3", "description": "Marginal zone lymphoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "453"}},
{"id": "9400/3", "description": "Astrocytoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "197"}},
{"id": "9709/3", "description": "Primary cutaneous peripheral T-cell lymphoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "10"}},
{"id": "8575/3", "description": "Metaplastic carcinoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "2"}},
{"id": "8980/3", "description": "Carcinosarcoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "4"}},
{"id": "9070/3", "description": "Embryonal carcinoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "9"}},
{"id": "8490/3", "description": "Signet ring cell carcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "3"}},
{"id": "9085/3", "description": "Mixed germ cell tumor", "reference": "reference genome", "size": { "variants": "-1", "samples": "36"}},
{"id": "9120/0", "description": "Hemangioma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "2"}},
{"id": "8200/3", "description": "Adenoid cystic carcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "69"}},
{"id": "9081/3", "description": "Teratocarcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "13"}},
{"id": "9582/0", "description": "Granular cell tumor", "reference": "reference genome", "size": { "variants": "-1", "samples": "2"}},
{"id": "9679/3", "description": "Mediastinal large B-cell lymphoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "40"}},
{"id": "9080/3", "description": "Teratoma, malignant, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "30"}},
{"id": "8000/3", "description": "Neoplasm, malignant", "reference": "reference genome", "size": { "variants": "-1", "samples": "11"}},
{"id": "9705/3", "description": "Peripheral T-cell lymphoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "159"}},
{"id": "8070/2", "description": "Squamous cell carcinoma in situ, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "65"}},
{"id": "9051/3", "description": "Desmoplastic mesothelioma", "reference": "reference genome", "size": { "variants": "-1", "samples": "8"}},
{"id": "9540/3", "description": "Malignant peripheral nerve sheath tumor", "reference": "reference genome", "size": { "variants": "-1", "samples": "95"}},
{"id": "9100/3", "description": "Choriocarcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "15"}},
{"id": "9522/3", "description": "Olfactory neuroblastoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "13"}},
{"id": "9181/3", "description": "Chondroblastic osteosarcoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "12"}},
{"id": "9733/3", "description": "Plasma cell leukemia", "reference": "reference genome", "size": { "variants": "-1", "samples": "17"}},
{"id": "9986/3", "description": "Myelodysplastic syndrome with 5q- syndrome", "reference": "reference genome", "size": { "variants": "-1", "samples": "3"}},
{"id": "8800/3", "description": "Sarcoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "45"}},
{"id": "9837/3", "description": "Precursor T-cell lymphoblastic leukemia", "reference": "reference genome", "size": { "variants": "-1", "samples": "104"}},
{"id": "8802/3", "description": "Giant cell sarcoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "1"}},
{"id": "9065/3", "description": "Germ cell tumor, nonseminomatous", "reference": "reference genome", "size": { "variants": "-1", "samples": "43"}},
{"id": "9701/3", "description": "Sezary syndrome", "reference": "reference genome", "size": { "variants": "-1", "samples": "72"}},
{"id": "0000/0", "description": "not classified in ICD-O 3 [e.g. non-neoplastic or benign]", "reference": "reference genome", "size": { "variants": "-1", "samples": "9165"}},
{"id": "8936/3", "description": "Gastrointestinal stromal tumor, malignant", "reference": "reference genome", "size": { "variants": "-1", "samples": "374"}},
{"id": "8246/3", "description": "Neuroendocrine carcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "12"}},
{"id": "9866/3", "description": "Acute promyelocytic leukemia [FAB type M3]", "reference": "reference genome", "size": { "variants": "-1", "samples": "61"}},
{"id": "9510/3", "description": "Retinoblastoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "24"}},
{"id": "8380/3", "description": "Endometrioid carcinoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "434"}},
{"id": "9757/3", "description": "Dendritic cell sarcoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "7"}},
{"id": "8500/2", "description": "Ductal carcinoma in situ, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "225"}},
{"id": "9700/3", "description": "mycosis fungoides", "reference": "reference genome", "size": { "variants": "-1", "samples": "63"}},
{"id": "8833/3", "description": "Pigmented dermatofibrosarcoma protuberans", "reference": "reference genome", "size": { "variants": "-1", "samples": "17"}},
{"id": "9180/3", "description": "Osteosarcoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "198"}},
{"id": "8140/1", "description": "atypical adenoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "53"}},
{"id": "8170/0", "description": "Hepatocellular adenoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "125"}},
{"id": "8460/3", "description": "Micropapillary serous carcinoma [C56.9]", "reference": "reference genome", "size": { "variants": "-1", "samples": "513"}},
{"id": "8501/2", "description": "DCIS, comedo type [C50._]", "reference": "reference genome", "size": { "variants": "-1", "samples": "2"}},
{"id": "8370/3", "description": "Adrenal cortical carcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "215"}},
{"id": "8046/3", "description": "Non-small cell carcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "1195"}},
{"id": "9391/3", "description": "Ependymoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "213"}},
{"id": "9860/3", "description": "Myeloid leukemia, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "5"}},
{"id": "9596/3", "description": "Composite Hodgkin and Non-Hodgkin lymphoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "2"}},
{"id": "8811/3", "description": "Myxoinflammatory fibroblastic sarcoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "58"}},
{"id": "9891/3", "description": "Acute monoblastic leukemia with differentiation [FAB M5b]", "reference": "reference genome", "size": { "variants": "-1", "samples": "15"}},
{"id": "9401/3", "description": "Astrocytoma, anaplastic", "reference": "reference genome", "size": { "variants": "-1", "samples": "114"}},
{"id": "8020/3", "description": "Carcinoma, undifferentiated type, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "3"}},
{"id": "8520/2", "description": "Lobular carcinoma in situ", "reference": "reference genome", "size": { "variants": "-1", "samples": "39"}},
{"id": "9421/1", "description": "Pilocytic astrocytoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "159"}},
{"id": "8480/3", "description": "Mucinous adenocarcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "132"}},
{"id": "9962/3", "description": "Essential thrombocythemia", "reference": "reference genome", "size": { "variants": "-1", "samples": "45"}},
{"id": "8730/3", "description": "Amelanotic melanoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "4"}},
{"id": "9530/0", "description": "meningioma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "284"}},
{"id": "9471/3", "description": "Medulloblastoma with extensive nodularity", "reference": "reference genome", "size": { "variants": "-1", "samples": "133"}},
{"id": "9473/3", "description": "Primitive neuroectodermal tumor, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "186"}},
{"id": "8130/3", "description": "Papillary transitional cell carcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "2"}},
{"id": "9591/3", "description": "Malignant lymphoma, B-cell NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "130"}},
{"id": "9430/3", "description": "Astroblastoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "3"}},
{"id": "8140/0", "description": "Adenoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "385"}},
{"id": "9716/3", "description": "Hepatosplenic gamma/delta T-cell lymphoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "9"}},
{"id": "8170/3", "description": "Hepatocellular carcinoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "860"}},
{"id": "9064/3", "description": "Germinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "1"}},
{"id": "8830/3", "description": "Fibrous histiocytoma, malignant", "reference": "reference genome", "size": { "variants": "-1", "samples": "1"}},
{"id": "9826/3", "description": "Acute lymphoblastic leukemia, mature B-cell type", "reference": "reference genome", "size": { "variants": "-1", "samples": "31"}},
{"id": "9863/3", "description": "Chronic myeloid leukemia, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "333"}},
{"id": "8144/3", "description": "Adenocarcinoma, intestinal type", "reference": "reference genome", "size": { "variants": "-1", "samples": "132"}},
{"id": "9718/3", "description": "Anaplastic large cell lymphoma, cutaneous type", "reference": "reference genome", "size": { "variants": "-1", "samples": "11"}},
{"id": "9130/3", "description": "Hemangioendothelioma, malignant", "reference": "reference genome", "size": { "variants": "-1", "samples": "1"}},
{"id": "8720/3", "description": "Malignant melanoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "1405"}},
{"id": "8260/4", "description": "Papillary adenocarcinoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "1"}},
{"id": "9540/0", "description": "Neurofibroma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "104"}},
{"id": "9440/3", "description": "Glioblastoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "2294"}},
{"id": "9714/3", "description": "Anaplastic large cell lymphoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "71"}},
{"id": "8982/0", "description": "Myoepithelioma", "reference": "reference genome", "size": { "variants": "-1", "samples": "20"}},
{"id": "9040/3", "description": "Synovial sarcoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "67"}},
{"id": "9732/3", "description": "Plasma cell myeloma", "reference": "reference genome", "size": { "variants": "-1", "samples": "561"}},
{"id": "8520/3", "description": "Invasive lobular carcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "65"}},
{"id": "9800/3", "description": "Leukemia, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "17"}},
{"id": "8247/3", "description": "Merkel cell carcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "26"}},
{"id": "9182/3", "description": "Fibroblastic osteosarcoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "3"}},
{"id": "8810/3", "description": "Fibrosarcoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "50"}},
{"id": "9989/3", "description": "Myelodysplastic syndrome, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "703"}},
{"id": "9728/3", "description": "Precursor B-cell lymphoblastic lymphoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "7"}},
{"id": "9220/3", "description": "Chondrosarcoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "108"}},
{"id": "", "description": "", "reference": "reference genome", "size": { "variants": "-1", "samples": "1041"}},
{"id": "9560/0", "description": "Schwannoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "5"}},
{"id": "9680/3", "description": "Diffuse large B-cell lymphoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "1044"}},
{"id": "8900/3", "description": "Rhabdomyosarcoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "71"}},
{"id": "8854/3", "description": "Liposarcoma, pleomorphic", "reference": "reference genome", "size": { "variants": "-1", "samples": "24"}},
{"id": "8260/10", "description": "Papillary adenocarcinoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "1"}},
{"id": "9690/3", "description": "follicular lymphoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "867"}},
{"id": "9945/3", "description": "Chronic myelomonocytic leukemia, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "69"}},
{"id": "9689/3", "description": "Splenic marginal zone lymphoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "441"}},
{"id": "9650/3", "description": "Hodgkin lymphoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "13"}},
{"id": "9020/3", "description": "Phyllodes tumor, malignant", "reference": "reference genome", "size": { "variants": "-1", "samples": "1"}},
{"id": "9500/3", "description": "Neuroblastoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "1333"}},
{"id": "8522/3", "description": "Infiltrating duct and lobular carcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "43"}},
{"id": "9064/2", "description": "Intratubular germ cell neoplasia [C62._]", "reference": "reference genome", "size": { "variants": "-1", "samples": "16"}},
{"id": "8012/3", "description": "Large cell carcinoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "46"}},
{"id": "9470/3", "description": "Medulloblastoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "2052"}},
{"id": "9451/3", "description": "Oligodendroglioma, anaplastic", "reference": "reference genome", "size": { "variants": "-1", "samples": "41"}},
{"id": "9695/3", "description": "Follicular lymphoma, grade 1", "reference": "reference genome", "size": { "variants": "-1", "samples": "13"}},
{"id": "8721/3", "description": "Nodular melanoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "4"}},
{"id": "8570/3", "description": "Adenocarcinoma with squamous metaplasia", "reference": "reference genome", "size": { "variants": "-1", "samples": "20"}},
{"id": "9061/3", "description": "Seminoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "17"}},
{"id": "8317/3", "description": "Renal cell carcinoma, chromophobe", "reference": "reference genome", "size": { "variants": "-1", "samples": "24"}},
{"id": "8850/3", "description": "Liposarcoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "38"}},
{"id": "null", "description": "null", "reference": "reference genome", "size": { "variants": "-1", "samples": "0"}},
{"id": "8120/3", "description": "Transitional cell carcinoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "447"}},
{"id": "8500/3", "description": "invasive carcinoma of no special type", "reference": "reference genome", "size": { "variants": "-1", "samples": "8171"}},
{"id": "9960/3", "description": "Chronic myeloproliferative disease, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "173"}},
{"id": "8260/7", "description": "Papillary adenocarcinoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "1"}},
{"id": "9961/3", "description": "Chronic idiopathic myelofibrosis", "reference": "reference genome", "size": { "variants": "-1", "samples": "47"}},
{"id": "9673/3", "description": "Mantle cell lymphoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "380"}},
{"id": "9687/3", "description": "Burkitt lymphoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "108"}},
{"id": "8562/3", "description": "Myoepithelial carcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "14"}},
{"id": "9950/3", "description": "Polycythemia vera", "reference": "reference genome", "size": { "variants": "-1", "samples": "45"}},
{"id": "9450/3", "description": "Oligodendroglioma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "161"}},
{"id": "8260/9", "description": "Papillary adenocarcinoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "1"}},
{"id": "8010/3", "description": "Carcinoma, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "1570"}},
{"id": "8524/3", "description": "Infiltrating lobular mixed with other types of carcinoma", "reference": "reference genome", "size": { "variants": "-1", "samples": "1"}},
{"id": "9984/3", "description": "Refractory anemia with excess blasts in transformation [RAEBT]", "reference": "reference genome", "size": { "variants": "-1", "samples": "1"}},
{"id": "9835/3", "description": "Acute lymphoblastic leukemia, NOS", "reference": "reference genome", "size": { "variants": "-1", "samples": "1789"}},