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Merge pull request #219 from CBIIT/EVSSIP-274-Update-mapping-for-GDC-…
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…release-2.5.0

EVS SIP 274 - GDC Mapping Update for NCIt 22.08e
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@fmanuelos
fmanuelos authored Nov 7, 2022
2 parents f8cdd7e + 371c0bf commit b4e1cbf
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Showing 5 changed files with 232 additions and 79 deletions.
2 changes: 1 addition & 1 deletion server/data_files/GDC/gdc_props.js
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2 changes: 1 addition & 1 deletion server/data_files/GDC/gdc_values.js
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2 changes: 1 addition & 1 deletion server/data_files/GDC/ncit_details.js
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302 changes: 227 additions & 75 deletions server/service/search/controller.js
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Original file line number Diff line number Diff line change
Expand Up @@ -629,15 +629,15 @@ const synchronziedLoadSynonmysfromNCIT = (ncitids, idx, next) => {
d.synonyms.forEach((data) => {
if (
checker_arr.indexOf(
(data.name + "@#$" + data.termGroup + "@#$" + data.source)
(data.name + "@#$" + data.termType + "@#$" + data.source)
.trim()
.toLowerCase()
) !== -1
)
return;
let obj = {};
obj.termName = data.name;
obj.termGroup = data.termGroup;
obj.termGroup = data.termType;
obj.termSource = data.source;
//only keep NCI synonyms
if (obj.termSource == "NCI") {
Expand All @@ -648,7 +648,7 @@ const synchronziedLoadSynonmysfromNCIT = (ncitids, idx, next) => {
}
}
checker_arr.push(
(data.name + "@#$" + data.termGroup + "@#$" + data.source)
(data.name + "@#$" + data.termType + "@#$" + data.source)
.trim()
.toLowerCase()
);
Expand Down Expand Up @@ -1290,92 +1290,243 @@ const exportAllCompareResult = async function(req, res){
res.send(report);
}

const generateProperties = async function(req, res) {
const dataset = [];
let output_file_path = path.join(__dirname, '..', '..', 'data_files', 'GDC', 'gdc_values_updated.js');
let GDCDict = await shared.getGDCDictionaryByVersion("2.4.1");

for(let node in GDCDict){
let entry = GDCDict[node];
let uid = node + "/" + entry.category + "/gdc";
if(entry.properties){
let prop_dict = entry.properties;
for(let prop in prop_dict){
let tmp = {};
tmp.category = entry.category;
tmp.node = node;
tmp.property = prop;
let dict = prop_dict[prop];
tmp.ncit = dict.termDef && dict.termDef.source && dict.termDef.source == "NCIt" ? (dict.termDef.term_id || dict.termDef.cde_id ) : "";
dataset.push(tmp);
}
}
}
const generateGDCPropertiesReport = async function(req, res) {
const dataset = [];
let GDCDict = await shared.getGDCDictionaryByVersion("2.5.0");
let prop_mapping = shared.readGDCProps();

for(let node in GDCDict){
let entry = GDCDict[node];
if(entry.properties){
let prop_dict = entry.properties;
for(let prop in prop_dict){
let tmp = {};
let uid = entry.category + "." + node + "." + prop;
tmp.category = entry.category;
tmp.node = node;
tmp.property = prop;
let dict = prop_dict[prop];
tmp.ncit = prop_mapping[uid] !== undefined ? prop_mapping[uid] : '';
tmp.cdeid = dict.termDef && dict.termDef.source && dict.termDef.source === "caDSR" ? (dict.termDef.cde_id) : "";
dataset.push(tmp);
}
}
}

// You can define styles as json object
const styles = {
const styles = {
cellPink: {
fill: {
fgColor: {
rgb: 'FF00FF00'
}
fgColor: {
rgb: '1F497D'
}
},
font:{
color: {
rgb: 'FFFFFF'
}
}
}
};
};

//Array of objects representing heading rows (very top)
const heading = [
];
//Array of objects representing heading rows (very top)
const heading = [
];

//Here you specify the export structure
const specification = {
category: { // <- the key should match the actual data key
displayName: 'Category', // <- Here you specify the column header
headerStyle: styles.cellPink, // <- Header style
width: 220 // <- width in pixels
},
node: {
displayName: 'Node',
headerStyle: styles.cellPink,
width: 220 // <- width in chars (when the number is passed as string)
},
property: {
displayName: 'Property',
headerStyle: styles.cellPink,
width: 220 // <- width in pixels
},
ncit: {
displayName: 'NCIt Code',
headerStyle: styles.cellPink,
width: 220 // <- width in pixels
}
//Here you specify the export structure
const specification = {
category: { // <- the key should match the actual data key
displayName: 'Category', // <- Here you specify the column header
headerStyle: styles.cellPink, // <- Header style
width: 220 // <- width in pixels
},
node: {
displayName: 'Node',
headerStyle: styles.cellPink,
width: 220 // <- width in chars (when the number is passed as string)
},
property: {
displayName: 'Property',
headerStyle: styles.cellPink,
width: 220 // <- width in pixels
},
ncit: {
displayName: 'NCIt Code',
headerStyle: styles.cellPink,
width: 220 // <- width in pixels
},
cdeid: {
displayName: 'CDE ID',
headerStyle: styles.cellPink,
width: 220 // <- width in pixels
}
}

// Define an array of merges. 1-1 = A:1
// The merges are independent of the data.
// A merge will overwrite all data _not_ in the top-left cell.
const merges = [];

// Create the excel report.
// This function will return Buffer
const report = export_excel.buildExport(
[ // <- Notice that this is an array. Pass multiple sheets to create multi sheet report
{
name: 'Report', // <- Specify sheet name (optional)
heading: heading, // <- Raw heading array (optional)
merges: merges, // <- Merge cell ranges
specification: specification, // <- Report specification
data: dataset // <-- Report data
// Define an array of merges. 1-1 = A:1
// The merges are independent of the data.
// A merge will overwrite all data _not_ in the top-left cell.
const merges = [];

// Create the excel report.
// This function will return Buffer
const report = export_excel.buildExport(
[ // <- Notice that this is an array. Pass multiple sheets to create multi sheet report
{
name: 'Report', // <- Specify sheet name (optional)
heading: heading, // <- Raw heading array (optional)
merges: merges, // <- Merge cell ranges
specification: specification, // <- Report specification
data: dataset // <-- Report data
}
]
);

// You can then return this straight
res.attachment('GDC_Properties_Data_Mapping.xlsx'); // This is sails.js specific (in general you need to set headers)
res.send(report);
}


const generateGDCValuesReport = async function(req, res) {
const dataset = [];
let GDCDict = await shared.getGDCDictionaryByVersion("2.5.0");
let gdc_values = shared.readGDCValues();
let syns = shared.readNCItDetails();

for(let node in GDCDict){
let entry = GDCDict[node];
if(entry.properties){
let prop_dict = entry.properties;
for(let prop in prop_dict){
let uid = entry.category + "." + node + "." + prop;
let prop_enum = prop_dict[prop] !== undefined && prop_dict[prop].enum !== undefined && prop_dict[prop].enum.length > 0 ? prop_dict[prop].enum : [];
prop_enum = prop_dict[prop] !== undefined && prop_dict[prop].items !== undefined && prop_dict[prop].items.enum !== undefined && prop_dict[prop].items.enum.length > 0 ? prop_dict[prop].items.enum : prop_enum;

let mappings = gdc_values[uid] !== undefined ? gdc_values[uid] : [];
let deprecated_enum = prop_dict[prop] !== undefined && prop_dict[prop].deprecated_enum !== undefined && prop_dict[prop].deprecated_enum.length > 0 ? prop_dict[prop].deprecated_enum : [];

for(let value of prop_enum){
let tmp = {};
tmp.category = entry.category;
tmp.node = node;
tmp.property = prop;
tmp.value = value;
tmp.ncit = [];
tmp.icdo3 = '';
tmp.icdoS = [];
tmp.ncitPV = [];

if (deprecated_enum.includes(value)) {
continue;
}

let map = mappings.find(({ nm }) => nm === value);
if(map !== undefined){
tmp.ncit = Array.isArray(map.n_c) ? map.n_c.join('|') : '';
tmp.icdo3 = map.i_c;
tmp.icdoS = Array.isArray(map.i_c_s) ? map.i_c_s.join('|') : ''
for(let code of map.n_c){
tmp.ncitPV.push(syns[code] !== undefined ? syns[code].label : '');
}
tmp.ncitPV = Array.isArray(tmp.ncitPV) ? tmp.ncitPV.join('|') : '';
}

dataset.push(tmp);
}
}
]
);
}
}

// You can define styles as json object
const styles = {
cellPink: {
fill: {
fgColor: {
rgb: '1F497D'
}
},
font:{
color: {
rgb: 'FFFFFF'
}
}
}
};

// You can then return this straight
res.attachment('report.xlsx'); // This is sails.js specific (in general you need to set headers)
res.send(report);
//Array of objects representing heading rows (very top)
const heading = [
];

//Here you specify the export structure
const specification = {
category: { // <- the key should match the actual data key
displayName: 'Category', // <- Here you specify the column header
headerStyle: styles.cellPink, // <- Header style
width: 220 // <- width in pixels
},
node: {
displayName: 'Node',
headerStyle: styles.cellPink,
width: 220 // <- width in chars (when the number is passed as string)
},
property: {
displayName: 'Property',
headerStyle: styles.cellPink,
width: 220 // <- width in pixels
},
value: {
displayName: 'GDC Values',
headerStyle: styles.cellPink,
width: 220 // <- width in pixels
},
ncit: {
displayName: 'NCIt Code',
headerStyle: styles.cellPink,
width: 220 // <- width in pixels
},
ncitPV: {
displayName: 'NCIt PV',
headerStyle: styles.cellPink,
width: 220 // <- width in pixels
},
icdo3: {
displayName: 'ICDO3 Code',
headerStyle: styles.cellPink,
width: 220 // <- width in pixels
},
icdoS: {
displayName: 'ICDO3 String',
headerStyle: styles.cellPink,
width: 220 // <- width in pixels
}
}

// Define an array of merges. 1-1 = A:1
// The merges are independent of the data.
// A merge will overwrite all data _not_ in the top-left cell.
const merges = [];

// Create the excel report.
// This function will return Buffer
const report = export_excel.buildExport(
[ // <- Notice that this is an array. Pass multiple sheets to create multi sheet report
{
name: 'Report', // <- Specify sheet name (optional)
heading: heading, // <- Raw heading array (optional)
merges: merges, // <- Merge cell ranges
specification: specification, // <- Report specification
data: dataset // <-- Report data
}
]
);

// You can then return this straight
res.attachment('GDC_Values_Data_Mapping.xlsx'); // This is sails.js specific (in general you need to set headers)
res.send(report);
}



const generateCompareProperties = async function(req, res) {
try {
const datasetnew = {};
Expand Down Expand Up @@ -1959,7 +2110,8 @@ module.exports = {
compareAllWithGDCDictionary,
exportCompareResult,
exportAllCompareResult,
generateProperties,
generateGDCPropertiesReport,
generateGDCValuesReport,
generateCompareProperties,
generateCompareNodes,
updateGDCPropertyMappings,
Expand Down
3 changes: 2 additions & 1 deletion server/service/search/index.js
View file
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,8 @@ router.get("/p/local/vs", controller.getGDCData);
router.get('/compareAllWithGDCDictionary', controller.compareAllWithGDCDictionary);
router.get('/exportCompareResult', controller.exportCompareResult);
router.get('/exportAllCompareResult', controller.exportAllCompareResult);
//router.get('/generateProperties', controller.generateProperties);
//router.get('/generateGDCPropertiesReport', controller.generateGDCPropertiesReport);
router.get('/generateGDCValuesReport', controller.generateGDCValuesReport);
//router.get('/generateCompareProperties', controller.generateCompareProperties);
//router.get('/generateCompareNodes', controller.generateCompareNodes);
//router.get('/updateGDCPropertyMappings', controller.updateGDCPropertyMappings);
Expand Down

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