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merge EVS-SIP-275 into EVS-sIP-274
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@fmanuelos
fmanuelos committed Oct 20, 2022
2 parents 3af6ae8 + 80da557 commit ad703f4
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Showing 7 changed files with 285 additions and 114 deletions.
2 changes: 1 addition & 1 deletion package-lock.json
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2 changes: 1 addition & 1 deletion package.json
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{
"name": "evs-sip",
"version": "v3.0.0",
"version": "v3.0.1",
"private": true,
"homepage": "/evssip/",
"dependencies": {
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24 changes: 15 additions & 9 deletions server/service/esapi/esapicontroller.js
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Original file line number Diff line number Diff line change
Expand Up @@ -374,18 +374,18 @@ const getGraphicalPCDCDictionary = (project = null, node, prop) => {
};
let result;

// TODO - fix result being empty after making same request for 2nd time
// if (project) {
// result = cache.getValue(`pcdc_dict_${project}`);
// } else {
// result = cache.getValue("pcdc_dict");
// }
// Read from cache
if (project) {
result = cache.getValue(`public_pcdc_dict_${project}`);
} else {
result = cache.getValue("public_pcdc_dict");
}

if (true || result === undefined) {
let jsonData = shared.readPCDCMapping();
result = generatePCDCData(jsonData, {});
//result = generatePCDCData(jsonData, {Relationships: {}});
cache.setValue("pcdc_dict", result, config.item_ttl);
cache.setValue("public_pcdc_dict", result, config.item_ttl);
}

// Obtain nodes from specified project
Expand Down Expand Up @@ -417,7 +417,13 @@ const getGraphicalPCDCDictionary = (project = null, node, prop) => {
project_result[n].links.push(linkItem);
}
});
cache.setValue("pcdc_dict_" + project, project_result, config.item_ttl);

// Cache the results
if (project) {
cache.setValue(`public_pcdc_dict_${project}`, project_result, config.item_ttl);
} else {
cache.setValue("public_pcdc_dict", project_result, config.item_ttl);
}

// Handle empty results
if (project_result.results.length === 0 ) {
Expand All @@ -442,7 +448,7 @@ const getPcdcNodes = (nodes, desiredNode, desiredProp) => {
const desiredNodes = [];

// Gather desired nodes into an array
for(const nodeName in nodes) {
for (const nodeName in nodes) {
const node = nodes[nodeName];
const isCorrectNode = node.node_name?.toLowerCase() === desiredNode?.toLowerCase();

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291 changes: 218 additions & 73 deletions server/service/search/controller.js
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Original file line number Diff line number Diff line change
Expand Up @@ -468,7 +468,7 @@ const getGraphicalCTDCDictionary = (req, res) => {
};

const getGraphicalPCDCDictionary = (req, res) => {
let project = req.query.project == "" ? "AML" : req.query.project;
let project = (req.query.project !== undefined && req.query.project !== '') ? req.query.project : 'AML';
let jsonData = shared.getGraphicalPCDCDictionary(project);
res.json(jsonData);
};
Expand Down Expand Up @@ -1290,92 +1290,236 @@ 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 : [];
let mappings = gdc_values[uid] !== undefined ? gdc_values[uid] : [];

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 = [];

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 +2103,8 @@ module.exports = {
compareAllWithGDCDictionary,
exportCompareResult,
exportAllCompareResult,
generateProperties,
generateGDCPropertiesReport,
generateGDCValuesReport,
generateCompareProperties,
generateCompareNodes,
updateGDCPropertyMappings,
Expand Down
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