@gen3/core 0.11.31 → 0.11.33

package/dist/cjs/index.js

@@ -6,18 +6,18 @@ var cookiesNext = require('cookies-next');
 var query = require('@reduxjs/toolkit/query');
 var reactRedux = require('react-redux');
 var React = require('react');
+var graphql = require('graphql');
+var jsonpathPlus = require('jsonpath-plus');
 var nanoid$1 = require('nanoid');
 var useSWR = require('swr');
 var lodash = require('lodash');
 var flat = require('flat');
 var Papa = require('papaparse');
-var jsonpathPlus = require('jsonpath-plus');
 var reduxPersist = require('redux-persist');
 var createWebStorage = require('redux-persist/lib/storage/createWebStorage');
 var react$1 = require('redux-persist/integration/react');
 var idb = require('idb');
 var useDeepCompare = require('use-deep-compare');
-var graphql = require('graphql');
 var uuid = require('uuid');
 var reactCookie = require('react-cookie');
 var Queue = require('queue');
@@ -806,6 +806,15 @@ const selectRequestedWorkspaceStatusTimestamp = (state)=>state.activeWorkspace.r
                 data: await response.json()
             };
         } catch (e) {
+            if (e instanceof graphql.GraphQLError) {
+                return {
+                    error: {
+                        message: e.message,
+                        locations: e.locations,
+                        path: e.path
+                    }
+                };
+            }
             if (e instanceof Error) return {
                 error: e.message
             };
@@ -1615,6 +1624,36 @@ const filterSetToOperation = (fs)=>{
     }
     return undefined;
 };
+/**
+ * Constructs a nested operation object based on the provided field and leaf operand.
+ * If the field does not contain a dot '.', it either assigns the field to the leaf operand (if applicable)
+ * or returns the leaf operand as is. When the field contains dots, it splits the field into parts,
+ * creates a "nested" operation for the root field, and recursively constructs the nested structure
+ * for the remaining portion of the field.
+ *
+ * @param {string} field - The hierarchical field path, with segments separated by dots (e.g., "root.child").
+ * @param {Operation} leafOperand - The operation to be nested within the specified path.
+ * @param parentPath - The parent path of the current field. Guppy nested filters require a parent path.
+ * @param depth
+ * @returns {Operation} A nested operation object that represents the structured path and operand.
+ */ const buildNestedGQLFilter = (field, leafOperand, parentPath = undefined)=>{
+    if (!field.includes('.')) {
+        return leafOperand;
+    }
+    const splitFieldArray = field.split('.');
+    const nextField = splitFieldArray.shift();
+    if (!nextField) {
+        console.warn('Invalid field path:', field);
+        return leafOperand;
+    }
+    const currentPath = parentPath ? `${parentPath}.${nextField}` : nextField;
+    return {
+        nested: {
+            path: currentPath,
+            ...buildNestedGQLFilter(splitFieldArray.join('.'), leafOperand, currentPath)
+        }
+    };
+};
 
 const isFilterSet = (input)=>{
     if (typeof input !== 'object' || input === null) {
@@ -1669,7 +1708,7 @@ const COMMON_PREPOSITIONS = [
     'up',
     'yet'
 ];
-const capitalize = (s)=>s.length > 0 ? s[0].toUpperCase() + s.slice(1) : '';
+const capitalize$1 = (s)=>s.length > 0 ? s[0].toUpperCase() + s.slice(1) : '';
 const trimFirstFieldNameToTitle = (fieldName, trim = false)=>{
     if (trim) {
         const source = fieldName.slice(fieldName.indexOf('.') + 1);
@@ -1688,7 +1727,7 @@ const trimFirstFieldNameToTitle = (fieldName, trim = false)=>{
         return FieldNameOverrides[fieldName];
     }
     if (fieldName === undefined) return 'No Title';
-    return fieldName.split('.').slice(-sections).map((s)=>s.split('_')).flat().map((word)=>COMMON_PREPOSITIONS.includes(word) ? word : capitalize(word)).join(' ');
+    return fieldName.split('.').slice(-sections).map((s)=>s.split('_')).flat().map((word)=>COMMON_PREPOSITIONS.includes(word) ? word : capitalize$1(word)).join(' ');
 };
 /**
  * Extracts the index name from the field name
@@ -1870,14 +1909,22 @@ function isHttpStatusError(error) {
  * @param {string} csrfToken - The CSRF token to include in the request headers.
  * @returns {FetchConfig} - The prepared fetch configuration object.
  */ const prepareFetchConfig = (parameters, csrfToken)=>{
+    const headers = new Headers({
+        Accept: 'application/json',
+        'Content-Type': 'application/json',
+        ...csrfToken !== undefined && {
+            'X-CSRF-Token': csrfToken
+        }
+    });
+    if (process.env.NODE_ENV === 'development') {
+        // NOTE: This cookie can only be accessed from the client side
+        // in development mode. Otherwise, the cookie is set as httpOnly
+        const accessToken = cookiesNext.getCookie('credentials_token');
+        if (accessToken) headers.set('Authorization', `Bearer ${accessToken}`);
+    }
     return {
         method: 'POST',
-        headers: {
-            'Content-Type': 'application/json',
-            ...csrfToken !== undefined && {
-                'X-CSRF-Token': csrfToken
-            }
-        },
+        headers: headers,
         body: JSON.stringify({
             type: parameters.type,
             filter: convertFilterSetToGqlFilter(parameters.filter),
@@ -2062,6 +2109,88 @@ const groupSharedFields = (data)=>{
     return data;
 };
 
+const customQueryStrForField = (field, query, depth = 0)=>{
+    const indent = '  '.repeat(depth);
+    const splittedFieldArray = field.split('.');
+    const splittedField = splittedFieldArray.shift();
+    if (splittedFieldArray.length === 0) {
+        return `${indent}${splittedField} ${query}`;
+    }
+    return `${indent}${splittedField} {
+${customQueryStrForField(splittedFieldArray.join('.'), query, depth + 1)}
+${indent}}`;
+};
+// TODO: refactor the function below using customQueryStrForEachField and a wrapper function that passes the query
+const histogramQueryStrForEachField = (field)=>{
+    const splittedFieldArray = field.split('.');
+    const splittedField = splittedFieldArray.shift();
+    if (splittedFieldArray.length === 0) {
+        return `
+    ${splittedField} {
+      histogram {
+        key
+        count
+      }
+    }`;
+    }
+    return `
+  ${splittedField} {
+    ${histogramQueryStrForEachField(splittedFieldArray.join('.'))}
+  }`;
+};
+const statsQueryStrForEachField = (field)=>{
+    const splittedFieldArray = field.split('.');
+    const splittedField = splittedFieldArray.shift();
+    if (splittedFieldArray.length === 0) {
+        return `
+    ${splittedField} {
+      histogram {
+                count
+                min
+                max
+                avg
+                sum
+      }
+    }`;
+    }
+    return `
+  ${splittedField} {
+    ${statsQueryStrForEachField(splittedFieldArray.join('.'))}
+  }`;
+};
+const nestedHistogramQueryStrForEachField = (mainField, numericAggAsText)=>`
+  ${mainField} {
+    ${numericAggAsText ? 'asTextHistogram' : 'histogram'} {
+      key
+      count
+      missingFields {
+        field
+        count
+      }
+      termsFields {
+        field
+        count
+        terms {
+          key
+          count
+        }
+      }
+    }
+  }`;
+const rawDataQueryStrForEachField = (field)=>{
+    const splitFieldArray = field.split('.');
+    const splitField = splitFieldArray.shift();
+    if (splitFieldArray.length === 0) {
+        return `
+    ${splitField}
+    `;
+    }
+    return `
+  ${splitField} {
+    ${rawDataQueryStrForEachField(splitFieldArray.join('.'))}
+  }`;
+};
+
 const statusEndpoint = '/_status';
 const fetchJson = async (url)=>{
     const res = await fetch(url, {
@@ -2342,75 +2471,6 @@ const explorerTags = guppyApi.enhanceEndpoints({
             })
         })
 });
-const histogramQueryStrForEachField = (field)=>{
-    const splittedFieldArray = field.split('.');
-    const splittedField = splittedFieldArray.shift();
-    if (splittedFieldArray.length === 0) {
-        return `
-    ${splittedField} {
-      histogram {
-        key
-        count
-      }
-    }`;
-    }
-    return `
-  ${splittedField} {
-    ${histogramQueryStrForEachField(splittedFieldArray.join('.'))}
-  }`;
-};
-const statsQueryStrForEachField = (field)=>{
-    const splittedFieldArray = field.split('.');
-    const splittedField = splittedFieldArray.shift();
-    if (splittedFieldArray.length === 0) {
-        return `
-    ${splittedField} {
-      histogram {
-                count
-                min
-                max
-                avg
-                sum
-      }
-    }`;
-    }
-    return `
-  ${splittedField} {
-    ${statsQueryStrForEachField(splittedFieldArray.join('.'))}
-  }`;
-};
-const nestedHistogramQueryStrForEachField = (mainField, numericAggAsText)=>`
-  ${mainField} {
-    ${numericAggAsText ? 'asTextHistogram' : 'histogram'} {
-      key
-      count
-      missingFields {
-        field
-        count
-      }
-      termsFields {
-        field
-        count
-        terms {
-          key
-          count
-        }
-      }
-    }
-  }`;
-const rawDataQueryStrForEachField = (field)=>{
-    const splitFieldArray = field.split('.');
-    const splitField = splitFieldArray.shift();
-    if (splitFieldArray.length === 0) {
-        return `
-    ${splitField}
-    `;
-    }
-    return `
-  ${splitField} {
-    ${rawDataQueryStrForEachField(splitFieldArray.join('.'))}
-  }`;
-};
 const useGetArrayTypes = ()=>{
     {
         const { data, error } = useGetStatus();
@@ -2762,6 +2822,28 @@ const fetchFencePresignedURL = async ({ guid, method = 'GET', onAbort = ()=>null
     return await response.json();
 };
 
+const extractValuesFromObject = (jsonPathMappings, obj)=>{
+    const result = {};
+    const extractObjectValue = (jsonPath, obj)=>{
+        const extractedValues = jsonpathPlus.JSONPath({
+            path: jsonPath,
+            json: obj
+        });
+        return extractedValues.length > 0 ? extractedValues[0] : undefined;
+    };
+    for(const key in jsonPathMappings){
+        if (key in Object.keys(jsonPathMappings)) {
+            // Extract value from an object and store it in the result.
+            result[key] = extractObjectValue(jsonPathMappings[key], obj);
+        }
+    }
+    return result;
+};
+const ExtractValueFromObject = (obj, key, valueIfNotFound)=>{
+    return obj?.[key] ?? valueIfNotFound;
+};
+
+const DAYS_IN_YEAR = 365.25;
 /**
  * Converts HistogramData to HistogramDataAsStringKey by ensuring the key is a string.
  * If the key is already a string, it's used as is.
@@ -2777,6 +2859,79 @@ const fetchFencePresignedURL = async ({ guid, method = 'GET', onAbort = ()=>null
 };
 const calculatePercentageAsNumber = (count, total)=>count ? count / total * 100 : 0;
 const calculatePercentageAsString = (count, total)=>`${(count / total * 100).toFixed(2)}%`;
+const capitalize = (original)=>{
+    const customCapitalizations = {
+        id: 'ID',
+        uuid: 'UUID',
+        dna: 'DNA',
+        dbsnp: 'dbSNP',
+        cosmic: 'COSMIC',
+        civic: 'CIViC',
+        dbgap: 'dbGaP',
+        ecog: 'ECOG',
+        bmi: 'BMI',
+        gdc: 'GDC',
+        cnv: 'CNV',
+        ssm: 'SSM',
+        aa: 'AA'
+    };
+    return original.split(' ').map((word)=>customCapitalizations[word.toLowerCase()] || `${word.charAt(0).toUpperCase()}${word.slice(1)}`).join(' ');
+};
+const humanify = ({ term = '', capitalize: cap = true, facetTerm = false })=>{
+    let original;
+    let humanified;
+    if (facetTerm) {
+        // Splits on capital letters followed by lowercase letters to find
+        // words squished together in a string.
+        original = term?.split(/(?=[A-Z][a-z])/).join(' ');
+        humanified = term?.replace(/\./g, ' ').replace(/_/g, ' ').trim();
+    } else {
+        const split = (original || term)?.split('.');
+        humanified = split[split.length - 1]?.replace(/_/g, ' ').trim();
+        // Special case 'name' to include any parent nested for sake of
+        // specificity in the UI
+        if (humanified === 'name' && split?.length > 1) {
+            humanified = `${split[split?.length - 2]} ${humanified}`;
+        }
+    }
+    return cap ? capitalize(humanified) : humanified;
+};
+/*https://github.com/NCI-GDC/portal-ui/blob/develop/src/packages/%40ncigdc/utils/ageDisplay.js*/ /**
+ * Converts age in days into a human-readable format.
+ *
+ * @param ageInDays - The age in days.
+ * @param yearsOnly - If true, only display years.
+ *   @defaultValue false
+ * @param defaultValue - The default value to return if ageInDays is falsy.
+ *   @defaultValue "--"
+ * @returns The formatted age string.
+ */ const ageDisplay = (ageInDays, yearsOnly = false, defaultValue = '--')=>{
+    if (ageInDays !== 0 && !ageInDays) {
+        return defaultValue;
+    }
+    const calculateYearsAndDays = (years, days)=>days === 365 ? [
+            years + 1,
+            0
+        ] : [
+            years,
+            days
+        ];
+    const ABS_AGE_DAYS = Math.abs(ageInDays);
+    const [years, remainingDays] = calculateYearsAndDays(Math.floor(ABS_AGE_DAYS / DAYS_IN_YEAR), Math.ceil(ABS_AGE_DAYS % DAYS_IN_YEAR));
+    const formattedYears = years === 0 ? '' : `${years} ${years === 1 ? 'year' : 'years'}`;
+    const formattedDays = !yearsOnly && remainingDays > 0 ? `${remainingDays} ${remainingDays === 1 ? 'day' : 'days'}` : years === 0 && remainingDays === 0 ? '0 days' : '';
+    const ageString = [
+        formattedYears,
+        formattedDays
+    ].filter(Boolean).join(' ');
+    return ageInDays >= 0 ? ageString : `-${ageString}`;
+};
+/**
+ * Given an object of JSON, stringify it into a string.
+ * @param obj - the object to stringify
+ * @param defaults - the default value to return if the object is undefined
+ * @category Utility
+ */ const stringifyJSONParam = (obj, defaults = '{}')=>obj ? JSON.stringify(obj) : defaults;
 
 const queryWTSFederatedLoginStatus = async (signal)=>{
     try {
@@ -4768,7 +4923,7 @@ const { useGraphQLQuery } = graphQLAPI;
                     return {
                         url: `${GEN3_GUPPY_API}/download`,
                         method: 'POST',
-                        body: JSON.stringify(queryBody),
+                        body: queryBody,
                         cache: 'no-cache'
                     };
                 },
@@ -5321,24 +5476,6 @@ const userHasMethodOnAnyProject = (method, userAuthMapping = {})=>{
 };
 const userHasCreateOrUpdateOnAnyProject = (userAuthMapping = {})=>userHasMethodOnAnyProject('create', userAuthMapping) || userHasMethodOnAnyProject('update', userAuthMapping);
 
-const extractValuesFromObject = (jsonPathMappings, obj)=>{
-    const result = {};
-    const extractObjectValue = (jsonPath, obj)=>{
-        const extractedValues = jsonpathPlus.JSONPath({
-            path: jsonPath,
-            json: obj
-        });
-        return extractedValues.length > 0 ? extractedValues[0] : undefined;
-    };
-    for(const key in jsonPathMappings){
-        if (key in Object.keys(jsonPathMappings)) {
-            // Extract value from an object and store it in the result.
-            result[key] = extractObjectValue(jsonPathMappings[key], obj);
-        }
-    }
-    return result;
-};
-
 const SubmissionGraphqlQuery = `query transactionList {
     transactionList: transaction_log(last: 20) {
       id
@@ -5624,10 +5761,12 @@ const isWorkspaceRunningOrStopping = (status)=>status === WorkspaceStatus.Runnin
 exports.Accessibility = Accessibility;
 exports.CohortStorage = CohortStorage;
 exports.CoreProvider = CoreProvider;
+exports.DAYS_IN_YEAR = DAYS_IN_YEAR;
 exports.DataLibraryStoreMode = DataLibraryStoreMode;
 exports.EmptyFilterSet = EmptyFilterSet;
 exports.EmptyWorkspaceStatusResponse = EmptyWorkspaceStatusResponse;
 exports.EnumValueExtractorHandler = EnumValueExtractorHandler;
+exports.ExtractValueFromObject = ExtractValueFromObject;
 exports.GEN3_API = GEN3_API;
 exports.GEN3_AUTHZ_API = GEN3_AUTHZ_API;
 exports.GEN3_COMMONS_NAME = GEN3_COMMONS_NAME;
@@ -5653,12 +5792,15 @@ exports.RequestedWorkspaceStatus = RequestedWorkspaceStatus;
 exports.ToGqlHandler = ToGqlHandler;
 exports.ValueExtractorHandler = ValueExtractorHandler;
 exports.WorkspaceStatus = WorkspaceStatus;
+exports.ageDisplay = ageDisplay;
 exports.appendFilterToOperation = appendFilterToOperation;
 exports.buildGetAggregationQuery = buildGetAggregationQuery;
 exports.buildGetStatsAggregationQuery = buildGetStatsAggregationQuery;
 exports.buildListItemsGroupedByDataset = buildListItemsGroupedByDataset;
+exports.buildNestedGQLFilter = buildNestedGQLFilter;
 exports.calculatePercentageAsNumber = calculatePercentageAsNumber;
 exports.calculatePercentageAsString = calculatePercentageAsString;
+exports.capitalize = capitalize;
 exports.clearActiveWorkspaceId = clearActiveWorkspaceId;
 exports.clearCohortFilters = clearCohortFilters;
 exports.cohortReducer = cohortReducer;
@@ -5674,6 +5816,7 @@ exports.createGen3App = createGen3App;
 exports.createGen3AppWithOwnStore = createGen3AppWithOwnStore;
 exports.createNewCohort = createNewCohort;
 exports.createUseCoreDataHook = createUseCoreDataHook;
+exports.customQueryStrForField = customQueryStrForField;
 exports.defaultCohortNameGenerator = defaultCohortNameGenerator;
 exports.downloadFromGuppyToBlob = downloadFromGuppyToBlob;
 exports.downloadJSONDataFromGuppy = downloadJSONDataFromGuppy;
@@ -5714,6 +5857,7 @@ exports.handleGqlOperation = handleGqlOperation;
 exports.handleOperation = handleOperation;
 exports.hideModal = hideModal;
 exports.histogramQueryStrForEachField = histogramQueryStrForEachField;
+exports.humanify = humanify;
 exports.isAdditionalDataItem = isAdditionalDataItem;
 exports.isArray = isArray;
 exports.isAuthenticated = isAuthenticated;
@@ -5834,6 +5978,7 @@ exports.setShouldShareFilters = setShouldShareFilters;
 exports.setupCoreStore = setupCoreStore;
 exports.showModal = showModal;
 exports.statsQueryStrForEachField = statsQueryStrForEachField;
+exports.stringifyJSONParam = stringifyJSONParam;
 exports.submissionApi = submissionApi;
 exports.toggleCohortBuilderAllFilters = toggleCohortBuilderAllFilters;
 exports.toggleCohortBuilderCategoryFilter = toggleCohortBuilderCategoryFilter;