Merge pull request #150 from bcgsc/release/v7.4.0

v7.4.0

Author: brayden-bcgsc

app/api/graphkb.js

@@ -59,48 +59,6 @@ const graphkbAutocomplete = async (targetType, graphkbToken, keyword = null) =>
   });
 };
 
-/**
- * Get review status of entries from GraphKB
- *
- * @param {string} graphkbToken the Authorization token for the connection to GraphKB
- * @param {array} graphkbEntries array of graphkb results from IPR database
- *
- * @returns {object} response body from graphkb
- */
-const graphkbReviewStatus = async (graphkbToken, graphkbEntries) => {
-  const {uri} = CONFIG.get('graphkb');
-
-  const filters = {
-    '@rid': graphkbEntries
-      .reduce((filtered, {kbStatementId}) => {
-        if (kbStatementId.match(/^#\d+:\d+$/)) {
-          filtered.push(kbStatementId);
-        }
-        return filtered;
-      }, []),
-    operator: 'IN',
-  };
-  const query = {
-    target: 'Statement',
-    filters,
-    returnProperties: ['@class', '@rid', 'reviewStatus'],
-    orderBy: ['@rid'],
-  };
-
-  const {result} = await request({
-    url: `${uri}/query`,
-    method: 'POST',
-    body: JSON.stringify(query),
-    json: true,
-    headers: {
-      Authorization: graphkbToken,
-      'Content-Type': 'application/json',
-    },
-  });
-
-  return result;
-};
-
 /* Get IPR evidence level descriptions from GraphKB
  *
  * @param {string} graphkbToken the Authorization token for the connection to GraphKB
@@ -138,5 +96,4 @@ const graphkbEvidenceLevels = async (graphkbToken) => {
 module.exports = {
   graphkbAutocomplete,
   graphkbEvidenceLevels,
-  graphkbReviewStatus,
 };

app/constants.js

@@ -26,7 +26,7 @@ module.exports = {
     'mutationBurden\\.(barplot|density|legend)_(sv|snv|indel|snv_indel)\\.(primary|secondary|tertiary|quaternary)',
     'circosSv\\.(genome|transcriptome)',
     'expDensity\\.(histogram|violin\\.(tcga|gtex|cser|hartwig|pediatric))\\.\\S+',
-    'expression\\.(chart|legend|spearman\\.(tcga|gtex|cser|hartwig|target))',
+    'expression\\.(chart|legend|spearman\\.(tcga|gtex|cser|hartwig|target|pediatric))',
     'microbial\\.circos\\.(genome|transcriptome)',
     'cibersort\\.(cd8_positive|combined)_t-cell_scatter',
     'mixcr\\.circos_trb_vj_gene_usage',

app/libs/image.js

@@ -15,7 +15,7 @@ const db = require('../models');
  */
 const processImage = async (image, width, height, format = 'png') => {
   const imageData = await sharp(image)
-    .resize(width, height, {fit: 'inside'})
+    .resize(width, height, {fit: 'inside', withoutEnlargement: true})
     .toFormat(format.toLowerCase())
     .toBuffer();
 

app/models/clearCache.js

@@ -169,20 +169,28 @@ module.exports = async (instance, method) => {
     case 'signatures':
       return removeKeys(`/reports/${report.ident}/signatures`);
     case 'smallMutations':
-      return removeKeys(`/reports/${report.ident}/small-mutations`);
+      return Promise.all([
+        batchDeleteKeysByPattern(`/reports/${report.ident}/kb-matches*`),
+        removeKeys(`/reports/${report.ident}/small-mutations`),
+      ]);
     case 'copyVariants':
     case 'expressionVariants':
     case 'structuralVariants':
+    case 'proteinVariants':
     case 'kbMatches':
-      return removeKeys([
-        `/reports/${report.ident}/copy-variants`,
-        `/reports/${report.ident}/expression-variants`,
-        `/reports/${report.ident}/small-mutations`,
-        `/reports/${report.ident}/structural-variants`,
+      return Promise.all([
+        batchDeleteKeysByPattern(`/reports/${report.ident}/kb-matches*`),
+        removeKeys([
+          `/reports/${report.ident}/copy-variants`,
+          `/reports/${report.ident}/expression-variants`,
+          `/reports/${report.ident}/small-mutations`,
+          `/reports/${report.ident}/structural-variants`,
+        ]),
       ]);
     case 'genes':
       return Promise.all([
         batchDeleteKeysByPattern(`/reports/${report.ident}/genes*`),
+        batchDeleteKeysByPattern(`/reports/${report.ident}/kb-matches*`),
         removeKeys([
           `/reports/${report.ident}/copy-variants`,
           `/reports/${report.ident}/expression-variants`,

app/models/reports/copyVariants.js

@@ -64,6 +64,9 @@ module.exports = (sequelize, Sq) => {
     cna: {
       type: Sq.NUMERIC,
     },
+    germline: {
+      type: Sq.BOOLEAN,
+    },
   }, {
     ...DEFAULT_REPORT_OPTIONS,
     tableName: 'reports_copy_variants',

app/models/reports/expressionVariants.js

@@ -140,6 +140,9 @@ module.exports = (sequelize, Sq) => {
       field: 'kb_category',
       type: Sq.TEXT,
     },
+    germline: {
+      type: Sq.BOOLEAN,
+    },
   }, {
     ...DEFAULT_REPORT_OPTIONS,
     tableName: 'reports_expression_variants',

app/models/reports/genomic/summary/genomicAlterationsIdentified.js

@@ -16,6 +16,9 @@ module.exports = (sequelize, Sq) => {
       type: Sq.TEXT,
       allowNull: false,
     },
+    germline: {
+      type: Sq.BOOLEAN,
+    },
   }, {
     ...DEFAULT_REPORT_OPTIONS,
     tableName: 'reports_summary_genomic_alterations_identified',

app/models/reports/kbMatches.js

@@ -116,6 +116,11 @@ module.exports = (sequelize, Sq) => {
       field: 'external_statement_id',
       type: Sq.TEXT,
     },
+    reviewStatus: {
+      name: 'reviewStatus',
+      field: 'review_status',
+      type: Sq.TEXT,
+    },
   }, {
     ...DEFAULT_REPORT_OPTIONS,
     tableName: 'reports_kb_matches',

app/models/reports/probeTestInformation.js

@@ -54,6 +54,20 @@ module.exports = (sequelize, Sq) => {
       allowNull: false,
       defaultValue: -1,
     },
+    cancerGenes: {
+      name: 'cancerGenes',
+      field: 'cancer_genes',
+      type: Sq.INTEGER,
+      allowNull: false,
+      defaultValue: -1,
+    },
+    cancerVars: {
+      name: 'cancerVars',
+      field: 'cancer_vars',
+      type: Sq.INTEGER,
+      allowNull: false,
+      defaultValue: -1,
+    },
     pharmacogenomicGenes: {
       name: 'pharmacogenomicGenes',
       field: 'pharmacogenomic_genes',

app/models/reports/proteinVariants.js

@@ -66,6 +66,9 @@ module.exports = (sequelize, Sq) => {
       field: 'kb_category',
       type: Sq.TEXT,
     },
+    germline: {
+      type: Sq.BOOLEAN,
+    },
   }, {
     ...DEFAULT_REPORT_OPTIONS,
     tableName: 'reports_protein_variants',