@sjcrh/proteinpaint-server 2.14.4 → 2.16.0

package/genome/genome.sql

@@ -0,0 +1,54 @@
+CREATE TABLE genes (
+  name character varying(50) collate nocase primary key not null,
+  isoform character varying(50) collate nocase,
+  isdefault smallint,
+  genemodel json
+);
+CREATE INDEX geneisoform on genes(isoform collate nocase);
+
+
+CREATE TABLE genealias (
+  alias character varying(50) collate nocase,
+  name character varying(50) collate nocase,
+  foreign key(name) references genes(name) on delete cascade on update cascade
+);
+CREATE INDEX aliastext on genealias(alias collate nocase);
+
+
+CREATE TABLE gene2canonicalisoform (
+	gene character collate nocase primary key not null,
+	isoform character collate nocase,
+    foreign key(gene) references genes(name) on delete cascade on update cascade
+
+);
+
+CREATE TABLE gene2coord (
+  name char(100) collate nocase primary key not null,
+  chr char(100) collate nocase,
+  start INTEGER,
+  stop INTEGER,
+  foreign key(name) references genes(name) on delete cascade on update cascade
+
+);
+
+CREATE TABLE refseq2ensembl (
+  ensembl char(100) collate nocase,
+  refseq char(100) collate nocase
+);
+CREATE INDEX r2er on refseq2ensembl(refseq);
+CREATE INDEX r2ee on refseq2ensembl(ensembl);
+
+CREATE TABLE isoform2gene (
+	gene character collate nocase,
+	isoform character collate nocase,
+    foreign key(gene) references genes(name) on delete cascade on update cascade
+
+);
+CREATE INDEX isoform2gene_isoform on isoform2gene(isoform);
+
+
+
+
+
+
+

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.14.4",
+  "version": "2.16.0",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "server.js",
   "bin": "start.js",
@@ -10,10 +10,10 @@
   },
   "scripts": {
     "dev": "webpack --env NODE_ENV=development --watch --color",
-    "start": "nodemon server.js --watch ./server*.js* --watch genome --watch dataset",
+    "start": "nodemon --enable-source-maps server.js --watch ./server*.js* --watch genome --watch dataset",
     "pretest": "./test/pretest.js",
-    "test": "webpack --env NODE_ENV=test exportsFilename=all-test-context.js && node test/serverTests.js",
-    "test:unit": "webpack --env NODE_ENV=test exportsFilename=unit-test-context.js && node test/serverTests.js",
+    "test": "webpack --env NODE_ENV=test exportsFilename=all-test-context.js && node --enable-source-maps test/serverTests.js",
+    "test:unit": "webpack --env NODE_ENV=test exportsFilename=unit-test-context.js && node --enable-source-maps test/serverTests.js",
     "test:integration": "echo 'TODO: server integration tests'",
     "prepack": "webpack --env NODE_ENV=production",
     "response": "nodemon modules/test/test.server.js --watch src",
@@ -38,7 +38,7 @@
     "webpack-notifier": "^1.15.0"
   },
   "dependencies": {
-    "@sjcrh/proteinpaint-rust": "2.11.1",
+    "@sjcrh/proteinpaint-rust": "2.12.0",
     "better-sqlite3": "^7.5.3",
     "body-parser": "^1.15.2",
     "canvas": "~2.9.3",