@sjcrh/proteinpaint-server 2.16.0 → 2.17.0

package/shared/common.js

@@ -428,6 +428,10 @@ morigin[morigingermline] = {
 		'A constitutional variant found in a normal sample. The proportion is indicated by the span of the solid arc within the whole circle.',
 	legend: germlinelegend
 }
+
+morigin.germline = morigin[morigingermline]
+morigin.somatic = morigin[moriginsomatic]
+
 export const moriginrelapse = 'R'
 morigin[moriginrelapse] = {
 	label: 'Relapse',

package/src/serverconfig.js

@@ -177,7 +177,7 @@ if (!serverconfig.features) {
 	serverconfig.features = {}
 }
 
-if (!serverconfig.backend_only) {
+if (!serverconfig.backend_only && fs.existsSync(path.join(process.cwd(), './public'))) {
 	const defaultTarget = path.join(serverconfig.binpath, 'cards')
 	if (!serverconfig.cards) {
 		serverconfig.cards = {
@@ -187,9 +187,17 @@ if (!serverconfig.backend_only) {
 	}
 	const cards = serverconfig.cards
 	const cardsPath = path.join(process.cwd(), './public/', cards.path)
+
+	let cardsSymlink
+	try {
+		cardsSymlink = fs.lstatSync(cardsPath)
+	} catch (e) {
+		cardsSymlink = false
+	}
+
 	// only set up the symlink if the user doesn't already have a custom public/${cards.path} directory
 	// a user may also not specify cards.path for other reasons, in that case no need for symlink
-	if (cards.path && !fs.existsSync(cardsPath)) {
+	if (cards.path && !fs.existsSync(cardsPath) && !cardsSymlink) {
 		// a user may only wish to use a different public path for the cards
 		// and keep the defaulf of using server/cards
 		if (!cards.target) cards.target = defaultTarget

package/genome/genome.sql

@@ -1,54 +0,0 @@
-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);
-
-
-
-
-
-
-