Merge pull request #1159 from dondi/beta

v7.2 release candidate

.github/workflows/node.js.yml

@@ -0,0 +1,35 @@
+# This workflow will do a clean installation of node dependencies, cache/restore them, build the source code and run tests across different versions of node
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-nodejs
+
+name: Node.js CI
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        node-version: [18.x, 20.x, 22.x]
+
+    steps:
+    - uses: actions/checkout@v4
+    # install system dependencies needed by the 'canvas' package
+    - name: Install dependencies for canvas
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y libcairo2-dev libpango1.0-dev libjpeg62 libgif-dev librsvg2-dev
+    - name: Use Node.js ${{ matrix.node-version }}
+      uses: actions/setup-node@v4
+      with:
+        node-version: ${{ matrix.node-version }}
+        cache: 'npm'
+
+    - run: npm ci
+    - run: npm run lint 
+    - run: npm run build --if-present
+    - run: npm test
+
+

README.md

@@ -3,6 +3,7 @@ GRNsight
 [![DOI](https://zenodo.org/badge/16195791.svg)](https://zenodo.org/badge/latestdoi/16195791)
 [![Build Status](https://app.travis-ci.com/dondi/GRNsight.svg?branch=master)](https://app.travis-ci.com/dondi/GRNsight)
 [![Coverage Status](https://coveralls.io/repos/github/dondi/GRNsight/badge.svg?branch=master)](https://coveralls.io/github/dondi/GRNsight?branch=master)
+[![Node.js CI](https://github.com/dondi/GRNsight/actions/workflows/node.js.yml/badge.svg)](https://github.com/dondi/GRNsight/actions/workflows/node.js.yml)
 
 http://dondi.github.io/GRNsight/
 

database/network-database/schema.sql

@@ -20,6 +20,6 @@ CREATE TABLE gene_regulatory_network.network (
   time_stamp TIMESTAMP WITH TIME ZONE,
   source VARCHAR,
   FOREIGN KEY (regulator_gene_id, taxon_id) REFERENCES gene_regulatory_network.gene(gene_id, taxon_id),
-  FOREIGN KEY (target_gene_id, taxon_id) REFERENCES gene_regulatory_network_testing.gene(gene_id, taxon_id),
-  FOREIGN KEY (time_stamp, source) REFERENCES gene_regulatory_network_testing.source(time_stamp, source)
+  FOREIGN KEY (target_gene_id, taxon_id) REFERENCES gene_regulatory_network.gene(gene_id, taxon_id),
+  FOREIGN KEY (time_stamp, source) REFERENCES gene_regulatory_network.source(time_stamp, source)
 ); 

database/protein-protein-database/schema.sql

@@ -20,7 +20,7 @@ CREATE TABLE protein_protein_interactions.protein (
   molecular_weight FLOAT,
   PI FLOAT,
   taxon_id VARCHAR,
-  FOREIGN KEY (gene_systematic_name, taxon_id) REFERENCES protein_protein_interactions_testing.gene(gene_id, taxon_id)
+  FOREIGN KEY (gene_systematic_name, taxon_id) REFERENCES protein_protein_interactions.gene(gene_id, taxon_id)
 );
 
 CREATE TABLE protein_protein_interactions.physical_interactions (
@@ -30,8 +30,8 @@ CREATE TABLE protein_protein_interactions.physical_interactions (
   experiment_name VARCHAR,
   time_stamp TIMESTAMP WITH TIME ZONE,
   source VARCHAR,
-  FOREIGN KEY (protein1) REFERENCES protein_protein_interactions_testing.protein(standard_name),
-  FOREIGN KEY (protein2) REFERENCES protein_protein_interactions_testing.protein(standard_name),
-  FOREIGN KEY (time_stamp, source) REFERENCES protein_protein_interactions_testing.source(time_stamp, source),
+  FOREIGN KEY (protein1) REFERENCES protein_protein_interactions.protein(standard_name),
+  FOREIGN KEY (protein2) REFERENCES protein_protein_interactions.protein(standard_name),
+  FOREIGN KEY (time_stamp, source) REFERENCES protein_protein_interactions.source(time_stamp, source),
   CONSTRAINT unique_physical_interaction UNIQUE (protein1, protein2, interaction_detection_methods_identifier, experiment_name, time_stamp, source)
 );