.gitlab-ci.yml

@@ -3,6 +3,7 @@ stages:
   - prettier
   - test
   - deploy
+  - packaging
 cache:
   paths:
     - ~/.cache
@@ -75,3 +76,22 @@ deploy_staging:
     - vercel pull --yes --environment=production --token=$VERCEL_TOKEN
     - vercel build --prod --token=$VERCEL_TOKEN
     - vercel deploy --prebuilt --prod --token=$VERCEL_TOKEN
+
+build:deb:
+  image: node:16.16.0
+  stage: packaging
+  only:
+    - tags
+    - development
+  before_script:
+    - apt-get update
+    - DEBIAN_FRONTEND=noninteractive apt-get install -y dh-make build-essential lintian devscripts xsltproc fakeroot xsltproc docbook-xsl curl gnupg git zip
+  artifacts:
+    # you cannot enforce never here yet
+    expire_in: 1000 yrs
+    paths:
+      - 'debian/*.deb'
+  script:
+    - export DEBFULLNAME="Piotr Gawron"
+    - export DEBEMAIL="piotr.gawron@uni.lu"
+    - debian/create-debian-pkg.sh

CHANGELOG

+minerva-front (18.0.0~beta.5) stable; urgency=medium
+  * Small improvements: when exporting map as image provide default selections
+    in for format and submap  (#295)
+  * Small improvements: dropdown sections in exporting map as image are
+    unfolded permanently (#296)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 04 Oct 2024 13:00:00 +0200
+
+minerva-front (18.0.0~beta.4) stable; urgency=medium
+  * Bugfix: connectivity issue should report a problem with network instead of
+    submitting error report(#293)
+  * Bugfix: source map for js was missing (#292)
+  * Bugfix: sometimes project don't have link to disease or organism, this
+    crashed listing of projects after log in (#290)
+  * Bugfix: show proper message when there is a problem with overlay data
+    instead error report form (#291)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 02 Oct 2024 13:00:00 +0200
+
+minerva-front (18.0.0~beta.3) stable; urgency=medium
+  * Bugfix: link to download project source was invalid
+  * Bugfix: change background to empty after overlay is loaded so there is no
+    blank background (#285)
+  * Bugfix: license info styling (#280)
+  * Bugfix: list of plugins did not contain version (#287)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 26 Sep 2024 13:00:00 +0200
+
+minerva-front (18.0.0~beta.2) stable; urgency=medium
+  * Feature: minerva frontend - first version
+  * Bugfix: when opening overlay provide loading info (#285)
+  * Bugfix: problem with reporting errors in minervanet (#284)
+  * Bugfix: license info styling (#284)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 19 Sep 2024 13:00:00 +0200

debian/create-debian-pkg.sh

+#!/bin/bash
+
+set -e
+
+#Where source file of the debian package should be placed
+SRC_DIR=debian/src
+
+ROOT_DIR=`pwd`
+
+#clean build directories
+rm -rf $SRC_DIR debian/minerva-front*
+
+#recreate directory
+mkdir $SRC_DIR
+
+export APP_PREFIX=/minerva
+npm install
+npm run build
+cp -r out $SRC_DIR/front
+
+cd $SRC_DIR
+zip -r front.zip front
+rm -r front
+cd $ROOT_DIR
+
+#copy changelog file
+cp CHANGELOG $ROOT_DIR/debian/template/changelog
+
+current_version=`cat CHANGELOG |grep minerva-front |head -1 | cut -f2 -d'(' | cut -f1 -d')'`
+
+echo "Current version: " $current_version
+
+#dh_make requires directory name to be like <package>-<version>
+# this points to the directory
+DEBIAN_DIR=debian/minerva-front-$current_version/
+
+mkdir $DEBIAN_DIR
+
+# copy all source files to this directory
+cp $SRC_DIR/* $DEBIAN_DIR
+
+#because dh_make works only from within directory where
+#package data will be generated we need to change it
+cd $DEBIAN_DIR
+#this should be improved (to include src properly)
+dh_make -s --createorig -e piotr.gawron@uni.lu -y -t $ROOT_DIR/debian/template
+
+echo "1.0" > debian/source/format
+
+#remove example files generated by dh_make
+find -name '*.ex' ! -name 'minerva-front*' -type f -exec rm -f {} +
+
+#set proper architecture
+arch=`dpkg --print-architecture`
+echo "Architecture: $arch" >>debian/control
+
+#remove some sample file
+rm debian/*.ex debian/*.EX debian/README.Debian debian/README.source debian/minerva-front-docs.docs
+
+#build debian package
+debuild -us -uc --lintian-opts --suppress-tags bad-distribution-in-changes-file
+
+#run separately to fail on errors (does not work on old debian)
+#lintian --suppress-tags bad-distribution-in-changes-file --no-tag-display-limit
+
+# remove temporary changelog
+rm $ROOT_DIR/debian/template/changelog

debian/template/compat

+10

debian/template/control

+Source: minerva-front
+Section: science
+Priority: optional
+Maintainer: Piotr Gawron <piotr.gawron@uni.lu>
+Standards-Version: 3.9.7
+Vcs-Browser: https://gitlab.lcsb.uni.lu/minerva/frontend
+Build-Depends: debhelper (>=10)
+
+Package: minerva-front
+Priority: optional
+Description: Frontend for standalone web application for visualization,
+ exploration and management of molecular networks encoded in SBGN-compliant
+ format. After installation, the resource is used and managed via a web browser,
+ under the default address 'http://localhost:8080/minerva/'. Full documentation
+ can be found here: https://minerva.pages.uni.lu/doc/
+Homepage: https://minerva.pages.uni.lu/
+Depends: ${misc:Depends}

debian/template/copyright

+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: minerva-front
+Source: https://minerva.pages.uni.lu/doc/
+
+Files: front.zip
+Copyright: 2024 Piotr Gawron <piotr.gawron@uni.lu>
+License: AGPL-3.0
+Comment: Manual for the package.
+
+Files: debian/*
+Copyright: 2024 Piotr Gawron <piotr.gawron@uni.lu>
+License: AGPL-3.0
+
+License: AGPL-3.0
+ Copyright (C) 2024 Piotr Gawron
+ .
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Affero General Public License as
+ published by the Free Software Foundation, either version 3 of the
+ License, or (at your option) any later version.
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU Affero General Public License for more details.
+ .
+ You should have received a copy of the GNU Affero General Public License
+ along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ .

debian/template/install

+front.zip /usr/share/minerva/

debian/template/rules

+#!/usr/bin/make -f
+
+%:
+	dh $@

next.config.js

@@ -3,6 +3,7 @@ const nextConfig = {
   reactStrictMode: true,
   basePath: process.env.APP_PREFIX ? process.env.APP_PREFIX + '/index.html' : '',
   assetPrefix: process.env.APP_PREFIX ? process.env.APP_PREFIX : '',
+  productionBrowserSourceMaps: true,
   output: 'export',
   images: {
     unoptimized: true,

public/config.js

@@ -2,6 +2,6 @@ window.config = {
   BASE_API_URL: 'https://lux1.atcomp.pl/minerva/api',
   BASE_NEW_API_URL: 'https://lux1.atcomp.pl/minerva/new_api/',
   BASE_MAP_IMAGES_URL: 'https://lux1.atcomp.pl/',
-  DEFAULT_PROJECT_ID: 'pdmap_appu_test',
+  DEFAULT_PROJECT_ID: 'sample',
   ADMIN_PANEL_URL: 'https://lux1.atcomp.pl/minerva/admin.xhtml',
 };

src/components/FunctionalArea/Modal/ErrorReportModal/ErroReportModal.component.tsx

@@ -28,7 +28,6 @@ export const ErrorReportModal: React.FC = () => {
   const javaStacktrace = getValue(errorData?.javaStacktrace);
   const stacktrace = getValue(errorData?.stacktrace);
   const version = getValue(errorData?.version);
-  const message = getValue(errorData?.message);
   const timestamp = errorData ? errorData.timestamp : Math.floor(+new Date() / ONE_THOUSAND);
 
   // eslint-disable-next-line @typescript-eslint/no-unused-vars
@@ -42,7 +41,6 @@ export const ErrorReportModal: React.FC = () => {
     stacktrace,
     version,
     timestamp,
-    message,
   });
 
   const handleChange = (e: React.ChangeEvent<HTMLInputElement>): void => {
@@ -77,7 +75,6 @@ export const ErrorReportModal: React.FC = () => {
   return (
     <div className="w-[800px] border border-t-[#E1E0E6] bg-white">
       <form onSubmit={handleSubmit} className="p-4">
-        <p className="my-4 font-bold"> {errorDataToSend.message}</p>
         <p className="my-4">
           If you agree to submit the following information to the minerva maintainers please uncheck
           all boxes that might contain sensitive data.

src/components/Map/Drawer/AvailablePluginsDrawer/AvailablePluginsDrawer.component.test.tsx

@@ -48,7 +48,7 @@ describe('AvailablePluginsDrawer - component', () => {
           },
         });
 
-        const pluginLabel = screen.getByText(currentPlugin.name);
+        const pluginLabel = screen.getByText(`${currentPlugin.name} (${currentPlugin.version})`);
         expect(pluginLabel).toBeInTheDocument();
       },
     );

src/components/Map/Drawer/AvailablePluginsDrawer/LoadPlugin/LoadPlugin.component.test.tsx

@@ -43,7 +43,7 @@ describe('LoadPlugin - component', () => {
     it('renders plugin name', () => {
       renderComponent({ plugin });
 
-      const title = screen.getByText(plugin.name);
+      const title = screen.getByText(`${plugin.name} (${plugin.version})`);
       expect(title).toBeInTheDocument();
     });
 

src/components/Map/Drawer/AvailablePluginsDrawer/LoadPlugin/LoadPlugin.component.tsx

@@ -22,7 +22,9 @@ export const LoadPlugin = ({ plugin }: Props): JSX.Element => {
 
   return (
     <div className="flex w-full items-center justify-between text-sm">
-      <span className="text-cetacean-blue">{plugin.name}</span>
+      <span className="text-cetacean-blue">
+        {plugin.name} ({plugin.version})
+      </span>
       <Button
         variantStyles="secondary"
         className="h-10 self-end rounded-e rounded-s text-xs font-medium"

src/components/Map/Drawer/ExportDrawer/CollapsibleSection/CollapsibleSection.component.tsx

@@ -12,12 +12,14 @@ type CollapsibleSectionProps = {
   title: string;
   children: React.ReactNode;
   onOpened?(): void;
+  dangerouslySetExpanded?: boolean;
 };
 
 export const CollapsibleSection = ({
   title,
   children,
   onOpened,
+  dangerouslySetExpanded,
 }: CollapsibleSectionProps): React.ReactNode => {
   const handleOnChange = (ids: ID[]): void => {
     const hasBeenOpened = ids.length > ZERO;
@@ -29,7 +31,7 @@ export const CollapsibleSection = ({
 
   return (
     <Accordion allowZeroExpanded onChange={handleOnChange}>
-      <AccordionItem>
+      <AccordionItem dangerouslySetExpanded={dangerouslySetExpanded}>
         <AccordionItemHeading>
           <AccordionItemButton>{title}</AccordionItemButton>
         </AccordionItemHeading>

src/components/Map/Drawer/ExportDrawer/ExportCompound/ImageFormat/ImageFormat.component.test.tsx

@@ -40,8 +40,6 @@ describe('ImageFormat - component', () => {
       },
     });
 
-    expect(screen.queryByTestId('checkbox-filter')).not.toBeVisible();
-
     const navigationButton = screen.getByTestId('accordion-item-button');
 
     act(() => {

src/components/Map/Drawer/ExportDrawer/ExportCompound/ImageFormat/ImageFormat.component.tsx

@@ -4,7 +4,8 @@ import {
   loadingConfigurationMainSelector,
 } from '@/redux/configuration/configuration.selectors';
 import { useAppSelector } from '@/redux/hooks/useAppSelector';
-import { useContext } from 'react';
+import { useContext, useState } from 'react';
+import { CheckboxItem } from '@/components/Map/Drawer/ExportDrawer/CheckboxFilter/CheckboxFilter.types';
 import { CheckboxFilter } from '../../CheckboxFilter';
 import { CollapsibleSection } from '../../CollapsibleSection';
 import { ExportContext } from '../ExportCompound.context';
@@ -23,8 +24,18 @@ export const ImageFormat = (): React.ReactNode => {
       label: name,
     }));
 
+  const options = useState<CheckboxItem[]>(mappedElementAnnotations);
+  if (
+    !isPending &&
+    currentImageFormats.length === ZERO &&
+    options.length > ZERO &&
+    options[ZERO].length > ZERO
+  ) {
+    setImageFormats([options[ZERO][ZERO]]);
+  }
+
   return (
-    <CollapsibleSection title="Image format">
+    <CollapsibleSection title="Image format" dangerouslySetExpanded>
       {isPending && <p>Loading...</p>}
       {!isPending && mappedElementAnnotations.length > ZERO && (
         <CheckboxFilter

src/components/Map/Drawer/ExportDrawer/ExportCompound/ImageSize/ImageSize.component.tsx

@@ -5,7 +5,7 @@ export const ImageSize = (): React.ReactNode => {
   const { width, height, handleChangeHeight, handleChangeWidth } = useImageSize();
 
   return (
-    <CollapsibleSection title="Image size">
+    <CollapsibleSection title="Image size" dangerouslySetExpanded>
       <div className="flex flex-col gap-4">
         <label className="flex h-9 items-center gap-4">
           <span className="w-12">Width:&nbsp;</span>

src/components/Map/Drawer/ExportDrawer/ExportCompound/Submap/Submap.component.test.tsx

@@ -39,8 +39,6 @@ describe('Submap - component', () => {
       },
     });
 
-    expect(screen.queryByTestId('checkbox-filter')).not.toBeVisible();
-
     const navigationButton = screen.getByTestId('accordion-item-button');
 
     act(() => {

src/components/Map/Drawer/ExportDrawer/ExportCompound/Submap/Submap.component.tsx

 import { ZERO } from '@/constants/common';
 import { useAppSelector } from '@/redux/hooks/useAppSelector';
 import { loadingModelsSelector, modelsDataSelector } from '@/redux/models/models.selectors';
-import { useContext } from 'react';
+import { useContext, useState } from 'react';
+import { CheckboxItem } from '@/components/Map/Drawer/ExportDrawer/CheckboxFilter/CheckboxFilter.types';
 import { CheckboxFilter } from '../../CheckboxFilter';
 import { CollapsibleSection } from '../../CollapsibleSection';
 import { ExportContext } from '../ExportCompound.context';
@@ -18,8 +19,18 @@ export const Submap = (): React.ReactNode => {
     label: name,
   }));
 
+  const options = useState<CheckboxItem[]>(mappedElementAnnotations);
+  if (
+    !isPending &&
+    currentSelectedModels.length === ZERO &&
+    options.length > ZERO &&
+    options[ZERO].length > ZERO
+  ) {
+    setModels([options[ZERO][ZERO]]);
+  }
+
   return (
-    <CollapsibleSection title="Submap">
+    <CollapsibleSection title="Submap" dangerouslySetExpanded>
       {isPending && <p>Loading...</p>}
       {!isPending && mappedElementAnnotations && mappedElementAnnotations.length > ZERO && (
         <CheckboxFilter