Feature/dockerize ruby

.github/workflows/node.js.yml

@@ -54,6 +54,7 @@ jobs:
       run: |
           cd app/assets/javascripts/3dbio_viewer
           yarn install
+          yarn localize
           yarn build
     - name: Check build dependency versions (3dbioviewer)
       run: |

Gemfile

@@ -4,7 +4,7 @@ ruby '3.3.1'
 gem 'rails', '7.1.3.2'
 
 #gem 'mysql2', '0.4.10'
-gem 'mysql2', '0.5'
+gem 'mysql2', '0.5.6'
 gem 'sqlite3', '1.4.2'
 
 gem 'haml'

Gemfile.lock

@@ -133,7 +133,7 @@ GEM
     mini_mime (1.1.5)
     minitest (5.22.3)
     mutex_m (0.2.0)
-    mysql2 (0.5.0)
+    mysql2 (0.5.6)
     net-imap (0.4.10)
       date
       net-protocol
@@ -257,7 +257,7 @@ DEPENDENCIES
   haml
   jquery-rails (= 4.6.0)
   json
-  mysql2 (= 0.5)
+  mysql2 (= 0.5.6)
   nori
   passenger (= 5.1.12)
   rack-cors

README.md

@@ -18,7 +18,6 @@
 Use rvm or rbenv to select the Ruby version specified in Gemfile and then run:
 
 ```
-$ git submodule update --recursive --init
 $ rvm install ruby-3.3.1
 $ gem install bundler:2.5.10
 $ sudo apt install libmysqlclient-dev # Debian/Ubuntu
@@ -35,10 +34,9 @@ Before you start your setup, make sure you have homebrew, ruby, rvm and python2
 Use rvm or rbenv to select the Ruby version specified in Gemfile and then run:
 
 ```
-$ git submodule update --recursive --init
 $ rvm install ruby-3.3.1
 $ gem install bundler:2.2.15
-$ brew install gsl mysql
+$ brew install mysql
 $ gem install bundler:2.0.0.pre.3
 ```
 

app/assets/config/manifest.js

@@ -59,7 +59,4 @@
 
 //= link webserver/viewer.css
 //= link application.css
-//= link application.js
-
-//= link_tree ../javascripts/3dbio_viewer/build
-//= link_tree ../javascripts/covid19/build
+//= link application.js

app/assets/javascripts/3dbio_viewer/package.json

@@ -4,7 +4,7 @@
     "private": true,
     "dependencies": {
         "@3dbionotes/pdbe-molstar": "3.1.0-est-2",
-        "@3dbionotes/protvista-pdb": "2.0.1-est-2-beta.1",
+        "@3dbionotes/protvista-pdb": "2.0.1-est-2-beta.2",
         "@material-ui/core": "^4.11.2",
         "@material-ui/data-grid": "4.0.0-alpha.35",
         "@material-ui/icons": "^4.11.2",

app/assets/javascripts/3dbio_viewer/public/index.html

@@ -17,7 +17,7 @@
             type="text/css"
         />
 
-        <script src="/protvista-pdb/protvista-pdb-2.0.1-est-2-beta.1.js"></script>
+        <script src="/protvista-pdb/protvista-pdb-2.0.1-est-2-beta.2.js"></script>
         <script src="/pdbe-molstar/pdbe-molstar-plugin-3.1.0-est-2.js"></script>
 
         <title>3dbio Viewer</title>

app/assets/javascripts/3dbio_viewer/src/data/PdbLigands.ts

@@ -93,7 +93,6 @@ const publicationC = Codec.interface({
     doi: string,
     pubMedId: string,
     PMCId: string,
-    abstract: string,
     authors: array(authorC),
 });
 
@@ -129,7 +128,7 @@ export const commonLigand = {
     imageLink: string,
     externalLink: string,
     pubChemCompoundId: string,
-    IUPACInChI: string,
+    IUPACInChI: optional(string),
     isomericSMILES: string,
     canonicalSMILES: string,
 };

app/assets/javascripts/3dbio_viewer/src/data/PdbPublications.ts

@@ -1,6 +1,7 @@
 import { Codec, GetType, array, nullType, number, string } from "purify-ts";
 import { maybe } from "./PdbLigands";
 import { PdbPublication } from "../domain/entities/Pdb";
+import _ from "lodash";
 
 export const publicationsCodec = array(
     //using so many "maybe" from examples: 7O7Z, 6ABA, 7SUB
@@ -21,11 +22,11 @@ export const publicationsCodec = array(
             year: maybe(number),
         }),
         abstract: Codec.interface({
-            background: nullType,
-            objective: nullType,
-            methods: nullType,
-            results: nullType,
-            conclusions: nullType,
+            background: maybe(string),
+            objective: maybe(string),
+            methods: maybe(string),
+            results: maybe(string),
+            conclusions: maybe(string),
             unassigned: maybe(string),
         }),
         author_list: array(
@@ -62,6 +63,15 @@ export function getPublications(publications: PublicationsCodec): PdbPublication
             abstract,
             author_list,
         }) => {
+            const description = _.compact([
+                abstract.background,
+                abstract.conclusions,
+                abstract.methods,
+                abstract.objective,
+                abstract.results,
+                abstract.unassigned,
+            ]).join(" "); //possibly "" if all are null
+
             return {
                 title,
                 type,
@@ -78,9 +88,7 @@ export function getPublications(publications: PublicationsCodec): PdbPublication
                     issue: journal_info.issue ?? undefined,
                     year: journal_info.year ?? undefined,
                 },
-                abstract: {
-                    unassigned: abstract.unassigned ?? undefined,
-                },
+                abstract: description || undefined,
                 authors: author_list.map(author => author.full_name),
             };
         }

app/assets/javascripts/3dbio_viewer/src/domain/entities/Pdb.ts

@@ -90,9 +90,7 @@ export interface PdbPublication {
         issue?: string;
         year?: number;
     };
-    abstract: {
-        unassigned?: string;
-    };
+    abstract?: string;
     authors: string[];
 }
 

app/assets/javascripts/3dbio_viewer/src/webapp/components/BasicInfoEntry.tsx

@@ -97,7 +97,7 @@ export const BasicInfoEntry: React.FC<BlockComponentProps> = React.memo(props =>
 function getItems(publication: PdbPublication) {
     const items: Item[] = _.compact([
         { name: i18n.t("Title"), value: escapeHTML(publication.title) },
-        { name: i18n.t("Abstract"), value: escapeHTML(publication.abstract.unassigned) },
+        { name: i18n.t("Abstract"), value: escapeHTML(publication.abstract) },
         { name: i18n.t("Authors"), value: publication.authors.join(", ") },
         {
             name: i18n.t("Journal"),

app/assets/javascripts/3dbio_viewer/yarn.lock

@@ -15,10 +15,10 @@
     lodash "^4.17.21"
     molstar "3.15.0"
 
-"@3dbionotes/[email protected].1":
-  version "2.0.1-est-2-beta.1"
-  resolved "https://registry.yarnpkg.com/@3dbionotes/protvista-pdb/-/protvista-pdb-2.0.1-est-2-beta.1.tgz#9db59040a702a4b9bd5b4283e4d6ae1d63cd26ad"
-  integrity sha512-EuW6xY0ZlhKhUqievJPSmBqXPeE+LHK8oGku78yE5RGgCePaHYnBff0X1PL/lvhRBU968bxiZls2z1HOyKU8mQ==
+"@3dbionotes/[email protected].2":
+  version "2.0.1-est-2-beta.2"
+  resolved "https://registry.yarnpkg.com/@3dbionotes/protvista-pdb/-/protvista-pdb-2.0.1-est-2-beta.2.tgz#83cbb6a6a56c1138de67c9263053ee7b73e48f89"
+  integrity sha512-3qCQWWIf1Rjpz1FEdcKzOi/CjcaZQc0VgPMYgxMpc2qZhuIcFQ8NRYIC4q1Zl5glui0nFM/DjMoTOCH2tXjx+A==
   dependencies:
     lodash-es "^4.17.11"
     protvista-filter "2.0.0"

app/assets/javascripts/covid19/i18n/en.pot

@@ -297,9 +297,6 @@ msgstr ""
 msgid "Journal"
 msgstr ""
 
-msgid "Abstract"
-msgstr ""
-
 msgid "Date"
 msgstr ""
 

app/assets/javascripts/covid19/src/data/Covid19Data.types.ts

@@ -109,7 +109,6 @@ export interface RefDoc {
     pmID: string;
     title: string;
     authors: string[];
-    abstract?: string;
     journal: string;
     pubDate: string;
     pmidLink?: Url;

app/assets/javascripts/covid19/src/data/LigandToImageData.ts

@@ -89,7 +89,6 @@ const publicationC = Codec.interface({
     doi: string,
     pubMedId: string,
     PMCId: string,
-    abstract: string,
     authors: array(authorC),
 });
 
@@ -125,7 +124,7 @@ export const commonLigand = {
     imageLink: string,
     externalLink: string,
     pubChemCompoundId: string,
-    IUPACInChI: string,
+    IUPACInChI: optional(string),
     isomericSMILES: string,
     canonicalSMILES: string,
 };