v1.4.0

* upd VERSION tag * upd CHANGELOG * drop chemotion_ELN plugins: clean JS code
ComPlat · Sep 26, 2022 · a6e2533 · a6e2533
1 parent 9a6c244
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diff --git a/.env.production.example b/.env.production.example
@@ -1,7 +1,32 @@
-SFTP_HOST=sftp-host-production
-SFTP_PORT=sftp-port-production
-SFTP_UPLOAD_FOLDER=sftp-upload-folder # e.g. uploads
-SFTP_USER=sftp-user-production
+# default uri of your Chemotion ELN for http links in e-mails and notification:
+PUBLIC_URL='http://sld.tld' 
+# senders e-mail:
+DEVISE_SENDER='[email protected]' 
+
+## SMTP config 
+# Remote mail server
+SMTP_ADDRESS='smtp.sld.tld'
+SMTP_PORT=587
+# login user name & password:
+SMTP_USERNAME='[email protected]' 
+SMTP_PASSWORD='s3cr3tPW'
+# optional, HELO domain
+SMTP_DOMAIN='sld.tld'
+# detect STARTTLS
+SMTP_TLS=true
+# authentication type ('plain' 'login' (Base64 encoded) or 'cram_md5')
+SMTP_AUTH='plain'
+# how OpenSSL checks the certificate  ('none' or 'peer') 
+SMTP_SSL_MODE='none'
+
+# disable mail delivery
+# DISABLE_MAIL_DELIVERY='nomail'
+
+
+#SFTP_HOST=sftp-host-production
+#SFTP_PORT=sftp-port-production
+#SFTP_UPLOAD_FOLDER=sftp-upload-folder # e.g. uploads
+#SFTP_USER=sftp-user-production
 
 # Choose between password and ssh-key authentication.
 # The default key locations are ~/.ssh/id_rsa,~/.ssh/id_dsa. If you want to use

diff --git a/.eslintrc b/.eslintrc
@@ -1,5 +1,5 @@
 {
-  "parser": "babel-eslint",
+  "parser": "@babel/eslint-parser",
   "plugins": [
     "react"
   ],

diff --git a/.nvmrc b/.nvmrc
@@ -1 +1 @@
-v14.16.0
+v14.20.0
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,7 +10,35 @@
 * Fixes
 
 
-# [v1.3.1-pre]
+## [v1.4.0]
+> 2022-09-26
+
+* Important for admin and developers:
+  * change of environment variable: use PUBLIC_URL instead of HOST and SMTP_HOST
+  * nodejs upd to 14.20.0
+  * drop support for bionic
+
+* Features and Improvements:
+  * ketcherservice: server generation of sample svg
+  * Reaction coefficient: improve yield calculation (https://github.com/ComPlat/chemotion_ELN/issues/544)
+  * Metadata-converter: v0.6.0
+  * Chemspectra: v0.10.15 (allow reprocessing, read Bruker processed files if present)
+  * Inbox: delete multiple attachments at once (https://github.com/ComPlat/chemotion_ELN/issues/571)
+  * research-plan: improve context-menu in tables
+
+
+* Fixes:
+  * SVG generation for sample and reaction: (https://github.com/ComPlat/chemotion_ELN/issues/846)
+  * Sample amount metric 
+  * report svg composer: skip image if image file does not exist.
+  * chemspectra: duplicate image generation
+
+
+
+
+
+
+## [v1.3.1]
 > 2022-07-07
 
 * Features and Improvements:

diff --git a/VERSION b/VERSION
@@ -1,3 +1,3 @@
-version: 1.3.1
-base_revision: d7c0c64dda79f938430e5236ce7559ab3bc17242
+version: 1.4.0
+base_revision: 9a6c2441a52356989aa69da67f8283a27a279ff6
 current_revision: 0
diff --git a/app/packs/src/components/CollectionManagement.js b/app/packs/src/components/CollectionManagement.js
@@ -5,7 +5,6 @@ import MyCollections from './collection_management/MyCollections';
 import MySharedCollections from './collection_management/MySharedCollections';
 import SharedWithMeCollections from './collection_management/SharedWithMeCollections';
 import SyncWithMeCollections from './collection_management/SyncWithMeCollections';
-import XTabs from './extra/CollectionManagementXTabs';
 
 const CollectionManagement = () => {
   const tabContents = [
@@ -14,17 +13,6 @@ const CollectionManagement = () => {
     <Tab eventKey={2} key={2} title="Collections shared with me "><SharedWithMeCollections /></Tab>,
     <Tab eventKey={3} key={3} title="Collections synchronized with me "><SyncWithMeCollections /></Tab>,
   ];
-  const offset = tabContents.length;
-  for (let j = 0; j < XTabs.count; j += 1) {
-    if (XTabs[`on${j}`]()) {
-      const NoName = XTabs[`content${j}`];
-      tabContents.push((
-        <Tab eventKey={offset + j} key={offset + j} title={XTabs[`title${j}`]} >
-          <NoName />
-        </Tab>
-      ));
-    }
-  }
 
   return (
     <div id="collection-management">

diff --git a/app/packs/src/components/CollectionTree.js b/app/packs/src/components/CollectionTree.js
@@ -10,7 +10,6 @@ import LoadingActions from './actions/LoadingActions';
 import UIStore from './stores/UIStore';
 import ElementStore from './stores/ElementStore';
 import InboxStore from './stores/InboxStore';
-import Xdiv from './extra/CollectionTreeXdiv';
 import UserInfos from './UserInfos';
 
 import DeviceBox from './inbox/DeviceBox';
@@ -287,11 +286,6 @@ export default class CollectionTree extends React.Component {
 
   render() {
     let {ownCollectionVisible, inboxVisible, inbox} = this.state
-    let extraDiv = [];
-    for (let j=0;j < Xdiv.count;j++){
-      let NoName = Xdiv["content"+j];
-      extraDiv.push(<NoName key={"Xdiv"+j} />);
-    }
 
     const ownCollectionDisplay = ownCollectionVisible ? '' : 'none';
     const inboxDisplay = inboxVisible ? '' : 'none';
@@ -320,7 +314,6 @@ export default class CollectionTree extends React.Component {
         <div className="tree-wrapper">
           {this.remoteSyncInSubtrees()}
         </div>
-        {extraDiv.map((e)=>{return e})}
         <div className="tree-view">
           <div className="title" style={{ backgroundColor: 'white' }}>
             <button

diff --git a/app/packs/src/components/ElementsTableEntries.js b/app/packs/src/components/ElementsTableEntries.js
@@ -14,7 +14,6 @@ import ElementStore from './stores/ElementStore';
 import KeyboardStore from './stores/KeyboardStore';
 
 import DragDropItemTypes from './DragDropItemTypes';
-import XTdCont from './extra/ElementsTableEntriesXTdCont';
 import { elementShowOrNew } from './routesUtils';
 import SvgWithPopover from './common/SvgWithPopover';
 import UserStore from './stores/UserStore';
@@ -190,33 +189,26 @@ export default class ElementsTableEntries extends Component {
       textAlign: 'center',
       cursor: 'pointer'
     };
-    let tdExtraContents = [];
-    for (let j=0;j < XTdCont.count;j++){
-      let NoName = XTdCont["content"+j];
-      tdExtraContents.push(<NoName element={element}/>);
-    }
+
 
     const {showPreviews} = UIStore.getState();
     const clickToShowDetails = e => this.showDetails(element);
     if (showPreviews && (element.type == 'reaction')) {
       return (
         <td style={svgContainerStyle} onClick={e => this.showDetails(element)}>
           <SVG src={element.svgPath} className={classNames} key={element.svgPath}/>
-          {tdExtraContents.map((e)=>{return e;})}
         </td>
       );
     } else if (element.type === 'research_plan') {
       if (element.thumb_svg !== 'not available') {
         return (
           <td style={svgContainerStyle} onClick={e => this.showDetails(element)}>
             <img src={`data:image/png;base64,${element.thumb_svg}`} alt="" style={{ cursor: 'pointer' }} />
-            {tdExtraContents.map((e) => { return e; })}
           </td>
         );
       }
       return (
         <td style={svgContainerStyle} onClick={e => this.showDetails(element)}>
-          {tdExtraContents.map((e) => { return e; })}
         </td>
       );
     }

diff --git a/app/packs/src/components/ElementsTableSampleEntries.js b/app/packs/src/components/ElementsTableSampleEntries.js
@@ -19,7 +19,6 @@ import KeyboardStore from './stores/KeyboardStore';
 
 import DragDropItemTypes from './DragDropItemTypes';
 import SampleName from './common/SampleName';
-import XMolHeadCont from './extra/ElementsTableSampleEntriesXMolHeadCont';
 import { sampleShowOrNew } from './routesUtils';
 import SvgWithPopover from './common/SvgWithPopover';
 import { ShowUserLabels } from './UserLabels';
@@ -140,12 +139,6 @@ const svgPreview = (showPreviews, sample) => (
 
 const MoleculeHeader = ({ sample, show, showDragColumn, onClick, targetType }) => {
   const showIndicator = (show) ? 'glyphicon-chevron-down' : 'glyphicon-chevron-right';
-  const tdExtraContents = [];
-
-  for (let j = 0; j < XMolHeadCont.count; j++) {
-    const NoName = XMolHeadCont[`content${j}`];
-    tdExtraContents.push(<NoName element={sample} key={`exMolHead${j}`} />);
-  }
 
   const { collId, showPreviews } = UIStore.getState();
   return (
@@ -170,7 +163,6 @@ const MoleculeHeader = ({ sample, show, showDragColumn, onClick, targetType }) =
             </div>
             <div style={{ position: 'absolute', top: '10px', right: '25px', float: 'right' }} >
               <ChemrepoLabels chemrepoId={sample.molecule.chem_repo && sample.molecule.chem_repo.id} />
-              {tdExtraContents.map(e => e)}
               <PubchemLabels element={sample} />
             </div>
             <div style={{ position: 'absolute', bottom: '10px', right: '25px', float: 'right' }} >

diff --git a/app/packs/src/components/ReactionDetails.js b/app/packs/src/components/ReactionDetails.js
@@ -20,7 +20,6 @@ import ReactionDetailsProperties from './ReactionDetailsProperties';
 import GreenChemistry from './green_chem/GreenChemistry';
 import Utils from './utils/Functions';
 import PrintCodeButton from './common/PrintCodeButton';
-import XTabs from './extra/ReactionDetailsXTabs';
 import UIStore from './stores/UIStore';
 import UIActions from './actions/UIActions';
 import { setReactionByType } from './ReactionDetailsShare';
@@ -231,19 +230,6 @@ export default class ReactionDetails extends Component {
     );
   }
 
-  extraTab(ind) {
-    const reaction = this.state.reaction || {};
-    const num = ind;
-    const NoName = XTabs["content"+num];
-    const TabName = XTabs["title"+num];
-    return (
-      <Tab eventKey={ind + 5} title={TabName} key={`sampleDetailsTab${ind + 3}`} >
-        <ListGroupItem style={{ paddingBottom: 20 }}>
-          <NoName reaction={reaction} />
-        </ListGroupItem>
-      </Tab>
-    );
-  }
 
   reactionSVG(reaction) {
     if(!reaction.svgPath) {
@@ -450,19 +436,6 @@ export default class ReactionDetails extends Component {
       green_chemistry: 'Green Chemistry'
     }
 
-    for (let j = 0; j < XTabs.count; j += 1) {
-      if (XTabs[`on${j}`](reaction)) {
-        const NoName = XTabs[`content${j}`];
-        tabContentsMap[`xtab_${j}`] = (
-          <Tab eventKey={`xtab_${j}`} key={`xtab_${j}`} title={XTabs[`title${j}`]} >
-            <ListGroupItem style={{ paddingBottom: 20 }} >
-              <NoName reaction={reaction} />
-            </ListGroupItem>
-          </Tab>
-        );
-        tabTitlesMap[`xtab_${j}`] = XTabs[`title${j}`];
-      }
-    }
 
     addSegmentTabs(reaction, this.handleSegmentsChange, tabContentsMap);
 

diff --git a/app/packs/src/components/SampleDetails.js b/app/packs/src/components/SampleDetails.js
@@ -34,9 +34,6 @@ import PubchemLabels from './PubchemLabels';
 import ElementReactionLabels from './ElementReactionLabels';
 import SampleDetailsContainers from './SampleDetailsContainers';
 
-import XLabels from './extra/SampleDetailsXLabels';
-import XTabs from './extra/SampleDetailsXTabs';
-
 import StructureEditorModal from './structure_editor/StructureEditorModal';
 
 import Sample from './models/Sample';
@@ -557,7 +554,6 @@ export default class SampleDetails extends React.Component {
           {colLabel}
           <ElementAnalysesLabels element={sample} key={`${sample.id}_analyses`} />
           <PubchemLabels element={sample} />
-          {this.extraLabels().map((Lab, i) => <Lab key={i} element={sample} />)}
         </div>
         <ShowUserLabels element={sample} />
       </div>
@@ -1136,13 +1132,6 @@ export default class SampleDetails extends React.Component {
     );
   }
 
-  extraLabels() {
-    let labels = [];
-    for (let j = 0; j < XLabels.count; j += 1) {
-      labels.push(XLabels[`content${j}`]);
-    }
-    return labels;
-  }
 
   sampleIsValid() {
     const { sample, loadingMolecule, quickCreator } = this.state;
@@ -1295,19 +1284,6 @@ export default class SampleDetails extends React.Component {
       measurements: 'Measurements!'
     };
 
-    for (let j = 0; j < XTabs.count; j += 1) {
-      if (XTabs[`on${j}`](sample)) {
-        const NoName = XTabs[`content${j}`];
-        tabContentsMap[`xtab_${j}`] = (
-          <Tab eventKey={`xtab_${j}`} key={`xtab_${j}`} title={XTabs[`title${j}`]} >
-            <ListGroupItem style={{ paddingBottom: 20 }} >
-              <NoName sample={sample} />
-            </ListGroupItem>
-          </Tab>
-        );
-        tabTitlesMap[`xtab_${j}`] = XTabs[`title${j}`];
-      }
-    }
 
     addSegmentTabs(sample, this.handleSegmentsChange, tabContentsMap);
     const stb = [];

diff --git a/app/packs/src/components/inbox/InboxModal.js b/app/packs/src/components/inbox/InboxModal.js
@@ -9,8 +9,6 @@ import LoadingActions from '../actions/LoadingActions';
 import DeviceBox from '../inbox/DeviceBox';
 import UnsortedBox from '../inbox/UnsortedBox';
 
-import Xdiv from '../extra/CollectionTreeXdiv';
-
 export default class InboxModal extends React.Component {
   constructor(props) {
     super(props);
@@ -90,11 +88,6 @@ export default class InboxModal extends React.Component {
     const { showCollectionTree } = this.props;
     const { visible, inboxVisible } = this.state;
 
-    const extraDiv = [];
-    for (let j = 0; j < Xdiv.count; j += 1) {
-      const NoName = Xdiv[`Xdiv${j}`];
-      extraDiv.push(<NoName key={`Xdiv${j}`} />);
-    }
 
     const panelClass = showCollectionTree ? 'small-col col-md-6' : 'small-col col-md-5';
     const inboxDisplay = inboxVisible ? '' : 'none';

diff --git a/app/packs/src/components/routes.js b/app/packs/src/components/routes.js
@@ -5,18 +5,11 @@ import UserStore from './stores/UserStore';
 import UIActions from './actions/UIActions';
 import UserActions from './actions/UserActions';
 import ElementActions from './actions/ElementActions';
-import rXr from './extra/routesXroutes';
 import * as routesUtils from './routesUtils';
 import UIFetcher from './fetchers/UIFetcher';
 import klasses from '../../../../config/klasses.json';
 
 
-const allRoutes = (r) => {
-  let rts = { ...r };
-  for (let i = 0; i < rXr.count; i++) { rts = { ...rts, ...rXr[`content${i}`] }; }
-  return rts;
-}
-
 const routes = {
   '/': 'root',
   target: {
@@ -134,5 +127,5 @@ klasses && klasses.forEach((klass) => {
 export default function() {
   Aviator.root = '/mydb';
   Aviator.pushStateEnabled = true;
-  Aviator.setRoutes(allRoutes(routes));
+  Aviator.setRoutes(routes);
 }
diff --git a/app/packs/src/components/search/SearchFilter.js b/app/packs/src/components/search/SearchFilter.js
@@ -2,7 +2,7 @@ import React from 'react'
 import {Button, FormControl} from 'react-bootstrap'
 import Select from 'react-select'
 import UIActions from '../actions/UIActions';
-import XSearchParams from "../extra/AdvancedSearchXSearchParams";
+
 
 export default class SearchFilter extends React.Component {
   constructor(props) {
@@ -60,11 +60,7 @@ export default class SearchFilter extends React.Component {
       }
     ];
 
-    for (let i = 0; i < XSearchParams.count; i++){
-      if (XSearchParams[`on${i}`]) {
-        this.listOptions = this.listOptions.concat(XSearchParams[`content${i}`])
-      }
-    }
+
 
     this.andOrOps = [
       { value: "AND", label: "AND" },