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Chemotion_ELN Changelog

[v1.6.0]

2023-05-09

  • Features and Improvements:

  • Fixes

    • port fixes from v1.5.3 v1.5.4

[v1.5.4]

2023-05-09

  • Admin: it is possible to reprocess SVGs images of molecules and samples (see docs)

  • Fixes

    • datacollector: find user by insensitive case name_abbreviation #1302
    • eln to work with onlyoffice 7 #1278
    • correct url building for inbox item notification #1299
    • Cas datamodel change #1287
    • Migration fixes #1307
    • reactants from reagent list do not appear above reaction arrow #1308
    • Search api: fix ActiveRecord::UnknownAttributeReference on sum-formulae #1310

[v1.5.3]

2023-04-21

  • Fixes
    • analyses-dataset issue #1271
    • missing index in container entity #1277
    • Report of samples with reaction description: fix calling of descripti..1281
    • fix crash when open and save nmrium #1275
    • Mail-collector: write tmp file to pass path #1284
    • New purification method of Precipitation #1290
    • 1285 do no cache the welcome message #1286
    • 1289 saving wellplate causes white screen #1295
    • Chemdraw JS doesn't work on Google Chrome 111.05563.x #1266
    • show results from calculations #1291
    • report issue fix #1296

[v1.6.0-rc1]

2023-04-11

  • Fixes
    • port fixes from v1.5.2

[v1.5.2]

2023-04-11

  • Fixes
    • AttachmentAPI: quote filename in content-dispostion header #1250
    • spectra: fix cannot sync 1d data #1227
    • Ease shrine derivative access #1255
    • update chem-spectra-app to version 0.11.2 #1263
    • Literature entity to return reference data and doi #1257
    • 1260 report UI to not break if a report template cannot be found #1261
    • Fix the creation of sample with invalid label 'NEW SAMPLE' #1240
    • Use db-generated uuid for building the attachment shrine id #1259

[v1.6.0-rc0]

2023-03-28

  • Features and Improvements:

    • Shibboleth authentication #1239

  • Fixes

    • content-disposition header preventing fetching image properly #1250

[v1.5.1]

2023-03-24

  • Fixes
    • omniauth provider entity fix #1217
    • PDF attachments in Analyses Tab now readable #1197
    • reset melting & boiling point for products on reaction copy #1221
    • Minor image annotation fixes #1223
    • cannot save 2D data #1178
    • tab layout popups #1212
    • cannot work with Bruker FID #1232
    • Update sample task api for changes in Chemobile App #1216
    • white screen on the homepage after login #1231
    • Set default search type value (EXACT) #1224
    • Updated welcome message to point to new docs URL #1236
    • export wellplate samples error fix by #1235

[v1.5.0]

2023-03-14

  • Important for admin and developers:

    • Gem Shrine is now used to handle attachment files:
      • if you use a custom config/storage.yml file, ensure your shrine config/shrine.yml is correct or DB migrations will fail
    • Upgrade Rails to 6.1

  • Features and Improvements:

    • Image Annotation tool (docs)
    • collection archiving to RADAR (RADAR account needed)
    • NMRium: NMR data can be processed in NMRium (docs)
    • Integration of Chem-converter v0.9.0 (docs
    • Wellplate/Screen/ResearchPlan Workflow
    • Chemspectra: better UI for Cyclic Volt.
    • add cas to sample export

  • Fixes

    • Chemspectra: The issue of multiplicities on chemspectra frontend are not removed when changing between layouts with the old JCAMP design is fixed
    • Chemspectra: Spectra can be processed even when the molfile is invalid (ComPlat#951) (Warning: update chem-spectra-app service to 0.11.0)
    • Affiliation autocomplete (sign up page)
    • CAS not searchable (index search might need to be rebuilt)
    • molecule image cropped in chemspectra
    • others

[v1.4.1]

2022-11-09

  • Features and Improvements:

  • Fixes:

    • An incomplete SVG file is generated after sanitizing the SVG
    • chemspectra on Reaction and ResearchPlan analyses
    • chemspectra display of XRD data
    • DataCollector: deletion of folder
    • Incorrect application root url in Jobs
    • client handling of attachment hyperlinks
    • misleading tooltip in the user list (Admin UI)
    • proper version of chemspectra app

[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 (ComPlat#544)
    • Metadata-converter: v0.6.0
    • Chemspectra: v0.10.15 (allow reprocessing, read Bruker processed files if present)
    • Inbox: delete multiple attachments at once (ComPlat#571)
    • research-plan: improve context-menu in tables

  • Fixes:

    • SVG generation for sample and reaction: (ComPlat#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:

    • Download of large dataset as background job to avoid timeout (ComPlat#785)

  • Fixes:

[v1.3.0]

2022-07-05

  • Features and Improvements:

    • dataset selection in chemspectra viewer dataset selection in chemspectra viewer #715
    • Screens:
      • Research Plans may be added to Screens
      • Associated Research Plans may be edited from Screens
    • Research Plans:
      • Wellplates may be added to Research Plans
    • Wellplates:
      • Add short label with user prefix and user's Wellplate count
      • Wells have multiple readouts now
      • Add title for readouts and display of multiple readouts in designer and list
      • Add attachments
      • Add import for well data from .xlsx and import template .xlsx
    • Collection Tag for research-plan screen (ComPlat#774)
    • Chemspectra : Cyclic Voltametry (Warning: upd chem-spectra-app service to 0.10.14)
    • ResearchPlan link to reactions and samples (ComPlat#666)
    • No reaction-svg when no material present (ComPlat#691)

  • Fixes

[v1.2.1]

2022-05-10

  • Fixes
    • export dataset attachments with no hyperlink present
    • analysis: preview latest processed image
    • rails patch upd
    • npx audit fix

[v1.2.0]

2022-04-14

  • Features and Improvements:
    • fast input: sample creation
      • users can create samples by entering the CAS Registry Number or SMILES
    • SciFinder-n Search: integrate SciFinder-n into ELN and user can search in SciFinder for substances/reactions/references/suppliers by structure
    • analytics converter integration
    • OIDC signin

[v1.1.4]

2022-04-14

  • Fixes
    • Ketcher icons missing (since 1.1.3)

[v1.1.3]

2022-04-05

  • Fixes
    • npx-audit and Gem patches
    • migration
    • reaction prediction UI

[v1.1.2]

2022-03-25

  • Fixes
    • upd chemspectra client: XRD d-value
    • add product to reaction

[v1.1.1]

2022-03-08

  • Fixes
    • uniq sample short-label while creating reaction
    • customized toolbar refresh issue in quill editor
    • rendering of the group list when deleting multiple groups
    • permission to add elements to sync-collections

[v1.1.0]

2022-01-18

  • NB:

    • Admin: if applicable, chemspectra backend should be updated to version 0.10.13
    • Developers: reactjs updated to 17

  • Features and Improvements:

    • export sample: literature option for excel list ComPlat#554
    • report: Add literature section in standard sample report ComPlat#554
    • report: Add more information to standard reaction report ComPlat#523
    • attachments-inbox: filename matching with sample’s “name” or “external name”. ComPlat#537
    • attachments-inbox: case-insensitive matching ComPlat#537
    • attachments-inbox: added labels “product” or “start material” if applicable ComPlat#537
    • attachments-inbox: when the assignment is completed, send a notification to user’s message box ComPlat#537
    • attachments-inbox: filename matching to support files from ELA system.
    • chemspectra: UV-vis layout extension (part of ComPlat#531 )
    • chemspectra: Add further functions to XRD layout ComPlat#532
    • wellplate designer: select info and colour to be displayed in well (ComPlat#556, ComPlat#558)
    • wellplate designer: print wellplate as pdf (ComPlat#555)
    • name_abbreviation regexp validation is configurable
    • swagger documentation: visibility of endpoints doc customizable
    • rename tab 'literature' to 'references'. Please update the current profile_default.yml with the new one.
    • Admin user management: add multiple users from file.

  • Fixes

[v1.0.3]

2021-10-21: https://github.com/ComPlat/chemotion_ELN/releases/tag/v1.0.3

  • Fixes
    • reseach-plan .docx export: convert SVG to PNG sample/reaction images
    • collection import with sample missing molecule_name: use default value
    • structure editors: added public/editors to ease set up
    • node post-install fx to resolve node_modules path when located outside of app (docker)

[v1.0.2]

2021-10-19: https://github.com/ComPlat/chemotion_ELN/releases/tag/v1.0.2

  • Fixes
    • DB migration: fix typo that could prevent updating from 0.9.1
    • structure editor: chemdrawjs-20 support
    • gate transfer: attachment checksum bckwrd compatibility

[v1.0.1]

2021-10-11: https://github.com/ComPlat/chemotion_ELN/releases/tag/v1.0.1

  • Improvements

    • LCSS display info only from ECHA source
    • QuillEditor: added special characters menu for ResearchPlan

  • Fixes

    • postinstall rewrite of some imports in citation.js to fix wbpk assets compilation
    • Reaction SVG refresh after editing or adding samples
    • Fix Cron Jobs for LCSS and Pubchem Info
    • dev: fix reaction seeds

[v1.0.0]

2021-09-22: https://github.com/ComPlat/chemotion_ELN/releases/tag/v1.0.0

[v1.0.0-beta]

2021-08-26

[v0.9.1]

2021-06-04: https://github.com/ComPlat/chemotion_ELN/releases/tag/v0.9.1

  • Fixes
    • sync/share deletion permission
    • Admin: segment deletion

[v0.9.0]

2021-05-26: https://github.com/ComPlat/chemotion_ELN/releases/tag/v0.9.0

  • Features

    • Decoupled sample: molfile-less sample creation
    • Generic-element/segment (Beta): customizable data structure

  • Fixes

    • serialization of sdf-imported molecules with improper file encoding

[v0.8.0]

2021-04-28: https://github.com/ComPlat/chemotion_ELN/releases/tag/v0.8.0

  • Features

    • option to decouple sample from molfile defined molecule - enable user custom MW input (Admin has to enable the feature)
    • research-plan table: switch to using ag-grid - enable moving row/columns with d-n-d
    • nmr_sim ELN plugin installed by default

  • Fixes

    • Add configurable default profile for Element-Detail tab sortings
    • slow opening of reaction panel: rm debounce
    • green-chemistry: fix checkbox rerendering in table cell
    • Analytics atom count scenari
    • default favicon if none present

[v0.7.1]

2021-03-26: https://github.com/ComPlat/chemotion_ELN/releases/tag/v0.7.1

  • Features

    • sorting of tabs in Element-detail Panel (Sample, Reaction,...)

  • Fixes

    • mimemagic gem updated due to previous version forced retirement
    • research-plan table: cell focus input
    • slow opening of reaction panel: rm debounce

[v0.7.0]

2021-03-15: https://github.com/ComPlat/chemotion_ELN/releases/tag/v0.7.0

[v0.6.0]

2019-12-16: https://github.com/ComPlat/chemotion_ELN/releases/tag/v0.6.0

  • Features
  • minor UX improvements
  • admin UI for data-collector and noVNC connection
  • improve report UI performance

[v0.5.0]

2019-10-08

  • Features

    • Analysis type according to Chemical Ontology (owl)
    • export data from whole collections as zip (and import them)
    • server notification system to users. E.g: user get notified when:
      • the report generation is done
      • it needs to refresh the browsers page to reload the cached application (update)
    • Admin UI:
      • NB: migrations will seed a default admin account => you need to change its password email: [email protected] , pw: PleaseChangeYourPassword
      • basic user management functions + direct notification to user
      • DataCollector device configuration
      • global notification to users
    • Green Chemistry calculator for reaction
    • RInChI integration
    • new reporting functions
    • sample/reaction large image preview from their element lists on hover
    • clone samples/reactions to one's Chemotion Repository account (chemotion.net)

  • Upgrade Notes:

    • must do: change the default password of the default admin account (vide supra)
    • should do: reports are now stored as attachments run rake task data:ver_20180812115719_add_colums_to_attachment to ensure the retrievability of previously generated reports

[v0.4.0]

yyyy-mm-dd

  • Features

    • Element list: added time range filter / product filter
    • enhanced data collector, new configuration (Breaking change)
    • Export reactions as reaction smiles
    • Extract RSMI from docx embedded cdx object

  • Fixes

    • Report formating
    • shared collection from deleted account

[v0.3.dev]

yyyy-mm-dd

  • Features

    • upg Rails to 4.2.10 nvm to 6.10.2

  • Fixes

    • Docker: node_modules as volume
    • collection_tag update after element re-assignmnet to former collection

[v0.3.0]

2017-11-15: https://github.com/ComPlat/chemotion_ELN/releases/tag/v0.3.0

  • Features

    • Export reaction smiles
    • reporting: revamp of UI
    • reporting: analysis metadata formating
    • user affiliations management
    • revamp of sample/reaction detail UI
    • select the sample molecule_name to display
    • fetch CAS from pubchem
    • uuid (qr code) for each element (sample, reaction, analyse)
    • export samples as sdf
    • adv search
    • Docker install

  • Fixes

    • search result element ordering
    • dependent destroy of collections-elements
    • sample density default set to 0
    • react production build

[v0.2.1]

2016-11-02

  • Features

    • Temperature Chart with unit converter (°C, °F , K) for reaction
    • Import molecules and create samples from a sd file (R group and polymer support are not supported)
    • Images in report doc are from eps files
    • rearrange the reaction list for a report by Drag-and-drop -ing
    • Text editing and formating tool bar for the reaction description

  • Fixes

    • upgrade to Ruby 2.3.1
    • The Upload of analyses files does not fail if the thumbnail creation does

[v0.2.0]

2016-10-17: https://github.com/ComPlat/chemotion_ELN/releases/tag/v0.2.0

  • Features

    • sharing data with a group of users
    • substructure search with fingerprint algorithm
    • multiple solvents for reactions
    • drag-and-drop of sample to reaction solvent
    • user-defined chemical structure templates
    • common chemical structure templates
    • synchronized collections
    • added full-screeen button to element view
    • database and attachments backups
    • better import feature
    • advanced export options
    • generate reports in .doc format
    • different naming for reaction product
    • add concentration to sample in solution
    • updates in reporting system
    • molecular weight calculation in real time Ketcherails v0.1.1
    • molecular weight calculation for selected structure part in real time Ketcherails v0.1.1
    • warning for user when editing parent/child sample: parent/child samples structures are not automatically updated
    • reactants are not appearing in the samples list anymore
    • added more details to sample analyses header
    • style and user interface improvements
    • zooming of reactions SVGs

  • Fixes

    • user created samples counter is not decremented on deletion
    • add material for reaction
    • do not show non-saved collection in collection tree
    • edit sample from reaction
    • better scaling of sample and reaction SVG images
    • multiple bug fixes

[v0.1.0]

2016-05-31: https://github.com/ComPlat/chemotion_ELN/releases/tag/v0.1.0

  • Features

    • ELN for (organic) chemistry ton to element view
    • database and attachments backups
    • better import feature
    • advanced export options
    • generate reports in .doc format
    • different naming for reaction product
    • add concentration to sample in solution
    • updates in reporting system
    • molecular weight calculation in real time Ketcherails v0.1.1
    • molecular weight calculation for selected structure part in real time Ketcherails v0.1.1
    • warning for user when editing parent/child sample: parent/child samples structures are not automatically updated
    • reactants are not appearing in the samples list anymore
    • added more details to sample analyses header
    • style and user interface improvements
    • zooming of reactions SVGs

  • Fixes

    • user created samples counter is not decremented on deletion
    • add material for reaction
    • do not show non-saved collection in collection tree
    • edit sample from reaction
    • better scaling of sample and reaction SVG images
    • multiple bug fixes

[v0.1.0]

2016-05-31: https://github.com/ComPlat/chemotion_ELN/releases/tag/v0.1.0

  • Features
    • ELN for (organic) chemistry