Chemotion Repository 2.2.0

What's Changed

• Features and Enhancements:

  • Adjusted the button layout for preview images on the publication page.
  • Expanded coverage of Ontology Terminology in metadata.
  • Reduced paragraph spacing in the quill-viewer for space efficiency.
  • Added ontology terminology to JSON-LD metadata based on template definitions.
  • Introduced the StartingMaterial4Chem identifier to the publication list.
  • A submission feature with dataset copy capability.
  • Decoupled sample information in the Publication and Review pages, enhancing data clarity and management.
  • Updated Schema.org JSON-LD metadata to enhance data interoperability and search engine optimization.
  • Added functionality to add or remove reviewers during the review process.
  • Enabled NMRium functionality on the Data Publications page.
  • Enhanced preview capabilities for anonymous users.
  • Added additional information settings for StartingMaterial4Chem.
  • Refined JSON-LD metadata to further improve data interoperability and search engine optimization.
  • Added advertisement for the NFDI4Chem award.
  • Added StartingMaterial4Chem support for Buchler and Carbolution.
  • Included the Chemotion LabIMotion version 1.3.0.

• Bug Fixes:

  • Fixed an issue where clicking on embargo review.
  • Fixed issue with uploading attachments.
  • Fixed conversion failure while fetching thumbnails.
  • Resolved blank page issue when clicking "Keep Changes" on the submit modal.
  • Fixed issue where reviewers could not add an author.
  • Corrected incorrect affiliation ID format.
  • Fixed issue where submission failed when no review information was provided.
  • Fixed an issue where the sample name was missing on the review page.
  • Fixed an issue where importing collections failed when multiple collections were provided.

• Chores:

  • Improved performance with preload.
  • Upgraded react-molviewer
  • Upgraded chem-generic-ui-viewer
  • Upgraded Quill for the quill-viewer function.
  • Removed redundant code.
  • Included the Chemotion ELN version 1.9.2.
  • Included the Chemotion ELN version 1.9.1.
  • Included the Chemotion ELN version 1.9.0.

Chemotion Repository 2.1.0

What's Changed

• Features and Enhancements:

  • Use public domain icon to represent No License.
  • Use ORCID iD to refer to the ORCID identifier.
  • Group analysis attachments.
  • Introduced spectra viewer on the publication page without login required.
  • Introduced the embargo overview page, which enables scientists to review their submission status and providing an overview for the reviewers.
  • Implemented the review comment function for the embargo collection.
  • Enhanced the publication page performance by using cache mechanism.
  • Implemented streaming data transfer from Chemotion ELN.
  • Introduced a new confirmation and welcome email. [Chemotion_Repository#74].
  • Introduced preservation strategy for the Chemotion Repository.
  • LabIMotion 1.1.4.

• Bug Fixes:

  • Fixed svg scrubber.
  • Fixed the missing confirmation dialog when canceling an account.
  • Fixed the missing DOI information in the SI.
  • Fixed the publication page shows no entries.
  • Fixed downloading files via the pop-up modal fails on the publication page. [Chemotion_Repository#96].
  • Disabled annotate button for the publication.
  • Fixed initial load hang issue.
  • Fixed the incorrect format of the sign-up terms and conditions content [Chemotion_Repository#83].
  • Fixed a flaw in the similarity search function that caused the error. [Chemotion_Repository#91].
  • Fixed the missing warning dialog before canceling an account. [Chemotion_Repository#78].

• Chores:

  • Updated API document.
  • Reorganize partners section on homepage.
  • Disabled DOI List.
  • Upgraded Labimotion.
  • chore: remove duplicate codes.
  • Updated API document. [Chemotion_Repository#67].
  • Upgraded lodash from 4.17.20 to 4.17.21.
  • Upgraded puma from 5.6.7 to 5.6.8.
  • Upgraded follow-redirects from 1.14.9 to 1.15.5.
  • Upgraded ruby from 2.7.7 to 2.7.8.
  • Upgraded node from 18.18.2 to 18.19.1.

Chemotion Repository 2.0.0

What's Changed

• Features and enhancements:

  • Dataset Excel improvement: More information is provided in the Description sheet. See the documentation here.
  • Inbox Converter: The device files are converted automatically when they arrive in the inbox.
  • Introduced Repo Search Tool: A search tool is now accessible on the Chemotion Repository Home page. This tool enables searches by author, chemical methods ontology, IUPAC, InChi, SMILES, or even allows users to draw a structure for searching in Data Publications or Molecule Archive.
  • Enhanced JSON-LD Option: An additional option has been incorporated into JSON-LD, allowing users to view all samples of the published reaction.
  • JSON-LD Format Support: Data Publications now support the JSON-LD format. We are continually refining this function to align more closely with schema.org standards.
  • Introduced Review Guidelines and Reviewers' Introduction Section: We have added a dedicated section to clearly outline the review guidelines and provide an introduction for reviewers.
  • LabIMotion Hub UI Optimization: We have optimized the LabIMotion Hub UI to improve user experience.
  • Implemented Lock mechanism: The original sample or reaction is automatically locked upon submission. Submitters have the option to unlock it for further editing.
  • Enhanced the front-end code to eliminate the 'unique key of child' warning.
  • Introduced Generic Dataset section in Publication Page: Generic datasets are now displayed on the publication page, enhancing the overall user experience. Example link: Reaction DOI.
  • Introduced Generic Dataset in Review Page: Similarly, Generic Datasets are visible on the review page, providing comprehensive information to reviewers.
  • Refactored Submission Data Check Modal: The submission data check modal has been refactored for better user experience.
  • Always Create a New Record for Review Comments: A new record is now created for each review comment. This feature is applicable for actions taken after deployment.
  • Introduced Converter Feature for Inbox Data: A converter feature has been added to facilitate easy conversion of inbox data, streamlining data processing tasks.
  • Made Temperature, Duration, and Description Optional for Submission: Users now have the flexibility to submit data without providing temperature, duration, and description, simplifying the submission process.
  • Re-packed the MolViewer to deal with cif file.
  • Invisibility of Temperature, Duration, and Description on Publication Page: If no data is available, temperature, duration, and description fields are now invisible on the publication page, providing a cleaner and more concise presentation.
  • Introduced Review Comment Ownership feature: User can now create review comments to maintain ownership and clarity.
  • Enhanced Review Comments: Added the capability to attach review comments to the physical properties of the sample.
  • Improved User Comment Modal: The User Comment Modal can now be dragged and ensures the background remains visible.
  • Automatic Closure of Review Modal: The Review Modal now closes automatically when the user closes the element on the review page.
  • Improved the Submission Check view: The Submission Check view has been enhanced to provide a better user experience.
  • Introduced Download Metadata and Data: Users have the ability to acquire metadata in xlsx format(Dataset Excel). Furthermore, an option is provided for users to download both the data and metadata together as a compressed zip file.
  • Implemented a feature for global user labeling: Authorized users can now define a global label that is accessible to all users.
  • Introduced LabIMotion Template Hub: The LabIMotion Template Hub is now available for users to access and download templates. See here for more information.
  • Added license to the linked data.
  • Added X-Vial to the Publication Page.
  • Introduced MolViewer: Users can now use the button Viewer to view molecules structure in the MolViewer.
  • Added .tool-versions file to the repository.

• Bug fixes:

  • Resolved a bug causing an invalid date format in certain cases.
  • Addressed an issue where reviewers encountered an empty embargo list.
  • Fixed a bug where scientists organizing report content experienced page breaks.
  • Corrected Navigation URLs: Navigation URLs have been reviewed and corrected to prevent incorrect redirects, ensuring seamless browsing for users.
  • Fixed Issue with Missing File Extensions: An issue occurring when filenames lacked file extensions has been resolved. Files are now handled correctly regardless of the presence of an extension.
  • Text Copying Issue Resolved: The problem with copying text in the User Comment Modal has been fixed.
  • Fixed the issue where the unit data cannot be displayed in the publication page.
  • Addressed an issue where terminology data was not retained following import.
  • Resolved an issue where users were unable to utilize the 'Compare View' feature to assess the disparities between the submitted data and the current working version.
  • Fixed the issue that different molecule shows the same structure in the MolViewer.
  • Corrected dataCatalog syntax error.

• Chores:

  • Upgraded ChemSpectra.
  • Upgraded Converter.
  • Upgraded Labimotion.
  • Upgraded NMRium.
  • Upgraded node version.
  • Upgraded Ruby version.
  • Included the Chemotion ELN version 1.8.1.

Chemotion Repository 1.2.0

Chemotion Repository 1.2.0 brings a variety of significant enhancements to improve user experience and functionality. The following key improvements have been introduced:

Enhancements:

• The update includes the adoption of the ISO8601 time format, providing improved consistency and standardization.
• The publication page and review page now include essential physical properties such as melting point and boiling point information. This addition enhances the comprehensiveness of the data presented, enabling users to access crucial details more conveniently.
• A new data protection mechanism has been introduced, ensuring the security and integrity of user-submitted work. After scientists submit their work, the system automatically locks the data, preventing modifications. However, users retain the ability to unseal the data for editing purposes, providing a flexible and secure workflow.
• Introduction of the feature that users can view the information from the original data source within the repository and conveniently redirect to the ELN instance by clicking on it. This integration streamlines data management processes and facilitates efficient collaboration between different platforms.
• The default chosen license has been changed from 'CC BY-SA' to 'CC BY'.

Chemotion Repository 1.1.0

Chemotion Repository 1.1.0 introduces a range of significant enhancements and bug fixes. The update includes the following key improvements:

Enhancements:

• Integration of Molecule Archive to enhance data visibility and management capabilities.
• Support for assigning Collection DOIs, enabling persistent identification of collections.
• Shibboleth support for streamlined authentication and authorization processes.
• JSON-LD format support for enriched metadata representation.
• Open API for convenient downloading of metadata in JSON-LD format.
• Addition of group leader review functionality, facilitating improved collaboration and oversight.
• Support for publishing MOF reactions.
• Introduction of the Converter service, enabling format conversion for data.
• Introduction of the Ketcher backend service.
• Enriched metadata support for various types of published samples.
• Redesigned sample representation on the landing page for improved usability.
• Support for ORCID authentication, providing seamless user identification.
• Upgraded Chemspectra function.
• Styling improvements to enhance the user experience.

Bug Fixes:

• Addressed an issue with the exporting function when data includes hyperlinks.
• Resolved a QC issue related to the usage of 'mass spectrometry' and 'IR'.
• Corrected the nmrium aasm_state to ensure accurate representation.
• Fixed an issue where the embargo job would get stuck if the mail server did not respond.

Contributors:

• Chia-Lin Lin
• Pei-Chi Huang
• Pierre Tremouilhac
• Lan Le

1.0.1: Extending chemotion_ELN with Repository functions

In short:
- data submission feature added to user ELN page
- Review page for internal reviewing
- Public page to browse published sample/reaction data

Contributors:
Chia-Lin Lin
Pei-Chi Huang
Pierre Tremouilhac