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Chemotion_Repository Changelog

[2.2.0]

2024-11-06

  • 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:

[2.1.0]

2024-08-05

  • 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.

[2.0.0]

2024-01-15

  • 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.

[1.2.0]

2023-06-29

  • Enhancements:

    • published on ISO8601. #46
    • Add physical properties which are melting point and boiling point information to the publication page and review page.
    • Introduction of the data protection mechanism where the system automatically locks data after scientists submit their work; they can unseal the data for editing.
    • publish sample: pre-chosen license. #27
    • Introduction of the feature that users can see the information from the original one after transferring the data from ELN and click on it to redirect to the ELN instance.
    • Upgrade node version.

[1.1.0]

2023-06-12

  • 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.

  • Fixes

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