Releases

An ’Submit new version’ action has been added to the Configuration Manager. When enabled, authors are able to submit a new version without requiring an editor submitted a decision verdict (accept, revise or reject).

ThreadedDiscussion form field engagement history is now displayed across versions.

Easily unassign Editor roles from the Control panel>Teams>Assign Editors dropdown menu using the cancel action.

Other;

• Node has been upgraded to version 16. This was done in conjunction with a Cypress Docker upgrade.
• XSweet has been added as a microservice.

Bug fixes;

• Publish action is now working again on the aperture and colab instance archetypes.
• Task Manager; error message erroneously indicating that email notifications are not being sent has been fixed.
• A record of unresponsive reviewers are now kept across versions. Access to a review is restricted to Reviewers who have ‘accepted’ an invitation to peer review (version 1, for example), have done so after a new version of the manuscript has been submitted (version 2, for example).
• Numerous updates and fixes to aperture Cypress tests.
• Fix for JATS generation, and
• better handling of broken images in Wax.

A Peer review workflow dashboard has also been added to the Control panel to give editors oversight of reviewers at each phase of a peer review cycle per version. Click on user cards to see the Review status, review feedback, ‘shared review’ controls and more.

The Control panel has been further segregated into the Team, Decision, Manuscripts text, Metadata and Tasks & Notifications pages to improve usability. The ‘Team’ page replaces the ‘Workflow’ page and includes the new ‘Reviewer status’ Dashboard. The ‘Decision’ page displays all completed reviews, Decision form and Publishing action.

The author, reviewer and editor Dashboard views have also been separated out to improve usability. Easily use pagination, filters and keyword search to display a list of manuscripts as required.

A frontend Configuration Manager; is now accessible via the Menu>Settings>Configuration page. All instance configuration variables will be accessible per workflow from the Configuration Manager. The .env file will only be used where necessary moving forward. Here’s an overview of core workflows (instance archetypes) currently in use.

You are only able to edit variables with respect to the workflow type you have chosen (instance archetype). You are not able to switch between workflow types (instance archetypes). In the future, you will be able to select and modify workflows and variables per group. More on this in our next major release which will support multitenancy, where there will be support for multiple separate groups on a single instance of Kotahi.

Bug fixes;

• A fix for a JATS generation error.
• Improved error handling when publishing fails on the elife instance archetype. Error messages are now displayed in a pop-up on the Manuscripts page.
• Fix that automatically navigates users to any incomplete required fields after clicking on the submit action.
• Fix for Manuscript page ‘Select’ action, where a single click now applies the freeform label.

Task Manager notifications;    can now be scheduled and reminder email notifications sent from all tasks added from the Menu>Tasks and the Control panel>Tasks & Notifications page.

As an Admin, you can create a task and select an email notification reminder to be scheduled when a task is added to a Task template.

As an editor, you can add an assignee to an existing task and click ‘Start’ when you’re ready. Editors can also create new tasks, schedule reminder notifications or send an action email notification immediately (e.g. Reviewer invitation) from the Task & Notifications page.

Clicking on ‘Start’ applies the ‘Duration’ count selected in the Task builder, and sets the ‘Due date’. Email notifications will be sent ‘x’ days ‘before’/‘after’ a ‘Due date’ is met. Marking a task as ‘Complete’ suppresses email notifications from being sent.

Setting a task ‘Duration’ to ‘None’ implies that the task is to be actioned immediately. ‘Due dates’ cannot be applied to action tasks, only to scheduled tasks where a ‘Duration’ value of 0 (zero) and upwards is selected.

Plugin architecture this markup provides a technical overview for handling both Wax and generic plugins in Kotahi; https://docs.coko.foundation/s/f961fad5-f903-4561-9d22-b723129edf15

Bug fixes;

• MathML displays in PDFs generated from the Production editor.
• Footnotes are now displayed in PDFs generated from the Production editor.
• For Docx submissions; additional Regex to handle math incorrectly wrapped in <h3> tags. Regex now handles <h1> to <h6>.
• Various fixes to get Cypress test running on the elife instance.

Bug fixes;

• Fix for the intermittent crashing of the frontpage.
• Admin discussion error no longer displays when there are too many messages.
• Setting automated archiving of manuscripts to only run when ARCHIVE_PERIOD_DAYS has a positive numeric value.

Automated citation parser; has been added to the Production editor. Highlighting citation text and applying the ‘Automated citation parser’ tags a citation using AnyStyle.io. Use the existing citation annotation toolkit to edit citation markup as required for export to JATS.

You will be able to run a single entry or a list of citations through the Automated parser. When applying the parser to a list of references note that citations will be tagged however, AnyStyle does know how to apply list styling thereafter - so you’ll need to apply bulleted/numbered or another list styling manually.

Bug fixes;

• Fix for importing a manuscript containing MathML equations; the centre-aligned equations ($$) are not rendered. This was due to malformed HTML coming from XSweet. By replacing <h4><h4> and </h4></h4> with <p> and </p> respectively the parsing works as expected.
• Email notifications are being sent again from the colab archetype. The system now fetches authors where team members have accepted status.

DocMaps; can now be generated on publish action for the elife instance archetype. A DocMap is a framework for describing the processes used to create a document in a machine-readable way.

This is an example GraphQL query to Kotahi to obtain a docmap:

query {
  docmap(externalId: "https://www.biorxiv.org/content/10.1234/2022.12.20.123456v1")
}

And it returns the following JSON DocMap:

{
  "@context": "https://w3id.org/docmaps/context.jsonld",
  "id": "8cae22e2096db",
  "type": "docmap",
  "publisher": {
    "id": "https://example.com/",
    "name": "Your Journal Name",
    "homepage": "https://example.com/"
  },
  "first-step": "_:b0",
  "steps": {
    "_:b0": {
      "assertions": [],
      "inputs": [
        {
          "doi": "10.1234/2022.12.20.123456",
          "url": "https://biorxiv.org/content/10.1234/2022.12.20.123456v1"
        }
      ],
      "actions": [
        {
          "participants": [
            {
              "actor": {
                "name": "<p>Annie Adams</p>",
                "type": "person",
                "_relatesToOrganization": "<p>University of Otago</p>"
              },
              "role": "peer-reviewer"
            }
          ],
          "outputs": [
            {
              "type": "review-article",
              "content": [
                {
                  "type": "web-page",
                  "url": "https://hypothes.is/a/iRAQ_J0nEe2mijMkkjnKAh"
                },
                {
                  "type": "web-page",
                  "url": "https://mykotahi.com/versions/dc439175-c14a-4f50-8d1a-adf8e1bf9b95/artifacts/819cb7fd-eade-4dd5-9cfc-86c2dc9756b4"
                }
              ],
              "published": "2023-01-26T03:47:15.786Z"
            }
          ]
        },
        {
          "participants": [
            {
              "actor": {
                "name": "<p>Ben Briggs</p>",
                "type": "person",
                "_relatesToOrganization": ""
              },
              "role": "peer-reviewer"
            }
          ],
          "outputs": [
            {
              "type": "review-article",
              "content": [
                {
                  "type": "web-page",
                  "url": "https://hypothes.is/a/ialvLJ0nEe2XeMunC4CmA7"
                },
                {
                  "type": "web-page",
                  "url": "https://mykotahi.com/versions/dc439175-c14a-4f50-8d1a-adf8e1bf9b95/artifacts/5b542cdc-3634-48c2-af8b-0add2d83c064"
                }
              ],
              "published": "2023-01-26T03:47:15.883Z"
            },
            {
              "type": "review-article",
              "content": [
                {
                  "type": "web-page",
                  "url": "https://hypothes.is/a/iSJByJ0nEe2nVEt_9jIEA-"
                },
                {
                  "type": "web-page",
                  "url": "https://mykotahi.com/versions/dc439175-c14a-4f50-8d1a-adf8e1bf9b95/artifacts/93752612-ceb3-4079-a954-eaa27ac062b4"
                }
              ],
              "published": "2023-01-26T03:47:16.409Z"
            }
          ]
        }
      ]
    }
  },
  "created": "2023-01-26T03:14:26.065Z",
  "updated": "2023-01-26T03:47:16.421Z"
}

A screenshot of Kotahi’s Frontpage;

A screenshot of an artefact page (e.g a review) linked from the Frontpage;

Bug fixes:

• Pagedjs: partial fix for splitting tables over multiple pages.
• Pagedjs: output in the template now specifies <ol> elements should have a list style type.
• Review page: fix for review page re-rendering when editing a text field.
• Wax: fix to remove $$ appearing at the start of both block-level and inline equations. Note this effects Kotahi and not XSweet pipeline.
• Wax: action to close JATS generation is now working as intended.

UI enhancements; were made to the Submission, Review and Decision forms to improve the user experience when reading and editing forms.

• Spacing, colour and fonts were adjusted for improving design continuity and usability.
• Required fields are now labelled with an ‘*’.

Bug fixes;

• Review invitations and review data are now being captured and displayed per manuscript version.
• Archived Manuscripts are no longer being displayed on the Dashboard.
• The ‘Label citation’ annotation is now applying the correct reference tag when generating JATS.

ManuscriptFile; form field type has been added to the form builder. Manuscripts file submission e.g. Word, PDF, LaTeX etc. will now display as an attachment on the submission form. Admins can 'hide this form ‘Hide from reviewers?’ Y/N using the form field settings.

Bug fixes;

• The file picker refreshes after uploading an image file.
• Semantic Scholar imports are now based on the most recent 100 selected preprints.
• Reviewer invitation status is now captured on the Control panel>Workflow>Manage reviewers page.

Task Manager; can be used by the editorial team to create and track important peer reviews or other workflow deliverables. You can find the task list on the Control panel>Task & Notifications page.

As an editor assigned to a manuscript you can;

1. Access a task list
2. Create, modify or delete a task
3. Add a title
4. Add an assignee
5. Assign a due date
6. Set a status

Tasks are automatically marked as overdue once a due date has been met. Overdue tasks are highlighted by a red accent.

Hover your mouse over the due date, a tooltip displays the due date and time in your timezone. The default timezone is UTC. If your team works in a single location you can set a timezone using a .env file configuration - see the CHANGES.md update.

As an admin, you can create a ‘Task template’ using the Task builder located in the Menu>Settings>Tasks page. Here you can create a task list that will appear on the Task & Notifications page for all new submissions (in the case of the aperture / traditional journal publishing workflow archetype) and for all ‘selected’ preprints (in the case of the colab / preprint workflow archetype).

As an admin you are able to;

1. Create and or modify a task template
2. Add an assignee
3. Set a task duration (for example; if a manuscript is uploaded/preprint ‘selected’ and a duration of 14 days has been applied to a task, then the due date would be automatically set for 14 days from the submission/selection date)
4. Mark a task as complete using the checkbox or setting the status to ‘Done’

Notifications have been removed from the Control panel>Workflow page and are now accessible from the Control panel>Task & Notifications page. Making it easier for the editorial team to send email notifications related to workflow tasks.

Keyword search; added to Manuscripts page. Journal Managers/Curators can now easily search for objects listed in the Manuscripts table. You can also filter/sort search results.

Search results are ranked based on relevance. Relevance is based on the prevalence of the search terms in the title and abstract fields. You can also search using a ‘manuscripts number’, ‘id’ or ‘submitter’ name.

Here is an overview of the Search syntax;

• Terms separated by spaces are all required (treated as AND)
• Terms inside double quotes are phrases that have to be matched with words in the given order, e.g. “exact phrase”
• You can allow matching of just one out of two or more subqueries using capital OR, e.g. “climate change” OR albedo warming OR “fossil fuel” pricing will match any of the three options
• Subqueries can also be created in brackets, e.g. repayment (loan OR mortgage OR “personal debt”) - directly before a term, phrase or bracketed subquery indicates that term/phrase/subquery should NOT be present, e.g. bank deposit -“river bank”
• The stopwords list is; I me my myself we our ours ourselves you your yours yourself yourselves he him his himself she her hers herself it its it itself they them their theirs themselves what which who whom this that these those am is are was were be been being have has had having do does did doing a an the and but if or because as until while of at by for with about against between into through during before after above below to from up down in out on off over under again further then once here there when where why how all any both each few more most other some such no nor not only own same so than too very can can’t will just don’t should now

Automated import of preprints from bioRxiv & Semantic Scholar; has now been added to instances utilising the colab archetype.

Preprints are imported from bioRxiv based on specific subject matter categories. Preprints are imported and are accessible via the Manuscripts page. A curator (admin role) is able to ‘Select’ preprints on the Manuscripts page. Recommended preprints are imported from Semantic Scholar based on these pre-selected items. Preprints imported from Semantic Scholar are identifiable by the icon displayed in the Title column.

The import action can be set to run and at a specific time each day using a configuration setting.

Date selection filter; added to the ‘updated’ and ‘created’ columns on the Manuscripts page. Journal Managers/Curators can easily filter views by the date a manuscript entered the system or when it was last updated.

Click on the calendar icon to choose a date range manually or select from a list of presets.

Manuscripts can now be archived; from the Manuscripts page. These manuscripts are removed from the list of Manuscripts page list but are still stored in the database.

The following JATS annotations have been added to the Production editor; glossary, keywords, funders and a dedicated Citation toolbar including author name, journal title, issue, year and DOI tags. Citation annotations can now also be applied to footnotes.

The menu has been reorganised; to better accommodate the additional pages. ‘My profile’ is now accessed by clicking on the profile picture. ‘Forms’, Users and soon ‘Tasks’ are nested in the ‘Settings’ dropdown menu.

'Reviewer invitation’ email notification; has now been added to the Control panel>Workflow>Notifications page.

If you’ve selected a manuscript or preprint for review, you can now invite a new user to participate in a peer review by using the ‘reviewer invitation’ email notification template.

A reviewer can ‘accept’ or ‘decline’ the invitation from links embedded in the email notification. Accepting the invitation automatically links the review to the manuscript in Kotahi. Editors can track the ‘accept’ or ‘decline’ response from the Control panel>Reviews page.

A reviewer can log in and see their review on the Dashboard. They can access the review form, complete all required fields, accept the T&Cs and submit.

Share/publish Submission and Decision form fields; using an advanced setting ‘Include when sharing or publishing?’ Yes/No. This setting can enable/disable sharing/publishing to an endpoint when clicking on the Control panel>Workflow>‘Publish’ action. This can be applied per form field with the exception SupplementaryFiles.

Threaded Discussion form field; can now be added to a Decision form. This form field type allows an editor to share a decision or summary report with the author. The author now has the option to provide inline feedback. The editorial team can also provide feedback on an author’s response. Individual discussion posts can be selected and shared/published when clicking on the Control panel>Workflow>‘Publish’ action.

Bug fix; Review page authentication error resolved. Reviewers are now authorised to submit review feedback and can now access the review form.

Customisable Review and Decision forms; will replace the hardcoded Review and Decision feedback pages. Easily select for fields, and settings to create bespoke Review and Decision forms.

All current form field types will be available in both Review and Decision form builders; Supplementary Files, AbstractEditor, VisualAbstract, Authors Input, Links Input, Text Field, Checkbox Group, Select & Radio button Group options. Along with various advanced settings for ‘required fields’ or ‘DOI validation’ etc.

Capturing of Review and Decision form data in a structured manner offers an opportunity for more versatile and innovative publishing actions. With the ability to select and send feedback components to specific endpoints as desired.

'Author invitation’ email notification; has now been added to the Control panel>Workflow>Notifications page.

If you’ve selected a preprint for review, you can now request permission to peer review a manuscript by using the ‘author invitation’ email notification template. An author can ‘accept’ or ‘decline’ the invitation from links embedded in the email notification. Accepting the invitation automatically links the author to the manuscript in Kotahi.

An author can log in and see their manuscript on the Dashboard. They can access the submission form, complete all requisite metadata fields, accept the T&Cs and submit for peer review.

If an author declines, they will be redirected to a landing page where they can provide feedback and opt-out from further communication.

The ‘Author invitation’ email template can be personalised (customised) per instance.

Download JATS; from the Wax Production editor. Valid JATS is generated on download from the Production editor. Images folder contains all of the image converted on submission of a docx file and supplementary files attached on submission will also be included.

The download action results in a shareable URL, that persists for 24 hours and can be shared publicly as required.

This latest release includes the following enhancements;

• Object store; organises images and supplementary files for access in the Wax word processor as well as scaling images for export to various endpoints. On submission, all images inserted into Word documents (JPEG, PNG, SVG, TIFF, EPS & GIF) will be retained in the original format in the Object Store. On conversion to HTML, images are converted to “medium” size format (JPEG or PNG) for access in the Wax word processor. Images will be also accessible in multiple quality formats (size “small”, “medium” and “original”) for export to the web, print-ready PDF or JATS XML (as a zipped file component).
• Wax Asset Manager; supports the management of image files (upload, insert and delete actions) from within the Wax word processer.

The Kotahi 1.0.0-beta.1 is here! :rocket:

A month after the release of the 1.0.0-alpha.1 the first beta release of Kotahi is here!

The most important new features are:

• Infinite versions of manuscript submissions
• Visual abstract
• Initial permissions and restrictions
• yarn console for easy access command line access to all models
• Simplification of viewing a manuscript and controlling its workflow
• Double chat interface (one with authors, one with the editorial team)

This release also includes many fixes including:

• Better form validation support
• Better management of uploaded files
• Numerous fixes across the board

Hope you like it! Feel free to reach out in the issues with ideas, bugs or comments.

This is the first alpha release of Kotahi, an open source application to manage research publication workflows.

This release is not ready for general use. It does, however, include many features such as:

• Customisable submission form
• Real-time chat with authors, editors and reviewers
• A dashboard and several admin screens
• Review and decision workflows
• Supplementary file uploads
• DOCX to HTML conversion with XSweet
• Multiple link/research object submission
• Basic frontpage/public-facing page
• Logging in with ORCID
• Profile pictures

And more. :rocket:

Upcoming milestones can be seen here: https://gitlab.coko.foundation/kotahi/kotahi/-/milestones. The first beta is planned for end of August and will include many stability/UX and security improvements.