Releases

Reference parser has been updated! You can now use the ‘Reference’ annotation tool in the Production editor to parse citations via Crossref.

Group Managers can select single/multiple references in a reference list and click on ‘Reference’ to run the AnyStyle and Crossref parser. Once the results are loaded, you’ll be able to click on a reference to select and/or edit as required. Clicking ‘Apply’ inserts the updated citation into the Reference list.

Configuration>Production offers controls to select the citation style, number of results and language locale. To note that an ordered list cannot be applied to parsed citations.

@mentions are now supported in Discussion channels. Users are subscribed to a channel based on role or participation. Type ‘@’ into the editor to get a list of 5 subscribed users. Continue typing to search for other subscribed users. Select a username and on the 'Send action an email notification will be sent to the @mentioned user.

Use the Configuration control to assign the ‘@mention notification’ email notification template.

Updates have also been made to the scheduler that sends email notifications for new messages posted to a Discussion channel;

• Only subscribed users will receive notifications.
• The scheduler checks to see if there have been any new posts made every 30mins. If a new message is present a ‘Discussion notification’ is sent. Once this initial email has been sent a subsequent email will be sent the next day.

Users can now edit and/or delete their own Discussion messages. Hover over a message to see the ellipses menu and the actions to ‘Edit’ or ‘Delete’ a post.

Admin users are able to delete any message.

Users are also now able to pause (mute) email notifications sent per Discussion channel.

Bug fixes;

• Formulas and equations are now displaying in Flax.
• The display of tables column and row width & height in Flax has been improved.
• Task Manager; email notifications records now display the sender username. Scheduled notifications; ‘Kotahi’ and notifications sent manually; ‘Username’ e.g. ‘Ryan Dix’.
• Fix to clean up malformed formulas containing an additional \ coming out of XSweet.
• ‘Suggested’ changes are visible in the Wax editor again.
• Fix for filtering status on Dashboard and Manuscripts pages for groups using the aperture or colab instance archetypes.

• Fix Flax version

• Improved stability for import plugins importing very large numbers of manuscripts.
• Fixed metadata inconsistencies in Flax publishing.

Multitenancy is now supported! The database has been refactored to support multiple separate groups on a single instance of Kotahi.

• Frontpage allows new/existing users to access the login page for each Group e.g. https://yourserver.co/

• Login page allows new/existing users to log in to a specific Group e.g. https://https://kotahi.yourserver.co/groupx/login

• Publishing page (Homepage) has been built using Flax, displaying manuscript content or form data published to the web per Group e.g. https://yourserver.co/groupx

New Groups can be created using the .env file - see CHANGES.md for more detail on how to add/remove groups. A frontend Configuration Manager has already been implemented to customise workflow settings as required.

The Admin role has been modified to access all Groups on a single instance. The role has also been enhanced to serve an overarching system administration function;

• The Admin will see all users (global) when accessing the User page.
• The Admin will be able to assign other Admin and/or Group Managers roles per Group.

A new Group Manager role has been created** to serve as the administrator, curator, and journal manager per Group.

• Group Managers will see all users in their Group.
• Group Managers will be able to assign other Group Managers in their Group only.

A Content Management System allows Group Managers to create/edit and publish webpages in Flax (static website builder) from Settings>CMS. Use the CMS>Pages to create/edit webpages linked from the Header/footer. Use the CMS>Layout features to organise webpages and add brand partners/affiliations.

Utilise the aperture or colab instance archetype to publish and display manuscript content, metadata, reviews and/or decision/summaries in Flax. Publishing controls reside within the form builder from field settings.

This release targets instances that have not yet upgraded to v2.0.0

Patch release includes the following:

• Prevent invitations from being unintentionally declined by the link-prefetch feature of some email services. Now a person must click a button to decline, once they reach the decline page.
• Fix instability in CrossRef publishing

Patch release to fix instabilities in the Manuscripts page and author invitation process.

Email notification templates are accessible in a read-only format from the Settings>Email page. Templates include expressions representing the data mapping.

Assign an email template to an event from the Configuration>Email page.

Discussion email notifications will be sent to;

• Authors and Editors are subscribed to the Author discussion thread per manuscript.
• Editors and Reviewers are subscribed to the Editors discussion thread per manuscript.
• Admins are subscribed to the Admin discussion thread.
• Admin who have posted to an Editor discussion thread.

New discussion posts will be labelled as ‘Unread’.

Users can mute chat notifications from the User profile page.

Bug fixes;

• Fix that ensures Threaded Discussions persist across manuscript versions.
• Fix that ensures Task lists persist across manuscript versions.
• Fix error when displaying anonymous reviews on the /submit page.

Bug fixes;

• The ability to enable individual review submissions as ‘Shared’ has been fixed. When enabled, reviewers can access and read other submitted reviews that have been marked as ‘Shared’.
• Chat text editor stays in focus after a user clicks enter or on ‘send’.
• Fix for Cypress test to run on Firefox.
• Update to wmf regex to handle emf files on conversion. Unsupported image files are replaced with a ‘broken image’ icon for ease of reference.
• Fix to correctly display task lists across versions.
• Fix for the inclusion of the Funding source element on export to JATS.

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.