Kotahi issueshttps://gitlab.coko.foundation/kotahi/kotahi/-/issues2023-12-06T10:43:12Zhttps://gitlab.coko.foundation/kotahi/kotahi/-/issues/1306[CoLab] Hide option for editors to 'Publish' from Control panel2023-12-06T10:43:12ZRyan Dix-Peek[CoLab] Hide option for editors to 'Publish' from Control panelOnly admin should be able to publish content to an endpoint. Currently, editors and admin are able to see the 'Publish' action.
Suggested solution; for a Configuration>Control panel setting; 'Only admins can Publish articles/reviews'Only admin should be able to publish content to an endpoint. Currently, editors and admin are able to see the 'Publish' action.
Suggested solution; for a Configuration>Control panel setting; 'Only admins can Publish articles/reviews'CoLab Biophysics v7https://gitlab.coko.foundation/kotahi/kotahi/-/issues/1305[CoLab] Ability to see changes made to Decision form data (divs)2023-12-06T10:43:19ZRyan Dix-Peek[CoLab] Ability to see changes made to Decision form data (divs)CoLab Biophysics v7https://gitlab.coko.foundation/kotahi/kotahi/-/issues/1304[CoLab] Hide option to 'Delete' submitted reviews2023-12-06T10:43:32ZRyan Dix-Peek[CoLab] Hide option to 'Delete' submitted reviewsEditors should not be able to delete submitted reviews from the Control panel>Team page. These are seen as formal submissions - and a record should always be kept.
Suggested solution; add a Configuration>Control page setting; 'Editors ...Editors should not be able to delete submitted reviews from the Control panel>Team page. These are seen as formal submissions - and a record should always be kept.
Suggested solution; add a Configuration>Control page setting; 'Editors can 'delete' submitted reviews'
![Screenshot_2023-05-22_at_15.16.59](/uploads/3fd55db00a4fb3acd68ac899ce57d2ff/Screenshot_2023-05-22_at_15.16.59.png)CoLab Biophysics v7https://gitlab.coko.foundation/kotahi/kotahi/-/issues/1296Support for multiple submissions froms2024-02-15T06:49:38ZAdam Hydeadam@coko.foundationSupport for multiple submissions fromsWe need to support multiple submission types within each group. I recommend a management interface in the submission form settings where submissions that will be surfaced can be selected/unselected. We will need to put a name for each ('...We need to support multiple submission types within each group. I recommend a management interface in the submission form settings where submissions that will be surfaced can be selected/unselected. We will need to put a name for each ('submission type'). The submission type should be surfaced as a drop down at the first submission screen:
![Screenshot_from_2023-05-18_17-18-32](/uploads/24db9ecd01ffb0c52066016de5cc6914/Screenshot_from_2023-05-18_17-18-32.png)
we will also need to work out how to manage the display of these within the manuscripts page, as it is likely not all submission types have the same data profile.Amnet multi-tenancy v2https://gitlab.coko.foundation/kotahi/kotahi/-/issues/1290Add datatype drop downs to form builder2023-08-22T01:52:32ZAdam Hydeadam@coko.foundationAdd datatype drop downs to form builderWe need to add datatypes to the form fields for a number of reasons, mainly:
* to map incoming entities extracted from the submission (eg via AI parsing of a manuscript) to form fields to pre-populate the forms
* to map the data in the f...We need to add datatypes to the form fields for a number of reasons, mainly:
* to map incoming entities extracted from the submission (eg via AI parsing of a manuscript) to form fields to pre-populate the forms
* to map the data in the form fields to the outgoing formats
What I dont want is to build multiple different types of form fields each hard coded and related to a specific JATS attribute. We need to build a drop down that is part of the form element config that allows users to choose the datatype. This dropdown is to be pre-populated with attribute types (eg JATS elements) but also can be identified by a user-defined entry.
I recommend we do this sooner rather than later so we can start planning to use AI to pre-populate the submission from.Amnet multi-tenancy v2Ben WhitmoreBen Whitmorehttps://gitlab.coko.foundation/kotahi/kotahi/-/issues/1289Turn the Task List into a kanban board2023-12-06T10:44:15ZAdam Hydeadam@coko.foundationTurn the Task List into a kanban boardThe current task manager is awesome, but hard to grok if there is a lot of items in the list. I believe we will need to enable the user to segment the tasks into as they like into groupings which may reflect (for example) workflow stages...The current task manager is awesome, but hard to grok if there is a lot of items in the list. I believe we will need to enable the user to segment the tasks into as they like into groupings which may reflect (for example) workflow stages. TO make this even more readable and useful it would be very good to allow the groups to happen by creating vertical columns that can be named by the user to reflect their workflow. In this way we are effectively converting the current task manager into a kanban board (see trello).
We can then considering the form factor of tasks and designing them to look more like 'cards' (also as per trello).
Lastly, at a much later date we could use this format to populate user defined columns of 'cards' which would effectively reflect their to-dos. I am including two videos here of the Aperta system - IMHO these concepts are extremely powerful, and if we can move their in stages we would have a tremendously powerful paradigm for managing workflow.
![demo_part_1](/uploads/be2ed3af63829e99256a95a31e6020b5/demo_part_1.webm)
![demo_part_2](/uploads/9d5e46ad978f0f1bbcc74af18e5f8450/demo_part_2.webm)CoLab Biophysics v7https://gitlab.coko.foundation/kotahi/kotahi/-/issues/1256[Task builder] Action to update all unmodified tasks2023-12-06T10:44:23ZRyan Dix-Peek[Task builder] Action to update all unmodified tasksCoLab Biophysics v7https://gitlab.coko.foundation/kotahi/kotahi/-/issues/1226[Production editor] Add feature to remove annotations2023-03-07T19:41:06ZRyan Dix-Peek[Production editor] Add feature to remove annotationsCurrently, in a new session when accessing the Production editor; users are unable to remove annotations applied to paragraph text. Only annotations applied in the same session can be removed using the 'undo' action. This is problematic ...Currently, in a new session when accessing the Production editor; users are unable to remove annotations applied to paragraph text. Only annotations applied in the same session can be removed using the 'undo' action. This is problematic as an incorrectly applied annotation cannot be removed.
**Suggested solution;** clicking on the annotated area displays a cancel action on the top-right, clicking on cancel would remove the annotation.Amnet Production Editor v2https://gitlab.coko.foundation/kotahi/kotahi/-/issues/1213[CoLab] Apply styling to email notification templates2023-12-06T10:44:31ZRyan Dix-Peek[CoLab] Apply styling to email notification templatesFor `colab` archetype notifications; support for email content styling (fonts, line spacing) needs to be retained as far as is reasonably possible.
- Font; Helvetica Neue (fall back is Arial)
- Line spacing; 1.3For `colab` archetype notifications; support for email content styling (fonts, line spacing) needs to be retained as far as is reasonably possible.
- Font; Helvetica Neue (fall back is Arial)
- Line spacing; 1.3CoLab Biophysics v7https://gitlab.coko.foundation/kotahi/kotahi/-/issues/1207[CoLab] Ability to add metadata to a User profile page2023-12-06T10:44:37ZRyan Dix-Peek[CoLab] Ability to add metadata to a User profile page**Description** editorial teams want to collect specific user data to support editor/reviewer selection. The suggested solution is to create a 'Profile builder'; where an admin can create a form that will be visible on the User profile p...**Description** editorial teams want to collect specific user data to support editor/reviewer selection. The suggested solution is to create a 'Profile builder'; where an admin can create a form that will be visible on the User profile page.
Users will be able to navigate to the profile page, and complete fields e.g. select from a list of topics of expertise etc. These fields can also be required, and ade compulsory for all new users to complete on first login.CoLab Biophysics v7https://gitlab.coko.foundation/kotahi/kotahi/-/issues/1192[CoLab] Submitter and author in conflict when sending author invitation2023-12-06T10:44:44ZRyan Dix-Peek[CoLab] Submitter and author in conflict when sending author invitationCoLab Biophysics v7https://gitlab.coko.foundation/kotahi/kotahi/-/issues/1169Send emails using generic SMTP2023-12-06T10:44:52ZBen WhitmoreSend emails using generic SMTPCurrently the sending of emails is only supported using Gmail. But `coko-server` [provides easy functionality to send emails](https://dev.coko.foundation/?path=/docs/common-libraries-server--page#sendemail) using standard SMTP, and we sh...Currently the sending of emails is only supported using Gmail. But `coko-server` [provides easy functionality to send emails](https://dev.coko.foundation/?path=/docs/common-libraries-server--page#sendemail) using standard SMTP, and we should support that. This is how it is configured in the [.env](https://gitlab.coko.foundation/hhmi/hhmi/-/blob/master/docker-compose.yml#L76-80) and in [custom-environment-variables.js](https://gitlab.coko.foundation/hhmi/hhmi/-/blob/master/packages/server/config/custom-environment-variables.js#L45-55)
We can use https://ethereal.email/ for local development.
We should consider, before we _remove_ gmail-specific support, whether gmail provides possible benefits in terms of whitelisting against spam filters etc and whether we can make an equivalent connection to gmail using normal SMTP. It may be that some customers wish to continue with the gmail service.CoLab Biophysics v7https://gitlab.coko.foundation/kotahi/kotahi/-/issues/1144[Task builder] Add task start date2023-12-06T10:44:58ZRyan Dix-Peek[Task builder] Add task start date**Description;** the purpose of this task is to include features that support the configuration of task due dates based on a predefined start date. Currently, only a task duration can be added and enabled on the 'Start' action.
Admin v...**Description;** the purpose of this task is to include features that support the configuration of task due dates based on a predefined start date. Currently, only a task duration can be added and enabled on the 'Start' action.
Admin view;
![CoLab___PM_to-do_list-Admin-Add](/uploads/0dfeb5fca6fe9b52edfe78bf7d6860c7/CoLab___PM_to-do_list-Admin-Add.jpg)
![CoLab___PM_to-do_list-Admin_v2](/uploads/c2a321f7036d17bf79b87510668b6377/CoLab___PM_to-do_list-Admin_v2.jpg)
Editor view;
![CoLab___PM_to-do_list-Editor_view__3_](/uploads/b111244e0072ffc4a028828293b8209b/CoLab___PM_to-do_list-Editor_view__3_.jpg)
**Acceptance criteria;**
- [ ] An admin should be able to set a start date using the counter in the Settinsg>Task builder. The counter calculation is the number of days after the manuscripts was submitted (`aperture`) or Selected (`colab`).
- [ ] An editor should be able to edit the start date counter in the Tasks&Notifications>Tasks> Settings modal.
- [ ] An admin can set a duration. A duration count is added to a start date and displays the due date (Tasks&NOtifications>Task>Due date) based on this calculation.
- [ ] Configuration setting should `ENABLE_TASK_DATE`=true/falseCoLab Biophysics v7https://gitlab.coko.foundation/kotahi/kotahi/-/issues/1121[CoLab] Replace submission.link with DOI URL for preprints imported from Sema...2023-12-06T10:45:05ZRyan Dix-Peek[CoLab] Replace submission.link with DOI URL for preprints imported from Semantic ScholarPublishing to Hypothesis displays an error because `submission.link` points to the Semetaic Scholar domain for all preprints imported from Semantic Scholar. the user is required to manually insert the DOI URL into the submission.link fie...Publishing to Hypothesis displays an error because `submission.link` points to the Semetaic Scholar domain for all preprints imported from Semantic Scholar. the user is required to manually insert the DOI URL into the submission.link field, then publish.
Is it possible to automatically replace the submission.link field with URL that DOI points to for all preprints imported from Semantic Scholar?
![Screenshot_2022-11-09_at_10.24.37](/uploads/7228a20653a7c11bcfc1ca9f88fd6f2f/Screenshot_2022-11-09_at_10.24.37.png)CoLab Biophysics v7https://gitlab.coko.foundation/kotahi/kotahi/-/issues/1113[CoLab] Add ability for editor to rescind reviewer invitation2023-12-06T10:45:12ZRyan Dix-Peek[CoLab] Add ability for editor to rescind reviewer invitationCurrently, a reviewer's access to a review page can be revoked by deleting the reviewer from the Control panel>Manage reviewers page. It is not currently possible to revoke a 'reviewer invitation' email notification.
Solution; a 'delet...Currently, a reviewer's access to a review page can be revoked by deleting the reviewer from the Control panel>Manage reviewers page. It is not currently possible to revoke a 'reviewer invitation' email notification.
Solution; a 'delete' action should also be available in the Control panel once the email notification is sent. This feature can be used by the editor to rescind the invitation.
The email notification may have still been sent, but clicking on the accept/decline should not display a notification that access to the review has been revoked.
Current state, control panel does not include a 'delete' (rescind) action;
![Screenshot_2023-01-16_at_12.50.36](/uploads/79004397df4a78f51424222c7cf70bbc/Screenshot_2023-01-16_at_12.50.36.png)
Current state, 'access revoked' error handling display;
![Screenshot_2023-01-16_at_12.53.24](/uploads/a132085f3368918de2b437daa6dac7b6/Screenshot_2023-01-16_at_12.53.24.png)CoLab Biophysics v7https://gitlab.coko.foundation/kotahi/kotahi/-/issues/1103[eLife] Use a configuration setting to inlcude/remove pages form the control ...2022-10-27T12:45:01ZRyan Dix-Peek[eLife] Use a configuration setting to inlcude/remove pages form the control panel**Description;** instances using the `elife` archetype make use of the Evaluation page to capture and publish reviews. The control panel pages; workflow, manuscript text and metadata are not visible to the end user. The purpose of this t...**Description;** instances using the `elife` archetype make use of the Evaluation page to capture and publish reviews. The control panel pages; workflow, manuscript text and metadata are not visible to the end user. The purpose of this task would be to allow an instance to allow pages to be visible as required using a configuration variable in the .env file.
For example; the elife team could benefit from features such as assigning a reviewer or using creating a task list. Currently, these features are inaccessible because the control panel is hidden in elife archetype.eLife v1https://gitlab.coko.foundation/kotahi/kotahi/-/issues/1095[CoLab] Submitting a new version should prevent automated import of the same ...2023-12-06T10:45:19ZRyan Dix-Peek[CoLab] Submitting a new version should prevent automated import of the same preprint from bioRxiv**Description;** currently, we prevent the importing of duplicates from bioRxiv based on the `submission.link` and from Semantic Scholar based on `submission.doi`.
A key outcome of the Colab peer review cycle is to ensure an author sub...**Description;** currently, we prevent the importing of duplicates from bioRxiv based on the `submission.link` and from Semantic Scholar based on `submission.doi`.
A key outcome of the Colab peer review cycle is to ensure an author submits an updated version of their manuscripts to a preprint server. The purpose of this task is to ensure that we do not automatically import the updated version of the preprint (e.g. https://www.biorxiv.org/content/10.1101/2021.01.10.426076v2) into Kotahi if the preprint has been submitted as part of the initial version/1st review cycle.
Suggested solution; preprionts imported automatically are validated against against `submission.link` field captured in the database. A validation error should display for all `submission.url` fields where a duplication is present in the system - this will allow an Editor to manually varify and archive the duplicate.CoLab Biophysics v7https://gitlab.coko.foundation/kotahi/kotahi/-/issues/1070[Production editor] Add the ability to apply inline callouts in a random order2022-10-11T12:29:15ZRyan Dix-Peek[Production editor] Add the ability to apply inline callouts in a random orderTo be specced -
Uses would like to apply footnote references inline in random order. Wax footnote callout logic only supports chronological ordering at this stage. This needs to be discussed as to how best to do this.To be specced -
Uses would like to apply footnote references inline in random order. Wax footnote callout logic only supports chronological ordering at this stage. This needs to be discussed as to how best to do this.Amnet Production Editor v2https://gitlab.coko.foundation/kotahi/kotahi/-/issues/1067[CoLab] Validate DOIs submitted manually2023-12-06T10:45:26ZRyan Dix-Peek[CoLab] Validate DOIs submitted manually**Description;** For the `colab` archetype configuration; Manuscripts can be imported automatically or submitted manually. We have a use case where authors, editors and or curators may submit a manuscript manually for review. This submis...**Description;** For the `colab` archetype configuration; Manuscripts can be imported automatically or submitted manually. We have a use case where authors, editors and or curators may submit a manuscript manually for review. This submission may already have been imported automatically into kotahi - we need to account for this duplicate in the system, as the manuscript may have already been considered for review, reviewed and/or rejected.
The most common identifier is the DOI. A suggestion is to validate the DOI captured against DOIs currently in the Manuscripts page or archived in the database.
We could display an alert at the form field level; 'Duplicate of manuscript number 1015' or 'Duplicate of manuscript number 1015 (ARCHIVED)'
![Screenshot_2022-10-10_at_14.32.08](/uploads/bfa23908dd1372784d64acecdf5e391b/Screenshot_2022-10-10_at_14.32.08.png)CoLab Biophysics v7https://gitlab.coko.foundation/kotahi/kotahi/-/issues/975[eLife] Add 'Upload image' plugin to AbstractEditor2022-08-03T05:27:06ZRyan Dix-Peek[eLife] Add 'Upload image' plugin to AbstractEditorAs an admin, I would like to embed images when reviewing content, and publish to Hypothe.is.
**Acceptance criteria;**
- [ ] `upload-file` feature is accessible in the Basic Wax editor when editing content in an `AbstractEditor`.
- [ ]...As an admin, I would like to embed images when reviewing content, and publish to Hypothe.is.
**Acceptance criteria;**
- [ ] `upload-file` feature is accessible in the Basic Wax editor when editing content in an `AbstractEditor`.
- [ ] An editor is able to use the Asset Manager to source & manage images.
- [ ] An Author is able to use a file picker to locate and add image files.eLife v1