Kotahi issueshttps://gitlab.coko.foundation/kotahi/kotahi/-/issues2024-03-28T03:54:25Zhttps://gitlab.coko.foundation/kotahi/kotahi/-/issues/1521OpenAI-Kotahi production editor integration2024-03-28T03:54:25ZRyan Dix-PeekOpenAI-Kotahi production editor integration1. Update Cokoserver (latest version) to ensure that this renders as fast as possible.
1. Add Open AI chat, and 'rendered' Preview to Production editor per article.
2. Label as a Beta feature.1. Update Cokoserver (latest version) to ensure that this renders as fast as possible.
1. Add Open AI chat, and 'rendered' Preview to Production editor per article.
2. Label as a Beta feature.MRdevTaggMRdevTagghttps://gitlab.coko.foundation/kotahi/kotahi/-/issues/769Running this application on my local machine to development2021-12-16T09:57:03ZWahyu Nur FadillahRunning this application on my local machine to developmentI am Wahyu from Indonesia, I was ordered by Mr. Oka to learn about this project. So I want to ask how can I run this app on my local machine? and carry out development if needed
thank youI am Wahyu from Indonesia, I was ordered by Mr. Oka to learn about this project. So I want to ask how can I run this app on my local machine? and carry out development if needed
thank youhttps://gitlab.coko.foundation/kotahi/kotahi/-/issues/691Clearer prompt to enter email address2021-11-18T06:50:10ZBen WhitmoreClearer prompt to enter email addressUpon first logging in, if Kotahi cannot retrieve a user's email address from their ORCID account, the user is presented with this page:
![image](/uploads/253b80746d4ca0b420f52c14d48eed8d/image.png)
If they try to navigate by clicking an...Upon first logging in, if Kotahi cannot retrieve a user's email address from their ORCID account, the user is presented with this page:
![image](/uploads/253b80746d4ca0b420f52c14d48eed8d/image.png)
If they try to navigate by clicking any of the menu items, this does not work; they remain on the same page.
Kotahi wants them to enter an email address and hit "Change", but it doesn't make this clear enough, and users typically don't know what is expected of them.
Because this step must be completed before _any_ other actions can be taken, it's misleading to show any other active navigation options. We should show something like a modal dialog with a textbox for email address, a "Save email address" button, and instructions along the lines of "Please register your email address to continue". Probably the rest of the screen should be greyed out behind with an alpha transparency. The modal dialog should disappear upon an email address being entered and "Save email address" being clicked.
We will probably want to reuse modal dialogs for other purposes, so the modal dialog should be built as a reusable component. Regarding styling, in general prefer simple, clean layouts that use whitespace rather than lines to create separation. We have configured colours and grid [here](https://gitlab.coko.foundation/kotahi/kotahi/blob/2ce939d19221b931696f3e870c077bcb721cdbb7/app/theme/index.js) -- see [this example](https://gitlab.coko.foundation/kotahi/kotahi/blob/28e106553c31e90c732643255a441e7f4296b502/app/components/Menu.js) of how these are used.Yash Guptayash.wit2021@gmail.comYash Guptayash.wit2021@gmail.comhttps://gitlab.coko.foundation/kotahi/kotahi/-/issues/606Error occured while trying to proxy to: localhost:4000/graphql2021-11-23T04:32:37ZMladen BabicError occured while trying to proxy to: localhost:4000/graphqlHi all,
I'm trying to start Kotahi project but without success. I've followed instructions in the Readme file, the server starts normally but when I try to request http://localhost:4000 it gives me:
`{"graphQLErrors":[],"networkError":...Hi all,
I'm trying to start Kotahi project but without success. I've followed instructions in the Readme file, the server starts normally but when I try to request http://localhost:4000 it gives me:
`{"graphQLErrors":[],"networkError":{"name":"ServerParseError","response":{},"statusCode":504,"bodyText":"Error occured while trying to proxy to: localhost:4000/graphql"},"message":"Unexpected token E in JSON at position 0"}`
Any help regarding to this?Yannis BarlasYannis Barlashttps://gitlab.coko.foundation/kotahi/kotahi/-/issues/1566[Sciety-Colab] Invited author assigned as reviewer2024-03-27T11:28:29ZRyan Dix-Peek[Sciety-Colab] Invited author assigned as reviewer## Expected behaviour
When inviting authors to participate in a peer review; multiple user users (existing/new) can be invited, the user who accepts the invitation should be assigned as the author. A record of the accept or reject actio...## Expected behaviour
When inviting authors to participate in a peer review; multiple user users (existing/new) can be invited, the user who accepts the invitation should be assigned as the author. A record of the accept or reject action is displayed in the Decision>Completed reviews section.
## Current behaviour
When inviting authors to participate in a peer review; if an 'Author invitation' email notification is sent, the second time the author notification is sent to new (different) user, the user appears to be assigned as a reviewer on the Teams>Reviewer Status section.
## Steps to reproduce
1. Editor sends an author invitation to user 1
1. Ueer 1 accepts author invitation
2. Editor sends an author invitation to user 2
3. User 2 is assigned as reviwer on the Control panel>Teams>Reviwer status (review does not appear in Users 2 Dashboard>To review list)
## Possible solution
Ahen an author is invited, this action should not be recorded and displayed on the Team>Reviwer status kanban board.
![Screenshot_2024-03-22_at_11.54.48](/uploads/5d16e75d6082a7cb0113549b690b8b26/Screenshot_2024-03-22_at_11.54.48.png)
![Screenshot_2024-03-22_at_12.13.28](/uploads/97d0368b60e450909718a7316ea61b10/Screenshot_2024-03-22_at_12.13.28.png)Vignesh DevendranVignesh Devendranhttps://gitlab.coko.foundation/kotahi/kotahi/-/issues/1557Reviewers should only be able to be invited manually or using the Reviewer in...2024-03-27T11:47:01ZRyan Dix-PeekReviewers should only be able to be invited manually or using the Reviewer invitation## Expected behaviour
An editor should only be able to invite a single user once to participate in a round of review.
## Current behaviour
Currently, a user editor can be assigned manually and using the 'Reviewer invitation' email noti...## Expected behaviour
An editor should only be able to invite a single user once to participate in a round of review.
## Current behaviour
Currently, a user editor can be assigned manually and using the 'Reviewer invitation' email notification template.
## Steps to reproduce
1. Assign a reviewer from the Control panel>Teams page>Invite reviewers section, ensure 'Email notification' is unselected
2. Assign the same user from the Control panel>Teams page>Invite reviewers section and select 'Email notification' for the Invite reviwer modal.
3. Notice both users appear in the Control panel>Teams page>Reviwer stutas>'Invited' column
## Possible solution
- A user should only be able to be assigned once to a round of review. The user card should only appear once in the 'Invited' list (column).
- If a user is invited they should be able to receive multiple email notifications to participate in a single round of review.
- If a user is invited manually and sent a 'Reviewer invitation' email notification thereafter, the same user card should be updated to reflect 'Invoted via email'.
![Screenshot_2024-03-11_at_08.02.36](/uploads/b6c2c1cf2e7d5dc6c7316fcff1d947a1/Screenshot_2024-03-11_at_08.02.36.png)Vignesh DevendranVignesh Devendranhttps://gitlab.coko.foundation/kotahi/kotahi/-/issues/1555Unsubmitted reviews are not being saved2024-03-27T11:39:54ZRyan Dix-PeekUnsubmitted reviews are not being saved## Expected behaviour
Reviwes accessing and editing the Review page>Review tab should be able to edit form content, end session and return to their review and data should be saved and editable.
## Current behaviour
Data input into th...## Expected behaviour
Reviwes accessing and editing the Review page>Review tab should be able to edit form content, end session and return to their review and data should be saved and editable.
## Current behaviour
Data input into the review page is not saved and not submitted is not saved when the reviewers ends the session.
## Steps to reproduce
<!-- Required. Provide a link to a live example or screenshots, and the steps to reproduce this bug.]-->
1. Assign a reviewer to a review
2. Reviewers access the review page and inputs data into any field
3. navigate to the dashboard or click refresh
## Possible solution
Data should saved on blurVignesh DevendranVignesh Devendranhttps://gitlab.coko.foundation/kotahi/kotahi/-/issues/1551[Sciety Preprints] Hide published articles from web crawlers2024-03-13T05:52:46ZRyan Dix-Peek[Sciety Preprints] Hide published articles from web crawlersDisallow all paths, and update robot.txt file accordingly. Linked MR; https://gitlab.coko.foundation/kotahi/kotahi/-/merge_requests/1158Disallow all paths, and update robot.txt file accordingly. Linked MR; https://gitlab.coko.foundation/kotahi/kotahi/-/merge_requests/1158Ben WhitmoreBen Whitmorehttps://gitlab.coko.foundation/kotahi/kotahi/-/issues/1548Reference parser modal display enhancements2024-03-27T11:39:51ZRyan Dix-PeekReference parser modal display enhancements# Improve the user experience of the parser modal for editing Original, AnyStyle and/or Crossref citations
## Context
The user experience of working with the 'Orginal' citation is challenging. Currently, if you edit the 'Orginal' citati...# Improve the user experience of the parser modal for editing Original, AnyStyle and/or Crossref citations
## Context
The user experience of working with the 'Orginal' citation is challenging. Currently, if you edit the 'Orginal' citation when editing any form field the content displayed is blank and changes made are saved and displayed on blur. Also, (n.d.) is displayed because there is no date provided.
A suggestion was made to combine the 'Aystyle' and 'Original', however, we know that data can be lost when using the AnyStyle parser (or any parser) - so there is value in keeping the original citation as a visual reference for users. So we should retain the display of the Original, AnyStyle and Crossref selection options as per the current state.
## Proposal
To add the 'Original' display alongside an 'edit view' of the citation for the Original, AnyStyle and Crossref selection options.
We could also improve the experience of editing the Original form by prepopulating the field using the AnyStyle parser.
## Solution
1. Display the 'Original' citation below the edited view.
2. The 'Original' citation should be visually distinguishable from the edited display and remain static.
3. Edits made to data capture in the form should be reflected in the 'edit view' in real time.
![Screenshot_2024-02-29_at_09.25.13](/uploads/c6466130a8f6e4b2f73661e80f9f4d07/Screenshot_2024-02-29_at_09.25.13.png)Vignesh DevendranVignesh Devendranhttps://gitlab.coko.foundation/kotahi/kotahi/-/issues/1547Email notification data mapping issue2024-03-27T12:08:56ZRyan Dix-PeekEmail notification data mapping issueI received a 'Submitted review' email notification and none of the manuscript metadata was present in the email I received.
## Expected behaviour
Metadata should be mapped and displayed in the email notification I receive.
## Current...I received a 'Submitted review' email notification and none of the manuscript metadata was present in the email I received.
## Expected behaviour
Metadata should be mapped and displayed in the email notification I receive.
## Current behaviour
Metadata mapped in the email notification template is not being input into the email notification sent from Kotahi
Example; https://kotahi.kotahidev.cloud68.co/kotahi/versions/dbd0fdef-d63d-4bba-92aa-c30bdf8383cb/decision
## Steps to reproduce
1. On Kotahidev; complete a submission form and submit
2. Go to Control>Decision page
3. Select a decision (accept, revise or reject) and submit
4. navigate to email inbox
5. open email and metadata is missing
## Other information
- The issue persists for all `journal` archetype-specific email notifications; Submitted manuscript, Submitted review and Reviewer rejects an invitation to review.
- If the email is sent from the Control panel>Tasks&Notifcation page manually the metadata is mapped and displayed in the email notification as intended.
- the Configuration?Emails>'Submitted review' should be changed to 'Submitted decision' (there is no trigger events for a submitted review).
![Screenshot_2024-02-29_at_08.15.25](/uploads/f030936882999beb6b9189bef83cf39d/Screenshot_2024-02-29_at_08.15.25.png)Vignesh DevendranVignesh Devendranhttps://gitlab.coko.foundation/kotahi/kotahi/-/issues/1545Support for CMS article template per group2024-03-11T06:59:39ZRyan Dix-PeekSupport for CMS article template per grouphttps://gitlab.coko.foundation/kotahi/kotahi/-/issues/1539Error in decision page for group manager, when the reviewer declines the invi...2024-02-27T06:04:19ZSidorela UkuError in decision page for group manager, when the reviewer declines the invitation<!-- Required. Provide a general summary of the issue in the title above -->
## Expected behaviour
A group manager can invite users to review a manuscript from the Manuscripts>Control>Team. The user declines the invitation and it shoul...<!-- Required. Provide a general summary of the issue in the title above -->
## Expected behaviour
A group manager can invite users to review a manuscript from the Manuscripts>Control>Team. The user declines the invitation and it should be listed at team page of declined request.
## Current behaviour
The reviewer gets the email and declined it. When the group manager refreshes the page it sees an blank page with an error that something went wrong.
## Steps to reproduce
1. Login as group manager
2. Submit a manuscript
3. Go to Manuscripts>Control
4. Invite a reviewer
5. Reviewer checks email and clicks Decline which will require login
6. Go back to /decision page for the group manager and refresh the page while at Team tab.
7. A blank page that something went wrong will appear.
![image](/uploads/fbf5a18168f81a910456a1330de1065e/image.png)
The test site link: https://kotahi.kotahidev.cloud68.co/kotahi/versions/9a6106d4-bc90-452f-b227-58ff3ba4a4d3/decision
Manuscript with title: Test of decline invite.
## Environment
Firefox, Brave and Chrome browsers. Tested both in site linked above and in the local deployment.
## Possible solution
<!-- If known, provide details on how to fix the bug.-->
<!-- After creating this issue you can link other related or blocking issues with the Gitlab's Linked issues functionality. -->https://gitlab.coko.foundation/kotahi/kotahi/-/issues/1538Hide author proofing email notifications from the Task&Notifications page2024-03-11T06:58:12ZRyan Dix-PeekHide author proofing email notifications from the Task&Notifications page1. An Admin/Group Manager should not be able to select the 'Author proofing invitation' or 'Author proofing submitted' from the Tasks>Edit>Select email template dropdown
![Screenshot_2024-02-20_at_07.30.38](/uploads/59de338c84dc29f8a587...1. An Admin/Group Manager should not be able to select the 'Author proofing invitation' or 'Author proofing submitted' from the Tasks>Edit>Select email template dropdown
![Screenshot_2024-02-20_at_07.30.38](/uploads/59de338c84dc29f8a587a1ed1cb981df/Screenshot_2024-02-20_at_07.30.38.png)
2. An Editor Manager should not be able to select the 'Author proofing invitation' or 'Author proofing submitted' from the Control panel>Tasks&Notifications>NOtifications>Choose template notifications dropdown AND Tasks>Edit>Select email template dropdown
![Screenshot_2024-02-20_at_07.33.06](/uploads/b5a05de2140dd4de9e9e2ac79979771a/Screenshot_2024-02-20_at_07.33.06.png)
![Screenshot_2024-02-20_at_07.34.27](/uploads/4829622fbd6dc1173892a5b68c27f38f/Screenshot_2024-02-20_at_07.34.27.png)Vignesh DevendranVignesh Devendranhttps://gitlab.coko.foundation/kotahi/kotahi/-/issues/1536[ejpimport] Update import script2024-03-19T15:24:23ZRyan Dix-Peek[ejpimport] Update import scriptGoals;
- Support to have changes made to the data mapping on imports _ we should be able to identify changes made to data mapping in elifes datahub that breaks import into Kotahi.
- Import should be running. Only importing objects that ...Goals;
- Support to have changes made to the data mapping on imports _ we should be able to identify changes made to data mapping in elifes datahub that breaks import into Kotahi.
- Import should be running. Only importing objects that have review and/or reviews + assessments.
- Update imports. Known issues; unable import preprint version URL, publishing or peer review state data.
## Introduced changes
The result of the overall refactoring of the plugin introduced changes in the way the plugin should be configured.
When it comes to deployments, the sys-admin should be responsible to always pull the latest version of the plugin from its [repo](https://gitlab.coko.foundation/kotahi/import-from-docmap/-/tree/main)
The path on host where the code of the plugin resides should be mounted in Kotahi's server container e.g. `host_plugin_path:/home/node/app/config/plugins/import-from-docmap`
A configuration file should exist also on the host's side with content:
```
module.exports = {
'import-from-docmaps': {
dataHubURL:
'URL value of Data hub',
dataHubUsername: 'given_username',
dataHubPassword: 'given_password',
crossrefURL: 'URL value of Crossref',
},
}
```
The above file should also be mounted in Kotahi's server container e.g. `host_config_file_path:/home/node/app/config/local.js`
Also a file which will represent the plugins_manifest should be mounted in the container:
```
[
{
"groupName": "kotahi",
"plugins": [
{
"name": "Import preprints from DataHub Docmaps",
"folderName": "import-from-docmap"
}
]
}
]
```
That file should be mounted `host_manifest_path:/home/node/app/config/plugins/plugins_manifest.json`Alexandros GeorgantasAlexandros Georgantashttps://gitlab.coko.foundation/kotahi/kotahi/-/issues/1535Research options to convert binary math (MathType)2024-03-27T12:06:00ZRyan Dix-PeekResearch options to convert binary math (MathType)The purpose of this task is to investigate the work required to convert binary math and allow the output to be accessible in Wax.
Some initial work was done by Suki and @bharathydasan in this regard; https://gitlab.coko.foundation/XSwe...The purpose of this task is to investigate the work required to convert binary math and allow the output to be accessible in Wax.
Some initial work was done by Suki and @bharathydasan in this regard; https://gitlab.coko.foundation/XSweet/XSweet/-/blob/mtef/applications/math/mtef/README.md
It's not clear if we can use/build on this code to support the conversion of MathType content.Dan ViselDan Viselhttps://gitlab.coko.foundation/kotahi/kotahi/-/issues/1534Footer images saved in CMS are not displayed in Flax2024-02-17T16:23:19ZRyan Dix-PeekFooter images saved in CMS are not displayed in FlaxImages uploaded and saved in CMS>Laypout>Footer appear as broken image files in Flax.
![Screenshot_2024-02-16_at_06.45.10](/uploads/378f755f2a6b5724dbf613c0a006ed2e/Screenshot_2024-02-16_at_06.45.10.png)Images uploaded and saved in CMS>Laypout>Footer appear as broken image files in Flax.
![Screenshot_2024-02-16_at_06.45.10](/uploads/378f755f2a6b5724dbf613c0a006ed2e/Screenshot_2024-02-16_at_06.45.10.png)Ben WhitmoreGiannis Kopanasjkopanas@gmail.comBen Whitmorehttps://gitlab.coko.foundation/kotahi/kotahi/-/issues/1532ORICD null in Users2024-02-16T10:02:36ZCloud68 Support teamORICD null in Users<!-- Required. Provide a general summary of the issue in the title above -->
## Expected behaviour
<!-- Required. Tell us what should happen -->
## Current behaviour
<!-- Required. Tell us what happens instead of the expected behavio...<!-- Required. Provide a general summary of the issue in the title above -->
## Expected behaviour
<!-- Required. Tell us what should happen -->
## Current behaviour
<!-- Required. Tell us what happens instead of the expected behaviour -->
Users ORICD are null on users menu and not shown at all at the Manuscrips
## Steps to reproduce
<!-- Required. Provide a link to a live example or screenshots, and the steps to reproduce this bug.]-->
1. Build on v3.0.0 or main
2. login with oricd
3. all users are missing oricd
## Environment
<!-- Required. Provide relevant information such as browser name and version, PC or Mac use, internet speed, etc.]-->
## Possible solution
<!-- If known, provide details on how to fix the bug.-->
<!-- After creating this issue you can link other related or blocking issues with the Gitlab's Linked issues functionality. -->Vignesh DevendranVignesh Devendranhttps://gitlab.coko.foundation/kotahi/kotahi/-/issues/1530Errors publishing to Flax2024-02-16T10:07:47ZRyan Dix-PeekErrors publishing to FlaxFor the `journal` archetype; if the`submission.dateAccepted` field is blank, or the formatting is not yyyy-mm-DD then publishing to Flax doesn't work. The field should be published irrespective of the date format.
Secondly, on publish ...For the `journal` archetype; if the`submission.dateAccepted` field is blank, or the formatting is not yyyy-mm-DD then publishing to Flax doesn't work. The field should be published irrespective of the date format.
Secondly, on publish action the Control panel notification indicates that the publishing action was successful when it was not. If an article is not published then 'Posting to publishing CMS' should not be 'green'.
![Screenshot_2024-02-14_at_21.03.11](/uploads/4fee5b5694ced8d20c2f440e115460fe/Screenshot_2024-02-14_at_21.03.11.png)
Error messages on Publish/Republish action;
![Screenshot_2024-02-15_at_07.58.24](/uploads/8ae53014c378857d6fd3fc946d384b51/Screenshot_2024-02-15_at_07.58.24.png)
![Screenshot_2024-02-14_at_19.39.14](/uploads/c4509009afe318a08c3b3e5983d5b07d/Screenshot_2024-02-14_at_19.39.14.png)Ben WhitmoreBen Whitmorehttps://gitlab.coko.foundation/kotahi/kotahi/-/issues/1529Email notification sent on accept action2024-02-15T07:42:23ZRyan Dix-PeekEmail notification sent on accept actionI receive a random email notification despite not being assigned to a manuscript (as an editor). Steps to recreate the bug;
1. As a Group Manager create a new submission
1. upload a docx file and do NOT submit
1. Navigate to Control pa...I receive a random email notification despite not being assigned to a manuscript (as an editor). Steps to recreate the bug;
1. As a Group Manager create a new submission
1. upload a docx file and do NOT submit
1. Navigate to Control panel>Decision, select accept and click 'Submit'
1. I receive email notification; Test
Example; https://kotahi.kotahidev.cloud68.co/kotahi/versions/b2fec8aa-eed9-430d-8285-499a91212cfb/decision
This email is also being sent despite there being no email notification selected in Configuration>Event Notifications>Submitted manuscripthttps://gitlab.coko.foundation/kotahi/kotahi/-/issues/1528Manuscript versioning is not being save correctly2024-02-15T03:50:33ZRyan Dix-PeekManuscript versioning is not being save correctlyUsing the `journal` archetype; As an author, I can see the status 'Revise', I click on manuscript, go to the submission page and click on 'Create new submission' (version 2) and submit. When I access the manuscript from my dashboard I ca...Using the `journal` archetype; As an author, I can see the status 'Revise', I click on manuscript, go to the submission page and click on 'Create new submission' (version 2) and submit. When I access the manuscript from my dashboard I can only see version 1 as a dropdown selection option, and this version contains my version 2 changes.
Somehow the version is not being saved correctly. There is only a single version option, when there should be 2 i.e. version 1 and version 2. This also impacts the Dashboard and not the Control panel;
![Screen_Recording_2024-02-13_at_14.10.09](/uploads/7f28f9ae55ab0c08af9e0fddaa237e9c/Screen_Recording_2024-02-13_at_14.10.09.mov)Ben WhitmoreBen Whitmore