Kotahi issueshttps://gitlab.coko.foundation/kotahi/kotahi/-/issues2023-03-08T09:10:04Zhttps://gitlab.coko.foundation/kotahi/kotahi/-/issues/1102[eLife] Include editor metadata on publish action2023-03-08T09:10:04ZRyan Dix-Peek[eLife] Include editor metadata on publish action**Issue description;** Elife team would like to include editor metadata when publishing to Sciety. An option is to add the Control panel>Workflow (soon to be 'Teams') page to the `elife` archetype using a configuration setting. The edito...**Issue description;** Elife team would like to include editor metadata when publishing to Sciety. An option is to add the Control panel>Workflow (soon to be 'Teams') page to the `elife` archetype using a configuration setting. The editor can be assigned from the Control panel>Workflow>Assign editors dropdown menu.
On the publish action; the editor metadata needs to be sent to Hypothesis and structured in a way that can be consumed in DOCMAPS syntax by Sciety APIeLife v1Ben WhitmoreBen Whitmorehttps://gitlab.coko.foundation/kotahi/kotahi/-/issues/300avatar upload should use S3/Minio2022-10-26T08:15:28ZMihailGorceagENavatar upload should use S3/MinioeLife v1https://gitlab.coko.foundation/kotahi/kotahi/-/issues/987[eLife] Add config control to reverse order of publishing to Hypothes.is2022-08-16T08:37:05ZRyan Dix-Peek[eLife] Add config control to reverse order of publishing to Hypothes.isCurrently, publishing of content from the Submission form has been reversed to resolve #986. Content from the Submission form is published in chronological order, from top to bottom, with the most recent component at the bottom. BioRxivs...Currently, publishing of content from the Submission form has been reversed to resolve #986. Content from the Submission form is published in chronological order, from top to bottom, with the most recent component at the bottom. BioRxivs TRiP inverts this order to display bottom to top, with the most recent annotation at the bottom.
The purpose of this task is to create a configuration control that can be added to the elife instance .env file that can invert the publishing order to Hypothe.is only.
Example; https://www.biorxiv.org/content/10.1101/2021.05.05.442713v1eLife v1https://gitlab.coko.foundation/kotahi/kotahi/-/issues/757App to provision list of DOIs for retrieval by Sciety API2022-03-02T10:26:36ZRyan Dix-PeekApp to provision list of DOIs for retrieval by Sciety API**Description;** Sciety team would like to access a list of preprint DOIs from Kotahi. The idea is Sciety Groups (in this case CoLab Biophysics and NCRC) want to be able to display a list of the articles they have selected for review bu...**Description;** Sciety team would like to access a list of preprint DOIs from Kotahi. The idea is Sciety Groups (in this case CoLab Biophysics and NCRC) want to be able to display a list of the articles they have selected for review but have not actually reviewed. So all preprints selected/labelled as 'ready for review' in the manuscripts view need to be accessible via an API/App.
Suggested solution; from Ben
> we could retrieve with a graphql query, but we would have to add session header info to the query to get access (basically so our query is "logged in"). This would be relatively simple if the graphql playground were running, but this tool is only available in dev mode. So we'd essentially have to write or obtain a small app to run the query for us. We only expose published files via the API. Submitted files are not retrievable via the API until they've been published.eLife v1Ben WhitmoreBen Whitmorehttps://gitlab.coko.foundation/kotahi/kotahi/-/issues/387[eLife] Validate bioRxiv URLs before publish2021-06-11T14:16:58ZRyan Dix-Peek[eLife] Validate bioRxiv URLs before publish**User story;** as a Kotahi system administrator, I would like to know that I have published evaluations against a valid URL, to avoid mistakenly publishing a blank evaluation.
**Description;** a system administrator mistakingly insert...**User story;** as a Kotahi system administrator, I would like to know that I have published evaluations against a valid URL, to avoid mistakenly publishing a blank evaluation.
**Description;** a system administrator mistakingly inserted the incorrect article URL (biorxiv.org/content/10.1101/2021.03.16.435665v1.full) into the submission form. The '.full' URL extension resulted in the evaluation being published in Kotahi but not to the Hypothesis endpoint. The idea here is to consider a solution that caters for all Kotahi users. This solution should be available to the user when they are editing an element in the form builder.
**Proposed solution;**
- add URL validation parameters to the form validate dropdown menu when adding to a new element e.g TextField.
![Screenshot_2021-06-01_at_12.41.01](/uploads/d68f702bf732d351fe33268ecfd41c9e/Screenshot_2021-06-01_at_12.41.01.png)eLife v1Beatrice-Emanuela SuarasanBeatrice-Emanuela Suarasanhttps://gitlab.coko.foundation/kotahi/kotahi/-/issues/406[eLife] Republish sequence should be respected2021-06-09T13:18:13ZEugeniu Stribitchi[eLife] Republish sequence should be respectedAll republished articles, should be published in a sequence, so that on Hypothesis it will repeat the sequence from Kotahi:
1. Summery
2. Review # 3
3. Review # 2
4. Review # 1All republished articles, should be published in a sequence, so that on Hypothesis it will repeat the sequence from Kotahi:
1. Summery
2. Review # 3
3. Review # 2
4. Review # 1eLife v1Beatrice-Emanuela SuarasanBeatrice-Emanuela Suarasanhttps://gitlab.coko.foundation/kotahi/kotahi/-/issues/395[eLife] Ordering of evaluations in Hypothesis2021-06-09T13:18:10ZRyan Dix-Peek[eLife] Ordering of evaluations in Hypothesis**User story;** as a system administrator, I ant the evaluation annotations published in Hypothesis to be ordered as follows; 1) Evaluation summary, 2) Review 1, 3) Review 2 and 4) Review 3, in order to present a logically flow for reade...**User story;** as a system administrator, I ant the evaluation annotations published in Hypothesis to be ordered as follows; 1) Evaluation summary, 2) Review 1, 3) Review 2 and 4) Review 3, in order to present a logically flow for readers.
**Description;** Currently the order of evaluations captured in Kotahi eLife form does not match how the annotations are published on Hypothesis e.g. https://www.biorxiv.org/content/10.1101/2021.04.18.440347v1#annotations:LLfdBsRUEeuWyfOxhTz4qg published from https://elife.kotahi.cloud/kotahi/versions/ebf84647-21e6-4e61-993e-14d6be26b89a/evaluation
**Suggestion solution**
- Assumption; Hypothesis API uses time in minutes (not seconds) to order annotations. Adding a time delay (e.g. 1 minute) to the time captured when a Review is inserted in the form could be utilised to order the annotations as required.eLife v1sebastianrad1sebastianrad1https://gitlab.coko.foundation/kotahi/kotahi/-/issues/327[eLife] Evaluations page2021-06-03T14:23:42ZEugeniu Stribitchi[eLife] Evaluations pageAs User I would like to have separate pages for each evaluation of article so that those links could be used for DOI registration
**Acceptance Criteria:**
- [x] Each evaluations (Review 1,2,3 & summery should have unique URL)
- [x] Ev...As User I would like to have separate pages for each evaluation of article so that those links could be used for DOI registration
**Acceptance Criteria:**
- [x] Each evaluations (Review 1,2,3 & summery should have unique URL)
- [x] Evaluation page link should be concatenation between baseUrl & Article ID & counter (ex. https://elife.kotahi.cloud/29f7a475-7e0a-440e-a601-db8b492d1fc2) (**1** from screenshots)
**Evaluation Page**
- [x] Evaluation title should be Article description from Submission form(**2** from screenshots)
- [x] Evaluation type should be outputted under page title(**4** from screenshots) (based on evaluation type )
- [x] Review date from submission form should be outputted on left of title(**3** from screenshots)
- [x] Review text is the Evaluation text that Evaluators work on(**5** from screenshots)
- [x] "Link to original article" should point to DOI form submission page.(**6** from screenshots)
![image](/uploads/f798f386bbd40eefcda5cde5eb3877c2/image.png)eLife v1sebastianrad1sebastianrad1https://gitlab.coko.foundation/kotahi/kotahi/-/issues/220[eLife] Publishing over Crossref API2021-06-03T08:01:42ZEugeniu Stribitchi[eLife] Publishing over Crossref API**API description:**
https://www.crossref.org/education/content-registration/content-type-markup-guide/peer-reviews/
**Field Mapping:**
https://docs.google.com/spreadsheets/d/1CBkfIVhJA94aIAjlKkdZEBGEmUg0QqbdKQlE5Bt5MY4/edit#gid=0
...**API description:**
https://www.crossref.org/education/content-registration/content-type-markup-guide/peer-reviews/
**Field Mapping:**
https://docs.google.com/spreadsheets/d/1CBkfIVhJA94aIAjlKkdZEBGEmUg0QqbdKQlE5Bt5MY4/edit#gid=0
**Assets:**
https://www.crossref.org/services/content-registration/
https://www.crossref.org/education/member-setup/constructing-your-dois/
https://www.crossref.org/education/retrieve-metadata/rest-api/
https://github.com/CrossRef/rest-api-doc.eLife v1sebastianrad1sebastianrad1https://gitlab.coko.foundation/kotahi/kotahi/-/issues/307[eLife] Kotahi Publishing page2021-06-03T07:59:36ZEugeniu Stribitchi[eLife] Kotahi Publishing pageAs User I would like to publish evaluations on Kotahi webpage so that evaluations would be accessible for unregistered users.
**Workflow:**
1. Open Kotahi root page (ex. http://kotahidev.cloud68.co/)
2. Click on any title from the lis...As User I would like to publish evaluations on Kotahi webpage so that evaluations would be accessible for unregistered users.
**Workflow:**
1. Open Kotahi root page (ex. http://kotahidev.cloud68.co/)
2. Click on any title from the list
3. Redirected to Evaluation page
**Acceptance Criteria:**
- [x] Only evaluations that are not empty should be published
- [x] Only articles that have no error during publishing (hypothesis and crossref) should be visible on this page.
- [x] Published evaluation title is Article description
- [x] Next to evaluation type should be a link to the Evaluation page
- [x] Summary or Review n - on click should expand evaluation text (**2** from screenshots)
- [x] If text is expanded on "Summary or Review n" click should close expanded text
![image](/uploads/bc490c9acc6a64ded30787b115a10d26/image.png)eLife v1sebastianrad1sebastianrad1https://gitlab.coko.foundation/kotahi/kotahi/-/issues/316[eLife] registering multiple peer review DOIs in Crossref from a single form2021-06-03T07:58:50ZRyan Dix-Peek[eLife] registering multiple peer review DOIs in Crossref from a single form**User story;** as a system administrator I would like to publish multiple peer reviews at one time in order to minimise the opportunity for errors and speed-up the submission process.
**Workflow:**
1. Submit article
2. Evaluate artic...**User story;** as a system administrator I would like to publish multiple peer reviews at one time in order to minimise the opportunity for errors and speed-up the submission process.
**Workflow:**
1. Submit article
2. Evaluate article
3. Publish
**Expected result:**
After publishing, each of article review and summery should retrieve DOI over Crossref API. #220
**Description;** This task is considering #315 implemented and review form contains all reviews and summery in a single form.eLife v1sebastianrad1sebastianrad1https://gitlab.coko.foundation/kotahi/kotahi/-/issues/329[eLife] republishing enhancements2021-06-03T07:56:25ZEugeniu Stribitchi[eLife] republishing enhancementsAs Kotahi User I would like to have possibility to republish Article evaluations using common submission/evaluation form
**Acceptance criteria:**
- [x] Evaluations that been published and have text, should be updated
- [x] Evaluations...As Kotahi User I would like to have possibility to republish Article evaluations using common submission/evaluation form
**Acceptance criteria:**
- [x] Evaluations that been published and have text, should be updated
- [x] Evaluations that been published and on republish have no text should be deleted from Hypothesis
- [x] Evaluations that were not been published before but currently have text, should be published
- [x] Actions for UPDATE & DELETE should be applied over Hypothesis and Kotahi homepage
- [x] In case if all evaluations were deleted, article should revert back to evaluated stepeLife v1sebastianrad1sebastianrad1https://gitlab.coko.foundation/kotahi/kotahi/-/issues/328[eLife] Hypothesis publishing enhancements2021-06-02T13:56:18ZEugeniu Stribitchi[eLife] Hypothesis publishing enhancementsAs Kotahi User, I would like to publish to Hypothesis separate article evaluations entered to the submission/evaluation form.
**Acceptance criteria:**
- [x] Only evaluations that are not empty should be publishedAs Kotahi User, I would like to publish to Hypothesis separate article evaluations entered to the submission/evaluation form.
**Acceptance criteria:**
- [x] Only evaluations that are not empty should be publishedeLife v1sebastianrad1sebastianrad1https://gitlab.coko.foundation/kotahi/kotahi/-/issues/361[eLife] - Review Date for each evaluation2021-06-02T11:14:38ZEugeniu Stribitchi[eLife] - Review Date for each evaluationAs, Kotahi User, I would like to register review date for each review and summary fields, so that published information would be more accurate.
**Current state:**
At this moment, we have only 1 review date that is applied for every re...As, Kotahi User, I would like to register review date for each review and summary fields, so that published information would be more accurate.
**Current state:**
At this moment, we have only 1 review date that is applied for every review and summary.
**Acceptance criteria:**
- [x] Review date as text field should be added to the submission and evaluation field for each review and summary
- [x] This field shouldn't be required
- [x] Remove common review date from submission/evaluation form
- [x] For Crossref publishing tickets #220 #316 #329 review date for each publishing evaluation should be taken from review date attached to the evaluation set of fields.
**Assets:**
![Kotahi-Elements-submission_form](/uploads/1e65638ba18284eeb8b43b447817f41c/Kotahi-Elements-submission_form.png)eLife v1sebastianrad1sebastianrad1https://gitlab.coko.foundation/kotahi/kotahi/-/issues/315[eLife] submit and publish multiple reviews in a single form submission2021-06-02T11:13:47ZRyan Dix-Peek[eLife] submit and publish multiple reviews in a single form submission**User story;** as a system administrator I would like to register multiple evaluations at one time in order to minimize the opportunity for errors and speed-up the submission process.
**Description;** current state requires a single fo...**User story;** as a system administrator I would like to register multiple evaluations at one time in order to minimize the opportunity for errors and speed-up the submission process.
**Description;** current state requires a single form to be submitted per peer review. A single article registered in the system may require multiple reviews. This requirement needs to cater for handling the capturing of multiple reviews against a single article, in a single submission.
Each of the [Review 1 & Creator] & [Review 2 & Creator] & [Review 3 & Creator] & [Review summary & creator] will be published separate probably Creators should be connected somehow to review/summary text.
**Additional info:**
- [x] Submission form should contain 4 collections of data [Review 1 & Creator] & [Review 2 & Creator] & [Review 3 & Creator] & [Review summary & creator]
- [x] New form doesn't need **review type** field
**Assets:**
![Kotahi-Elements-1](/uploads/fa5795adeb29917442918db176f9ba28/Kotahi-Elements-1.png)eLife v1sebastianrad1sebastianrad1https://gitlab.coko.foundation/kotahi/kotahi/-/issues/336[eLife] POC Crossref XML Generation2021-05-18T14:03:25ZEugeniu Stribitchi[eLife] POC Crossref XML GenerationUsing evaluations from this page https://sciety.org/articles/activity/10.1101/2021.01.15.21249881, need to generate XMLs that should be used to retrieve DOIs from CrossrefUsing evaluations from this page https://sciety.org/articles/activity/10.1101/2021.01.15.21249881, need to generate XMLs that should be used to retrieve DOIs from CrossrefeLife v1MihailGorceagENMihailGorceagENhttps://gitlab.coko.foundation/kotahi/kotahi/-/issues/272[eLife&NCRC] Manuscripts view Publish action enhancements2021-04-23T11:16:15ZEugeniu Stribitchi[eLife&NCRC] Manuscripts view Publish action enhancementsAs User I would like to use Publish action only for Evaluated articles
Acceptance Criteria:
- [ ] Publish option should be visible only for the articles with Evaluated state.As User I would like to use Publish action only for Evaluated articles
Acceptance Criteria:
- [ ] Publish option should be visible only for the articles with Evaluated state.eLife v1sebastianrad1sebastianrad1https://gitlab.coko.foundation/kotahi/kotahi/-/issues/266[eLife] Evaluations don't publish to Hypothesis when using a DOI URL2021-04-22T14:13:59ZRyan Dix-Peek[eLife] Evaluations don't publish to Hypothesis when using a DOI URL**Issue;** Evaluations don't publish to hypothesis when using a DOI URL as an endpoint. It also appears as though DOI URLS are static and do not account for articles with multiple published versions.
**Description;** evaluators are abl...**Issue;** Evaluations don't publish to hypothesis when using a DOI URL as an endpoint. It also appears as though DOI URLS are static and do not account for articles with multiple published versions.
**Description;** evaluators are able capture an endpoint URL upon article registration and the evaluation should publish to the desired endpoint via Hypothesis API.
Here's an example of an article with multiple versions; https://www.biorxiv.org/content/10.1101/695049v2.article-info
To note;
- The DOI URL = https://doi.org/10.1101/695049
- Published URL = https://www.biorxiv.org/content/10.1101/695049v2
An additional field has been added to the eLife 'Evaluation Form' to capture the bioRxiv end point URL where the evaluation should be accessible via Hypothesis.
**Desired outcome;**
1. User logins
1. User completes and submits an Evaluation Form
1. User publishes evaluation
1. User logs into 'myelifetestemail' Hypothesis test account
1. User clicks on 'Visit annotations in context' in Hypothesis and sees the evaluation Note within context of the correct bioRxiv article version.eLife v1sebastianrad1sebastianrad1https://gitlab.coko.foundation/kotahi/kotahi/-/issues/267[eLife & NCRC] Manuscripts view enhancements2021-04-22T08:03:26ZRyan Dix-Peek[eLife & NCRC] Manuscripts view enhancements**Story;** as user I want to be able to access a published evaluation to review form content for reference purposes.
**Description;** currently in the Manuscripts view for the published articles, there is no possibility to read the con...**Story;** as user I want to be able to access a published evaluation to review form content for reference purposes.
**Description;** currently in the Manuscripts view for the published articles, there is no possibility to read the content of the evaluation.
**Suggested solution:** on the `Manuscripts` page;
- Once article is published Hide publishing option.
- Show "Evaluation" that will output submission form with read only possibility.eLife v1Beatrice-Emanuela SuarasanBeatrice-Emanuela Suarasan