Kotahi issueshttps://gitlab.coko.foundation/kotahi/kotahi/-/issues2023-11-22T12:30:20Zhttps://gitlab.coko.foundation/kotahi/kotahi/-/issues/1369DOAJ Indexing2023-11-22T12:30:20ZRavindhar RangarajanDOAJ Indexing**1. Introduction**
Nvcleus Publishing Platform seeks to promote open access and increased visibility of its scholarly articles by indexing them on the Directory of Open Access Journals (DOAJ). This specification document outlines the pr...**1. Introduction**
Nvcleus Publishing Platform seeks to promote open access and increased visibility of its scholarly articles by indexing them on the Directory of Open Access Journals (DOAJ). This specification document outlines the process of registering a publisher account on DOAJ and the procedure to submit articles using the existing CrossRef schema or by structuring the XML in a specific format.
**Reference Links:**
https://doaj.org/docs/faq/
https://doaj.org/api/v3/docs
https://www.crossref.org/documentation/schema-library/xsd-schema-quick-reference/
https://doaj.org/docs/xml/#example-doaj-xml-file
**2. Registering a Publisher Account on DOAJ**
To begin indexing articles on DOAJ, Nvcleus Publishing Platform must first register a publisher account using the following link: https://doaj.org/publisher/
**3. CrossRef Schema for Article Submission**
The Nvcleus Journals Platform already utilizes the CrossRef schema for registering its journals (contact Ravindhar for more info); it can use the same schema to submit articles to DOAJ. The CrossRef schema includes essential metadata fields such as DOI, title, authors, affiliations, abstract, full-text URL, and keywords.
**4. Structuring XML for Article Submission**
If Nvcleus Publishing Platform does not use the CrossRef schema, articles can be submitted to DOAJ by structuring the XML in the format provided below:
```
<?xml version="1.0" encoding="UTF-8"?>
<records>
<record>
<language>[Language]</language>
<publisher>[Publisher Name]</publisher>
<journalTitle>[Journal Title]</journalTitle>
<issn>[Print ISSN]</issn>
<eissn>[Electronic ISSN]</eissn>
<publicationDate>[Publication Date - YYYY-MM-DD]</publicationDate>
<volume>[Volume Number]</volume>
<issue>[Issue Number]</issue>
<startPage>[Start Page]</startPage>
<endPage>[End Page]</endPage>
<doi>[DOI]</doi>
<publisherRecordId>[Publisher Record ID]</publisherRecordId>
<documentType>[Document Type - e.g., article]</documentType>
<title language="[Language]">[Article Title]</title>
<authors>
<author>
<name>[Author Name]</name>
<affiliationId>[Affiliation ID]</affiliationId>
<orcid_id>[ORCID ID]</orcid_id>
</author>
<!-- Additional authors, if applicable -->
</authors>
<affiliationsList>
<affiliationName affiliationId="[Affiliation ID]">[Affiliation Name]</affiliationName>
<!-- Additional affiliations, if applicable -->
</affiliationsList>
<abstract language="[Language]">[Abstract Text]</abstract>
<fullTextUrl format="[File Format]">[Full Text URL]</fullTextUrl>
<keywords language="[Language]">
<keyword>[Keyword 1]</keyword>
<keyword>[Keyword 2]</keyword>
<!-- Additional keywords, if applicable -->
</keywords>
</record>
<!-- Additional records for other articles, if applicable -->
</records>
```
**5. XML Elements Explanation**
[Language]: Language code of the article (e.g., "eng" for English).
[Publisher Name]: Name of the publishing platform (Nvcleus Publishing Platform).
[Journal Title]: Title of the journal in which the article is published.
[Print ISSN]: Print ISSN of the journal.
[Electronic ISSN]: Electronic ISSN of the journal.
[Publication Date - YYYY-MM-DD]: Publication date of the article in the format "YYYY-MM-DD".
[Volume Number]: Volume number of the journal.
[Issue Number]: Issue number of the journal.
[Start Page]: Starting page number of the article in the journal.
[End Page]: Ending page number of the article in the journal.
[DOI]: Digital Object Identifier of the article.
[Publisher Record ID]: Unique record identifier used by the publisher.
[Document Type]: Type of the document, e.g., "article".
[Article Title]: Title of the article.
[Author Name]: Name of the article's author.
[Affiliation ID]: Unique ID for the author's affiliation.
[ORCID ID]: ORCID ID of the author (if available).
[Abstract Text]: Abstract of the article.
[File Format]: Format of the full text file (e.g., "pdf").
[Full Text URL]: URL to access the full text of the article.
**6: Obtain API Credentials**
To use the DOAJ API, you need to obtain API credentials, which typically include an API key or an access token. You can request these credentials by registering as a publisher on DOAJ and obtaining API access.
More detailed information on this link: https://doaj.org/api/v3/docs
**6. Article Submission Process**
Once the XML file is structured according to the provided format, Nvcleus Publishing Platform can submit to the DOAJ using the API.
**Example API call: **
Assuming you have obtained your API key and saved your article metadata in an XML file called article.xml, you can use cURL to make the API request as follows:
`curl -X POST -H "Content-Type: application/xml" -H "Authorization: API_KEY_YOUR_API_KEY" --data-binary "@article.xml" `https://doaj.org/api/v1/articles/
Replace YOUR_API_KEY with your actual API key.
**7. Conclusion**
By adhering to the specifications provided in this document, Nvcleus Publishing Platform can effectively index its articles on the Directory of Open Access Journals (DOAJ), ensuring increased visibility and accessibility of scholarly content to the global research community. Proper indexing on DOAJ contributes to the promotion of open access and the dissemination of valuable research publications.https://gitlab.coko.foundation/kotahi/kotahi/-/issues/1368Google Scholar Indexing - HTML output2023-11-22T12:30:18ZRavindhar RangarajanGoogle Scholar Indexing - HTML output**1. Introduction**
Nvcleus Publishing Platform is a web-based platform that allows users to publish academic journals and books directly onto the website. To ensure proper indexing and visibility on search engines, including Google Sch...**1. Introduction**
Nvcleus Publishing Platform is a web-based platform that allows users to publish academic journals and books directly onto the website. To ensure proper indexing and visibility on search engines, including Google Scholar, we need to structure the HTML meta tags in a specific way. This specification document outlines the required meta tags and their structure for effective indexing on Google Scholar.
**Reference Links:**
https://docs.pkp.sfu.ca/google-scholar/en/#introduction
https://scholar.google.com/intl/en/scholar/inclusion.html#indexing
**2. Meta Tag Structure**
The following are the meta tags that should be structured within the HTML code of each published article or book:
**2.1. Title of the Publication**
`<meta name="citation_title" content="[Publication Title]">`
Replace [Publication Title] with the actual title of the article or book.
**2.2. Authors**
`<meta name="citation_author" content="[Author Name]">`
Include one tag for each author of the publication. Replace [Author Name] with the full name of the author.
**2.3. Publication Date**
`<meta name="citation_publication_date" content="[YYYY/MM/DD]">`
Replace [YYYY/MM/DD] with the publication date of the article or book in the format year/month/day (e.g., 1996/05/17).
**2.4. Journal Title (for Journals)**
`<meta name="citation_journal_title" content="[Journal Title]">`
Replace [Journal Title] with the title of the journal in which the article was published. This tag is not needed for books.
**2.5. Volume (for Journals)**
`<meta name="citation_volume" content="[Volume Number]">`
Replace [Volume Number] with the volume number of the journal. This tag is not needed for books.
**2.6. Issue (for Journals)**
`<meta name="citation_issue" content="[Issue Number]">`
Replace [Issue Number] with the issue number of the journal. This tag is not needed for books.
**2.7. First Page and Last Page (for Journals)**
```
<meta name="citation_firstpage" content="[First Page Number]">
<meta name="citation_lastpage" content="[Last Page Number]">
```
Replace [First Page Number] and [Last Page Number] with the respective page numbers of the article in the journal. These tags are not needed for books.
**2.8. PDF URL**
`<meta name="citation_pdf_url" content="[URL to PDF]">`
Replace [URL to PDF] with the direct URL to the full PDF version of the article or book.
**2.9. Marking the references**
Mark the section of the paper that contains references to other works with a standard heading, such as "References" or "Bibliography", on a line just by itself. Individual references inside this section should be either numbered "1. - 2. - 3." or "[1] - [2] - [3]" in PDF, or put inside an "<ol>" list in HTML. The text of each reference must be a formal bibliographic citation in a commonly used format, without free-form commentary.
Please understand that the references are identified automatically by the parser software; they're not entered or corrected by human operators. While we try to support the most common reference formats, it is not possible to guarantee that all references are identified correctly; and incorrect identification of references could lead to exclusion of your papers from Google Scholar or to low ranking of your papers in the search results.
**3. Usage Example**
Here's an example of how the meta tags should be implemented in the HTML code of a published article:
```
<head>
<meta name="citation_title" content="The testis isoform of the phosphorylase kinase catalytic subunit (PhK-T) plays a critical role in regulation of glycogen mobilization in developing lung">
<meta name="citation_author" content="Liu, Li">
<meta name="citation_author" content="Rannels, Stephen R.">
<meta name="citation_author" content="Falconieri, Mary">
<meta name="citation_author" content="Phillips, Karen S.">
<meta name="citation_author" content="Wolpert, Ellen B.">
<meta name="citation_author" content="Weaver, Timothy E.">
<meta name="citation_publication_date" content="1996/05/17">
<meta name="citation_journal_title" content="Journal of Biological Chemistry">
<meta name="citation_volume" content="271">
<meta name="citation_issue" content="20">
<meta name="citation_firstpage" content="11761">
<meta name="citation_lastpage" content="11766">
<meta name="citation_pdf_url" content="http://www.example.com/content/271/20/11761.full.pdf">
</head>
```
**4. Conclusion**
By adhering to this specification, articles published on the Nvcleus Publishing Platform will have properly structured meta tags for Google Scholar to easily index and display them in its search results. This will improve the visibility and discoverability of the content for researchers and readers worldwide.https://gitlab.coko.foundation/kotahi/kotahi/-/issues/1343Author Proofing Workflow2024-03-20T05:19:18ZRavindhar RangarajanAuthor Proofing Workflow**1. Introduction**
The purpose of this specification document is to outline the requirements and functionality of the Author Proofing Module for the Nvcleus Journal Publishing Platform. This module facilitates the author-proofing workfl...**1. Introduction**
The purpose of this specification document is to outline the requirements and functionality of the Author Proofing Module for the Nvcleus Journal Publishing Platform. This module facilitates the author-proofing workflow after the production process is complete. The Author Proofing Module will utilize the Wax Editor with limited functionality, supporting only suggesting mode and comments.
**2. Scope**
The Author Proofing Module will provide authors with a user-friendly interface to review and provide feedback on the finalized version of their published article. It will enable authors to suggest edits, make comments, and collaborate with the editorial team to ensure the accuracy and quality of the published work.
**3. Requirements**
3.1 Author assignment
Currently, Kotahi has the option only to assign editors and reviewers. We need the option to assign authors to the specific manuscript from the control window as shown below.
![Screenshot_4](/uploads/572713cca2c54038230a3f6b140f81ee/Screenshot_4.png)
If the manuscript has been submitted by an author, the respective author's name should be available by default under the Authors section.
**3.2 Author proofing stage**
Once the production process is completed, there will be a section under control options, where the journal manager or admin can move a submitted manuscript to the author-proofing stage as shown below. This stage will be enabled only when the production process is complete.
![Screenshot_5](/uploads/5a03df93191b9cf3e5768096239a803f/Screenshot_5.png)
**3.3 Wax Editor Integration**
The Author Proofing Module will utilize the Wax Editor, which supports only suggesting modes and comments. The following requirements should be considered:
**3.3.1 Suggesting Mode**
- The Wax Editor will be configured to allow authors to suggest edits to the text without directly modifying the published version.
- Authors can insert, delete, or modify text while clearly indicating the changes they propose.
- Suggested edits should be visually distinguishable from the original text which is already available in the wax editor.
**3.3.2 Comments**
- Authors and the editorial team should be able to add comments to specific sections of the article.
- Comments should provide a text input field for entering the comment text.
- Comments should be visible to all relevant parties and easily distinguishable from the main text.
- These are also already available in the Wax editor.
**3.4 Author Proofing Workflow**
The Author Proofing Module will follow a structured workflow to ensure efficient collaboration between authors and the editorial team. The workflow will include the following steps:
**3.4.1 Notification**
Authors will receive a notification when the production process is complete and their article is ready for proofreading.
The notification will contain instructions on accessing the Author Proofing Module and rules set by the publisher.
**3.4.2 Accessing the Module**
Authors will be able to access the Author Proofing Module through their Nvcleus account.
Upon logging in, authors will be presented with a list of their published articles that are ready for proofreading.
![proof_reading](/uploads/1a33e4884601ac0f8ed6acbaa9160dc3/proof_reading.jpg)
Clicking on the manuscript title will open the wax editor in suggesting mode.
**3.4.3 Reviewing the Article**
Authors can select an article from the list to enter the proofreading interface.
The article will be displayed in the Wax Editor with the finalized version.
Authors can navigate through the article, read the text, and make suggestions or comments as necessary.
Only the suggesting mode will be enabled and the author cannot have the option to change it to editing mode.
**3.4.5 Submitting Suggestions and Comments**
Author Proofing Form: Just like the reviewer form, we should have an author proofing form where the author can submit the comments and any supplementary files and complete the author proofing stage. Only this is done, the editorial team can take it up for review.
**3.4.5 Editorial Team Review**
The editorial team will receive notifications when authors submit their suggestions and comments.
The team can access the Author Proofing Module and view the author's feedback on the article.
The team can respond to suggestions and comments, provide clarifications, or request further revisions.
**4. Conclusion**
The Author Proofing Module for the Nvcleus Journal Publishing Platform will provide a robust workflow for authors to review and provide feedback on the finalized version of their articles. By leveraging the Wax Editor's suggesting mode and comment features, authors can suggest edits, make comments, and collaborate effectively with the editorial team. The module aims to enhance the overall quality and accuracy of published articles while ensuring a user-friendly experience for authors and the editorial team.https://gitlab.coko.foundation/kotahi/kotahi/-/issues/958JATS should download automatically2022-07-06T08:26:57ZRyan Dix-PeekJATS should download automaticallyhttps://gitlab.coko.foundation/kotahi/kotahi/-/issues/863Implement DSD XML validation inline2022-04-11T09:07:38ZRyan Dix-PeekImplement DSD XML validation inlinehttps://gitlab.coko.foundation/kotahi/kotahi/-/issues/776Tack changes permissions [WIP]2021-12-21T10:18:02ZRyan Dix-PeekTack changes permissions [WIP]- An an editor i cant accept track changes
- as a reviewer I can see track changes ont the review page- An an editor i cant accept track changes
- as a reviewer I can see track changes ont the review pagehttps://gitlab.coko.foundation/kotahi/kotahi/-/issues/775Add spell checker to Wax2021-12-21T09:22:03ZRyan Dix-PeekAdd spell checker to Wax**Description;** browser extensions, such as Grammarly, can currently be utilised with editing content in the Wax word processor. The purpose of this task is to address use cases that cannot be supported by such solutions. The primary us...**Description;** browser extensions, such as Grammarly, can currently be utilised with editing content in the Wax word processor. The purpose of this task is to address use cases that cannot be supported by such solutions. The primary use of the spell check will be the Production teams for Qa and copyediting purposes.
For example;
- Ability to add custom dictionaries
- exclude suggested, deleted text from correction
A suggested alternative solution is the [Language Tool proofreading API](https://languagetool.org/proofreading-api).https://gitlab.coko.foundation/kotahi/kotahi/-/issues/772[Production page] Add Author notes annotations2022-10-14T11:02:15ZRyan Dix-Peek[Production page] Add Author notes annotations**Description;** production editorial staff would like to tag 'Author notes' for conversion to JATS; `<author-notes>`. The purpose of the task is to add an 'Author notes' annotation to the Front matter menu in the Production editor. Refe...**Description;** production editorial staff would like to tag 'Author notes' for conversion to JATS; `<author-notes>`. The purpose of the task is to add an 'Author notes' annotation to the Front matter menu in the Production editor. Reference; https://jats.nlm.nih.gov/archiving/tag-library/1.1/element/author-notes.html
**Acceptance criteria;**
- [ ] Ability to Highlight text in the Notes (footnotes) section and apply the 'Author note' annotation converts the annotated content to valid JATS when exporting XML.
- [ ] When exporting as JATS XML; `author-note` appear in the `front` matter, and should not be wrapped in an `fn-group`. [TBC]
- [ ] When exporting as JATS XML; `correp` (author name & email address) should be included as an attribute in an `author-note` element.
![Screenshot_2021-12-15_at_15.18.03](/uploads/9323e2e23cfbac597d028800518ef4dc/Screenshot_2021-12-15_at_15.18.03.png)
Example;
```
<author-notes>
<fn id="fn1" fn-type="other"><label>*</label><p>Official English translation from the original Spanish manuscript made by the Pan American Health Organization. In case of discrepancy, the original version shall prevail. Access to original manuscript: <ext-link ext-link-type="uri" xlink:href="https://doi.org/10.26633/RPSP.2021.19">https://doi.org/10.26633/RPSP.2021.19</ext-link></p></fn>
<corresp id="c1">Pilar Torres-Pereda, <email>pilar.torres@insp.mx</email></corresp>
</author-notes>Amnet Production Editor v2https://gitlab.coko.foundation/kotahi/kotahi/-/issues/696[Wax] Annotating and adding comment alignment issue2021-11-05T07:32:32ZRyan Dix-Peek[Wax] Annotating and adding comment alignment issue**Issue description;** annotated text and the comment icon are not aligned. The alignment should be as per the [wax-demo editor](http://wax-demo.coko.foundation/).
Wax demo editor;
![Screenshot_2021-11-03_at_14.14.23](/uploads/39282c9c...**Issue description;** annotated text and the comment icon are not aligned. The alignment should be as per the [wax-demo editor](http://wax-demo.coko.foundation/).
Wax demo editor;
![Screenshot_2021-11-03_at_14.14.23](/uploads/39282c9c98740ee895a4b4d5428f05da/Screenshot_2021-11-03_at_14.14.23.png)
Kotahi wax editor examples;
![Screenshot_2021-11-03_at_14.26.34](/uploads/de2739858fe8a2e779a0d68a608b7acf/Screenshot_2021-11-03_at_14.26.34.png)
![Screenshot_2021-11-03_at_14.15.11](/uploads/3eed2b00e253303617ad6c27a6d72d03/Screenshot_2021-11-03_at_14.15.11.png)
![Screenshot_2021-11-03_at_14.12.33](/uploads/b502d5a419d6e586e6c8739c46496cb7/Screenshot_2021-11-03_at_14.12.33.png)https://gitlab.coko.foundation/kotahi/kotahi/-/issues/694[Wax] Text should wrap on smaller screen sizes2021-11-12T02:47:32ZRyan Dix-Peek[Wax] Text should wrap on smaller screen sizes**Issue description;** text/content visible in the wax editor should be responsive to the size of the screen and not overlap with the scroll bars (both on the righthand side and the bottom).
![Screenshot_from_2021-11-02_17-43-47](/uploa...**Issue description;** text/content visible in the wax editor should be responsive to the size of the screen and not overlap with the scroll bars (both on the righthand side and the bottom).
![Screenshot_from_2021-11-02_17-43-47](/uploads/b0880d37326a8878f090e5daa586f9c6/Screenshot_from_2021-11-02_17-43-47.png)https://gitlab.coko.foundation/kotahi/kotahi/-/issues/633Add links to Production page from Dashboard & Control panel2021-09-15T11:04:49ZRyan Dix-PeekAdd links to Production page from Dashboard & Control panel**Context;** the purpose of this task is to create a link between a manuscript and the Production interface.
**Proposal;** to include a button that links to the Production interface from the Dashboard and Control panel. The link should...**Context;** the purpose of this task is to create a link between a manuscript and the Production interface.
**Proposal;** to include a button that links to the Production interface from the Dashboard and Control panel. The link should always open the most recent version of the manuscript text.
Control panel; TBC
Dashboard; ![Screenshot_2021-09-02_at_15.31.40](/uploads/16f55cbb87126488221e4d6402afbfaa/Screenshot_2021-09-02_at_15.31.40.png)https://gitlab.coko.foundation/kotahi/kotahi/-/issues/627Support for Amnet extraction tool to call data from submission form2021-09-08T14:39:24ZRyan Dix-PeekSupport for Amnet extraction tool to call data from submission form**Description;** Kotahi has a good submission workflow. But as soon as you upload a manuscript, you have to fill out a form as per the publisher needs as extra metadata. These could be used later in the workflow to create a JATS XML outp...**Description;** Kotahi has a good submission workflow. But as soon as you upload a manuscript, you have to fill out a form as per the publisher needs as extra metadata. These could be used later in the workflow to create a JATS XML output or for any other downstream processing. If we could help out the authors by pre-filling this form as much as possible, it would be of great use to the author. With Machine Learning (ML) we can train and extract this information from the submitted manuscript and use that information to pre-fill the form.
[Reference document](https://docs.google.com/document/d/1mbDCLVIKm2EixyrOV9hcpXP98FYOZMwm0XYOLVSjLe8/)
**Acceptance criteria;**
- [ ] Amnet deliverable; to create a metadata xtraction microservice that takes in a raw manuscript [Docx] and extracts key information from it.
- [ ] Coko deliverable; create a feature in kotahi to call this service on import and use the metadata to auto-populate form fields upon submission.https://gitlab.coko.foundation/kotahi/kotahi/-/issues/619Merge the form and manuscript data for export2021-09-03T04:27:47ZRyan Dix-PeekMerge the form and manuscript data for exporthttps://gitlab.coko.foundation/kotahi/kotahi/-/issues/618[Production page] Insert 'Author names' placeholder component in Wax2022-10-14T11:02:27ZRyan Dix-Peek[Production page] Insert 'Author names' placeholder component in Wax**Description;** placeholder components are visual indicators nested within the manuscript. The purpose of the placeholder component is to offer Production editors the ability to identify, add and/or organise metadata captured in the sub...**Description;** placeholder components are visual indicators nested within the manuscript. The purpose of the placeholder component is to offer Production editors the ability to identify, add and/or organise metadata captured in the submission form in the Production editor (Wax).
Manuscript content displayed in Wax serves as the canonical manuscript view. Even though placeholder content is not editable in Wax, there is a need for the component to be visible and represent the structure of the manuscript as accurately as possible. If an author first/last name, email or affiliation are modified this updated data will reflect at the endpoint (Flax, PDF etc.)
UI; TBC
**Acceptance criteria;**
- [ ] In the Submission form; Admins should be able to enable an advanced form field setting; 'Include in the Production editor' Yes/No.
- [ ] Placeholder components (box) should span the width of the page (Wax viewport) with a border. The placeholder box are should be fixed to the top of the Wax viewport.
- [ ] Placeholder components that are enabled should appear in the same order as they do in the Submission form.Amnet Production Editor v2