...

Why? OJS is freeand open source software (FOSS) platform reliably updated by its developing team. Sometimes  Sometimes it's not straightforwardly intuitive, but this is why we are gathering the knowledge here, so we can quickly find what you need if one of us knows  

This is a living document and work-in-progress documentation .

Backend - OJS Database

Automatizable tasks and schedule

...

• setting_name = "familyName", "givenName", "affiliation", "country", "orcid", "url" or "biography"

• setting_value = correspondent values (e.g. "Delgado Mas", "Elisabet", "University of Vienna", "AT")

Queries:

SELECT * FROM ojs.authors

...

authors

...

authors

Links author_id with:

email

publication_id

...

A single user / author / standard student has two rows in this table, and two different author_id values! One row is for their first year publication and the other for their second. 

• Example: Elisabet Delgado Mas (a12013592 add unet.univie.ac.at) has one row in the authors table with author_id = 270 and publication_id = 147 ("EMG reproducibility using neuronavigated TMS"), and another row with author_id = 525 and publication_id = 328 ("Human-AI Interaction").

...

Queries:

-- Check main table related to authors.

SELECT * FROM ojs.author_settings

-- Note that the table author_settings ≠ table authors, where you can find the email. 

SELECT * FROM ojs.authors

-- Note table authors ≠ table Authors.

SELECT * FROM ojs.Authors

-- Given one of the user's author_id, get email.

SELECT email FROM ojs.authors x WHERE author_id = 256

publication_settings 

Nested structure: columns setting_name and setting_value, linked by publication_id (≠submission_id) .

• setting_name = "abstract", "title", "prefix", "subtitle", "categoryIds"

• setting_value = correspondent values (e.g. "

publication_settings 

Nested structure: columns setting_name and setting_value, linked by publication_id (≠submission_id) .

• setting_name = "abstract", "title", "prefix", "subtitle", "categoryIds"

• setting_value = correspondent values (e.g. "Delgado Mas", "Elisabet", "University of Vienna", "AT")

...

last_modified can be used in the query as a filter for the submissions of the current year (e.g. AND p.last_modified >= '2024-03-03 00:00:00';).

submission_id can be used to create the links to the backend and the frontend of each submission:

...

Links user_id with everything else related to a user, including:

username

password

username = elisabet

password = (encripted) $2y$16$m2Wp95TAKo9Fg8V7hCoCEuC/3Z8zCDC/q8f2Py6C3Yl1LxC2kGnIG   

email = a000000000@unet.univie.ac.atemail

date_registered = YYYY-MM-DD HH:MM:SS.000    

date_last_login    login = YYYY-MM-DD HH:MM:SS.000

user_settings

Similar to author_settings. Nested structure: columns setting_name and setting_value, linked by user_id.

• setting_name = "familyName", "givenName", "affiliation" + "preferredPublicName", "signature", "orcid"

• setting_value = correspondent values (e.g. "Delgado Mas", "Elisabet", "University of Vienna", "", "", "")

sections

(journal_id = 3, ours)
3
4
7
8
(journal_id = 4, who knows)
5
6

...

It means order.
Values: 1,2,3,4
Section_idsids: 7, 8, 3, 4
Corresponding to: Workshops, plenary talks, talks, posters.

...

• File-paths-given-issue.sql
• ...

Scripts Documentation

Single line comments start with --

...

• get-author-id-by-email.sql

...

• get-

...

• authors-

...

• and-

...

• submissions.sql
• get-authors-email-family_name-given_name.sql
• get-submissions-date-range.sql
• get-urls_submission-id.sql
• 05-01_authors_registration.sql

Scripts Documentation

Single line comments start with --

File-paths-given-issue.sql

File-paths-given-issue.sql

f.f.path from (select publication_id from publication_settings 

...

--We have published . 
Issue 2023
where setting_name = 'issueID' and setting_value = 13
Issue 2022
where setting_name = 'issueID' and setting_value = 8

get-authors-and-submissions.sql

(almost ready, on Eli's laptop)

authors-registration.sql

05-01_authors_registration.sql

...

On the making

Scripts we have not yet managed to finish.

• ...

Quick useful queries

-- Given submission_id, provide the backend and frontend links of its submission. Change 368 for your n.

SELECT p.submission_id,

p.publication_id,

CONCAT('https://journals.phl.univie.ac.at/meicogsci/workflow/access/', p.submission_id) as 'url_backend',

CONCAT('https://journals.phl.univie.ac.at/meicogsci/article/view/', p.submission_id) as 'url_frontend'

FROM publications p

WHERE p.submission_id = 368

-- WHERE p.publication_id = 328

...

Given a list of emails, returns a table with all the submissions by those authors, the user_id, givenName, familyName, email, university, publication_id, submission_id, title (of the abstract), abstract, last_modified (date), and a quick access URL to the public view and the dashboard view of that submission.

get-authors-email-family_name-given_name.sql

Smaller script: Returns the email, family name and given name of an author, which are values found at different tables of the database (email in users and names in user_settings).

get-author-id-by-email.sql

Smaller script: Returns the author_id, given name, family name, email, university, publication_id, submission_id and country, given an email address.

get-urls_submission-id.sql

Smaller script: Generates the URLs for quick access of a given submission both in the public face of the website (or its preview) and the admin dashboard.

get-submissions-date-range.sql

Gets submissions within a date range and their data. 

This is important as a constrain because until the submissions have been reviewed and approved, we cannot filter them by issue (merely because they have not yet been assigned to an issue, which is a manual process done one by one).

On the making

Scripts we have not yet managed to finish, if any.

• 05-01_authors_registration.sql
  • We would like it to track: Author, email address, submission ID (& link), submission title, if the submission abstract text field is filled, and if they actually pressed the button to submit).

Quick useful queries

-- Given submission_id, provide the backend and frontend links of its submission. Change 368 for your n.

SELECT p.submission_id,

p.publication_id,

CONCAT('https://journals.phl.univie.ac.at/meicogsci/workflow/access/', p.submission_id) as 'url_backend',

CONCAT('https://journals.phl.univie.ac.at/meicogsci/article/view/', p.submission_id) as 'url_frontend'

FROM publications p

WHERE p.submission_id = 368

-- WHERE p.publication_id = 328

-- Given one of the user's author_id, show their email and both publications. Change 270 for your n.

SELECT a.email, a.author_id, a.publication_id

FROM authors a

WHERE email = (SELECT email FROM authors WHERE author_id = "270")

-- Given one of the user's author_id, show their data (familyName, givenName, affiliation, country) for both publications. Change 270 for your n.

SELECT DISTINCT a.email, a.author_id, a.publication_id, ase.setting_value

FROM authors a, author_settings ase

JOIN (SELECT author_id, setting_value FROM author_settings WHERE author_id = "270") as aaf

ON ase.author_id = aaf.author_id

WHERE email = (SELECT email FROM authors WHERE author_id = "270")

-- Check which users have the permission most tutors had.

SELECT * FROM authors WHERE user_group_id = 36;

Annexes

Tables used

These are the tables in our database.

1. Most of these might be empty or merely not used. 
2. We highlight in bold the ones we have been using in successful queries.
3. We highlight in italics the ones in which we have found data that we have not yet managed to explain, but which may become relevant.

• Authors
• access_keys
• announcement_settings
• announcement_type_settings
• announcement_types
• announcements
• auth_sources
• author_settings
• authors
• books_for_review
• books_for_review_authors
• books_for_review_settings
• captchas
• categories
• category_settings
• citation_settings
• citations
• comments
• completed_payments
• controlled_vocab_entries
• controlled_vocab_entry_settings
• controlled_vocabs
• custom_issue_orders
• custom_section_orders
• data_object_tombstone_oai_set_objects
• data_object_tombstone_settings
• data_object_tombstones
•  dataverse_files
•  dataverse_studies
•  edit_assignments
•  edit_decisions
•  email_log
•  email_log_users  
•  email_templates
•  email_templates_default
•  email_templates_default_data
•  external_feeds 
•  external_feed_settings 
•  email_templates_settings 
•  event_log 
•  event_log_settings 
•  failed_jobs
•  files 
•  filter_groups 
•  filter_settings 
•  filters 
•  genre_settings 
•  genres 
•  group_memberships 
•  group_settings 
•  groups 
•  institutional_subscription_ip 
•  institutional_subscriptions 
•  issue_files 
•  issue_galley_settings 
•  issue_galleys 
•  issue_settings 
•  issues 
•  item_views 
•  jobs 
•  journal_settings 
•  journals 
•  library_file_settings 
•  library_files 
•  metadata_description_settings 
•  metadata_descriptions 
•  metrics 
•  mutex 
•  navigation_menu_item_assignment_settings 
• navigation_menu_item_assignments
•  navigation_menu_item_settings 
•  navigation_menu_items 
•  navigation_menus 
•  notes 
•  notification_mail_list 
•  notification_settings 
•  notification_subscription_settings 
•  notifications 
•  oai_resumption_tokens 
•  object_for_review_assignments 
•  object_for_review_persons 
•  object_for_review_settings 
•  objects_for_review 
•  paypal_transactions 
•  pln_deposit_objects 
•  pln_deposits 
•  plugin_settings 
•  processes 
•  publication_categories 
•  publication_galley_settings 
•  publication_galleys 
•  publication_settings 
•  publications 
•  queries 
•  query_participants 
•  queued_payments 
•  referral_settings 
•  referrals 
•  review_assignments 
•  review_files 
•  review_form_element_settings
•  referral_settings 
•  referrals 
•  review_assignments 
• review_files
• review_form_element_settings
•  review_form_elements           
•  review_form_responses                    
•  review_form_settings 
•  review_forms 
•  review_object_metadata 
•  review_object_metadata_settings 
•  review_object_type_settings 
•  review_object_types 
•  review_round_files 
•  review_rounds 
•  roles 
•  rt_contexts 
•  rt_searches 
•  rt_versions 
•  scheduled_tasks 
•  section_settings 
•  sections 
•  sessions 
•  site 
•  site_settings 
•  stage_assignments 
•  static_page_settings 
•  static_pages 
•  subeditor_submission_group 
•  submission_artwork_files 
•  submission_comments 
•  submission_file_revisions 
•  submission_file_settings 
•  submission_files 
•  submission_search_keyword_list 
•  submission_search_object_keywords
•  submission_search_objects 
•  submission_settings 
•  submission_supplementary_files 
•  submission_tombstones 
•  submission_xml_galleys 
•  submissions 
•  subscription_type_settings 
•  subscription_types 
•  subscriptions 
•  temporary_files 
•  theses 
•  usage_stats_temporary_records 
•  user_group_settings 
•  user_group_stage 
•  user_groups 
•  user_interests 
•  user_settings 
•  user_user_groups 
•  users 

Backend - OJS Exports

We have prepared a sample of exports here, protected by password. 

The folders in which they are contained include descriptions of the items selected for export and the encountered problems.

At this point, the main issue with OJS exports is that this mainly focus on published articles already assigned to an issue, a step undertaken only after the review phase.

They have been obtained through:

TOOLS

Exporting XML tools, basically.
https://journals.phl.univie.ac.at/meicogsci/management/tools

    Crossref XML Export Plugin: Export

SELECT a.email, a.author_id, a.publication_id

FROM authors a

WHERE email = (SELECT email FROM authors WHERE author_id = "270")

-- Given one of the user's author_id, show their data (familyName, givenName, affiliation, country) for both publications. Change 270 for your n.

SELECT DISTINCT a.email, a.author_id, a.publication_id, ase.setting_value

FROM authors a, author_settings ase

JOIN (SELECT author_id, setting_value FROM author_settings WHERE author_id = "270") as aaf

ON ase.author_id = aaf.author_id

WHERE email = (SELECT email FROM authors WHERE author_id = "270")

-- Check which users have the permission most tutors had.

SELECT * FROM authors WHERE user_group_id = 36;

Annexes

Tables used

These are the tables in our database.

1. Most of these might be empty or merely not used. 
2. We highlight in bold the ones we have been using in successful queries.
3. We highlight in italics the ones in which we have found data that we have not yet managed to explain, but which may become relevant.

• Authors
• access_keys
• announcement_settings
• announcement_type_settings
• announcement_types
• announcements
• auth_sources
• author_settings
• authors
• books_for_review
• books_for_review_authors
• books_for_review_settings
• captchas
• categories
• category_settings
• citation_settings
• citations
• comments
• completed_payments
• controlled_vocab_entries
• controlled_vocab_entry_settings
• controlled_vocabs
• custom_issue_orders
• custom_section_orders
• data_object_tombstone_oai_set_objects
• data_object_tombstone_settings
• data_object_tombstones
•  dataverse_files
•  dataverse_studies
•  edit_assignments
•  edit_decisions
•  email_log
•  email_log_users  
•  email_templates
•  email_templates_default
•  email_templates_default_data
•  external_feeds 
•  external_feed_settings 
•  email_templates_settings 
•  event_log 
•  event_log_settings 
•  failed_jobs
•  files 
•  filter_groups 
•  filter_settings 
•  filters 
•  genre_settings 
•  genres 
•  group_memberships 
•  group_settings 
•  groups 
•  institutional_subscription_ip 
•  institutional_subscriptions 
•  issue_files 
•  issue_galley_settings 
•  issue_galleys 
•  issue_settings 
•  issues 
•  item_views 
•  jobs 
•  journal_settings 
•  journals 
•  library_file_settings 
•  library_files 
•  metadata_description_settings 
•  metadata_descriptions 
•  metrics 
•  mutex 
•  navigation_menu_item_assignment_settings 
• navigation_menu_item_assignments
•  navigation_menu_item_settings 
•  navigation_menu_items 
•  navigation_menus 
•  notes 
•  notification_mail_list 
•  notification_settings 
•  notification_subscription_settings 
•  notifications 
•  oai_resumption_tokens 
•  object_for_review_assignments 
•  object_for_review_persons 
•  object_for_review_settings 
•  objects_for_review 
•  paypal_transactions 
•  pln_deposit_objects 
•  pln_deposits 
•  plugin_settings 
•  processes 
•  publication_categories 
•  publication_galley_settings 
•  publication_galleys 
•  publication_settings 
•  publications 
•  queries 
•  query_participants 
•  queued_payments 
•  referral_settings 
•  referrals 
•  review_assignments 
•  review_files 
•  review_form_element_settings
•  referral_settings 
•  referrals 
•  review_assignments 
• review_files
• review_form_element_settings
•  review_form_elements           
•  review_form_responses                    
•  review_form_settings 
•  review_forms 
•  review_object_metadata 
•  review_object_metadata_settings 
•  review_object_type_settings 
•  review_object_types 
•  review_round_files 
•  review_rounds 
•  roles 
•  rt_contexts 
•  rt_searches 
•  rt_versions 
•  scheduled_tasks 
•  section_settings 
•  sections 
•  sessions 
•  site 
•  site_settings 
•  stage_assignments 
•  static_page_settings 
•  static_pages 
•  subeditor_submission_group 
•  submission_artwork_files 
•  submission_comments 
•  submission_file_revisions 
•  submission_file_settings 
•  submission_files 
•  submission_search_keyword_list 
•  submission_search_object_keywords
•  submission_search_objects 
•  submission_settings 
•  submission_supplementary_files 
•  submission_tombstones 
•  submission_xml_galleys 
•  submissions 
•  subscription_type_settings 
•  subscription_types 
•  subscriptions 
•  temporary_files 
•  theses 
•  usage_stats_temporary_records 
•  user_group_settings 
•  user_group_stage 
•  user_groups 
•  user_interests 
•  user_settings 
•  user_user_groups 
•  users 

Backend - OJS Exports

We have prepared a sample of exports here, protected by password. 

The folders in which they are contained include descriptions of the items selected for export and the encountered problems.

At this point, the main issue with OJS exports is that this mainly focus on published articles already assigned to an issue, a step undertaken only after the review phase.

They have been obtained through:

TOOLS

Exporting XML tools, basically.
https://journals.phl.univie.ac.at/meicogsci/management/tools

    Crossref XML Export Plugin: Export article metadata in Crossref XML format.
    DataCite Export/Registration Plugin: Export or register issue, article, galley and supplementary file metadata in DataCite format.
    PubMed XML Export Plugin: Export article metadata in PubMed XML format for indexing in MEDLINE.
    DOAJ Export Plugin: Export Journal for DOAJ.
    Native XML Plugin: Import and export articles and issues in OJS's native XML format.
    Users XML Plugin: Import and export users

...

• Select all the content, copy it.
• Go to your Google Sheets spreadsheet (or elsewhere).
  • Paste it.
  • If you need to keep the format (https://support.google.com/docs/thread/54946749/paste-special-paste-values-only-does-not-work-in-google-sheet?hl=en) paste it on another sheet inside of the document first (e.g. a sheet with conditional formatting: Edit > Paste values).

Voilà, congratulations 

Frontend

...

- OJS Website & Dashboard

...

View of the homepage of the website (left) and the dashboard (right) of an advanced user. The changes in the website have to be done and saved from the dashboard. Find below a written tutorial on where to find what.

...

In this section there are many many tabs, sometimes inside of other tabs. This is why we will structure this section on the wiki not by tabs but by where you can find each feature, so it's most helpful  

Design

Change some of the design of the homepage, how the whole website looks and how to customize its design:

Menus & URLs

 
 Change the structure/architecture/navigation (what page is inside of which and its URL) of the website:

Eli's note:

Beware there are two sections called "Setup". In the picture we are in SETTINGS: WEBSITE (left bar) > APPEARANCE (tab in the upper part) > SETUP (tab inside appearance, on the lef-central part) > "Logo".

Image Removed

...

> PLUGINS

STATISTICS
Menu arquitecture
Permisions

SUBMISSIONS

It's where you can see and do everything related to the particular submissions of the author abstracts and reviews.

ISSUES

Mostly relevant just before the last step for publishing the issue (June), to rearrange what you see here:

Image Removed

...

Edit the configuration of an issue (name, date of publication, volume - formal number).

Add a cover image and some text about this issue.

...

Order the abstracts within each section in the right order.

In 2024, by author surname, manually once an issue is created and after all submissions have been assigned.

...

Order the sections.

In 2024, the order set is:

• Editorial 
• Plenary Talks
• Workshops
• Poster Abstracts
• Talk Abstracts

...

Eli's note:

Beware there are two sections called "Setup". In the picture we are in SETTINGS: WEBSITE (left bar) > APPEARANCE (tab in the upper part) > SETUP (tab inside appearance, on the lef-central part) > "Logo".

Image Added

> SETUP

> PLUGINS

SETTINGS: WORKFLOW

It's where you find most of the stuff related to author guidelines and the review phase, but also about submission settings (e.g. confirmation statement component).

*Eli's note for the 2025 team, most interesting:

Review forms are in SETTINGS: WORKFLOW > REVIEW (upper tab) > REVIEW FORMS (left tab). Once a review form has been used to review by any user, it cannot be edited anymore! 

There may be a way to set automatic reminders in SETTINGS: WORKFLOW > REVIEW (upper tab) > SETUP (left tab). 

•  Response Reminder: Send an email reminder if a reviewer has not responded to a review request this manydays after the response due date.
•  Review Reminder: Send an email reminder if a reviewer has not submitted a recommendation within this many days after the review's due date.

We can set and change friendlier and more customized templates for emails and reminders that can be sent automatically within the system: https://journals.phl.univie.ac.at/meicogsci/management/settings/manageEmails

SETTINGS: USERS & ROLES

You can browse specific users in the first upper tab, and see the role possibilities in the second.

Permissions are divided in four categories or stages: 

All roles are a combination of these categories or stages (which for our purposes, is not most helpful).

There are currently 17 roles, and any given user can have multiple roles assigned. Each role has an associated permission level.

Permission levels are:

SUBMISSIONS

It's where you can see and do everything related to the particular submissions of the author abstracts and reviews.

ISSUES

Mostly relevant just before the last step for publishing the issue (June), to rearrange what you see here:

Image Added

Image AddedImage AddedImage Added

Eli's note for team 2025:

It's worth noticing the actual issue ID in the URL is not the same as the formal number "Identification Volume". E.g. 

• Issue "Vol. 18 No. 1 (2024): Proceedings of the MEi:CogSci Conference" (18th MEi:CogSci Conference) has the ID 17 in its URL https://journals.phl.univie.ac.at/meicogsci/issue/view/17 
• Issue "Vol. 17 No. 1 (2023): Proceedings of the MEi:CogSci Conference" (17th MEi:CogSci Conference) has the ID 13 in its URL https://journals.phl.univie.ac.at/meicogsci/issue/view/13

And the ID in the URL changes every time the issue is unpublished and published again (be wary of this).

ANNOUNCEMENTS

Add or modify the announcements / posts that appear in the website.

STATISTICS

About the number of users, editorial activity etc. Mostly exportable in CSV format (and from there to Excel).

Interestingly:
-Most visited articles
https://journals.phl.univie.ac.at/meicogsci/stats/publications/publications 

Image Added

Activity Log

16.07.2024

Elisabet, @Elisabeth, @Evelyn, @Odin

•  Meeting and sharing content with the Bratislava team (@Martin & @Kika).

15.07.2024

Elisabet Delgado Mas Evelyn Fischer

•  Backend documentation on OJS web scrapping, and link to scripts.
•  Create queries that:
  •  Given submission_id, provides the backend and frontend links of its submission.
  •  Given one of the user's author_id, show their email and both publications.
  •  Given one of the user's author_id, show their data (familyName, givenName, affiliation, country) for both publications

Image RemovedImage RemovedImage Removed

Eli's note for team 2025:

It's worth noticing the actual issue ID in the URL is not the same as the formal number "Identification Volume". E.g. 

• Issue "Vol. 18 No. 1 (2024): Proceedings of the MEi:CogSci Conference" (18th MEi:CogSci Conference) has the ID 17 in its URL https://journals.phl.univie.ac.at/meicogsci/issue/view/17 
• Issue "Vol. 17 No. 1 (2023): Proceedings of the MEi:CogSci Conference" (17th MEi:CogSci Conference) has the ID 13 in its URL https://journals.phl.univie.ac.at/meicogsci/issue/view/13

And the ID in the URL changes every time the issue is unpublished and published again (be wary of this).

ANNOUNCEMENTS

Add or modify the announcements / posts that appear in the website.

STATISTICS

About the number of users, editorial activity etc. Mostly exportable in CSV format (and from there to Excel).

Interestingly:
-Most visited articles
https://journals.phl.univie.ac.at/meicogsci/stats/publications/publications 

Image Removed

Activity Log

15.07.2024

Elisabet, @Elisabeth, @Evelyn, @Odin

•  Meeting and sharing content with the Bratislava team (@Martin & @Kika).

15.07.2024

Elisabet Delgado Mas

•  General structure and order.
•  Backend documentation on OJS web scrapping.

09.07.2024

Elisabet Delgado Mas

•  Backend documentation on OJS exports.

02.07.2024

Elisabet Delgado Mas

•  Frontend documentation on OJS.

27.03.2024

Elisabet Delgado Mas

• Goal: Explore database, create table documentation, get first scripts.
  
  •  Elisabet Delgado Mas Create table documentation.
  •  Elisabet Delgado Mas Create queries that:
    •  Given submission_id, provides the backend and frontend links of its submission.
    •  Given one of the user's author_id, show their email and both publications.
    •  Given one of the user's author_id, show their data (familyName, givenName, affiliation, country) for both publications.
    •  Give list of users with a given permission.
  •  Elisabet Delgado Mas Create script that gets authors and submissions.

19.03.2024

Elisabet Delgado Mas Evelyn Fischer

• Goal: Start new scripts based on the Schedule.
• Homework:
  •  Evelyn Fischer Delete outdated tutorial. 
  •  Elisabet Delgado Mas Create updated tutorial and follow-up content from our meeting.
  •  Arrange next meeting (any hour, Tue or Wed). https://univienna.zoom.us/j/66408236619?pwd=WFZEclF6bGNXUlJaellNbnYrTkMxUT09
    Time: Mar 19, 2024 02:00 PM, Meeting ID: 664 0823 6619,  Passcode: 444917
  •  Elisabet Delgado Mas Check DBeaver https://dbeaver.com/docs/dbeaver/Data-transfer/

12.03.2024

Elisabet Delgado Mas Evelyn Fischer

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