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# Documentation history
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This section includes **out-of-date** documetation for record purposes only.
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[[_TOC_]]
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## Create and sign up to organizations
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NBCI's requirements regarding registering users and adding them to organisations:
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* Org admins should not be able to see all users in the system. This means that Org Admins can't add users by searching for existing users in the system.
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* The NCBI team don't want the task of associating users to an Org to be their responsibility by default because that will create a lot work for their team, especially at scale.
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* The use case of a user belonging to multiple organisation is not common.
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* user authentication must work with MyNCBI
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![NCBI-register](/uploads/571f3dc15841e39b8b61afaf70a7fd22/NCBI-register.jpg)
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An organisation must exist before users can sign up.
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The **workflow for creating and signing up to organisations** would be:
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* System admin creates organisation →
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* this makes the org name available in the dropdown list on the sign up page and sends an email to the address used to set up the org "Your organisation has been created" →
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* Org admin signs up →
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* sys admin approves the org admin →
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* all other users sign up (selecting their org in the process) →
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* Org admin accepts/rejects the users requests to join the team
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If a user wants to join another org, they send a request to that org after signing up (this would happen is a "User account/profile" page not currently prioritised)
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## Manage organization (Sys admin POV)
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Tasks on this page:
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1. See all organisations, and click through to each org and its users
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1. Search by organisation name and email
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2. Access the modal to create a new organisation
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3. Access the "Users" page to view and manage *all* users in the system
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4. Change the status of the agreement from "pending" to "signed". Sys admins will, for the time being, change the status manually. This will be automated later with an integration with NCBI's other systems.
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5. Delete organisations
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![Sys_admin_org_overview_page](/uploads/a8d4a9b93b62e8bc9a08dc5f6737f9fe/Sys_admin_org_overview_page.jpg)
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**Create new organisation**
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Clicking the "New organisation" button takes the Sys Admin here. Tasks on this page:
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1. Create organisation
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2. Change the status of the agreement from "pending" to "signed".
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On save, an email is sent to the email provided "[Organisation name] is active". When the organisation has been created, the organisation name is available for users to select and join from the sign up page.
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![Sys_admin_new_org](/uploads/20c2357349573ccbaac67c6f7d40c310/Sys_admin_new_org.jpg)
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**View of one organisation**
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Clicking on one organisation row (see first wireframe above) takes the Sys Admin here.
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Tasks on this page:
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1. Edit organisation data
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1. Search and view all users in the organisation
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2. Change status of agreement
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3. Delete organisation
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4. Accept users requests to join organisation
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5. Make users organisation admins
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6. Add accepted users to organisation teams
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7. Click through to users data
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![Sys_admin_user_page](/uploads/44e58b2c5a8a0ca9fa80437e593119b6/Sys_admin_user_page.jpg)
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Clicking on one user row opens the view of that user's information for the relevant organisation.
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Tasks on this page:
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1. View the users data
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1. Edit the users data (troubleshooting purposes)
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1. Make a user an organisation admin
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1. Add or remove the accepted user to organisation teams
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1. Disable the accepted user
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![Sys_admin_user_popup](/uploads/ca81591caf664a17d36c4a893c89d756/Sys_admin_user_popup.jpg)
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**View and manage all users**
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*[Not scheduled for development]*
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Clicking the "Users" button (see first wireframe above) takes the Sys Admin here.
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![Sys_admin_all_users_page](/uploads/e61f68062817230f697848fd581d6d3f/Sys_admin_all_users_page.jpg)
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**View and manage a user**
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*[Not scheduled for development]*
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Clicking on one row opens the view of that user's information across all organisations.
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![Sys_admin_all_users_page_-_popup](/uploads/172f8b7c367211a67db4b2c8d1210cb2/Sys_admin_all_users_page_-_popup.jpg)
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## Manage organization (Org admin POV)
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Shows only the relevant organisation's details and users. Org admins cannot:
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* delete the organisation or users.
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* edit a user's name, email, etc.
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* change the status of the organisation agreement
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Tasks on this page:
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1. Edit organisation data
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1. Search and view all users in the organisation
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1. Accept users requests to join organisation
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1. Make users organisation admins
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1. Add accepted users to organisation teams
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1. Click through to users data
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![Org_admin_user_page_v2](/uploads/ff51ffd9ea9b2fc124de0c5b49b3455a/Org_admin_user_page_v2.jpg)
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Clicking on one user row opens the view of that user's information for the relevant organisation.
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Tasks on this page:
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1. View the users data
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1. Make a user an organisation admin
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1. Add or remove the accepted user to organisation teams
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1. Disable the accepted user
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![Org_admin_user_page_-_popup](/uploads/055d515a4f783dee6803efcfcc86ba2e/Org_admin_user_page_-_popup.jpg)
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## Assign organisation and content roles
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This documents the workflow of assigning roles to accepted users of an organisation for the Word workflow as discussed in #59.
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**Organisation roles**
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Org roles are assigned in the Admin UI. The Word workflow includes two org roles:
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* Org Admin
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* Editor
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When a user is given the org role 'Editor', this means that she is able to create collections and books for the organisation, and be added as an Editor to content.
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If an Org admin turns off a user's 'Editor' org role, she won't be able to create collections and books or be assigned as an Editor to content.
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**Content roles**
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Once Editors are assigned in the Admin page, they can assign all further roles to users according to which content they need to access. The Editor does this in the relevant Team modal for the collection or book.
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**Book team modal**
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![image](uploads/da4600f6eea9df049c559ed15a3104e4/image.png)
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* Multiple roles can be assigned to a user. See the 'Role permissions' section on the [wiki homepage](https://gitlab.coko.foundation/ncbi/ncbi/-/wikis/home/).
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* The Editor who created the book is listed in the team modal (i.e the Editor does not need to add herself to the team).
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* V1 dev includes adding (co) Editors, Authors, and Previewers to the book's team.
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* V1 dev doesn't include sorting or filtering the list of users.
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**Assign content roles to specific book components**
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* Certain roles (e.g. Previewers, Reviewers, and Copy-editors) won't see any book components in the Book Manager until they have been assigned to the relevant components.
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* Additionally, co-authors (any author that did not create the book component) need to be given access to specific book components.
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This assignment can be done:
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* for individual book components in the 'manage team' tab
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* for multiple book components is the 'assign team' modal
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**Manage team tab**
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* The Editor's of the book, and the author who created the book component are listed in the manage team tab.
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* The Editors and author add further users to the specific book component:
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* Username dropdown lists all users associated with the book
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* Role dropdown lists the roles of the selected user (i.e the role the user has been assigned in the team modal)
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* If a user has been assigned more than one role on the book, the Editor is prompted to select the role for this book component **before** the user is added to the book component team.
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* When a new version of the book component is created, the team listed is copied to the current version -- so there is no need to reassign users.
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* V1 release does not include the "Approval required before publishing" column
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![manage_team](uploads/570e161087b653b4043abc675b19915e/manage_team.jpg)
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**Assign team modal**
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* From the book manager page, the Editor selects multiple book components, then then selects the 'Assign team' button.
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![Previewing_workflow-A](uploads/53f87952f9d355833253b36bb83e9b5c/Previewing_workflow-A.jpg)
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* The 'Assign team' button opens the modal below.
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* The modal lists all the selected chapters
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* The users then adds users to the book components, in the same way as done for individual book components.
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* The users assigned in this modal are listed in the 'manage team' tab of the relevant book components.
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* V1 release does not include the "Approval required before publishing" column
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![assign_chapters](uploads/a8870ade12d3023a69ae9476454248cd/assign_chapters.png)
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## Book manager structure
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![01-NCBI_General_Book_Manager](/uploads/a4d9b5703098035646134ca084215301/01-NCBI_General_Book_Manager.jpg)
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* The Book manager shows each book component and its related information listed in a table. There is a table for each book section: Front/Body/Back
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* Tasks that apply to the full book (Team, Settings, Metadata, Bulk upload) are shown in the top bar. Editors and Org Admins see these.
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* Expanding the current book component version row will open to show the previous version only, and a button to "show all versions". (V1 development will include current version only.)
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* V1 will include columns as shown above (errors will not have any data).
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* V1 will not include 'Download' and 'Archive' bulk actions.
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### Book component cards
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![11-NCBI_Bulk_upload_workflow_step_7](/uploads/4ad3a701590229cf98d499168b1992c4/11-NCBI_Bulk_upload_workflow_step_7.jpg)
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* Clicking on a row in the table opens a card for that book component version, showing its information.
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* Users can move through these cards (prev and next) to view each component easily.
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* **Answer to questions in call**: Moving through the cards will work for all the book components, not just the book components in one section. We will add the sections (Front/Body/Back) to the cards.
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* Users who have permission to see previous versions can do so using the version buttons shown in the bottom left (not for development in V1 of BCMS)
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* Design for the "files" tab to be confirmed
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* The "Metadata tab below shows the min required book component metadata (#22) and `abstract`
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![12-NCBI_Book_Component_metadata_modal](/uploads/c4ebdfce9f3504e790845e5924b3abb4/12-NCBI_Book_Component_metadata_modal.jpg)
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## Workflow step: create new book
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![Create_new_book_record_in_SFM-20200402](uploads/82c459f65268315e954d7c4709ec32e4/Create_new_book_record_in_SFM-20200402.png)
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* The Sys Admin, Org Admin and Editor have permission to create a book.
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* When the book is created, the book’s ID is created and passed to NCBI. It is possible for a book to exist in the SMF before it is a record in NCBI’s system.
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* When a book is created, a row is added to the table of records in the Dashboard
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### Dashboard
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![Bookshelf_SFM_-_Dashboard_-_V2](uploads/84c62af3a5efab327e009aa38fa4fad2/Bookshelf_SFM_-_Dashboard_-_V2.jpg)
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* The Dashboard shows an overview of an Organisation's books and collections. A book row open the Book Manager page; a collection row opens the Collection Manager page.
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* The view of the dashboard will vary depending on the users' roles and which assets (books and collections) they have been associated with. For example, system admins can see all assets in all organisations.
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For this step in the workflow, the following table columns will be developed:
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* Workflow type: The same organisation may use multiple workflows (Word/PDF/XML). Since there are different conversion processes required for each workflow, the Org Admin and Editor will want to see at a glance which workflow applies to each book and filter by this workflow. At this stage only "Word" will show.
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* Content type: Book or collection as shown by the icons. At this stage only books will shown.
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* Title and organisation name
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* Activity: latest activity on the book record.
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### Dashboard: New book modal
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![Bookshelf_SFM_-_New_book_-_V2](uploads/5051e02d11e0b0e2111602eafd329f75/Bookshelf_SFM_-_New_book_-_V2.jpg)
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---
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*Update not shown in above wireframe*
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It is possible for a user to belong to more than one organisation. If a user is accepted to more than one org, and that user has the permission to create books in both these organisations, then we need to show a dropdown box so the user can select the organisation name when creating the book.
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---
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The options available in this modal will depend on which conversion workflow is selected. The source-type (and its conversion workflow) is consistent across the whole book, i.e. it is not possible for one chapter to be submitted as a Word file and another chapter as a PDF. There are VERY rare cases where the NCBI needs to change the workflow for a book. In these cases a new book record is created.
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**Word to XML workflow**
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* All Word-source books are processed at the book-part level. This means that each chapter can be published independently. Selecting the "Word to XML" conversion workflow turns ON the setting 'Publish chapters independently'. This setting cannot be turned off.
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* Some books will require multiple published versions of each book-part to be available on NCBI's Bookshelf, as shown in the 'Version History' section of [this book](https://www.ncbi.nlm.nih.gov/books/NBK65761/). Organisations can choose to support multiple published versions or not.
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* Some organisations will require a PDF version of the book to be published, as shown in the 'Views' section of [this book](https://www.ncbi.nlm.nih.gov/books/NBK84114/). Organisations can choose to have a PDF version of the book published for 1) each chapter 2) the complete book 3) both 1 and 2.
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* PDF versions are created by NCBI as part of the conversion process. These are available to view when a preview of the book is generated at `https://www.preview.ncbi.nlm.nih.gov/books/...`
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**PDF to XML workflow**
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* PDF-source books can be published at the book-part level or book level. I.e. the organisation can choose to 'publish chapters independently' or not.
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* When the 'publish chapters independently' setting is turned ON, organisations can choose to support multiple published versions or not.
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* Often organisations that submit PDF files will choose to publish this file for download, so NCBI does not needs to create the PDF as part of the conversion workflow. When the user selects the conversion workflow 'PDF to XML' an additional option should be available so that the user can choose 'supply PDF' or 'create PDF'.
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**PDF to XML, and XML workflows via FTP**
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* PDF- and XML-source books via FTP can be processed at the book-part level or book level.
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* The once-off book settings shown in the 'New book' modal could be provided in the FTP package (e.g. in a config file). These details will be worked out at a later date.
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* Additionally, for XML-source books, these settings should include an option to skip the review process and publish the book directly to the live Bookshelf website.
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## Create book components in bulk
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This documents the workflow of creating book components in bulk for the Word workflow.
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**Summary**
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One book component version = multiple Source files + any converted files derived from the source files + metadata extracted from Source file and added in the metadata UI + uploaded supplementary files + image files extracted during the conversion process + associated "reviewer-version" files.
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1. Users can bulk upload Word files which creates a book component.
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1. Files that are bulk uploaded are automatically send to NCBI for conversion and ingest into PMC. The results are passed back to us.
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* Success = xml file created, with no errors reported, and Preview generated
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* Failure = xml file created with errors reported (Sometimes a failure can happen to prevent an xml file from being created during conversion - such as a Word read-only property that prevents the converter from opening the file or when a server is down, etc.)
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1. Images that are extracted from the source files are stored and available for certain users to view. Author would need to replace any images in the Word doc and upload.
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1. Supplementary and associated "reviewer-version" files are uploaded in separate step, per book component.
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**Wireframes**
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Selecting the "bulk upload" button open the modal
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![05-NCBI_Bulk_upload_workflow_step_1](/uploads/3022ff711578603d4f5b000a1129090d/05-NCBI_Bulk_upload_workflow_step_1.jpg)
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![06-NCBI_Bulk_upload_workflow_step_2](/uploads/1c3b098f0ce19d5eed0a415cdb4ec135/06-NCBI_Bulk_upload_workflow_step_2.jpg)
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An Author (or Editor) uploads Word source files in bulk. These files are styled according the NCBI's conversion requirements, and the conversion is initiated at this point. One book component is created for each file. This is the 1st version of the book component and the file.
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![07-NCBI_Bulk_upload_workflow_step_3](/uploads/d48bcbc0a233f0c0deb9b75527e704e6/07-NCBI_Bulk_upload_workflow_step_3.jpg)
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Processing information that will show here depends on the info NCBI sends back to us, and at which point.
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![08-NCBI_Bulk_upload_workflow_step_4](/uploads/2f1892a966253892cc599d949e5f9656/08-NCBI_Bulk_upload_workflow_step_4.jpg)
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Users can minimise the 'Bulk upload' modal and continue to work while the upload in is progress.
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![09-NCBI_Bulk_upload_workflow_step_5](/uploads/ff420bb8c1cb7f682f92ec24d8d75cad/09-NCBI_Bulk_upload_workflow_step_5.jpg)
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* Once the process is complete, users will see a success message if they have the book manager page open. Future iterations will in include email notifications to users.
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* Users will see how many files failed.
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![10-NCBI_Bulk_upload_workflow_step_6](/uploads/4579b1e65186f3e6d2277391a28c8983/10-NCBI_Bulk_upload_workflow_step_6.jpg)
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* Clicking the "show all failures" button filters the content in the tables to show only the failures.
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* If the files don't include the Document Type, meaning that the system does not know if it should be placed in Front/Body/Back, it will shown in the Body by default until the Document type is known, or the Editor drags and drops the component to the correct section.
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* Files that process successfully have the status "Previewing"; files that fail have the status "Failed".
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* V1 will not include failed files or error reporting.
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## Create book components individually [draft]
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One book component version = multiple Source files + any converted files derived from the source files + metadata extracted from Source file and added in the metadata UI + uploaded supplementary files + image files extracted during the conversion process + associated "reviewer-version" files.
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In our UI it needs to be clear to the user:
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* This source file = this converted file
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* These "reviewer-version" files relates to this source file
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* This source file and converted file is published.
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Authors need to create new book components one by one. Here the need is different to bulk uploads because some files will need to go through a peer review and copyediting process before they are styled according the NCBI's conversion requirements.
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* Author select "Add new book component" button in the relevant book section (front, body, back) and inserts the title. One book component is created
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* Author uploads Source file but this does not auto convert because the Author chooses to "Send to Peer Reviewer" or "Create Preview" depending on the need.
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* "Send to Peer Reviewer" creates a copy of the file. These "reviewer-version" files are separate from the book component file versions. There can be multiple "reviewer-version" files associated with a book component version. These files are never converted.
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* The Author implements all feedback from Reviewers into one file and uploads the latest version of the book component file.
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* The process continues until an approved file is successfully converted, the Preview approved and published. (As described above).
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## Book metadata
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![03-NCBI_Book_metadata_modal](/uploads/a1d0af5e652639ed00b8b0580a92d655/03-NCBI_Book_metadata_modal.jpg)
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* The Org admin and Editor can add and edit metadata for the book
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* V1 dev includes the min required book metadata (#22) and `abstract`
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## Book settings
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### Publishing setting
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* As per requirements discussed in #60, the Editor manages the setting for the book.
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* Most of the Publishing Settings are made at the step of creating the book. Settings that only the Sys Admin can change are locked.
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![image](uploads/5fa2eae81b313846082e1ee21b7f6793/image.png)
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### TOC settings
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**Part sections on TOC**
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1. Chapters of the book be grouped into parts ([as in this example](https://www.ncbi.nlm.nih.gov/books/NBK5330/))
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2. Parts ordered alphabetically or the editor chooses the order manually ([as in this example](https://www.ncbi.nlm.nih.gov/books/NBK278943/))
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**Order of chapters**
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* Alphabetically ([as in this example](https://www.ncbi.nlm.nih.gov/books/NBK278943/))
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* by chapter number
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* descending order by date created ([as in this example](https://www.ncbi.nlm.nih.gov/books/NBK43420/))
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* descending order by date updated
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* custom/manual order by editor
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**Display headings in TOC**
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For each chapter, list headings on the TOC:
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* Chapter title only
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* Chapter title and main section heading ([as in this example](https://www.ncbi.nlm.nih.gov/books/NBK555156/))
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**Display book component metadata**
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For each chapter, include metadata:
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* Author(s)
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* Date updated
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* Date created
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* Subtitle
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* Alt-titles ([as in this example](https://www.ncbi.nlm.nih.gov/books/NBK5330/))
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**Version 1**
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The TOC settings for V1 include:
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* Order chapters by: manual
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* Display headings (depth)
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* Display chapter metadata
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## Order and preview TOC
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The book manager lists all the book's components for a particular book. The order of these components is the order of the TOC. Users can manually order these by dragging them into the correct place, as indicated by the drag/move icon.
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![NCBI-TOC](/uploads/e85e99c68f7cb4fb87a55c389a4d6b66/NCBI-TOC.jpg)
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In the top right of the screen, there is a "Preview TOC" button. Selecting this would open the modal below. The preview shows the current version of all the book components in the Book Manger, irrespective of their status. What's shown here will depend on the settings that the Editor has chosen in the Setting modal (e.g. display 'date created').
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![NCBI-TOC-preview-final](/uploads/2d142ac77932922391ef7b3bee97c88a/NCBI-TOC-preview-final.jpg)
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This modal can be extended in future iterations if necessary, but for now the aim is to provide a quick way for the Editor to preview the TOC on the fly.
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## Upload and manage files
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The book component files that users upload in bulk are shown in the files tab. Users can upload new file version individually -- these are stored and then sent to NCBI conversion. The result is shown in the Status column.
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**File sections**
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* Book component: The files versions that comprise the book component version
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* Supplementary: files that relate to the book component version
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* Images: images that are extracted from the book component files (source)
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* Support: support file that are send to system when book component source is converted (only visible to system admins)
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The V1 release will include the 'Book component' section.
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**Post V1 features**
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* The sections 'Images' Supplementary' and 'Support' show the current version by default with the options to 'Show all versions'
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* Bulk action 'Download' button: users would use the select checkbox to download the relevant files. (In a later version we can add a 'Download all' button which would download all the files for that book component version).
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* Upload, replace, delete supplementary files
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* The ability to edit the file name of a supplementary file
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![files-A](/uploads/e8092bf09f03b8b6b5e536f643d48aad/files-A.jpg)
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![files-B](/uploads/8f1745a4b987b3f767e728c485254025/files-B.jpg)
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![files-C](/uploads/14b64d5c5eb99fe27f0468928a850b3e/files-C.jpg)
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![files-D](/uploads/31f565f40a7f43c7a2d902a88630c026/files-D.jpg)
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## Publish book components
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**Publishing a book component individually**
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On the preview tab, after the Editor has selected the 'Ready to publish' button, the 'Publish' button is active.
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![Preview](/uploads/2f8a253f23beeefc57a59ef40cbe6c9d/Preview.jpg)
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* Selecting the 'Publish' button opens this modal. The Editor will see this modal the first time *any* book component is published, and when all subsequent versions are publish *if* the book has the setting "Support multiple published versions" turned OFF.
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* The placeholder text [book component title] will show the actual title.
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![Publish-A](/uploads/775871bdfea8aaf0d45c5e3da09b5638/Publish-A.jpg)
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* The Editor will see this modal when all subsequent versions are published *if* the book has the setting "Support multiple published versions" turned ON.
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* The Editor chooses whether to publish:
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* as an replacement of the current published version
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* as a new published version
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* The V1 release will not include this modal since we are only publishing for the first time.
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![Publish-B](/uploads/3cad5ba79ed3a22e141df6ca72100b42/Publish-B.jpg)
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![Publish-C](/uploads/701a5198a073085dcaaf1ab73dadd25b/Publish-C.jpg)
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**Publishing book components in bulk**
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* On the book manager page, after the Editor has selected the 'Ready to publish' button, the 'Publish' button is active.
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* The Editor selects the book components that she wants to publish. To avoid human error the 'Publish' button will become inactive if the Editor selects any components that don't have the status 'Ready to publish'. The Editor would also be able to filter by Status 'Ready to publish' and then select all.
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![Previewing_workflow-A](/uploads/c16bc06cab50e1b753e2098698109d2b/Previewing_workflow-A.jpg)
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* Selecting the 'Publish' button opens this modal. Shown here is the view of the modal *if* the book has the setting "Support multiple published versions" turned ON.
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* The Editor chooses "replacement" or "new published version" for each book component. To speed up this task the Editor can also select an option from any one of the dropdowns, and then check the 'Apply selection to all' box.
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* As discussed, we could choose a default option for the dropdown box -- but we won't know which option is the most common use case until after user testing.
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* If this is the first time the components are being published (i.e. V1), the dropdown will be set to "new published version" and will not be editable.
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* *If* the book has the setting "Support multiple published versions" turned OFF, the 'Publish as' column won't appear.
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* If for some reason the Editor decides that she doesn't want to publish one or more of the selected components, she can untick the relevant components. The avoids the Editor having to close the modal and reselect the book components.
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![Publish-D](/uploads/79546c6fe0ce910d7228fdcdc5c88ee9/Publish-D.jpg)
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The above modal will include the following explainer text:
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Publishing as a replacement updates your chapter on Bookshelf with the revisions you've made. The previous version will no longer be accessible on Bookshelf. Publishing as a new published version creates a new version of your chapter on Bookshelf that contains your substantive updates. Previous versions will also be accessible on Bookshelf since they are part of the scientific record. |