Documents Management
View, Edit, Publish
Summary
This guide provides a description of the web interface for viewing and managing documents .
Operations
Edit
Users with Editor or Reviewer permission can modify the properties of a document with status Draft. See Permissions and Publication Flow for more information.
Publish
Users with Reviewer permission can publish a document with status Under Review.
Note
When a collected dataset is published, its associated study must also be published to update its inferred annotations. It is only during this process that list of variable annotations are collected.
Unpublish
Users with Reviewer permission can unpublish an already published document.
Delete
Users with Reviewer permission can delete a document with status Deleted.
Status Change
Users with Editor or Reviewer permission can change the status of a document. See Publication Flow for more information.
Network Operations
Manage Contacts
Users with Editor or Reviewer permission can manage (add/remove/edit) the list of contacts.
Manage Investigators
Users with Editor or Reviewer permission can manage the list of investigators.
Manage Studies
Users with Editor or Reviewer permission can manage the list of studies.
Manage Networks
Users with Editor or Reviewer permission can manage the list of networks.
Individual Study Operations
Manage Contacts
Users with Editor or Reviewer permission can manage (add/remove/edit) the list of contacts. Manage InvestigatorsUsers with Editor or Reviewer permission can manage the list of investigators.
Manage Populations
Users with Editor or Reviewer permission can manage the list of populations.
Manage Data Collection Events
Users with Editor or Reviewer permission can manage the list of data collection events of a population.
Manage Annotations
Users with Editor or Reviewer permission can manage the list of annotations. The list of annotations can be customized to include a subset of variable taxonomies. See the Content configurations in the administration section
Harmonization Initiative Operations
Manage Contacts
Users with Editor or Reviewer permission can manage (add/remove/edit) the list of contacts.
Manage Investigators
Users with Editor or Reviewer permission can manage the list of investigators.
Collected Dataset Operations
Manage Study Table
Users with Editor or Reviewer permission can manage (add/remove/edit) the associated study table.
Harmonization Protocol Operations
Manage Study Tables
Users with Editor or Reviewer permission can manage (add/remove/edit) the list of study tables. This operation only applies to harmonization protocols having a collection of study tables.
Revisions
Summary
Each time a document is edited a new history revision is added. The revisions are ordered from the most recent (current) to the oldest. If the document is published, a star indicates which revision is currently online.
Operations
View
Shows a read-only view of the network of the selected revision.
Restore
Restores the selected revision by replacing the current document. This operation is tracked as a new revision.
Files
Summary
Mica File System is a repository of files associated with all Mica domain documents . Similar to their associated documents, files have a publication flow and history revisions. The publication flow can apply to one or a group of files. Folders can be used to organize and group files into logical hierarchies but do not represent real data and therefore some operations such as searching do not apply to them.
Operations
Status Change
Refer to Publication Flow page for details.
Rename
Users with Editor or Reviewer permission on the containing document can rename a File and Folder. Names cannot contain the following
characters: $ / % #
.
Copy
Selected files and folders can be copied and pasted in other folders.
Move
Selected files and folders can cut and pasted in other folders.
File Specific Operations
Upload
A file from the local file system can be uploaded into the selected folder in the Mica file system.
Download
A file from Mica file system can be download into the local file system.
Search
Files can be searched in two ways:
free-text where the keyword is matched against the file name , type or description .
predefined searches listed in the search panel.
The predefined searches are all recursive in that the search query matches all files in all folder hierarchies. By toggling the Recursive button a free-text search can be recursive or applied to the current folder.
Type Edition
File types can be considered as tags and are a comma separated list of keywords associated with a file. They can be edited in the file detailpanel.
Description Edition
File description is localized and can be edited in the file detail panel.
Folder Specific Operations
Folder Creation
Folders can added as a single folder ( baseline ) or in form of a path ( baseline/temp ).
Batch Operations
Operations such as copy, move and publication flow can be performed in batch mode when they are applied to a group of selected files and/or folders.
Draft Permissions
The following tables describe file and folder draft permissions:
File Permissions
Role |
Description |
---|---|
Reader |
Can only view and download a file. |
Editor |
Can only edit, download and change the status of a file. |
Reviewer |
All operations are permitted. |
Folder Permissions
Role |
Description |
---|---|
Reader |
Can only view and download a folder. |
Editor |
Can only edit, download, change the status and upload files into a folder. |
Reviewer |
All operations are permitted. |
Note
File permissions are inherited from their parent folder unless specified.
Publication Access
Publication access makes folders and files available to everyone.
Note
Publication access is only available if Mica content is not configured for open access.
Permissions
Summary
Access to each publishable documents can be controlled. There are actually two sets of privileges:
permissions that apply to draft documents: only users having a permission on the draft document can see it,
accesses that apply to published documents: by default published documents are open access, i.e. anyone (even a anonymous web portal visitor) can see the publications. This setting
Open access
can be changed in the General.
Operations
Add Permission
Adding a permission gives a role to a named user or group of users on the draft document. The available roles are:
Role |
Description |
---|---|
Reader |
Read-only access to the document in draft mode with its revisions and its associated files. |
Editor |
Edit access to the document in draft mode with its revisions and its associated files. Publication or permanent deletion are not permitted. |
Reviewer |
Full access to the document, including its publication, permanent deletion and permissions. |
Edit Permission
selected permission role can be modified.
Delete Permission
Delete selected permission.
Add Access
This operation is only available if the Open access
general setting has been disabled. Adding an access gives the right to see the published
document to a named user or group of users. As the Files permissions on the associated files can be managed independently, when adding an access there is an option for applying same access to all the files (selected by default). Note that user (or group) name * (star) is an alias for Anyone (or Any group ).
Delete Access
Delete selected access.
Comments
Summary
All Mica domain documents can be commented on by all users with the proper permissions. The content can be pure text or in Markdown format.
Operations
Comment
The entered text (markdown) will be associated with the current document.
Preview
A preview of the rendered markdown text is presented.
Edit
The comment text can be updated and previewed.
Delete
Deletes the selected comment.
Permissions
Role
Description
Reader
Can add, edit and delete own comment. Can view comments of others.
Editor
Can add, edit and delete own comment. Can view comments of others.
Reviewer
Can add, edit and delete own comment. Can view comments of others.
Administrator
Can view, add, edit and delete all comments.