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login, user-groups added at-glance changed

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# 1 DAISY at a Glance
This section contains a brief description of DAISY functions listed in the application's menu bar (image below) and some tips how to effectively familiarise with DAISY application.
DAISY is a tool that assists GDPR compliance by keeping a register of personal data used in research. DAISY's application menu Bar lists the main functions provided.
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<span style="display:block; text-align:center">![Alt](../img/menubar.png "DAISY Menu bar"){:width="800px"}<br/><small>DAISY Menu bar</small></span>
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![Alt](../img/menubar.png "DAISY Menubar")
<center>DAISY Menubar</center>
* [_Datasets Management_](#4-dataset-management) module allows for the recording of personal data held by the institution. The dataset may or may not fall in the context of a particular project. DAISY allows datasets to be defined in a granular way; where - if desired - each data subset, called a *data declaration*, can be listed individually. These declarations may list data from a particular partner, data of a particular cohort or data of a particular type.
* _Project Management_ module allows for the recording of research activities as projects. Documenting projects is critical for GDPR compliance as projects constitute the purpose and the context of use of personal data. Any document supporting the legal and ethical basis for data use can be stored in DAISY. Examples are ethics approvals, consent configurations, or subject information sheets.
* _Dataset Management_ module allows for the recording of personal data held by the institution. The dataset may or may not fall in the context of a particular project. DAISY allows Datasets to be defined in a granular way; where - if desired - each data subset, called a data declaration, can be listed individually. These declarations may list data from a particular partner, data of a particular cohort or data of a particular type.
* _Contract Management_ module allows the recording and storage of legal contracts of various types that have been signed with partner institutes or suppliers. Consortium agreements, data sharing agreements, material transfer agreements are examples of contracts. For GDPR compliance contracts become useful when documenting the source of datasets received or the target datasets transferred.
* _Definitions Management_. DAISY comes pre-packed with default lookup lists; these can be changed during application deployment. Lookup lists are used when defining contracts, projects or datasets. The definitions module of the DAISY application allows the management of dynamic lookup lists, specifically those of cohorts, partner institutes and contact persons.
* [_Projects Management_](#3-project-management) module allows for the recording of research activities as projects. Documenting projects is critical for GDPR compliance as projects constitute the purpose and the context of use of the personal data.
Any document supporting the legal and ethical basis for data use can be stored in DAISY (e.g. ethics approvals, consent configurations or subject information sheets).
The dependencies between DAISY modules is given below. There are no hard dependencies between the Projects, Contracts and Datasets modules. In principle you may start using any of these modules once DAISY is deployed with pre-packed definitions.
* [_Contracts Management_](#5-contract-management) module allows for the recording and storage of legal contracts of various types that have been signed with partner institutes or suppliers. Consortium agreements, data sharing agreements, material transfer agreements are the examples of the contracts.
<!-- For GDPR compliance the contracts become useful when documenting the source of received datasets or the target datasets transferred. -->
For GDPR compliance the contracts become useful in case of documenting the received datasets source or transferred datasets target.
![Alt](../img/dependencies.png "DAISY module dependencies")
<center>DAISY module dependencies</center>
* [_Definitions Management_](#6-definitions-management) - DAISY comes pre-packed with the default lookup lists; these can be changed during the application deployment. Lookup lists are used when defining the contracts, projects or datasets. The definitions module of the DAISY application allows on the management of dynamic lookup lists, specifically those of the cohorts, partner institutes and contact persons.
<mark>Our suggestion to first-time users is the following</mark>:
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1. Familiarise yourself with DAISY's interface conventions by reading the [relevant section of this guide](#DIC).
2. Login to DAISY with a user that has Administrator or VIP privileges. E.g. In the demo deployment the _admin_ user has Administrator privileges and _alice.white_ has VIP privileges.
3. Use Project Management to [create a project](#PM1).
4. Use Dataset Management to [create a dataset](#PM21) within the defined project.
<mark>Our suggestion to the first-time users:</mark>
1. Familiarise yourself with DAISY's layout by reading the next section [Interface Conventions](#2-daisy-interface-conventions).
2. Login to DAISY as standard user and VIP user on your DAISY instance.
3. Use Project Management to [create a project](#31-create-new-project).
4. Use Dataset Management to [create a dataset]({{ "/manual/project_management_details/#321-add-project-dataset" | relative_url }}) within the defined project.
<!-- 1. Familiarise yourself with DAISY's interface conventions by reading the [relevant section of this guide](#DIC). -->
<!-- 2. Login to DAISY with a user that has Administrator or VIP privileges. E.g. In the demo deployment the _admin_ user has Administrator privileges and _alice.white_ has VIP privileges. -->
<!-- 3. Use Project Management to [create a project](#PM1). -->
<!-- 4. Use Dataset Management to [create a dataset](#PM21) within the defined project. -->
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<div style="text-align: right;"> <a href="#top">Back to top</a> </div>
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---
<div style="text-align: right"> <strong><a href="#top">Back to top</a></strong></div>
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---
layout: page
title: User guide
permalink: /manual/
order: 2
---
# <a name="top"></a>DAISY User Guide
{:.no_toc}
This howto-card is the user guide for the Data Information System (DAISY). If it is your first time with the guide then start with Section **DAISY at a Glance**.
Welcome to the user guide for the DAta Information SYstem (DAISY). DAISY is a tool that assists GDPR compliance by keeping a register of personal data used in research.
<!-- If it is your first time with the guide, start with [DAISY at a Glance](#1-daisy-at-a-glance) section. -->
If it is your first time with the guide, it is recommended to start with:
1. How to [login](#login-to-daisy)?
2. Find out what are [the users groups](#what-are-the-users-groups).
3. Read [DAISY at a Glance](#1-daisy-at-a-glance) section.
---
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**Table of content**
* TOC
{:toc}
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{% include_relative user_login.md %}
{% include_relative users_group.md %}
{% include_relative at_a_glance.md %}
{% include_relative interface_conventions.md %}
{% include_relative project_management.md %}
......@@ -34,4 +51,3 @@ This howto-card is the user guide for the Data Information System (DAISY). If it
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-->
# Login to DAISY
Upon successful installation of DAISY, go to the web address
`https://${IP_ADDRESS_OR_NAME_OF_DEPLOYMENT_SERVER}`, where you should display the login page.
<!-- If you are University of Luxembourg staff you can go to [https://daisy.lcsb.uni.lu/](https://daisy.lcsb.uni.lu/). -->
<!-- You can also check [DAISY demo deployment](https://daisy-demo.elixir-luxembourg.org/). -->
Based on the authentication configuration made for your deployment, you may log in by:
* the user definitions in an existing LDAP directory, e.g. institutional/uni credentials.
* the user definitions maintained within the DAISY database.
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<span style="display:block;text-align:center">![Alt]({{ "img/login.png" | relative_url }}){:width="800px"}<br/><small>DAISY Login Page</small></span>
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After successful login, you see DAISY home page.
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<span style="display:block;text-align:center">![Alt]({{ "img/after_login.png" | relative_url }}){:width="800px"}<br/><small>DAISY Home Page</small></span>
---
<div style="text-align: right"> <strong><a href="#top">Back to top</a></strong></div>
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# What are the users groups?
DAISY provides various types of users accounts with assigned different sets of users actions. Generally, any user can view DAISY records and create a project, thus become the project's *owner*. The owner is granted for managing the project. If *standard user* is appointed as project's *local custodian*, his privileges become equal to project's owner - thus he can manage the project too. Standard user by default is not allowed to access the documents attachments.
The extension of standard user is *VIP user*. By default, if VIP user is project's owner or local custodian, he is granted for project's administrator, thus can manage users access/permissions for the project. Moreover, VIP has access to view and manage the documents attachments.
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Below we specified the users privileges:
<!-- This is the default role assigned to all users. All DAISY users can view all Dataset, Project, Contract and Definitions. The document attachments of records are excluded from this view permission. -->
- **Standard user**
The default role assigned to all users. All DAISY standard users can:
- view any *Dataset*, *Project*, *Contract* or *Definition* (further called *modules* or *records*). The documents attachments of the records are protected, thus excluded from the view permission.
- create any module.
- edit and delete any module the user has created.
- if user is assigned as *Local Custodian*, he is granted for the permissions to edit and delete the module.
- has no access to grant other users with the projects's permissions (even for the modules the user owns or is *Local Custodian*).
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- **VIP user**
This role is typically given to research principle investigators. VIP users have:
- all privileges (view, add, edit, remove) on the records they own, meaning the records where the user has been appointed as the *Local Custodian* or the projects he created.
- view and manage the protected documents attachments of modules he owns.
- grant other users with permissions on the datasets and projects he owns (VIP is the project's administrator).
NOTE: Being a local custodian or owner extends the users permissions in the similar way. For the standard user, it grants for edit and delete records. For VIP user to edit, delete records and project/dataset administration.
- **Legal user**
This role is given to users that will be managing *Contract* records. Legal personnel can:
- add, view, edit and remove any contract.
- grant the other users with an access for the contract.
- view all records in DAISY and manage their documents attachments.
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If you are legal user we suggest to read firstly [DAISY at a Glance](#1-daisy-at-a-glance) section and then [Contract Management](#5-contract-management) section.
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For more details go to section [Types of Users and Permissions]({{ "/manual/#7-types-of-users-and-permissions" | relative_url }}) (recommended for DAISY Administrator).
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