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.aspell.en.pws
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personal_ws-1.1 en 0 utf-8
Affero
AGPL
alice
Alper
Backend
backend
backends
Biomedicine
Christophe
DAISY’s
DAta
Dataset
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datasets
Datasets
datatypes
Ded
DOI
du
GDPR
GigaScience
github
giz
Grouès
howto
Jacek
Jarosz
jekyll
Kavita
lcsb
LCSB's
LDAP
Lebioda
LuxPARK
Menubar
Pinar
pre
projects’s
Rege
Reinhard
repo
Sandrine
Satagopam
STDOUT
Storages
SYSCID
SYstem
TBC
Trefois
Université
unlinked
Venkata
Vilem
vip
Yohan
YYYY
Quickstart
.gitlab-ci.yml
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# In case something goes horribly wrong, you can fall back to `image: ruby:latest`
image: git-r3lab.uni.lu:4567/r3/docker/jekyll-lcsb:1.0
image: git-r3lab.uni.lu:4567/r3/docker/jekyll-lcsb:1.5
build:
stage: build
......
README.md 0 → 100644
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# Daisy documentation
## How to get started
1. clone the repository
2. install dependencies using bundler
```bash
bundle install --path vendor/bundle
```
1. run server locally
```bash
bundle exec jekyll server
```
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index.md
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# DAISY - introduction
DAta Information SYstem is an open-source web application that allows biomedical research institutions to map their data and data flows in accordance with General Data Protection Regulation (GDPR) requirements.
DAISY is a commercial tool, created in response to the novel principle - *accountability*, introduced by the GDPR in May 2018. Accountability requires the demonstration of the compliance with all data protection principles and moreover, to record all data processing. DAISY fulfils GDPR requirements effectively, what we observe by analysing the transparency and record-keeping obligations of each GDPR principle. DAISY as well enhances the collaboration between partners and allows the institutions to create their GDPR data registers. DAISY is a tool tailored specifically for the biomedical research, supporting their complex data flows and tagging projects with controlled vocabulary terms to denote the study features.
DAISY is a tool, created in response to the novel principle - *accountability*, introduced by the GDPR in May 2018. Accountability requires the demonstration of the compliance with all data protection principles and moreover, to record all data processing. DAISY fulfils GDPR requirements effectively, what we observe by analysing the transparency and record-keeping obligations of each GDPR principle. DAISY as well enhances the collaboration between partners and allows the institutions to create their GDPR data registers. DAISY is a tool tailored specifically for the biomedical research, supporting their complex data flows and tagging projects with controlled vocabulary terms to denote the study features.
The application is available as a free and open source tool on [Github](https://github.com/elixir-luxembourg/daisy/) and the issue tracker is open to everyone.
DAISY is actively being used at the [Luxembourg Centre for Systems Biomedicine](https://wwwen.uni.lu/lcsb) and the [ELIXIR-Luxembourg](https://elixir-luxembourg.org) data hub.
## Upcoming events
<a style="color: red"> Online workshop </a>
__Best practices in research data management and stewardship__
[(click here for more details)](https://elixir-luxembourg.org/events/2020_01_27_research_data_management)
start: 19th May 2020
## License
DAISY is licensed under [GNU Affero General Public License v3.0 (AGPL 3.0)](https://www.gnu.org/licenses/agpl-3.0.en.html).
......
manual/contract_management.md deleted 100644 → 0
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<a name="CM"></a>
# 5 Contract Management
The Contract Management module allows recording legal documents signed in the context of research activities. Contracts are typically linked to Projects and provide the necessary traceability for the GDPR compliant provision and transfer of data.
<a name="CM1"></a>
## 5.1 Create New Contract
<mark>In order to create a new contract</mark>:
1. Click Contracts from the Menu Bar.<br />
![Alt](../img/contract_menubar.png)
2. Click the add button from the Contract Search Page.<br />
![Alt](../img/add_button.png)
3. You will see an empty Contract Form. The _Project_ field is optional, meanwhile, in practice most contracts are signed in the context of a research project. In the _Roles_ field, you are expected to select one or more GDPR role that identifies your institutions roles as described in the Contract. In the _Other comments_ section you may describe the nature of the document or if the document has an ID/REF e.g. from a document management system, you may put it in. Just like projects and datasets, when creating contracts you are expected to provide a local responsible in the _Local Custodians_ field. As stated before, one of the Local Custodians must be a user with VIP Privileges. E.g. in the demo deployment _alice.white_ is a research principle investigator and is a VIP user.<br />
![Alt](../img/contract_add_form.png)
4. Click SUBMIT. Once you successfully save the form, you will be taken to the newly created contract's details page, as seen below.<br />
![Alt](../img/contract_created.png)
<a name="CM2"></a>
## 5.2 Manage Contract Details
After initial creation the contract will be in a skeletal form and would need further input on its signatories and document attachments.
### 5.2.1 Manage Contract Partners (Signatories)
Contracts have multiple signatories. These can be managed via the **Partners (Signatories)** detail box.
1. Click the plus button on the **Partners (Signatories)** details box, as seen below.<br />
![Alt](../img/contract_add_partner.png)
2. You will see the **Partner and role** addition form. In this form, you will be asked to select the _Partner_ as well as the GDPR _Roles_ that this partner assumes in the contract. You can select more than one role. It is also mandatory to provide a contact person that is with the selected partner institute. You can either select from the list or you can add a new contact if it does not already exist.
![Alt](../img/contract_add_partner_form.png)
3. Once you fill in the information and click SUBMIT the partner will be added to the list of signatories, as seen below. Partners can be removed from a contract by clicking on the trash icon that will appear when hovering over the items in the **Partner and role detail box**.<br />
![Alt](../img/project_ref_user_search.png)
### 5.2.2 Manage Contract Documents
You may attach PDF, word documents, scans, via the **Documents** detail box. Document management is common throughout DAISY modules. It is described [here](#PM25).
<br />
<br />
<br />
<div style="text-align: right;"> <a href="#top">Back to top</a> </div>
<br />
<br />
<br />
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---
layout: page
title: Contract management details
permalink: /manual/contract_management_details/
order: -1
---
<small>
[User guide]({{ "/manual/" | relative_url }}) &raquo; [*Contracts (**GO BACK to main page**)*]({{ "/manual/#23-contracts" | relative_url }})
</small>
---
<br/>
{:.no_toc}
* TOC
{:toc}
---
<br/>
# 5 Contract Management
The *Contract Management* module allows recording legal documents signed in the context of research activities. Contracts are typically linked to *Projects* and provide the necessary traceability for the GDPR compliant provision and transfer of data.
## 5.1 Create New Contract
<mark>In order to create a new contract:</mark>
1. Click Contracts from the Menu Bar.<br />
<span style="display:block;text-align:center">![Alt]({{ "img/contract_menubar.png" | relative_url }}){:width="800px"}</span>
2. Click the add button from the Contract Search Page.<br />
<span style="display:block;text-align:left">![Alt]({{ "img/add_button.png" | relative_url }}){:width="100px"}</span>
3. You will see an empty Contract Form. The *Project* field is optional, meanwhile, in practice most contracts are signed in the context of a research project. In the *Roles* field, you are expected to select one or more GDPR role that identifies your institutions roles as described in the Contract. The roles are: *Controller*, *Joint Controller* and *Processor* ([find out more about the GDPR roles](https://edps.europa.eu/sites/edp/files/publication/19-11-07_edps_guidelines_on_controller_processor_and_jc_reg_2018_1725_en.pdf)).
In the *Other comments* section you may describe the nature of the document or if the document has an ID/REF e.g. from a document management system, you may put it in. Just like projects and datasets, when creating contracts you are expected to provide a local responsible in the *Local Custodians* field. As stated before, one of the Local Custodians must be a user with VIP Privileges.<br />
<span style="display:block;text-align:center">![Alt]({{ "img/contract_add_form.png" | relative_url }}){:width="800px"}</span>
1. Click SUBMIT. Once you successfully save the form, you will be taken to the newly created
contract's details page, as seen below.<br />
<span style="display:block;text-align:center">![Alt]({{ "img/contract_created.png" | relative_url }}){:width="800px"}</span>
## 5.2 Manage Contract Details
After initial creation the contract will be in a skeletal form and would need further input on its signatories and document attachments. As per above image, you can add following contract details:
- Participants
Contracts have multiple signatories. These can be managed via the *Partners (Signatories)* detail box.
1. Click the plus button on the *Partners (Signatories)* details box, as seen below.<br />
<span style="display:block;text-align:center">![Alt]({{ "img/contract_add_partner.png" | relative_url }}){:width="800px"}</span>
2. You will see the *Partner and role* addition form. In this form, you will be asked to select the _Partner_ as well as the GDPR _Roles_ that this partner assumes in the contract. You can select more than one role. It is also mandatory to provide a contact person that is with the selected partner institute. You can either select from the list or you can add a new contact if it does not already exist.
<span style="display:block;text-align:center">![Alt]({{ "img/contract_add_partner_form.png" | relative_url }}){:width="800px"}</span>
3. Once you fill in the information and click SUBMIT the partner will be added to the list of signatories, as seen below. Partners can be removed from a contract by clicking on the trash icon that will appear when hovering over the items in the *Partner and role detail box*.<br />
<span style="display:block;text-align:left">![Alt]({{ "img/contract_add_partner_result.png" | relative_url }}){:width="800px"}</span>
- Documents
You may attach PDF, word documents, scans, via the *Documents* detail box. Document management is common throughout DAISY modules. More details in section [Manage Project Documentation]({{ "/manual/project_management_details/#325-manage-project-documentation" | relative_url }})).
---
<div style="text-align: right"> <strong><a href="#top">Back to top</a></strong></div>
<br>
manual/daisy.md
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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.
---
<br>
**Table of content**
<br/>
* TOC
{:toc}
<br>
{% 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 %}
{% include_relative dataset_management.md %}
{% include_relative contract_management.md %}
{% include_relative definitions_management.md %}
{% include_relative user_management.md %}
<!--- Below fragment is needed for TOC in iAWriter PDF export
<br/>
{{TOC}}
/at_a_glance.md "DAISY at a glance"
/interface_conventions.md "Interface Conventions"
/project_management.md "Project Management"
/dataset_management.md "Dataset Management"
/contract_management.md "Contract Management"
/definitions_management.md "Definitions Management"
/user_management.md "User and Permission Management"
{% include_relative quickstart.md %}
{% include_relative users_modules.md %}
+++
-->
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<a name="DM"></a>
# 4 Dataset Management
<a name="DM1"></a>
## 4.1 Create New Dataset
In order to create a new Dataset:
1. Click Datasets from the Menu Bar.<br />
![Alt](../img/dataset_menubar.png)
2. Click the add button from the Dataset Search Page.<br />
![Alt](../img/add_button.png)
3. You will see the **Dataset Creation Quick Form**<br />
![Alt](../img/dataset_quick_form.png)
4. Click SUBMIT. Once you successfully save the form, you will be taken to the newly created dataset's details page, as seen below. <br />
![Alt](../img/dataset_details.png)
<a name="DM2"></a>
## 4.2 Declare Data within the Dataset
After initial creation the dataset will be in a skeletal form. The dataset needs to be fleshed out with further information on the characteristics of the data it contains. We do this by creating **data declarations** within the dataset, by following these steps.
1. Click the plus button on the **Data declarations** details box.<br />
![Alt](../img/datadec_empty.png)
2. You will see the **Data declaration Creation Quick Form** as below. With the **Data declaration Creation Quick Form** you are asked for a **Title** for the declaration and denote where the data was **Obtained from** by selecting one of three options. For the **Title** one can use the same title you used earlier when creating the dataset. However, if you're going to have multiple declarations within a dataset you can give them names based on their source or their type (e.g. Helsinki Cohort, Parkinson Study-2, LuxPARK PARK2 Cell lines etc). It is important that the **Title** is a name that is familiar to you and your research group as it will be used in free text search over datasets. The options for the **Obtained from** field is described in detail [in the remainder of this section](#DDEC_OPTIONS). <br />
![Alt](../img/datadec_quick_form.png)
3. Click SUBMIT. The data declaration will be created you will be taken to the **Data Declaration Editor Page**.
Before we describe the details of data declaration editing we will discuss the three different options for specifying the origin of data in DAISY.
<a name="DDEC_OPTIONS"></a> <mark>The <strong>Obtained from</strong> field captures important information, but, for the first-time users of DAISY it can be difficult to populate. Your choice among the three options will determine if and how your dataset will be linked to other entities in DAISY. If you are a first-time user and you're creating records for learning purposes, we suggest that you choose the option "Other" for simplicity.</mark>
<span>&#9675; </span><mark><strong>From existing data/samples:</strong></mark> When you state that the data is obtained from existing data/samples in your institution, DAISY will prompt you (as below) to search for and choose the data record which is the origin for your current declaration.
![Alt](../img/datadec_from_existing.png)
You will be provided a searchable selection box, through which you can find existing data records by their Project, by responsible PI or by their title. As you will be making a selection from existing records, with this option, it is necessary that origin data had been entered into DAISY earlier.
By choosing the **from existing data/samples:** you will link the newly created data declaration to an existing data declaration in daisy, as depicted below.
![Alt](../img/from_existing_topology.png)
<span>&#9675;</span><mark><strong>Newly incoming data/samples:</strong></mark> When you select this option, it means you are obtaining data from a collaborator institute or from a repository and this data is being recorded for the first time in DAISY. With this option DAISY will first ask you to select a partner (institutes and repositories are both in the partner list). Once you select a partner DAISY will then list all those contracts that are in the system involving this partner and that have local custodians overlapping with the custodians of the dataset you're detailing. If there are no such contracts or if none of the existing contracts foresee the receipt of this data, then you have to option to create an empty contract. You can later on provide the details and documentation for this empty contract. It is possible that in some DAISY deployments the _Contract Management_ module, in that case the empty contract acts as a link to the source partner for the data.
![Alt](../img/datadec_newly_incoming.png)
When the **newly incoming data/samples** option is chose, DAISY will link the newly created data declaration to a Contract and and associated Partner(s), as depicted below.
![Alt](../img/newly_incoming_topology.png)
<span>&#9675;</span><mark><strong>Other:</strong></mark> When you select this option, it means you do not want to create any structured DAISY records to denote the origin of data being declared. DAISY will prompt you to provide a free-text description of the origin of data as seen below.
![Alt](../img/datadec_other.png)
Data declared with the **Other** option will not have links to any other records as to its origin.
![Alt](../img/other_topology.png)
After selecting any one of the options and creating the data declaration, you will be taken back to the Dataset Details Page. You can see the newly added declaration listed in the **Data Declarations** detail box. This box also provides action buttons for editing, deleting, and cloning data declarations, as seen below.
![Alt](../img/datadec_added.png)
Once created you're advised to edit the declaration to provide further information about the data. Data declarations have several fields in addition to the title and origin supplied during their creation.
![Alt](../img/datadec_edit_1.png)
## 4.3 Manage Dataset Locations
As per GDPR, the storage of personal data is considered as a``data processing'' and needs tone recorded. The **Storage Locations detail box** allows you to do this. In order to record a new storage location:
1. click the plus button on the **Storage Locations** detail box depicted below. <br />
![Alt](../img/dataset_add_location.png)
2. You will see the location creation form asking you for the _Storage Backend_ and the _Nature of data copy_ the _Stored datatypes_ (optional) and _Location of the data_ for the paper. The backends box will list storage platforms for your institution, you need to select one and in the location box you're expected to provide information on where the data can be found on the selected platform. Please note that you are not expected to document individual files. E.g. it is good practice to record the top level folder in which a certain dataset exists. The datatypes are optional and if you're not separately storing data subsets by type then there is no need to specify datatype information for a location.
![Alt](../img/dataset_add_location_form.png)
3. Click SUBMIT and the new location will be listed as below. Storage locations can be deleted by clicking on the trash icon that will appear when hovering over items in the **Storage Locations detail box**. <br />
![Alt](../img/dataset_remove_location.png)
## 4.4 Manage Dataset Accesses
As per GDPR, any access to personal data held in an institution needs to be recorded. The **Accesses detail box** allows you to do this. **IMPORTANT NOTE: Before recording access, make sure you have recorded storage locations of data.**
In order to add a new access record:
1. Click the plus button on the **Accesses** detail box depicted below.<br />
![Alt](../img/dataset_add_access.png)
2. You will see the access creation form. Access is defined over a specific storage location, so you'd need to select one from the _Data Locations_ list. In addition you'd need to document the access control policy in the _Remarks_ section. If access is time-limited you may specify the start and end dates for its validity. By default all accesses recorded will fall under the scope of the project, which owns the dataset. It is also possible to record accesses, in the scope of other projects, to do so you must select one from the _Project_ list. We discuss access across projects later in this section.<br />
![Alt](../img/dataset_add_access_form.png)
3. Click SUBMIT and the new access will be recorded and listed on the dataset's page as below. Accesses can be deleted by clicking on the trash icon that will appear when hovering over items in the **Accesses detail box**. <br />
![Alt](../img/dataset_remove_access.png)
As discussed above, when data of one project is being access in the context of another project, this can be specified by in the access creation form by selecting a Project (see below left). When you create access records in this way, the dataset will be linked to the project accessing it. This dataset will be listed in the **Data used from other projects** detail box (see below right).
![Alt](../img/dataset_access_other_project.png)
<br />
<br />
<br />
<div style="text-align: right;"> <a href="#top">Back to top</a> </div>
<br />
<br />
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---
layout: page
title: Dataset management details
permalink: /manual/dataset_management_details/
order: -1
---
<small>
[User guide]({{ "/manual/" | relative_url }}) &raquo; [*Datasets (**GO BACK to main page**)*]({{ "/manual/#22-datasets" | relative_url }})
</small>
---
<br/>
{:.no_toc}
* TOC
{:toc}
---
# 4 Dataset Management
## 4.1 Create New Dataset
<mark>In order to create a new Dataset:</mark>
1. Click Datasets from the Menu Bar.<br />
<span style="display:block;text-align:center">![Alt]({{ "img/dataset_menubar.png" | relative_url }}){:width="800px"}</span>
2. Click the add button (in the right bottom corner) from the *Dataset Search Page*.<br />
<span style="display:block;text-align:left">![Alt]({{ "img/add_button.png" | relative_url }}){:width="100px"}</span>
3. You will see the *Dataset Creation Quick Form*. Fill the fields and click SUBMIT. <br />
<span style="display:block;text-align:center">![Alt]({{ "img/dataset_quick_form.png" | relative_url }}){:width="800px"}</span><br />
4. Once you successfully save the form, you will be taken to the newly created dataset's details page, as seen below. <br />
<span style="display:block;text-align:center">![Alt]({{ "img/dataset_details.png" | relative_url }}){:width="800px"}</span>
<br>
## 4.2 Manage Dataset Details
Dataset entity details box are displayed in dataset page, where you can add, edit or remove following details:
- Data declarations
- Legal bases
- Storages
- Accesses
- Transfers
<span style="display:block;text-align:center">![Alt]({{ "img/dataset_entities.png" | relative_url }}){:width="800px"}<br/><small>Dataset's entities detail boxes</small></span>
<br/>
After initial creation the dataset will be in a skeletal form. The dataset needs to be fleshed out with further information on the characteristics of the data it contains.
## 4.2.1 Declare Data within the Dataset
<mark> To add new data declaration: </mark>
1. Click the plus button on the *Data declarations* details box.<br />
<span style="display:block;text-align:center">![Alt]({{ "img/datadec_empty.png" | relative_url }}){:width="700px"}</span>
2. You will see the *Data declaration Creation Quick Form* as below. With the *Data declaration Creation Quick Form* you are asked for a *Title* for the declaration and denote where the data was *Obtained from* by selecting one of three options. For the *Title* one can use the same title you used earlier when creating the dataset. However, if you're going to have multiple declarations within a dataset you can give them names based on their source or their type (e.g. Helsinki Cohort, Parkinson Study-2, LuxPARK PARK2 Cell lines etc). It is important that the *Title* is a name that is familiar to you and your research group as it will be used in free text search over datasets. The options for the *Obtained from* field is described in detail below.
<br>
<span style="display:block;text-align:center">![Alt]({{ "img/datadec_quick_form.png" | relative_url }}){:width="600px"}</span>
3. Click SUBMIT. The data declaration will be created and you will be taken to the *Data Declaration Editor Page*.
<br>
<big> **Obtained from** field</big>
This field captures important information, but, for the first-time users of DAISY it can be difficult to populate. Your choice among the three options will determine if and how your dataset will be linked to other entities in DAISY. If you are a first-time user and you are creating records for learning purposes, we suggest that you choose the option *Other* for simplicity.
- **From existing data/samples**
When you state that the data is obtained from existing data/samples in your institution, DAISY will prompt you (as below) to search for and choose the data record which is the origin for your current declaration.
<span style="display:block;text-align:center">![Alt]({{ "img/datadec_from_existing.png" | relative_url }}){:width="800px"}</span>
You will be provided a searchable selection box, through which you can find existing data records by their Project, by responsible PI or by their title. As you will be making a selection from existing records, with this option, it is necessary that origin data had been entered into DAISY earlier.
<br>
<br>
By choosing the **from existing data/samples:** you will link the newly created data declaration to an existing data declaration in daisy, as depicted below. <span style="display:block;text-align:center">![Alt]({{ "img/from_existing_topology.png" | relative_url }}){:width="800px"}</span>
<br>
- **Newly incoming data/samples**
When you select this option, it means you are obtaining data from a collaborator institute or from a repository and this data is being recorded for the first time in DAISY. With this option DAISY will first ask you to select a partner (institutes and repositories are both in the partner list). Once you select a partner DAISY will then list all those contracts that are in the system involving this partner and that have local custodians overlapping with the custodians of the dataset you're detailing. If there are no such contracts or if none of the existing contracts foresee the receipt of this data, then you have to option to create an empty contract. You can later on provide the details and documentation for this empty contract. In that case the empty contract acts as a link to the source partner for the data.
<span style="display:block;text-align:center">![Alt]({{ "img/datadec_newly_incoming.png" | relative_url }}){:width="800px"}</span>
<br>
<br>
When the **newly incoming data/samples** option is chose, DAISY will link the newly created data declaration to a Contract and and associated Partner(s), as depicted below.
<span style="display:block;text-align:center">![Alt]({{ "img/newly_incoming_topology.png" | relative_url }}){:width="800px"}</span>
- **Other**
When you select this option, it means you do not want to create any structured DAISY records to denote the origin of data being declared. DAISY will prompt you to provide a free-text description of the origin of data as seen below.
<span style="display:block;text-align:center">![Alt]({{ "img/datadec_other.png" | relative_url }}){:width="800px"}</span>
<br>
Data declared with the **Other** option will not have links to any other records as to its origin.
<span style="display:block;text-align:left">![Alt]({{ "img/other_topology.png" | relative_url }}){:width="200px"}</span>
<br>
After selecting any one of the options and creating the data declaration, you will be taken back to the *Dataset Details Page*. You can see the newly added declaration listed in the *Data Declarations* detail box. This box also provides action buttons for editing, deleting, and cloning data declarations, as seen below.
<span style="display:block;text-align:center">![Alt]({{ "img/datadec_added.png" | relative_url }}){:width="800px"}</span>
Once created you are advised to edit the declaration to provide further information about the data. Data declarations have a rich set of fields in addition to the title and origin supplied during their creation.
<span style="display:block;text-align:center">![Alt]({{ "img/datadec_edit_1.png" | relative_url }}){:width="800px"}</span>
<br>
---
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<br />
## 4.2.2 Manage Dataset Legal basis
GDPR outlines six legal basis under which data processing is legally permitted ([find out more about the Legal basis](https://gdpr-info.eu/art-6-gdpr/)).
<mark> To add new data legal bases: </mark>
1. Click the plus button on the Legal bases details box.
<span style="display:block;text-align:left">![Alt]({{ "img/dataset_add_legal_bases.png" | relative_url }}){:width="800px"}</span>
2. The *Legal base create form* will be displayed. Fill in the fields. The *Legal Bases* is mandatory and multiple choices field.
<span style="display:block;text-align:left">![Alt]({{ "img/dataset_add_legal_bases_form.png" | relative_url }}){:width="400px"}</span>
3. Click SUBMIT. In the *Dataset Search Page* you will see legal bases you have just added. It can be edited or deleted by clicking on the pencil/trash icons.
<span style="display:block;text-align:left">![Alt]({{ "img/dataset_add_legal_bases_result.png" | relative_url }}){:width="800px"}</span>
---
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<br />
## 4.2.3 Manage Dataset Storages
As per GDPR, the storage of personal data is considered as a `data processing` and needs tone recorded. The *Storages detail box* allows you to do this. In order to record a new storage location:
1. Click the plus button on the *Storages* detail box depicted below.
<span style="display:block;text-align:left">![Alt]({{ "img/dataset_add_location.png" | relative_url }}){:width="400px"}</span>
2. You will see the location creation form asking you for the *Storage back-end* and the *Nature of data copy* the *Stored datatypes* (optional) and *Location of the data* for the paper. The backend box will list storage platforms for your institution, you need to select one and in the location box you are expected to provide information on where the data can be found on the selected platform. Note that you are not expected to document the individual files. E.g. it is good practice to record the top level folder in which a certain dataset exists. The datatypes are optional and if you are not separately storing data subsets by type then there is no need to specify datatype information for a location.
<span style="display:block;text-align:left">![Alt]({{ "img/dataset_add_location_form.png" | relative_url }}){:width="600px"}</span>
3. Click SUBMIT and the new location will be listed as below. Storage locations can be edited or deleted by clicking on the pencil/trash icon in the *Storages detail box*. <br />
<span style="display:block;text-align:left">![Alt]({{ "img/dataset_remove_location.png" | relative_url }}){:width="400px"}</span>
<br>
---
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<br />
## 4.2.4 Manage Dataset Accesses
As per GDPR, any access to personal data held in an institution needs to be recorded. The *Accesses detail box* allows you to do this.
**IMPORTANT NOTE: Before recording access, make sure you have recorded storage locations of data.**
<mark>In order to add a new access record:</mark>
1. Click the plus button on the *Accesses* detail box depicted below.<br />
<span style="display:block;text-align:left">![Alt]({{ "img/dataset_add_access.png" | relative_url }}){:width="400px"}</span>
2. You will see the access creation form. Access is defined over a specific storage location, so you'd need to select one from the _Data Locations_ list. In addition you'd need to document the access control policy in the _Remarks_ section. If access is time-limited you may specify the start and end dates for its validity. By default all accesses recorded will fall under the scope of the project, which owns the dataset. It is also possible to record accesses, in the scope of other projects, to do so you must select one from the _Project_ list. We discuss access across projects later in this section.<br />
<span style="display:block;text-align:left">![Alt]({{ "img/dataset_add_access_form.png" | relative_url }}){:width="400px"}</span>
3. Click SUBMIT and the new access will be recorded and listed on the dataset's page as below. Accesses can be edited or deleted by clicking on the pencil/trash icons in the *Accesses detail box*. <br>
<span style="display:block;text-align:left">![Alt]({{ "img/dataset_remove_access.png" | relative_url }}){:width="400px"}</span>
<br>
As discussed above, when data of one project is being accessed in the context of another project, this can be specified in the access creation form by selecting a Project (see below left). When you create access records in this way, the dataset will be linked to the project accessing it. This dataset will be listed in the **Data used from other projects** detail box (see below right).
<span style="display:block;text-align:left">![Alt]({{ "img/dataset_access_other_project.png" | relative_url }}){:width="800px"}</span>
---
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<br />
## 4.2.5 Manage Dataset Transfers
*Transfers* holds information on datasets flow between project's parties and details on datasets access by external partners. Dataset can be transferred to the external partners or they can get access to view the datasets.
<mark> To add new data transfer: </mark>
1. Click the plus button on the Transfers details box.
<span style="display:block;text-align:left">![Alt]({{ "img/dataset_add_transfer.png" | relative_url }}){:width="800px"}</span>
2. The *Transfer create form* will be displayed. Fill in the fields. Note that *Partner* is a mandatory field.
<span style="display:block;text-align:left">![Alt]({{ "img/dataset_add_transfer_form.png" | relative_url }}){:width="400px"}</span>
3. Click SUBMIT. In the *Dataset Search Page* you will see the transfer you have just added. Transfers can be edited or deleted by clicking on the pencil/trash icons in the *Transfers detail box*.
<span style="display:block;text-align:left">![Alt]({{ "img/dataset_add_transfer_result.png" | relative_url }}){:width="800px"}</span>
---
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<br />
## **4.2.6 Appendix for VIP user**
By clicking *eye button* in the dataset overview box, VIP user can enter *Change permission* page.
The management of the dataset's access permissions is alike to project's permissions described in
[**3.2.7 VIP appendix**]({{ "/manual/project_management_details/#327-appendix-for-vip-users" | relative_url }}).
<!-- This section describes management of the dataset's access permissions. If VIP user (check [users groups here]({{ "manual/#what-are-the-users-groups" | relative_url }})) owns a dataset or is its Local Custodian, he can grant other users with permissions for the dataset.
By clicking *eye button* in the dataset overview box, VIP user can enter *Change permission* page.
<span style="display:block;text-align:center">![Alt]({{ "img/change_permissions_dataset.png" | relative_url }}){:width="800px"}</span>
#### Permissions
- **Admin**
Grant the right to change permissions on this dataset and grant all other permissions.
- **Edit**
Grant the right to edit this dataset.
- **Delete**
Grant the right to delete this dataset.
- **View**
Grant the right to view this dataset.
- **Protected**
Grant the right to access protected information on this dataset. -->
---
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<a name="DEF_M"></a>
# 6 Definitions Management
With the _Definitions_ module, DAISY allows the management of _Contacts, _Cohorts_ and _Partners_. All pages within _Definitions_ operate according to the interface conventions given in the [relevant section of this guide](#DIC). In the following sections we only discuss what information is held in these definitions.
<a name="COH_M"></a>
## 6.1 Cohorts Management
Cohort is a study that collects data and/or bio-samples from a group of participants (e.g. longitudinal case-control or family studies). A cohort is linked to the creation of data and is considered its ultimate source.
In order to effectively handle data subjects' requests, as per GDPR, it is crucial that an institution keeps track of what data it keeps from which cohorts. Inline with this, DAISY allows maintaining a list of _Cohorts_ and link _Datasets_ to _Cohorts_.
The information kept on cohorts can be seen in the associated _Editor Page_ seen below. Cohorts are expected to have a _Title_ unique to them, and they are linked to one or more _Cohort Owners_, which are that are Principle Investigators, Clinicians running the study. Cohorts owners are kept as _Contacts_ in DAISY. In order to maintain a controlled list of cohorts, the administrator for the DAISY deployment may assign an accession number to the _Cohort_, which would be the unique identifier for this Cohort. <br />
![Alt](../img/cohort_edit_form.png)
<a name="PAR_M"></a>
## 6.2 Partners Management
A _Partner_ is a research collaborator that is the source and/or recipient of human data. Partners are also legal entities with whom contracts are signed. Clinical entities that run longitudinal cohorts, research institutes, or data hubs are all examples of Partners.
In accordance, when maintaining _Dataset_ source info, _Dataset_ transfer info or when creating _Contract_ records, you will be asked to select Partners.
The information kept on partners can be seen in the associated _Editor Page_ seen below. <br />
![Alt](../img/partner_edit_form.png)
<a name="CONN_M"></a>
## 6.3 Contacts Management
DAISY allows keeping an address book of all contact persons related to the _Projects_, _Datasets_, _Cohorts_ and _Contracts_.
The information kept on contacts is pretty standard as can be seen in the associated _Editor Page_ given below. <br />
![Alt](../img/contact_edit_form.png)
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---
layout: page
title: Definitions management details
permalink: /manual/definitions_management_details/
order: -1
---
<small>
[User guide]({{ "/manual/" | relative_url }}) &raquo; [*Definitions (**GO BACK to main page**)*]({{ "/manual/#24-definitions" | relative_url }})
</small>
---
<br>
# 6 Definitions Management
{:.no_toc}
* TOC
{:toc}
---
<br>
DAISY *Definitions* module allows for the management of *Contacts*, *Cohorts* and *Partners*.
<!-- <a name="COH_M"></a> -->
## 6.1 Cohorts
Cohort is a study that collects data and/or bio-samples from a group of participants (e.g. longitudinal case-control or family studies). A cohort is linked to the creation of data and is considered its ultimate source.
In order to effectively handle data subjects' requests, as per GDPR, it is crucial that an institution keeps track of what data it keeps from which cohorts. Inline with this, DAISY allows maintaining a list of *Cohorts* and link *Datasets* to *Cohorts*.
The information kept on cohorts can be seen in the associated *Editor Page* seen below. Cohorts are expected to have a *Title* unique to them, and they are linked to one or more *Cohort Owners*, which are that are Principle Investigators, Clinicians running the study. Cohorts owners are kept as *Contacts* in DAISY. In order to maintain a controlled list of cohorts, the administrator for the DAISY deployment may assign an accession number to the *Cohort*, which would be the unique identifier for this Cohort. <br />
<span style="display:block;text-align:center">![Alt]({{ "img/cohort_edit_form.png" | relative_url }}){:width="800px"}</span>
<!-- <a name="PAR_M"></a> -->
## 6.2 Partners
A *Partner* is a research collaborator that is the source and/or recipient of human data. Partners are also legal entities with whom contracts are signed. Clinical entities that run longitudinal cohorts, research institutes, or data hubs are all examples of Partners.
In accordance, when maintaining *Data Declaration's* data source, *Dataset* transfer or when creating *Contract* records, you will be asked to select Partners.
The information kept on partners can be seen in the associated *Editor Page* seen below.
<br />
<span style="display:block;text-align:center">![Alt]({{ "img/partner_edit_form.png" | relative_url }}){:width="800px"}</span>
<!-- <a name="CONN_M"></a> -->
## 6.3 Contacts
*Contacts* are people affiliated with the external partner institutions (e.g. collaborator principle investigators, project officers at the EU).
DAISY keeps the contact details (e.g email address, affiliations) of external collaborators related to the *Projects*, *Datasets*, *Cohorts* and *Contracts*.
Standard information is kept on contacts as can be seen in the associated *Editor Page* given below.
<br />
<span style="display:block;text-align:center">![Alt]({{ "img/contact_edit_form.png" | relative_url }}){:width="800px"}</span>
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manual/interface_conventions.md
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<a name="DIC"></a>
<!-- <a name="DIC"></a> -->
# 2 DAISY Interface Conventions
<!-- This section has three paragraphs. -->
The main view of each DAISY module is called [Search Page](#21-search-pages), where you choose entity you are interested in (or create a new module). You can inspect a particular entity details in [Entity Details Pages](#22-entity-details-pages) and edit them in [Entity Editor Pages](#23-entity-editor-pages).
<a name="SP"></a>
<!-- <a name="SP"></a> -->
## 2.1 Search Pages
DAISY provides search pages for all entities manageable via modules. Currently these modules are: *Datasets*, *Projects*, *Contracts* and under *Definitions*: *Cohorts*, *Partners*, *Contacts*. All search pages have similar layout and operational conventions. Search pages are also the only entry point for the functions in a module. When you select a module from the menu bar, you will be taken to the search page for the entity managed by that module.
As an example, the screenshot of the search page for Projects is given below.
Each search page is headed with the help text containing a brief description. On the left hand side of the page there are search facets and on the right - the search results are displayed.
DAISY provides search pages for all entities manageable via modules. Currently these are: _Projects, Contracts, Datasets_, and, under definitions, _Partners, Cohorts, Contacts_. All search pages have similar layout and operational conventions. Search pages are also the only entry point for the functions in a module. When you select a module from the menu bar, you will be taken to the search page for the entity managed by that module.
<span style="display:block; text-align:center">![Alt](../img/search_page.png "Search Page for Projects"){:width="900px"}<br/><small>Search page for Projects</small></span>
<br>
A screenshot of the search page for Projects is given below.
Each search page is headed with _help text search facets on the left hand side and search results on the right hand side.
By default, all entities (in our example - projects) will be listed on the search page. The list can be filtered by either selecting one or more facet from the left hand side or by typing in a keyword into the search box. Note that currently **DAISY search does not support partial matching**. Instead, the entire keyword will be matched in a case insensitive manner.
![Alt](../img/search_page.png)
<center>Search Page for Projects</center>
On the top right section of search results a few attributes are listed. Clicking on these attributes repeatedly will respectively (1) enable the ordering; (2) change order to ascending/descending; (3) disable ordering for the clicked attribute.
By default, all entities - in our example, all projects- will be listed on the search page. The list can be filtered by either selecting one or more facet from the left hand side or by typing in a keyword into the search box. Currently DAISY search does not support partial matching; instead the entire keyword will be matched in a case insensitive manner.
Each entity listed in the search results is displayed in a shaded box, containing few of its attributes. In our example these are the project's name and the number of publications. Each result box will also contain a *DETAILS* link, through which you can go to the [Entity Details Page](#22-entity-details-pages).
On the top right section of search results a few attributes will be listed. Clicking on these attributes repeatedly will respectively (1) enable the ordering either (2) change order to ascending/descending (3) disable ordering for the clicked attribute.
Depending on the permissions associated with your user type, you may see a **add button (denoted with a plus sign)** at the bottom right section of the search page. You can add a new entity by clicking the plus button, which will open up an empty editor form for you to fill in.
Each entity listed in the search results will be displayed in a shaded box are listing few of attributes; in our example the project's name and number of publications are listed. Each result box will also contain a "DETAILS" link, through which you can go to the [Entity Details Page](#EDP).
Depending on the permissions associated with your user type, you may see a **add button (denoted with a plus sign)** at the bottom right section of the search page. You can add a new entity by clicking the plus button, which will open up an empty editor form for you to fill in.
<a name="EDP"></a>
<br>
<!-- <a name="EDP"></a> -->
## 2.2 Entity Details Pages
Clicking the *DETAILS* button in the search result box takes you to *Details Page*, which contains the information about the chosen entity. An example of details page for *Project* named 'SYSCID' is given below.
Information about a single entity is provided through a Details Page. As example page for a _Project_ named ``SYSCID'' is given below.
<span style="display:block; text-align:center">![Alt](../img/details_page.png "Details page of a Project in DAISY"){:width="900px"}<br/><small>Details page of a Project in DAISY</small></span>
<br>
![Alt](../img/details_page.png)
<center>Details page of a Project in DAISY</center>
You may end up on an *Entity Details Page* through:
* the *DETAILS* link of a search results in a search page.
* the links on details pages of other (linked) entities in DAISY.
You may end up on an Entity Details Page in two primary ways. (1) Through the ``DETAILS'' link of a search results in a search page (2) Through links on details pages of other (linked) entities in DAISY.
Each Details Page is headed with an **entity overview box** listing some of the entity's attributes (e.g. local custodians, start date) and allows to modify the entity. Depending on users permissions (see [users groups](#what-are-the-users-groups)) in the right bottom corner of the overview box you may see:
* permissions button (denoted with an eye icon),
* edit entity button (denoted with a pencil icon),
* remove entity button (denoted with a bin icon).
Each Details Page is headed with an **overview box) listing some of the entity's attributes. Depending on the permissions associated with your user type, you may see an **edit entity button (denoted with a pencil icon)** and an **permissions button (denoted with an eye icon)**. These will take you to the Entity Editor Page and the Permissions Management Page respectively.
<!-- Each Details Page is headed with an overview box) listing some of the entity’s attributes. Depending on the permissions associated with your user type, you may see an **edit entity button (denoted with a pencil icon) and an permissions button (denoted with an eye icon). These will take you to the Entity Editor Page and the Permissions Management Page respectively. -->
Beneath the overview box several information boxes will be listed displaying further details of the entity.
If you have edit permissions for the entity, then at the top right corner of some detail boxes you will see an **add detail button (denoted with a plus sign)**. Via this button you can do the following:
Beneath the entity overview box there are several information boxes, which display the further details of the entity (e.g. personnel, ethics).
If you have edit permissions for the entity, then at the top right corner of particular detail boxes you will see an **add detail button (denoted with a plus sign)**. Via this button you can do the following:
* create links to other entities e.g. link contacts with projects.
* create (inline) detail records to the current entity e.g. one or more publications to a project.
<a name="EEP"></a>
<br>
<!-- <a name="EEP"></a> -->
## 2.3 Entity Editor Pages
When you click the edit button on the Details Page of an entity, you will be taken to the Editor Page containing a form for entity update. An example of **editor form** is given below.
<span style="display:block; text-align:center">![Alt](../img/editor_form.png "Editor page of a Project"){:width="900px"}<br/><small>Editor page of a Project</small></span>
<br>
When you click the edit button on the Details Page of an entity, you will be taken to the Editor Page containing a form for entity update. An example is given below.
![Alt](../img/editor_form.png)
<center>Editor page of a Project</center>
Each field in the form is be listed with a **name**, a **value** and a **help text**. Names of the fields that are required to have a value, are marked with a red asterisk (e.g. Title).
Each field in the form will be listed with a **Name**, a **Value** and a **Help text**. Names of fields that are required to have a value will end with a red asterisk.
Editor forms can be saved by pressing **SUBMIT** button at the bottom of the page. The forms will be validated upon the submission. If the validation fails for one or more fields, these will be highlighted with inline validation error message, illustrated below.
Editor forms can be saved by pressing the **SUBMIT** button found at the bottom of the page. Forms will be validated upon submission. If validation fails for one or more fields, these will be highlighted with inline validation _ERROR_ messages, illustrated below.
<!-- ![Alt](../img/validation_error.png)
<center>Field validation error</center> -->
![Alt](../img/validation_error.png)
<center>Field validation error</center>
<span style="display:block; text-align:center">![Alt](../img/validation_error.png "Field validation error"){:width="800px"}<br/><small>Field validation error message</small></span>
<br>
Upon successful save of a form, you will be returned to the entity details page. DAISY may give **SUCCESS** and/or **WARNING** messages upon form save; these will be displayed at the top of the page, as illustrated below.
Upon successful submission of a form, you will be returned to the Entity Details page.
DAISY may give success and/or warning messages upon the form submission; these will be displayed at the top of the page, as illustrated below.
![Alt](../img/page_messages.png)
<center>Message display in DAISY</center>
<!-- ![Alt](../img/page_messages.png) -->
<!-- <center>Message display in DAISY</center> -->
<br>
<span style="display:block; text-align:center">![Alt](../img/page_messages.png "Message display in DAISY"){:width="800px"}<br/><small>Status message displayed in DAISY</small></span>
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<!-- <a name="PM"></a> -->
# 3 Project Management
This section describes how to add a new project. Adding a project is available for standard user and VIP user.
<!-- <a name="PM1"></a> -->
## 3.1 Create New Project
<!-- <mark>In order to create a new project</mark>: -->
In order to create a new project:
1. Click Projects from the Menu Bar to enter Project Search Page.<br />
<span style="display:block; text-align:center">![Alt](../img/project_menubar.png "project menubar"){:width="800px"}</span>
2. Click the add button in the right bottom corner.<br />
![Alt](../img/add_button.png)
3. You will see an empty Project Form. *Acronym*, *Title* and *Local Custodians* are mandatory fields, whereas the others are optional. Provide the values for the fields. Note that at least one of the Local Custodians **must be VIP user**. E.g. in the demo deployment *alice.white* is a research principle investigator and VIP user.<br />
<!-- ![Alt](../img/project_custodians.png) -->
<span style="display:block; text-align:center">![Alt](../img/project_custodians.png "Project custodians"){:width="800px"}<br/></span>
4. Click SUBMIT. Once you successfully save the form, you will be taken to the newly create project's details page, as see below.<br />
<!-- ![Alt](../img/project_created.png) -->
<span style="display:block; text-align:center">![Alt](../img/project_created.png "Project created "){:width="800px"}<br/></span>
<br>
<!-- <a name="PM2"></a> -->
## 3.2 Manage Project Details
[**See full section here.**]({{ "/manual/project_management_details/" | relative_url }})
When you first create a *Project* in DAISY, it will be isolated, with no links to other entities. The project page provides shortcuts to create (and edit) following entities: dataset, contract, personnel, contacts, documentation and publications. If you use these shortcuts the newly created entities will automatically be linked to the project.
To add some details, click plus button in the particular entity box.
<span style="display:block;text-align:left">![Alt]({{ "img/add_details_button.png" | relative_url }}){:width="400px"}</span>
[**See full section here.**]({{ "/manual/project_management_details/" | relative_url }})
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---
<small>
[User guide]({{ "/manual/" | relative_url }}) &raquo; [*3. Project Management*]({{ "/manual/#3-project-management" | relative_url }}) &raquo; [*3.2 Manage Project Details (**GO BACK to main page**)*]({{ "/manual/#32-manage-project-details" | relative_url }})
[User guide]({{ "/manual/" | relative_url }}) &raquo; [*Projects (**GO BACK to main page**)*]({{ "/manual/#21-projects" | relative_url }})
</small>
---
<br>
<br/>
## 3.2 Manage Project Details
{:.no_toc}
* TOC
......@@ -22,6 +20,37 @@ order: -1
---
# 3 Project Management
This section describes how to add a new project. Adding a project is available for standard user and VIP user.
## 3.1 Create New Project
In order to create a new project:
1. Click Projects from the Menu Bar to enter Project Search Page.<br />
<span style="display:block; text-align:center">![Alt]({{ "img/project_menubar.png" | relative_url }}){:width="800px"}</span>
2. Click the add button in the right bottom corner.<br />
<span style="display:block; text-align:left">![Alt]({{ "img/add_button.png" | relative_url }}){:width="100px"}</span>
3. You will see an empty Project Form. *Acronym*, *Title* and *Local Custodians* are mandatory fields, whereas the others are optional. Provide the values for the fields. Note that at least one of the Local Custodians **must be VIP user**.<br />
<span style="display:block; text-align:center">![Alt]({{"img/project_custodians.png" | relative_url }}){:width="800px"}<br/></span>
4. Click SUBMIT. Once you successfully save the form, you will be taken to the newly create project's details page, as see below.<br />
<span style="display:block; text-align:center">![Alt]({{"img/project_created.png" | relative_url }}){:width="800px"}<br/></span>
<br>
## 3.2 Manage Project Details
When you first create a *Project* in DAISY, it will be isolated, with no links to other entities. The project page provides shortcuts to create (and edit) following entities: dataset, contract, personnel, contacts, documentation and publications. If you use these shortcuts the newly created entities will automatically be linked to the project.
To add some details, click plus button in the particular entity box.
<span style="display:block;text-align:left">![Alt]({{ "img/add_details_button.png" | relative_url }}){:width="400px"}</span>
## 3.2 Manage Project Details
<br>
This section describes how to manage the project's entities details. Newly created project in DAISY has no links to other entities (e.g. personnel). Simply by clicking the plus button in the entity details box, you can create entity, which will automatically be linked to the project.
......@@ -45,14 +74,13 @@ When a project is created, it will have no associated datasets. On the project's
2. You will see the **Dataset Creation Quick Form** as below. The *Project* field will be auto-selected, in addition you need to provide *Local Custodians* and a *Title* for your dataset. Typically the local custodians would be the same as the project, but you are free to choose any user as the custodian. Remember that one of the custodians needs to be a VIP user. Provide the field values and press submit.
<span style="display:block;text-align:center">![Alt]({{ "img/project_add_dataset_form.png" | relative_url }}){:width="800px"}</span>
3. Once the dataset is created, you will be taken to the **Dataset's Details Page**, seen below. You can continue working on the data set as described in [section Dataset Management]({{ "/manual/#4-dataset-management" | relative_url }}).
3. Once the dataset is created, you will be taken to the **Dataset's Details Page**, seen below. You can continue working on the data set as described in [section Dataset Management]({{ "/manual/dataset_management_details/" | relative_url }}).
If you want to go back to the Project that owns this dataset, then you can click the project link in the dataset's overview box, highlighted below.<br />
![Alt]({{ "img/project_add_dataset_result.png" | relative_url }})
<br>
<!-- <a name="PM22"></a> -->
### 3.2.2 Add Project Contract
Contract allows for recording legal documents signed in the context of research activities. It provides the necessary traceability for the GDPR compliant provision and transfer of data.
......@@ -66,11 +94,10 @@ Contract allows for recording legal documents signed in the context of research
Remember that one of the custodians needs to be a VIP user. Provide the field values and press submit.
<span style="display:block;text-align:center">![Alt]({{ "img/project_add_contract_form.png" | relative_url }}){:width="800px"}</span>
3. The contract can be viewed by clicking its name in the detail box. (More details [here]({{ "/manual/#5-contract-management" | relative_url }}).) The contract can be removed from a project by clicking on the trash icon that will appear when hovering over the items in the *Contracts* detail box.
1. The contract can be viewed by clicking its name in the detail box. (See section [Contract Management]({{ "/manual/contract_management_details" | relative_url }}).) The contract can be removed from a project by clicking on the trash icon that will appear when hovering over the items in the *Contracts* detail box.
<span style="display:block;text-align:center">![Alt]({{ "img/project_remove_contract.png" | relative_url }}){:width="800px"}</span>
<!-- <a name="PM23"></a> -->
### 3.2.3 Add Project Personnel
A project's *Personnel* refer to those persons that work on the project, we assume that these persons will all have a user account for the DAISY system. The *Personnel* detail box on the *Project* page also allows linking DAISY *Users* as personnel of a project.
......@@ -88,17 +115,16 @@ Personnel can be unlinked from a Project by clicking on the trash icon that will
<br>
<!-- <a name="PM24"></a> -->
### 3.2.4 Manage Project Contacts
A project's *Contacts* refer to those persons that are associated with the project, but that **are not a user** of the DAISY system. Under the *Definitions Management* module, it is possible to manage *Contacts* and search for them. The *Contacts* detail box on the *Project* page also allows on contact management.
A project's *Contacts* refer to those persons that are associated with the project, but these **are not users** of the DAISY system. Under the [*Definitions Management*]({{ "/manual/definitions_management_details" | relative_url }}) module, it is possible to manage *Contacts* and search for them. Management of contacts can be also done directly on *Project's* page via The *Contacts* detail box.
<mark>To add project's contact details:</mark>
1. Click the plus button on the Contacts details box. You will be given the options to either **Link to existing contact** or **Create a new contact**, as seen below.<br />
<span style="display:block;text-align:left">![Alt]({{ "img/project_add_contact.png" | relative_url }}){:width="400px"}</span>
2. If you choose to link, you will be asked to select one contact from the dropdown list of existing contacts. Contacts will be listed with their name, surname and role as seen below. Make a selection and click SUBMIT.<br />
2. If you choose to link, you will be asked to select one contact from the drop down list of existing contacts. Contacts will be listed with their name, surname and role as seen below. Make a selection and click SUBMIT.<br />
<span style="display:block;text-align:left">![Alt]({{ "img/project_ref_contact.png" | relative_url }}){:width="400px"}</span>
3. If you choose to create new one, you will see the contact creation form. Once you fill in the details and click SUBMIT a new contact will be created and automatically linked to the project.<br />
......@@ -110,7 +136,6 @@ Contacts can be unlinked from a Project by clicking on the trash icon that will
<br>
<!-- <a name="PM25"></a> -->
### 3.2.5 Manage Project Documentation
Document management is done via the *Documents* detail box. You can attach documents to a project record in DAISY. Some examples of the documents are listed below:
......@@ -128,7 +153,7 @@ The format of the documents is not limited, these can be PDF, Word or images. If
1. Click the plus button on the *Documents* detail box.<br />
<span style="display:block;text-align:left">![Alt]({{ "img/project_add_document.png" | relative_url }}){:width="800px"}</span>
2. You will see the *Document creation form*. Either select *Content* to upload a file or paste the document link (if exists in an external system). You will be required to provide a brief description of the document in *Document Notes*. Also you will also be required to select a *Domain Type* for the document. <br />
2. You will see the *Document creation form*. Either select *Content* to upload a file or paste the document link (if exists in an external system). You will be required to provide a brief description of the document in *Document Notes*. You will be also required to select a *Domain Type* for the document. <br />
<span style="display:block;text-align:left">![Alt]({{ "img/project_add_document_form.png" | relative_url }}){:width="400px"}</span>
3. Click SUBMIT and the new document will be listed as below. Documents can be deleted by clicking on the trash icon beside each document. The document information can be edited by clicking the pencil icon.<br />
......@@ -137,7 +162,6 @@ The format of the documents is not limited, these can be PDF, Word or images. If
<br>
### 3.2.6 Manage Project Publications
<!-- <a name="PM26"></a> -->
A project's *Publications* can be managed via the *Publications detail box*.
......@@ -161,7 +185,7 @@ Publications can be unlinked from a project by clicking on the trash icon that w
### **3.2.7 Appendix for VIP users**
This section describes management of the project's access permissions. If VIP user (check [users groups here]({{ "manual/#what-are-the-users-groups" | relative_url }})) owns a project or is its Local Custodian, he can grant users with the project's privileges.
This section describes management of the project's access permissions. If VIP user owns a project or is its Local Custodian, he can grant users with the project's privileges.
By clicking *eye button* in the project overview box, VIP user can enter *Change permission* page.
......
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# 1 Quickstart
## 1.1 Login and User Homepage
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.
<br/>
<span style="display:block;text-align:center">![Alt]({{ "img/login.png" | relative_url }}){:width="800px"}<br/><small>DAISY Login Page</small></span>
<br/>
After successful login, you see DAISY home page.
<br/>
<span style="display:block;text-align:center">![Alt]({{ "img/after_login.png" | relative_url }}){:width="800px"}<br/><small>DAISY User Home Page</small></span>
---
<div style="text-align: right"> <strong><a href="#top">Back to top</a></strong></div>
<br />
## 1.2 DAISY Interface Conventions
The main view of each DAISY module is called [Search Page](#search-pages), where you choose entity you are interested in (or create a new module). You can inspect a particular entity details in [Entity Details Pages](#entity-details-pages) and edit them in [Entity Editor Pages](#entity-editor-pages).
### Search Pages
DAISY provides search pages for all entities manageable via modules. Currently these modules are: *Datasets*, *Projects*, *Contracts* and under *Definitions*: *Cohorts*, *Partners*, *Contacts*. All search pages have similar layout and operational conventions. Search pages are also the only entry point for the functions in a module. When you select a module from the menu bar, you will be taken to the search page for the entity managed by that module.
As an example, the screenshot of the search page for Projects is given below.
Each search page is headed with the help text containing a brief description. On the left hand side of the page there are search facets and on the right - the search results are displayed.
<span style="display:block; text-align:center">![Alt](../img/search_page.png "Search Page for Projects"){:width="900px"}<br/><small>Search page for Projects</small></span>
<br/>
By default, all entities (in our example - projects) will be listed on the search page. The list can be filtered by either selecting one or more facet from the left hand side or by typing in a keyword into the search box. Note that currently **DAISY search does not support partial matching**. Instead, the entire keyword will be matched in a case insensitive manner.
On the top right section of search results a few attributes are listed. Clicking on these attributes repeatedly will respectively (1) enable the ordering; (2) change order to ascending/descending; (3) disable ordering for the clicked attribute.
Each entity listed in the search results is displayed in a shaded box, containing few of its attributes. In our example these are the project's name and the number of publications. Each result box will also contain a *DETAILS* link, through which you can go to the [Entity Details Page](#entity-details-pages).
Depending on the permissions associated with your user type, you may see a **add button (denoted with a plus sign)** at the bottom right section of the search page. You can add a new entity by clicking the plus button, which will open up an empty editor form for you to fill in.
<br/>
### Entity Details Pages
Clicking the *DETAILS* button in the search result box takes you to *Details Page*, which contains the information about the chosen entity. An example of details page for *Project* named 'SYSCID' is given below.
<span style="display:block; text-align:center">![Alt](../img/details_page.png "Details page of a Project in DAISY"){:width="900px"}<br/><small>Details page of a Project in DAISY</small></span>
<br/>
You may end up on an *Entity Details Page* through:
* the *DETAILS* link of a search results in a search page.
* the links on details pages of other (linked) entities in DAISY.
Each Details Page is headed with an **entity overview box** listing some of the entity's attributes (e.g. local custodians, start date) and allows to modify the entity. Depending on users permissions (see [users groups](#3-different-types-of-daisy-users)) in the right bottom corner of the overview box you may see:
* permissions button (denoted with an eye icon),
* edit entity button (denoted with a pencil icon),
* remove entity button (denoted with a bin icon).
Beneath the entity overview box there are several information boxes, which display the further details of the entity (e.g. personnel, ethics).
If you have edit permissions for the entity, then at the top right corner of particular detail boxes you will see an **add detail button (denoted with a plus sign)**. Via this button you can do the following:
* create links to other entities e.g. link contacts with projects.
* create (inline) detail records to the current entity e.g. one or more publications to a project.
<br/>
### Entity Editor Pages
When you click the edit button on the Details Page of an entity, you will be taken to the Editor Page containing a form for entity update. An example of **editor form** is given below.
<span style="display:block; text-align:center">![Alt](../img/editor_form.png "Editor page of a Project"){:width="900px"}<br/><small>Editor page of a Project</small></span>
<br/>
Each field in the form is be listed with a **name**, a **value** and a **help text**. Names of the fields that are required to have a value, are marked with a red asterisk (e.g. Title).
Editor forms can be saved by pressing **SUBMIT** button at the bottom of the page. The forms will be validated upon the submission. If the validation fails for one or more fields, these will be highlighted with inline validation error message, illustrated below.
<span style="display:block; text-align:center">![Alt](../img/validation_error.png "Field validation error"){:width="800px"}<br/><small>Field validation error message</small></span>
<br/>
Upon successful submission of a form, you will be returned to the Entity Details page.
DAISY may give success and/or warning messages upon the form submission; these will be displayed at the top of the page, as illustrated below.
<br/>
<span style="display:block; text-align:center">![Alt](../img/page_messages.png "Message display in DAISY"){:width="800px"}<br/><small>Status message displayed in DAISY</small></span>
<br/>
---
<div style="text-align: right"> <strong><a href="#top">Back to top</a></strong></div>
<br />
manual/user_management.md → manual/user_management_details.md
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---
layout: page
title: Login and users types
permalink: /manual/user_management_details/
order: -1
---
# 7 Login, Types of Users and Permissions
<small>
[User guide]({{ "/manual/" | relative_url }}) &raquo; [*3 Different types of DAISY users (**GO BACK to main page**)*]({{ "manual/#3-different-types-of-daisy-users" | relative_url }})
</small>
---
Upon successful installation of DAISY, going to the web address ```https://${IP_ADDRESS_OR_NAME_OF_DEPLOYMENT_SERVER}```
should display the login page.
<br>
![Alt](../img/login.png)
<center>DAISY Login Page</center>
# Users Groups and Permissions
{:.no_toc}
Based on the authentication configuration made for your deployment, you may login by:
* TOC
{:toc}
* user definitions in an existing LDAP directory, e.g. institutional/uni credentials
* user definitions maintained within the DAISY database.
---
<br>
DAISY is intended to be used mostly by three categories of end users in a biomedical research institutions:
- Research staff (e.g. principle investigators, lab members)
- Legal support team
- IT and data management specialists
<mark>DAISY is intended to be used mostly by three categories of end users in a Biomedical research institution</mark>; primarily Research staff e.g. principle investigators, lab members, legal support team, and IT and data management specialists.
Specifically, DAISY has the following **user groups** to support record access control;
Above categories are assigned to particular DAISY **user groups**, which support the control of records access:
- **Standard**
This is the default group that users are mainly assigned to. All DAISY users can view all *Dataset*, *Project*, *Contract* and *Definitions* (*Cohorts*, *Partners*, *Contacts*). The document attachments of the records are excluded from this view permission.
<br>
- **VIP**
The research principle investigators are typically assigned to this group. VIP users have all privileges on the records they own, meaning the records where the user has been appointed as the `Local Custodian`. They also have the right to give permissions to others on these records.
<br>
- **Legal**
This group allows users to manage *Contract* records. Legal personnel will be able to create view and edit contract as well as view all other records in DAISY and manage their document attachments
<br>
- **Auditor**
This role would designed to an external person, who is given view-only temporary access to all DAISY records. This is typically happening during an audit scenario.
* **standard**: This is the default role assigned to all users. All DAISY users can view all Dataset, Project, Contract and Definitions (Cohorts, Partner, Contact). The document attachments of records are excluded from this view permission.
* **vip**: This role is typically given to research principle investigators. VIP users have all privileges on the records they own, meaning the records where the user has been appointed as the ``Local Custodian``. They also have the right to give permissions to others on these records.
* **legal**: This role is given to users that will be managing _Contract_ records. Legal personnel will be able to create view and edit contract as well as view all other records in DAISY and manage their document attachments
* **auditor**: This role would designed to an external person, who is given view-only temporary access to all DAISY records. This would typically happening an audit scenario.
Inside the group a user can be assigned with a specific **role**, which specifies his project's permissions:
- Project's owner
- Local Custodian
- Regular user
The *back end user* is called *superuser* and is granted with *all* DAISY privileges - to manage the application's content and administer DAISY settings.
DAISY supports fine-grained permission management with the following categories of permissible actions. The ability to _View_ records, _View Document_ attachments of records, ability to _Edit_ and _Delete_ records. The ability to _Administer Permissions_.
<br>
DAISY supports fine-grained permission management with the following categories of permissible actions.
The users permissions are summed up in the below table:
<span style="display:block;text-align:center">![Alt]({{ "img/permissions_table.png" | relative_url }}){:width="900px"}<br/><small>Users permissions</small></span>
| User Category | Administer Permissions | Delete | Edit | View | View Document Attachments |
<!-- | User Category | Administer Permissions | Delete | Edit | View | View Document Attachments |
| -------------|:-------------:|:-------------:|:-------------:|:-------------:|:-----|
| superuser | P<sub>all</sub>, D<sub>all</sub>, C<sub>all</sub>, Def<sub>all</sub> | P<sub>all</sub>, D<sub>all</sub>, C<sub>all</sub>, Def<sub>all</sub>| P<sub>all</sub>, D<sub>all</sub>, C<sub>all</sub>, Def<sub>all</sub>| P<sub>all</sub>, D<sub>all</sub>, C<sub>all</sub>, Def<sub>all</sub> | P<sub>all</sub>, D<sub>all</sub>, C<sub>all</sub>, Def<sub>all</sub>|
| standard | | | | P<sub>all</sub>, D<sub>all</sub>, C<sub>all</sub>, Def<sub>all</sub> | |
| vip | P<sub>own</sub>, D<sub>own</sub> | P<sub>own</sub>, D<sub>own</sub>| P<sub>own</sub>, D<sub>own</sub>| P<sub>all</sub>, D<sub>all</sub>, C<sub>all</sub>, Def<sub>all</sub> | P<sub>own</sub>, D<sub>own</sub>, C<sub>own</sub> |
| auditor | | | |P<sub>all</sub>, D<sub>all</sub>, C<sub>all</sub>, Def<sub>all</sub>| P<sub>all</sub>, D<sub>all</sub>, C<sub>all</sub>, Def<sub>all</sub> |
| legal | C<sub>all</sub> | C<sub>all</sub> | P<sub>all</sub>, D<sub>all</sub>, C<sub>all</sub>, Def<sub>all</sub> | P<sub>all</sub>, D<sub>all</sub>, C<sub>all</sub>, Def<sub>all</sub> | P<sub>all</sub>, D<sub>all</sub>, C<sub>all</sub>, Def<sub>all</sub> |
| legal | C<sub>all</sub> | C<sub>all</sub> | P<sub>all</sub>, D<sub>all</sub>, C<sub>all</sub>, Def<sub>all</sub> | P<sub>all</sub>, D<sub>all</sub>, C<sub>all</sub>, Def<sub>all</sub> | P<sub>all</sub>, D<sub>all</sub>, C<sub>all</sub>, Def<sub>all</sub> | -->
<br />
---
<br />
<br />
<br />
<div style="text-align: right;"> <a href="#top">Back to top</a> </div>
<br />
<br />
<br />
\ No newline at end of file
<!-- WHERE PUT THAT ? -->
<!-- The dependencies between DAISY modules are given below. There are no hard dependencies between Projects, Contracts and Datasets modules. In principle you may start using any of these modules once DAISY is deployed with the pre-packed definitions. -->
<!-- ![Alt](../img/dependencies.png "DAISY module dependencies") -->
<!-- <center>DAISY module dependencies</center> -->
<!-- <span style="display:block; text-align:center">![Alt](../img/dependencies.png "DAISY module dependencies"){:width="800px"}<br/><small>DAISY module dependencies</small></span>
<br /> -->
manual/users_group.md
View file @ 8b364eca
......@@ -10,7 +10,7 @@ The extension of standard user is *VIP user*. By default, if VIP user is project
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:
The default group that users are assigned to. 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.
......@@ -18,7 +18,7 @@ The default role assigned to all users. All DAISY standard users can:
- has no access to grant other users with the projects's permissions (even for the modules the user owns or is *Local Custodian*).
<br>
- **VIP user**
This role is typically given to research principle investigators. VIP users have:
The research principle investigators are typically assigned to this group. 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).
......@@ -26,7 +26,7 @@ This role is typically given to research principle investigators. VIP users have
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:
The users assigned to this group can are allowed to manage *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.
......@@ -35,7 +35,7 @@ This role is given to users that will be managing *Contract* records. Legal pers
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.
<br>
For more details go to section [Types of Users and Permissions]({{ "/manual/#7-types-of-users-and-permissions" | relative_url }}) (recommended for DAISY Administrator).
For more details go to [Users Groups and Permissions]({{ "/manual/user_management_details/" | relative_url }}) (recommended for DAISY superuser).
---
......
manual/users_modules.md 0 → 100644
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# 2 What records can be kept with DAISY?
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.
<br>
<span style="display:block; text-align:center">![Alt](../img/menubar.png "DAISY Menu bar"){:width="800px"}<br/><small>DAISY Menu bar</small></span>
<br>
## 2.1 Projects
Projects 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). [**Go to Project Management**]({{ "/manual/project_management_details/" | relative_url }})
## 2.2 Datasets
Datasets 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.
[**Go to Dataset Management**]({{ "/manual/dataset_management_details" | relative_url }})
## 2.3 Contracts
Contracts 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. [**Go to Contracts Management**]({{ "/manual/contract_management_details" | relative_url }})
## 2.4 Definitions
Definitions Management module allows the maintenance of secondary entities, which are used when defining the contracts, projects or datasets. Users can manage cohorts, partner institutes and contact persons via the definitions module.
[**Go to Definitions Management**]({{ "/manual/definitions_management_details" | relative_url }})
---
<div style="text-align: right"> <strong><a href="#top">Back to top</a></strong></div>
<br />
# 3 Different types of DAISY users
Any user with an account can login to DAISY and start creating records. Users that create a record become the record's *owner* and will be able to change and delete the record at any time.
In DAISY, a records owner, however, is not the one with the utmost privileges. DAISY provides various types of users accounts, and associated privileges.
<br/>
<!-- 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 type of user is a standard user. Standard users can:
- view any *Dataset*, *Project*, *Contract* or *Definition* record in DAISY, including those created by others. The documents attachments on the records are, however, protected, and they are not visible to other standard users.
- create records of their own.
- edit and delete records of their own.
- **VIP user**
The research principle investigators are VIP type users. Whenever a *Dataset*, *Project*, *Contract* record gets created in DAISY, a VIP user **must be designated** as the record's **Local Custodian**. Records cannot be created without a local custodian.
In addition to the privileges of the standard user, the VIP Users have the following rights:
- view, edit and delete records under his custodianship,
- view and manage the document attachments of records under their custodianship,
- grant other users permissions on the records under his custodianship.
- **Legal user**
The users assigned to this group can are allowed to manage *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.
<br />
<br>
For more details go to [Users Groups and Permissions]({{ "/manual/user_management_details/" | relative_url }}) (recommended for those administering DAISY deployments).
---
<div style="text-align: right"> <strong><a href="#top">Back to top</a></strong></div>
<br />