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Restructuring 1

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README.md
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2. install dependencies using bundler
```bash
bundle install --path /vendor/bundle
bundle install --path vendor/bundle
```
1. run server locally
......
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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 />
<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 />
![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. 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>
<!-- <a name="CM2"></a> -->
## 5.2 Manage Contract Details
<!-- [**See how to manage contract details here.**]({{ "/manual/contract_management_details" | relative_url }}) -->
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 ([**more details here**]({{ "/manual/contract_management_details" | relative_url }})).
- Documents (described in section [Manage Project Documentation]({{ "/manual/project_management_details/#325-manage-project-documentation" | relative_url }})).
<!--
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 describe [here](#325-manage-project-documentation).
<!-- [here](#PM25). -->
---
<div style="text-align: right"> <strong><a href="#top">Back to top</a></strong></div>
<br />
manual/contract_management_details.md
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---
<small>
[User guide]({{ "/manual/" | relative_url }}) &raquo; [*5. Contract Management*]({{ "/manual/#5-contract-management" | relative_url }}) &raquo; [*5.2 Manage Contract Details (**GO BACK to main page**)*]({{ "/manual/#52-manage-contract-details" | relative_url }})
[User guide]({{ "/manual/" | relative_url }}) &raquo; [*Contracts (**GO BACK to main page**)*]({{ "/manual/#23-contracts" | relative_url }})
</small>
---
<br>
<br/>
## 5.2 Manage Contract Details
{:.no_toc}
* TOC
......@@ -21,28 +21,51 @@ order: -1
---
<br>
<br/>
# 5 Contract Management
### 5.2.1 Manage Contract Participants
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.
Contracts have multiple signatories. These can be managed via the *Participants* detail box.
## 5.1 Create New Contract
<mark>In order to create a new contract:</mark>
1. Click the plus button on the *Participants* details box, as seen below.<br />
<span style="display:block;text-align:center">![Alt]({{ "img/contract_add_partner.png" | relative_url }}){:width="800px"}</span>
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 />
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 Participants, as seen below. Partners can be removed from a contract by clicking on the trash icon that is displayed in the *Participants* detail box.<br />
<span style="display:block;text-align:center">![Alt]({{ "img/contract_add_partner_result.png" | relative_url }}){:width="800px"}</span>
<span style="display:block;text-align:center">![Alt]({{ "img/contract_add_form.png" | relative_url }}){:width="800px"}</span>
### 5.2.2 Manage Contract Documents
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 />
You may attach PDF file, Word documents or scans via the *Documents* detail box. Document management is common throughout DAISY modules. It is describe [here]({{ "/manual/project_management_details/#325-manage-project-documentation" | relative_url }}).
<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>
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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 %}
<!--- 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
<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 />
![Alt](../img/add_button.png)
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>
[**See full section Dataset Management**]({{ "/manual/dataset_management_details" | relative_url }})
---
<div style="text-align: right"> <strong><a href="#top">Back to top</a></strong></div>
<br />
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---
<small>
[User guide]({{ "/manual/" | relative_url }}) &raquo; [*4. Dataset Management*]({{ "/manual/#4-dataset-management" | relative_url }}) &raquo; [*4.2 Manage Dataset Details (**GO BACK to main page**)*]({{ "/manual/#42-manage-dataset-details" | relative_url }})
[User guide]({{ "/manual/" | relative_url }}) &raquo; [*Datasets (**GO BACK to main page**)*]({{ "/manual/#22-datasets" | relative_url }})
</small>
---
<br>
<br/>
## 4.2 Manage Dataset Details
{:.no_toc}
* TOC
......@@ -21,10 +20,40 @@ order: -1
---
# 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.
<!-- <a name="DM2"></a> -->
## 4.2.1 Declare Data within the Dataset
<mark> To add new data declaration: </mark>
......@@ -41,12 +70,10 @@ After initial creation the dataset will be in a skeletal form. The dataset needs
<br>
<!-- <a name="DDEC_OPTIONS"></a> -->
<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.
<!-- <span> &#9675; </span> -->
- **From existing data/samples**
- **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.
......@@ -56,7 +83,6 @@ This field captures important information, but, for the first-time users of DAIS
<br>
<!-- <span>&#9675;</span><mark><strong></strong></mark> -->
- **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>
......@@ -66,9 +92,6 @@ This field captures important information, but, for the first-time users of DAIS
<span style="display:block;text-align:center">![Alt]({{ "img/newly_incoming_topology.png" | relative_url }}){:width="800px"}</span>
<!-- <span>&#9675;</span><mark><strong>Other:</strong></mark> -->
- **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>
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## **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. appendix**]({{ "/manual/project_management_details/#327-appendix-for-vip-users**" | relative_url }}).
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.
......
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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](#2-daisy-interface-conventions). In this sections we only discuss what information is held in these definitions.
[**See full section Definitions Management.**]({{ "/manual/definitions_management_details" | relative_url }})
---
<div style="text-align: right"> <strong><a href="#top">Back to top</a></strong></div>
<br />
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---
<small>
[User guide]({{ "/manual/" | relative_url }}) &raquo; [*6 Definitions Management (**GO BACK to main page**)*]({{ "/manual/#6-definitions-management" | relative_url }})
[User guide]({{ "/manual/" | relative_url }}) &raquo; [*Definitions (**GO BACK to main page**)*]({{ "/manual/#24-definitions" | relative_url }})
</small>
---
<br>
## 6 Definitions Management
# 6 Definitions Management
{:.no_toc}
* TOC
......@@ -23,10 +23,10 @@ order: -1
<br>
DAISY *Definitions* module allows for the management of *Contacts*, *Cohorts* and *Partners*. Here we only discuss what information is held in these definitions.
DAISY *Definitions* module allows for the management of *Contacts*, *Cohorts* and *Partners*.
<!-- <a name="COH_M"></a> -->
### 6.1 Cohorts Management
## 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*.
......@@ -37,7 +37,7 @@ The information kept on cohorts can be seen in the associated *Editor Page* seen
<!-- <a name="PAR_M"></a> -->
### 6.2 Partners Management
## 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.
......@@ -48,7 +48,7 @@ The information kept on partners can be seen in the associated *Editor Page* see
<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 Management
## 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*.
......
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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**.<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
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 Project Management**]({{ "/manual/project_management_details/" | relative_url }})
---
<div style="text-align: right"> <strong><a href="#top">Back to top</a></strong></div>
<br />
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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>
1. The contract can be viewed by clicking its name in the detail box. (See section [Contract Management]({{ "/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.
......@@ -88,7 +115,6 @@ 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 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.
......@@ -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:
......@@ -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 />
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<!--
# 7 Users Groups and Permissions
This paragraph is recommended for DAISY superuser. [**Click here**]({{ "/manual/user_management_details/" | relative_url }}) to find out about DAISY end users and their privileges.
---
<div style="text-align: right"> <strong><a href="#top">Back to top</a></strong></div>
<br /> -->
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......@@ -6,7 +6,7 @@ order: -1
---
<small>
[User guide]({{ "/manual/" | relative_url }}) &raquo; [*What are the users groups (**GO BACK to main page**)*]({{ "manual/#what-are-the-users-groups" | relative_url }})
[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>
---
......@@ -31,10 +31,13 @@ DAISY is intended to be used mostly by three categories of end users in a biomed
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.
......@@ -43,33 +46,17 @@ Inside the group a user can be assigned with a specific **role**, which specifie
- Local Custodian
- Regular user
<br>
The *back end user* is called *superuser* and is granted with *all* DAISY privileges - to manage the application's content and administer DAISY settings.
<br>
DAISY supports fine-grained permission management with the following categories of permissible actions.
The right to *View*, *Edit* and *Delete* records; to *View Document attachments of records* and to *Administer Permissions*.
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>
<!-- Project permissions:
Permissions
- Admin
Grant the right to change permissions on this dataset and grant all other permissions.
- Delete
Grant the right to delete this dataset.
- Edit
Grant the right to edit this dataset.
- Protected
Grant the right to access protected information on this dataset.\
- View
Grant the right to view this dataset. -->
<!-- | User Category | Administer Permissions | Delete | Edit | View | View Document Attachments |
......@@ -80,8 +67,6 @@ Permissions
| 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> | -->
<br />
---
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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 />
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