Commit a1840f56 authored by Pinar Alper's avatar Pinar Alper
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first version of DAISY support pages with manual moved ver from howto cards

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# Gitlab pages
Welcome to an example page! Below you will find a detailed instruction on how to set-up your own Jekyll website with Gitlab-CI and our LCSB template.
# DAISY support pages
Sources for this page are [available in Gitlab](https://git-r3lab.uni.lu/core-services/pages-jekyll-lcsb-template).
If you are interested, have found any issues with the layout or have a helpful suggestion, you can also navigate to the [repository for theme](https://git-r3lab.uni.lu/core-services/jekyll-theme-lcsb-default).
Welcome! The user manual for DAISY can be found [here](./manual/)
# Setting up your web page
## The whole process to deploy your website
0. Make sure that you have access to our [LCSB's Gitlab - https://git-r3lab.uni.lu/](https://git-r3lab.uni.lu/). If you ever cloned a repository or set-up a new one there, then you should be fine. If you don't have it, either contact the sysadmins (`lcsb-sysadmins (at) uni.lu`) or open a ticket at [https://service.uni.lu](https://service.uni.lu).
1. [Create an empty repository in Gitlab](https://git-r3lab.uni.lu/projects/new). Please bear in mind, that the both names of the namespace and the project influence
final address of the page - it will internally follow the `https://<namespace>.pages.uni.lu/<project_name>` convention. (Note, that in the very last step, SIU can set a new alias/URL for your website)
![image](assets/screenshots/new_project.png)
2. On your computer, clone this very repository using: `git clone ssh://git@git-r3lab-server.uni.lu:8022/core-services/pages-jekyll-lcsb-template.git`.
3. Once cloned, navigate into cloned repository (`cd pages-jekyll-lcsb-template`) and remove the _remote_ - `git remote rm origin` (so that you update your repository, and not this very page).
4. Set a new remote (so that you push to your new repository) - `git remote add origin ssh://git@git-r3lab-server.uni.lu:8022/firstname.surname/your_projects_name.git`. You can find the correct remote address in Gitlab just after creating new repository, as in the following image:
![image](assets/screenshots/remote.png)
5. Modify site's settings (`_config.yml`) to match your needs. Refer to the next section for help.
6. Modify the index page. Modify (or delete) help and about pages. Add your own content.
7. Add your changes (`git add .`), commit (`git commit -m "Initial commit"`) and push (`git push --set-upstream origin master`) to the repository.
8. Your page is published! Go to `https://<namespace>.pages.uni.lu/name-of-repository` in your favourite browser, or the URL you specified in the SIU ticket.
9. In gitlab, go to **Settings** (under left-hand menu) > **General** > **Advanced** (hit `Expand` button) > **Remove fork relationship** (red button), then follow the instructions from the pop-up.
10. If you want to have your page publicly available - contact us (`lcsb-sysadmins (at) uni.lu`), we will make a ticket to SIU.
## What should you change in settings file?
We used to require a change in `url` and `baseurl` - but not anymore :)
However, you still might want to change:
* `title` field
* `e-mail` field
* `description` field
* `date` field
* `banner` field - if you want to have your own banner (the text next to _uni.lu_ logo), please contact us.
## Testing the web page locally
You can test your website locally (on your machine).
* First, make sure that you have Ruby installed. If not - please [install it](https://www.ruby-lang.org/en/downloads/).
* Then, from terminal install _bundler_ - `gem install bundler`.
* Navigate into a directory with your website
* Initialize the site with: `bundle install`.
* Finally, run the site: `bundle exec jekyll serve`.
## Please don't change/remove Gemfile and .gitlab-ci.yml files
They are mandatory in order for the website to work. First one contains the website dependencies, the second is responsible for building the website.
## Common problems
### *The website is not updated after commiting to the repository!*
Did you push the commit? If yes, then you probably changed/deleted `.gitlab-ci.yml` file.
### *The website looks broken! There are no images, no colors etc.*
You probably didn't configure `baseurl` parameter in the settings or configured it wrongly. Please take a look on `_settings.yml` file.
### *The links in the menu are not working (they point to "404: Not found").*
You probably didn't add `permalink` attribute. Or the post has `published: false` or `draft: true` set. Please take a look on the post file.
### *Something goes wrong with Gitlab-CI*
It never happened before, please notify us immediately.
### Other problems?
Please send us an email! (`lcsb-sysadmins (at) uni.lu`)
If you need help in registering your data to LCSB's DAISY instance, please contact [LCSB data stewards](mailto:lcsb-datastewards@uni.lu).
# 1 DAISY at a Glance
DAISY is a tool that assists GDPR compliance by keeping a register of personal data used in research. DAISY's application menu Bar lists the main functions provided.
![Alt](../img/img/menubar.png "DAISY Menubar")
<center>DAISY Menubar</center>
* _Project Management_ module allows for the recording of research activities as projects. Documenting projects is critical for GDPR compliance as projects constitute the purpose and the context of use of personal data. Any document supporting the legal and ethical basis for data use can be stored in DAISY. Examples are ethics approvals, consent configurations, or subject information sheets.
* _Dataset Management_ module allows for the recording of personal data held by the institution. The dataset may or may not fall in the context of a particular project. DAISY allows Datasets to be defined in a granular way; where - if desired - each data subset, called a data declaration, can be listed individually. These declarations may list data from a particular partner, data of a particular cohort or data of a particular type.
* _Contract Management_ module allows the recording and storage of legal contracts of various types that have been signed with partner institutes or suppliers. Consortium agreements, data sharing agreements, material transfer agreements are examples of contracts. For GDPR compliance contracts become useful when documenting the source of datasets received or the target datasets transferred.
* _Definitions Management_. DAISY comes pre-packed with default lookup lists; these can be changed during application deployment. Lookup lists are used when defining contracts, projects or datasets. The definitions module of the DAISY application allows the management of dynamic lookup lists, specifically those of cohorts, partner institutes and contact persons.
The dependencies between DAISY modules is given below. There are no hard dependencies between the Projects, Contracts and Datasets modules. In principle you may start using any of these modules once DAISY is deployed with pre-packed definitions.
![Alt](../img/img/dependencies.png "DAISY module dependencies")
<center>DAISY module dependencies</center>
<mark>Our suggestion to first-time users is the following</mark>:
1. Familiarise yourself with DAISY's interface conventions by reading the [relevant section of this guide](#DIC).
2. Login to DAISY with a user that has Administrator or VIP privileges. E.g. In the demo deployment the _admin_ user has Administrator privileges and _alice.white_ has VIP privileges.
3. Use Project Management to [create a project](#PM1).
4. Use Dataset Management to [create a dataset](#PM21) within the defined project.
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# 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)
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## 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).
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