Merge branch 'filter-daisy-merged' into 'develop'

integrate DAISY labcard

See merge request R3/labCards!9

external/daisy/interface_conventions.md

+
+<a name="DIC"></a>
+# 2 DAISY Interface Conventions 
+
+<a name="SP"></a> 
+## 2.1 Search Pages 
+
+
+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.
+
+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.
+
+
+ ![Alt](./images/search_page.png)
+ <center>Search Page for Projects</center>
+
+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.
+
+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. 
+
+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> 
+## 2.2 Entity Details Pages 
+
+Information about a single entity is provided through a Details Page. As example page for a _Project_ named ``SYSCID'' is given below.
+
+![Alt](./images/details_page.png)
+<center>Details page of a Project in DAISY</center>
+
+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 **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:
+
+* 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> 
+## 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 is given below.
+
+![Alt](./images/editor_form.png)
+<center>Editor page of a Project</center>
+
+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 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](./images/validation_error.png)
+<center>Field validation error</center>
+
+ 
+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.
+
+ ![Alt](./images/page_messages.png)
+<center>Message display in DAISY</center>
+
+
+<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

external/daisy/project_management.md

+
+<a name="PM"></a>
+# 3 Project Management
+ 
+ <a name="PM1"></a>
+## 3.1 Create New Project
+
+<mark>In order  to create a new project</mark>:
+
+1. Click Projects from the Menu Bar.<br />
+ ![Alt](./images/project_menubar.png)
+2. Click the add button from the Project Search Page.<br />
+ ![Alt](./images/add_button.png)
+3. You will see an empty Project Form. _Acronym, Title_ and _Local Custodians_  are mandatory fields, whereas others are optional. Provide values for fields. Please note that 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](./images/project_custodians.png)
+4. Click SUBMIT. Once you successfully save the form, you will be taken to the newly create project's details page, as seen below.<br />
+![Alt](./images/project_created.png)
+
+
+<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 such entities, most importantly Datasets and Contracts. If you use these shortcuts the newly created entities will automatically be linked to the project.  In the following section we describe how such shortcuts work.
+<a name="PM21"></a>
+### 3.2.1 Add Dataset to Project
+
+
+When a project is created, it will have no associated Datasets. On the project's details page this situation will be highlighted in the **Data of this project** detail box as follows:
+
+ ![Alt](./images/project_add_dataset.png)
+ 
+ <mark>In order to create a Dataset and automatically link it to the project</mark>:
+ 
+ 1. Click the **Add** button pointed by the arrow  in the **Data of this project** detail box.
+ 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.\
+  ![Alt](./images/project_add_dataset_form.png)
+  
+  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 [this part of the guide](#DM). If you want to go pack to the Project that owns this dataset, then you can click the project link in the dataset's overview box, highlighted below.<br />
+  ![Alt](./images/project_add_dataset_result.png)
+
+<a name="PM22"></a>
+### 3.2.2 Add Contract to Project
+
+TBC
+
+<a name="PM23"></a>
+### 3.2.3 Add Personnel to Project
+
+
+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, to do so;
+
+ 
+1. Click the plus button  on the **Personnel** details box, as seen below.<br />
+ ![Alt](./images/project_ref_user.png)
+2. You will be asked to select one user from a searchable list of existing users. Users will be listed with their name and surname. Make a selection and click SUBMIT. <br />
+ ![Alt](./images/project_ref_user_search.png)
+ 
+
+ Personnel can be unlinked from a Project by clicking on the trash icon that will appear when hovering over items in the  **Personnel detail box**, as seen below. Note that the personnel will not be deleted from the system, it will simply be unlinked.<br />
+ 
+ 
+  ![Alt](./images/project_remove_user.png)
+
+<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 contact management, as follows; 
+ 
+ 1. Click the plus button  on the **Contacts** details box. You will be given the options to either **Create a new contact** or **Reference an existing contact** as seen below.<br />
+ ![Alt](./images/project_add_contact.png)
+ 
+ 2. If you choose to reference, you will be asked to select one contact from a searchable list of existing contacts. Contacts will be listed with their name, surname and role as seen below. Make a selection and click SUBMIT.<br />
+ ![Alt](./images/project_ref_contact.png)
+ 
+ 3. If you choose to create new, 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 />
+ ![Alt](./images/project_add_contact_form.png)
+ 
+ 
+ Contacts can be unlinked from a Project by clicking on the trash icon that will appear when hovering over items in the  **Contacts detail box**, as seen below. Note that the contact will not be deleted from the system, it will simply be unlinked.<br />
+![Alt](./images/project_remove_contact.png)
+
+
+<a name="PM25"></a> 
+### 3.2.5 Manage Project Documentation 
+
+
+You can attach documents to a project record in DAISY. Examples of documents are the Project Proposal, Ethics Approvals, Templates of Consent Form or the Subject Information Sheet. Documents can be in any format, PDF, Word or scans. If the document is stored already in an external system, you can also record its link in DAISY. 
+
+Document management is done via the **Documents** detail box, as follows:
+
+1. Click the plus button on the **Documents** detail box.<br />
+![Alt](./images/project_add_document.png)
+
+2. You will see the _Document_ creation form. Either select _Content_, i.e. file to upload, or paste the document link (if in 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 _Type_ for the document. <br />
+![Alt](./images/project_add_document_form.png)
+
+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, also document information can be edited by clicking the pencil icon.<br />
+![Alt](./images/project_remove_document.png)
+
+  
+  
+### 3.2.6 Manage Project Publications 
+<a name="PM26"></a>
+
+A project's _Publications_ can be managed via the **Publications detail box**, as follows: 
+ 
+ 1. Click the plus button  on the **Publications** detail box. You will be given the options to either **Create a new publication** or **Reference an existing publication** as seen below.<br />
+ ![Alt](./images/project_add_publication.png)
+ 
+ 2. If you choose to reference, you will be asked to select one publication from a searchable list of existing publications. Publications will be listed with their citation string. Make a selection and click SUBMIT.<br />
+ ![Alt](./images/project_ref_publication.png)
+ 
+ 3. If you choose to create new, you will see the publication creation form asking you for the _Citation string_ and the  _DOI_ for the paper. Once you fill in the details and click SUBMIT a new publication will be created and automatically linked to the project.<br />
+ ![Alt](./images/project_add_publication_form.png)
+ 
+ 
+ Publications can be unlinked from a Project by clicking on the trash icon that will appear when hovering over items in the **Publications detail box**, as seen below. Note that the publication will not be deleted from the system, it will simply be unlinked.<br />
+ 
+
+![Alt](./images/project_remove_publication.png)
+
+
+<br />
+<br />
+<br />
+<div style="text-align: right;"> <a href="#top">Back to top</a> </div>
+<br />
+<br />
+<br />
+
+

external/daisy/user_management.md

+
+# 7 Login, Types of Users and Permissions
+ 
+ 
+Upon successful installation of DAISY, going to the web address ```https://${IP_ADDRESS_OR_NAME_OF_DEPLOYMENT_SERVER}```
+should display the login page.
+
+ ![Alt](./images/login.png) 
+ <center>DAISY Login Page</center>
+ 
+Based on the authentication configuration made for your deployment, you may login by:
+
+* user definitions in an existing LDAP directory, e.g. institutional/uni credentials
+* user definitions maintained within the DAISY database.
+
+
+<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;
+
+* **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. 
+
+
+
+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_.
+
+
+ 
+| 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> |
+
+
+
+<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

index.md

@@ -11,3 +11,4 @@ Bioinformatics Core assists Luxembourg Centre for Systems Biomedicine ([LCSB](ht
 ## Current LabCards
 
   * [Exchange data with collaborators](./external/exchange-channels/)
+  * [Registering human-subject data to DAISY](./external/daisy/)