Merge branch 'restructuring-1' into 'restructuring-1'

Restructuring 1

See merge request elixir/daisy-doc!10

README.md

@@ -7,7 +7,7 @@
 2. install dependencies using bundler
 
 ```bash
-bundle install --path /vendor/bundle
+bundle install --path vendor/bundle
 ```
 
 1. run server locally

manual/definitions_management_details.md

@@ -13,7 +13,7 @@ order: -1
 
 <br>
 
-## 6 Definitions Management
+# 6 Definitions Management
 {:.no_toc}
 
 * TOC
@@ -26,7 +26,7 @@ order: -1
 DAISY *Definitions* module allows for the management of *Contacts*, *Cohorts* and *Partners*. 
 
 <!-- <a name="COH_M"></a> -->
-### 6.1 Cohorts 
+## 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 
+## 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 
+## 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*.

manual/quickstart.md

@@ -12,7 +12,7 @@ Based on the authentication configuration made for your deployment, you may log
 * the user definitions maintained within the DAISY database.
 
 <br/>
-<span style="display:block;text-align:center">![Alt]({{ "img/login.png" | relative_url }})<br/><small>DAISY Login Page</small></span>
+<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.
@@ -29,7 +29,7 @@ After successful login, you see DAISY home page.
 <!-- <a name="DIC"></a> -->
 ## 1.2 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).
+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).
 
 <!-- <a name="SP"></a> -->
 ### Search Pages
@@ -46,7 +46,7 @@ By default, all entities (in our example - projects) will be listed on the searc
 
 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](#22-entity-details-pages).
+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.
 
@@ -62,7 +62,7 @@ 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](#what-are-the-users-groups)) in the right bottom corner of the overview box you may see:
+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).