Merge branch 'manual-update1' into 'manual-update1'

Manual update1 - minor changes

See merge request !6

README.md

+# 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
+```
+

manual/dataset_management.md

@@ -22,8 +22,6 @@
 
 ## 4.2 Manage Dataset Details
 
-[**See how to manage dataset details here.**]({{ "/manual/dataset_management_details" | relative_url }})    
-
 Dataset entity details box are displayed in dataset page, where you can add, edit or remove following details:  
 - Data declarations
 - Legal bases
@@ -33,7 +31,7 @@ Dataset entity details box are displayed in dataset page, where you can add, edi
 
 <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 how to manage dataset details here.**]({{ "/manual/dataset_management_details" | relative_url }})
+[**See full section Dataset Management**]({{ "/manual/dataset_management_details" | relative_url }})
 
 
 ---

manual/dataset_management_details.md

@@ -32,12 +32,12 @@ After initial creation the dataset will be in a skeletal form. The dataset needs
 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 further in this paragraph.    
+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>
 <!-- The options for the *Obtained from* field is described in detail [in the remainder of this section](#DDEC_OPTIONS). <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 you will be taken to the *Data Declaration Editor Page*.    
+3. Click SUBMIT. The data declaration will be created and 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. -->
@@ -82,7 +82,7 @@ This field captures important information, but, for the first-time users of DAIS
 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 several fields in addition to the title and origin supplied during their creation.
+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>
@@ -149,7 +149,7 @@ As per GDPR, any access to personal data held in an institution needs to be reco
 <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 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).  
+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>
 
 

manual/definitions_management_details.md

@@ -52,7 +52,7 @@ The information kept on partners can be seen in the associated *Editor Page* see
 
 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.
+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>

manual/interface_conventions.md

@@ -19,7 +19,7 @@ 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 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](#22-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.
 
@@ -67,8 +67,8 @@ Editor forms can be saved by pressing **SUBMIT** button at the bottom of the pag
 <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 the 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> -->

manual/project_management_details.md

@@ -66,7 +66,7 @@ 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/#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.    
 <span style="display:block;text-align:center">![Alt]({{ "img/project_remove_contract.png" | relative_url }}){:width="800px"}</span>
 
 
@@ -91,7 +91,7 @@ Personnel can be unlinked from a Project by clicking on the trash icon that will
 <!-- <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* module, it is possible to manage *Contacts* and search for them. The *Contacts* detail box on the *Project* page also allows on contact management.    
 
 <mark>To add project's contact details:</mark>
 
@@ -128,7 +128,7 @@ 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 />