Merge branch 'manual-update' into 'master'

Spell check added

See merge request elixir/daisy-doc!4

.aspell.en.pws

+personal_ws-1.1 en 0 utf-8
+alice
+Backend
+backends
+DAISY’s
+DAta
+Dataset
+dataset
+Dataset’s
+dataset’s
+datasets
+Datasets
+datatypes
+DOI
+du
+GDPR
+GigaScience
+github
+giz
+howto
+jekyll
+lcsb
+LCSB's
+LDAP
+LuxPARK
+Menubar
+pre
+repo
+STDOUT
+SYSCID
+SYstem
+TBC
+Université
+unlinked
+vip
+YYYY

.gitlab-ci.yml

 # In case something goes horribly wrong, you can fall back to `image: ruby:latest`
 image: git-r3lab.uni.lu:4567/r3/docker/jekyll-lcsb:1.0
 
-build the website:
+build:
   stage: build
   before_script:
   - gem install bundler -v2.0.2
@@ -18,6 +18,20 @@ build the website:
   variables:
     JEKYLL_ENV: production
 
+
+test_spell_check:
+  image: debian
+  stage: test
+  dependencies:
+     - build
+  script:
+  - apt-get update
+  - apt-get install -y aspell aspell-en
+  - ./test_spell_check.sh
+  except:
+  - master
+
+
 pages:
   stage: deploy
   only:

_config.yml

 # This config file is meant to be edited once, before the site is deployed.
-# After that, new edits are rarely needed. 
+# After that, new edits are rarely needed.
 
 # Usually, you need only to change `title`, `email`, `description`, `baseurl`, `url` and `date`.
 # To see complete guide, please take a look into `readme.md` file.
@@ -12,14 +12,14 @@
 # you will see them accessed via {{ site.title }}, {{ site.email }}, and so on.
 # You can create any custom variable you would like, and they will be accessible
 # in the templates via {{ site.myvariable }}.
-title: Blank template using LCSB theme.
-email: your-email@example.com
+title: DAta Information SYstem (DAISY)
+email: pinar.alper@uni.lu
 description: >- # this means to ignore newlines until "baseurl:"
-  Write an awesome description for your new site here. You can edit this
-  line in _config.yml. It will appear in your document head meta (for
-  Google search results) and in your feed.xml site description.
+  The user guide for the DAta Information SYstem (DAISY). It allows to manage your research data
+  in a GDPR-compliant manner and share the projects with your collaboration partners.
 
-# URL settings that will be used to access on your local machine 
+
+# URL settings that will be used to access on your local machine
 # Note #1: by default you will need to use port 4000 (https://localhost:4000/website) to access the website in your browser running on your machine with `bundle exec jekyll serve`
 # Note #2: the configuration used in GitlabCI is generated in `.gitlab-ci.yml` file automatically for you, if you need to change that - do it there
 baseurl: "/website"
@@ -39,17 +39,17 @@ linkedin_schoolname: university-of-luxembourg
 permalink: /:year/:month/:title.html
 
 # Pagination Settings
-pagination:
-  enabled: true
-  title: ':title - page :num of :max'
-  per_page: 7
-  permalink: '/page/:num/'
-  limit: 0
-  sort_field: 'date'
-  sort_reverse: true
-  trail:
-    before: 2
-    after: 2
+# pagination:
+#   enabled: true
+#   title: ':title - page :num of :max'
+#   per_page: 7
+#   permalink: '/page/:num/'
+#   limit: 0
+#   sort_field: 'date'
+#   sort_reverse: true
+#   trail:
+#     before: 2
+#     after: 2
 
 # Build settings (no need to touch these)
 markdown: kramdown

manual/at_a_glance.md

 
-
 # 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")
+ ![Alt](../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.
@@ -14,7 +13,7 @@ DAISY is a tool that assists GDPR compliance by keeping a register of personal d
 
 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")
+![Alt](../img/dependencies.png "DAISY module dependencies")
  <center>DAISY module dependencies</center>
 
 <mark>Our suggestion to first-time users is the following</mark>:

manual/dataset_management.md

@@ -102,7 +102,7 @@ In order to add a new access record:
    ![Alt](../img/dataset_remove_access.png)
 
 
-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 **Dat used from other projects** detail box (see below right).
+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).
    ![Alt](../img/dataset_access_other_project.png)
 
 
@@ -115,6 +115,3 @@ As discussed above, when data of one project is being access in the context of a
 <br />
 <br />
 <br />
-
-
-

test_spell_check.sh

+#!/bin/bash
+set -e
+
+#set en_GB for British English
+aspell_lang=en
+
+echo "Spell checking"
+spell_check_code=0
+for x in $(find test/ -name '*.html');
+do
+	lines=`cat $x|aspell --lang=$aspell_lang --encoding=utf-8 --mode html --add-extra-dicts=./.aspell.en.pws list 2>errors.txt |wc -l`
+	if [ $lines -gt 0 ]
+	then
+		echo $x:
+		cat $x | aspell --lang=$aspell_lang --encoding=utf-8 --mode html --add-extra-dicts=./.aspell.en.pws list
+		spell_check_code=1
+		echo
+	fi
+# we need to check stderr - in case something really bad happens there will be output there
+        lines=`cat errors.txt | wc -l`
+	if [ $lines -gt 0 ]
+	then
+        	cat errors.txt
+		spell_check_code=1
+	fi
+done
+
+if [ $spell_check_code -gt 0 ]
+then
+	echo "Spell check found some problems. Either fix them or add exceptions to the dictionary file: .aspell.en.pws"
+fi
+rm errors.txt
+exit $spell_check_code