Merge pull request #500 from deNBI/staging

Staging

config.yml

@@ -29,21 +29,24 @@ repo_name: 'deNBI/cloud-user-docs'
 repo_url: 'https://github.com/deNBI/cloud-user-docs'
 edit_uri: blob/master/wiki/
 use_directory_urls: true
-site_url: !ENV [SITE_URL, 'https://cloud.denbi.de/wiki/']
+site_url: !ENV [ SITE_URL, 'https://cloud.denbi.de/wiki/' ]
 
 plugins:
   - search
   - glightbox
   - macros
   - git-revision-date-localized:
-        fallback_to_build_date: true
+      fallback_to_build_date: true
   - htmlproofer:
-      enabled: !ENV [ENABLED_HTMLPROOFER,False]
-      raise_error: True
+      enabled: !ENV [ ENABLED_HTMLPROOFER,False ]
+      raise_error_after_finish: True
       raise_error_excludes:
-        -1: ["https://cloud.denbi.de/portal/webapp/#/userinfo","http://169.254.169.254","https://login.elixir-czech.org/oidc/","https://spreg-legacy.aai.elixir-czech.org/spreg/auth/requests/new","https://spreg-legacy.aai.elixir-czech.org/spreg/auth/facilities/myServices","http://BIBIGRID_MASTER/ganglia"]
-        400: ["http://169.254.169.254"]
-        500: ["https://cloud.denbi.de/register", "https://signup.aai.lifescience-ri.eu/fed/registrar/?vo=elixir_test"]
+        -1: [ "https://cloud.denbi.de/portal/webapp/#/userinfo","http://169.254.169.254","https://login.elixir-czech.org/oidc/","https://spreg-legacy.aai.elixir-czech.org/spreg/auth/requests/new","https://spreg-legacy.aai.elixir-czech.org/spreg/auth/facilities/myServices","http://BIBIGRID_MASTER/ganglia" ]
+        400: [ "http://169.254.169.254" ]
+        403: [ "https://s3.denbi.uni-tuebingen.de" ]
+        500: [ "https://cloud.denbi.de/register", "https://signup.aai.lifescience-ri.eu/fed/registrar/?vo=elixir_test" ]
+        504: [ "https://cloud.denbi.de/about/credits-calculator/", "https://packages.ubuntu.com/","https://denbi-cloud.bihealth.org","http://apt-cache.bi.denbi.de:9999","http://129.70.51.2:9999","https://cloud.denbi.dkfz-heidelberg.de","https://denbi-cloud.bioquant.uni-heidelberg.de","https://denbi-cloud.bioquant.uni-heidelberg.de" ]
+
 markdown_extensions:
   - abbr
   - attr_list
@@ -103,64 +106,64 @@ extra:
       name: de.NBI on YouTube
     - icon: fontawesome/brands/wikipedia-w
       link: https://en.wikipedia.org/wiki/German_Network_for_Bioinformatics_Infrastructure
-      name: de.NBI on Wikipedia  
-  simplevm_wiki_link: !ENV [SIMPLE_VM_WIKI_LINK, 'https://simplevm.denbi.de/wiki/']
+      name: de.NBI on Wikipedia
+  simplevm_wiki_link: !ENV [ SIMPLE_VM_WIKI_LINK, 'https://simplevm.denbi.de/wiki/' ]
 
 nav:
-  - 'Home' : index.md
-  - 'Registration' : registration.md
+  - 'Home': index.md
+  - 'Registration': registration.md
   - 'Citation and publication': citation_and_publication.md
-  - 'Portal' :
-    - 'Allocation': portal/allocation.md
-    - 'Resource/Lifetime Modifications': portal/modification.md
-    - 'Project Termination' : portal/termination.md
-    - 'Project Overview': portal/project_overview.md
-    - 'Profile Page': portal/user_information.md
-    - 'Using Vault': portal/vault_user.md
-    - 'Cloud Credits': portal/credits.md
-    - 'Personal Data': portal/personal_data.md
+  - 'Portal':
+      - 'Allocation': portal/allocation.md
+      - 'Resource/Lifetime Modifications': portal/modification.md
+      - 'Project Termination': portal/termination.md
+      - 'Project Overview': portal/project_overview.md
+      - 'Profile Page': portal/user_information.md
+      - 'Using Vault': portal/vault_user.md
+      - 'Cloud Credits': portal/credits.md
+      - 'Personal Data': portal/personal_data.md
   - 'Simple VM':
       - simple_vm/index.md
-  - 'OpenStack Quickstart' : quickstart.md
-  - 'Security' : security.md
-  - 'Concept' :
-    - 'OpenStack Basics' : Concept/basics.md
-    - 'OpenStack Components' : Concept/openstack.md
-    - 'Flavors' : Concept/flavors.md
-    - 'Images' : Concept/images.md
-  - 'Tutorials' :
-    - 'Tutorials': Tutorials/index.md
-    - 'Access de.NBI Virtual Machines from Windows 10' : Tutorials/Win10_SSH/index.md
-    - 'Access project infrastructure with sshuttle' : Tutorials/Sshuttle/index.md
-    - 'Ansible Automation' : Tutorials/Ansible/index.md
-    - 'Bibigrid' : Tutorials/BiBiGrid/index.md
-    - 'Blast on BiBiGrid' : Tutorials/BlastOnBiBiGrid/index.md
-    - 'Hybridcloud' : Tutorials/Hybridcloud/index.md
-    - 'Install latest CUDA version' : Tutorials/CUDA/index.md
-    - 'JupyterHub' : Tutorials/JupyterHub/index.md
-    - 'Kubermatic' : Tutorials/Kubermatic/index.md
-    - 'Loadbalancer' : Tutorials/Loadbalancer/index.md
-    - 'Object Storage' : Tutorials/ObjectStorage/index.md
-    - 'Public Web Server' : Tutorials/PublicWebServer/index.md
-    - 'Reverse Proxy with Elixir AAI': Tutorials/Elixir_AAI/Elixir_AAI.md
-    - 'Save FloatingIPs' : Tutorials/SaveFloatingIPs/index.md
-    - 'Set up RStudio' : Tutorials/RStudio_Server/index.md
-    - 'Persistent SSH Sessions' : Tutorials/Persistent_SSH_Sessions/index.md
-    - 'Theia Web IDE': Tutorials/TheiaIde/index.md
-    - 'UserData' : Tutorials/UserData/index.md
-    - 'Using X2GO': Tutorials/X2GO/x2go.md
-  - 'FAQ' : 'FAQ.md'
-  - 'Compute Center Specific' :
-    - 'Berlin' : Compute_Center/Berlin.md
-    - 'Bielefeld' : Compute_Center/Bielefeld.md
-    - 'EMBL' : Compute_Center/EMBL.md
-    - 'Freiburg' : Compute_Center/Freiburg.md
-    - 'Giessen' : Compute_Center/Giessen.md
-    - 'Heidelberg Uni' : Compute_Center/Heidelberg.md
-    - 'Heidelberg DKFZ' : Compute_Center/Heidelberg-DKFZ.md
-    - 'Tuebingen' : Compute_Center/Tuebingen.md
+  - 'OpenStack Quickstart': quickstart.md
+  - 'Security': security.md
+  - 'Concept':
+      - 'OpenStack Basics': Concept/basics.md
+      - 'OpenStack Components': Concept/openstack.md
+      - 'Flavors': Concept/flavors.md
+      - 'Images': Concept/images.md
+  - 'Tutorials':
+      - 'Tutorials': Tutorials/index.md
+      - 'Access de.NBI Virtual Machines from Windows 10': Tutorials/Win10_SSH/index.md
+      - 'Access project infrastructure with sshuttle': Tutorials/Sshuttle/index.md
+      - 'Ansible Automation': Tutorials/Ansible/index.md
+      - 'Bibigrid': Tutorials/BiBiGrid/index.md
+      - 'Blast on BiBiGrid': Tutorials/BlastOnBiBiGrid/index.md
+      - 'Hybridcloud': Tutorials/Hybridcloud/index.md
+      - 'Install latest CUDA version': Tutorials/CUDA/index.md
+      - 'JupyterHub': Tutorials/JupyterHub/index.md
+      - 'Kubermatic': Tutorials/Kubermatic/index.md
+      - 'Loadbalancer': Tutorials/Loadbalancer/index.md
+      - 'Object Storage': Tutorials/ObjectStorage/index.md
+      - 'Public Web Server': Tutorials/PublicWebServer/index.md
+      - 'Reverse Proxy with Elixir AAI': Tutorials/Elixir_AAI/Elixir_AAI.md
+      - 'Save FloatingIPs': Tutorials/SaveFloatingIPs/index.md
+      - 'Set up RStudio': Tutorials/RStudio_Server/index.md
+      - 'Persistent SSH Sessions': Tutorials/Persistent_SSH_Sessions/index.md
+      - 'Theia Web IDE': Tutorials/TheiaIde/index.md
+      - 'UserData': Tutorials/UserData/index.md
+      - 'Using X2GO': Tutorials/X2GO/x2go.md
+  - 'FAQ': 'FAQ.md'
+  - 'Compute Center Specific':
+      - 'Berlin': Compute_Center/Berlin.md
+      - 'Bielefeld': Compute_Center/Bielefeld.md
+      - 'EMBL': Compute_Center/EMBL.md
+      - 'Freiburg': Compute_Center/Freiburg.md
+      - 'Giessen': Compute_Center/Giessen.md
+      - 'Heidelberg Uni': Compute_Center/Heidelberg.md
+      - 'Heidelberg DKFZ': Compute_Center/Heidelberg-DKFZ.md
+      - 'Tuebingen': Compute_Center/Tuebingen.md
   - 'Cloud Admin':
-    - 'Configure OpenStack to use Elixir AAI via OpenID Connect': cloud_admin/elixir_OIDC.md
-    - 'Register your identity provider for ELIXIR': cloud_admin/identity_provider.md
-    - 'News management': cloud_admin/news_management.md
-    - 'Vault management': cloud_admin/vault_admin.md
+      - 'Configure OpenStack to use Elixir AAI via OpenID Connect': cloud_admin/elixir_OIDC.md
+      - 'Register your identity provider for ELIXIR': cloud_admin/identity_provider.md
+      - 'News management': cloud_admin/news_management.md
+      - 'Vault management': cloud_admin/vault_admin.md

wiki/FAQ.md

@@ -23,7 +23,7 @@ If this does not bring the desired success, the reasons can be manifold.
 Make sure that you use the correct SSH key!
 If you have changed your SSH key in the portal since creating the machine, it will not be automatically changed on this machine. The connection to this VM still requires the key that was set at the time of creation. The private key is always used to connect to the machine.
 
-You can find more about SSH keys [here](./simple_vm/keypairs.md#ssh-keys-and-sharing-access).
+You can find more about SSH keys [here]({{extra.simplevm_wiki_link}simple_vm/keypairs/).
 
 Maintenance may be performed at the site where your machines are running. Occasionally, malfunctions also occur during regular service.
 Check your project site's [Facility News](https://cloud.denbi.de/news/facility-news/) page - downtimes are usually announced on this page.

wiki/Tutorials/Elixir_AAI/Elixir_AAI.md

@@ -12,7 +12,7 @@ In this section you can see an illustration of our finished architecture.
 ![](Goal_Architecture.png)
 ​
 ## What do we need before we start?
-1. We need a running virtual instance that is accessible from the web. You can find a tutorial on how to create one in the de.NBI wiki: <https://cloud.denbi.de/wiki/simple_vm/new_instance/>. The hardware specs we used for this project are: OS: Ubuntu 18.04 LTS; RAM: 4GB; HDD: 20 GB. 
+1. We need a running virtual instance that is accessible from the web. You can find a tutorial on how to create one in the de.NBI SimpleVM wiki: <https://simplevm.denbi.de/wiki/simple_vm/create_instance/>. The hardware specs we used for this project are: OS: Ubuntu 18.04 LTS; RAM: 4GB; HDD: 20 GB. 
 2. You need a registered Elixir client. You can register here: <https://elixir-europe.org/register>. After the registration you can access your personal profile via this link: <https://profile.aai.lifescience-ri.eu/profile>. Here you can find e.g . your personal Elixir client ID. 
 3. Create an Elixir service you will use to authenticate at the reverse proxy later on. This service can be registered here: <https://spreg-legacy.aai.elixir-czech.org/spreg/auth/requests/new>. 
 4. To be able to access the services in the test environment, you need to register to a special "virtual organization" representing this environment. You can register at: <https://signup.aai.lifescience-ri.eu/fed/registrar/?vo=elixir_test>. Note: The membership in this VO is valid for one month and has to be extended to be able to use the test environment in the future. 

wiki/Tutorials/ObjectStorage/index.md

@@ -18,7 +18,7 @@ A caveat on object stores is the possible higher network latency between the sto
 ### Object storage access 
 
 Depending on the cloud site the object storage is based on different storage backends. It can be accessed using 
-the [https://docs.aws.amazon.com/AmazonS3/latest/API/Welcome.html](S3-API). SThese APIs differ in
+the [S3-API](https://docs.aws.amazon.com/AmazonS3/latest/API/Welcome.html). These APIs differ in
 their terminology, capabilities and respective tools: Objects are stored in containers (swift) or buckets (s3).
 Access is controlled via access control lists (s3 and swift) or via policies (only s3).
 

wiki/Tutorials/Persistent_SSH_Sessions/index.md

@@ -80,7 +80,7 @@ This way you can easily create persistent sessions with screen that are independ
 - Screen Cheatsheet - https://quickref.me/screen
 
 
-- Manpage: [Screen](https://linux.die.net/man/1/screen) or
+- Manpage:
 ```bash 
 $ man screen
 

wiki/Tutorials/RStudio_Server/index.md

@@ -165,4 +165,4 @@ sudo apt-get install libcurl4-gnutls-dev libssl-dev libcurl4-openssl-dev libxml2
 After the installation of these packages, try to re-install the R packages in RStudio Server. Hopefully the error vanished now!
 
 ## 6. Further Reading
-For more information on RStudio and the RStudio Server please have a look at their documentation at ([https://support.rstudio.com/hc/en-us/categories/200035113-Documentation](https://support.rstudio.com/hc/en-us/categories/200035113-Documentation))
+For more information on RStudio and the RStudio Server please have a look at their documentation at ([https://docs.posit.co/ide/user/](https://docs.posit.co/ide/user/))

wiki/Tutorials/index.md

@@ -1,7 +1,7 @@
 # Tutorials
 
 Welcome to the tutorials section! Explore the guides below to enhance your knowledge and skills in various topics.
-SimpleVM-specific Tutorials can be found in the SimpleVM-Wiki [tutorial section]({{extra.simplevm_wiki_link}}/Tutorials)
+SimpleVM-specific Tutorials can be found in the SimpleVM-Wiki [tutorial section]({{extra.simplevm_wiki_link}}Tutorials/)
 
 
 - [Access de.NBI Virtual Machines from Windows 10](Win10_SSH/index.md)
@@ -22,4 +22,3 @@ SimpleVM-specific Tutorials can be found in the SimpleVM-Wiki [tutorial section]
 - [Persistent SSH Sessions](Persistent_SSH_Sessions/index.md)
 - [Theia Web IDE](TheiaIde/index.md)
 - [UserData](UserData/index.md)
-- [Using X2GO](X2GO/x2go.md)

wiki/portal/user_information.md

@@ -32,8 +32,8 @@ https://signup.aai.lifescience-ri.eu/fed/registrar/?vo=anonymize
 ### SSH Key
 ![setcopypublickey](img/profile_page.png)
 
-You have the possibility to view, copy and deposit your public ssh key. An uploaded public key is required for starting machines. 
-Read more about it [here](../simple_vm/new_instance.md#3-grant-access-for-project-members).
+
+You have the possibility to view, copy and deposit your public ssh key.
 If you don't know how to generate a ssh key, you can read the [instructions](../quickstart.md#generate-ssh-keys) on our quickstart page.
 
 Alternatively you are also able to have a ECDSA key generated for you. Click on the `Generate Key` button and read and confirm the notification.