diff --git a/CONTRIBUTORS.yaml b/CONTRIBUTORS.yaml index c9a29fc..72081a9 100644 --- a/CONTRIBUTORS.yaml +++ b/CONTRIBUTORS.yaml @@ -42,3 +42,33 @@ silviabah: email: sbahena@ebi.ac.uk orcid: 0000-0002-2734-0449 elixir_node: embl + +ahornos: + name: Albert Hornos Vidal + email: ahornos@bsc.es + orcid: 0000-0002-7330-668X + elixir_node: es + +blankdots: + name: Stefan Negru + email: + orcid: + elixir_node: fi + +alex-dem: + name: Alexandros Dimopoulos + email: dimopoulos@fleming.gr + orcid: 0000-0002-4602-2040 + elixir_node: gr + +d-salgado: + name: David Salgado + email: david.salgado@france-bioinformatique.fr + orcid: 0000-0002-5905-3591 + elixir_node: fr + +lilachic: + name: Liisa Lado-Villar + email: liisa.lado-villar@csc.fi + orcid: + elixir_node: fi diff --git a/docs/search.html b/docs/search.html new file mode 100755 index 0000000..b06e38e --- /dev/null +++ b/docs/search.html @@ -0,0 +1,89 @@ +--- +layout: base +title: Search +nav_exclude: true +search_exclude: true +--- + +

Search Results

+ +
+ Enter a search query in the search box on the left. +
+ + + + diff --git a/docs/search_data.json b/docs/search_data.json new file mode 100644 index 0000000..639c8a4 --- /dev/null +++ b/docs/search_data.json @@ -0,0 +1,32 @@ +--- +layout: null +nav_exclude: true +search_exclude: true +--- +{ +{%- for site_page in site.pages %} +{%- unless site_page.search_exclude == true %} + "{{ site_page.url | slugify }}": { + "title": "{{ site_page.title | xml_escape }}", + "content": {{site_page.content | markdownify | newline_to_br | replace: '
', ' ' | strip_html | normalize_whitespace | jsonify }}, + "url": " {{ site_page.url | xml_escape }}", + "author": "{{ site_page.author | xml_escape }}" + }, +{%- endunless %} +{%- endfor %} +{%- for site_post in site.posts %} +{%- unless site_page.search_exclude == true %} + "{{ site_post.url | slugify }}": { + "title": "{{ site_post.title | xml_escape }}", + "content": {{site_post.content | markdownify | newline_to_br | replace: '
', ' ' | strip_html | normalize_whitespace | jsonify }}, + "url": " {{ site_post.url | xml_escape }}", + "author": "{{ site_post.author | xml_escape }}" + }{%- unless forloop.last %},{%- endunless %} +{%- endunless %} +{%- else %} + {%- comment %} Dirty trick: There is a comma at the end of the sites loop, so we need at least one entry after {% endcomment %} + ".": { + ".": "." + } +{%- endfor %} +} diff --git a/docs/topics/technical-operational/countries_tech_stack/component_description.html b/docs/topics/technical-operational/countries_tech_stack/component_description.html new file mode 100644 index 0000000..c07e433 --- /dev/null +++ b/docs/topics/technical-operational/countries_tech_stack/component_description.html @@ -0,0 +1,153 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
#ComponentDescriptionRequiredLink to
1URLOfficial website for documentation-
2CredentialsFor connecting to Central EGA there are 2 types of credentials required:
User API for identifying and validating in Submitter Inbox the cEGA accounts
cEGA MQ credentials for connecting FEGA Node MQ		Y
3FEGA Node Encryption key pairA Crypt4GH key pair generated by the FEGA Node, and the public is shared with the Submitter so that files are sent encrypted for the FEGA NodeY
4FEGA Node MQRabbitMQ which is connected in shovel and federation mechanism with the cEGA MQY2
5Submitter InboxAn Inbox solution for the Researcher to submit files to a specific Node (e.g. SFTP, REST API).
The Inbox needs to be accessible by a Researcher via an URL.		Y2, 3
6Ingest PipelineMeans of interfacing with the cEGA so that the required messages are being sent at relevant steps of the submission process. https://localega.readthedocs.io/en/latest/amqp.html Y4, 7, 8, 9
7Archive storageStorage solution for storing archived files. e.g. S3, POSIX etc.Y6
8Archive File DatabaseMeans of storing information about the archived files and their AccessionIDs and dataset IDs mapping to AccessionIDs (file to dataset mapping).
Note: other details can be stored in the database e.g. checksums, timestamps, headers of crypt4gh file etc.		Y6
9Backup StorageStorage solution for storing a backup of the archived files. e.g. S3, POSIX etc.
Note: A file needs to be backed up in a different location than the Archive		Y6
10Main Source Code RepositoryWhere the source code can be foundN
11Main Programming LanguageMain programming language for the technical stack pipeline-
12Deployment MethodMeans which technology is used to put in production different components-
13Helpdesk Management SystemMain tool for user/helpdesk communicationN
14Helpdesk Portal TechnologyFederated EGA node helpedesk will provide means of interacting with submitter, registering DPA, establisng DACs and monitoring submissions.N15
15Monitoring ToolMeans of providing an overview of the status of submissions.
Good also for auditing purposes.		N14
16Metadata Submission MethodMeans how the researchers will send the metadata to Central EGA through a cEGA submitter portal, node portal or another solutionY
17Download SolutionMeans for a Requester to access the data once approval has been granted.Y7, 8, 18
18Data Access ToolMeans of enabling Requesters to Download the archived data.
tool for facilitating DACs		N
19General ContactEmail or website to contact the team deploying the solutionY
diff --git a/docs/topics/technical-operational/countries_tech_stack/finland_tech_stack.html b/docs/topics/technical-operational/countries_tech_stack/finland_tech_stack.html new file mode 100644 index 0000000..92bfaf5 --- /dev/null +++ b/docs/topics/technical-operational/countries_tech_stack/finland_tech_stack.html @@ -0,0 +1,106 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
#ComponentFinland
1URLhttps://research.csc.fi/-/fega
2Credentials
3FEGA Node Encryption key pair
4FEGA Node MQ
5Submitter InboxSFTP
6Ingest Pipeline
7Archive storagePOSIX / S3(dev)
8Archive File Database
9Backup StorageTape
10Main Source Code Repositoryhttps://github.com/neicnordic/sda-pipeline
11Main Programming LanguageGolang
12Deployment MethodKubernetes
13Helpdesk Management SystemRT - request tracker
14Helpdesk Portal Technology
15Monitoring Tool
16Metadata Submission MethodCentral EGA submitter Portal / Planning Developement of own Portal
17Download Solutionhttps://docs.csc.fi/data/sensitive-data/fega_application/
18Data Access Toolhttps://github.com/CSCfi/rems
19General Contact
diff --git a/docs/topics/technical-operational/countries_tech_stack/germany_tech_stack.html b/docs/topics/technical-operational/countries_tech_stack/germany_tech_stack.html new file mode 100644 index 0000000..36e720d --- /dev/null +++ b/docs/topics/technical-operational/countries_tech_stack/germany_tech_stack.html @@ -0,0 +1,111 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
#ComponentGermany
1URLhttps://www.ghga.de/
2Credentials
3FEGA Node Encryption key pair
4FEGA Node MQ
5Submitter Inbox
6Ingest Pipeline
7Archive storage
8Archive File Database
9Backup Storage
10Main Source Code Repository
11Main Programming Language
12Deployment Method
13Helpdesk Management SystemZammad
14Helpdesk Portal Technology
15Monitoring Tool
16Metadata Submission Method
17Download Solution
18Data Access Tool
19General Contact
diff --git a/docs/topics/technical-operational/countries_tech_stack/national_nodes_technical_stack.html b/docs/topics/technical-operational/countries_tech_stack/national_nodes_technical_stack.html new file mode 100644 index 0000000..2acbc76 --- /dev/null +++ b/docs/topics/technical-operational/countries_tech_stack/national_nodes_technical_stack.html @@ -0,0 +1,243 @@ + + +
+ + + + + + + + + + + + + + +
+ + {% include_relative countries_tech_stack/component_description.html %} + +
+ + +
+ {% include_relative countries_tech_stack/finland_tech_stack.html %} +
+ + +
+ {% include_relative countries_tech_stack/norway_tech_stack.html %} +
+ + +
+ {% include_relative countries_tech_stack/sweden_tech_stack.html %} +
+ + +
+ {% include_relative countries_tech_stack/germany_tech_stack.html %} +
+ + +
+ {% include_relative countries_tech_stack/spain_tech_stack.html %} +
+
diff --git a/docs/topics/technical-operational/countries_tech_stack/norway_tech_stack.html b/docs/topics/technical-operational/countries_tech_stack/norway_tech_stack.html new file mode 100644 index 0000000..346f108 --- /dev/null +++ b/docs/topics/technical-operational/countries_tech_stack/norway_tech_stack.html @@ -0,0 +1,106 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
#ComponentNorway
1URLhttps://ega.elixir.no/
2Credentials
3FEGA Node Encryption key pair
4FEGA Node MQ
5Submitter InboxREST API
6Ingest Pipeline
7Archive storageS3
8Archive File Database
9Backup Storage
10Main Source Code Repositoryhttps://github.com/neicnordic/sda-pipeline
11Main Programming LanguageGolang
12Deployment MethodDocker Swarm
13Helpdesk Management SystemRT - request tracker
14Helpdesk Portal Technology
15Monitoring Tool
16Metadata Submission MethodCentral EGA submitter Portal
17Download Solution
18Data Access Toolhttps://ega.elixir.no/retrieval.html
19General Contact
diff --git a/docs/topics/technical-operational/countries_tech_stack/spain_tech_stack.html b/docs/topics/technical-operational/countries_tech_stack/spain_tech_stack.html new file mode 100644 index 0000000..e7ba213 --- /dev/null +++ b/docs/topics/technical-operational/countries_tech_stack/spain_tech_stack.html @@ -0,0 +1,106 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
#ComponentSpain
1URLhttps://fega-test.bsc.es/docs/
2Credentials
3FEGA Node Encryption key pair
4FEGA Node MQ
5Submitter InboxSFTP
6Ingest Pipeline
7Archive storageGPFS
8Archive File Database
9Backup Storage
10Main Source Code Repositoryhttps://github.com/EGA-archive/LocalEGA
11Main Programming LanguagePython
12Deployment MethodDocker-Compose
13Helpdesk Management SystemRT - request tracker
14Helpdesk Portal Technology
15Monitoring Tool
16Metadata Submission MethodCentral EGA submitter Portal
17Download SolutionNextcloud
18Data Access Tool
19General Contacthttps://fega-test.bsc.es/docs/contact.html
diff --git a/docs/topics/technical-operational/countries_tech_stack/sweden_tech_stack.html b/docs/topics/technical-operational/countries_tech_stack/sweden_tech_stack.html new file mode 100644 index 0000000..7e36034 --- /dev/null +++ b/docs/topics/technical-operational/countries_tech_stack/sweden_tech_stack.html @@ -0,0 +1,106 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
#ComponentSweden
1URLhttps://nbis.se/infrastructure/sensitive-data-archive.html
2Credentials
3FEGA Node Encryption key pair
4FEGA Node MQ
5Submitter InboxS3 Proxy
6Ingest Pipeline
7Archive storageS3
8Archive File Database
9Backup Storage
10Main Source Code Repositoryhttps://github.com/neicnordic/sda-pipeline
11Main Programming LanguageGolang
12Deployment MethodKubernetes
13Helpdesk Management SystemRedmine
14Helpdesk Portal Technology
15Monitoring Tool
16Metadata Submission MethodCentral EGA submitter Portal
17Download Solution
18Data Access Tool
19General Contact
diff --git a/docs/topics/technical-operational/index.md b/docs/topics/technical-operational/index.md index 9f71457..f6a587d 100644 --- a/docs/topics/technical-operational/index.md +++ b/docs/topics/technical-operational/index.md @@ -12,7 +12,7 @@ Welcome! If you are involved in technical or operational aspects of establishing **You might find this page useful if you are:** - a technical team leader -- responsible for procuring resources +- responsible for procuring resources - a software developer or engineer - a bioinformatician - a support officer @@ -67,12 +67,18 @@ Central EGA Helpdesk have developed a set of SOPs to harmonise both user-facing ## 2. Learn from current node implementations Check-out current Federated EGA node implementations from some of the first established nodes: + - Finnish FEGA Node - German Human Genome-phenome Archive (GHGA) - Federated EGA Norway - Spanish FEGA (es-FEGA) - Swedish Sensitive Data Archive +### Technical requirements + +{% include_relative countries_tech_stack/national_nodes_technical_stack.html %} + + Hear more details about node implementations: - Norway, Sweden, and Finland FEGA node architecture and implementations (19 June 2020) - Further details on the Norwegian node (19 June 2020)