Added endpoint doc to wiki

.gitignore

 ## Generated
 site/
+node_modules/
+*.bkp
 
 ## Core latex/pdflatex auxiliary files:
 *.aux

Makefile

@@ -8,5 +8,12 @@ build:
 run: build
 	docker-compose up
 
+docs:
+	widdershins --environment ./misc/env.json ./misc/api-authentication.yaml -o ./docs/operation/authentication.md
+	widdershins --environment ./misc/env.json ./misc/api-container.yaml -o ./docs/operation/container.md
+	widdershins --environment ./misc/env.json ./misc/api-database.yaml -o ./docs/operation/database.md
+	widdershins --environment ./misc/env.json ./misc/api-identifier.yaml -o ./docs/operation/identifier.md
+	widdershins --environment ./misc/env.json ./misc/api-query.yaml -o ./docs/operation/query.md
+
 deploy: run
 	sudo cp -r ./site/* /usr/share/nginx/html/
\ No newline at end of file

docs/contact.md

+---
+hide:
+
+- navigation
+
+---
+
+# Contact
+
+Ao.Univ.Prof. Dipl.-Ing. Dr.techn. Andreas Rauber<br />
+[Technische Universität Wien](https://ror.org/04d836q62)<br />
+[Information and Software Engineering Group](https://informatics.tuwien.ac.at/orgs/e194-01)<br />
+Favoritenstraße 9-11<br />
+A-1040 Vienna, Austria
+
+Mail: [andreas.rauber@tuwien.ac.at](mailto:andreas.rauber@tuwien.ac.at)
\ No newline at end of file

docs/index.md

@@ -14,16 +14,17 @@ databases accessible in their collection. Challenges revolve around organizing,
 within databases and constitute a major technical burden as their internal representation greatly differs from static
 documents most digital repositories are designed for.
 
+[Get Started](/getting-started){ .action-button .md-button .md-button--primary }
+
 ## Application Areas
 
 We present a database repository system that allows researchers to ingest data into a central, versioned repository
 through common interfaces, provides efficient access to arbitrary subsets of data even when the underlying data store is
 evolving, allows reproducing of query results and supports findable-, accessible-, interoperable- and reusable data.
 
-[Get Started](/getting-started){ .action-button .md-button .md-button--primary } [PDF](/pdf/document.pdf){ .action-button .md-button .md-button--secondary }
-
-## Demo
-
-Public demonstration instance [https://dbrepo.ossdip.at](https://dbrepo.ossdip.at)
+## More Information
 
-![Image](/images/logos_1035_142.png)
+- This documentation can be downloaded as [PDF](/pdf/document.pdf)
\ No newline at end of file
+- Public demonstration instance [https://dbrepo.ossdip.at](https://dbrepo.ossdip.at)
+- Join our [mailing list](https://lists.univie.ac.at/mailman/listinfo/fairdata_dbrepo) to receive bi-monthly updates
+  about the progress, new features and events!
\ No newline at end of file

docs/operation.md → docs/operation/index.md

----
-hide:
-
-- navigation
-
----
-
 # Operation
 
 ## Deploy

docs/system.md

@@ -9,6 +9,100 @@ hide:
 
 ## Architecture
 
+The repository is designed as a microservice architecture to ensure scalability and the utilization of various
+technologies. The conceptualized microservices operate the basic database operations, data versioning as well as
+*findability*, *accessability*, *interoperability* and *reuseability* (FAIR).
+
+<figure markdown>
+![Microservice cloud architecture](/images/dia_architecture.png) 
+<figcaption>Microservice cloud architecture</figcaption>
+</figure>
+
+### Discovery Service
+
+This microservice allows service discovery and registration of containers that provide services.
+
+### Gateway Service
+
+Provides a single point of access to the *application programming interface* (API).
+
+### Authentication Service
+
+Very specific to the deployment of the organization. In our reference implementation we implement a *security assertion
+markup language* (SAML) service provider and use our institutional SAML identity provider for obtaining account data
+through an encrypted channel.
+
+### Metadata Database
+
+is the core component of the project. It is a relational database that contains metadata about all researcher databases
+created in the database repository like column names, check expressions, value enumerations or key/value constraints and
+relevant data for citing data sets. Additionally, the concept, e.g. URI of units of measurements of numerical columns is
+stored in the Metadata Database in order to provide semantic knowledge context. We
+use [PostgreSQL](https://www.postgresql.org/) for its rich capabilities in the reference implementation.
+
+### Unit Service
+
+It is designed to map terms in the domain of units of measurement to controlled vocabulary, modelled in
+the [ontology of units of measure](https://github.com/HajoRijgersberg/OM). This service validates researcher provided in
+units and provides a *uniform resource identifier* (URI) to the related concept, which will be stored in the system.
+Furthermore, there is a method for auto-completing text and listing a description as well as commonly used unit symbols.
+
+### Identifier Service
+
+This microservice is responsible for creating and resolving a *persistent identifier* (PID) attached to a query to
+obtain the metadata attached to it and allow re-execution of a query. We store both the query and hashes of the query
+and result set to allow equality checks of the originally obtained result set and the currently obtained result set. In
+the reference implementation we currently only use a numerical id column and plan to integrate *digital object
+identifier* (DOI) through our institutional library soon.
+
+### Search Service
+
+It processes search requests from the Gateway Service for full-text lookups in the Metadata Database. We use
+[Elasticsearch](https://www.elastic.co/) in the reference implementation.
+
+### Container Service
+
+It is responsible for Docker container lifecycle operations and updating the local copy of the Docker images.
+
+### Database Service
+
+It creates the databases inside a Docker container and the Query Store. Currently we only
+support [MariaDB](https://mariadb.org/) images that allow table versioning with low programmatic effort.
+
+### Table Service
+
+This microservice handles table operations inside a database that is managed by the Database Service. We
+use [Hibernate](https://hibernate.org/orm/) for schema and data ingest operations.
+
+### Broker Service
+
+It holds exchanges and topics responsible for holding AMQP messages for later consumption. We
+use [RabbitMQ](https://www.rabbitmq.com/) in the reference implementation.
+
+### Query Service
+
+It provides an interface to insert data into the tables created by the Table Service. It also allows for view-only,
+paginated and versioned query execution to the raw data and consumes messages in the message queue from the Broker
+Service.
+
+### Portal
+
+It provides a *graphical user interface* (GUI) for a researcher to interact with the database repository's API.
+
+### Analyse Service
+
+It suggests data types for the FAIR Portal when creating a table from a *comma separated values* (CSV) file. It
+recommends enumerations for columns and returns e.g. a list of potential primary key candidates. The researcher is able
+to confirm these suggestions manually. Moreover, the *Analyze Service* determines basic statistical properties of
+numerical columns.
+
+### User Database
+
+This container runs a relational database engine that allows data versioning and contains the Query Store, a special
+table that stores all queries issued to the Researcher Database along with metadata. We store the queries here and not
+in the metadata database level to ensure that they are preserved along with the original database for a regular backup
+and archival together with the original database once the container is retired.
+
 ### Technical
 
 We use Docker for deployment. The containers are packing all runtime dependencies, when starting them all necessary

misc/diagrams.drawio

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id="SixR3OZ22FMnOk72hDml" 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\ No newline at end of file

misc/env.json

+{
+  "language_tabs": [
+    {
+      "python": "Python"
+    },{
+      "java": "Java"
+    }
+  ]
+}

mkdocs.yml

@@ -2,22 +2,25 @@ site_name: Database Repository
 repo_url: https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services
 repo_name: fda-services
 site_author: FAIR Data Austria
-copyright: CC-BY 4.0
+copyright: CC-BY 4.0 Technische Universität Wien & Universität Wien
 extra:
   homepage: https://dbrepo.tuwien.ac.at
   social:
     - icon: fontawesome/brands/gitlab
       link: https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services
-    - icon: fontawesome/brands/twitter
-      link: https://twitter.com/RDMTUWien
-    - icon: fontawesome/solid/globe
-      link: https://forschungsdaten.at/fda/
 nav:
   - Home: index.md
   - getting-started.md
   - system.md
-  - operation.md
+  - Operation:
+      - operation/index.md
+      - operation/authentication.md
+      - operation/container.md
+      - operation/database.md
+      - operation/identifier.md
+      - operation/query.md
   - publications.md
+  - contact.md
 extra_css:
   - stylesheets/extra.css
 theme: