Feature/update readme and swagger (#151)

* swagger endpoint doc

* swagger

* trivy

* annotation controller swagger

* digital media swagger

* digital specimen swagger

* mjr swagger

* readme

* code review

* trivy

README.md

@@ -7,40 +7,31 @@ In general, the find/search APIs are open, and APIs for create, update and delet
 
 All endpoints are based on the [JSON:API](https://jsonapi.org/) specification.
 It follows the guidelines and best practices described in [BiCIKL Deliverable 1.3](https://docs.google.com/document/d/1RgngKSPabEs-Pir6vA25iFDgVorbEZe7duT7L7vQ7QI)
-The organisation endpoints are an exception.
 
 The backend provides APIs for the following objects:
 - Digital Specimens
 - Digital Media Objects
 - Annotations
-- Users
-- Organisations
 
 ## Storage solutions
 In general, there are three places where data is stored:
-- Postgres database
-The Postgres database stores the latest active version of the object.
+- **Postgres database**: The Postgres database stores the latest active version of the object.
 It is used in retrieving a specific object based on the id.
 It can also be used to combine objects based on their relationships.
 
-- Elasticsearch
-This data storage is used for searching and aggregating.
+- **Elasticsearch**: This data storage is used for searching and aggregating.
 It is used for data discovery and provides endpoints for the filters and search fields.
 In general, it does not return a single object, but a paginated list of objects.
 Additionally, it can provide aggregations showing how many items comply to the search criteria.
 
-- MongoDB
-MongoDB is used for provenance storage and stores the historical data.
+- **MongoDB**: MongoDB is used for provenance storage and stores the historical data.
 This data storage is used for displaying previous versions of the data.
 
 ## API documentation
 The APIs are documented through code-generated OpenAPI v3 and Swagger.
 - The swagger endpoint is: https://sandbox.dissco.tech/api/swagger-ui/index.html#/
 - The OpenAPI endpoint is: https://sandbox.dissco.tech/api/v3/api-docs
 
-As we use generic objects, the API documentation is not as detailed as we would like.
-We are looking at additional options for more detailed documentation.
-
 ### Digital Specimens
 For Digital Specimen, we only provide search and read functionality through the APIs.
 It follows a generic structure.
@@ -79,24 +70,10 @@ The create, update and tombstone endpoints are protected through authentication.
 The actions posted to these endpoints are forwarded to the annotation processor.
 This processor manages all the annotations and is the only application authorized to create or change annotations.
 
-### User
-For users, we provide a set of read, create, update and delete functionality through the APIs.
-When a new user is registered it will be created in the database.
-A user can update his or her information through the profile page.
-The backend will then update the user information in the database.
-
-### Organisation
-The organisation endpoints provide read functionality for the organisations.
-These organisations are inserted in the database and need to be updated manually.
-The organisation endpoints can be used by forms.
-
-### Organisation document
-The organisation documents can be used to insert documents for a particular organisation.
-These endpoints can be used to insert the result of forms.
-
 ## Run locally
 To run the system locally, it can be run from an IDEA.
 Clone the code and fill in the application properties (see below).
+The application requires a connection to an elastic search instance and a mongodb instance.
 The application needs a connection to a Postgres database, MongoDB and Elasticsearch.
 For creation and modification of annotations it needs a reachable annotation processor service.
 
@@ -121,10 +98,23 @@ elasticsearch.port=# The port of the Elasticsearch cluster
 #Oauth properties
 spring.security.oauth2.resourceserver.jwt.issuer-uri=# The URI to the JWT issuer
 spring.security.oauth2.authorizationserver.endpoint.jwk-set-uri=# The URI to the JWT OpenId certifications 
+token.secret=# Keycloak secret
+token.id=# Keycloak client id
+token.grant-type= # Keycloak grant type
+
+#Kafka properties
+kafka.publisher.host=# Endpoint for kafka publisher
 
 #MongoDB properties
 mongo.connection-string=# Connection string to MongoDB
 mongo.database=# Database name of MongoDB
 
 #Feign clients
-feign.annotations=# Path to annotation proccessor endpoint
+feign.annotations=# Path to annotation proccessor endpoint
+
+#Endpoints
+endpoint.handle-endpoint=# Endpoint to handle API
+endpoint.token-endpoint=# Endpoint to keycloak authenticator
+
+#Application Properties
+application.base-url=# The url of the application (used to build JsonApiLinks objects)

pom.xml

@@ -90,6 +90,11 @@
       <artifactId>springdoc-openapi-starter-webmvc-ui</artifactId>
       <version>${springdoc.version}</version>
     </dependency>
+    <dependency>
+      <groupId>org.springdoc</groupId>
+      <artifactId>springdoc-openapi-starter-webflux-ui</artifactId>
+      <version>${springdoc.version}</version>
+    </dependency>
     <dependency>
       <groupId>org.springframework.boot</groupId>
       <artifactId>spring-boot-starter-webflux</artifactId>
@@ -249,6 +254,24 @@
           <useSystemClassLoader>false</useSystemClassLoader>
         </configuration>
       </plugin>
+      <plugin>
+        <groupId>org.springdoc</groupId>
+        <artifactId>springdoc-openapi-maven-plugin</artifactId>
+        <version>1.4</version>
+        <executions>
+          <execution>
+            <id>integration-test</id>
+            <goals>
+              <goal>generate</goal>
+            </goals>
+            <configuration>
+              <outputFileName>openapi.yaml</outputFileName>
+              <outputDir>${project.build.directory}</outputDir>
+            </configuration>
+          </execution>
+        </executions>
+      </plugin>
+
       <plugin>
         <groupId>org.codehaus.mojo</groupId>
         <artifactId>exec-maven-plugin</artifactId>