index file for API documentation

web/src/main/asciidoc/index.adoc

+= Rest API Documentation
+Piotr Gawron
+v{project-version} {build-time}
+:toc: left
+:sectnums:
+
+
+== Introduction
+
+Rest API is located in /api/ path of the deployed application. For instance, Rest API of pdmap project that can be browsed using https://pdmap.uni.lu/minerva/ will be located here: https://pdmap.uni.lu/minerva/api/
+
+Rest API tries to follow link:https://cloud.google.com/apis/design/[API Design Guide] by Google.
+
+For API calls that require authentication MINERVA_AUTH_TOKEN obtained during login process must be included.
+
+
+== QuickStart guide
+Here is sample example that shows information about all projects accessible by guest account (anonymous user):
+
+include::{snippets}/projects/project_data/list/curl-request.adoc[]
+
+If we are interested in the API calls that require more privileges than anonymous user we need to login first:
+
+include::{snippets}/authentication/login/curl-request.adoc[]
+
+include::{snippets}/authentication/login/response-body.adoc[]
+
+The response creates an authentication token and puts it into a cookie MINERVA_AUTH_TOKEN=xxxxxxxx. When using console curl command this cookie must be attached to every query that follows. When we have authentication token we can access information about specific user on the server:
+
+include::{snippets}/user/get_user/curl-request.adoc[]
+
+== Categories
+
+=== <<authentication.adoc#,Authentication>> 
+=== <<configuration.adoc#,Configuration>>
+Methods allowing to obtain configuration information from server and updating it with proper privileges
+
+=== <<converter.adoc#,Converter>>
+Conversion API provides access to MINERVA’s ability to convert between different systems biology network formats and to export of layouts to different graphical formats
+
+=== <<file.adoc#,Files>>
+Methods that allow to upload files into the system
+
+=== <<genomics.adoc#,Genomics>>
+Methods allowing to access genome data
+
+=== <<mesh.adoc#,Mesh>>
+Methods allowing to access info about mesh data
+
+=== <<plugin.adoc#,Plugins>>
+Methods allowing to store some data for plugin infrastructure
+
+=== <<project.adoc#,Project>>
+Set of methods allowing to obtain information about projects and allowing to create new project and modifying existing ones
+
+=== <<taxonomy.adoc#,Taxonomy>>
+Methods allowing to access info about taxonomy data
+
+=== <<user.adoc#,Users>>
+Set of methods allowing to obtain and manage users and their access control

web/src/main/asciidoc/project.adoc

+= Rest API Documentation - Project
+Piotr Gawron
+v{project-version} {build-time}
+:toc: left
+:sectnums:
+
+
+=== <<project_data.adoc#,Project Data>> 
+=== <<project_chemicals.adoc#,Project Chemicals>>
+=== <<project_comments.adoc#,Project Comments>>
+=== <<project_drugs.adoc#,Project Drugs>>
+=== <<project_maps.adoc#,Project Maps>>
+=== <<project_mirna.adoc#,Project Micro RNA>>
+=== <<project_overlays.adoc#,Project Overlays>>
+=== <<project_privileges.adoc#,Project Privileges>>