fix: Path in docs (#208)

backend/app/api/api_v1/api.py

@@ -48,9 +48,20 @@
 
 
 class OrcidOpenId(OpenID):
-    """Custom OrcID OpenID client that fetches the user's email from the OrcID API.
-
+    """
+    Custom OrcID OpenID client that fetches the user's email from the OrcID API.
     Note that users must have given access to their email address for "trusted parties".
+
+    :param client_id: client ID
+    :type client_id: str
+    :param client_secret: client secret
+    :type client_secret: str
+    :param openid_configuration_endpoint: OpenID configuration endpoint
+    :type openid_configuration_endpoint: str
+    :param name: name of the provider
+    :type name: str
+    :param base_scopes: base scopes
+    :type base_scopes: list, optional
     """
 
     def __init__(

backend/app/api/internal/api.py

@@ -15,7 +15,12 @@
 @api_router.get("/version")
 @api_router.post("/version")
 async def version():
-    """Return REEV software version"""
+    """
+    Return reev version.
+
+    :return: reev version
+    :rtype: str
+    """
     if settings.REEV_VERSION:
         version = settings.REEV_VERSION
     else:
@@ -26,7 +31,12 @@ async def version():
 @api_router.get("/frontend-settings")
 @api_router.post("/frontend-settings")
 async def matomo():
-    """Return Frontend settings"""
+    """
+    Return frontend settings.
+
+    :return: frontend settings
+    :rtype: dict
+    """
     frontend_settings = {
         "matomo_host": settings.MATOMO_HOST,
         "matomo_site_id": settings.MATOMO_SITE_ID,

backend/app/api/internal/endpoints/proxy.py

@@ -13,7 +13,20 @@
 @router.get("/{path:path}")
 @router.post("/{path:path}")
 async def reverse_proxy(request: Request) -> Response:
-    """Implement reverse proxy for internal backend services."""
+    """
+    Reverse proxy to internal services.
+    Supported services:
+    - AnnoNARS
+    - MeHARI
+    - Viguno
+    - NGINX
+    - Dotty
+
+    :param request: request
+    :type request: :class:`fastapi.Request`
+    :return: response
+    :rtype: :class:`fastapi.Response`
+    """
     url = request.url
     backend_url = None
 

backend/app/api/internal/endpoints/remote.py

@@ -72,7 +72,17 @@ def get_legacy_session():
 
 @router.get("/variantvalidator/{path:path}")
 async def variantvalidator(request: Request, path: str):
-    """Implement reverse proxy for variantvalidator.org."""
+    """
+    Implement VariantValidator API. Proxy requests to the
+    `VariantValidator <https://rest.variantvalidator.org/>`_ backend.
+
+    :param request: request
+    :type request: :class:`fastapi.Request`
+    :param path: path to append to the backend URL
+    :type path: str
+    :return: response
+    :rtype: :class:`fastapi.responses.StreamingResponse`
+    """
     url = request.url
 
     # change grch to GRCh and strip "chr" prefixes
@@ -97,7 +107,15 @@ async def variantvalidator(request: Request, path: str):
 
 @router.get("/acmg/{path:path}")
 async def acmg(request: Request):
-    """Implement searching for ACMG classification."""
+    """
+    Implement searching for ACMG classification for SNVs and indels.
+    Proxy requests to the `WinterVar <http://wintervar.wglab.org/>`_ backend.
+
+    :param request: request
+    :type request: :class:`fastapi.Request`
+    :return: ACMG classification
+    :rtype: dict
+    """
     query_params = request.query_params
     chromosome = query_params.get("chromosome")
     position = query_params.get("position")
@@ -128,7 +146,15 @@ async def acmg(request: Request):
 
 @router.get("/cnv/acmg/{path:path}")
 async def cnv_acmg(request: Request):
-    """Implement searching for ACMG classification for CNVs."""
+    """
+    Implement searching for ACMG classification for CNVs.
+    Proxy requests to the `WinterVar <http://wintervar.wglab.org/>`_ backend.
+
+    :param request: request
+    :type request: :class:`fastapi.Request`
+    :return: ACMG classification
+    :rtype: dict
+    """
     query_params = request.query_params
     chromosome = query_params.get("chromosome")
     start = query_params.get("start")

docs/api_api_v1.rst

@@ -10,7 +10,7 @@ app.api.api_v1
 app.api.api_v1.endpoints.adminmsgs
 ----------------------------------
 
-.. automodule:: backend.app.api.api_v1.endpoints.adminmsgs
+.. automodule:: app.api.api_v1.endpoints.adminmsgs
     :members:
     :undoc-members:
     :show-inheritance:
@@ -20,7 +20,7 @@ app.api.api_v1.endpoints.adminmsgs
 app.api.api_v1.endpoints.auth
 -----------------------------
 
-.. automodule:: backend.app.api.api_v1.endpoints.auth
+.. automodule:: app.api.api_v1.endpoints.auth
     :members:
     :undoc-members:
     :show-inheritance:
@@ -30,7 +30,7 @@ app.api.api_v1.endpoints.auth
 app.api.api_v1.endpoints.bookmarks
 ----------------------------------
 
-.. automodule:: backend.app.api.api_v1.endpoints.bookmarks
+.. automodule:: app.api.api_v1.endpoints.bookmarks
     :members:
     :undoc-members:
     :show-inheritance:
@@ -40,7 +40,7 @@ app.api.api_v1.endpoints.bookmarks
 app.api.api_v1.endpoints.caseinfo
 ---------------------------------
 
-.. automodule:: backend.app.api.api_v1.endpoints.caseinfo
+.. automodule:: app.api.api_v1.endpoints.caseinfo
     :members:
     :undoc-members:
     :show-inheritance:
@@ -50,7 +50,7 @@ app.api.api_v1.endpoints.caseinfo
 app.api.api_v1.endpoints.utils
 ------------------------------
 
-.. automodule:: backend.app.api.api_v1.endpoints.utils
+.. automodule:: app.api.api_v1.endpoints.utils
     :members:
     :undoc-members:
     :show-inheritance:

docs/api_internal.rst

@@ -10,7 +10,7 @@ app.api.internal
 app.api.internal.endpoints.remote
 ---------------------------------
 
-.. automodule:: backend.app.api.internal.endpoints.remote
+.. automodule:: app.api.internal.endpoints.remote
     :members:
     :undoc-members:
     :show-inheritance:

docs/api_models.rst

@@ -10,26 +10,26 @@ app.models
 app.models.adminmsg
 -------------------
 
-.. automodule:: backend.app.models.adminmsg
+.. automodule:: app.models.adminmsg
     :members:
 
 -------------------
 app.models.bookmark
 -------------------
 
-.. automodule:: backend.app.models.bookmark
+.. automodule:: app.models.bookmark
     :members:
 
 ---------------
 app.models.user
 ---------------
 
-.. automodule:: backend.app.models.user
+.. automodule:: app.models.user
     :members:
 
 -------------------
 app.models.caseinfo
 -------------------
 
-.. automodule:: backend.app.models.caseinfo
+.. automodule:: app.models.caseinfo
     :members: