Add custom urls for reev microservices (#224)

.env.dev

@@ -6,4 +6,4 @@ USE_CACHE=0
 API_REEV_URL=https://reev.cubi.bihealth.org/internal/proxy
 # Default path to seqrepo data for Docker. Change it to your local development path.
 # It can look like this: "/home/<username>/seqrepo/master"
-SEQREPO_DATA_DIR=
+AUTO_ACMG_SEQREPO_DATA_DIR=

docs/usage.rst

@@ -71,7 +71,7 @@ them with the following command:
     tar -czvf seqrepo_master.tar.gz .dev/volumes/seqrepo/master --strip-components=1
 
 Finally, you should have the following directories structures in ``/usr/local/share/seqrepo`` (local):
-and SEQREPO_DATA_DIR (master):
+and AUTO_ACMG_SEQREPO_DATA_DIR (master):
 
 
 .. code-block:: bash
@@ -133,7 +133,7 @@ The application can be configured using environment variables. An example config
     API_REEV_URL=https://reev.cubi.bihealth.org/internal/proxy
     # Default path to seqrepo data for Docker. Change it to your local development path.
     # It can look like this: "/home/<username>/seqrepo/master"
-    SEQREPO_DATA_DIR=/home/gromdimon/Custom/seqrepo/master
+    AUTO_ACMG_SEQREPO_DATA_DIR=/home/gromdimon/Custom/seqrepo/master
 
 Adjust the values according to your environment. Here are brief descriptions of the variables. Note
 that not all variables are required for the application to run. More info below.:
@@ -143,15 +143,15 @@ that not all variables are required for the application to run. More info below.
 - ``CACHE_DIR``: Path to the cache directory.
 - ``API_V1_STR``: Base path for API endpoints.
 - ``API_REEV_URL``: URL of the REEV API.
-- ``SEQREPO_DATA_DIR``: Path to the project-specific SeqRepo data directory.
+- ``AUTO_ACMG_SEQREPO_DATA_DIR``: Path to the project-specific SeqRepo data directory.
 - ``GENEBE_API_KEY``: API key for the GeneBE service. You'll need it for running the benchmarks.
 - ``GENEBE_USERNAME``: Username for the GeneBE service. You'll need it for running the benchmarks.
 
 You will most likely need to set the following variables:
 
 - ``DEBUG``: Set to ``1`` to enable debug mode.
 - ``USE_CACHE``: Set to ``1`` to enable caching. This is recommended only for development.
-- ``SEQREPO_DATA_DIR``: Set to the path of the custom project SeqRepo data directory.
+- ``AUTO_ACMG_SEQREPO_DATA_DIR``: Set to the path of the custom project SeqRepo data directory.
 
 To pass this configuration to the Docker container, ensure the ``.env`` file is located where
 you run the ``docker run`` command or specify the correct path to the file using the ``--env-file``

src/api/reev/annonars.py

@@ -16,7 +16,7 @@
 from src.defs.strucvar import StrucVar
 
 #: Annonars API base URL
-ANNONARS_API_BASE_URL = f"{settings.API_REEV_URL}/annonars"
+ANNONARS_API_BASE_URL = settings.AUTO_ACMG_API_ANNONARS_URL or f"{settings.API_REEV_URL}/annonars"
 
 
 class AnnonarsClient:

src/api/reev/dotty.py

@@ -12,7 +12,7 @@
 from src.defs.genome_builds import GenomeRelease
 
 #: Dotty API base URL
-DOTTI_API_BASE_URL = f"{settings.API_REEV_URL}/dotty"
+DOTTI_API_BASE_URL = settings.AUTO_ACMG_API_DOTTY_URL or f"{settings.API_REEV_URL}/dotty"
 
 
 class DottyClient:

src/api/reev/mehari.py

@@ -15,7 +15,7 @@
 from src.defs.strucvar import StrucVar
 
 #: Mehari API base URL
-MEHARI_API_BASE_URL = f"{settings.API_REEV_URL}/mehari"
+MEHARI_API_BASE_URL = settings.AUTO_ACMG_API_MEHARI_URL or f"{settings.API_REEV_URL}/mehari"
 
 
 class MehariClient:

src/core/config.py

@@ -33,8 +33,20 @@ class Settings(BaseSettings):
     #: Base URL to reev
     API_REEV_URL: str = ""
 
+    # Keep this setting empty. It is used for the reev-docker-compose.
+    #: Base URL to annonars
+    AUTO_ACMG_API_ANNONARS_URL: str = ""
+
+    # Keep this setting empty. It is used for the reev-docker-compose.
+    #: Base URL to mehari
+    AUTO_ACMG_API_MEHARI_URL: str = ""
+
+    # Keep this setting empty. It is used for the reev-docker-compose.
+    #: Base URL to dotty
+    AUTO_ACMG_API_DOTTY_URL: str = ""
+
     #: Path to seqrepo data directory
-    SEQREPO_DATA_DIR: str = ""
+    AUTO_ACMG_SEQREPO_DATA_DIR: str = ""
 
     #: API key for genebe
     GENEBE_API_KEY: str = ""
@@ -74,7 +86,7 @@ class Config(BaseModel):
     api_base_url_dotty: Optional[str] = None
 
     #: Path to the seqrepo data directory.
-    seqrepo_data_dir: Optional[str] = settings.SEQREPO_DATA_DIR
+    seqrepo_data_dir: Optional[str] = settings.AUTO_ACMG_SEQREPO_DATA_DIR
 
     @model_validator(mode="before")
     @classmethod