Switch to ENV config

README.rst

@@ -24,6 +24,16 @@ The easiest way to install PyHPO-API is via pip
     pip install pyhpoapi
 
 
+.. note::
+
+    **PyHPO-API** ships with ``pyhpo`` as the underlying Ontology by default. it is also possible to use `hpo3 <https://pypi.org/project/hpo3/>`_ instead. ``hpo3`` is a drop-in replacement of ``pyhpo`` written in Rust and is much faster. It is not 100% feature complete, so use it with caution. To switch to ``hpo3`` unintstall pyhpo and then install hpo3
+
+    .. code:: bash
+
+        pip uninstall -y pyhpo
+        pip install hpo3
+
+
 Usage
 =====
 
@@ -53,13 +63,11 @@ you can run PyHPO-API with multiple workers
 
 CORS
 ----
-If you need to allow cross-origin requests, you can simply create
-a ``config.ini`` file in your working directory and specify CORS settings::
+If you need to allow cross-origin requests, you specify CORS settings through environment variables::
 
-    [default]
-    cors-origins = *
-    cors-methods = GET,POST
-    cors-headers = *
+    export PYHPOAPI_CORS_ORIGINS="*"
+    export PYHPOAPI_CORS_METHODS="GET,POST"
+    export PYHPOAPI_CORS_HEADERS="*"
 
 
 Dev

pyhpoapi/config.py

@@ -4,7 +4,6 @@
 """
 
 import os
-import configparser
 from typing import Any, List
 
 
@@ -15,27 +14,20 @@ def config_item_list(value: str, convert=str) -> List[Any]:
     return [convert(x) for x in value.split(',')]
 
 
-local_config = os.path.join(
-    os.getcwd(),
-    'config.ini'
-    )
+VERSION = "2.0.0"
 
-
-config = configparser.ConfigParser()
-if os.path.exists(local_config):
-    config.read(local_config)
-
-
-VERSION = config.get('default', 'version', fallback='1.2.2')
+MASTER_DATA = os.environ.get("PYHPOAPI_DATA_DIR", "")
 
 CORS_ORIGINS = config_item_list(
-    config.get('default', 'cors-origins', fallback='')
+    os.environ.get("PYHPOAPI_CORS_ORIGINS", "")
 )
+
 CORS_METHODS = config_item_list(
-    config.get('default', 'cors-methods', fallback='')
+    os.environ.get("PYHPOAPI_CORS_METHODS", "")
 )
+
 CORS_HEADERS = config_item_list(
-    config.get('default', 'cors-headers', fallback='')
+    os.environ.get("PYHPOAPI_CORS_HEADERS", "")
 )
 
 OPENAPI_TAGS = [

pyhpoapi/server.py

@@ -42,10 +42,15 @@ def custom_openapi():
 
 
 def initialize_ontology() -> None:
-    data_dir = os.environ.get("PYHPOAPI_DATA_DIR", "")
-    logger.debug(f"Loading Ontology from {data_dir}")
+    data_dir = config.MASTER_DATA
+
+    if data_dir == "":
+        logger.debug("Using builtin standard ontology")
+        _ = Ontology()
+    else:
+        logger.info(f"Loading Ontology from {data_dir}")
+        _ = Ontology(data_dir)
 
-    _ = Ontology(data_dir)
     terms.gene_model = EnrichmentModel('gene')
     terms.omim_model = EnrichmentModel('omim')
     terms.hpo_model_genes = HPOEnrichment('gene')