Merge pull request #37 from bento-platform/fix-service-info-env

fix: service-info environment + other misc changes
bento-platform · Mar 28, 2023 · 3a02946 · 3a02946
2 parents df0fba5 + 3b89d4d
commit 3a02946
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Showing 5 changed files with 157 additions and 120 deletions.
diff --git a/bento_wes/app.py b/bento_wes/app.py
@@ -53,19 +53,15 @@ def __call__(self, *args, **kwargs):
     else:
         update_db()
 
-    if application.config["IS_RUNNING_DEV"]:
-        app_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
-        subprocess.run(["git", "config", "--global", "--add", "safe.directory", str(app_dir)])
-
 
 # TODO: Not compatible with GA4GH WES due to conflict with GA4GH service-info (preferred)
 @application.route("/service-info", methods=["GET"])
 def service_info():
     info: GA4GHServiceInfo = {
-        "id": application.config["SERVICE_ID"],
+        "id": current_app.config["SERVICE_ID"],
         "name": SERVICE_NAME,  # TODO: Should be globally unique?
         "type": SERVICE_TYPE,
-        "description": "Workflow execution service for a CHORD application.",
+        "description": "Workflow execution service for a Bento instance.",
         "organization": {
             "name": "C3G",
             "url": "https://www.computationalgenomics.ca"
@@ -78,7 +74,8 @@ def service_info():
             "gitRepository": "https://github.com/bento-platform/bento_wes",
         },
     }
-    if not application.config["IS_RUNNING_DEV"]:
+
+    if not current_app.config["IS_RUNNING_DEV"]:
         return jsonify(info)
 
     info["environment"] = "dev"

diff --git a/bento_wes/config.py b/bento_wes/config.py
@@ -1,5 +1,7 @@
 import os
 
+from typing import Optional, Tuple
+
 from .constants import SERVICE_ID
 
 
@@ -14,45 +16,47 @@
 
 
 class Config:
-    CHORD_URL = os.environ.get("CHORD_URL", "http://127.0.0.1:5000/")
+    CHORD_URL: str = os.environ.get("CHORD_URL", "http://127.0.0.1:5000/")
 
-    BENTO_DEBUG = os.environ.get(
+    BENTO_DEBUG: bool = os.environ.get(
         "BENTO_DEBUG",
         os.environ.get(
             "CHORD_DEBUG",
             os.environ.get("FLASK_DEBUG", "false"))).strip().lower() in TRUTH_VALUES
-    BENTO_VALIDATE_SSL = os.environ.get("BENTO_VALIDATE_SSL", str(not BENTO_DEBUG)).strip().lower() in TRUTH_VALUES
+    BENTO_VALIDATE_SSL: bool = os.environ.get(
+        "BENTO_VALIDATE_SSL", str(not BENTO_DEBUG)).strip().lower() in TRUTH_VALUES
 
-    IS_RUNNING_DEV = os.environ.get("FLASK_DEBUG", "false").strip().lower() in ("true", "1")
+    IS_RUNNING_DEV: bool = os.environ.get("FLASK_DEBUG", "false").strip().lower() in TRUTH_VALUES
 
-    DATABASE = os.environ.get("DATABASE", "bento_wes.db")
+    DATABASE: str = os.environ.get("DATABASE", "bento_wes.db")
     SERVICE_ID = SERVICE_ID
-    SERVICE_TEMP = os.environ.get("SERVICE_TEMP", "tmp")
-    SERVICE_URL_BASE_PATH = os.environ.get("SERVICE_URL_BASE_PATH", "/")
+    SERVICE_TEMP: str = os.environ.get("SERVICE_TEMP", "tmp")
+    SERVICE_URL_BASE_PATH: str = os.environ.get("SERVICE_URL_BASE_PATH", "/")
 
     # WDL-file-related configuration
-    WOM_TOOL_LOCATION = os.environ.get("WOM_TOOL_LOCATION")
-    WORKFLOW_HOST_ALLOW_LIST = os.environ.get("WORKFLOW_HOST_ALLOW_LIST")
+    WOM_TOOL_LOCATION: Optional[str] = os.environ.get("WOM_TOOL_LOCATION")
+    WORKFLOW_HOST_ALLOW_LIST: Optional[str] = os.environ.get("WORKFLOW_HOST_ALLOW_LIST")
 
     # Backend configuration
-    CROMWELL_LOCATION = os.environ.get("CROMWELL_LOCATION", "/cromwell.jar")
+    CROMWELL_LOCATION: str = os.environ.get("CROMWELL_LOCATION", "/cromwell.jar")
 
     # OTT-related configuration
-    OTT_ENDPOINT_NAMESPACE = os.environ.get("OTT_ENDPOINT_NAMESPACE", f"{CHORD_URL}api/auth/ott/")
+    OTT_ENDPOINT_NAMESPACE: str = os.environ.get("OTT_ENDPOINT_NAMESPACE", f"{CHORD_URL}api/auth/ott/")
 
     # TT (temporary token)-related config
-    TT_ENDPOINT_NAMESPACE = os.environ.get("TT_ENDPOINT_NAMESPACE", f"{CHORD_URL}api/auth/tt/")
+    TT_ENDPOINT_NAMESPACE: str = os.environ.get("TT_ENDPOINT_NAMESPACE", f"{CHORD_URL}api/auth/tt/")
 
     # DRS-related configuration
-    DRS_URL = os.environ.get("DRS_URL", f"{CHORD_URL}api/drs").strip().rstrip("/")
-    WRITE_OUTPUT_TO_DRS = os.environ.get("WRITE_OUTPUT_TO_DRS", "false").lower().strip() == "true"
-    DRS_DEDUPLICATE = os.environ.get("DRS_DEDUPLICATE", "true").lower().strip() == "true"
-    DRS_SKIP_TYPES = tuple(t.strip() for t in os.environ.get("DRS_SKIP_TYPES", "").split(",") if t.strip())
+    DRS_URL: str = os.environ.get("DRS_URL", f"{CHORD_URL}api/drs").strip().rstrip("/")
+    WRITE_OUTPUT_TO_DRS: bool = os.environ.get("WRITE_OUTPUT_TO_DRS", "false").lower().strip() in TRUTH_VALUES
+    DRS_DEDUPLICATE: bool = os.environ.get("DRS_DEDUPLICATE", "true").lower().strip() in TRUTH_VALUES
+    DRS_SKIP_TYPES: Tuple[str, ...] = tuple(
+        t.strip() for t in os.environ.get("DRS_SKIP_TYPES", "").split(",") if t.strip())
 
     # Other services, used for interpolating workflow variables
-    METADATA_URL = os.environ.get("METADATA_URL", f"{CHORD_URL}api/metadata").strip().rstrip("/")
+    METADATA_URL: str = os.environ.get("METADATA_URL", f"{CHORD_URL}api/metadata").strip().rstrip("/")
 
     # VEP-related configuration
-    VEP_CACHE_DIR = os.environ.get("VEP_CACHE_DIR")
+    VEP_CACHE_DIR: Optional[str] = os.environ.get("VEP_CACHE_DIR")
 
-    INGEST_POST_TIMEOUT = 60 * 60  # 1 hour
+    INGEST_POST_TIMEOUT: int = 60 * 60  # 1 hour