Update sample registry lib and tests

Dockerfile

@@ -5,7 +5,7 @@ WORKDIR /app
 COPY . .
 
 RUN pip install -r requirements.txt
-RUN pip install /app/app/sample_registry
+RUN pip install /app/app/sample_registry/
 
 ENTRYPOINT [ "python" ]
 CMD [ "app/app.py" ]

app/app.py

@@ -129,6 +129,9 @@ def show_tags(tag=None, val=None):
 @app.route("/runs")
 @app.route("/runs/<run_acc>")
 def show_runs(run_acc=None):
+    if run_acc:
+        run_acc = "".join(filter(str.isdigit, run_acc.strip()))  # Sanitize run_acc
+
     if request.path.endswith(".json"):
         run = db.session.query(Run).filter(Run.run_accession == run_acc).all()
         with open(f"run_{run_acc}", "wb") as f:  # TEMP
@@ -176,7 +179,7 @@ def show_runs(run_acc=None):
 def show_stats():
     num_samples = db.session.query(Sample).count()
     num_samples_with_sampletype = (
-        db.session.query(Sample).filter(Sample.sample_type != None).count()
+        db.session.query(Sample).filter(Sample.sample_type is not None).count()
     )
     num_samples_with_standard_sampletype = (
         db.session.query(Sample)

app/sample_registry/src/sample_registry/__init__.py

@@ -11,21 +11,31 @@ def sample_registry_version():
     sys.stderr.write(__version__)
 
 
-try:
-    db_host = os.environ["DB_HOST"]
-    db_user = os.environ["DB_USER"]
-    db_name = os.environ["DB_NAME"]
-    db_pswd = os.environ["DB_PSWD"]
-    SQLALCHEMY_DATABASE_URI = f"postgresql://{db_user}:{db_pswd}@{db_host}/{db_name}"
-except KeyError:
-    # For development purposes, use a SQLite db prefilled with some demo data
-    sys.stdout.write(
-        "Missing database connection information in environment, using test SQLite database\n"
-    )
-    sys.stdout.write(
-        f"DB_HOST: {os.environ.get('DB_HOST')}\nDB_USER: {os.environ.get('DB_USER')}\nDB_NAME: {os.environ.get('DB_NAME')}\nDB_PSWD: {os.environ.get('DB_PSWD')}\n"
-    )
-    SQLALCHEMY_DATABASE_URI = f"sqlite:///{Path(__file__).parent.parent.parent.parent.parent.resolve()}/sample_registry.sqlite3"
+print({k: v for k, v in os.environ.items() if "PYTEST" in k})
+
+if "PYTEST_VERSION" in os.environ:
+    # Set SQLALCHEMY_DATABASE_URI to an in-memory SQLite database for testing
+    SQLALCHEMY_DATABASE_URI = "sqlite:///:memory:"
+else:
+    try:
+        db_host = os.environ["DB_HOST"]
+        db_user = os.environ["DB_USER"]
+        db_name = os.environ["DB_NAME"]
+        db_pswd = os.environ["DB_PSWD"]
+        SQLALCHEMY_DATABASE_URI = (
+            f"postgresql://{db_user}:{db_pswd}@{db_host}/{db_name}"
+        )
+    except KeyError:
+        # For development purposes, use a SQLite db prefilled with some demo data
+        sys.stdout.write(
+            "Missing database connection information in environment, using test SQLite database\n"
+        )
+        sys.stdout.write(
+            f"DB_HOST: {os.environ.get('DB_HOST')}\nDB_USER: {os.environ.get('DB_USER')}\nDB_NAME: {os.environ.get('DB_NAME')}\nDB_PSWD: {os.environ.get('DB_PSWD')}\n"
+        )
+        SQLALCHEMY_DATABASE_URI = f"sqlite:///{Path(__file__).parent.parent.parent.parent.parent.resolve()}/sample_registry.sqlite3"
+
+print(SQLALCHEMY_DATABASE_URI)
 
 # Create database engine
 engine = create_engine(SQLALCHEMY_DATABASE_URI, echo=False)