Fetch sampledata

* gn3/api/sampledata.py (get_sampledata): New end-point.
* gn3/app.py: Register above end-point.
* gn3/settings.py: Add new conf variable for LMDB.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>

3 files changed, 28 insertions, 0 deletions

diff --git a/gn3/api/sampledata.py b/gn3/api/sampledata.py
new file mode 100644
index 0000000..5b09b52
--- /dev/null
+++ b/gn3/api/sampledata.py
@@ -0,0 +1,23 @@
+"""API for fetching sampledata from a given trait"""
+import os
+from flask import Blueprint
+from flask import jsonify
+from flask import current_app
+
+from gn3.db.matrix import get_current_matrix
+
+
+sampledata = Blueprint("sampledata", __name__)
+
+
+@sampledata.route("/dataset/<dataset_name>/trait/<trait_name>", methods=["GET"])
+def get_sampledata(dataset_name, trait_name):
+    """Fetch a trait's sampledata as a matrix."""
+    return jsonify(
+        get_current_matrix(
+            os.path.join(
+                current_app.config.get("LMDB_PATH"),
+                dataset_name, trait_name
+            )
+        )
+    )
diff --git a/gn3/app.py b/gn3/app.py
index 72d76c2..0c2f9f9 100644
--- a/gn3/app.py
+++ b/gn3/app.py
@@ -20,6 +20,7 @@ from gn3.api.async_commands import async_commands
 from gn3.api.menu import menu
 from gn3.api.search import search
 from gn3.api.metadata import metadata
+from gn3.api.sampledata import sampledata
 from gn3.auth import oauth2
 from gn3.auth.authentication.oauth2.server import setup_oauth2_server
 
@@ -59,6 +60,7 @@ def create_app(config: Union[Dict, str, None] = None) -> Flask:
     app.register_blueprint(menu, url_prefix="/api/menu")
     app.register_blueprint(search, url_prefix="/api/search")
     app.register_blueprint(metadata, url_prefix="/api/metadata")
+    app.register_blueprint(sampledata, url_prefix="/api/sampledata")
     app.register_blueprint(oauth2, url_prefix="/api/oauth2")
 
     register_error_handlers(app)
diff --git a/gn3/settings.py b/gn3/settings.py
index 5fec562..1de4d27 100644
--- a/gn3/settings.py
+++ b/gn3/settings.py
@@ -15,6 +15,9 @@ RQTL_WRAPPER = "rqtl_wrapper.R"
 
 # SPARQL endpoint
 SPARQL_ENDPOINT = "http://localhost:8891/sparql"
+# LMDB path
+LMDB_PATH = os.environ.get(
+    "LMDB_PATH", f"{os.environ.get('HOME')}/tmp/dataset")
 
 # SQL confs
 SQL_URI = os.environ.get(