Added endpoint to lookup samples based on sequencer run id search

ExonCov/api_views.py

@@ -138,7 +138,7 @@ def get_sample_by_sample_name_api(sample_name):
 
 @app.route('/api/samples/run/id/<int:run_id>')
 @token_required
-def get_summary_by_run_id_api(run_id):
+def get_summary_by_run_db_id_api(run_id):
     """
         Look up samples by its run database ID
 
@@ -160,3 +160,29 @@ def get_summary_by_run_id_api(run_id):
         samples_list = generate_not_found_dict()
 
     return jsonify(samples_list)
+
+
+@app.route('/api/samples/run/seqid/<string:seq_run_id>')
+@token_required
+def get_summary_by_run_seq_id_api(seq_run_id):
+    """
+        Look up samples by its sequencer run ID
+
+        Args:
+            run_id (str): run sequencer id
+
+        Returns:
+            A list of sample as a JSON object if there are any found in the database
+        """
+    samples = get_sample_by_like_run_id(seq_run_id)
+    samples_list = []
+
+    for sample in samples:
+        sample = model_to_dict(sample)
+        sample.pop("import_command")
+        samples_list.append(sample)
+
+    if len(samples_list) == 0:
+        samples_list = generate_not_found_dict()
+
+    return jsonify(samples_list)

ExonCov/services.py

@@ -90,7 +90,20 @@ def get_sample_by_like_run_id(run_id):
         .options(joinedload(Sample.project))
     )
 
-    samples = samples.filter(SequencingRun.id.like('%{0}%'.format(run_id)))
+    samples = samples.filter(SequencingRun.platform_unit.like('%{0}%'.format(run_id)))
+    return samples
+
+
+def get_sample_by_like_run_db_id(run_id):
+    samples = (
+        Sample.query
+        .order_by(Sample.import_date.desc())
+        .order_by(Sample.name.asc())
+        .options(joinedload(Sample.sequencing_runs))
+        .options(joinedload(Sample.project))
+    )
+
+    samples = samples.filter(SequencingRun.id == run_id)
     return samples