diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/auth/authorisation/data/views.py | 18 |
1 files changed, 12 insertions, 6 deletions
diff --git a/gn3/auth/authorisation/data/views.py b/gn3/auth/authorisation/data/views.py index d84b080..6431389 100644 --- a/gn3/auth/authorisation/data/views.py +++ b/gn3/auth/authorisation/data/views.py @@ -175,7 +175,7 @@ def __search_genotypes__(): limit=limit, offset=offset) return jsonify(with_db_connection(__ungrouped__)) -def __search_phenotypes__(): +def __search_xapian__(): # launch the external process to search for phenotypes redisuri = app.config["REDIS_URI"] with redis.Redis.from_url(redisuri, decode_responses=True) as redisconn: @@ -184,6 +184,7 @@ def __search_phenotypes__(): command =[ sys.executable, "-m", "scripts.search_phenotypes", __request_key__("species_name"), + __request_key__("dataset_type"), __request_key__("query"), str(job_id), f"--host={__request_key__('gn3_server_uri')}", @@ -193,6 +194,10 @@ def __search_phenotypes__(): f"--per-page={__request_key__('per_page')}"] +( [f"--selected={json.dumps(selected)}"] if len(selected) > 0 else []) + print("+++++++++++++++++++++++++++++++++++++++++++++++++++++++++") + import shlex + print(shlex.join(command)) + print("+++++++++++++++++++++++++++++++++++++++++++++++++++++++++") jobs.create_job(redisconn, { "job_id": job_id, "command": command, "status": "queued", "search_results": tuple()}) @@ -203,20 +208,21 @@ def __search_phenotypes__(): "command": command }) -@data.route("/search", methods=["GET"]) +@data.route("/search", methods=["POST"]) @require_oauth("profile group resource") +@require_json def search_unlinked_data(): """Search for various unlinked data.""" dataset_type = request.json["dataset_type"] search_fns = { "mrna": __search_mrna__, - "genotype": __search_genotypes__, - "phenotype": __search_phenotypes__ + "genotype": __search_xapian__, + "phenotype": __search_xapian__ } return search_fns[dataset_type]() -@data.route("/search/phenotype/<uuid:job_id>", methods=["GET"]) -def pheno_search_results(job_id: uuid.UUID) -> Response: +@data.route("/search/results/<uuid:job_id>", methods=["GET"]) +def search_job_results(job_id: uuid.UUID) -> Response: """Get the search results from the external script""" def __search_error__(err): raise NotFoundError(err["error_description"]) |