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authorMunyoki Kilyungi2022-11-23 12:19:02 +0300
committerBonfaceKilz2022-11-23 12:47:39 +0300
commitd0d08d513e403f7836da450a1d05eaeb89a5ba30 (patch)
treec37e42a2c0b1893fd90eb0282257351beb680f2b /gn3
parenta93e8cc48815bd7e9b64c634ad808ddbfa85cd4b (diff)
downloadgenenetwork3-d0d08d513e403f7836da450a1d05eaeb89a5ba30.tar.gz
Create a new REST endpoint for fetching a phenotype's metadata
* gn3/api/general.py: (dataset_metadata) Delete. * gn3/api/metadata.py: Import Blueprint, jsonify, current_app, SPARQLWrapper and get_dataset_metadata. (metadata): New Blueprint (jsonify_dataset_metadata): New function/end-point. * gn3/app.py: Import metadata (create_app): Register metadata blueprint.
Diffstat (limited to 'gn3')
-rw-r--r--gn3/api/general.py5
-rw-r--r--gn3/api/metadata.py22
-rw-r--r--gn3/app.py3
3 files changed, 26 insertions, 4 deletions
diff --git a/gn3/api/general.py b/gn3/api/general.py
index 68b128b..f904ffe 100644
--- a/gn3/api/general.py
+++ b/gn3/api/general.py
@@ -69,7 +69,4 @@ def run_r_qtl(geno_filestr, pheno_filestr):
f"{geno_filestr} {pheno_filestr}")
return jsonify(run_cmd(cmd)), 201
-@general.route("/dataset/<accession_id>")
-def dataset_metadata(accession_id):
- """Return info as JSON for dataset with ACCESSION_ID."""
- return jsonify(rdf.get_dataset_metadata(accession_id).data)
+
diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py
new file mode 100644
index 0000000..4fe9e67
--- /dev/null
+++ b/gn3/api/metadata.py
@@ -0,0 +1,22 @@
+"""API for fetching metadata using an API"""
+from flask import Blueprint
+from flask import jsonify
+from flask import current_app
+
+from SPARQLWrapper import SPARQLWrapper
+
+from gn3.db.rdf import get_dataset_metadata
+
+
+metadata = Blueprint("metadata", __name__)
+
+
+@metadata.route("/dataset/<accession_id>", methods=["GET"])
+def jsonify_dataset_metadata(accession_id):
+ """Fetch a dataset's metadata given it's ACCESSION_ID"""
+ return jsonify(get_dataset_metadata(
+ SPARQLWrapper(current_app
+ .config
+ .get("SPARQL_ENDPOINT")),
+ accession_id
+ ).data)
diff --git a/gn3/app.py b/gn3/app.py
index 6c7e483..a187e54 100644
--- a/gn3/app.py
+++ b/gn3/app.py
@@ -18,6 +18,8 @@ from gn3.api.ctl import ctl
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
+
def create_app(config: Union[Dict, str, None] = None) -> Flask:
"""Create a new flask object"""
@@ -53,4 +55,5 @@ def create_app(config: Union[Dict, str, None] = None) -> Flask:
app.register_blueprint(async_commands, url_prefix="/api/async_commands")
app.register_blueprint(menu, url_prefix="/api/menu")
app.register_blueprint(search, url_prefix="/api/search")
+ app.register_blueprint(metadata, url_prefix="/api/metadata")
return app