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Graph route #63

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b339232
Bump version for Lomikel and add Janusgraph
JulienPeloton May 23, 2025
a7cd4f2
Initial Graph route
JulienPeloton May 23, 2025
4fc9787
Add default classifier
JulienPeloton May 23, 2025
ee3284e
Add default classifier
JulienPeloton May 23, 2025
69dcc33
Fix typo
JulienPeloton May 23, 2025
d80b68b
Register the route
JulienPeloton May 23, 2025
a6517be
Ruff
JulienPeloton May 23, 2025
530dcca
Update with new version of graph client
JulienPeloton May 26, 2025
c838676
Fix tablename
JulienPeloton May 26, 2025
8a86e4b
Fix new syntax
JulienPeloton May 26, 2025
06ba9b2
PEP8
JulienPeloton Jun 25, 2025
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2 changes: 2 additions & 0 deletions app.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@
from apps.routes.v1.anomaly.api import ns as ns_anomaly
from apps.routes.v1.ssoft.api import ns as ns_ssoft
from apps.routes.v1.metadata.api import ns as ns_metadata
from apps.routes.v1.recommender.api import ns as ns_recommender

config = extract_configuration("config.yml")

Expand Down Expand Up @@ -79,6 +80,7 @@ def after_request(response):
api.add_namespace(ns_anomaly)
api.add_namespace(ns_ssoft)
api.add_namespace(ns_metadata)
api.add_namespace(ns_recommender)

# Register blueprint
app.register_blueprint(blueprint)
Expand Down
129 changes: 129 additions & 0 deletions apps/routes/v1/recommender/README.md
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@@ -0,0 +1,129 @@
# Recommender system

Here are the first applications for the graph component in Fink.

## Tag-based analysis

Idea: users tag objects. From these tags, they can search for closest objects in the graph. We start from a few tags (the seed), and as we acquire more tags, the search should become more personnalised (from seed to tree).

Question:
- how many tags are required to get relevant results?
- how many tags should be available?
- how to handle different tags for the same object?
- can we also automatise some tagging mechanism (i.e. from manual tag assignment to automatic science module)?

## Classification transfer

Goal: compare two classification schemes (how C0 and C1 relates to each other).

## Todo

todo:
- [ ] `recommender` route in the API to get similar objects
- [ ] New HBase table to store obj/tags
- [ ] Add tag button in web portal
- [ ] Add tag as classification mechanism based on tags in graph tools
- [ ] Contact pilot teams to test capabilities

## Profiling

```python
Total time: 0.26651 s
File: /opt/fink-object-api/apps/utils/client.py
Function: connect_to_graph at line 60

Line # Hits Time Per Hit % Time Line Contents
==============================================================
60 @profile
61 def connect_to_graph():
62 """Return a client connected to a graph"""
63 1 5578.6 5578.6 2.1 config = extract_configuration("config.yml")
64 1 240.1 240.1 0.1 gateway = JavaGateway(auto_convert=True)
65
66 1 256935.3 256935.3 96.4 jc = gateway.jvm.com.Lomikel.Januser.JanusClient(config["PRO…
67
68 # TODO: add definition of IP/PORT/TABLE/SCHEMA here in new v…
69 1 2468.6 2468.6 0.9 gr = gateway.jvm.com.astrolabsoftware.FinkBrowser.Januser.Fi…
70
71 1 1287.6 1287.6 0.5 return gr, gateway.jvm.com.astrolabsoftware.FinkBrowser.Janu…


Total time: 1.60666 s
File: /opt/fink-object-api/apps/routes/v1/recommender/utils.py
Function: extract_similar_objects at line 24

Line # Hits Time Per Hit % Time Line Contents
==============================================================
24 @profile
25 def extract_similar_objects(payload: dict) -> pd.DataFrame:
26 """Extract similar objects returned by JanusGraph and format…
27
28 Data is from /api/v1/recommender
29
30 Parameters
31 ----------
32 payload: dict
33 See https://api.fink-portal.org
34
35 Return
36 ----------
37 out: pandas dataframe
38 """
39 1 1.2 1.2 0.0 if "n" not in payload:
40 1 0.5 0.5 0.0 nobjects = 10
41 else:
42 nobjects = int(payload["n"])
43
44 1 0.2 0.2 0.0 if "classifier" not in payload:
45 1 0.2 0.2 0.0 classifier_name = "FINK_PORTAL"
46 else:
47 classifier_name = payload["classifier"]
48
49 1 7097.0 7097.0 0.4 user_config = extract_configuration("config.yml")
50
51 1 266750.0 266750.0 16.6 gr, classifiers = connect_to_graph()
52
53 # Classify source
54 1 377.3 377.3 0.0 func = getattr(classifiers, classifier_name)
55 2 1110560.4 555280.2 69.1 gr.classifySource(
56 1 0.7 0.7 0.0 func,
57 1 1.3 1.3 0.0 payload["objectId"],
58 2 26.3 13.2 0.0 '{}:{}:{}'.format(
59 1 1.5 1.5 0.0 user_config["HBASEIP"],
60 1 1.7 1.7 0.0 user_config["ZOOPORT"],
61 1 1.0 1.0 0.0 user_config["SCHEMAVER"]
62 ),
63 1 1.0 1.0 0.0 False,
64 1 0.6 0.6 0.0 None
65 )
66
67 2 206912.5 103456.3 12.9 closest_sources = gr.sourceNeighborhood(
68 1 2.3 2.3 0.0 payload["objectId"],
69 1 0.7 0.7 0.0 classifier_name
70 )
71 1 3.0 3.0 0.0 out = {"i:objectId": [], "v:distance": [], "v:classification…
72 1 871.1 871.1 0.1 for index, (oid, distance) in enumerate(closest_sources.item…
73 if index > nobjects:
74 break
75
76 r = requests.post(
77 "https://api.fink-portal.org/api/v1/objects",
78 json={
79 "objectId": oid,
80 "output-format": "json"
81 }
82 )
83 out["v:classification"].append(r.json()[0]["v:classifica…
84 out["i:objectId"].append(oid)
85 out["v:distance"].append(distance)
86
87 1 1211.7 1211.7 0.1 pdf = pd.DataFrame(out)
88
89 1 12835.5 12835.5 0.8 gr.close()
90
91 1 3.8 3.8 0.0 return pdf


0.27 seconds - /opt/fink-object-api/apps/utils/client.py:60 - connect_to_graph
1.61 seconds - /opt/fink-object-api/apps/routes/v1/recommender/utils.py:24 - extract_similar_objects
```
Empty file added apps/routes/v1/recommender/__init__.py
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85 changes: 85 additions & 0 deletions apps/routes/v1/recommender/api.py
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# Copyright 2025 AstroLab Software
# Author: Julien Peloton
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from flask import Response, request
from flask_restx import Namespace, Resource, fields

from apps.utils.utils import check_args
from apps.utils.utils import send_tabular_data

from apps.routes.v1.recommender.utils import extract_similar_objects

ns = Namespace("api/v1/recommender", "Get similar objects via Fink recommender system")

ARGS = ns.model(
"objects",
{
"objectId": fields.String(
description="ZTF Object ID",
example="ZTF21abfmbix",
required=True,
),
"classifier": fields.String(
description="Edge classifier to use: FINK_PORTAL or FEATURES",
example="FINK_PORTAL",
required=True,
),
"n": fields.Integer(
description="N closest objects (upper bound). Default is 10",
example=10,
required=False,
),
"output-format": fields.String(
description="Output format among json[default], csv, parquet, votable.",
example="json",
required=False,
),
},
)


@ns.route("")
@ns.doc(params={k: ARGS[k].description for k in ARGS})
class Recommender(Resource):
def get(self):
"""Retrieve similar objects via Fink recommender system"""
payload = request.args
if len(payload) > 0:
# POST from query URL
return self.post()
else:
return Response(ns.description, 200)

@ns.expect(ARGS, location="json", as_dict=True)
def post(self):
"""Retrieve similar objects via Fink recommender system"""
# get payload from the query URL
payload = request.args

if payload is None or len(payload) == 0:
# if no payload, try the JSON blob
payload = request.json

rep = check_args(ARGS, payload)
if rep["status"] != "ok":
return Response(str(rep), 400)

out = extract_similar_objects(payload)

# Error propagation
if isinstance(out, Response):
return out

output_format = payload.get("output-format", "json")
return send_tabular_data(out, output_format)
23 changes: 23 additions & 0 deletions apps/routes/v1/recommender/profiling.py
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# Copyright 2025 AstroLab Software
# Author: Julien Peloton
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""Call extract_similar_objects"""

from apps.routes.v1.recommender.utils import extract_similar_objects

payload = {
"objectId": "ZTF21abfmbix",
}

extract_similar_objects(payload)
90 changes: 90 additions & 0 deletions apps/routes/v1/recommender/test.py
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# Copyright 2025 AstroLab Software
# Author: Julien Peloton
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import requests
import pandas as pd

import io
import sys

APIURL = sys.argv[1]

# Implement random name generator
OID = "ZTF21abfmbix"


def get_recommendation(
oid="ZTF21abfmbix",
classifier="FINK_CLASS",
nobjects=10,
output_format="json",
):
"""Get recommendation from the classification graph using the Fink REST API"""
payload = {
"objectId": oid,
"classifier": classifier,
"n": nobjects,
"output-format": output_format,
}

r = requests.post("{}/api/v1/recommender".format(APIURL), json=payload)

assert r.status_code == 200, r.content

if output_format == "json":
# Format output in a DataFrame
pdf = pd.read_json(io.BytesIO(r.content))
elif output_format == "csv":
pdf = pd.read_csv(io.BytesIO(r.content))
elif output_format == "parquet":
pdf = pd.read_parquet(io.BytesIO(r.content))

return pdf


def test_object() -> None:
"""
Examples
--------
>>> test_object()
"""
pdf = get_recommendation(oid=OID)

assert not pdf.empty

assert len(pdf) == 10, len(pdf)


def test_stability() -> None:
"""
Examples
--------
>>> test_n_object()
"""
pdf1 = get_recommendation(oid=OID, n=20)
pdf2 = get_recommendation(oid=OID, n=10)

assert len(pdf1) == 20, len(pdf1)
assert len(pdf2) == 10, len(pdf2)

# first 10 must be the same
assert pdf1.head(10).equals(pdf2), (pdf1, pdf2)


if __name__ == "__main__":
""" Execute the test suite """
import sys
import doctest

sys.exit(doctest.testmod()[0])
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