diff --git a/.github/livestream_targets.png b/.github/livestream_targets.png new file mode 100644 index 0000000..b1a7fa7 Binary files /dev/null and b/.github/livestream_targets.png differ diff --git a/README.md b/README.md index 4c86b3e..8f54944 100644 --- a/README.md +++ b/README.md @@ -4,24 +4,22 @@ [![Codacy Badge](https://app.codacy.com/project/badge/Grade/43466ecc9ffe4622b3492625a137a70c)](https://www.codacy.com/gh/TOMToolkit/tom_fink/dashboard?utm_source=github.com&utm_medium=referral&utm_content=TOMToolkit/tom_fink&utm_campaign=Badge_Grade) [![Coverage Status](https://coveralls.io/repos/github/TOMToolkit/tom_fink/badge.svg?branch=main)](https://coveralls.io/github/TOMToolkit/tom_fink?branch=main) -This repository hosts the Fink Alert Broker Module for the TOM Toolkit. Fink is a broker currently connected to ZTF. More information on Fink at https://fink-broker.org/. +This repository hosts the Fink Alert Broker Module for the TOM Toolkit. Fink is a broker currently connected to ZTF, and that will handle the massive alert stream from LSST. More information on Fink at https://fink-broker.org/. You can easily install the module using pip: -As of version 0.4, the module simply uses the Fink REST API to retrieve alerts. Note that the Fink databases are updated once a day with the previous night alert data (hence you do not get live alerts for the moment). Users can perform: +```bash +pip install tom-fink +``` + +## Polling data from the REST API + +As of `tom-fink` version 0.4, the module simply uses the [Fink REST API](https://fink-broker.readthedocs.io/en/latest/services/science_portal/) to retrieve alerts. Note that the Fink databases are updated **once a day** with the previous night alert data (hence you do not get live alerts for the moment). Users can perform: - Search by ZTF object ID - Cone Search - Search by Date - Search by derived alert class - Search by Solar System name -## How to use the Fink module inside your TOM - -First, install the module using pip - -```bash -pip install tom-fink -``` - -then you need to declare it in your running TOM instance. To do so just add `tom_fink.fink.FinkBroker` to the `TOM_ALERT_CLASSES` in your TOM's `settings.py`: +You need to declare the `FinkBroker` class in your running TOM instance. To do so just add `tom_fink.fink.FinkBroker` to the `TOM_ALERT_CLASSES` in your TOM's `settings.py`: ```python TOM_ALERT_CLASSES = [ @@ -37,9 +35,116 @@ and finally relaunch your TOM: ./manage.py runserver ``` +## Polling data from the Fink livestream service + +Alternatively from `tom_fink` version 0.6.0, users can poll Fink substreams in real-time, using the [livestream service](https://fink-broker.readthedocs.io/en/latest/services/livestream/). First you need to add `tom_alertstreams` and `tom_fink` to your `INSTALLED_APPS` setting in your project `settings.py`: + +```python +INSTALLED_APPS = [ + ... + 'tom_alertstreams', + 'tom_fink' +] +``` + +Then add the following block to your `settings.py`: + +```python +ALERT_STREAMS = [ + { + 'ACTIVE': True, + 'NAME': 'tom_fink.alertstream.FinkAlertStream', + 'OPTIONS': { + 'URL': os.getenv('FINK_CREDENTIAL_URL', 'set FINK_CREDENTIAL_URL value in environment'), + 'USERNAME': os.getenv('FINK_CREDENTIAL_USERNAME', 'set FINK_CREDENTIAL_USERNAME value in environment'), + 'GROUP_ID': os.getenv('FINK_CREDENTIAL_GROUP_ID', 'set FINK_CREDENTIAL_GROUP_ID value in environment'), + 'TOPIC': os.getenv('FINK_TOPIC', 'set FINK_TOPIC value in environment'), + 'MAX_POLL_NUMBER': os.getenv("FINK_MAX_POLL_NUMBER", 1e10), + 'TIMEOUT': os.getenv('FINK_TIMEOUT', 10), + 'TOPIC_HANDLERS': { + 'fink.stream': 'tom_fink.alertstream.alert_logger', + }, + }, + }, +] +``` + +and declare the following variables in your `~/.bash_profile`: + +```bash +export FINK_CREDENTIAL_USERNAME= # provided when registering to Fink livestream +export FINK_CREDENTIAL_GROUP_ID= # provided when registering to Fink livestream +export FINK_CREDENTIAL_URL= # provided when registering to Fink livestream +export FINK_TOPIC= # str, topic name to poll +export FINK_MAX_POLL_NUMBER= # int, number maximum of alerts to poll before closing the connection. Default is 1e10 (never stops). +export FINK_TIMEOUT= # int, in seconds. Default is 10 seconds if not set +``` + +Credentials are provided when registering to Fink livestream (see https://fink-broker.readthedocs.io/en/latest/services/livestream). The available topic names and description can be found at https://fink-broker.readthedocs.io/en/latest/services/livestream. Note that we currently allow to poll only one topic at once (multi-topic is planned for later). Then launch the `readstreams` service: + +```bash +./manage.py readstreams +``` + +You should see a log similar to: + +```bash +registering new views: args: ('groups', , 'groups'), kwargs: {} +registering new views: args: ('targets', , 'targets'), kwargs: {} +registering new views: args: ('targetextra', , 'targetextra'), kwargs: {} +registering new views: args: ('targetname', , 'targetname'), kwargs: {} +registering new views: args: ('targetlist', , 'targetlist'), kwargs: {} +registering new views: args: ('observations', , 'observations'), kwargs: {} +registering new views: args: ('dataproducts', , 'dataproducts'), kwargs: {} +registering new views: args: ('reduceddatums', , 'reduceddatums'), kwargs: {} +NumExpr defaulting to 8 threads. +FinkAlertStream.listen opening stream: IP:PORT with group_id: julien6 (call number: 0) +read_streams FinkAlertStream TID=378166 ; thread identifier=125271444649536 +readstreams Command.handle() returning... +fink.alert_logger topic: fink_sso_ztf_candidates_ztf +fink.alert_logger value: ZTF24aakwfsz emitted 2024-04-23 07:26:57.998412 (received 2024-04-29 10:45:01) +FinkAlertStream.listen opening stream: IP:PORT with group_id: julien6 (call number: 1) +fink.alert_logger topic: fink_sso_ztf_candidates_ztf +fink.alert_logger value: ZTF24aakwftv emitted 2024-04-23 07:27:39.003823 (received 2024-04-29 10:45:01) +... +``` + +Each new alert will be saved as a `Target`. If more than one alert with the name `objectId` are emitted, you will be warned: + +```bash +fink.alert_logger value: ZTF24aakwfsu emitted 2024-04-23 07:26:57.998412 (received 2024-04-29 08:18:07) +Target ZTF24aakwfsu already in the database +``` + +and the program will continue. Probably we should group these in the future, instead of ignoring subsequent alerts. Then launch the app (do not close the previous process!): + +```bash +./manage.py runserver +``` + +and you should have access to your targets, that are accessible from their topic name: + +![targets](.github/livestream_targets.png) + +### Testing & debugging the connection + +Before running in production, we advise to make tests using a test stream, and polling a few alerts: + +```bash +export FINK_CREDENTIAL_USERNAME= # provided when registering to Fink livestream +export FINK_CREDENTIAL_GROUP_ID= # provided when registering to Fink livestream +export FINK_CREDENTIAL_URL= # provided when registering to Fink livestream +export FINK_TOPIC=fink_sso_ztf_candidates_ztf +export FINK_MAX_POLL_NUMBER=2 +export FINK_TIMEOUT=10 +``` + +This way, you will poll alerts two-by-two, and you will have a reservoir of thousands of alerts (solar system objects)! + ## Todo list - [ ] Add a test suite (preferably running on GitHub Actions) - [x] Add a linter (preferably running on GitHub Actions) - [x] Update the Query Form with all API features -- [ ] Enable querying livestreams using the Fink Kafka client +- [x] Enable querying live streams using the Fink Kafka client +- [x] Update visualisation of targets from the livestream service diff --git a/poetry.lock b/poetry.lock index ef27b8a..5e01374 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,9 +1,32 @@ -# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. +# This file is automatically @generated by Poetry and should not be changed by hand. + +[[package]] +name = "adc-streaming" +version = "2.3.2" +description = "Astronomy Data Commons streaming client libraries" +category = "main" +optional = false +python-versions = "*" +files = [ + {file = "adc-streaming-2.3.2.tar.gz", hash = "sha256:0f7097f5ed6d56a31c1a91d2ddbfb18b64ed651c175a43dd982be01002f16ce3"}, + {file = "adc_streaming-2.3.2-py3-none-any.whl", hash = "sha256:9b010c01e08c761a1173bd05068b0a4f31c88b1c12b9c9554924b2de478fddbf"}, +] + 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Python programs" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1616,10 +2447,26 @@ files = [ {file = "pyflakes-3.2.0.tar.gz", hash = "sha256:1c61603ff154621fb2a9172037d84dca3500def8c8b630657d1701f026f8af3f"}, ] +[[package]] +name = "pyparsing" +version = "3.1.2" +description = "pyparsing module - Classes and methods to define and execute parsing grammars" +category = "main" +optional = false +python-versions = ">=3.6.8" +files = [ + {file = "pyparsing-3.1.2-py3-none-any.whl", hash = "sha256:f9db75911801ed778fe61bb643079ff86601aca99fcae6345aa67292038fb742"}, + {file = "pyparsing-3.1.2.tar.gz", hash = "sha256:a1bac0ce561155ecc3ed78ca94d3c9378656ad4c94c1270de543f621420f94ad"}, +] + +[package.extras] +diagrams = ["jinja2", "railroad-diagrams"] + [[package]] name = "pyrsistent" version = "0.20.0" description = "Persistent/Functional/Immutable data structures" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1661,6 +2508,7 @@ files = [ 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description = "YAML parser and emitter for Python" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1777,6 +2629,7 @@ files = [ name = "redis" version = "5.0.3" description = "Python client for Redis database and key-value store" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1795,6 +2648,7 @@ ocsp = ["cryptography (>=36.0.1)", "pyopenssl (==20.0.1)", "requests (>=2.26.0)" name = "requests" version = "2.31.0" description = "Python HTTP for Humans." +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1816,6 +2670,7 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"] name = "scipy" version = "1.10.1" description = "Fundamental algorithms for scientific computing in Python" +category = "main" optional = false python-versions = "<3.12,>=3.8" files = [ @@ -1854,6 +2709,7 @@ test = ["asv", "gmpy2", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeo name = "secretstorage" version = "3.3.3" description = "Python bindings to FreeDesktop.org Secret Service API" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1869,6 +2725,7 @@ jeepney = ">=0.6" name = "semantic-version" version = "2.10.0" description = "A library implementing the 'SemVer' scheme." +category = "main" optional = false python-versions = ">=2.7" files = [ @@ -1884,6 +2741,7 @@ doc = ["Sphinx", "sphinx-rtd-theme"] name = "setuptools" version = "69.2.0" description = "Easily download, build, install, upgrade, and uninstall Python packages" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1900,6 +2758,7 @@ testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jar name = "six" version = "1.16.0" description = "Python 2 and 3 compatibility utilities" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -1911,6 +2770,7 @@ files = [ name = "soupsieve" version = "2.5" description = "A modern CSS selector implementation for Beautiful Soup." +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1922,6 +2782,7 @@ files = [ name = "specutils" version = "1.13.0" description = "Package for spectroscopic astronomical data" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1947,6 +2808,7 @@ test = ["matplotlib", "pytest-astropy", "spectral-cube", "tox"] name = "sqlparse" version = "0.4.4" description = "A non-validating SQL parser." +category = "main" optional = false python-versions = ">=3.5" files = [ @@ -1959,10 +2821,26 @@ dev = ["build", "flake8"] doc = ["sphinx"] test = ["pytest", "pytest-cov"] +[[package]] +name = "tabulate" +version = "0.9.0" +description = "Pretty-print tabular data" +category = "main" +optional = false +python-versions = ">=3.7" +files = [ + {file = "tabulate-0.9.0-py3-none-any.whl", hash = "sha256:024ca478df22e9340661486f85298cff5f6dcdba14f3813e8830015b9ed1948f"}, + {file = "tabulate-0.9.0.tar.gz", hash = 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">=2.10,<3.0" + +[[package]] +name = "toml" +version = "0.10.2" +description = "Python Library for Tom's Obvious, Minimal Language" +category = "main" +optional = false +python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" +files = [ + {file = "toml-0.10.2-py2.py3-none-any.whl", hash = "sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b"}, + {file = "toml-0.10.2.tar.gz", hash = "sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f"}, +] + [[package]] name = "tomtoolkit" version = "2.17.2" description = "TOM Toolkit and base modules" +category = "main" optional = false python-versions = ">=3.8.1,<3.12" files = [ @@ -2010,10 +2919,32 @@ python-dateutil = "<3" requests = "<3" specutils = "<2" +[[package]] +name = "tqdm" +version = "4.66.2" +description = "Fast, Extensible Progress Meter" +category = "main" +optional = false +python-versions = ">=3.7" +files = [ + {file = "tqdm-4.66.2-py3-none-any.whl", hash = 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more." +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2053,6 +2986,7 @@ zstd = ["zstandard (>=0.18.0)"] name = "watchdog" version = "4.0.0" description = "Filesystem events monitoring" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2094,6 +3028,7 @@ watchmedo = ["PyYAML (>=3.10)"] name = "watchdog-gevent" version = "0.1.1" description = "A gevent-based observer for watchdog." +category = "main" optional = false python-versions = "*" files = [ @@ -2109,6 +3044,7 @@ watchdog = ">=0.8" name = "webencodings" version = "0.5.1" description = "Character encoding aliases for legacy web content" +category = "main" optional = false python-versions = "*" files = [ @@ -2116,10 +3052,23 @@ files = [ {file = "webencodings-0.5.1.tar.gz", hash = "sha256:b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923"}, ] +[[package]] +name = "xmltodict" +version = "0.13.0" +description = "Makes working with XML feel like you are working with JSON" +category = "main" +optional = false +python-versions = ">=3.4" +files = [ + {file = "xmltodict-0.13.0-py2.py3-none-any.whl", hash = "sha256:aa89e8fd76320154a40d19a0df04a4695fb9dc5ba977cbb68ab3e4eb225e7852"}, + {file = "xmltodict-0.13.0.tar.gz", hash = "sha256:341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56"}, +] + [[package]] name = "zipp" version = "3.18.1" description = "Backport of pathlib-compatible object wrapper for zip files" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2135,6 +3084,7 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p name = "zope-event" version = "5.0" description = "Very basic event publishing system" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2153,6 +3103,7 @@ test = ["zope.testrunner"] name = "zope-interface" version = "6.2" description = "Interfaces for Python" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2205,4 +3156,4 @@ testing = ["coverage (>=5.0.3)", "zope.event", "zope.testing"] [metadata] lock-version = "2.0" python-versions = ">=3.8.1,<3.12" -content-hash = "ec92daee221b3b5b02e56723678f740c4321203c45e31bfabe61bb4dfe4a01e8" +content-hash = "817a614e1c2df22670c3e23b9613fc8d5fcd5be7171940c91654c1d4882e98aa" diff --git a/pyproject.toml b/pyproject.toml index 2726771..9277f79 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -40,6 +40,8 @@ python = ">=3.8.1,<3.12" tomtoolkit = "^2.17.2" elasticsearch-dsl = "^8.12.0" Markdown = "^3.5.2" +fink-client = "^7.2" +tom-alertstreams = "^0.6.2" [tool.poetry.group.test.dependencies] factory_boy = ">=3.1,<3.3" diff --git a/tom_fink/alertstream.py b/tom_fink/alertstream.py new file mode 100644 index 0000000..41475c9 --- /dev/null +++ b/tom_fink/alertstream.py @@ -0,0 +1,166 @@ +# Copyright (c) 2024 Julien Peloton +# +# This file is part of TOM Toolkit +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +import time +import logging +import traceback + +from fink_client.consumer import AlertConsumer + +from tom_alertstreams.alertstreams.alertstream import AlertStream +from tom_targets.models import Target, TargetList + +from psycopg2.errors import UniqueViolation +from django.db.utils import IntegrityError as DJ_IntegrityError +from sqlite3 import IntegrityError as SQL_IntegrityError +from django.contrib.auth.models import Group +from guardian.shortcuts import assign_perm + +logger = logging.getLogger(__name__) + + +class FinkAlertStream(AlertStream): + """Poll alerts from a stream generated by Fink""" + + required_keys = [ + "URL", + "GROUP_ID", + "USERNAME", + "TOPIC", + "TOPIC_HANDLERS", + "MAX_POLL_NUMBER", + "TIMEOUT", + ] + allowed_keys = [ + "URL", + "GROUP_ID", + "USERNAME", + "PASSWORD", + "TOPIC", + "TOPIC_HANDLERS", + "MAX_POLL_NUMBER", + "TIMEOUT", + ] + + def __init__(self, *args, **kwargs) -> None: + """Initialise credentials and target list""" + super().__init__(*args, **kwargs) + + # Define target list based on topics + public_group, _ = Group.objects.get_or_create(name="Public") + tl, is_created = TargetList.objects.get_or_create(name=self.topic) + assign_perm("tom_targets.view_targetlist", public_group, tl) + + def listen(self): + """Listen to one topic from Fink Kafka server + + Each alert is saved into the target list named from + the topic. + + Note + ---------- + This only handles one topic at once for the moment. + """ + super().listen() + + myconfig = { + "username": self.username, + "bootstrap.servers": self.url, + "group_id": self.group_id, + } + + consumer = AlertConsumer([self.topic], myconfig, schema_path=None) + + poll_number = 0 + while poll_number < int(self.max_poll_number): + try: + logger.info( + "FinkAlertStream.listen opening stream: {} with group_id: {} (call number: {})".format( + self.url, + self.group_id, + poll_number + ) + ) + topic, alert, key = consumer.poll(timeout=int(self.timeout)) + + if topic is not None: + # TODO: handle MMA vs regular streams + self.alert_handler["fink.stream"](alert, topic) + else: + logger.info("No alerts received") + poll_number += 1 + except Exception as ex: + logger.error(f"FinkAlertStream.listen: {ex}") + logger.error(traceback.format_exc()) + break + consumer.close() + + +def alert_logger(alert, topic): + """Basic alert handler for Fink + + This alert handler simply display on screen basic information, + and save the alert as a new Target. + + Parameters + ---------- + alert: dic + Dictionary containing alert data. See `consumer.poll`. + topic: str + Topic name + + Warnings + ---------- + UniqueViolation, SQL_IntegrityError, DJ_IntegrityError + If the target is already saved + + Raises + ---------- + Exception (base) + for any other failures than name clash when + saving the target in the database. + + """ + utc = time.strftime("%Y-%m-%d %H:%M:%S", time.gmtime()) + logger.info("fink.alert_logger topic: {}".format(topic)) + logger.info( + "fink.alert_logger value: {} emitted {} (received {})".format( + alert["objectId"], alert["timestamp"], utc + ) + ) + + mytarget = Target( + name=alert["objectId"], + type="SIDEREAL", + ra=alert["candidate"]["ra"], + dec=alert["candidate"]["dec"], + epoch=alert["candidate"]["jd"], + ) + + try: + mytarget.save( + extras={ + "fink broker link": "https://fink-portal.org/{}".format( + alert["objectId"] + ) + } + ) + except (UniqueViolation, SQL_IntegrityError, DJ_IntegrityError): + logger.warning(f"Target {mytarget} already in the database") + pass + except Exception: + logger.error("error when trying to save new alerts in the db", exc_info=1) + logger.error(traceback.format_exc())