From 3c1cfb5125d299b5dba4d01cd197e5b9e5688062 Mon Sep 17 00:00:00 2001 From: JulienPeloton Date: Tue, 18 Jun 2024 08:56:54 +0200 Subject: [PATCH 1/7] Fix syntax for group_id in recent version of fink-client --- tom_fink/alertstream.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tom_fink/alertstream.py b/tom_fink/alertstream.py index 9d3287a..65fba4e 100644 --- a/tom_fink/alertstream.py +++ b/tom_fink/alertstream.py @@ -79,7 +79,7 @@ def listen(self): myconfig = { "username": self.username, "bootstrap.servers": self.url, - "group_id": self.group_id, + "group.id": self.group_id, } consumer = AlertConsumer([self.topic], myconfig, schema_path=None) @@ -88,7 +88,7 @@ def listen(self): while poll_number < int(self.max_poll_number): try: logger.info( - "FinkAlertStream.listen opening stream: {} with group_id: {} (call number: {})".format( + "FinkAlertStream.listen opening stream: {} with group.id: {} (call number: {})".format( self.url, self.group_id, poll_number From 5fa31cefd7080fe698e5759ca53e4af4f4adf287 Mon Sep 17 00:00:00 2001 From: JulienPeloton Date: Tue, 18 Jun 2024 08:57:21 +0200 Subject: [PATCH 2/7] UPdate requirement for fink-client --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 9277f79..f9446b5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -40,7 +40,7 @@ python = ">=3.8.1,<3.12" tomtoolkit = "^2.17.2" elasticsearch-dsl = "^8.12.0" Markdown = "^3.5.2" -fink-client = "^7.2" +fink-client = "^8.2" tom-alertstreams = "^0.6.2" [tool.poetry.group.test.dependencies] From 6493090a467eb786aa6be351ac319daee9bf2b83 Mon Sep 17 00:00:00 2001 From: JulienPeloton Date: Tue, 18 Jun 2024 09:37:10 +0200 Subject: [PATCH 3/7] Bump fink-client version --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index f9446b5..e77845a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -40,7 +40,7 @@ python = ">=3.8.1,<3.12" tomtoolkit = "^2.17.2" elasticsearch-dsl = "^8.12.0" Markdown = "^3.5.2" -fink-client = "^8.2" +fink-client = "^8.3" tom-alertstreams = "^0.6.2" [tool.poetry.group.test.dependencies] From 0514aedd706962d0a0fb936b262049b7398b0578 Mon Sep 17 00:00:00 2001 From: JulienPeloton Date: Tue, 18 Jun 2024 11:42:02 +0200 Subject: [PATCH 4/7] Update dependency files --- poetry.lock | 1789 +++++++++++++++++++++++------------------------- pyproject.toml | 4 +- 2 files changed, 876 insertions(+), 917 deletions(-) diff --git a/poetry.lock b/poetry.lock index 4f9040f..be14d28 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,14 +1,15 @@ -# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. +# This file is automatically @generated by Poetry and should not be changed by hand. 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+fink-client = "^8.5" tom-alertstreams = "^0.6.2" [tool.poetry.group.test.dependencies] From b660711ee0491d74032f4bf5bb8760561380f0a0 Mon Sep 17 00:00:00 2001 From: JulienPeloton Date: Tue, 18 Jun 2024 22:16:39 +0200 Subject: [PATCH 5/7] Run ruff for code formatting --- tom_fink/alertstream.py | 6 ++---- tom_fink/fink.py | 17 +++++++++-------- 2 files changed, 11 insertions(+), 12 deletions(-) diff --git a/tom_fink/alertstream.py b/tom_fink/alertstream.py index 65fba4e..a17ad53 100644 --- a/tom_fink/alertstream.py +++ b/tom_fink/alertstream.py @@ -89,9 +89,7 @@ def listen(self): try: logger.info( "FinkAlertStream.listen opening stream: {} with group.id: {} (call number: {})".format( - self.url, - self.group_id, - poll_number + self.url, self.group_id, poll_number ) ) topic, alert, key = consumer.poll(timeout=int(self.timeout)) @@ -128,7 +126,7 @@ def alert_logger(alert, topic): If the target is already saved Raises - ---------- + ------ Exception (base) for any other failures than name clash when saving the target in the database. diff --git a/tom_fink/fink.py b/tom_fink/fink.py index 2230c0d..fa19af6 100644 --- a/tom_fink/fink.py +++ b/tom_fink/fink.py @@ -30,12 +30,13 @@ class FinkQueryForm(GenericQueryForm): - """ Class to organise the Query Form for Fink. + """Class to organise the Query Form for Fink. It currently contains forms for * ObjectId search """ + help_objectid = """ Enter a valid object ID to access its data, e.g. try: - ZTF19acmdpyr, ZTF19acnjwgm, ZTF17aaaabte, ZTF20abqehqf, ZTF18acuajcr @@ -216,7 +217,7 @@ class FinkBroker(GenericBroker): form = FinkQueryForm def fetch_alerts(self, parameters: dict) -> iter: - """ Call the Fink API based on parameters from the Query Form. + """Call the Fink API based on parameters from the Query Form. Parameters ---------- @@ -229,7 +230,7 @@ def fetch_alerts(self, parameters: dict) -> iter: } Returns - ---------- + ------- out: iter Iterable on alert data (list of dictionary). Alert data is in the form {column name: value}. @@ -337,14 +338,14 @@ def fetch_alerts(self, parameters: dict) -> iter: return iter(data) def fetch_alert(self, id: str): - """ Call the Fink API based on parameters from the Query Form. + """Call the Fink API based on parameters from the Query Form. Parameters ---------- parameters: str Returns - ---------- + ------- out: iter Iterable on alert data (list of dictionary). Alert data is in the form {column name: value}. @@ -364,7 +365,7 @@ def process_reduced_data(self, target, alert=None): pass def to_target(self, alert: dict) -> Target: - """ Redirect query result to a Target + """Redirect query result to a Target Parameters ---------- @@ -381,7 +382,7 @@ def to_target(self, alert: dict) -> Target: return target def to_generic_alert(self, alert): - """ Extract relevant parameters from the Fink alert to the TOM interface + """Extract relevant parameters from the Fink alert to the TOM interface Parameters ---------- @@ -390,7 +391,7 @@ def to_generic_alert(self, alert): `self.fetch_alerts` for more information. Returns - ---------- + ------- out: GenericAlert Alert columns to be displayed on the TOM interface """ From 96f7debd11c20d74d7a3c4bd59d363866e7df8b8 Mon Sep 17 00:00:00 2001 From: JulienPeloton Date: Tue, 18 Jun 2024 22:18:29 +0200 Subject: [PATCH 6/7] Use f-string when possible --- tom_fink/alertstream.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/tom_fink/alertstream.py b/tom_fink/alertstream.py index a17ad53..4fe1b69 100644 --- a/tom_fink/alertstream.py +++ b/tom_fink/alertstream.py @@ -88,9 +88,7 @@ def listen(self): 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 - ) + f"FinkAlertStream.listen opening stream: {self.url} with group.id: {self.group_id} (call number: {poll_number})" ) topic, alert, key = consumer.poll(timeout=int(self.timeout)) @@ -133,7 +131,7 @@ def alert_logger(alert, topic): """ utc = time.strftime("%Y-%m-%d %H:%M:%S", time.gmtime()) - logger.info("fink.alert_logger topic: {}".format(topic)) + logger.info(f"fink.alert_logger topic: {topic}") logger.info( "fink.alert_logger value: {} emitted {} JD (received {})".format( alert["objectId"], alert["candidate"]["jd"], utc From 6b5937acd1764cf782e1d8851ce9a66d3f331454 Mon Sep 17 00:00:00 2001 From: JulienPeloton Date: Tue, 18 Jun 2024 22:25:38 +0200 Subject: [PATCH 7/7] Run Ruff formatting on files --- .ruff.toml | 85 ++++++++++++++++++ tom_fink/alertstream.py | 5 +- tom_fink/fink.py | 189 +++++++++++++++------------------------- 3 files changed, 157 insertions(+), 122 deletions(-) create mode 100644 .ruff.toml diff --git a/.ruff.toml b/.ruff.toml new file mode 100644 index 0000000..5849525 --- /dev/null +++ b/.ruff.toml @@ -0,0 +1,85 @@ +# Exclude a variety of commonly ignored directories. +exclude = [ + ".bzr", + ".direnv", + ".eggs", + ".git", + ".git-rewrite", + ".hg", + ".ipynb_checkpoints", + ".mypy_cache", + ".nox", + ".pants.d", + ".pyenv", + ".pytest_cache", + ".pytype", + ".ruff_cache", + ".svn", + ".tox", + ".venv", + ".vscode", + "__pypackages__", + "_build", + "buck-out", + "build", + "dist", + "node_modules", + "site-packages", + "venv", +] + +# Same as Black. +line-length = 88 +indent-width = 4 + +# Assume Python 3.8 +target-version = "py38" + +[lint] +# Rules can be found at https://docs.astral.sh/ruff/rules +select = ["E4", "E7", "E9", "F", "E1", "E2", "W", "N", "D", "B", "C4", "PD", "PERF"] +ignore = [ + "C408", "C901", + "D400", "D401", "D100", "D102", "D103", "D104", "D415", "D419", + "E731", + "N812", "N806", "N803", + "PD901", + "PLR0913" +] + +# Allow fix for all enabled rules (when `--fix`) is provided. +fixable = ["ALL"] +unfixable = [] + +# Allow unused variables when underscore-prefixed. +dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$" + +[format] +# Like Black, use double quotes for strings. +quote-style = "double" + +# Like Black, indent with spaces, rather than tabs. +indent-style = "space" + +# Like Black, respect magic trailing commas. +skip-magic-trailing-comma = false + +# Like Black, automatically detect the appropriate line ending. +line-ending = "auto" + +# Enable auto-formatting of code examples in docstrings. Markdown, +# reStructuredText code/literal blocks and doctests are all supported. +# +# This is currently disabled by default, but it is planned for this +# to be opt-out in the future. +docstring-code-format = false + +# Set the line length limit used when formatting code snippets in +# docstrings. +# +# This only has an effect when the `docstring-code-format` setting is +# enabled. +docstring-code-line-length = "dynamic" + +[lint.pydocstyle] +convention = "numpy" diff --git a/tom_fink/alertstream.py b/tom_fink/alertstream.py index 4fe1b69..c69c2e0 100644 --- a/tom_fink/alertstream.py +++ b/tom_fink/alertstream.py @@ -85,10 +85,11 @@ def listen(self): consumer = AlertConsumer([self.topic], myconfig, schema_path=None) poll_number = 0 + header = "FinkAlertStream.listen" while poll_number < int(self.max_poll_number): try: logger.info( - f"FinkAlertStream.listen opening stream: {self.url} with group.id: {self.group_id} (call number: {poll_number})" + f"{header} opening stream: {self.url} with group.id: {self.group_id} (call number: {poll_number})" ) topic, alert, key = consumer.poll(timeout=int(self.timeout)) @@ -99,7 +100,7 @@ def listen(self): logger.info("No alerts received") poll_number += 1 except Exception as ex: - logger.error(f"FinkAlertStream.listen: {ex}") + logger.error(f"{header}: {ex}") logger.error(traceback.format_exc()) break consumer.close() diff --git a/tom_fink/fink.py b/tom_fink/fink.py index fa19af6..f519f90 100644 --- a/tom_fink/fink.py +++ b/tom_fink/fink.py @@ -26,7 +26,7 @@ from astropy.time import Time FINK_URL = "https://fink-portal.org" -COLUMNS = 'i:candid,d:rf_snia_vs_nonia,i:ra,i:dec,i:jd,i:magpsf,i:objectId,d:cdsxmatch' +COLUMNS = "i:candid,d:rf_snia_vs_nonia,i:ra,i:dec,i:jd,i:magpsf,i:objectId,d:cdsxmatch" class FinkQueryForm(GenericQueryForm): @@ -44,13 +44,9 @@ class FinkQueryForm(GenericQueryForm): """ objectId = forms.CharField( required=False, - label='ZTF Object ID', - widget=forms.TextInput( - attrs={'placeholder': 'enter a valid ZTF object ID'} - ), - help_text=md.markdown( - help_objectid - ), + label="ZTF Object ID", + widget=forms.TextInput(attrs={"placeholder": "enter a valid ZTF object ID"}), + help_text=md.markdown(help_objectid), ) help_conesearch = """ @@ -66,15 +62,9 @@ class FinkQueryForm(GenericQueryForm): """ conesearch = forms.CharField( required=False, - label='Cone Search', - help_text=md.markdown( - help_conesearch - ), - widget=forms.TextInput( - attrs={ - 'placeholder': 'RA, Dec, radius' - } - ) + label="Cone Search", + help_text=md.markdown(help_conesearch), + widget=forms.TextInput(attrs={"placeholder": "RA, Dec, radius"}), ) help_datesearch = """ @@ -90,15 +80,9 @@ class FinkQueryForm(GenericQueryForm): """ datesearch = forms.CharField( required=False, - label='Date Search', - help_text=md.markdown( - help_datesearch - ), - widget=forms.TextInput( - attrs={ - 'placeholder': 'startdate, window' - } - ) + label="Date Search", + help_text=md.markdown(help_datesearch), + widget=forms.TextInput(attrs={"placeholder": "startdate, window"}), ) help_classsearch = f""" @@ -111,15 +95,9 @@ class FinkQueryForm(GenericQueryForm): """ classsearch = forms.CharField( required=False, - label='Class Search by number', - help_text=md.markdown( - help_classsearch - ), - widget=forms.TextInput( - attrs={ - 'placeholder': 'class, n_alert' - } - ) + label="Class Search by number", + help_text=md.markdown(help_classsearch), + widget=forms.TextInput(attrs={"placeholder": "class, n_alert"}), ) help_classsearchdate = f""" @@ -131,15 +109,9 @@ class FinkQueryForm(GenericQueryForm): """ classsearchdate = forms.CharField( required=False, - label='Class Search by date', - help_text=md.markdown( - help_classsearchdate - ), - widget=forms.TextInput( - attrs={ - 'placeholder': 'class, n_days_in_past' - } - ) + label="Class Search by date", + help_text=md.markdown(help_classsearchdate), + widget=forms.TextInput(attrs={"placeholder": "class, n_days_in_past"}), ) help_ssosearch = f""" @@ -166,21 +138,15 @@ class FinkQueryForm(GenericQueryForm): """ ssosearch = forms.CharField( required=False, - label='Solar System Objects Search', - help_text=md.markdown( - help_ssosearch - ), - widget=forms.TextInput( - attrs={ - 'placeholder': 'sso_name' - } - ) + label="Solar System Objects Search", + help_text=md.markdown(help_ssosearch), + widget=forms.TextInput(attrs={"placeholder": "sso_name"}), ) def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) self.helper.layout = Layout( - HTML(f''' + HTML(f"""

TOM Toolkit Broker Module @@ -192,15 +158,15 @@ def __init__(self, *args, **kwargs): Please see the Fink API homepage for a detailed description of this broker.

- '''), + """), self.common_layout, Fieldset( None, - 'objectId', - 'conesearch', - 'datesearch', - 'classsearchdate', - 'ssosearch' + "objectId", + "conesearch", + "datesearch", + "classsearchdate", + "ssosearch", ), ) @@ -213,7 +179,7 @@ class FinkBroker(GenericBroker): filters for querying, please see http://134.158.75.151:24000/api """ - name = 'Fink' + name = "Fink" form = FinkQueryForm def fetch_alerts(self, parameters: dict) -> iter: @@ -237,8 +203,12 @@ def fetch_alerts(self, parameters: dict) -> iter: """ # Check the user fills only one query form allowed_search = [ - 'objectId', 'conesearch', 'datesearch', - 'classsearch', 'classsearchdate', 'ssosearch' + "objectId", + "conesearch", + "datesearch", + "classsearch", + "classsearchdate", + "ssosearch", ] nquery = np.sum([len(parameters[i].strip()) > 0 for i in allowed_search]) if nquery > 1: @@ -254,75 +224,58 @@ def fetch_alerts(self, parameters: dict) -> iter: """ raise NotImplementedError(msg) - if len(parameters['objectId'].strip()) > 0: + if len(parameters["objectId"].strip()) > 0: r = requests.post( - FINK_URL + '/api/v1/objects', - json={ - 'objectId': parameters['objectId'].strip(), - 'columns': COLUMNS - } + FINK_URL + "/api/v1/objects", + json={"objectId": parameters["objectId"].strip(), "columns": COLUMNS}, ) - elif len(parameters['conesearch'].strip()) > 0: + elif len(parameters["conesearch"].strip()) > 0: try: - ra, dec, radius = parameters['conesearch'].split(',') + ra, dec, radius = parameters["conesearch"].split(",") except ValueError: raise r = requests.post( - FINK_URL + '/api/v1/explorer', - json={ - 'ra': ra, - 'dec': dec, - 'radius': radius - } + FINK_URL + "/api/v1/explorer", + json={"ra": ra, "dec": dec, "radius": radius}, ) - elif len(parameters['datesearch'].strip()) > 0: + elif len(parameters["datesearch"].strip()) > 0: try: - startdate, window = parameters['datesearch'].split(',') + startdate, window = parameters["datesearch"].split(",") except ValueError: raise r = requests.post( - FINK_URL + '/api/v1/explorer', - json={ - 'startdate': startdate, - 'window': window - } + FINK_URL + "/api/v1/explorer", + json={"startdate": startdate, "window": window}, ) - elif len(parameters['classsearch'].strip()) > 0: + elif len(parameters["classsearch"].strip()) > 0: try: - class_name, n_alert = parameters['classsearch'].split(',') + class_name, n_alert = parameters["classsearch"].split(",") except ValueError: raise r = requests.post( - FINK_URL + '/api/v1/latests', - json={ - 'class': class_name, - 'n': n_alert - } + FINK_URL + "/api/v1/latests", json={"class": class_name, "n": n_alert} ) - elif len(parameters['classsearchdate'].strip()) > 0: + elif len(parameters["classsearchdate"].strip()) > 0: try: - class_name, n_days_in_past = parameters['classsearchdate'].split(',') + class_name, n_days_in_past = parameters["classsearchdate"].split(",") except ValueError: raise now = Time.now() - start = Time(now.jd - float(n_days_in_past), format='jd').iso + start = Time(now.jd - float(n_days_in_past), format="jd").iso end = now.iso r = requests.post( - FINK_URL + '/api/v1/latests', + FINK_URL + "/api/v1/latests", json={ - 'class': class_name, - 'n': 1000, - 'startdate': start, - 'stopdate': end - } + "class": class_name, + "n": 1000, + "startdate": start, + "stopdate": end, + }, ) - elif len(parameters['ssosearch'].strip()) > 0: + elif len(parameters["ssosearch"].strip()) > 0: r = requests.post( - FINK_URL + '/api/v1/sso', - json={ - 'n_or_d': parameters['ssosearch'].strip(), - 'columns': COLUMNS - } + FINK_URL + "/api/v1/sso", + json={"n_or_d": parameters["ssosearch"].strip(), "columns": COLUMNS}, ) else: msg = """ @@ -351,11 +304,7 @@ def fetch_alert(self, id: str): the form {column name: value}. """ r = requests.post( - FINK_URL + '/api/v1/explorer', - json={ - 'objectId': id, - 'columns': COLUMNS - } + FINK_URL + "/api/v1/explorer", json={"objectId": id, "columns": COLUMNS} ) r.raise_for_status() data = r.json() @@ -375,7 +324,7 @@ def to_target(self, alert: dict) -> Target: """ target = Target.objects.create( name=alert.name, - type='SIDEREAL', + type="SIDEREAL", ra=alert.ra, dec=alert.dec, ) @@ -396,15 +345,15 @@ def to_generic_alert(self, alert): Alert columns to be displayed on the TOM interface """ # This URL points to the objectId page in the Fink Science Portal - url = '{}/{}'.format(FINK_URL, alert['i:objectId']) + url = "{}/{}".format(FINK_URL, alert["i:objectId"]) return GenericAlert( - timestamp=alert['i:jd'], - id=alert['i:candid'], + timestamp=alert["i:jd"], + id=alert["i:candid"], url=url, - name=alert['i:objectId'], - ra=alert['i:ra'], - dec=alert['i:dec'], - mag=alert['i:magpsf'], - score=alert.get('d:rf_snia_vs_nonia', 0) + name=alert["i:objectId"], + ra=alert["i:ra"], + dec=alert["i:dec"], + mag=alert["i:magpsf"], + score=alert.get("d:rf_snia_vs_nonia", 0), )