From da7799849602b2529b6a8cf972d6ad24eaec3cdd Mon Sep 17 00:00:00 2001 From: "Adam Ginsburg (keflavich)" Date: Thu, 3 Jan 2019 16:35:23 -0700 Subject: [PATCH 01/13] add HiGal module --- astroquery/higal/__init__.py | 39 +++ astroquery/higal/core.py | 260 ++++++++++++++++++++ astroquery/higal/tests/__init__.py | 0 astroquery/higal/tests/setup_package.py | 15 ++ astroquery/higal/tests/test_higal.py | 85 +++++++ astroquery/higal/tests/test_higal_remote.py | 34 +++ astroquery/template_module/core.py | 2 +- 7 files changed, 434 insertions(+), 1 deletion(-) create mode 100644 astroquery/higal/__init__.py create mode 100644 astroquery/higal/core.py create mode 100644 astroquery/higal/tests/__init__.py create mode 100644 astroquery/higal/tests/setup_package.py create mode 100644 astroquery/higal/tests/test_higal.py create mode 100644 astroquery/higal/tests/test_higal_remote.py diff --git a/astroquery/higal/__init__.py b/astroquery/higal/__init__.py new file mode 100644 index 0000000000..5dd60d26af --- /dev/null +++ b/astroquery/higal/__init__.py @@ -0,0 +1,39 @@ +# Licensed under a 3-clause BSD style license - see LICENSE.rst + +""" +HiGal cutout service +-------------------- + +:author: Adam Ginsburg +""" + +# Make the URL of the server, timeout and other items configurable +# See +# for docs and examples on how to do this +# Below is a common use case +from astropy import config as _config + + +class Conf(_config.ConfigNamespace): + """ + Configuration parameters for `astroquery.higal`. + """ + server = _config.ConfigItem( + ['https://tools.ssdc.asi.it/', + ], + 'Name of the higal server to use.') + + timeout = _config.ConfigItem( + 30, + 'Time limit for connecting to template_module server.') + + +conf = Conf() + +# Now import your public class +# Should probably have the same name as your module +from .core import HiGal, HiGalClass + +__all__ = ['HiGal', 'HiGalClass', + 'Conf', 'conf', + ] diff --git a/astroquery/higal/core.py b/astroquery/higal/core.py new file mode 100644 index 0000000000..c0c505955d --- /dev/null +++ b/astroquery/higal/core.py @@ -0,0 +1,260 @@ +# Licensed under a 3-clause BSD style license - see LICENSE.rst +from __future__ import print_function + +import json +from six.moves.urllib.parse import urljoin +import io + +import astropy.units as u +from astropy import coordinates +import astropy.io.votable as votable +from astropy.table import Table +from astropy.io import fits + +from ..query import BaseQuery +from ..utils import commons +from ..utils import prepend_docstr_nosections +from ..utils import async_to_sync +from . import conf + +__all__ = ['HiGal', 'HiGalClass'] + +# declare global variables and constants if any + + +# Now begin your main class +# should be decorated with the async_to_sync imported previously +@async_to_sync +class HiGalClass(BaseQuery): + + """ + Not all the methods below are necessary but these cover most of the common + cases, new methods may be added if necessary, follow the guidelines at + + """ + # use the Configuration Items imported from __init__.py to set the URL, + # TIMEOUT, etc. + URL = conf.server + "HiGALSearch.jsp" + TIMEOUT = conf.timeout + CATALOG_URL = conf.server + "MMCAjaxFunction" + #https://tools.ssdc.asi.it/MMCAjaxFunction? + #&mission=Hi-GAL&action=getMMCCatalogData&catalogId=4048&radius=10&ra=281.85238759&dec=-1.93488693&_=1546540568988 + HIGAL_CATALOGS = {'blue': 4047, + 'red': 4051, + 'psw': 4050, + 'pmw': 4049, + 'plw': 4048, + } + HIGAL_WAVELENGTHS = {'blue': '070', + 'red': '160', + 'psw': '250', + 'pmw': '350', + 'plw': '500', + } + + def query_region_async(self, coordinates, radius, + catalog='blue', + catalog_query=True, + get_query_payload=False, cache=True): + """ + Queries a region around the specified coordinates. + + Parameters + ---------- + coordinates : str or `astropy.coordinates`. + coordinates around which to query + radius : str or `astropy.units.Quantity`. + the radius of the cone search + catalog_query : bool + Query the catalog or the generic search interface? No parser + is implemented for the generic search interface yet. + catalog : 'blue', 'red', 'psw', 'pmw', or 'plw' + Which HiGal catalog to query. + get_query_payload : bool, optional + Just return the dict of HTTP request parameters. + verbose : bool, optional + Display VOTable warnings or not. + + Returns + ------- + response : `requests.Response` + The HTTP response returned from the service. + All async methods should return the raw HTTP response. + """ + request_payload = self._args_to_payload(coords=coordinates, + radius=radius, + catalog_id=self.HIGAL_CATALOGS[catalog.lower()], + catalog_query=catalog_query, + ) + if get_query_payload: + return request_payload + + if catalog_query: + response = self._request('GET', self.CATALOG_URL, params=request_payload, + timeout=self.TIMEOUT, cache=cache) + else: + response = self._request('POST', self.URL, params=request_payload, + timeout=self.TIMEOUT, cache=cache) + + response.raise_for_status() + + return response + + # as we mentioned earlier use various python regular expressions, etc + # to create the dict of HTTP request parameters by parsing the user + # entered values. For cleaner code keep this as a separate private method: + + def _args_to_payload(self, coords=None, name=None, radius=10*u.arcmin, + catalog_id=None, catalog_query=True, *args, **kwargs): + + if not hasattr(self, '_session_id'): + # set up session: get cookies + initial_response = self._request('GET', self.URL, cache=False, + timeout=self.TIMEOUT) + + # multiple cookies are returned + self._session_id = self._session.cookies.values()[1] + + # remove the bad session ID associated with CAS rather + # than root; this may confuse later download attempts + for cookie in self._session.cookies: + if cookie.name == 'JSESSIONID': + if cookie.path == '/cas/': + self._session.cookies.clear(cookie.domain, + cookie.path, + cookie.name) + + + if name is not None: + coords = coordinates.SkyCoord.from_name(name) + + if catalog_query: + request_payload = { + 'mission':'Hi-GAL', + 'action': 'getMMCCatalogData', + 'catalogId': catalog_id, #[4048-4051 + "radius": "{0}".format(radius.to(u.arcmin).value), + "ra": coords.fk5.ra.value, + "dec": coords.fk5.dec.value, + } + else: + # this is the "default" query to the service that produces + # the cutouts; it's needed by get_images + request_payload = { + "coordobjc": "{0} {1}".format(coords.fk5.ra.value, + coords.fk5.dec.value), + "RA": coords.fk5.ra.value, + "DEC": coords.fk5.dec.value, + "coordsType": "RADEC", # or "LB" + "NameResolverLOCAL": "LOCAL", + "radius": "arcmin", + "size": "", + "radiusInput": "{0}".format(radius.to(u.arcmin).value), + "radius_all": "{0}".format(radius.to(u.arcmin).value), + "HIGAL": "HIGAL", + "catalog": [4047, 4048, 4049, 4050, 4051], + "catalog_radius_4047": 1.0, + "catalog_radius_4051": 1.0, + "catalog_radius_4050": 1.0, + "catalog_radius_4049": 1.0, + "catalog_radius_4048": 1.0, + "resolution": "", + "sourceString": "", + "sessionId": self._session_id, + "editId": "", + } + + return request_payload + + def _parse_result(self, response, verbose=False): + jdata = response.json() + + return Table(jdata['aaData']) + + def get_images(self, coordinates, radius, get_query_payload=False, + cache=False): + """ + A query function that searches for image cut-outs around coordinates + + Parameters + ---------- + coordinates : str or `astropy.coordinates`. + coordinates around which to query + radius : str or `astropy.units.Quantity`. + the radius of the cone search + get_query_payload : bool, optional + If true than returns the dictionary of query parameters, posted to + remote server. Defaults to `False`. + + Returns + ------- + A list of `astropy.fits.HDUList` objects + """ + responses = self.get_images_async(coordinates, radius, + get_query_payload=get_query_payload, + cache=cache) + if get_query_payload: + return responses + return [fits.open(io.BytesIO(response.content)) for response in responses] + + @prepend_docstr_nosections(get_images.__doc__) + def get_images_async(self, coordinates, radius, get_query_payload=False, + cache=False): + """ + Returns + ------- + A list of context-managers that yield readable file-like objects + """ + image_urls = self.get_image_list(coordinates, radius, + get_query_payload=get_query_payload) + if get_query_payload: + return image_urls + + responses = [] + for url in image_urls: + response = self._request('GET', url, timeout=self.TIMEOUT, + cache=cache) + response.raise_for_status() + responses.append(response) + + return responses + + @prepend_docstr_nosections(get_images.__doc__) + def get_image_list(self, coordinates, radius, get_query_payload=False, + cache=True): + """ + Returns + ------- + list of image urls + """ + if get_query_payload: + return {} + + base_response = self.query_region_async(coordinates=coordinates, + radius=radius, + catalog_query=False, + cache=False, + ) + base_response.raise_for_status() + + lines = base_response.text.split("\n") + dataline = [line for line in lines if 'fitsHeaders = JSON.parse(\'' in line][0] + + json_data = dataline.split('fitsHeaders = JSON.parse(\'')[1].strip('\');') + + jdict = json.loads(json_data) + filename = jdict['4048']['FILENAME'] + + assert self._session_id in filename + + image_list = [urljoin(conf.server, + filename + .replace("PLW", wlname.upper()) + .replace("500", wlval) + .replace('jpeg', 'fits')) + for wlname, wlval in self.HIGAL_WAVELENGTHS.items()] + + return image_list + + +HiGal = HiGalClass() diff --git a/astroquery/higal/tests/__init__.py b/astroquery/higal/tests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/astroquery/higal/tests/setup_package.py b/astroquery/higal/tests/setup_package.py new file mode 100644 index 0000000000..7585ada1b3 --- /dev/null +++ b/astroquery/higal/tests/setup_package.py @@ -0,0 +1,15 @@ +# Licensed under a 3-clause BSD style license - see LICENSE.rst +from __future__ import absolute_import + +import os + + +# setup paths to the test data +# can specify a single file or a list of files +def get_package_data(): + paths = [os.path.join('data', '*.dat'), + os.path.join('data', '*.xml'), + ] # etc, add other extensions + # you can also enlist files individually by names + # finally construct and return a dict for the sub module + return {'astroquery.template_module.tests': paths} diff --git a/astroquery/higal/tests/test_higal.py b/astroquery/higal/tests/test_higal.py new file mode 100644 index 0000000000..9af0fd283b --- /dev/null +++ b/astroquery/higal/tests/test_higal.py @@ -0,0 +1,85 @@ +# Licensed under a 3-clause BSD style license - see LICENSE.rst +from __future__ import print_function + +# astroquery uses the pytest framework for testing +# this is already available in astropy and does +# not require a separate install. Import it using: +import pytest + +# It would be best if tests are separated in two +# modules. This module performs tests on local data +# by mocking HTTP requests and responses. To test the +# same functions on the remote server, put the relevant +# tests in the 'test_module_remote.py' + +# Now import other commonly used modules for tests +import os +import requests + +from numpy import testing as npt +from astropy.table import Table +import astropy.coordinates as coord +import astropy.units as u + +from ...utils.testing_tools import MockResponse + +# finally import the module which is to be tested +# and the various configuration items created +from ... import template_module +from ...template_module import conf + +# Local tests should have the corresponding data stored +# in the ./data folder. This is the actual HTTP response +# one would expect from the server when a valid query is made. +# Its best to keep the data file small, so that testing is +# quicker. When running tests locally the stored data is used +# to mock the HTTP requests and response part of the query +# thereby saving time and bypassing unreliability for +# an actual remote network query. + +DATA_FILES = {'GET': + # You might have a different response for each URL you're + # querying: + {'http://dummy_server_mirror_1': + 'dummy.dat'}} + + +# ./setup_package.py helps the test function locate the data file +# define a function that can construct the full path to the file in the +# ./data directory: +def data_path(filename): + data_dir = os.path.join(os.path.dirname(__file__), 'data') + return os.path.join(data_dir, filename) + + +# define a monkeypatch replacement request function that returns the +# dummy HTTP response for the dummy 'get' function, by +# reading in data from some data file: +def nonremote_request(self, request_type, url, **kwargs): + # kwargs are ignored in this case, but they don't have to be + # (you could use them to define which data file to read) + with open(data_path(DATA_FILES[request_type][url]), 'rb') as f: + response = MockResponse(content=f.read(), url=url) + return response + + +# use a pytest fixture to create a dummy 'requests.get' function, +# that mocks(monkeypatches) the actual 'requests.get' function: +@pytest.fixture +def patch_request(request): + try: + mp = request.getfixturevalue("monkeypatch") + except AttributeError: # pytest < 3 + mp = request.getfuncargvalue("monkeypatch") + mp.setattr(template_module.core.TemplateClass, '_request', + nonremote_request) + return mp + + +# finally test the methods using the mock HTTP response +def test_query_object(patch_request): + result = template_module.core.TemplateClass().query_object('m1') + assert isinstance(result, Table) + +# similarly fill in tests for each of the methods +# look at tests in existing modules for more examples diff --git a/astroquery/higal/tests/test_higal_remote.py b/astroquery/higal/tests/test_higal_remote.py new file mode 100644 index 0000000000..7ef8142526 --- /dev/null +++ b/astroquery/higal/tests/test_higal_remote.py @@ -0,0 +1,34 @@ +# Licensed under a 3-clause BSD style license - see LICENSE.rst +from __future__ import print_function + +from astropy.tests.helper import remote_data + +from astropy import coordinates +from astropy import units as u + +from ..core import HiGal + +@remote_data +class TestTemplateClass: + def test_basic_query(self): + crd = coordinates.SkyCoord(*(281.85238759, -1.93488693), frame='fk5', + unit=(u.deg, u.deg)) + + # check cutout response + base_response = HiGal.query_region_async(crd, radius=10*u.arcmin, + cache=False, + catalog_query=False) + + # this text is where the filename JSON data is hidden + assert 'fitsHeaders = JSON.parse(\'' in base_response.text + + def test_catalog_query(self): + crd = coordinates.SkyCoord(*(281.85238759, -1.93488693), frame='fk5', + unit=(u.deg, u.deg)) + + # check catalog response + catalog = HiGal.query_region_async(crd, radius=10*u.arcmin, + catalog='blue', + cache=False, catalog_query=True) + + assert 'HIGALPB030.6606-0.0878' in catalog['DESIGNATION'] diff --git a/astroquery/template_module/core.py b/astroquery/template_module/core.py index bdda6c8678..094a09a414 100644 --- a/astroquery/template_module/core.py +++ b/astroquery/template_module/core.py @@ -227,7 +227,7 @@ def _parse_result(self, response, *, verbose=False): # the downloaded images to a preferred location. Here we look at the # skeleton code for image services - def get_images(self, coordinates, radius, get_query_payload): + def get_images(self, coordinates, radius, get_query_payload=False): """ A query function that searches for image cut-outs around coordinates From 8c7db3266bc44741a5a16f3bd4228bbdb6c29192 Mon Sep 17 00:00:00 2001 From: "Adam Ginsburg (keflavich)" Date: Thu, 3 Jan 2019 16:35:50 -0700 Subject: [PATCH 02/13] more cleanup --- astroquery/higal/__init__.py | 6 ------ 1 file changed, 6 deletions(-) diff --git a/astroquery/higal/__init__.py b/astroquery/higal/__init__.py index 5dd60d26af..73c80e7b14 100644 --- a/astroquery/higal/__init__.py +++ b/astroquery/higal/__init__.py @@ -7,10 +7,6 @@ :author: Adam Ginsburg """ -# Make the URL of the server, timeout and other items configurable -# See -# for docs and examples on how to do this -# Below is a common use case from astropy import config as _config @@ -30,8 +26,6 @@ class Conf(_config.ConfigNamespace): conf = Conf() -# Now import your public class -# Should probably have the same name as your module from .core import HiGal, HiGalClass __all__ = ['HiGal', 'HiGalClass', From 74f40265072bc0af97a2466813671be98c3e33c1 Mon Sep 17 00:00:00 2001 From: "Adam Ginsburg (keflavich)" Date: Thu, 3 Jan 2019 16:39:55 -0700 Subject: [PATCH 03/13] add changelog --- CHANGES.rst | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/CHANGES.rst b/CHANGES.rst index 3becc87463..ab14d2a31a 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -1189,6 +1189,11 @@ noirlab - Module added to access the NOIRLab (formally NOAO) archive. [#1638] +higal +^^^^^ + +- Herschel Hi-Gal catalog & cutout service [#1324] + Service fixes and enhancements ------------------------------ From 4871638c1e9e9e971a8a5bb7dd424d23fd14031d Mon Sep 17 00:00:00 2001 From: "Adam Ginsburg (keflavich)" Date: Thu, 3 Jan 2019 17:02:36 -0700 Subject: [PATCH 04/13] it is possible for a cutout to be missing; we need to allow for that. Also, the hack I had before isn't needed when you appropriately query for multiple wavelengths --- astroquery/higal/core.py | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/astroquery/higal/core.py b/astroquery/higal/core.py index c0c505955d..4c1ac334cf 100644 --- a/astroquery/higal/core.py +++ b/astroquery/higal/core.py @@ -243,16 +243,15 @@ def get_image_list(self, coordinates, radius, get_query_payload=False, json_data = dataline.split('fitsHeaders = JSON.parse(\'')[1].strip('\');') jdict = json.loads(json_data) - filename = jdict['4048']['FILENAME'] - - assert self._session_id in filename + filenames = {wlname: jdict[str(wlnum)]['FILENAME'] + for wlname, wlnum in self.HIGAL_CATALOGS.items() + if str(wlnum) in jdict} image_list = [urljoin(conf.server, - filename - .replace("PLW", wlname.upper()) - .replace("500", wlval) - .replace('jpeg', 'fits')) - for wlname, wlval in self.HIGAL_WAVELENGTHS.items()] + filenames[wlname].replace('jpeg', 'fits')) + for wlname in self.HIGAL_CATALOGS + if wlname in filenames + ] return image_list From 80247e50190e8e8cbe03126b8992212fe98560fb Mon Sep 17 00:00:00 2001 From: "Adam Ginsburg (keflavich)" Date: Wed, 27 Feb 2019 17:28:13 -0700 Subject: [PATCH 05/13] remove some comments, still not done with the PR --- astroquery/higal/core.py | 5 +---- astroquery/higal/tests/test_higal.py | 23 ++++------------------- 2 files changed, 5 insertions(+), 23 deletions(-) diff --git a/astroquery/higal/core.py b/astroquery/higal/core.py index 4c1ac334cf..3ce96b02ee 100644 --- a/astroquery/higal/core.py +++ b/astroquery/higal/core.py @@ -100,10 +100,6 @@ def query_region_async(self, coordinates, radius, return response - # as we mentioned earlier use various python regular expressions, etc - # to create the dict of HTTP request parameters by parsing the user - # entered values. For cleaner code keep this as a separate private method: - def _args_to_payload(self, coords=None, name=None, radius=10*u.arcmin, catalog_id=None, catalog_query=True, *args, **kwargs): @@ -111,6 +107,7 @@ def _args_to_payload(self, coords=None, name=None, radius=10*u.arcmin, # set up session: get cookies initial_response = self._request('GET', self.URL, cache=False, timeout=self.TIMEOUT) + initial_response.raise_for_status() # multiple cookies are returned self._session_id = self._session.cookies.values()[1] diff --git a/astroquery/higal/tests/test_higal.py b/astroquery/higal/tests/test_higal.py index 9af0fd283b..fabfcc61c3 100644 --- a/astroquery/higal/tests/test_higal.py +++ b/astroquery/higal/tests/test_higal.py @@ -1,18 +1,8 @@ # Licensed under a 3-clause BSD style license - see LICENSE.rst from __future__ import print_function -# astroquery uses the pytest framework for testing -# this is already available in astropy and does -# not require a separate install. Import it using: import pytest -# It would be best if tests are separated in two -# modules. This module performs tests on local data -# by mocking HTTP requests and responses. To test the -# same functions on the remote server, put the relevant -# tests in the 'test_module_remote.py' - -# Now import other commonly used modules for tests import os import requests @@ -23,10 +13,8 @@ from ...utils.testing_tools import MockResponse -# finally import the module which is to be tested -# and the various configuration items created -from ... import template_module -from ...template_module import conf +from ... import higal +from ...higal import conf # Local tests should have the corresponding data stored # in the ./data folder. This is the actual HTTP response @@ -71,15 +59,12 @@ def patch_request(request): mp = request.getfixturevalue("monkeypatch") except AttributeError: # pytest < 3 mp = request.getfuncargvalue("monkeypatch") - mp.setattr(template_module.core.TemplateClass, '_request', + mp.setattr(higal.core.HiGalClass, '_request', nonremote_request) return mp # finally test the methods using the mock HTTP response def test_query_object(patch_request): - result = template_module.core.TemplateClass().query_object('m1') + result = higal.core.HiGalClass().query_object('m1') assert isinstance(result, Table) - -# similarly fill in tests for each of the methods -# look at tests in existing modules for more examples From 1f42cecfdb6eeea2010d4201bde63d231e990d66 Mon Sep 17 00:00:00 2001 From: "Adam Ginsburg (keflavich)" Date: Thu, 28 Feb 2019 10:21:01 -0700 Subject: [PATCH 06/13] minor correction --- astroquery/higal/tests/test_higal.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/astroquery/higal/tests/test_higal.py b/astroquery/higal/tests/test_higal.py index fabfcc61c3..03c23be660 100644 --- a/astroquery/higal/tests/test_higal.py +++ b/astroquery/higal/tests/test_higal.py @@ -65,6 +65,6 @@ def patch_request(request): # finally test the methods using the mock HTTP response -def test_query_object(patch_request): - result = higal.core.HiGalClass().query_object('m1') +def test_query_region(patch_request): + result = higal.core.HiGalClass().query_region('m1') assert isinstance(result, Table) From e1b2b0947d8dba7e48c1b1937371d5645c49d6a3 Mon Sep 17 00:00:00 2001 From: "Adam Ginsburg (keflavich)" Date: Sun, 3 Mar 2019 19:34:39 -0700 Subject: [PATCH 07/13] added basic docs --- docs/higal/higal.rst | 51 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 docs/higal/higal.rst diff --git a/docs/higal/higal.rst b/docs/higal/higal.rst new file mode 100644 index 0000000000..72378f18a0 --- /dev/null +++ b/docs/higal/higal.rst @@ -0,0 +1,51 @@ +.. doctest-skip-all + +.. _astroquery.higal: + +************************************** +HiGal Image Cutout and Catalog service +************************************** + +Getting started +=============== + +The HiGal image cutout service is a sub-service of the Space Science Data +Center Sky Explorer (https://tools.ssdc.asi.it/). It enables image cutout +queries and catalog queries. + +An example catalog query: + +.. python:: + >>> from astroquery.higal import HiGal + >>> from astropy import units as u, coordinates + >>> target = coordinates.SkyCoord(49.5, -0.3, frame='galactic', unit=(u.deg, u.deg)) + >>> result = HiGal.query_region(coordinates=target, radius=0.25*u.deg) + >>> result + + DEC DESIGNATION ERR_FINT ERR_FPEAK FINT FPEAK FWHMA FWHMB GLAT GLON NAME PA RA RMS_SURROUND rowid + float64 str22 float64 float64 float64 float64 float64 float64 float64 float64 str10 float64 float64 float64 int64 + --------- ---------------------- -------- --------- -------- -------- ------- ------- --------- --------- ---------- ------- --------- ------------ ----- + 14.335341 HIGALPB049.3443-0.4849 0.171 11.126 2.66513 203.692 22.77 17.43 -0.484918 49.344287 HIGAL_BLUE -74.4 290.95059 28.8882 5567 + 14.358867 HIGALPB049.3808-0.5031 0.158 14.851 3.72149 425.767 15.18 17.28 -0.503143 49.380769 HIGAL_BLUE 64.1 290.98497 56.3716 5513 + ... + + +And an example image query: + +.. python:: + >>> from astroquery.higal import HiGal + >>> from astropy import units as u, coordinates + >>> target = coordinates.SkyCoord(49.5, -0.3, frame='galactic', unit=(u.deg, u.deg)) + >>> result = HiGal.get_images(coordinates=target, radius=0.25*u.deg) + [[], + [], + [], + [], + []] + + +Reference/API +============= + +.. automodapi:: astroquery.higal + :no-inheritance-diagram: From 68b7a08065a2b1d54763a050c6e926c0c7a671c2 Mon Sep 17 00:00:00 2001 From: "Adam Ginsburg (keflavich)" Date: Sun, 3 Mar 2019 20:30:06 -0700 Subject: [PATCH 08/13] pep8 fixes. The bracket closures DO match the indentation, though. pep8 lies sometimes. --- astroquery/higal/core.py | 11 +++++------ astroquery/higal/tests/test_higal_remote.py | 1 + 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/astroquery/higal/core.py b/astroquery/higal/core.py index 3ce96b02ee..6b6159fb97 100644 --- a/astroquery/higal/core.py +++ b/astroquery/higal/core.py @@ -37,8 +37,8 @@ class HiGalClass(BaseQuery): URL = conf.server + "HiGALSearch.jsp" TIMEOUT = conf.timeout CATALOG_URL = conf.server + "MMCAjaxFunction" - #https://tools.ssdc.asi.it/MMCAjaxFunction? - #&mission=Hi-GAL&action=getMMCCatalogData&catalogId=4048&radius=10&ra=281.85238759&dec=-1.93488693&_=1546540568988 + # https://tools.ssdc.asi.it/MMCAjaxFunction? + # &mission=Hi-GAL&action=getMMCCatalogData&catalogId=4048&radius=10&ra=281.85238759&dec=-1.93488693&_=1546540568988 HIGAL_CATALOGS = {'blue': 4047, 'red': 4051, 'psw': 4050, @@ -121,15 +121,14 @@ def _args_to_payload(self, coords=None, name=None, radius=10*u.arcmin, cookie.path, cookie.name) - if name is not None: coords = coordinates.SkyCoord.from_name(name) if catalog_query: request_payload = { - 'mission':'Hi-GAL', + 'mission': 'Hi-GAL', 'action': 'getMMCCatalogData', - 'catalogId': catalog_id, #[4048-4051 + 'catalogId': catalog_id, #[4048-4051 "radius": "{0}".format(radius.to(u.arcmin).value), "ra": coords.fk5.ra.value, "dec": coords.fk5.dec.value, @@ -142,7 +141,7 @@ def _args_to_payload(self, coords=None, name=None, radius=10*u.arcmin, coords.fk5.dec.value), "RA": coords.fk5.ra.value, "DEC": coords.fk5.dec.value, - "coordsType": "RADEC", # or "LB" + "coordsType": "RADEC", # or "LB" "NameResolverLOCAL": "LOCAL", "radius": "arcmin", "size": "", diff --git a/astroquery/higal/tests/test_higal_remote.py b/astroquery/higal/tests/test_higal_remote.py index 7ef8142526..3547819952 100644 --- a/astroquery/higal/tests/test_higal_remote.py +++ b/astroquery/higal/tests/test_higal_remote.py @@ -8,6 +8,7 @@ from ..core import HiGal + @remote_data class TestTemplateClass: def test_basic_query(self): From ceb12735a4dda82524ab0185b15d484087645523 Mon Sep 17 00:00:00 2001 From: "Adam Ginsburg (keflavich)" Date: Sun, 3 Mar 2019 20:53:24 -0700 Subject: [PATCH 09/13] add local tests and cleanup some testing --- astroquery/higal/core.py | 8 +- astroquery/higal/tests/data/frontpage.html | 316 ++++++++++++++++++++ astroquery/higal/tests/data/g49.html | 1 + astroquery/higal/tests/setup_package.py | 11 +- astroquery/higal/tests/test_higal.py | 62 ++-- astroquery/higal/tests/test_higal_remote.py | 12 + 6 files changed, 378 insertions(+), 32 deletions(-) create mode 100644 astroquery/higal/tests/data/frontpage.html create mode 100644 astroquery/higal/tests/data/g49.html diff --git a/astroquery/higal/core.py b/astroquery/higal/core.py index 6b6159fb97..8f31ee7cac 100644 --- a/astroquery/higal/core.py +++ b/astroquery/higal/core.py @@ -105,9 +105,11 @@ def _args_to_payload(self, coords=None, name=None, radius=10*u.arcmin, if not hasattr(self, '_session_id'): # set up session: get cookies - initial_response = self._request('GET', self.URL, cache=False, - timeout=self.TIMEOUT) - initial_response.raise_for_status() + # (save _initial_response for later debugging) + self._initial_response = self._request('GET', self.URL, + cache=False, + timeout=self.TIMEOUT) + self._initial_response.raise_for_status() # multiple cookies are returned self._session_id = self._session.cookies.values()[1] diff --git a/astroquery/higal/tests/data/frontpage.html b/astroquery/higal/tests/data/frontpage.html new file mode 100644 index 0000000000..fc52cc676b --- /dev/null +++ b/astroquery/higal/tests/data/frontpage.html @@ -0,0 +1,316 @@ + + + + + + + + + + + + + + + + + + + Hi-GAL Catalogs and Image Server + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + logo_higal_header.png + + + + + + + Version 1.0.2 +
+ + + +
+
+ + + +
+ +
+
+ + + + + + + + + + + + + + + + + + + +
Hi-GAL Catalogs and Image Server
+ + +
+ Coordinates/Object: + + + RA DEC + L B +

+ Name Resolver: + Local + SIMBAD + NED +

+ + +  Radius: + + +  (Arcmin max 30) + +

+
+ + + + + + + + + + +
+ + + Available Catalogs +
+
+ + + + + + +
+
+ + + HIGAL:  + +
+ + + + + + + + + + + + +
+ + + + HIGAL_BLUE    +
+ + + + + + + + +
+ + + + HIGAL_RED    +
+ + + + + + + + +
+ + + + HIGAL_PSW    +
+ + + + + + + + +
+ + + + HIGAL_PMW    +
+ + + + + + + + +
+ + + + HIGAL_PLW    +
+ + + + +
+
+ + + + +
+
+ +
+ + +
+ +
  + + + + + + + + +
+
+
    +
  • Radius:    + + +
    • +
+
+
+

+
+

© SSDC

+
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\ No newline at end of file diff --git a/astroquery/higal/tests/setup_package.py b/astroquery/higal/tests/setup_package.py index 7585ada1b3..1e51d86bad 100644 --- a/astroquery/higal/tests/setup_package.py +++ b/astroquery/higal/tests/setup_package.py @@ -4,12 +4,7 @@ import os -# setup paths to the test data -# can specify a single file or a list of files def get_package_data(): - paths = [os.path.join('data', '*.dat'), - os.path.join('data', '*.xml'), - ] # etc, add other extensions - # you can also enlist files individually by names - # finally construct and return a dict for the sub module - return {'astroquery.template_module.tests': paths} + paths = [os.path.join('data', '*.html'), + ] + return {'astroquery.higal.tests': paths} diff --git a/astroquery/higal/tests/test_higal.py b/astroquery/higal/tests/test_higal.py index 03c23be660..1be44a77d6 100644 --- a/astroquery/higal/tests/test_higal.py +++ b/astroquery/higal/tests/test_higal.py @@ -16,25 +16,18 @@ from ... import higal from ...higal import conf -# Local tests should have the corresponding data stored -# in the ./data folder. This is the actual HTTP response -# one would expect from the server when a valid query is made. -# Its best to keep the data file small, so that testing is -# quicker. When running tests locally the stored data is used -# to mock the HTTP requests and response part of the query -# thereby saving time and bypassing unreliability for -# an actual remote network query. - -DATA_FILES = {'GET': - # You might have a different response for each URL you're - # querying: - {'http://dummy_server_mirror_1': - 'dummy.dat'}} - - -# ./setup_package.py helps the test function locate the data file -# define a function that can construct the full path to the file in the -# ./data directory: +DATA_FILES = {'POST': + {'https://tools.ssdc.asi.it/HiGALSearch.jsp': + 'g49.html'}, + 'GET': + {'https://tools.ssdc.asi.it/MMCAjaxFunction': + 'g49.html', + 'https://tools.ssdc.asi.it/HiGALSearch.jsp': + 'frontpage.html', + } + } + + def data_path(filename): data_dir = os.path.join(os.path.dirname(__file__), 'data') return os.path.join(data_dir, filename) @@ -63,8 +56,35 @@ def patch_request(request): nonremote_request) return mp +class FakeCookieJar(list): + def values(self): + return self + + def clear(self, arg1, arg2, arg3, **kwargs): + return + +class FakeCookie(object): + def __init__(self): + self.name = "JSESSIONID" + self.path = '/cas/' + self.domain = "" + -# finally test the methods using the mock HTTP response def test_query_region(patch_request): - result = higal.core.HiGalClass().query_region('m1') + target = coord.SkyCoord(49.5, -0.3, frame='galactic', unit=(u.deg, u.deg)) + hg = higal.core.HiGalClass() + hg._session.cookies = FakeCookieJar([FakeCookie()]*2) + + result = hg.query_region(coordinates=target, radius=0.25*u.deg, catalog_query=True) + assert isinstance(result, Table) + + result = hg.query_region(coordinates=target, radius=0.25*u.deg, catalog_query=False) assert isinstance(result, Table) + +# these tests are challenging to do locally; we'll rely on the remote ones for +# now =( +# def test_get_images(patch_request): +# target = coord.SkyCoord(49.5, -0.3, frame='galactic', unit=(u.deg, u.deg)) +# result = higal.core.HiGalClass().get_images(coordinates=target, +# radius=0.25*u.deg) +# assert isinstance(result, Table) diff --git a/astroquery/higal/tests/test_higal_remote.py b/astroquery/higal/tests/test_higal_remote.py index 3547819952..785f7b35a3 100644 --- a/astroquery/higal/tests/test_higal_remote.py +++ b/astroquery/higal/tests/test_higal_remote.py @@ -5,6 +5,7 @@ from astropy import coordinates from astropy import units as u +from astropy.io import fits from ..core import HiGal @@ -33,3 +34,14 @@ def test_catalog_query(self): cache=False, catalog_query=True) assert 'HIGALPB030.6606-0.0878' in catalog['DESIGNATION'] + + def test_get_images(self): + crd = coordinates.SkyCoord(49.5, -0.3, frame='galactic', + unit=(u.deg, u.deg)) + + imlist = HiGal.get_images(crd, radius=3*u.arcmin) + + assert len(imlist) == 5 + + for im in imlist: + assert isinstance(im, fits.HDUList) From 66cae7a054485f792e07f512ab7085c2e1a34db6 Mon Sep 17 00:00:00 2001 From: "Adam Ginsburg (keflavich)" Date: Sat, 4 May 2019 11:59:45 -0600 Subject: [PATCH 10/13] more interactive tests revealed that my hacks didn't really work, this commit has some fixes --- astroquery/higal/core.py | 28 +++++++++++++++++++--------- 1 file changed, 19 insertions(+), 9 deletions(-) diff --git a/astroquery/higal/core.py b/astroquery/higal/core.py index 8f31ee7cac..f9a571a347 100644 --- a/astroquery/higal/core.py +++ b/astroquery/higal/core.py @@ -11,7 +11,7 @@ from astropy.table import Table from astropy.io import fits -from ..query import BaseQuery +from ..query import BaseQuery, AstroQuery from ..utils import commons from ..utils import prepend_docstr_nosections from ..utils import async_to_sync @@ -188,34 +188,44 @@ def get_images(self, coordinates, radius, get_query_payload=False, ------- A list of `astropy.fits.HDUList` objects """ - responses = self.get_images_async(coordinates, radius, + filenames = self.get_images_async(coordinates, radius, get_query_payload=get_query_payload, cache=cache) if get_query_payload: - return responses - return [fits.open(io.BytesIO(response.content)) for response in responses] + return filenames + return [fits.open(fn) for fn in filenames] @prepend_docstr_nosections(get_images.__doc__) def get_images_async(self, coordinates, radius, get_query_payload=False, - cache=False): + cache=False, timeout=None): """ Returns ------- A list of context-managers that yield readable file-like objects """ + print(f"Getting image list at {coordinates} with {radius}") image_urls = self.get_image_list(coordinates, radius, get_query_payload=get_query_payload) if get_query_payload: return image_urls responses = [] + filenames = [] for url in image_urls: - response = self._request('GET', url, timeout=self.TIMEOUT, - cache=cache) - response.raise_for_status() + print("Downloading URL {0}".format(url)) + query = AstroQuery('GET', url) + cachefile = query.request_file(self.cache_location) + response = self._download_file(url, cachefile, cache=cache, + timeout=timeout or self.TIMEOUT, + close_response=False + ) + filenames.append(cachefile) + #response = self._request('GET', url, timeout=self.TIMEOUT, + # cache=cache) + #response.raise_for_status() responses.append(response) - return responses + return filenames @prepend_docstr_nosections(get_images.__doc__) def get_image_list(self, coordinates, radius, get_query_payload=False, From e330c204d2668d6e7362e4a4a29c81c4bd4344ab Mon Sep 17 00:00:00 2001 From: "Adam Ginsburg (keflavich)" Date: Sat, 8 May 2021 16:08:05 -0400 Subject: [PATCH 11/13] move everything into astroquery.herschel.higal --- astroquery/{ => herschel}/higal/__init__.py | 0 astroquery/{ => herschel}/higal/core.py | 0 astroquery/{ => herschel}/higal/tests/__init__.py | 0 astroquery/{ => herschel}/higal/tests/data/frontpage.html | 0 astroquery/{ => herschel}/higal/tests/data/g49.html | 0 astroquery/{ => herschel}/higal/tests/setup_package.py | 0 astroquery/{ => herschel}/higal/tests/test_higal.py | 0 astroquery/{ => herschel}/higal/tests/test_higal_remote.py | 0 8 files changed, 0 insertions(+), 0 deletions(-) rename astroquery/{ => herschel}/higal/__init__.py (100%) rename astroquery/{ => herschel}/higal/core.py (100%) rename astroquery/{ => herschel}/higal/tests/__init__.py (100%) rename astroquery/{ => herschel}/higal/tests/data/frontpage.html (100%) rename astroquery/{ => herschel}/higal/tests/data/g49.html (100%) rename astroquery/{ => herschel}/higal/tests/setup_package.py (100%) rename astroquery/{ => herschel}/higal/tests/test_higal.py (100%) rename astroquery/{ => herschel}/higal/tests/test_higal_remote.py (100%) diff --git a/astroquery/higal/__init__.py b/astroquery/herschel/higal/__init__.py similarity index 100% rename from astroquery/higal/__init__.py rename to astroquery/herschel/higal/__init__.py diff --git a/astroquery/higal/core.py b/astroquery/herschel/higal/core.py similarity index 100% rename from astroquery/higal/core.py rename to astroquery/herschel/higal/core.py diff --git a/astroquery/higal/tests/__init__.py b/astroquery/herschel/higal/tests/__init__.py similarity index 100% rename from astroquery/higal/tests/__init__.py rename to astroquery/herschel/higal/tests/__init__.py diff --git a/astroquery/higal/tests/data/frontpage.html b/astroquery/herschel/higal/tests/data/frontpage.html similarity index 100% rename from astroquery/higal/tests/data/frontpage.html rename to astroquery/herschel/higal/tests/data/frontpage.html diff --git a/astroquery/higal/tests/data/g49.html b/astroquery/herschel/higal/tests/data/g49.html similarity index 100% rename from astroquery/higal/tests/data/g49.html rename to astroquery/herschel/higal/tests/data/g49.html diff --git a/astroquery/higal/tests/setup_package.py b/astroquery/herschel/higal/tests/setup_package.py similarity index 100% rename from astroquery/higal/tests/setup_package.py rename to astroquery/herschel/higal/tests/setup_package.py diff --git a/astroquery/higal/tests/test_higal.py b/astroquery/herschel/higal/tests/test_higal.py similarity index 100% rename from astroquery/higal/tests/test_higal.py rename to astroquery/herschel/higal/tests/test_higal.py diff --git a/astroquery/higal/tests/test_higal_remote.py b/astroquery/herschel/higal/tests/test_higal_remote.py similarity index 100% rename from astroquery/higal/tests/test_higal_remote.py rename to astroquery/herschel/higal/tests/test_higal_remote.py From bb7020779ad6b4b982c9bcc715b9d04244e3062a Mon Sep 17 00:00:00 2001 From: "Adam Ginsburg (keflavich)" Date: Sat, 8 May 2021 16:17:30 -0400 Subject: [PATCH 12/13] update relative paths --- astroquery/herschel/higal/core.py | 8 ++++---- astroquery/herschel/higal/tests/test_higal.py | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/astroquery/herschel/higal/core.py b/astroquery/herschel/higal/core.py index f9a571a347..1a81d2dbe5 100644 --- a/astroquery/herschel/higal/core.py +++ b/astroquery/herschel/higal/core.py @@ -11,10 +11,10 @@ from astropy.table import Table from astropy.io import fits -from ..query import BaseQuery, AstroQuery -from ..utils import commons -from ..utils import prepend_docstr_nosections -from ..utils import async_to_sync +from ...query import BaseQuery, AstroQuery +from ...utils import commons +from ...utils import prepend_docstr_nosections +from ...utils import async_to_sync from . import conf __all__ = ['HiGal', 'HiGalClass'] diff --git a/astroquery/herschel/higal/tests/test_higal.py b/astroquery/herschel/higal/tests/test_higal.py index 1be44a77d6..7d89cf4ff0 100644 --- a/astroquery/herschel/higal/tests/test_higal.py +++ b/astroquery/herschel/higal/tests/test_higal.py @@ -11,7 +11,7 @@ import astropy.coordinates as coord import astropy.units as u -from ...utils.testing_tools import MockResponse +from ....utils.testing_tools import MockResponse from ... import higal from ...higal import conf From 42580cba571e086a250cc82a2bc48ad8e5d9ceb3 Mon Sep 17 00:00:00 2001 From: "Adam Ginsburg (keflavich)" Date: Tue, 27 Feb 2024 17:03:31 -0500 Subject: [PATCH 13/13] whitespace --- astroquery/splatalogue/core.py | 1 + 1 file changed, 1 insertion(+) diff --git a/astroquery/splatalogue/core.py b/astroquery/splatalogue/core.py index 49273c2da2..8ed5a2f26f 100644 --- a/astroquery/splatalogue/core.py +++ b/astroquery/splatalogue/core.py @@ -281,6 +281,7 @@ def _parse_kwargs(self, *, min_frequency=None, max_frequency=None, """ + payload = {"searchSpecies": "", "speciesSelectBox": [], "dataVersion": "v3.0",