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Merge pull request #567 from msdemlei/speed-up-registry-doctest
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Speed up registry doctest
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@bsipocz
bsipocz authored Jul 2, 2024
2 parents ec1bc1a + 580d75c commit f2d6b7d
Showing 1 changed file with 47 additions and 44 deletions.
91 changes: 47 additions & 44 deletions docs/registry/index.rst
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Expand Up @@ -34,7 +34,9 @@ Basic interface


The main interface for the module is :py:meth:`pyvo.registry.search`;
the examples below assume::
the examples below assume:

.. doctest::

>>> from pyvo import registry

Expand Down Expand Up @@ -101,13 +103,15 @@ the keyword arguments; for instance:

.. doctest-remote-data::

>>> resources = registry.search(registry.Waveband("Radio", "Millimeter"))
>>> resources = registry.search(registry.Waveband("Radio", "Millimeter"),
... registry.Author("%Miller%"))

is equivalent to:

.. doctest-remote-data::

>>> resources = registry.search(waveband=["Radio", "Millimeter"])
>>> resources = registry.search(waveband=["Radio", "Millimeter"],
... author='%Miller%')

There is also :py:meth:`~pyvo.registry.get_RegTAP_query`, accepting the
same arguments as :py:meth:`pyvo.registry.search`. This function simply
Expand All @@ -127,7 +131,7 @@ you would say:
.. doctest-remote-data::

>>> resources = registry.search(registry.UCD("src.redshift"),
... registry.Freetext("supernova"))
... registry.Freetext("AGB"))

After that, ``resources`` is an instance of
:py:class:`~pyvo.registry.regtap.RegistryResults`, which you can iterate over. In
Expand All @@ -137,29 +141,30 @@ interactive data discovery, however, it is usually preferable to use the
.. doctest-remote-data::

>>> resources.to_table() # doctest: +IGNORE_OUTPUT
<Table length=158>
title ... interfaces
str67 ... str24
--------------------------------------------------------------- ... ------------------------
Asiago Supernova Catalogue (Barbon et al., 1999-) ... conesearch, tap#aux, web
Asiago Supernova Catalogue (Version 2008-Mar) ... conesearch, tap#aux, web
Sloan Digital Sky Survey-II Supernova Survey (Sako+, 2018) ... conesearch, tap#aux, web
<Table length=9>
ivoid ...
...
object ...
--------------------------------- ...
ivo://cds.vizier/j/a+a/392/1 ...
ivo://cds.vizier/j/a+a/566/a95 ...
ivo://cds.vizier/j/aj/151/146 ...
ivo://cds.vizier/j/apj/727/14 ...
...

And to look for tap resources *in* a specific cone, you would do

.. doctest-remote-data::

>>> from astropy.coordinates import SkyCoord
>>> registry.search(registry.Servicetype("tap"),
... registry.Spatial((SkyCoord("23d +3d"), 3), intersect="enclosed"),
... includeaux=True) # doctest: +IGNORE_OUTPUT
>>> registry.search(registry.Freetext("Wolf-Rayet"),
... registry.Spatial((SkyCoord("23d +3d"), 3), intersect="enclosed")) # doctest: +IGNORE_OUTPUT
<DALResultsTable length=1>
ivoid res_type short_name res_title ... intf_types intf_roles alt_identifier
...
object object object object ... object object object
------------------------------ ----------------- ------------- ------------------------------------------- ... ------------ ---------- --------------------------------
ivo://cds.vizier/j/apj/835/123 vs:catalogservice J/ApJ/835/123 Globular clusters in NGC 474 from CFHT obs. ... vs:paramhttp std doi:10.26093/cds/vizier.18350123
ivoid ...
...
object ...
---------------------------- ...
ivo://cds.vizier/j/aj/166/68 ...

Where ``intersect`` can take the following values:
* 'covers' is the default and returns resources that cover the geometry provided,
Expand Down Expand Up @@ -190,14 +195,14 @@ thus say:

.. doctest-remote-data::

>>> voresource = resources["II/283"]
>>> voresource.get_service(service_type="conesearch").search(pos=(120, 73), sr=1)
>>> voresource = resources["J/ApJ/727/14"]
>>> voresource.get_service(service_type="conesearch").search(pos=(257.41, 64.345), sr=0.01)
<DALResultsTable length=1>
_RAJ2000 _DEJ2000 _r recno ... NED RAJ2000 DEJ2000
deg deg ...
float64 float64 float64 int32 ... str3 str12 str12
------------ ------------ -------- ----- ... ---- ------------ ------------
117.98645833 73.00961111 0.588592 986 ... NED 07 51 56.750 +73 00 34.60
_r recno f_ID ID RAJ2000 ... SED DR7 Sloan Simbad
deg ...
float64 int32 str1 str18 float64 ... str3 str3 str5 str6
-------- ----- ---- ------------------ --------- ... ---- ---- ----- ------
0.000618 1 P 170938.52+642044.1 257.41049 ... SED DR7 Sloan Simbad

This method will raise an error if there is more than one service of the desired
type. If you know for sure that all declared conesearch will be the same, you can
Expand All @@ -216,8 +221,8 @@ constraint on the description ``get_service(service_type='conesearch', keyword='
>>> for interface in voresource.list_interfaces():
... print(interface)
Interface(type='tap#aux', description='', url='http://tapvizier.cds.unistra.fr/TAPVizieR/tap')
Interface(type='vr:webbrowser', description='', url='http://vizier.cds.unistra.fr/viz-bin/VizieR-2?-source=II/283')
Interface(type='conesearch', description='Cone search capability for table II/283/sncat (List of SNe arranged in chronological order)', url='http://vizier.cds.unistra.fr/viz-bin/conesearch/II/283/sncat?')
Interface(type='vr:webbrowser', description='', url='http://vizier.cds.unistra.fr/viz-bin/VizieR-2?-source=J/ApJ/727/14')
Interface(type='conesearch', description='Cone search capability for table J/ApJ/727/14/table2 (AKARI IRC 3-24{mu}m, and Spitzer MIPS 24/70{mu}m photometry of Abell 2255 member galaxies)', url='http://vizier.cds.unistra.fr/viz-bin/conesearch/J/ApJ/727/14/table2?')

Or construct the service object directly from the list of interfaces with:

Expand All @@ -241,27 +246,25 @@ attribute, but you can take a shortcut and call a RegistryResource's

.. doctest-remote-data::

>>> tables = resources["II/283"].get_tables() # doctest: +IGNORE_WARNINGS
>>> tables = resources["J/ApJ/727/14"].get_tables() # doctest: +IGNORE_WARNINGS
>>> list(tables.keys())
['II/283/sncat']
>>> sorted(c.name for c in tables['II/283/sncat'].columns)
['band', 'bmag', 'deg', 'dej2000', 'disc', 'epmax', 'galaxy', 'hrv', 'i', 'logd25', 'maxmag', 'mtype', 'n_bmag', 'n_sn', 'n_x', 'n_y', 'ned', 'pa', 'rag', 'raj2000', 'recno', 'simbad', 'sn', 't', 'type', 'u_epmax', 'u_maxmag', 'u_sn', 'u_y', 'u_z', 'x', 'y', 'z']
['J/ApJ/727/14/table2']
>>> sorted(c.name for c in tables["J/ApJ/727/14/table2"].columns)
['[24]', '[70]', 'dej2000', 'dr7', 'e_[24]', 'e_[70]', 'e_l15', 'e_l24', 'e_n3', 'e_n4', 'e_s11', 'e_s7', 'f_id', 'gmag', 'id', 'imag', 'l15', 'l24', 'n3', 'n4', 'raj2000', 'recno', 'rmag', 's11', 's7', 'sed', 'simbad', 'sloan', 'umag', 'y03', 'z', 'zmag']


In this case, this is a table with one of VizieR's somewhat funky names.
To run a TAP query based on this metadata, do something like:

.. doctest-remote-data::

>>> resources["II/283"].get_service(service_type="tap#aux").run_sync(
... 'SELECT sn, z FROM "J/A+A/437/789/table2" WHERE z>0.04')
<DALResultsTable length=4>
SN z
object float64
------ -------
1992bh 0.045
1992bp 0.079
1993ag 0.049
1993O 0.051
>>> resources["J/ApJ/727/14"].get_service(service_type="tap#aux").run_sync(
... 'SELECT id, z FROM "J/ApJ/727/14/table2" WHERE z>0.09 and umag<18')
<DALResultsTable length=1>
ID z
object float64
------------------ -------
171319.90+635428.0 0.09043

A special sort of access mode is ``web``, which represents some facility related
to the resource that works in a web browser. You can ask for a
Expand All @@ -271,7 +274,7 @@ with the query facility (this uses python's ``webbrowser`` module):

.. doctest-skip::

>>> resources["II/283"].get_service(service_type="web").search() # doctest: +IGNORE_OUTPUT
>>> resources["J/ApJ/727/14"].get_service(service_type="web").search() # doctest: +IGNORE_OUTPUT

Note that for interactive data discovery in the VO Registry, you may
also want to have a look at Aladin's discovery tree, TOPCAT's VO menu,
Expand Down Expand Up @@ -627,7 +630,7 @@ run all-VO queries without reading at least this sentence):
... # some service is broken; you *should* complain, but
... #print(" Broken: {} ({}). Complain to {}.\n".format(
... pass # svc_rec.ivoid, msg, svc_rec.get_contact()))
... if i == 5:
... if i == 2:
... break
>>> total_result = vstack(results) # doctest: +IGNORE_WARNINGS
>>> total_result # doctest: +IGNORE_OUTPUT
Expand Down

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