Source code for pyvo.dal.tap

# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
A module for accessing remote source and observation catalogs
"""


import requests
import astropy
import functools
from astropy.table import Column
from datetime import datetime
import time

from . import query
from .query import DALServiceError, DALQueryError
from ..tools import vosi, uws

__all__ = ["search", "escape",
    "TAPService", "TAPQuery", "AsyncTAPJob", "TAPResults"]

def _fix_upload(upload):
    if type(upload) is not tuple:
        upload = ('uri', upload)
    if type(upload[1]) == TAPResults:
        upload = ('uri', upload[1].result_uri)
    return upload

def _fileobj(s):
    if type(s) == astropy.table.table.Table:
        from io import StringIO
        f = StringIO()
        s.write(output = f, format = "votable")
        f.seek(0)
        return f
    try:
        s = open(s)
    finally:
        return s

[docs]def escape(term): """ escapes a term for use in ADQL """ return str(term).replace("'", "''")
[docs]class TAPResults(query.DALResults): @property def infos(self): """ return the info element as dictionary """ return getattr(self, "_infos", {}) @property def query_status(self): """ return the query status """ return getattr(self, "_infos", {}).get("QUERY_STATUS", None)
[docs]class TAPQuery(query.DALQuery): RESULTS_CLASS = TAPResults def __init__(self, baseurl, query, mode="sync", language="ADQL", maxrec=None, uploads = None): """ initialize the query object with the given parameters Parameters ---------- baseurl : str the TAP baseurl query : str the query string / parameters mode : str the query mode (sync | async). default "sync" language : str the query language. defaults to ADQL maxrec : int the amount of records to fetch uploads : dict Files to upload. Uses table name as key and file name as value """ super(TAPQuery, self).__init__(baseurl, "TAP", "1.0") self._query = query self._mode = mode if mode in ("sync", "async") else "sync" self._language = language self._uploads = uploads or {} self._uploads = {k: _fix_upload(v) for k, v in list(self._uploads.items())} self._maxrec = maxrec self["REQUEST"] = "doQuery" self["LANG"] = language if maxrec: self["MAXREC"] = maxrec if isinstance(query, dict): self.update(query) else: self["QUERY"] = query if self._uploads: upload_param = ';'.join( ['{0},{1}{2}'.format( k, 'param:' if v[0] == 'inline' else '', v[1] if v[0] == 'uri' else k ) for k, v in list(self._uploads.items())]) self["UPLOAD"] = upload_param
[docs] def getqueryurl(self): return '{0}/{1}'.format(self.baseurl, self._mode)
[docs] def execute_stream(self): """ submit the query and return the raw VOTable XML as a file stream Raises ------ DALServiceError for errors connecting to or communicating with the service DALQueryError for errors in the input query syntax """ if self._mode != "sync": raise DALServiceError( "Cannot execute a non-synchronous query. Use submit instead") url = self.getqueryurl() try: return self.submit().raw except requests.RequestException as ex: raise DALServiceError.from_except(ex, url, self.protocol, self.version)
[docs] def submit(self): """ does the actual request """ url = self.getqueryurl() files = {k: _fileobj(v[1]) for k, v in [x for x in list(self._uploads.items()) if x[1][0] == 'inline']} r = requests.post(url, data = self, stream = True, files = files) r.raise_for_status() # requests doesn't decode the content by default r.raw.read = functools.partial(r.raw.read, decode_content=True) return r
[docs]class TAPService(query.DALService): """ a representation of a Table Access Protocol service """ QUERY_CLASS = TAPQuery _availability = (None, None) _capabilities = None _tables = None def __init__(self, baseurl): """ instantiate a Tablee Access Protocol service Parameters ---------- baseurl : str the base URL that should be used for forming queries to the service. """ super(TAPService, self).__init__(baseurl, "TAP", "1.0") @property def availability(self): """ returns availability as a tuple in the following form: Returns ------- [0] : bool whether the service is available or not [1] : datetime the time since the server is running """ if self._availability == (None, None): r = requests.get( '{0}/availability'.format(self.baseurl), stream = True) # requests doesn't decode the content by default r.raw.read = functools.partial(r.raw.read, decode_content=True) self._availability = vosi.parse_availability(r.raw) return self._availability @property def available(self): """ True if the service is available, False otherwise """ return self.availability[0] @property def up_since(self): """ datetime the service was started """ return self.availability[1] @property def capabilities(self): """returns capabilities as a nested dictionary Known keys include: * outputs_formats * languages: { 'ADQL-2.0': { 'features': 'ivo://ivoa.net/std/TAPRegExt#features-adqlgeo': [], 'ivo://ivoa.net/std/TAPRegExt#features-udf': [], } """ if self._capabilities is None: r = requests.get( '{0}/capabilities'.format(self.baseurl), stream = True) # requests doesn't decode the content by default r.raw.read = functools.partial(r.raw.read, decode_content=True) self._capabilities = vosi.parse_capabilities(r.raw) return self._capabilities @property def tables(self): """ returns tables as a flat OrderedDict """ if self._tables is None: r = requests.get('{0}/tables'.format(self.baseurl), stream = True) # requests doesn't decode the content by default r.raw.read = functools.partial(r.raw.read, decode_content=True) self._tables = vosi.parse_tables(r.raw) return self._tables @property def maxrec(self): """ the default output limit. Raises ------ DALServiceError if the property is not exposed by the service """ try: for capa in self.capabilities: if "outputLimit" in capa: return capa["outputLimit"]["default"]["value"] except KeyError: pass raise DALServiceError("Default limit not exposed by the service") @property def hardlimit(self): """ the hard output limit. Raises ------ DALServiceError if the property is not exposed by the service """ try: for capa in self.capabilities: if "outputLimit" in capa: return capa["outputLimit"]["hard"]["value"] except KeyError: pass raise DALServiceError("Hard limit not exposed by the service") @property def upload_methods(self): """ a list of upload methods in form of IVOA identifiers """ _upload_methods = [] for capa in self.capabilities: if "uploadMethods" in capa: _upload_methods += capa["uploadMethods"] return _upload_methods
[docs] def run_sync(self, query, language="ADQL", maxrec=None, uploads=None): """ runs sync query and returns its result Parameters ---------- query : str The query language : str specifies the query language, default ADQL. useful for services which allow to use the backend query language. maxrec : int specifies the maximum records to return. defaults to the service default uploads : dict a mapping from table names to file like objects containing a votable Returns ------- TAPResults the query result See Also -------- TAPResults """ q = self.QUERY_CLASS( self.baseurl, query, language=language, maxrec=maxrec, uploads=uploads) return q.execute()
#alias for service discovery search = run_sync
[docs] def run_async(self, query, language="ADQL", maxrec=None, uploads=None): """ runs async query and returns its result Parameters ---------- query : str, dict the query string / parameters language : str specifies the query language, default ADQL. useful for services which allow to use the backend query language. maxrec : int specifies the maximum records to return. defaults to the service default uploads : dict a mapping from table names to file like objects containing a votable Returns ------- TAPResult the query instance Raises ------ DALServiceError for errors connecting to or communicating with the service DALQueryError for errors either in the input query syntax or other user errors detected by the service DALFormatError for errors parsing the VOTable response See Also -------- AsyncTAPJob """ job = AsyncTAPJob.create(self.baseurl, query, language, maxrec, uploads) job = job.run().wait() job.raise_if_error() result = job.fetch_result() return result
[docs] def submit_job(self, query, language="ADQL", maxrec=None, uploads=None): """ submit a async query without starting it and returns a AsyncTAPJob object Parameters ---------- query : str the query string / parameters language : str specifies the query language, default ADQL. useful for services which allow to use the backend query language. maxrec : int specifies the maximum records to return. defaults to the service default uploads : dict a mapping from table names to file like objects containing a votable Returns ------- AsyncTAPJob the query instance See Also -------- AsyncTAPJob """ return AsyncTAPJob.create(self.baseurl, query, language, maxrec, uploads)
[docs]class AsyncTAPJob(object): _job = {} @classmethod
[docs] def create(cls, baseurl, query, language="ADQL", maxrec = None, uploads = None): """ creates a async tap job on the server unter `baseurl` Parameters ---------- baseurl : str the TAP baseurl query : str the query string language : str specifies the query language, default ADQL. useful for services which allow to use the backend query language. maxrec : int specifies the maximum records to return. defaults to the service default uploads : dict a mapping from table names to file like objects containing a votable """ query = TAPService.QUERY_CLASS( baseurl, query, mode="async", language=language, maxrec=maxrec, uploads=uploads) response = query.submit() job = cls(response.url) return job
def __init__(self, url): """ initialize the job object with the given url and fetch the remote values Parameters ---------- url : str the job url """ self._url = url self._update() def _update(self): """ updates local job infos with remote values """ try: r = requests.get(self.url, stream = True) r.raise_for_status() except requests.exceptions.RequestException as ex: raise DALServiceError.from_except(ex, self.url, "TAP", "1.0") # requests doesn't decode the content by default r.raw.read = functools.partial(r.raw.read, decode_content=True) self._job.update(uws.parse_job(r.raw)) @property def job(self): """ all up-to-date uws job infos as dictionary """ #keep it up to date self._update() return self._job @property def url(self): """ the job url """ return self._url @property def jobId(self): """ the job id """ return self._job["jobId"] @property def phase(self): """ the current query phase """ self._update() return self._job["phase"] @property def execution_duration(self): """ maximum execution duration. read-write """ self._update() return self._job["executionDuration"] @execution_duration.setter def execution_duration(self, value): """ maximum execution duration. read-write Parameters ---------- value : int seconds after the query execution is aborted """ try: r = requests.post("{}/executionduration".format(self.url), data = {"EXECUTIONDURATION": str(value)}) r.raise_for_status() except requests.exceptions.RequestException as ex: raise DALServiceError.from_except(ex, self.url, "TAP", "1.0") self._job["executionDuration"] = value @property def destruction(self): """ datetime after which the job results are deleted automatically. read-write """ self._update() return self._job["destruction"] @destruction.setter def destruction(self, value): """ datetime after which the job results are deleted automatically. read-write Parameters ---------- value : datetime datetime after which the job results are deleted automatically """ try: #is string? easier to ask for forgiveness value = datetime.strptime(value, "%Y-%m-%dT%H:%M:%SZ") except: pass try: r = requests.post("{}/destruction".format(self.url), data = {"DESTRUCTION": value.strftime("%Y-%m-%dT%H:%M:%SZ")}) r.raise_for_status() except requests.exceptions.RequestException as ex: raise DALServiceError.from_except(ex, self.url, "TAP", "1.0") self._job["destruction"] = value @property def quote(self): """ estimated runtime """ self._update() return self._job["quote"] @property def owner(self): """ job owner (if applicable) """ self._update() return self._job["owner"] @property def result_uris(self): """ a list of the last result uri's """ self.raise_if_error() return self._job["results"] @property def result_uri(self): """ the first result uri """ try: return next(iter(list(self.result_uris.values()))) except StopIteration: return None
[docs] def run(self): """ starts the job / change phase to RUN """ try: r = requests.post('{}/phase'.format(self.url), data = {"PHASE": "RUN"}) r.raise_for_status() except requests.exceptions.RequestException as ex: raise DALServiceError.from_except(ex, self.url, "TAP", "1.0") return self
[docs] def abort(self): """ aborts the job / change phase to ABORT """ try: r = requests.post('{}/phase'.format(self.url), data = {"PHASE": "ABORT"}) r.raise_for_status() except requests.exceptions.RequestException as ex: raise DALServiceError.from_except(ex, self.url, self.protocol, self.version) return self
[docs] def wait( self, phases={"COMPLETED", "ABORTED", "ERROR"}, interval=1.0, increment=1.2, giveup_after=None, timeout=None): """ waits for the job to reach the given phases. Parameters ---------- phases : list phases to wait for interval : float poll interval in seconds. defaults to 1 increment : float poll interval increments. defaults to 1.2 giveup_after : int raise an :py:class`~pyvo.dal.query.DALServiceError` after n tries timeout : float raise an :py:class`~pyvo.dal.query.DALServiceError` after n seconds Raises ------ DALServiceError if the timeout is exceeded """ attempts = 0 start_time = time.time() while True: cur_phase = self.phase if cur_phase in phases: break time.sleep(interval) interval = min(120, interval * increment) attempts += 1 if any(( giveup_after and attempts > giveup_after, timeout and start_time + timeout < time.time() )): raise DALServiceError( "None of the states in {0} were reached in time.".format( repr(phases)), self.url, "TAP", "1.0") return self
[docs] def delete(self): """ deletes the job. this object will become invalid. """ try: r = requests.post(self.url, data = {"ACTION": "DELETE"}) r.raise_for_status() except requests.exceptions.RequestException as ex: raise DALServiceError.from_except(ex, self.url, "TAP", "1.0") self._url = None
[docs] def raise_if_error(self): """ raise a exception if theres an error Raises ------ DALQueryError if theres an error """ if self.phase in ["ERROR", "ABORTED"]: raise DALQueryError( self._job.get("message", "Query was aborted."), self.phase, self.url, "TAP", "1.0")
[docs] def fetch_result(self): """ returns the result votable if query is finished """ try: response = requests.get(self.result_uri, stream = True) response.raise_for_status() except IOError as ex: self._update() # we propably got a 404 because query error. raise with error msg self.raise_if_error() raise DALServiceError.from_except(ex, self.url, "TAP", "1.0") response.raw.read = functools.partial( response.raw.read, decode_content=True) return TAPResults( query._votableparse(response.raw.read), self.result_uri, "TAP", "1.0")