def search(self, template: str) -> Result:
"""Search the :class:`Element <Element>` for the given Parse template.
:param template: The Parse template to use.
"""
return parse_search(template, self.html)
def search(self, template: str) -> Result:
"""Search the :class:`Element <Element>` for the given Parse template.
:param template: The Parse template to use.
"""
return parse_search(template, self.html)
def search(self,
term,
db="pubmed",
field=None,
daterange=None,
dbtype=None):
set_klass = _get_recordset_constructor(db, dbtype)
infile = self.eutils.esearch(
term=term,
db=db,
field=field,
retstart=0,
retmax=0,
daterange=daterange,
usehistory=1,
webenv=self.webenv_ref[0],
)
searchinfo = parse.parse_search(infile, self.webenv_ref)
if searchinfo.query_key is not None:
cookie = HistoryCookie(db, self.webenv_ref, searchinfo.query_key)
else:
assert searchinfo.count == 0
cookie = HistoryCookie(db, None, None)
recordset = set_klass(self.eutils, cookie, 0, searchinfo.count,
searchinfo)
# won't have a query_key if the search turned up empty
if searchinfo.query_key is not None:
self._check_for_cache_reset(searchinfo.query_key)
self.query_history[searchinfo.query_key] = recordset
return recordset
def search(self, template):
"""Search the :class:`Element <Element>` for the given Parse template.
:param template: The Parse template to use.
"""
if not isinstance(template, str):
raise TypeError("Expected string, got %r" % type(template))
return parse_search(template, self.html)
def search(self,
term,
db = "pubmed",
field = None,
retstart = 0,
retmax = 20,
daterange = None,
dbtype = None,
):
"""do an Entrez search
The parameters are:
'term' -- the query string in the Entrez query language; see
http://www.ncbi.nlm.nih.gov/entrez/query/static/help/pmhelp.html
'db' -- the database to search
'field' -- the field to use for unqualified words
Eg, "dalke[au] AND gene" with field==None becomes
dalke[au] AND (genes[MeSH Terms] OR gene[Text Word]
and "dalke[au] AND gene" with field=="au" becomes
dalke[au] AND genes[Author]
(Yes, I think the first "au" should be "Author" too)
'retstart' -- include identifiers in the output, starting with
position 'retstart' (normally starts with 0)
'retmax' -- return at most 'retmax' identifiers in the output
(if not specified, NCBI returns 20 identifiers)
'daterange' -- a date restriction; either WithinNDays or DateRange
'dbtype' -- (optional) the database type (Config.PUBLICATION_TYPE
or SEQUENCE_TYPE). Overrides the type based on the 'db'
"""
set_klass = _get_recordset_constructor(db, dbtype)
infile = self.eutils.esearch(
term = term,
db = db,
field = field,
retstart = retstart,
retmax = retmax,
daterange = daterange)
searchinfo = parse.parse_search(infile, [None])
dbids = Datatypes.DBIds(db, searchinfo.ids)
return set_klass(self.eutils, dbids, searchinfo)
def search(
self,
term,
db="pubmed",
field=None,
retstart=0,
retmax=20,
daterange=None,
dbtype=None,
):
"""do an Entrez search
The parameters are:
'term' -- the query string in the Entrez query language; see
http://www.ncbi.nlm.nih.gov/entrez/query/static/help/pmhelp.html
'db' -- the database to search
'field' -- the field to use for unqualified words
Eg, "dalke[au] AND gene" with field==None becomes
dalke[au] AND (genes[MeSH Terms] OR gene[Text Word]
and "dalke[au] AND gene" with field=="au" becomes
dalke[au] AND genes[Author]
(Yes, I think the first "au" should be "Author" too)
'retstart' -- include identifiers in the output, starting with
position 'retstart' (normally starts with 0)
'retmax' -- return at most 'retmax' identifiers in the output
(if not specified, NCBI returns 20 identifiers)
'daterange' -- a date restriction; either WithinNDays or DateRange
'dbtype' -- (optional) the database type (Config.PUBLICATION_TYPE
or SEQUENCE_TYPE). Overrides the type based on the 'db'
"""
set_klass = _get_recordset_constructor(db, dbtype)
infile = self.eutils.esearch(term=term,
db=db,
field=field,
retstart=retstart,
retmax=retmax,
daterange=daterange)
searchinfo = parse.parse_search(infile, [None])
dbids = Datatypes.DBIds(db, searchinfo.ids)
return set_klass(self.eutils, dbids, searchinfo)
def search(self,
term,
db = "pubmed",
field = None,
daterange = None,
dbtype = None
):
set_klass = _get_recordset_constructor(db, dbtype)
infile = self.eutils.esearch(
term = term,
db = db,
field = field,
retstart = 0,
retmax = 0,
daterange = daterange,
usehistory = 1,
webenv = self.webenv_ref[0],
)
searchinfo = parse.parse_search(infile, self.webenv_ref)
if searchinfo.query_key is not None:
cookie = HistoryCookie(db, self.webenv_ref, searchinfo.query_key)
else:
assert searchinfo.count == 0
cookie = HistoryCookie(db, None, None)
recordset = set_klass(self.eutils, cookie, 0, searchinfo.count,
searchinfo)
# won't have a query_key if the search turned up empty
if searchinfo.query_key is not None:
self._check_for_cache_reset(searchinfo.query_key)
self.query_history[searchinfo.query_key] = recordset
return recordset
def search(self, template):
"""Searches the element for the given parse template."""
return parse_search(template, self.html)
def search(self, template):
"""Searches the :class:`Element <Element>` for the given parse template."""
return parse_search(template, self.html)
def parse(self, template: str):
return parse_search(template, self.html)[0]
def search(self, template: str) -> Result:
"""Searches the :class:`Element <Element>` for the given parse template."""
return parse_search(template, self.html)
