def assign_simple_handler(self, widget_name, model_attr, validator=None):
'''
Assign handlers to widgets to change fields in the model.
:param widget_name:
:param model_attr:
:param validator:
Note: Where widget is a gtk.ComboBox or gtk.ComboBoxEntry then
the value is assumed to be stored in model[row][0]
'''
widget = self.view.widgets[widget_name]
check(widget is not None, _('no widget with name %s') % widget_name)
class ProblemValidator(Validator):
def __init__(self, presenter, wrapped):
self.presenter = presenter
self.wrapped = wrapped
def to_python(self, value):
try:
value = self.wrapped.to_python(value)
self.presenter.remove_problem('BAD_VALUE_%s' \
% model_attr,widget)
except Exception, e:
self.presenter.add_problem('BAD_VALUE_%s' \
% model_attr, widget)
raise
return value
def invoke(self, search_strategy):
"""
update search_strategy object with statement results
Queries can use more database specific features. This also
means that the same query might not work the same on different
database types. For example, on a PostgreSQL database you can
use ilike but this would raise an error on SQLite.
"""
domain = self.domain
check(
domain in search_strategy._domains
or domain in search_strategy._shorthand,
'Unknown search domain: %s' % domain)
self.domain = search_strategy._shorthand.get(domain, domain)
self.domain = search_strategy._domains[domain][0]
self.search_strategy = search_strategy
result = set()
if search_strategy._session is not None:
self.domains = self.filter.needs_join(self)
self.session = search_strategy._session
records = self.filter.evaluate(self).all()
result.update(records)
return result
def range_builder(text):
"""Return a list of numbers from a string range of the form 1-3,4,5
"""
from pyparsing import Word, Group, Suppress, delimitedList, nums, \
ParseException, ParseResults
rng = Group(Word(nums) + Suppress('-') + Word(nums))
range_list = delimitedList(rng | Word(nums))
token = None
try:
tokens = range_list.parseString(text)
except (AttributeError, ParseException) as e:
return []
values = set()
for rng in tokens:
if isinstance(rng, ParseResults):
# get here if the token is a range
start = int(rng[0])
end = int(rng[1]) + 1
check(start<end, 'start must be less than end')
values.update(range(start, end))
else:
# get here if the token is an integer
values.add(int(rng))
return list(values)
def add_meta(self, domain, cls, properties):
"""Add a domain to the search space
an example of domain is a database table, where the properties would
be the table columns to consider in the search. continuing this
example, a record is be selected if any of the fields matches the
searched value.
:param domain: a string, list or tuple of domains that will resolve
a search string to cls. domain act as a shorthand to
the class name.
:param cls: the class the domain will resolve to
:param properties: a list of string names of the properties to
search by default
"""
logger.debug('%s.add_meta(%s, %s, %s)' %
(self, domain, cls, properties))
check(
isinstance(properties, list),
_('MapperSearch.add_meta(): '
'default_columns argument must be list'))
check(
len(properties) > 0,
_('MapperSearch.add_meta(): '
'default_columns argument cannot be empty'))
if isinstance(domain, (list, tuple)):
self._domains[domain[0]] = cls, properties
for d in domain[1:]:
self._shorthand[d] = domain[0]
else:
self._domains[domain] = cls, properties
self._properties[cls] = properties
def invoke(self, search_strategy):
"""
update search_strategy object with statement results
Queries can use more database specific features. This also
means that the same query might not work the same on different
database types. For example, on a PostgreSQL database you can
use ilike but this would raise an error on SQLite.
"""
domain = self.domain
check(domain in search_strategy._domains or
domain in search_strategy._shorthand,
'Unknown search domain: %s' % domain)
self.domain = search_strategy._shorthand.get(domain, domain)
self.domain = search_strategy._domains[domain][0]
self.search_strategy = search_strategy
result = set()
if search_strategy._session is not None:
self.domains = self.filter.needs_join(self)
self.session = search_strategy._session
records = self.filter.evaluate(self).all()
result.update(records)
return result
def add_meta(self, domain, cls, properties):
"""
Adds search meta to the domain
:param domain: a string, list or tuple of domains that will resolve
to cls a search string, domain act as a shorthand to the class name
:param cls: the class the domain will resolve to
:param properties: a list of string names of the properties to
search by default
"""
check(
isinstance(properties, list),
_('MapperSearch.add_meta(): '
'default_columns argument must be list'))
check(
len(properties) > 0,
_('MapperSearch.add_meta(): '
'default_columns argument cannot be empty'))
if isinstance(domain, (list, tuple)):
# domain[0] is the result key
self._result_keys[cls] = domain[0]
self._domains[domain[0]] = cls, properties
for d in domain[1:]:
self._shorthand[d] = domain[0]
else:
self._result_keys[cls] = domain
self._domains[d] = cls, properties
self._properties[cls] = properties
def add_meta(self, domain, cls, properties):
"""Add a domain to the search space
an example of domain is a database table, where the properties would
be the table columns to consider in the search. continuing this
example, a record is be selected if any of the fields matches the
searched value.
:param domain: a string, list or tuple of domains that will resolve
a search string to cls. domain act as a shorthand to
the class name.
:param cls: the class the domain will resolve to
:param properties: a list of string names of the properties to
search by default
"""
logger.debug('%s.add_meta(%s, %s, %s)' %
(self, domain, cls, properties))
check(isinstance(properties, list),
_('MapperSearch.add_meta(): '
'default_columns argument must be list'))
check(len(properties) > 0,
_('MapperSearch.add_meta(): '
'default_columns argument cannot be empty'))
if isinstance(domain, (list, tuple)):
self._domains[domain[0]] = cls, properties
for d in domain[1:]:
self._shorthand[d] = domain[0]
else:
self._domains[domain] = cls, properties
self._properties[cls] = properties
def make_label_clickable(label, on_clicked, *args):
"""
:param label: a gtk.Label that has a gtk.EventBox as its parent
:param on_clicked: callback to be called when the label is clicked
on_clicked(label, event, data)
"""
eventbox = label.parent
check(eventbox is not None, 'label must have a parent')
check(isinstance(eventbox, gtk.EventBox),
'label must have an gtk.EventBox as its parent')
label.__pressed = False
def on_enter_notify(*args):
label.modify_fg(gtk.STATE_NORMAL, gtk.gdk.color_parse("blue"))
def on_leave_notify(*args):
label.modify_fg(gtk.STATE_NORMAL, None)
label.__pressed = False
def on_press(*args):
label.__pressed = True
def on_release(widget, event, *args):
if label.__pressed:
label.__pressed = False
label.modify_fg(gtk.STATE_NORMAL, None)
on_clicked(label, event, *args)
eventbox.connect('enter_notify_event', on_enter_notify)
eventbox.connect('leave_notify_event', on_leave_notify)
eventbox.connect('button_press_event', on_press)
eventbox.connect('button_release_event', on_release, *args)
def make_label_clickable(label, on_clicked, *args):
"""
:param label: a gtk.Label that has a gtk.EventBox as its parent
:param on_clicked: callback to be called when the label is clicked
on_clicked(label, event, data)
"""
eventbox = label.parent
check(eventbox is not None, 'label must have a parent')
check(isinstance(eventbox, gtk.EventBox),
'label must have an gtk.EventBox as its parent')
label.__pressed = False
def on_enter_notify(*args):
label.modify_fg(gtk.STATE_NORMAL, gtk.gdk.color_parse("blue"))
def on_leave_notify(*args):
label.modify_fg(gtk.STATE_NORMAL, None)
label.__pressed = False
def on_press(*args):
label.__pressed = True
def on_release(widget, event, *args):
if label.__pressed:
label.__pressed = False
label.modify_fg(gtk.STATE_NORMAL, None)
on_clicked(label, event, *args)
eventbox.connect('enter_notify_event', on_enter_notify)
eventbox.connect('leave_notify_event', on_leave_notify)
eventbox.connect('button_press_event', on_press)
eventbox.connect('button_release_event', on_release, *args)
def append_children(self, model, parent, kids):
"""
append object to a parent iter in the model
:param model: the model the append to
:param parent: the parent gtk.TreeIter
:param kids: a list of kids to append
@return: the model with the kids appended
"""
check(parent is not None, "append_children(): need a parent")
for k in kids:
i = model.append(parent, [k])
if self.view_meta[type(k)].children is not None:
model.append(i, ["_dummy"])
return model
def append_children(self, model, parent, kids):
"""
append object to a parent iter in the model
:param model: the model the append to
:param parent: the parent gtk.TreeIter
:param kids: a list of kids to append
@return: the model with the kids appended
"""
check(parent is not None, "append_children(): need a parent")
for k in kids:
i = model.append(parent, [k])
if self.view_meta[type(k)].children is not None:
model.append(i, ["_dummy"])
return model
def set_active_connection_by_name(self, name):
"""
sets the name of the connection in the name combo, this
causes on_changed_name_combo to be fired which changes the param
box type and set the connection parameters
"""
check(hasattr(self, "name_combo"))
i = 0
active = 0
conn_list = prefs.prefs[bauble.conn_list_pref]
if conn_list is None:
return
for conn in conn_list:
self.name_combo.insert_text(i, conn)
if conn == name:
active = i
i += 1
self.name_combo.set_active(active)
def set_active_connection_by_name(self, name):
"""
sets the name of the connection in the name combo, this
causes on_changed_name_combo to be fired which changes the param
box type and set the connection parameters
"""
check(hasattr(self, "name_combo"))
i = 0
active = 0
conn_list = prefs.prefs[bauble.conn_list_pref]
if conn_list is None:
return
for conn in conn_list:
self.name_combo.insert_text(i, conn)
if conn == name:
active = i
i += 1
self.name_combo.set_active(active)
def make_label_clickable(label, on_clicked, *args):
"""
:param label: a gtk.Label that has a gtk.EventBox as its parent
:param on_clicked: callback to be called when the label is clicked
on_clicked(label, event, data)
"""
eventbox = label.parent
check(eventbox is not None, 'label must have a parent')
check(isinstance(eventbox, gtk.EventBox),
'label must have an gtk.EventBox as its parent')
label.__pressed = False
def on_enter_notify(widget, *args):
widget.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse("#faf8f7"))
label.modify_fg(gtk.STATE_NORMAL, gtk.gdk.color_parse("blue"))
def on_leave_notify(widget, *args):
widget.modify_bg(gtk.STATE_NORMAL, None)
label.modify_fg(gtk.STATE_NORMAL, None)
label.__pressed = False
def on_press(*args):
label.__pressed = True
def on_release(widget, event, *args):
if label.__pressed:
label.__pressed = False
label.modify_fg(gtk.STATE_NORMAL, None)
on_clicked(label, event, *args)
try:
eventbox.disconnect(label.__on_event)
logger.debug('disconnected previous release-event handler')
label.__on_event = eventbox.connect(
'button_release_event', on_release, *args)
except AttributeError:
logger.debug('defining handlers')
label.__on_event = eventbox.connect(
'button_release_event', on_release, *args)
eventbox.connect('enter_notify_event', on_enter_notify)
eventbox.connect('leave_notify_event', on_leave_notify)
eventbox.connect('button_press_event', on_press)
def make_label_clickable(label, on_clicked, *args):
"""
:param label: a gtk.Label that has a gtk.EventBox as its parent
:param on_clicked: callback to be called when the label is clicked
on_clicked(label, event, data)
"""
eventbox = label.parent
check(eventbox is not None, 'label must have a parent')
check(isinstance(eventbox, gtk.EventBox),
'label must have an gtk.EventBox as its parent')
label.__pressed = False
def on_enter_notify(widget, *args):
widget.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse("#faf8f7"))
label.modify_fg(gtk.STATE_NORMAL, gtk.gdk.color_parse("blue"))
def on_leave_notify(widget, *args):
widget.modify_bg(gtk.STATE_NORMAL, None)
label.modify_fg(gtk.STATE_NORMAL, None)
label.__pressed = False
def on_press(*args):
label.__pressed = True
def on_release(widget, event, *args):
if label.__pressed:
label.__pressed = False
label.modify_fg(gtk.STATE_NORMAL, None)
on_clicked(label, event, *args)
try:
eventbox.disconnect(label.__on_event)
logger.debug('disconnected previous release-event handler')
label.__on_event = eventbox.connect(
'button_release_event', on_release, *args)
except AttributeError:
logger.debug('defining handlers')
label.__on_event = eventbox.connect(
'button_release_event', on_release, *args)
eventbox.connect('enter_notify_event', on_enter_notify)
eventbox.connect('leave_notify_event', on_leave_notify)
eventbox.connect('button_press_event', on_press)
def add_meta(self, domain, cls, properties):
"""
Adds search meta to the domain
:param domain: a string, list or tuple of domains that will resolve
to cls a search string, domain act as a shorthand to the class name
:param cls: the class the domain will resolve to
:param properties: a list of string names of the properties to
search by default
"""
check(isinstance(properties, list), _('MapperSearch.add_meta(): '\
'default_columns argument must be list'))
check(len(properties) > 0, _('MapperSearch.add_meta(): '\
'default_columns argument cannot be empty'))
if isinstance(domain, (list, tuple)):
self._domains[domain[0]] = cls, properties
for d in domain[1:]:
self._shorthand[d] = domain[0]
else:
self._domains[d] = cls, properties
self._properties[cls] = properties
def select_in_search_results(obj):
"""
:param obj: the object the select
@returns: a gtk.TreeIter to the selected row
Search the tree model for obj if it exists then select it if not
then add it and select it.
The the obj is not in the model then we add it.
"""
check(obj is not None, 'select_in_search_results: arg is None')
view = bauble.gui.get_view()
if not isinstance(view, SearchView):
return None
model = view.results_view.get_model()
found = utils.search_tree_model(model, obj)
row_iter = None
if len(found) > 0:
row_iter = found[0]
else:
row_iter = model.append(None, [obj])
model.append(row_iter, ['-'])
view.results_view.set_cursor(model.get_path(row_iter))
return row_iter
def select_in_search_results(obj):
"""
:param obj: the object the select
@returns: a gtk.TreeIter to the selected row
Search the tree model for obj if it exists then select it if not
then add it and select it.
The the obj is not in the model then we add it.
"""
check(obj is not None, 'select_in_search_results: arg is None')
view = bauble.gui.get_view()
if not isinstance(view, SearchView):
return None
model = view.results_view.get_model()
found = utils.search_tree_model(model, obj)
row_iter = None
if len(found) > 0:
row_iter = found[0]
else:
row_iter = model.append(None, [obj])
model.append(row_iter, ['-'])
view.results_view.set_cursor(model.get_path(row_iter))
return row_iter
rng = Group(Word(nums) + Suppress("-") + Word(nums))
range_list = delimitedList(rng | Word(nums))
token = None
try:
tokens = range_list.parseString(text)
except (AttributeError, ParseException), e:
logger.debug(e)
return []
values = set()
for rng in tokens:
if isinstance(rng, ParseResults):
# get here if the token is a range
start = int(rng[0])
end = int(rng[1]) + 1
check(start < end, "start must be less than end")
values.update(range(start, end))
else:
# get here if the token is an integer
values.add(int(rng))
return list(values)
def gc_objects_by_type(tipe):
"""
Return a list of objects from the garbage collector by type.
"""
import inspect
import gc
if isinstance(tipe, basestring):
def set_privilege(role, privilege):
"""Set the role's privileges.
Arguments:
- `role`:
- `privilege`:
"""
check(privilege in ('read', 'write', 'admin', None),
'invalid privilege: %s' % privilege)
conn = db.engine.connect()
trans = conn.begin()
if privilege:
privs = _privileges[privilege]
try:
# revoke everything first
for table in db.metadata.sorted_tables:
stmt = 'revoke all on table %s from %s;' % (table.name, role)
conn.execute(stmt)
for col in table.c:
if hasattr(col, 'sequence'):
stmt = 'revoke all on sequence %s from %s' % \
(col.sequence.name, role)
conn.execute(stmt)
stmt = 'revoke all on database %s from %s' \
% (bauble.db.engine.url.database, role)
conn.execute(stmt)
stmt = 'alter role %s with nocreaterole' % role
conn.execute(stmt)
# privilege is None so all permissions are revoked
if not privilege:
trans.commit()
conn.close()
return
# change privileges on the database
if privilege == 'admin':
stmt = 'grant all on database %s to %s' % \
(bauble.db.engine.url.database, role)
if privilege == 'admin':
stmt += ' with grant option'
conn.execute(stmt)
stmt = 'alter role %s with createuser' % role
conn.execute(stmt)
# grant privileges on the tables and sequences
for table in bauble.db.metadata.sorted_tables:
tbl_privs = filter(lambda x: x.lower() in _table_privs, privs)
for priv in tbl_privs:
stmt = 'grant %s on %s to %s' % (priv, table.name, role)
if privilege == 'admin':
stmt += ' with grant option'
#debug(stmt)
conn.execute(stmt)
for col in table.c:
seq_privs = filter(lambda x: x.lower() in __sequence_privs,
privs)
for priv in seq_privs:
if hasattr(col, 'sequence'):
stmt = 'grant %s on sequence %s to %s' % \
(priv, col.sequence.name, role)
#debug(stmt)
if privilege == 'admin':
stmt += ' with grant option'
conn.execute(stmt)
except Exception, e:
error('users.set_privilege(): %s' % utils.utf8(e))
trans.rollback()
raise
rng = Group(Word(nums) + Suppress('-') + Word(nums))
range_list = delimitedList(rng | Word(nums))
token = None
try:
tokens = range_list.parseString(text)
except (AttributeError, ParseException), e:
logger.debug(e)
return []
values = set()
for rng in tokens:
if isinstance(rng, ParseResults):
# get here if the token is a range
start = int(rng[0])
end = int(rng[1]) + 1
check(start < end, 'start must be less than end')
values.update(range(start, end))
else:
# get here if the token is an integer
values.add(int(rng))
return list(values)
def gc_objects_by_type(tipe):
"""
Return a list of objects from the garbage collector by type.
"""
import inspect
import gc
if isinstance(tipe, basestring):
return [o for o in gc.get_objects() if type(o).__name__ == tipe]
def on_query(self, s, loc, tokens):
"""
Called when the parser hits a query token.
Queries can use more database specific features. This also
means that the same query might not work the same on different
database types. For example, on a PostgreSQL database you can
use ilike but this would raise an error on SQLite.
"""
# The method requires that the underlying database support
# union and intersect. At the time of writing this MySQL
# didn't.
# TODO: support 'not' a boolean op as well, e.g sp where
# genus.genus=Maxillaria and not genus.family=Orchidaceae
domain, expr = tokens
check(domain in self._domains or domain in self._shorthand,
'Unknown search domain: %s' % domain)
if domain in self._shorthand:
domain = self._shorthand[domain]
cls = self._domains[domain][0]
main_query = self._session.query(cls)
mapper = class_mapper(cls)
expr_iter = iter(expr)
boolop = None
for e in expr_iter:
idents, cond, val = e
# debug('cls: %s, idents: %s, cond: %s, val: %s'
# % (cls.__name__, idents, cond, val))
if val == 'None':
val = None
if cond == 'is':
cond = '='
elif cond == 'is not':
cond = '!='
elif cond in ('ilike', 'icontains', 'ihas'):
cond = lambda col: \
lambda val: utils.ilike(col, '%s' % val)
if len(idents) == 1:
# we get here when the idents only refer to a property
# on the mapper table..i.e. a column
col = idents[0]
msg = _('The %(tablename)s table does not have a '\
'column named "%(columname)s"') % \
dict(tablename=mapper.local_table.name,
columname=col)
check(col in mapper.c, msg)
if isinstance(cond, str):
clause = getattr(cls, col).op(cond)(utils.utf8(val))
else:
clause = cond(getattr(cls, col))(utils.utf8(val))
query = self._session.query(cls).filter(clause).order_by(None)
else:
# we get here when the idents refer to a relation on a
# mapper/table
relations = idents[:-1]
col = idents[-1]
query = self._session.query(cls)
query = query.join(*relations)
# NOTE: SA07 - this depends on Query._joinpoint not changing,
# it changed in SA05 which broke this
local_table = query._joinpoint['prev'][0][1].local_table
if isinstance(cond, str):
clause = local_table.c[col].op(cond)(utils.utf8(val))
else:
clause = cond(local_table.c[col])(utils.utf8(val))
query = query.filter(clause).order_by(None)
if boolop == 'or':
main_query = main_query.union(query)
elif boolop == 'and':
main_query = main_query.intersect(query)
else:
main_query = query
try:
boolop = expr_iter.next()
except StopIteration:
pass
self._results.update(main_query.order_by(None).all())
def create_abcd(decorated_objects, authors=True, validate=True):
"""
:param objects: a list/tuple of objects that implement the ABCDDecorator
interface
:param authors: flag to control whether to include the authors in the
species name
:param validate: whether we should validate the data before returning
:returns: a valid ABCD ElementTree
"""
import bauble.plugins.garden.institution as institution
inst = institution.Institution()
if not verify_institution(inst):
msg = _('Some or all of the information about your institution or ' \
'business is not complete. Please make sure that the ' \
'Name, Technical Contact, Email, Contact and Institution '
'Code fields are filled in.')
utils.message_dialog(msg)
institution.InstitutionEditor().start()
return create_abcd(decorated_objects, authors, validate)
datasets = DataSets()
ds = ABCDElement(datasets, 'DataSet')
tech_contacts = ABCDElement(ds, 'TechnicalContacts')
tech_contact = ABCDElement(tech_contacts, 'TechnicalContact')
# TODO: need to include contact information in bauble meta when
# creating a new database
ABCDElement(tech_contact, 'Name', text=inst.inst_technical_contact)
ABCDElement(tech_contact, 'Email', text=inst.inst_email)
cont_contacts = ABCDElement(ds, 'ContentContacts')
cont_contact = ABCDElement(cont_contacts, 'ContentContact')
ABCDElement(cont_contact, 'Name', text=inst.inst_contact)
ABCDElement(cont_contact, 'Email', text=inst.inst_email)
metadata = ABCDElement(
ds,
'Metadata',
)
description = ABCDElement(metadata, 'Description')
# TODO: need to get the localized language
representation = ABCDElement(description,
'Representation',
attrib={'language': 'en'})
revision = ABCDElement(metadata, 'RevisionData')
ABCDElement(revision, 'DateModified', text='2001-03-01T00:00:00')
title = ABCDElement(representation, 'Title', text='TheTitle')
units = ABCDElement(ds, 'Units')
# build the ABCD unit
for obj in decorated_objects:
unit = ABCDElement(units, 'Unit')
ABCDElement(unit, 'SourceInstitutionID', text=inst.inst_code)
# TODO: don't really understand the SourceID element
ABCDElement(unit, 'SourceID', text='Bauble')
unit_id = ABCDElement(unit, 'UnitID', text=obj.get_UnitID())
ABCDElement(unit, 'DateLastEdited', text=obj.get_DateLastEdited())
# TODO: add list of verifications to Identifications
# scientific name identification
identifications = ABCDElement(unit, 'Identifications')
identification = ABCDElement(identifications, 'Identification')
result = ABCDElement(identification, 'Result')
taxon_identified = ABCDElement(result, 'TaxonIdentified')
higher_taxa = ABCDElement(taxon_identified, 'HigherTaxa')
higher_taxon = ABCDElement(higher_taxa, 'HigherTaxon')
# TODO: ABCDDecorator should provide an iterator so that we can
# have multiple HigherTaxonName's
higher_taxon_name = ABCDElement(higher_taxon,
'HigherTaxonName',
text=obj.get_family())
higher_taxon_rank = ABCDElement(higher_taxon,
'HigherTaxonRank',
text='familia')
scientific_name = ABCDElement(taxon_identified, 'ScientificName')
ABCDElement(scientific_name,
'FullScientificNameString',
text=obj.get_FullScientificNameString(authors))
name_atomised = ABCDElement(scientific_name, 'NameAtomised')
botanical = ABCDElement(name_atomised, 'Botanical')
ABCDElement(botanical,
'GenusOrMonomial',
text=obj.get_GenusOrMonomial())
ABCDElement(botanical, 'FirstEpithet', text=obj.get_FirstEpithet())
author_team = obj.get_AuthorTeam()
if author_team is not None:
ABCDElement(botanical, 'AuthorTeam', text=author_team)
ABCDElement(identification, 'PreferredFlag', text='true')
# vernacular name identification
# TODO: should we include all the vernacular names or only the default
# one
vernacular_name = obj.get_InformalNameString()
if vernacular_name is not None:
identification = ABCDElement(identifications, 'Identification')
result = ABCDElement(identification, 'Result')
taxon_identified = ABCDElement(result, 'TaxonIdentified')
ABCDElement(taxon_identified,
'InformalNameString',
text=vernacular_name)
# add all the extra non standard elements
obj.extra_elements(unit)
# TODO: handle verifiers/identifiers
# TODO: RecordBasis
# notes are last in the schema and extra_elements() shouldn't
# add anything that comes past Notes, e.g. RecordURI,
# EAnnotations, UnitExtension
notes = obj.get_Notes()
if notes:
ABCDElement(unit, 'Notes', text=notes)
if validate:
check(validate_xml(datasets), 'ABCD data not valid')
return ElementTree(datasets)
def create_abcd(decorated_objects, authors=True, validate=True):
"""
:param objects: a list/tuple of objects that implement the ABCDDecorator
interface
:param authors: flag to control whether to include the authors in the
species name
:param validate: whether we should validate the data before returning
:returns: a valid ABCD ElementTree
"""
import bauble.plugins.garden.institution as institution
inst = institution.Institution()
if not verify_institution(inst):
msg = _('Some or all of the information about your institution or ' \
'business is not complete. Please make sure that the ' \
'Name, Technical Contact, Email, Contact and Institution '
'Code fields are filled in.')
utils.message_dialog(msg)
institution.InstitutionEditor().start()
return create_abcd(decorated_objects, authors, validate)
datasets = DataSets()
ds = ABCDElement(datasets, 'DataSet')
tech_contacts = ABCDElement(ds, 'TechnicalContacts')
tech_contact = ABCDElement(tech_contacts, 'TechnicalContact')
# TODO: need to include contact information in bauble meta when
# creating a new database
ABCDElement(tech_contact, 'Name', text=inst.inst_technical_contact)
ABCDElement(tech_contact, 'Email', text=inst.inst_email)
cont_contacts = ABCDElement(ds, 'ContentContacts')
cont_contact = ABCDElement(cont_contacts, 'ContentContact')
ABCDElement(cont_contact, 'Name', text=inst.inst_contact)
ABCDElement(cont_contact, 'Email', text=inst.inst_email)
metadata = ABCDElement(ds, 'Metadata', )
description = ABCDElement(metadata, 'Description')
# TODO: need to get the localized language
representation = ABCDElement(description, 'Representation',
attrib={'language': 'en'})
revision = ABCDElement(metadata, 'RevisionData')
ABCDElement(revision, 'DateModified', text='2001-03-01T00:00:00')
title = ABCDElement(representation, 'Title', text='TheTitle')
units = ABCDElement(ds, 'Units')
# build the ABCD unit
for obj in decorated_objects:
unit = ABCDElement(units, 'Unit')
ABCDElement(unit, 'SourceInstitutionID', text=inst.inst_code)
# TODO: don't really understand the SourceID element
ABCDElement(unit, 'SourceID', text='Bauble')
unit_id = ABCDElement(unit, 'UnitID', text=obj.get_UnitID())
ABCDElement(unit, 'DateLastEdited', text=obj.get_DateLastEdited())
# TODO: add list of verifications to Identifications
# scientific name identification
identifications = ABCDElement(unit, 'Identifications')
identification = ABCDElement(identifications, 'Identification')
result = ABCDElement(identification, 'Result')
taxon_identified = ABCDElement(result, 'TaxonIdentified')
higher_taxa = ABCDElement(taxon_identified, 'HigherTaxa')
higher_taxon = ABCDElement(higher_taxa, 'HigherTaxon')
# TODO: ABCDDecorator should provide an iterator so that we can
# have multiple HigherTaxonName's
higher_taxon_name = ABCDElement(higher_taxon, 'HigherTaxonName',
text=obj.get_family())
higher_taxon_rank = ABCDElement(higher_taxon, 'HigherTaxonRank',
text='familia')
scientific_name = ABCDElement(taxon_identified, 'ScientificName')
ABCDElement(scientific_name, 'FullScientificNameString',
text=obj.get_FullScientificNameString(authors))
name_atomised = ABCDElement(scientific_name, 'NameAtomised')
botanical = ABCDElement(name_atomised, 'Botanical')
ABCDElement(botanical, 'GenusOrMonomial',
text=obj.get_GenusOrMonomial())
ABCDElement(botanical, 'FirstEpithet', text=obj.get_FirstEpithet())
author_team = obj.get_AuthorTeam()
if author_team is not None:
ABCDElement(botanical, 'AuthorTeam', text=author_team)
ABCDElement(identification, 'PreferredFlag', text='true')
# vernacular name identification
# TODO: should we include all the vernacular names or only the default
# one
vernacular_name = obj.get_InformalNameString()
if vernacular_name is not None:
identification = ABCDElement(identifications, 'Identification')
result = ABCDElement(identification, 'Result')
taxon_identified = ABCDElement(result, 'TaxonIdentified')
ABCDElement(taxon_identified, 'InformalNameString',
text=vernacular_name)
# add all the extra non standard elements
obj.extra_elements(unit)
# TODO: handle verifiers/identifiers
# TODO: RecordBasis
# notes are last in the schema and extra_elements() shouldn't
# add anything that comes past Notes, e.g. RecordURI,
# EAnnotations, UnitExtension
notes = obj.get_Notes()
if notes:
ABCDElement(unit, 'Notes', text=notes)
if validate:
check(validate_xml(datasets), 'ABCD data not valid')
return ElementTree(datasets)
def set_privilege(role, privilege):
"""Set the role's privileges.
Arguments:
- `role`:
- `privilege`:
"""
check(privilege in ("read", "write", "admin", None), "invalid privilege: %s" % privilege)
conn = db.engine.connect()
trans = conn.begin()
if privilege:
privs = _privileges[privilege]
try:
# revoke everything first
for table in db.metadata.sorted_tables:
stmt = "revoke all on table %s from %s;" % (table.name, role)
conn.execute(stmt)
for col in table.c:
if hasattr(col, "sequence"):
stmt = "revoke all on sequence %s from %s" % (col.sequence.name, role)
conn.execute(stmt)
stmt = "revoke all on database %s from %s" % (bauble.db.engine.url.database, role)
conn.execute(stmt)
stmt = "alter role %s with nocreaterole" % role
conn.execute(stmt)
# privilege is None so all permissions are revoked
if not privilege:
trans.commit()
conn.close()
return
# change privileges on the database
if privilege == "admin":
stmt = "grant all on database %s to %s" % (bauble.db.engine.url.database, role)
if privilege == "admin":
stmt += " with grant option"
conn.execute(stmt)
stmt = "alter role %s with createuser" % role
conn.execute(stmt)
# grant privileges on the tables and sequences
for table in bauble.db.metadata.sorted_tables:
tbl_privs = filter(lambda x: x.lower() in _table_privs, privs)
for priv in tbl_privs:
stmt = "grant %s on %s to %s" % (priv, table.name, role)
if privilege == "admin":
stmt += " with grant option"
# debug(stmt)
conn.execute(stmt)
for col in table.c:
seq_privs = filter(lambda x: x.lower() in __sequence_privs, privs)
for priv in seq_privs:
if hasattr(col, "sequence"):
stmt = "grant %s on sequence %s to %s" % (priv, col.sequence.name, role)
# debug(stmt)
if privilege == "admin":
stmt += " with grant option"
conn.execute(stmt)
except Exception, e:
error("users.set_privilege(): %s" % utils.utf8(e))
trans.rollback()
raise
rng = Group(Word(nums) + Suppress('-') + Word(nums))
range_list = delimitedList(rng | Word(nums))
token = None
try:
tokens = range_list.parseString(text)
except (AttributeError, ParseException), e:
logger.debug(e)
return []
values = set()
for rng in tokens:
if isinstance(rng, ParseResults):
# get here if the token is a range
start = int(rng[0])
end = int(rng[1]) + 1
check(start < end, 'start must be less than end')
values.update(range(start, end))
else:
# get here if the token is an integer
values.add(int(rng))
return list(values)
def gc_objects_by_type(tipe):
"""
Return a list of objects from the garbage collector by type.
"""
import inspect
import gc
if isinstance(tipe, basestring):
return [o for o in gc.get_objects() if type(o).__name__ == tipe]
def on_query(self, s, loc, tokens):
"""
Called when the parser hits a query token.
Queries can use more database specific features. This also
means that the same query might not work the same on different
database types. For example, on a PostgreSQL database you can
use ilike but this would raise an error on SQLite.
"""
# The method requires that the underlying database support
# union and intersect. At the time of writing this MySQL
# didn't.
# TODO: support 'not' a boolean op as well, e.g sp where
# genus.genus=Maxillaria and not genus.family=Orchidaceae
domain, expr = tokens
check(domain in self._domains or domain in self._shorthand,
'Unknown search domain: %s' % domain)
if domain in self._shorthand:
domain = self._shorthand[domain]
cls = self._domains[domain][0]
main_query = self._session.query(cls)
mapper = class_mapper(cls)
expr_iter = iter(expr)
boolop = None
for e in expr_iter:
idents, cond, val = e
# debug('cls: %s, idents: %s, cond: %s, val: %s'
# % (cls.__name__, idents, cond, val))
if val == 'None':
val = None
if cond == 'is':
cond = '='
elif cond == 'is not':
cond = '!='
elif cond in ('ilike', 'icontains', 'ihas'):
return col.op.ilike(val)
# cond = lambda col: \
# lambda val: utils.ilike(col, '%s' % val)
if len(idents) == 1:
# we get here when the idents only refer to a property
# on the mapper table..i.e. a column
col = idents[0]
msg = _('The %(tablename)s table does not have a '\
'column named "%(columname)s"') % \
dict(tablename=mapper.local_table.name,
columname=col)
check(col in mapper.c, msg)
if isinstance(cond, str):
#clause = getattr(cls, col).op(cond)(utils.utf8(val))
clause = getattr(cls, col).op(cond)(val)
else:
#clause = cond(getattr(cls, col))(utils.utf8(val))
clause = cond(getattr(cls, col))(val)
query = self._session.query(cls).filter(clause).order_by(None)
else:
# we get here when the idents refer to a relation on a
# mapper/table
relations = idents[:-1]
col = idents[-1]
query = self._session.query(cls)
query = query.join(*relations)
# NOTE: SA07 - this depends on Query._joinpoint not changing,
# it changed in SA05 which broke this
local_table = query._joinpoint['prev'][0][1].local_table
if isinstance(cond, str):
#clause = local_table.c[col].op(cond)(utils.utf8(val))
clause = local_table.c[col].op(cond)(val)
else:
#clause = cond(local_table.c[col])(utils.utf8(val))
clause = cond(local_table.c[col])(val)
query = query.filter(clause).order_by(None)
if boolop == 'or':
main_query = main_query.union(query)
elif boolop == 'and':
main_query = main_query.intersect(query)
else:
main_query = query
try:
boolop = next(expr_iter)
except StopIteration:
pass
self._results[self._result_keys[cls]] = main_query.order_by(None).all()
def get_objects(self):
'''return the list of objects to be exported
if "based_on" is "selection", return the top level selection only.
if "based_on" is something else, return all that is needed to create
a complete export.
'''
if self._choices['based_on'] == 'selection':
class EmptySelectionException(Exception):
pass
from bauble.view import SearchView
view = bauble.gui.get_view()
try:
check(isinstance(view, SearchView))
tree_view = view.results_view.get_model()
check(tree_view is not None)
except CheckConditionError:
utils.message_dialog(_('Search for something first.'))
return
return [row[0] for row in tree_view]
## export disregarding selection
result = []
if self._choices['based_on'] == 'plants':
plants = self.session.query(Plant).order_by(Plant.code).join(
Accession).order_by(Accession.code).all()
plantnotes = self.session.query(PlantNote).all()
## only used locations and accessions
locations = self.session.query(Location).filter(
Location.id.in_([j.location_id for j in plants])).all()
accessions = self.session.query(Accession).filter(
Accession.id.in_([j.accession_id for j in plants])).order_by(
Accession.code).all()
## notes are linked in opposite direction
accessionnotes = self.session.query(AccessionNote).filter(
AccessionNote.accession_id.in_(
[j.id for j in accessions])).all()
# extend results with things not further used
result.extend(locations)
result.extend(plants)
result.extend(plantnotes)
elif self._choices['based_on'] == 'accessions':
accessions = self.session.query(Accession).order_by(
Accession.code).all()
accessionnotes = self.session.query(AccessionNote).all()
## now the taxonomy, based either on all species or on the ones used
if self._choices['based_on'] == 'taxa':
species = self.session.query(Species).order_by(
Species.sp).all()
else:
# prepend results with accession data
result = accessions + accessionnotes + result
species = self.session.query(Species).filter(
Species.id.in_([j.species_id for j in accessions])).order_by(
Species.sp).all()
## and all used genera and families
genera = self.session.query(Genus).filter(
Genus.id.in_([j.genus_id for j in species])).order_by(
Genus.genus).all()
families = self.session.query(Familia).filter(
Familia.id.in_([j.family_id for j in genera])).order_by(
Familia.family).all()
## prepend the result with the taxonomic information
result = families + genera + species + result
## done, return the result
return result
def assign_completions_handler(self, widget, get_completions,
on_select=lambda v: v):
"""
Dynamically handle completions on a gtk.Entry.
:param widget: a gtk.Entry instance or widget name
:param get_completions: the method to call when a list of
completions is requested, returns a list of completions
:param on_select: callback for when a value is selected from
the list of completions
"""
if not isinstance(widget, gtk.Entry):
widget = self.view.widgets[widget]
PROBLEM = hash(widget.get_name())
def add_completions(text):
if get_completions is None:
# get_completions is None usually means that the
# completions model already has a static list of
# completions
return
# get the completions using [0:key_length] as the start of
# the string
def idle_callback(values):
completion = widget.get_completion()
utils.clear_model(completion)
completion_model = gtk.ListStore(object)
for v in values:
completion_model.append([v])
completion.set_model(completion_model)
key_length = widget.get_completion().props.minimum_key_length
values = get_completions(text[:key_length])
gobject.idle_add(idle_callback, values)
def on_changed(entry, *args):
text = entry.get_text()
comp = entry.get_completion()
comp_model = comp.get_model()
found = []
if comp_model:
# search the tree model to see if the text in the
# entry matches one of the completions, if so then
# emit the match-selected signal, this allows us to
# type a match in the entry without having to select
# it from the popup
def _cmp(row, data):
return utils.utf8(row[0]) == text
found = utils.search_tree_model(comp_model, text, _cmp)
if len(found) == 1:
v = comp.get_model()[found[0]][0]
# only auto select if the full string has been entered
if text.lower() == utils.utf8(v).lower():
comp.emit('match-selected', comp.get_model(), found[0])
else:
found = None
if text != '' and not found and PROBLEM not in self.problems:
self.add_problem(PROBLEM, widget)
on_select(None)
key_length = widget.get_completion().props.minimum_key_length
if (not comp_model and len(text)>key_length) or \
len(text) == key_length:
add_completions(text)
# if entry is empty select nothing and remove all problem
if text == '':
on_select(None)
self.remove_problem(PROBLEM, widget)
return True
def on_match_select(completion, compl_model, treeiter):
value = compl_model[treeiter][0]
# temporarily block the changed ID so that this function
# doesn't get called twice
widget.handler_block(_changed_sid)
widget.props.text = utils.utf8(value)
widget.handler_unblock(_changed_sid)
self.remove_problem(PROBLEM, widget)
on_select(value)
return True # return True or on_changed() will be called with ''
completion = widget.get_completion()
check(completion is not None, 'the gtk.Entry %s doesn\'t have a '\
'completion attached to it' % widget.get_name())
_changed_sid = self.view.connect(widget, 'changed', on_changed)
self.view.connect(completion, 'match-selected', on_match_select)
