def test_get_species_pertinent_to_lists(self):
"""
Test getting the species from different types
"""
get_ids = lambda objs: sorted([o.id for o in objs])
family = self.session.query(Family).get(1)
ids = get_ids(get_species_pertinent_to([family], self.session))
self.assert_(ids == range(1, 5), ids)
family = self.session.query(Family).get(1)
family2 = self.session.query(Family).get(2)
ids = get_ids(get_species_pertinent_to([family, family2],
self.session))
self.assert_(ids == range(1, 9), ids)
genus = self.session.query(Genus).get(1)
ids = get_ids(get_species_pertinent_to([genus], self.session))
self.assert_(ids == [1, 2], ids)
species = self.session.query(Species).get(1)
ids = get_ids(get_species_pertinent_to([species], self.session))
self.assert_(ids == [1], ids)
accession = self.session.query(Accession).get(1)
ids = get_ids(get_species_pertinent_to([accession], self.session))
self.assert_(ids == [1], ids)
plant = self.session.query(Plant).get(1)
ids = get_ids(get_species_pertinent_to([plant], self.session))
self.assert_(ids == [1], ids)
location = self.session.query(Location).get(1)
ids = get_ids(get_species_pertinent_to([location], self.session))
self.assert_(ids == [1], ids)
vn = self.session.query(VernacularName).get(1)
ids = get_ids(get_species_pertinent_to([vn], self.session))
self.assert_(ids == [1], ids)
tag_objects('test', [family, genus])
tag = self.session.query(Tag).filter_by(tag=u'test').one()
ids = get_ids(get_species_pertinent_to([tag], self.session))
self.assert_(ids == range(1, 5), ids)
# now test all the objects
ids = get_ids(
get_species_pertinent_to(
[family, genus, species, accession, plant, location],
self.session))
self.assert_(ids == range(1, 5), ids)
def test_get_species_pertinent_to_lists(self):
"""
Test getting the species from different types
"""
get_ids = lambda objs: sorted([o.id for o in objs])
family = self.session.query(Family).get(1)
ids = get_ids(get_species_pertinent_to([family], self.session))
self.assert_(ids == range(1, 5), ids)
family = self.session.query(Family).get(1)
family2 = self.session.query(Family).get(2)
ids = get_ids(
get_species_pertinent_to([family, family2], self.session))
self.assert_(ids == range(1, 9), ids)
genus = self.session.query(Genus).get(1)
ids = get_ids(get_species_pertinent_to([genus], self.session))
self.assert_(ids == [1, 2], ids)
species = self.session.query(Species).get(1)
ids = get_ids(get_species_pertinent_to([species], self.session))
self.assert_(ids == [1], ids)
accession = self.session.query(Accession).get(1)
ids = get_ids(get_species_pertinent_to([accession], self.session))
self.assert_(ids == [1], ids)
plant = self.session.query(Plant).get(1)
ids = get_ids(get_species_pertinent_to([plant], self.session))
self.assert_(ids == [1], ids)
location = self.session.query(Location).get(1)
ids = get_ids(get_species_pertinent_to([location], self.session))
self.assert_(ids == [1], ids)
vn = self.session.query(VernacularName).get(1)
ids = get_ids(get_species_pertinent_to([vn], self.session))
self.assert_(ids == [1], ids)
tag_objects('test', [family, genus])
tag = self.session.query(Tag).filter_by(tag=u'test').one()
ids = get_ids(get_species_pertinent_to([tag], self.session))
self.assert_(ids == range(1, 5), ids)
# now test all the objects
ids = get_ids(get_species_pertinent_to(
[family, genus, species, accession, plant, location],
self.session))
self.assert_(ids == range(1, 5), ids)
def test_get_species_pertinent_to_element(self):
"""
Test getting the species from different types
"""
get_ids = lambda objs: sorted([o.id for o in objs])
family = self.session.query(Family).get(1)
ids = get_ids(get_species_pertinent_to(family, self.session))
self.assert_(ids == range(1, 5), ids)
def test_get_species_pertinent_to_element(self):
"""
Test getting the species from different types
"""
get_ids = lambda objs: sorted([o.id for o in objs])
family = self.session.query(Family).get(1)
ids = get_ids(get_species_pertinent_to(family, self.session))
self.assert_(ids == range(1, 5), ids)
def format(objs, **kwargs):
# debug('format(%s)' % kwargs)
stylesheet = kwargs['stylesheet']
authors = kwargs['authors']
renderer = kwargs['renderer']
source_type = kwargs['source_type']
use_private = kwargs['private']
error_msg = None
if not stylesheet:
error_msg = _('Please select a stylesheet.')
elif not renderer:
error_msg = _('Please select a a renderer')
if error_msg is not None:
utils.message_dialog(error_msg, gtk.MESSAGE_WARNING)
return False
fo_cmd = renderers_map[renderer]
exe = fo_cmd.split(' ')[0]
if not on_path(exe):
utils.message_dialog(
_('Could not find the command "%(exe)s" to '
'start the %(renderer_name)s '
'renderer.') % ({
'exe': exe,
'renderer_name': renderer
}), gtk.MESSAGE_ERROR)
return False
session = db.Session()
# convert objects to ABCDAdapters depending on source type for
# passing to create_abcd
adapted = []
if source_type == plant_source_type:
plants = sorted(get_plants_pertinent_to(objs, session=session),
key=utils.natsort_key)
if len(plants) == 0:
utils.message_dialog(
_('There are no plants in the search '
'results. Please try another search.'))
return False
for p in plants:
if use_private:
adapted.append(PlantABCDAdapter(p, for_labels=True))
elif not p.accession.private:
adapted.append(PlantABCDAdapter(p, for_labels=True))
elif source_type == species_source_type:
species = sorted(get_species_pertinent_to(objs, session=session),
key=utils.natsort_key)
if len(species) == 0:
utils.message_dialog(
_('There are no species in the search '
'results. Please try another search.'))
return False
for s in species:
adapted.append(SpeciesABCDAdapter(s, for_labels=True))
elif source_type == accession_source_type:
accessions = sorted(get_accessions_pertinent_to(objs,
session=session),
key=utils.natsort_key)
if len(accessions) == 0:
utils.message_dialog(
_('There are no accessions in the search '
'results. Please try another search.'))
return False
for a in accessions:
if use_private:
adapted.append(AccessionABCDAdapter(a, for_labels=True))
elif not a.private:
adapted.append(AccessionABCDAdapter(a, for_labels=True))
else:
raise NotImplementedError('unknown source type')
if len(adapted) == 0:
# nothing adapted....possibly everything was private
# TODO: if everything was private and that is really why we got
# here then it is probably better to show a dialog with a message
# and raise and exception which appears as an error
raise Exception('No objects could be adapted to ABCD units.')
abcd_data = create_abcd(adapted, authors=authors, validate=False)
session.close()
logger.debug(etree.dump(abcd_data.getroot()))
# create xsl fo file
dummy, fo_filename = tempfile.mkstemp()
style_etree = etree.parse(stylesheet)
transform = etree.XSLT(style_etree)
result = transform(abcd_data)
fo_outfile = open(fo_filename, 'w')
fo_outfile.write(str(result))
fo_outfile.close()
dummy, filename = tempfile.mkstemp()
filename = '%s.pdf' % filename
# TODO: checkout pyexpect for spawning processes
# run the report to produce the pdf file, the command has to be
# on the path for this to work
fo_cmd = fo_cmd % ({
'fo_filename': fo_filename,
'out_filename': filename
})
logger.debug(fo_cmd)
# TODO: use popen to get output
os.system(fo_cmd)
logger.debug(filename)
if not os.path.exists(filename):
utils.message_dialog(
_('Error creating the PDF file. Please '
'ensure that your PDF formatter is '
'properly installed.'), gtk.MESSAGE_ERROR)
return False
else:
try:
desktop.open(filename)
except OSError:
utils.message_dialog(
_('Could not open the report with the '
'default program. You can open the '
'file manually at %s') % filename)
return True
def format(objs, **kwargs):
# debug('format(%s)' % kwargs)
stylesheet = kwargs['stylesheet']
authors = kwargs['authors']
renderer = kwargs['renderer']
source_type = kwargs['source_type']
use_private = kwargs['private']
error_msg = None
if not stylesheet:
error_msg = _('Please select a stylesheet.')
elif not renderer:
error_msg = _('Please select a a renderer')
if error_msg is not None:
utils.message_dialog(error_msg, gtk.MESSAGE_WARNING)
return False
fo_cmd = renderers_map[renderer]
exe = fo_cmd.split(' ')[0]
if not on_path(exe):
utils.message_dialog(_('Could not find the command "%(exe)s" to '
'start the %(renderer_name)s '
'renderer.') %
({'exe': exe, 'renderer_name': renderer}),
gtk.MESSAGE_ERROR)
return False
session = db.Session()
# convert objects to ABCDAdapters depending on source type for
# passing to create_abcd
adapted = []
if source_type == plant_source_type:
plants = sorted(get_plants_pertinent_to(objs, session=session),
key=utils.natsort_key)
if len(plants) == 0:
utils.message_dialog(_('There are no plants in the search '
'results. Please try another search.'))
return False
for p in plants:
if use_private:
adapted.append(PlantABCDAdapter(p, for_labels=True))
elif not p.accession.private:
adapted.append(PlantABCDAdapter(p, for_labels=True))
elif source_type == species_source_type:
species = sorted(get_species_pertinent_to(objs, session=session),
key=utils.natsort_key)
if len(species) == 0:
utils.message_dialog(_('There are no species in the search '
'results. Please try another search.'))
return False
for s in species:
adapted.append(SpeciesABCDAdapter(s, for_labels=True))
elif source_type == accession_source_type:
accessions = sorted(get_accessions_pertinent_to(objs,
session=session),
key=utils.natsort_key)
if len(accessions) == 0:
utils.message_dialog(_('There are no accessions in the search '
'results. Please try another search.'))
return False
for a in accessions:
if use_private:
adapted.append(AccessionABCDAdapter(a, for_labels=True))
elif not a.private:
adapted.append(AccessionABCDAdapter(a, for_labels=True))
else:
raise NotImplementedError('unknown source type')
if len(adapted) == 0:
# nothing adapted....possibly everything was private
# TODO: if everything was private and that is really why we got
# here then it is probably better to show a dialog with a message
# and raise and exception which appears as an error
raise Exception('No objects could be adapted to ABCD units.')
abcd_data = create_abcd(adapted, authors=authors, validate=False)
session.close()
# logger.debug(etree.dump(abcd_data.getroot()))
# create xsl fo file
dummy, fo_filename = tempfile.mkstemp()
style_etree = etree.parse(stylesheet)
transform = etree.XSLT(style_etree)
result = transform(abcd_data)
fo_outfile = open(fo_filename, 'w')
fo_outfile.write(str(result))
fo_outfile.close()
dummy, filename = tempfile.mkstemp()
filename = '%s.pdf' % filename
# TODO: checkout pyexpect for spawning processes
# run the report to produce the pdf file, the command has to be
# on the path for this to work
fo_cmd = fo_cmd % ({'fo_filename': fo_filename,
'out_filename': filename})
# print fo_cmd
# debug(fo_cmd)
# TODO: use popen to get output
os.system(fo_cmd)
# print filename
if not os.path.exists(filename):
utils.message_dialog(_('Error creating the PDF file. Please '
'ensure that your PDF formatter is '
'properly installed.'), gtk.MESSAGE_ERROR)
return False
else:
try:
desktop.open(filename)
except OSError:
utils.message_dialog(_('Could not open the report with the '
'default program. You can open the '
'file manually at %s') % filename)
return True
def test_get_species_pertinent_to_sessionless(self):
get_ids = lambda objs: sorted([o.id for o in objs])
family = self.session.query(Family).get(1)
ids = get_ids(get_species_pertinent_to([family]))
self.assert_(ids == range(1, 5), ids)
def test_get_species_pertinent_to_sessionless(self):
get_ids = lambda objs: sorted([o.id for o in objs])
family = self.session.query(Family).get(1)
ids = get_ids(get_species_pertinent_to([family]))
self.assert_(ids == range(1, 5), ids)
