def remove_callback(locations):
loc = locations[0]
s = '%s: %s' % (loc.__class__.__name__, str(loc))
if len(loc.plants) > 0:
msg = _('Please remove the plants from <b>%(location)s</b> '
'before deleting it.') % {
'location': loc
}
utils.message_dialog(msg, gtk.MESSAGE_WARNING)
return
msg = _("Are you sure you want to remove %s?") % \
utils.xml_safe(s)
if not utils.yes_no_dialog(msg):
return
try:
session = db.Session()
obj = session.query(Location).get(loc.id)
session.delete(obj)
session.commit()
except Exception, e:
msg = _('Could not delete.\n\n%s') % utils.xml_safe(e)
utils.message_details_dialog(msg,
traceback.format_exc(),
type=gtk.MESSAGE_ERROR)
def run(self):
ssn = db.Session()
value, = ssn.execute(self.query).first()
idle_add(lambda x: self.widget.set_text(str(x)), value)
ssn.close()
def update(self):
'''
'''
logger.debug('SplashInfoBox::update')
statusbar = bauble.gui.widgets.statusbar
sbcontext_id = statusbar.get_context_id('searchview.nresults')
statusbar.pop(sbcontext_id)
bauble.gui.widgets.main_comboentry.child.set_text('')
ssn = db.Session()
q = ssn.query(bauble.meta.BaubleMeta)
q = q.filter(bauble.meta.BaubleMeta.name.startswith(u'stqr_'))
name_tooltip_query = dict(
(int(i.name[5:]), (i.value.split(':', 2))) for i in q.all())
ssn.close()
for i in range(1, 11):
wname = "stqr_%02d_button" % i
widget = getattr(self.widgets, wname)
name, tooltip, query = name_tooltip_query.get(
i, (_('<empty>'), '', ''))
widget.set_label(name)
widget.set_tooltip_text(tooltip)
self.name_tooltip_query = name_tooltip_query
# LabelUpdater objects **can** run in a thread.
if 'GardenPlugin' in pluginmgr.plugins:
LabelUpdater(self.widgets.splash_nplttot,
"select count(*) from plant").run()
self.start_thread(
LabelUpdater(self.widgets.splash_npltuse,
"select count(*) from plant where quantity>0"))
self.start_thread(
LabelUpdater(self.widgets.splash_npltnot,
"select count(*) from plant where quantity=0"))
LabelUpdater(self.widgets.splash_nacctot,
"select count(*) from accession").run()
self.start_thread(
LabelUpdater(
self.widgets.splash_naccuse,
"select count(distinct accession.id) "
"from accession "
"join plant on plant.accession_id=accession.id "
"where plant.quantity>0"))
self.start_thread(
LabelUpdater(
self.widgets.splash_naccnot, "select count(id) "
"from accession "
"where id not in "
"(select accession_id from plant "
" where plant.quantity>0)"))
LabelUpdater(self.widgets.splash_nloctot,
"select count(*) from location").run()
self.start_thread(
LabelUpdater(
self.widgets.splash_nlocuse,
"select count(distinct location.id) "
"from location "
"join plant on plant.location_id=location.id "
"where plant.quantity>0"))
self.start_thread(
LabelUpdater(
self.widgets.splash_nlocnot, "select count(id) "
"from location "
"where id not in "
"(select location_id from plant "
" where plant.quantity>0)"))
self.start_thread(
LabelUpdater(
self.widgets.splash_nspcuse,
"select count(distinct species.id) "
"from species join accession "
"on accession.species_id=species.id"))
self.start_thread(
LabelUpdater(
self.widgets.splash_ngenuse,
"select count(distinct species.genus_id) "
"from species join accession "
"on accession.species_id=species.id"))
self.start_thread(
LabelUpdater(
self.widgets.splash_nfamuse,
"select count(distinct genus.family_id) from genus "
"join species on species.genus_id=genus.id "
"join accession on accession.species_id=species.id "))
LabelUpdater(self.widgets.splash_nspctot,
"select count(*) from species").run()
LabelUpdater(self.widgets.splash_ngentot,
"select count(*) from genus").run()
LabelUpdater(self.widgets.splash_nfamtot,
"select count(*) from family").run()
self.start_thread(
LabelUpdater(
self.widgets.splash_nspcnot, "select count(id) from species "
"where id not in "
"(select distinct species.id "
" from species join accession "
" on accession.species_id=species.id)"))
self.start_thread(
LabelUpdater(
self.widgets.splash_ngennot, "select count(id) from genus "
"where id not in "
"(select distinct species.genus_id "
" from species join accession "
" on accession.species_id=species.id)"))
self.start_thread(
LabelUpdater(
self.widgets.splash_nfamnot, "select count(id) from family "
"where id not in "
"(select distinct genus.family_id from genus "
"join species on species.genus_id=genus.id "
"join accession on accession.species_id=species.id)"))
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 update(self, row):
'''
update the expander
:param row: the row to get the values from
'''
self.current_obj = row
# TODO: how do we put the genus in a seperate label so it
# can be clickable but still respect the text wrap to wrap
# around and indent from the genus name instead of from the
# species name
session = db.Session()
self.widget_set_value('sp_name_data',
'<big>%s</big>' % row.markup(True),
markup=True)
awards = ''
if row.awards:
awards = utils.utf8(row.awards)
self.widget_set_value('sp_awards_data', awards)
logger.debug('setting cites data from row %s' % row)
cites = ''
if row.cites:
cites = utils.utf8(row.cites)
self.widget_set_value('sp_cites_data', cites)
# zone = ''
# if row.hardiness_zone:
# awards = utils.utf8(row.hardiness_zone)
# self.widget_set_value('sp_hardiness_data', zone)
habit = ''
if row.habit:
habit = utils.utf8(row.habit)
self.widget_set_value('sp_habit_data', habit)
dist = ''
if row.distribution:
dist = utils.utf8(row.distribution_str())
self.widget_set_value('sp_dist_data', dist)
dist = ''
if row.label_distribution:
dist = row.label_distribution
self.widget_set_value('sp_labeldist_data', dist)
# stop here if not GardenPluin
if 'GardenPlugin' not in pluginmgr.plugins:
return
from bauble.plugins.garden.accession import Accession
from bauble.plugins.garden.plant import Plant
nacc = session.query(Accession).join('species').\
filter_by(id=row.id).count()
self.widget_set_value('sp_nacc_data', nacc)
nplants = session.query(Plant).join('accession', 'species').\
filter_by(id=row.id).count()
if nplants == 0:
self.widget_set_value('sp_nplants_data', nplants)
else:
nacc_in_plants = session.query(Plant.accession_id).\
join('accession', 'species').\
filter_by(id=row.id).distinct().count()
self.widget_set_value(
'sp_nplants_data',
'%s in %s accessions' % (nplants, nacc_in_plants))
session.close()
return plants.Species.retrieve_or_create(ssn, {
'object': 'taxon',
'rank': 'species',
'ht-epithet': gen_epithet,
'epithet': sp_epithet,
'ht-rank': 'genus'
},
create=create)
def species_to_add(s):
return species_to_fix(s, create=True)
db.open("sqlite:////home/mario/.bauble/cuchubo-corrected.db")
ssn = db.Session()
import codecs
with codecs.open("/tmp/complete.csv", 'r', 'utf16') as f:
keys = f.readline().strip().split('\t')
for l in f.readlines():
l = l.strip()
values = [i.strip() for i in l.split("\t")]
fields = dict(zip(keys, values))
print fields['Name_submitted'], fields['Name_matched']
obj = species_to_fix(fields['Name_submitted'])
if obj is None:
print fields['Name_submitted']
continue
gen_epithet, sp_epithet = fields['Name_matched'].split(' ')
def setUp(self):
assert uri is not None, "The database URI is not set"
init_bauble(uri)
self.session = db.Session()