def test_install_with_problem(self):
"bauble.pluginmgr.init() using plugin which can't install"
db.open(uri, verify=False)
db.create(False)
bauble.pluginmgr.plugins[FailingInstallPlugin.__name__] = FailingInstallPlugin()
bauble.pluginmgr.plugins[DependsOnFailingInstallPlugin.__name__] = DependsOnFailingInstallPlugin()
self.assertRaises(BaubleError, bauble.pluginmgr.init, force=True)
def test_install_with_problem(self):
"bauble.pluginmgr.init() using plugin which can't install"
db.open(uri, verify=False)
db.create(False)
bauble.pluginmgr.plugins[
FailingInstallPlugin.__name__] = FailingInstallPlugin()
bauble.pluginmgr.plugins[DependsOnFailingInstallPlugin.
__name__] = DependsOnFailingInstallPlugin()
self.assertRaises(BaubleError, bauble.pluginmgr.init, force=True)
def test_init(self):
"""
Test bauble.pluginmgr.init()
"""
db.open(uri, verify=False)
db.create(False)
bauble.pluginmgr.plugins[C.__name__] = C
bauble.pluginmgr.plugins[B.__name__] = B
bauble.pluginmgr.plugins[A.__name__] = A
bauble.pluginmgr.init(force=True)
self.assert_(A.initialized and B.initialized and C.initialized)
def test_successfulinit(self):
"bauble.pluginmgr.init() should be successful"
db.open(uri, verify=False)
db.create(False)
bauble.pluginmgr.plugins[C.__name__] = C()
bauble.pluginmgr.plugins[B.__name__] = B()
bauble.pluginmgr.plugins[A.__name__] = A()
bauble.pluginmgr.init(force=True)
self.assertTrue(A.initialized)
self.assertTrue(B.initialized)
self.assertTrue(C.initialized)
def test_successfulinit(self):
"bauble.pluginmgr.init() should be successful"
db.open(uri, verify=False)
db.create(False)
bauble.pluginmgr.plugins[C.__name__] = C()
bauble.pluginmgr.plugins[B.__name__] = B()
bauble.pluginmgr.plugins[A.__name__] = A()
bauble.pluginmgr.init(force=True)
self.assertTrue(A.initialized)
self.assertTrue(B.initialized)
self.assertTrue(C.initialized)
def test_dependencies_CA(self):
"test that loading C will also load A"
pA = A()
pB = B()
pC = C()
bauble.pluginmgr.plugins[B.__name__] = pB
bauble.pluginmgr.plugins[A.__name__] = pA
bauble.pluginmgr.plugins[C.__name__] = pC
db.open(uri, verify=False)
db.create(False)
## should try to load the A plugin
self.assertRaises(KeyError, bauble.pluginmgr.install, (pC, ), force=True)
def test_dependencies_CA(self):
"test that loading C will also load A"
pA = A()
pB = B()
pC = C()
bauble.pluginmgr.plugins[B.__name__] = pB
bauble.pluginmgr.plugins[A.__name__] = pA
bauble.pluginmgr.plugins[C.__name__] = pC
db.open(uri, verify=False)
db.create(False)
## should try to load the A plugin
self.assertRaises(KeyError,
bauble.pluginmgr.install, (pC, ), force=True)
def test_install(self):
"""
Test bauble.pluginmgr.install()
"""
pA = A()
pB = B()
pC = C()
bauble.pluginmgr.plugins[C.__name__] = pC
bauble.pluginmgr.plugins[B.__name__] = pB
bauble.pluginmgr.plugins[A.__name__] = pA
db.open(uri, verify=False)
db.create(False)
bauble.pluginmgr.install((pA, pB, pC), force=True)
self.assert_(A.installed and B.installed and C.installed)
def test_install(self):
"""
Test bauble.pluginmgr.install()
"""
pA = A()
pB = B()
pC = C()
bauble.pluginmgr.plugins[C.__name__] = pC
bauble.pluginmgr.plugins[B.__name__] = pB
bauble.pluginmgr.plugins[A.__name__] = pA
db.open(uri, verify=False)
db.create(False)
bauble.pluginmgr.install((pA, pB, pC), force=True)
self.assert_(A.installed and B.installed and C.installed)
def test_init_with_problem(self):
"bauble.pluginmgr.init() using plugin which can't initialize"
old_dialog = utils.message_details_dialog
self.invoked = False
def fake_dialog(a,b,c):
"trap dialog box invocation"
self.invoked = True
utils.message_details_dialog = fake_dialog
db.open(uri, verify=False)
db.create(False)
bauble.pluginmgr.plugins[FailingInitPlugin.__name__] = FailingInitPlugin()
bauble.pluginmgr.plugins[DependsOnFailingInitPlugin.__name__] = DependsOnFailingInitPlugin()
bauble.pluginmgr.init(force=True)
self.assertTrue(self.invoked)
# self.assertFalse(FailingInitPlugin.initialized) # irrelevant
self.assertFalse(DependsOnFailingInitPlugin.initialized)
utils.message_details_dialog = old_dialog
def test_init_with_problem(self):
"bauble.pluginmgr.init() using plugin which can't initialize"
old_dialog = utils.message_details_dialog
self.invoked = False
def fake_dialog(a, b, c):
"trap dialog box invocation"
self.invoked = True
utils.message_details_dialog = fake_dialog
db.open(uri, verify=False)
db.create(False)
bauble.pluginmgr.plugins[
FailingInitPlugin.__name__] = FailingInitPlugin()
bauble.pluginmgr.plugins[DependsOnFailingInitPlugin.
__name__] = DependsOnFailingInitPlugin()
bauble.pluginmgr.init(force=True)
self.assertTrue(self.invoked)
# self.assertFalse(FailingInitPlugin.initialized) # irrelevant
self.assertFalse(DependsOnFailingInitPlugin.initialized)
utils.message_details_dialog = old_dialog
def on_file_menu_open(self, widget, data=None):
"""
Open the connection manager.
"""
from connmgr import ConnMgrPresenter
default_conn = prefs[bauble.conn_default_pref]
cm = ConnMgrPresenter(default=default_conn)
name, uri = cm.start()
if name is None:
return
engine = None
try:
engine = db.open(uri, True, True)
except Exception, e:
# we don't do anything to handle the exception since db.open()
# should have shown an error dialog if there was a problem
# opening the database as long as the show_error_dialogs
# parameter is True
logger.warning(e)
def on_file_menu_open(self, widget, data=None):
"""
Open the connection manager.
"""
from connmgr import ConnMgrPresenter
default_conn = prefs[bauble.conn_default_pref]
cm = ConnMgrPresenter(default=default_conn)
name, uri = cm.start()
if name is None:
return
engine = None
try:
engine = db.open(uri, True, True)
except Exception, e:
# we don't do anything to handle the exception since db.open()
# should have shown an error dialog if there was a problem
# opening the database as long as the show_error_dialogs
# parameter is True
logger.warning(e)
def init_bauble(uri, create=False):
try:
db.open(uri, verify=False)
except Exception, e:
print >>sys.stderr, e
def species_to_fix(s, create=False):
gen_epithet, sp_epithet = s.split(' ')
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/jbdm.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))
if float(fields['Overall_score']) <= 0.9:
print fields['Name_submitted']
continue
obj = species_to_fix(fields['Name_submitted'])
def species_to_fix(s, create=False):
gen_epithet, sp_epithet = s.split(' ', 1)
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
def init_bauble(uri, create=False):
try:
db.open(uri, verify=False)
except Exception, e:
print >> sys.stderr, e
import os, sys
import xml.sax.saxutils as saxutils
sys.path.append('.')
import sqlalchemy as sa
from sqlalchemy.orm import *
from sqlalchemy.orm.mapper import _mapper_registry
from sqlalchemy.orm.properties import *
import bauble
import bauble.db as db
import bauble.pluginmgr as pluginmgr
from bauble.prefs import prefs
import bauble.view as view
uri = 'sqlite:///:memory:'
db.open(uri, verify=False)
prefs.init()
pluginmgr.load()
db.create(False)
pluginmgr.init(True)
def column_type_str(col):
print type(col)
if isinstance(col, sa.String):
return 'string'
elif isinstance(col, sa.Unicode):
return 'unicode'
elif isinstance(col, sa.Integer):
return 'integer'
elif isinstance(col, sa.ForeignKey):
return 'foreign key(int)'
# intialize the user preferences
prefs.init()
open_exc = None
# open default database
if uri is None:
from bauble.connmgr import ConnectionManager
default_conn = prefs[conn_default_pref]
while True:
if not uri or not conn_name:
cm = ConnectionManager(default_conn)
conn_name, uri = cm.start()
if conn_name is None:
quit()
try:
if db.open(uri, True, True):
prefs[conn_default_pref] = conn_name
break
else:
uri = conn_name = None
except err.VersionError, e:
warning(e)
db.open(uri, False)
break
except (err.EmptyDatabaseError, err.MetaTableError,
err.VersionError, err.TimestampError,
err.RegistryError), e:
warning(e)
open_exc = e
# reopen without verification so that db.Session and
# db.engine, db.metadata will be bound to an engine
gen_epithet, sp_epithet = s.split(' ', 1)
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
import os, sys
import xml.sax.saxutils as saxutils
sys.path.append('.')
import sqlalchemy as sa
from sqlalchemy.orm import *
from sqlalchemy.orm.mapper import _mapper_registry
from sqlalchemy.orm.properties import *
import bauble
import bauble.db as db
import bauble.pluginmgr as pluginmgr
from bauble.prefs import prefs
import bauble.view as view
uri = 'sqlite:///:memory:'
db.open(uri, verify=False)
prefs.init()
pluginmgr.load()
db.create(False)
pluginmgr.init(True)
def column_type_str(col):
print type(col)
if isinstance(col, sa.String):
return 'string'
elif isinstance(col, sa.Unicode):
return 'unicode'
elif isinstance(col, sa.Integer):
return 'integer'
elif isinstance(col, sa.ForeignKey):
# declare module level variables
global gui, default_icon, conn_name
default_icon = os.path.join(paths.lib_dir(), "images", "icon.svg")
open_exc = None
# open default database
if uri is None:
from bauble.connmgr import start_connection_manager
while True:
if not uri or not conn_name:
conn_name, uri = start_connection_manager()
if conn_name is None:
quit()
try:
if db.open(uri, True, True):
prefs[conn_default_pref] = conn_name
break
else:
uri = conn_name = None
except err.VersionError, e:
logger.warning("%s(%s)" % (type(e), e))
db.open(uri, False)
break
except (err.EmptyDatabaseError, err.MetaTableError,
err.VersionError, err.TimestampError,
err.RegistryError), e:
logger.info("%s(%s)" % (type(e), e))
open_exc = e
# reopen without verification so that db.Session and
# db.engine, db.metadata will be bound to an engine