def do_genus(filename):
"""
Convert genus.txt
"""
from bauble.plugins.plants import Genus, GenusNote
reader = UnicodeReader(open(filename))
genus_filename = os.path.join(dst_path, 'genus.txt')
genus_writer = UnicodeWriter(open(genus_filename, "wb"))
genus_columns = ['id', 'genus', 'hybrid', 'author', 'qualifier',
'family_id', '_created', '_last_updated']
genus_writer.writerow(genus_columns)
note_filename = os.path.join(dst_path, 'genus_note.txt')
note_writer = NoteWriter(note_filename, 'genus_id')
for line in reader:
note = line.pop('notes')
genus_writer.writerow([line['id'], line['genus'], line['hybrid'],
line['author'], line['qualifier'],
line['family_id'], line['_created'],
line['_last_updated']])
if note:
note_writer.write(note, line['id'])
def do_species(filename):
"""
Convert species.txt
"""
from bauble.plugins.plants import Species, SpeciesNote
reader = UnicodeReader(open(filename))
species_filename = os.path.join(dst_path, 'species.txt')
species_writer = UnicodeWriter(open(species_filename, "wb"))
species_columns = ['id', 'sp', 'sp2', 'sp_author', 'hybrid', 'sp_qual',
'cv_group', 'trade_name', 'infrasp1', 'infrasp1_rank',
'infrasp1_author', 'infrasp2', 'infrasp2_rank',
'infrasp2_author', 'infrasp3', 'infrasp3_rank',
'infrasp3_author', 'infrasp4', 'infrasp4_rank',
'infrasp4_author', 'genus_id', 'label_distribution',
'habit_id', 'flower_color_id', 'awards', '_created',
'_last_updated']
species_writer.writerow(species_columns)
note_filename = os.path.join(dst_path, 'species_note.txt')
note_writer = NoteWriter(note_filename, 'species_id')
for line in reader:
# in bauble 0.9 if sp_hybrid was not None then the infrasp held sp2
hybrid = False
if line['sp_hybrid']:
hybrid = True
if line['infrasp_rank'] or line['infrasp_author']:
print '**', line['sp'], line['infrasp'], line['infrasp_rank'], \
line['infrasp_author']
sp2 = line['infrasp']
infrasp1 = None
else:
sp2 = None
infrasp1 = line['infrasp']
species_writer.writerow([line['id'], line['sp'], sp2,
line['sp_author'], hybrid,
line['sp_qual'], line['cv_group'],
line['trade_name'], infrasp1,
line['infrasp_rank'], line['infrasp_author'],
None, None, None, # infrasp2
None, None, None, # infrasp3
None, None, None, # infrasp4
line['genus_id'],
None, # label_distribution
None, # habit_id,
None, # flower_color_id
None, # awards
line['_created'], line['_last_updated']])
note = line.pop('notes')
if note:
note_writer.write(note, line['id'])
def do_family(filename):
"""
Convert the family.txt
"""
reader = UnicodeReader(open(filename))
family_filename = os.path.join(dst_path, 'family.txt')
family_writer = UnicodeWriter(open(family_filename, "wb"))
family_columns = ['id', 'epithet', 'hybrid_marker', 'author', 'aggregate',
'_created', '_last_updated']
family_writer.writerow(family_columns)
for line in reader:
family_writer.writerow([line['id'], line['family'], '', '', '',
line['_created'], line['_last_updated']])
print 'done'
def do_family(filename):
"""
Convert the family.txt
"""
from bauble.plugins.plants import Family, FamilyNote, FamilySynonym
reader = UnicodeReader(open(filename))
family_filename = os.path.join(dst_path, 'family.txt')
family_writer = UnicodeWriter(open(family_filename, "wb"))
family_columns = ['id', 'family', 'qualifier', '_created', '_last_updated']
family_writer.writerow(family_columns)
note_filename = os.path.join(dst_path, 'family_note.txt')
note_writer = NoteWriter(note_filename, 'family_id')
for line in reader:
note = line.pop('notes')
family_writer.writerow([line['id'], line['family'], line['qualifier'],
line['_created'], line['_last_updated']])
if note:
note_writer.write(note, line['id'])
def do_genus(filename):
"""
Convert genus.txt
"""
reader = UnicodeReader(open(filename))
genus_filename = os.path.join(dst_path, 'genus.txt')
genus_writer = UnicodeWriter(open(genus_filename, "wb"))
genus_columns = [
'id', 'epithet', 'hybrid_marker', 'author', 'aggregate',
'family_id', '_created', '_last_updated']
genus_writer.writerow(genus_columns)
for line in reader:
genus_writer.writerow(
[line['id'], line['genus'], '',
line['author'], line['qualifier'],
line['family_id'], line['_created'],
line['_last_updated']])
print 'done'
def do_genus(filename):
"""
Convert genus.txt
"""
from bauble.plugins.plants import Genus, GenusNote
reader = UnicodeReader(open(filename))
genus_filename = os.path.join(dst_path, 'genus.txt')
genus_writer = UnicodeWriter(open(genus_filename, "wb"))
genus_columns = ['id', 'genus', 'hybrid', 'author', 'qualifier',
'family_id', '_created', '_last_updated']
genus_writer.writerow(genus_columns)
note_filename = os.path.join(dst_path, 'genus_note.txt')
note_writer = NoteWriter(note_filename, 'genus_id')
for line in reader:
note = line.pop('notes')
genus_writer.writerow([line['id'], line['genus'], line['hybrid'],
line['author'], line['qualifier'],
line['family_id'], line['_created'],
line['_last_updated']])
if note:
note_writer.write(note, line['id'])
def do_species(filename):
"""
Convert species.txt
"""
reader = UnicodeReader(open(filename))
species_filename = os.path.join(dst_path, 'species.txt')
writer = UnicodeWriter(open(species_filename, "wb"))
columns = [
'id', 'epithet', 'hybrid_marker', 'author', 'aggregate', 'cv_group',
'trade_name', 'infrasp1', 'infrasp1_rank', 'infrasp1_author',
'infrasp2', 'infrasp2_rank', 'infrasp2_author',
'infrasp3', 'infrasp3_rank', 'infrasp3_author',
'infrasp4', 'infrasp4_rank', 'infrasp4_author',
'genus_id', 'label_distribution', 'bc_distribution', 'habit_id',
'flower_color_id', 'awards', '_created', '_last_updated']
writer.writerow(columns)
post_process_hyop = []
for line in reader:
line = dict(line)
if line['sp'] and (line['sp'].find(u'×') > 0):
line['hybrid_marker'] = 'H'
line['epithet'] = ''
post_process_hyop.append(dict(line))
else:
line['hybrid_marker'] = (line['hybrid'] == 'True') and u'×' or ''
line['epithet'] = line['sp']
line['author'] = line['sp_author']
line['aggregate'] = line['sp_qual']
writer.writerow([line[k] for k in columns])
hybrid_operand = os.path.join(dst_path, 'hybrid_operands.txt')
hyop_columns = ['child_id', 'parent_id', 'role']
hyop_writer = create_writer(hybrid_operand, hyop_columns)
if post_process_hyop:
print post_process_hyop
print 'done'
def do_species(filename):
"""
Convert species.txt
"""
from bauble.plugins.plants import Species, SpeciesNote
reader = UnicodeReader(open(filename))
species_filename = os.path.join(dst_path, 'species.txt')
species_writer = UnicodeWriter(open(species_filename, "wb"))
species_columns = ['id', 'sp', 'sp2', 'sp_author', 'hybrid', 'sp_qual',
'cv_group', 'trade_name', 'infrasp1', 'infrasp1_rank',
'infrasp1_author', 'infrasp2', 'infrasp2_rank',
'infrasp2_author', 'infrasp3', 'infrasp3_rank',
'infrasp3_author', 'infrasp4', 'infrasp4_rank',
'infrasp4_author', 'genus_id', 'label_distribution',
'habit_id', 'flower_color_id', 'awards', '_created',
'_last_updated']
species_writer.writerow(species_columns)
note_filename = os.path.join(dst_path, 'species_note.txt')
note_writer = NoteWriter(note_filename, 'species_id')
for line in reader:
# in bauble 0.9 if sp_hybrid was not None then the infrasp held sp2
hybrid = False
if line['sp_hybrid']:
hybrid = True
if line['infrasp_rank'] or line['infrasp_author']:
print '**', line['sp'], line['infrasp'], line['infrasp_rank'], \
line['infrasp_author']
sp2 = line['infrasp']
infrasp1 = None
else:
sp2 = None
infrasp1 = line['infrasp']
species_writer.writerow([line['id'], line['sp'], sp2,
line['sp_author'], hybrid,
line['sp_qual'], line['cv_group'],
line['trade_name'], infrasp1,
line['infrasp_rank'], line['infrasp_author'],
None, None, None, # infrasp2
None, None, None, # infrasp3
None, None, None, # infrasp4
line['genus_id'],
None, # label_distribution
None, # habit_id,
None, # flower_color_id
None, # awards
line['_created'], line['_last_updated']])
note = line.pop('notes')
if note:
note_writer.write(note, line['id'])
def do_family(filename):
"""
Convert the family.txt
"""
reader = UnicodeReader(open(filename))
family_filename = os.path.join(dst_path, 'family.txt')
family_writer = UnicodeWriter(open(family_filename, "wb"))
family_columns = [
'id', 'epithet', 'hybrid_marker', 'author', 'aggregate', '_created',
'_last_updated'
]
family_writer.writerow(family_columns)
for line in reader:
family_writer.writerow([
line['id'], line['family'], '', '', '', line['_created'],
line['_last_updated']
])
print 'done'
def do_family(filename):
"""
Convert the family.txt
"""
from bauble.plugins.plants import Family, FamilyNote, FamilySynonym
reader = UnicodeReader(open(filename))
family_filename = os.path.join(dst_path, 'family.txt')
family_writer = UnicodeWriter(open(family_filename, "wb"))
family_columns = ['id', 'family', 'qualifier', '_created', '_last_updated']
family_writer.writerow(family_columns)
note_filename = os.path.join(dst_path, 'family_note.txt')
note_writer = NoteWriter(note_filename, 'family_id')
for line in reader:
note = line.pop('notes')
family_writer.writerow([line['id'], line['family'], line['qualifier'],
line['_created'], line['_last_updated']])
if note:
note_writer.write(note, line['id'])
def do_genus(filename):
"""
Convert genus.txt
"""
reader = UnicodeReader(open(filename))
genus_filename = os.path.join(dst_path, 'genus.txt')
genus_writer = UnicodeWriter(open(genus_filename, "wb"))
genus_columns = [
'id', 'epithet', 'hybrid_marker', 'author', 'aggregate', 'family_id',
'_created', '_last_updated'
]
genus_writer.writerow(genus_columns)
for line in reader:
genus_writer.writerow([
line['id'], line['genus'], '', line['author'], line['qualifier'],
line['family_id'], line['_created'], line['_last_updated']
])
print 'done'
def do_species(filename):
"""
Convert species.txt
"""
reader = UnicodeReader(open(filename))
species_filename = os.path.join(dst_path, 'species.txt')
writer = UnicodeWriter(open(species_filename, "wb"))
columns = [
'id', 'epithet', 'hybrid_marker', 'author', 'aggregate', 'cv_group',
'trade_name', 'infrasp1', 'infrasp1_rank', 'infrasp1_author',
'infrasp2', 'infrasp2_rank', 'infrasp2_author', 'infrasp3',
'infrasp3_rank', 'infrasp3_author', 'infrasp4', 'infrasp4_rank',
'infrasp4_author', 'genus_id', 'label_distribution', 'bc_distribution',
'habit_id', 'flower_color_id', 'awards', '_created', '_last_updated'
]
writer.writerow(columns)
post_process_hyop = []
for line in reader:
line = dict(line)
if line['sp'] and (line['sp'].find(u'×') > 0):
line['hybrid_marker'] = 'H'
line['epithet'] = ''
post_process_hyop.append(dict(line))
else:
line['hybrid_marker'] = (line['hybrid'] == 'True') and u'×' or ''
line['epithet'] = line['sp']
line['author'] = line['sp_author']
line['aggregate'] = line['sp_qual']
writer.writerow([line[k] for k in columns])
hybrid_operand = os.path.join(dst_path, 'hybrid_operands.txt')
hyop_columns = ['child_id', 'parent_id', 'role']
hyop_writer = create_writer(hybrid_operand, hyop_columns)
if post_process_hyop:
print post_process_hyop
print 'done'
def create_writer(filename, columns):
writer = UnicodeWriter(open(filename, "a+b"))
writer.writerow(columns)
return writer
def create_writer(filename, columns):
writer = UnicodeWriter(open(filename, "a+b"))
writer.writerow(columns)
return writer
