def load_analyses(self, p, header_idx=1):
self._path = p
parser = XLSParser()
parser.load(p, header_idx)
self.header_offset = header_idx + 1
self.parser = parser
return True
def load_analyses(self, p, header_idx=1):
self._path = p
parser = XLSParser()
parser.load(p, header_idx)
self.header_offset = header_idx + 1
self.parser = parser
return True
def _import_environment_sheet(self, manager, p, sheet, tag):
xp = XLSParser()
xp.load(p, sheet=sheet)
db = manager.db
with db.session_ctx():
# progress = manager.open_progress(xp.nrows)
for args in xp.itervalues():
sample = args['sample']
sample = '{}-{:03d}'.format(tag, int(sample))
# progress.change_message('Setting environment for {}'.format(sample))
dbsample = db.get_sample(sample, project='Minna Bluff', verbose=False)
if dbsample:
mapf = args['MapFea'].lower()
env = None
if 'subaerial' in mapf:
env = 'subaerial'
elif 'hyaloclastite' in mapf:
env = 'subglacial'
elif 'quenched' in mapf:
env = 'mixed'
if env:
self.debug('setting sample: {} environment: {}'.format(sample, env))
dbsample.environment = env
else:
self.debug('no sample in db for {}'.format(sample))
def _import_rock_type(self, manager, p):
xp = XLSParser()
xp.load(p)
db = manager.db
rock_type_map = {'L': 'Lava',
'LAg': 'Lava/Agglutinate',
'L(gl)': 'Lava glassy',
'B': 'Autobreccia',
'B(gl)': 'Hyaloclastite Breccia',
'D': 'Dike',
'VZI': 'Vent zone intrusion',
'T': 'Pyroclastic Tuff or Lapilli Tuff',
'S': 'Polymict sediment',
'T(gl)': 'Hydrovolcanic tuff aka hyalotuff'}
with db.session_ctx():
progress = manager.open_progress(xp.nrows)
for args in xp.itervalues(keys=['ID', 'MapCode']):
sample = args['ID']
sample = '{}-{}'.format(sample[:4], sample[4:])
progress.change_message('Setting sample {}'.format(sample))
dbsample = db.get_sample(sample, project='Minna Bluff', verbose=False)
if dbsample:
# rock_type = rock_type_map[args['MapCode']]
rock_type = args['MapCode'].strip()
if rock_type in rock_type_map:
dbsample.rock_type = rock_type
else:
dbsample.rock_type = ''
# print sample, rock_type
else:
print 'no sample in db for {}'.format(sample)
progress.close()
def _import_lithologies(self, manager, p):
xp = XLSParser()
xp.load(p)
db = manager.db
with db.session_ctx():
progress = manager.open_progress(xp.nrows)
for args in xp.itervalues(keys=['sample', 'lithology']):
sample = args['sample']
progress.change_message('Setting sample {}'.format(sample))
dbsample = db.get_sample(sample, project='Minna Bluff', verbose=False)
if dbsample:
dbsample.lithology = args['lithology']
else:
print 'no sample in db for {}'.format(sample)
progress.close()
def do_loading(self,
manager,
db,
path,
dry=True,
use_progress=True,
quiet=False):
if not quiet:
option = self.options
info = option.edit_traits()
if not info.result:
return
dry = option.dry
if not os.path.isfile(path):
self.warning('No file located at {}'.format(path))
xp = XLSParser()
xp.load(path)
add_samples = True
if manager and use_progress:
db = manager.db
progress = manager.open_progress(xp.nrows)
progress.position = (100, 100)
added_projects = []
added_materials = []
with db.session_ctx(commit=not dry):
keys = ('sample', 'project', 'material')
for args in xp.itervalues(keys=keys):
sample, project, material = args['sample'], args[
'project'], args['material']
# check if project exists
if project not in added_projects:
dbproject = db.get_project(project)
if not dbproject:
if quiet or self.confirmation_dialog(
'"{}" does not exist. Add to database?'.format(
project)):
added_projects.append(project)
db.add_project(project)
else:
continue
# check if material exists
if material not in added_materials:
dbmaterial = db.get_material(material)
if not dbmaterial:
if quiet or self.confirmation_dialog(
'"{}" does not exist. Add to database?'.format(
material)):
added_materials.append(material)
db.add_material(material)
else:
continue
if use_progress:
progress.change_message('Setting sample {}'.format(sample))
if not dry:
db.flush()
dbsample = db.get_sample(sample,
project,
material,
verbose=False)
if not dbsample:
if add_samples:
# print 'trying to add sample {} {} {}'.format(sample,project, material)
dbsample = db.add_sample(sample, project, material)
if use_progress:
progress.close()
def do_loading(self, manager, db, path, dry=True, use_progress=True, quiet=False):
if not quiet:
option = self.options
info = option.edit_traits()
if not info.result:
return
dry = option.dry
if not os.path.isfile(path):
self.warning('No file located at {}'.format(path))
xp = XLSParser()
xp.load(path)
add_samples = True
if manager and use_progress:
db = manager.db
progress = manager.open_progress(xp.nrows)
progress.position = (100,100)
added_projects = []
added_materials = []
with db.session_ctx(commit=not dry):
keys = ('sample', 'project', 'material')
for args in xp.itervalues(keys=keys):
sample, project, material = args['sample'], args['project'], args['material']
# check if project exists
if project not in added_projects:
dbproject = db.get_project(project)
if not dbproject:
if quiet or self.confirmation_dialog('"{}" does not exist. Add to database?'.format(project)):
added_projects.append(project)
db.add_project(project)
else:
continue
# check if material exists
if material not in added_materials:
dbmaterial = db.get_material(material)
if not dbmaterial:
if quiet or self.confirmation_dialog('"{}" does not exist. Add to database?'.format(material)):
added_materials.append(material)
db.add_material(material)
else:
continue
if use_progress:
progress.change_message('Setting sample {}'.format(sample))
if not dry:
db.flush()
dbsample = db.get_sample(sample, project, material, verbose=False)
if not dbsample:
if add_samples:
# print 'trying to add sample {} {} {}'.format(sample,project, material)
dbsample = db.add_sample(sample, project, material)
if use_progress:
progress.close()
def do_import(self, manager, p):
# self._import_lithologies(manager,p)
# self._import_tas(manager, p)
# self._import_environment(manager, p)
self._import_rock_type(manager, p)
return
xp = XLSParser()
xp.load(p, header_idx=2)
overwrite_meta = True
overwrite_alt_name = True
add_samples = True
db = manager.db
progress = manager.open_progress(xp.nrows)
self._import_lithologies(manager, db, xp)
with db.session_ctx():
ellps = xp.get_value(0, 1)
zone = xp.get_value(1, 1)
convert_coordinates = xp.has_key('E') and xp.has_key('N')
self._ref_system = pyproj.Proj(proj='utm', zone=zone, ellps=ellps.upper())
self._wgs84 = pyproj.Proj(init='EPSG:4326')
if convert_coordinates:
keys = ('sample', 'alt_name', 'project', 'material')
else:
keys = ('sample', 'alt_name', 'project', 'material',
'lithology',
'lat', 'long', 'elevation', 'location', 'igsn', 'note')
for args in xp.itervalues(keys=keys):
sample, project, material = args['sample'], args['project'], args['material']
progress.change_message('Setting sample {}'.format(sample))
dbsample = db.get_sample(sample, project, material, verbose=False)
# if not dbsample:
# self.info('adding sample {} project={} material={}'.format(sample, project, material))
# dbsample=db.add_sample(sample, project, material)
alt_name = args['alt_name']
alt_names = None
if alt_name:
head, tail = alt_name.split('-')
try:
itail = int(tail)
padded_alt_name = '{}-{:03d}'.format(head, itail)
non_padded_alt_name = '{}-{:01d}'.format(head, itail)
except ValueError:
padded_alt_name, non_padded_alt_name = '', ''
alt_names = (alt_name, padded_alt_name, non_padded_alt_name)
if not dbsample:
if alt_names:
for a in alt_names:
dbsample = db.get_sample(a, project, material, verbose=False)
if dbsample:
if overwrite_alt_name:
self.debug('setting name={} alt_name={}, padded_alt_name={}'.format(sample,
a,
padded_alt_name))
dbsample.name = sample
dbsample.alt_name = padded_alt_name
break
if not dbsample:
if alt_names:
for a in alt_names:
dbsample = db.get_sample(a, project, material, verbose=False)
if dbsample:
break
if not dbsample:
if add_samples:
if args['lat'] and args['long']:
dbsample = db.add_sample(sample, project, material)
if alt_name:
dbsample.alt_name = padded_alt_name
if not dbsample:
continue
if overwrite_meta:
if convert_coordinates:
lon, lat = self._convert_coordinates(args['E'], args['N'])
else:
lat, lon = args['lat'], args['long']
dbsample.lat = lat
dbsample.long = lon
dbsample.elevation = args['elevation']
dbsample.location = args['location']
dbsample.igsn = args['igsn']
dbsample.note = args['note']
dbsample.lithology = args['lithology']
progress.close()