def _get_obj_from_row(self, row, parent):
# row = (type, id, info, data)
if row is None:
return None
args = {}
args['info'] = json.loads(zlib.decompress(row[2]).decode('utf-8'))
otype = str(row[0])
if otype == 'peak':
args['data'] = decompress_to_ts(row[3])
elif otype == 'spectrum':
args['data'] = decompress_to_spec(row[3])
else:
args['data'] = str(row[3])
args['parent'] = parent
args['db'] = (self, row[1])
if otype == 'file':
return ftype_to_class(args['info']['s-file-type'])(**args)
elif otype == 'peak':
from aston.peaks.Peak import Peak
return Peak(**args)
elif otype == 'spectrum':
from aston.spectra.Spectrum import Spectrum
return Spectrum(**args)
elif otype == 'method':
from aston.features.Other import Method
return Method(**args)
elif otype == 'compound':
from aston.features.Other import Compound
return Compound(**args)
else:
from aston.features.DBObject import DBObject
return DBObject(**args)
def files_to_update(self, path, name_to_dbid, remove=False):
"""
Makes sure the database is in sync with the file system.
"""
ext2ftype = ext_to_classtable()
dnames = set(name_to_dbid.keys())
#TODO: this needs to run in a separate thread
#extract a list of lists of file names in my directory
foldname = os.path.dirname(path)
if foldname == '':
foldname = os.curdir
datafiles = []
for fold, dirs, files in os.walk(foldname):
for filename in files:
ext, magic = get_magic(os.path.join(fold, filename))
#TODO: this MWD stuff is kludgy and will probably break
if ext == 'CH':
if filename[:3].upper() == 'MWD':
filename = 'mwd1A.ch'
elif filename[:3].upper() == 'DAD':
filename = 'dad1A.ch'
ftype = None
if magic is not None:
ftype = ext2ftype.get(ext + '.' + magic, None)
if ftype is None:
ftype = ext2ftype.get(ext, None)
#if it's a supported file, add it in
if ftype is not None:
fn = os.path.join(fold, filename)
datafiles.append(fn)
if fn in dnames:
#TODO: update old database entries with new metadata
# if the metadata has changed
#yield (name_to_dbid[fn], new_obj)
pass
else:
# update dnames, so we won't find *.CH multiple times
if filename in ['mwd1A.ch', 'dad1A.ch']:
dnames.update([fn])
#TODO: generate projects and project_ids based on
# folder names?
fdate = datetime.fromtimestamp(os.path.getctime(fn))
fdate = fdate.replace(microsecond=0).isoformat(' ')
name = os.path.splitext(os.path.basename(fn))[0]
info = {'s-file-type': ftype, 'traces': \
'TIC', 'name': name, 'r-date': fdate}
obj = ftype_to_class(info['s-file-type'])(info, fn)
obj._update_info_from_file()
yield (None, obj)
#obj.db, obj._parent = self, self
#obj.parent = self
#self.save_object(obj)
for d in dirs:
if d.startswith('.') or d.startswith('_'):
dirs.remove(d)
#compare the two lists -> remove deleted files from the database
if remove:
for fn in dnames.difference(set(datafiles)):
yield (name_to_dbid[fn], None)
