def read_directory(path, db, group=None):
# TODO: update with group also for permissions support
ftype_to_cls = {tf.__name__: tf for tf in tfclasses()}
# create blank project
if db.execute('SELECT 1 FROM projects WHERE name = ""').scalar() is None:
p = Project(name='', directory=op.abspath(path))
if group is not None:
p.group = group
db.add(p)
for fold, dirs, files in os.walk(path):
# for some reason, the scanning code at the end of this loop
# doesn't always work?
if '/_' in fold or '/.' in fold:
continue
curpath = op.relpath(fold, path).split(op.sep)
# extract a run name
try:
runname = [i for i in curpath if
i.endswith(('.d', '.D', '.raw', '.RAW'))][-1]
except IndexError:
runname = ''
# extract a project name
if curpath[0] == op.curdir or curpath[0] == runname:
projname = ''
projpath = op.abspath(path)
else:
projname = curpath[0]
projpath = op.abspath(op.join(path, projname))
for filename in files:
# deal with CH files for each wavelength; merge
if filename.upper().endswith('.CH'):
ufn = filename.upper()
if (ufn.startswith('MWD') and ufn != 'MWD1A.CH') or \
(ufn.startswith('DAD') and ufn != 'DAD1A.CH'):
continue
# figure out if this is a chromatography file
ftype = file_type(op.join(fold, filename))
if ftype is None:
continue
tf = ftype_to_cls[ftype](op.join(fold, filename))
tf.info['filename'] = op.relpath(op.join(fold, filename), path)
add_analysis(db, projname, projpath, runname, tf, group)
db.commit()
db.flush()
def __init__(self, filename=None, ftype=None, data=None):
self.filename = filename
self.ftype = ''
self._data = None
# try to automatically change my class to reflect
# whatever type of file I'm pointing at if not provided
if type(self) is TraceFile:
if data is not None:
self._data = data
if filename is None:
return
ftype = file_type(filename)
if ftype is not None:
# try to automatically subclass myself to provided type
for cls in tfclasses():
if cls.__name__ == ftype:
self.__class__ = cls
self.ftype = ftype
else:
self.ftype = self.__class__.__name__