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'''
scilo - A scientific workflow and efficiency library
Copyright (C) 2012 Joseph Hunkeler <jhunkeler@gmail.com>
This file is part of scilo.
scilo is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
scilo is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with scilo. If not, see <http://www.gnu.org/licenses/>.
'''
import database
import numpy
import glob
import os
class settings(object):
def __init__(self, path_start):
# Define generic directory structure
self.path = path_start
self.directories = {
'data':False,
'result':False,
'npz':False
}
for key in self.directories.iterkeys():
d = os.path.join(self.path, key)
self.directories[key] = d
class mtimedb:
def __init__(self, **kwargs):
self.settings = kwargs
self._path_database = os.path.join(self.settings['npz'], 'npz_mtime.db')
self.db = database.s3(self._path_database)
self.populate()
def populate(self):
#if not os.path.exists(self._path_database):
if os.path.getsize(self._path_database) == 0:
print("Creating file tracking database...")
try:
self.db.cursor.execute("CREATE TABLE npz(file, mtime)")
for f in glob.glob(os.path.join(self.settings['data'], "*.*")):
print("File: %s\tmtime: %f" % (os.path.basename(f), os.path.getmtime(f)))
self.insert(f, os.path.getmtime(f))
self.db.connection.commit()
except:
raise
return
def insert(self, path, mtime):
values = (path, mtime,)
self.db.cursor.execute("INSERT INTO npz VALUES (?,?)", values)
self.db.connection.commit()
def update(self, path, stored, current):
values = (path, current, path, stored)
self.db.cursor("UPDATE npz SET file=?, mtime=? WHERE file==? AND mtime==?", values)
self.db.connection.commit()
print("'%s' updated mtime: %f" % (path, current))
def delete(self, path):
values = (path,)
self.db.cursor.execute("DELETE FROM npz WHERE file==?", (values))
self.db.connection.commit()
print("'%s' removed from mtime database" % path)
return
def check(self):
mtime_stored = []
mtime_current = []
self.db.cursor.execute("SELECT file, mtime FROM npz")
files = glob.glob(os.path.join(self.settings['data'], '*.*'))
for f in files:
mtime_current.append([f, os.path.getmtime(f)])
for f, mtime in self.db.cursor.fetchall():
mtime_stored.append([str(f), mtime])
for stored_file, stored_mtime in mtime_stored:
for current_file, current_mtime in mtime_current:
if not os.path.exists(stored_file) or not os.path.exists(current_file):
print("Missing data file: '%s'" % stored_file)
self.delete(stored_file)
self.drop(stored_file)
break
if current_file == stored_file:
if current_mtime != stored_mtime:
print("'%s' differs" % current_file)
self.update(current_file, stored_mtime, current_mtime)
print("Rebuilding numpy cache for '%s'" % current_file)
self.build(current_file)
return
class cache:
def __init__(self, **kwargs):
self.settings = kwargs
self.files = glob.glob(os.path.join(self.settings['npz'], "*.npz"))
self.files_total = len(self.files)
pass
def build(self, path):
''' Generate 'path' npz file in npz directory'''
temp = numpy.loadtxt(path)
if numpy.savez(os.path.join(self.settings['npz'], os.path.basename(path)), temp) == False:
return False
return True
def drop(self, path):
''' Remove 'path' from npz directory '''
# For security reasons, you are only allowed to unlink files in the 'npz' directory
if os.path.dirname(path) == 'npz':
print("Unlinking '%s'" % (path))
os.unlink(path)
def drop_all(self):
''' Remove all npz files '''
files = glob.glob(os.path.join(self.settings['npz'], '*.npz'))
if files:
[os.unlink(f) for f in files]
def populate(self):
files = glob.glob(os.path.join(self.settings['data'], '*.*'))
file_total = len(files)
file_current = 1
for f in files:
exists = os.path.exists(os.path.join(self.settings['npz'], os.path.basename(f) + '.npz'))
if exists:
file_total -= 1
continue
print("NPZ %d of %d: '%s'" % (file_current, file_total, os.path.basename(f))),
if not self.build(f):
print("... FAIL")
print("")
file_current += 1
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