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page.py
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page.py
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import os,time,gzip
import hashlib
import numpy as np
import sys
def id_to_path(num,nchar=3):
sss=str(num)[::-1]
sss=[sss[i:i+nchar][::-1] for i in range(0,len(sss),nchar)][::-1]
sss=['0'+a for a in sss[:-1]]+sss[-1:]
return os.path.join(*sss)
def hashfile(sha,fpath,BUF_SIZE = 65536):
with open(fpath, 'rb') as f:
while True:
data = f.read(BUF_SIZE)
if not data:
break
sha.update(data)
return sha
def split_string_utf32(sss):
sss=[a for a in sss.decode('utf-32').split('\0') if len(a)>0]
return sss
def split_string(sss):
sss=[a for a in sss.split('\0') if len(a)>0]
return sss
class Page(object):
def __init__(self,pagedir,pageid,
idxtype,count,idxa,idxb,
rectype,reclen,recsize,comp,checksum,check=False):
self.pageid=pageid
self.pagedir=pagedir
self.rectype=rectype
self.reclen=reclen
self.idxtype=idxtype
self.count=count
self.idxa=idxa
self.idxb=idxb
self.recsize=recsize
self.comp=comp
self.checksum=checksum
base=os.path.join(pagedir,id_to_path(self.pageid))
self.pagepath=os.path.split(base)[0]
self.recpath=os.path.join(base+'.rec')
self.idxpath=os.path.join(base+'.idx')
if self.reclen == -1:
self.lenpath=os.path.join(base+'.len')
if check and self.checksum is not None:
assert self.check()
@classmethod
def from_data(cls,idx,rec,pagedir,pageid,comp=None):
count=len(idx)
if count==0 or len(rec)!=count:
msg="Error creating Page %s: idx,rec length mismatch %d!=%d"
raise ValueError(msg%(pageid,len(idx),len(rec)))
lengths=[len(rrr) if hasattr(rrr,'__len__') else 0 for rrr in rec]
if len(set(lengths))>1:
reclen=-1
out=[]
nlengths=[]
for rrr in rec:
rrr=np.array(rrr)
# for string, save data in zero terminated strings
if 'S' in rrr.dtype.str:
nt=str(int(rrr.dtype.str[2:])+1)
rrr=np.array([rrr],dtype='S'+nt).view('S1').flatten()
elif 'U' in rrr.dtype.str:
nt=str(int(rrr.dtype.str[2:])+1)
rrr=np.array([rrr],dtype='U'+nt).view('U1').flatten()
out.append(rrr)
nlengths.append(len(rrr))
rec=out
lengths=np.array(nlengths,dtype='<i8')
rectypes=[rrr.dtype.str for rrr in rec]
if len(set(rectypes))>1:
msg="type mismatch in variable length data: %s"%rectypes
raise ValueError(msg)
rectype=rectypes[0]
recsize=sum(lengths)*rec[0].dtype.itemsize
else:
rec=np.array(rec)
recsize=rec.nbytes
rectype=rec.dtype.str
if rec.ndim==1:
reclen=0
else:
reclen=rec.shape[1]
idx=np.array(idx)
idxtype=idx.dtype.str
self=cls(pagedir,pageid,idxtype,count,idx[0],idx[-1],
rectype,reclen,int(recsize),comp,None)
if not os.path.isdir(self.pagepath):
os.makedirs(self.pagepath)
idx.tofile(self.idxpath)
sha = hashlib.md5()
sha=hashfile(sha,self.idxpath)
if reclen==-1:
recfh=open(self.recpath,'wb')
lengths.tofile(self.lenpath)
sha=hashfile(sha,self.lenpath)
[ rrr.tofile(recfh) for rrr in rec]
recfh.close()
else:
if recsize>0:
rec.tofile(self.recpath)
if recsize>0:
sha=hashfile(sha,self.recpath)
if comp=='gzip':
os.system("gzip %s"%self.recpath)
self.checksum=sha.hexdigest()
return self
def get_all(self):
return self.get_idx_all(),self.get_rec_all()
def get_rec_all(self):
if self.recsize==0:
rec=np.array([[]]*self.count,dtype=self.rectype)
else:
if self.comp=='gzip':
os.system("gunzip %s.gz"%self.recpath)
cc=self.count
reclen=self.reclen
if reclen==-1:
lengths=np.fromfile(self.lenpath,dtype='<i8',count=cc)
recfh=open(self.recpath)
rec=[np.fromfile(recfh,dtype=self.rectype,count=cc)
for cc in lengths]
recfh.close()
if 'S' in self.rectype:
rec=[split_string(rrr.tostring()) for rrr in rec]
elif 'U' in self.rectype:
rec=[split_string_utf32(rrr.tostring()) for rrr in rec]
elif reclen==0:
rec=np.fromfile(self.recpath,dtype=self.rectype,count=cc)
else:
rec=np.fromfile(self.recpath,dtype=self.rectype,
count=cc*reclen)
if len(rec)<cc*reclen:
msg="Error in Page %s: not enough records:%d!=%d*%d"
raise IOError(msg%(self.pageid,cc*reclen,cc,reclen))
rec=rec.reshape(cc,reclen)
if len(rec)!=self.count:
msg='Error: Record mismatch in Page %d: %d read vs %d'
raise IOError(msg%(self.pageid,len(rec),self.count))
return rec
def get_idx_all(self):
cc=self.count
idx=np.fromfile(self.idxpath,dtype=self.idxtype,count=cc)
if len(idx)!=cc:
msg='Error: Index mismatch in Page %d: %d read vs %d'
raise IOError(msg%(self.pageid,len(idx),cc))
return idx
def delete(self):
os.unlink(self.recpath)
os.unlink(self.idxpath)
if self.reclen==-1:
os.unlink(self.lenpath)
def _tolist(self):
timestamp=os.path.getmtime(self.idxpath)
return [self.pageid,self.idxtype,self.count,self.idxa,self.idxb,
self.rectype,self.reclen,self.recsize,self.comp,
timestamp,self.checksum]
def get(self,idxa,idxb,skip=1):
idx,rec=self.get_all()
a=idx.searchsorted(idxa,side='left')
b=idx.searchsorted(idxb,side='right')
return idx[a:b:skip],rec[a:b:skip]
def get_idx(self,idxa,idxb,skip=1):
idx=self.get_idx_all()
a=idx.searchsorted(idxa,side='left')
b=idx.searchsorted(idxb,side='right')
return idx[a:b:skip]
def get_range(self,idxa,idxb):
a=idx.searchsorted(idxa,side='left')
b=idx.searchsorted(idxb,side='right')
return a,b
def get_count(self,idxa,idxb,skip=1):
return len(self.get_idx(idxa,idxb,skip=skip))
def get_recsize(self,idxa,idxb,skip=1):
if self.reclen>=0:
itemsize=self.recsize/self.count
return self.count(idxa,idxb,skip=skip)*itemsize
else:
a,b=self.get_range(idxa,idxb)
items=np.sum(np.fromfile(self.lenpath,
dtype='<i8',count=cc)[a:b:skip])
return items*np.dtype(self.rectype).itemsize
def check(self):
sha=hashlib.md5()
sha=hashfile(sha,self.idxpath)
if self.reclen==-1:
sha=hashfile(sha,self.lenpath)
if self.comp=='gzip':
sha=hashfile(sha,self.recpath+'.gz')
else:
sha=hashfile(sha,self.recpath)
res=sha.hexdigest()==self.checksum
if res==False:
print("Checksum failsed for page %s"%self.pageid)
return res