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pagestore.py
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pagestore.py
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import os
import sys
import shutil
import tempfile
import sqlite3
import numpy as np
from .page import Page
def isstr(s):
return isinstance(s, str)
def merge(idx0, rec0, idx1, rec1):
sel = {}
val = [rec0, rec1]
for ii, iv in enumerate(idx0):
sel[iv] = (0, ii)
for ii, iv in enumerate(idx1):
sel[iv] = (1, ii)
idx = []
rec = []
for sv, (ir, ii) in sorted(sel.items()):
idx.append(sv)
rec.append(val[ir][ii])
return idx, rec
def concatenate(val):
try:
return np.concatenate(val)
except ValueError:
out = []
for vv in val:
out.extend(vv)
return out
_suffixes = ["bytes", "KiB", "MiB", "GiB", "TiB", "EiB", "ZiB"]
def human_readable(size, suffixes=" kMGTEZ"):
order = int(np.log10(size) / 3) if size else 0
return (
"%.4g%s" % (size / (10.0 ** (order * 3)), suffixes[order])
).rstrip()
class PageStore(object):
def __repr__(self):
fmt = "PageStore(%r,pagedir=%r,maxpagesize=%r)"
return fmt % (self.dbname, self.pagedir, self.maxpagesize)
def __init__(
self,
dbname,
pagedir,
maxpagesize=None,
checksum=False,
keep_deleted_pages=False,
readonly=False,
):
try:
if dbname.startswith("file:"):
if readonly:
dbname += "?mode=ro"
self.db = sqlite3.connect(
dbname, isolation_level="IMMEDIATE", uri=True
)
else:
if readonly:
tmp = tempfile.mktemp()
shutil.copy2(dbname, tmp)
dbname = tmp
self.db = sqlite3.connect(dbname, isolation_level="IMMEDIATE")
except sqlite3.Error as e:
print(e.msg)
print("Error creating database %s" % dbname)
sys.exit(1)
self.dbname = dbname
self.create_db()
self.set_pagedir(pagedir)
self.set_var("maxpagesize", maxpagesize, 2 ** 24)
self.checksum = checksum
self.keep_deleted_pages = keep_deleted_pages
def create_db(self):
sql = """
CREATE TABLE IF NOT EXISTS pages(
name STRING,
pageid INTEGER,
idxtype STRING,
count INTEGER,
idxa NUMERIC,
idxb NUMERIC,
rectype STRING,
reclen INTEGER,
recsize INTEGER,
comp STRING,
created NUMERIC,
checksum STRING,
deleted NUMERIC);
CREATE INDEX IF NOT EXISTS page_index ON pages(pageid);
CREATE TABLE IF NOT EXISTS conf(
variable STRING,
value STRING,
timestamp STRING);"""
self.db.executescript(sql)
self.db.commit()
return self
def set_var(self, name, value, default=None):
if value is None:
value = self.get_var(name)
if value is None:
value = default
setattr(self, name, value)
return value
def store_var(self, name, value):
cur = self.db.cursor()
sql = "INSERT INTO conf VALUES (?,?,datetime('now'))"
cur.execute(sql, (name, value))
self.db.commit()
def set_pagedir(self, dirpath):
if dirpath is None:
dirpath = self.get_var("pagedir", "data")
if not os.path.isdir(dirpath):
os.mkdir(dirpath)
dirpath = os.path.abspath(dirpath)
self.set_var("pagedir", dirpath)
def get_var(self, name, default=None):
cur = self.db.cursor()
sql = """SELECT value FROM conf
WHERE variable=? ORDER BY timestamp DESC LIMIT 1"""
ret = cur.execute(sql, (name,)).fetchone()
if ret:
return ret[0]
else:
return default
def get_vars(self):
cur = self.db.cursor()
sql = """SELECT * FROM conf
ORDER BY variable,timestamp"""
ret = list(cur.execute(sql))
return ret
def get_last_pageid(self):
cur = self.db.cursor()
lastid = cur.execute("SELECT MAX(pageid) FROM pages").fetchone()[0]
if lastid is None:
return 0
return lastid
def delete(self):
if os.path.exists(self.pagedir):
shutil.rmtree(self.pagedir)
os.unlink(self.dbname)
def store_page(self, variable, idx, rec, commit=True):
# print("Store page %s"%variable)
pageid = self.get_last_pageid() + 1
page = Page.from_data(idx, rec, self.pagedir, pageid)
sql = """INSERT INTO pages VALUES
(?,?,?,?,?,?,?,?,?,?,?,?,?)"""
self.db.execute(sql, [variable] + page._tolist() + [None])
if commit:
self.db.commit()
def get_pages(self, variable, idxa=None, idxb=None):
cur = self.db.cursor()
idxa, idxb = self.get_lim(variable, idxa, idxb)
sql = """SELECT pageid,idxtype,count,idxa,idxb,
rectype,reclen,recsize,comp,checksum
FROM pages WHERE name==? AND idxb>=? AND idxa<=?
AND deleted IS NULL
ORDER BY idxa"""
pages = list(cur.execute(sql, [variable, idxa, idxb]))
return pages
def get(self, variables, idxa=None, idxb=None):
data = {}
if isstr(variables):
varlist = self.search(variables)
elif isinstance(variables, (list, tuple)):
varlist = variables
for variable in varlist:
data[variable] = self.get_variable(variable, idxa=idxa, idxb=idxb)
return data
def get_variable(self, variable, idxa=None, idxb=None):
idxa, idxb = self.get_lim(variable, idxa, idxb)
pages = self.get_pages(variable, idxa, idxb)
if len(pages) > 0:
page = Page(self.pagedir, *pages[0], check=True)
out = [page.get(idxa, idxb)]
for res in pages[1:-1]:
page = Page(self.pagedir, *res, check=True)
out.append(page.get_all())
if len(pages) > 1:
page = Page(self.pagedir, *pages[-1], check=True)
out.append(page.get(idxa, idxb))
idx, rec = zip(*out)
idx = concatenate(idx)
rec = concatenate(rec)
else:
idx = np.array([])
rec = np.array([])
return idx, rec
def get_idx(self, variable, idxa=None, idxb=None):
idxa, idxb = self.get_lim(variable, idxa, idxb)
pages = self.get_pages(variable, idxa, idxb)
page = Page(self.pagedir, *pages[0])
out = [page.get_idx(idxa, idxb)]
for res in pages[1:-1]:
page = Page(self.pagedir, *res)
out.append(page.get_idx_all())
if len(pages) > 1:
page = Page(self.pagedir, *pages[-1])
out.append(page.get_idx(idxa, idxb))
return concatenate(out)
def count(self, variable, idxa=None, idxb=None):
idxa, idxb = self.get_lim(variable, idxa, idxb)
pages = self.get_pages(variable, idxa, idxb)
if len(pages) > 0:
page = Page(self.pagedir, *pages[0])
tot = page.get_count(idxa, idxb)
for res in pages[1:-1]:
tot += res[2] # to change when using named_tupled
if len(pages) > 1:
page = Page(self.pagedir, *pages[-1])
tot += page.get_count(idxa, idxb)
return tot
else:
return 0
def get_page(self, pageid):
cur = self.db.cursor()
sql = """SELECT pageid,idxtype,count,idxa,idxb,
rectype,reclen,recsize,comp,checksum
FROM pages WHERE pageid=?"""
page = cur.execute(sql, [pageid]).fetchone()
return Page(self.pagedir, *page)
def delete_page(self, page):
cur = self.db.cursor()
if self.keep_deleted_pages:
sql = """UPDATE pages SET deleted=strftime('%s','now')
WHERE pageid==?"""
else:
sql = """DELETE FROM pages WHERE pageid==?"""
# print("Delete page %s"%page.pageid)
cur.execute(sql, [page.pageid])
self.db.commit()
if self.keep_deleted_pages is False:
page.delete()
def delete_variable(self, variable):
for page in self.get_pages(variable):
page = Page(self.pagedir, *page)
self.delete_page(page)
def store(self, data):
for variable, (idx, rec) in data.items():
self.store_variable(variable, idx, rec)
def store_variable(self, variable, idx, rec):
count = len(idx)
idx = np.array(idx)
if count > 0:
if len(rec) != count:
msg = "idx,rec length mismatch %d!=%d" % (len(idx), len(rec))
raise ValueError(msg)
idxa = idx[0]
idxb = idx[-1]
pages = self.get_pages(variable, idxa, idxb)
pages = [Page(self.pagedir, *res) for res in pages]
for page in pages:
if len(idx) > 0:
# if idx[0]<page.idxa:
# cut=idx.searchsorted(page.idxa)
# # self.merge_page(variable,page,idx[:cut],rec[:cut])
# self.store_page(variable,idx[:cut],rec[:cut])
# idx=idx[cut:];rec=rec[cut:]
if idx[0] <= page.idxb:
cut = idx.searchsorted(page.idxb, side="right")
self.merge_page(variable, page, idx[:cut], rec[:cut])
idx = idx[cut:]
rec = rec[cut:]
if len(idx) > 0:
self.store_page(variable, idx, rec)
if self.maxpagesize > 0:
self.rebalance(variable, self.maxpagesize)
def merge_page(self, variable, page, idx, rec):
pidx, prec = page.get_all()
nidx, nrec = merge(pidx, prec, idx, rec)
self.store_page(variable, nidx, nrec, commit=False)
self.delete_page(page)
def search(self, searchexp="%"):
cur = self.db.cursor()
sql = """SELECT DISTINCT name FROM pages WHERE name LIKE ?"""
res = cur.execute(sql, [str(searchexp)]).fetchall()
return [rr[0] for rr in res]
def get_lim(self, variable, idxa=None, idxb=None):
cur = self.db.cursor()
if idxa is None:
sql = """SELECT MIN(idxa) FROM PAGES WHERE name==?"""
idxa = cur.execute(sql, [variable]).fetchone()[0]
if idxb is None:
sql = """SELECT MAX(idxb) FROM PAGES WHERE name==?"""
idxb = cur.execute(sql, [variable]).fetchone()[0]
return idxa, idxb
def rebalance(self, variables, maxpagesize):
for variable in self.search(variables):
self.rebalance_variable(variable, maxpagesize)
def rebalance_variable(self, variable, maxpagesize):
print("Rebalance %s" % variable)
acc = 0
tomerge = []
for pagedata in self.get_pages(variable):
page = Page(self.pagedir, *pagedata)
if acc != 0 or page.recsize < maxpagesize / 2:
acc += page.recsize
tomerge.append(page)
if acc > maxpagesize:
self.merge_pages(variable, tomerge)
acc = 0
tomerge = []
if len(tomerge) > 1:
self.merge_pages(variable, tomerge)
return self
def get_info(self, variable=None):
cur = self.db.cursor()
suf = "FROM pages"
if variable is not None:
suf += ' WHERE name=="%s"' % variable
out = ""
else:
nvars = cur.execute(
"SELECT COUNT(DISTINCT name) FROM pages"
).fetchone()[0]
out = "%s variables, " % (human_readable(nvars))
npages = cur.execute("SELECT COUNT(*)" + suf).fetchone()[0]
nrecords = cur.execute("SELECT SUM(count)" + suf).fetchone()[0]
nsize = cur.execute("SELECT SUM(recsize)" + suf).fetchone()[0]
asize = cur.execute("SELECT AVG(recsize)" + suf).fetchone()[0]
if npages > 0:
data = tuple(map(human_readable, (npages, nrecords, nsize, asize)))
out += "%s pages, %s records, %sB total, %sB/page" % data
return out
def merge_pages(self, variable, pages):
print("Merging %d pages" % len(pages))
out = [page.get_all() for page in pages]
idxlist, reclist = zip(*out)
self.store_page(variable, concatenate(idxlist), concatenate(reclist))
for page in pages:
self.delete_page(page)
def split_pages(self, variable, maxsize):
for pagedata in self.get_pages(variable):
page = Page(self.pagedir, *pagedata)
if page.recsize > maxsize:
chunks = int(page.recsize / maxsize)
step = int(page.count / chunks)
print("Splitting in %d pages" % chunks)
for i in range(0, page.count, step):
idx, rec = page.get_all()
self.store_page(
variable, idx[i : i + step], rec[i : i + step]
)
self.delete_page(page)
def prune_delete_pages(self, timestamp=None):
cur = self.db.cursor()
if timestamp is None:
timestamp = "now"
sql = """SELECT pageid,idxtype,count,idxa,idxb,
rectype,reclen,recsize,comp,checksum
FROM pages WHERE
deleted < strftime('%s',?)
"""
pages = list(cur.execute(sql, [timestamp]))
for pagedata in pages:
page = Page(self.pagedir, *pagedata)
self.delete_page(page)