Totally rewrote recovery script to use an entirely different approach

based on:

  - transaction iteration/copy

  - scanning for transactions after bad data

This should allow recovery of data when:

  - only data records are damaged and when

  - multiple parts of a file are damaged

The interface has changed to not modify in place.

Other features:

  - Progress indicator

  - Verbose output

  - optional packing

  - index creation

src/ZODB/fsrecover.py

@@ -82,13 +82,320 @@
 # attributions are listed in the accompanying credits file.
 # 
 ##############################################################################
+
+
 """Simple script for repairing damaged FileStorage files.
+
+Usage: %s [-f] input output
+
+Recover data from a FileStorage data file, skipping over damaged
+data. Any damaged data will be lost. This could lead to useless output
+of critical data were lost.
+
+Options:
+
+    -f
+       Force output to putput file even if it exists
+
+    -v level
+
+       Set the verbosity level:
+
+         0 -- Show progress indicator (default)
+
+         1 -- Show transaction times and sizes
+
+         2 -- Show transaction times and sizes, and
+              show object (record) ids, versions, and sizes.
+
+    -p
+
+       Copy partial transactions. If a data record in the middle of a
+       transaction is bad, the data up to the bad data are packed. The
+       output record is marked as packed. If this option is not used,
+       transaction with any bad data are skipped.
+
+    -P t
+
+       Pack data to t seconds in the past. Note that is the "-p"
+       option is used, then t should be 0.
+
+    
+Important note: The ZODB package must be imporable.  You may need
+                to adjust the Python path accordingly.
+
 """
 
-import sys
+# Algorithm:
+# 
+#     position to start of input
+#     while 1:
+#         if end of file: break
+#          try: copy_transaction
+#          except:
+#                 scan for transaction
+#                 continue
+
+import sys, os
+
+if __name__ == '__main__' and len(sys.argv) < 3:
+    print __doc__ % sys.argv[0]
+
+def die(mess=''):
+    if not mess: mess="%s: %s" % sys.exc_info()[:2]
+    print mess+'\n'
+    sys.exit(1)
+
+try: import ZODB
+except ImportError:
+    if os.path.exists('ZODB'): sys.path.append('.')
+    elif os.path.exists('FileStorage.py'):  sys.path.append('..')
+    import ZODB
+
+            
+import getopt, ZODB.FileStorage, struct, time
+from struct import unpack
+from ZODB.utils import t32, p64, U64
+from ZODB.TimeStamp import TimeStamp
+from cPickle import loads
+from ZODB.FileStorage import RecordIterator
+
+class EOF(Exception): pass
+class ErrorFound(Exception): pass
+
+def error(mess, *args):
+    raise ErrorFound(mess % args)
+
+def read_transaction_header(file, pos, file_size):
+    # Read the transaction record
+    seek=file.seek
+    read=file.read
+
+    seek(pos)
+    h=read(23)
+    if len(h) < 23: raise EOF
+
+    tid, stl, status, ul, dl, el = unpack(">8s8scHHH",h)
+    if el < 0: el=t32-el
+
+    tl=U64(stl)
+
+    if status=='c': raise EOF
+
+    if pos+(tl+8) > file_size:
+        error("bad transaction length at %s", pos)
+
+    if status not in ' up':
+        error('invalid status, %s, at %s', status, pos)
+
+    if tl < (23+ul+dl+el):
+        error('invalid transaction length, %s, at %s', tl, pos)
+
+    tpos=pos
+    tend=tpos+tl
+
+    if status=='u':
+        # Undone transaction, skip it
+        seek(tend)
+        h=read(8)
+        if h != stl: error('inconsistent transaction length at %s', pos)
+        pos=tend+8
+        return pos, None
+
+    pos=tpos+(23+ul+dl+el)
+    user=read(ul)
+    description=read(dl)
+    if el:
+        try: e=loads(read(el))
+        except: e={}
+    else: e={}
+
+    result=RecordIterator(
+        tid, status, user, description, e,
+        pos, (tend, file, seek, read,
+              tpos,
+              )
+        )
+
+    pos=tend
+
+    # Read the (intentionally redundant) transaction length
+    seek(pos)
+    h=read(8)
+    if h != stl:
+        error("redundant transaction length check failed at %s", pos)
+    pos=pos+8
+
+    return pos, result
+
+def scan(file, pos, file_size):
+    seek=file.seek
+    read=file.read
+    while 1:
+        seek(pos)
+        data=read(8096)
+        if not data: return 0
+
+        s=0
+        while 1:
+            l=data.find('.', s)
+            if l < 0:
+                pos=pos+8096
+                break
+            if l > 8080:
+                pos = pos + l
+                break
+            s=l+1
+            tl=U64(data[s:s+8])
+            if tl < pos:
+                return pos + s + 8
+
+def iprogress(i):
+    if i%2: print '.',
+    else: print (i/2)%10,
+    sys.stdout.flush()
+
+def progress(p):
+    for i in range(p): iprogress(i) 
+
+def recover(argv=sys.argv):
+
+    try:
+        opts, (inp, outp) = getopt.getopt(argv[1:], 'fv:pP:')
+        force = partial = verbose = 0
+        pack = None
+        for opt, v in opts:
+            if opt == '-v': verbose = int(v)
+            elif opt == '-p': partial=1
+            elif opt == '-f': force=1
+            elif opt == '-P': pack=time.time()-float(v)
+
+        
+        force = filter(lambda opt: opt[0]=='-f', opts)
+        partial = filter(lambda opt: opt[0]=='-p', opts)
+        verbose = filter(lambda opt: opt[0]=='-v', opts)
+        verbose = verbose and int(verbose[0][1]) or 0
+        print 'Recovering', inp, 'into', outp
+    except:
+        die()
+        print __doc__ % argv[0]
+        
+
+    if os.path.exists(outp) and not force:
+        die("%s exists" % outp)
+
+    file=open(inp, "rb")
+    seek=file.seek
+    read=file.read
+    if read(4) != ZODB.FileStorage.packed_version:
+        die("input is not a file storage")
+
+    seek(0,2)
+    file_size=file.tell()
+
+    ofs=ZODB.FileStorage.FileStorage(outp, create=1)
+    _ts=None
+    ok=1
+    prog1=0
+    preindex={}; preget=preindex.get   # waaaa
+    undone=0
+
+    pos=4
+    while pos:
+
+        try:
+            npos, transaction = read_transaction_header(file, pos, file_size)
+        except EOF:
+            break
+        except:
+            print "\n%s: %s\n" % sys.exc_info()[:2]
+            if not verbose: progress(prog1)
+            pos = scan(file, pos, file_size)
+            continue
+
+        if transaction is None:
+            undone = undone + npos - pos
+            pos=npos
+            continue
+        else:
+            pos=npos
+
+        tid=transaction.tid
+
+        if _ts is None:
+            _ts=TimeStamp(tid)
+        else:
+            t=TimeStamp(tid)
+            if t <= _ts:
+                if ok: print ('Time stamps out of order %s, %s' % (_ts, t))
+                ok=0
+                _ts=t.laterThan(_ts)
+                tid=`_ts`
+            else:
+                _ts = t
+                if not ok:
+                    print ('Time stamps back in order %s' % (t))
+                    ok=1
+
+        if verbose:
+            print 'begin', 
+            if verbose > 1: print
+            sys.stdout.flush()
+
+        ofs.tpc_begin(transaction, tid, transaction.status)
+
+        if verbose:
+            print 'begin', pos, _ts,
+            if verbose > 1: print
+            sys.stdout.flush()
+
+        nrec=0
+        try:
+            for r in transaction:
+                oid=r.oid
+                if verbose > 1: print U64(oid), r.version, len(r.data)
+                pre=preget(oid, None)
+                s=ofs.store(oid, pre, r.data, r.version, transaction)
+                preindex[oid]=s
+                nrec=nrec+1
+        except:
+            if partial and nrec:
+                ofs._status='p'
+                ofs.tpc_vote(transaction)
+                ofs.tpc_finish(transaction)
+                if verbose: print 'partial'
+            else:
+                ofs.tpc_abort(transaction)
+            print "\n%s: %s\n" % sys.exc_info()[:2]
+            if not verbose: progress(prog1)
+            pos = scan(file, pos, file_size)
+        else:
+            ofs.tpc_vote(transaction)
+            ofs.tpc_finish(transaction)
+            if verbose:
+                print 'finish'
+                sys.stdout.flush()
+
+        if not verbose:
+            prog = pos * 20l / file_size
+            while prog > prog1:
+                prog1 = prog1 + 1
+                iprogress(prog1)
+
+
+    bad = file_size - undone - ofs._pos
+
+    print "\n%s bytes removed during recovery" % bad
+    if undone:
+        print "%s bytes of undone transaction data were skipped" % undone
+    
+    if pack is not None:
+        print "Packing ..."
+        from ZODB.referencesf import referencesf
+        ofs.pack(pack, referencesf)
+
+    ofs.close()
                 
-sys.path.append('.')
 
-import FileStorage
+if __name__=='__main__': recover()
 
-FileStorage.recover(sys.argv[1])