Let's say we have a test.zip file and we update a file:
zfh = zipfile.ZipFile("test.zip", mode = "a")
zfh.write("/home/msala/test.txt")
zfh.close()
Repeating a few times this "update", using the builtin method printdir()
I see in the archive there are stored not only the last one "test.txt" but also all the previous copies of the file.
Ok, I understand the zipfile library hasn't a delete method.
Questions:
if I call the builtin method extract("/home/msala/test.txt"),
which copy of the file is extracted and written to the file system ?
inside the zip archive, is there any flag telling that old copies .. are old copies, superseded by the last one ?
At the moment I list all the stored files and sort them by filename, last modification time...
The tl;dr is no, you can't do this without building a bit of extra info—but that can be done without sorting, and, even if you did have to sort, the performance cost would be irrelevant.
First, let me explain how zipfiles work. (Even if you understand this, later readers with the same problem may not.)
Unfortunately, the specification is a copyrighted and paywalled ISO document, so I can't link to it or quote it. The original PKZip APPNOTE.TXT which is the de facto pro-standardization standard is available, however. And numerous sites like Wikipedia have nice summaries.
A zipfile is 0 or more fragments, followed by a central directory.
Fragments are just treated as if they were all concatenated into one big file.
The body of the file can contain zip entries, in arbitrary order, along with anything you want. (This is how DOS/Windows self-extracting archives work—the unzip executable comes at the start of the first fragment.) Anything that looks like a zip entry, but isn't referenced by the central directory, is not treated as a zip entry (except when repairing a corrupted zipfile.)
Each zip entries starts with a header that gives you the filename, compression format, etc. of the following data.
The directory is a list of directory entries that contain most of the same information, plus a pointer to where to find the zip entry.
It's the order of directory entries that determines the order of the files in the archive.
if I call the builtin method extract("/home/msala/test.txt"), which copy of the file is extracted and written to the file system ?
The behavior isn't really specified anywhere.
Extracting the whole archive should extract both files, in the order present in the zip directory (the same order given by infolist), with the second one overwriting the first.
But extracting by name doesn't have to give you both—it could give you the last one, or the first, or pick one at random.
Python gives you the last. The way this works is that, when reading the directory, it builds a dict mapping filenames to ZipInfos, just adding them as encountered, so the last one will overwrite the previous ones. (Here's the 3.7 code.) Whenever you try to access something by filename, it just looks up the filename in that dict to get the ZipInfo.
But is that something you want to rely on? I'm not sure. On the one hand, this behavior has been the same from Python 1.6 to 3.7, which is usually a good sign that it's not going to change, even if it's never been documented. On the other hand, there are open issues—including #6818, which is intended to add deletion support to the library one way or another—that could change it.
And it's really not that hard to do the same thing yourself. With the added benefit that you can use a different rule—always keep the first, always keep the one with the latest mod time, etc.
You seem to be worried about the performance cost of sorting the infolist, which is probably not worth worrying about. The time it takes to read and parse the zip directory is going to make the cost of your sort virtually invisible.
But you don't really need to sort here. After all, you don't want to be able to get all of the entries with a given name in some order, you just want to get one particular entry for each name. So, you can just do what ZipFile does internally, which takes only linear time to build, and constant time each time you search it. And you can use any rule you want here.
entries = {}
for entry in zfh.infolist():
if entry.filename not in entries:
entries[entry.filename] = entries
This keeps the first entry for any name. If you want to keep the last, just remove the if. If you want to keep the latest by modtime, just change it if entry.date_time > entries[entry.filename].date_time:. And so on.
Now, instead of relying on what happens when you call extract("home/msala/test.txt"), you can call extract(entries["home/msala/test.txt"]) and know that you're getting the first/last/latest/whatever file of that name.
inside the zip archive, is there any flag telling that old copies .. are old copies, superseded by the last one ?
No, not really.
The way to delete a file is to remove it from the central directory. Which you do just by rewriting the central directory. Since it comes at the end of the zipfile, and is almost always more than small enough to fit on even the smallest floppy, this was generally considered fine even back in the DOS days.
(But notice that if you unplug the computer in the middle of it, you've got a zipfile without a central directory, which has to be rebuilt by scanning all of the file entries. So, many newer tools will instead, at least for smaller files, rewrite the whole file to a tempfile then rename it over the original, to guarantee a safe, atomic write.)
At least some early tools would sometimes, especially for gigantic archives, rewrite the entry's pathname's first byte with a NUL. But this doesn't really mark the entry as deleted, it just renames it to "\0ome/msala/test.txt". And many modern tools will in fact treat it as meaning exactly that and give you weird errors telling you they can't find a directory named 'ome' or '' or something else fun. Plus, this means the filename in the directory entry no longer matches the filename in the file entry header, which will cause many modern tools to flag the zipfile as corrupted.
At any rate, Python's zipfile module doesn't do either of these, so you'd need to subclass ZipFile to add the support yourself.
I solved this way, similar to database records management.
Adding a file to the archive, I look for previous stored copies (same filename).
For each of them, I set their field "comment" to a specific marker, for example "deleted".
We add the new file, with comment = empty.
As we like, we can "vacuum": shrink the zip archive using the usually tools (under the hood a new archive is created, discarding the files having the comment set to "deleted").
This way, we have also a simple "versioning".
We have all the previous files copies, until the vacuum.
Related
For a unit test, I need a zipfile that contains directory entries. In a pinch, I could create one manually and keep it in the repo in binary form, but I'd rather create it dynamically as part of the test setup.
Neither the zipfile module nor shutil.make_archive seems to be able to create directory entries. Is there a native-python solution?
Instinctively I would go with your approach "keep it in the repor in binary form", especially since it would be quite small and guaranteed to be identical across platforms.
For dynamically creating such a ZIP file, you probably need to go the "long way" to first the target structure on disc. For that, I would be using os.makedirs within a tempfile.TemporaryDirectory, then compressing it.
I am currently working on a script that automatically syncs files from the Documents and Picture directory with an USB stick that I use as sort of an "essentials backup". In practice, this should identify filenames and some information about them (like last time edited etc.) in the directories that I choose to sync.
If a file exists in one directory, but not in the other (i.e. it's on my computer but not on my USB drive), it should automatically copy that file to the USB as well. Likewise, if a file exists in both directories, but has different mod-times, it should replace the older with the newer one.
However, I have some issues with storing that information for the purpose of comparing those files. I initially thought about a file class, that stores all that information and through which I can compare objects with the same name.
Problem 1 with that approach is, that if I create an object, how do I name it? Do I name it like the file? I then would have to remove the file-extension like .txt or .py, because I'd run into trouble with my code. but I might have a notes.odt and a notes.jpg, which would be problem 2.
I am pretty new to Python, so my imagination is probably limited by my lack of knowledge. Any pointers on how I could make that work?
I'm trying to get the time of last modification (os.stat.st_mtime) of a particular directory. My issue is I have added a few metadata files that are hidden (they start with .). If I use os.stat(directory).st_mtime I get the date at which I updated the metadata file, not the date that a non-hidden file was modified in the directory. I would like to get the most recent time of modification for all of the other files in the directory other than the hidden metadata files.
I figure it's possible to write my own function, something along the lines of:
for file in folder:
if not file starts with '.':
modified_times.append(os.path.getmtime('/path/to/file')
last_time = most recent of modified_times
However, is it possible to do this natively in python? Or do I need to write my own function like the pseudocode above (or something like this question)?
Your desired outcome is impossible. The most recent modification time of all non-hidden files doesn't necessarily correspond to the virtual "last modified time of a directory ignoring hidden files". The problem is that directories are modified when files are moved in and out of them, but the file timestamps aren't changed (the file was moved, but not modified). So your proposed solution is at best a heuristic; you can hope it's correct, but there is no way to be sure.
In any event, no, there is no built-in that provides this heuristic. The concept of hidden vs. non-hidden files is OS and file system dependent, and Python provides no built-in API that cares about the distinction. If you want to make a "last_modified_guess" function, you'll have to write it yourself (I recommend basing it on os.scandir for efficiency).
Something as simple as:
last_time = max(entry.stat().st_mtime for entry in os.scandir(somedir) if not entry.name.startswith('.'))
would get you the most recent last modified time (in seconds since the epoch) of your non-hidden directory entries.
Update: On further reflection, the glob module does include a concept of . prefix meaning "hidden", so you could use glob.glob/glob.iglob of os.path.join(somedir, '*') to have it filter out the "hidden" files for you. That said, by doing so, you give up some of the potential benefits of os.scandir (free or cached stat results, free type checks, etc.), so if all you need is "hidden" filtering, a simple .startswith('.') check is not worth giving that up.
I'm aware of os.listdir, but as far as I can gather, that gets all the filenames in a directory into memory, and then returns the list. What I want, is a way to yield a filename, work on it, and then yield the next one, without reading them all into memory.
Is there any way to do this? I worry about the case where filenames change, new files are added, and files are deleted using such a method. Some iterators prevent you from modifying the collection during iteration, essentially by taking a snapshot of the state of the collection at the beginning, and comparing that state on each move operation. If there is an iterator capable of yielding filenames from a path, does it raise an error if there are filesystem changes (add, remove, rename files within the iterated directory) which modify the collection?
There could potentially be a few cases that could cause the iterator to fail, and it all depends on how the iterator maintains state. Using S.Lotts example:
filea.txt
fileb.txt
filec.txt
Iterator yields filea.txt. During processing, filea.txt is renamed to filey.txt and fileb.txt is renamed to filez.txt. When the iterator attempts to get the next file, if it were to use the filename filea.txt to find it's current position in order to find the next file and filea.txt is not there, what would happen? It may not be able to recover it's position in the collection. Similarly, if the iterator were to fetch fileb.txt when yielding filea.txt, it could look up the position of fileb.txt, fail, and produce an error.
If the iterator instead was able to somehow maintain an index dir.get_file(0), then maintaining positional state would not be affected, but some files could be missed, as their indexes could be moved to an index 'behind' the iterator.
This is all theoretical of course, since there appears to be no built-in (python) way of iterating over the files in a directory. There are some great answers below, however, that solve the problem by using queues and notifications.
Edit:
The OS of concern is Redhat. My use case is this:
Process A is continuously writing files to a storage location.
Process B (the one I'm writing), will be iterating over these files, doing some processing based on the filename, and moving the files to another location.
Edit:
Definition of valid:
Adjective
1. Well grounded or justifiable, pertinent.
(Sorry S.Lott, I couldn't resist).
I've edited the paragraph in question above.
tl;dr <update>: As of Python 3.5 (currently in beta) just use os.scandir
</update>
As I've written earlier, since "iglob" is just a facade for a real iterator, you will have to call low level system functions in order to get one at a time like you want. Fortunately, calling low level functions is doable from Python.
The low level functions are different for Windows and Posix/Linux systems.
If you are on Windows, you should check if win32api has any call to read "the next entry from a dir" or how to proceed otherwise.
If you are on Posix/Linux, you can proceed to call libc functions straight through ctypes and get a file-dir entry (including naming information) a time.
The documentation on the C functions is here:
http://www.gnu.org/s/libc/manual/html_node/Opening-a-Directory.html#Opening-a-Directory
http://www.gnu.org/s/libc/manual/html_node/Reading_002fClosing-Directory.html#Reading_002fClosing-Directory
I have provided a snippet of Python code that demonstrates how to call the low-level C functions on my system but this code snippet may not work on your system[footnote-1]. I recommend opening your /usr/include/dirent.h header file and verifying the Python snippet is correct (your Python Structure must match the C struct) before using the snippet.
Here is the snippet using ctypes and libc I've put together that allow you to get each filename, and perform actions on it. Note that ctypes automatically gives you a Python string when you do str(...) on the char array defined on the structure. (I am using the print statement, which implicitly calls Python's str)
#!/usr/bin/env python2
from ctypes import *
libc = cdll.LoadLibrary( "libc.so.6")
dir_ = c_voidp( libc.opendir("/home/jsbueno"))
class Dirent(Structure):
_fields_ = [("d_ino", c_voidp),
("off_t", c_int64),
("d_reclen", c_ushort),
("d_type", c_ubyte),
("d_name", c_char * 2048)
]
while True:
p = libc.readdir64(dir_)
if not p:
break
entry = Dirent.from_address( p)
print entry.d_name
update: Python 3.5 is now in beta - and in Python 3.5 the new os.scandir function call is available as the materialization of PEP 471 ("a better and faster directory iterator") which does exactly what is asked for here, besides a lot other optimizations that can deliver up to 9 fold speed increase over os.listdir on large-directories listing under Windows (2-3 fold increase in Posix systems).
[footnote-1] The dirent64 C struct is determined at C compile time for each system.
The glob module Python from 2.5 onwards has an iglob method which returns an iterator.
An iterator is exactly for the purposes of not storing huge values in memory.
glob.iglob(pathname)
Return an iterator which yields the same values as glob() without
actually storing them all simultaneously.
For example:
import glob
for eachfile in glob.iglob('*'):
# act upon eachfile
Since you are using Linux, you might want to look at pyinotify.
It would allow you to write a Python script which monitors a directory for filesystem changes -- such as the creation, modification or deletion of files.
Every time such a filesystem event occurs, you can arrange for the Python script to call a function. This would be roughly like yielding each filename once, while being able to react to modifications and deletions.
It sounds like you already have a million files sitting in a directory. In this case, if you were to move all those files to a new, pyinotify-monitored directory, then the filesystem events generated by the creation of new files would yield the filenames as desired.
#jsbueno's post is really useful, but is still kind of slow on slow disks since libc readdir() only ready 32K of disk entries at a time. I am not an expert on making system calls directly in python, but I outlined how to write code in C that will list a directory with millions of files, in a blog post at: http://www.olark.com/spw/2011/08/you-can-list-a-directory-with-8-million-files-but-not-with-ls/.
The ideal case would be to call getdents() directly in python (http://www.kernel.org/doc/man-pages/online/pages/man2/getdents.2.html) so you can specify a read buffer size when loading directory entries from disk.
Rather than calling readdir() which as far as I can tell has a buffer size defined at compile time.
What I want, is a way to yield a filename, work on it, and then yield the next one, without reading them all into memory.
No method will reveal a filename which "changed". It's not even clear what you mean by this "filenames change, new files are added, and files are deleted"? What is your use case?
Let's say you have three files: a.a, b.b, c.c.
Your magical "iterator" starts with a.a. You process it.
The magical "iterator" moves to b.b. You're processing it.
Meanwhile a.a is copied to a1.a1, a.a is deleted. What now? What does your magical iterator do with these? It's already passed a.a. Since a1.a1 is before b.b, it will never see it. What's supposed to happen for "filenames change, new files are added, and files are deleted"?
The magical "iterator" moves to c.c. What was supposed to happen to the other files? And how were you supposed to find out about the deletion?
Process A is continuously writing files to a storage location. Process B (the one I'm writing), will be iterating over these files, doing some processing based on the filename, and moving the files to another location.
Don't use the naked file system for coordination.
Use a queue.
Process A writes files and enqueues the add/change/delete memento onto a queue.
Process B reads the memento from queue and then does the follow-on processing on the file named in the memento.
I think what you are asking is impossible due to the nature of file IO. Once python has retrieved the listing of a directory it cannot maintain a view of the actual directory on disk, nor is there any way for python to insist that the OS inform it of any modifications to the directory.
All python can do is ask for periodic listings and diff the results to see if there have been any changes.
The best you can do is create a semaphore file in the directory which lets other processes know that your python process desires that no other process modify the directory. Of course they will only observe the semaphore if you have explicitly programmed them to.
I'm aware of os.listdir, but as far as I can gather, that gets all the filenames in a directory into memory, and then returns the list. What I want, is a way to yield a filename, work on it, and then yield the next one, without reading them all into memory.
Is there any way to do this? I worry about the case where filenames change, new files are added, and files are deleted using such a method. Some iterators prevent you from modifying the collection during iteration, essentially by taking a snapshot of the state of the collection at the beginning, and comparing that state on each move operation. If there is an iterator capable of yielding filenames from a path, does it raise an error if there are filesystem changes (add, remove, rename files within the iterated directory) which modify the collection?
There could potentially be a few cases that could cause the iterator to fail, and it all depends on how the iterator maintains state. Using S.Lotts example:
filea.txt
fileb.txt
filec.txt
Iterator yields filea.txt. During processing, filea.txt is renamed to filey.txt and fileb.txt is renamed to filez.txt. When the iterator attempts to get the next file, if it were to use the filename filea.txt to find it's current position in order to find the next file and filea.txt is not there, what would happen? It may not be able to recover it's position in the collection. Similarly, if the iterator were to fetch fileb.txt when yielding filea.txt, it could look up the position of fileb.txt, fail, and produce an error.
If the iterator instead was able to somehow maintain an index dir.get_file(0), then maintaining positional state would not be affected, but some files could be missed, as their indexes could be moved to an index 'behind' the iterator.
This is all theoretical of course, since there appears to be no built-in (python) way of iterating over the files in a directory. There are some great answers below, however, that solve the problem by using queues and notifications.
Edit:
The OS of concern is Redhat. My use case is this:
Process A is continuously writing files to a storage location.
Process B (the one I'm writing), will be iterating over these files, doing some processing based on the filename, and moving the files to another location.
Edit:
Definition of valid:
Adjective
1. Well grounded or justifiable, pertinent.
(Sorry S.Lott, I couldn't resist).
I've edited the paragraph in question above.
tl;dr <update>: As of Python 3.5 (currently in beta) just use os.scandir
</update>
As I've written earlier, since "iglob" is just a facade for a real iterator, you will have to call low level system functions in order to get one at a time like you want. Fortunately, calling low level functions is doable from Python.
The low level functions are different for Windows and Posix/Linux systems.
If you are on Windows, you should check if win32api has any call to read "the next entry from a dir" or how to proceed otherwise.
If you are on Posix/Linux, you can proceed to call libc functions straight through ctypes and get a file-dir entry (including naming information) a time.
The documentation on the C functions is here:
http://www.gnu.org/s/libc/manual/html_node/Opening-a-Directory.html#Opening-a-Directory
http://www.gnu.org/s/libc/manual/html_node/Reading_002fClosing-Directory.html#Reading_002fClosing-Directory
I have provided a snippet of Python code that demonstrates how to call the low-level C functions on my system but this code snippet may not work on your system[footnote-1]. I recommend opening your /usr/include/dirent.h header file and verifying the Python snippet is correct (your Python Structure must match the C struct) before using the snippet.
Here is the snippet using ctypes and libc I've put together that allow you to get each filename, and perform actions on it. Note that ctypes automatically gives you a Python string when you do str(...) on the char array defined on the structure. (I am using the print statement, which implicitly calls Python's str)
#!/usr/bin/env python2
from ctypes import *
libc = cdll.LoadLibrary( "libc.so.6")
dir_ = c_voidp( libc.opendir("/home/jsbueno"))
class Dirent(Structure):
_fields_ = [("d_ino", c_voidp),
("off_t", c_int64),
("d_reclen", c_ushort),
("d_type", c_ubyte),
("d_name", c_char * 2048)
]
while True:
p = libc.readdir64(dir_)
if not p:
break
entry = Dirent.from_address( p)
print entry.d_name
update: Python 3.5 is now in beta - and in Python 3.5 the new os.scandir function call is available as the materialization of PEP 471 ("a better and faster directory iterator") which does exactly what is asked for here, besides a lot other optimizations that can deliver up to 9 fold speed increase over os.listdir on large-directories listing under Windows (2-3 fold increase in Posix systems).
[footnote-1] The dirent64 C struct is determined at C compile time for each system.
The glob module Python from 2.5 onwards has an iglob method which returns an iterator.
An iterator is exactly for the purposes of not storing huge values in memory.
glob.iglob(pathname)
Return an iterator which yields the same values as glob() without
actually storing them all simultaneously.
For example:
import glob
for eachfile in glob.iglob('*'):
# act upon eachfile
Since you are using Linux, you might want to look at pyinotify.
It would allow you to write a Python script which monitors a directory for filesystem changes -- such as the creation, modification or deletion of files.
Every time such a filesystem event occurs, you can arrange for the Python script to call a function. This would be roughly like yielding each filename once, while being able to react to modifications and deletions.
It sounds like you already have a million files sitting in a directory. In this case, if you were to move all those files to a new, pyinotify-monitored directory, then the filesystem events generated by the creation of new files would yield the filenames as desired.
#jsbueno's post is really useful, but is still kind of slow on slow disks since libc readdir() only ready 32K of disk entries at a time. I am not an expert on making system calls directly in python, but I outlined how to write code in C that will list a directory with millions of files, in a blog post at: http://www.olark.com/spw/2011/08/you-can-list-a-directory-with-8-million-files-but-not-with-ls/.
The ideal case would be to call getdents() directly in python (http://www.kernel.org/doc/man-pages/online/pages/man2/getdents.2.html) so you can specify a read buffer size when loading directory entries from disk.
Rather than calling readdir() which as far as I can tell has a buffer size defined at compile time.
What I want, is a way to yield a filename, work on it, and then yield the next one, without reading them all into memory.
No method will reveal a filename which "changed". It's not even clear what you mean by this "filenames change, new files are added, and files are deleted"? What is your use case?
Let's say you have three files: a.a, b.b, c.c.
Your magical "iterator" starts with a.a. You process it.
The magical "iterator" moves to b.b. You're processing it.
Meanwhile a.a is copied to a1.a1, a.a is deleted. What now? What does your magical iterator do with these? It's already passed a.a. Since a1.a1 is before b.b, it will never see it. What's supposed to happen for "filenames change, new files are added, and files are deleted"?
The magical "iterator" moves to c.c. What was supposed to happen to the other files? And how were you supposed to find out about the deletion?
Process A is continuously writing files to a storage location. Process B (the one I'm writing), will be iterating over these files, doing some processing based on the filename, and moving the files to another location.
Don't use the naked file system for coordination.
Use a queue.
Process A writes files and enqueues the add/change/delete memento onto a queue.
Process B reads the memento from queue and then does the follow-on processing on the file named in the memento.
I think what you are asking is impossible due to the nature of file IO. Once python has retrieved the listing of a directory it cannot maintain a view of the actual directory on disk, nor is there any way for python to insist that the OS inform it of any modifications to the directory.
All python can do is ask for periodic listings and diff the results to see if there have been any changes.
The best you can do is create a semaphore file in the directory which lets other processes know that your python process desires that no other process modify the directory. Of course they will only observe the semaphore if you have explicitly programmed them to.