What kind of password hash/encryption is this? - sql

Trying to find out what kind of hash/encryption this is in a SQL db. We want to create an app to do password resets but I cannot for the life of me find how they are generating this value.
Here are multiple examples
{enc:1}gdyb21LQTcIANtvYMT7QVQ==
{enc:1}ZEImYhrd/Ot/LcewJCFdMw==
{enc:1}+IOSBzegAx7nSytO1J3GEw==
{enc:1}6ULa1IFMxavY7SE66K3UDg==
{enc:1}UEFeGim2M8d0Iee7ejFRUw==
{enc:1}RjqL5rXOBpqJAKPjYkwLtw==
{enc:1}V/PEslecyYxFki03H4ctAQ==
{enc:1}VDEm9QmD+L7tsqcPz/S9XQ==
{enc:1}YkQuEPpL6dRfDLwKMEVMMg==
{enc:1}86rG96EP7T3tx9e8C7513g==
{enc:1}xvSwvsmkgwtXwVISvg7mJQ==
{enc:1}KjCF0RD4tcUGEP4Bpafw5A==
{enc:1}z9pGrdm4QAoomrFCJCXQIQ==
{enc:1}yhLv0HeW90FENKJjV9Nb+g==
{enc:1}EtYMl5FOW+zdpVvWsIj3Rw==

Let's take it apart:
{enc:1}gdyb21LQTcIANtvYMT7QVQ==
The {enc:1} part is likely to be versioning of some form. This is reasonably common so that you can upgrade whatever hashing/encryption algorithm you use over time. Each value identifies the algorithm used to produce the hash - if the implementation decides to use a different approach, it would know to validate a password using the first version, but could then replace the {enc:1} with {enc:2} or whatever, along with the new form of the hash.
The rest is base64 - and it's 24 characters ending in ==, which means the original value is 16 bytes.
So it's a 16 byte (128 bit) hash of some kind, with a versioning prefix. That's pretty much all we can tell... it could be any 128 bit hash, or possibly 128 bits of a longer hash (although you'd have to wonder why they threw away data at that point).
You could perform further tests if you can create your own users with passwords. For example, do two users with the same password end up with the same hash? If not, if you change from password X to password Y and then back to password X for a single user, does that get to the same hash? (There's no obvious salt in the value, although the username could be used as the salt.)

Related

Is 128-bit md5 do full mapping for 128-bit binary set?

I'm writing a utility to convert md5 (or sha1) digest to a distinguishable image, something like ssh-keygen -lv. Usually, similar messages can have digests very different, but hackers can modify the message bit by bit to try to get a similar but still different md5 digest to mock the original one. When matching is done by machine, the trick will certainly fail. But when matching is done by human eye, user could be fooled.
To avoid of such trick, the convert program can generate the image from a modified digest as follow:
image = generateImage( md5(md5 + Random_Secret) )
The Random_Secret will reshape the digest, the similarity introduced by hacker will be removed after the transformation.
Now comes the question, since the final md5() take input of another md5 variable, which is only 128-bit length, (here ignore the Random_Secret which is a constant in all) is it safe to generate enough different values for feeding generateImage()?
Question also for other digest algorithms: sha1, etc.
A hash function should have the following properties, among others:
In cryptography, the avalanche effect is the desirable property of cryptographic algorithms, typically block ciphers and cryptographic hash functions, wherein if an input is changed slightly (for example, flipping a single bit), the output changes significantly (e.g., half the output bits flip).
see https://en.wikipedia.org/wiki/Avalanche_effect
Thus, hackers should not be able to slightly modify the message to obtain a similar digest unless the hash function is broken. Also it should not be possible to create a message that results in a specific hash value (so it should resist preimage attacks, see https://en.wikipedia.org/wiki/Preimage_attack).
md5 is cryptographically broken
So would the use of a simple md5 hash already be sufficient?
No. Although md5 is a widely used hash function, it has the problem that it is cryptographically broken and therefore insecure.
One basic requirement of any cryptographic hash function is that it should be computationally infeasible to find two distinct messages that hash to the same value. MD5 fails this requirement catastrophically; such collisions can be found in seconds on an ordinary home computer.
see https://en.wikipedia.org/wiki/MD5
Therefore, it is generally recommended to stop using md5 in a cryptographic context.
Since such a collision would result in the same hash in the first inner hash operation in your approach, the repeated hash with an additional constant random secret would also be the same. This means that this attack can successfully exchange the message or file with a different one.
The other hash algorithm you mentioned, SHA-1, is also cryptographically broken.
In this context, there is a worth reading article from Arstechnica from 2008 about the exploitation of md5 collisions to create bogus CA intermediate certificates.
Example of a hash collision
Finally to illustrate a hash collision, here are two .jpg files with the same md5 hash. The collision was created using the following open source project published on Github: https://github.com/cr-marcstevens/hashclash.
The following small Python program writes the files yes.jpg and no.jpg into the current directory to be able to compare the files visually, and then calculates the md5 hash for them - which results in exactly the same value for both files.
import binascii
import hashlib
yes = b'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no = b'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def write_file(filename, data):
with open(filename, 'wb') as f:
f.write(data)
if __name__ == '__main__':
yes_data = binascii.unhexlify(yes)
write_file("yes.jpg", yes_data)
no_data = binascii.unhexlify(no)
write_file("no.jpg", no_data)
md5_yes = hashlib.md5(yes_data).hexdigest()
md5_no = hashlib.md5(no_data).hexdigest()
print("yes.jpg, md5 =", md5_yes)
print("no.jpg, md5 =", md5_no)

How to extract encryption and MAC keys using KDF (X9.63) defined by javacardx.security.derivation

As per Java Card v3.1 new package is defined javacardx.security.derivation
https://docs.oracle.com/en/java/javacard/3.1/jc_api_srvc/api_classic/javacardx/security/derivation/package-summary.html
KDF X9.63 works on three inputs: input secret, counter and shared info.
Depends on length of generated key material, multiple rounds on hash is carried out to generated final output.
I am using this KDF via JC API to generated 64 bytes of output (which is carried out by 2 rounds of SHA-256) for a 16 bytes-Encryption Key, a 16 bytes-IV, and a 32 bytes-MAC Key.
Note: This is just pseudo code to put my question with necessary details.
DerivationFunction df = DerivationFunction.getInstance(DerivationFunction.ALG_KDF_ANSI_X9_63, false);
df.init(KDFAnsiX963Spec(MessageDigest.ALG_SHA_256, input, sharedInfo, (short) 64);
SecretKey encKey = KeyBuilder.buildKey(KeyBuilder.TYPE_AES, (short)16, false);
SecretKey macKey = KeyBuilder.buildKey(KeyBuilder.TYPE_HMAC, (short)32, false);
df.nextBytes(encKey);
df.nextBytes(IVBuffer, (short)0, (short)16);
df.lastBytes(macKey);
I have the following questions:
When rounds of KDF are performed? Are these performed during df.init() or during df.nextBytes() & df.lastBytes()?
One KDF round will generate 32 bytes output (considering SHA-256 algorithm) then how API's df.nextBytes() & df.lastBytes() will work with any output expected length < 32 bytes?
In this KDF counter is incremented in every next round then how counter will be managed between df.nextBytes() & df.lastBytes() API's?
When rounds of KDF are performed? Are these performed during df.init() or during df.nextBytes() & df.lastBytes()?
That seems to be implementation specific to me. It will probably be faster to perform all the calculations at one time, but in that case it still makes sense to wait for the first request of the bytes. On the other hand RAM is also often an issue, so on demand generation also makes some sense. That requires a somewhat trickier implementation though.
The fact that the output size is pre-specified probably indicates that the simpler method of generating all the key material at once is at least foreseen by the API designers (they probably created an implementation before subjecting it to peer review in the JCF).
One KDF round will generate 32 bytes output (considering SHA-256 algorithm) then how API's df.nextBytes() & df.lastBytes() will work with any output expected length < 32 bytes?
It will commonly return the leftmost bytes (of the hash output) and likely leave the rest of the bytes in a buffer. This buffer will likely be destroyed together with the rest of the state when lastBytes is called (so don't forget to do so).
Note that the API clearly states that you have to re-initialize the DerivationFunction instance if you want to use it again. So that is a very strong indication that they though of destruction of key material (something that is required by FIPS and Common Criteria certification, not just common sense).
Other KDF's could have a different way of returning bytes, but using the leftmost bytes and then add rounds to the right is so common you can call it universal. For the ANSI X9.63 KDF this is certainly the case and it is clearly specified in the standard that way.
In this KDF counter is incremented in every next round then how counter will be managed between df.nextBytes() & df.lastBytes() API's?
These are methods of the same class and cannot be viewed separately, so they are not separate API's. Class instances can keep state in anyway they want. It might simply hold the counter as class variable, but if it decided to generate the bytes during init or the first nextBytes / lastBytes call then the counter is not even required anymore.

how to represent message as an integer between 1 and n-1?

I am trying to implement simple El-Gamal cryptosystem.
And I can't understand how to represent message as an integer between 1 and n-1.
The only thing that comes to my mind is:
if n bit length is k, then divide input message m on t | t < k bits and each piece of bits use as integer number.
I think It is wrong.
So how to represent message as an integer between 1 and n-1?
You could do that which is essentially the equivalent of using ECB mode in block ciphers, but there are attacks on this. An attacker may reorder the different blocks of the ciphertext and you would decrypt it without problem, but the received plaintext would be broken without you knowing this. This may also open the door for replay attacks since the blocks are all encrypted independently. You would need some kind of authenticated encryption.
Back to your original question. Such a problem is usually solved by using hybrid encryption. A block cipher like AES is used to encrypt the whole plaintext with a random key. This random key is in turn encrypted through ElGamal since the key is small enough to be represented in < k bits.
Now depending on the mode of operation of the block cipher this could still be malleable. You would either need to put a hash of the ciphertext/plaintext next to the random key as an integrity check. Or otherwise use an authenticated mode of operation like GCM and add the resulting tag next to the random key. Depending on k, this should fit.
Note that you should use some kind of padding for random key | hash/tag if it doesn't reach k.

PBKDF2 with HMAC in Java

I am working on a Java project where I must ensure the confidentiality and integrity of users password saved in a plaintext file.
To do so, I will write only a hash of the password in the file. More specifically, my intention is to write the hash of the password and a random salt, plus the random salt itself, to avoid the use of rainbow and lookup tables. I also want to use key-stretching with PBKDF2, to make the computation of the hash computationally expensive.
Finally, I would like to use a keyed hash algorithm, HMAC, for a final layer of protection.
I am trying to implement my thoughts in a Java code, and I have found some examples of the operations that I have presented above:
private static byte[] pbkdf2(char[] password, byte[] salt, int iterations, int bytes)
throws NoSuchAlgorithmException, InvalidKeySpecException
{
PBEKeySpec spec = new PBEKeySpec(password, salt, iterations, bytes * 8);
SecretKeyFactory skf = SecretKeyFactory.getInstance("PBKDF2WithHmacSHA1");
return skf.generateSecret(spec).getEncoded();
}
The thing that I really cannot understand is how to input my secret key as the key used by the HMAC algorithm, as it doesn't seem an input to the function. I have looked through the Java documentation, but I cannot find a solution to my question.
At this point, I am not really sure if I understood correctly how the different part of the encryption mechanism work, so I would accept any help on the topic.
I think I see the confusion. You're apparently expecting your code to apply PBKDF2 then HMAC-SHA-1. That's not how it works: HMAC-SHA-1 is used inside PBKDF2.
The gist of PBKDF2 is to apply a function repeatedly which has the following properties:
it takes two arguments;
it returns a fixed-size value;
it is practically undistinguishable from a pseudo-random function.
HMAC-SHA-1 is such a function, and a common choice. There are other variants of PBKDF2, using HMAC-MD5, HMAC-SHA-256, or other functions (but these variants aren't in the basic Java library).
PBKDF2 takes two data inputs (plus some configuration inputs): the password, and a salt. If you want to include a secret value in the calculation, PBKDF2's input is the place for it: don't tack on a custom scheme on top of that (doing your own crypto is a recipe for doing it wrong). Append the pepper (secret value common to all accounts) to the salt (public value that varies between accounts).
Note that pepper is of limited usefulness. It's only useful if the hashes and the pepper secret value are stored in different places — for example, if the hashes are in a database and the pepper is in a disk file that is not directly vulnerable to SQL injection attacks.

Collision Attacks, Message Digests and a Possible solution

I've been doing some preliminary research in the area of message digests. Specifically collision attacks of cryptographic hash functions such as MD5 and SHA-1, such as the Postscript example and X.509 certificate duplicate.
From what I can tell in the case of the postscript attack, specific data was generated and embedded within the header of the postscript file (which is ignored during rendering) which brought about the internal state of the md5 to a state such that the modified wording of the document would lead to a final MD value equivalent to the original postscript file.
The X.509 took a similar approach where by data was injected within the comment/whitespace sections of the certificate.
Ok so here is my question, and I can't seem to find anyone asking this question:
Why isn't the length of ONLY the data being consumed added as a final block to the MD calculation?
In the case of X.509 - Why is the whitespace and comments being taken into account as part of the MD?
Wouldn't a simple processes such as one of the following be enough to resolve the proposed collision attacks:
MD(M + |M|) = xyz
MD(M + |M| + |M| * magicseed_0 +...+ |M| * magicseed_n) = xyz
where :
M : is the message
|M| : size of the message
MD : is the message digest function (eg: md5, sha, whirlpool etc)
xyz : is the pairing of the acutal message digest value for the message M and |M|. <M,|M|>
magicseed_{i}: Is a set of random values generated with seed based on the internal-state prior to the size being added.
This technqiue should work, as to date all such collision attacks rely on adding more data to the original message.
In short, the level of difficulty involved in generating a collision message such that:
It not only generates the same MD
But is also comprehensible/parsible/compliant
and is also the same size as the original message,
is immensely difficult if not near impossible. Has this approach ever been discussed? Any links to papers etc would be nice.
Further Question: What is the lower bound for collisions of messages of common length for a hash function H chosen randomly from U, where U is the set of universal hash functions ?
Is it 1/N (where N is 2^(|M|)) or is it greater? If it is greater, that implies there is more than 1 message of length N that will map to the same MD value for a given H.
If that is the case, how practical is it to find these other messages? bruteforce would be of O(2^N), is there a method of time complexity less than bruteforce?
Can't speak for the rest of the questions, but the first one is fairly simple - adding length data to the input of the md5, at any stage of the hashing process (1st block, Nth block, final block) just changes the output hash. You couldn't retrieve that length from the output hash string afterwards. It's also not inconceivable that a collision couldn't be produced from another string with the exact same length in the first place, so saying "the original string was 17 bytes" is meaningless, because the colliding string could also be 17 bytes.
e.g.
md5("abce(17bytes)fghi") = md5("abdefghi<long sequence of text to produce collision>")
is still possible.
In the case of X.509 certificates specifically, the "comments" are not comments in the programming language sense: they are simply additional attributes with an OID that indicates they are to be interpreted as comments. The signature on a certificate is defined to be over the DER representation of the entire tbsCertificate ('to be signed' certificate) structure which includes all the additional attributes.
Hash function design is pretty deep theory, though, and might be better served on the Theoretical CS Stack Exchange.
As #Marc points out, though, as long as more bits can be modified than the output of the hash function contains, then by the pigeonhole principle a collision must exist for some pair of inputs. Because cryptographic hash functions are in general designed to behave pseudo-randomly over their inputs, collisions will tend toward being uniformly distributed over possible inputs.
EDIT: Incorporating the message length into the final block of the hash function would be equivalent to appending the length of everything that has gone before to the input message, so there's no real need to modify the hash function to do this itself; rather, specify it as part of the usage in a given context. I can see where this would make some types of collision attacks harder to pull off, since if you change the message length there's a changed field "downstream" of the area modified by the attack. However, this wouldn't necessarily impede the X.509 intermediate CA forgery attack since the length of the tbsCertificate is not modified.