Add precert handling.

4 files changed, 389 insertions, 167 deletions

diff --git a/src/catlfish.erl b/src/catlfish.erl
index 2fd9dc7..3b81baa 100644
--- a/src/catlfish.erl
+++ b/src/catlfish.erl
@@ -2,7 +2,7 @@
 %%% See LICENSE for licensing information.
 
 -module(catlfish).
--export([add_chain/2, entries/2, entry_and_proof/2]).
+-export([add_chain/3, entries/2, entry_and_proof/2]).
 -export([known_roots/0, update_known_roots/0]).
 -export([init_cache_table/0]).
 -include_lib("eunit/include/eunit.hrl").
@@ -21,53 +21,89 @@
 
 -record(timestamped_entry, {timestamp :: integer(),
                             entry_type :: entry_type(),
-                            signed_entry :: binary(),
+                            signed_entry :: signed_x509_entry() |
+                                            signed_precert_entry(),
                             extensions = <<>> :: binary()}).
 -type timestamped_entry() :: #timestamped_entry{}.
 
--spec serialise(mtl() | timestamped_entry()) -> binary().
-serialise(#timestamped_entry{timestamp = Timestamp} = E) ->
-    list_to_binary(
-      [<<Timestamp:64>>,
-       serialise_entry_type(E#timestamped_entry.entry_type),
-       encode_tls_vector(E#timestamped_entry.signed_entry, 3),
-       encode_tls_vector(E#timestamped_entry.extensions, 2)]);
+-record(signed_x509_entry, {asn1_cert :: binary()}).
+-type signed_x509_entry() :: #signed_x509_entry{}.
+-record(signed_precert_entry, {issuer_key_hash :: binary(),
+                               tbs_certificate :: binary()}).
+-type signed_precert_entry() :: #signed_precert_entry{}.
+
+-spec serialise(mtl() | timestamped_entry() |
+                signed_x509_entry() | signed_precert_entry()) -> binary().
+%% @doc Serialise a MerkleTreeLeaf as per RFC6962 Section 3.4.
 serialise(#mtl{leaf_version = LeafVersion,
                leaf_type = LeafType,
                entry = TimestampedEntry}) ->
     list_to_binary(
       [serialise_leaf_version(LeafVersion),
        serialise_leaf_type(LeafType),
-       serialise(TimestampedEntry)]).
+       serialise(TimestampedEntry)]);
+%% @doc Serialise a TimestampedEntry as per RFC6962 Section 3.4.
+serialise(#timestamped_entry{timestamp = Timestamp,
+                             entry_type = EntryType,
+                             signed_entry = SignedEntry,
+                             extensions = Extensions}) ->
+    list_to_binary(
+      [<<Timestamp:64>>,
+       serialise_entry_type(EntryType),
+       serialise(SignedEntry),
+       encode_tls_vector(Extensions, 2)]);
+%% @doc Serialise an ASN1.Cert as per RFC6962 Section 3.1.
+serialise(#signed_x509_entry{asn1_cert = Cert}) ->
+    encode_tls_vector(Cert, 3);
+%% @doc Serialise a PreCert as per RFC6962 Section 3.2.
+serialise(#signed_precert_entry{
+             issuer_key_hash = IssuerKeyHash,
+             tbs_certificate = TBSCertificate}) when is_binary(IssuerKeyHash),
+                                                     size(IssuerKeyHash) == 32 ->
+    list_to_binary(
+      [IssuerKeyHash,
+       encode_tls_vector(TBSCertificate, 3)]).
 
 serialise_leaf_version(v1) ->
     <<0:8>>;
 serialise_leaf_version(v2) ->
     <<1:8>>.
+deserialise_leaf_version(<<0:8>>) ->
+    v1;
+deserialise_leaf_version(<<1:8>>) ->
+    v2.
 
 serialise_leaf_type(timestamped_entry) ->
     <<0:8>>.
-%% serialise_leaf_type(_) ->
-%%     <<>>.
+deserialise_leaf_type(<<0:8>>) ->
+    timestamped_entry.
 
 serialise_entry_type(x509_entry) ->
     <<0:16>>;
 serialise_entry_type(precert_entry) ->
     <<1:16>>.
+deserialise_entry_type(<<0:16>>) ->
+    x509_entry;
+deserialise_entry_type(<<1:16>>) ->
+    precert_entry.
 
 serialise_signature_type(certificate_timestamp) ->
     <<0:8>>;
 serialise_signature_type(tree_hash) ->
     <<1:8>>.
+%% deserialise_signature_type(<<0:8>>) ->
+%%     certificate_timestamp;
+%% deserialise_signature_type(<<1:8>>) ->
+%%     tree_hash.
 
-build_mtl(Timestamp, LeafCert) ->
-    TSE = #timestamped_entry{timestamp = Timestamp,
-                             entry_type = x509_entry,
-                             signed_entry = LeafCert},
-    MTL = #mtl{leaf_version = v1,
-               leaf_type = timestamped_entry,
-               entry = TSE},
-    serialise(MTL).
+%% build_mtl(Timestamp, LeafCert) ->
+%%     TSE = #timestamped_entry{timestamp = Timestamp,
+%%                              entry_type = x509_entry,
+%%                              signed_entry = LeafCert},
+%%     MTL = #mtl{leaf_version = v1,
+%%                leaf_type = timestamped_entry,
+%%                entry = TSE},
+%%     serialise(MTL).
 
 calc_sct(TimestampedEntry) ->
     plop:serialise(plop:spt(list_to_binary([<<?PROTOCOL_VERSION:8>>,
@@ -86,37 +122,48 @@ get_sct(Hash, TimestampedEntry) ->
                     SCT
             end;
         _ ->
-            SCT = calc_sct(TimestampedEntry)
+            calc_sct(TimestampedEntry)
     end.
 
--spec add_chain(binary(), [binary()]) -> nonempty_string().
-add_chain(LeafCert, CertChain) ->
+-spec add_chain(binary(), [binary()], normal|precert) -> nonempty_string().
+add_chain(LeafCert, CertChain, Type) ->
     EntryHash = crypto:hash(sha256, [LeafCert | CertChain]),
+    EntryType = case Type of
+                    normal -> x509_entry;
+                    precert -> precert_entry
+                end,
     {TimestampedEntry, Hash} =
         case plop:get(EntryHash) of
             notfound ->
                 Timestamp = plop:generate_timestamp(),
-                TSE = #timestamped_entry{timestamp = Timestamp,
-                                         entry_type = x509_entry,
-                                         signed_entry = LeafCert},
-                MTL = #mtl{leaf_version = v1,
-                           leaf_type = timestamped_entry,
-                           entry = TSE},
-                MTLHash = ht:leaf_hash(serialise(MTL)),
-                ok = plop:add(
-                       serialise_logentry(Timestamp, LeafCert, CertChain),
-                       MTLHash,
-                       EntryHash),
+                TSE = timestamped_entry(Timestamp, EntryType, LeafCert, CertChain),
+                MTLText = serialise(#mtl{leaf_version = v1,
+                                         leaf_type = timestamped_entry,
+                                         entry = TSE}),
+                MTLHash = ht:leaf_hash(MTLText),
+                ExtraData = 
+                    case Type of
+                        normal -> CertChain;
+                        precert -> [LeafCert | CertChain]
+                    end,
+                LogEntry =
+                    list_to_binary(
+                      [encode_tls_vector(MTLText, 4),
+                       encode_tls_vector(
+                         encode_tls_vector(
+                           list_to_binary(
+                             [encode_tls_vector(C, 3) || C <- ExtraData]),
+                           3),
+                         4)]),
+                ok = plop:add(LogEntry, MTLHash, EntryHash),
                 {TSE, MTLHash};
-            {_Index, MTLHash, Entry} ->
-                <<Timestamp:64, _LogEntry/binary>> = Entry,
-                %% TODO: Perform a costly db consistency check against
-                %% unpacked LogEntry (w/ LeafCert and CertChain)
-                {#timestamped_entry{timestamp = Timestamp,
-                                    entry_type = x509_entry,
-                                    signed_entry = LeafCert},
-                 MTLHash}
+            {_Index, MTLHash, DBEntry} ->
+                {MTLText, _ExtraData} = unpack_entry(DBEntry),
+                MTL = deserialise_mtl(MTLText),
+                MTLText = serialise(MTL),       % verify FIXME: remove
+                {MTL#mtl.entry, MTLHash}
         end,
+
     SCT_sig = get_sct(Hash, TimestampedEntry),
     {[{sct_version, ?PROTOCOL_VERSION},
       {id, base64:encode(plop:get_logid())},
@@ -124,15 +171,73 @@ add_chain(LeafCert, CertChain) ->
       {extensions, base64:encode(<<>>)},
       {signature, base64:encode(SCT_sig)}]}.
 
--spec serialise_logentry(integer(), binary(), [binary()]) -> binary().
-serialise_logentry(Timestamp, LeafCert, CertChain) ->
-    list_to_binary(
-      [<<Timestamp:64>>,
-       list_to_binary(
-         [encode_tls_vector(LeafCert, 3),
-          encode_tls_vector(
-            list_to_binary(
-              [encode_tls_vector(X, 3) || X <- CertChain]), 3)])]).
+-spec timestamped_entry(integer(), entry_type(), binary(), binary()) ->
+                               timestamped_entry().
+timestamped_entry(Timestamp, EntryType, LeafCert, CertChain) ->
+    SignedEntry =
+        case EntryType of
+            x509_entry ->
+                #signed_x509_entry{asn1_cert = LeafCert};
+            precert_entry ->
+                {DetoxedLeafTBSCert, IssuerKeyHash} =
+                    x509:detox(LeafCert, CertChain),
+                #signed_precert_entry{
+                   issuer_key_hash = IssuerKeyHash,
+                   tbs_certificate = DetoxedLeafTBSCert}
+        end,
+    #timestamped_entry{timestamp = Timestamp,
+                       entry_type = EntryType,
+                       signed_entry = SignedEntry}.
+
+%% -spec serialise_logentry(integer(), binary(), [binary()]) -> binary().
+%% serialise_logentry(Timestamp, LeafCert, CertChain) ->
+%%     list_to_binary(
+%%       [<<Timestamp:64>>,
+%%        list_to_binary(
+%%          [encode_tls_vector(LeafCert, 3),
+%%           encode_tls_vector(
+%%             list_to_binary(
+%%               [encode_tls_vector(X, 3) || X <- CertChain]), 3)])]).
+
+-spec deserialise_mtl(binary()) -> mtl().
+deserialise_mtl(Data) ->
+    <<LeafVersionBin:1/binary,
+      LeafTypeBin:1/binary,
+      TimestampedEntryBin/binary>> = Data,
+    #mtl{leaf_version = deserialise_leaf_version(LeafVersionBin),
+         leaf_type = deserialise_leaf_type(LeafTypeBin),
+         entry = deserialise_timestampedentry(TimestampedEntryBin)}.
+
+-spec deserialise_timestampedentry(binary()) -> timestamped_entry().
+deserialise_timestampedentry(Data) ->
+    <<Timestamp:64, EntryTypeBin:2/binary, RestData/binary>> = Data,
+    EntryType = deserialise_entry_type(EntryTypeBin),
+    {SignedEntry, ExtensionsBin} =
+        case EntryType of
+            x509_entry ->
+                deserialise_signed_x509_entry(RestData);
+            precert_entry ->
+                deserialise_signed_precert_entry(RestData)
+        end,
+    {Extensions, <<>>} = decode_tls_vector(ExtensionsBin, 2),
+    #timestamped_entry{timestamp = Timestamp,
+                       entry_type = EntryType,
+                       signed_entry = SignedEntry,
+                       extensions = Extensions}.
+
+-spec deserialise_signed_x509_entry(binary()) -> {signed_x509_entry(), binary()}.
+deserialise_signed_x509_entry(Data) ->
+    {E, D} = decode_tls_vector(Data, 3),
+    {#signed_x509_entry{asn1_cert = E}, D}.
+
+-spec deserialise_signed_precert_entry(binary()) ->
+                                              {signed_precert_entry(), binary()}.
+deserialise_signed_precert_entry(Data) ->
+    <<IssuerKeyHash:32/binary, RestData/binary>> = Data,
+    {TBSCertificate, RestData2} = decode_tls_vector(RestData, 3),
+    {#signed_precert_entry{issuer_key_hash = IssuerKeyHash,
+                           tbs_certificate = TBSCertificate},
+     RestData2}.    
 
 -spec entries(non_neg_integer(), non_neg_integer()) -> list().
 entries(Start, End) ->
@@ -142,10 +247,9 @@ entries(Start, End) ->
 entry_and_proof(Index, TreeSize) ->
     case plop:inclusion_and_entry(Index, TreeSize) of
         {ok, Entry, Path} ->
-            {Timestamp, LeafCertVector, CertChainVector} = unpack_entry(Entry),
-            MTL = build_mtl(Timestamp, LeafCertVector),
+            {MTL, ExtraData} = unpack_entry(Entry),
             {[{leaf_input, base64:encode(MTL)},
-              {extra_data, base64:encode(CertChainVector)},
+              {extra_data, base64:encode(ExtraData)},
               {audit_path, [base64:encode(X) || X <- Path]}]};
         {notfound, Msg} ->
             {[{success, false},
@@ -161,20 +265,20 @@ init_cache_table() ->
     ets:new(?CACHE_TABLE, [set, public, named_table]).
 
 %% Private functions.
+-spec unpack_entry(binary()) -> {binary(), binary()}.
 unpack_entry(Entry) ->
-    <<Timestamp:64, LogEntry/binary>> = Entry,
-    {LeafCertVector, CertChainVector} = decode_tls_vector(LogEntry, 3),
-    {Timestamp, LeafCertVector, CertChainVector}.
+    {MTL, Rest} = decode_tls_vector(Entry, 4),
+    {ExtraData, <<>>} = decode_tls_vector(Rest, 4),
+    {MTL, ExtraData}.
 
 -spec x_entries([{non_neg_integer(), binary(), binary()}]) -> list().
 x_entries([]) ->
     [];
 x_entries([H|T]) ->
     {_Index, _Hash, Entry} = H,
-    {Timestamp, LeafCertVector, CertChainVector} = unpack_entry(Entry),
-    MTL = build_mtl(Timestamp, LeafCertVector),
-    [{[{leaf_input, base64:encode(MTL)}, {extra_data, base64:encode(CertChainVector)}]} |
-     x_entries(T)].
+    {MTL, ExtraData} = unpack_entry(Entry),
+    [{[{leaf_input, base64:encode(MTL)},
+       {extra_data, base64:encode(ExtraData)}]} | x_entries(T)].
 
 -spec encode_tls_vector(binary(), non_neg_integer()) -> binary().
 encode_tls_vector(Binary, LengthLen) ->
diff --git a/src/v1.erl b/src/v1.erl
index 006990d..e672182 100644
--- a/src/v1.erl
+++ b/src/v1.erl
@@ -9,34 +9,10 @@
 
 %% Public functions, i.e. part of URL.
 request(post, "ct/v1/add-chain", Input) ->
-    case (catch mochijson2:decode(Input)) of
-        {error, E} ->
-            html("add-chain: bad input:", E);
-        {struct, [{<<"chain">>, ChainBase64}]} ->
-            case (catch [base64:decode(X) || X <- ChainBase64]) of
-                {'EXIT', _} ->
-                    html("add-chain: invalid base64-encoded chain: ",
-                         [ChainBase64]);
-                [LeafCert | CertChain] ->
-                    Roots = catlfish:known_roots(),
-                    case x509:normalise_chain(Roots, [LeafCert|CertChain]) of
-                        {ok, [Leaf | Chain]} ->
-                            lager:info("adding ~p",
-                                           [x509:cert_string(LeafCert)]),
-                            success(catlfish:add_chain(Leaf, Chain));
-                        {error, Reason} ->
-                            lager:info("rejecting ~p: ~p",
-                                       [x509:cert_string(LeafCert), Reason]),
-                            html("add-chain: invalid chain", Reason)
-                    end;
-                Invalid ->
-                    html("add-chain: chain is not a list: ", [Invalid])
-            end;
-        _ -> html("add-chain: missing input: chain", Input)
-    end;
+    add_chain(Input, normal);
 
-request(post, "ct/v1/add-pre-chain", _Input) ->
-    niy();
+request(post, "ct/v1/add-pre-chain", Input) ->
+    add_chain(Input, precert);
 
 request(get, "ct/v1/get-sth", _Query) ->
     R = plop:sth(),
@@ -130,8 +106,33 @@ html(Text, Input) ->
            "~p~n" ++
            "</body></html>~n", [Text, Input])}.
 
-niy() ->
-    html("NIY - Not Implemented Yet|", []).
-
 success(Data) ->
     {200, [{"Content-Type", "text/json"}], mochijson2:encode(Data)}.
+
+-spec add_chain(any(), normal|precert) -> any().
+add_chain(Input, Type) ->
+    case (catch mochijson2:decode(Input)) of
+        {error, E} ->
+            html("add-chain: bad input:", E);
+        {struct, [{<<"chain">>, ChainBase64}]} ->
+            case (catch [base64:decode(X) || X <- ChainBase64]) of
+                {'EXIT', _} ->
+                    html("add-chain: invalid base64-encoded chain: ",
+                         [ChainBase64]);
+                [LeafCert | CertChain] ->
+                    case x509:normalise_chain(catlfish:known_roots(),
+                                              [LeafCert|CertChain]) of
+                        {ok, [Leaf | Chain]} ->
+                            lager:info("adding ~p cert ~p",
+                                       [Type, x509:cert_string(LeafCert)]),
+                            success(catlfish:add_chain(Leaf, Chain, Type));
+                        {error, Reason} ->
+                            lager:info("rejecting ~p: ~p",
+                                       [x509:cert_string(LeafCert), Reason]),
+                            html("add-chain: invalid chain", Reason)
+                    end;
+                Invalid ->
+                    html("add-chain: chain is not a list: ", [Invalid])
+            end;
+        _ -> html("add-chain: missing input: chain", Input)
+    end.
diff --git a/src/x509.erl b/src/x509.erl
index 5a0e871..43b90b3 100644
--- a/src/x509.erl
+++ b/src/x509.erl
@@ -3,10 +3,10 @@
 
 -module(x509).
 -export([normalise_chain/2, cert_string/1, read_pemfiles_from_dir/1,
-         self_signed/1]).
-
+         self_signed/1, detox/2]).
 -include_lib("public_key/include/public_key.hrl").
 -include_lib("eunit/include/eunit.hrl").
+-import(lists, [nth/2, filter/2]).
 
 -type reason() :: {chain_too_long |
                    root_unknown |
@@ -18,15 +18,49 @@
 -spec normalise_chain([binary()], [binary()]) -> {ok, [binary()]} |
                                                  {error, reason()}.
 normalise_chain(AcceptableRootCerts, CertChain) ->
-    case valid_chain_p(AcceptableRootCerts, CertChain, ?MAX_CHAIN_LENGTH) of
+    case normalise_chain(AcceptableRootCerts, CertChain, ?MAX_CHAIN_LENGTH) of
         {false, Reason} ->
             {error, Reason};
         {true, Root} ->
-            [Leaf | Chain] = CertChain,
-            {ok, [detox_precert(Leaf) | Chain] ++ Root}
+            {ok, CertChain ++ Root}
     end.
 
-%%%%%%%%%%%%%%%%%%%%
+cert_string(Der) ->
+    mochihex:to_hex(crypto:hash(sha, Der)).
+
+-spec read_pemfiles_from_dir(file:filename()) -> [binary()].
+%% @doc Reading certificates from files. Flattening the result -- all
+%% certs in all files are returned in a single list.
+read_pemfiles_from_dir(Dir) ->
+    case file:list_dir(Dir) of
+        {error, enoent} ->
+            lager:error("directory does not exist: ~p", [Dir]),
+            [];
+        {error, Reason} ->
+            lager:error("unable to read directory ~p: ~p", [Dir, Reason]),
+            [];
+        {ok, Filenames} ->
+            Files = lists:filter(
+                      fun(F) ->
+                              string:equal(".pem", filename:extension(F))
+                      end,
+                      Filenames),
+            ders_from_pemfiles(Dir, Files)
+    end.
+
+-spec self_signed([binary()]) -> [binary()].
+%% @doc Return a list of certs in L that are self signed.
+self_signed(L) ->
+    lists:filter(fun(Cert) -> signed_by_p(Cert, Cert) end, L).
+
+%% @doc Return the detoxed cet in LeafDer and the issuer leaf hash.
+-spec detox(binary(), [binary()]) -> {binary(), binary()}.
+detox(LeafDer, ChainDer) ->
+    detox_precert(LeafDer, nth(1, ChainDer), nth(2, ChainDer)).
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% Private functions.
+
 %% @doc Verify that the leaf cert or precert has a valid chain back to
 %% an acceptable root cert. The order of certificates in the second
 %% argument is: leaf cert in head, chain in tail. Order of first
@@ -37,12 +71,12 @@ normalise_chain(AcceptableRootCerts, CertChain) ->
 %% amongst the acceptable root certs. Otherwise it contains exactly
 %% one element, a CA cert from the acceptable root certs signing the
 %% root of the chain.
--spec valid_chain_p([binary()], [binary()], integer()) ->
-                           {false, reason()} | {true, list()}.
-valid_chain_p(_, _, MaxChainLength) when MaxChainLength =< 0 ->
+-spec normalise_chain([binary()], [binary()], integer()) ->
+                             {false, reason()} | {true, list()}.
+normalise_chain(_, _, MaxChainLength) when MaxChainLength =< 0 ->
     %% Chain too long.
     {false, chain_too_long};
-valid_chain_p(AcceptableRootCerts, [TopCert], MaxChainLength) ->
+normalise_chain(AcceptableRootCerts, [TopCert], MaxChainLength) ->
     %% Check root of chain.
     case lists:member(TopCert, AcceptableRootCerts) of
         true ->
@@ -58,9 +92,9 @@ valid_chain_p(AcceptableRootCerts, [TopCert], MaxChainLength) ->
                 Root -> {true, [Root]}
             end
     end;
-valid_chain_p(AcceptableRootCerts, [BottomCert|Rest], MaxChainLength) ->
+normalise_chain(AcceptableRootCerts, [BottomCert|Rest], MaxChainLength) ->
     case signed_by_p(BottomCert, hd(Rest)) of
-        true -> valid_chain_p(AcceptableRootCerts, Rest, MaxChainLength - 1);
+        true -> normalise_chain(AcceptableRootCerts, Rest, MaxChainLength - 1);
         false -> {false, signature_mismatch}
     end.
 
@@ -90,9 +124,10 @@ encoded_tbs_cert(DerCert) ->
         PKIXCert,
     EncodedTBSCert.
 
+-spec extract_verify_data(#'Certificate'{}, binary()) -> {ok, tuple()} | error.
+%% @doc Return DER encoded TBScertificate, digest type and signature.
 %% Code from pubkey_cert:extract_verify_data/2.
--spec verifydata_from_cert(#'Certificate'{}, binary()) -> {ok, tuple()} | error.
-verifydata_from_cert(Cert, DerCert) ->
+extract_verify_data(Cert, DerCert) ->
     PlainText = encoded_tbs_cert(DerCert),
     {_, Sig} = Cert#'Certificate'.signature,
     SigAlgRecord = Cert#'Certificate'.signatureAlgorithm,
@@ -114,7 +149,7 @@ verify_sig(Cert, DerCert,                     % Certificate to verify.
               tbsCertificate = #'TBSCertificate'{
                                   subjectPublicKeyInfo = IssuerSPKI}}) ->
     %% Dig out digest, digest type and signature from Cert/DerCert.
-    case verifydata_from_cert(Cert, DerCert) of
+    case extract_verify_data(Cert, DerCert) of
         error -> false;
         {ok, Tuple} -> verify_sig2(IssuerSPKI, Tuple)
     end.
@@ -159,9 +194,6 @@ signed_by_p(DerCert, IssuerDerCert) when is_binary(DerCert),
                DerCert,
                public_key:pkix_decode_cert(IssuerDerCert, plain)).
 
-cert_string(Der) ->
-    mochihex:to_hex(crypto:hash(sha, Der)).
-
 parsable_cert_p(Der) ->
     case (catch public_key:pkix_decode_cert(Der, plain)) of
         #'Certificate'{} ->
@@ -175,54 +207,139 @@ parsable_cert_p(Der) ->
             false
     end.
 
--spec self_signed([binary()]) -> [binary()].
-self_signed(L) ->
-    lists:filter(fun(Cert) -> signed_by_p(Cert, Cert) end, L).
-
-%%%%%%%%%%%%%%%%%%%%
-%% Precertificates according to draft-ietf-trans-rfc6962-bis-04.
+%% Precerts according to RFC6962.
 
 %% Submitted precerts have a special critical poison extension -- OID
 %% 1.3.6.1.4.1.11129.2.4.3, whose extnValue OCTET STRING contains
 %% ASN.1 NULL data (0x05 0x00).
 
 %% They are signed with either the CA cert that will sign the final
-%% cert or Precertificate Signing Certificate directly signed by the
+%% cert or a Precertificate Signing Certificate directly signed by the
 %% CA cert that will sign the final cert. A Precertificate Signing
 %% Certificate has CA:true and Extended Key Usage: Certificate
 %% Transparency, OID 1.3.6.1.4.1.11129.2.4.4.
 
-%% A PreCert in a SignedCertificateTimestamp does _not_ contain the
-%% poison extension, nor a Precertificate Signing Certificate. This
-%% means that we might have to 1) remove poison extensions in leaf
-%% certs, 2) remove "poisoned signatures", 3) change issuer and
-%% Authority Key Identifier of leaf certs.
+%% PreCert in SignedCertificateTimestamp does _not_ contain the poison
+%% extension, nor does it have an issuer which is a Precertificate
+%% Signing Certificate. This means that we have to 1) remove the
+%% poison extension and 2) potentially change issuer and Authority Key
+%% Identifier. See RFC6962 Section 3.2.
+
+%% Changes in draft-ietf-trans-rfc6962-bis-??: TODO.
+
+-spec detox_precert(binary(), binary(), binary()) -> {binary(), binary()}.
+%% @doc Return {DetoxedLeaf, IssuerPubKeyHash} where i) DetoxedLeaf is
+%% the tbsCertificate w/o poison and adjusted issuer and authkeyid;
+%% and ii) IssuerPubKeyHash is the hash over issuing cert's public
+%% key.
+detox_precert(LeafDer, ParentDer, GrandParentDer) ->
+    Leaf = public_key:pkix_decode_cert(LeafDer, plain),
+    Parent = public_key:pkix_decode_cert(ParentDer, plain),
+    GrandParent = public_key:pkix_decode_cert(GrandParentDer, plain),
+    DetoxedLeafTBS = remove_poison_ext(Leaf),
+
+    %% If parent is a precert signing cert, change issuer and
+    %% potential authority key id to refer to grandparent.
+    {C, IssuerKeyHash} =
+        case is_precert_signer(Parent) of
+            true -> 
+                {set_issuer_and_authkeyid(DetoxedLeafTBS, Parent),
+                 extract_pub_key(GrandParent)};
+            false -> 
+                {DetoxedLeafTBS, extract_pub_key(Parent)}
+        end,
+    {public_key:pkix_encode('TBSCertificate', C, plain),
+     crypto:hash(sha256, public_key:pkix_encode(
+                           'SubjectPublicKeyInfo', IssuerKeyHash, plain))}.
+
+-spec extract_pub_key(#'Certificate'{}) -> #'SubjectPublicKeyInfo'{}.
+extract_pub_key(#'Certificate'{
+                   tbsCertificate = #'TBSCertificate'{
+                                       subjectPublicKeyInfo = SPKI}}) ->
+    SPKI.    
+
+-spec set_issuer_and_authkeyid(#'TBSCertificate'{}, #'Certificate'{}) ->
+                                      #'TBSCertificate'{}.
+%% @doc Return Cert with issuer and AuthorityKeyIdentifier from Parent.
+set_issuer_and_authkeyid(TBSCert,
+                         #'Certificate'{
+                            tbsCertificate =
+                                #'TBSCertificate'{
+                                   issuer = ParentIssuer,
+                                   extensions = ParentExtensions}}) ->
+    case pubkey_cert:select_extension(?'id-ce-authorityKeyIdentifier',
+                                      ParentExtensions) of
+        undefined ->
+            lager:debug("setting issuer only", []),
+            TBSCert#'TBSCertificate'{issuer = ParentIssuer};
+        ParentAuthKeyExt ->
+            NewExtensions =
+                lists:map(
+                  fun(E) ->
+                          case E of
+                              #'Extension'{extnID =
+                                               ?'id-ce-authorityKeyIdentifier'} ->
+                                  lager:debug("swapping auth key id to ~p",
+                                              [ParentAuthKeyExt]),
+                                  ParentAuthKeyExt;
+                              Orig ->
+                                  Orig
+                          end
+                  end,
+                  TBSCert#'TBSCertificate'.extensions),
+            TBSCert#'TBSCertificate'{issuer = ParentIssuer,
+                                     extensions = NewExtensions}
+    end.
 
--spec detox_precert([#'Certificate'{}]) -> [#'Certificate'{}].
-detox_precert(CertChain) ->
-    CertChain.                                  % NYI
+-define(CA_POISON_OID, {1,3,6,1,4,1,11129,2,4,4}).
+
+-spec is_precert_signer(#'Certificate'{}) -> boolean().
+is_precert_signer(#'Certificate'{tbsCertificate = TBSCert}) ->
+    Extensions = pubkey_cert:extensions_list(TBSCert#'TBSCertificate'.extensions),
+    %% NOTE: It's OK to look at only the first extension found since
+    %% "A certificate MUST NOT include more than one instance of a
+    %% particular extension." --RFC5280 Sect 4.2
+    case pubkey_cert:select_extension(?'id-ce-extKeyUsage', Extensions) of
+        #'Extension'{extnValue = Val} ->
+            case 'OTP-PUB-KEY':decode('ExtKeyUsageSyntax', Val) of
+                %% NOTE: We require that the poisoned OID is the
+                %% _only_ extkeyusage present. RFC6962 Sect 3.1 is not
+                %% really clear.
+                {ok, [?CA_POISON_OID]} -> is_ca(TBSCert);
+                _ -> false
+            end;
+        _ -> false
+    end.
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--spec read_pemfiles_from_dir(file:filename()) -> [binary()].
-%% @doc Reading certificates from files. Flattening the result -- all
-%% certs in all files are returned in a single list.
-read_pemfiles_from_dir(Dir) ->
-    case file:list_dir(Dir) of
-        {error, enoent} ->
-            lager:error("directory does not exist: ~p", [Dir]),
-            [];
-        {error, Reason} ->
-            lager:error("unable to read directory ~p: ~p", [Dir, Reason]),
-            [];
-        {ok, Filenames} ->
-            Files = lists:filter(
-                      fun(F) ->
-                              string:equal(".pem", filename:extension(F))
-                      end,
-                      Filenames),
-            ders_from_pemfiles(Dir, Files)
+is_ca(#'TBSCertificate'{extensions = Extensions}) ->
+    case pubkey_cert:select_extension(?'id-ce-basicConstraints', Extensions) of
+        #'Extension'{critical = true, extnValue = Val} ->
+            case 'OTP-PUB-KEY':decode('BasicConstraints', Val) of
+                {ok, {'BasicConstraints', true, _}} -> true;
+                _ -> false
+            end;
+        _ -> false
     end.
 
+-spec remove_poison_ext(#'Certificate'{}) -> #'TBSCertificate'{}.
+remove_poison_ext(#'Certificate'{tbsCertificate = TBSCert}) ->
+    Extensions = pubkey_cert:extensions_list(TBSCert#'TBSCertificate'.extensions),
+    SanitisedExtensions =
+        filter(fun(E) -> not poisoned_leaf_p(E) end, Extensions),
+    NewTBSCert = TBSCert#'TBSCertificate'{extensions = SanitisedExtensions},
+    NewTBSCert.
+
+-define(LEAF_POISON_OID, {1,3,6,1,4,1,11129,2,4,3}).
+-define(LEAF_POISON_VAL, [5,0]).
+
+poisoned_leaf_p(#'Extension'{extnID = ?LEAF_POISON_OID,
+                             critical = true,
+                             extnValue = ?LEAF_POISON_VAL}) ->
+    true;
+poisoned_leaf_p(_) ->
+    false.
+
+%%%% PEM files.
 ders_from_pemfiles(Dir, Filenames) ->
     lists:flatten(
       [ders_from_pemfile(filename:join(Dir, X)) || X <- Filenames]).
@@ -297,21 +414,21 @@ valid_cert_test_() ->
               %% 'OTP-PUB-KEY':Func('OTP-X520countryname', Value0)
               %% FIXME: This error doesn't make much sense -- is my
               %% environment borked?
-              ?_assertMatch({true, _}, valid_chain_p(lists:nth(1, Chains),
-                                                     lists:nth(1, Chains), 10)),
+              ?_assertMatch({true, _}, normalise_chain(lists:nth(1, Chains),
+                                                       lists:nth(1, Chains), 10)),
               %% Self-signed so fail.
               ?_assertMatch({false, root_unknown},
-                            valid_chain_p(KnownRoots,
-                                          lists:nth(2, Chains), 10)),
+                            normalise_chain(KnownRoots,
+                                            lists:nth(2, Chains), 10)),
               %% Leaf signed by known CA, pass.
-              ?_assertMatch({true, _}, valid_chain_p(KnownRoots,
-                                                     lists:nth(3, Chains), 10)),
+              ?_assertMatch({true, _}, normalise_chain(KnownRoots,
+                                                       lists:nth(3, Chains), 10)),
               %% Proper 3-depth chain with root in KnownRoots, pass.
               %% Bug CATLFISH-19 --> [info] rejecting "3ee62cb678014c14d22ebf96f44cc899adea72f1": chain_broken
               %% leaf sha1: 3ee62cb678014c14d22ebf96f44cc899adea72f1
               %% leaf Subject: C=KR, O=Government of Korea, OU=Group of Server, OU=\xEA\xB5\x90\xEC\x9C\xA1\xEA\xB3\xBC\xED\x95\x99\xEA\xB8\xB0\xEC\x88\xA0\xEB\xB6\x80, CN=www.berea.ac.kr, CN=haksa.bits.ac.kr
-              ?_assertMatch({true, _}, valid_chain_p(KnownRoots,
-                                                     lists:nth(4, Chains), 3)),
+              ?_assertMatch({true, _}, normalise_chain(KnownRoots,
+                                                       lists:nth(4, Chains), 3)),
               %% Verify against self, pass.
               %% Bug CATLFISH-??, can't handle issuer keytype ECPoint.
               %% Issuer sha1: 6969562e4080f424a1e7199f14baf3ee58ab6abb
@@ -333,21 +450,21 @@ chain_test_() ->
 chain_test(C0, C1) ->
     [
      %% Root not in chain but in trust store.
-     ?_assertEqual({true, [C1]}, valid_chain_p([C1], [C0], 10)),
-     ?_assertEqual({true, [C1]}, valid_chain_p([C1], [C0], 2)),
+     ?_assertEqual({true, [C1]}, normalise_chain([C1], [C0], 10)),
+     ?_assertEqual({true, [C1]}, normalise_chain([C1], [C0], 2)),
      %% Chain too long.
-     ?_assertMatch({false, chain_too_long}, valid_chain_p([C1], [C0], 1)),
+     ?_assertMatch({false, chain_too_long}, normalise_chain([C1], [C0], 1)),
      %% Root in chain and in trust store.
-     ?_assertEqual({true, []}, valid_chain_p([C1], [C0, C1], 2)),
+     ?_assertEqual({true, []}, normalise_chain([C1], [C0, C1], 2)),
      %% Chain too long.
-     ?_assertMatch({false, chain_too_long}, valid_chain_p([C1], [C0, C1], 1)),
+     ?_assertMatch({false, chain_too_long}, normalise_chain([C1], [C0, C1], 1)),
      %% Root not in trust store.
-     ?_assertMatch({false, root_unknown}, valid_chain_p([], [C0, C1], 10)),
+     ?_assertMatch({false, root_unknown}, normalise_chain([], [C0, C1], 10)),
      %% Selfsigned. Actually OK.
-     ?_assertMatch({true, []}, valid_chain_p([C0], [C0], 10)),
-     ?_assertMatch({true, []}, valid_chain_p([C0], [C0], 1)),
+     ?_assertMatch({true, []}, normalise_chain([C0], [C0], 10)),
+     ?_assertMatch({true, []}, normalise_chain([C0], [C0], 1)),
      %% Max chain length 0 is not OK.
-     ?_assertMatch({false, chain_too_long}, valid_chain_p([C0], [C0], 0))
+     ?_assertMatch({false, chain_too_long}, normalise_chain([C0], [C0], 0))
     ].
 
 %%-spec read_certs(file:filename()) -> [string:string()].
diff --git a/tools/certtools.py b/tools/certtools.py
index 222497f..0e639f2 100644
--- a/tools/certtools.py
+++ b/tools/certtools.py
@@ -6,6 +6,7 @@ import json
 import base64
 import urllib
 import urllib2
+import ssl
 import urlparse
 import struct
 import sys
@@ -79,7 +80,7 @@ def get_root_cert(issuer):
     return root_cert
 
 def get_sth(baseurl):
-    result = urllib2.urlopen(baseurl + "ct/v1/get-sth").read()
+    result = urllib2.urlopen(baseurl + "ct/v1/get-sth", context=ssl.SSLContext(ssl.PROTOCOL_TLSv1)).read()
     return json.loads(result)
 
 def get_proof_by_hash(baseurl, hash, tree_size):
@@ -87,7 +88,7 @@ def get_proof_by_hash(baseurl, hash, tree_size):
         params = urllib.urlencode({"hash":base64.b64encode(hash),
                                    "tree_size":tree_size})
         result = \
-          urllib2.urlopen(baseurl + "ct/v1/get-proof-by-hash?" + params).read()
+          urllib2.urlopen(baseurl + "ct/v1/get-proof-by-hash?" + params, context=ssl.SSLContext(ssl.PROTOCOL_TLSv1)).read()
         return json.loads(result)
     except urllib2.HTTPError, e:
         print "ERROR:", e.read()
@@ -98,7 +99,7 @@ def get_consistency_proof(baseurl, tree_size1, tree_size2):
         params = urllib.urlencode({"first":tree_size1,
                                    "second":tree_size2})
         result = \
-          urllib2.urlopen(baseurl + "ct/v1/get-sth-consistency?" + params).read()
+          urllib2.urlopen(baseurl + "ct/v1/get-sth-consistency?" + params, context=ssl.SSLContext(ssl.PROTOCOL_TLSv1)).read()
         return json.loads(result)["consistency"]
     except urllib2.HTTPError, e:
         print "ERROR:", e.read()
@@ -121,8 +122,7 @@ def unpack_tls_array(packed_data, length_len):
 
 def add_chain(baseurl, submission):
     try:
-        result = urllib2.urlopen(baseurl + "ct/v1/add-chain",
-            json.dumps(submission)).read()
+        result = urllib2.urlopen(baseurl + "ct/v1/add-chain", json.dumps(submission), context=ssl.SSLContext(ssl.PROTOCOL_TLSv1)).read()
         return json.loads(result)
     except urllib2.HTTPError, e:
         print "ERROR", e.code,":", e.read()
@@ -140,7 +140,7 @@ def add_chain(baseurl, submission):
 def get_entries(baseurl, start, end):
     try:
         params = urllib.urlencode({"start":start, "end":end})
-        result = urllib2.urlopen(baseurl + "ct/v1/get-entries?" + params).read()
+        result = urllib2.urlopen(baseurl + "ct/v1/get-entries?" + params, context=ssl.SSLContext(ssl.PROTOCOL_TLSv1)).read()
         return json.loads(result)
     except urllib2.HTTPError, e:
         print "ERROR:", e.read()
@@ -197,7 +197,7 @@ def http_request(url, data=None, key=None):
     signature = sk.sign("%s\0%s\0%s" % (method, parsed_url.path, data), hashfunc=hashlib.sha256,
                         sigencode=ecdsa.util.sigencode_der)
     req.add_header('X-Catlfish-Auth', base64.b64encode(signature) + ";key=" + keyname)
-    result = urllib2.urlopen(req).read()
+    result = urllib2.urlopen(req, context=ssl.SSLContext(ssl.PROTOCOL_TLSv1)).read()
     return result
 
 def get_signature(baseurl, data, key=None):