clone.c

#ifndef _GNU_SOURCE
#define _GNU_SOURCE 1
#endif

/* Beginning in libgit2 v1.4.5 and v1.5.1, libgit2 will now perform host key checking by default.
 * However on Windows libssh does not have access to the cert store */
#if defined(_WIN32)
#define SKIP_HOSTKEY_CHECK
#endif

#include <string.h>
#include "utils.h"
#include <Rversion.h>

/* Workaround for performance bug: https://github.com/libgit2/libgit2/issues/5725 */
#if AT_LEAST_LIBGIT2(0, 26)
#define USE_SUBMODULE_CACHE
#endif

#ifdef USE_SUBMODULE_CACHE
#include <git2/sys/repository.h>
#endif

#ifndef GIT_ERROR_CALLBACK
#define GIT_ERROR_CALLBACK GITERR_CALLBACK
#endif

#define print_if_verbose(...) print_log(verbose, __VA_ARGS__)

typedef struct {
  int verbose;
  int retries;
  SEXP getkey;
  SEXP getcred;
} auth_callback_data_t;

typedef struct {
  const char *key_path;
  const char *pubkey_path;
  const char *pass_phrase;
} auth_key_data;

static void print_log(int verbose, const char *fmt, ...){
  if(verbose){
    va_list args;
    va_start(args, fmt);
    REvprintf(fmt, args);
    va_end(args);
  }
}

static const char *session_keyphrase(const char *set){
  static char *key;
  if(set){
    key = strdup(set);
    return NULL;
  }
  return key;
}

static char* get_password(SEXP cb, const char *url, const char **username, int retries){
  if(!Rf_isFunction(cb))
    Rf_error("cb must be a function");
  int err;
  SEXP call = PROTECT(Rf_lang4(cb,
                               PROTECT(safe_string(url)),
                               PROTECT(safe_string(*username)),
                               PROTECT(Rf_ScalarInteger(retries))));
  SEXP res = PROTECT(R_tryEval(call, R_GlobalEnv, &err));
  if(err || !Rf_isString(res) || Rf_length(res) < 2){
    UNPROTECT(5);
    return NULL;
  }
  if(*username == NULL){
    *username = strdup(CHAR(STRING_ELT(res, 0)));
  }
  UNPROTECT(5);
  return strdup(CHAR(STRING_ELT(res, 1)));
}

static int get_key_files(SEXP cb, auth_key_data *out, int verbose){
  if(!Rf_isFunction(cb))
    Rf_error("cb must be a function");
  int err = 0;
  SEXP call = PROTECT(Rf_lcons(cb, R_NilValue));
  SEXP res = PROTECT(verbose ? R_tryEval(call, R_GlobalEnv, &err) :
                       R_tryEvalSilent(call, R_GlobalEnv, &err));
  if(res && Rf_inherits(res, "try-error")){
    static char custom_callback_error[1000] = {0};
    snprintf(custom_callback_error, 999, "SSH authentication failure: %s", CHAR(STRING_ELT(res, 0)));
    giterr_set_str(GIT_ERROR_CALLBACK, custom_callback_error);
    UNPROTECT(2);
    return -1;
  }
  if(err || !Rf_isString(res)){
    giterr_set_str(GIT_ERROR_CALLBACK, "Failed to read local SSH key from callback function");
    UNPROTECT(2);
    return -1;
  }
  /* Todo: Maybe strdup() in case res gets collected */
  out->pubkey_path = CHAR(STRING_ELT(res, 0));
  out->key_path = CHAR(STRING_ELT(res, 1));
  out->pass_phrase = CHAR(STRING_ELT(res, 2));
  UNPROTECT(2);
  return 0;
}

static void fin_git_repository(SEXP ptr){
  if(!R_ExternalPtrAddr(ptr)) return;
  git_repository_free(R_ExternalPtrAddr(ptr));
  R_ClearExternalPtr(ptr);
}

#ifdef SKIP_HOSTKEY_CHECK
static int skip_hostkey_check(struct git_cert *cert, int valid, const char *host, void *payload){
  if(cert->cert_type == GIT_CERT_HOSTKEY_LIBSSH2)
    return 0;
  return valid;
}
void set_verify_handler(git_remote_callbacks *callbacks){
  callbacks->certificate_check = skip_hostkey_check;
}
#else
#define set_verify_handler(x)
#endif

SEXP new_git_repository(git_repository *repo){
  SEXP ptr = PROTECT(R_MakeExternalPtr(repo, R_NilValue, R_NilValue));
  R_RegisterCFinalizerEx(ptr, fin_git_repository, 1);
  Rf_setAttrib(ptr, R_ClassSymbol, Rf_mkString("git_repo_ptr"));
  UNPROTECT(1);
  return ptr;
}

git_repository *get_git_repository(SEXP ptr){
  if(TYPEOF(ptr) != EXTPTRSXP || !Rf_inherits(ptr, "git_repo_ptr"))
    Rf_error("handle is not a git_repo_ptr");
  if(!R_ExternalPtrAddr(ptr))
    Rf_error("pointer is dead");
  return R_ExternalPtrAddr(ptr);
}

static int print_progress(unsigned int cur, unsigned int tot, size_t bytes, void *payload){
  R_CheckUserInterrupt();
  static size_t prev = 0;
  if(prev != cur){
    prev = cur;
    REprintf("\rTransferred %d of %d objects...", cur, tot);
    if(cur == tot)
      REprintf("done!\n");
  }
  return 0;
}

static int fetch_progress(const git_transfer_progress *stats, void *payload){
  return print_progress(stats->received_objects, stats->total_objects, 0, NULL);
}

static int remote_message(const char *refname, const char *status, void *data){
  REprintf("[status] %s: %s\n", refname, status ? status : "unchanged");
  return 0;
}

static void checkout_progress(const char *path, size_t cur, size_t tot, void *payload){
  R_CheckUserInterrupt();
  static size_t prev = 0;
  if(prev != cur){
    prev = cur;
    REprintf("\rChecked out %zu of %zu commits...", cur, tot);
    if(cur == tot)
      REprintf(" done!\n");
  }
}

/* Examples: https://github.com/libgit2/libgit2/blob/master/tests/online/clone.c */
static int auth_callback(git_cred **cred, const char *url, const char *username,
                               unsigned int allowed_types, void *payload){
  /* First get a username */
  auth_callback_data_t *cb_data = payload;
  const char * ssh_user = username ? username : "git";
  int verbose = cb_data->verbose;
  giterr_clear();


#if AT_LEAST_LIBGIT2(0, 20)

  /* This is for SSH remotes */
  if(allowed_types & GIT_CREDTYPE_SSH_KEY){
    // First try the ssh agent
    if(cb_data->retries == 0){
      cb_data->retries++;
      if(getenv("SSH_AUTH_SOCK")){
        if(git_cred_ssh_key_from_agent(cred, ssh_user) == 0){
          print_if_verbose("Trying to authenticate '%s' using ssh-agent...\n", ssh_user);
          return 0;
        } else {
          print_if_verbose("Failed to connect to ssh-agent: %s\n", giterr_last()->message);
        }
      } else {
        print_if_verbose("Unable to find ssh-agent (SSH_AUTH_SOCK undefined)\n");
      }
    }
    // Second try is with the user provided key
    if(cb_data->retries == 1) {
      cb_data->retries++;
      auth_key_data key_data = {0};
      if(!get_key_files(cb_data->getkey, &key_data, verbose) &&
         !git_cred_ssh_key_new(cred, ssh_user, key_data.pubkey_path,
                               key_data.key_path, key_data.pass_phrase)){
        print_if_verbose("Trying to authenticate '%s' using provided ssh-key...\n", ssh_user);
        return 0;
      }
    }

    // Third is just bail with an error
    if(cb_data->retries == 2) {
      print_if_verbose("Failed to authenticate over SSH. You either need to provide a key or setup ssh-agent\n");
      if(strcmp(ssh_user, "git"))
        print_if_verbose("Are you sure ssh address has username '%s'? (ssh remotes usually have username 'git')\n", ssh_user);
      goto failure;
    }
  }

#endif

  /* This is for HTTP remotes */
  if(allowed_types & GIT_CREDTYPE_USERPASS_PLAINTEXT){
    if(cb_data->retries > 3){
      print_if_verbose("Failed password authentiation %d times. Giving up\n", cb_data->retries - 1);
      cb_data->retries = 0;
    } else {
      cb_data->retries++;
      print_if_verbose("Looking up https credentials for %s\n", url);
      char *pass = get_password(cb_data->getcred, url, &username, cb_data->retries);
      if(!username || !pass){
        print_if_verbose("Credential lookup failed\n");
        giterr_set_str(GIT_ERROR_CALLBACK, "HTTPS Authentication failure");
        goto failure;
      } else {
        return git_cred_userpass_plaintext_new(cred, username, pass);
      }
    }
  }
  print_if_verbose("All authentication methods failed\n");
failure:
  return GIT_EAUTH;
}

static auth_callback_data_t auth_callback_data(SEXP getkey, SEXP getcred, int verbose){
  auth_callback_data_t data_cb;
  data_cb.verbose = verbose;
  data_cb.retries = 0;
  data_cb.getcred = getcred;
  data_cb.getkey = getkey;
  return data_cb;
}

SEXP R_git_repository_init(SEXP path, SEXP is_bare){
  git_repository *repo = NULL;
  bail_if(git_repository_init(&repo, CHAR(STRING_ELT(path, 0)), Rf_asLogical(is_bare)), "git_repository_init");
#ifdef USE_SUBMODULE_CACHE
  git_repository_submodule_cache_all(repo);
#endif
  return new_git_repository(repo);
}

SEXP R_git_repository_open(SEXP path, SEXP search){
  git_repository *repo = NULL;
  if(Rf_asLogical(search)){
    bail_if(git_repository_open_ext(&repo, CHAR(STRING_ELT(path, 0)), 0, NULL), "git_repository_open_ext");
  } else {
    bail_if(git_repository_open(&repo, CHAR(STRING_ELT(path, 0))), "git_repository_open");
  }
#ifdef USE_SUBMODULE_CACHE
  git_repository_submodule_cache_all(repo);
#endif
  return new_git_repository(repo);
}

SEXP R_git_repository_find(SEXP path){
  git_buf buf = {0};
  bail_if(git_repository_discover(&buf, CHAR(STRING_ELT(path, 0)), 0, NULL), "git_repository_discover");
  SEXP out = Rf_ScalarString(Rf_mkCharLenCE(buf.ptr, buf.size, CE_UTF8));
  git_buf_free(&buf);
  return out;
}

/* Based on code provided https://libgit2.org/docs/guides/101-samples/#repositories_clone_mirror */
int create_remote_mirror(git_remote **out, git_repository *repo, const char *name, const char *url, void *payload){
  int error = git_remote_create_with_fetchspec(out, repo, name, url, "+refs/*:refs/*");
  if (error < 0)
    return(error);

  git_config *cfg;
  error = git_repository_config(&cfg, repo);
  if (error < 0)
    return(error);

  char *mirror_config;
  if (asprintf(&mirror_config, "remote.%s.mirror", name) == -1) {
    giterr_set_str(GITERR_OS, "asprintf failed");
    git_config_free(cfg);
    return -1;
  }

  error = git_config_set_bool(cfg, mirror_config, TRUE);

  free(mirror_config);
  git_config_free(cfg);

  return error;
}

static int repository_enable_cache(git_repository **out, const char *path, int bare, void *payload) {
  int res = git_repository_init(out, path, bare);
#ifdef USE_SUBMODULE_CACHE
  git_repository_submodule_cache_all(*out);
#endif
  return res;
}

SEXP R_git_repository_clone(SEXP url, SEXP path, SEXP branch, SEXP getkey, SEXP getcred,
                            SEXP bare, SEXP mirror, SEXP depth, SEXP verbose){
  git_repository *repo = NULL;
  git_clone_options clone_opts = GIT_CLONE_OPTIONS_INIT;
  clone_opts.checkout_opts.checkout_strategy = GIT_CHECKOUT_SAFE;
  auth_callback_data_t data_cb = auth_callback_data(getkey, getcred, Rf_asLogical(verbose));
  clone_opts.fetch_opts.callbacks.payload = &data_cb;
  clone_opts.fetch_opts.callbacks.credentials = auth_callback;
  clone_opts.repository_cb = repository_enable_cache;

  set_verify_handler(&clone_opts.fetch_opts.callbacks);

  /* shallow clone: fetch only the last 'depth' commits (libgit2 >= 1.7) */
  int clone_depth = Rf_asInteger(depth);
  if(clone_depth > 0){
#if AT_LEAST_LIBGIT2(1, 7)
    clone_opts.fetch_opts.depth = clone_depth;
#else
    Rf_warning("Shallow clone (depth) requires libgit2 >= 1.7.0. Ignoring the depth parameter.");
#endif
  }

  /* Also enables download progress and user interrupt */
  if(Rf_asLogical(verbose)){
    clone_opts.checkout_opts.progress_cb = checkout_progress;
    clone_opts.fetch_opts.callbacks.transfer_progress = fetch_progress;
  }

  if(Rf_asLogical(bare) || Rf_asLogical(mirror))
    clone_opts.bare = TRUE;

  if(Rf_asLogical(mirror))
    clone_opts.remote_cb = create_remote_mirror;

  /* specify branch to checkout */
  if(Rf_length(branch))
    clone_opts.checkout_branch = CHAR(STRING_ELT(branch, 0));

  /* try to clone */
  bail_if(git_clone(&repo, CHAR(STRING_ELT(url, 0)), CHAR(STRING_ELT(path, 0)),
                    &clone_opts), "git_clone");
  bail_if_null(repo, "failed to clone repo");
  return new_git_repository(repo);
}

/* From: https://github.com/libgit2/libgit2/blob/master/examples/network/fetch.c */
static int update_cb(const char *refname, const git_oid *a, const git_oid *b, void *data){
  char a_str[GIT_OID_HEXSZ+1], b_str[GIT_OID_HEXSZ+1];
  git_oid_fmt(b_str, b);
  b_str[GIT_OID_HEXSZ] = '\0';
  if (git_oid_iszero(a)) {
    REprintf("[new]     %.20s %s\n", b_str, refname);
  } else {
    git_oid_fmt(a_str, a);
    a_str[GIT_OID_HEXSZ] = '\0';
    REprintf("[updated] %.10s..%.10s %s\n", a_str, b_str, refname);
  }
  return 0;
}

SEXP R_git_remote_fetch(SEXP ptr, SEXP name, SEXP refspec, SEXP getkey, SEXP getcred, SEXP prune, SEXP verbose){
  git_remote *remote = NULL;
  git_repository *repo = get_git_repository(ptr);
  if(git_remote_lookup(&remote, repo, CHAR(STRING_ELT(name, 0))) < 0){
    if(git_remote_create_anonymous(&remote, repo, CHAR(STRING_ELT(name, 0))) < 0)
      Rf_error("Remote must either be an existing remote or URL");
  }
  git_strarray *rs = Rf_length(refspec) ? files_to_array(refspec) : NULL;
  git_fetch_options opts = GIT_FETCH_OPTIONS_INIT;
  opts.download_tags = GIT_REMOTE_DOWNLOAD_TAGS_ALL;
  if(Rf_asLogical(prune))
    opts.prune = GIT_FETCH_PRUNE;
  opts.update_fetchhead = 1;
  auth_callback_data_t data_cb = auth_callback_data(getkey, getcred, Rf_asLogical(verbose));
  opts.callbacks.payload = &data_cb;
  opts.callbacks.credentials = auth_callback;
  set_verify_handler(&opts.callbacks);

  /* Also enables download progress and user interrupt */
  if(Rf_asLogical(verbose)){
    opts.callbacks.update_tips = &update_cb;
    opts.callbacks.transfer_progress = fetch_progress;
  }
  bail_if(git_remote_fetch(remote, rs, &opts, NULL), "git_remote_fetch");
  git_remote_free(remote);
  return ptr;
}

SEXP R_git_remote_push(SEXP ptr, SEXP name, SEXP refspec, SEXP getkey, SEXP getcred, SEXP verbose){
  git_remote *remote = NULL;
  git_repository *repo = get_git_repository(ptr);
  if(git_remote_lookup(&remote, repo, CHAR(STRING_ELT(name, 0))) < 0){
    if(git_remote_create_anonymous(&remote, repo, CHAR(STRING_ELT(name, 0))) < 0)
      Rf_error("Remote must either be an existing remote or URL");
  }
  git_strarray *rs = Rf_length(refspec) ? files_to_array(refspec) : NULL;
  git_push_options opts = GIT_PUSH_OPTIONS_INIT;
  auth_callback_data_t data_cb = auth_callback_data(getkey, getcred, Rf_asLogical(verbose));
  opts.callbacks.payload = &data_cb;
  opts.callbacks.credentials = auth_callback;

  /* Also enables download progress and user interrupt */
  if(Rf_asLogical(verbose)){
    opts.callbacks.update_tips = &update_cb;
    opts.callbacks.transfer_progress = fetch_progress;
    opts.callbacks.push_transfer_progress = print_progress;
    opts.callbacks.push_update_reference = remote_message;
  }
  set_verify_handler(&opts.callbacks);

  bail_if(git_remote_push(remote, rs, &opts), "git_remote_push");
  git_remote_free(remote);
  return ptr;
}

SEXP R_set_session_keyphrase(SEXP key){
  if(!Rf_length(key) || !Rf_isString(key))
    Rf_error("Need to pass a string");
  session_keyphrase(CHAR(STRING_ELT(key, 0)));
  return R_NilValue;
}

SEXP R_git_remote_ls(SEXP ptr, SEXP name, SEXP getkey, SEXP getcred, SEXP verbose){
  git_remote *remote = NULL;
  const char *remote_name = CHAR(STRING_ELT(name, 0));
  git_repository *repo = get_git_repository(ptr);
  if(git_remote_lookup(&remote, repo, remote_name) < 0){
    remote_name = NULL;
    if(git_remote_create_anonymous(&remote, repo, CHAR(STRING_ELT(name, 0))) < 0)
      Rf_error("Remote must either be an existing remote or URL");
  }
  git_remote_callbacks callbacks = GIT_REMOTE_CALLBACKS_INIT;
  auth_callback_data_t data_cb = auth_callback_data(getkey, getcred, Rf_asLogical(verbose));
  callbacks.payload = &data_cb;
  callbacks.credentials = auth_callback;
  set_verify_handler(&callbacks);

  /* Also enables download progress and user interrupt */
  if(Rf_asLogical(verbose)){
    callbacks.update_tips = &update_cb;
    callbacks.transfer_progress = fetch_progress;
    callbacks.push_transfer_progress = print_progress;
    callbacks.push_update_reference = remote_message;
  }
  bail_if(git_remote_connect(remote, GIT_DIRECTION_FETCH, &callbacks, NULL, NULL), "git_remote_connect");

  /* We are connected */
  size_t refs_len;
  const git_remote_head **refs;
  bail_if(git_remote_ls(&refs, &refs_len, remote), "git_remote_ls");

  /* Store the default branch (remote HEAD) */
  if (remote_name && refs_len && refs[0]->symref_target){
    char head[1000] = {0};
    char target[1000] = {0};
    snprintf(head, 1000, "refs/remotes/%s/HEAD", git_remote_name(remote));
    const char *symref = refs[0]->symref_target;
    if(strncmp(symref, "refs/heads/", 11) == 0){
      snprintf(target, 1000, "refs/remotes/%s/%s", git_remote_name(remote), symref + 11);
    } else {
      strcpy(target, symref);
    }
    git_object *revision = NULL;
    if(git_revparse_single(&revision, repo, target) == GIT_OK){
      git_object_free(revision);
      git_reference *ref = NULL;
      git_reference_symbolic_create(&ref, repo, head, target, 1, "Updated default branch!");
      git_reference_free(ref);
    } else {
      REprintf("Remote default branch %s not found locally (fetch first)\n", target);
    }
  }

  /* Collect references */
  SEXP names = PROTECT(Rf_allocVector(STRSXP, refs_len));
  SEXP oids = PROTECT(Rf_allocVector(STRSXP, refs_len));
  SEXP syms = PROTECT(Rf_allocVector(STRSXP, refs_len));
  for (int i = 0; i < refs_len; i++) {
    char oid[GIT_OID_HEXSZ + 1] = {0};
    git_oid_fmt(oid, &refs[i]->oid);
    SET_STRING_ELT(names, i, safe_char(refs[i]->name));
    SET_STRING_ELT(oids, i, safe_char(oid));
    SET_STRING_ELT(syms, i, safe_char(refs[i]->symref_target));
  }
  git_remote_free(remote);
  SEXP out = build_tibble(3, "ref", names, "symref", syms, "oid", oids);
  UNPROTECT(3);
  return out;
}