static void annotate_refs_with_symref_info(struct ref *ref)
{
struct string_list symref = STRING_LIST_INIT_DUP;
const char *feature_list = server_capabilities;
while (feature_list) {
int len;
const char *val;
val = parse_feature_value(feature_list, "symref", &len);
if (!val)
break;
parse_one_symref_info(&symref, val, len);
feature_list = val + 1;
}
sort_string_list(&symref);
for (; ref; ref = ref->next) {
struct string_list_item *item;
item = string_list_lookup(&symref, ref->name);
if (!item)
continue;
ref->symref = xstrdup((char *)item->util);
}
string_list_clear(&symref, 0);
}
int combine_notes_cat_sort_uniq(unsigned char *cur_sha1,
const unsigned char *new_sha1)
{
struct string_list sort_uniq_list = STRING_LIST_INIT_DUP;
struct strbuf buf = STRBUF_INIT;
int ret = 1;
/* read both note blob objects into unique_lines */
if (string_list_add_note_lines(&sort_uniq_list, cur_sha1))
goto out;
if (string_list_add_note_lines(&sort_uniq_list, new_sha1))
goto out;
string_list_remove_empty_items(&sort_uniq_list, 0);
sort_string_list(&sort_uniq_list);
string_list_remove_duplicates(&sort_uniq_list, 0);
/* create a new blob object from sort_uniq_list */
if (for_each_string_list(&sort_uniq_list,
string_list_join_lines_helper, &buf))
goto out;
ret = write_sha1_file(buf.buf, buf.len, blob_type, cur_sha1);
out:
strbuf_release(&buf);
string_list_clear(&sort_uniq_list, 0);
return ret;
}
static int prepare_repo_cmd(struct cgit_context *ctx)
{
char *tmp;
unsigned char sha1[20];
int nongit = 0;
int rc;
setenv("GIT_DIR", ctx->repo->path, 1);
setup_git_directory_gently(&nongit);
if (nongit) {
rc = errno;
ctx->page.title = fmt("%s - %s", ctx->cfg.root_title,
"config error");
tmp = fmt("Failed to open %s: %s",
ctx->repo->name,
rc ? strerror(rc) : "Not a valid git repository");
ctx->repo = NULL;
cgit_print_http_headers(ctx);
cgit_print_docstart(ctx);
cgit_print_pageheader(ctx);
cgit_print_error(tmp);
cgit_print_docend();
return 1;
}
ctx->page.title = fmt("%s - %s", ctx->repo->name, ctx->repo->desc);
if (!ctx->repo->defbranch)
ctx->repo->defbranch = guess_defbranch();
if (!ctx->qry.head) {
ctx->qry.nohead = 1;
ctx->qry.head = find_default_branch(ctx->repo);
}
if (!ctx->qry.head) {
cgit_print_http_headers(ctx);
cgit_print_docstart(ctx);
cgit_print_pageheader(ctx);
cgit_print_error("Repository seems to be empty");
cgit_print_docend();
return 1;
}
if (get_sha1(ctx->qry.head, sha1)) {
tmp = xstrdup(ctx->qry.head);
ctx->qry.head = ctx->repo->defbranch;
ctx->page.status = 404;
ctx->page.statusmsg = "Not found";
cgit_print_http_headers(ctx);
cgit_print_docstart(ctx);
cgit_print_pageheader(ctx);
cgit_print_error(fmt("Invalid branch: %s", tmp));
cgit_print_docend();
return 1;
}
sort_string_list(&ctx->repo->submodules);
cgit_prepare_repo_env(ctx->repo);
return 0;
}
static void check_aliased_updates(struct command *commands)
{
struct command *cmd;
struct string_list ref_list = STRING_LIST_INIT_NODUP;
for (cmd = commands; cmd; cmd = cmd->next) {
struct string_list_item *item =
string_list_append(&ref_list, cmd->ref_name);
item->util = (void *)cmd;
}
sort_string_list(&ref_list);
for (cmd = commands; cmd; cmd = cmd->next)
check_aliased_update(cmd, &ref_list);
string_list_clear(&ref_list, 0);
}
/****************************************************************************
* Read an alignment from a file. Sort the sequences by sequence name if
* requested. Remove all gap sequences if requested.
****************************************************************************/
ALIGNMENT_T* read_alignment_from_file
(char *filename,
BOOLEAN_T sort,
BOOLEAN_T remove_allgap_seqs,
int* ref_seq_index
)
{
int i;
// Read the sequences.
ALIGNMENT_T* alignment = read_alignment_from_clustalw_file(filename);
if (sort) {
// Create a temporary array to hold sorted sequence pointers.
int num_sequences = get_num_aligned_sequences(alignment);
SEQ_T** sequences = (SEQ_T**) mm_malloc(num_sequences * sizeof(SEQ_T*));
// Sort the sequences by name.
STRING_LIST_T* alignment_species = get_species_names(alignment);
// Store the name of the reference sequence.
char *ref_name = get_nth_string(*ref_seq_index, alignment_species);
sort_string_list(alignment_species); // keep species alphabetical
for (i=0; i<num_sequences; i++) {
char *name = get_nth_string(i, alignment_species);
sequences[i] = get_alignment_sequence_by_name(name, alignment);
}
myfree(alignment->sequences);
alignment->sequences = sequences;
// Find the new index of the reference sequence.
*ref_seq_index = get_index_in_string_list(ref_name, alignment_species);
}
if (remove_allgap_seqs) {
ALIGNMENT_T* new_alignment = remove_allgap_sequences(alignment);
if (new_alignment != alignment) {
free_alignment(alignment);
alignment = new_alignment;
}
}
return(alignment);
} // read_alignment_from_file
struct ref *fetch_pack(struct fetch_pack_args *args,
int fd[], struct child_process *conn,
const struct ref *ref,
const char *dest,
struct string_list *sought,
char **pack_lockfile)
{
struct stat st;
struct ref *ref_cpy;
fetch_pack_setup();
if (args->depth > 0) {
if (stat(git_path("shallow"), &st))
st.st_mtime = 0;
}
if (sought->nr) {
sort_string_list(sought);
string_list_remove_duplicates(sought, 0);
}
if (!ref) {
packet_flush(fd[1]);
die("no matching remote head");
}
ref_cpy = do_fetch_pack(args, fd, ref, sought, pack_lockfile);
if (args->depth > 0) {
static struct lock_file lock;
struct cache_time mtime;
struct strbuf sb = STRBUF_INIT;
char *shallow = git_path("shallow");
int fd;
mtime.sec = st.st_mtime;
mtime.nsec = ST_MTIME_NSEC(st);
if (stat(shallow, &st)) {
if (mtime.sec)
die("shallow file was removed during fetch");
} else if (st.st_mtime != mtime.sec
#ifdef USE_NSEC
|| ST_MTIME_NSEC(st) != mtime.nsec
#endif
)
die("shallow file was changed during fetch");
fd = hold_lock_file_for_update(&lock, shallow,
LOCK_DIE_ON_ERROR);
if (!write_shallow_commits(&sb, 0)
|| write_in_full(fd, sb.buf, sb.len) != sb.len) {
unlink_or_warn(shallow);
rollback_lock_file(&lock);
} else {
commit_lock_file(&lock);
}
strbuf_release(&sb);
}
reprepare_packed_git();
return ref_cpy;
}
