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// =============================================================== //
// //
// File : adChangeKey.cxx //
// Purpose : Changekey management //
// //
// Coded by Elmar Pruesse and Ralf Westram in May 2009 //
// Institute of Microbiology (Technical University Munich) //
// http://www.arb-home.de/ //
// //
// =============================================================== //
#include <arbdbt.h>
#include "gb_local.h"
// get the container of a species key description
GBDATA *GBT_get_changekey(GBDATA *gb_main, const char *key, const char *change_key_path) {
#if defined(WARN_TODO)
#warning check if search for CHANGEKEY_NAME should be case-sensitive!
#endif
GBDATA *gb_key = 0;
GBDATA *gb_key_data = GB_search(gb_main, change_key_path,
GB_CREATE_CONTAINER);
if (gb_key_data) {
GBDATA *gb_key_name = GB_find_string(gb_key_data, CHANGEKEY_NAME, key, GB_IGNORE_CASE, SEARCH_GRANDCHILD);
if (gb_key_name) {
gb_key = GB_get_father(gb_key_name);
}
}
return gb_key;
}
GB_TYPES GBT_get_type_of_changekey(GBDATA *gb_main, const char *field_name, const char *change_key_path) {
GB_TYPES type = GB_NONE;
GBDATA *gbd = GBT_get_changekey(gb_main, field_name, change_key_path);
if (gbd) {
long *typePtr = GBT_read_int(gbd, CHANGEKEY_TYPE);
if (typePtr) {
type = (GB_TYPES)*typePtr;
}
}
return type;
}
static GB_ERROR gbt_set_type_of_changekey(GBDATA *gb_main, const char *field_name, GB_TYPES type, const char *change_key_path) {
GB_ERROR error = NULL;
GBDATA *gbd = GBT_get_changekey(gb_main, field_name, change_key_path);
if (!gbd) {
error = GBS_global_string("Can't set type of nonexistent changekey " "\"%s\"", field_name);
}
else {
error = GBT_write_int(gbd, CHANGEKEY_TYPE, type);
}
return error;
}
GB_ERROR GBT_add_new_changekey_to_keypath(GBDATA *gb_main, const char *name, int type, const char *keypath) {
GB_ERROR error = NULL;
GBDATA *gb_key = GBT_get_changekey(gb_main, name, keypath);
const char *c = GB_first_non_key_char(name);
if (c) {
char *new_name = strdup(name);
*(char*)GB_first_non_key_char(new_name) = 0;
if (*c == '/') error = GBT_add_new_changekey(gb_main, new_name, GB_DB);
else if (*c == '-') error = GBT_add_new_changekey(gb_main, new_name, GB_LINK);
else error = GBS_global_string("Cannot add '%s' to your key list (illegal character '%c')", name, *c);
free(new_name);
}
if (!error) {
if (!gb_key) { // create new key
GBDATA *gb_key_data = GB_search(gb_main, keypath, GB_CREATE_CONTAINER);
gb_key = gb_key_data ? GB_create_container(gb_key_data, CHANGEKEY) : 0;
if (!gb_key) error = GB_await_error();
else {
error = GBT_write_string(gb_key, CHANGEKEY_NAME, name);
if (!error) error = GBT_write_int(gb_key, CHANGEKEY_TYPE, type);
}
}
else { // check type of existing key
long *elem_type = GBT_read_int(gb_key, CHANGEKEY_TYPE);
if (!elem_type) error = GB_await_error();
else if (*elem_type != type) error = GBS_global_string("Key '%s' exists, but has different type", name);
}
}
gb_assert(gb_key || error);
return error;
}
GB_ERROR GBT_add_new_changekey(GBDATA *gb_main, const char *name, int type) {
return GBT_add_new_changekey_to_keypath(gb_main, name, type, CHANGE_KEY_PATH);
}
GB_ERROR GBT_add_new_gene_changekey(GBDATA *gb_main, const char *name, int type) {
return GBT_add_new_changekey_to_keypath(gb_main, name, type, CHANGE_KEY_PATH_GENES);
}
GB_ERROR GBT_add_new_experiment_changekey(GBDATA *gb_main, const char *name, int type) {
return GBT_add_new_changekey_to_keypath(gb_main, name, type, CHANGE_KEY_PATH_EXPERIMENTS);
}
static GB_ERROR write_as_int(GBDATA *gbfield, const char *data, bool trimmed, size_t *rounded) {
char *end = 0;
unsigned long i = strtoul(data, &end, 10);
GB_ERROR error = NULL;
if (end == data || end[0] != 0) {
if (trimmed) {
// fallback: convert to double and round
double d = strtod(data, &end);
if (end == data || end[0] != 0) {
error = GBS_global_string("cannot convert '%s' to rounded numeric value", data);
}
else {
(*rounded)++;
i = d>0 ? (int)(d+0.5) : (int)(d-0.5);
error = GB_write_int(gbfield, i);
if (error) error = GBS_global_string("write error (%s)", error);
}
}
else {
char *trimmed_data = GBS_trim(data);
error = write_as_int(gbfield, trimmed_data, true, rounded);
free(trimmed_data);
}
}
else {
error = GB_write_int(gbfield, i);
if (error) error = GBS_global_string("write error (%s)", error);
}
return error;
}
static GB_ERROR write_as_float(GBDATA *gbfield, const char *data, bool trimmed) {
char *end = 0;
double d = strtod(data, &end);
GB_ERROR error = NULL;
if (end == data || end[0] != 0) {
if (trimmed) {
error = GBS_global_string("cannot convert '%s' to numeric value", data);
}
else {
char *trimmed_data = GBS_trim(data);
error = write_as_float(gbfield, trimmed_data, true);
free(trimmed_data);
}
}
else {
error = GB_write_float(gbfield, d);
if (error) error = GBS_global_string("write error (%s)", error);
}
return error;
}
GB_ERROR GBT_convert_changekey(GBDATA *gb_main, const char *name, GB_TYPES target_type) {
GB_ERROR error = GB_push_transaction(gb_main);
bool need_convert = true;
if (!error) {
GBDATA *gbkey = GBT_get_changekey(gb_main, name, CHANGE_KEY_PATH);
if (gbkey) {
GB_TYPES source_type = (GB_TYPES)*GBT_read_int(gbkey, CHANGEKEY_TYPE);
if (source_type == target_type) need_convert = false;
}
else {
error = GBS_global_string("Unknown changekey '%s'", name);
}
}
if (!error && need_convert) {
GBDATA *gbspec = GBT_first_species(gb_main);
size_t rounded = 0;
for (; gbspec; gbspec = GBT_next_species(gbspec)) {
GBDATA *gbfield = GB_entry(gbspec, name);
// If entry does not exist, no need to convert (sparse population is valid => 'NULL' value)
if (gbfield) {
char *data = GB_read_as_string(gbfield);
if (!data) {
error = GBS_global_string("read error (%s)", GB_await_error());
}
else {
error = GB_delete(gbfield);
if (!error) {
gbfield = GB_create(gbspec, name, target_type);
if (!gbfield) {
error = GBS_global_string("create error (%s)", GB_await_error());
}
else {
switch (target_type) {
case GB_INT:
error = write_as_int(gbfield, data, false, &rounded);
break;
case GB_FLOAT:
error = write_as_float(gbfield, data, false);
break;
case GB_STRING:
error = GB_write_string(gbfield, data);
if (error) error = GBS_global_string("write error (%s)", error);
break;
default:
error = "Conversion is not possible";
break;
}
}
}
free(data);
}
}
if (error) break;
}
if (error && gbspec) {
const char *spname = GBT_read_name(gbspec);
error = GBS_global_string("%s for species '%s'", error, spname);
}
if (!error) error = gbt_set_type_of_changekey(gb_main, name, target_type, CHANGE_KEY_PATH);
if (!error && rounded>0) {
GB_warningf("%zi values were rounded (loss of precision)", rounded);
}
}
if (error) error = GBS_global_string("GBT_convert: %s", error);
return GB_end_transaction(gb_main, error);
}
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