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Add file reading functionality and update script and database handling

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This commit is contained in:
Max Lübke 2024-03-19 13:11:42 +00:00
parent 8328fd1390
commit d77aad7d2e
2 changed files with 43 additions and 17 deletions
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2
ext/iphreeqc

@ -1 +1 @@
Subproject commit b34c327377e2e06fb1d79b546996b9b401e850bc
Subproject commit d6e7130746f9823e0bc5f711179e676e27ba3737

58
src/Init/GridInit.cpp
View File

@ -6,6 +6,7 @@
#include <Rcpp/vector/instantiation.h>
#include <map>
#include <regex>
#include <sstream>
#include <string>
#include <vector>
@ -73,24 +74,49 @@ getModuleSizes(IPhreeqcPOET &phreeqc, const Rcpp::List &initial_grid) {
return phreeqc.getModuleSizes(row_ids);
}
void InitialList::initGrid(const Rcpp::List &grid_input) {
// parse input values
const std::string script = Rcpp::as<std::string>(
grid_input[getGridMemberString(GridMembers::PQC_SCRIPT_FILE)]);
const std::string database = Rcpp::as<std::string>(
grid_input[getGridMemberString(GridMembers::PQC_DB_FILE)]);
static std::string readFile(const std::string &path) {
std::string string_rpath(PATH_MAX, '\0');
std::string script_rp(PATH_MAX, '\0');
std::string database_rp(PATH_MAX, '\0');
if (realpath(script.c_str(), script_rp.data()) == nullptr) {
throw std::runtime_error("Failed to resolve the path of the Phreeqc input" +
script);
if (realpath(path.c_str(), string_rpath.data()) == nullptr) {
throw std::runtime_error("Failed to resolve the realpath to file " + path);
}
if (realpath(database.c_str(), database_rp.data()) == nullptr) {
throw std::runtime_error("Failed to resolve the path of the database" +
database);
std::ifstream file(string_rpath);
if (!file.is_open()) {
throw std::runtime_error("Failed to open file: " + path);
}
std::stringstream buffer;
buffer << file.rdbuf();
return buffer.str();
}
void InitialList::initGrid(const Rcpp::List &grid_input) {
// parse input values
std::string script;
std::string database;
if (grid_input.containsElementNamed(
getGridMemberString(GridMembers::PQC_SCRIPT_FILE))) {
script = readFile(Rcpp::as<std::string>(
grid_input[getGridMemberString(GridMembers::PQC_SCRIPT_FILE)]));
} else {
script = Rcpp::as<std::string>(
grid_input[getGridMemberString(GridMembers::PQC_SCRIPT_STRING)]);
}
if (grid_input.containsElementNamed(
getGridMemberString(GridMembers::PQC_DB_FILE))) {
database = readFile(Rcpp::as<std::string>(
grid_input[getGridMemberString(GridMembers::PQC_DB_FILE)]));
} else {
database = Rcpp::as<std::string>(
grid_input[getGridMemberString(GridMembers::PQC_DB_STRING)]);
}
Rcpp::NumericMatrix grid_def =
@ -122,7 +148,7 @@ void InitialList::initGrid(const Rcpp::List &grid_input) {
throw std::runtime_error("Grid size must be positive.");
}
IPhreeqcPOET phreeqc(database_rp, script_rp);
IPhreeqcPOET phreeqc(database, script);
this->phreeqc_mat = pqcScriptToGrid(phreeqc, R);
this->initial_grid = matToGrid(R, this->phreeqc_mat, grid_def);