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Commits (7)
// From CLI11 examples
#include "CLI11.hpp"
#include "json.hpp"
// This example is only built on GCC 7 on Travis due to mismatch in stdlib
// for clang (CLI11 is forgiving about mismatches, json.hpp is not)
using nlohmann::json;
class ConfigJSON : public CLI::Config {
public:
std::string to_config(const CLI::App *app, bool default_also, bool, std::string) const override {
json j;
for(const CLI::Option *opt : app->get_options({})) {
// Only process option with a long-name and configurable
if(!opt->get_lnames().empty() && opt->get_configurable()) {
std::string name = opt->get_lnames()[0];
// Non-flags
if(opt->get_type_size() != 0) {
// If the option was found on command line
if(opt->count() == 1)
j[name] = opt->results().at(0);
else if(opt->count() > 1)
j[name] = opt->results();
// If the option has a default and is requested by optional argument
else if(default_also && !opt->get_defaultval().empty())
j[name] = opt->get_defaultval();
// Flag, one passed
} else if(opt->count() == 1) {
j[name] = true;
// Flag, multiple passed
} else if(opt->count() > 1) {
j[name] = opt->count();
// Flag, not present
} else if(opt->count() == 0 && default_also) {
j[name] = false;
}
}
}
for(const CLI::App *subcom : app->get_subcommands({}))
j[subcom->get_name()] = json(to_config(subcom, default_also, false, ""));
return j.dump(4);
}
std::vector<CLI::ConfigItem> from_config(std::istream &input) const override {
json j;
input >> j;
return _from_config(j);
}
std::vector<CLI::ConfigItem>
_from_config(json j, std::string name = "", std::vector<std::string> prefix = {}) const {
std::vector<CLI::ConfigItem> results;
if(j.is_object()) {
for(json::iterator item = j.begin(); item != j.end(); ++item) {
auto copy_prefix = prefix;
if(!name.empty())
copy_prefix.push_back(name);
auto sub_results = _from_config(*item, item.key(), copy_prefix);
results.insert(results.end(), sub_results.begin(), sub_results.end());
}
} else if(!name.empty()) {
results.emplace_back();
CLI::ConfigItem &res = results.back();
res.name = name;
res.parents = prefix;
if(j.is_boolean()) {
res.inputs = {j.get<bool>() ? "true" : "false"};
} else if(j.is_number()) {
std::stringstream ss;
ss << j.get<double>();
res.inputs = {ss.str()};
} else if(j.is_string()) {
res.inputs = {j.get<std::string>()};
} else if(j.is_array()) {
for(std::string ival : j)
res.inputs.push_back(ival);
} else {
throw CLI::ConversionError("Failed to convert " + name);
}
} else {
throw CLI::ConversionError("You must make all top level values objects in json!");
}
return results;
}
};
int testCLI11_json(int argc, char **argv) {
CLI::App app;
app.config_formatter(std::make_shared<ConfigJSON>());
int item;
app.add_flag("--simple");
app.add_option("--item", item);
app.set_config("--config");
CLI11_PARSE(app, argc, argv);
std::cout << app.config_to_str(true, true) << std::endl;
return 0;
}
class ConfigJSON : public CLI::Config {
std::string to_config(const CLI::App *app, bool default_also, bool, std::string) const override ;
std::vector<CLI::ConfigItem> from_config(std::istream &input) const override ;
} ;
{
"first-reads": 10,
"min-reads": "1",
"max-consensus": "1",
"cdr3": true
}
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH --config ../data/config.vidjil $VIDJIL_DATA/Stanford_S22.fasta
$ Analyze 10 reads (--first-reads)
: in 10 reads
$ Report a clone with one read (--min-reads)
1: Clone #001 .* 1 read
$ Compute a CDR3 (--cdr3)
1:CARVGSSWS#MLLIIW
$ Report only one clone (--max-consensus)
1: Clone #
......@@ -13,3 +13,14 @@ $ Segment two reads on IgVC/IgJC (second -g option)
1: IgVC .* -> .* 1
1: IgJC .* -> .* 1
!LAUNCH: cat out/config.vidjil
$ Both germlines are in out/config.vidjil
1: /germline"
1: /homo-sapiens-isotypes.g"
$ Check that some options are correctly reported
1: "max-consensus": "100"
1: "plain-index": false
1: "cdr3": false
......@@ -17,4 +17,4 @@ $ Display advanced options
: custom Cost
$ Correct number of options
52:^..-
53:^..-
......@@ -57,6 +57,7 @@
#include "lib/CLI11.hpp"
#include "lib/json.hpp"
#include "lib/CLI11_json.hpp"
#include "vidjil.h"
......@@ -104,6 +105,7 @@ enum { CMD_WINDOWS, CMD_CLONES, CMD_SEGMENT, CMD_GERMLINES } ;
#define AFFECTS_FILENAME ".affects"
#define EDGES_FILENAME ".edges"
#define COMP_FILENAME "comp.vidjil"
#define CONFIG_FILENAME "config.vidjil"
#define AIRR_SUFFIX ".tsv"
#define JSON_SUFFIX ".vidjil"
......@@ -229,6 +231,7 @@ int main (int argc, char **argv)
#endif
CLI::App app{"# vidjil-algo -- V(D)J recombinations analysis", argv[0]};
app.config_formatter(std::make_shared<ConfigJSON>());
app.get_formatter()->label("REQUIRED", "");
app.get_formatter()->label("Positionnals", "");
app.failure_message(failure_message_doc);
......@@ -266,6 +269,9 @@ int main (int argc, char **argv)
// ----------------------------------------------------------------------------------------------------------------------
group = "Input" ;
app.set_config("--config", "", "read a (.json) config.vidjil file with options") -> type_name("FILE")
-> group(group) -> level();
string read_header_separator = DEFAULT_READ_HEADER_SEPARATOR ;
app.add_option("--header-sep", read_header_separator, "separator for headers in the reads file", false)
-> group(group) -> level() -> type_name("CHAR='" DEFAULT_READ_HEADER_SEPARATOR "'");
......@@ -743,6 +749,13 @@ int main (int argc, char **argv)
}
cout << endl;
// Dump configuration
string f_config = out_dir + CONFIG_FILENAME ;
cout << " ==> " << f_config << endl ;
ofstream out_config(f_config.c_str());
out_config << app.config_to_str(true, true) << endl;
out_config.close();
//////////////////////////////////
// Display time and date
time_t rawtime;
......