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job.cpp
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job.cpp
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/*
Pheniqs : PHilology ENcoder wIth Quality Statistics
Copyright (C) 2018 Lior Galanti
NYU Center for Genetics and System Biology
Author: Lior Galanti <lior.galanti@nyu.edu>
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as
published by the Free Software Foundation, either version 3 of the
License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Affero General Public License for more details.
You should have received a copy of the GNU Affero General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#include "job.h"
Job::Job(Document& operation) try :
operation(move(operation)),
interactive(this->operation["interactive"]),
schema_repository(this->operation["schema"]),
projection_repository(this->operation["projection"]),
instruction(kObjectType),
ontology(kObjectType),
report(kObjectType) {
} catch(Error& error) {
error.push("Job");
throw;
};
Job::~Job() {
};
void Job::assemble() {
/* if a URL to an instruction file was provided in the interactive instruction,
load it and overlay on top of the ontology */
URL configuration_url;
if(decode_value_by_key< URL >("configuration url", configuration_url, interactive)) {
string buffer(configuration_url);
expand_shell(buffer);
normalize_standard_stream(buffer, IoDirection::IN);
URL resolved(buffer);
overlay_json_object(instruction, read_instruction_document(resolved));
sort_json_value(instruction, instruction);
}
};
void Job::compile() {
ontology.CopyFrom(instruction, ontology.GetAllocator());
remove_disabled_from_json_value(ontology, ontology);
clean_json_object(ontology, ontology);
validate();
};
void Job::describe() const {
};
void Job::execute() {
load();
start();
stop();
finalize();
};
void Job::write_result() const {
URL report_url(decode_value_by_key< URL >("report url", ontology));
if(!report_url.is_dev_null()) {
if(report_url.is_stdout()) {
print_json(report, cout, float_precision());
} else if(report_url.is_stderr()) {
print_json(report, cerr, float_precision());
} else {
print_json(report, report_url.path().c_str(), float_precision());
}
}
};
void Job::write_static_instruction() const {
Document assembled;
assembled.CopyFrom(instruction, assembled.GetAllocator());
apply_interactive_ontology(assembled);
sort_json_value(assembled, assembled);
clean_json_object(assembled, assembled);
print_json(assembled, cout);
};
void Job::write_compiled_instruction() const {
Document compiled;
compiled.CopyFrom(ontology, compiled.GetAllocator());
compiled.RemoveMember("application version");
compiled.RemoveMember("program");
compiled.RemoveMember("working directory");
sort_json_value(compiled, compiled);
print_json(compiled, cout, float_precision());
};
void Job::validate() {
};
void Job::load() {
};
void Job::start() {
};
void Job::stop() {
};
void Job::finalize() {
if(decode_value_by_key< bool >("include compiled job", ontology)) {
/* add a copy of the job document */
report.AddMember(
Value("job", report.GetAllocator()).Move(),
Value(ontology, report.GetAllocator()).Move(),
report.GetAllocator()
);
}
};
void Job::apply_default_ontology(Document& document) const {
/* if the operation defines a default instruction overlay it on top of the ontology */
Value::ConstMemberIterator reference = operation.FindMember("default");
if(reference != operation.MemberEnd()) {
merge_json_value(reference->value, document, document);
}
};
void Job::apply_interactive_ontology(Document& document) const {
Document adjusted;
adjusted.CopyFrom(interactive, adjusted.GetAllocator());
adjusted.RemoveMember("configuration url");
adjusted.RemoveMember("static only");
adjusted.RemoveMember("validate only");
adjusted.RemoveMember("compile only");
overlay_json_object(document, adjusted);
};
const Value* Job::find_schema(const string& key) const {
const Value* element(NULL);
if(schema_repository.IsObject()) {
Value::ConstMemberIterator reference = schema_repository.FindMember(key.c_str());
if(reference != schema_repository.MemberEnd()) {
if(reference->value.IsObject()) {
element = &reference->value;
}
}
}
return element;
};
const Value* Job::find_projection(const string& key) const {
const Value* element(NULL);
if(projection_repository.IsObject()) {
Value::ConstMemberIterator reference = projection_repository.FindMember(key.c_str());
if(reference != projection_repository.MemberEnd()) {
if(reference->value.IsObject()) {
element = &reference->value;
}
}
}
return element;
};
Document Job::read_instruction_document(const URL& url) {
set< URL > visited;
Document document(load_instruction_with_import(url, visited));
return document;
};
Document Job::load_instruction_with_import(const URL& url, set< URL >& visited) {
Document document(kNullType);
if(url.is_readable()) {
istream* stream(&cin);
ifstream* file(NULL);
if(!url.is_stdin()) {
file = new ifstream(url.path());
stream = file;
}
const string content((istreambuf_iterator< char >(*stream)), istreambuf_iterator< char >());
if(file != NULL) {
file->close();
delete file;
}
if(!document.Parse(content.c_str()).HasParseError()) {
const SchemaDocument* schema_document(get_schema_document("instruction:lax"));
if(schema_document != NULL) {
SchemaValidator validator(*schema_document);
if(document.Accept(validator)) {
visited.emplace(url);
list< string > import;
if(decode_value_by_key< list< string > >("import", import, document)) {
Document aggregated(kNullType);
for(auto& record : import) {
URL import_url(expand_shell(record));
/* import url is resolved relative to the dirname of the importing document */
import_url.relocate_sibling(url);
/* To avoid cyclical import a url is only visited once,
the first time it is encountered on a depth first recursion.
TODO: This should really use the inode number and not the url */
if(!visited.count(import_url)) {
Document imported(load_instruction_with_import(import_url, visited));
merge_json_value(aggregated, imported, imported);
aggregated.Swap(imported);
}
}
merge_json_value(aggregated, document, document);
}
document.RemoveMember("import");
} else {
Document error(encode_validation_error(validator, *find_schema("instruction:lax"), document));
encode_key_value("url", url, error, error);
throw ValidationError(error);
}
} else { throw InternalError("no schema instruction:lax"); }
} else {
string message(GetParseError_En(document.GetParseError()));
message += " at position ";
message += to_string(document.GetErrorOffset());
throw ConfigurationError(message);
}
} else { throw ConfigurationError("unable to read instruction file from " + string(url.path())); }
return document;
};
const SchemaDocument* Job::get_schema_document(const string& key) {
const SchemaDocument* schema_document(NULL);
auto record = schema_document_by_name.find(key);
if(record != schema_document_by_name.end()) {
schema_document = &record->second;
} else {
Value::ConstMemberIterator reference = schema_repository.FindMember(key.c_str());
if(reference != schema_repository.MemberEnd()) {
schema_document_by_name.emplace(make_pair(key, SchemaDocument(reference->value)));
record = schema_document_by_name.find(key);
if(record != schema_document_by_name.end()) {
schema_document = &record->second;
}
}
}
return schema_document;
};