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package org.cellocad.api;
import org.apache.commons.io.FileUtils;
import org.cellocad.BU.dom.DAGW;
import org.cellocad.BU.netsynth.NetSynth;
import org.cellocad.BU.netsynth.NetSynthSwitch;
import org.cellocad.BU.netsynth.Utilities;
import org.cellocad.MIT.dnacompiler.*;
import org.json.JSONArray;
import org.json.simple.JSONObject;
import org.springframework.web.bind.annotation.*;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Map;
/**
* Created by Bryan Der on 8/21/15.
*/
@RestController
public class MainController extends BaseController {
// @RequestMapping(value="",method= RequestMethod.GET)
// public @ResponseBody
// String dnaCompiler(
// @RequestHeader("Authorization") String basic
// ) {
// if(!auth.login(basic)) {
// throw new CelloUnauthorizedException("invalid username/password");
// }
// String username = auth.getUsername(basic);
// return "Welcome, " + username;
// }
@RequestMapping(value="/ping", method= RequestMethod.GET)
public @ResponseBody
String testPingPong(
@RequestHeader("Authorization") String basic
) throws IOException {
if(!auth.login(basic)) {
throw new CelloUnauthorizedException("invalid username/password");
}
return "pong";
}
@RequestMapping(value="/submit",method= RequestMethod.POST, produces = "application/json")
public @ResponseBody
JSONObject dnaCompiler(
@RequestHeader("Authorization") String basic,
@RequestParam Map<String, String> params
) {
if(!auth.login(basic)) {
throw new CelloUnauthorizedException("invalid username/password");
}
String username = auth.getUsername(basic);
String id = params.get("id");
String inputs = params.get("input_promoter_data");
String outputs = params.get("output_gene_data");
String verilog_text = params.get("verilog_text");
String options = params.get("options");
String user_directory = _resultPath + "/" + username + "/";
String output_directory = user_directory + id + "/";
File f = new File(user_directory);
if (!f.exists()) {
Util.createDirectory(user_directory);
}
File f2 = new File(output_directory);
if (f2.exists()) {
try {
FileUtils.deleteDirectory(f2);
} catch (IOException e) {
e.printStackTrace();
}
}
Util.createDirectory(output_directory);
JSONObject out = new JSONObject();
out.put("username", username);
out.put("id", id);
out.put("input_promoter_data", inputs);
out.put("output_gene_data", outputs);
out.put("verilog_text", verilog_text);
out.put("options", options);
String verilog_filename = output_directory + id + "_verilog.v";
String inputs_filename = output_directory + id + "_inputs.txt";
String outputs_filename = output_directory + id + "_outputs.txt";
Util.fileWriter(verilog_filename, verilog_text, false);
Util.fileWriter(inputs_filename, inputs, false);
Util.fileWriter(outputs_filename, outputs, false);
String all_options =
" -username " + username +
" -verilog " + verilog_filename +
" -jobID " + id +
" -output_directory " + output_directory +
" -input_promoters " + inputs_filename +
" -output_genes " + outputs_filename +
" -figures " + "true" +
" -plasmid " + "true" +
" " + options;
ArrayList<String> optList = Util.lineTokenizer(all_options);
String[] optArr = new String[optList.size()];
optArr = optList.toArray(optArr);
DNACompiler dnaCompiler = new DNACompiler(username);
dnaCompiler.run(optArr);
String message = "WARNING: Unknown result status.";
if(dnaCompiler.get_result_status() == DNACompiler.ResultStatus.success) {
message = "SUCCESS: job '" + id + "' finished";
}
else if(dnaCompiler.get_result_status() == DNACompiler.ResultStatus.wiring_diagram_invalid) {
message = "Wiring diagram invalid.";
}
else if(dnaCompiler.get_result_status() == DNACompiler.ResultStatus.ucf_invalid) {
message = "UCF invalid.";
}
else if(dnaCompiler.get_result_status() == DNACompiler.ResultStatus.not_enough_gates_in_library) {
message = "Not enough gates in library.";
}
else if(dnaCompiler.get_result_status() == DNACompiler.ResultStatus.no_assignments_found) {
message = "No assignments found.";
}
else if(dnaCompiler.get_result_status() == DNACompiler.ResultStatus.roadblocking_inputs) {
message = "WARNING: roadblocking inputs: job '" + id + "' finished";
}
else if(dnaCompiler.get_result_status() == DNACompiler.ResultStatus.abstract_only) {
message = "SUCCESS: abstract only.";
}
else if(dnaCompiler.get_result_status() == DNACompiler.ResultStatus.arguments_invalid) {
message = "Arguments invalid.";
}
else if(dnaCompiler.get_result_status() == DNACompiler.ResultStatus.breadth_first_not_allowed) {
message = "Breadth-first search not allowed due to memory usage.";
}
JSONObject response = new JSONObject();
response.put("message", message);
return response;
}
@RequestMapping(value="/netsynth",method= RequestMethod.POST)
public @ResponseBody
String getNetlist(
@RequestHeader("Authorization") String basic,
@RequestParam String verilog_text
) {
if(!auth.login(basic)) {
throw new CelloUnauthorizedException("invalid username/password");
}
String username = auth.getUsername(basic);
NetSynth netsynth = new NetSynth(username + "netSynthAPIcall");
DAGW GW = netsynth.runNetSynthCode(verilog_text, new ArrayList<NetSynthSwitch>(), new JSONArray());
netsynth.cleanDirectory();
org.cellocad.MIT.dnacompiler.LogicCircuit abstract_logic_circuit = new LogicCircuit(GW.Gates, GW.Wires);
LogicCircuitUtil.renameGatesWires(abstract_logic_circuit);
String netlist = Netlist.getNetlist(abstract_logic_circuit);
String netlist2 = abstract_logic_circuit.printNetlist();
if(netlist.contains("INPUT") && netlist.contains("OUTPUT")) {
String[] lines = netlist.split("\n");
for(int i=0; i<lines.length; ++i) {
String line = lines[i];
if(line.contains("INPUT")) {
continue;
}
if(!line.contains("(") || !line.contains(")")) {
return "Invalid netlist. Are any outputs always 0 or always 1?";
}
}
return netlist2;
}
return "NetSynth finished but the netlist is invalid";
}
public String newUserSetup(String username) {
String user_directory = _resultPath + "/" + username + "/";
File f = new File(user_directory);
if (!f.exists()) {
Util.createDirectory(user_directory);
}
String pTac = "pTac 0.0034 2.8 AACGATCGTTGGCTGTGTTGACAATTAATCATCGGCTCGTATAATGTGTGGAATTGTGAGCGCTCACAATT";
String pTet = "pTet 0.0013 4.4 TACTCCACCGTTGGCTTTTTTCCCTATCAGTGATAGAGATTGACATCCCTATCAGTGATAGAGATAATGAGCAC";
String pBAD = "pBAD 0.0082 2.5 ACTTTTCATACTCCCGCCATTCAGAGAAGAAACCAATTGTCCATATTGCATCAGACATTGCCGTCACTGCGTCTTTTACTGGCTCTTCTCGCTAACCAAACCGGTAACCCCGCTTATTAAAAGCATTCTGTAACAAAGCGGGACCAAAGCCATGACAAAAACGCGTAACAAAAGTGTCTATAATCACGGCAGAAAAGTCCACATTGATTATTTGCACGGCGTCACACTTTGCTATGCCATAGCATTTTTATCCATAAGATTAGCGGATCCTACCTGACGCTTTTTATCGCAACTCTCTACTGTTTCTCCATACCCGTTTTTTTGGGCTAGC";
String pLuxStar = "pLuxStar 0.025 0.31 ATAGCTTCTTACCGGACCTGTAGGATCGTACAGGTTTACGCAAGAAAATGGTTTGTTACTTTCGAATAAA";
String YFP = "YFP CTGAAGCTGTCACCGGATGTGCTTTCCGGTCTGATGAGTCCGTGAGGACGAAACAGCCTCTACAAATAATTTTGTTTAATACTAGAGAAAGAGGGGAAATACTAGATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACAGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCTTCGGCTACGGCCTGCAATGCTTCGCCCGCTACCCCGACCACATGAAGCTGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCAATCGGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTTAGCTACCAGTCCGCCCTGAGCAAAGACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACTCTCGGCATGGACGAGCTGTACAAGTAACTCGGTACCAAATTCCAGAAAAGAGGCCTCCCGAAAGGGGGGCCTTTTTTCGTTTTGGTCC";
String RFP = "RFP CTGAAGTGGTCGTGATCTGAAACTCGATCACCTGATGAGCTCAAGGCAGAGCGAAACCACCTCTACAAATAATTTTGTTTAATACTAGAGTCACACAGGAAAGTACTAGATGGCTTCCTCCGAAGACGTTATCAAAGAGTTCATGCGTTTCAAAGTTCGTATGGAAGGTTCCGTTAACGGTCACGAGTTCGAAATCGAAGGTGAAGGTGAAGGTCGTCCGTACGAAGGTACCCAGACCGCTAAACTGAAAGTTACCAAAGGTGGTCCGCTGCCGTTCGCTTGGGACATCCTGTCCCCGCAGTTCCAGTACGGTTCCAAAGCTTACGTTAAACACCCGGCTGACATCCCGGACTACCTGAAACTGTCCTTCCCGGAAGGTTTCAAATGGGAACGTGTTATGAACTTCGAAGACGGTGGTGTTGTTACCGTTACCCAGGACTCCTCCCTGCAAGACGGTGAGTTCATCTACAAAGTTAAACTGCGTGGTACCAACTTCCCGTCCGACGGTCCGGTTATGCAGAAAAAAACCATGGGTTGGGAAGCTTCCACCGAACGTATGTACCCGGAAGACGGTGCTCTGAAAGGTGAAATCAAAATGCGTCTGAAACTGAAAGACGGTGGTCACTACGACGCTGAAGTTAAAACCACCTACATGGCTAAAAAACCGGTTCAGCTGCCGGGTGCTTACAAAACCGACATCAAACTGGACATCACCTCCCACAACGAAGACTACACCATCGTTGAACAGTACGAACGTGCTGAAGGTCGTCACTCCACCGGTGCTTAATAACAGATAAAAAAAATCCTTAGCTTTCGCTAAGGATGATTTCT";
String BFP = "BFP CTGAAGTTCCAGTCGAGACCTGAAGTGGGTTTCCTGATGAGGCTGTGGAGAGAGCGAAAGCTTTACTCCCGCACAAGCCGAAACTGGAACCTCTACAAATAATTTTGTTTAAGAGTCACACAGGAAAGTACTAGATGAGCGAGCTGATTAAGGAGAACATGCACATGAAGCTGTACATGGAGGGCACCGTGGACAACCATCACTTCAAGTGCACATCCGAGGGCGAAGGCAAGCCCTACGAGGGCACCCAGACCATGAGAATCAAGGTGGTCGAGGGCGGCCCTCTCCCCTTCGCCTTCGACATCCTGGCTACTAGCTTCCTCTACGGCAGCAAGACCTTCATCAACCACACCCAGGGCATCCCCGACTTCTTCAAGCAGTCCTTCCCTGAGGGCTTCACATGGGAGAGAGTCACCACATACGAAGATGGGGGCGTGCTGACCGCTACCCAGGACACCAGCCTCCAGGACGGCTGCCTCATCTACAACGTCAAGATCAGAGGGGTGAACTTCACATCCAACGGCCCTGTGATGCAGAAGAAAACACTCGGCTGGGAGGCCTTCACCGAGACGCTGTACCCCGCTGACGGCGGCCTGGAAGGCAGAAACGACATGGCCCTGAAGCTCGTGGGCGGGAGCCATCTGATCGCAAACATCAAGACCACATATAGATCCAAGAAACCCGCTAAGAACCTCAAGATGCCTGGCGTCTACTATGTGGACTACAGACTGGAAAGAATCAAGGAGGCCAACAACGAGACCTACGTCGAGCAGCACGAGGTGGCAGTGGCCAGATACTGCGACCTCCCTAGCAAACTGGGGCACTAACCAGGCATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCTACTAGAGTCACACTGGCTCACCTTCGGGTGGGCCTTTCTGCGTTTATA";
String sigmaK1FR = "sigmaK1FR ATGAGCATCGCGGCGACCCTGGAGAACGATCTGGCGCGTCTGGAAAACGAAAACGCTCGTCTCGAAAAAGACATCGCGAACCTGGAACGTGACCTGGCGAAACTGGAGCGTGAAGAAGCGTACTTCGGAGGTTCAGGTGGTAAGAACACTGGTGAAATCTCTGAGAAAGTCAAGCTGGGCACTAAGGCACTGGCTGGTCAATGGCTGGCTTACGGTGTTACTCGCAGTGTGACTAAGCGTTCAGTCATGACGCTGGCTTACGGGTCCAAAGAGTTCGGCTTCCGTCAACAAGTGCTGGAAGATACCATTCAGCCAGCTATTGATTCCGGCAAGGGTCTGATGTTCACTCAGCCGAATCAGGCTGCTGGATACATGGCTAAGCTGATTTGGGAATCTGTGAGCGTGACGGTGGTAGCTGCGGTTGAAGCAATGAACTGGCTTAAGTCTGCTGCTAAGCTGCTGGCTGCTGAGGTCAAAGATAAGAAGACTGGAGAGATTCTTCGCAAGCGTTGCGCTGTGCATTGGGTAACTCCTGATGGTTTCCCTGTGTGGCAGGAATACAAGAAGCCTATTCAGACGCGCTTGAACCTGAGGTTCCTCGGTTCGTTCAACCTCCAGCCGACCGTCAACACCAACAAAGATAGCGAGATTGATGCACACAAACAGGAGTCTGGTATCGCTCCTAACTTTGTACACAGCCAAGACGGTAGCCACCTTCGTAAGACTGTAGTGTGGGCACACGAGAAGTACGGAATCGAATCTTTTGCACTGATTCACGACTCCTTCGGTACGATTCCGGCTGACGCTGCGAACCTGTTCAAAGCAGTGCGCGAAACTATGGTTGACACATATGAGTCTTGTGATGTACTGGCTGATTTCTACGACCAGTTCGCTGACCAGTTGCACGAGTCTCAATTGGACAAAATGCCAGCACTTCCGGCTAAAGGTAACTTGAACCTCCGTGACATCTTAGAGTCGGACTTCGCGTTCGCG";
String sigmaT3 = "sigmaT3 ATGAGCATCGCGGCGACCCTGGAGAACGATCTGGCGCGTCTGGAAAACGAAAACGCTCGTCTCGAAAAAGACATCGCGAACCTGGAACGTGACCTGGCGAAACTGGAGCGTGAAGAAGCGTACTTCGGAGGTTCAGGTGGTAAGAACACTGGTGAAATCTCTGAGAAAGTCAAGCTGGGCACTAAGGCACTGGCTGGTCAATGGCTGGCTTACGGTGTTACTCGCAGTGTGACTAAGCGTTCAGTCATGACGCTGGCTTACGGGTCCAAAGAGTTCGGCTTCCGTCAACAAGTGCTGGAAGATACCATTCAGCCAGCTATTGATTCCGGCAAGGGTCTGATGTTCACTCAGCCGAATCAGGCTGCTGGATACATGGCTAAGCTGATTTGGGAATCTGTGAGCGTGACGGTGGTAGCTGCGGTTGAAGCAATGAACTGGCTTAAGTCTGCTGCTAAGCTGCTGGCTGCTGAGGTCAAAGATAAGAAGACTGGAGAGATTCTTCGCAAGCGTTGCGCTGTGCATTGGGTAACTCCTGATGGTTTCCCTGTGTGGCAGGAATACAAGAAGCCTATTCAGAAGCGCCTGGACATGATTTTCTTGGGTCAATTTCGCTTGCAACCTACCATTAACACCAACAAAGATAGCGAGATTGATGCACACAAACAGGAGTCTGGTATCGCTCCTAACTTTGTACACAGCCAAGACGGTAGCCACCTTCGTAAGACTGTAGTGTGGGCACACGAGAAGTACGGAATCGAATCTTTTGCACTGATTCACGACTCCTTCGGTACGATTCCGGCTGACGCTGCGAACCTGTTCAAAGCAGTGCGCGAAACTATGGTTGACACATATGAGTCTTGTGATGTACTGGCTGATTTCTACGACCAGTTCGCTGACCAGTTGCACGAGTCTCAATTGGACAAAATGCCAGCACTTCCGGCTAAAGGTAACTTGAACCTCCGTGACATCTTAGAGTCGGACTTCGCGTTCGCG";
String sigmaT7 = "sigmaT7 ATGAGCATCGCGGCGACCCTGGAGAACGATCTGGCGCGTCTGGAAAACGAAAACGCTCGTCTCGAAAAAGACATCGCGAACCTGGAACGTGACCTGGCGAAACTGGAGCGTGAAGAAGCGTACTTCGGAGGTTCAGGTGGTAAGAACACTGGTGAAATCTCTGAGAAAGTCAAGCTGGGCACTAAGGCACTGGCTGGTCAATGGCTGGCTTACGGTGTTACTCGCAGTGTGACTAAGAGTTCAGTCATGACGCTGGCTTACGGGTCCAAAGAGTTCGGCTTCCGTCAACAAGTGCTGGAAGATACCATTCAGCCAGCTATTGATTCCGGCAAGGGTCTGATGTTCACTCAGCCGAATCAGGCTGCTGGATACATGGCTAAGCTGATTTGGGAATCTGTGAGCGTGACGGTGGTAGCTGCGGTTGAAGCAATGAACTGGCTTAAGTCTGCTGCTAAGCTGCTGGCTGCTGAGGTCAAAGATAAGAAGACTGGAGAGATTCTTCGCAAGCGTTGCGCTGTGCATTGGGTAACTCCTGATGGTTTCCCTGTGTGGCAGGAATACAAGAAGCCTATTCAGACGCGCTTGAACCTGATGTTCCTCGGTCAGTTCCGCTTACAGCCTACCATTAACACCAACAAAGATAGCGAGATTGATGCACACAAACAGGAGTCTGGTATCGCTCCTAACTTTGTACACAGCCAAGACGGTAGCCACCTTCGTAAGACTGTAGTGTGGGCACACGAGAAGTACGGAATCGAATCTTTTGCACTGATTCACGACTCCTTCGGTACGATTCCGGCTGACGCTGCGAACCTGTTCAAAGCAGTGCGCGAAACTATGGTTGACACATATGAGTCTTGTGATGTACTGGCTGATTTCTACGACCAGTTCGCTGACCAGTTGCACGAGTCTCAATTGGACAAAATGCCAGCACTTCCGGCTAAAGGTAACTTGAACCTCCGTGACATCTTAGAGTCGGACTTCGCGTTCGCG";
String sigmaCGG = "sigmaCGG ATGAGCATCGCGGCGACCCTGGAGAACGATCTGGCGCGTCTGGAAAACGAAAACGCTCGTCTCGAAAAAGACATCGCGAACCTGGAACGTGACCTGGCGAAACTGGAGCGTGAAGAAGCGTACTTCGGAGGTTCAGGTGGTAAGAACACTGGTGAAATCTCTGAGAAAGTCAAGCTGGGCACTAAGGCACTGGCTGGTCAATGGCTGGCTTACGGTGTTACTCGCAGTGTGACTAAGCGTTCAGTCATGACGCTGGCTTACGGGTCCAAAGAGTTCGGCTTCCGTCAACAAGTGCTGGAAGATACCATTCAGCCAGCTATTGATTCCGGCAAGGGTCTGATGTTCACTCAGCCGAATCAGGCTGCTGGATACATGGCTAAGCTGATTTGGGAATCTGTGAGCGTGACGGTGGTAGCTGCGGTTGAAGCAATGAACTGGCTTAAGTCTGCTGCTAAGCTGCTGGCTGCTGAGGTCAAAGATAAGAAGACTGGAGAGATTCTTCGCAAGCGTTGCGCTGTGCATTGGGTAACTCCTGATGGTTTCCCTGTGTGGCAGGAATACAAGAAGCCTATTAAAACGCGCGTGCATATTATGTTCCTCGGTCAGTTCGAAATGCAGCCTACCATTAACACCAACAAAGATAGCGAGATTGATGCACGCAAACAGGAGTCTGGTATCGCTCCTAACTTTGTACACAGCCAAGACGGTAGCCACCTTCGTAAGACTGTAGTGTGGGCACACGAGAAGTACGGAATCGAATCTTTTGCACTGATTCACGACTCCTTCGGTACGATTCCGGCTGACGCTGCGAACCTGTTCAAAGCAGTGCGCGAAACTATGGTTGACACATATGAGTCTTGTGATGTACTGGCTGATTTCTACGACCAGTTCGCTGACCAGTTGCACGAGTCTCAATTGGACAAAATGCCAGCACTTCCGGCTAAAGGTAACTTGAACCTCCGTGACATCTTAGAGTCGGACTTCGCGTTCGCG";
String pTac_file = user_directory + "input_pTac.txt";
String pTet_file = user_directory + "input_pTet.txt";
String pBAD_file = user_directory + "input_pBAD.txt";
String pLuxStar_file = user_directory + "input_pLuxStar.txt";
String YFP_file = user_directory + "output_YFP.txt";
String RFP_file = user_directory + "output_RFP.txt";
String BFP_file = user_directory + "output_BFP.txt";
String sigmaK1FR_file = user_directory + "output_sigmaK1FR.txt";
String sigmaT3_file = user_directory + "output_sigmaT3.txt";
String sigmaT7_file = user_directory + "output_sigmaT7.txt";
String sigmaCGG_file = user_directory + "output_sigmaCGG.txt";
Util.fileWriter(pTac_file, pTac + "\n", false);
Util.fileWriter(pTet_file, pTet + "\n", false);
Util.fileWriter(pBAD_file, pBAD + "\n", false);
Util.fileWriter(pLuxStar_file, pLuxStar + "\n", false);
Util.fileWriter(YFP_file, YFP + "\n", false);
Util.fileWriter(RFP_file, RFP + "\n", false);
Util.fileWriter(BFP_file, BFP + "\n", false);
Util.fileWriter(sigmaK1FR_file, sigmaK1FR + "\n", false);
Util.fileWriter(sigmaT3_file, sigmaT3 + "\n", false);
Util.fileWriter(sigmaT7_file, sigmaT7 + "\n", false);
Util.fileWriter(sigmaT7_file, sigmaT7 + "\n", false);
Util.fileWriter(sigmaCGG_file, sigmaCGG + "\n", false);
return "First login: creating default input promoters and output genes.";
}
}