static void Main(string[] args)
{
string input_notes_folder = ConfigurationManager.AppSettings["input_notes_folder"];
string cTakes_xml_folder = ConfigurationManager.AppSettings["cTakes_xml_folder"];
string cTakes_bin_folder = ConfigurationManager.AppSettings["cTakes_bin_folder"];
string parsed_service_folder = ConfigurationManager.AppSettings["parsed_service_folder"];
string output_notes_html_folder = ConfigurationManager.AppSettings["output_notes_html_folder"];
string bypass_umls = ConfigurationManager.AppSettings["bypass_umls"];
string new_file_txt = string.Empty;
string input_file_name = string.Empty;
string input_file_path = string.Empty;
Dictionary <string, int> input_dict_files;
Dictionary <string, int> converted_dict_files;
string indications_file = ConfigurationManager.AppSettings["indications_file"];
try
{
if (!string.IsNullOrEmpty(bypass_umls))
{
RunProcess(bypass_umls, "umlsmock.exe", false);
}
input_dict_files = SQLService.GetInputFileNames();
converted_dict_files = new Dictionary <string, int>();
if (input_dict_files != null && input_dict_files.Count > 0)
{
string[] input_file_entries = Directory.GetFiles(input_notes_folder);
if (input_file_entries.Length > 0)
{
Console.WriteLine(new string('-', 70));
Console.WriteLine("*** FILES CONVERSION ***");
Console.WriteLine(new string('-', 70));
Console.WriteLine();
Console.WriteLine("Start the file conversion process\r\n\r\nPlease wait.........");
foreach (string input_file in input_file_entries)
{
input_file_name = Path.GetFileName(input_file);
if (input_dict_files.ContainsKey(input_file_name))
{
new_file_txt = Path.GetFileNameWithoutExtension(input_file) + ".txt";
input_file_path = Path.Combine(input_notes_folder, new_file_txt);
FilesHelper.ConvertToTxt(input_file, input_notes_folder, input_file_path);
converted_dict_files.Add(new_file_txt, input_dict_files[input_file_name]);
}
}
Console.WriteLine("Finish the file conversion process");
Console.WriteLine();
}
Console.WriteLine(new string('-', 70));
Console.WriteLine("*** cTAKES PROCESSING ***");
Console.WriteLine(new string('-', 70));
Console.WriteLine();
RunProcess(cTakes_bin_folder, "runctakesCPE_CLI.bat", true);
Parser parser = new Parser();
string[] cTakes_file_entries = Directory.GetFiles(cTakes_xml_folder);
string file_without_ext = string.Empty;
int note_id = 0;
if (cTakes_file_entries.Length > 0)
{
Console.WriteLine("Start the cTakes .xml files processing\r\n\r\nPlease wait.........");
foreach (string xml_file in cTakes_file_entries)
{
file_without_ext = Path.GetFileNameWithoutExtension(xml_file);
if (converted_dict_files.ContainsKey(file_without_ext))
{
note_id = converted_dict_files[file_without_ext];
parser.ParseXML(xml_file, input_notes_folder, cTakes_xml_folder, parsed_service_folder, output_notes_html_folder, indications_file, note_id);
}
}
if (!string.IsNullOrEmpty(bypass_umls))
{
StopDummyServer("umlsmock");
}
Console.WriteLine("Finish the cTakes .xml files processing");
Console.WriteLine();
Console.WriteLine(new string('-', 70));
Console.WriteLine();
Console.WriteLine("THE PROCESS HAS BEEN FINISHED SUCCESSFULLY........");
Console.WriteLine("PRESS ANY KEY TO CLOSE THE PROGRAM.........");
}
else
{
Console.WriteLine("NO OUTPUT HTML FILES........");
Console.WriteLine("PRESS ANY KEY TO CLOSE THE PROGRAM........");
}
}
else
{
Console.WriteLine("No files to read.");
}
}
catch (Exception ex)
{
if (!string.IsNullOrEmpty(bypass_umls))
{
StopDummyServer("umlsmock");
}
LogHelper.SaveLogInfo(string.Format("Exception: {0}", ex.Message), ex.StackTrace);
Console.WriteLine(ex.Message);
}
Console.ReadKey();
}
public void ParseXML(string xml_file_name, string input_notes_folder, string cTakes_xml_folder, string parsed_service_folder, string output_notes_html_folder, string indications_file, int note_id)
{
try
{
ConsoleSpinner spin = new ConsoleSpinner();
lst_SNOMED_Codes = new List <dynamic>();
input_xml_fileName = Path.GetFileName(xml_file_name);
output_parsed_file = Path.Combine(parsed_service_folder, Path.GetFileNameWithoutExtension(xml_file_name));
Console.WriteLine("\r\nProcessing of the file: {0}.....\r\n", input_xml_fileName);
if (!string.IsNullOrEmpty(xml_file_name))
{
var excel_rows = GetExcelRows(indications_file)
.Select(dataRow => new
{
code = dataRow["Code"].ToString(),
name = dataRow["Name"].ToString().ToLower(),
confidence = dataRow["Confidence"].ToString(),
status = dataRow["Status"].ToString()
});
var indicationNames = excel_rows.Select(n => n.name.ToLower()).ToList();
if (!Directory.Exists(parsed_service_folder))
{
Directory.CreateDirectory(parsed_service_folder);
}
StringBuilder sb_descr = new StringBuilder();
sb_descr.AppendLine(DateTime.Now.ToString());
sb_descr.AppendLine(string.Format("Parsing of file: {0}", input_xml_fileName));
sb_descr.AppendLine(new string('-', 80));
sb_descr.AppendLine("Descriptions");
sb_descr.AppendLine(new string('-', 80));
sb_descr.AppendLine();
XDocument document = XDocument.Load(xml_file_name);
cTakesTextstring = document.Descendants("uima.cas.Sofa")
.Select(r => r.Attribute("sofaString").Value).FirstOrDefault();
if (!string.IsNullOrEmpty(cTakesTextstring))
{
var positions = document.Descendants("org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention")
.Select(r => new { begin = r.Attribute("begin").Value, end = r.Attribute("end").Value, arr_ref = r.Attribute("_ref_ontologyConceptArr").Value });
int descr_num = 1;
int cur_begin = -1;
int cur_end = -1;
int prev_begin = -1;
int prev_end = -1;
if (positions.Count() > 0)
{
var sentences = document.Descendants("org.apache.ctakes.typesystem.type.textspan.Sentence")
.Select(r => new { begin = int.Parse(r.Attribute("begin").Value), end = int.Parse(r.Attribute("end").Value), num = r.Attribute("sentenceNumber").Value });
var treebankNode = document.Descendants("org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode")
.Select(r => new { begin = int.Parse(r.Attribute("begin").Value), end = int.Parse(r.Attribute("end").Value), nodeValue = r.Attribute("nodeValue").Value.ToLower() });
var measurements = document.Descendants("org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation")
.Select(r => new { begin = int.Parse(r.Attribute("begin").Value), end = int.Parse(r.Attribute("end").Value), _id = r.Attribute("_id").Value.ToLower() });
var semantics = document.Descendants("org.apache.ctakes.typesystem.type.textsem.SemanticArgument")
.Select(r => new { begin = int.Parse(r.Attribute("begin").Value), end = int.Parse(r.Attribute("end").Value), _id = r.Attribute("_id").Value.ToLower() });
foreach (var result in positions)
{
spin.Turn();
cur_begin = int.Parse(result.begin);
cur_end = int.Parse(result.end);
var cur_sentence = sentences
.Where(e => e.begin <= cur_begin && e.end >= cur_end)
.Select(s => s);
var checkMeasurement = measurements
.Where(e => e.begin == cur_begin && e.end == cur_end)
.Select(e => e._id);
var checkSemantic = semantics
.Where(e => e.begin == cur_begin && e.end == cur_end)
.Select(e => e._id);
var cur_descr = treebankNode
.Where(e => e.begin >= cur_begin &&
e.end <= cur_end
&&
!(
e.begin >= prev_begin && e.end <= prev_end)
)
.Select(e => e.nodeValue + " ");
var indications = treebankNode
.Where(tb => cur_sentence.All(sent => (sent.begin <= tb.begin && sent.end >= tb.end)) &&
indicationNames.Contains(tb.nodeValue))
.Select(e => new { ind_name = e.nodeValue, begin = e.begin, end = e.end });
if (cur_descr.Count() > 0 && checkSemantic.Count() == 0 && checkMeasurement.Count() == 0)
{
string descr_val = "";
StringBuilder help_descr = new StringBuilder();
foreach (var d_itm in cur_descr)
{
descr_val += d_itm;
}
help_descr.AppendLine(string.Format("Begin: {0}; End: {1}", cur_begin, cur_end));
help_descr.AppendLine("Codes: ");
var cas_arr = document.Descendants("uima.cas.FSArray")
.Where(e => e.Attribute("_id").Value == result.arr_ref)
.Descendants("i")
.Select(e => e.Value);
int code_num = 1;
foreach (var id_itm in cas_arr)
{
spin.Turn();
string currCode = document.Descendants("org.apache.ctakes.typesystem.type.refsem.UmlsConcept")
.Where(e => e.Attribute("_id").Value == id_itm)
.Select(e => e.Attribute("code").Value).FirstOrDefault();
var curr_indication = indications.Count() > 0
?
excel_rows
.Where(ex => indications.Any(ind => ex.name == ind.ind_name))
:
null
;
// fill dynamic list
lst_SNOMED_Codes.Add(new
{
snomed_code = currCode,
text_descr = descr_val.Trim(),
pos_start = cur_begin,
pos_end = cur_end,
confidence = curr_indication == null ? "-" : curr_indication.Select(ex => ex.confidence).FirstOrDefault(),
status = curr_indication == null ? "-" : curr_indication.Select(ex => ex.status).FirstOrDefault()
});
string code_with_indications = curr_indication == null ? currCode : (currCode + curr_indication.Select(ex => " - " + ex.code + "(" + ex.name + ")").FirstOrDefault());
help_descr.AppendLine(string.Format("\t{0}) {1}", code_num, code_with_indications));
code_num++;
}
if (sb_descr.ToString().Contains(descr_val))
{
sb_descr.Replace(descr_val, descr_val + "\n" + help_descr.ToString());
}
else
{
sb_descr.AppendLine(string.Format("{0}. Description: {1}", descr_num, descr_val));
sb_descr.AppendLine(help_descr.ToString());
sb_descr.AppendLine();
descr_num++;
}
prev_begin = cur_begin;
prev_end = cur_end;
}
}
using (StreamWriter sw = new StreamWriter(output_parsed_file))
{
sw.Write(sb_descr.ToString());
}
FilesHelper.BackUpFiles(cTakes_xml_folder, xml_file_name);
string file_result_txt = Path.GetFileName(output_parsed_file);
string file_result_html = Path.GetFileNameWithoutExtension(output_parsed_file) + ".htm";
lst_result = SQLService.ExecuteCompareSQL(lst_SNOMED_Codes);
FilesHelper.CreateHtmlFile(lst_result, input_notes_folder, output_notes_html_folder, file_result_txt, file_result_html, cTakesTextstring, note_id);
SQLService.CreateNoteConditions(lst_result, file_result_html, note_id);
}
else
{
Console.WriteLine("cTakes text string is empty");
}
}
}
}
catch (Exception ex)
{
LogHelper.SaveLogInfo(string.Format("Exception: {0}", ex.Message), ex.StackTrace);
}
}
