static void Main(string[] args)
{
Entity.Preprocess();
int op = 3;
if (op > 0)
{
//TimeExtractor.Preprocessing.preprocess();
}
for (int packageNo = 1; packageNo <= 6; packageNo++)
{
string folder = "docs\\Package " + packageNo;
// string folder = "docs";
string[] files = Directory.GetFiles(folder, "*.txt");
foreach (string file in files)
{
switch (op)
{
case 0:
{
//Tag with stemmed PMT tags
Regex fileregex = new Regex(@"[0-9]+\.txt");
Match match = fileregex.Match(file);
if (match == null)
{
break;
}
string concept_filename = "concepts\\" + match.Value.Replace("txt", "con");
if (!File.Exists(concept_filename))
{
Console.WriteLine("Uoh, concept file \"" + concept_filename + "\" not found.");
break;
}
string[] cons = File.ReadAllLines(concept_filename);
List <Entity> entities = new List <Entity>();
foreach (string con in cons)
{
if (con.Length <= 0)
{
continue;
}
Entity entity = EntityUtil.I2b2formToEntity(con, file);
entities.Add(entity);
}
IEnumerable <Entity> PMTEntities =
from entity in entities
where entity.type == "problem" || entity.type == "treatment" || entity.type == "test"
select entity;
Annotator.Annotate(file, ".PMTstem.con", entities, true);
break;
}
case 1:
{
TimeExtractor.tools.Init.setFilePath(file);
TimeExtractor.TimeMapping.process(false);
List <SenseGroup> sensegroups = TimeVariables.TIME_ENTITIES;
List <Entity> timeEntities = new List <Entity>();
foreach (SenseGroup sg in sensegroups)
{
Entity entity = new TimeEntity();
entity.text = sg.getWords()[0];
entity.startLoc = sg.startLoc;
entity.endLoc = sg.endLoc;
entity.setTimePoint(sg.getTimePeriod().getFirstTimePoint());
timeEntities.Add(entity);
}
Annotator.Annotate(file, ".time.con", timeEntities, false);
break;
}
case 2:
{
//Tag with PMT tags + guessed classifications
Regex fileregex = new Regex(@"[0-9]+\.txt");
Match match = fileregex.Match(file);
if (match == null)
{
break;
}
string concept_filename = "concepts\\" + match.Value.Replace("txt", "con");
if (!File.Exists(concept_filename))
{
Console.WriteLine("Uoh, concept file \"" + concept_filename + "\" not found.");
break;
}
string sectionfile = file.Replace("txt", "section");
string[] sections = File.ReadAllLines(sectionfile);
string[] cons = File.ReadAllLines(concept_filename);
List <Entity> entities = new List <Entity>();
foreach (string con in cons)
{
if (con.Length <= 0)
{
continue;
}
PMTEntity entity = (PMTEntity)EntityUtil.I2b2formToEntity(con, file);
int lineNumber = entity.startLoc.line;
int ptab = sections[lineNumber - 1].IndexOf("\t");
string no = sections[lineNumber - 1].Substring(0, ptab);
string[] wa_nos = { "1.1", "5.34", "5.34.78", "5.34.78.93", "5.34.78.93.35", "5.34.78.93.38", "5.34.78.96", "5.34.78.96.45", "5.34.79", "5.34.79.103.60", "5.35", "5.35.84", "5.35.91.108" };
string[] a_nos = { "5.15", "5.22.44" };
string[] ad_nos = { "5.37.106.125" };
entities.Add(entity);
}
TimeExtractor.tools.Init.setFilePath(file);
TimeExtractor.TimeMapping.process(false);
List <SenseGroup> sensegroups = TimeVariables.TIME_ENTITIES;
foreach (SenseGroup sg in sensegroups)
{
Entity entity = new TimeEntity();
entity.text = sg.getWords()[0];
entity.startLoc = sg.startLoc;
entity.endLoc = sg.endLoc;
entity.setTimePoint(sg.getTimePeriod().getFirstTimePoint());
entities.Add(entity);
}
IEnumerable <Entity> PMTEntities =
from entity in entities
where entity.type == "problem" || entity.type == "treatment" || entity.type == "test" || entity.type == "time"
select entity;
Annotator.Annotate(file, ".PMTrelation.con", entities, false);
break;
}
case 3:
{
//From annotated time expression (including normalized) to concept files
string annotate_file = file.Replace(".txt", ".time.con");
string con_file = file.Replace(".txt", ".time-con");
Entity[] entities = Annotator.ReadAnnotate(annotate_file);
EntityUtil.ExportConcept(con_file, entities, false);
break;
}
case 4:
{
//Update the original data
//WARNING: THINK BEFORE YOU DO THIS
string annotate_file = file.Replace(".txt", ".time.con");
string raw_file = file;
Annotator.UpdateOriginalData(annotate_file, raw_file);
break;
}
case 5:
{
//Tag with standard PMT tags + revised time taggings (including normalizations)
string time_con_file = file.Replace(".txt", ".time-con");
string pmt_con_file = "concepts\\" + FileNameUtil.FileNameNoSuffix(file) + ".con";
Entity[] TIMEentities = EntityUtil.ImportConcept(time_con_file, "*.time-con", "*.txt");
Entity[] PMTentities = EntityUtil.ImportConcept(pmt_con_file, "*.con", "*.txt");
List <Entity> entities = new List <Entity>();
foreach (Entity entity in TIMEentities)
{
entities.Add(entity);
}
foreach (Entity entity in PMTentities)
{
entities.Add(entity);
}
Annotator.Annotate(file, ".PMTrelation.con", entities, false);
break;
}
}
}
}
}
public static Entity I2b2formToEntity(string i2b2str, string filename)
{
Entity ret = null;
if (i2b2str.IndexOf("three years prior") != -1)
{
ret = ret;
}
if (i2b2str.IndexOf("~~") == -1)
{
string[] terms = i2b2str.Split(new string[] { "||" }, StringSplitOptions.RemoveEmptyEntries);
Regex conregex = new Regex(@"""(?<con>[A-Za-z_]+)""");
Match matchcon = conregex.Match(terms[1]);
string con = matchcon.Groups["con"].Value;
if (con == "time")
{
ret = new TimeEntity();
for (int i = 2; i < terms.Length; i++)
{
Regex normRegex = new Regex(@"normalization=\((?<year>[0-9]+),(?<month>[0-9]+),(?<day>[0-9]+),(?<hour>[0-9]+),(?<minute>[0-9]+),(?<second>[0-9]+)\)");
Match normMatch = normRegex.Match(terms[i]);
int year = Convert.ToInt32(normMatch.Groups["year"].Value);
int month = Convert.ToInt32(normMatch.Groups["month"].Value);
int day = Convert.ToInt32(normMatch.Groups["day"].Value);
int hour = Convert.ToInt32(normMatch.Groups["hour"].Value);
int minute = Convert.ToInt32(normMatch.Groups["minute"].Value);
int second = Convert.ToInt32(normMatch.Groups["second"].Value);
TimePoint tp = new TimePoint(year, month, day, hour, minute, second);
ret.addTimePoint(tp);
}
ret.type = con;
}
else if (terms[0].StartsWith("sectime", StringComparison.CurrentCultureIgnoreCase))
{
Regex regex = new Regex(@"dvalue=""(?<year>[0-9]+)-(?<month>[0-9]+)-(?<day>[0-9]+)""");
Match match = regex.Match(terms[2]);
int year = Convert.ToInt32(match.Groups["year"].Value);
int month = Convert.ToInt32(match.Groups["month"].Value);
int day = Convert.ToInt32(match.Groups["day"].Value);
TimeEntity te = new TimeEntity();
te.mode = TimeEntityMode.NA;
te.type = TimeEntityType.DATE;
te.setTimePoint(new TimePoint(year, month, day));
ret = te;
ret.type = "time";
}
else if (con == "DATE" || con == "TIME" || con == "DURATION" || con == "FREQUENCY" || con == "RELATIVE")
{
TimeEntity te = new TimeEntity();
//value
if (terms.Length > 2)
{
string val = terms[2].Substring(5, terms[2].Length - 6);
ValGetTimeEntity(val, te);
}
//mode
if (terms.Length > 2)
{
Regex modeRegex = new Regex(@"""(?<mod>[A-Za-z]+)""$");
Match match = modeRegex.Match(terms[3]);
string mod = match.Groups["mod"].Value.ToUpper();
if (mod == "NA")
{
te.mode = TimeEntityMode.NA;
}
else if (mod == "APPROX")
{
te.mode = TimeEntityMode.APPROX;
}
else if (mod == "END")
{
te.mode = TimeEntityMode.END;
}
else if (mod == "LESS")
{
te.mode = TimeEntityMode.LESS;
}
else if (mod == "MORE")
{
te.mode = TimeEntityMode.MORE;
}
else if (mod == "MIDDLE")
{
te.mode = TimeEntityMode.MIDDLE;
}
else if (mod == "START")
{
te.mode = TimeEntityMode.START;
}
}
//type
if (con == "DATE")
{
te.type = TimeEntityType.DATE;
}
else if (con == "TIME")
{
te.type = TimeEntityType.TIME;
}
else if (con == "DURATION")
{
te.type = TimeEntityType.DURATION;
}
else if (con == "FREQUENCY")
{
te.type = TimeEntityType.FREQUENCY;
}
else
{
te.type = TimeEntityType.RELATIVE_TP;
}
if (terms[terms.Length - 1].IndexOf("relative") != -1)
{
te.is_relative_tp = true;
}
ret = te;
ret.type = con;
}
else if (con.ToUpper() == "IMPLICIT" || con.ToUpper() == "EXPLICIT" || con.ToUpper() == "TREATMENT" ||
con.ToUpper() == "CLINICAL_DEPT" || con.ToUpper() == "EVIDENTIAL" || con.ToUpper() == "OCCURRENCE")
{
PMTEntity pe = new PMTEntity();
pe.type = con.ToUpper();
//modality
if (terms.Length > 2)
{
Regex modRegex = new Regex(@"""(?<mod>[A-Za-z]+)""$");
Match match = modRegex.Match(terms[2]);
string mode = match.Groups["mod"].Value.ToUpper();
if (mode == "CONDITIONAL")
{
pe.modality = Modality.CONDITIONAL;
}
else if (mode == "FACTUAL" || mode == "ACTUAL")
{
pe.modality = Modality.FACTUAL;
}
else if (mode == "POSSIBLE")
{
pe.modality = Modality.POSSIBLE;
}
else
{
pe.modality = Modality.PROPOSED;
}
}
//polarity
if (terms.Length > 2)
{
Regex polRegex = new Regex(@"""(?<pol>[A-Za-z]+)""$");
Match match = polRegex.Match(terms[3]);
string pol = match.Groups["pol"].Value.ToUpper();
if (pol == "POS")
{
pe.polarity = Polarity.POS;
}
else
{
pe.polarity = Polarity.NEG;
}
}
//sec_time_rel
if (terms.Length > 4)
{
Regex secRegex = new Regex(@"""(?<sec>.+)""$");
Match match = secRegex.Match(terms[4]);
string sec = match.Groups["sec"].Value.ToUpper();
pe.sec_time_rel = sec;
}
ret = pe;
ret.type = con.ToUpper();
}
else
{
ret = new PMTEntity();
ret.type = con;
}
Regex textregex = new Regex(@"^[A-Za-z0-9]+\=""(?<text>.+)"" [0-9]+\:[0-9]+ [0-9]+\:[0-9]+$");
Match matchtext = textregex.Match(terms[0]);
ret.text = matchtext.Groups["text"].Value;
Regex posregex = new Regex(@"(?<sline>[0-9]+)[:](?<scol>[0-9]+) (?<eline>[0-9]+)[:](?<ecol>[0-9]+)");
Match matchpos = posregex.Match(terms[0]);
int sline = Convert.ToInt32(matchpos.Groups["sline"].Value);
int scol = Convert.ToInt32(matchpos.Groups["scol"].Value);
/* if (i2b2str.StartsWith("TIMEX3") || i2b2str.StartsWith("EVENT"))
* sline++;*/
ret.startLoc = new TextIdentifier(filename, sline, scol);
int eline = Convert.ToInt32(matchpos.Groups["eline"].Value);
int ecol = Convert.ToInt32(matchpos.Groups["ecol"].Value);
/* if (i2b2str.StartsWith("TIMEX3") || i2b2str.StartsWith("EVENT"))
* eline++;*/
ret.endLoc = new TextIdentifier(filename, eline, ecol);
}
if (ret == null)
{
ret = null;
}
return(ret);
}
