@Override
public void constructIndex() throws IOException {
String corpusFile = _options._corpusPrefix + "/";
System.out.println("Construct index from: " + corpusFile);
chooseFiles cf = new chooseFiles(_options);
int times = cf.writeTimes();
System.out.println(times);
FileOps filewriter = new FileOps(_options._indexPrefix + "/");
for (int i = 0; i < times; i++) {
Vector<String> files = cf.loadFile(i);
for (String name : files) {
String filepath = corpusFile + name;
File file = new File(filepath);
time = new Date().getTime();
String content = ProcessHtml.process(file);
totalTime += new Date().getTime() - time;
if (content != null) processDocument(content, name);
}
// System.out.println("Times here : " + i);
// System.out.println("processes:" + totalTime);
String name = "temp" + i + ".txt";
Map<String, String> content = new HashMap<String, String>();
for (String term : _index.keySet()) {
StringBuilder builder = new StringBuilder();
for (Integer x : _index.get(term)) {
builder.append(x + "|");
}
builder.deleteCharAt(builder.length() - 1);
content.put(term, builder.toString());
}
filewriter.write(name, content);
_index.clear();
_terms.clear();
}
String corpus_statistics = _options._indexPrefix + "/" + "statistics";
BufferedWriter outsta = new BufferedWriter(new FileWriter(corpus_statistics));
// the first line in the corpus_statistics is the number of docs in the corpus
outsta.write(_numDocs + "\n");
outsta.write(String.valueOf(_totalTermFrequency) + "\n");
outsta.close();
String[] files = new String[times];
for (int count = 0; count < times; count++) {
files[count] = "temp" + count + ".txt";
}
filewriter.merge(files, "index.txt", "|");
}
public void generateDataExchangeFiles() {
long startTime = System.currentTimeMillis();
if (CmlOptions.SHOW_LOGS)
System.out.print("- Generating SQLite DB from EPha drug interactions csv... ");
extractInteractionMap();
// Save interactions to DB
try {
// Create Sqlite database
createDB();
// CSV file
String csv_file = "";
//
int intercnt = 0;
for (Map.Entry<String, ArrayList<String>> entry : m_drug_interactions_map.entrySet()) {
String key = entry.getKey().toUpperCase();
ArrayList<String> value = entry.getValue();
System.out.println(++intercnt + ": " + key + " interacts with " + value.size() + " meds");
/*
key: ATC1
inter0: Name1
inter1: ATC2
inter2: Name2
inter3: Info
inter4: Mechanismus
inter5: Effekt
inter6: Massnahmen
inter7: Grad
*/
/*
Risikoklassen
-------------
A: Keine Massnahmen notwendig (grün)
B: Vorsichtsmassnahmen empfohlen (gelb)
C: Regelmässige Überwachung (orange)
D: Kombination vermeiden (pinky)
X: Kontraindiziert (hellrot)
0: Keine Angaben (grau)
*/
for (String s : value) {
String[] inter = s.split("\\|\\|");
String risk_class = "";
if (inter[7].equals("A")) risk_class = "Keine Massnahmen notwendig";
else if (inter[7].equals("B")) risk_class = "Vorsichtsmassnahmen empfohlen";
else if (inter[7].equals("C")) risk_class = "Regelmässige Überwachung";
else if (inter[7].equals("D")) risk_class = "Kombination vermeiden";
else if (inter[7].equals("X")) risk_class = "Kontraindiziert";
else if (inter[7].equals("0")) risk_class = "Keine Angaben";
String para_class = "paragraph" + inter[7];
String html_content =
"<div>"
+ "<div class=\""
+ para_class
+ "\" id=\""
+ key
+ "-"
+ inter[1]
+ "\">"
+ "<div class=\"absTitle\">"
+ key
+ " ["
+ inter[0]
+ "] → "
+ inter[1]
+ " ["
+ inter[2]
+ "]</div></div>"
+ "<p class=\"spacing2\">"
+ "<i>Risikoklasse:</i> "
+ risk_class
+ " ("
+ inter[7]
+ ")</p>"
+ "<p class=\"spacing2\">"
+ "<i>Möglicher Effekt:</i> "
+ inter[3]
+ "</p>"
+ "<p class=\"spacing2\">"
+ "<i>Mechanismus:</i> "
+ inter[4]
+ "</p>"
+ "<p class=\"spacing2\">"
+ "<i>Empfohlene Massnahmen:</i> "
+ inter[6]
+ "</p></div>";
// Add to sqlite database
addDB(key, inter[0], inter[1], inter[2], html_content);
// Add to csv file
csv_file += key + "||" + inter[1] + "||" + html_content + "\n";
// Add to atc code - html map
String atc1_atc2_key = key + "-" + inter[1];
if (atc1_atc2_key != null) {
ArrayList<String> interaction_html = m_atc1_atc2_html_map.get(atc1_atc2_key);
if (interaction_html == null) interaction_html = new ArrayList<String>();
interaction_html.add(html_content);
m_atc1_atc2_html_map.put(atc1_atc2_key, interaction_html);
}
}
// Assume batch size of 20
if (batch_cnt > 20) {
conn.setAutoCommit(false);
prep.executeBatch();
conn.setAutoCommit(true);
batch_cnt = 0;
}
batch_cnt++;
}
// Add the rest
conn.setAutoCommit(false);
prep.executeBatch();
conn.setAutoCommit(true);
// Compress
stat.executeUpdate("VACUUM;");
// Write CSV to file
FileOps.writeToFile(
csv_file,
Constants.DIR_OUTPUT,
"drug_interactions_csv_" + CmlOptions.DB_LANGUAGE + ".csv");
// Zip file
FileOps.zipToFile(
Constants.DIR_OUTPUT, "drug_interactions_csv_" + CmlOptions.DB_LANGUAGE + ".csv");
// Generate report
if (CmlOptions.GENERATE_REPORTS == true) {
// Create interactions error report file
InteractionsReport interactions_errors =
new InteractionsReport(
Constants.FILE_INTERACTIONS_REPORT, CmlOptions.DB_LANGUAGE, "html");
String report_style_str = FileOps.readCSSfromFile(Constants.FILE_REPORT_CSS_BASE + ".css");
interactions_errors.addStyleSheet(report_style_str);
if (CmlOptions.DB_LANGUAGE.equals("de"))
interactions_errors.addHtmlHeader(
"Schweizer Arzneimittel-Kompendium", Constants.FI_DB_VERSION);
else if (CmlOptions.DB_LANGUAGE.equals("fr"))
interactions_errors.addHtmlHeader(
"Compendium des Médicaments Suisse", Constants.FI_DB_VERSION);
interactions_errors.append(interactions_errors.treemapToHtmlTable(m_atc1_atc2_html_map));
interactions_errors.writeHtmlToFile();
interactions_errors.getBWriter().close();
}
} catch (IOException e) {
e.printStackTrace();
} catch (SQLException e) {
System.out.println("SQLException!");
} catch (ClassNotFoundException e) {
System.out.println("ClassNotFoundException!");
}
long stopTime = System.currentTimeMillis();
if (CmlOptions.SHOW_LOGS) {
System.out.println(
"processed "
+ m_drug_interactions_map.size()
+ " drug interactions in "
+ (stopTime - startTime) / 1000.0f
+ " sec");
}
}
