Newer
Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
package smash.appointment.parse;
import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.text.SimpleDateFormat;
import java.time.format.DateTimeFormatter;
import java.util.ArrayList;
import java.util.Calendar;
import java.util.List;
import org.apache.log4j.Logger;
public class RedcapCalendarParser {
Logger logger = Logger.getLogger(RedcapCalendarParser.class);
private SubjectDao subjectDao;
DateTimeFormatter formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd HH:mm:ss");
SimpleDateFormat dateFormatter = new SimpleDateFormat("yyyy-MM-dd");
public List<AppointmentEntry> parse(String filename, Calendar minDate) throws FileNotFoundException, IOException {
List<AppointmentEntry> result = new ArrayList<>();
try (BufferedReader br = new BufferedReader(new FileReader(filename))) {
String line;
while ((line = br.readLine()) != null) {
if (!line.startsWith("INSERT INTO")) {
continue;
}
String tmp[] = line.substring(line.indexOf("(")).split("\\),\\(", -1);
for (String string : tmp) {
AppointmentEntry entry = processEntry(string, minDate);
if (entry != null) {
result.add(entry);
}
}
}
}
return result;
}
private AppointmentEntry processEntry(String string, Calendar minDate) {
AppointmentEntry result = new AppointmentEntry();
if (string.startsWith("(")) {
string = string.substring(1);
}
if (string.endsWith(")")) {
string = string.substring(0, string.length() - 1);
}
string = string.replaceAll("\\\\'", "__quota__");
string = string.replaceAll("'", "\"");
string = string.replaceAll("__quota__", "'");
String fields[] = string.split(",(?=(?:[^\"]*\"[^\"]*\")*[^\"]*$)", -1);
String ndNumber = fields[1].replaceAll("\"", "");
String day = fields[6].replaceAll("\"", "");
String time = fields[7].replaceAll("\"", "");
String query = fields[10].replaceAll("\"", "");
if (query.equals("") || query.equals("NULL")) {
return null;
}
if (minDate != null) {
if (day.compareTo(dateFormatter.format(minDate.getTime())) < 0) {
return null;
}
}
if (ndNumber.equals("NDtest_internal") || ndNumber.equals("NDtest_external")) {
return null;
}
Subject subject = null;
if (!ndNumber.equalsIgnoreCase("NULL")) {
subject = subjectDao.getByNdNumber(ndNumber);
if (subject == null) {
logger.warn("Cannot find subject with nd number: " + ndNumber);
}
}
if (subject == null) {
subject = findSubject(query);
}
if (subject != null && !subject.getToBeSeenAt().equalsIgnoreCase("LIH")) {
return null;
}
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
result.setDay(day);
result.setTime(time);
result.setSource("From redcap: " + query);
result.setSubject(subject);
result.addTypes(getTypes(query));
if (result.getTypes().contains(AppointmentType.OTHER)) {
logger.warn("Cannot find types for: " + query);
}
return result;
}
CellParser cellParser = new CellParser();
private List<AppointmentType> getTypes(String query) {
List<AppointmentType> result = new ArrayList<>();
AppointmentTypeCollection collection = cellParser.extractType(query);
if (collection == null) {
int index = query.indexOf("_");
if (index >= 0) {
query = query.substring(index);
if (query.startsWith("_lev a_")) {
collection = AppointmentTypeCollection.LEVEL_A;
}
}
if (collection == null) {
collection = AppointmentTypeCollection.OTHER;
}
}
for (AppointmentType appointmentType : collection.getTypes()) {
result.add(appointmentType);
}
return result;
}
private Subject findSubject(String query) {
String id = query.split("_")[0];
id = "L-" + id;
Subject result = subjectDao.getByScreeningNumber(id);
if (result == null) {
logger.warn("Cannot find subject for query: " + query);
}
return result;
}
/**
* @return the subjectDao
* @see #subjectDao
*/
public SubjectDao getSubjectDao() {
return subjectDao;
}
/**
* @param subjectDao
* the subjectDao to set
* @see #subjectDao
*/
public void setSubjectDao(SubjectDao subjectDao) {
this.subjectDao = subjectDao;
}
}