From 0b436ed76e5dca781a50f58b52027101bb0477ad Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 27 Feb 2017 16:24:01 +0100
Subject: [PATCH] lih data parser added
---
.../parse/LihControlMappingParser.java | 136 +++++++++++++
.../appointment/parse/LihControlParser.java | 179 ++++++++++++++++++
.../java/smash/appointment/parse/Main.java | 24 +++
.../appointment/parse/PrcControlParser.java | 10 +-
.../appointment/parse/PrcFlyingParser.java | 9 +-
.../appointment/parse/PrcSubjectsParser.java | 15 +-
.../appointment/parse/SubjectParser.java | 17 ++
.../smash/appointment/parse/AllTests.java | 3 +
.../parse/LihControlMappingParserTest.java | 58 ++++++
.../parse/LihControlParserTest.java | 64 +++++++
.../testFiles/lihControlExample.xlsx | Bin 0 -> 9814 bytes
11 files changed, 512 insertions(+), 3 deletions(-)
create mode 100644 appointment-import/src/main/java/smash/appointment/parse/LihControlMappingParser.java
create mode 100644 appointment-import/src/main/java/smash/appointment/parse/LihControlParser.java
create mode 100644 appointment-import/src/test/java/smash/appointment/parse/LihControlMappingParserTest.java
create mode 100644 appointment-import/src/test/java/smash/appointment/parse/LihControlParserTest.java
create mode 100644 appointment-import/testFiles/lihControlExample.xlsx
diff --git a/appointment-import/src/main/java/smash/appointment/parse/LihControlMappingParser.java b/appointment-import/src/main/java/smash/appointment/parse/LihControlMappingParser.java
new file mode 100644
index 00000000..8f5b0e2d
--- /dev/null
+++ b/appointment-import/src/main/java/smash/appointment/parse/LihControlMappingParser.java
@@ -0,0 +1,136 @@
+package smash.appointment.parse;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.poi.ss.usermodel.Row;
+
+public class LihControlMappingParser extends SubjectParser {
+
+ @Override
+ protected String parseScreeningNumber(Row row) {
+ String number = getString(row.getCell(0));
+ if (number.trim().isEmpty()) {
+ return "";
+ } else {
+ if (number.length() == 1) {
+ number = "00" + number;
+ } else if (number.length() == 2) {
+ number = "0" + number;
+ }
+ return "L-" + number;
+ }
+ }
+
+ @Override
+ protected String parseName(Row row) {
+ return getString(row.getCell(8));
+ }
+
+ @Override
+ protected String parseSurname(Row row) {
+ return getString(row.getCell(9));
+ }
+
+ @Override
+ protected String parseNdNumber(Row row) {
+ return getString(row.getCell(7));
+ }
+
+ @Override
+ protected String getSheetName() {
+ return "Sheet1";
+ }
+
+ @Override
+ protected int getInitRow() {
+ return 1;
+ }
+
+ @Override
+ protected String parseBirthDate(Row row) {
+ return "";
+ }
+
+ @Override
+ protected String parsemPowerId(Row row) {
+ return "";
+ }
+
+ @Override
+ protected String parseAddDate(Row row) {
+ return getDate(row.getCell(1));
+ }
+
+ @Override
+ protected String parseReferal(Row row) {
+ return "";
+ }
+
+ @Override
+ protected String parseDiagnosisYear(Row row) {
+ return "";
+ }
+
+ @Override
+ protected String parseMail(Row row) {
+ return "";
+ }
+
+ @Override
+ protected String parsePhone3(Row row) {
+ return "";
+ }
+
+ @Override
+ protected String parsePhone2(Row row) {
+ return "";
+ }
+
+ @Override
+ protected String parsePhone1(Row row) {
+ return getString(row.getCell(10));
+ }
+
+ @Override
+ protected String parseCity(Row row) {
+ return "";
+
+ }
+
+ @Override
+ protected String parseCountry(Row row) {
+ return "";
+ }
+
+ @Override
+ protected String parseZipCode(Row row) {
+ return "";
+ }
+
+ @Override
+ protected String parseAddress(Row row) {
+ return "";
+ }
+
+ @Override
+ protected String parseRemarks(Row row) {
+ return "";
+ }
+
+ @Override
+ protected String parseDiagnosis(Row row) {
+ return "";
+ }
+
+ @Override
+ protected SubjectType parseType(Row row) {
+ return SubjectType.CONTROL;
+ }
+
+ @Override
+ protected List<String> parseLanguages(Row row) {
+ return new ArrayList<>();
+ }
+
+}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/LihControlParser.java b/appointment-import/src/main/java/smash/appointment/parse/LihControlParser.java
new file mode 100644
index 00000000..82955aa2
--- /dev/null
+++ b/appointment-import/src/main/java/smash/appointment/parse/LihControlParser.java
@@ -0,0 +1,179 @@
+package smash.appointment.parse;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.poi.ss.usermodel.Row;
+
+public class LihControlParser extends SubjectParser {
+
+ @Override
+ protected String parseScreeningNumber(Row row) {
+ String number = getString(row.getCell(0));
+ if (number.trim().isEmpty()) {
+ return "";
+ } else {
+ return "L-" + number;
+ }
+ }
+
+ @Override
+ protected String parseName(Row row) {
+ return getString(row.getCell(2));
+ }
+
+ @Override
+ protected String parseSurname(Row row) {
+ return getString(row.getCell(1));
+ }
+
+ @Override
+ protected String parseNdNumber(Row row) {
+ return "";
+ }
+
+ @Override
+ protected String getSheetName() {
+ return "Screening log";
+ }
+
+ @Override
+ protected int getInitRow() {
+ return 1;
+ }
+
+ @Override
+ protected String parseBirthDate(Row row) {
+ return getDate(row.getCell(5));
+ }
+
+ @Override
+ protected String parsemPowerId(Row row) {
+ return "";
+ }
+
+ @Override
+ protected String parseAddDate(Row row) {
+ return "";
+ }
+
+ @Override
+ protected String parseReferal(Row row) {
+ return "";
+ }
+
+ @Override
+ protected String parseDiagnosisYear(Row row) {
+ return "";
+ }
+
+ @Override
+ protected String parseMail(Row row) {
+ return getString(row.getCell(8));
+ }
+
+ @Override
+ protected String parsePhone3(Row row) {
+ return "";
+ }
+
+ @Override
+ protected String parsePhone2(Row row) {
+ return getString(row.getCell(7));
+ }
+
+ @Override
+ protected String parsePhone1(Row row) {
+ return getString(row.getCell(6));
+ }
+
+ @Override
+ protected String parseCity(Row row) {
+ return getString(row.getCell(12));
+
+ }
+
+ @Override
+ protected String parseCountry(Row row) {
+ return "";
+ }
+
+ @Override
+ protected String parseZipCode(Row row) {
+ return getString(row.getCell(11));
+ }
+
+ @Override
+ protected String parseAddress(Row row) {
+ return getString(row.getCell(9)) + ", " + getString(row.getCell(10));
+ }
+
+ @Override
+ protected String parseRemarks(Row row) {
+ List<String> remarks = new ArrayList<>();
+ String info = getString(row.getCell(4));
+ if (!info.trim().isEmpty()) {
+ remarks.add("PD family relation=" + info);
+ }
+ remarks.add(getString(row.getCell(13)));
+ remarks.add(getComments(row.getCell(14)));
+ remarks.add(getComments(row.getCell(15)));
+ remarks.add(getComments(row.getCell(16)));
+ remarks.add(getString(row.getCell(18)));
+ remarks.add(getString(row.getCell(19)));
+ String result = "";
+ for (String string : remarks) {
+ if (!string.trim().isEmpty()) {
+ result += string.trim() + "\n";
+ }
+ }
+ return result;
+ }
+
+ @Override
+ protected String parseDiagnosis(Row row) {
+ return "";
+ }
+
+ @Override
+ protected SubjectType parseType(Row row) {
+ return SubjectType.CONTROL;
+ }
+
+ @Override
+ protected List<String> parseLanguages(Row row) {
+ List<String> result = new ArrayList<>();
+
+ String languages = getString(row.getCell(3));
+ String langAbbreviations[] = new String[] {};
+ if (languages.indexOf(",") >= 0) {
+ langAbbreviations = languages.split(",");
+ } else {
+ langAbbreviations = languages.split("/");
+ }
+ for (String string : langAbbreviations) {
+ if (!string.trim().isEmpty()) {
+ result.add(getMappedLanguage(string.trim()));
+ }
+ }
+ return result;
+ }
+
+ private String getMappedLanguage(String abbreviation) {
+ switch (abbreviation.toUpperCase()) {
+ case ("F"):
+ return "French";
+ case ("D"):
+ return "German";
+ case ("GB"):
+ return "English";
+ case ("P"):
+ return "Portuguese";
+ case ("ENG"):
+ return "English";
+ }
+ logger.warn("Unknown language abbreviation: " + abbreviation);
+ return "";
+ }
+
+}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/Main.java b/appointment-import/src/main/java/smash/appointment/parse/Main.java
index 96965759..5c6f94cb 100644
--- a/appointment-import/src/main/java/smash/appointment/parse/Main.java
+++ b/appointment-import/src/main/java/smash/appointment/parse/Main.java
@@ -27,10 +27,14 @@ public class Main {
Option subjects = Option.builder().required().argName("file").hasArg().desc("PRC subjects").longOpt("subjects").build();
Option controls = Option.builder().required().argName("file").hasArg().desc("PRC controls").longOpt("controls").build();
Option flyingTeam = Option.builder().required().argName("file").hasArg().desc("PRC flying-team").longOpt("flying-team").build();
+ Option lihControls = Option.builder().required().argName("file").hasArg().desc("LIH controls").longOpt("lih-controls").build();
+ Option lihMappingControls = Option.builder().required().argName("file").hasArg().desc("LIH controls mapping").longOpt("lih-mapping").build();
options.addOption(agenda);
options.addOption(subjects);
options.addOption(controls);
options.addOption(flyingTeam);
+ options.addOption(lihControls);
+ options.addOption(lihMappingControls);
CommandLineParser parser = new DefaultParser();
try {
@@ -51,6 +55,16 @@ public class Main {
subjectDao.addSubject(subject, "[" + flyingTeamFile + ";" + subject.getScreeningNumber() + ";" + subject.getName() + " " + subject.getSurname() + "]");
}
+ String lihMappingControlsFile = line.getOptionValue("lih-mapping");
+ for (Subject subject : processLihMappingControls(lihMappingControlsFile)) {
+ subjectDao.addSubject(subject, "[" + lihMappingControlsFile + ";" + subject.getScreeningNumber() + ";" + subject.getName() + " " + subject.getSurname() + "]");
+ }
+
+ String lihControlsFile = line.getOptionValue("lih-controls");
+ for (Subject subject : processLihControls(lihControlsFile)) {
+ subjectDao.addSubject(subject, "[" + lihControlsFile + ";" + subject.getScreeningNumber() + ";" + subject.getName() + " " + subject.getSurname() + "]");
+ }
+
logger.debug("SUBJECTS: ");
for (Subject subject : subjectDao.getSubjects()) {
logger.debug(subject);
@@ -66,6 +80,16 @@ public class Main {
}
}
+ private List<Subject> processLihMappingControls(String lihMappingControlsFile) throws Exception{
+ LihControlMappingParser parser = new LihControlMappingParser();
+ return parser.processExcel(lihMappingControlsFile);
+ }
+
+ private List<Subject> processLihControls(String lihControlsFile) throws Exception{
+ LihControlParser parser = new LihControlParser();
+ return parser.processExcel(lihControlsFile);
+ }
+
private List<Subject> processFlyingTeamControls(String flyingTeamFile) throws Exception {
PrcFlyingParser parser = new PrcFlyingParser();
return parser.processExcel(flyingTeamFile);
diff --git a/appointment-import/src/main/java/smash/appointment/parse/PrcControlParser.java b/appointment-import/src/main/java/smash/appointment/parse/PrcControlParser.java
index 44496a88..dbf0dc8c 100644
--- a/appointment-import/src/main/java/smash/appointment/parse/PrcControlParser.java
+++ b/appointment-import/src/main/java/smash/appointment/parse/PrcControlParser.java
@@ -1,5 +1,8 @@
package smash.appointment.parse;
+import java.util.ArrayList;
+import java.util.List;
+
import org.apache.poi.ss.usermodel.Cell;
import org.apache.poi.ss.usermodel.Row;
@@ -8,7 +11,7 @@ public class PrcControlParser extends SubjectParser {
@Override
protected String parseScreeningNumber(Row row) {
String number = getString(row.getCell(16));
- if (number.isEmpty()) {
+ if (number.trim().isEmpty()) {
return "";
} else {
return "P-" + number;
@@ -153,4 +156,9 @@ public class PrcControlParser extends SubjectParser {
return SubjectType.CONTROL;
}
+ @Override
+ protected List<String> parseLanguages(Row row) {
+ return new ArrayList<>();
+ }
+
}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/PrcFlyingParser.java b/appointment-import/src/main/java/smash/appointment/parse/PrcFlyingParser.java
index 5e27552d..ff69003a 100644
--- a/appointment-import/src/main/java/smash/appointment/parse/PrcFlyingParser.java
+++ b/appointment-import/src/main/java/smash/appointment/parse/PrcFlyingParser.java
@@ -1,5 +1,8 @@
package smash.appointment.parse;
+import java.util.ArrayList;
+import java.util.List;
+
import org.apache.poi.ss.usermodel.Cell;
import org.apache.poi.ss.usermodel.Row;
@@ -8,7 +11,7 @@ public class PrcFlyingParser extends SubjectParser {
@Override
protected String parseScreeningNumber(Row row) {
String number = getString(row.getCell(25));
- if (number.isEmpty()) {
+ if (number.trim().isEmpty()) {
return "";
} else {
return "P-" + number;
@@ -142,5 +145,9 @@ public class PrcFlyingParser extends SubjectParser {
protected SubjectType parseType(Row row) {
return null;
}
+ @Override
+ protected List<String> parseLanguages(Row row) {
+ return new ArrayList<>();
+ }
}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/PrcSubjectsParser.java b/appointment-import/src/main/java/smash/appointment/parse/PrcSubjectsParser.java
index 7b76573f..c2aea102 100644
--- a/appointment-import/src/main/java/smash/appointment/parse/PrcSubjectsParser.java
+++ b/appointment-import/src/main/java/smash/appointment/parse/PrcSubjectsParser.java
@@ -1,5 +1,8 @@
package smash.appointment.parse;
+import java.util.ArrayList;
+import java.util.List;
+
import org.apache.poi.ss.usermodel.Cell;
import org.apache.poi.ss.usermodel.Row;
@@ -7,7 +10,12 @@ public class PrcSubjectsParser extends SubjectParser {
@Override
protected String parseScreeningNumber(Row row) {
- return "P-" + getString(row.getCell(25));
+ String number = getString(row.getCell(25));
+ if (number.trim().isEmpty()) {
+ return "";
+ } else {
+ return "P-" + number;
+ }
}
@Override
@@ -125,4 +133,9 @@ public class PrcSubjectsParser extends SubjectParser {
return SubjectType.SUBJECT;
}
+ @Override
+ protected List<String> parseLanguages(Row row) {
+ return new ArrayList<>();
+ }
+
}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/SubjectParser.java b/appointment-import/src/main/java/smash/appointment/parse/SubjectParser.java
index 6b218352..3d5652f6 100644
--- a/appointment-import/src/main/java/smash/appointment/parse/SubjectParser.java
+++ b/appointment-import/src/main/java/smash/appointment/parse/SubjectParser.java
@@ -16,7 +16,9 @@ import org.apache.poi.hssf.usermodel.HSSFDateUtil;
import org.apache.poi.openxml4j.exceptions.InvalidFormatException;
import org.apache.poi.ss.usermodel.Cell;
import org.apache.poi.ss.usermodel.CellType;
+import org.apache.poi.ss.usermodel.Comment;
import org.apache.poi.ss.usermodel.DataFormatter;
+import org.apache.poi.ss.usermodel.RichTextString;
import org.apache.poi.ss.usermodel.Row;
import org.apache.poi.ss.usermodel.Sheet;
import org.apache.poi.ss.usermodel.Workbook;
@@ -84,10 +86,13 @@ public abstract class SubjectParser {
result.setmPowerId(parsemPowerId(row));
result.setBirthDate(parseBirthDate(row));
result.setType(parseType(row));
+ result.setLanguages(parseLanguages(row));
return result;
}
+ protected abstract List<String> parseLanguages(Row row);
+
protected abstract SubjectType parseType(Row row);
protected abstract String parseBirthDate(Row row);
@@ -142,6 +147,18 @@ public abstract class SubjectParser {
return df.formatCellValue(cell).trim();
}
+ protected String getComments(Cell cell) {
+ Comment comment = cell.getCellComment();
+ if (comment != null) {
+ RichTextString richTextString = comment.getString();
+ if (richTextString != null) {
+ return richTextString.getString();
+
+ }
+ }
+ return "";
+ }
+
protected String getDate(Cell cell) {
if (cell == null) {
return "";
diff --git a/appointment-import/src/test/java/smash/appointment/parse/AllTests.java b/appointment-import/src/test/java/smash/appointment/parse/AllTests.java
index 5aaea5c9..71c7e659 100644
--- a/appointment-import/src/test/java/smash/appointment/parse/AllTests.java
+++ b/appointment-import/src/test/java/smash/appointment/parse/AllTests.java
@@ -6,6 +6,8 @@ import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({ CellParserTest.class, //
+ LihControlMappingParserTest.class, //
+ LihControlParserTest.class, //
PrcFlyingParserTest.class, //
PrcSubjectsParserTest.class, //
RedcapParserTest.class, //
@@ -14,6 +16,7 @@ import org.junit.runners.Suite.SuiteClasses;
SubjectParserTest.class, //
XlsxCalendarProcessorTest.class, //
})
+
public class AllTests {
}
diff --git a/appointment-import/src/test/java/smash/appointment/parse/LihControlMappingParserTest.java b/appointment-import/src/test/java/smash/appointment/parse/LihControlMappingParserTest.java
new file mode 100644
index 00000000..33d36da9
--- /dev/null
+++ b/appointment-import/src/test/java/smash/appointment/parse/LihControlMappingParserTest.java
@@ -0,0 +1,58 @@
+package smash.appointment.parse;
+
+import static org.junit.Assert.*;
+
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+public class LihControlMappingParserTest extends TestBase {
+ Logger logger = Logger.getLogger(LihControlMappingParserTest.class);
+
+ LihControlMappingParser processor = new LihControlMappingParser();
+
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() {
+ super.setUp();
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void test() throws Exception {
+ List<Subject> entries = processor.processExcel("testFiles/lihControlMappingExample.xlsx");
+ assertTrue(entries.size() > 0);
+
+ Subject subject = entries.get(0);
+ assertEquals("L-001", subject.getScreeningNumber());
+ assertEquals("Piotrek", subject.getName());
+ assertEquals("Gawron", subject.getSurname());
+ assertEquals("", subject.getAddress());
+ assertEquals("", subject.getZipCode());
+ assertEquals("", subject.getCity());
+ assertEquals("", subject.getCountry());
+ assertEquals("343", subject.getPhone1());
+ assertEquals("", subject.getPhone2());
+ assertEquals("", subject.getPhone3());
+ assertEquals("", subject.getMail());
+ assertEquals("", subject.getDiagnosisYear());
+ assertEquals("", subject.getDiagnosis());
+ assertEquals("", subject.getReferal());
+ assertEquals("2015-08-03", subject.getAddDate());
+ assertEquals("ND3333", subject.getNdNumber());
+ assertEquals("", subject.getBirthDate());
+ }
+
+
+}
diff --git a/appointment-import/src/test/java/smash/appointment/parse/LihControlParserTest.java b/appointment-import/src/test/java/smash/appointment/parse/LihControlParserTest.java
new file mode 100644
index 00000000..b610128e
--- /dev/null
+++ b/appointment-import/src/test/java/smash/appointment/parse/LihControlParserTest.java
@@ -0,0 +1,64 @@
+package smash.appointment.parse;
+
+import static org.junit.Assert.*;
+
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+public class LihControlParserTest extends TestBase {
+ Logger logger = Logger.getLogger(LihControlParserTest.class);
+
+ LihControlParser processor = new LihControlParser();
+
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() {
+ super.setUp();
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void test() throws Exception {
+ List<Subject> entries = processor.processExcel("testFiles/lihControlExample.xlsx");
+ assertTrue(entries.size() > 0);
+
+ Subject subject = entries.get(0);
+ assertEquals("L-001", subject.getScreeningNumber());
+ assertEquals("Name", subject.getName());
+ assertEquals("Surname", subject.getSurname());
+ assertTrue(subject.getRemarks().contains("001 rdv 01/09/2015 9h jyf"));
+ assertTrue(subject.getRemarks().contains("PD family relation=pd info"));
+ assertEquals("11, Rue blabla", subject.getAddress());
+ assertEquals("L-3322", subject.getZipCode());
+ assertEquals("Luxembourg", subject.getCity());
+ assertEquals("", subject.getCountry());
+ assertEquals("123456789", subject.getPhone1());
+ assertEquals("321654", subject.getPhone2());
+ assertEquals("", subject.getPhone3());
+ assertEquals("email@pt.lu", subject.getMail());
+ assertEquals("", subject.getDiagnosisYear());
+ assertEquals("", subject.getDiagnosis());
+ assertEquals("", subject.getReferal());
+ assertEquals("", subject.getAddDate());
+ assertEquals("", subject.getNdNumber());
+ assertEquals("1937-01-03", subject.getBirthDate());
+ assertTrue(subject.getRemarks().contains("some other remark"));
+ assertTrue(subject.getRemarks().contains("at home: NMS + RFQ 1 + RFQ 2 + REM + PDSS: manque une page ds RFQ => Linda pr level b 09/09/15"));
+ assertTrue(subject.getLanguages().contains("French"));
+ assertTrue(subject.getLanguages().contains("German"));
+ }
+
+
+}
diff --git a/appointment-import/testFiles/lihControlExample.xlsx b/appointment-import/testFiles/lihControlExample.xlsx
new file mode 100644
index 0000000000000000000000000000000000000000..526e749bdf8cb818d13e98b763afb22b3ec3b071
GIT binary patch
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--
GitLab