diff --git a/appointment-import/.classpath b/appointment-import/.classpath
deleted file mode 100644
index f7b62f180179a74fbb8400870e0e56b071065daa..0000000000000000000000000000000000000000
--- a/appointment-import/.classpath
+++ /dev/null
@@ -1,36 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
- <classpathentry kind="src" output="target/classes" path="src/main/java">
- <attributes>
- <attribute name="optional" value="true"/>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="src" output="target/test-classes" path="src/test/java">
- <attributes>
- <attribute name="optional" value="true"/>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7">
- <attributes>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
- <attributes>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
- <attributes>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
- <attributes>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="output" path="target/classes"/>
-</classpath>
diff --git a/appointment-import/.gitignore b/appointment-import/.gitignore
deleted file mode 100644
index ad708984880d5452a04d9a6a243c0c0cde201ce7..0000000000000000000000000000000000000000
--- a/appointment-import/.gitignore
+++ /dev/null
@@ -1,2 +0,0 @@
-/target/
-/log.txt
diff --git a/appointment-import/.project b/appointment-import/.project
deleted file mode 100644
index eee5e1c7df61a5e6865e9a8584bb8c4c4becfe6a..0000000000000000000000000000000000000000
--- a/appointment-import/.project
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
- <name>appointment-import</name>
- <comment></comment>
- <projects>
- </projects>
- <buildSpec>
- <buildCommand>
- <name>org.eclipse.jdt.core.javabuilder</name>
- <arguments>
- </arguments>
- </buildCommand>
- <buildCommand>
- <name>org.eclipse.m2e.core.maven2Builder</name>
- <arguments>
- </arguments>
- </buildCommand>
- </buildSpec>
- <natures>
- <nature>org.eclipse.jdt.core.javanature</nature>
- <nature>org.eclipse.m2e.core.maven2Nature</nature>
- </natures>
-</projectDescription>
diff --git a/appointment-import/.settings/org.eclipse.core.resources.prefs b/appointment-import/.settings/org.eclipse.core.resources.prefs
deleted file mode 100644
index 04cfa2c1a8566d64dd12fcf7a8e895fe02e1856f..0000000000000000000000000000000000000000
--- a/appointment-import/.settings/org.eclipse.core.resources.prefs
+++ /dev/null
@@ -1,6 +0,0 @@
-eclipse.preferences.version=1
-encoding//src/main/java=UTF-8
-encoding//src/main/resources=UTF-8
-encoding//src/test/java=UTF-8
-encoding//src/test/resources=UTF-8
-encoding/<project>=UTF-8
diff --git a/appointment-import/.settings/org.eclipse.jdt.core.prefs b/appointment-import/.settings/org.eclipse.jdt.core.prefs
deleted file mode 100644
index bbcbc93486d53c73668b275ea5daf41b66ba9c41..0000000000000000000000000000000000000000
--- a/appointment-import/.settings/org.eclipse.jdt.core.prefs
+++ /dev/null
@@ -1,5 +0,0 @@
-eclipse.preferences.version=1
-org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7
-org.eclipse.jdt.core.compiler.compliance=1.7
-org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
-org.eclipse.jdt.core.compiler.source=1.7
diff --git a/appointment-import/.settings/org.eclipse.m2e.core.prefs b/appointment-import/.settings/org.eclipse.m2e.core.prefs
deleted file mode 100644
index 14b697b7bbb0d85e8d8ee19141a2a92d9ce211be..0000000000000000000000000000000000000000
--- a/appointment-import/.settings/org.eclipse.m2e.core.prefs
+++ /dev/null
@@ -1,4 +0,0 @@
-activeProfiles=
-eclipse.preferences.version=1
-resolveWorkspaceProjects=true
-version=1
diff --git a/appointment-import/pom.xml b/appointment-import/pom.xml
deleted file mode 100644
index a2244ee9c27fc393f0190108de420b7cb272a67c..0000000000000000000000000000000000000000
--- a/appointment-import/pom.xml
+++ /dev/null
@@ -1,72 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
-
- <groupId>smash</groupId>
- <artifactId>appointment-import</artifactId>
- <version>0.0.1-SNAPSHOT</version>
- <packaging>jar</packaging>
-
- <name>appointment-import</name>
- <url>http://maven.apache.org</url>
-
- <properties>
- <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
- </properties>
-
- <dependencies>
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>4.12</version>
- <scope>test</scope>
- </dependency>
-<dependency>
- <groupId>log4j</groupId>
- <artifactId>log4j</artifactId>
- <version>1.2.17</version>
-</dependency>
-<dependency>
- <groupId>org.apache.poi</groupId>
- <artifactId>poi-ooxml</artifactId>
- <version>3.15</version>
-</dependency>
-<dependency>
- <groupId>commons-cli</groupId>
- <artifactId>commons-cli</artifactId>
- <version>1.3.1</version>
-</dependency>
- </dependencies>
-
- <build>
- <plugins>
-<plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-compiler-plugin</artifactId>
- <version>3.5.1</version>
- <configuration>
- <source>1.7</source>
- <target>1.7</target>
- </configuration>
-</plugin>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-assembly-plugin</artifactId>
- <configuration>
- <source>1.7</source>
- <target>1.7</target>
- <archive>
- <manifest>
- <addClasspath>true</addClasspath>
- <mainClass>smash.appointment.parse.Main</mainClass>
- </manifest>
- </archive>
- <descriptorRefs>
- <descriptorRef>jar-with-dependencies</descriptorRef>
- </descriptorRefs>
- </configuration>
- </plugin>
- </plugins>
- </build>
-
-</project>
diff --git a/appointment-import/src/main/java/smash/appointment/parse/AppointmentDao.java b/appointment-import/src/main/java/smash/appointment/parse/AppointmentDao.java
deleted file mode 100644
index ab5871502c8445b74fb03c13d8f988b1a8acb664..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/java/smash/appointment/parse/AppointmentDao.java
+++ /dev/null
@@ -1,142 +0,0 @@
-package smash.appointment.parse;
-
-import java.text.ParseException;
-import java.text.SimpleDateFormat;
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-
-public class AppointmentDao {
- Logger logger = Logger.getLogger(AppointmentDao.class);
- private List<AppointmentEntry> appointments = new ArrayList<>();
-
- public void addAppointments(List<AppointmentEntry> appointmentsToAdd) {
- for (AppointmentEntry appointmentEntry : appointmentsToAdd) {
- addAppointment(appointmentEntry);
- }
- }
-
- /**
- * @return the appointments
- * @see #appointments
- */
- public List<AppointmentEntry> getAppointments() {
- return appointments;
- }
-
- /**
- * @param appointments
- * the appointments to set
- * @see #appointments
- */
- public void setAppointments(List<AppointmentEntry> appointments) {
- this.appointments = appointments;
- }
-
- public List<Visit> getVisits() throws ParseException {
- List<Visit> result = new ArrayList<>();
- Map<Subject, List<AppointmentEntry>> subjectAppointments = new HashMap<>();
- for (AppointmentEntry entry : appointments) {
- if (subjectAppointments.get(entry.getSubject()) == null) {
- subjectAppointments.put(entry.getSubject(), new ArrayList<AppointmentEntry>());
- }
- subjectAppointments.get(entry.getSubject()).add(entry);
- }
- for (Subject subject : subjectAppointments.keySet()) {
- result.addAll(getVisitsForSubject(subject, subjectAppointments.get(subject)));
- }
- return result;
- }
-
- private List<Visit> getVisitsForSubject(Subject subject, List<AppointmentEntry> list) throws ParseException {
- Comparator<AppointmentEntry> comparator = new Comparator<AppointmentEntry>() {
-
- @Override
- public int compare(AppointmentEntry o1, AppointmentEntry o2) {
- String date1 = o1.getDay().substring(0, 10);
- String date2 = o2.getDay().substring(0, 10);
- if (date1.compareTo(date2) == 0) {
- if (o1.getTypes().contains(AppointmentType.LEVEL_AQUEST) || o1.getTypes().contains(AppointmentType.LEVEL_A_TQ)) {
- return -1;
- } else if (o2.getTypes().contains(AppointmentType.LEVEL_AQUEST) || o2.getTypes().contains(AppointmentType.LEVEL_A_TQ)) {
- return 1;
- } else {
- return 0;
- }
- } else {
- return date1.compareTo(date2);
- }
- }
- };
- Collections.sort(list, comparator);
-
- List<Visit> result = new ArrayList<>();
- Visit currentVisit = new Visit(subject);
- for (AppointmentEntry appointmentEntry : list) {
- if (appointmentEntry.getTypes().contains(AppointmentType.LEVEL_AQUEST) || appointmentEntry.getTypes().contains(AppointmentType.LEVEL_A_TQ)) {
- if (currentVisit.getAppointments().size() > 0) {
- if (shouldBeFinished(currentVisit.getEndDate())) {
- currentVisit.setFinished(true);
- }
- result.add(currentVisit);
- }
-
- currentVisit = new Visit(subject);
- currentVisit.addAppointment(appointmentEntry);
- } else {
- String date = currentVisit.getLastAppointmentDate();
- if (date.equals(appointmentEntry.getDay().substring(0, 10))) {
- currentVisit.getLastAppointment().addTypes(appointmentEntry.getTypes());
- String source = appointmentEntry.getSource() + "\n" + currentVisit.getLastAppointment().getSource();
- currentVisit.getLastAppointment().setSource(source);
- } else {
- currentVisit.addAppointment(appointmentEntry);
- }
- }
- }
- if (currentVisit.getAppointments().size() > 0) {
- result.add(currentVisit);
- }
- if (shouldBeFinished(currentVisit.getEndDate())) {
- currentVisit.setFinished(true);
- if (!subject.isDead() && !subject.isResigned()) {
- result.add(createNextVisit(currentVisit));
- }
- }
- return result;
- }
-
- protected Visit createNextVisit(Visit currentVisit) throws ParseException {
- Visit visit = new Visit(currentVisit.getSubject());
- Calendar date = Calendar.getInstance();
- String dateStr = currentVisit.getStartDate();
- date.setTime(DATE_FORMATTER.parse(dateStr));
- if (currentVisit.getSubject().getType().equals(SubjectType.CONTROL)) {
- date.add(Calendar.YEAR, 4);
- } else {
- date.add(Calendar.YEAR, 1);
- }
- visit.setStartDate(DATE_FORMATTER.format(date.getTime()));
- return visit;
- }
-
- private static final SimpleDateFormat DATE_FORMATTER = new SimpleDateFormat("yyyy-MM-dd");
-
- protected boolean shouldBeFinished(String endDate) {
- Calendar today_minus_two_months = Calendar.getInstance();
- today_minus_two_months.add(Calendar.MONTH, -2);
- return DATE_FORMATTER.format(today_minus_two_months.getTime()).compareTo(endDate) > 0;
- }
-
- public void addAppointment(AppointmentEntry appointment) {
- appointments.add(appointment);
-
- }
-
-}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/AppointmentEntry.java b/appointment-import/src/main/java/smash/appointment/parse/AppointmentEntry.java
deleted file mode 100644
index 4b8001727ff44fdd7e46e3a9fa5f35695d0e02e7..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/java/smash/appointment/parse/AppointmentEntry.java
+++ /dev/null
@@ -1,165 +0,0 @@
-package smash.appointment.parse;
-
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-public class AppointmentEntry {
- private String day;
- private String time;
- private String duration;
- private Subject subject;
- private Set<AppointmentType> types = new HashSet<>();
- private String source;
- private String location;
-
-
- /**
- * @return the time
- * @see #time
- */
- public String getTime() {
- if (time == null || time.trim().isEmpty()) {
- return "09:00";
- } else {
- return time;
- }
- }
-
- /**
- * @param time
- * the time to set
- * @see #time
- */
- public void setTime(String time) {
- this.time = time;
- }
-
- /**
- * @return the subject
- * @see #subject
- */
- public Subject getSubject() {
- return subject;
- }
-
- /**
- * @param subject
- * the subject to set
- * @see #subject
- */
- public void setSubject(Subject subject) {
- this.subject = subject;
- }
-
- /**
- * @return the type
- * @see #type
- */
- public Set<AppointmentType> getTypes() {
- return types;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void addType(AppointmentType type) {
- this.types.add(type);
- }
-
- /**
- * @return the day
- * @see #day
- */
- public String getDay() {
- return day;
- }
-
- /**
- * @param day
- * the day to set
- * @see #day
- */
- public void setDay(String day) {
- this.day = day;
- }
-
- /**
- * @return the source
- * @see #source
- */
- public String getSource() {
- return source;
- }
-
- /**
- * @param source
- * the source to set
- * @see #source
- */
- public void setSource(String source) {
- this.source = source;
- }
-
- @Override
- public String toString() {
- return day + " " + time + " " + subject + " " + types + "\t\t[source: " + source + "]";
- }
-
- /**
- * @return the duration
- * @see #duration
- */
- public String getDuration() {
- if (duration == null || duration.trim().isEmpty()) {
- int count = 0;
- for (AppointmentType type : types) {
- count += type.getTime();
- }
- return count + "";
- }
- return duration;
- }
-
- /**
- * @param duration
- * the duration to set
- * @see #duration
- */
- public void setDuration(String duration) {
- this.duration = duration;
- }
-
- public void addTypes(AppointmentType[] typesToAdd) {
- for (AppointmentType appointmentType : typesToAdd) {
- addType(appointmentType);
- }
-
- }
-
- public void addTypes(Collection<AppointmentType> typesToAdd) {
- for (AppointmentType appointmentType : typesToAdd) {
- addType(appointmentType);
- }
-
- }
-
- /**
- * @return the location
- * @see #location
- */
- public String getLocation() {
- return location;
- }
-
- /**
- * @param location the location to set
- * @see #location
- */
- public void setLocation(String location) {
- this.location = location;
- }
-}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/AppointmentSqlExporter.java b/appointment-import/src/main/java/smash/appointment/parse/AppointmentSqlExporter.java
deleted file mode 100644
index 4c669334a76b25c7a1ebe5959bbb4e771df61346..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/java/smash/appointment/parse/AppointmentSqlExporter.java
+++ /dev/null
@@ -1,56 +0,0 @@
-package smash.appointment.parse;
-
-import java.util.Calendar;
-
-public class AppointmentSqlExporter extends SqlExporter {
-
- public String toSql(AppointmentEntry appointment) {
- StringBuilder result = new StringBuilder("");
-
- result.append("insert into web_appointment (");
- result.append("datetime_when, ");
- result.append("length, ");
- result.append("status, ");
- result.append("comment, ");
- result.append("location_id, ");
- result.append("visit_id) ");
-
- result.append("values (");
- result.append(getStringVal(appointment.getDay() + " " + appointment.getTime() + "+00") + ",");
- result.append(getStringVal(appointment.getDuration()) + ",");
- if (isBefore(appointment, Calendar.getInstance())) {
- result.append("'FINISHED',");
- } else {
- result.append("'SCHEDULED',");
- }
- result.append(getStringVal(appointment.getSource()) + ",");
- switch (appointment.getLocation().substring(0, 1)) {
- case ("L"):
- result.append("(select id from web_location where name = 'LIH'),");
- break;
- case ("F"):
- result.append("(select id from web_location where name = 'Flying Team'),");
- break;
- case ("P"):
- result.append("(select id from web_location where name = 'PRC'),");
- break;
- default:
- throw new RuntimeException("Unknown location: " + appointment.getLocation());
- }
- result.append("(select max(id) from web_visit)");
- result.append(");\n");
-
- for (AppointmentType type : appointment.getTypes()) {
- result.append("\tinsert into web_appointment_appointment_types (");
- result.append("appointment_id, ");
- result.append("appointmenttype_id) ");
- result.append("values (");
- result.append("(select max(id) from web_appointment),");
- result.append("(select id from web_appointmenttype where code=" + getStringVal(type.getAbbreviation()) + ") ");
- result.append(");\n");
- }
-
- return result.toString();
- }
-
-}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/AppointmentType.java b/appointment-import/src/main/java/smash/appointment/parse/AppointmentType.java
deleted file mode 100644
index a4e9aec8774b7cec2379e17d3e78ae89c7f42168..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/java/smash/appointment/parse/AppointmentType.java
+++ /dev/null
@@ -1,33 +0,0 @@
-package smash.appointment.parse;
-
-public enum AppointmentType {
- LEVEL_BV(90,"BV"), //
- LEVEL_BG(30,"BG"), //
- LEVEL_SB(30,"SB"), //
-
- LEVEL_A_TQ(120,"A_TQ"), //
- LEVEL_AN(60,"AN"), //
- LEVEL_ANP(60,"ANP"), //
- LEVEL_ASAMP(60,"ASAMP"), //
- LEVEL_AWELC(15,"AWELC"), //
- LEVEL_AQUEST(0,"AQUEST"), //
- LEVEL_B(90,"B"), //
- LEVEL_B_M_POWER(70,"mPower"), //
- OTHER(60,"OTHER"), //
- ;
-
- private int time;
- private String abbreviation;
-
- private AppointmentType(int defaultTime, String abbreviation) {
- this.time=defaultTime;
- this.abbreviation=abbreviation;
- }
- public int getTime() {
- return time;
- }
- public String getAbbreviation() {
- return abbreviation;
- }
-
-}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/AppointmentTypeCollection.java b/appointment-import/src/main/java/smash/appointment/parse/AppointmentTypeCollection.java
deleted file mode 100644
index 0799c0e5124e2c6eefb519059962135947c39885..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/java/smash/appointment/parse/AppointmentTypeCollection.java
+++ /dev/null
@@ -1,82 +0,0 @@
-package smash.appointment.parse;
-
-public enum AppointmentTypeCollection {
- LEVEL_A_BV_BG(new AppointmentType[] { AppointmentType.LEVEL_ANP, AppointmentType.LEVEL_BV, AppointmentType.LEVEL_BG }, //
- new String[] { "BV + BG + neuro level A" }), //
- LEVEL_A_B(new AppointmentType[] { AppointmentType.LEVEL_ANP, AppointmentType.LEVEL_B }, //
- new String[] { "level B + level A neuro" }), //
-
- LEVEL_B_BV_SB(new AppointmentType[] { AppointmentType.LEVEL_B, AppointmentType.LEVEL_BV, AppointmentType.LEVEL_SB }, //
- new String[] { "level B + BV + SB" }), //
-
- LEVEL_B_BV_BG(new AppointmentType[] { AppointmentType.LEVEL_B, AppointmentType.LEVEL_BV, AppointmentType.LEVEL_BG }, //
- new String[] { "level B + BV + BG" }), //
-
- LEVEL_B_BG(new AppointmentType[] { AppointmentType.LEVEL_B, AppointmentType.LEVEL_BG }, //
- new String[] { "level B + BG" }), //
-
- LEVEL_B_BV(new AppointmentType[] { AppointmentType.LEVEL_B, AppointmentType.LEVEL_BV }, //
- new String[] { "level B + BV" }), //
-
- LEVEL_BV_BG_SB_MPOWER(
- new AppointmentType[] { AppointmentType.LEVEL_BV, AppointmentType.LEVEL_BG, AppointmentType.LEVEL_SB, AppointmentType.LEVEL_B_M_POWER, }, //
- new String[] { "evel BV + BG + SB + mPower", "BV + BG + SB + mPower" }), //
-
- LEVEL_BG_SB_MPOWER(
- new AppointmentType[] { AppointmentType.LEVEL_BG, AppointmentType.LEVEL_SB, AppointmentType.LEVEL_B_M_POWER, }, //
- new String[] { "level BG + SB + mPower" }), //
- LEVEL_BV_BG_SB(new AppointmentType[] { AppointmentType.LEVEL_BV, AppointmentType.LEVEL_BG, AppointmentType.LEVEL_SB }, //
- new String[] { "evel BV + BG + SB", "BV + BG + SB" }), //
- LEVEL_BV_SB_NEURO(new AppointmentType[] { AppointmentType.LEVEL_BV, AppointmentType.LEVEL_SB, AppointmentType.LEVEL_AN }, //
- new String[] { "BV + SB + neuro" }), //
- LEVEL_BV_SB_M_POWER(new AppointmentType[] { AppointmentType.LEVEL_BV, AppointmentType.LEVEL_SB, AppointmentType.LEVEL_B_M_POWER}, //
- new String[] { "BV + SB + mPower" }), //
- LEVEL_BV_SB(new AppointmentType[] { AppointmentType.LEVEL_BV, AppointmentType.LEVEL_SB }, //
- new String[] { "evel BV + SB", "BV + SB" }), //
- LEVEL_BV_BG(new AppointmentType[] { AppointmentType.LEVEL_BV, AppointmentType.LEVEL_BG }, //
- new String[] { "evel BV + BG", "BV + BG" }), //
- LEVEL_BG_SB(new AppointmentType[] { AppointmentType.LEVEL_BG, AppointmentType.LEVEL_SB }, //
- new String[] { "evel BG + SB", "BG + SB" }), //
- LEVEL_BV(new AppointmentType[] { AppointmentType.LEVEL_BV }, //
- new String[] { "evel BV", "BV" }), //
- LEVEL_BG(new AppointmentType[] { AppointmentType.LEVEL_BG }, //
- new String[] { "evel BG", "BG" }), //
- LEVEL_SB(new AppointmentType[] { AppointmentType.LEVEL_SB }, //
- new String[] { "evel SB", "SB" }), //
-
- LEVEL_A_TQ(new AppointmentType[] { AppointmentType.LEVEL_A_TQ }, //
- new String[] { "TQ" }), //
- LEVEL_A(new AppointmentType[] { AppointmentType.LEVEL_AWELC, AppointmentType.LEVEL_AN, AppointmentType.LEVEL_ANP, AppointmentType.LEVEL_AQUEST, AppointmentType.LEVEL_ASAMP, }, //
- new String[] { "level A" }), //
- LEVEL_B(new AppointmentType[] { AppointmentType.LEVEL_B }, //
- new String[] { "evel B" }), //
- LEVEL_B_M_POWER(new AppointmentType[] { AppointmentType.LEVEL_B_M_POWER }, //
- new String[] { "mPower" }), //
- OTHER(new AppointmentType[] {AppointmentType.OTHER}, //
- new String[] {}), //
- ;
- private String[] queryStrings;
- private AppointmentType[] types;
-
- private AppointmentTypeCollection(AppointmentType[] types, String[] queryStrings) {
- this.queryStrings = queryStrings;
- this.types = types;
- }
-
- /**
- * @return the queryStrings
- * @see #queryStrings
- */
- public String[] getQueryStrings() {
- return queryStrings;
- }
-
- /**
- * @return the types
- * @see #types
- */
- public AppointmentType[] getTypes() {
- return types;
- }
-
-}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/CellParser.java b/appointment-import/src/main/java/smash/appointment/parse/CellParser.java
deleted file mode 100644
index bfd6940fcf13b38ed6c8e2279e953bc515f70192..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/java/smash/appointment/parse/CellParser.java
+++ /dev/null
@@ -1,167 +0,0 @@
-package smash.appointment.parse;
-
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import org.apache.log4j.Logger;
-
-public class CellParser {
- Logger logger = Logger.getLogger(CellParser.class);
-
- private SubjectDao subjectDao;
-
- Pattern timePattern = Pattern.compile("^[0-9][0-9]\\:[0-9][0-9]");
-
- public String extractTime(String content) {
- String result = null;
- Matcher matcher = timePattern.matcher(content);
- if (matcher.find()) {
- result = matcher.group();
- }
- return result;
- }
-
- public String removeTime(String content) {
- Matcher matcher = timePattern.matcher(content);
- if (matcher.find()) {
- content = matcher.replaceFirst("").trim();
- }
- return content;
- }
-
- public AppointmentEntry parseAppointment(String query, String defaultTime) {
- AppointmentEntry result = new AppointmentEntry();
-
- String time = extractTime(query);
- if (time != null) {
- query = removeTime(query);
- } else {
- time = defaultTime;
- }
- result.setTime(time);
-
- Subject subject = extractSubject(query);
- result.setSubject(subject);
- if (subject!=null) {
- result.setLocation(subject.getToBeSeenAt());
- } else {
- result.setLocation("PRC");
- }
-
- AppointmentTypeCollection type = extractType(query);
- if (type == null) {
- result.addType(AppointmentType.OTHER);
- } else {
- result.addTypes(type.getTypes());
- }
-
- result.setSource(query);
- return result;
- }
-
- public AppointmentTypeCollection extractType(String query) {
-
- String simplifiedQuery = Utils.simplifyString(query);
-
- AppointmentTypeCollection result = null;
-
- String usedString = null;
- for (AppointmentTypeCollection type : AppointmentTypeCollection.values()) {
- boolean matchFound = false;
- for (String string : type.getQueryStrings()) {
- if (!matchFound) {
- String simplifiedString = Utils.simplifyString(string);
-
- if (simplifiedQuery.contains(simplifiedString)) {
- matchFound = true;
- if (result == null) {
- result = type;
- usedString = string;
- } else {
- if (string.contains(usedString)) {
- result = type;
- usedString = string;
- } else if (usedString.contains(string)) {
- // new one is a substring of old
- } else { // if there is no substring then we might have a problem
- AppointmentTypeCollection newType = result;
- if (usedString.length() < string.length()) {
- usedString = string;
- newType = type;
- }
- logger.warn("More than one type possible for query: " + query + ". Type 1: " + result + ". Type 2: " + type + ". Choosing: " + newType);
- result = newType;
- }
- }
-
- }
- }
- }
- }
- return result;
- }
-
- private Subject extractSubject(String query) {
- Subject result = null;
- String simplifiedQuery = Utils.simplifyString(query);
-
- SubjectIndexer[] mainIndices = new SubjectIndexer[] { //
- new NameSurnameIndexer(), //
- new SurnameNameIndexer(), //
- new NdNumberIndexer(),//
- };
-
- result = getByIndices(query, simplifiedQuery, mainIndices);
- if (result == null) {
- SubjectIndexer[] secondaryIndices = new SubjectIndexer[] { //
- new SurnameIndexer(), //
- };
- result = getByIndices(query, simplifiedQuery, secondaryIndices);
- }
- return result;
- }
-
- private Subject getByIndices(String query, String simplifiedQuery, SubjectIndexer[] mainIndices) {
- Subject result = null;
- for (Subject subject : subjectDao.getSubjects()) {
- boolean matchFound = false;
- for (SubjectIndexer indexer : mainIndices) {
- if (!matchFound) {
- if (indexer.match(subject, simplifiedQuery)) {
- matchFound = true;
- if (result == null) {
- result = subject;
- } else {
- Subject newResult = result;
- if (indexer.isBetter(subject, result)) {
- newResult = subject;
- }
- logger.warn(
- "[" + indexer.getClass().getSimpleName() + "]" + "More than one subject possible for query: " + query + ". Subject 1: " + result
- + ". Subject 2: " + subject + ". Choosing: " + newResult);
- result = newResult;
- }
- }
- }
- }
- }
- 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;
- }
-}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/DuplicateRemoveParser.java b/appointment-import/src/main/java/smash/appointment/parse/DuplicateRemoveParser.java
deleted file mode 100644
index 42fd910a1072f1c6a5e9b34353e655086c93344f..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/java/smash/appointment/parse/DuplicateRemoveParser.java
+++ /dev/null
@@ -1,48 +0,0 @@
-package smash.appointment.parse;
-
-import java.io.BufferedReader;
-import java.io.FileReader;
-import java.io.IOException;
-
-public class DuplicateRemoveParser {
- private SubjectDao subjectDao;
-
- public void removeDuplicates(String filename) throws IOException {
- try (BufferedReader br = new BufferedReader(new FileReader(filename))) {
- String line;
- while ((line = br.readLine()) != null) {
- String tmp[] = line.split("\t");
- Subject subject = subjectDao.getByScreeningNumber(tmp[0]);
- if (subject == null) {
- throw new InvalidArgumentException("Cannot find subject with id: " + tmp[0]);
- }
- for (int i = 1; i < tmp.length; i++) {
- Subject duplicate = subjectDao.getByScreeningNumber(tmp[i]);
-
- if (duplicate == null) {
- throw new InvalidArgumentException("Cannot find subject with id: " + tmp[i]);
- }
- subjectDao.removeDuplicate(subject, duplicate, "DUPLICATES: " + tmp[0] + ", " + tmp[i]);
- }
- }
- }
-
- }
-
- /**
- * @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;
- }
-}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/InvalidArgumentException.java b/appointment-import/src/main/java/smash/appointment/parse/InvalidArgumentException.java
deleted file mode 100644
index 7ae0e2d841f43d0e697de94a088e2091823cda56..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/java/smash/appointment/parse/InvalidArgumentException.java
+++ /dev/null
@@ -1,14 +0,0 @@
-package smash.appointment.parse;
-
-public class InvalidArgumentException extends RuntimeException {
-
- public InvalidArgumentException(String string) {
- super(string);
- }
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
-}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/LihControlMappingParser.java b/appointment-import/src/main/java/smash/appointment/parse/LihControlMappingParser.java
deleted file mode 100644
index f0dc3de54d5f514defb6c882e3a20abb4d7dbd47..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/java/smash/appointment/parse/LihControlMappingParser.java
+++ /dev/null
@@ -1,162 +0,0 @@
-package smash.appointment.parse;
-
-import java.util.ArrayList;
-import java.util.Calendar;
-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) {
- String number = getString(row.getCell(7));
-
- if (number.equalsIgnoreCase("PK") ||number.equalsIgnoreCase("CHEM") || number.equalsIgnoreCase("Flying Team")) {
- number = "";
- }
- return number;
- }
-
- @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), Calendar.getInstance());
- }
-
- @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<>();
- }
-
- @Override
- protected String parseToBeSeenAt(Row row) {
- return "L";
- }
-
- @Override
- protected boolean parseDead(Row row) {
- return false;
- }
-
- @Override
- protected boolean parseResigned(Row row) {
- return false;
- }
-
- @Override
- protected boolean parsePostponed(Row row) {
- return false;
- }
-
-}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/LihControlParser.java b/appointment-import/src/main/java/smash/appointment/parse/LihControlParser.java
deleted file mode 100644
index 5dd580f688af72c2d69b5b346a94110e14cbddd7..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/java/smash/appointment/parse/LihControlParser.java
+++ /dev/null
@@ -1,273 +0,0 @@
-package smash.appointment.parse;
-
-import java.text.SimpleDateFormat;
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.List;
-
-import org.apache.poi.ss.usermodel.Color;
-import org.apache.poi.ss.usermodel.Row;
-import org.apache.poi.xssf.usermodel.XSSFColor;
-
-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), null);
- }
-
- @Override
- protected String parsemPowerId(Row row) {
- return "";
- }
-
- private static final SimpleDateFormat DATE_FORMATTER = new SimpleDateFormat("yyyy-MM-dd");
-
- @Override
- protected String parseAddDate(Row row) {
- return DATE_FORMATTER.format(Calendar.getInstance().getTime());
- }
-
- @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) {
- String zipCode = parseZipCode(row);
- if (zipCode!=null) {
- if (zipCode.startsWith("L")) {
- return "Luxembourg";
- } else if (zipCode.startsWith("D")){
- return "Deutschland";
- } else if (zipCode.startsWith("F")){
- return "France";
- } else if (zipCode.startsWith("B")){
- return "Belgique";
- }
- }
- 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("Inclusion="+getString(row.getCell(17)));
- 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 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;
- }
-
- protected String getMappedLanguage(String abbreviation) {
- switch (abbreviation.toUpperCase()) {
- case ("F"):
- return "French";
- case ("D"):
- return "German";
- case ("A"):
- return "German";
- case ("E"):
- return "Spanish";
- case ("ALL"):
- return "German";
- case ("GB"):
- return "English";
- case ("P"):
- return "Portuguese";
- case ("PT"):
- return "Portuguese";
- case ("ENG"):
- return "English";
- case ("EN"):
- return "English";
- case ("FR"):
- return "French";
- case ("L"):
- return "Luxembourgish";
- case ("LUX"):
- return "Luxembourgish";
- }
- logger.warn("Unknown language abbreviation: " + abbreviation);
- return "";
- }
-
- @Override
- protected String parseToBeSeenAt(Row row) {
- return "L";
- }
-
- @Override
- protected boolean parseDead(Row row) {
- return false;
- }
-
- @Override
- protected boolean parsePostponed(Row row) {
- Color color = row.getCell(0).getCellStyle().getFillForegroundColorColor();
- if (color == null) {
- return false;
- }
-
- XSSFColor c = (XSSFColor) color;
- String colorString = c.getARGBHex().substring(2);
- switch (colorString) {
- case ("FFC000"):// orange
- return false;
- case ("FFFF00"):// yellow
- return false;
- case ("FF0000"):// red
- return false;
- case ("FF3399"):// pink
- return true;
- case ("00B050"):// green
- return false;
- }
- throw new RuntimeException(parseName(row) + " " + parseSurname(row) + ": Unknown color: " + colorString);
- }
-
- @Override
- protected boolean parseResigned(Row row) {
- Color color = row.getCell(0).getCellStyle().getFillForegroundColorColor();
- if (color == null) {
- return false;
- }
-
- XSSFColor c = (XSSFColor) color;
- String colorString = c.getARGBHex().substring(2);
- switch (colorString) {
- case ("FFC000"):// orange
- return false;
- case ("FFFF00"):// yellow
- return false;
- case ("FF0000"):// red
- return true;
- case ("FF3399"):// pink
- return false;
- case ("00B050"):// green
- return false;
- }
- throw new RuntimeException(parseName(row) + " " + parseSurname(row) + ": Unknown color: " + colorString);
- }
-}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/Main.java b/appointment-import/src/main/java/smash/appointment/parse/Main.java
deleted file mode 100644
index 8db86858cfbbcdc461ed881ffc9775cb65551231..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/java/smash/appointment/parse/Main.java
+++ /dev/null
@@ -1,185 +0,0 @@
-package smash.appointment.parse;
-
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.util.Calendar;
-import java.util.List;
-
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.DefaultParser;
-import org.apache.commons.cli.HelpFormatter;
-import org.apache.commons.cli.Option;
-import org.apache.commons.cli.Options;
-import org.apache.commons.cli.ParseException;
-import org.apache.log4j.Logger;
-
-public class Main {
- private static Logger logger = Logger.getLogger(Main.class);
-
- SubjectDao subjectDao = new SubjectDao();
- AppointmentDao appointmentDao = new AppointmentDao();
-
- public void run(String[] args) throws Exception {
-
- Options options = new Options();
- Option agenda = Option.builder().required().argName("file").hasArg().desc("PRC agenda").longOpt("agenda").build();
- 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();
- Option redCap = Option.builder().required().argName("file").hasArg().desc("RedCap appointments").longOpt("red-cap").build();
- Option redCapCalendar = Option.builder().required().argName("file").hasArg().desc("RedCap calendar sql").longOpt("red-cap-calendar").build();
- Option duplicates = Option.builder().required().argName("file").hasArg().desc("duplicates").longOpt("duplicates").build();
- options.addOption(agenda);
-
- options.addOption(subjects);
- options.addOption(controls);
- options.addOption(flyingTeam);
- options.addOption(lihControls);
- options.addOption(lihMappingControls);
- options.addOption(redCap);
- options.addOption(redCapCalendar);
- options.addOption(duplicates);
-
- CommandLineParser parser = new DefaultParser();
- try {
- CommandLine line = parser.parse(options, args);
-
- String subjectsFile = line.getOptionValue("subjects");
- for (Subject subject : processPrcSubjects(subjectsFile)) {
- subjectDao.addSubject(subject, "[" + subjectsFile + ";" + subject.getScreeningNumber() + ";" + subject.getName() + " " + subject.getSurname() + "]");
- }
-
- String controlsFile = line.getOptionValue("controls");
- for (Subject subject : processPrcControls(controlsFile)) {
- subjectDao.addSubject(subject, "[" + controlsFile + ";" + subject.getScreeningNumber() + ";" + subject.getName() + " " + subject.getSurname() + "]");
- }
-
- String flyingTeamFile = line.getOptionValue("flying-team");
- for (Subject subject : processFlyingTeamControls(flyingTeamFile)) {
- 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() + "]");
- }
-
- String duplicatesFile = line.getOptionValue("duplicates");
- removeDuplicates(duplicatesFile);
-
- subjectDao.addSubject(Visit.UNKNOWN, "");
-
- String agendaFile = line.getOptionValue("agenda");
- Calendar today = Calendar.getInstance();
- today.set(Calendar.HOUR, 5);
- appointmentDao.addAppointments(processPrcAppointments(agendaFile, today));
-
- String redCapFile = line.getOptionValue("red-cap");
- appointmentDao.addAppointments(processRedCapAppointments(redCapFile));
-
- String redCapCalendarFile = line.getOptionValue("red-cap-calendar");
- appointmentDao.addAppointments(processRedCapCalendar(redCapCalendarFile));
-
- System.out.println("delete from web_visit_appointment_types;");
- System.out.println("delete from web_appointment_appointment_types;");
- System.out.println("delete from web_subject_languages;");
- System.out.println("delete from web_appointment;");
- System.out.println("delete from web_visit;");
- System.out.println("delete from web_subject;");
-
- SubjectSqlExporter subjectSqlExporter = new SubjectSqlExporter();
- // logger.debug("SUBJECTS: ");
- for (Subject subject : subjectDao.getSubjects()) {
- System.out.println(subjectSqlExporter.toSql(subject));
- }
-
- VisitSqlExporter visitSqlExporter = new VisitSqlExporter();
- List<Visit> visits = appointmentDao.getVisits();
- for (int i = 0; i < visits.size(); i++) {
- Visit visit = visits.get(i);
- System.out.println(visitSqlExporter.toSql(visit));
- }
-
- } catch (ParseException exp) {
- System.out.println(exp.getMessage());
- HelpFormatter formatter = new HelpFormatter();
- formatter.printHelp("java -jar file.jar", options);
- }
- }
-
- private List<AppointmentEntry> processRedCapCalendar(String redCapCalendarFile) throws FileNotFoundException, IOException {
- RedcapCalendarParser redcapCalendarParser = new RedcapCalendarParser();
- redcapCalendarParser.setSubjectDao(subjectDao);
- Calendar date = Calendar.getInstance();
- date.set(Calendar.HOUR, 0);
- return redcapCalendarParser.parse(redCapCalendarFile, date);
- }
-
- private void removeDuplicates(String duplicatesFile) throws IOException {
- logger.info("PROCESSING FILE: " + duplicatesFile);
- DuplicateRemoveParser parser = new DuplicateRemoveParser();
- parser.setSubjectDao(subjectDao);
- parser.removeDuplicates(duplicatesFile);
- }
-
- private List<AppointmentEntry> processRedCapAppointments(String agendaFile) throws Exception {
- logger.info("PROCESSING FILE: " + agendaFile);
- RedcapParser parser = new RedcapParser();
- parser.setSubjectDao(subjectDao);
- return parser.parse(agendaFile);
- }
-
- private List<Subject> processLihMappingControls(String lihMappingControlsFile) throws Exception {
- logger.info("PROCESSING FILE: " + lihMappingControlsFile);
- LihControlMappingParser parser = new LihControlMappingParser();
- return parser.processExcel(lihMappingControlsFile);
- }
-
- private List<Subject> processLihControls(String lihControlsFile) throws Exception {
- logger.info("PROCESSING FILE: " + lihControlsFile);
- LihControlParser parser = new LihControlParser();
- return parser.processExcel(lihControlsFile);
- }
-
- private List<Subject> processFlyingTeamControls(String flyingTeamFile) throws Exception {
- logger.info("PROCESSING FILE: " + flyingTeamFile);
- PrcFlyingParser parser = new PrcFlyingParser();
- return parser.processExcel(flyingTeamFile);
- }
-
- private List<Subject> processPrcControls(String controlsFile) throws Exception {
- logger.info("PROCESSING FILE: " + controlsFile);
- PrcControlParser parser = new PrcControlParser();
- return parser.processExcel(controlsFile);
- }
-
- private List<AppointmentEntry> processPrcAppointments(String agendaFile, Calendar minDate) throws Exception {
- logger.info("PROCESSING FILE: " + agendaFile);
- XlsxCalendarProcessor processor = new XlsxCalendarProcessor();
- processor.setSubjectDao(subjectDao);
- List<AppointmentEntry> entries = processor.processExcel(agendaFile, minDate);
-
- return entries;
- }
-
- public static void main(String[] args) throws Exception {
- new Main().run(args);
- }
-
- private List<Subject> processPrcSubjects(String subjectsFile) throws Exception {
- logger.info("PROCESSING FILE: " + subjectsFile);
- PrcSubjectsParser parser = new PrcSubjectsParser();
- return parser.processExcel(subjectsFile);
- }
-
-}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/NameSurnameIndexer.java b/appointment-import/src/main/java/smash/appointment/parse/NameSurnameIndexer.java
deleted file mode 100644
index 2ed820ad2e1b4609692d2eaf7233254a6784c0fc..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/java/smash/appointment/parse/NameSurnameIndexer.java
+++ /dev/null
@@ -1,9 +0,0 @@
-package smash.appointment.parse;
-
-public class NameSurnameIndexer extends SubjectIndexer {
-
- public String getIndexedString(Subject subject) {
- return Utils.simplifyString(subject.getName() + subject.getSurname());
- }
-
-}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/NdNumberIndexer.java b/appointment-import/src/main/java/smash/appointment/parse/NdNumberIndexer.java
deleted file mode 100644
index cd96a4a1a0149f439d7436689350279fe87d92fb..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/java/smash/appointment/parse/NdNumberIndexer.java
+++ /dev/null
@@ -1,9 +0,0 @@
-package smash.appointment.parse;
-
-public class NdNumberIndexer extends SubjectIndexer {
-
- public String getIndexedString(Subject subject) {
- return Utils.simplifyString(subject.getNdNumber());
- }
-
-}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/PrcControlParser.java b/appointment-import/src/main/java/smash/appointment/parse/PrcControlParser.java
deleted file mode 100644
index 7a7ec376543578b77ca3db1e2fb2206e79479f89..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/java/smash/appointment/parse/PrcControlParser.java
+++ /dev/null
@@ -1,165 +0,0 @@
-package smash.appointment.parse;
-
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.List;
-
-import org.apache.poi.ss.usermodel.Cell;
-import org.apache.poi.ss.usermodel.Row;
-
-public class PrcControlParser extends SubjectParser {
-
- @Override
- protected String parseScreeningNumber(Row row) {
- String number = getString(row.getCell(13));
- if (number.trim().isEmpty()) {
- return "";
- } else {
- if (number.length() == 1) {
- number = "00" + number;
- } else if (number.length() == 2) {
- number = "0" + number;
- }
- return "P-" + number;
- }
- }
-
- @Override
- protected String parseName(Row row) {
- return getString(row.getCell(1));
- }
-
- @Override
- protected String parseSurname(Row row) {
- return getString(row.getCell(0));
- }
-
- @Override
- protected String parseNdNumber(Row row) {
- return getString(row.getCell(12));
- }
-
- @Override
- protected String getSheetName() {
- return "Contrôles";
- }
-
- @Override
- protected int getInitRow() {
- return 1;
- }
-
- @Override
- protected String parseBirthDate(Row row) {
- return parseDateOfBirth(row.getCell(11));
- }
-
- @Override
- protected String parsemPowerId(Row row) {
- return "";
- }
-
- @Override
- protected String parseAddDate(Row row) {
- return getDate(row.getCell(9), Calendar.getInstance());
- }
-
- @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(4));
- }
-
- @Override
- protected String parseCountry(Row row) {
- return getString(row.getCell(5));
- }
-
- @Override
- protected String parseZipCode(Row row) {
- return getString(row.getCell(3));
- }
-
- @Override
- protected String parseAddress(Row row) {
- return getString(row.getCell(2));
- }
-
- @Override
- protected String parseRemarks(Row row) {
- String remark1 = getString(row.getCell(10));
- String remark2 = "";
-
- String result = "";
- if (!remark1.trim().isEmpty()) {
- result = result + remark1 + "\n";
- }
- if (!remark2.trim().isEmpty()) {
- result = result + remark2 + "\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) {
- return new ArrayList<>();
- }
-
- @Override
- protected String parseToBeSeenAt(Row row) {
- return "P";
- }
- @Override
- protected boolean parseDead(Row row) {
- return false;
- }
-
- @Override
- protected boolean parseResigned(Row row) {
- return false;
- }
-
- @Override
- protected boolean parsePostponed(Row row) {
- return false;
- }
-}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/PrcFlyingParser.java b/appointment-import/src/main/java/smash/appointment/parse/PrcFlyingParser.java
deleted file mode 100644
index 1ee25fa2de02e448063e86233b9bf137288c0a65..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/java/smash/appointment/parse/PrcFlyingParser.java
+++ /dev/null
@@ -1,171 +0,0 @@
-package smash.appointment.parse;
-
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.List;
-
-import org.apache.poi.ss.usermodel.Cell;
-import org.apache.poi.ss.usermodel.Row;
-
-public class PrcFlyingParser extends SubjectParser {
-
- @Override
- protected String parseScreeningNumber(Row row) {
- String number = getString(row.getCell(22));
- if (number.trim().isEmpty()) {
- return "";
- } else {
- if (number.length() == 1) {
- number = "00" + number;
- } else if (number.length() == 2) {
- number = "0" + number;
- }
- return "F-" + number;
- }
- }
-
- @Override
- protected String parseName(Row row) {
- return getString(row.getCell(1));
- }
-
- @Override
- protected String parseSurname(Row row) {
- return getString(row.getCell(0));
- }
-
- @Override
- protected String parseNdNumber(Row row) {
- return getString(row.getCell(21));
- }
-
- @Override
- protected String getSheetName() {
- return "Leudelange";
- }
-
- @Override
- protected int getInitRow() {
- return 2;
- }
-
- @Override
- protected String parseBirthDate(Row row) {
- return parseDateOfBirth(row.getCell(23));
- }
-
- @Override
- protected String parsemPowerId(Row row) {
- return "";
- }
-
- @Override
- protected String parseAddDate(Row row) {
- return getDate(row.getCell(13),Calendar.getInstance());
- }
-
- @Override
- protected String parseReferal(Row row) {
- return getString(row.getCell(12));
- }
-
- @Override
- protected String parseDiagnosisYear(Row row) {
- return "";
- }
-
- @Override
- protected String parseMail(Row row) {
- return getString(row.getCell(9));
- }
-
- @Override
- protected String parsePhone3(Row row) {
- return "";
- }
-
- @Override
- protected String parsePhone2(Row row) {
- return getString(row.getCell(8));
- }
-
- @Override
- protected String parsePhone1(Row row) {
- return getString(row.getCell(7));
- }
-
- @Override
- protected String parseCity(Row row) {
- return getString(row.getCell(5));
- }
-
- @Override
- protected String parseCountry(Row row) {
- return getString(row.getCell(6));
- }
-
- @Override
- protected String parseZipCode(Row row) {
- return getString(row.getCell(4));
- }
-
- @Override
- protected String parseAddress(Row row) {
- return getString(row.getCell(3));
- }
-
- @Override
- protected String parseRemarks(Row row) {
- String remark1 = getString(row.getCell(10));
- String remark2 = getString(row.getCell(19));
-
- String result = "";
- if (!remark1.trim().isEmpty()) {
- result = result + remark1 + "\n";
- }
- if (!remark2.trim().isEmpty()) {
- result = result + remark2 + "\n";
- }
- return result;
- }
-
- @Override
- protected String parseDiagnosis(Row row) {
- return getString(row.getCell(11));
- }
-
- @Override
- protected SubjectType parseType(Row row) {
- String str = getString(row.getCell(2)).toLowerCase().trim();
- if (str.startsWith("c")) {
- return SubjectType.CONTROL;
- } else if (str.startsWith("p")) {
- return SubjectType.PATIENT;
- }
- return SubjectType.PATIENT;
- }
-
- @Override
- protected List<String> parseLanguages(Row row) {
- return new ArrayList<>();
- }
- @Override
- protected String parseToBeSeenAt(Row row) {
- return "F";
- }
-
- @Override
- protected boolean parseDead(Row row) {
- return false;
- }
-
- @Override
- protected boolean parseResigned(Row row) {
- return false;
- }
- @Override
- protected boolean parsePostponed(Row row) {
- return false;
- }
-
-}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/PrcSubjectsParser.java b/appointment-import/src/main/java/smash/appointment/parse/PrcSubjectsParser.java
deleted file mode 100644
index 5badd40394a25d065d17796f3547427dc34c6d42..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/java/smash/appointment/parse/PrcSubjectsParser.java
+++ /dev/null
@@ -1,213 +0,0 @@
-package smash.appointment.parse;
-
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.List;
-
-import org.apache.poi.hssf.util.HSSFColor;
-import org.apache.poi.ss.usermodel.Color;
-import org.apache.poi.ss.usermodel.IndexedColors;
-import org.apache.poi.ss.usermodel.Row;
-import org.apache.poi.xssf.usermodel.XSSFColor;
-
-public class PrcSubjectsParser extends SubjectParser {
-
- @Override
- protected String parseScreeningNumber(Row row) {
- String number = getString(row.getCell(25));
- if (number.trim().isEmpty()) {
- return "";
- } else {
- if (number.length() == 1) {
- number = "00" + number;
- } else if (number.length() == 2) {
- number = "0" + number;
- }
- return "P-" + number;
- }
- }
-
- @Override
- protected String parseName(Row row) {
- return getString(row.getCell(1));
- }
-
- @Override
- protected String parseSurname(Row row) {
- return getString(row.getCell(0));
- }
-
- @Override
- protected String parseNdNumber(Row row) {
- return getString(row.getCell(22));
- }
-
- @Override
- protected String getSheetName() {
- return "Feuil1";
- }
-
- @Override
- protected int getInitRow() {
- return 1;
- }
-
- @Override
- protected String parseBirthDate(Row row) {
- return parseDateOfBirth(row.getCell(27));
- }
-
- @Override
- protected String parsemPowerId(Row row) {
- return getString(row.getCell(23));
- }
-
- @Override
- protected String parseAddDate(Row row) {
- return getDate(row.getCell(14), Calendar.getInstance());
- }
-
- @Override
- protected String parseReferal(Row row) {
- return getString(row.getCell(13));
- }
-
- @Override
- protected String parseDiagnosisYear(Row row) {
- return getString(row.getCell(11));
- }
-
- @Override
- protected String parseMail(Row row) {
- return getString(row.getCell(10));
- }
-
- @Override
- protected String parsePhone3(Row row) {
- return getString(row.getCell(9));
- }
-
- @Override
- protected String parsePhone2(Row row) {
- return getString(row.getCell(8));
- }
-
- @Override
- protected String parsePhone1(Row row) {
- return getString(row.getCell(7));
- }
-
- @Override
- protected String parseCity(Row row) {
- return getString(row.getCell(5));
- }
-
- @Override
- protected String parseCountry(Row row) {
- return getString(row.getCell(6));
- }
-
- @Override
- protected String parseZipCode(Row row) {
- return getString(row.getCell(4));
- }
-
- @Override
- protected String parseAddress(Row row) {
- return getString(row.getCell(3));
- }
-
- @Override
- protected String parseRemarks(Row row) {
- String remark1 = getString(row.getCell(2));
- String remark2 = getString(row.getCell(20));
-
- String result = "";
- if (!remark1.trim().isEmpty()) {
- result = result + remark1 + "\n";
- }
- if (!remark2.trim().isEmpty()) {
- result = result + remark2 + "\n";
- }
- return result;
- }
-
- @Override
- protected String parseDiagnosis(Row row) {
- return getString(row.getCell(12));
- }
-
- @Override
- protected SubjectType parseType(Row row) {
- return SubjectType.PATIENT;
- }
-
- @Override
- protected List<String> parseLanguages(Row row) {
- return new ArrayList<>();
- }
-
- @Override
- protected String parseToBeSeenAt(Row row) {
- return "P";
- }
-
- @Override
- protected boolean parseDead(Row row) {
- Color color = row.getCell(0).getCellStyle().getFillForegroundColorColor();
- if (color == null) {
- return false;
- }
- if (color instanceof XSSFColor) {
- return true;
- }
- if (color instanceof HSSFColor) {
- HSSFColor hssfColor = (HSSFColor) color;
- if (hssfColor.getHexString().equalsIgnoreCase("0:0:0")) {
- return false;
- } else {
- return true;
- }
- }
- return false;
- }
-
- @Override
- protected boolean parseResigned(Row row) {
- try {
- int colorId = row.getSheet().getWorkbook().getFontAt(row.getCell(0).getCellStyle().getFontIndex()).getColor();
- // special case for black
- if (colorId == 32767) {
- return false;
- }
- IndexedColors color = IndexedColors.fromInt(colorId);
- switch (color) {
- case RED:
- return true;
- case SEA_GREEN:
- return false;
- case PINK:
- return false;
- case PLUM:
- return false;
- case BLUE:
- return false;
- case BLACK:
- return false;
- case GREEN:
- return false;
- default:
- logger.debug("Unknown font color: " + color);
- return false;
- }
- } catch (Exception e) {
- logger.error("Problem with parsing color for subject: " + parseName(row) + " " + parseSurname(row), e);
- return false;
- }
- }
-
- @Override
- protected boolean parsePostponed(Row row) {
- return false;
- }
-}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/RedcapCalendarParser.java b/appointment-import/src/main/java/smash/appointment/parse/RedcapCalendarParser.java
deleted file mode 100644
index e9b86aee73fc5c1b014fbef24a416eb8e8b8ec08..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/java/smash/appointment/parse/RedcapCalendarParser.java
+++ /dev/null
@@ -1,162 +0,0 @@
-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().toLowerCase().startsWith("l")) {
- return null;
- }
- result.setLocation("LIH");
- 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);
- }
- if (result.getTypes().contains(AppointmentType.LEVEL_ASAMP)) {
- return result;
- } else {
- logger.debug("Skipping LIH appointment: " + query);
- return null;
- }
- }
-
- 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;
- } else {
- index = query.indexOf("_", 1);
- 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;
- }
-}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/RedcapMissingSqlExporter.java b/appointment-import/src/main/java/smash/appointment/parse/RedcapMissingSqlExporter.java
deleted file mode 100644
index 3a15d6c16bf49e2e55f8f5562b3e0439696fb95c..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/java/smash/appointment/parse/RedcapMissingSqlExporter.java
+++ /dev/null
@@ -1,52 +0,0 @@
-package smash.appointment.parse;
-
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.List;
-
-public class RedcapMissingSqlExporter {
- static SubjectDao subjectDao = new SubjectDao();
-
- public static void main(String[] args) throws Exception {
- List<Subject> subjects = new ArrayList<>();
- for (int count =0 ;count<10000;count++) {
- String nd = count+"";
- while (nd.length()<4) {
- nd = "0"+nd;
- }
- Subject subject = new Subject("name "+nd, "surname"+nd, "ND"+nd, count+"");
-
- String screening = nd;
- if (screening.startsWith("0")) {
- screening = screening.substring(1);
- }
- subject.setScreeningNumber("P-"+screening);
- subject.setToBeSeenAt("PRC");
- if (count>=3000) {
- screening=screening.substring(1);
- subject.setScreeningNumber("L-"+screening);
- subject.setToBeSeenAt("LIH");
- }
- if (count>=7000) {
- subject.setScreeningNumber("F-"+nd);
- subject.setToBeSeenAt("FLYING TEAM");
- }
- subjects.add(subject);
- }
- subjectDao.setSubjects(subjects);
-
- RedcapCalendarParser parser = new RedcapCalendarParser();
- parser.setSubjectDao(subjectDao);
- Calendar date = Calendar.getInstance();
- date.set(2017, 2, 21, 1, 0, 0);
- List<AppointmentEntry> entries = parser.parse("E:/redcap_events_calendar-20032017.sql", date);
-
- VisitSqlExporter sqlExporter = new VisitSqlExporter();
- for (AppointmentEntry entry: entries) {
- Visit visit = new Visit(entry.getSubject());
- visit.addAppointment(entry);
- visit.setStartDate(entry.getDay());
- System.out.println(sqlExporter.toSql(visit));
- }
- }
-}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/RedcapParser.java b/appointment-import/src/main/java/smash/appointment/parse/RedcapParser.java
deleted file mode 100644
index 77daba4800f5cb51d19bd23ef250805d335e67d0..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/java/smash/appointment/parse/RedcapParser.java
+++ /dev/null
@@ -1,212 +0,0 @@
-package smash.appointment.parse;
-
-import java.io.BufferedReader;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-import java.time.LocalDateTime;
-import java.time.format.DateTimeFormatter;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-public class RedcapParser {
- Logger logger = Logger.getLogger(RedcapParser.class);
-
- private SubjectDao subjectDao;
-
- public List<AppointmentEntry> parse(String filename) throws FileNotFoundException, IOException {
- List<AppointmentEntry> result = new ArrayList<>();
- try (BufferedReader br = new BufferedReader(new FileReader(filename))) {
- int lineNumber = 0;
- String line;
- while ((line = br.readLine()) != null) {
- lineNumber++;
- if (lineNumber == 1) {
- continue;
- }
- String tmp[] = line.split("\t", -1);
-
- String ndNumber = tmp[0];
- Subject subject = subjectDao.getByNdNumber(ndNumber);
- if (subject == null) {
- logger.warn("Cannot find subject with id: " + ndNumber);
- } else {
- if (tmp.length < 8) {
- logger.warn("Invalid row (not enough cells): " + line);
- } else {
- subject.addLanguage(tmp[4]);
- subject.addLanguage(tmp[5]);
- subject.addLanguage(tmp[6]);
- subject.addLanguage(tmp[7]);
- if (!tmp[3].trim().isEmpty()) {
- subject.setSex(tmp[3]);
- }
- if (!tmp[2].trim().isEmpty()) {
- subject.setBirthDate(tmp[2]);
- }
-
- List<AppointmentEntry> subjectAppointments = new ArrayList<>();
- if (!tmp[9].isEmpty()) {
- subjectAppointments.add(createEntryLevelA(tmp[9], tmp[10], subject));
- }
-
- if (!tmp[13].isEmpty()) {
- subjectAppointments.add(createEntryLevelB(tmp[13], tmp[14], subject));
- }
-
- if (!tmp[17].isEmpty()) {
- subjectAppointments.add(createEntryLevelBG(tmp[17], tmp[18], subject));
- }
-
- if (!tmp[21].isEmpty()) {
- subjectAppointments.add(createEntryLevelBV(tmp[21], tmp[22], subject));
- }
-
- if (!tmp[41].isEmpty()) {
- subjectAppointments.add(createEntryLevelSB(tmp[41], subject));
- }
-
- if (!tmp[45].isEmpty()) {
- subjectAppointments.add(createEntryLevelMPower(tmp[45], subject));
- }
-
- result.addAll(subjectAppointments);
- }
- }
-
- }
- }
- return result;
-
- }
-
- private AppointmentEntry createEntryLevelMPower(String from, Subject subject) {
- AppointmentEntry entry = new AppointmentEntry();
- String date = getDate(from);
- entry.setDay(date);
- entry.setSubject(subject);
- entry.setSource("Imported from RedCap");
- entry.addType(AppointmentType.LEVEL_B_M_POWER);
- entry.setLocation(subject.getToBeSeenAt());
- return entry;
- }
-
- private AppointmentEntry createEntryLevelSB(String from, Subject subject) {
- AppointmentEntry entry = new AppointmentEntry();
- String date = getDate(from);
- entry.setDay(date);
- entry.setSubject(subject);
- entry.setSource("Imported from RedCap");
- entry.addType(AppointmentType.LEVEL_SB);
- entry.setLocation(subject.getToBeSeenAt());
- return entry;
- }
-
- private AppointmentEntry createEntryLevelBV(String from, String to, Subject subject) {
- AppointmentEntry entry = new AppointmentEntry();
- String date = getDate(from);
- String date2 = getDate(to);
- if (!date.equals(date2)) {
- logger.warn("Different start and end date for level BV appointment. Subject: " + subject.getNdNumber());
- }
- entry.setDay(date);
- entry.setSubject(subject);
- entry.setSource("Imported from RedCap");
- entry.addType(AppointmentType.LEVEL_BV);
- entry.setLocation(subject.getToBeSeenAt());
- return entry;
- }
-
- private AppointmentEntry createEntryLevelBG(String from, String to, Subject subject) {
- AppointmentEntry entry = new AppointmentEntry();
- String date = getDate(from);
- String date2 = getDate(to);
- if (!date.equals(date2)) {
- logger.warn("Different start and end date for level BG appointment. Subject: " + subject.getNdNumber());
- }
- entry.setDay(date);
- entry.setSubject(subject);
- entry.setSource("Imported from RedCap");
- entry.addType(AppointmentType.LEVEL_BG);
- entry.setLocation(subject.getToBeSeenAt());
- return entry;
- }
-
- private AppointmentEntry createEntryLevelB(String from, String to, Subject subject) {
- AppointmentEntry entry = new AppointmentEntry();
- String date = getDate(from);
- String date2 = getDate(to);
- if (!date.equals(date2)) {
- logger.warn("Different start and end date for level B appointment. Subject: " + subject.getNdNumber());
- }
- entry.setDay(date);
- entry.setSubject(subject);
- entry.setSource("Imported from RedCap");
- entry.addType(AppointmentType.LEVEL_B);
- entry.setLocation(subject.getToBeSeenAt());
- return entry;
- }
-
- private AppointmentEntry createEntryLevelA(String from, String to, Subject subject) {
- AppointmentEntry entry = new AppointmentEntry();
- String date = getDate(from);
- String date2 = getDate(to);
- if (!date.equals(date2)) {
- logger.warn("Different start and end date for level A appointment. Subject: " + subject.getNdNumber() + "; " + date + ", " + date2);
- }
- String time = getTime(from);
- String duration = getDuration(from, to);
- entry.setDay(date);
- entry.setDuration(duration);
- entry.setSubject(subject);
- entry.setSource("Imported from RedCap");
- entry.setTime(time);
- entry.addTypes(AppointmentTypeCollection.LEVEL_A.getTypes());
- entry.setLocation(subject.getToBeSeenAt());
- return entry;
- }
-
- private String getDuration(String string, String string2) {
- if (string2.isEmpty()) {
- return null;
- }
- String time1 = getTime(string);
- String time2 = getTime(string2);
-
- DateTimeFormatter formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd HH:mm:ss");
-
- LocalDateTime dateTime1 = LocalDateTime.parse("2014-11-25 " + time1 + ":00", formatter);
- LocalDateTime dateTime2 = LocalDateTime.parse("2014-11-25 " + time2 + ":00", formatter);
-
- long diffInMinutes = java.time.Duration.between(dateTime1, dateTime2).toMinutes();
-
- return diffInMinutes + "";
- }
-
- private String getTime(String string) {
- return string.split(" ")[1];
- }
-
- private String getDate(String string) {
- return string.split(" ")[0];
- }
-
- /**
- * @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;
- }
-}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/SqlExporter.java b/appointment-import/src/main/java/smash/appointment/parse/SqlExporter.java
deleted file mode 100644
index a5c19bb25f2b4a06d5d88b9cedcce94ae89d028b..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/java/smash/appointment/parse/SqlExporter.java
+++ /dev/null
@@ -1,52 +0,0 @@
-package smash.appointment.parse;
-
-import java.text.SimpleDateFormat;
-import java.util.Calendar;
-
-public class SqlExporter {
-
- private static final SimpleDateFormat DATE_FORMATTER = new SimpleDateFormat("yyyy-MM-dd");
-
- public SqlExporter() {
- super();
- }
-
- protected boolean isBefore(AppointmentEntry entry, Calendar minDate) {
- String entryDate = entry.getDay();
- String beforeDate = DATE_FORMATTER.format(minDate.getTime());
- if (entryDate.compareTo(beforeDate) < 0) {
- return true;
- } else {
- return false;
- }
- }
-
- protected String getStringVal(String arg) {
- if (arg == null) {
- return "null";
- } else if (arg.isEmpty()) {
- return "''";
- } else {
- return "'" + arg.replace("'", "''") + "'";
- }
- }
-
- protected String getIntVal(String diagnosisYear) {
- if (diagnosisYear == null || diagnosisYear.trim().isEmpty()) {
- return "0";
- } else {
- return diagnosisYear;
- }
- }
-
- protected String getDateVal(String arg) {
- if (arg == null) {
- return "null";
- } else if (arg.isEmpty()) {
- return "null";
- } else {
- return "'" + arg + "'";
- }
- }
-
-}
\ No newline at end of file
diff --git a/appointment-import/src/main/java/smash/appointment/parse/Subject.java b/appointment-import/src/main/java/smash/appointment/parse/Subject.java
deleted file mode 100644
index ec606f964af36cd450bff91e7b022663a8df5fe9..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/java/smash/appointment/parse/Subject.java
+++ /dev/null
@@ -1,598 +0,0 @@
-package smash.appointment.parse;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-public class Subject {
- Logger logger = Logger.getLogger(Subject.class);
-
- private String name;
- private String surname;
- private String ndNumber;
- private String screeningNumber;
- private String sex = "";
- private String remarks;
- private String birthDate;
- private String address;
- private String zipCode;
- private String country;
- private String city;
- private String phone1;
- private String phone2;
- private String phone3;
- private String mail;
- private String diagnosisYear;
- private String diagnosis;
- private String referal;
- private String addDate;
- private String mPowerId;
- private SubjectType type;
- private String toBeSeenAt;
- private boolean dead = false;
- private boolean resigned = false;
- private boolean postponed = false;
-
- private List<String> languages = new ArrayList<>();
-
- public Subject(String name, String surname, String ndNumber, String screeningNumber) {
- this.setName(name);
- this.setSurname(surname);
- this.setNdNumber(ndNumber);
- this.setScreeningNumber(screeningNumber);
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- if (name != null && name.length() > 50) {
- logger.warn("Name too long. Trimming: " + name);
- name = name.substring(0, 50);
- }
- this.name = name;
- }
-
- /**
- * @return the surname
- * @see #surname
- */
- public String getSurname() {
- return surname;
- }
-
- /**
- * @param surname
- * the surname to set
- * @see #surname
- */
- public void setSurname(String surname) {
- if (surname != null && surname.length() > 50) {
- logger.warn("Surname too long. Trimming: " + surname);
- surname = surname.substring(0, 50);
- }
- this.surname = surname;
- }
-
- /**
- * @return the ndNumber
- * @see #ndNumber
- */
- public String getNdNumber() {
- return ndNumber;
- }
-
- /**
- * @param ndNumber
- * the ndNumber to set
- * @see #ndNumber
- */
- public void setNdNumber(String ndNumber) {
- this.ndNumber = ndNumber;
- }
-
- /**
- * @return the screeningNumber
- * @see #screeningNumber
- */
- public String getScreeningNumber() {
- return screeningNumber;
- }
-
- /**
- * @param screeningNumber
- * the screeningNumber to set
- * @see #screeningNumber
- */
- public void setScreeningNumber(String screeningNumber) {
- this.screeningNumber = screeningNumber;
- }
-
- @Override
- public String toString() {
- return this.getName() + " " + this.getSurname() + " (" + this.getNdNumber() + "; " + this.getScreeningNumber() + ")";
- }
-
- public void addLanguage(String string) {
- if (!string.trim().isEmpty() && !string.equalsIgnoreCase("OTHER")) {
- if (!languages.contains(string)) {
- this.languages.add(string);
- }
- }
- }
-
- /**
- * @return the sex
- * @see #sex
- */
- public String getSex() {
- return sex;
- }
-
- /**
- * @param sex
- * the sex to set
- * @see #sex
- */
- public void setSex(String sex) {
- this.sex = sex;
- }
-
- /**
- * @return the birthDate
- * @see #birthDate
- */
- public String getBirthDate() {
- return birthDate;
- }
-
- /**
- * @param birthDate
- * the birthDate to set
- * @see #birthDate
- */
- public void setBirthDate(String birthDate) {
- this.birthDate = birthDate;
- }
-
- /**
- * @return the languages
- * @see #languages
- */
- public List<String> getLanguages() {
- return languages;
- }
-
- /**
- * @param languages
- * the languages to set
- * @see #languages
- */
- public void setLanguages(List<String> languages) {
- this.languages = languages;
- }
-
- /**
- * @return the remarks
- * @see #remarks
- */
- public String getRemarks() {
- return remarks;
- }
-
- /**
- * @param remarks
- * the remarks to set
- * @see #remarks
- */
- public void setRemarks(String remarks) {
- this.remarks = remarks;
- }
-
- /**
- * @return the address
- * @see #address
- */
- public String getAddress() {
- return address;
- }
-
- /**
- * @param address
- * the address to set
- * @see #address
- */
- public void setAddress(String address) {
- this.address = address;
- }
-
- /**
- * @return the zipCode
- * @see #zipCode
- */
- public String getZipCode() {
- return zipCode;
- }
-
- /**
- * @param zipCode
- * the zipCode to set
- * @see #zipCode
- */
- public void setZipCode(String zipCode) {
- if (zipCode != null && zipCode.length() > 7) {
- logger.warn("Surname too long. Ignoring: " + zipCode);
- this.zipCode = "";
- } else {
- this.zipCode = zipCode;
- }
- }
-
- /**
- * @return the country
- * @see #country
- */
- public String getCountry() {
- return country;
- }
-
- /**
- * @param country
- * the country to set
- * @see #country
- */
- public void setCountry(String country) {
- this.country = country;
- }
-
- /**
- * @return the city
- * @see #city
- */
- public String getCity() {
- return city;
- }
-
- /**
- * @param city
- * the city to set
- * @see #city
- */
- public void setCity(String city) {
- this.city = city;
- }
-
- /**
- * @return the phone1
- * @see #phone1
- */
- public String getPhone1() {
- return phone1;
- }
-
- /**
- * @param phone1
- * the phone1 to set
- * @see #phone1
- */
- public void setPhone1(String phone1) {
- if (phone1 != null && phone1.length() > 20) {
- logger.warn("Invalid phone. Ignoring: " + phone1);
- } else if (phone1 != null) {
- this.phone1 = phone1.replace(",", "").replace(" ", "");
- }
- }
-
- /**
- * @return the phone2
- * @see #phone2
- */
- public String getPhone2() {
- return phone2;
- }
-
- /**
- * @param phone2
- * the phone2 to set
- * @see #phone2
- */
- public void setPhone2(String phone2) {
- if (phone2 != null && phone2.length() > 20) {
- logger.warn("Invalid phone. Ignoring: " + phone2);
- } else if (phone2 != null) {
- this.phone2 = phone2.replace(",", "").replace(" ", "");
- }
- }
-
- /**
- * @return the phone3
- * @see #phone3
- */
- public String getPhone3() {
- return phone3;
- }
-
- /**
- * @param phone3
- * the phone3 to set
- * @see #phone3
- */
- public void setPhone3(String phone3) {
- if (phone3 != null && phone3.length() > 20) {
- logger.warn("Invalid phone. Ignoring: " + phone3);
- } else if (phone3 != null) {
- this.phone3 = phone3.replace(",", "").replace(" ", "");
- }
- }
-
- /**
- * @return the mail
- * @see #mail
- */
- public String getMail() {
- return mail;
- }
-
- /**
- * @param mail
- * the mail to set
- * @see #mail
- */
- public void setMail(String mail) {
- this.mail = mail;
- }
-
- /**
- * @return the diagnosisYear
- * @see #diagnosisYear
- */
- public String getDiagnosisYear() {
- return diagnosisYear;
- }
-
- /**
- * @param diagnosisYear
- * the diagnosisYear to set
- * @see #diagnosisYear
- */
- public void setDiagnosisYear(String diagnosisYear) {
- this.diagnosisYear = diagnosisYear;
- }
-
- /**
- * @return the diagnosis
- * @see #diagnosis
- */
- public String getDiagnosis() {
- return diagnosis;
- }
-
- /**
- * @param diagnosis
- * the diagnosis to set
- * @see #diagnosis
- */
- public void setDiagnosis(String diagnosis) {
- this.diagnosis = diagnosis;
- }
-
- /**
- * @return the referal
- * @see #referal
- */
- public String getReferal() {
- return referal;
- }
-
- /**
- * @param referal
- * the referal to set
- * @see #referal
- */
- public void setReferal(String referal) {
- this.referal = referal;
- }
-
- /**
- * @return the mPowerId
- * @see #mPowerId
- */
- public String getmPowerId() {
- return mPowerId;
- }
-
- /**
- * @param mPowerId
- * the mPowerId to set
- * @see #mPowerId
- */
- public void setmPowerId(String mPowerId) {
- this.mPowerId = mPowerId;
- }
-
- /**
- * @return the addDate
- * @see #addDate
- */
- public String getAddDate() {
- return addDate;
- }
-
- /**
- * @param addDate
- * the addDate to set
- * @see #addDate
- */
- public void setAddDate(String addDate) {
- this.addDate = addDate;
- }
-
- /**
- * @return the type
- * @see #type
- */
- public SubjectType getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(SubjectType type) {
- this.type = type;
- }
-
- public void update(Subject subject, String errorPrefix) {
- setName(getMergedValue("name", this.getName(), subject.getName(), errorPrefix));
- setSurname(getMergedValue("surname", this.getSurname(), subject.getSurname(), errorPrefix));
- setNdNumber(getMergedValue("ndNumber", this.getNdNumber(), subject.getNdNumber(), errorPrefix));
- setScreeningNumber(getMergedValue("screeningNumber", this.getScreeningNumber(), subject.getScreeningNumber(), errorPrefix));
- setSex(getMergedValue("sex", this.getSex(), subject.getSex(), errorPrefix));
- setRemarks(getMergedValue("remarks", this.getRemarks(), subject.getRemarks(), errorPrefix));
- setBirthDate(getMergedValue("birthDate", this.getBirthDate(), subject.getBirthDate(), errorPrefix));
- setAddress(getMergedValue("address", this.getAddress(), subject.getAddress(), errorPrefix));
- setZipCode(getMergedValue("zipCode", this.getZipCode(), subject.getZipCode(), errorPrefix));
- setCountry(getMergedValue("country", this.getCountry(), subject.getCountry(), errorPrefix));
- setCity(getMergedValue("city", this.getCity(), subject.getCity(), errorPrefix));
- setPhone1(getMergedValue("phone1", this.getPhone1(), subject.getPhone1(), errorPrefix));
- setPhone2(getMergedValue("phone2", this.getPhone2(), subject.getPhone2(), errorPrefix));
- setPhone3(getMergedValue("phone3", this.getPhone3(), subject.getPhone3(), errorPrefix));
- setMail(getMergedValue("mail", this.getMail(), subject.getMail(), errorPrefix));
- setDiagnosisYear(getMergedValue("diagnosisYear", this.getDiagnosisYear(), subject.getDiagnosisYear(), errorPrefix));
- setDiagnosis(getMergedValue("diagnosis", this.getDiagnosis(), subject.getDiagnosis(), errorPrefix));
- setReferal(getMergedValue("referal", this.getReferal(), subject.getReferal(), errorPrefix));
- setAddDate(getMergedValue("addDate", this.getAddDate(), subject.getAddDate(), errorPrefix, true));
- setmPowerId(getMergedValue("mPowerId", this.getmPowerId(), subject.getmPowerId(), errorPrefix));
- setType(getMergedValue("type", this.getType(), subject.getType(), errorPrefix));
- setResigned(this.isResigned() && subject.isResigned());
- setDead(this.isDead() || subject.isDead());
- setPostponed(this.isPostponed() && subject.isPostponed());
- // override only when to be seen by flying team
- if (subject.getToBeSeenAt() != null && subject.getToBeSeenAt().equals("F")) {
- setToBeSeenAt(subject.getToBeSeenAt());
- }
- addLanguages(subject.getLanguages());
- }
-
- private SubjectType getMergedValue(String string, SubjectType existingValue, SubjectType newValue, String errorPrefix) {
- if (existingValue == null) {
- return newValue;
- } else if (newValue == null) {
- return existingValue;
- } else if (existingValue.equals(newValue)) {
- return existingValue;
- } else {
- logger.warn(errorPrefix + "New " + string + " differs from old one. (new: " + newValue + ", " + existingValue + "). Skipping");
- return existingValue;
- }
- }
-
- private String getMergedValue(String string, String existingValue, String newValue, String errorPrefix) {
- return getMergedValue(string, existingValue, newValue, errorPrefix, false);
- }
-
- private String getMergedValue(String string, String existingValue, String newValue, String errorPrefix, boolean ignoreMessage) {
- if (existingValue == null || existingValue.trim().isEmpty()) {
- return newValue;
- } else if (newValue == null || newValue.trim().isEmpty()) {
- return existingValue;
- } else if (existingValue.trim().toLowerCase().contains(newValue.trim().toLowerCase())) {
- return existingValue;
- } else if (newValue.trim().toLowerCase().contains(existingValue.trim().toLowerCase())) {
- return newValue;
- } else {
- if (!ignoreMessage) {
- logger.warn(errorPrefix + "New " + string + " differs from old one. (new: " + newValue + ", " + existingValue + "). Skipping");
- }
- return existingValue;
- }
- }
-
- /**
- * @return the toBeSeenAt
- * @see #toBeSeenAt
- */
- public String getToBeSeenAt() {
- return toBeSeenAt;
- }
-
- /**
- * @param toBeSeenAt
- * the toBeSeenAt to set
- * @see #toBeSeenAt
- */
- public void setToBeSeenAt(String toBeSeenAt) {
- this.toBeSeenAt = toBeSeenAt;
- }
-
- /**
- * @return the dead
- * @see #dead
- */
- public boolean isDead() {
- return dead;
- }
-
- /**
- * @param dead
- * the dead to set
- * @see #dead
- */
- public void setDead(boolean dead) {
- this.dead = dead;
- }
-
- /**
- * @return the resigned
- * @see #resigned
- */
- public boolean isResigned() {
- return resigned;
- }
-
- /**
- * @param resigned
- * the resigned to set
- * @see #resigned
- */
- public void setResigned(boolean resigned) {
- this.resigned = resigned;
- }
-
- public void addLanguages(List<String> langs) {
- for (String string : langs) {
- addLanguage(string);
- }
- }
-
- /**
- * @return the postponed
- * @see #postponed
- */
- public boolean isPostponed() {
- return postponed;
- }
-
- /**
- * @param postponed
- * the postponed to set
- * @see #postponed
- */
- public void setPostponed(boolean postponed) {
- this.postponed = postponed;
- }
-
-}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/SubjectDao.java b/appointment-import/src/main/java/smash/appointment/parse/SubjectDao.java
deleted file mode 100644
index 7d78c4d363d6509150f560fd46445fbd59fa670e..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/java/smash/appointment/parse/SubjectDao.java
+++ /dev/null
@@ -1,113 +0,0 @@
-package smash.appointment.parse;
-
-import java.io.BufferedReader;
-import java.io.FileReader;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-public class SubjectDao {
- Logger logger = Logger.getLogger(SubjectDao.class);
- private List<Subject> subjects = new ArrayList<>();
-
- public void addSubject(Subject subject, String errorPrefix) {
- if (subject.getNdNumber() != null && !Utils.simplifyString(subject.getNdNumber()).isEmpty()) {
- Subject existing = getByNdNumber(subject.getNdNumber());
- if (existing != null) {
- if (!existing.getScreeningNumber().equals(subject.getScreeningNumber())) {
- logger.error(errorPrefix + " Nd number taken by subject: " + existing.getScreeningNumber());
- return;
- }
- }
- }
- Subject existing = getByScreeningNumber(subject.getScreeningNumber());
- if (existing != null) {
- existing.update(subject, errorPrefix);
- } else {
- subjects.add(subject);
- }
- }
-
- Subject getByScreeningNumber(String screeningNumber) {
- for (Subject s : subjects) {
- for (String number: s.getScreeningNumber().split(";")) {
- if (screeningNumber.equals(number.trim())) {
- return s;
- }
- }
- }
- return null;
- }
-
- public void readFile(String filename) throws IOException {
- try (BufferedReader br = new BufferedReader(new FileReader(filename))) {
- String line;
- int lineCount = 1;
- while ((line = br.readLine()) != null) {
- String tmp[] = line.split("\t");
- addSubject(new Subject(tmp[0], tmp[1], tmp[2], tmp[3]), "[" + filename + ":" + lineCount + "]");
- lineCount++;
- }
- }
- }
-
- /**
- * @return the subjects
- * @see #subjects
- */
- public List<Subject> getSubjects() {
- return subjects;
- }
-
- /**
- * @param subjects
- * the subjects to set
- * @see #subjects
- */
- public void setSubjects(List<Subject> subjects) {
- this.subjects = subjects;
- }
-
- public Subject getByNdNumber(String ndNumber) {
- ndNumber = Utils.simplifyString(ndNumber);
- for (Subject s : subjects) {
- if (ndNumber.equalsIgnoreCase(s.getNdNumber())) {
- return s;
- }
- }
- return null;
- }
-
- public void addSubjects(List<Subject> processPrcSubjects, String errorPrefix) {
- for (Subject subject : processPrcSubjects) {
- addSubject(subject, errorPrefix);
- }
- }
-
- public void removeDuplicate(Subject subject1, Subject subject2, String errorPrefix) {
- String screeningNumber1 = subject1.getScreeningNumber().trim();
- String screeningNumber2 = subject2.getScreeningNumber().trim();
- String screeningNumber = null;
- if (screeningNumber1.toLowerCase().contains(screeningNumber2.toLowerCase())) {
- screeningNumber = screeningNumber1;
- } else if (screeningNumber2.toLowerCase().contains(screeningNumber1.toLowerCase())) {
- screeningNumber = screeningNumber2;
- } else {
- screeningNumber = screeningNumber1 + "; " + screeningNumber2;
- }
- subject1.setScreeningNumber(screeningNumber);
- subject2.setScreeningNumber(screeningNumber);
- if (!subject1.getNdNumber().trim().isEmpty() && !subject2.getNdNumber().trim().isEmpty()
- && !subject1.getNdNumber().trim().equals(subject2.getNdNumber().trim())) {
- throw new InvalidArgumentException("Two different nd numbers: " + subject1.getNdNumber() + ", " + subject2.getNdNumber());
- }
-
- String remarks = (subject1.getRemarks()+"\n"+subject2.getRemarks()).trim();
- subject1.setRemarks(remarks);
- subject1.update(subject2, errorPrefix);
- subjects.remove(subject2);
- }
-
-}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/SubjectIndexer.java b/appointment-import/src/main/java/smash/appointment/parse/SubjectIndexer.java
deleted file mode 100644
index b120fdc9ccb1cf77902c71b1427d8fdde344801d..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/java/smash/appointment/parse/SubjectIndexer.java
+++ /dev/null
@@ -1,25 +0,0 @@
-package smash.appointment.parse;
-
-import org.apache.log4j.Logger;
-
-public abstract class SubjectIndexer {
- Logger logger = Logger.getLogger(SubjectIndexer.class);
-
- public abstract String getIndexedString(Subject subject);
-
- public boolean match(Subject subject, String simplifiedQuery) {
- String indexedString = getIndexedString(subject);
- if (indexedString.length() == 0) {
- return false;
- }
- // logger.debug("Check: " + simplifiedQuery + " against: " + indexedString);
- if (simplifiedQuery.startsWith(indexedString)) {
- return true;
- }
- return false;
- }
-
- public boolean isBetter(Subject subject, Subject oldSubject) {
- return getIndexedString(subject).length() > getIndexedString(oldSubject).length();
- }
-}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/SubjectParser.java b/appointment-import/src/main/java/smash/appointment/parse/SubjectParser.java
deleted file mode 100644
index 557f48063f285a57e2196c23d1b29f1a0786fdc9..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/java/smash/appointment/parse/SubjectParser.java
+++ /dev/null
@@ -1,250 +0,0 @@
-package smash.appointment.parse;
-
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.text.ParseException;
-import java.text.SimpleDateFormat;
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.Date;
-import java.util.Iterator;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.apache.poi.EncryptedDocumentException;
-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;
-import org.apache.poi.ss.usermodel.WorkbookFactory;
-
-public abstract class SubjectParser {
- private static final SimpleDateFormat DATE_FORMATTER = new SimpleDateFormat("yyyy-MM-dd");
- Logger logger = Logger.getLogger(SubjectParser.class);
- DataFormatter df = new DataFormatter();
-
- public List<Subject> processExcel(String filename) throws EncryptedDocumentException, InvalidFormatException, IOException, ParseException {
- List<Subject> result = new ArrayList<>();
- InputStream inp = new FileInputStream(filename);
- Workbook workbook = WorkbookFactory.create(inp);
- Iterator<Sheet> sheetIter = workbook.sheetIterator();
- while (sheetIter.hasNext()) {
- Sheet sheet = sheetIter.next();
- String name = sheet.getSheetName().trim();
- if (name.trim().toLowerCase().equals(getSheetName().toLowerCase())) {
- result.addAll(processSheet(sheet));
- } else {
- logger.debug(filename + "Skipping sheet: " + name);
- }
- }
- return result;
- }
-
- private List<Subject> processSheet(Sheet sheet) {
- List<Subject> result = new ArrayList<>();
- int rowCount = sheet.getPhysicalNumberOfRows();
- for (int rowId = getInitRow(); rowId < rowCount; rowId++) {
- Row subjectRow = sheet.getRow(rowId);
- Subject subject = parseSubject(subjectRow);
- if (subject != null) {
- result.add(subject);
- }
- }
- return result;
- }
-
- private Subject parseSubject(Row row) {
- String screeningNumber = parseScreeningNumber(row);
- if (screeningNumber == null || screeningNumber.isEmpty()) {
- String name = getString(row.getCell(0)) + " " + getString(row.getCell(1));
- if (!name.trim().isEmpty()) {
- logger.debug("Skipping row: (" + name + ")");
- }
- return null;
- }
- String name = parseName(row);
- String surname = parseSurname(row);
- String ndNumber = parseNdNumber(row);
- Subject result = new Subject(name, surname, ndNumber, screeningNumber);
-
- result.setRemarks(parseRemarks(row));
- result.setAddress(parseAddress(row));
- result.setZipCode(parseZipCode(row));
- result.setCity(parseCity(row));
- result.setCountry(parseCountry(row));
- result.setPhone1(parsePhone1(row));
- result.setPhone2(parsePhone2(row));
- result.setPhone3(parsePhone3(row));
- result.setMail(parseMail(row));
- result.setDiagnosisYear(parseDiagnosisYear(row));
- result.setDiagnosis(parseDiagnosis(row));
- result.setReferal(parseReferal(row));
- result.setAddDate(parseAddDate(row));
- result.setmPowerId(parsemPowerId(row));
- result.setBirthDate(parseBirthDate(row));
- result.setType(parseType(row));
- result.addLanguages(parseLanguages(row));
- result.setToBeSeenAt(parseToBeSeenAt(row));
- result.setDead(parseDead(row));
- result.setResigned(parseResigned(row));
- result.setPostponed(parsePostponed(row));
-
- return result;
- }
-
- protected abstract boolean parseDead(Row row);
-
- protected abstract boolean parsePostponed(Row row);
-
- protected abstract boolean parseResigned(Row row);
-
- protected abstract String parseToBeSeenAt(Row row);
-
- protected abstract List<String> parseLanguages(Row row);
-
- protected abstract SubjectType parseType(Row row);
-
- protected abstract String parseBirthDate(Row row);
-
- protected abstract String parsemPowerId(Row row);
-
- protected abstract String parseAddDate(Row row);
-
- protected abstract String parseReferal(Row row);
-
- protected abstract String parseDiagnosisYear(Row row);
-
- protected abstract String parseDiagnosis(Row row);
-
- protected abstract String parseMail(Row row);
-
- protected abstract String parsePhone3(Row row);
-
- protected abstract String parsePhone2(Row row);
-
- protected abstract String parsePhone1(Row row);
-
- protected abstract String parseCity(Row row);
-
- protected abstract String parseCountry(Row row);
-
- protected abstract String parseZipCode(Row row);
-
- protected abstract String parseAddress(Row row);
-
- protected abstract String parseRemarks(Row row);
-
- protected abstract String parseScreeningNumber(Row row);
-
- protected abstract String parseName(Row row);
-
- protected abstract String parseSurname(Row row);
-
- protected abstract String parseNdNumber(Row row);
-
- protected abstract String getSheetName();
-
- protected abstract int getInitRow();
-
- protected String getString(Cell cell) {
- if (cell == null) {
- return "";
- }
- if (cell.getCellTypeEnum().equals(CellType.STRING)) {
- return cell.getStringCellValue().trim();
- }
- 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, Calendar defaultDate) {
- String defaultDateString = "";
- if (defaultDate != null) {
- defaultDateString = DATE_FORMATTER.format(defaultDate.getTime());
- }
- if (cell == null) {
- return defaultDateString;
- }
- String result = null;
- if (cell.getCellTypeEnum().equals(CellType.STRING)) {
- result = getString(cell);
- } else if (HSSFDateUtil.isCellDateFormatted(cell)) {
- Date date = cell.getDateCellValue();
- if (date != null) {
- result = DATE_FORMATTER.format(date);
- } else {
- result = defaultDateString;
- }
- } else {
- result = getString(cell);
- }
- if (result == null || result.trim().isEmpty()) {
- result = defaultDateString;
- }
- result = fixDate(result, defaultDateString);
- return result;
- }
-
- protected String fixDate(String result) {
- return fixDate(result, null);
- }
-
- protected String fixDate(String result, String defaultDateString) {
- result = result.replaceAll("\\?", "");
- result = result.replaceAll("jan", "01");
- result = result.replaceAll("fev", "02");
- result = result.replaceAll("mar", "03");
- result = result.replaceAll("avr", "04");
- result = result.replaceAll("may", "05");
- result = result.replaceAll("aou", "08");
- result = result.replaceAll("cot", "08");
- result = result.replaceAll("sep", "09");
- result = result.replaceAll("oct", "10");
- if (result.trim().isEmpty()) {
- result = defaultDateString;
- } else if (result.length() != 10) {
- logger.warn("Invalid date. Ignoring: " + result);
- result = defaultDateString;
- }
- if (result.indexOf("/") >= 0) {
- String tmp[] = result.split("/");
- result = tmp[2] + "-" + tmp[1] + "-" + tmp[0];
- }
- if (result.length() == 10 && result.charAt(2) == '-') {
- String tmp[] = result.split("-");
- result = tmp[2] + "-" + tmp[1] + "-" + tmp[0];
- }
- return result;
- }
-
- protected String parseDateOfBirth(Cell cell) {
- String date = getString(cell).replaceAll(" ", "");
- if (date.length() < 8) {
- return "";
- }
- String year = date.substring(0, 4);
- String month = date.substring(4, 6);
- String day = date.substring(6, 8);
- String result = year + "-" + month + "-" + day;
- return result;
- }
-
-}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/SubjectSqlExporter.java b/appointment-import/src/main/java/smash/appointment/parse/SubjectSqlExporter.java
deleted file mode 100644
index 5c59412dfbd387afab381b8e4d824dc47a7baa4d..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/java/smash/appointment/parse/SubjectSqlExporter.java
+++ /dev/null
@@ -1,95 +0,0 @@
-package smash.appointment.parse;
-
-public class SubjectSqlExporter extends SqlExporter {
-
- public String toSql(Subject subject) {
- StringBuilder result = new StringBuilder("");
-
- result.append("insert into web_subject (");
- result.append("sex, ");
- result.append("last_name, ");
- result.append("first_name, ");
- result.append("comments,");
- result.append("address,");
- result.append("postal_code, ");
- result.append("city, ");
- result.append("country, ");
- result.append("phone_number,");
- result.append("phone_number_2,");
- result.append("phone_number_3,");
- result.append("email,");
- result.append("year_of_diagnosis,");
- result.append("diagnosis,");
- result.append("referral,");
- result.append("date_added,");
- result.append("nd_number,");
- result.append("mpower_id,");
- result.append("screening_number,");
- result.append("default_location_id,");
- result.append("type,");
- result.append("dead,");
- result.append("default_written_communication_language_id,");
- result.append("resigned,");
- result.append("postponed,");
- result.append("date_born) ");
-
- result.append("values (");
- result.append(getStringVal(subject.getSex()) + ",");
- result.append(getStringVal(subject.getSurname()) + ",");
- result.append(getStringVal(subject.getName()) + ",");
- result.append(getStringVal(subject.getRemarks()) + ",");
- result.append(getStringVal(subject.getAddress()) + ",");
- result.append(getStringVal(subject.getZipCode()) + ",");
- result.append(getStringVal(subject.getCity()) + ",");
- result.append(getStringVal(subject.getCountry()) + ",");
- result.append(getStringVal(subject.getPhone1()) + ",");
- result.append(getStringVal(subject.getPhone2()) + ",");
- result.append(getStringVal(subject.getPhone3()) + ",");
- result.append(getStringVal(subject.getMail()) + ",");
- result.append(getIntVal(subject.getDiagnosisYear()) + ",");
- result.append(getStringVal(subject.getDiagnosis()) + ",");
- result.append(getStringVal(subject.getReferal()) + ",");
- result.append(getDateVal(subject.getAddDate()) + ",");
- result.append(getStringVal(subject.getNdNumber()) + ",");
- result.append(getStringVal(subject.getmPowerId()) + ",");
- result.append(getStringVal(subject.getScreeningNumber()) + ",");
- switch (subject.getToBeSeenAt()) {
- case ("L"):
- result.append("(select id from web_location where name = 'LIH'),");
- break;
- case ("F"):
- result.append("(select id from web_location where name = 'Flying Team'),");
- break;
- case ("P"):
- result.append("(select id from web_location where name = 'PRC'),");
- break;
- default:
- throw new RuntimeException("Unknown location: " + subject.getToBeSeenAt());
- }
-
- result.append(getStringVal(subject.getType().toString().substring(0, 1)) + ",");
- result.append(subject.isDead() + ",");
- if (subject.getLanguages().size()>0) {
- result.append("(select id from web_language where name=" + getStringVal(subject.getLanguages().get(0)) + "),");
- } else {
- result.append("null,");
- }
- result.append(subject.isResigned() + ",");
- result.append(subject.isPostponed() + ",");
- result.append(getDateVal(subject.getBirthDate()));
- result.append(");\n");
-
- for (String langueage : subject.getLanguages()) {
- result.append("insert into web_subject_languages (");
- result.append("subject_id, ");
- result.append("language_id) ");
- result.append("values (");
- result.append("(select max(id) from web_subject), ");
- result.append("(select id from web_language where name=" + getStringVal(langueage) + ") ");
- result.append(");\n");
- }
-
- return result.toString();
- }
-
-}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/SubjectType.java b/appointment-import/src/main/java/smash/appointment/parse/SubjectType.java
deleted file mode 100644
index a1ef995b0ccebeb8a0500126b8df6cad8f95177d..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/java/smash/appointment/parse/SubjectType.java
+++ /dev/null
@@ -1,5 +0,0 @@
-package smash.appointment.parse;
-
-public enum SubjectType {
- PATIENT, CONTROL;
-}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/SurnameIndexer.java b/appointment-import/src/main/java/smash/appointment/parse/SurnameIndexer.java
deleted file mode 100644
index 10c1a29f3e39236ed33c0c819e6a30d4420de99c..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/java/smash/appointment/parse/SurnameIndexer.java
+++ /dev/null
@@ -1,9 +0,0 @@
-package smash.appointment.parse;
-
-public class SurnameIndexer extends SubjectIndexer {
-
- public String getIndexedString(Subject subject) {
- return Utils.simplifyString(subject.getSurname());
- }
-
-}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/SurnameNameIndexer.java b/appointment-import/src/main/java/smash/appointment/parse/SurnameNameIndexer.java
deleted file mode 100644
index 7de6d7c4ef96e23ee9b75a72fa5d32eb1f6b5ad1..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/java/smash/appointment/parse/SurnameNameIndexer.java
+++ /dev/null
@@ -1,9 +0,0 @@
-package smash.appointment.parse;
-
-public class SurnameNameIndexer extends SubjectIndexer {
-
- public String getIndexedString(Subject subject) {
- return Utils.simplifyString(subject.getSurname() + subject.getName());
- }
-
-}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/Utils.java b/appointment-import/src/main/java/smash/appointment/parse/Utils.java
deleted file mode 100644
index 916487ba6948c86609d8a4e273f5b4bed574121b..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/java/smash/appointment/parse/Utils.java
+++ /dev/null
@@ -1,7 +0,0 @@
-package smash.appointment.parse;
-
-public class Utils {
- public static String simplifyString(String query) {
- return query.replaceAll("[\\s\\-©]", "").toLowerCase().replaceAll("\\(c\\)", "");
- }
-}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/Visit.java b/appointment-import/src/main/java/smash/appointment/parse/Visit.java
deleted file mode 100644
index 98b2a896b1b67821ce78a64ec5901a4f2344aeee..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/java/smash/appointment/parse/Visit.java
+++ /dev/null
@@ -1,134 +0,0 @@
-package smash.appointment.parse;
-
-import java.text.ParseException;
-import java.text.SimpleDateFormat;
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-public class Visit {
- static Subject UNKNOWN;
- static {
- UNKNOWN = new Subject("NOBODY", "", "", "---");
- UNKNOWN.setType(SubjectType.CONTROL);
- UNKNOWN.setAddDate("1900-01-01");
- UNKNOWN.setAddress("");
- UNKNOWN.setZipCode("");
- UNKNOWN.setCity("");
- UNKNOWN.setCountry("");
- UNKNOWN.setmPowerId("");
- UNKNOWN.setReferal("");
- UNKNOWN.setRemarks("");
- UNKNOWN.setDiagnosis("");
- UNKNOWN.setToBeSeenAt("P");
- }
- Logger logger = Logger.getLogger(Visit.class);
-
- private Subject subject;
- private List<AppointmentEntry> appointments = new ArrayList<>();
-
- private String startDate;
- private boolean finished = false;
-
- public Visit(Subject subject) {
- if (subject == null) {
- subject = UNKNOWN;
- }
- this.subject = subject;
- }
-
- public void addAppointment(AppointmentEntry entry) {
- appointments.add(entry);
- }
-
- /**
- * @return the appointments
- * @see #appointments
- */
- public List<AppointmentEntry> getAppointments() {
- return appointments;
- }
-
- /**
- * @param appointments
- * the appointments to set
- * @see #appointments
- */
- public void setAppointments(List<AppointmentEntry> appointments) {
- this.appointments = appointments;
- }
-
- public String getLastAppointmentDate() {
- if (appointments.size() == 0) {
- return "1900-01-01";
- }
- return getLastAppointment().getDay().substring(0, 10);
- }
-
- public AppointmentEntry getLastAppointment() {
- if (appointments.size() > 0) {
- return appointments.get(appointments.size() - 1);
- } else {
- return null;
- }
- }
-
- public String getStartDate() {
- if (appointments.size() > 0) {
- return appointments.get(0).getDay().substring(0, 10);
- } else if (startDate == null) {
- return "1900-01-01";
- } else {
- return startDate;
- }
- }
-
- private static final SimpleDateFormat DATE_FORMATTER = new SimpleDateFormat("yyyy-MM-dd");
-
- public String getEndDate() throws ParseException {
- Calendar calendar = Calendar.getInstance();
- calendar.setTime(DATE_FORMATTER.parse(getStartDate()));
- calendar.add(Calendar.MONTH, 3);
- return DATE_FORMATTER.format(calendar.getTime());
- }
-
- /**
- * @return the subject
- * @see #subject
- */
- public Subject getSubject() {
- return subject;
- }
-
- /**
- * @param subject
- * the subject to set
- * @see #subject
- */
- public void setSubject(Subject subject) {
- this.subject = subject;
- }
-
- public void setStartDate(String newDate) {
- this.startDate = newDate;
- }
-
- /**
- * @return the finished
- * @see #finished
- */
- public boolean isFinished() {
- return finished;
- }
-
- /**
- * @param finished the finished to set
- * @see #finished
- */
- public void setFinished(boolean finished) {
- this.finished = finished;
- }
-
-}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/VisitSqlExporter.java b/appointment-import/src/main/java/smash/appointment/parse/VisitSqlExporter.java
deleted file mode 100644
index ad544f75172a77252da124a601d60cccff4d87d5..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/java/smash/appointment/parse/VisitSqlExporter.java
+++ /dev/null
@@ -1,31 +0,0 @@
-package smash.appointment.parse;
-
-import java.text.ParseException;
-import java.util.Calendar;
-
-public class VisitSqlExporter extends SqlExporter {
- AppointmentSqlExporter appointmentSqlExporter = new AppointmentSqlExporter();
- public String toSql(Visit visit) throws ParseException {
- StringBuilder result = new StringBuilder("");
-
- result.append("insert into web_visit (");
- result.append("subject_id, ");
- result.append("datetime_begin, ");
- result.append("datetime_end, ");
- result.append("post_mail_sent, ");
- result.append("is_finished)");
-
- result.append("values (");
- result.append("(SELECT id from web_subject where screening_number like "+getStringVal('%'+visit.getSubject().getScreeningNumber()+'%') + "),");
- result.append(getStringVal(visit.getStartDate()) + ",");
- result.append(getStringVal(visit.getEndDate()) + ",");
- result.append("false,");
- result.append(visit.isFinished());
- result.append(");\n");
- for (AppointmentEntry entry: visit.getAppointments()) {
- result.append(appointmentSqlExporter.toSql(entry)+"\n");
- }
-
- return result.toString();
- }
-}
diff --git a/appointment-import/src/main/java/smash/appointment/parse/XlsxCalendarProcessor.java b/appointment-import/src/main/java/smash/appointment/parse/XlsxCalendarProcessor.java
deleted file mode 100644
index 57040b275b38bed01495b615d2a2e94b66b5c6fc..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/java/smash/appointment/parse/XlsxCalendarProcessor.java
+++ /dev/null
@@ -1,181 +0,0 @@
-package smash.appointment.parse;
-
-import java.io.FileInputStream;
-import java.io.InputStream;
-import java.text.ParseException;
-import java.text.SimpleDateFormat;
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.Date;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Locale;
-import java.util.Set;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import org.apache.log4j.Logger;
-import org.apache.poi.ss.usermodel.Cell;
-import org.apache.poi.ss.usermodel.CellType;
-import org.apache.poi.ss.usermodel.FormulaEvaluator;
-import org.apache.poi.ss.usermodel.Row;
-import org.apache.poi.ss.usermodel.Sheet;
-import org.apache.poi.ss.usermodel.Workbook;
-import org.apache.poi.ss.usermodel.WorkbookFactory;
-
-public class XlsxCalendarProcessor {
- Logger logger = Logger.getLogger(XlsxCalendarProcessor.class);
-
- private SubjectDao subjectDao;
-
- public List<AppointmentEntry> processExcel(String filename, Calendar minDate) throws Exception {
- List<AppointmentEntry> result = new ArrayList<AppointmentEntry>();
- InputStream inp = new FileInputStream(filename);
- Workbook workbook = WorkbookFactory.create(inp);
- Iterator<Sheet> sheetIter = workbook.sheetIterator();
- while (sheetIter.hasNext()) {
- Sheet sheet = sheetIter.next();
- String name = sheet.getSheetName().trim();
- if (name.contains("2017")) {
- String monthName = name.split(" ")[0];
- String monthNumber = parseMonth(monthName);
- result.addAll(processSheet(sheet, "2017-" + monthNumber));
- } else {
- logger.debug("Skipping sheet: " + name);
- }
- }
- if (minDate != null) {
- Set<AppointmentEntry> toBeRemoved = new HashSet<>();
-
- for (AppointmentEntry entry : result) {
- if (isBefore(entry, minDate)) {
- toBeRemoved.add(entry);
- }
- }
- result.removeAll(toBeRemoved);
- }
-
- return result;
- }
-
- private static final SimpleDateFormat DATE_FORMATTER = new SimpleDateFormat("yyyy-MM-dd");
-
- private boolean isBefore(AppointmentEntry entry, Calendar minDate) {
- String entryDate = entry.getDay();
- String beforeDate = DATE_FORMATTER.format(minDate.getTime());
- if (entryDate.compareTo(beforeDate) < 0) {
- return true;
- } else {
- return false;
- }
- }
-
- int[] dayColumns = new int[] { 3, 4, 5, 6, 7 };
-
- int[] weekStartRows = new int[] { 5, 23, 41, 59, 77, 95 };
-
- int hourColum = 0;
- int dayOfMonthRowOffset = 0;
- int calendarRowStartOffset = 3;
- int calendarRowEndOffset = 18;
-
- private List<AppointmentEntry> processSheet(Sheet sheet, String string) {
- FormulaEvaluator evaluator = sheet.getWorkbook().getCreationHelper().createFormulaEvaluator();
-
- List<AppointmentEntry> result = new ArrayList<AppointmentEntry>();
-
- CellParser parser = new CellParser();
- parser.setSubjectDao(subjectDao);
-
- for (int weekOffset : weekStartRows) {
- Row weekRow = sheet.getRow(weekOffset + dayOfMonthRowOffset);
- for (int dayColumnOffset : dayColumns) {
- Cell dayCell = weekRow.getCell(dayColumnOffset);
- String dayOfMonth = "0";
- evaluator.evaluateInCell(dayCell);
- if (dayCell.getCellTypeEnum().equals(CellType.NUMERIC)) {
- dayOfMonth = ((int) dayCell.getNumericCellValue()) + "";
- } else {
- dayOfMonth = dayCell.getStringCellValue();
- }
- if (dayOfMonth.length() == 1) {
- dayOfMonth = "0" + dayOfMonth;
- }
- if (!dayOfMonth.equals("00") && !dayOfMonth.trim().isEmpty()) {
- String day = string + "-" + dayOfMonth;
-
- String hour = "08:00";
- for (int hourOffset = calendarRowStartOffset; hourOffset < calendarRowEndOffset; hourOffset++) {
- Row hourRow = sheet.getRow(weekOffset + hourOffset);
-
- Cell hourCell = hourRow.getCell(hourColum);
- if (hourCell.getCellTypeEnum().equals(CellType.NUMERIC)) {
-
- SimpleDateFormat formatTime = new SimpleDateFormat("HH:mm");
- String hourString = formatTime.format(hourCell.getDateCellValue());
-
- if (isHour(hourString)) {
- hour = hourString;
- }
- }
-
- Cell queryCell = hourRow.getCell(dayColumnOffset);
- if (queryCell != null) {
- if (queryCell.getCellTypeEnum().equals(CellType.STRING)) {
- String query = queryCell.getStringCellValue();
-
- if (query != null && !query.isEmpty()) {
- AppointmentEntry entry = parser.parseAppointment(query, hour);
- entry.setDay(day);
-
- result.add(entry);
- }
- } else if (!queryCell.getCellTypeEnum().equals(CellType.BLANK)) {
- logger
- .warn("Skipping cell: " + queryCell.getAddress() + ", " + queryCell.getSheet().getSheetName() + ", type: " + queryCell.getCellTypeEnum());
- }
- }
- }
- }
- }
-
- }
- return result;
- }
-
- Pattern timePattern = Pattern.compile("^[0-9][0-9]\\:[0-9][0-9]");
-
- private boolean isHour(String hourString) {
- Matcher matcher = timePattern.matcher(hourString);
- return matcher.find();
- }
-
- private String parseMonth(String monthName) throws ParseException {
- Date date = new SimpleDateFormat("MMMM", Locale.ENGLISH).parse(monthName);
- Calendar cal = Calendar.getInstance();
- cal.setTime(date);
- String result = (cal.get(Calendar.MONTH) + 1) + "";
- if (result.length() == 1) {
- result = "0" + result;
- }
- 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;
- }
-}
diff --git a/appointment-import/src/main/resources/log4j.properties b/appointment-import/src/main/resources/log4j.properties
deleted file mode 100644
index 7ad74adebca3440ce16615072190de60dbdf4fc9..0000000000000000000000000000000000000000
--- a/appointment-import/src/main/resources/log4j.properties
+++ /dev/null
@@ -1,15 +0,0 @@
-log4j.rootLogger=CONSOLE, R
-
-#Set the behavior of the CONSOLE appender
-log4j.appender.CONSOLE=org.apache.log4j.ConsoleAppender
-log4j.appender.CONSOLE.Threshold=FATAL
-log4j.appender.CONSOLE.layout=org.apache.log4j.PatternLayout
-log4j.appender.CONSOLE.layout.ConversionPattern=%d %5p [%t] (%F:%L) - %m%n
-#log4j.appender.CONSOLE.layout.ConversionPattern=%m%n
-
-#Set the behavior of the FILE appender
-log4j.appender.R=org.apache.log4j.FileAppender
-log4j.appender.R.File=log.txt
-log4j.appender.R.layout=org.apache.log4j.PatternLayout
-log4j.appender.R.layout.ConversionPattern=%d %5p [%t] (%F:%L) - %m%n
-log4j.appender.R.Threshold=DEBUG
diff --git a/appointment-import/src/test/java/smash/appointment/parse/AllTests.java b/appointment-import/src/test/java/smash/appointment/parse/AllTests.java
deleted file mode 100644
index e9008b24281f818d57cc80746159043bb57a33cc..0000000000000000000000000000000000000000
--- a/appointment-import/src/test/java/smash/appointment/parse/AllTests.java
+++ /dev/null
@@ -1,27 +0,0 @@
-package smash.appointment.parse;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AppointmentDaoTest.class, //
- CellParserTest.class, //
- DuplicateRemoveParserTest.class, //
- LihControlMappingParserTest.class, //
- LihControlParserTest.class, //
- PrcControlParserTest.class, //
- PrcFlyingParserTest.class, //
- PrcSubjectsParserTest.class, //
- RedcapCalendarParserTest.class, //
- RedcapParserTest.class, //
-
- SubjectDaoTest.class, //
- SubjectParserTest.class, //
- VisitTest.class, //
- XlsxCalendarProcessorTest.class, //
-})
-
-public class AllTests {
-
-}
diff --git a/appointment-import/src/test/java/smash/appointment/parse/AppointmentDaoTest.java b/appointment-import/src/test/java/smash/appointment/parse/AppointmentDaoTest.java
deleted file mode 100644
index c0339f690a2c346a0aaf65a7865f8824996bd79b..0000000000000000000000000000000000000000
--- a/appointment-import/src/test/java/smash/appointment/parse/AppointmentDaoTest.java
+++ /dev/null
@@ -1,120 +0,0 @@
-package smash.appointment.parse;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.text.ParseException;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class AppointmentDaoTest {
- Logger logger = Logger.getLogger(AppointmentDaoTest.class);
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void getVisits() throws ParseException {
- Subject subject1 = new Subject("a", "b", "c", "d");
- AppointmentEntry appointment = new AppointmentEntry();
- appointment.setSubject(subject1);
- appointment.setDay("2026-02-02");
- appointment.addType(AppointmentType.LEVEL_AQUEST);
-
- AppointmentEntry appointment2 = new AppointmentEntry();
- appointment2.setSubject(subject1);
- appointment2.setDay("2026-02-02");
- appointment2.addType(AppointmentType.LEVEL_B);
-
- AppointmentEntry appointment3 = new AppointmentEntry();
- appointment3.setSubject(subject1);
- appointment3.setDay("2021-02-02");
- appointment3.addType(AppointmentType.LEVEL_AQUEST);
-
- AppointmentDao appointmentDao = new AppointmentDao();
- appointmentDao.addAppointment(appointment);
- appointmentDao.addAppointment(appointment2);
- appointmentDao.addAppointment(appointment3);
- assertEquals(2, appointmentDao.getVisits().size());
- }
-
- @Test
- public void getVisits2() throws ParseException {
- Subject subject1 = new Subject("a", "b", "c", "d");
- Subject subject2 = new Subject("a1", "b1", "c1", "d1");
- AppointmentEntry appointment = new AppointmentEntry();
- appointment.setSubject(subject1);
- appointment.setDay("2026-02-02");
- appointment.addType(AppointmentType.LEVEL_AQUEST);
-
- AppointmentEntry appointment3 = new AppointmentEntry();
- appointment3.setSubject(subject2);
- appointment3.setDay("2026-02-02");
- appointment3.addType(AppointmentType.LEVEL_B);
-
- AppointmentDao appointmentDao = new AppointmentDao();
- appointmentDao.addAppointment(appointment);
- appointmentDao.addAppointment(appointment3);
- assertEquals(2, appointmentDao.getVisits().size());
- }
-
- @Test
- public void getShouldBeFinished() {
- AppointmentDao appointmentDao = new AppointmentDao();
- assertTrue(appointmentDao.shouldBeFinished("2014-01-01"));
- assertTrue(appointmentDao.shouldBeFinished("2017-01-01"));
- assertFalse(appointmentDao.shouldBeFinished("2018-01-01"));
- }
-
- @Test
- public void createNextVisitForControl() throws ParseException {
- Subject subject = new Subject("a", "b", "c", "d");
- subject.setType(SubjectType.CONTROL);
- AppointmentEntry appointment3 = new AppointmentEntry();
- appointment3.setSubject(subject);
- appointment3.setDay("2016-02-02");
- appointment3.addType(AppointmentType.LEVEL_B);
-
- Visit visit = new Visit(subject);
- visit.addAppointment(appointment3);
-
- AppointmentDao appointmentDao = new AppointmentDao();
- Visit nextVisit = appointmentDao.createNextVisit(visit);
- assertNotNull(nextVisit);
- assertTrue(nextVisit.getStartDate().startsWith("2020"));
- }
-
- @Test
- public void createNextVisitForPatient() throws ParseException {
- Subject subject = new Subject("a", "b", "c", "d");
- subject.setType(SubjectType.PATIENT);
- AppointmentEntry appointment3 = new AppointmentEntry();
- appointment3.setSubject(subject);
- appointment3.setDay("2016-02-02");
- appointment3.addType(AppointmentType.LEVEL_B);
-
- Visit visit = new Visit(subject);
- visit.addAppointment(appointment3);
-
- AppointmentDao appointmentDao = new AppointmentDao();
- Visit nextVisit = appointmentDao.createNextVisit(visit);
- assertNotNull(nextVisit);
- assertTrue(nextVisit.getStartDate().startsWith("2017"));
- }
-
-}
diff --git a/appointment-import/src/test/java/smash/appointment/parse/CellParseTestCase.java b/appointment-import/src/test/java/smash/appointment/parse/CellParseTestCase.java
deleted file mode 100644
index a43dcbc578952867a0cd36fcbd74d1284fbc3466..0000000000000000000000000000000000000000
--- a/appointment-import/src/test/java/smash/appointment/parse/CellParseTestCase.java
+++ /dev/null
@@ -1,15 +0,0 @@
-package smash.appointment.parse;
-
-class CellParseTestCase {
- String query;
- Subject subject;
- String time;
- AppointmentType[] types;
-
- public CellParseTestCase(String query, Subject subject, String time, AppointmentType[] types) {
- this.query = query;
- this.subject = subject;
- this.time = time;
- this.types = types;
- }
-};
diff --git a/appointment-import/src/test/java/smash/appointment/parse/CellParserTest.java b/appointment-import/src/test/java/smash/appointment/parse/CellParserTest.java
deleted file mode 100644
index 1c0290fe7f9426312100b8adf7654d94586fb4c9..0000000000000000000000000000000000000000
--- a/appointment-import/src/test/java/smash/appointment/parse/CellParserTest.java
+++ /dev/null
@@ -1,157 +0,0 @@
-package smash.appointment.parse;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.junit.Before;
-import org.junit.Test;
-
-public class CellParserTest extends TestBase {
- Logger logger = Logger.getLogger(CellParserTest.class);
-
- List<CellParseTestCase> testCases;
- CellParser parser;
-
- @Before
- public void setUp() {
- super.setUp();
-
- parser = new CellParser();
- parser.setSubjectDao(subjectDao);
-
- testCases = new ArrayList<CellParseTestCase>();
-
- testCases.add(new CellParseTestCase("Piotr Gawron level A FU V3", piotrGawron, null, AppointmentTypeCollection.LEVEL_A.getTypes()));
- testCases.add(new CellParseTestCase("09:00 Jan Kowalski-Nowak level A", janKowalskiNowak, "09:00", AppointmentTypeCollection.LEVEL_A.getTypes()));
- testCases.add(
- new CellParseTestCase(
- "ND0002 l664574645 (sms)evel BV © + SB ©", janKowalskiNowak, null, new AppointmentType[] { AppointmentType.LEVEL_BV, AppointmentType.LEVEL_SB }));
- testCases.add(new CellParseTestCase("ND0001 654654631 level B ©", piotrGawron, null, new AppointmentType[] { AppointmentType.LEVEL_B }));
- testCases.add(
- new CellParseTestCase(
- "John Doe BV + BG + SB", johnDoe, null, new AppointmentType[] { AppointmentType.LEVEL_BV, AppointmentType.LEVEL_BG, AppointmentType.LEVEL_SB }));
- testCases.add(new CellParseTestCase("Kowalski-Nowak m-Power", janKowalskiNowak, null, new AppointmentType[] { AppointmentType.LEVEL_B_M_POWER }));
- testCases.add(new CellParseTestCase("ND0004 Name BV ©", cateKowalsky, null, new AppointmentType[] { AppointmentType.LEVEL_BV }));
- testCases.add(
- new CellParseTestCase("ND0004 level BV (c) + SB ©", cateKowalsky, null, new AppointmentType[] { AppointmentType.LEVEL_BV, AppointmentType.LEVEL_SB }));
- testCases.add(
- new CellParseTestCase(
- "Cate Kowalsky level BV + BG + SB + m-Power", cateKowalsky, null,
- new AppointmentType[] { AppointmentType.LEVEL_BV, AppointmentType.LEVEL_BG, AppointmentType.LEVEL_SB, AppointmentType.LEVEL_B_M_POWER }));
- testCases.add(new CellParseTestCase("sb name level A", null, null, AppointmentTypeCollection.LEVEL_A.getTypes()));
- testCases.add(new CellParseTestCase("Andrew Dude level A FU V3", andrewDude, null, AppointmentTypeCollection.LEVEL_A.getTypes()));
- testCases.add(
- new CellParseTestCase(
- "Gawron Piotr BV + BG + neuro level A (FU)", piotrGawron, null,
- new AppointmentType[] { AppointmentType.LEVEL_ANP, AppointmentType.LEVEL_BV, AppointmentType.LEVEL_BG }));
-
- testCases.add(
- new CellParseTestCase(
- "Gawron Piotr level B © + level A neuro ©", piotrGawron, null, new AppointmentType[] { AppointmentType.LEVEL_ANP, AppointmentType.LEVEL_B }));
-
- testCases.add(
- new CellParseTestCase(
- "Gawron Piotr level B © + BV © + SB ©", piotrGawron, null,
- new AppointmentType[] { AppointmentType.LEVEL_B, AppointmentType.LEVEL_BV, AppointmentType.LEVEL_SB }));
-
- testCases.add(
- new CellParseTestCase(
- "Gawron Piotr level B + BV + BG", piotrGawron, null,
- new AppointmentType[] { AppointmentType.LEVEL_B, AppointmentType.LEVEL_BV, AppointmentType.LEVEL_BG }));
-
- testCases.add(
- new CellParseTestCase("Gawron Piotr level B + BG", piotrGawron, null, new AppointmentType[] { AppointmentType.LEVEL_B, AppointmentType.LEVEL_BG }));
- testCases.add(
- new CellParseTestCase(
- "Gawron Piotr level B © + BV © + SB ©", piotrGawron, null,
- new AppointmentType[] { AppointmentType.LEVEL_B, AppointmentType.LEVEL_BV, AppointmentType.LEVEL_SB }));
- testCases.add(
- new CellParseTestCase(
- "Gawron Piotr level BG + SB + M-Power", piotrGawron, null,
- new AppointmentType[] { AppointmentType.LEVEL_BG, AppointmentType.LEVEL_SB, AppointmentType.LEVEL_B_M_POWER }));
-
- testCases.add(
- new CellParseTestCase("Gawron Piotr level B + BV", piotrGawron, null, new AppointmentType[] { AppointmentType.LEVEL_B, AppointmentType.LEVEL_BV }));
- testCases.add(
- new CellParseTestCase(
- "Gawron Piotr level BG + SB + M-Power", piotrGawron, null,
- new AppointmentType[] { AppointmentType.LEVEL_BG, AppointmentType.LEVEL_SB, AppointmentType.LEVEL_B_M_POWER }));
- testCases.add(
- new CellParseTestCase(
- "Gawron Piotr BV © + SB © + neuro", piotrGawron, null,
- new AppointmentType[] { AppointmentType.LEVEL_BV, AppointmentType.LEVEL_SB, AppointmentType.LEVEL_AN }));
- testCases.add(
- new CellParseTestCase(
- "Gawron Piotr BV © + SB © + M-Power", piotrGawron, null,
- new AppointmentType[] { AppointmentType.LEVEL_BV, AppointmentType.LEVEL_SB, AppointmentType.LEVEL_B_M_POWER }));
-
-
-
- }
-
- @Test
- public void testExtractTime() {
- for (CellParseTestCase testCase : testCases) {
- String result = parser.extractTime(testCase.query);
- assertEquals("Invalid time parsed from query: " + testCase.query, testCase.time, result);
- }
- }
-
- @Test
- public void testRemoveTime() {
- for (CellParseTestCase testCase : testCases) {
- String result = parser.removeTime(testCase.query);
- if (testCase.time == null) {
- assertEquals("query after removing time should be the same for query: " + testCase.query, testCase.query, result);
- } else {
- assertFalse(testCase.query.equals(result));
- }
- }
- }
-
- @Test
- public void testRemoveTime2() {
- String result = parser.removeTime("09:00 John Doe level B");
- assertEquals("John Doe level B", result);
- }
-
- @Test
- public void testExtractAppointment() {
- String defaultTime = "23:55";
- for (CellParseTestCase testCase : testCases) {
- AppointmentEntry appointment = parser.parseAppointment(testCase.query, defaultTime);
- if (testCase.time != null) {
- assertEquals("Invalid time parsed from query: " + testCase.query, testCase.time, appointment.getTime());
- } else {
- assertEquals("Invalid time parsed from query (default value expected): " + testCase.query, defaultTime, appointment.getTime());
- }
- assertEquals("Invalid subject parsed from query: " + testCase.query, testCase.subject, appointment.getSubject());
- assertTrue(
- "Invalid type parsed from query: " + testCase.query + " expected: " + Arrays.asList(testCase.types) + "; found: " + appointment.getTypes(),
- equalTypes(Arrays.asList(testCase.types), appointment.getTypes()));
- }
- }
-
- private boolean equalTypes(List<AppointmentType> types, Collection<AppointmentType> types2) {
- for (AppointmentType type : types) {
- if (!types2.contains(type)) {
- return false;
- }
- }
- for (AppointmentType type : types2) {
- if (!types.contains(type)) {
- return false;
- }
- }
-
- return true;
- }
-
-}
diff --git a/appointment-import/src/test/java/smash/appointment/parse/DuplicateRemoveParserTest.java b/appointment-import/src/test/java/smash/appointment/parse/DuplicateRemoveParserTest.java
deleted file mode 100644
index 7b0786742db14bd4b5f49b4636cfbe99dab481bf..0000000000000000000000000000000000000000
--- a/appointment-import/src/test/java/smash/appointment/parse/DuplicateRemoveParserTest.java
+++ /dev/null
@@ -1,45 +0,0 @@
-package smash.appointment.parse;
-
-import static org.junit.Assert.*;
-
-import java.io.IOException;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class DuplicateRemoveParserTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void test() throws IOException {
- DuplicateRemoveParser parser = new DuplicateRemoveParser();
-
- SubjectDao subjectDao = new SubjectDao();
-
- subjectDao.addSubject(new Subject("First", "Last", "","P-113"), null);
- subjectDao.addSubject(new Subject("First", "Last", "","P-114"), null);
- subjectDao.addSubject(new Subject("A", "B", "","P-115"), null);
- subjectDao.addSubject(new Subject("C", "D", "","P-116"), null);
-
- assertEquals(4, subjectDao.getSubjects().size());
-
- parser.setSubjectDao(subjectDao);
- parser.removeDuplicates("testFiles/duplicates.txt");
-
- assertEquals(2, subjectDao.getSubjects().size());
- }
-
-}
diff --git a/appointment-import/src/test/java/smash/appointment/parse/LihControlMappingParserTest.java b/appointment-import/src/test/java/smash/appointment/parse/LihControlMappingParserTest.java
deleted file mode 100644
index b281fe89d51262e0f562e36a481c3124b0567d7c..0000000000000000000000000000000000000000
--- a/appointment-import/src/test/java/smash/appointment/parse/LihControlMappingParserTest.java
+++ /dev/null
@@ -1,80 +0,0 @@
-package smash.appointment.parse;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-
-import java.text.SimpleDateFormat;
-import java.util.Date;
-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 {
- }
-
- private static final SimpleDateFormat DATE_FORMATTER = new SimpleDateFormat("yyyy-MM-dd");
-
- @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());
-
- for (Subject s:entries) {
- DATE_FORMATTER.parse(s.getAddDate());
- }
- }
-
-
- @Test
- public void testFixDate() throws Exception {
- DATE_FORMATTER.parse(processor.fixDate("2016-cot-31"));
- Date d = DATE_FORMATTER.parse(processor.fixDate("25-11-1951"));
- assertEquals("1951-11-25",DATE_FORMATTER.format(d));
- DATE_FORMATTER.parse(processor.fixDate("1957??-10-25"));
- DATE_FORMATTER.parse(processor.fixDate("2016?-sep-12"));
- DATE_FORMATTER.parse(processor.fixDate("2016-aou-26"));
- DATE_FORMATTER.parse(processor.fixDate("2016-avr-14"));
- DATE_FORMATTER.parse(processor.fixDate("2016-fev-03"));
- DATE_FORMATTER.parse(processor.fixDate("-","2016-01-01"));
- }
-
-}
diff --git a/appointment-import/src/test/java/smash/appointment/parse/LihControlParserTest.java b/appointment-import/src/test/java/smash/appointment/parse/LihControlParserTest.java
deleted file mode 100644
index 9cd3eb203b49d97fd123e824112c6a952d55e983..0000000000000000000000000000000000000000
--- a/appointment-import/src/test/java/smash/appointment/parse/LihControlParserTest.java
+++ /dev/null
@@ -1,68 +0,0 @@
-package smash.appointment.parse;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-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 testParseLang() throws Exception {
- assertEquals("English", processor.getMappedLanguage("EN"));
- }
-
- @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("Luxembourg", 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());
- assertNotNull(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/src/test/java/smash/appointment/parse/PrcControlParserTest.java b/appointment-import/src/test/java/smash/appointment/parse/PrcControlParserTest.java
deleted file mode 100644
index 8c44d431a5bd0ff46906d9394ae003a13436e5a1..0000000000000000000000000000000000000000
--- a/appointment-import/src/test/java/smash/appointment/parse/PrcControlParserTest.java
+++ /dev/null
@@ -1,59 +0,0 @@
-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 PrcControlParserTest extends TestBase {
- Logger logger = Logger.getLogger(PrcSubjectsParserTest.class);
-
- PrcControlParser processor = new PrcControlParser();
-
-
- @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/prcControlesExample.xlsx");
- assertTrue(entries.size() > 0);
-
- Subject subject = entries.get(0);
- assertEquals("P-333", subject.getScreeningNumber());
- assertEquals("CCC", subject.getName());
- assertEquals("BBB", subject.getSurname());
- assertTrue(subject.getRemarks().contains("note"));
- assertEquals("DDD", subject.getAddress());
- assertEquals("L-2423", subject.getZipCode());
- assertEquals("Luxembourg", subject.getCity());
- assertEquals("Luxembourg", subject.getCountry());
- assertEquals("123", subject.getPhone1());
- assertEquals("456", subject.getPhone2());
- assertEquals("", subject.getPhone3());
- assertEquals("mail@mail.lu", subject.getMail());
- assertEquals("", subject.getDiagnosisYear());
- assertEquals("", subject.getDiagnosis());
- assertEquals("", subject.getReferal());
- assertEquals("2016-03-29", subject.getAddDate());
- assertEquals("ND3333", subject.getNdNumber());
- assertEquals("1999-09-10", subject.getBirthDate());
- }
-
-
-}
diff --git a/appointment-import/src/test/java/smash/appointment/parse/PrcFlyingParserTest.java b/appointment-import/src/test/java/smash/appointment/parse/PrcFlyingParserTest.java
deleted file mode 100644
index 6c34a90a4af6520dc27a332f18662fc711e06d90..0000000000000000000000000000000000000000
--- a/appointment-import/src/test/java/smash/appointment/parse/PrcFlyingParserTest.java
+++ /dev/null
@@ -1,61 +0,0 @@
-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 PrcFlyingParserTest extends TestBase {
- Logger logger = Logger.getLogger(PrcSubjectsParserTest.class);
-
- PrcFlyingParser processor = new PrcFlyingParser();
-
-
- @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/prcFlyingTeam.xlsx");
- assertTrue(entries.size() > 0);
-
- Subject subject = entries.get(0);
- assertEquals("F-222", subject.getScreeningNumber());
- assertEquals(SubjectType.CONTROL, subject.getType());
- assertEquals("DOE", subject.getSurname());
- assertEquals("John", subject.getName());
- assertTrue(subject.getRemarks().contains("notes"));
- assertEquals("8, rue des Nowhere", subject.getAddress());
- assertEquals("F-57100", subject.getZipCode());
- assertEquals("Paris", subject.getCity());
- assertEquals("France", subject.getCountry());
- assertEquals("001234325435", subject.getPhone1());
- assertEquals("666", subject.getPhone2());
- assertEquals("", subject.getPhone3());
- assertEquals("mail@address.lu", subject.getMail());
- assertEquals("", subject.getDiagnosisYear());
- assertEquals("BLA", subject.getDiagnosis());
- assertEquals("DR", subject.getReferal());
- assertEquals("2016-07-06", subject.getAddDate());
- assertTrue(subject.getRemarks().contains("Questionnaires OK"));
- assertEquals("ND2222", subject.getNdNumber());
- assertEquals("1945-01-02", subject.getBirthDate());
- }
-
-
-}
diff --git a/appointment-import/src/test/java/smash/appointment/parse/PrcSubjectsParserTest.java b/appointment-import/src/test/java/smash/appointment/parse/PrcSubjectsParserTest.java
deleted file mode 100644
index 86f9568717977c12266a21fccd6e6f0c1acaabaf..0000000000000000000000000000000000000000
--- a/appointment-import/src/test/java/smash/appointment/parse/PrcSubjectsParserTest.java
+++ /dev/null
@@ -1,85 +0,0 @@
-package smash.appointment.parse;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-
-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 PrcSubjectsParserTest extends TestBase {
- Logger logger = Logger.getLogger(PrcSubjectsParserTest.class);
-
- PrcSubjectsParser processor = new PrcSubjectsParser();
-
- @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/prcSubjectsExample.xlsx");
- assertTrue(entries.size() > 0);
-
- Subject subject = entries.get(0);
- assertEquals("P-111", subject.getScreeningNumber());
- assertEquals("abcdef", subject.getSurname());
- assertEquals("Piotr", subject.getName());
- assertTrue(subject.getRemarks().contains("this is remark"));
- assertEquals("Jaskolki, 6", subject.getAddress());
- assertEquals("D-66636", subject.getZipCode());
- assertEquals("Trier", subject.getCity());
- assertEquals("Deutschland", subject.getCountry());
- assertEquals("0049123455676", subject.getPhone1());
- assertEquals("tel2", subject.getPhone2());
- assertEquals("tel3", subject.getPhone3());
- assertEquals("piotr.cos@uni.lu", subject.getMail());
- assertEquals("1999", subject.getDiagnosisYear());
- assertEquals("unknown", subject.getDiagnosis());
- assertEquals("PG", subject.getReferal());
- assertEquals("2015-10-14", subject.getAddDate());
- assertTrue(subject.getRemarks().contains("Questionnaires OK"));
- assertEquals("ND1111", subject.getNdNumber());
- assertEquals("m_id", subject.getmPowerId());
- assertEquals("1972-01-02", subject.getBirthDate());
- assertFalse(subject.isDead());
- assertFalse(subject.isResigned());
-
- subject = entries.get(1);
- assertTrue(subject.isDead());
- assertTrue(subject.isResigned());
-
- subject = entries.get(2);
- assertFalse(subject.isDead());
- assertFalse(subject.isResigned());
-
- subject = entries.get(3);
- assertFalse(subject.isDead());
- assertFalse(subject.isResigned());
-
- subject = entries.get(4);
- assertFalse(subject.isDead());
- assertTrue(subject.isResigned());
-
-
- subject = entries.get(5);
- assertFalse(subject.isDead());
-
- subject = entries.get(6);
- assertFalse(subject.isDead());
- }
-}
diff --git a/appointment-import/src/test/java/smash/appointment/parse/RedcapCalendarParserTest.java b/appointment-import/src/test/java/smash/appointment/parse/RedcapCalendarParserTest.java
deleted file mode 100644
index 2a9a17fae5e05b342e817ba4fd29e4d0d7bf8d49..0000000000000000000000000000000000000000
--- a/appointment-import/src/test/java/smash/appointment/parse/RedcapCalendarParserTest.java
+++ /dev/null
@@ -1,76 +0,0 @@
-package smash.appointment.parse;
-
-import static org.junit.Assert.*;
-
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.List;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class RedcapCalendarParserTest extends TestBase{
- RedcapCalendarParser parser = new RedcapCalendarParser();
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() {
- super.setUp();
- parser.setSubjectDao(subjectDao);
- List<Subject> subjects = new ArrayList<>();
- for (int count =0 ;count<10000;count++) {
- String nd = count+"";
- while (nd.length()<4) {
- nd = "0"+nd;
- }
- Subject subject = new Subject("name "+nd, "surname"+nd, "ND"+nd, count+"");
-
- String screening = nd;
- if (screening.startsWith("0")) {
- screening = screening.substring(1);
- }
- subject.setScreeningNumber("P-"+screening);
- subject.setToBeSeenAt("PRC");
- if (count>=3000) {
- screening=screening.substring(1);
- subject.setScreeningNumber("L-"+screening);
- subject.setToBeSeenAt("LIH");
- }
- if (count>=7000) {
- subject.setScreeningNumber("F-"+nd);
- subject.setToBeSeenAt("FLYING TEAM");
- }
- subjects.add(subject);
- }
- subjectDao.setSubjects(subjects);
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParse() throws Exception{
- List<AppointmentEntry> result = parser.parse("testFiles/redcap_calendar.sql", null);
- assertEquals(2, result.size());
- }
-
-// @Test
-// public void test() throws Exception{
-// List<AppointmentEntry> result = parser.parse("c:/Users/piotr.gawron/Desktop/tmp/prc/redcap_events_calendar.sql", Calendar.getInstance());
-// }
-
- @Test
- public void testParse2() throws Exception{
- Calendar future =Calendar.getInstance();
- future.set(Calendar.YEAR, 4000);
- List<AppointmentEntry> result = parser.parse("testFiles/redcap_calendar.sql", future);
- assertEquals(0, result.size());
- }
-
-}
diff --git a/appointment-import/src/test/java/smash/appointment/parse/RedcapParserTest.java b/appointment-import/src/test/java/smash/appointment/parse/RedcapParserTest.java
deleted file mode 100644
index ba1be9f13d5c784e651537a48585808616e1cba9..0000000000000000000000000000000000000000
--- a/appointment-import/src/test/java/smash/appointment/parse/RedcapParserTest.java
+++ /dev/null
@@ -1,74 +0,0 @@
-package smash.appointment.parse;
-
-import static org.junit.Assert.*;
-
-import java.io.FileNotFoundException;
-import java.io.IOException;
-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 RedcapParserTest extends TestBase{
- Logger logger = Logger.getLogger(RedcapParserTest.class);
- RedcapParser parser = new RedcapParser();
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() {
- super.setUp();
- parser.setSubjectDao(subjectDao);
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParseFile() throws FileNotFoundException, IOException {
- List<AppointmentEntry> entries = parser.parse("testFiles/redcap_imp.txt");
- assertTrue(entries.size() > 0);
- assertEquals(3, subjectDao.getByNdNumber("ND0001").getLanguages().size());
-
- int levelACount = 0;
- int levelBCount = 0;
- int levelBVCount = 0;
- int levelBGCount = 0;
- int levelSBCount = 0;
- int levelMPowerCount = 0;
- for (AppointmentEntry appointmentEntry : entries) {
- if (appointmentEntry.getTypes().contains(AppointmentType.LEVEL_AQUEST)) {
- levelACount++;
- }
- if (appointmentEntry.getTypes().contains(AppointmentType.LEVEL_B)) {
- levelBCount++;
- }
- if (appointmentEntry.getTypes().contains(AppointmentType.LEVEL_BG)) {
- levelBGCount++;
- }
- if (appointmentEntry.getTypes().contains(AppointmentType.LEVEL_BV)) {
- levelBVCount++;
- }
- if (appointmentEntry.getTypes().contains(AppointmentType.LEVEL_SB)) {
- levelSBCount++;
- }
- if (appointmentEntry.getTypes().contains(AppointmentType.LEVEL_B_M_POWER)) {
- levelMPowerCount++;
- }
- }
- assertTrue(levelACount > 0);
- assertTrue(levelBCount > 0);
- assertTrue(levelBVCount > 0);
- assertTrue(levelBGCount > 0);
- assertTrue(levelSBCount > 0);
- assertTrue(levelMPowerCount > 0);
-
- }
-
-}
diff --git a/appointment-import/src/test/java/smash/appointment/parse/SubjectDaoTest.java b/appointment-import/src/test/java/smash/appointment/parse/SubjectDaoTest.java
deleted file mode 100644
index 0585aa0d9e9f918d3cb37745ea58a8c81b3e0826..0000000000000000000000000000000000000000
--- a/appointment-import/src/test/java/smash/appointment/parse/SubjectDaoTest.java
+++ /dev/null
@@ -1,88 +0,0 @@
-package smash.appointment.parse;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class SubjectDaoTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testReadFile() throws Exception {
- SubjectDao subjectDao = new SubjectDao();
- subjectDao.readFile("testFiles/subjects.txt");
- assertEquals(2, subjectDao.getSubjects().size());
- assertEquals("Piotr", subjectDao.getSubjects().get(0).getName());
- }
-
- @Test
- public void testDuplicateRem() throws Exception {
- Subject subject1 = new Subject("A", "B", "C", "D");
- subject1.setToBeSeenAt("");
- Subject subject2 = new Subject("A", "B", "", "E");
- subject2.setToBeSeenAt("");
- SubjectDao subjectDao = new SubjectDao();
-
- subjectDao.addSubject(subject1, null);
- subjectDao.addSubject(subject2, null);
- subjectDao.removeDuplicate(subject1, subject2, null);
-
- assertEquals(1, subjectDao.getSubjects().size());
- assertTrue(subject1.getScreeningNumber().contains("D"));
- assertTrue(subject1.getScreeningNumber().contains("E"));
- assertEquals("C", subject1.getNdNumber());
- }
-
- @Test
- public void testDuplicateRem2() throws Exception {
- Subject subject1 = new Subject("A", "B", "C", "D");
- subject1.setToBeSeenAt("");
- Subject subject2 = new Subject("A", "B", "", "E");
- subject2.setToBeSeenAt("");
- SubjectDao subjectDao = new SubjectDao();
-
- subjectDao.addSubject(subject1, null);
- subjectDao.addSubject(subject2, null);
- subjectDao.removeDuplicate(subject2, subject1, null);
-
- assertEquals(1, subjectDao.getSubjects().size());
- assertTrue(subject2.getScreeningNumber().contains("D"));
- assertTrue(subject2.getScreeningNumber().contains("E"));
- assertEquals("C", subject2.getNdNumber());
- }
-
- @Test
- public void testDuplicateRem3() throws Exception {
- try {
- Subject subject1 = new Subject("A", "B", "C", "D");
- subject1.setToBeSeenAt("");
- Subject subject2 = new Subject("A", "B", "X", "E");
- subject2.setToBeSeenAt("");
- SubjectDao subjectDao = new SubjectDao();
-
- subjectDao.addSubject(subject1, null);
- subjectDao.addSubject(subject2, null);
- subjectDao.removeDuplicate(subject2, subject1, null);
-
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- }
-
-}
diff --git a/appointment-import/src/test/java/smash/appointment/parse/SubjectParserTest.java b/appointment-import/src/test/java/smash/appointment/parse/SubjectParserTest.java
deleted file mode 100644
index a9efafaf25f0c43f333bd4afa97c370dddc5c4ce..0000000000000000000000000000000000000000
--- a/appointment-import/src/test/java/smash/appointment/parse/SubjectParserTest.java
+++ /dev/null
@@ -1,32 +0,0 @@
-package smash.appointment.parse;
-
-import static org.junit.Assert.*;
-
-import java.util.Calendar;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class SubjectParserTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParseDate() {
- SubjectParser parser = new PrcControlParser();
- assertEquals("", parser.getDate(null, null));
- }
-
-}
diff --git a/appointment-import/src/test/java/smash/appointment/parse/TestBase.java b/appointment-import/src/test/java/smash/appointment/parse/TestBase.java
deleted file mode 100644
index b9663f46e9e6dfe9a395fecd0166b97de4ef75e0..0000000000000000000000000000000000000000
--- a/appointment-import/src/test/java/smash/appointment/parse/TestBase.java
+++ /dev/null
@@ -1,25 +0,0 @@
-package smash.appointment.parse;
-
-public class TestBase {
- SubjectDao subjectDao;
-
- Subject piotrGawron = new Subject("Piotr", "Gawron", "ND0001", "1");
- Subject janKowalskiNowak = new Subject("Jan", "Kowalski-Nowak", "ND0002", "2");
- Subject johnDoe = new Subject("John", "Doe", "ND0003", "3");
- Subject cateKowalsky = new Subject("Cate", "Kowalsky", "ND0004", "4");
- Subject andrewDude = new Subject(" Andrew ", " Dude ", "ND0005", "5");
- Subject unknownDude = new Subject(" Unknownnnnnnnn ", " Dude ", "ND0006", "6");
-
- public void setUp() {
- subjectDao = new SubjectDao();
-
- subjectDao.addSubject(new Subject("Piotr Marcin", "Gawron", "ND1005", "1005"), null);
- subjectDao.addSubject(piotrGawron, null);
- subjectDao.addSubject(janKowalskiNowak, null);
- subjectDao.addSubject(johnDoe, null);
- subjectDao.addSubject(cateKowalsky, null);
- subjectDao.addSubject(andrewDude, null);
- subjectDao.addSubject(unknownDude, null);
- }
-
-}
diff --git a/appointment-import/src/test/java/smash/appointment/parse/VisitTest.java b/appointment-import/src/test/java/smash/appointment/parse/VisitTest.java
deleted file mode 100644
index fd3eb2d963d5699e12d1abc642d67070226e9a3a..0000000000000000000000000000000000000000
--- a/appointment-import/src/test/java/smash/appointment/parse/VisitTest.java
+++ /dev/null
@@ -1,48 +0,0 @@
-package smash.appointment.parse;
-
-import static org.junit.Assert.*;
-
-import java.text.ParseException;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class VisitTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetStartDate() {
- Subject subject = new Subject("!", "", "4", "5");
- Visit visit = new Visit(subject);
- AppointmentEntry entry = new AppointmentEntry();
- entry.setSubject(subject);
- entry.setDay("2015-02-01 8:00");
- visit.addAppointment(entry);
- assertEquals("2015-02-01", visit.getStartDate());
- }
-
- @Test
- public void testGetEndDate() throws ParseException {
- Subject subject = new Subject("!", "", "4", "5");
- Visit visit = new Visit(subject);
- AppointmentEntry entry = new AppointmentEntry();
- entry.setSubject(subject);
- entry.setDay("2015-02-01 8:00");
- visit.addAppointment(entry);
- assertEquals("2015-05-01", visit.getEndDate());
- }
-
-}
diff --git a/appointment-import/src/test/java/smash/appointment/parse/XlsxCalendarProcessorTest.java b/appointment-import/src/test/java/smash/appointment/parse/XlsxCalendarProcessorTest.java
deleted file mode 100644
index 8e23b0a920bfd4ef3d4f0c218a767e502bae523b..0000000000000000000000000000000000000000
--- a/appointment-import/src/test/java/smash/appointment/parse/XlsxCalendarProcessorTest.java
+++ /dev/null
@@ -1,41 +0,0 @@
-package smash.appointment.parse;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-
-import java.io.FileNotFoundException;
-import java.util.Calendar;
-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 XlsxCalendarProcessorTest extends TestBase {
- Logger logger = Logger.getLogger(XlsxCalendarProcessorTest.class);
-
- XlsxCalendarProcessor processor = new XlsxCalendarProcessor();
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() {
- super.setUp();
- processor.setSubjectDao(subjectDao);
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testReadExcel() throws Exception {
- List<AppointmentEntry> entries = processor.processExcel("testFiles/calendarExample.xlsx", Calendar.getInstance());
- assertTrue(entries.size() > 0);
- }
-
-}
diff --git a/appointment-import/src/test/resources/log4j.properties b/appointment-import/src/test/resources/log4j.properties
deleted file mode 100644
index e108a78cf8570a6f5bfc3e00dfaee3c45a1e829e..0000000000000000000000000000000000000000
--- a/appointment-import/src/test/resources/log4j.properties
+++ /dev/null
@@ -1,8 +0,0 @@
-#Set root logger 's level and its appender to an appender called CONSOLE which is defined below.
-log4j.rootLogger=debug, CONSOLE
-
-#Set the behavior of the CONSOLE appender
-log4j.appender.CONSOLE=org.apache.log4j.ConsoleAppender
-log4j.appender.CONSOLE.layout=org.apache.log4j.PatternLayout
-log4j.appender.CONSOLE.layout.ConversionPattern=%d %5p [%t] (%F:%L) - %m%n
-#log4j.appender.CONSOLE.layout.ConversionPattern=%m%n
diff --git a/appointment-import/testFiles/calendarExample.xlsx b/appointment-import/testFiles/calendarExample.xlsx
deleted file mode 100644
index b8a0e42b59245f10692d9739ade2a0e8e4cc8b03..0000000000000000000000000000000000000000
Binary files a/appointment-import/testFiles/calendarExample.xlsx and /dev/null differ
diff --git a/appointment-import/testFiles/duplicates.txt b/appointment-import/testFiles/duplicates.txt
deleted file mode 100644
index 3c7625d5e81df7be3e2efea220146ef0a1fda1f7..0000000000000000000000000000000000000000
--- a/appointment-import/testFiles/duplicates.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-P-113 P-114
-P-115 P-116
\ No newline at end of file
diff --git a/appointment-import/testFiles/lihControlExample.xlsx b/appointment-import/testFiles/lihControlExample.xlsx
deleted file mode 100644
index 526e749bdf8cb818d13e98b763afb22b3ec3b071..0000000000000000000000000000000000000000
Binary files a/appointment-import/testFiles/lihControlExample.xlsx and /dev/null differ
diff --git a/appointment-import/testFiles/lihControlMappingExample.xlsx b/appointment-import/testFiles/lihControlMappingExample.xlsx
deleted file mode 100644
index 4d54795013bdb361399cc256f0c51ae913af2cf5..0000000000000000000000000000000000000000
Binary files a/appointment-import/testFiles/lihControlMappingExample.xlsx and /dev/null differ
diff --git a/appointment-import/testFiles/prcControlesExample.xlsx b/appointment-import/testFiles/prcControlesExample.xlsx
deleted file mode 100644
index a3143cb40d39499dd598cea9f473fe6c49f1f2f3..0000000000000000000000000000000000000000
Binary files a/appointment-import/testFiles/prcControlesExample.xlsx and /dev/null differ
diff --git a/appointment-import/testFiles/prcFlyingTeam.xlsx b/appointment-import/testFiles/prcFlyingTeam.xlsx
deleted file mode 100644
index 891faa078123cf6c7d6d0b676afc1ce763df549a..0000000000000000000000000000000000000000
Binary files a/appointment-import/testFiles/prcFlyingTeam.xlsx and /dev/null differ
diff --git a/appointment-import/testFiles/prcSubjectsExample.xlsx b/appointment-import/testFiles/prcSubjectsExample.xlsx
deleted file mode 100644
index 986303d98419537e3952a2d557457cb85f468693..0000000000000000000000000000000000000000
Binary files a/appointment-import/testFiles/prcSubjectsExample.xlsx and /dev/null differ
diff --git a/appointment-import/testFiles/redcap_calendar.sql b/appointment-import/testFiles/redcap_calendar.sql
deleted file mode 100644
index c6586541fe09946d50bf9716e3fa1652a3f2eafd..0000000000000000000000000000000000000000
--- a/appointment-import/testFiles/redcap_calendar.sql
+++ /dev/null
@@ -1,68 +0,0 @@
--- MySQL dump 10.13 Distrib 5.5.54, for debian-linux-gnu (x86_64)
---
--- Host: localhost Database: redcap
--- ------------------------------------------------------
--- Server version 5.5.54-0ubuntu0.14.04.1
-
-/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
-/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
-/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */;
-/*!40101 SET NAMES utf8 */;
-/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */;
-/*!40103 SET TIME_ZONE='+00:00' */;
-/*!40014 SET @OLD_UNIQUE_CHECKS=@@UNIQUE_CHECKS, UNIQUE_CHECKS=0 */;
-/*!40014 SET @OLD_FOREIGN_KEY_CHECKS=@@FOREIGN_KEY_CHECKS, FOREIGN_KEY_CHECKS=0 */;
-/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='NO_AUTO_VALUE_ON_ZERO' */;
-/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */;
-
---
--- Table structure for table `redcap_events_calendar`
---
-
-DROP TABLE IF EXISTS `redcap_events_calendar`;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `redcap_events_calendar` (
- `cal_id` int(10) NOT NULL AUTO_INCREMENT,
- `record` varchar(50) COLLATE utf8_unicode_ci DEFAULT NULL,
- `project_id` int(10) DEFAULT NULL,
- `event_id` int(10) DEFAULT NULL,
- `baseline_date` date DEFAULT NULL,
- `group_id` int(10) DEFAULT NULL,
- `event_date` date DEFAULT NULL,
- `event_time` varchar(5) COLLATE utf8_unicode_ci DEFAULT NULL COMMENT 'HH:MM',
- `event_status` int(2) DEFAULT NULL COMMENT 'NULL=Ad Hoc, 0=Due Date, 1=Scheduled, 2=Confirmed, 3=Cancelled, 4=No Show',
- `note_type` int(2) DEFAULT NULL,
- `notes` text COLLATE utf8_unicode_ci,
- `extra_notes` text COLLATE utf8_unicode_ci,
- PRIMARY KEY (`cal_id`),
- KEY `event_id` (`event_id`),
- KEY `group_id` (`group_id`),
- KEY `project_date` (`project_id`,`event_date`),
- KEY `project_record` (`project_id`,`record`),
- CONSTRAINT `redcap_events_calendar_ibfk_1` FOREIGN KEY (`event_id`) REFERENCES `redcap_events_metadata` (`event_id`) ON DELETE CASCADE ON UPDATE CASCADE,
- CONSTRAINT `redcap_events_calendar_ibfk_2` FOREIGN KEY (`group_id`) REFERENCES `redcap_data_access_groups` (`group_id`) ON DELETE SET NULL ON UPDATE CASCADE,
- CONSTRAINT `redcap_events_calendar_ibfk_3` FOREIGN KEY (`project_id`) REFERENCES `redcap_projects` (`project_id`) ON DELETE CASCADE ON UPDATE CASCADE
-) ENGINE=InnoDB AUTO_INCREMENT=2107 DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci COMMENT='Calendar Data';
-/*!40101 SET character_set_client = @saved_cs_client */;
-
---
--- Dumping data for table `redcap_events_calendar`
---
-
-LOCK TABLES `redcap_events_calendar` WRITE;
-/*!40000 ALTER TABLE `redcap_events_calendar` DISABLE KEYS */;
-INSERT INTO `redcap_events_calendar` VALUES (7,NULL,12,NULL,NULL,NULL,'2015-05-06','08:00',NULL,NULL,'Patient, Level A',NULL),(8,NULL,12,NULL,NULL,NULL,'2015-05-06','12:00',NULL,NULL,'Patient Level A',NULL),(1336,'ND0333',12,41,'2016-10-27',NULL,'2018-09-07','',0,NULL,'',NULL);
-/*!40000 ALTER TABLE `redcap_events_calendar` ENABLE KEYS */;
-UNLOCK TABLES;
-/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */;
-
-/*!40101 SET SQL_MODE=@OLD_SQL_MODE */;
-/*!40014 SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS */;
-/*!40014 SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS */;
-/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */;
-/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */;
-/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
-/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
-
--- Dump completed on 2017-03-03 15:52:47
diff --git a/appointment-import/testFiles/redcap_imp.txt b/appointment-import/testFiles/redcap_imp.txt
deleted file mode 100644
index 8065e5c6c17ca5d0d5803ba08831feb0798a0406..0000000000000000000000000000000000000000
--- a/appointment-import/testFiles/redcap_imp.txt
+++ /dev/null
@@ -1,8 +0,0 @@
-Subject ID Event Name Date/Time of Birth Sex Language: most fluent Language: second most fluent Language: third most fluent Language: fourth most fluent Basic assessment (Level A) Basic assessment: start date Basic assessment: end date Basic assessment: number of visits Detailed neuropsychological assessment (Level B) Detailed neuropsychological assessment: start date Detailed neuropsychological assessment: end date Detailed neuropsychological assessment: number of visits Detailed motor assessment (Level B) Detailed motor assessment: start date Detailed motor assessment: end date Detailed motor assessment: number of visits Detailed sensory assessment (Level B) Detailed sensory assessment: start date Detailed sensory assessment: end date Detailed sensory assessment: number of visits PSP (Level B) PSP: start date PSP: end date PSP: number of visits Blood Blood: date Urine Urine: date CSF CSF: date Imaging Imaging: date Stool Stool: collection acceptance by patient Stool: collection date proposed Stool: date collected Skin biopsy Skin biopsy: date Saliva Saliva: date mPower mPower: date
-ND0001 Visit 1 1955-10-24 10:44 M Polish German French Yes 2015-01-04 10:14 2015-03-04 14:18 1 Yes 2015-03-04 Yes 2015-03-04 Yes 2016-10-20 Yes 2015-03-04 2015-03-11
-ND0001 Visit 2 Yes 2016-12-12 09:34 2017-01-24 10:46 2
-ND0002 Visit 1 1956-05-22 14:53 M Polish Yes 2015-03-04 14:56 2015-03-04 17:43 1 Yes 2015-07-29 2015-07-29 1 No No No Yes 2015-05-13 Yes 2015-05-13 No No No No Yes 2015-05-13
-ND0002 Visit 2 Yes 2016-01-18 10:00 2016-01-18 13:10 1 Yes 2016-05-26 2016-05-26 1 Yes 2016-01-18 Yes 2016-01-18 Yes Yes 2016-05-26 2016-05-26 Yes 2016-05-26 Yes 2016-01-18
-ND0003 Visit 1 1957-07-15 09:21 F Polish German Rusian English Yes 2015-03-11 09:25 2015-03-11 14:58 1 Yes 2015-11-12 2015-11-12 1 Yes 2015-03-11 Yes 2015-03-11 Yes 2015-03-11
-ND0003 Visit 2 Yes 2016-04-27 11:31 2016-05-11 13:30 2 Yes 2016-06-16 2016-06-16 1 Yes 2016-08-18 2016-08-18 1 Yes 2016-04-27 Yes 2016-04-27 Yes Yes 2016-04-27 2016-04-28 Yes 2016-07-28 Yes 2016-04-27
-ND0003 Visit 3
\ No newline at end of file
diff --git a/appointment-import/testFiles/subjects.txt b/appointment-import/testFiles/subjects.txt
deleted file mode 100644
index c55594f7ee41d31b0b81aaf1b38b46eb949d5bb4..0000000000000000000000000000000000000000
--- a/appointment-import/testFiles/subjects.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-Piotr Gawron ND0001 1
-John Doe ND0002 2