chore: fix warnings ♻️ (#6)

* chore: fix warnings (WIP)

* chore: fix warnings (WIP)

* chore: fix deprecated methods

* chore: fix warnings (WIP)

* chore: fix warnings (WIP)

* chore: fix warnings (WIP)

* chore: remove TODO

* ci: update Github Actions

.github/dependabot.yml

@@ -5,14 +5,62 @@
 
 version: 2
 updates:
-# Files stored in repository root
+# Files stored in repository builder
   - package-ecosystem: "maven"
     directory: "/builder"
     commit-message:
       prefix: chore
       include: "scope"
     schedule:
       interval: "weekly"
+# Files stored in repository super
+  - package-ecosystem: "maven"
+    directory: "/super"
+    commit-message:
+      prefix: chore
+      include: "scope"
+    schedule:
+      interval: "weekly"
+# Files stored in repository core
+  - package-ecosystem: "maven"
+    directory: "/core"
+    commit-message:
+      prefix: chore
+      include: "scope"
+    schedule:
+      interval: "weekly"
+# Files stored in repository ehconnector
+  - package-ecosystem: "maven"
+    directory: "/ehconnector"
+    commit-message:
+      prefix: chore
+      include: "scope"
+    schedule:
+      interval: "weekly"
+# Files stored in repository viewer
+  - package-ecosystem: "maven"
+    directory: "/viewer"
+    commit-message:
+      prefix: chore
+      include: "scope"
+    schedule:
+      interval: "weekly"
+# Files stored in repository datagenerator
+  - package-ecosystem: "maven"
+    directory: "/datagenerator"
+    commit-message:
+      prefix: chore
+      include: "scope"
+    schedule:
+      interval: "weekly"
+# Files stored in repository distribution
+  - package-ecosystem: "maven"
+    directory: "/distribution"
+    commit-message:
+      prefix: chore
+      include: "scope"
+    schedule:
+      interval: "weekly"
 # Workflow files stored in the default location of `.github/workflows`
   - package-ecosystem: "github-actions"
     directory: "/"

.github/workflows/pr-comment-artifact-url.yml

@@ -17,6 +17,9 @@ jobs:
     steps:
       - uses: 8BitJonny/[email protected]
         id: PR
+        with:
+          # Only return if PR is still open. (By default it returns PRs in any state.)
+          filterOutClosed: true
       - name: Get Artifact URL & PR Info
         if: steps.PR.outputs.pr_found == 'true'
         env:

core/src/main/java/org/imec/ivlab/core/RangeChecker.java

@@ -22,6 +22,7 @@
 import org.joda.time.Days;
 import org.joda.time.Months;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 import java.util.Set;
 
@@ -447,14 +448,10 @@ public LocalDate calculateEndDateForDuration(LocalDate startDate, Duration durat
 
         }
 
-        switch (durationUnit) {
-
-            case A:
-            case MO:
-            case WK:
-            case D:
-                endDate = endDate.minusDays(1);
-
+        // Vitalink/EVS in the past substract one day for authorized units, to compute the endDate properly
+        List<TimeUnit> unitsToSubtractOneDay = Arrays.asList(TimeUnit.A, TimeUnit.MO, TimeUnit.WK, TimeUnit.D);
+        if (unitsToSubtractOneDay.contains(durationUnit)) {
+            endDate = endDate.minusDays(1);
         }
 
         return endDate.toLocalDate();

core/src/main/java/org/imec/ivlab/core/kmehr/KmehrMarshaller.java

@@ -2,7 +2,8 @@
 
 import be.fgov.ehealth.standards.kmehr.schema.v1.Kmehrmessage;
 import javax.xml.bind.JAXBException;
-import org.apache.commons.lang3.StringUtils;
+
+import org.apache.commons.lang3.RegExUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.imec.ivlab.core.exceptions.TransformationException;
@@ -37,11 +38,11 @@ public static String resetNamespaces(String kmehrContent) {
     }
 
     private static String removeNamespaceUsage(String kmehrContent) {
-        return StringUtils.replacePattern(kmehrContent, "(<|<\\/)(ns\\d*:)", "$1");
+        return RegExUtils.replacePattern(kmehrContent, "(<|<\\/)(ns\\d*:)", "$1");
     }
 
     private static String setDefaultNamespace(String kmehrContent) {
-        return StringUtils.replacePattern(kmehrContent, "<kmehrmessage(?:[^>]*)>", KMEHRMESSAGE_TAG_WITH_DEFAULT_NAMESPACES);
+        return RegExUtils.replacePattern(kmehrContent, "<kmehrmessage(?:[^>]*)>", KMEHRMESSAGE_TAG_WITH_DEFAULT_NAMESPACES);
     }
 
 }

core/src/main/java/org/imec/ivlab/core/kmehr/model/localid/util/URIConverter.java

@@ -1,13 +1,13 @@
 package org.imec.ivlab.core.kmehr.model.localid.util;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
+//import org.apache.logging.log4j.LogManager;
+//import org.apache.logging.log4j.Logger;
 import org.imec.ivlab.core.kmehr.model.localid.URI;
 import org.imec.ivlab.core.kmehr.model.localid.URIType;
 
 public class URIConverter {
 
-    private final static Logger log = LogManager.getLogger(URIConverter.class);
+    //private final static Logger log = LogManager.getLogger(URIConverter.class);
 
 
     public static URI convertToUpdate(URI uri) {

core/src/main/java/org/imec/ivlab/core/model/upload/KmehrWithReferenceList.java

@@ -17,6 +17,7 @@ public void setList(List<KmehrWithReference> list) {
     }
 
     @Override
+    @SuppressWarnings({"unchecked" })
     public List<KmehrWithReference> getIdentifiables() {
         return list;
     }

core/src/main/java/org/imec/ivlab/core/model/upload/msentrylist/MSEntryList.java

@@ -20,6 +20,7 @@ public void setMsEntries(List<MSEntry> msEntries) {
 
 
     @Override
+    @SuppressWarnings({"unchecked" })
     public List<MSEntry> getIdentifiables() {
         return msEntries;
     }

core/src/main/java/org/imec/ivlab/core/model/upload/msentrylist/ReferenceDateUtil.java

@@ -26,7 +26,6 @@ public static void setReferenceDate(Kmehrmessage kmehrmessage, LocalDate referen
             patient = new PersonType();
         }
 
-        // TODO To fix
         patient.setRecorddatetime(
             new DateTime(
                 referenceDate.getYear(),

core/src/main/java/org/imec/ivlab/core/util/ClassesUtil.java

@@ -15,6 +15,7 @@ public class ClassesUtil {
 
     private final static Logger log = LogManager.getLogger(ClassesUtil.class);
 
+    @SuppressWarnings({ "unchecked"})
     public static <T> List<Class<T>> getClasses(String packagePath, Class<T> clazzFilter) {
 
         List<Class<T>> testClasses = new ArrayList<>();

core/src/main/java/org/imec/ivlab/core/util/DateUtils.java

@@ -108,7 +108,6 @@ public static LocalDateTime toLocalDateTime(Calendar calendar) {
         return LocalDateTime.ofInstant(calendar.toInstant(), ZoneId.systemDefault());
     }
 
-    // TODO issue here
     public static LocalDateTime toLocalDateTime(org.joda.time.DateTime calendar) {
         if (calendar == null) {
             return null;

core/src/main/java/org/imec/ivlab/core/util/FileUtil.java

@@ -8,10 +8,10 @@
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
 import java.io.IOException;
-import java.io.RandomAccessFile;
 import java.nio.channels.FileChannel;
 import java.nio.channels.FileLock;
 import java.nio.channels.OverlappingFileLockException;
+import java.nio.file.StandardOpenOption;
 
 public class FileUtil {
 
@@ -23,19 +23,10 @@ public static void copyFile(File sourceFile, File destFile) throws IOException {
             destFile.createNewFile();
         }
 
-        FileChannel source = null;
-        FileChannel destination = null;
-
-        try {
-            source = new FileInputStream(sourceFile).getChannel();
-            destination = new FileOutputStream(destFile).getChannel();
-            destination.transferFrom(source, 0, source.size());
-        } finally {
-            if (source != null) {
-                source.close();
-            }
-            if (destination != null) {
-                destination.close();
+        try(FileInputStream source = new FileInputStream(sourceFile)) {
+            try(FileOutputStream destination = new FileOutputStream(destFile)) {
+                FileChannel sourceChannel = source.getChannel();
+                destination.getChannel().transferFrom(sourceChannel, 0, sourceChannel.size());
             }
         }
     }
@@ -67,42 +58,23 @@ public static void createDirectoriesRecursively(String directoryPath) {
 
     public static boolean isLocked(File file) {
 
-        FileLock lock = null;
-        FileChannel channel = null;
-
-        try { // Get a file channel for the file
-            channel = new RandomAccessFile(file, "rw").getChannel();
-
-            // Try acquiring the lock without blocking.
-            // lock is null or exception if the file is already locked.
-            try {
-                lock = channel.tryLock();
-            } catch (OverlappingFileLockException e){
-                return true;
+        try (FileChannel channel = FileChannel.open(file.toPath(), StandardOpenOption.READ, StandardOpenOption.WRITE)) {
+            FileLock lock = channel.tryLock();
+            if (lock != null) {
+                lock.release(); // Release the lock immediately
+                return false; // File is not locked
+            } else {
+                return true; // File is locked
             }
-
-        } catch (Exception e) {
+        } catch (OverlappingFileLockException e) {
+            return true;
+        } catch (IOException e) {
+            // Handle any exceptions
             log.error("Error when checking if file is locked: ", e);
-        } finally {
-            if (lock != null && lock.isValid()) {
-                try {
-                    lock.release();
-                } catch (IOException e1) {
-                    log.error("Error when trying to release lock", e1);
-                }
-            }
-            if (channel != null && channel.isOpen()) {
-                try {
-                    channel.close();
-                } catch (IOException e) {
-                    log.error("Error when trying to close channel", e);
-                }
-            }
         }
 
-        return false;
-
-    }
+        return false; // Unable to determine lock status, assuming not locked
+}
 
     public static File appendTextToFilename(File file, String textToAppend) {
         return new File(FilenameUtils.getFullPath(file.getAbsolutePath()) + FilenameUtils.getBaseName(file.getAbsolutePath()) + textToAppend + "." +  FilenameUtils.getExtension(file.getAbsolutePath()));

core/src/main/java/org/imec/ivlab/core/util/JAXBUtils.java

@@ -81,7 +81,8 @@ public static String marshal(Object o, String rootName) throws JAXBException {
 
         QName qName = new QName(nsURI, rootName);
 
-        JAXBElement root = new JAXBElement(qName, o.getClass(), o);
+        @SuppressWarnings({ "rawtypes", "unchecked" })
+        JAXBElement<?> root = new JAXBElement(qName, o.getClass(), o);
 
         jaxbMarshaller.marshal(root, writer);
 

core/src/main/java/org/imec/ivlab/core/util/PathUtils.java

@@ -62,7 +62,6 @@ public static String commonParent(String[] files) {
         outerloop:
         while (charPosition < shortestPathLength) {
             Character charPosFirstPath = paths[0].charAt(charPosition);
-            innerloop:
             for (int i = 0; i < paths.length; i++) {
                 char charAtPosition = paths[i].charAt(charPosition);
                 if (charAtPosition != charPosFirstPath) {

core/src/main/java/org/imec/ivlab/core/util/ResourceResolver.java

@@ -35,7 +35,7 @@ public static File getProjectDirectoryAsFile(String relativeProjectDirectory) {
         // found resource inside jar
         File fileAsInternalResource = getProjectDirectoryJarMode(relativeProjectDirectory);
         if (fileAsInternalResource != null && fileAsInternalResource.exists()) {
-            log.info("Running as jar. Found resource: " + fileAsExternalResource.getAbsolutePath());
+            log.info("Running as jar. Found resource: " + fileAsInternalResource.getAbsolutePath());
             return fileAsInternalResource;
         }
 

core/src/main/java/org/imec/ivlab/core/util/TemplateEngineUtils.java

@@ -30,11 +30,11 @@ private TemplateEngineUtils() {
 
     public static String generate(Map<String, Object> ctx, String templateLocation) {
         VelocityContext context = new VelocityContext();
-        Iterator template = ctx.entrySet().iterator();
+        Iterator<Map.Entry<String, Object>> template = ctx.entrySet().iterator();
 
         while(template.hasNext()) {
-            Map.Entry writer = (Map.Entry)template.next();
-            context.put((String)writer.getKey(), writer.getValue());
+            Map.Entry<String, Object> writer = template.next();
+            context.put(writer.getKey(), writer.getValue());
         }
 
         if (!templateCache.containsKey(templateLocation)) {

core/src/main/java/org/imec/ivlab/core/vaccination/VaccinationMappingReader.java

@@ -15,7 +15,7 @@
 import java.util.Map;
 import java.util.stream.Collectors;
 import lombok.Getter;
-import lombok.extern.log4j.Log4j2;
+//import lombok.extern.log4j.Log4j2;
 import org.apache.poi.ss.usermodel.Cell;
 import org.apache.poi.ss.usermodel.Row;
 import org.apache.poi.ss.usermodel.Row.MissingCellPolicy;
@@ -24,7 +24,7 @@
 import org.apache.poi.xssf.usermodel.XSSFWorkbook;
 import org.imec.ivlab.core.util.IOUtils;
 
-@Log4j2
+//@Log4j2
 @Getter
 public class VaccinationMappingReader {
 

core/src/test/java/org/imec/ivlab/core/model/evsref/extractor/impl/DiaryNoteEVSRefExtractorTest.java

@@ -22,10 +22,10 @@
 import be.fgov.ehealth.standards.kmehr.schema.v1.Kmehrmessage;
 import be.fgov.ehealth.standards.kmehr.schema.v1.TextWithLayoutType;
 import be.fgov.ehealth.standards.kmehr.schema.v1.TransactionType;
-import lombok.extern.log4j.Log4j2;
+//import lombok.extern.log4j.Log4j2;
 
 @Test
-@Log4j2
+//@Log4j2
 public class DiaryNoteEVSRefExtractorTest extends TestCase {
 
   private EVSREF evsref = new EVSREF("TESTREF");

datagenerator/src/main/java/org/imec/ivlab/datagenerator/audittrail/AuditTrailLogger.java

@@ -38,22 +38,21 @@ public void logPatientAuditTrail(Patient patient, String actorId) throws Gateway
 
         if (patientAuditTrail == null || patientAuditTrail.getTransactionaccesslist() == null || patientAuditTrail.getTransactionaccesslist().getTransactionaccesses() == null) {
             LOG.info("No audit trail found for patient: " + patient.inReadableFormat());
-        }
-
-        for (Transactionaccess transactionaccess : patientAuditTrail.getTransactionaccesslist().getTransactionaccesses()) {
-            LOG.info("------------- Audit trail entry -------------");
-            LOG.info("accessed at: " + transactionaccess.getAccessdatetime());
-            if (transactionaccess.getHcparties() != null) {
-                for (HcpartyType hcpartyType : transactionaccess.getHcparties()) {
-                    LOG.info("Accessed by: " + org.imec.ivlab.core.util.StringUtils.joinWith(" ", hcpartyType.getFirstname(), hcpartyType.getFamilyname(), hcpartyType.getName()));
+        } else {
+            for (Transactionaccess transactionaccess : patientAuditTrail.getTransactionaccesslist().getTransactionaccesses()) {
+                LOG.info("------------- Audit trail entry -------------");
+                LOG.info("accessed at: " + transactionaccess.getAccessdatetime());
+                if (transactionaccess.getHcparties() != null) {
+                    for (HcpartyType hcpartyType : transactionaccess.getHcparties()) {
+                        LOG.info("Accessed by: " + org.imec.ivlab.core.util.StringUtils.joinWith(" ", hcpartyType.getFirstname(), hcpartyType.getFamilyname(), hcpartyType.getName()));
+                    }
                 }
+                LOG.info("break the glass info: " + transactionaccess.getBreaktheglass());
+                LOG.info("patient: " + transactionaccess.getPatient().getIds().get(0).getValue());
+                LOG.info("transaction: " + transactionaccess.getTransaction().getIds().get(0).getValue());
             }
-            LOG.info("break the glass info: " + transactionaccess.getBreaktheglass());
-            LOG.info("patient: " + transactionaccess.getPatient().getIds().get(0).getValue());
-            LOG.info("transaction: " + transactionaccess.getTransaction().getIds().get(0).getValue());
         }
 
-
     }
 
 }

datagenerator/src/main/java/org/imec/ivlab/datagenerator/exporter/VaultExporterRunnable.java

@@ -77,7 +77,7 @@ public void run() {
 
         boolean incurableErrorOccurred = false;
         Throwable incurableError = null;
-        boolean breakTheGlass = false;
+        //boolean breakTheGlass = false;
 
         File outputDirectory = new File(exportInstruction.getExportDir().getAbsolutePath() + File.separator + monitorInstruction.getPatient().getKey());