Merge pull request #437 from buschlab/renovate/com.github.ngeor-check…

…style-rules-7.x Update dependency com.github.ngeor:checkstyle-rules to v7
buschlab · Sep 3, 2024 · a00bd65 · a00bd65
2 parents 0b9ab5f + eb74b8e
commit a00bd65
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Showing 16 changed files with 41 additions and 56 deletions.
diff --git a/pom.xml b/pom.xml
@@ -127,7 +127,7 @@
                   <dependency>
                     <groupId>com.github.ngeor</groupId>
                     <artifactId>checkstyle-rules</artifactId>
-                    <version>6.7.2</version>
+                    <version>7.0.0</version>
                   </dependency>
                 </dependencies>
                 <configuration>

diff --git a/src/main/java/fhirspark/JsonFhirMapper.java b/src/main/java/fhirspark/JsonFhirMapper.java
@@ -22,6 +22,16 @@
 import fhirspark.restmodel.Mtb;
 import fhirspark.restmodel.TherapyRecommendation;
 import fhirspark.settings.Settings;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Comparator;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
 import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
@@ -36,17 +46,6 @@
 import org.hl7.fhir.r4.model.RelatedArtifact;
 import org.hl7.fhir.r4.model.RelatedArtifact.RelatedArtifactType;
 
-import java.io.FileWriter;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Comparator;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
 /**
  * Fulfils the persistence in HL7 FHIR resources.
  */

diff --git a/src/main/java/fhirspark/adapter/ClinicalTrialAdapter.java b/src/main/java/fhirspark/adapter/ClinicalTrialAdapter.java
@@ -3,11 +3,10 @@
 import fhirspark.definitions.GenomicsReportingEnum;
 import fhirspark.definitions.UriEnum;
 import fhirspark.restmodel.ClinicalTrial;
-import org.hl7.fhir.r4.model.Coding;
-import org.hl7.fhir.r4.model.Observation.ObservationComponentComponent;
-
 import java.util.ArrayList;
 import java.util.List;
+import org.hl7.fhir.r4.model.Coding;
+import org.hl7.fhir.r4.model.Observation.ObservationComponentComponent;
 
 public final class ClinicalTrialAdapter {
 

diff --git a/src/main/java/fhirspark/adapter/FollowUpAdapter.java b/src/main/java/fhirspark/adapter/FollowUpAdapter.java
@@ -11,6 +11,11 @@
 import fhirspark.restmodel.TherapyRecommendation;
 import fhirspark.settings.Regex;
 import fhirspark.settings.Settings;
+import java.lang.reflect.InvocationTargetException;
+import java.text.SimpleDateFormat;
+import java.util.ArrayList;
+import java.util.Calendar;
+import java.util.List;
 import org.hl7.fhir.r4.model.Annotation;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.CodeableConcept;
@@ -22,12 +27,6 @@
 import org.hl7.fhir.r4.model.Practitioner;
 import org.hl7.fhir.r4.model.Reference;
 
-import java.lang.reflect.InvocationTargetException;
-import java.text.SimpleDateFormat;
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.List;
-
 public final class FollowUpAdapter {
 
     private static IGenericClient client;

diff --git a/src/main/java/fhirspark/adapter/MtbAdapter.java b/src/main/java/fhirspark/adapter/MtbAdapter.java
@@ -10,6 +10,12 @@
 import fhirspark.restmodel.TherapyRecommendation;
 import fhirspark.settings.Regex;
 import fhirspark.settings.Settings;
+import java.text.SimpleDateFormat;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.DiagnosticReport;
@@ -27,13 +33,6 @@
 import org.hl7.fhir.r4.model.Task.TaskIntent;
 import org.hl7.fhir.r4.model.Task.TaskStatus;
 
-import java.text.SimpleDateFormat;
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
 public final class MtbAdapter {
 
     private static IGenericClient client;

diff --git a/src/main/java/fhirspark/adapter/ReasoningAdapter.java b/src/main/java/fhirspark/adapter/ReasoningAdapter.java
@@ -7,19 +7,18 @@
 import fhirspark.restmodel.GeneticAlteration;
 import fhirspark.restmodel.Reasoning;
 import fhirspark.settings.Regex;
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.IdType;
 import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Reference;
 import org.hl7.fhir.r4.model.Resource;
 import org.hl7.fhir.r4.model.Specimen;
 
-import java.lang.reflect.InvocationTargetException;
-import java.lang.reflect.Method;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-
 public final class ReasoningAdapter {
 
     private ReasoningAdapter() {

diff --git a/src/main/java/fhirspark/adapter/RegexAdapter.java b/src/main/java/fhirspark/adapter/RegexAdapter.java
@@ -1,7 +1,6 @@
 package fhirspark.adapter;
 
 import fhirspark.settings.Regex;
-
 import java.util.List;
 
 public final class RegexAdapter {

diff --git a/src/main/java/fhirspark/adapter/SpecimenAdapter.java b/src/main/java/fhirspark/adapter/SpecimenAdapter.java
@@ -3,15 +3,14 @@
 import fhirspark.definitions.GenomicsReportingEnum;
 import fhirspark.definitions.Hl7TerminologyEnum;
 import fhirspark.settings.Regex;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
 import org.hl7.fhir.r4.model.IdType;
 import org.hl7.fhir.r4.model.Identifier;
 import org.hl7.fhir.r4.model.Reference;
 import org.hl7.fhir.r4.model.Specimen;
 
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
 /**
  * Builds a HL7 FHIR Speciment object with the provided specimen id.
  */

diff --git a/src/main/java/fhirspark/adapter/TherapyRecommendationAdapter.java b/src/main/java/fhirspark/adapter/TherapyRecommendationAdapter.java
@@ -11,6 +11,10 @@
 import fhirspark.restmodel.TherapyRecommendation;
 import fhirspark.restmodel.Treatment;
 import fhirspark.settings.Regex;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
 import org.hl7.fhir.r4.model.Annotation;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Coding;
@@ -29,11 +33,6 @@
 import org.hl7.fhir.r4.model.ResearchStudy;
 import org.hl7.fhir.r4.model.codesystems.ObservationCategory;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Map;
-
 public final class TherapyRecommendationAdapter {
 
     private static PubmedPublication pubmedResolver = new PubmedPublication();

diff --git a/src/main/java/fhirspark/adapter/clinicaldata/ClinicalDataAdapter.java b/src/main/java/fhirspark/adapter/clinicaldata/ClinicalDataAdapter.java
@@ -3,12 +3,11 @@
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import fhirspark.restmodel.ClinicalDatum;
 import fhirspark.settings.Regex;
+import java.util.List;
 import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Reference;
 import org.hl7.fhir.r4.model.Resource;
 
-import java.util.List;
-
 /**
  * General interface for all adapters of clinical data.
  */

diff --git a/src/main/java/fhirspark/adapter/clinicaldata/GenericAdapter.java b/src/main/java/fhirspark/adapter/clinicaldata/GenericAdapter.java
@@ -6,6 +6,7 @@
 import fhirspark.definitions.LoincEnum;
 import fhirspark.restmodel.ClinicalDatum;
 import fhirspark.settings.Regex;
+import java.util.List;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.CodeableConcept;
 import org.hl7.fhir.r4.model.Observation;
@@ -14,8 +15,6 @@
 import org.hl7.fhir.r4.model.Resource;
 import org.hl7.fhir.r4.model.Specimen;
 
-import java.util.List;
-
 /**
  * Generic adapter for clinical data. Also fallback if other adapter was not
  * found.

diff --git a/src/main/java/fhirspark/resolver/HgncGeneName.java b/src/main/java/fhirspark/resolver/HgncGeneName.java
@@ -3,7 +3,6 @@
 import com.fasterxml.jackson.dataformat.csv.CsvMapper;
 import com.fasterxml.jackson.dataformat.csv.CsvSchema;
 import fhirspark.resolver.model.Genenames;
-
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.util.HashMap;

diff --git a/src/main/java/fhirspark/resolver/OncoKbDrug.java b/src/main/java/fhirspark/resolver/OncoKbDrug.java
@@ -3,7 +3,6 @@
 import com.fasterxml.jackson.core.type.TypeReference;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import fhirspark.resolver.model.Drug;
-
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.util.HashMap;

diff --git a/src/main/java/fhirspark/resolver/PubmedPublication.java b/src/main/java/fhirspark/resolver/PubmedPublication.java
@@ -8,9 +8,8 @@
 import com.sun.jersey.api.client.ClientResponse;
 import com.sun.jersey.api.client.UniformInterfaceException;
 import com.sun.jersey.api.client.WebResource;
-import org.eclipse.jetty.http.HttpStatus;
-
 import java.io.IOException;
+import org.eclipse.jetty.http.HttpStatus;
 
 /**
  * Resolves the title of a pubmed publication if it was not provided.

diff --git a/src/main/java/fhirspark/settings/ConfigurationLoader.java b/src/main/java/fhirspark/settings/ConfigurationLoader.java
@@ -3,13 +3,12 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.dataformat.yaml.YAMLFactory;
 import com.google.common.io.ByteStreams;
-import org.apache.commons.text.StringSubstitutor;
-import org.apache.commons.text.lookup.StringLookupFactory;
-
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.UncheckedIOException;
 import java.nio.charset.StandardCharsets;
+import org.apache.commons.text.StringSubstitutor;
+import org.apache.commons.text.lookup.StringLookupFactory;
 
 /**
  * Class that enables the use of environment variables in the settings.yaml

diff --git a/src/main/java/fhirspark/settings/Settings.java b/src/main/java/fhirspark/settings/Settings.java
@@ -4,7 +4,6 @@
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonProperty;
 import com.fasterxml.jackson.annotation.JsonPropertyOrder;
-
 import java.util.List;
 
 /**