https://github.com/metadatacenter/cedar-project/issues/1198

metadatacenter · Nov 8, 2023 · 28599bc · 28599bc
1 parent 537b5c9
commit 28599bc
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Showing 21 changed files with 78 additions and 164 deletions.
diff --git a/...rc/main/java/org/metadatacenter/submission/resources/ImmPortSubmissionServerResource.java b/...rc/main/java/org/metadatacenter/submission/resources/ImmPortSubmissionServerResource.java
@@ -146,7 +146,7 @@ public Response immPortWorkspaces() throws CedarException {
     c.must(c.user()).be(LoggedIn);
 
     Optional<String> immPortBearerToken = immPortUtil.getImmPortBearerToken();
-    if (!immPortBearerToken.isPresent()) {
+    if (immPortBearerToken.isEmpty()) {
       logger.warn("Could not get an ImmPort token");
       return CedarResponse.status(CedarResponseStatus.INTERNAL_SERVER_ERROR).build();  // TODO CEDAR error response
     }
@@ -189,7 +189,7 @@ public Response submitImmPort() throws CedarException {
     c.must(c.user()).be(LoggedIn);
 
     Optional<String> immPortBearerToken = immPortUtil.getImmPortBearerToken();
-    if (!immPortBearerToken.isPresent()) {
+    if (immPortBearerToken.isEmpty()) {
       logger.warn("No ImmPort token found");
       return CedarResponse.status(CedarResponseStatus.INTERNAL_SERVER_ERROR).build(); // TODO CEDAR error response
     }
@@ -275,7 +275,7 @@ public Response submitImmPortOld() throws CedarException {
     }
 
     Optional<String> immPortBearerToken = immPortUtil.getImmPortBearerToken();
-    if (!immPortBearerToken.isPresent()) {
+    if (immPortBearerToken.isEmpty()) {
       logger.warn("No ImmPort token found");
       return CedarResponse.status(CedarResponseStatus.INTERNAL_SERVER_ERROR).build(); // TODO CEDAR error response
     }

diff --git a/cedar-submission-server-core/pom.xml b/cedar-submission-server-core/pom.xml
@@ -47,8 +47,8 @@
     </dependency>
 
     <dependency>
-      <groupId>org.apache.httpcomponents</groupId>
-      <artifactId>httpclient</artifactId>
+      <groupId>org.apache.httpcomponents.client5</groupId>
+      <artifactId>httpclient5</artifactId>
     </dependency>
 
     <dependency>

diff --git a/...bmission-server-core/src/main/java/org/metadatacenter/submission/immport/ImmPortUtil.java b/...bmission-server-core/src/main/java/org/metadatacenter/submission/immport/ImmPortUtil.java
@@ -56,7 +56,7 @@ public SubmissionStatus getImmPortSubmissionStatus(String submissionID) {
     CloseableHttpClient client = null;
 
     Optional<String> token = getImmPortBearerToken();
-    if (!token.isPresent()) {
+    if (token.isEmpty()) {
       logger.warn("Could not get an ImmPort token");
       return new SubmissionStatus(submissionID, SubmissionState.ERROR, "Could not get an ImmPort token");
     }
@@ -109,11 +109,11 @@ public Optional<String> getImmPortBearerToken() {
         ImmPortGetTokenResponse immPortGetTokenResponse = MAPPER
             .readValue(entity.getContent(), ImmPortGetTokenResponse.class);
 
-        if (immPortGetTokenResponse.getStatus().intValue() == 200) {
+        if (immPortGetTokenResponse.getStatus() == 200) {
           return Optional.of(immPortGetTokenResponse.getToken());
         } else {
           logger.warn("Failed to get token from host " + submissionUrl + "; ImmPort status code="
-              + immPortGetTokenResponse.getStatus().intValue() + ", error=" + immPortGetTokenResponse.getError());
+              + immPortGetTokenResponse.getStatus() + ", error=" + immPortGetTokenResponse.getError());
           return Optional.empty();
         }
       } else {

diff --git a/...e/src/main/java/org/metadatacenter/submission/ncbi/pipelines/NcbiPipelinesCommonUtil.java b/...e/src/main/java/org/metadatacenter/submission/ncbi/pipelines/NcbiPipelinesCommonUtil.java
@@ -104,11 +104,10 @@ public static List<String> extractSraFileNames(JsonNode instance, String sraElem
 
     for (JsonNode sra : sras) {
 
-      if (sra.hasNonNull(sraFieldNameField) && sra.get(sraFieldNameField).size() > 0) {
-        Iterator<JsonNode> fileNameFieldsIt = sra.get(sraFieldNameField).iterator();
+      if (sra.hasNonNull(sraFieldNameField) && !sra.get(sraFieldNameField).isEmpty()) {
 
-        while (fileNameFieldsIt.hasNext()) {
-          String fileNameField = fileNameFieldsIt.next().asText();
+        for (JsonNode jsonNode : sra.get(sraFieldNameField)) {
+          String fileNameField = jsonNode.asText();
           Optional<String> fileName = NcbiPipelinesCommonUtil.getTemplateFieldValue(sra, fileNameField);
           sraFileNames.add(fileName.get());
         }

diff --git a/.../main/java/org/metadatacenter/submission/ncbi/pipelines/NcbiPipelinesCommonValidator.java b/.../main/java/org/metadatacenter/submission/ncbi/pipelines/NcbiPipelinesCommonValidator.java
@@ -4,8 +4,6 @@
 
 import java.util.*;
 
-import static org.metadatacenter.submission.ncbi.pipelines.cairr.NcbiCairrConstants.*;
-
 public class NcbiPipelinesCommonValidator {
 
   public static List<String> validateBioproject(JsonNode bioproject, List<String> bioprojectFields, List<String> bioprojectRequiredFieldValues) {
@@ -39,11 +37,10 @@ public static List<String> validateSra(JsonNode sras, List<String> sraFields, St
         }
       }
       // File type and file names
-      Iterator<JsonNode> fileNamesIt = sra.get(sraFileNameField).iterator();
-      while (fileNamesIt.hasNext()) {
-        String fileNameField = fileNamesIt.next().asText();
+      for (JsonNode jsonNode : sra.get(sraFileNameField)) {
+        String fileNameField = jsonNode.asText();
         Optional<String> fileName = NcbiPipelinesCommonUtil.getTemplateFieldValue(sra, fileNameField);
-        if (!fileName.isPresent()) {
+        if (fileName.isEmpty()) {
           messages.add("File name field not present: " + fileNameField);
         }
       }

diff --git a/.../src/main/java/org/metadatacenter/submission/ncbi/pipelines/cairr/NcbiCairrConstants.java b/.../src/main/java/org/metadatacenter/submission/ncbi/pipelines/cairr/NcbiCairrConstants.java
@@ -34,19 +34,19 @@ public class NcbiCairrConstants {
 
 
   protected static final List<String> BIOPROJECT_FIELDS =
-      Collections.unmodifiableList(Arrays.asList(
+      List.of(
           BIOPROJECT_STUDY_ID_FIELD,
           BIOPROJECT_CONTACT_INFO_FIELD,
           BIOPROJECT_LAB_NAME_FIELD
-      ));
+      );
 
 
   protected static final List<String> BIOPROJECT_REQUIRED_FIELD_VALUES =
-      Collections.unmodifiableList(Arrays.asList(
+      List.of(
           BIOPROJECT_STUDY_ID_FIELD,
           BIOPROJECT_CONTACT_INFO_FIELD,
           BIOPROJECT_LAB_NAME_FIELD
-      ));
+      );
 
   /*** BioSample section ***/
   // Subject
@@ -97,7 +97,7 @@ public class NcbiCairrConstants {
   protected static final String BIOSAMPLE_OPTIONAL_ATTRIBUTE_FIELD = "Optional BioSample Attribute";
 
   protected static final List<String> BIOSAMPLE_FIELDS =
-      Collections.unmodifiableList(Arrays.asList(
+      List.of(
           BIOSAMPLE_SUBJECT_ID_FIELD,
           BIOSAMPLE_SYNTHETIC_LIBRARY_FIELD,
           BIOSAMPLE_ORGANISM_FIELD,
@@ -138,10 +138,10 @@ public class NcbiCairrConstants {
           BIOSAMPLE_CELL_ISOLATION_FIELD,
           BIOSAMPLE_PROCESSING_PROTOCOL_FIELD,
           BIOSAMPLE_OPTIONAL_ATTRIBUTE_FIELD
-      ));
+      );
 
   protected static final List<String> BIOSAMPLE_REQUIRED_FIELD_VALUES =
-      Collections.unmodifiableList(Arrays.asList(
+      List.of(
           BIOSAMPLE_SUBJECT_ID_FIELD,
           BIOSAMPLE_SYNTHETIC_LIBRARY_FIELD,
           BIOSAMPLE_ORGANISM_FIELD,
@@ -180,7 +180,7 @@ public class NcbiCairrConstants {
           BIOSAMPLE_CELL_QUALITY_FIELD,
           BIOSAMPLE_CELL_ISOLATION_FIELD,
           BIOSAMPLE_PROCESSING_PROTOCOL_FIELD
-      ));
+      );
 
   /*** SRA section ***/
   protected static final String SRA_ELEMENT = "Sequence Read Archive for AIRR NCBI";
@@ -211,7 +211,7 @@ public class NcbiCairrConstants {
   protected static final String SRA_FILE_TYPE_FIELD = "File Type";
   protected static final String SRA_FILE_NAME_FIELD = "filename";
 
-  protected static final List<String> SRA_FIELDS = Collections.unmodifiableList(Arrays.asList(
+  protected static final List<String> SRA_FIELDS = List.of(
       SRA_SAMPLE_ID_FIELD,
       SRA_TARGET_SUBSTRATE_FIELD,
       SRA_TARGET_SUBSTRATE_QUALITY_FIELD,
@@ -238,7 +238,7 @@ public class NcbiCairrConstants {
       SRA_SEQUENCING_KIT_FIELD,
       SRA_FILE_TYPE_FIELD,
       SRA_FILE_NAME_FIELD
-  ));
+  );
 
   protected static final List<String> SRA_REQUIRED_FIELD_VALUES = SRA_FIELDS;
 

diff --git a/...etadatacenter/submission/ncbi/pipelines/cairr/NcbiCairrTemplateInstance2XMLConverter.java b/...etadatacenter/submission/ncbi/pipelines/cairr/NcbiCairrTemplateInstance2XMLConverter.java
@@ -139,11 +139,9 @@ public String convertTemplateInstanceToXML(JsonNode instance) throws JAXBExcepti
 
         if (sra.hasNonNull(SRA_FILE_NAME_FIELD) && sra.get(SRA_FILE_NAME_FIELD).size() > 0) {
 
-          Iterator<JsonNode> fileNameFieldsIt = sra.get(SRA_FILE_NAME_FIELD).iterator();
+          for (JsonNode jsonNode : sra.get(SRA_FILE_NAME_FIELD)) {
 
-          while (fileNameFieldsIt.hasNext()) {
-
-            String fileNameField = fileNameFieldsIt.next().asText();
+            String fileNameField = jsonNode.asText();
 
             Optional<String> fileName = NcbiPipelinesCommonUtil.getTemplateFieldValue(sra, fileNameField);
 

diff --git a/.../main/java/org/metadatacenter/submission/ncbi/pipelines/generic/NcbiGenericConstants.java b/.../main/java/org/metadatacenter/submission/ncbi/pipelines/generic/NcbiGenericConstants.java
@@ -33,20 +33,20 @@ public class NcbiGenericConstants {
   protected static final String BIOPROJECT_RELEVANT_PUBLICATIONS_FIELD = "Relevant Publications";
 
   protected static final List<String> BIOPROJECT_FIELDS =
-      Collections.unmodifiableList(Arrays.asList(
+      List.of(
           BIOPROJECT_STUDY_ID_FIELD,
           BIOPROJECT_CONTACT_INFO_FIELD,
           BIOPROJECT_CONTACT_EMAIL_FIELD,
           BIOPROJECT_LAB_NAME_FIELD
-      ));
+      );
 
   protected static final List<String> BIOPROJECT_REQUIRED_FIELD_VALUES =
-      Collections.unmodifiableList(Arrays.asList(
+      List.of(
           BIOPROJECT_STUDY_ID_FIELD,
           BIOPROJECT_CONTACT_INFO_FIELD,
           BIOPROJECT_CONTACT_EMAIL_FIELD,
           BIOPROJECT_LAB_NAME_FIELD
-      ));
+      );
 
 
   /*** BioSample section ***/
@@ -78,7 +78,7 @@ public class NcbiGenericConstants {
   protected static final String BIOSAMPLE_DESCRIPTION_FIELD = "Sample Description";
 
   protected static final List<String> BIOSAMPLE_FIELDS =
-      Collections.unmodifiableList(Arrays.asList(
+      List.of(
           BIOSAMPLE_SAMPLE_NAME_FIELD,
           BIOSAMPLE_SAMPLE_TITLE_FIELD,
           BIOSAMPLE_ORGANISM_FIELD,
@@ -103,18 +103,18 @@ public class NcbiGenericConstants {
           BIOSAMPLE_SAMPLE_TYPE_FIELD,
           BIOSAMPLE_TREATMENT_FIELD,
           BIOSAMPLE_DESCRIPTION_FIELD
-      ));
+      );
 
   protected static final List<String> BIOSAMPLE_REQUIRED_FIELD_VALUES =
-      Collections.unmodifiableList(Arrays.asList(
+      List.of(
           BIOSAMPLE_SAMPLE_NAME_FIELD,
           BIOSAMPLE_ORGANISM_FIELD,
           BIOSAMPLE_ISOLATE_FIELD,
           BIOSAMPLE_AGE_FIELD,
           BIOSAMPLE_BIOMATERIAL_PROVIDER_FIELD,
           BIOSAMPLE_SEX_FIELD,
           BIOSAMPLE_TISSUE_FIELD
-      ));
+      );
 
   /*** SRA section ***/
   protected static final String SRA_ELEMENT = "NCBI SRA for Human Tissue";
@@ -132,7 +132,7 @@ public class NcbiGenericConstants {
   protected static final String SRA_FILE_NAME_FIELD = "File Name";
 
   protected static final List<String> SRA_FIELDS =
-      Collections.unmodifiableList(Arrays.asList(
+      List.of(
           SRA_SAMPLE_NAME_FIELD,
           SRA_LIBRARY_ID_FIELD,
           SRA_TITLE_FIELD,
@@ -145,10 +145,10 @@ public class NcbiGenericConstants {
           SRA_DESIGN_DESCRIPTION_FIELD,
           SRA_FILE_TYPE_FIELD,
           SRA_FILE_NAME_FIELD
-      ));
+      );
 
   protected static final List<String> SRA_REQUIRED_FIELD_VALUES =
-      Collections.unmodifiableList(Arrays.asList(
+      List.of(
           SRA_SAMPLE_NAME_FIELD,
           SRA_LIBRARY_ID_FIELD,
           SRA_TITLE_FIELD,
@@ -161,7 +161,7 @@ public class NcbiGenericConstants {
           SRA_DESIGN_DESCRIPTION_FIELD,
           SRA_FILE_TYPE_FIELD,
           SRA_FILE_NAME_FIELD
-      ));
+      );
 
   // PRIVATE //
 

diff --git a/...tadatacenter/submission/ncbi/pipelines/generic/NcbiGenericSubmissionXMLFileGenerator.java b/...tadatacenter/submission/ncbi/pipelines/generic/NcbiGenericSubmissionXMLFileGenerator.java
@@ -5,7 +5,6 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 import org.apache.commons.io.FileUtils;
 import org.metadatacenter.submission.ncbi.NcbiConstants;
-import org.metadatacenter.util.json.JsonMapper;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

diff --git a/...atacenter/submission/ncbi/pipelines/generic/NcbiGenericTemplateInstance2XMLConverter.java b/...atacenter/submission/ncbi/pipelines/generic/NcbiGenericTemplateInstance2XMLConverter.java
@@ -139,11 +139,9 @@ public String convertTemplateInstanceToXML(JsonNode instance) throws JAXBExcepti
 
         if (sra.hasNonNull(SRA_FILE_NAME_FIELD) && sra.get(SRA_FILE_NAME_FIELD).size() > 0) {
 
-          Iterator<JsonNode> fileNameFieldsIt = sra.get(SRA_FILE_NAME_FIELD).iterator();
+          for (JsonNode jsonNode : sra.get(SRA_FILE_NAME_FIELD)) {
 
-          while (fileNameFieldsIt.hasNext()) {
-
-            String fileNameField = fileNameFieldsIt.next().asText();
+            String fileNameField = jsonNode.asText();
 
             Optional<String> fileName = NcbiPipelinesCommonUtil.getTemplateFieldValue(sra, fileNameField);
 

diff --git a/...core/src/main/java/org/metadatacenter/submission/ncbi/queue/NcbiSubmissionQueueEvent.java b/...core/src/main/java/org/metadatacenter/submission/ncbi/queue/NcbiSubmissionQueueEvent.java
@@ -1,6 +1,5 @@
 package org.metadatacenter.submission.ncbi.queue;
 
-import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import org.metadatacenter.constant.CedarConstants;
 import org.metadatacenter.submission.ncbi.NcbiSubmission;
 

diff --git a/...er-core/src/main/java/org/metadatacenter/submission/ncbi/status/NcbiFtpStatusChecker.java b/...er-core/src/main/java/org/metadatacenter/submission/ncbi/status/NcbiFtpStatusChecker.java
@@ -75,7 +75,7 @@ public static SubmissionStatus getNcbiSubmissionStatus(String submissionID, FTPC
           SubmissionStatusDescriptor submissionStatusDescriptor = SubmissionStatusManager.getInstance()
               .getCurrentSubmissions().get(submissionID);
           NcbiSubmissionStatusTask statusTask = (NcbiSubmissionStatusTask) submissionStatusDescriptor
-              .getSubmissionStatusTask();
+              .submissionStatusTask();
           statusTask.setLastStatusReportFile(mostRecentReportFileName.get());
 
           // generate submission status from the most recent report file
@@ -86,7 +86,7 @@ public static SubmissionStatus getNcbiSubmissionStatus(String submissionID, FTPC
           logger.info(submissionStatus.toString());
         } else { // the report file has already been checked so the status will be the same
           submissionStatus =
-              SubmissionStatusManager.getInstance().getCurrentSubmissions().get(submissionID).getSubmissionStatus();
+              SubmissionStatusManager.getInstance().getCurrentSubmissions().get(submissionID).submissionStatus();
         }
       } else { // the folder does not contain any report file yet
         String message = SubmissionStatusUtil.getShortStatusMessage(submissionID, SubmissionState.PROCESSING)

diff --git a/...ore/src/main/java/org/metadatacenter/submission/ncbi/status/NcbiSubmissionStatusUtil.java b/...ore/src/main/java/org/metadatacenter/submission/ncbi/status/NcbiSubmissionStatusUtil.java
@@ -22,13 +22,13 @@ public class NcbiSubmissionStatusUtil {
 
   public static SubmissionStatus toSubmissionStatus(String submissionId, NcbiSubmissionStatusReport report) {
     SubmissionState submissionState = null;
-    if (report.getState().equals(NcbiSubmissionState.SUBMITTED)) {
+    if (report.state().equals(NcbiSubmissionState.SUBMITTED)) {
       submissionState = SubmissionState.PROCESSING;
-    } else if (report.getState().equals(NcbiSubmissionState.PROCESSING)) {
+    } else if (report.state().equals(NcbiSubmissionState.PROCESSING)) {
       submissionState = SubmissionState.PROCESSING;
-    } else if (report.getState().equals(NcbiSubmissionState.PROCESSED_ERROR)) {
+    } else if (report.state().equals(NcbiSubmissionState.PROCESSED_ERROR)) {
       submissionState = SubmissionState.ERROR;
-    } else if (report.getState().equals(NcbiSubmissionState.FAILED)) {
+    } else if (report.state().equals(NcbiSubmissionState.FAILED)) {
       submissionState = SubmissionState.REJECTED;
     }
     // TODO: complete with all NCBI states
@@ -37,7 +37,7 @@ public static SubmissionStatus toSubmissionStatus(String submissionId, NcbiSubmi
     }
 
     String message = SubmissionStatusUtil.getShortStatusMessage(submissionId, submissionState) +
-        "\nNCBI STATUS REPORT\n==================" + report.getTextReport();
+        "\nNCBI STATUS REPORT\n==================" + report.textReport();
 
     return new SubmissionStatus(submissionId, submissionState, message);
   }

diff --git a/...ain/java/org/metadatacenter/submission/ncbi/status/report/NcbiSubmissionStatusReport.java b/...ain/java/org/metadatacenter/submission/ncbi/status/report/NcbiSubmissionStatusReport.java
@@ -2,28 +2,9 @@
 
 /**
  * This class represents the submission status extracted from a report.[number].xml file
+ *
+ * @param textReport generated from the xml report
  */
-public class NcbiSubmissionStatusReport {
+public record NcbiSubmissionStatusReport(NcbiSubmissionState state, String xmlReport, String textReport) {
 
-  private final NcbiSubmissionState state;
-  private final String xmlReport;
-  private final String textReport; // generated from the xml report
-
-  public NcbiSubmissionStatusReport(NcbiSubmissionState state, String xmlReport, String textReport) {
-    this.state = state;
-    this.xmlReport = xmlReport;
-    this.textReport = textReport;
-  }
-
-  public NcbiSubmissionState getState() {
-    return state;
-  }
-
-  public String getXmlReport() {
-    return xmlReport;
-  }
-
-  public String getTextReport() {
-    return textReport;
-  }
 }
diff --git a/...-core/src/main/java/org/metadatacenter/submission/ncbi/validation/BioSampleValidator.java b/...-core/src/main/java/org/metadatacenter/submission/ncbi/validation/BioSampleValidator.java
@@ -14,7 +14,6 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import javax.ws.rs.core.Response;
 import javax.xml.bind.JAXBContext;
 import javax.xml.bind.JAXBException;
 import javax.xml.bind.Unmarshaller;
@@ -23,7 +22,6 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.PrintWriter;
-import java.text.ParseException;
 import java.util.ArrayList;
 import java.util.List;