Merge pull request #13 from phac-nml/fix/sync

Fix/sync
phac-nml · Jan 21, 2024 · fd24a76 · fd24a76
2 parents ea264b6 + 623d54e
commit fd24a76
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diff --git a/plugins/nf-iridanext/src/main/nextflow/iridanext/IridaNextJSONOutput.groovy b/plugins/nf-iridanext/src/main/nextflow/iridanext/IridaNextJSONOutput.groovy
@@ -170,6 +170,7 @@ class IridaNextJSONOutput {
         try {
             // validate all JSON against passed schema prior to writing
             if (validate && jsonSchema != null) {
+                log.debug "Validating IRIDA Next output against schema ${jsonSchema.getUri()} prior to writing to ${path}"
                 validateJson(jsonString)
                 log.debug "Validation successfull against schema ${jsonSchema.getUri()} for JSON prior to writing to ${path}"
             } else {

diff --git a/plugins/nf-iridanext/src/main/nextflow/iridanext/IridaNextObserver.groovy b/plugins/nf-iridanext/src/main/nextflow/iridanext/IridaNextObserver.groovy
@@ -24,6 +24,7 @@ import java.nio.file.PathMatcher
 import java.net.URI
 
 import groovy.transform.CompileStatic
+import groovy.transform.Synchronized
 import groovy.util.logging.Slf4j
 import groovy.json.JsonOutput
 import nextflow.Session
@@ -51,6 +52,8 @@ import nextflow.iridanext.MetadataParserJSON
 @Slf4j
 @CompileStatic
 class IridaNextObserver implements TraceObserver {
+    private static final tasksLock = new Object[0]
+    private static final publishedFilesLock = new Object[0]
 
     private Map<Path,Path> publishedFiles = [:]
     private List<TaskRun> tasks = []
@@ -98,13 +101,15 @@ class IridaNextObserver implements TraceObserver {
     }
 
     @Override
+    @Synchronized("tasksLock")
     void onProcessComplete(TaskHandler handler, TraceRecord trace) {
         log.trace "onProcessComplete: ${handler.task}"
         tasks << handler.task
         traces << trace
     }
 
     @Override
+    @Synchronized("tasksLock")
     void onProcessCached(TaskHandler handler, TraceRecord trace) {
         log.trace "onProcessCached: ${handler.task}"
         tasks << handler.task
@@ -217,6 +222,7 @@ class IridaNextObserver implements TraceObserver {
     }
 
     @Override
+    @Synchronized("publishedFilesLock")
     void onFilePublish(Path destination, Path source) {
         if (publishedFiles.containsKey(source)) {
             throw new Exception("Error: file with source=${source} was already published")