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Fix/sync #13

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merged 3 commits into from
Jan 21, 2024
Merged

Fix/sync #13

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f36852e
Added some additional logging
apetkau Jan 21, 2024
5fc5466
Added synchronized sections
apetkau Jan 21, 2024
623d54e
Named lock for published files
apetkau Jan 21, 2024
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1 change: 1 addition & 0 deletions plugins/nf-iridanext/src/main/nextflow/iridanext/IridaNextJSONOutput.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -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 {
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6 changes: 6 additions & 0 deletions plugins/nf-iridanext/src/main/nextflow/iridanext/IridaNextObserver.groovy
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Expand Up @@ -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
Expand Down Expand Up @@ -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 = []
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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")
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