Merge pull request #1506 from phac-nml/fix_early_file_processor

Fix file processor running on files that are on unfinished upload runs.

CHANGELOG.md

@@ -3,6 +3,7 @@
 # [23.10.1] - 2023/12/07
 * [UI]: Fixed issue where filter inputs required focus when they are opened on the project samples page. See [PR 1503](https://github.com/phac-nml/irida/pull/1503)
 * [UI]: Fixed bug preventing sorting and paging on the project members page. See [PR 1504](https://github.com/phac-nml/irida/pull/1504)
+* [Developer]: Fixed race condition where FastQC file processor would start on incomplete file by filtering out files on non complete sequencing runs. [PR 1506](https://github.com/phac-nml/irida/pull/1506)
 
 ## [23.10] - 2023/10/15
 * [Developer]: Added functionality to delete sequence files from file system when a sequence run is removed. [See PR 1468](https://github.com/phac-nml/irida/pull/1468)

src/main/java/ca/corefacility/bioinformatics/irida/service/SequencingObjectProcessingService.java

@@ -1,6 +1,7 @@
 package ca.corefacility.bioinformatics.irida.service;
 
 import ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject;
+import ca.corefacility.bioinformatics.irida.model.enums.SequencingRunUploadStatus;
 import ca.corefacility.bioinformatics.irida.processing.FileProcessingChain;
 import ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequencingObjectRepository;
 import ca.corefacility.bioinformatics.irida.service.impl.processor.SequenceFileProcessorLauncher;
@@ -66,6 +67,12 @@ public synchronized void findFilesToProcess() {
 		List<SequencingObject> toProcess = sequencingObjectRepository
 				.getSequencingObjectsWithProcessingState(SequencingObject.ProcessingState.UNPROCESSED);
 
+		// filter out sequencing objects on a SequencingRun that is not in a COMPLETE state
+		toProcess.removeIf(seqObj -> (
+				(seqObj.getSequencingRun() != null) &&
+				(!seqObj.getSequencingRun().getUploadStatus().equals(SequencingRunUploadStatus.COMPLETE))
+		));
+
 		// individually loop through and mark the ones we're going to process.  Looping individually so 2 processes are less likely to write at the same time.
 		Iterator<SequencingObject> iterator = toProcess.iterator();