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Fix file processor running on files that are on unfinished upload runs. #1506

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merged 6 commits into from
Dec 14, 2023
Merged

Fix file processor running on files that are on unfinished upload runs. #1506

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94c5068
first cut
JeffreyThiessen Dec 13, 2023
f7a1942
fix working
JeffreyThiessen Dec 13, 2023
50a1b97
remove comment
JeffreyThiessen Dec 13, 2023
173053f
Use list filter instead of if inside loop
JeffreyThiessen Dec 13, 2023
9f07657
Merge branch 'main' of github.com:phac-nml/irida into fix_early_file_…
JeffreyThiessen Dec 14, 2023
997fa5e
update changelog
JeffreyThiessen Dec 14, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -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)
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7 changes: 7 additions & 0 deletions .../java/ca/corefacility/bioinformatics/irida/service/SequencingObjectProcessingService.java
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@@ -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;
Expand Down Expand Up @@ -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();

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