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TASK-5858 - Fix alignment and coverage index analyses in blob storage #2416

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merged 7 commits into from
Apr 19, 2024
Merged

TASK-5858 - Fix alignment and coverage index analyses in blob storage #2416

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060c26f
analysis: improve alignment and coverage index by taking into account…
jtarraga Mar 14, 2024
57fbbe1
tests: add Junit tests, #TASK-5858
jtarraga Mar 25, 2024
c550fd3
client: generate clients, #TASK-5858
jtarraga Mar 25, 2024
f26c9e8
core: fix Integer conversion, #TASK-5858
jtarraga Mar 25, 2024
1e5f15b
analysis: remove jobID check from OpenCgaTool, #TASK-5858
jtarraga Mar 25, 2024
80a2e9a
Merge branch 'release-2.12.x' into TASK-5858
jtarraga Apr 16, 2024
313ae7f
Merge branch 'release-2.12.x' into TASK-5858
jtarraga Apr 17, 2024
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16 changes: 9 additions & 7 deletions ...alysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentCoverageAnalysis.java
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Original file line number Diff line number Diff line change
Expand Up @@ -168,20 +168,22 @@ protected void run() throws Exception {
+ ") was not create, please, check log files.");
}

// Try to copy the BW file into the BAM file directory
// Try to move the BW file into the BAM file directory
boolean moveSuccessful = false;
Path targetPath = Paths.get(bamCatalogFile.getUri()).getParent().resolve(bwPath.getFileName());
try {
Files.move(bwPath, targetPath);
Path movedPath = Files.move(bwPath, targetPath);
moveSuccessful = targetPath.equals(movedPath);
} catch (Exception e) {
// Do nothing
logger.info("Moving from {} to {}: {}", bwPath, targetPath, e.getMessage());
// Log message
logger.info("Error moving the coverage file into the BAM folder {} to {}", bwPath, targetPath, e);
}

if (targetPath.toFile().exists()) {
if (moveSuccessful) {
bwPath = targetPath;
logger.info("Coverage file was copied into the BAM folder: {}", bwPath);
logger.info("Coverage file was moved into the BAM folder: {}", bwPath);
} else {
logger.info("Couldn't copy the coverage file into the BAM folder. The coverage file is in the job folder instead: {}",
logger.info("Couldn't move the coverage file into the BAM folder. The coverage file is in the job folder instead: {}",
bwPath);
}

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16 changes: 9 additions & 7 deletions ...analysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentIndexOperation.java
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Original file line number Diff line number Diff line change
Expand Up @@ -85,20 +85,22 @@ protected void run() throws Exception {
throw new ToolException("Something wrong happened when computing index file for '" + inputFile + "'");
}

// Try to copy the BAI file into the BAM file directory
// Try to move the BAI file into the BAM file directory
boolean moveSuccessful = false;
Path targetPath = inputPath.getParent().resolve(outputPath.getFileName());
try {
Files.move(outputPath, targetPath);
Path movedPath = Files.move(outputPath, targetPath);
moveSuccessful = targetPath.equals(movedPath);
} catch (Exception e) {
// Do nothing
logger.info("Moving from {} to {}: {}", outputPath, targetPath, e.getMessage());
// Log message
logger.info("Error moving from {} to {}", outputPath, targetPath, e);
}

if (targetPath.toFile().exists()) {
if (moveSuccessful) {
outputPath = targetPath;
logger.info("Alignment index file was copied into the BAM folder: {}", outputPath);
logger.info("Alignment index file was moved into the BAM folder: {}", outputPath);
} else {
logger.info("Couldn't copy the alignment index file into the BAM folder. The index file is in the job folder instead: {}",
logger.info("Couldn't move the alignment index file into the BAM folder. The index file is in the job folder instead: {}",
outputPath);
}

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