From e4dfdd82c497d889dcb7c876f21080feef004a41 Mon Sep 17 00:00:00 2001 From: vagisha Date: Tue, 4 Feb 2025 14:32:03 -0800 Subject: [PATCH 1/3] Fix ExpRuns's FilePathRoot. --- experiment/src/org/labkey/experiment/XarReader.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/experiment/src/org/labkey/experiment/XarReader.java b/experiment/src/org/labkey/experiment/XarReader.java index 62ffa397eab..68a2187f54b 100644 --- a/experiment/src/org/labkey/experiment/XarReader.java +++ b/experiment/src/org/labkey/experiment/XarReader.java @@ -1109,7 +1109,8 @@ private void loadExperimentRun(ExperimentRunType a, List startingMa vals.setProtocolLSID(protocol.getLSID()); vals.setComments(trimString(a.getComments())); - vals.setFilePathRoot(FileUtil.getAbsolutePath(_xarSource.getRootPath())); // FileUtil.getAbsolutePath(runContext.getContainer(), _job.getPipeRoot().getRootNioPath())); + // vals.setFilePathRoot(FileUtil.getAbsolutePath(_xarSource.getRootPath())); // FileUtil.getAbsolutePath(runContext.getContainer(), _job.getPipeRoot().getRootNioPath())); + vals.setFilePathRoot(FileUtil.getAbsolutePath(runContext.getContainer(), _job.getPipeRoot().getRootNioPath())); vals.setContainer(getContainer()); String workflowTaskLSID = a.getWorkflowTaskLSID(); From d990456d1ae424742b71cececb5be65f36002287 Mon Sep 17 00:00:00 2001 From: vagisha Date: Wed, 5 Feb 2025 11:35:45 -0800 Subject: [PATCH 2/3] Added getJobRootPath() to XarSource. Use this to set the FilePathRoot on ExpRun. --- api/src/org/labkey/api/exp/XarSource.java | 2 ++ experiment/src/org/labkey/experiment/XarReader.java | 2 +- .../src/org/labkey/experiment/pipeline/MoveRunsTask.java | 9 +++++++++ 3 files changed, 12 insertions(+), 1 deletion(-) diff --git a/api/src/org/labkey/api/exp/XarSource.java b/api/src/org/labkey/api/exp/XarSource.java index 38ec6ec1868..1d0853be740 100644 --- a/api/src/org/labkey/api/exp/XarSource.java +++ b/api/src/org/labkey/api/exp/XarSource.java @@ -84,6 +84,8 @@ public XarSource(PipelineJob job) public abstract Path getRootPath(); + public Path getJobRootPath() { return getRootPath(); } + /** * Should be true if this was uploaded XML that was not part of a full XAR */ diff --git a/experiment/src/org/labkey/experiment/XarReader.java b/experiment/src/org/labkey/experiment/XarReader.java index 68a2187f54b..5f889f8f2c1 100644 --- a/experiment/src/org/labkey/experiment/XarReader.java +++ b/experiment/src/org/labkey/experiment/XarReader.java @@ -1110,7 +1110,7 @@ private void loadExperimentRun(ExperimentRunType a, List startingMa vals.setComments(trimString(a.getComments())); // vals.setFilePathRoot(FileUtil.getAbsolutePath(_xarSource.getRootPath())); // FileUtil.getAbsolutePath(runContext.getContainer(), _job.getPipeRoot().getRootNioPath())); - vals.setFilePathRoot(FileUtil.getAbsolutePath(runContext.getContainer(), _job.getPipeRoot().getRootNioPath())); + vals.setFilePathRoot(FileUtil.getAbsolutePath(_xarSource.getJobRootPath())); vals.setContainer(getContainer()); String workflowTaskLSID = a.getWorkflowTaskLSID(); diff --git a/experiment/src/org/labkey/experiment/pipeline/MoveRunsTask.java b/experiment/src/org/labkey/experiment/pipeline/MoveRunsTask.java index 1a5e8af2faa..2f3badf00c2 100644 --- a/experiment/src/org/labkey/experiment/pipeline/MoveRunsTask.java +++ b/experiment/src/org/labkey/experiment/pipeline/MoveRunsTask.java @@ -220,6 +220,15 @@ public Path getRootPath() return FileUtil.stringToPath(_sourceContainer, _root); } + @Override + public Path getJobRootPath() + { + var pipelineJob = getXarContext().getJob(); + return pipelineJob != null + ? FileUtil.stringToPath(getXarContext().getContainer(), pipelineJob.getPipeRoot().getRootFileLike().toNioPathForRead().toString()) + : getRootPath(); + } + @Override public boolean shouldIgnoreDataFiles() { From eca8bb20b1959d09834d349a5da98dccae23371a Mon Sep 17 00:00:00 2001 From: vagisha Date: Sun, 9 Feb 2025 13:02:53 -0800 Subject: [PATCH 3/3] CR changes --- experiment/src/org/labkey/experiment/XarReader.java | 1 - .../src/org/labkey/experiment/pipeline/MoveRunsTask.java | 4 ++-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/experiment/src/org/labkey/experiment/XarReader.java b/experiment/src/org/labkey/experiment/XarReader.java index 5f889f8f2c1..e7744f755f8 100644 --- a/experiment/src/org/labkey/experiment/XarReader.java +++ b/experiment/src/org/labkey/experiment/XarReader.java @@ -1109,7 +1109,6 @@ private void loadExperimentRun(ExperimentRunType a, List startingMa vals.setProtocolLSID(protocol.getLSID()); vals.setComments(trimString(a.getComments())); - // vals.setFilePathRoot(FileUtil.getAbsolutePath(_xarSource.getRootPath())); // FileUtil.getAbsolutePath(runContext.getContainer(), _job.getPipeRoot().getRootNioPath())); vals.setFilePathRoot(FileUtil.getAbsolutePath(_xarSource.getJobRootPath())); vals.setContainer(getContainer()); String workflowTaskLSID = a.getWorkflowTaskLSID(); diff --git a/experiment/src/org/labkey/experiment/pipeline/MoveRunsTask.java b/experiment/src/org/labkey/experiment/pipeline/MoveRunsTask.java index 2f3badf00c2..e36410dc529 100644 --- a/experiment/src/org/labkey/experiment/pipeline/MoveRunsTask.java +++ b/experiment/src/org/labkey/experiment/pipeline/MoveRunsTask.java @@ -225,8 +225,8 @@ public Path getJobRootPath() { var pipelineJob = getXarContext().getJob(); return pipelineJob != null - ? FileUtil.stringToPath(getXarContext().getContainer(), pipelineJob.getPipeRoot().getRootFileLike().toNioPathForRead().toString()) - : getRootPath(); + ? pipelineJob.getPipeRoot().getRootFileLike().toNioPathForRead() + : super.getJobRootPath(); } @Override