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Adopt FileLike for more pipeline APIs #183

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Merged
labkey-jeckels merged 5 commits into from
Nov 5, 2025
Merged

Adopt FileLike for more pipeline APIs #183

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0bb0cd0
More file path improvements, mostly around pipeline jobs
labkey-jeckels Oct 18, 2025
e8be0dc
Test fixes,
labkey-jeckels Oct 19, 2025
4b1351d
More FileLike
labkey-jeckels Oct 21, 2025
68b1217
Merge branch 'develop' into fb_pipelineFileLike
labkey-jeckels Oct 27, 2025
fd6c856
Merge branch 'develop' into fb_pipelineFileLike
labkey-jeckels Oct 31, 2025
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27 changes: 9 additions & 18 deletions genotyping/src/org/labkey/genotyping/GenotypingController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -973,8 +973,8 @@ public boolean handlePost(ImportReadsForm form, BindException errors) throws Exc
{
if (null == form.getReadsPath())
{
File readsFile = form.getValidatedSingleFile(getContainer());
form.setReadsPath(readsFile.getPath());
FileLike readsFile = form.getValidatedSingleFile(getContainer());
form.setReadsPath(readsFile.toNioPathForRead().toFile().getPath());
return false;
}

Expand Down Expand Up @@ -1395,24 +1395,15 @@ public boolean handlePost(PipelinePathForm form, BindException errors) throws IO
{
Container container = getContainer();
// Manual upload of genotyping analysis; pipeline provider posts to this action with matches file.
Path singleFile = form.getValidatedSinglePath(container);
FileLike singleFile = form.getValidatedSingleFile(container);
FileLike analysisDir = singleFile.getParent();

if (form.getPipeRoot(container).getRootFileLike().isDescendant(singleFile.toUri()))
{

FileLike matches = form.getPipeRoot(container).resolvePathToFileLike(singleFile.toString());
FileLike analysisDir = matches.getParent();
// Load properties to determine the run.
Properties props = GenotypingManager.get().readProperties(analysisDir);
int analysisId = Integer.parseInt((String) props.get("analysis"));
importAnalysis(analysisId, analysisDir, getUser());

// Load properties to determine the run.
Properties props = GenotypingManager.get().readProperties(analysisDir);
int analysisId = Integer.parseInt((String) props.get("analysis"));
importAnalysis(analysisId, analysisDir, getUser());

return true;
}

errors.reject(ERROR_MSG, "File was not found under the pipeline root");
return false;
return true;
}

@Override
Expand Down
9 changes: 4 additions & 5 deletions genotyping/src/org/labkey/genotyping/Import454ReadsJob.java
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@

import com.fasterxml.jackson.annotation.JsonCreator;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Strings;
import org.labkey.api.data.DbScope;
import org.labkey.api.data.RuntimeSQLException;
import org.labkey.api.data.Table;
Expand Down Expand Up @@ -69,7 +69,7 @@ public Import454ReadsJob(ViewBackgroundInfo info, PipeRoot root, File reads, Gen
super(Import454ReadsPipelineProvider.NAME, info, root, run);
FileLike verifiedFileLike = FileSystemLike.getVerifiedFileLike(root.getContainer(), reads.getAbsolutePath());
_reads = FileSystemLike.toFile(verifiedFileLike);
setLogFile(verifiedFileLike.getParent().resolveChild(FileUtil.makeFileNameWithTimestamp("import_reads", "log")).toNioPathForWrite());
setLogFile(verifiedFileLike.getParent().resolveChild(FileUtil.makeFileNameWithTimestamp("import_reads", "log")));
}

@Override
Expand All @@ -91,7 +91,7 @@ public void run()
}
catch (SQLException se)
{
if (RuntimeSQLException.isConstraintException(se) && StringUtils.containsIgnoreCase(se.getMessage(), "uq_reads_name"))
if (RuntimeSQLException.isConstraintException(se) && Strings.CI.contains(se.getMessage(), "uq_reads_name"))
throw new RuntimeException("A readname in this file already exists in the database; this run may have been imported previously", se);
else
throw se;
Expand Down Expand Up @@ -126,8 +126,7 @@ private void importReads() throws IOException, SQLException, PipelineJobExceptio

try (TabLoader loader = new TabLoader(_reads, true))
{
List<ColumnDescriptor> columns = new ArrayList<>();
columns.addAll(Arrays.asList(loader.getColumns()));
List<ColumnDescriptor> columns = new ArrayList<>(Arrays.asList(loader.getColumns()));

for (ColumnDescriptor col : columns)
{
Expand Down
2 changes: 1 addition & 1 deletion genotyping/src/org/labkey/genotyping/ImportAnalysisJob.java
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Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,7 @@ public ImportAnalysisJob(ViewBackgroundInfo info, PipeRoot root, FileLike pipeli
super("Import Analysis", info, root);
_dir = pipelineDir;
_analysis = analysis;
setLogFile(_dir.resolveChild(FileUtil.makeFileNameWithTimestamp("import_analysis", "log")).toNioPathForWrite());
setLogFile(_dir.resolveChild(FileUtil.makeFileNameWithTimestamp("import_analysis", "log")));

if (!_dir.exists())
throw new IllegalArgumentException("Pipeline directory does not exist: " + _dir.toNioPathForRead().toAbsolutePath());
Expand Down
2 changes: 1 addition & 1 deletion genotyping/src/org/labkey/genotyping/ImportIlluminaReadsJob.java
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Original file line number Diff line number Diff line change
Expand Up @@ -77,7 +77,7 @@ public ImportIlluminaReadsJob(ViewBackgroundInfo info, PipeRoot root, File sampl
FileLike verifiedFileLike = FileSystemLike.getVerifiedFileLike(root.getContainer(), sampleFile.getAbsolutePath());
_sampleFile = FileSystemLike.toFile(verifiedFileLike);
_fastqPrefix = fastqPrefix;
setLogFile(verifiedFileLike.getParent().resolveChild(FileUtil.makeFileNameWithTimestamp("import_reads", "log")).toNioPathForWrite());
setLogFile(verifiedFileLike.getParent().resolveChild(FileUtil.makeFileNameWithTimestamp("import_reads", "log")));
}

@Override
Expand Down
2 changes: 1 addition & 1 deletion genotyping/src/org/labkey/genotyping/ImportPacBioReadsJob.java
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Original file line number Diff line number Diff line change
Expand Up @@ -73,7 +73,7 @@ public ImportPacBioReadsJob(ViewBackgroundInfo info, PipeRoot root, File sampleF
FileLike verifiedFileLike = FileSystemLike.getVerifiedFileLike(root.getContainer(), sampleFile.getAbsolutePath());
_sampleFile = FileSystemLike.toFile(verifiedFileLike);
_fastqPrefix = fastqPrefix;
setLogFile(verifiedFileLike.getParent().resolveChild(FileUtil.makeFileNameWithTimestamp("import_pacbio_reads", "log")).toNioPathForWrite());
setLogFile(verifiedFileLike.getParent().resolveChild(FileUtil.makeFileNameWithTimestamp("import_pacbio_reads", "log")));
}

@Override
Expand Down
2 changes: 1 addition & 1 deletion genotyping/src/org/labkey/genotyping/SubmitAnalysisJob.java
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Original file line number Diff line number Diff line change
Expand Up @@ -110,7 +110,7 @@ public SubmitAnalysisJob(ViewBackgroundInfo info, PipeRoot root, FileLike reads,
throw new MinorConfigurationException("Can't create analysis directory: " + _analysisDir.getPath());
}

setLogFile(_analysisDir.resolveChild(FileUtil.makeFileNameWithTimestamp("submit_analysis", "log")).toNioPathForWrite());
setLogFile(_analysisDir.resolveChild(FileUtil.makeFileNameWithTimestamp("submit_analysis", "log")));
info("Creating analysis directory: " + _analysisDir.getName());
_analysis.setPath(FileUtil.getAbsolutePath(_analysisDir.toNioPathForRead()));
_analysis.setFileName(_analysisDir.getName());
Expand Down