Skip to content

Allow transformed run properties to be imported based on property name, label, or import alias #6025

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
cnathe merged 2 commits into from
Nov 6, 2024
Merged

Allow transformed run properties to be imported based on property name, label, or import alias #6025

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
34653ed
Allow transformed run properties to be imported based on property nam…
cnathe Nov 5, 2024
1c1ac92
Merge branch 'develop' into fb_transformRunPropAlias
cnathe Nov 5, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
23 changes: 15 additions & 8 deletions api/src/org/labkey/api/qc/TsvDataExchangeHandler.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@
import org.labkey.api.assay.TsvDataHandler;
import org.labkey.api.assay.actions.AssayRunUploadForm;
import org.labkey.api.assay.actions.ProtocolIdForm;
import org.labkey.api.collections.CaseInsensitiveHashMap;
import org.labkey.api.data.Container;
import org.labkey.api.data.TSVWriter;
import org.labkey.api.dataiterator.DataIterator;
Expand All @@ -49,6 +50,7 @@
import org.labkey.api.exp.api.ExperimentService;
import org.labkey.api.exp.property.Domain;
import org.labkey.api.exp.property.DomainProperty;
import org.labkey.api.exp.property.PropertyService;
import org.labkey.api.pipeline.PipeRoot;
import org.labkey.api.pipeline.PipelineService;
import org.labkey.api.query.PropertyValidationError;
Expand Down Expand Up @@ -1112,7 +1114,7 @@ else if (String.valueOf(row.get("name")).equalsIgnoreCase(Props.runDataUploadedF

if (transformedRunProps != null && transformedRunProps.exists())
{
transformedProps = new HashMap<>();
transformedProps = new CaseInsensitiveHashMap<>();
for (Map<String, Object> row : parseRunInfo(transformedRunProps))
{
String name = row.get("name") == null ? null : String.valueOf(row.get("name"));
Expand All @@ -1128,13 +1130,18 @@ else if (String.valueOf(row.get("name")).equalsIgnoreCase(Props.runDataUploadedF
Map<DomainProperty, String> runProperties = !result.getRunProperties().isEmpty() ? result.getRunProperties() : getRunProperties(context);
for (Map.Entry<DomainProperty, String> entry : runProperties.entrySet())
{
String propName = entry.getKey().getName();
if (transformedProps.containsKey(propName))
Set<String> propAliases = PropertyService.get().getDomainPropertyImportAliases(entry.getKey());
boolean transformedPropFound = false;
for (String propAlias : propAliases)
{
runProps.put(entry.getKey(), transformedProps.get(propName));
runPropTransformed = true;
if (transformedProps.containsKey(propAlias))
{
runProps.put(entry.getKey(), transformedProps.get(propAlias));
runPropTransformed = true;
transformedPropFound = true;
}
}
else
if (!transformedPropFound)
runProps.put(entry.getKey(), entry.getValue());
}

Expand Down Expand Up @@ -1165,8 +1172,8 @@ else if (String.valueOf(row.get("name")).equalsIgnoreCase(Props.runDataUploadedF
if (!runDataUploadedFiles.isEmpty())
result.setUploadedFiles(FileSystemLike.wrapFiles(runDataUploadedFiles));

// Don't offer up input or other files as "outputs" of the script
tempOutputFiles.removeAll(_filesToIgnore);
// Don't offer up input or other files as "outputs" of the script
tempOutputFiles.removeAll(_filesToIgnore);

processWarningsOutput(result, transformedProps, info, transErrorFile, transformedFile, tempOutputFiles);
}
Expand Down