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Avoid copying referenceStudy on dev machines where source root and pipeline root match #244

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Merged
labkey-jeckels merged 2 commits into from
Sep 30, 2021
Merged

Avoid copying referenceStudy on dev machines where source root and pipeline root match #244

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cc3a12e
Avoid infinite recursion on dev machines when pipeline root is pointe…
Sep 30, 2021
c908ddf
DirectoryResource instead of FileResource
Sep 30, 2021
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27 changes: 21 additions & 6 deletions ehr/src/org/labkey/ehr/EHRServiceImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -58,6 +58,8 @@
import org.labkey.api.query.FieldKey;
import org.labkey.api.query.QueryService;
import org.labkey.api.query.UserSchema;
import org.labkey.api.resource.DirectoryResource;
import org.labkey.api.resource.FileResource;
import org.labkey.api.resource.Resource;
import org.labkey.api.security.SecurableResource;
import org.labkey.api.security.SecurityPolicy;
Expand Down Expand Up @@ -866,16 +868,29 @@ public void importStudyDefinition(Container container, User user, Module m, Path
Resource root = m.getModuleResource(sourceStudyDirPath);
PipeRoot pipeRoot = PipelineService.get().findPipelineRoot(container);
java.nio.file.Path pipeRootPath = pipeRoot.getRootNioPath();
java.nio.file.Path studyPath = pipeRootPath.resolve("upgradeStudyImport");
if (Files.exists(studyPath))

java.nio.file.Path studyXmlPath;

if (root instanceof DirectoryResource && ((DirectoryResource)root).getDir().equals(pipeRootPath.toFile()))
{
// The pipeline root is already pointed at the study definition's folder, like it might be on a dev machine.
// No need to copy, especially since copying can cause infinite recursion when the paths are nested
studyXmlPath = pipeRootPath.resolve("study.xml");
}
else
{
FileUtil.deleteDir(studyPath);
java.nio.file.Path studyPath = pipeRootPath.resolve("moduleStudyImport");
studyXmlPath = studyPath.resolve("study.xml");
if (Files.exists(studyPath))
{
FileUtil.deleteDir(studyPath);
}
copyResourceToPath(root, studyPath);
}
copyResourceToPath(root, studyPath);
java.nio.file.Path studyXmlPath = studyPath.resolve("study.xml");

if (!Files.exists(studyXmlPath))
{
throw new FileNotFoundException("Couldn't find an extracted " + studyPath);
throw new FileNotFoundException("Couldn't find an extracted " + studyXmlPath);
}
ImportOptions options = new ImportOptions(container.getId(), user.getUserId());
options.setSkipQueryValidation(true);
Expand Down