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Prevent shared EHR properties from moving out of /Shared #168

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Merged
labkey-jeckels merged 1 commit into from
Apr 18, 2021
Merged

Prevent shared EHR properties from moving out of /Shared #168

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80 changes: 37 additions & 43 deletions ehr/src/org/labkey/ehr/EHRManager.java
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Original file line number Diff line number Diff line change
Expand Up @@ -488,21 +488,20 @@ public List<String> ensureDatasetPropertyDescriptors(Container c, User u, boolea

List<? extends Dataset> datasets = study.getDatasets();

// Hack - adding a shared EHR property to a domain ends up reparenting it to the EHR folder. They
// need to keep living in the /Shared project. Rather than introducing a brand new API for adding a shared
// PD to an existing domain, we'll directly update the owning container afterwards
Set<PropertyDescriptor> pdsToReparentInShared = new HashSet<>();

for (Dataset dataset : datasets)
{
Domain domain = dataset.getDomain();
List<? extends DomainProperty> dprops = domain.getProperties();
if (dprops == null)
{
_log.error("domain.getProperties() was null for: " + domain.getName());
continue;
}

boolean changed = false;
List<PropertyDescriptor> toUpdate = new ArrayList<>();

List<PropertyDescriptor> props = new ArrayList<>();
props.addAll(properties);
List<PropertyDescriptor> props = new ArrayList<>(properties);
if (dataset.getCategory() != null && dataset.getCategory().equals("ClinPath") && !dataset.getName().equalsIgnoreCase("Clinpath Runs"))
{
String propertyURI = EHRProperties.RUNID.getPropertyDescriptor().getPropertyURI();
Expand Down Expand Up @@ -555,11 +554,6 @@ public List<String> ensureDatasetPropertyDescriptors(Container c, User u, boolea
}
}

// if (!pd.getContainer().equals(dp.getContainer()) && !pd.getProject().equals(ContainerManager.getSharedContainer()))
// {
// messages.add("Containers do not match for: " + dp.getName() + ". Expected: " + dp.getContainer().getPath() + ", but was: " + pd.getContainer().getPath() + ".");
// }

if (!dp.getName().equals(pd.getName()))
{
messages.add("Case mismatch for property in dataset: " + dataset.getName() + ". Expected: " + pd.getName() + ", but was: " + dp.getName() + ". This has not been automatically changed");
Expand All @@ -576,6 +570,7 @@ public List<String> ensureDatasetPropertyDescriptors(Container c, User u, boolea
d.setPropertyURI(pd.getPropertyURI());
d.setRangeURI(pd.getRangeURI());
d.setName(pd.getName());
pdsToReparentInShared.add(pd);
changed = true;
}
}
Expand Down Expand Up @@ -611,19 +606,27 @@ public List<String> ensureDatasetPropertyDescriptors(Container c, User u, boolea
}
}

if (commitChanges)
{
for (PropertyDescriptor sharedPD : pdsToReparentInShared)
{
sharedPD.setContainer(ContainerManager.getSharedContainer());
sharedPD.setProject(ContainerManager.getSharedContainer());
OntologyManager.updatePropertyDescriptor(sharedPD);
}
}

//ensure keymanagement type
if (commitChanges)
{
DbSchema studySchema = DbSchema.get("study");
SQLFragment sql = new SQLFragment("UPDATE study.dataset SET keymanagementtype=?, keypropertyname=? WHERE demographicdata=? AND container=?", "GUID", "objectid", false, c.getEntityId());
long total = new SqlExecutor(studySchema).execute(sql);
long total = new SqlExecutor(StudyService.get().getDatasetSchema()).execute(sql);
messages.add("Non-demographics datasets updated to use objectId as a managed key: "+ total);
}
else
{
DbSchema studySchema = DbSchema.get("study");
SQLFragment sql = new SQLFragment("SELECT * FROM study.dataset WHERE keymanagementtype!=? AND demographicdata=? AND container=?", "GUID", false, c.getEntityId());
long total = new SqlExecutor(studySchema).execute(sql);
long total = new SqlExecutor(StudyService.get().getDatasetSchema()).execute(sql);
if (total > 0)
messages.add("Non-demographics datasets that are not using objectId as a managed key: " + total);
}
Expand Down Expand Up @@ -1127,8 +1130,7 @@ private void rebuildIndex(String table, String indexName)
//NOTE: this assumes the property already exists
private void updatePropertyURI(Domain d, PropertyDescriptor pd) throws SQLException
{
DbSchema expSchema = DbSchema.get(ExpSchema.SCHEMA_NAME);
TableInfo propertyDomain = expSchema.getTable("propertydomain");
DbSchema expSchema = ExperimentService.get().getSchema();
TableInfo propertyDescriptor = expSchema.getTable("propertydescriptor");

//find propertyId
Expand Down Expand Up @@ -1279,47 +1281,39 @@ public int discardTask(Container c, User u, String taskId) throws SQLException
@Override
public void exec(Map<String, Object> map)
{
Map<String, Object> row = new CaseInsensitiveHashMap<>();
row.putAll(map);
Map<String, Object> row = new CaseInsensitiveHashMap<>();
row.putAll(map);

if (row.containsKey("requestid") && row.get("requestid") != null)
{
row.put("requestid", null);
row.put("qcstate", null);
row.put("taskid", null);
row.put("qcstateLabel", "Request: Approved");
if (row.containsKey("requestid") && row.get("requestid") != null)
{
row.put("requestid", null);
row.put("qcstate", null);
row.put("taskid", null);
row.put("qcstateLabel", "Request: Approved");

requestsToQueue.add(row);
}
else
{
keysToDelete.add(row);
}
requestsToQueue.add(row);
}
else
{
keysToDelete.add(row);
}
}
});

try
{
if (!keysToDelete.isEmpty())
{
ti.getUpdateService().deleteRows(u, c, keysToDelete, null, new HashMap<String, Object>());
ti.getUpdateService().deleteRows(u, c, keysToDelete, null, new HashMap<>());
}


if (!requestsToQueue.isEmpty())
{
ti.getUpdateService().updateRows(u, c, requestsToQueue, requestsToQueue, null, new HashMap<String, Object>());
ti.getUpdateService().updateRows(u, c, requestsToQueue, requestsToQueue, null, new HashMap<>());
}
}
catch (InvalidKeyException e)
{
throw new RuntimeException(e);
}
catch (QueryUpdateServiceException e)
{
throw new RuntimeException(e);
}
catch (BatchValidationException e)
catch (InvalidKeyException | QueryUpdateServiceException | BatchValidationException e)
{
throw new RuntimeException(e);
}
Expand Down