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Merged
labkey-adam merged 2 commits into from
Dec 18, 2025
Merged

Remove unused User parameters from service methods #968

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16364ea
Migrate away from deprecated SampleTypeService methods
labkey-adam Dec 16, 2025
cb34ad4
Update FlowProtocol.getSampleType() callers to not pass User
labkey-adam Dec 16, 2025
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2 changes: 1 addition & 1 deletion flow/src/org/labkey/flow/controllers/protocol/EditICSMetadataForm.java
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Expand Up @@ -228,7 +228,7 @@ public Map<FieldKey, String> getKeywordAndSampleFieldMap(boolean includeStatisti
}

FieldKey sampleProperty = FieldKey.fromParts("FCSFile", "Sample");
ExpSampleType sampleType = getProtocol().getSampleType(getUser());
ExpSampleType sampleType = getProtocol().getSampleType();
if (sampleType != null)
{
if (sampleType.hasNameAsIdCol())
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2 changes: 1 addition & 1 deletion flow/src/org/labkey/flow/controllers/protocol/JoinSampleTypeForm.java
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Expand Up @@ -69,7 +69,7 @@ public Map<String, String> getAvailableSampleKeyFields()
{
LinkedHashMap<String,String> ret = new LinkedHashMap<>();
ret.put("", "");
ExpSampleType sampleType = getProtocol().getSampleType(getUser());
ExpSampleType sampleType = getProtocol().getSampleType();
if (sampleType != null)
{
if (sampleType.hasNameAsIdCol())
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2 changes: 1 addition & 1 deletion flow/src/org/labkey/flow/controllers/protocol/joinSampleType.jsp
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Expand Up @@ -24,7 +24,7 @@
<%
JoinSampleTypeForm form = (JoinSampleTypeForm) __form;

if (form.getProtocol().getSampleType(getUser()) == null)
if (form.getProtocol().getSampleType() == null)
{
%>
<p>You must first upload a sample type before specifying how to match samples to FCS files.</p>
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2 changes: 1 addition & 1 deletion flow/src/org/labkey/flow/controllers/protocol/showProtocol.jsp
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Expand Up @@ -27,7 +27,7 @@
<%
ProtocolForm form = (ProtocolForm) __form;
FlowProtocol protocol = form.getProtocol();
ExpSampleType sampleType = protocol.getSampleType(getUser());
ExpSampleType sampleType = protocol.getSampleType();
%>
<p>
The Flow Protocol describes sample information and metadata about the experiment.
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2 changes: 1 addition & 1 deletion flow/src/org/labkey/flow/controllers/protocol/showSamples2.jsp
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Expand Up @@ -37,7 +37,7 @@
<%
ProtocolForm form = (ProtocolForm) __form;
FlowProtocol protocol = form.getProtocol();
ExpSampleType st = protocol.getSampleType(getUser());
ExpSampleType st = protocol.getSampleType();

ExperimentUrls expUrls = urlProvider(ExperimentUrls.class);

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2 changes: 1 addition & 1 deletion flow/src/org/labkey/flow/controllers/protocol/updateSamples.jsp
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Expand Up @@ -25,5 +25,5 @@
<%= form.fileCount%> FCS files were linked to samples in this sample type.
</p>
<p><a href="<%=h(form.getProtocol().urlShowSamples())%>">Show linked samples</a><br>
<a href="<%=h(form.getProtocol().getSampleType(getUser()).detailsURL())%>">Show all samples</a><br>
<a href="<%=h(form.getProtocol().getSampleType().detailsURL())%>">Show all samples</a><br>
<a href="<%=h(form.getProtocol().urlFor(ProtocolController.JoinSampleTypeAction.class))%>">Edit join properties</a></p>
26 changes: 15 additions & 11 deletions flow/src/org/labkey/flow/data/FlowProtocol.java
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Expand Up @@ -257,7 +257,11 @@ public FlowProtocolStep getStep()
*/
public ExpSampleType getSampleType(User user)
{
return SampleTypeService.get().getSampleType(getContainer(), user, SAMPLETYPE_NAME);
return SampleTypeService.get().getSampleType(getContainer(), SAMPLETYPE_NAME, true);
}
public ExpSampleType getSampleType()
{
return SampleTypeService.get().getSampleType(getContainer(), SAMPLETYPE_NAME, true);
}

/**
Expand Down Expand Up @@ -305,14 +309,14 @@ public Map<String, FieldKey> getSampleTypeJoinFields()
return ret;
}

public String getSampleTypeLSID(User user)
public String getSampleTypeLSID()
{
String propValue = (String) getProperty(ExperimentProperty.SampleTypeLSID.getPropertyDescriptor());
if (propValue != null)
return propValue;

// get lsid for sample type with name "Samples"
ExpSampleType sampleType = getSampleType(user);
ExpSampleType sampleType = getSampleType();
if (sampleType != null)
return sampleType.getLSID();

Expand All @@ -328,7 +332,7 @@ public void setSampleTypeJoinFields(User user, Map<String, FieldKey> values) thr
}
String value = StringUtils.join(strings.iterator(), "&");
setProperty(user, FlowProperty.SampleTypeJoin.getPropertyDescriptor(), value);
setProperty(user, ExperimentProperty.SampleTypeLSID.getPropertyDescriptor(), getSampleTypeLSID(user));
setProperty(user, ExperimentProperty.SampleTypeLSID.getPropertyDescriptor(), getSampleTypeLSID());
FlowManager.get().flowObjectModified();
}

Expand All @@ -352,7 +356,7 @@ public ActionURL urlShowSamples()

public Map<SampleKey, ExpMaterial> getSampleMap(User user)
{
ExpSampleType st = getSampleType(user);
ExpSampleType st = getSampleType();
if (st == null)
return Collections.emptyMap();
Set<String> propertyNames = getSampleTypeJoinFields().keySet();
Expand Down Expand Up @@ -433,7 +437,7 @@ public int updateSampleIds(User user)
Map<SampleKey, ExpMaterial> sampleMap = getSampleMap(user);
_log.debug("sampleMap=" + sampleMap.size());

ExpSampleType st = getSampleType(user);
ExpSampleType st = getSampleType();
_log.debug("sampleType=" + (st == null ? "<none>" : st.getName()) + ", lsid=" + (st == null ? "<none>" : st.getLSID()));

FlowSchema schema = new FlowSchema(user, getContainer());
Expand Down Expand Up @@ -604,7 +608,7 @@ public FCSFilesGroupedBySample getFCSFilesGroupedBySample(User user, Container c
"__FCSFiles.Sample = M.RowId\n" +
"ORDER BY M.Name, __FCSFiles.RowId";

ExpSampleType sampleType = getSampleType(user);
ExpSampleType sampleType = getSampleType();
ContainerFilter cf = getContainerFilter(sampleType, user);
UserSchema userSchema = QueryService.get().getUserSchema(user, getContainer(), SamplesSchema.SCHEMA_NAME);
TableInfo sampleTable = userSchema.getTable(SAMPLETYPE_NAME, cf);
Expand Down Expand Up @@ -1017,8 +1021,8 @@ public void testSampleJoin() throws Exception
assertEquals(0, fcsFiles[1].getSamples().size());

// create sample type
assertNull(protocol.getSampleType(user));
String sampleTypeLSID = protocol.getSampleTypeLSID(user);
assertNull(protocol.getSampleType());
String sampleTypeLSID = protocol.getSampleTypeLSID();
assertNull(sampleTypeLSID);

List<GWTPropertyDescriptor> props = List.of(
Expand All @@ -1029,9 +1033,9 @@ public void testSampleJoin() throws Exception
);
ExpSampleType st = SampleTypeService.get().createSampleType(c, user, SAMPLETYPE_NAME, null,
props, List.of(), -1,-1,-1,-1,null);
assertNotNull(protocol.getSampleType(user));
assertNotNull(protocol.getSampleType());

sampleTypeLSID = protocol.getSampleTypeLSID(user);
sampleTypeLSID = protocol.getSampleTypeLSID();
assertNotNull(sampleTypeLSID);

// add join fields
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10 changes: 0 additions & 10 deletions flow/src/org/labkey/flow/persist/FlowKeywordAuditProvider.java
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Expand Up @@ -99,16 +99,6 @@ public String getDescription()
return "Displays information about keyword changes.";
}

@Override
public Map<FieldKey, String> legacyNameMap()
{
Map<FieldKey, String> legacyNames = super.legacyNameMap();
legacyNames.put(FieldKey.fromParts("key1"), COLUMN_NAME_DIRECTORY);
legacyNames.put(FieldKey.fromParts("key2"), COLUMN_NAME_FILE);
legacyNames.put(FieldKey.fromParts("key3"), COLUMN_NAME_KEYWORD_NAME);
return legacyNames;
}

@Override
public <K extends AuditTypeEvent> Class<K> getEventClass()
{
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2 changes: 1 addition & 1 deletion flow/src/org/labkey/flow/persist/FlowManager.java
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Expand Up @@ -1359,7 +1359,7 @@ public Map<String, Object> getUsageMetrics(User user, Container c, boolean inclu
FlowProtocol protocol = FlowProtocol.getForContainer(c);
if (protocol != null)
{
ExpSampleType st = protocol.getSampleType(user);
ExpSampleType st = protocol.getSampleType();
if (st != null)
{
// put sample count at top-level since it isn't really specific to the protocol
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2 changes: 1 addition & 1 deletion flow/src/org/labkey/flow/query/FlowSchema.java
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Expand Up @@ -1518,7 +1518,7 @@ public FlowDataTable createFCSFileTable(String name, ContainerFilter cf, boolean
ExpSampleType st = null;
if (_protocol != null)
{
st = _protocol.getSampleType(getUser());
st = _protocol.getSampleType();
}
var colMaterialInput = ret.addMaterialInputColumn("Sample", new SamplesSchema(getUser(), getContainer()), ExpMaterialRunInput.DEFAULT_ROLE, st);
if (st == null)
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2 changes: 1 addition & 1 deletion flow/src/org/labkey/flow/reports/statPicker.jsp
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Expand Up @@ -68,7 +68,7 @@

Collection<String> sampleTypeProperties = new ArrayList<>();
FlowProtocol protocol = FlowProtocol.ensureForContainer(getUser(), getContainer());
ExpSampleType sampleType = protocol.getSampleType(getUser());
ExpSampleType sampleType = protocol.getSampleType();
if (sampleType != null)
{
for (DomainProperty dp : sampleType.getDomain().getProperties())
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2 changes: 1 addition & 1 deletion flow/src/org/labkey/flow/webparts/FlowOverview.java
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Expand Up @@ -190,7 +190,7 @@ private Step getSamplesStep()
Step ret = new Step("Assign additional meanings to keywords", status);
if (protocol != null)
{
ExpSampleType st = protocol.getSampleType(getUser());
ExpSampleType st = protocol.getSampleType();
if (st != null)
{
HtmlStringBuilder sb = HtmlStringBuilder.of();
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2 changes: 1 addition & 1 deletion flow/src/org/labkey/flow/webparts/FlowSummary.jsp
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Expand Up @@ -76,7 +76,7 @@
//int _flaggedCount = FlowManager.get().getFlaggedCount(c);

FlowProtocol _protocol = FlowProtocol.getForContainer(c);
ExpSampleType _sampleType = _protocol != null ? _protocol.getSampleType(getUser()) : null;
ExpSampleType _sampleType = _protocol != null ? _protocol.getSampleType() : null;
List<? extends ExpMaterial> _sampleTypeSamples = _sampleType == null ? null : _protocol.getSamples(_sampleType, user);
ActionURL _sampleTypeDetailsUrl = _sampleType != null ? _protocol.getSampleTypeDetailsURL(_sampleType, getContainer()) : null;

Expand Down