public void testBlankInputs()
{
InMemoryDataProvider provider = new InMemoryDataProvider("test", "1.0");
StagingTable table = new StagingTable();
table.setId("table_input1");
StagingColumnDefinition def1 = new StagingColumnDefinition();
def1.setKey("input1");
def1.setName("Input 1");
def1.setType(ColumnType.INPUT);
StagingColumnDefinition def2 = new StagingColumnDefinition();
def2.setKey("result1");
def2.setName("Result1");
def2.setType(ColumnType.DESCRIPTION);
table.setColumnDefinitions(new List <IColumnDefinition>()
{
def1, def2
});
table.setRawRows(new List <List <String> >());
table.getRawRows().Add(new List <String>()
{
"1", "ONE"
});
table.getRawRows().Add(new List <String>()
{
"2", "TWO"
});
provider.addTable(table);
table = new StagingTable();
table.setId("table_input2");
def1 = new StagingColumnDefinition();
def1.setKey("input2");
def1.setName("Input 2");
def1.setType(ColumnType.INPUT);
def2 = new StagingColumnDefinition();
def2.setKey("result2");
def2.setName("Result2");
def2.setType(ColumnType.DESCRIPTION);
table.setColumnDefinitions(new List <IColumnDefinition>()
{
def1, def2
});
table.setRawRows(new List <List <String> >());
table.getRawRows().Add(new List <String>()
{
"", "Blank"
});
table.getRawRows().Add(new List <String>()
{
"A", "Letter A"
});
table.getRawRows().Add(new List <String>()
{
"B", "Letter B"
});
provider.addTable(table);
table = new StagingTable();
table.setId("table_selection");
def1 = new StagingColumnDefinition();
def1.setKey("input1");
def1.setName("Input 1");
def1.setType(ColumnType.INPUT);
table.setColumnDefinitions(new List <IColumnDefinition>()
{
def1
});
table.setRawRows(new List <List <String> >());
table.getRawRows().Add(new List <String>()
{
"*"
});
provider.addTable(table);
table = new StagingTable();
table.setId("primary_site");
def1 = new StagingColumnDefinition();
def1.setKey("site");
def1.setName("Site");
def1.setType(ColumnType.INPUT);
table.setColumnDefinitions(new List <IColumnDefinition>()
{
def1
});
table.setRawRows(new List <List <String> >());
table.getRawRows().Add(new List <String>()
{
"C509"
});
provider.addTable(table);
table = new StagingTable();
table.setId("histology");
def1 = new StagingColumnDefinition();
def1.setKey("hist");
def1.setName("Histology");
def1.setType(ColumnType.INPUT);
table.setColumnDefinitions(new List <IColumnDefinition>()
{
def1
});
table.setRawRows(new List <List <String> >());
table.getRawRows().Add(new List <String>()
{
"8000"
});
provider.addTable(table);
table = new StagingTable();
table.setId("table_year_dx");
def1 = new StagingColumnDefinition();
def1.setKey("year_dx");
def1.setName("Year DX");
def1.setType(ColumnType.INPUT);
table.setColumnDefinitions(new List <IColumnDefinition>()
{
def1
});
table.setRawRows(new List <List <String> >());
table.getRawRows().Add(new List <String>()
{
"1900-2100"
});
provider.addTable(table);
StagingSchema schema = new StagingSchema();
schema.setId("schema_test");
schema.setSchemaSelectionTable("table_selection");
List <StagingSchemaInput> inputs = new List <StagingSchemaInput>();
inputs.Add(new StagingSchemaInput("site", "Primary Site", "primary_site"));
inputs.Add(new StagingSchemaInput("hist", "Hist", "histology"));
inputs.Add(new StagingSchemaInput("year_dx", "Year DX", "table_year_dx"));
inputs.Add(new StagingSchemaInput("input1", "Input 1", "table_input1"));
inputs.Add(new StagingSchemaInput("input2", "Input 2", "table_input2"));
schema.setInputs(inputs);
provider.addSchema(schema);
TNMStagingCSharp.Src.Staging.Staging staging = TNMStagingCSharp.Src.Staging.Staging.getInstance(provider);
Assert.AreEqual("schema_test", staging.getSchema("schema_test").getId());
// check case where required input field not supplied (i.e. no default); since there are is no workflow defined, this should
// not cause an error
StagingData data = new StagingData("C509", "8000");
data.setInput("year_dx", "2018");
data.setInput("input1", "1");
staging.stage(data);
Assert.AreEqual(StagingData.Result.STAGED, data.getResult());
// pass in blank for "input2"
data = new StagingData("C509", "8000");
data.setInput("year_dx", "2018");
data.setInput("input1", "1");
data.setInput("input2", "");
staging.stage(data);
Assert.AreEqual(StagingData.Result.STAGED, data.getResult());
// pass in null for "input2"
data = new StagingData("C509", "8000");
data.setInput("year_dx", "2018");
data.setInput("input1", "1");
data.setInput("input2", null);
staging.stage(data);
Assert.AreEqual(StagingData.Result.STAGED, data.getResult());
}
public static void MultiTask_TaskCompute(int id, Object task_data)
{
MultiTask_DataObj thisDataObj = (MultiTask_DataObj)task_data;
try
{
// load up inputs
TnmStagingData data = new TnmStagingData();
foreach (KeyValuePair <TnmInput, String> kp in thisDataObj.mInputValues)
{
data.setInput(kp.Key, kp.Value);
}
// save the expected outputs
Dictionary <String, String> output = new Dictionary <String, String>(100, StringComparer.Ordinal);
String sKeyValue = "";
foreach (KeyValuePair <TnmOutput, String> entry in thisDataObj.mOutputValues)
{
sKeyValue = entry.Key.toString();
output[sKeyValue] = entry.Value;
}
// run collaborative stage; if no schema found, set the output to empty
SchemaLookup lookup = new SchemaLookup(data.getInput(TnmInput.PRIMARY_SITE), data.getInput(TnmInput.HISTOLOGY));
lookup.setInput(TnmStagingData.SEX_KEY, data.getInput(TnmInput.SEX));
lookup.setInput(TnmStagingData.SSF25_KEY, data.getInput(TnmInput.SSF25));
List <StagingSchema> schemas = mMultiTask_Staging.lookupSchema(lookup);
if (schemas.Count == 1)
{
mMultiTask_Staging.stage(data);
}
else
{
Dictionary <String, String> outResult = new Dictionary <String, String>(2, StringComparer.Ordinal);
outResult["schema_id"] = "<invalid>";
data.setOutput(outResult);
}
List <String> mismatches = new List <String>();
// compare results
if (!thisDataObj.mbJSONFormat)
{
String sNewResultStr = "";
String sOldResultStr = thisDataObj.msExpectedResult.Trim();
if (data.getResult() == StagingData.Result.STAGED)
{
sNewResultStr = "STAGED";
}
else if (data.getResult() == StagingData.Result.FAILED_MISSING_SITE_OR_HISTOLOGY)
{
sNewResultStr = "FAILED_MISSING_SITE_OR_HISTOLOGY";
}
else if (data.getResult() == StagingData.Result.FAILED_NO_MATCHING_SCHEMA)
{
sNewResultStr = "FAILED_NO_MATCHING_SCHEMA";
}
else if (data.getResult() == StagingData.Result.FAILED_MULITPLE_MATCHING_SCHEMAS)
{
sNewResultStr = "FAILED_MULITPLE_MATCHING_SCHEMAS";
}
else if (data.getResult() == StagingData.Result.FAILED_INVALID_YEAR_DX)
{
sNewResultStr = "FAILED_INVALID_YEAR_DX";
}
else if (data.getResult() == StagingData.Result.FAILED_INVALID_INPUT)
{
sNewResultStr = "FAILED_INVALID_INPUT";
}
if (sNewResultStr != sOldResultStr)
{
mismatches.Add(" " + thisDataObj.miLineNum + " --> Result: EXPECTED '" + sOldResultStr + "' ACTUAL: '" + sNewResultStr + "'");
}
}
// compare output
foreach (KeyValuePair <String, String> entry in output)
{
String expected = "";
output.TryGetValue(entry.Key, out expected);
if (expected == null)
{
expected = "";
}
expected = expected.Trim();
String actual = "";
data.getOutput().TryGetValue(entry.Key, out actual);
if (actual == null)
{
actual = "";
}
actual = actual.Trim();
if (expected != actual)
{
mismatches.Add(" " + thisDataObj.miLineNum + " --> " + entry.Key + ": EXPECTED '" + expected + "' ACTUAL: '" + actual + "'");
}
}
if (mismatches.Count != 0)
{
String sSchemaIDValue = data.getSchemaId();
IntegrationUtils.WritelineToLog(" " + thisDataObj.miLineNum + " --> [" + sSchemaIDValue + "] Mismatches in " + thisDataObj.msFileName);
foreach (String mismatch in mismatches)
{
IntegrationUtils.WritelineToLog(mismatch);
}
IntegrationUtils.WritelineToLog(" " + thisDataObj.miLineNum + " *** RESULT: " + data.getResult());
IntegrationUtils.WritelineToLog(" " + thisDataObj.miLineNum + " --> Input: " + IntegrationUtils.convertInputMap(data.getInput()));
IntegrationUtils.WritelineToLog(" " + thisDataObj.miLineNum + " --> Output: " + IntegrationUtils.convertInputMap(data.getOutput()));
if (data.getErrors().Count > 0)
{
IntegrationUtils.WritelineToLog(" " + thisDataObj.miLineNum + " --> ERRORS: ");
foreach (Error e in data.getErrors())
{
IntegrationUtils.WritelineToLog(" " + thisDataObj.miLineNum + " --> (" + e.getTable() + ": " + e.getMessage() + ") ");
}
}
Interlocked.Increment(ref miMultiTask_FailedCases);
}
}
catch (Exception e)
{
IntegrationUtils.WritelineToLog(" " + thisDataObj.miLineNum + " --> Exception processing " + thisDataObj.msFileName + " : " + e.Message);
Interlocked.Increment(ref miMultiTask_FailedCases);
}
Interlocked.Increment(ref miMultiTask_ThreadProcessedCases);
}
public static void MultiTask_TaskCompute(int id, Object task_data)
{
MultiTask_DataObj thisDataObj = (MultiTask_DataObj)task_data;
//IntegrationUtils.WritelineToLog("Task " + id + " - Executing Line " + thisDataObj.miLineNum + " - " + DateTime.Now.ToString("HH:mm:ss.ffff"));
// load up inputs
CsStagingData data = new CsStagingData();
data.setInput(CsInput.PRIMARY_SITE, thisDataObj.mValues[0]);
data.setInput(CsInput.HISTOLOGY, thisDataObj.mValues[1]);
data.setInput(CsInput.DX_YEAR, thisDataObj.mValues[2]);
data.setInput(CsInput.CS_VERSION_ORIGINAL, thisDataObj.mValues[3]);
data.setInput(CsInput.BEHAVIOR, thisDataObj.mValues[4]);
data.setInput(CsInput.GRADE, thisDataObj.mValues[5]);
data.setInput(CsInput.AGE_AT_DX, thisDataObj.mValues[6]);
data.setInput(CsInput.LVI, thisDataObj.mValues[7]);
data.setInput(CsInput.TUMOR_SIZE, thisDataObj.mValues[8]);
data.setInput(CsInput.EXTENSION, thisDataObj.mValues[9]);
data.setInput(CsInput.EXTENSION_EVAL, thisDataObj.mValues[10]);
data.setInput(CsInput.LYMPH_NODES, thisDataObj.mValues[11]);
data.setInput(CsInput.LYMPH_NODES_EVAL, thisDataObj.mValues[12]);
data.setInput(CsInput.REGIONAL_NODES_POSITIVE, thisDataObj.mValues[13]);
data.setInput(CsInput.REGIONAL_NODES_EXAMINED, thisDataObj.mValues[14]);
data.setInput(CsInput.METS_AT_DX, thisDataObj.mValues[15]);
data.setInput(CsInput.METS_EVAL, thisDataObj.mValues[16]);
data.setInput(CsInput.SSF1, thisDataObj.mValues[17]);
data.setInput(CsInput.SSF2, thisDataObj.mValues[18]);
data.setInput(CsInput.SSF3, thisDataObj.mValues[19]);
data.setInput(CsInput.SSF4, thisDataObj.mValues[20]);
data.setInput(CsInput.SSF5, thisDataObj.mValues[21]);
data.setInput(CsInput.SSF6, thisDataObj.mValues[22]);
data.setInput(CsInput.SSF7, thisDataObj.mValues[23]);
data.setInput(CsInput.SSF8, thisDataObj.mValues[24]);
data.setInput(CsInput.SSF9, thisDataObj.mValues[25]);
data.setInput(CsInput.SSF10, thisDataObj.mValues[26]);
data.setInput(CsInput.SSF11, thisDataObj.mValues[27]);
data.setInput(CsInput.SSF12, thisDataObj.mValues[28]);
data.setInput(CsInput.SSF13, thisDataObj.mValues[29]);
data.setInput(CsInput.SSF14, thisDataObj.mValues[30]);
data.setInput(CsInput.SSF15, thisDataObj.mValues[31]);
data.setInput(CsInput.SSF16, thisDataObj.mValues[32]);
data.setInput(CsInput.SSF17, thisDataObj.mValues[33]);
data.setInput(CsInput.SSF18, thisDataObj.mValues[34]);
data.setInput(CsInput.SSF19, thisDataObj.mValues[35]);
data.setInput(CsInput.SSF20, thisDataObj.mValues[36]);
data.setInput(CsInput.SSF21, thisDataObj.mValues[37]);
data.setInput(CsInput.SSF22, thisDataObj.mValues[38]);
data.setInput(CsInput.SSF23, thisDataObj.mValues[39]);
data.setInput(CsInput.SSF24, thisDataObj.mValues[40]);
data.setInput(CsInput.SSF25, thisDataObj.mValues[41]);
try
{
// save the expected outputs
Dictionary <String, String> output = new Dictionary <String, String>(100, StringComparer.Ordinal);
String sKeyValue = "";
foreach (KeyValuePair <CsOutput, int> entry in thisDataObj.mMappings)
{
sKeyValue = entry.Key.toString();
output[sKeyValue] = thisDataObj.mValues[entry.Value];
}
// run collaborative stage; if no schema found, set the output to empty
SchemaLookup lookup = new SchemaLookup(data.getInput(CsInput.PRIMARY_SITE), data.getInput(CsInput.HISTOLOGY));
lookup.setInput(CsStagingData.SSF25_KEY, data.getInput(CsInput.SSF25));
List <StagingSchema> schemas = mMultiTask_Staging.lookupSchema(lookup);
if (schemas.Count == 1)
{
mMultiTask_Staging.stage(data);
}
else
{
Dictionary <String, String> outResult = new Dictionary <String, String>(2, StringComparer.Ordinal);
outResult["schema_id"] = "<invalid>";
data.setOutput(outResult);
}
List <String> mismatches = new List <String>();
// compare results
foreach (KeyValuePair <String, String> entry in output)
{
String expected = "";
output.TryGetValue(entry.Key, out expected);
if (expected == null)
{
expected = "";
}
expected = expected.Trim();
String actual = "";
data.getOutput().TryGetValue(entry.Key, out actual);
if (actual == null)
{
actual = "";
}
actual = actual.Trim();
if (expected != actual)
{
mismatches.Add(" " + thisDataObj.miLineNum + " --> " + entry.Key + ": EXPECTED '" + expected + "' ACTUAL: '" + actual + "'");
}
}
if (mismatches.Count != 0)
{
String sSchemaIDValue = data.getSchemaId();
IntegrationUtils.WritelineToLog(" " + thisDataObj.miLineNum + " --> [" + sSchemaIDValue + "] Mismatches in " + thisDataObj.msFileName);
foreach (String mismatch in mismatches)
{
IntegrationUtils.WritelineToLog(mismatch);
}
IntegrationUtils.WritelineToLog(" " + thisDataObj.miLineNum + " *** RESULT: " + data.getResult());
IntegrationUtils.WritelineToLog(" " + thisDataObj.miLineNum + " --> " + IntegrationUtils.convertInputMap(data.getInput()));
if (data.getErrors().Count > 0)
{
IntegrationUtils.WritelineToLog(" " + thisDataObj.miLineNum + " --> ERRORS: ");
foreach (Error e in data.getErrors())
{
IntegrationUtils.WritelineToLog(" " + thisDataObj.miLineNum + " --> (" + e.getTable() + ": " + e.getMessage() + ") ");
}
}
Interlocked.Increment(ref miMultiTask_FailedCases);
}
}
catch (Exception e)
{
IntegrationUtils.WritelineToLog(" " + thisDataObj.miLineNum + " --> Exception processing " + thisDataObj.msFileName + " : " + e.Message);
Interlocked.Increment(ref miMultiTask_FailedCases);
}
Interlocked.Increment(ref miMultiTask_ThreadProcessedCases);
}
public void testExternalLoad()
{
Assert.AreEqual("testing", _STAGING.getAlgorithm());
Assert.AreEqual("99.99", _STAGING.getVersion());
Assert.AreEqual(1, _STAGING.getSchemaIds().Count);
Assert.AreEqual(62, _STAGING.getTableIds().Count);
StagingSchema schema = _STAGING.getSchema("urethra");
Assert.IsNotNull(schema);
Assert.AreEqual("testing", schema.getAlgorithm());
Assert.AreEqual("99.99", schema.getVersion());
StagingTable table = _STAGING.getTable("ajcc_descriptor_codes");
Assert.IsNotNull(table);
Assert.AreEqual("testing", table.getAlgorithm());
Assert.AreEqual("99.99", table.getVersion());
Assert.AreEqual(6, table.getTableRows().Count);
HashSet <String> involved = _STAGING.getInvolvedTables("urethra");
Assert.AreEqual(62, involved.Count);
Assert.IsTrue(involved.Contains("mets_eval_ipa"));
StagingData data = new StagingData();
data.setInput("site", "C680");
data.setInput("hist", "8000");
data.setInput("behavior", "3");
data.setInput("grade", "9");
data.setInput("year_dx", "2013");
data.setInput("cs_input_version_original", "020550");
data.setInput("extension", "100");
data.setInput("extension_eval", "9");
data.setInput("nodes", "100");
data.setInput("nodes_eval", "9");
data.setInput("mets", "10");
data.setInput("mets_eval", "9");
// perform the staging
_STAGING.stage(data);
Assert.AreEqual(StagingData.Result.STAGED, data.getResult());
Assert.AreEqual("urethra", data.getSchemaId());
Assert.AreEqual(0, data.getErrors().Count);
Assert.AreEqual(37, data.getPath().Count);
// check output
Assert.AreEqual("129", data.getOutput("schema_number"));
Assert.AreEqual("020550", data.getOutput("csver_derived"));
// AJCC 6
Assert.AreEqual("70", data.getOutput("stor_ajcc6_stage"));
// AJCC 7
Assert.AreEqual("700", data.getOutput("stor_ajcc7_stage"));
// Summary Stage
Assert.AreEqual("7", data.getOutput("stor_ss77"));
Assert.AreEqual("7", data.getOutput("stor_ss2000"));
}
