public void testTableRowParsing()
{
StagingTable table = new StagingTable();
table.setId("test_table");
table.setColumnDefinitions(new List <IColumnDefinition>()
{
new StagingColumnDefinition("key1", "Input 1", ColumnType.INPUT)
});
table.setRawRows(new List <List <String> >());
table.getRawRows().Add(new List <String>()
{
",1,2,3"
});
table.getRawRows().Add(new List <String>()
{
"1,2,3,"
});
StagingDataProvider.initTable(table);
Assert.AreEqual(2, table.getTableRows().Count);
//StagingTableRow
List <ITableRow> tablerows = table.getTableRows();
StagingTableRow row = (tablerows[0] as StagingTableRow);
Assert.AreEqual(4, row.getInputs()["key1"].Count);
row = (tablerows[1] as StagingTableRow);
Assert.AreEqual(4, row.getInputs()["key1"].Count);
}
public void testNumericRangeTableMatch()
{
InMemoryDataProvider provider = new InMemoryDataProvider("test", "1.0");
StagingTable table = new StagingTable();
table.setId("psa");
StagingColumnDefinition def1 = new StagingColumnDefinition();
def1.setKey("psa");
def1.setName("PSA Value");
def1.setType(ColumnType.INPUT);
StagingColumnDefinition def2 = new StagingColumnDefinition();
def2.setKey("description");
def2.setName("PSA Description");
def2.setType(ColumnType.DESCRIPTION);
table.setColumnDefinitions(new List <IColumnDefinition>()
{
def1, def2
});
table.setRawRows(new List <List <String> >());
table.getRawRows().Add(new List <String>()
{
"0.1", "0.1 or less nanograms/milliliter (ng/ml)"
});
table.getRawRows().Add(new List <String>()
{
"0.2-999.9", "0.2 – 999.9 ng/ml"
});
provider.addTable(table);
TNMStagingCSharp.Src.Staging.Staging staging = TNMStagingCSharp.Src.Staging.Staging.getInstance(provider);
Assert.AreEqual(0, staging.findMatchingTableRow("psa", "psa", "0.1"));
Assert.AreEqual(1, staging.findMatchingTableRow("psa", "psa", "0.2"));
Assert.AreEqual(1, staging.findMatchingTableRow("psa", "psa", "500"));
Assert.AreEqual(1, staging.findMatchingTableRow("psa", "psa", "500.99"));
Assert.AreEqual(1, staging.findMatchingTableRow("psa", "psa", "500.0001"));
Assert.AreEqual(1, staging.findMatchingTableRow("psa", "psa", "999.9"));
Assert.AreEqual(-1, staging.findMatchingTableRow("psa", "psa", "1000"));
Assert.AreEqual(-1, staging.findMatchingTableRow("psa", "psa", "-1"));
Assert.AreEqual(-1, staging.findMatchingTableRow("psa", "psa", "0.01"));
}
public void testInvalidContext()
{
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);
table.setColumnDefinitions(new List <IColumnDefinition>()
{
def1
});
table.setRawRows(new List <List <String> >());
table.getRawRows().Add(new List <String>()
{
"1"
});
table.getRawRows().Add(new List <String>()
{
"2"
});
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("table_mapping");
def1 = new StagingColumnDefinition();
def1.setKey("input1");
def1.setName("Input 1");
def1.setType(ColumnType.INPUT);
StagingColumnDefinition def2 = new StagingColumnDefinition();
def2.setKey("final_output");
def2.setName("Output");
def2.setType(ColumnType.ENDPOINT);
table.setColumnDefinitions(new List <IColumnDefinition>()
{
def1, def2
});
table.setRawRows(new List <List <String> >());
table.getRawRows().Add(new List <String>()
{
"*", "VALUE:ABC"
});
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("input1", "Input 1", "table_input1"));
schema.setInputs(inputs);
List <StagingSchemaOutput> outputs = new List <StagingSchemaOutput>();
outputs.Add(new StagingSchemaOutput("final_output", "Final Output"));
schema.setOutputs(outputs);
StagingMapping mapping = new StagingMapping();
mapping.setId("m1");
List <IKeyValue> mapInitialContext = new List <IKeyValue>();
mapInitialContext.Add(new StagingKeyValue("input1", "XXX"));
mapping.setInitialContext(mapInitialContext);
StagingTablePath path = new StagingTablePath();
path.setId("table_mapping");
HashSet <String> pathInputs = new HashSet <String>();
pathInputs.Add("input1");
path.setInputs(pathInputs);
HashSet <String> pathOutputs = new HashSet <String>();
pathOutputs.Add("final_output");
path.setOutputs(pathOutputs);
List <ITablePath> mapTablePaths = new List <ITablePath>();
mapTablePaths.Add(path);
mapping.setTablePaths(mapTablePaths);
List <IMapping> schemaMappings = new List <IMapping>();
schemaMappings.Add(mapping);
schema.setMappings(schemaMappings);
try
{
provider.addSchema(schema);
Assert.Fail("Add Schema should have thrown an exception.");
} catch (System.InvalidOperationException e)
{
Assert.IsTrue(e.Message.Contains("not allowed since it is also defined as an input"));
}
}
public void testGetInputsWithContext()
{
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);
table.setColumnDefinitions(new List <IColumnDefinition>()
{
def1
});
table.setRawRows(new List <List <String> >());
table.getRawRows().Add(new List <String>()
{
"1"
});
table.getRawRows().Add(new List <String>()
{
"2"
});
provider.addTable(table);
table = new StagingTable();
table.setId("table_input2");
def1 = new StagingColumnDefinition();
def1.setKey("input1");
def1.setName("Input 2");
def1.setType(ColumnType.INPUT);
table.setColumnDefinitions(new List <IColumnDefinition>()
{
def1
});
table.setRawRows(new List <List <String> >());
table.getRawRows().Add(new List <String>()
{
""
});
table.getRawRows().Add(new List <String>()
{
"A"
});
table.getRawRows().Add(new List <String>()
{
"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("table_mapping");
def1 = new StagingColumnDefinition();
def1.setKey("input1");
def1.setName("Input 1");
def1.setType(ColumnType.INPUT);
StagingColumnDefinition def2 = new StagingColumnDefinition();
def2.setKey("input2");
def2.setName("Input 2");
def2.setType(ColumnType.INPUT);
StagingColumnDefinition def3 = new StagingColumnDefinition();
def3.setKey("mapped_field");
def3.setName("Temp value");
def3.setType(ColumnType.INPUT);
StagingColumnDefinition def4 = new StagingColumnDefinition();
def4.setKey("final_output");
def4.setName("Output");
def4.setType(ColumnType.ENDPOINT);
table.setColumnDefinitions(new List <IColumnDefinition>()
{
def1, def2, def3, def4
});
table.setRawRows(new List <List <String> >());
table.getRawRows().Add(new List <String>()
{
"*", "*", "*", "VALUE:ABC"
});
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("input1", "Input 1", "table_input1"));
inputs.Add(new StagingSchemaInput("input2", "Input 2", "table_input2"));
schema.setInputs(inputs);
List <StagingSchemaOutput> outputs = new List <StagingSchemaOutput>();
outputs.Add(new StagingSchemaOutput("final_output", "Final Output"));
schema.setOutputs(outputs);
StagingMapping mapping = new StagingMapping();
mapping.setId("m1");
List <IKeyValue> mapInitialContext = new List <IKeyValue>();
mapInitialContext.Add(new StagingKeyValue("tmp_field", null));
mapping.setInitialContext(mapInitialContext);
StagingTablePath path = new StagingTablePath();
path.setId("table_mapping");
HashSet <IKeyMapping> pathInputMap = new HashSet <IKeyMapping>();
pathInputMap.Add(new StagingKeyMapping("tmp_field", "mapped_field"));
path.setInputMapping(pathInputMap);
HashSet <String> pathInputs = new HashSet <String>();
pathInputs.Add("input1");
pathInputs.Add("input2");
pathInputs.Add("tmp_field");
path.setInputs(pathInputs);
HashSet <String> pathOutputs = new HashSet <String>();
pathOutputs.Add("final_output");
path.setOutputs(pathOutputs);
List <ITablePath> mapTablePaths = new List <ITablePath>();
mapTablePaths.Add(path);
mapping.setTablePaths(mapTablePaths);
List <IMapping> schemaMappings = new List <IMapping>();
schemaMappings.Add(mapping);
schema.setMappings(schemaMappings);
provider.addSchema(schema);
TNMStagingCSharp.Src.Staging.Staging staging = TNMStagingCSharp.Src.Staging.Staging.getInstance(provider);
HashSet <String> testSet1 = staging.getInputs(staging.getSchema("schema_test"));
HashSet <String> testSet2 = new HashSet <String>();
testSet2.Add("input1");
testSet2.Add("input2");
// should only return the "real" inputs and not the temp field set in initial context
Assert.IsTrue(testSet1.SetEquals(testSet2));
}
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 void testExtraInput()
{
StagingTable table = new StagingTable();
table.setId("test_table");
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.ENDPOINT);
table.setColumnDefinitions(new List <IColumnDefinition>()
{
def1, def2
});
table.setRawRows(new List <List <String> >());
table.getRawRows().Add(new List <String>()
{
"1", "MATCH"
});
table.getRawRows().Add(new List <String>()
{
"2", "VALUE:{{extra1}}"
});
table.getRawRows().Add(new List <String>()
{
"{{extra2}}", "MATCH"
});
table.getRawRows().Add(new List <String>()
{
"{{ctx_year_current}}", "MATCH"
});
table.getRawRows().Add(new List <String>()
{
"5", "VALUE:{{ctx_year_current}}"
});
table.getRawRows().Add(new List <String>()
{
"6", "MATCH:{{match_extra}}"
});
table.getRawRows().Add(new List <String>()
{
"7", "ERROR:{{error_extra}}"
});
StagingDataProvider.initTable(table);
HashSet <String> hash1 = new HashSet <String>()
{
"extra1", "extra2"
};
HashSet <String> hash2 = table.getExtraInput();
// since context variables are not user-supplied, they should not be included in the extra input
Assert.IsTrue(hash1.SetEquals(hash2));
table.setRawRows(new List <List <String> >());
table.getRawRows().Add(new List <String>()
{
"{{ctx_year_current}}", "MATCH"
});
StagingDataProvider.initTable(table);
Assert.IsNull(table.getExtraInput());
}