@Test
public void testProviderOutputFormatter() throws IOException, SQLException {
config.setRowDimension(OutputConfiguration.RowDimension.PROVIDER);
formatter = new DataOutputFormatter(config, data);
String expected =
"\"Provider_name\",\"Concept_3\",\"Concept_1_value\",\"Concept_1_units\",\"Concept_1_value\",\"Concept_1_units\",\"Concept_1_value\",\"Concept_1_units\",\"Concept_2_max\",\"Concept_2_units\",\"Systolic_value\",\"Systolic_start\",\"Systolic_end\",\"Systolic_value\",\"Systolic_start\",\"Systolic_end\",\"Diastolic_value\",\"Diastolic_start\",\"Diastolic_end\",\"Diastolic_value\",\"Diastolic_start\",\"Diastolic_end\"\n"
+ "\"SMITH, JOHN\",\"true\",\"200\",\"U\",\"100\",\"U\",\"(NULL)\",\"(NULL)\",\"1.75\",\"X\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\"\n"
+ "\"DOE, JANE\",\"false\",\"300\",\"U\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\"\n"
+ "\"SALK, JONAS\",\"false\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"1.8\",\"X\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\"\n"
+ "\"HIPPOCRATES, BRIAN\",\"true\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"140\",\"2013-07-07T09:00:00.000-0400\",\"2013-07-07T10:00:00.000-0400\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"90\",\"2013-07-07T09:00:00.000-0400\",\"2013-07-07T10:00:00.000-0400\",\"(NULL)\",\"(NULL)\",\"(NULL)\"\n";
Assert.assertEquals(expected, formatString(formatter));
}
@Test
public void testPatientOutputFormatter() throws IOException, SQLException {
config.setRowDimension(OutputConfiguration.RowDimension.PATIENT);
formatter = new DataOutputFormatter(config, data);
String expected =
"\"Patient_id\",\"Concept_3\",\"Concept_1_value\",\"Concept_1_units\",\"Concept_1_value\",\"Concept_1_units\",\"Concept_1_value\",\"Concept_1_units\",\"Concept_2_max\",\"Concept_2_units\",\"Systolic_value\",\"Systolic_start\",\"Systolic_end\",\"Systolic_value\",\"Systolic_start\",\"Systolic_end\",\"Diastolic_value\",\"Diastolic_start\",\"Diastolic_end\",\"Diastolic_value\",\"Diastolic_start\",\"Diastolic_end\"\n"
+ "\"P1\",\"true\",\"300\",\"U\",\"200\",\"U\",\"100\",\"U\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\"\n"
+ "\"P2\",\"false\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"1.8\",\"X\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\"\n"
+ "\"P3\",\"true\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"140\",\"2013-07-07T09:00:00.000-0400\",\"2013-07-07T10:00:00.000-0400\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"90\",\"2013-07-07T09:00:00.000-0400\",\"2013-07-07T10:00:00.000-0400\",\"(NULL)\",\"(NULL)\",\"(NULL)\"\n";
Assert.assertEquals(expected, formatString(formatter));
}
@Test
public void testVisitOutputFormatter() throws IOException, SQLException {
config.setRowDimension(OutputConfiguration.RowDimension.VISIT);
formatter = new DataOutputFormatter(config, data);
String expected =
"\"Patient_id\",\"Visit_id\",\"Visit_start\",\"Visit_end\",\"Concept_3\",\"Concept_1_value\",\"Concept_1_units\",\"Concept_1_value\",\"Concept_1_units\",\"Concept_1_value\",\"Concept_1_units\",\"Concept_2_max\",\"Concept_2_units\",\"Systolic_value\",\"Systolic_start\",\"Systolic_end\",\"Systolic_value\",\"Systolic_start\",\"Systolic_end\",\"Diastolic_value\",\"Diastolic_start\",\"Diastolic_end\",\"Diastolic_value\",\"Diastolic_start\",\"Diastolic_end\"\n"
+ "\"P1\",\"E11\",\"2013-01-01T09:00:00.000-0500\",\"2013-01-01T14:00:00.000-0500\",\"false\",\"100\",\"U\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\"\n"
+ "\"P1\",\"E12\",\"2013-02-02T09:00:00.000-0500\",\"2013-02-02T14:00:00.000-0500\",\"false\",\"200\",\"U\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\"\n"
+ "\"P1\",\"E13\",\"2013-03-03T09:00:00.000-0500\",\"2013-03-03T14:00:00.000-0500\",\"true\",\"300\",\"U\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\"\n"
+ "\"P2\",\"E21\",\"2013-04-04T09:00:00.000-0400\",\"2013-04-04T14:00:00.000-0400\",\"false\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"1.0\",\"X\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\"\n"
+ "\"P2\",\"E22\",\"2013-05-05T09:00:00.000-0400\",\"2013-05-05T14:00:00.000-0400\",\"false\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"1.8\",\"X\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\"\n"
+ "\"P2\",\"E23\",\"2013-06-06T09:00:00.000-0400\",\"2013-06-06T14:00:00.000-0400\",\"false\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"1.75\",\"X\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\"\n"
+ "\"P3\",\"E31\",\"2013-07-07T09:00:00.000-0400\",\"2013-07-07T14:00:00.000-0400\",\"true\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"140\",\"2013-07-07T09:00:00.000-0400\",\"2013-07-07T10:00:00.000-0400\",\"(NULL)\",\"(NULL)\",\"(NULL)\",\"90\",\"2013-07-07T09:00:00.000-0400\",\"2013-07-07T10:00:00.000-0400\",\"(NULL)\",\"(NULL)\",\"(NULL)\"\n";
Assert.assertEquals(expected, formatString(formatter));
}
public DataOutputFormatterTest() throws ParseException {
DateFormat fmt = new SimpleDateFormat(I2b2CommUtil.I2B2_DATE_FMT);
config = new OutputConfiguration();
config.setUsername("i2b2");
config.setName("foo");
config.setMissingValue("(NULL)");
config.setSeparator(",");
config.setQuoteChar("\"");
config.setWhitespaceReplacement("_");
config.setColumnConfigs(new ArrayList<OutputColumnConfiguration>());
Collection<Patient> patients = new ArrayList<>();
Patient p1 = new Patient.Builder("P1").build();
Patient p2 = new Patient.Builder("P2").build();
Patient p3 = new Patient.Builder("P3").build();
patients.add(p1);
patients.add(p2);
patients.add(p3);
Collection<Event> visits = new ArrayList<>();
// patient 1
Event e11 =
new Event.Builder("E11", p1)
.startDate(fmt.parse("2013-01-01T09:00:00.000-0500"))
.endDate(fmt.parse("2013-01-01T14:00:00.000-0500"))
.build();
Event e12 =
new Event.Builder("E12", p1)
.startDate(fmt.parse("2013-02-02T09:00:00.000-0500"))
.endDate(fmt.parse("2013-02-02T14:00:00.000-0500"))
.build();
Event e13 =
new Event.Builder("E13", p1)
.startDate(fmt.parse("2013-03-03T09:00:00.000-0500"))
.endDate(fmt.parse("2013-03-03T14:00:00.000-0500"))
.build();
visits.add(e11);
visits.add(e12);
visits.add(e13);
p1.addEvent(e11);
p1.addEvent(e12);
p1.addEvent(e13);
// patient 2
Event e21 =
new Event.Builder("E21", p2)
.startDate(fmt.parse("2013-04-04T09:00:00.000-0400"))
.endDate(fmt.parse("2013-04-04T14:00:00.000-0400"))
.build();
Event e22 =
new Event.Builder("E22", p2)
.startDate(fmt.parse("2013-05-05T09:00:00.000-0400"))
.endDate(fmt.parse("2013-05-05T14:00:00.000-0400"))
.build();
Event e23 =
new Event.Builder("E23", p2)
.startDate(fmt.parse("2013-06-06T09:00:00.000-0400"))
.endDate(fmt.parse("2013-06-06T14:00:00.000-0400"))
.build();
visits.add(e21);
visits.add(e22);
visits.add(e23);
p2.addEvent(e21);
p2.addEvent(e22);
p2.addEvent(e23);
// patient 3
Event e31 =
new Event.Builder("E31", p3)
.startDate(fmt.parse("2013-07-07T09:00:00.000-0400"))
.endDate(fmt.parse("2013-07-07T14:00:00.000-0400"))
.build();
visits.add(e31);
p3.addEvent(e31);
Collection<Observer> providers = new ArrayList<>();
Observer o1 =
new Observer.Builder(
"\\i2b2INTERNAL|Provider\\i2b2INTERNAL|Provider|S\\i2b2INTERNAL|Provider:SMITH, JOHN",
"i2b2INTERNAL|Provider:SMITH, JOHN")
.name("SMITH, JOHN")
.build();
Observer o2 =
new Observer.Builder(
"\\i2b2INTERNAL|Provider\\i2b2INTERNAL|Provider|D\\i2b2INTERNAL|Provider:DOE, JANE",
"i2b2INTERNAL|Provider:DOE, JANE")
.name("DOE, JANE")
.build();
Observer o3 =
new Observer.Builder(
"\\i2b2INTERNAL|Provider\\i2b2INTERNAL|Provider|S\\i2b2INTERNAL|Provider:SALK, JONAS",
"i2b2INTERNAL|Provider:SALK, JONAS")
.name("SALK, JONAS")
.build();
Observer o4 =
new Observer.Builder(
"\\i2b2INTERNAL|Provider\\i2b2INTERNAL|Provider|H\\i2b2INTERNAL|Provider:HIPPOCRATES, BRIAN",
"i2b2INTERAL|Provider:HIPPOCRATES, BRIAN")
.name("HIPPOCRATES, BRIAN")
.build();
providers.add(o1);
providers.add(o2);
providers.add(o3);
providers.add(o4);
Collection<Observation> observations = new ArrayList<>();
// patient 1
Observation obx1 =
new Observation.Builder(e11)
.conceptPath("\\\\i2b2\\Concepts\\MyConcept1")
.startDate(fmt.parse("2013-01-01T09:00:00.000-0500"))
.endDate(fmt.parse("2013-01-01T10:00:00.000-0500"))
.tval("100")
.nval("100")
.valuetype("N")
.units("U")
.build();
Observation obx2 =
new Observation.Builder(e12)
.conceptPath("\\\\i2b2\\Concepts\\MyConcept1")
.startDate(fmt.parse("2013-02-02T09:00:00.000-0500"))
.endDate(fmt.parse("2013-02-02T10:00:00.000-0500"))
.tval("200")
.nval("200")
.valuetype("N")
.units("U")
.build();
Observation obx3 =
new Observation.Builder(e13)
.conceptPath("\\\\i2b2\\Concepts\\MyConcept1")
.startDate(fmt.parse("2013-03-03T09:00:00.000-0500"))
.endDate(fmt.parse("2013-03-03T10:00:00.000-0500"))
.tval("300")
.nval("300")
.valuetype("N")
.units("U")
.build();
Observation obx4 =
new Observation.Builder(e13)
.conceptPath("\\\\i2b2\\Concepts\\MyConcept3")
.startDate(fmt.parse("2013-03-03T09:00:00.000-0500"))
.endDate(fmt.parse("2013-03-03T10:00:00.000-0500"))
.build();
e11.addObservation(obx1);
e12.addObservation(obx2);
e13.addObservation(obx3);
e13.addObservation(obx4);
o1.addObservation(obx1);
o1.addObservation(obx2);
o2.addObservation(obx3);
o1.addObservation(obx4);
// patient 2
Observation obx5 =
new Observation.Builder(e21)
.conceptPath("\\\\i2b2\\Concepts\\MyConcept2")
.startDate(fmt.parse("2013-04-04T09:00:00.000-0400"))
.endDate(fmt.parse("2013-04-04T09:05:00.000-0400"))
.tval("1.0")
.nval("1.0")
.valuetype("N")
.units("X")
.build();
Observation obx6 =
new Observation.Builder(e22)
.conceptPath("\\\\i2b2\\Concepts\\MyConcept2")
.startDate(fmt.parse("2013-05-05T09:00:00.000-0400"))
.endDate(fmt.parse("2013-05-05T09:05:00.000-0400"))
.tval("1.5")
.nval("1.5")
.valuetype("N")
.units("X")
.build();
Observation obx7 =
new Observation.Builder(e22)
.conceptPath("\\\\i2b2\\Concepts\\MyConcept2")
.startDate(fmt.parse("2013-06-06T09:00:00.000-0400"))
.endDate(fmt.parse("2013-06-06T09:05:00.000-0400"))
.tval("1.8")
.nval("1.8")
.valuetype("N")
.units("X")
.build();
Observation obx8 =
new Observation.Builder(e23)
.conceptPath("\\\\i2b2\\Concepts\\MyConcept2")
.startDate(fmt.parse("2013-04-04T09:00:00.000-0400"))
.endDate(fmt.parse("2013-04-04T09:05:00.000-0400"))
.tval("1.75")
.nval("1.75")
.valuetype("N")
.units("X")
.build();
e21.addObservation(obx5);
e22.addObservation(obx6);
e22.addObservation(obx7);
e23.addObservation(obx8);
o3.addObservation(obx5);
o3.addObservation(obx6);
o3.addObservation(obx7);
o1.addObservation(obx8);
// patient 3
Observation obx9 =
new Observation.Builder(e31)
.conceptPath("\\\\i2b2\\Concepts\\MyConcept4")
.startDate(fmt.parse("2013-07-07T09:00:00.000-0400"))
.endDate(fmt.parse("2013-07-07T10:00:00.000-0400"))
.tval("140")
.nval("140")
.valuetype("N")
.units("mm Hg")
.build();
Observation obxA =
new Observation.Builder(e31)
.conceptPath("\\\\i2b2\\Concepts\\MyConcept5")
.startDate(fmt.parse("2013-07-07T09:00:00.000-0400"))
.endDate(fmt.parse("2013-07-07T10:00:00.000-0400"))
.tval("90")
.nval("90")
.valuetype("N")
.units("mm Hg")
.build();
Observation obxB =
new Observation.Builder(e31)
.conceptPath("\\\\i2b2\\Concepts\\MyConcept3")
.startDate(fmt.parse("2013-07-07T09:00:00.000-0400"))
.endDate(fmt.parse("2013-07-07T10:00:00.000-0400"))
.build();
e31.addObservation(obx9);
e31.addObservation(obxA);
e31.addObservation(obxB);
o4.addObservation(obx9);
o4.addObservation(obxA);
o4.addObservation(obxB);
observations.add(obx1);
observations.add(obx2);
observations.add(obx3);
observations.add(obx4);
observations.add(obx5);
observations.add(obx6);
observations.add(obx7);
observations.add(obx8);
observations.add(obx9);
observations.add(obxA);
observations.add(obxB);
data = new I2b2PdoResults(patients, visits, providers, observations);
OutputColumnConfiguration colConfig1 = new OutputColumnConfiguration();
colConfig1.setOutputConfig(config);
colConfig1.setColumnOrder(1);
I2b2Concept concept1 =
new I2b2Concept(
"\\\\i2b2\\Concepts\\MyConcept3", 2, "concept_dimension", "MyConcept3", "N");
colConfig1.setI2b2Concept(concept1);
colConfig1.setColumnName("Concept 3");
colConfig1.setDisplayFormat(OutputColumnConfiguration.DisplayFormat.EXISTENCE);
OutputColumnConfiguration colConfig2 = new OutputColumnConfiguration();
colConfig2.setOutputConfig(config);
colConfig2.setColumnOrder(2);
I2b2Concept concept2 =
new I2b2Concept(
"\\\\i2b2\\Concepts\\MyConcept1", 2, "concept_dimension", "MyConcept1", "N");
colConfig2.setI2b2Concept(concept2);
colConfig2.setColumnName("Concept 1");
colConfig2.setDisplayFormat(OutputColumnConfiguration.DisplayFormat.VALUE);
colConfig2.setHowMany(3);
colConfig2.setIncludeUnits(true);
colConfig2.setIncludeTimeRange(false);
OutputColumnConfiguration colConfig3 = new OutputColumnConfiguration();
colConfig3.setOutputConfig(config);
colConfig3.setColumnOrder(3);
I2b2Concept concept3 =
new I2b2Concept(
"\\\\i2b2\\Concepts\\MyConcept2", 2, "concept_dimension", "MyConcept2", "N");
colConfig3.setI2b2Concept(concept3);
colConfig3.setColumnName("Concept 2");
colConfig3.setDisplayFormat(OutputColumnConfiguration.DisplayFormat.AGGREGATION);
colConfig3.setAggregation(OutputColumnConfiguration.AggregationType.MAX);
colConfig3.setIncludeUnits(true);
OutputColumnConfiguration colConfig4 = new OutputColumnConfiguration();
colConfig4.setOutputConfig(config);
colConfig4.setColumnOrder(4);
I2b2Concept concept4 =
new I2b2Concept(
"\\\\i2b2\\Concepts\\MyConcept4", 2, "concept_dimension", "MyConcept4", "N");
colConfig4.setI2b2Concept(concept4);
colConfig4.setColumnName("Systolic");
colConfig4.setDisplayFormat(OutputColumnConfiguration.DisplayFormat.VALUE);
colConfig4.setIncludeTimeRange(true);
colConfig4.setIncludeUnits(false);
colConfig4.setHowMany(2);
OutputColumnConfiguration colConfig5 = new OutputColumnConfiguration();
colConfig5.setOutputConfig(config);
colConfig5.setColumnOrder(5);
I2b2Concept concept5 =
new I2b2Concept(
"\\\\i2b2\\Concepts\\MyConcept5", 2, "concept_dimension", "MyConcept5", "N");
colConfig5.setI2b2Concept(concept5);
colConfig5.setColumnName("Diastolic");
colConfig5.setDisplayFormat(OutputColumnConfiguration.DisplayFormat.VALUE);
colConfig5.setIncludeTimeRange(true);
colConfig5.setIncludeUnits(false);
colConfig5.setHowMany(2);
config.getColumnConfigs().add(colConfig1);
config.getColumnConfigs().add(colConfig2);
config.getColumnConfigs().add(colConfig3);
config.getColumnConfigs().add(colConfig4);
config.getColumnConfigs().add(colConfig5);
}