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Merge pull request #1148 from dlutz2/export-cmd-bugfixes
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Export cmd bugfixes
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@jamesaoverton
jamesaoverton authored Sep 20, 2023
2 parents 07a2b59 + a7b50d7 commit fa04ed6
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Showing 4 changed files with 999 additions and 17 deletions.
42 changes: 29 additions & 13 deletions robot-core/src/main/java/org/obolibrary/robot/ExportOperation.java
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Original file line number Diff line number Diff line change
Expand Up @@ -724,6 +724,11 @@ private static Set<String> getRestrictionFillers(
}
}
break;
// TODO
case DATA_HAS_VALUE:
break;
default:
break;
}
}
return fillers;
Expand Down Expand Up @@ -831,10 +836,25 @@ private static Set<String> getRestrictionFillers(
}
}
break;
// TODO
case OBJECT_HAS_VALUE:
// property value instance
case OBJECT_COMPLEMENT_OF:
// not ce
case OBJECT_HAS_SELF:
// property Self
// this requires the subject entity to render
case OBJECT_ONE_OF:
// {instance, instance,...}
// this should not occur
case OBJECT_UNION_OF:
// ce or ce or ce
// this should not occur
case OBJECT_INTERSECTION_OF:
// TODO
// ce and ce and ce
// this should not occur
break;
default:
break;
}
}
Expand Down Expand Up @@ -1095,18 +1115,8 @@ private static Row getRow(OWLOntology ontology, Table table, OWLEntity entity) t
case "http://www.w3.org/2002/07/owl#equivalentProperty":
// Equivalent Properties
if (entity.isOWLAnnotationProperty()) {
Collection<OWLAnnotationProperty> eqs =
EntitySearcher.getEquivalentProperties(entity.asOWLAnnotationProperty(), ontology);
row.add(
getObjectCell(
eqs,
col,
displayRendererType,
sortRendererType,
provider,
includeNamed,
includeAnonymous));

// no equivalent annotation property in OWL
break;
} else if (entity.isOWLDataProperty()) {
Collection<OWLDataPropertyExpression> eqs =
EntitySearcher.getEquivalentProperties(entity.asOWLDataProperty(), ontology);
Expand Down Expand Up @@ -1140,6 +1150,8 @@ private static Row getRow(OWLOntology ontology, Table table, OWLEntity entity) t
if (entity.isOWLClass()) {
Collection<OWLClassExpression> disjoints =
EntitySearcher.getDisjointClasses(entity.asOWLClass(), ontology);
// remove self-disjoint
disjoints.remove(entity.asOWLClass());
row.add(
getObjectCell(
disjoints,
Expand All @@ -1153,6 +1165,8 @@ private static Row getRow(OWLOntology ontology, Table table, OWLEntity entity) t
} else if (entity.isOWLDataProperty()) {
Collection<OWLDataPropertyExpression> disjoints =
EntitySearcher.getDisjointProperties(entity.asOWLDataProperty(), ontology);
// remove self-disjoint
disjoints.remove(entity.asOWLDataProperty());
row.add(
getObjectCell(
disjoints,
Expand All @@ -1166,6 +1180,8 @@ private static Row getRow(OWLOntology ontology, Table table, OWLEntity entity) t
} else if (entity.isOWLObjectProperty()) {
Collection<OWLObjectPropertyExpression> disjoints =
EntitySearcher.getDisjointProperties(entity.asOWLObjectProperty(), ontology);
// remove self-disjoint
disjoints.remove(entity.asOWLObjectProperty());
row.add(
getObjectCell(
disjoints,
Expand Down
21 changes: 17 additions & 4 deletions robot-core/src/main/java/org/obolibrary/robot/export/Row.java
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Original file line number Diff line number Diff line change
Expand Up @@ -82,8 +82,8 @@ public void addToWorkbook(Workbook wb, List<Column> columns, String split) {

String value;
String comment = null;
CellStyle style = wb.createCellStyle();
Font font = wb.createFont();
CellStyle style = null;
Font font = null;
if (cell != null) {
List<String> values = cell.getDisplayValues();
if (values.size() > 1) {
Expand All @@ -109,20 +109,34 @@ public void addToWorkbook(Workbook wb, List<Column> columns, String split) {
}

if (cellColor != null) {
if (style == null) {
style = wb.createCellStyle();
}
style.setFillForegroundColor(cellColor.getIndex());
}

FillPatternType cellPattern = cell.getCellPattern();
if (cellColor != null && cellPattern == null) {
cellPattern = FillPatternType.SOLID_FOREGROUND;
}

if (cellPattern != null) {
if (style == null) {
style = wb.createCellStyle();
}
style.setFillPattern(cellPattern);
}

IndexedColors fontColor = cell.getFontColor();
if (fontColor != null) {
if (style == null) {
style = wb.createCellStyle();
}
if (font == null) {
font = wb.createFont();
}
font.setColor(fontColor.getIndex());
style.setFont(font);
}

// Maybe get a comment or null
Expand All @@ -135,8 +149,7 @@ public void addToWorkbook(Workbook wb, List<Column> columns, String split) {
// Add value to cell
xlsxCell.setCellValue(value);

// Add style to cell
style.setFont(font);
// Add style to cell, null is OK
xlsxCell.setCellStyle(style);

// Maybe add a comment
Expand Down
204 changes: 204 additions & 0 deletions robot-core/src/test/java/org/obolibrary/robot/ExportOperationTest.java
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Original file line number Diff line number Diff line change
@@ -1,14 +1,26 @@
package org.obolibrary.robot;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.apache.poi.ss.usermodel.Cell;
import org.apache.poi.ss.usermodel.Row;
import org.apache.poi.ss.usermodel.Sheet;
import org.apache.poi.ss.usermodel.Workbook;
import org.junit.Test;
import org.obolibrary.robot.export.Table;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.model.AxiomType;
import org.semanticweb.owlapi.model.OWLClass;
import org.semanticweb.owlapi.model.OWLEntity;
import org.semanticweb.owlapi.model.OWLObjectProperty;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.model.OWLSubClassOfAxiom;
import org.semanticweb.owlapi.model.parameters.Imports;
import org.semanticweb.owlapi.util.DefaultPrefixManager;

/**
* Tests ExportOperation.
Expand Down Expand Up @@ -53,4 +65,196 @@ public void testExportToXLSX() throws Exception {
v2 = r2.getCell(1).getStringCellValue();
assert (v2.equals("simple:test1"));
}

/**
* Test exporting to Excel with > 64,000 exported records.
*
* @throws Exception on any problem
*/
@Test
public void testLargeExcelExport() throws Exception {

// how many many axioms to create
int axiomCount = 64002;

IOHelper ioHelper = new IOHelper();
ioHelper.addPrefix(
"simple", "https://github.com/ontodev/robot/robot-core/src/test/resources/simple.owl#");

DefaultPrefixManager pfm = ioHelper.getPrefixManager();

OWLOntologyManager owlm = OWLManager.createOWLOntologyManager();
OWLOntology ontology = owlm.createOntology();

// add axiomCount subclass axioms to ontology
// first the super class
OWLClass superClass = CoreTest.dataFactory.getOWLClass("simple:super", pfm);

// then all the subs and axioms
for (int i = 0; i < axiomCount; i++) {
OWLClass subClass = CoreTest.dataFactory.getOWLClass("simple:sub_" + i, pfm);
OWLSubClassOfAxiom subAxiom =
CoreTest.dataFactory.getOWLSubClassOfAxiom(subClass, superClass);
owlm.addAxiom(ontology, subAxiom);
}

// export just the classes and their subclasses
List<String> columns = Arrays.asList("ID", "SubClass Of [ID]");
Map<String, String> options = ExportOperation.getDefaultOptions();
options.put("include", "classes");

// Create the table and render it as a Workbook
Table t = ExportOperation.createExportTable(ontology, ioHelper, columns, options);
Workbook wb = t.asWorkbook("|");

// get the first sheet
Sheet s = wb.getSheetAt(0);

// There should be same number of rows as subclass axioms + 1 for the header row
assert (s.getLastRowNum() == ontology.getAxiomCount(AxiomType.SUBCLASS_OF) + 1);
}

/**
* Test exporting all named headings using simple ontology.
*
* @throws Exception on any problem
*/
@Test
public void testExportNamedHeadingsSimple() throws Exception {
OWLOntology ontology = loadOntology("/simple.owl");
IOHelper ioHelper = new IOHelper();
ioHelper.addPrefix(
"simple", "https://github.com/ontodev/robot/robot-core/src/test/resources/simple.owl#");

// every named header
List<String> columns =
Arrays.asList(
"ID",
"LABEL",
"IRI",
"CURIE",
"Type",
"SYNONYMS",
"SUBCLASSES",
"SubClass Of",
"SubProperty Of",
"Equivalent Class",
"Equivalent Property",
"Disjoint With",
"Domain",
"Range");

// export everything
Map<String, String> options = ExportOperation.getDefaultOptions();
options.put("include", "classes individuals properties");

// Create the table and render it as a Workbook
Table t = ExportOperation.createExportTable(ontology, ioHelper, columns, options);
Workbook wb = t.asWorkbook("|");

Sheet s = wb.getSheetAt(0);
// There should be three rows (0, 1, 2)
assert (s.getLastRowNum() == 3);

// Validate header
// should match size and label
org.apache.poi.ss.usermodel.Row header = s.getRow(0);

short minColIx = header.getFirstCellNum();
short maxColIx = header.getLastCellNum();
int numCol = maxColIx - minColIx;
// same width
assert (numCol == columns.size());

// column header labels should match
for (short colIx = minColIx; colIx < maxColIx; colIx++) {
Cell cell = header.getCell(colIx);
if (cell == null) {
continue;
}
String foundHeader = cell.getStringCellValue();
String expectedHeader = columns.get(colIx);
assert (foundHeader.equals(expectedHeader));
}
}

/**
* Test exporting all named headings and object properties seen in the all-axioms ontology.
*
* @throws Exception on any problem
*/
@Test
public void testExportNamedHeadingsAllAxioms() throws Exception {
OWLOntology ontology = loadOntology("/axioms.owl");
Set<OWLEntity> signature = ontology.getSignature();
// remove datatypes
signature.removeAll(ontology.getDatatypesInSignature());
int entityCount = signature.size();

Set<OWLObjectProperty> properties = ontology.getObjectPropertiesInSignature(Imports.EXCLUDED);

IOHelper ioHelper = new IOHelper();
ioHelper.addPrefix("ax", "https://http://robot.obolibrary.org/export_test/");

// every named header
List<String> columns = new ArrayList<String>();

List<String> hdrLabels =
Arrays.asList(
"ID",
"LABEL",
"Type",
"IRI",
"CURIE",
"SYNONYMS",
"SUBCLASSES",
"SubClass Of",
"SubProperty Of",
"Equivalent Class",
"Equivalent Property",
"Disjoint With",
"Domain",
"Range");

columns.addAll(hdrLabels);

// add all the object properties to the header
for (OWLObjectProperty op : properties) {
String shrt = ioHelper.getPrefixManager().getShortForm(op.getIRI());
columns.add(shrt);
}

// export everything
Map<String, String> options = ExportOperation.getDefaultOptions();
options.put("include", "classes individuals properties");

// Create the table and render it as a Workbook
Table t = ExportOperation.createExportTable(ontology, ioHelper, columns, options);
Workbook wb = t.asWorkbook("|");

Sheet s = wb.getSheetAt(0);
// There should be same number of rows as class,properties and instances in signature
assert (s.getLastRowNum() == entityCount);

// Validate header
// should match size and label
org.apache.poi.ss.usermodel.Row header = s.getRow(0);

short minColIx = header.getFirstCellNum();
short maxColIx = header.getLastCellNum();
int numCol = maxColIx - minColIx;
// should be same width
assert (numCol == columns.size());

// column header labels should match workbook
for (short colIx = minColIx; colIx < maxColIx; colIx++) {
Cell cell = header.getCell(colIx);
if (cell == null) {
continue;
}
String foundHeader = cell.getStringCellValue();
String expectedHeader = columns.get(colIx);
assert (foundHeader.equals(expectedHeader));
}
}
}
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