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Multi annotation column #1205

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759a8e5
Multi-Annotations in single column update
pk-mitre Apr 17, 2024
4ad9529
multi_annotations : updated file names and content
pk-mitre Apr 17, 2024
ff9c7a4
Merge branch 'ontodev:master' into multi-annotation-column
pk-mitre Jun 19, 2024
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4 changes: 4 additions & 0 deletions docs/examples/multi_annotations_header_new.tsv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
Term Term ID Annotations
LABEL ID AP


2 changes: 2 additions & 0 deletions docs/examples/multi_annotations_header_old.tsv
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@@ -0,0 +1,2 @@
LABEL ID A acme:p-0000000049 A acme:p-0000000050 A acme:p-0000000051

67 changes: 67 additions & 0 deletions docs/examples/multi_annotations_new.owl
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@@ -0,0 +1,67 @@
<?xml version="1.0"?>
<rdf:RDF xmlns="http://www.w3.org/2002/07/owl#"
xml:base="http://www.w3.org/2002/07/owl"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:acme="https://shangrila.ef.zz/ontology/acme/"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
<Ontology/>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Annotation properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->




<!-- https://shangrila.ef.zz/ontology/acme/p-0000000049 -->

<AnnotationProperty rdf:about="https://shangrila.ef.zz/ontology/acme/p-0000000049"/>



<!-- https://shangrila.ef.zz/ontology/acme/p-0000000050 -->

<AnnotationProperty rdf:about="https://shangrila.ef.zz/ontology/acme/p-0000000050"/>



<!-- https://shangrila.ef.zz/ontology/acme/p-0000000051 -->

<AnnotationProperty rdf:about="https://shangrila.ef.zz/ontology/acme/p-0000000051"/>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Classes
//
///////////////////////////////////////////////////////////////////////////////////////
-->




<!-- https://shangrila.ef.zz/ontology/acme/s-0000014176 -->

<Class rdf:about="https://shangrila.ef.zz/ontology/acme/s-0000014176">
<rdfs:label>ACME Communications INC</rdfs:label>
<acme:p-0000000049> Value ZZ</acme:p-0000000049>
<acme:p-0000000050>ABCD 1234</acme:p-0000000050>
<acme:p-0000000051>CBS ABC,CNN,PBS</acme:p-0000000051>
</Class>
</rdf:RDF>



<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->

2 changes: 2 additions & 0 deletions docs/examples/multi_annotations_new.tsv
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Term Term ID Annotations
ACME Communications INC acme:s-0000014176 acme:p-0000000049 " Value ZZ"|acme:p-0000000050 "ABCD 1234"|acme:p-0000000051 "CBS ABC,CNN,PBS"
67 changes: 67 additions & 0 deletions docs/examples/multi_annotations_old.owl
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<?xml version="1.0"?>
<rdf:RDF xmlns="http://www.w3.org/2002/07/owl#"
xml:base="http://www.w3.org/2002/07/owl"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:acme="https://shangrila.ef.zz/ontology/acme/"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
<Ontology/>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Annotation properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->




<!-- https://shangrila.ef.zz/ontology/acme/p-0000000049 -->

<AnnotationProperty rdf:about="https://shangrila.ef.zz/ontology/acme/p-0000000049"/>



<!-- https://shangrila.ef.zz/ontology/acme/p-0000000050 -->

<AnnotationProperty rdf:about="https://shangrila.ef.zz/ontology/acme/p-0000000050"/>



<!-- https://shangrila.ef.zz/ontology/acme/p-0000000051 -->

<AnnotationProperty rdf:about="https://shangrila.ef.zz/ontology/acme/p-0000000051"/>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Classes
//
///////////////////////////////////////////////////////////////////////////////////////
-->




<!-- https://shangrila.ef.zz/ontology/acme/s-0000014176 -->

<Class rdf:about="https://shangrila.ef.zz/ontology/acme/s-0000014176">
<rdfs:label>ACME Communications INC</rdfs:label>
<acme:p-0000000049> Value ZZ</acme:p-0000000049>
<acme:p-0000000050>ABCD 1234</acme:p-0000000050>
<acme:p-0000000051>CBS ABC,CNN,PBS</acme:p-0000000051>
</Class>
</rdf:RDF>



<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->

2 changes: 2 additions & 0 deletions docs/examples/multi_annotations_old.tsv
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Term Term ID classification1 classification2 classification3
ACME Communications INC acme:s-0000014176 (U) CBS ABC,CNN,PBS
6 changes: 6 additions & 0 deletions docs/template.md
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Expand Up @@ -236,6 +236,12 @@ robot template --template animals_template_error.tsv \
--ext-template animals_ext_template.tsv \
--output results/animals_ext_template.owl
```
MEKS ROBOT multi annotation in a single column

robot template --prefix "acme: https://shangrila.ef.zz/ontology/acme/" \
--template multi_annotations_new.tsv \
--external-template multi_annotations_header_new.tsv
--output results/multi_annotations_new.owl


\* NOTE: the imports would be merged into the output if `--collapse-import-closure true` is included instead.
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32 changes: 30 additions & 2 deletions robot-core/src/main/java/org/obolibrary/robot/Template.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,7 @@
package org.obolibrary.robot;

import java.text.CharacterIterator;
import java.text.StringCharacterIterator;
import java.util.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
Expand Down Expand Up @@ -877,8 +879,34 @@ private void addClassAxioms(IRI iri, List<String> row) throws Exception {
if (value == null || value.trim().isEmpty()) {
continue;
}

if (template.startsWith("A") || template.startsWith("LABEL")) {
if (template.equals("AP")) {
// split multi annotation string
// Ex meks:p-0000000049 "(U)"|meks:p-0000000050 "KECF6"|meks:p-0000000051 "SATL,COMMO,RODNIK
CharacterIterator it = new StringCharacterIterator(value);

// Iterate and print current character
String token = new String();
List<String> annotation_list = new ArrayList<>();
while (it.current() != CharacterIterator.DONE) {
if (it.current() != '|') {
token += it.current();
} else {
annotation_list.add(token);
token = "";
}
it.next();
}
annotation_list.add(token);
// ListString annotation_list[] = value.split("|");
Set<OWLAnnotation> annotations = new HashSet<>();
for (String annotation : annotation_list) {
annotations.addAll(getAnnotations(template, annotation, row, column));
}
// MultiAnnotation
for (OWLAnnotation annotation : annotations) {
axioms.add(dataFactory.getOWLAnnotationAssertionAxiom(iri, annotation));
}
} else if (template.startsWith("A") || template.startsWith("LABEL")) {
// Handle class annotations
Set<OWLAnnotation> annotations = getAnnotations(template, value, row, column);
for (OWLAnnotation annotation : annotations) {
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13 changes: 11 additions & 2 deletions robot-core/src/main/java/org/obolibrary/robot/TemplateHelper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -186,8 +186,10 @@ public static Set<OWLAnnotation> getAnnotations(
if (template.startsWith(">")) {
template = template.substring(1);
}

if (template.startsWith("A ") || template.startsWith("C ")) {
if (template.equals("AP")) {
// MultiAnnotation
return getStringAnnotations(checker, template, split, value, column);
} else if (template.startsWith("A ") || template.startsWith("C ")) {
return getStringAnnotations(checker, template, split, value, column);
} else if (template.startsWith("AT ") || template.startsWith("CT ")) {
if (template.contains("^^")) {
Expand Down Expand Up @@ -717,6 +719,10 @@ public static Set<OWLAnnotation> getStringAnnotations(
if (template.equals("LABEL")) {
// Handle special LABEL case
property = dataFactory.getRDFSLabel();
} else if (template.equals("AP")) {
String name = value.split(" ")[0];
value = value.substring(name.length() + 2).replaceAll("^\"|\"$", "");
property = getAnnotationProperty(checker, name, column);
} else {
String name = template.substring(1).trim();
property = getAnnotationProperty(checker, name, column);
Expand Down Expand Up @@ -930,6 +936,9 @@ public static boolean validateTemplateString(String template) {
} else if (template.matches("^(P .*|PI.?|[SEDI]P .*)")) {
// Properties can be P, PI (does not need to be followed by space), SP, EP, DP, or IP
return true;
} else if (template.equals("AP")) {
// AP multi annotation type
return true;
} else
// Individuals can be I, II (does not need to be followed by space), SI, or DI
return template.matches("^(I .*|II.?|[TSD]I .*)");
Expand Down
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