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Merge branch 'dev' into enhance-curie-logic-tests-api
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@haideriqbal
haideriqbal committed Oct 30, 2024
2 parents f66af0d + 4aef53d commit 211bdaa
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Showing 50 changed files with 261 additions and 197 deletions.
5 changes: 4 additions & 1 deletion apitester4/src/main/java/uk/ac/ebi/ols/apitester/RecursiveJsonDiff.java
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Expand Up @@ -63,10 +63,13 @@ public boolean diff() throws FileNotFoundException {
continue;
}

if(!jsonA.equals(jsonB)) {
if(jsonA.equals(jsonB)) {
System.out.println(inputDir + filename + " was equal to " + expectedDir + filename);
} else {
System.out.println(inputDir + filename + " differed from " + expectedDir + filename);
success = false;
}

}

return success;
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4 changes: 3 additions & 1 deletion dataload/rdf2json/src/main/java/uk/ac/ebi/rdf2json/annotators/ShortFormAnnotator.java
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Expand Up @@ -37,7 +37,7 @@ public static void annotateShortForms(OntologyGraph graph) {
}

String shortForm = extractShortForm(graph, ontologyBaseUris, preferredPrefix, c.uri);

/*
CURIEs are formed by following rules:
If there is only one underscore "_" AND the characters before the underscore are PreferredPrefix then replace the underscore with colon ":"
Expand Down Expand Up @@ -71,6 +71,8 @@ public static void annotateShortForms(OntologyGraph graph) {
}
long endTime3 = System.nanoTime();
logger.info("annotate short forms: {}", ((endTime3 - startTime3) / 1000 / 1000 / 1000));


}

private static String extractShortForm(OntologyGraph graph, Set<String> ontologyBaseUris, String preferredPrefix,
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4 changes: 2 additions & 2 deletions testcases_expected_output/annotation-properties/gitIssue502/ontologies.json
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Expand Up @@ -78852,7 +78852,7 @@
"type": [
"literal"
],
"value": "excluded_subClassOf"
"value": "excluded:subClassOf"
},
"directAncestor": [],
"hasDirectChildren": false,
Expand Down Expand Up @@ -78908,7 +78908,7 @@
"type": [
"literal"
],
"value": "should_conform_to"
"value": "should:conform_to"
},
"directAncestor": [],
"hasDirectChildren": false,
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20 changes: 10 additions & 10 deletions testcases_expected_output/annotation-properties/gitIssue502/ontologies_linked.json
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Expand Up @@ -76637,7 +76637,7 @@
"type": [
"literal"
],
"value": "excluded_subClassOf"
"value": "excluded:subClassOf"
},
"type": [
"property",
Expand Down Expand Up @@ -84439,7 +84439,7 @@
"type": [
"literal"
],
"value": "excluded_subClassOf"
"value": "excluded:subClassOf"
},
"type": [
"property",
Expand Down Expand Up @@ -86426,7 +86426,7 @@
"type": [
"literal"
],
"value": "excluded_subClassOf"
"value": "excluded:subClassOf"
},
"type": [
"property",
Expand Down Expand Up @@ -91845,7 +91845,7 @@
"type": [
"literal"
],
"value": "excluded_subClassOf"
"value": "excluded:subClassOf"
},
"type": [
"property",
Expand Down Expand Up @@ -100909,7 +100909,7 @@
"type": [
"literal"
],
"value": "should_conform_to"
"value": "should:conform_to"
},
"type": [
"property",
Expand Down Expand Up @@ -103239,7 +103239,7 @@
"type": [
"literal"
],
"value": "excluded_subClassOf"
"value": "excluded:subClassOf"
},
"type": [
"property",
Expand Down Expand Up @@ -106019,7 +106019,7 @@
"type": [
"literal"
],
"value": "excluded_subClassOf"
"value": "excluded:subClassOf"
},
"type": [
"property",
Expand Down Expand Up @@ -113652,7 +113652,7 @@
"type": [
"literal"
],
"value": "excluded_subClassOf"
"value": "excluded:subClassOf"
},
"type": [
"property",
Expand Down Expand Up @@ -196156,7 +196156,7 @@
"type": [
"literal"
],
"value": "excluded_subClassOf"
"value": "excluded:subClassOf"
},
"directAncestor": [],
"hasDirectChildren": false,
Expand Down Expand Up @@ -196217,7 +196217,7 @@
"type": [
"literal"
],
"value": "should_conform_to"
"value": "should:conform_to"
},
"directAncestor": [],
"hasDirectChildren": false,
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16 changes: 8 additions & 8 deletions testcases_expected_output/duo/classes.jsonl
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16 changes: 8 additions & 8 deletions testcases_expected_output/duo/duo_classes.csv
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6 changes: 3 additions & 3 deletions testcases_expected_output/duo/duo_properties.csv
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16 changes: 8 additions & 8 deletions testcases_expected_output/duo/ontologies.json
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Expand Up @@ -175,7 +175,7 @@
"type": [
"literal"
],
"value": "APOLLO_SV:00000008"
"value": "APOLLO:SV_00000008"
},
"definition": {
"type": [
Expand Down Expand Up @@ -372,7 +372,7 @@
"type": [
"literal"
],
"value": "APOLLO_SV:00000032"
"value": "APOLLO:SV_00000032"
},
"definition": {
"type": [
Expand Down Expand Up @@ -525,7 +525,7 @@
"type": [
"literal"
],
"value": "APOLLO_SV:00000033"
"value": "APOLLO:SV_00000033"
},
"definition": {
"type": [
Expand Down Expand Up @@ -686,7 +686,7 @@
"type": [
"literal"
],
"value": "APOLLO_SV:00000522"
"value": "APOLLO:SV_00000522"
},
"definition": [
{
Expand Down Expand Up @@ -918,7 +918,7 @@
"type": [
"literal"
],
"value": "APOLLO_SV:00000524"
"value": "APOLLO:SV_00000524"
},
"definition": [
{
Expand Down Expand Up @@ -1138,7 +1138,7 @@
"type": [
"literal"
],
"value": "APOLLO_SV:00000796"
"value": "APOLLO:SV_00000796"
},
"definition": {
"type": [
Expand Down Expand Up @@ -78590,7 +78590,7 @@
"type": [
"literal"
],
"value": "created_by"
"value": "created:by"
},
"directAncestor": [],
"hasDirectChildren": false,
Expand Down Expand Up @@ -78646,7 +78646,7 @@
"type": [
"literal"
],
"value": "creation_date"
"value": "creation:date"
},
"directAncestor": [],
"hasDirectChildren": false,
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28 changes: 14 additions & 14 deletions testcases_expected_output/duo/ontologies_linked.json
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Expand Up @@ -177,7 +177,7 @@
"type": [
"literal"
],
"value": "APOLLO_SV:00000008"
"value": "APOLLO:SV_00000008"
},
"definition": {
"type": [
Expand Down Expand Up @@ -653,7 +653,7 @@
"type": [
"literal"
],
"value": "APOLLO_SV:00000032"
"value": "APOLLO:SV_00000032"
},
"definition": {
"type": [
Expand Down Expand Up @@ -1017,7 +1017,7 @@
"type": [
"literal"
],
"value": "APOLLO_SV:00000033"
"value": "APOLLO:SV_00000033"
},
"type": [
"class",
Expand Down Expand Up @@ -1079,7 +1079,7 @@
"type": [
"literal"
],
"value": "APOLLO_SV:00000033"
"value": "APOLLO:SV_00000033"
},
"definition": {
"type": [
Expand Down Expand Up @@ -1457,7 +1457,7 @@
"type": [
"literal"
],
"value": "APOLLO_SV:00000032"
"value": "APOLLO:SV_00000032"
},
"type": [
"class",
Expand Down Expand Up @@ -1497,7 +1497,7 @@
"type": [
"literal"
],
"value": "APOLLO_SV:00000522"
"value": "APOLLO:SV_00000522"
},
"definition": [
{
Expand Down Expand Up @@ -2046,7 +2046,7 @@
"type": [
"literal"
],
"value": "APOLLO_SV:00000524"
"value": "APOLLO:SV_00000524"
},
"definition": [
{
Expand Down Expand Up @@ -2366,7 +2366,7 @@
"type": [
"literal"
],
"value": "APOLLO_SV:00000008"
"value": "APOLLO:SV_00000008"
},
"type": [
"class",
Expand Down Expand Up @@ -2583,7 +2583,7 @@
"type": [
"literal"
],
"value": "APOLLO_SV:00000796"
"value": "APOLLO:SV_00000796"
},
"definition": {
"type": [
Expand Down Expand Up @@ -49533,7 +49533,7 @@
"type": [
"literal"
],
"value": "APOLLO_SV:00000522"
"value": "APOLLO:SV_00000522"
},
"type": [
"class",
Expand Down Expand Up @@ -61396,7 +61396,7 @@
"type": [
"literal"
],
"value": "APOLLO_SV:00000522"
"value": "APOLLO:SV_00000522"
},
"type": [
"class",
Expand Down Expand Up @@ -174717,7 +174717,7 @@
"type": [
"literal"
],
"value": "created_by"
"value": "created:by"
},
"type": [
"property",
Expand Down Expand Up @@ -184244,7 +184244,7 @@
"type": [
"literal"
],
"value": "created_by"
"value": "created:by"
},
"directAncestor": [],
"hasDirectChildren": false,
Expand Down Expand Up @@ -184305,7 +184305,7 @@
"type": [
"literal"
],
"value": "creation_date"
"value": "creation:date"
},
"directAncestor": [],
"hasDirectChildren": false,
Expand Down
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