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update master with many changes on dev #343

Merged
merged 43 commits into from
Aug 19, 2020
Merged

update master with many changes on dev #343

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7028d18
added root-type to default m3batch response
goodb Jun 12, 2020
66478d7
test doesn't instantiate the map first
goodb Jun 12, 2020
baa5c78
some change from golr
goodb Jun 12, 2020
6a1cbb9
baby proofing to suit test
goodb Jun 12, 2020
497e0d0
Merge pull request #327 from geneontology/issue-325-fast-types
kltm Jun 12, 2020
e593d65
adding a shex validator test into minerva-core
goodb Jun 28, 2020
1fe3b6e
local neo owl ontology no longer needed
goodb Jun 28, 2020
db5580a
adding test fail file - repinging travis
goodb Jun 28, 2020
cc19da2
fun linux mac difference - for travis
goodb Jun 28, 2020
6cae08f
release lock on go_lego journal file
goodb Jun 28, 2020
5f802ca
Merge pull request #329 from geneontology/shex-validation-model-metadata
goodb Jun 28, 2020
dd60344
Now capturing cardinality for explanation
goodb Jun 30, 2020
079fc66
now catching cardinality violations in constraint objects
goodb Jun 30, 2020
aad0541
updating to correct tests
goodb Jul 2, 2020
f7d2a3e
Update test-multi-org-1.ttl
goodb Jul 2, 2020
5a3ea75
updated tests
goodb Jul 3, 2020
fb08e88
resolved search test error introduced by accident..
goodb Jul 3, 2020
bebdc86
Merge pull request #331 from geneontology/add-cardinality-to-shex-val…
goodb Jul 3, 2020
dc7cc68
add search by model id
goodb Jul 17, 2020
931e624
Merge pull request #334 from geneontology/search-by-id
goodb Jul 17, 2020
2c97e57
allow for multiple ids in search
goodb Jul 21, 2020
567d6a0
Merge pull request #336 from geneontology/search-by-id
goodb Jul 21, 2020
e7ededc
adding root types for partial responses.
goodb Jul 23, 2020
7304c44
Merge pull request #340 from geneontology/add-root-types-for-partial-…
goodb Jul 23, 2020
98a3905
basic object model for go-cams populated from OWL model
goodb Jul 24, 2020
4c0228f
expanded statistics for go-cam measurements
goodb Jul 28, 2020
d814335
moving gocam model stats out into its own object
goodb Jul 31, 2020
6d191c0
added model stats to command line results when running shex validation
goodb Aug 4, 2020
136865e
fix up depth recursion
goodb Aug 5, 2020
ad88d63
bumping owlapi from 4.5.13 to 4.5.15
goodb Aug 17, 2020
effe013
Added stats as a default behavior for the command line validator
goodb Aug 17, 2020
108e884
cleaning up tmp testing files
goodb Aug 17, 2020
2103aff
added method to gpadrender to gain access to the GPADData objects
goodb Aug 17, 2020
858d852
not returning anonymous classes as types for instances
goodb Aug 17, 2020
dd2c7d6
added hacky method to try to cure ontology loader problems
goodb Aug 17, 2020
d6d754e
filling in pieces of the gocam model
goodb Aug 17, 2020
af63064
removing unused temporary test method
goodb Aug 17, 2020
e7581e2
cleaning up test
goodb Aug 17, 2020
50613b1
cleaning OWL fail output so it doesn't break the table
goodb Aug 17, 2020
b3842e1
added activity-level file to report folder
goodb Aug 17, 2020
c3a3972
dealing with deprecated classes in gocams
goodb Aug 17, 2020
6942937
more dealing with deprecation and adding an identifier for uris with …
goodb Aug 17, 2020
e5429eb
Merge pull request #342 from geneontology/model-measurements
goodb Aug 18, 2020
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212 changes: 140 additions & 72 deletions minerva-cli/src/main/java/org/geneontology/minerva/cli/CommandLineInterface.java
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11 changes: 8 additions & 3 deletions minerva-converter/src/main/java/org/geneontology/minerva/legacy/sparql/GPADSPARQLExport.java
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Original file line number Diff line number Diff line change
Expand Up @@ -103,8 +103,13 @@ public GPADSPARQLExport(CurieHandler handler, Map<IRI, String> shorthandIndex, M
this.doNotAnnotateSubset = doNotAnnotateSubset;
}

/* This is a bit convoluted in order to minimize redundant queries, for performance reasons. */
public String exportGPAD(WorkingMemory wm, IRI modelIRI) throws InconsistentOntologyException {
Set<GPADData> annotations = getGPAD(wm, modelIRI);
return new GPADRenderer(curieHandler, relationShorthandIndex).renderAll(annotations);
}

/* This is a bit convoluted in order to minimize redundant queries, for performance reasons. */
public Set<GPADData> getGPAD(WorkingMemory wm, IRI modelIRI) throws InconsistentOntologyException {
Model model = ModelFactory.createDefaultModel();
model.add(JavaConverters.setAsJavaSetConverter(wm.facts()).asJava().stream().map(t -> model.asStatement(Bridge.jenaFromTriple(t))).collect(Collectors.toList()));
if (!isConsistent(model)) throw new InconsistentOntologyException();
Expand Down Expand Up @@ -185,7 +190,7 @@ public String exportGPAD(WorkingMemory wm, IRI modelIRI) throws InconsistentOnto
}
}
}
return new GPADRenderer(curieHandler, relationShorthandIndex).renderAll(annotations);
return annotations;
}

private Map<String, String> getModelAnnotations(Model model) {
Expand All @@ -202,7 +207,7 @@ private Map<String, String> getModelAnnotations(Model model) {
String providedBy = qs.getLiteral("provided_by").getLexicalForm();
modelAnnotations.put("assigned-by", providedBy);
}
break;
//break;
}
return modelAnnotations;
}
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6 changes: 6 additions & 0 deletions minerva-core/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -76,5 +76,11 @@
<artifactId>elk-owlapi</artifactId>
<version>0.4.3</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-math3 -->
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math3</artifactId>
<version>3.6.1</version>
</dependency>
</dependencies>
</project>
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