Skip to content

Commit

Permalink
Merge pull request #52 from halcyon-project/develop
Browse files Browse the repository at this point in the history 
Develop
  • Loading branch information
@ebremer
ebremer authored Dec 15, 2023
2 parents 4078793 + 594acbb commit 3b32f8c
Show file tree
Hide file tree
Showing 12 changed files with 35 additions and 67 deletions.
3 changes: 1 addition & 2 deletions Halcyon/src/main/java/com/ebremer/halcyon/gui/CollectionActionPanel.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -73,8 +73,7 @@ public void onClick() {
DataCore.getInstance().ReloadSECM();
AccessCachePool.getPool().getKeys().forEach(k->{
System.out.println("Clear key pool --> "+k);
AccessCachePool.getPool().clear(k);

AccessCachePool.getPool().clear(k);
});
}
};
Expand Down
6 changes: 3 additions & 3 deletions Halcyon/src/main/java/com/ebremer/halcyon/puffin/Puffin.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -27,16 +27,16 @@ public Puffin() {
ds.end();
RDFDataMgr.write(System.out, m, Lang.TURTLE);
Model target = ModelFactory.createDefaultModel();
Resource r = target.createResource("https://www.ebremer.com/myfirstcolorlist");
Resource r = target.createResource("https://halcyon.is/res/myfirstcolorlist");
r.addProperty(RDF.type, HAL.AnnotationClassList);
r.addProperty(SchemaDO.name, "My first annotation class list!");
r.addProperty(SchemaDO.name, r.getModel().createResource("http://www.google.com"));
r.addProperty(SchemaDO.name, "HI!");
Resource bn = target.createResource();
bn.addProperty(HAL.hasClassification, SNO.Lymphocytes).addProperty(HAL.color, "#0000ff").addProperty(RDF.type, HAL.AnnotationClass);
bn.addProperty(HAL.classification, SNO.Lymphocytes).addProperty(HAL.color, "#0000ff").addProperty(RDF.type, HAL.AnnotationClass);
r.addProperty(HAL.hasAnnotationClass, bn);
bn = target.createResource();
bn.addProperty(HAL.hasClassification, SNO.Necrosis).addProperty(HAL.color, "#00ff00").addProperty(RDF.type, HAL.AnnotationClass);
bn.addProperty(HAL.classification, SNO.Necrosis).addProperty(HAL.color, "#00ff00").addProperty(RDF.type, HAL.AnnotationClass);
r.addProperty(HAL.hasAnnotationClass, bn);
SHACLForm sf = new SHACLForm("sform", r, HAL.AnnotationClassListShape.asNode(), null);
add(sf);
Expand Down
2 changes: 1 addition & 1 deletion Halcyon/src/main/java/com/ebremer/halcyon/server/Main.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -186,7 +186,7 @@ public FilterRegistrationBean<HALKeycloakOIDCFilter> KeycloakOIDCFilterFilterReg
registration.addUrlPatterns("/*");
registration.setOrder(Ordered.HIGHEST_PRECEDENCE);
registration.addInitParameter(KeycloakOIDCFilter.CONFIG_FILE_PARAM, "keycloak.json");
registration.addInitParameter(KeycloakOIDCFilter.SKIP_PATTERN_PARAM, "(^/skunkworks/.*|^/puffin.*|^/threejs/.*|^/halcyon.*|^/zephyr/.*|^/rdf.*|^/talon/.*|/;jsessionid=.*|/gui/images/halcyon.png|^/wicket/resource/.*|^/multi-viewer.*|^/iiif.*|^/|^/about|^/ListImages.*|^/wicket/resource/com.*\\.css||^/auth/.*|^/favicon.ico)");
registration.addInitParameter(KeycloakOIDCFilter.SKIP_PATTERN_PARAM, "(^/h2.*|^/skunkworks/.*|^/puffin.*|^/threejs/.*|^/halcyon.*|^/zephyr/.*|^/rdf.*|^/talon/.*|/;jsessionid=.*|/gui/images/halcyon.png|^/wicket/resource/.*|^/multi-viewer.*|^/iiif.*|^/|^/about|^/ListImages.*|^/wicket/resource/com.*\\.css||^/auth/.*|^/favicon.ico)");
registration.setEnabled(true);
return registration;
}
Expand Down
2 changes: 1 addition & 1 deletion Halcyon/src/main/java/com/ebremer/halcyon/server/Wicket.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ public FilterRegistrationBean<WicketFilter> wicketFilterRegistration(){
registration.setOrder(5000);
registration.addInitParameter(ContextParamWebApplicationFactory.APP_CLASS_PARAM, HalcyonApplication.class.getName());
registration.addInitParameter(WicketFilter.FILTER_MAPPING_PARAM, "/*");
registration.addInitParameter(IGNORE_PATHS_PARAM, "/skunkworks,/login,/auth,/three.js/,/multi-viewer/,/iiif/,/halcyon/,/images/,/favicon.ico,/rdf,/talon/,/threejs/,/zephyr/,/rdf/");
registration.addInitParameter(IGNORE_PATHS_PARAM, "/h2,/skunkworks,/login,/auth,/three.js/,/multi-viewer/,/iiif/,/halcyon/,/images/,/favicon.ico,/rdf,/talon/,/threejs/,/zephyr/,/rdf/");
return registration;
}
}
3 changes: 2 additions & 1 deletion Halcyon/src/main/java/com/ebremer/halcyon/sparql/Sparql.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -21,14 +21,15 @@ <h2>SPARQL Endpoint</h2>
var tab = yasgui.getTab();
//tab.setQuery("select *\nwhere {graph ?g {?s ?p ?o}}\nlimit 20");
tab.yasqe.addPrefixes({ so: "https://schema.org/" });
tab.yasqe.addPrefixes({hal: "https://www.ebremer.com/halcyon/ns/" });
tab.yasqe.addPrefixes({hal: "https://halcyon.is/ns/" });
tab.yasqe.addPrefixes({rdfs: "http://www.w3.org/2000/01/rdf-schema#" });
tab.yasqe.addPrefixes({rdf: "http://www.w3.org/1999/02/22-rdf-syntax-ns#" });
tab.yasqe.addPrefixes({exif: "http://www.w3.org/2003/12/exif/ns#" });
tab.yasqe.addPrefixes({owl: "http://www.w3.org/2002/07/owl#" });
tab.yasqe.addPrefixes({loc: "http://id.loc.gov/vocabulary/preservation/cryptographicHashFunctions/" });
tab.yasqe.addPrefixes({geo: "http://www.opengis.net/ont/geosparql#" });
tab.yasqe.addPrefixes({dct: "http://purl.org/dc/terms/" });
tab.yasqe.addPrefixes({prov: "http://www.w3.org/ns/prov#" });
tab.yasqe.collapsePrefixes(true);
</script>
</wicket:extend>
Expand Down
9 changes: 5 additions & 4 deletions Halcyon/src/main/java/com/ebremer/halcyon/wicket/FeatureManager.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -27,8 +27,6 @@
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.logging.Level;
import java.util.logging.Logger;
import org.apache.jena.query.Dataset;
import org.apache.jena.query.DatasetFactory;
import org.apache.jena.query.ParameterizedSparqlString;
Expand All @@ -46,6 +44,7 @@
import org.apache.jena.vocabulary.RDF;
import org.apache.jena.vocabulary.RDFS;
import org.apache.jena.vocabulary.SchemaDO;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
Expand All @@ -54,7 +53,7 @@
*/
public class FeatureManager {

private static final org.slf4j.Logger logger = LoggerFactory.getLogger(FeatureManager.class);
private static final Logger logger = LoggerFactory.getLogger(FeatureManager.class);

public static String getFeatures(HashSet<String> features, String urn) {
Dataset ds = DataCore.getInstance().getDataset();
Expand Down Expand Up @@ -89,6 +88,7 @@ public static String getFeatures(HashSet<String> features, String urn) {
pss.setIri("image", urn);
pss.setValues("selected", createactions);
ds.begin(ReadWrite.READ);
logger.debug(pss.toString());
ResultSet results = QueryExecutionFactory.create(pss.toString(), ds).execSelect().materialise();
ds.end();
ArrayList<RDFNode> roc = new ArrayList<>();
Expand All @@ -111,6 +111,7 @@ public static String getFeatures(HashSet<String> features, String urn) {
pss.setNsPrefix("rdf", RDF.uri);
pss.setValues("selected", roc);
ds.begin(ReadWrite.READ);
logger.debug(pss.toString());
ResultSet rs = QueryExecutionFactory.create(pss.toString(), ds).execSelect().materialise();
ds.end();
record ColorCode(String color, int code, String name) {}
Expand Down Expand Up @@ -258,7 +259,7 @@ record ColorCode(String color, int code, String name) {}
out.writeObject(jo);
hold = new String(baos.toByteArray());
} catch (JsonLdError ex) {
Logger.getLogger(FeatureManager.class.getName()).log(Level.SEVERE, null, ex);
logger.error(ex.toString());
}
return HFrame.wow(hold);
}
Expand Down
2 changes: 1 addition & 1 deletion Halcyon/src/main/resources/application.yml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@ logging:
max-history: 10
level:
root: ERROR
com.ebremer.halcyon: ERROR
com.ebremer.halcyon: DEBUG
com.ebremer.beakgraph: ERROR
#org.apache.wicket.Application: ERROR
#org.keycloak.adapters: TRACE
Expand Down
14 changes: 10 additions & 4 deletions halcyon-core/src/main/java/com/ebremer/halcyon/FL/FLHeatmap.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,6 @@
import com.ebremer.halcyon.raptor.Objects.Scale;
import com.ebremer.halcyon.lib.GeometryTools;
import com.ebremer.ns.GEO;
import com.ebremer.ns.PROVO;
import jakarta.json.Json;
import jakarta.json.JsonArray;
import jakarta.json.JsonObject;
Expand Down Expand Up @@ -54,7 +53,6 @@
import org.apache.jena.sparql.vocabulary.DOAP;
import org.apache.jena.vocabulary.DCTerms;
import org.apache.jena.vocabulary.RDF;
import org.apache.jena.vocabulary.RDFS;
import org.apache.jena.vocabulary.SchemaDO;
import org.locationtech.jts.geom.Envelope;
import org.locationtech.jts.geom.Polygon;
Expand Down Expand Up @@ -277,6 +275,13 @@ private Model LoadManifest() {

@Override
public Model LoadExtendedManifest() {
logger.info("Loading ROCrate Manifest");
Model hh = ModelFactory.createDefaultModel();
BeakGraph bg = BeakGraphPool.getPool().borrowObject(uri);
hh.add(bg.getReader().getManifest());
BeakGraphPool.getPool().returnObject(uri, bg);
return hh;
/*
Model hh = ModelFactory.createDefaultModel();
BeakGraph bg = BeakGraphPool.getPool().borrowObject(uri);
Dataset ds = DatasetFactory.wrap(new BGDatasetGraph(bg));
Expand All @@ -289,7 +294,7 @@ public Model LoadExtendedManifest() {
dct:title ?title;
prov:wasGeneratedBy [ a prov:Activity; prov:used ?used; prov:wasAssociatedWith ?wasAssociatedWith ] .
?fc dct:creator ?creator .
?fc dct:publisherr ?publisher .
?fc dct:publisher ?publisher .
?fc dct:references ?references .
?fc hal:hasClassification ?hasClassification .
?fc dct:contributor ?contributor .
Expand All @@ -300,7 +305,7 @@ public Model LoadExtendedManifest() {
dct:title ?title;
prov:wasGeneratedBy [ a prov:Activity; prov:used ?used; prov:wasAssociatedWith ?wasAssociatedWith ] .
optional { ?fc dct:creator ?creator }
optional { ?fc dct:publisherr ?publisherr }
optional { ?fc dct:publisher ?publisher }
optional { ?fc dct:references ?references }
optional { ?fc hal:hasClassification ?hasClassification }
optional { ?fc dct:contributor ?contributor }
Expand All @@ -315,6 +320,7 @@ public Model LoadExtendedManifest() {
pss.setNsPrefix("rdfs", RDFS.uri);
pss.setNsPrefix("prov", PROVO.NS);
return QueryExecutionFactory.create(pss.toString(), hh).execConstruct();
*/
}

@Override
Expand Down
18 changes: 10 additions & 8 deletions halcyon-core/src/main/java/com/ebremer/halcyon/FL/FLSegmentation.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,6 @@
import com.ebremer.halcyon.lib.GeometryTools;
import com.ebremer.halcyon.utils.ImageTools;
import com.ebremer.ns.GEO;
import com.ebremer.ns.PROVO;
import jakarta.json.Json;
import jakarta.json.JsonArray;
import jakarta.json.JsonObject;
Expand Down Expand Up @@ -60,7 +59,6 @@
import org.apache.jena.sparql.vocabulary.DOAP;
import org.apache.jena.vocabulary.DCTerms;
import org.apache.jena.vocabulary.RDF;
import org.apache.jena.vocabulary.RDFS;
import org.apache.jena.vocabulary.SchemaDO;
import org.locationtech.jts.geom.Polygon;
import org.slf4j.Logger;
Expand Down Expand Up @@ -236,18 +234,21 @@ private Model LoadManifest() {
public Model LoadExtendedManifest() {
logger.info("Loading ROCrate Manifest");
Model hh = ModelFactory.createDefaultModel();
BeakGraph bg = BeakGraphPool.getPool().borrowObject(uri);
Dataset ds = DatasetFactory.wrap(new BGDatasetGraph(bg));
hh.add(ds.getDefaultModel());
BeakGraphPool.getPool().returnObject(uri, bg);
BeakGraph bg = BeakGraphPool.getPool().borrowObject(uri);
//Dataset ds = DatasetFactory.wrap(new BGDatasetGraph(bg));
//hh.add(ds.getDefaultModel());
hh.add(bg.getReader().getManifest());
BeakGraphPool.getPool().returnObject(uri, bg);
return hh;
/*
ParameterizedSparqlString pss = new ParameterizedSparqlString(
"""
construct {
?fc a geo:FeatureCollection;
dct:title ?title;
prov:wasGeneratedBy [ a prov:Activity; prov:used ?used; prov:wasAssociatedWith ?wasAssociatedWith ] .
?fc dct:creator ?creator .
?fc dct:publisherr ?publisher .
?fc dct:publisher ?publisher .
?fc dct:references ?references .
?fc hal:hasClassification ?hasClassification .
?fc dct:contributor ?contributor .
Expand All @@ -258,7 +259,7 @@ public Model LoadExtendedManifest() {
dct:title ?title;
prov:wasGeneratedBy [ a prov:Activity; prov:used ?used; prov:wasAssociatedWith ?wasAssociatedWith ] .
optional { ?fc dct:creator ?creator }
optional { ?fc dct:publisherr ?publisherr }
optional { ?fc dct:publisher ?publisher }
optional { ?fc dct:references ?references }
optional { ?fc hal:hasClassification ?hasClassification }
optional { ?fc dct:contributor ?contributor }
Expand All @@ -273,6 +274,7 @@ public Model LoadExtendedManifest() {
pss.setNsPrefix("rdfs", RDFS.uri);
pss.setNsPrefix("prov", PROVO.NS);
return QueryExecutionFactory.create(pss.toString(), hh).execConstruct();
*/
}

@Override
Expand Down
3 changes: 0 additions & 3 deletions halcyon-core/src/main/java/com/ebremer/halcyon/raptor/HeatmapProcess.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -218,9 +218,6 @@ public void Process(BeakWriter bw, Dataset ds) {
Resource FC = last.listResourcesWithProperty(RDF.type, GEO.FeatureCollection).next();
FC.addProperty(RDFS.member, bw.getTarget());
bw.getROC().getManifest().getManifestModel().add(last);
//Model man = bw.getROC().getManifest().getManifestModel();
//man.setNsPrefix("bg", BG.NS);
//man.setNsPrefix("prov", PROVO.NS);
logger.debug("Heatmap process finished...");
}
}
11 changes: 1 addition & 10 deletions halcyon-core/src/main/java/com/ebremer/halcyon/raptor/SegmentationProcess.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -87,8 +87,7 @@ public void FindClassifications(Dataset ds) {
?featureCollection hal:hasClassification ?class
}
where {
?featureCollection
a geo:FeatureCollection;
?featureCollection a geo:FeatureCollection;
rdfs:member ?feature .
?feature hal:classification ?class
}
Expand Down Expand Up @@ -420,9 +419,6 @@ public void Process(BeakWriter bw, Dataset ds) {
}
"""
);
// ?featureCollection a geo:FeatureCollection; prov:wasGeneratedBy ?activity; hal:hasClassification ?classification .
//?activity a prov:Activity; prov:used ?used; prov:wasAssociatedWith ?wasAssociatedWith .
//?used ?up ?uo
pssx.setNsPrefix("so", SchemaDO.NS);
pssx.setNsPrefix("geo", GEO.NS);
pssx.setNsPrefix("dcterms", DCTerms.NS);
Expand Down Expand Up @@ -463,13 +459,8 @@ public void Process(BeakWriter bw, Dataset ds) {
pssx.setNsPrefix("dcterms", DCTerms.NS);
qe = QueryExecutionFactory.create(pssx.toString(), ds.getDefaultModel());
last.add(qe.execConstruct());
//Resource activity = last.listResourcesWithProperty(RDF.type, PROVO.Activity).next();
Resource FC = last.listResourcesWithProperty(RDF.type, GEO.FeatureCollection).next();
//activity.addProperty(SchemaDO.result, bw.getTarget());
FC.addProperty(RDFS.member, bw.getTarget());
bw.getROC().getManifest().getManifestModel().add(last);
//Model man = bw.getROC().getManifest().getManifestModel();
//man.setNsPrefix("bg", BG.NS);
//man.setNsPrefix("prov", PROVO.NS);
}
}
29 changes: 0 additions & 29 deletions ingest/src/main/java/com/ebremer/halcyon/converters/NS2GS.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,6 @@
import org.apache.jena.vocabulary.RDFS;
import org.apache.jena.vocabulary.SchemaDO;
import org.apache.jena.vocabulary.XSD;
import org.slf4j.LoggerFactory;

/**
*
Expand Down Expand Up @@ -264,31 +263,3 @@ public Model call() {
}
}
}

/*
Resource root = m.createResource()
.addProperty(SchemaDO.creator, m.createResource("http://orcid.org/0000-0003-0223-1059"))
.addProperty(RDF.type, SchemaDO.Dataset)
.addLiteral(SchemaDO.keywords, "Whole Slide Imaging")
.addLiteral(SchemaDO.keywords, "pathology")
.addProperty(SchemaDO.datePublished, dateTimeLiteral)
.addLiteral(SchemaDO.keywords, "nuclear segmentation")
.addLiteral(SchemaDO.description, "Nuclear segmentation of TCGA cancer types")
.addLiteral(SchemaDO.name, "cnn-nuclear-segmentations-2019")
.addProperty(SchemaDO.instrument, m.createResource("https://github.com/SBU-BMI/quip_cnn_segmentation/releases/tag/v1.1"))
.addProperty(SchemaDO.publisher, m.createResource("https://ror.org/05qghxh33"))
.addProperty(SchemaDO.publisher, m.createResource("https://ror.org/01882y777"));
root.addProperty(SchemaDO.hasPart, CA);
*/

/*
Resource CA = m.createResource()
.addProperty(RDF.type, SchemaDO.CreateAction)
.addLiteral(SchemaDO.name, "cnn-nuclear-segmentations-2019")
.addLiteral(SchemaDO.description, "cnn-nuclear-segmentations-2019")
.addProperty(SchemaDO.object, image)
.addProperty(SchemaDO.result, SpatialObjectCollection);
*/

0 comments on commit 3b32f8c

Please sign in to comment.