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Arbitrary uris dc #96

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Arbitrary uris dc #96

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9636eb2
Allow arbitrary uris
IKCAP Feb 25, 2019
6fe7e2c
Merge branch 'dev' into arbitrary_uris_dc
mosoriob Feb 27, 2019
47f644a
Merge branch 'dev' into arbitrary_uris_dc
mosoriob Feb 27, 2019
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4 changes: 2 additions & 2 deletions planner/src/main/java/edu/isi/wings/catalog/component/api/impl/kb/ComponentKB.java
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Original file line number Diff line number Diff line change
Expand Up @@ -648,8 +648,8 @@ protected ComponentRole getRole(KBObject argobj) {
arg.setParam(true);
else if (type.getID().equals(this.pcns + "DataArgument"))
arg.setParam(false);
else if (type.getNamespace().equals(this.dcdomns)
|| type.getNamespace().equals(this.dcns))
else /*if (type.getNamespace().equals(this.dcdomns)
|| type.getNamespace().equals(this.dcns))*/
arg.setType(type.getID());
}
KBObject role = kb.getPropertyValue(argobj, argidProp);
Expand Down
18 changes: 10 additions & 8 deletions planner/src/main/java/edu/isi/wings/catalog/component/api/impl/kb/ComponentReasoningKB.java
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Expand Up @@ -91,7 +91,7 @@ private void initializeMetrics() {
}

protected KBObject copyObjectIntoKB(String id, KBObject obj, KBAPI tkb, String includeNS,
String excludeNS, boolean direct) {
ArrayList<String> excludeNS, boolean direct) {
// Add component to the temporary KB (add all its classes explicitly)
for(KBTriple triple : this.getTriplesForObject(id, obj, includeNS, excludeNS, direct)) {
tkb.addTriple(triple);
Expand All @@ -100,7 +100,7 @@ protected KBObject copyObjectIntoKB(String id, KBObject obj, KBAPI tkb, String i
}

protected KBObject copyObjectClassesIntoKB(String id, KBObject obj, KBAPI tkb, String includeNS,
String excludeNS, boolean direct) {
ArrayList<String> excludeNS, boolean direct) {
// Add component to the temporary KB (add all its classes explicitly)
for(KBTriple triple : this.getObjectClassTriples(id, obj, includeNS, excludeNS, direct)) {
tkb.addTriple(triple);
Expand Down Expand Up @@ -129,7 +129,7 @@ protected ArrayList<String> getConcreteComponentsForAbstract(String id) {
}

protected ArrayList<KBTriple> getTriplesForObject(String id, KBObject obj,
String includeNS, String excludeNS, boolean direct) {
String includeNS, ArrayList<String> excludeNS, boolean direct) {
ArrayList<KBTriple> triples = new ArrayList<KBTriple>();
triples.add(ontologyFactory.getTriple(
ontologyFactory.getObject(id),
Expand All @@ -140,7 +140,7 @@ protected ArrayList<KBTriple> getTriplesForObject(String id, KBObject obj,
}

protected ArrayList<KBTriple> getObjectClassTriples(String id, KBObject obj,
String includeNS, String excludeNS, boolean direct) {
String includeNS, ArrayList<String> excludeNS, boolean direct) {
// Add component to the temporary KB (add all its classes explicitly)
ArrayList<KBTriple> triples = new ArrayList<KBTriple>();

Expand All @@ -158,8 +158,8 @@ protected ArrayList<KBTriple> getObjectClassTriples(String id, KBObject obj,
ArrayList<KBObject> objclses =
this.getAllCachedClassesOfInstance(obj.getID(), direct);
for (KBObject objcls : objclses) {
if ((includeNS != null && objcls.getNamespace().equals(includeNS))
|| (excludeNS != null && !objcls.getNamespace().equals(excludeNS))) {
if ( (includeNS != null && objcls.getNamespace().equals(includeNS))
|| (excludeNS != null && !excludeNS.contains(objcls.getNamespace())) ) {
triples.add(ontologyFactory.getTriple(
tobj, ontologyFactory.getObject(KBUtils.RDF + "type"), objcls));
}
Expand Down Expand Up @@ -426,8 +426,10 @@ public ArrayList<ComponentPacket> findDataDetails(ComponentPacket details, boole

// Copy over the argument's classes to the variable
KBObject argobj = this.kb.getIndividual(arg.getID());
KBObject varobj = this.copyObjectClassesIntoKB(varid, argobj, tkb, this.dcdomns,
null, false);
ArrayList<String> excludeNS = new ArrayList<String>();
excludeNS.add(this.pcns);
excludeNS.add(this.dcns);
KBObject varobj = this.copyObjectClassesIntoKB(varid, argobj, tkb, null, excludeNS, false);
if(varobj == null)
continue;

Expand Down
11 changes: 8 additions & 3 deletions planner/src/main/java/edu/isi/wings/catalog/data/api/impl/kb/DataCreationKB.java
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Original file line number Diff line number Diff line change
Expand Up @@ -102,7 +102,7 @@ public ArrayList<String> getAllDatatypeIds() {
"SELECT ?type\n" +
"WHERE {\n" +
"?type a <"+KBUtils.OWL+"Class> .\n" +
"FILTER ( STRSTARTS(STR(?type), \"" + this.dcdomns + "\"))\n" +
//"FILTER ( STRSTARTS(STR(?type), \"" + this.dcdomns + "\"))\n" +
"}";

this.start_read();
Expand All @@ -114,7 +114,8 @@ public ArrayList<String> getAllDatatypeIds() {
if(vals.get("type") == null)
continue;
String typeid = vals.get("type").getID();
list.add(typeid);
if(!typeid.equals(this.dcns + "Metrics"))
list.add(typeid);
}
this.end();
return list;
Expand Down Expand Up @@ -719,9 +720,11 @@ private DataTree createHierarchy(String classid, boolean types_only) {
}
ArrayList<KBObject> subclasses = this.getSubClasses(cls);
for (KBObject subcls : subclasses) {
/*
if (!subcls.getNamespace().equals(this.dcdomns)
&& !subcls.getNamespace().equals(this.dcdomns))
&& !subcls.getNamespace().equals(this.dcns))
continue;
*/
DataItem institem = new DataItem(subcls.getID(), DataItem.DATATYPE);
DataTreeNode childnode = new DataTreeNode(institem);
node.addChild(childnode);
Expand Down Expand Up @@ -775,8 +778,10 @@ private ArrayList<MetadataProperty> createMetadataProperties(ArrayList<KBObject>
ArrayList<MetadataProperty> list = new ArrayList<MetadataProperty>();
for (KBObject property : properties) {
// Ignore properties not declared in this domain
/*
if (!property.getNamespace().equals(this.dcdomns))
continue;
*/
MetadataProperty prop = this.createMetadataProperty(property);
if (prop != null)
list.add(prop);
Expand Down
3 changes: 3 additions & 0 deletions planner/src/main/java/edu/isi/wings/planner/api/impl/kb/WorkflowGenerationKB.java
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Original file line number Diff line number Diff line change
Expand Up @@ -388,9 +388,11 @@ private ArrayList<VariableBindingsList> selectInputDataForVariables(
}

Variable[] variables = specializedTemplate.getVariables();
String varNS = null;
ArrayList<String> blacklist = new ArrayList<String>(variables.length);
String variableNS = null;
for (Variable variable : variables) {
varNS = variable.getNamespace();
blacklist.add(variable.getID());
variableNS = variable.getNamespace();
}
Expand Down Expand Up @@ -487,6 +489,7 @@ private ArrayList<VariableBindingsList> selectInputDataForVariables(

this.addExplanation("Querying the DataReasoningAPI with the following constraints: <br/>"
+ inputConstraints.toString().replaceAll(",", "<br/>"));

ArrayList<VariableBindingsList> partialList = dc.findDataSources(inputConstraints, variableNS);

if (partialList == null
Expand Down
8 changes: 1 addition & 7 deletions portal/src/main/java/edu/isi/wings/portal/controllers/DataController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -42,10 +42,7 @@
import edu.isi.wings.catalog.provenance.api.ProvenanceAPI;
import edu.isi.wings.catalog.provenance.classes.ProvActivity;
import edu.isi.wings.catalog.provenance.classes.Provenance;
import edu.isi.wings.catalog.resource.classes.GridkitCloud;
import edu.isi.wings.catalog.resource.classes.Machine;
import edu.isi.wings.common.kb.KBUtils;
import edu.isi.wings.opmm.HashUtils;
import edu.isi.wings.portal.classes.config.Config;
import edu.isi.wings.portal.classes.config.ServerDetails;
import edu.isi.wings.portal.classes.JsonHandler;
Expand All @@ -57,13 +54,10 @@
import com.google.gson.JsonParser;

import java.io.File;
import java.io.IOException;
import java.net.URL;
import java.util.concurrent.ExecutionException;

import org.asynchttpclient.*;
import org.asynchttpclient.request.body.multipart.InputStreamPart;
import org.tukaani.xz.check.None;

import static java.nio.charset.StandardCharsets.UTF_8;
import static org.asynchttpclient.Dsl.basicAuthRealm;
Expand Down Expand Up @@ -171,7 +165,7 @@ public String publishData(String dataid) {
return null;
}
}
return null;
return null;
}

private String uploadFile(ServerDetails server, File datafile) {
Expand Down
62 changes: 46 additions & 16 deletions portal/src/main/webapp/js/gui/DataViewer.js
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Original file line number Diff line number Diff line change
Expand Up @@ -264,13 +264,13 @@ DataViewer.prototype.openDataTypeEditor = function(args) {
}
if (mine)
myProperties.push({
prop: getLocalName(prop.id),
range: This.getPrefixedDataRange(prop.range)
prop: prop.id,
range: This.getPrefixedDataRange(prop.range)
});
else
inhProperties.push({
prop: getLocalName(prop.id),
range: This.getPrefixedDataRange(prop.range)
prop: prop.id,
range: This.getPrefixedDataRange(prop.range)
});
});

Expand Down Expand Up @@ -298,10 +298,10 @@ DataViewer.prototype.openDataTypeEditor = function(args) {
rec.set('prop', sdata.prop);
var mod = rec.modified;
if (!mod.prop && !mod.range) {
propmods.addedProperties[This.ontns + sdata.prop] = sdata;
propmods.addedProperties[sdata.prop] = sdata;
} else {
var prop = mod.prop ? mod.prop: sdata.prop;
propmods.modifiedProperties[This.ontns + prop] = sdata;
propmods.modifiedProperties[prop] = sdata;
}
}
});
Expand Down Expand Up @@ -445,6 +445,7 @@ DataViewer.prototype.openDataTypeEditor = function(args) {

var typeTabPanel = new Ext.tab.Panel({
plain: true,
region: 'center',
margin: 5
});

Expand Down Expand Up @@ -474,6 +475,7 @@ DataViewer.prototype.openDataTypeEditor = function(args) {
handler: function() {
var p = new dataPropRange();
p.set('range', "xsd:string");
p.set('prop', This.ontns);
var pos = dataTypeStore.getCount();
editorPlugin.cancelEdit();
dataTypeStore.insert(pos, p);
Expand All @@ -498,7 +500,7 @@ DataViewer.prototype.openDataTypeEditor = function(args) {
// This property was just added, don't mark it as a
// deletedProperty for the server
} else if (prop != "") {
propmods.deletedProperties[This.ontns + prop] = 1;
propmods.deletedProperties[prop] = 1;
}
dataTypeStore.remove(r);
}
Expand All @@ -517,6 +519,9 @@ DataViewer.prototype.openDataTypeEditor = function(args) {
flex: 1,
header: 'Property',
editor: propEditor,
renderer: function(url) {
return getLocalName(url);
},
editable: This.advanced_user ? true: false,
menuDisabled: true
}, {
Expand Down Expand Up @@ -609,7 +614,22 @@ DataViewer.prototype.openDataTypeEditor = function(args) {
layout: 'fit',
tbar: mainTbar,
//autoScroll: true,
items: typeTabPanel
items: [
{
layout: 'border',
border: false,
items: [
typeTabPanel,
{
html: '<a href="'+id+'">'+id+'</a>',
margins: '0 0 6 6',
border: false,
region: 'south',
bodyStyle: { background: 'transparent' }
}
]
}
]
});
tab.add(mainPanel);
};
Expand Down Expand Up @@ -666,14 +686,19 @@ DataViewer.prototype.confirmAndRenameDatatype = function(node) {

var dtypeid = node.data.id;
var dtypeName = getLocalName(dtypeid);
var title = "Rename " + dtypeName;
for(var i=0; i<150; i++)
title += "&nbsp;";
title += ".";

Ext.Msg.prompt("Rename " + dtypeName, "Enter new name:", function(btn, text) {
Ext.Msg.prompt(title, "Enter new name:", function(btn, text) {
if (btn == 'ok' && text) {
var newName = getRDFID(text);
var newid = This.ontns + newName;
var newName = getRDFID(getLocalName(text));
var newid = getNamespace(text) + newName;

var enode = This.dataTreePanel.getStore().getNodeById(newid);
if (enode) {
showError(getRDFID(text) + ' already exists ! Choose a different name.');
showError(newName + ' already exists ! Choose a different name.');
This.confirmAndRenameDatatype(node);
return;
}
Expand Down Expand Up @@ -704,7 +729,7 @@ DataViewer.prototype.confirmAndRenameDatatype = function(node) {
}
});
}
}, this, false, dtypeName);
}, this, false, dtypeid);
};

DataViewer.prototype.confirmAndDeleteData = function(node) {
Expand Down Expand Up @@ -1500,9 +1525,14 @@ DataViewer.prototype.addDatatype = function(parentNode) {
}
var parentType = parentNode.data.id;

Ext.Msg.prompt("Add Datatype", "Enter name for the new Datatype:", function(btn, text) {
var title = "Add Datatype";
for(var i=0; i<150; i++)
title += "&nbsp;";
title += ".";

Ext.Msg.prompt(title, "Enter name for the new Datatype:", function(btn, text) {
if (btn == 'ok' && text) {
var newid = This.ontns + getRDFID(text);
var newid = getNamespace(text) + getRDFID(getLocalName(text));
var enode = This.dataTreePanel.getStore().getNodeById(newid);
if (enode) {
showError('Datatype ' + text + ' already exists');
Expand Down Expand Up @@ -1540,7 +1570,7 @@ DataViewer.prototype.addDatatype = function(parentNode) {
}
});
}
}, window, false);
}, window, false, this.ontns);
};

DataViewer.prototype.saveDatatype = function(
Expand Down