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Workflow inst data & fix var binding id issues
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@hvarg
hvarg committed Feb 20, 2024
1 parent e823e77 commit 78e5788
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Showing 16 changed files with 545 additions and 414 deletions.
3 changes: 1 addition & 2 deletions server/src/main/java/org/diskproject/server/api/impl/DiskResource.java
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,6 @@
import org.diskproject.shared.classes.util.WorkflowTemplateResponse;
import org.diskproject.shared.classes.vocabulary.Vocabulary;
import org.diskproject.shared.classes.workflow.WorkflowVariable;
import org.diskproject.shared.classes.workflow.WorkflowTemplate;
import org.diskproject.shared.classes.workflow.WorkflowRun;

import com.fasterxml.jackson.annotation.JsonProperty;
Expand Down Expand Up @@ -174,7 +173,7 @@ public List<TriggeredLOI> queryGoal(
response.setContentType("application/json");
response.setCharacterEncoding("utf-8");
try {
return this.repo.queryHypothesis(id);
return this.repo.queryGoal(id);
} catch (NotFoundException e) {
try {
ErrorMessage error = new ErrorMessage(e.getMessage());
Expand Down
42 changes: 23 additions & 19 deletions server/src/main/java/org/diskproject/server/db/DiskDB.java
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,8 @@
import java.util.Date;
import java.util.List;

import org.checkerframework.checker.units.qual.t;

import org.diskproject.server.repository.DiskRDF;
import org.diskproject.server.util.KBCache;
import org.diskproject.server.util.KBUtils;
Expand Down Expand Up @@ -530,7 +532,7 @@ private DataQueryTemplate loadDataQueryTemplate (KBObject objTemplate) {
}

private KBObject writeDataQueryResults (DataQueryResult queryResults) {
KBObject dq = domainKB.createObjectOfClass(GUID.randomId("dqt"), DISKOnt.getClass(DISK.DATA_QUERY_TEMPLATE));
KBObject dq = domainKB.createObjectOfClass(GUID.randomId("dqr"), DISKOnt.getClass(DISK.DATA_QUERY_RESULTS));
KBObject qr = _writeDataQueryTemplate(queryResults, dq);
if (queryResults.getQuery() != null)
domainKB.setPropertyValue(qr, DISKOnt.getProperty(DISK.HAS_QUERY), domainKB.createLiteral(queryResults.getQuery()));
Expand Down Expand Up @@ -700,10 +702,10 @@ public List<LineOfInquiry> listLOIPreviews() {
private KBObject writeWorkflowSeed (WorkflowSeed seed, String parentId) {
String prefix = parentId != null ? parentId + "/seeds/" : null;
KBObject seedObj = domainKB.createObjectOfClass(prefix != null ? prefix + GUID.randomId("") : null , DISKOnt.getClass(DISK.WORKFLOW_SEED));
return _writeWorkflowSeed(seed, seedObj, parentId);
return _writeWorkflowSeed(seed, seedObj);
}

private KBObject _writeWorkflowSeed (WorkflowSeed seed, KBObject seedObj, String parentId) {
private KBObject _writeWorkflowSeed (WorkflowSeed seed, KBObject seedObj) {
if (seed.getName() != null)
domainKB.setLabel(seedObj, seed.getName());
if (seed.getDescription() != null)
Expand All @@ -717,19 +719,19 @@ private KBObject _writeWorkflowSeed (WorkflowSeed seed, KBObject seedObj, String
if (parameters != null && parameters.size() > 0) {
for (VariableBinding vBinding: parameters) {
domainKB.addPropertyValue(seedObj, DISKOnt.getProperty(DISK.HAS_PARAMETER),
writeVariableBinding(vBinding, parentId));
writeVariableBinding(vBinding, seedObj.getID()));
}
}
if (inputs != null && inputs.size() > 0) {
for (VariableBinding vBinding: inputs) {
domainKB.addPropertyValue(seedObj, DISKOnt.getProperty(DISK.HAS_INPUT),
writeVariableBinding(vBinding, parentId));
writeVariableBinding(vBinding, seedObj.getID()));
}
}
if (outputs != null && outputs.size() > 0) {
for (VariableBinding vBinding: outputs) {
domainKB.addPropertyValue(seedObj, DISKOnt.getProperty(DISK.HAS_OUTPUT),
writeVariableBinding(vBinding, parentId));
writeVariableBinding(vBinding, seedObj.getID()));
}
}
return seedObj;
Expand Down Expand Up @@ -775,7 +777,8 @@ private WorkflowSeed loadWorkflowSeed (KBObject seedObj) {
private KBObject writeWorkflowInstantiation (WorkflowInstantiation inst, String parentId) {
String prefix = parentId != null ? parentId + "/instantiations/" : null;
KBObject seedObj = domainKB.createObjectOfClass(prefix != null ? prefix + GUID.randomId("") : null , DISKOnt.getClass(DISK.WORKFLOW_INSTANTIATION));
KBObject instObj = _writeWorkflowSeed(inst, seedObj, parentId);
KBObject instObj = _writeWorkflowSeed(inst, seedObj);
String instId = instObj.getID();

if (inst.getStatus() != null)
domainKB.setPropertyValue(instObj, DISKOnt.getClass(DISK.HAS_STATUS), domainKB.createLiteral(getStringFromStatus(inst.getStatus())) );
Expand All @@ -784,15 +787,15 @@ private KBObject writeWorkflowInstantiation (WorkflowInstantiation inst, String
if (data != null && data.size() > 0) {
for (VariableBinding vBinding: data) {
domainKB.addPropertyValue(instObj, DISKOnt.getProperty(DISK.HAS_DATA_BINDINGS),
writeVariableBinding(vBinding, parentId));
writeVariableBinding(vBinding, instId));
}
}

List<Execution> execs = inst.getExecutions();
if (execs != null && execs.size() > 0) {
for (Execution exec: execs) {
domainKB.addPropertyValue(instObj, DISKOnt.getProperty(DISK.HAS_EXECUTION),
writeExecution(exec, parentId));
writeExecution(exec, instId));
}
}
return instObj;
Expand Down Expand Up @@ -1052,7 +1055,6 @@ public boolean writeTLOI(TriggeredLOI tloi) {
Boolean newTLOI = tloi.getId() == null || tloi.getId().equals("");
if (newTLOI) tloi.setId(createTloiURI(GUID.randomId("TriggeredLOI")));
String tloiId = tloi.getId();
//if (domainKB == null) return false;

this.rdf.startWrite();
KBObject tloiItem = writeCommonResource(tloi, tloiId, DISKOnt.getClass(DISK.TRIGGERED_LINE_OF_INQUIRY));
Expand Down Expand Up @@ -1112,27 +1114,27 @@ public TriggeredLOI loadTLOI(String id) {
KBObject status = domainKB.getPropertyValue(obj, DISKOnt.getProperty(DISK.HAS_STATUS));
if (status != null)
tloi.setStatus(getStatusFromString(status.getValueAsString()));
KBObject queryResult = domainKB.getPropertyValue(obj, DISKOnt.getProperty(DISK.HAS_RESULT));
KBObject queryResult = domainKB.getPropertyValue(obj, DISKOnt.getProperty(DISK.HAS_QUERY_RESULTS));
if (queryResult != null)
tloi.setQueryResults(loadDataQueryResult(queryResult));

List<KBObject> wfInst = domainKB.getPropertyValues(obj, DISKOnt.getProperty(DISK.HAS_WORKFLOW_INST));
List<KBObject> mwfInst = domainKB.getPropertyValues(obj, DISKOnt.getProperty(DISK.HAS_META_WORKFLOW_INST));
List<WorkflowInstantiation> wfList = new ArrayList<WorkflowInstantiation>();
List<WorkflowInstantiation> metaWfList = new ArrayList<WorkflowInstantiation>();

if (wfInst != null && wfInst.size() > 0) {
List<WorkflowInstantiation> list = new ArrayList<WorkflowInstantiation>();
for (KBObject t : wfInst) {
list.add(loadWorkflowInstantiation(t));
wfList.add(loadWorkflowInstantiation(t));
}
tloi.setWorkflows(list);
}
if (mwfInst != null && mwfInst.size() > 0) {
List<WorkflowInstantiation> list = new ArrayList<WorkflowInstantiation>();
for (KBObject t : mwfInst) {
list.add(loadWorkflowInstantiation(t));
metaWfList.add(loadWorkflowInstantiation(t));
}
tloi.setMetaWorkflows(list);
}
tloi.setWorkflows(wfList);
tloi.setMetaWorkflows(metaWfList);

this.rdf.end();
return tloi;
Expand Down Expand Up @@ -1167,9 +1169,11 @@ public List<TriggeredLOI> listTLOIs() {
List<String> ids = listObjectIdPerClass(DISKOnt.getClass(DISK.TRIGGERED_LINE_OF_INQUIRY));
for (String fullId: ids) {
String id = getLocalId(fullId);
list.add(this.loadTLOI(id));
TriggeredLOI cur = this.loadTLOI(id);
if (cur != null) {
list.add(cur);
}
}
//TriggeredLOI tloi = loadTLOI(username, tloiId.replaceAll("^.*\\/", ""));
return list;
}

Expand Down
5 changes: 0 additions & 5 deletions server/src/main/java/org/diskproject/server/db/DiskOrchestrator.java
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This file was deleted.

10 changes: 9 additions & 1 deletion server/src/main/java/org/diskproject/server/db/QuestionDB.java
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Original file line number Diff line number Diff line change
Expand Up @@ -280,7 +280,7 @@ public QuestionVariable LoadQuestionVariableFromKB (KBObject var, KBAPI kb) {
return null;
}

public List<Question> listHypothesesQuestions() {
public List<Question> listQuestions() {
return new ArrayList<Question>(this.allQuestions.values());
}

Expand Down Expand Up @@ -356,6 +356,14 @@ private List<VariableOption> queryForOptions (String varName, String query) thro
return options;
}

public Question getQuestion (String id) {
return this.allQuestions.get(id);
}

public QuestionVariable getVariable (String id) {
return this.allVariables.get(id);
}

public String createQuestionOptionsQuery (Question q, List<QuestionVariable> includedVariables) {
if (q != null) {
String queryConstraint = q.getConstraint();
Expand Down
48 changes: 47 additions & 1 deletion server/src/main/java/org/diskproject/server/managers/DataAdapterManager.java
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Original file line number Diff line number Diff line change
Expand Up @@ -12,9 +12,12 @@
import org.diskproject.server.util.ConfigKeys;
import org.diskproject.shared.classes.adapters.DataAdapter;
import org.diskproject.shared.classes.common.Endpoint;
import org.diskproject.shared.classes.loi.DataQueryTemplate;
import org.diskproject.shared.classes.loi.LineOfInquiry;

public class DataAdapterManager {
protected Map<String, DataAdapter> byUrl, byName;
protected Map<String, DataAdapter> byId; // By endpoints ID

public DataAdapterManager () {
this.byUrl = new HashMap<String, DataAdapter>();
Expand Down Expand Up @@ -87,10 +90,53 @@ public Collection<DataAdapter> values () {
return this.byUrl.values();
}

/**
* Create records for each adapter into the RDF database.
* @param db Diskdb where to register the adapters.
*/
public void registerAdapters (DiskDB db) {
this.byId = new HashMap<String, DataAdapter>();
for (DataAdapter adp: this.values()) {
Endpoint cur = db.registerEndpoint(new Endpoint(adp.getName(), adp.getEndpointUrl()));
adp.setId(cur.getId());
String id = cur.getId();
adp.setId(id);
this.byId.put(id, adp);
}
}

/**
* Finds a data adapter by their endpoint id.
* Only works after registerAdapters, as the id is dependent of the database.
* @param id Id of the endpoint that represents the data adapter.
* @return The data adater with that endpoint id.
*/
public DataAdapter getMethodAdapterById (String id) {
if (this.byId != null && this.byId.containsKey(id))
return this.byId.get(id);
return null;
}

/**
* Finds a data adapter by their endpoint.
* Only works after registerAdapters, as endpoints are dependent of the database.
* @param endpoint Endpoint that represents the data adapter.
* @return The data adater for that endpoint.
*/
public DataAdapter getMethodAdapterByEndpoint (Endpoint endpoint) {
if (endpoint != null && endpoint.getId() != null)
return this.getMethodAdapterById(endpoint.getId());
return null;
}

/**
* Finds a data adapter by their endpoint.
* Only works after registerAdapters, as endpoints are dependent of the database.
* @param endpoint Endpoint that represents the data adapter.
* @return The data adater for that endpoint.
*/
public DataAdapter getMethodAdapterByLOI (LineOfInquiry loi) {
DataQueryTemplate dqt = loi.getDataQueryTemplate();
Endpoint e = dqt == null ? null : dqt.getEndpoint();
return e == null ? null : getMethodAdapterByEndpoint(e);
}
}
42 changes: 41 additions & 1 deletion server/src/main/java/org/diskproject/server/managers/MethodAdapterManager.java
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,11 @@

public class MethodAdapterManager {
protected Map<String, MethodAdapter> byUrl, byName;
protected Map<String, MethodAdapter> byId; // By endpoints ID

/**
* Manages and indexes a group of method adapters.
*/
public MethodAdapterManager () {
this.byUrl = new HashMap<String, MethodAdapter>();
this.byName = new HashMap<String, MethodAdapter>();
Expand Down Expand Up @@ -63,6 +67,11 @@ public MethodAdapter getMethodAdapterByUrl (String url) {
return null;
}

/**
* Finds a method adapter by its name.
* @param name Name of the method adapter.
* @return The method adater with that name.
*/
public MethodAdapter getMethodAdapterByName (String name) {
if (this.byName.containsKey(name))
return this.byName.get(name);
Expand Down Expand Up @@ -107,10 +116,41 @@ public String toString () {
return txt;
}

/**
* Create records for each adapter into the RDF database.
* @param db Diskdb where to register the adapters.
*/
public void registerAdapters (DiskDB db) {
this.byId = new HashMap<String, MethodAdapter>();
for (MethodAdapter adp: this.values()) {
Endpoint cur = db.registerEndpoint(new Endpoint(adp.getName(), adp.getEndpointUrl()));
adp.setId(cur.getId());
String id = cur.getId();
adp.setId(id);
byId.put(id, adp);
}
}

/**
* Finds a method adapter by their endpoint id.
* Only works after registerAdapters, as the id is dependent of the database.
* @param id Id of the endpoint that represents the method adapter.
* @return The method adater with that endpoint id.
*/
public MethodAdapter getMethodAdapterById (String id) {
if (this.byId != null && this.byId.containsKey(id))
return this.byId.get(id);
return null;
}

/**
* Finds a method adapter by their endpoint.
* Only works after registerAdapters, as endpoints are dependent of the database.
* @param endpoint Endpoint that represents the method adapter.
* @return The method adater for that endpoint.
*/
public MethodAdapter getMethodAdapterByEndpoint (Endpoint endpoint) {
if (endpoint != null && endpoint.getId() != null)
return this.getMethodAdapterById(endpoint.getId());
return null;
}
}
2 changes: 1 addition & 1 deletion server/src/main/java/org/diskproject/server/managers/VocabularyManager.java
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Original file line number Diff line number Diff line change
Expand Up @@ -106,7 +106,7 @@ private Vocabulary initializeVocabularyFromKB(KBAPI kb, String ns, String prefix
public String getPrefixes() {
String txt = "";
for (Vocabulary v: this.vocabularies.values()) {
txt += String.format("PREFIX %s: <%s>\n", v.getNamespace(), v.getPrefix());
txt += String.format("PREFIX %s: <%s>\n", v.getPrefix(), v.getNamespace());
}
return txt;
}
Expand Down
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