Examples with BioModelInfo org.vcell.util.document.BioModelInfo used on opensource projects

Example 46 with BioModelInfo

use of org.vcell.util.document.BioModelInfo in project vcell by virtualcell.

the class DatabaseWindowManager method findModelsUsingSelectedGeometry.

/**
 * Insert the method's description here.
 * Creation date: (11/6/2005 9:15:25 AM)
 */
public void findModelsUsingSelectedGeometry() {
    AsynchClientTask findModelsTask = new AsynchClientTask("Finding Models...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            VCDocumentInfo selectedDocument = getPanelSelection();
            if (!(selectedDocument instanceof GeometryInfo)) {
                PopupGenerator.showErrorDialog(DatabaseWindowManager.this, "DatabaseWindowManager.findModelsUsingSelectedGeometry expected a GeometryInfo\nbut got type=" + selectedDocument.getClass().getName() + " instead");
                return;
            }
            ReferenceQuerySpec rqs = new ReferenceQuerySpec(VersionableType.Geometry, selectedDocument.getVersion().getVersionKey());
            // try{
            ReferenceQueryResult rqr = getRequestManager().getDocumentManager().findReferences(rqs);
            // cbit.vcell.modeldb.VersionableTypeVersion[] children = (rqr.getVersionableFamily().bChildren()?rqr.getVersionableFamily().getUniqueChildren():null);
            VersionableTypeVersion[] dependants = (rqr.getVersionableFamily().bDependants() ? rqr.getVersionableFamily().getUniqueDependants() : null);
            // System.out.println("\n");
            // if(children != null){
            // for(int i=0;i<children.length;i+= 1){
            // if( children[i] != rqr.getVersionableFamily().getTarget()){
            // System.out.println("Children "+children[i]+" key="+children[i].getVersion().getVersionKey()+" date="+children[i].getVersion().getDate());
            // }
            // }
            // }else{
            // System.out.println("No Children");
            // }
            // if(dependants != null){
            // for(int i=0;i<dependants.length;i+= 1){
            // if( dependants[i] != rqr.getVersionableFamily().getTarget()){
            // System.out.println("Dependants "+dependants[i]+" key="+dependants[i].getVersion().getVersionKey()+" date="+dependants[i].getVersion().getDate());
            // }
            // }
            // }else{
            // System.out.println("No Dependants");
            // }
            // System.out.println("\nVersionableRelationships");
            // cbit.vcell.modeldb.VersionableRelationship[] vrArr = rqr.getVersionableFamily().getDependantRelationships();
            // for(int i=0;i<vrArr.length;i+= 1){
            // System.out.println(vrArr[i].from() +" -> "+vrArr[i].to());
            // }
            Hashtable<String, Object> choices = new Hashtable<String, Object>();
            if (dependants != null) {
                // System.out.println("\nMajor Relationships");
                for (int i = 0; i < dependants.length; i += 1) {
                    boolean isBioModel = dependants[i].getVType().equals(VersionableType.BioModelMetaData);
                    boolean isTop = isBioModel || dependants[i].getVType().equals(VersionableType.MathModelMetaData);
                    if (isTop) {
                        VersionableRelationship[] vrArr2 = rqr.getVersionableFamily().getDependantRelationships();
                        for (int j = 0; j < vrArr2.length; j += 1) {
                            if ((vrArr2[j].from() == dependants[i]) && vrArr2[j].to().getVType().equals((isBioModel ? VersionableType.SimulationContext : VersionableType.MathDescription))) {
                                for (int k = 0; k < vrArr2.length; k += 1) {
                                    if ((vrArr2[k].from() == vrArr2[j].to()) && vrArr2[k].to().getVType().equals(VersionableType.Geometry)) {
                                        String s = (isBioModel ? "BioModel" : "MathModel") + "  " + "\"" + dependants[i].getVersion().getName() + "\"  (" + dependants[i].getVersion().getDate() + ")" + (isBioModel ? " (App=\"" + vrArr2[k].from().getVersion().getName() + "\")" : /*+" -> "*/
                                        "");
                                        // +" Geometry="+vrArr2[k].to().getVersion().getName()+" "+vrArr2[k].to().getVersion().getDate();
                                        choices.put(s, dependants[i]);
                                    // System.out.println(s);
                                    }
                                }
                            }
                        }
                    }
                }
            }
            if (choices.size() > 0) {
                Object[] listObj = choices.keySet().toArray();
                Object o = DialogUtils.showListDialog(getComponent(), listObj, "Models Referencing Geometry (Select To Open) " + selectedDocument.getVersion().getName() + " " + selectedDocument.getVersion().getDate());
                if (o != null) {
                    VersionableTypeVersion v = (VersionableTypeVersion) choices.get(o);
                    // System.out.println(v);
                    if (v.getVType().equals(VersionableType.BioModelMetaData)) {
                        BioModelInfo bmi = getRequestManager().getDocumentManager().getBioModelInfo(v.getVersion().getVersionKey());
                        getRequestManager().openDocument(bmi, DatabaseWindowManager.this, true);
                    } else if (v.getVType().equals(VersionableType.MathModelMetaData)) {
                        MathModelInfo mmi = getRequestManager().getDocumentManager().getMathModelInfo(v.getVersion().getVersionKey());
                        getRequestManager().openDocument(mmi, DatabaseWindowManager.this, true);
                    }
                }
            } else {
                if (dependants == null) {
                    DialogUtils.showInfoDialog(getComponent(), "No Model references found.\n" + (rqr.getVersionableFamily().getTarget().getVersion().getFlag().isArchived() ? "Info: Not Deletable (key=" + rqr.getVersionableFamily().getTarget().getVersion().getVersionKey() + ") because legacy ARCHIVE set" : ""));
                } else {
                    DialogUtils.showInfoDialog(getComponent(), "No current Model references found.\n" + "Geometry has internal database references from\n" + "previously linked Model(s).\n" + "Not Deletable until database is culled (daily).");
                }
            // return;
            }
        // }catch(DataAccessException e){
        // DialogUtils.showErrorDialog(getComponent(), "Error find Geometry Model references\n"+e.getClass().getName()+"\n"+e.getMessage());
        // }
        }
    };
    ClientTaskDispatcher.dispatch(getComponent(), new Hashtable<String, Object>(), new AsynchClientTask[] { findModelsTask }, false);
}

Example 47 with BioModelInfo

use of org.vcell.util.document.BioModelInfo in project vcell by virtualcell.

the class DatabaseWindowManager method compareAnotherEdition.

/**
 * Comment
 */
public void compareAnotherEdition() {
    // 
    if (getPanelSelection() == null) {
        PopupGenerator.showErrorDialog(this, "Error Comparing documents : No first document selected");
        return;
    }
    VCDocumentInfo thisDocumentInfo = getPanelSelection();
    // 
    // Get the previous version of the documentInfo
    // 
    VCDocumentInfo[] documentVersionsList = null;
    try {
        documentVersionsList = getDocumentVersionDates(thisDocumentInfo);
    } catch (DataAccessException e) {
        PopupGenerator.showErrorDialog(this, "Error accessing second document!");
    }
    if (documentVersionsList == null || documentVersionsList.length == 0) {
        PopupGenerator.showErrorDialog(this, "Error Comparing documents : Not Enough Versions to Compare!");
        return;
    }
    // 
    // Obtaining the Dates of the versions as a String, to be displayed as a list
    // 
    String[] versionDatesList = new String[documentVersionsList.length];
    for (int i = 0; i < documentVersionsList.length; i++) {
        versionDatesList[i] = documentVersionsList[i].getVersion().getDate().toString();
    }
    // 
    // Get the user's choice of document version from the list box, use it to get the documentInfo for the
    // corresponding version
    // 
    String newVersionChoice = (String) PopupGenerator.showListDialog(this, versionDatesList, "Please select edition");
    if (newVersionChoice == null) {
        PopupGenerator.showErrorDialog(this, "Error Comparing documents : Second document not selected!");
        return;
    }
    int versionIndex = -1;
    for (int i = 0; i < versionDatesList.length; i++) {
        if (versionDatesList[i].equals(newVersionChoice)) {
            versionIndex = i;
        }
    }
    if (versionIndex == -1) {
        PopupGenerator.showErrorDialog(this, "Error Comparing documents : No such Version Exists " + newVersionChoice);
        return;
    }
    VCDocumentInfo anotherDocumentInfo = documentVersionsList[versionIndex];
    // Check if both document types are of the same kind. If not, throw an error.
    if (((thisDocumentInfo instanceof BioModelInfo) && !(anotherDocumentInfo instanceof BioModelInfo)) || ((thisDocumentInfo instanceof MathModelInfo) && !(anotherDocumentInfo instanceof MathModelInfo)) || ((thisDocumentInfo instanceof GeometryInfo) && !(anotherDocumentInfo instanceof GeometryInfo))) {
        PopupGenerator.showErrorDialog(this, "Error Comparing documents : The two documents are not of the same type!");
        return;
    }
    // Now that we have both the document versions to be compared, do the comparison and display the result
    compareWithOther(anotherDocumentInfo, thisDocumentInfo);
}

Example 48 with BioModelInfo

use of org.vcell.util.document.BioModelInfo in project vcell by virtualcell.

the class DatabaseWindowManager method compareLatestEdition.

/**
 * Comment
 */
public void compareLatestEdition() {
    // 
    if (getPanelSelection() == null) {
        PopupGenerator.showErrorDialog(this, "Error Comparing documents : No first document selected");
        return;
    }
    VCDocumentInfo thisDocumentInfo = getPanelSelection();
    // 
    // Get the latest version of the documentInfo
    // 
    VCDocumentInfo[] documentVersionsList = null;
    try {
        documentVersionsList = getDocumentVersionDates(thisDocumentInfo);
    } catch (DataAccessException e) {
        PopupGenerator.showErrorDialog(this, "Error accessing second document!");
    }
    if (documentVersionsList == null || documentVersionsList.length == 0) {
        PopupGenerator.showErrorDialog(this, "Error Comparing documents : Not Enough Versions to Compare!");
        return;
    }
    // 
    // Obtaining the latest version of the current documentInfo
    // 
    VCDocumentInfo latestDocumentInfo = documentVersionsList[documentVersionsList.length - 1];
    for (int i = 0; i < documentVersionsList.length; i++) {
        if (documentVersionsList[i].getVersion().getDate().after(latestDocumentInfo.getVersion().getDate())) {
            latestDocumentInfo = documentVersionsList[i];
        }
    }
    if (thisDocumentInfo.getVersion().getDate().after(latestDocumentInfo.getVersion().getDate())) {
        PopupGenerator.showErrorDialog(this, "Current Version is the latest! Choose another Version or Model to compare!");
        return;
    }
    // Check if both document types are of the same kind. If not, throw an error.
    if (((thisDocumentInfo instanceof BioModelInfo) && !(latestDocumentInfo instanceof BioModelInfo)) || ((thisDocumentInfo instanceof MathModelInfo) && !(latestDocumentInfo instanceof MathModelInfo)) || ((thisDocumentInfo instanceof GeometryInfo) && !(latestDocumentInfo instanceof GeometryInfo))) {
        PopupGenerator.showErrorDialog(this, "Error Comparing documents : The two documents are not of the same type!");
        return;
    }
    // 
    // Now that we have both the document versions to be compared, do the comparison and display the result
    // 
    compareWithOther(latestDocumentInfo, thisDocumentInfo);
}

Example 49 with BioModelInfo

use of org.vcell.util.document.BioModelInfo in project vcell by virtualcell.

the class FieldDataWindowManager method findReferencingModels.

public boolean findReferencingModels(final ExternalDataIdentifier targetExtDataID, boolean bShowReferencingModelsList) throws DataAccessException, UserCancelException {
    ReferenceQuerySpec rqs = new ReferenceQuerySpec(targetExtDataID);
    ReferenceQueryResult rqr = getRequestManager().getDocumentManager().findReferences(rqs);
    VersionableTypeVersion[] dependants = null;
    Hashtable<VersionableTypeVersion, String[]> choices = new Hashtable<VersionableTypeVersion, String[]>();
    boolean bDanglingReferences = false;
    VersionableType bioModelType = VersionableType.BioModelMetaData;
    VersionableType mathModelType = VersionableType.MathModelMetaData;
    if (rqr != null) {
        dependants = (rqr.getVersionableFamily().bDependants() ? rqr.getVersionableFamily().getUniqueDependants() : null);
        if (dependants != null) {
            for (int i = 0; i < dependants.length; i += 1) {
                boolean isBioModel = dependants[i].getVType().equals(bioModelType);
                boolean isTop = isBioModel || dependants[i].getVType().equals(mathModelType);
                if (isTop) {
                    VersionableRelationship[] vrArr2 = rqr.getVersionableFamily().getDependantRelationships();
                    for (int j = 0; j < vrArr2.length; j += 1) {
                        if ((vrArr2[j].from() == dependants[i]) && vrArr2[j].to().getVType().equals((isBioModel ? VersionableType.SimulationContext : VersionableType.MathDescription))) {
                            for (int k = 0; k < vrArr2.length; k += 1) {
                                boolean bAdd = false;
                                if (k == j && vrArr2[k].from().getVType().equals(mathModelType)) {
                                    bAdd = true;
                                }
                                if ((vrArr2[k].from() == vrArr2[j].to()) && vrArr2[k].to().getVType().equals(VersionableType.MathDescription)) {
                                    bAdd = true;
                                }
                                if (bAdd) {
                                    choices.put(dependants[i], new String[] { dependants[i].getVersion().getName(), (isBioModel ? bioModelType.getTypeName() : mathModelType.getTypeName()), (isBioModel ? vrArr2[k].from().getVersion().getName() : ""), dependants[i].getVersion().getVersionKey().toString() });
                                }
                            }
                        }
                    }
                }
            }
            bDanglingReferences = (choices.size() == 0);
        } else {
            bDanglingReferences = true;
        }
    }
    // FieldDataFileOperationResults fdfor = getRequestManager().getDocumentManager().fieldDataFileOperation(
    // FieldDataFileOperationSpec.createDependantFuncsFieldDataFileOperationSpec(targetExtDataID));
    FieldDataFileOperationResults fdfor = null;
    boolean bHasReferences = false;
    if (choices.size() > 0 || fdfor != null) {
        bHasReferences = true;
        if (bShowReferencingModelsList) {
            String[] columnNames = new String[] { "Model", "Type", "Description" };
            Vector<VersionableType> varTypeV = new Vector<VersionableType>();
            Vector<KeyValue> keyValV = new Vector<KeyValue>();
            Vector<String[]> choicesV = new Vector<String[]>();
            String[][] modelListData = choices.values().toArray(new String[0][0]);
            for (int i = 0; i < modelListData.length; i++) {
                choicesV.add(new String[] { modelListData[i][0], modelListData[i][1], "Model Variable - " + (modelListData[i][2].length() == 0 ? "" : "App='" + modelListData[i][2] + "'") + " version[" + modelListData[i][3] + "]" });
                varTypeV.add((modelListData[i][1].equals(bioModelType.getTypeName()) ? bioModelType : mathModelType));
                keyValV.add(new KeyValue(modelListData[i][3]));
            }
            for (int i = 0; fdfor != null && i < fdfor.dependantFunctionInfo.length; i++) {
                String functionNames = "";
                for (int j = 0; j < fdfor.dependantFunctionInfo[i].funcNames.length; j++) {
                    functionNames += (j > 0 ? "," : "") + fdfor.dependantFunctionInfo[i].funcNames[j];
                }
                choicesV.add(new String[] { fdfor.dependantFunctionInfo[i].referenceSourceName, fdfor.dependantFunctionInfo[i].referenceSourceType, "Data Viewer Function(s) '" + functionNames + "' - " + (fdfor.dependantFunctionInfo[i].applicationName == null ? "" : "App='" + fdfor.dependantFunctionInfo[i].applicationName + "' ") + (fdfor.dependantFunctionInfo[i].simulationName == null ? "" : "Sim='" + fdfor.dependantFunctionInfo[i].simulationName + "' ") + "version[" + fdfor.dependantFunctionInfo[i].refSourceVersionDate + "]" });
                if (fdfor.dependantFunctionInfo[i].referenceSourceType.equals(FieldDataFileOperationResults.FieldDataReferenceInfo.FIELDDATATYPENAME)) {
                    varTypeV.add(null);
                } else if (fdfor.dependantFunctionInfo[i].referenceSourceType.equals(bioModelType.getTypeName())) {
                    varTypeV.add(bioModelType);
                } else if (fdfor.dependantFunctionInfo[i].referenceSourceType.equals(mathModelType.getTypeName())) {
                    varTypeV.add(mathModelType);
                } else {
                    throw new IllegalArgumentException("Unknown reference source type " + fdfor.dependantFunctionInfo[i].referenceSourceType);
                }
                keyValV.add(fdfor.dependantFunctionInfo[i].refSourceVersionKey);
            }
            int[] selectionArr = PopupGenerator.showComponentOKCancelTableList(getComponent(), "References to Field Data (Select To Open) " + targetExtDataID.getName(), columnNames, choicesV.toArray(new String[0][0]), ListSelectionModel.SINGLE_SELECTION);
            if (selectionArr != null && selectionArr.length > 0) {
                if (varTypeV.elementAt(selectionArr[0]) != null) {
                    if (varTypeV.elementAt(selectionArr[0]).equals(bioModelType)) {
                        BioModelInfo bmi = getRequestManager().getDocumentManager().getBioModelInfo(keyValV.elementAt(selectionArr[0]));
                        getRequestManager().openDocument(bmi, FieldDataWindowManager.this, true);
                    } else if (varTypeV.elementAt(selectionArr[0]).equals(mathModelType)) {
                        MathModelInfo mmi = getRequestManager().getDocumentManager().getMathModelInfo(keyValV.elementAt(selectionArr[0]));
                        getRequestManager().openDocument(mmi, FieldDataWindowManager.this, true);
                    } else {
                        throw new IllegalArgumentException("Not expecting varType " + varTypeV.elementAt(selectionArr[0]));
                    }
                } else {
                    PopupGenerator.showInfoDialog(this, "use FiledDataManager to view FieldData '" + choicesV.elementAt(selectionArr[0])[0] + "'");
                }
            }
        }
    } else {
        if (!bDanglingReferences) {
            bHasReferences = false;
            if (bShowReferencingModelsList) {
                PopupGenerator.showInfoDialog(this, "No Model references found for Field Data " + targetExtDataID.getName());
            }
        } else {
            bHasReferences = true;
            if (bShowReferencingModelsList) {
                PopupGenerator.showInfoDialog(this, "No current Model references found.\n" + "Field Data has internal database references from\n" + "previously linked Model(s) that have been deleted.\n" + "Note: Field Data '" + targetExtDataID.getName() + "' is not deletable\n" + "until database is culled (daily).");
            }
        }
    }
    return bHasReferences;
}

Example 50 with BioModelInfo

use of org.vcell.util.document.BioModelInfo in project vcell by virtualcell.

the class TestingFrameworkWindowManager method generateTestCaseReport.

/**
 * Insert the method's description here.
 * Creation date: (8/18/2003 5:36:47 PM)
 */
public String generateTestCaseReport(TestCaseNew testCase, TestCriteriaNew onlyThisTCrit, ClientTaskStatusSupport pp, TFGenerateReport.VCDocumentAndSimInfo userDefinedRefSimInfo) {
    StringBuffer reportTCBuffer = new StringBuffer();
    if (testCase == null) {
        reportTCBuffer.append("\n\tTEST CASE :\tERROR: Test Case is NULL\n");
    } else {
        pp.setMessage(testCase.getVersion().getName() + " " + testCase.getType() + " Getting Simulations");
        // Get the Simulations
        Simulation[] sims = null;
        reportTCBuffer.append("\n\tTEST CASE : " + (testCase.getVersion() != null ? testCase.getVersion().getName() : "Null") + "\n\tAnnotation : " + testCase.getAnnotation() + "\n");
        try {
            if (testCase instanceof TestCaseNewMathModel) {
                MathModelInfo mmInfo = ((TestCaseNewMathModel) testCase).getMathModelInfo();
                MathModel mathModel = getRequestManager().getDocumentManager().getMathModel(mmInfo);
                sims = mathModel.getSimulations();
                reportTCBuffer.append("\tMathModel : " + mmInfo.getVersion().getName() + ", " + mmInfo.getVersion().getDate().toString() + "\n");
            } else if (testCase instanceof TestCaseNewBioModel) {
                TestCaseNewBioModel bioTestCase = (TestCaseNewBioModel) testCase;
                // bioTestCase.
                BioModelInfo bmInfo = bioTestCase.getBioModelInfo();
                BioModel bioModel = getRequestManager().getDocumentManager().getBioModel(bmInfo);
                SimulationContext[] simContextArr = bioModel.getSimulationContexts();
                if (simContextArr != null && simContextArr.length > 0) {
                    SimulationContext simContext = null;
                    for (int i = 0; i < simContextArr.length; i += 1) {
                        if (simContextArr[i].getVersion().getVersionKey().compareEqual(bioTestCase.getSimContextKey())) {
                            simContext = simContextArr[i];
                            break;
                        }
                    }
                    if (simContext != null) {
                        sims = bioModel.getSimulations(simContext);
                        reportTCBuffer.append("\tBioModel : " + bmInfo.getVersion().getName() + ", " + bmInfo.getVersion().getDate().toString() + "\n");
                    }
                }
            }
            if (sims == null || sims.length == 0) {
                reportTCBuffer.append("\tERROR " + "No sims found for TestCase " + (testCase.getVersion() != null ? "name=" + testCase.getVersion().getName() : "key=" + testCase.getTCKey()) + "\n");
            }
            if (testCase.getTestCriterias() == null || sims.length != testCase.getTestCriterias().length) {
                reportTCBuffer.append("\tNote " + "Num sims=" + sims.length + " does not match testCriteria length=" + (testCase.getTestCriterias() != null ? testCase.getTestCriterias().length + "" : "null") + " for TestCase " + (testCase.getVersion() != null ? "name=" + testCase.getVersion().getName() : "key=" + testCase.getTCKey()) + "\n");
            }
            // Sort
            if (sims.length > 0) {
                java.util.Arrays.sort(sims, new java.util.Comparator<Simulation>() {

                    public int compare(Simulation si1, Simulation si2) {
                        return si1.getName().compareTo(si2.getName());
                    }

                    public boolean equals(Object obj) {
                        return false;
                    }
                });
            }
            TestCriteriaNew[] testCriterias = (onlyThisTCrit != null ? new TestCriteriaNew[] { onlyThisTCrit } : testCase.getTestCriterias());
            for (int k = 0; k < sims.length; k++) {
                TestCriteriaNew testCriteria = getMatchingTestCriteria(sims[k], testCriterias);
                if (testCriteria != null) {
                    pp.setMessage((testCase instanceof TestCaseNewMathModel ? "(MM)" : "(BM)") + " " + (onlyThisTCrit == null ? "sim " + (k + 1) + " of " + sims.length : "sim=" + onlyThisTCrit.getSimInfo().getName()) + "  " + testCase.getVersion().getName() + " " + testCase.getType());
                    reportTCBuffer.append(generateTestCriteriaReport(testCase, testCriteria, sims[k], userDefinedRefSimInfo));
                }
            }
        } catch (UserCancelException e) {
            throw e;
        } catch (Throwable e) {
            e.printStackTrace();
            reportTCBuffer.append("\tERROR " + e.getClass().getName() + " mesg=" + e.getMessage() + "\n");
            try {
                if (onlyThisTCrit != null) {
                    updateTCritStatus(onlyThisTCrit, TestCriteriaNew.TCRIT_STATUS_RPERROR, "TestCase Error " + e.getClass().getName() + " " + e.getMessage());
                } else if (testCase.getTestCriterias() != null) {
                    for (int i = 0; i < testCase.getTestCriterias().length; i += 1) {
                        updateTCritStatus(testCase.getTestCriterias()[i], TestCriteriaNew.TCRIT_STATUS_RPERROR, "TestCase Error " + e.getClass().getName() + " " + e.getMessage());
                    }
                }
            } catch (Throwable e2) {
            // 
            }
        }
    }
    return reportTCBuffer.toString();
}