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

Example 46 with MathModelInfo

use of org.vcell.util.document.MathModelInfo 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 47 with MathModelInfo

use of org.vcell.util.document.MathModelInfo 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 48 with MathModelInfo

use of org.vcell.util.document.MathModelInfo 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 49 with MathModelInfo

use of org.vcell.util.document.MathModelInfo 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();
}

Example 50 with MathModelInfo

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

the class TestingFrameworkWindowManager method getUserSelectedRefSimInfo.

public SimulationInfo getUserSelectedRefSimInfo(RequestManager currentRequstManager, VCDocumentInfo vcDocInfo) throws Exception {
    final int MODELTYPE_INDEX = 0;
    final int MODELKEY_INDEX = 2;
    final int SIMNAME_INDEX = 5;
    final String[] ROWDATACOLNAMES = new String[] { "Type", "Model", "Model Key", "Owner", "App", "Sim", "Date" };
    Vector<Object[]> simInfoV = new Vector<Object[]>();
    // BioModelMetaData[] bmMetaDataArr = getRequestManager().getDocumentManager().getSessionManager().getUserMetaDbServer().getBioModelMetaDatas(true);
    // bmMetaDataArr[0].
    BioModelInfo[] bioModelInfoArr = null;
    if (vcDocInfo == null) {
        bioModelInfoArr = currentRequstManager.getDocumentManager().getBioModelInfos();
    } else if (vcDocInfo instanceof BioModelInfo) {
        bioModelInfoArr = new BioModelInfo[] { (BioModelInfo) vcDocInfo };
    }
    for (int i = 0; bioModelInfoArr != null && i < bioModelInfoArr.length; i++) {
        if (bioModelInfoArr[i].getBioModelChildSummary() != null) {
            String[] bmSimContextNamesArr = bioModelInfoArr[i].getBioModelChildSummary().getSimulationContextNames();
            for (int j = 0; bmSimContextNamesArr != null && j < bmSimContextNamesArr.length; j++) {
                String[] bmSimNamesArr = bioModelInfoArr[i].getBioModelChildSummary().getSimulationNames(bmSimContextNamesArr[j]);
                for (int k = 0; bmSimNamesArr != null && k < bmSimNamesArr.length; k++) {
                    // System.out.println("BM "+
                    // bioModelInfoArr[i].getVersion().getOwner().getName()+" "+
                    // bioModelInfoArr[i].getVersion().getName()+
                    // " app="+bmSimContextNamesArr[j]+
                    // " sim="+bmSimNamesArr[k]);
                    simInfoV.add(new Object[] { "BM", bioModelInfoArr[i].getVersion().getName(), bioModelInfoArr[i].getVersion().getVersionKey(), bioModelInfoArr[i].getVersion().getOwner().getName(), bmSimContextNamesArr[j], bmSimNamesArr[k], bioModelInfoArr[i].getVersion().getDate() });
                }
            }
        }
    }
    MathModelInfo[] mathModelInfoArr = null;
    if (vcDocInfo == null) {
        mathModelInfoArr = currentRequstManager.getDocumentManager().getMathModelInfos();
    } else if (vcDocInfo instanceof MathModelInfo) {
        mathModelInfoArr = new MathModelInfo[] { (MathModelInfo) vcDocInfo };
    }
    for (int i = 0; mathModelInfoArr != null && i < mathModelInfoArr.length; i++) {
        if (mathModelInfoArr[i].getMathModelChildSummary() != null) {
            String[] mathSimNamesArr = mathModelInfoArr[i].getMathModelChildSummary().getSimulationNames();
            for (int j = 0; mathSimNamesArr != null && j < mathSimNamesArr.length; j++) {
                // System.out.println("MM "+
                // mathModelInfoArr[i].getVersion().getOwner().getName()+" "+
                // mathModelInfoArr[i].getVersion().getName()+
                // " sim="+mathSimNamesArr[j]);
                simInfoV.add(new Object[] { "MM", mathModelInfoArr[i].getVersion().getName(), mathModelInfoArr[i].getVersion().getVersionKey(), mathModelInfoArr[i].getVersion().getOwner().getName(), null, mathSimNamesArr[j], mathModelInfoArr[i].getVersion().getDate() });
            }
        }
    }
    Object[][] rowData = new Object[simInfoV.size()][ROWDATACOLNAMES.length];
    simInfoV.copyInto(rowData);
    int[] simSelection = DialogUtils.showComponentOKCancelTableList(getComponent(), "Choose Ref Simulation", ROWDATACOLNAMES, rowData, ListSelectionModel.SINGLE_SELECTION);
    if (simSelection == null || simSelection.length == 0) {
        throw UserCancelException.CANCEL_GENERIC;
    }
    Simulation[] simArr = null;
    if (rowData[simSelection[0]][MODELTYPE_INDEX].equals("BM")) {
        BioModel bm = currentRequstManager.getDocumentManager().getBioModel((KeyValue) rowData[simSelection[0]][MODELKEY_INDEX]);
        simArr = bm.getSimulations();
    } else {
        MathModel mm = currentRequstManager.getDocumentManager().getMathModel((KeyValue) rowData[simSelection[0]][MODELKEY_INDEX]);
        simArr = mm.getSimulations();
    }
    for (int i = 0; simArr != null && i < simArr.length; i++) {
        if (simArr[i].getName().equals(rowData[simSelection[0]][SIMNAME_INDEX])) {
            return simArr[i].getSimulationInfo();
        }
    }
    throw new Exception("Couldn't find selected simulation");
}