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

Example 26 with BioModelInfo

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

the class BioModelEditor method setRightBottomPanelOnSelection.

@Override
protected void setRightBottomPanelOnSelection(Object[] selections) {
    if (selections == null) {
        return;
    }
    JComponent bottomComponent = rightBottomEmptyPanel;
    int destComponentIndex = DocumentEditorTabID.object_properties.ordinal();
    boolean bShowInDatabaseProperties = false;
    boolean bShowPathway = false;
    if (selections.length == 1) {
        Object singleSelection = selections[0];
        if (singleSelection instanceof ReactionStep) {
            bottomComponent = getReactionPropertiesPanel();
        } else if (singleSelection instanceof ReactionRule) {
            bottomComponent = getReactionRulePropertiesPanel();
        } else if (singleSelection instanceof SpeciesContext) {
            bottomComponent = getSpeciesPropertiesPanel();
        } else if (singleSelection instanceof MolecularType) {
            bottomComponent = getMolecularTypePropertiesPanel();
        } else if (singleSelection instanceof RbmObservable) {
            bottomComponent = getObservablePropertiesPanel();
        } else if (singleSelection instanceof Structure) {
            bottomComponent = getStructurePropertiesPanel();
            getStructurePropertiesPanel().setModel(bioModel.getModel());
        } else if (singleSelection instanceof Parameter) {
            bottomComponent = getParameterPropertiesPanel();
        } else if (singleSelection instanceof SimulationContext) {
            bottomComponent = getApplicationPropertiesPanel();
        } else if (singleSelection instanceof ParameterEstimationTask) {
            bottomComponent = parameterEstimationTaskPropertiesPanel;
        } else if (singleSelection instanceof Product || singleSelection instanceof Reactant) {
            bottomComponent = getReactionParticipantPropertiesPanel();
        } else if (singleSelection instanceof BioModelInfo) {
            bShowInDatabaseProperties = true;
            bottomComponent = bioModelMetaDataPanel;
        } else if (singleSelection instanceof MathModelInfo) {
            bShowInDatabaseProperties = true;
            bottomComponent = mathModelMetaDataPanel;
        } else if (singleSelection instanceof GeometryInfo) {
            bShowInDatabaseProperties = true;
            bottomComponent = geometryMetaDataPanel;
        } else if (singleSelection instanceof SpeciesContextSpec) {
            bottomComponent = getSpeciesContextSpecPanel();
        } else if (singleSelection instanceof ReactionSpec) {
            bottomComponent = getKineticsTypeTemplatePanel();
        } else if (singleSelection instanceof ReactionRuleSpec) {
            // 
            bottomComponent = getReactionRuleSpecPropertiesPanel();
        } else if (singleSelection instanceof BioModelsNetModelInfo) {
            bShowInDatabaseProperties = true;
            bottomComponent = getBioModelsNetPropertiesPanel();
        } else if (singleSelection instanceof Simulation) {
            bottomComponent = getSimulationSummaryPanel();
        } else if (singleSelection instanceof DataSymbol) {
            bottomComponent = getDataSymbolsSpecPanel();
        } else if (singleSelection instanceof BioEvent) {
            bottomComponent = getEventPanel();
        } else if (singleSelection instanceof SpatialObject) {
            bottomComponent = getSpatialObjectPropertyPanel();
        } else if (singleSelection instanceof SpatialProcess) {
            bottomComponent = getSpatialProcessPropertyPanel();
        } else if (singleSelection instanceof BioPaxObject) {
            bottomComponent = bioPaxObjectPropertiesPanel;
        } else if (singleSelection instanceof BioModel || singleSelection instanceof VCMetaData) {
            bottomComponent = bioModelEditorAnnotationPanel;
        } else if (singleSelection instanceof PathwayData) {
            bShowPathway = true;
            bottomComponent = getBioModelEditorPathwayPanel();
        } else if (singleSelection instanceof Model) {
        } else if (singleSelection instanceof RuleParticipantSignature) {
            bottomComponent = getReactionRuleParticipantSignaturePropertiesPanel();
        } else if (singleSelection instanceof CSGObject) {
            bottomComponent = csgObjectPropertiesPanel;
            csgObjectPropertiesPanel.setSimulationContext(getSelectedSimulationContext());
        } else if (singleSelection instanceof DocumentEditorTreeFolderNode) {
            DocumentEditorTreeFolderClass folderClass = ((DocumentEditorTreeFolderNode) singleSelection).getFolderClass();
            if ((folderClass == DocumentEditorTreeFolderClass.REACTIONS_NODE) && !(singleSelection instanceof ReactionRule)) {
                bottomComponent = getReactionPropertiesPanel();
            } else if ((folderClass == DocumentEditorTreeFolderClass.REACTIONS_NODE) && (singleSelection instanceof ReactionRule)) {
                bottomComponent = getReactionRulePropertiesPanel();
            } else if (folderClass == DocumentEditorTreeFolderClass.STRUCTURES_NODE) {
                bottomComponent = getStructurePropertiesPanel();
            } else if (folderClass == DocumentEditorTreeFolderClass.SPECIES_NODE) {
                bottomComponent = getSpeciesPropertiesPanel();
            } else if (folderClass == DocumentEditorTreeFolderClass.MOLECULAR_TYPES_NODE) {
                bottomComponent = getMolecularTypePropertiesPanel();
            } else if (folderClass == DocumentEditorTreeFolderClass.OBSERVABLES_NODE) {
                bottomComponent = getObservablePropertiesPanel();
            } else if (folderClass == DocumentEditorTreeFolderClass.APPLICATIONS_NODE) {
                bottomComponent = getApplicationsPropertiesPanel();
                getApplicationsPropertiesPanel().setBioModel(bioModel);
            } else if (folderClass == DocumentEditorTreeFolderClass.PARAMETER_ESTIMATION_NODE) {
                bottomComponent = parameterEstimationTaskPropertiesPanel;
            }
        }
    }
    if (bShowPathway) {
        for (destComponentIndex = 0; destComponentIndex < rightBottomTabbedPane.getTabCount(); destComponentIndex++) {
            if (rightBottomTabbedPane.getComponentAt(destComponentIndex) == bottomComponent) {
                break;
            }
        }
        String tabTitle = "Pathway Preview";
        if (rightBottomTabbedPane.getTabCount() == destComponentIndex) {
            rightBottomTabbedPane.addTab(tabTitle, new TabCloseIcon(), bottomComponent);
        }
    } else if (bShowInDatabaseProperties) {
        for (destComponentIndex = 0; destComponentIndex < rightBottomTabbedPane.getTabCount(); destComponentIndex++) {
            Component c = rightBottomTabbedPane.getComponentAt(destComponentIndex);
            if (c == bioModelMetaDataPanel || c == mathModelMetaDataPanel || c == geometryMetaDataPanel || c == getBioModelsNetPropertiesPanel()) {
                break;
            }
        }
        if (rightBottomTabbedPane.getTabCount() == destComponentIndex) {
            rightBottomTabbedPane.addTab(DATABASE_PROPERTIES_TAB_TITLE, new TabCloseIcon(), bottomComponent);
        }
    }
    if (rightBottomTabbedPane.getComponentAt(destComponentIndex) != bottomComponent) {
        bottomComponent.setBorder(GuiConstants.TAB_PANEL_BORDER);
        rightBottomTabbedPane.setComponentAt(destComponentIndex, bottomComponent);
        rightSplitPane.repaint();
    }
    if (rightBottomTabbedPane.getSelectedComponent() != bottomComponent) {
        rightBottomTabbedPane.setSelectedComponent(bottomComponent);
    }
}

Example 27 with BioModelInfo

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

the class DatabaseWindowPanel method dbTreePanelActionPerformed.

private void dbTreePanelActionPerformed(java.awt.event.ActionEvent e) {
    String actionCommand = e.getActionCommand();
    if (actionCommand.equals("Open") || actionCommand.equals(DatabaseWindowManager.BM_MM_GM_DOUBLE_CLICK_ACTION)) {
        // check to see if open in new or this window
        BioModelEditor bioModelEditor = null;
        Container c = this;
        while (c != null) {
            if (c instanceof BioModelEditor) {
                bioModelEditor = (BioModelEditor) c;
                break;
            }
            c = c.getParent();
        }
        if (bioModelEditor != null && getSelectedDocumentInfo() instanceof BioModelInfo) {
            if (bioModelEditor.getBioModelWindowManager().hasBlankDocument()) {
                getDatabaseWindowManager().openSelected(bioModelEditor.getBioModelWindowManager(), false);
            } else {
                getDatabaseWindowManager().openSelected(bioModelEditor.getBioModelWindowManager(), true);
            }
        } else {
            getDatabaseWindowManager().openSelected();
        }
    } else if (actionCommand.equals("Delete")) {
        getDatabaseWindowManager().deleteSelected();
    } else if (actionCommand.equals("Permission")) {
        getDatabaseWindowManager().accessPermissions();
    } else if (actionCommand.equals("Export")) {
        getDatabaseWindowManager().exportDocument();
    } else if (actionCommand.equals("Latest Edition")) {
        getDatabaseWindowManager().compareLatestEdition();
    } else if (actionCommand.equals("Previous Edition")) {
        getDatabaseWindowManager().comparePreviousEdition();
    } else if (actionCommand.equals("Another Edition...")) {
        getDatabaseWindowManager().compareAnotherEdition();
    } else if (actionCommand.equals("Another Model...")) {
        getDatabaseWindowManager().compareAnotherModel();
    } else if (actionCommand.equals("Models Using Geometry")) {
        getDatabaseWindowManager().findModelsUsingSelectedGeometry();
    } else if (actionCommand.equals("Archive")) {
        getDatabaseWindowManager().archive();
    } else if (actionCommand.equals("Publish")) {
        getDatabaseWindowManager().publish();
    } else if (actionCommand.equals(NEW_GEOMETRY)) {
        getDatabaseWindowManager().createNewGeometry();
    }
}

Example 28 with BioModelInfo

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

the class DatabaseWindowPanel method currentDocumentInfo.

/**
 * Comment
 */
private void currentDocumentInfo() {
    VCDocumentInfo selectedDocInfo = null;
    switch(getJTabbedPane1().getSelectedIndex()) {
        case 0:
            {
                // VCDocumentType.BIOMODEL_DOC
                selectedDocInfo = (BioModelInfo) getBioModelDbTreePanel1().getSelectedVersionInfo();
                break;
            }
        case 1:
            {
                // VCDocumentType.MATHMODEL_DOC
                selectedDocInfo = (MathModelInfo) getMathModelDbTreePanel1().getSelectedVersionInfo();
                break;
            }
        case 2:
            {
                // VCDocumentType.GEOMETRY_DOC
                selectedDocInfo = (GeometryInfo) getGeometryTreePanel1().getSelectedVersionInfo();
                break;
            }
    }
    setSelectedDocumentInfo(selectedDocInfo);
}

Example 29 with BioModelInfo

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

the class MathVerifier method testDocumentLoad.

private void testDocumentLoad(boolean bUpdateDatabase, User user, VCDocumentInfo documentInfo, VCDocument vcDocumentFromDBCache) {
    KeyValue versionKey = documentInfo.getVersion().getVersionKey();
    // try{
    // String vcDocumentXMLFromDBCacheRoundtrip = null;
    // Compare self same
    Exception bSameCachedAndNotCachedXMLExc = null;
    Exception bSameCachedAndNotCachedObjExc = null;
    Exception bSameSelfXMLCachedRoundtripExc = null;
    Boolean bSameCachedAndNotCachedXML = null;
    Boolean bSameCachedAndNotCachedObj = null;
    Boolean bSameSelfCachedRoundtrip = null;
    // Boolean bSameSelfObjCachedRoundTrip = null;
    long startTime = 0;
    // Long compareXMLTime = null;
    // Long compareObjTime = null;
    // Long loadOriginalXMLTime = null;
    Long loadUnresolvedTime = null;
    if (documentInfo instanceof BioModelInfo) {
        Level existingLogLevel = VCMLComparator.getLogLevel();
        try {
            String xmlRndTrip0 = XmlHelper.bioModelToXML((BioModel) vcDocumentFromDBCache);
            BioModel bioModelRndTrip0 = XmlHelper.XMLToBioModel(new XMLSource(xmlRndTrip0));
            String xmlRndTrip1 = XmlHelper.bioModelToXML((BioModel) bioModelRndTrip0);
            BioModel bioModelRndTrip1 = XmlHelper.XMLToBioModel(new XMLSource(xmlRndTrip1));
            if (Compare.logger != null) {
                Compare.loggingEnabled = true;
                VCMLComparator.setLogLevel(Level.DEBUG);
            }
            bSameSelfCachedRoundtrip = VCMLComparator.compareEquals(xmlRndTrip0, xmlRndTrip1, true);
            System.out.println("----------XML same=" + bSameSelfCachedRoundtrip);
            boolean objectSame = bioModelRndTrip0.compareEqual(bioModelRndTrip1);
            System.out.println("----------Objects same=" + objectSame);
            bSameSelfCachedRoundtrip = bSameSelfCachedRoundtrip && objectSame;
        } catch (Exception e) {
            bSameSelfCachedRoundtrip = null;
            lg.error(e.getMessage(), e);
            bSameSelfXMLCachedRoundtripExc = e;
        } finally {
            Compare.loggingEnabled = false;
            VCMLComparator.setLogLevel(existingLogLevel);
        }
        String fromDBBioModelUnresolvedXML = null;
        try {
            startTime = System.currentTimeMillis();
            fromDBBioModelUnresolvedXML = dbServerImpl.getServerDocumentManager().getBioModelUnresolved(new QueryHashtable(), user, versionKey);
            BioModel vcDocumentFromDBNotCached = XmlHelper.XMLToBioModel(new XMLSource(fromDBBioModelUnresolvedXML));
            loadUnresolvedTime = System.currentTimeMillis() - startTime;
            bSameCachedAndNotCachedObj = vcDocumentFromDBCache.compareEqual(vcDocumentFromDBNotCached);
        } catch (Exception e) {
            lg.error(e.getMessage(), e);
            bSameCachedAndNotCachedObjExc = e;
        }
        if (fromDBBioModelUnresolvedXML != null) {
            try {
                String vcDocumentXMLFromDBCacheRegenerate = XmlHelper.bioModelToXML((BioModel) vcDocumentFromDBCache);
                bSameCachedAndNotCachedXML = VCMLComparator.compareEquals(vcDocumentXMLFromDBCacheRegenerate, fromDBBioModelUnresolvedXML, true);
            } catch (Exception e) {
                lg.error(e.getMessage(), e);
                bSameCachedAndNotCachedXMLExc = e;
            }
        }
    } else {
        Level existingLogLevel = VCMLComparator.getLogLevel();
        try {
            String xmlRndTrip0 = XmlHelper.mathModelToXML((MathModel) vcDocumentFromDBCache);
            MathModel mathModelRndTrip0 = XmlHelper.XMLToMathModel(new XMLSource(xmlRndTrip0));
            String xmlRndTrip1 = XmlHelper.mathModelToXML((MathModel) mathModelRndTrip0);
            MathModel mathModelRndTrip1 = XmlHelper.XMLToMathModel(new XMLSource(xmlRndTrip1));
            if (Compare.logger != null) {
                Compare.loggingEnabled = true;
                VCMLComparator.setLogLevel(Level.DEBUG);
            }
            bSameSelfCachedRoundtrip = VCMLComparator.compareEquals(xmlRndTrip0, xmlRndTrip1, true);
            bSameSelfCachedRoundtrip = bSameSelfCachedRoundtrip && mathModelRndTrip0.compareEqual(mathModelRndTrip1);
        } catch (Exception e) {
            bSameSelfCachedRoundtrip = null;
            lg.error(e.getMessage(), e);
            bSameSelfXMLCachedRoundtripExc = e;
        } finally {
            Compare.loggingEnabled = false;
            VCMLComparator.setLogLevel(existingLogLevel);
        }
        String fromDBMathModelUnresolvedXML = null;
        try {
            startTime = System.currentTimeMillis();
            MathModel vcDocumentFromDBNotCached = dbServerImpl.getServerDocumentManager().getMathModelUnresolved(new QueryHashtable(), user, versionKey);
            loadUnresolvedTime = System.currentTimeMillis() - startTime;
            fromDBMathModelUnresolvedXML = XmlHelper.mathModelToXML(vcDocumentFromDBNotCached);
            bSameCachedAndNotCachedObj = vcDocumentFromDBCache.compareEqual(vcDocumentFromDBNotCached);
        } catch (Exception e) {
            lg.error(e.getMessage(), e);
            bSameCachedAndNotCachedObjExc = e;
        }
        if (fromDBMathModelUnresolvedXML != null) {
            try {
                String vcDocumentXMLFromDBCacheRegenerate = XmlHelper.mathModelToXML((MathModel) vcDocumentFromDBCache);
                bSameCachedAndNotCachedXML = VCMLComparator.compareEquals(vcDocumentXMLFromDBCacheRegenerate, fromDBMathModelUnresolvedXML, true);
            } catch (Exception e) {
                lg.error(e.getMessage(), e);
                bSameCachedAndNotCachedXMLExc = e;
            }
        }
    }
    if (bUpdateDatabase) {
        updateLoadModelsStatTable_CompareTest(versionKey, null, /*loadOriginalXMLTime*/
        loadUnresolvedTime, bSameCachedAndNotCachedXML, bSameCachedAndNotCachedObj, bSameSelfCachedRoundtrip, bSameCachedAndNotCachedXMLExc, bSameCachedAndNotCachedObjExc, bSameSelfXMLCachedRoundtripExc);
    } else {
        System.out.println("loadOriginalXMLTime=" + null + /*loadOriginalXMLTime*/
        " loadUnresolvedTime=" + loadUnresolvedTime);
        System.out.println("bSameCachedAndNotCachedXML=" + bSameCachedAndNotCachedXML + " bSameCachedAndNotCachedObj=" + bSameCachedAndNotCachedObj + " bSameSelfXMLCachedRoundtrip=" + bSameSelfCachedRoundtrip);
        System.out.println("bSameCachedAndNotCachedXMLExc=" + bSameCachedAndNotCachedXMLExc + "\nbSameCachedAndNotCachedObjExc=" + bSameCachedAndNotCachedObjExc + "\nbSameSelfXMLCachedRoundtripExc=" + bSameSelfXMLCachedRoundtripExc);
        System.out.println();
    }
}

Example 30 with BioModelInfo

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

the class MathVerifier method scan.

/**
 * Insert the method's description here.
 * Creation date: (2/2/01 3:40:29 PM)
 */
public void scan(User[] users, boolean bUpdateDatabase, KeyValue[] bioAndMathModelKeys) throws MathException, MappingException, SQLException, DataAccessException, ModelException, ExpressionException {
    // java.util.Calendar calendar = java.util.GregorianCalendar.getInstance();
    // //	calendar.set(2002,java.util.Calendar.MAY,7+1);
    // calendar.set(2002,java.util.Calendar.JULY,1);
    // final java.util.Date fluxCorrectionOrDisablingBugFixDate = calendar.getTime();
    // //	calendar.set(2001,java.util.Calendar.JUNE,13+1);
    // calendar.set(2002,java.util.Calendar.JANUARY,1);
    // final java.util.Date totalVolumeCorrectionFixDate = calendar.getTime();
    KeyValue[] sortedBioAndMathModelKeys = null;
    if (bioAndMathModelKeys != null) {
        sortedBioAndMathModelKeys = bioAndMathModelKeys.clone();
        Arrays.sort(sortedBioAndMathModelKeys, keyValueCpmparator);
    }
    for (int i = 0; i < users.length; i++) {
        User user = users[i];
        BioModelInfo[] bioModelInfos0 = dbServerImpl.getBioModelInfos(user, false);
        MathModelInfo[] mathModelInfos0 = dbServerImpl.getMathModelInfos(user, false);
        if (lg.isTraceEnabled())
            lg.trace("Testing user '" + user + "'");
        Vector<VCDocumentInfo> userBioAndMathModelInfoV = new Vector<VCDocumentInfo>();
        userBioAndMathModelInfoV.addAll(Arrays.asList(bioModelInfos0));
        userBioAndMathModelInfoV.addAll(Arrays.asList(mathModelInfos0));
        // 
        for (int j = 0; j < userBioAndMathModelInfoV.size(); j++) {
            // 
            // if certain Bio or Math models are requested, then filter all else out
            // 
            VCDocumentInfo documentInfo = userBioAndMathModelInfoV.elementAt(j);
            KeyValue versionKey = documentInfo.getVersion().getVersionKey();
            if (sortedBioAndMathModelKeys != null) {
                int srch = Arrays.binarySearch(sortedBioAndMathModelKeys, versionKey, keyValueCpmparator);
                if (srch < 0) {
                    continue;
                }
            }
            if (!(documentInfo instanceof BioModelInfo)) {
                continue;
            }
            // 
            if (skipHash.contains(versionKey)) {
                System.out.println("skipping " + (documentInfo instanceof BioModelInfo ? "BioModel" : "MathModel") + " with key '" + versionKey + "'");
                continue;
            }
            try {
                // 
                // read in the BioModel and MathModel from the database
                // 
                VCDocument vcDocumentFromDBCache = null;
                BigString vcDocumentXMLFromDBCache = null;
                try {
                    long startTime = System.currentTimeMillis();
                    if (documentInfo instanceof BioModelInfo) {
                        vcDocumentXMLFromDBCache = new BigString(dbServerImpl.getServerDocumentManager().getBioModelXML(new QueryHashtable(), user, versionKey, false));
                        vcDocumentFromDBCache = XmlHelper.XMLToBioModel(new XMLSource(vcDocumentXMLFromDBCache.toString()));
                    } else {
                        vcDocumentXMLFromDBCache = new BigString(dbServerImpl.getServerDocumentManager().getMathModelXML(new QueryHashtable(), user, versionKey, false));
                        vcDocumentFromDBCache = XmlHelper.XMLToMathModel(new XMLSource(vcDocumentXMLFromDBCache.toString()));
                    }
                    if (bUpdateDatabase && testFlag.equals(MathVerifier.MV_LOAD_XML)) {
                        updateLoadModelsStatTable_LoadTest(System.currentTimeMillis() - startTime, versionKey, null);
                    }
                } catch (Exception e) {
                    lg.error(e.getMessage(), e);
                    if (bUpdateDatabase && testFlag.equals(MathVerifier.MV_LOAD_XML)) {
                        updateLoadModelsStatTable_LoadTest(0, versionKey, e);
                    }
                }
                if (testFlag.equals(MathVerifier.MV_LOAD_XML)) {
                    // 
                    if (vcDocumentXMLFromDBCache != null) {
                        testDocumentLoad(bUpdateDatabase, user, documentInfo, vcDocumentFromDBCache);
                    }
                } else if (testFlag.equals(MathVerifier.MV_DEFAULT)) {
                    // 
                    if (vcDocumentFromDBCache instanceof BioModel) {
                        BioModel bioModel = (BioModel) vcDocumentFromDBCache;
                        checkMathForBioModel(vcDocumentXMLFromDBCache, bioModel, user, bUpdateDatabase);
                    }
                }
            } catch (Throwable e) {
                // exception in whole BioModel
                lg.error(e.getMessage(), e);
            // can't update anything in database, since we don't know what simcontexts are involved
            }
        }
    }
}