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

Example 36 with Version

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

the class BioModelTable method getInfo.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.geometry.GeometryInfo
 * @param rset java.sql.ResultSet
 * @param log cbit.vcell.server.SessionLog
 */
public VersionInfo getInfo(ResultSet rset, Connection con, DatabaseSyntax dbSyntax) throws SQLException, org.vcell.util.DataAccessException {
    KeyValue modelRef = new KeyValue(rset.getBigDecimal(table.modelRef.toString()));
    BigDecimal groupid = rset.getBigDecimal(VersionTable.privacy_ColumnName);
    Version version = getVersion(rset, DbDriver.getGroupAccessFromGroupID(con, groupid));
    String softwareVersion = rset.getString(SoftwareVersionTable.table.softwareVersion.toString());
    VCellSoftwareVersion vcSoftwareVersion = VCellSoftwareVersion.fromString(softwareVersion);
    String serialDbChildSummary = DbDriver.varchar2_CLOB_get(rset, BioModelTable.table.childSummarySmall, BioModelTable.table.childSummaryLarge, dbSyntax);
    return new org.vcell.util.document.BioModelInfo(version, modelRef, serialDbChildSummary, vcSoftwareVersion);
}

Example 37 with Version

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

the class BioModelTable method getBioModelMetaData.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.math.MathDescription
 * @param user cbit.vcell.server.User
 * @param rset java.sql.ResultSet
 */
public BioModelMetaData getBioModelMetaData(ResultSet rset, BioModelDbDriver bioModelDbDriver, Connection con, DatabaseSyntax dbSyntax) throws SQLException, DataAccessException {
    // 
    // Get Version
    // 
    BigDecimal groupid = rset.getBigDecimal(VersionTable.privacy_ColumnName);
    Version version = getVersion(rset, DbDriver.getGroupAccessFromGroupID(con, groupid));
    KeyValue bioModelKey = version.getVersionKey();
    KeyValue modelRef = new KeyValue(rset.getBigDecimal(table.modelRef.toString()));
    // 
    // get Simulation Keys for bioModelKey
    // 
    KeyValue[] simKeys = bioModelDbDriver.getSimulationEntriesFromBioModel(con, bioModelKey);
    // 
    // get SimulationContext Keys for bioModelKey
    // 
    KeyValue[] simContextKeys = bioModelDbDriver.getSimContextEntriesFromBioModel(con, bioModelKey);
    // 
    // Get VCMetaData XML
    // 
    String vcMetaDataXML = VCMetaDataTable.getVCMetaDataXML(rset, dbSyntax);
    BioModelMetaData bioModelMetaData = new BioModelMetaData(version, modelRef, simContextKeys, simKeys, vcMetaDataXML);
    return bioModelMetaData;
}

Example 38 with Version

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

the class BioModelPropertiesPanel method updateInterface.

/**
 * Comment
 */
private void updateInterface() {
    if (bioModel == null || bioModelWindowManager == null) {
        return;
    }
    nameLabel.setText(bioModel.getName());
    Version version = bioModel.getVersion();
    if (version != null) {
        ownerLabel.setText(version.getOwner().getName());
        lastModifiedLabel.setText(version.getDate().toString());
        try {
            BioModelInfo bioModelInfo = bioModelWindowManager.getRequestManager().getDocumentManager().getBioModelInfo(version.getVersionKey());
            permissionLabel.setText(bioModelInfo.getVersion().getGroupAccess().getDescription());
        } catch (DataAccessException e) {
            e.printStackTrace();
        }
        changePermissionButton.setEnabled(true);
    }
    webLinksPanel.removeAll();
    webLinksPanel.setLayout(new GridLayout(0, 1));
    Set<MiriamRefGroup> resources = new HashSet<MiriamRefGroup>();
    Set<MiriamRefGroup> isDescribedByAnnotation = bioModel.getVCMetaData().getMiriamManager().getMiriamRefGroups(bioModel, MIRIAMQualifier.MODEL_isDescribedBy);
    Set<MiriamRefGroup> isAnnotation = bioModel.getVCMetaData().getMiriamManager().getMiriamRefGroups(bioModel, MIRIAMQualifier.MODEL_is);
    resources.addAll(isDescribedByAnnotation);
    resources.addAll(isAnnotation);
    for (MiriamRefGroup refGroup : resources) {
        for (MiriamResource miriamResources : refGroup.getMiriamRefs()) {
            LinkNode linkNode = new MiriamTreeModel.LinkNode(MIRIAMQualifier.MODEL_isDescribedBy, miriamResources);
            final String link = linkNode.getLink();
            String labelText = miriamResources.getDataType() == null ? "" : miriamResources.getDataType().getDataTypeName();
            String toolTip = null;
            if (link != null) {
                toolTip = "double-click to open link " + link;
                labelText = "<html><b>" + labelText + "</b>&nbsp;" + "<font color=blue><a href=" + link + ">" + link + "</a></font></html>";
            }
            JLabel label = new JLabel(labelText);
            label.addMouseListener(new MouseListener() {

                public void mouseReleased(MouseEvent e) {
                }

                public void mousePressed(MouseEvent e) {
                }

                public void mouseExited(MouseEvent e) {
                }

                public void mouseEntered(MouseEvent e) {
                }

                public void mouseClicked(MouseEvent e) {
                    if (e.getClickCount() == 2) {
                        DialogUtils.browserLauncher(BioModelPropertiesPanel.this, link, "failed to open " + link);
                    }
                }
            });
            label.setToolTipText(toolTip);
            webLinksPanel.add(label);
        }
    }
    applicationsPanel.removeAll();
    int gridy = 0;
    SimulationContext[] simulationContexts = bioModel.getSimulationContexts();
    if (simulationContexts != null) {
        for (int i = 0; i < simulationContexts.length; i++) {
            SimulationContext simContext = simulationContexts[i];
            JLabel label = new JLabel(simContext.getName());
            label.setFont(label.getFont().deriveFont(Font.BOLD));
            if (simContext.isRuleBased()) {
                if (simContext.getGeometry().getDimension() == 0) {
                    label.setIcon(VCellIcons.appRbmNonspIcon);
                }
            } else if (simContext.isStoch()) {
                if (simContext.getGeometry().getDimension() == 0) {
                    label.setIcon(VCellIcons.appStoNonspIcon);
                } else {
                    label.setIcon(VCellIcons.appStoSpatialIcon);
                }
            } else {
                // deterministic
                if (simContext.getGeometry().getDimension() == 0) {
                    label.setIcon(VCellIcons.appDetNonspIcon);
                } else {
                    label.setIcon(VCellIcons.appDetSpatialIcon);
                }
            }
            GridBagConstraints gbc = new java.awt.GridBagConstraints();
            gbc.gridx = 0;
            gbc.gridy = gridy++;
            gbc.weightx = 1.0;
            gbc.fill = GridBagConstraints.HORIZONTAL;
            gbc.anchor = GridBagConstraints.FIRST_LINE_START;
            if (i > 0) {
                gbc.insets = new Insets(4, 0, 0, 0);
            }
            applicationsPanel.add(label, gbc);
            Geometry geometry = simContext.getGeometry();
            String geometryText = "Compartmental geometry";
            if (geometry != null) {
                Version geometryVersion = geometry.getVersion();
                int dimension = geometry.getDimension();
                if (dimension > 0) {
                    String description = geometry.getDimension() + "D " + (geometry.getGeometrySpec().hasImage() ? "image" : "analytic") + " geometry";
                    geometryText = description;
                    if (geometryVersion != null) {
                        geometryText += " - " + geometryVersion.getName();
                    }
                }
            }
            JLabel geometryLabel = new JLabel(geometryText);
            geometryLabel.setIcon(VCellIcons.geometryIcon);
            JLabel detStochLabel = new JLabel(simContext.getMathType().getDescription());
            detStochLabel.setIcon(VCellIcons.mathTypeIcon);
            gbc.insets = new Insets(2, 20, 2, 2);
            gbc.gridy = gridy++;
            applicationsPanel.add(detStochLabel, gbc);
            gbc.gridy = gridy++;
            if (i == simulationContexts.length - 1) {
                gbc.weighty = 1.0;
            }
            applicationsPanel.add(geometryLabel, gbc);
        }
    }
}

Example 39 with Version

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

the class XmlReader method getMathDescription.

/**
 * This method returns a MathDescription from a XML element.
 * Creation date: (4/26/2001 12:11:14 PM)
 * @return cbit.vcell.math.MathDescription
 * @param param org.jdom.Element
 * @exception cbit.vcell.xml.XmlParseException The exception description.
 */
MathDescription getMathDescription(Element param, Geometry geometry) throws XmlParseException {
    MathDescription mathdes = null;
    Element tempelement;
    // Retrieve Metadata(Version)
    Version version = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace));
    // Retrieve attributes
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    // Create new MathDescription
    if (version != null) {
        mathdes = new MathDescription(version);
    } else {
        mathdes = new MathDescription(name);
    }
    try {
        // this step is needed!
        mathdes.setGeometry(geometry);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("a PropertyVetoException was fired when setting the Geometry to the Mathdescription in the simContext " + name, e);
    }
    // set attributes
    try {
        mathdes.setName(name);
        // String annotation = param.getAttributeValue(XMLTags.AnnotationAttrTag);
        // if (annotation!=null) {
        // mathdes.setDescription(unMangle(annotation));
        // }
        // add Annotation
        String annotationText = param.getChildText(XMLTags.AnnotationTag, vcNamespace);
        if (annotationText != null && annotationText.length() > 0) {
            mathdes.setDescription(unMangle(annotationText));
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("A PropertyVetoException was fired when setting the name " + name + ", to a new MathDescription!", e);
    }
    VariableHash varHash = new VariableHash();
    // Retrieve Constant
    Iterator<Element> iterator = param.getChildren(XMLTags.ConstantTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getConstant(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // Retrieve FilamentRegionVariables
    iterator = param.getChildren(XMLTags.FilamentRegionVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getFilamentRegionVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // Retrieve FilamentVariables
    iterator = param.getChildren(XMLTags.FilamentVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getFilamentVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // retrieve InsideVariables
    // **** This variables are for internal USE ******
    // Retrieve MembraneRegionVariable
    iterator = param.getChildren(XMLTags.MembraneRegionVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getMembraneRegionVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // Retrieve MembraneVariable
    iterator = param.getChildren(XMLTags.MembraneVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getMemVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // Retrieve PointVariable
    iterator = param.getChildren(XMLTags.PointVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getPointVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // retrieve OutsideVariables
    // **** This variables are for internal USE ******
    // Retrieve Volume Region variable
    iterator = param.getChildren(XMLTags.VolumeRegionVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getVolumeRegionVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // Retrieve VolumeVariable
    iterator = param.getChildren(XMLTags.VolumeVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getVolVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // Retrieve StochVolVariable
    iterator = param.getChildren(XMLTags.StochVolVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getStochVolVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // Retrieve all the Functions //This needs to be processed before all the variables are read!
    iterator = param.getChildren(XMLTags.FunctionTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getFunction(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    iterator = param.getChildren(XMLTags.VolumeRandomVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getRandomVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    iterator = param.getChildren(XMLTags.MembraneRandomVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getRandomVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    iterator = param.getChildren(XMLTags.VolumeParticleVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getVolumeParticalVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    iterator = param.getChildren(XMLTags.MembraneParticleVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getMembraneParticalVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // ParticleMolecularTypeTag       getParticleMolecularTypes
    // has to be done before VolumeParticleSpeciesPattern and VolumeParticleObservable
    iterator = param.getChildren(XMLTags.ParticleMolecularTypeTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        mathdes.addParticleMolecularType(getParticleMolecularType(tempelement));
    }
    // VolumeParticleSpeciesPatternTag
    iterator = param.getChildren(XMLTags.VolumeParticleSpeciesPatternTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getVolumeParticleSpeciesPattern(tempelement, mathdes));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // VolumeParticleObservableTag    getParticleObservables
    iterator = param.getChildren(XMLTags.VolumeParticleObservableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getVolumeParticleObservable(tempelement, varHash));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // 
    try {
        mathdes.setAllVariables(varHash.getAlphabeticallyOrderedVariables());
    } catch (MathException e) {
        e.printStackTrace();
        throw new XmlParseException("Error adding the Function variables to the MathDescription " + name, e);
    } catch (ExpressionBindingException e) {
        e.printStackTrace();
        throw new XmlParseException("Error adding the Function variables to the MathDescription " + name, e);
    }
    // Retrieve CompartmentsSubdomains
    iterator = param.getChildren(XMLTags.CompartmentSubDomainTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            mathdes.addSubDomain(getCompartmentSubDomain(tempelement, mathdes));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("Error adding a new CompartmentSubDomain to the MathDescription " + name, e);
        }
    }
    // Retrieve MembraneSubdomains
    iterator = param.getChildren(XMLTags.MembraneSubDomainTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            mathdes.addSubDomain(getMembraneSubDomain(tempelement, mathdes));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("Error adding a new MembraneSubDomain to the MathDescription " + name, e);
        }
    }
    // Retrieve the FilamentSubdomain (if any)
    tempelement = param.getChild(XMLTags.FilamentSubDomainTag, vcNamespace);
    if (tempelement != null) {
        try {
            mathdes.addSubDomain(getFilamentSubDomain(tempelement, mathdes));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("Error adding a new FilamentSubDomain to the MathDescription " + name, e);
        }
    }
    // Retrieve the PointSubdomain (if any)
    tempelement = param.getChild(XMLTags.PointSubDomainTag, vcNamespace);
    if (tempelement != null) {
        try {
            mathdes.addSubDomain(getPointSubDomain(tempelement, mathdes));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("Error adding a new PointSubDomain to the MathDescription " + name, e);
        }
    }
    iterator = param.getChildren(XMLTags.EventTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        Event event = getEvent(mathdes, tempelement);
        try {
            mathdes.addEvent(event);
        } catch (MathException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException(e);
        }
    }
    iterator = param.getChildren(XMLTags.PostProcessingBlock, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        getPostProcessingBlock(mathdes, tempelement);
    }
    return mathdes;
}

Example 40 with Version

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

the class XmlReader method getVCImage.

/**
 * This method returns a VCIMage object from a XML representation.
 * Creation date: (3/16/2001 3:41:24 PM)
 * @return VCImage
 * @param param org.jdom.Element
 */
VCImage getVCImage(Element param, Extent extent) throws XmlParseException {
    // try to get metadata(version)
    Version version = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace));
    // get the attributes
    Element tempelement = param.getChild(XMLTags.ImageDataTag, vcNamespace);
    int aNumX = Integer.parseInt(tempelement.getAttributeValue(XMLTags.XAttrTag));
    int aNumY = Integer.parseInt(tempelement.getAttributeValue(XMLTags.YAttrTag));
    int aNumZ = Integer.parseInt(tempelement.getAttributeValue(XMLTags.ZAttrTag));
    // getpixels
    String temp = tempelement.getText();
    // decode
    byte[] data = Hex.toBytes(temp);
    // create the VCImage object
    VCImageCompressed newimage = null;
    try {
        newimage = new VCImageCompressed(version, data, extent, aNumX, aNumY, aNumZ);
    } catch (ImageException e) {
        e.printStackTrace();
        throw new XmlParseException("An imageException occurred while trying to create a VCImage!", e);
    }
    // set attributes
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    try {
        newimage.setName(name);
        // String annotation = param.getAttributeValue(XMLTags.AnnotationAttrTag);
        // if (annotation!=null) {
        // newimage.setDescription(unMangle(annotation));
        // }
        // read the annotation
        String annotation = param.getChildText(XMLTags.AnnotationTag, vcNamespace);
        if (annotation != null && annotation.length() > 0) {
            newimage.setDescription(unMangle(annotation));
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new XmlParseException(e);
    }
    // get PixelClasses
    List<Element> pixelClassList = param.getChildren(XMLTags.PixelClassTag, vcNamespace);
    if (pixelClassList.size() != 0) {
        VCPixelClass[] pixelClassArray = new VCPixelClass[pixelClassList.size()];
        int pixelClassCounter = 0;
        for (Element pcElement : pixelClassList) {
            pixelClassArray[pixelClassCounter] = getPixelClass(pcElement);
            pixelClassCounter++;
        }
        try {
            newimage.setPixelClasses(pixelClassArray);
        } catch (java.beans.PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException(e);
        }
    } else {
        // Invalid format
        System.out.println("Format Error! No <PixelClass> references found inside <Image name=\"" + name + "\">!");
        System.out.println("Valid format for images is:");
        System.out.println("<Image Name=\"??\">");
        System.out.println(" <ImageData Z=\"?\" Y=\"?\" Z=\"?\" CompressedSize=\"?\">");
        System.out.println("     ......Image content...");
        System.out.println(" </ImageData>");
        System.out.println(" <PixelClass Name=\"?\" ImagePixelValue=\"?\"/>");
        System.out.println("  ...");
        System.out.println(" <PixelClass Name=\"?\" ImagePixelValue=\"?\"/>");
        System.out.println(" <Version Name=\"?\"/>");
        System.out.println("</Image>");
        throw new XmlParseException("Invalid VCML format error!\nNo <PixelClass> references found inside <Image name=\"" + name + "\">!");
    }
    return newimage;
}