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Example 46 with Attribute

use of org.jdom.Attribute in project intellij-plugins by StepicOrg.

the class StudySerializationUtils method getSectionNodes.

private static List<Element> getSectionNodes(@NotNull Element stepManager) throws StudyUnrecognizedFormatException {
    Element defaultLang = getFieldWithNameOrNull(stepManager, DEFAULT_LANG);
    if (defaultLang == null) {
        defaultLang = createField(stepManager, DEFAULT_LANG, INVALID);
    }
    Attribute defaultLangValue = defaultLang.getAttribute(VALUE);
    replaceLanguage(defaultLangValue);
    Element courseNode = getCourseNode(stepManager);
    return getListFieldWithNameOrNull(courseNode, SECTIONS_NODES, SECTION_NODE_CLASS);
}
Also used : Attribute(org.jdom.Attribute) Element(org.jdom.Element)

Example 47 with Attribute

use of org.jdom.Attribute in project intellij-plugins by JetBrains.

the class OsgiRunConfiguration method readExternal.

@Override
public void readExternal(final Element element) throws InvalidDataException {
    workingDir = element.getAttributeValue(WORKING_DIR_ATTRIBUTE);
    vmParameters = element.getAttributeValue(VM_PARAMETERS_ATTRIBUTE);
    programParameters = element.getAttributeValue(PROGRAM_PARAMETERS_ATTRIBUTE);
    includeAllBundlesInClassPath = Boolean.valueOf(element.getAttributeValue(INCLUDE_ALL_BUNDLES_IN_CLASS_PATH_ATTRIBUTE, "false"));
    useAlternativeJre = Boolean.valueOf(element.getAttributeValue(USE_ALTERNATIVE_JRE_ATTRIBUTE, "false"));
    alternativeJrePath = element.getAttributeValue(ALTERNATIVE_JRE_PATH, "");
    generateWorkingDir = Boolean.valueOf(element.getAttributeValue(GENERATE_WORKING_DIR_ATTRIBUTE));
    try {
        frameworkStartLevel = Integer.parseInt(element.getAttributeValue(FRAMEWORK_START_LEVEL, "1"));
    } catch (NumberFormatException e) {
        frameworkStartLevel = 1;
    }
    try {
        defaultStartLevel = Integer.parseInt(element.getAttributeValue(DEFAULT_START_LEVEL, "5"));
    } catch (NumberFormatException e) {
        defaultStartLevel = 5;
    }
    List<Element> children = element.getChildren(BUNDLE_ELEMENT);
    bundlesToDeploy.clear();
    for (Element child : children) {
        String name = child.getAttributeValue(NAME_ATTRIBUTE);
        String url = child.getAttributeValue(URL_ATTRIBUTE);
        String startLevel = child.getAttributeValue(START_LEVEL_ATTRIBUTE);
        String typeName = child.getAttributeValue(TYPE_ATTRIBUTE);
        SelectedBundle.BundleType type;
        try {
            type = SelectedBundle.BundleType.valueOf(typeName);
        } catch (IllegalArgumentException e) {
            LOG.error("unexpected bundle type '" + typeName + "'");
            type = SelectedBundle.BundleType.Module;
        }
        String path = url != null ? VfsUtilCore.urlToPath(url) : null;
        SelectedBundle selectedBundle = new SelectedBundle(type, name, path);
        if (startLevel != null) {
            try {
                selectedBundle.setStartLevel(Integer.parseInt(startLevel));
            } catch (NumberFormatException ignored) {
            }
        }
        String startAfterInstallationString = child.getAttributeValue(START_AFTER_INSTALLATION_ATTRIBUTE);
        if (startAfterInstallationString != null) {
            selectedBundle.setStartAfterInstallation(Boolean.parseBoolean(startAfterInstallationString));
        }
        bundlesToDeploy.add(selectedBundle);
    }
    // try to load the framework instance
    Element framework = element.getChild(FRAMEWORK_ELEMENT);
    if (framework != null) {
        String name = framework.getAttributeValue(INSTANCE_ATTRIBUTE);
        if (name != null) {
            ApplicationSettings settings = ServiceManager.getService(ApplicationSettings.class);
            instanceToUse = settings.getFrameworkInstance(name);
        }
    }
    Element additionalProperties = element.getChild(ADDITIONAL_PROPERTIES_ELEMENT);
    if (additionalProperties == null) {
        //noinspection SpellCheckingInspection
        additionalProperties = element.getChild("additinalProperties");
    }
    if (additionalProperties != null) {
        List<Attribute> attributes = additionalProperties.getAttributes();
        for (Attribute attribute : attributes) {
            this.additionalProperties.put(attribute.getName(), attribute.getValue());
        }
    }
    super.readExternal(element);
}
Also used : ApplicationSettings(org.osmorc.settings.ApplicationSettings) SelectedBundle(org.osmorc.run.ui.SelectedBundle) Attribute(org.jdom.Attribute) Element(org.jdom.Element)

Example 48 with Attribute

use of org.jdom.Attribute in project vcell by virtualcell.

the class XmlReader method getMathOverrides.

/**
 * This method returns a MathOverrides object from a XML Element.
 * Creation date: (5/21/2001 3:05:17 PM)
 * @return cbit.vcell.solver.MathOverrides
 * @param param org.jdom.Element
 */
private MathOverrides getMathOverrides(Element param, Simulation simulation) throws XmlParseException {
    MathOverrides mathOverrides = null;
    try {
        // Get the constants
        Object[] elements = param.getChildren().toArray();
        Vector<ConstantArraySpec> v1 = new Vector<ConstantArraySpec>();
        Vector<Constant> v2 = new Vector<Constant>();
        for (int i = 0; i < elements.length; i++) {
            Element e = (Element) elements[i];
            Attribute array = e.getAttribute(XMLTags.ConstantArraySpec);
            if (array != null) {
                // collect scan overrides
                String name = e.getAttributeValue(XMLTags.NameAttrTag);
                int type = array.getIntValue();
                v1.add(ConstantArraySpec.createFromString(name, e.getText(), type));
            } else {
                // collect regular overrides
                v2.add(getConstant(e));
            }
        }
        Constant[] constants = (Constant[]) BeanUtils.getArray(v2, Constant.class);
        ConstantArraySpec[] specs = (ConstantArraySpec[]) BeanUtils.getArray(v1, ConstantArraySpec.class);
        // create new MathOverrides object
        mathOverrides = new MathOverrides(simulation, constants, specs);
    } catch (ExpressionException e) {
        e.printStackTrace();
        throw new XmlParseException("A ExpressionException was fired when adding a Constant to the MathOverrides", e);
    } catch (DataConversionException e2) {
        e2.printStackTrace();
        throw new XmlParseException("A DataConversionException occured when reading a ConstantArraySpec type", e2);
    }
    return mathOverrides;
}
Also used : Attribute(org.jdom.Attribute) MacroscopicRateConstant(cbit.vcell.math.MacroscopicRateConstant) Constant(cbit.vcell.math.Constant) Element(org.jdom.Element) ConstantArraySpec(cbit.vcell.solver.ConstantArraySpec) ExpressionException(cbit.vcell.parser.ExpressionException) MathOverrides(cbit.vcell.solver.MathOverrides) VolumeRegionObject(cbit.vcell.mapping.spatial.VolumeRegionObject) PointObject(cbit.vcell.mapping.spatial.PointObject) SpatialObject(cbit.vcell.mapping.spatial.SpatialObject) SurfaceRegionObject(cbit.vcell.mapping.spatial.SurfaceRegionObject) CSGObject(cbit.vcell.geometry.CSGObject) DataConversionException(org.jdom.DataConversionException) Vector(java.util.Vector)

Example 49 with Attribute

use of org.jdom.Attribute in project vcell by virtualcell.

the class XmlTreeDiff method mergeAttrList.

/**
 * This method merges to attributes list into one.
 * Creation date: (8/29/2001 2:51:33 PM)
 * @return java.util.List
 * @param listA java.util.List
 * @param listB java.util.List
 */
private List mergeAttrList(List listA, List listB, DiffConfiguration comparisonSetting) {
    List result = new java.util.ArrayList();
    XmlElementComparator comparator = new XmlElementComparator(this);
    Iterator i = listA.iterator();
    while (i.hasNext()) {
        Attribute temp = (Attribute) (i.next());
        if (temp.getName().equals(XMLTags.KeyValueAttrTag) && ignoreVersionInfo) {
            if (DiffConfiguration.COMPARE_DOCS_SAVED == comparisonSetting) {
                result.add(new NodeInfo(temp, NodeInfo.STATUS_NORMAL));
            }
            i.remove();
            continue;
        } else {
            int index = comparator.getindexof(temp, listB);
            if (index >= 0) {
                // this attribute exists in both!
                result.add(new NodeInfo(temp, NodeInfo.STATUS_NORMAL));
                i.remove();
                listB.remove(index);
            }
        }
    }
    // If there are already Attributes in ListA, try to find similars in ListB
    i = listA.iterator();
    while (i.hasNext()) {
        Attribute temp = (Attribute) (i.next());
        int index = comparator.getsimilarAttr(temp, listB);
        if (index >= 0) {
            result.add(new ChangedNodeInfo(temp, (Attribute) listB.get(index)));
            // I found one similar
            listB.remove(index);
        } else {
            // It seems that this nodes only exist in ListA
            result.add(new NodeInfo(temp, NodeInfo.STATUS_REMOVED));
        }
    }
    // Add the remaining of listB
    i = listB.iterator();
    while (i.hasNext()) {
        // these nodes only exists in ListB
        Attribute tempAtt = (Attribute) i.next();
        if (tempAtt.getName().equals(XMLTags.KeyValueAttrTag) && ignoreVersionInfo) {
            // ignore keys in the modified
            if (DiffConfiguration.COMPARE_DOCS_OTHER == comparisonSetting) {
                result.add(new NodeInfo((tempAtt), NodeInfo.STATUS_NORMAL));
            }
            continue;
        }
        result.add(new NodeInfo((tempAtt), NodeInfo.STATUS_NEW));
    }
    return result;
}
Also used : Attribute(org.jdom.Attribute) ArrayList(java.util.ArrayList) Iterator(java.util.Iterator) List(java.util.List) ArrayList(java.util.ArrayList)

Example 50 with Attribute

use of org.jdom.Attribute in project vcell by virtualcell.

the class XmlTreeDiff method createNodes.

/**
 * Insert the method's description here.
 * Creation date: (8/29/2001 2:41:50 PM)
 * @return cbit.xml.merge.NodeInfo
 * @param parsed org.jdom.Element
 * @param status int
 */
private NodeInfo createNodes(org.jdom.Element parsed, int status, String nodeSource) {
    NodeInfo parent = null;
    NodeInfo temp;
    if (parsed != null) {
        parent = new NodeInfo(parsed, status);
        // get all the attributes children
        List children = parsed.getAttributes();
        if (!children.isEmpty()) {
            Iterator i = children.iterator();
            while (i.hasNext()) {
                Attribute atchild = (Attribute) i.next();
                if (atchild.getName().equals(XMLTags.KeyValueAttrTag) && ignoreVersionInfo) {
                    // keep the read-only key values for the baseline.
                    if (nodeSource.equals(this.BASELINE_NODE)) {
                        parent.add(new NodeInfo(atchild, NodeInfo.STATUS_NORMAL));
                    } else {
                        // ignore all the modified key values.
                        continue;
                    }
                } else {
                    parent.add(new NodeInfo(atchild, status));
                }
            }
        }
        // get all the element children
        List elementchildren = parsed.getChildren();
        if (!elementchildren.isEmpty()) {
            Iterator i = elementchildren.iterator();
            while (i.hasNext()) {
                Element child = (Element) i.next();
                // ignore all version info.
                if (child.getName().equals(XMLTags.VersionTag) && ignoreVersionInfo) {
                    if (nodeSource.equals(BASELINE_NODE)) {
                        // keep the baseline versions, but they are all 'normal'
                        temp = createNodes(child, NodeInfo.STATUS_NORMAL, nodeSource);
                        parent.add(temp);
                    } else if (nodeSource.equals(MODIFIED_NODE)) {
                        // ignore version info for the modified.
                        continue;
                    }
                } else {
                    temp = createNodes(child, status, nodeSource);
                    parent.add(temp);
                }
            }
        }
    }
    return parent;
}
Also used : Attribute(org.jdom.Attribute) Element(org.jdom.Element) Iterator(java.util.Iterator) List(java.util.List) ArrayList(java.util.ArrayList)

Aggregations

Attribute (org.jdom.Attribute)57 Element (org.jdom.Element)40 ArrayList (java.util.ArrayList)10 DataConversionException (org.jdom.DataConversionException)7 Iterator (java.util.Iterator)4 List (java.util.List)4 Document (org.jdom.Document)4 Namespace (org.jdom.Namespace)3 SAXBuilder (org.jdom.input.SAXBuilder)3 NotNull (org.jetbrains.annotations.NotNull)3 MacroscopicRateConstant (cbit.vcell.math.MacroscopicRateConstant)2 ExpressionException (cbit.vcell.parser.ExpressionException)2 PathMacrosImpl (com.intellij.application.options.PathMacrosImpl)2 PathMacroFilter (com.intellij.openapi.application.PathMacroFilter)2 VirtualFile (com.intellij.openapi.vfs.VirtualFile)2 Content (org.jdom.Content)2 Text (org.jdom.Text)2 BioPaxObject (org.vcell.pathway.BioPaxObject)2 RdfObjectProxy (org.vcell.pathway.persistence.BiopaxProxy.RdfObjectProxy)2 JDOMTreeWalker (cbit.util.xml.JDOMTreeWalker)1