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

Example 11 with PublicationInfo

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

the class VcmlOmexConverter method getMetadata.

private static String getMetadata(String vcmlName, BioModel bioModel) {
    String ret = "";
    String ns = DefaultNameSpaces.EX.uri;
    Graph graph = new HashGraph();
    Graph schema = new HashGraph();
    // recover the bioModelInfo
    // we first assume that vcml name is the model id
    BioModelInfo bioModelInfo = bioModelInfoMap.get(vcmlName);
    if (bioModelInfo == null) {
        // if not, we try based on biomodel name
        bioModelInfo = bioModelInfoMap2.get(vcmlName);
    }
    if (bioModelInfo == null) {
        // perhaps it's not public, in which case is not in the map
        // make an empty rdf file
        String description = "http://omex-library.org/" + vcmlName + ".omex";
        URI descriptionURI = ValueFactoryImpl.getInstance().createURI(description);
        graph.add(descriptionURI, RDF.TYPE, PubMet.Description);
        try {
            Map<String, String> nsMap = DefaultNameSpaces.defaultMap.convertToMap();
            ret = SesameRioUtil.writeRDFToString(graph, nsMap, RDFFormat.RDFXML);
            SesameRioUtil.writeRDFToStream(System.out, graph, nsMap, RDFFormat.RDFXML);
        } catch (RDFHandlerException e) {
            e.printStackTrace();
        }
        return ret;
    }
    PublicationInfo[] publicationInfos = bioModelInfo.getPublicationInfos();
    if (publicationInfos == null || publicationInfos.length == 0) {
        // we may not have PublicationInfo
        // make an empty rdf file
        String description = "http://omex-library.org/" + vcmlName + ".omex";
        URI descriptionURI = ValueFactoryImpl.getInstance().createURI(description);
        graph.add(descriptionURI, RDF.TYPE, PubMet.Description);
        try {
            Map<String, String> nsMap = DefaultNameSpaces.defaultMap.convertToMap();
            ret = SesameRioUtil.writeRDFToString(graph, nsMap, RDFFormat.RDFXML);
            SesameRioUtil.writeRDFToStream(System.out, graph, nsMap, RDFFormat.RDFXML);
        } catch (RDFHandlerException e) {
            e.printStackTrace();
        }
        return ret;
    }
    PublicationInfo publicationInfo = publicationInfos[0];
    String bioModelName = bioModel.getName();
    Version version = bioModelInfo.getVersion();
    String[] creators = publicationInfo.getAuthors();
    String citation = publicationInfo.getCitation();
    String doi = publicationInfo.getDoi();
    Date pubDate = publicationInfo.getPubDate();
    String pubmedid = publicationInfo.getPubmedid();
    String sTitle = publicationInfo.getTitle();
    String url = publicationInfo.getUrl();
    List<String> contributors = new ArrayList<>();
    contributors.add("Dan Vasilescu");
    contributors.add("Michael Blinov");
    contributors.add("Ion Moraru");
    // "http://omex-library.org/biomodel_12345678.omex";
    String description = "http://omex-library.org/" + vcmlName + ".omex";
    URI descriptionURI = ValueFactoryImpl.getInstance().createURI(description);
    Literal descTitle = OntUtil.createTypedString(schema, sTitle);
    // <rdf:Description rdf:about='http://omex-library.org/Monkeyflower_pigmentation_v2.omex'>
    graph.add(descriptionURI, RDF.TYPE, PubMet.Description);
    graph.add(descriptionURI, PubMet.Title, descTitle);
    try {
        Map<String, String> nsMap = DefaultNameSpaces.defaultMap.convertToMap();
        ret = SesameRioUtil.writeRDFToString(graph, nsMap, RDFFormat.RDFXML);
    // SesameRioUtil.writeRDFToStream(System.out, graph, nsMap, RDFFormat.RDFXML);
    } catch (RDFHandlerException e) {
        e.printStackTrace();
    }
    String end = "\n\n" + ret.substring(ret.indexOf(PubMet.EndDescription0));
    ret = ret.substring(0, ret.indexOf(PubMet.EndDescription0));
    ret += PubMet.CommentTaxon;
    ret += PubMet.CommentOther;
    ret += PubMet.StartIs;
    ret += PubMet.StartDescription;
    ret += PubMet.StartIdentifier;
    ret += PubMet.ResourceIdentifier;
    String isLabel = "vcell:" + version.getVersionKey();
    ret += isLabel;
    ret += PubMet.EndIdentifier;
    ret += PubMet.StartLabel;
    ret += isLabel;
    ret += PubMet.EndLabel;
    ret += PubMet.EndDescription;
    ret += PubMet.EndIs;
    ret += PubMet.StartIsDescribedBy;
    ret += PubMet.StartDescription;
    ret += PubMet.StartIdentifier;
    ret += PubMet.ResourceIdentifier;
    String pubmed = "pubmed:" + pubmedid;
    ret += pubmed;
    ret += PubMet.EndIdentifier;
    ret += PubMet.StartLabel;
    ret += pubmed;
    ret += PubMet.EndLabel;
    ret += PubMet.EndDescription;
    ret += PubMet.EndIsDescribedBy;
    ret += PubMet.CommentCreator;
    for (String creator : creators) {
        ret += PubMet.StartCreator;
        ret += PubMet.StartDescription;
        ret += PubMet.StartName;
        ret += creator;
        ret += PubMet.EndName;
        ret += PubMet.StartLabel;
        ret += creator;
        ret += PubMet.EndLabel;
        ret += PubMet.EndDescription;
        ret += PubMet.EndCreator;
    }
    ret += PubMet.CommentContributor;
    for (String contributor : contributors) {
        ret += PubMet.StartContributor;
        ret += PubMet.StartDescription;
        ret += PubMet.StartName;
        ret += contributor;
        ret += PubMet.EndName;
        ret += PubMet.StartLabel;
        ret += contributor;
        ret += PubMet.EndLabel;
        ret += PubMet.EndDescription;
        ret += PubMet.EndContributor;
    }
    ret += PubMet.CommentCitations;
    ret += PubMet.StartIsDescribedBy;
    ret += PubMet.StartDescription;
    ret += PubMet.StartIdentifier;
    ret += PubMet.ResourceIdentifier;
    String sdoi = "doi:" + doi;
    ret += sdoi;
    ret += PubMet.EndIdentifier;
    ret += PubMet.StartLabel;
    ret += citation;
    ret += PubMet.EndLabel;
    ret += PubMet.EndDescription;
    ret += PubMet.EndIsDescribedBy;
    ret += PubMet.CommentLicense;
    ret += PubMet.StartLicense;
    ret += PubMet.StartDescription;
    ret += PubMet.StartIdentifier;
    ret += PubMet.ResourceIdentifier;
    String lic = "spdx:" + "CC0-1.0";
    ret += lic;
    ret += PubMet.EndIdentifier;
    ret += PubMet.StartLabel;
    ret += "CC0-1.0";
    ret += PubMet.EndLabel;
    ret += PubMet.EndDescription;
    ret += PubMet.EndLicense;
    String sPubDate = new SimpleDateFormat("yyyy-MM-dd").format(pubDate);
    ret += PubMet.CommentCreated;
    ret += PubMet.StartCreated;
    ret += PubMet.StartDescription;
    ret += PubMet.PrefixCreated;
    ret += new SimpleDateFormat("yyyy-MM-dd").format(pubDate);
    ret += PubMet.SuffixCreated;
    ret += PubMet.EndDescription;
    ret += PubMet.EndCreated;
    Calendar calendar = Calendar.getInstance();
    Date today = calendar.getTime();
    ret += PubMet.CommentModified;
    ret += PubMet.StartModified;
    ret += PubMet.StartDescription;
    ret += PubMet.PrefixModified;
    ret += new SimpleDateFormat("yyyy-MM-dd").format(today);
    ret += PubMet.SuffixModified;
    ret += PubMet.EndDescription;
    ret += PubMet.EndModified;
    ret += end;
    System.out.println(ret);
    System.out.println("");
    return (ret);
}

Example 12 with PublicationInfo

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

the class BioModelInfoCellRenderer method getTreeCellRendererComponent.

/**
 * Insert the method's description here.
 * Creation date: (7/27/2000 6:41:57 PM)
 * @return java.awt.Component
 */
public java.awt.Component getTreeCellRendererComponent(JTree tree, Object value, boolean sel, boolean expanded, boolean leaf, int row, boolean hasFocus) {
    JLabel component = (JLabel) super.getTreeCellRendererComponent(tree, value, sel, expanded, leaf, row, hasFocus);
    // 
    if (!leaf && expanded) {
        setIcon(fieldFolderOpenIcon);
    } else if (!leaf && !expanded) {
        setIcon(fieldFolderClosedIcon);
    }
    try {
        if (value instanceof BioModelNode) {
            BioModelNode node = (BioModelNode) value;
            boolean bLoaded = false;
            // 
            if (node.getUserObject() instanceof String && "Geometry".equals(node.getRenderHint("type"))) {
                String label = (String) node.getUserObject();
                component.setToolTipText("Geometry");
                component.setText(label);
                setIcon(fieldGeometryIcon);
            } else if (node.getUserObject() instanceof String && "Applications".equals(node.getRenderHint("type"))) {
                String label = (String) node.getUserObject();
                component.setToolTipText("Applications List");
                component.setText("<html><b>" + label + "</b></html>");
                setIcon(fieldTextIcon);
            } else if (node.getUserObject() instanceof String && "SimulationContext".equals(node.getRenderHint("type"))) {
                String label = (String) node.getUserObject();
                component.setToolTipText("Application");
                component.setText(label);
                if (MathType.RuleBased.getDescription().equals(node.getRenderHint("appType"))) {
                    setIcon(VCellIcons.appRbmNonspIcon);
                } else if (MathType.Stochastic.getDescription().equals(node.getRenderHint("appType"))) {
                    if ("0".equals(node.getRenderHint("dimension"))) {
                        setIcon(VCellIcons.appStoNonspIcon);
                    } else {
                        setIcon(VCellIcons.appStoSpatialIcon);
                    }
                } else if (MathType.Deterministic.getDescription().equals(node.getRenderHint("appType"))) {
                    if ("0".equals(node.getRenderHint("dimension"))) {
                        setIcon(VCellIcons.appDetNonspIcon);
                    } else {
                        setIcon(VCellIcons.appDetSpatialIcon);
                    }
                } else {
                    // don't know what it is, use old "generic" icon
                    setIcon(fieldSimulationContextIcon);
                }
            } else if (node.getUserObject() instanceof String && "Simulation".equals(node.getRenderHint("type"))) {
                String label = (String) node.getUserObject();
                component.setToolTipText("Simulation");
                component.setText(label);
                setIcon(fieldSimulationIcon);
            } else if (node.getUserObject() instanceof String && "AppType".equals(node.getRenderHint("type"))) {
                String label = (String) node.getUserObject();
                component.setToolTipText("Simulation");
                component.setText(label);
                setIcon(fieldAppTypeIcon);
            } else if (node.getUserObject() instanceof String && "Provenance".equals(node.getRenderHint("type"))) {
                String label = (String) node.getUserObject();
                component.setToolTipText("Provenance");
                component.setText("<html><b>" + label + "</b></html>");
                setIcon(fieldTextIcon);
            } else if (node.getUserObject() instanceof Annotation) {
                String label = ((Annotation) node.getUserObject()).toString();
                component.setToolTipText("Version Annotation");
                component.setText(label);
                setIcon(null);
            } else if (node.getUserObject() instanceof String && "PublicationsInfo".equals(node.getRenderHint("type"))) {
                String label = (String) node.getUserObject();
                component.setToolTipText("Publications Info");
                component.setText("<html><b>" + label + "</b></html>");
                setIcon(fieldTextIcon);
            } else if (node.getUserObject() instanceof PublicationInfo && "PublicationInfoTitle".equals(node.getRenderHint("type"))) {
                PublicationInfo info = (PublicationInfo) node.getUserObject();
                component.setToolTipText("Title");
                String text = "<b>" + info.getTitle() + "</b>";
                component.setText("<html>" + text + "</html>");
                setIcon(fieldTextIcon);
            } else if (node.getUserObject() instanceof PublicationInfo && "PublicationInfoAuthors".equals(node.getRenderHint("type"))) {
                PublicationInfo info = (PublicationInfo) node.getUserObject();
                component.setToolTipText("Authors");
                String text = "";
                int count = 0;
                for (String author : info.getAuthors()) {
                    if (count > 0) {
                        text += "; ";
                    }
                    text += author;
                    count++;
                }
                component.setText("<html>" + text + "</html>");
                setIcon(null);
            } else if (node.getUserObject() instanceof PublicationInfo && "PublicationInfoCitation".equals(node.getRenderHint("type"))) {
                PublicationInfo info = (PublicationInfo) node.getUserObject();
                component.setToolTipText("Citation");
                String text = "";
                text += info.getCitation();
                component.setText("<html>" + text + "</html>");
                setIcon(null);
            } else if (node.getUserObject() instanceof PublicationInfo && "PublicationInfoDoi".equals(node.getRenderHint("type"))) {
                PublicationInfo info = (PublicationInfo) node.getUserObject();
                component.setToolTipText("DOI");
                String text = "<a href=\"" + BeanUtils.getDynamicClientProperties().getProperty(PropertyLoader.DOI_URL) + info.getDoi() + "\">" + "DOI: " + info.getDoi() + "</a>";
                component.setText("<html>" + text + "</html>");
                setIcon(null);
            } else if (node.getUserObject() instanceof PublicationInfo && "PublicationInfoUrl".equals(node.getRenderHint("type"))) {
                PublicationInfo info = (PublicationInfo) node.getUserObject();
                component.setToolTipText("PMID");
                // we know from the tree model that this is not null or empty
                String pmid = info.getUrl();
                if (pmid.contains("list_uids=")) {
                    // ex: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12644446
                    pmid = pmid.substring(pmid.lastIndexOf("list_uids=") + "list_uids=".length());
                } else if (pmid.contains("pubmed/")) {
                    // ex: http://www.ncbi.nlm.nih.gov/pubmed/23093806
                    pmid = pmid.substring(pmid.lastIndexOf("/") + 1);
                } else if (pmid.contains("pubmed.ncbi")) {
                    // ex: https://pubmed.ncbi.nlm.nih.gov/34360784/
                    if (pmid.endsWith("/")) {
                        pmid = pmid.substring(0, pmid.length() - 1);
                    }
                    pmid = pmid.substring(pmid.lastIndexOf("/") + 1);
                } else {
                    // something that we don't know how to parse
                    pmid = "?";
                }
                String text = "<a href=\"" + info.getUrl() + "\">" + "PubMed PMID: " + pmid + "</a>";
                component.setText("<html>" + text + "</html>");
                setIcon(null);
            } else if (node.getUserObject() instanceof String && "GeneralFileInfo".equals(node.getRenderHint("type"))) {
                component.setToolTipText("Database File Info");
                String text = "<b>" + (String) node.getUserObject() + "</b>";
                component.setText("<html>" + text + "</html>");
                setIcon(fieldDatabaseIcon);
            } else if (node.getUserObject() instanceof String && "ModelName".equals(node.getRenderHint("type"))) {
                component.setToolTipText("BioModel Name");
                String text = "<b>" + (String) node.getUserObject() + "</b>";
                component.setText("<html>" + text + "</html>");
            // setIcon(fieldTextIcon);
            } else if (node.getUserObject() instanceof KeyValue && "VCellIdentifier".equals(node.getRenderHint("type"))) {
                component.setToolTipText("Virtual Cell Identifier");
                KeyValue key = (KeyValue) node.getUserObject();
                String text = "biomodel-" + key;
                component.setText("<html>" + text + "</html>");
                setIcon(fieldDatabaseModelKeyIcon);
            } else if (node.getUserObject() instanceof User && "ModelOwner".equals(node.getRenderHint("type"))) {
                String label = ((User) node.getUserObject()).getName();
                component.setToolTipText("Model Owner");
                component.setText("<html>" + label + "</html>");
                setIcon(fieldUserIcon);
            } else if (node.getUserObject() instanceof Date && "ModelDate".equals(node.getRenderHint("type"))) {
                Date date = (Date) node.getUserObject();
                component.setToolTipText("Last Modified");
                component.setText("<html>" + date + "</html>");
                setIcon(fieldCalendarIcon);
            } else if (node.getUserObject() instanceof String && "Permissions".equals(node.getRenderHint("type"))) {
                component.setToolTipText("Permissions");
                String text = (String) node.getUserObject();
                component.setText("<html>" + text + "</html>");
                setIcon(fieldPermissionsIcon);
            } else if (node.getUserObject() instanceof String && "Annotations".equals(node.getRenderHint("type"))) {
                // deprecated; we don't show annotation icon(s), neither for notes nor for links
                component.setToolTipText("Text Annotation");
                String text = (String) node.getUserObject();
                component.setText("<html>" + text + "</html>");
                setIcon(VCellIcons.noteIcon);
            } else {
                setComponentProperties(component, node.getUserObject());
            }
            if (selectedFont == null && component.getFont() != null) {
                selectedFont = component.getFont().deriveFont(Font.BOLD);
            }
            if (unselectedFont == null && component.getFont() != null) {
                unselectedFont = component.getFont().deriveFont(Font.PLAIN);
            }
            if (bLoaded) {
                component.setFont(selectedFont);
            } else {
                component.setFont(unselectedFont);
            }
        }
    } catch (Throwable e) {
        e.printStackTrace(System.out);
    }
    // 
    return component;
}

Example 13 with PublicationInfo

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

the class PublicationInfoNodeTreeModel method createVersionSubTree.

private BioModelNode createVersionSubTree(BioModelNode publicationsInfoNode) throws DataAccessException {
    BioModelNode versionNode = new BioModelNode("Root", true);
    Object uo = publicationsInfoNode.getUserObject();
    if (!(uo instanceof PublicationInfo)) {
        String title = "PublicationInfo missing";
        publicationNode = new BioModelNode(title, false);
        versionNode.add(publicationNode);
        return versionNode;
    }
    publicationNode = null;
    modelsNode = null;
    PublicationInfo pi = (PublicationInfo) uo;
    publicationNode = new BioModelNode("Publication", true);
    publicationNode.setRenderHint("type", "PublicationsInfo");
    BioModelNode piTitleNode = new BioModelNode(pi, true);
    piTitleNode.setRenderHint("type", "PublicationInfoTitle");
    publicationNode.add(piTitleNode);
    BioModelNode piAuthorsNode = new BioModelNode(pi, false);
    piAuthorsNode.setRenderHint("type", "PublicationInfoAuthors");
    piTitleNode.add(piAuthorsNode);
    BioModelNode piCitationNode = new BioModelNode(pi, false);
    piCitationNode.setRenderHint("type", "PublicationInfoCitation");
    piTitleNode.add(piCitationNode);
    BioModelNode piDoiNode = new BioModelNode(pi, false);
    piDoiNode.setRenderHint("type", "PublicationInfoDoi");
    piTitleNode.add(piDoiNode);
    if (pi.getUrl() != null && !pi.getUrl().isEmpty()) {
        if (pi.getUrl().contains("pubmed") || pi.getUrl().contains("PubMed")) {
            BioModelNode piUrlNode = new BioModelNode(pi, false);
            piUrlNode.setRenderHint("type", "PublicationInfoUrl");
            piTitleNode.add(piUrlNode);
        }
    }
    versionNode.add(publicationNode);
    String name = publicationsInfoNode.getChildCount() > 1 ? "Models" : "Model";
    modelsNode = new BioModelNode(name, true);
    modelsNode.setRenderHint("type", "ModelsList");
    for (int i = 0; i < publicationsInfoNode.getChildCount(); i++) {
        TreeNode child = publicationsInfoNode.getChildAt(i);
        if (!(child instanceof BioModelNode)) {
            versionNode.add(modelsNode);
            return versionNode;
        }
        BioModelNode modelNode = (BioModelNode) child;
        uo = modelNode.getUserObject();
        if (!(uo instanceof VCDocumentInfoNode)) {
            versionNode.add(modelsNode);
            return versionNode;
        }
        VCDocumentInfoNode din = (VCDocumentInfoNode) uo;
        Version version = din.getVCDocumentInfo().getVersion();
        BioModelNode mNameNode = new BioModelNode(version.getName(), true);
        mNameNode.setRenderHint("type", "ModelName");
        VCDocumentInfo di = din.getVCDocumentInfo();
        if (di instanceof BioModelInfo) {
            mNameNode.setRenderHint("category", "BioModel");
        } else if (di instanceof MathModelInfo) {
            mNameNode.setRenderHint("category", "MathModel");
        } else if (di instanceof GeometryInfo) {
            mNameNode.setRenderHint("category", "Geometry");
        }
        modelsNode.add(mNameNode);
        BioModelNode mOwnerNode = new BioModelNode(version.getOwner(), true);
        mOwnerNode.setRenderHint("type", "ModelOwner");
        mNameNode.add(mOwnerNode);
        BioModelNode mDateNode = new BioModelNode(version.getDate(), true);
        mDateNode.setRenderHint("type", "ModelDate");
        mNameNode.add(mDateNode);
    }
    versionNode.add(modelsNode);
    return versionNode;
}

Example 14 with PublicationInfo

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

the class BioModelDbTreePanel method treeSelection.

/**
 * Comment
 */
protected void treeSelection() {
    TreePath treePath = getJTree1().getSelectionPath();
    if (treePath == null) {
        setSelectedVersionInfo(null);
        return;
    }
    BioModelNode bioModelNode = (BioModelNode) treePath.getLastPathComponent();
    Object object = bioModelNode.getUserObject();
    if (object instanceof PublicationInfo) {
        setSelectedVersionInfo(null);
        setSelectedPublicationInfo(bioModelNode);
    } else if (object instanceof BioModelInfo) {
        setSelectedVersionInfo((VersionInfo) object);
    } else if (object instanceof VCDocumentInfoNode && bioModelNode.getChildCount() > 0 && ((BioModelNode) bioModelNode.getChildAt(0)).getUserObject() instanceof BioModelInfo) {
        BioModelInfo bioModelInfo = (BioModelInfo) ((BioModelNode) bioModelNode.getChildAt(0)).getUserObject();
        setSelectedVersionInfo(bioModelInfo);
    } else if (object instanceof BioModelMetaData) {
        BioModelInfo bioModelInfo = (BioModelInfo) ((BioModelNode) bioModelNode.getParent()).getUserObject();
        setSelectedVersionInfo(bioModelInfo);
    } else {
        setSelectedVersionInfo(null);
    }
}

Example 15 with PublicationInfo

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

the class BioModelCellRenderer method getTreeCellRendererComponent.

/**
 * Insert the method's description here.
 * Creation date: (7/27/2000 6:41:57 PM)
 * @return java.awt.Component
 */
public java.awt.Component getTreeCellRendererComponent(JTree tree, Object value, boolean sel, boolean expanded, boolean leaf, int row, boolean hasFocus) {
    JLabel component = (JLabel) super.getTreeCellRendererComponent(tree, value, sel, expanded, leaf, row, hasFocus);
    // 
    try {
        if (value instanceof DateNode) {
            DateNode dateNode = (DateNode) value;
            AnnotationQualifier qualifier = dateNode.getDateQualifier();
            String colorString = (sel) ? "white" : "black";
            component.setText("<html>" + qualifier.getDescription() + "&nbsp;<font color=\"" + colorString + "\">" + dateNode.getDate().getDateString() + "</font></html>");
        } else if (value instanceof LinkNode) {
            LinkNode ln = (LinkNode) value;
            String link = ln.getLink();
            String text = ln.getText();
            MIRIAMQualifier mQualifier = ln.getMiriamQualifier();
            String qualifier = "";
            if (mQualifier.equals(MIRIAMQualifier.MODEL_isDescribedBy)) {
                String colorString = (sel) ? "white" : "black";
                qualifier = "<font color=\"" + colorString + "\">" + mQualifier.getDescription() + "</font>";
            } else {
                String colorString = (sel) ? "white" : "#8B0000";
                qualifier = "<font color=\"" + colorString + "\">" + mQualifier.getDescription() + "</font>";
            }
            if (link != null) {
                String colorString = (sel) ? "white" : "blue";
                component.setToolTipText("Double-click to open link");
                component.setText("<html>" + qualifier + "&nbsp;<font color=\"" + colorString + "\"><a href=" + link + ">" + text + "</a></font></html>");
            } else {
                String colorString = (sel) ? "white" : "black";
                component.setText("<html>" + qualifier + "&nbsp;<font color=\"" + colorString + "\">" + text + "</font></html>");
            }
        } else if (value instanceof PublicationInfoNode) {
            BioModelNode node = (PublicationInfoNode) value;
            PublicationInfo pi = (PublicationInfo) node.getUserObject();
            String label = pi.getTitle();
            String name = "";
            if (pi.getAuthors() != null && pi.getAuthors().length > 0) {
                name = pi.getAuthors()[0];
            }
            if (name.contains(",")) {
                name = name.substring(0, name.indexOf(","));
            }
            int year = Integer.parseInt((new SimpleDateFormat("yyyy")).format(pi.getPubDate()));
            String label2 = name + " " + year + " " + label;
            int maxLen = MaxPublicationLabelLength + (node.getChildCount() > 1 ? 0 : 4);
            if (label2.length() > maxLen) {
                label2 = label2.substring(0, maxLen) + "...";
            }
            if (node.getChildCount() > 1) {
                String prefix = sel ? "" : "<span style=\"color:#8B0000\">";
                String suffix = sel ? "" : "</span>";
                label += prefix + " (" + node.getChildCount() + ")" + suffix;
                label2 += prefix + " (" + node.getChildCount() + ")" + suffix;
            }
            component.setText("<html>" + label2 + "</html>");
            component.setToolTipText("<html>" + label + "</html>");
            if (pi.getPubDate().compareTo(Calendar.getInstance().getTime()) > 0) {
                // sanity check
                setIcon(fieldFolderWarningIcon);
            } else if (pi.getDoi() == null) {
                setIcon(fieldFolderWarningIcon);
            } else if (name.contains(" ")) {
                setIcon(fieldFolderWarningIcon);
            } else {
                // publications have their own icon
                setIcon(fieldPublishedPublicationIcon);
            }
        } else if (value instanceof UserNameNode) {
            UserNameNode node = (UserNameNode) value;
            String label = (String) node.getUserObject();
            String qualifier = "";
            if (sessionUser != null && sessionUser.getName().contentEquals(label)) {
                String colorString = (sel) ? "white" : "#8B0000";
                qualifier = "<font color=\"" + colorString + "\"><b>" + label + "</b></font>";
            } else {
                String colorString = (sel) ? "white" : "black";
                qualifier = "<font color=\"" + colorString + "\">" + label + "</font>";
            }
            component.setToolTipText(label);
            component.setText("<html>" + qualifier + " (" + node.getChildCount() + ")" + "</html>");
            component.setIcon(fieldFolderUserIcon);
        } else if (value instanceof BioModelNode) {
            BioModelNode node = (BioModelNode) value;
            Object userObject = node.getUserObject();
            if (userObject instanceof User) {
                String label = null;
                if (sessionUser != null && sessionUser.compareEqual((User) userObject)) {
                    label = "My BioModels (" + ((User) userObject).getName() + ") (" + node.getChildCount() + ")";
                } else {
                    label = ((User) userObject).getName() + "(abcdefghijklmnopq)(000000)";
                }
                component.setToolTipText(label);
                component.setText(label);
            } else if (userObject instanceof BioModelInfo) {
                BioModelInfo biomodelInfo = (BioModelInfo) userObject;
                if (biomodelInfo.getPublicationInfos() != null && biomodelInfo.getPublicationInfos().length > 0) {
                    if (biomodelInfo.getVersion().getFlag().compareEqual(org.vcell.util.document.VersionFlag.Published)) {
                        component.setText("(Published) " + component.getText());
                    } else {
                        component.setText("(Curated) " + component.getText());
                    }
                } else if (biomodelInfo.getVersion().getFlag().compareEqual(org.vcell.util.document.VersionFlag.Archived)) {
                    component.setText("(Archived) " + component.getText());
                }
                String str = component.getToolTipText();
                if (str != null && !str.isEmpty()) {
                    component.setToolTipText(str + " " + biomodelInfo.getVersion().getVersionKey());
                }
                // we change color of version if it's in the Other folder (Uncurated) and belongs to login user
                Object pNode = node.getParent();
                if (pNode instanceof BioModelNode) {
                    pNode = ((BioModelNode) pNode).getParent();
                    if (pNode instanceof BioModelNode && ((BioModelNode) pNode).getUserObject() instanceof String) {
                        str = (String) ((BioModelNode) pNode).getUserObject();
                        if (str.equals(VCDocumentDbTreeModel.ModelBricks) && sessionUser.getName().contentEquals(VCDocumentDbTreeModel.USER_modelBricks)) {
                            // GRAY
                            String prefix = sel ? "" : "<span style=\"color:#808080\">";
                            String suffix = sel ? "" : "</span>";
                            String str1 = prefix + component.getText() + suffix;
                            setText("<html>" + str1 + "</html>");
                        } else {
                            pNode = ((BioModelNode) pNode).getParent();
                            if (((BioModelNode) pNode).getUserObject() instanceof String && str.equalsIgnoreCase(sessionUser.getName())) {
                                str = (String) ((BioModelNode) pNode).getUserObject();
                                if (str.equals(VCDocumentDbTreeModel.Other_BioModels)) {
                                    // GRAY
                                    String prefix = sel ? "" : "<span style=\"color:#808080\">";
                                    String suffix = sel ? "" : "</span>";
                                    String str1 = prefix + component.getText() + suffix;
                                    setText("<html>" + str1 + "</html>");
                                }
                            }
                        }
                    }
                }
            } else if (userObject instanceof Geometry) {
                Geometry geo = (Geometry) userObject;
                String label = "";
                // geomety info, when spatial--shows name+1D/2D/3D
                if (geo.getDimension() > 0) {
                    label = geo.getName() + " (" + geo.getDimension() + "D)";
                } else {
                    label = BioModelChildSummary.COMPARTMENTAL_GEO_STR;
                }
                component.setToolTipText("Geometry");
                component.setText(label);
                setIcon(fieldGeometryIcon);
            } else if (userObject instanceof String && "AppType".equals(node.getRenderHint("type"))) {
                String label = (String) userObject;
                component.setToolTipText("Application type");
                component.setText(label);
                setIcon(VCellIcons.mathTypeIcon);
            } else if (userObject instanceof VCDocumentInfoNode) {
                VCDocumentInfoNode infonode = (VCDocumentInfoNode) userObject;
                User nodeUser = infonode.getVCDocumentInfo().getVersion().getOwner();
                String modelName = infonode.getVCDocumentInfo().getVersion().getName();
                String username = nodeUser.getName();
                if (username.equals(VCDocumentDbTreeModel.USER_tutorial) || // || username.equals(VCDocumentDbTreeModel.USER_Education)
                username.equals(VCDocumentDbTreeModel.USER_tutorial610) || username.equals(VCDocumentDbTreeModel.USER_tutorial611)) {
                    if (node.getParent() instanceof BioModelNode && ((BioModelNode) node.getParent()).getUserObject() instanceof String) {
                        String pName = (String) ((BioModelNode) node.getParent()).getUserObject();
                        if (pName.equals(VCDocumentDbTreeModel.Curated_BioModels)) {
                            // we add the user name to Curated
                            setText("<html><b>" + nodeUser.getName() + " </b> : " + modelName + "</html>");
                        } else {
                            // keep it simple for Education and Tutorial
                            component.setText(modelName);
                        }
                    } else {
                        component.setText(modelName);
                    }
                } else if (username.equals(VCDocumentDbTreeModel.USER_modelBricks)) {
                    if (node.getParent() instanceof UserNameNode && sessionUser.getName().contentEquals(VCDocumentDbTreeModel.USER_modelBricks)) {
                        // login user is ModelBrick, must gray everything in the Other (Uncurated) folder
                        // ATTANTION: the Uncurated folder is populated with bricks only in the versions of vCell where the ModelBricks
                        // folder is missing !!!
                        String toolTip = modelName;
                        // GRAY
                        String prefix = sel ? "" : "<span style=\"color:#808080\">";
                        String suffix = sel ? "" : "</span>";
                        String str1 = prefix + modelName + suffix;
                        component.setText("<html>" + str1 + "</html>");
                        component.setToolTipText(toolTip);
                    } else if (node.getParent() instanceof BioModelNode && ((BioModelNode) node.getParent()).getUserObject() instanceof String && sessionUser.getName().contentEquals(VCDocumentDbTreeModel.USER_modelBricks) && ((String) ((BioModelNode) node.getParent()).getUserObject()).equals(VCDocumentDbTreeModel.ModelBricks)) {
                        // login user is ModelBrick, and the model Bricks folder is present -> we must gray everything in it
                        // do exactly what we did for the "Other" folder, just above
                        String toolTip = modelName;
                        // GRAY
                        String prefix = sel ? "" : "<span style=\"color:#808080\">";
                        String suffix = sel ? "" : "</span>";
                        String str1 = prefix + modelName + suffix;
                        component.setText("<html>" + str1 + "</html>");
                        component.setToolTipText(toolTip);
                    } else if (node.getParent() instanceof BioModelNode && ((BioModelNode) node.getParent()).getUserObject() instanceof String) {
                        String pName = (String) ((BioModelNode) node.getParent()).getUserObject();
                        String toolTip = modelName;
                        if (!sessionUser.getName().contentEquals(VCDocumentDbTreeModel.USER_modelBricks) && modelName.contains(VCDocumentDbTreeModel.ModelBricksNameSeparator)) {
                            modelName = modelName.substring(modelName.indexOf(VCDocumentDbTreeModel.ModelBricksNameSeparator) + VCDocumentDbTreeModel.ModelBricksNameSeparator.length());
                            String prefix = toolTip.substring(0, toolTip.indexOf(VCDocumentDbTreeModel.ModelBricksNameSeparator));
                            toolTip = "id: " + prefix + ", name: " + modelName;
                        }
                        if (pName.equals(VCDocumentDbTreeModel.Curated_BioModels)) {
                            // we add the user name to Curated
                            setText("<html><b>" + nodeUser.getName() + " </b> : " + modelName + "</html>");
                            component.setToolTipText(toolTip);
                        } else if (pName.equals(VCDocumentDbTreeModel.ModelBricks)) {
                            component.setText(modelName);
                            component.setToolTipText(toolTip);
                        } else {
                            String str = modelName;
                            if (node.getChildCount() > 1) {
                                String prefix = sel ? "" : "<span style=\"color:#8B0000\">";
                                String suffix = sel ? "" : "</span>";
                                str += prefix + " (" + node.getChildCount() + ")" + suffix;
                            }
                            component.setText("<html>" + str + "</html>");
                            component.setToolTipText(toolTip);
                        }
                    } else {
                        component.setText(modelName);
                    }
                } else if (nodeUser.compareEqual(sessionUser)) {
                    Object pNode = node.getParent();
                    if (pNode instanceof BioModelNode) {
                        BioModelNode parent = (BioModelNode) pNode;
                        // TODO: do this differently
                        if (parent.getUserObject() instanceof String) {
                            // the Published, Curated and Other folders are the only
                            // ones where the user object is a String
                            String str = (String) parent.getUserObject();
                            if (str.equals(VCDocumentDbTreeModel.Published_BioModels) || str.equals(VCDocumentDbTreeModel.Curated_BioModels)) /*|| str.equals(VCDocumentDbTreeModel.Other_BioModels)*/
                            {
                                String prefix = sel ? "" : "<span style=\"color:#8B0000\">";
                                String suffix = sel ? "" : "</span>";
                                setText("<html><b>" + prefix + nodeUser.getName() + suffix + "</b>  : " + modelName + "</html>");
                            } else {
                                // in the Other folder / owner folder
                                // GRAY
                                String prefix = sel ? "" : "<span style=\"color:#808080\">";
                                String suffix = sel ? "" : "</span>";
                                String str1 = prefix + modelName + suffix;
                                if (node.getChildCount() > 1) {
                                    prefix = sel ? "" : "<span style=\"color:#8B0000\">";
                                    suffix = sel ? "" : "</span>";
                                    str1 += prefix + " (" + node.getChildCount() + ")" + suffix;
                                }
                                // the name of the model container - which holds the versions
                                setText("<html>" + str1 + "</html>");
                            }
                        } else if (parent.getUserObject() instanceof PublicationInfo) {
                            String prefix = sel ? "" : "<span style=\"color:#8B0000\">";
                            String suffix = sel ? "" : "</span>";
                            setText("<html><b>" + prefix + nodeUser.getName() + suffix + "</b>  : " + modelName + "</html>");
                        } else {
                            String str = modelName;
                            if (node.getChildCount() > 1) {
                                String prefix = sel ? "" : "<span style=\"color:#8B0000\">";
                                String suffix = sel ? "" : "</span>";
                                str += prefix + " (" + node.getChildCount() + ")" + suffix;
                            }
                            setText("<html>" + str + "</html>");
                        }
                    } else {
                        // unreachable
                        setText(modelName);
                    }
                } else {
                    Object pNode = node.getParent();
                    if (pNode instanceof UserNameNode) {
                        // if we are inside an UserName folder (like Shared or Uncurated public),
                        // don't prefix again the model with the user name
                        String str = modelName;
                        if (node.getChildCount() > 1) {
                            String prefix = sel ? "" : "<span style=\"color:#8B0000\">";
                            String suffix = sel ? "" : "</span>";
                            str += prefix + " (" + node.getChildCount() + ")" + suffix;
                        }
                        setText("<html>" + str + "</html>");
                    } else {
                        // content of "Published" folder
                        setText("<html><b>" + nodeUser.getName() + " </b> : " + modelName + "</html>");
                    }
                }
            }
        }
    } catch (Throwable e) {
        e.printStackTrace(System.out);
    }
    // 
    if (component.getToolTipText() == null || component.getToolTipText().length() == 0) {
        component.setToolTipText(component.getText());
    }
    return component;
}