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

Example 6 with PublicationInfo

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

the class MathModelDbTreePanel 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) {
        // TODO: is this line needed?
        setSelectedVersionInfo(null);
        setSelectedPublicationInfo(bioModelNode);
    } else if (object instanceof VersionInfo) {
        setSelectedVersionInfo((VersionInfo) object);
    } else if (object instanceof VCDocumentInfoNode && bioModelNode.getChildCount() > 0 && ((BioModelNode) bioModelNode.getChildAt(0)).getUserObject() instanceof MathModelInfo) {
        MathModelInfo mathModelInfo = (MathModelInfo) ((BioModelNode) bioModelNode.getChildAt(0)).getUserObject();
        setSelectedVersionInfo(mathModelInfo);
    } else {
        setSelectedVersionInfo(null);
    }
}

Example 7 with PublicationInfo

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

the class DbDriver method getVCInfoContainer.

/**
 * Insert the method's description here.
 * Creation date: (9/24/2003 12:54:32 PM)
 * @return cbit.vcell.modeldb.VCInfoContainer
 */
public static VCInfoContainer getVCInfoContainer(User user, Connection con, DatabaseSyntax dbSyntax, int whichExtraInfo) throws SQLException, DataAccessException {
    VCInfoContainer results = null;
    // 
    VCImageInfo[] vcImageInfos = null;
    GeometryInfo[] geometryInfos = null;
    MathModelInfo[] mathModelInfos = null;
    BioModelInfo[] bioModelInfos = null;
    PublicationInfo[] publicationInfos = null;
    // 
    StringBuffer sql = null;
    String special = null;
    ResultSet rset = null;
    boolean enableSpecial = true;
    boolean enableDistinct = true;
    Statement stmt = con.createStatement();
    stmt.setFetchSize(500);
    try {
        String aliasSimName = "aliasSimName";
        String aliasSimID = "aliasSimID";
        String aliasSCName = "aliasSCName";
        String aliasSVName = "aliasSVName";
        // 
        // BioModelInfos
        // 
        {
            double beginTime = System.currentTimeMillis();
            special = " ORDER BY " + BioModelTable.table.name.getQualifiedColName() + "," + BioModelTable.table.versionBranchID.getQualifiedColName() + "," + BioModelTable.table.versionDate.getQualifiedColName();
            sql = new StringBuffer(BioModelTable.table.getInfoSQL(user, null, (enableSpecial ? special : null), dbSyntax));
            sql.insert(7, Table.SQL_GLOBAL_HINT);
            rset = stmt.executeQuery(sql.toString());
            TreeMap<BigDecimal, BioModelInfo> mapBmToBioModelInfo = new TreeMap<BigDecimal, BioModelInfo>();
            while (rset.next()) {
                BigDecimal bmID = rset.getBigDecimal(VersionTable.id_ColumnName);
                if (!mapBmToBioModelInfo.containsKey(bmID)) {
                    BioModelInfo versionInfo = (BioModelInfo) BioModelTable.table.getInfo(rset, con, dbSyntax);
                    mapBmToBioModelInfo.put(bmID, versionInfo);
                }
            }
            rset.close();
            if (whichExtraInfo != 0) {
                // Add mapping simName->SimID
                try {
                    // String aliasUserKey = "aliasUserKey";
                    sql = new StringBuffer("SELECT " + SimContextTable.table.id.getQualifiedColName() + "," + SimContextTable.table.name.getQualifiedColName() + " " + aliasSCName + "," + BioModelSimContextLinkTable.table.bioModelRef.getQualifiedColName() + "," + SimulationTable.table.name.getQualifiedColName() + " " + aliasSimName + "," + SimulationTable.table.id.getQualifiedColName() + " " + aliasSimID + (whichExtraInfo == 0xFF ? "," + ApplicationMathTable.table.outputFuncLarge.getQualifiedColName() + "," + ApplicationMathTable.table.outputFuncSmall.getQualifiedColName() + "," + SimulationTable.table.mathOverridesSmall + "," + SimulationTable.table.mathOverridesLarge + "," + SubVolumeTable.table.handle.getQualifiedColName() + "," + SubVolumeTable.table.name.getQualifiedColName() + " " + aliasSVName : // SubVolumeTable.table.ordinal.getQualifiedColName()+
                    "") + " FROM " + SimContextTable.table.getTableName() + "," + BioModelSimContextLinkTable.table.getTableName() + "," + BioModelSimulationLinkTable.table.getTableName() + "," + SimulationTable.table.getTableName() + (whichExtraInfo == 0xFF ? "," + ApplicationMathTable.table.getTableName() + "," + // GeometricRegionTable.table.getTableName()+","+
                    SubVolumeTable.table.getTableName() : "") + " WHERE " + BioModelSimContextLinkTable.table.simContextRef.getQualifiedColName() + " = " + SimContextTable.table.id.getQualifiedColName() + " AND " + SimulationTable.table.id.getQualifiedColName() + " = " + BioModelSimulationLinkTable.table.simRef.getQualifiedColName() + " AND " + BioModelSimulationLinkTable.table.bioModelRef.getQualifiedColName() + " = " + BioModelSimContextLinkTable.table.bioModelRef.getQualifiedColName() + " AND " + SimContextTable.table.mathRef.getQualifiedColName() + " = " + SimulationTable.table.mathRef.getQualifiedColName() + (whichExtraInfo == 0xFF ? " AND " + SimContextTable.table.id.getQualifiedColName() + " = " + ApplicationMathTable.table.simContextRef.getQualifiedColName() + " (+)" + // " AND "+SubVolumeTable.table.geometryRef.getQualifiedColName()+" = "+GeometricRegionTable.table.geometryRef.getQualifiedColName()
                    " AND " + SimContextTable.table.geometryRef.getQualifiedColName() + " = " + SubVolumeTable.table.geometryRef.getQualifiedColName() + " (+)" : ""));
                    final BigDecimal[] array = mapBmToBioModelInfo.keySet().toArray(new BigDecimal[0]);
                    final int MAX_LIST = 500;
                    for (int i = 0; i < array.length; i += MAX_LIST) {
                        StringBuffer bmListStr = new StringBuffer();
                        for (int j = 0; (i + j) < array.length && j < MAX_LIST; j++) {
                            bmListStr.append((j != 0 ? "," : "") + array[i + j].toString());
                        }
                        final String sql2 = sql.toString() + " AND " + BioModelSimulationLinkTable.table.bioModelRef.getQualifiedColName() + " IN (" + bmListStr.toString() + ")" + " ORDER BY " + BioModelSimulationLinkTable.table.bioModelRef.getQualifiedColName() + "," + SimContextTable.table.id.getQualifiedColName() + "," + SimulationTable.table.id.getQualifiedColName();
                        rset = stmt.executeQuery(sql2);
                        BioModelInfo bmInfo = null;
                        while (rset.next()) {
                            final BigDecimal bmID = rset.getBigDecimal(BioModelSimContextLinkTable.table.bioModelRef.toString());
                            bmInfo = mapBmToBioModelInfo.get(bmID);
                            if (bmInfo != null) {
                                final BigDecimal scID = rset.getBigDecimal(SimContextTable.table.id.toString());
                                final String scName = rset.getString(aliasSCName);
                                bmInfo.addSCID(scName, scID);
                                if ((whichExtraInfo & EXTRAINFO_ANNOTFUNC) != 0) {
                                    if (!bmInfo.hasSCIDForAnnotFunc(scID)) {
                                        String outputFunctionsXML = DbDriver.varchar2_CLOB_get(rset, ApplicationMathTable.table.outputFuncSmall, ApplicationMathTable.table.outputFuncLarge, dbSyntax);
                                        if (outputFunctionsXML != null) {
                                            bmInfo.addAnnotatedFunctionsStr(scName, scID, outputFunctionsXML);
                                        }
                                    }
                                }
                                final String simName = rset.getString(aliasSimName);
                                if (bmInfo.getSimID(simName) == null) {
                                    final BigDecimal simID = rset.getBigDecimal(aliasSimID);
                                    bmInfo.addSimID(simName, simID);
                                    if ((whichExtraInfo & EXTRAINFO_MATHOVERRIDES) != 0) {
                                        CommentStringTokenizer mathOverridesTokenizer = SimulationTable.getMathOverridesTokenizer(rset, dbSyntax);
                                        List<Element> mathOverrideElements = MathOverrides.parseOverrideElementsFromVCML(mathOverridesTokenizer);
                                        // int scanCount=1;
                                        // for(Element ele:mathOverrideElements) {
                                        // if(ele.getSpec() != null) {
                                        // scanCount*=ele.getSpec().getNumValues();
                                        // //										if(scanCount==0) {
                                        // //											scanCount=ele.getSpec().getNumValues();
                                        // //										}else {
                                        // //											scanCount*=ele.getSpec().getNumValues();
                                        // //										}
                                        // }
                                        // }
                                        // //							if(scanCount > 1) {
                                        // //								System.out.println("bmid="+bmID+" simid="+simID+" scans="+scanCount+" "+simName);
                                        // //							}
                                        bmInfo.addMathOverrides(simName, mathOverrideElements);
                                    }
                                }
                                if ((whichExtraInfo & EXTRAINFO_SUBVOLUMES) != 0) {
                                    final int subVolumeID = rset.getInt(SubVolumeTable.table.handle.toString());
                                    if (bmInfo.getSubVolumeName(subVolumeID) == null) {
                                        bmInfo.addSubVolume(subVolumeID, rset.getString(aliasSVName));
                                    }
                                }
                            }
                        }
                        rset.close();
                    }
                } catch (Exception e) {
                    e.printStackTrace();
                // ignore
                }
            }
            if (mapBmToBioModelInfo.size() > 0) {
                bioModelInfos = new BioModelInfo[mapBmToBioModelInfo.size()];
                mapBmToBioModelInfo.values().toArray(bioModelInfos);
            }
            // }
            if (lg.isInfoEnabled()) {
                lg.info("BioModelInfo Time=" + (((double) System.currentTimeMillis() - beginTime) / (double) 1000));
            }
        }
        // 
        // MathModelInfos
        // 
        {
            double beginTime = System.currentTimeMillis();
            special = " ORDER BY " + MathModelTable.table.name.getQualifiedColName() + "," + MathModelTable.table.versionBranchID.getQualifiedColName() + "," + MathModelTable.table.versionDate.getQualifiedColName();
            sql = new StringBuffer(MathModelTable.table.getInfoSQL(user, null, (enableSpecial ? special : null), dbSyntax));
            sql.insert(7, Table.SQL_GLOBAL_HINT);
            TreeMap<BigDecimal, MathModelInfo> mapMmToMathModelInfo = new TreeMap<BigDecimal, MathModelInfo>();
            rset = stmt.executeQuery(sql.toString());
            ArrayList<MathModelInfo> tempInfos = new ArrayList<MathModelInfo>();
            Set<String> distinctV = new HashSet<String>();
            while (rset.next()) {
                MathModelInfo versionInfo = (MathModelInfo) MathModelTable.table.getInfo(rset, con, dbSyntax);
                if (!distinctV.contains(versionInfo.getVersion().getVersionKey().toString())) {
                    tempInfos.add(versionInfo);
                    distinctV.add(versionInfo.getVersion().getVersionKey().toString());
                    mapMmToMathModelInfo.put(BigDecimal.valueOf(Long.parseLong(versionInfo.getVersion().getVersionKey().toString())), versionInfo);
                }
            }
            rset.close();
            if (whichExtraInfo != 0) {
                // Add mapping simName->SimID
                try {
                    // String aliasUserKey = "aliasUserKey";
                    sql = new StringBuffer("SELECT " + MathModelSimulationLinkTable.table.mathModelRef.getQualifiedColName() + "," + ApplicationMathTable.table.outputFuncLarge.getQualifiedColName() + "," + ApplicationMathTable.table.outputFuncSmall.getQualifiedColName() + "," + SimulationTable.table.name.getQualifiedColName() + " " + aliasSimName + "," + SimulationTable.table.id.getQualifiedColName() + " " + aliasSimID + "," + SimulationTable.table.mathOverridesSmall + "," + SimulationTable.table.mathOverridesLarge + "," + SubVolumeTable.table.handle.getQualifiedColName() + "," + SubVolumeTable.table.name.getQualifiedColName() + " " + aliasSVName + " FROM " + MathModelTable.table.getTableName() + "," + MathDescTable.table.getTableName() + "," + MathModelSimulationLinkTable.table.getTableName() + "," + ApplicationMathTable.table.getTableName() + "," + SimulationTable.table.getTableName() + "," + SubVolumeTable.table.getTableName() + " WHERE " + MathModelSimulationLinkTable.table.mathModelRef.getQualifiedColName() + " = " + ApplicationMathTable.table.mathModelRef.getQualifiedColName() + " (+)" + " AND " + MathModelTable.table.id.getQualifiedColName() + " = " + MathModelSimulationLinkTable.table.mathModelRef.getQualifiedColName() + " AND " + SimulationTable.table.id.getQualifiedColName() + " = " + MathModelSimulationLinkTable.table.simRef.getQualifiedColName() + " AND " + MathDescTable.table.id.getQualifiedColName() + " = " + MathModelTable.table.mathRef.getQualifiedColName() + " AND " + MathDescTable.table.geometryRef.getQualifiedColName() + " = " + SubVolumeTable.table.geometryRef.getQualifiedColName() + " (+)");
                    final BigDecimal[] array = mapMmToMathModelInfo.keySet().toArray(new BigDecimal[0]);
                    final int MAX_LIST = 500;
                    for (int i = 0; i < array.length; i += MAX_LIST) {
                        StringBuffer mmListStr = new StringBuffer();
                        for (int j = 0; (i + j) < array.length && j < MAX_LIST; j++) {
                            mmListStr.append((j != 0 ? "," : "") + array[i + j].toString());
                        }
                        final String sql2 = sql.toString() + " AND " + MathModelSimulationLinkTable.table.mathModelRef.getQualifiedColName() + " IN (" + mmListStr.toString() + ")" + " ORDER BY " + MathModelSimulationLinkTable.table.mathModelRef.getQualifiedColName() + "," + SimulationTable.table.id.getQualifiedColName();
                        rset = stmt.executeQuery(sql2);
                        MathModelInfo mmInfo = null;
                        while (rset.next()) {
                            final BigDecimal mmID = rset.getBigDecimal(MathModelSimulationLinkTable.table.mathModelRef.toString());
                            mmInfo = mapMmToMathModelInfo.get(mmID);
                            if (mmInfo != null) {
                                if (mmInfo.getAnnotatedFunctionsStr() == null) {
                                    String outputFunctionsXML = DbDriver.varchar2_CLOB_get(rset, ApplicationMathTable.table.outputFuncSmall, ApplicationMathTable.table.outputFuncLarge, dbSyntax);
                                    if (outputFunctionsXML != null) {
                                        mmInfo.setAnnotatedFunctionsStr(outputFunctionsXML);
                                    }
                                }
                                final String simName = rset.getString(aliasSimName);
                                if (mmInfo.getSimID(simName) == null) {
                                    final BigDecimal simID = rset.getBigDecimal(aliasSimID);
                                    CommentStringTokenizer mathOverridesTokenizer = SimulationTable.getMathOverridesTokenizer(rset, dbSyntax);
                                    List<Element> mathOverrideElements = MathOverrides.parseOverrideElementsFromVCML(mathOverridesTokenizer);
                                    // int scanCount=1;
                                    // for(Element ele:mathOverrideElements) {
                                    // if(ele.getSpec() != null) {
                                    // scanCount*=ele.getSpec().getNumValues();
                                    // }
                                    // }
                                    mmInfo.addSimID(simName, simID, mathOverrideElements);
                                }
                                final int subVolumeID = rset.getInt(SubVolumeTable.table.handle.toString());
                                if (mmInfo.getSubVolumeName(subVolumeID) == null) {
                                    mmInfo.addSubVolume(subVolumeID, rset.getString(aliasSVName));
                                }
                            }
                        }
                        rset.close();
                    }
                } catch (Exception e) {
                    e.printStackTrace();
                // ignore
                }
            }
            if (tempInfos.size() > 0) {
                mathModelInfos = new MathModelInfo[tempInfos.size()];
                tempInfos.toArray(mathModelInfos);
            }
            if (lg.isInfoEnabled()) {
                lg.info("MathModelInfo Time=" + (((double) System.currentTimeMillis() - beginTime) / (double) 1000));
            }
        }
        // 
        // VCImageInfos
        // 
        {
            double beginTime = System.currentTimeMillis();
            special = " ORDER BY " + ImageTable.table.name.getQualifiedColName() + "," + ImageTable.table.versionBranchID.getQualifiedColName() + "," + ImageTable.table.versionDate.getQualifiedColName();
            sql = new StringBuffer(ImageTable.table.getInfoSQL(user, null, (enableSpecial ? special : null), true, dbSyntax));
            sql.insert(7, Table.SQL_GLOBAL_HINT);
            rset = stmt.executeQuery(sql.toString());
            ArrayList<VCImageInfo> tempInfos = new ArrayList<VCImageInfo>();
            Set<String> distinctV = new HashSet<String>();
            while (rset.next()) {
                VCImageInfo versionInfo = (VCImageInfo) ImageTable.table.getInfo(rset, con, dbSyntax);
                if (!distinctV.contains(versionInfo.getVersion().getVersionKey().toString())) {
                    tempInfos.add(versionInfo);
                    distinctV.add(versionInfo.getVersion().getVersionKey().toString());
                }
            }
            rset.close();
            if (tempInfos.size() > 0) {
                vcImageInfos = new VCImageInfo[tempInfos.size()];
                tempInfos.toArray(vcImageInfos);
            }
            if (lg.isInfoEnabled()) {
                lg.info("ImageInfo Time=" + (((double) System.currentTimeMillis() - beginTime) / (double) 1000));
            }
        }
        // 
        // GeometeryInfos
        // 
        {
            double beginTime = System.currentTimeMillis();
            special = " ORDER BY " + GeometryTable.table.name.getQualifiedColName() + "," + GeometryTable.table.versionBranchID.getQualifiedColName() + "," + GeometryTable.table.versionDate.getQualifiedColName();
            sql = new StringBuffer(GeometryTable.table.getInfoSQL(user, null, (enableSpecial ? special : null), true, dbSyntax));
            sql.insert(7, Table.SQL_GLOBAL_HINT + (enableDistinct ? "DISTINCT " : ""));
            rset = stmt.executeQuery(sql.toString());
            ArrayList<GeometryInfo> tempInfos = new ArrayList<GeometryInfo>();
            Set<String> distinctV = new HashSet<String>();
            while (rset.next()) {
                GeometryInfo versionInfo = (GeometryInfo) GeometryTable.table.getInfo(rset, con);
                if (!distinctV.contains(versionInfo.getVersion().getVersionKey().toString())) {
                    tempInfos.add(versionInfo);
                    distinctV.add(versionInfo.getVersion().getVersionKey().toString());
                }
            }
            rset.close();
            if (tempInfos.size() > 0) {
                geometryInfos = new GeometryInfo[tempInfos.size()];
                tempInfos.toArray(geometryInfos);
            }
            if (lg.isInfoEnabled()) {
                lg.info("GeometryInfo Time=" + (((double) System.currentTimeMillis() - beginTime) / (double) 1000));
            }
        }
        try {
            Vector<VersionInfo> bm_mm_VCDocumentInfos = new Vector<>();
            bm_mm_VCDocumentInfos.addAll(Arrays.asList((bioModelInfos != null ? bioModelInfos : new BioModelInfo[0])));
            bm_mm_VCDocumentInfos.addAll(Arrays.asList((mathModelInfos != null ? mathModelInfos : new MathModelInfo[0])));
            DbDriver.addPublicationInfos(con, stmt, bm_mm_VCDocumentInfos);
        } catch (Exception e) {
            e.printStackTrace();
        // Don't fail if something goes wrong with setting publication info
        }
    } finally {
        if (stmt != null) {
            stmt.close();
        }
    }
    results = new VCInfoContainer(user, vcImageInfos, geometryInfos, mathModelInfos, bioModelInfos);
    return results;
}

Example 8 with PublicationInfo

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

the class MathModelMetaDataPanel method getJTree1.

private JTree getJTree1() {
    if (tree == null) {
        try {
            tree = new JTree();
            tree.setName("JTree1");
            tree.setEnabled(true);
            tree.setRootVisible(false);
            tree.setRequestFocusEnabled(false);
            tree.addMouseListener(new MouseAdapter() {

                @Override
                public void mouseClicked(MouseEvent e) {
                    if (e.getClickCount() == 1) {
                        DefaultMutableTreeNode value = (DefaultMutableTreeNode) tree.getLastSelectedPathComponent();
                        if (value instanceof BioModelNode) {
                            BioModelNode node = (BioModelNode) value;
                            try {
                                if (node.getUserObject() instanceof PublicationInfo && "PublicationInfoDoi".equals(node.getRenderHint("type"))) {
                                    PublicationInfo info = (PublicationInfo) node.getUserObject();
                                    Desktop.getDesktop().browse(new URI(BeanUtils.getDynamicClientProperties().getProperty(PropertyLoader.DOI_URL) + info.getDoi()));
                                } else if (node.getUserObject() instanceof PublicationInfo && "PublicationInfoUrl".equals(node.getRenderHint("type"))) {
                                    PublicationInfo info = (PublicationInfo) node.getUserObject();
                                    Desktop.getDesktop().browse(new URI(info.getUrl()));
                                }
                            } catch (URISyntaxException | IOException ex) {
                                handleException(ex);
                            }
                        }
                    }
                }
            });
        } catch (java.lang.Throwable ivjExc) {
            handleException(ivjExc);
        }
    }
    return tree;
}

Example 9 with PublicationInfo

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

the class PublicationInfoNodeCellRenderer method getTreeCellRendererComponent.

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;
            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 String && "ModelsList".equals(node.getRenderHint("type"))) {
                String label = (String) node.getUserObject();
                component.setToolTipText("Model(s) mentioned in this Publication");
                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 && "ModelName".equals(node.getRenderHint("type"))) {
                String label = (String) node.getUserObject();
                component.setToolTipText("Model Name");
                component.setText("<html><b>" + label + "</b></html>");
                if ("BioModel".equals(node.getRenderHint("category"))) {
                    component.setToolTipText("BioModel Name");
                    setIcon(fieldBioModelIcon);
                } else if ("MathModel".equals(node.getRenderHint("category"))) {
                    component.setToolTipText("MathModel Name");
                    setIcon(fieldMathModelIcon);
                } else if ("Geometry".equals(node.getRenderHint("category"))) {
                    component.setToolTipText("Geometry Name");
                    setIcon(fieldGeometryIcon);
                } else {
                    component.setToolTipText("Document Name");
                    setIcon(fieldTextIcon);
                }
            } 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(fieldUsersIcon);
            } else if (node.getUserObject() instanceof Date && "ModelDate".equals(node.getRenderHint("type"))) {
                Date date = (Date) node.getUserObject();
                component.setToolTipText("Model Creation Date");
                component.setText("<html>" + date + "</html>");
                setIcon(fieldCalendarIcon);
            } 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);
            }
            component.setFont(unselectedFont);
        }
    } catch (Throwable e) {
        e.printStackTrace(System.out);
    }
    // 
    return component;
}

Example 10 with PublicationInfo

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

the class DbDriver method addPublicationInfos.

public static void addPublicationInfos(Connection con, Statement stmt, Vector<VersionInfo> mm_and_bm_VersionInfos) throws SQLException, DataAccessException {
    TreeMap<Long, VersionInfo> mapModelIdToVersionInfo = new TreeMap<>(new Comparator<Long>() {

        @Override
        public int compare(Long o1, Long o2) {
            return o1.compareTo(o2);
        }
    });
    for (int i = 0; i < mm_and_bm_VersionInfos.size(); i++) {
        mapModelIdToVersionInfo.put(Long.parseLong(mm_and_bm_VersionInfos.get(i).getVersion().getVersionKey().toString()), mm_and_bm_VersionInfos.get(i));
    }
    // 
    // PublicationInfos
    // 
    final String DOCTYPE_COL = "doctype";
    final String DOCID_COL = "docid";
    String sql = new String("select vc_publication.*,'bm' " + DOCTYPE_COL + ",vc_biomodel.id " + DOCID_COL + ",vc_biomodel.ownerref,vc_userinfo.userid" + " from vc_publication,vc_publicationmodellink,vc_biomodel,vc_userinfo" + " where" + " vc_biomodel.id=vc_publicationmodellink.biomodelref and vc_userinfo.id=vc_biomodel.ownerref" + " and vc_publication.id=vc_publicationmodellink.pubref and vc_publicationmodellink.pubref is not null" + " and vc_publicationmodellink.biomodelref is not null" + " UNION ALL" + " select vc_publication.*,'mm' " + DOCTYPE_COL + ",vc_mathmodel.id " + DOCID_COL + ",vc_mathmodel.ownerref,vc_userinfo.userid" + " from vc_publication,vc_publicationmodellink,vc_mathmodel,vc_userinfo" + " where" + " vc_mathmodel.id=vc_publicationmodellink.mathmodelref and vc_userinfo.id=vc_mathmodel.ownerref" + " and vc_publication.id=vc_publicationmodellink.pubref and vc_publicationmodellink.pubref is not null" + " and vc_publicationmodellink.mathmodelref is not null");
    System.out.println(sql);
    ResultSet rset = null;
    try {
        rset = stmt.executeQuery(sql);
        while (rset.next()) {
            Publication publication = PublicationTable.table.getInfo(rset, con);
            String docType = rset.getString(DOCTYPE_COL);
            BigDecimal modelVersionID = rset.getBigDecimal(DOCID_COL);
            KeyValue versionKey = new KeyValue(modelVersionID);
            Timestamp timestamp = rset.getTimestamp("pubdate");
            PublicationInfo publicationInfo = new PublicationInfo(publication.key, versionKey, publication.title, publication.authors, publication.citation, publication.pubmedid, publication.doi, publication.url, (docType.equals("bm") ? VCDocumentType.BIOMODEL_DOC : VCDocumentType.MATHMODEL_DOC), new User(rset.getString(UserTable.table.userid.getUnqualifiedColName()), new KeyValue(rset.getBigDecimal("ownerref").toString())), timestamp);
            if (mapModelIdToVersionInfo.containsKey(modelVersionID.longValue()) && mapModelIdToVersionInfo.get(modelVersionID.longValue()) instanceof VCDocumentInfo) {
                ((VCDocumentInfo) mapModelIdToVersionInfo.get(modelVersionID.longValue())).addPublicationInfo(publicationInfo);
            }
        // publicationInfoArr.add(publicationInfo);
        }
    } catch (Exception e) {
        e.printStackTrace();
        throw new DataAccessException(DbDriver.class.getName() + ".getPublicationInfo(...) Error -" + e.getMessage(), e);
    } finally {
        if (rset != null) {
            rset.close();
        }
    }
// return publicationInfoArr.toArray(new PublicationInfo[0]);
}