Examples with ExternalDocInfo cbit.vcell.xml.ExternalDocInfo used on opensource projects

Example 6 with ExternalDocInfo

use of cbit.vcell.xml.ExternalDocInfo in project vcell by virtualcell.

the class BioModelsNetJPanel method searchImport.

private void searchImport() {
    AsynchClientTask searchTask = new AsynchClientTask("Search BioModels", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Hashtable<String, String> vcellCompatibleBioModels_ID_Name_Hash = readVCellCompatibleBioModels_ID_Name_Hash();
            ClientTaskStatusSupport clientTaskStatusSupport = getClientTaskStatusSupport();
            // clientTaskStatusSupport.setProgress(0);
            clientTaskStatusSupport.setMessage("Initializing BioModels Search...");
            BioModelsWebServicesServiceLocator bioModelsWebServicesServiceLocator = new BioModelsWebServicesServiceLocator();
            BioModelsWebServices bioModelsWebServices = bioModelsWebServicesServiceLocator.getBioModelsWebServices();
            // clientTaskStatusSupport.setProgress(10);
            clientTaskStatusSupport.setMessage("Executing BioModels Search...");
            TreeSet<String> modelIDsMergedSearch = new TreeSet<String>();
            boolean bHasModelEntryID = modelEntryIDTextField.getText() != null && modelEntryIDTextField.getText().length() > 0;
            if (bHasModelEntryID) {
                clientTaskStatusSupport.setMessage("Executing BioModels Search (Model ID matches)...");
                // String[] modelIDsAll = bioModelsWebServices.getAllModelsId();
                String[] modelIDsAll = vcellCompatibleBioModels_ID_Name_Hash.keySet().toArray(new String[0]);
                for (int i = 0; i < modelIDsAll.length; i++) {
                    if (modelIDsAll[i].toUpperCase().indexOf(modelEntryIDTextField.getText().toUpperCase()) != -1) {
                        modelIDsMergedSearch.add(modelIDsAll[i]);
                    }
                }
            }
            boolean bHasModelName = modelNameTextField.getText() != null && modelNameTextField.getText().length() > 0;
            if (bHasModelName) {
                clientTaskStatusSupport.setMessage("Executing BioModels Search (Model Name matches)...");
                TreeSet<String> modelIDsByNameSet = new TreeSet<String>();
                // String[] modelIDsByName = bioModelsWebServices.getModelsIdByName(modelNameTextField.getText());
                String[] modelIDsAll = vcellCompatibleBioModels_ID_Name_Hash.keySet().toArray(new String[0]);
                for (int i = 0; i < modelIDsAll.length; i++) {
                    if (vcellCompatibleBioModels_ID_Name_Hash.get(modelIDsAll[i]).toUpperCase().indexOf(modelNameTextField.getText().toUpperCase()) != -1) {
                        modelIDsByNameSet.add(modelIDsAll[i]);
                    }
                }
                // }
                if (bHasModelEntryID) {
                    // intersection
                    modelIDsMergedSearch.retainAll(modelIDsByNameSet);
                } else {
                    modelIDsMergedSearch = modelIDsByNameSet;
                }
            }
            boolean bHasModelPublication = publicationTextField.getText() != null && publicationTextField.getText().length() > 0;
            if (bHasModelPublication) {
                clientTaskStatusSupport.setMessage("Executing BioModels Search (Publication matches)...");
                TreeSet<String> modelIDsByPublicationSet = new TreeSet<String>();
                String[] modelIDsbyPublication = bioModelsWebServices.getModelsIdByPublication(publicationTextField.getText());
                for (int i = 0; i < modelIDsbyPublication.length; i++) {
                    modelIDsByPublicationSet.add(modelIDsbyPublication[i]);
                }
                if (bHasModelEntryID || bHasModelName) {
                    // intersection
                    modelIDsMergedSearch.retainAll(modelIDsByPublicationSet);
                } else {
                    modelIDsMergedSearch = modelIDsByPublicationSet;
                }
            }
            if (!(bHasModelEntryID || bHasModelName || bHasModelPublication)) {
                // Get all models
                // modelIDsMergedSearch.addAll(Arrays.asList(bioModelsWebServices.getAllModelsId()));
                modelIDsMergedSearch.addAll(Arrays.asList(vcellCompatibleBioModels_ID_Name_Hash.keySet().toArray(new String[0])));
            }
            // clientTaskStatusSupport.setProgress(COLLECTION_PROGRESS);
            if (modelIDsMergedSearch.size() > 0) {
                // Intersect with supported BioModel IDs
                modelIDsMergedSearch.retainAll(Arrays.asList(vcellCompatibleBioModels_ID_Name_Hash.keySet().toArray(new String[0])));
                clientTaskStatusSupport.setMessage("Found " + modelIDsMergedSearch.size() + " VCell compatible BioModels");
                String[] modelIDMergedSearchArr = modelIDsMergedSearch.toArray(new String[0]);
                TreeMap<String, String> model_ID_Name_Map = new TreeMap<String, String>();
                String nameNotfound = "NameNotFound_0";
                for (int i = 0; i < modelIDMergedSearchArr.length; i++) {
                    if (clientTaskStatusSupport.isInterrupted()) {
                        // DialogUtils.showWarningDialog(BioModelsNetJPanel.this, "Search Cancelled");
                        throw UserCancelException.CANCEL_GENERIC;
                    }
                    try {
                        // clientTaskStatusSupport.setMessage("Retrieving "+modelIDMergedSearchArr[i]+" "+(i+1)+" of "+modelIDMergedSearchArr.length);
                        // String modelName = bioModelsWebServices.getModelNameById(modelIDMergedSearchArr[i]);
                        String modelName = vcellCompatibleBioModels_ID_Name_Hash.get(modelIDMergedSearchArr[i]);
                        // Assume model names are unique
                        model_ID_Name_Map.put(modelName, modelIDMergedSearchArr[i]);
                    } catch (Exception e) {
                        // For some reason Web Service API sometimes throws java.util.NoSuchElementException
                        // if id exists but name can't be found.
                        e.printStackTrace();
                        model_ID_Name_Map.put(nameNotfound, modelIDMergedSearchArr[i]);
                        nameNotfound = TokenMangler.getNextEnumeratedToken(nameNotfound);
                    }
                }
                // Make name,id rowdata for tablelist to allow user selection
                String[] sortedModelNames = model_ID_Name_Map.keySet().toArray(new String[0]);
                final String[][] rowData = new String[sortedModelNames.length][2];
                for (int i = 0; i < sortedModelNames.length; i++) {
                    rowData[i][0] = sortedModelNames[i];
                    rowData[i][1] = model_ID_Name_Map.get(sortedModelNames[i]);
                }
                // Allow user to select model for opening
                final String importNow = "Import";
                final String cancel = "Cancel";
                DialogUtils.TableListResult result = DialogUtils.showComponentOptionsTableList(BioModelsNetJPanel.this, "Select a BioModel to import", new String[] { "Model Names", "BioModels Entry ID" }, rowData, ListSelectionModel.SINGLE_SELECTION, null, new String[] { importNow, cancel }, importNow, new Comparator<Object>() {

                    public int compare(Object o1, Object o2) {
                        if (o1 instanceof String && o2 instanceof String) {
                            return ((String) o1).compareTo((String) o2);
                        }
                        throw new RuntimeException("row data should only be String");
                    }
                });
                if (result.selectedOption != null && result.selectedOption.equals(importNow)) {
                    // Close Dialog showing "this" panel so ProgressPopup not obscured during openDocument
                    SwingUtilities.invokeAndWait(new Runnable() {

                        public void run() {
                            disposeParentDialog();
                        }
                    });
                    closeClientTaskStatusSupport(clientTaskStatusSupport);
                    // Download and open (in new window) SBML document selected by user
                    String bioModelSBML = bioModelsWebServices.getModelSBMLById(rowData[result.selectedTableRows[0]][1]);
                    final ExternalDocInfo externalDocInfo = new ExternalDocInfo(bioModelSBML, sortedModelNames[result.selectedTableRows[0]]);
                    new Thread(new Runnable() {

                        public void run() {
                            documentWindow.getTopLevelWindowManager().getRequestManager().openDocument(externalDocInfo, documentWindow.getTopLevelWindowManager(), true);
                        }
                    }).start();
                }
            } else {
                closeClientTaskStatusSupport(clientTaskStatusSupport);
                DialogUtils.showWarningDialog(BioModelsNetJPanel.this, "No BioModels found matching current search criteria.");
                throw UserCancelException.CANCEL_GENERIC;
            }
        }
    };
    ClientTaskDispatcher.dispatch(BioModelsNetJPanel.this, new Hashtable<String, Object>(), new AsynchClientTask[] { searchTask }, true, true, null, true);
}

Example 7 with ExternalDocInfo

use of cbit.vcell.xml.ExternalDocInfo in project vcell by virtualcell.

the class BioModelsNetPanel method importFromBioModelsNet.

public void importFromBioModelsNet() {
    Object obj = tree.getLastSelectedPathComponent();
    if (obj == null || !(obj instanceof BioModelNode)) {
        return;
    }
    BioModelNode selectedNode = (BioModelNode) obj;
    Object userObject = selectedNode.getUserObject();
    if (!(userObject instanceof BioModelsNetModelInfo)) {
        return;
    }
    BioModelsNetModelInfo bioModelsNetInfo = (BioModelsNetModelInfo) userObject;
    String name = bioModelsNetInfo.getName();
    String id = bioModelsNetInfo.getId();
    AsynchClientTask task1 = new AsynchClientTask("Importing " + name, AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            ExternalDocInfo externalDocInfo = download(name, id);
            if (externalDocInfo != null) {
                hashTable.put("externalDocInfo", externalDocInfo);
            }
            System.out.println("done downloading");
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("Opening", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            ExternalDocInfo externalDocInfo = (ExternalDocInfo) hashTable.get("externalDocInfo");
            if (externalDocInfo == null) {
                return;
            }
            documentWindowManager.getRequestManager().openDocument(externalDocInfo, documentWindowManager, true);
        }
    };
    ClientTaskDispatcher.dispatch(documentWindowManager.getComponent(), new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 }, false);
}

Example 8 with ExternalDocInfo

use of cbit.vcell.xml.ExternalDocInfo in project vcell by virtualcell.

the class BioModelsNetPanel method download.

private ExternalDocInfo download(String name, String id) throws Exception {
    // C:\Users\vasilescu\.vcell\simdata
    String simDataDir = ResourceUtil.getLocalRootDir().getAbsolutePath();
    String tempDir = simDataDir + File.separator + "temp";
    String destDirectory = tempDir + File.separator + id;
    String zipFilePath = destDirectory + ".zip";
    Path tempDirPath = Paths.get(tempDir);
    // temp may not be there, we make it
    Files.createDirectories(tempDirPath);
    byte[] responseContent = null;
    URL url = new URL(BeanUtils.getDynamicClientProperties().getProperty(PropertyLoader.BMDB_DOWNLOAD_URL) + id);
    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    InputStream is = null;
    try {
        try {
            is = url.openStream();
        } catch (Exception e) {
            e.printStackTrace();
            if (is != null) {
                is.close();
            }
            // Try with http instead of https
            String newUrlString = url.toString().replaceFirst("^https", "http");
            url = new URL(newUrlString);
            is = url.openStream();
        }
        // Or whatever size you want to read in at a time.
        byte[] byteChunk = new byte[4096];
        int n;
        while ((n = is.read(byteChunk)) > 0) {
            baos.write(byteChunk, 0, n);
        }
        responseContent = baos.toByteArray();
    } catch (IOException e) {
        System.err.printf("Failed while reading bytes from %s: %s", url.toExternalForm(), e.getMessage());
        // e.printStackTrace ();
        throw new RuntimeException("Failed while reading bytes from: " + url.toExternalForm());
    } finally {
        if (is != null) {
            is.close();
        }
    }
    if (responseContent == null) {
        throw new RuntimeException("Failed while reading bytes from: " + url.toExternalForm());
    }
    try {
        File file = new File(zipFilePath);
        Files.write(file.toPath(), responseContent, StandardOpenOption.CREATE, StandardOpenOption.WRITE, StandardOpenOption.TRUNCATE_EXISTING);
        UnzipUtility uu = new UnzipUtility();
        uu.unzip(zipFilePath, destDirectory);
    } catch (IOException e) {
        e.printStackTrace();
    }
    String unzippedPath = destDirectory + File.separator + id + ".xml";
    String bioModelSBML = new String(Files.readAllBytes(Paths.get(unzippedPath)), StandardCharsets.UTF_8);
    // bioModelSBML = bioModelSBML.replace("<notanumber/>", "<ci> a </ci>");
    try {
        // the original zip file
        Files.deleteIfExists(Paths.get(zipFilePath));
        // the unzipped SBML file
        Files.deleteIfExists(Paths.get(unzippedPath));
        // its directory
        Files.deleteIfExists(Paths.get(destDirectory));
    // Files.deleteIfExists(Paths.get(prettyXML));			// the pretty xml
    } catch (IOException e) {
        e.printStackTrace();
    }
    ExternalDocInfo externalDocInfo = ExternalDocInfo.createBioModelsNetExternalDocInfo(bioModelSBML, name);
    return externalDocInfo;
}

Example 9 with ExternalDocInfo

use of cbit.vcell.xml.ExternalDocInfo in project vcell by virtualcell.

the class BioModelsNetPanel method importFromBioModelsNetTest.

public void importFromBioModelsNetTest() {
    try {
        int i = 731;
        String name = "tested" + i;
        String id = "BIOMD0000000" + i;
        AsynchClientTask task1 = new AsynchClientTask("Importing " + name, AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                ExternalDocInfo externalDocInfo = download(name, id);
                if (externalDocInfo != null) {
                    hashTable.put("externalDocInfo", externalDocInfo);
                }
                System.out.println("done downloading: " + id);
            }
        };
        AsynchClientTask task2 = new AsynchClientTask("Opening", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                ExternalDocInfo externalDocInfo = (ExternalDocInfo) hashTable.get("externalDocInfo");
                if (externalDocInfo == null) {
                    return;
                }
                documentWindowManager.getRequestManager().openDocument(externalDocInfo, documentWindowManager, true);
                System.out.println("opened: " + id);
            }
        };
        ClientTaskDispatcher.dispatch(documentWindowManager.getComponent(), new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 }, false);
        System.out.println("task dispatched for " + id);
    } catch (Exception e) {
        System.err.println(e.getMessage());
    }
}

Example 10 with ExternalDocInfo

use of cbit.vcell.xml.ExternalDocInfo in project vcell by virtualcell.

the class BioModelsNetPropertiesPanel method importFromBioModelsNet.

public void importFromBioModelsNet() {
    AsynchClientTask task1 = new AsynchClientTask("Importing " + bioModelsNetModelInfo.getName(), AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            BioModelsWebServicesServiceLocator bioModelsWebServicesServiceLocator = new BioModelsWebServicesServiceLocator();
            BioModelsWebServices bioModelsWebServices = bioModelsWebServicesServiceLocator.getBioModelsWebServices();
            String bioModelSBML = bioModelsWebServices.getModelSBMLById(bioModelsNetModelInfo.getId());
            ExternalDocInfo externalDocInfo = new ExternalDocInfo(bioModelSBML, bioModelsNetModelInfo.getName());
            if (externalDocInfo != null) {
                hashTable.put("externalDocInfo", externalDocInfo);
            }
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("Opening", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            ExternalDocInfo externalDocInfo = (ExternalDocInfo) hashTable.get("externalDocInfo");
            if (externalDocInfo == null) {
                return;
            }
            documentWindowManager.getRequestManager().openDocument(externalDocInfo, documentWindowManager, true);
        }
    };
    ClientTaskDispatcher.dispatch(documentWindowManager.getComponent(), new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 }, false);
}