Examples with TemplateThing ini.trakem2.tree.TemplateThing used on opensource projects

Example 1 with TemplateThing

use of ini.trakem2.tree.TemplateThing in project TrakEM2 by trakem2.

the class DBLoader method getChildrenTemplateThings.

/**
 * Recursive into children.
 */
private ArrayList getChildrenTemplateThings(Project project, long parent_id) throws Exception {
    ArrayList al = new ArrayList();
    ResultSet r = connection.prepareStatement("SELECT * FROM ab_things WHERE parent_id=" + parent_id).executeQuery();
    while (r.next()) {
        long id = r.getLong("id");
        String type = r.getString("type");
        TemplateThing tt = new TemplateThing(type, project, id);
        tt.setup(getChildrenTemplateThings(project, id));
        al.add(tt);
    }
    r.close();
    return al;
}

Example 2 with TemplateThing

use of ini.trakem2.tree.TemplateThing in project TrakEM2 by trakem2.

the class DBLoader method getProjectThing.

private ProjectThing getProjectThing(ResultSet r, Project project, HashMap<String, TemplateThing> hs_tt, HashMap<Long, Displayable> hs_d) throws Exception {
    long id = r.getLong("id");
    String type = r.getString("type");
    TemplateThing tt = (TemplateThing) hs_tt.get(type);
    if (null == tt) {
        Utils.log("Loader.getProjectThing: can not find a proper TemplateThing of type " + type + " for the ProjectThing of id=" + id);
        return null;
    }
    long object_id = r.getLong("object_id");
    // may be null
    Object ob = r.getString("title");
    if (-1 != object_id) {
        ob = getProjectObject(project, object_id);
        if (ob instanceof Displayable)
            hs_d.put(new Long(((Displayable) ob).getId()), (Displayable) ob);
        else
            Utils.log("Loader.getProjectThing: not adding to hs_d: " + ob);
    }
    return new ProjectThing(tt, project, id, ob, getChildrenProjectThings(project, id, type, hs_tt, hs_d));
}

Example 3 with TemplateThing

use of ini.trakem2.tree.TemplateThing in project TrakEM2 by trakem2.

the class DBLoader method getLayerThing.

private LayerThing getLayerThing(ResultSet r, Project project, HashMap hs_pt, TemplateThing layer_set_tt, TemplateThing layer_tt) throws Exception {
    long id = r.getLong("id");
    String type = r.getString("type");
    // if not a "Layer", then it's a "Layer Set"
    TemplateThing template = type.equals("layer_set") ? layer_set_tt : layer_tt;
    // HERE the order of the arguments layer_set_tt and layer_tt was inverted, and it worked??? There was a compensating bug, incredibly enough, in the type.equals(.. above.
    return new LayerThing(template, project, id, r.getString("title"), getLayerThingObject(project, r.getLong("object_id"), template, hs_pt), getChildrenLayerThing(project, id, hs_pt, layer_set_tt, layer_tt));
}

Example 4 with TemplateThing

use of ini.trakem2.tree.TemplateThing in project TrakEM2 by trakem2.

the class DBLoader method upgradeProjectsTable.

/**
 * Used to upgrade old databases.
 */
private boolean upgradeProjectsTable() throws Exception {
    // Upgrade database if necessary: set a version field, create the TemplateThing entries in the database for each project from its XML template file, and delete the xml_template column
    // Check columns: see if trakem2_version is there
    ResultSet r = connection.prepareStatement("SELECT column_name FROM information_schema.columns WHERE table_name='ab_projects' AND column_name='xml_template'").executeQuery();
    if (r.next()) {
        YesNoCancelDialog yn = new YesNoCancelDialog(IJ.getInstance(), "Upgrade", "Need to upgrade table projects.\nNo data will be lost, but reorganized.\nProceed?");
        if (!yn.yesPressed()) {
            return false;
        }
        // retrieve and parse XML template from each project
        ResultSet r1 = connection.prepareStatement("SELECT * FROM ab_projects").executeQuery();
        while (r1.next()) {
            long project_id = r1.getLong("id");
            // parse the XML file stored in the db and save the TemplateThing into the ab_things table
            InputStream xml_stream = null;
            try {
                String query = "SELECT xml_template FROM ab_projects WHERE id=" + project_id;
                ResultSet result = connection.prepareStatement(query).executeQuery();
                if (result.next()) {
                    xml_stream = result.getBinaryStream("xml_template");
                }
                result.close();
            } catch (Exception e) {
                IJError.print(e);
                return false;
            }
            if (null == xml_stream) {
                Utils.showMessage("Failed to upgrade the database schema: XML template stream is null.");
                return false;
            }
            TemplateThing template_root = new TrakEM2MLParser(xml_stream).getTemplateRoot();
            if (null == template_root) {
                Utils.showMessage("Failed to upgrade the database schema: root TemplateThing is null.");
                return false;
            }
            Project project = new Project(project_id, r1.getString("title"));
            project.setTempLoader(this);
            template_root.addToDatabase(project);
        }
        r1.close();
        // remove the XML column
        connection.prepareStatement("ALTER TABLE ab_projects DROP xml_template").execute();
        // org.postgresql.util.PSQLException: ERROR: adding columns with defaults is not implemented in 7.4.* (only in 8.1.4+)
        // connection.prepareStatement("ALTER TABLE ab_projects ADD version text default '" + Utils.version + "'").execute();
        // so: workaround
        connection.prepareStatement("ALTER TABLE ab_projects ADD version TEXT").execute();
        connection.prepareStatement("ALTER TABLE ab_projects ALTER COLUMN version SET DEFAULT '" + Utils.version + "'").execute();
    }
    r.close();
    // success!
    return true;
}

Example 5 with TemplateThing

use of ini.trakem2.tree.TemplateThing in project TrakEM2 by trakem2.

the class DBLoader method getRootLayerThing.

/**
 * Fetches the root LayerSet, fills it with children (recursively) and uses the profiles, pipes, etc., from the project_thing. Will reconnect the links and open Displays for the layers that have one.
 */
public LayerThing getRootLayerThing(Project project, ProjectThing project_thing, TemplateThing layer_set_tt, TemplateThing layer_tt) {
    synchronized (db_lock) {
        // connect if disconnected
        if (!connectToDatabase()) {
            return null;
        }
        HashMap hs_pt = new HashMap();
        unpack(project_thing, hs_pt);
        LayerThing root = null;
        try {
            // -1 signals root
            ResultSet r = connection.prepareStatement("SELECT * FROM ab_things WHERE project_id=" + project.getId() + " AND type='layer_set' AND parent_id=-1").executeQuery();
            if (r.next()) {
                root = getLayerThing(r, project, hs_pt, layer_set_tt, layer_tt);
            }
            r.close();
            if (null == root) {
                Utils.log("Loader.getRootLayerThing: can't find it for project id=" + project.getId());
                return null;
            }
            // Redo the links! hs_pt contains now all Displayable objects.
            ResultSet rl = connection.prepareStatement("SELECT * FROM ab_links WHERE project_id=" + project.getId()).executeQuery();
            while (rl.next()) {
                Long id1 = new Long(rl.getLong("id1"));
                Long id2 = new Long(rl.getLong("id2"));
                Object ob1 = hs_pt.get(id1);
                Object ob2 = hs_pt.get(id2);
                if (null != ob1 && null != ob2) {
                    Displayable d = (Displayable) ob1;
                    d.link((Displayable) ob2, false);
                } else {
                    Utils.log("Loader: broken link between " + id1 + " and " + id2);
                }
            }
            rl.close();
        } catch (Exception e) {
            IJError.print(e);
            return null;
        }
        return root;
    }
}