Examples with HPO_Class_Found org.monarchinitiative.loinc2hpo.util.HPO_Class_Found used on opensource projects

Example 1 with HPO_Class_Found

use of org.monarchinitiative.loinc2hpo.util.HPO_Class_Found in project loinc2hpo by monarch-initiative.

the class AnnotateTabController method updateHpoTermListView.

private void updateHpoTermListView(LoincEntry entry) {
    if (SparqlQuery.model == null) {
        Alert alert = new Alert(Alert.AlertType.INFORMATION);
        alert.setTitle("HPO Model Undefined");
        alert.setHeaderText("Create HPO model first before querying");
        alert.setContentText("Click \"Initialize HPO model\" to create an" + " HPO model for Sparql query. Click and query again.");
        alert.showAndWait();
        return;
    }
    String name = entry.getLongName();
    hpoListView.getItems().clear();
    sparqlQueryResult.clear();
    sparqlQueryResult.addAll(SparqlQuery.query_auto(name));
    sparqlQueryResult.sort((o1, o2) -> o2.getScore() - o1.getScore());
    // SparqlQuery.query_auto(name).stream().forEach(sparqlQueryResult::add);
    logger.trace("sparqlQueryResult size: " + sparqlQueryResult.size());
    if (sparqlQueryResult.size() == 0) {
        String noHPOfoundMessage = "0 HPO class is found. Try manual search with " + "alternative keys (synonyms)";
        sparqlQueryResult.add(new HPO_Class_Found(noHPOfoundMessage, null, null, null));
    }
    hpoListView.setItems(sparqlQueryResult);
}

Example 2 with HPO_Class_Found

use of org.monarchinitiative.loinc2hpo.util.HPO_Class_Found in project loinc2hpo by monarch-initiative.

the class AnnotateTabController method suggestNewChildTerm.

@FXML
private void suggestNewChildTerm(ActionEvent e) {
    e.consume();
    initializeGitHubLabelsIfNecessary();
    LoincEntry loincEntrySelected = loincTableView.getSelectionModel().getSelectedItem();
    if (loincEntrySelected == null) {
        logger.error("Select a loinc code before making a suggestion");
        PopUps.showInfoMessage("Please select a loinc code before creating GitHub issue", "Error: No HPO Term selected");
        return;
    }
    loincIdSelected = loincEntrySelected.getLOINC_Number();
    logger.info("Selected loinc to create github issue for: " + loincIdSelected);
    HPO_Class_Found hpoSelected = (HPO_Class_Found) hpoListView.getSelectionModel().getSelectedItem();
    if (hpoSelected == null) {
        HPO_TreeView hpoSelectedInTree = treeView.getSelectionModel().getSelectedItem().getValue();
        hpoSelected = hpoSelectedInTree.hpo_class_found;
    }
    if (hpoSelected == null) {
        logger.error("Select a hpo term before making a suggestion");
        PopUps.showInfoMessage("Please select a hpo term before creating GitHub issue", "Error: No HPO Term selected");
        return;
    }
    HpoTerm hpoTerm = model.getTermMap().get(hpoSelected.getLabel());
    GitHubPopup popup = new GitHubPopup(loincEntrySelected, hpoTerm, true);
    initializeGitHubLabelsIfNecessary();
    popup.setLabels(model.getGithublabels());
    popup.setupGithubUsernamePassword(githubUsername, githubPassword);
    popup.setBiocuratorId(model.getBiocuratorID());
    logger.debug("get biocurator id from model: " + model.getBiocuratorID());
    popup.displayWindow(Main.getPrimarystage());
    String githubissue = popup.retrieveGitHubIssue();
    if (githubissue == null) {
        logger.trace("got back null github issue");
        return;
    }
    List<String> labels = popup.getGitHubLabels();
    // String title = String.format("NTR for Loinc %s:  \"%s\"", loincIdSelected, popup.retrieveSuggestedTerm());
    String title = String.format("Loinc %s:  \"%s\"", loincIdSelected, loincEntrySelected.getLongName());
    postGitHubIssue(githubissue, title, popup.getGitHubUserName(), popup.getGitHubPassWord(), labels);
}

Example 3 with HPO_Class_Found

use of org.monarchinitiative.loinc2hpo.util.HPO_Class_Found in project loinc2hpo by monarch-initiative.

the class AnnotateTabController method handleManualQueryButton.

@FXML
private void handleManualQueryButton(ActionEvent e) {
    e.consume();
    if (SparqlQuery.model == null) {
        Alert alert = new Alert(Alert.AlertType.INFORMATION);
        alert.setTitle("HPO Model Undefined");
        alert.setHeaderText("Create HPO model first before querying");
        alert.setContentText("Click \"Initialize HPO model\" to create an" + " HPO model for Sparql query. Click and query again.");
        alert.showAndWait();
        return;
    }
    // for now, force user choose a loinc entry. TODO: user may or may not
    // choose a loinc term.
    LoincEntry entry = loincTableView.getSelectionModel().getSelectedItem();
    if (entry == null) {
        noLoincEntryAlert();
        return;
    }
    if (model.getLoincUnderEditing() != null && !model.getLoincUnderEditing().equals(entry)) {
        PopUps.showInfoMessage("You are currently editing " + model.getLoincUnderEditing().getLOINC_Number() + ". Save or cancel editing current loinc annotation before switching to others", "Under Editing mode");
        return;
    }
    String userInput = userInputForManualQuery.getText();
    if (userInput == null || userInput.trim().length() < 2) {
        Alert alert = new Alert(Alert.AlertType.INFORMATION);
        alert.setTitle("Input Error");
        alert.setHeaderText("Type in keys for manual query");
        alert.setContentText("Provide comma seperated keys for query. Do " + "not use quotes(\"\"). Avoid non-specific words " + "or numbers. Synonyms are strongly recommended if " + "auto-query is not working.");
        alert.showAndWait();
        return;
    }
    String[] keys = userInput.split(",");
    List<String> keysInList = new ArrayList<>();
    for (String key : keys) {
        if (key.length() > 0) {
            keysInList.add(key);
        }
    }
    String name = entry.getLongName();
    LoincCodeClass loincCodeClass = LoincLongNameParser.parse(name);
    List<HPO_Class_Found> queryResults = SparqlQuery.query_manual(keysInList, loincCodeClass);
    if (queryResults.size() != 0) {
        ObservableList<HPO_Class_Found> items = FXCollections.observableArrayList();
        for (HPO_Class_Found candidate : queryResults) {
            items.add(candidate);
        }
        this.hpoListView.setItems(items);
        userInputForManualQuery.clear();
    // items.add("0 result is found. Try manual search with synonyms.");
    } else {
        ObservableList<String> items = FXCollections.observableArrayList();
        items.add("0 HPO class is found. Try manual search with " + "alternative keys (synonyms)");
        this.hpoListView.setItems(items);
    }
    // clear text in abnormality text fields if not currently editing a term
    if (!createAnnotationButton.getText().equals("Save")) {
        // Got user feedback that they do not want to clear the field when doing manual query
        // clearAbnormalityTextField();
        // inialize the flag field
        flagForAnnotation.setIndeterminate(false);
        flagForAnnotation.setSelected(false);
        createAnnotationSuccess.setFill(Color.WHITE);
        annotationNoteField.setText("");
    }
}

Example 4 with HPO_Class_Found

use of org.monarchinitiative.loinc2hpo.util.HPO_Class_Found in project loinc2hpo by monarch-initiative.

the class AnnotateTabController method initialize.

@FXML
private void initialize() {
    if (model != null) {
        // weird line. model is set by main controller; this line never runs
        setModel(model);
    // currentAnnotationController.setModel(model); //let current annotation stage have access to model
    }
    // currentAnnotationController.setModel(model); //let current annotation stage have access to model
    suggestHPOButton.setTooltip(new Tooltip("Suggest new HPO terms"));
    filterButton.setTooltip(new Tooltip("Filter Loinc by providing a Loinc list in txt file"));
    addCodedAnnotationButton.setTooltip(new Tooltip("Add current annotation"));
    flagForAnnotation.setTooltip(new Tooltip("Check if you are not confident"));
    clearButton.setTooltip(new Tooltip("Clear all textfields"));
    allAnnotationsButton.setTooltip(new Tooltip("Display annotations for currently selected Loinc code"));
    initLOINCtableButton.setTooltip(new Tooltip("Initialize Loinc Core Table. Download it first."));
    IntializeHPOmodelbutton.setTooltip(new Tooltip("Load hp.owl as a RDF model for query"));
    searchForLOINCIdButton.setTooltip(new Tooltip("Search Loinc with a Loinc code or name"));
    modeButton.setTooltip(new Tooltip("Switch between basic and advanced annotation mode"));
    autoQueryButton.setTooltip(new Tooltip("Find candidate HPO terms with automatically generated keys"));
    manualQueryButton.setTooltip(new Tooltip("Find candidate HPO terms with manually typed keys"));
    hpoListView.setCellFactory(new Callback<ListView<HPO_Class_Found>, ListCell<HPO_Class_Found>>() {

        @Override
        public ListCell<HPO_Class_Found> call(ListView<HPO_Class_Found> param) {
            return new ListCell<HPO_Class_Found>() {

                @Override
                public void updateItem(HPO_Class_Found hpo, boolean empty) {
                    super.updateItem(hpo, empty);
                    if (hpo != null) {
                        setText(hpo.toString());
                        Tooltip tooltip = new Tooltip(hpo.getDefinition());
                        tooltip.setPrefWidth(300);
                        tooltip.setWrapText(true);
                        setTooltip(tooltip);
                    } else {
                        setText(null);
                    }
                }
            };
        }
    });
    treeView.setCellFactory(new Callback<TreeView<HPO_TreeView>, TreeCell<HPO_TreeView>>() {

        @Override
        public TreeCell<HPO_TreeView> call(TreeView<HPO_TreeView> param) {
            return new TreeCell<HPO_TreeView>() {

                @Override
                public void updateItem(HPO_TreeView hpo, boolean empty) {
                    super.updateItem(hpo, empty);
                    if (empty) {
                        setText(null);
                        setGraphic(null);
                    } else {
                        if (hpo != null && hpo.hpo_class_found == null) {
                            setText("root");
                        }
                        if (hpo != null && hpo.hpo_class_found != null) {
                            setText(hpo.toString());
                            if (hpo.hpo_class_found.getDefinition() != null) {
                                Tooltip tooltip = new Tooltip(hpo.hpo_class_found.getDefinition());
                                tooltip.setPrefWidth(300);
                                tooltip.setWrapText(true);
                                setTooltip(tooltip);
                            }
                        }
                    }
                }
            };
        }
    });
    // if user creates a new Loinc group, add two menuitems for it, and specify the actions when those menuitems are
    // clicked
    userCreatedLoincLists.addListener(new ListChangeListener<String>() {

        @Override
        public void onChanged(Change<? extends String> c) {
            while (c.next()) {
                if (c.wasAdded()) {
                    logger.trace(c + " was added");
                    c.getAddedSubList().stream().filter(p -> !model.getUserCreatedLoincLists().containsKey(p)).forEach(p -> {
                        model.addUserCreatedLoincList(p, new LinkedHashSet<>());
                        MenuItem newListMenuItem = new MenuItem(p);
                        userCreatedLoincListsButton.getItems().add(newListMenuItem);
                        newListMenuItem.setOnAction((event -> {
                            logger.trace("action detected");
                            if (loincTableView.getSelectionModel().getSelectedItem() != null) {
                                LoincId loincId = loincTableView.getSelectionModel().getSelectedItem().getLOINC_Number();
                                if (model.getUserCreatedLoincLists().get(p).contains(loincId)) {
                                    model.getUserCreatedLoincLists().get(p).remove(loincId);
                                    logger.trace(String.format("LOINC: %s removed from %s", loincId, p));
                                } else {
                                    model.getUserCreatedLoincLists().get(p).add(loincId);
                                    logger.trace(String.format("LOINC: %s added to %s", loincId, p));
                                }
                                changeColorLoincTableView();
                                model.setSessionChanged(true);
                            }
                        }));
                        MenuItem newExportMenuItem = new MenuItem(p);
                        exportLoincListButton.getItems().add(newExportMenuItem);
                        newExportMenuItem.setOnAction((event -> {
                            logger.trace("action detected");
                            if (loincTableView.getSelectionModel().getSelectedItem() != null) {
                                Set<LoincId> loincIds = model.getUserCreatedLoincLists().get(p);
                                if (loincIds.isEmpty()) {
                                    return;
                                }
                                FileChooser chooser = new FileChooser();
                                chooser.setTitle("Save Loinc List: ");
                                chooser.getExtensionFilters().add(new FileChooser.ExtensionFilter("TSV files (*.txt)", "*.txt"));
                                chooser.setInitialFileName(p);
                                File f = chooser.showSaveDialog(null);
                                String filepath;
                                if (f == null) {
                                    return;
                                } else {
                                    filepath = f.getAbsolutePath();
                                }
                                StringBuilder builder = new StringBuilder();
                                loincIds.forEach(l -> {
                                    builder.append(l);
                                    builder.append("\n");
                                });
                                WriteToFile.writeToFile(builder.toString().trim(), filepath);
                            }
                        }));
                        MenuItem newImportMenuItem = new MenuItem(p);
                        importLoincGroupButton.getItems().add(newImportMenuItem);
                        newImportMenuItem.setOnAction((event) -> {
                            logger.trace("user wants to import " + p);
                            FileChooser chooser = new FileChooser();
                            chooser.setTitle("Select file to import from");
                            File f = chooser.showOpenDialog(null);
                            if (f == null) {
                                return;
                            }
                            List<String> malformed = new ArrayList<>();
                            List<String> notFound = new ArrayList<>();
                            try {
                                LoincOfInterest loincSet = new LoincOfInterest(f.getAbsolutePath());
                                Set<String> loincIds = loincSet.getLoincOfInterest();
                                loincIds.forEach(l -> {
                                    LoincId loincId = null;
                                    try {
                                        loincId = new LoincId(l);
                                    } catch (MalformedLoincCodeException e) {
                                        malformed.add(l);
                                    }
                                    if (model.getLoincEntryMap().containsKey(loincId)) {
                                        model.getUserCreatedLoincLists().get(p).add(loincId);
                                    } else {
                                        notFound.add(l);
                                    }
                                    changeColorLoincTableView();
                                });
                            } catch (FileNotFoundException e) {
                                logger.error("File not found. Should never happen");
                            }
                            if (!malformed.isEmpty() || !notFound.isEmpty()) {
                                String malformedString = String.join("\n", malformed);
                                String notFoundString = String.join("\n", notFound);
                                PopUps.showInfoMessage(String.format("Malformed Loinc: %d\n%s\nNot Found: %d\n%s", malformed.size(), malformedString, notFound.size(), notFoundString), "Error during importing");
                            }
                        });
                    });
                } else {
                    logger.error("This should never happen");
                }
            }
        }
    });
    initadvancedAnnotationTable();
}

Example 5 with HPO_Class_Found

use of org.monarchinitiative.loinc2hpo.util.HPO_Class_Found in project loinc2hpo by monarch-initiative.

the class SparqlQueryTest method testQuery_auto.

@Test
public void testQuery_auto() {
    // String loinc_name = "Testosterone Free [Mass/volume] in Serum or Plasma";
    // SparqlQuery.query_auto(loinc_name);
    // String loinc_name = "Erythrocyte distribution width [Ratio] in blood or serum by Automated count";
    // String loinc_name = "Carbon dioxide, total [Moles/volume] in Serum or Plasma";
    // List<HPO_Class_Found> hpo_clsses_found = new ArrayList<>();
    /**
     *        System.out.println("Find Carbon dioxide, total [Moles/volume] in Serum or Plasma: ");
     *        SparqlQuery.query_auto("Carbon dioxide, total [Moles/volume] in Serum or Plasma");
     *        System.out.println("Find Anion gap 3 in Serum or Plasma: ");
     *        SparqlQuery.query_auto("Anion gap 3 in Serum or Plasma");
     */
    // System.out.println("Find \"Potassium [Moles/volume] in Serum or Plasma\": ");
    List<HPO_Class_Found> hpo_clsses_found = SparqlQuery.query_auto("Potassium [Moles/volume] in Serum or Plasma");
    for (HPO_Class_Found HPO_class : hpo_clsses_found) {
        StringBuilder outContent = new StringBuilder();
        // outContent.append(newline);
        // outContent.append("\t");
        outContent.append(HPO_class.getScore() + "\t");
        outContent.append(HPO_class.getId() + "\t");
        outContent.append(HPO_class.getLabel() + "\t");
        if (HPO_class.getDefinition() != null) {
            outContent.append(HPO_class.getDefinition());
        }
        outContent.append("\n");
    // System.out.println(outContent.toString());
    }
}