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

Example 1 with LoincCodeClass

use of org.monarchinitiative.loinc2hpo.util.LoincCodeClass 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 2 with LoincCodeClass

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

the class LoincLongNameParserTest method testString13.

@Test
public void testString13() {
    String name = "pH of Urine by Test strip";
    LoincCodeClass loinc = LoincLongNameParser.parse(name);
    assertEquals("pH", loinc.getLoincParameter());
    assertEquals("Urine", loinc.getLoincTissue());
    assertEquals("", loinc.getLoincType());
    assertEquals("Test strip", loinc.getLoincMethod());
}

Example 3 with LoincCodeClass

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

the class LoincLongNameParserTest method testString15.

@Test
public void testString15() {
    String name = "little i Ag [Presence] on Red Blood Cells from donor";
    LoincCodeClass loinc = LoincLongNameParser.parse(name);
    assertEquals("little i Ag", loinc.getLoincParameter());
    assertEquals("Red Blood Cells", loinc.getLoincTissue());
    assertEquals("Presence", loinc.getLoincType());
    assertEquals("", loinc.getLoincMethod());
}

Example 4 with LoincCodeClass

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

the class LoincLongNameParserTest method testString3.

@Test
public void testString3() {
    String name = "Platelet mean volume [Entitic volume] in Blood by Automated count";
    LoincCodeClass loinc = LoincLongNameParser.parse(name);
    assertEquals("Platelet mean volume", loinc.getLoincParameter());
    assertEquals("Blood", loinc.getLoincTissue());
    assertEquals("Entitic volume", loinc.getLoincType());
    assertEquals("Automated count", loinc.getLoincMethod());
}

Example 5 with LoincCodeClass

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

the class LoincLongNameParserTest method testString14.

@Test
public void testString14() {
    String name = "Appearance of Cerebral spinal fluid";
    LoincCodeClass loinc = LoincLongNameParser.parse(name);
    assertEquals("Appearance", loinc.getLoincParameter());
    assertEquals("Cerebral spinal fluid", loinc.getLoincTissue());
    assertEquals("", loinc.getLoincType());
    assertEquals("", loinc.getLoincMethod());
}