Examples with HpoTerm com.github.phenomics.ontolib.formats.hpo.HpoTerm used on opensource projects

Example 1 with HpoTerm

use of com.github.phenomics.ontolib.formats.hpo.HpoTerm in project loinc2hpo by monarch-initiative.

the class AnnotateTabController method handleAnnotateCodedValue.

@FXML
private void handleAnnotateCodedValue(ActionEvent e) {
    e.consume();
    // do nothing if it is the basic mode
    if (!advancedAnnotationModeSelected)
        return;
    Annotation annotation = null;
    String system = annotationTextFieldLeft.getText().trim().toLowerCase();
    // case sensitive
    String codeId = annotationTextFieldMiddle.getText().trim();
    Code code = null;
    if (system != null && !system.isEmpty() && codeId != null && !codeId.isEmpty()) {
        code = Code.getNewCode().setSystem(system).setCode(codeId);
    }
    String candidateHPO = annotationTextFieldRight.getText();
    HpoTerm hpoterm = model.getTermMap().get(stripEN(candidateHPO));
    if (hpoterm == null)
        logger.error("hpoterm is null");
    if (code != null && hpoterm != null) {
        annotation = new Annotation(code, new HpoTermId4LoincTest(hpoterm, inverseChecker.isSelected()));
    }
    tempAdvancedAnnotations.add(annotation);
    // add annotated value to the advanced table view
    // initadvancedAnnotationTable();
    accordion.setExpandedPane(advancedAnnotationTitledPane);
    inverseChecker.setSelected(false);
    model.setTempAdvancedAnnotation(new HashMap<>());
    model.setInversedAdvancedMode(false);
}

Example 2 with HpoTerm

use of com.github.phenomics.ontolib.formats.hpo.HpoTerm 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 HpoTerm

use of com.github.phenomics.ontolib.formats.hpo.HpoTerm in project loinc2hpo by monarch-initiative.

the class UniversalLoinc2HPOAnnotationTest method testToString.

@Test
public void testToString() throws Exception {
    Map<String, HpoTerm> hpoTermMap;
    String hpo_obo = FhirObservationAnalyzerTest.class.getClassLoader().getResource("obo/hp.obo").getPath();
    HpoOboParser hpoOboParser = new HpoOboParser(new File(hpo_obo));
    HpoOntology hpo = null;
    try {
        hpo = hpoOboParser.parse();
    } catch (IOException e) {
        e.printStackTrace();
    }
    ImmutableMap.Builder<String, HpoTerm> termmap = new ImmutableMap.Builder<>();
    if (hpo != null) {
        List<HpoTerm> res = hpo.getTermMap().values().stream().distinct().collect(Collectors.toList());
        res.forEach(term -> termmap.put(term.getName(), term));
    }
    hpoTermMap = termmap.build();
    Map<LoincId, UniversalLoinc2HPOAnnotation> testmap = new HashMap<>();
    LoincId loincId = new LoincId("15074-8");
    LoincScale loincScale = LoincScale.string2enum("Qn");
    HpoTerm low = hpoTermMap.get("Hypoglycemia");
    HpoTerm normal = hpoTermMap.get("Abnormality of blood glucose concentration");
    HpoTerm hi = hpoTermMap.get("Hyperglycemia");
    Map<String, Code> internalCodes = CodeSystemConvertor.getCodeContainer().getCodeSystemMap().get(Loinc2HPOCodedValue.CODESYSTEM);
    UniversalLoinc2HPOAnnotation glucoseAnnotation = new UniversalLoinc2HPOAnnotation.Builder().setLoincId(loincId).setLoincScale(loincScale).setLowValueHpoTerm(low).setIntermediateValueHpoTerm(normal).setHighValueHpoTerm(hi).setIntermediateNegated(true).build();
    testmap.put(loincId, glucoseAnnotation);
    loincId = new LoincId("600-7");
    loincScale = LoincScale.string2enum("Nom");
    HpoTerm forCode1 = hpoTermMap.get("Recurrent E. coli infections");
    HpoTerm forCode2 = hpoTermMap.get("Recurrent Staphylococcus aureus infections");
    HpoTerm positive = hpoTermMap.get("Recurrent bacterial infections");
    Code code1 = Code.getNewCode().setSystem("http://snomed.info/sct").setCode("112283007");
    Code code2 = Code.getNewCode().setSystem("http://snomed.info/sct").setCode("3092008");
    UniversalLoinc2HPOAnnotation bacterialAnnotation = new UniversalLoinc2HPOAnnotation.Builder().setLoincId(loincId).setLoincScale(loincScale).addAdvancedAnnotation(code1, new HpoTermId4LoincTest(forCode1, false)).addAdvancedAnnotation(code2, new HpoTermId4LoincTest(forCode2, false)).addAdvancedAnnotation(internalCodes.get("P"), new HpoTermId4LoincTest(positive, false)).build();
    testmap.put(loincId, bacterialAnnotation);
    // testmap.entrySet().forEach(System.out::println);
    String path = temporaryFolder.newFile("testoutput.tsv").getPath();
    WriteToFile.writeToFile("", path);
    testmap.forEach((k, v) -> {
        WriteToFile.appendToFile(v.toString(), path);
        WriteToFile.appendToFile("\n", path);
    });
    // WriteToFile.appendToFile(glucoseAnnotation.toString(), path);
    BufferedReader reader = new BufferedReader(new FileReader(path));
    // System.out.println(UniversalLoinc2HPOAnnotation.getHeaderAdvanced());
    // reader.lines().forEach(System.out::println);
    String content = "15074-8\tQn\thttp://jax.org/loinc2hpo\tL\tHP:0001943\tfalse\tnull\tfalse\t0.0\tnull\tnull\tnull\tnull\n" + "15074-8\tQn\thttp://jax.org/loinc2hpo\tN\tHP:0011015\ttrue\tnull\tfalse\t0.0\tnull\tnull\tnull\tnull\n" + "15074-8\tQn\thttp://jax.org/loinc2hpo\tH\tHP:0003074\tfalse\tnull\tfalse\t0.0\tnull\tnull\tnull\tnull\n" + "15074-8\tQn\thttp://jax.org/loinc2hpo\tA\tHP:0011015\tfalse\tnull\tfalse\t0.0\tnull\tnull\tnull\tnull\n" + "600-7\tNom\thttp://snomed.info/sct\t112283007\tHP:0002740\tfalse\tnull\tfalse\t0.0\tnull\tnull\tnull\tnull\n" + "600-7\tNom\thttp://jax.org/loinc2hpo\tP\tHP:0002718\tfalse\tnull\tfalse\t0.0\tnull\tnull\tnull\tnull\n" + "600-7\tNom\thttp://snomed.info/sct\t3092008\tHP:0002726\tfalse\tnull\tfalse\t0.0\tnull\tnull\tnull\tnull";
    assertEquals(9, reader.lines().collect(Collectors.toList()).size());
}

Example 4 with HpoTerm

use of com.github.phenomics.ontolib.formats.hpo.HpoTerm in project loinc2hpo by monarch-initiative.

the class UniversalLoinc2HPOAnnotationTest method testBuilderForBasicAnnotation.

@Test
public void testBuilderForBasicAnnotation() throws Exception {
    Map<String, HpoTerm> hpoTermMap;
    String hpo_obo = FhirObservationAnalyzerTest.class.getClassLoader().getResource("obo/hp.obo").getPath();
    HpoOboParser hpoOboParser = new HpoOboParser(new File(hpo_obo));
    HpoOntology hpo = null;
    try {
        hpo = hpoOboParser.parse();
    } catch (IOException e) {
        e.printStackTrace();
    }
    ImmutableMap.Builder<String, HpoTerm> termmap = new ImmutableMap.Builder<>();
    if (hpo != null) {
        List<HpoTerm> res = hpo.getTermMap().values().stream().distinct().collect(Collectors.toList());
        res.forEach(term -> termmap.put(term.getName(), term));
    }
    hpoTermMap = termmap.build();
    UniversalLoinc2HPOAnnotation.Builder loinc2HpoAnnotationBuilder = new UniversalLoinc2HPOAnnotation.Builder();
    LoincId loincId = new LoincId("15074-8");
    LoincScale loincScale = LoincScale.string2enum("Qn");
    HpoTerm low = hpoTermMap.get("Hypoglycemia");
    HpoTerm normal = hpoTermMap.get("Abnormality of blood glucose concentration");
    HpoTerm hi = hpoTermMap.get("Hyperglycemia");
    loinc2HpoAnnotationBuilder.setLoincId(loincId).setLoincScale(loincScale).setLowValueHpoTerm(low).setIntermediateValueHpoTerm(normal).setIntermediateNegated(true).setHighValueHpoTerm(hi);
    UniversalLoinc2HPOAnnotation annotation15074 = loinc2HpoAnnotationBuilder.build();
    assertEquals("15074-8", annotation15074.getLoincId().toString());
    assertEquals("Qn", annotation15074.getLoincScale().toString());
    Map<String, Code> internalCodes = CodeSystemConvertor.getCodeContainer().getCodeSystemMap().get(Loinc2HPOCodedValue.CODESYSTEM);
    Code code4low = internalCodes.get("L");
    assertEquals(low.getId().getIdWithPrefix(), annotation15074.getCandidateHpoTerms().get(code4low).getHpoTerm().getId().getIdWithPrefix());
    assertEquals(false, annotation15074.getCandidateHpoTerms().get(code4low).isNegated());
    Code code4high = internalCodes.get("H");
    assertEquals(hi.getId().getIdWithPrefix(), annotation15074.getCandidateHpoTerms().get(code4high).getHpoTerm().getId().getIdWithPrefix());
    assertEquals(false, annotation15074.getCandidateHpoTerms().get(code4high).isNegated());
    Code code4normal = internalCodes.get("N");
    assertEquals(normal.getId().getIdWithPrefix(), annotation15074.getCandidateHpoTerms().get(code4normal).getHpoTerm().getId().getIdWithPrefix());
    assertEquals(true, annotation15074.getCandidateHpoTerms().get(code4normal).isNegated());
    Code code4Pos = internalCodes.get("P");
    assertEquals(hi.getId().getIdWithPrefix(), annotation15074.getCandidateHpoTerms().get(code4Pos).getHpoTerm().getId().getIdWithPrefix());
    assertEquals(false, annotation15074.getCandidateHpoTerms().get(code4Pos).isNegated());
    Code code4NP = internalCodes.get("NP");
    assertEquals(normal.getId().getIdWithPrefix(), annotation15074.getCandidateHpoTerms().get(code4NP).getHpoTerm().getId().getIdWithPrefix());
    assertEquals(true, annotation15074.getCandidateHpoTerms().get(code4NP).isNegated());
}

Example 5 with HpoTerm

use of com.github.phenomics.ontolib.formats.hpo.HpoTerm in project loinc2hpo by monarch-initiative.

the class WriteToFile method fromTSV.

/**
 * A method to deserialize annotation map from a TSV file.
 * @param path filepath to the TSV
 * @param hpoTermMap a HPO map from TermId to HpoTerm. Note: the key is TermId, instead of TermName
 * @return an annotation map
 * @throws FileNotFoundException
 */
public static Map<LoincId, UniversalLoinc2HPOAnnotation> fromTSV(String path, Map<TermId, HpoTerm> hpoTermMap) throws FileNotFoundException {
    Map<LoincId, UniversalLoinc2HPOAnnotation> deserializedMap = new LinkedHashMap<>();
    Map<LoincId, UniversalLoinc2HPOAnnotation.Builder> builderMap = new HashMap<>();
    Map<String, Code> internalCode = CodeSystemConvertor.getCodeContainer().getCodeSystemMap().get(Loinc2HPOCodedValue.CODESYSTEM);
    BufferedReader reader = new BufferedReader(new FileReader(path));
    reader.lines().forEach(serialized -> {
        String[] elements = serialized.split("\\t");
        if (elements.length == 13 && !serialized.startsWith("loincId")) {
            try {
                LoincId loincId = new LoincId(elements[0]);
                LoincScale loincScale = LoincScale.string2enum(elements[1]);
                String codeSystem = elements[2];
                String codeId = elements[3];
                TermPrefix prefix = new ImmutableTermPrefix(elements[4].substring(0, 2));
                String id = elements[4].substring(3);
                HpoTerm hpoTerm = hpoTermMap.get(new ImmutableTermId(prefix, id));
                boolean inverse = Boolean.parseBoolean(elements[5]);
                String note = elements[6].equals(MISSINGVALUE) ? null : elements[6];
                boolean flag = Boolean.parseBoolean(elements[7]);
                double version = Double.parseDouble(elements[8]);
                LocalDateTime createdOn = elements[9].equals(MISSINGVALUE) ? null : LocalDateTime.parse(elements[9]);
                String createdBy = elements[10].equals(MISSINGVALUE) ? null : elements[10];
                LocalDateTime lastEditedOn = elements[11].equals(MISSINGVALUE) ? null : LocalDateTime.parse(elements[11]);
                String lastEditedBy = elements[12].equals(MISSINGVALUE) ? null : elements[12];
                if (!builderMap.containsKey(loincId)) {
                    UniversalLoinc2HPOAnnotation.Builder builder = new UniversalLoinc2HPOAnnotation.Builder().setLoincId(loincId).setLoincScale(loincScale).setNote(note).setFlag(flag).setVersion(version).setCreatedOn(createdOn).setCreatedBy(createdBy).setLastEditedOn(lastEditedOn).setLastEditedBy(lastEditedBy);
                    builderMap.put(loincId, builder);
                }
                Code code = Code.getNewCode().setSystem(codeSystem).setCode(codeId);
                HpoTermId4LoincTest hpoTermId4LoincTest = new HpoTermId4LoincTest(hpoTerm, inverse);
                if (code.equals(internalCode.get("L"))) {
                    builderMap.get(loincId).setLowValueHpoTerm(hpoTermId4LoincTest.getHpoTerm());
                }
                if (code.equals(internalCode.get("N"))) {
                    builderMap.get(loincId).setIntermediateValueHpoTerm(hpoTermId4LoincTest.getHpoTerm());
                    builderMap.get(loincId).setIntermediateNegated(hpoTermId4LoincTest.isNegated());
                }
                if (code.equals(internalCode.get("H"))) {
                    builderMap.get(loincId).setHighValueHpoTerm(hpoTermId4LoincTest.getHpoTerm());
                }
                if (code.equals(internalCode.get("A")) || code.equals(internalCode.get("P")) || code.equals(internalCode.get("NP"))) {
                    // currently, we neglect those codes
                    // it will be wrong to do so if the user has manually changed what map to them
                    logger.info("!!!!!!!!!!!annotation neglected. MAY BE WRONG!!!!!!!!!!!!!!!");
                } else {
                    builderMap.get(loincId).addAdvancedAnnotation(code, hpoTermId4LoincTest);
                }
            } catch (MalformedLoincCodeException e) {
                logger.error("Malformed loinc code line: " + serialized);
            }
        } else {
            if (elements.length != 13) {
                logger.error(String.format("line does not have 13 elements, but has %d elements. Line: %s", elements.length, serialized));
            } else {
                logger.info("line is header: " + serialized);
            }
        }
    });
    try {
        reader.close();
    } catch (IOException e) {
        e.printStackTrace();
    }
    builderMap.entrySet().forEach(b -> deserializedMap.put(b.getKey(), b.getValue().build()));
    return deserializedMap;
}