Examples with StringUtils.trim org.apache.commons.lang3.StringUtils.trim used on opensource projects

Example 6 with StringUtils.trim

use of org.apache.commons.lang3.StringUtils.trim in project eol-globi-data by jhpoelen.

the class StudyImporterForHurlbert method importInteraction.

protected void importInteraction(Set<String> regions, Set<String> locales, Set<String> habitats, Record record, Study study, String preyTaxonName, String predatorName) throws StudyImporterException {
    try {
        Taxon predatorTaxon = new TaxonImpl(predatorName);
        Specimen predatorSpecimen = nodeFactory.createSpecimen(study, predatorTaxon);
        setBasisOfRecordAsLiterature(predatorSpecimen);
        Taxon preyTaxon = new TaxonImpl(preyTaxonName);
        String preyNameId = StringUtils.trim(columnValueOrNull(record, "Prey_Name_ITIS_ID"));
        if (NumberUtils.isDigits(preyNameId)) {
            preyTaxon.setExternalId(TaxonomyProvider.ITIS.getIdPrefix() + preyNameId);
        }
        Specimen preySpecimen = nodeFactory.createSpecimen(study, preyTaxon);
        setBasisOfRecordAsLiterature(preySpecimen);
        String preyStage = StringUtils.trim(columnValueOrNull(record, "Prey_Stage"));
        if (StringUtils.isNotBlank(preyStage)) {
            Term lifeStage = nodeFactory.getOrCreateLifeStage("HULBERT:" + StringUtils.replace(preyStage, " ", "_"), preyStage);
            preySpecimen.setLifeStage(lifeStage);
        }
        String preyPart = StringUtils.trim(columnValueOrNull(record, "Prey_Part"));
        if (StringUtils.isNotBlank(preyPart)) {
            Term term = nodeFactory.getOrCreateBodyPart("HULBERT:" + StringUtils.replace(preyPart, " ", "_"), preyPart);
            preySpecimen.setBodyPart(term);
        }
        Date date = addCollectionDate(record, study);
        nodeFactory.setUnixEpochProperty(predatorSpecimen, date);
        nodeFactory.setUnixEpochProperty(preySpecimen, date);
        LocationImpl location = new LocationImpl(null, null, null, null);
        String longitude = columnValueOrNull(record, "Longitude_dd");
        String latitude = columnValueOrNull(record, "Latitude_dd");
        if (NumberUtils.isNumber(latitude) && NumberUtils.isNumber(longitude)) {
            try {
                LatLng latLng = LocationUtil.parseLatLng(latitude, longitude);
                String altitude = columnValueOrNull(record, "Altitude_mean_m");
                Double altitudeD = NumberUtils.isNumber(altitude) ? Double.parseDouble(altitude) : null;
                location = new LocationImpl(latLng.getLat(), latLng.getLng(), altitudeD, null);
            } catch (InvalidLocationException e) {
                getLogger().warn(study, "found invalid (lat,lng) pair: (" + latitude + "," + longitude + ")");
            }
        }
        String locationRegion = columnValueOrNull(record, "Location_Region");
        String locationSpecific = columnValueOrNull(record, "Location_Specific");
        location.setLocality(StringUtils.join(Arrays.asList(locationRegion, locationSpecific), ":"));
        Location locationNode = nodeFactory.getOrCreateLocation(location);
        String habitat_type = columnValueOrNull(record, "Habitat_type");
        List<Term> habitatList = Arrays.stream(StringUtils.split(StringUtils.defaultIfBlank(habitat_type, ""), ";")).map(StringUtils::trim).map(habitat -> new TermImpl(idForHabitat(habitat), habitat)).collect(Collectors.toList());
        nodeFactory.addEnvironmentToLocation(locationNode, habitatList);
        preySpecimen.caughtIn(locationNode);
        predatorSpecimen.caughtIn(locationNode);
        predatorSpecimen.ate(preySpecimen);
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("failed to create interaction between [" + predatorName + "] and [" + preyTaxonName + "]", e);
    }
}

Example 7 with StringUtils.trim

use of org.apache.commons.lang3.StringUtils.trim in project AntennaPod by AntennaPod.

the class FeedInfoActivity method onCreate.

@Override
protected void onCreate(Bundle savedInstanceState) {
    setTheme(UserPreferences.getTheme());
    super.onCreate(savedInstanceState);
    setContentView(R.layout.feedinfo);
    getSupportActionBar().setDisplayHomeAsUpEnabled(true);
    long feedId = getIntent().getLongExtra(EXTRA_FEED_ID, -1);
    imgvCover = (ImageView) findViewById(R.id.imgvCover);
    txtvTitle = (TextView) findViewById(R.id.txtvTitle);
    txtvDescription = (TextView) findViewById(R.id.txtvDescription);
    lblLanguage = (TextView) findViewById(R.id.lblLanguage);
    txtvLanguage = (TextView) findViewById(R.id.txtvLanguage);
    lblAuthor = (TextView) findViewById(R.id.lblAuthor);
    txtvAuthor = (TextView) findViewById(R.id.txtvAuthor);
    txtvUrl = (TextView) findViewById(R.id.txtvUrl);
    cbxAutoDownload = (CheckBox) findViewById(R.id.cbxAutoDownload);
    cbxKeepUpdated = (CheckBox) findViewById(R.id.cbxKeepUpdated);
    spnAutoDelete = (Spinner) findViewById(R.id.spnAutoDelete);
    etxtUsername = (EditText) findViewById(R.id.etxtUsername);
    etxtPassword = (EditText) findViewById(R.id.etxtPassword);
    etxtFilterText = (EditText) findViewById(R.id.etxtEpisodeFilterText);
    rdoFilterInclude = (RadioButton) findViewById(R.id.radio_filter_include);
    rdoFilterInclude.setOnClickListener(v -> {
        filterInclude = true;
        filterTextChanged = true;
    });
    rdoFilterExclude = (RadioButton) findViewById(R.id.radio_filter_exclude);
    rdoFilterExclude.setOnClickListener(v -> {
        filterInclude = false;
        filterTextChanged = true;
    });
    txtvUrl.setOnClickListener(copyUrlToClipboard);
    subscription = Observable.fromCallable(() -> DBReader.getFeed(feedId)).subscribeOn(Schedulers.newThread()).observeOn(AndroidSchedulers.mainThread()).subscribe(result -> {
        if (result == null) {
            Log.e(TAG, "Activity was started with invalid arguments");
            finish();
        }
        feed = result;
        Log.d(TAG, "Language is " + feed.getLanguage());
        Log.d(TAG, "Author is " + feed.getAuthor());
        Log.d(TAG, "URL is " + feed.getDownload_url());
        FeedPreferences prefs = feed.getPreferences();
        Glide.with(FeedInfoActivity.this).load(feed.getImageLocation()).placeholder(R.color.light_gray).error(R.color.light_gray).diskCacheStrategy(ApGlideSettings.AP_DISK_CACHE_STRATEGY).fitCenter().dontAnimate().into(imgvCover);
        txtvTitle.setText(feed.getTitle());
        String description = feed.getDescription();
        if (description != null) {
            if (Feed.TYPE_ATOM1.equals(feed.getType())) {
                HtmlToPlainText formatter = new HtmlToPlainText();
                Document feedDescription = Jsoup.parse(feed.getDescription());
                description = StringUtils.trim(formatter.getPlainText(feedDescription));
            }
        } else {
            description = "";
        }
        txtvDescription.setText(description);
        if (!TextUtils.isEmpty(feed.getAuthor())) {
            txtvAuthor.setText(feed.getAuthor());
        } else {
            lblAuthor.setVisibility(View.GONE);
            txtvAuthor.setVisibility(View.GONE);
        }
        if (!TextUtils.isEmpty(feed.getLanguage())) {
            txtvLanguage.setText(LangUtils.getLanguageString(feed.getLanguage()));
        } else {
            lblLanguage.setVisibility(View.GONE);
            txtvLanguage.setVisibility(View.GONE);
        }
        txtvUrl.setText(feed.getDownload_url() + " {fa-paperclip}");
        Iconify.addIcons(txtvUrl);
        cbxAutoDownload.setEnabled(UserPreferences.isEnableAutodownload());
        cbxAutoDownload.setChecked(prefs.getAutoDownload());
        cbxAutoDownload.setOnCheckedChangeListener((compoundButton, checked) -> {
            feed.getPreferences().setAutoDownload(checked);
            feed.savePreferences(FeedInfoActivity.this);
            updateAutoDownloadSettings();
            ApplyToEpisodesDialog dialog = new ApplyToEpisodesDialog(FeedInfoActivity.this, feed, checked);
            dialog.createNewDialog().show();
        });
        cbxKeepUpdated.setChecked(prefs.getKeepUpdated());
        cbxKeepUpdated.setOnCheckedChangeListener((compoundButton, checked) -> {
            feed.getPreferences().setKeepUpdated(checked);
            feed.savePreferences(FeedInfoActivity.this);
        });
        spnAutoDelete.setOnItemSelectedListener(new OnItemSelectedListener() {

            @Override
            public void onItemSelected(AdapterView<?> parent, View view, int pos, long id) {
                FeedPreferences.AutoDeleteAction auto_delete_action;
                switch(parent.getSelectedItemPosition()) {
                    case 0:
                        auto_delete_action = FeedPreferences.AutoDeleteAction.GLOBAL;
                        break;
                    case 1:
                        auto_delete_action = FeedPreferences.AutoDeleteAction.YES;
                        break;
                    case 2:
                        auto_delete_action = FeedPreferences.AutoDeleteAction.NO;
                        break;
                    default:
                        return;
                }
                feed.getPreferences().setAutoDeleteAction(auto_delete_action);
                autoDeleteChanged = true;
            }

            @Override
            public void onNothingSelected(AdapterView<?> parent) {
            }
        });
        spnAutoDelete.setSelection(prefs.getAutoDeleteAction().ordinal());
        etxtUsername.setText(prefs.getUsername());
        etxtPassword.setText(prefs.getPassword());
        etxtUsername.addTextChangedListener(authTextWatcher);
        etxtPassword.addTextChangedListener(authTextWatcher);
        FeedFilter filter = prefs.getFilter();
        if (filter.includeOnly()) {
            etxtFilterText.setText(filter.getIncludeFilter());
            rdoFilterInclude.setChecked(true);
            rdoFilterExclude.setChecked(false);
            filterInclude = true;
        } else if (filter.excludeOnly()) {
            etxtFilterText.setText(filter.getExcludeFilter());
            rdoFilterInclude.setChecked(false);
            rdoFilterExclude.setChecked(true);
            filterInclude = false;
        } else {
            Log.d(TAG, "No filter set");
            rdoFilterInclude.setChecked(false);
            rdoFilterExclude.setChecked(false);
            etxtFilterText.setText("");
        }
        etxtFilterText.addTextChangedListener(filterTextWatcher);
        supportInvalidateOptionsMenu();
        updateAutoDownloadSettings();
    }, error -> {
        Log.d(TAG, Log.getStackTraceString(error));
        finish();
    });
}

Example 8 with StringUtils.trim

use of org.apache.commons.lang3.StringUtils.trim in project gatk-protected by broadinstitute.

the class PoNTestUtils method readTsvIntoMatrix.

/**
     * Reads a very basic tsv (numbers separated by tabs) into a RealMatrix.
     * <p>Very little error checking happens in this method</p>
     *
     * @param inputFile readable file.  Not {@code null}
     * @return never {@code null}
     */
public static RealMatrix readTsvIntoMatrix(final File inputFile) {
    IOUtils.canReadFile(inputFile);
    final List<double[]> allData = new ArrayList<>();
    int ctr = 0;
    try {
        final CSVReader reader = new CSVReader(new FileReader(inputFile), '\t', CSVWriter.NO_QUOTE_CHARACTER);
        String[] nextLine;
        while ((nextLine = reader.readNext()) != null) {
            ctr++;
            allData.add(Arrays.stream(nextLine).filter(s -> StringUtils.trim(s).length() > 0).map(s -> Double.parseDouble(StringUtils.trim(s))).mapToDouble(d -> d).toArray());
        }
    } catch (final IOException ioe) {
        Assert.fail("Could not open test file: " + inputFile, ioe);
    }
    final RealMatrix result = new Array2DRowRealMatrix(allData.size(), allData.get(0).length);
    for (int i = 0; i < result.getRowDimension(); i++) {
        result.setRow(i, allData.get(i));
    }
    return result;
}