Examples with PropertyEnricherException org.eol.globi.service.PropertyEnricherException used on opensource projects

Example 6 with PropertyEnricherException

use of org.eol.globi.service.PropertyEnricherException in project eol-globi-data by jhpoelen.

the class EOLService method getPageId.

protected Long getPageId(String taxonName, boolean shouldFollowAlternate) throws PropertyEnricherException {
    try {
        URI uri = createSearchURI(taxonName);
        String response = getResponse(uri);
        Long smallestPageId = null;
        if (response != null) {
            // pick first of non empty result, assuming that exact match parameter is yielding a valid result
            if (!response.contains("totalResults>0<")) {
                smallestPageId = findSmallestPageId(response);
            } else if (shouldFollowAlternate) {
                String[] alternates = response.split("<link rel=\"alternate\" href=\"http://eol.org/api/search/1.0/");
                if (alternates.length > 1) {
                    String[] urlSplit = alternates[1].split("\"");
                    if (urlSplit.length > 1) {
                        String alternateTaxonName = urlSplit[0];
                        try {
                            String decodedName = URLDecoder.decode(alternateTaxonName, "UTF-8");
                            decodedName = decodedName.replace("/", "");
                            if (!decodedName.equals(taxonName)) {
                                smallestPageId = getPageId(decodedName, false);
                            }
                        } catch (UnsupportedEncodingException e) {
                            throw new PropertyEnricherException("failed to decode [" + alternateTaxonName + "]", e);
                        }
                    }
                }
            }
        }
        return smallestPageId;
    } catch (URISyntaxException e) {
        throw new PropertyEnricherException("failed to fetch pageid for [" + taxonName + "]", e);
    }
}

Example 7 with PropertyEnricherException

use of org.eol.globi.service.PropertyEnricherException in project eol-globi-data by jhpoelen.

the class ResolvingTaxonIndex method resolveAndIndex.

private TaxonNode resolveAndIndex(Taxon origTaxon, Taxon taxon) throws NodeFactoryException {
    TaxonNode indexedTaxon = findTaxon(taxon);
    while (indexedTaxon == null) {
        try {
            taxon = TaxonUtil.enrich(enricher, taxon);
        } catch (PropertyEnricherException e) {
            throw new NodeFactoryException("failed to enrich taxon with name [" + taxon.getName() + "]", e);
        }
        indexedTaxon = findTaxon(taxon);
        if (indexedTaxon == null) {
            if (TaxonUtil.isResolved(taxon)) {
                indexedTaxon = createAndIndexTaxon(origTaxon, taxon);
            } else {
                String truncatedName = NodeUtil.truncateTaxonName(taxon.getName());
                if (StringUtils.equals(truncatedName, taxon.getName())) {
                    if (isIndexResolvedOnly()) {
                        break;
                    } else {
                        indexedTaxon = addNoMatchTaxon(origTaxon);
                    }
                } else {
                    taxon = new TaxonImpl();
                    taxon.setName(truncatedName);
                    indexedTaxon = findTaxonByName(taxon.getName());
                }
            }
        }
    }
    return indexedTaxon;
}

Example 8 with PropertyEnricherException

use of org.eol.globi.service.PropertyEnricherException in project eol-globi-data by jhpoelen.

the class EOLService method getResponse.

private String getResponse(URI uri) throws PropertyEnricherException {
    HttpGet get = new HttpGet(uri);
    BasicResponseHandler responseHandler = new BasicResponseHandler();
    String response = null;
    try {
        response = HttpUtil.executeWithTimer(get, responseHandler);
    } catch (HttpResponseException e) {
        if (e.getStatusCode() != 406 && e.getStatusCode() != 404) {
            throw new PropertyEnricherException("failed to lookup [" + uri.toString() + "]: http status [" + e.getStatusCode() + "]   ", e);
        }
    } catch (ClientProtocolException e) {
        throw new PropertyEnricherException("failed to lookup [" + uri.toString() + "]", e);
    } catch (IOException e) {
        throw new PropertyEnricherException("failed to lookup [" + uri.toString() + "]", e);
    }
    return response;
}

Example 9 with PropertyEnricherException

use of org.eol.globi.service.PropertyEnricherException in project eol-globi-data by jhpoelen.

the class EOLService method addTaxonInfo.

protected void addTaxonInfo(Long pageId, Map<String, String> properties) throws PropertyEnricherException {
    try {
        URI uri = new URI("http", null, "eol.org", 80, "/api/pages/1.0/" + pageId + ".json", "images=1&videos=0&sounds=0&maps=0&text=0&iucn=false&subjects=overview&licenses=all&details=false&common_names=true&synonyms=false&references=false&taxonomy=true&format=json", null);
        String response = getResponse(uri);
        if (response != null) {
            addCanonicalNamesAndRanks(properties, response);
            StringBuilder commonNames = new StringBuilder();
            addCommonNames(commonNames, response);
            if (commonNames.length() > 0) {
                properties.put(PropertyAndValueDictionary.COMMON_NAMES, commonNames.toString());
            }
        }
    } catch (URISyntaxException e) {
        throw new PropertyEnricherException("failed to create uri", e);
    } catch (JsonProcessingException e) {
        throw new PropertyEnricherException("failed to parse response", e);
    } catch (IOException e) {
        throw new PropertyEnricherException("failed to get response", e);
    }
}

Example 10 with PropertyEnricherException

use of org.eol.globi.service.PropertyEnricherException in project eol-globi-data by jhpoelen.

the class EOLService method getPageIdFromProvider.

private Long getPageIdFromProvider(int eolProviderId, String providerTaxonId) throws PropertyEnricherException {
    Long eolPageId = null;
    try {
        URI uri1 = new URI("http://eol.org/api/search_by_provider/1.0/" + providerTaxonId + ".json?hierarchy_id=" + eolProviderId);
        String response1 = getResponse(uri1);
        if (response1 == null) {
            throw new PropertyEnricherException("failed to retrieve response for [" + uri1 + "]");
        }
        JsonNode jsonNode = new ObjectMapper().readTree(response1);
        if (jsonNode.isArray() && jsonNode.size() > 0) {
            JsonNode jsonNode1 = jsonNode.get(0);
            if (jsonNode1.has("eol_page_id")) {
                eolPageId = Long.parseLong(jsonNode1.get("eol_page_id").asText());
            }
        }
    } catch (JsonProcessingException ex) {
        throw new PropertyEnricherException("failed to create uri", ex);
    } catch (URISyntaxException ex) {
        throw new PropertyEnricherException("failed to create uri", ex);
    } catch (IOException e) {
        throw new PropertyEnricherException("failed to get response", e);
    } catch (NumberFormatException e) {
        throw new PropertyEnricherException("invalid page id", e);
    }
    return eolPageId;
}