Revision 55b8caff
Added by Andreas Müller over 6 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/edaphobase/EdaphobaseTaxonImport.java | ||
|---|---|---|
| 72 | 72 |
|
| 73 | 73 |
@Override |
| 74 | 74 |
protected String getRecordQuery(EdaphobaseImportConfigurator config) {
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| 75 |
String result = " SELECT DISTINCT t.*, r.value as rankStr, pr.value as parentRankStr, ppr.value as grandParentRankStr, "
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String result = " SELECT DISTINCT t.*, r.value_summary as rankStr, pr.value_summary as parentRankStr, ppr.value_summary as grandParentRankStr, "
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| 76 | 76 |
+ " pt.name as parentName, ppt.name as grandParentName " |
| 77 | 77 |
+ " FROM tax_taxon t " |
| 78 | 78 |
+ " LEFT JOIN tax_taxon pt ON t.parent_taxon_fk = pt.taxon_id " |
| 79 | 79 |
+ " LEFT JOIN tax_taxon ppt ON pt.parent_taxon_fk = ppt.taxon_id" |
| 80 |
+ " LEFT OUTER JOIN tax_rank_en r ON r.element_id = t.tax_rank_fk "
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+ " LEFT OUTER JOIN tax_rank_en pr ON pr.element_id = pt.tax_rank_fk "
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+ " LEFT OUTER JOIN tax_rank_en ppr ON ppr.element_id = ppt.tax_rank_fk "
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+ " LEFT OUTER JOIN selective_list.element r ON r.element_id = t.tax_rank_fk "
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+ " LEFT OUTER JOIN selective_list.element pr ON pr.element_id = pt.tax_rank_fk "
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+ " LEFT OUTER JOIN selective_list.element ppr ON ppr.element_id = ppt.tax_rank_fk "
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| 83 | 83 |
+ " WHERE t.taxon_id IN (@IDSET)"; |
| 84 | 84 |
result = result.replace("@IDSET", IPartitionedIO.ID_LIST_TOKEN);
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| 85 | 85 |
return result; |
| ... | ... | |
| 143 | 143 |
|
| 144 | 144 |
TaxonBase<?> taxonBase; |
| 145 | 145 |
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rankStr= extractEnglish(rankStr); |
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parentRankStr= extractEnglish(parentRankStr); |
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grandParentRankStr= extractEnglish(grandParentRankStr); |
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//Name etc. |
| 147 | 151 |
Rank rank = makeRank(state, rankStr); |
| 148 | 152 |
checkRankMarker(state, rank); |
| ... | ... | |
| 205 | 209 |
} |
| 206 | 210 |
|
| 207 | 211 |
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/** |
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* @param rankStr |
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* @return |
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*/ |
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private String extractEnglish(String rankStr) {
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if (rankStr == null){
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return null; |
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} |
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String[] splits = rankStr.split(", ");
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if (splits.length != 3){
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String message = "Wrong rank format: "+ rankStr; |
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logger.error(message); |
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return null; |
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} |
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return splits[1].trim(); |
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} |
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static Map<Integer,UUID> idMap = new HashMap<>(); |
| 209 | 231 |
static{
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idMap.put(86594, UUID.fromString("715c2370-45a4-450c-99f7-e196758979ca")); //Aporrectodea caliginosa
|
| ... | ... | |
| 337 | 359 |
if (StringUtils.isBlank(name.getGenusOrUninomial())){
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| 338 | 360 |
name.setGenusOrUninomial(nameStr); |
| 339 | 361 |
} |
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}else if (rank.isInfraGeneric()){
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}else if (rank.isInfraGenericButNotSpeciesGroup()){
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| 341 | 363 |
if (StringUtils.isBlank(name.getInfraGenericEpithet())){
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| 342 | 364 |
name.setInfraGenericEpithet(nameStr); |
| 343 | 365 |
} |
Also available in: Unified diff
ref #5499 latest Edaphobase import changes