Revision 2f628c0c
Added by Andreas Müller over 4 years ago
cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/ErmsImportActivator.java | ||
---|---|---|
59 | 59 |
|
60 | 60 |
// ***************** ALL ************************************************// |
61 | 61 |
|
62 |
static final DO_REFERENCES doReferences = DO_REFERENCES.NONE;
|
|
62 |
static final DO_REFERENCES doReferences = DO_REFERENCES.ALL;
|
|
63 | 63 |
static final boolean doTaxa = true; |
64 | 64 |
static final boolean doRelTaxa = doTaxa; //should always run with doTaxa because dependent on state from doTaxa |
65 | 65 |
static final boolean doSourceUse = true; |
... | ... | |
84 | 84 |
private static DbSchemaValidation hbm2dll = (doReferences == DO_REFERENCES.ALL)? DbSchemaValidation.CREATE:DbSchemaValidation.VALIDATE; |
85 | 85 |
|
86 | 86 |
private void doImport(Source source, ICdmDataSource destination, DbSchemaValidation hbm2dll){ |
87 |
System.out.println("Start import from ("+ ermsSource.getDatabase() + ") to " + cdmDestination.getDatabase() + " ..." );
|
|
87 |
System.out.println("Start import from ("+ ermsSource.getDatabase() + ") to " + destination.getDatabase() + " ..." );
|
|
88 | 88 |
|
89 | 89 |
//make ERMS Source |
90 | 90 |
|
... | ... | |
126 | 126 |
// app = ermsImport.getCdmAppController(); |
127 | 127 |
// app.getFeatureTreeService().saveOrUpdate(tree); |
128 | 128 |
} |
129 |
System.out.println("End import from ("+ source.getDatabase() + ") to "+cdmDestination.getDatabase() + "...");
|
|
129 |
System.out.println("End import from ("+ source.getDatabase() + ") to " + destination.getDatabase() + "...");
|
|
130 | 130 |
} |
131 | 131 |
|
132 | 132 |
public static void main(String[] args) { |
cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/PesiExportActivatorERMS.java | ||
---|---|---|
62 | 62 |
|
63 | 63 |
static boolean doPureNames = false; //ERMS has no pure names |
64 | 64 |
|
65 |
//check - export
|
|
66 |
static final CHECK check = CHECK.EXPORT_WITHOUT_CHECK;
|
|
65 |
//check - export
|
|
66 |
static final CHECK check = CHECK.EXPORT_WITHOUT_CHECK;
|
|
67 | 67 |
|
68 |
//Taxon names can't be mapped to their CDM ids as PESI Taxon table mainly holds taxa and there IDs. We ad nameIdStart to the TaxonName id to get a unique id
|
|
69 |
static final int nameIdStart = 10000000;
|
|
70 |
static final IdType idType = IdType.CDM_ID_WITH_EXCEPTIONS;
|
|
68 |
//Taxon names can't be mapped to their CDM ids as PESI Taxon table mainly holds taxa and there IDs. We ad nameIdStart to the TaxonName id to get a unique id
|
|
69 |
static final int nameIdStart = 10000000;
|
|
70 |
static final IdType idType = IdType.CDM_ID_WITH_EXCEPTIONS;
|
|
71 | 71 |
|
72 |
static final int partitionSize = 1000;
|
|
72 |
static final int partitionSize = 1000;
|
|
73 | 73 |
|
74 | 74 |
public boolean doExport(ICdmDataSource source, Source destination){ |
75 | 75 |
System.out.println("Start export from " + source.getDatabase() + " to PESI ("+ pesiDestination.getDatabase() + ") ..."); |
cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/PesiSources.java | ||
---|---|---|
62 | 62 |
String userName = "WebUser"; |
63 | 63 |
return ImportUtils.makeSource(dbms, strServer, strDB, port, userName, null); |
64 | 64 |
} |
65 |
public static Source faunaEu_old(){ |
|
66 |
// Fauna Europaea |
|
67 |
String dbms = Source.SQL_SERVER_2008; |
|
68 |
String strServer = "BGBM42"; // "192.168.1.36"; |
|
69 |
String strDB = "FaunaEu_1_3"; |
|
70 |
int port = 1433; |
|
71 |
String userName = "WebUser"; |
|
72 |
return ImportUtils.makeSource(dbms, strServer, strDB, port, userName, null); |
|
73 |
} |
|
74 | 65 |
|
75 | 66 |
public static Source PESI_ERMS(){ |
76 | 67 |
// BerlinModel - Pesi-ERMS |
cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsTaxonImport.java | ||
---|---|---|
341 | 341 |
logger.warn("Set name cache: " + displayName + "; id =" + meId); |
342 | 342 |
} |
343 | 343 |
if (!taxonName.getNameCache().equals(displayName)){ |
344 |
logger.warn("Computed name cache differs.\n Computed : " + taxonName.getNameCache()+"\n DisplayName: " +displayName); |
|
344 |
int pos = CdmUtils.diffIndex(taxonName.getNameCache(), displayName); |
|
345 |
logger.warn("Computed name cache differs at "+pos+".\n Computed : " + taxonName.getNameCache()+"\n DisplayName: " +displayName); |
|
345 | 346 |
taxonName.setNameCache(displayName, true); |
346 | 347 |
} |
347 | 348 |
taxonName.getTitleCache(); |
348 | 349 |
return taxonName; |
349 | 350 |
} |
350 | 351 |
|
351 |
|
|
352 | 352 |
@SuppressWarnings("unused") //used by MethodMapper |
353 | 353 |
private static TaxonBase<?> testTitleCache(ResultSet rs, ErmsImportState state) throws SQLException{ |
354 | 354 |
TaxonBase<?> taxon = (TaxonBase<?>)state.getRelatedObject(DbImportStateBase.CURRENT_OBJECT_NAMESPACE, DbImportStateBase.CURRENT_OBJECT_ID); |
cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiExportBase.java | ||
---|---|---|
380 | 380 |
* @param taxonBase |
381 | 381 |
* @return |
382 | 382 |
*/ |
383 |
protected static boolean isPesiTaxon(TaxonBase taxonBase, boolean excludeMisappliedNames) { |
|
383 |
protected static boolean isPesiTaxon(TaxonBase<?> taxonBase, boolean excludeMisappliedNames) {
|
|
384 | 384 |
if (taxonBase == null){ |
385 | 385 |
return false; |
386 | 386 |
} |
... | ... | |
614 | 614 |
// Sources from TaxonName |
615 | 615 |
TaxonName taxonName = CdmBase.deproxy(identifiableEntity, TaxonName.class); |
616 | 616 |
Set<IdentifiableSource> testSources = identifiableEntity.getSources(); |
617 |
sources = filterPesiSources(identifiableEntity.getSources());
|
|
617 |
sources = filterPesiSources(testSources);
|
|
618 | 618 |
|
619 | 619 |
if (sources.size() == 0 && testSources.size()>0){ |
620 | 620 |
IdentifiableSource source = testSources.iterator().next(); |
... | ... | |
627 | 627 |
// name has no PESI source, take sources from TaxonBase |
628 | 628 |
if (sources == null || sources.isEmpty()) { |
629 | 629 |
Set<TaxonBase> taxa = taxonName.getTaxonBases(); |
630 |
for (TaxonBase taxonBase: taxa){ |
|
630 |
for (TaxonBase<?> taxonBase: taxa){
|
|
631 | 631 |
sources.addAll(filterPesiSources(taxonBase.getSources())); |
632 | 632 |
} |
633 | 633 |
} |
cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiSourceExport.java | ||
---|---|---|
94 | 94 |
try{ |
95 | 95 |
logger.info("*** Started Making " + pluralString + " ..."); |
96 | 96 |
|
97 |
PesiExportConfigurator pesiExportConfigurator = state.getConfig(); |
|
98 |
|
|
99 | 97 |
// Get the limit for objects to save within a single transaction. |
100 | 98 |
int limit = modCount;//pesiExportConfigurator.getLimitSave(); |
101 | 99 |
|
... | ... | |
117 | 115 |
TransactionStatus txStatus = null; |
118 | 116 |
List<Reference> list = null; |
119 | 117 |
|
120 |
// logger.error("PHASE 1...");
|
|
118 |
// logger.warn("PHASE 1...");
|
|
121 | 119 |
// Start transaction |
122 | 120 |
txStatus = startTransaction(true); |
123 | 121 |
logger.info("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") ..."); |
cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiTransformer.java | ||
---|---|---|
601 | 601 |
private final Map<Integer, String> areaCacheMap = new HashMap<>(); |
602 | 602 |
private final Map<Integer, String> languageCacheMap = new HashMap<>(); |
603 | 603 |
private static final Map<String,Integer> languageCodeToKeyMap = new HashMap<>(); |
604 |
|
|
604 | 605 |
private final Map<Integer, String> featureCacheMap = new HashMap<>(); |
605 | 606 |
private final Map<Integer, String> nameStatusCacheMap = new HashMap<>(); |
606 | 607 |
private final Map<Integer, String> qualityStatusCacheMap = new HashMap<>(); |
cdm-pesi/src/main/resources/log4j.properties | ||
---|---|---|
57 | 57 |
|
58 | 58 |
### ***HIBERNATE ************ ### |
59 | 59 |
log4j.logger.org.hibernate=warn |
60 |
log4j.logger.org.hibernate.engine.StatefulPersistenceContext.ProxyWarnLog=error |
|
60 |
log4j.logger.org.hibernate.engine.internal.StatefulPersistenceContext=error |
|
61 |
|
|
61 | 62 |
log4j.logger.org.hibernate.orm.deprecation = error |
62 | 63 |
|
63 | 64 |
|
Also available in: Unified diff
cleanup