Revision f12ac52e
Added by Katja Luther about 7 years ago
| eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/io/wizard/ExcelNormalExplicitTaxaImportWizard.java | ||
|---|---|---|
| 13 | 13 |
import java.io.FileInputStream; |
| 14 | 14 |
import java.io.FileNotFoundException; |
| 15 | 15 |
import java.net.URI; |
| 16 |
import org.apache.log4j.Logger; |
|
| 17 | 16 |
|
| 17 |
import org.apache.log4j.Logger; |
|
| 18 | 18 |
import org.eclipse.core.runtime.jobs.Job; |
| 19 | 19 |
import org.eclipse.jface.viewers.IStructuredSelection; |
| 20 | 20 |
import org.eclipse.jface.viewers.TreeSelection; |
| ... | ... | |
| 24 | 24 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator.SOURCE_TYPE; |
| 25 | 25 |
import eu.etaxonomy.cdm.io.excel.taxa.NormalExplicitImportConfigurator; |
| 26 | 26 |
import eu.etaxonomy.cdm.model.taxon.TaxonNode; |
| 27 |
|
|
| 28 | 27 |
import eu.etaxonomy.taxeditor.store.CdmStore; |
| 29 | 28 |
|
| 30 | 29 |
|
| ... | ... | |
| 68 | 67 |
} catch (FileNotFoundException e) {
|
| 69 | 68 |
logger.error("Error while reading file" + source.toString());
|
| 70 | 69 |
} |
| 71 |
|
|
| 72 |
Job job = CdmStore.getImportManager().createIOServiceJob(configurator,file , SOURCE_TYPE.INPUTSTREAM);
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|
| 70 |
|
|
| 71 |
Job job = CdmStore.getImportManager().createIOServiceJob(configurator,fis , SOURCE_TYPE.INPUTSTREAM);
|
|
| 73 | 72 |
CdmStore.getImportManager().run(job); |
| 74 |
|
|
| 73 |
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|
| 75 | 74 |
return true; |
| 76 | 75 |
} |
| 77 | 76 |
|
| eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/dataimport/SaveImportedSpecimenAction.java | ||
|---|---|---|
| 9 | 9 |
import java.util.HashSet; |
| 10 | 10 |
import java.util.List; |
| 11 | 11 |
import java.util.Set; |
| 12 |
import java.util.UUID; |
|
| 13 | 12 |
|
| 14 | 13 |
import org.apache.http.client.ClientProtocolException; |
| 15 | 14 |
import org.apache.log4j.Logger; |
| 16 | 15 |
import org.eclipse.core.runtime.jobs.Job; |
| 17 | 16 |
import org.eclipse.jface.action.Action; |
| 18 |
import org.eclipse.jface.text.source.Annotation; |
|
| 19 |
import org.eclipse.swt.widgets.Event; |
|
| 20 | 17 |
import org.eclipse.swt.widgets.Table; |
| 21 | 18 |
import org.eclipse.swt.widgets.TableItem; |
| 22 | 19 |
import org.eclipse.ui.IWorkbenchPart; |
| ... | ... | |
| 24 | 21 |
import org.eclipse.ui.PlatformUI; |
| 25 | 22 |
|
| 26 | 23 |
import eu.etaxonomy.cdm.api.conversation.ConversationHolder; |
| 27 |
import eu.etaxonomy.cdm.api.service.IClassificationService; |
|
| 28 |
import eu.etaxonomy.cdm.api.service.IOccurrenceService; |
|
| 29 | 24 |
import eu.etaxonomy.cdm.api.service.ITermService; |
| 30 | 25 |
import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery; |
| 31 | 26 |
import eu.etaxonomy.cdm.ext.occurrence.gbif.DataSetResponse; |
| ... | ... | |
| 33 | 28 |
import eu.etaxonomy.cdm.ext.occurrence.gbif.GbifQueryServiceWrapper; |
| 34 | 29 |
import eu.etaxonomy.cdm.ext.occurrence.gbif.GbifResponse; |
| 35 | 30 |
import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportConfigurator; |
| 36 |
import eu.etaxonomy.cdm.io.specimen.gbif.in.*;
|
|
| 31 |
import eu.etaxonomy.cdm.io.specimen.gbif.in.GbifImportConfigurator;
|
|
| 37 | 32 |
import eu.etaxonomy.cdm.model.common.DefinedTermBase; |
| 38 |
import eu.etaxonomy.cdm.model.common.ICdmBase; |
|
| 39 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
|
| 40 |
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase; |
|
| 41 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
|
| 42 | 33 |
import eu.etaxonomy.taxeditor.store.CdmStore; |
| 43 |
import eu.etaxonomy.taxeditor.ui.dialog.selection.SelectionDialogFactory; |
|
| 44 | 34 |
|
| 45 | 35 |
public class SaveImportedSpecimenAction extends Action {
|
| 46 | 36 |
|
| 47 | 37 |
private final Logger logger = Logger.getLogger(SaveImportedSpecimenAction.class); |
| 48 |
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| 38 |
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|
| 49 | 39 |
private Comparator<GbifResponse> comparator; |
| 50 | 40 |
|
| 51 | 41 |
/* (non-Javadoc) |
| ... | ... | |
| 63 | 53 |
Set<String[]> unitIdsGbif = new HashSet<String[]>(); |
| 64 | 54 |
Set<String[]> unitIdsBioCase = new HashSet<String[]>(); |
| 65 | 55 |
List<GbifResponse> biocaseResponses = new ArrayList<GbifResponse>(); |
| 66 |
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|
| 56 |
|
|
| 67 | 57 |
for(TableItem item:table.getItems()){
|
| 68 | 58 |
if(item.getChecked()){
|
| 69 | 59 |
//Save Specimen |
| ... | ... | |
| 77 | 67 |
for (GbifResponse response:checkedResults){
|
| 78 | 68 |
if (response != null){
|
| 79 | 69 |
tripleId = response.getTripleID(); |
| 80 |
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|
| 70 |
|
|
| 81 | 71 |
if (response.getDataSetProtocol().equals(GbifDataSetProtocol.BIOCASE)){
|
| 82 | 72 |
biocaseResponses.add(response); |
| 83 |
|
|
| 73 |
|
|
| 84 | 74 |
}else{
|
| 85 | 75 |
unitIdsGbif.add(tripleId); |
| 86 | 76 |
} |
| 87 |
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|
| 88 |
|
|
| 77 |
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|
| 78 |
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|
| 89 | 79 |
} |
| 90 | 80 |
} |
| 91 |
Collections.sort(biocaseResponses, getComparator());
|
|
| 81 |
Collections.sort(biocaseResponses, getComparator()); |
|
| 92 | 82 |
URI dataSetUri = null; |
| 93 | 83 |
Abcd206ImportConfigurator configuratorAbcd; |
| 94 |
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|
| 84 |
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|
| 95 | 85 |
List<Abcd206ImportConfigurator> abcdConfigurators = new ArrayList<Abcd206ImportConfigurator>(); |
| 96 | 86 |
DataSetResponse dataSetResponse; |
| 97 | 87 |
OccurenceQuery bioCaseOccurrenceQuery = null; |
| ... | ... | |
| 109 | 99 |
if (!response.getDataSetUri().equals(dataSetUri)){
|
| 110 | 100 |
configuratorAbcd = Abcd206ImportConfigurator.NewInstance(dataSetUri, null, false); |
| 111 | 101 |
configuratorAbcd.addMediaAsMediaSpecimen(true); |
| 102 |
configuratorAbcd.setIgnoreAuthorship(true); |
|
| 103 |
configuratorAbcd.setMoveNewTaxaToDefaultClassification(false); |
|
| 112 | 104 |
if (configuratorAbcd != null){
|
| 113 | 105 |
abcdConfigurators.add(configuratorAbcd); |
| 114 | 106 |
} |
| ... | ... | |
| 118 | 110 |
if (dataImportView.getClassification() != null){
|
| 119 | 111 |
configuratorAbcd.setClassificationUuid(dataImportView.getClassification().getUuid()); |
| 120 | 112 |
} |
| 121 |
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|
| 113 |
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|
| 122 | 114 |
} |
| 123 | 115 |
tripleId = response.getTripleID(); |
| 124 | 116 |
unitIdsBioCase.add(tripleId); |
| 125 | 117 |
} |
| 126 |
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|
| 118 |
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|
| 127 | 119 |
OccurenceQuery query = new OccurenceQuery(unitIdsGbif); |
| 128 | 120 |
GbifImportConfigurator configurator = GbifImportConfigurator.newInstance(query); |
| 129 | 121 |
configurator.setSourceReferenceTitle("Import Gbif data");
|
| 130 |
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| 131 |
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| 132 |
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| 122 |
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| 123 |
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| 124 |
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| 133 | 125 |
// configurator.setQuery(query); |
| 134 |
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|
| 126 |
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|
| 135 | 127 |
Job bioCaseJob = CdmStore.getImportManager().createIOServiceJob(abcdConfigurators); |
| 136 | 128 |
CdmStore.getImportManager().run(bioCaseJob); |
| 137 |
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|
| 129 |
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|
| 138 | 130 |
Job gbifJob = CdmStore.getImportManager().createIOServiceJob(configurator); |
| 139 | 131 |
CdmStore.getImportManager().run(gbifJob); |
| 140 |
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| 141 |
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| 142 |
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| 132 |
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| 143 | 135 |
} |
| 144 | 136 |
} |
| 145 |
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| 146 |
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| 137 |
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| 138 |
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| 147 | 139 |
private void persistTerm(DefinedTermBase<?> term, ITermService termService, ConversationHolder conversation){
|
| 148 | 140 |
if(term!=null){
|
| 149 | 141 |
//if the term does not exist in the DB save it |
| ... | ... | |
| 152 | 144 |
} |
| 153 | 145 |
} |
| 154 | 146 |
} |
| 155 |
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|
| 147 |
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|
| 156 | 148 |
/* (non-Javadoc) |
| 157 | 149 |
* @see org.eclipse.jface.action.Action#getText() |
| 158 | 150 |
*/ |
| ... | ... | |
| 160 | 152 |
public String getText() {
|
| 161 | 153 |
return "Import"; |
| 162 | 154 |
} |
| 163 |
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| 155 |
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| 164 | 156 |
private Comparator<GbifResponse> getComparator(){
|
| 165 | 157 |
if (comparator == null){
|
| 166 | 158 |
comparator = new GbifResponseComparator(); |
| 167 | 159 |
} |
| 168 | 160 |
return comparator; |
| 169 | 161 |
} |
| 170 |
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| 172 | 164 |
} |
| eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/dataimport/SpecimenImportView.java | ||
|---|---|---|
| 15 | 15 |
import java.util.Collection; |
| 16 | 16 |
|
| 17 | 17 |
import org.apache.http.client.ClientProtocolException; |
| 18 |
import org.eclipse.core.runtime.jobs.Job; |
|
| 18 |
import org.w3c.dom.Element; |
|
| 19 |
import org.w3c.dom.NodeList; |
|
| 19 | 20 |
|
| 20 | 21 |
import eu.etaxonomy.cdm.ext.occurrence.bioCase.BioCaseQueryServiceWrapper; |
| 21 |
import eu.etaxonomy.cdm.io.common.CdmDefaultImport; |
|
| 22 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator.SOURCE_TYPE; |
|
| 22 |
import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206DataHolder; |
|
| 23 | 23 |
import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportConfigurator; |
| 24 |
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase; |
|
| 25 |
import eu.etaxonomy.taxeditor.store.CdmStore; |
|
| 24 |
import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportParser; |
|
| 25 |
import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportState; |
|
| 26 |
import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206XMLFieldGetter; |
|
| 27 |
import eu.etaxonomy.cdm.io.specimen.abcd206.in.AbcdParseUtility; |
|
| 28 |
import eu.etaxonomy.cdm.io.specimen.abcd206.in.UnitAssociationWrapper; |
|
| 26 | 29 |
|
| 27 | 30 |
/** |
| 28 | 31 |
* @author pplitzner |
| 29 | 32 |
* @date Sep 3, 2014 |
| 30 | 33 |
* |
| 31 | 34 |
*/ |
| 32 |
public class SpecimenImportView extends DataImportView<SpecimenOrObservationBase<?>> {
|
|
| 35 |
public class SpecimenImportView extends DataImportView<Abcd206DataHolder> {
|
|
| 33 | 36 |
|
| 34 | 37 |
public static final String ID = "eu.etaxonomy.taxeditor.view.dataimport.SpecimenImportView"; //$NON-NLS-1$ |
| 35 | 38 |
|
| ... | ... | |
| 49 | 52 |
* @see eu.etaxonomy.taxeditor.view.dataimport.DataImportView#getTextForTableItem(java.lang.Object) |
| 50 | 53 |
*/ |
| 51 | 54 |
@Override |
| 52 |
protected String getTextForTableItem(SpecimenOrObservationBase<?> item) {
|
|
| 53 |
return item.getTitleCache(); |
|
| 55 |
protected String getTextForTableItem(Abcd206DataHolder item) {
|
|
| 56 |
//TODO: define a suitable toString method |
|
| 57 |
return item.toString(); |
|
| 54 | 58 |
} |
| 55 | 59 |
|
| 56 | 60 |
/* (non-Javadoc) |
| ... | ... | |
| 60 | 64 |
public void query() {
|
| 61 | 65 |
String errorMessage = "Could not execute query " + query; |
| 62 | 66 |
|
| 63 |
Collection<SpecimenOrObservationBase<?>> results = new ArrayList<SpecimenOrObservationBase<?>>();
|
|
| 67 |
Collection<Abcd206DataHolder> results = new ArrayList<Abcd206DataHolder>();
|
|
| 64 | 68 |
try {
|
| 65 | 69 |
//FIXME move ABCD import to cdmlib -> this will also get rid of the transient services |
| 66 | 70 |
InputStream resultStream; |
| 67 | 71 |
resultStream = new BioCaseQueryServiceWrapper().query(query, endPoint); |
| 68 | 72 |
Abcd206ImportConfigurator configurator = Abcd206ImportConfigurator.NewInstance(null, null); |
| 69 |
// TransientCdmRepository repo = |
|
| 73 |
configurator.setSourceUri(endPoint); |
|
| 74 |
|
|
| 75 |
// TransientCdmRepository repo = |
|
| 70 | 76 |
// new TransientCdmRepository(CdmStore.getCurrentApplicationConfiguration()); |
| 71 | 77 |
//configurator.setCdmAppController(repo); |
| 78 |
|
|
| 79 |
//TODO: do not query all data but with the selected triple IDs -> see GbifResponseImportView |
|
| 72 | 80 |
configurator.setAddMediaAsMediaSpecimen(true); |
| 73 | 81 |
configurator.setAllowReuseOtherClassifications(true); |
| 74 |
|
|
| 75 |
Job job = CdmStore.getImportManager().createIOServiceJob(configurator, resultStream, SOURCE_TYPE.INPUTSTREAM); |
|
| 76 |
CdmStore.getImportManager().run(job); |
|
| 77 |
|
|
| 82 |
configurator.setMoveNewTaxaToDefaultClassification(false); |
|
| 83 |
UnitAssociationWrapper unitAssociationWrapper = AbcdParseUtility.parseUnitsNodeList(resultStream, null); |
|
| 84 |
NodeList unitsList = unitAssociationWrapper.getAssociatedUnits(); |
|
| 85 |
Abcd206DataHolder dataHolder = new Abcd206DataHolder(); |
|
| 86 |
Abcd206XMLFieldGetter abcdFieldGetter = new Abcd206XMLFieldGetter(dataHolder, unitAssociationWrapper.getPrefix()); |
|
| 87 |
Abcd206ImportState state = new Abcd206ImportState(configurator); |
|
| 88 |
state.setDataHolder(dataHolder); |
|
| 89 |
for (int i = 0; i <unitsList.getLength(); i++){
|
|
| 90 |
Element item = (Element) unitsList.item(i); |
|
| 91 |
//dataHolder = new Abcd206DataHolder(); |
|
| 92 |
Abcd206ImportParser.setUnitPropertiesXML(item, abcdFieldGetter, state); |
|
| 93 |
results.add(dataHolder); |
|
| 94 |
} |
|
| 95 |
|
|
| 96 |
// Job job = CdmStore.getImportManager().createIOServiceJob(configurator, resultStream, SOURCE_TYPE.INPUTSTREAM); |
|
| 97 |
// CdmStore.getImportManager().run(job); |
|
| 98 |
|
|
| 78 | 99 |
setResults(results); |
| 79 | 100 |
} catch (ClientProtocolException e) {
|
| 80 | 101 |
logger.error(errorMessage, e); |
| ... | ... | |
| 82 | 103 |
logger.error(errorMessage, e); |
| 83 | 104 |
} |
| 84 | 105 |
|
| 85 |
setResults(results); |
|
| 106 |
// setResults(results);
|
|
| 86 | 107 |
|
| 87 | 108 |
} |
| 88 | 109 |
|
| eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/dataimport/SpecimenSearchWizard.java | ||
|---|---|---|
| 33 | 33 |
import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery; |
| 34 | 34 |
import eu.etaxonomy.cdm.ext.occurrence.bioCase.BioCaseQueryServiceWrapper; |
| 35 | 35 |
import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportConfigurator; |
| 36 |
|
|
| 37 | 36 |
import eu.etaxonomy.cdm.io.specimen.abcd206.in.AbcdParseUtility; |
| 38 | 37 |
import eu.etaxonomy.cdm.io.specimen.abcd206.in.SpecimenImportReport; |
| 39 | 38 |
import eu.etaxonomy.cdm.io.specimen.abcd206.in.UnitAssociationWrapper; |
| ... | ... | |
| 80 | 79 |
configurator.setAddMediaAsMediaSpecimen(true); |
| 81 | 80 |
configurator.setDbSchemaValidation(DbSchemaValidation.CREATE); |
| 82 | 81 |
configurator.setIgnoreAuthorship(true); |
| 83 |
|
|
| 82 |
configurator.setMoveNewTaxaToDefaultClassification(false); |
|
| 83 |
|
|
| 84 |
|
|
| 84 | 85 |
//Job job = CdmStore.getImportManager().createIOServiceJob(configurator, new File(source), SOURCE_TYPE.INPUTSTREAM); |
| 85 | 86 |
//CdmStore.getImportManager().run(job); |
| 86 | 87 |
try {
|
| ... | ... | |
| 96 | 97 |
NodeList nodeList = unitNodesList.getAssociatedUnits(); |
| 97 | 98 |
String prefix = unitNodesList.getPrefix(); |
| 98 | 99 |
String associationType = unitNodesList.getAssociationType(); |
| 99 |
URI uri =AbcdParseUtility.parseFirstUri(nodeList, report); |
|
| 100 |
String content = AbcdParseUtility.parseFirstTextContent(nodeList); |
|
| 101 |
System.out.println(content); |
|
| 100 |
if (nodeList != null){
|
|
| 101 |
URI uri =AbcdParseUtility.parseFirstUri(nodeList, report); |
|
| 102 |
String content = AbcdParseUtility.parseFirstTextContent(nodeList); |
|
| 103 |
System.out.println(content); |
|
| 104 |
} |
|
| 105 |
|
|
| 102 | 106 |
|
| 103 | 107 |
|
| 104 | 108 |
SpecimenImportView specimenImportView = new SpecimenImportView(); |
| ... | ... | |
| 115 | 119 |
|
| 116 | 120 |
} else{
|
| 117 | 121 |
try {
|
| 118 |
|
|
| 122 |
|
|
| 119 | 123 |
dataImportView = (GbifResponseImportView) activePart.showView(GbifResponseImportView.ID, "query_"+query.toString().replaceAll(",", ""), IWorkbenchPage.VIEW_ACTIVATE);
|
| 120 |
dataImportView.setQuery(query);
|
|
| 124 |
dataImportView.setQuery(query); |
|
| 121 | 125 |
// (GbifResponseImportView) activePart.showView(GbifResponseImportView.ID);getWorkbench().getActiveWorkbenchWindow().getActivePage() |
| 122 | 126 |
// .showView(GbifResponseImportView.ID, "query_"+query.toString().replaceAll(",", ""),IWorkbenchPage.VIEW_ACTIVATE);
|
| 123 | 127 |
|
| ... | ... | |
| 134 | 138 |
e.printStackTrace(); |
| 135 | 139 |
} |
| 136 | 140 |
// CdmStore.getImportManager().run(configurator); |
| 137 |
|
|
| 141 |
|
|
| 138 | 142 |
// try {
|
| 139 | 143 |
// switch (providerSelectionPage.getQueryType()) {
|
| 140 | 144 |
// case BIOCASE: |
| ... | ... | |
| 162 | 166 |
//// } |
| 163 | 167 |
//// }); |
| 164 | 168 |
Job queryJob = new QueryJob("Query specimen provider", dataImportView);
|
| 165 |
queryJob.schedule();
|
|
| 169 |
queryJob.schedule(); |
|
| 166 | 170 |
|
| 167 | 171 |
return true; |
| 168 | 172 |
} |
Also available in: Unified diff
some changes for specimen import