Revision f3715fb4
Added by Patricia Kelbert about 10 years ago
| .gitattributes | ||
|---|---|---|
| 1 | 1 |
* text=auto !eol |
| 2 |
/LICENSE.TXT -text |
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| 3 |
/README.TXT -text |
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| 2 | 4 |
XperCdmIntegration/pom.xml -text |
| 3 | 5 |
XperCdmIntegration/src/main/java/eu/etaxonomy/cdm/io/xper/BaseCdm.java -text |
| 4 | 6 |
XperCdmIntegration/src/main/java/eu/etaxonomy/cdm/io/xper/CdmXperAdapter.java -text |
| ... | ... | |
| 411 | 413 |
cdm-pesi/src/test/java/eu/etaxonomy/cdm/io/erms/ermsErrors.txt -text |
| 412 | 414 |
cdm-pesi/src/test/resources/sql/Check_Import_Master.sql -text |
| 413 | 415 |
cdmapps-parent/pom.xml -text |
| 416 |
/pom.xml -text |
|
| LICENSE.TXT | ||
|---|---|---|
| 1 |
The contents of this file are subject to the Mozilla Public License |
|
| 2 |
Version 1.1 (the "License"); you may not use this file except in |
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| 3 |
compliance with the License. You may obtain a copy of the License at |
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| 4 |
http://www.mozilla.org/MPL/ |
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| 5 |
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| 6 |
Software distributed under the License is distributed on an "AS IS" |
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| 7 |
basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the |
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| 8 |
License for the specific language governing rights and limitations |
|
| 9 |
under the License. |
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| README.TXT | ||
|---|---|---|
| 1 |
The project uses Maven2 and AspectJ. |
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| 2 |
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| 3 |
Please see http://dev.e-taxonomy.eu/trac/wiki/CdmLibrary for details on installation and usage |
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| XperCdmIntegration/pom.xml | ||
|---|---|---|
| 14 | 14 |
<modelVersion>4.0.0</modelVersion> |
| 15 | 15 |
<artifactId>xper2-cdm-integration</artifactId> |
| 16 | 16 |
<name>xper2 Cdm Integration</name> |
| 17 |
<description>The Xper integration package for EDIT's CdmLibrary</description>
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|
| 17 |
<description>The import-export package for EDIT's cdmLibrary</description>
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|
| 18 | 18 |
<scm> |
| 19 | 19 |
<connection>scm:svn:http://dev.e-taxonomy.eu/svn/trunk/cdmlib-apps/XperCdmIntegration/</connection> |
| 20 | 20 |
<developerConnection>scm:svn:https://dev.e-taxonomy.eu/svn/trunk/cdmlib-apps/XperCdmIntegration/</developerConnection> |
| app-import/src/main/java/eu/etaxonomy/cdm/app/abcdImport/SpecimenImport.java | ||
|---|---|---|
| 25 | 25 |
private static Logger logger = Logger.getLogger(SpecimenImport.class); |
| 26 | 26 |
|
| 27 | 27 |
//database validation status (create, update, validate ...) |
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static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
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static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;
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| 29 | 29 |
// final static String xmlSource = "/home/patricia/Desktop/multiABCD.xml"; |
| 30 | 30 |
//final static String xmlSource = "D:\\_Tagungen\\2010-09 TDWG 2010\\Workshop\\data\\specimen\\Picris pauciflora\\B-W14632-000_B-W14632-010_B100097145_B100097146_B100326668_B180004364_B180017717_.xml"; |
| 31 | 31 |
// final static String xmlSource = "/home/pkelbert/workspace/proibiosphere/cdmlib-io/src/test/resources/eu/etaxonomy/cdm/io/specimen/abcd206/in/SpecimenImportConfiguratorTest-input.xml"; |
| ... | ... | |
| 54 | 54 |
ICdmDataSource destination = cdmDestination; |
| 55 | 55 |
Abcd206ImportConfigurator specimenImportConfigurator = Abcd206ImportConfigurator.NewInstance(source, destination); |
| 56 | 56 |
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// specimenImportConfigurator.setClassificationName(specimenImportConfigurator.getSourceReferenceTitle()); |
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//// specimenImportConfigurator.setClassificationName(specimenImportConfigurator.getSourceReferenceTitle());
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| 58 | 58 |
specimenImportConfigurator.setSourceSecId("specimen");
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| 59 | 59 |
specimenImportConfigurator.setCheck(check); |
| 60 | 60 |
specimenImportConfigurator.setDbSchemaValidation(hbm2dll); |
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specimenImportConfigurator.setParseNameAutomatically(false);
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specimenImportConfigurator.setParseNameAutomatically(true);
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| 62 | 62 |
specimenImportConfigurator.setReuseExistingMetadata(true); |
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specimenImportConfigurator.reuseExistingDescriptiveGroups(false);
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specimenImportConfigurator.reuseExistingDescriptiveGroups(true);
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// |
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specimenImportConfigurator.setReuseExistingTaxaWhenPossible(true); |
| 66 |
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// |
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| 67 | 67 |
specimenImportConfigurator.setAddIndividualsAssociationsSuchAsSpecimenAndObservations(true); |
| 68 | 68 |
specimenImportConfigurator.setUseClassification(true); |
| 69 | 69 |
specimenImportConfigurator.setInteractWithUser(true); |
| 70 |
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// |
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| 71 | 71 |
specimenImportConfigurator.setSourceReference(null); |
| 72 | 72 |
specimenImportConfigurator.setTaxonReference(null); |
| 73 | 73 |
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| app-import/src/main/java/eu/etaxonomy/cdm/app/abcdImport/SynthesysCacheActivator.java | ||
|---|---|---|
| 42 | 42 |
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| 43 | 43 |
// static final ICdmDataSource cdmDestination = CdmDestinations.mon_cdm(); |
| 44 | 44 |
// static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE; |
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static final ICdmDataSource cdmDestination = CdmDestinations.proibiosphere_local(); |
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static final ICdmDataSource cdmDestination = CdmDestinations.proibiosphere_chenopodium_local();
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| 46 | 46 |
static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE; |
| 47 | 47 |
static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK; |
| 48 | 48 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/common/CdmDestinations.java | ||
|---|---|---|
| 1 | 1 |
/** |
| 2 | 2 |
* Copyright (C) 2007 EDIT |
| 3 |
* European Distributed Institute of Taxonomy
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* European Distributed Institute of Taxonomy |
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| 4 | 4 |
* http://www.e-taxonomy.eu |
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*
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* |
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| 6 | 6 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
| 7 | 7 |
* See LICENSE.TXT at the top of this package for the full license terms. |
| 8 | 8 |
*/ |
| ... | ... | |
| 22 | 22 |
public class CdmDestinations {
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| 23 | 23 |
@SuppressWarnings("unused")
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private static Logger logger = Logger.getLogger(CdmDestinations.class); |
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/** |
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* Intended to be used for imports |
| 28 | 28 |
*/ |
| ... | ... | |
| 37 | 37 |
public static ICdmDataSource cdm_test_alex(){
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| 38 | 38 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 39 | 39 |
String cdmServer = "192.168.2.10"; |
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String cdmDB = "cdm_production_palmae";
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String cdmDB = "cdm_production_palmae"; |
|
| 41 | 41 |
String cdmUserName = "edit"; |
| 42 | 42 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 43 | 43 |
} |
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| 45 | 45 |
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public static ICdmDataSource cdm_test_useSummary(){
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| 47 | 47 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 48 | 48 |
String cdmServer = "localhost"; |
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String cdmDB = "palmae_2011_07_17";
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String cdmDB = "palmae_2011_07_17"; |
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| 50 | 50 |
String cdmUserName = "root"; |
| 51 | 51 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 52 | 52 |
} |
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| 54 | 54 |
public static ICdmDataSource cdm_test_local_mysql(){
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| 55 | 55 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 56 | 56 |
String cdmServer = "127.0.0.1"; |
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String cdmDB = "cdm_test";
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String cdmDB = "cdm_test"; |
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| 58 | 58 |
String cdmUserName = "edit"; |
| 59 | 59 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 60 | 60 |
} |
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public static ICdmDataSource cdm_test_local_mysql_moose(){
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| 64 | 64 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 65 | 65 |
String cdmServer = "127.0.0.1"; |
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String cdmDB = "moose";
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String cdmDB = "moose"; |
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String cdmUserName = "root"; |
| 68 | 68 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 69 | 69 |
} |
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public static ICdmDataSource cdm_test_local_mysql_standardliste(){
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DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 73 | 73 |
String cdmServer = "127.0.0.1"; |
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String cdmDB = "standardliste";
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String cdmDB = "standardliste"; |
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String cdmUserName = "root"; |
| 76 | 76 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 77 | 77 |
} |
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public static ICdmDataSource cdm_test_local_mysql_standardliste2(){
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DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 81 | 80 |
String cdmServer = "127.0.0.1"; |
| ... | ... | |
| 84 | 83 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 85 | 84 |
} |
| 86 | 85 |
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| 87 | 87 |
public static ICdmDataSource cdm_test_local_mysql_dwca(){
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DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 89 | 89 |
String cdmServer = "127.0.0.1"; |
| 90 |
String cdmDB = "dwca";
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String cdmDB = "dwca"; |
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String cdmUserName = "edit"; |
| 92 | 92 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 93 | 93 |
} |
| 94 | 94 |
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public static ICdmDataSource cdm_test_local_mysql_fdac(){
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| 97 | 97 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 98 | 98 |
String cdmServer = "127.0.0.1"; |
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String cdmDB = "fdac";
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String cdmDB = "fdac"; |
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| 100 | 100 |
String cdmUserName = "edit"; |
| 101 | 101 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 102 | 102 |
} |
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| 104 | 104 |
public static ICdmDataSource cdm_test_local_mysql_test(){
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| 105 | 105 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 106 | 106 |
String cdmServer = "127.0.0.1"; |
| 107 |
String cdmDB = "test";
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String cdmDB = "test"; |
|
| 108 | 108 |
String cdmUserName = "edit"; |
| 109 | 109 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 110 | 110 |
} |
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| 112 | 112 |
public static ICdmDataSource cdm_corvidae_dev(){
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| 113 | 113 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 114 | 114 |
String cdmServer = "160.45.63.201"; |
| 115 |
String cdmDB = "cdm_corvidae";
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String cdmDB = "cdm_corvidae"; |
|
| 116 | 116 |
String cdmUserName = "edit"; |
| 117 | 117 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 118 | 118 |
} |
| ... | ... | |
| 124 | 124 |
String cdmUserName = "edit"; |
| 125 | 125 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 126 | 126 |
} |
| 127 |
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| 128 | 128 |
// |
| 129 | 129 |
// public static ICdmDataSource cdm_ildis_production(){
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| 130 | 130 |
// DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| ... | ... | |
| 133 | 133 |
// String cdmUserName = "edit"; |
| 134 | 134 |
// return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 135 | 135 |
// } |
| 136 |
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| 137 | 137 |
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| 138 | 138 |
public static ICdmDataSource cdm_redlist_moose_dev(){
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| 139 | 139 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| ... | ... | |
| 142 | 142 |
String cdmUserName = "edit"; |
| 143 | 143 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 144 | 144 |
} |
| 145 |
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| 146 | 146 |
public static ICdmDataSource cdm_redlist_standardlist_dev(){
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| 147 | 147 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 148 | 148 |
String cdmServer = "160.45.63.201"; |
| ... | ... | |
| 150 | 150 |
String cdmUserName = "edit"; |
| 151 | 151 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 152 | 152 |
} |
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public static ICdmDataSource cdm_cyprus_dev(){
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| 155 | 155 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 156 | 156 |
String cdmServer = "160.45.63.201"; |
| ... | ... | |
| 158 | 158 |
String cdmUserName = "edit"; |
| 159 | 159 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 160 | 160 |
} |
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public static ICdmDataSource cdm_cyprus_production(){
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DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 164 | 164 |
String cdmServer = "160.45.63.171"; |
| ... | ... | |
| 175 | 175 |
String cdmUserName = "edit"; |
| 176 | 176 |
return makeDestination(dbType, cdmServer, cdmDB, port, cdmUserName, null); |
| 177 | 177 |
} |
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public static ICdmDataSource cdm_cyprus_dev_tunnel(){
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| 180 | 180 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 181 | 181 |
String cdmServer = "127.0.0.1"; |
| ... | ... | |
| 184 | 184 |
String cdmUserName = "edit"; |
| 185 | 185 |
return makeDestination(dbType, cdmServer, cdmDB, port, cdmUserName, null); |
| 186 | 186 |
} |
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public static ICdmDataSource cdm_campanulaceae_production(){
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| 189 | 189 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 190 | 190 |
String cdmServer = "160.45.63.171"; |
| ... | ... | |
| 192 | 192 |
String cdmUserName = "edit"; |
| 193 | 193 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 194 | 194 |
} |
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public static ICdmDataSource cdm_flora_malesiana_preview(){
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| 197 | 197 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 198 | 198 |
String cdmServer = "160.45.63.201"; |
| ... | ... | |
| 208 | 208 |
String cdmUserName = "edit"; |
| 209 | 209 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 210 | 210 |
} |
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public static ICdmDataSource cdm_flora_central_africa_preview(){
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DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 214 | 214 |
String cdmServer = "160.45.63.201"; |
| ... | ... | |
| 216 | 216 |
String cdmUserName = "edit"; |
| 217 | 217 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 218 | 218 |
} |
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public static ICdmDataSource cdm_flora_central_africa_production(){
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| 221 | 221 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 222 | 222 |
String cdmServer = "160.45.63.171"; |
| ... | ... | |
| 224 | 224 |
String cdmUserName = "edit"; |
| 225 | 225 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 226 | 226 |
} |
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public static ICdmDataSource cdm_pesi_euroMed(){
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| 229 | 229 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 230 | 230 |
String cdmServer = "192.168.2.10"; |
| ... | ... | |
| 232 | 232 |
String cdmUserName = "edit"; |
| 233 | 233 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 234 | 234 |
} |
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public static ICdmDataSource cdm_pesi_all(){
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| 237 | 237 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 238 | 238 |
String cdmServer = "192.168.2.10"; |
| ... | ... | |
| 240 | 240 |
String cdmUserName = "edit"; |
| 241 | 241 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 242 | 242 |
} |
| 243 |
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| 244 | 244 |
public static ICdmDataSource cdm_portal_test_localhost(){
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| 245 | 245 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 246 | 246 |
String cdmServer = "127.0.0.1"; |
| ... | ... | |
| 248 | 248 |
String cdmUserName = "edit"; |
| 249 | 249 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 250 | 250 |
} |
| 251 |
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| 252 | 252 |
public static ICdmDataSource cdm_portal_test_localhost2(){
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| 253 | 253 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 254 | 254 |
String cdmServer = "127.0.0.1"; |
| ... | ... | |
| 256 | 256 |
String cdmUserName = "edit"; |
| 257 | 257 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 258 | 258 |
} |
| 259 |
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| 260 | 260 |
public static ICdmDataSource cdm_local_cichorieae(){
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| 261 | 261 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 262 | 262 |
String cdmServer = "127.0.0.1"; |
| ... | ... | |
| 264 | 264 |
String cdmUserName = "edit"; |
| 265 | 265 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 266 | 266 |
} |
| 267 |
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public static ICdmDataSource cdm_local_dipera(){
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| 269 | 269 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 270 | 270 |
String cdmServer = "127.0.0.1"; |
| ... | ... | |
| 272 | 272 |
String cdmUserName = "edit"; |
| 273 | 273 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 274 | 274 |
} |
| 275 |
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| 275 |
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| 276 | 276 |
public static ICdmDataSource cdm_local_palmae(){
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| 277 | 277 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 278 | 278 |
String cdmServer = "127.0.0.1"; |
| ... | ... | |
| 280 | 280 |
String cdmUserName = "edit"; |
| 281 | 281 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 282 | 282 |
} |
| 283 |
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| 284 | 284 |
public static ICdmDataSource cdm_globis_dev(){
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| 285 | 285 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 286 | 286 |
String cdmServer = "160.45.63.201"; |
| ... | ... | |
| 288 | 288 |
String cdmUserName = "edit"; |
| 289 | 289 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 290 | 290 |
} |
| 291 |
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| 291 |
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| 292 | 292 |
public static ICdmDataSource cdm_local_globis(){
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| 293 | 293 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 294 | 294 |
String cdmServer = "127.0.0.1"; |
| ... | ... | |
| 312 | 312 |
String cdmUserName = "edit"; |
| 313 | 313 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 314 | 314 |
} |
| 315 |
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| 317 | 317 |
public static ICdmDataSource NULL(){
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| 318 | 318 |
return null; |
| 319 | 319 |
} |
| 320 |
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| 321 |
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| 320 |
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| 321 |
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| 322 | 322 |
public static ICdmDataSource localH2(){
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| 323 | 323 |
return CdmDataSource.NewH2EmbeddedInstance("cdm", "sa", "");
|
| 324 | 324 |
} |
| 325 |
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| 325 |
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| 326 | 326 |
public static ICdmDataSource localH2(String database, String username, String filePath){
|
| 327 | 327 |
return CdmDataSource.NewH2EmbeddedInstance(database, "sa", "", filePath, null); |
| 328 | 328 |
} |
| 329 |
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| 329 |
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| 330 | 330 |
public static ICdmDataSource localH2Salvador(){
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| 331 | 331 |
return CdmDataSource.NewH2EmbeddedInstance("salvador", "sa", "");
|
| 332 | 332 |
} |
| 333 |
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| 333 |
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|
| 334 | 334 |
public static ICdmDataSource localH2Diptera(){
|
| 335 | 335 |
return CdmDataSource.NewH2EmbeddedInstance("diptera", "sa", "");
|
| 336 | 336 |
} |
| 337 |
|
|
| 338 |
|
|
| 337 |
|
|
| 338 |
|
|
| 339 | 339 |
public static ICdmDataSource localH2Cichorieae(){
|
| 340 | 340 |
return CdmDataSource.NewH2EmbeddedInstance("cichorieae", "sa", "");
|
| 341 | 341 |
} |
| 342 |
|
|
| 342 |
|
|
| 343 | 343 |
public static ICdmDataSource localH2Palmae(){
|
| 344 | 344 |
return CdmDataSource.NewH2EmbeddedInstance("palmae", "sa", "");
|
| 345 | 345 |
} |
| 346 |
|
|
| 346 |
|
|
| 347 | 347 |
public static ICdmDataSource localH2EuroMed(){
|
| 348 | 348 |
return CdmDataSource.NewH2EmbeddedInstance("euroMed", "sa", "");
|
| 349 | 349 |
} |
| 350 |
|
|
| 350 |
|
|
| 351 | 351 |
public static ICdmDataSource localH2Erms(){
|
| 352 | 352 |
return CdmDataSource.NewH2EmbeddedInstance("erms", "sa", "");
|
| 353 | 353 |
} |
| 354 |
|
|
| 354 |
|
|
| 355 | 355 |
public static ICdmDataSource localH2_viola(){
|
| 356 | 356 |
return CdmDataSource.NewH2EmbeddedInstance("testViola", "sa", "");
|
| 357 | 357 |
} |
| 358 |
|
|
| 358 |
|
|
| 359 | 359 |
public static ICdmDataSource localH2_LIAS(){
|
| 360 | 360 |
return CdmDataSource.NewH2EmbeddedInstance("testLIAS", "sa", "");
|
| 361 | 361 |
} |
| 362 |
|
|
| 362 |
|
|
| 363 | 363 |
public static ICdmDataSource localH2_Erythroneura(){
|
| 364 | 364 |
return CdmDataSource.NewH2EmbeddedInstance("testErythroneura", "sa", "");
|
| 365 | 365 |
} |
| 366 |
|
|
| 366 |
|
|
| 367 | 367 |
public static ICdmDataSource localH2_Cicad(){
|
| 368 | 368 |
return CdmDataSource.NewH2EmbeddedInstance("testCicad", "sa", "");
|
| 369 | 369 |
} |
| 370 |
|
|
| 370 |
|
|
| 371 | 371 |
public static ICdmDataSource localH2_ValRosandraFRIDAKey(){
|
| 372 | 372 |
return CdmDataSource.NewH2EmbeddedInstance("testValRosandraFRIDAKey", "sa", "");
|
| 373 | 373 |
} |
| 374 |
|
|
| 374 |
|
|
| 375 | 375 |
public static ICdmDataSource localH2_FreshwaterAquaticInsects(){
|
| 376 | 376 |
return CdmDataSource.NewH2EmbeddedInstance("testFreshwaterAquaticInsects", "sa", "");
|
| 377 | 377 |
} |
| ... | ... | |
| 379 | 379 |
public static ICdmDataSource cdm_algaterra_preview(){
|
| 380 | 380 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 381 | 381 |
String cdmServer = "160.45.63.201"; |
| 382 |
String cdmDB = "cdm_edit_algaterra";
|
|
| 382 |
String cdmDB = "cdm_edit_algaterra"; |
|
| 383 | 383 |
String cdmUserName = "edit"; |
| 384 | 384 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 385 | 385 |
} |
| ... | ... | |
| 387 | 387 |
public static ICdmDataSource cdm_algaterra_production(){
|
| 388 | 388 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 389 | 389 |
String cdmServer = "160.45.63.171"; |
| 390 |
String cdmDB = "cdm_production_algaterra";
|
|
| 390 |
String cdmDB = "cdm_production_algaterra"; |
|
| 391 | 391 |
String cdmUserName = "edit"; |
| 392 | 392 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 393 | 393 |
} |
| 394 |
|
|
| 394 |
|
|
| 395 | 395 |
public static ICdmDataSource cdm_edit_cichorieae_local_PG(){
|
| 396 | 396 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.PostgreSQL; |
| 397 | 397 |
String cdmServer = "127.0.0.1"; |
| 398 |
String cdmDB = "cdm_edit_cichorieae_a";
|
|
| 398 |
String cdmDB = "cdm_edit_cichorieae_a"; |
|
| 399 | 399 |
String cdmUserName = "edit"; |
| 400 | 400 |
int port = 15432; |
| 401 | 401 |
return makeDestination(dbType, cdmServer, cdmDB, port, cdmUserName, null); |
| ... | ... | |
| 404 | 404 |
public static ICdmDataSource cdm_cichorieae_preview(){
|
| 405 | 405 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 406 | 406 |
String cdmServer = "160.45.63.201"; |
| 407 |
String cdmDB = "cdm_edit_cichorieae";
|
|
| 407 |
String cdmDB = "cdm_edit_cichorieae"; |
|
| 408 | 408 |
String cdmUserName = "edit"; |
| 409 | 409 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 410 | 410 |
} |
| 411 |
|
|
| 411 |
|
|
| 412 | 412 |
public static ICdmDataSource cdm_production_cichorieae(){
|
| 413 | 413 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 414 | 414 |
String cdmServer = "160.45.63.171"; |
| 415 | 415 |
// String cdmServer = "127.0.0.1"; |
| 416 |
String cdmDB = "cdm_production_cichorieae";
|
|
| 416 |
String cdmDB = "cdm_production_cichorieae"; |
|
| 417 | 417 |
String cdmUserName = "edit"; |
| 418 | 418 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 419 | 419 |
} |
| 420 |
|
|
| 420 |
|
|
| 421 | 421 |
public static ICdmDataSource cdm_production_palmae(){
|
| 422 | 422 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 423 | 423 |
String cdmServer = "160.45.63.171"; |
| 424 |
String cdmDB = "cdm_production_palmae";
|
|
| 424 |
String cdmDB = "cdm_production_palmae"; |
|
| 425 | 425 |
String cdmUserName = "edit"; |
| 426 | 426 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 427 | 427 |
} |
| 428 |
|
|
| 429 |
|
|
| 428 |
|
|
| 429 |
|
|
| 430 | 430 |
public static ICdmDataSource cdm_production_diptera(){
|
| 431 | 431 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 432 | 432 |
String cdmServer = "160.45.63.171"; |
| 433 |
String cdmDB = "cdm_production_diptera";
|
|
| 433 |
String cdmDB = "cdm_production_diptera"; |
|
| 434 | 434 |
String cdmUserName = "edit"; |
| 435 | 435 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 436 | 436 |
} |
| 437 |
|
|
| 437 |
|
|
| 438 | 438 |
public static ICdmDataSource local_cdm_edit_cichorieae_a(){
|
| 439 | 439 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 440 | 440 |
String cdmServer = "127.0.0.1"; |
| 441 |
String cdmDB = "cdm_edit_cichorieae_a";
|
|
| 441 |
String cdmDB = "cdm_edit_cichorieae_a"; |
|
| 442 | 442 |
String cdmUserName = "edit"; |
| 443 | 443 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 444 | 444 |
} |
| ... | ... | |
| 450 | 450 |
String cdmUserName = "edit"; |
| 451 | 451 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 452 | 452 |
} |
| 453 |
|
|
| 453 |
|
|
| 454 | 454 |
public static ICdmDataSource cdm_edit_cichorieae_preview(){
|
| 455 | 455 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 456 | 456 |
String cdmServer = "127.0.0.1"; |
| 457 |
String cdmDB = "cdm_edit_cichorieae";
|
|
| 457 |
String cdmDB = "cdm_edit_cichorieae"; |
|
| 458 | 458 |
String cdmUserName = "edit"; |
| 459 | 459 |
int port = 13306; |
| 460 | 460 |
return makeDestination(dbType, cdmServer, cdmDB, port, cdmUserName, null); |
| 461 | 461 |
} |
| 462 |
|
|
| 462 |
|
|
| 463 | 463 |
public static ICdmDataSource cdm_edit_cichorieae_preview_direct(){
|
| 464 | 464 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 465 | 465 |
String cdmServer = "160.45.63.201"; |
| 466 |
String cdmDB = "cdm_edit_cichorieae";
|
|
| 466 |
String cdmDB = "cdm_edit_cichorieae"; |
|
| 467 | 467 |
String cdmUserName = "edit"; |
| 468 | 468 |
int port = 3306; |
| 469 | 469 |
return makeDestination(dbType, cdmServer, cdmDB, port, cdmUserName, null); |
| 470 | 470 |
} |
| 471 |
|
|
| 471 |
|
|
| 472 | 472 |
public static ICdmDataSource cdm_edit_cichorieae_integration(){
|
| 473 | 473 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 474 | 474 |
String cdmServer = "127.0.0.1"; |
| 475 |
String cdmDB = "cdm_integration_cichorieae";
|
|
| 475 |
String cdmDB = "cdm_integration_cichorieae"; |
|
| 476 | 476 |
String cdmUserName = "edit"; |
| 477 | 477 |
int port = 13306; |
| 478 | 478 |
return makeDestination(dbType, cdmServer, cdmDB, port, cdmUserName, null); |
| ... | ... | |
| 481 | 481 |
public static ICdmDataSource cdm_edit_palmae_preview(){
|
| 482 | 482 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 483 | 483 |
String cdmServer = "127.0.0.1"; |
| 484 |
String cdmDB = "cdm_edit_palmae";
|
|
| 484 |
String cdmDB = "cdm_edit_palmae"; |
|
| 485 | 485 |
String cdmUserName = "edit"; |
| 486 | 486 |
int port = 13306; |
| 487 | 487 |
return makeDestination(dbType, cdmServer, cdmDB, port, cdmUserName, null); |
| 488 |
}
|
|
| 489 |
|
|
| 488 |
} |
|
| 489 |
|
|
| 490 | 490 |
public static ICdmDataSource cdm_edit_salvador(){
|
| 491 | 491 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 492 | 492 |
String cdmServer = "192.168.2.10"; |
| 493 |
String cdmDB = "cdm_edit_salvador";
|
|
| 493 |
String cdmDB = "cdm_edit_salvador"; |
|
| 494 | 494 |
String cdmUserName = "edit"; |
| 495 | 495 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 496 | 496 |
} |
| 497 |
|
|
| 497 |
|
|
| 498 | 498 |
public static ICdmDataSource cdm_import_salvador() {
|
| 499 | 499 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 500 | 500 |
String cdmServer = "192.168.2.10"; |
| 501 |
String cdmDB = "cdm_import_salvador";
|
|
| 501 |
String cdmDB = "cdm_import_salvador"; |
|
| 502 | 502 |
String cdmUserName = "edit"; |
| 503 | 503 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 504 | 504 |
} |
| 505 |
|
|
| 505 |
|
|
| 506 | 506 |
public static ICdmDataSource cdm_salvador_production() {
|
| 507 | 507 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 508 | 508 |
String cdmServer = "192.168.2.10"; |
| 509 |
String cdmDB = "salvador_cdm";
|
|
| 509 |
String cdmDB = "salvador_cdm"; |
|
| 510 | 510 |
String cdmUserName = "salvador"; |
| 511 | 511 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 512 | 512 |
} |
| 513 |
|
|
| 513 |
|
|
| 514 | 514 |
/** |
| 515 | 515 |
* patricia |
| 516 | 516 |
*/ |
| ... | ... | |
| 521 | 521 |
String cdmUserName = "root"; |
| 522 | 522 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 523 | 523 |
} |
| 524 |
|
|
| 525 |
public static ICdmDataSource proibiosphere_local() {
|
|
| 524 |
|
|
| 525 |
public static ICdmDataSource mon_corvids() {
|
|
| 526 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
|
| 527 |
String cdmServer = "localhost"; |
|
| 528 |
String cdmDB = "cdm_production_corvidae"; |
|
| 529 |
String cdmUserName = "root"; |
|
| 530 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, "mysqlr00t"); |
|
| 531 |
} |
|
| 532 |
|
|
| 533 |
public static ICdmDataSource proibiosphere_chenopodium_local() {
|
|
| 526 | 534 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 527 | 535 |
String cdmServer = "localhost"; |
| 528 | 536 |
String cdmDB = "cdm_production_proibiosphere_chenopodium_pilot"; |
| 529 | 537 |
String cdmUserName = "root"; |
| 530 | 538 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 531 | 539 |
} |
| 532 |
|
|
| 540 |
|
|
| 541 |
public static ICdmDataSource proibiosphere_ants_local() {
|
|
| 542 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
|
| 543 |
String cdmServer = "localhost"; |
|
| 544 |
String cdmDB = "cdm_production_proibiosphere_ants_pilot"; |
|
| 545 |
String cdmUserName = "root"; |
|
| 546 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
|
| 547 |
} |
|
| 548 |
|
|
| 549 |
public static ICdmDataSource proibiosphere_fungi_local() {
|
|
| 550 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
|
| 551 |
String cdmServer = "localhost"; |
|
| 552 |
String cdmDB = "cdm_production_proibiosphere_fungi_pilot"; |
|
| 553 |
String cdmUserName = "root"; |
|
| 554 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
|
| 555 |
} |
|
| 556 |
|
|
| 557 |
public static ICdmDataSource proibiosphere_campylopus_local() {
|
|
| 558 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
|
| 559 |
String cdmServer = "localhost"; |
|
| 560 |
String cdmDB = "cdm_production_proibiosphere_campylopus_pilot"; |
|
| 561 |
String cdmUserName = "root"; |
|
| 562 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
|
| 563 |
} |
|
| 564 |
|
|
| 565 |
|
|
| 566 |
public static ICdmDataSource proibiosphere_eupolybothrus_local() {
|
|
| 567 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
|
| 568 |
String cdmServer = "localhost"; |
|
| 569 |
String cdmDB = "cdm_production_proibiosphere_eupolybothrus_pilot"; |
|
| 570 |
String cdmUserName = "root"; |
|
| 571 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
|
| 572 |
} |
|
| 573 |
|
|
| 574 |
public static ICdmDataSource proibiosphere_spiders_local() {
|
|
| 575 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
|
| 576 |
String cdmServer = "localhost"; |
|
| 577 |
String cdmDB = "cdm_production_proibiosphere_spiders_pilot"; |
|
| 578 |
String cdmUserName = "root"; |
|
| 579 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
|
| 580 |
} |
|
| 533 | 581 |
// public static ICdmDataSource LAPTOP_HP(){
|
| 534 | 582 |
// DatabaseTypeEnum dbType = DatabaseTypeEnum.SqlServer2005; |
| 535 | 583 |
// String cdmServer = "LAPTOPHP"; |
| 536 |
// String cdmDB = "cdmTest";
|
|
| 584 |
// String cdmDB = "cdmTest"; |
|
| 537 | 585 |
// String cdmUserName = "edit"; |
| 538 | 586 |
// return makeDestination(cdmServer, cdmDB, -1, cdmUserName, null); |
| 539 | 587 |
// } |
| 540 |
|
|
| 541 |
|
|
| 542 | 588 |
|
| 543 |
|
|
| 589 |
|
|
| 590 |
|
|
| 591 |
|
|
| 544 | 592 |
/** |
| 545 | 593 |
* initializes source |
| 546 | 594 |
* TODO only supports MySQL and PostgreSQL |
| 547 |
*
|
|
| 595 |
* |
|
| 548 | 596 |
* @param dbType |
| 549 | 597 |
* @param cdmServer |
| 550 | 598 |
* @param cdmDB |
| ... | ... | |
| 558 | 606 |
pwd = AccountStore.readOrStorePassword(cdmServer, cdmDB, cdmUserName, pwd); |
| 559 | 607 |
ICdmDataSource destination; |
| 560 | 608 |
if(dbType.equals(DatabaseTypeEnum.MySQL)){
|
| 561 |
destination = CdmDataSource.NewMySqlInstance(cdmServer, cdmDB, port, cdmUserName, pwd, null);
|
|
| 609 |
destination = CdmDataSource.NewMySqlInstance(cdmServer, cdmDB, port, cdmUserName, pwd, null); |
|
| 562 | 610 |
} else if(dbType.equals(DatabaseTypeEnum.PostgreSQL)){
|
| 563 |
destination = CdmDataSource.NewPostgreSQLInstance(cdmServer, cdmDB, port, cdmUserName, pwd, null);
|
|
| 611 |
destination = CdmDataSource.NewPostgreSQLInstance(cdmServer, cdmDB, port, cdmUserName, pwd, null); |
|
| 564 | 612 |
} else {
|
| 565 | 613 |
//TODO others |
| 566 | 614 |
throw new RuntimeException("Unsupported DatabaseType");
|
| ... | ... | |
| 571 | 619 |
|
| 572 | 620 |
|
| 573 | 621 |
/** |
| 574 |
* Accepts a string array and tries to find a method returning an ICdmDataSource with
|
|
| 622 |
* Accepts a string array and tries to find a method returning an ICdmDataSource with |
|
| 575 | 623 |
* the name of the given first string in the array |
| 576 |
*
|
|
| 624 |
* |
|
| 577 | 625 |
* @param args |
| 578 | 626 |
* @return |
| 579 | 627 |
*/ |
| 580 | 628 |
public static ICdmDataSource chooseDestination(String[] args) {
|
| 581 |
if(args == null) |
|
| 582 |
return null; |
|
| 583 |
|
|
| 584 |
if(args.length != 1) |
|
| 585 |
return null; |
|
| 586 |
|
|
| 629 |
if(args == null) {
|
|
| 630 |
return null; |
|
| 631 |
} |
|
| 632 |
|
|
| 633 |
if(args.length != 1) {
|
|
| 634 |
return null; |
|
| 635 |
} |
|
| 636 |
|
|
| 587 | 637 |
String possibleDestination = args[0]; |
| 588 |
|
|
| 638 |
|
|
| 589 | 639 |
Method[] methods = CdmDestinations.class.getMethods(); |
| 590 |
|
|
| 640 |
|
|
| 591 | 641 |
for (Method method : methods){
|
| 592 | 642 |
if(method.getName().equals(possibleDestination)){
|
| 593 | 643 |
try {
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/excelImport/taxa/NormalExplicitActivator.java | ||
|---|---|---|
| 1 | 1 |
/** |
| 2 | 2 |
* Copyright (C) 2007 EDIT |
| 3 |
* European Distributed Institute of Taxonomy
|
|
| 3 |
* European Distributed Institute of Taxonomy |
|
| 4 | 4 |
* http://www.e-taxonomy.eu |
| 5 |
*
|
|
| 5 |
* |
|
| 6 | 6 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
| 7 | 7 |
* See LICENSE.TXT at the top of this package for the full license terms. |
| 8 | 8 |
*/ |
| ... | ... | |
| 27 | 27 |
*/ |
| 28 | 28 |
public class NormalExplicitActivator {
|
| 29 | 29 |
private static final Logger logger = Logger.getLogger(NormalExplicitActivator.class); |
| 30 |
|
|
| 31 |
// private static String fileName =
|
|
| 30 |
|
|
| 31 |
// private static String fileName = |
|
| 32 | 32 |
// new String("D:\\_Tagungen\\2010-09 TDWG 2010\\Workshop\\data\\NormalExplicit.xls");
|
| 33 |
|
|
| 34 |
private static URI source = |
|
| 35 |
URI.create("file:/C:/localCopy/meetings_workshops/2011_G�ttingen/GermanSL12/GermanSL.xls");
|
|
| 33 |
|
|
| 34 |
private static URI source = |
|
| 35 |
// URI.create("file:/C:/localCopy/meetings_workshops/2011_G�ttingen/GermanSL12/GermanSL.xls");
|
|
| 36 |
URI.create("/home/pkelbert/Documents/Proibiosphere/Presentations/Demo/Excel/Cichorium_simple.xls");
|
|
| 36 | 37 |
|
| 37 | 38 |
private static DbSchemaValidation dbSchemaValidation = DbSchemaValidation.CREATE; |
| 38 |
|
|
| 39 |
|
|
| 39 | 40 |
// private static final ICdmDataSource destinationDb = CdmDestinations.cdm_test_jaxb(); |
| 40 |
private static final ICdmDataSource destinationDb = CdmDestinations.cdm_test_local_mysql();
|
|
| 41 |
|
|
| 41 |
private static final ICdmDataSource destinationDb = CdmDestinations.mon_cdm();
|
|
| 42 |
|
|
| 42 | 43 |
public static void main(String[] args) {
|
| 43 | 44 |
|
| 44 | 45 |
NomenclaturalCode code = NomenclaturalCode.ICNAFP; |
| 45 | 46 |
URI uri = source; |
| 46 |
NormalExplicitImportConfigurator normalExplicitImportConfigurator =
|
|
| 47 |
NormalExplicitImportConfigurator normalExplicitImportConfigurator = |
|
| 47 | 48 |
NormalExplicitImportConfigurator.NewInstance(uri, destinationDb, code,dbSchemaValidation); |
| 48 | 49 |
|
| 49 |
CdmDefaultImport<NormalExplicitImportConfigurator> normalExplicitImport =
|
|
| 50 |
CdmDefaultImport<NormalExplicitImportConfigurator> normalExplicitImport = |
|
| 50 | 51 |
new CdmDefaultImport<NormalExplicitImportConfigurator>(); |
| 51 | 52 |
|
| 52 | 53 |
// invoke import |
| 53 | 54 |
logger.debug("Invoking Normal Explicit Excel import");
|
| 54 | 55 |
normalExplicitImport.invoke(normalExplicitImportConfigurator); |
| 55 |
|
|
| 56 |
|
|
| 56 | 57 |
} |
| 57 | 58 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/app/proibiosphere/SpecimenImportActivator.java | ||
|---|---|---|
| 30 | 30 |
|
| 31 | 31 |
//database validation status (create, update, validate ...) |
| 32 | 32 |
static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE; |
| 33 |
final static String excelSource = "/home/pkelbert/Documents/Proibiosphere/ChenopodiumQuentin/dca_UK_records.xls";
|
|
| 34 |
// final static String excelSource = "/home/pkelbert/Documents/Proibiosphere/ChenopodiumQuentin/dca_UK_specimens.xls"; |
|
| 33 |
final static String excelSource = "/home/pkelbert/Documents/Proibiosphere/ChenopodiumQuentin/dca_UK_records.xls"; |
|
| 34 |
// final static String excelSource = "/home/pkelbert/Documents/Proibiosphere/ChenopodiumQuentin/dca_UK_specimens.xls";
|
|
| 35 | 35 |
|
| 36 | 36 |
// final static String xmlSource = "C:\\localCopy\\eclipse\\cdmlib\\app-import\\src\\main\\resources\\specimenABCD\\CDMtabular9c04a474e2_23_09_08.xls"; |
| 37 | 37 |
|
| 38 | 38 |
|
| 39 | 39 |
|
| 40 |
static final ICdmDataSource cdmDestination = CdmDestinations.proibiosphere_local(); |
|
| 40 |
static final ICdmDataSource cdmDestination = CdmDestinations.proibiosphere_chenopodium_local();
|
|
| 41 | 41 |
//check - import |
| 42 | 42 |
static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK; |
| 43 | 43 |
|
| ... | ... | |
| 68 | 68 |
// specimenImportConfigurator.setDoCreateIndividualsAssociations(true); |
| 69 | 69 |
|
| 70 | 70 |
Reference<?> ref = ReferenceFactory.newBook(); |
| 71 |
ref.setUuid(UUID.fromString("98b0a618-a95b-464e-943a-25aaaef202f6"));//observations
|
|
| 72 |
ref.setTitle("Chenopodium vulvaria observations from the British Isles");
|
|
| 71 |
ref.setUuid(UUID.fromString("98b0a618-a95b-464e-943a-25aaaef202f6"));//observations
|
|
| 72 |
ref.setTitle("Chenopodium vulvaria observations from the British Isles");
|
|
| 73 | 73 |
// |
| 74 |
// ref.setUuid(UUID.fromString("5480eed1-1a23-4ce8-ac4d-c2893e178dea"));//specimens
|
|
| 75 |
// ref.setTitle("Chenopodium vulvaria specimens from the British Isles");
|
|
| 74 |
// ref.setUuid(UUID.fromString("5480eed1-1a23-4ce8-ac4d-c2893e178dea"));//specimens
|
|
| 75 |
// ref.setTitle("Chenopodium vulvaria specimens from the British Isles");
|
|
| 76 | 76 |
|
| 77 | 77 |
specimenImportConfigurator.setDataReference(ref); |
| 78 | 78 |
specimenImportConfigurator.setSourceReference(null); |
| app-import/src/main/java/eu/etaxonomy/cdm/app/proibiosphere/SynthesysCacheActivator.java | ||
|---|---|---|
| 39 | 39 |
|
| 40 | 40 |
//database validation status (create, update, validate ...) |
| 41 | 41 |
|
| 42 |
// final static String xmlSource = "/home/pkelbert/workspace/proibiosphere/cdmlib-io/target/test-classes/eu/etaxonomy/cdm/io/specimen/excel/in/ExcelImportConfiguratorTest-input.xls"; |
|
| 42 |
// final static String xmlSource = "/home/pkelbert/workspace/proibiosphere/cdmlib-io/target/test-classes/eu/etaxonomy/cdm/io/specimen/excel/in/ExcelImportConfiguratorTest-input.xls";
|
|
| 43 | 43 |
final static String xmlSource = "/home/pkelbert/Documents/Proibiosphere/ChenopodiumQuentin/dca UK records.xls"; |
| 44 | 44 |
|
| 45 | 45 |
|
| 46 | 46 |
static final ICdmDataSource cdmDestination = CdmDestinations.mon_cdm(); |
| 47 | 47 |
static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE; |
| 48 |
// static final ICdmDataSource cdmDestination = CdmDestinations.proibiosphere_local(); |
|
| 49 |
// static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE; |
|
| 48 |
// static final ICdmDataSource cdmDestination = CdmDestinations.proibiosphere_local();
|
|
| 49 |
// static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;
|
|
| 50 | 50 |
static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK; |
| 51 | 51 |
|
| 52 | 52 |
/** |
| ... | ... | |
| 70 | 70 |
specimenImportConfigurator.setReUseExistingMetadata(true); |
| 71 | 71 |
specimenImportConfigurator.setAskForDate(true); |
| 72 | 72 |
specimenImportConfigurator.setDefaultAuthor("L.");
|
| 73 |
// specimenImportConfigurator.setClassificationName("Chenopodium");
|
|
| 73 |
// specimenImportConfigurator.setClassificationName("Chenopodium");
|
|
| 74 | 74 |
|
| 75 | 75 |
specimenImportConfigurator.setReUseTaxon(true); |
| 76 | 76 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/proibiosphere/TaxonXImportLauncher.java | ||
|---|---|---|
| 53 | 53 |
// private static final Logger log = Logger.getLogger(CdmEntityDaoBase.class); |
| 54 | 54 |
|
| 55 | 55 |
//database validation status (create, update, validate ...) |
| 56 |
static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;
|
|
| 57 |
static final ICdmDataSource cdmDestination = CdmDestinations.proibiosphere_local();
|
|
| 56 |
static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
|
|
| 57 |
static final ICdmDataSource cdmDestination = CdmDestinations.mon_cdm();
|
|
| 58 | 58 |
|
| 59 | 59 |
static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK; |
| 60 | 60 |
|
| 61 | 61 |
|
| 62 |
static String plaziUrl = "http://plazi.cs.umb.edu/GgServer/search?taxonomicName.isNomenclature=true&taxonomicName.exactMatch=true&indexName=0&subIndexName=taxonomicName&subIndexName=MODS&minSubResultSize=1&searchMode=index&resultFormat=xml&xsltUrl=http%3A%2F%2Fplazi.cs.umb.edu%2FGgServer%2Fresources%2FsrsWebPortalData%2FCdmSyncTreatmentList.xslt&taxonomicName.taxonomicName="; |
|
| 63 |
static String plaziUrlDoc = "http://plazi.cs.umb.edu/GgServer/search?taxonomicName.isNomenclature=true&taxonomicName.exactMatch=true&indexName=0&subIndexName=taxonomicName&subIndexName=MODS&minSubResultSize=1&searchMode=index&resultFormat=xml&xsltUrl=http%3A%2F%2Fplazi.cs.umb.edu%2FGgServer%2Fresources%2FsrsWebPortalData%2FCdmSyncTreatmentList.xslt&MODS.ModsDocID="; |
|
| 64 |
|
|
| 65 |
|
|
| 62 | 66 |
private static String askQuestion(String question){
|
| 63 | 67 |
Scanner scan = new Scanner(System.in); |
| 64 | 68 |
System.out.println(question); |
| ... | ... | |
| 67 | 71 |
} |
| 68 | 72 |
|
| 69 | 73 |
public static void main(String[] args) {
|
| 74 |
String[] taxonList = new String[] {"Polybothrus","Eupolybothrus"};
|
|
| 75 |
// /*ants*/ String[] modsList = new String[] {"3924", "3743", "4375","6757","6752","3481","21401_fisher_smith_plos_2008","2592","4096","6877","6192","8071"};
|
|
| 76 |
// String[] modsList = new String[] {"FloNuttDuWin1838"};
|
|
| 77 |
// modsList = new String[] {"Zapparoli-1986-Eupolybothrus-fasciatus"};
|
|
| 78 |
String tnomenclature = "ICZN"; |
|
| 70 | 79 |
|
| 71 |
String plaziUrl = "http://plazi.cs.umb.edu/GgServer/search?taxonomicName.isNomenclature=true&taxonomicName.exactMatch=true&indexName=0&subIndexName=taxonomicName&subIndexName=MODS&minSubResultSize=1&searchMode=index&resultFormat=xml&xsltUrl=http%3A%2F%2Fplazi.cs.umb.edu%2FGgServer%2FsrsWebPortalData%2FCdmSyncTreatmentList.xslt&taxonomicName.taxonomicName="; |
|
| 72 |
String plaziUrlDoc = "http://plazi.cs.umb.edu/GgServer/search?taxonomicName.isNomenclature=true&taxonomicName.exactMatch=true&indexName=0&subIndexName=taxonomicName&subIndexName=MODS&minSubResultSize=1&searchMode=index&resultFormat=xml&xsltUrl=http%3A%2F%2Fplazi.cs.umb.edu%2FGgServer%2FsrsWebPortalData%2FCdmSyncTreatmentList.xslt&MODS.ModsDocID="; |
|
| 73 |
// String plaziUrl = "http://plazi.cs.umb.edu/GgServer/xslt/E01DD5BE427421156E0C0BAC56389E0D?xsltUrl=http%3A%2F%2Fplazi.cs.umb.edu%2FGgServer%2FsrsWebPortalData%2FLinkers%2FXmlDocumentLinkerData%2Fgg2taxonx.xsl"; |
|
| 74 |
List<String> sourcesStr = new ArrayList<String>(); |
|
| 75 |
boolean plaziNotServer=false; |
|
| 80 |
String defaultClassif="Eupolybothrus and Polybothrus"; |
|
| 76 | 81 |
|
| 77 | 82 |
Map<String,List<String>> documents = new HashMap<String,List<String>>(); |
| 78 |
// plaziUrl=plaziUrl+"Chenopodium"; |
|
| 79 |
plaziUrl=plaziUrlDoc+"0910-2878-5652"; |
|
| 83 |
HashMap<String,List<URI>>documentMap = new HashMap<String, List<URI>>(); |
|
| 80 | 84 |
|
| 81 | 85 |
/*HOW TO HANDLE SECUNDUM REFERENCE*/ |
| 82 | 86 |
boolean reuseSecundum = askIfReuseSecundum(); |
| ... | ... | |
| 85 | 89 |
secundum = askForSecundum(); |
| 86 | 90 |
} |
| 87 | 91 |
|
| 88 |
String tnomenclature = "ICBN"; |
|
| 92 |
checkTreatmentPresence("taxon",taxonList, documents,documentMap);
|
|
| 93 |
// checkTreatmentPresence("modsid",modsList, documents,documentMap);
|
|
| 94 |
|
|
| 95 |
TaxonXImportConfigurator taxonxImportConfigurator =null; |
|
| 96 |
CdmDefaultImport<TaxonXImportConfigurator> taxonImport = new CdmDefaultImport<TaxonXImportConfigurator>(); |
|
| 97 |
|
|
| 98 |
ICdmDataSource destination = cdmDestination; |
|
| 99 |
taxonxImportConfigurator = prepareTaxonXImport(destination,reuseSecundum, secundum); |
|
| 100 |
|
|
| 101 |
taxonxImportConfigurator.setImportClassificationName(defaultClassif); |
|
| 102 |
log.info("Start import from TaxonX Data");
|
|
| 103 |
|
|
| 104 |
taxonxImportConfigurator.setLastImport(false); |
|
| 105 |
|
|
| 106 |
int j=0; |
|
| 107 |
for (String document:documentMap.keySet()){
|
|
| 108 |
j++; |
|
| 109 |
if (doImportDocument(document, documentMap.get(document).size())){
|
|
| 110 |
int i=0; |
|
| 111 |
for (URI source:documentMap.get(document)){
|
|
| 112 |
System.out.println("START "+i+" ("+(documentMap.get(document)).size()+"): "+source.getPath());
|
|
| 113 |
i++; |
|
| 114 |
if (j==documentMap.keySet().size() && i==documentMap.get(document).size()) {
|
|
| 115 |
taxonxImportConfigurator.setLastImport(true); |
|
| 116 |
} |
|
| 117 |
prepareReferenceAndSource(taxonxImportConfigurator,source); |
|
| 118 |
prepareNomenclature(taxonxImportConfigurator,tnomenclature); |
|
| 119 |
// taxonxImportConfigurator.setTaxonReference(null); |
|
| 120 |
taxonImport.invoke(taxonxImportConfigurator); |
|
| 121 |
log.info("End import from SpecimenData ("+ source.toString() + ")...");
|
|
| 122 |
|
|
| 123 |
// //deduplicate |
|
| 124 |
// ICdmApplicationConfiguration app = taxonImport.getCdmAppController(); |
|
| 125 |
// int count = app.getAgentService().deduplicate(Person.class, null, null); |
|
| 126 |
// logger.warn("Deduplicated " + count + " persons.");
|
|
| 127 |
// count = app.getReferenceService().deduplicate(Reference.class, null, null); |
|
| 128 |
// logger.warn("Deduplicated " + count + " references.");
|
|
| 129 |
} |
|
| 130 |
} |
|
| 131 |
} |
|
| 132 |
} |
|
| 133 |
|
|
| 134 |
|
|
| 135 |
|
|
| 136 |
/** |
|
| 137 |
* @param taxonxImportConfigurator |
|
| 138 |
* @param tnomenclature |
|
| 139 |
*/ |
|
| 140 |
private static void prepareNomenclature(TaxonXImportConfigurator taxonxImportConfigurator, String tnomenclature) {
|
|
| 141 |
// String tnomenclature = askQuestion("ICBN or ICZN ?");
|
|
| 142 |
taxonxImportConfigurator.setNomenclaturalCode(NomenclaturalCode.ICNAFP); |
|
| 143 |
if (tnomenclature.equalsIgnoreCase("ICBN")) {
|
|
| 144 |
taxonxImportConfigurator.setNomenclaturalCode(NomenclaturalCode.ICNAFP); |
|
| 145 |
// taxonxImportConfigurator.setClassificationName("Chenopodiaceae");
|
|
| 146 |
} |
|
| 147 |
if(tnomenclature.equalsIgnoreCase("ICZN")){
|
|
| 148 |
taxonxImportConfigurator.setNomenclaturalCode(NomenclaturalCode.ICZN); |
|
| 149 |
// taxonxImportConfigurator.setClassificationName("Ants");
|
|
| 150 |
} |
|
| 151 |
if(tnomenclature.equalsIgnoreCase("ICNB")){
|
|
| 152 |
taxonxImportConfigurator.setNomenclaturalCode(NomenclaturalCode.ICNB); |
|
| 153 |
// taxonxImportConfigurator.setClassificationName("Bacteria");
|
|
| 154 |
} |
|
| 155 |
|
|
| 156 |
} |
|
| 157 |
|
|
| 158 |
/** |
|
| 159 |
* @param taxonxImportConfigurator |
|
| 160 |
* @param source |
|
| 161 |
* |
|
| 162 |
*/ |
|
| 163 |
private static void prepareReferenceAndSource(TaxonXImportConfigurator taxonxImportConfigurator, URI source) {
|
|
| 164 |
Reference<?> reference = ReferenceFactory.newGeneric(); |
|
| 165 |
// String tref = askQuestion("Import source? (ie Plazi document ID)");
|
|
| 166 |
String tref="PLAZI - "+source.getPath().split("/")[source.getPath().split("/").length-1];
|
|
| 167 |
reference.setTitleCache(tref,true); |
|
| 168 |
reference.setTitle(tref); |
|
| 169 |
reference.generateTitle(); |
|
| 170 |
|
|
| 171 |
taxonxImportConfigurator.setSourceReference(reference); |
|
| 172 |
TaxonXImportConfigurator.setSourceRef(reference); |
|
| 173 |
|
|
| 174 |
Reference<?> referenceUrl = ReferenceFactory.newWebPage(); |
|
| 175 |
referenceUrl.setTitleCache(source.toString(), true); |
|
| 176 |
referenceUrl.setTitle(source.toString()); |
|
| 177 |
reference.setUri(source); |
|
| 178 |
referenceUrl.generateTitle(); |
|
| 179 |
|
|
| 180 |
taxonxImportConfigurator.addOriginalSource(referenceUrl); |
|
| 181 |
taxonxImportConfigurator.setSource(source); |
|
| 182 |
} |
|
| 183 |
|
|
| 184 |
/** |
|
| 185 |
* @param destination |
|
| 186 |
* @param reuseSecundum |
|
| 187 |
* @param secundum |
|
| 188 |
* @return |
|
| 189 |
*/ |
|
| 190 |
private static TaxonXImportConfigurator prepareTaxonXImport(ICdmDataSource destination, boolean reuseSecundum, Reference<?> secundum) {
|
|
| 191 |
TaxonXImportConfigurator taxonxImportConfigurator = TaxonXImportConfigurator.NewInstance(destination); |
|
| 192 |
|
|
| 193 |
// taxonxImportConfigurator.setClassificationName(taxonxImportConfigurator.getSourceReferenceTitle()); |
|
| 194 |
taxonxImportConfigurator.setCheck(check); |
|
| 195 |
taxonxImportConfigurator.setDbSchemaValidation(hbm2dll); |
|
| 196 |
taxonxImportConfigurator.setDoAutomaticParsing(true); |
|
| 197 |
|
|
| 198 |
taxonxImportConfigurator.setInteractWithUser(true); |
|
| 199 |
|
|
| 200 |
|
|
| 201 |
taxonxImportConfigurator.setKeepOriginalSecundum(reuseSecundum); |
|
| 202 |
if (!reuseSecundum) {
|
|
| 203 |
taxonxImportConfigurator.setSecundum(secundum); |
|
| 204 |
} |
|
| 205 |
|
|
| 206 |
// taxonxImportConfigurator.setDoMatchTaxa(true); |
|
| 207 |
// taxonxImportConfigurator.setReUseTaxon(true); |
|
| 208 |
return taxonxImportConfigurator; |
|
| 209 |
} |
|
| 210 |
|
|
| 211 |
/** |
|
| 212 |
* @param importFilter |
|
| 213 |
* @param modsList |
|
| 214 |
* @param documents |
|
| 215 |
* @param documentMap |
|
| 216 |
* @return |
|
| 217 |
*/ |
|
| 218 |
private static HashMap<String, List<URI>> checkTreatmentPresence(String importFilter, String[] modsList, Map<String, List<String>> documents, HashMap<String, List<URI>> documentMap) {
|
|
| 89 | 219 |
URL plaziURL; |
| 90 |
try {
|
|
| 91 |
plaziURL = new URL(plaziUrl); |
|
| 92 |
BufferedReader in = new BufferedReader(new InputStreamReader(plaziURL.openStream())); |
|
| 220 |
// System.out.println(plaziUrl); |
|
| 93 | 221 |
|
| 222 |
Map<String, List<String>> docs = new HashMap<String, List<String>>(); |
|
| 223 |
try {
|
|
| 224 |
BufferedReader in=null; |
|
| 94 | 225 |
List<String> docList; |
| 95 | 226 |
String inputLine; |
| 96 | 227 |
String docID; |
| ... | ... | |
| 98 | 229 |
String pageEnd; |
| 99 | 230 |
String taxon; |
| 100 | 231 |
String link; |
| 101 |
//TODO lastUpdate field |
|
| 102 |
if(!plaziNotServer){
|
|
| 232 |
String urlstr=""; |
|
| 233 |
|
|
| 234 |
for(String modsID : modsList){
|
|
| 235 |
// plaziUrl=plaziUrl+"Eupolybothrus"; |
|
| 236 |
if (importFilter.equalsIgnoreCase("modsid")) {
|
|
| 237 |
urlstr=plaziUrlDoc+modsID; |
|
| 238 |
} |
|
| 239 |
if (importFilter.equalsIgnoreCase("taxon")) {
|
|
| 240 |
urlstr=plaziUrl+modsID; |
|
| 241 |
} |
|
| 242 |
// System.out.println(url); |
|
| 243 |
|
|
| 244 |
plaziURL = new URL(urlstr); |
|
| 245 |
in = new BufferedReader(new InputStreamReader(plaziURL.openStream())); |
|
| 246 |
|
|
| 247 |
|
|
| 248 |
//TODO lastUpdate field |
|
| 249 |
// if(!plaziNotServer){
|
|
| 103 | 250 |
while ((inputLine = in.readLine()) != null) {
|
| 251 |
System.out.println(inputLine); |
|
| 104 | 252 |
if (inputLine.startsWith("<treatment ")){
|
| 105 | 253 |
taxon = inputLine.split("taxon=\"")[1].split("\"")[0];
|
| 106 | 254 |
docID=inputLine.split("docId=\"")[1].split("\"")[0];
|
| 255 |
System.out.println("docID: "+docID);
|
|
| 107 | 256 |
link=inputLine.split("link=\"")[1].split("\"")[0];
|
| 108 | 257 |
pageStart = inputLine.split("startPage=\"")[1].split("\"")[0];
|
| 109 | 258 |
pageEnd = inputLine.split("endPage=\"")[1].split("\"")[0];
|
| ... | ... | |
| 116 | 265 |
} |
| 117 | 266 |
} |
| 118 | 267 |
} |
| 268 |
System.out.println("hop");
|
|
| 269 |
|
|
| 270 |
|
|
| 271 |
|
|
| 119 | 272 |
for (String docId:documents.keySet()){
|
| 120 | 273 |
in = new BufferedReader(new InputStreamReader(new URL(plaziUrlDoc+docId).openStream())); |
| 121 | 274 |
while ((inputLine = in.readLine()) != null) {
|
| ... | ... | |
| 130 | 283 |
docList = new ArrayList<String>(); |
| 131 | 284 |
} |
| 132 | 285 |
docList.add(pageStart+"---"+pageEnd+"---"+taxon+"---"+link); |
| 133 |
documents.put(docID,docList);
|
|
| 286 |
docs.put(docID,docList); |
|
| 134 | 287 |
} |
| 135 | 288 |
} |
| 136 | 289 |
} |
| 137 |
if(plaziNotServer) {
|
|
| 138 |
sourcesStr.add(plaziUrl); |
|
| 139 |
} |
|
| 140 |
in.close(); |
|
| 290 |
// if(plaziNotServer) {
|
|
| 291 |
// sourcesStr.add(plaziUrl);
|
|
| 292 |
// }
|
|
| 293 |
// in.close();
|
|
| 141 | 294 |
} catch (MalformedURLException e1) {
|
| 142 | 295 |
// TODO Auto-generated catch block |
| 143 | 296 |
e1.printStackTrace(); |
| ... | ... | |
| 150 | 303 |
|
| 151 | 304 |
// sourcesStr.add("/home/pkelbert/Documents/Proibiosphere/ChenopodiumXML/1362148061170_Chenopodium_K_hn_U_1993_tx.xml");
|
| 152 | 305 |
|
| 153 |
for (String docId : documents.keySet()){
|
|
| 154 |
/*remove documents bad quality*/ |
|
| 155 |
log.info(docId); |
|
| 156 |
// if (!docId.equalsIgnoreCase("3891-7797-6564")){
|
|
| 157 |
log.info("document "+docId);
|
|
| 158 |
List<String> treatments = new ArrayList<String>(new HashSet<String>(documents.get(docId))); |
|
| 159 |
|
|
| 160 |
Map<Integer, List<String>> startPages = new HashMap<Integer, List<String>>(); |
|
| 161 |
for (String treatment:treatments) {
|
|
| 162 |
List<String>tmplist = startPages.get(Integer.valueOf(treatment.split("---")[0]));
|
|
| 163 |
if (tmplist == null) {
|
|
| 164 |
tmplist = new ArrayList<String>(); |
|
| 165 |
} |
|
| 166 |
tmplist.add(treatment.split("---")[3]);
|
|
| 167 |
startPages.put(Integer.valueOf(treatment.split("---")[0]),tmplist);
|
|
| 306 |
//System.out.println(documents); |
|
| 307 |
for (String docId : docs.keySet()){
|
|
| 308 |
List<String> treatments = new ArrayList<String>(new HashSet<String>(docs.get(docId))); |
|
| 309 |
|
|
| 310 |
Map<Integer, List<String>> startPages = new HashMap<Integer, List<String>>(); |
|
| 311 |
for (String treatment:treatments) {
|
|
| 312 |
List<String>tmplist = startPages.get(Integer.valueOf(treatment.split("---")[0]));
|
|
| 313 |
if (tmplist == null) {
|
|
| 314 |
tmplist = new ArrayList<String>(); |
|
| 168 | 315 |
} |
| 169 |
List<Integer> pages = new ArrayList<Integer>(); |
|
| 170 |
pages.addAll(startPages.keySet()); |
|
| 171 |
|
|
| 172 |
Collections.sort(pages); |
|
| 173 |
// log.info(pages); |
|
| 174 |
|
|
| 175 |
log.info("Document "+docId+" should have "+treatments.size()+" treatments");
|
|
| 176 |
int cnt=0; |
|
| 177 |
for (String source:treatments){
|
|
| 178 |
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); |
|
| 179 |
DocumentBuilder builder; |
|
| 180 |
URL url; |
|
| 181 |
|
|
| 182 |
try {
|
|
| 183 |
builder = factory.newDocumentBuilder(); |
|
| 184 |
url = new URL(source.split("---")[3]);
|
|
| 185 |
Object o = url.getContent(); |
|
| 186 |
InputStream is = (InputStream) o; |
|
| 187 |
Document document = builder.parse(is); |
|
| 188 |
cnt++; |
|
| 189 |
}catch(Exception e){
|
|
| 190 |
// e.printStackTrace(); |
|
| 191 |
log.warn(e); |
|
| 192 |
} |
|
| 316 |
tmplist.add(treatment.split("---")[3]);
|
|
| 317 |
startPages.put(Integer.valueOf(treatment.split("---")[0]),tmplist);
|
|
| 318 |
} |
|
| 319 |
List<Integer> pages = new ArrayList<Integer>(); |
|
| 320 |
pages.addAll(startPages.keySet()); |
|
| 321 |
|
|
| 322 |
Collections.sort(pages); |
|
| 323 |
// log.info(pages); |
|
| 324 |
|
|
| 325 |
log.info("Document "+docId+" should have "+treatments.size()+" treatments");
|
|
| 326 |
int cnt=0; |
|
| 327 |
if(treatments.size()<150){
|
|
| 328 |
|
|
| 329 |
for (String source:treatments){
|
|
| 330 |
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); |
|
| 331 |
DocumentBuilder builder; |
|
| 332 |
URL url; |
|
| 333 |
|
|
| 334 |
try {
|
|
| 335 |
builder = factory.newDocumentBuilder(); |
|
| 336 |
url = new URL(source.split("---")[3]);
|
|
| 337 |
Object o = url.getContent(); |
|
| 338 |
InputStream is = (InputStream) o; |
|
| 339 |
Document document = builder.parse(is); |
|
| 340 |
cnt++; |
|
| 341 |
}catch(Exception e){
|
|
| 342 |
// e.printStackTrace(); |
|
| 343 |
log.warn(e); |
|
| 344 |
} |
|
| 345 |
} |
|
| 346 |
log.info("Document "+docId+" has "+cnt+" treatments available");
|
|
| 347 |
} |
|
| 348 |
if(treatments.size() != cnt) |
|
| 349 |
{
|
|
| 350 |
File file = new File("/home/pkelbert/Bureau/urlTaxonXToDoLater.txt");
|
|
| 351 |
FileWriter writer; |
|
| 352 |
try {
|
|
| 353 |
writer = new FileWriter(file ,true); |
|
| 354 |
writer.write(docId+"\n"); |
|
| 355 |
writer.flush(); |
|
| 356 |
writer.close(); |
|
| 357 |
} catch (IOException e1) {
|
|
| 358 |
// TODO Auto-generated catch block |
|
| 359 |
e1.printStackTrace(); |
|
| 193 | 360 |
} |
| 194 |
log.info("Document "+docId+" has "+cnt+" treatments available");
|
|
| 195 |
if(treatments.size() != cnt) |
|
| 196 |
{
|
|
| 197 |
File file = new File("/home/pkelbert/Bureau/urlTaxonXToDoLater.txt");
|
|
| 198 |
FileWriter writer; |
|
| 199 |
try {
|
|
| 200 |
writer = new FileWriter(file ,true); |
|
| 201 |
writer.write(docId+"\n"); |
|
| 202 |
writer.flush(); |
|
| 203 |
writer.close(); |
|
| 204 |
} catch (IOException e1) {
|
|
| 205 |
// TODO Auto-generated catch block |
|
| 206 |
e1.printStackTrace(); |
|
| 207 |
} |
|
| 208 | 361 |
|
| 362 |
} |
|
| 363 |
else{
|
|
| 364 |
List<URI> uritmp = documentMap.get(docId); |
|
| 365 |
if (uritmp == null) {
|
|
| 366 |
uritmp = new ArrayList<URI>(); |
|
| 209 | 367 |
} |
| 210 |
else{
|
|
| 211 |
for (int page:pages) {
|
|
| 212 |
for (String treatment: startPages.get(page)) {
|
|
| 213 |
sourcesStr.add(treatment); |
|
| 368 |
for (int page:pages) {
|
|
| 369 |
for (String treatment: startPages.get(page)) {
|
|
| 370 |
try {
|
|
| 371 |
uritmp.add(new URL(treatment).toURI()); |
|
| 372 |
} catch (MalformedURLException e) {
|
|
| 373 |
// TODO Auto-generated catch block |
|
| 374 |
e.printStackTrace(); |
|
| 375 |
} catch (URISyntaxException e) {
|
|
| 376 |
// TODO Auto-generated catch block |
|
| 377 |
e.printStackTrace(); |
|
| 214 | 378 |
} |
| 215 | 379 |
} |
| 216 | 380 |
} |
| 217 |
// } |
|
| 218 |
} |
|
| 219 |
log.info("NB SOURCES : "+sourcesStr.size());
|
|
| 220 |
// sourcesStr = new ArrayList<String>(); |
|
| 221 |
// sourcesStr.add("http://plazi.cs.umb.edu/exist/rest/db/taxonx_docs/cdmSync/4E7390346C05780D32283CCF6F5E4431_tx.xml");
|
|
| 222 |
|
|
| 223 |
List<URI> sources = new ArrayList<URI>(); |
|
| 224 |
for (String src: sourcesStr){
|
|
| 225 |
URI uri; |
|
| 226 |
try {
|
|
| 227 |
uri = new URL(src).toURI(); |
|
| 228 |
sources.add(new URI(uri.toString())); |
|
| 229 |
} catch (MalformedURLException e1) {
|
|
| 230 |
// TODO Auto-generated catch block |
|
| 231 |
e1.printStackTrace(); |
|
| 232 |
} catch (URISyntaxException e1) {
|
|
| 233 |
// TODO Auto-generated catch block |
|
| 234 |
e1.printStackTrace(); |
|
| 381 |
documentMap.put(docId, uritmp); |
|
| 235 | 382 |
} |
| 236 |
} |
|
| 237 | 383 |
|
| 238 |
log.info("Start import from TaxonX Data");
|
|
| 239 | 384 |
|
| 240 |
ICdmDataSource destination = cdmDestination; |
|
| 241 |
TaxonXImportConfigurator taxonxImportConfigurator = TaxonXImportConfigurator.NewInstance(destination); |
|
| 242 |
|
|
| 243 |
// taxonxImportConfigurator.setClassificationName(taxonxImportConfigurator.getSourceReferenceTitle()); |
|
| 244 |
taxonxImportConfigurator.setCheck(check); |
|
| 245 |
taxonxImportConfigurator.setDbSchemaValidation(hbm2dll); |
|
| 246 |
taxonxImportConfigurator.setDoAutomaticParsing(true); |
|
| 247 | 385 |
|
| 248 |
// invoke import |
|
| 249 |
CdmDefaultImport<TaxonXImportConfigurator> taxonImport = new CdmDefaultImport<TaxonXImportConfigurator>(); |
|
| 250 | 386 |
|
| 251 |
taxonxImportConfigurator.setKeepOriginalSecundum(reuseSecundum); |
|
| 252 |
if (!reuseSecundum) {
|
|
| 253 |
taxonxImportConfigurator.setSecundum(secundum); |
|
| 254 | 387 |
} |
| 388 |
////// log.info("NB SOURCES : "+sourcesStr.size());
|
|
| 389 |
// List<URI> sourcesStr = new ArrayList<URI>(); |
|
| 390 |
// try {
|
|
| 391 |
//// documentMap = new HashMap<String, List<URI>>(); |
|
| 392 |
// sourcesStr.add(new URI("http://plazi.cs.umb.edu/GgServer/cdmSync/8F5B3EA099D371BC41CC5DDBFEDCFBED"));
|
|
| 393 |
// documentMap.put("singlesource", sourcesStr);
|
|
| 394 |
// } catch (URISyntaxException e) {
|
|
| 395 |
// // TODO Auto-generated catch block |
|
| 396 |
// e.printStackTrace(); |
|
| 397 |
// } |
|
| 398 |
|
|
| 399 |
return documentMap; |
|
| 255 | 400 |
|
| 401 |
} |
|
| 256 | 402 |
|
| 257 |
// taxonxImportConfigurator.setDoMatchTaxa(true); |
|
| 258 |
// taxonxImportConfigurator.setReUseTaxon(true); |
|
| 259 |
|
|
| 260 |
for (URI source:sources){
|
|
| 261 |
log.info("START : "+source.getPath());
|
|
| 262 |
taxonxImportConfigurator.setSource(source); |
|
| 263 |
|
|
| 264 |
Reference<?> reference = ReferenceFactory.newGeneric(); |
|
| 265 |
// String tref = askQuestion("Import source? (ie Plazi document ID)");
|
|
| 266 |
String tref="PLAZI - "+source.getPath().split("/")[source.getPath().split("/").length-1];
|
|
| 267 |
reference.setTitleCache(tref,true); |
|
| 268 |
reference.setTitle(tref); |
|
| 269 |
reference.generateTitle(); |
|
| 270 |
|
|
| 271 |
taxonxImportConfigurator.setSourceReference(reference); |
|
| 272 |
taxonxImportConfigurator.setSourceRef(reference); |
|
| 273 |
|
|
| 274 |
// String tnomenclature = askQuestion("ICBN or ICZN ?");
|
|
| 275 |
|
|
| 276 |
if (tnomenclature.equalsIgnoreCase("ICBN")) {
|
|
| 277 |
taxonxImportConfigurator.setNomenclaturalCode(NomenclaturalCode.ICNAFP); |
|
| 278 |
// taxonxImportConfigurator.setClassificationName("Chenopodiaceae");
|
|
| 279 |
} |
|
| 280 |
if(tnomenclature.equalsIgnoreCase("ICZN")){
|
|
| 281 |
taxonxImportConfigurator.setNomenclaturalCode(NomenclaturalCode.ICZN); |
|
| 282 |
// taxonxImportConfigurator.setClassificationName("Ants");
|
|
| 283 |
} |
|
| 284 |
|
|
| 285 |
// taxonxImportConfigurator.setTaxonReference(null); |
|
| 286 |
|
|
| 287 |
// log.info("INVOKE");
|
|
| 288 |
|
|
| 289 |
taxonImport.invoke(taxonxImportConfigurator); |
|
| 290 |
log.info("End import from SpecimenData ("+ source.toString() + ")...");
|
|
| 291 |
|
|
| 292 |
// //deduplicate |
|
| 293 |
// ICdmApplicationConfiguration app = taxonImport.getCdmAppController(); |
|
| 294 |
// int count = app.getAgentService().deduplicate(Person.class, null, null); |
|
| 295 |
// logger.warn("Deduplicated " + count + " persons.");
|
|
| 296 |
// count = app.getReferenceService().deduplicate(Reference.class, null, null); |
|
| 297 |
// logger.warn("Deduplicated " + count + " references.");
|
|
| 403 |
/** |
|
| 404 |
* @param document |
|
| 405 |
* @return |
|
| 406 |
*/ |
|
| 407 |
private static boolean doImportDocument(String document, int nbtreatments) {
|
|
| 408 |
return true; |
|
| 409 |
/* |
|
| 410 |
// List<String> docDone = Arrays.asList(new String[]{"3540555099", "0910-2878-5652", "5012-9059-4108",
|
|
| 411 |
// "3784-0748-2261","3-201-00728-5", "FloNuttDuWin1838", "FlNordica_chenop","2580-1363-7530", |
|
| 412 |
// "1842460692","5161-7797-8064","FlCaboVerde_Chen","2819-9661-8339","2626-3794-9273"});//, |
|
| 413 |
// // "8776-7797-8303"}); |
|
| 414 |
// if (docDone.contains(document)) {
|
|
| 415 |
// return false; |
|
| 416 |
// } |
|
| 417 |
|
|
| 418 |
JTextArea textArea = new JTextArea("Should this document be imported ("+nbtreatments+")? \n'"+document+"'");
|
|
| 419 |
JScrollPane scrollPane = new JScrollPane(textArea); |
|
| 420 |
textArea.setLineWrap(true); |
|
| 421 |
textArea.setWrapStyleWord(true); |
|
| 422 |
scrollPane.setPreferredSize( new Dimension( 700, 70 ) ); |
|
| 423 |
|
|
| 424 |
// JFrame frame = new JFrame("I have a question");
|
|
| 425 |
// frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); |
|
| 426 |
int s = JOptionPane.showConfirmDialog(null, scrollPane); |
|
| 427 |
if (s==0) {
|
|
| 428 |
return true; |
|
| 429 |
} else {
|
|
| 430 |
return false; |
|
| 298 | 431 |
} |
| 299 |
|
|
| 300 |
|
|
| 432 |
*/ |
|
| 301 | 433 |
} |
| 302 | 434 |
|
| 303 |
|
|
| 304 |
|
|
| 305 | 435 |
/** |
| 306 | 436 |
* @return |
| 307 | 437 |
*/ |
| 308 | 438 |
private static boolean askIfReuseSecundum() {
|
| 309 |
// logger.info("getFullReference for "+ name);
|
|
| 310 |
JTextArea textArea = new JTextArea("Reuse the secundum present in the current classification? " +
|
|
| 311 |
"\n Click Yes to reuse it, click No or Cancel to create a new one.");
|
|
| 312 |
JScrollPane scrollPane = new JScrollPane(textArea);
|
|
| 313 |
textArea.setLineWrap(true);
|
|
| 314 |
textArea.setWrapStyleWord(true);
|
|
| 315 |
scrollPane.setPreferredSize( new Dimension( 700, 100 ) );
|
|
| 316 |
|
|
| 317 |
// JFrame frame = new JFrame("I have a question");
|
|
| 318 |
// frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
|
|
| 319 |
int s = JOptionPane.showConfirmDialog(null, scrollPane);
|
|
| 320 |
if (s==0) {
|
|
| 439 |
// logger.info("getFullReference for "+ name);
|
|
| 440 |
JTextArea textArea = new JTextArea("Reuse the secundum present in the current classification? " +
|
|
| 441 |
"\n Click Yes to reuse it, click No or Cancel to create a new one.\nA default secundum will be created if needed.");
|
|
| 442 |
JScrollPane scrollPane = new JScrollPane(textArea); |
|
| 443 |
textArea.setLineWrap(true); |
|
| 444 |
textArea.setWrapStyleWord(true); |
|
| 445 |
scrollPane.setPreferredSize( new Dimension( 700, 70 ) );
|
|
| 446 |
|
|
| 447 |
// JFrame frame = new JFrame("I have a question");
|
|
| 448 |
// frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); |
|
| 449 |
int s = JOptionPane.showConfirmDialog(null, scrollPane); |
|
| 450 |
if (s==0) {
|
|
| 321 | 451 |
return true; |
| 322 | 452 |
} else {
|
| 323 | 453 |
return false; |
| ... | ... | |
| 328 | 458 |
* @return |
| 329 | 459 |
*/ |
| 330 | 460 |
private static Reference<?> askForSecundum() {
|
| 331 |
// logger.info("getFullReference for "+ name);
|
|
| 332 |
JTextArea textArea = new JTextArea("Enter the secundum name");
|
|
| 333 |
JScrollPane scrollPane = new JScrollPane(textArea); |
|
| 334 |
textArea.setLineWrap(true); |
|
| 335 |
textArea.setWrapStyleWord(true); |
|
| 336 |
scrollPane.setPreferredSize( new Dimension( 700, 100 ) ); |
|
| 337 |
|
|
| 338 |
// JFrame frame = new JFrame("I have a question");
|
|
| 339 |
// frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); |
|
| 340 |
String s = (String) JOptionPane.showInputDialog( |
|
| 341 |
null, |
|
| 342 |
scrollPane, |
|
| 343 |
"", |
|
| 344 |
JOptionPane.PLAIN_MESSAGE, |
|
| 345 |
null, |
|
| 346 |
null, |
|
| 347 |
null); |
|
| 348 |
Reference<?> ref = ReferenceFactory.newGeneric(); |
|
| 349 |
ref.setTitle(s); |
|
| 350 |
return ref; |
|
| 461 |
// logger.info("getFullReference for "+ name);
|
|
| 462 |
JTextArea textArea = new JTextArea("Enter the secundum name");
|
|
| 463 |
JScrollPane scrollPane = new JScrollPane(textArea); |
|
| 464 |
textArea.setLineWrap(true); |
|
| 465 |
textArea.setWrapStyleWord(true); |
|
| 466 |
scrollPane.setPreferredSize( new Dimension( 700, 100 ) ); |
|
| 467 |
|
|
Also available in: Unified diff
reintegrate cdmlib-apps patricia into trunk