Revision 138715e0
Added by Andreas Müller over 3 years ago
cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/geo/CondensedDistributionRecipe.java | ||
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22 | 22 |
* For reference see: |
23 | 23 |
* <ul> |
24 | 24 |
* <li>{@link http://ww2.bgbm.org/EuroPlusMed/explanations.asp}</li> |
25 |
* <li>{@link http://dev.e-taxonomy.eu/trac/ticket/3907}</li>
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25 |
* <li>{@link https://dev.e-taxonomy.eu/redmine/issues/3907}</li>
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26 | 26 |
* </ul> |
27 | 27 |
*/ |
28 | 28 |
EuroPlusMed(EuroPlusMedCondensedDistributionComposer.class), |
cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/geo/EuroPlusMedCondensedDistributionComposer.java | ||
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48 | 48 |
static { |
49 | 49 |
|
50 | 50 |
// ================================================== |
51 |
// Mapping as defined in ticket http://dev.e-taxonomy.eu/trac/ticket/3907
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51 |
// Mapping as defined in ticket https://dev.e-taxonomy.eu/redmine/issues/3907
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52 | 52 |
// ================================================== |
53 | 53 |
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54 | 54 |
statusSymbols = new HashMap<> (); |
cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/geo/FloraCubaCondensedDistributionComposer.java | ||
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50 | 50 |
static { |
51 | 51 |
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52 | 52 |
// ================================================== |
53 |
// Mapping as defined in ticket http://dev.e-taxonomy.eu/trac/ticket/5682
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53 |
// Mapping as defined in ticket https://dev.e-taxonomy.eu/redmine/issues/5682
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54 | 54 |
// ================================================== |
55 | 55 |
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56 | 56 |
statusSymbols = new HashMap<> (); |
cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/geo/FloraCubaCondensedDistributionComposerOld.java | ||
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50 | 50 |
static { |
51 | 51 |
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52 | 52 |
// ================================================== |
53 |
// Mapping as defined in ticket http://dev.e-taxonomy.eu/trac/ticket/5682
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53 |
// Mapping as defined in ticket https://dev.e-taxonomy.eu/redmine/issues/5682
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54 | 54 |
// ================================================== |
55 | 55 |
|
56 | 56 |
statusSymbols = new HashMap<UUID, String> (); |
cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/geo/GeoServiceArea.java | ||
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38 | 38 |
* that is the combination of GeoServiceType, URL and layer would be a unique key. |
39 | 39 |
* This is however conflicting with the concept of the subAreas which allows to combine multiple |
40 | 40 |
* polygons from different layers. |
41 |
* see also http://dev.e-taxonomy.eu/trac/ticket/4263 |
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41 |
* <BR><BR> |
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42 |
* see also https://dev.e-taxonomy.eu/redmine/issues/4263 |
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42 | 43 |
* |
43 | 44 |
* @author a.mueller |
44 | 45 |
* @since 11.08.2011 |
cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/geo/ShpAttributesToNamedAreaMapper.java | ||
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139 | 139 |
|
140 | 140 |
if(matchIdCode != null){ |
141 | 141 |
//TODO need to clear the area mapping since the mapping impl can not distinguish multiple layers |
142 |
// see http://dev.e-taxonomy.eu/trac/ticket/4263
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142 |
// see https://dev.e-taxonomy.eu/redmine/issues/4263
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143 | 143 |
areaMapping.clear(a); |
144 | 144 |
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145 | 145 |
GeoServiceArea geoServiceArea; |
cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/SpecimenImportBase.java | ||
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546 | 546 |
|
547 | 547 |
/** |
548 | 548 |
* Very fast and dirty implementation to allow handling of transient objects as described in |
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* https://dev.e-taxonomy.eu/trac/ticket/3726
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* https://dev.e-taxonomy.eu/redmine/issues/3726
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550 | 550 |
* |
551 | 551 |
* Not yet complete. |
552 | 552 |
* |
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/ICdmBase.java | ||
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48 | 48 |
* Sets the timestamp this object was created. |
49 | 49 |
* Most databases cannot store milliseconds, so they are removed by this method. |
50 | 50 |
* Caution: We are planning to replace the Calendar class with a different datetime representation which is more suitable for hibernate |
51 |
* see {@link http://dev.e-taxonomy.eu/trac/ticket/247 TRAC ticket}
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* see {@link https://dev.e-taxonomy.eu/redmine/issues/247 TRAC ticket}
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52 | 52 |
* |
53 | 53 |
* @param created |
54 | 54 |
*/ |
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/PresenceAbsenceTerm.java | ||
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59 | 59 |
* naturalized => non invasive - invasive<BR> |
60 | 60 |
* invasive => not harmful - transformers - weeds |
61 | 61 |
* |
62 |
* @see http://dev.e-taxonomy.eu/redmine/issues/6000 |
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62 |
* @see https://dev.e-taxonomy.eu/redmine/issues/6000
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63 | 63 |
* |
64 | 64 |
* @author m.doering |
65 | 65 |
* @since 08-Nov-2007 13:06:44 |
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/Amplification.java | ||
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66 | 66 |
* PCR itself is not persistent we do not store further information on it in the CDM and do not handle |
67 | 67 |
* {@link AmplificationResult} as a {@link DerivedUnit}. |
68 | 68 |
* <BR> |
69 |
* This may change in future: http://dev.e-taxonomy.eu/trac/ticket/3717.
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69 |
* This may change in future: https://dev.e-taxonomy.eu/redmine/issues/3717.
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70 | 70 |
* <BR> |
71 | 71 |
* |
72 | 72 |
* @author a.mueller |
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/AmplificationResult.java | ||
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68 | 68 |
* PCR itself is not persistent we do not store further information on it in the CDM and do not handle |
69 | 69 |
* {@link AmplificationResult} as a {@link DerivedUnit}. |
70 | 70 |
* <BR> |
71 |
* This may change in future: http://dev.e-taxonomy.eu/trac/ticket/3717.
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71 |
* This may change in future: https://dev.e-taxonomy.eu/redmine/issues/3717.
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72 | 72 |
* <BR> |
73 | 73 |
* |
74 | 74 |
* @author a.mueller |
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/HomotypicalGroupNameComparator.java | ||
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35 | 35 |
* the replacement name comes later as this reflects the order of publication</li> |
36 | 36 |
* </ul> |
37 | 37 |
* |
38 |
* Details on ordering are explained at http://dev.e-taxonomy.eu/trac/ticket/3338<BR>
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38 |
* Details on ordering are explained at https://dev.e-taxonomy.eu/redmine/issues/3338<BR>
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39 | 39 |
* |
40 | 40 |
* @author k.luther |
41 | 41 |
* @since 20.03.2017 |
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/ITypeDesignation.java | ||
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40 | 40 |
// * @see #getTypeSpecimen() |
41 | 41 |
// * @deprecated homotypical group can not be set and always seems to be <code>null</code>. |
42 | 42 |
// * Probably it is a relict of an old version. |
43 |
// * See also http://dev.e-taxonomy.eu/trac/ticket/2173
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43 |
// * See also https://dev.e-taxonomy.eu/redmine/issues/2173
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44 | 44 |
// */ |
45 | 45 |
// public HomotypicalGroup getHomotypicalGroup(); |
46 | 46 |
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cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/RankClass.java | ||
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26 | 26 |
* usually needed for correct formatting of taxon name text representations by using e.g. |
27 | 27 |
* {@link Rank#isSupraGeneric()} . Prior to v3.3 this was computed by comparison of ranks. |
28 | 28 |
* The current solution makes such methods less dependend on term loading.<BR> |
29 |
* @see http://dev.e-taxonomy.eu/trac/ticket/3521
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29 |
* @see https://dev.e-taxonomy.eu/redmine/issues/3521
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30 | 30 |
* |
31 | 31 |
* @author a.mueller |
32 | 32 |
* @since 11.06.2013 |
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/occurrence/SpecimenOrObservationBase.java | ||
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181 | 181 |
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182 | 182 |
/** |
183 | 183 |
* The preferred stable identifier (URI) as discussed in |
184 |
* {@link http://dev.e-taxonomy.eu/trac/ticket/5606}
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184 |
* {@link https://dev.e-taxonomy.eu/redmine/issues/5606}
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185 | 185 |
*/ |
186 | 186 |
@XmlElement(name = "PreferredStableUri") |
187 | 187 |
@Field(analyze = Analyze.NO) |
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/reference/ReferenceType.java | ||
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34 | 34 |
* @since 20.09.2009 |
35 | 35 |
*/ |
36 | 36 |
|
37 |
//TODO hierarchies, see http://dev.e-taxonomy.eu/trac/ticket/3619
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37 |
//TODO hierarchies, see https://dev.e-taxonomy.eu/redmine/issues/3619
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38 | 38 |
@XmlEnum |
39 | 39 |
public enum ReferenceType implements IEnumTerm<ReferenceType>, Serializable{ |
40 | 40 |
|
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/HomotypicGroupTaxonComparator.java | ||
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35 | 35 |
* the replacement name comes later as this reflects the order of publication</li> |
36 | 36 |
* </ul> |
37 | 37 |
* |
38 |
* Details on ordering are explained at http://dev.e-taxonomy.eu/trac/ticket/3338<BR>
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38 |
* Details on ordering are explained at https://dev.e-taxonomy.eu/redmine/issues/3338<BR>
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39 | 39 |
* |
40 | 40 |
* @author a.mueller |
41 | 41 |
* @since 02.03.2016 |
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonNode.java | ||
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139 | 139 |
@XmlElement(name = "childNode") |
140 | 140 |
@XmlIDREF |
141 | 141 |
@XmlSchemaType(name = "IDREF") |
142 |
//see https://dev.e-taxonomy.eu/trac/ticket/3722
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142 |
//see https://dev.e-taxonomy.eu/redmine/issues/3722
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143 | 143 |
@OrderColumn(name="sortIndex") |
144 | 144 |
@OrderBy("sortIndex") |
145 | 145 |
@OneToMany(mappedBy="parent", fetch=FetchType.LAZY) |
146 | 146 |
//@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE}) |
147 | 147 |
private List<TaxonNode> childNodes = new ArrayList<>(); |
148 | 148 |
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149 |
//see https://dev.e-taxonomy.eu/trac/ticket/3722
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150 |
//see https://dev.e-taxonomy.eu/trac/ticket/4200
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149 |
//see https://dev.e-taxonomy.eu/redmine/issues/3722
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150 |
//see https://dev.e-taxonomy.eu/redmine/issues/4200
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151 | 151 |
private Integer sortIndex = -1; |
152 | 152 |
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153 | 153 |
// //the source for this placement |
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/term/TermNode.java | ||
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94 | 94 |
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95 | 95 |
@XmlElementWrapper(name = "Children") |
96 | 96 |
@XmlElement(name = "Child") |
97 |
//see https://dev.e-taxonomy.eu/trac/ticket/3722
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97 |
//see https://dev.e-taxonomy.eu/redmine/issues/3722
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98 | 98 |
@OrderColumn(name="sortIndex") |
99 | 99 |
@OrderBy("sortIndex") |
100 | 100 |
@OneToMany(fetch = FetchType.LAZY, mappedBy="parent", targetEntity=TermNode.class) |
101 | 101 |
@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE}) |
102 | 102 |
private List<TermNode<T>> children = new ArrayList<>(); |
103 | 103 |
|
104 |
//see https://dev.e-taxonomy.eu/trac/ticket/3722
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104 |
//see https://dev.e-taxonomy.eu/redmine/issues/3722
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105 | 105 |
private Integer sortIndex; |
106 | 106 |
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107 | 107 |
@XmlElementWrapper(name = "OnlyApplicableIf") |
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/term/TermVocabulary.java | ||
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216 | 216 |
String label = csvLine.get(2).trim(); |
217 | 217 |
String description = csvLine.get(3); |
218 | 218 |
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219 |
//see http://dev.e-taxonomy.eu/trac/ticket/3550
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219 |
//see https://dev.e-taxonomy.eu/redmine/issues/3550
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220 | 220 |
this.addRepresentation(Representation.NewInstance(description, label, null, lang) ); |
221 | 221 |
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222 | 222 |
TermType termType = TermType.getByKey(csvLine.get(4)); |
cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/cache/reference/DefaultReferenceCacheStrategy.java | ||
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686 | 686 |
result = result.replace(beforeMicroReference + INomenclaturalReference.MICRO_REFERENCE_TOKEN, INomenclaturalReference.MICRO_REFERENCE_TOKEN); |
687 | 687 |
} |
688 | 688 |
} |
689 |
//FIXME: vol. etc., http://dev.e-taxonomy.eu/trac/ticket/2862
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689 |
//FIXME: vol. etc., https://dev.e-taxonomy.eu/redmine/issues/2862
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690 | 690 |
|
691 | 691 |
result = getInRefAuthorPart(thisRef.getInReference(), afterInRefAuthor) + result; |
692 | 692 |
result = "in " + result; |
... | ... | |
711 | 711 |
+ " nomenclatural reference. This is not correct or not handled yet." |
712 | 712 |
+ " Generic titleWithoutYearAndAuthor used instead"); |
713 | 713 |
result = getTitleWithoutYearAndAuthorGeneric(inInRef, true); |
714 |
//FIXME: vol. etc., http://dev.e-taxonomy.eu/trac/ticket/2862 (comment taken from super.getTokenizedNomenclaturalTitel())
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714 |
//FIXME: vol. etc., https://dev.e-taxonomy.eu/redmine/issues/2862 (comment taken from super.getTokenizedNomenclaturalTitel())
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715 | 715 |
}else{ |
716 | 716 |
result = getTitleWithoutYearAndAuthor(inRef, true); |
717 | 717 |
} |
cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/location/PointTest.java | ||
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1 | 1 |
/** |
2 | 2 |
* Copyright (C) 2009 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 |
5 |
*
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5 |
* |
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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 |
*/ |
... | ... | |
32 | 32 |
|
33 | 33 |
private Point point1; |
34 | 34 |
private Point point2; |
35 |
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35 |
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36 | 36 |
private Integer errorRadius; |
37 | 37 |
private Double longitude1; |
38 | 38 |
private Double latitude1; |
39 | 39 |
private Double longitude2; |
40 | 40 |
private Double latitude2; |
41 |
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41 |
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42 | 42 |
private ReferenceSystem referenceSystem; |
43 |
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44 |
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43 |
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44 |
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45 | 45 |
/** |
46 | 46 |
* @throws java.lang.Exception |
47 | 47 |
*/ |
... | ... | |
59 | 59 |
public void setUp() throws Exception { |
60 | 60 |
longitude1 = 23.123556; |
61 | 61 |
latitude1 = -13.975556; |
62 |
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62 |
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63 | 63 |
longitude2 = 28.48556; |
64 | 64 |
latitude2 = 12.656; |
65 |
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65 |
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66 | 66 |
errorRadius = 5; |
67 | 67 |
referenceSystem = ReferenceSystem.GOOGLE_EARTH(); |
68 |
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68 |
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69 | 69 |
point1 = Point.NewInstance(longitude1, latitude1, referenceSystem, errorRadius); |
70 | 70 |
point2 = Point.NewInstance(); |
71 |
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72 |
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73 |
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71 |
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72 |
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73 |
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74 | 74 |
} |
75 | 75 |
|
76 |
//********************** TESTS *****************************
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77 |
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76 |
//********************** TESTS ***************************** |
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77 |
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78 | 78 |
@Test |
79 | 79 |
public void testNewInstance(){ |
80 | 80 |
Assert.assertNotNull("ReferenceSystem must not be null", referenceSystem); |
... | ... | |
85 | 85 |
Assert.assertEquals("", latitude1, point1.getLatitude()); |
86 | 86 |
Assert.assertEquals("", errorRadius, point1.getErrorRadius()); |
87 | 87 |
Assert.assertEquals("", referenceSystem, point1.getReferenceSystem()); |
88 |
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88 |
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89 | 89 |
Assert.assertNull("LongitudeSexagesimal should be null", point2.getLongitudeSexagesimal()); |
90 | 90 |
Assert.assertNull("LatitudeSexagesimal should be null", point2.getLatitudeSexagesimal()); |
91 | 91 |
} |
... | ... | |
105 | 105 |
point2.setLatitude(null); |
106 | 106 |
Assert.assertEquals(null, point2.getLatitude()); |
107 | 107 |
} |
108 |
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108 |
|
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109 | 109 |
@Test |
110 | 110 |
public void testGetSetErrorRadius(){ |
111 | 111 |
point2.setErrorRadius(7); |
... | ... | |
113 | 113 |
point2.setErrorRadius(null); |
114 | 114 |
Assert.assertEquals(null, point2.getErrorRadius()); |
115 | 115 |
} |
116 |
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116 |
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117 | 117 |
@Test |
118 | 118 |
public void testGetSetReferenceSystem(){ |
119 | 119 |
ReferenceSystem newRefSystem = ReferenceSystem.NewInstance(); |
... | ... | |
122 | 122 |
point2.setReferenceSystem(null); |
123 | 123 |
Assert.assertEquals(null, point2.getReferenceSystem()); |
124 | 124 |
} |
125 |
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125 |
|
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126 | 126 |
@Test |
127 | 127 |
public void testGetLongitudeSexagesimal(){ |
128 | 128 |
Assert.assertEquals("23\u00B07'24.801\"E", point1.getLongitudeSexagesimal().toString(true, false)); |
129 |
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130 |
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129 |
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130 |
|
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131 | 131 |
point2.setLongitudeSexagesimal(Sexagesimal.NewInstance(5, 22, null, Direction.WEST)); |
132 | 132 |
Assert.assertEquals((Integer)22, point2.getLongitudeSexagesimal().minutes); |
133 | 133 |
Assert.assertEquals((Integer)0, point2.getLongitudeSexagesimal().seconds); |
134 |
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135 |
Double latitudeDouble = -45.57389326;
|
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134 |
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135 |
Double latitudeDouble = -45.57389326; |
|
136 | 136 |
point1.setLatitudeSexagesimal(Sexagesimal.valueOf(latitudeDouble, true)); |
137 | 137 |
//Not true because of rounding errors |
138 | 138 |
// Assert.assertEquals("latitudeDouble must be equal", latitudeDouble, point1.getLatitude()); |
139 |
|
|
139 |
|
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140 | 140 |
Sexagesimal sexagesimal1 = Sexagesimal.NewInstance(0, 0, 0, Direction.WEST); |
141 | 141 |
Sexagesimal sexagesimal2 = Sexagesimal.NewInstance(2, 2, 2, Direction.WEST); |
142 | 142 |
Assert.assertNotSame("", sexagesimal1, sexagesimal2); |
143 |
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144 |
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143 |
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144 |
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145 | 145 |
} |
146 | 146 |
|
147 | 147 |
@Test |
... | ... | |
178 | 178 |
try { |
179 | 179 |
point1.setLatitudeByParsing("37\u00B07'44\"N"); |
180 | 180 |
Assert.assertEquals("Result should be 37\u00B07'44\"N not 37\u00B07'44.999\"N", "37\u00B07'44\"N", point1.getLatitudeSexagesimal().toString()); |
181 |
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181 |
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182 | 182 |
point1.setLatitudeByParsing("37\u00B07'45\"N"); |
183 | 183 |
Assert.assertEquals("Result should be 37\u00B07'45\"N not 37\u00B07'45.\"N", "37\u00B07'45\"N", point1.getLatitudeSexagesimal().toString()); |
184 |
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184 |
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185 | 185 |
} catch (ParseException e) { |
186 | 186 |
Assert.fail("No parsing error should occur"); |
187 | 187 |
} |
188 |
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189 |
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190 |
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191 | 188 |
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192 | 189 |
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193 |
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194 |
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195 |
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190 |
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191 |
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192 |
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193 |
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194 |
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195 |
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196 | 196 |
// Assert.assertTrue("Southern must be negative", conversionResults.convertedCoord < 0); |
197 | 197 |
// Assert.assertFalse("Southern must be latitude", conversionResults.isLongitude); |
198 | 198 |
// |
... | ... | |
203 | 203 |
// conversionResults = coordinateConverter.tryConvert("95\u00B034.744"); |
204 | 204 |
// Assert.assertTrue("Longitude must be defined", conversionResults.isLongitude); |
205 | 205 |
// |
206 |
//
|
|
206 |
// |
|
207 | 207 |
// conversionResults = coordinateConverter.tryConvert("-35\u00B034'55.67S"); |
208 | 208 |
// Assert.assertTrue(conversionResults.conversionComments, conversionResults.patternRecognised); |
209 | 209 |
// |
... | ... | |
212 | 212 |
// |
213 | 213 |
// conversionResults = coordinateConverter.tryConvert("35\u00B011'34.744SW"); |
214 | 214 |
// Assert.assertTrue("Western must be longitude", conversionResults.isLongitude); |
215 |
//
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|
215 |
// |
|
216 | 216 |
// conversionResults = coordinateConverter.tryConvert("35D11M34.744S"); |
217 | 217 |
// Assert.assertNull("isLongitude must be undefined. S stands for second.", conversionResults.isLongitude); |
218 | 218 |
|
219 | 219 |
} |
220 |
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220 |
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221 | 221 |
|
222 | 222 |
@Test |
223 | 223 |
public void testDoubleParsing(){ |
... | ... | |
233 | 233 |
} catch (ParseException e) { |
234 | 234 |
Assert.fail("No parsing error should occur"); |
235 | 235 |
} |
236 |
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236 |
|
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237 | 237 |
try { |
238 | 238 |
point1.setLongitudeByParsing("-120.4"); |
239 | 239 |
Assert.assertEquals("", "-120.4", point1.getLongitude().toString()); |
... | ... | |
248 | 248 |
} catch (ParseException e) { |
249 | 249 |
Assert.assertTrue("Latitude can not be > 90", true); |
250 | 250 |
} |
251 |
|
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251 |
|
|
252 | 252 |
try { |
253 | 253 |
point1.setLongitudeByParsing("191"); |
254 | 254 |
Assert.fail("Longitude can be > 180°"); |
... | ... | |
261 | 261 |
Assert.fail("String '2°39'38,5956\"S'should be parsable"); |
262 | 262 |
} |
263 | 263 |
} |
264 |
|
|
264 |
|
|
265 | 265 |
/** |
266 | 266 |
* I don't exactly know what should happen here. |
267 |
* Please see http://dev.e-taxonomy.eu/trac/ticket/2267#comment:3 on why this test was created
|
|
268 |
*
|
|
267 |
* Please see https://dev.e-taxonomy.eu/redmine/issues/2267#comment:3 on why this test was created
|
|
268 |
* |
|
269 | 269 |
* @throws ParseException |
270 | 270 |
*/ |
271 | 271 |
@Test |
... | ... | |
274 | 274 |
point1.setLatitudeByParsing(example); |
275 | 275 |
Assert.assertEquals(example, point1.getLatitudeSexagesimal().toString()); |
276 | 276 |
} |
277 |
|
|
277 |
|
|
278 | 278 |
@Test |
279 | 279 |
public void testStaticParsing(){ |
280 | 280 |
try{ |
... | ... | |
285 | 285 |
Assert.fail("No parsing error should occur"); |
286 | 286 |
} |
287 | 287 |
} |
288 |
|
|
289 |
|
|
290 |
|
|
288 |
|
|
289 |
|
|
290 |
|
|
291 | 291 |
} |
cdmlib-model/src/test/java/eu/etaxonomy/cdm/strategy/parser/NonViralNameParserImplTest.java | ||
---|---|---|
514 | 514 |
assertEquals("Uninomial must be 'Aegilops'", "Aegilops", name1.getGenusOrUninomial()); |
515 | 515 |
|
516 | 516 |
//Subspecies hybrid with hybrid sign |
517 |
//maybe false: see http://dev.e-taxonomy.eu/trac/ticket/3868
|
|
517 |
//maybe false: see https://dev.e-taxonomy.eu/redmine/issues/3868
|
|
518 | 518 |
name1 = parser.parseFullName("Aegilops insulae subsp. X abies Scholz", botanicCode, null); |
519 | 519 |
assertFalse("Name must not have monom hybrid bit set", name1.isMonomHybrid()); |
520 | 520 |
assertFalse("Name must not have binom hybrid bit set", name1.isBinomHybrid()); |
... | ... | |
1638 | 1638 |
|
1639 | 1639 |
/** |
1640 | 1640 |
* Test author with name parts van, von, de, de la, d', da, del. |
1641 |
* See also http://dev.e-taxonomy.eu/trac/ticket/3373
|
|
1641 |
* See also https://dev.e-taxonomy.eu/redmine/issues/3373
|
|
1642 | 1642 |
*/ |
1643 | 1643 |
@Test |
1644 | 1644 |
public final void testComposedAuthorNames(){ |
1645 | 1645 |
|
1646 |
//van author (see https://dev.e-taxonomy.eu/trac/ticket/3373)
|
|
1646 |
//van author (see https://dev.e-taxonomy.eu/redmine/issues/3373)
|
|
1647 | 1647 |
String testParsable = "Aphelocoma unicolor subsp. griscomi van Rossem, 1928"; |
1648 | 1648 |
assertTrue("Author with 'van' should be parsable", isParsable(testParsable, ICZN)); |
1649 | 1649 |
|
1650 |
//von author (see https://dev.e-taxonomy.eu/trac/ticket/3373)
|
|
1650 |
//von author (see https://dev.e-taxonomy.eu/redmine/issues/3373)
|
|
1651 | 1651 |
testParsable = "Aphelocoma unicolor subsp. griscomi von Rossem, 1928"; |
1652 | 1652 |
assertTrue("Author with 'von' should be parsable", isParsable(testParsable, ICZN)); |
1653 | 1653 |
|
1654 |
//de author (see https://dev.e-taxonomy.eu/trac/ticket/3373)
|
|
1654 |
//de author (see https://dev.e-taxonomy.eu/redmine/issues/3373)
|
|
1655 | 1655 |
testParsable = "Aphelocoma unicolor subsp. griscomi de Rossem, 1928"; |
1656 | 1656 |
assertTrue("Author with 'de' should be parsable", isParsable(testParsable, ICZN)); |
1657 | 1657 |
|
1658 |
//de la author (see https://dev.e-taxonomy.eu/trac/ticket/3373)
|
|
1658 |
//de la author (see https://dev.e-taxonomy.eu/redmine/issues/3373)
|
|
1659 | 1659 |
testParsable = "Aphelocoma unicolor subsp. griscomi de la Rossem, 1928"; |
1660 | 1660 |
assertTrue("Author with 'de la' should be parsable", isParsable(testParsable, ICZN)); |
1661 | 1661 |
|
1662 |
//d' author (see https://dev.e-taxonomy.eu/trac/ticket/3373)
|
|
1662 |
//d' author (see https://dev.e-taxonomy.eu/redmine/issues/3373)
|
|
1663 | 1663 |
testParsable = "Aphelocoma unicolor subsp. griscomi d'Rossem, 1928"; |
1664 | 1664 |
assertTrue("Author with \"'d'\" should be parsable", isParsable(testParsable, ICZN)); |
1665 | 1665 |
|
1666 |
//da author (see https://dev.e-taxonomy.eu/trac/ticket/3373)
|
|
1666 |
//da author (see https://dev.e-taxonomy.eu/redmine/issues/3373)
|
|
1667 | 1667 |
testParsable = "Aphelocoma unicolor subsp. griscomi da Rossem, 1928"; |
1668 | 1668 |
assertTrue("Author with 'da' should be parsable", isParsable(testParsable, ICZN)); |
1669 | 1669 |
|
1670 |
//del author (see https://dev.e-taxonomy.eu/trac/ticket/3373)
|
|
1670 |
//del author (see https://dev.e-taxonomy.eu/redmine/issues/3373)
|
|
1671 | 1671 |
testParsable = "Aphelocoma unicolor subsp. griscomi del Rossem, 1928"; |
1672 | 1672 |
assertTrue("Author with 'del' should be parsable", isParsable(testParsable, ICZN)); |
1673 | 1673 |
|
1674 |
//O' author (see https://dev.e-taxonomy.eu/trac/ticket/4759)
|
|
1674 |
//O' author (see https://dev.e-taxonomy.eu/redmine/issues/4759)
|
|
1675 | 1675 |
testParsable = "Aphelocoma unicolor subsp. griscomi O'Connor, 1928"; |
1676 | 1676 |
assertTrue("Author with 'O'' should be parsable", isParsable(testParsable, ICZN)); |
1677 | 1677 |
|
1678 |
//del author (see https://dev.e-taxonomy.eu/trac/ticket/4759)
|
|
1678 |
//del author (see https://dev.e-taxonomy.eu/redmine/issues/4759)
|
|
1679 | 1679 |
testParsable = "Aphelocoma unicolor subsp. griscomi zur Strassen, 1928"; |
1680 | 1680 |
assertTrue("Author with 'zur' should be parsable", isParsable(testParsable, ICZN)); |
1681 | 1681 |
|
... | ... | |
1720 | 1720 |
|
1721 | 1721 |
@Test |
1722 | 1722 |
public void testNeverEndingParsing(){ |
1723 |
//some full titles result in never ending parsing process https://dev.e-taxonomy.eu/trac/ticket/1556
|
|
1723 |
//some full titles result in never ending parsing process https://dev.e-taxonomy.eu/redmine/issues/1556
|
|
1724 | 1724 |
|
1725 | 1725 |
String irinaExample = "Milichiidae Sharp, 1899, Insects. Part II. Hymenopteracontinued (Tubulifera and Aculeata), Coleoptera, Strepsiptera, Lepidoptera, Diptera, Aphaniptera, Thysanoptera, Hemiptera, Anoplura 6: 504. 1899"; |
1726 | 1726 |
// irinaExample = "Milichiidae Sharp, 1899, Insects. Part II. Uiuis Iuiui Hymenopteracontinued (Tubulifera and Aculeata), Coleoptera, Strepsiptera, Lepidoptera, Diptera, Aphaniptera, Thysanoptera, Hemiptera, Anoplura 6: 504. 1899"; |
cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/v30_40/SchemaUpdater_31_33.java | ||
---|---|---|
1139 | 1139 |
|
1140 | 1140 |
// update length of all title caches and full title cache in names |
1141 | 1141 |
// TODO test for H2, Postgres, SqlServer |
1142 |
// https://dev.e-taxonomy.eu/trac/ticket/1592
|
|
1142 |
// https://dev.e-taxonomy.eu/redmine/issues/1592
|
|
1143 | 1143 |
private void updateTitleCacheLength(List<ISchemaUpdaterStep> stepList) { |
1144 | 1144 |
String stepName; |
1145 | 1145 |
String tableName; |
cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/term/DefinedTermDaoImpl.java | ||
---|---|---|
605 | 605 |
} |
606 | 606 |
|
607 | 607 |
/** |
608 |
* Workaround for http://dev.e-taxonomy.eu/trac/ticket/5871 and #5945
|
|
608 |
* Workaround for https://dev.e-taxonomy.eu/redmine/issues/5871 and #5945
|
|
609 | 609 |
* Terms with multiple representations return identical duplicates |
610 | 610 |
* due to eager representation loading. We expect these duplicates to appear |
611 | 611 |
* in line wo we only compare one term with its predecessor. If it already |
cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/hibernate/CdmSecurityHibernateInterceptor.java | ||
---|---|---|
64 | 64 |
public static final Map<Class<? extends CdmBase>, Set<String>> exculdeMap = new HashMap<Class<? extends CdmBase>, Set<String>>(); |
65 | 65 |
|
66 | 66 |
static{ |
67 |
// disabled since no longer needed, see https://dev.e-taxonomy.eu/trac/ticket/4111#comment:8
|
|
67 |
// disabled since no longer needed, see https://dev.e-taxonomy.eu/redmine/issues/4111#comment:8
|
|
68 | 68 |
// exculdeMap.put(TaxonName.class, new HashSet<>()); |
69 | 69 |
|
70 | 70 |
Set<String> defaultExculdes = new HashSet<>(); |
cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/persistence/dao/hibernate/taxon/ClassificationDaoHibernateImplTest.java | ||
---|---|---|
66 | 66 |
} |
67 | 67 |
|
68 | 68 |
/** |
69 |
* see http://dev.e-taxonomy.eu/trac/ticket/2778
|
|
69 |
* see https://dev.e-taxonomy.eu/redmine/issues/2778
|
|
70 | 70 |
* Classification/{uuid}/childNodesAt/{rank-uuid} fails if only species in database |
71 | 71 |
*/ |
72 | 72 |
@Test |
... | ... | |
78 | 78 |
Classification classification = classificationDao.load(FLAT_CLASSIFICATION_UUID); |
79 | 79 |
|
80 | 80 |
includeUnpublished = true; |
81 |
// test for the bug in http://dev.e-taxonomy.eu/trac/ticket/2778
|
|
81 |
// test for the bug in https://dev.e-taxonomy.eu/redmine/issues/2778
|
|
82 | 82 |
Rank rank = Rank.GENUS(); |
83 | 83 |
// run both queries in dao method since rank != null |
84 | 84 |
List<TaxonNode> rootNodes = classificationDao.listRankSpecificRootNodes(classification, null, rank, includeUnpublished, |
... | ... | |
340 | 340 |
|
341 | 341 |
|
342 | 342 |
/** |
343 |
* At the moment the data created is special to the issue http://dev.e-taxonomy.eu/trac/ticket/2778
|
|
343 |
* At the moment the data created is special to the issue https://dev.e-taxonomy.eu/redmine/issues/2778
|
|
344 | 344 |
* ClassificationDaoHibernateImplTest.issue2778.xml |
345 | 345 |
* |
346 | 346 |
* {@inheritDoc} |
cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/application/FirstDataInserter.java | ||
---|---|---|
167 | 167 |
/* TODO set up work amount, currently the amount of work ticks is hard coded |
168 | 168 |
* in {@link CdmApplicationControllersetNewDataSource}, but we need some means to register |
169 | 169 |
* additional ticks. |
170 |
* see http://dev.e-taxonomy.eu/trac/ticket/3140 (generic way to obtain work ticks of application startup for monitoring)
|
|
170 |
* see https://dev.e-taxonomy.eu/redmine/issues/3140 (generic way to obtain work ticks of application startup for monitoring)
|
|
171 | 171 |
* |
172 | 172 |
*/ |
173 | 173 |
} else { |
cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/utility/DescriptionUtility.java | ||
---|---|---|
48 | 48 |
* An area is a <b>fallback area</b> if it is marked to be hidden and if it has at least one of |
49 | 49 |
* sub area which is not marked to be hidden. The fallback area will be show if there is no {@link Distribution} |
50 | 50 |
* for any of the non hidden sub-areas. For more detailed discussion on fallback areas see |
51 |
* https://dev.e-taxonomy.eu/trac/ticket/4408</li>
|
|
51 |
* https://dev.e-taxonomy.eu/redmine/issues/4408</li>
|
|
52 | 52 |
* <li><b>Prefer computed rule</b>:Computed distributions are preferred over entered or imported elements. |
53 | 53 |
* (Computed description elements are identified by the {@link |
54 | 54 |
* MarkerType.COMPUTED()}). This means if a entered or imported status |
... | ... | |
67 | 67 |
* <code>subAreaPreference</code>. Can be run separately from the other filters. |
68 | 68 |
* This rule affects any distribution, |
69 | 69 |
* that is to computed and edited equally. For more details see |
70 |
* {@link https://dev.e-taxonomy.eu/trac/ticket/5050})</li>
|
|
70 |
* {@link https://dev.e-taxonomy.eu/redmine/issues/5050})</li>
|
|
71 | 71 |
* </ol> |
72 | 72 |
* |
73 | 73 |
* @param distributions |
cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/facade/DerivedUnitFacadeTest.java | ||
---|---|---|
1789 | 1789 |
|
1790 | 1790 |
/** |
1791 | 1791 |
* |
1792 |
* See https://dev.e-taxonomy.eu/trac/ticket/2426
|
|
1792 |
* See https://dev.e-taxonomy.eu/redmine/issues/2426
|
|
1793 | 1793 |
* This test doesn't handle the above issue yet as it doesn't fire events as |
1794 | 1794 |
* expected (at least it does not reproduce the behaviour in the Taxonomic Editor). |
1795 | 1795 |
* In the meanwhile the property change framework for the facade has been changed |
cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/SecurityTest.java | ||
---|---|---|
209 | 209 |
|
210 | 210 |
@Test |
211 | 211 |
@DataSet |
212 |
@Ignore // FIXME http://dev.e-taxonomy.eu/trac/ticket/3098
|
|
212 |
@Ignore // FIXME https://dev.e-taxonomy.eu/redmine/issues/3098
|
|
213 | 213 |
public void testHasPermissions(){ |
214 | 214 |
|
215 | 215 |
Taxon taxon = Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(Rank.GENUS()),null); |
... | ... | |
912 | 912 |
|
913 | 913 |
} |
914 | 914 |
|
915 |
// @Ignore // FIXME http://dev.e-taxonomy.eu/trac/ticket/4081 : #4081 (TaxonNodeServiceImpl.makeTaxonNodeASynonymOfAnotherTaxonNode() requires TAXONNAME.[UPDATE])
|
|
915 |
// @Ignore // FIXME https://dev.e-taxonomy.eu/redmine/issues/4081 : #4081 (TaxonNodeServiceImpl.makeTaxonNodeASynonymOfAnotherTaxonNode() requires TAXONNAME.[UPDATE])
|
|
916 | 916 |
@Test |
917 | 917 |
public void testAcceptedTaxonToSynomym(){ |
918 | 918 |
|
cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/TaxonServiceSearchTest.java | ||
---|---|---|
1389 | 1389 |
|
1390 | 1390 |
@Test |
1391 | 1391 |
@DataSet |
1392 |
//http://dev.e-taxonomy.eu/trac/ticket/5477
|
|
1392 |
//https://dev.e-taxonomy.eu/redmine/issues/5477
|
|
1393 | 1393 |
public final void testFindTaxaAndNamesByFullText_AreaFilter_issue5477() throws IOException, LuceneParseException, LuceneMultiSearchException { |
1394 | 1394 |
|
1395 | 1395 |
TaxonNode subtree = null; |
cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/description/DistributionAggregationTest.java | ||
---|---|---|
543 | 543 |
/** |
544 | 544 |
* Variant of {@link #testArea_rank_and_area_1()} with alternate source references to |
545 | 545 |
* check the handling of the case where the target taxon already has the distribution which is the |
546 |
* result of the aggregation (see http://dev.e-taxonomy.eu/trac/ticket/4366#comment:12)
|
|
546 |
* result of the aggregation (see https://dev.e-taxonomy.eu/redmine/issues/4366#comment:12)
|
|
547 | 547 |
* |
548 | 548 |
* This test relies on {@link #testArea_rank_and_area_1()} |
549 | 549 |
* an makes assertions only on the alternative source references |
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