Revision 55109
Added by Alessia Bardi about 5 years ago
modules/dnet-openaireplus-profiles/trunk/src/main/resources/eu/dnetlib/test/profiles/TransformationRuleDSResources/TransformationRuleDSResourceType/xslt_cleaning_ORP-biotools.xml | ||
---|---|---|
1 |
<RESOURCE_PROFILE> |
|
2 |
<HEADER> |
|
3 |
<RESOURCE_IDENTIFIER value="b703be53-e2e9-4de3-ba94-210ea4a96b82_VHJhbnNmb3JtYXRpb25SdWxlRFNSZXNvdXJjZXMvVHJhbnNmb3JtYXRpb25SdWxlRFNSZXNvdXJjZVR5cGU="/> |
|
4 |
<RESOURCE_TYPE value="TransformationRuleDSResourceType"/> |
|
5 |
<RESOURCE_KIND value="TransformationRuleDSResources"/> |
|
6 |
<RESOURCE_URI value=""/> |
|
7 |
<DATE_OF_CREATION value="2019-03-27T09:42:01+00:00"/> |
|
8 |
</HEADER> |
|
9 |
<BODY> |
|
10 |
<CONFIGURATION> |
|
11 |
<IMPORTED/> |
|
12 |
<SCRIPT> |
|
13 |
<TITLE>xslt_cleaning_ORP-biotools</TITLE> |
|
14 |
<CODE> |
|
15 |
<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" version="1.1" |
|
16 |
xmlns:oaf="http://namespace.openaire.eu/oaf" |
|
17 |
xmlns:dr="http://www.driver-repository.eu/namespace/dr" |
|
18 |
xmlns:datacite="http://datacite.org/schema/kernel-4" |
|
19 |
xmlns:TransformationFunction="eu.dnetlib.data.collective.transformation.core.xsl.ext.TransformationFunctionProxy" |
|
20 |
extension-element-prefixes="TransformationFunction" |
|
21 |
exclude-result-prefixes="TransformationFunction"> |
|
22 |
|
|
23 |
<xsl:param name="varOfficialName"/> |
|
24 |
<xsl:param name="varDsType"/> |
|
25 |
<xsl:param name="varDataSourceId"/> |
|
26 |
<xsl:param name="index" select="0"/> |
|
27 |
<xsl:param name="transDate" select="current-dateTime()"/> |
|
28 |
<xsl:variable name="tf" select="TransformationFunction:getInstance()"/> |
|
29 |
|
|
30 |
<xsl:template match="/"> |
|
31 |
<xsl:variable name="datasourcePrefix" |
|
32 |
select="normalize-space(//oaf:datasourceprefix)"/> |
|
33 |
<xsl:call-template name="validRecord"/> |
|
34 |
</xsl:template> |
|
35 |
|
|
36 |
<xsl:template name="terminate"> |
|
37 |
<xsl:message terminate="yes"> |
|
38 |
record is not compliant, transformation is interrupted. |
|
39 |
</xsl:message> |
|
40 |
</xsl:template> |
|
41 |
|
|
42 |
<xsl:template name="validRecord"> |
|
43 |
<record> |
|
44 |
<xsl:apply-templates select="//*[local-name() = 'header']"/> |
|
45 |
|
|
46 |
<metadata> |
|
47 |
|
|
48 |
<!-- |
|
49 |
<xsl:apply-templates select="//*[local-name() = 'metadata']//*[local-name() = 'list']"/> |
|
50 |
--> |
|
51 |
|
|
52 |
<datacite:resource> |
|
53 |
|
|
54 |
|
|
55 |
<datacite:resourceType> |
|
56 |
<xsl:attribute name="resourceTypeGeneral" select="'Software'"/> |
|
57 |
<xsl:value-of select="//*[local-name() = 'toolType']"/> |
|
58 |
</datacite:resourceType> |
|
59 |
|
|
60 |
<xsl:for-each select="//*[local-name() = 'language']"> |
|
61 |
<datacite:format> |
|
62 |
<xsl:value-of select="."/> |
|
63 |
</datacite:format> |
|
64 |
</xsl:for-each> |
|
65 |
|
|
66 |
<!-- DOE CODE does not state languages; projects/funding: funders not known to OpenAIRE |
|
67 |
--> |
|
68 |
|
|
69 |
<datacite:publisher> |
|
70 |
<xsl:value-of select="$varOfficialName"/> |
|
71 |
</datacite:publisher> |
|
72 |
|
|
73 |
<datacite:relatedIdentifiers> |
|
74 |
<xsl:for-each select="//*[local-name() = 'documentation'][not(./*[local-name() = 'type'] = ('Terms of use', 'Citation instructions', 'Contributions policy', 'Governance'))]"> |
|
75 |
<datacite:relatedIdentifier> |
|
76 |
<xsl:attribute name="relatedIdentifierType" select="'URL'"/> |
|
77 |
<xsl:attribute name="relationType" select="'IsDocumentedBy'"/> |
|
78 |
<xsl:value-of select="./*[local-name() = 'url']"/> |
|
79 |
</datacite:relatedIdentifier> |
|
80 |
</xsl:for-each> |
|
81 |
<!-- paper references --> |
|
82 |
<xsl:call-template name="relatedPaper"/> |
|
83 |
</datacite:relatedIdentifiers> |
|
84 |
|
|
85 |
<datacite:alternateIdentifiers> |
|
86 |
<!-- landing page, documentation, distribution --> |
|
87 |
<datacite:alternateIdentifier> |
|
88 |
<xsl:attribute name="alternateIdentifierType" select="'LandingPage'"/> |
|
89 |
<xsl:value-of select="concat('https://bio.tools/', //*[local-name() = 'id'])"/> |
|
90 |
</datacite:alternateIdentifier> |
|
91 |
|
|
92 |
<!-- |
|
93 |
<xsl:for-each select="distinct-values((//*[local-name() = 'link'][./*[local-name() = 'type' and . = 'Repository']]/*[local-name() = 'url'], //*[local-name() = 'link'][./*[local-name() = 'url' and starts-with(., 'https://github.com/')]]/*[local-name() = 'url']/replace(., '(https://github.com/[^/]*/[^/]*)(/.*)?', '$1')))"> |
|
94 |
--> |
|
95 |
<xsl:for-each select="distinct-values((//*[local-name() = 'link'][./*[local-name() = 'type' and . = 'Repository']]/*[local-name() = 'url'], //*[starts-with(., 'https://github.com/') and contains(., concat('/', //*[local-name() = 'id']))]/replace(., '(https://github.com/[^/]*/[^/]*)(/.*)?', '$1')))"> |
|
96 |
<datacite:alternateIdentifier> |
|
97 |
<xsl:attribute name="alternateIdentifierType" select="'DistributionLocation'"/> |
|
98 |
<xsl:value-of select="."/> |
|
99 |
</datacite:alternateIdentifier> |
|
100 |
</xsl:for-each> |
|
101 |
|
|
102 |
<!-- identifier --> |
|
103 |
<datacite:alternateIdentifier> |
|
104 |
<xsl:attribute name="alternateIdentifierType" select="'local accession id'"/> |
|
105 |
<xsl:value-of select="//*[local-name() = 'id']"/> |
|
106 |
</datacite:alternateIdentifier> |
|
107 |
</datacite:alternateIdentifiers> |
|
108 |
|
|
109 |
<datacite:identifier> |
|
110 |
<xsl:attribute name="identifierType" select="'URL'"/> |
|
111 |
<xsl:value-of select="concat('https://bio.tools/', //*[local-name() = 'id'])"/> |
|
112 |
</datacite:identifier> |
|
113 |
|
|
114 |
<!-- title --> |
|
115 |
<datacite:titles> |
|
116 |
<datacite:title> |
|
117 |
<xsl:value-of select="//*[local-name() = 'list']/*[local-name() = 'name']"/> |
|
118 |
</datacite:title> |
|
119 |
</datacite:titles> |
|
120 |
|
|
121 |
<!-- version --> |
|
122 |
<xsl:if test="//*[local-name() = 'list']/*[local-name() = 'version'][not(. = 'null')]"> |
|
123 |
<datacite:version> |
|
124 |
<xsl:value-of select="//*[local-name() = 'list']/*[local-name() = 'version'][not(. = 'null')]"/> |
|
125 |
</datacite:version> |
|
126 |
</xsl:if> |
|
127 |
|
|
128 |
<!-- bio.tools' credit/typeRole Developer/... is not identical with statements on GitHub ??? (Scoary) --> |
|
129 |
<xsl:call-template name="authors"/> |
|
130 |
|
|
131 |
<datacite:contributors> |
|
132 |
<xsl:for-each select="//*[local-name() = 'contact']/*[local-name() = 'name' and not(. = 'null')]"> |
|
133 |
<xsl:variable name="varContributorName" select="TransformationFunction:convertString($tf, ., 'Person')"/> |
|
134 |
<datacite:contributor> |
|
135 |
<xsl:attribute name="contributorType" select="'ContactPerson'"/> |
|
136 |
<datacite:contributorName> |
|
137 |
<xsl:value-of select="$varContributorName"/> |
|
138 |
</datacite:contributorName> |
|
139 |
<datacite:givenName> |
|
140 |
<xsl:value-of select="substring-after($varContributorName, ', ')"/> |
|
141 |
</datacite:givenName> |
|
142 |
<datacite:familyName> |
|
143 |
<xsl:value-of select="substring-before($varContributorName, ', ')"/> |
|
144 |
</datacite:familyName> |
|
145 |
</datacite:contributor> |
|
146 |
</xsl:for-each> |
|
147 |
</datacite:contributors> |
|
148 |
|
|
149 |
<datacite:descriptions> |
|
150 |
<datacite:description> |
|
151 |
<xsl:attribute name="descriptionType"> |
|
152 |
<xsl:value-of select="'Abstract'"/> |
|
153 |
</xsl:attribute> |
|
154 |
<xsl:value-of select="//*[local-name() = 'description']"/> |
|
155 |
</datacite:description> |
|
156 |
|
|
157 |
<!-- |
|
158 |
<xsl:for-each select="//*[local-name() = 'operatingSystem'], //*[local-name() = 'function']/*[local-name() = 'comment' and not(. = 'null')]"> |
|
159 |
--> |
|
160 |
|
|
161 |
<xsl:for-each select="//*[local-name() = 'function']/*[local-name() = 'comment' and not(. = 'null')]"> |
|
162 |
<datacite:description> |
|
163 |
<xsl:attribute name="descriptionType" select="'Abstract'"/> |
|
164 |
<xsl:value-of select="."/> |
|
165 |
</datacite:description> |
|
166 |
</xsl:for-each> |
|
167 |
|
|
168 |
<xsl:for-each select="//*[local-name() = 'operatingSystem']"> |
|
169 |
<datacite:description> |
|
170 |
<xsl:attribute name="descriptionType" select="'TechnicalInfo'"/> |
|
171 |
<xsl:value-of select="."/> |
|
172 |
</datacite:description> |
|
173 |
</xsl:for-each> |
|
174 |
|
|
175 |
</datacite:descriptions> |
|
176 |
|
|
177 |
<!-- subject --> |
|
178 |
<!-- dropping duplicate topics - funny that this seemingly works --> |
|
179 |
<datacite:subjects> |
|
180 |
<xsl:for-each select="//*[local-name() = 'topic'][index-of(distinct-values(//*[local-name() = 'topic']/*[local-name() = 'uri']), ./*[local-name() = 'uri'])]"> |
|
181 |
<xsl:if test="."> |
|
182 |
<datacite:subject> |
|
183 |
<xsl:attribute name="subjectScheme" select="'EDAM Ontology'"/> |
|
184 |
<xsl:attribute name="schemeURI" select="'http://edamontology.org'"/> |
|
185 |
<xsl:attribute name="valueURI" select="./*[local-name() = 'uri']"/> |
|
186 |
<xsl:value-of select="./*[local-name() = 'term']"/> |
|
187 |
</datacite:subject> |
|
188 |
</xsl:if> |
|
189 |
</xsl:for-each> |
|
190 |
</datacite:subjects> |
|
191 |
|
|
192 |
</datacite:resource> |
|
193 |
|
|
194 |
<!-- |
|
195 |
CobjCategory, SuperType |
|
196 |
--> |
|
197 |
<xsl:variable name='varCobjCategory' select="'0029'"/> |
|
198 |
<xsl:variable name='varSuperType' select="TransformationFunction:convertString($tf, $varCobjCategory, 'SuperTypes')"/> |
|
199 |
<dr:CobjCategory> |
|
200 |
<xsl:attribute name="type" select="$varSuperType"/> |
|
201 |
<xsl:value-of select="$varCobjCategory"/> |
|
202 |
</dr:CobjCategory> |
|
203 |
|
|
204 |
<!-- |
|
205 |
access rights, licenses |
|
206 |
--> |
|
207 |
<xsl:for-each select="//*[local-name() = ('license', 'accessibility') and not(. = 'null')]"> |
|
208 |
<oaf:accessrights> |
|
209 |
<xsl:variable name='varAccessRights' select="TransformationFunction:convertString($tf, ., 'AccessRights')"/> |
|
210 |
<xsl:choose> |
|
211 |
<xsl:when test="$varAccessRights = ('OPEN', 'OPEN SOURCE') and $varSuperType = 'software'"> |
|
212 |
<xsl:value-of select="'OPEN SOURCE'"/> |
|
213 |
</xsl:when> |
|
214 |
<xsl:otherwise> |
|
215 |
<xsl:value-of select="$varAccessRights"/> |
|
216 |
</xsl:otherwise> |
|
217 |
</xsl:choose> |
|
218 |
</oaf:accessrights> |
|
219 |
</xsl:for-each> |
|
220 |
|
|
221 |
<xsl:for-each select="//*[local-name() = 'license' and not(. = 'null')]"> |
|
222 |
<oaf:license> |
|
223 |
<xsl:value-of select="."/> |
|
224 |
</oaf:license> |
|
225 |
</xsl:for-each> |
|
226 |
|
|
227 |
<oaf:hostedBy> |
|
228 |
<xsl:attribute name="name" select="$varOfficialName"/> |
|
229 |
<xsl:attribute name="id" select="$varDataSourceId"/> |
|
230 |
</oaf:hostedBy> |
|
231 |
<oaf:collectedFrom> |
|
232 |
<xsl:attribute name="name" select="$varOfficialName"/> |
|
233 |
<xsl:attribute name="id" select="$varDataSourceId"/> |
|
234 |
</oaf:collectedFrom> |
|
235 |
|
|
236 |
<!-- |
|
237 |
<oaf:identifier> |
|
238 |
<xsl:value-of select="//*[local-name() = 'id']"/> |
|
239 |
</oaf:identifier> |
|
240 |
--> |
|
241 |
|
|
242 |
|
|
243 |
<oaf:concept> |
|
244 |
<xsl:attribute name="id" select="'elixir-gr'"/> |
|
245 |
</oaf:concept> |
|
246 |
|
|
247 |
|
|
248 |
<!-- date --> |
|
249 |
<oaf:dateAccepted> |
|
250 |
<xsl:value-of select="//*[local-name() = 'additionDate']/substring-before(., 'T')"/> |
|
251 |
</oaf:dateAccepted> |
|
252 |
|
|
253 |
</metadata> |
|
254 |
<xsl:copy-of select="//*[local-name() = 'about']"/> |
|
255 |
</record> |
|
256 |
|
|
257 |
</xsl:template> |
|
258 |
|
|
259 |
<xsl:template match="node()|@*"> |
|
260 |
<xsl:copy> |
|
261 |
<xsl:apply-templates select="node()|@*"/> |
|
262 |
</xsl:copy> |
|
263 |
</xsl:template> |
|
264 |
|
|
265 |
<xsl:template match="//*[local-name() = 'metadata']//*[local-name() = 'resource']"> |
|
266 |
<xsl:copy> |
|
267 |
<xsl:apply-templates select="node()|@*"/> |
|
268 |
</xsl:copy> |
|
269 |
</xsl:template> |
|
270 |
|
|
271 |
<xsl:template match="//*[local-name() = 'header']"> |
|
272 |
<xsl:copy> |
|
273 |
<xsl:apply-templates select="node()|@*"/> |
|
274 |
<xsl:element name="dr:dateOfTransformation"> |
|
275 |
<xsl:value-of select="$transDate"/> |
|
276 |
</xsl:element> |
|
277 |
</xsl:copy> |
|
278 |
</xsl:template> |
|
279 |
|
|
280 |
<!-- |
|
281 |
<xsl:template match="//*[local-name() = 'authors']"> |
|
282 |
--> |
|
283 |
<xsl:template name="authors"> |
|
284 |
<xsl:choose> |
|
285 |
<xsl:when test="not(//*[local-name() = 'credit'][./*[local-name() = 'typeRole' and . = 'Developer']][./*[local-name() = 'name' and not(. = 'null')]])"> |
|
286 |
<xsl:call-template name="terminate"/> |
|
287 |
</xsl:when> |
|
288 |
<xsl:otherwise> |
|
289 |
<datacite:creators> |
|
290 |
<xsl:for-each select="//*[local-name() = 'credit'][./*[local-name() = 'typeRole' and . = 'Developer']]/*[local-name() = 'name' and not(. = 'null')]"> |
|
291 |
<xsl:for-each select="tokenize(., ', ')"> |
|
292 |
<xsl:variable name="varDeveloperName" select="TransformationFunction:convertString($tf, normalize-space(.), 'Person')"/> |
|
293 |
<datacite:creator> |
|
294 |
<datacite:creatorName> |
|
295 |
<xsl:value-of select="$varDeveloperName"/> |
|
296 |
</datacite:creatorName> |
|
297 |
<datacite:givenName> |
|
298 |
<xsl:value-of select="substring-after($varDeveloperName, ', ')"/> |
|
299 |
</datacite:givenName> |
|
300 |
<datacite:familyName> |
|
301 |
<xsl:value-of select="substring-before($varDeveloperName, ', ')"/> |
|
302 |
</datacite:familyName> |
|
303 |
<!-- |
|
304 |
<xsl:if test="string-length(./*[local-name() = 'orcid']) > 0"> |
|
305 |
<xsl:element name="datacite:nameIdentifier"> |
|
306 |
<xsl:attribute name="nameIdentifierScheme" select="'ORCID'"/> |
|
307 |
<xsl:attribute name="schemeURI" select="'http://orcid.org'"/> |
|
308 |
<xsl:value-of select="./*[local-name()='orcid']"/> |
|
309 |
</xsl:element> |
|
310 |
</xsl:if> |
|
311 |
<xsl:for-each select="./*[local-name() = 'affiliations'][string-length(.) > 0]"> |
|
312 |
<xsl:element name="datacite:affiliation"> |
|
313 |
<xsl:value-of select="."/> |
|
314 |
</xsl:element> |
|
315 |
</xsl:for-each> |
|
316 |
--> |
|
317 |
</datacite:creator> |
|
318 |
</xsl:for-each> |
|
319 |
</xsl:for-each> |
|
320 |
</datacite:creators> |
|
321 |
</xsl:otherwise> |
|
322 |
</xsl:choose> |
|
323 |
</xsl:template> |
|
324 |
|
|
325 |
<!-- |
|
326 |
<xsl:template match="//*[local-name() = 'DOI']"> |
|
327 |
--> |
|
328 |
<xsl:template name="relatedPaper"> |
|
329 |
<xsl:for-each select="//*[local-name() = 'publication']/*[local-name() = ('doi', 'pmid', 'pmcid') and not(. = 'null')]"> |
|
330 |
<xsl:element name="datacite:relatedIdentifier"> |
|
331 |
<xsl:attribute name="relatedIdentifierType" select="upper-case(local-name())"/> |
|
332 |
<xsl:attribute name="relationType"> |
|
333 |
<xsl:choose> |
|
334 |
<xsl:when test="../*[local-name() = 'type'] = 'Primary'"> |
|
335 |
<xsl:value-of select="'isSupplementTo'"/> |
|
336 |
</xsl:when> |
|
337 |
<xsl:when test="../*[local-name() = 'type'] = ('Review', 'Benchmark', 'Comparison')"> |
|
338 |
<xsl:value-of select="'isReviewedBy'"/> |
|
339 |
</xsl:when> |
|
340 |
<xsl:when test="../*[local-name() = 'type'] = 'Usage'"> |
|
341 |
<xsl:value-of select="'isReferencedBy'"/> |
|
342 |
</xsl:when> |
|
343 |
<xsl:when test="../*[local-name() = 'type'] = 'Method'"> |
|
344 |
<xsl:value-of select="'references'"/> |
|
345 |
</xsl:when> |
|
346 |
<xsl:otherwise> |
|
347 |
<xsl:value-of select="'isReferencedBy'"/> |
|
348 |
</xsl:otherwise> |
|
349 |
</xsl:choose> |
|
350 |
</xsl:attribute> |
|
351 |
<xsl:value-of select="."/> |
|
352 |
</xsl:element> |
|
353 |
</xsl:for-each> |
|
354 |
</xsl:template> |
|
355 |
|
|
356 |
</xsl:stylesheet> |
|
357 |
</CODE> |
|
358 |
</SCRIPT> |
|
359 |
</CONFIGURATION> |
|
360 |
<STATUS/> |
|
361 |
<SECURITY_PARAMETERS/> |
|
362 |
</BODY> |
|
363 |
</RESOURCE_PROFILE> |
Also available in: Unified diff
TDS for biotools