Revision 58056
Added by Alessia Bardi about 4 years ago
| xslt_cleaning_ORP-biotools.xml | ||
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| 1 | 1 |
<RESOURCE_PROFILE> |
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<HEADER> |
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<RESOURCE_IDENTIFIER value="b703be53-e2e9-4de3-ba94-210ea4a96b82_VHJhbnNmb3JtYXRpb25SdWxlRFNSZXNvdXJjZXMvVHJhbnNmb3JtYXRpb25SdWxlRFNSZXNvdXJjZVR5cGU="/> |
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<RESOURCE_TYPE value="TransformationRuleDSResourceType"/> |
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<RESOURCE_KIND value="TransformationRuleDSResources"/> |
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<RESOURCE_URI value=""/> |
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<DATE_OF_CREATION value="2019-03-27T09:42:01+00:00"/> |
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</HEADER> |
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<BODY> |
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<CONFIGURATION> |
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<IMPORTED/> |
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<SCRIPT> |
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<TITLE>xslt_cleaning_ORP-biotools</TITLE> |
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<CODE> |
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<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:oaf="http://namespace.openaire.eu/oaf" xmlns:datacite="http://datacite.org/schema/kernel-4" xmlns:functx="http://www.functx.com" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:TransformationFunction="eu.dnetlib.data.collective.transformation.core.xsl.ext.TransformationFunctionProxy" xmlns:dr="http://www.driver-repository.eu/namespace/dr" exclude-result-prefixes="TransformationFunction" extension-element-prefixes="TransformationFunction" version="2.0"> |
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<HEADER> |
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<RESOURCE_IDENTIFIER |
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value="b703be53-e2e9-4de3-ba94-210ea4a96b82_VHJhbnNmb3JtYXRpb25SdWxlRFNSZXNvdXJjZXMvVHJhbnNmb3JtYXRpb25SdWxlRFNSZXNvdXJjZVR5cGU="/> |
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<RESOURCE_TYPE value="TransformationRuleDSResourceType"/> |
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<RESOURCE_KIND value="TransformationRuleDSResources"/> |
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<RESOURCE_URI value=""/> |
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<DATE_OF_CREATION value="2019-06-21T12:30:02+00:00"/> |
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</HEADER> |
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<BODY> |
|
| 11 |
<CONFIGURATION> |
|
| 12 |
<IMPORTED/> |
|
| 13 |
<SCRIPT> |
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<TITLE>xslt_cleaning_ORP-biotools</TITLE> |
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<CODE> |
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<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" |
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xmlns:oaf="http://namespace.openaire.eu/oaf" |
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xmlns:datacite="http://datacite.org/schema/kernel-4" |
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xmlns:functx="http://www.functx.com" xmlns:xs="http://www.w3.org/2001/XMLSchema" |
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xmlns:TransformationFunction="eu.dnetlib.data.collective.transformation.core.xsl.ext.TransformationFunctionProxy" |
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xmlns:dr="http://www.driver-repository.eu/namespace/dr" |
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exclude-result-prefixes="TransformationFunction" |
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extension-element-prefixes="TransformationFunction" version="2.0"> |
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| 16 | 24 |
<xsl:function as="xs:anyAtomicType*" name="functx:value-intersect"> |
| 17 | 25 |
<xsl:param as="xs:anyAtomicType*" name="arg1"/> |
| 18 | 26 |
<xsl:param as="xs:anyAtomicType*" name="arg2"/> |
| ... | ... | |
| 29 | 37 |
<xsl:call-template name="validRecord"/> |
| 30 | 38 |
</xsl:template> |
| 31 | 39 |
<xsl:template name="terminate"> |
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<xsl:message terminate="yes"> record is not compliant, transformation is interrupted.
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</xsl:message> |
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<xsl:message terminate="yes">record is not compliant, transformation is interrupted. |
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</xsl:message>
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| 34 | 42 |
</xsl:template> |
| 35 | 43 |
<xsl:template name="validRecord"> |
| 36 | 44 |
<record> |
| ... | ... | |
| 53 | 61 |
<xsl:value-of select="$varOfficialName"/> |
| 54 | 62 |
</datacite:publisher> |
| 55 | 63 |
<datacite:relatedIdentifiers> |
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<xsl:for-each select="//*[local-name() = 'documentation'][not(./*[local-name() = 'type'] = ('Terms of use', 'Citation instructions', 'Contributions policy', 'Governance'))]">
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<xsl:for-each |
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select="//*[local-name() = 'documentation'][not(./*[local-name() = 'type'] = ('Terms of use', 'Citation instructions', 'Contributions policy', 'Governance'))]">
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|
| 57 | 66 |
<datacite:relatedIdentifier> |
| 58 | 67 |
<xsl:attribute name="relatedIdentifierType" select="'URL'"/> |
| 59 | 68 |
<xsl:attribute name="relationType" select="'IsDocumentedBy'"/> |
| ... | ... | |
| 65 | 74 |
<datacite:alternateIdentifiers><!-- landing page, documentation, distribution --> |
| 66 | 75 |
<datacite:alternateIdentifier> |
| 67 | 76 |
<xsl:attribute name="alternateIdentifierType" select="'LandingPage'"/> |
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<xsl:value-of select="concat('https://bio.tools/', //*[local-name() = 'biotoolsID'])"/>
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<xsl:value-of |
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select="concat('https://bio.tools/', //*[local-name() = 'biotoolsID'][0])"/>
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| 69 | 79 |
</datacite:alternateIdentifier><!-- |
| 70 | 80 |
<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')))"> |
| 71 | 81 |
--> |
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<!--
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<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')))">
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<xsl:for-each
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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')))">
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| 74 | 84 |
<datacite:alternateIdentifier> |
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<xsl:attribute name="alternateIdentifierType" select="'DistributionLocation'"/> |
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<xsl:attribute name="alternateIdentifierType" |
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select="'DistributionLocation'"/> |
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| 76 | 87 |
<xsl:value-of select="."/> |
| 77 | 88 |
</datacite:alternateIdentifier> |
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</xsl:for-each>--><!-- identifier --> |
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<datacite:alternateIdentifier> |
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<xsl:attribute name="alternateIdentifierType" select="'biotoolsID'"/> |
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<xsl:value-of select="//*[local-name() = 'biotoolsID']"/> |
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</datacite:alternateIdentifier> |
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</xsl:for-each> |
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| 84 | 90 |
</datacite:alternateIdentifiers> |
| 85 | 91 |
<datacite:identifier> |
| 86 | 92 |
<xsl:attribute name="identifierType" select="'URL'"/> |
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<xsl:value-of select="concat('https://bio.tools/', //*[local-name() = 'biotoolsID'])"/>
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<xsl:value-of |
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select="concat('https://bio.tools/', //*[local-name() = 'biotoolsID'][0])"/>
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| 88 | 95 |
</datacite:identifier><!-- title --> |
| 89 | 96 |
<datacite:titles> |
| 90 | 97 |
<datacite:title> |
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<xsl:value-of select="//*[local-name() = 'list']/*[local-name() = 'name']"/> |
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<xsl:value-of |
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select="//*[local-name() = 'list']/*[local-name() = 'name']"/> |
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| 92 | 100 |
</datacite:title> |
| 93 | 101 |
</datacite:titles><!-- version --> |
| 94 | 102 |
<xsl:if test="//*[local-name() = 'list']/*[local-name() = 'version'][not(. = 'null')]"> |
| 95 | 103 |
<datacite:version> |
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<xsl:value-of select="//*[local-name() = 'list']/*[local-name() = 'version'][not(. = 'null')]"/> |
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<xsl:value-of |
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select="//*[local-name() = 'list']/*[local-name() = 'version'][not(. = 'null')]"/> |
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| 97 | 106 |
</datacite:version> |
| 98 | 107 |
</xsl:if><!-- bio.tools' credit/typeRole Developer/... is not identical with statements on GitHub ??? (Scoary) --> |
| 99 | 108 |
<xsl:call-template name="authors"/> |
| 100 | 109 |
<datacite:contributors> |
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<xsl:for-each select="//*[local-name() = 'contact']/*[local-name() = 'name' and not(. = 'null')]"> |
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<xsl:variable name="varContributorName" select="TransformationFunction:convertString($tf, ., 'Person')"/> |
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<xsl:for-each |
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select="//*[local-name() = 'contact']/*[local-name() = 'name' and not(. = 'null')]"> |
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<xsl:variable name="varContributorName" |
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select="TransformationFunction:convertString($tf, ., 'Person')"/> |
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| 103 | 114 |
<datacite:contributor> |
| 104 | 115 |
<xsl:attribute name="contributorType" select="'ContactPerson'"/> |
| 105 | 116 |
<datacite:contributorName> |
| 106 | 117 |
<xsl:value-of select="$varContributorName"/> |
| 107 | 118 |
</datacite:contributorName> |
| 108 | 119 |
<datacite:givenName> |
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<xsl:value-of select="substring-after($varContributorName, ', ')"/> |
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<xsl:value-of |
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select="substring-after($varContributorName, ', ')"/> |
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| 110 | 122 |
</datacite:givenName> |
| 111 | 123 |
<datacite:familyName> |
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<xsl:value-of select="substring-before($varContributorName, ', ')"/> |
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<xsl:value-of |
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select="substring-before($varContributorName, ', ')"/> |
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| 113 | 126 |
</datacite:familyName> |
| 114 | 127 |
</datacite:contributor> |
| 115 | 128 |
</xsl:for-each> |
| ... | ... | |
| 123 | 136 |
</datacite:description><!-- |
| 124 | 137 |
<xsl:for-each select="//*[local-name() = 'operatingSystem'], //*[local-name() = 'function']/*[local-name() = 'comment' and not(. = 'null')]"> |
| 125 | 138 |
--> |
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<xsl:for-each select="//*[local-name() = 'function']/*[local-name() = 'comment' and not(. = 'null')]"> |
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<xsl:for-each |
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select="//*[local-name() = 'function']/*[local-name() = 'comment' and not(. = 'null')]"> |
|
| 127 | 141 |
<datacite:description> |
| 128 | 142 |
<xsl:attribute name="descriptionType" select="'Abstract'"/> |
| 129 | 143 |
<xsl:value-of select="."/> |
| ... | ... | |
| 137 | 151 |
</xsl:for-each> |
| 138 | 152 |
</datacite:descriptions><!-- subject --><!-- dropping duplicate topics - funny that this seemingly works --> |
| 139 | 153 |
<datacite:subjects> |
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<xsl:for-each select="//*[local-name() = 'topic'][index-of(distinct-values(//*[local-name() = 'topic']/*[local-name() = 'uri']), ./*[local-name() = 'uri'])]"> |
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<xsl:for-each |
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select="//*[local-name() = 'topic'][index-of(distinct-values(//*[local-name() = 'topic']/*[local-name() = 'uri']), ./*[local-name() = 'uri'])]"> |
|
| 141 | 156 |
<xsl:if test="."> |
| 142 | 157 |
<datacite:subject> |
| 143 | 158 |
<xsl:attribute name="subjectScheme" select="'EDAM Ontology'"/> |
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<xsl:attribute name="schemeURI" select="'http://edamontology.org'"/> |
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<xsl:attribute name="valueURI" select="./*[local-name() = 'uri']"/> |
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<xsl:attribute name="schemeURI" |
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select="'http://edamontology.org'"/> |
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<xsl:attribute name="valueURI" |
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select="./*[local-name() = 'uri']"/> |
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| 146 | 163 |
<xsl:value-of select="./*[local-name() = 'term']"/> |
| 147 | 164 |
</datacite:subject> |
| 148 | 165 |
</xsl:if> |
| ... | ... | |
| 152 | 169 |
CobjCategory, SuperType |
| 153 | 170 |
--> |
| 154 | 171 |
<xsl:variable name="varCobjCategory" select="'0029'"/> |
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<xsl:variable name="varSuperType" select="TransformationFunction:convertString($tf, $varCobjCategory, 'SuperTypes')"/> |
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<xsl:variable name="varSuperType" |
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select="TransformationFunction:convertString($tf, $varCobjCategory, 'SuperTypes')"/> |
|
| 156 | 174 |
<dr:CobjCategory> |
| 157 | 175 |
<xsl:attribute name="type" select="$varSuperType"/> |
| 158 | 176 |
<xsl:value-of select="$varCobjCategory"/> |
| 159 | 177 |
</dr:CobjCategory><!-- |
| 160 | 178 |
access rights, licenses |
| 161 | 179 |
--> |
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<xsl:for-each select="//*[local-name() = ('license', 'accessibility') and not(. = 'null')]">
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<xsl:for-each |
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select="//*[local-name() = ('license', 'accessibility') and not(. = 'null')]">
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| 163 | 182 |
<oaf:accessrights> |
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<xsl:variable name="varAccessRights" select="TransformationFunction:convertString($tf, ., 'AccessRights')"/> |
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<xsl:variable name="varAccessRights" |
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select="TransformationFunction:convertString($tf, ., 'AccessRights')"/> |
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| 165 | 185 |
<xsl:choose> |
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<xsl:when test="$varAccessRights = ('OPEN', 'OPEN SOURCE') and $varSuperType = 'software'">
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<xsl:when |
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test="$varAccessRights = ('OPEN', 'OPEN SOURCE') and $varSuperType = 'software'">
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| 167 | 188 |
<xsl:value-of select="'OPEN SOURCE'"/> |
| 168 | 189 |
</xsl:when> |
| 169 | 190 |
<xsl:otherwise> |
| ... | ... | |
| 184 | 205 |
<oaf:collectedFrom> |
| 185 | 206 |
<xsl:attribute name="name" select="$varOfficialName"/> |
| 186 | 207 |
<xsl:attribute name="id" select="$varDataSourceId"/> |
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</oaf:collectedFrom><!-- |
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<oaf:identifier> |
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<xsl:value-of select="//*[local-name() = 'id']"/> |
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</oaf:identifier> |
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--> |
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<xsl:variable name="elixirGRAuthorMails" select="()"/> |
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<xsl:variable name="elixirGRTools" select="('3DMem-enzyme','ACT','Align Paths','AMYL-PRED 2','ANASTASIA','BioTextQuest(+)','BioTranslator','BiP finder','BPM','BUFET','CHRONOS','DEsubs','DIANA-LNCBase','DIANA-microT','DIANA-mirExTra','DIANA-mirExTra v2.0','DIANA-miRGen','DIANA-miRGen v3.0','DIANA-mirPath','DIANA-miRPath v3','DruGeVar','easyFRAP','ePGA','FINDbase','g-Class','G-Class','GprotPRED','GWAR','GWAS Training','haplotypeAnalysisPipeline','M-IOLITE','MESBL GC-MS metabolite peak database','METAGEN','metaseqR','Micro-CTvlab','microTSS','MiGA','mirPub','MR-microT','MR-microT','Mutations-Meta-Analyser','Mutations-Meta-Analyser ','MXM','Network Analyzer','OMPdb','PICKLE','PRED-LIPO','PRED-SIGNAL','PRED-TAT','PRED-TMBB2','Proteosign','recoup','RNEA','SCENERY','SymCurv','TRES','Variant Ranker')"/>
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</oaf:collectedFrom><!-- Check for person emails, tool name and elixirNode if we can set the concept for ELIXIR-GR --> |
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<xsl:variable name="elixirGRAuthorMails" |
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select="('achatzi@eie.gr','artemis.hatzigeorgiou@gmail.com','balomenos@upatras.gr','bezer@upatras.gr','D.R.Westhead@leeds.ac.uk','diwis@imis.athena-innovation.gr','epilalis@eie.gr','fpsom@issel.ee.auth.gr','geo.papoutsoglou@gmail.com','gpatrinos@upatras.gr','ikavakiotis@gmail.com','iliopj@med.uoc.gr','imichalop@bioacademy.gr','keklikoglou@hcmr.gr','lygerou@upatras.gr','mklapa@iceht.forth.gr','moulos@fleming.gr','mtheodo@biol.uoa.gr','mtsagris@yahoo.gr','n_moschonas@med.upatras.gr','nikolaou@uoc.gr','npapand@biol.uoa.gr','pbagos@compgen.org','ppaschou@mbg.duth.gr','secretariat@goldenhelix.org','sonja.althammer@gmail.com','thkoutsandreas@eie.gr','tsamard.it@gmail.com','vbur@iceht.forth.gr')"/><!-- List of tools provided by Elixir-GR RCD manager -->
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<xsl:variable name="elixirGRTools" |
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select="('3DMem-enzyme','ACT','Align Paths','AMYL-PRED 2','ANASTASIA','BioTextQuest(+)','BioTranslator','BiP finder','BPM','BUFET','CHRONOS','DEsubs','DIANA-LNCBase','DIANA-microT','DIANA-mirExTra','DIANA-mirExTra v2.0','DIANA-miRGen','DIANA-miRGen v3.0','DIANA-mirPath','DIANA-miRPath v3','DruGeVar','easyFRAP','ePGA','FINDbase','g-Class','G-Class','GprotPRED','GWAR','GWAS Training','haplotypeAnalysisPipeline','M-IOLITE','MESBL GC-MS metabolite peak database','METAGEN','metaseqR','Micro-CTvlab','microTSS','MiGA','mirPub','MR-microT','MR-microT','Mutations-Meta-Analyser','Mutations-Meta-Analyser ','MXM','Network Analyzer','OMPdb','PICKLE','PRED-LIPO','PRED-SIGNAL','PRED-TAT','PRED-TMBB2','Proteosign','recoup','RNEA','SCENERY','SymCurv','TRES','Variant Ranker')"/>
|
|
| 194 | 213 |
<xsl:variable name="authorMails" select="//credit/email"/> |
| 195 | 214 |
<xsl:if test="//elixirNode/text() = 'Greece' or $elixirGRTools=/list/name/text() or count(functx:value-intersect($authorMails, $elixirGRAuthorMails)) > 0"> |
| 196 | 215 |
<oaf:concept> |
| ... | ... | |
| 198 | 217 |
</oaf:concept> |
| 199 | 218 |
</xsl:if><!-- date --> |
| 200 | 219 |
<oaf:dateAccepted> |
| 201 |
<xsl:value-of select="//*[local-name() = 'additionDate']/substring-before(., 'T')"/> |
|
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<xsl:value-of |
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select="//*[local-name() = 'additionDate']/substring-before(., 'T')"/> |
|
| 202 | 222 |
</oaf:dateAccepted> |
| 203 | 223 |
</metadata> |
| 204 | 224 |
<xsl:copy-of select="//*[local-name() = 'about']"/> |
| ... | ... | |
| 233 | 253 |
We'll consider Developer and Primary Contact as authors. |
| 234 | 254 |
--> |
| 235 | 255 |
<xsl:choose> |
| 236 |
<xsl:when test="not(//*[local-name() = 'credit'][./*[local-name() = 'typeRole' and (. = 'Developer' or . = 'Primary contact')]][./*[local-name() = 'name' and not(. = 'null')]])"> |
|
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<xsl:when |
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test="not(//*[local-name() = 'credit'][./*[local-name() = 'typeRole' and (. = 'Developer' or . = 'Primary contact')]][./*[local-name() = 'name' and not(. = 'null')]])"> |
|
| 237 | 258 |
<xsl:call-template name="terminate"/> |
| 238 | 259 |
</xsl:when> |
| 239 | 260 |
<xsl:otherwise> |
| 240 | 261 |
<creators> |
| 241 |
<xsl:for-each select="//*[local-name() = 'credit'][./*[local-name() = 'typeRole' and (. = 'Developer' or . = 'Primary contact')]]/*[local-name() = 'name' and not(. = 'null')]"> |
|
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<xsl:for-each |
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select="//*[local-name() = 'credit'][./*[local-name() = 'typeRole' and (. = 'Developer' or . = 'Primary contact')]]/*[local-name() = 'name' and not(. = 'null')]"> |
|
| 242 | 264 |
<xsl:for-each select="tokenize(., ', ')"> |
| 243 |
<xsl:variable name="varDeveloperName" select="TransformationFunction:convertString($tf, normalize-space(.), 'Person')"/> |
|
| 265 |
<xsl:variable name="varDeveloperName" |
|
| 266 |
select="TransformationFunction:convertString($tf, normalize-space(.), 'Person')"/> |
|
| 244 | 267 |
<creator> |
| 245 | 268 |
<creatorName> |
| 246 | 269 |
<xsl:value-of select="$varDeveloperName"/> |
| 247 | 270 |
</creatorName> |
| 248 | 271 |
<givenName> |
| 249 |
<xsl:value-of select="substring-after($varDeveloperName, ', ')"/> |
|
| 272 |
<xsl:value-of |
|
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select="substring-after($varDeveloperName, ', ')"/> |
|
| 250 | 274 |
</givenName> |
| 251 | 275 |
<familyName> |
| 252 |
<xsl:value-of select="substring-before($varDeveloperName, ', ')"/> |
|
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<xsl:value-of |
|
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select="substring-before($varDeveloperName, ', ')"/> |
|
| 253 | 278 |
</familyName> |
| 254 | 279 |
</creator> |
| 255 | 280 |
</xsl:for-each> |
| ... | ... | |
| 261 | 286 |
<xsl:template match="//*[local-name() = 'DOI']"> |
| 262 | 287 |
--> |
| 263 | 288 |
<xsl:template name="relatedPaper"> |
| 264 |
<xsl:for-each select="//*[local-name() = 'publication']/*[local-name() = ('doi', 'pmid', 'pmcid') and not(. = 'null')]">
|
|
| 289 |
<xsl:for-each |
|
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select="//*[local-name() = 'publication']/*[local-name() = ('doi', 'pmid', 'pmcid') and not(. = 'null')]">
|
|
| 265 | 291 |
<xsl:element name="datacite:relatedIdentifier"> |
| 266 | 292 |
<xsl:attribute name="relatedIdentifierType" select="upper-case(local-name())"/> |
| 267 | 293 |
<xsl:attribute name="relationType"> |
| ... | ... | |
| 269 | 295 |
<xsl:when test="../*[local-name() = 'type'] = 'Primary'"> |
| 270 | 296 |
<xsl:value-of select="'isSupplementTo'"/> |
| 271 | 297 |
</xsl:when> |
| 272 |
<xsl:when test="../*[local-name() = 'type'] = ('Review', 'Benchmark', 'Comparison')">
|
|
| 298 |
<xsl:when |
|
| 299 |
test="../*[local-name() = 'type'] = ('Review', 'Benchmark', 'Comparison')">
|
|
| 273 | 300 |
<xsl:value-of select="'isReviewedBy'"/> |
| 274 | 301 |
</xsl:when> |
| 275 | 302 |
<xsl:when test="../*[local-name() = 'type'] = 'Usage'"> |
| ... | ... | |
| 288 | 315 |
</xsl:for-each> |
| 289 | 316 |
</xsl:template> |
| 290 | 317 |
</xsl:stylesheet> |
| 291 |
</CODE>
|
|
| 292 |
</SCRIPT>
|
|
| 293 |
</CONFIGURATION>
|
|
| 294 |
<STATUS/>
|
|
| 295 |
<SECURITY_PARAMETERS/>
|
|
| 296 |
</BODY>
|
|
| 318 |
</CODE>
|
|
| 319 |
</SCRIPT>
|
|
| 320 |
</CONFIGURATION>
|
|
| 321 |
<STATUS/>
|
|
| 322 |
<SECURITY_PARAMETERS/>
|
|
| 323 |
</BODY>
|
|
| 297 | 324 |
</RESOURCE_PROFILE> |
Also available in: Unified diff
it looks like some records have two biotoolsID, hence let's take the first one.