November 2007 - tdwg-tag - lists.tdwg.org

[tdwg-tapir] Interpretation of TAPIR filters
by Renato De Giovanni 04 Dec '07

04 Dec '07

Dear all, I came across an issue that I know it was discussed before, but I couldn't find anything about it in the spec and I couldn't find a message with a final agreement/solution. The issue is: How should TAPIR filters be interpreted if they reference concepts that are not understood by providers or if they reference parameters that were not passed? Query templates may often include parameterized filters with many conditions, such as: <filter> <and> <equals> <concept id="http://rs.tdwg.org/dwc/dwcore/Genus"/> <parameter name="genus"/> </equals> <equals> <concept id="http://rs.tdwg.org/dwc/dwcore/SpecificEpithet"/> <parameter name="species"/> </equals> <equals> <concept id="http://rs.tdwg.org/dwc/dwcore/Country"/> <parameter name="country"/> </equals> </and> </filter> And it's important to be able to use the same query template even when not all parameters are passed, such as allowing all these calls: http://myprovider.org/tapir?op=search&t=mytemplate&genus=x http://myprovider.org/tapir?op=search&t=mytemplate&genus=x&species=y http://myprovider.org/tapir?op=search&t=mytemplate&country=z and so on... Otherwise we would need a different template for each combination of parameters, which would certainly make clients very unhappy. I've been discussing this with Markus and we're leaning towards the following suggestion about how to interpret filters: 1- Comparative operators (COPs) that reference unspecified parameters should be simply dropped from the filter. 2- COPs must evaluate to false if they reference a concept that is not understood by the provider, unless they also reference an unspecified parameter - in which case the COP must be dropped from the filter. 3- After dropping a COP, if it was part of a logical operator (LOP) then the LOP should also be dropped if there are no boolean operators left inside the LOP. 4- After dropping a LOP, if it was part of another LOP, then the parent LOP should also be dropped if there are no boolean operators left inside the parent LOP. There's clearly a gap in the specification about this and we need to fix it, so please let me know if you have any thoughts about this. If there are no objections or better suggestions, then I'll probably use the proposal above to amend the spec. Many thanks! -- Renato

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RE: [tdwg-guid] TDWG LSID Resolver broken?
by Richard Pyle 03 Dec '07

03 Dec '07

VERY strange! This LSID does not work: http://lsid.tdwg.org/urn:lsid:zoobank.org:act:20889795-7EC7-42F3-A4C3-D1D977 04A609 But this one does: http://lsid.tdwg.org/urn:lsid:bishopmuseum.org:tnu:20889795-7EC7-42F3-A4C3-D 1D97704A609 Even though these are the exact same record from the exact same database, and the latter resolver was created from the exact same source code as the former. Both seem to work fine on Rod's tester page, except the latter has one failure (5a), while in the former it is just a warning. Go figure.... Rich ________________________________ From: Paul Kirk [mailto:p.kirk@cabi.org] Sent: Wednesday, November 28, 2007 11:57 AM To: Richard Pyle Subject: RE: [tdwg-guid] TDWG LSID Resolver broken? Hi Rich, works OK for IF LSIDs http://lsid.tdwg.org/urn:lsid:indexfungorum.org:names:296755 <http://lsid.tdwg.org/urn:lsid:indexfungorum.org:names:296755> Cheers, Paul ________________________________ From: tdwg-guid-bounces(a)lists.tdwg.org on behalf of Richard Pyle Sent: Wed 28/11/2007 21:52 To: tdwg-guid(a)lists.tdwg.org Subject: [tdwg-guid] TDWG LSID Resolver broken? Hi All, I'm testing the ZooBank LSID resolver, and I can't seem to get any of my LSIDs to work with the TDWG LSID resolver (http://lsid.tdwg.org/) They used to work a couple months ago, but now they don't. For example: urn:lsid:zoobank.org:act:20889795-7EC7-42F3-A4C3-D1D97704A609 This works fine on Rod's Tester site: http://linnaeus.zoology.gla.ac.uk/~rpage/lsid/tester/ Any ideas??? Thanks, Rich Richard L. Pyle, PhD Database Coordinator for Natural Sciences and Associate Zoologist in Ichthyology Department of Natural Sciences, Bishop Museum 1525 Bernice St., Honolulu, HI 96817 Ph: (808)848-4115, Fax: (808)847-8252 email: deepreef(a)bishopmuseum.org http://hbs.bishopmuseum.org/staff/pylerichard.html _______________________________________________ tdwg-guid mailing list tdwg-guid(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-guid P Think Green - don't print this email unless you really need to ************************************************************************ The information contained in this e-mail and any files transmitted with it is confidential and is for the exclusive use of the intended recipient. If you are not the intended recipient please note that any distribution, copying or use of this communication or the information in it is prohibited. Whilst CAB International trading as CABI takes steps to prevent the transmission of viruses via e-mail, we cannot guarantee that any e-mail or attachment is free from computer viruses and you are strongly advised to undertake your own anti-virus precautions. If you have received this communication in error, please notify us by e-mail at cabi(a)cabi.org or by telephone on +44 (0)1491 829199 and then delete the e-mail and any copies of it. CABI is an International Organization recognised by the UK Government under Statutory Instrument 1982 No. 1071. **************************************************************************

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[tdwg-guid] How to create resource that is not defined in Jena's vocabulary
by Chaohong Xie 28 Nov '07

28 Nov '07

Hi guys, I met the same problem as Peter wrote in the following link: http://lists.tdwg.org/pipermail/tdwg-guid/2006-September/000496.html. Unfortunately, I didn't get the final solution in it. I'm not sure Peter, Ben and Steve are still in this mail group or not. Anyway, can anybody help me solve this problem? Thanks a lot. My code is attached as well. What I want is outputing my vocabulary "Manifest" instead of "rdf:Description". Map<String, String> ns = new HashMap<String, String>(); ns.put("", "http://www.test.com/2007/08/test-vocabulary#"); ns.put("rdfs", "http://www.w3.org/2000/01/rdf-schema#"); ns.put("rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#"); Model model = ModelFactory.createDefaultModel(); model.setNsPrefixes(ns); Resource r = model.createResource(" http://www.test.com/2007/08/test_config#MyNodeID").addProperty(model.createProperty("http://www.w3.org/1999/02/22-rdf-syntax-ns#type"), "http://www.test.com/2007/08/test-vocabulary#Manifest"); Property p = model.createProperty(" http://www.test.com/2007/08/test-vocabulary#created_by"); Statement s = model.createStatement(r, p, "Chaohong"); model.add(s); RDFWriter w = model.getWriter("RDF/XML-ABBREV"); w.setProperty("showXMLDeclaration", "true"); w.setProperty("tab", "2"); w.setProperty("xmlbase", "http://www.test.com/2007/08/test_config#"); w.write(model, System.out, "http://www.test.com/2007/08/test-vocabulary #"); Chaohong

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"Quality" in TDWG Standards
by Roger Hyam 25 Nov '07

25 Nov '07

Dear Tags, Bob Morris and Chuck Miller have made some interesting comments on this page in the wiki: http://wiki.tdwg.org/twiki/bin/view/TAG/QualityAssurance I'd like to throw this open to a wider audience as I am aware that many of you are not on the notify list of the wiki pages. The question in hand (as I see it) is this. The TAG has a role to play maintaining the "quality" of TDWG standards. If the executive (or any other member of TDWG) asks the TAG what its opinion on a particular standard or proposed activity is how should the TAG respond. 1) Should it have a list of criteria that guide it in assessing the standard/activity? 2) Should it take a completely ad hoc approach to each request? My opinion is that we should have at least a list of basic criteria even if some of those criteria are not appropriate to all situations. Before we embark on building such a list does anyone disagree with the notion of having a list at all? I'll take a week of silence as assent. Many thanks for you brain cycles on this, Roger

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[tdwg-tapir] r1351 - tapir/dev/schema
by svn＠rs.tdwg.org 22 Nov '07

22 Nov '07

Author: RenatoDeGiovanni Date: 2007-11-22 13:21:45 +0100 (Thu, 22 Nov 2007) New Revision: 1351 Modified: tapir/dev/schema/tapir.xsd Log: Schema was forcing all indexingPreferences' attributes to be present - which was clearly not our original intention (providers may wish to specify only a frequency or a maximum duration or just indicate the preferred start time). Modified: tapir/dev/schema/tapir.xsd =================================================================== --- tapir/dev/schema/tapir.xsd 2007-11-22 12:18:38 UTC (rev 1350) +++ tapir/dev/schema/tapir.xsd 2007-11-22 12:21:45 UTC (rev 1351) @@ -8,7 +8,7 @@ xmlns:geo="http://www.w3.org/2003/01/geo/wgs84_pos#" xmlns:vcard="http://www.w3.org/2001/vcard-rdf/3.0#" elementFormDefault="qualified" - attributeFormDefault="unqualified" version="1.0.3" xml:lang="EN" > + attributeFormDefault="unqualified" version="1.0.4" xml:lang="EN" > <xsd:annotation> <xsd:documentation xml:lang="en"> TAPIR XML Schema. TAPIR is an acronym for TDWG Access Protocol for Information Retrieval. @@ -1666,9 +1666,9 @@ </xsd:element> <xsd:element name="indexingPreferences" minOccurs="0"> <xsd:complexType> - <xsd:attribute name="startTime" type="xsd:time"/> - <xsd:attribute name="maxDuration" type="xsd:duration"/> - <xsd:attribute name="frequency" type="xsd:duration" /> + <xsd:attribute name="startTime" type="xsd:time" use="optional"/> + <xsd:attribute name="maxDuration" type="xsd:duration" use="optional"/> + <xsd:attribute name="frequency" type="xsd:duration" use="optional"/> </xsd:complexType> </xsd:element> <xsd:element name="relatedEntity" type="relatedEntityInformationType" maxOccurs="unbounded">

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Quality Assurance in TDWG standards and activities
by Roger Hyam 20 Nov '07

20 Nov '07

Dear Tag, There has been some discussion concerning quality assurance in TDWG standards. You may have seen the new wiki page that has been introduced on the subject. http://wiki.tdwg.org/twiki/bin/view/TAG/QualityAssurance The executive committee is required to ask the TAG its opinion on the formation of new Task and Interest Groups and also on the passing of new standards. The TAG needs a framework for expressing this opinion. People submitting new group charters and standards need to know what the TAG will be looking for when it assesses their proposal The wiki page contains a provisional list of these criteria. These will form the basis of a brief document that Jim Graham and I will put together over the next couple of weeks to act as a more formal guide to other members of TDWG. Please review the list on the page and add your comments and changes. We will probably only have time to briefly circulate the document for review so it would be really helpful if you could get your comments in now. Many thanks, Roger

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Updating ontology space
by Roger Hyam 15 Nov '07

15 Nov '07

Dear Taggie, I am going to make changes to the ontology environment today in order to implement better change management. You can read about the plan here: http://wiki.tdwg.org/twiki/bin/view/TAG/TDWGOntologyGovernance You should not notice changes to the live system at first but some or the unused or purely experimental concepts may disappear from the live branch over the next few days. Please email the list if anything disappears that you rely on - it shouldn't. All the best, Roger

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[tdwg-tapir] xsd:any element processing
by Dave Vieglais 14 Nov '07

14 Nov '07

Hi, In http://rs.tdwg.org/tapir/1.0/schema/tapir.xsd, the definition of the <custom> element is such that any elements may be included, however the <xsd:any> element definition does not include a "processContents" attribute, in which case a validator will use the default of "strict" which requires that a definition of the contents are available and valid (i.e. an appropriate schema is available to validate the element content). The relevant XML schema reference is: http://www.w3.org/TR/2004/REC-xmlschema-1-20041028/structures.html#element-… I'm curious if that was the intent of the TAPIR design? If not, then including an attribute in <xsd:any> of processContents="lax" (validate if possible but ignore problems) or processContents="skip" (don't validate) would enable quick evaluation of TAPIR response documents using xml schema validation tools without requiring that providers explicitly include a schema defining the content of the <custom> element (which seems overly restrictive). An appropriate change could be: <xsd:element name="custom"> <xsd:annotation> <xsd:documentation>Extension slot for additional information not defined in the schema.</xsd:documentation> </xsd:annotation> <xsd:complexType> <xsd:sequence> <xsd:any minOccurs="0" maxOccurs="unbounded" processContents="lax" > <xsd:annotation> <xsd:documentation>For any custom extension. E.g what security related capabilities does the provider have? Encryption, access restriction, etc.</xsd:documentation> </xsd:annotation> </xsd:any> </xsd:sequence> </xsd:complexType> </xsd:element> I do not believe this will change any functionality of TAPIR providers, but it will enable validation of responses such as: <?xml version="1.0" encoding="utf-8" ?> <response xmlns="http://rs.tdwg.org/tapir/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation=" http://rs.tdwg.org/tapir/1.0/schema/tapir.xsd"> <header> <source accesspoint=" http://lsid.herbimi.info/TapirDotNET/tapir.aspx/herbIMI" sendtime="2007-11-09T05:15:05"> <software name="TapirDotNET" version="0.1 (revision )"/> </source> <destination>128.111.242.127</destination> <custom><skin>default</skin></custom> </header> <pong/> </response> which does not validate according to the current TAPIR schema. Other places in the schema that may be a problem (because processContents is not explicitly stated) are: /xsd:schema/xsd:group[1]/xsd:sequence[1]/xsd:element[1]/xsd:complexType[1]/xsd:choice[1]/xsd:any[1] /xsd:schema/xsd:complexType[34]/xsd:sequence[1] regards, Dave V.

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[tdwg-tapir] r1343 - tapir/dev/schema
by svn＠rs.tdwg.org 13 Nov '07

13 Nov '07

Author: RenatoDeGiovanni Date: 2007-11-13 17:12:24 +0100 (Tue, 13 Nov 2007) New Revision: 1343 Modified: tapir/dev/schema/tapir.xsd Log: Updated schema version. Modified: tapir/dev/schema/tapir.xsd =================================================================== --- tapir/dev/schema/tapir.xsd 2007-11-13 16:09:15 UTC (rev 1342) +++ tapir/dev/schema/tapir.xsd 2007-11-13 16:12:24 UTC (rev 1343) @@ -8,7 +8,7 @@ xmlns:geo="http://www.w3.org/2003/01/geo/wgs84_pos#" xmlns:vcard="http://www.w3.org/2001/vcard-rdf/3.0#" elementFormDefault="qualified" - attributeFormDefault="unqualified" version="1.0.2" xml:lang="EN" > + attributeFormDefault="unqualified" version="1.0.3" xml:lang="EN" > <xsd:annotation> <xsd:documentation xml:lang="en"> TAPIR XML Schema. TAPIR is an acronym for TDWG Access Protocol for Information Retrieval.

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[tdwg-tapir] r1342 - tapir/dev/schema
by svn＠rs.tdwg.org 13 Nov '07

13 Nov '07

Author: RenatoDeGiovanni Date: 2007-11-13 17:09:15 +0100 (Tue, 13 Nov 2007) New Revision: 1342 Modified: tapir/dev/schema/tapir.xsd Log: Avoid strict schema validation in search results that include the TAPIR envelope, but require a different namespace for the elements (note: omit-ns can only be used when the TAPIR envelope is turned off). Modified: tapir/dev/schema/tapir.xsd =================================================================== --- tapir/dev/schema/tapir.xsd 2007-11-13 16:01:09 UTC (rev 1341) +++ tapir/dev/schema/tapir.xsd 2007-11-13 16:09:15 UTC (rev 1342) @@ -1828,7 +1828,7 @@ <xsd:documentation>Format of search operation result.</xsd:documentation> </xsd:annotation> <xsd:sequence> - <xsd:any/> + <xsd:any processContents="lax" namespace="##other"/> <xsd:element name="summary" type="resultSummaryType"> <xsd:annotation> <xsd:documentation>Used to show information about the number of records for

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