April 2014 - IPT - lists.gbif.org

IPT v2.1 released
by Kyle Braak [GBIF] 23 Apr '14

23 Apr '14

Dear IPT users, The GBIF Secretariat is pleased to announce that a new release of the Integrated Publishing Toolkit (IPT v2.1) is now available for download here. For information about how to upgrade your installation, you can check out the Release Notes. Added to this version, is support for Microsoft Excel files as data sources, and the ability to validate that each record within a dataset has a unique identifier. To find out what else is new, you can check out the latest post on the GBIF Developer Blog. New users should follow the installation guidelines in the IPT User Manual that has been updated for this version. Thank you once again for using the IPT, and we hope you enjoy the latest version. With kind regards, Kyle, on behalf of the GBIF development team and the GBIF Secretariat

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Pre-release testing, IPT v2.1
by Kyle Braak [GBIF] 09 Apr '14

09 Apr '14

Dear IPT users, A pre-release version of IPT v2.1 is online for wider testing at http://ipt-uat.gbif.org I would greatly appreciate your help with testing, if you have a little time to spare. To login, you can use your existing account on http://ipt.gbif.org/. If you need an account setup, or if you need a password reminder, just let me know. Here are a few of the new features we need help testing: Identifier validation: when the occurrenceID/taxonID is mapped, the IPT will validate that each record has an ID, and each ID is unique Excel file support: Excel files can now be uploaded as source data Interface in Japanese: making the interface available in 6 languages now As always, our aim is to ensure that the released version is as sturdy as possible. We are currently putting the release candidate through rigorous testing too. In testing this morning, we successfully published a copy of the EOD-eBird Observation Dataset with 151 million records (check out the attached screenshot). We want to be confident that the identifier validation will scale up, and the initial tests look positive. If no major issues are uncovered during testing, IPT v2.1 will be released next week. Thank you for your assistance, Kyle, on behalf of the IPT development team and the GBIF Secretariat

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Re: [IPT] How to add his own/custom extension
by Julien Husson 09 Apr '14

09 Apr '14

Hi Tim, thanks for your prompt answer. It's not really what i expected, to be more specific > First, i have to harvest lot of data from multiple DB (remote or not) with, of course, different structures/models and format of datas ... sometimes no DB just flat CSV/xsl files... That's why i use an IPT to create data mapping and to standardize the data stream into Dwc standard. (I'm talking about millions of specimen) Secondly, i build specific indexes of harvested data with a custom harvester using canadensys-harvester lib. ( Thanks to Christian). It's at this point that it's begin to be difficult with a denormalized view of the data from IPT Dwc-A. 'Cause i need to transform this denormalized view or raw model into a normalize view that match with my big relational database model which become the new repository. That's why i thought that the custom extensions could be make my life easier. On Fri, Mar 14, 2014 at 5:12 PM, Julien Husson <biology.info(a)gmail.com>wrote: > Hi Tim, thanks for your prompt answer. > > It's not really what i expected, to be more specific > > > First, i have to harvest lot of data from multiple DB (remote or not) > with, of course, different structures/models and format of datas ... > sometimes no DB just flat CSV/xsl files... > That's why i use an IPT to create data mapping and to standardize the data > stream into Dwc standard. > (I'm talking about millions of specimen) > > Secondly, i build specific indexes of harvested data with a custom > harvester using canadensys-harvester lib. ( Thanks to Christian). It's at > this point that it's begin to be difficult with a denormalized view of the > data from IPT Dwc-A. > 'Cause i need to transform this denormalized view or raw model into a > normalize view that match with my big relational database model which > become the new repository. > > That's why i thought that the custom extensions could be make my life > easier. > > > > > On Fri, Mar 14, 2014 at 4:32 PM, Tim Robertson [GBIF] <trobertson(a)gbif.org > > wrote: > >> Hi Julien, >> >> Thanks for your question. It really depends on what you are trying to >> publish. We can add extensions of course, but without knowing the >> specifics it is difficult to comment. >> >> However, a "specimen, event, location" DB model would typically map to an >> Occurrence core with no extensions required - this is the most common use >> case of Darwin Core and the IPT. An Occurrence core is basically a >> denormalized view of the data. >> >> If I were the data manager, I would probably consider that I was >> publishing a "DwC Occurrence view" of my more complex model and as such >> would keep a view in the database along the lines of: >> >> CREATE VIEW view_dwc_occurrence AS >> SELECT >> specimen.bar_code AS occurrenceID, >> specimen.name AS scientificName, >> location.latitude AS decimalLatitude, >> location.longitude AS decimalLongitude, >> event.year AS year >> FROM >> specimen >> JOIN event ON ... >> JOIN location ON ... >> WHERE >> <insert any conditions for record inclusion, such as non endangered etc> >> >> Then in my IPT I would simply do "SELECT * FROM view_dwc_occurrence". >> Here you are flattening the normalised model into a denormalized DwC view >> of the data. >> >> Maintaining a view in the database layer as opposed to a custom mapping >> in the IPT benefits you by: >> i) catching issues early with database schema changes since the DB will >> likely stop you with an error >> ii) offering an easy mapping of DB table field names, to DwC terms in a >> language I find very familiar (SQL) >> iii) a super simple IPT mapping, as all columns will map automatically >> in the IPT since they are DwC recognised terms already >> >> Does that help in any way? If not, could you please elaborate on the >> model and what you are trying to achieve and we'll do all we can. >> >> Thanks, >> Tim >> >> >> >> On 14 Mar 2014, at 16:06, Julien Husson <biology.info(a)gmail.com> wrote: >> >> Hi, >> >> I use Dwc-A to feed my BD. >> >> We know the limits of the Dwc star schema to represent a relationnal >> database. >> >> For example in the case of 1-n cardinality : specimen --- event/record >> --- location. >> If i understand the concept, I need to use the Darwin *Core* *Occurrence* >> *extension*, denormalize my relational model in a big raw model and >> transform / re-normalize this model to match with my DB model. >> >> In order to reduce cost*, *dev and optimize sql statement, it will be >> grandly appreciate to add custom extension. In this case, i can to be >> very close of my relational database model and avoid multiple step of dev. >> >> I discovered this link but explanantion is now deprecated >> >> http://dag-endresen.blogspot.fr/2009/06/adding-extension-for-germplasm-to-g… >> >> Thanks, >> >> J. >> _______________________________________________ >> IPT mailing list >> IPT(a)lists.gbif.org >> http://lists.gbif.org/mailman/listinfo/ipt >> >> >> >

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