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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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How to add his own/custom extension
by Julien Husson 14 Mar '14

14 Mar '14

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.

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Happy new year, two questions
by Michel Kapel 03 Jan '14

03 Jan '14

Happy new year everybody. I have two questions here. 1. I am searching for DarwinCore element "verbatim_scientific_name" is this available somewhere? 2. I have a need for a non DarwinCore field namely "WaterBodyType" with values such as (RIVER|LAKE|ESTUARY|SEA|...) I have looked but it does not seem to exist in DarwinCore. WaterBody does exist but this refers to the name of the water body such as "Nile river" or "Ganges river" or just "Amazon" . I want something that just specifies the type. Would it be possible to define such a field and add it to the mapping interface? Thanks in advance for any info. Michel K.

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Happy new year and two questions
by Michel Kapel 02 Jan '14

02 Jan '14

Happy new year everybody. I have two questions here. 1. I am searching for DarwinCore element "verbatim_scientific_name" is this available somewhere? 2. I have a need for a non DarwinCore field namely "WaterBodyType" with values such as (RIVER|LAKE|ESTUARY|SEA|...) I have looked but it does not seem to exist in DarwinCore. WaterBody does exist but this refers to the name of the water body such as "Nile river" or "Ganges river" or just "Amazon" . I want something that just specifies the type. Would it be possible to define such a field and add it to the mapping interface? Thanks in advance for any info. Michel K.

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use of extensions; how can duplication of rows be avoided?
by "Dröge, Gabriele" 02 Jan '14

02 Jan '14

Dear all, I have a general question on Darwin Core and the use of Darwin Core extensions. E.g. I want to use the Occurrence Core and Simple Images with a mysql database. Problem: Only a few of my occurrences have images. The Darwin Core Archive creates a large images file with all occurrence IDs and only a few have also Image urls. But I did expect a file with the image urls only (so much shorter) and all occurrences (with or without image) in the occurrences file. The same problem appears for the identification extension the other way round (duplication of occurrence rows for multiple identifications) and every other extension I've tested... But I am a bit confused how this can be done with only one big sql query (with some left joins). Do I have to use multiple resources to use multiple sql queries? Or is this a problem/bug of IPT? Best, Gabi

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Conflict "Darwin Core Sample Extension" and "Darwin Core Sample Core"
by "Dröge, Gabriele" 23 Oct '13

23 Oct '13

Dear all, I have another question concerning IPT and the Darwin Core extensions. For my test mapping I am using the Occurrences Core. Using the "Darwin Core Sample Extension" works in principal but unfortunately it is changed to "Darwin Core Sample Core" today (and can therefore not be used). Due to the similar name there seems to be a technical conflict. Could you please check this? Best, Gabi

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IPT bug -> MySQL
by "Dröge, Gabriele" 17 Oct '13

17 Oct '13

Dear all, I've downloaded the latest IPT version 2.0.5-r4398 and tried to map my data. I want to use a MySQL database, but there seems to be a bug in IPT concerning MySQL. IPT is not able to handle the SQL statement even though it is correct (tested on the MySQL server directly) Log file says: 1. Error in SQL (there is definitely no error in the sql statement) 2. IPT expects one more column than the sql statement queries for (unclear why) 3. IPT can't handle datetime (unclear why) A CSV file and a connection to a MS SQL Server did work. Preview looks like this: [cid:image001.jpg@01CECB47.70BB6950] It would be great if someone could fix those bugs. Thanks in advance! Best wishes, Gabi ----------------------------------------------------------------- Gabriele Droege Coordinator - DNA Bank Network Global Genome Biodiversity Network (GGBN) Berlin-Dahlem DNA Bank Deputy Women's Officer ZE BGBM Botanic Garden and Botanical Museum Berlin-Dahlem Freie Universität Berlin Koenigin-Luise-Str. 6-8 14195 Berlin Germany +49 30 838 50 139 www.dnabank-network.org<http://www.dnabank-network.org> www.ggbn.org<http://www.ggbn.org> www.bgbm.org<http://www.bgbm.org>

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mapping to the wrong datatypes
by BROSENS, Dimitri 03 Oct '13

03 Oct '13

* modified is mapped to values with the wrong data type. * eventDate is mapped to values with the wrong data type. * individualCount is mapped to values with the wrong data type. Dear, Here, we have chosen the wrong data type on purpose. For the terms eventDate and modified, the reason is that we sometimes have very vague dates. (ex: Winter 1921) and for individualCount we would like to use "unknown". (As the field is empty in the original data) Would this create any problems during the indexing? Can we just leave it like that? In the standard it is not specified which type the data has to be... only "best practices". Kind regards, Dimi * * * * * * * * * * * * * D I S C L A I M E R * * * * * * * * * * * * * Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document.

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