- IPT - lists.gbif.org

New IPT version: 2.4.0.
by Matthew Blissett 01 Aug '19

01 Aug '19

Dear IPT users, A new version of the IPT has been released, version 2.4.0. This version includes security updates from Struts and Jackson (code libraries the IPT uses). For this reason, all users should upgrade. It also includes support for DataCite's new API for issuing DOIs, since the old API has been switched off. The new version is available for download herehttps://repository.gbif.org/content/groups/gbif/org/gbif/ipt/2.4.0/ipt-… <http://repository.gbif.org/content/groups/gbif/org/gbif/ipt/2.3.4/ipt-2.3.4…> . New CentOS packages and Docker containers have also been generated, please see https://github.com/gbif/ipt/blob/master/package/rpm/README.md and https://github.com/gbif/docker-ipt. Please read the release notes, particularly if you are not upgrading from the previous release, 2.3.6:https://github.com/gbif/ipt/wiki/IPTReleaseNotes233.wiki Sincerely, Matthew Blissett GBIF Secretariat

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Re: [IPT] EZID, ARK and DOI
by Gamble, Beth 08 Jul '19

08 Jul '19

Hello Tim, The Smithsonian Institution National Museum of Natural History (NMNH) uses EZIDs as our unique identifiers. What EZID capability are you removing from IPT? Beth :-) Beth Gamble Senior Systems Analyst IT - Informatics Office w 202.633.0851 e gambleb(a)si.edu SMITHSONIAN INSTITUTION NATIONAL MUSEUM OF NATURAL HISTORY Facebook | Twitter | Instagram -----Original Message----- Date: Wed, 19 Jun 2019 08:38:01 +0000 From: Tim Robertson <trobertson(a)gbif.org> To: "ipt(a)lists.gbif.org" <ipt(a)lists.gbif.org> Cc: informatics <informatics(a)gbif.org> Subject: [IPT] EZID, ARK and DOI Message-ID: <E8F22A9E-D94A-430E-AE4A-BB7138ADB521(a)gbif.org> Content-Type: text/plain; charset="utf-8" Dear all, This email only affects those of you using DOI or EZID directly with your IPT. The next release of the IPT will be prepared to accommodate recent changes in the DataCite API who have deprecated their public API. In addition we are aware that EZID have reduced their capabilities with respect to DOIs. We are not aware of anyone using EZID as an identity service for ARKs. We therefore propose to remove EZID capabilities from the IPT 2.4 release as we are not aware that it is in use by anyone. If you are using EZID with your IPT can you please let me know asap and elaborate on which identifier scheme you are using so we can reconsider? Many thanks, Tim

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EZID, ARK and DOI
by Tim Robertson 19 Jun '19

19 Jun '19

Dear all, This email only affects those of you using DOI or EZID directly with your IPT. The next release of the IPT will be prepared to accommodate recent changes in the DataCite API who have deprecated their public API. In addition we are aware that EZID have reduced their capabilities with respect to DOIs. We are not aware of anyone using EZID as an identity service for ARKs. We therefore propose to remove EZID capabilities from the IPT 2.4 release as we are not aware that it is in use by anyone. If you are using EZID with your IPT can you please let me know asap and elaborate on which identifier scheme you are using so we can reconsider? Many thanks, Tim

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Re: [IPT] Daily feeds and archive history
by Kennedy, Jonathan 19 Feb '19

19 Feb '19

Thanks very much, this is helpful feedback. On a related note, Harvard-IQSS created a platform called Dataverse (https://dataverse.org/about) around 2007 and one interesting element is that they published a method for hashing datasets. This is done for the purpose of creating a citation element that can be used to verify that you have downloaded the same data. Passing along in case this is of interest to the group: http://best-practices.dataverse.org/data-citation/ Best regards, Jonathan A. Kennedy Director of Biodiversity Informatics Harvard University Herbaria, Department of Organismic and Evolutionary Biology From: Daniel Noesgaard <dnoesgaard(a)gbif.org> Date: Tuesday, February 19, 2019 at 3:22 AM To: Quentin Groom <quentin.groom(a)plantentuinmeise.be>, Tim Robertson <trobertson(a)gbif.org> Cc: "Kennedy, Jonathan" <jonathan_kennedy(a)harvard.edu>, "ipt(a)lists.gbif.org list" <ipt(a)lists.gbif.org>, helpdesk <helpdesk(a)gbif.org> Subject: Re: [IPT] Daily feeds and archive history I might also add that every download from GBIF.org–be it a single dataset or an aggregate–is archived and given a unique, persistent DOI for citation. And that citations of downloads count against all the datasets that contributed to that download. -- Daniel Noesgaard Science Communications Coordinator GBIF | Global Biodiversity Information Facility - Secretariat Universitetsparken 15 DK-2100 Copenhagen, Denmark E: dnoesgaard(a)gbif.org<mailto:dnoesgaard@gbif.org> W: www.gbif.org T: +45 35 32 08 74 From: Quentin Groom <quentin.groom(a)plantentuinmeise.be> Date: Tuesday, 19 February 2019 at 08.38 To: Tim Robertson <trobertson(a)gbif.org> Cc: "Kennedy, Jonathan" <jonathan_kennedy(a)harvard.edu>, "ipt(a)lists.gbif.org list" <ipt(a)lists.gbif.org>, helpdesk <helpdesk(a)gbif.org>, Daniel Noesgaard <dnoesgaard(a)gbif.org> Subject: Re: [IPT] Daily feeds and archive history While it would be great to have versioned datasets I generally create a snapshot of the data used in a paper and archive this in Zenodo. This gives complete reproducibility without putting extra demands on the data providers. I do however need to cite the source and the snapshot. Regards Quentin On Mon, 18 Feb 2019, 17:45 Tim Robertson <trobertson(a)gbif.org<mailto:trobertson@gbif.org> wrote: Hi Jonathan (adding GBIF helpdesk to the CC) This is just a quick answer which I expect will result in follow up questions. In terms of citation, we use a DOI to identify the concept of a dataset, not the specific version. E.g. https://doi.org/10.15468/cup0nk<https://urldefense.proofpoint.com/v2/url?u=https-3A__doi.org_10.15468_cup0n…> If you start deleting copies of data (e.g. a background housekeeping task) what will break are links to the downloads in the IPT pages. https://ipt.huh.harvard.edu/ipt/resource?r=huh_all_records&v=1.3 This may or may not be considered a problem for you. I think others might have contacted you about suggestions for improving the dataset titles being used but if not I would suggest considering correctly formatted titles as they are used in many places (https://www.gbif.org/dataset/4e4f97d2-4670-4b24-b982-261e0a450faf)<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.gbif.org_dataset_4…>. I hope this helps as a start, Tim From: IPT <ipt-bounces(a)lists.gbif.org<mailto:ipt-bounces@lists.gbif.org>> on behalf of "Kennedy, Jonathan" <jonathan_kennedy(a)harvard.edu<mailto:jonathan_kennedy@harvard.edu>> Date: Monday, 18 February 2019 at 18.31 To: "ipt(a)lists.gbif.org<mailto:ipt@lists.gbif.org>" <ipt(a)lists.gbif.org<mailto:ipt@lists.gbif.org>> Subject: [IPT] Daily feeds and archive history Hi All, I am finishing an upgrade to the Harvard University Herbaria IPT instance and have configured our feeds for daily auto-publish. The HUH has invested in a mass digitization workflow and we are currently creating ~20,000 new vascular records per month (with minimal data), so we do have new records on a daily basis. However, our DwC archives are fairly large (100MB+), so we can’t keep the daily archive history. I am looking for guidance on how it will work with GBIF dataset citation if we do not preserve each daily archive. It seems problematic if a version of our dataset is used and cited but cannot be reconstructed. Best regards, Jonathan A. Kennedy Director of Biodiversity Informatics Harvard University Herbaria, Department of Organismic and Evolutionary Biology _______________________________________________ IPT mailing list IPT(a)lists.gbif.org<mailto:IPT@lists.gbif.org> https://lists.gbif.org/mailman/listinfo/ipt<https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.gbif.org_mailman…>

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Re: [IPT] Daily feeds and archive history
by Tim Robertson 19 Feb '19

19 Feb '19

Hi Jonathan (adding GBIF helpdesk to the CC) This is just a quick answer which I expect will result in follow up questions. In terms of citation, we use a DOI to identify the concept of a dataset, not the specific version. E.g. https://doi.org/10.15468/cup0nk If you start deleting copies of data (e.g. a background housekeeping task) what will break are links to the downloads in the IPT pages. https://ipt.huh.harvard.edu/ipt/resource?r=huh_all_records&v=1.3 This may or may not be considered a problem for you. I think others might have contacted you about suggestions for improving the dataset titles being used but if not I would suggest considering correctly formatted titles as they are used in many places (https://www.gbif.org/dataset/4e4f97d2-4670-4b24-b982-261e0a450faf) I hope this helps as a start, Tim From: IPT <ipt-bounces(a)lists.gbif.org> on behalf of "Kennedy, Jonathan" <jonathan_kennedy(a)harvard.edu> Date: Monday, 18 February 2019 at 18.31 To: "ipt(a)lists.gbif.org" <ipt(a)lists.gbif.org> Subject: [IPT] Daily feeds and archive history Hi All, I am finishing an upgrade to the Harvard University Herbaria IPT instance and have configured our feeds for daily auto-publish. The HUH has invested in a mass digitization workflow and we are currently creating ~20,000 new vascular records per month (with minimal data), so we do have new records on a daily basis. However, our DwC archives are fairly large (100MB+), so we can’t keep the daily archive history. I am looking for guidance on how it will work with GBIF dataset citation if we do not preserve each daily archive. It seems problematic if a version of our dataset is used and cited but cannot be reconstructed. Best regards, Jonathan A. Kennedy Director of Biodiversity Informatics Harvard University Herbaria, Department of Organismic and Evolutionary Biology

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Daily feeds and archive history
by Kennedy, Jonathan 18 Feb '19

18 Feb '19

Hi All, I am finishing an upgrade to the Harvard University Herbaria IPT instance and have configured our feeds for daily auto-publish. The HUH has invested in a mass digitization workflow and we are currently creating ~20,000 new vascular records per month (with minimal data), so we do have new records on a daily basis. However, our DwC archives are fairly large (100MB+), so we can’t keep the daily archive history. I am looking for guidance on how it will work with GBIF dataset citation if we do not preserve each daily archive. It seems problematic if a version of our dataset is used and cited but cannot be reconstructed. Best regards, Jonathan A. Kennedy Director of Biodiversity Informatics Harvard University Herbaria, Department of Organismic and Evolutionary Biology

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migrate dataset from one IPT to another
by Rui Figueira 26 Sep '18

26 Sep '18

Dear IPT list, We want to migrate several datasets from http://maerua.iict.pt/ipt to http://ipt.gbif.pt. The datasets are already registered with GBIF, and there will be no change of the publishing organisation. We are thinking in transferring the resources to the new host IPT by importing the DwC-A from the old IPT. The questions is how to publish the datasets in the new hosting IPT, without creating a duplication in the GBIF registration? I tried to find a solution for this in https://github.com/gbif/ipt/wiki/FAQ.wiki, but none of the answers seems to apply. Thanks, Rui -- Rui Figueira Coordenador do Nó Português do GBIF ruifigueira(a)isa.ulisboa.pt Instituto Superior de Agronomia Herbário Tapada da Ajuda, 1300-344 Lisboa, Portugal Tel. +351 213653165 | Fax. +351 213653195 http://www.gbif.pt http://www.isa.ulisboa.pt

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schedule time for weekly auto-publish
by Matthew Neilson 21 Aug '18

21 Aug '18

Greetings, Is there a way to have more control over the time that an auto-publish occurs? I'd like to be able to schedule the auto-publish to occur outside of business hours. Thanks, -Matt -------------------------------------------------- *Matthew Neilson, PhD* U.S. Geological Survey Nonindigenous Aquatic Species Program Wetlands and Aquatic Research Center 7920 NW 71st Street Gainesville, FL 32653 -------------------------------------------------- (352) 264-3519 mneilson(a)usgs.gov http://nas.er.usgs.gov http://orcid.org/0000-0002-5139-5677

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update of Darwin Core Resource Relationship extension
by Rui Figueira 04 Jul '18

04 Jul '18

Hi IPT list members, Could anyone help me to understand what are the implications of doing an update of the Darwin Core Resource Relationship extension, that our IPT installation is asking to update? I am particularly concerned with the dataset http://ipt.gbif.pt/ipt/resource?r=edp_tua_arthropoda_eia, that is using this extension. The table resourcerelationship.txt in the dataset uses the term scientificName to identify the name of the tree where larva of butterflies feed on. This is reflected in the occurrence data at gbif.org, for example, in this record: https://www.gbif.org/occurrence/1585354292. I noticed that the update of the extension dropped the term scientificName. So, could anyone guide me on the changes that I need to do in the dataset, in order to be able to update the extension and have the same or equivalent information about the relationship in the record at https://www.gbif.org/occurrence/1585354292? Best regards, Rui -- ------------------ Rui Figueira Coordenador do Nó Português do GBIF ruifigueira(a)isa.ulisboa.pt Instituto Superior de Agronomia Herbário Tapada da Ajuda, 1349-017 Lisboa, Portugal Tel. +351 213653165 | Fax. +351 213653195 http://www.gbif.pt http://www.isa.ulisboa.pt

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FAIL - Application at context path /ipt could not be started
by Erik Jan Hofmeyer 24 May '18

24 May '18

Hi, I’m having trouble installing IPT on our Ubuntu server I get this error: FAIL - Application at context path /ipt could not be started Found the solution to this error here ( https://share.polymail.io/v1/z/b/NWIwNDI0ZGQwNDhj/iKquJarUXsATD5nggMoRwOZsf… ) , but none of the suggestions are helping me solve the problem. Are there other causes for this error? Kind regards, Erik Jan Hofmeyer De Vlinderstichting

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