- IPT - lists.gbif.org

IPT 3.1.0 release
by Mikhail Podolskiy 16 Oct '24

16 Oct '24

Dear IPT users, We are pleased to announce the release of version 3.1.0 of the Integrated Publishing Toolkit (IPT). While supporting all previous functions, IPT 3.1.0 now includes support for the EML 2.2.0 [1]. In total, the new version release of the IPT resolves 48 issues [2]. All users are encouraged to upgrade to this version. New or current IPT administrators will want to consult the updated IPT documentation, which contains specific instructions on how to install the IPT [3] or upgrade an existing installation [4]. Please remember to check your data directory backup is working before starting the upgrade. Managers and users of GBIF-hosted IPT installations can already take advantage of the new functionality, as these instances have all been upgraded. If you have any questions feel free to contact us. Best regards, Mikhail Podolskiy [1] https://eml.ecoinformatics.org/eml-ecological-metadata-language [2] https://github.com/gbif/ipt/milestone/60?closed=1 [3] https://ipt.gbif.org/manual/en/ipt/latest/installation [4] https://ipt.gbif.org/manual/en/ipt/latest/release-notes

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IPT Install not accessible by GBIF
by jwfetz＠hotmail.com 29 Aug '24

29 Aug '24

Hi All, I am trying to install an instance of IPT. I'm working on a Win11 laptop and have installed Tomcat 9. If I go to "localhost:8080" I can see that Tomcat has installed just fine. However, when I go to manager app to install the "ipt.war" file, using the "war file to deploy" file upload, after hitting the deploy button the browser errors out with a message that it "can't reach this page" and "the connection was reset". So, to get around this, I copied the ipt.war file to the Tomcat webapps folder and then restarted Tomcat. This installed/deployed the ipt folder and I can access the ipt pages at localhost:8080/ipt. However, when I try to enter the public URL for the ITP in the settings, it gives an error "The Public URL does not point to an IPT installation that is accessible from this computer. http://{public ip address}:8080/ipt". I have opened port 8080 for incoming and outgoing connections for both TCP and UDP in the windows 11 firewall and have also enabled port forwarding for that port on my router so the connection will pass to the laptop. If I enter the {public ip address}:8080, it will display the Tomcat Home screen, but when I add the "/ipt" to the address, it says "you are not authorized to view this page". Does anyone know what I need to do to allow a connection to the IPT pages from an outside IP address? Is there some setting in Tomcat that needs to be changed? Thanks! Jim

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Re: [IPT] IPT Digest, Vol 101, Issue 2
by katia＠gbif.es 05 Apr '24

05 Apr '24

Thanks for reporting Rui! Katia Cezón Unidad de Coordinación de GBIF España (GBIF.ES – CSIC) Tel: +34 91 568 00 88 katia(a)gbif.es C/ Joaquín Costa, 22. 28002 Madrid (Spain) www.gbif.es datos.gbif.es twitter.com/GbifEs -----Mensaje original----- De: IPT <ipt-bounces(a)lists.gbif.org> En nombre de ipt-request(a)lists.gbif.org Enviado el: viernes, 5 de abril de 2024 14:00 Para: ipt(a)lists.gbif.org Asunto: IPT Digest, Vol 101, Issue 2 Send IPT mailing list submissions to ipt(a)lists.gbif.org To subscribe or unsubscribe via the World Wide Web, visit https://lists.gbif.org/mailman/listinfo/ipt or, via email, send a message with subject or body 'help' to ipt-request(a)lists.gbif.org You can reach the person managing the list at ipt-owner(a)lists.gbif.org When replying, please edit your Subject line so it is more specific than "Re: Contents of IPT digest..." Today's Topics: 1. Re: error in communication with gbif registry (Rui Figueira) ---------------------------------------------------------------------- Message: 1 Date: Thu, 4 Apr 2024 19:00:13 +0100 From: Rui Figueira <ruifigueira(a)isa.ulisboa.pt> To: ipt(a)lists.gbif.org Subject: Re: [IPT] error in communication with gbif registry Message-ID: <2c45c881-e7ea-4946-92dd-a32ed3a43f6e(a)isa.ulisboa.pt> Content-Type: text/plain; charset="utf-8"; Format="flowed" Dear list, I am replying to myself, to report the solution that I found for the issue. The problem was that as java version we are using is old (8u131), and it had no support for more recent SSL certificates used by the GBIF. The solution was to update java to recognize the GBIF certificate. For that, I followed the directions by https://magicmonster.com/kb/prg/java/ssl/pkix_path_building_failed/. Before doing that, I also updated java to a more recent version (8u402), by Amazon Correto, as pointed out by colleagues from GBIF France, but it seemed that alone this was not to be sufficient to solve the problem. Best, 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 On 4/3/24 18:00, Rui Figueira via IPT wrote: > > Dear IPT list, > > My IPT 2.7.6 installation on a debian server with java JRE 8 and > tomcat7 show the following error: > > An IO error occurred while trying to communicate with the GBIF > Registry. [https://gbrds.gbif.org/registry/network.json] > > When I did a restart of the tomcat service, I got the following error > in the log file > > ERROR 03-Apr-2024 17:29:35 > [org.gbif.ipt.service.admin.impl.VocabulariesManagerImpl] - An IO > error occurred while trying to communicate with the GBIF Registry. > [https://gbrds.gbif.org/registry/thesauri.json] > org.gbif.ipt.service.RegistryException: > sun.security.validator.ValidatorException: PKIX path building failed: > sun.security.provider.certpath.SunCertPathBuilderException: unable to > find valid certification path to requested target > > As a consequence, the IPT is unable to show any of the existing > resources. > > Have you seen this error, and know how to solve it? Notice that the > server has no ssl certificate installed. > > Thanks, > > 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 > > _______________________________________________ > IPT mailing list > IPT(a)lists.gbif.org > https://lists.gbif.org/mailman/listinfo/ipt

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error in communication with gbif registry
by Rui Figueira 04 Apr '24

04 Apr '24

Dear IPT list, My IPT 2.7.6 installation on a debian server with java JRE 8 and tomcat7 show the following error: An IO error occurred while trying to communicate with the GBIF Registry. [https://gbrds.gbif.org/registry/network.json] When I did a restart of the tomcat service, I got the following error in the log file ERROR 03-Apr-2024 17:29:35 [org.gbif.ipt.service.admin.impl.VocabulariesManagerImpl] - An IO error occurred while trying to communicate with the GBIF Registry. [https://gbrds.gbif.org/registry/thesauri.json] org.gbif.ipt.service.RegistryException: sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target As a consequence, the IPT is unable to show any of the existing resources. Have you seen this error, and know how to solve it? Notice that the server has no ssl certificate installed. Thanks, 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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IPT 3 release
by Mikhail Podolskiy 14 Feb '24

14 Feb '24

Dear IPT users, We are pleased to announce the release of version 3 of the Integrated Publishing Toolkit (IPT), which extends new data publishing capabilities beyond the Darwin Core Archive format while retaining full backwards compatibility [1]. IPT 3 includes support for new Frictionless Data Packages [2] that eliminate the constraints of the star schema at the heart of Darwin Core. The first supported data package is the Camera Trap Data Packages (Camtrap DP) [3], while others—including ColDP [4], used for sharing taxonomic data to and from ChecklistBank [5] —are undergoing testing for inclusion in the near future, but already available in the test mode. IPT 3 fully supports previous functions of the software, enabling any user to continue to accept spreadsheet uploads, connect to databases, perform data validation and create and publish Darwin Core archives. In total, the version 3 release of the IPT resolves more than 140 issues [6]. All users are encouraged to upgrade to this version. New or current IPT administrators will want to consult the updated IPT documentation, which contains specific instructions on how to install the IPT [7] or upgrade an existing installation [8]. Please remember to check your data directory backup is working before starting the upgrade. Managers and users of GBIF-hosted IPT installations can already take advantage of the new functionality, as these instances have all been upgraded to version 3. If you have any questions feel free to contact us. Best regards, Mikhail Podolskiy ---- Mikhail Podolskiy Developer GBIF Secretariat Universitetsparken 15 DK-2100 Copenhagen Ø DENMARK e-mail: mpodolskiy(a)gbif.org<mailto:mpodolskiy@gbif.org> www.gbif.org<http://www.gbif.org> [1] https://www.gbif.org/news/3b0zVJSYPpzuFQ83F8v13q/gbif-releases-ipt-version-3 [2] https://specs.frictionlessdata.io/data-package/ [3] https://camtrap-dp.tdwg.org/ [4] https://github.com/CatalogueOfLife/coldp [5] https://www.checklistbank.org/ [6] https://github.com/gbif/ipt/milestone/38?closed=1 [7] https://ipt.gbif.org/manual/en/ipt/latest/installation [8] https://ipt.gbif.org/manual/en/ipt/latest/release-notes

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IPT release 2.7.6
by Mikhail Podolskiy 26 Sep '23

26 Sep '23

Dear IPT users, We have released a new version of the IPT, version 2.7.6 [1]. This version mostly brings bug fixes and small improvements. A full list of addressed issues can be found here [2] All users are encouraged to upgrade to this version. Upgrade and installation instructions are in the manual [1]. Please remember to check your data directory backup is working before starting the upgrade. [1] https://ipt.gbif.org/manual/en/ipt/latest/releases#2-7-6-september-2023 [2] https://github.com/gbif/ipt/milestone/49?closed=1 Best regards, Mikhail ---- Mikhail Podolskiy Developer GBIF Secretariat Universitetsparken 15 DK-2100 Copenhagen Ø DENMARK e-mail: mpodolskiy(a)gbif.org<mailto:mpodolskiy@gbif.org> www.gbif.org<http://www.gbif.org>

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IPT v3 Release Candidate
by Mikhail Podolskiy 04 Sep '23

04 Sep '23

Dear IPT users, I’m happy to announce the availability of a preview release for the Integrated Publishing Toolkit Version 3.0-RC1. We’ve opted to name this version 3 as it brings in a new capability that goes beyond the Darwin Core Archive format. IPT version 3 will still provide all the functions of previous versions, but will additionally allow a user to map datasets to supported Frictionless Data [1] schemas. The first of these are the Camera Trap Data Package (Camtrap DP) [2, 3] and Catalogue of Life Data Package (CoL DP) [4]. This version also introduces a new core for Darwin Core Archives, for MaterialEntity [5], which is in preparation for the outputs of the Darwin Core Material task group. In addition, the installation requirements have been updated. Java 11 or 17 is now recommended, and Tomcat 9 or later. A Docker package for the release candidate version has been created, as well as CentOS Stream 8 and 9 test packages. Please note that this is a release candidate and is intended for testing and preview purposes only. It's NOT for production use — the IPT should be set up in test mode to register published datasets to the test system, gbif-uat.org. Documentation in the user manual for the new features is not yet available. Feedback is appreciated through issues on the GitHub issue tracker [6], or by email. If you have any questions or suggestions feel free to contact us. Best regards, Mikhail Podolskiy ---- Mikhail Podolskiy Developer GBIF Secretariat Universitetsparken 15 DK-2100 Copenhagen Ø DENMARK e-mail: mpodolskiy(a)gbif.org<mailto:mpodolskiy@gbif.org> www.gbif.org<http://www.gbif.org> [1] https://frictionlessdata.io/ [2] https://tdwg.github.io/camtrap-dp/ [3] https://github.com/tdwg/camtrap-dp [4] https://github.com/CatalogueOfLife/coldp#name [5] https://rs.gbif.org/sandbox/core/dwc_material_2023-04-29.xml [6] https://github.com/gbif/ipt/issues

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Update docker tomcat?
by Roger W. J. Alterskjær 23 Dec '22

23 Dec '22

Our university IT-security guys have noticed that our docker container for gbif/ipt is running a vulnerable version of Tomcat: Apache Tomcat 8.5.x < 8.5.83 which is vulnerable to "Request Smuggling Vulnerability" (CVE-2022-42252). They say that Tomcat 8.5.84 is the latest version of 8.5. I see that we’re using maven:3.8-jdk-8 with hasn’t been updated for five months… -Roger A

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missing organization in the ECA-IPT
by Andreas Allspach 01 Jun '22

01 Jun '22

Dear Admins, I want to insert the Basic Metadata for a resource in the ECA-IPT, but cannot select an organization. Where can I add my organization or has this to be done by you? I want to select "Senckenberg", the provider with following URL: (https://www.gbif.org/publisher/c76cf030-2a95-11da-9cc1-b8a03c50a862) Many thanks for your help and kind regards Andreas ☀☀☀☀☀☀☀☀☀☀☀☀☀☀☀☀☀☀☀☀☀☀☀☀☀☀☀☀ Andreas Allspach Collections Manager Senckenberg Forschungsinstitut und Naturmuseum Frankfurt Senckenberganlage 25 60325 Frankfurt am Main Tel. +49-69-7542-1369 Fax: +49-69-1437 Email: andreas.allspach(a)senckenberg.de Senckenberg Gesellschaft für Naturforschung (Rechtsfähiger Verein gemäß § 22 BGB) Senckenberganlage 25 60325 Frankfurt www.senckenberg.de Direktorium: Prof. Dr. Klement Tockner, Prof. Dr. Angelika Brandt, Dr. Martin Mittelbach, Prof. Dr. Andreas Mulch, Prof. Dr. Karsten Wesche; Präsidentin: Dr. h.c. Beate Heraeus; Aufsichtsbehörde: Magistrat der Stadt Frankfurt am Main (Ordnungsamt) Mitglied der Leibniz-Gemeinschaft Senckenberg forscht für Ihr Leben gern! www.senckenberg.de ***************************************************** P Drucken Sie bitte nur, wenn es wirklich notwendig ist: Sparen Sie pro Seite ca. 200 ml Wasser, 2 g CO2 und 2 g Holz.

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Proxy disabled due to 404 response
by Yasuhiko Fujita 04 Apr '22

04 Apr '22

Dear IPT admins, I am getting the following error in my IPT 2.5.5 (Test mode). - IPT startup warnings. For additional help diagnosing the problem(s), please see logs. After fixing the problem(s), please restart your web server. - admin.config.error.connectionRefused From the logs, it seems that the proxy settings are disabled because [https://gbrds.gbif-uat.org] is getting a 404 error. ==== INFO [org.gbif.ipt.service.admin.impl.ConfigManagerImpl] - Configuring http proxy ... INFO [org.gbif.ipt.service.admin.impl.ConfigManagerImpl] - Testing new proxy by fetching https://gbrds.gbif-uat.org with 4 second timeout DEBUG [org.gbif.utils.PreemptiveAuthenticationInterceptor] - GET / HTTP/1.1 INFO [org.gbif.ipt.service.admin.impl.ConfigManagerImpl] - Proxy response is HTTP/1.1 404 Not Found INFO [org.gbif.ipt.service.admin.impl.ConfigManagerImpl] - Proxy could not be validated (tried to retrieve https://gbrds.gbif-uat.org) , reverting to previous proxy setting on HTTP client: <...masked...> WARN [org.gbif.ipt.config.ConfigWarnings] - org.gbif.ipt.service.InvalidConfigException: admin.config.error.connectionRefused ==== Could anyone help to sort out how to resolve this problem? Does anyone know what is happening to gbrds.gbif-uat.org site? Best regards, Yasuhiko Fujita

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