From tero.mononen at uef.fi Fri Mar 9 09:35:08 2012 From: tero.mononen at uef.fi (Tero Mononen) Date: Fri, 9 Mar 2012 10:35:08 +0200 Subject: [IPT] All space-characters in metadata are replaced to plus-character Message-ID: <7E11F47B5584C642AEBB77967228BE532E837FC9@EXCVS1.uefad.uef.fi> Hi We have used this IPT-setup without any problems till now. System: Version 2.0.2-r3306 Apache Tomcat/6.0.24 JVM 1.6.0_29-b1 Problem: All space-characters in metadata are replaced to plus-character. For example title "foo bar car" is saved as "foo+bar+car". It affects in every text field in metadata. If I include at least one plus-char in a text value, it prevents the space replacement. For example "foo bar car+dar" is saved as it is. I think this is related to Java/Tomcat/urlencode. Do you have suggestions how to fix this problem? Best Regards, Tero Mononen -- Digitarium Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) FI-80101 Joensuu http://www.digitarium.fi/ Tero Mononen, Analyst Programmer tero.mononen at uef.fi +358-50-5631788 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gbif.org/pipermail/ipt/attachments/20120309/26724c63/attachment.html From trobertson at gbif.org Fri Mar 9 09:36:56 2012 From: trobertson at gbif.org (Tim Robertson [GBIF]) Date: Fri, 9 Mar 2012 09:36:56 +0100 Subject: [IPT] All space-characters in metadata are replaced to plus-character In-Reply-To: <7E11F47B5584C642AEBB77967228BE532E837FC9@EXCVS1.uefad.uef.fi> References: <7E11F47B5584C642AEBB77967228BE532E837FC9@EXCVS1.uefad.uef.fi> Message-ID: Dear Tero, Could you please provide a link to an example file? We'll investigate, but this is not a behavior I have ever seen with a Tomcat application. Do you run any proxies or mod_jk or anything like that? Thanks, Tim On Mar 9, 2012, at 9:35 AM, Tero Mononen wrote: > Hi > > We have used this IPT-setup without any problems till now. > > System: > Version 2.0.2-r3306 > Apache Tomcat/6.0.24 > JVM 1.6.0_29-b1 > > Problem: > All space-characters in metadata are replaced to plus-character. For example title ?foo bar car? is saved as ?foo+bar+car?. It affects in every text field in metadata. > > If I include at least one plus-char in a text value, it prevents the space replacement. For example ?foo bar car+dar? is saved as it is. > > I think this is related to Java/Tomcat/urlencode. Do you have suggestions how to fix this problem? > > > Best Regards, > Tero Mononen > > -- > Digitarium > Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) > FI-80101 Joensuu > http://www.digitarium.fi/ > > Tero Mononen, Analyst Programmer > tero.mononen at uef.fi > +358-50-5631788 > > _______________________________________________ > IPT mailing list > IPT at lists.gbif.org > http://lists.gbif.org/mailman/listinfo/ipt -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gbif.org/pipermail/ipt/attachments/20120309/175e4c95/attachment.html From tero.mononen at uef.fi Fri Mar 9 09:44:11 2012 From: tero.mononen at uef.fi (Tero Mononen) Date: Fri, 9 Mar 2012 10:44:11 +0200 Subject: [IPT] All space-characters in metadata are replaced to plus-character In-Reply-To: References: <7E11F47B5584C642AEBB77967228BE532E837FC9@EXCVS1.uefad.uef.fi> Message-ID: <7E11F47B5584C642AEBB77967228BE532E837FDB@EXCVS1.uefad.uef.fi> Dear Tim, There's only public example (Title: William+Nylander+lichen+collection): http://db.digitarium.fi:8080/ipt/resource.do?r=nylander It's interesting, eml.xml on file system contains line: William+Nylander+lichen+collection But eml via IPT/Tomcat offers line: William Nylander lichen collection It's pure Tomcat without proxies. BR, Tero Mononen From: Tim Robertson [GBIF] [mailto:trobertson at gbif.org] Sent: Friday, March 09, 2012 10:37 AM To: Tero Mononen Cc: ipt at lists.gbif.org Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character Dear Tero, Could you please provide a link to an example file? We'll investigate, but this is not a behavior I have ever seen with a Tomcat application. Do you run any proxies or mod_jk or anything like that? Thanks, Tim On Mar 9, 2012, at 9:35 AM, Tero Mononen wrote: Hi We have used this IPT-setup without any problems till now. System: Version 2.0.2-r3306 Apache Tomcat/6.0.24 JVM 1.6.0_29-b1 Problem: All space-characters in metadata are replaced to plus-character. For example title "foo bar car" is saved as "foo+bar+car". It affects in every text field in metadata. If I include at least one plus-char in a text value, it prevents the space replacement. For example "foo bar car+dar" is saved as it is. I think this is related to Java/Tomcat/urlencode. Do you have suggestions how to fix this problem? Best Regards, Tero Mononen -- Digitarium Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) FI-80101 Joensuu http://www.digitarium.fi/ Tero Mononen, Analyst Programmer tero.mononen at uef.fi +358-50-5631788 _______________________________________________ IPT mailing list IPT at lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gbif.org/pipermail/ipt/attachments/20120309/9ee77495/attachment-0001.html From trobertson at gbif.org Fri Mar 9 10:05:40 2012 From: trobertson at gbif.org (Tim Robertson [GBIF]) Date: Fri, 9 Mar 2012 10:05:40 +0100 Subject: [IPT] All space-characters in metadata are replaced to plus-character In-Reply-To: <7E11F47B5584C642AEBB77967228BE532E837FDB@EXCVS1.uefad.uef.fi> References: <7E11F47B5584C642AEBB77967228BE532E837FC9@EXCVS1.uefad.uef.fi> <7E11F47B5584C642AEBB77967228BE532E837FDB@EXCVS1.uefad.uef.fi> Message-ID: <845F06C4-1971-48B1-A696-72A0F1ACDB54@gbif.org> Hi Tero, How very strange. Given this is public anyway (http://db.digitarium.fi:8080/ipt/eml.do?r=nylander) would you mind attaching the file from the filesystem please? I'd like to look at the file encoding etc. Thanks, Tim On Mar 9, 2012, at 9:44 AM, Tero Mononen wrote: > Dear Tim, > > There?s only public example (Title: William+Nylander+lichen+collection): > http://db.digitarium.fi:8080/ipt/resource.do?r=nylander > > It?s interesting, eml.xml on file system contains line: > William+Nylander+lichen+collection > > But eml via IPT/Tomcat offers line: > William Nylander lichen collection > > It?s pure Tomcat without proxies. > > > BR, > Tero Mononen > > From: Tim Robertson [GBIF] [mailto:trobertson at gbif.org] > Sent: Friday, March 09, 2012 10:37 AM > To: Tero Mononen > Cc: ipt at lists.gbif.org > Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character > > Dear Tero, > > Could you please provide a link to an example file? We'll investigate, but this is not a behavior I have ever seen with a Tomcat application. > > Do you run any proxies or mod_jk or anything like that? > > Thanks, > Tim > > > On Mar 9, 2012, at 9:35 AM, Tero Mononen wrote: > > > Hi > > We have used this IPT-setup without any problems till now. > > System: > Version 2.0.2-r3306 > Apache Tomcat/6.0.24 > JVM 1.6.0_29-b1 > > Problem: > All space-characters in metadata are replaced to plus-character. For example title ?foo bar car? is saved as ?foo+bar+car?. It affects in every text field in metadata. > > If I include at least one plus-char in a text value, it prevents the space replacement. For example ?foo bar car+dar? is saved as it is. > > I think this is related to Java/Tomcat/urlencode. Do you have suggestions how to fix this problem? > > > Best Regards, > Tero Mononen > > -- > Digitarium > Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) > FI-80101 Joensuu > http://www.digitarium.fi/ > > Tero Mononen, Analyst Programmer > tero.mononen at uef.fi > +358-50-5631788 > > _______________________________________________ > IPT mailing list > IPT at lists.gbif.org > http://lists.gbif.org/mailman/listinfo/ipt -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gbif.org/pipermail/ipt/attachments/20120309/81fd3118/attachment.html From tero.mononen at uef.fi Fri Mar 9 10:15:40 2012 From: tero.mononen at uef.fi (Tero Mononen) Date: Fri, 9 Mar 2012 11:15:40 +0200 Subject: [IPT] All space-characters in metadata are replaced to plus-character In-Reply-To: <845F06C4-1971-48B1-A696-72A0F1ACDB54@gbif.org> References: <7E11F47B5584C642AEBB77967228BE532E837FC9@EXCVS1.uefad.uef.fi> <7E11F47B5584C642AEBB77967228BE532E837FDB@EXCVS1.uefad.uef.fi> <845F06C4-1971-48B1-A696-72A0F1ACDB54@gbif.org> Message-ID: <4F59CA3C.1030501@uef.fi> Hi There is the original eml.xml. Is that the only file you are interested in? BR, Tero On 03/09/2012 11:05 AM, Tim Robertson [GBIF] wrote: Hi Tero, How very strange. Given this is public anyway (http://db.digitarium.fi:8080/ipt/eml.do?r=nylander) would you mind attaching the file from the filesystem please? I'd like to look at the file encoding etc. Thanks, Tim On Mar 9, 2012, at 9:44 AM, Tero Mononen wrote: Dear Tim, There?s only public example (Title: William+Nylander+lichen+collection): http://db.digitarium.fi:8080/ipt/resource.do?r=nylander It?s interesting, eml.xml on file system contains line: William+Nylander+lichen+collection But eml via IPT/Tomcat offers line: William Nylander lichen collection It?s pure Tomcat without proxies. BR, Tero Mononen From: Tim Robertson [GBIF] [mailto:trobertson at gbif.org] Sent: Friday, March 09, 2012 10:37 AM To: Tero Mononen Cc: ipt at lists.gbif.org Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character Dear Tero, Could you please provide a link to an example file? We'll investigate, but this is not a behavior I have ever seen with a Tomcat application. Do you run any proxies or mod_jk or anything like that? Thanks, Tim On Mar 9, 2012, at 9:35 AM, Tero Mononen wrote: Hi We have used this IPT-setup without any problems till now. System: Version 2.0.2-r3306 Apache Tomcat/6.0.24 JVM 1.6.0_29-b1 Problem: All space-characters in metadata are replaced to plus-character. For example title ?foo bar car? is saved as ?foo+bar+car?. It affects in every text field in metadata. If I include at least one plus-char in a text value, it prevents the space replacement. For example ?foo bar car+dar? is saved as it is. I think this is related to Java/Tomcat/urlencode. Do you have suggestions how to fix this problem? Best Regards, Tero Mononen -- Digitarium Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) FI-80101 Joensuu http://www.digitarium.fi/ Tero Mononen, Analyst Programmer tero.mononen at uef.fi +358-50-5631788 _______________________________________________ IPT mailing list IPT at lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt -- Digitarium Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) FI-80101 Joensuu http://www.digitarium.fi/ Tero Mononen, Analyst Programmer tero.mononen at uef.fi +358-50-5631788 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gbif.org/pipermail/ipt/attachments/20120309/0eaf236b/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: eml.xml Type: text/xml Size: 5028 bytes Desc: eml.xml Url : http://lists.gbif.org/pipermail/ipt/attachments/20120309/0eaf236b/attachment-0001.xml From trobertson at gbif.org Fri Mar 9 10:40:15 2012 From: trobertson at gbif.org (Tim Robertson [GBIF]) Date: Fri, 9 Mar 2012 10:40:15 +0100 Subject: [IPT] All space-characters in metadata are replaced to plus-character In-Reply-To: <4F59CA3C.1030501@uef.fi> References: <7E11F47B5584C642AEBB77967228BE532E837FC9@EXCVS1.uefad.uef.fi> <7E11F47B5584C642AEBB77967228BE532E837FDB@EXCVS1.uefad.uef.fi> <845F06C4-1971-48B1-A696-72A0F1ACDB54@gbif.org> <4F59CA3C.1030501@uef.fi> Message-ID: <8E6E552E-5A05-467D-BC5E-6522DE0DC6A3@gbif.org> Thanks Tero Very curious indeed. The single input fields are represented with + but the description field which is a Textarea on the form is not. We'll look more into it. Cheers, Tim On Mar 9, 2012, at 10:15 AM, Tero Mononen wrote: > Hi > > There is the original eml.xml. Is that the only file you are interested in? > > > BR, > Tero > > On 03/09/2012 11:05 AM, Tim Robertson [GBIF] wrote: >> >> Hi Tero, >> >> How very strange. >> Given this is public anyway (http://db.digitarium.fi:8080/ipt/eml.do?r=nylander) would you mind attaching the file from the filesystem please? I'd like to look at the file encoding etc. >> >> Thanks, >> Tim >> >> >> On Mar 9, 2012, at 9:44 AM, Tero Mononen wrote: >> >>> Dear Tim, >>> >>> There?s only public example (Title: William+Nylander+lichen+collection): >>> http://db.digitarium.fi:8080/ipt/resource.do?r=nylander >>> >>> It?s interesting, eml.xml on file system contains line: >>> William+Nylander+lichen+collection >>> >>> But eml via IPT/Tomcat offers line: >>> William Nylander lichen collection >>> >>> It?s pure Tomcat without proxies. >>> >>> >>> BR, >>> Tero Mononen >>> >>> From: Tim Robertson [GBIF] [mailto:trobertson at gbif.org] >>> Sent: Friday, March 09, 2012 10:37 AM >>> To: Tero Mononen >>> Cc: ipt at lists.gbif.org >>> Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character >>> >>> Dear Tero, >>> >>> Could you please provide a link to an example file? We'll investigate, but this is not a behavior I have ever seen with a Tomcat application. >>> >>> Do you run any proxies or mod_jk or anything like that? >>> >>> Thanks, >>> Tim >>> >>> >>> On Mar 9, 2012, at 9:35 AM, Tero Mononen wrote: >>> >>> >>> Hi >>> >>> We have used this IPT-setup without any problems till now. >>> >>> System: >>> Version 2.0.2-r3306 >>> Apache Tomcat/6.0.24 >>> JVM 1.6.0_29-b1 >>> >>> Problem: >>> All space-characters in metadata are replaced to plus-character. For example title ?foo bar car? is saved as ?foo+bar+car?. It affects in every text field in metadata. >>> >>> If I include at least one plus-char in a text value, it prevents the space replacement. For example ?foo bar car+dar? is saved as it is. >>> >>> I think this is related to Java/Tomcat/urlencode. Do you have suggestions how to fix this problem? >>> >>> >>> Best Regards, >>> Tero Mononen >>> >>> -- >>> Digitarium >>> Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) >>> FI-80101 Joensuu >>> http://www.digitarium.fi/ >>> >>> Tero Mononen, Analyst Programmer >>> tero.mononen at uef.fi >>> +358-50-5631788 >>> >>> _______________________________________________ >>> IPT mailing list >>> IPT at lists.gbif.org >>> http://lists.gbif.org/mailman/listinfo/ipt >> > > -- > Digitarium > Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) > FI-80101 Joensuu > http://www.digitarium.fi/ > > Tero Mononen, Analyst Programmer > tero.mononen at uef.fi > +358-50-5631788 > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gbif.org/pipermail/ipt/attachments/20120309/cfbc5d5d/attachment-0001.html From kbraak at gbif.org Fri Mar 9 10:54:00 2012 From: kbraak at gbif.org (Kyle Braak [GBIF]) Date: Fri, 9 Mar 2012 10:54:00 +0100 Subject: [IPT] All space-characters in metadata are replaced to plus-character In-Reply-To: <8E6E552E-5A05-467D-BC5E-6522DE0DC6A3@gbif.org> References: <7E11F47B5584C642AEBB77967228BE532E837FC9@EXCVS1.uefad.uef.fi> <7E11F47B5584C642AEBB77967228BE532E837FDB@EXCVS1.uefad.uef.fi> <845F06C4-1971-48B1-A696-72A0F1ACDB54@gbif.org> <4F59CA3C.1030501@uef.fi> <8E6E552E-5A05-467D-BC5E-6522DE0DC6A3@gbif.org> Message-ID: Dear Tero, Can I kindly ask you to fill in a bug report on the IPT Project Site: http://code.google.com/p/gbif-providertoolkit/issues/entry In addition to the IPT version, Java version, and Tomcat version, can you also specify the Operating System you are using (with version), as well as the browser (with version) that you are using to fill in the metadata? Out of curiosity, have you tried entering metadata through different browsers (Chrome, Firefox, IE)? This will help us try and reproduce the problem ourselves so that if there is something wrong with the application we can fix it ASAP. Thanks a lot, Kyle On Mar 9, 2012, at 10:40 AM, Tim Robertson [GBIF] wrote: > Thanks Tero > > Very curious indeed. The single input fields are represented with + but the description field which is a Textarea on the form is not. > > We'll look more into it. > > Cheers, > Tim > > > On Mar 9, 2012, at 10:15 AM, Tero Mononen wrote: > >> Hi >> >> There is the original eml.xml. Is that the only file you are interested in? >> >> >> BR, >> Tero >> >> On 03/09/2012 11:05 AM, Tim Robertson [GBIF] wrote: >>> >>> Hi Tero, >>> >>> How very strange. >>> Given this is public anyway (http://db.digitarium.fi:8080/ipt/eml.do?r=nylander) would you mind attaching the file from the filesystem please? I'd like to look at the file encoding etc. >>> >>> Thanks, >>> Tim >>> >>> >>> On Mar 9, 2012, at 9:44 AM, Tero Mononen wrote: >>> >>>> Dear Tim, >>>> >>>> There?s only public example (Title: William+Nylander+lichen+collection): >>>> http://db.digitarium.fi:8080/ipt/resource.do?r=nylander >>>> >>>> It?s interesting, eml.xml on file system contains line: >>>> William+Nylander+lichen+collection >>>> >>>> But eml via IPT/Tomcat offers line: >>>> William Nylander lichen collection >>>> >>>> It?s pure Tomcat without proxies. >>>> >>>> >>>> BR, >>>> Tero Mononen >>>> >>>> From: Tim Robertson [GBIF] [mailto:trobertson at gbif.org] >>>> Sent: Friday, March 09, 2012 10:37 AM >>>> To: Tero Mononen >>>> Cc: ipt at lists.gbif.org >>>> Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character >>>> >>>> Dear Tero, >>>> >>>> Could you please provide a link to an example file? We'll investigate, but this is not a behavior I have ever seen with a Tomcat application. >>>> >>>> Do you run any proxies or mod_jk or anything like that? >>>> >>>> Thanks, >>>> Tim >>>> >>>> >>>> On Mar 9, 2012, at 9:35 AM, Tero Mononen wrote: >>>> >>>> >>>> Hi >>>> >>>> We have used this IPT-setup without any problems till now. >>>> >>>> System: >>>> Version 2.0.2-r3306 >>>> Apache Tomcat/6.0.24 >>>> JVM 1.6.0_29-b1 >>>> >>>> Problem: >>>> All space-characters in metadata are replaced to plus-character. For example title ?foo bar car? is saved as ?foo+bar+car?. It affects in every text field in metadata. >>>> >>>> If I include at least one plus-char in a text value, it prevents the space replacement. For example ?foo bar car+dar? is saved as it is. >>>> >>>> I think this is related to Java/Tomcat/urlencode. Do you have suggestions how to fix this problem? >>>> >>>> >>>> Best Regards, >>>> Tero Mononen >>>> >>>> -- >>>> Digitarium >>>> Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) >>>> FI-80101 Joensuu >>>> http://www.digitarium.fi/ >>>> >>>> Tero Mononen, Analyst Programmer >>>> tero.mononen at uef.fi >>>> +358-50-5631788 >>>> >>>> _______________________________________________ >>>> IPT mailing list >>>> IPT at lists.gbif.org >>>> http://lists.gbif.org/mailman/listinfo/ipt >>> >> >> -- >> Digitarium >> Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) >> FI-80101 Joensuu >> http://www.digitarium.fi/ >> >> Tero Mononen, Analyst Programmer >> tero.mononen at uef.fi >> +358-50-5631788 >> > > _______________________________________________ > IPT mailing list > IPT at lists.gbif.org > http://lists.gbif.org/mailman/listinfo/ipt -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gbif.org/pipermail/ipt/attachments/20120309/1f897b7c/attachment-0001.html From tero.mononen at uef.fi Fri Mar 9 11:22:58 2012 From: tero.mononen at uef.fi (Tero Mononen) Date: Fri, 9 Mar 2012 12:22:58 +0200 Subject: [IPT] All space-characters in metadata are replaced to plus-character In-Reply-To: References: <7E11F47B5584C642AEBB77967228BE532E837FC9@EXCVS1.uefad.uef.fi> <7E11F47B5584C642AEBB77967228BE532E837FDB@EXCVS1.uefad.uef.fi> <845F06C4-1971-48B1-A696-72A0F1ACDB54@gbif.org> <4F59CA3C.1030501@uef.fi> <8E6E552E-5A05-467D-BC5E-6522DE0DC6A3@gbif.org> Message-ID: <7E11F47B5584C642AEBB77967228BE532E83807B@EXCVS1.uefad.uef.fi> Hi Thank you, I made new issue (http://code.google.com/p/gbif-providertoolkit/issues/detail?id=845). We have tested many browsers on Windows and Linux. I think the reproduction is hard because it did work on our system well and then something weird happened causing this... BR, Tero From: Kyle Braak [GBIF] [mailto:kbraak at gbif.org] Sent: Friday, March 09, 2012 11:54 AM To: Tero Mononen Cc: ipt at lists.gbif.org; Tim Robertson [GBIF] Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character Dear Tero, Can I kindly ask you to fill in a bug report on the IPT Project Site: http://code.google.com/p/gbif-providertoolkit/issues/entry In addition to the IPT version, Java version, and Tomcat version, can you also specify the Operating System you are using (with version), as well as the browser (with version) that you are using to fill in the metadata? Out of curiosity, have you tried entering metadata through different browsers (Chrome, Firefox, IE)? This will help us try and reproduce the problem ourselves so that if there is something wrong with the application we can fix it ASAP. Thanks a lot, Kyle On Mar 9, 2012, at 10:40 AM, Tim Robertson [GBIF] wrote: Thanks Tero Very curious indeed. The single input fields are represented with + but the description field which is a Textarea on the form is not. We'll look more into it. Cheers, Tim On Mar 9, 2012, at 10:15 AM, Tero Mononen wrote: Hi There is the original eml.xml. Is that the only file you are interested in? BR, Tero On 03/09/2012 11:05 AM, Tim Robertson [GBIF] wrote: Hi Tero, How very strange. Given this is public anyway (http://db.digitarium.fi:8080/ipt/eml.do?r=nylander) would you mind attaching the file from the filesystem please? I'd like to look at the file encoding etc. Thanks, Tim On Mar 9, 2012, at 9:44 AM, Tero Mononen wrote: Dear Tim, There's only public example (Title: William+Nylander+lichen+collection): http://db.digitarium.fi:8080/ipt/resource.do?r=nylander It's interesting, eml.xml on file system contains line: William+Nylander+lichen+collection But eml via IPT/Tomcat offers line: William Nylander lichen collection It's pure Tomcat without proxies. BR, Tero Mononen From: Tim Robertson [GBIF] [mailto:trobertson at gbif.org] Sent: Friday, March 09, 2012 10:37 AM To: Tero Mononen Cc: ipt at lists.gbif.org Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character Dear Tero, Could you please provide a link to an example file? We'll investigate, but this is not a behavior I have ever seen with a Tomcat application. Do you run any proxies or mod_jk or anything like that? Thanks, Tim On Mar 9, 2012, at 9:35 AM, Tero Mononen wrote: Hi We have used this IPT-setup without any problems till now. System: Version 2.0.2-r3306 Apache Tomcat/6.0.24 JVM 1.6.0_29-b1 Problem: All space-characters in metadata are replaced to plus-character. For example title "foo bar car" is saved as "foo+bar+car". It affects in every text field in metadata. If I include at least one plus-char in a text value, it prevents the space replacement. For example "foo bar car+dar" is saved as it is. I think this is related to Java/Tomcat/urlencode. Do you have suggestions how to fix this problem? Best Regards, Tero Mononen -- Digitarium Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) FI-80101 Joensuu http://www.digitarium.fi/ Tero Mononen, Analyst Programmer tero.mononen at uef.fi +358-50-5631788 _______________________________________________ IPT mailing list IPT at lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt -- Digitarium Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) FI-80101 Joensuu http://www.digitarium.fi/ Tero Mononen, Analyst Programmer tero.mononen at uef.fi +358-50-5631788 _______________________________________________ IPT mailing list IPT at lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gbif.org/pipermail/ipt/attachments/20120309/ed370c89/attachment.html From trobertson at gbif.org Fri Mar 9 11:47:38 2012 From: trobertson at gbif.org (Tim Robertson [GBIF]) Date: Fri, 9 Mar 2012 11:47:38 +0100 Subject: [IPT] All space-characters in metadata are replaced to plus-character In-Reply-To: <7E11F47B5584C642AEBB77967228BE532E83807B@EXCVS1.uefad.uef.fi> References: <7E11F47B5584C642AEBB77967228BE532E837FC9@EXCVS1.uefad.uef.fi> <7E11F47B5584C642AEBB77967228BE532E837FDB@EXCVS1.uefad.uef.fi> <845F06C4-1971-48B1-A696-72A0F1ACDB54@gbif.org> <4F59CA3C.1030501@uef.fi> <8E6E552E-5A05-467D-BC5E-6522DE0DC6A3@gbif.org> <7E11F47B5584C642AEBB77967228BE532E83807B@EXCVS1.uefad.uef.fi> Message-ID: <989C4CCB-087A-4AF5-9E78-19ABB05AC146@gbif.org> > Hi > > Thank you, I made new issue (http://code.google.com/p/gbif-providertoolkit/issues/detail?id=845). > > We have tested many browsers on Windows and Linux. I think the reproduction is hard because it did work on our system well and then something weird happened causing this? Hi Tero, What changed between it working well, and then this happening please? OS upgrades, OS changes, Tomcat upgrades, Java updates etc The *good* news is the IPT still works - the EML is correct when accessed through Tomcat. Of course we want to fix the direct file access route, but the IPT is operating correctly through the IPT interface (e.g. http://db.digitarium.fi:8080/ipt/eml.do?r=nylander is correct ) Thanks, Tim > > > BR, > Tero > > From: Kyle Braak [GBIF] [mailto:kbraak at gbif.org] > Sent: Friday, March 09, 2012 11:54 AM > To: Tero Mononen > Cc: ipt at lists.gbif.org; Tim Robertson [GBIF] > Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character > > Dear Tero, > > Can I kindly ask you to fill in a bug report on the IPT Project Site: http://code.google.com/p/gbif-providertoolkit/issues/entry > > In addition to the IPT version, Java version, and Tomcat version, can you also specify the Operating System you are using (with version), as well as the browser (with version) that you are using to fill in the metadata? Out of curiosity, have you tried entering metadata through different browsers (Chrome, Firefox, IE)? > > This will help us try and reproduce the problem ourselves so that if there is something wrong with the application we can fix it ASAP. > > Thanks a lot, > > Kyle > On Mar 9, 2012, at 10:40 AM, Tim Robertson [GBIF] wrote: > > > Thanks Tero > > Very curious indeed. The single input fields are represented with + but the description field which is a Textarea on the form is not. > > We'll look more into it. > > Cheers, > Tim > > > On Mar 9, 2012, at 10:15 AM, Tero Mononen wrote: > > > Hi > > There is the original eml.xml. Is that the only file you are interested in? > > > BR, > Tero > > On 03/09/2012 11:05 AM, Tim Robertson [GBIF] wrote: > Hi Tero, > > How very strange. > Given this is public anyway (http://db.digitarium.fi:8080/ipt/eml.do?r=nylander) would you mind attaching the file from the filesystem please? I'd like to look at the file encoding etc. > > Thanks, > Tim > > > On Mar 9, 2012, at 9:44 AM, Tero Mononen wrote: > > > Dear Tim, > > There?s only public example (Title: William+Nylander+lichen+collection): > http://db.digitarium.fi:8080/ipt/resource.do?r=nylander > > It?s interesting, eml.xml on file system contains line: > William+Nylander+lichen+collection > > But eml via IPT/Tomcat offers line: > William Nylander lichen collection > > It?s pure Tomcat without proxies. > > > BR, > Tero Mononen > > From: Tim Robertson [GBIF] [mailto:trobertson at gbif.org] > Sent: Friday, March 09, 2012 10:37 AM > To: Tero Mononen > Cc: ipt at lists.gbif.org > Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character > > Dear Tero, > > Could you please provide a link to an example file? We'll investigate, but this is not a behavior I have ever seen with a Tomcat application. > > Do you run any proxies or mod_jk or anything like that? > > Thanks, > Tim > > > On Mar 9, 2012, at 9:35 AM, Tero Mononen wrote: > > > > Hi > > We have used this IPT-setup without any problems till now. > > System: > Version 2.0.2-r3306 > Apache Tomcat/6.0.24 > JVM 1.6.0_29-b1 > > Problem: > All space-characters in metadata are replaced to plus-character. For example title ?foo bar car? is saved as ?foo+bar+car?. It affects in every text field in metadata. > > If I include at least one plus-char in a text value, it prevents the space replacement. For example ?foo bar car+dar? is saved as it is. > > I think this is related to Java/Tomcat/urlencode. Do you have suggestions how to fix this problem? > > > Best Regards, > Tero Mononen > > -- > Digitarium > Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) > FI-80101 Joensuu > http://www.digitarium.fi/ > > Tero Mononen, Analyst Programmer > tero.mononen at uef.fi > +358-50-5631788 > > _______________________________________________ > IPT mailing list > IPT at lists.gbif.org > http://lists.gbif.org/mailman/listinfo/ipt > > > > -- > Digitarium > Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) > FI-80101 Joensuu > http://www.digitarium.fi/ > > Tero Mononen, Analyst Programmer > tero.mononen at uef.fi > +358-50-5631788 > > > _______________________________________________ > IPT mailing list > IPT at lists.gbif.org > http://lists.gbif.org/mailman/listinfo/ipt -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gbif.org/pipermail/ipt/attachments/20120309/42864c05/attachment-0001.html From hannu.saarenmaa at helsinki.fi Fri Mar 9 12:03:02 2012 From: hannu.saarenmaa at helsinki.fi (Hannu Saarenmaa) Date: Fri, 09 Mar 2012 13:03:02 +0200 Subject: [IPT] All space-characters in metadata are replaced to plus-character In-Reply-To: <7E11F47B5584C642AEBB77967228BE532E837FDB@EXCVS1.uefad.uef.fi> References: <7E11F47B5584C642AEBB77967228BE532E837FC9@EXCVS1.uefad.uef.fi> <7E11F47B5584C642AEBB77967228BE532E837FDB@EXCVS1.uefad.uef.fi> Message-ID: <4F59E366.3070502@helsinki.fi> This EML is older than the edited metadata. It was made before the problem appeared. I just made a new EML in http://db.digitarium.fi:8080/ipt/resource.do?r=test The pluses do go in this. Hannu On 2012-03-09 10:44, Tero Mononen wrote: > > Dear Tim, > > There's only public example (Title: William+Nylander+lichen+collection): > > http://db.digitarium.fi:8080/ipt/resource.do?r=nylander > > It's interesting, eml.xml on file system contains line: > > William+Nylander+lichen+collection > > But eml via IPT/Tomcat offers line: > > William Nylander lichen collection > > It's pure Tomcat without proxies. > > BR, > > Tero Mononen > > *From:*Tim Robertson [GBIF] [mailto:trobertson at gbif.org] > *Sent:* Friday, March 09, 2012 10:37 AM > *To:* Tero Mononen > *Cc:* ipt at lists.gbif.org > *Subject:* Re: [IPT] All space-characters in metadata are replaced to > plus-character > > Dear Tero, > > Could you please provide a link to an example file? We'll > investigate, but this is not a behavior I have ever seen with a Tomcat > application. > > Do you run any proxies or mod_jk or anything like that? > > Thanks, > > Tim > > On Mar 9, 2012, at 9:35 AM, Tero Mononen wrote: > > > > Hi > > We have used this IPT-setup without any problems till now. > > System: > > Version 2.0.2-r3306 > > Apache Tomcat/6.0.24 > > JVM 1.6.0_29-b1 > > Problem: > > All space-characters in metadata are replaced to plus-character. For > example title "foo bar car" is saved as "foo+bar+car". It affects in > every text field in metadata. > > If I include at least one plus-char in a text value, it prevents the > space replacement. For example "foo bar car+dar" is saved as it is. > > I think this is related to Java/Tomcat/urlencode. Do you have > suggestions how to fix this problem? > > Best Regards, > > Tero Mononen > > -- > > Digitarium > > Digitisation Centre of the Finnish Museum of Natural History and the > University of Eastern Finland Faculty of Science and Forestry, Joensuu > Science Park L?nsikatu 15 (P.O. Box 111) > > FI-80101 Joensuu > > http://www.digitarium.fi/ > > Tero Mononen, Analyst Programmer > > tero.mononen at uef.fi > > +358-50-5631788 > > _______________________________________________ > IPT mailing list > IPT at lists.gbif.org > http://lists.gbif.org/mailman/listinfo/ipt > > > _______________________________________________ > IPT mailing list > IPT at lists.gbif.org > http://lists.gbif.org/mailman/listinfo/ipt -- Digitarium - Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland School of Computing, SIB-labs, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) FIN-80101 Joensuu http://www.digitarium.fi/ Hannu Saarenmaa, Project Manager hannu.saarenmaa at helsinki.fi Skypename hsaarenmaa Mobile +358-50-4479668 GBIF Node Manager for Finland http://www.gbif.fi/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gbif.org/pipermail/ipt/attachments/20120309/5813bfd7/attachment.html From hannu.saarenmaa at helsinki.fi Fri Mar 9 12:13:44 2012 From: hannu.saarenmaa at helsinki.fi (Hannu Saarenmaa) Date: Fri, 09 Mar 2012 13:13:44 +0200 Subject: [IPT] All space-characters in metadata are replaced to plus-character In-Reply-To: References: <7E11F47B5584C642AEBB77967228BE532E837FC9@EXCVS1.uefad.uef.fi> <7E11F47B5584C642AEBB77967228BE532E837FDB@EXCVS1.uefad.uef.fi> <845F06C4-1971-48B1-A696-72A0F1ACDB54@gbif.org> <4F59CA3C.1030501@uef.fi> <8E6E552E-5A05-467D-BC5E-6522DE0DC6A3@gbif.org> Message-ID: <4F59E5E8.9050206@helsinki.fi> I have tried Firfefox and IE on Win7 and Firefox on Linux. Behavior is the same. Hannu On 2012-03-09 11:54, Kyle Braak [GBIF] wrote: > Dear Tero, > > Can I kindly ask you to fill in a bug report on the IPT Project Site: > http://code.google.com/p/gbif-providertoolkit/issues/entry > > In addition to the IPT version, Java version, and Tomcat version, can > you also specify the Operating System you are using (with version), as > well as the browser (with version) that you are using to fill in the > metadata? Out of curiosity, have you tried entering metadata through > different browsers (Chrome, Firefox, IE)? > > This will help us try and reproduce the problem ourselves so that if > there is something wrong with the application we can fix it ASAP. > > Thanks a lot, > > Kyle > On Mar 9, 2012, at 10:40 AM, Tim Robertson [GBIF] wrote: > >> Thanks Tero >> >> Very curious indeed. The single input fields are represented with + >> but the description field which is a Textarea on the form is not. >> >> We'll look more into it. >> >> Cheers, >> Tim >> >> >> On Mar 9, 2012, at 10:15 AM, Tero Mononen wrote: >> >>> Hi >>> >>> There is the original eml.xml. Is that the only file you are >>> interested in? >>> >>> >>> BR, >>> Tero >>> >>> On 03/09/2012 11:05 AM, Tim Robertson [GBIF] wrote: >>>> Hi Tero, >>>> >>>> How very strange. >>>> Given this is public anyway >>>> (http://db.digitarium.fi:8080/ipt/eml.do?r=nylander) would you mind >>>> attaching the file from the filesystem please? I'd like to look at >>>> the file encoding etc. >>>> >>>> Thanks, >>>> Tim >>>> >>>> >>>> On Mar 9, 2012, at 9:44 AM, Tero Mononen wrote: >>>> >>>>> Dear Tim, >>>>> There?s only public example (Title: >>>>> William+Nylander+lichen+collection): >>>>> http://db.digitarium.fi:8080/ipt/resource.do?r=nylander >>>>> It?s interesting, eml.xml on file system contains line: >>>>> William+Nylander+lichen+collection >>>>> But eml via IPT/Tomcat offers line: >>>>> William Nylander lichen collection >>>>> It?s pure Tomcat without proxies. >>>>> BR, >>>>> Tero Mononen >>>>> *From:*Tim Robertson [GBIF] [mailto:trobertson at gbif.org] >>>>> *Sent:*Friday, March 09, 2012 10:37 AM >>>>> *To:*Tero Mononen >>>>> *Cc:*ipt at lists.gbif.org >>>>> *Subject:*Re: [IPT] All space-characters in metadata are replaced >>>>> to plus-character >>>>> Dear Tero, >>>>> Could you please provide a link to an example file? We'll >>>>> investigate, but this is not a behavior I have ever seen with a >>>>> Tomcat application. >>>>> Do you run any proxies or mod_jk or anything like that? >>>>> Thanks, >>>>> Tim >>>>> On Mar 9, 2012, at 9:35 AM, Tero Mononen wrote: >>>>> >>>>> >>>>> Hi >>>>> We have used this IPT-setup without any problems till now. >>>>> System: >>>>> Version 2.0.2-r3306 >>>>> Apache Tomcat/6.0.24 >>>>> JVM 1.6.0_29-b1 >>>>> Problem: >>>>> All space-characters in metadata are replaced to plus-character. >>>>> For example title ?foo bar car? is saved as ?foo+bar+car?. It >>>>> affects in every text field in metadata. >>>>> If I include at least one plus-char in a text value, it prevents >>>>> the space replacement. For example ?foo bar car+dar? is saved as >>>>> it is. >>>>> I think this is related to Java/Tomcat/urlencode. Do you have >>>>> suggestions how to fix this problem? >>>>> Best Regards, >>>>> Tero Mononen >>>>> -- >>>>> Digitarium >>>>> Digitisation Centre of the Finnish Museum of Natural History and >>>>> the University of Eastern Finland Faculty of Science and Forestry, >>>>> Joensuu Science Park L?nsikatu 15 (P.O. Box 111) >>>>> FI-80101 Joensuu >>>>> http://www.digitarium.fi/ >>>>> Tero Mononen, Analyst Programmer >>>>> tero.mononen at uef.fi >>>>> +358-50-5631788 >>>>> _______________________________________________ >>>>> IPT mailing list >>>>> IPT at lists.gbif.org >>>>> http://lists.gbif.org/mailman/listinfo/ipt >>>> >>> >>> -- >>> Digitarium >>> Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) >>> FI-80101 Joensuu >>> http://www.digitarium.fi/ >>> >>> Tero Mononen, Analyst Programmer >>> tero.mononen at uef.fi >>> +358-50-5631788 >>> >> >> _______________________________________________ >> IPT mailing list >> IPT at lists.gbif.org >> http://lists.gbif.org/mailman/listinfo/ipt > > > _______________________________________________ > IPT mailing list > IPT at lists.gbif.org > http://lists.gbif.org/mailman/listinfo/ipt -- Digitarium - Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland School of Computing, SIB-labs, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) FIN-80101 Joensuu http://www.digitarium.fi/ Hannu Saarenmaa, Project Manager hannu.saarenmaa at helsinki.fi Skypename hsaarenmaa Mobile +358-50-4479668 GBIF Node Manager for Finland http://www.gbif.fi/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gbif.org/pipermail/ipt/attachments/20120309/1aab26af/attachment-0001.html From tero.mononen at uef.fi Fri Mar 9 12:25:03 2012 From: tero.mononen at uef.fi (Tero Mononen) Date: Fri, 9 Mar 2012 13:25:03 +0200 Subject: [IPT] All space-characters in metadata are replaced to plus-character In-Reply-To: <989C4CCB-087A-4AF5-9E78-19ABB05AC146@gbif.org> References: <7E11F47B5584C642AEBB77967228BE532E837FC9@EXCVS1.uefad.uef.fi> <7E11F47B5584C642AEBB77967228BE532E837FDB@EXCVS1.uefad.uef.fi> <845F06C4-1971-48B1-A696-72A0F1ACDB54@gbif.org> <4F59CA3C.1030501@uef.fi> <8E6E552E-5A05-467D-BC5E-6522DE0DC6A3@gbif.org> <7E11F47B5584C642AEBB77967228BE532E83807B@EXCVS1.uefad.uef.fi> <989C4CCB-087A-4AF5-9E78-19ABB05AC146@gbif.org> Message-ID: <7E11F47B5584C642AEBB77967228BE532E8380E8@EXCVS1.uefad.uef.fi> Hi Only very minor updates from openSUSE to tomcat6 and kernel 2.6.34. Tomcat from version 6.0.24-5.14.1 to version 6.0.24-5.16.1. Kernel 2.6.34.10-0.4.1 -> 2.6.34.10-0.6.1 BR, Tero From: Tim Robertson [GBIF] [mailto:trobertson at gbif.org] Sent: Friday, March 09, 2012 12:48 PM To: Tero Mononen Cc: Kyle Braak [GBIF]; ipt at lists.gbif.org Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character Hi Thank you, I made new issue (http://code.google.com/p/gbif-providertoolkit/issues/detail?id=845). We have tested many browsers on Windows and Linux. I think the reproduction is hard because it did work on our system well and then something weird happened causing this... Hi Tero, What changed between it working well, and then this happening please? OS upgrades, OS changes, Tomcat upgrades, Java updates etc The *good* news is the IPT still works - the EML is correct when accessed through Tomcat. Of course we want to fix the direct file access route, but the IPT is operating correctly through the IPT interface (e.g. http://db.digitarium.fi:8080/ipt/eml.do?r=nylander is correct ) Thanks, Tim BR, Tero From: Kyle Braak [GBIF] [mailto:kbraak at gbif.org] Sent: Friday, March 09, 2012 11:54 AM To: Tero Mononen Cc: ipt at lists.gbif.org; Tim Robertson [GBIF] Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character Dear Tero, Can I kindly ask you to fill in a bug report on the IPT Project Site: http://code.google.com/p/gbif-providertoolkit/issues/entry In addition to the IPT version, Java version, and Tomcat version, can you also specify the Operating System you are using (with version), as well as the browser (with version) that you are using to fill in the metadata? Out of curiosity, have you tried entering metadata through different browsers (Chrome, Firefox, IE)? This will help us try and reproduce the problem ourselves so that if there is something wrong with the application we can fix it ASAP. Thanks a lot, Kyle On Mar 9, 2012, at 10:40 AM, Tim Robertson [GBIF] wrote: Thanks Tero Very curious indeed. The single input fields are represented with + but the description field which is a Textarea on the form is not. We'll look more into it. Cheers, Tim On Mar 9, 2012, at 10:15 AM, Tero Mononen wrote: Hi There is the original eml.xml. Is that the only file you are interested in? BR, Tero On 03/09/2012 11:05 AM, Tim Robertson [GBIF] wrote: Hi Tero, How very strange. Given this is public anyway (http://db.digitarium.fi:8080/ipt/eml.do?r=nylander) would you mind attaching the file from the filesystem please? I'd like to look at the file encoding etc. Thanks, Tim On Mar 9, 2012, at 9:44 AM, Tero Mononen wrote: Dear Tim, There's only public example (Title: William+Nylander+lichen+collection): http://db.digitarium.fi:8080/ipt/resource.do?r=nylander It's interesting, eml.xml on file system contains line: William+Nylander+lichen+collection But eml via IPT/Tomcat offers line: William Nylander lichen collection It's pure Tomcat without proxies. BR, Tero Mononen From: Tim Robertson [GBIF] [mailto:trobertson at gbif.org] Sent: Friday, March 09, 2012 10:37 AM To: Tero Mononen Cc: ipt at lists.gbif.org Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character Dear Tero, Could you please provide a link to an example file? We'll investigate, but this is not a behavior I have ever seen with a Tomcat application. Do you run any proxies or mod_jk or anything like that? Thanks, Tim On Mar 9, 2012, at 9:35 AM, Tero Mononen wrote: Hi We have used this IPT-setup without any problems till now. System: Version 2.0.2-r3306 Apache Tomcat/6.0.24 JVM 1.6.0_29-b1 Problem: All space-characters in metadata are replaced to plus-character. For example title "foo bar car" is saved as "foo+bar+car". It affects in every text field in metadata. If I include at least one plus-char in a text value, it prevents the space replacement. For example "foo bar car+dar" is saved as it is. I think this is related to Java/Tomcat/urlencode. Do you have suggestions how to fix this problem? Best Regards, Tero Mononen -- Digitarium Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) FI-80101 Joensuu http://www.digitarium.fi/ Tero Mononen, Analyst Programmer tero.mononen at uef.fi +358-50-5631788 _______________________________________________ IPT mailing list IPT at lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt -- Digitarium Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) FI-80101 Joensuu http://www.digitarium.fi/ Tero Mononen, Analyst Programmer tero.mononen at uef.fi +358-50-5631788 _______________________________________________ IPT mailing list IPT at lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gbif.org/pipermail/ipt/attachments/20120309/8c651577/attachment-0001.html From trobertson at gbif.org Fri Mar 9 12:43:59 2012 From: trobertson at gbif.org (Tim Robertson [GBIF]) Date: Fri, 9 Mar 2012 12:43:59 +0100 Subject: [IPT] All space-characters in metadata are replaced to plus-character In-Reply-To: <7E11F47B5584C642AEBB77967228BE532E8380E8@EXCVS1.uefad.uef.fi> References: <7E11F47B5584C642AEBB77967228BE532E837FC9@EXCVS1.uefad.uef.fi> <7E11F47B5584C642AEBB77967228BE532E837FDB@EXCVS1.uefad.uef.fi> <845F06C4-1971-48B1-A696-72A0F1ACDB54@gbif.org> <4F59CA3C.1030501@uef.fi> <8E6E552E-5A05-467D-BC5E-6522DE0DC6A3@gbif.org> <7E11F47B5584C642AEBB77967228BE532E83807B@EXCVS1.uefad.uef.fi> <989C4CCB-087A-4AF5-9E78-19ABB05AC146@gbif.org> <7E11F47B5584C642AEBB77967228BE532E8380E8@EXCVS1.uefad.uef.fi> Message-ID: <659C0C7C-EEB6-41B9-8FA3-266C8A6EE339@gbif.org> This looks like you are hitting this Tomcat6 / OpenSUSE bug: http://stackoverflow.com/questions/9290745/tomcat-6-doesnt-decode-to-space-in-parameter-values Can you please try the suggested fix? Thanks, Tim On Mar 9, 2012, at 12:25 PM, Tero Mononen wrote: > Hi > > Only very minor updates from openSUSE to tomcat6 and kernel 2.6.34. > > Tomcat from version 6.0.24-5.14.1 to version 6.0.24-5.16.1. > Kernel 2.6.34.10-0.4.1 -> 2.6.34.10-0.6.1 > > > BR, > Tero > > From: Tim Robertson [GBIF] [mailto:trobertson at gbif.org] > Sent: Friday, March 09, 2012 12:48 PM > To: Tero Mononen > Cc: Kyle Braak [GBIF]; ipt at lists.gbif.org > Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character > > Hi > > Thank you, I made new issue (http://code.google.com/p/gbif-providertoolkit/issues/detail?id=845). > > We have tested many browsers on Windows and Linux. I think the reproduction is hard because it did work on our system well and then something weird happened causing this? > > Hi Tero, > > What changed between it working well, and then this happening please? OS upgrades, OS changes, Tomcat upgrades, Java updates etc > > The *good* news is the IPT still works - the EML is correct when accessed through Tomcat. Of course we want to fix the direct file access route, but the IPT is operating correctly through the IPT interface (e.g. http://db.digitarium.fi:8080/ipt/eml.do?r=nylander is correct ) > > Thanks, > Tim > > > > > BR, > Tero > > From: Kyle Braak [GBIF] [mailto:kbraak at gbif.org] > Sent: Friday, March 09, 2012 11:54 AM > To: Tero Mononen > Cc: ipt at lists.gbif.org; Tim Robertson [GBIF] > Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character > > Dear Tero, > > Can I kindly ask you to fill in a bug report on the IPT Project Site: http://code.google.com/p/gbif-providertoolkit/issues/entry > > In addition to the IPT version, Java version, and Tomcat version, can you also specify the Operating System you are using (with version), as well as the browser (with version) that you are using to fill in the metadata? Out of curiosity, have you tried entering metadata through different browsers (Chrome, Firefox, IE)? > > This will help us try and reproduce the problem ourselves so that if there is something wrong with the application we can fix it ASAP. > > Thanks a lot, > > Kyle > On Mar 9, 2012, at 10:40 AM, Tim Robertson [GBIF] wrote: > > > > Thanks Tero > > Very curious indeed. The single input fields are represented with + but the description field which is a Textarea on the form is not. > > We'll look more into it. > > Cheers, > Tim > > > On Mar 9, 2012, at 10:15 AM, Tero Mononen wrote: > > > > Hi > > There is the original eml.xml. Is that the only file you are interested in? > > > BR, > Tero > > On 03/09/2012 11:05 AM, Tim Robertson [GBIF] wrote: > Hi Tero, > > How very strange. > Given this is public anyway (http://db.digitarium.fi:8080/ipt/eml.do?r=nylander) would you mind attaching the file from the filesystem please? I'd like to look at the file encoding etc. > > Thanks, > Tim > > > On Mar 9, 2012, at 9:44 AM, Tero Mononen wrote: > > > > Dear Tim, > > There?s only public example (Title: William+Nylander+lichen+collection): > http://db.digitarium.fi:8080/ipt/resource.do?r=nylander > > It?s interesting, eml.xml on file system contains line: > William+Nylander+lichen+collection > > But eml via IPT/Tomcat offers line: > William Nylander lichen collection > > It?s pure Tomcat without proxies. > > > BR, > Tero Mononen > > From: Tim Robertson [GBIF] [mailto:trobertson at gbif.org] > Sent: Friday, March 09, 2012 10:37 AM > To: Tero Mononen > Cc: ipt at lists.gbif.org > Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character > > Dear Tero, > > Could you please provide a link to an example file? We'll investigate, but this is not a behavior I have ever seen with a Tomcat application. > > Do you run any proxies or mod_jk or anything like that? > > Thanks, > Tim > > > On Mar 9, 2012, at 9:35 AM, Tero Mononen wrote: > > > > > Hi > > We have used this IPT-setup without any problems till now. > > System: > Version 2.0.2-r3306 > Apache Tomcat/6.0.24 > JVM 1.6.0_29-b1 > > Problem: > All space-characters in metadata are replaced to plus-character. For example title ?foo bar car? is saved as ?foo+bar+car?. It affects in every text field in metadata. > > If I include at least one plus-char in a text value, it prevents the space replacement. For example ?foo bar car+dar? is saved as it is. > > I think this is related to Java/Tomcat/urlencode. Do you have suggestions how to fix this problem? > > > Best Regards, > Tero Mononen > > -- > Digitarium > Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) > FI-80101 Joensuu > http://www.digitarium.fi/ > > Tero Mononen, Analyst Programmer > tero.mononen at uef.fi > +358-50-5631788 > > _______________________________________________ > IPT mailing list > IPT at lists.gbif.org > http://lists.gbif.org/mailman/listinfo/ipt > > > > > -- > Digitarium > Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) > FI-80101 Joensuu > http://www.digitarium.fi/ > > Tero Mononen, Analyst Programmer > tero.mononen at uef.fi > +358-50-5631788 > > > _______________________________________________ > IPT mailing list > IPT at lists.gbif.org > http://lists.gbif.org/mailman/listinfo/ipt -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gbif.org/pipermail/ipt/attachments/20120309/206bf92d/attachment-0001.html From kbraak at gbif.org Fri Mar 9 12:48:48 2012 From: kbraak at gbif.org (Kyle Braak [GBIF]) Date: Fri, 9 Mar 2012 12:48:48 +0100 Subject: [IPT] All space-characters in metadata are replaced to plus-character In-Reply-To: <659C0C7C-EEB6-41B9-8FA3-266C8A6EE339@gbif.org> References: <7E11F47B5584C642AEBB77967228BE532E837FC9@EXCVS1.uefad.uef.fi> <7E11F47B5584C642AEBB77967228BE532E837FDB@EXCVS1.uefad.uef.fi> <845F06C4-1971-48B1-A696-72A0F1ACDB54@gbif.org> <4F59CA3C.1030501@uef.fi> <8E6E552E-5A05-467D-BC5E-6522DE0DC6A3@gbif.org> <7E11F47B5584C642AEBB77967228BE532E83807B@EXCVS1.uefad.uef.fi> <989C4CCB-087A-4AF5-9E78-19ABB05AC146@gbif.org> <7E11F47B5584C642AEBB77967228BE532E8380E8@EXCVS1.uefad.uef.fi> <659C0C7C-EEB6-41B9-8FA3-266C8A6EE339@gbif.org> Message-ID: <49B8C51D-B126-4EFA-B4F1-B372C1C6B2F1@gbif.org> Hi Tero, It's nice that we might be on the verge of solving this now.. When you have this working, I recommend an upgrade from 2.0.2 to 2.0.3. The upgrade is relatively painless. To do so, a) back up your current data directory to somewhere safe b) download the 2.0.3 war file, and rename it to ipt.war c) stop tomcat, remove ipt/ and ipt.war from the tomcat webapps folder, and add the new ipt.war file d) start tomcat, and open up the IPT in a browser e) presented with the 1st setup page, enter the location of your existing data directory f) press continue to proceed, then visit the Administration page and press the button "Publish all resources" (this may take a few moments as it will republish all resources. Caution: There is a known bug with the upgrade where a taxonomic resources switches to type occurrence. I know that you have purely occurrence resources, but if this switch happens, just try the upgrade again but de-select the subtype (and be sure to save) for each resource before going through the steps. Best of luck, Kyle On Mar 9, 2012, at 12:43 PM, Tim Robertson [GBIF] wrote: > This looks like you are hitting this Tomcat6 / OpenSUSE bug: > http://stackoverflow.com/questions/9290745/tomcat-6-doesnt-decode-to-space-in-parameter-values > > Can you please try the suggested fix? > > Thanks, > Tim > > > > On Mar 9, 2012, at 12:25 PM, Tero Mononen wrote: > >> Hi >> >> Only very minor updates from openSUSE to tomcat6 and kernel 2.6.34. >> >> Tomcat from version 6.0.24-5.14.1 to version 6.0.24-5.16.1. >> Kernel 2.6.34.10-0.4.1 -> 2.6.34.10-0.6.1 >> >> >> BR, >> Tero >> >> From: Tim Robertson [GBIF] [mailto:trobertson at gbif.org] >> Sent: Friday, March 09, 2012 12:48 PM >> To: Tero Mononen >> Cc: Kyle Braak [GBIF]; ipt at lists.gbif.org >> Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character >> >> Hi >> >> Thank you, I made new issue (http://code.google.com/p/gbif-providertoolkit/issues/detail?id=845). >> >> We have tested many browsers on Windows and Linux. I think the reproduction is hard because it did work on our system well and then something weird happened causing this? >> >> Hi Tero, >> >> What changed between it working well, and then this happening please? OS upgrades, OS changes, Tomcat upgrades, Java updates etc >> >> The *good* news is the IPT still works - the EML is correct when accessed through Tomcat. Of course we want to fix the direct file access route, but the IPT is operating correctly through the IPT interface (e.g. http://db.digitarium.fi:8080/ipt/eml.do?r=nylander is correct ) >> >> Thanks, >> Tim >> >> >> >> >> BR, >> Tero >> >> From: Kyle Braak [GBIF] [mailto:kbraak at gbif.org] >> Sent: Friday, March 09, 2012 11:54 AM >> To: Tero Mononen >> Cc: ipt at lists.gbif.org; Tim Robertson [GBIF] >> Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character >> >> Dear Tero, >> >> Can I kindly ask you to fill in a bug report on the IPT Project Site: http://code.google.com/p/gbif-providertoolkit/issues/entry >> >> In addition to the IPT version, Java version, and Tomcat version, can you also specify the Operating System you are using (with version), as well as the browser (with version) that you are using to fill in the metadata? Out of curiosity, have you tried entering metadata through different browsers (Chrome, Firefox, IE)? >> >> This will help us try and reproduce the problem ourselves so that if there is something wrong with the application we can fix it ASAP. >> >> Thanks a lot, >> >> Kyle >> On Mar 9, 2012, at 10:40 AM, Tim Robertson [GBIF] wrote: >> >> >> >> Thanks Tero >> >> Very curious indeed. The single input fields are represented with + but the description field which is a Textarea on the form is not. >> >> We'll look more into it. >> >> Cheers, >> Tim >> >> >> On Mar 9, 2012, at 10:15 AM, Tero Mononen wrote: >> >> >> >> Hi >> >> There is the original eml.xml. Is that the only file you are interested in? >> >> >> BR, >> Tero >> >> On 03/09/2012 11:05 AM, Tim Robertson [GBIF] wrote: >> Hi Tero, >> >> How very strange. >> Given this is public anyway (http://db.digitarium.fi:8080/ipt/eml.do?r=nylander) would you mind attaching the file from the filesystem please? I'd like to look at the file encoding etc. >> >> Thanks, >> Tim >> >> >> On Mar 9, 2012, at 9:44 AM, Tero Mononen wrote: >> >> >> >> Dear Tim, >> >> There?s only public example (Title: William+Nylander+lichen+collection): >> http://db.digitarium.fi:8080/ipt/resource.do?r=nylander >> >> It?s interesting, eml.xml on file system contains line: >> William+Nylander+lichen+collection >> >> But eml via IPT/Tomcat offers line: >> William Nylander lichen collection >> >> It?s pure Tomcat without proxies. >> >> >> BR, >> Tero Mononen >> >> From: Tim Robertson [GBIF] [mailto:trobertson at gbif.org] >> Sent: Friday, March 09, 2012 10:37 AM >> To: Tero Mononen >> Cc: ipt at lists.gbif.org >> Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character >> >> Dear Tero, >> >> Could you please provide a link to an example file? We'll investigate, but this is not a behavior I have ever seen with a Tomcat application. >> >> Do you run any proxies or mod_jk or anything like that? >> >> Thanks, >> Tim >> >> >> On Mar 9, 2012, at 9:35 AM, Tero Mononen wrote: >> >> >> >> >> Hi >> >> We have used this IPT-setup without any problems till now. >> >> System: >> Version 2.0.2-r3306 >> Apache Tomcat/6.0.24 >> JVM 1.6.0_29-b1 >> >> Problem: >> All space-characters in metadata are replaced to plus-character. For example title ?foo bar car? is saved as ?foo+bar+car?. It affects in every text field in metadata. >> >> If I include at least one plus-char in a text value, it prevents the space replacement. For example ?foo bar car+dar? is saved as it is. >> >> I think this is related to Java/Tomcat/urlencode. Do you have suggestions how to fix this problem? >> >> >> Best Regards, >> Tero Mononen >> >> -- >> Digitarium >> Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) >> FI-80101 Joensuu >> http://www.digitarium.fi/ >> >> Tero Mononen, Analyst Programmer >> tero.mononen at uef.fi >> +358-50-5631788 >> >> _______________________________________________ >> IPT mailing list >> IPT at lists.gbif.org >> http://lists.gbif.org/mailman/listinfo/ipt >> >> >> >> >> -- >> Digitarium >> Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) >> FI-80101 Joensuu >> http://www.digitarium.fi/ >> >> Tero Mononen, Analyst Programmer >> tero.mononen at uef.fi >> +358-50-5631788 >> >> >> _______________________________________________ >> IPT mailing list >> IPT at lists.gbif.org >> http://lists.gbif.org/mailman/listinfo/ipt > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gbif.org/pipermail/ipt/attachments/20120309/9f635652/attachment-0001.html From tero.mononen at uef.fi Fri Mar 9 13:45:03 2012 From: tero.mononen at uef.fi (Tero Mononen) Date: Fri, 9 Mar 2012 14:45:03 +0200 Subject: [IPT] All space-characters in metadata are replaced to plus-character In-Reply-To: <49B8C51D-B126-4EFA-B4F1-B372C1C6B2F1@gbif.org> References: <7E11F47B5584C642AEBB77967228BE532E837FC9@EXCVS1.uefad.uef.fi> <7E11F47B5584C642AEBB77967228BE532E837FDB@EXCVS1.uefad.uef.fi> <845F06C4-1971-48B1-A696-72A0F1ACDB54@gbif.org> <4F59CA3C.1030501@uef.fi> <8E6E552E-5A05-467D-BC5E-6522DE0DC6A3@gbif.org> <7E11F47B5584C642AEBB77967228BE532E83807B@EXCVS1.uefad.uef.fi> <989C4CCB-087A-4AF5-9E78-19ABB05AC146@gbif.org> <7E11F47B5584C642AEBB77967228BE532E8380E8@EXCVS1.uefad.uef.fi> <659C0C7C-EEB6-41B9-8FA3-266C8A6EE339@gbif.org> <49B8C51D-B126-4EFA-B4F1-B372C1C6B2F1@gbif.org> Message-ID: <7E11F47B5584C642AEBB77967228BE532E83816B@EXCVS1.uefad.uef.fi> Hi I added the URIEncoding="UTF-8" to the connector and sadly it does not helped. In POST-data spaces are coded using '+' in IPT. I did send POST data using %20-coding and it works. Normally I've used percent-based url-coding. BR, Tero From: Kyle Braak [GBIF] [mailto:kbraak at gbif.org] Sent: Friday, March 09, 2012 1:49 PM To: Tero Mononen Cc: ipt at lists.gbif.org; Tim Robertson [GBIF] Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character Hi Tero,? It's nice that we might be on the verge of solving this now.. When you have this working,?I recommend an upgrade from 2.0.2 to 2.0.3. The upgrade is relatively painless.? To do so,? a) back up your current data directory to somewhere safe b) download the 2.0.3 war file, and rename it to ipt.war c) stop tomcat, remove ipt/ and ipt.war from the tomcat webapps folder, and add the new ipt.war file d) start tomcat, and open up the IPT in a browser e) presented with the 1st setup page, enter the location of your existing data directory f) press continue to proceed, then visit the Administration page and press the button "Publish all resources" (this may take a few moments as it will republish all resources.? Caution: There is a known?bug?with the upgrade where a taxonomic resources switches to type occurrence. I know that you have purely occurrence resources, but if this switch happens, just try the upgrade again but de-select the subtype (and be sure to save) for each resource before going through the steps.? Best of luck, Kyle On Mar 9, 2012, at 12:43 PM, Tim Robertson [GBIF] wrote: This looks like you are hitting this Tomcat6 / OpenSUSE bug: http://stackoverflow.com/questions/9290745/tomcat-6-doesnt-decode-to-space-in-parameter-values Can you please try the suggested fix? Thanks, Tim On Mar 9, 2012, at 12:25 PM, Tero Mononen wrote: Hi ? Only very minor updates from openSUSE to tomcat6 and kernel 2.6.34. ? Tomcat from version 6.0.24-5.14.1 to version 6.0.24-5.16.1. Kernel 2.6.34.10-0.4.1 -> 2.6.34.10-0.6.1 ? ? BR, Tero ? From:?Tim Robertson [GBIF] [mailto:trobertson at gbif.org]? Sent:?Friday, March 09, 2012 12:48 PM To:?Tero Mononen Cc:?Kyle Braak [GBIF]; ipt at lists.gbif.org Subject:?Re: [IPT] All space-characters in metadata are replaced to plus-character ? Hi ? Thank you, I made new issue (http://code.google.com/p/gbif-providertoolkit/issues/detail?id=845). ? We have tested many browsers on Windows and Linux. I think the reproduction is hard because it did work on our system well and then something weird happened causing this. ? Hi Tero, ? What changed between it working well, and then this happening please? ?OS upgrades, OS changes, Tomcat upgrades, Java updates etc ? The *good* news is the IPT still works - the EML is correct when accessed through Tomcat. ?Of course we want to fix the direct file access route, but the IPT is operating correctly through the IPT interface (e.g.?http://db.digitarium.fi:8080/ipt/eml.do?r=nylander?is correct?) ? Thanks, Tim ? ? BR, Tero ? From:?Kyle Braak [GBIF] [mailto:kbraak at gbif.org]? Sent:?Friday, March 09, 2012 11:54 AM To:?Tero Mononen Cc:?ipt at lists.gbif.org; Tim Robertson [GBIF] Subject:?Re: [IPT] All space-characters in metadata are replaced to plus-character ? Dear Tero,? ? Can I kindly ask you to fill in a bug report on the IPT Project Site:?http://code.google.com/p/gbif-providertoolkit/issues/entry ? In addition to the IPT version, Java version, and Tomcat version, can you also specify the Operating System you are using (with version), as well as the browser ?(with version) that you are using to fill in the metadata? Out of curiosity, have you tried entering metadata through different browsers (Chrome, Firefox, IE)?? ? This will help us try and reproduce the problem ourselves so that if there is something wrong with the application we can fix it ASAP. ? Thanks a lot, ? Kyle On Mar 9, 2012, at 10:40 AM, Tim Robertson [GBIF] wrote: Thanks Tero ? Very curious indeed. ?The single input fields are represented with + but the description field which is a Textarea on the form is not. ? We'll look more into it. ? Cheers, Tim ? ? On Mar 9, 2012, at 10:15 AM, Tero Mononen wrote: Hi There is the original eml.xml. Is that the only file you are interested in? BR, Tero On 03/09/2012 11:05 AM, Tim Robertson [GBIF] wrote: Hi Tero, ? How very strange. Given this is public anyway (http://db.digitarium.fi:8080/ipt/eml.do?r=nylander) would you mind attaching the file from the filesystem please? ?I'd like to look at the file encoding etc. ? Thanks, Tim ? ? On Mar 9, 2012, at 9:44 AM, Tero Mononen wrote: Dear Tim, ? There's only public example (Title: William+Nylander+lichen+collection): http://db.digitarium.fi:8080/ipt/resource.do?r=nylander ? It's interesting, eml.xml on file system contains line: William+Nylander+lichen+collection ? But eml via IPT/Tomcat offers line: William Nylander lichen collection ? It's pure Tomcat without proxies. ? ? BR, Tero Mononen ? From:?Tim Robertson [GBIF] [mailto:trobertson at gbif.org]? Sent:?Friday, March 09, 2012 10:37 AM To:?Tero Mononen Cc:?ipt at lists.gbif.org Subject:?Re: [IPT] All space-characters in metadata are replaced to plus-character ? Dear Tero, ? Could you please provide a link to an example file? ?We'll investigate, but this is not a behavior I have ever seen with a Tomcat application. ? Do you run any proxies or mod_jk or anything like that? ? Thanks, Tim ? ? On Mar 9, 2012, at 9:35 AM, Tero Mononen wrote: Hi ? We have used this IPT-setup without any problems till now. ? System: Version 2.0.2-r3306 Apache Tomcat/6.0.24 JVM 1.6.0_29-b1 ? Problem: All space-characters in metadata are replaced to plus-character. For example title "foo bar car" is saved as "foo+bar+car". It affects in every text field in metadata. ? If I include at least one plus-char in a text value, it prevents the space replacement. For example "foo bar car+dar" is saved as it is. ? I think this is related to Java/Tomcat/urlencode. Do you have suggestions how to fix this problem? ? ? Best Regards, Tero Mononen ? -- Digitarium Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) FI-80101 Joensuu http://www.digitarium.fi/ ? Tero Mononen, Analyst Programmer tero.mononen at uef.fi +358-50-5631788 ? _______________________________________________ IPT mailing list IPT at lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt ? -- Digitarium Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) FI-80101 Joensuu http://www.digitarium.fi/ ? Tero Mononen, Analyst Programmer tero.mononen at uef.fi +358-50-5631788 ? _______________________________________________ IPT mailing list IPT at lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt From trobertson at gbif.org Fri Mar 9 13:51:30 2012 From: trobertson at gbif.org (Tim Robertson [GBIF]) Date: Fri, 9 Mar 2012 13:51:30 +0100 Subject: [IPT] All space-characters in metadata are replaced to plus-character In-Reply-To: <7E11F47B5584C642AEBB77967228BE532E83816B@EXCVS1.uefad.uef.fi> References: <7E11F47B5584C642AEBB77967228BE532E837FC9@EXCVS1.uefad.uef.fi> <7E11F47B5584C642AEBB77967228BE532E837FDB@EXCVS1.uefad.uef.fi> <845F06C4-1971-48B1-A696-72A0F1ACDB54@gbif.org> <4F59CA3C.1030501@uef.fi> <8E6E552E-5A05-467D-BC5E-6522DE0DC6A3@gbif.org> <7E11F47B5584C642AEBB77967228BE532E83807B@EXCVS1.uefad.uef.fi> <989C4CCB-087A-4AF5-9E78-19ABB05AC146@gbif.org> <7E11F47B5584C642AEBB77967228BE532E8380E8@EXCVS1.uefad.uef.fi> <659C0C7C-EEB6-41B9-8FA3-266C8A6EE339@gbif.org> <49B8C51D-B126-4EFA-B4F1-B372C1C6B2F1@gbif.org> <7E11F47B5584C642AEBB77967228BE532E83816B@EXCVS1.uefad.uef.fi> Message-ID: <6276EDF4-A2B2-44EB-B7F9-F349D1CA82FA@gbif.org> Thanks for testing that Tero, I've been hunting around on OpenSuse and Tomcat forums and can't find much on this bug. Could you run a test on Tomcat7 at all? It might be worth posting this to any OpenSuse lists you are on as it is seemingly not an IPT specific issue - we are of course keen to see this sorted and help as much as possible. Thanks, Tim On Mar 9, 2012, at 1:45 PM, Tero Mononen wrote: > Hi > > I added the URIEncoding="UTF-8" to the connector and sadly it does not helped. > > In POST-data spaces are coded using '+' in IPT. I did send POST data using %20-coding and it works. Normally I've used percent-based url-coding. > > > BR, > Tero > > From: Kyle Braak [GBIF] [mailto:kbraak at gbif.org] > Sent: Friday, March 09, 2012 1:49 PM > To: Tero Mononen > Cc: ipt at lists.gbif.org; Tim Robertson [GBIF] > Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character > > Hi Tero, > > It's nice that we might be on the verge of solving this now.. > > When you have this working, I recommend an upgrade from 2.0.2 to 2.0.3. The upgrade is relatively painless. > > To do so, > > a) back up your current data directory to somewhere safe > b) download the 2.0.3 war file, and rename it to ipt.war > c) stop tomcat, remove ipt/ and ipt.war from the tomcat webapps folder, and add the new ipt.war file > d) start tomcat, and open up the IPT in a browser > e) presented with the 1st setup page, enter the location of your existing data directory > f) press continue to proceed, then visit the Administration page and press the button "Publish all resources" (this may take a few moments as it will republish all resources. > > Caution: There is a known bug with the upgrade where a taxonomic resources switches to type occurrence. I know that you have purely occurrence resources, but if this switch happens, just try the upgrade again but de-select the subtype (and be sure to save) for each resource before going through the steps. > > Best of luck, > > Kyle > On Mar 9, 2012, at 12:43 PM, Tim Robertson [GBIF] wrote: > > > This looks like you are hitting this Tomcat6 / OpenSUSE bug: > http://stackoverflow.com/questions/9290745/tomcat-6-doesnt-decode-to-space-in-parameter-values > > Can you please try the suggested fix? > > Thanks, > Tim > > > > On Mar 9, 2012, at 12:25 PM, Tero Mononen wrote: > > > Hi > > Only very minor updates from openSUSE to tomcat6 and kernel 2.6.34. > > Tomcat from version 6.0.24-5.14.1 to version 6.0.24-5.16.1. > Kernel 2.6.34.10-0.4.1 -> 2.6.34.10-0.6.1 > > > BR, > Tero > > From: Tim Robertson [GBIF] [mailto:trobertson at gbif.org] > Sent: Friday, March 09, 2012 12:48 PM > To: Tero Mononen > Cc: Kyle Braak [GBIF]; ipt at lists.gbif.org > Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character > > Hi > > Thank you, I made new issue (http://code.google.com/p/gbif-providertoolkit/issues/detail?id=845). > > We have tested many browsers on Windows and Linux. I think the reproduction is hard because it did work on our system well and then something weird happened causing this. > > Hi Tero, > > What changed between it working well, and then this happening please? OS upgrades, OS changes, Tomcat upgrades, Java updates etc > > The *good* news is the IPT still works - the EML is correct when accessed through Tomcat. Of course we want to fix the direct file access route, but the IPT is operating correctly through the IPT interface (e.g. http://db.digitarium.fi:8080/ipt/eml.do?r=nylander is correct ) > > Thanks, > Tim > > > > > > BR, > Tero > > From: Kyle Braak [GBIF] [mailto:kbraak at gbif.org] > Sent: Friday, March 09, 2012 11:54 AM > To: Tero Mononen > Cc: ipt at lists.gbif.org; Tim Robertson [GBIF] > Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character > > Dear Tero, > > Can I kindly ask you to fill in a bug report on the IPT Project Site: http://code.google.com/p/gbif-providertoolkit/issues/entry > > In addition to the IPT version, Java version, and Tomcat version, can you also specify the Operating System you are using (with version), as well as the browser (with version) that you are using to fill in the metadata? Out of curiosity, have you tried entering metadata through different browsers (Chrome, Firefox, IE)? > > This will help us try and reproduce the problem ourselves so that if there is something wrong with the application we can fix it ASAP. > > Thanks a lot, > > Kyle > On Mar 9, 2012, at 10:40 AM, Tim Robertson [GBIF] wrote: > > > > > Thanks Tero > > Very curious indeed. The single input fields are represented with + but the description field which is a Textarea on the form is not. > > We'll look more into it. > > Cheers, > Tim > > > On Mar 9, 2012, at 10:15 AM, Tero Mononen wrote: > > > > > Hi > > There is the original eml.xml. Is that the only file you are interested in? > > > BR, > Tero > > On 03/09/2012 11:05 AM, Tim Robertson [GBIF] wrote: > Hi Tero, > > How very strange. > Given this is public anyway (http://db.digitarium.fi:8080/ipt/eml.do?r=nylander) would you mind attaching the file from the filesystem please? I'd like to look at the file encoding etc. > > Thanks, > Tim > > > On Mar 9, 2012, at 9:44 AM, Tero Mononen wrote: > > > > > Dear Tim, > > There's only public example (Title: William+Nylander+lichen+collection): > http://db.digitarium.fi:8080/ipt/resource.do?r=nylander > > It's interesting, eml.xml on file system contains line: > William+Nylander+lichen+collection > > But eml via IPT/Tomcat offers line: > William Nylander lichen collection > > It's pure Tomcat without proxies. > > > BR, > Tero Mononen > > From: Tim Robertson [GBIF] [mailto:trobertson at gbif.org] > Sent: Friday, March 09, 2012 10:37 AM > To: Tero Mononen > Cc: ipt at lists.gbif.org > Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character > > Dear Tero, > > Could you please provide a link to an example file? We'll investigate, but this is not a behavior I have ever seen with a Tomcat application. > > Do you run any proxies or mod_jk or anything like that? > > Thanks, > Tim > > > On Mar 9, 2012, at 9:35 AM, Tero Mononen wrote: > > > > > > Hi > > We have used this IPT-setup without any problems till now. > > System: > Version 2.0.2-r3306 > Apache Tomcat/6.0.24 > JVM 1.6.0_29-b1 > > Problem: > All space-characters in metadata are replaced to plus-character. For example title "foo bar car" is saved as "foo+bar+car". It affects in every text field in metadata. > > If I include at least one plus-char in a text value, it prevents the space replacement. For example "foo bar car+dar" is saved as it is. > > I think this is related to Java/Tomcat/urlencode. Do you have suggestions how to fix this problem? > > > Best Regards, > Tero Mononen > > -- > Digitarium > Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) > FI-80101 Joensuu > http://www.digitarium.fi/ > > Tero Mononen, Analyst Programmer > tero.mononen at uef.fi > +358-50-5631788 > > _______________________________________________ > IPT mailing list > IPT at lists.gbif.org > http://lists.gbif.org/mailman/listinfo/ipt > > > > > > -- > Digitarium > Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) > FI-80101 Joensuu > http://www.digitarium.fi/ > > Tero Mononen, Analyst Programmer > tero.mononen at uef.fi > +358-50-5631788 > > > _______________________________________________ > IPT mailing list > IPT at lists.gbif.org > http://lists.gbif.org/mailman/listinfo/ipt > > > From tero.mononen at uef.fi Fri Mar 9 13:54:57 2012 From: tero.mononen at uef.fi (Tero Mononen) Date: Fri, 9 Mar 2012 14:54:57 +0200 Subject: [IPT] All space-characters in metadata are replaced to plus-character In-Reply-To: <6276EDF4-A2B2-44EB-B7F9-F349D1CA82FA@gbif.org> References: <7E11F47B5584C642AEBB77967228BE532E837FC9@EXCVS1.uefad.uef.fi> <7E11F47B5584C642AEBB77967228BE532E837FDB@EXCVS1.uefad.uef.fi> <845F06C4-1971-48B1-A696-72A0F1ACDB54@gbif.org> <4F59CA3C.1030501@uef.fi> <8E6E552E-5A05-467D-BC5E-6522DE0DC6A3@gbif.org> <7E11F47B5584C642AEBB77967228BE532E83807B@EXCVS1.uefad.uef.fi> <989C4CCB-087A-4AF5-9E78-19ABB05AC146@gbif.org> <7E11F47B5584C642AEBB77967228BE532E8380E8@EXCVS1.uefad.uef.fi> <659C0C7C-EEB6-41B9-8FA3-266C8A6EE339@gbif.org> <49B8C51D-B126-4EFA-B4F1-B372C1C6B2F1@gbif.org> <7E11F47B5584C642AEBB77967228BE532E83816B@EXCVS1.uefad.uef.fi> <6276EDF4-A2B2-44EB-B7F9-F349D1CA82FA@gbif.org> Message-ID: <7E11F47B5584C642AEBB77967228BE532E838179@EXCVS1.uefad.uef.fi> Hi, That's true, I have to make some new installations. I'll inform you if the problem was entirely from Tomcat. Thank you a lot for helping. :) BR, Tero -----Original Message----- From: Tim Robertson [GBIF] [mailto:trobertson at gbif.org] Sent: Friday, March 09, 2012 2:52 PM To: Tero Mononen Cc: Kyle Braak [GBIF]; ipt at lists.gbif.org Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character Thanks for testing that Tero, I've been hunting around on OpenSuse and Tomcat forums and can't find much on this bug. Could you run a test on Tomcat7 at all? It might be worth posting this to any OpenSuse lists you are on as it is seemingly not an IPT specific issue - we are of course keen to see this sorted and help as much as possible. Thanks, Tim On Mar 9, 2012, at 1:45 PM, Tero Mononen wrote: > Hi > > I added the URIEncoding="UTF-8" to the connector and sadly it does not helped. > > In POST-data spaces are coded using '+' in IPT. I did send POST data using %20-coding and it works. Normally I've used percent-based url-coding. > > > BR, > Tero > > From: Kyle Braak [GBIF] [mailto:kbraak at gbif.org] > Sent: Friday, March 09, 2012 1:49 PM > To: Tero Mononen > Cc: ipt at lists.gbif.org; Tim Robertson [GBIF] > Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character > > Hi Tero, > > It's nice that we might be on the verge of solving this now.. > > When you have this working, I recommend an upgrade from 2.0.2 to 2.0.3. The upgrade is relatively painless. > > To do so, > > a) back up your current data directory to somewhere safe > b) download the 2.0.3 war file, and rename it to ipt.war > c) stop tomcat, remove ipt/ and ipt.war from the tomcat webapps folder, and add the new ipt.war file > d) start tomcat, and open up the IPT in a browser > e) presented with the 1st setup page, enter the location of your existing data directory > f) press continue to proceed, then visit the Administration page and press the button "Publish all resources" (this may take a few moments as it will republish all resources. > > Caution: There is a known bug with the upgrade where a taxonomic resources switches to type occurrence. I know that you have purely occurrence resources, but if this switch happens, just try the upgrade again but de-select the subtype (and be sure to save) for each resource before going through the steps. > > Best of luck, > > Kyle > On Mar 9, 2012, at 12:43 PM, Tim Robertson [GBIF] wrote: > > > This looks like you are hitting this Tomcat6 / OpenSUSE bug: > http://stackoverflow.com/questions/9290745/tomcat-6-doesnt-decode-to-space-in-parameter-values > > Can you please try the suggested fix? > > Thanks, > Tim > > > > On Mar 9, 2012, at 12:25 PM, Tero Mononen wrote: > > > Hi > > Only very minor updates from openSUSE to tomcat6 and kernel 2.6.34. > > Tomcat from version 6.0.24-5.14.1 to version 6.0.24-5.16.1. > Kernel 2.6.34.10-0.4.1 -> 2.6.34.10-0.6.1 > > > BR, > Tero > > From: Tim Robertson [GBIF] [mailto:trobertson at gbif.org] > Sent: Friday, March 09, 2012 12:48 PM > To: Tero Mononen > Cc: Kyle Braak [GBIF]; ipt at lists.gbif.org > Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character > > Hi > > Thank you, I made new issue (http://code.google.com/p/gbif-providertoolkit/issues/detail?id=845). > > We have tested many browsers on Windows and Linux. I think the reproduction is hard because it did work on our system well and then something weird happened causing this. > > Hi Tero, > > What changed between it working well, and then this happening please? OS upgrades, OS changes, Tomcat upgrades, Java updates etc > > The *good* news is the IPT still works - the EML is correct when accessed through Tomcat. Of course we want to fix the direct file access route, but the IPT is operating correctly through the IPT interface (e.g. http://db.digitarium.fi:8080/ipt/eml.do?r=nylander is correct ) > > Thanks, > Tim > > > > > > BR, > Tero > > From: Kyle Braak [GBIF] [mailto:kbraak at gbif.org] > Sent: Friday, March 09, 2012 11:54 AM > To: Tero Mononen > Cc: ipt at lists.gbif.org; Tim Robertson [GBIF] > Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character > > Dear Tero, > > Can I kindly ask you to fill in a bug report on the IPT Project Site: http://code.google.com/p/gbif-providertoolkit/issues/entry > > In addition to the IPT version, Java version, and Tomcat version, can you also specify the Operating System you are using (with version), as well as the browser (with version) that you are using to fill in the metadata? Out of curiosity, have you tried entering metadata through different browsers (Chrome, Firefox, IE)? > > This will help us try and reproduce the problem ourselves so that if there is something wrong with the application we can fix it ASAP. > > Thanks a lot, > > Kyle > On Mar 9, 2012, at 10:40 AM, Tim Robertson [GBIF] wrote: > > > > > Thanks Tero > > Very curious indeed. The single input fields are represented with + but the description field which is a Textarea on the form is not. > > We'll look more into it. > > Cheers, > Tim > > > On Mar 9, 2012, at 10:15 AM, Tero Mononen wrote: > > > > > Hi > > There is the original eml.xml. Is that the only file you are interested in? > > > BR, > Tero > > On 03/09/2012 11:05 AM, Tim Robertson [GBIF] wrote: > Hi Tero, > > How very strange. > Given this is public anyway (http://db.digitarium.fi:8080/ipt/eml.do?r=nylander) would you mind attaching the file from the filesystem please? I'd like to look at the file encoding etc. > > Thanks, > Tim > > > On Mar 9, 2012, at 9:44 AM, Tero Mononen wrote: > > > > > Dear Tim, > > There's only public example (Title: William+Nylander+lichen+collection): > http://db.digitarium.fi:8080/ipt/resource.do?r=nylander > > It's interesting, eml.xml on file system contains line: > William+Nylander+lichen+collection > > But eml via IPT/Tomcat offers line: > William Nylander lichen collection > > It's pure Tomcat without proxies. > > > BR, > Tero Mononen > > From: Tim Robertson [GBIF] [mailto:trobertson at gbif.org] > Sent: Friday, March 09, 2012 10:37 AM > To: Tero Mononen > Cc: ipt at lists.gbif.org > Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character > > Dear Tero, > > Could you please provide a link to an example file? We'll investigate, but this is not a behavior I have ever seen with a Tomcat application. > > Do you run any proxies or mod_jk or anything like that? > > Thanks, > Tim > > > On Mar 9, 2012, at 9:35 AM, Tero Mononen wrote: > > > > > > Hi > > We have used this IPT-setup without any problems till now. > > System: > Version 2.0.2-r3306 > Apache Tomcat/6.0.24 > JVM 1.6.0_29-b1 > > Problem: > All space-characters in metadata are replaced to plus-character. For example title "foo bar car" is saved as "foo+bar+car". It affects in every text field in metadata. > > If I include at least one plus-char in a text value, it prevents the space replacement. For example "foo bar car+dar" is saved as it is. > > I think this is related to Java/Tomcat/urlencode. Do you have suggestions how to fix this problem? > > > Best Regards, > Tero Mononen > > -- > Digitarium > Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) > FI-80101 Joensuu > http://www.digitarium.fi/ > > Tero Mononen, Analyst Programmer > tero.mononen at uef.fi > +358-50-5631788 > > _______________________________________________ > IPT mailing list > IPT at lists.gbif.org > http://lists.gbif.org/mailman/listinfo/ipt > > > > > > -- > Digitarium > Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) > FI-80101 Joensuu > http://www.digitarium.fi/ > > Tero Mononen, Analyst Programmer > tero.mononen at uef.fi > +358-50-5631788 > > > _______________________________________________ > IPT mailing list > IPT at lists.gbif.org > http://lists.gbif.org/mailman/listinfo/ipt > > > From tero.mononen at uef.fi Sat Mar 10 10:58:51 2012 From: tero.mononen at uef.fi (Tero Mononen) Date: Sat, 10 Mar 2012 11:58:51 +0200 Subject: [IPT] All space-characters in metadata are replaced to plus-character In-Reply-To: <7E11F47B5584C642AEBB77967228BE532E838179@EXCVS1.uefad.uef.fi> References: <7E11F47B5584C642AEBB77967228BE532E837FC9@EXCVS1.uefad.uef.fi> <7E11F47B5584C642AEBB77967228BE532E837FDB@EXCVS1.uefad.uef.fi> <845F06C4-1971-48B1-A696-72A0F1ACDB54@gbif.org> <4F59CA3C.1030501@uef.fi> <8E6E552E-5A05-467D-BC5E-6522DE0DC6A3@gbif.org> <7E11F47B5584C642AEBB77967228BE532E83807B@EXCVS1.uefad.uef.fi> <989C4CCB-087A-4AF5-9E78-19ABB05AC146@gbif.org> <7E11F47B5584C642AEBB77967228BE532E8380E8@EXCVS1.uefad.uef.fi> <659C0C7C-EEB6-41B9-8FA3-266C8A6EE339@gbif.org> <49B8C51D-B126-4EFA-B4F1-B372C1C6B2F1@gbif.org> <7E11F47B5584C642AEBB77967228BE532E83816B@EXCVS1.uefad.uef.fi> <6276EDF4-A2B2-44EB-B7F9-F349D1CA82FA@gbif.org> <7E11F47B5584C642AEBB77967228BE532E838179@EXCVS1.uefad.uef.fi> Message-ID: <4F5B25DB.8090809@uef.fi> Hi Tomcat upgrade to version 7 really fixed this issue! Damn openSUSE or Tomcat :) Thanks, Tero Mononen On 03/09/2012 02:54 PM, Tero Mononen wrote: > Hi, > > That's true, I have to make some new installations. I'll inform you if the problem was entirely from Tomcat. Thank you a lot for helping. :) > > > BR, > Tero > > -----Original Message----- > From: Tim Robertson [GBIF] [mailto:trobertson at gbif.org] > Sent: Friday, March 09, 2012 2:52 PM > To: Tero Mononen > Cc: Kyle Braak [GBIF]; ipt at lists.gbif.org > Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character > > Thanks for testing that Tero, > > I've been hunting around on OpenSuse and Tomcat forums and can't find much on this bug. Could you run a test on Tomcat7 at all? > It might be worth posting this to any OpenSuse lists you are on as it is seemingly not an IPT specific issue - we are of course keen to see this sorted and help as much as possible. > > Thanks, > Tim > > > > On Mar 9, 2012, at 1:45 PM, Tero Mononen wrote: > >> Hi >> >> I added the URIEncoding="UTF-8" to the connector and sadly it does not helped. >> >> In POST-data spaces are coded using '+' in IPT. I did send POST data using %20-coding and it works. Normally I've used percent-based url-coding. >> >> >> BR, >> Tero >> >> From: Kyle Braak [GBIF] [mailto:kbraak at gbif.org] >> Sent: Friday, March 09, 2012 1:49 PM >> To: Tero Mononen >> Cc: ipt at lists.gbif.org; Tim Robertson [GBIF] >> Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character >> >> Hi Tero, >> >> It's nice that we might be on the verge of solving this now.. >> >> When you have this working, I recommend an upgrade from 2.0.2 to 2.0.3. The upgrade is relatively painless. >> >> To do so, >> >> a) back up your current data directory to somewhere safe >> b) download the 2.0.3 war file, and rename it to ipt.war >> c) stop tomcat, remove ipt/ and ipt.war from the tomcat webapps folder, and add the new ipt.war file >> d) start tomcat, and open up the IPT in a browser >> e) presented with the 1st setup page, enter the location of your existing data directory >> f) press continue to proceed, then visit the Administration page and press the button "Publish all resources" (this may take a few moments as it will republish all resources. >> >> Caution: There is a known bug with the upgrade where a taxonomic resources switches to type occurrence. I know that you have purely occurrence resources, but if this switch happens, just try the upgrade again but de-select the subtype (and be sure to save) for each resource before going through the steps. >> >> Best of luck, >> >> Kyle >> On Mar 9, 2012, at 12:43 PM, Tim Robertson [GBIF] wrote: >> >> >> This looks like you are hitting this Tomcat6 / OpenSUSE bug: >> http://stackoverflow.com/questions/9290745/tomcat-6-doesnt-decode-to-space-in-parameter-values >> >> Can you please try the suggested fix? >> >> Thanks, >> Tim >> >> >> >> On Mar 9, 2012, at 12:25 PM, Tero Mononen wrote: >> >> >> Hi >> >> Only very minor updates from openSUSE to tomcat6 and kernel 2.6.34. >> >> Tomcat from version 6.0.24-5.14.1 to version 6.0.24-5.16.1. >> Kernel 2.6.34.10-0.4.1 -> 2.6.34.10-0.6.1 >> >> >> BR, >> Tero >> >> From: Tim Robertson [GBIF] [mailto:trobertson at gbif.org] >> Sent: Friday, March 09, 2012 12:48 PM >> To: Tero Mononen >> Cc: Kyle Braak [GBIF]; ipt at lists.gbif.org >> Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character >> >> Hi >> >> Thank you, I made new issue (http://code.google.com/p/gbif-providertoolkit/issues/detail?id=845). >> >> We have tested many browsers on Windows and Linux. I think the reproduction is hard because it did work on our system well and then something weird happened causing this. >> >> Hi Tero, >> >> What changed between it working well, and then this happening please? OS upgrades, OS changes, Tomcat upgrades, Java updates etc >> >> The *good* news is the IPT still works - the EML is correct when accessed through Tomcat. Of course we want to fix the direct file access route, but the IPT is operating correctly through the IPT interface (e.g. http://db.digitarium.fi:8080/ipt/eml.do?r=nylander is correct ) >> >> Thanks, >> Tim >> >> >> >> >> >> BR, >> Tero >> >> From: Kyle Braak [GBIF] [mailto:kbraak at gbif.org] >> Sent: Friday, March 09, 2012 11:54 AM >> To: Tero Mononen >> Cc: ipt at lists.gbif.org; Tim Robertson [GBIF] >> Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character >> >> Dear Tero, >> >> Can I kindly ask you to fill in a bug report on the IPT Project Site: http://code.google.com/p/gbif-providertoolkit/issues/entry >> >> In addition to the IPT version, Java version, and Tomcat version, can you also specify the Operating System you are using (with version), as well as the browser (with version) that you are using to fill in the metadata? Out of curiosity, have you tried entering metadata through different browsers (Chrome, Firefox, IE)? >> >> This will help us try and reproduce the problem ourselves so that if there is something wrong with the application we can fix it ASAP. >> >> Thanks a lot, >> >> Kyle >> On Mar 9, 2012, at 10:40 AM, Tim Robertson [GBIF] wrote: >> >> >> >> >> Thanks Tero >> >> Very curious indeed. The single input fields are represented with + but the description field which is a Textarea on the form is not. >> >> We'll look more into it. >> >> Cheers, >> Tim >> >> >> On Mar 9, 2012, at 10:15 AM, Tero Mononen wrote: >> >> >> >> >> Hi >> >> There is the original eml.xml. Is that the only file you are interested in? >> >> >> BR, >> Tero >> >> On 03/09/2012 11:05 AM, Tim Robertson [GBIF] wrote: >> Hi Tero, >> >> How very strange. >> Given this is public anyway (http://db.digitarium.fi:8080/ipt/eml.do?r=nylander) would you mind attaching the file from the filesystem please? I'd like to look at the file encoding etc. >> >> Thanks, >> Tim >> >> >> On Mar 9, 2012, at 9:44 AM, Tero Mononen wrote: >> >> >> >> >> Dear Tim, >> >> There's only public example (Title: William+Nylander+lichen+collection): >> http://db.digitarium.fi:8080/ipt/resource.do?r=nylander >> >> It's interesting, eml.xml on file system contains line: >> William+Nylander+lichen+collection >> >> But eml via IPT/Tomcat offers line: >> William Nylander lichen collection >> >> It's pure Tomcat without proxies. >> >> >> BR, >> Tero Mononen >> >> From: Tim Robertson [GBIF] [mailto:trobertson at gbif.org] >> Sent: Friday, March 09, 2012 10:37 AM >> To: Tero Mononen >> Cc: ipt at lists.gbif.org >> Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character >> >> Dear Tero, >> >> Could you please provide a link to an example file? We'll investigate, but this is not a behavior I have ever seen with a Tomcat application. >> >> Do you run any proxies or mod_jk or anything like that? >> >> Thanks, >> Tim >> >> >> On Mar 9, 2012, at 9:35 AM, Tero Mononen wrote: >> >> >> >> >> >> Hi >> >> We have used this IPT-setup without any problems till now. >> >> System: >> Version 2.0.2-r3306 >> Apache Tomcat/6.0.24 >> JVM 1.6.0_29-b1 >> >> Problem: >> All space-characters in metadata are replaced to plus-character. For example title "foo bar car" is saved as "foo+bar+car". It affects in every text field in metadata. >> >> If I include at least one plus-char in a text value, it prevents the space replacement. For example "foo bar car+dar" is saved as it is. >> >> I think this is related to Java/Tomcat/urlencode. Do you have suggestions how to fix this problem? >> >> >> Best Regards, >> Tero Mononen >> >> -- >> Digitarium >> Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) >> FI-80101 Joensuu >> http://www.digitarium.fi/ >> >> Tero Mononen, Analyst Programmer >> tero.mononen at uef.fi >> +358-50-5631788 >> >> _______________________________________________ >> IPT mailing list >> IPT at lists.gbif.org >> http://lists.gbif.org/mailman/listinfo/ipt >> >> >> >> >> >> -- >> Digitarium >> Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) >> FI-80101 Joensuu >> http://www.digitarium.fi/ >> >> Tero Mononen, Analyst Programmer >> tero.mononen at uef.fi >> +358-50-5631788 >> >> >> _______________________________________________ >> IPT mailing list >> IPT at lists.gbif.org >> http://lists.gbif.org/mailman/listinfo/ipt >> >> >> > _______________________________________________ > IPT mailing list > IPT at lists.gbif.org > http://lists.gbif.org/mailman/listinfo/ipt -- Digitarium Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) FI-80101 Joensuu http://www.digitarium.fi/ Tero Mononen, Analyst Programmer tero.mononen at uef.fi +358-50-5631788 From trobertson at gbif.org Sat Mar 10 17:22:50 2012 From: trobertson at gbif.org (Tim Robertson [GBIF]) Date: Sat, 10 Mar 2012 17:22:50 +0100 Subject: [IPT] All space-characters in metadata are replaced to plus-character In-Reply-To: <4F5B25DB.8090809@uef.fi> References: <7E11F47B5584C642AEBB77967228BE532E837FC9@EXCVS1.uefad.uef.fi> <7E11F47B5584C642AEBB77967228BE532E837FDB@EXCVS1.uefad.uef.fi> <845F06C4-1971-48B1-A696-72A0F1ACDB54@gbif.org> <4F59CA3C.1030501@uef.fi> <8E6E552E-5A05-467D-BC5E-6522DE0DC6A3@gbif.org> <7E11F47B5584C642AEBB77967228BE532E83807B@EXCVS1.uefad.uef.fi> <989C4CCB-087A-4AF5-9E78-19ABB05AC146@gbif.org> <7E11F47B5584C642AEBB77967228BE532E8380E8@EXCVS1.uefad.uef.fi> <659C0C7C-EEB6-41B9-8FA3-266C8A6EE339@gbif.org> <49B8C51D-B126-4EFA-B4F1-B372C1C6B2F1@gbif.org> <7E11F47B5584C642AEBB77967228BE532E83816B@EXCVS1.uefad.uef.fi> <6276EDF4-A2B2-44EB-B7F9-F349D1CA82FA@gbif.org> <7E11F47B5584C642AEBB77967228BE532E838179@EXCVS1.uefad.uef.fi> <4F5B25DB.8090809@uef.fi> Message-ID: <79035395-F88F-4829-BDB4-B4B37460F6CE@gbif.org> Great! Glad it was so simple in the end. Tim On Mar 10, 2012, at 10:58 AM, Tero Mononen wrote: > Hi > > Tomcat upgrade to version 7 really fixed this issue! > > Damn openSUSE or Tomcat :) > > > Thanks, > Tero Mononen > > On 03/09/2012 02:54 PM, Tero Mononen wrote: >> Hi, >> >> That's true, I have to make some new installations. I'll inform you if the problem was entirely from Tomcat. Thank you a lot for helping. :) >> >> >> BR, >> Tero >> >> -----Original Message----- >> From: Tim Robertson [GBIF] [mailto:trobertson at gbif.org] >> Sent: Friday, March 09, 2012 2:52 PM >> To: Tero Mononen >> Cc: Kyle Braak [GBIF]; ipt at lists.gbif.org >> Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character >> >> Thanks for testing that Tero, >> >> I've been hunting around on OpenSuse and Tomcat forums and can't find much on this bug. Could you run a test on Tomcat7 at all? >> It might be worth posting this to any OpenSuse lists you are on as it is seemingly not an IPT specific issue - we are of course keen to see this sorted and help as much as possible. >> >> Thanks, >> Tim >> >> >> >> On Mar 9, 2012, at 1:45 PM, Tero Mononen wrote: >> >>> Hi >>> >>> I added the URIEncoding="UTF-8" to the connector and sadly it does not helped. >>> >>> In POST-data spaces are coded using '+' in IPT. I did send POST data using %20-coding and it works. Normally I've used percent-based url-coding. >>> >>> >>> BR, >>> Tero >>> >>> From: Kyle Braak [GBIF] [mailto:kbraak at gbif.org] >>> Sent: Friday, March 09, 2012 1:49 PM >>> To: Tero Mononen >>> Cc: ipt at lists.gbif.org; Tim Robertson [GBIF] >>> Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character >>> >>> Hi Tero, >>> >>> It's nice that we might be on the verge of solving this now.. >>> >>> When you have this working, I recommend an upgrade from 2.0.2 to 2.0.3. The upgrade is relatively painless. >>> >>> To do so, >>> >>> a) back up your current data directory to somewhere safe >>> b) download the 2.0.3 war file, and rename it to ipt.war >>> c) stop tomcat, remove ipt/ and ipt.war from the tomcat webapps folder, and add the new ipt.war file >>> d) start tomcat, and open up the IPT in a browser >>> e) presented with the 1st setup page, enter the location of your existing data directory >>> f) press continue to proceed, then visit the Administration page and press the button "Publish all resources" (this may take a few moments as it will republish all resources. >>> >>> Caution: There is a known bug with the upgrade where a taxonomic resources switches to type occurrence. I know that you have purely occurrence resources, but if this switch happens, just try the upgrade again but de-select the subtype (and be sure to save) for each resource before going through the steps. >>> >>> Best of luck, >>> >>> Kyle >>> On Mar 9, 2012, at 12:43 PM, Tim Robertson [GBIF] wrote: >>> >>> >>> This looks like you are hitting this Tomcat6 / OpenSUSE bug: >>> http://stackoverflow.com/questions/9290745/tomcat-6-doesnt-decode-to-space-in-parameter-values >>> >>> Can you please try the suggested fix? >>> >>> Thanks, >>> Tim >>> >>> >>> >>> On Mar 9, 2012, at 12:25 PM, Tero Mononen wrote: >>> >>> >>> Hi >>> >>> Only very minor updates from openSUSE to tomcat6 and kernel 2.6.34. >>> >>> Tomcat from version 6.0.24-5.14.1 to version 6.0.24-5.16.1. >>> Kernel 2.6.34.10-0.4.1 -> 2.6.34.10-0.6.1 >>> >>> >>> BR, >>> Tero >>> >>> From: Tim Robertson [GBIF] [mailto:trobertson at gbif.org] >>> Sent: Friday, March 09, 2012 12:48 PM >>> To: Tero Mononen >>> Cc: Kyle Braak [GBIF]; ipt at lists.gbif.org >>> Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character >>> >>> Hi >>> >>> Thank you, I made new issue (http://code.google.com/p/gbif-providertoolkit/issues/detail?id=845). >>> >>> We have tested many browsers on Windows and Linux. I think the reproduction is hard because it did work on our system well and then something weird happened causing this. >>> >>> Hi Tero, >>> >>> What changed between it working well, and then this happening please? OS upgrades, OS changes, Tomcat upgrades, Java updates etc >>> >>> The *good* news is the IPT still works - the EML is correct when accessed through Tomcat. Of course we want to fix the direct file access route, but the IPT is operating correctly through the IPT interface (e.g. http://db.digitarium.fi:8080/ipt/eml.do?r=nylander is correct ) >>> >>> Thanks, >>> Tim >>> >>> >>> >>> >>> >>> BR, >>> Tero >>> >>> From: Kyle Braak [GBIF] [mailto:kbraak at gbif.org] >>> Sent: Friday, March 09, 2012 11:54 AM >>> To: Tero Mononen >>> Cc: ipt at lists.gbif.org; Tim Robertson [GBIF] >>> Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character >>> >>> Dear Tero, >>> >>> Can I kindly ask you to fill in a bug report on the IPT Project Site: http://code.google.com/p/gbif-providertoolkit/issues/entry >>> >>> In addition to the IPT version, Java version, and Tomcat version, can you also specify the Operating System you are using (with version), as well as the browser (with version) that you are using to fill in the metadata? Out of curiosity, have you tried entering metadata through different browsers (Chrome, Firefox, IE)? >>> >>> This will help us try and reproduce the problem ourselves so that if there is something wrong with the application we can fix it ASAP. >>> >>> Thanks a lot, >>> >>> Kyle >>> On Mar 9, 2012, at 10:40 AM, Tim Robertson [GBIF] wrote: >>> >>> >>> >>> >>> Thanks Tero >>> >>> Very curious indeed. The single input fields are represented with + but the description field which is a Textarea on the form is not. >>> >>> We'll look more into it. >>> >>> Cheers, >>> Tim >>> >>> >>> On Mar 9, 2012, at 10:15 AM, Tero Mononen wrote: >>> >>> >>> >>> >>> Hi >>> >>> There is the original eml.xml. Is that the only file you are interested in? >>> >>> >>> BR, >>> Tero >>> >>> On 03/09/2012 11:05 AM, Tim Robertson [GBIF] wrote: >>> Hi Tero, >>> >>> How very strange. >>> Given this is public anyway (http://db.digitarium.fi:8080/ipt/eml.do?r=nylander) would you mind attaching the file from the filesystem please? I'd like to look at the file encoding etc. >>> >>> Thanks, >>> Tim >>> >>> >>> On Mar 9, 2012, at 9:44 AM, Tero Mononen wrote: >>> >>> >>> >>> >>> Dear Tim, >>> >>> There's only public example (Title: William+Nylander+lichen+collection): >>> http://db.digitarium.fi:8080/ipt/resource.do?r=nylander >>> >>> It's interesting, eml.xml on file system contains line: >>> William+Nylander+lichen+collection >>> >>> But eml via IPT/Tomcat offers line: >>> William Nylander lichen collection >>> >>> It's pure Tomcat without proxies. >>> >>> >>> BR, >>> Tero Mononen >>> >>> From: Tim Robertson [GBIF] [mailto:trobertson at gbif.org] >>> Sent: Friday, March 09, 2012 10:37 AM >>> To: Tero Mononen >>> Cc: ipt at lists.gbif.org >>> Subject: Re: [IPT] All space-characters in metadata are replaced to plus-character >>> >>> Dear Tero, >>> >>> Could you please provide a link to an example file? We'll investigate, but this is not a behavior I have ever seen with a Tomcat application. >>> >>> Do you run any proxies or mod_jk or anything like that? >>> >>> Thanks, >>> Tim >>> >>> >>> On Mar 9, 2012, at 9:35 AM, Tero Mononen wrote: >>> >>> >>> >>> >>> >>> Hi >>> >>> We have used this IPT-setup without any problems till now. >>> >>> System: >>> Version 2.0.2-r3306 >>> Apache Tomcat/6.0.24 >>> JVM 1.6.0_29-b1 >>> >>> Problem: >>> All space-characters in metadata are replaced to plus-character. For example title "foo bar car" is saved as "foo+bar+car". It affects in every text field in metadata. >>> >>> If I include at least one plus-char in a text value, it prevents the space replacement. For example "foo bar car+dar" is saved as it is. >>> >>> I think this is related to Java/Tomcat/urlencode. Do you have suggestions how to fix this problem? >>> >>> >>> Best Regards, >>> Tero Mononen >>> >>> -- >>> Digitarium >>> Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) >>> FI-80101 Joensuu >>> http://www.digitarium.fi/ >>> >>> Tero Mononen, Analyst Programmer >>> tero.mononen at uef.fi >>> +358-50-5631788 >>> >>> _______________________________________________ >>> IPT mailing list >>> IPT at lists.gbif.org >>> http://lists.gbif.org/mailman/listinfo/ipt >>> >>> >>> >>> >>> >>> -- >>> Digitarium >>> Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) >>> FI-80101 Joensuu >>> http://www.digitarium.fi/ >>> >>> Tero Mononen, Analyst Programmer >>> tero.mononen at uef.fi >>> +358-50-5631788 >>> >>> >>> _______________________________________________ >>> IPT mailing list >>> IPT at lists.gbif.org >>> http://lists.gbif.org/mailman/listinfo/ipt >>> >>> >>> >> _______________________________________________ >> IPT mailing list >> IPT at lists.gbif.org >> http://lists.gbif.org/mailman/listinfo/ipt > > -- > Digitarium > Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park L?nsikatu 15 (P.O. Box 111) > FI-80101 Joensuu > http://www.digitarium.fi/ > > Tero Mononen, Analyst Programmer > tero.mononen at uef.fi > +358-50-5631788 > From larussell at vertnet.org Fri Mar 23 17:57:22 2012 From: larussell at vertnet.org (Laura Russell) Date: Fri, 23 Mar 2012 11:57:22 -0500 Subject: [IPT] CentOS IPT Install Message-ID: I'm having difficulty with a CentOS IPT Install that I'm doing for the Field Museum (in Chicago, I'm remote to their server from Kansas). The Field IT staff enabled their Tomcat on the server. And I've deployed the IPT. Permissions on the iptdata folder seem to be okay as it created all the folders and extension files in the first step. They are running CentOS 5.2 Tomcat 5.5.23 Java 1.6 I'm getting the following error when trying to complete the second setup page on the IPT. "The Base URL does not point to an IPT installation that is accessible from this computer." The URL is accessible outside of the firewall. I've also tried it with the IP address and get the same error. I chatted with Tim Robertson a bit yesterday and I've had the Field IT staff check that the port is open for both incoming and outgoing connections. They do not think their firewall is the issue so I'm looking at other possibilities. I've attached the Catalina.out file and the IPT Admin and Debug logs. Any assistance is appreciated. Thanks. Laura Russell VertNet Programmer Biodiversity Institute University of Kansas Dyche Hall 1345 Jayhawk Blvd., Room 606 Lawrence, KS 66045 Phone: 785.864.4681 Fax: 785.864.5335 Email: larussell at vertnet.org Email: larussell at ku.edu Google Chat: larussell at vertnet.org Skype: laura.anne.russell URL: http://www.vertnet.org VertNet Portals: MaNIS: http://www.manisnet.org HerpNET: http://www.herpnet.org ORNIS: http://www.ornisnet.org FishNet2: http://www.fishnet2.net -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gbif.org/pipermail/ipt/attachments/20120323/e93aaa18/attachment.html -------------- next part -------------- A non-text attachment was scrubbed... Name: FieldIPTerrors.zip Type: application/zip Size: 3054 bytes Desc: not available Url : http://lists.gbif.org/pipermail/ipt/attachments/20120323/e93aaa18/attachment.zip From kbraak at gbif.org Fri Mar 23 18:32:08 2012 From: kbraak at gbif.org (Kyle Braak [GBIF]) Date: Fri, 23 Mar 2012 18:32:08 +0100 Subject: [IPT] CentOS IPT Install In-Reply-To: References: Message-ID: Dear Laura, The debug.log says: "WARN Localhost used as base url, IPT will not be visible to the outside!" I wonder if this is the value saved in the /home/iptdata/config/ipt.properties file? You could always try overwriting that ipt.baseURL property (stopping Tomcat, changing the property, restarting Tomcat) or doing a fresh install to change this value. Please, ensure of course that on a fresh install, the production checkbox is checked (if that's what you want), and that the URL you choose is resolvable from your end first before trying to save setup page II. Best of luck, Kyle On Mar 23, 2012, at 5:57 PM, Laura Russell wrote: > I'm having difficulty with a CentOS IPT Install that I'm doing for the Field Museum (in Chicago, I'm remote to their server from Kansas). The Field IT staff enabled their Tomcat on the server. And I've deployed the IPT. Permissions on the iptdata folder seem to be okay as it created all the folders and extension files in the first step. > > They are running > CentOS 5.2 > Tomcat 5.5.23 > Java 1.6 > > I'm getting the following error when trying to complete the second setup page on the IPT. > > "The Base URL does not point to an IPT installation that is accessible from this computer." > > The URL is accessible outside of the firewall. I've also tried it with the IP address and get the same error. > > I chatted with Tim Robertson a bit yesterday and I've had the Field IT staff check that the port is open for both incoming and outgoing connections. They do not think their firewall is the issue so I'm looking at other possibilities. > > I've attached the Catalina.out file and the IPT Admin and Debug logs. > > Any assistance is appreciated. > > Thanks. > > > Laura Russell > VertNet Programmer > Biodiversity Institute > University of Kansas > Dyche Hall > 1345 Jayhawk Blvd., Room 606 > Lawrence, KS 66045 > > Phone: 785.864.4681 > Fax: 785.864.5335 > > Email: larussell at vertnet.org > Email: larussell at ku.edu > Google Chat: larussell at vertnet.org > Skype: laura.anne.russell > > URL: http://www.vertnet.org > > VertNet Portals: > MaNIS: http://www.manisnet.org > HerpNET: http://www.herpnet.org > ORNIS: http://www.ornisnet.org > FishNet2: http://www.fishnet2.net > > _______________________________________________ > IPT mailing list > IPT at lists.gbif.org > http://lists.gbif.org/mailman/listinfo/ipt -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gbif.org/pipermail/ipt/attachments/20120323/c2ba4df2/attachment.html From trobertson at gbif.org Mon Mar 26 09:10:51 2012 From: trobertson at gbif.org (Tim Robertson [GBIF]) Date: Mon, 26 Mar 2012 09:10:51 +0200 Subject: [IPT] CentOS IPT Install In-Reply-To: References: Message-ID: <64A1811C-2316-409C-8B2E-43BB67B6BDCC@gbif.org> Hi Laura After our Skype session, is this still an issue? For the benefit of the list: We found that using the terminal the machine could not open connections to itself on port 8080. We found this using curl Cheers, Tim On Mar 23, 2012, at 5:57 PM, Laura Russell wrote: > I'm having difficulty with a CentOS IPT Install that I'm doing for the Field Museum (in Chicago, I'm remote to their server from Kansas). The Field IT staff enabled their Tomcat on the server. And I've deployed the IPT. Permissions on the iptdata folder seem to be okay as it created all the folders and extension files in the first step. > > They are running > CentOS 5.2 > Tomcat 5.5.23 > Java 1.6 > > I'm getting the following error when trying to complete the second setup page on the IPT. > > "The Base URL does not point to an IPT installation that is accessible from this computer." > > The URL is accessible outside of the firewall. I've also tried it with the IP address and get the same error. > > I chatted with Tim Robertson a bit yesterday and I've had the Field IT staff check that the port is open for both incoming and outgoing connections. They do not think their firewall is the issue so I'm looking at other possibilities. > > I've attached the Catalina.out file and the IPT Admin and Debug logs. > > Any assistance is appreciated. > > Thanks. > > > Laura Russell > VertNet Programmer > Biodiversity Institute > University of Kansas > Dyche Hall > 1345 Jayhawk Blvd., Room 606 > Lawrence, KS 66045 > > Phone: 785.864.4681 > Fax: 785.864.5335 > > Email: larussell at vertnet.org > Email: larussell at ku.edu > Google Chat: larussell at vertnet.org > Skype: laura.anne.russell > > URL: http://www.vertnet.org > > VertNet Portals: > MaNIS: http://www.manisnet.org > HerpNET: http://www.herpnet.org > ORNIS: http://www.ornisnet.org > FishNet2: http://www.fishnet2.net > > _______________________________________________ > IPT mailing list > IPT at lists.gbif.org > http://lists.gbif.org/mailman/listinfo/ipt -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gbif.org/pipermail/ipt/attachments/20120326/e4d78474/attachment.html From larussell at vertnet.org Mon Mar 26 16:51:52 2012 From: larussell at vertnet.org (Laura Russell) Date: Mon, 26 Mar 2012 09:51:52 -0500 Subject: [IPT] CentOS IPT Install In-Reply-To: <3F5B44F8-40F3-4872-BC2A-716763CEE7D7@gbif.org> Message-ID: Hi Tim and Burke, Yes still having issues. Tried Kyle's suggestion on Friday. Didn't work, but did cause a connection refused error in Apache. I just read Burke's suggestion below and my our IT admin here at KU just suggested the same thing. Going to recommend to Field IT. Stan Blum also indicated that he had issues with CentOS 5 and Tomcat 5 and went with fresh installs on a virtual server and Tomcat 6. Can't do a fresh system install in this situation, but might be able to update to Tomcat 6. Going to investigate the SELinux policy settings first. I'll keep the list posted as to the resolution. Thanks. Laura Russell VertNet Programmer Biodiversity Institute University of Kansas Dyche Hall 1345 Jayhawk Blvd., Room 606 Lawrence, KS 66045 Phone: 785.864.4681 Fax: 785.864.5335 Email: larussell at vertnet.org Email: larussell at ku.edu Google Chat: larussell at vertnet.org Skype: laura.anne.russell URL: http://www.vertnet.org VertNet Portals: MaNIS: http://www.manisnet.org HerpNET: http://www.herpnet.org ORNIS: http://www.ornisnet.org FishNet2: http://www.fishnet2.net From: "Burke Chih-Jen Ko [GBIF]" Date: Mon, 26 Mar 2012 11:38:55 +0200 To: Laura Russell Cc: "Tim Robertson [GBIF]" Subject: Re: [IPT] CentOS IPT Install Hi Laura, Perhaps you would also want to check the SELINUX policy settings on the CentOS box. I happened to similar situations when every setting is honoured and it turns out the SELINUX add another layer of filtering communications of the linux box. Cheers, Burke On Mar 26, 2012, at 9:10 AM, Tim Robertson [GBIF] wrote: > Hi Laura > > After our Skype session, is this still an issue? > > For the benefit of the list: We found that using the terminal the machine > could not open connections to itself on port 8080. We found this using curl > > Cheers, > Tim > > > > On Mar 23, 2012, at 5:57 PM, Laura Russell wrote: > >> I'm having difficulty with a CentOS IPT Install that I'm doing for the Field >> Museum (in Chicago, I'm remote to their server from Kansas). The Field IT >> staff enabled their Tomcat on the server. And I've deployed the IPT. >> Permissions on the iptdata folder seem to be okay as it created all the >> folders and extension files in the first step. >> >> They are running >> CentOS 5.2 >> Tomcat 5.5.23 >> Java 1.6 >> >> I'm getting the following error when trying to complete the second setup page >> on the IPT. >> >> "The Base URL does not point to an IPT installation that is accessible from >> this computer." >> >> The URL is accessible outside of the firewall. I've also tried it with the >> IP address and get the same error. >> >> I chatted with Tim Robertson a bit yesterday and I've had the Field IT staff >> check that the port is open for both incoming and outgoing connections. They >> do not think their firewall is the issue so I'm looking at other >> possibilities. >> >> I've attached the Catalina.out file and the IPT Admin and Debug logs. >> >> Any assistance is appreciated. >> >> Thanks. >> >> >> Laura Russell >> VertNet Programmer >> Biodiversity Institute >> University of Kansas >> Dyche Hall >> 1345 Jayhawk Blvd., Room 606 >> Lawrence, KS 66045 >> >> Phone: 785.864.4681 >> Fax: 785.864.5335 >> >> Email: larussell at vertnet.org >> Email: larussell at ku.edu >> Google Chat: larussell at vertnet.org >> Skype: laura.anne.russell >> >> URL: http://www.vertnet.org >> >> VertNet Portals: >> MaNIS: http://www.manisnet.org >> HerpNET: http://www.herpnet.org >> ORNIS: http://www.ornisnet.org >> FishNet2: http://www.fishnet2.net >> >> _______________________________________________ >> IPT mailing list >> IPT at lists.gbif.org >> http://lists.gbif.org/mailman/listinfo/ipt > > _______________________________________________ > IPT mailing list > IPT at lists.gbif.org > http://lists.gbif.org/mailman/listinfo/ipt -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gbif.org/pipermail/ipt/attachments/20120326/57ff2f26/attachment.html From janno at ut.ee Mon Mar 26 22:31:57 2012 From: janno at ut.ee (=?ISO-8859-1?Q?janno_j=F5geva?=) Date: Mon, 26 Mar 2012 23:31:57 +0300 Subject: [IPT] CentOS IPT Install In-Reply-To: References: <3F5B44F8-40F3-4872-BC2A-716763CEE7D7@gbif.org> Message-ID: Hi, I am not sure where you are in your testing but this might be useful: When playing around with SELinux then the first thing to give you an idea if SELinux might be an issue would be to go: "sudo setenforce 0" Try to do what didn't work before. "sudo setenforce 1" This will give you an idea if your installation would work without SELinux. If this is the case then you could use "sudo audit2allow -a" to find the issue for your installation. Hope this helps, Janno J?geva NHM of University of Tartu 2012/3/26 Laura Russell : > Hi Tim and Burke, > > Yes still having issues. ?Tried Kyle's suggestion on Friday. ?Didn't work, > but did cause a connection refused error in Apache. ?I just read Burke's > suggestion below and my our IT admin here at KU just suggested the same > thing. ?Going to recommend to Field IT. ?Stan Blum also indicated that he > had issues with CentOS 5 and Tomcat 5 and went with fresh installs on a > virtual server and Tomcat 6. ?Can't do a fresh system install in this > situation, but might be able to update to Tomcat 6. ?Going to investigate > the SELinux policy settings first. ?I'll keep the list posted as to the > resolution. > > Thanks. > > Laura Russell > VertNet Programmer > Biodiversity Institute > University of Kansas > Dyche Hall > 1345 Jayhawk Blvd., Room 606 > Lawrence, KS 66045 > > Phone: 785.864.4681 > Fax: 785.864.5335 > > Email: larussell at vertnet.org > Email: larussell at ku.edu > Google Chat: larussell at vertnet.org > Skype: laura.anne.russell > > URL: http://www.vertnet.org > > VertNet Portals: > MaNIS: http://www.manisnet.org > HerpNET: http://www.herpnet.org > ORNIS: http://www.ornisnet.org > FishNet2: http://www.fishnet2.net > > > From: "Burke Chih-Jen Ko [GBIF]" > Date: Mon, 26 Mar 2012 11:38:55 +0200 > To: Laura Russell > Cc: "Tim Robertson [GBIF]" > Subject: Re: [IPT] CentOS IPT Install > > Hi Laura, > > Perhaps you would also want to check the SELINUX policy settings on the > CentOS box. I happened to similar situations when every setting is honoured > and it turns out the SELINUX add another layer of filtering communications > of the linux box. > > Cheers, > > Burke > > On Mar 26, 2012, at 9:10 AM, Tim Robertson [GBIF] wrote: > > Hi Laura > > After our Skype session, is this still an issue? > > For the benefit of the list: We found that using the terminal the machine > could not open connections to itself on port 8080. ?We found this using curl > > Cheers, > Tim > > > > On Mar 23, 2012, at 5:57 PM, Laura Russell wrote: > > I'm having difficulty with a CentOS IPT Install that I'm doing for the Field > Museum (in Chicago, I'm remote to their server from Kansas). ?The Field IT > staff enabled their Tomcat on the server. And I've deployed the IPT. > ?Permissions on the iptdata folder seem to be okay as it created all the > folders and extension files in the first step. > > They are running > CentOS 5.2 > Tomcat?5.5.23 > Java ?1.6 > > I'm getting the following error when trying to complete the second setup > page on the IPT. > > "The Base URL does not point to an IPT installation that is accessible from > this computer." > > The URL is accessible outside of the firewall. ?I've also tried it with the > IP address and get the same error. > > I chatted with Tim Robertson a bit yesterday and I've had the Field IT staff > check that the port is open for both incoming and outgoing connections. > ?They do not think their firewall is the issue so I'm looking at other > possibilities. > > I've attached the Catalina.out file and the IPT Admin and Debug logs. > > Any assistance is appreciated. > > Thanks. > > > Laura Russell > VertNet Programmer > Biodiversity Institute > University of Kansas > Dyche Hall > 1345 Jayhawk Blvd., Room 606 > Lawrence, KS 66045 > > Phone: 785.864.4681 > Fax: 785.864.5335 > > Email: larussell at vertnet.org > Email: larussell at ku.edu > Google Chat: larussell at vertnet.org > Skype: laura.anne.russell > > URL: http://www.vertnet.org > > VertNet Portals: > MaNIS: http://www.manisnet.org > HerpNET: http://www.herpnet.org > ORNIS: http://www.ornisnet.org > FishNet2: http://www.fishnet2.net > > _______________________________________________ > IPT mailing list > IPT at lists.gbif.org > http://lists.gbif.org/mailman/listinfo/ipt > > > _______________________________________________ > IPT mailing list > IPT at lists.gbif.org > http://lists.gbif.org/mailman/listinfo/ipt > > > > _______________________________________________ > IPT mailing list > IPT at lists.gbif.org > http://lists.gbif.org/mailman/listinfo/ipt >