Mickael, I looked at the source again and the IPT really doesn't log any errors when changing the db connection. This is obviously not very helpful, so I've updated the code already to do so. I will upload a new war file today, so if you like you can try this version and hopefully find the reason for your connection problem. Will post the links later. many thanks, Markus On May 11, 2009, at 6:03 PM, Tim Robertson wrote:

Hej Mickael,

Can you please post the logs you get when you configure and save the database connection?

Many thanks,

Tim

On 11 May 2009, at 14:36, Mickael Graf wrote:

...

Sorry for posting at the wrong place.

The database name is correct, and IPT runs on the same server as the mysql database. This database works perfectly with our TAPIRLink provider.

The MySQL server version is 5.0.45 and Connector/J has version 5.1.7. It has been tested against Java 1.6.0 (OpenJDK) and against Sun Java 6 Update 12. None of this worked.

Cheers, Mickaël

On Mon, 2009-05-11 at 10:49 +0200, Tim Robertson wrote:

...

Hi Mickael,

Please always post questions to the list, to help us keep an FAQ up to date and allow for others to search etc.

I have just tested it myself with the following:

Database connection URL: jdbc:mysql://localhost:3306/portal Database User: tim Database Password: password

and it worked... so, to get started debugging your issue may I please ask some basic questions:

- You wrote "jdbc:mysql://localhost:3306/databasename" - is your database name correct? - You are running the IPT on the same machine as the database? - You are using mysql?

Cheers,

Tim

On 11 May 2009, at 10:26, Mickael Graf wrote:

...

Hi Tim,

I'm trying to create a resource in IPT but I encounter a problem while creating the link to the database: in "Source Data" it is written under "SQL Data Sources" I have the message "No Database connected. Please adjust connection parameters to use SQL sources" while it keeps my settings correctly. I hope I wrote the jdbc string well: jdbc:mysql://localhost:3306/databasename.

I surprised because I am using the same parameters as with TAPIRLink in which I don't have any problem. I don't think I should make any changes in my grants on my database.

Cheers, Mickaël

-- --------------------------------- Mickaël Graf Database developper, GBIF Sweden - http://www.gbif.se tel: +46 8 5195 4045 mailto:mickael.graf@nrm.se

Swedish Museum of Natural History - http://www.nrm.se Box 50007 SE-104 05 Stockholm Sweden

-- --------------------------------- Mickaël Graf Database developper, GBIF Sweden - http://www.gbif.se tel: +46 8 5195 4045 mailto:mickael.graf@nrm.se

Swedish Museum of Natural History - http://www.nrm.se Box 50007 SE-104 05 Stockholm Sweden

_______________________________________________ IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt

Mickael, the latest IPT war snapshot can be found here: ftp://ftp.gbif.org/projects/ipt/downloads/ipt-1.0RC2-SNAPSHOT.war This version logs connection problems and also uses in addition to tomcat logging an ipt.log file inside the data/logging dir. It also shows a simple message if you configure a bad connection in the manager UI. If you have time, please use this to find out more about your mysql conenction problem. thanks, Markus On May 12, 2009, at 10:17 AM, Markus Döring (GBIF) wrote:

Mickael, I looked at the source again and the IPT really doesn't log any errors when changing the db connection. This is obviously not very helpful, so I've updated the code already to do so. I will upload a new war file today, so if you like you can try this version and hopefully find the reason for your connection problem. Will post the links later.

many thanks, Markus

On May 11, 2009, at 6:03 PM, Tim Robertson wrote:

...

Hej Mickael,

Can you please post the logs you get when you configure and save the database connection?

Many thanks,

Tim

On 11 May 2009, at 14:36, Mickael Graf wrote:

...

Sorry for posting at the wrong place.

The database name is correct, and IPT runs on the same server as the mysql database. This database works perfectly with our TAPIRLink provider.

The MySQL server version is 5.0.45 and Connector/J has version 5.1.7. It has been tested against Java 1.6.0 (OpenJDK) and against Sun Java 6 Update 12. None of this worked.

Cheers, Mickaël

On Mon, 2009-05-11 at 10:49 +0200, Tim Robertson wrote:

...

Hi Mickael,

Please always post questions to the list, to help us keep an FAQ up to date and allow for others to search etc.

I have just tested it myself with the following:

Database connection URL: jdbc:mysql://localhost:3306/portal Database User: tim Database Password: password

and it worked... so, to get started debugging your issue may I please ask some basic questions:

- You wrote "jdbc:mysql://localhost:3306/databasename" - is your database name correct? - You are running the IPT on the same machine as the database? - You are using mysql?

Cheers,

Tim

On 11 May 2009, at 10:26, Mickael Graf wrote:

...

Hi Tim,

I'm trying to create a resource in IPT but I encounter a problem while creating the link to the database: in "Source Data" it is written under "SQL Data Sources" I have the message "No Database connected. Please adjust connection parameters to use SQL sources" while it keeps my settings correctly. I hope I wrote the jdbc string well: jdbc:mysql://localhost:3306/databasename.

I surprised because I am using the same parameters as with TAPIRLink in which I don't have any problem. I don't think I should make any changes in my grants on my database.

Cheers, Mickaël

-- --------------------------------- Mickaël Graf Database developper, GBIF Sweden - http://www.gbif.se tel: +46 8 5195 4045 mailto:mickael.graf@nrm.se

Swedish Museum of Natural History - http://www.nrm.se Box 50007 SE-104 05 Stockholm Sweden

-- --------------------------------- Mickaël Graf Database developper, GBIF Sweden - http://www.gbif.se tel: +46 8 5195 4045 mailto:mickael.graf@nrm.se

Swedish Museum of Natural History - http://www.nrm.se Box 50007 SE-104 05 Stockholm Sweden

_______________________________________________ IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt

Dear Mickael, just a small hint... in a former version I also had some problems with SQL connections: http://code.google.com/p/gbif-providertoolkit/issues/detail?id=121 Maybe try to restart tomcat to make sure it's not the same problem. Just an idea, Jörg -----Ursprüngliche Nachricht----- Von: ipt-bounces@lists.gbif.org [mailto:ipt-bounces@lists.gbif.org]Im Auftrag von Mickael Graf Gesendet: Dienstag, 12. Mai 2009 13:28 An: "Markus Döring (GBIF)" Cc: ipt@lists.gbif.org Betreff: Re: [IPT] IPT connection problem Markus, I undeployed RC1 and deployed RC2 and it creates a logfile ipt.log. But it doesn't log any error at all related to the connection problem. BTW, I never wrote it before but the message is "No Database connected. Please adjust connection parameters to use SQL sources" I send you the logfile in case of there is something useful in it. Cheers Mickaël On Tue, 2009-05-12 at 11:47 +0200, "Markus Döring (GBIF)" wrote:

Mickael, the latest IPT war snapshot can be found here:

ftp://ftp.gbif.org/projects/ipt/downloads/ipt-1.0RC2-SNAPSHOT.war

This version logs connection problems and also uses in addition to tomcat logging an ipt.log file inside the data/logging dir. It also shows a simple message if you configure a bad connection in the manager UI. If you have time, please use this to find out more about your mysql conenction problem.

thanks, Markus

On May 12, 2009, at 10:17 AM, Markus Döring (GBIF) wrote:

...

Mickael, I looked at the source again and the IPT really doesn't log any errors when changing the db connection. This is obviously not very helpful, so I've updated the code already to do so. I will upload a new war file today, so if you like you can try this version and hopefully find the reason for your connection problem. Will post the links later.

many thanks, Markus

On May 11, 2009, at 6:03 PM, Tim Robertson wrote:

...

Hej Mickael,

Can you please post the logs you get when you configure and save the database connection?

Many thanks,

Tim

On 11 May 2009, at 14:36, Mickael Graf wrote:

...

Sorry for posting at the wrong place.

The database name is correct, and IPT runs on the same server as the mysql database. This database works perfectly with our TAPIRLink provider.

The MySQL server version is 5.0.45 and Connector/J has version 5.1.7. It has been tested against Java 1.6.0 (OpenJDK) and against Sun Java 6 Update 12. None of this worked.

Cheers, Mickaël

On Mon, 2009-05-11 at 10:49 +0200, Tim Robertson wrote:

...

Hi Mickael,

Please always post questions to the list, to help us keep an FAQ up to date and allow for others to search etc.

I have just tested it myself with the following:

Database connection URL: jdbc:mysql://localhost:3306/portal Database User: tim Database Password: password

and it worked... so, to get started debugging your issue may I please ask some basic questions:

- You wrote "jdbc:mysql://localhost:3306/databasename" - is your database name correct? - You are running the IPT on the same machine as the database? - You are using mysql?

Cheers,

Tim

On 11 May 2009, at 10:26, Mickael Graf wrote:

...

Hi Tim,

I'm trying to create a resource in IPT but I encounter a problem while creating the link to the database: in "Source Data" it is written under "SQL Data Sources" I have the message "No Database connected. Please adjust connection parameters to use SQL sources" while it keeps my settings correctly. I hope I wrote the jdbc string well: jdbc:mysql://localhost:3306/databasename.

I surprised because I am using the same parameters as with TAPIRLink in which I don't have any problem. I don't think I should make any changes in my grants on my database.

Cheers, Mickaël

-- --------------------------------- Mickaël Graf Database developper, GBIF Sweden - http://www.gbif.se tel: +46 8 5195 4045 mailto:mickael.graf@nrm.se

Swedish Museum of Natural History - http://www.nrm.se Box 50007 SE-104 05 Stockholm Sweden

-- --------------------------------- Mickaël Graf Database developper, GBIF Sweden - http://www.gbif.se tel: +46 8 5195 4045 mailto:mickael.graf@nrm.se

Swedish Museum of Natural History - http://www.nrm.se Box 50007 SE-104 05 Stockholm Sweden

_______________________________________________ IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt

-- --------------------------------- Mickaël Graf Database developper, GBIF Sweden - http://www.gbif.se tel: +46 8 5195 4045 mailto:mickael.graf@nrm.se Swedish Museum of Natural History - http://www.nrm.se Box 50007 SE-104 05 Stockholm Sweden

Hi all,

PS. I agree with Jörg that a convenient way to keep the old data directory when upgrading the IPT would be cute.

This is indeed the case. We will aim wherever possible to make upgrading as simple as it can be. For bug fix releases, such as this snapshot, with no structural change the data directory can be migrated directly. In future releases, we might require a "one time" migration task be run. I anticipate the first one being required when the DwC standard is ratified.

PPS. And a convinient way to add a thematic extension to the DwC (for testing and demonstration) would also be very useful. I am thinking of the draft DwC germplasm extension - as well as a new draft for germplasm trait observation data I have started to work on. I assume this perhaps could be done as an addition in the IPT code somewhere around "WEB-INF/classes/org/gbif/provider/model/" ...?

A good suggestion. We should look at setting up some sandbox repository for exactly this purpose. Dag, for testing and demonstration you could do the following, but please be very careful not to register these datasets with GBIF. - The IPT will call (http://gbrds.gbif.org/registry/ipt/ extensions.json and http://gbrds.gbif.org/registry/ipt/thesauri.json) to get the extensions and the thesauri. - The response is fairly self explanatory, and for a test, you could override gbrds.gbif.org in you host file, and put up a different version locally for example referencing your test extensions. - Then simply update your extensions through the IPT. - Sorry, not the easiest work around, but might get you able to demonstrate how you can start to build your community without waiting for the sandbox repository. Best wishes, Tim

From: Holetschek, Jörg [mailto:j.holetschek@bgbm.org] To: 'Mickael Graf' [mailto:mickael.graf@nrm.se], "\"Markus Döring (GBIF)\"" [mailto:mdoering@gbif.org] Cc: ipt@lists.gbif.org [mailto:ipt@lists.gbif.org] Sent: Tue, 12 May 2009 13:55:36 +0200 Subject: Re: [IPT] IPT connection problem

Dear Mickael,

just a small hint... in a former version I also had some problems with SQL connections: http://code.google.com/p/gbif-providertoolkit/issues/detail?id=121

Maybe try to restart tomcat to make sure it's not the same problem.

Just an idea, Jörg

-----Ursprüngliche Nachricht----- Von: ipt-bounces@lists.gbif.org [mailto:ipt-bounces@lists.gbif.org]Im Auftrag von Mickael Graf Gesendet: Dienstag, 12. Mai 2009 13:28 An: "Markus Döring (GBIF)" Cc: ipt@lists.gbif.org Betreff: Re: [IPT] IPT connection problem

Markus,

I undeployed RC1 and deployed RC2 and it creates a logfile ipt.log. But it doesn't log any error at all related to the connection problem.

BTW, I never wrote it before but the message is "No Database connected. Please adjust connection parameters to use SQL sources"

I send you the logfile in case of there is something useful in it.

Cheers Mickaël

On Tue, 2009-05-12 at 11:47 +0200, "Markus Döring (GBIF)" wrote:

...

Mickael, the latest IPT war snapshot can be found here:

ftp://ftp.gbif.org/projects/ipt/downloads/ipt-1.0RC2-SNAPSHOT.war

This version logs connection problems and also uses in addition to tomcat logging an ipt.log file inside the data/logging dir. It also shows a simple message if you configure a bad connection in the manager UI. If you have time, please use this to find out more about your mysql conenction problem.

thanks, Markus

On May 12, 2009, at 10:17 AM, Markus Döring (GBIF) wrote:

...

Mickael, I looked at the source again and the IPT really doesn't log any errors when changing the db connection. This is obviously not very helpful, so I've updated the code already to do so. I will upload a new war file today, so if you like you can try this version and hopefully find the reason for your connection problem. Will post the links later.

many thanks, Markus

On May 11, 2009, at 6:03 PM, Tim Robertson wrote:

...

Hej Mickael,

Can you please post the logs you get when you configure and save the database connection?

Many thanks,

Tim

On 11 May 2009, at 14:36, Mickael Graf wrote:

...

Sorry for posting at the wrong place.

The database name is correct, and IPT runs on the same server as the mysql database. This database works perfectly with our TAPIRLink provider.

The MySQL server version is 5.0.45 and Connector/J has version 5.1.7. It has been tested against Java 1.6.0 (OpenJDK) and against Sun Java 6 Update 12. None of this worked.

Cheers, Mickaël

On Mon, 2009-05-11 at 10:49 +0200, Tim Robertson wrote:

...

Hi Mickael,

Please always post questions to the list, to help us keep an FAQ up to date and allow for others to search etc.

I have just tested it myself with the following:

Database connection URL: jdbc:mysql://localhost:3306/portal Database User: tim Database Password: password

and it worked... so, to get started debugging your issue may I please ask some basic questions:

- You wrote "jdbc:mysql://localhost:3306/databasename" - is your database name correct? - You are running the IPT on the same machine as the database? - You are using mysql?

Cheers,

Tim

On 11 May 2009, at 10:26, Mickael Graf wrote:

> Hi Tim, > > I'm trying to create a resource in IPT but I encounter a problem > while > creating the link to the database: in "Source Data" it is written > under > "SQL Data Sources" I have the message "No Database connected. > Please > adjust connection parameters to use SQL sources" while it keeps my > settings correctly. I hope I wrote the jdbc string well: > jdbc:mysql://localhost:3306/databasename. > > I surprised because I am using the same parameters as with > TAPIRLink > in > which I don't have any problem. I don't think I should make any > changes > in my grants on my database. > > Cheers, > Mickaël > > -- > --------------------------------- > Mickaël Graf > Database developper, GBIF Sweden - http://www.gbif.se > tel: +46 8 5195 4045 > mailto:mickael.graf@nrm.se > > Swedish Museum of Natural History - http://www.nrm.se > Box 50007 > SE-104 05 Stockholm > Sweden > > >

-- --------------------------------- Mickaël Graf Database developper, GBIF Sweden - http://www.gbif.se tel: +46 8 5195 4045 mailto:mickael.graf@nrm.se

Swedish Museum of Natural History - http://www.nrm.se Box 50007 SE-104 05 Stockholm Sweden

_______________________________________________ IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt

-- --------------------------------- Mickaël Graf Database developper, GBIF Sweden - http://www.gbif.se tel: +46 8 5195 4045 mailto:mickael.graf@nrm.se

Swedish Museum of Natural History - http://www.nrm.se Box 50007 SE-104 05 Stockholm Sweden _______________________________________________ IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt _______________________________________________ IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt

Dag, Eli, I've checked the IPT code again for the extension registry URL and I was actually wrong. The current version *does* make use of the ipt.properties settings. The standard GBIF URL that is used in the ipt.properties should be: registryUrl=http://gbrds.gbif.org/registry The registry then returns a JSON list of all known extensions located at: http://gbrds.gbif.org/registry/ipt/extensions.json So to test your own extensions you can modify this json list to include entries for your own (pointing to your extension xml definitions hosted on some URL), upload that json file to some http server and modify the ipt.properties setting to point to your registry, e.g.: registryUrl=http://dev.eol.org/ipt that will finally point to the file http://dev.eol.org/ipt/ipt/extensions.json To get everything working this registry base URL should also deal with other things, e.g. the registry of resources, organisations, services, etc. But in order to test the extensions this should still work. If you give it a try, please report your findings back to this list. cheers, Markus On May 12, 2009, at 6:05 PM, Markus Döring (GBIF) wrote:

...

...

PS. I agree with Jörg that a convenient way to keep the old data directory when upgrading the IPT would be cute.

This is indeed the case. We will aim wherever possible to make upgrading as simple as it can be. For bug fix releases, such as this snapshot, with no structural change the data directory can be migrated directly. In future releases, we might require a "one time" migration task be run. I anticipate the first one being required when the DwC standard is ratified.

if you look into your ipt.properties file you can modify the following settings:

dataDir=${ipt.datadir} registryUrl=${ipt.registry.url}

the dataDir should be an absolute path pointing to your data dir (defaults to the ipt webapp data subfolder). the registry URL can point to a development registry - unfortunately the extensions and vocabs currently dont use this setting, only the UDDI style registration of resources and organisations. We will make sure that the IPT uses this setting also for the extension registration, so you can easily point it to an alternative extension site for testing.

markus

This is really excellent to see Dag - really well done and thank you for taking the time to post those instructions. Tim On 15 May 2009, at 15:07, Dag Terje Filip Endresen wrote:

Hi Markus and Tim,

Thanks a lot for your help! I followed your instructions and successfully added my DRAFT version of a DarwinCore extension for germplasm to the IPT. I have listed a brief summary of each of the steps I followed below.

If you are interested, you may visit the IPT from NordGen with a DEMO dataset mapped to terms from this DRAFT Darwin Core extension for germplasm at: http://atlas.nordgen.org/ipt/occResource.html?resource_id=77

1. Schema I built a suggestion to a DRAFT Darwin Core extansion for germplasm http://code.google.com/p/darwincore/source/browse/trunk/xsd/profiles/germpla... http://wwwdev.ngb.se/portal/rs/dwc_germplasm.xsd

2. XML definition for IPT Listing the terms to use from the suggested DRAFT DarwinCore extension http://wwwdev.ngb.se/portal/rs/ipt_germplasm.xml

3. Add this XML definition to a copy of extensions.json Starting with "http://gbrds.gbif.org/registry/ipt/extensions.json" Add text {"title":"Germplasm","url":"http://wwwdev.ngb.se/portal/rs/ipt_germplasm.xml ","id":9} Saved as: http://wwwdev.ngb.se/portal/rs/ipt/extensions.json

4. Modify ipt.properties PATH_TO_TOMCAT_WEBAPPS/ipt/WEB-INF/classes/ipt.properties Line 7: "registryUrl=http://gbrds.gbif.org/registry" modified to "registryUrl=http://wwwdev.ngb.se/portal/rs"

5. Restart Tomcat (reload ipt) The new ipt.properties settings does not seem to be loaded without restart of tomcat

6. Add/load the new extension to IPT Login with admin permissions http://your_server_name/ipt/admin/extensions.html Click "Check for all available extensions" Select the name of the new extension Select "install" and "Done"

7. Mapping of terms to your data Select the new extension under "Add New Mapping" Click "Add" button to the right Select and map terms

I selected the "publish" button and hope that this will not cause this dataset to be registered at the GBIF registry...? Without selecting the "publish" button the dataset is not listed from the menu item "explore". I was missing the option to publish a dataset under this "explore", but not not to register with the GBIF registry...? Should there not be one more step to this procedure?

Cheers Dag Terje

PS. I have noticed that the right side context menu is very sensitive to missing data (Navigate Taxonomy, Navigate Geography). If some of the higher taxonomic levels is missing I get an error message instead of the context menu. For example I did not have phylum for the genebank dataset and the error message on "Navigate Taxonomy" untill I added data for this term. Similar I did not have continent causing the "Navigate Geography" context menu to start at country. When continent and/or country is missing, the "Navigate Geography" context menu creates a top node for the lowest level available - sometimes even the coordinate is displayed as the top node here. Would be cute if the IPT could default to "unknown continent", "unknown country"; "unknown phylum", ... or something similar.

PPS. NB! This DRAFT extension for germplasm is still under development and I am sure that I still duplicate some terms from DarwinCore or other extensions! I did not yet work much with the terms for trait observations on germplasm, but added most of the terms from the new proposed draft standard for these data for the European genebank community.

From: "Markus Döring (GBIF)" [mailto:mdoering@gbif.org] To: Dag Terje Filip Endresen [mailto:dag.endresen@nordgen.org], Eli Agbayani [mailto:eagbayani@eol.org] Cc: ipt@lists.gbif.org Sent: Wed, 13 May 2009 00:05:33 +0200 Subject: Re: [IPT] IPT connection problem

Dag, Eli, I've checked the IPT code again for the extension registry URL and I was actually wrong. The current version *does* make use of the ipt.properties settings.

The standard GBIF URL that is used in the ipt.properties should be: registryUrl=http://gbrds.gbif.org/registry

The registry then returns a JSON list of all known extensions located at: http://gbrds.gbif.org/registry/ipt/extensions.json

So to test your own extensions you can modify this json list to include entries for your own (pointing to your extension xml definitions hosted on some URL), upload that json file to some http server and modify the ipt.properties setting to point to your registry, e.g.: registryUrl=http://dev.eol.org/ipt

that will finally point to the file http://dev.eol.org/ipt/ipt/extensions.json

To get everything working this registry base URL should also deal with other things, e.g. the registry of resources, organisations, services, etc. But in order to test the extensions this should still work.

If you give it a try, please report your findings back to this list.

cheers, Markus

On May 12, 2009, at 6:05 PM, Markus Döring (GBIF) wrote:

...

...

...

PS. I agree with Jörg that a convenient way to keep the old data directory when upgrading the IPT would be cute.

This is indeed the case. We will aim wherever possible to make upgrading as simple as it can be. For bug fix releases, such as this snapshot, with no structural change the data directory can be migrated directly. In future releases, we might require a "one time" migration task be run. I anticipate the first one being required when the DwC standard is ratified.

if you look into your ipt.properties file you can modify the following settings:

dataDir=${ipt.datadir} registryUrl=${ipt.registry.url}

the dataDir should be an absolute path pointing to your data dir (defaults to the ipt webapp data subfolder). the registry URL can point to a development registry - unfortunately the extensions and vocabs currently dont use this setting, only the UDDI style registration of resources and organisations. We will make sure that the IPT uses this setting also for the extension registration, so you can easily point it to an alternative extension site for testing.

markus

_______________________________________________ IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt

Hi Dag, My database and IPT are on the same machine, as well as my TAPIRLink provider. The database name, username and password are the ones used successfully with TAPIRLink so this shouldn't be a permission issue. Cheers, Mickaël On Tue, 2009-05-12 at 14:48 +0200, Dag Terje Filip Endresen wrote:

Hi Mickael,

Just another thought. Is the MySQL database on localhost (same computer as the ipt)? As you get the error on "No Database connected", perhaps it is the permission settings for your database not allowing connections from the computer where you have installed the IPT. I am using a PostgreSQL (not on localhost) and saw this error message before I added the permissions for the computer running the ipt to connect to the database (hba.conf for PostgreSQL).

Dag Terje

PS. I agree with Jörg that a convenient way to keep the old data directory when upgrading the IPT would be cute. PPS. And a convinient way to add a thematic extension to the DwC (for testing and demonstration) would also be very useful. I am thinking of the draft DwC germplasm extension - as well as a new draft for germplasm trait observation data I have started to work on. I assume this perhaps could be done as an addition in the IPT code somewhere around "WEB-INF/classes/org/gbif/provider/model/" ...?

______________________________________________________________ From: Holetschek, Jörg [mailto:j.holetschek@bgbm.org] To: 'Mickael Graf' [mailto:mickael.graf@nrm.se], "\"Markus Döring (GBIF)\"" [mailto:mdoering@gbif.org] Cc: ipt@lists.gbif.org [mailto:ipt@lists.gbif.org] Sent: Tue, 12 May 2009 13:55:36 +0200 Subject: Re: [IPT] IPT connection problem

Dear Mickael,

just a small hint... in a former version I also had some problems with SQL connections: http://code.google.com/p/gbif-providertoolkit/issues/detail?id=121

Maybe try to restart tomcat to make sure it's not the same problem.

Just an idea, Jörg

-----Ursprüngliche Nachricht----- Von: ipt-bounces@lists.gbif.org [mailto:ipt-bounces@lists.gbif.org]Im Auftrag von Mickael Graf Gesendet: Dienstag, 12. Mai 2009 13:28 An: "Markus Döring (GBIF)" Cc: ipt@lists.gbif.org Betreff: Re: [IPT] IPT connection problem

Markus,

I undeployed RC1 and deployed RC2 and it creates a logfile ipt.log. But it doesn't log any error at all related to the connection problem.

BTW, I never wrote it before but the message is "No Database connected. Please adjust connection parameters to use SQL sources"

I send you the logfile in case of there is something useful in it.

Cheers Mickaël

On Tue, 2009-05-12 at 11:47 +0200, "Markus Döring (GBIF)" wrote: > Mickael, > the latest IPT war snapshot can be found here: > > ftp://ftp.gbif.org/projects/ipt/downloads/ipt-1.0RC2-SNAPSHOT.war > > This version logs connection problems and also uses in addition to > tomcat logging an ipt.log file inside the data/logging dir. > It also shows a simple message if you configure a bad connection in > the manager UI. > If you have time, please use this to find out more about your mysql > conenction problem. > > thanks, > Markus > > > > On May 12, 2009, at 10:17 AM, Markus Döring (GBIF) wrote: > > > Mickael, > > I looked at the source again and the IPT really doesn't log any > > errors when changing the db connection. > > This is obviously not very helpful, so I've updated the code already > > to do so. I will upload a new war file today, so if you like you can > > try this version and hopefully find the reason for your connection > > problem. Will post the links later. > > > > many thanks, > > Markus > > > > > > > > On May 11, 2009, at 6:03 PM, Tim Robertson wrote: > > > >> Hej Mickael, > >> > >> Can you please post the logs you get when you configure and save the > >> database connection? > >> > >> Many thanks, > >> > >> Tim > >> > >> > >> > >> On 11 May 2009, at 14:36, Mickael Graf wrote: > >> > >>> Sorry for posting at the wrong place. > >>> > >>> The database name is correct, and IPT runs on the same server as the > >>> mysql database. This database works perfectly with our TAPIRLink > >>> provider. > >>> > >>> The MySQL server version is 5.0.45 and Connector/J has version > >>> 5.1.7. It > >>> has been tested against Java 1.6.0 (OpenJDK) and against Sun Java 6 > >>> Update 12. None of this worked. > >>> > >>> > >>> Cheers, > >>> Mickaël > >>> > >>> > >>> On Mon, 2009-05-11 at 10:49 +0200, Tim Robertson wrote: > >>>> Hi Mickael, > >>>> > >>>> > >>>> Please always post questions to the list, to help us keep an FAQ up > >>>> to > >>>> date and allow for others to search etc. > >>>> > >>>> > >>>> I have just tested it myself with the following: > >>>> > >>>> > >>>> Database connection URL: jdbc:mysql://localhost:3306/portal > >>>> Database User: tim > >>>> Database Password: password > >>>> > >>>> > >>>> and it worked... so, to get started debugging your issue may I > >>>> please > >>>> ask some basic questions: > >>>> > >>>> > >>>> - You wrote "jdbc:mysql://localhost:3306/databasename" - is your > >>>> database name correct? > >>>> - You are running the IPT on the same machine as the database? > >>>> - You are using mysql? > >>>> > >>>> > >>>> Cheers, > >>>> > >>>> > >>>> Tim > >>>> > >>>> > >>>> > >>>> On 11 May 2009, at 10:26, Mickael Graf wrote: > >>>> > >>>>> Hi Tim, > >>>>> > >>>>> I'm trying to create a resource in IPT but I encounter a problem > >>>>> while > >>>>> creating the link to the database: in "Source Data" it is written > >>>>> under > >>>>> "SQL Data Sources" I have the message "No Database connected. > >>>>> Please > >>>>> adjust connection parameters to use SQL sources" while it keeps my > >>>>> settings correctly. I hope I wrote the jdbc string well: > >>>>> jdbc:mysql://localhost:3306/databasename. > >>>>> > >>>>> I surprised because I am using the same parameters as with > >>>>> TAPIRLink > >>>>> in > >>>>> which I don't have any problem. I don't think I should make any > >>>>> changes > >>>>> in my grants on my database. > >>>>> > >>>>> Cheers, > >>>>> Mickaël > >>>>> > >>>>> -- > >>>>> --------------------------------- > >>>>> Mickaël Graf > >>>>> Database developper, GBIF Sweden - http://www.gbif.se > >>>>> tel: +46 8 5195 4045 > >>>>> mailto:mickael.graf@nrm.se > >>>>> > >>>>> Swedish Museum of Natural History - http://www.nrm.se > >>>>> Box 50007 > >>>>> SE-104 05 Stockholm > >>>>> Sweden > >>>>> > >>>>> > >>>>> > >>>> > >>>> > >>> -- > >>> --------------------------------- > >>> Mickaël Graf > >>> Database developper, GBIF Sweden - http://www.gbif.se > >>> tel: +46 8 5195 4045 > >>> mailto:mickael.graf@nrm.se > >>> > >>> Swedish Museum of Natural History - http://www.nrm.se > >>> Box 50007 > >>> SE-104 05 Stockholm > >>> Sweden > >>> > >>> > >> > >> _______________________________________________ > >> IPT mailing list > >> IPT@lists.gbif.org > >> http://lists.gbif.org/mailman/listinfo/ipt > >> > > > -- --------------------------------- Mickaël Graf Database developper, GBIF Sweden - http://www.gbif.se tel: +46 8 5195 4045 mailto:mickael.graf@nrm.se

Swedish Museum of Natural History - http://www.nrm.se Box 50007 SE-104 05 Stockholm Sweden _______________________________________________ IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt --

Mickaël Graf, Database developper GBIF Sweden - http://www.gbif.se mailto:mickael.graf@nrm.se tel: +46 8 5195 4045 Swedish Museum of Natural History - http://www.nrm.se Box 50007 SE-104 05 Stockholm Sweden

from RC1 on there hasn't been a change in the data dir, so yes, you should be able to use your existing data dir without a problem. Probably the best is to keep it outside of the webapps folder and update the ipt.properties Markus On May 12, 2009, at 2:05 PM, Holetschek, Jörg wrote:

Hi Markus,

is it possible to keep the old data directory with the new RC?

Jörg

-----Ursprüngliche Nachricht----- Von: ipt-bounces@lists.gbif.org [mailto:ipt-bounces@lists.gbif.org]Im Auftrag von "Markus Döring (GBIF)" Gesendet: Dienstag, 12. Mai 2009 11:48 An: Mickael Graf Cc: ipt@lists.gbif.org Betreff: Re: [IPT] IPT connection problem

Mickael, the latest IPT war snapshot can be found here:

ftp://ftp.gbif.org/projects/ipt/downloads/ipt-1.0RC2-SNAPSHOT.war

This version logs connection problems and also uses in addition to tomcat logging an ipt.log file inside the data/logging dir. It also shows a simple message if you configure a bad connection in the manager UI. If you have time, please use this to find out more about your mysql conenction problem.

thanks, Markus

On May 12, 2009, at 10:17 AM, Markus Döring (GBIF) wrote:

...

Mickael, I looked at the source again and the IPT really doesn't log any errors when changing the db connection. This is obviously not very helpful, so I've updated the code already to do so. I will upload a new war file today, so if you like you can try this version and hopefully find the reason for your connection problem. Will post the links later.

many thanks, Markus

On May 11, 2009, at 6:03 PM, Tim Robertson wrote:

...

Hej Mickael,

Can you please post the logs you get when you configure and save the database connection?

Many thanks,

Tim

On 11 May 2009, at 14:36, Mickael Graf wrote:

...

Sorry for posting at the wrong place.

The database name is correct, and IPT runs on the same server as the mysql database. This database works perfectly with our TAPIRLink provider.

The MySQL server version is 5.0.45 and Connector/J has version 5.1.7. It has been tested against Java 1.6.0 (OpenJDK) and against Sun Java 6 Update 12. None of this worked.

Cheers, Mickaël

On Mon, 2009-05-11 at 10:49 +0200, Tim Robertson wrote:

...

Hi Mickael,

Please always post questions to the list, to help us keep an FAQ up to date and allow for others to search etc.

I have just tested it myself with the following:

Database connection URL: jdbc:mysql://localhost:3306/portal Database User: tim Database Password: password

and it worked... so, to get started debugging your issue may I please ask some basic questions:

- You wrote "jdbc:mysql://localhost:3306/databasename" - is your database name correct? - You are running the IPT on the same machine as the database? - You are using mysql?

Cheers,

Tim

On 11 May 2009, at 10:26, Mickael Graf wrote:

...

Hi Tim,

I'm trying to create a resource in IPT but I encounter a problem while creating the link to the database: in "Source Data" it is written under "SQL Data Sources" I have the message "No Database connected. Please adjust connection parameters to use SQL sources" while it keeps my settings correctly. I hope I wrote the jdbc string well: jdbc:mysql://localhost:3306/databasename.

I surprised because I am using the same parameters as with TAPIRLink in which I don't have any problem. I don't think I should make any changes in my grants on my database.

Cheers, Mickaël

-- --------------------------------- Mickaël Graf Database developper, GBIF Sweden - http://www.gbif.se tel: +46 8 5195 4045 mailto:mickael.graf@nrm.se

Swedish Museum of Natural History - http://www.nrm.se Box 50007 SE-104 05 Stockholm Sweden

-- --------------------------------- Mickaël Graf Database developper, GBIF Sweden - http://www.gbif.se tel: +46 8 5195 4045 mailto:mickael.graf@nrm.se

Swedish Museum of Natural History - http://www.nrm.se Box 50007 SE-104 05 Stockholm Sweden

_______________________________________________ IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt

_______________________________________________ IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt

Mickael, do you get any feedback a) in the UI when saving a sql connection b) in the logs? if not, how did you upgrade your installation? You might want to try: - stop tomcat - copy your existing data dir somewhere else - remove the exploded webapps folder - remove the cached version in tomcat/work/Catalina/localhost/ipt - start tomcat with ipt.war inside webapps - stop tomcat - update webapps/ipt/WEB-INF/classes/ipt.properties to point to your saved data dir - start tomcat thats the procedure for upgrading to a new IPT version while keeping your data if its still living within the default webapps folder. Did you do this and still get no message when saving a not working db connection? Markus On May 13, 2009, at 12:24 PM, Mickael Graf wrote:

Markus,

The RC2 didn't help much, I'm totally blind as to find where the problem comes from.

I was wondering if you could tell me which files are involved in the process so I can get a better understanding?

Cheers, Mickaël

On Tue, 2009-05-12 at 11:47 +0200, "Markus Döring (GBIF)" wrote:

...

Mickael, the latest IPT war snapshot can be found here:

ftp://ftp.gbif.org/projects/ipt/downloads/ipt-1.0RC2-SNAPSHOT.war

This version logs connection problems and also uses in addition to tomcat logging an ipt.log file inside the data/logging dir. It also shows a simple message if you configure a bad connection in the manager UI. If you have time, please use this to find out more about your mysql conenction problem.

thanks, Markus

On May 12, 2009, at 10:17 AM, Markus Döring (GBIF) wrote:

...

Mickael, I looked at the source again and the IPT really doesn't log any errors when changing the db connection. This is obviously not very helpful, so I've updated the code already to do so. I will upload a new war file today, so if you like you can try this version and hopefully find the reason for your connection problem. Will post the links later.

many thanks, Markus

On May 11, 2009, at 6:03 PM, Tim Robertson wrote:

...

Hej Mickael,

Can you please post the logs you get when you configure and save the database connection?

Many thanks,

Tim

On 11 May 2009, at 14:36, Mickael Graf wrote:

...

Sorry for posting at the wrong place.

The database name is correct, and IPT runs on the same server as the mysql database. This database works perfectly with our TAPIRLink provider.

The MySQL server version is 5.0.45 and Connector/J has version 5.1.7. It has been tested against Java 1.6.0 (OpenJDK) and against Sun Java 6 Update 12. None of this worked.

Cheers, Mickaël

On Mon, 2009-05-11 at 10:49 +0200, Tim Robertson wrote:

...

Hi Mickael,

Please always post questions to the list, to help us keep an FAQ up to date and allow for others to search etc.

I have just tested it myself with the following:

Database connection URL: jdbc:mysql://localhost:3306/portal Database User: tim Database Password: password

and it worked... so, to get started debugging your issue may I please ask some basic questions:

- You wrote "jdbc:mysql://localhost:3306/databasename" - is your database name correct? - You are running the IPT on the same machine as the database? - You are using mysql?

Cheers,

Tim

On 11 May 2009, at 10:26, Mickael Graf wrote:

> Hi Tim, > > I'm trying to create a resource in IPT but I encounter a problem > while > creating the link to the database: in "Source Data" it is > written > under > "SQL Data Sources" I have the message "No Database connected. > Please > adjust connection parameters to use SQL sources" while it > keeps my > settings correctly. I hope I wrote the jdbc string well: > jdbc:mysql://localhost:3306/databasename. > > I surprised because I am using the same parameters as with > TAPIRLink > in > which I don't have any problem. I don't think I should make any > changes > in my grants on my database. > > Cheers, > Mickaël > > -- > --------------------------------- > Mickaël Graf > Database developper, GBIF Sweden - http://www.gbif.se > tel: +46 8 5195 4045 > mailto:mickael.graf@nrm.se > > Swedish Museum of Natural History - http://www.nrm.se > Box 50007 > SE-104 05 Stockholm > Sweden > > >

-- --------------------------------- Mickaël Graf Database developper, GBIF Sweden - http://www.gbif.se tel: +46 8 5195 4045 mailto:mickael.graf@nrm.se

Swedish Museum of Natural History - http://www.nrm.se Box 50007 SE-104 05 Stockholm Sweden

_______________________________________________ IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt

-- --------------------------------- Mickaël Graf, Database developper GBIF Sweden - http://www.gbif.se mailto:mickael.graf@nrm.se tel: +46 8 5195 4045 Swedish Museum of Natural History - http://www.nrm.se Box 50007 SE-104 05 Stockholm Sweden

Mickael, real sorry from my side. Seemed that I've uploaded a wrong snapshot version to our ftp server. The war there didnt give any message to me neither. I've updated the file and the current ftp war (same name) does work for me now. But I really had to remove tomcats cached work folder files in order to be taken up, pretty stupid, but well. You mentioned pointing IPT to a data dir outside didnt work? That would be a serious issue, but I cant reproduce that. If that still is true for you, can you please let us know what exactly happens? cheers, Markus On May 14, 2009, at 11:56, Mickael Graf wrote:

Markus,

I undeployed IPT from the manager interface of tomcat. Then I uploaded the RC2 file from the same interface. This removed all the settings.

Since then I restarted tomcat numerous times. I removed the cache this morning but nothing changed.

Now I just did what you wrote below, but I copied back the data directory because IPT didn't like having dataDir pointing to another place.

So when I come to my existing resource, under Source Data/SQL Data Sources I get the following message: "No Database connected. Please adjust connection parameters to use SQL sources"

The I click on Edit, all my parameters are in place and I save it. Then I come back to the previous page I get the message "Resource has been updated successfully." but the message under SQL Data Sources is the same as before.

This is what is logged after starting tomcat, login and getting to the resource and saving the database information, and it's not much:

INFO main-AppConfig.reloadLogger(416) | Reloaded log4j settings from /usr/share/tomcat5/webapps/ipt/data/logging/ipt-developer.xml INFO main-AppConfig.<init>(57) | -------------------- IPT_DATA_DIR: /usr/share/tomcat5/webapps/ipt/data IPT_WEBAPP_DIR: /usr/share/tomcat5/webapps/ipt IPT_BASE_URL: http://www.gbif.se:8080/ipt IPT_GEOSERVER_URL: http://www.gbif.se:8080/geoserver IPT_GEOSERVER_DATA_DIR: /usr/share/tomcat5/webapps/geoserver/data --------------------

Cheers, Mickaël

On Wed, 2009-05-13 at 21:21 +0200, "Markus Döring (GBIF)" wrote:

...

Mickael, do you get any feedback a) in the UI when saving a sql connection b) in the logs?

if not, how did you upgrade your installation? You might want to try: - stop tomcat - copy your existing data dir somewhere else - remove the exploded webapps folder - remove the cached version in tomcat/work/Catalina/localhost/ipt - start tomcat with ipt.war inside webapps - stop tomcat - update webapps/ipt/WEB-INF/classes/ipt.properties to point to your saved data dir - start tomcat

thats the procedure for upgrading to a new IPT version while keeping your data if its still living within the default webapps folder. Did you do this and still get no message when saving a not working db connection?

Markus

On May 13, 2009, at 12:24 PM, Mickael Graf wrote:

...

Markus,

The RC2 didn't help much, I'm totally blind as to find where the problem comes from.

I was wondering if you could tell me which files are involved in the process so I can get a better understanding?

Cheers, Mickaël

On Tue, 2009-05-12 at 11:47 +0200, "Markus Döring (GBIF)" wrote:

...

Mickael, the latest IPT war snapshot can be found here:

ftp://ftp.gbif.org/projects/ipt/downloads/ipt-1.0RC2-SNAPSHOT.war

This version logs connection problems and also uses in addition to tomcat logging an ipt.log file inside the data/logging dir. It also shows a simple message if you configure a bad connection in the manager UI. If you have time, please use this to find out more about your mysql conenction problem.

thanks, Markus

On May 12, 2009, at 10:17 AM, Markus Döring (GBIF) wrote:

...

Mickael, I looked at the source again and the IPT really doesn't log any errors when changing the db connection. This is obviously not very helpful, so I've updated the code already to do so. I will upload a new war file today, so if you like you can try this version and hopefully find the reason for your connection problem. Will post the links later.

many thanks, Markus

On May 11, 2009, at 6:03 PM, Tim Robertson wrote:

...

Hej Mickael,

Can you please post the logs you get when you configure and save the database connection?

Many thanks,

Tim

On 11 May 2009, at 14:36, Mickael Graf wrote:

> Sorry for posting at the wrong place. > > The database name is correct, and IPT runs on the same server as > the > mysql database. This database works perfectly with our TAPIRLink > provider. > > The MySQL server version is 5.0.45 and Connector/J has version > 5.1.7. It > has been tested against Java 1.6.0 (OpenJDK) and against Sun > Java 6 > Update 12. None of this worked. > > > Cheers, > Mickaël > > > On Mon, 2009-05-11 at 10:49 +0200, Tim Robertson wrote: >> Hi Mickael, >> >> >> Please always post questions to the list, to help us keep an >> FAQ up >> to >> date and allow for others to search etc. >> >> >> I have just tested it myself with the following: >> >> >> Database connection URL: jdbc:mysql://localhost:3306/portal >> Database User: tim >> Database Password: password >> >> >> and it worked... so, to get started debugging your issue may I >> please >> ask some basic questions: >> >> >> - You wrote "jdbc:mysql://localhost:3306/databasename" - is >> your >> database name correct? >> - You are running the IPT on the same machine as the database? >> - You are using mysql? >> >> >> Cheers, >> >> >> Tim >> >> >> >> On 11 May 2009, at 10:26, Mickael Graf wrote: >> >>> Hi Tim, >>> >>> I'm trying to create a resource in IPT but I encounter a >>> problem >>> while >>> creating the link to the database: in "Source Data" it is >>> written >>> under >>> "SQL Data Sources" I have the message "No Database connected. >>> Please >>> adjust connection parameters to use SQL sources" while it >>> keeps my >>> settings correctly. I hope I wrote the jdbc string well: >>> jdbc:mysql://localhost:3306/databasename. >>> >>> I surprised because I am using the same parameters as with >>> TAPIRLink >>> in >>> which I don't have any problem. I don't think I should make >>> any >>> changes >>> in my grants on my database. >>> >>> Cheers, >>> Mickaël >>> >>> -- >>> --------------------------------- >>> Mickaël Graf >>> Database developper, GBIF Sweden - http://www.gbif.se >>> tel: +46 8 5195 4045 >>> mailto:mickael.graf@nrm.se >>> >>> Swedish Museum of Natural History - http://www.nrm.se >>> Box 50007 >>> SE-104 05 Stockholm >>> Sweden >>> >>> >>> >> >> > -- > --------------------------------- > Mickaël Graf > Database developper, GBIF Sweden - http://www.gbif.se > tel: +46 8 5195 4045 > mailto:mickael.graf@nrm.se > > Swedish Museum of Natural History - http://www.nrm.se > Box 50007 > SE-104 05 Stockholm > Sweden > >

_______________________________________________ IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt

-- --------------------------------- Mickaël Graf, Database developper GBIF Sweden - http://www.gbif.se mailto:mickael.graf@nrm.se tel: +46 8 5195 4045 Swedish Museum of Natural History - http://www.nrm.se Box 50007 SE-104 05 Stockholm Sweden

-- --------------------------------- Mickaël Graf, Database developper GBIF Sweden - http://www.gbif.se mailto:mickael.graf@nrm.se tel: +46 8 5195 4045 Swedish Museum of Natural History - http://www.nrm.se Box 50007 SE-104 05 Stockholm Sweden

Hi Mickael, So, something on the machine is blocking Tomcat from talking to mysql ("Caused by: java.net.ConnectException: Connection refused"). It could be something like a firewall or perhaps you have a rule in the /etc/hosts.deny ? I have never had to but I read that adding 127.0.0.1 to /etc/ hosts.allow might be required. Cheers, Tim On 18 May 2009, at 16:42, Mickael Graf wrote:

Hello Markus

The issue of data dir outside not working was an issue of ownership. This one is solved.

About the connection, the IPT interface provides med with "Could not establish db connection: Communications link failure Last packet sent to the server was 0 ms ago."

The log file is compressed and attached to this mail.

Thanks, Mickaël

On Mon, 2009-05-18 at 15:20 +0200, "Markus Döring (GBIF)" wrote:

...

Mickael, real sorry from my side. Seemed that I've uploaded a wrong snapshot version to our ftp server. The war there didnt give any message to me neither. I've updated the file and the current ftp war (same name) does work for me now. But I really had to remove tomcats cached work folder files in order to be taken up, pretty stupid, but well.

You mentioned pointing IPT to a data dir outside didnt work? That would be a serious issue, but I cant reproduce that. If that still is true for you, can you please let us know what exactly happens?

cheers, Markus

On May 14, 2009, at 11:56, Mickael Graf wrote:

...

Markus,

I undeployed IPT from the manager interface of tomcat. Then I uploaded the RC2 file from the same interface. This removed all the settings.

Since then I restarted tomcat numerous times. I removed the cache this morning but nothing changed.

Now I just did what you wrote below, but I copied back the data directory because IPT didn't like having dataDir pointing to another place.

So when I come to my existing resource, under Source Data/SQL Data Sources I get the following message: "No Database connected. Please adjust connection parameters to use SQL sources"

The I click on Edit, all my parameters are in place and I save it. Then I come back to the previous page I get the message "Resource has been updated successfully." but the message under SQL Data Sources is the same as before.

This is what is logged after starting tomcat, login and getting to the resource and saving the database information, and it's not much:

INFO main-AppConfig.reloadLogger(416) | Reloaded log4j settings from /usr/share/tomcat5/webapps/ipt/data/logging/ipt-developer.xml INFO main-AppConfig.<init>(57) | -------------------- IPT_DATA_DIR: /usr/share/tomcat5/webapps/ipt/data IPT_WEBAPP_DIR: /usr/share/tomcat5/webapps/ipt IPT_BASE_URL: http://www.gbif.se:8080/ipt IPT_GEOSERVER_URL: http://www.gbif.se:8080/geoserver IPT_GEOSERVER_DATA_DIR: /usr/share/tomcat5/webapps/geoserver/data --------------------

Cheers, Mickaël

On Wed, 2009-05-13 at 21:21 +0200, "Markus Döring (GBIF)" wrote:

...

Mickael, do you get any feedback a) in the UI when saving a sql connection b) in the logs?

if not, how did you upgrade your installation? You might want to try: - stop tomcat - copy your existing data dir somewhere else - remove the exploded webapps folder - remove the cached version in tomcat/work/Catalina/localhost/ipt - start tomcat with ipt.war inside webapps - stop tomcat - update webapps/ipt/WEB-INF/classes/ipt.properties to point to your saved data dir - start tomcat

thats the procedure for upgrading to a new IPT version while keeping your data if its still living within the default webapps folder. Did you do this and still get no message when saving a not working db connection?

Markus

On May 13, 2009, at 12:24 PM, Mickael Graf wrote:

...

Markus,

The RC2 didn't help much, I'm totally blind as to find where the problem comes from.

I was wondering if you could tell me which files are involved in the process so I can get a better understanding?

Cheers, Mickaël

On Tue, 2009-05-12 at 11:47 +0200, "Markus Döring (GBIF)" wrote:

...

Mickael, the latest IPT war snapshot can be found here:

ftp://ftp.gbif.org/projects/ipt/downloads/ipt-1.0RC2-SNAPSHOT.war

This version logs connection problems and also uses in addition to tomcat logging an ipt.log file inside the data/logging dir. It also shows a simple message if you configure a bad connection in the manager UI. If you have time, please use this to find out more about your mysql conenction problem.

thanks, Markus

On May 12, 2009, at 10:17 AM, Markus Döring (GBIF) wrote:

> Mickael, > I looked at the source again and the IPT really doesn't log any > errors when changing the db connection. > This is obviously not very helpful, so I've updated the code > already > to do so. I will upload a new war file today, so if you like you > can > try this version and hopefully find the reason for your > connection > problem. Will post the links later. > > many thanks, > Markus > > > > On May 11, 2009, at 6:03 PM, Tim Robertson wrote: > >> Hej Mickael, >> >> Can you please post the logs you get when you configure and >> save >> the >> database connection? >> >> Many thanks, >> >> Tim >> >> >> >> On 11 May 2009, at 14:36, Mickael Graf wrote: >> >>> Sorry for posting at the wrong place. >>> >>> The database name is correct, and IPT runs on the same >>> server as >>> the >>> mysql database. This database works perfectly with our >>> TAPIRLink >>> provider. >>> >>> The MySQL server version is 5.0.45 and Connector/J has version >>> 5.1.7. It >>> has been tested against Java 1.6.0 (OpenJDK) and against Sun >>> Java 6 >>> Update 12. None of this worked. >>> >>> >>> Cheers, >>> Mickaël >>> >>> >>> On Mon, 2009-05-11 at 10:49 +0200, Tim Robertson wrote: >>>> Hi Mickael, >>>> >>>> >>>> Please always post questions to the list, to help us keep an >>>> FAQ up >>>> to >>>> date and allow for others to search etc. >>>> >>>> >>>> I have just tested it myself with the following: >>>> >>>> >>>> Database connection URL: jdbc:mysql://localhost:3306/portal >>>> Database User: tim >>>> Database Password: password >>>> >>>> >>>> and it worked... so, to get started debugging your issue >>>> may I >>>> please >>>> ask some basic questions: >>>> >>>> >>>> - You wrote "jdbc:mysql://localhost:3306/databasename" - is >>>> your >>>> database name correct? >>>> - You are running the IPT on the same machine as the >>>> database? >>>> - You are using mysql? >>>> >>>> >>>> Cheers, >>>> >>>> >>>> Tim >>>> >>>> >>>> >>>> On 11 May 2009, at 10:26, Mickael Graf wrote: >>>> >>>>> Hi Tim, >>>>> >>>>> I'm trying to create a resource in IPT but I encounter a >>>>> problem >>>>> while >>>>> creating the link to the database: in "Source Data" it is >>>>> written >>>>> under >>>>> "SQL Data Sources" I have the message "No Database >>>>> connected. >>>>> Please >>>>> adjust connection parameters to use SQL sources" while it >>>>> keeps my >>>>> settings correctly. I hope I wrote the jdbc string well: >>>>> jdbc:mysql://localhost:3306/databasename. >>>>> >>>>> I surprised because I am using the same parameters as with >>>>> TAPIRLink >>>>> in >>>>> which I don't have any problem. I don't think I should make >>>>> any >>>>> changes >>>>> in my grants on my database. >>>>> >>>>> Cheers, >>>>> Mickaël >>>>> >>>>> -- >>>>> --------------------------------- >>>>> Mickaël Graf >>>>> Database developper, GBIF Sweden - http://www.gbif.se >>>>> tel: +46 8 5195 4045 >>>>> mailto:mickael.graf@nrm.se >>>>> >>>>> Swedish Museum of Natural History - http://www.nrm.se >>>>> Box 50007 >>>>> SE-104 05 Stockholm >>>>> Sweden >>>>> >>>>> >>>>> >>>> >>>> >>> -- >>> --------------------------------- >>> Mickaël Graf >>> Database developper, GBIF Sweden - http://www.gbif.se >>> tel: +46 8 5195 4045 >>> mailto:mickael.graf@nrm.se >>> >>> Swedish Museum of Natural History - http://www.nrm.se >>> Box 50007 >>> SE-104 05 Stockholm >>> Sweden >>> >>> >> >> _______________________________________________ >> IPT mailing list >> IPT@lists.gbif.org >> http://lists.gbif.org/mailman/listinfo/ipt >> >

-- --------------------------------- Mickaël Graf, Database developper GBIF Sweden - http://www.gbif.se mailto:mickael.graf@nrm.se tel: +46 8 5195 4045 Swedish Museum of Natural History - http://www.nrm.se Box 50007 SE-104 05 Stockholm Sweden

-- --------------------------------- Mickaël Graf, Database developper GBIF Sweden - http://www.gbif.se mailto:mickael.graf@nrm.se tel: +46 8 5195 4045 Swedish Museum of Natural History - http://www.nrm.se Box 50007 SE-104 05 Stockholm Sweden

_______________________________________________ IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt --

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Mickaël Graf, Database developper GBIF Sweden - http://www.gbif.se mailto:mickael.graf@nrm.se tel: +46 8 5195 4045 Swedish Museum of Natural History - http://www.nrm.se Box 50007 SE-104 05 Stockholm Sweden <ipt.log.tar.bz2>_______________________________________________ IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt