問答集

There is one important directory that contains all the IPT’s configuration and resources: the IPT’s data directory. If you ensure this directory is regularly backed-up somewhere safe, you’ll never lose any data.

To move the IPT to a different server, just make sure that you copy the entire contents of the IPT’s data directory over to the new server. It is important to preserve the same folder/file permissions. Then, install the IPT on the new server, using this directory as the data directory.

Some default configurations of Apache Tomcat come with very little allocated memory. In order to increase performance, this amount should be increased depending on the amount of physical memory on the server. If the server has at least 4GB of RAM, the available memory should be increased to 2GB. For more information on how to do it, see the Tomcat FAQ

The following is known to run:

This also applies to similar errors for creating files, like RollingFileManager … unable to create manager for … debug.log.

Assuming you are running Tomcat, you need to ensure the user running Tomcat has permissions on the directory. To find out the user running Tomcat on Linux, open a shell and enter the following command:

If the user is "tomcatuser", and this user belongs to group "tomcatgroup" then change the ownership of the IPT data directory (and its child folders and files) by entering the following command:

To ensure only this user has write permission, enter the following command:

Note that if you are running your IPT on a Windows operating system, you will need to check that your folder didn’t revert to read-only permissions.

Some Linux systems have additional protections, called security sandboxing. In this case, you usually need to grant additional permissions for Tomcat to access the data directory. For example, on Debian and Ubuntu you need to add a SystemD override:

The IPT’s default language is English, but it can be easily changed via the user interface (Administration→IPT Settings→Default Language).

For older IPT versions, it can be changed by manual configuration. To change the default language from English to Portuguese for example, first locate the struts.properties file (if the IPT is deployed in Tomcat for example, it would be located in tomcat/webapps/ipt/WEB-INF/classes). Then update the struts.locale property to:

Restart Tomcat, and the IPT will startup in Portuguese.

Please note the two-letter language code must match the code used by the IPT. The languages currently supported are Portuguese (pt), Japanese (ja), French (fr), Spanish (es), Traditional Chinese (zh), and Russian (ru).

Please note that every time you upgrade to a new version of the IPT, you will have to apply the same change.

Switching the IPT from test mode to production mode cannot be done automatically. This is by design, because each mode connects to a different registry (test mode uses the GBIF UAT Registry while production mode uses the GBIF Live Registry).

Therefore to switch to production mode you need to setup an entirely new IPT instance in production mode.

To save time recreating resources, you can try transferring your 'test' resources to the production IPT. To do this simply "upload an existing IPT resource using its zipped resource configuration folder." There are complete instructions on how to do this here.

During setup, and in test mode, the IPT makes secure HTTPS outgoing connections to https://gbrds.gbif-uat.org and https://tools.gbif.org.

If configured in production mode, the IPT makes secure HTTPS outgoing connections to https://gbrds.gbif.org.

In both modes, the IPT makes normal HTTP outgoing connections to http://rs.gbif.org. If you install particular additional vocabularies, the IPT will retrieve them from raw.githubusercontent.com or eol.org.

We recommend configuring your firewall to allow outbound access on ports 80 and 443 to all GBIF servers: 130.225.43.0/24.

Before version 2.3.4, connections were made using HTTP, rather than HTTPS, to http://gbrds.gbif.org and http://gbrdsdev.gbif.org. HTTP connections use port 80.

Refer to the DOI 工作流程.

The IPT does not support source files that have multi-line fields (fields that include a newline character (\n) or carriage return (\r)) even if you have specified a field quote (a single character that encloses every field/column in a row) in the source’s configuration.

Unless these line breaking characters are removed, the IPT will publish files with broken lines (the columns will appear mixed up).

To solve this, you can remove these line breaking characters from the source file, replace the source file with the new one, and republish the resource. Remember that when uploading a source file, you can tell the IPT to replace the file with a new one as long as they both have the same name. That way the mappings don’t have to be redone.

Check the publication log for exceptions such as:

that means you have invalid date value in your data source, which, in this case, is 0000-00-00 00:00:00.

To solve this, you can update the value with "Null" value, and update the resource. Usually, you can rely on the log message to identify the column of interest, like in the example above, it says "column 65," which is the 65th column in the data source.

The 0000-00-00 00:00:00 value in your SQL table could be resulted when importing, while having defined the column with "Not Null" and default value as 0000-00-00 00:00:00.

If you found an exception such as:

in your publication log file, it means there is no space left in the disk partition that contains your IPT data directory.

To solve this, you can:

Ideally, the publishing organization should not be changed after the resource has been either registered with GBIF or assigned a DOI.

That being said, there are two ways to change the publishing organization.

The easiest way is to republish the resource and then reset the desired publishing organization. To simplify the process, you can recreate the dataset from its zipped IPT resource folder. Instructions on how to do that can be found here. If you migrate the resource from the old publishing organization to the new publishing organization by following these instructions: Please pay careful attention to step 5, where you will have to ask the GBIF Help Desk to update the GBIF Registry.

The other way to proceed is to work directly in the IPT directory. Before you start anything, make a backup of your archives. Then, edit the resource.xml file of the dataset that you would like to work on (on your server in your IPT folder):

In addition to that, please contact the GBIF Help Desk and ask that the organization be updated in the GBIF Registry (this part is very important).

The type of a resource is derived from its core mapping:

Therefore to change the type of a resource, you need to change its core mapping. To change an occurrence resource to type checklist, for example, simply delete all core mappings to the Occurrence extension, and then recreate new core mappings to the Taxon extension. A new version of the resource should be published in order to finalize the change. If the resource has been registered with GBIF, its type will be automatically updated after it has been re-published.

Datasets can change over time. Keeping the dataset metadata up to date can be a burden, as inconsistencies can begin to creep in over time. Below is a list of tricks you can use to simplify the authoring of metadata and make it easier to maintain over time:

First, ensure the desired hosting organization has been added to your IPT. You can do this through the user interface. For help adding a new organization to your IPT, refer to this section of the user manual.

Next, perform the following 2 manual changes to the registration2.xml file located inside the /config folder of your IPT Data Directory:

Restart Tomcat.

Last, press the "update registration" button on the Edit GBIF Registration page. This will propagate the change to the GBIF Registry. For further information about what this update does, you can refer to this section of the user manual.

If you have forgotten the admin password, the server administrator will need to reset it.

Using a text editor, open the file config/users.xml contained in the IPT data directory. Find the admin user (with role="Admin"), and replace the encrypted password with $2a$12$FxYdvOAlQ4cP8q1qU77fZePpdwrXS5PC3zmSYgdZuWlU6XUUe6FRu. Restart the IPT. You can then log in as the admin user with the password Ga_1bxiedrvNHSyK — of course, this password should then be changed.

This migration process must be done directly on the server following the next steps:

The answer depends on how long GBIF’s indexing queue is, how big your dataset it and whether GBIF’s indexing service is turned on.

Normally it will take between 5-60 minutes for GBIF to start indexing your dataset. It can take several hours to finish indexing large datasets once started (those with several million records) so please be patient. At the bottom of the GBIF health page the length of the indexing queue is shown, and the full queue can be seen on the Crawl Monitor.

If you believe GBIF failed to index your dataset successfully, please submit feedback directly via GBIF.org, or send an email to the GBIF Help Desk <helpdesk@gbif.org> to investigate what happened. If you are interested in finding out why GBIF may not have (re)indexed your dataset, please see 2 below.

Occasionally, GBIF turns off its indexing service for maintenance (see the links in the previous question). This is the most common reason why datasets aren’t indexed as quickly as expected.

If you believe GBIF failed to index your dataset, please submit feedback directly via GBIF.org, or send an email directly to the GBIF Help Desk <helpdesk@gbif.org> to investigate what happened.

GBIF automatically attempts to reindex a registered dataset each time its registration is updated. This happens each time the dataset gets republished via the IPT.

To cater to datasets not published using the IPT, GBIF automatically attempts to reindex all registered datasets every 7 days.

GBIF supports 4 classes of datasets described here. GBIF currently only indexes species occurrence records, which can be provided as either core records or as extension records. In the case of sampling-event datasets, species occurrences in extension records will be augmented with information coming from its core event record wherever possible.

The IPT supports free-text dataset citations, however, these get overwritten on the GBIF.org dataset page. You can find out why in the GBIF.org FAQ.

This is usually due to a misconfiguration in the webserver (Apache, IIS, Tomcat etc). Ensure you can access your server through the command line (curl https://ipt.example.org), from computers outside your organization’s network (e.g. from a personal phone) and run an SSL Server Test.

Any errors like "unable to get local issuer certificate" or "certificate chain incomplete" will usually prevent GBIF’s systems from accessing your IPT.

To fix them, see the documentation of your webserver, or ask your IT department for advice. These problems are generally not related to the IPT.

A useful resource for configuring many web servers is the Mozilla SSL Configuration Generator, and a quick test for the most common issue is available at What’s My Chain Cert.

Some organizations need to index their own IPT, often to include records of each resource in a public open data system or similar. The IPT supports DCAT (Data Catalog Vocabulary) to allow this. The DCAT export is available at /dcat, for example https://ipt.gbif.org/dcat.

An alternative is the GBIF Registry Installations API, though this will only include datasets published to GBIF.