FAQ :: GBIF IPT User Manual (original) (raw)

Why do published files contain broken lines?

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.

Why do published files not include all records?

Check the publication log for exceptions such as:

java.sql.SQLException: Cannot convert value '0000-00-00 00:00:00' from column 65 to TIMESTAMP

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.

What does the error "No space left on device" mean and how do I fix it?

If you found an exception such as:

Caused by: java.io.IOException: No space left on device

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:

• Allocate more space to this partition.
• Move your IPT data directory to another partition where there is more space available. (Refer to the installation instructions to change the location of the data directory).
• Free up disk space (e.g. deleting temporary files, remove unused applications, etc)

How do I change the publishing organization of my resource? The drop down on the Basic Metadata page is disabled.

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 several ways to change the publishing organization.

In the most recent versions of the IPT (3+) publishing organization can be changed at the overview page in the Publication section.

For versions before version 3, 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 <organisation>, replace the current UUID by the UUID of the organization you would like to be the new publishing organization,
• Restart the IPT (restart Tomcat, restart the IPT service, etc),
• Check that no error message appears in your IPT when you click publish.

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).

How do I change the type of existing resource?

The type of resource is derived from its core mapping:

• If the core mapping is to the Occurrence extension, the type is equal to "occurrence".
• If the core mapping is to the Taxon extension, the type is equal to "checklist".
• If the core mapping is to the Event extension, the type is equal to "sampling-event".
• If the core mapping is not equal to one of the IPT’s default cores (Occurrence, Taxon, or Event) the type is equal to "other".

Therefore, to change the type of 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.

How do I change the existing Occurrence dataset to Camtrap DP?

You cannot directly convert an Occurrence dataset to Camtrap DP one. However, it is possible to associate an existing GBIF dataset with a new resource in the IPT.

Steps:

• Delete the current version of the resource from the IPT (Delete from IPT only option). Make sure the resource is backed up.
• Create a Camtrap DP version of the resource. You can use the same shortname if you deleted the resource in the previous step. Otherwise, use another shortname.
• Add related identifier to the new Camtrap DP resource. Fill the related identifier field with your GBIF URL and select the related identifier type as URL. The relation type can be any. See the image below.

• Publish the new Camtrap DP resource.
• Register the new Camtrap DP resource. You should see a confirmation message, like: "Resource matched an existing registered resource (UUID=…​) owned by …​ Consequently, this resource will be associated to the existing registered resource, instead of registering a new resource."

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:

• use a contact’s ORCID instead of supplying their email and other fields which are likely change if the person changes jobs. For more information about how to supply an ORCID see here.
• for datasets that continue to change/grow (versus static datasets) avoid specifying exact counts in textual descriptions, e.g. for record or taxa counts.
• use the IPT’s citation Auto-generation feature instead of supplying a manually created data citation.
• use the IPT’s import by Taxon list feature instead of supplying each taxon manually one at a time when entering the taxonomic coverage.

How do I change the hosting organization of my IPT?

| | the instructions below assume your IPT has already been registered and involve manual changes requiring technical competence. | | -------------------------------------------------------------------------------------------------------------------------------- |

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:

1. ```

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.

How do I reset the admin password?

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.

How do I migrate a dataset from one IPT installation to another?

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

1. Shut down the old IPT server; just to check no-one makes any changes.
2. In the old IPT go to /old-ipt-datadir/resources/[dataset_name] and copy the whole dataset folder
3. In the new IPT go to /new-ipt-datadir/resources/ and paste the dataset folder
4. Restart the new IPT server
5. Publish the dataset in the new IPT (updates the endpoint).