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This page gathers known issues of the onboarding process and the reccomended solutions or work-arounds for the given issue. If the issue you are facing does not appear on the list here, please contact HRI service desk at servicedesk@health-ri.nl and we will assist you.
Upgrading your FDP shapes
By default, the FDP reference implementation ships with so-called default shapes out of the box, based on DCAT 2. To upgrade them to the Health-RI model, see below.
Upgrade to Health-RI model v1.0.0
https://github.com/Health-RI/health-ri-metadata/blob/v1.0.0/README.md
Log in as an admin user
Click on the profile button on the top right of the user interface, and navigate to metadata schemas
Select the Resource schema
In the v1.0.0 model, copy the contents of the Resource shape
In the FDP, paste the contents in the Form Definition area.
Click Save and release on the bottom of the page.
Enter a description to indicate the use of the v1.0.0 model.
Select an appropriate version number.
Click Release.
Repeat for Catalog, Dataset, Distribution, and DataService.
Solve “unable to get data” on existing metadata after a model upgrade
🚧 TODO describe steps in detail.
FDP
Date and DateTime errors when editing
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| Code Block | ||
|---|---|---|
| ||
> use fdp
> db.metadata.deleteOne({ "uri": "<http://localhost/dataset/6dba4d3e-888a-4b8d-bacf-0fd322bef2f7>" }) |
Properties not showing in forms
Sometimes properties will not show when viewing or editing metadata. Possible causes are:
The property does not have a
dash:viewerordash:editordefined in the metadata schema. The solution is to update the property’s attributes in the appropriate metadata schema.Properties defined on a higher level in the hierarchy are not inherited in the extending classes. This seems to be a bug in the FDP reference implementation. An issue is filed in the FDP github repository, you can check on the progress there: https://github.com/FAIRDataTeam/FAIRDataPoint/issues/580
Publicly hosted FDP shows localhost urls
When an FDP is hosted on a public accessible domain (or IP address), subjects or some links in the UI can show up as localhost. A possible solution is to configure the instance.clientUrl and instance.persistentUrl properties in application.yml is not configured properly. These values should reflect the domain (or IP address) the FDP is available at.
After updating the instance.clientUrl and instance.persistentUrl properties, the FDP can show error messages like “Unable to get data”. Possible solutions:
Clean the triplestore and mongo database and restart the application. This is a viable solution if there is no metadata entered in the system yet. For a local setup using Docker Compose with GraphDB and Mongo:
docker compose downremove the volumes for graphdb and mongo
docker compose up -d
Upgrading your FDP shapes
By default, the FDP reference implementation ships with so-called default shapes out of the box, based on DCAT 2. To upgrade them to the Health-RI model, see below.
Upgrade to Health-RI model v1.0.0
https://github.com/Health-RI/health-ri-metadata/blob/v1.0.0/README.md
Log in as an admin user
Click on the profile button on the top right of the user interface, and navigate to metadata schemas
Select the Resource schema
In the v1.0.0 model, copy the contents of the Resource shape
In the FDP, paste the contents in the Form Definition area.
Click Save and release on the bottom of the page.
Enter a description to indicate the use of the v1.0.0 model.
Select an appropriate version number.
Click Release.
Repeat for Catalog, Dataset, Distribution, and DataService.
Solve “Unable to update entity data.” on existing metadata after the v1.0.0 upgrade
Version 1.0.0 introduced a new mandatory property on publisher; identifier. While https://github.com/FAIRDataTeam/FAIRDataPoint/issues/580 is not solved, the user interface will not allow this value to be filled by a user.
If you have access to the underlying triple store and have the right to execute a SPARQL Update query, the following query will add a default value:
| Code Block | ||
|---|---|---|
| ||
PREFIX dct: <http://purl.org/dc/terms/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
INSERT {
GRAPH ?g {
?s dct:identifier "DEFAULT-IDENTIFIER"
}
} WHERE {
GRAPH ?g {
?s a foaf:Agent
FILTER NOT EXISTS { ?s dct:identifier ?id }
}
} |
If you do not have access to the underlying triplestore, the known workaround is to manually disable the sh:minCount constraints on both the Agent definitions; one in Dataset (https://github.com/Health-RI/health-ri-metadata/blob/v1.0.0/Formalisation(shacl)/Core/PiecesShape/Dataset.ttl#L144) and one in Catalog (https://github.com/Health-RI/health-ri-metadata/blob/v1.0.0/Formalisation(shacl)/Core/PiecesShape/Catalog.ttl#L76).
Solve “unable to get data” on existing metadata after a model upgrade
Catalog shape works after upgrading from default shape to v1 shape. Manual edit lets the user enter an identifier for the publisher.
dataset shape works after upgrading from default shape to v1 shape.
dist shape works after upgrading from default shape to v1 shape. Manual edit lets user add access url and media type.
Moving from v1 to v2(draft)
catalog v2-draft upgrade works
dataset v2-draft upgrade breaks. Modified is mandatory, which the user can fill in. There is an issue in the v2-draft model for Dataset, specifically on
dcat:distribution(see https://github.com/Health-RI/health-ri-metadata/blob/develop/Formalisation(shacl)/Core/PiecesShape/Dataset.ttl#L102-L105).distribution v2-draft upgrade works.
Cannot edit Dataset that contains distributions after a v1.0.0 model upgrade
When a Dataset resource that contains Distributions is saved, the form displays a Unable to update entity data. error. This is caused by the issue reported in https://github.com/FAIRDataTeam/FAIRDataPoint/issues/445.
The workaround for this issue is manually editing the Dataset metadata schema to disable the sh:class constraint, on line 97: https://github.com/Health-RI/health-ri-metadata/blob/v1.0.0/Formalisation(shacl)/Core/PiecesShape/Dataset.ttl#L97.
ELSI
Email address visibility
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