Publishing
What is content?
The information on a Tripal site is categorized into different content types. Examples are Organism, Publication, Project, or Analysis. Additional content types can be added by another module, or created by a site administrator.
A single record for each of these content types is displayed on the site by an entity, you can think of an entity as “the page”. On each entity you will have multiple fields. Each field will present a particular type of information, such as the tile, or a description. Fields may contain a single record or multiple records. A field for a particular entity may also contain no records, in which case, we typically do not show the field on the entity page.
As an example, this is a project entity page, and it is displaying three fields: title, description, and a link to a related publication.
What does publishing mean?
Biological data on a Tripal site is usually stored in the database in the Chado schema. Publishing refers to the process where this information is made visible to site visitors. During the process of publishing some particular content type, an entity is created for each corresponding record in the database, and all fields that are present on each entity are populated with information from the database.
Note
Publishing or unpublishing only affects what content is visible on the web site. It does not affect the records stored in the underlying Chado database.
Publishing through the user interface
To publish through the user interface, go to
Tripal → Content → +Publish Tripal Content
and select the content type you wish to publish.
You will want to have Republish Existing Content active if you have changed the entity title format, or added any fields to the content type. In other cases it can be turned off, which may reduce the time required to run the publish job.
The migration file option is used only when migrating a Tripal 3 site. For more information on how this option works, see Migrating Chado.
Tip
If for some reason you run out of available memory when publishing, you can reduce the batch size and try again.
Publishing with a drush command
You can publish a content type with a simple drush command. For example, to publish the Project content type:
drush trp-chado-publish project
or to republish
drush trp-chado-publish project --republish
Other drush publish options can be listed with:
drush trp-chado-publish --help
Unpublishing
When Chado records are updated or removed, published content may no longer be synchronized with the contents of the Chado database.
If some records that are shown in fields were updated or removed, the republish option of publish will synchronize them.
If some records that define an entity were deleted, these are termed orphaned entities.
They can be selectively unpublished without danger of removing valid records. Go to
Tripal → Content → +Unpublish Tripal Content
and by leaving the Only unpublish orphaned content option checked, existing content still present in the Chado database will not be affected, only orphaned content will be unpublished.
Limiting publishing when there are too many records
Because a single field can refer to multiple records of the same type, a mechanism exists to limit publishing when there are too many records for the web site to display. For example, a Genome Annotation entity may have annotated all genes in a genome, which could easily be 30,000 genes or more. Displaying this many records in a field is impossible, so the publish function will limit how many records can be published. This limit is configurable.
Publish global limit
Access the global limit at
Tripal → Configuration → Tripal Entity Settings
There you will find these options that can be configured:
The second option exists for the case where you prefer to publish no records when the limit is exceeded. For the 30,000 gene example, you may prefer to not publish a subset, and provide some other mechanism on your site for accessing the gene records.
Publish limit for individual fields
If you wish to override this global limit for any particular field, you can do so. Go to
Tripal → Page Structure
For the content type of interest, select Manage Fields.
For the field of interest, select Edit.
Change the cardinality from:
to whatever value you desire, for example 50:
