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Drupal 8 Module Development. Drupal 8 comes with a release cycle that allows for new functionality to be added at a much faster pace. This book updates the first edition and includes the new functionality introduced in. The following descriptions assume some familiarity with the PHP language. Each content type in Tripal corresponds roughly to a table module in Chado. It is normally easy to identify which Tripal module, and hence which content type corresponds to each Chado module as the naming is consistent i.
Tripal exports automatically the data needed for each content type template. In the template file, each of these sections is defined by div tags with special CSS class names. First is the details section:. Also, within this div block are several print theme statements one of which is as follows:. These statements instruct Drupal to load subtemplates. These subtemplates are used to house the code for subcontent and are intended to keep the primary node template concise and from becoming excessively long.
More on these subtemplates is described in a later section. By default, some conditional logic is present in the template for filtering large datasets. This is because those datasets typically have very large sequences that would be too slow for the page. Finally, the resources side-bar is the last thing defined in the default node templates.
The code is as follows:. This empty list is where the list of resources will appear. For example, the following screen shot shows the resources sidebar on an organism page of the Citrus Genome Database. The code to add these links is as follows:. This ensures that the custom links will appear in the list where other Chado content is added. But notice that the External links appear as a separate ul block.
In the template layout section described previously it was shown how subtemplates are incorporated into the principle template file. These subtemplates are included using PHP print theme statements within the details div block. For the feature content type of Tripal v1. Each of these subtemplates adds to the details section of the page a specific category of data. Both of these data are extracted directly from tables in Chado through foreign key relationships.
By default, the first subtemplate included in the details section is displayed when the page is first loaded. Content from the other subtemplates are then visible by clicking the links in the resources side bar.
These links are added automatically for all subtemplates to the sidebar using Javascript described in the next section. All subtemplates for a content type should be stored in a directory with a similar name as that of the content type.
The same is true for all content types. You may have noticed that here we use an include statement for the subtemplate file rather than use a print theme statement as with other subtemplates. This is because we are adding a single template which is managed by a Tripal module.
Not all of the subtemplates appear in the content section at one time. Only content from one subtemplate will be shown at a time. The Resources sidebar on the right is used for interactive cycling through the content contributed by each subtemplate. When the page first loads, the Javascript hides all of the sub template content with the following statement:. It then iterates through each subtemplate and adds the title to the Resources side-bar, adds a javascript function to each link to make it visible when clicked, sets the first subtemplate as visible and adjusts the height of the Resources side-bar.
As mentioned previously, Tripal automatically exports the data needed for each content type template. By default Tripal will populate this variable with the record from the appropriate Chado table. The record is then available in the template in the following way:. The fields for the record can then be accessed in the following way:. For example, the feature table in Chado has a foreign key relationship with the organism table. The fields for the organism record are then available through the field that participates in the foreign-key relationship.
Therefore, you can access the organism fields in the following way:. However, not all fields within a record are available by default. Large text fields and one-to-many foreign-key relationships are not automatically provided. If the text field is very large e. Therefore, these are purposely not included. This function take the following arguments:.
The function returns the associative array, passed as the first argument, but with the requested expansion. For example, in the feature table the nucleotide or peptide sequences are stored in the residues field. This is a text field and not automatically included in the record.
To get this information we can expand the record in the following way:. Using the example code above we are able to add in the residues information to our feature record and then use it within our template file. Adding information from a one-to-many relationship is performed using the same function.
For example, a feature may have more than one synonym one-to-many. We can therefore obtain the list of synonyms for a feature with the following example code:. Unlike field expansion, records from a one-to-many relationship are accessed using the name of the table. For example:.
The results from a one-to-many relationship are available as a single value if only one record was returned or as an array if multiple records were returned. Therefore, the following code example converts the results into an array to make it easy to iterate over the results:. Below is example code for retrieving the set of synonyms as an array:. When expanding tables in a one-to-many relationship it is possible to return hundreds or thousands or more records.
There are two problems that can occur when large datasets are returned. Here, the featuremap may be a genetic map and we want to expand the featurepos table to include the features that are found on the map. Here we specify which fields of the featurepos table we want to recurse. We want the type and organism information for the landmark feature of the map. It will not recurse further than those table.
But, because we did not specify to expand that relationship it is not expanded. The pager is quite easy to create. As shown in the code above, a pager is created by including the pager option.
It has subkeys the limit or the number of records to return and the element which is a unique integer identifying the pager. If you have multiple pagers on a page then each one must have a unique element number.
Finally, to generate the HTML for the pager the following line is used in the code above:. Notice in this line the final argument is an array. Here we provide any arguments to add to the URL when any link in the pager is clicked. As described above, each element of the resources side-bar is managed by JavaScript.
If we simply refresh the page it will return to the first element. When the user clicks on an element in the pager we want the page to refresh and return to the same resource block. In the case of the feature map page, the name for the block on which the pager resides is 'featurepos'.
In some cases, a record may have a corresponding Drupal page or node and we would like to provide a link to that page. For example, for features, there is always a corresponding organism page. By default, Tripal will automatically populate the node information for one-to-one relationships. The code below shows how to obtain the node ID of the organism to which a feature belongs:. Even though the nid field is not part of the organism table, it is always available in the record if a Drupal node exists.
In one-to-many relationships however, the node information may not be automatically populated. This information can be obtained by expanding the record as done previously. Notice the second argument is node and the third argument is the Chado table. Using this code, the node information will be added if it doesn't already exists.
In order to use the Tripal API for module development the developer should have the following skills:. It is best to have a basic understanding of Drupal module development to help understand the remainder of this document. Drupal provides an API for anyone to create new modules to extend the functionality of Drupal. Tripal is itself a collection of modules that use the Drupal API. Tripal provides several major groups of functionality through the API. These include the following:.
Materialized Views MViews are useful when querying the Chado database is slow. Chado is highly normalized which makes it a great data storage platform, but as a result can cause some queries to be slow. For web visitors slow queries may not be acceptable. Therefore, materialized views were introduced to Chado to alleviate search time.
A materialized view is essentially a new database table that agglomerates data from multiple existing tables into a single table for easier access. The materialized view is typically populated from a single SQL query.
The materialized view becomes a reformatted copy of existing data. Because the materialized view is a copy of existing data it must be updated and refreshed to include new data added to the normal Chado tables. For example, the Tripal Feature module uses an MView to provide a count of the number of sequence types an organism has in the feature table.
Below is the SQL query used for to extract this information:. This query is too slow to execute for each visitor to the site, therefore an MView would be an appropriate solution.
Therefore, the above query is only executed one time, and the results needed to display on the page are easy available through a much simpler select statement in the new MView table. Tripal provides a web-interface to allow a site administrator to create a materialized view using a custom SQL query. A mechanism for updating stale MViews is also available. Chado makes heavy use of vocabularies. The cvterm table is where the terms from controlled vocabularies and ontologies are stored.
Examples of publicly curated ontologies include the Relationship , Sequence , and the Gene Ontology. All of the property tables e. When possible a public ontology or vocabulary should be used.
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