README

Tripal Fields Generator

This is a CLI tool to help automate the generation of Tripal fields for use in Tripal 3 development. We highly recommend you read the developer handbook before attempting to use this tool. It supports creating both Tripal and Chado fields.

Documentation

Installation

Using Composer

The easiest way to install Tripal Fields Generator is using Composer.

Install command

composer global require "statonlab/fields_generator:~0.1"

Update command

composer global update

Note: make sure you export the composer bin directory by running the following command:

# Add this line to your .bashrc or .bash_profile to persist between shell sessions.
export PATH="$PATH:~/.composer/vendor/bin"

Manual installation

You can download this tool using the "Clone or download" button above or cloning the repository using Git.

git clone https://github.com/statonlab/fields_generator.git

Usage

Generate a new field by running the following command and answering a few questions. By default, Tripal Fields Generator will generate a Chado field, but it can also generate Tripal fields.

# If installed globally with composer
makefield [--output|-o=/full/path/to/module]

# If installed manually without composer
./makefield [--output|-o=/full/path/to/module]

The generator will ask you for both the DB name and the CV name: these names correspond to the chado.db and chado.cv tables. If you aren't sure what these values are, you can use the EBI Ontology lookup Service CVterm entry as a guide: the DB name is the value in the orange box, and the CV name is the value in the teal box. For a full explanation, please read the CV guide.

Alternatively, the below table shows the DB and CV values for commonly used ontologies in Tripal 3.

FULL NAME	DB	CV
DCMI metadata terms	dc	dc
Eagle-I Research Ontology	ERO	ero
EDAM data	data	EDAM
EDAM format	format	EDAM
EDAM operation	operation	EDAM
EDAM topic	topic	EDAM
Friend of a Friend	foaf	foaf
Gene ontology biological process	GO	biological_process
Gene ontology cellular component	GO	cellular_component
Gene ontology molecular function	GO	molecular_function
hydra	hydra	hydra
Information Artifact Ontology	IAO	IAO
local	local	local
Ontology for Biomedical Investigation	OBI	OBI
Ontology for genetic interval	OGI	ogi
Ontology of Biological and Clinical Statistics	OBCS	OBCS
Relationship ontology (legacy)	RO	ro
Resource Description Framework Schema	rdfs	rdfs
schema	schema	schema
Semanticscience Integrated Ontology	SIO	SIO
Sequence ontology	SO	sequence
Software Ontology	SWO	swo
Systems Biology	SBO	sbo
Taxonomic Rank	TAXRANK	taxonomic_rank

In order for Drupal to recognize your fields, you must...

Place the file generated by this tool in the correct location (see below)
Specify which bundles your field will attach to. Fields generated by this tool attach to the organism bundle by default.
Clear the cache (drush cc all).
Add the field in Structure->Tripal_Content

Options

Option	default	description	example
--output (-o)	Current working directory	The path to the module responsible for the field.	`makefield -o="/var/www/html/sites/all/modules/my_module"`
--type (-t)	`chado`	The type of field to generate. Choose between Chado which would extend ChadoField or Tripal to extend TripalField	`makefield -t=tripal`

Output

Tripal Fields Generator will create four files that define your field. For the custom controlled vocabulary (CV) term example defined in the local CV, the field is defined in three files:

The Fields class, local__example.inc
The field formatter, local__example_formatter.inc
The field widget, local__example_widget.inc

Additionally, a fields file stub describing the fields declared in your module is generated: for this example module, the file might be tripal_example_module.fields.inc. Note that all of the fields in your module are described here: running Tripal Fields Generator multiple times will require you to combine this file for each field. The final structure of your fields should look like the example below, with a given field CV__CVTERM in module/includes/TripalFields/CV_CVterm, and the module.fields.inc located in module/includes. For a full example of a field please visit the Tripal Example Module repository by @laceysanderson.

Output file structure

By default, the module-level field file (moduleName.fields.inc) will be placed in CV__CVterm_output, and the classes defining your field will be in the field folder CV__CVterm_output/CV__CVterm. Note that the value of CV corresponds to what you enter for the DB, not the CV table!

CV__CVterm_output/
├── CV__CVterm/
│   ├── CV__CVterm.inc
│   ├── CV__CVterm_formatter.inc
│   └── CV__CVterm_widget.inc  
└── module.fields.inc

You will need to move these files to conform to the pattern in the previous section. Alternatively, you may specify a different output path using the output flag, -o="/path/to/module" or --output="/path/to/module". This will automatically define your fields in the correct place. In either case, your final module field structure should look like the example below.

module/
├── includes/
│   ├── TripalFields/
│   │   └── CV__CVterm/
│   │       ├── CV__CVterm.inc
│   │       ├── CV__CVterm_formatter.inc
│   │       └── CV__CVterm_widget.inc
│   └── module.fields.inc
└── rest of my module...

Terms

The below terms must be provided for each field you generate.

Field Label: A human readable label for the field. e,g. Germplasm Summary
Field Description: A human readable description of the field
Module Name: The machine name of the module this field is distributed with. e,g. tripal_germplasm_module
Database name:
CV name:
Controlled Vocabulary Term: The term name. e,g. germplasm_summary
Accession: The accession number for this term in the vocabulary, e,g. 30021. This must match the dbxref value in Chado. Biological CVs will always use numeric CVterms. Semantic CVs will generally use strings.

Examples

Contributing

Contributions are highly welcomed and recommended.

Fork the repository.
Create a branch that contains your code.
Create a pull request with a clear description of your contribution for us to review.

License

The Tripal Fields Generator "logo" is derived from the collectible card game Hearthstone, copyright © Blizzard Entertainment, Inc. Hearthstone® is a registered trademark of Blizzard Entertainment, Inc. Tripal Fields Generator is not affiliated or associated with or endorsed by Hearthstone® or Blizzard Entertainment, Inc.

statonlab / fields_generator

Maintainers

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