Validating definition files
Workflow and run definitions can grow pretty big, especially for complex experiments.
It becomes easy to do a typing mistake that could invalidate them.
Accio client comes with an
accio validate command that allows to check those files are correct without actually using them.
This command will not create or update anything on the cluster, but only check for the validity of definition files.
Here is a non exhaustive list of things this command will check:
- JSON is syntaxically correct
- names of nodes, parameters, etc. are valid
- graph of operators is acyclic
- references to other nodes, ports, parameters are valid (i.e., they exist) and allowed (i.e., data types match)
- values for inputs or parameters are allowed (i.e., data types match)
- all inputs have a value, whether it is a default or a user-specified one
- usage of deprecated operators
Once files are validated, they are guaranteed to be accepted. In case of an error, this command will do its best to provide meaningful information to help fixing the errors. This command issues two kinds of messages: errors and warnings. While errors have to be fixed for the file to be valid, warnings do not impact the usability of the definition. However, it is recommended to take into account warnings (e.g., using a deprecated operator can break at any time, since they might be removed).
Writing workflows and runs involves referencing existing objects by their names.
accio get command can be of a great help to find relevant resources, whether it is a workflow or an operator.
accio get operators returns a list of all known operators.
While there is a reference list of operators, the cluster you are interacting with can provide a slightly different version of operators, or contain custom operators installed by your system administrator.
In case of disagreement between the documentation and the command-line result, the command-line is assumed to provide the most accurate information for your particular Accio installation.
accio describe command is used to more details about a specific resource.
It is especially useful to get the list of parameters a workflow accepts, or the inputs and outputs exposed by an operator.
accio describe operator EventSource gives you a description of what this operator does, inputs it consumes and outputs it produces.