Object Model

Sequencing / IRIDA Objects

These objects are used to store the data of a sequencing run before uploading to IRIDA.

They each include a uploadable_schema which uses cerberus to define valid objects. Object validity is checked in core/model_validator.py, along with some extra edge case tests to ensure the built object model is ready for upload.

SequencingRun model/sequencing_run.py

Each upload needs a single SequencingRun object that acts as the root for the tree of data.

It contains a project_list which relate to the IRIDA projects that samples will be uploaded to.

The metadata dict is mostly unused, but must include layoutType as either PAIRED_END or SINGLE_END, this determines if the samples within the sequencing run are paired end or single end reads.

Project model/project.py

The Project object relates to a project on IRIDA.

The id field identifies what project number on IRIDA the samples are going to.

The sample_list list contains the Sample objects that will be uploaded.

When creating a new project on IRIDA using the API, a name at least 5 characters long must be given.

Sample model/sample.py

The Sample object includes:

  • name : How the sample is identified on IRIDA
  • description : the description of the sample on IRIDA
  • sequence_file : A SequenceFile object that holds the files to upload.
  • sample_dict : a meta data dictionary

When using the API to get samples from IRIDA, the get_irida_id method can be used to get the samples numerical identification number.

SequenceFile model/sequence_file.py

The SeuqenceFile holds the file paths to the sequence data to be uploaded.

It has a file_list list that can hold multiple files. Currently IRIDA only supports single end and paired end files (1 or 2 files) for upload.

It also includes a properties_dict that is used to store meta data, and is filled with required values by the API or Parsers before uploading.

Metadata model/metadata.py

The Metadata object defines and stores additional metadata for upload to IRIDA in a key-value dictionary.

When using the API and the send_metadata method, a Metadata object must be passed to the method.

Other Objects

DirectoryStatus model/directory_status.py

DirectoryStatus objects contain a directory, a status and a message

The progress modules makes use of them.

These are used when deciding if a run has been uploaded, partially uploaded, is a new run, or is invalid.

The directory field holds the path to the directory of some potential sequencing run.

The status field can hold the following options, defined in the file. (e.g. DirectoryStatus.NEW)

  • NEW
    • New runs, ready to upload
  • INVALID
    • Used when a run directory does not have the base requirements to act as a run
    • This is never written to a status file, as reading a status file as invalid will not allow a run to be uploaded using the --force option. When a run cannot be uploaded, ERROR is instead written to file.
  • PARTIAL
    • Parsing/Upload has started/partially completed for this run
  • ERROR
    • Parsing/Upload has stopped because of some error.
  • COMPLETE
    • Parsing/Upload has completed successfully

The message field is only filled if a run is "invalid", and contains information on why a run is invalid.

ValidationResult model/validation_result.py

ValidationResult objects contain an error_list with multiple errors. These are used to collect multiple ModelValidationErrors together so that all the validation issues can be seen at once.

Exceptions

ModelValidationError model/exceptions/model_validation_result.py

When validating the object model, A ModelValidationError will be thrown. It contains a message with information on the issue, and an object that holds the invalid object.