dina-py

Python access to the DINA API

Current Features

JSON-API serializer and deserializer with Marshmallow JSON-API

• Currently supported schemas:
  • Collecting Event
  • Storage Unit Usage
  • Person
  • Material Sample
  • Metadata
  • Storage Unit
  • Form Template
  • Split Configuration

DINA APIs

• Currently supported APIs:
  • Agent API
    • Person
  • Collection API
    • CollectingEvent
    • StorageUnit
    • StorageUnitUsage
    • FormTemplate
    • SplitConfiguration
    • MaterialSample
    • Organism
  • Object Store API
    • Any Object Store API endpoint using ObjectStoreApi's CRUD methods
  • SeqDB API
    • PCR Batch
    • PCR Batch Item
    • SEQ Reaction
  • Export API
    • Any Export API endpoint using DinaExportApi's CRUD methods

DINA_API_CLIENT

Currently supported operations:

upload_file:

• metavar="<file_path> : (str) = Path to the file to be uploaded.",
• help="Upload a file to Object Store. Argument: file_path"

upload_dir:

• metavar="<dir_path> : (str) = Path to the directory to be uploaded.",
• help="Upload all files in a directory to Object Store",

verbose:

• help="Verbosity of logs. Primarily for debugging.",
• action="store_true",

create_metadatas:

• metavar="<dir_path> : (str) = Path to the directory to be uploaded.",
• help="Upload all files in a directory to Object Store and create metadatas according to constants defined in ./dina-api-config.yml",

create_form_template:

• metavar="<file_path> : (str) = Path to the file to be parsed and created.",
• help="Create a form template according to specs defined in a yaml file such as ./form-template-sample.yml",

create_split_configuration:

• metavar="<file_path> : (str) = Path to the file to be parsed and created.",
• help="Create a split configuration according to specs defined in a yaml file such as ./split-configuration-sample.yml",

TEST COVERAGE

• APIs (Unit Test with Magic Mock):
  • Collection API
    • Collecting Event
    • Managed Attributes
    • Material Sample
    • Organism
  • Object Store API
    • Metadata
    • Object Export
  • Agent API
    • Person
  • Export API
    • Data Export
• Schemas:
  • Collecting Event
  • Form Template
  • Managed Attribute
  • Material Sample
  • Metadata
  • Person
  • Split Configuration
  • Storage Unit Usage

Installation Instructions

Local Install

Before installing, it's recommended to use a virtual environment in python but not required. create a virtual environment for the dependencies required.

sudo apt install python3.10-venv
python3 -m venv env
source env/bin/activate

From inside of the dina-py root folder, install the library and all required dependencies:

pip install -e .
pip install -r requirements.txt

The username and password are set via environment variables. This can be done via the command line:

set keycloak_username=username
set keycloak_password=password

Or programmatically using:

os.environ["keycloak_username"] = "username"
os.environ["keycloak_password"] = "password"

• Make a copy of keycloak-config-sample.yml and rename to keycloak-config.yml in the root of dina-py directory, open keycloak-config.yml using Notepad
• In keycloak-config.yml, change url, keycloak_username, keycloak_password as needed
• Make a copy of dina-api-config-sample.yml and rename to dina-api-config.yml in the root of dina-py directory, open dina-api-config.yml using Notepad

Sample usage of DINA_API_CLIENT:

(.venv) C:\Users\<your_account>\dina-py> python .\dinapy\client\dina_api_client.py -upload_dir '<object_upload_dir>'

• Or run the following command to upload a specific file:

(.venv) C:\Users\<your_account>\dina-py> python .\dinapy\client\dina_api_client.py -upload_file '<object_upload_dir>/<file_name>'

Example API Usage

In code:

def test_create_delete_entity(self):
   schema = MaterialSampleSchema()
   material_sample_api = MaterialSampleAPI()
   try:
      material_sample_attributes = MaterialSampleAttributesDTOBuilder().group("aafc").materialSampleName("test").materialSampleType("WHOLE_ORGANISM")\
      .build()
      material_sample = MaterialSampleDTOBuilder().attributes(material_sample_attributes).build()
      serialized_material_sample = schema.dump(material_sample)
      pp = pprint.PrettyPrinter(indent=0)
      pp.pprint(serialized_material_sample)
      response = material_sample_api.create_entity(serialized_material_sample)
      id = response.json()['data']['id']
      if response.status_code == 201:
         response = material_sample_api.remove_entity(id)
         self.assertEqual(response.status_code,204)
   except ValidationError as e:
      self.fail(f"Validation failed with error: {e.messages}")