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Metadata Migration

metadata-migration is a proof of concept library demonstrating Human Cell Altas metadata migration based on "exact" and "best effort" strategies. Further, it provides a contract programming module that allows users to check invariant assertions about what schemas and instances of metadata provide.

Contents

  1. Migration
  2. Contracts

Migration

This section introduces concepts and modules for migration.

class MetadataView

A MetadataView blob of metadata migrated to a new schema version. It is a "view" on the unmigrated metadata because, often, migrations cannot guarantee that the original metadata uploader would have uploaded identical metadata under the target schema version.

Migration Information

metadata-migration uses POC migration syntax to migrate metadata. A sample migration from donor_organism v6.0.0 to a hypothetical v6.0.1 is shown below.

{
  "source_ref": "https://schema.humancellatlas.org/type/biomaterial/6.0.0/donor_organism",
  "destination_ref": "https://schema.humancellatlas.org/type/biomaterial/6.0.1/donor_organism",
  "task_groups": [
    {
      "tasks": [
        {
          "function": "pounds_to_kilograms",
          "parameters": [
            "weight",
            "weight_unit.text"
          ]
        },
        {
          "function": "move",
          "parameters": [
            "weight",
            "mass"
          ]
        },
        {
          "function": "move",
          "parameters": [
            "weight_unit",
            "mass_unit"
          ]
        }
      ]
    }
  ]
}

parameters refer to keys in the metadata. Functions are implemented as simple python functions.

task_groups are groups of operations that need to be completed as a transaction for the change to the metadata to be committed. This will be discussed further in the migration strategy section.

class MetadataMigrator

Metadata migrator accepts a MetadataView and attempts to migrate it to a specified version. The migrator can both upgrade and downgrade metadata. It can migrate between any two metadata versions so long as the graph of migration information spans the two version schemas.

Below is a sample v6.0.0 donor organism.

{
  "describedBy": "https://schema.humancellatlas.org/type/biomaterial/6.0.0/donor_organism",
  "schema_type": "biomaterial",
  "biomaterial_core": {
    "biomaterial_id": "Q4_DEMO-donor_MGH30",
    "biomaterial_name": "Q4 DEMO donor MGH30",
    "ncbi_taxon_id": [
      9606
    ]
  },
  "genus_species": [
    {
      "text": "Homo sapiens"
    }
  ],
  "organism_age": "29",
  "organism_age_unit": "year",
  "height": "178",
  "height_unit": "centimeter",
  "is_living": true,
  "biological_sex": "male",
  "weight": "160",
  "weight_unit": {
    "text": "lbs"
  },
  "provenance": {
    "document_id": "dcbe0115-7871-41de-8502-b68f6ca024ab",
    "submission_date": "2018-07-22T23:38:35.835Z",
    "update_date": "2018-07-22T23:38:44.151Z"
  }
}

To migrate this metadata to a different version, we load migration information, select the migration and apply it.

metadata_view_6_0_0 = MetadataView.from_file('./test/fixtures/donor_organism_6_0_0.json')
migration_catalog = MigrationCatalog.from_file('./test/fixtures/migrations.json')
metadata_migrator = MetadataMigrator(migration_catalog)
metadata_migrator.migrate_to_version(metadata_view_6_0_0, '6.0.1')
{
  "describedBy": "https://schema.humancellatlas.org/type/biomaterial/6.0.1/donor_organism",
  "schema_type": "biomaterial",
  "biomaterial_core": {
    "biomaterial_id": "Q4_DEMO-donor_MGH30",
    "biomaterial_name": "Q4 DEMO donor MGH30",
    "ncbi_taxon_id": [
      9606
    ]
  },
  "genus_species": [
    {
      "text": "Homo sapiens"
    }
  ],
  "organism_age": "29",
  "organism_age_unit": "year",
  "height": "178",
  "height_unit": "centimeter",
  "is_living": true,
  "biological_sex": "male",
  "mass": "72.57472",
  "mass_unit": {
    "text": "kgs"
  },
  "provenance": {
    "document_id": "dcbe0115-7871-41de-8502-b68f6ca024ab",
    "submission_date": "2018-07-22T23:38:35.835Z",
    "update_date": "2018-07-22T23:38:44.151Z"
  }
}

Notice that the weight and weight_unit fields have been migrated to mass and mass_unit respectively.

MigrationStrategy

Metadata migrator has two migration strategies shown below.

  1. MigrationStrategy.EXACT raises and exception if any of the migration tasks fail.
  2. MigrationStrategy.BEST_EFFORT applies task groups one at a time. If one fails, its changes are not committed to the migrating MetadataView and the subsequent task groups are attempted.

Contracts

class Condition

A condition is an element of a contract. It accepts a path of a part of the metadata and kwargs key value pairs that form assertions about a Schema or MetadataView.

# Condition: schema must have required string field at path biomaterial_core.biomaterial_id
# parameters: path, **kwargs
c = Condition('biomaterial_core.biomaterial_id', value_type='string', required=True)
c.validate(schema)

The keys of kwargs refer to keys in the dictionary pointed to by the path parameter (part of the Schema or MetadataView). If the value of a kwargs pair has a value type, equality is tested between that value and the value in the dictionary. If the value of a kwargs is a function that returns a boolean, that function is used to test the value in the dictionary.

# Condition: submission must have been created in the last two weeks
from dateutil.parser import parse as parse_datetime
from datetime import datetime, timedelta
c = Condition(
    'provenance',
    submission_date=lambda x: parse_datetime(x) > datetime.utcnow() - timedelta(days=14)
)
c.validate(metadata_view)

class Contract

A contract is simply a collection of conditions that can be used to make assertions about different parts of a Schema or MetadataView.

# Contract: instance of MetadataView has weight and weight_unit info in lbs
c = Contract(
    title='metadata_view_has_weight_lbs',
    conditions=[
        Condition(path=None, weight=lambda x: isinstance(x, str)),
        Condition('weight_unit', text='lbs')
    ]
)
c.validate(metadata_view)

This allows developers a way to easily check if a Schema or MetadataView conforms to their expectations before processing it.