[mehalter]

TO TEST

Ran this locally. Feel free to recreate:

>>> from capepy.aws.dynamodb import PipelineTable
>>> pt=PipelineTable(table_name="cape-dap-registry-DataAnalysisPipelineRegistry")
>>> import pprint
>>> from capepy.aws.dynamodb import PipelineTable
>>> 
>>> 
>>> pt.get_pipeline("bactopia-ont-v3.2.0")
{'version': 'v3.2.0', 'pipeline_type': 'nextflow', 'pipeline_name': 'Bactopia ONT Sample', 'pipeline_runnable': True, 'pipeline_id': 'bactopia-ont-v3.2.0', 'profile': {'pipelineName': 'Bactopia ONT Sample', 'parametersSchema': {'allOf': [{'$ref': '#/$defs/bactopia-base-3.2.0'}], '$schema': 'https://json-schema.org/draft/2020-12/schema', '$defs': {'bactopia-base-3.2.0': {'$defs': {}, '$schema': 'https://json-schema.org/draft/2020-12/schema', 'type': 'object', 'properties': {'--aws_volumes': {'const': '/opt/conda:/mnt/conda,/mnt/nextflow_shared_data:/mnt/nextflow_shared_data:ro', 'default': '/opt/conda:/mnt/conda,/mnt/nextflow_shared_data:/mnt/nextflow_shared_data:ro'}, '-profile': {'const': 'aws', 'default': 'aws'}}}}, 'type': 'object', 'properties': {'--outdir': {'type': 'string', 'title': 'S3 Location of the output directory'}, '--max_memory': {'type': 'string', 'title': 'Max Memory', 'default': '24.GB'}, '--ont': {'type': 'string', 'title': 'ONT'}, '--max_cpus': {'default': Decimal('8'), 'type': 'integer', 'title': 'Max CPUs', 'minimum': Decimal('1')}, '--sample': {'type': 'string', 'title': 'Sample Name'}}, 'unevaluatedProperties': False, 'required': ['--sample', '--ont', '--outdir']}, 'pipelineDescription': "Execute Bactopia's ONT sample sequencing workflow with v3.2.0", 'uiSchema': {'type': 'VerticalLayout', 'elements': [{'type': 'Control', 'scope': '#/properties/--max_cpus'}, {'type': 'Control', 'scope': '#/properties/--max_memory'}, {'type': 'Control', 'scope': '#/properties/--ont'}, {'type': 'Control', 'scope': '#/properties/--sample'}]}, 'project': 'bactopia/bactopia', 'submission': {'encoding': 'cli-string', 'optionsFieldName': 'nextflowOptions'}, 'pipelineType': 'nextflow', 'version': 'v3.2.0', 'inherits': ['bactopia-base-3.2.0'], 'pipelineRunnable': True, 'pipelineId': 'bactopia-ont-v3.2.0'}, 'nextflow_config': {'aws': {'batch': {'cliPath': '/usr/bin/aws', 'delayBetweenAttempts': '5 sec', 'maxTransferAttempts': Decimal('3')}, 'client': {'uploadStorageClass': 'INTELLIGENT_TIERING', 'connectionTimeout': Decimal('10000'), 'storageEncryption': 'AES256', 'maxConnections': Decimal('20')}, 'secretKey': '<YOUR S3 SECRET KEY>', 'region': 'us-east-2', 'accessKey': '<YOUR S3 ACCESS KEY>'}}, 'project': 'bactopia/bactopia'}
>>> 
>>> 
>>> 
>>> items = pt.get_pipelines_by_name("Bactopia ONT Sample")
>>> len(items)
2
>>> items
[{'profile': {'parametersSchema': {'allOf': [{'$ref': '#/$defs/bactopia-base-dev'}], '$schema': 'https://json-schema.org/draft/2020-12/schema', '$defs': {'bactopia-base-dev': {'$defs': {}, '$schema': 'https://json-schema.org/draft/2020-12/schema', 'type': 'object', 'properties': {'--aws_volumes': {'const': '/opt/conda:/mnt/conda,/mnt/nextflow_shared_data:/mnt/nextflow_shared_data:ro', 'default': '/opt/conda:/mnt/conda,/mnt/nextflow_shared_data:/mnt/nextflow_shared_data:ro'}, '-profile': {'const': 'aws', 'default': 'aws'}}}}, 'type': 'object', 'required': ['--sample', '--ont', '--outdir'], 'properties': {'--outdir': {'title': 'S3 Location of the output directory', 'type': 'string'}, '--max_memory': {'title': 'Max Memory', 'type': 'string', 'default': '24.GB'}, '--max_cpus': {'default': Decimal('8'), 'type': 'integer', 'title': 'Max CPUs', 'minimum': Decimal('1')}, '--ont': {'type': 'string', 'title': 'ONT'}, '--sample': {'type': 'string', 'title': 'Sample Name'}}, 'unevaluatedProperties': False}, 'pipelineName': 'Bactopia ONT Sample', 'pipelineDescription': "Execute Bactopia's ONT sample sequencing workflow with the development release", 'uiSchema': {'type': 'VerticalLayout', 'elements': [{'type': 'Control', 'scope': '#/properties/--max_cpus'}, {'type': 'Control', 'scope': '#/properties/--max_memory'}, {'type': 'Control', 'scope': '#/properties/--ont'}, {'type': 'Control', 'scope': '#/properties/--sample'}]}, 'project': 'bactopia/bactopia', 'submission': {'encoding': 'cli-string', 'optionsFieldName': 'nextflowOptions'}, 'pipelineType': 'nextflow', 'version': 'dev', 'inherits': ['bactopia-base-dev'], 'pipelineRunnable': True, 'pipelineId': 'bactopia-ont-dev'}, 'project': 'bactopia/bactopia', 'pipeline_name': 'Bactopia ONT Sample', 'pipeline_runnable': True, 'version': 'dev', 'pipeline_id': 'bactopia-ont-dev', 'pipeline_type': 'nextflow', 'nextflow_config': {'aws': {'batch': {'cliPath': '/usr/bin/aws', 'delayBetweenAttempts': '5 sec', 'maxTransferAttempts': Decimal('3')}, 'client': {'uploadStorageClass': 'INTELLIGENT_TIERING', 'connectionTimeout': Decimal('10000'), 'storageEncryption': 'AES256', 'maxConnections': Decimal('20')}, 'secretKey': '<YOUR S3 SECRET KEY>', 'region': 'us-east-2', 'accessKey': '<YOUR S3 ACCESS KEY>'}}}, {'profile': {'pipelineName': 'Bactopia ONT Sample', 'parametersSchema': {'allOf': [{'$ref': '#/$defs/bactopia-base-3.2.0'}], '$schema': 'https://json-schema.org/draft/2020-12/schema', '$defs': {'bactopia-base-3.2.0': {'$defs': {}, '$schema': 'https://json-schema.org/draft/2020-12/schema', 'type': 'object', 'properties': {'--aws_volumes': {'const': '/opt/conda:/mnt/conda,/mnt/nextflow_shared_data:/mnt/nextflow_shared_data:ro', 'default': '/opt/conda:/mnt/conda,/mnt/nextflow_shared_data:/mnt/nextflow_shared_data:ro'}, '-profile': {'const': 'aws', 'default': 'aws'}}}}, 'type': 'object', 'properties': {'--outdir': {'type': 'string', 'title': 'S3 Location of the output directory'}, '--max_memory': {'type': 'string', 'title': 'Max Memory', 'default': '24.GB'}, '--ont': {'type': 'string', 'title': 'ONT'}, '--max_cpus': {'default': Decimal('8'), 'type': 'integer', 'title': 'Max CPUs', 'minimum': Decimal('1')}, '--sample': {'type': 'string', 'title': 'Sample Name'}}, 'unevaluatedProperties': False, 'required': ['--sample', '--ont', '--outdir']}, 'pipelineDescription': "Execute Bactopia's ONT sample sequencing workflow with v3.2.0", 'uiSchema': {'type': 'VerticalLayout', 'elements': [{'type': 'Control', 'scope': '#/properties/--max_cpus'}, {'type': 'Control', 'scope': '#/properties/--max_memory'}, {'type': 'Control', 'scope': '#/properties/--ont'}, {'type': 'Control', 'scope': '#/properties/--sample'}]}, 'project': 'bactopia/bactopia', 'submission': {'encoding': 'cli-string', 'optionsFieldName': 'nextflowOptions'}, 'pipelineType': 'nextflow', 'version': 'v3.2.0', 'inherits': ['bactopia-base-3.2.0'], 'pipelineRunnable': True, 'pipelineId': 'bactopia-ont-v3.2.0'}, 'pipeline_id': 'bactopia-ont-v3.2.0', 'project': 'bactopia/bactopia', 'pipeline_name': 'Bactopia ONT Sample', 'pipeline_runnable': True, 'pipeline_type': 'nextflow', 'version': 'v3.2.0', 'nextflow_config': {'aws': {'batch': {'cliPath': '/usr/bin/aws', 'delayBetweenAttempts': '5 sec', 'maxTransferAttempts': Decimal('3')}, 'client': {'uploadStorageClass': 'INTELLIGENT_TIERING', 'connectionTimeout': Decimal('10000'), 'storageEncryption': 'AES256', 'maxConnections': Decimal('20')}, 'secretKey': '<YOUR S3 SECRET KEY>', 'region': 'us-east-2', 'accessKey': '<YOUR S3 ACCESS KEY>'}}}]
>>> 
>>> 
>>> 
>>> item = pt.get_pipeline_by_name_ver("Bactopia ONT Sample", "v3.2.0")
>>> len(item)
1
>>> item
[{'pipeline_runnable': True, 'version': 'v3.2.0', 'nextflow_config': {'aws': {'batch': {'cliPath': '/usr/bin/aws', 'delayBetweenAttempts': '5 sec', 'maxTransferAttempts': Decimal('3')}, 'client': {'uploadStorageClass': 'INTELLIGENT_TIERING', 'connectionTimeout': Decimal('10000'), 'storageEncryption': 'AES256', 'maxConnections': Decimal('20')}, 'secretKey': '<YOUR S3 SECRET KEY>', 'region': 'us-east-2', 'accessKey': '<YOUR S3 ACCESS KEY>'}}, 'pipeline_name': 'Bactopia ONT Sample', 'project': 'bactopia/bactopia', 'pipeline_type': 'nextflow', 'pipeline_id': 'bactopia-ont-v3.2.0', 'profile': {'pipelineName': 'Bactopia ONT Sample', 'parametersSchema': {'allOf': [{'$ref': '#/$defs/bactopia-base-3.2.0'}], '$schema': 'https://json-schema.org/draft/2020-12/schema', '$defs': {'bactopia-base-3.2.0': {'$defs': {}, '$schema': 'https://json-schema.org/draft/2020-12/schema', 'type': 'object', 'properties': {'--aws_volumes': {'const': '/opt/conda:/mnt/conda,/mnt/nextflow_shared_data:/mnt/nextflow_shared_data:ro', 'default': '/opt/conda:/mnt/conda,/mnt/nextflow_shared_data:/mnt/nextflow_shared_data:ro'}, '-profile': {'const': 'aws', 'default': 'aws'}}}}, 'type': 'object', 'properties': {'--outdir': {'type': 'string', 'title': 'S3 Location of the output directory'}, '--max_memory': {'type': 'string', 'title': 'Max Memory', 'default': '24.GB'}, '--ont': {'type': 'string', 'title': 'ONT'}, '--max_cpus': {'default': Decimal('8'), 'type': 'integer', 'title': 'Max CPUs', 'minimum': Decimal('1')}, '--sample': {'type': 'string', 'title': 'Sample Name'}}, 'unevaluatedProperties': False, 'required': ['--sample', '--ont', '--outdir']}, 'pipelineDescription': "Execute Bactopia's ONT sample sequencing workflow with v3.2.0", 'uiSchema': {'type': 'VerticalLayout', 'elements': [{'type': 'Control', 'scope': '#/properties/--max_cpus'}, {'type': 'Control', 'scope': '#/properties/--max_memory'}, {'type': 'Control', 'scope': '#/properties/--ont'}, {'type': 'Control', 'scope': '#/properties/--sample'}]}, 'project': 'bactopia/bactopia', 'submission': {'encoding': 'cli-string', 'optionsFieldName': 'nextflowOptions'}, 'pipelineType': 'nextflow', 'version': 'v3.2.0', 'inherits': ['bactopia-base-3.2.0'], 'pipelineRunnable': True, 'pipelineId': 'bactopia-ont-v3.2.0'}}]
>>> 
>>> 
>>> 
>>> bad_vals = pt.get_pipeline("awsad")
>>> bad_vals
>>> bad_vals == None
True
>>> 
>>> 
>>> 
>>> bad_vals = pt.get_pipeline_by_name("awsad")
>>> bad_vals
[]
>>> bad_vals = pt.get_pipeline_by_name_ver("Bactopia ONT Sample", "awsad")
>>> bad_vals
[]

[mehalter]

this is a remerge of #21