trs_cli package

Submodules

trs_cli.client module

Class implementing TRS client.

class trs_cli.client.TRSClient(uri: str, port: int = None, base_path: str = 'ga4gh/trs/v2', use_http: bool = False, token: Optional[str] = None)

Bases: object

Client to communicate with a GA4GH TRS instance. Supports additional endpoints defined in TRS-Filer (https://github.com/elixir-cloud-aai/trs-filer).

Parameters:
  • uri – Either the base URI of the TRS instance to connect to in either ‘https’ or ‘http’ schema (note that fully compliant TRS instances will use ‘https’ exclusively), e.g., https://my-trs.app, OR a hostname-based TRS URI, cf. https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs_uris
  • port – Override default port at which the TRS instance can be accessed. Only required for TRS instances that are not fully spec-compliant, as the default port is defined in the TRS documentation, cf. https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs_uris
  • base-path – Override default path at which the TRS API is accessible at the given TRS instance. Only required for TRS instances that are not fully spec-compliant, as the default port is defined in the TRS documentation, cf. https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs_uris
  • use_http – Set the URI schema of the TRS instance to http instead of https`when a TRS URI was provided to `uri.
  • token – Bearer token to send along with TRS API requests. Set if required by TRS implementation. Alternatively, specify in API endpoint access methods.
uri

URI to TRS endpoints, built from uri, port and base_path, e.g.,”https://my-trs.app:443/ga4gh/trs/v2”.

token

Bearer token for gaining access to TRS endpoints.

headers

Dictionary of request headers.

classmethod config(debug: bool = False, no_validate: bool = False) → None

Class configuration.

Parameters:
  • debug – Set to print error tracebacks.
  • no_validate – Set to skip validation of error responses.
delete_tool(id: str, accept: str = 'application/json', token: Optional[str] = None) → str

Delete a tool.

id: A unique identifier of the tool to be deleted, scoped to this
registry OR a TRS URI. For more information on TRS URIs, cf. https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs_uris

accept: Requested content type. token: Bearer token for authentication. Set if required by TRS

implementation and if not provided when instatiating client or if expired.
Returns:

ID of deleted TRS tool in case of a 200 response, or an instance of Error for all other responses.

Raises:
  • requests.exceptions.ConnectionError – A connection to the provided TRS instance could not be established.
  • trs_cli.errors.InvalidResponseError – The response could not be validated against the API schema.
delete_tool_class(id: str, accept: str = 'application/json', token: Optional[str] = None) → str

Delete a tool class.

Parameters:
  • id – Identifier of tool class to be deleted.
  • accept – Requested content type.
  • token – Bearer token for authentication. Set if required by TRS implementation and if not provided when instatiating client or if expired.
Returns:

ID of deleted TRS toolClass in case of a 200 response, or an instance of Error for all other responses.

Raises:
  • requests.exceptions.ConnectionError – A connection to the provided TRS instance could not be established.
  • trs_cli.errors.InvalidResponseError – The response could not be validated against the API schema.
delete_version(id: str, version_id: Optional[str] = None, accept: str = 'application/json', token: Optional[str] = None) → str

Delete a tool version.

Parameters:
  • id – A unique identifier of the tool whose version is to be deleted, scoped to this registry OR a TRS URI. If a TRS URI is passed and includes the version identifier, passing a version_id is optional. For more information on TRS URIs, cf. https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs_uris
  • version_id – Identifier of the tool version to be deleted, scoped to this registry. It is optional if a TRS URI is passed and includes version information. If provided nevertheless, then the version_id retrieved from the TRS URI is overridden.
  • accept – Requested content type.
  • token – Bearer token for authentication. Set if required by TRS implementation and if not provided when instatiating client or if expired.
Returns:

ID of deleted TRS tool version in case of a 200 response, or an instance of Error for all other responses.

Raises:
  • requests.exceptions.ConnectionError – A connection to the provided TRS instance could not be established.
  • trs_cli.errors.InvalidResponseError – The response could not be validated against the API schema.
get_containerfiles(id: str, version_id: Optional[str] = None, accept: str = 'application/json', token: Optional[str] = None) → Union[List[trs_cli.models.FileWrapper], trs_cli.models.Error]

Retrieve the file wrappers for all containerfiles associated with a specified tool version.

Parameters:
  • id – A unique identifier of the tool, scoped to this registry OR a TRS URI. If a TRS URI is passed and includes the version identifier, passing a version_id is optional. For more information on TRS URIs, cf. https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs_uris
  • version_id – Identifier of the tool version, scoped to this registry. It is optional if a TRS URI is passed and includes version information. If provided nevertheless, then the version_id retrieved from the TRS URI is overridden.
  • accept – Requested content type.
  • token – Bearer token for authentication. Set if required by TRS implementation and if not provided when instatiating client or if expired.
Returns:

Unmarshalled TRS response as either a list of FileWrapper instances in case of a 200 response, or an instance of Error for all other JSON reponses.

Raises:
  • requests.exceptions.ConnectionError – A connection to the provided TRS instance could not be established.
  • trs_cli.errors.InvalidResponseError – The response could not be validated against the API schema.
get_descriptor(type: str, id: str, version_id: Optional[str] = None, accept: str = 'application/json', token: Optional[str] = None) → Union[trs_cli.models.Error, trs_cli.models.FileWrapper, str]

Retrieve the file wrapper for the primary descriptor of a specified tool version and descriptor type.

Parameters:
  • type – The output type of the descriptor. Plain types return the bare descriptor while the “non-plain” types return a descriptor wrapped with metadata. Allowed values include “CWL”, “WDL”, “NFL”, “GALAXY”, “SMK”, “PLAIN_CWL”, “PLAIN_WDL”, “PLAIN_NFL”, “PLAIN_GALAXY”, “PLAIN_SMK”.
  • id – A unique identifier of the tool, scoped to this registry OR a TRS URI. If a TRS URI is passed and includes the version identifier, passing a version_id is optional. For more information on TRS URIs, cf. https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs_uris
  • version_id – Identifier of the tool version, scoped to this registry. It is optional if a TRS URI is passed and includes version information. If provided nevertheless, then the version_id retrieved from the TRS URI is overridden.
  • accept – Requested content type.
  • token – Bearer token for authentication. Set if required by TRS implementation and if not provided when instatiating client or if expired.
Returns:

Unmarshalled TRS response as either an instance of FileWrapper in case of a 200 or 201 response, an instance of Error for all other JSON reponses, or a string with file contents for text/plain responses.

Raises:
  • requests.exceptions.ConnectionError – A connection to the provided TRS instance could not be established.
  • trs_cli.errors.InvalidResponseError – The response could not be validated against the API schema.
get_descriptor_by_path(type: str, path: str, id: str, version_id: Optional[str] = None, encode_path: bool = False, accept: Optional[str] = None, token: Optional[str] = None) → Union[trs_cli.models.Error, trs_cli.models.FileWrapper, str]

Retrieve the file wrapper for an indicated file for the specified tool version and descriptor type.

Parameters:
  • type – The output type of the descriptor. Plain types return the bare descriptor while the “non-plain” types return a descriptor wrapped with metadata. Allowed values include “CWL”, “WDL”, “NFL”, “GALAXY”, “SMK”, “PLAIN_CWL”, “PLAIN_WDL”, “PLAIN_NFL”, “PLAIN_GALAXY”, “PLAIN_SMK”. Setting one of the “PLAIN_” types will set the default accepted content type to “text/plain” (usually “application/json”).
  • path – Path, including filename, of descriptor or associated file relative to the primary descriptor file.
  • id – A unique identifier of the tool, scoped to this registry OR a TRS URI. If a TRS URI is passed and includes the version identifier, passing a version_id is optional. For more information on TRS URIs, cf. https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs_uris
  • version_id – Identifier of the tool version, scoped to this registry. It is optional if a TRS URI is passed and includes version information. If provided nevertheless, then the version_id retrieved from the TRS URI is overridden.
  • encode_path – Percent/URL-encode path (may be required by some TRS implementations).
  • accept – Requested content type.
  • token – Bearer token for authentication. Set if required by TRS implementation and if not provided when instatiating client or if expired.
Returns:

Unmarshalled TRS response as either an instance of FileWrapper in case of a 200 or 201 response, an instance of Error for all other JSON reponses, and a string with file contents for ‘text/plain’ responses.

Raises:
  • requests.exceptions.ConnectionError – A connection to the provided TRS instance could not be established.
  • trs_cli.errors.InvalidResponseError – The response could not be validated against the API schema.
get_files(type: str, id: str, version_id: Optional[str] = None, format: Optional[str] = None, outfile: Optional[pathlib.Path] = None, token: Optional[str] = None) → Union[List[trs_cli.models.ToolFile], trs_cli.models.Error, pathlib.Path, requests.models.Response]

Retrieve file information or ZIP archive of all files.

Parameters:
  • type – The output type of the descriptor. Plain types return the bare descriptor while the “non-plain” types return a descriptor wrapped with metadata. Allowed values include “CWL”, “WDL”, “NFL”, “GALAXY”, “SMK”, “PLAIN_CWL”, “PLAIN_WDL”, “PLAIN_NFL”, “PLAIN_GALAXY”, “PLAIN_SMK”.
  • id – A unique identifier of the tool, scoped to this registry OR a hostname-based TRS URI. If TRS URIs include the version information, passing a version_id is optional.
  • version_id – An optional identifier of the tool version, scoped to this registry. It is optional if version info is included in the TRS URI. If passed, then the existing version_id retreived from the TRS URI is overridden.
  • format – Returns a zip file of all files when format=zip is specified.
  • outfile – Name of zip archive when format is set to ‘zip’. Ignored otherwise. If not specified, the filename is set based on the URL by taking the part after the last ‘/’ and stored in the current working directory.
  • token – Bearer token for authentication. Set if required by TRS implementation and if not provided when instatiating client or if expired.
Returns:

Unmarshalled TRS response as either a list of instances of ToolFile in case of a 200 response, an instance of Error for all other JSON reponses, and the absolute path of the ZIP archive if format is set to ‘zip’.

Raises:
  • requests.exceptions.ConnectionError – A connection to the provided TRS instance could not be established.
  • trs_cli.errors.InvalidResponseError – The response could not be validated against the API schema.
  • IOError – The ZIP archive could not be written.
get_service_info(accept: str = 'application/json', token: Optional[str] = None) → Union[trs_cli.models.Service, trs_cli.models.Error]

Retrieve service info.

Parameters:
  • accept – Requested content type.
  • token – Bearer token for authentication. Set if required by TRS implementation and if not provided when instatiating client or if expired.
Returns:

Unmarshalled TRS response as either an instance of Service in case of a 200 response, or an instance of Error for all other JSON reponses.

Raises:
  • requests.exceptions.ConnectionError – A connection to the provided TRS instance could not be established.
  • trs_cli.errors.InvalidResponseError – The response could not be validated against the API schema.
get_tests(type: str, id: str, version_id: Optional[str] = None, accept: str = 'application/json', token: Optional[str] = None) → Union[trs_cli.models.Error, List[trs_cli.models.FileWrapper], str]

Retrieve the file wrappers for all tests associated with a specified tool version and descriptor type.

Parameters:
  • type – The output type of the descriptor. Plain types return the bare descriptor while the “non-plain” types return a descriptor wrapped with metadata. Allowed values include “CWL”, “WDL”, “NFL”, “GALAXY”, “SMK”, “PLAIN_CWL”, “PLAIN_WDL”, “PLAIN_NFL”, “PLAIN_GALAXY”, “PLAIN_SMK”.
  • id – A unique identifier of the tool, scoped to this registry OR a TRS URI. If a TRS URI is passed and includes the version identifier, passing a version_id is optional. For more information on TRS URIs, cf. https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs_uris
  • version_id – Identifier of the tool version, scoped to this registry. It is optional if a TRS URI is passed and includes version information. If provided nevertheless, then the version_id retrieved from the TRS URI is overridden.
  • accept – Requested content type.
  • token – Bearer token for authentication. Set if required by TRS implementation and if not provided when instatiating client or if expired.
Returns:

Unmarshalled TRS response as either a list of FileWrapper instances in case of a 200 or 201 response, an instance of Error for all other JSON reponses, and a string for ‘text/plain’ responses.

Raises:
  • requests.exceptions.ConnectionError – A connection to the provided TRS instance could not be established.
  • trs_cli.errors.InvalidResponseError – The response could not be validated against the API schema.
get_tool(id: str, accept: str = 'application/json', token: Optional[str] = None) → Union[trs_cli.models.Error, str, trs_cli.models.Tool]

Retrieve tool with the specified identifier.

Parameters:
  • id – A unique identifier of the tool, scoped to this registry OR a TRS URI. For more information on TRS URIs, cf. https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs_uris
  • accept – Requested content type.
  • token – Bearer token for authentication. Set if required by TRS implementation and if not provided when instatiating client or if expired.
Returns:

Unmarshalled TRS response as either an instance of Tool in case of a 200 or 201 response, an instance of Error for all other JSON reponses, and a string for ‘text/plain’ responses.

Raises:
  • requests.exceptions.ConnectionError – A connection to the provided TRS instance could not be established.
  • trs_cli.errors.InvalidResponseError – The response could not be validated against the API schema.
get_tool_classes(accept: str = 'application/json', token: Optional[str] = None) → Union[List[trs_cli.models.ToolClass], trs_cli.models.Error]

Retrieve tool classes.

Parameters:
  • accept – Requested content type.
  • token – Bearer token for authentication. Set if required by TRS implementation and if not provided when instatiating client or if expired.
Returns:

Unmarshalled TRS response as either a list of instances of ToolClass in case of a 200 response, or an instance of Error for all other JSON reponses.

Raises:
  • requests.exceptions.ConnectionError – A connection to the provided TRS instance could not be established.
  • trs_cli.errors.InvalidResponseError – The response could not be validated against the API schema.
get_tools(accept: str = 'application/json', token: Optional[str] = None, id: Optional[str] = None, alias: Optional[str] = None, toolClass: Optional[str] = None, descriptorType: Optional[str] = None, registry: Optional[str] = None, organization: Optional[str] = None, name: Optional[str] = None, toolname: Optional[str] = None, description: Optional[str] = None, author: Optional[str] = None, checker: Optional[bool] = None, limit: Optional[int] = None, offset: Optional[int] = None) → Union[List[trs_cli.models.Tool], trs_cli.models.Error]

List all tools.

Filter parameters to subset the tools list can be specified. Filter parameters are additive.

Parameters:
  • accept – Requested content type.
  • token – Bearer token for authentication. Set if required by TRS implementation and if not provided when instatiating client or if expired.
  • id – Return only entries with the given identifier.
  • alias – Return only entries with the given alias.
  • toolClass – Return only entries with the given subclass name.
  • descriptorType – Return only entries with the given descriptor type.
  • registry – Return only entries from the given registry.
  • organization – Return only entries from the given organization.
  • name – Return only entries with the given image name.
  • toolname – Return only entries with the given tool name.
  • description – Return only entries with the given description.
  • author – Return only entries from the given author.
  • checker – Return only checker workflows.
  • limit – Number of records when paginating results.
  • offset – Start index when paginating results.
Returns:

Unmarshalled TRS response as either a list of instances of Tool in case of a 200 response, or an instance of Error for all other JSON reponses.

Raises:
  • requests.exceptions.ConnectionError – A connection to the provided TRS instance could not be established.
  • trs_cli.errors.InvalidResponseError – The response could not be validated against the API schema.
get_version(id: str, version_id: Optional[str] = None, accept: str = 'application/json', token: Optional[str] = None) → Union[trs_cli.models.ToolVersion, trs_cli.models.Error]

Retrieve tool version with the specified identifiers.

Parameters:
  • id – A unique identifier of the tool, scoped to this registry OR a TRS URI. If a TRS URI is passed and includes the version identifier, passing a version_id is optional. For more information on TRS URIs, cf. https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs_uris
  • version_id – Identifier of the tool version, scoped to this registry. It is optional if a TRS URI is passed and includes version information. If provided nevertheless, then the version_id retrieved from the TRS URI is overridden.
  • accept – Requested content type.
  • token – Bearer token for authentication. Set if required by TRS implementation and if not provided when instatiating client or if expired.
Returns:

Unmarshalled TRS response as either an instance of ToolVersion in case of a 200 response, or an instance of Error for all other JSON reponses.

Raises:
  • requests.exceptions.ConnectionError – A connection to the provided TRS instance could not be established.
  • trs_cli.errors.InvalidResponseError – The response could not be validated against the API schema.
get_versions(id: str, accept: str = 'application/json', token: Optional[str] = None) → Union[List[trs_cli.models.ToolVersion], trs_cli.models.Error]

Returns all versions of the specified tool..

Parameters:
  • id – A unique identifier of the tool, scoped to this registry OR a TRS URI. For more information on TRS URIs, cf. https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs_uris
  • accept – Requested content type.
  • token – Bearer token for authentication. Set if required by TRS implementation and if not provided when instatiating client or if expired.
Returns:

Unmarshalled TRS response as either a list of instances of ToolVersion in case of a 200 response, or an instance of Error for all other JSON reponses.

Raises:
  • requests.exceptions.ConnectionError – A connection to the provided TRS instance could not be established.
  • trs_cli.errors.InvalidResponseError – The response could not be validated against the API schema.
no_validate = False
post_service_info(payload: Dict[KT, VT], token: Optional[str] = None) → None

Register service info.

Parameters:
  • payload – Service info data.
  • token – Bearer token for authentication. Set if required by TRS implementation and if not provided when instatiating client or if expired.
Raises:
  • requests.exceptions.ConnectionError – A connection to the provided TRS instance could not be established.
  • pydantic.ValidationError – The object data payload could not be validated against the API schema.
  • trs_cli.errors.InvalidResponseError – The response could not be validated against the API schema.
post_tool(payload: Dict[KT, VT], accept: str = 'application/json', token: Optional[str] = None) → str

Register a tool.

Parameters:
  • payload – Tool data.
  • accept – Requested content type.
  • token – Bearer token for authentication. Set if required by TRS implementation and if not provided when instatiating client or if expired.
Returns:

ID of registered TRS tool in case of a 200 response, or an instance of Error for all other responses.

Raises:
  • requests.exceptions.ConnectionError – A connection to the provided TRS instance could not be established.
  • pydantic.ValidationError – The object data payload could not be validated against the API schema.
  • trs_cli.errors.InvalidResponseError – The response could not be validated against the API schema.
post_tool_class(payload: Dict[KT, VT], accept: str = 'application/json', token: Optional[str] = None) → str

Register a tool class.

Parameters:
  • payload – Tool class data.
  • accept – Requested content type.
  • token – Bearer token for authentication. Set if required by TRS implementation and if not provided when instatiating client or if expired.
Returns:

ID of registered TRS toolClass in case of a 200 response, or an instance of Error for all other responses.

Raises:
  • requests.exceptions.ConnectionError – A connection to the provided TRS instance could not be established.
  • pydantic.ValidationError – The object data payload could not be validated against the API schema.
  • trs_cli.errors.InvalidResponseError – The response could not be validated against the API schema.
post_version(id: str, payload: Dict[KT, VT], accept: str = 'application/json', token: Optional[str] = None) → str

Register a tool version.

Parameters:
  • id – A unique identifier of the tool to be registered, scoped to this registry OR a TRS URI. For more information on TRS URIs, cf. https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs_uris
  • payload – Tool version data.
  • accept – Requested content type.
  • token – Bearer token for authentication. Set if required by TRS implementation and if not provided when instatiating client or if expired.
Returns:

ID of registered TRS tool version in case of a 200 response, or an instance of Error for all other responses.

Raises:
  • requests.exceptions.ConnectionError – A connection to the provided TRS instance could not be established.
  • pydantic.ValidationError – The object data payload could not be validated against the API schema.
  • trs_cli.errors.InvalidResponseError – The response could not be validated against the API schema.
put_tool(id: str, payload: Dict[KT, VT], accept: str = 'application/json', token: Optional[str] = None) → str

Create a tool object with a predefined ID. Overwrites any existing tool object with the same ID.

Parameters:
  • id – Identifier of tool to be created or overwritten.
  • payload – Tool data.
  • accept – Requested content type.
  • token – Bearer token for authentication. Set if required by TRS implementation and if not provided when instatiating client or if expired.
Returns:

ID of registered TRS tool in case of a 200 response, or an instance of Error for all other responses.

Raises:
  • requests.exceptions.ConnectionError – A connection to the provided TRS instance could not be established.
  • pydantic.ValidationError – The object data payload could not be validated against the API schema.
  • trs_cli.errors.InvalidResponseError – The response could not be validated against the API schema.
put_tool_class(id: str, payload: Dict[KT, VT], accept: str = 'application/json', token: Optional[str] = None) → str

Create a tool class with a predefined unique ID. Overwrites any existing tool object with the same ID.

Parameters:
  • id – Identifier of tool class to be created/overwritten.
  • payload – Tool class data.
  • accept – Requested content type.
  • token – Bearer token for authentication. Set if required by TRS implementation and if not provided when instatiating client or if expired.
Returns:

ID of registered TRS toolClass in case of a 200 response, or an instance of Error for all other responses.

Raises:
  • requests.exceptions.ConnectionError – A connection to the provided TRS instance could not be established.
  • pydantic.ValidationError – The object data payload could not be validated against the API schema.
  • trs_cli.errors.InvalidResponseError – The response could not be validated against the API schema.
put_version(id: str, version_id: str, payload: Dict[KT, VT], accept: str = 'application/json', token: Optional[str] = None) → str

Create a tool version object with a predefined ID. Overwrites any existing tool version object with the same ID.

Parameters:
  • id – A unique identifier of the tool to be registered, scoped to this registry OR a TRS URI. For more information on TRS URIs, cf. https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs_uris
  • version_id – Identifier of the tool version to be registered, scoped to this registry. It is optional if a TRS URI is passed and includes version information. If provided nevertheless, then the version_id retrieved from the TRS URI is overridden.
  • payload – Tool version data.
  • accept – Requested content type.
  • token – Bearer token for authentication. Set if required by TRS implementation and if not provided when instatiating client or if expired.
Returns:

ID of registered TRS tool version in case of a 200 response, or an instance of Error for all other responses.

Raises:
  • requests.exceptions.ConnectionError – A connection to the provided TRS instance could not be established.
  • pydantic.ValidationError – The object data payload could not be validated against the API schema.
  • trs_cli.errors.InvalidResponseError – The response could not be validated against the API schema.
retrieve_files(out_dir: Union[str, pathlib.Path], type: str, id: str, version_id: Optional[str] = None, encode_path: bool = False, token: Optional[str] = None) → Dict[str, List[str]]

Write tool version file contents for a given descriptor type to files.

DEPRECATED: Use .get_files with format=zip instead.

Parameters:
  • out_dir – Directory to write requested files to. Will be attempted to create if it does not exist.
  • type – The output type of the descriptor. Plain types return the bare descriptor while the “non-plain” types return a descriptor wrapped with metadata. Allowed values include “CWL”, “WDL”, “NFL”, “GALAXY”, “SMK”, “PLAIN_CWL”, “PLAIN_WDL”, “PLAIN_NFL”, “PLAIN_GALAXY”, “PLAIN_SMK”.
  • id – A unique identifier of the tool, scoped to this registry OR a hostname-based TRS URI. If TRS URIs include the version information, passing a version_id is optional.
  • version_id – An optional identifier of the tool version, scoped to this registry. It is optional if version info is included in the TRS URI. If passed, then the existing version_id retreived from the TRS URI is overridden.
  • encode_path – Percent/URL-encode relative paths of files (may be required by some TRS implementations).
Returns:

Dictionary of FileType enumerator values (e.g., TEST_FILE, PRIMARY_DESCRIPTOR) as keys and a list of paths, relative to out_dir as values.

trs_cli.errors module

exception trs_cli.errors.ContentTypeUnavailable

Bases: Exception

Exception raised when an unavailable content type is requested.

exception trs_cli.errors.FileInformationUnavailable

Bases: Exception

Exception raised when information for a file associated with a descriptor is unavailable.

exception trs_cli.errors.InvalidResourceIdentifier

Bases: Exception

Exception raised for invalid tool/version identifiers.

exception trs_cli.errors.InvalidResponseError

Bases: Exception

Exception raised when an invalid API response is encountered.

exception trs_cli.errors.InvalidURI

Bases: Exception

Exception raised for invalid URIs.

trs_cli.errors.exception_handler(_type: type, value: BaseException, traceback: traceback, print_traceback: bool = False) → None

Error handler for all exceptions.

trs_cli.models module

class trs_cli.models.Checksum

Bases: trs_cli.models.CustomBaseModel

class trs_cli.models.ChecksumRegister

Bases: trs_cli.models.CustomBaseModel

class trs_cli.models.CustomBaseModel

Bases: pydantic.main.BaseModel

Settings subclass.

class Config

Bases: object

Configuration for pydantic model class.

arbitrary_types_allowed = False
extra = 'forbid'
class trs_cli.models.DescriptorType

Bases: str, enum.Enum

An enumeration.

CWL = 'CWL'
GALAXY = 'GALAXY'
NFL = 'NFL'
SMK = 'SMK'
WDL = 'WDL'
class trs_cli.models.Error

Bases: trs_cli.models.CustomBaseModel

class trs_cli.models.FileType

Bases: enum.Enum

An enumeration.

CONTAINERFILE = 'CONTAINERFILE'
OTHER = 'OTHER'
PRIMARY_DESCRIPTOR = 'PRIMARY_DESCRIPTOR'
SECONDARY_DESCRIPTOR = 'SECONDARY_DESCRIPTOR'
TEST_FILE = 'TEST_FILE'
class trs_cli.models.FileType1

Bases: enum.Enum

An enumeration.

CONTAINERFILE = 'CONTAINERFILE'
OTHER = 'OTHER'
PRIMARY_DESCRIPTOR = 'PRIMARY_DESCRIPTOR'
SECONDARY_DESCRIPTOR = 'SECONDARY_DESCRIPTOR'
TEST_FILE = 'TEST_FILE'
class trs_cli.models.FileWrapper

Bases: trs_cli.models.CustomBaseModel

class trs_cli.models.FileWrapperRegister

Bases: trs_cli.models.CustomBaseModel

class trs_cli.models.FilesRegister

Bases: trs_cli.models.CustomBaseModel

class trs_cli.models.ImageData

Bases: trs_cli.models.CustomBaseModel

class trs_cli.models.ImageDataRegister

Bases: trs_cli.models.CustomBaseModel

class trs_cli.models.ImageType

Bases: str, enum.Enum

An enumeration.

Conda = 'Conda'
Docker = 'Docker'
Singularity = 'Singularity'
class trs_cli.models.Organization

Bases: trs_cli.models.CustomBaseModel

class trs_cli.models.Organization1

Bases: trs_cli.models.CustomBaseModel

class trs_cli.models.OtherType

Bases: enum.Enum

An enumeration.

JSON = 'JSON'
OTHER = 'OTHER'
class trs_cli.models.Service

Bases: trs_cli.models.CustomBaseModel

class trs_cli.models.ServiceRegister

Bases: trs_cli.models.CustomBaseModel

class trs_cli.models.ServiceType

Bases: trs_cli.models.CustomBaseModel

class trs_cli.models.ServiceTypeRegister

Bases: trs_cli.models.CustomBaseModel

class trs_cli.models.Tool

Bases: trs_cli.models.CustomBaseModel

class trs_cli.models.ToolClass

Bases: trs_cli.models.CustomBaseModel

class trs_cli.models.ToolClassRegister

Bases: trs_cli.models.CustomBaseModel

class trs_cli.models.ToolClassRegisterId

Bases: trs_cli.models.CustomBaseModel

class trs_cli.models.ToolFile

Bases: trs_cli.models.CustomBaseModel

class trs_cli.models.ToolFileRegister

Bases: trs_cli.models.CustomBaseModel

class trs_cli.models.ToolRegister

Bases: trs_cli.models.CustomBaseModel

class trs_cli.models.ToolVersion

Bases: trs_cli.models.CustomBaseModel

class trs_cli.models.ToolVersionRegister

Bases: trs_cli.models.CustomBaseModel

class trs_cli.models.ToolVersionRegisterId

Bases: trs_cli.models.CustomBaseModel

class trs_cli.models.TypeRegister

Bases: trs_cli.models.CustomBaseModel