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