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¶
Bases:
Exception
Exception raised when an unavailable content type is requested.
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
¶
-
class
trs_cli.models.
ChecksumRegister
¶
-
class
trs_cli.models.
CustomBaseModel
¶ Bases:
pydantic.main.BaseModel
Settings subclass.
-
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
¶
-
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
¶
-
class
trs_cli.models.
FileWrapperRegister
¶
-
class
trs_cli.models.
FilesRegister
¶
-
class
trs_cli.models.
ImageData
¶
-
class
trs_cli.models.
ImageDataRegister
¶
-
class
trs_cli.models.
ImageType
¶ Bases:
str
,enum.Enum
An enumeration.
-
Conda
= 'Conda'¶
-
Docker
= 'Docker'¶
-
Singularity
= 'Singularity'¶
-
-
class
trs_cli.models.
Organization
¶
-
class
trs_cli.models.
Organization1
¶
-
class
trs_cli.models.
Service
¶
-
class
trs_cli.models.
ServiceRegister
¶
-
class
trs_cli.models.
ServiceType
¶
-
class
trs_cli.models.
ServiceTypeRegister
¶
-
class
trs_cli.models.
Tool
¶
-
class
trs_cli.models.
ToolClass
¶
-
class
trs_cli.models.
ToolClassRegister
¶
-
class
trs_cli.models.
ToolClassRegisterId
¶
-
class
trs_cli.models.
ToolFile
¶
-
class
trs_cli.models.
ToolFileRegister
¶
-
class
trs_cli.models.
ToolRegister
¶
-
class
trs_cli.models.
ToolVersion
¶
-
class
trs_cli.models.
ToolVersionRegister
¶
-
class
trs_cli.models.
ToolVersionRegisterId
¶
-
class
trs_cli.models.
TypeRegister
¶