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client.py
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"""Class implementing TRS client."""
import json
import logging
from pathlib import Path
import re
import socket
import sys
from typing import (Dict, List, Optional, Tuple, Type, Union)
import urllib3
from urllib.parse import quote
import pydantic
from pydantic.main import ModelMetaclass
import requests
from trs_cli.errors import (
exception_handler,
ContentTypeUnavailable,
FileInformationUnavailable,
InvalidURI,
InvalidResourceIdentifier,
InvalidResponseError,
)
from trs_cli.models import (
Error,
FileType,
FileWrapper,
Service,
ServiceRegister,
Tool,
ToolClass,
ToolClassRegister,
ToolFile,
ToolRegister,
ToolVersion,
ToolVersionRegister,
)
logger = logging.getLogger(__name__)
sys.excepthook = exception_handler
class TRSClient():
"""Client to communicate with a GA4GH TRS instance. Supports additional
endpoints defined in TRS-Filer
(https://github.com/elixir-cloud-aai/trs-filer).
Arguments:
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.
Attributes:
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.
"""
# set regular expressions as private class variables
_RE_DOMAIN_PART = r'[a-z0-9]([a-z0-9-]{,61}[a-z0-9])?'
_RE_DOMAIN = rf"({_RE_DOMAIN_PART}\.)+{_RE_DOMAIN_PART}\.?"
_RE_TRS_ID = r'([a-z0-9-_~\.%#]+)'
_RE_VERSION_ID = rf"^(?P<version_id>{_RE_TRS_ID})$"
_RE_HOST = (
rf"^(?P<schema>trs|http|https):\/\/(?P<host>{_RE_DOMAIN})(\/\S+)?$"
)
_RE_TRS_URI_OR_TOOL_ID = (
rf"^(trs:\/\/{_RE_DOMAIN}\/)?(?P<tool_id>{_RE_TRS_ID})"
rf"(\/versions\/(?P<version_id>{_RE_TRS_ID}))?$"
)
def __init__(
self,
uri: str,
port: int = None,
base_path: str = 'ga4gh/trs/v2',
use_http: bool = False,
token: Optional[str] = None,
) -> None:
"""Class constructor."""
schema, host = self._get_host(uri)
if schema == 'trs':
schema = 'http' if use_http else 'https'
if port is None:
port = 80 if schema == 'http' else 443
self.uri = f"{schema}://{host}:{port}/{base_path}"
self.token = token
self.headers = {}
logger.info(f"Instantiated client for: {self.uri}")
def post_service_info(
self,
payload: Dict,
token: Optional[str] = None,
) -> None:
"""Register service info.
Arguments:
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.
"""
# validate requested content type and get request headers
self._get_headers(
content_type='application/json',
token=token,
)
# build request URL
url = f"{self.uri}/service-info"
logger.info(f"Connecting to '{url}'...")
# validate payload
ServiceRegister(**payload).dict()
# send request
response = self._send_request_and_validate_response(
url=url,
method='post',
payload=payload,
)
logger.info(
"Registered service info"
)
return response # type: ignore
def get_service_info(
self,
accept: str = 'application/json',
token: Optional[str] = None,
) -> Union[Service, Error]:
"""Retrieve service info.
Arguments:
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.
"""
# validate requested content type and get request headers
self._validate_content_type(
requested_type=accept,
available_types=['application/json', 'text/plain'],
)
self._get_headers(
content_accept=accept,
token=token,
)
# build request URL
url = f"{self.uri}/service-info"
logger.info(f"Connecting to '{url}'...")
# send request
response = self._send_request_and_validate_response(
url=url,
validation_class_ok=Service,
)
logger.info(
"Retrieved service info"
)
return response # type: ignore
def post_tool_class(
self,
payload: Dict,
accept: str = 'application/json',
token: Optional[str] = None,
) -> str:
"""Register a tool class.
Arguments:
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.
"""
# validate requested content type and get request headers
self._validate_content_type(
requested_type=accept,
available_types=['application/json'],
)
self._get_headers(
content_accept=accept,
content_type='application/json',
token=token,
)
# build request URL
url = f"{self.uri}/toolClasses"
logger.info(f"Connecting to '{url}'...")
# validate payload
ToolClassRegister(**payload).dict()
# send request
response = self._send_request_and_validate_response(
url=url,
method='post',
payload=payload,
validation_class_ok=str,
)
logger.info(
"Registered tool class"
)
return response # type: ignore
def put_tool_class(
self,
id: str,
payload: Dict,
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.
Arguments:
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.
"""
# validate requested content type and get request headers
self._validate_content_type(
requested_type=accept,
available_types=['application/json'],
)
self._get_headers(
content_accept=accept,
content_type='application/json',
token=token,
)
# build request URL
url = f"{self.uri}/toolClasses/{id}"
logger.info(f"Connecting to '{url}'...")
# validate payload
ToolClassRegister(**payload).dict()
# send request
response = self._send_request_and_validate_response(
url=url,
method='put',
payload=payload,
validation_class_ok=str,
)
logger.info(
f"Registered tool class with id : {id}"
)
return response # type: ignore
def delete_tool_class(
self,
id: str,
accept: str = 'application/json',
token: Optional[str] = None,
) -> str:
"""Delete a tool class.
Arguments:
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.
"""
# validate requested content type and get request headers
self._validate_content_type(
requested_type=accept,
available_types=['application/json'],
)
self._get_headers(
content_accept=accept,
token=token,
)
# build request URL
url = f"{self.uri}/toolClasses/{id}"
logger.info(f"Connecting to '{url}'...")
# send request
response = self._send_request_and_validate_response(
url=url,
method='delete',
validation_class_ok=str,
)
logger.info(
"Deleted tool class"
)
return response # type: ignore
def post_tool(
self,
payload: Dict,
accept: str = 'application/json',
token: Optional[str] = None,
) -> str:
"""Register a tool.
Arguments:
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.
"""
# validate requested content type and get request headers
self._validate_content_type(
requested_type=accept,
available_types=['application/json'],
)
self._get_headers(
content_accept=accept,
content_type='application/json',
token=token,
)
# build request URL
url = f"{self.uri}/tools"
logger.info(f"Connecting to '{url}'...")
# validate payload
ToolRegister(**payload).dict()
# send request
response = self._send_request_and_validate_response(
url=url,
method='post',
payload=payload,
validation_class_ok=str,
)
logger.info(
"Registered tool"
)
return response # type: ignore
def put_tool(
self,
id: str,
payload: Dict,
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.
Arguments:
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.
"""
# validate requested content type and get request headers
self._validate_content_type(
requested_type=accept,
available_types=['application/json'],
)
self._get_headers(
content_accept=accept,
content_type='application/json',
token=token,
)
# build request URL
url = f"{self.uri}/tools/{id}"
logger.info(f"Connecting to '{url}'...")
# validate payload
ToolRegister(**payload).dict()
# send request
response = self._send_request_and_validate_response(
url=url,
method='put',
payload=payload,
validation_class_ok=str,
)
logger.info(
f"Registered tool with id: {id}"
)
return response # type: ignore
def delete_tool(
self,
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.
"""
# validate requested content type and get request headers
self._validate_content_type(
requested_type=accept,
available_types=['application/json'],
)
self._get_headers(
content_accept=accept,
token=token,
)
# get/sanitize tool and version identifiers
_id, _ = self._get_tool_id_version_id(tool_id=id)
# build request URL
url = f"{self.uri}/tools/{_id}"
logger.info(f"Connecting to '{url}'...")
# send request
response = self._send_request_and_validate_response(
url=url,
method='delete',
validation_class_ok=str,
)
logger.info(
"Deleted tool"
)
return response # type: ignore
def post_version(
self,
id: str,
payload: Dict,
accept: str = 'application/json',
token: Optional[str] = None,
) -> str:
"""Register a tool version.
Arguments:
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.
"""
# validate requested content type and get request headers
self._validate_content_type(
requested_type=accept,
available_types=['application/json'],
)
self._get_headers(
content_accept=accept,
content_type='application/json',
token=token,
)
# build request URL
url = f"{self.uri}/tools/{id}/versions"
logger.info(f"Connecting to '{url}'...")
# validate payload
ToolVersionRegister(**payload).dict()
# send request
response = self._send_request_and_validate_response(
url=url,
method='post',
payload=payload,
validation_class_ok=str,
)
logger.info(
"Registered tool version"
)
return response # type: ignore
def put_version(
self,
id: str,
version_id: str,
payload: Dict,
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.
Arguments:
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.
"""
# validate requested content type and get request headers
self._validate_content_type(
requested_type=accept,
available_types=['application/json'],
)
self._get_headers(
content_accept=accept,
content_type='application/json',
token=token,
)
# build request URL
url = f"{self.uri}/tools/{id}/versions/{version_id}"
logger.info(f"Connecting to '{url}'...")
# validate payload
ToolVersionRegister(**payload).dict()
# send request
response = self._send_request_and_validate_response(
url=url,
method='put',
payload=payload,
validation_class_ok=str,
)
logger.info(
f"Registered tool version with id {version_id} for tool {id}"
)
return response # type: ignore
def delete_version(
self,
id: str,
version_id: Optional[str] = None,
accept: str = 'application/json',
token: Optional[str] = None,
) -> str:
"""Delete a tool version.
Arguments:
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.
"""
# validate requested content type and get request headers
self._validate_content_type(
requested_type=accept,
available_types=['application/json'],
)
self._get_headers(
content_accept=accept,
content_type='application/json',
token=token,
)
# get/sanitize tool and version identifiers
_id, _version_id = self._get_tool_id_version_id(
tool_id=id,
version_id=version_id,
)
# build request URL
url = f"{self.uri}/tools/{_id}/versions/{_version_id}"
logger.info(f"Connecting to '{url}'...")
# send request
response = self._send_request_and_validate_response(
url=url,
method='delete',
validation_class_ok=str,
)
logger.info(
"Deleted tool version"
)
return response # type: ignore
def get_tool_classes(
self,
accept: str = 'application/json',
token: Optional[str] = None
) -> Union[List[ToolClass], Error]:
"""Retrieve tool classes.
Arguments:
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.
"""
# validate requested content type and get request headers
self._validate_content_type(
requested_type=accept,
available_types=['application/json', 'text/plain'],
)
self._get_headers(
content_accept=accept,
token=token,
)
# build request URL
url = f"{self.uri}/toolClasses"
logger.info(f"Connecting to '{url}'...")
# send request
response = self._send_request_and_validate_response(
url=url,
validation_class_ok=(ToolClass, ),
)
logger.info(
"Retrieved tool classes"
)
return response # type: ignore
def get_tools(
self,
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[Tool], Error]:
"""List all tools.
Filter parameters to subset the tools list can be specified. Filter
parameters are additive.
Args:
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.
"""
# validate requested content type and get request headers
self._validate_content_type(
requested_type=accept,
available_types=['application/json', 'text/plain'],
)
self._get_headers(
content_accept=accept,
token=token,
)
# build request URL
query_args = (
'id',
'alias',
'toolClass',
'descriptorType',
'registry',
'organization',
'name',
'toolname',
'description',
'author',
'checker',
'limit',
'offset',
)
query_params = '&'.join(
[
f"{k}={quote(str(v), safe='')}"
for k, v in locals().items()
if k in query_args
and v is not None
]
)
url = '?'.join(filter(None, [f"{self.uri}/tools", query_params]))
logger.info(f"Connecting to '{url}'...")
# send request
response = self._send_request_and_validate_response(
url=url,
validation_class_ok=(Tool, ),
)
logger.info(
"Retrieved tools"
)
return response # type: ignore
def get_tool(
self,
id: str,
accept: str = 'application/json',
token: Optional[str] = None,
) -> Union[Tool, Error]:
"""Retrieve tool with the specified identifier.
Arguments:
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` 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.
"""
# validate requested content type and get request headers
self._validate_content_type(
requested_type=accept,
available_types=['application/json', 'text/plain'],
)
self._get_headers(
content_accept=accept,
token=token,
)
# get/sanitize tool identifier
_id, _ = self._get_tool_id_version_id(tool_id=id)
# build request URL
url = f"{self.uri}/tools/{_id}"
logger.info(f"Connecting to '{url}'...")
# send request
response = self._send_request_and_validate_response(
url=url,
validation_class_ok=Tool,
)
logger.info(
"Retrieved tool"
)
return response # type: ignore
def get_versions(
self,
id: str,
accept: str = 'application/json',
token: Optional[str] = None,
) -> Union[List[ToolVersion], Error]:
"""Returns all versions of the specified tool..
Arguments:
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.
"""
# validate requested content type and get request headers
self._validate_content_type(
requested_type=accept,
available_types=['application/json', 'text/plain'],
)
self._get_headers(
content_accept=accept,
token=token,
)
# get/sanitize tool identifier
_id, _ = self._get_tool_id_version_id(tool_id=id)
# build request URL
url = f"{self.uri}/tools/{_id}/versions"
logger.info(f"Connecting to '{url}'...")
# send request
response = self._send_request_and_validate_response(
url=url,
validation_class_ok=(ToolVersion, ),
)
logger.info(
"Retrieved tool versions"
)
return response # type: ignore
def get_version(
self,
id: str,
version_id: Optional[str] = None,
accept: str = 'application/json',
token: Optional[str] = None,
) -> Union[ToolVersion, Error]: