Make some fixes to API client

[juanneilson]

• Fix those tests that are failing in PR Adds methods for plates #43
• Implement plates functionalities on BUILD

Some methods fail because they are related to specific ids
Ex:

api-client/teselagen/api/tests/test_build_client.py

Lines 314 to 330 in 6070f52

	# TODO: It would be better to dynamically define IDs, so to not be restricted to a specific instance
	@pytest.mark.parametrize(
	'aliquot_id',
	[
	'13758', # Lab Group: Common
	'13760', # Lab Group: Common
	],
	ids=[
	'one_aliquot',
	'another_aliquot',
	],
	)
	def test_get_aliquot_by_id(
	self,
	aliquot_id: str,
	logged_build_client: BUILDClient,
	) -> None:

[juanneilson]

Failures

Test failures

=============================================================================== FAILURES ================================================================================
__________________________________________________________ TestBUILDClient.test_get_aliquot_by_id[one_aliquot] __________________________________________________________
[gw0] linux -- Python 3.9.9 /usr/bin/python3

self = <teselagen.api.build_client.BUILDClient object at 0x7f7be2fa5400>, aliquot_id = '13758'

    def get_aliquot(
        self,
        aliquot_id: AliquotID,
    ) -> AliquotRecord:
        """This function returns a single aliquot record.

        Args:
            aliquot_id (str): The id of the aliquot record you want to retrieve.

        Returns:
            AliquotRecord: Aliquot record.

        Raises:
            AliquotNotFoundError: If the aliquot record is not found.
        """
        output_aliquot: AliquotRecord | None = None

        try:
            url: str = self.aliquot_url.format(str(aliquot_id))
>           response: ResponseDict = get(
                url=url,
                headers=self.headers,
            )

teselagen/api/build_client.py:299:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

kwargs = {'headers': {'Content-Type': 'application/json', 'x-tg-cli-token': 'eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJ2ZXJzaW9uI...d9.480nPZ8hj0PhrD1KnWbRJCg7km-ipbP2ppedFTCwMHc'}, 'url': 'https://platform.teselagen.com/build/cli-api/aliquots/13758'}
url = 'https://platform.teselagen.com/build/cli-api/aliquots/13758'

    def wrapper(**kwargs: Any) -> Union[ParsedJSONResponse, Dict[str, Any]]:

        if 'url' not in kwargs.keys():
            raise Exception('url MUST be specified as keyword argument')

        url: str = kwargs['url']
>       response: requests.Response = func(**kwargs)

teselagen/utils/utils.py:362:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

kwargs = {'headers': {'Content-Type': 'application/json', 'x-tg-cli-token': 'eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJ2ZXJzaW9uI...X0NSRUFUT1IiLCJNRU1CRVIiXSwiaWF0IjoxNjUwNDg0OTk3LCJleHAiOjE2NTA0ODY3OTd9.480nPZ8hj0PhrD1KnWbRJCg7km-ipbP2ppedFTCwMHc'}}
url = 'https://platform.teselagen.com/build/cli-api/aliquots/13758', response = <Response [404]>

    def wrapper(**kwargs: Any) -> requests.Response:
        if 'url' not in kwargs.keys():
            raise Exception('url MUST be specified as keyword argument')

        url: str = kwargs.pop('url')

        try:
            response: requests.Response = func(url, **kwargs)

            if response.ok:
                return response

            elif response.status_code == 400:
                resp = json.loads(response.content)
                raise Exception(f"{response.reason}: {resp['error']}")

            elif response.status_code == 401:
                raise Exception(f'URL : {url} access is unauthorized.')

            elif response.status_code == 404:
>               raise Exception(f'URL : {url} cannot be found.')
E               Exception: URL : https://platform.teselagen.com/build/cli-api/aliquots/13758 cannot be found.

teselagen/utils/utils.py:337: Exception

The above exception was the direct cause of the following exception:

self = <teselagen.api.tests.test_build_client.TestBUILDClient object at 0x7f7be2fa59a0>, aliquot_id = '13758'
logged_build_client = <teselagen.api.build_client.BUILDClient object at 0x7f7be2fa5400>

    @pytest.mark.parametrize(
        'aliquot_id',
        [
            '13758',  # Lab Group: Common
            '13760',  # Lab Group: Common
        ],
        ids=[
            'one_aliquot',
            'another_aliquot',
        ],
    )
    def test_get_aliquot_by_id(
        self,
        aliquot_id: str,
        logged_build_client: BUILDClient,
    ) -> None:
        """Test getting aliquots by id."""
        client = logged_build_client

>       response = client.get_aliquot(aliquot_id=aliquot_id)

teselagen/api/tests/test_build_client.py:334:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <teselagen.api.build_client.BUILDClient object at 0x7f7be2fa5400>, aliquot_id = '13758'

    def get_aliquot(
        self,
        aliquot_id: AliquotID,
    ) -> AliquotRecord:
        """This function returns a single aliquot record.

        Args:
            aliquot_id (str): The id of the aliquot record you want to retrieve.

        Returns:
            AliquotRecord: Aliquot record.

        Raises:
            AliquotNotFoundError: If the aliquot record is not found.
        """
        output_aliquot: AliquotRecord | None = None

        try:
            url: str = self.aliquot_url.format(str(aliquot_id))
            response: ResponseDict = get(
                url=url,
                headers=self.headers,
            )
            assert response['content'] is not None  # noqa: S101
            output_aliquot = cast(AliquotRecord, json.loads(response['content']))

        except Exception as _exc:
            # fallback to bruteforce if an error occurs

            # NOTE: Since when using a method to get a single record, the user only have control over the id parameter,
            #       we can't use the same parameters as for the method to get many records. So, we choose to use the
            #       default parameters for the method to get many records.
            #       Except for the `gqlFilter` parameter, which is used for efficient querying.
            get_records = wrapped_partial(self.get_aliquots, gqlFilter=json.dumps({'id': str(aliquot_id)}))

            output_aliquot = get_record(
                get_records=get_records,
                record_id=aliquot_id,
            )

            if output_aliquot is None:
>               raise AliquotNotFoundError(f'Aliquot {aliquot_id} not found.') from _exc
E               teselagen.api.build_client.AliquotNotFoundError: Aliquot 13758 not found.

teselagen/api/build_client.py:321: AliquotNotFoundError
------------------------------------------------------------------------- Captured stdout setup -------------------------------------------------------------------------
Connection Accepted at https://platform.teselagen.com
Selected Lab: Common
----------------------------------------------------------------------- Captured stdout teardown ------------------------------------------------------------------------
Connection Accepted at https://platform.teselagen.com
________________________________________________________ TestBUILDClient.test_get_aliquot_by_id[another_aliquot] ________________________________________________________
[gw0] linux -- Python 3.9.9 /usr/bin/python3

self = <teselagen.api.build_client.BUILDClient object at 0x7f7be2f030d0>, aliquot_id = '13760'

    def get_aliquot(
        self,
        aliquot_id: AliquotID,
    ) -> AliquotRecord:
        """This function returns a single aliquot record.

        Args:
            aliquot_id (str): The id of the aliquot record you want to retrieve.

        Returns:
            AliquotRecord: Aliquot record.

        Raises:
            AliquotNotFoundError: If the aliquot record is not found.
        """
        output_aliquot: AliquotRecord | None = None

        try:
            url: str = self.aliquot_url.format(str(aliquot_id))
>           response: ResponseDict = get(
                url=url,
                headers=self.headers,
            )

teselagen/api/build_client.py:299:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

kwargs = {'headers': {'Content-Type': 'application/json', 'x-tg-cli-token': 'eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJ2ZXJzaW9uI...F9.ChtLr34NYtOLvqt7s4yPWoIxf49UFIrgG0kAtNaHy4o'}, 'url': 'https://platform.teselagen.com/build/cli-api/aliquots/13760'}
url = 'https://platform.teselagen.com/build/cli-api/aliquots/13760'

    def wrapper(**kwargs: Any) -> Union[ParsedJSONResponse, Dict[str, Any]]:

        if 'url' not in kwargs.keys():
            raise Exception('url MUST be specified as keyword argument')

        url: str = kwargs['url']
>       response: requests.Response = func(**kwargs)

teselagen/utils/utils.py:362:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

kwargs = {'headers': {'Content-Type': 'application/json', 'x-tg-cli-token': 'eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJ2ZXJzaW9uI...X0NSRUFUT1IiLCJNRU1CRVIiXSwiaWF0IjoxNjUwNDg1MDAxLCJleHAiOjE2NTA0ODY4MDF9.ChtLr34NYtOLvqt7s4yPWoIxf49UFIrgG0kAtNaHy4o'}}
url = 'https://platform.teselagen.com/build/cli-api/aliquots/13760', response = <Response [404]>

    def wrapper(**kwargs: Any) -> requests.Response:
        if 'url' not in kwargs.keys():
            raise Exception('url MUST be specified as keyword argument')

        url: str = kwargs.pop('url')

        try:
            response: requests.Response = func(url, **kwargs)

            if response.ok:
                return response

            elif response.status_code == 400:
                resp = json.loads(response.content)
                raise Exception(f"{response.reason}: {resp['error']}")

            elif response.status_code == 401:
                raise Exception(f'URL : {url} access is unauthorized.')

            elif response.status_code == 404:
>               raise Exception(f'URL : {url} cannot be found.')
E               Exception: URL : https://platform.teselagen.com/build/cli-api/aliquots/13760 cannot be found.

teselagen/utils/utils.py:337: Exception

The above exception was the direct cause of the following exception:

self = <teselagen.api.tests.test_build_client.TestBUILDClient object at 0x7f7be2f03a30>, aliquot_id = '13760'
logged_build_client = <teselagen.api.build_client.BUILDClient object at 0x7f7be2f030d0>

    @pytest.mark.parametrize(
        'aliquot_id',
        [
            '13758',  # Lab Group: Common
            '13760',  # Lab Group: Common
        ],
        ids=[
            'one_aliquot',
            'another_aliquot',
        ],
    )
    def test_get_aliquot_by_id(
        self,
        aliquot_id: str,
        logged_build_client: BUILDClient,
    ) -> None:
        """Test getting aliquots by id."""
        client = logged_build_client

>       response = client.get_aliquot(aliquot_id=aliquot_id)

teselagen/api/tests/test_build_client.py:334:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <teselagen.api.build_client.BUILDClient object at 0x7f7be2f030d0>, aliquot_id = '13760'

    def get_aliquot(
        self,
        aliquot_id: AliquotID,
    ) -> AliquotRecord:
        """This function returns a single aliquot record.

        Args:
            aliquot_id (str): The id of the aliquot record you want to retrieve.

        Returns:
            AliquotRecord: Aliquot record.

        Raises:
            AliquotNotFoundError: If the aliquot record is not found.
        """
        output_aliquot: AliquotRecord | None = None

        try:
            url: str = self.aliquot_url.format(str(aliquot_id))
            response: ResponseDict = get(
                url=url,
                headers=self.headers,
            )
            assert response['content'] is not None  # noqa: S101
            output_aliquot = cast(AliquotRecord, json.loads(response['content']))

        except Exception as _exc:
            # fallback to bruteforce if an error occurs

            # NOTE: Since when using a method to get a single record, the user only have control over the id parameter,
            #       we can't use the same parameters as for the method to get many records. So, we choose to use the
            #       default parameters for the method to get many records.
            #       Except for the `gqlFilter` parameter, which is used for efficient querying.
            get_records = wrapped_partial(self.get_aliquots, gqlFilter=json.dumps({'id': str(aliquot_id)}))

            output_aliquot = get_record(
                get_records=get_records,
                record_id=aliquot_id,
            )

            if output_aliquot is None:
>               raise AliquotNotFoundError(f'Aliquot {aliquot_id} not found.') from _exc
E               teselagen.api.build_client.AliquotNotFoundError: Aliquot 13760 not found.

teselagen/api/build_client.py:321: AliquotNotFoundError
------------------------------------------------------------------------- Captured stdout setup -------------------------------------------------------------------------
Connection Accepted at https://platform.teselagen.com
Selected Lab: Common
----------------------------------------------------------------------- Captured stdout teardown ------------------------------------------------------------------------
Connection Accepted at https://platform.teselagen.com
___________________________________________________________ TestBUILDClient.test_get_sample_by_id[one_sample] ___________________________________________________________
[gw0] linux -- Python 3.9.9 /usr/bin/python3

self = <teselagen.api.build_client.BUILDClient object at 0x7f7be2ef7250>, sample_id = '19152'

    def get_sample(
        self,
        sample_id: SampleID,
    ) -> SampleRecord:
        """This function returns a single sample by id.

        Args:
            sample_id (SampleID): The id of the sample to return.

        Returns:
            SampleRecord: Sample record.

        Raises:
            SampleNotFoundError: If the sample record is not found.
        """
        output_sample: SampleRecord | None = None

        try:
            url: str = self.sample_url.format(str(sample_id))
>           response: ResponseDict = get(
                url=url,
                headers=self.headers,
            )

teselagen/api/build_client.py:394:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

kwargs = {'headers': {'Content-Type': 'application/json', 'x-tg-cli-token': 'eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJ2ZXJzaW9uI...jV9.gLOIGeDjw-Le-lb5dkEW-LpFv1gWDfhBRyR6JtzNveY'}, 'url': 'https://platform.teselagen.com/build/cli-api/samples/19152'}
url = 'https://platform.teselagen.com/build/cli-api/samples/19152'

    def wrapper(**kwargs: Any) -> Union[ParsedJSONResponse, Dict[str, Any]]:

        if 'url' not in kwargs.keys():
            raise Exception('url MUST be specified as keyword argument')

        url: str = kwargs['url']
>       response: requests.Response = func(**kwargs)

teselagen/utils/utils.py:362:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

kwargs = {'headers': {'Content-Type': 'application/json', 'x-tg-cli-token': 'eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJ2ZXJzaW9uI...X0NSRUFUT1IiLCJNRU1CRVIiXSwiaWF0IjoxNjUwNDg1MDI1LCJleHAiOjE2NTA0ODY4MjV9.gLOIGeDjw-Le-lb5dkEW-LpFv1gWDfhBRyR6JtzNveY'}}
url = 'https://platform.teselagen.com/build/cli-api/samples/19152', response = <Response [404]>

    def wrapper(**kwargs: Any) -> requests.Response:
        if 'url' not in kwargs.keys():
            raise Exception('url MUST be specified as keyword argument')

        url: str = kwargs.pop('url')

        try:
            response: requests.Response = func(url, **kwargs)

            if response.ok:
                return response

            elif response.status_code == 400:
                resp = json.loads(response.content)
                raise Exception(f"{response.reason}: {resp['error']}")

            elif response.status_code == 401:
                raise Exception(f'URL : {url} access is unauthorized.')

            elif response.status_code == 404:
>               raise Exception(f'URL : {url} cannot be found.')
E               Exception: URL : https://platform.teselagen.com/build/cli-api/samples/19152 cannot be found.

teselagen/utils/utils.py:337: Exception

The above exception was the direct cause of the following exception:

self = <teselagen.api.tests.test_build_client.TestBUILDClient object at 0x7f7be2ef7e20>, sample_id = '19152'
logged_build_client = <teselagen.api.build_client.BUILDClient object at 0x7f7be2ef7250>

    @pytest.mark.parametrize(
        'sample_id',
        [
            '19152',  # Lab Group: Common
            '16457',  # Lab Group: Common
        ],
        ids=[
            'one_sample',
            'another_sample',
        ],
    )
    def test_get_sample_by_id(
        self,
        sample_id: str,
        logged_build_client: BUILDClient,
    ) -> None:
        """Test getting samples by id."""
        client = logged_build_client

>       response = client.get_sample(sample_id=sample_id)

teselagen/api/tests/test_build_client.py:403:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <teselagen.api.build_client.BUILDClient object at 0x7f7be2ef7250>, sample_id = '19152'

    def get_sample(
        self,
        sample_id: SampleID,
    ) -> SampleRecord:
        """This function returns a single sample by id.

        Args:
            sample_id (SampleID): The id of the sample to return.

        Returns:
            SampleRecord: Sample record.

        Raises:
            SampleNotFoundError: If the sample record is not found.
        """
        output_sample: SampleRecord | None = None

        try:
            url: str = self.sample_url.format(str(sample_id))
            response: ResponseDict = get(
                url=url,
                headers=self.headers,
            )
            assert response['content'] is not None  # noqa: S101
            output_sample = cast(SampleRecord, json.loads(response['content']))

        except Exception as _exc:
            # fallback to bruteforce if an error occurs

            # NOTE: Since when using a method to get a single record, the user only have control over the id parameter,
            #       we can't use the same parameters as for the method to get many records. So, we choose to use the
            #       default parameters for the method to get many records.
            #       Except for the `gqlFilter` parameter, which is used for efficient querying.
            get_records = wrapped_partial(self.get_samples, gqlFilter=json.dumps({'id': str(sample_id)}))

            output_sample = get_record(
                get_records=get_records,
                record_id=sample_id,
            )

            if output_sample is None:
>               raise SampleNotFoundError(f'Sample {sample_id} not found.') from _exc
E               teselagen.api.build_client.SampleNotFoundError: Sample 19152 not found.

teselagen/api/build_client.py:416: SampleNotFoundError
------------------------------------------------------------------------- Captured stdout setup -------------------------------------------------------------------------
Connection Accepted at https://platform.teselagen.com
Selected Lab: Common
----------------------------------------------------------------------- Captured stdout teardown ------------------------------------------------------------------------
Connection Accepted at https://platform.teselagen.com
_________________________________________________________ TestBUILDClient.test_get_sample_by_id[another_sample] _________________________________________________________
[gw0] linux -- Python 3.9.9 /usr/bin/python3

self = <teselagen.api.build_client.BUILDClient object at 0x7f7be2e587c0>, sample_id = '16457'

    def get_sample(
        self,
        sample_id: SampleID,
    ) -> SampleRecord:
        """This function returns a single sample by id.

        Args:
            sample_id (SampleID): The id of the sample to return.

        Returns:
            SampleRecord: Sample record.

        Raises:
            SampleNotFoundError: If the sample record is not found.
        """
        output_sample: SampleRecord | None = None

        try:
            url: str = self.sample_url.format(str(sample_id))
>           response: ResponseDict = get(
                url=url,
                headers=self.headers,
            )

teselagen/api/build_client.py:394:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

kwargs = {'headers': {'Content-Type': 'application/json', 'x-tg-cli-token': 'eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJ2ZXJzaW9uI...zB9.WHQCJ0y7sOfhryufd70jKUWSwsWtnnrUEE4KFqo4fJQ'}, 'url': 'https://platform.teselagen.com/build/cli-api/samples/16457'}
url = 'https://platform.teselagen.com/build/cli-api/samples/16457'

    def wrapper(**kwargs: Any) -> Union[ParsedJSONResponse, Dict[str, Any]]:

        if 'url' not in kwargs.keys():
            raise Exception('url MUST be specified as keyword argument')

        url: str = kwargs['url']
>       response: requests.Response = func(**kwargs)

teselagen/utils/utils.py:362:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

kwargs = {'headers': {'Content-Type': 'application/json', 'x-tg-cli-token': 'eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJ2ZXJzaW9uI...X0NSRUFUT1IiLCJNRU1CRVIiXSwiaWF0IjoxNjUwNDg1MDMwLCJleHAiOjE2NTA0ODY4MzB9.WHQCJ0y7sOfhryufd70jKUWSwsWtnnrUEE4KFqo4fJQ'}}
url = 'https://platform.teselagen.com/build/cli-api/samples/16457', response = <Response [404]>

    def wrapper(**kwargs: Any) -> requests.Response:
        if 'url' not in kwargs.keys():
            raise Exception('url MUST be specified as keyword argument')

        url: str = kwargs.pop('url')

        try:
            response: requests.Response = func(url, **kwargs)

            if response.ok:
                return response

            elif response.status_code == 400:
                resp = json.loads(response.content)
                raise Exception(f"{response.reason}: {resp['error']}")

            elif response.status_code == 401:
                raise Exception(f'URL : {url} access is unauthorized.')

            elif response.status_code == 404:
>               raise Exception(f'URL : {url} cannot be found.')
E               Exception: URL : https://platform.teselagen.com/build/cli-api/samples/16457 cannot be found.

teselagen/utils/utils.py:337: Exception

The above exception was the direct cause of the following exception:

self = <teselagen.api.tests.test_build_client.TestBUILDClient object at 0x7f7be2e58be0>, sample_id = '16457'
logged_build_client = <teselagen.api.build_client.BUILDClient object at 0x7f7be2e587c0>

    @pytest.mark.parametrize(
        'sample_id',
        [
            '19152',  # Lab Group: Common
            '16457',  # Lab Group: Common
        ],
        ids=[
            'one_sample',
            'another_sample',
        ],
    )
    def test_get_sample_by_id(
        self,
        sample_id: str,
        logged_build_client: BUILDClient,
    ) -> None:
        """Test getting samples by id."""
        client = logged_build_client

>       response = client.get_sample(sample_id=sample_id)

teselagen/api/tests/test_build_client.py:403:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <teselagen.api.build_client.BUILDClient object at 0x7f7be2e587c0>, sample_id = '16457'

    def get_sample(
        self,
        sample_id: SampleID,
    ) -> SampleRecord:
        """This function returns a single sample by id.

        Args:
            sample_id (SampleID): The id of the sample to return.

        Returns:
            SampleRecord: Sample record.

        Raises:
            SampleNotFoundError: If the sample record is not found.
        """
        output_sample: SampleRecord | None = None

        try:
            url: str = self.sample_url.format(str(sample_id))
            response: ResponseDict = get(
                url=url,
                headers=self.headers,
            )
            assert response['content'] is not None  # noqa: S101
            output_sample = cast(SampleRecord, json.loads(response['content']))

        except Exception as _exc:
            # fallback to bruteforce if an error occurs

            # NOTE: Since when using a method to get a single record, the user only have control over the id parameter,
            #       we can't use the same parameters as for the method to get many records. So, we choose to use the
            #       default parameters for the method to get many records.
            #       Except for the `gqlFilter` parameter, which is used for efficient querying.
            get_records = wrapped_partial(self.get_samples, gqlFilter=json.dumps({'id': str(sample_id)}))

            output_sample = get_record(
                get_records=get_records,
                record_id=sample_id,
            )

            if output_sample is None:
>               raise SampleNotFoundError(f'Sample {sample_id} not found.') from _exc
E               teselagen.api.build_client.SampleNotFoundError: Sample 16457 not found.

teselagen/api/build_client.py:416: SampleNotFoundError
------------------------------------------------------------------------- Captured stdout setup -------------------------------------------------------------------------
Connection Accepted at https://platform.teselagen.com
Selected Lab: Common
----------------------------------------------------------------------- Captured stdout teardown ------------------------------------------------------------------------
Connection Accepted at https://platform.teselagen.com
__________________________________________________________________ TestTESTClient.test_get_experiments __________________________________________________________________
[gw0] linux -- Python 3.9.9 /usr/bin/python3

self = <teselagen.api.tests.test_test_client.TestTESTClient object at 0x7f7be2e02eb0>, logged_client = <teselagen.api.client.TeselaGenClient object at 0x7f7be2e02a60>
select_laboratory = None

    def test_get_experiments(
        self,
        logged_client: TeselaGenClient,
        select_laboratory,
    ) -> None:
        client: TESTClient = logged_client.test
        response = client.get_experiments()

        assert isinstance(response, list)
>       assert len(response) > 0
E       assert 0 > 0
E        +  where 0 = len([])

teselagen/api/tests/test_test_client.py:302: AssertionError
------------------------------------------------------------------------- Captured stdout setup -------------------------------------------------------------------------
Connection Accepted at https://platform.teselagen.com
Selected Lab: P&G
----------------------------------------------------------------------- Captured stdout teardown ------------------------------------------------------------------------
Connection Accepted at https://platform.teselagen.com
___________________________________________________________ notebook: nbregression(Hello_World_BUILD_module) ____________________________________________________________
[gw0] linux -- Python 3.9.9 /usr/bin/python3
nbconvert.preprocessors.execute.CellExecutionError: An error occurred while executing the following cell:
------------------
list(features)
------------------

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
/tmp/ipykernel_85020/715497681.py in <module>
----> 1 list(features)

NameError: name 'features' is not defined
NameError: name 'features' is not defined
------------------------------------------------------------------------- Captured stderr call --------------------------------------------------------------------------
Diff up to exception:

--- expected
+++ obtained

___________________________________________________________ notebook: nbregression(Hello_World_DESIGN_module) ___________________________________________________________
[gw0] linux -- Python 3.9.9 /usr/bin/python3
nbconvert.preprocessors.execute.CellExecutionError: An error occurred while executing the following cell:
------------------
# The following list contains a list with the uploaded sequence id
ids_list = [int(result['existingAminoAcidSequences'][0]['id'])]
result = client.design.export_aa_sequences(ids_list)
------------------

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
/tmp/ipykernel_85183/255074899.py in <module>
      1 # The following list contains a list with the uploaded sequence id
----> 2 ids_list = [int(result['existingAminoAcidSequences'][0]['id'])]
      3 result = client.design.export_aa_sequences(ids_list)

ValueError: invalid literal for int() with base 10: '7b241b27-ddaf-4c8b-b19c-33c5f264a813'
ValueError: invalid literal for int() with base 10: '7b241b27-ddaf-4c8b-b19c-33c5f264a813'
------------------------------------------------------------------------- Captured stderr call --------------------------------------------------------------------------
Diff up to exception:

--- expected
+++ obtained

=========================================================================== warnings summary ============================================================================
../usr/local/lib/python3.9/dist-packages/pytest_notebook/notebook.py:145
  /usr/local/lib/python3.9/dist-packages/pytest_notebook/notebook.py:145: DeprecationWarning: read_text is deprecated. Use files() instead. Refer to https://importlib-resources.readthedocs.io/en/latest/using.html#migrating-from-legacy for migration advice.
    importlib_resources.read_text(resources, "nb_metadata.schema.json")

../usr/local/lib/python3.9/dist-packages/importlib_resources/_legacy.py:80
  /usr/local/lib/python3.9/dist-packages/importlib_resources/_legacy.py:80: DeprecationWarning: open_text is deprecated. Use files() instead. Refer to https://importlib-resources.readthedocs.io/en/latest/using.html#migrating-from-legacy for migration advice.
    with open_text(package, resource, encoding, errors) as fp:

teselagen/api/tests/test_build_client.py::TestBUILDClient::test_get_aliquots_with_default_query_params
conftest.py:112
conftest.py:112
  /home/conftest.py:112: UserWarning: Host URL was set to: https://platform.teselagen.com/
    warnings.warn(f"Host URL was set to: {configuration['host_url']}")

teselagen/api/tests/test_build_client.py::TestBUILDClient::test_get_aliquot_by_id[one_aliquot]
teselagen/api/tests/test_build_client.py::TestBUILDClient::test_get_aliquot_by_id[another_aliquot]
  /home/teselagen/api/build_client.py:221: UserWarning: An error occured while calling get_aliquots, fallback to bruteforce.
    warnings.warn(f'An error occured while calling {get_func_name(get_records)}, fallback to bruteforce.')

teselagen/api/tests/test_build_client.py::TestBUILDClient::test_get_sample_by_id[one_sample]
teselagen/api/tests/test_build_client.py::TestBUILDClient::test_get_sample_by_id[another_sample]
  /home/teselagen/api/build_client.py:221: UserWarning: An error occured while calling get_samples, fallback to bruteforce.
    warnings.warn(f'An error occured while calling {get_func_name(get_records)}, fallback to bruteforce.')

teselagen/examples/pytested/CRISPR-Tool.ipynb: 9 warnings
teselagen/examples/pytested/Closing-the-DBTL-Cycle.ipynb: 7 warnings
teselagen/examples/pytested/Hello-World-TEST-module.ipynb: 14 warnings
teselagen/examples/pytested/Hello_World_BUILD_module.ipynb: 10 warnings
teselagen/examples/pytested/Hello_World_DESIGN_module.ipynb: 18 warnings
  /usr/local/lib/python3.9/dist-packages/jsonschema/validators.py:188: DeprecationWarning: Passing a schema to Validator.iter_errors is deprecated and will be removed in a future release. Call validator.evolve(schema=new_schema).iter_errors(...) instead.
    warnings.warn(

-- Docs: https://docs.pytest.org/en/stable/warnings.html
========================================================================= slowest 10 durations ==========================================================================
252.04s call     teselagen/examples/pytested/Hello_World_DESIGN_module.ipynb::nbregression(Hello_World_DESIGN_module)
23.10s call     teselagen/examples/pytested/CRISPR-Tool.ipynb::nbregression(CRISPR-Tool)
22.58s call     teselagen/api/tests/test_discover_client.py::TestDISCOVERClient::test_design_crispr_grnas
20.22s setup    teselagen/api/tests/test_multiomics.py::TestTESTClientMultiomicsData::test_experiment_description_upload
18.96s call     teselagen/examples/pytested/Hello_World_BUILD_module.ipynb::nbregression(Hello_World_BUILD_module)
15.41s setup    teselagen/api/tests/test_multiomics.py::TestTESTClientMultiomicsData::test_upload_transcriptomics
14.71s setup    teselagen/api/tests/test_multiomics.py::TestTESTClientMultiomicsData::test_upload_external_metabolites
13.12s call     teselagen/examples/pytested/Hello-World-TEST-module.ipynb::nbregression(Hello-World-TEST-module)
10.11s setup    teselagen/api/tests/test_multiomics.py::TestTESTClientMultiomicsData::test_optical_density_upload
10.08s call     teselagen/api/tests/test_multiomics.py::TestTESTClientMultiomicsData::test_download_data
======================================================================== short test summary info ========================================================================
SKIPPED [1] teselagen/api/tests/test_client.py:192: Implement Test
SKIPPED [1] teselagen/api/tests/test_design_client.py:145: This test should be skipped until we have some way to ensure there is a report in database
SKIPPED [1] teselagen/api/tests/test_design_client.py:184: This test should be skipped until we know a dna sequence id in db
SKIPPED [1] teselagen/api/tests/test_test_client.py:391: We need to create a test experiment first
SKIPPED [1] teselagen/api/tests/test_test_client.py:429: We don't know which experiment and parser IDs to use
FAILED teselagen/api/tests/test_build_client.py::TestBUILDClient::test_get_aliquot_by_id[one_aliquot] - teselagen.api.build_client.AliquotNotFoundError: Aliquot 13758...
FAILED teselagen/api/tests/test_build_client.py::TestBUILDClient::test_get_aliquot_by_id[another_aliquot] - teselagen.api.build_client.AliquotNotFoundError: Aliquot 1...
FAILED teselagen/api/tests/test_build_client.py::TestBUILDClient::test_get_sample_by_id[one_sample] - teselagen.api.build_client.SampleNotFoundError: Sample 19152 not...
FAILED teselagen/api/tests/test_build_client.py::TestBUILDClient::test_get_sample_by_id[another_sample] - teselagen.api.build_client.SampleNotFoundError: Sample 16457...
FAILED teselagen/api/tests/test_test_client.py::TestTESTClient::test_get_experiments - assert 0 > 0
FAILED teselagen/examples/pytested/Hello_World_BUILD_module.ipynb::nbregression(Hello_World_BUILD_module)
FAILED teselagen/examples/pytested/Hello_World_DESIGN_module.ipynb::nbregression(Hello_World_DESIGN_module)