pybiolib 1.1.2123__py3-none-any.whl → 1.1.2135__py3-none-any.whl

biolib/__init__.py

@@ -12,7 +12,7 @@ from biolib.experiments.experiment import Experiment
 from biolib.biolib_api_client import BiolibApiClient as _BioLibApiClient, App
 from biolib.jobs import Job as _Job
 from biolib import user as _user
-from biolib.typing_utils import List, Optional
+from biolib.typing_utils import List, Optional, cast as _cast
 from biolib._data_record.data_record import DataRecord as _DataRecord
 
 import biolib.api
@@ -57,8 +57,11 @@ def fetch_data_records(uri: Optional[str] = None, count: Optional[int] = None) -
     return _DataRecord.fetch(uri, count)
 
 
-def get_experiment(name: str) -> Experiment:
-    return Experiment(name)
+def get_experiment(uri: Optional[str] = None, name: Optional[str] = None) -> Experiment:
+    if (not uri and not name) or (uri and name):
+        raise ValueError('Must provide either uri or name')
+
+    return Experiment.get_by_uri(uri=_cast(str, uri or name))
 
 
 def show_jobs(count: int = 25) -> None:

biolib/_internal/types/__init__.py

@@ -1 +1,2 @@
-from .resources import *  # noqa: F403
+from .data_record import *  # noqa: F403
+from .resource import *  # noqa: F403

biolib/_internal/types/data_record.py

@@ -0,0 +1,12 @@
+from .typing import Dict, List, TypedDict
+
+
+class DataRecordValidationRuleDict(TypedDict):
+    path: str
+    type: str
+    rule: Dict
+
+
+class DataRecordTypeDict(TypedDict):
+    name: str
+    validation_rules: List[Dict]

biolib/experiments/experiment.py

@@ -3,9 +3,7 @@ from collections import OrderedDict
 
 import biolib._internal.types as _types
 from biolib import api
-from biolib._internal.http_client import HttpError
-from biolib.biolib_errors import BioLibError, NotFound
-from biolib.experiments.types import ExperimentDict
+from biolib.biolib_errors import BioLibError
 from biolib.jobs.job import Job
 from biolib.jobs.types import JobsPaginatedResponse
 from biolib.tables import BioLibTable
@@ -24,11 +22,8 @@ class Experiment:
         }
     )
 
-    def __init__(self, uri: str, _experiment_dict: Optional[ExperimentDict] = None):
-        if not _experiment_dict:
-            self._experiment_dict: ExperimentDict = self._get_or_create_by_uri(uri)
-        else:
-            self._experiment_dict = _experiment_dict
+    def __init__(self, uri: str, _resource_dict: Optional[_types.ResourceDict] = None):
+        self._resource_dict: _types.ResourceDict = _resource_dict or self._get_or_create_resource_dict(uri)
 
     def __enter__(self):
         Experiment._BIOLIB_EXPERIMENTS.append(self)
@@ -37,18 +32,29 @@ class Experiment:
         Experiment._BIOLIB_EXPERIMENTS.pop()
 
     def __str__(self):
-        return f'Experiment: {self.name}'
+        return f'Experiment: {self.uri}'
 
     def __repr__(self):
-        return f'Experiment: {self.name}'
+        return f'Experiment: {self.uri}'
 
     @property
     def uuid(self) -> str:
-        return self._experiment_dict['uuid']
+        return self._resource_dict['uuid']
 
     @property
     def name(self) -> str:
-        return self._experiment_dict['name']
+        return self._resource_dict['name']
+
+    @property
+    def uri(self) -> str:
+        return self._resource_dict['uri']
+
+    @property
+    def _experiment_dict(self) -> _types.ExperimentDict:
+        if not self._resource_dict['experiment']:
+            raise ValueError(f'Resource {self.uri} is not an Experiment')
+
+        return self._resource_dict['experiment']
 
     @staticmethod
     def get_experiment_in_context() -> Optional['Experiment']:
@@ -68,25 +74,19 @@ class Experiment:
 
     @staticmethod
     def get_by_uri(uri: str) -> 'Experiment':
-        resource_dict: _types.ResourceDict = api.client.get('/resources/', params={'uri': uri}).json()
+        query_param_key = 'uri' if '/' in uri else 'name'
+        resource_dict: _types.ResourceDict = api.client.get('/resource/', params={query_param_key: uri}).json()
         if not resource_dict['experiment']:
-            raise ValueError('Resource from URI is not an experiment')
+            raise ValueError(f'Resource {uri} is not an experiment')
 
-        legacy_experiment_dict = ExperimentDict(
-            created_at=resource_dict['created_at'],
-            job_count=resource_dict['experiment']['job_count'],
-            job_running_count=resource_dict['experiment']['job_running_count'],
-            name=resource_dict['name'],
-            uuid=resource_dict['uuid'],
-        )
-        return Experiment(uri=resource_dict['uri'], _experiment_dict=legacy_experiment_dict)
+        return Experiment(uri=resource_dict['uri'], _resource_dict=resource_dict)
 
     def wait(self) -> None:
-        self._refetch_experiment_dict()
+        self._refetch()
         while self._experiment_dict['job_running_count'] > 0:
             print(f"Waiting for {self._experiment_dict['job_running_count']} jobs to finish", end='\r')
             time.sleep(5)
-            self._refetch_experiment_dict()
+            self._refetch()
 
         print(f'All jobs of experiment {self.name} have finished')
 
@@ -171,34 +171,22 @@ class Experiment:
 
         return jobs
 
-    def rename(self, name: Optional[str] = None, destination: Optional[str] = None) -> None:
-        if destination:
-            try:
-                account_id = api.client.get(path=f'/account/{destination}/').json()['uuid']
-            except HttpError as error:
-                if error.code == 404:
-                    raise NotFound(f'Destination "{destination}" not found.') from None
-                else:
-                    raise error
-
-            api.client.patch(
-                path=f'/apps/{self.uuid}/',
-                data={'account_id': account_id},
-                params={'resource_type': 'experiment'},
-            )
+    def rename(self, destination: str) -> None:
+        api.client.patch(f'/resources/{self.uuid}/', data={'uri': destination})
+        self._refetch()
 
-        if name:
-            api.client.patch(path=f'/apps/{self.uuid}/', data={'name': name}, params={'resource_type': 'experiment'})
+    @staticmethod
+    def _get_resource_dict_by_uuid(uuid: str) -> _types.ResourceDict:
+        resource_dict: _types.ResourceDict = api.client.get(f'/resources/{uuid}/').json()
+        if not resource_dict['experiment']:
+            raise ValueError('Resource from URI is not an experiment')
 
-        self._refetch_experiment_dict()
+        return resource_dict
 
     @staticmethod
-    def _get_or_create_by_uri(uri: str) -> ExperimentDict:
-        experiment_dict: ExperimentDict = api.client.post(
-            path='/experiments/',
-            data={'uri' if '/' in uri else 'name': uri},
-        ).json()
-        return experiment_dict
+    def _get_or_create_resource_dict(uri: str) -> _types.ResourceDict:
+        response_dict = api.client.post(path='/experiments/', data={'uri' if '/' in uri else 'name': uri}).json()
+        return Experiment._get_resource_dict_by_uuid(uuid=response_dict['uuid'])
 
-    def _refetch_experiment_dict(self) -> None:
-        self._experiment_dict = api.client.get(path=f'/experiments/{self.uuid}/').json()
+    def _refetch(self) -> None:
+        self._resource_dict = self._get_resource_dict_by_uuid(uuid=self._resource_dict['uuid'])

{pybiolib-1.1.2123.dist-info → pybiolib-1.1.2135.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.2123
+Version: 1.1.2135
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.1.2123.dist-info → pybiolib-1.1.2135.dist-info}/RECORD

@@ -1,6 +1,6 @@
 LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
 README.md,sha256=_IH7pxFiqy2bIAmaVeA-iVTyUwWRjMIlfgtUbYTtmls,368
-biolib/__init__.py,sha256=yX8w8bDiY7CIxfKHFRF0U1hhwgCCIXtVr18Td5iNLp8,4135
+biolib/__init__.py,sha256=_tThyzISH81yS9KXP_X3qEiKXmsIp5XOBcJIODfLVnc,4338
 biolib/_data_record/data_record.py,sha256=jUeCQjnVQLNLmlXO3rREEUnjXjOYuaQjBO7R66P6wFU,8909
 biolib/_internal/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/_internal/data_record/__init__.py,sha256=0T0CV6PfKc8itjMu-48sCJjcZQEzXl1ZLBqG_LjJTqQ,82
@@ -16,8 +16,9 @@ biolib/_internal/libs/__init__.py,sha256=Jdf4tNPqe_oIIf6zYml6TiqhL_02Vyqwge6IELr
 biolib/_internal/libs/fusepy/__init__.py,sha256=AWDzNFS-XV_5yKb0Qx7kggIhPzq1nj_BZS5y2Nso08k,41944
 biolib/_internal/push_application.py,sha256=8P7eXvySn7CRp5XBDkO3xjTGixS8g7-jD-_iwzM_XDI,10020
 biolib/_internal/runtime.py,sha256=9pZ3s3L7LGxdqOgnHh1KK3Jjyn_9MjhQmKHI-6hMT3U,448
-biolib/_internal/types/__init__.py,sha256=h2I2aupN01HbhBelL-qQa8FLuXiH1tB3kKl8dPdhmnc,39
-biolib/_internal/types/resources.py,sha256=LlxuiesDDv3TvfEmz_BCCxH0V650bNHtS_LpBMA25T4,256
+biolib/_internal/types/__init__.py,sha256=yVxn48Z7N240X5yVYM-gsbqXDyLF9VJ6-mbNpFvVzgU,79
+biolib/_internal/types/data_record.py,sha256=fPtWmrgL29zKGrzifr-4JOcpVp_4vVY0lNg8v6H_Bc8,220
+biolib/_internal/types/resource.py,sha256=LlxuiesDDv3TvfEmz_BCCxH0V650bNHtS_LpBMA25T4,256
 biolib/_internal/types/typing.py,sha256=D4EKKEe7kDx0K6lJi-H_XLtk-8w6nu2fdqn9bvzI-Xo,288
 biolib/_internal/utils/__init__.py,sha256=p5vsIFyu-zYqBgdSMfwW9NC_jk7rXvvCbV4Bzd3As7c,630
 biolib/_runtime/runtime.py,sha256=zy9HrE4X5hBqm8doUHkckyflquSBDSXV3REhT2MQGas,2767
@@ -94,8 +95,7 @@ biolib/compute_node/webserver/webserver_types.py,sha256=2t8EaFKESnves3BA_NBdnS2y
 biolib/compute_node/webserver/webserver_utils.py,sha256=XWvwYPbWNR3qS0FYbLLp-MDDfVk0QdaAmg3xPrT0H2s,4234
 biolib/compute_node/webserver/worker_thread.py,sha256=26tG73TADnOcXsAr7Iyf6smrLlCqB4x-vvmpUb8WqnA,11569
 biolib/experiments/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-biolib/experiments/experiment.py,sha256=o2gXMJVwK2SFljZ9RdTYFRH3jGKJmg3P39oERhEnZMQ,8126
-biolib/experiments/types.py,sha256=n9GxdFA7cLMfHvLLqLmZzX31ELeSSkMXFoEEdFsdWGY,171
+biolib/experiments/experiment.py,sha256=4VkeRMxDnROQ0CE_su299FjzODEHwpvlLH-h4-TFPNQ,7610
 biolib/jobs/__init__.py,sha256=aIb2H2DHjQbM2Bs-dysFijhwFcL58Blp0Co0gimED3w,32
 biolib/jobs/job.py,sha256=OfG8cLd3AjGjiMWRlJRZdVVbLsRWSX-OM5nxJhR6mPQ,19136
 biolib/jobs/job_result.py,sha256=rALHiKYNaC9lHi_JJqBob1RubzNLwG9Z386kwRJjd2M,5885
@@ -114,8 +114,8 @@ biolib/utils/cache_state.py,sha256=u256F37QSRIVwqKlbnCyzAX4EMI-kl6Dwu6qwj-Qmag,3
 biolib/utils/multipart_uploader.py,sha256=XvGP1I8tQuKhAH-QugPRoEsCi9qvbRk-DVBs5PNwwJo,8452
 biolib/utils/seq_util.py,sha256=jC5WhH63FTD7SLFJbxQGA2hOt9NTwq9zHl_BEec1Z0c,4907
 biolib/utils/zip/remote_zip.py,sha256=0wErYlxir5921agfFeV1xVjf29l9VNgGQvNlWOlj2Yc,23232
-pybiolib-1.1.2123.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.1.2123.dist-info/METADATA,sha256=aKfd3kBoe55TCBeMBPtX0GTAfUOVHfw_jXauy_dSlkI,1508
-pybiolib-1.1.2123.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-pybiolib-1.1.2123.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.1.2123.dist-info/RECORD,,
+pybiolib-1.1.2135.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.1.2135.dist-info/METADATA,sha256=FdkUDiSOcWBss6_5vClW1valODFetu3Soa8jNm29IE4,1508
+pybiolib-1.1.2135.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+pybiolib-1.1.2135.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.1.2135.dist-info/RECORD,,

biolib/experiments/types.py

@@ -1,9 +0,0 @@
-from biolib.typing_utils import TypedDict
-
-
-class ExperimentDict(TypedDict):
-    created_at: str
-    job_count: int
-    job_running_count: int
-    name: str
-    uuid: str