labkey 3.0.0__py3-none-any.whl → 3.2.0__py3-none-any.whl

labkey/__init__.py

@@ -14,6 +14,6 @@
 # limitations under the License.
 #
 __title__ = "labkey"
-__version__ = "3.0.0"
+__version__ = "3.2.0"
 __author__ = "LabKey"
 __license__ = "Apache License 2.0"

labkey/api_wrapper.py

@@ -22,6 +22,7 @@ class APIWrapper:
         verify_ssl=True,
         api_key=None,
         disable_csrf=False,
+        allow_redirects=False,
     ):
         self.server_context = ServerContext(
             domain=domain,
@@ -31,6 +32,7 @@ class APIWrapper:
             verify_ssl=verify_ssl,
             api_key=api_key,
             disable_csrf=disable_csrf,
+            allow_redirects=allow_redirects,
         )
         self.container = ContainerWrapper(self.server_context)
         self.domain = DomainWrapper(self.server_context)

labkey/exceptions.py

@@ -47,7 +47,22 @@ class RequestError(exceptions.RequestException):
             self.message = "No response received"
 
     def __str__(self):
-        return repr(self.message)
+        return str(self.message)
+
+
+class UnexpectedRedirectError(RequestError):
+    default_msg = "Unexpected redirect occurred"
+
+    def __init__(self, server_response, **kwargs):
+        super().__init__(server_response, **kwargs)
+
+        location = server_response.headers.get("Location", "")
+
+        # If the server is redirecting from http to https the user probably has a misconfigured ServerContext with use_ssl=False
+        if server_response.url.startswith("http://") and location.startswith("https://"):
+            self.message = "Redirected from http to https, set use_ssl=True in your APIWrapper or ServerContext"
+        elif location != "":
+            self.message = f"Unexpected redirect to: {location}"
 
 
 class QueryNotFoundError(RequestError):

labkey/experiment.py

@@ -218,6 +218,70 @@ def save_batches(
     return None
 
 
+def lineage(
+    server_context: ServerContext,
+    lsids: List[str],
+    children: bool = None,
+    container_path: str = None,
+    cpas_type: str = None,
+    depth: int = None,
+    exp_type: str = None,
+    include_inputs_and_outputs: bool = None,
+    include_properties: bool = None,
+    include_run_steps: bool = None,
+    parents: bool = None,
+    run_protocol_lsid: str = None,
+):
+    """
+    :param server_context: A LabKey server context. See utils.create_server_context.
+    :param lsids: Array of LSIDs for the seed ExpData, ExpMaterials, or ExpRun
+    :param children: Include children in the lineage response. Defaults to true.
+    :param container_path: labkey container path if not already set in context
+    :param cpas_type: Optional LSID of a SampleSet or DataClass to filter the response. Defaults to include all.
+    :param depth: An optional depth argument. Defaults to include all.
+    :param exp_type: Optional experiment type to filter response -- either "Data", "Material", or "ExperimentRun".
+    Defaults to include all.
+    :param include_inputs_and_outputs: Include inputs and outputs in the lineage response.
+    :param include_properties: Include properties in the lineage response.
+    :param include_run_steps: Include run steps in the lineage response.
+    :param parents: Include parents in the lineage response. Defaults to true.
+    :param run_protocol_lsid: Optional Exp Run Protocol Lsid to filter response. Defaults to include all.
+    """
+    lineage_url = server_context.build_url(
+        "experiment", "lineage.api", container_path=container_path
+    )
+    payload = {"lsids": lsids}
+
+    if children is not None:
+        payload["children"] = children
+
+    if cpas_type is not None:
+        payload["cpasType"] = cpas_type
+
+    if depth is not None:
+        payload["depth"] = depth
+
+    if exp_type is not None:
+        payload["expType"] = exp_type
+
+    if include_inputs_and_outputs is not None:
+        payload["includeInputsAndOutputs"] = include_inputs_and_outputs
+
+    if include_properties is not None:
+        payload["includeProperties"] = include_properties
+
+    if include_run_steps is not None:
+        payload["includeRunSteps"] = include_run_steps
+
+    if parents is not None:
+        payload["parents"] = parents
+
+    if run_protocol_lsid is not None:
+        payload["runProtocolLsid"] = run_protocol_lsid
+
+    return server_context.make_request(lineage_url, payload=payload, method="POST")
+
+
 class ExperimentWrapper:
     """
     Wrapper for all of the API methods exposed in the experiment module. Used by the APIWrapper class.
@@ -237,3 +301,33 @@ class ExperimentWrapper:
     @functools.wraps(save_batches)
     def save_batches(self, assay_id: int, batches: List[Batch]) -> Optional[List[Batch]]:
         return save_batches(self.server_context, assay_id, batches)
+
+    @functools.wraps(lineage)
+    def lineage(
+        self,
+        lsids: List[str],
+        children: bool = None,
+        container_path: str = None,
+        cpas_type: str = None,
+        exp_type: str = None,
+        depth: int = None,
+        include_properties: bool = None,
+        include_inputs_and_outputs: bool = None,
+        include_run_steps: bool = None,
+        parents: bool = None,
+        run_protocol_lsid: str = None,
+    ):
+        return lineage(
+            self.server_context,
+            lsids,
+            children,
+            container_path,
+            cpas_type,
+            depth,
+            exp_type,
+            parents,
+            include_inputs_and_outputs,
+            include_properties,
+            include_run_steps,
+            run_protocol_lsid,
+        )

labkey/query.py

@@ -258,7 +258,7 @@ def execute_sql(
     parameters: dict = None,
     required_version: float = None,
     timeout: int = _default_timeout,
-    waf_encode_sql: bool = True
+    waf_encode_sql: bool = True,
 ):
     """
     Execute sql query against a LabKey server.
@@ -535,7 +535,12 @@ def move_rows(
     """
     url = server_context.build_url("query", "moveRows.api", container_path=container_path)
 
-    payload = {"targetContainerPath": target_container_path, "schemaName": schema_name, "queryName": query_name, "rows": rows}
+    payload = {
+        "targetContainerPath": target_container_path,
+        "schemaName": schema_name,
+        "queryName": query_name,
+        "rows": rows,
+    }
 
     if transacted is False:
         payload["transacted"] = transacted
@@ -582,7 +587,7 @@ class QueryWrapper:
             transacted,
             audit_behavior,
             audit_user_comment,
-            timeout
+            timeout,
         )
 
     @functools.wraps(truncate_table)
@@ -605,7 +610,7 @@ class QueryWrapper:
         parameters: dict = None,
         required_version: float = None,
         timeout: int = _default_timeout,
-        waf_encode_sql: bool = True
+        waf_encode_sql: bool = True,
     ):
         return execute_sql(
             self.server_context,
@@ -620,7 +625,7 @@ class QueryWrapper:
             parameters,
             required_version,
             timeout,
-            waf_encode_sql
+            waf_encode_sql,
         )
 
     @functools.wraps(insert_rows)
@@ -646,7 +651,7 @@ class QueryWrapper:
             transacted,
             audit_behavior,
             audit_user_comment,
-            timeout
+            timeout,
         )
 
     @functools.wraps(select_rows)
@@ -716,7 +721,7 @@ class QueryWrapper:
             transacted,
             audit_behavior,
             audit_user_comment,
-            timeout
+            timeout,
         )
 
     @functools.wraps(move_rows)
@@ -742,5 +747,5 @@ class QueryWrapper:
             transacted,
             audit_behavior,
             audit_user_comment,
-            timeout
+            timeout,
         )

labkey/security.py

@@ -279,7 +279,7 @@ def stop_impersonating(server_context: ServerContext):
     Stop impersonating a user while keeping the original user logged in.
     """
     url = server_context.build_url(LOGIN_CONTROLLER, "stopImpersonating.api")
-    return server_context.make_request(url)
+    return server_context.make_request(url, allow_redirects=True)
 
 
 @dataclass

labkey/server_context.py

@@ -8,6 +8,7 @@ from labkey.exceptions import (
     QueryNotFoundError,
     ServerContextError,
     ServerNotFoundError,
+    UnexpectedRedirectError,
 )
 
 API_KEY_TOKEN = "apikey"
@@ -29,7 +30,8 @@ def handle_response(response, non_json_response=False):
                 content=response.content,
             )
             return result
-
+    elif sc == 302:
+        raise UnexpectedRedirectError(response)
     elif sc == 401:
         raise RequestAuthorizationError(response)
     elif sc == 404:
@@ -62,6 +64,7 @@ class ServerContext:
         verify_ssl=True,
         api_key=None,
         disable_csrf=False,
+        allow_redirects=False,
     ):
         self._container_path = container_path
         self._context_path = context_path
@@ -70,6 +73,7 @@ class ServerContext:
         self._verify_ssl = verify_ssl
         self._api_key = api_key
         self._disable_csrf = disable_csrf
+        self.allow_redirects = allow_redirects
         self._session = requests.Session()
         self._session.headers.update({"User-Agent": f"LabKey Python API/{__version__}"})
 
@@ -174,7 +178,9 @@ class ServerContext:
         non_json_response: bool = False,
         file_payload: any = None,
         json: dict = None,
+        allow_redirects=False,
     ) -> any:
+        allow_redirects_ = allow_redirects or self.allow_redirects
         if self._api_key is not None:
             if self._session.headers.get(API_KEY_TOKEN) is not self._api_key:
                 self._session.headers.update({API_KEY_TOKEN: self._api_key})
@@ -189,7 +195,13 @@ class ServerContext:
 
         try:
             if method == "GET":
-                response = self._session.get(url, params=payload, headers=headers, timeout=timeout)
+                response = self._session.get(
+                    url,
+                    params=payload,
+                    headers=headers,
+                    timeout=timeout,
+                    allow_redirects=allow_redirects_,
+                )
             else:
                 if file_payload is not None:
                     response = self._session.post(
@@ -198,6 +210,7 @@ class ServerContext:
                         files=file_payload,
                         headers=headers,
                         timeout=timeout,
+                        allow_redirects=allow_redirects_,
                     )
                 elif json is not None:
                     if headers is None:
@@ -206,10 +219,20 @@ class ServerContext:
                     headers_ = {**headers, "Content-Type": "application/json"}
                     # sort_keys is a hack to make unit tests work
                     data = json_dumps(json, sort_keys=True)
-                    response = self._session.post(url, data=data, headers=headers_, timeout=timeout)
+                    response = self._session.post(
+                        url,
+                        data=data,
+                        headers=headers_,
+                        timeout=timeout,
+                        allow_redirects=allow_redirects_,
+                    )
                 else:
                     response = self._session.post(
-                        url, data=payload, headers=headers, timeout=timeout
+                        url,
+                        data=payload,
+                        headers=headers,
+                        timeout=timeout,
+                        allow_redirects=allow_redirects_,
                     )
             return handle_response(response, non_json_response)
         except RequestException as e:

{labkey-3.0.0.dist-info → labkey-3.2.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: labkey
-Version: 3.0.0
+Version: 3.2.0
 Summary: Python client API for LabKey Server
 Home-page: https://github.com/LabKey/labkey-api-python
 Author: LabKey
@@ -21,6 +21,17 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Topic :: Scientific/Engineering
 License-File: LICENSE.txt
 Requires-Dist: requests
+Provides-Extra: build
+Requires-Dist: setuptools ; extra == 'build'
+Requires-Dist: build ; extra == 'build'
+Requires-Dist: twine ; extra == 'build'
+Requires-Dist: wheel ; extra == 'build'
+Provides-Extra: dev
+Requires-Dist: pytest ; extra == 'dev'
+Requires-Dist: requests ; extra == 'dev'
+Requires-Dist: mock ; extra == 'dev'
+Requires-Dist: pytest-cov ; extra == 'dev'
+Requires-Dist: black ; extra == 'dev'
 Provides-Extra: test
 Requires-Dist: pytest ; extra == 'test'
 Requires-Dist: requests ; extra == 'test'

labkey-3.2.0.dist-info/RECORD

@@ -0,0 +1,16 @@
+labkey/__init__.py,sha256=BxplFb91voofYbNkCpovsh5LfOdvBLWqCmHPjhy2Lj0,695
+labkey/api_wrapper.py,sha256=OxnV6_5jONWiwsi24TOXTKP5inXtAfABGqXAPua3eCM,1427
+labkey/container.py,sha256=DXmLhGsNnN_QLXa_tMCM0Xf_Kkz7B8KjRFhJT5I4FtY,5497
+labkey/domain.py,sha256=SABG7BfSqQGJr8DPjUsvhi8C7xP2MTpkq24sdtAu4J8,22486
+labkey/exceptions.py,sha256=00x-4oP_2d0SfZKxsGIs8QGvXiNq2y7C5hAzuzT3Gkk,3619
+labkey/experiment.py,sha256=6U4BXnYHNXCUF_mee0maK_CZDVm_lbMjC82ywx9YCTE,12062
+labkey/query.py,sha256=w6vYDwiwnLalrDQ8pGY-c9DvoPQuMXaFXnZLRUiezuk,24041
+labkey/security.py,sha256=eMa2b_22FWB2rVvVpxTeWrK0VgGTszhRchsApbDR6sA,15306
+labkey/server_context.py,sha256=0YcA7BRijLMs172qTrTB12MlnIcqz4X9dkkCwSxxzaA,7741
+labkey/storage.py,sha256=WpgpTWQzgig_qJXMGszFcFjtf8oMd2-6TBehSkpJPUg,6144
+labkey/utils.py,sha256=oL6qmHkpzLTm_9c7gSEzumv_MVh5s8fj6bOrbuslrV0,3233
+labkey-3.2.0.dist-info/LICENSE.txt,sha256=xllut76FgcGL5zbIRvuRc7aezPbvlMUTWJPsVr2Sugg,11358
+labkey-3.2.0.dist-info/METADATA,sha256=0xOPpsSbHkT9ow_bUQeILdYVPAcFIwmr_KG1tlHHbxQ,1481
+labkey-3.2.0.dist-info/WHEEL,sha256=cVxcB9AmuTcXqmwrtPhNK88dr7IR_b6qagTj0UvIEbY,91
+labkey-3.2.0.dist-info/top_level.txt,sha256=DQIk1fQNg7NxxBsEt_K7k-aopiH87jmnU98zwDp0n04,7
+labkey-3.2.0.dist-info/RECORD,,

{labkey-3.0.0.dist-info → labkey-3.2.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.42.0)
+Generator: setuptools (74.1.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

labkey-3.0.0.dist-info/RECORD

@@ -1,16 +0,0 @@
-labkey/__init__.py,sha256=q1xx8gL3h06R1DGXoOOInvVNbmuIOmuCexBPMyEApxM,695
-labkey/api_wrapper.py,sha256=ks6q5qwcGkutg2m5sMdTvryhfK42yltfPCV5iLPi22k,1351
-labkey/container.py,sha256=DXmLhGsNnN_QLXa_tMCM0Xf_Kkz7B8KjRFhJT5I4FtY,5497
-labkey/domain.py,sha256=SABG7BfSqQGJr8DPjUsvhi8C7xP2MTpkq24sdtAu4J8,22486
-labkey/exceptions.py,sha256=VtuKphEczSsfHAXgWRv-2HRzxSiObBnOEC_sgEPPR3c,2929
-labkey/experiment.py,sha256=Wtuz52bhuvDWk_o2AbTw7SJnwEji2iD6Q04ct0PWSxE,8804
-labkey/query.py,sha256=0Hp8P-mFuqurGlVbF71BN3Woz6tZfdweRKW0s4GFsh4,23995
-labkey/security.py,sha256=cVrlYbb7Yogjo9L1exGKgpscRFEljBpzFITQZWHW2X8,15284
-labkey/server_context.py,sha256=UGf4fJ9Cw_YIM_DwdPVP8WgKORt5aO_4bFCz14rjsrg,6950
-labkey/storage.py,sha256=WpgpTWQzgig_qJXMGszFcFjtf8oMd2-6TBehSkpJPUg,6144
-labkey/utils.py,sha256=oL6qmHkpzLTm_9c7gSEzumv_MVh5s8fj6bOrbuslrV0,3233
-labkey-3.0.0.dist-info/LICENSE.txt,sha256=xllut76FgcGL5zbIRvuRc7aezPbvlMUTWJPsVr2Sugg,11358
-labkey-3.0.0.dist-info/METADATA,sha256=BtwRKk5F9ja7CD37QvyCljOi0_R9Dq-10uUS0OH3BHQ,1076
-labkey-3.0.0.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-labkey-3.0.0.dist-info/top_level.txt,sha256=DQIk1fQNg7NxxBsEt_K7k-aopiH87jmnU98zwDp0n04,7
-labkey-3.0.0.dist-info/RECORD,,