labkey 3.0.0__tar.gz → 3.2.0__tar.gz

{labkey-3.0.0 → labkey-3.2.0}/CHANGE.txt

@@ -2,6 +2,24 @@
 LabKey Python Client API News
 +++++++++++
 
+What's New in the LabKey 3.2.0 package
+==============================
+
+*Release date: 09/10/2024*
+- Add lineage API to experiment module
+    - Accessible via API wrappers e.g. api.experiment.lineage()
+
+What's New in the LabKey 3.1.0 package
+==============================
+
+*Release date: 04/03/2024*
+- ServerContext
+    - Add allow_redirects flag (defaults to False) to constructor
+    - Add allow_redirects flag to make_request
+- APIWrapper: Add allow_redirects flag (defaults to False)
+- Add UnexpectedRedirectError
+    - thrown when allow_redirects is False and the server issues a redirect
+
 What's New in the LabKey 3.0.0 package
 ==============================
 

{labkey-3.0.0/labkey.egg-info → labkey-3.2.0}/PKG-INFO

@@ -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
@@ -26,5 +26,16 @@ Requires-Dist: pytest; extra == "test"
 Requires-Dist: requests; extra == "test"
 Requires-Dist: mock; extra == "test"
 Requires-Dist: pytest-cov; extra == "test"
+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: build
+Requires-Dist: setuptools; extra == "build"
+Requires-Dist: build; extra == "build"
+Requires-Dist: twine; extra == "build"
+Requires-Dist: wheel; extra == "build"
 
 Python client API for LabKey Server. Supports query and experiment APIs.

{labkey-3.0.0 → labkey-3.2.0}/README.md

@@ -93,12 +93,16 @@ from labkey.api_wrapper import APIWrapper
 
 print("Create an APIWrapper")
 labkey_server = 'localhost:8080'
-project_name = 'ModuleAssayTest'  # Project folder name
+# in this example, Tutorials is a project name and HIV study is a subfolder under it.
+container_path = 'Tutorials/HIV Study'
 contextPath = 'labkey'
 schema = 'core'
 table = 'Users'
-api = APIWrapper(labkey_server, project_name, contextPath, use_ssl=False)
 
+# Note: If developing against localhost with https disabled, set use_ssl=False below
+api = APIWrapper(labkey_server, container_path, contextPath)
+
+# Makes an API request to https://www.example.com/labkey/tutorials/hiv%20study/query-getQuery.api
 result = api.query.select_rows(schema, table)
 
 if result is not None:
@@ -113,28 +117,29 @@ Python 3.7+ is fully supported.
 LabKey Server v15.1 and later.
 
 ## Contributing
-This package is maintained by [LabKey](http://www.labkey.com/). If you have any questions or need support, please use
-the [LabKey Server developer support forum](https://www.labkey.org/home/developer/forum/project-start.view).
-
-When contributing changes please use `Black` to format your code. To run Black follow these instructions:
-1. Install black: `pip install black`
-2. Run black: `black .`
-3. Commit the newly formatted code.
+This package is maintained by [LabKey](http://www.labkey.com/). If you have any questions or need support, please use the
+[LabKey Server developer support forum](https://www.labkey.org/home/developer/forum/project-start.view).
 
-### Testing
-If you are looking to contribute please run the tests before issuing a PR. The tests can be initiated by running
+### Setup
+To install the necessary dependencies for local development you can run the following command:
 
 ```bash
-$ python setup.py test
+pip install -e '.[dev]'
 ```
 
-This runs the tests using [pytest](https://docs.pytest.org/en/latest/contents.html). If you'd like to run pytest directly you can install the testing dependencies in your virtual environment with:
+
+### Formatting your code
+When contributing changes please use `Black` to format your code. To run Black you can run the following command:
 
 ```bash
-$ pip install -e .[test]
+black .
 ```
 
-Then, the tests can be run with
+After black has run it may have formatted some files, commit the changed files before opening a PR.
+
+### Testing
+If you are looking to contribute please run the tests before issuing a PR. The tests can be run with:
+
 ```bash
 $ pytest .
 ```
@@ -147,4 +152,22 @@ $ pytest . -m "integration"
 ```
 
 ### Maintainers
-Package maintainer's can reference the [Python Package Maintenance](https://docs.google.com/document/d/13nVxwyctH4YZ6gDhcrOu9Iz6qGFPAxicE1VHiVYpw9A/) document (requires permission) for updating releases.
+Package maintainer's can reference the [Python Package Maintenance](https://docs.google.com/document/d/13nVxwyctH4YZ6gDhcrOu9Iz6qGFPAxicE1VHiVYpw9A/) document (requires permission) for updating
+releases.
+
+To build the package before releasing you will need to install the build dependencies. This can be done by running:
+
+```bash
+pip install -e '.[build]'
+```
+
+To build the package you can run:
+
+```bash
+python -m build
+```
+
+You should now have a `dist/` folder with two files:
+
+1. `labkey-<version from __init__.py>.tar.gz` - This is the source distribution
+2. `labkey-<version from __init__.py>-py3-none-any.whl` - This is the wheel

{labkey-3.0.0 → labkey-3.2.0}/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-3.0.0 → labkey-3.2.0}/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-3.0.0 → labkey-3.2.0}/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-3.0.0 → labkey-3.2.0}/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-3.0.0 → labkey-3.2.0}/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-3.0.0 → labkey-3.2.0}/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-3.0.0 → labkey-3.2.0}/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 → labkey-3.2.0/labkey.egg-info}/PKG-INFO

@@ -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
@@ -26,5 +26,16 @@ Requires-Dist: pytest; extra == "test"
 Requires-Dist: requests; extra == "test"
 Requires-Dist: mock; extra == "test"
 Requires-Dist: pytest-cov; extra == "test"
+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: build
+Requires-Dist: setuptools; extra == "build"
+Requires-Dist: build; extra == "build"
+Requires-Dist: twine; extra == "build"
+Requires-Dist: wheel; extra == "build"
 
 Python client API for LabKey Server. Supports query and experiment APIs.

{labkey-3.0.0 → labkey-3.2.0}/labkey.egg-info/SOURCES.txt

@@ -2,6 +2,7 @@ CHANGE.txt
 LICENSE.txt
 MANIFEST.in
 README.md
+debug.txt
 pyproject.toml
 pytest.ini
 setup.cfg

labkey-3.2.0/labkey.egg-info/requires.txt

@@ -0,0 +1,20 @@
+requests
+
+[build]
+setuptools
+build
+twine
+wheel
+
+[dev]
+pytest
+requests
+mock
+pytest-cov
+black
+
+[test]
+pytest
+requests
+mock
+pytest-cov

labkey-3.2.0/setup.cfg

@@ -0,0 +1,7 @@
+[metadata]
+description_file = README.md
+
+[egg_info]
+tag_build = 
+tag_date = 0
+

{labkey-3.0.0 → labkey-3.2.0}/setup.py

@@ -33,6 +33,8 @@ if not version:
 long_desc = "Python client API for LabKey Server. Supports query and experiment APIs."
 
 tests_require = ["pytest", "requests", "mock", "pytest-cov"]
+dev_require = ["pytest", "requests", "mock", "pytest-cov", "black"]
+build_require = ["setuptools", "build", "twine", "wheel"]
 
 setup(
     name="labkey",
@@ -48,9 +50,7 @@ setup(
     packages=packages,
     package_data={},
     install_requires=["requests"],
-    tests_require=tests_require,
-    setup_requires=["pytest-runner"],
-    extras_require={"test": tests_require},
+    extras_require={"test": tests_require, "dev": dev_require, "build": build_require},
     keywords="labkey api client",
     classifiers=[
         "Development Status :: 4 - Beta",

labkey-3.0.0/labkey.egg-info/requires.txt

@@ -1,7 +0,0 @@
-requests
-
-[test]
-pytest
-requests
-mock
-pytest-cov

labkey-3.0.0/setup.cfg

@@ -1,14 +0,0 @@
-[metadata]
-description-file = README.md
-
-[aliases]
-test = pytest
-
-[coverage:html]
-directory = build/coverage_html
-title = Test coverage report for labkey
-
-[egg_info]
-tag_build = 
-tag_date = 0
-