labkey 3.1.0__tar.gz → 3.3.0__tar.gz

{labkey-3.1.0 → labkey-3.3.0}/CHANGE.txt

@@ -2,6 +2,20 @@
 LabKey Python Client API News
 +++++++++++
 
+What's New in the LabKey 3.3.0 package
+==============================
+
+*Release date: 12/3/2024*
+- Add import_rows API to query module
+    - Accessible via API wrappers e.g. api.query.import_rows
+
+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
 ==============================
 

{labkey-3.1.0/labkey.egg-info → labkey-3.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: labkey
-Version: 3.1.0
+Version: 3.3.0
 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-3.1.0 → labkey-3.3.0}/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-3.1.0 → labkey-3.3.0}/labkey/__init__.py

@@ -14,6 +14,6 @@
 # limitations under the License.
 #
 __title__ = "labkey"
-__version__ = "3.1.0"
+__version__ = "3.3.0"
 __author__ = "LabKey"
 __license__ = "Apache License 2.0"

{labkey-3.1.0 → labkey-3.3.0}/labkey/domain.py

@@ -14,7 +14,7 @@
 # limitations under the License.
 #
 import functools
-from typing import Dict, List, Union, Tuple
+from typing import Dict, List, Union, Tuple, TextIO
 
 from .server_context import ServerContext
 from labkey.query import QueryFilter
@@ -483,7 +483,7 @@ def get_domain_details(
 
 
 def infer_fields(
-    server_context: ServerContext, data_file: any, container_path: str = None
+    server_context: ServerContext, data_file: TextIO, container_path: str = None
 ) -> List[PropertyDescriptor]:
     """
     Infer fields for a domain from a file

{labkey-3.1.0 → labkey-3.3.0}/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-3.1.0 → labkey-3.3.0}/labkey/query.py

@@ -41,7 +41,7 @@ https://www.labkey.org/home/developer/forum/project-start.view
 ############################################################################
 """
 import functools
-from typing import List
+from typing import List, TextIO
 
 from .server_context import ServerContext
 from .utils import waf_encode
@@ -357,6 +357,56 @@ def insert_rows(
     )
 
 
+def import_rows(
+    server_context: ServerContext,
+    schema_name: str,
+    query_name: str,
+    data_file: TextIO,
+    container_path: str = None,
+    insert_option: str = None,
+    audit_behavior: str = None,
+    import_lookup_by_alternate_key: bool = False,
+):
+    """
+    Import row(s) into a table
+    :param server_context: A LabKey server context. See utils.create_server_context.
+    :param schema_name: schema of table
+    :param query_name: table name to import into
+    :param data_file: the file containing the rows to import. The column names in the file must match the column names
+    from the LabKey server.
+    :param container_path: labkey container path if not already set in context
+    :param insert_option: Whether the import action should be done as an insert, creating new rows for each provided row
+    of the data frame, or a merge. When merging during import, any data you provide for the rows representing records
+    that already exist will replace the previous values. Note that when updating an existing record, you only need to
+    provide the columns you wish to update, existing data for other columns will be left as is. Available options are
+    "INSERT" and "MERGE". Defaults to "INSERT".
+    :param audit_behavior: Set the level of auditing details for this import action. Available options are "SUMMARY" and
+    "DETAILED". SUMMARY - Audit log reflects that a change was made, but does not mention the nature of the change.
+    DETAILED - Provides full details on what change was made, including values before and after the change. Defaults to
+    the setting as specified by the LabKey query.
+    :param import_lookup_by_alternate_key: Allows lookup target rows to be resolved by values rather than the target's
+    primary key. This option will only be available for lookups that are configured with unique column information
+    :return:
+    """
+    url = server_context.build_url("query", "import.api", container_path=container_path)
+    file_payload = {"file": data_file}
+    payload = {
+        "schemaName": schema_name,
+        "queryName": query_name,
+    }
+
+    if insert_option is not None:
+        payload["insertOption"] = insert_option
+
+    if audit_behavior is not None:
+        payload["auditBehavior"] = audit_behavior
+
+    if import_lookup_by_alternate_key is not None:
+        payload["importLookupByAlternateKey"] = import_lookup_by_alternate_key
+
+    return server_context.make_request(url, payload, method="POST", file_payload=file_payload)
+
+
 def select_rows(
     server_context: ServerContext,
     schema_name: str,
@@ -654,6 +704,28 @@ class QueryWrapper:
             timeout,
         )
 
+    @functools.wraps(import_rows)
+    def import_rows(
+        self,
+        schema_name: str,
+        query_name: str,
+        data_file,
+        container_path: str = None,
+        insert_option: str = None,
+        audit_behavior: str = None,
+        import_lookup_by_alternate_key: bool = False,
+    ):
+        return import_rows(
+            self.server_context,
+            schema_name,
+            query_name,
+            data_file,
+            container_path,
+            insert_option,
+            audit_behavior,
+            import_lookup_by_alternate_key,
+        )
+
     @functools.wraps(select_rows)
     def select_rows(
         self,

{labkey-3.1.0 → labkey-3.3.0}/labkey/server_context.py

@@ -1,3 +1,4 @@
+from typing import Dict, TextIO
 from labkey.utils import json_dumps
 from . import __version__
 import requests
@@ -176,7 +177,7 @@ class ServerContext:
         timeout: int = 300,
         method: str = "POST",
         non_json_response: bool = False,
-        file_payload: any = None,
+        file_payload: Dict[str, TextIO] = None,
         json: dict = None,
         allow_redirects=False,
     ) -> any:

{labkey-3.1.0 → labkey-3.3.0/labkey.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: labkey
-Version: 3.1.0
+Version: 3.3.0
 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-3.1.0 → labkey-3.3.0}/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-3.3.0/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-3.3.0/setup.cfg

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

{labkey-3.1.0 → labkey-3.3.0}/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-3.1.0/labkey.egg-info/requires.txt

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

labkey-3.1.0/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
-