labkey 3.1.0__py3-none-any.whl → 3.3.0__py3-none-any.whl

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/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/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

@@ -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/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.dist-info → labkey-3.3.0.dist-info}/METADATA

@@ -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
@@ -22,9 +22,20 @@ Classifier: Topic :: Scientific/Engineering
 License-File: LICENSE.txt
 Requires-Dist: requests
 Provides-Extra: test
-Requires-Dist: pytest ; extra == 'test'
-Requires-Dist: requests ; extra == 'test'
-Requires-Dist: mock ; extra == 'test'
-Requires-Dist: pytest-cov ; extra == 'test'
+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-3.3.0.dist-info/RECORD

@@ -0,0 +1,16 @@
+labkey/__init__.py,sha256=TUjL83UivtADyginkvpkXQQdrAgJQNmNzevhchgQ3qQ,695
+labkey/api_wrapper.py,sha256=OxnV6_5jONWiwsi24TOXTKP5inXtAfABGqXAPua3eCM,1427
+labkey/container.py,sha256=DXmLhGsNnN_QLXa_tMCM0Xf_Kkz7B8KjRFhJT5I4FtY,5497
+labkey/domain.py,sha256=hcyHOg3KPZFyEMccOllp9OtXMWnuzIGkbHbn8dAyfOI,22497
+labkey/exceptions.py,sha256=00x-4oP_2d0SfZKxsGIs8QGvXiNq2y7C5hAzuzT3Gkk,3619
+labkey/experiment.py,sha256=6U4BXnYHNXCUF_mee0maK_CZDVm_lbMjC82ywx9YCTE,12062
+labkey/query.py,sha256=zQH7qO2UH8aSHLa8GhEklNvEb6fj2cjdB3AI4Q4m2n8,27133
+labkey/security.py,sha256=eMa2b_22FWB2rVvVpxTeWrK0VgGTszhRchsApbDR6sA,15306
+labkey/server_context.py,sha256=f0xjiE9NtoSVn6oN-C0LaJfSWaK3YgOOX5ouwLL0Szo,7787
+labkey/storage.py,sha256=WpgpTWQzgig_qJXMGszFcFjtf8oMd2-6TBehSkpJPUg,6144
+labkey/utils.py,sha256=oL6qmHkpzLTm_9c7gSEzumv_MVh5s8fj6bOrbuslrV0,3233
+labkey-3.3.0.dist-info/LICENSE.txt,sha256=xllut76FgcGL5zbIRvuRc7aezPbvlMUTWJPsVr2Sugg,11358
+labkey-3.3.0.dist-info/METADATA,sha256=z5Co-n5oSWKDje8-xR7yY_3MR-kJGr9O8Xc_QL2I_tw,1468
+labkey-3.3.0.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+labkey-3.3.0.dist-info/top_level.txt,sha256=DQIk1fQNg7NxxBsEt_K7k-aopiH87jmnU98zwDp0n04,7
+labkey-3.3.0.dist-info/RECORD,,

{labkey-3.1.0.dist-info → labkey-3.3.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.42.0)
+Generator: setuptools (75.6.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

labkey-3.1.0.dist-info/RECORD

@@ -1,16 +0,0 @@
-labkey/__init__.py,sha256=SjBskVArzIGzH9aIlUwSK246XoguCK7iCvEm0fXQAhQ,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=Wtuz52bhuvDWk_o2AbTw7SJnwEji2iD6Q04ct0PWSxE,8804
-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-3.1.0.dist-info/LICENSE.txt,sha256=xllut76FgcGL5zbIRvuRc7aezPbvlMUTWJPsVr2Sugg,11358
-labkey-3.1.0.dist-info/METADATA,sha256=8O6aEerFp6Qn5B18KBaa7GGKApoNCwDDWDpaB9atXwM,1076
-labkey-3.1.0.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-labkey-3.1.0.dist-info/top_level.txt,sha256=DQIk1fQNg7NxxBsEt_K7k-aopiH87jmnU98zwDp0n04,7
-labkey-3.1.0.dist-info/RECORD,,