labkey 2.6.0__py3-none-any.whl → 3.0.0__py3-none-any.whl

labkey/__init__.py

@@ -14,6 +14,6 @@
 # limitations under the License.
 #
 __title__ = "labkey"
-__version__ = "2.6.0"
+__version__ = "3.0.0"
 __author__ = "LabKey"
 __license__ = "Apache License 2.0"

labkey/query.py

@@ -44,6 +44,7 @@ import functools
 from typing import List
 
 from .server_context import ServerContext
+from .utils import waf_encode
 
 _default_timeout = 60 * 5  # 5 minutes
 
@@ -164,12 +165,25 @@ class QueryFilter:
         return "<QueryFilter [{} {} {}]>".format(self.column_name, self.filter_type, self.value)
 
 
+class AuditBehavior:
+    """
+    Enum of different auditing levels
+    """
+
+    DETAILED = "DETAILED"
+    NONE = "NONE"
+    SUMMARY = "SUMMARY"
+
+
 def delete_rows(
     server_context: ServerContext,
     schema_name: str,
     query_name: str,
     rows: any,
     container_path: str = None,
+    transacted: bool = True,
+    audit_behavior: AuditBehavior = None,
+    audit_user_comment: str = None,
     timeout: int = _default_timeout,
 ):
     """
@@ -179,12 +193,25 @@ def delete_rows(
     :param query_name: table name to delete from
     :param rows: Set of rows to delete
     :param container_path: labkey container path if not already set in context
+    :param transacted: whether all of the updates should be done in a single transaction
+    :param audit_behavior: used to override the audit behavior for the update. See class query.AuditBehavior
+    :param audit_user_comment: used to provide a comment that will be attached to certain detailed audit log records
     :param timeout: timeout of request in seconds (defaults to 30s)
     :return:
     """
     url = server_context.build_url("query", "deleteRows.api", container_path=container_path)
+
     payload = {"schemaName": schema_name, "queryName": query_name, "rows": rows}
 
+    if transacted is False:
+        payload["transacted"] = transacted
+
+    if audit_behavior is not None:
+        payload["auditBehavior"] = audit_behavior
+
+    if audit_user_comment is not None:
+        payload["auditUserComment"] = audit_user_comment
+
     return server_context.make_request(
         url,
         json=payload,
@@ -231,6 +258,7 @@ def execute_sql(
     parameters: dict = None,
     required_version: float = None,
     timeout: int = _default_timeout,
+    waf_encode_sql: bool = True
 ):
     """
     Execute sql query against a LabKey server.
@@ -248,11 +276,12 @@ def execute_sql(
     :param parameters: parameter values to pass through to a parameterized query
     :param required_version: Api version of response
     :param timeout: timeout of request in seconds (defaults to 30s)
+    :param waf_encode_sql: WAF encode sql in request (defaults to True)
     :return:
     """
     url = server_context.build_url("query", "executeSql.api", container_path=container_path)
 
-    payload = {"schemaName": schema_name, "sql": sql}
+    payload = {"schemaName": schema_name, "sql": waf_encode(sql) if waf_encode_sql else sql}
 
     if container_filter is not None:
         payload["containerFilter"] = container_filter
@@ -285,6 +314,10 @@ def insert_rows(
     query_name: str,
     rows: List[any],
     container_path: str = None,
+    skip_reselect_rows: bool = False,
+    transacted: bool = True,
+    audit_behavior: AuditBehavior = None,
+    audit_user_comment: str = None,
     timeout: int = _default_timeout,
 ):
     """
@@ -294,6 +327,10 @@ def insert_rows(
     :param query_name: table name to insert into
     :param rows: set of rows to insert
     :param container_path: labkey container path if not already set in context
+    :param skip_reselect_rows: whether the full detailed response for the insert can be skipped
+    :param transacted: whether all of the updates should be done in a single transaction
+    :param audit_behavior: used to override the audit behavior for the update. See class query.AuditBehavior
+    :param audit_user_comment: used to provide a comment that will be attached to certain detailed audit log records
     :param timeout: timeout of request in seconds (defaults to 30s)
     :return:
     """
@@ -301,6 +338,18 @@ def insert_rows(
 
     payload = {"schemaName": schema_name, "queryName": query_name, "rows": rows}
 
+    if skip_reselect_rows is True:
+        payload["skipReselectRows"] = skip_reselect_rows
+
+    if transacted is False:
+        payload["transacted"] = transacted
+
+    if audit_behavior is not None:
+        payload["auditBehavior"] = audit_behavior
+
+    if audit_user_comment is not None:
+        payload["auditUserComment"] = audit_user_comment
+
     return server_context.make_request(
         url,
         json=payload,
@@ -316,7 +365,7 @@ def select_rows(
     filter_array: List[QueryFilter] = None,
     container_path: str = None,
     columns=None,
-    max_rows: int = None,
+    max_rows: int = -1,
     sort: str = None,
     offset: int = None,
     container_filter: str = None,
@@ -339,7 +388,7 @@ def select_rows(
     :param filter_array: set of filter objects to apply
     :param container_path: folder path if not already part of server_context
     :param columns: set of columns to retrieve
-    :param max_rows: max number of rows to retrieve
+    :param max_rows: max number of rows to retrieve, defaults to -1 (unlimited)
     :param sort: comma separated list of column names to sort by, prefix a column with '-' to sort descending
     :param offset: number of rows to offset results by
     :param container_filter: enumeration of the various container filters available. See:
@@ -419,6 +468,9 @@ def update_rows(
     query_name: str,
     rows: List[any],
     container_path: str = None,
+    transacted: bool = True,
+    audit_behavior: AuditBehavior = None,
+    audit_user_comment: str = None,
     timeout: int = _default_timeout,
 ):
     """
@@ -429,6 +481,9 @@ def update_rows(
     :param query_name: table name to update
     :param rows: Set of rows to update
     :param container_path: labkey container path if not already set in context
+    :param transacted: whether all of the updates should be done in a single transaction
+    :param audit_behavior: used to override the audit behavior for the update. See class query.AuditBehavior
+    :param audit_user_comment: used to provide a comment that will be attached to certain detailed audit log records
     :param timeout: timeout of request in seconds (defaults to 30s)
     :return:
     """
@@ -436,6 +491,61 @@ def update_rows(
 
     payload = {"schemaName": schema_name, "queryName": query_name, "rows": rows}
 
+    if transacted is False:
+        payload["transacted"] = transacted
+
+    if audit_behavior is not None:
+        payload["auditBehavior"] = audit_behavior
+
+    if audit_user_comment is not None:
+        payload["auditUserComment"] = audit_user_comment
+
+    return server_context.make_request(
+        url,
+        json=payload,
+        timeout=timeout,
+    )
+
+
+def move_rows(
+    server_context: ServerContext,
+    target_container_path: str,
+    schema_name: str,
+    query_name: str,
+    rows: any,
+    container_path: str = None,
+    transacted: bool = True,
+    audit_behavior: AuditBehavior = None,
+    audit_user_comment: str = None,
+    timeout: int = _default_timeout,
+):
+    """
+    Move a set of rows from the schema.query
+    :param server_context: A LabKey server context. See utils.create_server_context.
+    :param target_container_path: target labkey container path for the move
+    :param schema_name: schema of table
+    :param query_name: table name to move from
+    :param rows: Set of rows to move
+    :param container_path: source labkey container path if not already set in context
+    :param transacted: whether all of the updates should be done in a single transaction
+    :param audit_behavior: used to override the audit behavior for the update. See class query.AuditBehavior
+    :param audit_user_comment: used to provide a comment that will be attached to certain detailed audit log records
+    :param timeout: timeout of request in seconds (defaults to 30s)
+    :return:
+    """
+    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}
+
+    if transacted is False:
+        payload["transacted"] = transacted
+
+    if audit_behavior is not None:
+        payload["auditBehavior"] = audit_behavior
+
+    if audit_user_comment is not None:
+        payload["auditUserComment"] = audit_user_comment
+
     return server_context.make_request(
         url,
         json=payload,
@@ -458,10 +568,21 @@ class QueryWrapper:
         query_name: str,
         rows: any,
         container_path: str = None,
+        transacted: bool = True,
+        audit_behavior: AuditBehavior = None,
+        audit_user_comment: str = None,
         timeout: int = _default_timeout,
     ):
         return delete_rows(
-            self.server_context, schema_name, query_name, rows, container_path, timeout
+            self.server_context,
+            schema_name,
+            query_name,
+            rows,
+            container_path,
+            transacted,
+            audit_behavior,
+            audit_user_comment,
+            timeout
         )
 
     @functools.wraps(truncate_table)
@@ -484,6 +605,7 @@ class QueryWrapper:
         parameters: dict = None,
         required_version: float = None,
         timeout: int = _default_timeout,
+        waf_encode_sql: bool = True
     ):
         return execute_sql(
             self.server_context,
@@ -498,6 +620,7 @@ class QueryWrapper:
             parameters,
             required_version,
             timeout,
+            waf_encode_sql
         )
 
     @functools.wraps(insert_rows)
@@ -507,10 +630,23 @@ class QueryWrapper:
         query_name: str,
         rows: List[any],
         container_path: str = None,
+        skip_reselect_rows: bool = False,
+        transacted: bool = True,
+        audit_behavior: AuditBehavior = None,
+        audit_user_comment: str = None,
         timeout: int = _default_timeout,
     ):
         return insert_rows(
-            self.server_context, schema_name, query_name, rows, container_path, timeout
+            self.server_context,
+            schema_name,
+            query_name,
+            rows,
+            container_path,
+            skip_reselect_rows,
+            transacted,
+            audit_behavior,
+            audit_user_comment,
+            timeout
         )
 
     @functools.wraps(select_rows)
@@ -522,7 +658,7 @@ class QueryWrapper:
         filter_array: List[QueryFilter] = None,
         container_path: str = None,
         columns=None,
-        max_rows: int = None,
+        max_rows: int = -1,
         sort: str = None,
         offset: int = None,
         container_filter: str = None,
@@ -566,8 +702,45 @@ class QueryWrapper:
         query_name: str,
         rows: List[any],
         container_path: str = None,
+        transacted: bool = True,
+        audit_behavior: AuditBehavior = None,
+        audit_user_comment: str = None,
         timeout: int = _default_timeout,
     ):
         return update_rows(
-            self.server_context, schema_name, query_name, rows, container_path, timeout
+            self.server_context,
+            schema_name,
+            query_name,
+            rows,
+            container_path,
+            transacted,
+            audit_behavior,
+            audit_user_comment,
+            timeout
+        )
+
+    @functools.wraps(move_rows)
+    def move_rows(
+        self,
+        target_container_path: str,
+        schema_name: str,
+        query_name: str,
+        rows: any,
+        container_path: str = None,
+        transacted: bool = True,
+        audit_behavior: AuditBehavior = None,
+        audit_user_comment: str = None,
+        timeout: int = _default_timeout,
+    ):
+        return move_rows(
+            self.server_context,
+            target_container_path,
+            schema_name,
+            query_name,
+            rows,
+            container_path,
+            transacted,
+            audit_behavior,
+            audit_user_comment,
+            timeout
         )

labkey/utils.py

@@ -16,6 +16,8 @@
 import json
 from functools import wraps
 from datetime import date, datetime
+from base64 import b64encode
+from urllib import parse
 
 
 # Issue #14: json.dumps on datetime throws TypeError
@@ -71,3 +73,21 @@ def transform_helper(user_transform_func, file_path_run_properties):
             row = [str(el).strip() for el in row]
             row = "\t".join(row)
             file_out.write(row + "\n")
+
+
+def btoa(value: str) -> str:
+    if not value:
+        return value
+    binary = value.encode("utf-8")
+    return b64encode(binary).decode()
+
+
+def encode_uri_component(value: str) -> str:
+    # https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/encodeURIComponent
+    return parse.quote(value, encoding="utf-8", safe="-_.!~*'()")
+
+
+def waf_encode(value: str) -> str:
+    if value:
+        return "/*{{base64/x-www-form-urlencoded/wafText}}*/" + btoa(encode_uri_component(value))
+    return value

{labkey-2.6.0.dist-info → labkey-3.0.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: labkey
-Version: 2.6.0
+Version: 3.0.0
 Summary: Python client API for LabKey Server
 Home-page: https://github.com/LabKey/labkey-api-python
 Author: LabKey
@@ -9,7 +9,6 @@ Maintainer: Alan Vezina
 Maintainer-email: alanv@labkey.com
 License: Apache License 2.0
 Keywords: labkey api client
-Platform: UNKNOWN
 Classifier: Development Status :: 4 - Beta
 Classifier: Environment :: Console
 Classifier: Intended Audience :: Science/Research
@@ -20,6 +19,7 @@ Classifier: Operating System :: Microsoft
 Classifier: Operating System :: POSIX
 Classifier: Programming Language :: Python :: 3
 Classifier: Topic :: Scientific/Engineering
+License-File: LICENSE.txt
 Requires-Dist: requests
 Provides-Extra: test
 Requires-Dist: pytest ; extra == 'test'
@@ -28,5 +28,3 @@ Requires-Dist: mock ; extra == 'test'
 Requires-Dist: pytest-cov ; extra == 'test'
 
 Python client API for LabKey Server. Supports query and experiment APIs.
-
-

{labkey-2.6.0.dist-info → labkey-3.0.0.dist-info}/RECORD

@@ -1,16 +1,16 @@
-labkey/__init__.py,sha256=tOjisNuXTI8emw2lhq5cv6P4e79bfS5tPyitf_9NoHY,695
+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=b4HJXCbwhFQbKnd1M9VbuvrDvfszpEBCH2I7Je4jE2U,18059
+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=rfZM1LT5iPOgVbKcOLUuWh59LqXYV-g3zoQUKwKcz-I,2651
-labkey-2.6.0.dist-info/LICENSE.txt,sha256=xllut76FgcGL5zbIRvuRc7aezPbvlMUTWJPsVr2Sugg,11358
-labkey-2.6.0.dist-info/METADATA,sha256=JLFyY0uy-EiA4s7V_6R87lYGjhDLaEuXBtEqAIHq5nY,1070
-labkey-2.6.0.dist-info/WHEEL,sha256=OqRkF0eY5GHssMorFjlbTIq072vpHpF60fIQA6lS9xA,92
-labkey-2.6.0.dist-info/top_level.txt,sha256=DQIk1fQNg7NxxBsEt_K7k-aopiH87jmnU98zwDp0n04,7
-labkey-2.6.0.dist-info/RECORD,,
+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,,

{labkey-2.6.0.dist-info → labkey-3.0.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.36.2)
+Generator: bdist_wheel (0.42.0)
 Root-Is-Purelib: true
 Tag: py3-none-any