labkey 2.6.1__py3-none-any.whl → 3.1.0__py3-none-any.whl

labkey/__init__.py

@@ -14,6 +14,6 @@
 # limitations under the License.
 #
 __title__ = "labkey"
-__version__ = "2.6.1"
+__version__ = "3.1.0"
 __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/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,
@@ -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 +491,66 @@ 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 +573,21 @@ 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 +610,7 @@ 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 +625,7 @@ class QueryWrapper:
             parameters,
             required_version,
             timeout,
+            waf_encode_sql,
         )
 
     @functools.wraps(insert_rows)
@@ -507,10 +635,23 @@ 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)
@@ -566,8 +707,45 @@ 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/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/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-2.6.1.dist-info → labkey-3.1.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: labkey
-Version: 2.6.1
+Version: 3.1.0
 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-3.1.0.dist-info/RECORD

@@ -0,0 +1,16 @@
+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,,

{labkey-2.6.1.dist-info → labkey-3.1.0.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
 

labkey-2.6.1.dist-info/RECORD

@@ -1,16 +0,0 @@
-labkey/__init__.py,sha256=kC19-fjUIjUmWaNbRLugYAwZn-jtYgZt-dd65OLQ6hw,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=ZUQLdfZOFJ07om1L0ARPlcLMXGIskxgGMJwuo5Y_L6Q,18083
-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-2.6.1.dist-info/LICENSE.txt,sha256=xllut76FgcGL5zbIRvuRc7aezPbvlMUTWJPsVr2Sugg,11358
-labkey-2.6.1.dist-info/METADATA,sha256=YZi0E0SrIagngSWsUND3mTI4D7jJzz7YZiYI_b1Rmbc,1070
-labkey-2.6.1.dist-info/WHEEL,sha256=OqRkF0eY5GHssMorFjlbTIq072vpHpF60fIQA6lS9xA,92
-labkey-2.6.1.dist-info/top_level.txt,sha256=DQIk1fQNg7NxxBsEt_K7k-aopiH87jmnU98zwDp0n04,7
-labkey-2.6.1.dist-info/RECORD,,