Merge branch 'main' into pr/vsoch/2305

CHANGELOG.md

@@ -1,5 +1,12 @@
 # Changelog
 
+## [7.32.2](https://github.com/snakemake/snakemake/compare/v7.32.1...v7.32.2) (2023-08-07)
+
+
+### Bug Fixes
+
+* unnecessary set Snakefile in AzBatch executor ([#2397](https://github.com/snakemake/snakemake/issues/2397)) ([78e6d6e](https://github.com/snakemake/snakemake/commit/78e6d6ec6a1ad930e40d6edfe9f7210232a674f2))
+
 ## [7.32.1](https://github.com/snakemake/snakemake/compare/v7.32.0...v7.32.1) (2023-08-05)
 
 

snakemake/executors/azure_batch.py

@@ -8,6 +8,7 @@
 import os
 import re
 import shutil
+import shlex
 import sys
 import tarfile
 import tempfile
@@ -31,7 +32,6 @@
 from snakemake.executors import sleep
 from snakemake.logging import logger
 
-
 AzBatchJob = namedtuple("AzBatchJob", "job jobid task_id callback error_callback")
 
 
@@ -290,9 +290,6 @@ def __init__(
 
         self.workdir = dirname
 
-        # Relative path for running on instance
-        self._set_snakefile()
-
         # Prepare workflow sources for build package
         self._set_workflow_sources()
 
@@ -399,7 +396,7 @@ def mask_dict_vals(mdict: dict, keys: list):
     # token information from being printed to the logs
     def mask_sas_urls(self, attrs: dict):
         attrs_new = attrs.copy()
-        sas_pattern = r"\?s[v|p]=.+(\'|\"|$)"
+        sas_pattern = r"\?[^=]+=([^?'\"]+)"
         mask = 10 * "*"
 
         for k, value in attrs.items():
@@ -441,7 +438,7 @@ def run(
                 continue
 
         exec_job = self.format_job_exec(job)
-        exec_job = f"/bin/sh -c 'tar xzf {self.resource_file.file_path} && {exec_job}'"
+        exec_job = f"/bin/bash -c 'tar xzf {self.resource_file.file_path} && {shlex.quote(exec_job)}'"
 
         # A string that uniquely identifies the Task within the Job.
         task_uuid = str(uuid.uuid1())
@@ -850,14 +847,6 @@ def validate_az_blob_credential_is_sas():
                     "AZ_BLOB_CREDENTIAL is not a valid storage account SAS token."
                 )
 
-    def _set_snakefile(self):
-        """The snakefile must be a relative path, which cannot be reliably
-        derived from the self.workflow.snakefile as we might have moved
-        execution into a temporary directory, and the initial Snakefile
-        was somewhere else on the system.
-        """
-        self.snakefile = os.path.basename(self.workflow.main_snakefile)
-
     # from google_lifesciences.py
     def _set_workflow_sources(self):
         """We only add files from the working directory that are config related