Drop job integrity checks

doc/source/admin/galaxy_options.rst

@@ -1167,39 +1167,6 @@
 :Type: str
 
 
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-``check_job_script_integrity``
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-:Description:
-    Set to false to disable various checks Galaxy will do to ensure it
-    can run job scripts before attempting to execute or submit them.
-:Default: ``true``
-:Type: bool
-
-
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-``check_job_script_integrity_count``
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-:Description:
-    Number of checks to execute if check_job_script_integrity is
-    enabled.
-:Default: ``35``
-:Type: int
-
-
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-``check_job_script_integrity_sleep``
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-:Description:
-    Time to sleep between checks if check_job_script_integrity is
-    enabled (in seconds).
-:Default: ``0.25``
-:Type: float
-
-
 ~~~~~~~~~~~~~~~~~~~~~
 ``default_job_shell``
 ~~~~~~~~~~~~~~~~~~~~~

lib/galaxy/app_unittest_utils/galaxy_mock.py

@@ -261,9 +261,6 @@ def __init__(self, **kwargs):
         self.enable_tool_document_cache = False
         self.tool_cache_data_dir = os.path.join(self.root, "tool_cache")
         self.external_chown_script = None
-        self.check_job_script_integrity = False
-        self.check_job_script_integrity_count = 0
-        self.check_job_script_integrity_sleep = 0
 
         self.default_panel_view = "default"
         self.panel_views_dir = ""

lib/galaxy/config/sample/galaxy.yml.sample

@@ -913,18 +913,6 @@ galaxy:
   # <cache_dir>.
   #template_cache_path: compiled_templates
 
-  # Set to false to disable various checks Galaxy will do to ensure it
-  # can run job scripts before attempting to execute or submit them.
-  #check_job_script_integrity: true
-
-  # Number of checks to execute if check_job_script_integrity is
-  # enabled.
-  #check_job_script_integrity_count: 35
-
-  # Time to sleep between checks if check_job_script_integrity is
-  # enabled (in seconds).
-  #check_job_script_integrity_sleep: 0.25
-
   # Set the default shell used by non-containerized jobs Galaxy-wide.
   # This defaults to bash for all jobs and can be overridden at the
   # destination level for heterogeneous clusters. conda job resolution

lib/galaxy/config/sample/tool_shed.yml.sample

@@ -54,6 +54,9 @@ tool_shed:
   # options.
   #whoosh_index_dir: database/toolshed_whoosh_indexes
 
+  # Cache directory for Pydantic model objects.
+  #model_cache_dir: database/model_cache
+
   # For searching repositories at /api/repositories:
   #repo_name_boost: 0.9
 

lib/galaxy/config/schemas/config_schema.yml

@@ -848,28 +848,6 @@ mapping:
           Mako templates are compiled as needed and cached for reuse, this directory is
           used for the cache
 
-      check_job_script_integrity:
-        type: bool
-        default: true
-        required: false
-        desc: |
-          Set to false to disable various checks Galaxy will do to ensure it
-          can run job scripts before attempting to execute or submit them.
-
-      check_job_script_integrity_count:
-        type: int
-        default: 35
-        required: false
-        desc: |
-          Number of checks to execute if check_job_script_integrity is enabled.
-
-      check_job_script_integrity_sleep:
-        type: float
-        default: .25
-        required: false
-        desc: |
-          Time to sleep between checks if check_job_script_integrity is enabled (in seconds).
-
       default_job_shell:
         type: str
         default: /bin/bash

lib/galaxy/job_execution/setup.py

@@ -79,9 +79,6 @@ class JobIO(UsesDictVisibleKeys):
         "len_file_path",
         "builds_file_path",
         "file_sources_dict",
-        "check_job_script_integrity",
-        "check_job_script_integrity_count",
-        "check_job_script_integrity_sleep",
         "tool_source",
         "tool_source_class",
         "tool_dir",
@@ -105,9 +102,6 @@ def __init__(
         new_file_path: str,
         len_file_path: str,
         builds_file_path: str,
-        check_job_script_integrity: bool,
-        check_job_script_integrity_count: int,
-        check_job_script_integrity_sleep: float,
         file_sources_dict: Dict[str, Any],
         user_context: Union[FileSourcesUserContext, Dict[str, Any]],
         tool_source: Optional[str] = None,
@@ -137,9 +131,6 @@ def __init__(
         self.new_file_path = new_file_path
         self.len_file_path = len_file_path
         self.builds_file_path = builds_file_path
-        self.check_job_script_integrity = check_job_script_integrity
-        self.check_job_script_integrity_count = check_job_script_integrity_count
-        self.check_job_script_integrity_sleep = check_job_script_integrity_sleep
         self.tool_dir = tool_dir
         self.is_task = is_task
         self.tool_source = tool_source

lib/galaxy/jobs/__init__.py

@@ -1083,9 +1083,6 @@ def job_io(self):
                 len_file_path=self.app.config.len_file_path,
                 file_sources_dict=self.app.file_sources.to_dict(for_serialization=True, user_context=user_context),
                 user_context=user_context,
-                check_job_script_integrity=self.app.config.check_job_script_integrity,
-                check_job_script_integrity_count=self.app.config.check_job_script_integrity_count,
-                check_job_script_integrity_sleep=self.app.config.check_job_script_integrity_sleep,
                 tool_source=tool_source,
                 tool_source_class=type(self.tool.tool_source).__name__ if self.tool else None,
                 tool_dir=self.tool and self.tool.tool_dir,

lib/galaxy/jobs/command_factory.py

@@ -13,11 +13,7 @@
 
 from galaxy import util
 from galaxy.job_execution.output_collect import default_exit_code_file
-from galaxy.jobs.runners.util.job_script import (
-    INTEGRITY_INJECTION,
-    ScriptIntegrityChecks,
-    write_script,
-)
+from galaxy.jobs.runners.util.job_script import write_script
 from galaxy.tool_util.deps.container_classes import (
     Container,
     TRAP_KILL_CONTAINER,
@@ -154,7 +150,7 @@ def build_command(
         relocate_contents = (
             "from galaxy_ext.cwl.handle_outputs import relocate_dynamic_outputs; relocate_dynamic_outputs()"
         )
-        write_script(relocate_script_file, relocate_contents, ScriptIntegrityChecks(check_job_script_integrity=False))
+        write_script(relocate_script_file, relocate_contents)
         commands_builder.append_command(SETUP_GALAXY_FOR_METADATA)
         commands_builder.append_command(f"python '{relocate_script_file}'")
 
@@ -184,8 +180,6 @@ def __externalize_commands(
     # for instance.
     if shell and shell.lower() == "none":
         return tool_commands
-    if job_wrapper.job_io.check_job_script_integrity:
-        integrity_injection = INTEGRITY_INJECTION
     set_e = ""
     if job_wrapper.strict_shell:
         set_e = "set -e\n"
@@ -196,7 +190,6 @@ def __externalize_commands(
     write_script(
         local_container_script,
         script_contents,
-        job_io=job_wrapper.job_io,
     )
     commands = f"{shell} {local_container_script}"
     # TODO: Cleanup for_pulsar hack.

lib/galaxy/jobs/runners/__init__.py

@@ -31,7 +31,6 @@
 from galaxy.jobs.runners.util import runner_states
 from galaxy.jobs.runners.util.env import env_to_statement
 from galaxy.jobs.runners.util.job_script import (
-    DescribesScriptIntegrityChecks,
     job_script,
     write_script,
 )
@@ -520,8 +519,8 @@ def get_job_file(self, job_wrapper: "MinimalJobWrapper", **kwds) -> str:
         options.update(**kwds)
         return job_script(**options)
 
-    def write_executable_script(self, path: str, contents: str, job_io: DescribesScriptIntegrityChecks) -> None:
-        write_script(path, contents, job_io)
+    def write_executable_script(self, path: str, contents: str) -> None:
+        write_script(path, contents)
 
     def _find_container(
         self,

lib/galaxy/jobs/runners/aws.py

@@ -605,5 +605,5 @@ def write_command(self, job_wrapper: "MinimalJobWrapper") -> str:
             "galaxy_virtual_env": None,
         }
         job_file_contents = self.get_job_file(job_wrapper, **job_script_props)
-        self.write_executable_script(job_file, job_file_contents, job_io=job_wrapper.job_io)
+        self.write_executable_script(job_file, job_file_contents)
         return job_file

lib/galaxy/jobs/runners/local.py

@@ -80,7 +80,7 @@ def __command_line(self, job_wrapper: "MinimalJobWrapper") -> Tuple[str, str]:
             "shell": job_wrapper.shell,
         }
         job_file_contents = self.get_job_file(job_wrapper, **job_script_props)
-        self.write_executable_script(job_file, job_file_contents, job_io=job_wrapper.job_io)
+        self.write_executable_script(job_file, job_file_contents)
         return job_file, exit_code_path
 
     def queue_job(self, job_wrapper):

lib/galaxy/jobs/runners/util/job_script/__init__.py

@@ -1,17 +1,11 @@
 import logging
 import os
-import subprocess
-import time
-from dataclasses import dataclass
 from string import Template
 from typing import (
     Any,
     Dict,
-    Optional,
 )
 
-from typing_extensions import Protocol
-
 from galaxy.util import (
     RWXR_XR_X,
     unicodify,
@@ -32,19 +26,6 @@
 GALAXY_SLOTS="1"
 """
 
-INTEGRITY_INJECTION = """
-# The following block can be used by the job system
-# to ensure this script is runnable before actually attempting
-# to run it.
-if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then
-    exit 42
-fi
-"""
-
-INTEGRITY_SYNC_COMMAND = "/bin/sync"
-DEFAULT_INTEGRITY_CHECK = True
-DEFAULT_INTEGRITY_COUNT = 35
-DEFAULT_INTEGRITY_SLEEP = 0.25
 REQUIRED_TEMPLATE_PARAMS = ["working_directory", "command"]
 OPTIONAL_TEMPLATE_PARAMS: Dict[str, Any] = {
     "galaxy_lib": None,
@@ -54,7 +35,6 @@
     "slots_statement": SLOTS_STATEMENT_CLUSTER_DEFAULT,
     "instrument_pre_commands": "",
     "instrument_post_commands": "",
-    "integrity_injection": INTEGRITY_INJECTION,
     "shell": DEFAULT_SHELL,
     "preserve_python_environment": True,
     "tmp_dir_creation_statement": '""',
@@ -113,67 +93,19 @@ def job_script(template=DEFAULT_JOB_FILE_TEMPLATE, **kwds):
     return template.safe_substitute(template_params)
 
 
-class DescribesScriptIntegrityChecks(Protocol):
-    check_job_script_integrity: bool
-    check_job_script_integrity_count: Optional[int]
-    check_job_script_integrity_sleep: Optional[float]
-
-
-@dataclass
-class ScriptIntegrityChecks:
-    """Minimal class implementing the DescribesScriptIntegrityChecks protocol"""
-
-    check_job_script_integrity: bool
-    check_job_script_integrity_count: Optional[int] = None
-    check_job_script_integrity_sleep: Optional[float] = None
-
-
-def write_script(path: str, contents, job_io: DescribesScriptIntegrityChecks, mode: int = RWXR_XR_X) -> None:
+def write_script(path: str, contents, mode: int = RWXR_XR_X, use_fork_safe_write=False) -> None:
     dir = os.path.dirname(path)
     if not os.path.exists(dir):
         os.makedirs(dir)
-    fork_safe_write(path, contents)
+    if use_fork_safe_write:
+        fork_safe_write(path, contents)
+    else:
+        with open(path, "w", encoding="utf-8") as f:
+            f.write(unicodify(contents))
     os.chmod(path, mode)
-    if job_io.check_job_script_integrity:
-        assert job_io.check_job_script_integrity_count is not None
-        assert job_io.check_job_script_integrity_sleep is not None
-        _handle_script_integrity(path, job_io.check_job_script_integrity_count, job_io.check_job_script_integrity_sleep)
-
-
-def _handle_script_integrity(
-    path: str, check_job_script_integrity_count: int, check_job_script_integrity_sleep: float
-) -> None:
-    script_integrity_verified = False
-    for _ in range(check_job_script_integrity_count):
-        try:
-            returncode = subprocess.call([path], env={"ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ": "1"})
-            if returncode == 42:
-                script_integrity_verified = True
-                break
-
-            log.debug("Script integrity error for file '%s': returncode was %d", path, returncode)
-
-            # Else we will sync and wait to see if the script becomes
-            # executable.
-            try:
-                # sync file system to avoid "Text file busy" problems.
-                # These have occurred both in Docker containers and on EC2 clusters
-                # under high load.
-                subprocess.check_call(INTEGRITY_SYNC_COMMAND)
-            except Exception as e:
-                log.debug("Error syncing the filesystem: %s", unicodify(e))
-
-        except Exception as exc:
-            log.debug("Script not available yet: %s", unicodify(exc))
-
-        time.sleep(check_job_script_integrity_sleep)
-
-    if not script_integrity_verified:
-        raise Exception(f"Failed to write job script '{path}', could not verify job script integrity.")
 
 
 __all__ = (
     "job_script",
     "write_script",
-    "INTEGRITY_INJECTION",
 )

test/unit/app/jobs/test_command_factory.py

@@ -220,11 +220,6 @@ def __init__(self, job_dir):
         self.working_directory = job_dir
         self.prepare_input_files_cmds = None
         self.commands_in_new_shell = False
-        self.app = Bunch(
-            config=Bunch(
-                check_job_script_integrity=False,
-            )
-        )
         self.shell = "/bin/sh"
         self.use_metadata_binary = False
         self.job_id = 1
@@ -248,7 +243,6 @@ def setup_external_metadata(self, *args, **kwds):
     def job_io(self):
         return Bunch(
             get_output_fnames=lambda: ["output1"],
-            check_job_script_integrity=False,
             version_path=None,
         )
 

test/unit/app/jobs/test_runner_local.py

@@ -189,9 +189,7 @@ def change_state(self, state, job=None):
 
     @property
     def job_io(self):
-        return bunch.Bunch(
-            get_output_fnames=lambda: [], check_job_script_integrity=False, version_path="/tmp/version_path"
-        )
+        return bunch.Bunch(get_output_fnames=lambda: [], version_path="/tmp/version_path")
 
     def get_job(self):
         return self.job

test/unit/job_execution/test_job_io.py

@@ -70,9 +70,6 @@ def job_io(app: FileSourcesMockApp, job: Job) -> JobIO:
         builds_file_path=WORKING_DIRECTORY,
         user_context=USER_CONTEXT,
         file_sources_dict=app.file_sources.to_dict(for_serialization=True, user_context=user_context),
-        check_job_script_integrity=False,
-        check_job_script_integrity_count=1,
-        check_job_script_integrity_sleep=1,
         tool_dir=WORKING_DIRECTORY,
         is_task=False,
     )