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Don't check availability of shellescape
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It is not used in the CWL branch any more.

cwltool removed shellescape as dependency in 3.1.20241007082533 , which causes
errors like the following in test_galaxy_packages tests:

```
_______________________________ test_tool_proxy ________________________________

    def test_tool_proxy():
        """Test that tool proxies load some valid tools correctly."""
>       tool_proxy(_cwl_tool_path("v1.0/v1.0/cat1-testcli.cwl"))

tests/tool_util/test_cwl.py:35:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
galaxy/tool_util/cwl/parser.py:726: in tool_proxy
    ensure_cwltool_available()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

    def ensure_cwltool_available():
        """Assert optional dependencies proxied via this module are available at runtime.

        Throw an ImportError with a description of the problem if they do not exist.
        """
        if main is None or workflow is None or shellescape is None:
            message = "This feature requires cwltool and dependencies to be available, they are not."
            if main is None:
                message += " cwltool is not unavailable."
            elif resolve_and_validate_document is None:
                message += " cwltool.load_tool.resolve_and_validate_document is unavailable - cwltool version is too old."
            if requests is None:
                message += " Library 'requests' unavailable."
            if shellescape is None:
                message += " Library 'shellescape' unavailable."
            if schema_salad is None:
                message += " Library 'schema_salad' unavailable."
>           raise ImportError(message)
E           ImportError: This feature requires cwltool and dependencies to be available, they are not. Library 'shellescape' unavailable.
```
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nsoranzo committed Oct 8, 2024
1 parent c0f4ba1 commit b0b9bbe
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Showing 2 changed files with 3 additions and 14 deletions.
6 changes: 1 addition & 5 deletions lib/galaxy/tool_util/cwl/__init__.py
Original file line number Diff line number Diff line change
@@ -1,7 +1,4 @@
from .cwltool_deps import (
needs_shell_quoting,
shellescape,
)
from .cwltool_deps import needs_shell_quoting
from .parser import (
tool_proxy,
tool_proxy_from_persistent_representation,
Expand All @@ -21,5 +18,4 @@
"to_cwl_job",
"to_galaxy_parameters",
"needs_shell_quoting",
"shellescape",
)
11 changes: 2 additions & 9 deletions lib/galaxy/tool_util/cwl/cwltool_deps.py
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
:func:`ensure_cwltool_available` before using any of the imported
functionality at runtime.
"""

import re
import warnings

Expand Down Expand Up @@ -70,11 +71,6 @@
visit_class = None # type: ignore[assignment]
normalizeFilesDirs = None # type: ignore[assignment]

try:
import shellescape
except ImportError:
shellescape = None

try:
import schema_salad
from schema_salad import (
Expand Down Expand Up @@ -104,16 +100,14 @@ def ensure_cwltool_available():
Throw an ImportError with a description of the problem if they do not exist.
"""
if main is None or workflow is None or shellescape is None:
if main is None or workflow is None:
message = "This feature requires cwltool and dependencies to be available, they are not."
if main is None:
message += " cwltool is not unavailable."
elif resolve_and_validate_document is None:
message += " cwltool.load_tool.resolve_and_validate_document is unavailable - cwltool version is too old."
if requests is None:
message += " Library 'requests' unavailable."
if shellescape is None:
message += " Library 'shellescape' unavailable."
if schema_salad is None:
message += " Library 'schema_salad' unavailable."
raise ImportError(message)
Expand All @@ -136,7 +130,6 @@ def ensure_cwltool_available():
"resolve_and_validate_document",
"RuntimeContext",
"schema_salad",
"shellescape",
"sourceline",
"StdFsAccess",
"visit_class",
Expand Down

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