Open poshul opened 3 weeks ago
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PR Description updated to latest commit (https://github.com/OpenMS/streamlit-template/commit/34503ac39bf44d6c050d2f47bac92b89c3337983)
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| ⏱️ Estimated effort to review [1-5] | 2, because the changes are localized to a specific functionality in the code, and the logic is straightforward. The PR modifies the command line flag handling in a Python script, which is a common task and should be relatively easy to review for an experienced developer. |
| 🧪 Relevant tests | No |
| ⚡ Possible issues | Possible Bug: The condition `if v != False:` might not behave as expected if `v` is `None` or an empty string, which are also falsy values in Python. This could lead to unintended flags being added to the command. |
| Code Clarity: The comment `# add the value if we aren't a flag` might be misleading because it's placed before a block that handles multiline strings, not specifically non-flag values. | |
| 🔒 Security concerns | No |
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| Category | Suggestions | ||||
| Best practice |
Use identity comparison for boolean checks.___ **Replace the checkif v != False with if v is not False to ensure that the comparison is done using identity rather than equality. This is more Pythonic and avoids potential issues with different types that may evaluate to false.** [src/workflow/CommandExecutor.py [170]](https://github.com/OpenMS/streamlit-template/pull/59/files#diff-8415106457fd9d1400b9074c525816f067a131350c54c9ec9927efbc2f32162aR170-R170) ```diff -if v != False: +if v is not False: ``` | ||||
| Enhancement |
Add a check for None values to prevent errors.___ **Consider adding a check forNone values before appending to the command list to avoid potential errors when None is inadvertently passed as a value.**
[src/workflow/CommandExecutor.py [179]](https://github.com/OpenMS/streamlit-template/pull/59/files#diff-8415106457fd9d1400b9074c525816f067a131350c54c9ec9927efbc2f32162aR179-R179)
```diff
-command += [str(v)]
+if v is not None:
+ command += [str(v)]
```
| Add error handling for file removal operations.___ **Ensure that the temporary file is safely removed by using a try-except block to handlepotential exceptions during the unlink operation.** [src/workflow/CommandExecutor.py [274]](https://github.com/OpenMS/streamlit-template/pull/59/files#diff-8415106457fd9d1400b9074c525816f067a131350c54c9ec9927efbc2f32162aR274-R274) ```diff -tmp_params_file.unlink() +try: + tmp_params_file.unlink() +except Exception as e: + print(f"Failed to unlink file: {e}") ``` Maintainability |
| Clarify the condition for handling boolean flags.___ **Use a more explicit condition check for boolean flags by checkingif isinstance(v, bool) and v: instead of just elif isinstance(v, bool):. This ensures that the logic is clear and only true boolean flags are considered.** [src/workflow/CommandExecutor.py [176]](https://github.com/OpenMS/streamlit-template/pull/59/files#diff-8415106457fd9d1400b9074c525816f067a131350c54c9ec9927efbc2f32162aR176-R176) ```diff -elif isinstance(v, bool): +elif isinstance(v, bool) and v: ```
| Refactor command construction into a separate method.___ **Refactor the command construction logic into a separate method to improve readability andmaintainability of the run_topp method.**
[src/workflow/CommandExecutor.py [167-179]](https://github.com/OpenMS/streamlit-template/pull/59/files#diff-8415106457fd9d1400b9074c525816f067a131350c54c9ec9927efbc2f32162aR167-R179)
```diff
-if tool in params.keys():
- for k, v in params[tool].items():
+def construct_command(params):
+ command = []
+ for k, v in params.items():
if v is not False:
- command += [f"-{k}"]
+ command.append(f"-{k}")
if isinstance(v, str) and "\n" in v:
- command += v.split("\n")
+ command.extend(v.split("\n"))
elif isinstance(v, bool) and v:
continue
else:
- command += [str(v)]
+ command.append(str(v))
+ return command
```
|
axelwalter
commented
2 weeks ago Running this with the example workflow results in errors for non-flag boolean values, which require "true" or "false" passed as string.
Invalid string parameter value '' for parameter 'enable_RT_filtering' given! Valid values are: 'false,true'. Updating failed!
axelwalter
commented
2 weeks ago Setting the value depending on bool or string type might solve it? https://github.com/OpenMS/streamlit-template/blob/bbbd104183a58aa8b2c975a6e9cf0fcfdbd0f4f2/src/workflow/StreamlitUI.py#L420
poshul
commented
2 weeks ago Running this with the example workflow results in errors for non-flag boolean values, which require "true" or "false" passed as string.
Invalid string parameter value '' for parameter 'enable_RT_filtering' given! Valid values are: 'false,true'. Updating failed!
Hmm, thats a problem. Underlying this is gonna be the fact that since ParamValue doesn't have a type for Bool (https://github.com/OpenMS/OpenMS/blob/develop/src/openms/include/OpenMS/DATASTRUCTURES/ParamValue.h#L37-L46) and the "type" field from the ini file doesn't get stored, that I don't think we can tell the difference between a flag and a string option that just has true or false as its options from the option itself.
Maybe we can check the allowable values as well to distinguish?
PR Type
enhancement
Description
CommandExecutor.py:Changes walkthrough 📝
CommandExecutor.py
Enhance Flag Handling in Command Constructionsrc/workflow/CommandExecutor.py
appropriately.
is added if the value is true.
formation.