Refactor bio.tools sync: add protected fields validation, BioToolsClient, and improve update logic#51
Open
anitamnd wants to merge 4 commits into
Open
Conversation
anitamnd
force-pushed
the
fix/gh2biotools
branch
from
6e9d5c7 to
23d29f5
Compare
Contributor
There was a problem hiding this comment.
Pull request overview
This PR refactors the gh2biotools sync script by introducing a BioToolsClient abstraction, adds retry/rate-limiting behavior, and introduces a shell validator to prevent modifications to protected fields in .biotools.json files (skipping checks for newly added files).
Changes:
- Added
scripts/runbiotools/validate-biotools-fields.shto detect protected-field changes betweenGITHUB_BEFORE_SHAand the current workspace. - Refactored
scripts/runbiotools/gh2biotools.pyinto aBioToolsClientwith improved logging, timeouts, and retry support. - Updated sync logic to categorize results and exit non-zero when failures occur.
Reviewed changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 5 comments.
| File | Description |
|---|---|
| scripts/runbiotools/validate-biotools-fields.sh | Adds protected-field diff validation for existing .biotools.json files. |
| scripts/runbiotools/gh2biotools.py | Refactors bio.tools syncing into a client class with retries, rate limiting, and improved reporting. |
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
Comment on lines
+100
to
+106
| elif response.status_code == 404: | ||
| return None | ||
| else: | ||
| logging.error( | ||
| f"Error retrieving tool {tool_id}: {response.status_code} {response.text}" | ||
| ) | ||
| return None |
Contributor
There was a problem hiding this comment.
@anitamnd this is a good point. if I get the logic correctly, if return code is not 200 nor 404 it should raise requests.RequestException right?
Comment on lines
+268
to
+279
| existing_tool_clean = remap(existing_tool, lambda p, k, v: bool(v)) | ||
| payload_dict_clean = remap(payload_dict, lambda p, k, v: bool(v)) | ||
|
|
||
| if existing_tool_clean == payload_dict_clean: | ||
| logging.info(f"Tool {tool_id} is unchanged") | ||
| return tool_id, "unchanged" | ||
|
|
||
| # Validate and update | ||
| if not self.validate_update(tool_id, payload_dict): | ||
| return tool_id, "failed_validation" | ||
|
|
||
| success = self.update_tool(payload_dict) |
Comment on lines
+30
to
+35
| # Check if this is a new file or existing file | ||
| if ! git show "${GITHUB_BEFORE_SHA}:${file}" > old.json 2>/dev/null; then | ||
| # NEW FILE | ||
| echo "ℹ New file detected: $file" | ||
| echo "ℹ Skipping validation for protected fields..." | ||
| else |
Comment on lines
+25
to
+49
| failed=false | ||
|
|
||
| for file in "$@"; do | ||
| echo "Validating $file..." | ||
|
|
||
| # Check if this is a new file or existing file | ||
| if ! git show "${GITHUB_BEFORE_SHA}:${file}" > old.json 2>/dev/null; then | ||
| # NEW FILE | ||
| echo "ℹ New file detected: $file" | ||
| echo "ℹ Skipping validation for protected fields..." | ||
| else | ||
| # EXISTING FILE | ||
| echo "ℹ Existing file: $file" | ||
| cat "$file" > new.json | ||
|
|
||
| for field in "${PROTECTED_FIELDS[@]}"; do | ||
| old_val=$(jq -r ".$field // empty" old.json 2>/dev/null) | ||
| new_val=$(jq -r ".$field // empty" new.json 2>/dev/null) | ||
| if [ "$old_val" != "$new_val" ]; then | ||
| echo "::error file=$file::Protected field '$field' was modified (old: '$old_val', new: '$new_val')" | ||
| failed=true | ||
| fi | ||
| done | ||
|
|
||
| rm -f old.json new.json |
Comment on lines
+40
to
+46
| for field in "${PROTECTED_FIELDS[@]}"; do | ||
| old_val=$(jq -r ".$field // empty" old.json 2>/dev/null) | ||
| new_val=$(jq -r ".$field // empty" new.json 2>/dev/null) | ||
| if [ "$old_val" != "$new_val" ]; then | ||
| echo "::error file=$file::Protected field '$field' was modified (old: '$old_val', new: '$new_val')" | ||
| failed=true | ||
| fi |
hmenager
requested changes
May 12, 2026
Comment on lines
+100
to
+106
| elif response.status_code == 404: | ||
| return None | ||
| else: | ||
| logging.error( | ||
| f"Error retrieving tool {tool_id}: {response.status_code} {response.text}" | ||
| ) | ||
| return None |
Contributor
There was a problem hiding this comment.
@anitamnd this is a good point. if I get the logic correctly, if return code is not 200 nor 404 it should raise requests.RequestException right?
Comment on lines
+268
to
+279
| existing_tool_clean = remap(existing_tool, lambda p, k, v: bool(v)) | ||
| payload_dict_clean = remap(payload_dict, lambda p, k, v: bool(v)) | ||
|
|
||
| if existing_tool_clean == payload_dict_clean: | ||
| logging.info(f"Tool {tool_id} is unchanged") | ||
| return tool_id, "unchanged" | ||
|
|
||
| # Validate and update | ||
| if not self.validate_update(tool_id, payload_dict): | ||
| return tool_id, "failed_validation" | ||
|
|
||
| success = self.update_tool(payload_dict) |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
This PR refactors the gh2biotools sync by introducing a BioToolsClient class while preserving the existing logic and brings some improvements: