Stream apis

[chakrabandla]

PR Type

enhancement, dependencies

---

Description

• Introduced streaming capabilities for both project and file metadata using new methods in Files and Project classes.
• Added new CLI commands to facilitate streaming of metadata to files.
• Enhanced utility functions to support asynchronous streaming with httpx.
• Updated dependencies to include httpx for handling asynchronous HTTP requests.
• Updated package version and author email in setup.py.

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Changes walkthrough 📝

	Relevant files
Enhancement	files.py Add streaming capability for file metadata                              pridepy/files/files.py Added a new method stream_all_files_metadata for streaming file metadata. Introduced V3_API_BASE_URL for API requests. +18/-0    pridepy.py Add CLI commands for streaming metadata                                    pridepy/pridepy.py Added CLI commands for streaming project and file metadata. Utilized asyncio for asynchronous operations. +38/-1    project.py Implement project metadata streaming functionality              pridepy/project/project.py Added stream_all_projects method for streaming project metadata. Introduced V3_API_BASE_URL for API requests. +14/-0    api_handling.py Add utility for handling streaming API responses                  pridepy/util/api_handling.py Added stream_response_to_file method for handling streaming responses. Utilized httpx for asynchronous HTTP requests. +29/-0
Miscellaneous	setup.py Update package version and author email                                    setup.py Updated package version to 0.0.5. Changed author email to [email protected]. +2/-2
Dependencies	environment.yml Add httpx to dependencies                                                                environment.yml Added httpx to the list of dependencies. +2/-1      requirements.txt Add httpx to requirements                                                                requirements.txt Added httpx to the list of dependencies. +2/-1

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⏱️ Estimated effort to review: 3 🔵🔵🔵⚪⚪

🧪 No relevant tests

🔒 No security concerns identified

⚡ Recommended focus areas for review Error Handling The new stream_all_files_metadata method lacks proper error handling for API requests and file operations. Input Validation The new CLI commands for streaming metadata lack input validation for the output file path. Resource Management The stream_response_to_file method doesn't use a context manager for file handling, which could lead to resource leaks.

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PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Score
Best practice	✅ Use a context manager for file operations to ensure proper resource management Suggestion Impact: The commit implemented the suggestion by replacing the manual file open and close operations with a context manager using 'with open(out_file, 'w') as cfile:'. code diff: - cfile = open(out_file, 'w') - # Iterate over the streaming content line by line - async for line in response.aiter_lines(): - if line: # Avoid printing empty lines (common with text/event-stream) - cfile.write(line + "\n") - # Check if the pattern exists in the string - if re.search(regex_search_pattern, line): - pbar.update(1) # Update progress bar by 1 for each detection - cfile.close() + with open(out_file, 'w') as cfile: Consider using a context manager for file operations to ensure proper file closure, even in case of exceptions. pridepy/util/api_handling.py [49-57] -cfile = open(out_file, 'w') -# ... file operations ... -cfile.close() +with open(out_file, 'w') as cfile: + # ... file operations ... Suggestion importance[1-10]: 8 Why: Implementing a context manager for file operations ensures that files are properly closed even if an exception occurs, which is a best practice for resource management.	8
Maintainability	Use a constant for API version to improve maintainability Consider using a constant for the API version number instead of hardcoding it in the URL. This will make it easier to update the API version across the entire codebase in the future. pridepy/files/files.py [53] -V3_API_BASE_URL = "https://www.ebi.ac.uk/pride/ws/archive/v3" +API_VERSION = "v3" +V3_API_BASE_URL = f"https://www.ebi.ac.uk/pride/ws/archive/{API_VERSION}" Apply this suggestion Suggestion importance[1-10]: 7 Why: Using a constant for the API version enhances maintainability by centralizing the version number, making future updates easier and reducing the risk of errors from hardcoded values.	7
Enhancement	✅ Use f-strings for string formatting to improve readability and performance Consider using f-strings for string formatting instead of the .format() method for improved readability and performance. pridepy/files/files.py [71-72] -request_url = ("{0}/files/all".format(self.V3_API_BASE_URL)) -count_request_url = ("{0}/files/count".format(self.V3_API_BASE_URL)) +request_url = f"{self.V3_API_BASE_URL}/files/all" +count_request_url = f"{self.V3_API_BASE_URL}/files/count" [Suggestion has been applied] Suggestion importance[1-10]: 6 Why: Replacing the .format() method with f-strings improves code readability and performance, aligning with modern Python practices.	6

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CI Failure Feedback 🧐

Action: build

Failed stage: Install mamba, boa and conda-build [❌]

Relevant error logs: 1: ##[group]Operating System 2: Ubuntu ... 405: download_only: False 406: dry_run: False 407: enable_private_envs: False 408: env_prompt: ({default_env}) 409: envs_dirs: 410: - /usr/share/miniconda/envs 411: - /home/runner/.conda/envs 412: envvars_force_uppercase: True 413: error_upload_url: https://conda.io/conda-post/unexpected-error ... 443: remote_connect_timeout_secs: 9.15 444: remote_max_retries: 3 445: remote_read_timeout_secs: 60.0 446: repodata_fns: 447: - current_repodata.json 448: - repodata.json 449: repodata_threads: None 450: repodata_use_zst: True 451: report_errors: None ... 747: Executing transaction: ...working... done 748: Channels: 749: - conda-forge 750: - defaults 751: - bioconda 752: Platform: linux-64 753: Collecting package metadata (repodata.json): ...working... done 754: warning libmamba Added empty dependency for problem type SOLVER_RULE_UPDATE 755: Solving environment: ...working... failed 756: LibMambaUnsatisfiableError: Encountered problems while solving: ... 813: │ ├─ conda-build [24.1.0|24.1.1|...|3.28.4], which can be installed (as previously explained); 814: │ ├─ conda-build [24.1.0|24.1.1|...|3.28.4], which can be installed (as previously explained); 815: │ └─ conda-build [24.1.0|24.1.1|...|24.5.1] would require 816: │ └─ python >=3.12,<3.13.0a0 , which can be installed; 817: └─ pin-1 is not installable because it requires 818: └─ python 3.13.* , which conflicts with any installable versions previously reported. 819: Pins seem to be involved in the conflict. Currently pinned specs: 820: - python 3.13.* (labeled as 'pin-1') 821: ##[error]Process completed with exit code 1.

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Action: build

Failed stage: Install mamba, boa and conda-build [❌]

Failure summary: The action failed due to a dependency resolution conflict in the Conda environment: The conda-build package requires python version >=3.12,<3.13.0a0. However, there is a pin on python version 3.13.*, which conflicts with the required version range for conda-build. This conflict resulted in a LibMambaUnsatisfiableError, preventing the environment from being solved.

Relevant error logs: 1: ##[group]Operating System 2: Ubuntu ... 405: download_only: False 406: dry_run: False 407: enable_private_envs: False 408: env_prompt: ({default_env}) 409: envs_dirs: 410: - /usr/share/miniconda/envs 411: - /home/runner/.conda/envs 412: envvars_force_uppercase: True 413: error_upload_url: https://conda.io/conda-post/unexpected-error ... 443: remote_connect_timeout_secs: 9.15 444: remote_max_retries: 3 445: remote_read_timeout_secs: 60.0 446: repodata_fns: 447: - current_repodata.json 448: - repodata.json 449: repodata_threads: None 450: repodata_use_zst: True 451: report_errors: None ... 747: Executing transaction: ...working... done 748: Channels: 749: - conda-forge 750: - defaults 751: - bioconda 752: Platform: linux-64 753: Collecting package metadata (repodata.json): ...working... done 754: warning libmamba Added empty dependency for problem type SOLVER_RULE_UPDATE 755: Solving environment: ...working... failed 756: LibMambaUnsatisfiableError: Encountered problems while solving: ... 813: │ ├─ conda-build [24.1.0|24.1.1|...|3.28.4], which can be installed (as previously explained); 814: │ ├─ conda-build [24.1.0|24.1.1|...|3.28.4], which can be installed (as previously explained); 815: │ └─ conda-build [24.1.0|24.1.1|...|24.5.1] would require 816: │ └─ python >=3.12,<3.13.0a0 , which can be installed; 817: └─ pin-1 is not installable because it requires 818: └─ python 3.13.* , which conflicts with any installable versions previously reported. 819: Pins seem to be involved in the conflict. Currently pinned specs: 820: - python 3.13.* (labeled as 'pin-1') 821: ##[error]Process completed with exit code 1.

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In addition to being automatically triggered, the tool can also be invoked manually by commenting on a PR:

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CI Failure Feedback 🧐

Action: build

Failed stage: Install mamba, boa and conda-build [❌]

Failure summary: The action failed due to a dependency resolution conflict in the Conda environment: The package conda-build requires python version >=3.12,<3.13.0a0. However, there is a pinned requirement for python version 3.13.*, which conflicts with the required version range for conda-build. This conflict resulted in a LibMambaUnsatisfiableError during the environment solving process.

Relevant error logs: 1: ##[group]Operating System 2: Ubuntu ... 405: download_only: False 406: dry_run: False 407: enable_private_envs: False 408: env_prompt: ({default_env}) 409: envs_dirs: 410: - /usr/share/miniconda/envs 411: - /home/runner/.conda/envs 412: envvars_force_uppercase: True 413: error_upload_url: https://conda.io/conda-post/unexpected-error ... 443: remote_connect_timeout_secs: 9.15 444: remote_max_retries: 3 445: remote_read_timeout_secs: 60.0 446: repodata_fns: 447: - current_repodata.json 448: - repodata.json 449: repodata_threads: None 450: repodata_use_zst: True 451: report_errors: None ... 747: Executing transaction: ...working... done 748: Channels: 749: - conda-forge 750: - defaults 751: - bioconda 752: Platform: linux-64 753: Collecting package metadata (repodata.json): ...working... done 754: warning libmamba Added empty dependency for problem type SOLVER_RULE_UPDATE 755: Solving environment: ...working... failed 756: LibMambaUnsatisfiableError: Encountered problems while solving: ... 813: │ ├─ conda-build [24.1.0|24.1.1|...|3.28.4], which can be installed (as previously explained); 814: │ ├─ conda-build [24.1.0|24.1.1|...|3.28.4], which can be installed (as previously explained); 815: │ └─ conda-build [24.1.0|24.1.1|...|24.5.1] would require 816: │ └─ python >=3.12,<3.13.0a0 , which can be installed; 817: └─ pin-1 is not installable because it requires 818: └─ python 3.13.* , which conflicts with any installable versions previously reported. 819: Pins seem to be involved in the conflict. Currently pinned specs: 820: - python 3.13.* (labeled as 'pin-1') 821: ##[error]Process completed with exit code 1.

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✨ CI feedback usage guide:

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The CI feedback tool (/checks) automatically triggers when a PR has a failed check.
The tool analyzes the failed checks and provides several feedbacks:

• Failed stage
• Failed test name
• Failure summary
• Relevant error logs

In addition to being automatically triggered, the tool can also be invoked manually by commenting on a PR:

/checks "https://github.com/{repo_name}/actions/runs/{run_number}/job/{job_number}"

where {repo_name} is the name of the repository, {run_number} is the run number of the failed check, and {job_number} is the job number of the failed check.

Configuration options

• enable_auto_checks_feedback - if set to true, the tool will automatically provide feedback when a check is failed. Default is true.
• excluded_checks_list - a list of checks to exclude from the feedback, for example: ["check1", "check2"]. Default is an empty list.
• enable_help_text - if set to true, the tool will provide a help message with the feedback. Default is true.
• persistent_comment - if set to true, the tool will overwrite a previous checks comment with the new feedback. Default is true.
• final_update_message - if persistent_comment is true and updating a previous checks message, the tool will also create a new message: "Persistent checks updated to latest commit". Default is true.

See more information about the checks tool in the docs.

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CI Failure Feedback 🧐

Action: build

Failed stage: Install mamba, boa and conda-build [❌]

Failure summary: The action failed due to a dependency conflict while solving the environment with conda: The package conda-build requires python version >=3.12,<3.13.0a0. However, there is a pin for python version 3.13.* which conflicts with the required version range for conda-build. This conflict resulted in a LibMambaUnsatisfiableError, preventing the environment from being solved successfully.

Relevant error logs: 1: ##[group]Operating System 2: Ubuntu ... 405: download_only: False 406: dry_run: False 407: enable_private_envs: False 408: env_prompt: ({default_env}) 409: envs_dirs: 410: - /usr/share/miniconda/envs 411: - /home/runner/.conda/envs 412: envvars_force_uppercase: True 413: error_upload_url: https://conda.io/conda-post/unexpected-error ... 443: remote_connect_timeout_secs: 9.15 444: remote_max_retries: 3 445: remote_read_timeout_secs: 60.0 446: repodata_fns: 447: - current_repodata.json 448: - repodata.json 449: repodata_threads: None 450: repodata_use_zst: True 451: report_errors: None ... 747: Executing transaction: ...working... done 748: Channels: 749: - conda-forge 750: - defaults 751: - bioconda 752: Platform: linux-64 753: Collecting package metadata (repodata.json): ...working... done 754: warning libmamba Added empty dependency for problem type SOLVER_RULE_UPDATE 755: Solving environment: ...working... failed 756: LibMambaUnsatisfiableError: Encountered problems while solving: ... 813: │ ├─ conda-build [24.1.0|24.1.1|...|3.28.4], which can be installed (as previously explained); 814: │ ├─ conda-build [24.1.0|24.1.1|...|3.28.4], which can be installed (as previously explained); 815: │ └─ conda-build [24.1.0|24.1.1|...|24.5.1] would require 816: │ └─ python >=3.12,<3.13.0a0 , which can be installed; 817: └─ pin-1 is not installable because it requires 818: └─ python 3.13.* , which conflicts with any installable versions previously reported. 819: Pins seem to be involved in the conflict. Currently pinned specs: 820: - python 3.13.* (labeled as 'pin-1') 821: ##[error]Process completed with exit code 1.

---

✨ CI feedback usage guide:

---

The CI feedback tool (/checks) automatically triggers when a PR has a failed check.
The tool analyzes the failed checks and provides several feedbacks:

• Failed stage
• Failed test name
• Failure summary
• Relevant error logs

In addition to being automatically triggered, the tool can also be invoked manually by commenting on a PR:

/checks "https://github.com/{repo_name}/actions/runs/{run_number}/job/{job_number}"

where {repo_name} is the name of the repository, {run_number} is the run number of the failed check, and {job_number} is the job number of the failed check.

Configuration options

• enable_auto_checks_feedback - if set to true, the tool will automatically provide feedback when a check is failed. Default is true.
• excluded_checks_list - a list of checks to exclude from the feedback, for example: ["check1", "check2"]. Default is an empty list.
• enable_help_text - if set to true, the tool will provide a help message with the feedback. Default is true.
• persistent_comment - if set to true, the tool will overwrite a previous checks comment with the new feedback. Default is true.
• final_update_message - if persistent_comment is true and updating a previous checks message, the tool will also create a new message: "Persistent checks updated to latest commit". Default is true.

See more information about the checks tool in the docs.