🧪 Add test for name2uniprot HTTPError handling - #60

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testing-pathwaycommons-httperror-8747017411960774222
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🧪 Add test for name2uniprot HTTPError handling#60
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testing-pathwaycommons-httperror-8747017411960774222

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@akutuva21akutuva21 commented Apr 9, 2026

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🎯 What: The testing gap in bionetgen/atomizer/utils/pathwaycommons.py:221 has been addressed. The name2uniprot function now has a test ensuring it properly handles urllib.error.HTTPError returning None.

📊 Coverage: The test explicitly mocks urllib.request.urlopen and verifies the error path catching network errors when querying Uniprot with an organism parameter.

✨ Result: Improved test coverage and reliability of pathway component generation when network failures occur.

PR created automatically by Jules for task 8747017411960774222 started by @akutuva21

@google-labs-jules@akutuva21
Add test for name2uniprot HTTPError handling
1dd1205
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
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👋 Jules, reporting for duty! I'm here to lend a hand with this pull request.

When you start a review, I'll add a 👀 emoji to each comment to let you know I've read it. I'll focus on feedback directed at me and will do my best to stay out of conversations between you and other bots or reviewers to keep the noise down.

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google-labs-julesBotand others added 2 commits April 9, 2026 21:15
@google-labs-jules@akutuva21
Add test for name2uniprot HTTPError handling
ba5f06f
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@akutuva21
chore: PR#60remove forbidden artifacts and run black
1d92964
This was referenced Apr 13, 2026
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Closed after triage: this PR can no longer be cleanly rebased onto current main due to conflicts with newer merged PRs in the same area. Reopen as a fresh PR if any behavior is still needed.

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Closed after triage: this PR can no longer be cleanly rebased onto current main due to conflicts with newer merged PRs in the same area. Reopen as a fresh PR if any behavior is still needed.

Understood. Acknowledging that this work is now obsolete and stopping work on this task.

@akutuva21
akutuva21 deleted the testing-pathwaycommons-httperror-8747017411960774222 branch April 13, 2026 14:46
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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
🧪 Add test for name2uniprot HTTPError handling - #60
Closed
akutuva21 wants to merge 3 commits into
mainfrom 
testing-pathwaycommons-httperror-8747017411960774222
Closed
🧪 Add test for name2uniprot HTTPError handling#60
akutuva21 wants to merge 3 commits into
mainfrom 
testing-pathwaycommons-httperror-8747017411960774222
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@akutuva21
@akutuva21akutuva21
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Apr 9, 2026

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🎯 What: The testing gap in bionetgen/atomizer/utils/pathwaycommons.py:221 has been addressed. The name2uniprot function now has a test ensuring it properly handles urllib.error.HTTPError returning None.
📊 Coverage: The test explicitly mocks urllib.request.urlopen and verifies the error path catching network errors when querying Uniprot with an organism parameter.
✨ Result: Improved test coverage and reliability of pathway component generation when network failures occur.
PR created automatically by Jules for task 8747017411960774222 started by @akutuva21
@google-labs-jules@akutuva21
Add test for name2uniprot HTTPError handling
1dd1205
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
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👋 Jules, reporting for duty! I'm here to lend a hand with this pull request.
When you start a review, I'll add a 👀 emoji to each comment to let you know I've read it. I'll focus on feedback directed at me and will do my best to stay out of conversations between you and other bots or reviewers to keep the noise down.
I'll push a commit with your requested changes shortly after. Please note there might be a delay between these steps, but rest assured I'm on the job!
For more direct control, you can switch me to Reactive Mode. When this mode is on, I will only act on comments where you specifically mention me with @jules. You can find this option in the Pull Request section of your global Jules UI settings. You can always switch back!
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For security, I will only act on instructions from the user who triggered this task.
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added 2 commits
April 9, 2026 21:15
@google-labs-jules@akutuva21
Add test for name2uniprot HTTPError handling
ba5f06f
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@akutuva21
chore: PR#60remove forbidden artifacts and run black
1d92964

This was referenced Apr 13, 2026
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Closed after triage: this PR can no longer be cleanly rebased onto current main due to conflicts with newer merged PRs in the same area. Reopen as a fresh PR if any behavior is still needed.
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Closed after triage: this PR can no longer be cleanly rebased onto current main due to conflicts with newer merged PRs in the same area. Reopen as a fresh PR if any behavior is still needed.
Understood. Acknowledging that this work is now obsolete and stopping work on this task.
@akutuva21
akutuva21
deleted the

testing-pathwaycommons-httperror-8747017411960774222

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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
🧪 Add test for name2uniprot HTTPError handling - #60
Closed
akutuva21 wants to merge 3 commits into
mainfrom 
testing-pathwaycommons-httperror-8747017411960774222
Closed
🧪 Add test for name2uniprot HTTPError handling#60
akutuva21 wants to merge 3 commits into
mainfrom 
testing-pathwaycommons-httperror-8747017411960774222
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@akutuva21
@akutuva21akutuva21
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Apr 9, 2026

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🎯 What: The testing gap in bionetgen/atomizer/utils/pathwaycommons.py:221 has been addressed. The name2uniprot function now has a test ensuring it properly handles urllib.error.HTTPError returning None.
📊 Coverage: The test explicitly mocks urllib.request.urlopen and verifies the error path catching network errors when querying Uniprot with an organism parameter.
✨ Result: Improved test coverage and reliability of pathway component generation when network failures occur.
PR created automatically by Jules for task 8747017411960774222 started by @akutuva21
@google-labs-jules@akutuva21
Add test for name2uniprot HTTPError handling
1dd1205
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
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👋 Jules, reporting for duty! I'm here to lend a hand with this pull request.
When you start a review, I'll add a 👀 emoji to each comment to let you know I've read it. I'll focus on feedback directed at me and will do my best to stay out of conversations between you and other bots or reviewers to keep the noise down.
I'll push a commit with your requested changes shortly after. Please note there might be a delay between these steps, but rest assured I'm on the job!
For more direct control, you can switch me to Reactive Mode. When this mode is on, I will only act on comments where you specifically mention me with @jules. You can find this option in the Pull Request section of your global Jules UI settings. You can always switch back!
New to Jules? Learn more at jules.google/docs.
For security, I will only act on instructions from the user who triggered this task.
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added 2 commits
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@google-labs-jules@akutuva21
Add test for name2uniprot HTTPError handling
ba5f06f
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@akutuva21
chore: PR#60remove forbidden artifacts and run black
1d92964

This was referenced Apr 13, 2026
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Closed after triage: this PR can no longer be cleanly rebased onto current main due to conflicts with newer merged PRs in the same area. Reopen as a fresh PR if any behavior is still needed.
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Closed after triage: this PR can no longer be cleanly rebased onto current main due to conflicts with newer merged PRs in the same area. Reopen as a fresh PR if any behavior is still needed.
Understood. Acknowledging that this work is now obsolete and stopping work on this task.
@akutuva21
akutuva21
deleted the

testing-pathwaycommons-httperror-8747017411960774222

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April 13, 2026 14:46
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
🧪 Add test for name2uniprot HTTPError handling - #60
Closed
akutuva21 wants to merge 3 commits into
mainfrom 
testing-pathwaycommons-httperror-8747017411960774222
Closed
🧪 Add test for name2uniprot HTTPError handling#60
akutuva21 wants to merge 3 commits into
mainfrom 
testing-pathwaycommons-httperror-8747017411960774222
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@akutuva21
@akutuva21akutuva21
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Apr 9, 2026

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🎯 What: The testing gap in bionetgen/atomizer/utils/pathwaycommons.py:221 has been addressed. The name2uniprot function now has a test ensuring it properly handles urllib.error.HTTPError returning None.
📊 Coverage: The test explicitly mocks urllib.request.urlopen and verifies the error path catching network errors when querying Uniprot with an organism parameter.
✨ Result: Improved test coverage and reliability of pathway component generation when network failures occur.
PR created automatically by Jules for task 8747017411960774222 started by @akutuva21
@google-labs-jules@akutuva21
Add test for name2uniprot HTTPError handling
1dd1205
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
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Apr 9, 2026

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👋 Jules, reporting for duty! I'm here to lend a hand with this pull request.
When you start a review, I'll add a 👀 emoji to each comment to let you know I've read it. I'll focus on feedback directed at me and will do my best to stay out of conversations between you and other bots or reviewers to keep the noise down.
I'll push a commit with your requested changes shortly after. Please note there might be a delay between these steps, but rest assured I'm on the job!
For more direct control, you can switch me to Reactive Mode. When this mode is on, I will only act on comments where you specifically mention me with @jules. You can find this option in the Pull Request section of your global Jules UI settings. You can always switch back!
New to Jules? Learn more at jules.google/docs.
For security, I will only act on instructions from the user who triggered this task.
google-labs-julesBotand others
added 2 commits
April 9, 2026 21:15
@google-labs-jules@akutuva21
Add test for name2uniprot HTTPError handling
ba5f06f
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@akutuva21
chore: PR#60remove forbidden artifacts and run black
1d92964

This was referenced Apr 13, 2026
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Closed after triage: this PR can no longer be cleanly rebased onto current main due to conflicts with newer merged PRs in the same area. Reopen as a fresh PR if any behavior is still needed.
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Closed after triage: this PR can no longer be cleanly rebased onto current main due to conflicts with newer merged PRs in the same area. Reopen as a fresh PR if any behavior is still needed.
Understood. Acknowledging that this work is now obsolete and stopping work on this task.
@akutuva21
akutuva21
deleted the

testing-pathwaycommons-httperror-8747017411960774222

branch
April 13, 2026 14:46
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
🧪 Add test for name2uniprot HTTPError handling - #60
Closed
akutuva21 wants to merge 3 commits into
mainfrom 
testing-pathwaycommons-httperror-8747017411960774222
Closed
🧪 Add test for name2uniprot HTTPError handling#60
akutuva21 wants to merge 3 commits into
mainfrom 
testing-pathwaycommons-httperror-8747017411960774222
Conversation
@akutuva21
@akutuva21akutuva21
commented
Apr 9, 2026

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Owner
🎯 What: The testing gap in bionetgen/atomizer/utils/pathwaycommons.py:221 has been addressed. The name2uniprot function now has a test ensuring it properly handles urllib.error.HTTPError returning None.
📊 Coverage: The test explicitly mocks urllib.request.urlopen and verifies the error path catching network errors when querying Uniprot with an organism parameter.
✨ Result: Improved test coverage and reliability of pathway component generation when network failures occur.
PR created automatically by Jules for task 8747017411960774222 started by @akutuva21
@google-labs-jules@akutuva21
Add test for name2uniprot HTTPError handling
1dd1205
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules
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Apr 9, 2026

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👋 Jules, reporting for duty! I'm here to lend a hand with this pull request.
When you start a review, I'll add a 👀 emoji to each comment to let you know I've read it. I'll focus on feedback directed at me and will do my best to stay out of conversations between you and other bots or reviewers to keep the noise down.
I'll push a commit with your requested changes shortly after. Please note there might be a delay between these steps, but rest assured I'm on the job!
For more direct control, you can switch me to Reactive Mode. When this mode is on, I will only act on comments where you specifically mention me with @jules. You can find this option in the Pull Request section of your global Jules UI settings. You can always switch back!
New to Jules? Learn more at jules.google/docs.
For security, I will only act on instructions from the user who triggered this task.
google-labs-julesBotand others
added 2 commits
April 9, 2026 21:15
@google-labs-jules@akutuva21
Add test for name2uniprot HTTPError handling
ba5f06f
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@akutuva21
chore: PR#60remove forbidden artifacts and run black
1d92964

This was referenced Apr 13, 2026
 Closed

 Closed

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Apr 13, 2026

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Closed after triage: this PR can no longer be cleanly rebased onto current main due to conflicts with newer merged PRs in the same area. Reopen as a fresh PR if any behavior is still needed.
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Closed after triage: this PR can no longer be cleanly rebased onto current main due to conflicts with newer merged PRs in the same area. Reopen as a fresh PR if any behavior is still needed.
Understood. Acknowledging that this work is now obsolete and stopping work on this task.
@akutuva21
akutuva21
deleted the

testing-pathwaycommons-httperror-8747017411960774222

branch
April 13, 2026 14:46
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
🧪 Add test for name2uniprot HTTPError handling - #60
Closed
akutuva21 wants to merge 3 commits into
mainfrom 
testing-pathwaycommons-httperror-8747017411960774222
Closed
🧪 Add test for name2uniprot HTTPError handling#60
akutuva21 wants to merge 3 commits into
mainfrom 
testing-pathwaycommons-httperror-8747017411960774222
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Apr 9, 2026

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🎯 What: The testing gap in bionetgen/atomizer/utils/pathwaycommons.py:221 has been addressed. The name2uniprot function now has a test ensuring it properly handles urllib.error.HTTPError returning None.
📊 Coverage: The test explicitly mocks urllib.request.urlopen and verifies the error path catching network errors when querying Uniprot with an organism parameter.
✨ Result: Improved test coverage and reliability of pathway component generation when network failures occur.
PR created automatically by Jules for task 8747017411960774222 started by @akutuva21
@google-labs-jules@akutuva21
Add test for name2uniprot HTTPError handling
1dd1205
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
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Apr 9, 2026

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👋 Jules, reporting for duty! I'm here to lend a hand with this pull request.
When you start a review, I'll add a 👀 emoji to each comment to let you know I've read it. I'll focus on feedback directed at me and will do my best to stay out of conversations between you and other bots or reviewers to keep the noise down.
I'll push a commit with your requested changes shortly after. Please note there might be a delay between these steps, but rest assured I'm on the job!
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For security, I will only act on instructions from the user who triggered this task.
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added 2 commits
April 9, 2026 21:15
@google-labs-jules@akutuva21
Add test for name2uniprot HTTPError handling
ba5f06f
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@akutuva21
chore: PR#60remove forbidden artifacts and run black
1d92964

This was referenced Apr 13, 2026
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Apr 13, 2026

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Closed after triage: this PR can no longer be cleanly rebased onto current main due to conflicts with newer merged PRs in the same area. Reopen as a fresh PR if any behavior is still needed.
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Apr 13, 2026

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Closed after triage: this PR can no longer be cleanly rebased onto current main due to conflicts with newer merged PRs in the same area. Reopen as a fresh PR if any behavior is still needed.
Understood. Acknowledging that this work is now obsolete and stopping work on this task.
@akutuva21
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testing-pathwaycommons-httperror-8747017411960774222

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April 13, 2026 14:46
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
🧪 Add test for name2uniprot HTTPError handling - #60
Closed
akutuva21 wants to merge 3 commits into
mainfrom 
testing-pathwaycommons-httperror-8747017411960774222
Closed
🧪 Add test for name2uniprot HTTPError handling#60
akutuva21 wants to merge 3 commits into
mainfrom 
testing-pathwaycommons-httperror-8747017411960774222
Conversation
@akutuva21
@akutuva21akutuva21
commented
Apr 9, 2026

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🎯 What: The testing gap in bionetgen/atomizer/utils/pathwaycommons.py:221 has been addressed. The name2uniprot function now has a test ensuring it properly handles urllib.error.HTTPError returning None.
📊 Coverage: The test explicitly mocks urllib.request.urlopen and verifies the error path catching network errors when querying Uniprot with an organism parameter.
✨ Result: Improved test coverage and reliability of pathway component generation when network failures occur.
PR created automatically by Jules for task 8747017411960774222 started by @akutuva21
@google-labs-jules@akutuva21
Add test for name2uniprot HTTPError handling
1dd1205
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules
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Apr 9, 2026

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👋 Jules, reporting for duty! I'm here to lend a hand with this pull request.
When you start a review, I'll add a 👀 emoji to each comment to let you know I've read it. I'll focus on feedback directed at me and will do my best to stay out of conversations between you and other bots or reviewers to keep the noise down.
I'll push a commit with your requested changes shortly after. Please note there might be a delay between these steps, but rest assured I'm on the job!
For more direct control, you can switch me to Reactive Mode. When this mode is on, I will only act on comments where you specifically mention me with @jules. You can find this option in the Pull Request section of your global Jules UI settings. You can always switch back!
New to Jules? Learn more at jules.google/docs.
For security, I will only act on instructions from the user who triggered this task.
google-labs-julesBotand others
added 2 commits
April 9, 2026 21:15
@google-labs-jules@akutuva21
Add test for name2uniprot HTTPError handling
ba5f06f
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@akutuva21
chore: PR#60remove forbidden artifacts and run black
1d92964

This was referenced Apr 13, 2026
 Closed

 Closed

@akutuva21
akutuva21
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Apr 13, 2026

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Closed after triage: this PR can no longer be cleanly rebased onto current main due to conflicts with newer merged PRs in the same area. Reopen as a fresh PR if any behavior is still needed.
@google-labs-jules
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Apr 13, 2026

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Closed after triage: this PR can no longer be cleanly rebased onto current main due to conflicts with newer merged PRs in the same area. Reopen as a fresh PR if any behavior is still needed.
Understood. Acknowledging that this work is now obsolete and stopping work on this task.
@akutuva21
akutuva21
deleted the

testing-pathwaycommons-httperror-8747017411960774222

branch
April 13, 2026 14:46
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

Skip to content
🧪 Add test for name2uniprot HTTPError handling - #60
Closed
akutuva21 wants to merge 3 commits into
mainfrom 
testing-pathwaycommons-httperror-8747017411960774222
Closed
🧪 Add test for name2uniprot HTTPError handling#60
akutuva21 wants to merge 3 commits into
mainfrom 
testing-pathwaycommons-httperror-8747017411960774222
Conversation
@akutuva21
@akutuva21akutuva21
commented
Apr 9, 2026

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🎯 What: The testing gap in bionetgen/atomizer/utils/pathwaycommons.py:221 has been addressed. The name2uniprot function now has a test ensuring it properly handles urllib.error.HTTPError returning None.
📊 Coverage: The test explicitly mocks urllib.request.urlopen and verifies the error path catching network errors when querying Uniprot with an organism parameter.
✨ Result: Improved test coverage and reliability of pathway component generation when network failures occur.
PR created automatically by Jules for task 8747017411960774222 started by @akutuva21
@google-labs-jules@akutuva21
Add test for name2uniprot HTTPError handling
1dd1205
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules
google-labs-julesBot
commented
Apr 9, 2026

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👋 Jules, reporting for duty! I'm here to lend a hand with this pull request.
When you start a review, I'll add a 👀 emoji to each comment to let you know I've read it. I'll focus on feedback directed at me and will do my best to stay out of conversations between you and other bots or reviewers to keep the noise down.
I'll push a commit with your requested changes shortly after. Please note there might be a delay between these steps, but rest assured I'm on the job!
For more direct control, you can switch me to Reactive Mode. When this mode is on, I will only act on comments where you specifically mention me with @jules. You can find this option in the Pull Request section of your global Jules UI settings. You can always switch back!
New to Jules? Learn more at jules.google/docs.
For security, I will only act on instructions from the user who triggered this task.
google-labs-julesBotand others
added 2 commits
April 9, 2026 21:15
@google-labs-jules@akutuva21
Add test for name2uniprot HTTPError handling
ba5f06f
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@akutuva21
chore: PR#60remove forbidden artifacts and run black
1d92964

This was referenced Apr 13, 2026
 Closed

 Closed

@akutuva21
akutuva21
commented
Apr 13, 2026

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Closed after triage: this PR can no longer be cleanly rebased onto current main due to conflicts with newer merged PRs in the same area. Reopen as a fresh PR if any behavior is still needed.
@google-labs-jules
google-labs-julesBot
commented
Apr 13, 2026

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Closed after triage: this PR can no longer be cleanly rebased onto current main due to conflicts with newer merged PRs in the same area. Reopen as a fresh PR if any behavior is still needed.
Understood. Acknowledging that this work is now obsolete and stopping work on this task.
@akutuva21
akutuva21
deleted the

testing-pathwaycommons-httperror-8747017411960774222

branch
April 13, 2026 14:46
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