🧪 Tests for name2uniprot in pathwaycommons - #53

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🧪 Tests for name2uniprot in pathwaycommons#53
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@akutuva21akutuva21 commented Apr 9, 2026

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🎯 What: The testing gap addressed
The name2uniprot function in bionetgen/atomizer/utils/pathwaycommons.py lacked test coverage and requires mocked HTTP calls to biogrid/uniprot to be tested safely. The correct signature is def name2uniprot(nameStr, organism) based on the active code in the repository.

📊 Coverage: What scenarios are now tested
Created tests mapping to five distinct scenarios using unittest.mock.patch for urllib.request.urlopen:

  1. Successful response when an organism is provided.
  2. Fallback response (no organism limitation query) when the organism query returns no results.
  3. Successful response when no organism is initially provided.
  4. Correct error handling (returning None) when an HTTPError occurs with an organism provided.
  5. Correct error handling when an HTTPError occurs without an organism provided.

✨ Result: The improvement in test coverage
Test coverage is significantly improved by isolating external network requests, leading to deterministic test execution for the name2uniprot function. We use byte-strings internally mapped with .decode('utf-8') for correctness since the responses come from urllib.request.urlopen().read().

PR created automatically by Jules for task 14141266211072448977 started by @akutuva21

@google-labs-jules@akutuva21
Add tests for name2uniprot in pathwaycommons.py
fe95bd2
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 20:40
@akutuva21

akutuva21 commented Apr 13, 2026

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Superseded by #60 pathwaycommons HTTPError test coverage.

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Superseded by #60 pathwaycommons HTTPError test coverage.

Understood. Acknowledging that this work is superseded by #60, and I will stop work on this task.

@akutuva21
akutuva21 deleted the testing/pathwaycommons-name2uniprot-14141266211072448977 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
🧪 Tests for name2uniprot in pathwaycommons - #53
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akutuva21 wants to merge 3 commits into
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testing/pathwaycommons-name2uniprot-14141266211072448977
Closed
🧪 Tests for name2uniprot in pathwaycommons#53
akutuva21 wants to merge 3 commits into
mainfrom 
testing/pathwaycommons-name2uniprot-14141266211072448977
Conversation
@akutuva21
@akutuva21akutuva21
commented
Apr 9, 2026

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Owner
🎯 What: The testing gap addressed

The name2uniprot function in bionetgen/atomizer/utils/pathwaycommons.py lacked test coverage and requires mocked HTTP calls to biogrid/uniprot to be tested safely. The correct signature is def name2uniprot(nameStr, organism) based on the active code in the repository.
📊 Coverage: What scenarios are now tested

Created tests mapping to five distinct scenarios using unittest.mock.patch for urllib.request.urlopen:
  1. Successful response when an organism is provided.
  2. Fallback response (no organism limitation query) when the organism query returns no results.
  3. Successful response when no organism is initially provided.
  4. Correct error handling (returning None) when an HTTPError occurs with an organism provided.
  5. Correct error handling when an HTTPError occurs without an organism provided.
✨ Result: The improvement in test coverage

Test coverage is significantly improved by isolating external network requests, leading to deterministic test execution for the name2uniprot function. We use byte-strings internally mapped with .decode('utf-8') for correctness since the responses come from urllib.request.urlopen().read().
PR created automatically by Jules for task 14141266211072448977 started by @akutuva21
@google-labs-jules@akutuva21
Add tests for name2uniprot in pathwaycommons.py
fe95bd2
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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April 9, 2026 20:40
@akutuva21
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Apr 13, 2026

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Superseded by #60 pathwaycommons HTTPError test coverage.
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Apr 13, 2026

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Superseded by #60 pathwaycommons HTTPError test coverage.
Understood. Acknowledging that this work is superseded by #60, and I will stop work on this task.
@akutuva21
akutuva21
deleted the

testing/pathwaycommons-name2uniprot-14141266211072448977

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April 13, 2026 14:46
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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
🧪 Tests for name2uniprot in pathwaycommons - #53
Closed
akutuva21 wants to merge 3 commits into
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testing/pathwaycommons-name2uniprot-14141266211072448977
Closed
🧪 Tests for name2uniprot in pathwaycommons#53
akutuva21 wants to merge 3 commits into
mainfrom 
testing/pathwaycommons-name2uniprot-14141266211072448977
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@akutuva21
@akutuva21akutuva21
commented
Apr 9, 2026

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Owner
🎯 What: The testing gap addressed

The name2uniprot function in bionetgen/atomizer/utils/pathwaycommons.py lacked test coverage and requires mocked HTTP calls to biogrid/uniprot to be tested safely. The correct signature is def name2uniprot(nameStr, organism) based on the active code in the repository.
📊 Coverage: What scenarios are now tested

Created tests mapping to five distinct scenarios using unittest.mock.patch for urllib.request.urlopen:
  1. Successful response when an organism is provided.
  2. Fallback response (no organism limitation query) when the organism query returns no results.
  3. Successful response when no organism is initially provided.
  4. Correct error handling (returning None) when an HTTPError occurs with an organism provided.
  5. Correct error handling when an HTTPError occurs without an organism provided.
✨ Result: The improvement in test coverage

Test coverage is significantly improved by isolating external network requests, leading to deterministic test execution for the name2uniprot function. We use byte-strings internally mapped with .decode('utf-8') for correctness since the responses come from urllib.request.urlopen().read().
PR created automatically by Jules for task 14141266211072448977 started by @akutuva21
@google-labs-jules@akutuva21
Add tests for name2uniprot in pathwaycommons.py
fe95bd2
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
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April 9, 2026 20:40
@akutuva21
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Apr 13, 2026

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Superseded by #60 pathwaycommons HTTPError test coverage.
@google-labs-jules
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Apr 13, 2026

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Superseded by #60 pathwaycommons HTTPError test coverage.
Understood. Acknowledging that this work is superseded by #60, and I will stop work on this task.
@akutuva21
akutuva21
deleted the

testing/pathwaycommons-name2uniprot-14141266211072448977

branch
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
🧪 Tests for name2uniprot in pathwaycommons - #53
Closed
akutuva21 wants to merge 3 commits into
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testing/pathwaycommons-name2uniprot-14141266211072448977
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🧪 Tests for name2uniprot in pathwaycommons#53
akutuva21 wants to merge 3 commits into
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@akutuva21
@akutuva21akutuva21
commented
Apr 9, 2026

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🎯 What: The testing gap addressed

The name2uniprot function in bionetgen/atomizer/utils/pathwaycommons.py lacked test coverage and requires mocked HTTP calls to biogrid/uniprot to be tested safely. The correct signature is def name2uniprot(nameStr, organism) based on the active code in the repository.
📊 Coverage: What scenarios are now tested

Created tests mapping to five distinct scenarios using unittest.mock.patch for urllib.request.urlopen:
  1. Successful response when an organism is provided.
  2. Fallback response (no organism limitation query) when the organism query returns no results.
  3. Successful response when no organism is initially provided.
  4. Correct error handling (returning None) when an HTTPError occurs with an organism provided.
  5. Correct error handling when an HTTPError occurs without an organism provided.
✨ Result: The improvement in test coverage

Test coverage is significantly improved by isolating external network requests, leading to deterministic test execution for the name2uniprot function. We use byte-strings internally mapped with .decode('utf-8') for correctness since the responses come from urllib.request.urlopen().read().
PR created automatically by Jules for task 14141266211072448977 started by @akutuva21
@google-labs-jules@akutuva21
Add tests for name2uniprot in pathwaycommons.py
fe95bd2
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules
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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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@akutuva21
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Superseded by #60 pathwaycommons HTTPError test coverage.
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Apr 13, 2026

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Superseded by #60 pathwaycommons HTTPError test coverage.
Understood. Acknowledging that this work is superseded by #60, and I will stop work on this task.
@akutuva21
akutuva21
deleted the

testing/pathwaycommons-name2uniprot-14141266211072448977

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
🧪 Tests for name2uniprot in pathwaycommons - #53
Closed
akutuva21 wants to merge 3 commits into
mainfrom 
testing/pathwaycommons-name2uniprot-14141266211072448977
Closed
🧪 Tests for name2uniprot in pathwaycommons#53
akutuva21 wants to merge 3 commits into
mainfrom 
testing/pathwaycommons-name2uniprot-14141266211072448977
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@akutuva21
@akutuva21akutuva21
commented
Apr 9, 2026

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Owner
🎯 What: The testing gap addressed

The name2uniprot function in bionetgen/atomizer/utils/pathwaycommons.py lacked test coverage and requires mocked HTTP calls to biogrid/uniprot to be tested safely. The correct signature is def name2uniprot(nameStr, organism) based on the active code in the repository.
📊 Coverage: What scenarios are now tested

Created tests mapping to five distinct scenarios using unittest.mock.patch for urllib.request.urlopen:
  1. Successful response when an organism is provided.
  2. Fallback response (no organism limitation query) when the organism query returns no results.
  3. Successful response when no organism is initially provided.
  4. Correct error handling (returning None) when an HTTPError occurs with an organism provided.
  5. Correct error handling when an HTTPError occurs without an organism provided.
✨ Result: The improvement in test coverage

Test coverage is significantly improved by isolating external network requests, leading to deterministic test execution for the name2uniprot function. We use byte-strings internally mapped with .decode('utf-8') for correctness since the responses come from urllib.request.urlopen().read().
PR created automatically by Jules for task 14141266211072448977 started by @akutuva21
@google-labs-jules@akutuva21
Add tests for name2uniprot in pathwaycommons.py
fe95bd2
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules
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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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Superseded by #60 pathwaycommons HTTPError test coverage.
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Superseded by #60 pathwaycommons HTTPError test coverage.
Understood. Acknowledging that this work is superseded by #60, and I will stop work on this task.
@akutuva21
akutuva21
deleted the

testing/pathwaycommons-name2uniprot-14141266211072448977

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
🧪 Tests for name2uniprot in pathwaycommons - #53
Closed
akutuva21 wants to merge 3 commits into
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testing/pathwaycommons-name2uniprot-14141266211072448977
Closed
🧪 Tests for name2uniprot in pathwaycommons#53
akutuva21 wants to merge 3 commits into
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@akutuva21
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Apr 9, 2026

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🎯 What: The testing gap addressed

The name2uniprot function in bionetgen/atomizer/utils/pathwaycommons.py lacked test coverage and requires mocked HTTP calls to biogrid/uniprot to be tested safely. The correct signature is def name2uniprot(nameStr, organism) based on the active code in the repository.
📊 Coverage: What scenarios are now tested

Created tests mapping to five distinct scenarios using unittest.mock.patch for urllib.request.urlopen:
  1. Successful response when an organism is provided.
  2. Fallback response (no organism limitation query) when the organism query returns no results.
  3. Successful response when no organism is initially provided.
  4. Correct error handling (returning None) when an HTTPError occurs with an organism provided.
  5. Correct error handling when an HTTPError occurs without an organism provided.
✨ Result: The improvement in test coverage

Test coverage is significantly improved by isolating external network requests, leading to deterministic test execution for the name2uniprot function. We use byte-strings internally mapped with .decode('utf-8') for correctness since the responses come from urllib.request.urlopen().read().
PR created automatically by Jules for task 14141266211072448977 started by @akutuva21
@google-labs-jules@akutuva21
Add tests for name2uniprot in pathwaycommons.py
fe95bd2
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!
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For security, I will only act on instructions from the user who triggered this task.
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April 9, 2026 20:40
@akutuva21
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Apr 13, 2026

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Superseded by #60 pathwaycommons HTTPError test coverage.
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Apr 13, 2026

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Superseded by #60 pathwaycommons HTTPError test coverage.
Understood. Acknowledging that this work is superseded by #60, and I will stop work on this task.
@akutuva21
akutuva21
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testing/pathwaycommons-name2uniprot-14141266211072448977

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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('^' + ".*" + '

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🧪 Tests for name2uniprot in pathwaycommons - #53
Closed
akutuva21 wants to merge 3 commits into
mainfrom 
testing/pathwaycommons-name2uniprot-14141266211072448977
Closed
🧪 Tests for name2uniprot in pathwaycommons#53
akutuva21 wants to merge 3 commits into
mainfrom 
testing/pathwaycommons-name2uniprot-14141266211072448977
Conversation
@akutuva21
@akutuva21akutuva21
commented
Apr 9, 2026

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Owner
🎯 What: The testing gap addressed

The name2uniprot function in bionetgen/atomizer/utils/pathwaycommons.py lacked test coverage and requires mocked HTTP calls to biogrid/uniprot to be tested safely. The correct signature is def name2uniprot(nameStr, organism) based on the active code in the repository.
📊 Coverage: What scenarios are now tested

Created tests mapping to five distinct scenarios using unittest.mock.patch for urllib.request.urlopen:
  1. Successful response when an organism is provided.
  2. Fallback response (no organism limitation query) when the organism query returns no results.
  3. Successful response when no organism is initially provided.
  4. Correct error handling (returning None) when an HTTPError occurs with an organism provided.
  5. Correct error handling when an HTTPError occurs without an organism provided.
✨ Result: The improvement in test coverage

Test coverage is significantly improved by isolating external network requests, leading to deterministic test execution for the name2uniprot function. We use byte-strings internally mapped with .decode('utf-8') for correctness since the responses come from urllib.request.urlopen().read().
PR created automatically by Jules for task 14141266211072448977 started by @akutuva21
@google-labs-jules@akutuva21
Add tests for name2uniprot in pathwaycommons.py
fe95bd2
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules
google-labs-julesBot
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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 20:40
@akutuva21
akutuva21
commented
Apr 13, 2026

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Superseded by #60 pathwaycommons HTTPError test coverage.
@google-labs-jules
google-labs-julesBot
commented
Apr 13, 2026

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Superseded by #60 pathwaycommons HTTPError test coverage.
Understood. Acknowledging that this work is superseded by #60, and I will stop work on this task.
@akutuva21
akutuva21
deleted the

testing/pathwaycommons-name2uniprot-14141266211072448977

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
🧪 Tests for name2uniprot in pathwaycommons - #53
Closed
akutuva21 wants to merge 3 commits into
mainfrom 
testing/pathwaycommons-name2uniprot-14141266211072448977
Closed
🧪 Tests for name2uniprot in pathwaycommons#53
akutuva21 wants to merge 3 commits into
mainfrom 
testing/pathwaycommons-name2uniprot-14141266211072448977
Conversation
@akutuva21
@akutuva21akutuva21
commented
Apr 9, 2026

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Owner
🎯 What: The testing gap addressed

The name2uniprot function in bionetgen/atomizer/utils/pathwaycommons.py lacked test coverage and requires mocked HTTP calls to biogrid/uniprot to be tested safely. The correct signature is def name2uniprot(nameStr, organism) based on the active code in the repository.
📊 Coverage: What scenarios are now tested

Created tests mapping to five distinct scenarios using unittest.mock.patch for urllib.request.urlopen:
  1. Successful response when an organism is provided.
  2. Fallback response (no organism limitation query) when the organism query returns no results.
  3. Successful response when no organism is initially provided.
  4. Correct error handling (returning None) when an HTTPError occurs with an organism provided.
  5. Correct error handling when an HTTPError occurs without an organism provided.
✨ Result: The improvement in test coverage

Test coverage is significantly improved by isolating external network requests, leading to deterministic test execution for the name2uniprot function. We use byte-strings internally mapped with .decode('utf-8') for correctness since the responses come from urllib.request.urlopen().read().
PR created automatically by Jules for task 14141266211072448977 started by @akutuva21
@google-labs-jules@akutuva21
Add tests for name2uniprot in pathwaycommons.py
fe95bd2
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 20:40
@akutuva21
akutuva21
commented
Apr 13, 2026

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OwnerAuthor
Superseded by #60 pathwaycommons HTTPError test coverage.
@google-labs-jules
google-labs-julesBot
commented
Apr 13, 2026

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Superseded by #60 pathwaycommons HTTPError test coverage.
Understood. Acknowledging that this work is superseded by #60, and I will stop work on this task.
@akutuva21
akutuva21
deleted the

testing/pathwaycommons-name2uniprot-14141266211072448977

branch
April 13, 2026 14:46
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