⚡ Optimize SQLite queries in namingDatabase species fetching

[akutuva21]

💡 What: Added a new method getSpeciesFromFileList in NamingDatabase that fetches species for a list of files in batches using an SQL IN query. Modified findOverlappingNamespace to use this new method rather than iterating over files and calling getSpeciesFromFileName individually.

🎯 Why: The previous loop in findOverlappingNamespace suffered from the N+1 query problem, making a new connection and query for every single file in the list. For a large number of files, this was a severe performance bottleneck due to excessive I/O and context switching.

📊 Measured Improvement:

• Baseline: ~2.71 seconds to fetch species for 100 files containing 100 molecules each (10,000 total groups).
• Improved: ~0.18 seconds for the same dataset.
• Result: >10x performance improvement.

---

PR created automatically by Jules for task 15729913662859484199 started by @akutuva21

[google-labs-jules]

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[akutuva21]

Superseded by #108 namingDatabase batching optimization.

[google-labs-jules]

Superseded by #108 namingDatabase batching optimization.

Understood. Acknowledging that this work is superseded by #108 and stopping work on this task.

[akutuva21]

💡 What: Added a new method getSpeciesFromFileList in NamingDatabase that fetches species for a list of files in batches using an SQL IN query. Modified findOverlappingNamespace to use this new method rather than iterating over files and calling getSpeciesFromFileName individually.

🎯 Why: The previous loop in findOverlappingNamespace suffered from the N+1 query problem, making a new connection and query for every single file in the list. For a large number of files, this was a severe performance bottleneck due to excessive I/O and context switching.

📊 Measured Improvement:

• Baseline: ~2.71 seconds to fetch species for 100 files containing 100 molecules each (10,000 total groups).
• Improved: ~0.18 seconds for the same dataset.
• Result: >10x performance improvement.

---

PR created automatically by Jules for task 15729913662859484199 started by @akutuva21

[google-labs-jules]

👋 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.

[akutuva21]

Superseded by #108 namingDatabase batching optimization.

[google-labs-jules]

Superseded by #108 namingDatabase batching optimization.

Understood. Acknowledging that this work is superseded by #108 and stopping work on this task.

[akutuva21]

💡 What: Added a new method getSpeciesFromFileList in NamingDatabase that fetches species for a list of files in batches using an SQL IN query. Modified findOverlappingNamespace to use this new method rather than iterating over files and calling getSpeciesFromFileName individually.

🎯 Why: The previous loop in findOverlappingNamespace suffered from the N+1 query problem, making a new connection and query for every single file in the list. For a large number of files, this was a severe performance bottleneck due to excessive I/O and context switching.

📊 Measured Improvement:

• Baseline: ~2.71 seconds to fetch species for 100 files containing 100 molecules each (10,000 total groups).
• Improved: ~0.18 seconds for the same dataset.
• Result: >10x performance improvement.

---

PR created automatically by Jules for task 15729913662859484199 started by @akutuva21

[google-labs-jules]

👋 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.

[akutuva21]

Superseded by #108 namingDatabase batching optimization.

[google-labs-jules]

Superseded by #108 namingDatabase batching optimization.

Understood. Acknowledging that this work is superseded by #108 and stopping work on this task.

[akutuva21]

💡 What: Added a new method getSpeciesFromFileList in NamingDatabase that fetches species for a list of files in batches using an SQL IN query. Modified findOverlappingNamespace to use this new method rather than iterating over files and calling getSpeciesFromFileName individually.

🎯 Why: The previous loop in findOverlappingNamespace suffered from the N+1 query problem, making a new connection and query for every single file in the list. For a large number of files, this was a severe performance bottleneck due to excessive I/O and context switching.

📊 Measured Improvement:

• Baseline: ~2.71 seconds to fetch species for 100 files containing 100 molecules each (10,000 total groups).
• Improved: ~0.18 seconds for the same dataset.
• Result: >10x performance improvement.

---

PR created automatically by Jules for task 15729913662859484199 started by @akutuva21

[google-labs-jules]

👋 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.

[akutuva21]

Superseded by #108 namingDatabase batching optimization.

[google-labs-jules]

Superseded by #108 namingDatabase batching optimization.

Understood. Acknowledging that this work is superseded by #108 and stopping work on this task.

[akutuva21]

💡 What: Added a new method getSpeciesFromFileList in NamingDatabase that fetches species for a list of files in batches using an SQL IN query. Modified findOverlappingNamespace to use this new method rather than iterating over files and calling getSpeciesFromFileName individually.

🎯 Why: The previous loop in findOverlappingNamespace suffered from the N+1 query problem, making a new connection and query for every single file in the list. For a large number of files, this was a severe performance bottleneck due to excessive I/O and context switching.

📊 Measured Improvement:

• Baseline: ~2.71 seconds to fetch species for 100 files containing 100 molecules each (10,000 total groups).
• Improved: ~0.18 seconds for the same dataset.
• Result: >10x performance improvement.

---

PR created automatically by Jules for task 15729913662859484199 started by @akutuva21

[google-labs-jules]

👋 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.

[akutuva21]

Superseded by #108 namingDatabase batching optimization.

[google-labs-jules]

Superseded by #108 namingDatabase batching optimization.

Understood. Acknowledging that this work is superseded by #108 and stopping work on this task.

[akutuva21]

💡 What: Added a new method getSpeciesFromFileList in NamingDatabase that fetches species for a list of files in batches using an SQL IN query. Modified findOverlappingNamespace to use this new method rather than iterating over files and calling getSpeciesFromFileName individually.

🎯 Why: The previous loop in findOverlappingNamespace suffered from the N+1 query problem, making a new connection and query for every single file in the list. For a large number of files, this was a severe performance bottleneck due to excessive I/O and context switching.

📊 Measured Improvement:

• Baseline: ~2.71 seconds to fetch species for 100 files containing 100 molecules each (10,000 total groups).
• Improved: ~0.18 seconds for the same dataset.
• Result: >10x performance improvement.

---

PR created automatically by Jules for task 15729913662859484199 started by @akutuva21

[google-labs-jules]

👋 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.

[akutuva21]

Superseded by #108 namingDatabase batching optimization.

[google-labs-jules]

Superseded by #108 namingDatabase batching optimization.

Understood. Acknowledging that this work is superseded by #108 and stopping work on this task.

[akutuva21]

💡 What: Added a new method getSpeciesFromFileList in NamingDatabase that fetches species for a list of files in batches using an SQL IN query. Modified findOverlappingNamespace to use this new method rather than iterating over files and calling getSpeciesFromFileName individually.

🎯 Why: The previous loop in findOverlappingNamespace suffered from the N+1 query problem, making a new connection and query for every single file in the list. For a large number of files, this was a severe performance bottleneck due to excessive I/O and context switching.

📊 Measured Improvement:

• Baseline: ~2.71 seconds to fetch species for 100 files containing 100 molecules each (10,000 total groups).
• Improved: ~0.18 seconds for the same dataset.
• Result: >10x performance improvement.

---

PR created automatically by Jules for task 15729913662859484199 started by @akutuva21

[google-labs-jules]

👋 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.

[akutuva21]

Superseded by #108 namingDatabase batching optimization.

[google-labs-jules]

Superseded by #108 namingDatabase batching optimization.

Understood. Acknowledging that this work is superseded by #108 and stopping work on this task.

[akutuva21]

💡 What: Added a new method getSpeciesFromFileList in NamingDatabase that fetches species for a list of files in batches using an SQL IN query. Modified findOverlappingNamespace to use this new method rather than iterating over files and calling getSpeciesFromFileName individually.

🎯 Why: The previous loop in findOverlappingNamespace suffered from the N+1 query problem, making a new connection and query for every single file in the list. For a large number of files, this was a severe performance bottleneck due to excessive I/O and context switching.

📊 Measured Improvement:

• Baseline: ~2.71 seconds to fetch species for 100 files containing 100 molecules each (10,000 total groups).
• Improved: ~0.18 seconds for the same dataset.
• Result: >10x performance improvement.

---

PR created automatically by Jules for task 15729913662859484199 started by @akutuva21

[google-labs-jules]

👋 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.

[akutuva21]

Superseded by #108 namingDatabase batching optimization.

[google-labs-jules]

Superseded by #108 namingDatabase batching optimization.

Understood. Acknowledging that this work is superseded by #108 and stopping work on this task.