Protein Geometry Database
Installation
Development Branch Installation
Master Branch Installation
Importing Data
Running Splicer From The Command Line
Example
Updating Protein Database
Site Specific Information
Virtual environments
Files generated during the update process
Differences between staging and production
Technologies Used By Protein Geometry Database
Django
jQuery
Raphael
Mysql
Terminology (WIP)
Code Modules
PGD Core
PGD Search
PGD Splicer
Protein Data Models
Protein
Chain
Residue
Optimization
Optimization: SQL Indexes
Protein
Residue Joined to Residue
SQL Aggregates
Statistics for Dihedral Angles
Average
Standard Deviation
Optimization: In Memory Tables
Indexing Memory Tables
Parallelization of Queries
Startup and Django Configuration Issues
Growth Concerns
Attempted Optimization: De-normalizing Residue Table
Table Size
Search Workflow
Models
Forms
Conversions
Workflow
Ramachandran Plots
Data Selection
Statistics Calculation
Coloring
Logarithmic Scale
Color Ranges
Algorithm
Search Statistics
Queries
Optimization
Data Dump
Selecting Data
Buffered Response
Browse
Selecting Data
Splicer
Task Structure
Developing Splicer
Django Settings
Running Components from the command line
Splicer Processor Task
Running From the command line
Libraries
Parsing PDBs
Example a3
Example: Ome
Example B-factor: Bm, Bs, Bg
Update Checking
Running Splicer
Slow FTP Issues
Maintaining Connections Between Workunits
Only Downloading New Files
Storing files in a network share
Workunit Thrashing Problem
Debugging Splicer
Running Splicer From The Command Line
Selecting Proteins
Options
Downloading PDB Files
Processing PDB Files
Parameters
Options
Example
Full Import
Update Only New
Update Skipping Download
Development workflow
Create an issue in the issue tracker if one does not already exist.
Create a branch from the develop branch based on the issue number.
Write the code, including tests and release notes entry if necessary.
Commit code and update the issue.
Request code review.
Merge changes back into the develop branch.
Hotfix Workflow
One or more show-stopping bugs are detected between releases
Create a hotfix branch off the master branch
Create bug branches off the hotfix branch
Merge resolved bugs back to hotfix branch and test on staging
When all bugs are resolved and merged, merge hotfix branch into master branch
Pull master on production and restart Apache
Merge hotfix branch back into develop
Release Workflow
Announce the upcoming release to the PGD list four weeks before release.
Impose a feature freeze on develop three weeks before release.
Start the release branch two weeks before release.
Freeze the release branch one week before release.
Release the software, close tickets and unfreeze develop on the release date.
Management Commands and Possible Redisign
Protein Geometry Database
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