NMPDR Version Rollover
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NMPDR Standard Operating Procedure SOP020
Contents |
Introduction
This standard operating procedure (SOP) describes the operations followed by NMPDR personnel for rolling over a new version of the NMPDR. Before this procedure can be applied, there must be a staged version of the site available. The process of creating a staged version is described in NMPDR SOP020.
Scope
This SOP applies to the procedures to publish a new version of the NMPDR web site.
Applicable Regulations and Guidelines
| NMPDR Contract | Delivery of NMPDR SOPs |
| BRC Metrics | Production of metrics |
| GO | List of GO terms |
| Transaction Logging | NMPDR Logging requirements |
Responsibility
This SOP applies to those members of the NMPDR research team involved in managing the web site. This includes the following:
- Bioinformaticians
Definitions
- Standard Operating Procedures (SOPs): Detailed, written instructions to achieve uniformity of the performance of a specific function.
- Subsystem: A collection of functional roles that together implement a specific biological process or structural complex.
- FigFam: Protein families. Each family is intended to contain a set of globally similar proteins that implement the same function.
- Annotation: A tuple consisting of a date, annotator name, and textual message.
- Structured Annotation: An annotation where the text is structured. There are two kinds of structured annotations
- Placement of a gene within a subsystem.
- Assignment of a function to a gene.
Process Overview
- Fix the FIG_Config.pm File.
- Change the site pointers.
- Create the dummy staging site.
- Delete the old previous site.
Context
Bioinformaticians use the NMPDR Version Rollover Procedure to publish a new, improved version of the NMPDR web site.
NMPDR Version Rollover
Each version of the NMPDR has a two-digit version number associated with it. Throughout this document, the version number will be rendered as NN.
This entire procedure is executed on the Production Server.
Fix the FIG_Config.pm File
On the Production Server, go to the /disks/nmpdr/ directory. Insure that you are sourced to the correct version of the NMPDR. If you have not already done so, execute
cd /disks/nmpdr/ source /disks/nmpdr/next/FIGdisk/config/fig-user-env.sh
Now use FigConfigFix to fix the config files.
FigConfigFix roll
Change the Site Pointers
The version number of the site being published is rendered as NN. Let N0 be the site that is currently published (N0 = NN - 1). Use the following commands to move the site pointers.
unlink next unlink cur unlink prev ln -s vN0 prev ln -s vNN cur
The new NMPDR version is now officially published and live.
Create the Dummy Staging Site
We put a special dummy home page in place of the staging site to let people know it's empty. First, create the directory for the next staging site and link it to the next symbol. Let NN be the version number of the site just published. The next version number is N1 (N1 = NN + 1). Use the following commands to create the dummy site.
mkdir vN1 ln -s vN1 next mkdir next/html cp cur/html/Blog/index.html next/html
Delete the Old Previous Site
The original site has now been set up as the new previous site. The old previous site can be deleted. This site has the version number NZ (NZ = NN - 2). First, delete the database. You will be asked if you are sure. Yes, you're sure.
mysqladmin --user=seed drop nmpdr_vNZ_sprout
Now delete as much of the directory tree as you can.
rm --force --recursive /disks/nmpdr/vNZ/*
If there are no errors, then do
rmdir /disks/nmpdr/vNZ
to delete the directory itself. This has never happened, however, because some web applications create undeletable files. If this is the case, rename the directory.
mv /disks/nmpdr/vNZ /disks/nmpdr/vNZ.bad
Eventually somebody with super-user privileges will delete the directory for you.