Lightweight Code Update for Staged NMPDR

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NMPDR Standard Operating Procedure SOP021

Contents 1 Introduction 2 Scope 3 Applicable Regulations and Guidelines 4 Responsibility 5 Definitions 6 Process Overview 7 Context 8 Lightweight Code Update for Staged NMPDR 8.1 Copy the Source Files 8.2 Fix the FIG_Config.pm File 8.3 Make the Source

Introduction

This standard operating procedure (SOP) describes the operations followed by NMPDR personnel for updating the staged version of the site from the development site. (The staged site is created using NMPDR SOP020.

Scope

This SOP applies to the procedures to fix problems in the staged version of the site. The fixes are installed and tested on the Development Server, and then copied to the staged site so that they will be incorporated in the new version of the NMPDR.

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
  1. Placement of a gene within a subsystem.
  2. Assignment of a function to a gene.

Process Overview

1. Copy the source files.
2. Fix the FIG_Config.pm file.
3. Make the source.

Context

Bioinformaticians use the Lightweight Code Update for the Staged NMPDR to copy fixes made on the Development Server over to the Production Server.

Lightweight Code Update for Staged NMPDR

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.

The entire procedure is executed on the Production Server.

Copy the Source Files

Use the command

 rsync --verbose --recursive --archive --exclude=*.dtx user@server.nmpdr.org:/disks/nmpdr/vNN/ /disks/nmpdr/vNN/

In this case, user must be your user name and server is the name of the Development Server. You will be prompted for a password. You may get messages about files in the 'Tmp directory with long hexadecimal names not being transferred. This is not a problem, because they are non-essential files.

Fix the FIG_Config.pm File

If you have not already done so, issue the following source command to insure you are connected to the correct directories.

 source /disks/nmpdr/next/FIGdisk/config/fig-user-env.sh

Use the FigConfigFix command to fix the site URL in the FIG_Config.pm file.

 cd /disks/nmpdr/next
 FigConfigFix stage

Make the Source

Use the following commands to update the source files for execution.

 cd /disks/nmpdr/next/dist/releases/current
 make