Server:

"Help / Read me Document"

Version A.01.00

Persistent Systems Private Limited

'Bhageerath', 402, Senapati Bapat Road,

Pune - 411 016, India.

Tel: +91 (20) 567 8900, Fax: +91 (20) 567 8901

Document Information

  ------------------------- ---------------------------------------------
  Filename                  ServerHelp.doc

  Current Owner             PSPL / WashU

  Product Identifier        

  Project Identifier        WashU

  Current Lifecycle Phase   Release
  ------------------------- ---------------------------------------------

Revision Log

  ---------- ------------ --------------------------- ---------------------------
  Revision   Date         Author                      Reason For Update

  A.01.00    2004.04.26   Divyabhanu Singh            Initial version.
  ---------- ------------ --------------------------- ---------------------------

**Table Of Contents**

[1 Introduction 4](#introduction)

[2 About \"Function Express Server\" 4](#about-function-express-server)

[Server Execution Modes 4](#server-execution-modes)

[3 Preinstallation tasks 5](#preinstallation-tasks)

[SetUp Requirements 5](#setup-requirements)

[4 Installation Instructions 5](#installation-instructions)

[Using Installer 5](#using-installer)

[5 Configuration Instructions 7](#configuration-instructions)

[Introduction 7](#introduction-1)

[Server.properties 7](#server.properties)

[Servergui.properties 7](#servergui.properties)

[Configure the Command File (CMDFile_X_X.txt)
8](#configure-the-command-file-cmdfile_x_x.txt)

[Setup ClassPath 9](#setup-classpath)

[Miscellaneous - Checklist 9](#miscellaneous---checklist)

[6 Run The Server From Command Prompt
9](#run-the-server-from-command-prompt)

[Linux/Solaris 10](#linuxsolaris)

[Windows 10](#windows)

[7 Run The Server GUI 10](#run-the-server-gui)

[Choose Mode 10](#choose-mode)

[Update Mode Screens 11](#update-mode-screens)

[Add Chiplibrary Mode Screen 13](#add-chiplibrary-mode-screen)

[Chip Format Description 13](#chip-format-description)

[8 Checklists Before Running Server
14](#checklists-before-running-server)

[Checklist Update Mode 14](#checklist-update-mode)

[Checklist AddChip Mode 14](#checklist-addchip-mode)

[9 Server Control Flow - Update Mode
15](#server-control-flow---update-mode)

[10 Server Control Flow - Add Chiplibrary Mode
17](#server-control-flow---add-chiplibrary-mode)

[11 Troubleshooting 18](#troubleshooting)

# Introduction

The \"Function Express Server\" help document talks about Server
Execution Modes, Steps to set up the Server, Configuration of Properties
files, Running the Server Executable through Command Prompt and GUI.
Finally, it discusses a few important steps before running the
application.

#  About \"Function Express Server\"

##  {#section .unnumbered}

## Server Execution Modes {#server-execution-modes .unnumbered}

The \"Function Express Server\" is meant to do the following tasks as 3
different modes:

![](media/image1.png){width="0.15625in" height="0.15625in"} **Create
Mode**

> In this mode it reads a set of XML files, which contain SQL
> statements, and creates the database schema required for the Chip
> Import Utility, gene annotation data, Function Express Application,
> Mutation Viewer.

![](media/image1.png){width="0.15625in" height="0.15625in"} **Update
Mode**

> In this mode it will download the public domain gene annotation data,
>
> Populates the base tables in database after parsing the data, Creates
> summary tables using the base table information, Sends a status mail
> to the required addresses as mentioned in the properties file.

![](media/image1.png){width="0.15625in" height="0.15625in"} **Add
Chiplibrary Mode**

> In this mode, it accepts a tab delimited text file in a few specific
> formats, based on which it populates the Chipinformation,
> Chipdescription, Geneinfo Summary tables, hence linking the Microarray
> Data with the Gene Annotation data. New Chiplibraries are added to the
> database using this mode. The user specifies format of the
> Chiplibrary. (E.g. AU /UA e.t.c)

# Preinstallation tasks 

## SetUp Requirements  {#setup-requirements .unnumbered}

> ![](media/image1.png){width="0.15625in" height="0.15625in"} Oracle
> database is installed.
>
> ![](media/image1.png){width="0.15625in" height="0.15625in"} The
> Tablespaces as mentioned in Appendix are present. (As per CHIPDB
> specifications). The tablespace names must be the same as the names at
> CHIPDB.MGA.WUSTL.EDU
>
> E.g. Refdata, Chipdata e.t.c.
>
> ![](media/image1.png){width="0.15625in" height="0.15625in"} Oracle
> home is set to the correct value. Check this using the command:
>
> \$ echo \$ORACLE_HOME
>
> The output should be a path where Oracle is installed. For example:
>
> /Oracle_Application/app/oracle/product/9.0.1
>
> If it is blank then set it to your oracle home by using the following
> command: (in
>
> bash shell)
>
> \$ export ORACLE_HOME=/Oracle_Application/app/oracle/product/9.0.1
>
> For Windows: Set the environment Variable ORACLE_HOME using My
> Computer Environment variable.
>
> ![](media/image1.png){width="0.15625in" height="0.15625in"} The
> \"Function Express Server\" expects the Mail Client also active on the
> machine.

# Installation Instructions

## Using Installer {#using-installer .unnumbered}

Install F.E. Server using the platform specific Installable available in
the CVS. The installer will create the following folder Hierarchy

![](media/image2.png)

The above folders would contains the following data:

+-----------------------------+----------------------------------------+
| **Folder Name**             | **Contents**                           |
+-----------------------------+----------------------------------------+
| Config                      | ![](media/image3.png)                  |
+-----------------------------+----------------------------------------+
| ErrorFiles                  | -   GeneMiner_xx files (Initially      |
|                             |     Empty)                             |
+-----------------------------+----------------------------------------+
| Lib                         | ![](media/image4.png)                  |
+-----------------------------+----------------------------------------+
| Logs                        | -   ErrorLog.txt                       |
|                             |                                        |
|                             | -   FileStatus.txt                     |
+-----------------------------+----------------------------------------+
| Scripts                     | ![](media/image5.png)                  |
+-----------------------------+----------------------------------------+
| UninstallerData             | ![](media/image6.png)                  |
+-----------------------------+----------------------------------------+

# Configuration Instructions

## Introduction {#introduction-1 .unnumbered}

Before we run F.E. Server we need to make some changes in the properties
files. Please note that only properties to be changed are mentioned.

## Server.properties {#server.properties .unnumbered}

This file contains Server Status Mail, Tablespace Related data. This
file is read at start up time irrespective of whether the Command line /
GUI option is used.

##Address to which mail is to be sent

toAddress = <divyabhanu_singh@persistent.co.in>

##Address of Mail Server

host = [www.pspl.co.in](http://www.pspl.co.in/) (mga.wustl.edu)

##Address from which mails are to be sent.

fromAddress = <divyabhanu_singh@persistent.co.in>

## Servergui.properties {#servergui.properties .unnumbered}

\## SID of the database to which to connect. This can be obtained from
\$ORACLE_HOME\\network\\admin\\tnsnames.ora

dburl = CHIPDB_MIRAMAR

##Database User login Name

dbloginname = WashU

\## Name of the driver (Should not be changed ideally)

dbdriver = oracle.jdbc.driver.OracleDriver

## Configure the Command File (CMDFile_X_X.txt) {#configure-the-command-file-cmdfile_x_x.txt .unnumbered}

The Function Express Server does require the file to be a valid Command
File.

Hence, it is recommended that users take care while changing its
Contents.

It is a simple TAB DELIMITED Text File consisting of Records. Please
note that the file can

also be changed intuitively using the GUI.

##The Structure of each Record is as Follows:

File to be ftp'd in **Update Mode**

SITE_URL ftp.ncbi.nih.gov

USER_ID anonymous

PASSWD phataka@pathbox.wustl.edu

BASE_DIR /repository/UniGene/

FILE Hs.data.gz

FILE Dr.data.gz

DATABASE UNIGENE

\####

**The End of Record is signified by \####**

For a Local File in **Update Mode**:

LOCAL_FILE E:\\smalldata\\LL_100.txt

DATABASE LOCUSLINK

\####

For a Chiplibrary which will be done only in **AddChipMode:**

LOCAL_FILE F:\\HU95A.txt

DATABASE CHIPINFORMATION

INPUT_FORMAT UA

\####

## Setup ClassPath {#setup-classpath .unnumbered}

Change the LAX.CLASS.PATH parameter in the file RunF.E.Server.lax and
add \$ORACLE_HOME\\jdbc\\lib\\classses12.zip to the start of the Line.
Hence now the entry in the above file would read:

\# LAX.CLASS.PATH

\# \-\-\-\-\-\-\-\-\-\-\-\-\--

\# The Java ClassPath necessary to run this application

\# Can be separated by colons (Mac OS/Unix) or semicolons (Windows)

lax.class.path=C:\\oracle\\jdbc\\lib\\classes12.jar; lib/activation.jar;
lib/mail.jar; ............

## Miscellaneous - Checklist {#miscellaneous---checklist .unnumbered}

Please note that incase of a Linux/Solaris Box, The user will have to
replace the classes12.zip" present in the lib directory by the latest
version from\
ORACLE_HOME\\jdbc\\lib.

Also, change the Permissions for the installer binary to +x using\
chmod +x installF_E_SERVER_Linux.bin

# Run The Server From Command Prompt

**Please refer to the [Checklist](#checklists-before-running-server)
before running Server**

Incase you want to run the Server using CommandLine option instead of
the GUI on a non Windows machine, you would need to:

-   Set the class path

-   Sets necessary environment variables e.g. ORACLE_HOME e.t.c

java com.dataminer.server.jobmanager.JobManager \<mode\>

\<dbUserId\> \<dbUserPassword\> \<dbName\> \<driverName\> \<dbURL\>
\[\<ftpCommandFile\>\]

> Mode: mode \[1=full update, 2=add chip,3=createDBSchema\]

dbUserId: database user name

dbUserPassword: database user\'s password

[]{#dbname .anchor}dbName: database SID \[CHIPDB.MGA.WUSTL.EDU\]

drivername: Oracle driver name \[oracle.jdbc.driver.OracleDriver\]

dbURL: URL for database constructed with passed parameters

ftpCommandFile: CommandFile.txt

## Linux/Solaris {#linuxsolaris .unnumbered}

To run F.E. Server on a non Windows machine using Command Prompt:

-   Copy the script .mylogin.sh from CVS folder
    [\\\\FEServer\\\\Installers](../../../../../../../..//Installers) to
    the F.E.Server installation directory -- parallel to Logs / Config
    folders.

-   Copy the Shell Script runServerCHIPDB.sh from CVS folder
    [\\\\FEServer\\\\Installers](../../../../../../../..//Installers) to
    the F.E.Server installation directory -- parallel to Logs / Config
    folders.

**Please note that both the above files are mere samples, the paths
present in the files will change depending on the machine variables.**

To run the Server from the Command Prompt just type the following
command

from the directory where you have placed the installation files.

\$ source ./runFEServer_X_X.sh

**Example:**

To run the Server in ADDCHIPMode :

\$ source. / runFEServer_ADDCHIP.sh

## Windows {#windows .unnumbered}

java com.dataminer.server.jobmanager.JobManager \<mode\> \<dbUserId\>
\<dbUserPassword\> \<dbName\> \<driverName\> \<dbURL\>
\[\<ftpCommandFile\>\]

# Run The Server GUI

**Please refer to the [Checklist](#checklists-before-running-server)
before running Server**.

##  {#section-1 .unnumbered}

## Choose Mode {#choose-mode .unnumbered}

Select one of the Radio Buttons to choose the Execution mode. Note that
the Text on the left changes as the selected radio button changes.

![](media/image7.png){width="5.5in" height="2.80625in"}

##  {#section-2 .unnumbered}

## Update Mode Screens {#update-mode-screens .unnumbered}

#### Set Configuration Parameters {#set-configuration-parameters .unnumbered}

This screen requires the user to enter the following parameters:

-   Path of the Command File (Can be done using Browse button)

-   Database [SID](#dbname) (From tnsnames.ora)

-   Database Driver Name

-   Database User Name

-   Database User Password

-   

![](media/image8.png){width="6.125in" height="3.2666666666666666in"}

#### Register Required Databases {#register-required-databases .unnumbered}

![](media/image9.png){width="6.125in" height="3.0625in"}

This screen will automatically fill up the requisite Fields from the
command file although the user would have option of changing it. Incase
of a Local File the UI will remain the same except the FTP_xx fields on
the left side would be missing.

## Add Chiplibrary Mode Screen {#add-chiplibrary-mode-screen .unnumbered}

![](media/image10.png){width="5.75in" height="3.24375in"}

In this Screen the user needs to specify the format in which the chip is
present.

## Chip Format Description {#chip-format-description .unnumbered}

The assumption is that the user submits a tab delimited file such that:

-   Chiptypes table has an entry for the Chiptypes whose library is
    being loaded.

-   First line contains name of the chiptype, which is same as its entry
    in the Chiptypes table.

-   First Column will always be Probeset and last column would always be
    Probeset description.

-   The user would specify the other columns in between these two
    columns.

    -   A -- Accession Number

    -   U -- Unigene Id

    -   L -- LocusLink Id

    -   O- Organism

> Hence, UA would mean that the file has columns in the order Probeset,
> UnigeneId, Accession Number, Probeset description.

# Checklists Before Running Server

## Checklist Update Mode {#checklist-update-mode .unnumbered}

Please ensure the following before running the Server in Update mode:

-   No tables with name %\_U are present. E.g. UniGene_U. This can be
    obtained by doing the query:\
    \
    select tname from tab where upper (tname) like \'%\_u\'\
    \
    Incase we have \_U tables present, then run the following scripts in
    the same order before running the server. The scripts are present in
    the folder
    [\\\\FEServer\\\\ImportantScripts](../../../../../../../..//ImportantScripts):

    -   drop_index_u.sql

    -   drop_u.sql

> **Please be very careful with the script names, as there are scripts
> present which when run indiscriminately can be dangerous.**

-   The Index IDX_CTD_ALL must be present on the table. Incase it is
    not, use the following query to create it\
    \
    create index idx_ctd_all on chipinfo_term_with_duplicates
    (ctd_chiptypeid, ctd_probeset, ctd_organism, ctd_termid) tablespace
    indx nologging

-   Incase the Server run is aborted midway or there are some errors\
    the \_U tables will remain created. The Server Status mail will
    always state whether the run was successful or not.

## Checklist AddChip Mode {#checklist-addchip-mode .unnumbered}

Please ensure the following before running the Server in Update mode:

-   Chiplibrary File is in correct format. i.e. there are no extra tabs
    / spaces.

-   There is an entry for the Chiptype in the Chiptypes table.

-   The Chip name mentioned in the chiptypes table is same as the name
    present in the

first line of the Chiplibrary file.

**Incase of Any Error please mail the logs back to
washu_pspl@persistent.co.in**

# Server Control Flow - Update Mode

The following flowchart demonstrates the broad working of Server in
Update Mode

# Server Control Flow - Add Chiplibrary Mode

The following flowchart demonstrates the broad working of Server in
AddChiplibrary Mode

# Troubleshooting

This section will be updated as and when required. As of now, Incase of
Any Error please mail the logs back to washu_pspl@persistent.co.in