biolockj.module.report

Class Email

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.report.Email

All Implemented Interfaces:

BioModule, Comparable<BioModule>

public class Email
extends BioModuleImpl

This BioModule is used to email the user the pipeline execution status and summary. If run on cluster, an scp command is included in the email that can be run to download analysis from the cluster.

GUI Module Name

Email

Field Summary

Fields

Modifier and Type	Field and Description
static String	CLUSTER_HOST Config String property: "cluster.host" The cluster host URL used for SSH and SCP connections.
protected static String	EMAIL_ENCRYPTED_PASSWORD Config String property: "mail.encryptedPassword" The Base 64 encrypted password is stored in the Config file using this property.
protected static String	EMAIL_FROM Config String property: "mail.from" Admin email address used to send user pipeline notifications.
protected static String	EMAIL_HOST Config String property: "mail.smtp.host" Session SMTP host
protected static String	EMAIL_PORT Config Integer property: "mail.smtp.port" Session SMTP port
protected static String	EMAIL_SMTP_AUTH Config Boolean property: "mail.smtp.auth" Session SMTP authorization flag, set to "Y" if required by "mail.smtp.host"
protected static String	EMAIL_START_TLS_ENABLE Config Boolean property: "mail.smtp.starttls.enable" Session SMTP TLS enable flag, set to "Y" if required by "mail.smtp.host"
protected static String	EMAIL_TO Config List property: "mail.to" This property defines the email recipients

Fields inherited from class biolockj.module.BioModuleImpl

GZIP_EXT, LOG_EXT, PDF_EXT, RETURN, SH_EXT, TAB_DELIM, TSV_EXT, TXT_EXT

Fields inherited from interface biolockj.module.BioModule

MAIN_SCRIPT_PREFIX, OUTPUT_DIR, TEMP_DIR

Constructor Summary

Constructors

Constructor and Description
Email()

Method Summary

Modifier and Type	Method and Description
void	checkDependencies() Verify required email Config properties exist and are properly formatted.
protected static String	encrypt(String password) Encrypt clear-text password
static void	encryptAndStoreEmailPassword() Read clear-text password by call to RuntimeParamUtil.getAdminEmailPassword() Encrypt password by call to encrypt(String)
void	executeTask() Set status member variable and send email pipeline summary to email addresses listed in: Config."mail.to"
protected javax.mail.Session	getSession() Build an authenticated javax.mail.Session using Config email properties
String	getSummary() Summary simply reports the status.

Methods inherited from class biolockj.module.BioModuleImpl

cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getFileCache, getID, getInputFiles, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getTempDir, init, isValidInputModule, toString, validateFileNameUnique

Methods inherited from class java.lang.Object

clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

CLUSTER_HOST

public static final String CLUSTER_HOST

Config String property: "cluster.host"
The cluster host URL used for SSH and SCP connections.

See Also:

Constant Field Values

EMAIL_ENCRYPTED_PASSWORD

protected static final String EMAIL_ENCRYPTED_PASSWORD

Config String property: "mail.encryptedPassword"
The Base 64 encrypted password is stored in the Config file using this property.

See Also:

Constant Field Values

EMAIL_FROM

protected static final String EMAIL_FROM

Config String property: "mail.from"
Admin email address used to send user pipeline notifications.

See Also:

Constant Field Values

EMAIL_HOST

protected static final String EMAIL_HOST

Config String property: "mail.smtp.host"
Session SMTP host

See Also:

Constant Field Values

EMAIL_PORT

protected static final String EMAIL_PORT

Config Integer property: "mail.smtp.port"
Session SMTP port

See Also:

Constant Field Values

EMAIL_SMTP_AUTH

protected static final String EMAIL_SMTP_AUTH

Config Boolean property: "mail.smtp.auth"
Session SMTP authorization flag, set to "Y" if required by "mail.smtp.host"

See Also:

Constant Field Values

EMAIL_START_TLS_ENABLE

protected static final String EMAIL_START_TLS_ENABLE

Config Boolean property: "mail.smtp.starttls.enable"
Session SMTP TLS enable flag, set to "Y" if required by "mail.smtp.host"

See Also:

Constant Field Values

EMAIL_TO

protected static final String EMAIL_TO

Config List property: "mail.to" This property defines the email recipients

See Also:

Constant Field Values

Constructor Detail

Email

public Email()

Method Detail

checkDependencies

public void checkDependencies()
                       throws Exception

Verify required email Config properties exist and are properly formatted.

1. Require Config.EMAIL_HOST
2. Require Config.EMAIL_PORT
3. Require Config.EMAIL_SMTP_AUTH
4. Require Config.EMAIL_START_TLS_ENABLE
5. Require Config.EMAIL_ENCRYPTED_PASSWORD
6. Require Config.EMAIL_FROM is a valid email address
7. Require Config.EMAIL_TO is a valid email address

Specified by:

checkDependencies in interface BioModule

Specified by:

checkDependencies in class BioModuleImpl

Throws:

Exception - thrown if missing or invalid dependencies are found

executeTask

public void executeTask()
                 throws Exception

Set status member variable and send email pipeline summary to email addresses listed in: Config."mail.to"

Specified by:

executeTask in interface BioModule

Specified by:

executeTask in class BioModuleImpl

Throws:

Exception - thrown if the module is unable to complete is task

getSummary

public String getSummary()
                  throws Exception

Summary simply reports the status.

Specified by:

getSummary in interface BioModule

Overrides:

getSummary in class BioModuleImpl

Returns:

Summary of BioModule execution

Throws:

Exception - if any error occurs

getSession

protected javax.mail.Session getSession()
                                 throws Exception

Build an authenticated javax.mail.Session using Config email properties

Returns:

javax.mail.Session required to send a MimeMessage

Throws:

Exception - if Config finds missing or invalid email properties

encryptAndStoreEmailPassword

public static void encryptAndStoreEmailPassword()
                                         throws Exception

Read clear-text password by call to RuntimeParamUtil.getAdminEmailPassword()
Encrypt password by call to encrypt(String)

Throws:

Exception - if unable to encrypt or store password

encrypt

protected static String encrypt(String password)
                         throws GeneralSecurityException,
                                UnsupportedEncodingException

Encrypt clear-text password

Parameters:

password - Clear-text password

Returns:

Encrypted password

Throws:

GeneralSecurityException - Encryption error

UnsupportedEncodingException - Encryption error