biolockj.module.report

Class Email

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.report.Email

All Implemented Interfaces:

ApiModule, BioModule, Comparable<BioModule>

public class Email
extends BioModuleImpl
implements ApiModule

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
protected static String	EMAIL_ENCRYPTED_PASSWORD Config String property: "mail.encryptedPassword"
protected static String	EMAIL_FROM Config String property: "mail.from"
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

LOG_DIR, MAIN_SCRIPT_PREFIX, NO_VERSION, OUTPUT_DIR, RES_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.
(package private) String	decrypt(String val) Used to authenticate the service email account defined in EMAIL_FROM.
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"
String	getCitationString() At a minimum, this should return the name and/or url for the wrapped tool.
String	getDescription() Briefly describe what this module does.
String	getDockerImageName() Get the docker image to use for this module.
String	getDockerImageOwner() Get the name of the docker hub user that owns the image to use for this module.
protected javax.mail.Session	getSession() Build an authenticated javax.mail.Session using Config email properties
String	getSummary() Summary simply reports the status.
String	version() Changes to a module class should be accompanied by a increment in version.

Methods inherited from class biolockj.module.BioModuleImpl

addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getDetails, getDockerImageTag, getFileCache, getID, getInputFiles, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getPropDescMap, getPropType, getPropTypeMap, getResourceDir, getTempDir, getTitle, hashCode, init, isValidInputModule, isValidProp, listProps, setAlias, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface biolockj.api.ApiModule

getDescription, getDetails, getMenuPlacement, getPropType, getTitle, isValidProp, listProps

Methods inherited from interface biolockj.module.BioModule

cleanUp, getAlias, getDockerImageTag, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getTempDir, init, isValidInputModule, setAlias

Field Detail

EMAIL_ENCRYPTED_PASSWORD

protected static final String EMAIL_ENCRYPTED_PASSWORD

Config String property: "mail.encryptedPassword"

See Also:

Constant Field Values

EMAIL_FROM

protected static final String EMAIL_FROM

Config String property: "mail.from"

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

decrypt

String decrypt(String val)

Used to authenticate the service email account defined in EMAIL_FROM. WARNING - This is a trivial level of encryption! Service email account should never send confidential information!

Parameters:

val - Encrypted password

Returns:

Clear-text password

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

getDockerImageOwner

public String getDockerImageOwner()

Description copied from interface: BioModule

Get the name of the docker hub user that owns the image to use for this module. Docker images from docker hub are specified using this syntax: /:

Specified by:

getDockerImageOwner in interface BioModule

Overrides:

getDockerImageOwner in class BioModuleImpl

Returns:

getDockerImageName

public String getDockerImageName()

Description copied from interface: BioModule

Get the docker image to use for this module. The owner and version/tag are specificed separately; this is just the image name. Docker images from docker hub are specified using this syntax: /:

Specified by:

getDockerImageName in interface BioModule

Returns:

getDescription

public String getDescription()

Description copied from interface: ApiModule

Briefly describe what this module does. A more detailed description may be returned by getDetails.

Specified by:

getDescription in interface ApiModule

Returns:

getCitationString

public String getCitationString()

Description copied from interface: ApiModule

At a minimum, this should return the name and/or url for the wrapped tool. For BioLockJ home-grown modules, it can cite BioLockJ and give the current version. Ideally this will include the version for the wrapped tool. Tool version may require using a stored variable that can be filled in during execution; and the string that is returned pre-execution may not have the version.

Specified by:

getCitationString in interface ApiModule

Returns:

version

public String version()

Description copied from interface: BioModule

Changes to a module class should be accompanied by a increment in version. The is a string and open form, but using the major.minor.patch semantic versioning is recommended.

Specified by:

version in interface BioModule

Returns: