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Add support for AWS SES as mail sending provider
This commits adds the support for AWS Simple Email Service as an alternative transport for sending notification emails from nextflow. The email is sent via AWS SES when using the nf-amazon plugin, and: - the NXF_ENABLE_AWS_SES=true environment variable is set - or, not `mail.smtp` setting is provided and the AWS_REGION or AWS_DEFAULT_REGION is set in the launching environment Signed-off-by: Paolo Di Tommaso <[email protected]>
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+369
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‎modules/nextflow/src/main/groovy/nextflow/mail/BaseMailProvider.groovy

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/*
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* Copyright 2020-2023, Seqera Labs
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*
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*/
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package nextflow.mail
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import javax.mail.MessagingException
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import javax.mail.internet.MimeMessage
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import groovy.transform.CompileStatic
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import nextflow.util.Duration
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/**
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* Base class or sending an email via sys command `mail` or `sendmail`
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*
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* @author Paolo Di Tommaso <[email protected]>
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*/
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@CompileStatic
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abstract class BaseMailProvider implements MailProvider {
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private long SEND_MAIL_TIMEOUT = 15_000
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/**
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* Send a email message by using system tool such as `sendmail` or `mail`
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*
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* @param message A {@link MimeMessage} object representing the email to send
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*/
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void send(MimeMessage message, Mailer mailer) {
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final cmd = [name(), '-t']
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final proc = new ProcessBuilder()
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.command(cmd)
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.redirectErrorStream(true)
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.start()
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// pipe the message to the sendmail stdin
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final stdout = new StringBuilder()
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final stdin = proc.getOutputStream()
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message.writeTo(stdin);
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stdin.close() // <-- don't forget otherwise it hangs
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// wait for the sending to complete
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final consumer = proc.consumeProcessOutputStream(stdout)
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proc.waitForOrKill(sendTimeout(mailer))
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def status = proc.exitValue()
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if( status != 0 ) {
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consumer.join()
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throw new MessagingException("Unable to send mail message\n $mailer exit status: $status\n reported error: $stdout")
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}
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}
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private long sendTimeout(Mailer mailer) {
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final timeout = mailer.config.sendMailTimeout as Duration
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return timeout ? timeout.toMillis() : SEND_MAIL_TIMEOUT
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}
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}

‎modules/nextflow/src/main/groovy/nextflow/mail/JavaMailProvider.groovy

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/*
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* Copyright 2020-2023, Seqera Labs
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*
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*/
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package nextflow.mail
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import javax.mail.internet.MimeMessage
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import groovy.transform.CompileStatic
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import groovy.util.logging.Slf4j
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/**
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* Implements a send mail provider based on Java Mail API
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*
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* @author Paolo Di Tommaso <[email protected]>
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*/
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@Slf4j
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@CompileStatic
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class JavaMailProvider implements MailProvider {
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@Override
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void send(MimeMessage message, Mailer mailer) {
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if( !message.getAllRecipients() )
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throw new IllegalArgumentException("Missing mail message recipient")
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final transport = mailer.getSession().getTransport()
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transport.connect(mailer.host, mailer.port as int, mailer.user, mailer.password)
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log.trace("Connected to host=$mailer.host port=$mailer.port")
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try {
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transport.sendMessage(message, message.getAllRecipients())
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}
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finally {
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transport.close()
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}
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}
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@Override
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String name() {
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return 'javamail'
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}
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@Override
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boolean textOnly() {
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return false
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}
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}

‎modules/nextflow/src/main/groovy/nextflow/mail/MailProvider.groovy

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/*
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* Copyright 2020-2023, Seqera Labs
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*
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*/
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package nextflow.mail
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import javax.mail.internet.MimeMessage
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import org.pf4j.ExtensionPoint
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/**
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* Define a generic interface to send an email modelled as a Mime message object
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*
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* @author Paolo Di Tommaso <[email protected]>
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*/
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interface MailProvider extends ExtensionPoint {
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void send(MimeMessage message, Mailer mailer)
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String name()
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boolean textOnly()
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}

‎modules/nextflow/src/main/groovy/nextflow/mail/Mailer.groovy

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@@ -15,6 +15,7 @@
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*/
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package nextflow.mail
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import javax.activation.DataHandler
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import javax.activation.URLDataSource
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import javax.mail.Message
@@ -34,7 +35,7 @@ import groovy.transform.CompileStatic
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import groovy.transform.Memoized
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import groovy.util.logging.Slf4j
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import nextflow.io.LogOutputStream
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import nextflow.util.Duration
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import nextflow.plugin.Plugins
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import org.jsoup.Jsoup
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import org.jsoup.nodes.Document
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import org.jsoup.parser.Parser
@@ -61,8 +62,6 @@ class Mailer {
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private final static Pattern HTML_PATTERN = Pattern.compile("("+TAG_START+".*"+TAG_END+")|("+TAG_SELF_CLOSING+")|("+HTML_ENTITY+")", Pattern.DOTALL )
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64-
private long SEND_MAIL_TIMEOUT = 15_000
65-
6665
private static String DEF_CHARSET = Charset.defaultCharset().toString()
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/**
@@ -87,6 +86,8 @@ class Mailer {
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return this
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}
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89+
Map getConfig() { config }
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protected String getSysMailer() {
9192
if( !fMailer )
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fMailer = findSysMailer()
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getConfig('password')
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}
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203-
protected getConfig(String name ) {
204+
protected getConfig(String name) {
204205
def key = "smtp.${name}"
205206
def value = config.navigate(key)
206207
if( !value ) {
@@ -210,58 +211,6 @@ class Mailer {
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return value
211212
}
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213-
/**
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* Send a email message by using the Java API
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*
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* @param message A {@link MimeMessage} object representing the email to send
217-
*/
218-
protected void sendViaJavaMail(MimeMessage message) {
219-
if( !message.getAllRecipients() )
220-
throw new IllegalArgumentException("Missing mail message recipient")
221-
222-
final transport = getSession().getTransport()
223-
transport.connect(host, port as int, user, password)
224-
log.trace("Connected to host=$host port=$port")
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try {
226-
transport.sendMessage(message, message.getAllRecipients())
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}
228-
finally {
229-
transport.close()
230-
}
231-
}
232-
233-
protected long getSendTimeout() {
234-
def timeout = config.sendMailTimeout as Duration
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return timeout ? timeout.toMillis() : SEND_MAIL_TIMEOUT
236-
}
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238-
/**
239-
* Send a email message by using system tool such as `sendmail` or `mail`
240-
*
241-
* @param message A {@link MimeMessage} object representing the email to send
242-
*/
243-
protected void sendViaSysMail(MimeMessage message) {
244-
final mailer = getSysMailer()
245-
final cmd = [mailer, '-t']
246-
final proc = new ProcessBuilder()
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.command(cmd)
248-
.redirectErrorStream(true)
249-
.start()
250-
// pipe the message to the sendmail stdin
251-
final stdout = new StringBuilder()
252-
final stdin = proc.getOutputStream()
253-
message.writeTo(stdin);
254-
stdin.close() // <-- don't forget otherwise it hangs
255-
// wait for the sending to complete
256-
final consumer = proc.consumeProcessOutputStream(stdout)
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proc.waitForOrKill(sendTimeout)
258-
def status = proc.exitValue()
259-
if( status != 0 ) {
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consumer.join()
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throw new MessagingException("Unable to send mail message\n $mailer exit status: $status\n reported error: $stdout")
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}
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}
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265214
/**
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* @return A multipart mime message representing the mail message to send
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*/
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guessHtml(str) ? 'text/html' : 'text/plain'
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}
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410-
/**
411-
* Send the mail given the provided config setting
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*/
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void send(Mail mail) {
414-
log.trace "Mailer config: $config -- mail: $mail"
359+
protected boolean detectAwsEnv() {
360+
if( env.get('AWS_REGION') ) return true
361+
if( env.get('AWS_DEFAULT_REGION') ) return true
362+
return false
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}
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365+
protected MailProvider provider() {
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// load all providers
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final providers = Plugins.getExtensions(MailProvider)
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// find the AWS provider
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final awsProvider = providers.find(it -> it.name()=='aws-ses')
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// check if it can use the aws provider
371+
if( env.get('NXF_ENABLE_AWS_SES')=='true' ) {
372+
if( awsProvider )
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return awsProvider
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else
375+
log.warn "Unable to load AWS Simple Email Service (SES) client"
376+
}
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416-
// if the user provided required configuration
417-
// send via Java Mail API
418378
if( config.containsKey('smtp') ) {
419-
log.trace "Mailer send via `javamail`"
420-
def msg = createMimeMessage(mail)
421-
sendViaJavaMail(msg)
422-
return
379+
return providers.find(it -> it.name()=='javamail')
423380
}
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425-
final mailer = getSysMailer()
426-
// otherwise fallback on system sendmail
427-
if( mailer == 'sendmail' ) {
428-
log.trace "Mailer send via `sendmail`"
429-
def msg = createMimeMessage(mail)
430-
sendViaSysMail(msg)
431-
return
382+
if( awsProvider && detectAwsEnv() ) {
383+
return awsProvider
432384
}
433385

434-
if( mailer == 'mail' ) {
435-
log.trace "Mailer send via `mail`"
436-
def msg = createTextMessage(mail)
437-
sendViaSysMail(msg)
386+
// detect the mailer type
387+
final type = getSysMailer()
388+
return providers.find(it -> it.name()==type)
389+
}
390+
391+
/**
392+
* Send the mail given the provided config setting
393+
*/
394+
void send(Mail mail) {
395+
log.trace "Mailer config: $config -- mail: $mail"
396+
397+
final p = provider()
398+
if( p != null ) {
399+
log.debug "Sending mail via `${p.name()}`"
400+
final msg = p.textOnly()
401+
? createTextMessage(mail)
402+
: createMimeMessage(mail)
403+
p.send(msg, this)
438404
return
439405
}
440406

441-
String msg = (mailer
442-
? "Unknown system mail tool: $mailer"
443-
: "Cannot send email message -- Make sure you have installed `sendmail` or `mail` program or configure a mail SMTP server in the nextflow config file"
444-
)
407+
final msg = "Cannot send email message -- Make sure you have installed `sendmail` or `mail` program or configure a mail SMTP server in the nextflow config file"
445408
throw new IllegalArgumentException(msg)
446409
}
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‎modules/nextflow/src/main/groovy/nextflow/mail/SendMailProvider.groovy

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/*
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* Copyright 2020-2023, Seqera Labs
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
5+
* you may not use this file except in compliance with the License.
6+
* You may obtain a copy of the License at
7+
*
8+
* http://www.apache.org/licenses/LICENSE-2.0
9+
*
10+
* Unless required by applicable law or agreed to in writing, software
11+
* distributed under the License is distributed on an "AS IS" BASIS,
12+
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
13+
* See the License for the specific language governing permissions and
14+
* limitations under the License.
15+
*
16+
*/
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18+
package nextflow.mail
19+
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/**
21+
* Send a mail using the `sendmail` sys tool
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*
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* @author Paolo Di Tommaso <[email protected]>
24+
*/
25+
class SendMailProvider extends BaseMailProvider {
26+
27+
@Override
28+
String name() {
29+
return 'sendmail'
30+
}
31+
32+
@Override
33+
boolean textOnly() {
34+
return false
35+
}
36+
}

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