Admin user authenication problems during initial deployment.

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Admin user authenication problems during initial deployment.

Raf Bruyndonckx

Hi all,

We are currently trying to deploy a Apollo 2.4.1 server.
The setup used is a RHEL 7.6 server, with Tomcat8 installed and Mysql as DBMS.

During initial deployment we encounter the follow problem:

The apollo.war was succesfully file without any errors or dependency issues.  The war file is being deployed to tomcat and we can reach the application in a browser.
During first connection, the admin wizard is presented to register a new admin user.  The user registration seems to go well but when we try to logon with the same user credentials the login fails.  The connection to the Mysql database works correclty since db tables are succesfully created in the emtpy database.

We have checked the Tomcat access log files during this process:


When registering the Admin user, this seems be successful:

"POST /apollo/login/registerAdmin?clientToken=9549879604280319441649035252 HTTP/1.1" 200 12

 

When trying to login with the admin user we get a status code 401

"POST /apollo/user/loadUsers/?clientToken=9549879604280319441649035252 HTTP/1.1" 401 -

 

Is this a known/common issue during deployment?  Could someone suggest a possible debugging procedure?

 

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Re: Admin user authenication problems during initial deployment.

nathandunn

Raf,

1 - what version of mysql are you using? 
2 - what do you see on startup?
3 - what does your apollo-config.groovy look like (minus passwords)? 

Thanks,

Nathan


On Aug 5, 2019, at 10:52 AM, Raf Bruyndonckx <[hidden email]> wrote:

Hi all,

We are currently trying to deploy a Apollo 2.4.1 server.
The setup used is a RHEL 7.6 server, with Tomcat8 installed and Mysql as DBMS.

During initial deployment we encounter the follow problem:

The apollo.war was succesfully file without any errors or dependency issues.  The war file is being deployed to tomcat and we can reach the application in a browser.
During first connection, the admin wizard is presented to register a new admin user.  The user registration seems to go well but when we try to logon with the same user credentials the login fails.  The connection to the Mysql database works correclty since db tables are succesfully created in the emtpy database.

We have checked the Tomcat access log files during this process:


When registering the Admin user, this seems be successful:

"POST /apollo/login/registerAdmin?clientToken=9549879604280319441649035252 HTTP/1.1" 200 12

 

When trying to login with the admin user we get a status code 401

"POST /apollo/user/loadUsers/?clientToken=9549879604280319441649035252 HTTP/1.1" 401 -

 

Is this a known/common issue during deployment?  Could someone suggest a possible debugging procedure?

 

--
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Re: Admin user authenication problems during initial deployment.

Raf Bruyndonckx
Hi Nathan,

1 - We are using MariaDB 5.5.60   (Same version/server as our Apollo 2.0.7 setup)
2 - When deploying the WAR file and opening up the application in a browser we get the following screen:

<a imageanchor="1" href="about:invalid#zClosurez" style="clear: left; margin-bottom: 1em; float: left; margin-right: 1em;">admin wizzard.png

after entering the requested admin user info a normal login screen appears but when typing in the exact same credentials these are rejected and the tomcat logs show a error 401.


3 - our apollo-config.groovy looks like this:



environments {
development {
// sample config to turn on debug logging in development e.g. for apollo run-local
log4j.main = {
debug "grails.app"
}
// sample config to edit apollo specific configs in development mode
apollo {
gff3.source = "testing"
}
dataSource{
dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''
username = "DBUSER"
password = "PASSWORD"
driverClassName = "com.mysql.jdbc.Driver"
dialect = org.hibernate.dialect.MySQL5InnoDBDialect
url = "jdbc:mysql://FQDN/DATABASENAME_TEST"
}
}
test {
dataSource{
dbCreate = "create-drop" // one of 'create', 'create-drop', 'update', 'validate', ''
username = "DBUSER"
password = "PASSWORD"
driverClassName = "com.mysql.jdbc.Driver"
dialect = org.hibernate.dialect.MySQL5InnoDBDialect
url = "jdbc:mysql://FQDN/DATABASENAME_TEST"
}
}
production {
dataSource{
dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''
username = "DBUSER"
password = "PASSWORD"
driverClassName = "com.mysql.jdbc.Driver"
dialect = org.hibernate.dialect.MySQL5InnoDBDialect
url = "jdbc:mysql://FQDN/DATABASENAME_PRODUCTION"
properties {
// See http://grails.org/doc/latest/guide/conf.html#dataSource for documentation
jmxEnabled = true
initialSize = 5
maxActive = 50
minIdle = 5
maxIdle = 25
maxWait = 10000
maxAge = 10 * 60000
timeBetweenEvictionRunsMillis = 5000
minEvictableIdleTimeMillis = 60000
validationQuery = "SELECT 1"
validationQueryTimeout = 3
validationInterval = 15000
testOnBorrow = true
testWhileIdle = true
testOnReturn = false
jdbcInterceptors = "ConnectionState"
defaultTransactionIsolation = java.sql.Connection.TRANSACTION_READ_COMMITTED
}
}
}
}
apollo{
apollo.phone.phoneHome = false
google_analytics = []
sequence_search_tools = [
blat_nuc: [
search_exe: "/usr/local/bin/blat",
search_class: "org.bbop.apollo.sequence.search.blat.BlatCommandLineNucleotideToNucleotide",
name: "Blat nucleotide",
params: "-minIdentity=50 -minScore=10"
],
blat_prot: [
search_exe: "/usr/local/bin/blat",
search_class: "org.bbop.apollo.sequence.search.blat.BlatCommandLineProteinToNucleotide",
name: "Blat protein",
params: "",
tmp_dir: "/opt/apollo-data/tmp" //optional param, uses system tmp dir by default
]
]
// authentications = [
// ["name":"Remote User Authenticator",
// "className":"remoteUserAuthenticatorService",
// "active":true,
// ]
// ,
// ["name":"Username Password Authenticator",
// "className":"usernamePasswordAuthenticatorService",
// "active":true,
// ]
// ]
// admin{
// username = "[hidden email]"
// password = System.getenv("APOLLO_ADMIN_PASSWORD")?:"demo"
// firstName = "Super"
// lastName = "Admin"
}
}

//apollo {
// only_owners_delete = true
// common_data_directory = "/opt/temporary/apollo"
// store_orig_id = false
// sequence_search_tools {
// blat_nuc {
// search_exe = "/usr/local/bin/blastn"
// search_class = "org.bbop.apollo.sequence.search.blast.BlastCommandLine"
// name = "Blast nucleotide"
// params = ""
// }
// blat_prot {
// search_exe = "/usr/local/bin/tblastn"
// search_class = "org.bbop.apollo.sequence.search.blast.BlastCommandLine"
// name = "Blast protein to translated nucleotide"
// params = ""
// //tmp_dir: "/opt/apollo/tmp" optional param
// }
// }
// extraTabs = [
// ['title': 'extra1', 'url': 'http://localhost:8080/apollo/annotator/report/'],
// ['title': 'extra2', 'content': '<b>Apollo</b> documentation <a href="http://genomearchitect.org" target="_blank">linked here</a>']
// ]
//
//// extraTabs = [
//// tab1: [
//// title : 'extra1',
//// url : 'http://localhost:8080/apollo/annotator/report/'
//// ],
//// tab2: ['title': 'extra2',
//// 'content': '<b>Some content</b><a href="http://google.com" target="_blank">Google</a>'
//// ]
//// ]
//}

// Uncomment to change the default memory configurations
//grails.project.fork = [
// test : false,
// // configure settings for the run-app JVM
// run : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false],
// // configure settings for the run-war JVM
// war : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false],
// // configure settings for the Console UI JVM
// console: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024]
//]

// Uncomment to make changes
//
//jbrowse {
// git {
// url= "https://github.com/GMOD/jbrowse"
// tag = "1.16.5-release"
//// branch = "dev"
//// hash = "09b71099bf73c50d37a0e911baf06b4975e3f6ca"
// alwaysPull = true
// alwaysRecheck = true
// }
// plugins {
// NeatHTMLFeatures{
// included = true
// }
// NeatCanvasFeatures{
// included = true
// }
// RegexSequenceSearch{
// included = true
// }
// HideTrackLabels{
// included = true
// }
//// MyVariantInfo {
//// git = 'https://github.com/GMOD/myvariantviewer'
//// branch = 'master'
//// alwaysRecheck = "true"
//// alwaysPull = "true"
//// }
//// SashimiPlot {
//// git = 'https://github.com/cmdcolin/sashimiplot'
//// branch = 'master'
//// alwaysPull = "true"
//// }
// }
//}


With best regards,

Raf




Op maandag 5 augustus 2019 22:50:54 UTC+2 schreef Nathan Dunn:

Raf,

1 - what version of mysql are you using? 
2 - what do you see on startup?
3 - what does your apollo-config.groovy look like (minus passwords)? 

Thanks,

Nathan


On Aug 5, 2019, at 10:52 AM, Raf Bruyndonckx <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="_CeMf_QgBQAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">raf.bru...@partners.basf.com> wrote:

Hi all,

We are currently trying to deploy a Apollo 2.4.1 server.
The setup used is a RHEL 7.6 server, with Tomcat8 installed and Mysql as DBMS.

During initial deployment we encounter the follow problem:

The apollo.war was succesfully file without any errors or dependency issues.  The war file is being deployed to tomcat and we can reach the application in a browser.
During first connection, the admin wizard is presented to register a new admin user.  The user registration seems to go well but when we try to logon with the same user credentials the login fails.  The connection to the Mysql database works correclty since db tables are succesfully created in the emtpy database.

We have checked the Tomcat access log files during this process:


When registering the Admin user, this seems be successful:

"POST /apollo/login/registerAdmin?clientToken=9549879604280319441649035252 HTTP/1.1" 200 12

 

When trying to login with the admin user we get a status code 401

"POST /apollo/user/loadUsers/?clientToken=9549879604280319441649035252 HTTP/1.1" 401 -

 

Is this a known/common issue during deployment?  Could someone suggest a possible debugging procedure?

 

--
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Re: Admin user authenication problems during initial deployment.

nathandunn


Raf,

I duplicated this setup using MariaDB 5.5 (https://hub.docker.com/r/cytopia/mariadb-5.5/

It actually worked fine for me (in dev mode, but shouldn’t make a difference). 


Some questions:

1 - were you able to have this work with the username DBUSER?
2 - can you confirm that the registered user made it into the database (select * from grails_user) ? 
3 - can you supply log files when starting up and when registered / logging in? 
  

Nathan

On Aug 6, 2019, at 1:00 PM, Raf Bruyndonckx <[hidden email]> wrote:

Hi Nathan,

1 - We are using MariaDB 5.5.60   (Same version/server as our Apollo 2.0.7 setup)
2 - When deploying the WAR file and opening up the application in a browser we get the following screen:

<a imageanchor="1" href="about:invalid#zClosurez" style="clear: left; margin-bottom: 1em; float: left; margin-right: 1em;" class=""><admin wizzard.png>

after entering the requested admin user info a normal login screen appears but when typing in the exact same credentials these are rejected and the tomcat logs show a error 401.


3 - our apollo-config.groovy looks like this:



environments {
development {
// sample config to turn on debug logging in development e.g. for apollo run-local
log4j.main = {
debug "grails.app"
}
// sample config to edit apollo specific configs in development mode
apollo {
gff3.source = "testing"
}
dataSource{
dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''
username = "DBUSER"
password = "PASSWORD"
driverClassName = "com.mysql.jdbc.Driver"
dialect = org.hibernate.dialect.MySQL5InnoDBDialect
url = "jdbc:<a href="mysql://FQDN/DATABASENAME_TEST" class="">mysql://FQDN/DATABASENAME_TEST"
}
}
test {
dataSource{
dbCreate = "create-drop" // one of 'create', 'create-drop', 'update', 'validate', ''
username = "DBUSER"
password = "PASSWORD"
driverClassName = "com.mysql.jdbc.Driver"
dialect = org.hibernate.dialect.MySQL5InnoDBDialect
url = "jdbc:<a href="mysql://FQDN/DATABASENAME_TEST" class="">mysql://FQDN/DATABASENAME_TEST"
}
}
production {
dataSource{
dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''
username = "DBUSER"
password = "PASSWORD"
driverClassName = "com.mysql.jdbc.Driver"
dialect = org.hibernate.dialect.MySQL5InnoDBDialect
url = "jdbc:<a href="mysql://FQDN/DATABASENAME_PRODUCTION" class="">mysql://FQDN/DATABASENAME_PRODUCTION"
properties {
jmxEnabled = true
initialSize = 5
maxActive = 50
minIdle = 5
maxIdle = 25
maxWait = 10000
maxAge = 10 * 60000
timeBetweenEvictionRunsMillis = 5000
minEvictableIdleTimeMillis = 60000
validationQuery = "SELECT 1"
validationQueryTimeout = 3
validationInterval = 15000
testOnBorrow = true
testWhileIdle = true
testOnReturn = false
jdbcInterceptors = "ConnectionState"
defaultTransactionIsolation = java.sql.Connection.TRANSACTION_READ_COMMITTED
}
}
}
}
apollo{
apollo.phone.phoneHome = false
google_analytics = []
sequence_search_tools = [
blat_nuc: [
search_exe: "/usr/local/bin/blat",
search_class: "org.bbop.apollo.sequence.search.blat.BlatCommandLineNucleotideToNucleotide",
name: "Blat nucleotide",
params: "-minIdentity=50 -minScore=10"
],
blat_prot: [
search_exe: "/usr/local/bin/blat",
search_class: "org.bbop.apollo.sequence.search.blat.BlatCommandLineProteinToNucleotide",
name: "Blat protein",
params: "",
tmp_dir: "/opt/apollo-data/tmp" //optional param, uses system tmp dir by default
]
]
// authentications = [
// ["name":"Remote User Authenticator",
// "className":"remoteUserAuthenticatorService",
// "active":true,
// ]
// ,
// ["name":"Username Password Authenticator",
// "className":"usernamePasswordAuthenticatorService",
// "active":true,
// ]
// ]
// admin{
// username = "[hidden email]"
// password = System.getenv("APOLLO_ADMIN_PASSWORD")?:"demo"
// firstName = "Super"
// lastName = "Admin"
}
}

//apollo {
// only_owners_delete = true
// common_data_directory = "/opt/temporary/apollo"
// store_orig_id = false
// sequence_search_tools {
// blat_nuc {
// search_exe = "/usr/local/bin/blastn"
// search_class = "org.bbop.apollo.sequence.search.blast.BlastCommandLine"
// name = "Blast nucleotide"
// params = ""
// }
// blat_prot {
// search_exe = "/usr/local/bin/tblastn"
// search_class = "org.bbop.apollo.sequence.search.blast.BlastCommandLine"
// name = "Blast protein to translated nucleotide"
// params = ""
// //tmp_dir: "/opt/apollo/tmp" optional param
// }
// }
// extraTabs = [
// ['title': 'extra1', 'url': 'http://localhost:8080/apollo/annotator/report/'],
// ['title': 'extra2', 'content': '<b>Apollo</b> documentation <a href="http://genomearchitect.org" target="_blank">linked here</a>']
// ]
//
//// extraTabs = [
//// tab1: [
//// title : 'extra1',
//// ],
//// tab2: ['title': 'extra2',
//// 'content': '<b>Some content</b><a href="http://google.com" target="_blank">Google</a>'
//// ]
//// ]
//}

// Uncomment to change the default memory configurations
//grails.project.fork = [
// test : false,
// // configure settings for the run-app JVM
// run : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false],
// // configure settings for the run-war JVM
// war : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false],
// // configure settings for the Console UI JVM
// console: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024]
//]

// Uncomment to make changes
//
//jbrowse {
// git {
// tag = "1.16.5-release"
//// branch = "dev"
//// hash = "09b71099bf73c50d37a0e911baf06b4975e3f6ca"
// alwaysPull = true
// alwaysRecheck = true
// }
// plugins {
// NeatHTMLFeatures{
// included = true
// }
// NeatCanvasFeatures{
// included = true
// }
// RegexSequenceSearch{
// included = true
// }
// HideTrackLabels{
// included = true
// }
//// MyVariantInfo {
//// branch = 'master'
//// alwaysRecheck = "true"
//// alwaysPull = "true"
//// }
//// SashimiPlot {
//// branch = 'master'
//// alwaysPull = "true"
//// }
// }
//}


With best regards,

Raf




Op maandag 5 augustus 2019 22:50:54 UTC+2 schreef Nathan Dunn:

Raf,

1 - what version of mysql are you using? 
2 - what do you see on startup?
3 - what does your apollo-config.groovy look like (minus passwords)? 

Thanks,

Nathan


On Aug 5, 2019, at 10:52 AM, Raf Bruyndonckx <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="_CeMf_QgBQAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;" class="">raf.bru...@partners.basf.com> wrote:

Hi all,

We are currently trying to deploy a Apollo 2.4.1 server.
The setup used is a RHEL 7.6 server, with Tomcat8 installed and Mysql as DBMS.

During initial deployment we encounter the follow problem:

The apollo.war was succesfully file without any errors or dependency issues.  The war file is being deployed to tomcat and we can reach the application in a browser.
During first connection, the admin wizard is presented to register a new admin user.  The user registration seems to go well but when we try to logon with the same user credentials the login fails.  The connection to the Mysql database works correclty since db tables are succesfully created in the emtpy database.

We have checked the Tomcat access log files during this process:


When registering the Admin user, this seems be successful:

"POST /apollo/login/registerAdmin?clientToken=9549879604280319441649035252 HTTP/1.1" 200 12

 

When trying to login with the admin user we get a status code 401

"POST /apollo/user/loadUsers/?clientToken=9549879604280319441649035252 HTTP/1.1" 401 -

 

Is this a known/common issue during deployment?  Could someone suggest a possible debugging procedure?

 

<admin wizzard.png>

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Re: Admin user authenication problems during initial deployment.

Raf Bruyndonckx
Hi Nathan,

It appears the user did not make it to the database, the grails_user table was empty.  Although the DBUSER user works because all other tables were created in the empty database.
It seems that the issue is related to using https.  When connecting using http the user does make it to the database and everything seems to work as expected.

We're figuring out what network/firewall related issue causes the https call to fail.

Raf


Op dinsdag 6 augustus 2019 23:43:42 UTC+2 schreef Nathan Dunn:


Raf,

I duplicated this setup using MariaDB 5.5 (<a href="https://hub.docker.com/r/cytopia/mariadb-5.5/" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fhub.docker.com%2Fr%2Fcytopia%2Fmariadb-5.5%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEtHOW6fVLXA-P3P_iurY2p5fYyCw&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fhub.docker.com%2Fr%2Fcytopia%2Fmariadb-5.5%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEtHOW6fVLXA-P3P_iurY2p5fYyCw&#39;;return true;">https://hub.docker.com/r/cytopia/mariadb-5.5/) 

It actually worked fine for me (in dev mode, but shouldn’t make a difference). 


Some questions:

1 - were you able to have this work with the username DBUSER?
2 - can you confirm that the registered user made it into the database (select * from grails_user) ? 
3 - can you supply log files when starting up and when registered / logging in? 
  

Nathan

On Aug 6, 2019, at 1:00 PM, Raf Bruyndonckx <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="dq02TTYhDwAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">raf.bru...@partners.basf.com> wrote:

Hi Nathan,

1 - We are using MariaDB 5.5.60   (Same version/server as our Apollo 2.0.7 setup)
2 - When deploying the WAR file and opening up the application in a browser we get the following screen:

<admin wizzard.png>

after entering the requested admin user info a normal login screen appears but when typing in the exact same credentials these are rejected and the tomcat logs show a error 401.


3 - our apollo-config.groovy looks like this:



environments {
development {
// sample config to turn on debug logging in development e.g. for apollo run-local
log4j.main = {
debug "grails.app"
}
// sample config to edit apollo specific configs in development mode
apollo {
gff3.source = "testing"
}
dataSource{
dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''
username = "DBUSER"
password = "PASSWORD"
driverClassName = "com.mysql.jdbc.Driver"
dialect = org.hibernate.dialect.MySQL5InnoDBDialect
}
}
test {
dataSource{
dbCreate = "create-drop" // one of 'create', 'create-drop', 'update', 'validate', ''
username = "DBUSER"
password = "PASSWORD"
driverClassName = "com.mysql.jdbc.Driver"
dialect = org.hibernate.dialect.MySQL5InnoDBDialect
}
}
production {
dataSource{
dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''
username = "DBUSER"
password = "PASSWORD"
driverClassName = "com.mysql.jdbc.Driver"
dialect = org.hibernate.dialect.MySQL5InnoDBDialect
properties {
// See <a href="http://grails.org/doc/latest/guide/conf.html#dataSource" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fgrails.org%2Fdoc%2Flatest%2Fguide%2Fconf.html%23dataSource\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNH2X-NZlCXt7FM5RcIHLdxGVI6oOw&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fgrails.org%2Fdoc%2Flatest%2Fguide%2Fconf.html%23dataSource\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNH2X-NZlCXt7FM5RcIHLdxGVI6oOw&#39;;return true;">http://grails.org/doc/latest/guide/conf.html#dataSource for documentation
jmxEnabled = true
initialSize = 5
maxActive = 50
minIdle = 5
maxIdle = 25
maxWait = 10000
maxAge = 10 * 60000
timeBetweenEvictionRunsMillis = 5000
minEvictableIdleTimeMillis = 60000
validationQuery = "SELECT 1"
validationQueryTimeout = 3
validationInterval = 15000
testOnBorrow = true
testWhileIdle = true
testOnReturn = false
jdbcInterceptors = "ConnectionState"
defaultTransactionIsolation = java.sql.Connection.TRANSACTION_READ_COMMITTED
}
}
}
}
apollo{
apollo.phone.phoneHome = false
google_analytics = []
sequence_search_tools = [
blat_nuc: [
search_exe: "/usr/local/bin/blat",
search_class: "org.bbop.apollo.sequence.search.blat.BlatCommandLineNucleotideToNucleotide",
name: "Blat nucleotide",
params: "-minIdentity=50 -minScore=10"
],
blat_prot: [
search_exe: "/usr/local/bin/blat",
search_class: "org.bbop.apollo.sequence.search.blat.BlatCommandLineProteinToNucleotide",
name: "Blat protein",
params: "",
tmp_dir: "/opt/apollo-data/tmp" //optional param, uses system tmp dir by default
]
]
// authentications = [
// ["name":"Remote User Authenticator",
// "className":"remoteUserAuthenticatorService",
// "active":true,
// ]
// ,
// ["name":"Username Password Authenticator",
// "className":"usernamePasswordAuthenticatorService",
// "active":true,
// ]
// ]
// admin{
// username = "<a href="javascript:" target="_blank" gdf-obfuscated-mailto="dq02TTYhDwAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">su...@..."
// password = System.getenv("APOLLO_ADMIN_PASSWORD")?:"demo"
// firstName = "Super"
// lastName = "Admin"
}
}

//apollo {
// only_owners_delete = true
// common_data_directory = "/opt/temporary/apollo"
// store_orig_id = false
// sequence_search_tools {
// blat_nuc {
// search_exe = "/usr/local/bin/blastn"
// search_class = "org.bbop.apollo.sequence.search.blast.BlastCommandLine"
// name = "Blast nucleotide"
// params = ""
// }
// blat_prot {
// search_exe = "/usr/local/bin/tblastn"
// search_class = "org.bbop.apollo.sequence.search.blast.BlastCommandLine"
// name = "Blast protein to translated nucleotide"
// params = ""
// //tmp_dir: "/opt/apollo/tmp" optional param
// }
// }
// extraTabs = [
// ['title': 'extra1', 'url': '<a href="http://localhost:8080/apollo/annotator/report/" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Flocalhost%3A8080%2Fapollo%2Fannotator%2Freport%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFIHyk17VFivCw1Vj0gOcx1vTHe7g&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Flocalhost%3A8080%2Fapollo%2Fannotator%2Freport%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFIHyk17VFivCw1Vj0gOcx1vTHe7g&#39;;return true;">http://localhost:8080/apollo/annotator/report/'],
// ['title': 'extra2', 'content': '<b>Apollo</b> documentation <a href="<a href="http://genomearchitect.org" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fgenomearchitect.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFTZ57a-ZtNViV1_cnsnzK77ceoZQ&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fgenomearchitect.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFTZ57a-ZtNViV1_cnsnzK77ceoZQ&#39;;return true;">http://genomearchitect.org" target="_blank">linked here</a>']
// ]
//
//// extraTabs = [
//// tab1: [
//// title : 'extra1',
//// url : '<a href="http://localhost:8080/apollo/annotator/report/" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Flocalhost%3A8080%2Fapollo%2Fannotator%2Freport%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFIHyk17VFivCw1Vj0gOcx1vTHe7g&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Flocalhost%3A8080%2Fapollo%2Fannotator%2Freport%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFIHyk17VFivCw1Vj0gOcx1vTHe7g&#39;;return true;">http://localhost:8080/apollo/annotator/report/'
//// ],
//// tab2: ['title': 'extra2',
//// 'content': '<b>Some content</b><a href="<a href="http://google.com" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://google.com&#39;;return true;" onclick="this.href=&#39;http://google.com&#39;;return true;">http://google.com" target="_blank">Google</a>'
//// ]
//// ]
//}

// Uncomment to change the default memory configurations
//grails.project.fork = [
// test : false,
// // configure settings for the run-app JVM
// run : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false],
// // configure settings for the run-war JVM
// war : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false],
// // configure settings for the Console UI JVM
// console: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024]
//]

// Uncomment to make changes
//
//jbrowse {
// git {
// url= "<a href="https://github.com/GMOD/jbrowse" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEFrXiFEyuJToF-kzkXnrrZSspAAA&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEFrXiFEyuJToF-kzkXnrrZSspAAA&#39;;return true;">https://github.com/GMOD/jbrowse"
// tag = "1.16.5-release"
//// branch = "dev"
//// hash = "09b71099bf73c50d37a0e911baf06b4975e3f6ca"
// alwaysPull = true
// alwaysRecheck = true
// }
// plugins {
// NeatHTMLFeatures{
// included = true
// }
// NeatCanvasFeatures{
// included = true
// }
// RegexSequenceSearch{
// included = true
// }
// HideTrackLabels{
// included = true
// }
//// MyVariantInfo {
//// git = '<a href="https://github.com/GMOD/myvariantviewer" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2Fmyvariantviewer\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEO5e8__auiEkIL2p61jwTfjXSGIg&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2Fmyvariantviewer\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEO5e8__auiEkIL2p61jwTfjXSGIg&#39;;return true;">https://github.com/GMOD/myvariantviewer'
//// branch = 'master'
//// alwaysRecheck = "true"
//// alwaysPull = "true"
//// }
//// SashimiPlot {
//// git = '<a href="https://github.com/cmdcolin/sashimiplot" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2Fcmdcolin%2Fsashimiplot\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGxWmhi1eYjVKoPKAmJUGhR8fJY8Q&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2Fcmdcolin%2Fsashimiplot\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGxWmhi1eYjVKoPKAmJUGhR8fJY8Q&#39;;return true;">https://github.com/cmdcolin/sashimiplot'
//// branch = 'master'
//// alwaysPull = "true"
//// }
// }
//}


With best regards,

Raf




Op maandag 5 augustus 2019 22:50:54 UTC+2 schreef Nathan Dunn:

Raf,

1 - what version of mysql are you using? 
2 - what do you see on startup?
3 - what does your apollo-config.groovy look like (minus passwords)? 

Thanks,

Nathan


On Aug 5, 2019, at 10:52 AM, Raf Bruyndonckx <[hidden email]> wrote:

Hi all,

We are currently trying to deploy a Apollo 2.4.1 server.
The setup used is a RHEL 7.6 server, with Tomcat8 installed and Mysql as DBMS.

During initial deployment we encounter the follow problem:

The apollo.war was succesfully file without any errors or dependency issues.  The war file is being deployed to tomcat and we can reach the application in a browser.
During first connection, the admin wizard is presented to register a new admin user.  The user registration seems to go well but when we try to logon with the same user credentials the login fails.  The connection to the Mysql database works correclty since db tables are succesfully created in the emtpy database.

We have checked the Tomcat access log files during this process:


When registering the Admin user, this seems be successful:

"POST /apollo/login/registerAdmin?clientToken=9549879604280319441649035252 HTTP/1.1" 200 12

 

When trying to login with the admin user we get a status code 401

"POST /apollo/user/loadUsers/?clientToken=9549879604280319441649035252 HTTP/1.1" 401 -

 

Is this a known/common issue during deployment?  Could someone suggest a possible debugging procedure?

 

<admin wizzard.png>

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Re: Admin user authenication problems during initial deployment.

nathandunn

Thanks for the update.  

Let us know if there is anything there that might be useful to other users. 

Nathan


On Aug 7, 2019, at 9:12 AM, Raf Bruyndonckx <[hidden email]> wrote:

Hi Nathan,

It appears the user did not make it to the database, the grails_user table was empty.  Although the DBUSER user works because all other tables were created in the empty database.
It seems that the issue is related to using https.  When connecting using http the user does make it to the database and everything seems to work as expected.

We're figuring out what network/firewall related issue causes the https call to fail.

Raf


Op dinsdag 6 augustus 2019 23:43:42 UTC+2 schreef Nathan Dunn:


Raf,

I duplicated this setup using MariaDB 5.5 (<a href="https://hub.docker.com/r/cytopia/mariadb-5.5/" target="_blank" rel="nofollow" onmousedown="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fhub.docker.com%2Fr%2Fcytopia%2Fmariadb-5.5%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEtHOW6fVLXA-P3P_iurY2p5fYyCw';return true;" onclick="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fhub.docker.com%2Fr%2Fcytopia%2Fmariadb-5.5%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEtHOW6fVLXA-P3P_iurY2p5fYyCw';return true;" class="">https://hub.docker.com/r/cytopia/mariadb-5.5/) 

It actually worked fine for me (in dev mode, but shouldn’t make a difference). 


Some questions:

1 - were you able to have this work with the username DBUSER?
2 - can you confirm that the registered user made it into the database (select * from grails_user) ? 
3 - can you supply log files when starting up and when registered / logging in? 
  

Nathan

On Aug 6, 2019, at 1:00 PM, Raf Bruyndonckx <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="dq02TTYhDwAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;" class="">raf.bru...@partners.basf.com> wrote:

Hi Nathan,

1 - We are using MariaDB 5.5.60   (Same version/server as our Apollo 2.0.7 setup)
2 - When deploying the WAR file and opening up the application in a browser we get the following screen:

<admin wizzard.png>

after entering the requested admin user info a normal login screen appears but when typing in the exact same credentials these are rejected and the tomcat logs show a error 401.


3 - our apollo-config.groovy looks like this:



environments {
development {
// sample config to turn on debug logging in development e.g. for apollo run-local
log4j.main = {
debug "grails.app"
}
// sample config to edit apollo specific configs in development mode
apollo {
gff3.source = "testing"
}
dataSource{
dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''
username = "DBUSER"
password = "PASSWORD"
driverClassName = "com.mysql.jdbc.Driver"
dialect = org.hibernate.dialect.MySQL5InnoDBDialect
}
}
test {
dataSource{
dbCreate = "create-drop" // one of 'create', 'create-drop', 'update', 'validate', ''
username = "DBUSER"
password = "PASSWORD"
driverClassName = "com.mysql.jdbc.Driver"
dialect = org.hibernate.dialect.MySQL5InnoDBDialect
}
}
production {
dataSource{
dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''
username = "DBUSER"
password = "PASSWORD"
driverClassName = "com.mysql.jdbc.Driver"
dialect = org.hibernate.dialect.MySQL5InnoDBDialect
properties {
// See <a href="http://grails.org/doc/latest/guide/conf.html#dataSource" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fgrails.org%2Fdoc%2Flatest%2Fguide%2Fconf.html%23dataSource\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNH2X-NZlCXt7FM5RcIHLdxGVI6oOw';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fgrails.org%2Fdoc%2Flatest%2Fguide%2Fconf.html%23dataSource\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNH2X-NZlCXt7FM5RcIHLdxGVI6oOw';return true;" class="">http://grails.org/doc/latest/guide/conf.html#dataSource for documentation
jmxEnabled = true
initialSize = 5
maxActive = 50
minIdle = 5
maxIdle = 25
maxWait = 10000
maxAge = 10 * 60000
timeBetweenEvictionRunsMillis = 5000
minEvictableIdleTimeMillis = 60000
validationQuery = "SELECT 1"
validationQueryTimeout = 3
validationInterval = 15000
testOnBorrow = true
testWhileIdle = true
testOnReturn = false
jdbcInterceptors = "ConnectionState"
defaultTransactionIsolation = java.sql.Connection.TRANSACTION_READ_COMMITTED
}
}
}
}
apollo{
apollo.phone.phoneHome = false
google_analytics = []
sequence_search_tools = [
blat_nuc: [
search_exe: "/usr/local/bin/blat",
search_class: "org.bbop.apollo.sequence.search.blat.BlatCommandLineNucleotideToNucleotide",
name: "Blat nucleotide",
params: "-minIdentity=50 -minScore=10"
],
blat_prot: [
search_exe: "/usr/local/bin/blat",
search_class: "org.bbop.apollo.sequence.search.blat.BlatCommandLineProteinToNucleotide",
name: "Blat protein",
params: "",
tmp_dir: "/opt/apollo-data/tmp" //optional param, uses system tmp dir by default
]
]
// authentications = [
// ["name":"Remote User Authenticator",
// "className":"remoteUserAuthenticatorService",
// "active":true,
// ]
// ,
// ["name":"Username Password Authenticator",
// "className":"usernamePasswordAuthenticatorService",
// "active":true,
// ]
// ]
// admin{
// username = "<a href="javascript:" target="_blank" gdf-obfuscated-mailto="dq02TTYhDwAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;" class="">su...@..."
// password = System.getenv("APOLLO_ADMIN_PASSWORD")?:"demo"
// firstName = "Super"
// lastName = "Admin"
}
}

//apollo {
// only_owners_delete = true
// common_data_directory = "/opt/temporary/apollo"
// store_orig_id = false
// sequence_search_tools {
// blat_nuc {
// search_exe = "/usr/local/bin/blastn"
// search_class = "org.bbop.apollo.sequence.search.blast.BlastCommandLine"
// name = "Blast nucleotide"
// params = ""
// }
// blat_prot {
// search_exe = "/usr/local/bin/tblastn"
// search_class = "org.bbop.apollo.sequence.search.blast.BlastCommandLine"
// name = "Blast protein to translated nucleotide"
// params = ""
// //tmp_dir: "/opt/apollo/tmp" optional param
// }
// }
// extraTabs = [
// ['title': 'extra1', 'url': '<a href="http://localhost:8080/apollo/annotator/report/" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Flocalhost%3A8080%2Fapollo%2Fannotator%2Freport%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFIHyk17VFivCw1Vj0gOcx1vTHe7g';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Flocalhost%3A8080%2Fapollo%2Fannotator%2Freport%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFIHyk17VFivCw1Vj0gOcx1vTHe7g';return true;" class="">http://localhost:8080/apollo/annotator/report/'],
// ['title': 'extra2', 'content': '<b>Apollo</b> documentation <a href="<a href="http://genomearchitect.org/" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fgenomearchitect.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFTZ57a-ZtNViV1_cnsnzK77ceoZQ';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fgenomearchitect.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFTZ57a-ZtNViV1_cnsnzK77ceoZQ';return true;" class="">http://genomearchitect.org" target="_blank">linked here</a>']
// ]
//
//// extraTabs = [
//// tab1: [
//// title : 'extra1',
//// url : '<a href="http://localhost:8080/apollo/annotator/report/" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Flocalhost%3A8080%2Fapollo%2Fannotator%2Freport%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFIHyk17VFivCw1Vj0gOcx1vTHe7g';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Flocalhost%3A8080%2Fapollo%2Fannotator%2Freport%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFIHyk17VFivCw1Vj0gOcx1vTHe7g';return true;" class="">http://localhost:8080/apollo/annotator/report/'
//// ],
//// tab2: ['title': 'extra2',
//// 'content': '<b>Some content</b><a href="<a href="http://google.com/" target="_blank" rel="nofollow" onmousedown="this.href='http://google.com';return true;" onclick="this.href='http://google.com';return true;" class="">http://google.com" target="_blank">Google</a>'
//// ]
//// ]
//}

// Uncomment to change the default memory configurations
//grails.project.fork = [
// test : false,
// // configure settings for the run-app JVM
// run : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false],
// // configure settings for the run-war JVM
// war : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false],
// // configure settings for the Console UI JVM
// console: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024]
//]

// Uncomment to make changes
//
//jbrowse {
// git {
// url= "<a href="https://github.com/GMOD/jbrowse" target="_blank" rel="nofollow" onmousedown="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEFrXiFEyuJToF-kzkXnrrZSspAAA';return true;" onclick="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEFrXiFEyuJToF-kzkXnrrZSspAAA';return true;" class="">https://github.com/GMOD/jbrowse"
// tag = "1.16.5-release"
//// branch = "dev"
//// hash = "09b71099bf73c50d37a0e911baf06b4975e3f6ca"
// alwaysPull = true
// alwaysRecheck = true
// }
// plugins {
// NeatHTMLFeatures{
// included = true
// }
// NeatCanvasFeatures{
// included = true
// }
// RegexSequenceSearch{
// included = true
// }
// HideTrackLabels{
// included = true
// }
//// MyVariantInfo {
//// git = '<a href="https://github.com/GMOD/myvariantviewer" target="_blank" rel="nofollow" onmousedown="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2Fmyvariantviewer\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEO5e8__auiEkIL2p61jwTfjXSGIg';return true;" onclick="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2Fmyvariantviewer\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEO5e8__auiEkIL2p61jwTfjXSGIg';return true;" class="">https://github.com/GMOD/myvariantviewer'
//// branch = 'master'
//// alwaysRecheck = "true"
//// alwaysPull = "true"
//// }
//// SashimiPlot {
//// git = '<a href="https://github.com/cmdcolin/sashimiplot" target="_blank" rel="nofollow" onmousedown="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2Fcmdcolin%2Fsashimiplot\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGxWmhi1eYjVKoPKAmJUGhR8fJY8Q';return true;" onclick="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2Fcmdcolin%2Fsashimiplot\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGxWmhi1eYjVKoPKAmJUGhR8fJY8Q';return true;" class="">https://github.com/cmdcolin/sashimiplot'
//// branch = 'master'
//// alwaysPull = "true"
//// }
// }
//}


With best regards,

Raf




Op maandag 5 augustus 2019 22:50:54 UTC+2 schreef Nathan Dunn:

Raf,

1 - what version of mysql are you using? 
2 - what do you see on startup?
3 - what does your apollo-config.groovy look like (minus passwords)? 

Thanks,

Nathan


On Aug 5, 2019, at 10:52 AM, Raf Bruyndonckx <[hidden email]> wrote:

Hi all,

We are currently trying to deploy a Apollo 2.4.1 server.
The setup used is a RHEL 7.6 server, with Tomcat8 installed and Mysql as DBMS.

During initial deployment we encounter the follow problem:

The apollo.war was succesfully file without any errors or dependency issues.  The war file is being deployed to tomcat and we can reach the application in a browser.
During first connection, the admin wizard is presented to register a new admin user.  The user registration seems to go well but when we try to logon with the same user credentials the login fails.  The connection to the Mysql database works correclty since db tables are succesfully created in the emtpy database.

We have checked the Tomcat access log files during this process:


When registering the Admin user, this seems be successful:

"POST /apollo/login/registerAdmin?clientToken=9549879604280319441649035252 HTTP/1.1" 200 12

 

When trying to login with the admin user we get a status code 401

"POST /apollo/user/loadUsers/?clientToken=9549879604280319441649035252 HTTP/1.1" 401 -

 

Is this a known/common issue during deployment?  Could someone suggest a possible debugging procedure?

 

<admin wizzard.png>


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