Clean restart #12

joshmoore · 2018-03-15T09:01:20Z

This branch attempts a couple of things:

Add a stable directory (/var/lib/apacheds) as a volume
Improve signal handling (with dumb-init)
Cleanly restart after a docker stop

joshmoore · 2018-03-15T09:02:06Z

Currently looking into

jvm 1    | [08:55:59] ERROR [org.apache.directory.server.wrapper.ApacheDsTanukiWrapper] - Failed to start the service.
jvm 1    | org.apache.directory.api.ldap.model.exception.LdapOtherException: ERR_250_ENTRY_ALREADY_EXISTS ou=system already exists!
jvm 1    |      at org.apache.directory.server.core.api.partition.AbstractPartition.initialize(AbstractPartition.java:94)
jvm 1    |      at org.apache.directory.server.core.DefaultDirectoryService.initialize(DefaultDirectoryService.java:1822)
jvm 1    |      at org.apache.directory.server.core.DefaultDirectoryService.startup(DefaultDirectoryService.java:1251)
jvm 1    |      at org.apache.directory.server.ApacheDsService.initDirectoryService(ApacheDsService.java:364)
jvm 1    |      at org.apache.directory.server.ApacheDsService.start(ApacheDsService.java:197)
jvm 1    |      at org.apache.directory.server.ApacheDsService.start(ApacheDsService.java:153)
jvm 1    |      at org.apache.directory.server.wrapper.ApacheDsTanukiWrapper.start(ApacheDsTanukiWrapper.java:175)
jvm 1    |      at org.tanukisoftware.wrapper.WrapperManager$12.run(WrapperManager.java:2788)
jvm 1    | Caused by: org.apache.directory.api.ldap.model.exception.LdapOtherException: ERR_250_ENTRY_ALREADY_EXISTS ou=system already exists!
jvm 1    |      at org.apache.directory.server.core.api.partition.AbstractPartition.initialize(AbstractPartition.java:94)
jvm 1    |      at org.apache.directory.server.core.shared.partition.DefaultPartitionNexus.addContextPartition(DefaultPartitionNexus.java:809)
jvm 1    |      at org.apache.directory.server.core.shared.partition.DefaultPartitionNexus.doInit(DefaultPartitionNexus.java:227)
jvm 1    |      at org.apache.directory.server.core.api.partition.AbstractPartition.initialize(AbstractPartition.java:89)
jvm 1    |      ... 7 more
jvm 1    | Caused by: org.apache.directory.api.ldap.model.exception.LdapEntryAlreadyExistsException: ERR_250_ENTRY_ALREADY_EXISTS ou=system already exists!
jvm 1    |      at org.apache.directory.server.core.partition.impl.btree.AbstractBTreePartition.add(AbstractBTreePartition.java:698)
jvm 1    |      at org.apache.directory.server.core.partition.impl.btree.jdbm.JdbmPartition.doInit(JdbmPartition.java:522)
jvm 1    |      at org.apache.directory.server.core.api.partition.AbstractPartition.initialize(AbstractPartition.java:89)
jvm 1    |      ... 10 more

See also:

Bump for testing ome/apacheds-docker#12

manics · 2018-03-16T16:28:18Z

Dockerfile

 ENV APACHEDS_USER apacheds
 ENV APACHEDS_GROUP apacheds

+RUN ln -s ${APACHEDS_DATA}-${APACHEDS_VERSION} ${APACHDS_DATA}


typo: APACHDS_DATA
so there appear to be two data directories:

root@63b43aeb4f88:/var/lib# ls -l apacheds* -d drwxr-xr-x 3 root root 4096 Mar 16 16:43 apacheds drwxr-xr-x 3 apacheds apacheds 4096 Mar 15 11:43 apacheds-2.0.0-M24 root@63b43aeb4f88:/var/lib# ls apacheds* apacheds: default apacheds-2.0.0-M24: default

manics · 2018-03-16T16:32:37Z

README.md

@@ -13,7 +13,7 @@ The project sources can be found on [GitHub](https://github.com/openmicroscopy/a

 ## Installation

-The folder */var/lib/apacheds-${APACHEDS_VERSION}* contains the runtime data and thus has been defined as a volume. A [volume container](https://docs.docker.com/userguide/dockervolumes/) could be used for that. The image uses exactly the file system structure defined by the [ApacheDS documentation](https://directory.apache.org/apacheds/advanced-ug/2.2.1-debian-instance-layout.html).
+The folder */var/lib/apacheds* contains the runtime data and thus has been defined as a volume. A [volume container](https://docs.docker.com/userguide/dockervolumes/) could be used for that. The image uses exactly the file system structure defined by the [ApacheDS documentation](https://directory.apache.org/apacheds/advanced-ug/2.2.1-debian-instance-layout.html).


https://docs.docker.com/userguide/dockervolumes/ is broken. In any case volume containers aren't needed anymore.

manics · 2018-03-16T16:36:06Z

Dockerfile

 #############################################
 # ApacheDS wrapper command
 #############################################

-CMD ${APACHEDS_CMD}


Since this is removed do you still need the configurability provided by ENV APACHEDS_CMD ENV APACHEDS_SCRIPT: https://github.com/openmicroscopy/apacheds-docker/pull/12/files#diff-3254677a7917c6c01f55212f86c57fbfL41 ?

I couldn't get the syntax right to put the environment variable as the entrypoint (at least not without reverting to bash -c. I'll drop the rest.

manics · 2018-03-16T17:08:53Z

scripts/run.sh

+}
+
+trap shutdown INT TERM
+tail --pid=$(cat $PIDFILE) -f /dev/null


There's also

/var/lib/apacheds/default/log/apacheds.log

/var/lib/apacheds/default/log/wrapper.log
Is one of these more useful?

Neither is good, but that's likely a log4j.properties issue. I'll use the more specific apacheds.log.

joshmoore · 2018-03-16T18:39:59Z

Pushed.

manics

👍

pwalczysko · 2018-03-22T13:47:08Z

I was asked to review here too, but did not get to it for IDR-reasons.

Also, I am just not sure aobut the workflow:

have a ldap DB on the apacheds docker (on outreach ?)
restart the apacheds docker (how to do this ?)
observe that the ldap DB was preserved

Is that right ? @joshmoore is the workflow correct and, after we have clarified the steps (see above) I can run it as a part of some trello card task (which one ?) ?

joshmoore · 2018-03-22T16:47:12Z

did not get to it for IDR-reasons.

No worries, @pwalczysko. Though I am looking forward to your showing me how this change could be better (which I'll happily implement and release incrementally) I was equally if not more interested in how you found the usability of the deployed service. (Can give you pointers to that off-PR)

Is that right ?

Roughly yes. What this work tries to enable (using your bullet list) is:

have an apacheds container with a persistent data directory (or "volume")
restart the apacheds container
observe that that the changes to ldap are preserved

This would be my hope that the mentioned service that I spun up will become a persistent way for us to maintain users, including multiple groups and perhaps even different styles of LDAP layouts.

joshmoore added 5 commits March 15, 2018 08:22

Use /var/lib/apacheds as the data volume

dc608cf

Install ldapmanager globally in image

025d65a

Add dumb-init for signal handling

e5d93f6

Cleanup pid after console exits

3c7916e

Attempt clean shutdown

9fef36f

joshmoore mentioned this pull request Mar 15, 2018

can't re-start after stop greggigon/apacheds#4

Open

joshmoore added 2 commits March 15, 2018 10:02

Use start and stop to prevent DB corruption

3014a42

Minor cleanup of hard-coded version

dc382ba

joshmoore added a commit to joshmoore/apacheds-k8s-app that referenced this pull request Mar 15, 2018

Temporarily use joshmoore repository

eac1cbb

Bump for testing ome/apacheds-docker#12

joshmoore mentioned this pull request Mar 15, 2018

Update apacheds version ome/apacheds-k8s-app#1

Merged

joshmoore added a commit to joshmoore/apacheds-k8s-app that referenced this pull request Mar 15, 2018

Temporarily use joshmoore repository

c64f01c

Bump for testing ome/apacheds-docker#12

manics suggested changes Mar 16, 2018

View reviewed changes

Improvements from Simon

5e02663

manics approved these changes Mar 19, 2018

View reviewed changes

joshmoore merged commit ede8d0d into ome:master Mar 19, 2018

joshmoore deleted the clean-restart branch March 19, 2018 11:08

ome deleted a comment from pwalczysko Mar 23, 2018

joshmoore mentioned this pull request May 17, 2018

Add apacheds k8s app ome/kubernetes-apps#6

Merged

joshmoore mentioned this pull request Jun 21, 2018

ERR_250_ENTRY_ALREADY_EXISTS ou=system already exists #15

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Clean restart #12

Clean restart #12

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Clean restart #12

Clean restart #12

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