Table doesn't exist error on trying to load Atom for the first time (i.e. install)

[axf...@gmail.com]

Hi folks,

Full disclosure -- I'm trying to install Atom on a Snow Leopard (10.6) Mac for a client because that's what they asked for (specifically, I'm trying to update from a local install of ICA-AtoM 1.2), and this may not be a good idea. I got all of the dependencies installed, mostly through homebrew, mostly following your documentation (it's a little incomplete on Mac in that it doesn't mention gearman, but it's pretty close if you cross-reference the Linux docs); I probably would've given up satisfying the Java 7 requirement for ElasticSearch if someone else in an SO thread hadn't edited some headers for it to build, but hey, so far so good.

A caveat: I know very, very little about nginx, php-fpm, and sockets. I had to change a number of paths by hand in various config files to reflect homebrew's /usr/local sandboxes and I'm not at all sure I did it right, but, I got as far as Atom showing a 500 error, with this in the nginx logs:

2015/08/04 14:01:30 [error] 34198#0: *59 FastCGI sent in stderr: "PHP message:  [wrapped: SQLSTATE[42S02]: Base table or view not found: 1146 Table 'atom.object' doesn't exist]" while reading response header from upstream, client: 127.0.0.1, server: _, request: "GET / HTTP/1.1", upstream: "fastcgi://unix:/usr/local/var/run/php5-fpm.atom.sock:", host: "localhost"

I'm going to assume that this is actually a rather spectacular and unlikely misfire causing Atom to somehow check for a table existing before it's actually run the commands to create that table. However, it still seems odd that it would throw this error on a totally fresh install, when I haven't even configured it to look for a database called atom. This is on a 2.2 tarball, for the record.

Any ideas? Should I just erase the past four hours and throw a Ubuntu VM or vagrant setup on here? Thanks!

[mi...@artefactual.com]

Hi,

Yeah, that's a pretty odd error if you're upgrading from 1.2 given that that table should exist even in 1.2. Maybe there's an issue with connecting to the database?

If you'd like you can email me your database, at mike at artefactual.com, and I can try to replicate the issue.

Cheers,

Mike

[dh...@artefactual.com]

I've encountered this now and again as well on installs... did it happen in the midst of the "web install" (GUI with fields you filled in with database name, port 3306 and so on)?
Or a clearer question might be, what step are you at in the process (installation instructions)?

If you indeed have a created but empty (no tables) 'atom' database, can probably create "start state" tables with the equivalent command of

sudo -u www-data php symfony tools:purge

(where e.g. www-data is the web server user as on many of our Ubuntu installations)
per https://www.accesstomemory.org/en/docs/2.1/admin-manual/maintenance/cli-tools/#purging-all-data

albeit then I guess we'd have to still create your Elasticsearch index by hand and so on? Probably worth your answering the first two questions before we speculate further....


Thanks,

      Dave Hume

On Tuesday, August 4, 2015 at 2:12:09 PM UTC-7, axf...@gmail.com wrote:

[Alex Garnett]

This is on trying to *load* the install page for the very first time, before having provided any database credentials; I've created an empty database, but otherwise this is not in any sense an upgrade (the old 1.2 instance is running on a separate SQL server), which is why it's very strange that it's expecting to connect to a database at all.

I'm perfectly happy throwing in the towel and loading a VM, but "encountered this now and again" is curious :)

-alex

[David Hume]

Hi Alex,

So you completed both steps of https://www.accesstomemory.org/en/docs/2.1/admin-manual/installation/linux/#create-the-database, and moving on to the web installer...

Nothing (or what) comes up in a browser for http://<server_name> (I guess same as http://localhost if browser also on the Mac)?

         Dave

[Alex Garnett]

500 error. With the Atom logo, at least :)

-alex

[David Hume]

Okay, any difference if you add the following

http://<server_name>/sfInstallPlugin

[Alex Garnett]

Just back at this today, but yep. That gets me to the regular install process, but on trying to provide SQL credentials, I get:

Unable to open PDO connection [wrapped: SQLSTATE[28000] [1045] Access denied for user 'root'@'localhost' (using password: NO)]

When I was actually using a password.

-alex

[Dan Gillean]

Hi Alex,

It might be possible that you are encountering an error that some of our other users have reported in 2.2? Or that the workaround suggested there will help you, even if its origination is different. For suggestions on how to resolve this, please see this thread:

• https://groups.google.com/d/topic/ica-atom-users/L3jB7FQMaN8/discussion

We're already working on preparing a 2.2.1 release that will include fixes for this issue. In the meantime, let us know if the workaround helps you move forward.

Cheers,

Dan Gillean, MAS, MLIS
AtoM Product Manager / Systems Analyst,
Artefactual Systems, Inc.
604-527-2056

@accesstomemory

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[Alex Garnett]

Aha -- that's probably it. I left the client machine I was working on running a tweaked version of the vagrant install in the meantime after I couldn't get this to work, and that's doing the job for now, but this would be good to revisit. Thanks.

-alex

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[John La]

Hi,

I am encountering similar problem.

Trying a new install in Ubuntu 14.04 server and atom 2.2.

There is currently the atom database with no table.

The error log say atom.object table does not exist when trying to install.

I don't understand the solution above with http://<server_name>/sfInstallPlugin

I tried http://<server_name>/plugins/sfInstallPlugin but only got a directory listing

Can someone explain this further?

thanks,

John

[Dan Gillean]

Hi John,

I would suggest the following workarounds for you:

Try deleting the following file in your AtoM folder:

• config/config.php

You may then also want to drop, and then recreate, your database:

mysql -h localhost -u root -p -e "DROP DATABASE atom;"

mysql -h localhost -u root -p -e "CREATE DATABASE atom CHARACTER SET utf8 COLLATE utf8_unicode_ci;"

Using your database name (i've used atom as the DB name in the above examples).

Let us know if that resolves the issue!

Cheers,

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056

@accesstomemory

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[John La]

Thanks Dan, now I can get to the install page.

However, I am stuck at the Search configuration page with 'Elasticsearch error'.

From the apache log, it states ' No connection information in your runtime configuration file for datasource [propel]'

I looked at some other postings with that error message but got stuck at a solution

looking for apps/qubit/config/propel.ini.tmpl.

Was there something else I need to install?

Thanks,

John

[David at Artefactual]

Hi John,

A config/propel.ini and config/config.php should be created by the installer after you submit the form with your database information (Note that neither should be in the apps/qubit/config directory).  If these files have not been created, I would check your directory/file permissions, to make sure your PHP user (www-data by default in Ubuntu) can create the files.  If the files *are* there you may be experiencing a caching problem.  Try clearing any caches by running the following commands:

• sudo -u www-data /usr/share/nginx/atom/symfony cc
• sudo service php5-fpm restart
• sudo service memcached restart

Hopefully that should do the trick.

Best regards,
David

[John La]

Thanks David,

I did find the propel file and did a copy propel.ini.tmpl to propel.ini

php symphony cc

 php symfony tools:purge cause message 'You must create a schema.yml or schema.xml file'.

I checked the /atom/config directory and it still contains a schema.yml

sudo service php5-fpm restart

sudo service memcached restart

Now if I try the install page again, I get 'settings.yml not writable'.

in log, still get No connection information in your runtime configuration file for datasource [propel]

Really confusing now.

[Dan Gillean]

Hi John, 

Did you double-check your filesystem permissions as David suggested? It sounds like there might still be an issue there. See:

• https://www.accesstomemory.org/docs/2.2/admin-manual/installation/linux/#filesystem-permissions

That's all I can think of off the top of my head; maybe one of our developers can provide more ideas... but we're also getting very close to when our staff starts leaving for the holidays! I myself will be out of office until the 4th after today, but trying to check email sporadically when possible.

Let me know if reapplying the filesystem permissions changes anything.

Cheers,

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056

@accesstomemory

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[John La]

Thanks Dan,

I re-ran the permission for the atom directory and it got me pass the settings.yml message.

However, the ' No connection information in your runtime configuration file for datasource [propel]' still exist along with the elasticsearch error.

Maybe you can tell me when that runtime configuration file is, so I can see if there really is no reference there.

Thanks for all your help Dan. Hope you have a good holiday.

[mi...@artefactual.com]

Hi John,

One thing you could try is deleting config/config.php which, if I recall correctly, will force you to re-enter your configuration info.

Cheers,

Mike

[John La]

Thanks Mike,

But I do that already, otherwise I cannot get the index.php to display properly.

John

[Dan Gillean]

I admit I don't myself know what the runtime configuration file refers to, John. I'd need some developer input. I do think that, now that you've fixed the permissions, you should run the web installer again and enter the proper configuration information, etc - that might help.

The other thing I noticed was that you mentioned you are using Apache. I wonder if there might be some difference here? For example, we provide a server configuration block we know works for Nginx, but just the suggestion of one for Apache, since we do not use Apache here in-house. (in fact, I think there is a typo i need to fix in the sample Apache virtual server - the path for the uploads directory references nginx, but it should be different for Apache - probably /var/www/atom/uploads - once I confirm that, I'll try to update it). See:

• https://www.accesstomemory.org/en/docs/2.2/admin-manual/installation/linux/#apache

We do mention some other dependencies and configuration suggestions there as well - maybe make sure they are installed? After that, I am out of ideas! I'll see what I can do about getting more information for you though.

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056

@accesstomemory

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[John La]

With more investigation, I found elasticsearch is not running.

When I ran sudo /etc/init.d/elasticsearch start, it say it is starting

But if I check the status, it say elasticsearch is not running.

There is no error on the screen nor in the log files.

I even change the permission by entering chown elasticsearch:elasticsearch elasticsearch in the /etc directory

and re-booting but still not running.

Any suggestions will be greatly appreciated.

John

[David Juhasz]

Hi John,

In my experience, when Elasticsearch is dying unexpectedly it's because it needs more memory.   How much RAM do you available on the server?

Best regards,

David

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[John La]

Hi David,

I have 1GB of ram on the server.

I will try and upgrade to 2GB tomorrow.

Thanks,

Johnny

[John La]

Hi David,

We upgraded the ram to 3GB.

Re-booted several times but still ElasticSsearch refuses to run.

John

...

[David Juhasz]

Hi John,

Hmm, 3GB should be plenty unless you have a *really* big index.   What version of Elasticsearch and Java are you running?   Elasticsearch 1.4 - 2.1 require Java 7+.

The top answer for this Stackoverflow question also has some suggestions on where to find information about Elasticsearch when it crashes:
http://stackoverflow.com/questions/15213764/elasticsearch-disappearing-crashing-cannot-find-log-files-or-any-other-info

I'm off for the holidays from Dec 24 - Jan 11, but somebody else at Artefactual should be able to pick up the thread next week if you are still having problems.

Happy Holidays, and best of luck!

David

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[John La]

Thanks David,

We have Elasticsearch 2.1.1 installed with Java 8.

This is a fresh install on Ubuntu 14.04.

I will look at the suggestions.

I will be off Christmas until Jan 4 too.

Happy holidays to you and your team.

thanks,

John

[Dan Gillean]

Hi John,

I will try to check in with our developers, but one option may be to try downgrading Elasticsearch - I think the newest version we have heard of working has been 1.7 or 1.8 - not sure if our developers have yet tested these versions either. It's possible that there is something in the 2.x version that is non-backwards compatible?

Cheers,

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056

@accesstomemory

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[John La]

Hi Dan,

Slightly better news today. I am able to get Elasticsearch to run.

I had to change elasticsearch.yml and set network.host: localhost.

However, I still get the same error messages as before even after re-booting.

[Tue Jan 05 11:06:27.030509 2016] [:error] [pid 14887] [client 142.219.72.73:56814]  [wrapped: SQLSTATE[42S02]: Base table or view not found: 1146 Table 'atom.object' doesn't exis
t]
[Tue Jan 05 11:09:23.486031 2016] [:error] [pid 14889] [client 142.219.72.73:56852] No connection information in your runtime configuration file for datasource [propel]

I re-check file permission and everything looks correct.

drwxr-xr-x 13 www-data www-data   4096 Dec 18 08:42 ./
drwxr-xr-x  4 root     root       4096 Dec 16 15:08 ../
drwxrwxr-x  3 www-data www-data   4096 Aug 27 11:06 apps/
drwxr-xr-x  5 www-data www-data   4096 Jan  5 11:09 cache/
drwxrwxr-x  3 www-data www-data   4096 Jan  5 11:09 config/
-rw-rw-r--  1 www-data www-data    485 Jul  8 11:20 CONTRIBUTING
-rw-rw-r--  1 www-data www-data   5198 Jul  8 11:20 COPYRIGHT
drwxrwxr-x  2 www-data www-data   4096 Aug 27 11:06 css/
drwxrwxr-x  9 www-data www-data   4096 Jan  5 11:09 data/
-rw-rw-r--  1 www-data www-data 182068 Jul  8 11:20 ead.dtd
-rw-rw-r--  1 www-data www-data   1150 Jul  8 11:20 favicon.ico
drwxrwxr-x  5 www-data www-data   4096 Aug 27 11:06 images/
-rw-rw-r--  1 www-data www-data    229 Jul  8 11:20 index.php
drwxrwxr-x  2 www-data www-data   4096 Aug 27 11:06 js/
drwxrwxr-x 16 www-data www-data   4096 Aug 27 11:06 lib/
-rw-rw-r--  1 www-data www-data  34519 Jul  8 11:20 LICENSE
drwxr-xr-x  2 www-data www-data   4096 Dec 17 14:31 log/
-rw-r--r--  1 www-data www-data     20 Dec 16 15:49 phpinfo.php
drwxrwxr-x 30 www-data www-data   4096 Aug 27 11:06 plugins/
-rw-rw-r--  1 www-data www-data    751 Jul  8 11:20 qubit_dev.php
-rw-rw-r--  1 www-data www-data    334 Jul  8 11:20 README
-rw-rw-r--  1 www-data www-data     26 Jul  8 11:20 robots.txt
lrwxrwxrwx  1 www-data www-data     40 Dec 18 08:42 sf -> /var/www/atom/vendor/symfony/data/web/sf/
-rwxrwxr-x  1 www-data www-data    445 Jul  8 11:20 symfony*
drwxrwxr-x 14 www-data www-data   4096 Aug 27 11:06 vendor/

www-data is the user of Apache.

[Dan Gillean]

Hi John,

Very strange - I'm glad you've gotten ES sorted though. Hopefully we can try the same solution as before?

I would suggest the following workarounds for you:

Try deleting the following file in your AtoM folder:

• config/config.php

You may then also want to drop, and then recreate, your database:

mysql -h localhost -u root -p -e "DROP DATABASE atom;"

mysql -h localhost -u root -p -e "CREATE DATABASE atom CHARACTER SET utf8 COLLATE utf8_unicode_ci;"

Using your database name (i've used atom as the DB name in the above examples).

Let us know if that resolves the issue!

I'm not sure why this problem came back for you, but I'm hoping that now that the ES issue is worked out, the same steps will help you solve the tables issue. Let me know!

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056

@accesstomemory

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[John La]

Hi Dan,

I tried that several times and still get 'Elasticsearch error' during the Search configuration step of the installation.

In apache's error.log still say

 No connection information in your runtime configuration file for datasource [propel]

[Dan Gillean]

Hi John,

Hmmm, I am stumped. Many of our AtoM developers are away this week, but I will see if anyone else has some further ideas next week when they've returned. Did you ever end up trying to downgrade ES to 1.8 or lower? 1.8 is the highest version we have heard reports of working. I also think it would be good if you could try manually going back to the web installer page... basically: [your AtoM address]/sfInstallPlugin should get you there - this way you can get to the stage where you re-enter your database credentials and ES ports, which will in turn recreate the config/config.php file.

I hope that helps! If not, I'll try to follow up with our developers next week!

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056

@accesstomemory

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[David Hume]

Hi John and Dan,

Sorry if this might be redundant, but after a quick read it *sounds* like if you've done Dan's "create database" steps you might very well have an AtoM database, but possibly empty? That is, if you go into MySQL as an authorized database user and do the following (again, assuming 'atom' as the database name, adjust accordingly)

mysql> use atom;

mysql> show tables;

IF the latter says "Empty set" (no tables) then hopefully changing to your AtoM directory and running the following will now work

% sudo -u www-data php symfony cc

% sudo -u www-data php symfony tools:purge

If we can get that far, can probably take it from there (e.g. can't remember off the top of my head, but I think there is a path with which we can skip right to the "make search index" part of the web installer, or otherwise move forward).

Cheers,

       David Hume, Artefactual Systems Administrator

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[John La]

Thank you David and Dan,

I tried what David suggested but got 'Database "propel" does not exist'.

I also tried typing in [atom address]/plugins/sfInstaffPlugin/ but got the directory listing only. Was there more to this?

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[Dan Gillean]

Hi John,

Hmmmmm... this suggests to me that there might be something amiss with your Apache configuration. This URL should have taken you back to the web installer. I'm not sure what to suggest since our developers use Nginx in testing, development, and production, and it is difficult to figure out what's going on without taking a look at your installation, something we can't offer via the User Forum.

I know we have a sample Apache virtual server configuration sample in our docs, but I can see one place in them already that refer to nginx, and therefore they probably need to be updated.

I wonder if anyone else on the list who is using Apache with AtoM might have suggestions for John?

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056

@accesstomemory

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[Dan Gillean]

Does it do anything different if you enter [AtoM address]/sfInstallPlugin/checkSystem   ?

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056

@accesstomemory

[John La]

Hi Dan,

It just returns Not Found

The requested URL /sfInstallPlugin/checksystem was not found on this server.

[John La]

Just found that if I include /index.php in front of it, then will take me to the stall page.

However, still failed with the Elasticsearch error.

[Dan Gillean]

Are you still running ES 2.1+ ? I am unfortunately running out of ideas, but you may want to try downgrading - we've never tested AtoM with a version of ES that high. I believe that we are using ES 1.4.2 in most of our AtoM 2.2 deployments.

Note that ES also requires that Java be installed - is it possible this is not the case on your system at the moment? Make sure that, in the web installer stage, you've properly configured the ES host, port, and index name - I don't know if some of the differences in your installation environment change these from our suggested defaults or not, however.

Not sure what else to suggest! I hope this works!

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056

@accesstomemory

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[John La]

Hi Dan,

Great news! You are right.

I took your advice and remove 2.1.1 and re-install 1.4.5.

Works and the installation is complete.

Thank you very much for all your help!

[Dan Gillean]

I'm glad to hear it! This also lets us know that we'll have to do further testing and updates before we can make AtoM work with more recent 2.x versions of Elasticsearch.

Glad you're out of the woods, John!

Cheers,

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056

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[venta...@gmail.com]

I did that, but does not work! I have the same problem.

[Dan Gillean]

Hi Rodrigo, 

Sorry, there is a lot of information from multiple different posters with different issues in this old thread. Can you please clarify for us exactly what steps you have taken, what problem you encountered, what you have tried to resolve it, and what your installation environment is like? Are you installing AtoM 2.4? More information will help us offer better suggestions. 

Thank you! 

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056

@accesstomemory

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[Rodrigo Souza]

Hi!

Problem: The web installer interface does not appear.

My environment

- Linux RedHat7

- 4 CPUs

- 15G RAM memory 

- MySQL server database located in other host.

- AtoM 2.3.1

Install Procedures

I follow the procedure contained at https://www.accesstomemory.org/en/docs/2.3/admin-manual/installation/linux/ubuntu-trusty/

Dependencies

MySQL - I instaled MySQL-Connector

Elasticsearch

Web Server - I installed Apache

Virtual host configuration

PHP - I installed PHP7

PHP-FPM

PHP-FMP.D atom.fpm

Download AtoM

Create database

I created a empty database

CREATE DATABASE IF NOT EXISTS #{new_resource.database_name} CHARACTER SET utf8 COLLATE utf8_unicode_ci;

Run the web installer

I dont acccess the web installer page:

The apache log says:

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[Dan Gillean]

Hi Rodrigo, 

Thank you so much for sharing so much detailed information. I will ask one of our developers to take a look and see if they can offer suggestions. 

We don't have as much experience working with RHEL or CentOS, and as you know we only maintain documentation for Ubuntu installs, as this is what use during development, testing, and production deployments. However, you might want to take a look through some of the previous threads available - I've tried to tag all posts related to RHEL and CentOS in the last year+ here: 

• https://groups.google.com/forum/#!tags/ica-atom-users/centOS
  

For example, another user has also shared some instructions on how they got AtoM working on RHEL 7.1, here: 

• https://groups.google.com/d/msg/ica-atom-users/lXfeWzAIETE/9-fTTArvAwAJ

We have not tested these instructions ourselves, but hopefully they will give you some ideas. There are 2 different guides in the thread, so you might want to read through - however, both install PHP 5.5 instead of PHP7, and I think the instructions still use Nginx instead of Elasticsearch.

I'll see if anything jumps out to our developers. 

Cheers,  

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056

@accesstomemory

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[Dan Gillean]

Hi again, 

I also just remembered this post from another RHEL user:

• https://groups.google.com/d/msg/ica-atom-users/7yorcAIznx8/tHrebEsvBQAJ
  

From the post:

Upgraded to PHP5.6 and it worked.
I tried going to PHP7.0 and it ran into requiring some stuff that hasn't been ported to PHP7 for RHEL6, so I stepped down to 5.6 instead. :)

I don't know if the related requirements have been ported to RHEL7, but if you continue to have issues, you might consider downgrading your PHP version for now?

Regards,  

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056

@accesstomemory

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[sbr...@artefactual.com]

Hi Rodrigo

Looking at the summary of the 2.3.1 installation there are a couple things I am noticing:

1) Your Elasticsearch version is older than expected at 1.5.  AtoM 2.3.1 will run with up to 1.7.x.  That said, I do not think this is the source of this issue - I would leave this for now.

2) The exact error is that Apache cannot find /var/www/basearch/atom-2.3.1/sfInstallPlugin.  My first guess is that this might indicate an Apache configuration problem - I would try some tests:

  --  Can you serve up a very basic 'hello world' html file with your SSL certificate configured as you have?

  --  Can you serve up a very basic 'hello world' php file with your SSL certificate configured as you have?

  --  Can you serve up AtoM using an Apache config script that doesn't use SSL?  If so then there might be an issue with the Apache config.

Hope this helps lead to some answers for you.

Steve

Steven Breker, BSc
AtoM Programmer
Artefactual Systems, Inc.
604-527-2056

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[Rodrigo Souza]

It doesent work. I saw the same sintom

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[Dan Gillean]

Hi Rodrigo, 

Sorry, can you be a bit more specific? What did you try exactly, and what was the result? Did you try the tests that Steve recommended?

  --  Can you serve up a very basic 'hello world' html file with your SSL certificate configured as you have?
  --  Can you serve up a very basic 'hello world' php file with your SSL certificate configured as you have?
  --  Can you serve up AtoM using an Apache config script that doesn't use SSL?  If so then there might be an issue with the Apache config.

Did any of these tests work? Did none of them?

Thanks! 

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056

@accesstomemory

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