text:
Restarting MYSQL failing : Fresh Install

Issue Type

Bug Report / Support Request

Your Environment
Vagrant 1.9.1
VirtualBox 5.1.14r112924
ansible 2.2.0.0
  config file =
  configured module search path = Default w/o overrides

Your OS

macOS (10.12.3)

Full console output
Command
$ blt vm:nuke && blt vm
RUNNING HANDLER [geerlingguy.mysql : restart mysql] ****************************
	to retry, use: --limit @/Users/justinwinter/Sites/wny/vendor/geerlingguy/drupal-vm/provisioning/playbook.retry

PLAY RECAP *********************************************************************
webny                      : ok=195  changed=92   unreachable=0    failed=1

Ansible failed to complete successfully. Any error output should be
visible above. Please fix these errors and try again.
[phingcall] /Users/justinwinter/Sites/wny/./vendor/acquia/blt/phing/tasks/vm.xml:127:129: Task exited with code 1

BUILD FAILED/Users/justinwinter/Sites/wny/./vendor/acquia/blt/phing/tasks/vm.xml:26:8: /Users/justinwinter/Sites/wny/./vendor/acquia/blt/phing/tasks/vm.xml:29:34: Execution of the target buildfile failed. Aborting.
; 22 minutes  7.38 seconds

Summary
Trying to get my VM up and running again after doing a vagrant reload --provision and I'm seeing the above error. I deleted my vendor folder and ran a composer update and I'm also on the latest stable BLT release.
...
"acquia/blt": "8.6.14",
 "geerlingguy/drupal-vm": "~4.2"
...

Any ideas why MYSQL might be failing here?

@justinlevi - Is there any other output above that mysql handler line? I'm guessing something else is actually failing prior to that handler; Ansible just shows that a handler isn't run at the end if something else fails before the playbook ends. That doesn't necessarily mean the handler failed.

Here's the full output
https://gist.github.com/justinlevi/f836a497e0941d6b79abdda3e4c64aea

@justinlevi - It looks like the failure is in the mailhog step:
TASK [geerlingguy.mailhog : Download MailHog and mhsendmail binaries.] *********
failed: [webny] (item={u'url': u'https://github.com/mailhog/MailHog/releases/download/v0.2.0/MailHog_linux_amd64', u'dest': u'/opt/mailhog/mailhog'}) => {"failed": true, "item": {"dest": "/opt/mailhog/mailhog", "url": "https://github.com/mailhog/MailHog/releases/download/v0.2.0/MailHog_linux_amd64"}, "msg": "failed to create temporary content file: The read operation timed out"}
changed: [webny] => (item={u'url': u'https://github.com/mailhog/mhsendmail/releases/download/v0.2.0/mhsendmail_linux_amd64', u'dest': u'/opt/mailhog/mhsendmail'})

I've been having some github connectivity issues here and there today... maybe it's just a temporary fluke? If you want the build to succeed, you can bypass mailhog by removing it from installed_extras temporarily, and overriding the php_sendmail_path.

@geerlingguy I'm not seeing the mailhog failure in my gist:
TASK [geerlingguy.mailhog : Ensure mailhog install directory exists.] **********
changed: [webny]

TASK [geerlingguy.mailhog : Download MailHog and mhsendmail binaries.] *********
changed: [webny] => (item={u'url': u'https://github.com/mailhog/MailHog/releases/download/v0.2.0/MailHog_linux_amd64', u'dest': u'/opt/mailhog/mailhog'})
changed: [webny] => (item={u'url': u'https://github.com/mailhog/mhsendmail/releases/download/v0.2.0/mhsendmail_linux_amd64', u'dest': u'/opt/mailhog/mhsendmail'})

TASK [geerlingguy.mailhog : Copy mailhog init script into place.] **************
changed: [webny]

TASK [geerlingguy.mailhog : Copy mailhog systemd unit file into place (for systemd systems).] ***
skipping: [webny]

TASK [geerlingguy.mailhog : Ensure mailhog is enabled and will start on boot.] *
changed: [webny]

Today I'm actually seeing another issue??
vagrant reload --provision
==> webny: [vagrant-hostsupdater] Removing hosts
Password:
==> webny: Attempting graceful shutdown of VM...
==> webny: Checking if box 'geerlingguy/ubuntu1404' is up to date...
==> webny: Clearing any previously set forwarded ports...
==> webny: Clearing any previously set network interfaces...
==> webny: Preparing network interfaces based on configuration...
    webny: Adapter 1: nat
    webny: Adapter 2: hostonly
==> webny: Forwarding ports...
    webny: 22 (guest) => 2222 (host) (adapter 1)
==> webny: Running 'pre-boot' VM customizations...
==> webny: Booting VM...
==> webny: Waiting for machine to boot. This may take a few minutes...
    webny: SSH address: 127.0.0.1:2222
    webny: SSH username: vagrant
    webny: SSH auth method: private key
==> webny: Machine booted and ready!
[webny] GuestAdditions 5.1.14 running --- OK.
==> webny: Checking for guest additions in VM...
==> webny: [vagrant-hostsupdater] Checking for host entries
==> webny: [vagrant-hostsupdater] Writing the following entries to (/etc/hosts)
==> webny: [vagrant-hostsupdater]   192.168.88.88  webny.dev  # VAGRANT: 12f45ea8233192517336ff6e8539e7c6 (webny) / d55b1cbe-ec1c-4112-b951-8e998d6cec26
==> webny: [vagrant-hostsupdater]   192.168.88.88  www.webny.dev  # VAGRANT: 12f45ea8233192517336ff6e8539e7c6 (webny) / d55b1cbe-ec1c-4112-b951-8e998d6cec26
==> webny: [vagrant-hostsupdater]   192.168.88.88  adminer.webny.dev  # VAGRANT: 12f45ea8233192517336ff6e8539e7c6 (webny) / d55b1cbe-ec1c-4112-b951-8e998d6cec26
==> webny: [vagrant-hostsupdater]   192.168.88.88  xhprof.webny.dev  # VAGRANT: 12f45ea8233192517336ff6e8539e7c6 (webny) / d55b1cbe-ec1c-4112-b951-8e998d6cec26
==> webny: [vagrant-hostsupdater]   192.168.88.88  pimpmylog.webny.dev  # VAGRANT: 12f45ea8233192517336ff6e8539e7c6 (webny) / d55b1cbe-ec1c-4112-b951-8e998d6cec26
==> webny: [vagrant-hostsupdater]   192.168.88.88  dashboard.webny.dev  # VAGRANT: 12f45ea8233192517336ff6e8539e7c6 (webny) / d55b1cbe-ec1c-4112-b951-8e998d6cec26
==> webny: [vagrant-hostsupdater] This operation requires administrative access. You may skip it by manually adding equivalent entries to the hosts file.
==> webny: Setting hostname...
==> webny: Configuring and enabling network interfaces...
==> webny: Exporting NFS shared folders...
==> webny: Preparing to edit /etc/exports. Administrator privileges will be required...
==> webny: Mounting NFS shared folders...
==> webny: Configuring cache buckets...
==> webny: Running provisioner: ansible...
    webny: Running ansible-playbook...

PLAY [all] *********************************************************************

TASK [setup] *******************************************************************
ok: [webny]

TASK [Include OS-specific variables.] ******************************************
ok: [webny]

TASK [Define config_dir.] ******************************************************
skipping: [webny]

TASK [include_vars] ************************************************************
ok: [webny] => (item=/Users/justinwinter/Sites/wny/box/config.yml)

TASK [Define fully qualified domain name.] *************************************
ok: [webny]

TASK [Define short hostname.] **************************************************
ok: [webny]

TASK [Add hostname to /etc/hosts.] *********************************************
ok: [webny]

TASK [Configure hostname.] *****************************************************
ok: [webny]

TASK [Set the hostname for current session.] ***********************************
skipping: [webny]

TASK [include] *****************************************************************
included: /Users/justinwinter/Sites/wny/vendor/geerlingguy/drupal-vm/provisioning/tasks/init-debian.yml for webny

TASK [Update apt cache if needed.] *********************************************
ok: [webny]

TASK [Install required dependencies.] ******************************************
ok: [webny] => (item=[u'curl', u'python-apt', u'python-pycurl', u'sudo', u'unzip', u'make'])

TASK [Configure /etc/mailname.] ************************************************
ok: [webny]

TASK [Add repository for Apache 2.4.9+ on Ubuntu 12 and 14.] *******************
ok: [webny]

TASK [Add repository for PHP 5.5, 5.6, 7.0 or 7.1.] ****************************
ok: [webny]

TASK [Add repository for PHP 5 compatibility packages.] ************************
ok: [webny]

TASK [Purge PHP version packages.] *********************************************
ok: [webny] => (item=[u'php5.5', u'php5.5-apcu', u'php5.5-cli', u'php5.5-common', u'php5.5-curl', u'php5.5-dev', u'php5.5-fpm', u'php5.5-gd', u'php5.5-imap', u'php5.5-json', u'php5.5-mbstring', u'php5.5-mcrypt', u'php5.5-opcache', u'php5.5-sqlite3', u'php5.5-xml', u'php5.5-yaml', u'php7.0', u'php7.0-apcu', u'php7.0-cli', u'php7.0-common', u'php7.0-curl', u'php7.0-dev', u'php7.0-fpm', u'php7.0-gd', u'php7.0-imap', u'php7.0-json', u'php7.0-mbstring', u'php7.0-mcrypt', u'php7.0-opcache', u'php7.0-sqlite3', u'php7.0-xml', u'php7.0-yaml', u'php7.1', u'php7.1-apcu', u'php7.1-cli', u'php7.1-common', u'php7.1-curl', u'php7.1-dev', u'php7.1-fpm', u'php7.1-gd', u'php7.1-imap', u'php7.1-json', u'php7.1-mbstring', u'php7.1-mcrypt', u'php7.1-opcache', u'php7.1-sqlite3', u'php7.1-xml', u'php7.1-yaml'])

TASK [Purge PHP packages installed by default on Ubuntu.] **********************
skipping: [webny] => (item=[])

TASK [Purge PHP modules directory.] ********************************************
skipping: [webny] => (item=/usr/lib/php5/modules)
skipping: [webny] => (item=/usr/lib/php/modules)

TASK [Define php_xhprof_html_dir.] *********************************************
skipping: [webny]

TASK [include] *****************************************************************
skipping: [webny]

TASK [Run configured pre-provision shell scripts.] *****************************

TASK [Run configured pre-provision ansible task files.] ************************

TASK [Set the PHP webserver daemon correctly when nginx is in use.] ************
skipping: [webny]

TASK [Set the correct XHProf package when PHP 5.5 or 5.6 is used.] *************
ok: [webny]

TASK [Ensure PHP version -specific workspace directory exists.] ****************
ok: [webny]

TASK [geerlingguy.repo-remi : Install remi repo.] ******************************
skipping: [webny]

TASK [geerlingguy.repo-remi : Import remi GPG key.] ****************************
skipping: [webny]

TASK [geerlingguy.firewall : Ensure iptables is installed.] ********************
ok: [webny]

TASK [geerlingguy.firewall : Flush iptables the first time playbook runs.] *****
ok: [webny]

TASK [geerlingguy.firewall : Copy firewall script into place.] *****************
ok: [webny]

TASK [geerlingguy.firewall : Copy firewall init script into place.] ************
ok: [webny]

TASK [geerlingguy.firewall : Copy firewall systemd unit file into place (for systemd systems).] ***
skipping: [webny]

TASK [geerlingguy.firewall : Ensure the firewall is enabled and will start on boot.] ***
ok: [webny]

TASK [geerlingguy.firewall : Check firewalld package is installed (on RHEL).] **
skipping: [webny]

TASK [geerlingguy.firewall : Disable the firewalld service (on RHEL, if configured).] ***
skipping: [webny]

TASK [geerlingguy.firewall : Check ufw package is installed (on Ubuntu).] ******
changed: [webny]

TASK [geerlingguy.firewall : Disable the ufw firewall (on Ubuntu, if configured).] ***
ok: [webny]

TASK [geerlingguy.git : Ensure git is installed (RedHat).] *********************
skipping: [webny] => (item=[])

TASK [geerlingguy.git : Update apt cache (Debian).] ****************************
ok: [webny]

TASK [geerlingguy.git : Ensure git is installed (Debian).] *********************
ok: [webny] => (item=[u'git', u'git-svn'])

TASK [geerlingguy.git : Ensure git's dependencies are installed (RedHat).] *****
skipping: [webny] => (item=[])

TASK [geerlingguy.git : Ensure git's dependencies are installed (Debian).] *****
skipping: [webny] => (item=[])

TASK [geerlingguy.git : Get installed version] *********************************
[DEPRECATION WARNING]: always_run is deprecated. Use check_mode = no instead..

This feature will be removed in version 2.4. Deprecation warnings can be
disabled by setting deprecation_warnings=False in ansible.cfg.
skipping: [webny]

TASK [geerlingguy.git : Force git install if the version numbers do not match] *
skipping: [webny]

TASK [geerlingguy.git : Download git.] *****************************************
skipping: [webny]

TASK [geerlingguy.git : Expand git archive.] ***********************************
skipping: [webny]

TASK [geerlingguy.git : Build git.] ********************************************
skipping: [webny] => (item=all)
skipping: [webny] => (item=install)

TASK [geerlingguy.postfix : Ensure postfix is installed (RedHat).] *************
skipping: [webny]

TASK [geerlingguy.postfix : Ensure postfix is installed (Debian).] *************
ok: [webny]

TASK [geerlingguy.postfix : Ensure postfix is started and enabled at boot.] ****
ok: [webny]

TASK [geerlingguy.apache : Include OS-specific variables.] *********************
ok: [webny]

TASK [geerlingguy.apache : Define apache_packages.] ****************************
ok: [webny]

TASK [geerlingguy.apache : include] ********************************************
included: /Users/justinwinter/Sites/wny/vendor/geerlingguy/drupal-vm/provisioning/roles/geerlingguy.apache/tasks/setup-Debian.yml for webny

TASK [geerlingguy.apache : Update apt cache.] **********************************
ok: [webny]

TASK [geerlingguy.apache : Ensure Apache is installed on Debian.] **************
ok: [webny] => (item=[u'apache2', u'apache2-utils'])

TASK [geerlingguy.apache : Get installed version of Apache.] *******************
[DEPRECATION WARNING]: always_run is deprecated. Use check_mode = no instead..

This feature will be removed in version 2.4. Deprecation warnings can be
disabled by setting deprecation_warnings=False in ansible.cfg.
ok: [webny]

TASK [geerlingguy.apache : Create apache_version variable.] ********************
ok: [webny]

TASK [geerlingguy.apache : include_vars] ***************************************
skipping: [webny]

TASK [geerlingguy.apache : include_vars] ***************************************
ok: [webny]

TASK [geerlingguy.apache : include] ********************************************
included: /Users/justinwinter/Sites/wny/vendor/geerlingguy/drupal-vm/provisioning/roles/geerlingguy.apache/tasks/configure-Debian.yml for webny

TASK [geerlingguy.apache : Configure Apache.] **********************************
ok: [webny] => (item={u'regexp': u'^Listen ', u'line': u'Listen 80'})

TASK [geerlingguy.apache : Enable Apache mods.] ********************************
ok: [webny] => (item=expires.load)
ok: [webny] => (item=ssl.load)
ok: [webny] => (item=rewrite.load)
ok: [webny] => (item=proxy.load)
ok: [webny] => (item=proxy_fcgi.load)

TASK [geerlingguy.apache : Disable Apache mods.] *******************************

TASK [geerlingguy.apache : Check whether certificates defined in vhosts exist.]

TASK [geerlingguy.apache : Add apache vhosts configuration.] *******************
ok: [webny]

TASK [geerlingguy.apache : Add vhost symlink in sites-enabled.] ****************
ok: [webny]

TASK [geerlingguy.apache : Remove default vhost in sites-enabled.] *************
ok: [webny]

TASK [geerlingguy.apache : Ensure Apache has selected state and enabled on boot.] ***
ok: [webny]

TASK [geerlingguy.apache : Include OS-specific variables.] *********************
ok: [webny]

TASK [geerlingguy.apache : Define apache_packages.] ****************************
skipping: [webny]

TASK [geerlingguy.apache : include] ********************************************
included: /Users/justinwinter/Sites/wny/vendor/geerlingguy/drupal-vm/provisioning/roles/geerlingguy.apache/tasks/setup-Debian.yml for webny

TASK [geerlingguy.apache : Update apt cache.] **********************************
ok: [webny]

TASK [geerlingguy.apache : Ensure Apache is installed on Debian.] **************
ok: [webny] => (item=[u'apache2', u'apache2-utils'])

TASK [geerlingguy.apache : Get installed version of Apache.] *******************
[DEPRECATION WARNING]: always_run is deprecated. Use check_mode = no instead..

This feature will be removed in version 2.4. Deprecation warnings can be
disabled by setting deprecation_warnings=False in ansible.cfg.
ok: [webny]

TASK [geerlingguy.apache : Create apache_version variable.] ********************
ok: [webny]

TASK [geerlingguy.apache : include_vars] ***************************************
skipping: [webny]

TASK [geerlingguy.apache : include_vars] ***************************************
ok: [webny]

TASK [geerlingguy.apache : include] ********************************************
included: /Users/justinwinter/Sites/wny/vendor/geerlingguy/drupal-vm/provisioning/roles/geerlingguy.apache/tasks/configure-Debian.yml for webny

TASK [geerlingguy.apache : Configure Apache.] **********************************
ok: [webny] => (item={u'regexp': u'^Listen ', u'line': u'Listen 80'})

TASK [geerlingguy.apache : Enable Apache mods.] ********************************
ok: [webny] => (item=expires.load)
ok: [webny] => (item=ssl.load)
ok: [webny] => (item=rewrite.load)
ok: [webny] => (item=proxy.load)
ok: [webny] => (item=proxy_fcgi.load)

TASK [geerlingguy.apache : Disable Apache mods.] *******************************

TASK [geerlingguy.apache : Check whether certificates defined in vhosts exist.]

TASK [geerlingguy.apache : Add apache vhosts configuration.] *******************
ok: [webny]

TASK [geerlingguy.apache : Add vhost symlink in sites-enabled.] ****************
ok: [webny]

TASK [geerlingguy.apache : Remove default vhost in sites-enabled.] *************
ok: [webny]

TASK [geerlingguy.apache : Ensure Apache has selected state and enabled on boot.] ***
ok: [webny]

TASK [geerlingguy.apache-php-fpm : Enable mod_proxy_fcgi.] *********************
ok: [webny] => (item=proxy.load)
ok: [webny] => (item=proxy_fcgi.load)

TASK [geerlingguy.nginx : Include OS-specific variables.] **********************
skipping: [webny]

TASK [geerlingguy.nginx : Define nginx_user.] **********************************
skipping: [webny]

TASK [geerlingguy.nginx : Enable nginx repo.] **********************************
skipping: [webny]

TASK [geerlingguy.nginx : Ensure nginx is installed.] **************************
skipping: [webny]

TASK [geerlingguy.nginx : Add PPA for Nginx.] **********************************
skipping: [webny]

TASK [geerlingguy.nginx : Ensure nginx will reinstall if the PPA was just added.] ***
skipping: [webny]

TASK [geerlingguy.nginx : Update apt cache.] ***********************************
skipping: [webny]

TASK [geerlingguy.nginx : Ensure nginx is installed.] **************************
skipping: [webny]

TASK [geerlingguy.nginx : Update pkg cache.] ***********************************
skipping: [webny]

TASK [geerlingguy.nginx : Ensure nginx is installed.] **************************
skipping: [webny]

TASK [geerlingguy.nginx : Create logs directory.] ******************************
skipping: [webny]

TASK [geerlingguy.nginx : Remove default nginx vhost config file (if configured).] ***
skipping: [webny]

TASK [geerlingguy.nginx : Ensure nginx_vhost_path exists.] *********************
skipping: [webny]

TASK [geerlingguy.nginx : Add managed vhost config file (if any vhosts are configured).] ***
skipping: [webny]

TASK [geerlingguy.nginx : Remove managed vhost config file (if no vhosts are configured).] ***
skipping: [webny]

TASK [geerlingguy.nginx : Copy nginx configuration in place.] ******************
skipping: [webny]

TASK [geerlingguy.nginx : Ensure nginx is started and enabled to start at boot.] ***
skipping: [webny]

TASK [geerlingguy.php : Include OS-specific variables.] ************************
ok: [webny]

TASK [geerlingguy.php : Define php_packages.] **********************************
skipping: [webny]

TASK [geerlingguy.php : Define extra php_packages.] ****************************
ok: [webny]

TASK [geerlingguy.php : Define php_webserver_daemon.] **************************
ok: [webny]

TASK [geerlingguy.php : Define php_conf_paths.] ********************************
skipping: [webny]

TASK [geerlingguy.php : Define php_extension_conf_paths.] **********************
skipping: [webny]

TASK [geerlingguy.php : Define php_apc_conf_filename.] *************************
ok: [webny]

TASK [geerlingguy.php : Define php_opcache_conf_filename (Ubuntu 16.04).] ******
skipping: [webny]

TASK [geerlingguy.php : Define php_opcache_conf_filename.] *********************
ok: [webny]

TASK [geerlingguy.php : Define php_fpm_conf_path.] *****************************
skipping: [webny]

TASK [geerlingguy.php : include] ***********************************************
skipping: [webny]

TASK [geerlingguy.php : include] ***********************************************
included: /Users/justinwinter/Sites/wny/vendor/geerlingguy/drupal-vm/provisioning/roles/geerlingguy.php/tasks/setup-Debian.yml for webny

TASK [geerlingguy.php : Update apt cache.] *************************************
ok: [webny]

TASK [geerlingguy.php : Ensure PHP packages are installed.] ********************
ok: [webny] => (item=[u'php5.6', u'php5.6-apcu', u'php5.6-cli', u'php5.6-common', u'php5.6-curl', u'php5.6-dev', u'php5.6-fpm', u'php5.6-gd', u'php5.6-imap', u'php5.6-json', u'php5.6-mbstring', u'php5.6-mcrypt', u'php5.6-opcache', u'php5.6-sqlite3', u'php5.6-xml', u'php5.6-yaml', u'php5.6-bz2'])

TASK [geerlingguy.php : Delete APCu configuration file if this role will provide one.] ***
skipping: [webny] => (item=/etc/php/5.6/fpm/conf.d)
skipping: [webny] => (item=/etc/php/5.6/apache2/conf.d)
skipping: [webny] => (item=/etc/php/5.6/cli/conf.d)

TASK [geerlingguy.php : Delete OpCache configuration file if this role will provide one.] ***
skipping: [webny] => (item=/etc/php/5.6/fpm/conf.d)
skipping: [webny] => (item=/etc/php/5.6/apache2/conf.d)
skipping: [webny] => (item=/etc/php/5.6/cli/conf.d)

TASK [geerlingguy.php : include] ***********************************************
skipping: [webny]

TASK [geerlingguy.php : include] ***********************************************
included: /Users/justinwinter/Sites/wny/vendor/geerlingguy/drupal-vm/provisioning/roles/geerlingguy.php/tasks/configure.yml for webny

TASK [geerlingguy.php : Ensure configuration directories exist.] ***************
ok: [webny] => (item=/etc/php/5.6/fpm)
ok: [webny] => (item=/etc/php/5.6/apache2)
ok: [webny] => (item=/etc/php/5.6/cli)
ok: [webny] => (item=/etc/php/5.6/fpm/conf.d)
ok: [webny] => (item=/etc/php/5.6/apache2/conf.d)
ok: [webny] => (item=/etc/php/5.6/cli/conf.d)

TASK [geerlingguy.php : Place PHP configuration file in place.] ****************
ok: [webny] => (item=/etc/php/5.6/fpm)
ok: [webny] => (item=/etc/php/5.6/apache2)
ok: [webny] => (item=/etc/php/5.6/cli)

TASK [geerlingguy.php : include] ***********************************************
included: /Users/justinwinter/Sites/wny/vendor/geerlingguy/drupal-vm/provisioning/roles/geerlingguy.php/tasks/configure-apcu.yml for webny

TASK [geerlingguy.php : Check for existing APCu config files.] *****************
ok: [webny] => (item=/etc/php/5.6/fpm/conf.d)
ok: [webny] => (item=/etc/php/5.6/apache2/conf.d)
ok: [webny] => (item=/etc/php/5.6/cli/conf.d)

TASK [geerlingguy.php : Remove any non-role-supplied APCu config files.] *******
skipping: [webny] => (item=({'_ansible_parsed': True, u'changed': False, '_ansible_no_log': False, '_ansible_item_result': True, 'item': u'/etc/php/5.6/fpm/conf.d', u'examined': 41, 'invocation': {'module_name': u'find', u'module_args': {u'paths': [u'/etc/php/5.6/fpm/conf.d'], u'file_type': u'file', u'age': None, u'contains': u'extension(\\s+)?=(\\s+)?apc[u]?\\.so', u'recurse': False, u'age_stamp': u'mtime', u'patterns': [u'*'], u'get_checksum': False, u'use_regex': False, u'follow': False, u'hidden': False, u'size': None}}, u'matched': 1, u'msg': u''}, {u'uid': 0, u'woth': False, u'mtime': 1489500768.242277, u'inode': 3934559, u'isgid': False, u'size': 66, u'isuid': False, u'isreg': True, u'gid': 0, u'ischr': False, u'wusr': True, u'xoth': False, u'islnk': False, u'nlink': 1, u'issock': False, u'rgrp': True, u'path': u'/etc/php/5.6/fpm/conf.d/20-apcu.ini', u'xusr': False, u'atime': 1489588357.212095, u'isdir': False, u'ctime': 1489500768.410277, u'isblk': False, u'wgrp': False, u'xgrp': False, u'dev': 64512, u'roth': True, u'isfifo': False, u'mode': u'0644', u'rusr': True}))
skipping: [webny] => (item=({'_ansible_parsed': True, u'changed': False, '_ansible_no_log': False, '_ansible_item_result': True, 'item': u'/etc/php/5.6/apache2/conf.d', u'examined': 3, 'invocation': {'module_name': u'find', u'module_args': {u'paths': [u'/etc/php/5.6/apache2/conf.d'], u'file_type': u'file', u'age': None, u'contains': u'extension(\\s+)?=(\\s+)?apc[u]?\\.so', u'recurse': False, u'age_stamp': u'mtime', u'patterns': [u'*'], u'get_checksum': False, u'use_regex': False, u'follow': False, u'hidden': False, u'size': None}}, u'matched': 1, u'msg': u''}, {u'uid': 0, u'woth': False, u'mtime': 1489500768.686277, u'inode': 3934560, u'isgid': False, u'size': 66, u'isuid': False, u'isreg': True, u'gid': 0, u'ischr': False, u'wusr': True, u'xoth': False, u'islnk': False, u'nlink': 1, u'issock': False, u'rgrp': True, u'path': u'/etc/php/5.6/apache2/conf.d/20-apcu.ini', u'xusr': False, u'atime': 1489588406.988656, u'isdir': False, u'ctime': 1489500768.850277, u'isblk': False, u'wgrp': False, u'xgrp': False, u'dev': 64512, u'roth': True, u'isfifo': False, u'mode': u'0644', u'rusr': True}))
skipping: [webny] => (item=({'_ansible_parsed': True, u'changed': False, '_ansible_no_log': False, '_ansible_item_result': True, 'item': u'/etc/php/5.6/cli/conf.d', u'examined': 41, 'invocation': {'module_name': u'find', u'module_args': {u'paths': [u'/etc/php/5.6/cli/conf.d'], u'file_type': u'file', u'age': None, u'contains': u'extension(\\s+)?=(\\s+)?apc[u]?\\.so', u'recurse': False, u'age_stamp': u'mtime', u'patterns': [u'*'], u'get_checksum': False, u'use_regex': False, u'follow': False, u'hidden': False, u'size': None}}, u'matched': 1, u'msg': u''}, {u'uid': 0, u'woth': False, u'mtime': 1489500769.114277, u'inode': 3934561, u'isgid': False, u'size': 66, u'isuid': False, u'isreg': True, u'gid': 0, u'ischr': False, u'wusr': True, u'xoth': False, u'islnk': False, u'nlink': 1, u'issock': False, u'rgrp': True, u'path': u'/etc/php/5.6/cli/conf.d/20-apcu.ini', u'xusr': False, u'atime': 1489588407.164656, u'isdir': False, u'ctime': 1489500769.310277, u'isblk': False, u'wgrp': False, u'xgrp': False, u'dev': 64512, u'roth': True, u'isfifo': False, u'mode': u'0644', u'rusr': True}))

TASK [geerlingguy.php : Ensure APCu config file is present.] *******************
ok: [webny] => (item=/etc/php/5.6/fpm/conf.d)
ok: [webny] => (item=/etc/php/5.6/apache2/conf.d)
ok: [webny] => (item=/etc/php/5.6/cli/conf.d)

TASK [geerlingguy.php : Remove APCu config file if APC is disabled.] ***********
skipping: [webny] => (item=/etc/php/5.6/fpm/conf.d)
skipping: [webny] => (item=/etc/php/5.6/apache2/conf.d)
skipping: [webny] => (item=/etc/php/5.6/cli/conf.d)

TASK [geerlingguy.php : include] ***********************************************
included: /Users/justinwinter/Sites/wny/vendor/geerlingguy/drupal-vm/provisioning/roles/geerlingguy.php/tasks/configure-opcache.yml for webny

TASK [geerlingguy.php : Check for existing OpCache config files.] **************
ok: [webny] => (item=/etc/php/5.6/fpm/conf.d)
ok: [webny] => (item=/etc/php/5.6/apache2/conf.d)
ok: [webny] => (item=/etc/php/5.6/cli/conf.d)

TASK [geerlingguy.php : Remove any non-role-supplied OpCache config files.] ****
skipping: [webny] => (item=({'_ansible_parsed': True, u'changed': False, '_ansible_no_log': False, '_ansible_item_result': True, 'item': u'/etc/php/5.6/fpm/conf.d', u'examined': 41, 'invocation': {'module_name': u'find', u'module_args': {u'paths': [u'/etc/php/5.6/fpm/conf.d'], u'file_type': u'file', u'age': None, u'contains': u'zend_extension(\\s+)?=(\\s+)?opcache\\.so', u'recurse': False, u'age_stamp': u'mtime', u'patterns': [u'*'], u'get_checksum': False, u'use_regex': False, u'follow': False, u'hidden': False, u'size': None}}, u'matched': 1, u'msg': u''}, {u'uid': 0, u'woth': False, u'mtime': 1489500771.538277, u'inode': 3934562, u'isgid': False, u'size': 303, u'isuid': False, u'isreg': True, u'gid': 0, u'ischr': False, u'wusr': True, u'xoth': False, u'islnk': False, u'nlink': 1, u'issock': False, u'rgrp': True, u'path': u'/etc/php/5.6/fpm/conf.d/05-opcache.ini', u'xusr': False, u'atime': 1489588357.192095, u'isdir': False, u'ctime': 1489500771.710277, u'isblk': False, u'wgrp': False, u'xgrp': False, u'dev': 64512, u'roth': True, u'isfifo': False, u'mode': u'0644', u'rusr': True}))
skipping: [webny] => (item=({'_ansible_parsed': True, u'changed': False, '_ansible_no_log': False, '_ansible_item_result': True, 'item': u'/etc/php/5.6/apache2/conf.d', u'examined': 3, 'invocation': {'module_name': u'find', u'module_args': {u'paths': [u'/etc/php/5.6/apache2/conf.d'], u'file_type': u'file', u'age': None, u'contains': u'zend_extension(\\s+)?=(\\s+)?opcache\\.so', u'recurse': False, u'age_stamp': u'mtime', u'patterns': [u'*'], u'get_checksum': False, u'use_regex': False, u'follow': False, u'hidden': False, u'size': None}}, u'matched': 1, u'msg': u''}, {u'uid': 0, u'woth': False, u'mtime': 1489500771.962277, u'inode': 3934563, u'isgid': False, u'size': 303, u'isuid': False, u'isreg': True, u'gid': 0, u'ischr': False, u'wusr': True, u'xoth': False, u'islnk': False, u'nlink': 1, u'issock': False, u'rgrp': True, u'path': u'/etc/php/5.6/apache2/conf.d/05-opcache.ini', u'xusr': False, u'atime': 1489588741.726332, u'isdir': False, u'ctime': 1489500772.130277, u'isblk': False, u'wgrp': False, u'xgrp': False, u'dev': 64512, u'roth': True, u'isfifo': False, u'mode': u'0644', u'rusr': True}))
skipping: [webny] => (item=({'_ansible_parsed': True, u'changed': False, '_ansible_no_log': False, '_ansible_item_result': True, 'item': u'/etc/php/5.6/cli/conf.d', u'examined': 41, 'invocation': {'module_name': u'find', u'module_args': {u'paths': [u'/etc/php/5.6/cli/conf.d'], u'file_type': u'file', u'age': None, u'contains': u'zend_extension(\\s+)?=(\\s+)?opcache\\.so', u'recurse': False, u'age_stamp': u'mtime', u'patterns': [u'*'], u'get_checksum': False, u'use_regex': False, u'follow': False, u'hidden': False, u'size': None}}, u'matched': 1, u'msg': u''}, {u'uid': 0, u'woth': False, u'mtime': 1489500772.378277, u'inode': 3934564, u'isgid': False, u'size': 303, u'isuid': False, u'isreg': True, u'gid': 0, u'ischr': False, u'wusr': True, u'xoth': False, u'islnk': False, u'nlink': 1, u'issock': False, u'rgrp': True, u'path': u'/etc/php/5.6/cli/conf.d/05-opcache.ini', u'xusr': False, u'atime': 1489588407.164656, u'isdir': False, u'ctime': 1489500772.538277, u'isblk': False, u'wgrp': False, u'xgrp': False, u'dev': 64512, u'roth': True, u'isfifo': False, u'mode': u'0644', u'rusr': True}))

TASK [geerlingguy.php : Ensure OpCache config file is present.] ****************
ok: [webny] => (item=/etc/php/5.6/fpm/conf.d)
ok: [webny] => (item=/etc/php/5.6/apache2/conf.d)
ok: [webny] => (item=/etc/php/5.6/cli/conf.d)

TASK [geerlingguy.php : Remove OpCache config file if OpCache is disabled.] ****
skipping: [webny] => (item=/etc/php/5.6/cli/conf.d)
skipping: [webny] => (item=/etc/php/5.6/apache2/conf.d)
skipping: [webny] => (item=/etc/php/5.6/fpm/conf.d)

TASK [geerlingguy.php : include] ***********************************************
included: /Users/justinwinter/Sites/wny/vendor/geerlingguy/drupal-vm/provisioning/roles/geerlingguy.php/tasks/configure-fpm.yml for webny

TASK [geerlingguy.php : Define php_fpm_daemon.] ********************************
skipping: [webny]

TASK [geerlingguy.php : Define php_fpm_pool_conf_path.] ************************
skipping: [webny]

TASK [geerlingguy.php : Define php_fpm_pool_user.] *****************************
ok: [webny]

TASK [geerlingguy.php : Define php_fpm_pool_group.] ****************************
ok: [webny]

TASK [geerlingguy.php : Stat php_fpm_pool_conf_path] ***************************
ok: [webny]

TASK [geerlingguy.php : Ensure the default pool directory exists.] *************
skipping: [webny]

TASK [geerlingguy.php : Ensure the default pool exists.] ***********************
ok: [webny]

TASK [geerlingguy.php : Configure php-fpm pool (if enabled).] ******************
ok: [webny] => (item={u'regexp': u'^user.?=.+$', u'line': u'user = www-data'})
ok: [webny] => (item={u'regexp': u'^group.?=.+$', u'line': u'group = www-data'})
ok: [webny] => (item={u'regexp': u'^listen.?=.+$', u'line': u'listen = 127.0.0.1:9000'})
ok: [webny] => (item={u'regexp': u'^listen\\.allowed_clients.?=.+$', u'line': u'listen.allowed_clients = 127.0.0.1'})
ok: [webny] => (item={u'regexp': u'^pm\\.max_children.?=.+$', u'line': u'pm.max_children = 50'})
ok: [webny] => (item={u'regexp': u'^pm\\.start_servers.?=.+$', u'line': u'pm.start_servers = 5'})
ok: [webny] => (item={u'regexp': u'^pm\\.min_spare_servers.?=.+$', u'line': u'pm.min_spare_servers = 5'})
ok: [webny] => (item={u'regexp': u'^pm\\.max_spare_servers.?=.+$', u'line': u'pm.max_spare_servers = 5'})

TASK [geerlingguy.php : Ensure php-fpm is started and enabled at boot (if configured).] ***
ok: [webny]

TASK [geerlingguy.php : Include OS-specific variables.] ************************
ok: [webny]

TASK [geerlingguy.php : Define php_packages.] **********************************
skipping: [webny]

TASK [geerlingguy.php : Define extra php_packages.] ****************************
ok: [webny]

TASK [geerlingguy.php : Define php_webserver_daemon.] **************************
skipping: [webny]

TASK [geerlingguy.php : Define php_conf_paths.] ********************************
skipping: [webny]

TASK [geerlingguy.php : Define php_extension_conf_paths.] **********************
skipping: [webny]

TASK [geerlingguy.php : Define php_apc_conf_filename.] *************************
skipping: [webny]

TASK [geerlingguy.php : Define php_opcache_conf_filename (Ubuntu 16.04).] ******
skipping: [webny]

TASK [geerlingguy.php : Define php_opcache_conf_filename.] *********************
skipping: [webny]

TASK [geerlingguy.php : Define php_fpm_conf_path.] *****************************
skipping: [webny]

TASK [geerlingguy.php : include] ***********************************************
skipping: [webny]

TASK [geerlingguy.php : include] ***********************************************
included: /Users/justinwinter/Sites/wny/vendor/geerlingguy/drupal-vm/provisioning/roles/geerlingguy.php/tasks/setup-Debian.yml for webny

TASK [geerlingguy.php : Update apt cache.] *************************************
ok: [webny]

TASK [geerlingguy.php : Ensure PHP packages are installed.] ********************
ok: [webny] => (item=[u'php5.6', u'php5.6-apcu', u'php5.6-cli', u'php5.6-common', u'php5.6-curl', u'php5.6-dev', u'php5.6-fpm', u'php5.6-gd', u'php5.6-imap', u'php5.6-json', u'php5.6-mbstring', u'php5.6-mcrypt', u'php5.6-opcache', u'php5.6-sqlite3', u'php5.6-xml', u'php5.6-yaml', u'php5.6-bz2', u'php5.6-bz2'])

TASK [geerlingguy.php : Delete APCu configuration file if this role will provide one.] ***
skipping: [webny] => (item=/etc/php/5.6/fpm/conf.d)
skipping: [webny] => (item=/etc/php/5.6/apache2/conf.d)
skipping: [webny] => (item=/etc/php/5.6/cli/conf.d)

TASK [geerlingguy.php : Delete OpCache configuration file if this role will provide one.] ***
skipping: [webny] => (item=/etc/php/5.6/fpm/conf.d)
skipping: [webny] => (item=/etc/php/5.6/apache2/conf.d)
skipping: [webny] => (item=/etc/php/5.6/cli/conf.d)

TASK [geerlingguy.php : include] ***********************************************
skipping: [webny]

TASK [geerlingguy.php : include] ***********************************************
included: /Users/justinwinter/Sites/wny/vendor/geerlingguy/drupal-vm/provisioning/roles/geerlingguy.php/tasks/configure.yml for webny

TASK [geerlingguy.php : Ensure configuration directories exist.] ***************
ok: [webny] => (item=/etc/php/5.6/fpm)
ok: [webny] => (item=/etc/php/5.6/apache2)
ok: [webny] => (item=/etc/php/5.6/cli)
ok: [webny] => (item=/etc/php/5.6/fpm/conf.d)
ok: [webny] => (item=/etc/php/5.6/apache2/conf.d)
ok: [webny] => (item=/etc/php/5.6/cli/conf.d)

TASK [geerlingguy.php : Place PHP configuration file in place.] ****************
ok: [webny] => (item=/etc/php/5.6/fpm)
ok: [webny] => (item=/etc/php/5.6/apache2)
ok: [webny] => (item=/etc/php/5.6/cli)

TASK [geerlingguy.php : include] ***********************************************
included: /Users/justinwinter/Sites/wny/vendor/geerlingguy/drupal-vm/provisioning/roles/geerlingguy.php/tasks/configure-apcu.yml for webny

TASK [geerlingguy.php : Check for existing APCu config files.] *****************
ok: [webny] => (item=/etc/php/5.6/fpm/conf.d)
ok: [webny] => (item=/etc/php/5.6/apache2/conf.d)
ok: [webny] => (item=/etc/php/5.6/cli/conf.d)

TASK [geerlingguy.php : Remove any non-role-supplied APCu config files.] *******
skipping: [webny] => (item=({'_ansible_parsed': True, u'changed': False, '_ansible_no_log': False, '_ansible_item_result': True, 'item': u'/etc/php/5.6/fpm/conf.d', u'examined': 41, 'invocation': {'module_name': u'find', u'module_args': {u'paths': [u'/etc/php/5.6/fpm/conf.d'], u'file_type': u'file', u'age': None, u'contains': u'extension(\\s+)?=(\\s+)?apc[u]?\\.so', u'recurse': False, u'age_stamp': u'mtime', u'patterns': [u'*'], u'get_checksum': False, u'use_regex': False, u'follow': False, u'hidden': False, u'size': None}}, u'matched': 1, u'msg': u''}, {u'uid': 0, u'woth': False, u'mtime': 1489500768.242277, u'inode': 3934559, u'isgid': False, u'size': 66, u'isuid': False, u'isreg': True, u'gid': 0, u'ischr': False, u'wusr': True, u'xoth': False, u'islnk': False, u'nlink': 1, u'issock': False, u'rgrp': True, u'path': u'/etc/php/5.6/fpm/conf.d/20-apcu.ini', u'xusr': False, u'atime': 1489588357.212095, u'isdir': False, u'ctime': 1489500768.410277, u'isblk': False, u'wgrp': False, u'xgrp': False, u'dev': 64512, u'roth': True, u'isfifo': False, u'mode': u'0644', u'rusr': True}))
skipping: [webny] => (item=({'_ansible_parsed': True, u'changed': False, '_ansible_no_log': False, '_ansible_item_result': True, 'item': u'/etc/php/5.6/apache2/conf.d', u'examined': 3, 'invocation': {'module_name': u'find', u'module_args': {u'paths': [u'/etc/php/5.6/apache2/conf.d'], u'file_type': u'file', u'age': None, u'contains': u'extension(\\s+)?=(\\s+)?apc[u]?\\.so', u'recurse': False, u'age_stamp': u'mtime', u'patterns': [u'*'], u'get_checksum': False, u'use_regex': False, u'follow': False, u'hidden': False, u'size': None}}, u'matched': 1, u'msg': u''}, {u'uid': 0, u'woth': False, u'mtime': 1489500768.686277, u'inode': 3934560, u'isgid': False, u'size': 66, u'isuid': False, u'isreg': True, u'gid': 0, u'ischr': False, u'wusr': True, u'xoth': False, u'islnk': False, u'nlink': 1, u'issock': False, u'rgrp': True, u'path': u'/etc/php/5.6/apache2/conf.d/20-apcu.ini', u'xusr': False, u'atime': 1489588406.988656, u'isdir': False, u'ctime': 1489500768.850277, u'isblk': False, u'wgrp': False, u'xgrp': False, u'dev': 64512, u'roth': True, u'isfifo': False, u'mode': u'0644', u'rusr': True}))
skipping: [webny] => (item=({'_ansible_parsed': True, u'changed': False, '_ansible_no_log': False, '_ansible_item_result': True, 'item': u'/etc/php/5.6/cli/conf.d', u'examined': 41, 'invocation': {'module_name': u'find', u'module_args': {u'paths': [u'/etc/php/5.6/cli/conf.d'], u'file_type': u'file', u'age': None, u'contains': u'extension(\\s+)?=(\\s+)?apc[u]?\\.so', u'recurse': False, u'age_stamp': u'mtime', u'patterns': [u'*'], u'get_checksum': False, u'use_regex': False, u'follow': False, u'hidden': False, u'size': None}}, u'matched': 1, u'msg': u''}, {u'uid': 0, u'woth': False, u'mtime': 1489500769.114277, u'inode': 3934561, u'isgid': False, u'size': 66, u'isuid': False, u'isreg': True, u'gid': 0, u'ischr': False, u'wusr': True, u'xoth': False, u'islnk': False, u'nlink': 1, u'issock': False, u'rgrp': True, u'path': u'/etc/php/5.6/cli/conf.d/20-apcu.ini', u'xusr': False, u'atime': 1489588407.164656, u'isdir': False, u'ctime': 1489500769.310277, u'isblk': False, u'wgrp': False, u'xgrp': False, u'dev': 64512, u'roth': True, u'isfifo': False, u'mode': u'0644', u'rusr': True}))

TASK [geerlingguy.php : Ensure APCu config file is present.] *******************
ok: [webny] => (item=/etc/php/5.6/fpm/conf.d)
ok: [webny] => (item=/etc/php/5.6/apache2/conf.d)
ok: [webny] => (item=/etc/php/5.6/cli/conf.d)

TASK [geerlingguy.php : Remove APCu config file if APC is disabled.] ***********
skipping: [webny] => (item=/etc/php/5.6/fpm/conf.d)
skipping: [webny] => (item=/etc/php/5.6/apache2/conf.d)
skipping: [webny] => (item=/etc/php/5.6/cli/conf.d)

TASK [geerlingguy.php : include] ***********************************************
included: /Users/justinwinter/Sites/wny/vendor/geerlingguy/drupal-vm/provisioning/roles/geerlingguy.php/tasks/configure-opcache.yml for webny

TASK [geerlingguy.php : Check for existing OpCache config files.] **************
ok: [webny] => (item=/etc/php/5.6/fpm/conf.d)
ok: [webny] => (item=/etc/php/5.6/apache2/conf.d)
ok: [webny] => (item=/etc/php/5.6/cli/conf.d)

TASK [geerlingguy.php : Remove any non-role-supplied OpCache config files.] ****
skipping: [webny] => (item=({'_ansible_parsed': True, u'changed': False, '_ansible_no_log': False, '_ansible_item_result': True, 'item': u'/etc/php/5.6/fpm/conf.d', u'examined': 41, 'invocation': {'module_name': u'find', u'module_args': {u'paths': [u'/etc/php/5.6/fpm/conf.d'], u'file_type': u'file', u'age': None, u'contains': u'zend_extension(\\s+)?=(\\s+)?opcache\\.so', u'recurse': False, u'age_stamp': u'mtime', u'patterns': [u'*'], u'get_checksum': False, u'use_regex': False, u'follow': False, u'hidden': False, u'size': None}}, u'matched': 1, u'msg': u''}, {u'uid': 0, u'woth': False, u'mtime': 1489500771.538277, u'inode': 3934562, u'isgid': False, u'size': 303, u'isuid': False, u'isreg': True, u'gid': 0, u'ischr': False, u'wusr': True, u'xoth': False, u'islnk': False, u'nlink': 1, u'issock': False, u'rgrp': True, u'path': u'/etc/php/5.6/fpm/conf.d/05-opcache.ini', u'xusr': False, u'atime': 1489588357.192095, u'isdir': False, u'ctime': 1489500771.710277, u'isblk': False, u'wgrp': False, u'xgrp': False, u'dev': 64512, u'roth': True, u'isfifo': False, u'mode': u'0644', u'rusr': True}))
skipping: [webny] => (item=({'_ansible_parsed': True, u'changed': False, '_ansible_no_log': False, '_ansible_item_result': True, 'item': u'/etc/php/5.6/apache2/conf.d', u'examined': 3, 'invocation': {'module_name': u'find', u'module_args': {u'paths': [u'/etc/php/5.6/apache2/conf.d'], u'file_type': u'file', u'age': None, u'contains': u'zend_extension(\\s+)?=(\\s+)?opcache\\.so', u'recurse': False, u'age_stamp': u'mtime', u'patterns': [u'*'], u'get_checksum': False, u'use_regex': False, u'follow': False, u'hidden': False, u'size': None}}, u'matched': 1, u'msg': u''}, {u'uid': 0, u'woth': False, u'mtime': 1489500771.962277, u'inode': 3934563, u'isgid': False, u'size': 303, u'isuid': False, u'isreg': True, u'gid': 0, u'ischr': False, u'wusr': True, u'xoth': False, u'islnk': False, u'nlink': 1, u'issock': False, u'rgrp': True, u'path': u'/etc/php/5.6/apache2/conf.d/05-opcache.ini', u'xusr': False, u'atime': 1489588741.726332, u'isdir': False, u'ctime': 1489500772.130277, u'isblk': False, u'wgrp': False, u'xgrp': False, u'dev': 64512, u'roth': True, u'isfifo': False, u'mode': u'0644', u'rusr': True}))
skipping: [webny] => (item=({'_ansible_parsed': True, u'changed': False, '_ansible_no_log': False, '_ansible_item_result': True, 'item': u'/etc/php/5.6/cli/conf.d', u'examined': 41, 'invocation': {'module_name': u'find', u'module_args': {u'paths': [u'/etc/php/5.6/cli/conf.d'], u'file_type': u'file', u'age': None, u'contains': u'zend_extension(\\s+)?=(\\s+)?opcache\\.so', u'recurse': False, u'age_stamp': u'mtime', u'patterns': [u'*'], u'get_checksum': False, u'use_regex': False, u'follow': False, u'hidden': False, u'size': None}}, u'matched': 1, u'msg': u''}, {u'uid': 0, u'woth': False, u'mtime': 1489500772.378277, u'inode': 3934564, u'isgid': False, u'size': 303, u'isuid': False, u'isreg': True, u'gid': 0, u'ischr': False, u'wusr': True, u'xoth': False, u'islnk': False, u'nlink': 1, u'issock': False, u'rgrp': True, u'path': u'/etc/php/5.6/cli/conf.d/05-opcache.ini', u'xusr': False, u'atime': 1489588407.164656, u'isdir': False, u'ctime': 1489500772.538277, u'isblk': False, u'wgrp': False, u'xgrp': False, u'dev': 64512, u'roth': True, u'isfifo': False, u'mode': u'0644', u'rusr': True}))

TASK [geerlingguy.php : Ensure OpCache config file is present.] ****************
ok: [webny] => (item=/etc/php/5.6/fpm/conf.d)
ok: [webny] => (item=/etc/php/5.6/apache2/conf.d)
ok: [webny] => (item=/etc/php/5.6/cli/conf.d)

TASK [geerlingguy.php : Remove OpCache config file if OpCache is disabled.] ****
skipping: [webny] => (item=/etc/php/5.6/fpm/conf.d)
skipping: [webny] => (item=/etc/php/5.6/apache2/conf.d)
skipping: [webny] => (item=/etc/php/5.6/cli/conf.d)

TASK [geerlingguy.php : include] ***********************************************
included: /Users/justinwinter/Sites/wny/vendor/geerlingguy/drupal-vm/provisioning/roles/geerlingguy.php/tasks/configure-fpm.yml for webny

TASK [geerlingguy.php : Define php_fpm_daemon.] ********************************
skipping: [webny]

TASK [geerlingguy.php : Define php_fpm_pool_conf_path.] ************************
skipping: [webny]

TASK [geerlingguy.php : Define php_fpm_pool_user.] *****************************
skipping: [webny]

TASK [geerlingguy.php : Define php_fpm_pool_group.] ****************************
skipping: [webny]

TASK [geerlingguy.php : Stat php_fpm_pool_conf_path] ***************************
ok: [webny]

TASK [geerlingguy.php : Ensure the default pool directory exists.] *************
skipping: [webny]

TASK [geerlingguy.php : Ensure the default pool exists.] ***********************
ok: [webny]

TASK [geerlingguy.php : Configure php-fpm pool (if enabled).] ******************
ok: [webny] => (item={u'regexp': u'^user.?=.+$', u'line': u'user = www-data'})
ok: [webny] => (item={u'regexp': u'^group.?=.+$', u'line': u'group = www-data'})
ok: [webny] => (item={u'regexp': u'^listen.?=.+$', u'line': u'listen = 127.0.0.1:9000'})
ok: [webny] => (item={u'regexp': u'^listen\\.allowed_clients.?=.+$', u'line': u'listen.allowed_clients = 127.0.0.1'})
ok: [webny] => (item={u'regexp': u'^pm\\.max_children.?=.+$', u'line': u'pm.max_children = 50'})
ok: [webny] => (item={u'regexp': u'^pm\\.start_servers.?=.+$', u'line': u'pm.start_servers = 5'})
ok: [webny] => (item={u'regexp': u'^pm\\.min_spare_servers.?=.+$', u'line': u'pm.min_spare_servers = 5'})
ok: [webny] => (item={u'regexp': u'^pm\\.max_spare_servers.?=.+$', u'line': u'pm.max_spare_servers = 5'})

TASK [geerlingguy.php : Ensure php-fpm is started and enabled at boot (if configured).] ***
ok: [webny]

TASK [geerlingguy.php-pecl : Install PECL libaries.] ***************************

TASK [geerlingguy.composer : Set php_executable variable to a default if not defined.] ***
skipping: [webny]

TASK [geerlingguy.composer : Check if Composer is installed.] ******************
ok: [webny]

TASK [geerlingguy.composer : Download Composer installer.] *********************
skipping: [webny]

TASK [geerlingguy.composer : Run Composer installer.] **************************
skipping: [webny]

TASK [geerlingguy.composer : Move Composer into globally-accessible location.] *
skipping: [webny]

TASK [geerlingguy.composer : Update Composer to latest version (if configured).] ***
skipping: [webny]

TASK [geerlingguy.composer : Ensure composer directory exists.] ****************
ok: [webny]

TASK [geerlingguy.composer : Add GitHub OAuth token for Composer (if configured).] ***
skipping: [webny]

TASK [geerlingguy.composer : Install configured globally-required packages.] ***
ok: [webny] => (item={u'release': u'^0.3', u'name': u'hirak/prestissimo'})

TASK [geerlingguy.composer : Add composer_home_path bin directory to global $PATH.] ***
ok: [webny]

TASK [geerlingguy.composer : Add composer_project_path bin directory to global $PATH.] ***
skipping: [webny]

TASK [geerlingguy.mysql : Include OS-specific variables.] **********************
ok: [webny]

TASK [geerlingguy.mysql : Include OS-specific variables (RedHat).] *************
skipping: [webny]

TASK [geerlingguy.mysql : Define mysql_packages.] ******************************
ok: [webny]

TASK [geerlingguy.mysql : Define mysql_daemon.] ********************************
ok: [webny]

TASK [geerlingguy.mysql : Define mysql_slow_query_log_file.] *******************
ok: [webny]

TASK [geerlingguy.mysql : Define mysql_log_error.] *****************************
ok: [webny]

TASK [geerlingguy.mysql : Define mysql_syslog_tag.] ****************************
ok: [webny]

TASK [geerlingguy.mysql : Define mysql_pid_file.] ******************************
ok: [webny]

TASK [geerlingguy.mysql : Define mysql_config_file.] ***************************
ok: [webny]

TASK [geerlingguy.mysql : Define mysql_config_include_dir.] ********************
ok: [webny]

TASK [geerlingguy.mysql : Define mysql_socket.] ********************************
ok: [webny]

TASK [geerlingguy.mysql : Define mysql_supports_innodb_large_prefix.] **********
ok: [webny]

TASK [geerlingguy.mysql : include] *********************************************
skipping: [webny]

TASK [geerlingguy.mysql : include] *********************************************
included: /Users/justinwinter/Sites/wny/vendor/geerlingguy/drupal-vm/provisioning/roles/geerlingguy.mysql/tasks/setup-Debian.yml for webny

TASK [geerlingguy.mysql : Check if MySQL is already installed.] ****************
ok: [webny]

TASK [geerlingguy.mysql : Update apt cache if MySQL is not yet installed.] *****
skipping: [webny]

TASK [geerlingguy.mysql : Ensure MySQL Python libraries are installed.] ********
ok: [webny]

TASK [geerlingguy.mysql : Ensure MySQL packages are installed.] ****************
ok: [webny] => (item=[u'mysql-common', u'mysql-server'])

TASK [geerlingguy.mysql : Ensure MySQL is stopped after initial install.] ******
skipping: [webny]

TASK [geerlingguy.mysql : Delete innodb log files created by apt package after initial install.] ***
skipping: [webny] => (item=ib_logfile0)
skipping: [webny] => (item=ib_logfile1)

TASK [geerlingguy.mysql : Check if MySQL packages were installed.] *************
ok: [webny]

TASK [geerlingguy.mysql : Copy my.cnf global MySQL configuration.] *************
ok: [webny]

TASK [geerlingguy.mysql : Verify mysql include directory exists.] **************
skipping: [webny]

TASK [geerlingguy.mysql : Copy my.cnf override files into include directory.] **

TASK [geerlingguy.mysql : Create slow query log file (if configured).] *********
ok: [webny]

TASK [geerlingguy.mysql : Create datadir if it does not exist] *****************
ok: [webny]

TASK [geerlingguy.mysql : Set ownership on slow query log file (if configured).] ***
ok: [webny]

TASK [geerlingguy.mysql : Create error log file (if configured).] **************
ok: [webny]

TASK [geerlingguy.mysql : Set ownership on error log file (if configured).] ****
ok: [webny]

TASK [geerlingguy.mysql : Ensure MySQL is started and enabled on boot.] ********
ok: [webny]

TASK [geerlingguy.mysql : Get MySQL version.] **********************************
ok: [webny]

TASK [geerlingguy.mysql : Ensure default user is present.] *********************
skipping: [webny]

TASK [geerlingguy.mysql : Copy user-my.cnf file with password credentials.] ****
skipping: [webny]

TASK [geerlingguy.mysql : Disallow root login remotely] ************************
ok: [webny] => (item=DELETE FROM mysql.user WHERE User='root' AND Host NOT IN ('localhost', '127.0.0.1', '::1'))

TASK [geerlingguy.mysql : Get list of hosts for the root user.] ****************
[DEPRECATION WARNING]: always_run is deprecated. Use check_mode = no instead..

This feature will be removed in version 2.4. Deprecation warnings can be
disabled by setting deprecation_warnings=False in ansible.cfg.
skipping: [webny]

TASK [geerlingguy.mysql : Update MySQL root password for localhost root account (5.7.x).] ***

TASK [geerlingguy.mysql : Update MySQL root password for localhost root account (< 5.7.x).] ***

TASK [geerlingguy.mysql : Copy .my.cnf file with root password credentials.] ***
skipping: [webny]

TASK [geerlingguy.mysql : Get list of hosts for the anonymous user.] ***********
[DEPRECATION WARNING]: always_run is deprecated. Use check_mode = no instead..

This feature will be removed in version 2.4. Deprecation warnings can be
disabled by setting deprecation_warnings=False in ansible.cfg.
ok: [webny]

TASK [geerlingguy.mysql : Remove anonymous MySQL users.] ***********************

TASK [geerlingguy.mysql : Remove MySQL test database.] *************************
ok: [webny]

TASK [geerlingguy.mysql : Ensure MySQL databases are present.] *****************
ok: [webny] => (item={u'collation': u'utf8mb4_general_ci', u'name': u'drupal', u'encoding': u'utf8mb4'})

TASK [geerlingguy.mysql : Ensure MySQL users are present.] *********************
ok: [webny] => (item=(censored due to no_log))

TASK [geerlingguy.mysql : Ensure replication user exists on master.] ***********
skipping: [webny]

TASK [geerlingguy.mysql : Check slave replication status.] *********************
skipping: [webny]

TASK [geerlingguy.mysql : Check master replication status.] ********************
skipping: [webny]

TASK [geerlingguy.mysql : Configure replication on the slave.] *****************
skipping: [webny]

TASK [geerlingguy.mysql : Start replication.] **********************************
skipping: [webny]

TASK [geerlingguy.php-mysql : Include OS-specific variables.] ******************
ok: [webny]

TASK [geerlingguy.php-mysql : Define php_mysql_package.] ***********************
skipping: [webny]

TASK [geerlingguy.php-mysql : Install PHP MySQL dependencies (RedHat).] ********
skipping: [webny]

TASK [geerlingguy.php-mysql : Install PHP MySQL dependencies (Debian).] ********
ok: [webny]

TASK [geerlingguy.postgresql : include] ****************************************
skipping: [webny]

TASK [geerlingguy.postgresql : include] ****************************************
skipping: [webny]

TASK [geerlingguy.postgresql : include] ****************************************
skipping: [webny]

TASK [geerlingguy.postgresql : Set PostgreSQL environment variables.] **********
skipping: [webny]

TASK [geerlingguy.postgresql : Ensure PostgreSQL data directory exists.] *******
skipping: [webny]

TASK [geerlingguy.postgresql : Check if PostgreSQL database is initialized.] ***
skipping: [webny]

TASK [geerlingguy.postgresql : Ensure PostgreSQL database is initialized.] *****
skipping: [webny]

TASK [geerlingguy.postgresql : Configure global settings.] *********************
skipping: [webny] => (item={u'option': u'unix_socket_directories', u'value': u'/var/run/postgresql'})

TASK [geerlingguy.postgresql : Ensure PostgreSQL unix socket dirs exist.] ******
skipping: [webny] => (item=/var/run/postgresql)

TASK [geerlingguy.postgresql : Ensure PostgreSQL is started and enabled on boot.] ***
skipping: [webny]

TASK [geerlingguy.postgresql : Ensure PostgreSQL databases are present.] *******
skipping: [webny] => (item={u'name': u'drupal'})

TASK [geerlingguy.postgresql : Ensure PostgreSQL users are present.] ***********
skipping: [webny] => (item=(censored due to no_log))

TASK [geerlingguy.php-pgsql : Include OS-specific variables.] ******************
skipping: [webny]

TASK [geerlingguy.php-pgsql : Define php_pgsql_package.] ***********************
skipping: [webny]

TASK [geerlingguy.php-pgsql : Install PHP PostgreSQL dependencies (RedHat).] ***
skipping: [webny]

TASK [geerlingguy.php-pgsql : Install PHP PostgreSQL dependencies (Debian).] ***
skipping: [webny]

TASK [geerlingguy.drupal-console : Install Drupal Console.] ********************
skipping: [webny]

TASK [geerlingguy.drupal-console : Ensure Drupal Console is executable.] *******
skipping: [webny]

TASK [geerlingguy.drupal-console : Run Drupal Console init.] *******************
skipping: [webny]

TASK [geerlingguy.drupal-console : Update Drupal Console to latest version (if configured).] ***
skipping: [webny]

TASK [geerlingguy.drush : Install Drush.] **************************************
ok: [webny]

TASK [geerlingguy.drush : Ensure Drush is executable.] *************************
fatal: [webny]: FAILED! => {"changed": false, "failed": true, "msg": "src and dest are required for creating links"}
	to retry, use: --limit @/Users/justinwinter/Sites/wny/vendor/geerlingguy/drupal-vm/provisioning/playbook.retry

PLAY RECAP *********************************************************************
webny                      : ok=137  changed=1    unreachable=0    failed=1

Ansible failed to complete successfully. Any error output should be
visible above. Please fix these errors and try again.
justinwinter in ~/Sites/wny [-b feature/NDD-868-Video-Embed*]

Also, possibly unrelated, but if I comment out drush and mailhog in the config file
  # - drush
  # - mailhog

I now see this error:
TASK [geerlingguy.drupal : Install dependencies with composer require.] ********
failed: [webny] (item=drupal/devel:1.x-dev) => {"failed": true, "item": "drupal/devel:1.x-dev", "msg": "./composer.json has been updated Loading composer repositories with package information Installation failed, reverting ./composer.json to its original content. [RuntimeException] Failed to execute git clone --mirror 'git@github.com:ny/amber_alert_module.git' '/home/vagrant/.composer/cache/vcs/git-github.com-ny-amber-alert-module.git/' require [--dev] [--prefer-source] [--prefer-dist] [--no-progress] [--no-suggest] [--no-update] [--no-scripts] [--update-no-dev] [--update-with-dependencies] [--ignore-platform-reqs] [--prefer-stable] [--prefer-lowest] [--sort-packages] [-o|--optimize-autoloader] [-a|--classmap-authoritative] [--apcu-autoloader] [--] [<packages>]...", "stdout": "./composer.json has been updated\nLoading composer repositories with package information\n\nInstallation failed, reverting ./composer.json to its original content.\n\n                                                                                \n  [RuntimeException]                                                                                \n  Failed to execute git clone --mirror 'git@github.com:ny/amber_alert_module.git' '/home/vagrant/.composer/cache/vcs/git-github.com-ny-amber-alert-module.git/'  \n                                                                                \n\nrequire [--dev] [--prefer-source] [--prefer-dist] [--no-progress] [--no-suggest] [--no-update] [--no-scripts] [--update-no-dev] [--update-with-dependencies] [--ignore-platform-reqs] [--prefer-stable] [--prefer-lowest] [--sort-packages] [-o|--optimize-autoloader] [-a|--classmap-authoritative] [--apcu-autoloader] [--] [<packages>]...\n\n", "stdout_lines": ["./composer.json has been updated", "Loading composer repositories with package information", "", "Installation failed, reverting ./composer.json to its original content.", "", "                                                                                ", "  [RuntimeException]                                                                                ", "  Failed to execute git clone --mirror 'git@github.com:ny/amber_alert_module.git' '/home/vagrant/.composer/cache/vcs/git-github.com-ny-amber-alert-module.git/'  ", "                                                                                ", "", "require [--dev] [--prefer-source] [--prefer-dist] [--no-progress] [--no-suggest] [--no-update] [--no-scripts] [--update-no-dev] [--update-with-dependencies] [--ignore-platform-reqs] [--prefer-stable] [--prefer-lowest] [--sort-packages] [-o|--optimize-autoloader] [-a|--classmap-authoritative] [--apcu-autoloader] [--] [<packages>]...", ""]}
	to retry, use: --limit @/Users/justinwinter/Sites/wny/vendor/geerlingguy/drupal-vm/provisioning/playbook.retry

Seems that our custom amber alert module is having some issues getting cloned for some reason.

However, if I run composer update manually, I don't have any issues...

@justinlevi - It looks like you're managing your dependencies via composer.json on your own, so there's no need to have Drupal VM try to manage deps for you.
In this case, I'd say set drupal_composer_dependencies: [] in your config.yml

Oh wow... I didn't know about that config setting. Was that added recently?
I did upgrade drupal-vm recently and was wondering why I'm just seeing those composer issues now.

That's been in default.config.yml for a few releases now, since 4.0 I think? Anyways—does that get you through to the end now?

Yes, this can be closed. Thank you!
On Wed, Mar 15, 2017 at 2:39 PM Jeff Geerling notifications@github.com
wrote:

That's been in default.config.yml for a few releases now, since 4.0 I
think? Anyways—does that get you through to the end now?
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/geerlingguy/drupal-vm/issues/1216#issuecomment-286839680,
or mute the thread
https://github.com/notifications/unsubscribe-auth/ABEPJS4U8kb5vw1ZHYtwroa5hu_6JsMzks5rmDBQgaJpZM4McxdM
.

TASK [geerlingguy.drush : Install Drush.] **************************************
fatal: [drupalvm]: FAILED! => {"changed": false, "failed": true, "msg": "failed to create temporary content file: ('The read operation timed out',)"}
my os is ubuntu 16.04

@sudishth - That seems like a different problem besides MySQL restart failing. Can you try running vagrant provision again and see if it works? That error usually means your computer couldn't download Drush from GitHub for some reason (usually temporary).

authors: geerlingguy justinlevi sudishth

repo: geerlingguy/drupal-vm


text:
Adapts python plotting functionality to adhere to new tecplot output files

Hi Geir,
this PR adapts the python code to your new tecplot files and fixes Peter issue.
Cheers,
Rafael

Very good. Peter will be testing it :-)
Thanks a lot for contributing.

source: gharchive/pull-request

authors: geirev rafaeljmoraes

license: MIT

license_type: permissive

license_source: github-api


text:
misc: Add LULESH GPU tests

This adds the LULESH tests, which currently run successfully, though they still use the gem5-resources directory to build the binary used as opposed to using a pre-built binary
Change-Id: I91c511fe92b7f9d11dfb027f435573f826bc6714

Thanks for helping to move the GPU weekly tests out of the bash script! This looks fine for GCN3. One thing I would like though is to test the Vega ISA as well. I realize that will take more resources. @mattsinc and I have been planning to discuss in detail if GCN3 can be deprecated. I would also like to see Vega as part of the ALL build, which would further reduce compilation for testing, I think (not sure if each yaml file is rebuilding).
I have many more detailed thoughts on moving to Vega but it is probably better for a discussions thread rather than this PR.

Yes, this is something we can look into! I think if we do that, we can put it into a separate PR so we can update all the GPU tests to use Vega at the same time after we ensure it works locally first, unless you have other thoughts on that.

thanks! Please let @abmerop confirm before you merge in though.

done

FYI, when this is good to go (soon, I promise), i'll do a merge commit with this one so it'll be added to develop as one commit.
Just giving a heads up before people start to notice all the touch-up commits i've been doing.

Hi @Harshil2107 ,  I was actually just looking at this and was wondering how this command was even working. It seems it's not.  I will post a comment on what I suspect is the issue.

authors: BobbyRBruce abmerop mkjost0

license_source: bigquery


text:
02 09 Sampling

[x] Introduction
[x] SimPoint/LoopPoint
[x] SimPoint analysis
[x] SimPoint checkpointing
[x] Simpoint restoring
[x] ElFie
[x] ElFie example
[x] SMARTS
[x] SMARTS example
[x] Summary

What hasn't been done

Third party test on materials and go through slides
On slide 2 and  50, it is waiting for a visualization

@powerjg I removed the config files, removed the SimPoint3.2 source files, removed the checkpoints, and added -img to the image directory.


text:
Inconsistent documentation InformationService

Within the documentation on the main page it is written:
Information Service (information-service)
....
Limitations:
.....
 for record status it will always send HTTP code **200** (OK)

But  information/application.yaml says
      nested-responses:
        204:
          response:
            statusCode: **204**

Running actual Image deployment-1.0.8 repsonses with 204 and not 200

Hi @CEiderEVIDENT,
the documentation is updated with release version 1.0.12 - only the ReadMe wasn't updated accordingly after changing from 200 to 204 in previous API release.
--> https://github.com/gematik/epa-deployment/blob/main/README.md#information-service-information-service
Thanks for this finding and best regards,

source: gharchive/issue

authors: CEiderEVIDENT fnoGematik

repo: gematik/epa-deployment


text:
Annotated images in AmiGO

We'd like to have the ability to add annotated images that are displayable via the browser.
Discussion with @cmungall sounds like the ability to do something like a "gulp golr-load-image-annotations" where a tab delimited text file (format TBD) can be loaded into GOLR similar to how GAFs are done is the direction we'd like to head in.
Parts that I believe would need to be worked on include gulpfile changes to add the loading piece, actual code to load in GOLR, changes/addition to annotation pages in AmiGO to add the image type data, methods to display images (maybe carousel, maybe flat page with tables of images), probably other bits.
This is in conjunction with the image annotation work that @preecej is working on.
Also, time scale is pretty lax.  Just creating the issue so that work/thoughts can get started and we can brainstorm on how this will work.

As a first pass we can just overload golr bioentity_association documents (the bioentity would be an image rather than gene or germplasm). We can then reuse all the existing nice faceting mechanisms (e.g. when on the leaf page I can narrow my search dynamically to monocots).
I suggest using isa-partof closure but we need more requirements analysis here. If I am interested in leafs generally I will want to see images of subtypes of leaves. I will probably also be interested in images of parts of leafs too, but I'd get a bit uneasy if I jump too many levels of granularity.

Realistically, the code changes would be minimal if using 3rd-party storage. Most of these point could be covered with additional handler code. Adding a page base type similarly easy (although, maybe that should be abstracted out a bit more).
Also: https://github.com/geneontology/amigo/issues/341

In reference to work being done on Planteome.

(To mark the specific use case for planteome, I'd add it to the planteome amigo tracker and have it blocked with this as the upstream issue.)

I think the first step here is to see what kind of data would be loaded.
There are two possibilities here: an overloaded GAF-like (or whatever) thing that would take a custom loader or to overlay the image data on top of already-loaded annotation data (what the current demo does).
I suspect that once we have some fairly concrete data running around, or at format/approach, the code to get to basic usability would be pretty fast.

We may want to experiment with overlays later, but this is simpler. The subject/bioentity is an image denoted by a URL that resolves to a jpg or similar (let's say a thumbnail). Just using the default amigo view this would be behave as any other bioentity. We'd want to then enhance the display a bit, I don't have strong opinions here: just showing the thumbnail, carousel, ...?

@cmungall and I were just talking about this a second ago.  So, I think what we will have is some image URL that will display some term(s) so that people can see it and get a non-textual example of the term.  I think GAF may be an acceptable input format, we just have to have a new object type of image.  Maybe some client code that if the object type is an image to do something like make a thumbnail that links out to the source URL.  In other words, instead of At5g20800 in column 2 or 3 of the GAF, have the URL.  In column 12, have "image" as the object type, and then figure out how to make it look good in the browser.

The "carousel" has come up a couple of times here, and I don't quite understand--if it is a single object, what are the multiple things carouselling?
Otherwise, if we are literally treating these things as bioentities, then the code to detect an image URL ID would be very easy. Not so easy would be that have an ID component like that--it would likely throw a spanner into a lot of things. Preferable might be a standard bioentity document with an additional field that could act as the data overlay in a second loading step; population of the field would trigger the main effects.

This issue came up again in our ontology call this morning.  We are discussing some very complex Plant Ontology terms related to inflorescence axes and these definitions are accompanied with nice line-art diagrams of different types of inflorescences.  The textual definitions are complicated, and nuanced, but the images make it much clearer.  So being able to imbed an image would go a long way in clarifying the meaning of these terms.  This wouldn't require multiple images/carousel, rather just a single labeled image (from the NY crew).
Image example:
inflorescence_img_example.pdf

I think the addition is simple: add a new field, something like "auxiliary_external_reference_image" that is a remotely accessible PNG, etc. When the field is populated, AmiGO embeds whatever is at that end into the page. Simple.
Now, the hard part is to load that info into the store in the first place, which means we must descend into modifying the loader and loading a new file type (because GAF does not need a new field). That, or doing a second run over the index to populate it (like we did for the geo-spatial setup). If you want something out the door soon, the latter would be very very easy, especially if you don't have that many images.

When you say "new field" that would be a new field in what, exactly?
I think for a temporary solution, the example you outlined would work nicely.  To get a sense of scale, I'd say we will likely start with just a single image for each term in the PO (actually it would be fewer, as we would not have images for some categorical terms)  I could ask Dennis and his crew to gather the images that he would like to use, and deposit them somewhere on our repo (or elsewhere) with the PO:id in which they should be annotated to.
What format would be best?  We can just load all the images somewhere, and provide a delimited file with an ID and a URL to the image?

A new field in the Solr schema, as defined by the amigo metadata files.
If one were to move in this direction, and I won't have time really until after the GO meeting, I would tack towards getting all of the images into S3--I think we're talking about a few thousand here? Well, thinking about it, if you have a webserver (probably apache) up for AmiGO anyways, you could always server it out of the AmiGO static directory or apache as well.
As an experimental load format, let's say a JSON list along the lines of:
[
   {
      "index": "PO:0022008",
      "overlay": {
         "auxiliary_external_reference_image": "http://my.nifty/s3/url"
      }
   }
]

We can reuse this for other overlays in the future; I think that we can probably just reuse most of what was done for the geo-spatial here.

Excellent.  It will take some time to get images collected, and labeled correctly, so I'll see what can be done, then we can give it a whirl sometime in the semi-near future.
You're going to be in Corvallis this summer for the GO meeting, we can connect at that point.
Thanks for the explanation.

Yes, we can touch bases at Corvallis.
If there is a non-ontology label, or multiple images for a single term, a different overlay (or even strategy) would be necessary.

Yeah, and I'm sure that is in the long-term plan for the image annotation project, but if we could get just simple descriptive images imbedded in the term page on the browser, it would clear up a lot of the complex plant anatomy terms rapidly.

Well, yes, let's call this a one-off.
But for image annotations, we should revisit the work that has gone on with geospatial:
https://github.com/geneontology/amigo/issues/341

reiterating @austinmeier comments of displaying line diagrams etc. for explaining the anatomy terms on term detail pages. I recommend moving it up the priority.

Or, for that matter, thinking about #421, if we had a field that was essentially an overlay catch-all, a multivalued field (e.g. auxiliary_overlays) that could be loaded separately and incrementally, it could take a number of items to be render as needed. Each value could be like:
{
   "overlay": "auxiliary_external_reference_image",
   "index": "PO:0022008",
   "type": "image",
  "content": "http://snazzy.uri/foo/png"
}

or
{
   "overlay": "patter_description",
   "index": "PO:0022008",
   "type": "markdown",
  "content": "*** bleh"
}

authors: austinmeier cmungall elserj jaiswalp kltm

repo: geneontology/amigo


text:
Odd default namespace 2015-10-24 release

Looking in the header of gene_ontology_ext.obo
default-namespace: file:/Users/tanyaberardini/go_svn/ontology/extensions/ro_pending.obo
where it's usually
default-namespace: gene_ontology

Hi Jim,
As you've probably seen by now, Doug reported the same issue on the go-consortium mailing list, and it was fixed.
For reference, https://github.com/geneontology/go-ontology/issues/12141
Thanks for reporting.
Paola

authors: jimhu-tamu paolaroncaglia

repo: geneontology/go-ontology


text:
NTR: homotypic vesicle fusion and secretory granule maturation

Two new terms needed for annotation of Syt4 (Synaptotagmin-IV) in PMID:16618809:
homotypic vesicle fusion ; GO:NEW1
The fusion of two vesicle membranes to form a single vesicle.
GOC:bf, GOC:PARL
PMID:16618809
(Given that you’d have to have 2x ‘results_in_fusion_of: vesicle membrane’, I’m not sure I can currently create a decent logical definition for this).
secretory granule maturation ; GO:NEW2
Steps required to transform an immature secretory vesicle into a mature secretory vesicle. Typically proceeds through homotypic membrane fusion and membrane remodelling.
is_a: secretory granule organization ; GO:0033363
developmental maturation (GO:0021700) that results_in_organization_of: secretory granule ; GO:0030141
GOC:bf, GOC:PARL
PMID:16618809
is_a: child: dense core granule maturation ; GO:1990502
Note a similar logical definition could be added to dense core granule maturation ; GO:1990502
developmental maturation (GO:0021700) that results_in_organization_of: dense core granule ; GO:0031045
Thanks.

Including @dosumis because I'm sure he must have thought about this with respect to synaptic vesicles.
My hesitation with any of the 'homotypic' terms including the cell-cell adhesions terms is that at what level do we define the two entities as being the same. In the case of cell adhesion if two neurons bind one another, but they are distinct subtypes of neurons, is this homotypic? I have the same concerns with this term. In the ontology there is a rich substructure under membrane-bounded vesicle. At what point to we make the cut off for what is homotypic and what is heterotypic?
For the maturation term, we have 'synaptic vesicle maturation' and 'dense core granule maturation' as is_a children of 'vesicle organization'. We also have 'secretory granule organization' as a child. It seems like there are some patterns here of which we could take advantage. 'Synaptic vesicle maturation' is defined as 'developmental maturation' results_in_organization_of SOME 'synaptic vesicle' and is asserted as a subclass of 'vesicle organization'. There is also a term for 'synaptic vesicle coating' that has no relation to the maturation term. Any insights David?

I'd be reluctant to support a homotypic/heterotypic distinction if we can avoid it - for the resaons that @ukemi outlined above.
CC @Pimmelorus - General question about dense core vesicles here.  Any comments?  Could you see a need for a DCV maturation term for the Synapse work?

I see the problem with the 'homotypic' wording. How about making it more explicit in the GO term? It would go alongside the more specific instances of vesicle fusion:
E.g
vesicle fusion ; GO:0006906
--[isa]vesicle fusion with vesicle ; GO:NEW
--[isa]vesicle fusion to plasma membrane ; GO:0099500
--[isa]vesicle fusion with vacuole ; GO:0051469
--[isa]vesicle fusion with endoplasmic reticulum ; GO:0048279

I see the problem with the 'homotypic' wording. How about making it more explicit in the GO term? It would go alongside the more specific instances of vesicle fusion:
E.g
vesicle fusion ; GO:0006906
--[isa]vesicle fusion with vesicle ; GO:NEW
--[isa]vesicle fusion to plasma membrane ; GO:0099500
--[isa]vesicle fusion with vacuole ; GO:0051469
--[isa]vesicle fusion with endoplasmic reticulum ; GO:0048279

That looks fine.  I thought you were referring to vesicles of the same type.

Me too. This looks ok.
Added:
[Term]
+id: GO:0061782
+name: vesicle fusion with vesicle
+namespace: biological_process
+def: "Fusion of the membrane of a transport vesicle with a target membrane on another vesicle." [GOC:bf, GOC:PARL, PMID:16618809]
+synonym: "vesicle to vesicle fusion" EXACT [GOC:dph]
+synonym: "vesicle-vesicle fusion" EXACT [GOC:dph]
+is_a: GO:0006906 ! vesicle fusion
+created_by: dph
+creation_date: 2016-09-06T13:29:49Z
+

Thankyou! The authors were talking about two vesicles of the same type fusing, but vesicle-vesicle fusion is enough for me!

Added logical def to dense core granule term and:
[Term]
+id: GO:0061792
+name: secretory granule maturation
+namespace: biological_process
+def: "Steps required to transform an immature secretory vesicle into a mature secretory vesicle. Typically proceeds through homotypic membrane fusion and membrane remodelling." [GOC:bf, GOC:dph, GOC:PARL, PMID:16618809]
+is_a: GO:0033363 ! secretory granule organization
+intersection_of: GO:0021700 ! developmental maturation
+intersection_of: results_in_maturation_of GO:0030141 ! secretory granule
+created_by: dph
+creation_date: 2016-09-09T13:24:34Z

authors: dosumis rebeccafoulger ukemi


text:
Modified proteins proposal

Relevant GH tickets:
NTR: ubiquitinated protein binding
Parentage of glycoprotein binding
Question: adding new children of GO:0035064 methylated histone binding?
The proposalwas not well received by annotators at the GO meeting. The annotators thought that these terms were too important biologically for them not to be in the ontology. We need to come up with alternatives.
Continue to add these terms by hand. Unsustainable?
Figure out a way to add these terms automatically. Use PRO?, Chebi?, PsiMod?, will this lead to annotation inconsistency. Probably.
Only add a few very high-level terms. What is the specificity cut off and what happens when annotators make a case that the very specific term that they want is important.
Have do-not-annotate' terms that are generated automatically as in #1 below and categorize gene products by the entity that is captured in binding annotations.
We discussed three possible semantic interpretations of modified protein binding terms:
https://docs.google.com/document/d/1MAnnOfs-e2LY9MnqdCZscalbxbNUDSJ9pbMZ-f2WS9U/edit#heading=h.vzsyf1ss0k8h

Binds a protein that happens to have a modification, but not necessarily the modification site
Binds to the modified part of a protein <- Seems to be most broadly supported.
Binding to some specific protein partner is dependent on the modification state of the partner even if binding is not to the modified bit.  <- Some support.   DOS objection:  this seems like annotating a property of the bound protein. Also specific to one binding interaction (whereas 2 is likely to be a general function)

Number 2 in this list - binds to the modified part of a protein - had the most support. Example: SH2 domain confers binding to phospho-tryosine in the context of a specific peptide motif: https://en.wikipedia.org/wiki/SH2_domain
For terms like this, we could add a comment that it should only be used where there is high confidence that binding is to the modification + protein (simple dependency on phosphorylation of target is not sufficient but one that localizes the domain by deletion/mutagenesis analysis of the protein is). This still leaves the question of how detailed we should get in specifying the target (see histone binding).

Darren will join us on today's meeting to present his ideas.

This is what I mentioned to a few attendees at the USC GOC meeting. I'll summarize first, then give the reasoning by way of example.
Consider that "ubiquitinated protein binding" could be logically defined as something like ("protein binding to some ubiquitinated protein"). So ("ubiquitinated protein binding to some protein") is the same as ("protein binding to some ubiquitinated protein"). Given the confusion that currently holds when using these terms, this proposal provides the benefit that annotation is simplified. No information is lost, since terms like "ubiquitinated protein binding" are useful grouping terms that can be inferred
based on the binding partner indicated.
I would suggest that "protein binding" be used as the annotate-to term. Child terms of interest (such as "glycoprotein binding") stay, and new ones minted if desirable, but be marked as do-not-annotate.
Example:
Consider the case of USP15, a protein that binds to ubiquitinated histone H2B. This protein is annotated to GO:0061649 ("ubiquitinated histone binding"). For the moment, pretend that GO:0061649 can be a child of GO:0042393 ("histone binding") and the proposed term ("ubiquitinated protein binding"). The full hierarchy (after reasoning) would be:
protein binding
|_ ubiquitinated protein binding
|    |ubiquitinated histone binding
| histone binding
|_ubiquitinated histone binding
Consider a possible history for the annotation of USP15, from two different labs. Lab one and lab two each publish that USP15 binds protein, but don't know which protein. You'd get:
Lab1: USP15 protein binding some "protein"
Lab2: USP15 protein binding some "protein"
Lab1 then finds that USP15 binds to a ubiquitinated protein, while lab2 discovers that it binds to some histone. Now the annotation becomes:
Lab1: USP15 ubiquitinated protein binding some "ubiquitinated protein"
Lab2: USP15 histone binding some "histone"
Lab1 now finds that the specific type of ubiquitinated protein bound is histone, and Lab2 finds that the histone is ubiquitinated. Revised annotation:
Lab1: USP15 ubiquitinated histone binding some "ubiquitinated histone"
Lab2: USP15 ubiquitinated histone binding some "ubiquitinated histone"
Note that each new bit of information resulted in, for each lab, a change to both the GO term & the target (column 17). That means (for each lab) a total of 4 changes beyond the initial annotation.
A better, easier, more scalable solution would be to annotate ONLY to the parent protein binding term. The other GO terms stay but only as grouping terms. Specificity is given by the target. Thus, the history (for Lab1 only) would become:
A: USP15 protein binding some "protein"
B: USP15 protein binding some "ubiquitinated protein"
C: USP15 protein binding some "ubiquitinated histone"
Only 2 changes were necessary. Pros of this approach include fewer changes, clear guidance for GO term to use, and it's sustainable to any level of target specificity ("ubiquitinated histone" becomes "ubiquitinated histone H2B" becomes "histone H2B ubiquitinated at position 120" (as opposed to "histone H2B ubiquitinated at position 122"). I can think of only one con, which is that term enrichment becomes useless for specific types of protein binding. Of course, term enrichment could still be achieved, but there would be some overhead in calculating the correct sub-function.

On the call http://wiki.geneontology.org/index.php/Ontology_meeting_2016-11-10 @nataled clarified that in the above
A: USP15 protein binding to some "protein"
B: USP15 protein binding to some "ubiquitinated protein"
C: USP15 protein binding to some "ubiquitinated histone"

A, B and C are annotations made based on different evidence (different papers) through time, not one annotation evolving through time (though this would be possible too, provided the original paper contained the necessary information)

Notes from call (http://wiki.geneontology.org/index.php/Ontology_meeting_2016-11-10)
DOS:

Darren's suggested pattern in OWL:  GP (enables) 'protein binding' that has_input some PRO:'ubiquitinated protein'.
This corresponds to semantic interpretation 1: binds to some protein that happens to be ubiquitinated.  Binding doesn't have to be dependent on modification.  Are we sure we want this?
If we have the terms with logical defs in the ontology, then annotations with extensions will also work.  Might be worthwhile if we want to allow more specific pro terms to be used in extensions.

Action item:  We need more examples.  Ask Sylvan and Pascale to come to call to present examples.

The proposal was not well received by annotators at the GO meeting.
I'd like it to be recorded that this is not  true for PomBase curators.

I really like Darren's proposal. This is what we would do  anyway. The reason this solution was opposed was (by some) was because at the meeting it was not clear to all that  PRO could add generic
"ubiquitinated protein" terms.
Of course, tools would also need to catch up, but at present, I would not rely on GO to provide comprehensive lists of  modified protein binding partners.  The annotation would need to catch up in tandem to be realistically useful.  So in this situation we have a good opportunity to make the annotations in a more sustainable way without compromising what users can already do.

For example
GO:0051219 phosphoprotein binding
currently has
1 to 25 of 148 for 99 proteins
But I agree, @dosumis  we also need to be clear in these cases whether the binding is modification-dependent (when we make  these annotations using PRO IDs we translate has substrate into "active form" for our users
gene A protein binding "active form" PR:000045540  IPI  gene B
http://research.bioinformatics.udel.edu/pro/entry/PR%3A000045540/
(this isn't a real example, but I am sure we have done this for binding)

Hello,
Here's a version of the proposal, reviewed by the GO-editors and by @sylvainpoux

Background:
A number of proteins are known to specifically bind a protein that is modified, while not binding the unmodified form. The binding may occur at the site of the modification, but this is not an absolute requirement for a modification-specific binding; in some cases the binding occurs at another position on the target protein but is nevertheless dependent on the PTM.
Moreover (and very important for annotation), the information is not always complete: in some cases, the position of the binding relative to the modification is known, while in other cases, only the nature of the modification is known but not the binding site positions.
A number of domains are also known to specifically recognize and bind modified proteins, which is extremely important for recruitment of proteins and signaling (for example chromatin or DNA repair). Note that we do not always know whether these domains/proteins bind the modified part, but we usually know that they specifically recognize modified proteins.
The existence of these GO terms is extremely important for users, because it can really guide research. Moreover, resources like InterPro can generate electronic annotation for domains that bind modified proteins. Despite the usefulness of these terms, their ambiguous definitions has led to inconsistent usage.  Some terms have been created in GO to reflect modified protein binding: GO:0051219 phosphoprotein binding, GO:0061649 ubiquitinated histone binding etc. The definition does not clearly state that the binding must be modification-dependent, so it can be interpreted as 'protein x modified protein binding' to 'a protein that has the potential of bearing the modification'. This usage of the term is clearly incorrect.
On the other hand, other terms are missing from the ontology and curator use existing terms incorrectly to capture the information. For example, GO:0043130 ubiquitin binding could be both used for proteins that bind ubiquitinated proteins and free ubiquitin (both cases exist and are biologically important).
Proposal:
1.	Create a GO term
Modification-dependent protein binding:
Definition: Binding specifically to a protein that bears a post-translation modification.
Note: Does not bind the protein when not modified.
Annotation guidelines:
- The binding must be compared with and without the PTM in the interaction partner. If it is not shown that the binding is abolished in absence of the modification, this term cannot be used.
2.	Create a limited number of child terms for most common PTMs (fewer than 10)

Phosphorylated protein binding (would replace phosphoprotein binding)
Glycosylated protein binding (would replace glycoprotein binding)
Ubiquitinated protein binding (would be a child of ubiquitin binding and we would specify that ubiquitin binding is both for binding free ubiquitin and ubiquitinated proteins)
Methylated protein binding
Acylated protein binding
Acetylated protein binding

3.	Other PTMs:
To avoid unsustainable multiplication of terms, we can use 'Modified protein binding' with an ontology term in the extension (ontology to use remains to be defined). Until we choose the ontology, the parent term “modification-dependent protein binding” should be used for annotation.

Thanks, Pascale

Note: Send annotations to everyone to modify

here is list from PRO:
acetylation
ADP-ribosylation
amidation
bromination
cleavage
glycosylation
GPI-anchor
hydroxylation
methylation
phosphorylation
prenylation
sumoylation
ubiqitination
other

don't know how often bromination comes up, and the "cleavage"

Rename:
GO:0050815 phosphoserine binding ->   phosphoserine residue binding
GO:0050816 	phosphothreonine binding -> phosphothreonine residue binding
GO:0001784 phosphotyrosine binding -> phosphotyrosine  residue binding
On the May 9. 2017 annotation call, we agreed that the meaning of that terms was consistent with these changes.

Updated the definition to "Binding specifically to a protein dependent on the presence of a post-translation modification in the target protein. "

[Term]
+id: GO:0140030
+name: modification-dependent protein binding
+namespace: molecular_function
+def: "Binding specifically to a protein dependent on the presence of a post-translation modification in the target protein." [PMID:26060076]
+comment: This term should only be used when the binding is shown to required the post-translational modification: the interaction needs to be tested with and without the PTM. The binding does not need to be at the site of the modification. It may be that the PTM causes a conformation change that allows binding of the protein to another region; this type of modification-dependent protein binding is valid for annotation to this term.
+synonym: "modified protein binding" RELATED []
+is_a: GO:0005515 ! protein binding
+created_by: pg
+creation_date: 2017-05-17T11:50:41Z
+

Fixed ubiquitin protein binding:
id: GO:0031593
-name: polyubiquitin binding
+name: polyubiquitin modification-dependent protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a polymer of ubiqutin." [GOC:mah]
-synonym: "multiubiquitin binding" RELATED []
-is_a: GO:0043130 ! ubiquitin binding
+def: "Interacting selectively and non-covalently with a protein upon poly-ubiquitination of the target protein." [GOC:pg]
+is_a: GO:0140030 ! modification-dependent protein binding
[Term]
id: GO:0036435
-name: K48-linked polyubiquitin binding
+name: K48-polyubiquitin modification-dependent protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently and non-covalently with a polymer of ubiquitin formed by linkages between lysine residues at position 48 of the ubiquitin monomers." [GOC:al, PMID:20739285]
-is_a: GO:0031593 ! polyubiquitin binding
+def: "Interacting selectively and non-covalently with a protein upon poly-ubiquitination formed by linkages between lysine residues at position 48 in the target protein." [GOC:al, PMID:20739285]
+is_a: GO:0031593 ! polyubiquitin modification-dependent protein binding
created_by: rfoulger
creation_date: 2013-09-18T14:51:06Z
[Term]
id: GO:0070530
-name: K63-linked polyubiquitin binding
+name: K63-polyubiquitin modification-dependent protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently and non-covalently with a polymer of ubiquitin formed by linkages between lysine residues at position 63 of the ubiquitin monomers." [GOC:mah, PMID:15556404, PMID:17525341]
-is_a: GO:0031593 ! polyubiquitin binding
+def: "Interacting selectively and non-covalently with a protein upon poly-ubiquitination formed by linkages between lysine residues at position 63 in the target protein." [GOC:mah, PMID:15556404, PMID:17525341]
+is_a: GO:0031593 ! polyubiquitin modification-dependent protein binding
[Term]
id: GO:0071795
-name: K11-linked polyubiquitin binding
+name: K11-polyubiquitin modification-dependent protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently and non-covalently with a polymer of ubiquitin formed by linkages between lysine residues at position 11 of the ubiquitin monomers." [GOC:sp, PMID:18775313]
-is_a: GO:0031593 ! polyubiquitin binding
+def: "Interacting selectively and non-covalently with a protein upon poly-ubiquitination formed by linkages between lysine residues at position 11 in the target protein." [GOC:sp, PMID:18775313]
+is_a: GO:0031593 ! polyubiquitin modification-dependent protein binding
created_by: midori
creation_date: 2010-09-02T02:11:41Z
[Term]
id: GO:0071796
-name: K6-linked polyubiquitin binding
+name: K6-polyubiquitin modification-dependent protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently and non-covalently with a polymer of ubiquitin formed by linkages between lysine residues at position 6 of the ubiquitin monomers." [GOC:sp, PMID:17525341, PMID:20351172]
-is_a: GO:0031593 ! polyubiquitin binding
+def: "Interacting selectively and non-covalently with a protein upon poly-ubiquitination formed by linkages between lysine residues at position 6 in the target protein." [GOC:sp, PMID:17525341, PMID:20351172]
+is_a: GO:0031593 ! polyubiquitin modification-dependent protein binding
created_by: midori
creation_date: 2010-09-02T02:13:07Z
@@ -587346,7 +587345,7 @@ name: linear polyubiquitin binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with a linear polymer of ubiquitin. Linear ubiquitin polymers are formed by linking the amino-terminal methionine (M1) of one ubiquitin molecule to the carboxy-terminal glycine (G76) of the next." [GOC:bf, GOC:PARL, PMID:23453807]
synonym: "M1-linked ubiquitin chain binding" EXACT [PMID:23453807]
-is_a: GO:0031593 ! polyubiquitin binding
+is_a: GO:0043130 ! ubiquitin binding
created_by: bf
creation_date: 2014-08-06T11:10:26Z

Was the duplication of "and non-covalently" intentional?

probably not :) thanks for pointing out

In fact it was in the old definition ! (as you can see by the '-' sign at the beginning of the line.

I lose. My apologies.

As discussed in
https://github.com/geneontology/go-annotation/issues/1586
I will create
'glycosylated region binding' (similar to 'proline-rich region binding),
Proposed def: Interacting selectively and non-covalently with a glycosylated region of a protein.
Proposed parents:
protein binding + carbohydrate-derivative protein binding.

Pascale

New term:
+id: GO:0140081
+name: glycosylated region protein binding
+namespace: molecular_function
+def: "Interacting selectively and non-covalently with a glycosylated region of a protein." [GOC:pg]
+is_a: GO:0005515 ! protein binding
+is_a: GO:0097367 ! carbohydrate derivative binding
+created_by: pg
+creation_date: 2017-07-25T10:58:31Z

authors: ValWood dosumis hdrabkin mcourtot nataled pgaudet ukemi


text:
NTR:sexual macrocyst formation

Hello:
I would like to request a new GO term to describe the sexual reproductive phase of the Dictyostelium life cycle. This term is most commonly associated with D. discoideum, but applies to at least 3 additional species of Dictyostelids: D. giganteum, D. purpureum, and P. palladium. Please let me know if you have additional questions.
Thanks,
Bob Dodson
Name: sexual macrocyst formation
Ontology: process
Synonyms: macrocyst formation, sexual fusion
Definition: The fusion of haploid amoebae cells with matching mating types to form a larger cell, which ingests additional amoebae and forms a cellulose wall. The resulting macrocyst undergoes recombination and meiosis followed by release of haploid amoebae. An example of this process can be found in Dictyostelium discoideum.
Child of: GO:0019953 sexual reproduction
References:
PMID:16592095 Mating Types and Macrocyst Formation in Dictyostelium discoideum
PMID: 20089169 Phylogeography and sexual macrocyst formation in the social amoeba Dictyostelium giganteum.

Hi Bob !!
Here's the new term:
[Term]
+id: GO:0140084
+name: sexual macrocyst formation
+namespace: biological_process
+def: "The fusion of haploid amoebae cells with matching mating types to form a larger cell, which ingests additional amoebae and forms a cellulose wall. The resulting macrocyst undergoes recombination and meiosis followed by release of haploid amoebae. An example of this process can be found in Dictyostelium discoideum." [PMID:16592095, PMID:20089169]
+synonym: "macrocyst formation" RELATED []
+synonym: "sexual fusion" RELATED []
+is_a: GO:0019953 ! sexual reproduction
+created_by: pg
+creation_date: 2017-08-14T20:11:03Z
Thanks, Pascale

Thanks Pascale!

authors: pgaudet rjdodson


text:
astrocytes are not immune cells

GO:0045321 : immune cell activation (374)
GO:0048143 : astrocyte activation (5)
Astrocytes are glial cells (only exist in the brain and
support neurons; they are not found in the blood), so
they are currently mis-classified as immune cells.
Reported by: *anonymous
Original Ticket: "geneontology/ontology-requests/1627":https://sourceforge.net/p/geneontology/ontology-requests/1627

thanks www.movied.org

authors: gocentral linuxlovell