def test_configure_plugins_plugin_refresh(self):
_id = 0
plugin = Plugin()
plugin.name = "Foo"
#skip call to DB and return this Plugin stub instead
when(iondb.rundb.configure.views).get_object_or_404(Plugin,_id).thenReturn(plugin)
data = {}
response = self.client.get('configure/plugins/%s/refresh/' % _id, data)
self.assertEqual(response.status_code, 200)
self.assertEqual(response.context['plugin'], plugin)
self.assertEqual(response.context['action'], reverse('api_dispatch_info', kwargs={'resource_name': 'plugin', 'api_name': 'v1', 'pk': int(_id)}) + '?use_cache=false')
self.assertEqual(response.context['method'], 'get')
self.assertIn('Refresh Plugin %s Information' % plugin.name, response.content)
def validateStep(self):
"""This method overrides the abstract class'es implementation and will validate each of the plugins individually."""
# we don't need to perform this validation for templates
if self.sh_type in StepHelperType.TEMPLATE_TYPES:
return
self.updateSavedObjectsFromSavedFields()
# reset the validation errors
self.validationErrors.clear()
for plugin_id, values in self.savedObjects[
PluginFieldNames.PLUGINS].items():
plugin_model = Plugin.objects.get(id=plugin_id)
if values[PluginFieldNames.
SELECTED] and plugin_model.requires_configuration:
configuration = dict(
) if values[PluginFieldNames.CONFIG] is None else json.loads(
values[PluginFieldNames.CONFIG])
plugin_validation_errors = Plugin.validate(
plugin_id, configuration, 'Automatic')
if plugin_validation_errors:
self.validationErrors[values[PluginFieldNames.PLUGIN].
name] = plugin_validation_errors
def validate_plugin_configurations(selected_plugins):
"""this will validate all of the plugins as part of the plan. It returns a list of all of the validation error messages"""
validation_messages = list()
for name, plugin_parameters in selected_plugins.items():
try:
configuration = plugin_parameters.get('userInput', {}) or {}
plugin_model = Plugin.objects.get(name=plugin_parameters['name'], active=True)
validation_messages += Plugin.validate(plugin_model.id, configuration, 'pipeline')
except Exception as exc:
validation_messages += [str(exc)]
return validation_messages
def upgrade_helper(self, plugin, current_path=None):
# TODO: Rename this method to be _upgrade_helper
""" Handle additional tasks during upgrade of plugin.
Currently deactivates old versions of plugins to avoid version conflicts.
Pass in the new plugin object - the one you want to keep.
"""
from iondb.rundb.models import Plugin
# Some behavior here is just to disable old versions during upgrade.
count = 0
oldplugin = None
# Get all plugins with the same name and different version
for oldp in Plugin.objects.filter(name=plugin.name).exclude(
version=plugin.version):
# FIXME - multi-version support needs new behavior here
if oldp.active or oldp.path:
logger.info("Disabling old version of plugin %s v%s",
oldp.name, oldp.version)
count += 1
else:
continue
# Plugins other than our version are disabled
# Uninstall - Allows manual install of plugin previously installed via zeroinstall
# Careful not to delete new path if installed in-place!!!
current_path = current_path or plugin.path
if oldp.path and oldp.path != current_path:
# farm the uninstall off to the plugin daemon
Plugin.Uninstall(oldp.id)
else:
oldp.path = ""
if oldp.active:
oldp.active = False
oldp.save()
# Important! This is passed back to preserve autorun and selected settings
oldplugin = oldp
if count:
logger.debug(
"Deactivated %d old versions while upgrading to %s v%s",
count,
plugin.name,
plugin.version,
)
return count, oldplugin
def test_configure_plugins_plugin_refresh(self):
_id = 0
plugin = Plugin()
plugin.name = "Foo"
#skip call to DB and return this Plugin stub instead
when(iondb.rundb.configure.views).get_object_or_404(
Plugin, _id).thenReturn(plugin)
data = {}
response = self.client.get('configure/plugins/%s/refresh/' % _id, data)
self.assertEqual(response.status_code, 200)
self.assertEqual(response.context['plugin'], plugin)
self.assertEqual(
response.context['action'],
reverse('api_dispatch_info',
kwargs={
'resource_name': 'plugin',
'api_name': 'v1',
'pk': int(_id)
}) + '?use_cache=false')
self.assertEqual(response.context['method'], 'get')
self.assertIn('Refresh Plugin %s Information' % plugin.name,
response.content)
def validate_plugin_configurations(selected_plugins):
"""this will validate all of the plugins as part of the plan. It returns a list of all of the validation error messages"""
validation_messages = list()
if not selected_plugins:
return validation_messages
for name, plugin_parameters in list(selected_plugins.items()):
try:
configuration = plugin_parameters.get("userInput", {}) or {}
plugin_model = Plugin.objects.get(name=plugin_parameters["name"],
active=True)
if plugin_model.requires_configuration:
validation_messages += Plugin.validate(plugin_model.id,
configuration)
except Exception as exc:
validation_messages += [str(exc)]
return validation_messages
def validateStep(self):
"""This method overrides the abstract class'es implementation and will validate each of the plugins individually."""
# we don't need to perform this validation for templates
if self.sh_type in StepHelperType.TEMPLATE_TYPES:
return
self.updateSavedObjectsFromSavedFields()
# reset the validation errors
self.validationErrors.clear()
for plugin_id, values in self.savedObjects[PluginFieldNames.PLUGINS].items():
plugin_model = Plugin.objects.get(id=plugin_id)
if values[PluginFieldNames.SELECTED] and plugin_model.requires_configuration:
configuration = dict() if values[PluginFieldNames.CONFIG] is None else json.loads(values[PluginFieldNames.CONFIG])
plugin_validation_errors = Plugin.validate(plugin_id, configuration, 'Automatic')
if plugin_validation_errors:
self.validationErrors[values[PluginFieldNames.PLUGIN].name] = plugin_validation_errors
def launchPlugins(self,
result_pk,
plugins,
net_location,
username,
runlevel=RunLevel.DEFAULT,
params={}):
"""
Launch multiple plugins with dependencies
For multi-runlevel plugins the input 'plugins' is common for all runlevels
"""
msg = ''
logger.debug("[launchPlugins] result %s requested plugins: %s" %
(result_pk, ','.join(plugins.keys())))
try:
# get plugins to run for this runlevel
plugins, plugins_to_run, satisfied_dependencies = get_plugins_to_run(
plugins, result_pk, runlevel)
if len(plugins_to_run) > 0:
logger.debug(
"[launchPlugins] runlevel: %s, depsolved launch order: %s"
% (runlevel, ','.join(plugins_to_run)))
else:
logger.debug(
"[launchPlugins] no plugins to run at runlevel: %s" %
runlevel)
return plugins, msg
result = Results.objects.get(pk=result_pk)
report_dir = result.get_report_dir()
url_root = result.reportWebLink()
# get pluginresult owner - must be a valid TS user
try:
user = User.objects.get(username=username)
except User.DoesNotExist:
user = User.objects.get(pk=1)
logger.error(
"Invalid user specified for plugin launch: %s, will use %s"
% (username, user.username))
for name in plugins_to_run:
try:
p = plugins[name]
# get params for this plugin, make empty json value if doesn't exist
plugin_params = params.setdefault('plugins',
{}).setdefault(name, {})
# Get pluginresult for multi-runlevel plugins or if specified to be reused by manual launch
pr = None
pluginresult_pk = p.get(
'pluginresult') or plugin_params.get('pluginresult')
if pluginresult_pk:
logger.debug("Searching for PluginResult: %s",
pluginresult_pk)
try:
pr = result.pluginresult_set.get(
pk=pluginresult_pk)
except:
logger.error(
"Failed to find pluginresult for plugin %s, result %s: %s"
% (name, result.resultsName, pluginresult_pk))
pr = None
# Create new pluginresult - this is the most common path
if not pr:
pr = PluginResult.objects.create(result_id=result_pk,
plugin_id=p['id'],
owner=user)
logger.debug(
"New pluginresult id=%s created for plugin %s and result %s."
% (pr.pk, name, result.resultsName))
# Always create new, unique output folder.
# Never fallback to old *_out format.
plugin_output = pr.path(create=True, fallback=False)
else:
# Use existing output folder
plugin_output = pr.path(create=False)
p['results_dir'] = plugin_output
p['pluginresult'] = pr.pk
p, holding_for = add_hold_jid(p, plugins, runlevel,
satisfied_dependencies)
start_json = make_plugin_json(
result_pk, report_dir, p, plugin_output,
net_location, url_root, username, runlevel,
params.get('blockId', ''),
params.get('block_dirs', ["."]),
plugin_params.get('instance_config', {}))
# Pass on run_mode (launch source - manual/instance, pipeline)
run_mode = params.get('run_mode', '')
start_json['runplugin']['run_mode'] = run_mode
# add dependency info to startplugin json
if p.get('depends') and isinstance(p['depends'], list):
start_json['depends'] = {}
for depends_name in p['depends']:
if depends_name in satisfied_dependencies:
start_json['depends'][
depends_name] = satisfied_dependencies[
depends_name]
elif depends_name in plugins and plugins[
depends_name].get('pluginresult'):
start_json['depends'][depends_name] = {
'pluginresult':
plugins[depends_name]['pluginresult'],
'version':
plugins[depends_name].get('version', ''),
'pluginresult_path':
plugins[depends_name].get('results_dir')
}
# prepare for launch: updates config, sets pluginresults status, generates api key
pr.prepare()
# perform the validation of the plugin configuration here
pr.validation_errors = {
'validation_errors':
Plugin.validate(p['id'], start_json['pluginconfig'],
run_mode)
}
pr.save()
if pr.validation_errors.get('validation_errors', list()):
continue
# update startplugin json with pluginresult info
start_json['runinfo']['pluginresult'] = pr.pk
start_json['runinfo']['api_key'] = pr.apikey
# NOTE: Job is held on start, and subsequently released
# to avoid any race condition on updating job queue status
# launch plugin
jid = SGEPluginJob(start_json, hold=True)
if jid:
# Update pluginresult status
prj, created = PluginResultJob.objects.get_or_create(
plugin_result=pr,
run_level=runlevel,
grid_engine_jobid=jid,
state='Queued',
config=start_json['pluginconfig'],
)
prj.save()
# Release now that jobid and queued state are set.
_session.control(
jid,
drmaa.JobControlAction.RELEASE) # no return value
msg += 'Plugin: %s result: %s, jid %s, depends %s, holding for %s \n' % (
p.get('name', ''), result.resultsName, jid,
p.get('depends', []), holding_for)
if runlevel != RunLevel.BLOCK:
p['jid'] = jid
else:
p.setdefault('block_jid', []).append(jid)
except Exception as exc:
logger.error(traceback.format_exc())
msg += 'ERROR: Plugin %s failed to launch.\n' % p['name']
pr = PluginResult.objects.get(pk=pr.pk)
except:
logger.error(traceback.format_exc())
msg += 'ERROR: Failed to launch requested plugins.'
return plugins, msg
def install(self, pname, full_path, launch_script=None, info=None):
"""Install (or upgrade) a plugin given a src path.
Safe to use for already installed plugins, with these cautions:
* Will reactivate if previously marked inactive.
* May refresh pluginconfig or upgrade to new version if found.
TODO - handle embedded version number in path
"""
from iondb.rundb.models import Plugin
# Cleanup, normalize and validate inputs
pname = pname.strip()
full_path = os.path.normpath(full_path)
if not os.path.exists(full_path):
logger.error("Path specified for install does not exist '%s'",
full_path)
# Check Plugin Blacklist:
if pname in ("scratch", "implementations"):
logger.error(
"Scratch and Implementations are reserved folders, and cannot be installed."
)
return None, False
if not launch_script:
(launch_script,
isLaunch) = self.find_pluginscript(full_path, pname)
logger.debug("Plugin Info: %s", info)
if not info:
# Worst case, should have been pre-fetched above
logger.error("Need to rescan plugin info..")
info = PluginManager.get_plugininfo(pname,
launch_script,
existing_pk=None,
use_cache=False)
logger.debug("Plugin Rescan Info: %s", info)
if info is None:
raise ValueError("No plugininfo for '%s' in '%s'" %
(pname, launch_script))
version = info.get("version", "0")
majorBlock = info.get("major_block", False)
# Only used if new plugin record is created
packageName = getPackageName(full_path)
plugin_defaults = {
"path": full_path,
"date": datetime.datetime.now(),
"active": True, # auto activate new versions
"selected": True, # Auto enable new plugins
"majorBlock": majorBlock,
"description": info.get("docs", None),
"userinputfields": info.get("config", None),
"packageName":
packageName if not "ion-plugins" in packageName else "",
}
logger.debug("Plugin Install/Upgrade checking for plugin: %s %s",
pname, version)
# needs_save is aka created. Tracks if anything changed.
p, needs_save = Plugin.objects.get_or_create(name=pname,
version=version,
defaults=plugin_defaults)
# update the plugin package name
if plugin_defaults["packageName"] != p.packageName:
p.packageName = plugin_defaults["packageName"]
p.save()
if needs_save:
# Newly created plugin - never before seen with this name and version
logger.info("Installing New Plugin %s v%s at '%s'", pname, version,
full_path)
# Set pluginconfig.json if needed - only for new installs / version changes
if self.set_pluginconfig(p):
logger.info(
"Loaded new pluginconfig.json values for Plugin %s v%s at '%s'",
pname,
version,
full_path,
)
else:
logger.debug("Existing plugin found: %s %s [%d]", p.name,
p.version, p.pk)
p.updateFromInfo(info)
# Handle any upgrade behaviors - deactivating old versions, etc.
(count, oldp) = self.upgrade_helper(p, current_path=full_path)
# Preserve old selected/defaultSelected state
if count and oldp:
p.selected = oldp.selected
p.defaultSelected = oldp.defaultSelected
# Merge stock config with previous config, preserving user settings
p.config.update(oldp.config)
# Be careful with path handling -- FIXME
if not p.path:
# 1. path was empty - set path and reactivate
# Reinstall previously removed and inactive plugin - files were restored
logger.info(
"Reactivating previously uninstalled Plugin %s v%s at '%s'",
pname,
version,
full_path,
)
if self.enable(p, full_path):
needs_save = True
elif not os.path.exists(p.path):
# 2. path was set, but folder is missing - replace
# Prior path was invalid, but caller insists full_path exists
needs_save = p.path == full_path # only if changed
if needs_save:
logger.info(
"Changing Plugin path value %s v%s to '%s' (was '%s')",
pname,
version,
full_path,
p.path,
)
if os.path.exists(full_path):
self.enable(p, full_path)
elif p.path != full_path:
# 3. path was set and exists
# FIXME - for now, replace old plugin with new.
# TODO - With multi-version install, ignore duplicate of same version
logger.info(
"Found relocated Plugin %s v%s at '%s' (was '%s')",
pname,
version,
full_path,
p.path,
)
# uninstall the plugin
Plugin.Uninstall(p.id)
# And restore with full_path
self.enable(p, full_path)
# If the path exists, it is an active. Inactive plugins are removed
if not p.active and os.path.exists(p.path):
logger.info(
"Reactivating plugin marked inactive but present on filesystem %s v%s at '%s'",
pname,
version,
full_path,
)
self.enable(p)
if not p.script:
p.script = os.path.basename(launch_script)
if launch_script != os.path.join(p.path, p.script):
logger.error(
"Launch Script is not in plugin folder: '%s' '%s'",
p.path,
launch_script,
)
needs_save = True
# create media symlinks if needed
pluginMediaSrc = os.path.join(p.path, "pluginMedia")
if os.path.exists(pluginMediaSrc):
pluginMediaDst = os.path.join("/results/pluginMedia", p.name)
try:
if os.path.lexists(pluginMediaDst):
os.unlink(pluginMediaDst)
# note os.path.exists returns False for broken symlinks
os.symlink(
os.path.join(p.path, "pluginMedia"),
os.path.join("/results/pluginMedia", p.name),
)
except OSError:
logger.exception("Failed to create pluginMedia Symlink: %s",
pluginMediaDst)
# No need to set needs_save - no db data changed
# Update majorBlock to current setting
if p.majorBlock != majorBlock:
p.majorBlock = majorBlock
needs_save = True
if needs_save:
p.save()
# Return true if anything changed. Always return plugin object
return p, needs_save
def launchPlugins(self, result_pk, plugins, net_location, username, runlevel=RunLevel.DEFAULT, params={}):
"""
Launch multiple plugins with dependencies
For multi-runlevel plugins the input 'plugins' is common for all runlevels
"""
msg = ''
logger.debug("[launchPlugins] result %s requested plugins: %s" % (result_pk, ','.join(plugins.keys())))
try:
# get plugins to run for this runlevel
plugins, plugins_to_run, satisfied_dependencies = get_plugins_to_run(plugins, result_pk, runlevel)
if len(plugins_to_run) > 0:
logger.debug("[launchPlugins] runlevel: %s, depsolved launch order: %s" % (runlevel, ','.join(plugins_to_run)))
else:
logger.debug("[launchPlugins] no plugins to run at runlevel: %s" % runlevel)
return plugins, msg
result = Results.objects.get(pk=result_pk)
report_dir = result.get_report_dir()
url_root = result.reportWebLink()
# get pluginresult owner - must be a valid TS user
try:
user = User.objects.get(username=username)
except User.DoesNotExist:
user = User.objects.get(pk=1)
logger.error("Invalid user specified for plugin launch: %s, will use %s" % (username, user.username))
for name in plugins_to_run:
try:
p = plugins[name]
# get params for this plugin, make empty json value if doesn't exist
plugin_params = params.setdefault('plugins', {}).setdefault(name, {})
# Get pluginresult for multi-runlevel plugins or if specified to be reused by manual launch
pr = None
pluginresult_pk = p.get('pluginresult') or plugin_params.get('pluginresult')
if pluginresult_pk:
logger.debug("Searching for PluginResult: %s", pluginresult_pk)
try:
pr = result.pluginresult_set.get(pk=pluginresult_pk)
except:
logger.error("Failed to find pluginresult for plugin %s, result %s: %s" % (name, result.resultsName, pluginresult_pk))
pr = None
# Create new pluginresult - this is the most common path
if not pr:
pr = PluginResult.objects.create(result_id=result_pk, plugin_id=p['id'], owner=user)
logger.debug("New pluginresult id=%s created for plugin %s and result %s." % (pr.pk, name, result.resultsName))
# Always create new, unique output folder.
# Never fallback to old *_out format.
plugin_output = pr.path(create=True, fallback=False)
else:
# Use existing output folder
plugin_output = pr.path(create=False)
p['results_dir'] = plugin_output
p['pluginresult'] = pr.pk
p, holding_for = add_hold_jid(p, plugins, runlevel, satisfied_dependencies)
start_json = make_plugin_json(result_pk, report_dir, p, plugin_output, net_location, url_root, username, runlevel,
params.get('blockId', ''), params.get('block_dirs', ["."]), plugin_params.get('instance_config', {}))
# Pass on run_mode (launch source - manual/instance, pipeline)
run_mode = params.get('run_mode', '')
start_json['runplugin']['run_mode'] = run_mode
# add dependency info to startplugin json
if p.get('depends') and isinstance(p['depends'], list):
start_json['depends'] = {}
for depends_name in p['depends']:
if depends_name in satisfied_dependencies:
start_json['depends'][depends_name] = satisfied_dependencies[depends_name]
elif depends_name in plugins and plugins[depends_name].get('pluginresult'):
start_json['depends'][depends_name] = {
'pluginresult': plugins[depends_name]['pluginresult'],
'version': plugins[depends_name].get('version', ''),
'pluginresult_path': plugins[depends_name].get('results_dir')
}
# prepare for launch: updates config, sets pluginresults status, generates api key
pr.prepare()
# perform the validation of the plugin configuration here
pr.validation_errors = {
'validation_errors': Plugin.validate(p['id'], start_json['pluginconfig'], run_mode)
}
pr.save()
if pr.validation_errors.get('validation_errors', list()):
continue
# update startplugin json with pluginresult info
start_json['runinfo']['pluginresult'] = pr.pk
start_json['runinfo']['api_key'] = pr.apikey
# NOTE: Job is held on start, and subsequently released
# to avoid any race condition on updating job queue status
# launch plugin
jid = SGEPluginJob(start_json, hold=True)
if jid:
# Update pluginresult status
prj, created = PluginResultJob.objects.get_or_create(
plugin_result=pr,
run_level=runlevel,
grid_engine_jobid=jid,
state='Queued',
config=start_json['pluginconfig'],
)
prj.save()
# Release now that jobid and queued state are set.
_session.control(jid, drmaa.JobControlAction.RELEASE) # no return value
msg += 'Plugin: %s result: %s, jid %s, depends %s, holding for %s \n' % (p.get('name', ''), result.resultsName, jid, p.get('depends', []), holding_for)
if runlevel != RunLevel.BLOCK:
p['jid'] = jid
else:
p.setdefault('block_jid', []).append(jid)
except Exception as exc:
logger.error(traceback.format_exc())
msg += 'ERROR: Plugin %s failed to launch.\n' % p['name']
pr = PluginResult.objects.get(pk=pr.pk)
except:
logger.error(traceback.format_exc())
msg += 'ERROR: Failed to launch requested plugins.'
return plugins, msg