def SGEPluginJob(start_json):
"""
Spawn a thread that will start a SGE job, and wait for it to return
after it has return it will make a PUT the API using to update the status
of the run
args is a dict of all the args that are needed by for the plugin to run
"""
try:
os.umask(0000)
# Query some essential values
plugin = start_json['runinfo']['plugin']
resultpk = start_json['runinfo']['pk']
analysis_name = os.path.basename(start_json['runinfo']['analysis_dir'])
plugin_output = start_json['runinfo']['results_dir']
logger.debug("Getting ready for queue : %s %s", resultpk,
plugin['name'])
# Update pluginresult status
h = httplib2.Http()
headers = {
"Content-type": "application/json",
"Accept": "application/json"
}
url = 'http://localhost' + '/rundb/api/v1/results/%s/plugin/' % resultpk
data = {
plugin['name']: "Pending",
'owner': start_json.get('owner', None),
}
resp, content = h.request(url,
"PUT",
body=json.dumps(data),
headers=headers)
logger.debug("PluginResult Marked Queued : %s %s" % (resp, content))
#Make sure the dirs exist
if not os.path.exists(plugin_output):
os.makedirs(plugin_output, 0775)
# Write start_json to startplugin.json file.
startpluginjson = os.path.join(plugin_output, 'startplugin.json')
with open(startpluginjson, "w") as fp:
json.dump(start_json, fp, indent=2)
# Branch for launch.sh vs 3.0 plugin class
logger.debug("Finding plugin definition: '%s':'%s'", plugin['name'],
plugin['path'])
(launch,
isCompat) = pluginmanager.find_pluginscript(plugin['path'],
plugin['name'])
if not launch or not os.path.exists(launch):
logger.error(
"Analysis: %s. Path to plugin script: '%s' Does Not Exist!",
analysis_name, launch)
return 1
# Create individual launch script from template and plugin launch.sh
launcher = PluginRunner()
if isCompat:
launchScript = launcher.createPluginWrapper(launch, start_json)
else:
start_json.update({'command': ["python %s -vv" % launch]})
launchScript = launcher.createPluginWrapper(None, start_json)
launchWrapper = launcher.writePluginLauncher(plugin_output,
plugin['name'],
launchScript)
launcher.writePluginJson(start_json)
# Prepare drmaa Job - SGE/gridengine only
jt = _session.createJobTemplate()
jt.nativeSpecification = " -q %s" % ("plugin.q")
if constants.Feature.EXPORT in plugin['features']:
jt.nativeSpecification += ' -l ep=1 '
hold = plugin.get('hold_jid', [])
if hold:
jt.nativeSpecification += " -hold_jid " + ','.join(
str(jobid) for jobid in hold)
jt.workingDirectory = plugin_output
jt.outputPath = ":" + os.path.join(plugin_output, "drmaa_stdout.txt")
jt.joinFiles = True # Merge stdout and stderr
# Plugin command is: ion_pluginname_launch.sh -j startplugin.json
jt.remoteCommand = launchWrapper
jt.args = ["-j", startpluginjson]
# Submit the job to drmaa
jobid = _session.runJob(jt)
# Update pluginresult status
h = httplib2.Http()
headers = {
"Content-type": "application/json",
"Accept": "application/json"
}
url = 'http://localhost' + '/rundb/api/v1/results/%s/plugin/' % resultpk
resp, content = h.request(url,
"PUT",
body=json.dumps({plugin['name']: "Queued"}),
headers=headers)
logger.debug("PluginResult Marked Queued : %s %s" % (resp, content))
logger.info("Analysis: %s. Plugin: %s. Job: %s Queued." %
(analysis_name, plugin['name'], jobid))
_session.deleteJobTemplate(jt)
return jobid
except:
logger.critical("SGEPluginJob method failure")
logger.critical(traceback.format_exc())
def unzipPlugin(zipfile, logger=None):
if not logger:
logger = logging.getLogger(__name__)
## Extract plugin to scratch folder. When complete, move to final location.
plugin_path, ext = os.path.splitext(zipfile)
plugin_name = os.path.basename(plugin_path)
# ZIP file must named with plugin name - fragile
# FIXME - handle (1) additions (common for multiple downloads via browser)
# FIXME - handle version string in ZIP archive name
scratch_path = os.path.join(settings.PLUGIN_PATH, "scratch",
"install-temp", plugin_name)
(prefix, files) = extract_zip(zipfile,
scratch_path,
auto_prefix=True,
logger=logger)
if prefix:
plugin_name = os.path.basename(prefix)
plugin_temp_home = os.path.join(scratch_path, prefix)
try:
# Convert script into PluginClass, get info by introspection
from iondb.plugins.manager import pluginmanager
script, islaunch = pluginmanager.find_pluginscript(
plugin_temp_home, plugin_name)
logger.debug("Got script: %s", script)
from ion.plugin.loader import cache
ret = cache.load_module(plugin_name, script)
cls = cache.get_plugin(plugin_name)
p = cls()
final_name = p.name # what the plugin calls itself, regardless of ZIP file name
logger.info("Plugin calls itself: '%s'", final_name)
except:
logger.exception("Unable to interrogate plugin name from: '%s'",
zipfile)
final_name = plugin_name
#move to the plugin dir
# New extract_zip removes prefix from extracted files.
# But still writes to file_name
try:
final_install_dir = os.path.join(settings.PLUGIN_PATH, final_name)
if os.path.exists(final_install_dir) and (final_install_dir !=
settings.PLUGIN_PATH):
logger.info("Deleting old copy of plugin at '%s'",
final_install_dir)
delete_that_folder(
final_install_dir,
"Error Deleting old copy of plugin at '%s'" %
final_install_dir)
parent_folder = os.path.dirname(final_install_dir)
if not os.path.exists(parent_folder):
logger.info("Creating path for plugin '%s' for '%s'",
parent_folder, final_install_dir)
os.makedirs(parent_folder, 0555)
logger.info(
"Moving plugin from temp extract folder '%s' to final location: '%s'",
plugin_temp_home, final_install_dir)
shutil.move(plugin_temp_home, final_install_dir)
delete_that_folder(scratch_path,
"Deleting plugin install scratch folder")
except (IOError, OSError):
logger.exception(
"Failed to move plugin from temp extract folder '%s' to final location: '%s'",
plugin_temp_home, final_install_dir)
raise
# Now that it has been downloaded,
# convert pre-plugin into real db plugin object
try:
from iondb.plugins.manager import pluginmanager
(new_plugin, updated) = pluginmanager.install(final_name,
final_install_dir)
except ValueError:
logger.exception("Failed to install plugin")
#delete_that_folder(final_install_dir)
return {
"plugin": final_name,
"path": final_install_dir,
"files": files,
}
def unzipPlugin(zipfile, logger=None):
if not logger:
logger = logging.getLogger(__name__)
## Extract plugin to scratch folder. When complete, move to final location.
plugin_path, ext = os.path.splitext(zipfile)
plugin_name = os.path.basename(plugin_path)
# ZIP file must named with plugin name - fragile
# FIXME - handle (1) additions (common for multiple downloads via browser)
# FIXME - handle version string in ZIP archive name
scratch_path = os.path.join(settings.PLUGIN_PATH,"scratch","install-temp",plugin_name)
(prefix, files) = extract_zip(zipfile, scratch_path, auto_prefix=True, logger=logger)
if prefix:
plugin_name = os.path.basename(prefix)
plugin_temp_home = os.path.join(scratch_path, prefix)
try:
# Convert script into PluginClass, get info by introspection
from iondb.plugins.manager import pluginmanager
script, islaunch = pluginmanager.find_pluginscript(plugin_temp_home, plugin_name)
logger.debug("Got script: %s", script)
from ion.plugin.loader import cache
ret = cache.load_module(plugin_name, script)
cls = cache.get_plugin(plugin_name)
p = cls()
final_name = p.name # what the plugin calls itself, regardless of ZIP file name
logger.info("Plugin calls itself: '%s'", final_name)
except:
logger.exception("Unable to interrogate plugin name from: '%s'", zipfile)
final_name = plugin_name
#move to the plugin dir
# New extract_zip removes prefix from extracted files.
# But still writes to file_name
try:
final_install_dir = os.path.join(settings.PLUGIN_PATH, final_name)
if os.path.exists(final_install_dir) and (final_install_dir != settings.PLUGIN_PATH):
logger.info("Deleting old copy of plugin at '%s'", final_install_dir)
delete_that_folder(final_install_dir, "Error Deleting old copy of plugin at '%s'" % final_install_dir)
parent_folder = os.path.dirname(final_install_dir)
if not os.path.exists(parent_folder):
logger.info("Creating path for plugin '%s' for '%s'", parent_folder, final_install_dir)
os.makedirs(parent_folder, 0555)
logger.info("Moving plugin from temp extract folder '%s' to final location: '%s'", plugin_temp_home, final_install_dir)
shutil.move(plugin_temp_home, final_install_dir)
delete_that_folder(scratch_path, "Deleting plugin install scratch folder")
except (IOError, OSError):
logger.exception("Failed to move plugin from temp extract folder '%s' to final location: '%s'", plugin_temp_home, final_install_dir)
raise
# Now that it has been downloaded,
# convert pre-plugin into real db plugin object
try:
from iondb.plugins.manager import pluginmanager
(new_plugin, updated) = pluginmanager.install(final_name, final_install_dir)
except ValueError:
logger.exception("Failed to install plugin")
#delete_that_folder(final_install_dir)
return {
"plugin": final_name,
"path": final_install_dir,
"files": files,
}
def SGEPluginJob(start_json, hold=False):
"""
Spawn a thread that will start a SGE job, and wait for it to return
after it has return it will make a PUT the API using to update the status
of the run
args is a dict of all the args that are needed by for the plugin to run
"""
try:
os.umask(0000)
plugin_output = start_json['runinfo']['results_dir']
#Make sure the dirs exist
if not os.path.exists(plugin_output):
os.makedirs(plugin_output, 0775)
plugin = start_json['runinfo']['plugin']
logger.info("Preparing for SGE submission - plugin %s --v%s on result %s (%s)",
plugin['name'], plugin['version'], start_json['expmeta']['results_name'], start_json['runinfo']['pk'])
# Branch for launch.sh vs 3.0 plugin class
#logger.debug("Finding plugin definition: '%s':'%s'", plugin['name'], plugin['path'])
(launch, isCompat) = pluginmanager.find_pluginscript(plugin['path'], plugin['name'])
analysis_name = os.path.basename(start_json['runinfo']['analysis_dir'])
if not launch or not os.path.exists(launch):
logger.error("Analysis: %s. Path to plugin script: '%s' Does Not Exist!", analysis_name, launch)
return 1
# Create individual launch script from template and plugin launch.sh
launcher = PluginRunner()
if isCompat:
launchScript = launcher.createPluginWrapper(launch, start_json)
else:
start_json.update({'command': ["python %s -vv" % launch]})
launchScript = launcher.createPluginWrapper(None, start_json)
launchWrapper = launcher.writePluginLauncher(plugin_output, plugin['name'], launchScript)
# Returns filename of startpluginjson file, passed to script below
startpluginjson = launcher.writePluginJson(start_json)
# Prepare drmaa Job - SGE/gridengine only
jt = _session.createJobTemplate()
jt.nativeSpecification = " -q %s" % ("plugin.q")
if Feature.EXPORT in plugin['features']:
jt.nativeSpecification += ' -l ep=1 '
hold_jid = plugin.get('hold_jid', [])
if hold_jid:
jt.nativeSpecification += " -hold_jid " + ','.join(str(jobid) for jobid in hold_jid)
jt.workingDirectory = plugin_output
jt.outputPath = ":" + os.path.join(plugin_output, "drmaa_stdout.txt")
jt.joinFiles = True # Merge stdout and stderr
# Plugin command is: ion_pluginname_launch.sh -j startplugin.json
jt.remoteCommand = launchWrapper
jt.args = [ "-j", startpluginjson ]
if hold:
jt.jobSubmissionState = drmaa.JobSubmissionState.HOLD_STATE
# Submit the job to drmaa
jobid = _session.runJob(jt)
logger.info("Analysis: %s. Plugin: %s. Job: %s Queued." % (analysis_name, plugin['name'], jobid))
_session.deleteJobTemplate(jt)
return jobid
except:
logger.exception("SGEPluginJob method failure")
raise
def SGEPluginJob(start_json):
"""
Spawn a thread that will start a SGE job, and wait for it to return
after it has return it will make a PUT the API using to update the status
of the run
args is a dict of all the args that are needed by for the plugin to run
"""
try:
os.umask(0000)
# Query some essential values
plugin = start_json['runinfo']['plugin']
resultpk = start_json['runinfo']['pk']
analysis_name = os.path.basename(start_json['runinfo']['analysis_dir'])
plugin_output = start_json['runinfo']['results_dir']
logger.debug("Getting ready for queue : %s %s", resultpk, plugin['name'])
#Make sure the dirs exist
if not os.path.exists(plugin_output):
os.makedirs(plugin_output, 0755)
# Write start_json to startplugin.json file.
startpluginjson = os.path.join(plugin_output,'startplugin.json')
with open(startpluginjson,"w") as fp:
json.dump(start_json,fp,indent=2)
# Branch for launch.sh vs 3.0 plugin class
logger.debug("Finding plugin definition: '%s':'%s'", plugin['name'], plugin['path'])
(launch, isCompat) = pluginmanager.find_pluginscript(plugin['path'], plugin['name'])
if not launch or not os.path.exists(launch):
logger.error("Analysis: %s. Path to plugin script: '%s' Does Not Exist!", analysis_name, launch)
return 1
# Create individual launch script from template and plugin launch.sh
launcher = PluginRunner()
if isCompat:
launchScript = launcher.createPluginWrapper(launch, start_json)
else:
start_json.update({'command': ["python %s -vv" % launch]})
launchScript = launcher.createPluginWrapper(None, start_json)
launchWrapper = launcher.writePluginLauncher(plugin_output, plugin['name'], launchScript)
launcher.writePluginJson(start_json)
# Prepare drmaa Job - SGE/gridengine only
jt = _session.createJobTemplate()
jt.nativeSpecification = " -q %s" % ("plugin.q")
hold = plugin.get('hold_jid', [])
if hold:
jt.nativeSpecification += " -hold_jid " + ','.join(str(jobid) for jobid in hold)
jt.workingDirectory = plugin_output
jt.outputPath = ":" + os.path.join(plugin_output, "drmaa_stdout.txt")
jt.joinFiles = True # Merge stdout and stderr
# Plugin command is: ion_pluginname_launch.sh -j startplugin.json
jt.remoteCommand = launchWrapper
jt.args = [ "-j", startpluginjson ]
# Submit the job to drmaa
jobid = _session.runJob(jt)
# Update pluginresult status
h = httplib2.Http()
headers = {"Content-type": "application/json","Accept": "application/json"}
url = 'http://localhost' + '/rundb/api/v1/results/%s/plugin/' % resultpk
resp, content = h.request(url, "PUT", body=json.dumps({plugin['name']:"Queued"}), headers=headers)
logger.debug("PluginResult Marked Queued : %s %s" % (resp, content))
logger.info("Analysis: %s. Plugin: %s. Job: %s Queued." % (analysis_name, plugin['name'], jobid))
_session.deleteJobTemplate(jt)
return jobid
except:
logger.critical("SGEPluginJob method failure")
logger.critical(traceback.format_exc())
