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wfmng.py
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# Copyright (C) 2012 SCS srl <info@scsitaly.com>
"""
The **Workflow Manager** is a core *Hypermodel* Application.
It maps workflows and users, manages sessions, serializes workflows and
logs. Is the frontend for all other hypermodel application.
"""
import sys
import os
import smtplib
from datetime import datetime, timedelta
import argparse
from email.mime.text import MIMEText
from raven.contrib.flask import Sentry
from flask import Flask, render_template
try:
from flaskext.xmlrpc import XMLRPCHandler
except ImportError, e:
from flask.ext.xmlrpc import XMLRPCHandler
try:
from flaskext.sqlalchemy import SQLAlchemy
except ImportError, e:
from flask.ext.sqlalchemy import SQLAlchemy
try:
from flaskext.login import *
except ImportError, e:
from flask.ext.login import *
from flask.ext.login import UserMixin, login_required
from auth import extractUserFromTicket
import requests
# requirements for createOutputFolders
import xmltodict
import string
import base64
from cyfronet import easywebdav
from cfinterface import CloudFacadeInterface
import time
############################################################################
# create and configure main application
app = Flask(__name__)
# read configuration file
if os.path.exists("local.wfmng.cfg"):
app.config.from_pyfile("local.wfmng.cfg")
else:
app.config.from_pyfile("wfmng.cfg")
############################################################################
# connect xmlrpc handler to app
xmlrpc = XMLRPCHandler("xmlrpc")
xmlrpc.connect(app, '/api')
############################################################################
# create the Cloud server connector
serverManager = CloudFacadeInterface(app.config["CLOUDFACACE_URL"])
############################################################################
# configure database
# app.config['SQLALCHEMY_DATABASE_URI'] =
# 'postgresql://tiger:scot@localhost/wfmng'
# SQLAlchemy Database Connector
db = SQLAlchemy(app)
sentry = Sentry(app, dsn=app.config["SENTRY_DNS"])
class Workflow(db.Model):
"""
This class represents a Workfow into the database
Fields:
**workflowId** (string): the workflow unique identifier (primary key)
username (string): the workflow owner
title (string): the workflow title
status (string): the workflow status
createTime (string): the creation time iso-format string
startTime (string): the start time iso-format string
finishTime (string): the finish time iso-format string
expiry (string): the expiration time iso-format string
exitcode (string): the taverna command line exit code
stdout (string): the taverna command line standard out stream
stderr (string): the taverna command line standard error stream
output (string): xml document specifying the workflow outputs
"""
workflowRunId = db.Column(db.String(80), primary_key=True)
username = db.Column(db.String(80), primary_key=False)
title = db.Column(db.String(120), primary_key=False)
status = db.Column(db.String(20), primary_key=False)
createTime = db.Column(db.String(30), primary_key=False)
startTime = db.Column(db.String(30), primary_key=False)
finishTime = db.Column(db.String(30), primary_key=False)
expiry = db.Column(db.String(30), primary_key=False)
exitcode = db.Column(db.String(5), primary_key=False)
stdout = db.Column(db.String(2048), primary_key=False)
stderr = db.Column(db.String(2048), primary_key=False)
outputfolder = db.Column(db.String(2048), primary_key=False)
output = db.Column(db.String(2048), primary_key=False)
def __init__(self,
username,
workflowId,
title,
outputfolder,
status="Initialized",
createTime="",
startTime="",
finishTime="",
expiry="",
exitcode="",
stdout="",
stderr="",
output=""):
self.username = username
self.workflowRunId = workflowId
self.title = title
self.status = status
self.createTime = createTime
self.startTime = startTime
self.finishTime = finishTime
self.expiry = expiry
self.exitcode = exitcode
self.stdout = stdout
self.stderr = stderr
self.outputfolder = outputfolder
self.output = output
def __repr__(self):
return '<Workflow %r-%r>' % (self.username, self.workflowId)
def toDictionary(self):
""" return a dictionary with the given workflow """
ret = {'workflowId': self.workflowId,
'status': self.status,
'title': self.title,
'createTime': self.createTime,
'startTime': self.startTime,
'finishTime': self.finishTime,
'expiry': self.expiry,
'exitcode': self.exitcode,
'stdout': self.stdout,
'stderr': self.stderr,
'owner': self.username,
'outputfolder': self.outputfolder,
'output': self.output}
return ret
def update(self, d):
""" update the worfklow according to the given dictionary """
for key in dir(self):
if key in d:
setattr(self, key, d[key])
class SessionCache(db.Model):
""" This class caches a session item into the database.
It is not used for authentication purpose, it only caches useful information.
Fields:
**username** (string): the user identifier (primary key)
email (string): the user email address
tkt (string): the authentication ticket
"""
username = db.Column(db.String(80), primary_key=True)
email = db.Column(db.String(80), primary_key=False)
tkt = db.Column(db.String(), primary_key=False)
def __init__(self, username, email, tkt):
self.username = username
self.email = email
self.tkt = tkt
def __repr__(self):
return '<UserCache %r-%r>' % (self.username, self.tkt)
class Execution(db.Model):
username = db.Column(db.String(80), primary_key=False)
eid = db.Column(db.Integer(), primary_key=True)
status = db.Column(db.Integer(), primary_key=False)
tavernaId = db.Column(db.String(80), primary_key=False)
workflowRunId = db.Column(db.String(80), primary_key=False)
error = db.Column(db.Boolean(), primary_key=False)
error_msg = db.Column(db.String(80), primary_key=False)
def __init__(self,
username,
eid,
status=0,
tavernaId='',
workflowRunId=''):
self.username = username
self.eid = eid
self.status = status
self.tavernaId = tavernaId
self.workflowRunId = workflowRunId
self.error = False
self.error_msg = ''
class TavernaServer(db.Model):
""" This class represents a Taverna Server workflow (i.e. a workflow containing an AS running a Taverna Server) in the database
Fields:
**username** (string): the user identifier (primary key)
**url** (string): url for the web endpoint of the server
**workflowId** (string): id of the workflow containing the Taverna Server
**asConfigId** (string): configuration id of the atomic service running the server
**count** (integer): number of workflows running in the server at a given time
"""
username = db.Column(db.String(80), primary_key=True)
url = db.Column(db.String(80), primary_key=True)
workflowId = db.Column(db.String(80), primary_key=True)
asConfigId = db.Column(db.String(80), primary_key=True)
userAndPass = db.Column(db.String(80), primary_key=True)
tavernaServerCloudId = db.Column(db.String(80), primary_key=True)
valid = db.Column(db.Boolean())
def __init__(self,
username,
endpoint,
workflowId,
asConfigId,
tavernaServerCloudId,
tavernaUser='taverna',
tavernaPass='taverna'):
self.username = username
self.url = endpoint
self.workflowId = workflowId
self.asConfigId = asConfigId
self.userAndPass = base64.b64encode(tavernaUser + ":" + tavernaPass)
self.tavernaServerCloudId = tavernaServerCloudId
self.valid = False
def isAlive(self):
response = requests.get(
self.url,
headers={
'Authorization': 'Basic %s' % self.userAndPass,
'Accept': 'application/json'
},
verify=False)
if response.status_code == 200:
return True
return False
def isWorkflowAlive(self, wfRunId):
response = requests.get(
"%s/%s" % (self.url, wfRunId),
headers={
'Authorization': 'Basic %s' % self.userAndPass,
'Accept': 'application/json'
},
verify=False)
if response.status_code == 200:
return True
return False
def getWorkflowRunNumber(self):
response = requests.get(
"%s" % (self.url),
headers={
'Authorization': 'Basic %s' % self.userAndPass,
'Accept': 'application/json'
},
verify=False)
if response.status_code == 200:
ret = response.json()
if ret['runList'] == "":
return 0
listWf = ret['runList'].get('run', False)
if listWf:
if type(listWf) is list:
return len(listWf)
else:
return 1
return 0
def createWorkflow(self, workflowDefinition):
""" Create a new workflow according to the given definition string.
Arguments:
workflowDefinition (string): the workflow definition file string buffer
Returns:
dictionary::
Success -- 'workflow run id'
Failure -- raise Exception with possible error message
"""
wf = workflowDefinition
response = requests.post(
self.url,
data=wf,
headers={
'Content-type': 'application/vnd.taverna.t2flow+xml',
'Authorization': 'Basic %s' % self.userAndPass,
#'Accept': 'application/json'
},
allow_redirects=False,
verify=False)
if response.status_code in [201, 200]:
# workflow has been correctly created
wfRunId = response.headers['location'].split("/")[-1]
#wfRunId = response.url.split("/")[-1]
return wfRunId
raise Exception("Submitting workflow failed " + response.text)
def setPlugins(self, wfRunId, pluginDefinition):
""" Takes the contents of a plugin.xml file, and then creates this file in the server
Arguments:
workflowId (string): the workflow unique identifier
pluginDefinition (string): the plugin definition file string buffer
Returns:
dictionary::
Success -- True
Failure -- raise errors with message
"""
plugins = """<t2sr:upload t2sr:name="plugins.xml" xmlns:t2sr="http://ns.taverna.org.uk/2010/xml/server/rest/">%s</t2sr:upload>""" % base64.b64encode(
pluginDefinition)
response = requests.post(
"%s/%s/wd/plugins" % (self.url, wfRunId),
data=plugins,
headers={
"Content-type": "application/xml",
'Authorization': 'Basic %s' % self.userAndPass
},
allow_redirects=True,
verify=False)
if response.status_code == 201:
return True
raise Exception("Plugin setting failed " + response.text)
def setPluginProperties(self, wfRunId, propertiesFileName,
propertiesDefinition):
""" Creates a properties file with the specified filename and content, and uploads the file to the server
Arguments:
workflowId (string): the workflow unique identifier
propertiesFileName (string): the name of the properties file to be created
propertiesDefinition (string): the content of the properties file
Returns:
dictionary::
Success -- True
Failure -- Raise exception with message
"""
properties = """<t2sr:upload t2sr:name="%s" xmlns:t2sr="http://ns.taverna.org.uk/2010/xml/server/rest/">%s</t2sr:upload>""" % (
propertiesFileName, base64.b64encode(propertiesDefinition))
response = requests.post(
"%s/%s/wd/conf" % (self.url, wfRunId),
data=properties,
headers={
"Content-type": "application/xml",
'Authorization': 'Basic %s' % self.userAndPass
},
allow_redirects=True,
verify=False)
if response.status_code == 201:
return True
raise Exception("Plugin properties setting failed " + response.text)
def setTicket(self, wfRunId, ticket):
""" Stores the specified ticket in the working directory of the workflow with the specified id
Arguments:
workflowId (string): the workflow unique identifier
ticket (string): a valid authentication ticket
Returns:
dictionary::
Success -- True
Failure -- raise Exception with message
"""
credential = """<t2sr:upload t2sr:name="ticket" xmlns:t2sr="http://ns.taverna.org.uk/2010/xml/server/rest/">%s</t2sr:upload>""" % base64.b64encode(
ticket)
response = requests.post(
"%s/%s/wd/conf" % (self.url, wfRunId),
data=credential,
headers={
"Content-type": "application/xml",
'Authorization': 'Basic %s' % self.userAndPass
},
allow_redirects=True,
verify=False)
if response.status_code == 201:
return True
raise Exception("Ticket setting failed " + response.text)
def setTrustedIdentity(self, wfRunId, identityFileName,
identityDefinition):
""" Takes the name of the certificate file, reads the contents of the file and submits the file contents to the server
Arguments:
workflowId (string): the workflow unique identifier
identityFileName (string): name of the certificate file
identityDefinition (string): contents of the certificate file
Returns:
dictionary::
Success -- True
Failure -- raise Exception with message
"""
identity = """<t2sr:trustedIdentity xmlns:t2sr="http://ns.taverna.org.uk/2010/xml/server/" xmlns:t2s="http://ns.taverna.org.uk/2010/xml/server/"><t2s:certificateFile>%s</t2s:certificateFile><t2s:certificateBytes>%s</t2s:certificateBytes></t2sr:trustedIdentity>""" % (
base64.b64encode(identityFileName),
base64.b64encode(identityDefinition))
response = requests.post(
"%s/%s/security/trusts" % (self.url, wfRunId),
data=identity,
headers={
"Content-type": "application/xml",
'Authorization': 'Basic %s' % self.userAndPass
},
allow_redirects=True,
verify=False)
if response.status_code == 201:
return True
raise Exception("Trusted Identity setting failed " + response.text)
def setWorkflowInputs(self, wfRunId, inputDefinition):
""" Take the inputs definition string and create a baclava.xml file for the workflow with the given id.
Arguments:
workflowId (string): the workflowd unique identifier
workflowDefinition (string): the workflow definition file string buffer
inputDefinition (string): the input definition file string buffer:param workflowId: the id unique identifier
defaultInputMap (map): a map with the default inputs to be added to all (i.e. defaultInputMap = {'sessionTicket': <sessionTicket<, 'workflowId': >workflowId>, ...}
Returns:
dictionary::
Success -- True
Failure -- Raise Exception with message
"""
try:
baclava = """<t2sr:upload xmlns:t2sr="http://ns.taverna.org.uk/2010/xml/server/rest/" t2sr:name="baclava.xml">%s</t2sr:upload>""" % base64.b64encode(
inputDefinition)
response = requests.post(
"%s/%s/wd" % (self.url, wfRunId),
data=baclava,
headers={
"Content-type": "application/xml",
'Authorization': 'Basic %s' % self.userAndPass
},
allow_redirects=True,
verify=False)
if response.status_code == 201:
# PUT baclava
response2 = requests.put(
"%s/%s/input/baclava" % (self.url, wfRunId),
headers={
"Content-type": "text/plain",
'Authorization': 'Basic %s' % self.userAndPass
},
data="baclava.xml", )
if response2.status_code == 200:
return True
raise Exception("Workflow input setting failed " + response.text)
except Exception, e:
print e
raise Exception("Workflow input setting failed " + response.text)
def getWorkflowInputs(self, wfRunId):
"""
Retrieve the workflow inputs file from taverna server
:param workflowId:
:return:
"""
response = requests.get(
"%s/%s/wd/baclava.xml" % (self.url, wfRunId),
headers={
'Accept':
'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8',
'Authorization': 'Basic %s' % self.userAndPass
},
allow_redirects=True,
verify=False)
if response.status_code == 200:
return response.text
return ""
def getWorkflowOutput(self, wfRunId, port):
"""
Retrieves the value of a workflow port from taverna server
:param workflowId:
:param port:
:return:
"""
response = requests.get(
"%s/%s/wd/out/%s" % (self.url, wfRunId, port),
headers={
'Accept':
'text/plain,text/html,application/xml;q=0.9,*/*;q=0.8',
'Authorization': 'Basic %s' % self.userAndPass
},
allow_redirects=True,
verify=False)
if response.status_code == 200:
return response.text
return ""
def enhanceWorkflowOutputs(self, wfRunId, outputXML):
"""
Return an improved and simpler version of the specified output XML
:param workflowId:
:param outputXML:
:return:
"""
out = ""
try:
outputXMLContent = xmltodict.parse(outputXML)
if u'port:absent' in outputXMLContent[u'port:workflowOutputs'][
u'port:output']:
return outputXMLContent[u'port:workflowOutputs'][
u'port:output'][u'@port:name'] + "="
if outputXMLContent[u'port:workflowOutputs'][u'port:output'][
u'@port:depth'] == u'0':
port = outputXMLContent[u'port:workflowOutputs'][
u'port:output']
out = port[u'@port:name'] + "="
value = self.getWorkflowOutput(wfRunId, port[u'@port:name'])
out = out + value
if outputXMLContent[u'port:workflowOutputs'][u'port:output'][
u'@port:depth'] == u'1':
port = outputXMLContent[u'port:workflowOutputs'][
u'port:output']
count = int(port['port:list']['@port:length'])
value = ""
for i in range(count):
if out != "":
out = out + ", "
out = out + port[u'@port:name'] + "="
value = self.getWorkflowOutput(
wfRunId, port[u'@port:name'] + "/" + str(i + 1))
out = out + value
except Exception, e:
pass
out = "Could not parse: " + outputXML
return out
def getWorkflowDefinition(self, wfRunId):
"""
Retrieve the workflow file from taverna server
:param workflowId:
:return:
"""
response = requests.get(
"%s/%s/workflow" % (self.url, wfRunId),
headers={
"Content-type": "text/plain",
'Authorization': 'Basic %s' % self.userAndPass
},
allow_redirects=True,
verify=False)
if response.status_code == 200:
return response.text
return ""
def getRunInformations(self, wfRunId=''):
""" return the basic information associated to the given workflow id
Arguments:
workflowId (string): the workflow unique identifier
Returns:
dictionary::
Success -- {'workflowId':'a string value', 'info01':'a string value', 'info02':'a string value',..}
Failure -- {'workflowId':'', 'error.description':'', error.code:''}
"""
ret = {
'status': '',
'createTime': '',
'startTime': '',
'finishTime': '',
'expiry': '',
'exitcode': '',
'stdout': '',
'stderr': '',
'outputfolder': '',
'endpoint': '',
'workflowId': '',
'asConfigId': '',
'tavernaRunning': '',
'owner': '',
'wfRunning': '',
'output': ''
}
ret['endpoint'] = self.url
ret['workflowId'] = self.workflowId
ret['asConfigId'] = self.asConfigId
ret['tavernaRunning'] = self.isAlive()
ret['owner'] = self.username
if wfRunId:
wfJob = Workflow.query.filter_by(workflowRunId=wfRunId).first()
ret['wfRunning'] = self.isWorkflowAlive(wfRunId)
if wfJob:
ret['outputfolder'] = wfJob.outputfolder
else:
ret['wfRunning'] = False
return ret
if ret['wfRunning']:
infos = ["status", "createTime", "expiry", "startTime",
"finishTime"]
for info in infos:
headers = {"Content-type": "text/plain",
'Authorization': 'Basic %s' % self.userAndPass}
ret[info] = self.getInfo(wfRunId, info, headers)
additional_info = {'stderr': "listeners/io/properties/stderr",
'stdout': "listeners/io/properties/stdout",
'exitcode': "listeners/io/properties/exitcode"}
for info in additional_info.keys():
ret[info] = self.getInfo(wfRunId, additional_info[info],
headers)
headers = {"Content-type": "text/plain",
'Authorization': 'Basic %s' % self.userAndPass,
'Accept': 'application/xml'}
out = self.getInfo(wfRunId, "output", headers)
if out != "":
enhanced = self.enhanceWorkflowOutputs(wfRunId, out)
if len(enhanced) >= len(wfJob.output):
ret['output'] = enhanced # enhanced outputs should increase in lenght with time. A decrease is an indication of a prossible synchronization problem.
else:
ret['output'] = wfJob.output # when in doubt, use the previous value
else:
ret['output'] = wfJob.output
if wfJob:
wfJob.update(ret)
db.session.commit()
elif wfJob:
ret.update({
'status': wfJob.status,
'createTime': wfJob.createTime,
'startTime': wfJob.startTime,
'finishTime': wfJob.finishTime,
'expiry': wfJob.expiry,
'exitcode': wfJob.exitcode,
'stdout': wfJob.stdout,
'stderr': wfJob.stderr,
'outputfolder': wfJob.outputfolder,
'output': wfJob.output
})
return ret
def getInfo(self, wfRunId, info, headers):
""" return the workflow id requested info as a string
Arguments:
wfRunId (string): the workflow unique identifier
info (string): code name for the information requested
headers (string): headers for the GET operation
Returns:
string. The requested info as a string
"""
response = requests.get('%s/%s/%s' % (self.url, wfRunId, info),
headers=headers,
verify=False)
if response.status_code == 200:
return response.content
return ""
def startWorkflow(self, wfRunId):
""" start the workflow with the given workflow id
Arguments:
workflowId (string): the workflow unique identifier
Returns:
dictionary::
Success -- Ture
Failure -- False
"""
response = requests.put(
"%s/%s/status" % (self.url, wfRunId),
data="Operating",
headers={
"Content-type": "text/plain",
'Authorization': 'Basic %s' % self.userAndPass
},
verify=False)
if response.status_code in [200, 201, 202]:
return True
raise Exception('Error starting workflow on Taverna Server %s' %
response.status_code)
def setExpiry(self, wfRunId, expiry):
""" set a new expiry date
Arguments:
wfRunId (string): the workflow run unique identifier
Returns:
dictionary::
Success -- {'workflowId':'a string value', 'info01':'a string value', 'info02':'a string value',..}
Failure -- {'workflowId':'', 'error.description':'', error.code:''}
"""
response = requests.put(
"%s/%s/expiry" % (self.url, wfRunId),
data=expiry,
headers={
"Content-type": "text/plain",
'Authorization': 'Basic %s' % self.userAndPass
},
verify=False)
if response.status_code in [200, 201, 202]:
return True
return False
def deleteWorkflow(self, wfRunId):
""" delete the workflow with the given workflow id
Arguments:
workflowId (string): the workflow unique identifier
Returns:
dictionary::
Success -- True
Failure -- False
"""
if self.isWorkflowAlive(wfRunId):
response = requests.delete(
"%s/%s" % (self.url, wfRunId),
headers={
"Content-type": "text/plain",
'Authorization': 'Basic %s' % self.userAndPass
},
verify=False)
if response.status_code == 204:
return True
else:
return True
return False
def toDictionary(self):
""" return a dictionary with object properties"""
return {'username': self.username,
'url': self.url,
'workflowId': self.workflowId,
'asConfigId': self.asConfigId,
'count': self.count}
############################################################################
# html methods
@app.route("/")
def hello():
""" index method return the application title
Routed at: "/"
"""
return "Welcome to the VPH-Share Workflow Manager Application"
############################################################################
# utility methods
def alert_user_by_email(mail_from,
mail_to,
subject,
mail_template,
dictionary={}):
"""
Send an email to the user with the given template
This method will be replaced by the Master Interface notification service
"""
msg = MIMEText(render_template(mail_template, **dictionary), 'html')
msg['Subject'] = subject
msg['From'] = mail_from
msg['To'] = mail_to
try:
s = smtplib.SMTP(app.config.get('SMTP_HOST', '') or 'localhost')
s.sendmail(mail_from, mail_to, msg.as_string())
s.quit()
except BaseException, e:
pass
def notify_user_by_mi():
"""
send a notification message that will be shown to the Master interface
"""
def submition_work_around(execution, server, ticket, tavernaURL,
workflowDefinition):
workflow_worker_built_failed = True
while workflow_worker_built_failed:
serverManager.deleteWorkflow(server.workflowId, ticket)
server.valid = False
db.session.commit()
tavernaServerId = serverManager.createWorkflow(ticket)
atomicServiceConfigId = serverManager.getAtomicServiceConfigId(
server.tavernaServerCloudId, ticket)
if tavernaServerId and atomicServiceConfigId:
print "retry::Taverna Server id %s, atomic config id %s" % (
str(tavernaServerId), str(atomicServiceConfigId))
appliance_configuration_instance_id = serverManager.startAtomicService(
atomicServiceConfigId, tavernaServerId, ticket)
if appliance_configuration_instance_id:
endpoint = app.config["CLOUDFACACE_PROXY_ENDPOINT"] % str(
appliance_configuration_instance_id)
if endpoint:
if tavernaURL is not "":
endpoint = tavernaURL
print "retry::Taverna Server endpoint %s" % endpoint
# now it can be created Taverna server instance
server.url = endpoint
server.workflowId = tavernaServerId
server.asConfigId = atomicServiceConfigId
execution.tavernaId = tavernaServerId
db.session.commit()
else:
raise Exception('Error booting Taverna server')
else:
raise Exception('Error starting Atomic service')
else:
raise Exception('Error contacting cloud facade service')
timeout = 50
while server.isAlive() is not True and timeout > 0:
timeout -= 1
time.sleep(5)
if timeout == 0:
raise Exception('Taverna Server is not reachable.')
try:
return server.createWorkflow(workflowDefinition)
except Exception, e:
## here start the implementation of the workaround
# the workaround restart anytime the Taverna Server in the cloud
# until the WM is not able to submit the workflow.
sentry.captureException()
workflow_worker_built_failed = (
e.message ==
"Submitting workflow failed failed to build workflow run worker"
)
raise Exception("Submitting workflow failed")
############################################################################
# xmlrpc methods
def execute_workflow(ticket,
eid,
workflowTitle,
tavernaServerCloudId,
workflowDefinition,
inputDefinition,
tavernaURL="",
submitionWorkAround=False):
user = extractUserFromTicket(ticket)
execution = Execution.query.filter_by(username=user['username'],
eid=eid).first()
if execution is not None:
#reset execution before start
deleteExecution(eid, ticket)
execution = Execution(user['username'], eid)
db.session.add(execution)
db.session.commit()
#Now we don't have a stable taverna server then we have to create a new one for every execution
server = TavernaServer.query.filter_by(
username=user['username'],
tavernaServerCloudId=tavernaServerCloudId,
valid=True).first()
# remeber try execept
try:
if server is None or server.isAlive() is not True:
#if the server is not avaible ask to the cloud to start a new one
tavernaServerId = serverManager.createWorkflow(ticket)
atomicServiceConfigId = serverManager.getAtomicServiceConfigId(
tavernaServerCloudId, ticket)
if tavernaServerId and atomicServiceConfigId:
execution.status = 1
print "Taverna Server id %s, atomic config id %s" % (
str(tavernaServerId), str(atomicServiceConfigId))
db.session.commit()
appliance_configuration_instance_id = serverManager.startAtomicService(
atomicServiceConfigId, tavernaServerId, ticket)
if appliance_configuration_instance_id:
execution.status = 2
db.session.commit()
endpoint = app.config["CLOUDFACACE_PROXY_ENDPOINT"] % str(
appliance_configuration_instance_id)
if endpoint:
if tavernaURL is not "":
endpoint = tavernaURL
print "Taverna Server endpoint %s" % endpoint
# now it can be created Taverna server instance
server = TavernaServer(
user['username'], endpoint, tavernaServerId,
atomicServiceConfigId, tavernaServerCloudId)
execution.tavernaId = tavernaServerId
execution.status = 3
db.session.add(server)
db.session.commit()
else:
raise Exception('Error booting Taverna server')
else: