1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/38d9e07b58aa/ changeset: 38d9e07b58aa user: dannon date: 2012-06-15 20:51:12 summary: Rename 'cloud' controller to 'cloudlaunch' to avoid name collisions -- Cloudman interface for cloud instances, and /cloud redirect on main. affected #: 3 files

diff -r 5f3e2ffbae695cd7ae56b2ce4e4c0ed1182e2051 -r 38d9e07b58aa99ded2604cdd1aab4ca0f8761aa6 lib/galaxy/web/controllers/cloud.py --- a/lib/galaxy/web/controllers/cloud.py +++ /dev/null @@ -1,220 +0,0 @@ -""" -Cloud Controller: handles all cloud interactions. - -Adapted from Brad Chapman and Enis Afgan's BioCloudCentral -BioCloudCentral Source: https://github.com/chapmanb/biocloudcentral - -""" - -import datetime -import logging -import time -from galaxy import eggs -import pkg_resources -pkg_resources.require('boto') -import boto -from galaxy import web -from galaxy.web.base.controller import BaseUIController -from boto.ec2.regioninfo import RegionInfo -from boto.exception import EC2ResponseError - -log = logging.getLogger(__name__) - -class CloudController(BaseUIController): - def __init__(self, app): - BaseUIController.__init__(self, app) - - @web.expose - def index(self, trans): - return trans.fill_template("cloud/index.mako") - - @web.expose - def launch_instance(self, trans, cluster_name, password, key_id, secret, instance_type): - ec2_error = None - try: - # Create security group & key pair used when starting an instance - ec2_conn = connect_ec2(key_id, secret) - sg_name = create_cm_security_group(ec2_conn) - kp_name, kp_material = create_key_pair(ec2_conn) - except EC2ResponseError, err: - ec2_error = err.error_message - if ec2_error: - return trans.fill_template("cloud/run.mako", error = ec2_error) - else: - user_provided_data={'cluster_name':cluster_name, - 'access_key':key_id, - 'secret_key':secret, - 'instance_type':instance_type} - if password: - user_provided_data['password'] = password - rs = run_instance(ec2_conn=ec2_conn, - user_provided_data=user_provided_data, - key_name=kp_name, - security_groups=[sg_name]) - if rs: - instance = rs.instances[0] - ct = 0 - while not instance.public_dns_name: - # Can take a second to have public dns name registered. - # DBTODO, push this into a page update, this is not ideal. - instance.update() - ct +=1 - time.sleep(1) - return trans.fill_template("cloud/run.mako", - instance = rs.instances[0], - kp_name = kp_name, - kp_material = kp_material) - else: - return trans.fill_template("cloud/run.mako", - error = "Instance failure, but no specific error was detected. Please check your AWS Console.") - -# ## Cloud interaction methods -def connect_ec2(a_key, s_key): - """ Create and return an EC2 connection object. - """ - # Use variables for forward looking flexibility - # AWS connection values - region_name = 'us-east-1' - region_endpoint = 'ec2.amazonaws.com' - is_secure = True - ec2_port = None - ec2_conn_path = '/' - r = RegionInfo(name=region_name, endpoint=region_endpoint) - ec2_conn = boto.connect_ec2(aws_access_key_id=a_key, - aws_secret_access_key=s_key, - api_version='2011-11-01', # needed for availability zone support - is_secure=is_secure, - region=r, - port=ec2_port, - path=ec2_conn_path) - return ec2_conn - -def create_cm_security_group(ec2_conn, sg_name='CloudMan'): - """ Create a security group with all authorizations required to run CloudMan. - If the group already exists, check its rules and add the missing ones. - Return the name of the created security group. - """ - cmsg = None - # Check if this security group already exists - sgs = ec2_conn.get_all_security_groups() - for sg in sgs: - if sg.name == sg_name: - cmsg = sg - log.debug("Security group '%s' already exists; will add authorizations next." % sg_name) - break - # If it does not exist, create security group - if cmsg is None: - log.debug("Creating Security Group %s" % sg_name) - cmsg = ec2_conn.create_security_group(sg_name, 'A security group for CloudMan') - # Add appropriate authorization rules - # If these rules already exist, nothing will be changed in the SG - ports = (('80', '80'), # Web UI - ('20', '21'), # FTP - ('22', '22'), # ssh - ('30000', '30100'), # FTP transfer - ('42284', '42284')) # CloudMan UI - for port in ports: - try: - if not rule_exists(cmsg.rules, from_port=port[0], to_port=port[1]): - cmsg.authorize(ip_protocol='tcp', from_port=port[0], to_port=port[1], cidr_ip='0.0.0.0/0') - else: - log.debug("Rule (%s:%s) already exists in the SG" % (port[0], port[1])) - except EC2ResponseError, e: - log.error("A problem with security group authorizations: %s" % e) - # Add rule that allows communication between instances in the same SG - g_rule_exists = False # Flag to indicate if group rule already exists - for rule in cmsg.rules: - for grant in rule.grants: - if grant.name == cmsg.name: - g_rule_exists = True - log.debug("Group rule already exists in the SG") - if g_rule_exists: - break - if g_rule_exists is False: - try: - cmsg.authorize(src_group=cmsg) - except EC2ResponseError, e: - log.error("A problem w/ security group authorization: %s" % e) - log.info("Done configuring '%s' security group" % cmsg.name) - return cmsg.name - -def rule_exists(rules, from_port, to_port, ip_protocol='tcp', cidr_ip='0.0.0.0/0'): - """ A convenience method to check if an authorization rule in a security - group exists. - """ - for rule in rules: - if rule.ip_protocol == ip_protocol and rule.from_port == from_port and \ - rule.to_port == to_port and cidr_ip in [ip.cidr_ip for ip in rule.grants]: - return True - return False - -def create_key_pair(ec2_conn, key_name='cloudman_key_pair'): - """ Create a key pair with the provided name. - Return the name of the key or None if there was an error creating the key. - """ - kp = None - # Check if a key pair under the given name already exists. If it does not, - # create it, else return. - kps = ec2_conn.get_all_key_pairs() - for akp in kps: - if akp.name == key_name: - log.debug("Key pair '%s' already exists; not creating it again." % key_name) - return akp.name, None - try: - kp = ec2_conn.create_key_pair(key_name) - except EC2ResponseError, e: - log.error("Problem creating key pair '%s': %s" % (key_name, e)) - return None, None - return kp.name, kp.material - -def run_instance(ec2_conn, user_provided_data, image_id='ami-da58aab3', - kernel_id=None, ramdisk_id=None, key_name='cloudman_key_pair', - security_groups=['CloudMan']): - """ Start an instance. If instance start was OK, return the ResultSet object - else return None. - """ - rs = None - instance_type = user_provided_data['instance_type'] - # Remove 'instance_type' key from the dict before creating user data - del user_provided_data['instance_type'] - placement = _find_placement(ec2_conn, instance_type) - ud = "\n".join(['%s: %s' % (key, value) for key, value in user_provided_data.iteritems() if key != 'kp_material']) - try: - rs = ec2_conn.run_instances(image_id=image_id, - instance_type=instance_type, - key_name=key_name, - security_groups=security_groups, - user_data=ud, - kernel_id=kernel_id, - ramdisk_id=ramdisk_id, - placement=placement) - except EC2ResponseError, e: - log.error("Problem starting an instance: %s\n%s" % (e, e.body)) - if rs: - try: - log.info("Started an instance with ID %s" % rs.instances[0].id) - except Exception, e: - log.error("Problem with the started instance object: %s" % e) - else: - log.warning("Problem starting an instance?") - return rs - -def _find_placement(ec2_conn, instance_type): - """Find a region zone that supports our requested instance type. - - We need to check spot prices in the potential availability zones - for support before deciding on a region: - - http://blog.piefox.com/2011/07/ec2-availability-zones-and-instance.html - """ - base = ec2_conn.region.name - yesterday = datetime.datetime.now() - datetime.timedelta(1) - for loc_choice in ["b", "a", "c", "d"]: - cur_loc = "{base}{ext}".format(base=base, ext=loc_choice) - if len(ec2_conn.get_spot_price_history(instance_type=instance_type, - end_time=yesterday.isoformat(), - availability_zone=cur_loc)) > 0: - return cur_loc - log.error("Did not find availabilty zone in {0} for {1}".format(base, instance_type)) - return None -

diff -r 5f3e2ffbae695cd7ae56b2ce4e4c0ed1182e2051 -r 38d9e07b58aa99ded2604cdd1aab4ca0f8761aa6 lib/galaxy/web/controllers/cloudlaunch.py --- /dev/null +++ b/lib/galaxy/web/controllers/cloudlaunch.py @@ -0,0 +1,220 @@ +""" +Cloud Controller: handles all cloud interactions. + +Adapted from Brad Chapman and Enis Afgan's BioCloudCentral +BioCloudCentral Source: https://github.com/chapmanb/biocloudcentral + +""" + +import datetime +import logging +import time +from galaxy import eggs +import pkg_resources +pkg_resources.require('boto') +import boto +from galaxy import web +from galaxy.web.base.controller import BaseUIController +from boto.ec2.regioninfo import RegionInfo +from boto.exception import EC2ResponseError + +log = logging.getLogger(__name__) + +class CloudController(BaseUIController): + def __init__(self, app): + BaseUIController.__init__(self, app) + + @web.expose + def index(self, trans): + return trans.fill_template("cloud/index.mako") + + @web.expose + def launch_instance(self, trans, cluster_name, password, key_id, secret, instance_type): + ec2_error = None + try: + # Create security group & key pair used when starting an instance + ec2_conn = connect_ec2(key_id, secret) + sg_name = create_cm_security_group(ec2_conn) + kp_name, kp_material = create_key_pair(ec2_conn) + except EC2ResponseError, err: + ec2_error = err.error_message + if ec2_error: + return trans.fill_template("cloud/run.mako", error = ec2_error) + else: + user_provided_data={'cluster_name':cluster_name, + 'access_key':key_id, + 'secret_key':secret, + 'instance_type':instance_type} + if password: + user_provided_data['password'] = password + rs = run_instance(ec2_conn=ec2_conn, + user_provided_data=user_provided_data, + key_name=kp_name, + security_groups=[sg_name]) + if rs: + instance = rs.instances[0] + ct = 0 + while not instance.public_dns_name: + # Can take a second to have public dns name registered. + # DBTODO, push this into a page update, this is not ideal. + instance.update() + ct +=1 + time.sleep(1) + return trans.fill_template("cloud/run.mako", + instance = rs.instances[0], + kp_name = kp_name, + kp_material = kp_material) + else: + return trans.fill_template("cloud/run.mako", + error = "Instance failure, but no specific error was detected. Please check your AWS Console.") + +# ## Cloud interaction methods +def connect_ec2(a_key, s_key): + """ Create and return an EC2 connection object. + """ + # Use variables for forward looking flexibility + # AWS connection values + region_name = 'us-east-1' + region_endpoint = 'ec2.amazonaws.com' + is_secure = True + ec2_port = None + ec2_conn_path = '/' + r = RegionInfo(name=region_name, endpoint=region_endpoint) + ec2_conn = boto.connect_ec2(aws_access_key_id=a_key, + aws_secret_access_key=s_key, + api_version='2011-11-01', # needed for availability zone support + is_secure=is_secure, + region=r, + port=ec2_port, + path=ec2_conn_path) + return ec2_conn + +def create_cm_security_group(ec2_conn, sg_name='CloudMan'): + """ Create a security group with all authorizations required to run CloudMan. + If the group already exists, check its rules and add the missing ones. + Return the name of the created security group. + """ + cmsg = None + # Check if this security group already exists + sgs = ec2_conn.get_all_security_groups() + for sg in sgs: + if sg.name == sg_name: + cmsg = sg + log.debug("Security group '%s' already exists; will add authorizations next." % sg_name) + break + # If it does not exist, create security group + if cmsg is None: + log.debug("Creating Security Group %s" % sg_name) + cmsg = ec2_conn.create_security_group(sg_name, 'A security group for CloudMan') + # Add appropriate authorization rules + # If these rules already exist, nothing will be changed in the SG + ports = (('80', '80'), # Web UI + ('20', '21'), # FTP + ('22', '22'), # ssh + ('30000', '30100'), # FTP transfer + ('42284', '42284')) # CloudMan UI + for port in ports: + try: + if not rule_exists(cmsg.rules, from_port=port[0], to_port=port[1]): + cmsg.authorize(ip_protocol='tcp', from_port=port[0], to_port=port[1], cidr_ip='0.0.0.0/0') + else: + log.debug("Rule (%s:%s) already exists in the SG" % (port[0], port[1])) + except EC2ResponseError, e: + log.error("A problem with security group authorizations: %s" % e) + # Add rule that allows communication between instances in the same SG + g_rule_exists = False # Flag to indicate if group rule already exists + for rule in cmsg.rules: + for grant in rule.grants: + if grant.name == cmsg.name: + g_rule_exists = True + log.debug("Group rule already exists in the SG") + if g_rule_exists: + break + if g_rule_exists is False: + try: + cmsg.authorize(src_group=cmsg) + except EC2ResponseError, e: + log.error("A problem w/ security group authorization: %s" % e) + log.info("Done configuring '%s' security group" % cmsg.name) + return cmsg.name + +def rule_exists(rules, from_port, to_port, ip_protocol='tcp', cidr_ip='0.0.0.0/0'): + """ A convenience method to check if an authorization rule in a security + group exists. + """ + for rule in rules: + if rule.ip_protocol == ip_protocol and rule.from_port == from_port and \ + rule.to_port == to_port and cidr_ip in [ip.cidr_ip for ip in rule.grants]: + return True + return False + +def create_key_pair(ec2_conn, key_name='cloudman_key_pair'): + """ Create a key pair with the provided name. + Return the name of the key or None if there was an error creating the key. + """ + kp = None + # Check if a key pair under the given name already exists. If it does not, + # create it, else return. + kps = ec2_conn.get_all_key_pairs() + for akp in kps: + if akp.name == key_name: + log.debug("Key pair '%s' already exists; not creating it again." % key_name) + return akp.name, None + try: + kp = ec2_conn.create_key_pair(key_name) + except EC2ResponseError, e: + log.error("Problem creating key pair '%s': %s" % (key_name, e)) + return None, None + return kp.name, kp.material + +def run_instance(ec2_conn, user_provided_data, image_id='ami-da58aab3', + kernel_id=None, ramdisk_id=None, key_name='cloudman_key_pair', + security_groups=['CloudMan']): + """ Start an instance. If instance start was OK, return the ResultSet object + else return None. + """ + rs = None + instance_type = user_provided_data['instance_type'] + # Remove 'instance_type' key from the dict before creating user data + del user_provided_data['instance_type'] + placement = _find_placement(ec2_conn, instance_type) + ud = "\n".join(['%s: %s' % (key, value) for key, value in user_provided_data.iteritems() if key != 'kp_material']) + try: + rs = ec2_conn.run_instances(image_id=image_id, + instance_type=instance_type, + key_name=key_name, + security_groups=security_groups, + user_data=ud, + kernel_id=kernel_id, + ramdisk_id=ramdisk_id, + placement=placement) + except EC2ResponseError, e: + log.error("Problem starting an instance: %s\n%s" % (e, e.body)) + if rs: + try: + log.info("Started an instance with ID %s" % rs.instances[0].id) + except Exception, e: + log.error("Problem with the started instance object: %s" % e) + else: + log.warning("Problem starting an instance?") + return rs + +def _find_placement(ec2_conn, instance_type): + """Find a region zone that supports our requested instance type. + + We need to check spot prices in the potential availability zones + for support before deciding on a region: + + http://blog.piefox.com/2011/07/ec2-availability-zones-and-instance.html + """ + base = ec2_conn.region.name + yesterday = datetime.datetime.now() - datetime.timedelta(1) + for loc_choice in ["b", "a", "c", "d"]: + cur_loc = "{base}{ext}".format(base=base, ext=loc_choice) + if len(ec2_conn.get_spot_price_history(instance_type=instance_type, + end_time=yesterday.isoformat(), + availability_zone=cur_loc)) > 0: + return cur_loc + log.error("Did not find availabilty zone in {0} for {1}".format(base, instance_type)) + return None +

diff -r 5f3e2ffbae695cd7ae56b2ce4e4c0ed1182e2051 -r 38d9e07b58aa99ded2604cdd1aab4ca0f8761aa6 templates/cloud/index.mako --- a/templates/cloud/index.mako +++ b/templates/cloud/index.mako @@ -56,7 +56,7 @@ <div class="page-container" style="padding: 10px;"><h2>Launch a Galaxy Cloud Instance</h2><div class="toolForm"> - <form action="cloud/launch_instance" method="post"> + <form action="${h.url_for( controller='cloudlaunch', action='launch_instance' )}" method="post"><div class="form-row"><label for="id_cluster_name">Cluster Name</label><input type="text" size="80" name="cluster_name" id="id_cluster_name"/><br/>

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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