Re: [DISCUSS] Deprecate GRAM provider
+1 On Wed, Jul 30, 2014 at 8:57 PM, Lahiru Gunathilake wrote: > +1 > > > On Wed, Jul 30, 2014 at 8:08 PM, Suresh Marru wrote: > >> Hi All, >> >> Lately we haven’t been using/updating GRAM provider. From private >> conversions with the Globus team, I inferred GRAM will not be a key focus >> for future development. >> >> I would like to recommend deprecating support for GRAM beyond Airavata >> 0.13. Any opinions/comments/considerations? >> >> I will not call a formal VOTE unless we here otherwise, so please comment >> if you care about this support. >> >> Suresh >> >> > > > -- > System Analyst Programmer > PTI Lab > Indiana University >
Re: Registering ec2 application with app catalog
Hi suresh Thanks for the feedback. These are things i need so far nodeId executableLocation ExecutableType workingDirectory inputOutPutDirectories StandardError and StandardOut Directories CloudProvider name- for ec2 "aws-ec2" user account name in Node - for ec2 - "ec2-user" Perhaps all of these things can be saved with app-catalog already if so please correct me. So far i have mainly focused on ec2. but clearly with minimal effort we can used gfac provider with other jclouds Providers. if we take docker, the difference is creating the computingserviceContext, the provider name and the security details. and other things will remain same as long as the docker node is shell accessible. regards Nipun Udara On Thu, Jul 31, 2014 at 2:35 AM, Suresh Marru wrote: > Hi Nipun, > > Can you tell me what all information you will need to register EC2, > Rackspace? Lets quickly add it instead of you reverting to a old code. > > Which all JClouds providers did you try from > https://jclouds.apache.org/reference/providers/ ? > > Are you writing a generic JClouds GFac provider which will be easy to work > with the above listed jClouds providers? Taking an example, lets say docker > (https://jclouds.apache.org/guides/docker/), how much effort will be to > modify your provider and docker support? > > Suresh > > On Jul 30, 2014, at 3:41 PM, Nipun Udara wrote: > > > Hi all > > > > I have to test ec2 application registration with app catalog, and i have > look at the BetterGFacImpl and seems app-catalog intergration doenot > support ec2. > > > > So I would like to know whether i can continue rest of the work with the > old code . > > > > regards > > Nipun Udara > > -- Nipun Udara *Undergraduate* *Department of Computer Science & Engineering* *University of Moratuwa* *Sri Lanka*
Re: [DISCUSS] Deprecate GRAM provider
+1 On Wed, Jul 30, 2014 at 8:08 PM, Suresh Marru wrote: > Hi All, > > Lately we haven’t been using/updating GRAM provider. From private > conversions with the Globus team, I inferred GRAM will not be a key focus > for future development. > > I would like to recommend deprecating support for GRAM beyond Airavata > 0.13. Any opinions/comments/considerations? > > I will not call a formal VOTE unless we here otherwise, so please comment > if you care about this support. > > Suresh > > -- System Analyst Programmer PTI Lab Indiana University
[DISCUSS] Deprecate GRAM provider
Hi All, Lately we haven’t been using/updating GRAM provider. From private conversions with the Globus team, I inferred GRAM will not be a key focus for future development. I would like to recommend deprecating support for GRAM beyond Airavata 0.13. Any opinions/comments/considerations? I will not call a formal VOTE unless we here otherwise, so please comment if you care about this support. Suresh
[jira] [Commented] (AIRAVATA-465) ability to interact with outputs from individual tasks while executing
[ https://issues.apache.org/jira/browse/AIRAVATA-465?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14080260#comment-14080260 ] Pamidighantam, Sudhakar V commented on AIRAVATA-465: I will be out of office until Aug 15, 2014 with limited email access. Please contact h...@ncsa.illinois.edu if this require immediate attention. For SEAGrid/GridChem related issues please use the consulting portal at https://www.gridchem.org/consult/ Have a pleasant Summer 2014. Thanks, Sudhakar. > ability to interact with outputs from individual tasks while executing > -- > > Key: AIRAVATA-465 > URL: https://issues.apache.org/jira/browse/AIRAVATA-465 > Project: Airavata > Issue Type: New Feature > Components: Workflow Tracking >Affects Versions: 0.13 >Reporter: Sudhakar Pamidighantam >Assignee: Lahiru Gunathilake > Fix For: 0.15 > > > It will be useful to interact with the output of an individual task in a > workflow while the task is executing. Particularly for long running ( hours) > tasks some intermediate status echos will be very useful for the user to be > assured of the right progress of the task. In case of unsatisfactory progress > the user may want to stop/pause/kill the workflow and resubmit with modified > inputs. If there is a way to modify the inputs and the task rereads them at > the next cycle(step) during the execution then the workflow can be steered > toward the right (desired) direction by the user. -- This message was sent by Atlassian JIRA (v6.2#6252)
[jira] [Updated] (AIRAVATA-467) Allow user to set parameter options like -p -m to run jobs with GFAC
[ https://issues.apache.org/jira/browse/AIRAVATA-467?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Suresh Marru updated AIRAVATA-467: -- Fix Version/s: (was: 0.13) 0.14 > Allow user to set parameter options like -p -m to run jobs > with GFAC > > > Key: AIRAVATA-467 > URL: https://issues.apache.org/jira/browse/AIRAVATA-467 > Project: Airavata > Issue Type: Improvement > Components: GFac >Affects Versions: 0.4-INCUBATING >Reporter: Raminderjeet Singh >Assignee: Lahiru Gunathilake > Fix For: 0.14 > > > Some of the application need options before the parameter to run as shown in > example below. This requirement is true for different GFAC providers. > /home1/01437/ogce/biodrugscreen/bdsreening.py -p -m > -q -l -x -y -z -u > -v -- This message was sent by Atlassian JIRA (v6.2#6252)
[jira] [Updated] (AIRAVATA-465) ability to interact with outputs from individual tasks while executing
[ https://issues.apache.org/jira/browse/AIRAVATA-465?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Suresh Marru updated AIRAVATA-465: -- Fix Version/s: (was: 0.13) 0.15 > ability to interact with outputs from individual tasks while executing > -- > > Key: AIRAVATA-465 > URL: https://issues.apache.org/jira/browse/AIRAVATA-465 > Project: Airavata > Issue Type: New Feature > Components: Workflow Tracking >Affects Versions: 0.13 >Reporter: Sudhakar Pamidighantam >Assignee: Lahiru Gunathilake > Fix For: 0.15 > > > It will be useful to interact with the output of an individual task in a > workflow while the task is executing. Particularly for long running ( hours) > tasks some intermediate status echos will be very useful for the user to be > assured of the right progress of the task. In case of unsatisfactory progress > the user may want to stop/pause/kill the workflow and resubmit with modified > inputs. If there is a way to modify the inputs and the task rereads them at > the next cycle(step) during the execution then the workflow can be steered > toward the right (desired) direction by the user. -- This message was sent by Atlassian JIRA (v6.2#6252)
[jira] [Updated] (AIRAVATA-461) Allow users skip the workflow Nodes which already ran and invoke the rest of the Nodes
[ https://issues.apache.org/jira/browse/AIRAVATA-461?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Suresh Marru updated AIRAVATA-461: -- Fix Version/s: (was: 0.13) 0.14 > Allow users skip the workflow Nodes which already ran and invoke the rest of > the Nodes > -- > > Key: AIRAVATA-461 > URL: https://issues.apache.org/jira/browse/AIRAVATA-461 > Project: Airavata > Issue Type: Improvement > Components: Workflow Interpreter, XBaya >Affects Versions: 0.4-INCUBATING > Environment: $subject. So if you have a long running node which > already ran and if you are not changing the inputs for that node you can run > the workflow with same experiment ID and XBaya will not run the workflow > Nodes which already ran and will simply use the outputs gerated. > XBaya will load the outputs from Registry and use them. This will be useful > in-case XBaya or backend server crashed during a workflow run. > Lahiru >Reporter: Lahiru Gunathilake >Assignee: Saminda Wijeratne > Fix For: 0.14 > > -- This message was sent by Atlassian JIRA (v6.2#6252)
[jira] [Resolved] (AIRAVATA-454) Stopping Airavata service make Xbaya notification client give lot of errors.
[ https://issues.apache.org/jira/browse/AIRAVATA-454?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Suresh Marru resolved AIRAVATA-454. --- Resolution: Won't Fix Since ws-messenger is not bundled with latest code bases, this is irrelevant now. > Stopping Airavata service make Xbaya notification client give lot of errors. > > > Key: AIRAVATA-454 > URL: https://issues.apache.org/jira/browse/AIRAVATA-454 > Project: Airavata > Issue Type: Bug > Components: XBaya >Affects Versions: 0.3-INCUBATING, 0.4-INCUBATING >Reporter: Raminderjeet Singh > Labels: Contributor > Fix For: 0.13 > > > I stopped the airavata service to apply some code changes and Xbaya have > following exception on consol more than 1000 time in 5 mins. There is no way > to stop notification listener. > [Thread-12-async-msgbox-correlator] INFO httpclient.HttpMethodDirector - > I/O exception (java.net.ConnectException) caught when processing request: > Connection refused > [Thread-12-async-msgbox-correlator] INFO httpclient.HttpMethodDirector - > Retrying request > [Thread-12-async-msgbox-correlator] INFO httpclient.HttpMethodDirector - > I/O exception (java.net.ConnectException) caught when processing request: > Connection refused > [Thread-12-async-msgbox-correlator] INFO httpclient.HttpMethodDirector - > Retrying request > [Thread-12-async-msgbox-correlator] INFO httpclient.HttpMethodDirector - > I/O exception (java.net.ConnectException) caught when processing request: > Connection refused > [Thread-12-async-msgbox-correlator] INFO httpclient.HttpMethodDirector - > Retrying request > [Thread-12-async-msgbox-correlator] INFO http.HTTPSender - Unable to > sendViaPost to > url[http://localhost:8080/axis2/services/MsgBoxService/clientid/e2b5729d-2c82-41ab-b393-c39807337093] > java.net.ConnectException: Connection refused > at java.net.PlainSocketImpl.socketConnect(Native Method) > at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:351) > at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:213) > at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:200) > at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:432) > at java.net.Socket.connect(Socket.java:529) > at sun.reflect.GeneratedMethodAccessor27.invoke(Unknown Source) > at > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) > at java.lang.reflect.Method.invoke(Method.java:597) > at > org.apache.commons.httpclient.protocol.ReflectionSocketFactory.createSocket(ReflectionSocketFactory.java:140) > at > org.apache.commons.httpclient.protocol.DefaultProtocolSocketFactory.createSocket(DefaultProtocolSocketFactory.java:125) > at > org.apache.commons.httpclient.HttpConnection.open(HttpConnection.java:707) > at > org.apache.commons.httpclient.MultiThreadedHttpConnectionManager$HttpConnectionAdapter.open(MultiThreadedHttpConnectionManager.java:1361) > at > org.apache.commons.httpclient.HttpMethodDirector.executeWithRetry(HttpMethodDirector.java:387) > at > org.apache.commons.httpclient.HttpMethodDirector.executeMethod(HttpMethodDirector.java:171) > at > org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:397) > at > org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:346) > at > org.apache.axis2.transport.http.AbstractHTTPSender.executeMethod(AbstractHTTPSender.java:542) > at > org.apache.axis2.transport.http.HTTPSender.sendViaPost(HTTPSender.java:199) > at org.apache.axis2.transport.http.HTTPSender.send(HTTPSender.java:76) > at > org.apache.axis2.transport.http.CommonsHTTPTransportSender.writeMessageWithCommons(CommonsHTTPTransportSender.java:400) > at > org.apache.axis2.transport.http.CommonsHTTPTransportSender.invoke(CommonsHTTPTransportSender.java:225) > at org.apache.axis2.engine.AxisEngine.send(AxisEngine.java:435) > at > org.apache.axis2.description.OutInAxisOperationClient.send(OutInAxisOperation.java:402) > at > org.apache.axis2.description.OutInAxisOperationClient.executeImpl(OutInAxisOperation.java:229) > at > org.apache.axis2.client.OperationClient.execute(OperationClient.java:165) > at > org.apache.axis2.client.ServiceClient.sendReceive(ServiceClient.java:540) > at > org.apache.axis2.client.ServiceClient.sendReceive(ServiceClient.java:521) > at > org.apache.airavata.wsmg.msgbox.client.TakeMessages.execute(TakeMessages.java:76) > at > org.apache.airavata.wsmg.msgbox.client.MsgBoxClient.takeMessagesFromMsgBox(MsgBoxClient.java:56) > at > org.apache.airavata.xbaya.invoker.MsgBoxWsaResponsesCorrelator.run(MsgBoxWsaResp
[jira] [Updated] (AIRAVATA-439) GFAC/Orchestrator exception handling and notifications
[ https://issues.apache.org/jira/browse/AIRAVATA-439?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Suresh Marru updated AIRAVATA-439: -- Fix Version/s: (was: 0.13) 0.15 > GFAC/Orchestrator exception handling and notifications > -- > > Key: AIRAVATA-439 > URL: https://issues.apache.org/jira/browse/AIRAVATA-439 > Project: Airavata > Issue Type: Story >Reporter: Raminderjeet Singh >Assignee: Lahiru Gunathilake > Fix For: 0.15 > > > 1. Currently GFAC have ProviderException, ToolException, GFACException etc. > All of them have same methods or a minor variations. These need to be merged > or defined properly for developer to use. > 2. Error notification should be handled using a central method. Rest of the > components are responsible for throwing useful exceptions and is handled at > single place. -- This message was sent by Atlassian JIRA (v6.2#6252)
Re: [DISCUSS] Issues mailing list
+1 On Wed, Jul 30, 2014 at 5:53 PM, Suresh Marru wrote: > With no objections I will request a issues mailing list to be created. If > you think its a bad idea, please gripe. > > Suresh > > On Jul 22, 2014, at 8:36 AM, Marlon Pierce wrote: > > > +1 > > > > On 7/22/14, 6:47 AM, Suresh Marru wrote: > >> Hi All, > >> > >> To keep the dev list focussed on discussions and reduce the JIRA noise, > how about we create a new issues mailing list and have all JIRA’s send to > that mailing list. We need to make it mandatory for all PMC and committers > to subscribe to it and the community is welcome to join. It will be a > public mailing list. > >> > >> Thoughts? > >> Suresh > > > > -- System Analyst Programmer PTI Lab Indiana University
Re: Embedded ZK
Hi Danushka, Thats the plan. Regards Lahiru On Tue, Jul 29, 2014 at 1:51 PM, Danushka Menikkumbura < danushka.menikkumb...@gmail.com> wrote: > Nice! :-) > > I suggest we do a quick perf test just to get a sense of it. > > Danushka > > > On Tue, Jul 29, 2014 at 11:09 PM, Lahiru Gunathilake > wrote: > >> Hi Devs, >> >> I have added embedded ZK support to trunk. please stop your zk daemon >> with latest build and just use airavata-server.sh to start airavata. >> >> If you see any issues with this please let me know. >> >> Thanks >> Lahiru >> -- >> System Analyst Programmer >> PTI Lab >> Indiana University >> > > -- System Analyst Programmer PTI Lab Indiana University
[jira] [Resolved] (AIRAVATA-437) Stdout and stderr files are read as string and will be problem if the file are big
[ https://issues.apache.org/jira/browse/AIRAVATA-437?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Suresh Marru resolved AIRAVATA-437. --- Resolution: Won't Fix Since the issue is a concern on tomcat deployment, resolving for now. But the problem might exist neverthless. I suggets revisting this issue on a latest release and create a new jira with latest observations. > Stdout and stderr files are read as string and will be problem if the file > are big > -- > > Key: AIRAVATA-437 > URL: https://issues.apache.org/jira/browse/AIRAVATA-437 > Project: Airavata > Issue Type: Bug > Components: GFac >Affects Versions: 0.4-INCUBATING >Reporter: Raminderjeet Singh > Labels: Contributor > Fix For: 0.13 > > > Currently Stdout and stderr files are read as String to be evaluated against > regex to get output paramameters. These files can grow big and gfac may run > into out of memory. With the new infrastructure with all the services hosted > on same tomcat/axis2 server (may not be recommended but how its currently), > we need to be more careful about memory usage. -- This message was sent by Atlassian JIRA (v6.2#6252)
[jira] [Updated] (AIRAVATA-433) Providing Airavata API method to cancel a running job
[ https://issues.apache.org/jira/browse/AIRAVATA-433?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Suresh Marru updated AIRAVATA-433: -- Fix Version/s: (was: 0.13) 0.15 > Providing Airavata API method to cancel a running job > - > > Key: AIRAVATA-433 > URL: https://issues.apache.org/jira/browse/AIRAVATA-433 > Project: Airavata > Issue Type: Sub-task > Components: Airavata Client, GFac >Affects Versions: 0.4-INCUBATING >Reporter: Raminderjeet Singh >Assignee: Saminda Wijeratne > Fix For: 0.15 > > > Currently users need to login to remote resource to cancel a running job. > Gram have a method to cancel jobs remotely by passing job id. -- This message was sent by Atlassian JIRA (v6.2#6252)
[jira] [Updated] (AIRAVATA-402) Optional outputs from a application
[ https://issues.apache.org/jira/browse/AIRAVATA-402?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Suresh Marru updated AIRAVATA-402: -- Fix Version/s: (was: 0.13) 0.14 > Optional outputs from a application > --- > > Key: AIRAVATA-402 > URL: https://issues.apache.org/jira/browse/AIRAVATA-402 > Project: Airavata > Issue Type: Improvement > Components: GFac >Reporter: Raminderjeet Singh >Assignee: Lahiru Gunathilake > Fix For: 0.14 > > > Currently Gfac service fails if application did not produce a output > parameter in stdout file. User should be allowed to mark output parameter as > optional and/or provide default value. -- This message was sent by Atlassian JIRA (v6.2#6252)
[jira] [Resolved] (AIRAVATA-388) Store the fine grain workflow status in registry and when user load the workflow we should do coloring based on the status
[ https://issues.apache.org/jira/browse/AIRAVATA-388?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Suresh Marru resolved AIRAVATA-388. --- Resolution: Won't Fix The code base using these features changed significantly. > Store the fine grain workflow status in registry and when user load the > workflow we should do coloring based on the status > -- > > Key: AIRAVATA-388 > URL: https://issues.apache.org/jira/browse/AIRAVATA-388 > Project: Airavata > Issue Type: New Feature > Components: Registry API, XBaya >Affects Versions: 0.4-INCUBATING > Environment: mac >Reporter: Lahiru Gunathilake >Assignee: Lahiru Gunathilake > Fix For: 0.13 > > > $subject > After storing the fine grain statuses XBaya GUI should be able to show the > status of the workflow with proper coloring. > Lahiru -- This message was sent by Atlassian JIRA (v6.2#6252)
[jira] [Closed] (AIRAVATA-339) [GSoC] AMQP Messaging protocol support for Airavata WS-Messenger
[ https://issues.apache.org/jira/browse/AIRAVATA-339?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Suresh Marru closed AIRAVATA-339. - Resolution: Fixed This GSoC project is now concluded. > [GSoC] AMQP Messaging protocol support for Airavata WS-Messenger > > > Key: AIRAVATA-339 > URL: https://issues.apache.org/jira/browse/AIRAVATA-339 > Project: Airavata > Issue Type: New Feature >Reporter: Suresh Marru >Assignee: Lahiru Gunathilake > Labels: Contributor, gsoc2012, gsoc2013, mentor > Fix For: 0.13 > > Attachments: amqp-airavata-server.properties.patch, > amqp-ws-messenger-client-test.2.patch, amqp-ws-messenger-client-test.patch, > amqp-ws-messenger-client.patch, amqp-ws-messenger-messagebroker.patch > > > Airavata WS-Messenger is a Web Services-based Messaging System for > Service-Oriented Computing and is an implementation of WS-Notification and > WS-Eventing specifications. The message format can be automatically converted > between the two specifications. > With an increasing adoption of AMQP, Airavata community has interest to > support this protocol. The subscription request type can be AMQP or > Ws-Notification or WS-Eventing for a listener determines the message format > that the notification consumer will receive. Currently, if WS-Notification > subscription request is received by the broker, it will send WS-Notification > messages to the listener. Similarly, if WS-Eventing subscription is received > by the broker, the broker will produce WS-Eventing messages for that > listener. The publisher can publish messages in either format. The consumers > will receive messages in the format they subscribed irrespective of the > format the message is published. We want to extend this functionality to > interoperate with AMQP similarly. > There is extensive literature about Airavata WS Messenger including 4 > research papers. The Airavata community will provide guidance and assistance > with the project. > User community & Impact of the software: Airavata is primarily targeted to > build science gateways using computational resources from various > disciplines. The initial targeted set of gateways include projects supporting > research and education in chemistry, life sciences, biophysics, environmental > sciences, geosciences astronomy and nuclear physics. The goal of airavata is > to enhance productivity of these gateways to utilize cyberinfrastructure of > resources (e.g., local lab resources, the Extreme Science and Engineering > Discovery Environment (XSEDE), the Open Science Grid (OSG), University > Clusters, Academic and Commercial Computational Clouds like FutureGrid & > Amazon EC2). By using open community based software components and services > like Airavata, gateways will be able to focus on providing additional > scientific capabilities and to expanding the number of supported users. The > capabilities of these gateways will offer clear benefits to society. -- This message was sent by Atlassian JIRA (v6.2#6252)
[jira] [Closed] (AIRAVATA-331) Need to develop "shadow" MPI applications that illustrate basic executions on XSEDE and similar grids.
[ https://issues.apache.org/jira/browse/AIRAVATA-331?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Suresh Marru closed AIRAVATA-331. - Resolution: Fixed Refer - https://github.com/SciGaP/XSEDE-Job-Scripts > Need to develop "shadow" MPI applications that illustrate basic executions on > XSEDE and similar grids. > -- > > Key: AIRAVATA-331 > URL: https://issues.apache.org/jira/browse/AIRAVATA-331 > Project: Airavata > Issue Type: Story >Reporter: Marlon Pierce > Labels: Contributor > Fix For: 0.13 > > Attachments: airavata-331.patch > > -- This message was sent by Atlassian JIRA (v6.2#6252)
[jira] [Closed] (AIRAVATA-330) Create "shadow" applications that exercise the execution, host, and service description and execution facilities of airavata
[ https://issues.apache.org/jira/browse/AIRAVATA-330?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Suresh Marru closed AIRAVATA-330. - Resolution: Fixed These samples exist but outside the scope of Airavata. Refer scripts by [~yuma] on github - https://github.com/SciGaP/XSEDE-Job-Scripts > Create "shadow" applications that exercise the execution, host, and service > description and execution facilities of airavata > > > Key: AIRAVATA-330 > URL: https://issues.apache.org/jira/browse/AIRAVATA-330 > Project: Airavata > Issue Type: Epic >Reporter: Marlon Pierce > Labels: Contributor > Fix For: 0.13 > > > Develop simple MPI applications that echo the hostname on Ranger, Lonestar, > Trestles, (Blacklight). Run them on the command line using the queuing > system. Then run through Airavata. Check the examples into an appropriate > place on SVN. > As we encounter other patterns for codes, we will develop new shadow MPI > applications that mimic their execution profiles. -- This message was sent by Atlassian JIRA (v6.2#6252)
[jira] [Updated] (AIRAVATA-251) Integrate launched mechanim for foreach- parallel job submissions with the EC2 with oversubscribing
[ https://issues.apache.org/jira/browse/AIRAVATA-251?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Suresh Marru updated AIRAVATA-251: -- Fix Version/s: (was: 0.13) WISHLIST > Integrate launched mechanim for foreach- parallel job submissions with the > EC2 with oversubscribing > --- > > Key: AIRAVATA-251 > URL: https://issues.apache.org/jira/browse/AIRAVATA-251 > Project: Airavata > Issue Type: Improvement > Components: GFac, Workflow Interpreter >Reporter: Chathura Herath >Assignee: Heshan Suriyaarachchi > Labels: Contributor, EC2 > Fix For: WISHLIST > > > Heshan has done initial work on how to do parametric sweeps with > oversubscription in the nodes for maximum utilization as well as load > balancing. This need to be integration with the cartisian product and dot > product for-each evaluation of the engine. -- This message was sent by Atlassian JIRA (v6.2#6252)
[jira] [Updated] (AIRAVATA-282) Simple tutorial documentation and built-in test cases of the Provenance feature needs to be added to the website.
[ https://issues.apache.org/jira/browse/AIRAVATA-282?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Suresh Marru updated AIRAVATA-282: -- Fix Version/s: (was: 0.13) WISHLIST > Simple tutorial documentation and built-in test cases of the Provenance > feature needs to be added to the website. > - > > Key: AIRAVATA-282 > URL: https://issues.apache.org/jira/browse/AIRAVATA-282 > Project: Airavata > Issue Type: Improvement >Reporter: Marlon Pierce > Fix For: WISHLIST > > > Probably also there will need to be some sample cases checked into the SVN. -- This message was sent by Atlassian JIRA (v6.2#6252)
[jira] [Resolved] (AIRAVATA-1119) JPARegistry tests are failing
[ https://issues.apache.org/jira/browse/AIRAVATA-1119?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Suresh Marru resolved AIRAVATA-1119. Resolution: Fixed These tests seem to pass now. > JPARegistry tests are failing > - > > Key: AIRAVATA-1119 > URL: https://issues.apache.org/jira/browse/AIRAVATA-1119 > Project: Airavata > Issue Type: Bug > Components: Registry API >Affects Versions: 0.12 > Environment: mac >Reporter: Lahiru Gunathilake >Assignee: Saminda Wijeratne >Priority: Critical > Fix For: 0.13 > > > http://pastebin.com/6ije858z -- This message was sent by Atlassian JIRA (v6.2#6252)
[jira] [Updated] (AIRAVATA-281) Simple tutorial documentation and built-in test cases of the For-Each feature needs to be added to the website when For-Each is ready.
[ https://issues.apache.org/jira/browse/AIRAVATA-281?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Suresh Marru updated AIRAVATA-281: -- Fix Version/s: (was: 0.13) WISHLIST > Simple tutorial documentation and built-in test cases of the For-Each feature > needs to be added to the website when For-Each is ready. > -- > > Key: AIRAVATA-281 > URL: https://issues.apache.org/jira/browse/AIRAVATA-281 > Project: Airavata > Issue Type: Improvement >Reporter: Marlon Pierce > Fix For: WISHLIST > > > Probably also some simple tutorial/test cases will need to be checked into > SVN. -- This message was sent by Atlassian JIRA (v6.2#6252)
Re: [DISCUSS] Issues mailing list
With no objections I will request a issues mailing list to be created. If you think its a bad idea, please gripe. Suresh On Jul 22, 2014, at 8:36 AM, Marlon Pierce wrote: > +1 > > On 7/22/14, 6:47 AM, Suresh Marru wrote: >> Hi All, >> >> To keep the dev list focussed on discussions and reduce the JIRA noise, how >> about we create a new issues mailing list and have all JIRA’s send to that >> mailing list. We need to make it mandatory for all PMC and committers to >> subscribe to it and the community is welcome to join. It will be a public >> mailing list. >> >> Thoughts? >> Suresh >
[jira] [Updated] (AIRAVATA-1333) Can we have a way of searching for all the projects, experiments in the gateway?
[ https://issues.apache.org/jira/browse/AIRAVATA-1333?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Suresh Marru updated AIRAVATA-1333: --- Fix Version/s: (was: 0.13) 0.14 > Can we have a way of searching for all the projects, experiments in the > gateway? > > > Key: AIRAVATA-1333 > URL: https://issues.apache.org/jira/browse/AIRAVATA-1333 > Project: Airavata > Issue Type: Improvement >Affects Versions: 0.13 >Reporter: Eroma >Assignee: David Reagan > Fix For: 0.14 > > > Can we have a way of searching for all the projects, experiments in the > gateway? > May be using (*) as the search value to list all projects, experiments -- This message was sent by Atlassian JIRA (v6.2#6252)
Re: [SciGaP-Dev] CIPRES-Airavata integration proposal]]
Your repo got mangled, probably from the first build. Just delete the contents of that directory and it should rebuild correctly. However, there may be other problems lurking, so I recommend moving ~/.m2 to ~/.m2-30July2104 or something and rebuild from scratch. Marlon On 7/30/14, 5:01 PM, K Yoshimoto wrote: On Wed, Jul 30, 2014 at 04:52:35PM -0400, Marlon Pierce wrote: Does it work if you use mvn -o clean install? I get a bunch of test failures, with or without -o. Should I be concerned about these? What do you get when you run ls -tlr ~/.m2/repository/org/apache/airavata/airavata-client-api/0.14-SNAPSHOT/ ? ls -tlr ~/.m2/repository/org/apache/airavata/airavata-client-api/0.14-SNAPSHOT/ total 12 -rw-rw-r-- 1 john john 231 Jul 30 13:43 resolver-status.properties -rw-rw-r-- 1 john john 241 Jul 30 13:43 airavata-client-api-0.14-SNAPSHOT.pom.lastUpdated -rw-rw-r-- 1 john john 241 Jul 30 13:43 airavata-client-api-0.14-SNAPSHOT.jar.lastUpdated Kenneth Mine looks like this: mpierce$ ls -tlr ~/.m2/repository/org/apache/airavata/airavata-client-api/0.14-SNAPSHOT/ total 1432 -rw-r--r-- 1 mpierce staff5044 Jul 22 15:28 airavata-client-api-0.14-SNAPSHOT.pom -rw-r--r-- 1 mpierce staff 241 Jul 30 16:09 airavata-client-api-0.14-SNAPSHOT.pom.lastUpdated -rw-r--r-- 1 mpierce staff 241 Jul 30 16:09 airavata-client-api-0.14-SNAPSHOT.jar.lastUpdated -rw-r--r-- 1 mpierce staff 721 Jul 30 16:11 maven-metadata-local.xml -rw-r--r-- 1 mpierce staff 704373 Jul 30 16:11 airavata-client-api-0.14-SNAPSHOT.jar -rw-r--r-- 1 mpierce staff 206 Jul 30 16:11 _maven.repositories -rw-r--r-- 1 mpierce staff 231 Jul 30 16:49 resolver-status.properties On 7/30/14, 4:45 PM, K Yoshimoto wrote: I get a different error now: java-client-samples$ mvn clean install -U -DskipTests=true -f pom.xml [INFO] Scanning for projects... [INFO] [INFO] [INFO] Building Airavata Client Samples 0.14-SNAPSHOT [INFO] Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-data-models/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-api/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-model-utils/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-common-utils/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/commons/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-client-api/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-client-api/0.14-SNAPSHOT/airavata-client-api-0.14-SNAPSHOT.pom [WARNING] The POM for org.apache.airavata:airavata-client-api:jar:0.14-SNAPSHOT is missing, no dependency information available Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-gfac-schema-utils/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-jpa-registry/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/registry/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-registry-api/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-workflow-execution-context/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-credential-store/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-registry-cpi/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-api-stubs/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-client-configuration/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-configuration/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-client-api/0.14-SNAPSHOT/airavata-client-api-0.14-SNAPSHOT.jar [INFO] [INFO] BUILD FAILURE [INFO] [INFO] Total time: 6.780s [INFO] Finished at: Wed Jul 30 13:43:44 PDT 2014 [INFO] Final Memory: 8M/148M [INFO] -
Re: Registering ec2 application with app catalog
Hi Nipun, Can you tell me what all information you will need to register EC2, Rackspace? Lets quickly add it instead of you reverting to a old code. Which all JClouds providers did you try from https://jclouds.apache.org/reference/providers/ ? Are you writing a generic JClouds GFac provider which will be easy to work with the above listed jClouds providers? Taking an example, lets say docker (https://jclouds.apache.org/guides/docker/), how much effort will be to modify your provider and docker support? Suresh On Jul 30, 2014, at 3:41 PM, Nipun Udara wrote: > Hi all > > I have to test ec2 application registration with app catalog, and i have look > at the BetterGFacImpl and seems app-catalog intergration doenot support ec2. > > So I would like to know whether i can continue rest of the work with the old > code . > > regards > Nipun Udara
Re: [SciGaP-Dev] CIPRES-Airavata integration proposal]]
On Wed, Jul 30, 2014 at 04:52:35PM -0400, Marlon Pierce wrote: > Does it work if you use mvn -o clean install? I get a bunch of test failures, with or without -o. Should I be concerned about these? > > What do you get when you run ls -tlr > ~/.m2/repository/org/apache/airavata/airavata-client-api/0.14-SNAPSHOT/ ? ls -tlr ~/.m2/repository/org/apache/airavata/airavata-client-api/0.14-SNAPSHOT/ total 12 -rw-rw-r-- 1 john john 231 Jul 30 13:43 resolver-status.properties -rw-rw-r-- 1 john john 241 Jul 30 13:43 airavata-client-api-0.14-SNAPSHOT.pom.lastUpdated -rw-rw-r-- 1 john john 241 Jul 30 13:43 airavata-client-api-0.14-SNAPSHOT.jar.lastUpdated Kenneth > > Mine looks like this: > > mpierce$ ls -tlr > ~/.m2/repository/org/apache/airavata/airavata-client-api/0.14-SNAPSHOT/ > total 1432 > -rw-r--r-- 1 mpierce staff5044 Jul 22 15:28 > airavata-client-api-0.14-SNAPSHOT.pom > -rw-r--r-- 1 mpierce staff 241 Jul 30 16:09 > airavata-client-api-0.14-SNAPSHOT.pom.lastUpdated > -rw-r--r-- 1 mpierce staff 241 Jul 30 16:09 > airavata-client-api-0.14-SNAPSHOT.jar.lastUpdated > -rw-r--r-- 1 mpierce staff 721 Jul 30 16:11 maven-metadata-local.xml > -rw-r--r-- 1 mpierce staff 704373 Jul 30 16:11 > airavata-client-api-0.14-SNAPSHOT.jar > -rw-r--r-- 1 mpierce staff 206 Jul 30 16:11 _maven.repositories > -rw-r--r-- 1 mpierce staff 231 Jul 30 16:49 resolver-status.properties > > > On 7/30/14, 4:45 PM, K Yoshimoto wrote: > >I get a different error now: > > > >java-client-samples$ mvn clean install -U -DskipTests=true -f pom.xml > >[INFO] Scanning for projects... > >[INFO] > >[INFO] > > > >[INFO] Building Airavata Client Samples 0.14-SNAPSHOT > >[INFO] > > > >Downloading: > >http://repository.apache.org/snapshots/org/apache/airavata/airavata-data-models/0.14-SNAPSHOT/maven-metadata.xml > >Downloading: > >http://repository.apache.org/snapshots/org/apache/airavata/airavata-api/0.14-SNAPSHOT/maven-metadata.xml > >Downloading: > >http://repository.apache.org/snapshots/org/apache/airavata/airavata/0.14-SNAPSHOT/maven-metadata.xml > >Downloading: > >http://repository.apache.org/snapshots/org/apache/airavata/airavata-model-utils/0.14-SNAPSHOT/maven-metadata.xml > >Downloading: > >http://repository.apache.org/snapshots/org/apache/airavata/airavata-common-utils/0.14-SNAPSHOT/maven-metadata.xml > >Downloading: > >http://repository.apache.org/snapshots/org/apache/airavata/commons/0.14-SNAPSHOT/maven-metadata.xml > >Downloading: > >http://repository.apache.org/snapshots/org/apache/airavata/airavata-client-api/0.14-SNAPSHOT/maven-metadata.xml > >Downloading: > >http://repository.apache.org/snapshots/org/apache/airavata/airavata-client-api/0.14-SNAPSHOT/airavata-client-api-0.14-SNAPSHOT.pom > >[WARNING] The POM for > >org.apache.airavata:airavata-client-api:jar:0.14-SNAPSHOT is missing, no > >dependency information available > >Downloading: > >http://repository.apache.org/snapshots/org/apache/airavata/airavata-gfac-schema-utils/0.14-SNAPSHOT/maven-metadata.xml > >Downloading: > >http://repository.apache.org/snapshots/org/apache/airavata/airavata-jpa-registry/0.14-SNAPSHOT/maven-metadata.xml > >Downloading: > >http://repository.apache.org/snapshots/org/apache/airavata/registry/0.14-SNAPSHOT/maven-metadata.xml > >Downloading: > >http://repository.apache.org/snapshots/org/apache/airavata/airavata-registry-api/0.14-SNAPSHOT/maven-metadata.xml > >Downloading: > >http://repository.apache.org/snapshots/org/apache/airavata/airavata-workflow-execution-context/0.14-SNAPSHOT/maven-metadata.xml > >Downloading: > >http://repository.apache.org/snapshots/org/apache/airavata/airavata-credential-store/0.14-SNAPSHOT/maven-metadata.xml > >Downloading: > >http://repository.apache.org/snapshots/org/apache/airavata/airavata-registry-cpi/0.14-SNAPSHOT/maven-metadata.xml > >Downloading: > >http://repository.apache.org/snapshots/org/apache/airavata/airavata-api-stubs/0.14-SNAPSHOT/maven-metadata.xml > >Downloading: > >http://repository.apache.org/snapshots/org/apache/airavata/airavata-client-configuration/0.14-SNAPSHOT/maven-metadata.xml > >Downloading: > >http://repository.apache.org/snapshots/org/apache/airavata/airavata-configuration/0.14-SNAPSHOT/maven-metadata.xml > >Downloading: > >http://repository.apache.org/snapshots/org/apache/airavata/airavata-client-api/0.14-SNAPSHOT/airavata-client-api-0.14-SNAPSHOT.jar > >[INFO] > > > >[INFO] BUILD FAILURE > >[INFO] > > > >[INFO] Total time: 6.780s > >[INFO] Finished at: Wed Jul 30 13:43:44 PDT 2014 > >[INFO] Final Memory: 8M/148M > >[INFO] > > > >[ERROR] Failed to execute goal on pro
Re: [SciGaP-Dev] CIPRES-Airavata integration proposal]]
Does it work if you use mvn -o clean install? What do you get when you run ls -tlr ~/.m2/repository/org/apache/airavata/airavata-client-api/0.14-SNAPSHOT/ ? Mine looks like this: mpierce$ ls -tlr ~/.m2/repository/org/apache/airavata/airavata-client-api/0.14-SNAPSHOT/ total 1432 -rw-r--r-- 1 mpierce staff5044 Jul 22 15:28 airavata-client-api-0.14-SNAPSHOT.pom -rw-r--r-- 1 mpierce staff 241 Jul 30 16:09 airavata-client-api-0.14-SNAPSHOT.pom.lastUpdated -rw-r--r-- 1 mpierce staff 241 Jul 30 16:09 airavata-client-api-0.14-SNAPSHOT.jar.lastUpdated -rw-r--r-- 1 mpierce staff 721 Jul 30 16:11 maven-metadata-local.xml -rw-r--r-- 1 mpierce staff 704373 Jul 30 16:11 airavata-client-api-0.14-SNAPSHOT.jar -rw-r--r-- 1 mpierce staff 206 Jul 30 16:11 _maven.repositories -rw-r--r-- 1 mpierce staff 231 Jul 30 16:49 resolver-status.properties On 7/30/14, 4:45 PM, K Yoshimoto wrote: I get a different error now: java-client-samples$ mvn clean install -U -DskipTests=true -f pom.xml [INFO] Scanning for projects... [INFO] [INFO] [INFO] Building Airavata Client Samples 0.14-SNAPSHOT [INFO] Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-data-models/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-api/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-model-utils/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-common-utils/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/commons/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-client-api/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-client-api/0.14-SNAPSHOT/airavata-client-api-0.14-SNAPSHOT.pom [WARNING] The POM for org.apache.airavata:airavata-client-api:jar:0.14-SNAPSHOT is missing, no dependency information available Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-gfac-schema-utils/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-jpa-registry/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/registry/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-registry-api/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-workflow-execution-context/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-credential-store/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-registry-cpi/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-api-stubs/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-client-configuration/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-configuration/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-client-api/0.14-SNAPSHOT/airavata-client-api-0.14-SNAPSHOT.jar [INFO] [INFO] BUILD FAILURE [INFO] [INFO] Total time: 6.780s [INFO] Finished at: Wed Jul 30 13:43:44 PDT 2014 [INFO] Final Memory: 8M/148M [INFO] [ERROR] Failed to execute goal on project airavata-client-samples: Could not resolve dependencies for project org.apache.airavata:airavata-client-samples:jar:0.14-SNAPSHOT: Could not find artifact org.apache.airavata:airavata-client-api:jar:0.14-SNAPSHOT in apache.snapshots (http://repository.apache.org/snapshots) -> [Help 1] [ERROR] [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch. [ERROR] Re-run Maven using the -X switch to enable full debug logging. [ERROR] [ERROR] For more information about the errors and possible solutions, please read the following articles: [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException On Wed, Jul 30, 2014 at 04:20:01PM -0400, Marlon Pierce wrote: H
Re: [SciGaP-Dev] CIPRES-Airavata integration proposal]]
I get a different error now: java-client-samples$ mvn clean install -U -DskipTests=true -f pom.xml [INFO] Scanning for projects... [INFO] [INFO] [INFO] Building Airavata Client Samples 0.14-SNAPSHOT [INFO] Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-data-models/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-api/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-model-utils/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-common-utils/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/commons/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-client-api/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-client-api/0.14-SNAPSHOT/airavata-client-api-0.14-SNAPSHOT.pom [WARNING] The POM for org.apache.airavata:airavata-client-api:jar:0.14-SNAPSHOT is missing, no dependency information available Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-gfac-schema-utils/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-jpa-registry/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/registry/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-registry-api/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-workflow-execution-context/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-credential-store/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-registry-cpi/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-api-stubs/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-client-configuration/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-configuration/0.14-SNAPSHOT/maven-metadata.xml Downloading: http://repository.apache.org/snapshots/org/apache/airavata/airavata-client-api/0.14-SNAPSHOT/airavata-client-api-0.14-SNAPSHOT.jar [INFO] [INFO] BUILD FAILURE [INFO] [INFO] Total time: 6.780s [INFO] Finished at: Wed Jul 30 13:43:44 PDT 2014 [INFO] Final Memory: 8M/148M [INFO] [ERROR] Failed to execute goal on project airavata-client-samples: Could not resolve dependencies for project org.apache.airavata:airavata-client-samples:jar:0.14-SNAPSHOT: Could not find artifact org.apache.airavata:airavata-client-api:jar:0.14-SNAPSHOT in apache.snapshots (http://repository.apache.org/snapshots) -> [Help 1] [ERROR] [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch. [ERROR] Re-run Maven using the -X switch to enable full debug logging. [ERROR] [ERROR] For more information about the errors and possible solutions, please read the following articles: [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException On Wed, Jul 30, 2014 at 04:20:01PM -0400, Marlon Pierce wrote: > Hi Kenneth-- > > You should first build the entire Airavata project (mvn clean install at > the top level). This should fix the missing dependency problems you see > below. You can then do the java-client-samples only build as often as > you want from there. > > I just verified this, but let us know if you have problems. The build > took ~6 minutes on my laptop over wireless, but your first build may > take a little longer as you'll need additional jars. > > Marlon > > On 7/30/14, 4:05 PM, K Yoshimoto wrote: > >I wanted to play a bit more with the existing java client examples, > >in parallel with the new ones that are being written. I tried > >building them but got an error about missing files. > >This was run from airavata-api/airavata-client-sdks/java-client-samples. > > > > > >mvn clean install -DskipTests=true -f pom.xml[INFO] Scanning for > >projects... > >[INFO] > >
Re: [SciGaP-Dev] CIPRES-Airavata integration proposal]]
Hi Kenneth--
You should first build the entire Airavata project (mvn clean install at
the top level). This should fix the missing dependency problems you see
below. You can then do the java-client-samples only build as often as
you want from there.
I just verified this, but let us know if you have problems. The build
took ~6 minutes on my laptop over wireless, but your first build may
take a little longer as you'll need additional jars.
Marlon
On 7/30/14, 4:05 PM, K Yoshimoto wrote:
I wanted to play a bit more with the existing java client examples,
in parallel with the new ones that are being written. I tried
building them but got an error about missing files.
This was run from airavata-api/airavata-client-sdks/java-client-samples.
mvn clean install -DskipTests=true -f pom.xml[INFO] Scanning for projects...
[INFO]
[INFO] Building Airavata Client Samples
[INFO]task-segment: [clean, install]
[INFO]
[INFO] [clean:clean {execution: default-clean}]
[debug] execute contextualize
[INFO] [resources:copy-resources {execution: copy-resources}]
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory
/media/785F-C62B/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/assembly/dist
[INFO] [remote-resources:process {execution: default}]
Downloading:
http://repository.apache.org/snapshots/org/apache/airavata/airavata-data-models/0.14-SNAPSHOT/airavata-data-models-0.14-SNAPSHOT.pom
[INFO] Unable to find resource
'org.apache.airavata:airavata-data-models:pom:0.14-SNAPSHOT' in repository
apache.snapshots (http://repository.apache.org/snapshots)
Downloading:
http://repository.apache.org/snapshots/org/apache/airavata/airavata-model-utils/0.14-SNAPSHOT/airavata-model-utils-0.14-SNAPSHOT.pom
[INFO] Unable to find resource
'org.apache.airavata:airavata-model-utils:pom:0.14-SNAPSHOT' in repository
apache.snapshots (http://repository.apache.org/snapshots)
Downloading:
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apache.snapshots (http://repository.apache.org/snapshots)
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repository apache.snapshots (http://repository.apache.org/snapshots)
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apache.snapshots (http://repository.apache.org/snapshots)
Downloadi
Re: [SciGaP-Dev] CIPRES-Airavata integration proposal]]
I wanted to play a bit more with the existing java client examples,
in parallel with the new ones that are being written. I tried
building them but got an error about missing files.
This was run from airavata-api/airavata-client-sdks/java-client-samples.
mvn clean install -DskipTests=true -f pom.xml[INFO] Scanning for projects...
[INFO]
[INFO] Building Airavata Client Samples
[INFO]task-segment: [clean, install]
[INFO]
[INFO] [clean:clean {execution: default-clean}]
[debug] execute contextualize
[INFO] [resources:copy-resources {execution: copy-resources}]
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory
/media/785F-C62B/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/assembly/dist
[INFO] [remote-resources:process {execution: default}]
Downloading:
http://repository.apache.org/snapshots/org/apache/airavata/airavata-data-models/0.14-SNAPSHOT/airavata-data-models-0.14-SNAPSHOT.pom
[INFO] Unable to find resource
'org.apache.airavata:airavata-data-models:pom:0.14-SNAPSHOT' in repository
apache.snapshots (http://repository.apache.org/snapshots)
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apache.snapshots (http://repository.apache.org/snapshots)
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'org.apache.airavata:airavata-common-utils:pom:0.14-SNAPSHOT' in repository
apache.snapshots (http://repository.apache.org/snapshots)
Downloading:
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'org.apache.airavata:airavata-client-api:pom:0.14-SNAPSHOT' in repository
apache.snapshots (http://repository.apache.org/snapshots)
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'org.apache.airavata:airavata-gfac-schema-utils:pom:0.14-SNAPSHOT' in
repository apache.snapshots (http://repository.apache.org/snapshots)
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'org.apache.airavata:airavata-jpa-registry:pom:0.14-SNAPSHOT' in repository
apache.snapshots (http://repository.apache.org/snapshots)
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apache.snapshots (http://repository.apache.org/snapshots)
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repository apache.snapshots (http://repository.apache.org/snapshots)
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Registering ec2 application with app catalog
Hi all I have to test ec2 application registration with app catalog, and i have look at the BetterGFacImpl and seems app-catalog intergration doenot support ec2. So I would like to know whether i can continue rest of the work with the old code . regards Nipun Udara
[jira] [Created] (AIRAVATA-1368) In PHP gateway the cloned new experiment gets created at the wrong moment
Eroma created AIRAVATA-1368: --- Summary: In PHP gateway the cloned new experiment gets created at the wrong moment Key: AIRAVATA-1368 URL: https://issues.apache.org/jira/browse/AIRAVATA-1368 Project: Airavata Issue Type: Bug Affects Versions: 0.13 Reporter: Eroma In PHP gateway in Experiment Summary screen user can clone experiments. When user clicks on 'Clone' button the new experiment is credited. In edit mode it only updates the created experiment. If someone accidentally clicks on clone there is no turning back. Ideally when the clone is clicked it should create a new copy of the experiment but should not save it. when user modifies the details of the new experiment and clicks 'Save' or 'Save and Launch' then the experiment should get created. This way user can avoid unnecessary creation of records. -- This message was sent by Atlassian JIRA (v6.2#6252)
Re: Notion of user roles in the PHP Reference Gateway
Hi Supun--
I got things working, more or less. I had to "localize" the startup
scripts to get the API server to start; see my comments in github. The
PHP command line tools work fine, but I was not able to run the unit
tests (see attachment).
The core work looks good but you have several rough edges still. I may
have deeper comments about the core later.
Marlon
On 7/28/14, 9:48 AM, Supun Nakandala wrote:
Hi Marlon,
Please see the inline comments
On Mon, Jul 28, 2014 at 7:07 PM, Marlon Pierce wrote:
Hi Supun--
Nice progress and writeup. I'll test out with the php client samples. Some
small comments below.
* Does the "authenticateGateway()" method authenticate a user to a
particular gateway, or do I misunderstand?
authenticateGateway method is called for authenticating the gateway. Not
for authenticating a particular user. For authenticating a user
authenticateUser
method has to be used.
* You should add a "disableUser()" method. Hopefully this is easily
implemented in the IS. A disabled user may be able to authenticate but not
be able to do anything (no permissions), or he/she may simply be denied
authentication. But all the user's profile information and roles are
retained in case the account is re-enabled.
I did some research into this previously. But apparently there is no
explicit way of disabling a user. What they have suggested is to specify a
new role for disabled users and assign it. I'll see more into this. [
http://stackoverflow.com/questions/15420138/wso2-identity-server-deactivating-user-account
]
* Are you assigning permissions directly to the user object or indirectly
through roles. That is, the role has the permission and the user is
assigned to the role. The API implies it is assigned to the user directly
but it seems like a better design to assign these to the roles directly.
The permissions are added to roles. This has to be configured from the wso2
IS side. Not from the User API. From the user api gateways can assign roles
to users and remove them via the methods addUserToRole and
removeUserFromRole.
Marlon
On 7/25/14, 1:35 PM, Supun Nakandala wrote:
Hi All,
During the past few weeks I have done several changes to the airavata user
api. The new thrift interface descriptors can be found at
https://github.com/scnakandala/airavata-userapi/
tree/master/userapi/thrift-interface-descriptors
Most of the new changes are related to permissions and role.
- Earlier it was possible to create roles and delete them from the
user
api side. But now I have removed that. Now roles can be created and
deleted
only from the WSO2 IS management console.
- I have added addUserToRole ,
removeUserFromRole , getUserListOfRole , getRoleListOfUser , getAllRoleNames
- As per the gateway specific roles I have created the roles from the
WSO2 IS side specified by Suresh previously in this thread.
- In terms of permission validation I have added getUserPermissions
and
checkPermission methods.
- getUserPermissions returns an object (
https://github.com/scnakandala/airavata-userapi/
blob/master/userapi/thrift-interface-descriptors/userAPIModels.thrift#L50
)
which contains two maps of permissions sets one for airavata api and
other
for app catalog. The key value in these maps is the name of the api
method
and the value will be true if the user has permission else false. In
addition to these to maps it also has a string signature. I have
added this
signature so that this object can be verified by the server or any
intended
party. This addresses the issue of avoiding too many calls to server
as
Marlon mentioned previously in this thread. Currently this signature
is
prepared by concatenating the serialized strings of the two maps and
the
time stamp which is then encrypted using AES.
- checkPermission method can verify whether a user has a particular
permission. eg
getUserPermission('scnakandala','airavata-api/create_project',$token)
- Also now the authenticateUser method returns the same output as in
getUserPermissions if the authentication is successful.
I also looked into the concerns related to token generation.
Although wso2 IS provides OAuth based authentication/authorization there
is
a problem of using it in the user api. User api is operated by calling the
admin services of the wso2 IS under the cover. These services are soap
endpoints and cannot be accessed via oauth authorization. There are SCIM
REST services which can be accessed via oauth authorization but those
services are not sufficient for the user api functions.
Currently I have used http basic authentication. This means for every soap
call from user api to wso2 IS I send admin username and the password of
the
tenant in use. Since we are sending the username IS knows on which tenant
we are dealing with. This creates two possibilities for the communication
between gateway and the
Re: Notion of user roles in the PHP Reference Gateway
Hi Supun--
I'm adding some review comments to code lines in github. Do you use your
startup scripts in ./userapi/src/main/resources/bin/? Unless there is a
big difference between my Mac's bash shell and your environment, these
don't work.
Marlon
On 7/28/14, 9:48 AM, Supun Nakandala wrote:
Hi Marlon,
Please see the inline comments
On Mon, Jul 28, 2014 at 7:07 PM, Marlon Pierce wrote:
Hi Supun--
Nice progress and writeup. I'll test out with the php client samples. Some
small comments below.
* Does the "authenticateGateway()" method authenticate a user to a
particular gateway, or do I misunderstand?
authenticateGateway method is called for authenticating the gateway. Not
for authenticating a particular user. For authenticating a user
authenticateUser
method has to be used.
* You should add a "disableUser()" method. Hopefully this is easily
implemented in the IS. A disabled user may be able to authenticate but not
be able to do anything (no permissions), or he/she may simply be denied
authentication. But all the user's profile information and roles are
retained in case the account is re-enabled.
I did some research into this previously. But apparently there is no
explicit way of disabling a user. What they have suggested is to specify a
new role for disabled users and assign it. I'll see more into this. [
http://stackoverflow.com/questions/15420138/wso2-identity-server-deactivating-user-account
]
* Are you assigning permissions directly to the user object or indirectly
through roles. That is, the role has the permission and the user is
assigned to the role. The API implies it is assigned to the user directly
but it seems like a better design to assign these to the roles directly.
The permissions are added to roles. This has to be configured from the wso2
IS side. Not from the User API. From the user api gateways can assign roles
to users and remove them via the methods addUserToRole and
removeUserFromRole.
Marlon
On 7/25/14, 1:35 PM, Supun Nakandala wrote:
Hi All,
During the past few weeks I have done several changes to the airavata user
api. The new thrift interface descriptors can be found at
https://github.com/scnakandala/airavata-userapi/
tree/master/userapi/thrift-interface-descriptors
Most of the new changes are related to permissions and role.
- Earlier it was possible to create roles and delete them from the
user
api side. But now I have removed that. Now roles can be created and
deleted
only from the WSO2 IS management console.
- I have added addUserToRole ,
removeUserFromRole , getUserListOfRole , getRoleListOfUser , getAllRoleNames
- As per the gateway specific roles I have created the roles from the
WSO2 IS side specified by Suresh previously in this thread.
- In terms of permission validation I have added getUserPermissions
and
checkPermission methods.
- getUserPermissions returns an object (
https://github.com/scnakandala/airavata-userapi/
blob/master/userapi/thrift-interface-descriptors/userAPIModels.thrift#L50
)
which contains two maps of permissions sets one for airavata api and
other
for app catalog. The key value in these maps is the name of the api
method
and the value will be true if the user has permission else false. In
addition to these to maps it also has a string signature. I have
added this
signature so that this object can be verified by the server or any
intended
party. This addresses the issue of avoiding too many calls to server
as
Marlon mentioned previously in this thread. Currently this signature
is
prepared by concatenating the serialized strings of the two maps and
the
time stamp which is then encrypted using AES.
- checkPermission method can verify whether a user has a particular
permission. eg
getUserPermission('scnakandala','airavata-api/create_project',$token)
- Also now the authenticateUser method returns the same output as in
getUserPermissions if the authentication is successful.
I also looked into the concerns related to token generation.
Although wso2 IS provides OAuth based authentication/authorization there
is
a problem of using it in the user api. User api is operated by calling the
admin services of the wso2 IS under the cover. These services are soap
endpoints and cannot be accessed via oauth authorization. There are SCIM
REST services which can be accessed via oauth authorization but those
services are not sufficient for the user api functions.
Currently I have used http basic authentication. This means for every soap
call from user api to wso2 IS I send admin username and the password of
the
tenant in use. Since we are sending the username IS knows on which tenant
we are dealing with. This creates two possibilities for the communication
between gateway and the user api
1. gateway send tenant admin username and password with every request
to
the user api
2. user ap
