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D6.5: Production Deployment of User Access Systems

1. VPH Share ICT 269978 Integrated Project of the 7 Framework Programme COOPERATION THEME 3 Information amp Communication Technologies ICT 2009 5 3 Virtual Physiological Human VPH Share Work Package WP6 User Access Systems Deliverable D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share DOCUMENT INFORMATION IST Project Num Full title Project URL EU Project officer Work package Deliverable Date of delivery Status Nature Dissemination Level Authors Partner Responsible Author Abstract for dissemination Keywords FP7 ICT 269978 Acronym VPH Share Virtual Physiological Human Sharing for Healthcare A Research Environment http www vph share eu Robert Begier Number 6 Title User Access Systems Number 6 5 Title Production Deployment of User Access Systems Contractual 28 Feb 14 Actual 28 Feb 14 Version 1v2 Final Bd Prototype Bd ReportO Dissemination O Other O Public PU Bd Restricted to other Programme Participants PP LI Consortium CO LI Restricted to specified group RE LI Debora Testi CINECA Daniel Harezlak CYF Ernesto Coto USFD Juan Arenas USFD Vadim Surpin IITP Juan Arenas Email j arenas sheffield ac uk Partner USFD Phone 44 0 114 222 0166
2. FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 M Date 28 Feb 14 Sood VPH Share to retrieve the name of the applications that corresponds to the service being added so as to show the application name instead of the URL of the service in Taverna Workbench s GUI For this point on the user can more readily identify the applications and web services in the GUI 4 WORKFLOWS COMPOSITION INTEGRATION AND EXECUTION During the VPH Share project several tools have been developed to compose deploy and execute biomedical workflows Most of the work has been done behind the scenes to provide the user with friendly interfaces and reliable tools that are able to run smoothly through the VPH Share infostructure The following sections describe the developed tools in detail 4 1 Final architecture This section provides a brief review of the architecture leaving the more detailed description for the following sections The final architecture for workflow composition integration and execution is composed of client side and server side components see Figure 46 CLIENT SIDE SERVER SIDE Manager API D Server v Clinical Taverna Researcher Workbench Cloud Taverna p Facade On line Web based Remote ni Desktop Figure 46 Workflow Management Architecture overview On the client side a biomedical workflow can be composed and executed
3. amp le DUCE Data gt prov entity id df7197ce 6ae1 442b bbb9 7a7f2e0ac530 lt prov label gt OutputDescriptors lt prov label gt lt prov location gt loboder aneurist Geomerry Descriptors OutpurDescriptors ml chorowvilocations lt prov entity gt lt Entities used in derivation gt lt prov wasDerivedFrom gt lt prov generatedEntity prov ref df7197ce 6ael 442b bbb9 7a7f2e0ac530 lt prov usedEntity prov ref Dbee5df8 8c4c 46e0 a3c6 11597478d81b gt lt prov usedEntity prov ref 5b5a9dd2 be74 40a7 82d8 42cbc9368754 gt prov time 2014 02 24 15 49 57 lt prov time gt lt prov wasDerivedFrom gt lt prov document gt lt provenance gt lt rating gt 0 lt rating gt lt relatedResources gt lt semanticAnnotations gt lt status gt active lt status gt lt type gt File lt type gt lt updateDate gt 2014 02 24 15 11 42 288 lt updateDate gt lt views gt 0 lt views gt lt fileType gt XML lt fileType gt lt format gt XML lt format gt lt size gt 429 lt size gt subjectID lt file gt lt resource metadata gt Notice the highlighted field lt provenance gt which contains a provenance document following the PROV XML schema see http www w3 org TR prov xml The generated provenance document specifies the location of the file its owner its ID in the Catalogue and all the Page 75 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User A
4. e REST Endpoint an endpoint pointing to a REST resource optionally a WADL descriptor can be provided Each of the endpoint should have a port number assigned which is used when setting up redirections by the platform after an Application instance has started The endpoints are defined in the development mode and therefore can be instantly tested by developers According to the information provided in endpoint definitions the platform is able to produce valid URL and port mappings during runtime to target appropriate cloud instances 3 2 2 Generic Invoker In the generic invoker mode Applications tab in the main view regular users can instantiate and user available Applications A sample view of this mode is presented in Figure 44 Page 56 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 a VPH Share Workflows My Applications Name IP Location Status Actions WebDRS 10 100 8 3 Cyfronet active Web Applications DRS frontend http https Services Figure 44 Generic invoker view with a list of Appliance instances The details for each instance show the site where the instance 1s running and its current state After the instance becomes active all defined redirections are configured and the available endpoints are listed for easy access In the presented example the WebDRS Application exposes a web application available through http or
5. FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share The Refine options can be used to add additional filtering to the data by adding extra information The refinement is performed by inserting the text in the appropriate field and then pressing enter on the keyboard Filter By Dataset Workflow Atomic Sevice File SWS Application 9000080 User Refine Category Author mbalasso Figure 15 Filter and refine options in the plain search 2 3 3 2 Semantic Search The link to the Semantic search as user interface to the WP4 developed services 1s available just below the search button of the global search and it can be used for a more detailed search with respect to the free text one provided by the Plain search described above semantic search 1 Search dataset Select dataset Select concept Query dataset Search dataset Search Advanced search Figure 16 First step of the semantic search The first step allows the user to enter the semantic term or combination of terms The output will be the list of resources where the specific term 1s present anywhere in the resource information Page 33 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share 1 Search dataset 2 Select dataset Select concep
6. D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share e Users list of users using the cloud infrastructure e Virtual Machines list of virtual machines working for a given application 3 2 Overview of Cloud Management User Interface Cloud Management GUI offers graphical user interfaces to manage the life cycle of Application instances run on the cloud It works in three different modes which are shortly summarised below e Development mode in this mode a developer can instantiate both starting templates and existing Applications to perform development tasks leading to the creation of new Applications in this mode no optimisation is used and each instance of an Application has a corresponding physical machine running e Generic invoker mode this mode is intended for users who would like to instantiate individual Application instances and utilise their functionality in this mode platform optimisation is used which can result in instance reusing e Workflow mode this mode is used to view all started Application instances this does not include instances run in development and generic invoker modes on behalf of a given user which can be a result of using an external workflow management system The sections below contain screenshots with descriptions for each of the modes for completeness some of these were already presented from the user perspective in section 3 2 5 The main
7. In such a case the application communicates with the Cloud Facade through the Workflow Manager API The Cloud Fa ade will then start its own Taverna Server with an integrated VPH Share plugin and then submit the biomedical workflow to the server for execution In all cases the VPH Share plugin provides support for executing biomedical workflows with interactive and non interactive services as well as the execution of workflows in batch mode The results of the execution are accessible though the LOBCDER repository see Section 3 3 With the development of all the aforementioned processes and tools the VPH Share project provides the Clinical Researcher with a very versatile platform for execution and composition of biomedical workflows 4 2 GIMIAS WebServices plugin to make CLP tools available as Web Services The main goal of the GIMIAS WebServices plugin is to offer a mechanism to expose external tools command line tools as web services SOAP facilitating the integration of these tools on research workflows providing also an interface to support tools with long execution times The GIMIAS WebServices Plugin part of GIMIAS s extensions is able to expose as a web service any processor of any GIMIAS Plugin or Command Line Plugin CLP A list of available Plugins and CLPs is available at http sourceforge net apps mediawiki gimias index php title Users and instructions on how to create new CLPs can be found at http sourcefo
8. VM VMT VNC VTK WADL WebDAV FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 Smi VPH Share JavaScript Object Notation Large OBject Cloud Dataf storagE fedeRation Master Interface NX technology is a computer program that handles remote X Window System connections Open Service Gateway Initiative Data Access and Integration Public Key Infrastructure Resource Description Framework REpresentational State Transfer Simple Object Access Protocol SPARQL Protocol and RDF Query Language Structured Query Language Secure SHell Secure Socket Layout User Access System User Interface Uniform Resource Identifier Uniform Resource Locator Virtual Machine Virtual Machine Template Virtual Network Computing protocol Visualisation Toolkit www vtk org Web Application Description Language Web Distributed Authoring and Versioning Page 80 of 82 WebDRS WP WSDL WS XML XML RPC FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 Web Drug Ranking System a service from ViroLab Workpackage Web Service Description Language Web Service eXtensible Markup Language XML encoded Remote Procedure Call protocol VPH Share Page 81 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deploymen
9. so each one runs a test script using operations The script of the second service has been set to fail on purpose so as to test the reaction of the server to this failure Notice how the failed service is highlighted and its status is set to CRITICAL The system administrator received an alert e mail when the service failed The script of the third service has been set to be successful Notice how the service s status 1s set to OK Hrefox N Nagios Core 54 217 240 87 C E Google P f D N a 1 Oo S Current Network Status Host Status Totals Service Status Totals g Last Updated Wed Feb 26 11 13 49 GMT 2014 Up Down Unreachable Pending Ok Warning Unknown Critical Pending I Nagose Core 35 0 www nagis org BENE No EN J Logged in as nagiosadmin All Problems All Types All Problems All Types dera a a Documentation View History For all hosts View Notifications For All Hosts Current Status View Host Status Detail For All Hosts Tactical Overview z Service Status Details For All Hosts Map Hosts Limit Results 100 v Services Host Groups Host Service Status amp LastCheck Duration Attempt Status Information HTTPR HTTP OK HTTP 1 1 200 OK 615 bytes in 0 051 Summary VPH Share igi o 022 201 11 01 56 4d18h 1m6s 1 3 ere Grid portal vph share eu second response time Service Groups Webinject CRITICAL case 2 Failed HTTP Workflow Infrastructure 02 26 2014 03 14 43 4d
10. 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share The information currently includes the metadata below a revision of the metadata model is under finalisation and thus new metadata might be added in next versions of the system Y the resource title the resource description the associated information creation date language related citations type workflow data etc which are inserted at the upload time citations of publications related to the resource if there are other resources in some ways associated or related to the present one the views a counter of the number of visits to this resource which is automatically updated the version number the tags which can be used in the global search service the licence type and eventually the associated licence file available for download the semantic annotation URI eG AAR See amp On the left side at the bottom one or more buttons are present which allows you to access the resource The button will have a colour and an associated action depending on the permission the user has been granted on the specific resource If the user does not have the permissions to access the resource the button will allow the sending of a request for sharing to the resource owner where a personalised message can be added to the request to specify the purpose of the resource need When pressed the user
11. T2 Figure 56 Nagios Core web interface showing VPH Share service monitoring 76 LIST OF TABLES Table L WO Y or Ce VELWO MS R E E E uauaeers 1 Wale 2 WPO Cat Se a a PEE E A oce e N E A N EE A S 78 Page 8 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share EXECUTIVE SUMMARY This document presents the production version of the User Access System that has been developed by the WP6 in the context of the VPH Share project WP6 is an integration work package and therefore the multiple interactions with the other project work packages are also reflected in this document The main objective of this deliverable is to present the different features that have been developed along the project and that are going to be released as part of the production version of the user access system at the end of year 3 In addition the document outlines the future plans to support external users and use cases The following topics are addressed in this document An overview of the final features released via the project dedicated web portal Master Interface or MI and their APIs providing highlights about Final Architecture and API Web application Security and authentication 1 User interface User registration and access Discovery tools Resources management and their operation 4 Data Applications A
12. This document details the Production Deployment of User Access Systems from the technical and end users point of view It lists the status of each component produced by WP6 and the on going work for each of them Appliances for visualisation of physiological data scientific workflow composition management user interface usability semantic search annotation roles policies webservice taverna plugin security batch processing web composition The information in this document is provided as is and no guarantee or warranty is given that the information is fit for any particular purpose The user thereof uses the information at its sole risk and liability Its owner is not liable for damages resulting from the use of erroneous or incomplete confidential information Page 2 of 82 Version Log Issue Date 4 Oct 13 9 Oct 13 11 Dec 13 10 Jan 14 13 Jan 14 23 Jan 14 27 Jan 14 31 Jan 14 7 Feb 14 21 Feb 14 21 Feb 14 26 Feb 14 28 Feb 14 Version 0 1 0 2 0 3 0 4 0 5 0 6 0 7 0 8 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Author EC JA EC JA EC JA JA DT DH JA EC DH DT JA EC ES EC DH DT JA EC PMO Version 1v2 Date 28 Feb 14 VPH Share Change Initial draft for comments Initial draft after changes suggested by DT Initial draft of Chapter 5 Include MI initial content Chapter 3 Include Cloud Service
13. Workflows Owned resources 1 User care Use cases support External projects support External users support An overview of the final VPH Share Cloud services on which the MI relays for the iteration with the backend infostructure Final Architecture and API Overview of Cloud Management User Interface it is covered in more detail in WP2 s deliverable Development Mode Generic Invoker External Workflows LOBCDER repository Remote Desktop Access Webservice Catalogue An overview of the workflow services and management including 1 Final Architecture Page 9 of 82 bol fol rol fol bol fol bol bol FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 Smi VPH Share GIMAS WebServices plugin to make command line tools available as web services Specification of services requiring user interaction VPH Share plugin Desktop composition and execution tool Web composition and execution through Taverna Online Support for workflows with long execution times Workflow execution through the MI Batch execution Desktop batch execution Web batch execution Workflow Manager API Data Provenance and Semantic Workflow service monitoring A high level overview of the goals and work plan to be accomplished during year 4 This document is organised as follows Chapter 3 descri
14. b N fA _ VPH Share different Operating Systems with already configured all the necessary VPH Share services like the security proxy or the LODBCER data connection 2 3 5 2 Run an existing Application Applications that have been created and saved by developers may be used by any user of the platform There are several ways in which the VPH Share cloud platform enables use of Applications By asking a specific service to be instantiated using the so called Generic Invoker see section 3 2 2 for more details By authoring a Taverna workflow which makes use of the VPH Share Taverna plugin to automatically instantiate the required services By writing user owned software which communicates with the Cloud Facade interface of the Atmosphere platform and makes use of its API to instantiate and invoke services In this section we will focus on the Generic Invoker as a tool provided directly by the VPH Share platform and targeted for end users rather than application developers The Generic Invoker is a facility provided as part of the VPH Share Master Interface and enabling to use specific applications using a straightforward GUI without worrying about the technicalities of service instantiation and invocation Technically the Generic Invoker is part of the Cloud manager portlet Once the user has logged in he she can get the list of the available Appliances as reported in the Browsing section Start new application U
15. by a clinical researcher using two different applications Taverna Workbench and Taverna On line For this purpose the VPH Share plugin has been integrated into these two platforms Taverna Workbench is used for desktop composition and Taverna On line is used for web composition If the executing workflow requires user interaction the user is able to perform such interaction via NoMachine a web based remote desktop application which connects to the executing workflow Page 60 of 82 FP7 ICT 269978 VPH Share p WP6 User Access Systems A Je 3 D6 5 Production Deployment of User Access Systems 7 N Version 1v2 Date 28 Feb 14 VPH Share On the server side the Cloud Fa ade is the platform where the core of the biomedical workflow is executed This execution is controlled by exchanging information with the VPH Share plugin integrated into Taverna Workbench or Taverna On line If a biomedical workflow requires interaction a server side component inside the Cloud Fa ade is started to make the remote desktop communication possible Additionally a biomedical workflow can be executed directly from the Master Interface using the Workflow Manager In this case the Cloud Fa ade will start its own Taverna Server with an integrated VPH Share plugin and then submit the biomedical workflow to the server for execution Finally an external application on the client side can also start the execution of an already composed workflow
16. click on the details blue icon to learn about the possible ways in which he she may interact with the Application Instance The Cloud Management portlet will display a suitable dialog listing the interfaces provided by the instance tools Ts Workflows My Applications Name IP Location Status Actions AneuristGUl NoMachine NoUploadDelay 10 100 8 113 Cyfronet active th AsyncWeb Web Applications plugin http WS REST Services axis2 services wsGimias http Jaxis2 services ws Gimias http Other services ssh 149 156 10 132 12766 Figure 31 Invocation endpoints for an active application In this case the sample service provides access through SSH for administrative purposes as well as an HTTP redirection upon which a Web Application endpoint has been configured Clicking on the displayed link will take the user directly to the web application enabling to start using the service If the service provides a non Web interface for example a remote desktop the user will need a client appropriate for the type of interface in use e g VNC NoMachine Some services only provide programmatic access via APIs such as SOAP or REST in which case the service 1s intended to serve as a backend for other services While it may still be useful to instantiate such services in the Generic Invoker no end user interface is available In any case the detail page will provide the user with details on how to access any interface endpoint provided by your insta
17. computation resources The services are executed in the order specified by the Taverna workflow The output of each service as well as the final output of the Taverna workflow is stored in the LOBCDER see Figure 47 hitp vph cyfronet bost 149 156 10 132 o cyfronet pl Thanks for using NX Web mpanton Click on the button below to ext the pple applet t Yew Tools Selection Advanced Heip Workflow Nawgation F Manual neck cutting Aneurysm wih vessel For detailed information on ho 4eRngcut outputSurfaceMesh 5 Help and Acknowledgment Automatic Neck Cutting Select Neck Figure 48 Web based remote desktop connection via NX NoMachine If an Application requires user interaction a web browser window will automatically open in the user s desktop when the service is executed so that the user can perform the interaction The browser will start a web based remote desktop session via a NX NoMachine https www nomachine com client The client is available for all major platforms The NoMachine Web Companion java applet downloads and executes the appropriate version The end user experience is such that the remote application is run locally with a little slower response times dependent on the network throughput than a normal PC see Figure 48 An explanation on how to run an example workflow can be found at http vph share eu content running aneuristworkflow short workflow Page 65 of 82 FP7 I
18. for specific applications end points behaviour 1 e for web services 2 3 4 Resources Data 2 3 41 Remote visualisation For the unstructured data for each file there 1s also a new icon eye shape which allows the user to have a remote preview of the data This remote visualisation solution has been implemented by integrating ParaviewWeb Paraview is an open source multi platform data analysis and visualisation application It allows exploring and 3D visualisation of data or it allows creating batch script to process data The software package supports also big data thanks to a distributed calculation mechanisms which makes the system very efficient From its version 4 Paraview is distributed together with ParaviewWeb which makes available a series of tools for the rendering and sharing of 3D data and makes possible the integration of Paraview functionalities into a web browser API Javascript In the first implementation available in this production release the remote visualisation has been activated for a limited number of file types i e vtk and for a limited type of data structures i e structured grid polydata etc More data formats and data structures will be added in year 4 according to the beta users requests When the user clicks in the preview icon the data 1s loaded and a panel is opened in the top part of the page The data are transferred to the visualisation server where ParaviewWeb performs the selected renderin
19. in ParaviewWeb for potential exposure into the MI for the moment a limited number has been integrated for effort constraints and to wait for the user feedbacks on which might be the functionalities of interest for future implementation 2 3 4 2 Upload 2 3 4 2 1 Structured data DPS In VPH Share we primarily refer to tabular and potentially relational data sources such as CSV extracts and relational databases as Structured Data A desktop application Data Publication Suite has been developed as part of WP3 to support the process of publishing clinical or research data sets in a secure Internet accessible way The data once published may be browsed using an RDF Browser or queried using SPARQL and an SQL type protocol from the OGSA DAI project The general process for publication although many of them are not mandatory is as follows Import a data source Define relationships between the tables if they exist and are not automatically detected Semantically annotate the data Create a destination container of the server Create a new destination based on a data source Define a de identification profile for this destination Publish the data Manage the access list for the resource More information on the DPS technical details and its use can be found in WP3 deliverables On the MI side a page is available to users with a short description on the DPS links to the documentation and to download the application a
20. jcvv UAhUAg Z2vSI jpRhIDhvu7UXQLuQwSCF HSA SHA1 DSA Base64 Private key Figure 2 Ticket signature creation The authentication ticket is based on the Apache mod auth pubtkt technology The mod auth library5 a Python package to support the ticket creation and validation has been developed and integrated into the Master Interface The ticket is signed with the DSA Algorithm with a 2048 bytes key The ticket is then compressed in base64 to make easier the communication of different systems Anyone who has the below public key and a ticket can verify it and if valid it can open a session being sure that the information contained in it are safe and generated from the MI MIIDOZzCCAi4GByqGSMA4BAEwggIhAoIBAQD YHe5 IDKkW21i2bJTx4jcMERgLA77G 4 T13a2KhOw3ldl 7asktxZtvlJsxEpkdl TUTe2FFdssrcjQ bV ytBJgUf3KjfK 7rhK SuVLzNCO09Z73vjhr983WrBG7or7r hKjPlgaLsNNS1GVjHEHS jurGaE 4 7LhnX mfu ZALySwA2NQdbp 1 AbcQ6CjqXdtK Y w 7MQdj3cacM1PArWhnVDdPCO2TwZJA7ae40 1 WbPcUQmxtIM w3FYR5emjbz2C98 V Uv UdI6FbS 1 Qd V ZLPDP3j0IRcdQ RrnyMLtbN 32p H4xdrHbDQOnoRWhGhxcNp k xgJtHx2z lpbtU yCqP VOwsq6cO9AhUA ySB ytjH91Si TITUSmarwuAQECggEBALIIFPDXQTT4UpxkLer46K VOcnoek5 AbBNMFEh fKdm E2P9CzB gHLk Q1UiZRou7rRK vtvond4d7CeTK2X Va7uQMORbg1O7ABbczvh a04dW gegGAHr5rEZk6OBPzgW Y wvLEisF9f2vTufzWhAgOMUY WSI joc ILjFOuf TNLey2s7bjELP7nA6TmGrCtR XOHLPjIoA9OSTS YDHLMCq9r TGQEm 5 1 dh2Tfs KQnkbu OIt6ECr0t G 5chJin5 ROx5qO yqdywEzhhNwd G0eMc Y 6B aJwNn wNe zyuMenTy
21. portal vph structure share eu api deletegroup group lt group gt ticket lt ticket gt Method GET Parameters group the group name ticket your authentication ticket Returns Status code 200 WW OKU Status code 403 Ticket not valid or user not allowed to invoke the service Status code 500 2 2 2 5 api addtogroup Description It adds a user or a group to a group The requester must be one of the group managers the same user who has created the group With the recursive parameter if the group has any child group the user will be added to all of them as well Url structure portal vph share eu api addtogroup group group amp name name to add amp tick et ticket Page 15 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share Method GET Parameters group the group name name the user name or the group name to add recursive if present with any non empty value add user to all children group ticket your authentication ticket Returns Status code 200 Y OK Status code 403 Ticket not valid or user not allowed to invoke the service Status code 500 2 2 2 6 api removeuser Description It removes a user from a group The requester must be one of the group managers the same user who has created the group With the recursive parameter if the group has any child group the user will be removed from all of them as w
22. selected directory As in a standard file system removal of LOBCDER resources is possible The removal action can be applied to both files and directories In case of a directory all its contents contained files and subdirectories are recursively removed from the storage The action respects the permissions set on files and directories so only resources owned by a given user can be removed The user credentials are delegated down to the LOBCDER service with each request to be authorised Each of the files stored in LOBCDER can be annotated by a number of metadata properties The metadata engine implemented within LOBCDER offers an extendible API to support new properties The properties can be viewed and set 1f they are writable from the browser Page 57 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share by picking one of the files and going to the metadata view Metadata are managed by a dedicated REST service exposed by the LOBCDER component which is completely hidden from the end users by the browser The service also enables for requesting search queries on the metadata In such case the list of LOBCDER resources is filtered independently of the directory structure so all the files are always examined during searching 3 4 Remote Desktop Access To cover use cases where desktop based GUI applications are part of workflow exe
23. work together To this purpose the source code was shared with all the developer team on Github and two instances of the application were deployed A production instance reachable at portal vph share eu on which only consolidated features are deployed for end users evaluation A development instance at devel vph share eu which is used by the developers during the implementation to test the new functionalities and their integration The overall system is described in the next sections with preliminary technical information on the security and authentication layers 2 2 6 The security layer Security is an important aspect of the VPH Share platform The security proxy is implemented as part of WP2 and here just the aspects related to the Master Interface are described see D2 6 for more details on the security proxy Being the MI the point of access for the user the MI is responsible for passing to the other services the information on the user identity and granted permissions The Master interface uses Biomed Town as OpenID identity provider see next section for more details if the user is recognised as a valid one a session is opened in the MI and a valid ticket generated The authentication ticket holds all the information about the user and is signed by the MI to prove its authenticity The ticket is structured as the follow uid2 username validuntil2 expire time gt cip lt ip gt tokens lt roles gt udata lt userna
24. 1 A Re D a E m 39 DOs Resources AMP NC AO MG oooesetereo ncasdeemt amas ndav duse urea E EEEN ENTEROS 42 2 3 0 Resources workflows eeeseesesessssssesseeeeeeeeee eene nennen nennen 45 Zo AMunseqQwWedTesOUbCESoiscooeouormdi at susp goto tes sinat c co tar eu dese sc oe ieren 48 oS uic E 51 MED cc Fore oso Seg Bia ol ig ook ee eee een TO S OUT 22 o Apidae Mite CCl edd APT o aaeoeetetos oit Spusuelskuo beo cidebeebas NS 22 3 2 Overview of Cloud Management User Interface eseeeeeeeee 29 Page 4 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 SS PCV CVO DMC DU NOUE RTT 55 mu SCC TIC TINY ORG serseri serene deis E E EE EEE EEEE E 56 e JExternal WOPBSEIOQUS O A A A A 57 3 gt LOBCDER Fe POS OI y cress enir EEE E EAEE E 57 IA ROED S O S a deci ato mRNA rcd INI DLE PREIS Ucd NRI RE PARES MN ONORE 58 393 WED SERVICE ALA O ui m 59 4 Workflows composition integration and execution sese 60 AE eM ACN CS RR mU E 60 4 2 GIMIAS WebServices plugin to make CLP tools available as Web Services 61 4 3 Specification of services requiring user interaction eesssssssseeeressssssseeerrsssssseees 62 Lu ME uoi UAE 63 4 4 1 Desktop composition and execution OO eeeccccccccccceesseseseecceeeeseeaeeeeeeeeeees 64 4 4 2 Web composition and execution thr
25. 17h 59m6s 3 3 Response Code Verification received 302 Summary expecting 200 Grid Workflow Manager Weblnject OK All tests passed successfully in x 411 07 56 4d 17h 59m 6s Problems status fox iier 0 543 seconds Services Unhandled localhost lt gt ping ORI 02 24 2014 10 28 43 4d 18h 6m 6s PING OK Packet loss 0 RTA 0 05 ms Hosts Unhandled HTTP OK HTTP 1 1 200 OK 418 bytes in 0 006 Network Outages webserver HTTP 02 26 2014 03 18 43 1d 18h 38m 6s serm inc E Quick Search Results 1 5 of 5 Matching Services Reports Availability x Figure 56 Nagios Core web interface showing VPH Share service monitoring Page 76 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 5 YEAR 3 OUTCOMES WP6 Implementation WP6 Year 3 Achievements Team Roles O Owner C Contributor Results delivered Remote visualisation services based on Paraview LOBCDER web client GIMIAS Webservice wrapper extended to run long lasting requests VPH Share Taverna plugin extended to run long lasting request Workflow Manager Web Workflow composition services Workflow execution services integration on the MI Integration of new Atmosphere 2 0 API Integration of new Metadata Catalogue User cases and external projects support with bug fixing C New cloud management interface Initial implementation of services monitor
26. BDCER the user can browse the sub folders and for each folder the available files If the user has the permissions he she can download the file by clicking on the file name link The file owner can also delete or modify the file metadata respectively with the trash bin and pencil icons at the end of each row If the data format supports it the preview icon is also available to obtain the file remote visualisation as described in section 2 3 4 1 The tag icon allows the user to copy the path of the file or folder in the computer s clipboard so that it can be pasted afterwards 1n any other application This is especially useful for instance for the user to input paths to a workflow execution application see section 4 To add a new file the user can use the Add files green button or can create new directories with the top button Create directory inserting in the text box the name of the new older 2 3 5 Resources applications 2 3 5 1 Create a new Application The creation of a new Appliance is part of WP2 and just exposed into the MI Details on this can be found on WP2 deliverables and in section 3 2 1 In short the user can create his her instance of the Application VM and register it into the system This can be done also relying on a number of templates created by WP2 for the Page 42 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 W
27. CT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 ES Date 28 Feb 14 VPH Share 44 2 Web composition and execution through Taverna Online The architecture for web based workflow composition and execution is presented in Figure 49 Currently Taverna On line is supported via the High Performance Computing Online OnlineHPC site OnlineHPC s online scientific workflow editor is free of charge and it is available at http onlinehpc com CLIENT SIDE SERVER SIDE Cloud f Facade dt Researcher Workflow Taverna On line ise If ea cC gt poo s AS without LOBCDER AS with interaction interaction NoMachine connection Web based Remote Desktop Figure 49 Web based Workflow Management Architecture overview Once logged in OnlineHPC the user just needs to press the New Workflow button and name the new workflow Then the user will be presented with a working area as shown in Figure 50 If the user wants to include services provided by the VPH Share project it 1s only necessary to click on the VPHService icon inside the Processors box in the left side of the working area and then drag and drop it in the working area The result of this process is shown in Figure 50 Workflows v Components Processors n e ee Biomart ce WSDL E VPHSeni Vg 5 ervice p R Rshell uv p x Spreadsheetlmport E Tool 5 i lt
28. I RTI 34 Figure 19 Dataset internal query eesislsssssssseeeeeeeeeeeeeee nnne eene nn nnne essen nnns 34 Figure 20 Set value Tor 1n CIUSIOT Cret dessen esa oo arma den aene a ag Y r Fe RUNE Eee Eae 35 Figure 21 Data browsing per domain category eseseeesssssseseeeee nennen 35 Figure 22 Alphabetical data browsing ccccccccccccceesesseecceeeeceaaeeseeeceeeeesaaeeseeeeeeeeeeeaaaenees 36 Fiure 25 Work How D OWSIDIB secorir aE UEM Fa nr ulaksui uu teo ur eus pub Ub Fou cbas dU n cou aestus 36 Figure 22 Appliances ORO WSIS oeseri e iseTERm ESSO mud EI tust U I CIEN SU SUUMIM E UM OMM ENTUM aT Page 6 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 Fig re 25 Resource information DE BO cereos crisi cs yoearactueeeice somascacasenee ioi o PE Ree IHRE bU DUEe raran ekiri 57 Figure 26 Resource access buttons essssesesseeseesseeseseeeeeee esses eene nnne nnn n nn nnne eene eene 38 Figure 27 Preview of a polydata vtk file representing a human left ventricle 40 Figure 28 Preview of a 3D volume as slices along the coordinate axis The user can control direction and position of the slice with the bottom left controls esses 40 Figure 29 LOBDCER Interface soosqedinione ie cnu2indaqius thao nutdndant ie enun d as
29. PwoFZHm4PtxXjyuz0 4 1n39v0V5Rhc3 VC9OR27t0OwalhsDggEFAAKCAQBZ aQZsWveEV 2173QL8qb 9b EeG3GPEM 1H5AOxOqg rPRHS2 dJjiDvUeZD cDNW c 3 https neonl net mod auth pubtkt http pypi python org pypi mod auth library 1 0O http en wikipedia org wiki Digital Signature Algorithm Page 22 of 82 FP7 ICT 269978 VPH Share p WP6 User Access Systems A Je 3 D6 5 Production Deployment of User Access Systems Ey Version 1v2 Date 28 Feb 14 VPH Share EYv949skpIrZkthDiR W xaf 6ZmhAB66mg4dmgLJWtNOlIrYzD8nl RacHOHmBe20R8 DL UKBoyRIIB27IVLbFGCT177j YsDxP6Q7uLAkoJOKkN2FtY JCxqOMGAfhIqbtibg WJmICQAKYbOmON rTonOwzoK8GHtzqXtkbe Y 5HbBSOdiOHJCjtfFZDEZSOFaZXT OfULRFdOouooldiQyNxKsId pkL6hB XL6QvVzfVaGiESnhWsketmOsKanWWLeGtR svStH Xp48zLsDtXeFncp At the Master Interface level the same ticket is saved in a cookie named vph tkt and it validates it at each request of a page In fact the MI provides a ticket validation service that allows the ticket consumers to validate the ticket and to retrieve a JSON26 notation of the user attributes In accordance to the current regulations the user will have to explicitly accept the use of cookies for the correct functioning of the system The validation service receives the ticket to be validated as an URL parameter If the ticket 1s valid a JSON notation of the user information is returned username mbalasso language country ITALY role developer friend pos
30. Tid Dispatcher d Script z 9 a s XPathService PEST RESTSenice Utility components Ports and flow control e 66 of 82 Figure 50 Taverna On line working area FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share Following this the user must double click on the VPHService blue box on the working area and a configuration window will be presented The first time this is done the user must enter his Biomed Town credentials Once this is done the list of available Appliances will show up and the user can choose an endpoint Then the user should press the Get Operations button to retrieve the list of services available in the selected endpoint Once the list of operations is displayed the user can choose the service needed to build the workflow See Figure 51 for an illustration of this process For a guide on how to build workflows with OnlineHPC see the video at http www youtube com watch v 0n3 YhJjPBy8 Workflows Components VPHService Processo n M 5 d 3338 Bit Web service Advanced properties Input ports Output ports e 4 sancti Fassaden NR im Get oneentions AneuristGUIl Nolnteraction with LOBCDER Sp axis2 services wsGimias axis2 services wsGimias cp a Dig Operation Landmarking a BoundingBox s e XP GAR S i E lt _ Segmentation lt 5 Gaussian_Blur Utility cor Geometry Desc
31. Town i http www biomedtown org Page 24 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share community portal This has been a choice of opportunity to simplify access to the thousands of users of the biomedical community already subscribed to Biomed Town However the technical solution in place will allow in the future to update the MI to have others relying parties 2 3 Theuser interface In this and the following sub sections we will provide an overview of the available functionalities in the third year prototype of the MI and their user interfaces and we will always refer to the production instance of the Master Interface and associated services so to give a clear presentation on what a general user will get now by entering the VPH Share system A number of other services and improvements are already available in draft form in development and they will be mentioned just when appropriate to the user experience description The home page of the portal at https portal vph share eu shown in Figure 4 provides the user all most important links to the VPH Share infrastructure services at a glance oe W Y a ast 2 AT aim Help About Login Registration bam ie a NNI IINE DATA APPLICATIONS WORKFLOWS SEARCH i gt Q A Wwe VPH Share is an online environment for the development construction and storage of b
32. a instance xmins xsd http www w3 org 2001 XMLSchema xmlns prov http www w3 org ns provi xmins share http www vph share eu ns share gt 1 Person gt lt prov person prov id ecoto gt Page 74 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share lt prov role gt executor lt prov role gt lt prov person gt lt Webservice gt prov entity id e3cl17fe0 1657 4911 97d9 5148d78d5b74 gt prov label gt Geometry D soriptors provrlabel lt prov location gt https vph cyfronet pl api vl endpoints 188 descriptor lt orov ocaticn gt lt prov entity gt l Input Data gt prov entity id 2 Dbeeb5df8 8c4c 46e0 a3c6 11597478d81b Xprov label inputFileNameDomec prov label provilocation lobocderj aneurist Neckselsction outpursurfaceMesh vtk orovrlocstion lt prov entity gt lt Input Data gt lt prov entity id 5b5a9dd2 be74 40a7 82d8 42cbc9368754 gt lt prov label gt inputFileNameAneurysm lt prov label gt prov location gt loboder aneurist RingCut outputsurfaceMesh vtk eforov ilocatlon prov ientity lt Entities used in generation gt lt prov wasGeneratedBy gt prov entity prov ref ecoto gt Xprov entity prov ref e3cl7fe0 1657 4911 97d9 5148d78d5b74 provitimaea s2014 02 24 15749257 lt prov time gt lt prov wasGeneratedBy gt
33. alisation Capabilities euHeart services Cardiac Initialisation Cardiac Fitting Clinical Report Creation Other basic segmentation tools 1 Otsu Segmentation A Thresholding Segmentation Region growing Segmentation Currently GIMIAS provides a great interface to easily deploy any new external service on the VPH Share infostructure Interactive and non interactive services can be provided using the VPH Share Taverna Plugin both locally and on line via the two aforementioned Workflow Management Systems 4 3 Specification of services requiring user interaction If an Appliance is to expose a service that requires user interaction this needs to be advertised for the VPH Share Taverna Plugin to be able to provide the support for such interaction This can be easily configured by the Appliance developer through the Master Interface when adding the Web Service Endpoint of the Appliance in Development Mode The configuration consists on adding a string containing the list of interactive services to be exposed by the endpoint as part of the description field of the endpoint The string must start with the INTERACTIVE_SERVICES without quotes and then the list of interactive services Page 62 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems A Je 3 D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share names must follow with each service name separated fro
34. ample Workflow Sample workflow to test The workflow manager with baclava input file Figure 23 Workflow browsing Applications for the atomic services when the APPLICATIONS in the top bar link 1s clicked the first page shows the already running Applications for the specific user while clicking on the Start new application button provides the list of all the available tools 1n alphabetical order Each Application has a description provided by the service owner and the link to start the service if the user has the necessary permissions Page 36 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share Start new application Fitter applications Ubuntu 12 04 Work in progress template upon which B template with ATOS will install their security proxy Apache Pick initial configuration a 5298541bB554ER 1795002762 initial configuration Kate via NoMachine Offersthe KDE s kate application pm Meine the NoMachine remate desktop software Pick initial configuration Kate via NoMachine 4 initial configuration PmedVPHDemo v5 oncosimulator demo B Pick initial configuration a 51753ab7B6648B47800124ec initial configuration GIMIAS Full GIMIAS installation with powerful B Configuration Plugins with customized GUI and several cross platform Command line plugins Plugins Clinical Report CMGUI DICOM Generic segmentati
35. are platform workspace this link not yet active will lead to the page where the user can compose his her own data and tools to compose his her own workflows or to access the history of workflows executions a preliminary version is ready on development but not yet on production groups this link provides access to the institutions and groups management and subscription page search it sends you to the main global search services which allows to look for any type of resource hosted into the infrastructure When the website is opened at the top of the pages a warning is presented to the user on the fact that the website uses cookies and asks for acceptance on their use In collaboration with WP8 and the PMO a new version of the MI homepage is under design the aim is to make the first page where the user arrives more informative on the number and types of resources hosted 2 3 1 User registration Relying on the previously described authentication layer the user 1s allowed to register to the MI by clicking on the corresponding link in the home page A form will appear which asks the user to fill in a series of information username contact details e acceptance of the privacy terms security capture to avoid spam Page 26 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share Due to the fact that t
36. ata Sharing Agreement introducing Institutional policies Policies url Link to where Institutional Policy cocuments are available Admin fullname Acministration contact person fullname Acmin accress Acministration contact accress Acmin phone Acministration contact phone number Acmin email Administration contact email Formal fullname Formal contact person Fullname legally responsible person Formal address Formal contact accress Formal phone Formal contact phone number Formal email Formal contact email Breach fullname Breach contact person Fullname person to be notified in case of breach of security privacy detected or suspected Breach address Breach contact accress Breach phone Breach contact phone number Breach email Breach contact email submit your request Figure 12 The request institution view 2 3 3 Discovery tools The aim of VPH Share is to provide effective ways to the user to discover resources they might be interested in For this reason different discovery and search tools have been implemented and deployed In most of the cases the MI provides the User Interface while calling backend services developed by other WPs as shown in Figure 13 Page 31 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share 2 3 3 1 Plain Search This is a simple text search 1 e Google style The button to use it 1s in the right s
37. ated the user or members group receives an email and at the same time if he she loads a Master interface page a message popup appears The notification service can be performed by passing the ticket the recipient username or groupid the message and the subject as URL parameters It returns status code 200 if the notification is delivered 400 if there is a malformed request and 403 in case of error Bporral vele share eu api notify ticket lt ticket gt recipient lt recipient gt mess age lt message gt subject lt subject gt GET ticket your authentication ticket recipient the username or group id message the content of notification subject you have the possibility to specific a notification subject if need Status code 200 Status code 403 Ticket not valid Status code 400 Malformed request Page 20 of 82 FP7 ICT 269978 VPH Share 4 WP User Access Systems A Je 3 D6 5 Production Deployment of User Access Systems Y Version 1v2 Date 28 Feb 14 VPH Share 2 2 5 The web application The Master Interface represents the main access point for users to data workflows and services from the VPH Share Infostructure It 1s a web application which has been developed as part of Task 6 4 relying on the Django high level Python Web framework Due to the high level of interaction with all the technical WPs the set up of a collaborative environment was highly important to efficiently and productively
38. bes the Master Interface with an overview of the functionalities that have been released on the production version of the User Access System Chapter 4 describes the progress on VPH Share cloud infrastructure that 1s under the responsibility of WP6 but in close interaction with WP2 Chapter 5 describes the progress on the tools that have to facilitate the workflow integration workflow composition and execution Chapter 6 provides a high level overview of work accomplishments along year 3 Chapter 7 provides a high level overview of work plan for year 4 Page 10 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share 1 INTRODUCTION The User Access System is the main entry point for researchers and clinicians willing to access the VPH Share infrastructure services As such it should contain tools that enrich the user s experience and facilitate the interaction with the platform exposing in an intuitive way all the data and services that constitute the infrastructure According to the evolution of the project and the consequent level of maturity of the facilities provided by the other technical work packages a series of three incremental prototypes of the User Access System is being developed as defined in the project These incremental releases are allowing continuous feedback to be obtained from the users a
39. buntu 12 04 Work in progress template upon which B template with ATOS will install their security proxy Apache Pick initial configuration a 5298541bBB554BR 3795002 Tha initial configuration Kate via NaMachine Offersthe KDE s kate application mB through the NoMachine remote desktop software Pick initial configuration amp Kate via NoMachine 4 initial configuration PmedVPHDemo v5 oncosimulator demo mB Pick initial configuration a 51753ab7BE564BBA7B00124ec initial configuration GIMIAS Full GIMIAS installation with pawerful Dm Configuration Plugins with customized GUI and several cross platform Command line plugins Plugins Clinical Report CMGUI DICOM Generic Segmentation Image Tools MITK Manual Segmentation Start selected Cancel Page 43 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 i Date 28 Feb 14 VPH Share When the Start green arrow icon next to the selected service 1s pressed Atmosphere will prepare that service for user interaction The contents of the window will change to reflect the fact that a service is being spawned and inform the user when the service becomes available tools Pe aeucme Workflows My Applications Name IP Location Status Actions AneuristGUI NoMachine NoUploadDelay 10 100 8 113 Cyfronet active o AsyncWeb Figure 30 The application view after invocation At this point the user may
40. butes and it raises 403 if ticket is invalid Url portal vph share eu api validatetkt ticket ticket structure Method GET Parameters _ ticket your authentication ticket Returns Status code 200 username username Landguddget m Beo SEIT rodea developer friend 1m postcode ADS onn fullname Master Interface email mail example com Status code 403Ticket not valid Status code 500Any other kind of error 2 2 2 Groups Management 2 2 2 1 api searchuser Description It searches for users The provided term is searched in users email first name and last name The search is case insensitive Without any term the full list of users is returned It is available to all authenticated users A JSON list of user attributes is returned Url portal vph share eu api searchuser term term amp ticket ticket structure Method GET Parameters term the search term ticket your authentication ticket Page 13 of 82 Returns FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share Status code 200 username mbalasso email email email com adem enjeu Matteo a sso username testuser email emarl email com fullname Test User Status code 403 Ticket not valid Status code 500 2 2 2 2 api searchgroup Description Url structure Method Pa
41. c loading condition over 10 years A Final module calculates the risk of Fracture after 10 year of remodelling still under test ode Tag EB E GO CLN EE ee Enterta Licence 3 Upload licence Views 8 Published 05 24 7013 Category Workflow Type workflow Figure 38 Edit tags The description can be modified by clicking on the edit button The Tags can be removed or new ones can be added by using the Enter tag button Also the licence Page 49 of 82 FP7 ICT 269978 VPH Share WP User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 i Date 28 Feb 14 VPH Share associated to the resource can be changed using the Upload licence button Other information like the title or the category of the resource cannot be modified 3 Change access permissions orange icon Share tab the permissions associated to each resource can be edited by the owner and the managers If there are pending requests to be checked the user will be warned by a red exclamation mark close to the icon VPHOP workflow Author testi Published 2013 05 24 11 50 14 542 Details Share Share this resource with new user or group Reader O Editor O Manager m T and 7777 3 Editor Manager Reader master interface F Alfredo Saglimbenl F Y 7 Splras Koulouris VPH Share reviewer r Figure 39 Manage requests Using the available page the resource owner can search for a user group to be granted acc
42. ccess Systems Version 1v2 Date 28 Feb 14 VPH Share entities that were involved in the production of the file such as the web service that produced it and the files that were used as input to the web service With this information the user could re produce the file if needed In year 4 the user will be able to visualise this metadata and provenance information in the Master Interface 4 9 Workflow Monitoring The first attempts towards creating a Workflow Monitoring service have been carried out by deploying a Nagios Core engine for the project This is a free and open source solution monitoring system see http www nagios com products nagioscore The system supports the installation of specific purpose plugins from which the WeblInject plugin http www webinject org plugin html has been chosen for Workflow Monitoring The plugin will allow us to write a script with a series of steps for testing the workflow execution through the MI Each step in the script will use the REST interface of the Workflow Manager WM which will be available in year 4 to execute a method that will test the functionality and availability of the WM At the moment three test services have been setup See the three services under hosts VPH Share in Figure 56 The first one just checks that the portal vph share eu returns a valid HTTP response which indicates that this web page is up and reachable The second and third services use the WebInject plugin
43. cution in VPH Share a mechanism to support remote desktop access was implemented To make this even more convenient for end users a web based client was used to handle such scenarios The current implementation allows creating Applications which offer accessing native applications from the browser by clicking a generated link The communication is based on the SSH channel and the client is configured on the server side each time the user accesses the machine As the remote desktop technology NX NoMachine software was used The client is available for all major platforms and through the Web Companion web applet appropriate version is downloaded and executed The end user experience is such that the remote application is run locally with a little slower response times dependent on the network throughput This is possible due to the fact that only a given application window is transferred over the network without the necessity to show the whole desktop as with other such technologies The main difficulty overcome by this integration effort was to handle the dynamic nature of redirections of instances run in the cloud Each time an instance is started different redirection ports are assigned to the SSH channel which by default is executed on port 22 The combination of using the Cloud Fa ade API and passing of the current properties through REST services deployed on the machine instance allowed properly configuring all the components Thanks for usin
44. d endpoints returned by specifying the endpoint type or giving endpoint identification numbers The specification of the operation is as follows Operation GET appliance endpoints GET appliance endpoints endpoint type ws rest or webapp GET appliance endpoints endpoint type ws rest GET appliance endpoints endpoint id 1 3 7 Response appliance endpoints I wae iy name Foobar Appliance Type description Foobar Appliance Type description endpoints XO Ey name name of the endpoint description some descriptive text endpoint type ws rest or webapp urls urt to desorzpcor This operation is particularly used by the workflow composition tools Taverna Workbench and Taverna On line to present the user with a Web Service Catalogue a user friendly list of the available web services offered by VPH Share applications In Taverna On line this catalogue has been incorporated in the form of a dropdown list see Figure 51 When the user presses the Get Operations button the list of web services 1s displayed and then the user can browse through the services and choose the one to be used for workflow composition In Taverna Workbench it 1s not possible to browse the catalogue but when the user imports a VPH Share service using the VPH Share plugin as explained in http vph share eu content running aneuristworkflow short workflow the plugin accesses the catalogue Page 59 of 82
45. de obtaining information about all compute sites or about a specific one Operation GET compute sites Response comp te Sites Vad T oire IO GVIPOneL IOLSOm name Cyfronet locadrtron 2 Cracow SILe type privarte Ltechnology openstack GONT IGT Tp Page 53 of 82 FP7 ICT 269978 VPH Share P WP6 User Access Systems A Je 3 D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 cmm VPH Share Operation GET compute sites id Response OCONDHUCOe Sire ids I SlLe 10 S UOCUVLIONeC roLsSoON name Cyfronet Locations Cracow site Lupe privare Ltechnology openstack pontig Ue j j For each of the operations description URL and request response bodies are given to easily implement clients Authentication is done by passing a valid token obtained from the Master Interface see section 3 1 6 for details Other sections of the API include the following e Application Configuration Instances concrete application configurations with property placeholders replaced and with contents which is injected into running machines at boot time e Application Configuration Templates configuration templates holding property placeholders for a given application e Application Endpoints provides a list of application types with their endpoints e Application Sets groups applications for a given user can be of t
46. e see Figure 52 Moreover this behaviour is automatically available for any CLP published using the GIMAS WebServices Plugin Page 68 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 ES Workficw3 Neckselection De Execute service in non blocking mode Details VPH Share service https vph cyfronet pl api v1 endpoint k NackSalaction_VPHShare Geometry Descriplors VPHShara VPH Share service https vph cyfronet pl api v 1 endpoints 19 ra Configure Figure 52 Configuration dialog for the NeckSelection VPH Share service 4 5 Workflow execution through the MI Users can upload their composed Workflows to the MI and share them with other users Any user with access to a workflow can download it and load it into Taverna Workbench or Taverna On line for editing and or execution see section 3 2 6 for details on the user interface However if the user does not need to edit the workflow but only wishes to execute it using inputs stored in LOBCDER then the MI provides the Execute workflow button which can be used to execute the workflow 1n the MI The technology behind this button corresponds to the Workflow Manager WM Once the user enters the parameters for the execution and presses the nitialise execution button see Figure 33 the WM is activated behind the scenes see Figure 53 The WM communicate
47. e mediajlob al mediajlob mm b c media lob Added new value Edit value on right lt gt Load previous values lt gt Save values ati Use examples Run workflow 3 Cancel Figure 55 Taverna Workbench s Run Workflow dialog with input list For the first iteration all the necessary Applications will be created by the VPH Share Taverna Plugin All following iterations will re use the same Applications therefore saving the time and resources of continuously shutting down and re starting the same set of Applications If an Application requires user interaction a web browser window will automatically open in the user s desktop when the service 1s executed so that the user can perform the interaction The browser will start a web based remote desktop session via a NX NoMachine client see Figure 48 However since in batch execution mode services are executed several times the web client will open only once per Application The user must be careful not to close the browser tab although in such a case it could be easily recovered using the browser s history It is important to emphasise that the user must handle all the activations of the interactive service throughout all iterations for the workflow to finish successfully The outputs of each iteration intermediate and final workflow outputs are stored in the LOBCDER see Figure 47 However it 1s important to notice that Taverna Workbench will not do any automatic r
48. e log in the corresponding link at the top right side changes with the user name and provides a roll down menu which includes dashboard profile admin tools log out The dashboard is described in section 3 3 7 1 while the others will be described in the following sub sections Page 27 of 82 FP7 ICT 269978 VPH Share WP User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 y Date 28 Feb 14 VPH Share Z2 Profile If the user clicks on the profile link he she can get information on his her own account as provided at registration time get a copy of his her own authentication ticket for its use in the application deployment or access the groups page profile Your personal data Id 19 Username testi Email d testi scsitaly com First name Debora Last name Testi Country ITALY PostCode 40033 Last login time Jan 2 2014 8 43 a m Copy your Authentication Ticket to clipboard Groups Figure 6 The user profile page More information will be added in the future with the possibility also to edit update some of information provided at registration time 2 3 2 3 Groups The Master Interface does not only allow the user to register and access the system but it provides the user with the functionalities to manage and organise groups of users to assign access rights to the available resources Groups of users in the VPH Share infostructure have been
49. eb 14 VPH Share dashboard you don t have data yet you don t have applications yet VPHOP workflow Author testi Published 2013 05 24 11 50 14 542 Sample Workflow Author asagli Published 2013 11 29 15 37 51 21 aneuristWorkFlow Short Author ecoto Published 2013 06 07 15 47 51 156 Figure 37 Dashboard The page has two sections one for each resource type and each section can be expanded or collapsed with the right side arrow All the resources are presented in the same way so only one description is provided here For each of the resources the user can see the title name of the created resource its author with its username and the date the resource was published Three actions are possible for each resource with the two blue and orange icons visualise the resource information edit the resource tags and change the access permissions 1 Resource information blue icon which provides the visualisation of the resource common metadata as presented in the Resource Access section 2 3 3 4 2 Edit tags orange icon details tab once this is clicked a panel to edit the resource information is opened VPHOP workFlow Author testi Published 2013 05 24 11 50 14 542 Details Share Description This is the VPHOP workflow Taverna Files The workflow uses the SOAP version of Ehe services which are then r system The workflow starts From the patient data hosted on PhysiomeSpace applies the patient specifi
50. ell Url portal vph structure share eu api removeuser group Xgroup amp username username amp tick et ticket Method GET Parameters group the group name username the user name recursive if present with any non empty value remove user from all children group ticket your authentication ticket Returns Status code 200 LA OK Status code 403 Ticket not valid or user not allowed to invoke the service Status code 500 2 2 2 7 api groupmembers Description It searches for group members Given a group name the service returns all group members and children groups A JSON dictionary with the list of user attributes and the list of children groups is returned Url portal vph structure share eu api groupmembers group lt group gt amp ticket lt ticket gt Page 16 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share Method GET Parameters Group the group name ticket your authentication ticket Returns Status code 200 sere username mbalasso fullname Matteo Balasso email mail example com by username testuser tf ullname Trest User email mail example com V ONG OBDUO PM CQicOupman a8 FCs re GuaommouliOZ USsnloserioces s Status code 403 Ticket not valid or user not allowed to invoke the service Status code 404 Group with g
51. enaming of the output files on each iteration Therefore the user must take care to input files on different locations of the LOBCDER as otherwise the output files will be overwritten on each iteration If the user does not want to worry about this then the web execution tool can be used for it will automatically create separate output folders in the LOBCDER This is explained in the following section Page 72 of 82 FP7 ICT 269978 VPH Share P WP6 User Access Systems A Je 3 D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share 4 6 2 Web batch execution Web batch execution can also be accomplished by using the Workflow Manager WM available through the MI From the point of view of the user interface the process is exactly the same as executing a normal workflow using the Execute workflow button However two preconditions are necessary to accomplish web batch execution The first precondition 1s that the workflow chosen by the user through the MI must be already prepared to accept lists of depth 1 for input as explained in the previous section The second precondition is that the input baclava file must specify a list of input values not just one single value The user can upload to the MI such input baclava and workflow definition files and run the workflow directly in the VPH Share portal In addition if the workflow is expecting a list as input and a baclava file with only one
52. ents Data Manager which is used for managing file resources interfaces with the LOBCDER component directly by using a mixture of WebDAV and REST invocations The user is able to view upload and download files as well as edit their metadata Because LOBCDER offers a standard WebDAV interface many available clients can be used to access its resources The REST part of the interface is used to manage more complex metadata queries Authentication 1s implemented by delegating a user token obtained from the Master Interface server with each request Cloud manager uses the API offered by the Cloud Fa ade component which delivers a complete set of operations managing the life cycle of Appliances by utilising Cloud DB and Cloud Site components of the WP2 work package The facade is also intended to be used by other clients such as workflow management systems to provision resources required for workflow execution However in the scope of the Cloud Manager it is used to enable users with the possibility to manage individual instances of Applications and test them in the development mode http www webdav org WebDAV Resources I http www ics uci edu fielding pubs dissertation rest arch style htm Representational State Transfer Page 52 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 i Date 28 Feb 14 VPH Share Deployment of cloud components is
53. erna Workbench s edit input port dialog After this before the user starts running the Taverna workflow a list of values will be required as input in the Run Workflow dialog see Figure 55 The user can enter the list manually or the Load previous values button can be used to load a baclava file specifying the list of values See http dev mygrid org uk wiki display taverna DataViewer Tool for more details about baclava files After clicking on Run Workflow Taverna will start running the workflow using the implicit iterations approach During execution in the Graph tab Taverna will show progress bars and iterations numbers on each service that is performing implicit iteration Similar information is shown in the Progress Report tab For more details see the Pipelining section at http dev mygrid org uk wiki display taverna Implicit iteration In addition notice Page 71 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 i Date 28 Feb 14 VPH Share that Taverna will automatically perform implicit parallelisation to help increase data throughput see http taverna knowledgeblog org 2010 12 13 parallel service invocations for more details 3 amp Delete ati Add value Add file location QP Add URL T Imediallobcder aneuristitest RingCut outputSurfaceMesh vtk Habe mediajlab idi abi media lob abl
54. ess in the search box The list of matching users will appear at the bottom To add permissions the resource owner has to click on the role he she would like to assign Editor who can change the resource information Manager who can also modify the permissions Reader who can just download but nor modify the resource If the user wants to revoke permissions he she simply has to click again on a respective box and the permissions will be revoked 2 3 7 2 The workspace The workspace is the place where the user can Authoring and execute workflows Access to workflows outcomes Review history of workflow executions Create and manage new workflow composition and execution thanks to the Taverna Online integration see technical information in section 4 4 2 Page 50 of 82 FP7 ICT 269978 VPH Share P WP6 User Access Systems A Je 3 D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share Although the MI itself offer most of the components of the workspace our collaboration with the IITP ru to integrate web workflows composition services have bring us the opportunity to provide a more integrated workspace to VPH Share users at the same time that a great use case to demonstrate how an external application can integrate VPH Services and components However this is still a work in progress that will be completed early in Year 4 2 3 8 User care Being WP6 the work package devoted to the
55. fo error True time sleep 5 info getWorkflowInformation ret wfld userCredentials deleteExecution ret wfld userCredentials 4 8 Data Provenance and Semantic Currently the Taverna VPH Share plugin also incorporates functionality for creating metadata and provenance information for every single file that is produced in LOBCDER by the plugin That is for every file produced in LOBCDER an entry is automatically created in the Metadata Catalogue developed by WP4 which can then be used to publish the file and perform any intelligent data search that includes the file see WP4 deliverables for more detail An example entry for file Geometry Descriptors OutputDescriptors xml stored in LOBCDER is shown below If the file already exists the metadata information is just updated lt resource metadata file lt author gt ecoto lt author gt lt category gt GenericMetadata lt category gt lt creationDate gt 2014 02 24 15 11 42 288 lt creationDate gt lt description gt Taverna workflow output lt description gt globalID df7197ce 6ae1 442b bbb9 7a7f 2e0ac530 globalID linkedTo lt localID gt 7962 lt localID gt lt metadataCreationDate gt 2014 02 24 15 11 42 288 lt metadataCreationDate gt lt metadataUpdateDate gt 2014 02 24 15 11 42 287 lt metadataUpdateDate gt lt name gt Geometry Descriptors OutputDescriptors lt name gt lt provenance gt lt prov document xmlns xsi http www w3 org 2001 XMLSchem
56. g which is sent back to the MI panel where the user can interact with the visualisation i http www paraview org Page 39 of 82 FP7 ICT 269978 VPH Share WP User Access Systems D6 5 Production Deployment of User Access Systems X Version 1v2 NS Date 28 Feb 14 mm VPH Share Create directory Scalars View sice MOVE mouse amp press LEFT button rotate MIDDLE button pan RIGHT button zoom Name Owner Modified Size B Actions 5 0 1 testi 25 Sep 2013 1966341 E o P7 5 220 14 testi 25 Sep 2013 128681 ei sc CT SHORT mf asagli 19 Nov 2013 6060126 o P7 Create directory Slice 9 of 14 Window 0 494 Name Owner Modified Size B ac testi 25 Sep 2013 1966341 o F 5 220 1 vl testi 25 Sep 2013 128681 o F 5 ChestCT SHORT asagli 19 Nov 2013 6060126 a o 7 Page 40 of 82 FP7 ICT 269978 VPH Share p WP User Access Systems A Je 3 D6 5 Production Deployment of User Access Systems Y E M Version 1v2 Date 28 Feb 14 VPH Share The user can switch the visualisation from 3D rendering to slice rendering according to the type of data For the 3D rendering the user can also interact with the view by changing the point of view with the mouse standard pan and zoom interaction while for the slice rendering he she can move the slice direction and position and change the windowing moving the respective sliders Much more visualisation modalities and options are available
57. g Mx Web Companion Click on the button below to exit the applet KE Untitled modified Kate amp kabe via nomachinez c ve US z File Edit View Bookmarks Sessions Tools Settings Help oE 9 New in Open 4m Back EP Forward Save LA Save As Remote application on the cloud with two clicks by using VPH Share NOMACHINE 3 Documents For detailed information En Line 1 Cal 68 INS LINE UTF 8 Untitled E Terminal Figure 45 Sample remote application run on the cloud visible on the user computer as yet another local window Page 58 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share In Figure 45 a sample application was executed which presents itself as another locally executed window If a file would be saved in this application it would be stored on the machine instance run in the cloud This also makes it possible to save the results of running such application in LOBCDER cloud storage component given it is mounted on the cloud instance through the WebDAV driver This use case makes it very easy to use cloud resources both computation and storage in a seamless way 3 5 Web Service Catalogue One of the services provided by the Cloud Facade component is a list of the endpoints provided by the available applications It is possible to limit the number of applications types an
58. going to be submitted It produces as output among other things the identification of the submitted workflow stopWorkflow This method stops a specific workflow previously started with execute workflow It takes as input the user credentials and the identification of the workflow to be stopped getWorkflowInformation This method can be used to monitor the execution of a workflow previously started with execute workflow It returns information such as the status of the workflow execution the starting execution time the creation time any errors Page 73 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 i Date 28 Feb 14 VPH Share or warning messages triggered by the Taverna Server etc This information is also kept inside the MI for monitoring purposes deleteExecution This method stops a workflow and clears the information about the workflow stored in the MI With these methods it is possible to create a simple python script to execute workflows An example pseudo algorithm for such a script would be import wfmng wfDefinition open SampleWorkflow t2flow r read inputDefinition open SampleWorkflowlInputs xml r read ret execute workflow userCredentials wfTitle tavernaServer wfDefinition inputDefinition info getWorkflowInformation ret wfld userCredentials while info and info status Finished and in
59. he VPH Share system is meant to be used by professionals and the contact information will be used also by resource owner to take decisions for granting access the form is checked by a manual operator within 48 hours If the information is incorrect or incomplete i e an institutional email address is required the request 1s temporarily rejected with a request of update otherwise the request is approved and an email is sent to the user for the password set up Once the password is inserted into the system the user is automatically added to the VPH Share user database and he she can access all the information that requires a log in 2 3 2 User access 2 3 2 1 Login As much as possible of the VPH Share services and resources can be browsed and viewed without the need of an account but if the user would like to access specific resources he she needs first to register to the platform and then to login in the platform To access the web application a login button is available in the top right side of the page Help About Login Registration i Enter your BiomedTown username Are you an Internet Explorer user click here Figure 5 The login modal window The user can at this point insert his her own credentials as set at the registration step or as already set up for Biomed Town and accept the privacy policies to enter into the system The choice on the privacy policies will be required only at the first log in After th
60. hich the user s information is stored The Master Interface relies on this Identity Provider to assign the correct privileges to the user A schematic representation of the authentication method is presented below Figure 3 Identity Provider Relaying Party IP ch Request to be authenticated Redir IP henti 4 Request to trust the RP Redirect with signed parameters Li Li Login successful send session cookies lt lt yA Figure 3 Schematic representation of the OpenID authentication mechanism The main actors of this process are The User who wants to access the MI and needs to be authenticated The Identity Provider representing a trusted service where the User s identity is registered The Relying Party representing the service where the user wants to be authenticated in this case the MI The authentication mechanism works as follows when the user tries to login into the MI Relaying Party his her request is redirected to an external Identity Provider that shows the login dialog and handles the authentication process According to this authentication the Identity Provider assigns the appropriate privileges to the user These privileges are sent back to the MI that will now be able to successfully terminate the login process and open a dedicated session for the user according to his access rights Currently the only Identity Provider supported by VPH Share is the Biomed
61. https channels If the application 1s accessed by using the presented links inside the generic invoker view automatically a security token 1s attached to the request which 1s processed by the security proxy on the instance 3 2 3 External Workflows The third view which corresponds to the workflow mode allows for managing Application instances run from an external service e g workflow management system such as Taverna It is possible to see if any instances were run on behalf of a given user and if necessary remove them The view also gives details about the instances similar to the generic invoker view 3 3 LOBCDER repository Files present in the cloud storage resources WP2 LOBCDER component can be managed from the Data Manager view File upload and download is possible by using the WebDAV protocol hidden from users by the data browser The resources are structured into directories to resemble the standard file system structure A sample view of the data browser is presented in Figure 29 and described in section 3 2 4 2 Originally a flat file structure view was supported by the Data Manager however a requirement for structured data emerged to deal with the amount of data which eventually will be stored Structure of directories similar to standard file systems is used and the browser presents the contents of one of the directories at a time starting with the root location The upload action always uploads a given file to the currently
62. iances can be used at the same time A user can access the resources provided by the Cloud Facade by using the VPH Share Plugin to create and or execute a biomedical workflow The VPH Share Plugin integrates with Taverna Workbench for desktop workflow composition and execution and with Taverna On line for web based workflow composition and execution When a user wants to use a service provided by the Cloud Facade in a workflow a set of service definitions in WSDL format must be imported into the Workflow Management System being used While normally the entries of the WSDL would contain references to a running Web Service server endpoint in the VPH Share project the server is not yet running for it corresponds to a VM Instead the WSDL contains an identifier that indicates the VPH Share Plugin which VM to instantiate and which service to execute on that machine The URL for the WSDL of a given Appliance can be obtained from the Master Interface using one of the resource access buttons When the user executes a biomedical workflow using the VPH Share Plugin all the complexity of the execution process is handled by the plugin in the background to make things easy for the user The VPH Share Plugin instantiates the needed Applications waits for them to start up redirects the Web Service calls to the correct Application waits for each Application to finish its job and shuts it down when no longer needed manages the authentication of the user i
63. ication mechanism 24 Figure 4 Master interface home page for not logged user eeeessseeseeeeeeeeee 22 Figure 5 The login modal WINK OW EE 27 Figure 0 The user POU IS DIOC sssrinin ter ent tego l vase ER et Usa E n FUP DN MERE E 28 Fig te 7 SEDIS 1 hoy acl 6 ch rS 29 Figure 8 The institutions studies details ViCW cccecececeeeceeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeees 29 Figure 9 The institutions studies subscription VICW ccccceeeecccccccceceeeeeeeeeeesseeeeeeeeeeeeeeeeees 30 Figure 10 The institutions studies user management view cccccccccceeenteeeeteeeeeseeeeeeeeeeeeeees 30 Figure 11 The institutions studies creation study VICW ccccccccccccccceeeeeeeeetesseeeeeeeeeeeeeeeeees 30 Figure 12 The request institution VIeW ccccccccccssssssssssssssssescececceccccceeeseaaaauasssseseeeeeeeeeeeeeeees 3l Figure 15 Plam search Me ACC ivnciessinnssevedanndenatesecnsehensdasstesesncedewcdanatesacnachensdesoteasededonudeantesadt 32 Figure 14 Plon Sean Cy Ge SUN GAS ss ays vec come concn der Rubr EE E E EE ei DIE D Figure 15 Filter and refine options in the plain search eeeeeeeeeeeeeeee 33 Fagure 16 First step Of the semantic Sedre Ius coena oe en dante en e cesi dee abea hun eR aeisi 33 Figure 17 List of datasets corresponding to the semantic terms ccccssseeseeeeeeeeeeeeeeeees 34 TOUTS Ae Alas et MC
64. ide of the top bar The user is allowed to insert one or more textual terms By clicking on the drop down All resources menu the user is allowed to filter the search on a specific resource type 1 e Dataset for structured data All resources v Search Or use Semantic search Dataset Workflow Atomic Sevice File SWS Application User Figure 13 Plain search interface When the Search button is pressed the terms are searched on all the selected resource types and the results are presented search All resources test Search Or use Semantic search We ve found 67 results Filter By Dataset D sssSCS_test test description Workflow amp 8SCS_TEST2 Atomic Sevice O test File SSCS TEST3 SWS go m Application L6 SSSSCS test6 User Se TEST4 Description Test Description Test Description Test Description Test Description Test Descripti 555TB test alloc Refine Catego test For allocation gon Author sstest master an image to test script Licence Figure 14 Plain search result page On the right side of the page there are the additional filters that can be applied to the results list On the top the filter by options filters based on the type of resource The user can select more than one type at the time the selected types are shown with a blue back colour To deselect a type he she has just to click on it again As soon as a filter is applied the results list is automatically updated Page 32 of 82
65. ing Taverna server deployment 2 4 1 2 5 2 2 5 3 Initial implementation of provenance VPH Share webservice catalogue Messaging tool integration User registration tool Institutions and groups management in the MI Q cjo ote IHE MEN m elejo cjo oc cc cjo oci cce CcC cef l Oo cic oe oF o 0f cejoj MI UI improvements i e dashboard sharing Table 1 WP6 Year 3 Achievements Page 77 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share 6 WORK PLANNED FOR YEAR 4 WP6 Implementation WP6 Year 4 High level plan Team Roles O Owner C Contributor Results to be delivered list will be extended following requests from users and developments from other WPs User cases support External projects support Full integration with Taverna Online LOBCDER amp workflow repository Full implementation of provenance Visualisation REST interface to execute VPH Share workflows Extended user interface to execute workflows From MI Cloud Monitoring integration Cloud Billing Model New home page facelift Data browsing improvements Bug fixing and maintenance of the UI LL B z t Q D Lu a Em Ex o co EM on EN om Eu Usercasessupor EL suso aani aaa Fal mplementation of provenance ulster o REST interface terete VPH Share workowe o tended user inerface to execute
66. input value is used this input will be automatically converted into a list with only one item This mean that input baclava files for single execution can still be used with batch execution workflows Another difference between single and batch web execution relates to the output folder In single execution the WM will create one output folder in the LOBCDER using the unique identification string of the workflow and copy the output files directly into that folder However in batch execution multiple output files with the same name will be produced and this could pose a problem because the output files would be overwritten at the end of each iteration of the workflow In order to avoid this the WM creates subfolders within the workflow output folder Each subfolder is named after an iteration number and so the output files produced by each iteration will be saved inside the subfolder that corresponds to the iteration that produced them 4 7 Workflow Manager API There is also available a XML RPC API for the Workflow Manager which can be used to start monitor and stop workflows in the MI using a python script The most relevant methods available are execute workflow This method is able to start the execution of a workflow in a particular Taverna Server instance It takes as input the workflow definition file the input definition file the user credentials the workflow title and the details of the Taverna Server to which the workflow is
67. iomedical workflows It is designed to help researchers clinicians and software developers share resources data and tools to build workflows quickly and easily WORKSPACE SEARCH Terms oF use Privacy policy Cookie policy Security Figure 4 Master interface home page for not logged user Page 25 of 82 FP7 ICT 269978 VPH Share P WP6 User Access Systems A Je 3 D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share At the top right side the links to the help and documentation pages are available together with the log in registration In the top bar you can find links to all VPH Share resources data this links to the main data page which provides access to the main actions which can be executed on the data that VPH Share host browse search upload and manage applications this link provides after log in access to the services tools application deployed on the cloud platform and called also Appliances workflows this redirects to the main workflow pages where the user can find which actions are available on these resources browse search upload and manage search it sends to the main global search services which allows the users to look for any type of resource hosted into the infrastructure In the bottom of the page there are links to beta user program where the user can find information on how to be part of the beta evaluation of the VPH Sh
68. ion The given user is removed from the given group managers If the group has any child group the user will be removed from its managers as well Url portal vph structure share eu api downgradeuser group lt group gt username lt username gt t icket lt ticket gt Method GET Parameters username the user username group the group name ticket your authentication ticket Page 18 of 82 Returns FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share Status code 200 OK Status code 403 Ticket not valid or user not allowed to invoke the service Status code 500 2 2 3 Resource Access 2 2 3 1 api hasrole Description Url structure Method Parameters Returns It checks if the user is granted the target role over the given resources Resources can be referred by metadata global ids OR by local ids and resource type User authentication can be performed by passing the ticket as an URL parameter OR with http basic authentication username ticket It returns True if the user is granted the target role over the given resource False if not Porte ven share eu api hasrole local id 1local idl amp local id local id2 gt amp t ype lt type gt role lt role gt POrtaL vou share eu api hasrole global id global idl amp global id global id 2 gt amp role lt role gt GET global_id the resource globa
69. is notified by email that the request has been delivered At the same time the resource owner receives an email informing that there is a pending request in his her dashboard waiting for approval together with the text of the message typed by the user Once the request for sharing is sent the button will change state and the user will not be allowed to perform any further action until the resource owner approves or rejects the pending request Request for sharing Request sent Download Figure 26 Resource access buttons Page 38 of 82 FP7 ICT 269978 VPH Share P WP6 User Access Systems A Je 3 D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share As soon as the resource owner approves rejects the request the user will be notified by email and the button will change state and colour Also in this case the resource owner can motivate the rejection with a message or request for further details which will be delivered to the user together with the email notification At this point if the access has been granted the buttons can differ in type and number according to the resource type file unstructured data a download button dataset structured data a query button workflow a download button for the workflow file a download button for the input files and an execute button Application an invoke service button Other specific action buttons will be added
70. itialized Atomic service is started Taverna is ready Submitting Ehe workflow to Taverna Configuring the workflow Starting the Workflow Workflow is running Finished Figure 35 Workflow logs during execution Page 47 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share Workflow executions Sample WorkFlow execution 1 Status gt x 2 Su bmitting workflow Failed Failed to build workFlow run worker Status Details Created Atomic service is initialized Atomic service is started Taverna is ready Submitting workflow Failed Failed to build workflow run workers Configuring the workflow Starting the Workflow Workflow is running Finished Figure 36 Workflow execution error reporting If the workflow generates binary data during or after its execution the data can be found into the LOBDCER folder name with the same workflow Id 2 3 7 Manage owned resources 2 3 71 The dashboard The dashboard is the place in the VPH Share web portal where the user can access all the owned managed resources data applications and workflows The user can be assigned to be manager of a resource and thus have it in his her dashboard even if he she is not the resource owner Page 48 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 F
71. iven name does not exists Status code 500 2 2 2 8 api usergroups Description It searches for users group Given a username the service returns all groups the user is part of A JSON list of group names is returned Url portal vph structure share eu api usergroups username username amp ticket ticket Method GET Parameters username the user username ticket your authentication ticket Returns Status code 200 ogroupname MtestgroupooolT WSUS criber S mi by Page 17 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share Gqroupmame i te si gioupbit02 WSUS cum Demp et S Status code 403 Ticket not valid or user not allowed to invoke the service Status code 404 User with given username does not exists Status code 500 2 2 2 9 api promoteuser Description The given user is added to the given group managers If the group has or will have any child group the user will be manager of them as well Url portal vph structure share eu api promoteuser group lt group gt username lt username gt amp tic ket lt ticket gt Method GET Parameters username the user username group the group name ticket your authentication ticket Returns Status code 200 OK Status code 403 Ticket not valid or user not allowed to invoke the service Status code 500 2 2 2 10 api downgradeuser Descript
72. keletal Immunology p d M Oncology Multidisciplinary Information Pw i Technology Figure 21 Data browsing per domain category Page 35 of 82 browse A B C D E An axis2 services wsGimias 8443 ArchLinux 1366022614198 ArchLinux 1366195529363 ArchLinux 1367225436679 ArchLinux 1367996343998 ArchLinux 1367996837250 ArchLinux 1368021824769 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 G H I J K L M N o P Q R Figure 22 Alphabetical data browsing VPH Share Workflows the list of all the available workflows appears in the screen By clicking on the name the user can get information on the specific workflow while if the user is owner manager of a workflow an icon provides also access to the editing form search workflow We ve found 10 workflows CS TEST MASTER1 Test description Gaussian Blur Test WF VPHOP workflow This is the VPHOP workflow Taverna files The workflow uses the SOAP version of the services which a itianeuristWorkflow Aneurist Workflow updated z Test Test My Segmenation Workflow Thisisa test workflow with a segmentation tool My First Workflow Thisis my first workflow tianeuristWorkflow Short Short version of the neurist workflow My Segmenation Workflow Thisisa test workflow with asegmentation tool S
73. l id AATE local id the resource local id type the resource type role the user target role ticket your authentication ticket Status code 200 True Status code 200 False Status code 403 Ticket not valid Status code 404 Requested resources not found Status code 500 Any other kind of error 2 2 3 2 api resources Description Url It gets the list of the resources of the given type for which the user is granted the target role User authentication can be performed by passing the ticket as an URL parameter OR with http basic authentication username ticket It returns a JSON list of resources with their local and global ids portal vph share eu api resources type type amp role role Page 19 of 82 structure Method Parameters Returns FP7 ICT 269978 VPH Share WP User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share GET type the resource type role the user target role ticket user authentication ticket Status code 200 alin el Such ce ecdloxereu ate echec oon owe lacch Em boreeur suche ced oxeeubiolz oo c uethsiSeubeem T v Status code 403 Ticket not valid Status code 500 Any other kind of error 2 2 4 Notification Service 2 2 4 1 api notify Description Url structure Method Parameters Returns It provides the service to notify a specific user or a group member When the service is invoc
74. l input files required by the workflow The outputs of the workflow will also be copied in this folder In this way the user can easily locate the files that were produced by the execution of the workflow that he she chose Once the workflow is configured the WM indicates the Taverna Server to start running it The WM then request the server the status of the workflow executing every 5 seconds During this time if the user decides to run another workflow using the same server The WM will detect that a Taverna Server is already running and will reuse it meaning that it will submit the new workflow to the same server so as to save computational resources Once the server indicates that a workflow has finished its execution the WM will delete that workflow from the server releasing all resources allocated by it By this time the outputs of the workflow will be already copied in the output folder If the server 1s not running any other workflow then the WM will also shut down the appliance that is running the Taverna Server then again saving computational resources If an Application within a workflow requires user interaction the Master Interface notification service 1s used to send the user a link to the web based NX NoMachine client which can be used to open a remote desktop session to the Appliance Notifications reach the user by e mail as well as through the Master Interface s GUI see Section 2 2 4 In the case of the later the user ca
75. m the other by a coma For instance one of the appliances employed in the neurIST workflow specifies its interactive services as INTERACTIVE_SERVICES MeshEditing NeckSelection RingCut BoundingBox without quotes corresponding to the interactive services mentioned in the previous section Note that this process is only performed by the developer user that creates the Appliance in the VPH Share portal and it is only performed once before the Appliance is saved Any regular user of the Appliance does not have to perform any configuration task The INTERACTIVE_SERVICES string is automatically read by the VPH Share plugin during workflow execution and when an interactive service is to be executed the plugin detects it and provides remote desktop access to it as explained in the next section 4 4 VPH Share plugin The main goal of the VPH Share plugin is to facilitate integration of Web Services deployed on VPH Share on scientific workflows supporting for both composition and execution enabling VPH Share Web Services to be instantiated and released on demand In the VPH Share project a GIMIAS server is installed in a Virtual Machine VM that can be instantiated as often as needed and shutdown on demand Each VM is called an Application and it is managed by the Cloud Fa ade Many different Applications can be created exposing different sorts of services In order to make the services available to several users at a time several Appl
76. me gt lt fullname gt lt email gt lt language gt lt country gt lt p ostcode gt sig lt ticket signature gt The parts in bold are under discussion for removal from the ticket but the general structure of the ticket would not change uid username of the valid user validuntil timestamp indicating when the ticket validity ends at present this 1s set to 12 hours from its creation after this time it is refused as invalid in case of longer processes services are provided to automatically regenerate the ticket and not block the execution cip IP of the client which generated the ticket tokens here are inserted the roles and all the permissions assigned to the user The https www djangoproject com https github com b3c vphshare Page 21 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share permissions are used in particular by WP2 security proxy and are in the form lt nameresource gt _ lt typeresource gt _ lt permission admin read edit gt udata contains information on the user sign this is the ticket signature that is generated from the MI with a private key DSA 2048 bit This 1s used by all external services to verify the ticket validity Anatomy of a ticket uid mkasper cip 192 168 200 163 validunti L 1201383542 tokens foo bar udata mydata sig MCQ CFDkCxODPm1 cEvAu0 05w7
77. n click on the link and then a new web browser tab will open automatically starting the NX NoMachine client Then the user can interact with the AS see Figure 48 4 6 Batch execution With the tools created in the VPH Share project the user can also execute the same workflow multiple times without manual intervention This could be used for batch execution of the same workflow with a series of input data which is very useful for running tests on multiple subjects performing the same experiment multiple times and other common situations in the career of clinical researchers All Workflow Management Systems developed by Taverna have a built in support for dealing with lists of data values This means that automatically VPH Share services can be input lists of values instead of single values This later translates into what Taverna calls implicit iterations see http dev mygrid org uk wiki display taverna Implicit iteration This is due to the fact that normally VPH Share services have inputs of depth O single values and if the user feeds a workflow with an input of depth 1 a list Taverna will automatically apply the implicit iterations approach Page 70 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 i Date 28 Feb 14 VPH Share Normally if the Taverna workflow has a single input port this means that Taverna will perform as many iteratio
78. n the Cloud Facade and handles possible errors during the whole process Page 63 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 Snell VPH Share 44 1 Desktop composition and execution tool The architecture for desktop workflow composition and execution is presented in Figure 47 Currently Taverna Workbench 2 4 is the main tool supported for this purpose it is open source and is licensed under GPL license version 2 1 This tool can be obtained from http www taverna org uk download workbench 2 4 The first step for a user to build a workflow using Taverna Workbench is to download and install the software If the user wants to include services provided by the VPH Share project then the VPH Share Taverna Plugin must be installed For installing the plugin see Section Installing Taverna Plugin at http vph share eu content vph share taverna plugin CLIENT SIDE SERVER SIDE Taverna A pe Workbench Viet dnd ue Facade uim Workflow i SA 7 77 f _ Me i iem 4 GIMIAS CLPs C a C J pu 4 mo ST L d AS without LOBCDER AS with interaction interaction Web based Remote Desktop NoMachine connection Figure 47 Desktop Workflow Management Architecture overview After this the user can search the Master Interface for one or more Appliances that provide the required services For each Appliance the
79. nce Page 44 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share 2 3 6 Resources workflows 2 3 6 1 Upload a new workflow The user can use VPH Share infostructure to upload and share new workflows To do so from the Workflows page from the homepage an upload section 1s available for a new workflow creation When pressed this will open the form which allows inserting all the necessary information to completely define a workflow resource new Create new workflow Title Description Workflow description Taverna workflow Scegli file Nessun file selezionato Taverna workflow file t2flow Input definition Scegii file Nessun file selezionato Input definition file xml Category Workflow Category Tags Add tags separated by comma Semantic annotations Add the annotations uri separated by comma Licence licence type for this workflow es GPL BSD MIT Required fields Create Workflow Figure 32 New workflow upload form The mandatory fields are Title the name with which the workflow will appear in the available workflows list Description a summary of what the workflow does its input its output and any other information useful for others to understand it Taverna workflow the workflow description file in Taverna Workbench format Input definition the input
80. nd test data 2 3 4 2 2 Unstructured data LOBCDER In VPH Share we refer to medical images and binary information as unstructured data These are managed in the infostructure thanks to the LOBDCER service see section 3 3 for more technical details In the MI LOBDCER is presented similarly to a shared folder where sub folders and files can be created Page 41 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share lobcder Create directory Name Owner Modified Size B Actions BB ARTreat aneurist benchmark mcruzvilla 13 Feb 2014 0 gt Bs DRS Rulesets fajran 30 May 2013 0 7 gt B Literature Mining Abstracts fajran 30 May 2013 0 7 gt i STH mp1smw 29 May 2013 0 y iia Sage BioNetworks susheel 04 Feb 2014 0 7 gt Gs Tutorial malawski 03 Nov 2013 0 7 gt amp VPHDare_Data mp1smw 17 Feb 2014 0 7 Bs skoulouz skoulouz 27 Jan 2014 0 7 gt 5 31f43ed jpg testuser 16 Jul 2013 9616 7 gt D University of Sheffield logo png susheel 08 Nov 2013 20701 7 gt D File_100M_1 dharezlak 13 Feb 2014 104857600 NE D file 10M dharezlak 08 Oct 2013 10485760 7 5 file 15M dharezlak 19 Dec 2013 15728640 7 gt D File_1M dharezlak 10 Dec 2013 1048576 7 gt D lobcderStoryShort mp4 skoulouz 03 Feb 2014 96299398 7 D lobcderStoryShorter mp4 skoulouz 03 Feb 2014 73984014 7 Add files Figure 29 LOBDCER interface In the LO
81. ns of the workflow as the number of values in the input list That is Taverna will execute the workflow as many times as the number of items in the input list Each iteration takes as input one value from the input list However for a more detailed explanation on how implicit iterations are performed especially for workflows with multiple input ports see http dev mygrid org uk wiki display taverna Implicit iteration Batch execution of workflows can be performed either in the researcher s PC or on line as follows 4 6 1 Desktop batch execution For activating batch execution of a VPH Share workflow in Taverna Workbench the user simply has to edit the input port of the workflow In the Workflow explorer select the input port and press the right mouse button to open the pop up menu In that menu select Edit workflow input port In the dialog box that pops up select List of depth and enter a depth of 1 see Figure 54 for an example Press OK to finish editing Workflow explorer Details Validation report tz Workflow3 EM Workflow input ports LA inputRingcutMesh F i LH z i E Edit Workflow Input Port Set the workflow input port name Mame a plara uir c Type Single value List of depth i Depth 1is a list 2 is a list of lists etc EE Tate a S Geometry Descriptors VPHShare OutputDescriptors gt Geometry_Descripi 4 n j Figure 54 Tav
82. nse and continues the execution of the workflow This is implemented using the following GIMIAS CLPs WSAsyncRun This method can be used to start running a CLP asynchronously The name of the CLP and its parameters must be specified The method returns the identification number of the process that corresponds to the running CLP WSAsyncStatus This method can be used to inquire the execution status of a CLP previously started with WSAsyncRun The process identification number of the CLP must be specified Possible statuses are STATE _PENDING STATE ACTIVE and STATE FINISHED WSAsyncResults This method can be used to obtain the results of a CLP previously started with WSAsyncRun once the 9 WSAsyncStatus method returns STATE_FINISHED The process identification number of the CLP must be specified The results will be returned in the form of a string In this way the VPH Share Taverna plugin makes short and simple requests to the server every few seconds avoiding leaving the communication up for long times and therefore avoiding any timeouts This new mechanism can be easily activated in a per service base by selecting a service and then displaying its details In the Details tab a Configure button will show up By pressing this button the configuration dialog will appear in which the user can activate the non blocking behaviour by clicking on the check box next to Execute service in non blocking mod
83. of User Access Systems J Version 1v2 Date 28 Feb 14 VPH Share A short video showing the web composition and execution process is available at https dl dropboxusercontent com u 5233146 tavernaOnlineIntegration Sepl13 avi 44 3 Support for workflows with long execution times By default the execution of VPH Share services from Taverna Workbench or Taverna On line has a blocking behaviour This means that when the VPH Share plugin invokes a VPH Share service the plugin s execution is interrupted until the service returns a response This is perfectly valid for services that return a response promptly but it can pose a problem for those services with long execution times The problem is that while the VPH Share plugin is waiting for a response the connection to the web service is not used as no new information is communicated from either side Then the connection can be taken down by any intervening web proxies or firewalls as the communication is flagged as timed out This is the typical source of errors such as Bad gateway or Timeout when running VPH Share services In order to avoid this the VPH Share Taverna plugin has been upgraded to support a non blocking communication mechanism in which the plugin starts the execution of the service in an asynchronous fashion and then monitors the execution status of the service every few seconds When the plugin detects that the service is finished it collects the respo
84. of the workflow as saved by Taverna Workbench format Category standard categories for workflows defined by the domain experts Licence the level of permission associated to the workflow access use i e GPL BSD etc The user can eventually add also Tags and Semantic annotation URI both separated by commas which can be then used by search services to help user looking for specific services to retrieve the new workflow Page 45 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 y Date 28 Feb 14 a VPH Share 2 3 6 2 Run an existing workflow A workflow is the choreography of a series of components with a certain research aim Workflows can be created by composing Applications with Taverna Workbench and uploaded and shared in the Master Interface as previously described If a user has got permissions to access a workflow he she can download the workflow description file and its inputs so to execute the workflow locally from Taverna Workbench Otherwise he she can use the Execute workflow button to start its run connecting to the workflow manager technically described in section 5 4 Once the button is pressed a window opens to allow the user to configure the start of the workflow Some of the parameters can be used to run the workflow with custom input files or by using development mode Applications while others like the selection of the Taverna Se
85. on Image Tools MITK Manual Segmentation Start selected Cancel Figure 24 Appliances browsing 2 3 3 4 Resources access When browsing the VPH Share portal the user finds a resource of interest and visualises the information associated to it as recovered from the WP4 metadata services see D4 6 for more details All the resources data applications or workflows have the same presentation layout of the information which relies on the common metadata model provided by WP4 Thus we will here refer to a workflow as an example but the same information would be found for the other resource types estos a VPHOP workflow inca Description This is the VPHOP workflow Taverna Files The workflow uses the SOAP version of the services which are then running on Tags CINECA PLX HPC system The workflow starts From Ehe patient Fracture best WPHOP risk data hosted on PhysiomeSpace applies the patient specific loading conditions and performs the FE simulation over 10 years A Final module calculates the risk of Fracture after 10 year of remodelling Licence aso Download Date Created 05 24 2013 Semantic Annotations Language English This resource has not semantic annotations Status Published Execute workflow Citations STH2013 VPH Share Dataset CVBRU 2011 doi 33 55273 SHAR37 8542 95 Related Resources Download workflow File Download input File Figure 25 Resource information page Page 37 of 82 FP7 ICT
86. on through the NoMachine remote desktop DEM software Running Development Instances Name IP Location Status Actions Kate via NoMachine 10 100 8 2 Cyfronet active Start development instance Manage user keys Figure 43 Development mode view containing a list of applications owned by a given user and a list of running development instances The second section is a list of running development instances with details about the location and current status Also redirections and available endpoints can be edited for each of the items in this list After the item is expanded all the available redirections and endpoints for a given instance are presented which allows for testing the exposed services directly in development mode The development view also has two action buttons which are used to spawn new development instances and managing user keys Starting a new development instance ensures that always a fresh instance is run without any virtual machine reusing If more than one user key 1s added during booting a new instance a choice dialog is presented to pick one of them To register applications exposed a developer has to specify any number of the following endpoint types e Web Application Endpoint an endpoint pointing to a resource returning a web page e Web Service Endpoint an endpoint pointing to a Web Service resource for this endpoint a WSDL description should be provided optionally a description of the service can be provided
87. organised and implemented around the concepts of institution and study Institutions represent virtual or physical organisation representing a community of users like a university department a research project team Each institution can create and manage one or more studies Studies are a specific sub group of researchers typically working on the same research or clinical question When clicking on the Groups link the user is provided with the list of the available institutions and studies present into the system in green and blue background respectively Page 28 of 82 74 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share All Institutions Studies CINECA CISTIB DARE STH CINECA Italy UK fe A1 UK ry UK 45 45 Figure 7 The institutions studies S The institutions studies of which the user is member are marked with a green arrow If the name of the institution study is clicked its details are provided If the user is already part of the selected institution he she can see its members and the available studies while otherwise he she will have a link to request subscription to the institution If clicked the institution managers will receive a notification and will be able to accept or refuse the subscription Search CINECA Users CINECA ita Users 4 master interface Studies Test User tes Descrip
88. ough Taverna Online 66 4 4 3 Support for workflows with long execution times eeeeeeee 68 4 5 Workflow execution through the MI sssseeseeeeeenneneeeenn nnne 69 T0 BAU CIN CCC octane E enous oua cc doM ut A eei ise MIesnU Duca sa Po doH OR ND UOS 70 4 6 1 Desktop batch execution eessssssssssssseeeneneneeeenen nnne nennen nnn nnns 71 0 5 WED DALI EXE CUOI esee ce dont vens ont adecesecenesesoseuedseacennceeseadedeuenqneseasevedseaneneaces 73 47 Workflow Manager APIs cccewesndssnncencncuewarsssasdenettusese desnidanciseediadieanienetteeniadeseiianettews 73 AS Data Provenance and SermalitiCo uper cernes sets eo tu rtu bee teub ue Fere tua Fe seo nuu RENE xix Tees 74 49 Eos denim U 76 EE 7 io dress Em TI OO WOEDE TO du RETE 78 List of Key Words Abbreviations isis secu ssisbebisbce ses ensbebes aces etu sene ped u bas citta swxsiebestiasebuswsdiabieacesbia aude 79 Page 5 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 mum r VPH Share LIST OF FIGURES Figure 1 Master Interface component diagram cccccssseeeceeccccceeeeeeaaaaeaaseeseseeeseeeeeeeeeeees 12 Pisure 2 Ticket signature Cle ALON on i oro oci punc eere pit p RU erase ona EESE A EE Ei 22 Figure 3 Schematic representation of the OpenID authent
89. presented in Figure 41 All the cloud management views and Cloud Facade request handlers were encapsulated in a single Cloud Library run in the User Browser were necessary authentication credentials are obtained from the Token Store and delegated during direct communication with Cloud Fa ade Such setup allows bypassing the MI Server for cloud requests and greatly improving the responsiveness of cloud management views The Cloud Library itself is served by the MI server Master Interface User Browser Cloud Library VPH Token Store views Cloud Facade e g Cookies Store communication get token REST HTTPS HTTPS Cloud Facade MI Server static contents incl Cloud CORS Enabled Server Library Figure 41 CORS based cloud component deployment In order for the direct communication between the Cloud Library and the Cloud Fa ade component to work a CORS Cross Origin Resource Sharing mechanism had to be used as the MI Server and Cloud Facade servers are hosted by using different domains Additionally token authentication is used with each request to ensure proper resource access Cloud Fa ade component offers a REST interface for managing cloud resources The full API description is available online The API is divided into several sections each managing different aspects of the cloud infrastructure Here for reference the part responsible for obtaining information about compute sites is presented The available operations inclu
90. rameters Returns It searches for groups The search is case insensitive Without any term the full list of groups is returned A JSON list of group names is returned It is available to all authenticated users portal vph share eu api searchgroup term lt term gt ticket lt ticket gt GET Term the search term ticket your authentication ticket Status code 200 Meine oem es S Ss spere TS subscribers by toroupnamet testqroup0002 Mss orbem Status code 403 Ticket not valid Status code 500 2 2 2 5 api creategroup Description Url structure It creates a new group available only to staff users With the parent parameter provided the group is created as child of the given group portal vpl share eu api creategroup group group amp parent parent amp ticket ticket Page 14 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share Method GET Parameters group the group name must be globally unique parent the parent group name ticket your authentication ticket Returns Status code 200 VW QUE Status code 403 Ticket not valid or user not allowed to invoke the service Status code 500 2 2 2 4 api deletegroup Description It deletes an existing group available only to staff users Even after deletion the group name will not be available for new groups Url
91. rge net apps mediawiki gimias index php title How ToAddCommandLinePlug in The user just needs to activate in GIMIAS those plugins that are to be exposed and then activate the WebServices Plugin Then the WSDL generated by the WebServices Plugin can be used to reach the exposed Web Services In the VPH Share project GIMIAS is used as a server that acts as a Web Services provider Those services are used to compose biomedical workflows in different fields neurIST Page 61 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share euHeart VPH OP and Virolab flagship workflows The composition and execution of these workflows can be done using Taverna Workbench or Taverna On line Also any CLP already exposed through GIMAS can take benefit of the improved WSDL interface to support execution with long times in combination or not with the VPH Share Taverna Plugin The list of Web Services related to the VPH Share flagship workflows currently deployed includes neurlIST services not requiring user interaction GAR segmentation 1 Geometric Descriptors computation QneurIST services requiring user interaction Bounding Box selection Mesh editing ht Ring cut Neck selection Other Web Services that are available not directly related to any of the VPH Share flagship workflows include Basic Data Visu
92. riptors WSAsyncRun Ports and WSAsyncStatus WSAsyncResults Cancel Apply When the user executes the workflow composed in Taverna On line the VPH Share plugin communicates with the Cloud Facade and creates a VPH Share workflow which includes all the Applications needed to execute the Taverna workflow see Figure 49 The execution of each service in the Taverna workflow is delayed until the Application needed for this service is launched successfully If two or more services from the same Application are being used only one Application is created and then the services share it saving computation resources The services are executed in the order specified by the Taverna workflow The output of each service as well as the final output of the Taverna workflow is stored in the LOBCDER see Figure 49 If an Application requires user interaction the Master Interface notification service is used to send the user a link to the web based NX NoMachine client which can be used to open a remote desktop session to the Application Notifications reach the user by e mail as well as through the Master Interface s GUI see Section 2 2 4 In the case of the later the user can click on the link and then a new web browser tab will open automatically starting the NX NoMachine client Then the user can interact with the Application see Figure 48 Page 67 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems A Je 3 D6 5 Production Deployment
93. rver are temporarily present for debugging More work will be done in the future to provide an interface to customise the inputs of the workflow and in particular for the update addition deletion of parameters Sample Workflow Workflow Execution Title sample Workflow execution 1 Insert a meaningful name for this execution Choice Taverna server Taverna with helleworld app 7 Custom Taverna endpoint Set it only iF you start an atomic service in development mode Default Inputs Check iF you want Eo run Ehis workFlow with your inputs Initialize execution Figure 33 Workflow run configuration When the nitialise execution is pressed the workflow is added to the list of those ready for execution Each workflow has three action icons a green arrow to start the execution a red cross to delete the workflow execution and an orange icon to see the logs associated to the specific workflow execution in green the actions successfully completed and in red the errors Page 46 of 82 FP7 ICT 269978 VPH Share WP User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share The workFlow execution has been correctly created WorkFlow executions Sample WorkFlow execution 1 Status Created GEI Figure 34 Workflow execution list Workflow executions Sample Workflow execution 1 Status Submitting the workflow to Taverna E Status Details Created Atomic service is in
94. s content chapter 4 First consolidate version for review and comments from all WP members Update chapter 4 Hevision of MI sections Second consolidate version first for internal review Minor changes pending Comments from the internal reviewer Enrico Schileo Comments addressed and final version from co authors and partners Final review before submission to the PMO Submission Version Page 3 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 CONTENTS UY SNA eros iei cc sense E E 8005202 Up 10000 LIU a OUR IE URL AU CU dp cr TD R ER Dd LUS 9 EB c seio c 11 2 The Master MET Cecene R rA EEE annis Enia 12 2E Pal Aeee dno AE e E a 12 P2 AFE CPO ee A E A O 13 22 duthentcatmon TCC serprent n AEA E E eet bud ar E 13 222 Groups MOSS CEDOTID e aledeuctnctalcnenaawssuseseaianelncossuaases 13 2 2 9 BRESOUL CC CCC SS onetususp Emu iXImadi UI mU MINE I MM IESU M MIU IS I M MUEEE 19 L2 INOUHCAHORDLSCEVICE bestes ius uin toti nef aat henat as Cop eustu ia toni eui eati pus Ue UNE DN LEGE 20 2 2 2 MMC Web AIC dt EOBLo s oreaeiest sio itis tates sepu steptsdet EE rus cete cuu Pob E sUUT sob 21 2260 The security BURTON mMmSMR 21 2 2 Authentication mechanisms sssini enren nienn ase eek ieies 24 2o Teu Tl efl ACG e EEES uae 25 259 re O E A E EE E 26 PALA E a E E E E 27 Zo D Oe TOOLS e E E E E 3
95. s with the Cloud Facade to start a new Application that runs the Taverna Server specified by the user it waits for the server to be active and then submits to it the workflow selected by the user CLIENT SIDE SERVER SIDE ica Workflow TOR EE inica 3 Researcher SISHeBT D Server A Web based Remote Desktop Fa ade Figure 53 MI Workflow Execution Architecture overview If the submission of the workflow 1s successful the WM proceeds to configure the workflow execution This configuration process consist of specifying all necessary security parameters certificates for the workflow to be allowed to run in the Cloud Facade specifying the version and location of the VPH Share plugin that 1s going to be used during workflow execution specifying which services in the workflow require interaction and finally specifying what will be the input for the workflow in the form of a baclava file See Page 69 of 82 FP7 ICT 269978 VPH Share j WP6 User Access Systems A Je 3 D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share http dev mygrid org uk wiki display taverna DataViewer Tool for more details about baclava files In addition when the workflow is submitted to the server it 1s given a unique identification string Before executing the workflow the WM creates a new output folder in the LOBCDER using this identification string Then the WM copies into this folder al
96. seeeeeeeeeeaaas 56 Figure 44 Generic invoker view with a list of Appliance instances eseeeeesssss 57 Figure 45 Sample remote application run on the cloud visible on the user computer as yet zeros TOCA WING OW eee a T EEEE EEE ATE E EE EEEE 58 Figure 46 Workflow Management Architecture overview cccccccccceeeeeeeeeeseeseseseeeeeeeeeeeeees 60 Figure 47 Desktop Workflow Management Architecture overview essere 64 Page 7 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 antl VPH Share Figure 48 Web based remote desktop connection via NX NoMachine cccceeeeeeeeees 65 Figure 49 Web based Workflow Management Architecture overview ccssseeeeeeeeeeeees 66 Figure 50 Taverna On line working area eeesssssssssseeseeeeeee nennen nennen eene nennen 66 Figure 51 Importing VPH Share services in Taverna On line sees 67 Figure 52 Configuration dialog for the NeckSelection VPH Share service 69 Figure 53 MI Workflow Execution Architecture OVCrVICW ccccccccceeeeceeeeeeeeeeeeeeeeeeeeeeeeeees 69 Figure 54 Taverna Workbench s edit input port dialog ccccceseesesssncceeeeeeeeeeeeeeeeeeeeeeeens 71 Figure 55 Taverna Workbench s Run Workflow dialog with input list
97. sen on the left box and composed with AND and OR operators by dragging them in the right boxes The two right boxes are composed with the AND and the terms in each box are composed with an OR operator Page 34 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share When the concept is dragged a window is to set the value with exact match or inclusion criteria is shown Set Value Set the value for selected term 5 Inclusion match on EZB Figure 20 Set value for inclusion criteria After the selection of the criteria each one can be still edited or remove before pressing the Query dataset button 2 3 3 3 Browsing There is also the possibility for users to browse in each resource category all the available resources Data for the data resources the browsing can be achieved by domain category i e cardiovascular respiratory etc a carousel of images for the different medical domains the data can belong to is presented and by selecting one the user will be presented with data whose associated metadata are related to this category An Alternative browsing is the alphabetical listing the user can move from one initial to another using the top bar letters and click on the data name or icon to visualise the resource information and eventually access it Cardiovascular Respiratory Genetics Infection amp Musculos
98. t Query dataset patient Search Advanced search Results that match the following terms or query http ncicb nci nih gov xml owl EVS Thesaurus owl Patient Ed https vphsharedata1 sheffield ac uk woodreviewdemo2 Match 2 tH https vphsharedata1 sheffield ac uk woodreviewdemo Match 2 E3 https vphsharedata1 sheffield ac uk richtest Y Match 2 3e E https vphsharedata1 sheffield ac uk pvp Quey Match 120 atase Figure 17 List of datasets corresponding to the semantic terms From the list of the found resources the user can choose which one to further query based on the concepts used during the annotation phase Moreover he she can further refine the concepts or select one from the available list 1 Search dataset 2 Select dataset 3 Select concept Query dataset https vphsharedata1 sheffield ac uk woodreviewdemo2 Filter concepts Search Available Concepts Term description http ncicb nci nih gov xml owl EVS Thesaurus owl Patient Patient https vphsharedata1 sheffield ac uk woodreviewdemo2 unannotated patientimages_csv patientimages csv Figure 18 Dataset query 1 Search dataset 2 Select dataset 3 Select concept 4 Query dataset https vphsharedata1 sheffield ac uk woodreviewdemoz gt Patient Filter Annotations Search Reset Query Dataset Q ib Patient gt Address ib Patient gt Name ib Patient gt Identifier TERMS IN OR Figure 19 Dataset internal query The terms can be cho
99. t an early stage of development and to consider usability as one of the main drivers for the development of the system Furthermore in accordance to this attention towards end users and in close collaboration with WP8 after the release of each prototype users feedback report is issued in conjunction with WPS and circulated among the technical partners of the project for inclusion in the requirements for the next phase of software development In this document we provide a detailed description of the main tools and functionalities that constitute the production prototype of the User Access System describing its status and the current plans for its future development In particular in this deployment we have included the main facilities that permit the user to start using the infrastructure and implement basic use case scenarios According to this during this period we have improved services and functionalities that were already available as well as released new ones all of them are described in the following chapters Page 11 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share 2 THEMASTER INTERFACE As already mentioned the Master Interface 1s the entry point for the user into the VPH Share infostructure and it can be reached at portal vph share eu In particular it is a web application which besides providing its own func
100. t of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share This page was intentionally left blank Page 82 of 82
101. tcode 40033 fullname Matteo Balasso email m balasso scsitaly com j If the given ticket is not valid the HTTP 403 status code is returned If a user needs a copy of his her own actual ticket for example in the deployment of Applications Atomic services he she can copy it into the clipboard by using the button available 1n the user profile page Two APIs are available associated to the ticket 1 https devauth biomedtown org refresh_tkt ticket lt ticket gt It renews the ticket timeout for other 12 hours It accepts requests GET to be deprecated in the future and POST It returns a plain text answer with the new ticket 2 https devauth biomedtown org user login username username amp password pass word gt amp domain VPHSHARE It generates a valid ticket for the Master Interface It accepts requests GET to be deprecated in the future and POST It returns a plain text answer with the ticket http en wikipedia org wiki JSON Page 23 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share 2 2 7 Authentication mechanisms As already reported in D6 3 and repeated here for completeness the authentication mechanism provided by the MI uses a decentralised method based on the OpenID protocol The MI acts as the relaying party and the authentication is demanded to an external Identity Provider in w
102. test 15 Toi 21 ol 5 E 5 Figure 10 The institutions studies user management view Studies can be created by the institution managers with the form shown in Figure 11 Create a new study for CINECA Title Study title Managers Description Start date BP Study start date Finish date BP Study finish date Recurec field Figure 11 The institutions studies creation study view Page 30 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share If an institution of interest 1s not available in the system the user can request its creation by filling in the form provided see Figure 12 The portal administrators will then check the information and if appropriate approve the creation of the new group Resource owners can then use the available groups and studies to grant access permission to resources without having to select each user individually 2 3 2 4 Admin tools This page is available only to the portal administrator and it allows assigning specific permissions to subscribed users like the developer role or the administrator one to grant access and control on resources not opened to the standard users Request a new institution Name Managers Description Adcress Accress Country Country Logo Scegiif e Nessun ile selezionato Institution logo image Signed dsa Indicating that has signed D
103. tion Silvio Prosapio s_prosapic CINECA group e pori miae Debora Testi t Via magnanelli 6 3 Matteo Balasso mbalass ae Testi 4 Alfredo Saglimbeni asa 46 All Institutions Studies Request a new institution CINECA CISTIB DARE STH DARE PE CINECA Italy ts UK UK T UK test 1 i55 MES IS 25 ie 25 ma mA mA e Figure 8 The institutions studies details view Page 29 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share home groups CINECA Search In CINECA CINECA Italy Description CINECA group Address Subscribe Via magnanelli 6 3 Admin Debora Testi DSA No 26 4l All Institutions Studies L4 CINECA CISTIB DARE STH CINECA italy UK UK UK 46 e PE d 45 e 25 Figure 9 The institutions studies subscription view The managers can also remove or add new users with the provided management interface see Figure 10 CINECA tka Add users to institution CINECA Italy Studies Set as managers CESEW P Accepted users CINECA group 4 Alfredo Saglimbeni asaqli B Address mi Lestuser Via magnanelli 6 3 2 master interface mi te r Eg Admin Debora Testi 2 Debora Testi testi ga i 5s Silvio Prosapio s prosapio x create a new study Matteo Balasso mbalasso B Contact us to delete Y All Institutions Studies Request a new institution CINECA CISTIB DARE STH DARE PE CINECA Italy UK A UK UK
104. tionalities for example for user management and permission control it integrates and exposes the user interface for the services provided by the other technical WPs 2 1 Final Architecture and API The scheme below Figure 1 represents how the Master Interface 1s connected to other WPs or external services Master interface External services Resources Functionalities Access download WP2 WP3 ines i VO ParaviewWeb WP6 Creation Sharing Cloud platform WP2 Semantic services WP4 Upload _ Sharing Workflow manager WP6 Workfl 3 Groups institutions Dashboard arch amp annotation N A O p EM gt ee 5 o qp uo Biomed Town OpenID provider Django Python framework Figure 1 Master Interface component diagram The Master Interface is implemented as reported in the next section Some APIs to integrate or connect custom components to the MI are listed into the portal help pages and reported also here for completeness Any updates to the API will be documented at https portal vph share eu help api Page 12 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 2 2 API description 2 2 1 Authentication Ticket 2 2 11 api validatetkt also validatetkt works VPH Share Description It validates given authentication ticket it returns a JSON representation of the user attri
105. ts the issue on the Redmine system and assigns it to the proper member in the development team As soon as a solution is provided to the issue the user is notified by email A list of already notified known issues will be also kept on the MI web pages immediately after public release of the beta version to the general public together with a release note with the last development exposed into the interface Page 51 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 i Date 28 Feb 14 VPH Share 3 VPH SHARE CLOUD SERVICES 3 1 Final architecture and API Several views of the Master Interface in particular associated to the Application resources are cloud management graphical user interfaces GUIs which communicate with WP2 cloud components directly or through the Cloud Fa ade API module In Figure 40 a dependency overview among the components is presented followed by a short summary of core functionalities Master Interface Data Manager Cloud Manager upload download files development mode manage file metadata generic invoker search files workflow manager REST Cloud Facade Atomic Service lifecycle WebDav REST management SQL Cloud Client LOBCDER Cloud DB Cloud Sites file management cloud metadata JVidmanaoement file metadata management management 9 Figure 40 Architecture of cloud services and dependent compon
106. tu thaecnqt in fan ie cnuM nd Sue 42 Figure 30 The application view after invocation sese 44 Figure 31 Invocation endpoints for an active application eeeeeeeeeeeeeeere 44 Figure 32 New workflow upload form esee eee 45 Figure 33 Workflow run configuration eeeeeesssseseeseeseeeeeeeeeeee nennen nenne nnne enne nns 46 Figure 94 W OLRTIOW execution SE ouaiocoss oostin in eis commoti mia dine toos nudis comua ki quc Us HM SOUS ni dit dU 47 Figure 35 Workflow logs during execution 00cssssssseeeeeeeceeceecccccessceecascscsseeseseeeeceeeeees 47 Figure 36 Workflow execution error reporting sssssesseeeeeeeeeeeeeen nennen nennen nnns 48 Figure o e Dashboard osossesesesenute uses EEEE E RI DIPENDE EU EO SUONI HERR UUUE 49 USS 25 EU EIE E E sen E intesa ecu A EE rdi UN SE NU iMIUNUE 49 Figure 39 Manage Teque SES ereis i E a eai 50 Figure 40 Architecture of cloud services and dependent components 52 Figure 41 CORS based cloud component deployMent cc ceecccecccccceeeeeeeseeeeceeeeeaaeeeees 53 Figure 42 Main view of the cloud management GUI divided into three tabs corresponding to ditierent Workin TINO 0 CS NR M 55 Figure 43 Development mode view containing a list of applications owned by a given user and a list of running development instances ceececccccessseeseeccceeceeeaeeeeseeceeeeeeeeeae
107. user can obtain the URL address of its WSDL using one of the resource access buttons in the Master Interface This WSDL address can then be used to import the services provided by the Appliance in Taverna Workbench see Section Importing VPH Share services at http vph share eu content vph share taverna plugin As depicted in Figure 47 note that Taverna Workbench also supports other types of services such as any generic Web Service or the CLPs of a local GIMIAS installation All these services can be combined by the user into one or more biomedical workflows For a detailed explanation on how to build workflows with Taverna Workbench 2 4 see the user manual at http dev mygrid org uk wiki display taverna User Manual When the user executes the workflow composed in Taverna the VPH Share plugin communicates with the Cloud Facade and creates a VPH Share workflow which includes all Page 64 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 VPH Share the Applications needed to execute the Taverna workflow see Figure 47 The execution of each service in the Taverna workflow is delayed until the plugin has made sure that the Application needed for this service is launched successfully If two or more services from the same Application are being used only one Application is created and then the services share the Application saving
108. user interfaces development its activities 1n the last part of the project are mostly driven by the user s feedbacks and in synergy with WP8 As engagement with end users is particular relevant for VPH Share as a whole we particularly care about supporting users and take into proper consideration feedbacks coming from the testing phases As reported in WP8 beta user programme activities so far the system has been opened to the project partners but a public release is being launched soon For this reason a number of tools to get in contact with beta users have been deployed and proper procedure to process the feedbacks put into a place After a first evaluation of the getSatisfaction tool the consortium has decided that this was not completely satisfying the project needs as the direct interaction between the users and the development team was not straightforward Thus a new procedure has been put into place For internal users a Redmine tracking system is in place with two distinct sections for the users exemplary workflows users and the development team with the possibility to cross link the issues and their tracking For external users they are invited to write feedbacks or bug reporting to the support email the email is processed by a single person working on both WP6 and WP8 who takes care of clarifying unclear aspects replicating the issue and discussing with the user further details Once the issue is clear the support person pos
109. view of the cloud management interface consists of three tabs corresponding to each mode as presented in Figure 42 DYesfew nr Workflows My Applications Name IP Location Status Actions Kate via NoMachine 10 100 8 3 Cyfronet active Eo Start new application Figure 42 Main view of the cloud management GUI divided into three tabs corresponding to different working modes 3 2 1 Development Mode The development mode view denoted as My Applications tab 1s divided into two sections see Figure 43 The first section contains all the applications owned by a given user and allows changing its properties and associated initial configurations It is also possible to remove an Application which will also remove the image snapshot stored in the cloud infrastructure The set of properties for an Application include name description shared and scalable flags and the visibility which can be limited to the owner to users granted the developer role or to regular users Several initial configurations can be defined for a single Application and each can contain parameter placeholders which are replaced by user provided values during booting up new instances Page 55 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 Date 28 Feb 14 a VPH Share Applications Workflows BETIUPSYere Tes ea Owned Applications Kate via NoMachine Offers the KDE s kate applicati
110. workflows Fom Mi Boua montoring integration O GmdsiwMod 0 New home page facet O Data browsing mprovmens 700000000 Bug frang and maintenance ofthe UI Workfow aueue manager O Workflow queue manager Table 2 WP6 Year 4 Plan Page 78 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems D6 5 Production Deployment of User Access Systems Version 1v2 nus Date 28 Feb 14 a anal VPH Share LIST OF KEY WORDS ABBREVIATIONS 3DRA AIR AMS AS API AWS BSD CF CLP CRUD CSV DB DPS GAR GIMIAS GPL GUI HTTP HTTPS ITP JQUERY 3 Dimensional Rotational Angiography Adversarial information retrieval Application Management System Appliance Application Programming Interface Infrastructure services for cloud metadata management Infrastructure services for cloud site management Berkeley Software Distribution Cloud Fa ade Command Line Plugin Create Read Update and Delete operation Comma Separated Values Database Data Publication Suite Geodesic Active Regions Graphical Interface for Medical Image Analysis and Simulation GNU General Public License Graphical User Interface HyperText Transfer Protocol HyperText Transfer Protocol Secure Institute for Information Transmission Problems multi browser JavaScript library designed to simplify the client side scripting of HTM Page 79 of 82 JSON LOBCDER MI NX OGSI DAI PKI RDF REST SOAP SPARQL SQL SSH SSL UAS UI URI URL
111. ype portal workflow or development which changes the behaviour of optimisation mechanisms e Application Types describes applications including properties such as visibility sharing policy scalability or preferred resources e Application represents a list of running instances e Compute Sites list of compute sites available in the infrastructure e Development Mode Property Sets a structure with appliance type properties being a copy of the Application Type structure needed for instances run in the development mode e Endpoints list of endpoints representing HTTP based applications offered by a given application type e HTTP Mappings represents a list of HTTP redirections for applications running on private networks e Port Mapping Properties list of port mapping properties allowing for setting attributes such as timeouts e Port Mapping Templates a structure describing all necessary port mappings for a given application type e Port Mappings concrete port mappings containing source and destination port numbers for a running application instance e Security Policies repository for storing security policies used by the security proxy component while authorising requests e Security Proxies holds configuration parameters for security proxies e User Keys user public keys injected into running application instances Page 54 of 82 FP7 ICT 269978 VPH Share WP6 User Access Systems

D6.5: Production Deployment of User Access Systems

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