Manage your SAS Drug Development environment
Contents
1. lt group gt lt group gt lt group gt lt group gt lt folder gt The roles that are managed on the project or analysis level are included lt role gt lt Functionrole gt lt name gt Functionrole lt name gt lt adminworkitem gt true lt adminworkitem gt lt createworkitem gt true lt createworkitem gt lt disablevers gt true lt disablevers gt lt enablevers gt true lt enablevers gt lt managelock gt false lt managelock gt lt managememb gt false lt managememb gt lt managerole gt false lt managerole gt lt managestat gt false lt managestat gt lt managework gt true lt managework gt lt permdelitems gt false lt permdelitems gt lt resotreitemsdelbyoth gt false lt resotreitemsdelbyoth gt lt setsignfiles gt true lt setsignfiles gt lt assignedto gt lt assignedgroup gt Domain Expert lt assignedgroup gt lt assignedgroup gt GDM lt assignedgroup gt lt assignedgroup gt DML lt assignedgroup gt lt assignedgroup gt CP lt assignedgroup gt lt assignedgroup gt MBDD lt assignedgroup gt lt assignedgroup gt Medical Review lt assignedgroup gt lt assignedgroup gt eSubmission lt assignedgroup gt lt assignedgroup gt MA LIM lt assignedgroup gt lt assignedto gt lt role gt In the end groups from a higher level can be linked to groups in a lower level limiting the time needed for administrators when adding users to groups lt group hierarchy gt lt group pair gt lt so2. Bruxelles Work Phone XX XXX XXX XXX Email jean marc ferran businessdecision com Web www businessdecision lifesciences com 11
3. will be made to CDmation a Business amp Decision Life Sciences application The core focus will be on administrative tasks like user and group management privileges and permissions There will also be a chapter on the usage of programs jobs and workflows in relation to the environment This paper will not focus on how to build programs jobs and workflows in the system The last part of the paper will describe how the API functions allow external applications to interact with the environment To demonstrate the possibilities of these API functions some examples will be given One will be a simple example creating a user listing The other will be a fully integrated product CDmation What is SDD According to SAS SAS Drug Development enables the efficient development execution and management of analysis and reporting activities for clinical research SDD can be seen as fileserver and active directory versioning system and SAS server all in one SDD can be used to upload store and version files The SAS server allows for interaction with them The main difficulty is understanding the need of the users The system will have a variety of users with different roles in the company Not everyone will require the same functionality from the system Some will use the system to investigate data others will just use the system to upload and download files think about external partners Some will be programmers and develop SAS programs wi
4. PhUSE 2014 Paper TS08 Manage your SAS Drug Development environment First author Bart Van Win Business amp Decision Life Sciences Brussels Belgium Second author Jean Marc Ferran Qualiance Copenhagen Denmark Third author Sebastien Roland Business amp Decision Life Sciences Brussels Belgium ABSTRACT When the major players in the pharmaceutical industry start focusing on keeping data management processes internal instead of outsourcing having a dedicated environment is a plus SAS brings a new version of the product called SAS Drug Development i e version 4 x fulfilling many needs in the search for this platform This paper will focus on managing a SAS Drug Development 4 x environment In the paper following topics will be addressed e SDD environmental logic e Setting up a folder structure with group access and permissions e Program Job Workflow e Creating privileges and managing users e Using API functionalities to automate tasks e Using API functionalities to make user account listings While discussing these topics a link will be made with default environments fileserver SAS server to show the possibilities outside of SDD A custom application CDmation will be introduced as a part of the solution in managing the environment INTRODUCTION This paper will describe the usage and management of an SDD 4 x system Comparisons with other environments will be made where possible Sometimes a reference
5. ation_Start saa Ba PDF Ea RTF B exceptions sas bdat Validation result tet CONCLUSION The SAS Drug Development 4 x environment is a strong addition to the SDD series The SAS component lies much closer to the SAS Base environment that everyone is familiar with in comparison with older versions Additional to the SAS Base programs the system provides jobs and workflows as overlaying elements The file server component gives a lot of possibilities together with the user and group level privileges and permissions Where functionalities within SDD are missing the user is free to develop external applications Via these applications the user will be able to interact with the system with more functionalities than the standard SDD interface brings 10 CONTACT INFORMATION Contact the author at Bart Van Win Business amp Decision Life Sciences St Lambertusstraat 141 Rue Saint Lambert 1200 Brussel Bruxelles Work Phone 32 479 707 626 Email bart vanwin businessdecision com Web www businessdecision lifesciences com Contact the author at S bastien Roland Business amp Decision Life Sciences St Lambertusstraat 141 Rue Saint Lambert 1200 Brussel Bruxelles Work Phone 32 XXX XXX Xxx Email sebastien roland businessdecision com Web www businessdecision lifesciences com Contact the author at Jean Marc Ferran Business amp Decision Life Sciences St Lambertusstraat 141 Rue Saint Lambert 1200 Brussel
6. c will consist out of three parts 1 First the API functions of SDD will be described 2 The second part will give a simple example of how you can use JAVA API functions to read out the user management table In the example an excel table is created with all the necessary user info The SDD 4 2 system does not have an export functionality build in for this information but by using the API functions it can be done anyway 3 The third part will be a more complex example where Business amp Decision Life Sciences has created a fully SDD compatible environment to do Library Management Study Build and Management Data Validation and Issue Tracking The interaction with SDD is relying purely on these JAVA API functions With each version of SDD comes a constantly growing set of API functions both in JAVA as well as in SAS The JAVA set contains in each of the SDD versions a bigger list of functions than the SAS set Documentation is provided for both sets of functions For JAVA it is stored in the well known JAVA doc layout For SAS there is a user s manual in PDF format The goal of API functions is to allow the users access to the systems functions without having to use the system itself To list the always growing function set would be to list the whole SDD functionality In SDD 4 2 one of the earlier versions in the 4 x series the JAVA API functions already allow to create folders and files read out the audit trail do user management run
7. e privileges compare with the previous table to see the differences Disable Versioning FOLDER ACCESS AND PERMISSIONS Folder access is given on a group or user basis Every folder in the Permissions repository can be managed by using groups and users from that level or higher if pass through There are five different permissions that can be given to a group or user within a folder There is the admin read Owner Bart Van Win properties write content write and delete permission Read and Delete are self explanatory Content write means that the user can add and change files Properties write means that the user can change Current Default the properties of a file this is the metadata of a file Owner Every file type has a preset list of properties but more can be added with external attributes Members The Admin function allows a user to change permissions on a file or folder a Administrator For every folder there are two different permission sets There is the tech amp functional current permission set which allows the user to set the current permission meaning that if the permissions are changed the folder and files in the folder and subfolders if selected will have the new permissions The default permission contains the permissions for the new files in a folder Files can not have a default permission because they are not a container To clarify this with an example 1 Folder A current permissio
8. jobs A first easy example of using the JAVA API functions is creating a user listing report in Excel This functionality is not possible in the current SDD environment but can be done via external functions The user writes a program that accesses the UserService within SDD and extract the list of users With some additional JAVA coding this set of users can then be transformed into an excel file An example of this kind of listing is shown in the image underneath A B C E H J K 1 FirstNam LastNan Departmet IsActive IsLocked DisplayNam LastLogin L Accountl ype ha Administrat 16 User User BDLS Yes Yes User User Thu Jun 13 05 17 41 EDT 2013 INTERACTIVE No 53 User User BDLS Yes Yes User User Mon Sep 16 09 45 27 EDT 2013 INTERACTIVE Mo 58 User User BDLS Yes Yes User User Mon Apr 15 08 18 32 EDT 2013 INTERACTIVE Yes 66 User User BDLS Yes Noa User User Wed Sep 24 10 02 25 EDT 2014 INTERACTIVE Na oo User User BDLS Yes No User User Wed Sep 24 10 57 03 EDT 2014 INTERACTIVE No g7 User User BDLS Yes Mo User User Fri Sep 19 10 27 07 EDT 2014 INTERACTIVE Yes 93 User User BDLS Yes No User User Thu Mar 13 12 02 54 EDT 2014 INTERACTIVE No 99 User User BDLS Yes No User User Fri Sep 19 06 46 53 EDT 2014 INTERACTIVE Mo 103 User User BDLS Yes Yes User User Fri Feb 28 09 49 33 EST 2074 INTERACTIVE Yes 123 User User BDLS Yes No User User Mon Jul 26 10 20 11 EDT 2014 INTERACTIVE No 7A A second and more co
9. mplicated example can be CDmation a tool created by Business amp Decision Life Sciences as a means to interact with SDD and create a more user friendly environment for the otherwise long manual tasks A main functionality is the automatic creation of the folder structure One of the modules of CDmation reads in XML files and creates new Projects or Analysis with underlying folders accordingly Groups and roles are also set in the process The two images underneath will show the very simple interface while the images further down give an idea on how the folder structure information can be stored reateIDP Create study Create IDP Create study Create IDP Create IDP mee Upload XML template file bvanwin_Project_Folder_Structure xml uploaded Upload AML template file IDP TestiIDP DP Create IDP Create IDP lt folder gt lt folder gt lt folder gt lt folder gt lt folder gt lt folder gt lt folder gt lt folder gt lt folder gt lt folder gt lt folder gt lt folder gt lt folder gt lt folder gt lt folder gt lt folder gt lt folder gt lt folder gt lt folder gt lt folder gt Each folder is represented in the XML template lt xml version 1 0 encoding UIF amp gt lt folderstructure gt lt Documentation gt lt Documentation Notifications gt lt Documentation Notifications DML gt lt Documentation Notifications GDM gt lt Documentatio
10. n Notifications Domain Expert gt lt Documentation Notifications CRO gt lt Documentation Notifications PRK Office gt lt Documentation Notifications 5D Supplier gt lt Documentation Notifications Vendor gt lt Documentation Notifications IxR5 gt lt Documentation Notifications ESP gt lt Documentation Notifications CP gt lt Documentation Notifications MBDD gt lt Documentation Notifications Medical Review gt lt Documentation Notifications eSubmission gt lt Documentation Notifications IDMC gt lt Documentation Notifications BAN gt lt Documentation Notifications PGx gt Documentation Notifications MA LIM gt Production gt For each folder the different groups that will have access their permissions are set lt folder gt lt Staging DM CRO Metadata gt lt name gt Metadata lt name gt lt path gt Staging DM CRO lt path gt lt group gt lt groupname gt Administrator lt groupname gt lt admin gt true lt admin gt lt read gt true lt read gt lt propwrite gt true lt propwrite gt lt contwrite gt true lt contwrite gt lt delete gt true lt delete gt lt group gt lt group gt lt groupname gt DML lt groupname gt lt admin gt false lt admin gt lt read gt true lt read gt lt propwrite gt true lt propwrite gt lt contwrite gt true lt contwrite gt lt delete gt true lt delete gt
11. n is read write default permission is a e read Permissions Allow Deny 2 A new file is added to Folder A this file will now only have read ae permission Admin 3 The administrator changes the current permission to y read write delete 4 Now the file has the read write delete permission Content Write In most cases the current permission should be set equal to the default permission Sometimes there might be circumstances where they can Delet differ PROGRAM JOB WORKFLOW The SDD SAS programming environment is very close to the base SAS one The difference lies in the implementation Additional elements are added to the SDD environment Jobs and workflows In SDD a SAS program is the same as a base SAS program These SAS programs can be added to used by jobs Jobs can be set up with parameters that will be used as macro variables within the program The drawback is that jobs require a lot of metadata to work properly in the repository The highest level on top of jobs is workflows A workflow is an automation framework on top of SDD Workflows can send out messages give users tasks run jobs automatically etc Here also workflows require a lot of metadata setup The consensus here is that setting up jobs requires a lot of manual work This manual work can be simplified though Jobs can be copied from one study to another but then will still require additional changes The structure of the Job file allows a differen
12. nformation Manage the general information e mail name of a user account Manage User Accounts Manage information like the privileges lock account View Audit History View the audit history of the system View Item Audit Records View the audit history of items like IDP folders files Manage Checked out Files Uncheck checked out files to for example free up files when a person is on a long leave Manage Extended Attributes Change the Extended attributes for items Extended attributes are the extra information on top of the normal file information Manage My Schedules Manage your own schedules These privileges are set on a user level not by groups This can sometimes be a bit cumbersome For that reason it is a good idea to already sort out the privileges per group so that if new users require an account the privileges can be set correctly example underneath m ml mi zI uw oo Oo oO oo oO 3 3 a 3 DO O D D D o o oa a a Manage Dashboard Welcome Message px x Manage All SAS Sessions fot ty View Audit History eh i ae Manage My Schedules a ae ae we Manage All Subscriptions a he Create SAS Session i ae ae me e e Manage All Schedules ft ff fx Manage Checked out Files px x AccessWebDAV tx x x Ma nage Extended Attributes ret i tie Es EJ Manage User Accounts sJ View Item Audit Records Px of of Create Message EVES eT TEE TEE TTT S ferw LTTE TEE ET fer
13. os GROUPS Previous topic mentioned groups in the end Now the question is what are groups within SDD Is it similar to an active directory The answer is yes and no Groups can be used to give folder access more on this in the next topic but are handled in a unique way SDD has multiple levels within the folder structure Some folders in SDD aren t really seen as folders but more as manageable objects objects where you can define groups and link groups to roles and privileges These levels are the root project and analysis level Every level can be seen as its separate environment Lower levels can inherit groups and roles from higher levels Setting up groups in one of the levels can be done as follows 1 Add users as members only these users will be able to see use this level e g only the people that have to work on a project are added as members and will be able to see use the project SAS Drug Development View Administration Help 15 Dashboard E Repository C Workspace HH SAS x 45 Organization Members General m CRO 01 Members Groups Roles Assign Roles Projects Files Work Items Tasks CRO OS CRO 09 Event Subscriptions E CRO 10 CRO 11 Audit 2 Add users to groups SAS Drug Development View Tools Administration Help 33 Dashboard E Repository C3 Workspace SAS SE 6 amp 5 Organization Groups Group Members General aCROO1 r m E Member
14. s CRO 14 Groups CRO 15 Roles CRO 16 Assign Roles Domain Expert Projects ESP CRO 17 CRO 18 Files eSubmission CRO 19 le Re Re Re Re Re Re Re Work Items GDM CRO 20 IDMC Event Subscriptions E IxRS Audit JnJ Librarian MA LTM MBDD Medical Review Prey 3 Create roles which are combinations of privileges The privileges on these levels are different than the global privileges we have listed before More information on these privileges will follow iz Dashboard E Repository C3 Workspace lt SAS 5 Organization Roles Privileges General Adminrole Administer Work Items Members aE Create Work Items Groups FunctionRole Disable Versioning Roles System Administrator Enable Versioning Assign Roles test Manage Locking Projects Manage Membership Files Manage Roles Work Items Manage State Tasks PIR Manage Work Items Event Subscriptions Permanently Delete Items Audit Restore ltems Deleted by Others Sign Files 4 Add groups to roles Giving groups certain roles means giving the members of those groups users specific privileges 33 Dashboard amp Repository C Workspace HF SAS Sy Roles Members General Adminrole gt lt Librarian Groups FunctionRole Roles System Administrator Projects Files Work Items Tasks vent Subscriptions Audit lt was mentioned before that these privileges were different The table underneath gives an overview of thes
15. t approach A Job is an XML file This means that with a find and replace manual or programmatically new jobs can be created lt job releaseVersion 1 0 description executionMode SEQUENTILAL sddVersion 4 0 log S AS Files ShowFunctionality lst SA8 Files ShowF unctionality mnf SAS Files ShowFunctionality gt lt tasks gt lt task path SA5 Files ShowFunctionality program0 sas gt lt tasks gt lt taskSpecs gt lt inputSpec path SA5 Files ShowF unctionality program0 2 sas type FILE version includeSubFolders false gt lt taskSpecs gt lt otherSpecs gt lt inputSpec path SA5 Files ShowF unctionality inputdataset type CONTAINER version includeSubFolders false gt lt otherSpecs gt lt putputPaths gt lt outputPath path SAS Files ShowFunctionality outputdataset includeSubFolders false gt lt outputPaths gt lt outputSpec enableVersioningF orNewFiles false gt lt version ype type MAJOR gt lt outputSpec gt lt parameters gt job gt It is even possible by having a program scan the SAS program s and logs to automatically prepare the job Scanning of the program can for example be done via running the program with a scaproc procedure at the start and finish 2 3 proc scaproc record amp pathl record txt 2 run 6 run program code 2 3 proc scaproc 4 write 3 run API AUTOMATIONS This topi
16. thin SDD others will use it to store and share documents with the possibility of versioning an e signing PRIVILEGES AND USER MANAGEMENT User management in an SDD environment is separate from the companies environment The web application keeps its own user database Having dedicated people manage the system in an administrator role will be necessary User management consists out of different parts 1 First there is the user creation with all the standard user information like name e mail address account type etc 2 The second part is giving the privileges to the users In table underneath there is an overview of the different privileges Be aware that these privileges are the global privileges Later the paper will describe the privileges within the folder structure which are different Create Message Send a message to another user in the system the other user can see this message on his her dashboard running a job cancel submissions or end SAS sessions See and change scheduled jobs by other users also Manage All Subscriptions See set and change subscriptions forother users also Manage Checked out Files Uncheck checked out files to for example free up files when a person is on a long leave Manage Extended Attributes Change the Extended Attributes for items Extended Attributes are the extra information on top of the normal file information Manage My Schedules Manage your own schedules Manage User Account General I
17. urce gt DML lt source gt lt target gt DML lt target gt lt group pair gt lt group pair gt lt source gt Administrator lt source gt lt target gt Administrator lt target gt lt group pair gt lt group pair gt lt source gt Domain Expert lt source gt lt target gt Domain Expert lt target gt lt group pair gt lt group pair gt lt source gt GDM lt source gt lt target gt GDM lt target gt lt group pair gt lt group hierarchy gt Another important functionality of the tool is the automatic creation of jobs Creating jobs in the system can be very time consuming and this is time better spent elsewhere By using the API functions the JAVA application creates the job with the correct parametes inputs and outputs In the example given underneath pictures the job is validating elements in an oracle library The user has an element selected in the user interface and selects validate The application sets the validation status in the oracle database on pending After this the application will build the job and start the job At the end of the job the validation result is written to the database at which point the JAVA application picks up the result and demonstrates it in the user interface Image showing the functionality of the Validation Job creator import ixis New item Mey _2013 07 11_1 n26m105 j0D Locked Invalid Me Data Validity Checks E Create_Output_File sas Me EXCEL E Valid
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