Allocation of Libraries for Spectre

(Author: Roland Rashleigh-Berry Date: 21 Mar 2007)

Introduction

It is likely that you already have a method for allocating macros libraries, data libraries and format libraries. I know that changing your established system for doing this is going to be difficult but Spectre has some minimal needs that must be satisfied and these will be explained on this page.

Macros and the sasautos path

What Spectre needs from the autoexec.sas, and the only thing it needs, is for all the macros it might call to be declared to sasautos such that they are all allocated, and in the correct order, by the time autoexec.sas has finished processing. If you are doing study reporting then you will have to detect if sas is being invoked from a study reporting area and define all the macros relevant for that study. If you are invoking sas from an area that is nothing to do with study reporting then you will only need the Spectre macros and the supplied SASAUTOS defined to the sasautos path. You must set some system options for Spectre, namely "noovp nodate nonumber xsync noxwait", so this should also be in your autoexec.sas.

It is up to you whether you use a high-level autoexec.sas member for all users or place autoexec.sas in the directory from which you will invoke sas, in which case that one will be used instead. Maybe you will use a mix such that some study programs have their own autoexec while others use the high-level one. I am currently using a high-level autoexec on my PC and if I am in the study reporting area (the "pharma" directory hanging off the C: drive) then I assign study reporting macros. I list the contents of sasautos at the end and I recommend you do the same. Keeping in mind that this is for Windows-style path names, feel free to look at the code inside my autoexec.sas (best viewed as a source file).

%allocr and %allocw

Most of the Spectre scripts that call sas also call a macro named %allocr or %allocw (allocation macro for read and write respectively) and their code will have to be written for each site Spectre is installed. They allocate the dataset libraries and formats. Unless you want to change the shell scripts then these two macros are mandatory. It is important for QC purposes to have two macros, one to allocate datasets in read mode and the other in write mode, because you should not to allocate datasets in write mode for sas programs that only need read access.

It is possible to have these allocations macros as high-level macros but I am using low-level macros that do this. I have included two examples of these low-level macros below which are kept in one of my study increment macros directories on my PC. These macros are only good for the one study increment. They are not generic. They are not part of Spectre and not supported.
%allocr
%allocw

The Reporting Directory Structure

It will be helpful if you used a consistent directory structure. On my PC I have a folder named "pharma" in which all clinical reporting work is done. Underneath that I have a single imaginary client named "xenuyama" with an office in Tokyo. The have a drug named "DRUG001C" with a single protocol "DRUG001C3001" and for now, a "24weeks" increment. This is my directory structure downwards from the "pharma" directory. The output comes from the script dirtree.

xenuyama
    formats
    macros
    tokyo
        DRUG001
            DRUG001C3001
                24weeks
                    data
                        analysis
                        derived
                        raw
                    formats
                    macros
                    progs
                formats
                macros
            formats
            macros
        formats
        macros

Drug, study and increment macros

You will likely have reporting macros that must exist at the increment level, the study level and the drug level. Maybe even at the office level and client level if you have different clients. Macros stored at the lower levels should override those at the higher levels so they should be earlier in the sasautos path. You will have to be careful about your macro names so that you do not accidentally override the spectre macros when you need to use them, although on rare occasions you might need an amended version of a Spectre macro. All these macros should be assigned to the sasautos path in your autoexec.sas member if you are invoking sas from the clinical reporting area. Bearing in mind that I have Cygwin on my PC so all the directory names are Windows style, you can see the way I define the macros to the sasautos path it in my autoexec.sas (best viewed as a source file).

Conclusion

For Spectre to work correctly it was explained that all macros should be assigned to sasautos in the correct order in your autoexec.sas member. You might call another macro to set up sasautos within your autoexec.sas but when it completes it should have been done. Allocation of datasets and the format search path should be done in the allocation macros %allocr and %allocw.

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