Appion

Why do you have permission issue at the beginning?

when appionlib/apParam.py creates a directory, it is set to 0777

This bug surprised me because I knew that wasn't the default for us and I though Gabe must have made a mistake. However, when I looked at the source I found this horrible bit of code in the file apParam.py (source:/trunk/appion/appionlib/apParam.py@13489#L485)

def setUmask(msg=False):
        os.umask(0)
        os.umask(0)
        return
        if os.getgid() == 773:
                prev = os.umask(002)
                curr = os.umask(002)
        else:
                prev = os.umask(000)
                curr = os.umask(000)
        if msg is True:
                apDisplay.printMsg("Umask changed from "+str(prev)+" to "+str(curr))

So basically we're setting the umask to 002 if the user is in the Unix group 773, which is AMI here but could be anything somewhere else. That needs to be removed. Also, the umask should only be set to 000 if you want to ensure the file permission mode passed in a open() or other file/directory creation call isn't overridden by the users umask setting. However, you have to set that file permission mode when creating the file otherwise a file will have mode 666 and a directory will have mode 777 which is a very bad idea.

can we also change line 299 in apParam.py:
def createDirectory(path, mode=0777, warning=True):
to mode=0775?

Actually python's umask function works just as it should. The only place the setUmask()function is called on line 37 appion/appionlib/basicScript.py and createDirectory() is called in several places. As long as they are used it will work. The umask set by calling setUmask() doesn't work in the above code because it's forking a new shell to run the command. So if the user sets the umask in his startup scripts, that's the one that will be in effect when the chmod is executed. Neil's bit of code is unnecessary if you use the createDirectory() to create any directories.