Scripting DOS commands and DOS program input

[jly]

Hi all,

I just found out and tried to use AutoIt to script some intensive computational analysis programs I'm using. Basically, I'm trying to use the command console to run a program and then input commands into that program, and then trying to loop them together. I tried to use just SEND commands, but what I've found happens is that in random places within the script, the commands and the console get desynchronized, and I don't get the output I want, as gibberish goes into the console until it resets back to the proper state.

So for example, here's a chunk of my script:

expandcollapse popup

Send("dnapars{ENTER}")
SEND("test25-054.phy{ENTER}")
SEND("f{ENTER}")
SEND("test25-054.pars{ENTER}")
Send("o{ENTER}")
Send("44{ENTER}")
SEND("y{ENTER}")
SEND("f{ENTER}")
SEND("test25.parstree{ENTER}")
SEND("A{ENTER}")
SEND("{ENTER}")

Send("dnaml{ENTER}")
SEND("test25-054.phy{ENTER}")
SEND("f{ENTER}")
SEND("test25-054.ml{ENTER}")
Send("o{ENTER}")
Send("44{ENTER}")
SEND("y{ENTER}")
SEND("f{ENTER}")
SEND("test25.mltree{ENTER}")
SEND("A{ENTER}")
SEND("{ENTER}")

Send("dnadist{ENTER}")
SEND("test25-054.phy{ENTER}")
SEND("f{ENTER}")
SEND("test25-054.dist{ENTER}")
SEND("y{ENTER}")
SEND("{ENTER}")

Send("neighbor{ENTER}")
SEND("test25-054.dist{ENTER}")
SEND("f{ENTER}")
SEND("test25-054.nb{ENTER}")
SEND("y{ENTER}")
SEND("f{ENTER}")
SEND("test25.nbtree{ENTER}")
SEND("A{ENTER}")
SEND("{ENTER}")

dnapars, dnaml, dnadist, and neighbor are all .exes, the first filename entered in each block is an input file, the others are output files, and the other commands are just navigating the program's menus and options. (Some of you may recognize these as bioinformatics applications.)

Anyways, like I said, this code will work fine, but when I try to script together hundreds, it breaks down. I'm positive my script is consistent, since I generated it using Java loops, so are there other AutoIt commands I should be using, maybe to separate the .exe calls and the program inputs, or to check the output from each command before entering the next one (and program block if there's an error within)?

It's okay if the script misses some of the blocks, so long as output files aren't improperly generated, so I can go back and check which outputs need to be regenerated. What's not okay is if the script gets out of sync and responds with improper filenames and commands, since my output will be misleading.

Any help would be appreciated, thanks!

[martin]

Hi all,

I just found out and tried to use AutoIt to script some intensive computational analysis programs I'm using. Basically, I'm trying to use the command console to run a program and then input commands into that program, and then trying to loop them together. I tried to use just SEND commands, but what I've found happens is that in random places within the script, the commands and the console get desynchronized, and I don't get the output I want, as gibberish goes into the console until it resets back to the proper state.

So for example, here's a chunk of my script:

expandcollapse popup

Send("dnapars{ENTER}")
SEND("test25-054.phy{ENTER}")
SEND("f{ENTER}")
SEND("test25-054.pars{ENTER}")
Send("o{ENTER}")
Send("44{ENTER}")
SEND("y{ENTER}")
SEND("f{ENTER}")
SEND("test25.parstree{ENTER}")
SEND("A{ENTER}")
SEND("{ENTER}")

Send("dnaml{ENTER}")
SEND("test25-054.phy{ENTER}")
SEND("f{ENTER}")
SEND("test25-054.ml{ENTER}")
Send("o{ENTER}")
Send("44{ENTER}")
SEND("y{ENTER}")
SEND("f{ENTER}")
SEND("test25.mltree{ENTER}")
SEND("A{ENTER}")
SEND("{ENTER}")

Send("dnadist{ENTER}")
SEND("test25-054.phy{ENTER}")
SEND("f{ENTER}")
SEND("test25-054.dist{ENTER}")
SEND("y{ENTER}")
SEND("{ENTER}")

Send("neighbor{ENTER}")
SEND("test25-054.dist{ENTER}")
SEND("f{ENTER}")
SEND("test25-054.nb{ENTER}")
SEND("y{ENTER}")
SEND("f{ENTER}")
SEND("test25.nbtree{ENTER}")
SEND("A{ENTER}")
SEND("{ENTER}")

dnapars, dnaml, dnadist, and neighbor are all .exes, the first filename entered in each block is an input file, the others are output files, and the other commands are just navigating the program's menus and options. (Some of you may recognize these as bioinformatics applications.)

Anyways, like I said, this code will work fine, but when I try to script together hundreds, it breaks down. I'm positive my script is consistent, since I generated it using Java loops, so are there other AutoIt commands I should be using, maybe to separate the .exe calls and the program inputs, or to check the output from each command before entering the next one (and program block if there's an error within)?

It's okay if the script misses some of the blocks, so long as output files aren't improperly generated, so I can go back and check which outputs need to be regenerated. What's not okay is if the script gets out of sync and responds with improper filenames and commands, since my output will be misleading.

Any help would be appreciated, thanks!

I expect the problem is that you are firing lots of information using send without knowing that the application is in a stage where it can receive it or respond to it. At the very least maybe you could try adding some sleep statements in between each line to give the application you're talking to a chance to catch its breadth. But without anything to check the state of the application such as waiting for some change or response, it is always going to be unreliable.

If you are able to check something to tell you the effect of your Send then you would improve things a lot.

[jly]

I expect the problem is that you are firing lots of information using send without knowing that the application is in a stage where it can receive it or respond to it. At the very least maybe you could try adding some sleep statements in between each line to give the application you're talking to a chance to catch its breadth. But without anything to check the state of the application such as waiting for some change or response, it is always going to be unreliable.

If you are able to check something to tell you the effect of your Send then you would improve things a lot.

I can't realistically use sleep statements since I can't be sure of how long each run takes, since it's data-dependent.

Are there AutoIt commands I could use to check output? (The only outputs will be to the command console and newly created output files.)

[flyingboz]

I can't realistically use sleep statements since I can't be sure of how long each run takes, since it's data-dependent.

Are there AutoIt commands I could use to check output? (The only outputs will be to the command console and newly created output files.)

great improvements in handling stdout have been made3, look for runreadstd.au3 posts.....

[martin]

great improvements in handling stdout have been made3, look for runreadstd.au3 posts.....

runreadstd.au3 only seems to be found in this thread! Can you give a link flyingboz?

[flyingboz]

Can you give a link flyingboz?

http://www.autoitscript.com/forum/index.php?showtopic=41894