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Dave does not recognize some errors in Kilroy #63

Open leonardosepulveda opened 6 years ago

leonardosepulveda commented 6 years ago

(Add this in the future) I had errors in the Kilroy configuration file (Typo in one of the command names). Dave did not recognize this error and just stayed indefinitely in the step prior to the typo. It will be great to connect Kilroy and dave so that dave issues a warning or error message when Kilroy crashes, so I know that the run has crashed.

HazenBabcock commented 6 years ago

Did you run the validator in Dave before you started the run?

leonardosepulveda commented 6 years ago

I think I did, but I will verify.

On Mon, Oct 30, 2017 at 3:24 PM, Hazen Babcock notifications@github.com wrote:

Did you run the validator in Dave before you started the run?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ZhuangLab/storm-control/issues/63#issuecomment-340556543, or mute the thread https://github.com/notifications/unsubscribe-auth/AYzz_vKusFskhR8RVt1KnWCaE5ogmpZaks5sxiKGgaJpZM4QKZ7E .

leonardosepulveda commented 6 years ago

Hi Hazen,

I verified, and the validator did not catch the error.

The error was the following: I had this code in the Kilroy config file:

Set Hyb 8 1 mL/min 0.1 mL/min Stop Flow Seal Wash Buffer 0.5 mL/min 0.1 mL/min Stop Flow Seal Image Buffer 0.5 mL/min Stop Flow Seal

The error here is that I put "1 mL/min" instead of "1.0 mL/min". So, when the Hybridize 8 code was called, Kilroy stayed in the previous step (Set Hyb 8) indefinitely instead of crashing. So I arrived the next morning and my run was stuck in that step all night. Kilroy crashed, it says that "1 mL/min" was not a valid command. It is just that dave did not got that info.

Leonardo

On Mon, Oct 30, 2017 at 4:00 PM, Leonardo Sepúlveda Durán < leonardosepulveda@gmail.com> wrote:

I think I did, but I will verify.

On Mon, Oct 30, 2017 at 3:24 PM, Hazen Babcock notifications@github.com wrote:

Did you run the validator in Dave before you started the run?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ZhuangLab/storm-control/issues/63#issuecomment-340556543, or mute the thread https://github.com/notifications/unsubscribe-auth/AYzz_vKusFskhR8RVt1KnWCaE5ogmpZaks5sxiKGgaJpZM4QKZ7E .

jeffmoffitt commented 6 years ago

I see the issue. When you ask dave to validate a kilroy protocol request, it checks only the name of the protocol. Kilroy does not have a way to validate that all commands within a protocol are valid.

You should add it as an issue.

Best Jeff

On Mon, Oct 30, 2017 at 4:40 PM, leonardosepulveda <notifications@github.com

wrote:

Hi Hazen,

I verified, and the validator did not catch the error.

The error was the following: I had this code in the Kilroy config file:

Set Hyb 8 1 mL/min 0.1 mL/min Stop Flow Seal Wash Buffer 0.5 mL/min 0.1 mL/min Stop Flow Seal Image Buffer 0.5 mL/min Stop Flow Seal

The error here is that I put "1 mL/min" instead of "1.0 mL/min". So, when the Hybridize 8 code was called, Kilroy stayed in the previous step (Set Hyb 8) indefinitely instead of crashing. So I arrived the next morning and my run was stuck in that step all night. Kilroy crashed, it says that "1 mL/min" was not a valid command. It is just that dave did not got that info.

Leonardo

On Mon, Oct 30, 2017 at 4:00 PM, Leonardo Sepúlveda Durán < leonardosepulveda@gmail.com> wrote:

I think I did, but I will verify.

On Mon, Oct 30, 2017 at 3:24 PM, Hazen Babcock <notifications@github.com

wrote:

Did you run the validator in Dave before you started the run?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ZhuangLab/storm-control/issues/63# issuecomment-340556543, or mute the thread https://github.com/notifications/unsubscribe-auth/AYzz_ vKusFskhR8RVt1KnWCaE5ogmpZaks5sxiKGgaJpZM4QKZ7E .

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/ZhuangLab/storm-control/issues/63#issuecomment-340577387, or mute the thread https://github.com/notifications/unsubscribe-auth/ACiQXKDSSIMc3--Bbb34XnpCty0OL-ytks5sxjRGgaJpZM4QKZ7E .

HazenBabcock commented 6 years ago

This is also a related issue to #58.