Dave does not recognize some errors in Kilroy

[leonardosepulveda]

(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]

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

[leonardosepulveda]

I think I did, but I will verify.

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On Mon, Oct 30, 2017 at 3:24 PM, Hazen Babcock ***@***.***> 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 <#63 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AYzz_vKusFskhR8RVt1KnWCaE5ogmpZaks5sxiKGgaJpZM4QKZ7E> .

[leonardosepulveda]

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: <protocol name = "Hybridize 8"> <valve duration = "5">Set Hyb 8</valve> <pump duration = "180">1 mL/min</pump> <pump duration = "300">0.1 mL/min</pump> <pump duration = "600">Stop Flow</pump> <valve duration = "5">Seal</valve> <valve duration = "5">Wash Buffer</valve> <pump duration = "90">0.5 mL/min</pump> <pump duration = "300">0.1 mL/min</pump> <pump duration = "60">Stop Flow</pump> <valve duration = "5">Seal</valve> <valve duration = "5">Image Buffer</valve> <pump duration = "180">0.5 mL/min</pump> <pump duration = "60">Stop Flow</pump> <valve duration = "5">Seal</valve> </protocol> 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 < [email protected]> wrote:

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I think I did, but I will verify. On Mon, Oct 30, 2017 at 3:24 PM, Hazen Babcock ***@***.***> 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 > <#63 (comment)>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/AYzz_vKusFskhR8RVt1KnWCaE5ogmpZaks5sxiKGgaJpZM4QKZ7E> > . >

[jeffmoffitt]

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 <[email protected]

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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: <protocol name = "Hybridize 8"> <valve duration = "5">Set Hyb 8</valve> <pump duration = "180">1 mL/min</pump> <pump duration = "300">0.1 mL/min</pump> <pump duration = "600">Stop Flow</pump> <valve duration = "5">Seal</valve> <valve duration = "5">Wash Buffer</valve> <pump duration = "90">0.5 mL/min</pump> <pump duration = "300">0.1 mL/min</pump> <pump duration = "60">Stop Flow</pump> <valve duration = "5">Seal</valve> <valve duration = "5">Image Buffer</valve> <pump duration = "180">0.5 mL/min</pump> <pump duration = "60">Stop Flow</pump> <valve duration = "5">Seal</valve> </protocol> 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 < ***@***.***> wrote: > I think I did, but I will verify. > > On Mon, Oct 30, 2017 at 3:24 PM, Hazen Babcock ***@***.*** > > 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 >> <#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 <#63 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACiQXKDSSIMc3--Bbb34XnpCty0OL-ytks5sxjRGgaJpZM4QKZ7E> .

[HazenBabcock]

This is also a related issue to #58.