OSU ESElog test macros

[EvanKirshenbaum]

From Mike:

Ok, so, here is the macro that OSU would like to run for ESELog. I think I can figure this out given what you did for us last time (with the updates you are making), but thought I would put here for you as well.

1. The drop A (reagent) will move to the ESELog path for blank measurements (527 nm).

2. Second step Drop A will move out from the measuring region.

3. A drop from another well, B (DNA), will mix with drop A in a circular path for 1 minute, forming Drop AB, then rest for 3 minutes, and then move in a circular path again for 1 minute.

4. Next Step Drop AB will move to ESELog for measurement of fluorescence at 527 nm.

5. In the final step Drop AB will move out to waste.

This is relatively straightforward, but I'm running into compiler issues writing it out, so I figured I'd open an issue here.

Migrated from internal repository. Originally created by @EvanKirshenbaum on Jul 27, 2023 at 6:23 PM PDT.

[EvanKirshenbaum]

This issue was referenced by the following commits before migration:

• 8cd29673b1ea84473cbd5466de0a83ce589cd3c4 by @EvanKirshenbaum on Jul 28, 2023 at 9:42 AM PDT
• 059d2d3cfe00c5c7a65774bdee753fd8e74cc4f7 by @EvanKirshenbaum on Jul 28, 2023 at 6:08 PM PDT

[EvanKirshenbaum]

The "compiler issues" turned out to be me not noticing that I had spelled initial_fill as initial_file in its declaration, so of course it was undeclared, as was the function that used it. Sigh.

A couple of other things I tweaked in doing the example:

• There were no units for minutes and hours. There now are.
• You can now walk to a well. It aims for the exit pad.
  • I considered just allowing wells to convert to pads (as extraction points do), but I'm not sure that's such a good idea, so I special-cased it here.
  • I might want to do the same for extraction points.
• The () empty parameter list was somehow not optional in define (although it was in function and macro). It now is.
• Setting a well's reagent was, for some reason, also asserting the volume, which made it try to do a refill when the well wasn't empty. It now doesn't.
  • I suspect that this is a holdover from very early days, when we just wanted to pretend that the wells were full, and didn't show up because nobody tried to run a protocol twice or reset the reagent of a well.

In my example code (checked in as inputs/eselog-test.dml), I had to define a function for walking in a circle (square):

define circle(drop) {
  drop : right 4 : up 4 : left 4 : down 4;
}

because you can't (pedagogically clearly) define the path in the protocol function itself. What I wanted to be able to say was

   circle = right 4 : up 4 left 4 : down 4;

but if you do that, you get an undeclared variable warning. You can do it as

  local circle = right 4 : up 4 : left 4 : down 4;

but I didn't want to have to explain that. What I really want is (#282)

  path circle = right 4 : up 4 : left 4 : down 4;

but that's not in yet.

Migrated from internal repository. Originally created by @EvanKirshenbaum on Jul 28, 2023 at 11:29 AM PDT.

[EvanKirshenbaum]

Requested tweaks:

Macro Update request:

A = Fluorescent recorder molecule (syber green)

B = Sample (Plasma, pcr product, etc)

C = Buffer

1. Dispense drop from A and drop from C to form 2X drop AC
2. Mix AC in a circular path for 1 minute, then rest for 3 minutes, and then move in a circular path again for 1 minute.
3. Move AC to ESELog for measurement of fluorescence at 527 nm.
4. Move AC from the measuring region to waste well
5. Repeat steps 1-4 above with Reagent A and B instead of A and C.

   Migrated from internal repository. Originally created by @EvanKirshenbaum on Jul 28, 2023 at 5:22 PM PDT.