When a mouse dies in a surgery or for other reasons before the experiment of entirely carried out, flake should be able to skip the procedures that would have happened after the day it died. See in the screenshot attached. The mouse died on the same day as the surgery on 203-07-03, but the record simply continues with the normal procedure. This is dangerous for a careless user that doesn't double-check the output of flake.
The best is to have a condition checking if the date of death is before the last default procedure in the protocol, if yes, either (1) stop the record on that day, instead of "Sacrifice: perfusion" or whatever the default procedure is specified for this protocol, replace it with "Death: unexpected" (just added to the definitions now); or (2) have a prompt when this happens and let user choose between the option (1) and do nothing (as it is now) and ask the user to manually cure the entry.
When a mouse dies in a surgery or for other reasons before the experiment of entirely carried out, flake should be able to skip the procedures that would have happened after the day it died. See in the screenshot attached. The mouse died on the same day as the surgery on 203-07-03, but the record simply continues with the normal procedure. This is dangerous for a careless user that doesn't double-check the output of flake.
The best is to have a condition checking if the date of death is before the last default procedure in the protocol, if yes, either (1) stop the record on that day, instead of "Sacrifice: perfusion" or whatever the default procedure is specified for this protocol, replace it with "Death: unexpected" (just added to the definitions now); or (2) have a prompt when this happens and let user choose between the option (1) and do nothing (as it is now) and ask the user to manually cure the entry.
@maristany, what do you say?
That sounds good. The manual prompt would be quite a lot of work (especially when creating P9 for more than just one animal). What I could do, however, is to print a list of animals where the death date is before any other procedure and indicate that "Death: unexpected" was filled. If "Death: Unexpected" is not the correct choice for that animal, the user would have to fix their data manually (remove the procedures after the animals death, and add the correct procedure (if f.e. the animal was sacrificed with another procedure) and redo the document creation
That sounds good. The manual prompt would be quite a lot of work (especially when creating P9 for more than just one animal). What I could do, however, is to print a list of animals where the death date is before any other procedure and indicate that "Death: unexpected" was filled. If "Death: Unexpected" is not the correct choice for that animal, the user would have to fix their data manually (remove the procedures after the animals death, and add the correct procedure (if f.e. the animal was sacrificed with another procedure) and redo the document creation
So there is a first working version online for surgery sheets.
Maybe you could test it and give some feedback.
I was wondering whether it would be better to add the "Death: unexpected" to the unexpected area, instead of the procedures? What do you think?
So there is a first working version online for surgery sheets.
Maybe you could test it and give some feedback.
I was wondering whether it would be better to add the "Death: unexpected" to the unexpected area, instead of the procedures? What do you think?
I can test tmrw. I like your suggestion! Something along the line "Tier unerwartet verstorben am xxx" but in English. So the procedure can just stop with no additional entry about death, because it is stricly speaking not a procedure. No one did anything, the mouse died itself.
I can test tmrw. I like your suggestion! Something along the line "Tier unerwartet verstorben am xxx" but in English. So the procedure can just stop with no additional entry about death, because it is stricly speaking not a procedure. No one did anything, the mouse died itself.
the entries after the animal died are removed now, but not the procedure "sacrifice: perfusion". I think you can remove it entirely, so that the conducted procedure will end with "viral injection".
Also remove the entry under "C) Sacrifice of animal". It can stay empty.
Then add "unexpected death on dd.mm.yyyy" to the unexpected events.
What do you think?
the entries after the animal died are removed now, but not the procedure "sacrifice: perfusion". I think you can remove it entirely, so that the conducted procedure will end with "viral injection".
Also remove the entry under "C) Sacrifice of animal". It can stay empty.
Then add "unexpected death on dd.mm.yyyy" to the unexpected events.
What do you think?
Hey Meng, I thought, your suggestions sounded great and implemented all of them. I tested the results with your animal: MLA-023349
Maybe you could test one more time. In case everything is ok, I can work on implementing the fix for p9 also.
With this new implementation, I think it becomes obsolete to have a sacrifice named "Death: unexpected" and you can remove it from the definitions (since we don't add it when FLAKE fixes an invalid sacrifice date, we should also not add it in other cases).
Hey Meng, I thought, your suggestions sounded great and implemented all of them. I tested the results with your animal: MLA-023349
Maybe you could test one more time. In case everything is ok, I can work on implementing the fix for p9 also.
With this new implementation, I think it becomes obsolete to have a sacrifice named "Death: unexpected" and you can remove it from the definitions (since we don't add it when FLAKE fixes an invalid sacrifice date, we should also not add it in other cases).
Jan van Dick
When a mouse dies in a surgery or for other reasons before the experiment of entirely carried out, flake should be able to skip the procedures that would have happened after the day it died. See in the screenshot attached. The mouse died on the same day as the surgery on 203-07-03, but the record simply continues with the normal procedure. This is dangerous for a careless user that doesn't double-check the output of flake.
The best is to have a condition checking if the date of death is before the last default procedure in the protocol, if yes, either (1) stop the record on that day, instead of "Sacrifice: perfusion" or whatever the default procedure is specified for this protocol, replace it with "Death: unexpected" (just added to the definitions now); or (2) have a prompt when this happens and let user choose between the option (1) and do nothing (as it is now) and ask the user to manually cure the entry.
@maristany, what do you say?
That sounds good. The manual prompt would be quite a lot of work (especially when creating P9 for more than just one animal). What I could do, however, is to print a list of animals where the death date is before any other procedure and indicate that "Death: unexpected" was filled. If "Death: Unexpected" is not the correct choice for that animal, the user would have to fix their data manually (remove the procedures after the animals death, and add the correct procedure (if f.e. the animal was sacrificed with another procedure) and redo the document creation
Sounds good!
So there is a first working version online for surgery sheets. Maybe you could test it and give some feedback.
I was wondering whether it would be better to add the "Death: unexpected" to the unexpected area, instead of the procedures? What do you think?
I can test tmrw. I like your suggestion! Something along the line "Tier unerwartet verstorben am xxx" but in English. So the procedure can just stop with no additional entry about death, because it is stricly speaking not a procedure. No one did anything, the mouse died itself.
the entries after the animal died are removed now, but not the procedure "sacrifice: perfusion". I think you can remove it entirely, so that the conducted procedure will end with "viral injection".
Also remove the entry under "C) Sacrifice of animal". It can stay empty.
Then add "unexpected death on dd.mm.yyyy" to the unexpected events.
What do you think?
Hey Meng, I thought, your suggestions sounded great and implemented all of them. I tested the results with your animal: MLA-023349
Maybe you could test one more time. In case everything is ok, I can work on implementing the fix for p9 also.
With this new implementation, I think it becomes obsolete to have a sacrifice named "Death: unexpected" and you can remove it from the definitions (since we don't add it when FLAKE fixes an invalid sacrifice date, we should also not add it in other cases).