Error in the design pattern during the release

[LilyAndres]

I'm trying to run the make file, the command is:

./run.sh make all_modules

And I get the following error:

dosdp-tools generate --table-format=csv --template=patterns/chemical_concentration.yaml --outfile=modules/chemical_concentration.tmp.owl --obo-prefixes=true --infile=templates/chemical_concentration.csv
make: dosdp-tools: Permission denied
make: *** [Makefile:114: modules/chemical_concentration.owl] Error 127

[LilyAndres]

@kaiiam have you ever come across this type of error? Surely is not just about changing permissions...

[kaiiam]

This is probably a docker issue as I am able to run it on my computer. Perhaps something we should ask Nico for help with.

[LilyAndres]

@matentzn I'm having this error when I'm trying to run the modules, by any chance you know what could be happening?

[matentzn]

The error (127) means, usually, that, that a file was not found. So my guess is, given

dosdp-tools generate --table-format=csv --template=patterns/chemical_concentration.yaml --outfile=modules/chemical_concentration.tmp.owl --obo-prefixes=true --infile=templates/chemical_concentration.csv

That either:

• patterns/chemical_concentration.yaml or templates/chemical_concentration.csv does not exist or:
• the modules directory for modules/chemical_concentration.tmp.owl does not exist.

As an aside: pretty ancient ODK repo setup, could be updated

[kaiiam]

We think it's a docker issue as I was able to run it no problem on my computer, and lilly has also run it in the past. @LilyAndres perhaps you can just double check it by cloning the repo again and just running it to make sure it wasn't some silly file deletion issue on your branch?

As an aside: pretty ancient ODK repo setup, could be updated

We created CDNO with ODK about 2 years ago, I guess that makes it ancient now :P

[LilyAndres]

@kaiiam I just cloned the repo and I still have the issue. However, I don't remember:

• modules/chemical_concentration.tmp.owl

we don't have this file.

Question, should the concentration have these kind of permits:

I think is not reading the chemical_concentration.owl

[matentzn]

Does the modules directory exist?

[LilyAndres]

@matentzn yes, modules directory exist

[kaiiam]

Code works on my computer but not @LilyAndres I think this must be a docker issue or something like that. Can you update docker?

[matentzn]

I can recreate the issue: INCATools/ontology-development-kit#651

[LilyAndres]

@matentzn thanks a lot, I followed the changes you made in ENVO and it's working now :) I will close this issue now.

[kaiiam]

Excelent thank you very much @matentzn!