Too much quotation in generated configurations in .env.public

[cmungall]

linkml-project-cookiecutter/{{cookiecutter.project_name}}/.env.public

Lines 5 to 10 in 4e062ec

	LINKML_SCHEMA_NAME="{{cookiecutter.__project_slug}}"
	LINKML_SCHEMA_AUTHOR="{{cookiecutter.__author}}"
	LINKML_SCHEMA_DESCRIPTION="{{cookiecutter.project_description}}"
	LINKML_SCHEMA_SOURCE_PATH="{{cookiecutter.__source_path}}"
	LINKML_SCHEMA_GOOGLE_SHEET_ID="{{cookiecutter.google_sheet_id}}"
	LINKML_SCHEMA_GOOGLE_SHEET_TABS="{{cookiecutter.google_sheet_tabs}}"

The quotes don't function like normal quotes, they end up in the string

[sbliven]

I ran into this too. Makefiles expect variables not to be quoted. The default .env.public results in errors like

bash: -c: line 1: unexpected EOF while looking for matching `"'
make: *** [compile-sheets] Error 2

[noelmcloughlin]

I will have a look at this.

[amc-corey-cox]

Here is my full error message:

Writing lock file

Installing the current project: sepio_linkml (0.0.0.post2.dev0+842b967)
mkdir -p src/"sepio_linkml"/datamodel
poetry run sheets2linkml --gsheet-id "19Rp5DLFS3a1Yvvw84mPupgEkCMFRKax4LXCcwX84Vbg" "release_subset_v1" > "src/sepio_linkml/schema//release_subset_v1.yaml.tmp && mv "src/sepio_linkml/schema//release_subset_v1.yaml.tmp "src/sepio_linkml/schema//release_subset_v1.yaml
bash: -c: line 1: unexpected EOF while looking for matching `"'
make: *** [Makefile:116: compile-sheets] Error 2

[amc-corey-cox]

This looks like the quotes are somehow being dropped on the ends of variables when we run sheets2linkml. I got this when I ran make setup. I'll dig in to the .env file and see whether I can fix something there.

[amc-corey-cox]

This is the offending line in the Makefile:

$(RUN) sheets2linkml --gsheet-id $(SHEET_ID) $(SHEET_TABS) > $(SHEET_MODULE_PATH).tmp && mv $(SHEET_MODULE_PATH).tmp $(SHEET_MODULE_PATH)

I don't know why it is eating the " at the end of these variables from the variables defined at the top of the Makefile but it appears to be when we append text to the variable, so the statements $(SHEET_MODULE_PATH).tmp and $(SHEET_MODULE_PATH).tmp don't have closing ". Also, $(SHEET_MODULE_PATH) which is defined in the header as $(SOURCE_SCHEMA_DIR)/$(SHEET_MODULE).yaml has the same problem with missing the closing ".

As expected, since we have three opening " without closing " bash exits with an error stating there is a missing ", if it were an even number the line would execute but probably make a mess.

[amc-corey-cox]

Removing quotes from the variable definition for LINKML_SCHEMA_SOURCE_PATH in env.public solves the issue and allows make setup to run the line without issues related to ".

And here is a bit of a trace from that line to how it causes the issue in the Makefile:

SOURCE_SCHEMA_PATH = $(LINKML_SCHEMA_SOURCE_PATH)
SOURCE_SCHEMA_DIR = $(dir $(SOURCE_SCHEMA_PATH))
SHEET_MODULE_PATH = $(SOURCE_SCHEMA_DIR)/$(SHEET_MODULE).yaml

compile-sheets:
        $(RUN) sheets2linkml --gsheet-id $(SHEET_ID) $(SHEET_TABS) > $(SHEET_MODULE_PATH).tmp && mv $(SHEET_MODULE_PATH).tmp $(SHEET_MODULE_PATH)

I'm not very familiar with Makefile so I'm not sure how to solve this in the current infrastructure but I'd be happy to help.

[noelmcloughlin]

Thanks for feedback - unfortunately I am intermittent contributor (and my work laptop cannot access public GitHub, so I need to grab my neglected personal laptop). This issue was first raised in #106 so needs solution.

Would you be wiling to raise a PR to remove all quotes from .env.public file? @amc-corey-cox

This is acceptable regression as that file is my idea and needs incremental fixing.
I raised wider discussion here: https://github.com/orgs/linkml/discussions/2296

[amc-corey-cox]

@noelmcloughlin Sure, I'm happy to help out on this. I'll try just implementing your suggestion and see what we break.

[sbliven]

Makefile quoting is a mess. I think the normal suggestion is to not use quotes if there aren't any spaces in the variable (definitely true for the google vars, and likely true for the path)

[amc-corey-cox]

Looking a little deeper at this, this is actually a make file, not an environment file or a Bash script file. I think we should be more clear in how we define this.

At minimum, I will include a statement in the file that this is a make-file. I would prefer to change the name from .env.public to .vars.public.mk but I'm concerned this might cause unnecessary breakage for users using cruft to update their cookie-cutters.

For now, I'll remove the excess quotation and make a notation within the file that states it is a make-file not an env file or a bash script (it kinda looks like it could be either).

Please share your thoughts on changing the file name.

[noelmcloughlin]

Hi !!
The file originated from me and is not community driven request - i.e. nobody requested a make file with variables.
I was testing this project with different models and encountered various problems so I raised few Issues and lot of PRs.
I focused on setting environment variables manually and/or using that file and everything eventually seemed to work.
However, issues have emerged since -- so I think I need to rethink entire solution.

Feel free to rename file - I think nobody else cares at this point - they just want bug fixed I guess so that is why I suggested removing quotes as first step.

[noelmcloughlin]

I'm bit puzzled why I never saw errors when testing, usually I am thorough testing. Is there some extra tooling people use with makefiles? Maybe there is a linter for makefiles, I might investigate that also.