adapt error message

[ptrebert]

This raises even when the actual problem is that no base image has been built yet, which gives a misleading error message. There should be a point in the code where the decision can be made (= base image does not exist, raise)

https://github.com/core-unit-bioinformatics/reference-container/blob/11ca727a798b2673edf3077587644586d9d242d5/workflow/rules/functions.smk#L20

[svenwillger]

This issue required additional code at two different locations in the functions.smk

1. The original code in lines 19-20: https://github.com/core-unit-bioinformatics/reference-container/blob/11ca727a798b2673edf3077587644586d9d242d5/workflow/rules/functions.smk#L19-L20

has been changed to:

if not refcon_md:
        base_image_name = [(key.split('_')[-1], metadata) for key, metadata in config.items() if key.startswith('metadata_')]
        base_image_name = [(base_image, metadata) for base_image, metadata in base_image_name if base_image in select_names]
        base_container_path = pl.Path(f'container/{base_image_name}.sif')
        if not base_container_path.is_file():
            raise ValueError('No base container found. Please follow instructions above to create base container!')
        else:
            raise ValueError('No "metadata_" keys found in config. Did you forget to load a reference container config?')

2. The original code in lines 380-387: https://github.com/core-unit-bioinformatics/reference-container/blob/11ca727a798b2673edf3077587644586d9d242d5/workflow/rules/functions.smk#L380-L387

also triggered a misleading error message and where therefore changed into:

def select_container_readme(wildcards):

    _, refcon_md = _get_container_metadata(wildcards.rc_name_version)[0]
    if 'base' in {wildcards.rc_name_version}:
        base_container_path = pl.Path(f'container/{wildcards.rc_name_version}.sif')
        if not base_container_path.is_file():
            raise ValueError('No base container found. Please follow instructions above to create base container')
    if 'readme' in refcon_md:
        readme_path = f'container/{wildcards.rc_name_version}/README.txt'
    else:
        readme_path = []
    return readme_path

Now the error message looks like this and should make it clearer that an action is required to resolve the problem:

ACTION REQUIRED --- missing base container detected: base_v0.sif
Please run the following build command in the "container" folder:
$ cd /home/sven/Desktop/sandbox/ref-container/container
$ sudo singularity build base_v0.sif base_v0.def

InputFunctionException in line 42 of /home/sven/Desktop/sandbox/ref-container/workflow/rules/packaging.smk:
Error:
  ValueError: No base container found. Please follow instructions above to create base container
Wildcards:
  rc_name_version=base_v0
Traceback:
  File "/home/sven/Desktop/sandbox/ref-container/workflow/rules/functions.smk", line 388, in select_container_readme
  File "/home/sven/Desktop/sandbox/ref-container/workflow/rules/functions.smk", line 24, in _get_container_metadata

Commit message: added information when base container is missing