[BUG] arc export duplicates assay into new study

[floWetzels]

Describe the bug
When I run arc export on the proteomics samplearc (https://git.nfdi4plants.org/martinkuhl/SampleARC_Proteomics), the output json file contains two studies (see first screenshot):

• A "normal" study 01Minimal with filename 01Minimal/isa.study.xlsx
• A study assay with filename assay1/isa.assay.xlsx

However, the assay is actually registered in the study, as can be seen with arc a list or arc s list (see second screenshot). Therefore, there should only be one study containing the only assay. The study 01Minimal contains assay1 in the json output, but whithout a process sequence attached, whereas the assay itself (and therefore the second study) does contain the process sequence.

To Reproduce
Run arc export on the proteomics samplearc (https://git.nfdi4plants.org/martinkuhl/SampleARC_Proteomics).

Expected behavior
The output should only contain one assay and one study, with the only assay being part of the only study.

Screenshots

OS and framework information (please complete the following information):

• OS: Ubuntu
• OS Version 20.04

[Hannah-Doerpholz]

The same happened with my own test ARC when I wanted to export the ARC on my OS:

OS and framework information:
OS: Windows 10 Pro
OS Version: 21H1

[Brilator]

I think the duplication issue is fixed. However, arc study list stills throws the error

WARNING: The ARC contains following registered studies that have no associated file:

check arc s list on freshly re-built https://git.nfdi4plants.org/brilator/samplearc_rnaseq