acevedol
acevedol
The existing script worked, but is a massive memory hog and will not work for the next time with a bigger kg2pre. Per discussion with Steve, I am experimenting with...
```(venv) ubuntu@ip-172-31-50-177:~$ python3.7 -u ~/kg2-code/kg2_json_to_kgx_tsv.py ~/kg2-build/kg2-simplified.json ~/kg2-build/KGX/ Traceback (most recent call last): File "/home/ubuntu/kg2-code/kg2_json_to_kgx_tsv.py", line 128, in for item in nodes_data: File "/home/ubuntu/kg2-code/kg2_json_to_kgx_tsv.py", line 110, in nodes_data = (row for...
`Rule TSV` is in `Snakefile-post-etl`
Work for this ticket is in branch `issue-199`
I'm not sure about how much needs to be changed in kg_json_to_tsv.py. I added `has_chemical_role` as a list attribute to the header row, but it does not appear that the...
Because the error was on a few UBERON predicates in predicate-remap.yaml, we don't want to go through any of the extraction processes again. This build will also address issue 196,...
A dry build shows that the expected rules will run, so I am moving forward with a test run.
First issue: ``` [Fri May 6 19:09:06 2022] Error in rule UniProtKB_Conversion: jobid: 8 output: /home/ubuntu/kg2-build/kg2-uniprotkb.json log: /home/ubuntu/kg2-build/uniprotkb-dat-to-json.log (check log file(s) for error message) shell: /home/ubuntu/kg2-venv/bin/python3 -u /home/ubuntu/kg2-code/uniprotkb_dat_to_json.py /home/ubuntu/kg2-build/uniprotkb/uniprot_sprot.dat /home/ubuntu/kg2-build/kg2-uniprotkb.json...
Another error: ``` [Fri May 6 19:09:05 2022] Error in rule HMDB_Conversion: jobid: 18 output: /home/ubuntu/kg2-build/kg2-hmdb.json log: /home/ubuntu/kg2-build/hmdb-xml-to-kg-json.log (check log file(s) for error m essage) shell: /home/ubuntu/kg2-venv/bin/python3 -u /home/ubuntu/kg2-code/hmdb_xml_to_kg_json .py...
Error in `rule KEGG_Conversion`: ``` [Fri May 6 19:09:06 2022] Error in rule KEGG_Conversion: jobid: 26 output: /home/ubuntu/kg2-build/kg2-kegg.json shell: /home/ubuntu/kg2-venv/bin/python3 -u /home/ubuntu/kg2-code/kegg_json_to_kg_jso n.py /home/ubuntu/kg2-build/kegg.json /home/ubuntu/kg2-build/kg2-kegg.json (exited with non-zero exit code)...