Open ecwood opened 1 year ago
This error occurred during the build:
[Thu Jul 20 19:34:20 2023]
Error in rule SemMedDB:
jobid: 30
output: /home/ubuntu/kg2-build/semmeddb/kg2-semmeddb-tuplelist.json, /home/ubuntu/kg2-build/semmed-exclude-list.yaml
log: /home/ubuntu/kg2-build/extract-semmeddb.log (check log file(s) for error message)
shell:
bash -x /home/ubuntu/kg2-code/extract-semmeddb.sh /home/ubuntu/kg2-build/semmeddb/kg2-semmeddb-tuplelist.json /home/ubuntu/kg2-build/semmed-exclude-list.yaml > /home/ubuntu/kg2-build/extract-semmeddb.log 2>&1
(exited with non-zero exit code)
It is covered in more detail here: https://github.com/RTXteam/RTX-KG2/issues/294#issuecomment-1644489313
There was an error with SMPDB, which doesn't make sense since it was recently tested and worked the first time around:
[Thu Jul 20 21:02:58 2023]
Error in rule SMPDB:
jobid: 38
output: /home/ubuntu/kg2-build/smpdb/pathbank_pathways.csv
log: /home/ubuntu/kg2-build/extract-smpdb.log (check log file(s) for error message)
shell:
bash -x /home/ubuntu/kg2-code/extract-smpdb.sh /home/ubuntu/kg2-build/smpdb > /home/ubuntu/kg2-build/extract-smpdb.log 2>&1
(exited with non-zero exit code)
ubuntu@ip-172-31-62-73:~/kg2-build$ curl -L -f -k /home/ubuntu/kg2-build/smpdb/ https://pathbank.org/downloads/pathbank_all_pwml.zip
curl: (3) URL using bad/illegal format or missing URL
Warning: Binary output can mess up your terminal. Use "--output -" to tell
Warning: curl to output it to your terminal anyway, or consider "--output
Warning: <FILE>" to save to a file.
I am going to try restarting to see if that fixes it.
An error occurred in Ontologies and TTL, due to #303:
Traceback (most recent call last):
File "/home/ubuntu/kg2-code/multi_ont_to_json_kg.py", line 1391, in <module>
save_pickle)
File "/home/ubuntu/kg2-code/multi_ont_to_json_kg.py", line 142, in make_kg2
assert os.path.exists(ont_source_info_dict['file']), local_file_name
AssertionError: foodon.owl
download
in ont-load-inventory.yaml
needed to be set to true
to trigger the right if statement to use the pickle file. A better solution should be used in the future.
Here were the major report changes:
There was a significant drop in edges from infores:fma-umls in this build. The count dropped from 368827 to 290475
There was a significant drop in edges from infores:go in this build. The count dropped from 202983 to 132359
There was a significant drop in edges from infores:hgnc in this build. The count dropped from 42515 to 23262
There are no edges from infores:loinc-umls in this build. There were 2690586 in the previous build.
There was a significant drop in edges from infores:ncbi-taxon in this build. The count dropped from 3971385 to 1393247
There are no edges from infores:vandf-umls in this build. There were 140078 in the previous build.
1. Build and load KG2:
git clone https://github.com/RTXteam/RTX-KG2.git
bash -x clear-instance.sh
bash -x RTX-KG2/setup-kg2-build.sh
~/kg2-build/setup-kg2-build.log
to ensure setup completed successfullybash -x ~/kg2-code/build-kg2-snakemake.sh all -F -n
~/kg2-build/build-kg2-snakemake-n.log
to ensure all rules are includedtouch ~/kg2-build/minor-release
for a minor release ortouch ~/kg2-build/major-release
for a major release. If you don't want to change the version number, ignore this step.screen -S buildkg2
bash -x ~/kg2-code/build-kg2-snakemake.sh all -F
~/kg2-build/build-kg2-snakemake.log
~/kg2-build/kg2-version.txt
kg2-simplified-report.json
; compare against previouskg2-simplified-report.json
to identify any major changespython3 kg2_json_to_kgx_tsv.py kg2-simplified.json
content-metadata.json
on build instanceaws s3 /file/name s3://rtx-kg2-public
rtx.ai
underNetworking
on LightsailRTX-KG2/tsv-to-neo4j.sh > ~/kg2-build/tsv-to-neo4j.log 2>&1
kg2-versions.md
(see Cypher command below).Example Cypher to get versions of many of the knowledge sources in a specific build of KG2pre:
We're not planning to start this build immediately, I just want to have an issue to start tagging things with.