Error in `rule UMLS`

[acevedol]

[Mon Aug 22 16:46:17 2022] Error in rule UMLS: jobid: 27 output: /home/ubuntu/kg2-build/umls_cuis.tsv log: /home/ubuntu/kg2-build/extract-umls.log (check log file(s) for error message) shell: bash -x /home/ubuntu/kg2-code/extract-umls.sh /home/ubuntu/kg2-build /home/ubuntu/kg2-build/umls_cuis.tsv > /home/ubuntu/kg2-build/extract-umls.log 2>&1 (exited with non-zero exit code)

Originally posted by @acevedol in https://github.com/RTXteam/RTX-KG2/issues/221#issuecomment-1222625514 Build issue

[acevedol]

++ s3_bucket=rtx-kg2
...skipping...
                 unable to process umls-2022AA-metathesaurus.zip/META/CHANGE/MERGEDLUI.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/CHANGE/DELETEDCUI.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/indexes/PTR_AUI_RELA_MRHIER.x.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/indexes/CUI2_MRCUI.x.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/indexes/CODE_SAB_MRCONSO.x.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/indexes/CUI2_MRAUI.x.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/indexes/SCUI_SAB_MRCONSO.x.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/indexes/AUI_MRCONSO.x.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/indexes/SDUI_SAB_MRCONSO.x.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/indexes/MAPSETCUI_MRMAP.x.

[acevedol]

I am checking if there's a problem with the file in the s3 bucket. Removing, redownloading, and trying again because I haven't been able to resolve the issue within the instance.

[ecwood]

This seems to still be an issue. I'm trying to build (see #262) on kg2erica.rtx.ai from scratch. This is the error:

+ aws s3 cp --no-progress --region us-west-2 s3://rtx-kg2/umls-2022AA-metathesaurus.zip /home/ubuntu/kg2-build/umls/
download: s3://rtx-kg2/umls-2022AA-metathesaurus.zip to ../kg2-build/umls/umls-2022AA-metathesaurus.zip
+ cp /home/ubuntu/kg2-code/umls-config.prop /home/ubuntu/kg2-build/umls/config.prop
+ unzip /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip -d /home/ubuntu/kg2-build/umls/
Archive:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/.
  inflating: /home/ubuntu/kg2-build/umls/__MACOSX/._umls-2022AA-metathesaurus.zip  
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/Copyright_Notice.txt.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/.DS_Store.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/.
  inflating: /home/ubuntu/kg2-build/umls/__MACOSX/umls-2022AA-metathesaurus.zip/._META  
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/README.txt.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_ITA.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRHIST.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_RUS.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXNW_ENG.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/CHANGE/.
  inflating: /home/ubuntu/kg2-build/umls/__MACOSX/umls-2022AA-metathesaurus.zip/META/._CHANGE  
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRCONSO.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_LAV.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_TUR.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRCXT.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/.DS_Store.
  inflating: /home/ubuntu/kg2-build/umls/__MACOSX/umls-2022AA-metathesaurus.zip/META/._.DS_Store  
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_JPN.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_GER.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_ENG.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_POL.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/populate_oracle_db.bat.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRSTY.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_DAN.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_CZE.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_DAN.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRSTY.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_CZE.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_JPN.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_GER.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_ENG.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_POL.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_TUR.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXNW_ENG.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/oracle_indexes.sql.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRCONSO.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_LAV.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_RUS.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRHIST.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_ITA.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRFILES.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/README_DB.txt.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/oracle_tables.sql.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRCOLS.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/AMBIGSUI.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_EST.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_GRE.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_KOR.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_HUN.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_DUT.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_POR.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRDOC.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRMAP.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRREL.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRDEF.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_NOR.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/populate_mysql_db.bat.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_SWE.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRHIER.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_FRE.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRCUI.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_FIN.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_HEB.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_BAQ.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXNS_ENG.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_CHI.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_SCR.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/AMBIGLUI.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRSAT.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/populate_oracle_db.sh.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRRANK.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_SPA.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRAUI.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRSMAP.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/populate_mysql_db.sh.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRSAB.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRAUI.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRSMAP.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/config.prop.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRSAB.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/AMBIGLUI.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRSAT.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRRANK.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_SPA.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_HEB.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_FIN.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/mysql_tables.sql.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXNS_ENG.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_BAQ.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_CHI.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_SCR.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRHIER.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_FRE.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRCUI.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRREL.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRMAP.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRDEF.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_NOR.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_SWE.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRDOC.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_EST.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/AMBIGSUI.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_GRE.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_KOR.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_HUN.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_DUT.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRXW_POR.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/mysql_indexes.sql.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRFILES.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/indexes/.
  inflating: /home/ubuntu/kg2-build/umls/__MACOSX/umls-2022AA-metathesaurus.zip/META/._indexes  
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/MRCOLS.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/release.dat.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/CHANGE/MERGEDCUI.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/CHANGE/DELETEDSUI.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/CHANGE/DELETEDLUI.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/CHANGE/DELETEDLUI.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/CHANGE/DELETEDSUI.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/CHANGE/MERGEDCUI.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/CHANGE/DELETEDCUI.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/CHANGE/MERGEDLUI.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/CHANGE/MERGEDLUI.ctl.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/CHANGE/DELETEDCUI.RRF.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/indexes/PTR_AUI_RELA_MRHIER.x.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/indexes/CUI2_MRCUI.x.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/indexes/CODE_SAB_MRCONSO.x.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/indexes/CUI2_MRAUI.x.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/indexes/SCUI_SAB_MRCONSO.x.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/indexes/AUI_MRCONSO.x.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/indexes/SDUI_SAB_MRCONSO.x.
checkdir error:  /home/ubuntu/kg2-build/umls/umls-2022AA-metathesaurus.zip exists but is not directory
                 unable to process umls-2022AA-metathesaurus.zip/META/indexes/MAPSETCUI_MRMAP.x.

[ecwood]

This seems to be an issue with the version of UMLS in the S3 bucket. I copied the UMLS 2022AA copy from buildkg2.rtx.ai onto the S3 bucket as umls-2022AA-metathesaurus-buildkg2.zip and am using that for now. Also, we might want to consider upgrading to UMLS 2022AB anyways.

[ecwood]

There was also an issue relating to the pathway of the mv command being wrong. The folder is no longer the version but the entire name of the zip file. Another error occurred on rerun:

ERROR 2068 (HY000) at line 15: LOAD DATA LOCAL INFILE file request rejected due to restrictions on access.
Bye
finished loading tables ... Thu Jun 22 00:48:36 UTC 2023
finished indexes ... Thu Jun 22 00:48:36 UTC 2023
mysql: [Warning] Using a password on the command line interface can be insecure.
--------------
DROP TABLE IF EXISTS MRCXT
--------------

Query OK, 0 rows affected, 1 warning (0.04 sec)

Bye
----------------------------------------
There were one or more errors.  Please reference the mysql.log file for details.
Finished ... Thu Jun 22 00:48:36 UTC 2023
----------------------------------------

[ecwood]

I attempted the fix described here.

New error:

ERROR 3948 (42000) at line 15: Loading local data is disabled; this must be enabled on both the client and server sides
Bye
finished loading tables ... Thu Jun 22 16:23:18 UTC 2023
finished indexes ... Thu Jun 22 16:23:18 UTC 2023
mysql: [Warning] Using a password on the command line interface can be insecure.
--------------
DROP TABLE IF EXISTS MRCXT
--------------

Query OK, 0 rows affected, 1 warning (0.00 sec)

Bye
----------------------------------------
There were one or more errors.  Please reference the mysql.log file for details.
Finished ... Thu Jun 22 16:23:18 UTC 2023
----------------------------------------

[ecwood]

This script completed successfully on the KG2.8.4pre build so I am going to close out this issue.