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RTXteam / RTX-KG2

Build system for the RTX-KG2 biomedical knowledge graph, part of the ARAX reasoning system (https://github.com/RTXTeam/RTX)
MIT License
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Error in DrugCentral Extraction #295

Closed ecwood closed 11 months ago

ecwood commented 1 year ago

Here are the types of errors in DrugCentral's extract caused by problems with how postgres is installed:

ERROR:  syntax error at or near "LAMIVUDINE"
LINE 1: LAMIVUDINE TRIUMEQ PD VIIV HLTHCARE EQ 60MG BASE;
        ^
ERROR:  syntax error at or near "EQ"
LINE 1: EQ 5MG BASE;
        ^
ERROR:  trailing junk after numeric literal at or near "30M"
LINE 1: 30MG N 215413  2022-03-30 1 RX VIIV HEALTHCARE CO TABLET, FO...
        ^
ERROR:  syntax error at or near "DOLUTEGRAVIR"
LINE 1: DOLUTEGRAVIR SODIUM;
        ^
ERROR:  syntax error at or near "LAMIVUDINE"
LINE 1: LAMIVUDINE TRIUMEQ PD VIIV HLTHCARE EQ 60MG BASE;
        ^
ERROR:  syntax error at or near "EQ"
LINE 1: EQ 5MG BASE;
        ^
ERROR:  trailing junk after numeric literal at or near "30M"
LINE 1: 30MG N 215413  2022-03-30 1 RX VIIV HEALTHCARE CO TABLET, FO...
        ^
ERROR:  syntax error at or near "TADALAFIL"
LINE 1: TADALAFIL ENTADFI VERU 5MG;
        ^
ERROR:  trailing junk after numeric literal at or near "5M"
LINE 1: 5MG N 215423  2021-12-09 1 RX VERU INC CAPSULE ORAL 001
        ^
ERROR:  syntax error at or near "TADALAFIL"
LINE 1: TADALAFIL ENTADFI VERU 5MG;
        ^
ERROR:  trailing junk after numeric literal at or near "5M"
LINE 1: 5MG N 215423  2021-12-09 1 RX VERU INC CAPSULE ORAL 001

and

ERROR:  must be owner of schema public
ERROR:  permission denied for database drugcentral
ERROR:  must be owner of schema public
SET
SET
ERROR:  permission denied for schema public
LINE 1: CREATE TABLE public.act_table_full (
                     ^
ERROR:  relation "public.act_table_full" does not exist
ERROR:  permission denied for schema public
LINE 1: CREATE TABLE public.action_type (
                     ^
ERROR:  relation "public.action_type" does not exist
ERROR:  permission denied for schema public
ERROR:  relation "public.action_type_id_seq" does not exist
ERROR:  permission denied for schema public
LINE 1: CREATE TABLE public.active_ingredient (
                     ^
ERROR:  relation "public.active_ingredient" does not exist
ERROR:  permission denied for schema public
ERROR:  relation "public.active_ingredient_id_seq" does not exist
ERROR:  permission denied for schema public
LINE 1: CREATE TABLE public.approval (
                     ^
ERROR:  relation "public.approval" does not exist
ERROR:  permission denied for schema public
ERROR:  relation "public.approval_id_seq" does not exist
ERROR:  permission denied for schema public
LINE 1: CREATE TABLE public.approval_type (
                     ^
ERROR:  relation "public.approval_type" does not exist
ERROR:  permission denied for schema public
ERROR:  relation "public.approval_type_id_seq" does not exist
ERROR:  permission denied for schema public
LINE 1: CREATE TABLE public.atc (
                     ^
ERROR:  relation "public.atc" does not exist
ERROR:  permission denied for schema public
LINE 1: CREATE TABLE public.atc_ddd (
                     ^
ERROR:  relation "public.atc_ddd" does not exist
ERROR:  permission denied for schema public
ERROR:  relation "public.atc_ddd_id_seq" does not exist
ERROR:  permission denied for schema public
ERROR:  relation "public.atc_id_seq" does not exist

Originally posted by @ecwood in https://github.com/RTXteam/RTX-KG2/issues/262#issuecomment-1601826370

ecwood commented 1 year ago

With 515fed9, the extraction script finishes now.

ecwood commented 11 months ago

I am closing because this worked in KG2.8.4pre's build.