Comments (4)
Hi,
the error shows that it can't find the files. Where have you extracted the SNOMED CT release to?
from snomed-ct-database.
Hi,
I've re-extracted the SnomedCT_RF2Release_INT_20150131.zip
in /Users/enricopirani/download/SnomedCT_RF2Release_INT_20150131
and change the location in load-postgresql.sql
:
/* loads the SNOMED CT 'Full' release - replace filenames with relevant locations of base SNOMED CT release files*/
/* Filenames may need to change depending on the release you wish to upload, currently set to January 2015 release */
use snomedct;
COPY curr_concept_f(id, effectivetime, active, moduleid, definitionstatusid)
FROM '/Users/enricopirani/download/SnomedCT_RF2Release_INT_20150131/Full/Terminology/sct2_Concept_Full_INT_20150131.txt'
WITH DELIMITER '~';
CSV HEADER;
COPY curr_description_f(id, effectivetime, active, moduleid, conceptid, languagecode, typeid, term, casesignificanceid)
FROM '/Users/enricopirani/download/SnomedCT_RF2Release_INT_20150131/Full/Terminology/sct2_Description_Full-en_INT_20150131.txt'
WITH DELIMITER '~';
CSV HEADER;
COPY curr_textdefinition_f(id, effectivetime, active, moduleid, conceptid, languagecode, typeid, term, casesignificanceid)
FROM '/Users/enricopirani/download/SnomedCT_RF2Release_INT_20150131/Full/Terminology/sct2_TextDefinition_Full-en_INT_20150131.txt'
WITH DELIMITER '~';
CSV HEADER;
COPY curr_relationship_f(id, effectivetime, active, moduleid, sourceid, destinationid, relationshipgroup, typeid,characteristictypeid, modifierid)
FROM '/Users/enricopirani/download/SnomedCT_RF2Release_INT_20150131/Full/Terminology/sct2_Relationship_Full_INT_20150131.txt'
WITH DELIMITER '~';
CSV HEADER;
COPY curr_stated_relationship_f(id, effectivetime, active, moduleid, sourceid, destinationid, relationshipgroup, typeid, characteristictypeid, modifierid)
FROM '/Users/enricopirani/download/SnomedCT_RF2Release_INT_20150131/Full/Terminology/sct2_StatedRelationship_Full_INT_20150131.txt'
WITH DELIMITER '~';
CSV HEADER;
COPY curr_langrefset_f(id, effectivetime, active, moduleid, refsetid, referencedcomponentid, acceptabilityid)
FROM '/Users/enricopirani/download/SnomedCT_RF2Release_INT_20150131/Full/Refset/Language/der2_cRefset_LanguageFull-en_INT_20150131.txt'
WITH DELIMITER '~';
CSV HEADER;
COPY curr_associationrefset_d(id, effectivetime, active, moduleid, refsetid, referencedcomponentid, targetcomponentid)
FROM '/Users/enricopirani/download/SnomedCT_RF2Release_INT_20150131/Full/Refset/Content/der2_cRefset_AssociationReferenceFull_INT_20150131.txt'
WITH DELIMITER '~';
CSV HEADER;
COPY curr_attributevaluerefset_f(id, effectivetime, active, moduleid, refsetid, referencedcomponentid, valueid)
FROM '/Users/enricopirani/download/SnomedCT_RF2Release_INT_20150131/Full/Refset/Content/der2_cRefset_AttributeValueFull_INT_20150131.txt'
WITH DELIMITER '~';
CSV HEADER;
COPY curr_simplemaprefset_f(id, effectivetime, active, moduleid, refsetid, referencedcomponentid, maptarget);
FROM '/Users/enricopirani/download/SnomedCT_RF2Release_INT_20150131/Full/Refset/Crossmap/der2_sRefset_SimpleMapFull_INT_20150131.txt'
WITH DELIMITER '~';
CSV HEADER;
COPY curr_simplerefset_f(id, effectivetime, active, moduleid, refsetid, referencedcomponentid)
FROM '/Users/enricopirani/download/SnomedCT_RF2Release_INT_20150131/Full/Refset/Content/der2_Refset_SimpleFull_INT_20150131.txt'
WITH DELIMITER '~';
CSV HEADER;
COPY curr_complexmaprefset_f(id, effectivetime, active, moduleid, refsetid, referencedcomponentid, mapGroup, mapPriority, mapRule, mapAdvice, mapTarget, correlationId)
FROM '/Users/enricopirani/download/SnomedCT_RF2Release_INT_20150131/Full/Refset/Map/der2_iissscRefset_ComplexMapFull_INT_20150131.txt'
WITH DELIMITER '~';
CSV HEADER;
But still the same errors :
psql -d snomedct -f load-postgresql.sql
psql:load-postgresql.sql:4: ERROR: syntax error at or near "use"
LINE 3: use snomedct;
^
psql:load-postgresql.sql:8: ERROR: value too long for type character varying(18)
CONTEXT: COPY curr_concept_f, line 1, column id: "id effectiveTime active moduleId definitionStatusId"
psql:load-postgresql.sql:9: ERROR: syntax error at or near "CSV"
LINE 1: CSV HEADER;
^
psql:load-postgresql.sql:14: ERROR: value too long for type character varying(18)
CONTEXT: COPY curr_description_f, line 1, column id: "id effectiveTime active moduleId conceptId languageCode typeId term caseSignificanceId"
psql:load-postgresql.sql:15: ERROR: syntax error at or near "CSV"
LINE 1: CSV HEADER;
^
psql:load-postgresql.sql:20: ERROR: value too long for type character varying(18)
CONTEXT: COPY curr_textdefinition_f, line 1, column id: "id effectiveTime active moduleId conceptId languageCode typeId term caseSignificanceId"
psql:load-postgresql.sql:21: ERROR: syntax error at or near "CSV"
LINE 1: CSV HEADER;
^
psql:load-postgresql.sql:26: ERROR: value too long for type character varying(18)
CONTEXT: COPY curr_relationship_f, line 1, column id: "id effectiveTime active moduleId sourceId destinationId relationshipGroup typeId characteristicTypeI..."
psql:load-postgresql.sql:27: ERROR: syntax error at or near "CSV"
LINE 1: CSV HEADER;
^
psql:load-postgresql.sql:32: ERROR: relation "curr_stated_relationship_f" does not exist
psql:load-postgresql.sql:33: ERROR: syntax error at or near "CSV"
LINE 1: CSV HEADER;
^
psql:load-postgresql.sql:37: ERROR: value too long for type character varying(18)
CONTEXT: COPY curr_langrefset_f, line 1, column id: "id effectiveTime active moduleId refsetId referencedComponentId acceptabilityId"
psql:load-postgresql.sql:38: ERROR: syntax error at or near "CSV"
LINE 1: CSV HEADER;
^
psql:load-postgresql.sql:42: ERROR: value too long for type character varying(18)
CONTEXT: COPY curr_associationrefset_d, line 1, column id: "id effectiveTime active moduleId refsetId referencedComponentId targetComponentId"
psql:load-postgresql.sql:43: ERROR: syntax error at or near "CSV"
LINE 1: CSV HEADER;
^
psql:load-postgresql.sql:48: ERROR: value too long for type character varying(18)
CONTEXT: COPY curr_attributevaluerefset_f, line 1, column id: "id effectiveTime active moduleId refsetId referencedComponentId valueId"
psql:load-postgresql.sql:49: ERROR: syntax error at or near "CSV"
LINE 1: CSV HEADER;
^
psql:load-postgresql.sql:51: ERROR: syntax error at or near ";"
LINE 1: ...ive, moduleid, refsetid, referencedcomponentid, maptarget);
^
psql:load-postgresql.sql:53: ERROR: syntax error at or near "FROM"
LINE 1: FROM '/Users/enricopirani/download/SnomedCT_RF2Release_INT_2...
^
psql:load-postgresql.sql:54: ERROR: syntax error at or near "CSV"
LINE 1: CSV HEADER;
^
psql:load-postgresql.sql:58: ERROR: value too long for type character varying(18)
CONTEXT: COPY curr_simplerefset_f, line 1, column id: "id effectiveTime active moduleId refsetId referencedComponentId"
psql:load-postgresql.sql:59: ERROR: syntax error at or near "CSV"
LINE 1: CSV HEADER;
^
psql:load-postgresql.sql:63: ERROR: value too long for type character varying(18)
CONTEXT: COPY curr_complexmaprefset_f, line 1, column id: "id effectiveTime active moduleId refsetId referencedComponentId mapGroup mapPriority mapRule mapAdvi..."
psql:load-postgresql.sql:64: ERROR: syntax error at or near "CSV"
LINE 1: CSV HEADER;
^
from snomed-ct-database.
@Enrico68 I'm running into the same issue. Were you ever able to solve this?
from snomed-ct-database.
The repo has been updated now. Please have a go again.
from snomed-ct-database.
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