Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Postgres loader does not change the table suffixes in environment-postgresql.sql for different release types #59

Open
boxydog opened this issue Apr 17, 2023 · 2 comments
Open

Postgres loader does not change the table suffixes in environment-postgresql.sql for different release types #59

boxydog opened this issue Apr 17, 2023 · 2 comments

Comments

@boxydog
Copy link

boxydog commented Apr 17, 2023

In load_release-postgresql.sh, it asks for loadType (DELTA, SNAP, FULL, ALL), but then the code to adjust environment-postgresql.sql is commented out, so environment-postgresql.sql always has tables ending in _f, which only matches the FULL type.
@siamchen
Copy link
Contributor

Not sure about load_release-postgresq.sh but my way to load the RF2 files is to use the load-postgresql.sql scripts directly.
I'm currently only have the access to SNOMED CT-AU data files so not very sure if the INT release file structure is changed or not. If you can send a list of the INT release file structure then I may spend some time on update those outdated scripts.

@boxydog
Copy link
Author

boxydog commented Apr 17, 2023

In https://github.com/IHTSDO/snomed-database-loader/blob/master/PostgreSQL/README.md, it says to use load_release-postgresql.sh, so I was just doing whatever is documented.

If I should use load-postgresql.sql directly with hand-editing, perhaps change the README? That is what I ended up doing (hand-editing).

I am not using the INT structure, I'm using the US structure. If it helps, here it is:

$ unzip -l SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z.zip 
Archive:  SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z.zip
  Length      Date    Time    Name
---------  ---------- -----   ----
        0  02-20-2023 19:12   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/
     5641  02-20-2023 19:12   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Readme_en_20230301.txt
        0  02-20-2023 19:12   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Snapshot/
        0  02-20-2023 19:12   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Snapshot/Terminology/
 30527744  02-20-2023 19:12   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Snapshot/Terminology/sct2_Concept_Snapshot_US1000124_20230301.txt
214176051  02-20-2023 19:12   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Snapshot/Terminology/sct2_Description_Snapshot-en_US1000124_20230301.txt
       92  02-20-2023 19:12   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Snapshot/Terminology/sct2_Identifier_Snapshot_US1000124_20230301.txt
372965778  02-20-2023 19:12   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Snapshot/Terminology/sct2_Relationship_Snapshot_US1000124_20230301.txt
  3722541  02-20-2023 19:12   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Snapshot/Terminology/sct2_RelationshipConcreteValues_Snapshot_US1000124_20230301.txt
117383978  02-20-2023 19:12   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Snapshot/Terminology/sct2_StatedRelationship_Snapshot_US1000124_20230301.txt
  4169031  02-20-2023 19:12   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Snapshot/Terminology/sct2_TextDefinition_Snapshot-en_US1000124_20230301.txt
 92139770  02-20-2023 19:12   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Snapshot/Terminology/sct2_sRefset_OWLExpressionSnapshot_US1000124_20230301.txt
        0  02-20-2023 19:13   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Snapshot/Refset/
        0  02-20-2023 19:13   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Snapshot/Refset/Content/
 20812400  02-20-2023 19:13   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Snapshot/Refset/Content/der2_cRefset_AssociationSnapshot_US1000124_20230301.txt
 77667027  02-20-2023 19:13   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Snapshot/Refset/Content/der2_cRefset_AttributeValueSnapshot_US1000124_20230301.txt
  1863943  02-20-2023 19:13   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Snapshot/Refset/Content/der2_Refset_SimpleSnapshot_US1000124_20230301.txt
        0  02-20-2023 19:13   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Snapshot/Refset/Map/
128057044  02-20-2023 19:13   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Snapshot/Refset/Map/der2_iisssccRefset_ExtendedMapSnapshot_US1000124_20230301.txt
 54003519  02-20-2023 19:13   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Snapshot/Refset/Map/der2_sRefset_SimpleMapSnapshot_US1000124_20230301.txt
        0  02-20-2023 19:13   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Snapshot/Refset/Language/
363417770  02-20-2023 19:13   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Snapshot/Refset/Language/der2_cRefset_LanguageSnapshot-en_US1000124_20230301.txt
        0  02-20-2023 19:13   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Snapshot/Refset/Metadata/
    27713  02-20-2023 19:13   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Snapshot/Refset/Metadata/der2_cciRefset_RefsetDescriptorSnapshot_US1000124_20230301.txt
      489  02-20-2023 19:13   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Snapshot/Refset/Metadata/der2_ciRefset_DescriptionTypeSnapshot_US1000124_20230301.txt
     1046  02-20-2023 19:13   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Snapshot/Refset/Metadata/der2_ssRefset_ModuleDependencySnapshot_US1000124_20230301.txt
    91212  02-20-2023 19:13   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Snapshot/Refset/Metadata/der2_sssssssRefset_MRCMDomainSnapshot_US1000124_20230301.txt
    22005  02-20-2023 19:13   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Snapshot/Refset/Metadata/der2_cissccRefset_MRCMAttributeDomainSnapshot_US1000124_20230301.txt
    57413  02-20-2023 19:13   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Snapshot/Refset/Metadata/der2_ssccRefset_MRCMAttributeRangeSnapshot_US1000124_20230301.txt
      403  02-20-2023 19:13   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Snapshot/Refset/Metadata/der2_cRefset_MRCMModuleScopeSnapshot_US1000124_20230301.txt
        0  02-20-2023 19:13   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Full/
        0  02-20-2023 19:13   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Full/Terminology/
 40736607  02-20-2023 19:13   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Full/Terminology/sct2_Concept_Full_US1000124_20230301.txt
371488983  02-20-2023 19:13   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Full/Terminology/sct2_Description_Full-en_US1000124_20230301.txt
       92  02-20-2023 19:13   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Full/Terminology/sct2_Identifier_Full_US1000124_20230301.txt
706529597  02-20-2023 19:13   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Full/Terminology/sct2_Relationship_Full_US1000124_20230301.txt
  3802717  02-20-2023 19:14   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Full/Terminology/sct2_RelationshipConcreteValues_Full_US1000124_20230301.txt
236491109  02-20-2023 19:14   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Full/Terminology/sct2_StatedRelationship_Full_US1000124_20230301.txt
  4407323  02-20-2023 19:14   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Full/Terminology/sct2_TextDefinition_Full-en_US1000124_20230301.txt
128133790  02-20-2023 19:14   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Full/Terminology/sct2_sRefset_OWLExpressionFull_US1000124_20230301.txt
        0  02-20-2023 19:14   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Full/Refset/
        0  02-20-2023 19:14   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Full/Refset/Content/
 23956314  02-20-2023 19:14   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Full/Refset/Content/der2_cRefset_AssociationFull_US1000124_20230301.txt
 98983869  02-20-2023 19:14   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Full/Refset/Content/der2_cRefset_AttributeValueFull_US1000124_20230301.txt
  1938081  02-20-2023 19:14   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Full/Refset/Content/der2_Refset_SimpleFull_US1000124_20230301.txt
        0  02-20-2023 19:14   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Full/Refset/Map/
180176287  02-20-2023 19:14   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Full/Refset/Map/der2_iisssccRefset_ExtendedMapFull_US1000124_20230301.txt
 54271305  02-20-2023 19:14   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Full/Refset/Map/der2_sRefset_SimpleMapFull_US1000124_20230301.txt
        0  02-20-2023 19:14   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Full/Refset/Language/
433560717  02-20-2023 19:14   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Full/Refset/Language/der2_cRefset_LanguageFull-en_US1000124_20230301.txt
        0  02-20-2023 19:14   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Full/Refset/Metadata/
    31270  02-20-2023 19:14   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Full/Refset/Metadata/der2_cciRefset_RefsetDescriptorFull_US1000124_20230301.txt
      619  02-20-2023 19:14   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Full/Refset/Metadata/der2_ciRefset_DescriptionTypeFull_US1000124_20230301.txt
    22695  02-20-2023 19:14   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Full/Refset/Metadata/der2_ssRefset_ModuleDependencyFull_US1000124_20230301.txt
   417071  02-20-2023 19:14   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Full/Refset/Metadata/der2_sssssssRefset_MRCMDomainFull_US1000124_20230301.txt
    29161  02-20-2023 19:14   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Full/Refset/Metadata/der2_cissccRefset_MRCMAttributeDomainFull_US1000124_20230301.txt
   106807  02-20-2023 19:14   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Full/Refset/Metadata/der2_ssccRefset_MRCMAttributeRangeFull_US1000124_20230301.txt
      403  02-20-2023 19:14   SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20230301T120000Z/Full/Refset/Metadata/der2_cRefset_MRCMModuleScopeFull_US1000124_20230301.txt
---------                     -------
3766197427                     58 files

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@siamchen @boxydog