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Georgia Tech FHIR Server Web Page
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SchemaUpdate.java f_* tables #113

Open cnmaier opened 7 years ago

cnmaier commented 7 years ago

I am currently trying to set up your project with a standard installation of OMOP synpuf_cdm, however getting some errors on startup of the webapp:

2017-06-07 10:27:28.816 [localhost-startStop-1] ERROR o.h.tool.hbm2ddl.SchemaUpdate [SchemaUpdate.java:261] HHH000388: Unsuccessful: alter table condition_occurrence add constraint FK_l6vpcrfg21weo25qrnys952o1 foreign key (person_id) references f_person 2017-06-07 10:27:28.819 [localhost-startStop-1] ERROR o.h.tool.hbm2ddl.SchemaUpdate [SchemaUpdate.java:262] FEHLER: Einfügen oder Aktualisieren in Tabelle »condition_occurrence« verletzt Fremdschlüssel-Constraint »fk_l6vpcrfg21weo25qrnys952o1« **Detail: Key (person_id)=(453) is not present in »f_person« table.** 2017-06-07 10:27:28.822 [localhost-startStop-1] ERROR o.h.tool.hbm2ddl.SchemaUpdate [SchemaUpdate.java:261] HHH000388: Unsuccessful: alter table drug_exposure add constraint FK_pdjbpw6cpigr8oky0qjw25pxv foreign key (person_id) references f_person 2017-06-07 10:27:28.823 [localhost-startStop-1] ERROR o.h.tool.hbm2ddl.SchemaUpdate [SchemaUpdate.java:262] FEHLER: Einfügen oder Aktualisieren in Tabelle »drug_exposure« verletzt Fremdschlüssel-Constraint »fk_pdjbpw6cpigr8oky0qjw25pxv« Detail: Schlüssel (person_id)=(1172) ist nicht in Tabelle »f_person« vorhanden. 2017-06-07 10:27:28.828 [localhost-startStop-1] ERROR o.h.tool.hbm2ddl.SchemaUpdate [SchemaUpdate.java:261] HHH000388: Unsuccessful: alter table measurement add constraint FK_dwj6jftl6o0bb3v781tfnxhmd foreign key (person_id) references f_person 2017-06-07 10:27:28.830 [localhost-startStop-1] ERROR o.h.tool.hbm2ddl.SchemaUpdate [SchemaUpdate.java:262] FEHLER: Einfügen oder Aktualisieren in Tabelle »measurement« verletzt Fremdschlüssel-Constraint »fk_dwj6jftl6o0bb3v781tfnxhmd« Detail: Schlüssel (person_id)=(1265) ist nicht in Tabelle »f_person« vorhanden. 2017-06-07 10:27:28.832 [localhost-startStop-1] ERROR o.h.tool.hbm2ddl.SchemaUpdate [SchemaUpdate.java:261] HHH000388: Unsuccessful: alter table observation add constraint FK_2icte14g0f0j42nmrovgy8ptu foreign key (person_id) references f_person 2017-06-07 10:27:28.834 [localhost-startStop-1] ERROR o.h.tool.hbm2ddl.SchemaUpdate [SchemaUpdate.java:262] FEHLER: Einfügen oder Aktualisieren in Tabelle »observation« verletzt Fremdschlüssel-Constraint »fk_2icte14g0f0j42nmrovgy8ptu« Detail: Schlüssel (person_id)=(575) ist nicht in Tabelle »f_person« vorhanden. 2017-06-07 10:27:28.836 [localhost-startStop-1] ERROR o.h.tool.hbm2ddl.SchemaUpdate [SchemaUpdate.java:261] HHH000388: Unsuccessful: alter table procedure_occurrence add constraint FK_74ijltvx1uofohc2un9aolesw foreign key (person_id) references f_person 2017-06-07 10:27:28.837 [localhost-startStop-1] ERROR o.h.tool.hbm2ddl.SchemaUpdate [SchemaUpdate.java:262] FEHLER: Einfügen oder Aktualisieren in Tabelle »procedure_occurrence« verletzt Fremdschlüssel-Constraint »fk_74ijltvx1uofohc2un9aolesw« Detail: Schlüssel (person_id)=(941) ist nicht in Tabelle »f_person« vorhanden. 2017-06-07 10:27:30.016 [localhost-startStop-1] ERROR o.h.tool.hbm2ddl.SchemaUpdate [SchemaUpdate.java:261] HHH000388: Unsuccessful: alter table procedure_occurrence add constraint FK_nw5almj02oo3rjl54xyhiyup3 foreign key (procedure_concept_id) references concept 2017-06-07 10:27:30.017 [localhost-startStop-1] ERROR o.h.tool.hbm2ddl.SchemaUpdate [SchemaUpdate.java:262] FEHLER: Einfügen oder Aktualisieren in Tabelle »procedure_occurrence« verletzt Fremdschlüssel-Constraint »fk_nw5almj02oo3rjl54xyhiyup3« Detail: Schlüssel (procedure_concept_id)=(2211506) ist nicht in Tabelle »concept« vorhanden. 2017-06-07 10:27:31.118 [localhost-startStop-1] ERROR o.h.tool.hbm2ddl.SchemaUpdate [SchemaUpdate.java:261] HHH000388: Unsuccessful: alter table procedure_occurrence add constraint FK_imqm99ym8fl0jmlbh7rg0ew3l foreign key (procedure_source_concept_id) references concept 2017-06-07 10:27:31.121 [localhost-startStop-1] ERROR o.h.tool.hbm2ddl.SchemaUpdate [SchemaUpdate.java:262] FEHLER: Einfügen oder Aktualisieren in Tabelle »procedure_occurrence« verletzt Fremdschlüssel-Constraint »fk_imqm99ym8fl0jmlbh7rg0ew3l« Detail: Schlüssel (procedure_source_concept_id)=(2211506) ist nicht in Tabelle »concept« vorhanden. 2017-06-07 10:27:31.123 [localhost-startStop-1] ERROR o.h.tool.hbm2ddl.SchemaUpdate [SchemaUpdate.java:261] HHH000388: Unsuccessful: alter table visit_occurrence add constraint FK_gssbuvh60shtinbnlm07ygaer foreign key (person_id) references f_person 2017-06-07 10:27:31.123 [localhost-startStop-1] ERROR o.h.tool.hbm2ddl.SchemaUpdate [SchemaUpdate.java:262] FEHLER: Einfügen oder Aktualisieren in Tabelle »visit_occurrence« verletzt Fremdschlüssel-Constraint »fk_gssbuvh60shtinbnlm07ygaer« Detail: Schlüssel (person_id)=(71) ist nicht in Tabelle »f_person« vorhanden. 2017-06-07 10:27:31.124 [localhost-startStop-1] INFO o.h.tool.hbm2ddl.SchemaUpdate [SchemaUpdate.java:267] HHH000232: Schema update complete

It appears that the f_ (and probably the aud (?)) tables need to be filled with data, so that the foreign key constraints in the OMOP CDM tables can be created. The f* tables, however, are empty. So, do I have to fill them by myself?

When trying to query a patient on the frontend I do not get any results, although it is definitely in the CDM database. This is why I thought the errors above would be the reason.

myungchoi commented 7 years ago

f_person table must be populated. It's one-to-one table with person table. OMOP does not have person demographic information. You will need to assign them for each person in the f_person table.