HAPI 3.8.0 upgrade issues

[shi...@interopion.com]

Hi,

I am trying to upgrade our multi-tenant implementation of HAPI server to 3.8.0.  I have downloaded and ran the hapi-fhir-jpaserver-starter with recommended changes to use MySQL.

These are my hapi.properties settings:

datasource.driver=com.mysql.jdbc.Driver

datasource.url=jdbc:mysql://localhost:3306/hapi_dstu3

hibernate.dialect=org.hibernate.dialect.MySQL5InnoDBDialect

When I compared our current dstu3 schema to hapi_dstu3 schema, there were lots of schema differences.  I tried to do database migration through the hapi-fhir-cli, but it is not working.  I have tried a few commands with minor variations, but it is not working as expected.  It seems like it is not finding the tasks to migrate.  I double checked to see if it is able to find my database to migrate, by putting a non-existent database in the database url and I still got the same response.

2019-06-24 12:09:40 [main] INFO  c.u.f.j.m.Migrator Starting migration with 0 tasks

2019-06-24 12:09:40 [main] INFO  c.u.f.j.m.Migrator Finished migration of 0 tasks

2019-06-24 12:09:40 [main] INFO  ca.uhn.fhir.cli.App HAPI FHIR is shutting down...

These are the commands that I have tried on the hapi-fhir-cli

./hapi-fhir-cli migrate-database -d MYSQL_5_7 -u "jdbc:mysql://localhost:3306/hspc_8_Test0425" -n "abcd" -p "abcd" -f V3_7_0 -t V3_8_0

./hapi-fhir-cli migrate-database -d MYSQL_5_7 -u "jdbc:mysql://127.0.0.1:3306/hspc_8_Test0425?serverTimezone=America/Denver" -n "abcd" -p "abcd" -f V3_7_0 -t V3_8_0

java -cp ./hapi-fhir-cli.jar:mysql-connector-java-8.0.12.jar ca.uhn.fhir.cli.App migrate-database -d MYSQL_5_7 -u "jdbc:mysql://localhost:3306/hspc_8_Test0425" -n "abcd" -p "abcd" -f V3_7_0 -t V3_8_0

java -cp ./hapi-fhir-cli.jar:mysql-connector-java-8.0.12.jar ca.uhn.fhir.cli.App migrate-database -d MYSQL_5_7 -u "jdbc:mysql://127.0.0.1:3306/hspc_8_Test0425?serverTimezone=America/Denver" -n "abcd" -p "abcd" -f V3_7_0 -t V3_8_0

Please help me with this migration and also please guide me to the HAPI 3.8.0 upgrade process documentation as well.  

Thanks,

Shilpy

[James Agnew]

Hi Shilpy,

There are no schema changes between HAPI FHIR 3.7.0 and HAPI FHIR 3.8.0, and no database migration should be required.

Can you give an example of a schema change you are seeing?

Cheers,

James

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[Shilpy Sharma]

Hi James,

This is the result of database comparison.  There are lots of minor changes with the varchar and some default values, but the major ones are dropping tables (missing tables) HFJ_SEARCH_PARM and  SEQ_SEARCHPARM_ID, and creating some indexes and dropping some indexes.

USE hspc_8_CompareSTU3;

drop index IDX_FORCEDID_TYPE_FID on HFJ_FORCED_ID;

alter table HFJ_FORCED_ID engine=InnoDB;

alter table HFJ_FORCED_ID charset=utf8;

create unique index IDX_FORCEDID_TYPE_FID
on HFJ_FORCED_ID (RESOURCE_TYPE, FORCED_ID);

alter table HFJ_FORCED_ID
add constraint IDX_FORCEDID_TYPE_FID
unique (RESOURCE_TYPE, FORCED_ID);

alter table HFJ_FORCED_ID
add constraint FK_FORCEDID_RESOURCE
foreign key (RESOURCE_PID) references HFJ_RESOURCE (RES_ID);

alter table HFJ_HISTORY_TAG engine=InnoDB;

alter table HFJ_HISTORY_TAG charset=utf8;

alter table HFJ_HISTORY_TAG
add constraint FK_HISTORYTAG_HISTORY
foreign key (RES_VER_PID) references HFJ_RES_VER (PID);

alter table HFJ_HISTORY_TAG
add constraint FKtderym7awj6q8iq5c51xv4ndw
foreign key (TAG_ID) references HFJ_TAG_DEF (TAG_ID);

alter table HFJ_IDX_CMP_STRING_UNIQ modify IDX_STRING varchar(200) not null;

alter table HFJ_IDX_CMP_STRING_UNIQ engine=InnoDB;

alter table HFJ_IDX_CMP_STRING_UNIQ charset=utf8;

alter table HFJ_IDX_CMP_STRING_UNIQ
add constraint FK_IDXCMPSTRUNIQ_RES_ID
foreign key (RES_ID) references HFJ_RESOURCE (RES_ID);

alter table HFJ_RESOURCE drop column RES_TITLE;

alter table HFJ_RESOURCE engine=InnoDB;

alter table HFJ_RESOURCE charset=utf8;

alter table HFJ_RESOURCE
add constraint FKhjgj8cp879gfxko25cx5o692r
foreign key (FORCED_ID_PID) references HFJ_FORCED_ID (PID);

alter table HFJ_RES_LINK alter column SOURCE_RESOURCE_TYPE drop default;

alter table HFJ_RES_LINK alter column TARGET_RESOURCE_TYPE drop default;

alter table HFJ_RES_LINK engine=InnoDB;

alter table HFJ_RES_LINK charset=utf8;

alter table HFJ_RES_LINK
add constraint FK_RESLINK_SOURCE
foreign key (SRC_RESOURCE_ID) references HFJ_RESOURCE (RES_ID);

alter table HFJ_RES_LINK
add constraint FK_RESLINK_TARGET
foreign key (TARGET_RESOURCE_ID) references HFJ_RESOURCE (RES_ID);

alter table HFJ_RES_PARAM_PRESENT engine=InnoDB;

alter table HFJ_RES_PARAM_PRESENT charset=utf8;

alter table HFJ_RES_PARAM_PRESENT
add constraint FK_RESPARMPRES_RESID
foreign key (RES_ID) references HFJ_RESOURCE (RES_ID);

alter table HFJ_RES_REINDEX_JOB modify SUSPENDED_UNTIL datetime null;

alter table HFJ_RES_REINDEX_JOB modify UPDATE_THRESHOLD_HIGH datetime not null;

alter table HFJ_RES_REINDEX_JOB modify UPDATE_THRESHOLD_LOW datetime null;

alter table HFJ_RES_TAG engine=InnoDB;

alter table HFJ_RES_TAG charset=utf8;

alter table HFJ_RES_TAG
add constraint FK_RESTAG_RESOURCE
foreign key (RES_ID) references HFJ_RESOURCE (RES_ID);

alter table HFJ_RES_TAG
add constraint FKbfcjbaftmiwr3rxkwsy23vneo
foreign key (TAG_ID) references HFJ_TAG_DEF (TAG_ID);

alter table HFJ_RES_VER modify RES_ENCODING varchar(5) not null;

alter table HFJ_RES_VER drop column RES_TITLE;

alter table HFJ_RES_VER engine=InnoDB;

alter table HFJ_RES_VER charset=utf8;

alter table HFJ_RES_VER
add constraint FKh20i7lcbchkaxekvwg9ix4hc5
foreign key (FORCED_ID_PID) references HFJ_FORCED_ID (PID);

alter table HFJ_SEARCH modify SEARCH_UUID varchar(36) not null;

alter table HFJ_SEARCH engine=InnoDB;

alter table HFJ_SEARCH charset=utf8;

alter table HFJ_SEARCH_INCLUDE engine=InnoDB;

alter table HFJ_SEARCH_INCLUDE charset=utf8;

alter table HFJ_SEARCH_INCLUDE
add constraint FK_SEARCHINC_SEARCH
foreign key (SEARCH_PID) references HFJ_SEARCH (PID);

drop table HFJ_SEARCH_PARM;

alter table HFJ_SEARCH_RESULT engine=InnoDB;

alter table HFJ_SEARCH_RESULT charset=utf8;

alter table HFJ_SEARCH_RESULT
add constraint FK_SEARCHRES_RES
foreign key (RESOURCE_PID) references HFJ_RESOURCE (RES_ID);

alter table HFJ_SEARCH_RESULT
add constraint FK_SEARCHRES_SEARCH
foreign key (SEARCH_PID) references HFJ_SEARCH (PID);

alter table HFJ_SPIDX_COORDS engine=InnoDB;

alter table HFJ_SPIDX_COORDS charset=utf8;

alter table HFJ_SPIDX_COORDS
add constraint FKc97mpk37okwu8qvtceg2nh9vn
foreign key (RES_ID) references HFJ_RESOURCE (RES_ID);

drop index IDX_SP_DATE on hspc_8_CompareSTU3.HFJ_SPIDX_DATE;

alter table HFJ_SPIDX_DATE engine=InnoDB;

alter table HFJ_SPIDX_DATE charset=utf8;

alter table HFJ_SPIDX_DATE
add constraint FK17s70oa59rm9n61k9thjqrsqm
foreign key (RES_ID) references HFJ_RESOURCE (RES_ID);

alter table HFJ_SPIDX_NUMBER engine=InnoDB;

alter table HFJ_SPIDX_NUMBER charset=utf8;

alter table HFJ_SPIDX_NUMBER
add constraint FKcltihnc5tgprj9bhpt7xi5otb
foreign key (RES_ID) references HFJ_RESOURCE (RES_ID);

alter table HFJ_SPIDX_QUANTITY drop column HASH_UNITS_AND_VALPREFIX;

alter table HFJ_SPIDX_QUANTITY drop column HASH_VALPREFIX;

alter table HFJ_SPIDX_QUANTITY engine=InnoDB;

alter table HFJ_SPIDX_QUANTITY charset=utf8;

alter table HFJ_SPIDX_QUANTITY
add constraint FKn603wjjoi1a6asewxbbd78bi5
foreign key (RES_ID) references HFJ_RESOURCE (RES_ID);

alter table HFJ_SPIDX_STRING engine=InnoDB;

alter table HFJ_SPIDX_STRING charset=utf8;

create index IDX_SP_STRING_HASH_IDENT
on HFJ_SPIDX_STRING (HASH_IDENTITY);

alter table HFJ_SPIDX_STRING
add constraint FK_SPIDXSTR_RESOURCE
foreign key (RES_ID) references HFJ_RESOURCE (RES_ID);

alter table HFJ_SPIDX_TOKEN engine=InnoDB;

alter table HFJ_SPIDX_TOKEN charset=utf8;

alter table HFJ_SPIDX_TOKEN
add constraint FK7ulx3j1gg3v7maqrejgc7ybc4
foreign key (RES_ID) references HFJ_RESOURCE (RES_ID);

alter table HFJ_SPIDX_URI engine=InnoDB;

alter table HFJ_SPIDX_URI charset=utf8;

alter table HFJ_SPIDX_URI
add constraint FKgxsreutymmfjuwdswv3y887do
foreign key (RES_ID) references HFJ_RESOURCE (RES_ID);

alter table HFJ_SUBSCRIPTION_STATS engine=InnoDB;

alter table HFJ_SUBSCRIPTION_STATS charset=utf8;

alter table HFJ_SUBSCRIPTION_STATS
add constraint FK_SUBSC_RESOURCE_ID
foreign key (RES_ID) references HFJ_RESOURCE (RES_ID);

alter table HFJ_TAG_DEF drop column myHashCode;

alter table HFJ_TAG_DEF engine=InnoDB;

alter table HFJ_TAG_DEF charset=utf8;

drop table SEQ_SEARCHPARM_ID;

alter table TRM_CODESYSTEM engine=InnoDB;

alter table TRM_CODESYSTEM charset=utf8;

alter table TRM_CODESYSTEM
add constraint FK_TRMCODESYSTEM_CURVER
foreign key (CURRENT_VERSION_PID) references TRM_CODESYSTEM_VER (PID);

alter table TRM_CODESYSTEM
add constraint FK_TRMCODESYSTEM_RES
foreign key (RES_ID) references HFJ_RESOURCE (RES_ID);

alter table TRM_CODESYSTEM_VER engine=InnoDB;

alter table TRM_CODESYSTEM_VER charset=utf8;

alter table TRM_CODESYSTEM_VER
add constraint FK_CODESYSVER_CS_ID
foreign key (CODESYSTEM_PID) references TRM_CODESYSTEM (PID);

alter table TRM_CODESYSTEM_VER
add constraint FK_CODESYSVER_RES_ID
foreign key (RES_ID) references HFJ_RESOURCE (RES_ID);

alter table TRM_CONCEPT modify CODE varchar(500) not null;

alter table TRM_CONCEPT engine=InnoDB;

alter table TRM_CONCEPT charset=utf8;

alter table TRM_CONCEPT
add constraint FK_CONCEPT_PID_CS_PID
foreign key (CODESYSTEM_PID) references TRM_CODESYSTEM_VER (PID);

alter table TRM_CONCEPT_DESIG engine=InnoDB;

alter table TRM_CONCEPT_DESIG
add constraint FK_CONCEPTDESIG_CONCEPT
foreign key (CONCEPT_PID) references TRM_CONCEPT (PID);

alter table TRM_CONCEPT_DESIG
add constraint FK_CONCEPTDESIG_CSV
foreign key (CS_VER_PID) references TRM_CODESYSTEM_VER (PID);

alter table TRM_CONCEPT_MAP engine=InnoDB;

alter table TRM_CONCEPT_MAP
add constraint FK_TRMCONCEPTMAP_RES
foreign key (RES_ID) references HFJ_RESOURCE (RES_ID);

alter table TRM_CONCEPT_MAP_GROUP engine=InnoDB;

alter table TRM_CONCEPT_MAP_GROUP
add constraint FK_TCMGROUP_CONCEPTMAP
foreign key (CONCEPT_MAP_PID) references TRM_CONCEPT_MAP (PID);

alter table TRM_CONCEPT_MAP_GRP_ELEMENT engine=InnoDB;

create index IDX_CNCPT_MAP_GRP_CD
on TRM_CONCEPT_MAP_GRP_ELEMENT (SOURCE_CODE);

alter table TRM_CONCEPT_MAP_GRP_ELEMENT
add constraint FK_TCMGELEMENT_GROUP
foreign key (CONCEPT_MAP_GROUP_PID) references TRM_CONCEPT_MAP_GROUP (PID);

alter table TRM_CONCEPT_MAP_GRP_ELM_TGT engine=InnoDB;

create index IDX_CNCPT_MP_GRP_ELM_TGT_CD
on TRM_CONCEPT_MAP_GRP_ELM_TGT (TARGET_CODE);

alter table TRM_CONCEPT_MAP_GRP_ELM_TGT
add constraint FK_TCMGETARGET_ELEMENT
foreign key (CONCEPT_MAP_GRP_ELM_PID) references TRM_CONCEPT_MAP_GRP_ELEMENT (PID);

alter table TRM_CONCEPT_PC_LINK engine=InnoDB;

alter table TRM_CONCEPT_PC_LINK charset=utf8;

alter table TRM_CONCEPT_PC_LINK
add constraint FK_TERM_CONCEPTPC_CHILD
foreign key (CHILD_PID) references TRM_CONCEPT (PID);

alter table TRM_CONCEPT_PC_LINK
add constraint FK_TERM_CONCEPTPC_CS
foreign key (CODESYSTEM_PID) references TRM_CODESYSTEM_VER (PID);

alter table TRM_CONCEPT_PC_LINK
add constraint FK_TERM_CONCEPTPC_PARENT
foreign key (PARENT_PID) references TRM_CONCEPT (PID);

alter table TRM_CONCEPT_PROPERTY engine=InnoDB;

alter table TRM_CONCEPT_PROPERTY charset=utf8;

alter table TRM_CONCEPT_PROPERTY
add constraint FK_CONCEPTPROP_CONCEPT
foreign key (CONCEPT_PID) references TRM_CONCEPT (PID);

alter table TRM_CONCEPT_PROPERTY
add constraint FK_CONCEPTPROP_CSV
foreign key (CS_VER_PID) references TRM_CODESYSTEM_VER (PID);

[shi...@interopion.com]

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[James Agnew]

Something is definitely very wrong there...

Taking a random example from what you provided:

> add constraint FK_RESLINK_SOURCE

That constraint was added in 2017, in HAPI FHIR 2.5. So that's definitely not a valid schema for HAPI FHIR 3.7.0 if it was missing in your DB....

Cheers,

James

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[shi...@interopion.com]

Thanks for checking it.  I will be looking into what are we missing on our end.  

Shilpy