Remove dbSnp* and Oncotator* related fields in frontend and backend

[jagnathan]

Remove OncotatorProteinPosStar, OncotatorProteinPosEnd, getOncotatorRefseqMrnaId fields in frontend and backend

The changes require both frontend and backend changes. Frontend can be release ahead of backend or both releases have to happen in sync.

OncotatorProteinPosStart OncotatorProteinPosEnd refseqMrnaId - Has some frontend code as well

Removing oncotator fields

Backend changes:

• [ ] web/src/main/java/org/cbioportal/web/mixin/MutationMixin.java

• [ ] web/src/main/java/org/cbioportal/web/parameter/sort/MutationSortBy.java

• [ ] core/src/test/java/org/mskcc/cbio/portal/dao/TestDaoMutation.java

• [ ] core/src/main/java/org/mskcc/cbio/maf/MafRecord.java

• [ ] core/src/main/java/org/mskcc/cbio/maf/MafUtil.java

• [ ] core/src/main/java/org/mskcc/cbio/portal/dao/DaoMutation.java

• [ ] core/src/main/java/org/mskcc/cbio/portal/model/ExtendedMutation.java

• [ ] core/src/main/java/org/mskcc/cbio/portal/scripts/ImportExtendedMutationData.java

• [ ] core/src/main/java/org/mskcc/cbio/portal/util/ExtendedMutationUtil.java

• [ ] model/src/main/java/org/cbioportal/model/Mutation.java

• [ ] persistence/persistence-mybatis/src/test/java/org/cbioportal/persistence/mybatis/MutationMyBatisRepositoryTest.java

• [ ] persistence/persistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/MutationMapper.xml

SQL

• [ ] cgds.sql
• [ ] cgds-test.sql
• [ ] testSql.sql
• [ ] core/src/test/resources/seed_mini.sql

Frontend changes:

[jagnathan]

this issue is related to #9461

[jagnathan]

ONCOTATOR_DBSNP_RS and ONCOTATOR_UNIPROT_ENTRY_NAME are always null in the cbioportal.org database.

[jagnathan]

-- not empty ONCOTATOR_REFSEQ_MRNA_ID
-- not empty ONCOTATOR_CODON_CHANGE
-- not empty ONCOTATOR_UNIPROT_ACCESSION -- not empty ONCOTATOR_PROTEIN_POS_START -- not empty ONCOTATOR_PROTEIN_POS_END -- not empty DB_SNP_RS -- not empty DB_SNP_VAL_STATUS

Above fields have data in cbioportal.org database and therefore not removing them.

[jagnathan]

All columns that start with ONCOTATOR_ prefix replaced with MUTATION_ prefix.

[jagnathan]

In the file portal/src/org/mskcc/portal/model/MafRecord.java the prefix oncotator is replaced with prefix maf.

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[dippindots]

This is included in the v5.3.0, we can close this now.