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Remove dbSnp* and Oncotator* related fields in frontend and backend #9779
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this issue is related to #9461 |
ONCOTATOR_DBSNP_RS and ONCOTATOR_UNIPROT_ENTRY_NAME are always null in the cbioportal.org database. |
-- not empty ONCOTATOR_REFSEQ_MRNA_ID Above fields have data in cbioportal.org database and therefore not removing them. |
All columns that start with ONCOTATOR_ prefix replaced with MUTATION_ prefix. |
In the file portal/src/org/mskcc/portal/model/MafRecord.java the prefix oncotator is replaced with prefix maf. |
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. |
This is included in the |
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
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